2025-09-15 20:18:07.079 wdl.w:ptcp NOTICE workflow start :: name: "ptcp", source: "main.wdl", line: 8, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp"
2025-09-15 20:18:07.104 wdl.w:ptcp NOTICE miniwdl :: version: "v1.12.0", uname: "Linux mp-login9-2.nanofluidics.com 5.14.0-503.40.1.el9_5.x86_64 #1 SMP PREEMPT_DYNAMIC Wed Apr 30 17:38:54 UTC 2025 x86_64"
2025-09-15 20:18:07.104 wdl.w:ptcp INFO task thread pool initialized :: task_concurrency: 100
2025-09-15 20:18:07.110 wdl.w:ptcp INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:18:07.110 wdl.w:ptcp INFO visit :: node: "decl-fail_reads", values: "(((large)))"
2025-09-15 20:18:07.110 wdl.w:ptcp INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:18:07.110 wdl.w:ptcp INFO visit :: node: "decl-hifi_reads", values: "(((large)))"
2025-09-15 20:18:07.111 wdl.w:ptcp INFO visit :: node: "decl-log_level", values: {"log_level": "INFO"}
2025-09-15 20:18:07.111 wdl.w:ptcp INFO visit :: node: "decl-paraphase_annotation_vcf", values: {"paraphase_annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf"}
2025-09-15 20:18:07.111 wdl.w:ptcp INFO visit :: node: "decl-paraphase_config_yaml", values: {"paraphase_config_yaml": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml"}
2025-09-15 20:18:07.111 wdl.w:ptcp INFO visit :: node: "decl-pt_linear_regression", values: {"pt_linear_regression": null}
2025-09-15 20:18:07.111 wdl.w:ptcp INFO visit :: node: "decl-ptcp_qc_bed", values: {"ptcp_qc_bed": "/ptcp/meta/ptcp-qc/ptcp-qc.GRCh38.bed"}
2025-09-15 20:18:07.111 wdl.w:ptcp INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:18:07.111 wdl.w:ptcp INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:18:07.111 wdl.w:ptcp INFO visit :: node: "decl-sample_sheet", values: {"sample_sheet": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/sample_sheet.csv"}
2025-09-15 20:18:07.111 wdl.w:ptcp INFO visit :: node: "decl-trgt_bed", values: {"trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"}
2025-09-15 20:18:07.112 wdl.w:ptcp NOTICE ready :: job: "call-collect_inputs", callee: "collect_inputs"
2025-09-15 20:18:07.112 wdl.w:ptcp INFO input :: job: "call-collect_inputs", values: "(((large)))"
2025-09-15 20:18:07.118 wdl.w:ptcp.t:call-collect_inputs NOTICE task setup :: name: "collect_inputs", source: "./common.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs", thread: 140613838284352
2025-09-15 20:18:07.272 wdl.w:ptcp.t:call-collect_inputs NOTICE Singularity runtime initialized (BETA) :: singularity_version: "singularity-ce version 4.3.1-1.el9"
2025-09-15 20:18:07.277 wdl.w:ptcp.t:call-collect_inputs INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:18:07.277 wdl.w:ptcp.t:call-collect_inputs INFO input :: name: "fail_reads", value: "(((large)))"
2025-09-15 20:18:07.277 wdl.w:ptcp.t:call-collect_inputs INFO input :: name: "hifi_reads", value: "(((large)))"
2025-09-15 20:18:07.277 wdl.w:ptcp.t:call-collect_inputs INFO input :: name: "sample_sheet", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample_sheet.csv"
2025-09-15 20:18:07.277 wdl.w:ptcp.t:call-collect_inputs INFO eval :: name: "threads", value: 4
2025-09-15 20:18:07.277 wdl.w:ptcp.t:call-collect_inputs INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:18:07.279 wdl.w:ptcp.t:call-collect_inputs INFO eval :: name: "disk_size", value: 38
2025-09-15 20:18:07.280 wdl.w:ptcp.t:call-collect_inputs INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 4, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:18:07.280 wdl.w:ptcp.t:call-collect_inputs WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:18:07.284 wdl.w:ptcp.t:call-collect_inputs INFO provisioned :: seconds_waited: 0, cpu: 4, mem_bytes: 4000000000
2025-09-15 20:18:07.285 wdl.w:ptcp.t:call-collect_inputs INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:18:08.330 wdl.w:ptcp.t:call-collect_inputs INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 199, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/_singularity_tmpdir_h1j0zeoq"
2025-09-15 20:18:08.331 wdl.w:ptcp.t:call-collect_inputs INFO Slurm invocation: srun --job-name call-collect_inputs --partition compute,compute9 --cpus-per-task 4 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/r84036_20250809_035154/1_B01/fail_reads/m84036_250809_035451_s4.fail_reads.bc2152.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.fail_reads.bc2152.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/r84036_20250809_035154/1_B01/fail_reads/m84036_250809_035451_s4.fail_reads.bc2130.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.fail_reads.bc2130.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/r84036_20250809_035154/1_B01/fail_reads/m84036_250809_035451_s4.fail_reads.bc2173.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.fail_reads.bc2173.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/r84036_20250809_035154/1_B01/fail_reads/m84036_250809_035451_s4.fail_reads.bc2124.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.fail_reads.bc2124.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/r84036_20250809_035154/1_B01/fail_reads/m84036_250809_035451_s4.fail_reads.bc2101.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.fail_reads.bc2101.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/r84036_20250809_035154/1_B01/fail_reads/m84036_250809_035451_s4.fail_reads.bc2131.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.fail_reads.bc2131.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/r84036_20250809_035154/1_B01/fail_reads/m84036_250809_035451_s4.fail_reads.bc2109.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.fail_reads.bc2109.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/r84036_20250809_035154/1_B01/fail_reads/m84036_250809_035451_s4.fail_reads.bc2125.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.fail_reads.bc2125.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/r84036_20250809_035154/1_B01/fail_reads/m84036_250809_035451_s4.fail_reads.bc2106.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.fail_reads.bc2106.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/r84036_20250809_035154/1_B01/fail_reads/m84036_250809_035451_s4.fail_reads.bc2178.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.fail_reads.bc2178.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/r84036_20250809_035154/1_B01/fail_reads/m84036_250809_035451_s4.fail_reads.bc2133.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.fail_reads.bc2133.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/r84036_20250809_035154/1_B01/fail_reads/m84036_250809_035451_s4.fail_reads.bc2097.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.fail_reads.bc2097.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/r84036_20250809_035154/1_B01/fail_reads/m84036_250809_035451_s4.fail_reads.bc2154.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.fail_reads.bc2154.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/r84036_20250809_035154/1_B01/fail_reads/m84036_250809_035451_s4.fail_reads.bc2186.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.fail_reads.bc2186.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/r84036_20250809_035154/1_B01/fail_reads/m84036_250809_035451_s4.fail_reads.bc2170.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.fail_reads.bc2170.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/r84036_20250809_035154/1_B01/fail_reads/m84036_250809_035451_s4.fail_reads.bc2185.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.fail_reads.bc2185.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/r84036_20250809_035154/1_B01/fail_reads/m84036_250809_035451_s4.fail_reads.bc2136.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.fail_reads.bc2136.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/r84036_20250809_035154/1_B01/fail_reads/m84036_250809_035451_s4.fail_reads.bc2166.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.fail_reads.bc2166.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/r84036_20250809_035154/1_B01/fail_reads/m84036_250809_035451_s4.fail_reads.bc2118.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.fail_reads.bc2118.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/r84036_20250809_035154/1_B01/fail_reads/m84036_250809_035451_s4.fail_reads.bc2115.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.fail_reads.bc2115.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/r84036_20250809_035154/1_B01/fail_reads/m84036_250809_035451_s4.fail_reads.bc2140.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.fail_reads.bc2140.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/r84036_20250809_035154/1_B01/fail_reads/m84036_250809_035451_s4.fail_reads.bc2122.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.fail_reads.bc2122.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/r84036_20250809_035154/1_B01/fail_reads/m84036_250809_035451_s4.fail_reads.bc2168.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.fail_reads.bc2168.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/r84036_20250809_035154/1_B01/fail_reads/m84036_250809_035451_s4.fail_reads.bc2169.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.fail_reads.bc2169.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/r84036_20250809_035154/1_B01/fail_reads/m84036_250809_035451_s4.fail_reads.bc2127.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.fail_reads.bc2127.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/r84036_20250809_035154/1_B01/fail_reads/m84036_250809_035451_s4.fail_reads.bc2172.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.fail_reads.bc2172.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/r84036_20250809_035154/1_B01/fail_reads/m84036_250809_035451_s4.fail_reads.bc2142.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.fail_reads.bc2142.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/r84036_20250809_035154/1_B01/fail_reads/m84036_250809_035451_s4.fail_reads.bc2139.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.fail_reads.bc2139.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/r84036_20250809_035154/1_B01/fail_reads/m84036_250809_035451_s4.fail_reads.bc2150.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.fail_reads.bc2150.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/r84036_20250809_035154/1_B01/fail_reads/m84036_250809_035451_s4.fail_reads.bc2162.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.fail_reads.bc2162.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/r84036_20250809_035154/1_B01/fail_reads/m84036_250809_035451_s4.fail_reads.bc2191.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.fail_reads.bc2191.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/r84036_20250809_035154/1_B01/fail_reads/m84036_250809_035451_s4.fail_reads.bc2134.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.fail_reads.bc2134.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/r84036_20250809_035154/1_B01/fail_reads/m84036_250809_035451_s4.fail_reads.bc2117.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.fail_reads.bc2117.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/r84036_20250809_035154/1_B01/fail_reads/m84036_250809_035451_s4.fail_reads.bc2153.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.fail_reads.bc2153.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/r84036_20250809_035154/1_B01/fail_reads/m84036_250809_035451_s4.fail_reads.bc2175.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.fail_reads.bc2175.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/r84036_20250809_035154/1_B01/fail_reads/m84036_250809_035451_s4.fail_reads.bc2112.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.fail_reads.bc2112.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/r84036_20250809_035154/1_B01/fail_reads/m84036_250809_035451_s4.fail_reads.bc2132.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.fail_reads.bc2132.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/r84036_20250809_035154/1_B01/fail_reads/m84036_250809_035451_s4.fail_reads.bc2157.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.fail_reads.bc2157.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/r84036_20250809_035154/1_B01/fail_reads/m84036_250809_035451_s4.fail_reads.bc2190.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.fail_reads.bc2190.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/r84036_20250809_035154/1_B01/fail_reads/m84036_250809_035451_s4.fail_reads.bc2128.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.fail_reads.bc2128.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/r84036_20250809_035154/1_B01/fail_reads/m84036_250809_035451_s4.fail_reads.bc2113.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.fail_reads.bc2113.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/r84036_20250809_035154/1_B01/fail_reads/m84036_250809_035451_s4.fail_reads.bc2187.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.fail_reads.bc2187.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/r84036_20250809_035154/1_B01/fail_reads/m84036_250809_035451_s4.fail_reads.bc2161.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.fail_reads.bc2161.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/r84036_20250809_035154/1_B01/fail_reads/m84036_250809_035451_s4.fail_reads.bc2176.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.fail_reads.bc2176.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/r84036_20250809_035154/1_B01/fail_reads/m84036_250809_035451_s4.fail_reads.bc2177.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.fail_reads.bc2177.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/r84036_20250809_035154/1_B01/fail_reads/m84036_250809_035451_s4.fail_reads.bc2184.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.fail_reads.bc2184.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/r84036_20250809_035154/1_B01/fail_reads/m84036_250809_035451_s4.fail_reads.bc2108.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.fail_reads.bc2108.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/r84036_20250809_035154/1_B01/fail_reads/m84036_250809_035451_s4.fail_reads.bc2121.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.fail_reads.bc2121.bam:ro --bind 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/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/r84036_20250809_035154/1_B01/hifi_reads/m84036_250809_035451_s4.hifi_reads.bc2181.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.hifi_reads.bc2181.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/r84036_20250809_035154/1_B01/hifi_reads/m84036_250809_035451_s4.hifi_reads.bc2139.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.hifi_reads.bc2139.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/r84036_20250809_035154/1_B01/hifi_reads/m84036_250809_035451_s4.hifi_reads.bc2117.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.hifi_reads.bc2117.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/r84036_20250809_035154/1_B01/hifi_reads/m84036_250809_035451_s4.hifi_reads.bc2111.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.hifi_reads.bc2111.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/r84036_20250809_035154/1_B01/hifi_reads/m84036_250809_035451_s4.hifi_reads.bc2148.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.hifi_reads.bc2148.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/r84036_20250809_035154/1_B01/hifi_reads/m84036_250809_035451_s4.hifi_reads.bc2134.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.hifi_reads.bc2134.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/r84036_20250809_035154/1_B01/hifi_reads/m84036_250809_035451_s4.hifi_reads.bc2103.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.hifi_reads.bc2103.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/r84036_20250809_035154/1_B01/hifi_reads/m84036_250809_035451_s4.hifi_reads.bc2186.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.hifi_reads.bc2186.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/r84036_20250809_035154/1_B01/hifi_reads/m84036_250809_035451_s4.hifi_reads.bc2136.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.hifi_reads.bc2136.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/r84036_20250809_035154/1_B01/hifi_reads/m84036_250809_035451_s4.hifi_reads.bc2131.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.hifi_reads.bc2131.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/r84036_20250809_035154/1_B01/hifi_reads/m84036_250809_035451_s4.hifi_reads.bc2104.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.hifi_reads.bc2104.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/r84036_20250809_035154/1_B01/hifi_reads/m84036_250809_035451_s4.hifi_reads.bc2127.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.hifi_reads.bc2127.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/r84036_20250809_035154/1_B01/hifi_reads/m84036_250809_035451_s4.hifi_reads.bc2185.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.hifi_reads.bc2185.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/r84036_20250809_035154/1_B01/hifi_reads/m84036_250809_035451_s4.hifi_reads.bc2144.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.hifi_reads.bc2144.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/r84036_20250809_035154/1_B01/hifi_reads/m84036_250809_035451_s4.hifi_reads.bc2187.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.hifi_reads.bc2187.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/r84036_20250809_035154/1_B01/hifi_reads/m84036_250809_035451_s4.hifi_reads.bc2119.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.hifi_reads.bc2119.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/r84036_20250809_035154/1_B01/hifi_reads/m84036_250809_035451_s4.hifi_reads.bc2143.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.hifi_reads.bc2143.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/r84036_20250809_035154/1_B01/hifi_reads/m84036_250809_035451_s4.hifi_reads.bc2184.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.hifi_reads.bc2184.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/r84036_20250809_035154/1_B01/hifi_reads/m84036_250809_035451_s4.hifi_reads.bc2168.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.hifi_reads.bc2168.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/r84036_20250809_035154/1_B01/hifi_reads/m84036_250809_035451_s4.hifi_reads.bc2164.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.hifi_reads.bc2164.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/r84036_20250809_035154/1_B01/hifi_reads/m84036_250809_035451_s4.hifi_reads.bc2098.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.hifi_reads.bc2098.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/r84036_20250809_035154/1_B01/hifi_reads/m84036_250809_035451_s4.hifi_reads.bc2116.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.hifi_reads.bc2116.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/r84036_20250809_035154/1_B01/hifi_reads/m84036_250809_035451_s4.hifi_reads.bc2175.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.hifi_reads.bc2175.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/r84036_20250809_035154/1_B01/hifi_reads/m84036_250809_035451_s4.hifi_reads.bc2154.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.hifi_reads.bc2154.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/r84036_20250809_035154/1_B01/hifi_reads/m84036_250809_035451_s4.hifi_reads.bc2191.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.hifi_reads.bc2191.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/r84036_20250809_035154/1_B01/hifi_reads/m84036_250809_035451_s4.hifi_reads.bc2138.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.hifi_reads.bc2138.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/r84036_20250809_035154/1_B01/hifi_reads/m84036_250809_035451_s4.hifi_reads.bc2120.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.hifi_reads.bc2120.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/r84036_20250809_035154/1_B01/hifi_reads/m84036_250809_035451_s4.hifi_reads.bc2137.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.hifi_reads.bc2137.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/r84036_20250809_035154/1_B01/hifi_reads/m84036_250809_035451_s4.hifi_reads.bc2188.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.hifi_reads.bc2188.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/r84036_20250809_035154/1_B01/hifi_reads/m84036_250809_035451_s4.hifi_reads.bc2102.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.hifi_reads.bc2102.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/r84036_20250809_035154/1_B01/hifi_reads/m84036_250809_035451_s4.hifi_reads.bc2182.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.hifi_reads.bc2182.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/r84036_20250809_035154/1_B01/hifi_reads/m84036_250809_035451_s4.hifi_reads.bc2133.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.hifi_reads.bc2133.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/sample_sheet.csv:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample_sheet.csv:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/_singularity_tmpdir_h1j0zeoq/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/_singularity_tmpdir_h1j0zeoq/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:18:08.335 wdl.w:ptcp.t:call-collect_inputs NOTICE slurm_singularity run :: pid: 1195080, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/slurm_singularity.log.txt"
2025-09-15 20:18:09.344 wdl.w:ptcp.t:call-collect_inputs.slurm_singularity INFO srun: job 51797201 queued and waiting for resources
2025-09-15 20:18:09.344 wdl.w:ptcp.t:call-collect_inputs.slurm_singularity INFO srun: job 51797201 has been allocated resources
2025-09-15 20:18:10.355 wdl.w:ptcp.t:call-collect_inputs.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:18:30.573 wdl.w:ptcp.t:call-collect_inputs.stderr VERBOSE INFO:root:Merging 2 BAMs for sample m84036_250809_035451_s4.bc2097
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2025-09-15 20:18:54.917 wdl.w:ptcp.t:call-collect_inputs.stderr VERBOSE INFO:root:Merging 2 BAMs for sample m84036_250809_035451_s4.bc2108
2025-09-15 20:18:54.918 wdl.w:ptcp.t:call-collect_inputs.stderr VERBOSE INFO:root:Merging 2 BAMs for sample m84036_250809_035451_s4.bc2109
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2025-09-15 20:20:01.621 wdl.w:ptcp.t:call-collect_inputs.stderr VERBOSE INFO:root:Merging 2 BAMs for sample m84036_250809_035451_s4.bc2140
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2025-09-15 20:20:19.831 wdl.w:ptcp.t:call-collect_inputs.stderr VERBOSE INFO:root:Merging 2 BAMs for sample m84036_250809_035451_s4.bc2150
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2025-09-15 20:20:28.925 wdl.w:ptcp.t:call-collect_inputs.stderr VERBOSE INFO:root:Merging 2 BAMs for sample m84036_250809_035451_s4.bc2154
2025-09-15 20:20:28.925 wdl.w:ptcp.t:call-collect_inputs.stderr VERBOSE INFO:root:Merging 2 BAMs for sample m84036_250809_035451_s4.bc2155
2025-09-15 20:20:31.955 wdl.w:ptcp.t:call-collect_inputs.stderr VERBOSE INFO:root:Merging 2 BAMs for sample m84036_250809_035451_s4.bc2156
2025-09-15 20:20:34.987 wdl.w:ptcp.t:call-collect_inputs.stderr VERBOSE INFO:root:Merging 2 BAMs for sample m84036_250809_035451_s4.bc2157
2025-09-15 20:20:38.034 wdl.w:ptcp.t:call-collect_inputs.stderr VERBOSE INFO:root:Merging 2 BAMs for sample m84036_250809_035451_s4.bc2158
2025-09-15 20:20:38.034 wdl.w:ptcp.t:call-collect_inputs.stderr VERBOSE INFO:root:Merging 2 BAMs for sample m84036_250809_035451_s4.bc2159
2025-09-15 20:20:41.070 wdl.w:ptcp.t:call-collect_inputs.stderr VERBOSE INFO:root:Merging 2 BAMs for sample m84036_250809_035451_s4.bc2160
2025-09-15 20:20:44.102 wdl.w:ptcp.t:call-collect_inputs.stderr VERBOSE INFO:root:Merging 2 BAMs for sample m84036_250809_035451_s4.bc2161
2025-09-15 20:20:47.132 wdl.w:ptcp.t:call-collect_inputs.stderr VERBOSE INFO:root:Merging 2 BAMs for sample m84036_250809_035451_s4.bc2162
2025-09-15 20:20:50.165 wdl.w:ptcp.t:call-collect_inputs.stderr VERBOSE INFO:root:Merging 2 BAMs for sample m84036_250809_035451_s4.bc2163
2025-09-15 20:20:50.165 wdl.w:ptcp.t:call-collect_inputs.stderr VERBOSE INFO:root:Merging 2 BAMs for sample m84036_250809_035451_s4.bc2164
2025-09-15 20:20:53.199 wdl.w:ptcp.t:call-collect_inputs.stderr VERBOSE INFO:root:Merging 2 BAMs for sample m84036_250809_035451_s4.bc2165
2025-09-15 20:20:56.229 wdl.w:ptcp.t:call-collect_inputs.stderr VERBOSE INFO:root:Merging 2 BAMs for sample m84036_250809_035451_s4.bc2166
2025-09-15 20:20:59.262 wdl.w:ptcp.t:call-collect_inputs.stderr VERBOSE INFO:root:Merging 2 BAMs for sample m84036_250809_035451_s4.bc2167
2025-09-15 20:20:59.262 wdl.w:ptcp.t:call-collect_inputs.stderr VERBOSE INFO:root:Merging 2 BAMs for sample m84036_250809_035451_s4.bc2168
2025-09-15 20:21:02.296 wdl.w:ptcp.t:call-collect_inputs.stderr VERBOSE INFO:root:Merging 2 BAMs for sample m84036_250809_035451_s4.bc2169
2025-09-15 20:21:05.327 wdl.w:ptcp.t:call-collect_inputs.stderr VERBOSE INFO:root:Merging 2 BAMs for sample m84036_250809_035451_s4.bc2170
2025-09-15 20:21:08.359 wdl.w:ptcp.t:call-collect_inputs.stderr VERBOSE INFO:root:Merging 2 BAMs for sample m84036_250809_035451_s4.bc2171
2025-09-15 20:21:08.359 wdl.w:ptcp.t:call-collect_inputs.stderr VERBOSE INFO:root:Merging 2 BAMs for sample m84036_250809_035451_s4.bc2172
2025-09-15 20:21:11.393 wdl.w:ptcp.t:call-collect_inputs.stderr VERBOSE INFO:root:Merging 2 BAMs for sample m84036_250809_035451_s4.bc2173
2025-09-15 20:21:14.427 wdl.w:ptcp.t:call-collect_inputs.stderr VERBOSE INFO:root:Merging 2 BAMs for sample m84036_250809_035451_s4.bc2174
2025-09-15 20:21:17.457 wdl.w:ptcp.t:call-collect_inputs.stderr VERBOSE INFO:root:Merging 2 BAMs for sample m84036_250809_035451_s4.bc2175
2025-09-15 20:21:17.457 wdl.w:ptcp.t:call-collect_inputs.stderr VERBOSE INFO:root:Merging 2 BAMs for sample m84036_250809_035451_s4.bc2176
2025-09-15 20:21:20.494 wdl.w:ptcp.t:call-collect_inputs.stderr VERBOSE INFO:root:Merging 2 BAMs for sample m84036_250809_035451_s4.bc2177
2025-09-15 20:21:23.525 wdl.w:ptcp.t:call-collect_inputs.stderr VERBOSE INFO:root:Merging 2 BAMs for sample m84036_250809_035451_s4.bc2178
2025-09-15 20:21:26.553 wdl.w:ptcp.t:call-collect_inputs.stderr VERBOSE INFO:root:Merging 2 BAMs for sample m84036_250809_035451_s4.bc2179
2025-09-15 20:21:26.553 wdl.w:ptcp.t:call-collect_inputs.stderr VERBOSE INFO:root:Merging 2 BAMs for sample m84036_250809_035451_s4.bc2180
2025-09-15 20:21:29.584 wdl.w:ptcp.t:call-collect_inputs.stderr VERBOSE INFO:root:Merging 2 BAMs for sample m84036_250809_035451_s4.bc2181
2025-09-15 20:21:32.616 wdl.w:ptcp.t:call-collect_inputs.stderr VERBOSE INFO:root:Merging 2 BAMs for sample m84036_250809_035451_s4.bc2182
2025-09-15 20:21:35.648 wdl.w:ptcp.t:call-collect_inputs.stderr VERBOSE INFO:root:Merging 2 BAMs for sample m84036_250809_035451_s4.bc2183
2025-09-15 20:21:35.648 wdl.w:ptcp.t:call-collect_inputs.stderr VERBOSE INFO:root:Merging 2 BAMs for sample m84036_250809_035451_s4.bc2184
2025-09-15 20:21:38.680 wdl.w:ptcp.t:call-collect_inputs.stderr VERBOSE INFO:root:Merging 2 BAMs for sample m84036_250809_035451_s4.bc2185
2025-09-15 20:21:41.715 wdl.w:ptcp.t:call-collect_inputs.stderr VERBOSE INFO:root:Merging 2 BAMs for sample m84036_250809_035451_s4.bc2186
2025-09-15 20:21:44.745 wdl.w:ptcp.t:call-collect_inputs.stderr VERBOSE INFO:root:Merging 2 BAMs for sample m84036_250809_035451_s4.bc2187
2025-09-15 20:21:47.775 wdl.w:ptcp.t:call-collect_inputs.stderr VERBOSE INFO:root:Merging 2 BAMs for sample m84036_250809_035451_s4.bc2188
2025-09-15 20:21:50.808 wdl.w:ptcp.t:call-collect_inputs.stderr VERBOSE INFO:root:Merging 2 BAMs for sample m84036_250809_035451_s4.bc2189
2025-09-15 20:21:53.840 wdl.w:ptcp.t:call-collect_inputs.stderr VERBOSE INFO:root:Merging 2 BAMs for sample m84036_250809_035451_s4.bc2190
2025-09-15 20:21:53.840 wdl.w:ptcp.t:call-collect_inputs.stderr VERBOSE INFO:root:Merging 2 BAMs for sample m84036_250809_035451_s4.bc2191
2025-09-15 20:21:56.870 wdl.w:ptcp.t:call-collect_inputs.stderr VERBOSE INFO:root:Merging 2 BAMs for sample m84036_250809_035451_s4.bc2192
2025-09-15 20:21:59.901 wdl.w:ptcp.t:call-collect_inputs.stderr VERBOSE INFO:root:Wrote list of sample names to biosamples.txt
2025-09-15 20:22:00.824 wdl.w:ptcp.t:call-collect_inputs INFO output :: name: "chunks", value: "(((large)))"
2025-09-15 20:22:00.850 wdl.w:ptcp.t:call-collect_inputs INFO output :: name: "sample_names", value: ["m84036_250809_035451_s4.bc2097", "m84036_250809_035451_s4.bc2098", "m84036_250809_035451_s4.bc2099", "m84036_250809_035451_s4.bc2100", "m84036_250809_035451_s4.bc2101", "m84036_250809_035451_s4.bc2102", "m84036_250809_035451_s4.bc2103", "m84036_250809_035451_s4.bc2104", "m84036_250809_035451_s4.bc2105", "m84036_250809_035451_s4.bc2106", "m84036_250809_035451_s4.bc2107", "m84036_250809_035451_s4.bc2108", "m84036_250809_035451_s4.bc2109", "m84036_250809_035451_s4.bc2110", "m84036_250809_035451_s4.bc2111", "m84036_250809_035451_s4.bc2112", "m84036_250809_035451_s4.bc2113", "m84036_250809_035451_s4.bc2114", "m84036_250809_035451_s4.bc2115", "m84036_250809_035451_s4.bc2116", "m84036_250809_035451_s4.bc2117", "m84036_250809_035451_s4.bc2118", "m84036_250809_035451_s4.bc2119", "m84036_250809_035451_s4.bc2120", "m84036_250809_035451_s4.bc2121", "m84036_250809_035451_s4.bc2122", "m84036_250809_035451_s4.bc2123", "m84036_250809_035451_s4.bc2124", "m84036_250809_035451_s4.bc2125", "m84036_250809_035451_s4.bc2126", "m84036_250809_035451_s4.bc2127", "m84036_250809_035451_s4.bc2128", "m84036_250809_035451_s4.bc2129", "m84036_250809_035451_s4.bc2130", "m84036_250809_035451_s4.bc2131", "m84036_250809_035451_s4.bc2132", "m84036_250809_035451_s4.bc2133", "m84036_250809_035451_s4.bc2134", "m84036_250809_035451_s4.bc2135", "m84036_250809_035451_s4.bc2136", "m84036_250809_035451_s4.bc2137", "m84036_250809_035451_s4.bc2138", "m84036_250809_035451_s4.bc2139", "m84036_250809_035451_s4.bc2140", "m84036_250809_035451_s4.bc2141", "m84036_250809_035451_s4.bc2142", "m84036_250809_035451_s4.bc2143", "m84036_250809_035451_s4.bc2144", "m84036_250809_035451_s4.bc2145", "m84036_250809_035451_s4.bc2146", "m84036_250809_035451_s4.bc2147", "m84036_250809_035451_s4.bc2148", "m84036_250809_035451_s4.bc2149", "m84036_250809_035451_s4.bc2150", "m84036_250809_035451_s4.bc2151", "m84036_250809_035451_s4.bc2152", "m84036_250809_035451_s4.bc2153", "m84036_250809_035451_s4.bc2154", "m84036_250809_035451_s4.bc2155", "m84036_250809_035451_s4.bc2156", "m84036_250809_035451_s4.bc2157", "m84036_250809_035451_s4.bc2158", "m84036_250809_035451_s4.bc2159", "m84036_250809_035451_s4.bc2160", "m84036_250809_035451_s4.bc2161", "m84036_250809_035451_s4.bc2162", "m84036_250809_035451_s4.bc2163", "m84036_250809_035451_s4.bc2164", "m84036_250809_035451_s4.bc2165", "m84036_250809_035451_s4.bc2166", "m84036_250809_035451_s4.bc2167", "m84036_250809_035451_s4.bc2168", "m84036_250809_035451_s4.bc2169", "m84036_250809_035451_s4.bc2170", "m84036_250809_035451_s4.bc2171", "m84036_250809_035451_s4.bc2172", "m84036_250809_035451_s4.bc2173", "m84036_250809_035451_s4.bc2174", "m84036_250809_035451_s4.bc2175", "m84036_250809_035451_s4.bc2176", "m84036_250809_035451_s4.bc2177", "m84036_250809_035451_s4.bc2178", "m84036_250809_035451_s4.bc2179", "m84036_250809_035451_s4.bc2180", "m84036_250809_035451_s4.bc2181", "m84036_250809_035451_s4.bc2182", "m84036_250809_035451_s4.bc2183", "m84036_250809_035451_s4.bc2184", "m84036_250809_035451_s4.bc2185", "m84036_250809_035451_s4.bc2186", "m84036_250809_035451_s4.bc2187", "m84036_250809_035451_s4.bc2188", "m84036_250809_035451_s4.bc2189", "m84036_250809_035451_s4.bc2190", "m84036_250809_035451_s4.bc2191", "m84036_250809_035451_s4.bc2192"]
2025-09-15 20:22:00.854 wdl.w:ptcp.t:call-collect_inputs INFO output :: name: "sample_sexes", value: ["F", "F", "F", "F", "F", "F", "F", "F", "F", "F", "F", "F", "F", "F", "F", "F", "F", "F", "F", "F", "F", "F", "F", "F", "F", "F", "F", "F", "F", "F", "F", "F", "F", "F", "F", "F", "F", "F", "F", "F", "F", "F", "F", "F", "F", "F", "F", "F", "F", "F", "F", "F", "F", "F", "F", "F", "F", "F", "F", "F", "F", "F", "F", "F", "F", "F", "F", "F", "F", "F", "F", "F", "F", "F", "F", "F", "F", "F", "F", "F", "F", "F", "F", "F", "F", "F", "F", "F", "F", "F", "F", "F", "F", "F", "F", "F"]
2025-09-15 20:22:02.019 wdl.w:ptcp.t:call-collect_inputs NOTICE done
2025-09-15 20:22:02.060 wdl.w:ptcp NOTICE finish :: job: "call-collect_inputs"
2025-09-15 20:22:02.060 wdl.w:ptcp INFO output :: job: "call-collect_inputs", values: "(((large)))"
2025-09-15 20:22:02.060 wdl.w:ptcp INFO visit :: node: "output-sample_names", values: {"sample_names": ["m84036_250809_035451_s4.bc2097", "m84036_250809_035451_s4.bc2098", "m84036_250809_035451_s4.bc2099", "m84036_250809_035451_s4.bc2100", "m84036_250809_035451_s4.bc2101", "m84036_250809_035451_s4.bc2102", "m84036_250809_035451_s4.bc2103", "m84036_250809_035451_s4.bc2104", "m84036_250809_035451_s4.bc2105", "m84036_250809_035451_s4.bc2106", "m84036_250809_035451_s4.bc2107", "m84036_250809_035451_s4.bc2108", "m84036_250809_035451_s4.bc2109", "m84036_250809_035451_s4.bc2110", "m84036_250809_035451_s4.bc2111", "m84036_250809_035451_s4.bc2112", "m84036_250809_035451_s4.bc2113", "m84036_250809_035451_s4.bc2114", "m84036_250809_035451_s4.bc2115", "m84036_250809_035451_s4.bc2116", "m84036_250809_035451_s4.bc2117", "m84036_250809_035451_s4.bc2118", "m84036_250809_035451_s4.bc2119", "m84036_250809_035451_s4.bc2120", "m84036_250809_035451_s4.bc2121", "m84036_250809_035451_s4.bc2122", "m84036_250809_035451_s4.bc2123", "m84036_250809_035451_s4.bc2124", "m84036_250809_035451_s4.bc2125", "m84036_250809_035451_s4.bc2126", "m84036_250809_035451_s4.bc2127", "m84036_250809_035451_s4.bc2128", "m84036_250809_035451_s4.bc2129", "m84036_250809_035451_s4.bc2130", "m84036_250809_035451_s4.bc2131", "m84036_250809_035451_s4.bc2132", "m84036_250809_035451_s4.bc2133", "m84036_250809_035451_s4.bc2134", "m84036_250809_035451_s4.bc2135", "m84036_250809_035451_s4.bc2136", "m84036_250809_035451_s4.bc2137", "m84036_250809_035451_s4.bc2138", "m84036_250809_035451_s4.bc2139", "m84036_250809_035451_s4.bc2140", "m84036_250809_035451_s4.bc2141", "m84036_250809_035451_s4.bc2142", "m84036_250809_035451_s4.bc2143", "m84036_250809_035451_s4.bc2144", "m84036_250809_035451_s4.bc2145", "m84036_250809_035451_s4.bc2146", "m84036_250809_035451_s4.bc2147", "m84036_250809_035451_s4.bc2148", "m84036_250809_035451_s4.bc2149", "m84036_250809_035451_s4.bc2150", "m84036_250809_035451_s4.bc2151", "m84036_250809_035451_s4.bc2152", "m84036_250809_035451_s4.bc2153", "m84036_250809_035451_s4.bc2154", "m84036_250809_035451_s4.bc2155", "m84036_250809_035451_s4.bc2156", "m84036_250809_035451_s4.bc2157", "m84036_250809_035451_s4.bc2158", "m84036_250809_035451_s4.bc2159", "m84036_250809_035451_s4.bc2160", "m84036_250809_035451_s4.bc2161", "m84036_250809_035451_s4.bc2162", "m84036_250809_035451_s4.bc2163", "m84036_250809_035451_s4.bc2164", "m84036_250809_035451_s4.bc2165", "m84036_250809_035451_s4.bc2166", "m84036_250809_035451_s4.bc2167", "m84036_250809_035451_s4.bc2168", "m84036_250809_035451_s4.bc2169", "m84036_250809_035451_s4.bc2170", "m84036_250809_035451_s4.bc2171", "m84036_250809_035451_s4.bc2172", "m84036_250809_035451_s4.bc2173", "m84036_250809_035451_s4.bc2174", "m84036_250809_035451_s4.bc2175", "m84036_250809_035451_s4.bc2176", "m84036_250809_035451_s4.bc2177", "m84036_250809_035451_s4.bc2178", "m84036_250809_035451_s4.bc2179", "m84036_250809_035451_s4.bc2180", "m84036_250809_035451_s4.bc2181", "m84036_250809_035451_s4.bc2182", "m84036_250809_035451_s4.bc2183", "m84036_250809_035451_s4.bc2184", "m84036_250809_035451_s4.bc2185", "m84036_250809_035451_s4.bc2186", "m84036_250809_035451_s4.bc2187", "m84036_250809_035451_s4.bc2188", "m84036_250809_035451_s4.bc2189", "m84036_250809_035451_s4.bc2190", "m84036_250809_035451_s4.bc2191", "m84036_250809_035451_s4.bc2192"]}
2025-09-15 20:22:02.064 wdl.w:ptcp INFO visit :: node: "scatter-L178C3-i_chunk", values: {}
2025-09-15 20:22:02.065 wdl.w:ptcp INFO visit :: node: "decl-chunk_bam-00", values: {"chunk_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0001_m84036_250809_035451_s4.bc2097.unmapped.bam"}
2025-09-15 20:22:02.065 wdl.w:ptcp INFO visit :: node: "decl-chunk_bam-01", values: {"chunk_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0002_m84036_250809_035451_s4.bc2098.unmapped.bam"}
2025-09-15 20:22:02.065 wdl.w:ptcp INFO visit :: node: "decl-chunk_bam-02", values: {"chunk_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0003_m84036_250809_035451_s4.bc2099.unmapped.bam"}
2025-09-15 20:22:02.066 wdl.w:ptcp INFO visit :: node: "decl-chunk_bam-03", values: {"chunk_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0004_m84036_250809_035451_s4.bc2100.unmapped.bam"}
2025-09-15 20:22:02.066 wdl.w:ptcp INFO visit :: node: "decl-chunk_bam-04", values: {"chunk_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0005_m84036_250809_035451_s4.bc2101.unmapped.bam"}
2025-09-15 20:22:02.066 wdl.w:ptcp INFO visit :: node: "decl-chunk_bam-05", values: {"chunk_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0006_m84036_250809_035451_s4.bc2102.unmapped.bam"}
2025-09-15 20:22:02.066 wdl.w:ptcp INFO visit :: node: "decl-chunk_bam-06", values: {"chunk_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0007_m84036_250809_035451_s4.bc2103.unmapped.bam"}
2025-09-15 20:22:02.066 wdl.w:ptcp INFO visit :: node: "decl-chunk_bam-07", values: {"chunk_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0008_m84036_250809_035451_s4.bc2104.unmapped.bam"}
2025-09-15 20:22:02.066 wdl.w:ptcp INFO visit :: node: "decl-chunk_bam-08", values: {"chunk_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0009_m84036_250809_035451_s4.bc2105.unmapped.bam"}
2025-09-15 20:22:02.067 wdl.w:ptcp INFO visit :: node: "decl-chunk_bam-09", values: {"chunk_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0010_m84036_250809_035451_s4.bc2106.unmapped.bam"}
2025-09-15 20:22:02.067 wdl.w:ptcp INFO visit :: node: "decl-chunk_bam-10", values: {"chunk_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0011_m84036_250809_035451_s4.bc2107.unmapped.bam"}
2025-09-15 20:22:02.067 wdl.w:ptcp INFO visit :: node: "decl-chunk_bam-11", values: {"chunk_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0012_m84036_250809_035451_s4.bc2108.unmapped.bam"}
2025-09-15 20:22:02.067 wdl.w:ptcp INFO visit :: node: "decl-chunk_bam-12", values: {"chunk_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0013_m84036_250809_035451_s4.bc2109.unmapped.bam"}
2025-09-15 20:22:02.067 wdl.w:ptcp INFO visit :: node: "decl-chunk_bam-13", values: {"chunk_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0014_m84036_250809_035451_s4.bc2110.unmapped.bam"}
2025-09-15 20:22:02.068 wdl.w:ptcp INFO visit :: node: "decl-chunk_bam-14", values: {"chunk_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0015_m84036_250809_035451_s4.bc2111.unmapped.bam"}
2025-09-15 20:22:02.068 wdl.w:ptcp INFO visit :: node: "decl-chunk_bam-15", values: {"chunk_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0016_m84036_250809_035451_s4.bc2112.unmapped.bam"}
2025-09-15 20:22:02.068 wdl.w:ptcp INFO visit :: node: "decl-chunk_bam-16", values: {"chunk_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0017_m84036_250809_035451_s4.bc2113.unmapped.bam"}
2025-09-15 20:22:02.068 wdl.w:ptcp INFO visit :: node: "decl-chunk_bam-17", values: {"chunk_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0018_m84036_250809_035451_s4.bc2114.unmapped.bam"}
2025-09-15 20:22:02.068 wdl.w:ptcp INFO visit :: node: "decl-chunk_bam-18", values: {"chunk_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0019_m84036_250809_035451_s4.bc2115.unmapped.bam"}
2025-09-15 20:22:02.068 wdl.w:ptcp INFO visit :: node: "decl-chunk_bam-19", values: {"chunk_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0020_m84036_250809_035451_s4.bc2116.unmapped.bam"}
2025-09-15 20:22:02.069 wdl.w:ptcp INFO visit :: node: "decl-chunk_bam-20", values: {"chunk_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0021_m84036_250809_035451_s4.bc2117.unmapped.bam"}
2025-09-15 20:22:02.069 wdl.w:ptcp INFO visit :: node: "decl-chunk_bam-21", values: {"chunk_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0022_m84036_250809_035451_s4.bc2118.unmapped.bam"}
2025-09-15 20:22:02.069 wdl.w:ptcp INFO visit :: node: "decl-chunk_bam-22", values: {"chunk_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0023_m84036_250809_035451_s4.bc2119.unmapped.bam"}
2025-09-15 20:22:02.069 wdl.w:ptcp INFO visit :: node: "decl-chunk_bam-23", values: {"chunk_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0024_m84036_250809_035451_s4.bc2120.unmapped.bam"}
2025-09-15 20:22:02.069 wdl.w:ptcp INFO visit :: node: "decl-chunk_bam-24", values: {"chunk_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0025_m84036_250809_035451_s4.bc2121.unmapped.bam"}
2025-09-15 20:22:02.069 wdl.w:ptcp INFO visit :: node: "decl-chunk_bam-25", values: {"chunk_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0026_m84036_250809_035451_s4.bc2122.unmapped.bam"}
2025-09-15 20:22:02.070 wdl.w:ptcp INFO visit :: node: "decl-chunk_bam-26", values: {"chunk_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0027_m84036_250809_035451_s4.bc2123.unmapped.bam"}
2025-09-15 20:22:02.070 wdl.w:ptcp INFO visit :: node: "decl-chunk_bam-27", values: {"chunk_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0028_m84036_250809_035451_s4.bc2124.unmapped.bam"}
2025-09-15 20:22:02.070 wdl.w:ptcp INFO visit :: node: "decl-chunk_bam-28", values: {"chunk_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0029_m84036_250809_035451_s4.bc2125.unmapped.bam"}
2025-09-15 20:22:02.070 wdl.w:ptcp INFO visit :: node: "decl-chunk_bam-29", values: {"chunk_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0030_m84036_250809_035451_s4.bc2126.unmapped.bam"}
2025-09-15 20:22:02.070 wdl.w:ptcp INFO visit :: node: "decl-chunk_bam-30", values: {"chunk_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0031_m84036_250809_035451_s4.bc2127.unmapped.bam"}
2025-09-15 20:22:02.070 wdl.w:ptcp INFO visit :: node: "decl-chunk_bam-31", values: {"chunk_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0032_m84036_250809_035451_s4.bc2128.unmapped.bam"}
2025-09-15 20:22:02.071 wdl.w:ptcp INFO visit :: node: "decl-chunk_bam-32", values: {"chunk_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0033_m84036_250809_035451_s4.bc2129.unmapped.bam"}
2025-09-15 20:22:02.071 wdl.w:ptcp INFO visit :: node: "decl-chunk_bam-33", values: {"chunk_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0034_m84036_250809_035451_s4.bc2130.unmapped.bam"}
2025-09-15 20:22:02.071 wdl.w:ptcp INFO visit :: node: "decl-chunk_bam-34", values: {"chunk_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0035_m84036_250809_035451_s4.bc2131.unmapped.bam"}
2025-09-15 20:22:02.071 wdl.w:ptcp INFO visit :: node: "decl-chunk_bam-35", values: {"chunk_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0036_m84036_250809_035451_s4.bc2132.unmapped.bam"}
2025-09-15 20:22:02.071 wdl.w:ptcp INFO visit :: node: "decl-chunk_bam-36", values: {"chunk_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0037_m84036_250809_035451_s4.bc2133.unmapped.bam"}
2025-09-15 20:22:02.071 wdl.w:ptcp INFO visit :: node: "decl-chunk_bam-37", values: {"chunk_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0038_m84036_250809_035451_s4.bc2134.unmapped.bam"}
2025-09-15 20:22:02.072 wdl.w:ptcp INFO visit :: node: "decl-chunk_bam-38", values: {"chunk_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0039_m84036_250809_035451_s4.bc2135.unmapped.bam"}
2025-09-15 20:22:02.072 wdl.w:ptcp INFO visit :: node: "decl-chunk_bam-39", values: {"chunk_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0040_m84036_250809_035451_s4.bc2136.unmapped.bam"}
2025-09-15 20:22:02.072 wdl.w:ptcp INFO visit :: node: "decl-chunk_bam-40", values: {"chunk_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0041_m84036_250809_035451_s4.bc2137.unmapped.bam"}
2025-09-15 20:22:02.072 wdl.w:ptcp INFO visit :: node: "decl-chunk_bam-41", values: {"chunk_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0042_m84036_250809_035451_s4.bc2138.unmapped.bam"}
2025-09-15 20:22:02.072 wdl.w:ptcp INFO visit :: node: "decl-chunk_bam-42", values: {"chunk_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0043_m84036_250809_035451_s4.bc2139.unmapped.bam"}
2025-09-15 20:22:02.072 wdl.w:ptcp INFO visit :: node: "decl-chunk_bam-43", values: {"chunk_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0044_m84036_250809_035451_s4.bc2140.unmapped.bam"}
2025-09-15 20:22:02.073 wdl.w:ptcp INFO visit :: node: "decl-chunk_bam-44", values: {"chunk_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0045_m84036_250809_035451_s4.bc2141.unmapped.bam"}
2025-09-15 20:22:02.073 wdl.w:ptcp INFO visit :: node: "decl-chunk_bam-45", values: {"chunk_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0046_m84036_250809_035451_s4.bc2142.unmapped.bam"}
2025-09-15 20:22:02.073 wdl.w:ptcp INFO visit :: node: "decl-chunk_bam-46", values: {"chunk_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0047_m84036_250809_035451_s4.bc2143.unmapped.bam"}
2025-09-15 20:22:02.073 wdl.w:ptcp INFO visit :: node: "decl-chunk_bam-47", values: {"chunk_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0048_m84036_250809_035451_s4.bc2144.unmapped.bam"}
2025-09-15 20:22:02.073 wdl.w:ptcp INFO visit :: node: "decl-chunk_bam-48", values: {"chunk_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0049_m84036_250809_035451_s4.bc2145.unmapped.bam"}
2025-09-15 20:22:02.073 wdl.w:ptcp INFO visit :: node: "decl-chunk_bam-49", values: {"chunk_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0050_m84036_250809_035451_s4.bc2146.unmapped.bam"}
2025-09-15 20:22:02.073 wdl.w:ptcp INFO visit :: node: "decl-chunk_bam-50", values: {"chunk_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0051_m84036_250809_035451_s4.bc2147.unmapped.bam"}
2025-09-15 20:22:02.074 wdl.w:ptcp INFO visit :: node: "decl-chunk_bam-51", values: {"chunk_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0052_m84036_250809_035451_s4.bc2148.unmapped.bam"}
2025-09-15 20:22:02.074 wdl.w:ptcp INFO visit :: node: "decl-chunk_bam-52", values: {"chunk_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0053_m84036_250809_035451_s4.bc2149.unmapped.bam"}
2025-09-15 20:22:02.074 wdl.w:ptcp INFO visit :: node: "decl-chunk_bam-53", values: {"chunk_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0054_m84036_250809_035451_s4.bc2150.unmapped.bam"}
2025-09-15 20:22:02.074 wdl.w:ptcp INFO visit :: node: "decl-chunk_bam-54", values: {"chunk_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0055_m84036_250809_035451_s4.bc2151.unmapped.bam"}
2025-09-15 20:22:02.074 wdl.w:ptcp INFO visit :: node: "decl-chunk_bam-55", values: {"chunk_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0056_m84036_250809_035451_s4.bc2152.unmapped.bam"}
2025-09-15 20:22:02.074 wdl.w:ptcp INFO visit :: node: "decl-chunk_bam-56", values: {"chunk_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0057_m84036_250809_035451_s4.bc2153.unmapped.bam"}
2025-09-15 20:22:02.075 wdl.w:ptcp INFO visit :: node: "decl-chunk_bam-57", values: {"chunk_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0058_m84036_250809_035451_s4.bc2154.unmapped.bam"}
2025-09-15 20:22:02.075 wdl.w:ptcp INFO visit :: node: "decl-chunk_bam-58", values: {"chunk_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0059_m84036_250809_035451_s4.bc2155.unmapped.bam"}
2025-09-15 20:22:02.075 wdl.w:ptcp INFO visit :: node: "decl-chunk_bam-59", values: {"chunk_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0060_m84036_250809_035451_s4.bc2156.unmapped.bam"}
2025-09-15 20:22:02.075 wdl.w:ptcp INFO visit :: node: "decl-chunk_bam-60", values: {"chunk_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0061_m84036_250809_035451_s4.bc2157.unmapped.bam"}
2025-09-15 20:22:02.075 wdl.w:ptcp INFO visit :: node: "decl-chunk_bam-61", values: {"chunk_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0062_m84036_250809_035451_s4.bc2158.unmapped.bam"}
2025-09-15 20:22:02.075 wdl.w:ptcp INFO visit :: node: "decl-chunk_bam-62", values: {"chunk_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0063_m84036_250809_035451_s4.bc2159.unmapped.bam"}
2025-09-15 20:22:02.075 wdl.w:ptcp INFO visit :: node: "decl-chunk_bam-63", values: {"chunk_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0064_m84036_250809_035451_s4.bc2160.unmapped.bam"}
2025-09-15 20:22:02.076 wdl.w:ptcp INFO visit :: node: "decl-chunk_bam-64", values: {"chunk_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0065_m84036_250809_035451_s4.bc2161.unmapped.bam"}
2025-09-15 20:22:02.076 wdl.w:ptcp INFO visit :: node: "decl-chunk_bam-65", values: {"chunk_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0066_m84036_250809_035451_s4.bc2162.unmapped.bam"}
2025-09-15 20:22:02.076 wdl.w:ptcp INFO visit :: node: "decl-chunk_bam-66", values: {"chunk_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0067_m84036_250809_035451_s4.bc2163.unmapped.bam"}
2025-09-15 20:22:02.076 wdl.w:ptcp INFO visit :: node: "decl-chunk_bam-67", values: {"chunk_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0068_m84036_250809_035451_s4.bc2164.unmapped.bam"}
2025-09-15 20:22:02.076 wdl.w:ptcp INFO visit :: node: "decl-chunk_bam-68", values: {"chunk_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0069_m84036_250809_035451_s4.bc2165.unmapped.bam"}
2025-09-15 20:22:02.076 wdl.w:ptcp INFO visit :: node: "decl-chunk_bam-69", values: {"chunk_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0070_m84036_250809_035451_s4.bc2166.unmapped.bam"}
2025-09-15 20:22:02.077 wdl.w:ptcp INFO visit :: node: "decl-chunk_bam-70", values: {"chunk_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0071_m84036_250809_035451_s4.bc2167.unmapped.bam"}
2025-09-15 20:22:02.077 wdl.w:ptcp INFO visit :: node: "decl-chunk_bam-71", values: {"chunk_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0072_m84036_250809_035451_s4.bc2168.unmapped.bam"}
2025-09-15 20:22:02.077 wdl.w:ptcp INFO visit :: node: "decl-chunk_bam-72", values: {"chunk_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0073_m84036_250809_035451_s4.bc2169.unmapped.bam"}
2025-09-15 20:22:02.077 wdl.w:ptcp INFO visit :: node: "decl-chunk_bam-73", values: {"chunk_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0074_m84036_250809_035451_s4.bc2170.unmapped.bam"}
2025-09-15 20:22:02.077 wdl.w:ptcp INFO visit :: node: "decl-chunk_bam-74", values: {"chunk_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0075_m84036_250809_035451_s4.bc2171.unmapped.bam"}
2025-09-15 20:22:02.077 wdl.w:ptcp INFO visit :: node: "decl-chunk_bam-75", values: {"chunk_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0076_m84036_250809_035451_s4.bc2172.unmapped.bam"}
2025-09-15 20:22:02.077 wdl.w:ptcp INFO visit :: node: "decl-chunk_bam-76", values: {"chunk_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0077_m84036_250809_035451_s4.bc2173.unmapped.bam"}
2025-09-15 20:22:02.078 wdl.w:ptcp INFO visit :: node: "decl-chunk_bam-77", values: {"chunk_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0078_m84036_250809_035451_s4.bc2174.unmapped.bam"}
2025-09-15 20:22:02.078 wdl.w:ptcp INFO visit :: node: "decl-chunk_bam-78", values: {"chunk_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0079_m84036_250809_035451_s4.bc2175.unmapped.bam"}
2025-09-15 20:22:02.078 wdl.w:ptcp INFO visit :: node: "decl-chunk_bam-79", values: {"chunk_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0080_m84036_250809_035451_s4.bc2176.unmapped.bam"}
2025-09-15 20:22:02.078 wdl.w:ptcp INFO visit :: node: "decl-chunk_bam-80", values: {"chunk_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0081_m84036_250809_035451_s4.bc2177.unmapped.bam"}
2025-09-15 20:22:02.078 wdl.w:ptcp INFO visit :: node: "decl-chunk_bam-81", values: {"chunk_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0082_m84036_250809_035451_s4.bc2178.unmapped.bam"}
2025-09-15 20:22:02.078 wdl.w:ptcp INFO visit :: node: "decl-chunk_bam-82", values: {"chunk_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0083_m84036_250809_035451_s4.bc2179.unmapped.bam"}
2025-09-15 20:22:02.078 wdl.w:ptcp INFO visit :: node: "decl-chunk_bam-83", values: {"chunk_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0084_m84036_250809_035451_s4.bc2180.unmapped.bam"}
2025-09-15 20:22:02.079 wdl.w:ptcp INFO visit :: node: "decl-chunk_bam-84", values: {"chunk_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0085_m84036_250809_035451_s4.bc2181.unmapped.bam"}
2025-09-15 20:22:02.079 wdl.w:ptcp INFO visit :: node: "decl-chunk_bam-85", values: {"chunk_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0086_m84036_250809_035451_s4.bc2182.unmapped.bam"}
2025-09-15 20:22:02.079 wdl.w:ptcp INFO visit :: node: "decl-chunk_bam-86", values: {"chunk_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0087_m84036_250809_035451_s4.bc2183.unmapped.bam"}
2025-09-15 20:22:02.079 wdl.w:ptcp INFO visit :: node: "decl-chunk_bam-87", values: {"chunk_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0088_m84036_250809_035451_s4.bc2184.unmapped.bam"}
2025-09-15 20:22:02.079 wdl.w:ptcp INFO visit :: node: "decl-chunk_bam-88", values: {"chunk_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0089_m84036_250809_035451_s4.bc2185.unmapped.bam"}
2025-09-15 20:22:02.079 wdl.w:ptcp INFO visit :: node: "decl-chunk_bam-89", values: {"chunk_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0090_m84036_250809_035451_s4.bc2186.unmapped.bam"}
2025-09-15 20:22:02.079 wdl.w:ptcp INFO visit :: node: "decl-chunk_bam-90", values: {"chunk_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0091_m84036_250809_035451_s4.bc2187.unmapped.bam"}
2025-09-15 20:22:02.080 wdl.w:ptcp INFO visit :: node: "decl-chunk_bam-91", values: {"chunk_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0092_m84036_250809_035451_s4.bc2188.unmapped.bam"}
2025-09-15 20:22:02.080 wdl.w:ptcp INFO visit :: node: "decl-chunk_bam-92", values: {"chunk_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0093_m84036_250809_035451_s4.bc2189.unmapped.bam"}
2025-09-15 20:22:02.080 wdl.w:ptcp INFO visit :: node: "decl-chunk_bam-93", values: {"chunk_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0094_m84036_250809_035451_s4.bc2190.unmapped.bam"}
2025-09-15 20:22:02.080 wdl.w:ptcp INFO visit :: node: "decl-chunk_bam-94", values: {"chunk_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0095_m84036_250809_035451_s4.bc2191.unmapped.bam"}
2025-09-15 20:22:02.080 wdl.w:ptcp INFO visit :: node: "decl-chunk_bam-95", values: {"chunk_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0096_m84036_250809_035451_s4.bc2192.unmapped.bam"}
2025-09-15 20:22:02.080 wdl.w:ptcp INFO visit :: node: "decl-sample_name-00", values: {"sample_name": "m84036_250809_035451_s4.bc2097"}
2025-09-15 20:22:02.080 wdl.w:ptcp INFO visit :: node: "decl-sample_name-01", values: {"sample_name": "m84036_250809_035451_s4.bc2098"}
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2025-09-15 20:22:02.081 wdl.w:ptcp INFO visit :: node: "decl-sample_name-04", values: {"sample_name": "m84036_250809_035451_s4.bc2101"}
2025-09-15 20:22:02.081 wdl.w:ptcp INFO visit :: node: "decl-sample_name-05", values: {"sample_name": "m84036_250809_035451_s4.bc2102"}
2025-09-15 20:22:02.081 wdl.w:ptcp INFO visit :: node: "decl-sample_name-06", values: {"sample_name": "m84036_250809_035451_s4.bc2103"}
2025-09-15 20:22:02.082 wdl.w:ptcp INFO visit :: node: "decl-sample_name-07", values: {"sample_name": "m84036_250809_035451_s4.bc2104"}
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2025-09-15 20:22:02.082 wdl.w:ptcp INFO visit :: node: "decl-sample_name-09", values: {"sample_name": "m84036_250809_035451_s4.bc2106"}
2025-09-15 20:22:02.082 wdl.w:ptcp INFO visit :: node: "decl-sample_name-10", values: {"sample_name": "m84036_250809_035451_s4.bc2107"}
2025-09-15 20:22:02.082 wdl.w:ptcp INFO visit :: node: "decl-sample_name-11", values: {"sample_name": "m84036_250809_035451_s4.bc2108"}
2025-09-15 20:22:02.083 wdl.w:ptcp INFO visit :: node: "decl-sample_name-12", values: {"sample_name": "m84036_250809_035451_s4.bc2109"}
2025-09-15 20:22:02.083 wdl.w:ptcp INFO visit :: node: "decl-sample_name-13", values: {"sample_name": "m84036_250809_035451_s4.bc2110"}
2025-09-15 20:22:02.083 wdl.w:ptcp INFO visit :: node: "decl-sample_name-14", values: {"sample_name": "m84036_250809_035451_s4.bc2111"}
2025-09-15 20:22:02.083 wdl.w:ptcp INFO visit :: node: "decl-sample_name-15", values: {"sample_name": "m84036_250809_035451_s4.bc2112"}
2025-09-15 20:22:02.083 wdl.w:ptcp INFO visit :: node: "decl-sample_name-16", values: {"sample_name": "m84036_250809_035451_s4.bc2113"}
2025-09-15 20:22:02.083 wdl.w:ptcp INFO visit :: node: "decl-sample_name-17", values: {"sample_name": "m84036_250809_035451_s4.bc2114"}
2025-09-15 20:22:02.084 wdl.w:ptcp INFO visit :: node: "decl-sample_name-18", values: {"sample_name": "m84036_250809_035451_s4.bc2115"}
2025-09-15 20:22:02.084 wdl.w:ptcp INFO visit :: node: "decl-sample_name-19", values: {"sample_name": "m84036_250809_035451_s4.bc2116"}
2025-09-15 20:22:02.084 wdl.w:ptcp INFO visit :: node: "decl-sample_name-20", values: {"sample_name": "m84036_250809_035451_s4.bc2117"}
2025-09-15 20:22:02.084 wdl.w:ptcp INFO visit :: node: "decl-sample_name-21", values: {"sample_name": "m84036_250809_035451_s4.bc2118"}
2025-09-15 20:22:02.084 wdl.w:ptcp INFO visit :: node: "decl-sample_name-22", values: {"sample_name": "m84036_250809_035451_s4.bc2119"}
2025-09-15 20:22:02.084 wdl.w:ptcp INFO visit :: node: "decl-sample_name-23", values: {"sample_name": "m84036_250809_035451_s4.bc2120"}
2025-09-15 20:22:02.085 wdl.w:ptcp INFO visit :: node: "decl-sample_name-24", values: {"sample_name": "m84036_250809_035451_s4.bc2121"}
2025-09-15 20:22:02.085 wdl.w:ptcp INFO visit :: node: "decl-sample_name-25", values: {"sample_name": "m84036_250809_035451_s4.bc2122"}
2025-09-15 20:22:02.085 wdl.w:ptcp INFO visit :: node: "decl-sample_name-26", values: {"sample_name": "m84036_250809_035451_s4.bc2123"}
2025-09-15 20:22:02.085 wdl.w:ptcp INFO visit :: node: "decl-sample_name-27", values: {"sample_name": "m84036_250809_035451_s4.bc2124"}
2025-09-15 20:22:02.085 wdl.w:ptcp INFO visit :: node: "decl-sample_name-28", values: {"sample_name": "m84036_250809_035451_s4.bc2125"}
2025-09-15 20:22:02.085 wdl.w:ptcp INFO visit :: node: "decl-sample_name-29", values: {"sample_name": "m84036_250809_035451_s4.bc2126"}
2025-09-15 20:22:02.086 wdl.w:ptcp INFO visit :: node: "decl-sample_name-30", values: {"sample_name": "m84036_250809_035451_s4.bc2127"}
2025-09-15 20:22:02.086 wdl.w:ptcp INFO visit :: node: "decl-sample_name-31", values: {"sample_name": "m84036_250809_035451_s4.bc2128"}
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2025-09-15 20:22:02.086 wdl.w:ptcp INFO visit :: node: "decl-sample_name-35", values: {"sample_name": "m84036_250809_035451_s4.bc2132"}
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2025-09-15 20:22:02.087 wdl.w:ptcp INFO visit :: node: "decl-sample_name-37", values: {"sample_name": "m84036_250809_035451_s4.bc2134"}
2025-09-15 20:22:02.087 wdl.w:ptcp INFO visit :: node: "decl-sample_name-38", values: {"sample_name": "m84036_250809_035451_s4.bc2135"}
2025-09-15 20:22:02.087 wdl.w:ptcp INFO visit :: node: "decl-sample_name-39", values: {"sample_name": "m84036_250809_035451_s4.bc2136"}
2025-09-15 20:22:02.087 wdl.w:ptcp INFO visit :: node: "decl-sample_name-40", values: {"sample_name": "m84036_250809_035451_s4.bc2137"}
2025-09-15 20:22:02.087 wdl.w:ptcp INFO visit :: node: "decl-sample_name-41", values: {"sample_name": "m84036_250809_035451_s4.bc2138"}
2025-09-15 20:22:02.088 wdl.w:ptcp INFO visit :: node: "decl-sample_name-42", values: {"sample_name": "m84036_250809_035451_s4.bc2139"}
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2025-09-15 20:22:02.094 wdl.w:ptcp INFO visit :: node: "decl-sample_name-89", values: {"sample_name": "m84036_250809_035451_s4.bc2186"}
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2025-09-15 20:22:02.095 wdl.w:ptcp INFO visit :: node: "decl-sample_name-93", values: {"sample_name": "m84036_250809_035451_s4.bc2190"}
2025-09-15 20:22:02.095 wdl.w:ptcp INFO visit :: node: "decl-sample_name-94", values: {"sample_name": "m84036_250809_035451_s4.bc2191"}
2025-09-15 20:22:02.095 wdl.w:ptcp INFO visit :: node: "decl-sample_name-95", values: {"sample_name": "m84036_250809_035451_s4.bc2192"}
2025-09-15 20:22:02.095 wdl.w:ptcp INFO visit :: node: "decl-sample_sex-00", values: {"sample_sex": "F"}
2025-09-15 20:22:02.096 wdl.w:ptcp INFO visit :: node: "decl-sample_sex-01", values: {"sample_sex": "F"}
2025-09-15 20:22:02.096 wdl.w:ptcp INFO visit :: node: "decl-sample_sex-02", values: {"sample_sex": "F"}
2025-09-15 20:22:02.096 wdl.w:ptcp INFO visit :: node: "decl-sample_sex-03", values: {"sample_sex": "F"}
2025-09-15 20:22:02.096 wdl.w:ptcp INFO visit :: node: "decl-sample_sex-04", values: {"sample_sex": "F"}
2025-09-15 20:22:02.096 wdl.w:ptcp INFO visit :: node: "decl-sample_sex-05", values: {"sample_sex": "F"}
2025-09-15 20:22:02.097 wdl.w:ptcp INFO visit :: node: "decl-sample_sex-06", values: {"sample_sex": "F"}
2025-09-15 20:22:02.097 wdl.w:ptcp INFO visit :: node: "decl-sample_sex-07", values: {"sample_sex": "F"}
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2025-09-15 20:22:02.097 wdl.w:ptcp INFO visit :: node: "decl-sample_sex-09", values: {"sample_sex": "F"}
2025-09-15 20:22:02.097 wdl.w:ptcp INFO visit :: node: "decl-sample_sex-10", values: {"sample_sex": "F"}
2025-09-15 20:22:02.097 wdl.w:ptcp INFO visit :: node: "decl-sample_sex-11", values: {"sample_sex": "F"}
2025-09-15 20:22:02.098 wdl.w:ptcp INFO visit :: node: "decl-sample_sex-12", values: {"sample_sex": "F"}
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2025-09-15 20:22:02.098 wdl.w:ptcp INFO visit :: node: "decl-sample_sex-14", values: {"sample_sex": "F"}
2025-09-15 20:22:02.098 wdl.w:ptcp INFO visit :: node: "decl-sample_sex-15", values: {"sample_sex": "F"}
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2025-09-15 20:22:02.098 wdl.w:ptcp INFO visit :: node: "decl-sample_sex-17", values: {"sample_sex": "F"}
2025-09-15 20:22:02.099 wdl.w:ptcp INFO visit :: node: "decl-sample_sex-18", values: {"sample_sex": "F"}
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2025-09-15 20:22:02.099 wdl.w:ptcp INFO visit :: node: "decl-sample_sex-20", values: {"sample_sex": "F"}
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2025-09-15 20:22:02.100 wdl.w:ptcp INFO visit :: node: "decl-sample_sex-24", values: {"sample_sex": "F"}
2025-09-15 20:22:02.100 wdl.w:ptcp INFO visit :: node: "decl-sample_sex-25", values: {"sample_sex": "F"}
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2025-09-15 20:22:02.102 wdl.w:ptcp INFO visit :: node: "decl-sample_sex-37", values: {"sample_sex": "F"}
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2025-09-15 20:22:02.102 wdl.w:ptcp INFO visit :: node: "decl-sample_sex-42", values: {"sample_sex": "F"}
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2025-09-15 20:22:02.104 wdl.w:ptcp INFO visit :: node: "decl-sample_sex-55", values: {"sample_sex": "F"}
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2025-09-15 20:22:02.105 wdl.w:ptcp INFO visit :: node: "decl-sample_sex-57", values: {"sample_sex": "F"}
2025-09-15 20:22:02.105 wdl.w:ptcp INFO visit :: node: "decl-sample_sex-58", values: {"sample_sex": "F"}
2025-09-15 20:22:02.105 wdl.w:ptcp INFO visit :: node: "decl-sample_sex-59", values: {"sample_sex": "F"}
2025-09-15 20:22:02.105 wdl.w:ptcp INFO visit :: node: "decl-sample_sex-60", values: {"sample_sex": "F"}
2025-09-15 20:22:02.105 wdl.w:ptcp INFO visit :: node: "decl-sample_sex-61", values: {"sample_sex": "F"}
2025-09-15 20:22:02.105 wdl.w:ptcp INFO visit :: node: "decl-sample_sex-62", values: {"sample_sex": "F"}
2025-09-15 20:22:02.106 wdl.w:ptcp INFO visit :: node: "decl-sample_sex-63", values: {"sample_sex": "F"}
2025-09-15 20:22:02.106 wdl.w:ptcp INFO visit :: node: "decl-sample_sex-64", values: {"sample_sex": "F"}
2025-09-15 20:22:02.106 wdl.w:ptcp INFO visit :: node: "decl-sample_sex-65", values: {"sample_sex": "F"}
2025-09-15 20:22:02.106 wdl.w:ptcp INFO visit :: node: "decl-sample_sex-66", values: {"sample_sex": "F"}
2025-09-15 20:22:02.106 wdl.w:ptcp INFO visit :: node: "decl-sample_sex-67", values: {"sample_sex": "F"}
2025-09-15 20:22:02.106 wdl.w:ptcp INFO visit :: node: "decl-sample_sex-68", values: {"sample_sex": "F"}
2025-09-15 20:22:02.106 wdl.w:ptcp INFO visit :: node: "decl-sample_sex-69", values: {"sample_sex": "F"}
2025-09-15 20:22:02.107 wdl.w:ptcp INFO visit :: node: "decl-sample_sex-70", values: {"sample_sex": "F"}
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2025-09-15 20:22:02.107 wdl.w:ptcp INFO visit :: node: "decl-sample_sex-72", values: {"sample_sex": "F"}
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2025-09-15 20:22:02.109 wdl.w:ptcp INFO visit :: node: "decl-sample_sex-85", values: {"sample_sex": "F"}
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2025-09-15 20:22:02.109 wdl.w:ptcp INFO visit :: node: "decl-sample_sex-87", values: {"sample_sex": "F"}
2025-09-15 20:22:02.109 wdl.w:ptcp INFO visit :: node: "decl-sample_sex-88", values: {"sample_sex": "F"}
2025-09-15 20:22:02.109 wdl.w:ptcp INFO visit :: node: "decl-sample_sex-89", values: {"sample_sex": "F"}
2025-09-15 20:22:02.109 wdl.w:ptcp INFO visit :: node: "decl-sample_sex-90", values: {"sample_sex": "F"}
2025-09-15 20:22:02.110 wdl.w:ptcp INFO visit :: node: "decl-sample_sex-91", values: {"sample_sex": "F"}
2025-09-15 20:22:02.110 wdl.w:ptcp INFO visit :: node: "decl-sample_sex-92", values: {"sample_sex": "F"}
2025-09-15 20:22:02.110 wdl.w:ptcp INFO visit :: node: "decl-sample_sex-93", values: {"sample_sex": "F"}
2025-09-15 20:22:02.110 wdl.w:ptcp INFO visit :: node: "decl-sample_sex-94", values: {"sample_sex": "F"}
2025-09-15 20:22:02.110 wdl.w:ptcp INFO visit :: node: "decl-sample_sex-95", values: {"sample_sex": "F"}
2025-09-15 20:22:02.110 wdl.w:ptcp INFO visit :: node: "decl-unmapped_bam-00", values: {"unmapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0001_m84036_250809_035451_s4.bc2097.unmapped.bam"}
2025-09-15 20:22:02.111 wdl.w:ptcp INFO visit :: node: "decl-unmapped_bam-01", values: {"unmapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0002_m84036_250809_035451_s4.bc2098.unmapped.bam"}
2025-09-15 20:22:02.111 wdl.w:ptcp INFO visit :: node: "decl-unmapped_bam-02", values: {"unmapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0003_m84036_250809_035451_s4.bc2099.unmapped.bam"}
2025-09-15 20:22:02.111 wdl.w:ptcp INFO visit :: node: "decl-unmapped_bam-03", values: {"unmapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0004_m84036_250809_035451_s4.bc2100.unmapped.bam"}
2025-09-15 20:22:02.111 wdl.w:ptcp INFO visit :: node: "decl-unmapped_bam-04", values: {"unmapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0005_m84036_250809_035451_s4.bc2101.unmapped.bam"}
2025-09-15 20:22:02.111 wdl.w:ptcp INFO visit :: node: "decl-unmapped_bam-05", values: {"unmapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0006_m84036_250809_035451_s4.bc2102.unmapped.bam"}
2025-09-15 20:22:02.111 wdl.w:ptcp INFO visit :: node: "decl-unmapped_bam-06", values: {"unmapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0007_m84036_250809_035451_s4.bc2103.unmapped.bam"}
2025-09-15 20:22:02.111 wdl.w:ptcp INFO visit :: node: "decl-unmapped_bam-07", values: {"unmapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0008_m84036_250809_035451_s4.bc2104.unmapped.bam"}
2025-09-15 20:22:02.111 wdl.w:ptcp INFO visit :: node: "decl-unmapped_bam-08", values: {"unmapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0009_m84036_250809_035451_s4.bc2105.unmapped.bam"}
2025-09-15 20:22:02.111 wdl.w:ptcp INFO visit :: node: "decl-unmapped_bam-09", values: {"unmapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0010_m84036_250809_035451_s4.bc2106.unmapped.bam"}
2025-09-15 20:22:02.111 wdl.w:ptcp INFO visit :: node: "decl-unmapped_bam-10", values: {"unmapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0011_m84036_250809_035451_s4.bc2107.unmapped.bam"}
2025-09-15 20:22:02.111 wdl.w:ptcp INFO visit :: node: "decl-unmapped_bam-11", values: {"unmapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0012_m84036_250809_035451_s4.bc2108.unmapped.bam"}
2025-09-15 20:22:02.111 wdl.w:ptcp INFO visit :: node: "decl-unmapped_bam-12", values: {"unmapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0013_m84036_250809_035451_s4.bc2109.unmapped.bam"}
2025-09-15 20:22:02.111 wdl.w:ptcp INFO visit :: node: "decl-unmapped_bam-13", values: {"unmapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0014_m84036_250809_035451_s4.bc2110.unmapped.bam"}
2025-09-15 20:22:02.111 wdl.w:ptcp INFO visit :: node: "decl-unmapped_bam-14", values: {"unmapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0015_m84036_250809_035451_s4.bc2111.unmapped.bam"}
2025-09-15 20:22:02.111 wdl.w:ptcp INFO visit :: node: "decl-unmapped_bam-15", values: {"unmapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0016_m84036_250809_035451_s4.bc2112.unmapped.bam"}
2025-09-15 20:22:02.111 wdl.w:ptcp INFO visit :: node: "decl-unmapped_bam-16", values: {"unmapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0017_m84036_250809_035451_s4.bc2113.unmapped.bam"}
2025-09-15 20:22:02.111 wdl.w:ptcp INFO visit :: node: "decl-unmapped_bam-17", values: {"unmapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0018_m84036_250809_035451_s4.bc2114.unmapped.bam"}
2025-09-15 20:22:02.111 wdl.w:ptcp INFO visit :: node: "decl-unmapped_bam-18", values: {"unmapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0019_m84036_250809_035451_s4.bc2115.unmapped.bam"}
2025-09-15 20:22:02.111 wdl.w:ptcp INFO visit :: node: "decl-unmapped_bam-19", values: {"unmapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0020_m84036_250809_035451_s4.bc2116.unmapped.bam"}
2025-09-15 20:22:02.112 wdl.w:ptcp INFO visit :: node: "decl-unmapped_bam-20", values: {"unmapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0021_m84036_250809_035451_s4.bc2117.unmapped.bam"}
2025-09-15 20:22:02.112 wdl.w:ptcp INFO visit :: node: "decl-unmapped_bam-21", values: {"unmapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0022_m84036_250809_035451_s4.bc2118.unmapped.bam"}
2025-09-15 20:22:02.112 wdl.w:ptcp INFO visit :: node: "decl-unmapped_bam-22", values: {"unmapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0023_m84036_250809_035451_s4.bc2119.unmapped.bam"}
2025-09-15 20:22:02.112 wdl.w:ptcp INFO visit :: node: "decl-unmapped_bam-23", values: {"unmapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0024_m84036_250809_035451_s4.bc2120.unmapped.bam"}
2025-09-15 20:22:02.112 wdl.w:ptcp INFO visit :: node: "decl-unmapped_bam-24", values: {"unmapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0025_m84036_250809_035451_s4.bc2121.unmapped.bam"}
2025-09-15 20:22:02.112 wdl.w:ptcp INFO visit :: node: "decl-unmapped_bam-25", values: {"unmapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0026_m84036_250809_035451_s4.bc2122.unmapped.bam"}
2025-09-15 20:22:02.112 wdl.w:ptcp INFO visit :: node: "decl-unmapped_bam-26", values: {"unmapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0027_m84036_250809_035451_s4.bc2123.unmapped.bam"}
2025-09-15 20:22:02.112 wdl.w:ptcp INFO visit :: node: "decl-unmapped_bam-27", values: {"unmapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0028_m84036_250809_035451_s4.bc2124.unmapped.bam"}
2025-09-15 20:22:02.112 wdl.w:ptcp INFO visit :: node: "decl-unmapped_bam-28", values: {"unmapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0029_m84036_250809_035451_s4.bc2125.unmapped.bam"}
2025-09-15 20:22:02.112 wdl.w:ptcp INFO visit :: node: "decl-unmapped_bam-29", values: {"unmapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0030_m84036_250809_035451_s4.bc2126.unmapped.bam"}
2025-09-15 20:22:02.112 wdl.w:ptcp INFO visit :: node: "decl-unmapped_bam-30", values: {"unmapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0031_m84036_250809_035451_s4.bc2127.unmapped.bam"}
2025-09-15 20:22:02.112 wdl.w:ptcp INFO visit :: node: "decl-unmapped_bam-31", values: {"unmapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0032_m84036_250809_035451_s4.bc2128.unmapped.bam"}
2025-09-15 20:22:02.112 wdl.w:ptcp INFO visit :: node: "decl-unmapped_bam-32", values: {"unmapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0033_m84036_250809_035451_s4.bc2129.unmapped.bam"}
2025-09-15 20:22:02.112 wdl.w:ptcp INFO visit :: node: "decl-unmapped_bam-33", values: {"unmapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0034_m84036_250809_035451_s4.bc2130.unmapped.bam"}
2025-09-15 20:22:02.112 wdl.w:ptcp INFO visit :: node: "decl-unmapped_bam-34", values: {"unmapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0035_m84036_250809_035451_s4.bc2131.unmapped.bam"}
2025-09-15 20:22:02.112 wdl.w:ptcp INFO visit :: node: "decl-unmapped_bam-35", values: {"unmapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0036_m84036_250809_035451_s4.bc2132.unmapped.bam"}
2025-09-15 20:22:02.112 wdl.w:ptcp INFO visit :: node: "decl-unmapped_bam-36", values: {"unmapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0037_m84036_250809_035451_s4.bc2133.unmapped.bam"}
2025-09-15 20:22:02.112 wdl.w:ptcp INFO visit :: node: "decl-unmapped_bam-37", values: {"unmapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0038_m84036_250809_035451_s4.bc2134.unmapped.bam"}
2025-09-15 20:22:02.112 wdl.w:ptcp INFO visit :: node: "decl-unmapped_bam-38", values: {"unmapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0039_m84036_250809_035451_s4.bc2135.unmapped.bam"}
2025-09-15 20:22:02.112 wdl.w:ptcp INFO visit :: node: "decl-unmapped_bam-39", values: {"unmapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0040_m84036_250809_035451_s4.bc2136.unmapped.bam"}
2025-09-15 20:22:02.113 wdl.w:ptcp INFO visit :: node: "decl-unmapped_bam-40", values: {"unmapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0041_m84036_250809_035451_s4.bc2137.unmapped.bam"}
2025-09-15 20:22:02.113 wdl.w:ptcp INFO visit :: node: "decl-unmapped_bam-41", values: {"unmapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0042_m84036_250809_035451_s4.bc2138.unmapped.bam"}
2025-09-15 20:22:02.113 wdl.w:ptcp INFO visit :: node: "decl-unmapped_bam-42", values: {"unmapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0043_m84036_250809_035451_s4.bc2139.unmapped.bam"}
2025-09-15 20:22:02.113 wdl.w:ptcp INFO visit :: node: "decl-unmapped_bam-43", values: {"unmapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0044_m84036_250809_035451_s4.bc2140.unmapped.bam"}
2025-09-15 20:22:02.113 wdl.w:ptcp INFO visit :: node: "decl-unmapped_bam-44", values: {"unmapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0045_m84036_250809_035451_s4.bc2141.unmapped.bam"}
2025-09-15 20:22:02.113 wdl.w:ptcp INFO visit :: node: "decl-unmapped_bam-45", values: {"unmapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0046_m84036_250809_035451_s4.bc2142.unmapped.bam"}
2025-09-15 20:22:02.113 wdl.w:ptcp INFO visit :: node: "decl-unmapped_bam-46", values: {"unmapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0047_m84036_250809_035451_s4.bc2143.unmapped.bam"}
2025-09-15 20:22:02.113 wdl.w:ptcp INFO visit :: node: "decl-unmapped_bam-47", values: {"unmapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0048_m84036_250809_035451_s4.bc2144.unmapped.bam"}
2025-09-15 20:22:02.113 wdl.w:ptcp INFO visit :: node: "decl-unmapped_bam-48", values: {"unmapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0049_m84036_250809_035451_s4.bc2145.unmapped.bam"}
2025-09-15 20:22:02.113 wdl.w:ptcp INFO visit :: node: "decl-unmapped_bam-49", values: {"unmapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0050_m84036_250809_035451_s4.bc2146.unmapped.bam"}
2025-09-15 20:22:02.113 wdl.w:ptcp INFO visit :: node: "decl-unmapped_bam-50", values: {"unmapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0051_m84036_250809_035451_s4.bc2147.unmapped.bam"}
2025-09-15 20:22:02.113 wdl.w:ptcp INFO visit :: node: "decl-unmapped_bam-51", values: {"unmapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0052_m84036_250809_035451_s4.bc2148.unmapped.bam"}
2025-09-15 20:22:02.113 wdl.w:ptcp INFO visit :: node: "decl-unmapped_bam-52", values: {"unmapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0053_m84036_250809_035451_s4.bc2149.unmapped.bam"}
2025-09-15 20:22:02.113 wdl.w:ptcp INFO visit :: node: "decl-unmapped_bam-53", values: {"unmapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0054_m84036_250809_035451_s4.bc2150.unmapped.bam"}
2025-09-15 20:22:02.113 wdl.w:ptcp INFO visit :: node: "decl-unmapped_bam-54", values: {"unmapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0055_m84036_250809_035451_s4.bc2151.unmapped.bam"}
2025-09-15 20:22:02.113 wdl.w:ptcp INFO visit :: node: "decl-unmapped_bam-55", values: {"unmapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0056_m84036_250809_035451_s4.bc2152.unmapped.bam"}
2025-09-15 20:22:02.113 wdl.w:ptcp INFO visit :: node: "decl-unmapped_bam-56", values: {"unmapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0057_m84036_250809_035451_s4.bc2153.unmapped.bam"}
2025-09-15 20:22:02.113 wdl.w:ptcp INFO visit :: node: "decl-unmapped_bam-57", values: {"unmapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0058_m84036_250809_035451_s4.bc2154.unmapped.bam"}
2025-09-15 20:22:02.113 wdl.w:ptcp INFO visit :: node: "decl-unmapped_bam-58", values: {"unmapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0059_m84036_250809_035451_s4.bc2155.unmapped.bam"}
2025-09-15 20:22:02.113 wdl.w:ptcp INFO visit :: node: "decl-unmapped_bam-59", values: {"unmapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0060_m84036_250809_035451_s4.bc2156.unmapped.bam"}
2025-09-15 20:22:02.114 wdl.w:ptcp INFO visit :: node: "decl-unmapped_bam-60", values: {"unmapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0061_m84036_250809_035451_s4.bc2157.unmapped.bam"}
2025-09-15 20:22:02.114 wdl.w:ptcp INFO visit :: node: "decl-unmapped_bam-61", values: {"unmapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0062_m84036_250809_035451_s4.bc2158.unmapped.bam"}
2025-09-15 20:22:02.114 wdl.w:ptcp INFO visit :: node: "decl-unmapped_bam-62", values: {"unmapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0063_m84036_250809_035451_s4.bc2159.unmapped.bam"}
2025-09-15 20:22:02.114 wdl.w:ptcp INFO visit :: node: "decl-unmapped_bam-63", values: {"unmapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0064_m84036_250809_035451_s4.bc2160.unmapped.bam"}
2025-09-15 20:22:02.114 wdl.w:ptcp INFO visit :: node: "decl-unmapped_bam-64", values: {"unmapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0065_m84036_250809_035451_s4.bc2161.unmapped.bam"}
2025-09-15 20:22:02.114 wdl.w:ptcp INFO visit :: node: "decl-unmapped_bam-65", values: {"unmapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0066_m84036_250809_035451_s4.bc2162.unmapped.bam"}
2025-09-15 20:22:02.114 wdl.w:ptcp INFO visit :: node: "decl-unmapped_bam-66", values: {"unmapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0067_m84036_250809_035451_s4.bc2163.unmapped.bam"}
2025-09-15 20:22:02.114 wdl.w:ptcp INFO visit :: node: "decl-unmapped_bam-67", values: {"unmapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0068_m84036_250809_035451_s4.bc2164.unmapped.bam"}
2025-09-15 20:22:02.114 wdl.w:ptcp INFO visit :: node: "decl-unmapped_bam-68", values: {"unmapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0069_m84036_250809_035451_s4.bc2165.unmapped.bam"}
2025-09-15 20:22:02.114 wdl.w:ptcp INFO visit :: node: "decl-unmapped_bam-69", values: {"unmapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0070_m84036_250809_035451_s4.bc2166.unmapped.bam"}
2025-09-15 20:22:02.114 wdl.w:ptcp INFO visit :: node: "decl-unmapped_bam-70", values: {"unmapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0071_m84036_250809_035451_s4.bc2167.unmapped.bam"}
2025-09-15 20:22:02.114 wdl.w:ptcp INFO visit :: node: "decl-unmapped_bam-71", values: {"unmapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0072_m84036_250809_035451_s4.bc2168.unmapped.bam"}
2025-09-15 20:22:02.114 wdl.w:ptcp INFO visit :: node: "decl-unmapped_bam-72", values: {"unmapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0073_m84036_250809_035451_s4.bc2169.unmapped.bam"}
2025-09-15 20:22:02.114 wdl.w:ptcp INFO visit :: node: "decl-unmapped_bam-73", values: {"unmapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0074_m84036_250809_035451_s4.bc2170.unmapped.bam"}
2025-09-15 20:22:02.114 wdl.w:ptcp INFO visit :: node: "decl-unmapped_bam-74", values: {"unmapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0075_m84036_250809_035451_s4.bc2171.unmapped.bam"}
2025-09-15 20:22:02.114 wdl.w:ptcp INFO visit :: node: "decl-unmapped_bam-75", values: {"unmapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0076_m84036_250809_035451_s4.bc2172.unmapped.bam"}
2025-09-15 20:22:02.114 wdl.w:ptcp INFO visit :: node: "decl-unmapped_bam-76", values: {"unmapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0077_m84036_250809_035451_s4.bc2173.unmapped.bam"}
2025-09-15 20:22:02.114 wdl.w:ptcp INFO visit :: node: "decl-unmapped_bam-77", values: {"unmapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0078_m84036_250809_035451_s4.bc2174.unmapped.bam"}
2025-09-15 20:22:02.114 wdl.w:ptcp INFO visit :: node: "decl-unmapped_bam-78", values: {"unmapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0079_m84036_250809_035451_s4.bc2175.unmapped.bam"}
2025-09-15 20:22:02.115 wdl.w:ptcp INFO visit :: node: "decl-unmapped_bam-79", values: {"unmapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0080_m84036_250809_035451_s4.bc2176.unmapped.bam"}
2025-09-15 20:22:02.115 wdl.w:ptcp INFO visit :: node: "decl-unmapped_bam-80", values: {"unmapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0081_m84036_250809_035451_s4.bc2177.unmapped.bam"}
2025-09-15 20:22:02.115 wdl.w:ptcp INFO visit :: node: "decl-unmapped_bam-81", values: {"unmapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0082_m84036_250809_035451_s4.bc2178.unmapped.bam"}
2025-09-15 20:22:02.115 wdl.w:ptcp INFO visit :: node: "decl-unmapped_bam-82", values: {"unmapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0083_m84036_250809_035451_s4.bc2179.unmapped.bam"}
2025-09-15 20:22:02.115 wdl.w:ptcp INFO visit :: node: "decl-unmapped_bam-83", values: {"unmapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0084_m84036_250809_035451_s4.bc2180.unmapped.bam"}
2025-09-15 20:22:02.115 wdl.w:ptcp INFO visit :: node: "decl-unmapped_bam-84", values: {"unmapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0085_m84036_250809_035451_s4.bc2181.unmapped.bam"}
2025-09-15 20:22:02.115 wdl.w:ptcp INFO visit :: node: "decl-unmapped_bam-85", values: {"unmapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0086_m84036_250809_035451_s4.bc2182.unmapped.bam"}
2025-09-15 20:22:02.115 wdl.w:ptcp INFO visit :: node: "decl-unmapped_bam-86", values: {"unmapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0087_m84036_250809_035451_s4.bc2183.unmapped.bam"}
2025-09-15 20:22:02.115 wdl.w:ptcp INFO visit :: node: "decl-unmapped_bam-87", values: {"unmapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0088_m84036_250809_035451_s4.bc2184.unmapped.bam"}
2025-09-15 20:22:02.115 wdl.w:ptcp INFO visit :: node: "decl-unmapped_bam-88", values: {"unmapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0089_m84036_250809_035451_s4.bc2185.unmapped.bam"}
2025-09-15 20:22:02.115 wdl.w:ptcp INFO visit :: node: "decl-unmapped_bam-89", values: {"unmapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0090_m84036_250809_035451_s4.bc2186.unmapped.bam"}
2025-09-15 20:22:02.115 wdl.w:ptcp INFO visit :: node: "decl-unmapped_bam-90", values: {"unmapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0091_m84036_250809_035451_s4.bc2187.unmapped.bam"}
2025-09-15 20:22:02.115 wdl.w:ptcp INFO visit :: node: "decl-unmapped_bam-91", values: {"unmapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0092_m84036_250809_035451_s4.bc2188.unmapped.bam"}
2025-09-15 20:22:02.115 wdl.w:ptcp INFO visit :: node: "decl-unmapped_bam-92", values: {"unmapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0093_m84036_250809_035451_s4.bc2189.unmapped.bam"}
2025-09-15 20:22:02.115 wdl.w:ptcp INFO visit :: node: "decl-unmapped_bam-93", values: {"unmapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0094_m84036_250809_035451_s4.bc2190.unmapped.bam"}
2025-09-15 20:22:02.115 wdl.w:ptcp INFO visit :: node: "decl-unmapped_bam-94", values: {"unmapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0095_m84036_250809_035451_s4.bc2191.unmapped.bam"}
2025-09-15 20:22:02.115 wdl.w:ptcp INFO visit :: node: "decl-unmapped_bam-95", values: {"unmapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0096_m84036_250809_035451_s4.bc2192.unmapped.bam"}
2025-09-15 20:22:02.116 wdl.w:ptcp INFO visit :: node: "gather-decl-chunk_bam", values: "(((large)))"
2025-09-15 20:22:02.116 wdl.w:ptcp INFO visit :: node: "gather-decl-sample_name", values: {"sample_name": ["m84036_250809_035451_s4.bc2097", "m84036_250809_035451_s4.bc2098", "m84036_250809_035451_s4.bc2099", "m84036_250809_035451_s4.bc2100", "m84036_250809_035451_s4.bc2101", "m84036_250809_035451_s4.bc2102", "m84036_250809_035451_s4.bc2103", "m84036_250809_035451_s4.bc2104", "m84036_250809_035451_s4.bc2105", "m84036_250809_035451_s4.bc2106", "m84036_250809_035451_s4.bc2107", "m84036_250809_035451_s4.bc2108", "m84036_250809_035451_s4.bc2109", "m84036_250809_035451_s4.bc2110", "m84036_250809_035451_s4.bc2111", "m84036_250809_035451_s4.bc2112", "m84036_250809_035451_s4.bc2113", "m84036_250809_035451_s4.bc2114", "m84036_250809_035451_s4.bc2115", "m84036_250809_035451_s4.bc2116", "m84036_250809_035451_s4.bc2117", "m84036_250809_035451_s4.bc2118", "m84036_250809_035451_s4.bc2119", "m84036_250809_035451_s4.bc2120", "m84036_250809_035451_s4.bc2121", "m84036_250809_035451_s4.bc2122", "m84036_250809_035451_s4.bc2123", "m84036_250809_035451_s4.bc2124", "m84036_250809_035451_s4.bc2125", "m84036_250809_035451_s4.bc2126", "m84036_250809_035451_s4.bc2127", "m84036_250809_035451_s4.bc2128", "m84036_250809_035451_s4.bc2129", "m84036_250809_035451_s4.bc2130", "m84036_250809_035451_s4.bc2131", "m84036_250809_035451_s4.bc2132", "m84036_250809_035451_s4.bc2133", "m84036_250809_035451_s4.bc2134", "m84036_250809_035451_s4.bc2135", "m84036_250809_035451_s4.bc2136", "m84036_250809_035451_s4.bc2137", "m84036_250809_035451_s4.bc2138", "m84036_250809_035451_s4.bc2139", "m84036_250809_035451_s4.bc2140", "m84036_250809_035451_s4.bc2141", "m84036_250809_035451_s4.bc2142", "m84036_250809_035451_s4.bc2143", "m84036_250809_035451_s4.bc2144", "m84036_250809_035451_s4.bc2145", "m84036_250809_035451_s4.bc2146", "m84036_250809_035451_s4.bc2147", "m84036_250809_035451_s4.bc2148", "m84036_250809_035451_s4.bc2149", "m84036_250809_035451_s4.bc2150", "m84036_250809_035451_s4.bc2151", "m84036_250809_035451_s4.bc2152", "m84036_250809_035451_s4.bc2153", "m84036_250809_035451_s4.bc2154", "m84036_250809_035451_s4.bc2155", "m84036_250809_035451_s4.bc2156", "m84036_250809_035451_s4.bc2157", "m84036_250809_035451_s4.bc2158", "m84036_250809_035451_s4.bc2159", "m84036_250809_035451_s4.bc2160", "m84036_250809_035451_s4.bc2161", "m84036_250809_035451_s4.bc2162", "m84036_250809_035451_s4.bc2163", "m84036_250809_035451_s4.bc2164", "m84036_250809_035451_s4.bc2165", "m84036_250809_035451_s4.bc2166", "m84036_250809_035451_s4.bc2167", "m84036_250809_035451_s4.bc2168", "m84036_250809_035451_s4.bc2169", "m84036_250809_035451_s4.bc2170", "m84036_250809_035451_s4.bc2171", "m84036_250809_035451_s4.bc2172", "m84036_250809_035451_s4.bc2173", "m84036_250809_035451_s4.bc2174", "m84036_250809_035451_s4.bc2175", "m84036_250809_035451_s4.bc2176", "m84036_250809_035451_s4.bc2177", "m84036_250809_035451_s4.bc2178", "m84036_250809_035451_s4.bc2179", "m84036_250809_035451_s4.bc2180", "m84036_250809_035451_s4.bc2181", "m84036_250809_035451_s4.bc2182", "m84036_250809_035451_s4.bc2183", "m84036_250809_035451_s4.bc2184", "m84036_250809_035451_s4.bc2185", "m84036_250809_035451_s4.bc2186", "m84036_250809_035451_s4.bc2187", "m84036_250809_035451_s4.bc2188", "m84036_250809_035451_s4.bc2189", "m84036_250809_035451_s4.bc2190", "m84036_250809_035451_s4.bc2191", "m84036_250809_035451_s4.bc2192"]}
2025-09-15 20:22:02.116 wdl.w:ptcp INFO visit :: node: "gather-decl-sample_sex", values: {"sample_sex": ["F", "F", "F", "F", "F", "F", "F", "F", "F", "F", "F", "F", "F", "F", "F", "F", "F", "F", "F", "F", "F", "F", "F", "F", "F", "F", "F", "F", "F", "F", "F", "F", "F", "F", "F", "F", "F", "F", "F", "F", "F", "F", "F", "F", "F", "F", "F", "F", "F", "F", "F", "F", "F", "F", "F", "F", "F", "F", "F", "F", "F", "F", "F", "F", "F", "F", "F", "F", "F", "F", "F", "F", "F", "F", "F", "F", "F", "F", "F", "F", "F", "F", "F", "F", "F", "F", "F", "F", "F", "F", "F", "F", "F", "F", "F", "F"]}
2025-09-15 20:22:02.116 wdl.w:ptcp NOTICE ready :: job: "call-pbmm2_align_hifi-00", callee: "pbmm2_align_hifi"
2025-09-15 20:22:02.116 wdl.w:ptcp INFO input :: job: "call-pbmm2_align_hifi-00", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "log_level": "INFO", "out_prefix": "m84036_250809_035451_s4.bc2097.mapped", "ref_fasta": "/meta/refs/hg38.fa", "unmapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0001_m84036_250809_035451_s4.bc2097.unmapped.bam", "sample_name": "m84036_250809_035451_s4.bc2097"}
2025-09-15 20:22:02.117 wdl.w:ptcp NOTICE ready :: job: "call-pbmm2_align_hifi-01", callee: "pbmm2_align_hifi"
2025-09-15 20:22:02.118 wdl.w:ptcp INFO input :: job: "call-pbmm2_align_hifi-01", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "log_level": "INFO", "out_prefix": "m84036_250809_035451_s4.bc2098.mapped", "ref_fasta": "/meta/refs/hg38.fa", "unmapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0002_m84036_250809_035451_s4.bc2098.unmapped.bam", "sample_name": "m84036_250809_035451_s4.bc2098"}
2025-09-15 20:22:02.121 wdl.w:ptcp NOTICE ready :: job: "call-pbmm2_align_hifi-02", callee: "pbmm2_align_hifi"
2025-09-15 20:22:02.121 wdl.w:ptcp INFO input :: job: "call-pbmm2_align_hifi-02", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "log_level": "INFO", "out_prefix": "m84036_250809_035451_s4.bc2099.mapped", "ref_fasta": "/meta/refs/hg38.fa", "unmapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0003_m84036_250809_035451_s4.bc2099.unmapped.bam", "sample_name": "m84036_250809_035451_s4.bc2099"}
2025-09-15 20:22:02.124 wdl.w:ptcp NOTICE ready :: job: "call-pbmm2_align_hifi-03", callee: "pbmm2_align_hifi"
2025-09-15 20:22:02.124 wdl.w:ptcp INFO input :: job: "call-pbmm2_align_hifi-03", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "log_level": "INFO", "out_prefix": "m84036_250809_035451_s4.bc2100.mapped", "ref_fasta": "/meta/refs/hg38.fa", "unmapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0004_m84036_250809_035451_s4.bc2100.unmapped.bam", "sample_name": "m84036_250809_035451_s4.bc2100"}
2025-09-15 20:22:02.125 wdl.w:ptcp.t:call-pbmm2_align_hifi-00 NOTICE task setup :: name: "pbmm2_align_hifi", source: "./common.wdl", line: 170, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-00", thread: 140613838284352
2025-09-15 20:22:02.128 wdl.w:ptcp NOTICE ready :: job: "call-pbmm2_align_hifi-04", callee: "pbmm2_align_hifi"
2025-09-15 20:22:02.128 wdl.w:ptcp INFO input :: job: "call-pbmm2_align_hifi-04", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "log_level": "INFO", "out_prefix": "m84036_250809_035451_s4.bc2101.mapped", "ref_fasta": "/meta/refs/hg38.fa", "unmapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0005_m84036_250809_035451_s4.bc2101.unmapped.bam", "sample_name": "m84036_250809_035451_s4.bc2101"}
2025-09-15 20:22:02.128 wdl.w:ptcp.t:call-pbmm2_align_hifi-01 NOTICE task setup :: name: "pbmm2_align_hifi", source: "./common.wdl", line: 170, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-01", thread: 140613823374912
2025-09-15 20:22:02.131 wdl.w:ptcp NOTICE ready :: job: "call-pbmm2_align_hifi-05", callee: "pbmm2_align_hifi"
2025-09-15 20:22:02.131 wdl.w:ptcp INFO input :: job: "call-pbmm2_align_hifi-05", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "log_level": "INFO", "out_prefix": "m84036_250809_035451_s4.bc2102.mapped", "ref_fasta": "/meta/refs/hg38.fa", "unmapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0006_m84036_250809_035451_s4.bc2102.unmapped.bam", "sample_name": "m84036_250809_035451_s4.bc2102"}
2025-09-15 20:22:02.133 wdl.w:ptcp.t:call-pbmm2_align_hifi-02 NOTICE task setup :: name: "pbmm2_align_hifi", source: "./common.wdl", line: 170, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-02", thread: 140613605389888
2025-09-15 20:22:02.137 wdl.w:ptcp NOTICE ready :: job: "call-pbmm2_align_hifi-06", callee: "pbmm2_align_hifi"
2025-09-15 20:22:02.137 wdl.w:ptcp.t:call-pbmm2_align_hifi-03 NOTICE task setup :: name: "pbmm2_align_hifi", source: "./common.wdl", line: 170, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-03", thread: 140613596997184
2025-09-15 20:22:02.137 wdl.w:ptcp INFO input :: job: "call-pbmm2_align_hifi-06", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "log_level": "INFO", "out_prefix": "m84036_250809_035451_s4.bc2103.mapped", "ref_fasta": "/meta/refs/hg38.fa", "unmapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0007_m84036_250809_035451_s4.bc2103.unmapped.bam", "sample_name": "m84036_250809_035451_s4.bc2103"}
2025-09-15 20:22:02.139 wdl.w:ptcp.t:call-pbmm2_align_hifi-04 NOTICE task setup :: name: "pbmm2_align_hifi", source: "./common.wdl", line: 170, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-04", thread: 140613588604480
2025-09-15 20:22:02.140 wdl.w:ptcp NOTICE ready :: job: "call-pbmm2_align_hifi-07", callee: "pbmm2_align_hifi"
2025-09-15 20:22:02.141 wdl.w:ptcp INFO input :: job: "call-pbmm2_align_hifi-07", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "log_level": "INFO", "out_prefix": "m84036_250809_035451_s4.bc2104.mapped", "ref_fasta": "/meta/refs/hg38.fa", "unmapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0008_m84036_250809_035451_s4.bc2104.unmapped.bam", "sample_name": "m84036_250809_035451_s4.bc2104"}
2025-09-15 20:22:02.144 wdl.w:ptcp NOTICE ready :: job: "call-pbmm2_align_hifi-08", callee: "pbmm2_align_hifi"
2025-09-15 20:22:02.146 wdl.w:ptcp INFO input :: job: "call-pbmm2_align_hifi-08", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "log_level": "INFO", "out_prefix": "m84036_250809_035451_s4.bc2105.mapped", "ref_fasta": "/meta/refs/hg38.fa", "unmapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0009_m84036_250809_035451_s4.bc2105.unmapped.bam", "sample_name": "m84036_250809_035451_s4.bc2105"}
2025-09-15 20:22:02.145 wdl.w:ptcp.t:call-pbmm2_align_hifi-05 NOTICE task setup :: name: "pbmm2_align_hifi", source: "./common.wdl", line: 170, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-05", thread: 140613580211776
2025-09-15 20:22:02.147 wdl.w:ptcp.t:call-pbmm2_align_hifi-06 NOTICE task setup :: name: "pbmm2_align_hifi", source: "./common.wdl", line: 170, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-06", thread: 140613571819072
2025-09-15 20:22:02.148 wdl.w:ptcp NOTICE ready :: job: "call-pbmm2_align_hifi-09", callee: "pbmm2_align_hifi"
2025-09-15 20:22:02.149 wdl.w:ptcp INFO input :: job: "call-pbmm2_align_hifi-09", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "log_level": "INFO", "out_prefix": "m84036_250809_035451_s4.bc2106.mapped", "ref_fasta": "/meta/refs/hg38.fa", "unmapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0010_m84036_250809_035451_s4.bc2106.unmapped.bam", "sample_name": "m84036_250809_035451_s4.bc2106"}
2025-09-15 20:22:02.151 wdl.w:ptcp.t:call-pbmm2_align_hifi-07 NOTICE task setup :: name: "pbmm2_align_hifi", source: "./common.wdl", line: 170, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-07", thread: 140613563426368
2025-09-15 20:22:02.154 wdl.w:ptcp NOTICE ready :: job: "call-pbmm2_align_hifi-10", callee: "pbmm2_align_hifi"
2025-09-15 20:22:02.155 wdl.w:ptcp INFO input :: job: "call-pbmm2_align_hifi-10", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "log_level": "INFO", "out_prefix": "m84036_250809_035451_s4.bc2107.mapped", "ref_fasta": "/meta/refs/hg38.fa", "unmapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0011_m84036_250809_035451_s4.bc2107.unmapped.bam", "sample_name": "m84036_250809_035451_s4.bc2107"}
2025-09-15 20:22:02.158 wdl.w:ptcp.t:call-pbmm2_align_hifi-08 NOTICE task setup :: name: "pbmm2_align_hifi", source: "./common.wdl", line: 170, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-08", thread: 140613555033664
2025-09-15 20:22:02.160 wdl.w:ptcp NOTICE ready :: job: "call-pbmm2_align_hifi-11", callee: "pbmm2_align_hifi"
2025-09-15 20:22:02.162 wdl.w:ptcp INFO input :: job: "call-pbmm2_align_hifi-11", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "log_level": "INFO", "out_prefix": "m84036_250809_035451_s4.bc2108.mapped", "ref_fasta": "/meta/refs/hg38.fa", "unmapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0012_m84036_250809_035451_s4.bc2108.unmapped.bam", "sample_name": "m84036_250809_035451_s4.bc2108"}
2025-09-15 20:22:02.162 wdl.w:ptcp.t:call-pbmm2_align_hifi-09 NOTICE task setup :: name: "pbmm2_align_hifi", source: "./common.wdl", line: 170, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-09", thread: 140613068518976
2025-09-15 20:22:02.165 wdl.w:ptcp NOTICE ready :: job: "call-pbmm2_align_hifi-12", callee: "pbmm2_align_hifi"
2025-09-15 20:22:02.166 wdl.w:ptcp INFO input :: job: "call-pbmm2_align_hifi-12", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "log_level": "INFO", "out_prefix": "m84036_250809_035451_s4.bc2109.mapped", "ref_fasta": "/meta/refs/hg38.fa", "unmapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0013_m84036_250809_035451_s4.bc2109.unmapped.bam", "sample_name": "m84036_250809_035451_s4.bc2109"}
2025-09-15 20:22:02.167 wdl.w:ptcp.t:call-pbmm2_align_hifi-10 NOTICE task setup :: name: "pbmm2_align_hifi", source: "./common.wdl", line: 170, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-10", thread: 140613060126272
2025-09-15 20:22:02.171 wdl.w:ptcp NOTICE ready :: job: "call-pbmm2_align_hifi-13", callee: "pbmm2_align_hifi"
2025-09-15 20:22:02.172 wdl.w:ptcp INFO input :: job: "call-pbmm2_align_hifi-13", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "log_level": "INFO", "out_prefix": "m84036_250809_035451_s4.bc2110.mapped", "ref_fasta": "/meta/refs/hg38.fa", "unmapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0014_m84036_250809_035451_s4.bc2110.unmapped.bam", "sample_name": "m84036_250809_035451_s4.bc2110"}
2025-09-15 20:22:02.173 wdl.w:ptcp.t:call-pbmm2_align_hifi-11 NOTICE task setup :: name: "pbmm2_align_hifi", source: "./common.wdl", line: 170, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-11", thread: 140613051733568
2025-09-15 20:22:02.176 wdl.w:ptcp NOTICE ready :: job: "call-pbmm2_align_hifi-14", callee: "pbmm2_align_hifi"
2025-09-15 20:22:02.177 wdl.w:ptcp INFO input :: job: "call-pbmm2_align_hifi-14", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "log_level": "INFO", "out_prefix": "m84036_250809_035451_s4.bc2111.mapped", "ref_fasta": "/meta/refs/hg38.fa", "unmapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0015_m84036_250809_035451_s4.bc2111.unmapped.bam", "sample_name": "m84036_250809_035451_s4.bc2111"}
2025-09-15 20:22:02.179 wdl.w:ptcp.t:call-pbmm2_align_hifi-01 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:22:02.180 wdl.w:ptcp.t:call-pbmm2_align_hifi-12 NOTICE task setup :: name: "pbmm2_align_hifi", source: "./common.wdl", line: 170, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-12", thread: 140613043340864
2025-09-15 20:22:02.180 wdl.w:ptcp.t:call-pbmm2_align_hifi-02 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:22:02.184 wdl.w:ptcp NOTICE ready :: job: "call-pbmm2_align_hifi-15", callee: "pbmm2_align_hifi"
2025-09-15 20:22:02.184 wdl.w:ptcp.t:call-pbmm2_align_hifi-01 INFO input :: name: "log_level", value: "INFO"
2025-09-15 20:22:02.185 wdl.w:ptcp.t:call-pbmm2_align_hifi-13 NOTICE task setup :: name: "pbmm2_align_hifi", source: "./common.wdl", line: 170, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-13", thread: 140613034948160
2025-09-15 20:22:02.185 wdl.w:ptcp.t:call-pbmm2_align_hifi-00 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:22:02.187 wdl.w:ptcp.t:call-pbmm2_align_hifi-02 INFO input :: name: "log_level", value: "INFO"
2025-09-15 20:22:02.187 wdl.w:ptcp.t:call-pbmm2_align_hifi-03 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:22:02.188 wdl.w:ptcp INFO input :: job: "call-pbmm2_align_hifi-15", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "log_level": "INFO", "out_prefix": "m84036_250809_035451_s4.bc2112.mapped", "ref_fasta": "/meta/refs/hg38.fa", "unmapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0016_m84036_250809_035451_s4.bc2112.unmapped.bam", "sample_name": "m84036_250809_035451_s4.bc2112"}
2025-09-15 20:22:02.188 wdl.w:ptcp.t:call-pbmm2_align_hifi-01 INFO input :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2098.mapped"
2025-09-15 20:22:02.189 wdl.w:ptcp.t:call-pbmm2_align_hifi-14 NOTICE task setup :: name: "pbmm2_align_hifi", source: "./common.wdl", line: 170, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-14", thread: 140613026555456
2025-09-15 20:22:02.190 wdl.w:ptcp.t:call-pbmm2_align_hifi-00 INFO input :: name: "log_level", value: "INFO"
2025-09-15 20:22:02.192 wdl.w:ptcp.t:call-pbmm2_align_hifi-02 INFO input :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2099.mapped"
2025-09-15 20:22:02.192 wdl.w:ptcp.t:call-pbmm2_align_hifi-04 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:22:02.193 wdl.w:ptcp.t:call-pbmm2_align_hifi-03 INFO input :: name: "log_level", value: "INFO"
2025-09-15 20:22:02.195 wdl.w:ptcp.t:call-pbmm2_align_hifi-06 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:22:02.195 wdl.w:ptcp.t:call-pbmm2_align_hifi-01 INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:22:02.196 wdl.w:ptcp NOTICE ready :: job: "call-pbmm2_align_hifi-16", callee: "pbmm2_align_hifi"
2025-09-15 20:22:02.198 wdl.w:ptcp.t:call-pbmm2_align_hifi-00 INFO input :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2097.mapped"
2025-09-15 20:22:02.198 wdl.w:ptcp.t:call-pbmm2_align_hifi-05 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:22:02.198 wdl.w:ptcp.t:call-pbmm2_align_hifi-02 INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:22:02.199 wdl.w:ptcp.t:call-pbmm2_align_hifi-04 INFO input :: name: "log_level", value: "INFO"
2025-09-15 20:22:02.200 wdl.w:ptcp.t:call-pbmm2_align_hifi-03 INFO input :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2100.mapped"
2025-09-15 20:22:02.201 wdl.w:ptcp.t:call-pbmm2_align_hifi-06 INFO input :: name: "log_level", value: "INFO"
2025-09-15 20:22:02.201 wdl.w:ptcp.t:call-pbmm2_align_hifi-01 INFO input :: name: "unmapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0002_m84036_250809_035451_s4.bc2098.unmapped.bam"
2025-09-15 20:22:02.201 wdl.w:ptcp.t:call-pbmm2_align_hifi-07 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:22:02.202 wdl.w:ptcp INFO input :: job: "call-pbmm2_align_hifi-16", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "log_level": "INFO", "out_prefix": "m84036_250809_035451_s4.bc2113.mapped", "ref_fasta": "/meta/refs/hg38.fa", "unmapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0017_m84036_250809_035451_s4.bc2113.unmapped.bam", "sample_name": "m84036_250809_035451_s4.bc2113"}
2025-09-15 20:22:02.202 wdl.w:ptcp.t:call-pbmm2_align_hifi-15 NOTICE task setup :: name: "pbmm2_align_hifi", source: "./common.wdl", line: 170, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-15", thread: 140613018162752
2025-09-15 20:22:02.204 wdl.w:ptcp.t:call-pbmm2_align_hifi-00 INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:22:02.205 wdl.w:ptcp.t:call-pbmm2_align_hifi-05 INFO input :: name: "log_level", value: "INFO"
2025-09-15 20:22:02.206 wdl.w:ptcp.t:call-pbmm2_align_hifi-08 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:22:02.206 wdl.w:ptcp.t:call-pbmm2_align_hifi-02 INFO input :: name: "unmapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0003_m84036_250809_035451_s4.bc2099.unmapped.bam"
2025-09-15 20:22:02.206 wdl.w:ptcp.t:call-pbmm2_align_hifi-04 INFO input :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2101.mapped"
2025-09-15 20:22:02.208 wdl.w:ptcp.t:call-pbmm2_align_hifi-03 INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:22:02.208 wdl.w:ptcp.t:call-pbmm2_align_hifi-06 INFO input :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2103.mapped"
2025-09-15 20:22:02.209 wdl.w:ptcp.t:call-pbmm2_align_hifi-01 INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2098"
2025-09-15 20:22:02.210 wdl.w:ptcp.t:call-pbmm2_align_hifi-07 INFO input :: name: "log_level", value: "INFO"
2025-09-15 20:22:02.211 wdl.w:ptcp.t:call-pbmm2_align_hifi-00 INFO input :: name: "unmapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0001_m84036_250809_035451_s4.bc2097.unmapped.bam"
2025-09-15 20:22:02.211 wdl.w:ptcp.t:call-pbmm2_align_hifi-09 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:22:02.212 wdl.w:ptcp.t:call-pbmm2_align_hifi-05 INFO input :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2102.mapped"
2025-09-15 20:22:02.213 wdl.w:ptcp NOTICE ready :: job: "call-pbmm2_align_hifi-17", callee: "pbmm2_align_hifi"
2025-09-15 20:22:02.213 wdl.w:ptcp.t:call-pbmm2_align_hifi-08 INFO input :: name: "log_level", value: "INFO"
2025-09-15 20:22:02.214 wdl.w:ptcp.t:call-pbmm2_align_hifi-02 INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2099"
2025-09-15 20:22:02.214 wdl.w:ptcp.t:call-pbmm2_align_hifi-10 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:22:02.215 wdl.w:ptcp.t:call-pbmm2_align_hifi-04 INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:22:02.215 wdl.w:ptcp.t:call-pbmm2_align_hifi-03 INFO input :: name: "unmapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0004_m84036_250809_035451_s4.bc2100.unmapped.bam"
2025-09-15 20:22:02.215 wdl.w:ptcp.t:call-pbmm2_align_hifi-06 INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:22:02.216 wdl.w:ptcp.t:call-pbmm2_align_hifi-01 INFO eval :: name: "threads", value: 64
2025-09-15 20:22:02.216 wdl.w:ptcp.t:call-pbmm2_align_hifi-07 INFO input :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2104.mapped"
2025-09-15 20:22:02.216 wdl.w:ptcp.t:call-pbmm2_align_hifi-00 INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2097"
2025-09-15 20:22:02.217 wdl.w:ptcp.t:call-pbmm2_align_hifi-11 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:22:02.217 wdl.w:ptcp.t:call-pbmm2_align_hifi-09 INFO input :: name: "log_level", value: "INFO"
2025-09-15 20:22:02.218 wdl.w:ptcp.t:call-pbmm2_align_hifi-05 INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:22:02.218 wdl.w:ptcp INFO input :: job: "call-pbmm2_align_hifi-17", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "log_level": "INFO", "out_prefix": "m84036_250809_035451_s4.bc2114.mapped", "ref_fasta": "/meta/refs/hg38.fa", "unmapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0018_m84036_250809_035451_s4.bc2114.unmapped.bam", "sample_name": "m84036_250809_035451_s4.bc2114"}
2025-09-15 20:22:02.218 wdl.w:ptcp.t:call-pbmm2_align_hifi-08 INFO input :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2105.mapped"
2025-09-15 20:22:02.218 wdl.w:ptcp.t:call-pbmm2_align_hifi-16 NOTICE task setup :: name: "pbmm2_align_hifi", source: "./common.wdl", line: 170, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-16", thread: 140612531648064
2025-09-15 20:22:02.219 wdl.w:ptcp.t:call-pbmm2_align_hifi-02 INFO eval :: name: "threads", value: 64
2025-09-15 20:22:02.220 wdl.w:ptcp.t:call-pbmm2_align_hifi-10 INFO input :: name: "log_level", value: "INFO"
2025-09-15 20:22:02.221 wdl.w:ptcp.t:call-pbmm2_align_hifi-04 INFO input :: name: "unmapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0005_m84036_250809_035451_s4.bc2101.unmapped.bam"
2025-09-15 20:22:02.221 wdl.w:ptcp.t:call-pbmm2_align_hifi-03 INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2100"
2025-09-15 20:22:02.221 wdl.w:ptcp.t:call-pbmm2_align_hifi-06 INFO input :: name: "unmapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0007_m84036_250809_035451_s4.bc2103.unmapped.bam"
2025-09-15 20:22:02.221 wdl.w:ptcp.t:call-pbmm2_align_hifi-01 INFO eval :: name: "mem_gb", value: 64
2025-09-15 20:22:02.222 wdl.w:ptcp.t:call-pbmm2_align_hifi-07 INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:22:02.222 wdl.w:ptcp.t:call-pbmm2_align_hifi-00 INFO eval :: name: "threads", value: 64
2025-09-15 20:22:02.222 wdl.w:ptcp.t:call-pbmm2_align_hifi-11 INFO input :: name: "log_level", value: "INFO"
2025-09-15 20:22:02.223 wdl.w:ptcp.t:call-pbmm2_align_hifi-09 INFO input :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2106.mapped"
2025-09-15 20:22:02.223 wdl.w:ptcp.t:call-pbmm2_align_hifi-05 INFO input :: name: "unmapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0006_m84036_250809_035451_s4.bc2102.unmapped.bam"
2025-09-15 20:22:02.223 wdl.w:ptcp.t:call-pbmm2_align_hifi-08 INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:22:02.224 wdl.w:ptcp.t:call-pbmm2_align_hifi-12 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:22:02.225 wdl.w:ptcp.t:call-pbmm2_align_hifi-02 INFO eval :: name: "mem_gb", value: 64
2025-09-15 20:22:02.225 wdl.w:ptcp NOTICE ready :: job: "call-pbmm2_align_hifi-18", callee: "pbmm2_align_hifi"
2025-09-15 20:22:02.226 wdl.w:ptcp.t:call-pbmm2_align_hifi-10 INFO input :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2107.mapped"
2025-09-15 20:22:02.226 wdl.w:ptcp.t:call-pbmm2_align_hifi-04 INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2101"
2025-09-15 20:22:02.226 wdl.w:ptcp.t:call-pbmm2_align_hifi-03 INFO eval :: name: "threads", value: 64
2025-09-15 20:22:02.227 wdl.w:ptcp.t:call-pbmm2_align_hifi-06 INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2103"
2025-09-15 20:22:02.227 wdl.w:ptcp.t:call-pbmm2_align_hifi-13 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:22:02.228 wdl.w:ptcp.t:call-pbmm2_align_hifi-07 INFO input :: name: "unmapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0008_m84036_250809_035451_s4.bc2104.unmapped.bam"
2025-09-15 20:22:02.228 wdl.w:ptcp.t:call-pbmm2_align_hifi-00 INFO eval :: name: "mem_gb", value: 64
2025-09-15 20:22:02.229 wdl.w:ptcp.t:call-pbmm2_align_hifi-01 INFO eval :: name: "disk_size", value: 30
2025-09-15 20:22:02.229 wdl.w:ptcp.t:call-pbmm2_align_hifi-11 INFO input :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2108.mapped"
2025-09-15 20:22:02.229 wdl.w:ptcp.t:call-pbmm2_align_hifi-09 INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:22:02.229 wdl.w:ptcp.t:call-pbmm2_align_hifi-05 INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2102"
2025-09-15 20:22:02.229 wdl.w:ptcp.t:call-pbmm2_align_hifi-08 INFO input :: name: "unmapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0009_m84036_250809_035451_s4.bc2105.unmapped.bam"
2025-09-15 20:22:02.229 wdl.w:ptcp.t:call-pbmm2_align_hifi-12 INFO input :: name: "log_level", value: "INFO"
2025-09-15 20:22:02.230 wdl.w:ptcp INFO input :: job: "call-pbmm2_align_hifi-18", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "log_level": "INFO", "out_prefix": "m84036_250809_035451_s4.bc2115.mapped", "ref_fasta": "/meta/refs/hg38.fa", "unmapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0019_m84036_250809_035451_s4.bc2115.unmapped.bam", "sample_name": "m84036_250809_035451_s4.bc2115"}
2025-09-15 20:22:02.230 wdl.w:ptcp.t:call-pbmm2_align_hifi-10 INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:22:02.230 wdl.w:ptcp.t:call-pbmm2_align_hifi-02 INFO eval :: name: "disk_size", value: 30
2025-09-15 20:22:02.231 wdl.w:ptcp.t:call-pbmm2_align_hifi-17 NOTICE task setup :: name: "pbmm2_align_hifi", source: "./common.wdl", line: 170, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-17", thread: 140612523255360
2025-09-15 20:22:02.231 wdl.w:ptcp.t:call-pbmm2_align_hifi-04 INFO eval :: name: "threads", value: 64
2025-09-15 20:22:02.231 wdl.w:ptcp.t:call-pbmm2_align_hifi-14 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:22:02.231 wdl.w:ptcp.t:call-pbmm2_align_hifi-03 INFO eval :: name: "mem_gb", value: 64
2025-09-15 20:22:02.232 wdl.w:ptcp.t:call-pbmm2_align_hifi-06 INFO eval :: name: "threads", value: 64
2025-09-15 20:22:02.233 wdl.w:ptcp.t:call-pbmm2_align_hifi-13 INFO input :: name: "log_level", value: "INFO"
2025-09-15 20:22:02.233 wdl.w:ptcp.t:call-pbmm2_align_hifi-07 INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2104"
2025-09-15 20:22:02.233 wdl.w:ptcp.t:call-pbmm2_align_hifi-00 INFO eval :: name: "disk_size", value: 30
2025-09-15 20:22:02.234 wdl.w:ptcp.t:call-pbmm2_align_hifi-01 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 64, memory_reservation: 64000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:22:02.234 wdl.w:ptcp.t:call-pbmm2_align_hifi-11 INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:22:02.234 wdl.w:ptcp.t:call-pbmm2_align_hifi-09 INFO input :: name: "unmapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0010_m84036_250809_035451_s4.bc2106.unmapped.bam"
2025-09-15 20:22:02.235 wdl.w:ptcp.t:call-pbmm2_align_hifi-05 INFO eval :: name: "threads", value: 64
2025-09-15 20:22:02.235 wdl.w:ptcp.t:call-pbmm2_align_hifi-08 INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2105"
2025-09-15 20:22:02.235 wdl.w:ptcp.t:call-pbmm2_align_hifi-12 INFO input :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2109.mapped"
2025-09-15 20:22:02.235 wdl.w:ptcp.t:call-pbmm2_align_hifi-10 INFO input :: name: "unmapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0011_m84036_250809_035451_s4.bc2107.unmapped.bam"
2025-09-15 20:22:02.237 wdl.w:ptcp NOTICE ready :: job: "call-pbmm2_align_hifi-19", callee: "pbmm2_align_hifi"
2025-09-15 20:22:02.237 wdl.w:ptcp.t:call-pbmm2_align_hifi-04 INFO eval :: name: "mem_gb", value: 64
2025-09-15 20:22:02.237 wdl.w:ptcp.t:call-pbmm2_align_hifi-02 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 64, memory_reservation: 64000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:22:02.238 wdl.w:ptcp.t:call-pbmm2_align_hifi-14 INFO input :: name: "log_level", value: "INFO"
2025-09-15 20:22:02.238 wdl.w:ptcp.t:call-pbmm2_align_hifi-06 INFO eval :: name: "mem_gb", value: 64
2025-09-15 20:22:02.238 wdl.w:ptcp.t:call-pbmm2_align_hifi-03 INFO eval :: name: "disk_size", value: 30
2025-09-15 20:22:02.239 wdl.w:ptcp.t:call-pbmm2_align_hifi-13 INFO input :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2110.mapped"
2025-09-15 20:22:02.239 wdl.w:ptcp.t:call-pbmm2_align_hifi-07 INFO eval :: name: "threads", value: 64
2025-09-15 20:22:02.239 wdl.w:ptcp.t:call-pbmm2_align_hifi-01 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:22:02.240 wdl.w:ptcp.t:call-pbmm2_align_hifi-11 INFO input :: name: "unmapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0012_m84036_250809_035451_s4.bc2108.unmapped.bam"
2025-09-15 20:22:02.240 wdl.w:ptcp.t:call-pbmm2_align_hifi-00 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 64, memory_reservation: 64000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:22:02.240 wdl.w:ptcp.t:call-pbmm2_align_hifi-09 INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2106"
2025-09-15 20:22:02.241 wdl.w:ptcp.t:call-pbmm2_align_hifi-15 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:22:02.241 wdl.w:ptcp.t:call-pbmm2_align_hifi-05 INFO eval :: name: "mem_gb", value: 64
2025-09-15 20:22:02.241 wdl.w:ptcp.t:call-pbmm2_align_hifi-08 INFO eval :: name: "threads", value: 64
2025-09-15 20:22:02.242 wdl.w:ptcp.t:call-pbmm2_align_hifi-12 INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:22:02.242 wdl.w:ptcp.t:call-pbmm2_align_hifi-18 NOTICE task setup :: name: "pbmm2_align_hifi", source: "./common.wdl", line: 170, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-18", thread: 140612514862656
2025-09-15 20:22:02.242 wdl.w:ptcp.t:call-pbmm2_align_hifi-10 INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2107"
2025-09-15 20:22:02.242 wdl.w:ptcp INFO input :: job: "call-pbmm2_align_hifi-19", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "log_level": "INFO", "out_prefix": "m84036_250809_035451_s4.bc2116.mapped", "ref_fasta": "/meta/refs/hg38.fa", "unmapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0020_m84036_250809_035451_s4.bc2116.unmapped.bam", "sample_name": "m84036_250809_035451_s4.bc2116"}
2025-09-15 20:22:02.243 wdl.w:ptcp.t:call-pbmm2_align_hifi-02 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:22:02.243 wdl.w:ptcp.t:call-pbmm2_align_hifi-04 INFO eval :: name: "disk_size", value: 30
2025-09-15 20:22:02.243 wdl.w:ptcp.t:call-pbmm2_align_hifi-14 INFO input :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2111.mapped"
2025-09-15 20:22:02.244 wdl.w:ptcp.t:call-pbmm2_align_hifi-13 INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:22:02.244 wdl.w:ptcp.t:call-pbmm2_align_hifi-06 INFO eval :: name: "disk_size", value: 30
2025-09-15 20:22:02.244 wdl.w:ptcp.t:call-pbmm2_align_hifi-03 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 64, memory_reservation: 64000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:22:02.244 wdl.w:ptcp.t:call-pbmm2_align_hifi-07 INFO eval :: name: "mem_gb", value: 64
2025-09-15 20:22:02.245 wdl.w:ptcp.t:call-pbmm2_align_hifi-11 INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2108"
2025-09-15 20:22:02.245 wdl.w:ptcp.t:call-pbmm2_align_hifi-00 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:22:02.246 wdl.w:ptcp.t:call-pbmm2_align_hifi-09 INFO eval :: name: "threads", value: 64
2025-09-15 20:22:02.246 wdl.w:ptcp.t:call-pbmm2_align_hifi-15 INFO input :: name: "log_level", value: "INFO"
2025-09-15 20:22:02.246 wdl.w:ptcp.t:call-pbmm2_align_hifi-01 INFO provisioned :: seconds_waited: 0, cpu: 64, mem_bytes: 64000000000
2025-09-15 20:22:02.247 wdl.w:ptcp.t:call-pbmm2_align_hifi-08 INFO eval :: name: "mem_gb", value: 64
2025-09-15 20:22:02.247 wdl.w:ptcp.t:call-pbmm2_align_hifi-12 INFO input :: name: "unmapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0013_m84036_250809_035451_s4.bc2109.unmapped.bam"
2025-09-15 20:22:02.247 wdl.w:ptcp.t:call-pbmm2_align_hifi-05 INFO eval :: name: "disk_size", value: 30
2025-09-15 20:22:02.248 wdl.w:ptcp.t:call-pbmm2_align_hifi-10 INFO eval :: name: "threads", value: 64
2025-09-15 20:22:02.249 wdl.w:ptcp.t:call-pbmm2_align_hifi-14 INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:22:02.249 wdl.w:ptcp.t:call-pbmm2_align_hifi-13 INFO input :: name: "unmapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0014_m84036_250809_035451_s4.bc2110.unmapped.bam"
2025-09-15 20:22:02.250 wdl.w:ptcp NOTICE ready :: job: "call-pbmm2_align_hifi-20", callee: "pbmm2_align_hifi"
2025-09-15 20:22:02.250 wdl.w:ptcp.t:call-pbmm2_align_hifi-04 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 64, memory_reservation: 64000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:22:02.250 wdl.w:ptcp.t:call-pbmm2_align_hifi-03 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:22:02.251 wdl.w:ptcp.t:call-pbmm2_align_hifi-02 INFO provisioned :: seconds_waited: 0, cpu: 64, mem_bytes: 64000000000
2025-09-15 20:22:02.251 wdl.w:ptcp.t:call-pbmm2_align_hifi-06 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 64, memory_reservation: 64000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:22:02.251 wdl.w:ptcp.t:call-pbmm2_align_hifi-11 INFO eval :: name: "threads", value: 64
2025-09-15 20:22:02.252 wdl.w:ptcp.t:call-pbmm2_align_hifi-07 INFO eval :: name: "disk_size", value: 30
2025-09-15 20:22:02.252 wdl.w:ptcp.t:call-pbmm2_align_hifi-09 INFO eval :: name: "mem_gb", value: 64
2025-09-15 20:22:02.253 wdl.w:ptcp.t:call-pbmm2_align_hifi-00 INFO provisioned :: seconds_waited: 0, cpu: 64, mem_bytes: 64000000000
2025-09-15 20:22:02.253 wdl.w:ptcp.t:call-pbmm2_align_hifi-15 INFO input :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2112.mapped"
2025-09-15 20:22:02.253 wdl.w:ptcp.t:call-pbmm2_align_hifi-12 INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2109"
2025-09-15 20:22:02.254 wdl.w:ptcp.t:call-pbmm2_align_hifi-08 INFO eval :: name: "disk_size", value: 30
2025-09-15 20:22:02.254 wdl.w:ptcp.t:call-pbmm2_align_hifi-16 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:22:02.254 wdl.w:ptcp.t:call-pbmm2_align_hifi-01 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:22:02.254 wdl.w:ptcp.t:call-pbmm2_align_hifi-10 INFO eval :: name: "mem_gb", value: 64
2025-09-15 20:22:02.255 wdl.w:ptcp.t:call-pbmm2_align_hifi-14 INFO input :: name: "unmapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0015_m84036_250809_035451_s4.bc2111.unmapped.bam"
2025-09-15 20:22:02.255 wdl.w:ptcp.t:call-pbmm2_align_hifi-13 INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2110"
2025-09-15 20:22:02.255 wdl.w:ptcp.t:call-pbmm2_align_hifi-19 NOTICE task setup :: name: "pbmm2_align_hifi", source: "./common.wdl", line: 170, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-19", thread: 140612506469952
2025-09-15 20:22:02.255 wdl.w:ptcp.t:call-pbmm2_align_hifi-05 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 64, memory_reservation: 64000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:22:02.256 wdl.w:ptcp INFO input :: job: "call-pbmm2_align_hifi-20", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "log_level": "INFO", "out_prefix": "m84036_250809_035451_s4.bc2117.mapped", "ref_fasta": "/meta/refs/hg38.fa", "unmapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0021_m84036_250809_035451_s4.bc2117.unmapped.bam", "sample_name": "m84036_250809_035451_s4.bc2117"}
2025-09-15 20:22:02.256 wdl.w:ptcp.t:call-pbmm2_align_hifi-04 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:22:02.257 wdl.w:ptcp.t:call-pbmm2_align_hifi-02 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:22:02.257 wdl.w:ptcp.t:call-pbmm2_align_hifi-06 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:22:02.257 wdl.w:ptcp.t:call-pbmm2_align_hifi-03 INFO provisioned :: seconds_waited: 0, cpu: 64, mem_bytes: 64000000000
2025-09-15 20:22:02.257 wdl.w:ptcp.t:call-pbmm2_align_hifi-11 INFO eval :: name: "mem_gb", value: 64
2025-09-15 20:22:02.259 wdl.w:ptcp.t:call-pbmm2_align_hifi-09 INFO eval :: name: "disk_size", value: 30
2025-09-15 20:22:02.259 wdl.w:ptcp.t:call-pbmm2_align_hifi-00 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:22:02.259 wdl.w:ptcp.t:call-pbmm2_align_hifi-07 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 64, memory_reservation: 64000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:22:02.259 wdl.w:ptcp.t:call-pbmm2_align_hifi-15 INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:22:02.259 wdl.w:ptcp.t:call-pbmm2_align_hifi-12 INFO eval :: name: "threads", value: 64
2025-09-15 20:22:02.260 wdl.w:ptcp.t:call-pbmm2_align_hifi-16 INFO input :: name: "log_level", value: "INFO"
2025-09-15 20:22:02.260 wdl.w:ptcp.t:call-pbmm2_align_hifi-08 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 64, memory_reservation: 64000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:22:02.261 wdl.w:ptcp.t:call-pbmm2_align_hifi-14 INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2111"
2025-09-15 20:22:02.261 wdl.w:ptcp.t:call-pbmm2_align_hifi-10 INFO eval :: name: "disk_size", value: 30
2025-09-15 20:22:02.261 wdl.w:ptcp.t:call-pbmm2_align_hifi-13 INFO eval :: name: "threads", value: 64
2025-09-15 20:22:02.262 wdl.w:ptcp.t:call-pbmm2_align_hifi-05 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:22:02.264 wdl.w:ptcp NOTICE ready :: job: "call-pbmm2_align_hifi-21", callee: "pbmm2_align_hifi"
2025-09-15 20:22:02.264 wdl.w:ptcp.t:call-pbmm2_align_hifi-04 INFO provisioned :: seconds_waited: 0, cpu: 64, mem_bytes: 64000000000
2025-09-15 20:22:02.264 wdl.w:ptcp.t:call-pbmm2_align_hifi-03 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:22:02.267 wdl.w:ptcp.t:call-pbmm2_align_hifi-11 INFO eval :: name: "disk_size", value: 30
2025-09-15 20:22:02.267 wdl.w:ptcp.t:call-pbmm2_align_hifi-09 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 64, memory_reservation: 64000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:22:02.267 wdl.w:ptcp.t:call-pbmm2_align_hifi-07 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:22:02.267 wdl.w:ptcp.t:call-pbmm2_align_hifi-06 INFO provisioned :: seconds_waited: 0, cpu: 64, mem_bytes: 64000000000
2025-09-15 20:22:02.268 wdl.w:ptcp.t:call-pbmm2_align_hifi-15 INFO input :: name: "unmapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0016_m84036_250809_035451_s4.bc2112.unmapped.bam"
2025-09-15 20:22:02.268 wdl.w:ptcp.t:call-pbmm2_align_hifi-12 INFO eval :: name: "mem_gb", value: 64
2025-09-15 20:22:02.268 wdl.w:ptcp.t:call-pbmm2_align_hifi-16 INFO input :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2113.mapped"
2025-09-15 20:22:02.269 wdl.w:ptcp.t:call-pbmm2_align_hifi-08 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:22:02.269 wdl.w:ptcp.t:call-pbmm2_align_hifi-14 INFO eval :: name: "threads", value: 64
2025-09-15 20:22:02.269 wdl.w:ptcp.t:call-pbmm2_align_hifi-10 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 64, memory_reservation: 64000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:22:02.270 wdl.w:ptcp.t:call-pbmm2_align_hifi-13 INFO eval :: name: "mem_gb", value: 64
2025-09-15 20:22:02.270 wdl.w:ptcp INFO input :: job: "call-pbmm2_align_hifi-21", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "log_level": "INFO", "out_prefix": "m84036_250809_035451_s4.bc2118.mapped", "ref_fasta": "/meta/refs/hg38.fa", "unmapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0022_m84036_250809_035451_s4.bc2118.unmapped.bam", "sample_name": "m84036_250809_035451_s4.bc2118"}
2025-09-15 20:22:02.271 wdl.w:ptcp.t:call-pbmm2_align_hifi-04 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:22:02.271 wdl.w:ptcp.t:call-pbmm2_align_hifi-05 INFO provisioned :: seconds_waited: 0, cpu: 64, mem_bytes: 64000000000
2025-09-15 20:22:02.271 wdl.w:ptcp.t:call-pbmm2_align_hifi-17 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:22:02.272 wdl.w:ptcp.t:call-pbmm2_align_hifi-20 NOTICE task setup :: name: "pbmm2_align_hifi", source: "./common.wdl", line: 170, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-20", thread: 140612498077248
2025-09-15 20:22:02.273 wdl.w:ptcp.t:call-pbmm2_align_hifi-09 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:22:02.273 wdl.w:ptcp.t:call-pbmm2_align_hifi-11 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 64, memory_reservation: 64000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:22:02.273 wdl.w:ptcp.t:call-pbmm2_align_hifi-06 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:22:02.274 wdl.w:ptcp.t:call-pbmm2_align_hifi-15 INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2112"
2025-09-15 20:22:02.274 wdl.w:ptcp.t:call-pbmm2_align_hifi-07 INFO provisioned :: seconds_waited: 0, cpu: 64, mem_bytes: 64000000000
2025-09-15 20:22:02.274 wdl.w:ptcp.t:call-pbmm2_align_hifi-16 INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:22:02.274 wdl.w:ptcp.t:call-pbmm2_align_hifi-12 INFO eval :: name: "disk_size", value: 30
2025-09-15 20:22:02.275 wdl.w:ptcp.t:call-pbmm2_align_hifi-14 INFO eval :: name: "mem_gb", value: 64
2025-09-15 20:22:02.275 wdl.w:ptcp.t:call-pbmm2_align_hifi-10 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:22:02.276 wdl.w:ptcp.t:call-pbmm2_align_hifi-08 INFO provisioned :: seconds_waited: 0, cpu: 64, mem_bytes: 64000000000
2025-09-15 20:22:02.276 wdl.w:ptcp.t:call-pbmm2_align_hifi-13 INFO eval :: name: "disk_size", value: 30
2025-09-15 20:22:02.276 wdl.w:ptcp.t:call-pbmm2_align_hifi-05 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:22:02.276 wdl.w:ptcp.t:call-pbmm2_align_hifi-17 INFO input :: name: "log_level", value: "INFO"
2025-09-15 20:22:02.277 wdl.w:ptcp NOTICE ready :: job: "call-pbmm2_align_hifi-22", callee: "pbmm2_align_hifi"
2025-09-15 20:22:02.278 wdl.w:ptcp.t:call-pbmm2_align_hifi-11 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:22:02.279 wdl.w:ptcp.t:call-pbmm2_align_hifi-15 INFO eval :: name: "threads", value: 64
2025-09-15 20:22:02.279 wdl.w:ptcp.t:call-pbmm2_align_hifi-09 INFO provisioned :: seconds_waited: 0, cpu: 64, mem_bytes: 64000000000
2025-09-15 20:22:02.279 wdl.w:ptcp.t:call-pbmm2_align_hifi-07 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:22:02.279 wdl.w:ptcp.t:call-pbmm2_align_hifi-16 INFO input :: name: "unmapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0017_m84036_250809_035451_s4.bc2113.unmapped.bam"
2025-09-15 20:22:02.281 wdl.w:ptcp.t:call-pbmm2_align_hifi-12 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 64, memory_reservation: 64000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:22:02.281 wdl.w:ptcp.t:call-pbmm2_align_hifi-14 INFO eval :: name: "disk_size", value: 30
2025-09-15 20:22:02.281 wdl.w:ptcp.t:call-pbmm2_align_hifi-08 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:22:02.281 wdl.w:ptcp.t:call-pbmm2_align_hifi-18 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:22:02.283 wdl.w:ptcp.t:call-pbmm2_align_hifi-17 INFO input :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2114.mapped"
2025-09-15 20:22:02.283 wdl.w:ptcp INFO input :: job: "call-pbmm2_align_hifi-22", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "log_level": "INFO", "out_prefix": "m84036_250809_035451_s4.bc2119.mapped", "ref_fasta": "/meta/refs/hg38.fa", "unmapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0023_m84036_250809_035451_s4.bc2119.unmapped.bam", "sample_name": "m84036_250809_035451_s4.bc2119"}
2025-09-15 20:22:02.283 wdl.w:ptcp.t:call-pbmm2_align_hifi-10 INFO provisioned :: seconds_waited: 0, cpu: 64, mem_bytes: 64000000000
2025-09-15 20:22:02.283 wdl.w:ptcp.t:call-pbmm2_align_hifi-13 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 64, memory_reservation: 64000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:22:02.284 wdl.w:ptcp.t:call-pbmm2_align_hifi-15 INFO eval :: name: "mem_gb", value: 64
2025-09-15 20:22:02.285 wdl.w:ptcp.t:call-pbmm2_align_hifi-09 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:22:02.285 wdl.w:ptcp.t:call-pbmm2_align_hifi-11 INFO provisioned :: seconds_waited: 0, cpu: 64, mem_bytes: 64000000000
2025-09-15 20:22:02.285 wdl.w:ptcp.t:call-pbmm2_align_hifi-16 INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2113"
2025-09-15 20:22:02.285 wdl.w:ptcp.t:call-pbmm2_align_hifi-12 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:22:02.286 wdl.w:ptcp.t:call-pbmm2_align_hifi-18 INFO input :: name: "log_level", value: "INFO"
2025-09-15 20:22:02.286 wdl.w:ptcp.t:call-pbmm2_align_hifi-17 INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:22:02.287 wdl.w:ptcp.t:call-pbmm2_align_hifi-14 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 64, memory_reservation: 64000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:22:02.287 wdl.w:ptcp.t:call-pbmm2_align_hifi-10 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:22:02.287 wdl.w:ptcp.t:call-pbmm2_align_hifi-13 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:22:02.288 wdl.w:ptcp.t:call-pbmm2_align_hifi-15 INFO eval :: name: "disk_size", value: 30
2025-09-15 20:22:02.289 wdl.w:ptcp NOTICE ready :: job: "call-pbmm2_align_hifi-23", callee: "pbmm2_align_hifi"
2025-09-15 20:22:02.289 wdl.w:ptcp.t:call-pbmm2_align_hifi-11 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:22:02.289 wdl.w:ptcp.t:call-pbmm2_align_hifi-16 INFO eval :: name: "threads", value: 64
2025-09-15 20:22:02.290 wdl.w:ptcp.t:call-pbmm2_align_hifi-18 INFO input :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2115.mapped"
2025-09-15 20:22:02.290 wdl.w:ptcp.t:call-pbmm2_align_hifi-17 INFO input :: name: "unmapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0018_m84036_250809_035451_s4.bc2114.unmapped.bam"
2025-09-15 20:22:02.290 wdl.w:ptcp.t:call-pbmm2_align_hifi-14 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:22:02.290 wdl.w:ptcp.t:call-pbmm2_align_hifi-21 NOTICE task setup :: name: "pbmm2_align_hifi", source: "./common.wdl", line: 170, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-21", thread: 140612489684544
2025-09-15 20:22:02.291 wdl.w:ptcp.t:call-pbmm2_align_hifi-12 INFO provisioned :: seconds_waited: 0, cpu: 64, mem_bytes: 64000000000
2025-09-15 20:22:02.291 wdl.w:ptcp INFO input :: job: "call-pbmm2_align_hifi-23", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "log_level": "INFO", "out_prefix": "m84036_250809_035451_s4.bc2120.mapped", "ref_fasta": "/meta/refs/hg38.fa", "unmapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0024_m84036_250809_035451_s4.bc2120.unmapped.bam", "sample_name": "m84036_250809_035451_s4.bc2120"}
2025-09-15 20:22:02.292 wdl.w:ptcp.t:call-pbmm2_align_hifi-15 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 64, memory_reservation: 64000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:22:02.292 wdl.w:ptcp.t:call-pbmm2_align_hifi-16 INFO eval :: name: "mem_gb", value: 64
2025-09-15 20:22:02.292 wdl.w:ptcp.t:call-pbmm2_align_hifi-18 INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:22:02.292 wdl.w:ptcp.t:call-pbmm2_align_hifi-13 INFO provisioned :: seconds_waited: 0, cpu: 64, mem_bytes: 64000000000
2025-09-15 20:22:02.292 wdl.w:ptcp.t:call-pbmm2_align_hifi-17 INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2114"
2025-09-15 20:22:02.294 wdl.w:ptcp.t:call-pbmm2_align_hifi-12 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:22:02.294 wdl.w:ptcp.t:call-pbmm2_align_hifi-14 INFO provisioned :: seconds_waited: 0, cpu: 64, mem_bytes: 64000000000
2025-09-15 20:22:02.294 wdl.w:ptcp.t:call-pbmm2_align_hifi-15 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:22:02.295 wdl.w:ptcp.t:call-pbmm2_align_hifi-18 INFO input :: name: "unmapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0019_m84036_250809_035451_s4.bc2115.unmapped.bam"
2025-09-15 20:22:02.295 wdl.w:ptcp.t:call-pbmm2_align_hifi-16 INFO eval :: name: "disk_size", value: 30
2025-09-15 20:22:02.295 wdl.w:ptcp.t:call-pbmm2_align_hifi-19 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:22:02.296 wdl.w:ptcp.t:call-pbmm2_align_hifi-13 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:22:02.296 wdl.w:ptcp NOTICE ready :: job: "call-pbmm2_align_hifi-24", callee: "pbmm2_align_hifi"
2025-09-15 20:22:02.297 wdl.w:ptcp.t:call-pbmm2_align_hifi-17 INFO eval :: name: "threads", value: 64
2025-09-15 20:22:02.297 wdl.w:ptcp.t:call-pbmm2_align_hifi-14 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:22:02.297 wdl.w:ptcp.t:call-pbmm2_align_hifi-18 INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2115"
2025-09-15 20:22:02.299 wdl.w:ptcp INFO input :: job: "call-pbmm2_align_hifi-24", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "log_level": "INFO", "out_prefix": "m84036_250809_035451_s4.bc2121.mapped", "ref_fasta": "/meta/refs/hg38.fa", "unmapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0025_m84036_250809_035451_s4.bc2121.unmapped.bam", "sample_name": "m84036_250809_035451_s4.bc2121"}
2025-09-15 20:22:02.299 wdl.w:ptcp.t:call-pbmm2_align_hifi-17 INFO eval :: name: "mem_gb", value: 64
2025-09-15 20:22:02.298 wdl.w:ptcp.t:call-pbmm2_align_hifi-19 INFO input :: name: "log_level", value: "INFO"
2025-09-15 20:22:02.302 wdl.w:ptcp.t:call-pbmm2_align_hifi-19 INFO input :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2116.mapped"
2025-09-15 20:22:02.302 wdl.w:ptcp.t:call-pbmm2_align_hifi-17 INFO eval :: name: "disk_size", value: 30
2025-09-15 20:22:02.302 wdl.w:ptcp.t:call-pbmm2_align_hifi-19 INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:22:02.298 wdl.w:ptcp.t:call-pbmm2_align_hifi-16 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 64, memory_reservation: 64000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:22:02.300 wdl.w:ptcp.t:call-pbmm2_align_hifi-18 INFO eval :: name: "threads", value: 64
2025-09-15 20:22:02.303 wdl.w:ptcp.t:call-pbmm2_align_hifi-17 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 64, memory_reservation: 64000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:22:02.303 wdl.w:ptcp.t:call-pbmm2_align_hifi-19 INFO input :: name: "unmapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0020_m84036_250809_035451_s4.bc2116.unmapped.bam"
2025-09-15 20:22:02.303 wdl.w:ptcp.t:call-pbmm2_align_hifi-16 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:22:02.304 wdl.w:ptcp.t:call-pbmm2_align_hifi-18 INFO eval :: name: "mem_gb", value: 64
2025-09-15 20:22:02.304 wdl.w:ptcp.t:call-pbmm2_align_hifi-17 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:22:02.304 wdl.w:ptcp.t:call-pbmm2_align_hifi-19 INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2116"
2025-09-15 20:22:02.298 wdl.w:ptcp.t:call-pbmm2_align_hifi-15 INFO provisioned :: seconds_waited: 0, cpu: 64, mem_bytes: 64000000000
2025-09-15 20:22:02.305 wdl.w:ptcp.t:call-pbmm2_align_hifi-19 INFO eval :: name: "threads", value: 64
2025-09-15 20:22:02.306 wdl.w:ptcp.t:call-pbmm2_align_hifi-15 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:22:02.306 wdl.w:ptcp.t:call-pbmm2_align_hifi-16 INFO provisioned :: seconds_waited: 0, cpu: 64, mem_bytes: 64000000000
2025-09-15 20:22:02.306 wdl.w:ptcp.t:call-pbmm2_align_hifi-18 INFO eval :: name: "disk_size", value: 30
2025-09-15 20:22:02.306 wdl.w:ptcp.t:call-pbmm2_align_hifi-19 INFO eval :: name: "mem_gb", value: 64
2025-09-15 20:22:02.307 wdl.w:ptcp.t:call-pbmm2_align_hifi-17 INFO provisioned :: seconds_waited: 0, cpu: 64, mem_bytes: 64000000000
2025-09-15 20:22:02.307 wdl.w:ptcp.t:call-pbmm2_align_hifi-16 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:22:02.308 wdl.w:ptcp NOTICE ready :: job: "call-pbmm2_align_hifi-25", callee: "pbmm2_align_hifi"
2025-09-15 20:22:02.308 wdl.w:ptcp.t:call-pbmm2_align_hifi-22 NOTICE task setup :: name: "pbmm2_align_hifi", source: "./common.wdl", line: 170, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-22", thread: 140612481291840
2025-09-15 20:22:02.309 wdl.w:ptcp.t:call-pbmm2_align_hifi-18 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 64, memory_reservation: 64000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:22:02.309 wdl.w:ptcp.t:call-pbmm2_align_hifi-19 INFO eval :: name: "disk_size", value: 30
2025-09-15 20:22:02.309 wdl.w:ptcp.t:call-pbmm2_align_hifi-17 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:22:02.309 wdl.w:ptcp INFO input :: job: "call-pbmm2_align_hifi-25", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "log_level": "INFO", "out_prefix": "m84036_250809_035451_s4.bc2122.mapped", "ref_fasta": "/meta/refs/hg38.fa", "unmapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0026_m84036_250809_035451_s4.bc2122.unmapped.bam", "sample_name": "m84036_250809_035451_s4.bc2122"}
2025-09-15 20:22:02.310 wdl.w:ptcp.t:call-pbmm2_align_hifi-18 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:22:02.310 wdl.w:ptcp.t:call-pbmm2_align_hifi-19 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 64, memory_reservation: 64000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:22:02.311 wdl.w:ptcp.t:call-pbmm2_align_hifi-19 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:22:02.311 wdl.w:ptcp.t:call-pbmm2_align_hifi-18 INFO provisioned :: seconds_waited: 0, cpu: 64, mem_bytes: 64000000000
2025-09-15 20:22:02.311 wdl.w:ptcp.t:call-pbmm2_align_hifi-18 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:22:02.311 wdl.w:ptcp.t:call-pbmm2_align_hifi-19 INFO provisioned :: seconds_waited: 0, cpu: 64, mem_bytes: 64000000000
2025-09-15 20:22:02.312 wdl.w:ptcp.t:call-pbmm2_align_hifi-19 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:22:02.314 wdl.w:ptcp.t:call-pbmm2_align_hifi-20 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:22:02.314 wdl.w:ptcp.t:call-pbmm2_align_hifi-20 INFO input :: name: "log_level", value: "INFO"
2025-09-15 20:22:02.314 wdl.w:ptcp.t:call-pbmm2_align_hifi-20 INFO input :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2117.mapped"
2025-09-15 20:22:02.314 wdl.w:ptcp.t:call-pbmm2_align_hifi-20 INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:22:02.314 wdl.w:ptcp.t:call-pbmm2_align_hifi-20 INFO input :: name: "unmapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0021_m84036_250809_035451_s4.bc2117.unmapped.bam"
2025-09-15 20:22:02.314 wdl.w:ptcp.t:call-pbmm2_align_hifi-20 INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2117"
2025-09-15 20:22:02.315 wdl.w:ptcp.t:call-pbmm2_align_hifi-20 INFO eval :: name: "threads", value: 64
2025-09-15 20:22:02.315 wdl.w:ptcp.t:call-pbmm2_align_hifi-20 INFO eval :: name: "mem_gb", value: 64
2025-09-15 20:22:02.315 wdl.w:ptcp.t:call-pbmm2_align_hifi-20 INFO eval :: name: "disk_size", value: 30
2025-09-15 20:22:02.315 wdl.w:ptcp.t:call-pbmm2_align_hifi-20 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 64, memory_reservation: 64000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:22:02.315 wdl.w:ptcp.t:call-pbmm2_align_hifi-20 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:22:02.316 wdl.w:ptcp.t:call-pbmm2_align_hifi-20 INFO provisioned :: seconds_waited: 0, cpu: 64, mem_bytes: 64000000000
2025-09-15 20:22:02.316 wdl.w:ptcp.t:call-pbmm2_align_hifi-20 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:22:02.318 wdl.w:ptcp NOTICE ready :: job: "call-pbmm2_align_hifi-26", callee: "pbmm2_align_hifi"
2025-09-15 20:22:02.318 wdl.w:ptcp INFO input :: job: "call-pbmm2_align_hifi-26", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "log_level": "INFO", "out_prefix": "m84036_250809_035451_s4.bc2123.mapped", "ref_fasta": "/meta/refs/hg38.fa", "unmapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0027_m84036_250809_035451_s4.bc2123.unmapped.bam", "sample_name": "m84036_250809_035451_s4.bc2123"}
2025-09-15 20:22:02.322 wdl.w:ptcp NOTICE ready :: job: "call-pbmm2_align_hifi-27", callee: "pbmm2_align_hifi"
2025-09-15 20:22:02.322 wdl.w:ptcp INFO input :: job: "call-pbmm2_align_hifi-27", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "log_level": "INFO", "out_prefix": "m84036_250809_035451_s4.bc2124.mapped", "ref_fasta": "/meta/refs/hg38.fa", "unmapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0028_m84036_250809_035451_s4.bc2124.unmapped.bam", "sample_name": "m84036_250809_035451_s4.bc2124"}
2025-09-15 20:22:02.328 wdl.w:ptcp.t:call-pbmm2_align_hifi-21 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:22:02.328 wdl.w:ptcp.t:call-pbmm2_align_hifi-21 INFO input :: name: "log_level", value: "INFO"
2025-09-15 20:22:02.328 wdl.w:ptcp.t:call-pbmm2_align_hifi-21 INFO input :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2118.mapped"
2025-09-15 20:22:02.328 wdl.w:ptcp.t:call-pbmm2_align_hifi-21 INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:22:02.328 wdl.w:ptcp.t:call-pbmm2_align_hifi-21 INFO input :: name: "unmapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0022_m84036_250809_035451_s4.bc2118.unmapped.bam"
2025-09-15 20:22:02.328 wdl.w:ptcp.t:call-pbmm2_align_hifi-21 INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2118"
2025-09-15 20:22:02.329 wdl.w:ptcp.t:call-pbmm2_align_hifi-21 INFO eval :: name: "threads", value: 64
2025-09-15 20:22:02.329 wdl.w:ptcp.t:call-pbmm2_align_hifi-21 INFO eval :: name: "mem_gb", value: 64
2025-09-15 20:22:02.329 wdl.w:ptcp.t:call-pbmm2_align_hifi-21 INFO eval :: name: "disk_size", value: 30
2025-09-15 20:22:02.329 wdl.w:ptcp.t:call-pbmm2_align_hifi-23 NOTICE task setup :: name: "pbmm2_align_hifi", source: "./common.wdl", line: 170, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-23", thread: 140611994777152
2025-09-15 20:22:02.329 wdl.w:ptcp.t:call-pbmm2_align_hifi-21 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 64, memory_reservation: 64000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:22:02.330 wdl.w:ptcp.t:call-pbmm2_align_hifi-21 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:22:02.330 wdl.w:ptcp.t:call-pbmm2_align_hifi-21 INFO provisioned :: seconds_waited: 0, cpu: 64, mem_bytes: 64000000000
2025-09-15 20:22:02.330 wdl.w:ptcp.t:call-pbmm2_align_hifi-21 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:22:02.331 wdl.w:ptcp.t:call-pbmm2_align_hifi-24 NOTICE task setup :: name: "pbmm2_align_hifi", source: "./common.wdl", line: 170, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-24", thread: 140611986384448
2025-09-15 20:22:02.339 wdl.w:ptcp NOTICE ready :: job: "call-pbmm2_align_hifi-28", callee: "pbmm2_align_hifi"
2025-09-15 20:22:02.339 wdl.w:ptcp INFO input :: job: "call-pbmm2_align_hifi-28", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "log_level": "INFO", "out_prefix": "m84036_250809_035451_s4.bc2125.mapped", "ref_fasta": "/meta/refs/hg38.fa", "unmapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0029_m84036_250809_035451_s4.bc2125.unmapped.bam", "sample_name": "m84036_250809_035451_s4.bc2125"}
2025-09-15 20:22:02.339 wdl.w:ptcp.t:call-pbmm2_align_hifi-25 NOTICE task setup :: name: "pbmm2_align_hifi", source: "./common.wdl", line: 170, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-25", thread: 140611977991744
2025-09-15 20:22:02.346 wdl.w:ptcp.t:call-pbmm2_align_hifi-22 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:22:02.346 wdl.w:ptcp.t:call-pbmm2_align_hifi-22 INFO input :: name: "log_level", value: "INFO"
2025-09-15 20:22:02.346 wdl.w:ptcp.t:call-pbmm2_align_hifi-22 INFO input :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2119.mapped"
2025-09-15 20:22:02.346 wdl.w:ptcp.t:call-pbmm2_align_hifi-22 INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:22:02.346 wdl.w:ptcp.t:call-pbmm2_align_hifi-22 INFO input :: name: "unmapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0023_m84036_250809_035451_s4.bc2119.unmapped.bam"
2025-09-15 20:22:02.346 wdl.w:ptcp.t:call-pbmm2_align_hifi-22 INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2119"
2025-09-15 20:22:02.347 wdl.w:ptcp.t:call-pbmm2_align_hifi-22 INFO eval :: name: "threads", value: 64
2025-09-15 20:22:02.347 wdl.w:ptcp.t:call-pbmm2_align_hifi-22 INFO eval :: name: "mem_gb", value: 64
2025-09-15 20:22:02.347 wdl.w:ptcp.t:call-pbmm2_align_hifi-22 INFO eval :: name: "disk_size", value: 30
2025-09-15 20:22:02.347 wdl.w:ptcp.t:call-pbmm2_align_hifi-22 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 64, memory_reservation: 64000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:22:02.347 wdl.w:ptcp.t:call-pbmm2_align_hifi-22 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:22:02.348 wdl.w:ptcp.t:call-pbmm2_align_hifi-22 INFO provisioned :: seconds_waited: 0, cpu: 64, mem_bytes: 64000000000
2025-09-15 20:22:02.348 wdl.w:ptcp.t:call-pbmm2_align_hifi-26 NOTICE task setup :: name: "pbmm2_align_hifi", source: "./common.wdl", line: 170, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-26", thread: 140611969599040
2025-09-15 20:22:02.348 wdl.w:ptcp.t:call-pbmm2_align_hifi-22 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:22:02.359 wdl.w:ptcp NOTICE ready :: job: "call-pbmm2_align_hifi-29", callee: "pbmm2_align_hifi"
2025-09-15 20:22:02.360 wdl.w:ptcp INFO input :: job: "call-pbmm2_align_hifi-29", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "log_level": "INFO", "out_prefix": "m84036_250809_035451_s4.bc2126.mapped", "ref_fasta": "/meta/refs/hg38.fa", "unmapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0030_m84036_250809_035451_s4.bc2126.unmapped.bam", "sample_name": "m84036_250809_035451_s4.bc2126"}
2025-09-15 20:22:02.366 wdl.w:ptcp.t:call-pbmm2_align_hifi-27 NOTICE task setup :: name: "pbmm2_align_hifi", source: "./common.wdl", line: 170, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-27", thread: 140611961206336
2025-09-15 20:22:02.367 wdl.w:ptcp.t:call-pbmm2_align_hifi-24 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:22:02.368 wdl.w:ptcp.t:call-pbmm2_align_hifi-24 INFO input :: name: "log_level", value: "INFO"
2025-09-15 20:22:02.368 wdl.w:ptcp.t:call-pbmm2_align_hifi-24 INFO input :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2121.mapped"
2025-09-15 20:22:02.368 wdl.w:ptcp.t:call-pbmm2_align_hifi-02 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 8, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-02/_singularity_tmpdir_7ihnxtzt"
2025-09-15 20:22:02.368 wdl.w:ptcp.t:call-pbmm2_align_hifi-24 INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:22:02.369 wdl.w:ptcp.t:call-pbmm2_align_hifi-02 INFO Slurm invocation: srun --job-name call-pbmm2_align_hifi-02 --partition compute,compute9 --cpus-per-task 64 --mem 61035M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-02/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-02/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-02/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-02/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0003_m84036_250809_035451_s4.bc2099.unmapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0003_m84036_250809_035451_s4.bc2099.unmapped.bam:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-02/_singularity_tmpdir_7ihnxtzt/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-02/_singularity_tmpdir_7ihnxtzt/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:22:02.369 wdl.w:ptcp.t:call-pbmm2_align_hifi-24 INFO input :: name: "unmapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0025_m84036_250809_035451_s4.bc2121.unmapped.bam"
2025-09-15 20:22:02.369 wdl.w:ptcp.t:call-pbmm2_align_hifi-24 INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2121"
2025-09-15 20:22:02.369 wdl.w:ptcp.t:call-pbmm2_align_hifi-24 INFO eval :: name: "threads", value: 64
2025-09-15 20:22:02.371 wdl.w:ptcp.t:call-pbmm2_align_hifi-01 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 8, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-01/_singularity_tmpdir_wou59fe6"
2025-09-15 20:22:02.372 wdl.w:ptcp.t:call-pbmm2_align_hifi-24 INFO eval :: name: "mem_gb", value: 64
2025-09-15 20:22:02.372 wdl.w:ptcp.t:call-pbmm2_align_hifi-24 INFO eval :: name: "disk_size", value: 30
2025-09-15 20:22:02.373 wdl.w:ptcp.t:call-pbmm2_align_hifi-24 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 64, memory_reservation: 64000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:22:02.373 wdl.w:ptcp.t:call-pbmm2_align_hifi-24 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:22:02.373 wdl.w:ptcp.t:call-pbmm2_align_hifi-25 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:22:02.374 wdl.w:ptcp.t:call-pbmm2_align_hifi-25 INFO input :: name: "log_level", value: "INFO"
2025-09-15 20:22:02.374 wdl.w:ptcp.t:call-pbmm2_align_hifi-25 INFO input :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2122.mapped"
2025-09-15 20:22:02.374 wdl.w:ptcp.t:call-pbmm2_align_hifi-25 INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:22:02.374 wdl.w:ptcp.t:call-pbmm2_align_hifi-25 INFO input :: name: "unmapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0026_m84036_250809_035451_s4.bc2122.unmapped.bam"
2025-09-15 20:22:02.372 wdl.w:ptcp.t:call-pbmm2_align_hifi-01 INFO Slurm invocation: srun --job-name call-pbmm2_align_hifi-01 --partition compute,compute9 --cpus-per-task 64 --mem 61035M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-01/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-01/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-01/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-01/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0002_m84036_250809_035451_s4.bc2098.unmapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0002_m84036_250809_035451_s4.bc2098.unmapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-01/_singularity_tmpdir_wou59fe6/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-01/_singularity_tmpdir_wou59fe6/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:22:02.374 wdl.w:ptcp.t:call-pbmm2_align_hifi-25 INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2122"
2025-09-15 20:22:02.374 wdl.w:ptcp.t:call-pbmm2_align_hifi-24 INFO provisioned :: seconds_waited: 0, cpu: 64, mem_bytes: 64000000000
2025-09-15 20:22:02.375 wdl.w:ptcp.t:call-pbmm2_align_hifi-25 INFO eval :: name: "threads", value: 64
2025-09-15 20:22:02.375 wdl.w:ptcp.t:call-pbmm2_align_hifi-24 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:22:02.377 wdl.w:ptcp.t:call-pbmm2_align_hifi-25 INFO eval :: name: "mem_gb", value: 64
2025-09-15 20:22:02.378 wdl.w:ptcp.t:call-pbmm2_align_hifi-25 INFO eval :: name: "disk_size", value: 30
2025-09-15 20:22:02.378 wdl.w:ptcp.t:call-pbmm2_align_hifi-00 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 8, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-00/_singularity_tmpdir_p1tc9l60"
2025-09-15 20:22:02.379 wdl.w:ptcp.t:call-pbmm2_align_hifi-25 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 64, memory_reservation: 64000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:22:02.379 wdl.w:ptcp.t:call-pbmm2_align_hifi-00 INFO Slurm invocation: srun --job-name call-pbmm2_align_hifi-00 --partition compute,compute9 --cpus-per-task 64 --mem 61035M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-00/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-00/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-00/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-00/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0001_m84036_250809_035451_s4.bc2097.unmapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0001_m84036_250809_035451_s4.bc2097.unmapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-00/_singularity_tmpdir_p1tc9l60/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-00/_singularity_tmpdir_p1tc9l60/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:22:02.379 wdl.w:ptcp.t:call-pbmm2_align_hifi-25 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:22:02.380 wdl.w:ptcp.t:call-pbmm2_align_hifi-25 INFO provisioned :: seconds_waited: 0, cpu: 64, mem_bytes: 64000000000
2025-09-15 20:22:02.382 wdl.w:ptcp.t:call-pbmm2_align_hifi-25 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:22:02.385 wdl.w:ptcp NOTICE ready :: job: "call-pbmm2_align_hifi-30", callee: "pbmm2_align_hifi"
2025-09-15 20:22:02.385 wdl.w:ptcp INFO input :: job: "call-pbmm2_align_hifi-30", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "log_level": "INFO", "out_prefix": "m84036_250809_035451_s4.bc2127.mapped", "ref_fasta": "/meta/refs/hg38.fa", "unmapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0031_m84036_250809_035451_s4.bc2127.unmapped.bam", "sample_name": "m84036_250809_035451_s4.bc2127"}
2025-09-15 20:22:02.386 wdl.w:ptcp.t:call-pbmm2_align_hifi-03 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 8, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-03/_singularity_tmpdir_uu_7ttrl"
2025-09-15 20:22:02.387 wdl.w:ptcp.t:call-pbmm2_align_hifi-03 INFO Slurm invocation: srun --job-name call-pbmm2_align_hifi-03 --partition compute,compute9 --cpus-per-task 64 --mem 61035M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-03/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-03/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-03/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-03/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0004_m84036_250809_035451_s4.bc2100.unmapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0004_m84036_250809_035451_s4.bc2100.unmapped.bam:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-03/_singularity_tmpdir_uu_7ttrl/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-03/_singularity_tmpdir_uu_7ttrl/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:22:02.388 wdl.w:ptcp.t:call-pbmm2_align_hifi-23 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:22:02.391 wdl.w:ptcp.t:call-pbmm2_align_hifi-23 INFO input :: name: "log_level", value: "INFO"
2025-09-15 20:22:02.391 wdl.w:ptcp.t:call-pbmm2_align_hifi-23 INFO input :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2120.mapped"
2025-09-15 20:22:02.391 wdl.w:ptcp.t:call-pbmm2_align_hifi-23 INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:22:02.391 wdl.w:ptcp.t:call-pbmm2_align_hifi-23 INFO input :: name: "unmapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0024_m84036_250809_035451_s4.bc2120.unmapped.bam"
2025-09-15 20:22:02.391 wdl.w:ptcp.t:call-pbmm2_align_hifi-23 INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2120"
2025-09-15 20:22:02.391 wdl.w:ptcp.t:call-pbmm2_align_hifi-23 INFO eval :: name: "threads", value: 64
2025-09-15 20:22:02.392 wdl.w:ptcp.t:call-pbmm2_align_hifi-23 INFO eval :: name: "mem_gb", value: 64
2025-09-15 20:22:02.392 wdl.w:ptcp.t:call-pbmm2_align_hifi-28 NOTICE task setup :: name: "pbmm2_align_hifi", source: "./common.wdl", line: 170, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-28", thread: 140611952813632
2025-09-15 20:22:02.392 wdl.w:ptcp.t:call-pbmm2_align_hifi-26 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:22:02.393 wdl.w:ptcp.t:call-pbmm2_align_hifi-23 INFO eval :: name: "disk_size", value: 30
2025-09-15 20:22:02.393 wdl.w:ptcp.t:call-pbmm2_align_hifi-26 INFO input :: name: "log_level", value: "INFO"
2025-09-15 20:22:02.394 wdl.w:ptcp.t:call-pbmm2_align_hifi-26 INFO input :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2123.mapped"
2025-09-15 20:22:02.394 wdl.w:ptcp.t:call-pbmm2_align_hifi-23 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 64, memory_reservation: 64000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:22:02.394 wdl.w:ptcp.t:call-pbmm2_align_hifi-26 INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:22:02.394 wdl.w:ptcp.t:call-pbmm2_align_hifi-23 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:22:02.394 wdl.w:ptcp.t:call-pbmm2_align_hifi-26 INFO input :: name: "unmapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0027_m84036_250809_035451_s4.bc2123.unmapped.bam"
2025-09-15 20:22:02.395 wdl.w:ptcp.t:call-pbmm2_align_hifi-26 INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2123"
2025-09-15 20:22:02.395 wdl.w:ptcp.t:call-pbmm2_align_hifi-26 INFO eval :: name: "threads", value: 64
2025-09-15 20:22:02.395 wdl.w:ptcp.t:call-pbmm2_align_hifi-26 INFO eval :: name: "mem_gb", value: 64
2025-09-15 20:22:02.396 wdl.w:ptcp.t:call-pbmm2_align_hifi-23 INFO provisioned :: seconds_waited: 0, cpu: 64, mem_bytes: 64000000000
2025-09-15 20:22:02.396 wdl.w:ptcp.t:call-pbmm2_align_hifi-26 INFO eval :: name: "disk_size", value: 30
2025-09-15 20:22:02.396 wdl.w:ptcp.t:call-pbmm2_align_hifi-23 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:22:02.397 wdl.w:ptcp.t:call-pbmm2_align_hifi-26 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 64, memory_reservation: 64000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:22:02.397 wdl.w:ptcp.t:call-pbmm2_align_hifi-26 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:22:02.397 wdl.w:ptcp.t:call-pbmm2_align_hifi-26 INFO provisioned :: seconds_waited: 0, cpu: 64, mem_bytes: 64000000000
2025-09-15 20:22:02.397 wdl.w:ptcp.t:call-pbmm2_align_hifi-26 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:22:02.400 wdl.w:ptcp.t:call-pbmm2_align_hifi-27 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:22:02.400 wdl.w:ptcp.t:call-pbmm2_align_hifi-27 INFO input :: name: "log_level", value: "INFO"
2025-09-15 20:22:02.400 wdl.w:ptcp.t:call-pbmm2_align_hifi-27 INFO input :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2124.mapped"
2025-09-15 20:22:02.400 wdl.w:ptcp.t:call-pbmm2_align_hifi-27 INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:22:02.400 wdl.w:ptcp.t:call-pbmm2_align_hifi-27 INFO input :: name: "unmapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0028_m84036_250809_035451_s4.bc2124.unmapped.bam"
2025-09-15 20:22:02.400 wdl.w:ptcp.t:call-pbmm2_align_hifi-27 INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2124"
2025-09-15 20:22:02.401 wdl.w:ptcp.t:call-pbmm2_align_hifi-27 INFO eval :: name: "threads", value: 64
2025-09-15 20:22:02.401 wdl.w:ptcp.t:call-pbmm2_align_hifi-27 INFO eval :: name: "mem_gb", value: 64
2025-09-15 20:22:02.402 wdl.w:ptcp.t:call-pbmm2_align_hifi-27 INFO eval :: name: "disk_size", value: 30
2025-09-15 20:22:02.402 wdl.w:ptcp.t:call-pbmm2_align_hifi-27 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 64, memory_reservation: 64000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:22:02.402 wdl.w:ptcp.t:call-pbmm2_align_hifi-27 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:22:02.402 wdl.w:ptcp.t:call-pbmm2_align_hifi-27 INFO provisioned :: seconds_waited: 0, cpu: 64, mem_bytes: 64000000000
2025-09-15 20:22:02.402 wdl.w:ptcp.t:call-pbmm2_align_hifi-27 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:22:02.411 wdl.w:ptcp.t:call-pbmm2_align_hifi-02 NOTICE slurm_singularity run :: pid: 1197161, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-02/slurm_singularity.log.txt"
2025-09-15 20:22:02.412 wdl.w:ptcp.t:call-pbmm2_align_hifi-03 NOTICE slurm_singularity run :: pid: 1197165, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-03/slurm_singularity.log.txt"
2025-09-15 20:22:02.412 wdl.w:ptcp NOTICE ready :: job: "call-pbmm2_align_hifi-31", callee: "pbmm2_align_hifi"
2025-09-15 20:22:02.412 wdl.w:ptcp.t:call-pbmm2_align_hifi-00 NOTICE slurm_singularity run :: pid: 1197163, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-00/slurm_singularity.log.txt"
2025-09-15 20:22:02.412 wdl.w:ptcp.t:call-pbmm2_align_hifi-01 NOTICE slurm_singularity run :: pid: 1197162, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-01/slurm_singularity.log.txt"
2025-09-15 20:22:02.412 wdl.w:ptcp.t:call-pbmm2_align_hifi-04 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 8, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-04/_singularity_tmpdir_i4kc240f"
2025-09-15 20:22:02.413 wdl.w:ptcp INFO input :: job: "call-pbmm2_align_hifi-31", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "log_level": "INFO", "out_prefix": "m84036_250809_035451_s4.bc2128.mapped", "ref_fasta": "/meta/refs/hg38.fa", "unmapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0032_m84036_250809_035451_s4.bc2128.unmapped.bam", "sample_name": "m84036_250809_035451_s4.bc2128"}
2025-09-15 20:22:02.414 wdl.w:ptcp.t:call-pbmm2_align_hifi-04 INFO Slurm invocation: srun --job-name call-pbmm2_align_hifi-04 --partition compute,compute9 --cpus-per-task 64 --mem 61035M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-04/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-04/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-04/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-04/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0005_m84036_250809_035451_s4.bc2101.unmapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0005_m84036_250809_035451_s4.bc2101.unmapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-04/_singularity_tmpdir_i4kc240f/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-04/_singularity_tmpdir_i4kc240f/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:22:02.424 wdl.w:ptcp.t:call-pbmm2_align_hifi-29 NOTICE task setup :: name: "pbmm2_align_hifi", source: "./common.wdl", line: 170, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-29", thread: 140611944420928
2025-09-15 20:22:02.426 wdl.w:ptcp.t:call-pbmm2_align_hifi-06 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 8, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-06/_singularity_tmpdir_ljtdrdt2"
2025-09-15 20:22:02.427 wdl.w:ptcp NOTICE ready :: job: "call-pbmm2_align_hifi-32", callee: "pbmm2_align_hifi"
2025-09-15 20:22:02.427 wdl.w:ptcp.t:call-pbmm2_align_hifi-06 INFO Slurm invocation: srun --job-name call-pbmm2_align_hifi-06 --partition compute,compute9 --cpus-per-task 64 --mem 61035M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-06/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-06/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-06/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-06/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0007_m84036_250809_035451_s4.bc2103.unmapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0007_m84036_250809_035451_s4.bc2103.unmapped.bam:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-06/_singularity_tmpdir_ljtdrdt2/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-06/_singularity_tmpdir_ljtdrdt2/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:22:02.428 wdl.w:ptcp INFO input :: job: "call-pbmm2_align_hifi-32", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "log_level": "INFO", "out_prefix": "m84036_250809_035451_s4.bc2129.mapped", "ref_fasta": "/meta/refs/hg38.fa", "unmapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0033_m84036_250809_035451_s4.bc2129.unmapped.bam", "sample_name": "m84036_250809_035451_s4.bc2129"}
2025-09-15 20:22:02.428 wdl.w:ptcp.t:call-pbmm2_align_hifi-28 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:22:02.428 wdl.w:ptcp.t:call-pbmm2_align_hifi-28 INFO input :: name: "log_level", value: "INFO"
2025-09-15 20:22:02.428 wdl.w:ptcp.t:call-pbmm2_align_hifi-28 INFO input :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2125.mapped"
2025-09-15 20:22:02.431 wdl.w:ptcp.t:call-pbmm2_align_hifi-28 INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:22:02.431 wdl.w:ptcp.t:call-pbmm2_align_hifi-28 INFO input :: name: "unmapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0029_m84036_250809_035451_s4.bc2125.unmapped.bam"
2025-09-15 20:22:02.431 wdl.w:ptcp.t:call-pbmm2_align_hifi-28 INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2125"
2025-09-15 20:22:02.432 wdl.w:ptcp.t:call-pbmm2_align_hifi-28 INFO eval :: name: "threads", value: 64
2025-09-15 20:22:02.432 wdl.w:ptcp.t:call-pbmm2_align_hifi-28 INFO eval :: name: "mem_gb", value: 64
2025-09-15 20:22:02.432 wdl.w:ptcp.t:call-pbmm2_align_hifi-28 INFO eval :: name: "disk_size", value: 30
2025-09-15 20:22:02.432 wdl.w:ptcp.t:call-pbmm2_align_hifi-28 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 64, memory_reservation: 64000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:22:02.433 wdl.w:ptcp.t:call-pbmm2_align_hifi-28 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:22:02.433 wdl.w:ptcp.t:call-pbmm2_align_hifi-28 INFO provisioned :: seconds_waited: 0, cpu: 64, mem_bytes: 64000000000
2025-09-15 20:22:02.433 wdl.w:ptcp.t:call-pbmm2_align_hifi-28 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:22:02.440 wdl.w:ptcp NOTICE ready :: job: "call-pbmm2_align_hifi-33", callee: "pbmm2_align_hifi"
2025-09-15 20:22:02.440 wdl.w:ptcp INFO input :: job: "call-pbmm2_align_hifi-33", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "log_level": "INFO", "out_prefix": "m84036_250809_035451_s4.bc2130.mapped", "ref_fasta": "/meta/refs/hg38.fa", "unmapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0034_m84036_250809_035451_s4.bc2130.unmapped.bam", "sample_name": "m84036_250809_035451_s4.bc2130"}
2025-09-15 20:22:02.445 wdl.w:ptcp.t:call-pbmm2_align_hifi-30 NOTICE task setup :: name: "pbmm2_align_hifi", source: "./common.wdl", line: 170, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-30", thread: 140611457906240
2025-09-15 20:22:02.445 wdl.w:ptcp.t:call-pbmm2_align_hifi-05 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 8, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-05/_singularity_tmpdir_4leyced1"
2025-09-15 20:22:02.446 wdl.w:ptcp.t:call-pbmm2_align_hifi-05 INFO Slurm invocation: srun --job-name call-pbmm2_align_hifi-05 --partition compute,compute9 --cpus-per-task 64 --mem 61035M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-05/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-05/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-05/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-05/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0006_m84036_250809_035451_s4.bc2102.unmapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0006_m84036_250809_035451_s4.bc2102.unmapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-05/_singularity_tmpdir_4leyced1/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-05/_singularity_tmpdir_4leyced1/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:22:02.450 wdl.w:ptcp.t:call-pbmm2_align_hifi-09 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 8, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-09/_singularity_tmpdir_hjha1nbf"
2025-09-15 20:22:02.452 wdl.w:ptcp.t:call-pbmm2_align_hifi-07 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 8, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-07/_singularity_tmpdir_978r8v2x"
2025-09-15 20:22:02.453 wdl.w:ptcp.t:call-pbmm2_align_hifi-07 INFO Slurm invocation: srun --job-name call-pbmm2_align_hifi-07 --partition compute,compute9 --cpus-per-task 64 --mem 61035M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-07/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-07/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-07/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-07/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0008_m84036_250809_035451_s4.bc2104.unmapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0008_m84036_250809_035451_s4.bc2104.unmapped.bam:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-07/_singularity_tmpdir_978r8v2x/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-07/_singularity_tmpdir_978r8v2x/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:22:02.451 wdl.w:ptcp.t:call-pbmm2_align_hifi-09 INFO Slurm invocation: srun --job-name call-pbmm2_align_hifi-09 --partition compute,compute9 --cpus-per-task 64 --mem 61035M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-09/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-09/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-09/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-09/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0010_m84036_250809_035451_s4.bc2106.unmapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0010_m84036_250809_035451_s4.bc2106.unmapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-09/_singularity_tmpdir_hjha1nbf/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-09/_singularity_tmpdir_hjha1nbf/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:22:02.456 wdl.w:ptcp NOTICE ready :: job: "call-pbmm2_align_hifi-34", callee: "pbmm2_align_hifi"
2025-09-15 20:22:02.457 wdl.w:ptcp INFO input :: job: "call-pbmm2_align_hifi-34", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "log_level": "INFO", "out_prefix": "m84036_250809_035451_s4.bc2131.mapped", "ref_fasta": "/meta/refs/hg38.fa", "unmapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0035_m84036_250809_035451_s4.bc2131.unmapped.bam", "sample_name": "m84036_250809_035451_s4.bc2131"}
2025-09-15 20:22:02.461 wdl.w:ptcp.t:call-pbmm2_align_hifi-31 NOTICE task setup :: name: "pbmm2_align_hifi", source: "./common.wdl", line: 170, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-31", thread: 140611449513536
2025-09-15 20:22:02.461 wdl.w:ptcp.t:call-pbmm2_align_hifi-29 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:22:02.462 wdl.w:ptcp.t:call-pbmm2_align_hifi-29 INFO input :: name: "log_level", value: "INFO"
2025-09-15 20:22:02.462 wdl.w:ptcp.t:call-pbmm2_align_hifi-29 INFO input :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2126.mapped"
2025-09-15 20:22:02.462 wdl.w:ptcp.t:call-pbmm2_align_hifi-29 INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:22:02.462 wdl.w:ptcp.t:call-pbmm2_align_hifi-29 INFO input :: name: "unmapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0030_m84036_250809_035451_s4.bc2126.unmapped.bam"
2025-09-15 20:22:02.462 wdl.w:ptcp.t:call-pbmm2_align_hifi-29 INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2126"
2025-09-15 20:22:02.462 wdl.w:ptcp.t:call-pbmm2_align_hifi-29 INFO eval :: name: "threads", value: 64
2025-09-15 20:22:02.462 wdl.w:ptcp.t:call-pbmm2_align_hifi-29 INFO eval :: name: "mem_gb", value: 64
2025-09-15 20:22:02.462 wdl.w:ptcp.t:call-pbmm2_align_hifi-10 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 8, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-10/_singularity_tmpdir_xwty29su"
2025-09-15 20:22:02.462 wdl.w:ptcp.t:call-pbmm2_align_hifi-08 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 8, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-08/_singularity_tmpdir_qtkmegvh"
2025-09-15 20:22:02.463 wdl.w:ptcp.t:call-pbmm2_align_hifi-29 INFO eval :: name: "disk_size", value: 30
2025-09-15 20:22:02.463 wdl.w:ptcp.t:call-pbmm2_align_hifi-08 INFO Slurm invocation: srun --job-name call-pbmm2_align_hifi-08 --partition compute,compute9 --cpus-per-task 64 --mem 61035M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-08/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-08/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-08/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-08/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0009_m84036_250809_035451_s4.bc2105.unmapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0009_m84036_250809_035451_s4.bc2105.unmapped.bam:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-08/_singularity_tmpdir_qtkmegvh/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-08/_singularity_tmpdir_qtkmegvh/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:22:02.464 wdl.w:ptcp.t:call-pbmm2_align_hifi-29 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 64, memory_reservation: 64000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:22:02.463 wdl.w:ptcp.t:call-pbmm2_align_hifi-10 INFO Slurm invocation: srun --job-name call-pbmm2_align_hifi-10 --partition compute,compute9 --cpus-per-task 64 --mem 61035M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-10/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-10/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-10/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-10/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0011_m84036_250809_035451_s4.bc2107.unmapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0011_m84036_250809_035451_s4.bc2107.unmapped.bam:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-10/_singularity_tmpdir_xwty29su/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-10/_singularity_tmpdir_xwty29su/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:22:02.467 wdl.w:ptcp.t:call-pbmm2_align_hifi-29 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:22:02.468 wdl.w:ptcp.t:call-pbmm2_align_hifi-29 INFO provisioned :: seconds_waited: 0, cpu: 64, mem_bytes: 64000000000
2025-09-15 20:22:02.470 wdl.w:ptcp NOTICE ready :: job: "call-pbmm2_align_hifi-35", callee: "pbmm2_align_hifi"
2025-09-15 20:22:02.471 wdl.w:ptcp.t:call-pbmm2_align_hifi-29 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:22:02.471 wdl.w:ptcp INFO input :: job: "call-pbmm2_align_hifi-35", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "log_level": "INFO", "out_prefix": "m84036_250809_035451_s4.bc2132.mapped", "ref_fasta": "/meta/refs/hg38.fa", "unmapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0036_m84036_250809_035451_s4.bc2132.unmapped.bam", "sample_name": "m84036_250809_035451_s4.bc2132"}
2025-09-15 20:22:02.471 wdl.w:ptcp.t:call-pbmm2_align_hifi-04 NOTICE slurm_singularity run :: pid: 1197167, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-04/slurm_singularity.log.txt"
2025-09-15 20:22:02.474 wdl.w:ptcp NOTICE ready :: job: "call-pbmm2_align_hifi-36", callee: "pbmm2_align_hifi"
2025-09-15 20:22:02.474 wdl.w:ptcp INFO input :: job: "call-pbmm2_align_hifi-36", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "log_level": "INFO", "out_prefix": "m84036_250809_035451_s4.bc2133.mapped", "ref_fasta": "/meta/refs/hg38.fa", "unmapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0037_m84036_250809_035451_s4.bc2133.unmapped.bam", "sample_name": "m84036_250809_035451_s4.bc2133"}
2025-09-15 20:22:02.474 wdl.w:ptcp.t:call-pbmm2_align_hifi-05 NOTICE slurm_singularity run :: pid: 1197175, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-05/slurm_singularity.log.txt"
2025-09-15 20:22:02.474 wdl.w:ptcp.t:call-pbmm2_align_hifi-06 NOTICE slurm_singularity run :: pid: 1197173, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-06/slurm_singularity.log.txt"
2025-09-15 20:22:02.476 wdl.w:ptcp.t:call-pbmm2_align_hifi-13 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 8, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-13/_singularity_tmpdir_c4mfq_yc"
2025-09-15 20:22:02.476 wdl.w:ptcp.t:call-pbmm2_align_hifi-13 INFO Slurm invocation: srun --job-name call-pbmm2_align_hifi-13 --partition compute,compute9 --cpus-per-task 64 --mem 61035M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-13/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-13/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-13/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-13/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0014_m84036_250809_035451_s4.bc2110.unmapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0014_m84036_250809_035451_s4.bc2110.unmapped.bam:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-13/_singularity_tmpdir_c4mfq_yc/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-13/_singularity_tmpdir_c4mfq_yc/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:22:02.477 wdl.w:ptcp.t:call-pbmm2_align_hifi-12 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 8, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-12/_singularity_tmpdir_rfkx3hja"
2025-09-15 20:22:02.479 wdl.w:ptcp.t:call-pbmm2_align_hifi-11 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 8, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-11/_singularity_tmpdir_6vvqfo8o"
2025-09-15 20:22:02.479 wdl.w:ptcp.t:call-pbmm2_align_hifi-09 NOTICE slurm_singularity run :: pid: 1197178, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-09/slurm_singularity.log.txt"
2025-09-15 20:22:02.479 wdl.w:ptcp.t:call-pbmm2_align_hifi-07 NOTICE slurm_singularity run :: pid: 1197176, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-07/slurm_singularity.log.txt"
2025-09-15 20:22:02.480 wdl.w:ptcp.t:call-pbmm2_align_hifi-32 NOTICE task setup :: name: "pbmm2_align_hifi", source: "./common.wdl", line: 170, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-32", thread: 140611441120832
2025-09-15 20:22:02.480 wdl.w:ptcp.t:call-pbmm2_align_hifi-12 INFO Slurm invocation: srun --job-name call-pbmm2_align_hifi-12 --partition compute,compute9 --cpus-per-task 64 --mem 61035M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-12/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-12/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-12/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-12/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0013_m84036_250809_035451_s4.bc2109.unmapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0013_m84036_250809_035451_s4.bc2109.unmapped.bam:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-12/_singularity_tmpdir_rfkx3hja/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-12/_singularity_tmpdir_rfkx3hja/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:22:02.480 wdl.w:ptcp.t:call-pbmm2_align_hifi-11 INFO Slurm invocation: srun --job-name call-pbmm2_align_hifi-11 --partition compute,compute9 --cpus-per-task 64 --mem 61035M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-11/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-11/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-11/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-11/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0012_m84036_250809_035451_s4.bc2108.unmapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0012_m84036_250809_035451_s4.bc2108.unmapped.bam:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-11/_singularity_tmpdir_6vvqfo8o/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-11/_singularity_tmpdir_6vvqfo8o/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:22:02.481 wdl.w:ptcp.t:call-pbmm2_align_hifi-14 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 8, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-14/_singularity_tmpdir_7dtg2u17"
2025-09-15 20:22:02.482 wdl.w:ptcp.t:call-pbmm2_align_hifi-14 INFO Slurm invocation: srun --job-name call-pbmm2_align_hifi-14 --partition compute,compute9 --cpus-per-task 64 --mem 61035M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-14/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-14/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-14/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-14/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0015_m84036_250809_035451_s4.bc2111.unmapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0015_m84036_250809_035451_s4.bc2111.unmapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-14/_singularity_tmpdir_7dtg2u17/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-14/_singularity_tmpdir_7dtg2u17/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:22:02.482 wdl.w:ptcp.t:call-pbmm2_align_hifi-15 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 8, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-15/_singularity_tmpdir_nc2ys9zg"
2025-09-15 20:22:02.483 wdl.w:ptcp.t:call-pbmm2_align_hifi-33 NOTICE task setup :: name: "pbmm2_align_hifi", source: "./common.wdl", line: 170, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-33", thread: 140611432728128
2025-09-15 20:22:02.483 wdl.w:ptcp.t:call-pbmm2_align_hifi-18 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 8, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-18/_singularity_tmpdir_fp342tr7"
2025-09-15 20:22:02.485 wdl.w:ptcp.t:call-pbmm2_align_hifi-15 INFO Slurm invocation: srun --job-name call-pbmm2_align_hifi-15 --partition compute,compute9 --cpus-per-task 64 --mem 61035M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-15/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-15/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-15/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-15/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0016_m84036_250809_035451_s4.bc2112.unmapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0016_m84036_250809_035451_s4.bc2112.unmapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-15/_singularity_tmpdir_nc2ys9zg/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-15/_singularity_tmpdir_nc2ys9zg/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:22:02.485 wdl.w:ptcp NOTICE ready :: job: "call-pbmm2_align_hifi-37", callee: "pbmm2_align_hifi"
2025-09-15 20:22:02.486 wdl.w:ptcp.t:call-pbmm2_align_hifi-18 INFO Slurm invocation: srun --job-name call-pbmm2_align_hifi-18 --partition compute,compute9 --cpus-per-task 64 --mem 61035M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-18/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-18/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-18/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-18/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0019_m84036_250809_035451_s4.bc2115.unmapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0019_m84036_250809_035451_s4.bc2115.unmapped.bam:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-18/_singularity_tmpdir_fp342tr7/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-18/_singularity_tmpdir_fp342tr7/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:22:02.487 wdl.w:ptcp INFO input :: job: "call-pbmm2_align_hifi-37", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "log_level": "INFO", "out_prefix": "m84036_250809_035451_s4.bc2134.mapped", "ref_fasta": "/meta/refs/hg38.fa", "unmapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0038_m84036_250809_035451_s4.bc2134.unmapped.bam", "sample_name": "m84036_250809_035451_s4.bc2134"}
2025-09-15 20:22:02.494 wdl.w:ptcp.t:call-pbmm2_align_hifi-34 NOTICE task setup :: name: "pbmm2_align_hifi", source: "./common.wdl", line: 170, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-34", thread: 140611424335424
2025-09-15 20:22:02.494 wdl.w:ptcp NOTICE ready :: job: "call-pbmm2_align_hifi-38", callee: "pbmm2_align_hifi"
2025-09-15 20:22:02.494 wdl.w:ptcp INFO input :: job: "call-pbmm2_align_hifi-38", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "log_level": "INFO", "out_prefix": "m84036_250809_035451_s4.bc2135.mapped", "ref_fasta": "/meta/refs/hg38.fa", "unmapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0039_m84036_250809_035451_s4.bc2135.unmapped.bam", "sample_name": "m84036_250809_035451_s4.bc2135"}
2025-09-15 20:22:02.495 wdl.w:ptcp.t:call-pbmm2_align_hifi-30 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:22:02.495 wdl.w:ptcp.t:call-pbmm2_align_hifi-30 INFO input :: name: "log_level", value: "INFO"
2025-09-15 20:22:02.495 wdl.w:ptcp.t:call-pbmm2_align_hifi-30 INFO input :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2127.mapped"
2025-09-15 20:22:02.495 wdl.w:ptcp.t:call-pbmm2_align_hifi-30 INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:22:02.495 wdl.w:ptcp.t:call-pbmm2_align_hifi-30 INFO input :: name: "unmapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0031_m84036_250809_035451_s4.bc2127.unmapped.bam"
2025-09-15 20:22:02.495 wdl.w:ptcp.t:call-pbmm2_align_hifi-30 INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2127"
2025-09-15 20:22:02.496 wdl.w:ptcp.t:call-pbmm2_align_hifi-30 INFO eval :: name: "threads", value: 64
2025-09-15 20:22:02.496 wdl.w:ptcp.t:call-pbmm2_align_hifi-30 INFO eval :: name: "mem_gb", value: 64
2025-09-15 20:22:02.496 wdl.w:ptcp NOTICE ready :: job: "call-pbmm2_align_hifi-39", callee: "pbmm2_align_hifi"
2025-09-15 20:22:02.497 wdl.w:ptcp.t:call-pbmm2_align_hifi-35 NOTICE task setup :: name: "pbmm2_align_hifi", source: "./common.wdl", line: 170, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-35", thread: 140611415942720
2025-09-15 20:22:02.497 wdl.w:ptcp INFO input :: job: "call-pbmm2_align_hifi-39", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "log_level": "INFO", "out_prefix": "m84036_250809_035451_s4.bc2136.mapped", "ref_fasta": "/meta/refs/hg38.fa", "unmapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0040_m84036_250809_035451_s4.bc2136.unmapped.bam", "sample_name": "m84036_250809_035451_s4.bc2136"}
2025-09-15 20:22:02.497 wdl.w:ptcp.t:call-pbmm2_align_hifi-30 INFO eval :: name: "disk_size", value: 30
2025-09-15 20:22:02.497 wdl.w:ptcp.t:call-pbmm2_align_hifi-16 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 8, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-16/_singularity_tmpdir_gm0zdj3g"
2025-09-15 20:22:02.498 wdl.w:ptcp.t:call-pbmm2_align_hifi-16 INFO Slurm invocation: srun --job-name call-pbmm2_align_hifi-16 --partition compute,compute9 --cpus-per-task 64 --mem 61035M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-16/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-16/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-16/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-16/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0017_m84036_250809_035451_s4.bc2113.unmapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0017_m84036_250809_035451_s4.bc2113.unmapped.bam:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-16/_singularity_tmpdir_gm0zdj3g/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-16/_singularity_tmpdir_gm0zdj3g/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:22:02.498 wdl.w:ptcp.t:call-pbmm2_align_hifi-30 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 64, memory_reservation: 64000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:22:02.498 wdl.w:ptcp.t:call-pbmm2_align_hifi-30 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:22:02.499 wdl.w:ptcp.t:call-pbmm2_align_hifi-30 INFO provisioned :: seconds_waited: 0, cpu: 64, mem_bytes: 64000000000
2025-09-15 20:22:02.499 wdl.w:ptcp.t:call-pbmm2_align_hifi-19 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 8, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-19/_singularity_tmpdir_7be6nkyd"
2025-09-15 20:22:02.500 wdl.w:ptcp.t:call-pbmm2_align_hifi-31 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:22:02.501 wdl.w:ptcp.t:call-pbmm2_align_hifi-30 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:22:02.501 wdl.w:ptcp.t:call-pbmm2_align_hifi-31 INFO input :: name: "log_level", value: "INFO"
2025-09-15 20:22:02.501 wdl.w:ptcp.t:call-pbmm2_align_hifi-31 INFO input :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2128.mapped"
2025-09-15 20:22:02.501 wdl.w:ptcp.t:call-pbmm2_align_hifi-31 INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:22:02.501 wdl.w:ptcp.t:call-pbmm2_align_hifi-31 INFO input :: name: "unmapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0032_m84036_250809_035451_s4.bc2128.unmapped.bam"
2025-09-15 20:22:02.501 wdl.w:ptcp.t:call-pbmm2_align_hifi-31 INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2128"
2025-09-15 20:22:02.501 wdl.w:ptcp.t:call-pbmm2_align_hifi-31 INFO eval :: name: "threads", value: 64
2025-09-15 20:22:02.502 wdl.w:ptcp.t:call-pbmm2_align_hifi-31 INFO eval :: name: "mem_gb", value: 64
2025-09-15 20:22:02.502 wdl.w:ptcp.t:call-pbmm2_align_hifi-31 INFO eval :: name: "disk_size", value: 30
2025-09-15 20:22:02.502 wdl.w:ptcp.t:call-pbmm2_align_hifi-31 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 64, memory_reservation: 64000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:22:02.502 wdl.w:ptcp.t:call-pbmm2_align_hifi-31 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:22:02.503 wdl.w:ptcp.t:call-pbmm2_align_hifi-31 INFO provisioned :: seconds_waited: 0, cpu: 64, mem_bytes: 64000000000
2025-09-15 20:22:02.503 wdl.w:ptcp.t:call-pbmm2_align_hifi-31 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:22:02.501 wdl.w:ptcp.t:call-pbmm2_align_hifi-19 INFO Slurm invocation: srun --job-name call-pbmm2_align_hifi-19 --partition compute,compute9 --cpus-per-task 64 --mem 61035M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-19/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-19/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-19/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-19/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0020_m84036_250809_035451_s4.bc2116.unmapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0020_m84036_250809_035451_s4.bc2116.unmapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-19/_singularity_tmpdir_7be6nkyd/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-19/_singularity_tmpdir_7be6nkyd/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:22:02.507 wdl.w:ptcp NOTICE ready :: job: "call-pbmm2_align_hifi-40", callee: "pbmm2_align_hifi"
2025-09-15 20:22:02.508 wdl.w:ptcp INFO input :: job: "call-pbmm2_align_hifi-40", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "log_level": "INFO", "out_prefix": "m84036_250809_035451_s4.bc2137.mapped", "ref_fasta": "/meta/refs/hg38.fa", "unmapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0041_m84036_250809_035451_s4.bc2137.unmapped.bam", "sample_name": "m84036_250809_035451_s4.bc2137"}
2025-09-15 20:22:02.508 wdl.w:ptcp.t:call-pbmm2_align_hifi-36 NOTICE task setup :: name: "pbmm2_align_hifi", source: "./common.wdl", line: 170, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-36", thread: 140611407550016
2025-09-15 20:22:02.510 wdl.w:ptcp.t:call-pbmm2_align_hifi-17 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 8, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-17/_singularity_tmpdir_ln5cj4zh"
2025-09-15 20:22:02.511 wdl.w:ptcp.t:call-pbmm2_align_hifi-21 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 8, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-21/_singularity_tmpdir_bbe12uqf"
2025-09-15 20:22:02.511 wdl.w:ptcp NOTICE ready :: job: "call-pbmm2_align_hifi-41", callee: "pbmm2_align_hifi"
2025-09-15 20:22:02.511 wdl.w:ptcp.t:call-pbmm2_align_hifi-17 INFO Slurm invocation: srun --job-name call-pbmm2_align_hifi-17 --partition compute,compute9 --cpus-per-task 64 --mem 61035M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-17/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-17/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-17/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-17/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0018_m84036_250809_035451_s4.bc2114.unmapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0018_m84036_250809_035451_s4.bc2114.unmapped.bam:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-17/_singularity_tmpdir_ln5cj4zh/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-17/_singularity_tmpdir_ln5cj4zh/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:22:02.512 wdl.w:ptcp.t:call-pbmm2_align_hifi-21 INFO Slurm invocation: srun --job-name call-pbmm2_align_hifi-21 --partition compute,compute9 --cpus-per-task 64 --mem 61035M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-21/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-21/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-21/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-21/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0022_m84036_250809_035451_s4.bc2118.unmapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0022_m84036_250809_035451_s4.bc2118.unmapped.bam:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-21/_singularity_tmpdir_bbe12uqf/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-21/_singularity_tmpdir_bbe12uqf/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:22:02.512 wdl.w:ptcp.t:call-pbmm2_align_hifi-37 NOTICE task setup :: name: "pbmm2_align_hifi", source: "./common.wdl", line: 170, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-37", thread: 140610921035328
2025-09-15 20:22:02.512 wdl.w:ptcp INFO input :: job: "call-pbmm2_align_hifi-41", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "log_level": "INFO", "out_prefix": "m84036_250809_035451_s4.bc2138.mapped", "ref_fasta": "/meta/refs/hg38.fa", "unmapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0042_m84036_250809_035451_s4.bc2138.unmapped.bam", "sample_name": "m84036_250809_035451_s4.bc2138"}
2025-09-15 20:22:02.516 wdl.w:ptcp.t:call-pbmm2_align_hifi-38 NOTICE task setup :: name: "pbmm2_align_hifi", source: "./common.wdl", line: 170, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-38", thread: 140610912642624
2025-09-15 20:22:02.517 wdl.w:ptcp.t:call-pbmm2_align_hifi-20 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 8, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-20/_singularity_tmpdir_jbuiux57"
2025-09-15 20:22:02.517 wdl.w:ptcp.t:call-pbmm2_align_hifi-20 INFO Slurm invocation: srun --job-name call-pbmm2_align_hifi-20 --partition compute,compute9 --cpus-per-task 64 --mem 61035M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-20/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-20/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-20/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-20/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0021_m84036_250809_035451_s4.bc2117.unmapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0021_m84036_250809_035451_s4.bc2117.unmapped.bam:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-20/_singularity_tmpdir_jbuiux57/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-20/_singularity_tmpdir_jbuiux57/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:22:02.523 wdl.w:ptcp NOTICE ready :: job: "call-pbmm2_align_hifi-42", callee: "pbmm2_align_hifi"
2025-09-15 20:22:02.524 wdl.w:ptcp INFO input :: job: "call-pbmm2_align_hifi-42", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "log_level": "INFO", "out_prefix": "m84036_250809_035451_s4.bc2139.mapped", "ref_fasta": "/meta/refs/hg38.fa", "unmapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0043_m84036_250809_035451_s4.bc2139.unmapped.bam", "sample_name": "m84036_250809_035451_s4.bc2139"}
2025-09-15 20:22:02.525 wdl.w:ptcp.t:call-pbmm2_align_hifi-32 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:22:02.525 wdl.w:ptcp.t:call-pbmm2_align_hifi-32 INFO input :: name: "log_level", value: "INFO"
2025-09-15 20:22:02.526 wdl.w:ptcp.t:call-pbmm2_align_hifi-32 INFO input :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2129.mapped"
2025-09-15 20:22:02.526 wdl.w:ptcp.t:call-pbmm2_align_hifi-32 INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:22:02.526 wdl.w:ptcp.t:call-pbmm2_align_hifi-32 INFO input :: name: "unmapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0033_m84036_250809_035451_s4.bc2129.unmapped.bam"
2025-09-15 20:22:02.526 wdl.w:ptcp.t:call-pbmm2_align_hifi-32 INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2129"
2025-09-15 20:22:02.527 wdl.w:ptcp.t:call-pbmm2_align_hifi-32 INFO eval :: name: "threads", value: 64
2025-09-15 20:22:02.527 wdl.w:ptcp.t:call-pbmm2_align_hifi-32 INFO eval :: name: "mem_gb", value: 64
2025-09-15 20:22:02.528 wdl.w:ptcp.t:call-pbmm2_align_hifi-32 INFO eval :: name: "disk_size", value: 30
2025-09-15 20:22:02.528 wdl.w:ptcp.t:call-pbmm2_align_hifi-39 NOTICE task setup :: name: "pbmm2_align_hifi", source: "./common.wdl", line: 170, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-39", thread: 140610904249920
2025-09-15 20:22:02.529 wdl.w:ptcp.t:call-pbmm2_align_hifi-08 NOTICE slurm_singularity run :: pid: 1197180, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-08/slurm_singularity.log.txt"
2025-09-15 20:22:02.530 wdl.w:ptcp NOTICE ready :: job: "call-pbmm2_align_hifi-43", callee: "pbmm2_align_hifi"
2025-09-15 20:22:02.530 wdl.w:ptcp.t:call-pbmm2_align_hifi-33 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:22:02.531 wdl.w:ptcp.t:call-pbmm2_align_hifi-10 NOTICE slurm_singularity run :: pid: 1197182, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-10/slurm_singularity.log.txt"
2025-09-15 20:22:02.532 wdl.w:ptcp.t:call-pbmm2_align_hifi-13 NOTICE slurm_singularity run :: pid: 1197186, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-13/slurm_singularity.log.txt"
2025-09-15 20:22:02.532 wdl.w:ptcp.t:call-pbmm2_align_hifi-22 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 8, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-22/_singularity_tmpdir_diozgtcy"
2025-09-15 20:22:02.533 wdl.w:ptcp INFO input :: job: "call-pbmm2_align_hifi-43", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "log_level": "INFO", "out_prefix": "m84036_250809_035451_s4.bc2140.mapped", "ref_fasta": "/meta/refs/hg38.fa", "unmapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0044_m84036_250809_035451_s4.bc2140.unmapped.bam", "sample_name": "m84036_250809_035451_s4.bc2140"}
2025-09-15 20:22:02.533 wdl.w:ptcp.t:call-pbmm2_align_hifi-33 INFO input :: name: "log_level", value: "INFO"
2025-09-15 20:22:02.532 wdl.w:ptcp.t:call-pbmm2_align_hifi-32 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 64, memory_reservation: 64000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:22:02.533 wdl.w:ptcp.t:call-pbmm2_align_hifi-40 NOTICE task setup :: name: "pbmm2_align_hifi", source: "./common.wdl", line: 170, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-40", thread: 140610895857216
2025-09-15 20:22:02.534 wdl.w:ptcp.t:call-pbmm2_align_hifi-11 NOTICE slurm_singularity run :: pid: 1197189, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-11/slurm_singularity.log.txt"
2025-09-15 20:22:02.534 wdl.w:ptcp.t:call-pbmm2_align_hifi-12 NOTICE slurm_singularity run :: pid: 1197187, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-12/slurm_singularity.log.txt"
2025-09-15 20:22:02.534 wdl.w:ptcp.t:call-pbmm2_align_hifi-24 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 8, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-24/_singularity_tmpdir_416g52a1"
2025-09-15 20:22:02.536 wdl.w:ptcp.t:call-pbmm2_align_hifi-22 INFO Slurm invocation: srun --job-name call-pbmm2_align_hifi-22 --partition compute,compute9 --cpus-per-task 64 --mem 61035M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-22/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-22/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-22/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-22/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0023_m84036_250809_035451_s4.bc2119.unmapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0023_m84036_250809_035451_s4.bc2119.unmapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-22/_singularity_tmpdir_diozgtcy/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-22/_singularity_tmpdir_diozgtcy/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:22:02.536 wdl.w:ptcp.t:call-pbmm2_align_hifi-34 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:22:02.536 wdl.w:ptcp.t:call-pbmm2_align_hifi-14 NOTICE slurm_singularity run :: pid: 1197192, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-14/slurm_singularity.log.txt"
2025-09-15 20:22:02.537 wdl.w:ptcp.t:call-pbmm2_align_hifi-33 INFO input :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2130.mapped"
2025-09-15 20:22:02.537 wdl.w:ptcp.t:call-pbmm2_align_hifi-32 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:22:02.538 wdl.w:ptcp.t:call-pbmm2_align_hifi-24 INFO Slurm invocation: srun --job-name call-pbmm2_align_hifi-24 --partition compute,compute9 --cpus-per-task 64 --mem 61035M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-24/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-24/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-24/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-24/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0025_m84036_250809_035451_s4.bc2121.unmapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0025_m84036_250809_035451_s4.bc2121.unmapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-24/_singularity_tmpdir_416g52a1/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-24/_singularity_tmpdir_416g52a1/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:22:02.538 wdl.w:ptcp.t:call-pbmm2_align_hifi-15 NOTICE slurm_singularity run :: pid: 1197194, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-15/slurm_singularity.log.txt"
2025-09-15 20:22:02.538 wdl.w:ptcp.t:call-pbmm2_align_hifi-18 NOTICE slurm_singularity run :: pid: 1197196, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-18/slurm_singularity.log.txt"
2025-09-15 20:22:02.539 wdl.w:ptcp.t:call-pbmm2_align_hifi-25 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 8, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-25/_singularity_tmpdir_g12uzq7g"
2025-09-15 20:22:02.539 wdl.w:ptcp.t:call-pbmm2_align_hifi-34 INFO input :: name: "log_level", value: "INFO"
2025-09-15 20:22:02.540 wdl.w:ptcp NOTICE ready :: job: "call-pbmm2_align_hifi-44", callee: "pbmm2_align_hifi"
2025-09-15 20:22:02.539 wdl.w:ptcp.t:call-pbmm2_align_hifi-16 NOTICE slurm_singularity run :: pid: 1197199, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-16/slurm_singularity.log.txt"
2025-09-15 20:22:02.540 wdl.w:ptcp.t:call-pbmm2_align_hifi-41 NOTICE task setup :: name: "pbmm2_align_hifi", source: "./common.wdl", line: 170, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-41", thread: 140610887464512
2025-09-15 20:22:02.541 wdl.w:ptcp.t:call-pbmm2_align_hifi-33 INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:22:02.541 wdl.w:ptcp.t:call-pbmm2_align_hifi-35 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:22:02.542 wdl.w:ptcp.t:call-pbmm2_align_hifi-19 NOTICE slurm_singularity run :: pid: 1197200, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-19/slurm_singularity.log.txt"
2025-09-15 20:22:02.543 wdl.w:ptcp.t:call-pbmm2_align_hifi-32 INFO provisioned :: seconds_waited: 0, cpu: 64, mem_bytes: 64000000000
2025-09-15 20:22:02.543 wdl.w:ptcp.t:call-pbmm2_align_hifi-25 INFO Slurm invocation: srun --job-name call-pbmm2_align_hifi-25 --partition compute,compute9 --cpus-per-task 64 --mem 61035M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-25/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-25/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-25/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-25/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0026_m84036_250809_035451_s4.bc2122.unmapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0026_m84036_250809_035451_s4.bc2122.unmapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-25/_singularity_tmpdir_g12uzq7g/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-25/_singularity_tmpdir_g12uzq7g/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:22:02.544 wdl.w:ptcp.t:call-pbmm2_align_hifi-42 NOTICE task setup :: name: "pbmm2_align_hifi", source: "./common.wdl", line: 170, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-42", thread: 140610879071808
2025-09-15 20:22:02.544 wdl.w:ptcp.t:call-pbmm2_align_hifi-34 INFO input :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2131.mapped"
2025-09-15 20:22:02.544 wdl.w:ptcp INFO input :: job: "call-pbmm2_align_hifi-44", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "log_level": "INFO", "out_prefix": "m84036_250809_035451_s4.bc2141.mapped", "ref_fasta": "/meta/refs/hg38.fa", "unmapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0045_m84036_250809_035451_s4.bc2141.unmapped.bam", "sample_name": "m84036_250809_035451_s4.bc2141"}
2025-09-15 20:22:02.545 wdl.w:ptcp.t:call-pbmm2_align_hifi-33 INFO input :: name: "unmapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0034_m84036_250809_035451_s4.bc2130.unmapped.bam"
2025-09-15 20:22:02.546 wdl.w:ptcp.t:call-pbmm2_align_hifi-35 INFO input :: name: "log_level", value: "INFO"
2025-09-15 20:22:02.546 wdl.w:ptcp.t:call-pbmm2_align_hifi-32 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:22:02.547 wdl.w:ptcp.t:call-pbmm2_align_hifi-34 INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:22:02.547 wdl.w:ptcp.t:call-pbmm2_align_hifi-33 INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2130"
2025-09-15 20:22:02.548 wdl.w:ptcp.t:call-pbmm2_align_hifi-35 INFO input :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2132.mapped"
2025-09-15 20:22:02.550 wdl.w:ptcp.t:call-pbmm2_align_hifi-34 INFO input :: name: "unmapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0035_m84036_250809_035451_s4.bc2131.unmapped.bam"
2025-09-15 20:22:02.550 wdl.w:ptcp NOTICE ready :: job: "call-pbmm2_align_hifi-45", callee: "pbmm2_align_hifi"
2025-09-15 20:22:02.551 wdl.w:ptcp.t:call-pbmm2_align_hifi-33 INFO eval :: name: "threads", value: 64
2025-09-15 20:22:02.551 wdl.w:ptcp.t:call-pbmm2_align_hifi-27 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 8, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-27/_singularity_tmpdir_mov9jg26"
2025-09-15 20:22:02.551 wdl.w:ptcp.t:call-pbmm2_align_hifi-35 INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:22:02.552 wdl.w:ptcp.t:call-pbmm2_align_hifi-43 NOTICE task setup :: name: "pbmm2_align_hifi", source: "./common.wdl", line: 170, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-43", thread: 140610870679104
2025-09-15 20:22:02.552 wdl.w:ptcp.t:call-pbmm2_align_hifi-34 INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2131"
2025-09-15 20:22:02.552 wdl.w:ptcp.t:call-pbmm2_align_hifi-26 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 8, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-26/_singularity_tmpdir_odwqnygn"
2025-09-15 20:22:02.553 wdl.w:ptcp INFO input :: job: "call-pbmm2_align_hifi-45", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "log_level": "INFO", "out_prefix": "m84036_250809_035451_s4.bc2142.mapped", "ref_fasta": "/meta/refs/hg38.fa", "unmapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0046_m84036_250809_035451_s4.bc2142.unmapped.bam", "sample_name": "m84036_250809_035451_s4.bc2142"}
2025-09-15 20:22:02.553 wdl.w:ptcp.t:call-pbmm2_align_hifi-33 INFO eval :: name: "mem_gb", value: 64
2025-09-15 20:22:02.553 wdl.w:ptcp.t:call-pbmm2_align_hifi-27 INFO Slurm invocation: srun --job-name call-pbmm2_align_hifi-27 --partition compute,compute9 --cpus-per-task 64 --mem 61035M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-27/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-27/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-27/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-27/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0028_m84036_250809_035451_s4.bc2124.unmapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0028_m84036_250809_035451_s4.bc2124.unmapped.bam:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-27/_singularity_tmpdir_mov9jg26/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-27/_singularity_tmpdir_mov9jg26/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:22:02.554 wdl.w:ptcp.t:call-pbmm2_align_hifi-35 INFO input :: name: "unmapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0036_m84036_250809_035451_s4.bc2132.unmapped.bam"
2025-09-15 20:22:02.555 wdl.w:ptcp.t:call-pbmm2_align_hifi-34 INFO eval :: name: "threads", value: 64
2025-09-15 20:22:02.555 wdl.w:ptcp.t:call-pbmm2_align_hifi-26 INFO Slurm invocation: srun --job-name call-pbmm2_align_hifi-26 --partition compute,compute9 --cpus-per-task 64 --mem 61035M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-26/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-26/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-26/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-26/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0027_m84036_250809_035451_s4.bc2123.unmapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0027_m84036_250809_035451_s4.bc2123.unmapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-26/_singularity_tmpdir_odwqnygn/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-26/_singularity_tmpdir_odwqnygn/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:22:02.558 wdl.w:ptcp.t:call-pbmm2_align_hifi-35 INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2132"
2025-09-15 20:22:02.558 wdl.w:ptcp NOTICE ready :: job: "call-pbmm2_align_hifi-46", callee: "pbmm2_align_hifi"
2025-09-15 20:22:02.558 wdl.w:ptcp.t:call-pbmm2_align_hifi-33 INFO eval :: name: "disk_size", value: 30
2025-09-15 20:22:02.559 wdl.w:ptcp.t:call-pbmm2_align_hifi-34 INFO eval :: name: "mem_gb", value: 64
2025-09-15 20:22:02.561 wdl.w:ptcp.t:call-pbmm2_align_hifi-35 INFO eval :: name: "threads", value: 64
2025-09-15 20:22:02.560 wdl.w:ptcp.t:call-pbmm2_align_hifi-36 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:22:02.561 wdl.w:ptcp INFO input :: job: "call-pbmm2_align_hifi-46", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "log_level": "INFO", "out_prefix": "m84036_250809_035451_s4.bc2143.mapped", "ref_fasta": "/meta/refs/hg38.fa", "unmapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0047_m84036_250809_035451_s4.bc2143.unmapped.bam", "sample_name": "m84036_250809_035451_s4.bc2143"}
2025-09-15 20:22:02.576 wdl.w:ptcp.t:call-pbmm2_align_hifi-44 NOTICE task setup :: name: "pbmm2_align_hifi", source: "./common.wdl", line: 170, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-44", thread: 140610384164416
2025-09-15 20:22:02.578 wdl.w:ptcp.t:call-pbmm2_align_hifi-45 NOTICE task setup :: name: "pbmm2_align_hifi", source: "./common.wdl", line: 170, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-45", thread: 140610375771712
2025-09-15 20:22:02.577 wdl.w:ptcp.t:call-pbmm2_align_hifi-28 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 8, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-28/_singularity_tmpdir_bllzibop"
2025-09-15 20:22:02.578 wdl.w:ptcp.t:call-pbmm2_align_hifi-37 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:22:02.579 wdl.w:ptcp.t:call-pbmm2_align_hifi-35 INFO eval :: name: "mem_gb", value: 64
2025-09-15 20:22:02.580 wdl.w:ptcp.t:call-pbmm2_align_hifi-34 INFO eval :: name: "disk_size", value: 30
2025-09-15 20:22:02.580 wdl.w:ptcp.t:call-pbmm2_align_hifi-36 INFO input :: name: "log_level", value: "INFO"
2025-09-15 20:22:02.580 wdl.w:ptcp.t:call-pbmm2_align_hifi-33 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 64, memory_reservation: 64000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:22:02.581 wdl.w:ptcp.t:call-pbmm2_align_hifi-23 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 8, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-23/_singularity_tmpdir_2mdfyrr_"
2025-09-15 20:22:02.585 wdl.w:ptcp NOTICE ready :: job: "call-pbmm2_align_hifi-47", callee: "pbmm2_align_hifi"
2025-09-15 20:22:02.586 wdl.w:ptcp.t:call-pbmm2_align_hifi-38 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:22:02.587 wdl.w:ptcp.t:call-pbmm2_align_hifi-37 INFO input :: name: "log_level", value: "INFO"
2025-09-15 20:22:02.586 wdl.w:ptcp.t:call-pbmm2_align_hifi-28 INFO Slurm invocation: srun --job-name call-pbmm2_align_hifi-28 --partition compute,compute9 --cpus-per-task 64 --mem 61035M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-28/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-28/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-28/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-28/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0029_m84036_250809_035451_s4.bc2125.unmapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0029_m84036_250809_035451_s4.bc2125.unmapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-28/_singularity_tmpdir_bllzibop/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-28/_singularity_tmpdir_bllzibop/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:22:02.591 wdl.w:ptcp.t:call-pbmm2_align_hifi-36 INFO input :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2133.mapped"
2025-09-15 20:22:02.591 wdl.w:ptcp.t:call-pbmm2_align_hifi-35 INFO eval :: name: "disk_size", value: 30
2025-09-15 20:22:02.591 wdl.w:ptcp.t:call-pbmm2_align_hifi-34 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 64, memory_reservation: 64000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:22:02.592 wdl.w:ptcp.t:call-pbmm2_align_hifi-33 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:22:02.593 wdl.w:ptcp.t:call-pbmm2_align_hifi-23 INFO Slurm invocation: srun --job-name call-pbmm2_align_hifi-23 --partition compute,compute9 --cpus-per-task 64 --mem 61035M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-23/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-23/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-23/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-23/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0024_m84036_250809_035451_s4.bc2120.unmapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0024_m84036_250809_035451_s4.bc2120.unmapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-23/_singularity_tmpdir_2mdfyrr_/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-23/_singularity_tmpdir_2mdfyrr_/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:22:02.593 wdl.w:ptcp INFO input :: job: "call-pbmm2_align_hifi-47", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "log_level": "INFO", "out_prefix": "m84036_250809_035451_s4.bc2144.mapped", "ref_fasta": "/meta/refs/hg38.fa", "unmapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0048_m84036_250809_035451_s4.bc2144.unmapped.bam", "sample_name": "m84036_250809_035451_s4.bc2144"}
2025-09-15 20:22:02.594 wdl.w:ptcp.t:call-pbmm2_align_hifi-46 NOTICE task setup :: name: "pbmm2_align_hifi", source: "./common.wdl", line: 170, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-46", thread: 140610367379008
2025-09-15 20:22:02.595 wdl.w:ptcp.t:call-pbmm2_align_hifi-38 INFO input :: name: "log_level", value: "INFO"
2025-09-15 20:22:02.595 wdl.w:ptcp.t:call-pbmm2_align_hifi-37 INFO input :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2134.mapped"
2025-09-15 20:22:02.597 wdl.w:ptcp.t:call-pbmm2_align_hifi-36 INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:22:02.597 wdl.w:ptcp.t:call-pbmm2_align_hifi-39 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:22:02.598 wdl.w:ptcp.t:call-pbmm2_align_hifi-34 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:22:02.600 wdl.w:ptcp.t:call-pbmm2_align_hifi-29 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 8, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-29/_singularity_tmpdir_ozpgo8lf"
2025-09-15 20:22:02.601 wdl.w:ptcp.t:call-pbmm2_align_hifi-35 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 64, memory_reservation: 64000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:22:02.602 wdl.w:ptcp.t:call-pbmm2_align_hifi-38 INFO input :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2135.mapped"
2025-09-15 20:22:02.603 wdl.w:ptcp.t:call-pbmm2_align_hifi-33 INFO provisioned :: seconds_waited: 0, cpu: 64, mem_bytes: 64000000000
2025-09-15 20:22:02.603 wdl.w:ptcp.t:call-pbmm2_align_hifi-40 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:22:02.603 wdl.w:ptcp NOTICE ready :: job: "call-pbmm2_align_hifi-48", callee: "pbmm2_align_hifi"
2025-09-15 20:22:02.604 wdl.w:ptcp.t:call-pbmm2_align_hifi-37 INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:22:02.605 wdl.w:ptcp.t:call-pbmm2_align_hifi-36 INFO input :: name: "unmapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0037_m84036_250809_035451_s4.bc2133.unmapped.bam"
2025-09-15 20:22:02.606 wdl.w:ptcp.t:call-pbmm2_align_hifi-39 INFO input :: name: "log_level", value: "INFO"
2025-09-15 20:22:02.606 wdl.w:ptcp.t:call-pbmm2_align_hifi-29 INFO Slurm invocation: srun --job-name call-pbmm2_align_hifi-29 --partition compute,compute9 --cpus-per-task 64 --mem 61035M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-29/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-29/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-29/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-29/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0030_m84036_250809_035451_s4.bc2126.unmapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0030_m84036_250809_035451_s4.bc2126.unmapped.bam:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-29/_singularity_tmpdir_ozpgo8lf/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-29/_singularity_tmpdir_ozpgo8lf/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:22:02.607 wdl.w:ptcp.t:call-pbmm2_align_hifi-35 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:22:02.607 wdl.w:ptcp.t:call-pbmm2_align_hifi-38 INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:22:02.608 wdl.w:ptcp.t:call-pbmm2_align_hifi-21 NOTICE slurm_singularity run :: pid: 1197204, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-21/slurm_singularity.log.txt"
2025-09-15 20:22:02.608 wdl.w:ptcp.t:call-pbmm2_align_hifi-17 NOTICE slurm_singularity run :: pid: 1197203, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-17/slurm_singularity.log.txt"
2025-09-15 20:22:02.609 wdl.w:ptcp.t:call-pbmm2_align_hifi-34 INFO provisioned :: seconds_waited: 0, cpu: 64, mem_bytes: 64000000000
2025-09-15 20:22:02.608 wdl.w:ptcp.t:call-pbmm2_align_hifi-33 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:22:02.609 wdl.w:ptcp.t:call-pbmm2_align_hifi-42 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:22:02.610 wdl.w:ptcp.t:call-pbmm2_align_hifi-40 INFO input :: name: "log_level", value: "INFO"
2025-09-15 20:22:02.610 wdl.w:ptcp INFO input :: job: "call-pbmm2_align_hifi-48", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "log_level": "INFO", "out_prefix": "m84036_250809_035451_s4.bc2145.mapped", "ref_fasta": "/meta/refs/hg38.fa", "unmapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0049_m84036_250809_035451_s4.bc2145.unmapped.bam", "sample_name": "m84036_250809_035451_s4.bc2145"}
2025-09-15 20:22:02.610 wdl.w:ptcp.t:call-pbmm2_align_hifi-20 NOTICE slurm_singularity run :: pid: 1197205, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-20/slurm_singularity.log.txt"
2025-09-15 20:22:02.611 wdl.w:ptcp.t:call-pbmm2_align_hifi-22 NOTICE slurm_singularity run :: pid: 1197208, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-22/slurm_singularity.log.txt"
2025-09-15 20:22:02.611 wdl.w:ptcp.t:call-pbmm2_align_hifi-24 NOTICE slurm_singularity run :: pid: 1197213, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-24/slurm_singularity.log.txt"
2025-09-15 20:22:02.611 wdl.w:ptcp.t:call-pbmm2_align_hifi-25 NOTICE slurm_singularity run :: pid: 1197219, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-25/slurm_singularity.log.txt"
2025-09-15 20:22:02.612 wdl.w:ptcp.t:call-pbmm2_align_hifi-26 NOTICE slurm_singularity run :: pid: 1197226, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-26/slurm_singularity.log.txt"
2025-09-15 20:22:02.612 wdl.w:ptcp.t:call-pbmm2_align_hifi-37 INFO input :: name: "unmapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0038_m84036_250809_035451_s4.bc2134.unmapped.bam"
2025-09-15 20:22:02.612 wdl.w:ptcp.t:call-pbmm2_align_hifi-27 NOTICE slurm_singularity run :: pid: 1197225, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-27/slurm_singularity.log.txt"
2025-09-15 20:22:02.613 wdl.w:ptcp.t:call-pbmm2_align_hifi-36 INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2133"
2025-09-15 20:22:02.613 wdl.w:ptcp.t:call-pbmm2_align_hifi-31 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 8, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-31/_singularity_tmpdir_7cj6dmqa"
2025-09-15 20:22:02.613 wdl.w:ptcp.t:call-pbmm2_align_hifi-30 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 8, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-30/_singularity_tmpdir_o21kggzb"
2025-09-15 20:22:02.613 wdl.w:ptcp.t:call-pbmm2_align_hifi-47 NOTICE task setup :: name: "pbmm2_align_hifi", source: "./common.wdl", line: 170, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-47", thread: 140610358986304
2025-09-15 20:22:02.614 wdl.w:ptcp.t:call-pbmm2_align_hifi-39 INFO input :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2136.mapped"
2025-09-15 20:22:02.615 wdl.w:ptcp.t:call-pbmm2_align_hifi-41 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:22:02.615 wdl.w:ptcp.t:call-pbmm2_align_hifi-38 INFO input :: name: "unmapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0039_m84036_250809_035451_s4.bc2135.unmapped.bam"
2025-09-15 20:22:02.616 wdl.w:ptcp.t:call-pbmm2_align_hifi-35 INFO provisioned :: seconds_waited: 0, cpu: 64, mem_bytes: 64000000000
2025-09-15 20:22:02.617 wdl.w:ptcp.t:call-pbmm2_align_hifi-34 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:22:02.617 wdl.w:ptcp.t:call-pbmm2_align_hifi-43 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:22:02.618 wdl.w:ptcp.t:call-pbmm2_align_hifi-42 INFO input :: name: "log_level", value: "INFO"
2025-09-15 20:22:02.618 wdl.w:ptcp.t:call-pbmm2_align_hifi-40 INFO input :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2137.mapped"
2025-09-15 20:22:02.621 wdl.w:ptcp.t:call-pbmm2_align_hifi-37 INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2134"
2025-09-15 20:22:02.621 wdl.w:ptcp NOTICE ready :: job: "call-pbmm2_align_hifi-49", callee: "pbmm2_align_hifi"
2025-09-15 20:22:02.622 wdl.w:ptcp.t:call-pbmm2_align_hifi-36 INFO eval :: name: "threads", value: 64
2025-09-15 20:22:02.622 wdl.w:ptcp.t:call-pbmm2_align_hifi-31 INFO Slurm invocation: srun --job-name call-pbmm2_align_hifi-31 --partition compute,compute9 --cpus-per-task 64 --mem 61035M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-31/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-31/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-31/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-31/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0032_m84036_250809_035451_s4.bc2128.unmapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0032_m84036_250809_035451_s4.bc2128.unmapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-31/_singularity_tmpdir_7cj6dmqa/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-31/_singularity_tmpdir_7cj6dmqa/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:22:02.623 wdl.w:ptcp.t:call-pbmm2_align_hifi-30 INFO Slurm invocation: srun --job-name call-pbmm2_align_hifi-30 --partition compute,compute9 --cpus-per-task 64 --mem 61035M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-30/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-30/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-30/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-30/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0031_m84036_250809_035451_s4.bc2127.unmapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0031_m84036_250809_035451_s4.bc2127.unmapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-30/_singularity_tmpdir_o21kggzb/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-30/_singularity_tmpdir_o21kggzb/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:22:02.623 wdl.w:ptcp.t:call-pbmm2_align_hifi-39 INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:22:02.624 wdl.w:ptcp.t:call-pbmm2_align_hifi-41 INFO input :: name: "log_level", value: "INFO"
2025-09-15 20:22:02.624 wdl.w:ptcp.t:call-pbmm2_align_hifi-44 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:22:02.624 wdl.w:ptcp.t:call-pbmm2_align_hifi-38 INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2135"
2025-09-15 20:22:02.625 wdl.w:ptcp.t:call-pbmm2_align_hifi-35 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:22:02.625 wdl.w:ptcp.t:call-pbmm2_align_hifi-43 INFO input :: name: "log_level", value: "INFO"
2025-09-15 20:22:02.625 wdl.w:ptcp.t:call-pbmm2_align_hifi-42 INFO input :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2139.mapped"
2025-09-15 20:22:02.625 wdl.w:ptcp.t:call-pbmm2_align_hifi-37 INFO eval :: name: "threads", value: 64
2025-09-15 20:22:02.625 wdl.w:ptcp.t:call-pbmm2_align_hifi-40 INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:22:02.626 wdl.w:ptcp INFO input :: job: "call-pbmm2_align_hifi-49", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "log_level": "INFO", "out_prefix": "m84036_250809_035451_s4.bc2146.mapped", "ref_fasta": "/meta/refs/hg38.fa", "unmapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0050_m84036_250809_035451_s4.bc2146.unmapped.bam", "sample_name": "m84036_250809_035451_s4.bc2146"}
2025-09-15 20:22:02.626 wdl.w:ptcp.t:call-pbmm2_align_hifi-36 INFO eval :: name: "mem_gb", value: 64
2025-09-15 20:22:02.627 wdl.w:ptcp.t:call-pbmm2_align_hifi-39 INFO input :: name: "unmapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0040_m84036_250809_035451_s4.bc2136.unmapped.bam"
2025-09-15 20:22:02.627 wdl.w:ptcp.t:call-pbmm2_align_hifi-41 INFO input :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2138.mapped"
2025-09-15 20:22:02.627 wdl.w:ptcp.t:call-pbmm2_align_hifi-44 INFO input :: name: "log_level", value: "INFO"
2025-09-15 20:22:02.627 wdl.w:ptcp.t:call-pbmm2_align_hifi-38 INFO eval :: name: "threads", value: 64
2025-09-15 20:22:02.628 wdl.w:ptcp.t:call-pbmm2_align_hifi-45 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:22:02.628 wdl.w:ptcp.t:call-pbmm2_align_hifi-43 INFO input :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2140.mapped"
2025-09-15 20:22:02.628 wdl.w:ptcp.t:call-pbmm2_align_hifi-42 INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:22:02.628 wdl.w:ptcp.t:call-pbmm2_align_hifi-37 INFO eval :: name: "mem_gb", value: 64
2025-09-15 20:22:02.629 wdl.w:ptcp.t:call-pbmm2_align_hifi-48 NOTICE task setup :: name: "pbmm2_align_hifi", source: "./common.wdl", line: 170, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-48", thread: 140610350593600
2025-09-15 20:22:02.629 wdl.w:ptcp.t:call-pbmm2_align_hifi-40 INFO input :: name: "unmapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0041_m84036_250809_035451_s4.bc2137.unmapped.bam"
2025-09-15 20:22:02.630 wdl.w:ptcp.t:call-pbmm2_align_hifi-39 INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2136"
2025-09-15 20:22:02.630 wdl.w:ptcp.t:call-pbmm2_align_hifi-36 INFO eval :: name: "disk_size", value: 30
2025-09-15 20:22:02.630 wdl.w:ptcp.t:call-pbmm2_align_hifi-41 INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:22:02.631 wdl.w:ptcp NOTICE ready :: job: "call-pbmm2_align_hifi-50", callee: "pbmm2_align_hifi"
2025-09-15 20:22:02.631 wdl.w:ptcp.t:call-pbmm2_align_hifi-44 INFO input :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2141.mapped"
2025-09-15 20:22:02.631 wdl.w:ptcp.t:call-pbmm2_align_hifi-38 INFO eval :: name: "mem_gb", value: 64
2025-09-15 20:22:02.631 wdl.w:ptcp.t:call-pbmm2_align_hifi-45 INFO input :: name: "log_level", value: "INFO"
2025-09-15 20:22:02.631 wdl.w:ptcp.t:call-pbmm2_align_hifi-43 INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:22:02.632 wdl.w:ptcp.t:call-pbmm2_align_hifi-37 INFO eval :: name: "disk_size", value: 30
2025-09-15 20:22:02.632 wdl.w:ptcp.t:call-pbmm2_align_hifi-40 INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2137"
2025-09-15 20:22:02.633 wdl.w:ptcp.t:call-pbmm2_align_hifi-39 INFO eval :: name: "threads", value: 64
2025-09-15 20:22:02.633 wdl.w:ptcp.t:call-pbmm2_align_hifi-41 INFO input :: name: "unmapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0042_m84036_250809_035451_s4.bc2138.unmapped.bam"
2025-09-15 20:22:02.633 wdl.w:ptcp.t:call-pbmm2_align_hifi-36 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 64, memory_reservation: 64000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:22:02.634 wdl.w:ptcp INFO input :: job: "call-pbmm2_align_hifi-50", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "log_level": "INFO", "out_prefix": "m84036_250809_035451_s4.bc2147.mapped", "ref_fasta": "/meta/refs/hg38.fa", "unmapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0051_m84036_250809_035451_s4.bc2147.unmapped.bam", "sample_name": "m84036_250809_035451_s4.bc2147"}
2025-09-15 20:22:02.634 wdl.w:ptcp.t:call-pbmm2_align_hifi-44 INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:22:02.634 wdl.w:ptcp.t:call-pbmm2_align_hifi-45 INFO input :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2142.mapped"
2025-09-15 20:22:02.634 wdl.w:ptcp.t:call-pbmm2_align_hifi-43 INFO input :: name: "unmapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0044_m84036_250809_035451_s4.bc2140.unmapped.bam"
2025-09-15 20:22:02.634 wdl.w:ptcp.t:call-pbmm2_align_hifi-38 INFO eval :: name: "disk_size", value: 30
2025-09-15 20:22:02.635 wdl.w:ptcp.t:call-pbmm2_align_hifi-40 INFO eval :: name: "threads", value: 64
2025-09-15 20:22:02.631 wdl.w:ptcp.t:call-pbmm2_align_hifi-42 INFO input :: name: "unmapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0043_m84036_250809_035451_s4.bc2139.unmapped.bam"
2025-09-15 20:22:02.635 wdl.w:ptcp.t:call-pbmm2_align_hifi-37 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 64, memory_reservation: 64000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:22:02.635 wdl.w:ptcp.t:call-pbmm2_align_hifi-39 INFO eval :: name: "mem_gb", value: 64
2025-09-15 20:22:02.636 wdl.w:ptcp.t:call-pbmm2_align_hifi-46 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:22:02.636 wdl.w:ptcp.t:call-pbmm2_align_hifi-32 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 8, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-32/_singularity_tmpdir_6q66c6e3"
2025-09-15 20:22:02.636 wdl.w:ptcp.t:call-pbmm2_align_hifi-41 INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2138"
2025-09-15 20:22:02.636 wdl.w:ptcp.t:call-pbmm2_align_hifi-36 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:22:02.636 wdl.w:ptcp.t:call-pbmm2_align_hifi-44 INFO input :: name: "unmapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0045_m84036_250809_035451_s4.bc2141.unmapped.bam"
2025-09-15 20:22:02.636 wdl.w:ptcp.t:call-pbmm2_align_hifi-45 INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:22:02.636 wdl.w:ptcp.t:call-pbmm2_align_hifi-43 INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2140"
2025-09-15 20:22:02.637 wdl.w:ptcp.t:call-pbmm2_align_hifi-40 INFO eval :: name: "mem_gb", value: 64
2025-09-15 20:22:02.638 wdl.w:ptcp NOTICE ready :: job: "call-pbmm2_align_hifi-51", callee: "pbmm2_align_hifi"
2025-09-15 20:22:02.638 wdl.w:ptcp.t:call-pbmm2_align_hifi-42 INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2139"
2025-09-15 20:22:02.638 wdl.w:ptcp.t:call-pbmm2_align_hifi-38 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 64, memory_reservation: 64000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:22:02.638 wdl.w:ptcp.t:call-pbmm2_align_hifi-37 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:22:02.639 wdl.w:ptcp.t:call-pbmm2_align_hifi-46 INFO input :: name: "log_level", value: "INFO"
2025-09-15 20:22:02.639 wdl.w:ptcp.t:call-pbmm2_align_hifi-39 INFO eval :: name: "disk_size", value: 30
2025-09-15 20:22:02.639 wdl.w:ptcp.t:call-pbmm2_align_hifi-32 INFO Slurm invocation: srun --job-name call-pbmm2_align_hifi-32 --partition compute,compute9 --cpus-per-task 64 --mem 61035M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-32/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-32/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-32/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-32/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0033_m84036_250809_035451_s4.bc2129.unmapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0033_m84036_250809_035451_s4.bc2129.unmapped.bam:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-32/_singularity_tmpdir_6q66c6e3/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-32/_singularity_tmpdir_6q66c6e3/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:22:02.639 wdl.w:ptcp.t:call-pbmm2_align_hifi-41 INFO eval :: name: "threads", value: 64
2025-09-15 20:22:02.640 wdl.w:ptcp.t:call-pbmm2_align_hifi-44 INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2141"
2025-09-15 20:22:02.640 wdl.w:ptcp.t:call-pbmm2_align_hifi-43 INFO eval :: name: "threads", value: 64
2025-09-15 20:22:02.640 wdl.w:ptcp.t:call-pbmm2_align_hifi-36 INFO provisioned :: seconds_waited: 0, cpu: 64, mem_bytes: 64000000000
2025-09-15 20:22:02.641 wdl.w:ptcp.t:call-pbmm2_align_hifi-49 NOTICE task setup :: name: "pbmm2_align_hifi", source: "./common.wdl", line: 170, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-49", thread: 140610342200896
2025-09-15 20:22:02.641 wdl.w:ptcp INFO input :: job: "call-pbmm2_align_hifi-51", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "log_level": "INFO", "out_prefix": "m84036_250809_035451_s4.bc2148.mapped", "ref_fasta": "/meta/refs/hg38.fa", "unmapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0052_m84036_250809_035451_s4.bc2148.unmapped.bam", "sample_name": "m84036_250809_035451_s4.bc2148"}
2025-09-15 20:22:02.641 wdl.w:ptcp.t:call-pbmm2_align_hifi-40 INFO eval :: name: "disk_size", value: 30
2025-09-15 20:22:02.640 wdl.w:ptcp.t:call-pbmm2_align_hifi-45 INFO input :: name: "unmapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0046_m84036_250809_035451_s4.bc2142.unmapped.bam"
2025-09-15 20:22:02.642 wdl.w:ptcp.t:call-pbmm2_align_hifi-42 INFO eval :: name: "threads", value: 64
2025-09-15 20:22:02.642 wdl.w:ptcp.t:call-pbmm2_align_hifi-38 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:22:02.643 wdl.w:ptcp.t:call-pbmm2_align_hifi-46 INFO input :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2143.mapped"
2025-09-15 20:22:02.644 wdl.w:ptcp.t:call-pbmm2_align_hifi-41 INFO eval :: name: "mem_gb", value: 64
2025-09-15 20:22:02.644 wdl.w:ptcp.t:call-pbmm2_align_hifi-44 INFO eval :: name: "threads", value: 64
2025-09-15 20:22:02.644 wdl.w:ptcp.t:call-pbmm2_align_hifi-39 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 64, memory_reservation: 64000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:22:02.645 wdl.w:ptcp.t:call-pbmm2_align_hifi-37 INFO provisioned :: seconds_waited: 0, cpu: 64, mem_bytes: 64000000000
2025-09-15 20:22:02.645 wdl.w:ptcp.t:call-pbmm2_align_hifi-50 NOTICE task setup :: name: "pbmm2_align_hifi", source: "./common.wdl", line: 170, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-50", thread: 140610333808192
2025-09-15 20:22:02.645 wdl.w:ptcp.t:call-pbmm2_align_hifi-43 INFO eval :: name: "mem_gb", value: 64
2025-09-15 20:22:02.646 wdl.w:ptcp.t:call-pbmm2_align_hifi-36 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:22:02.647 wdl.w:ptcp.t:call-pbmm2_align_hifi-45 INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2142"
2025-09-15 20:22:02.647 wdl.w:ptcp.t:call-pbmm2_align_hifi-40 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 64, memory_reservation: 64000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:22:02.648 wdl.w:ptcp NOTICE ready :: job: "call-pbmm2_align_hifi-52", callee: "pbmm2_align_hifi"
2025-09-15 20:22:02.648 wdl.w:ptcp.t:call-pbmm2_align_hifi-42 INFO eval :: name: "mem_gb", value: 64
2025-09-15 20:22:02.649 wdl.w:ptcp.t:call-pbmm2_align_hifi-46 INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:22:02.650 wdl.w:ptcp.t:call-pbmm2_align_hifi-44 INFO eval :: name: "mem_gb", value: 64
2025-09-15 20:22:02.650 wdl.w:ptcp.t:call-pbmm2_align_hifi-38 INFO provisioned :: seconds_waited: 0, cpu: 64, mem_bytes: 64000000000
2025-09-15 20:22:02.651 wdl.w:ptcp.t:call-pbmm2_align_hifi-41 INFO eval :: name: "disk_size", value: 30
2025-09-15 20:22:02.651 wdl.w:ptcp.t:call-pbmm2_align_hifi-39 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:22:02.651 wdl.w:ptcp.t:call-pbmm2_align_hifi-37 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:22:02.653 wdl.w:ptcp.t:call-pbmm2_align_hifi-43 INFO eval :: name: "disk_size", value: 30
2025-09-15 20:22:02.654 wdl.w:ptcp.t:call-pbmm2_align_hifi-45 INFO eval :: name: "threads", value: 64
2025-09-15 20:22:02.654 wdl.w:ptcp.t:call-pbmm2_align_hifi-40 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:22:02.654 wdl.w:ptcp INFO input :: job: "call-pbmm2_align_hifi-52", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "log_level": "INFO", "out_prefix": "m84036_250809_035451_s4.bc2149.mapped", "ref_fasta": "/meta/refs/hg38.fa", "unmapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0053_m84036_250809_035451_s4.bc2149.unmapped.bam", "sample_name": "m84036_250809_035451_s4.bc2149"}
2025-09-15 20:22:02.655 wdl.w:ptcp.t:call-pbmm2_align_hifi-46 INFO input :: name: "unmapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0047_m84036_250809_035451_s4.bc2143.unmapped.bam"
2025-09-15 20:22:02.655 wdl.w:ptcp.t:call-pbmm2_align_hifi-42 INFO eval :: name: "disk_size", value: 30
2025-09-15 20:22:02.656 wdl.w:ptcp.t:call-pbmm2_align_hifi-51 NOTICE task setup :: name: "pbmm2_align_hifi", source: "./common.wdl", line: 170, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-51", thread: 140609847293504
2025-09-15 20:22:02.656 wdl.w:ptcp.t:call-pbmm2_align_hifi-38 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:22:02.656 wdl.w:ptcp.t:call-pbmm2_align_hifi-44 INFO eval :: name: "disk_size", value: 30
2025-09-15 20:22:02.658 wdl.w:ptcp.t:call-pbmm2_align_hifi-45 INFO eval :: name: "mem_gb", value: 64
2025-09-15 20:22:02.658 wdl.w:ptcp.t:call-pbmm2_align_hifi-41 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 64, memory_reservation: 64000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:22:02.660 wdl.w:ptcp.t:call-pbmm2_align_hifi-43 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 64, memory_reservation: 64000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:22:02.661 wdl.w:ptcp.t:call-pbmm2_align_hifi-47 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:22:02.661 wdl.w:ptcp.t:call-pbmm2_align_hifi-23 NOTICE slurm_singularity run :: pid: 1197229, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-23/slurm_singularity.log.txt"
2025-09-15 20:22:02.661 wdl.w:ptcp.t:call-pbmm2_align_hifi-46 INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2143"
2025-09-15 20:22:02.662 wdl.w:ptcp.t:call-pbmm2_align_hifi-39 INFO provisioned :: seconds_waited: 0, cpu: 64, mem_bytes: 64000000000
2025-09-15 20:22:02.663 wdl.w:ptcp NOTICE ready :: job: "call-pbmm2_align_hifi-53", callee: "pbmm2_align_hifi"
2025-09-15 20:22:02.663 wdl.w:ptcp.t:call-pbmm2_align_hifi-40 INFO provisioned :: seconds_waited: 0, cpu: 64, mem_bytes: 64000000000
2025-09-15 20:22:02.664 wdl.w:ptcp.t:call-pbmm2_align_hifi-42 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 64, memory_reservation: 64000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:22:02.664 wdl.w:ptcp.t:call-pbmm2_align_hifi-44 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 64, memory_reservation: 64000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:22:02.665 wdl.w:ptcp.t:call-pbmm2_align_hifi-45 INFO eval :: name: "disk_size", value: 30
2025-09-15 20:22:02.665 wdl.w:ptcp.t:call-pbmm2_align_hifi-28 NOTICE slurm_singularity run :: pid: 1197228, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-28/slurm_singularity.log.txt"
2025-09-15 20:22:02.666 wdl.w:ptcp.t:call-pbmm2_align_hifi-41 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:22:02.666 wdl.w:ptcp.t:call-pbmm2_align_hifi-43 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:22:02.667 wdl.w:ptcp.t:call-pbmm2_align_hifi-47 INFO input :: name: "log_level", value: "INFO"
2025-09-15 20:22:02.667 wdl.w:ptcp.t:call-pbmm2_align_hifi-46 INFO eval :: name: "threads", value: 64
2025-09-15 20:22:02.667 wdl.w:ptcp.t:call-pbmm2_align_hifi-39 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:22:02.668 wdl.w:ptcp INFO input :: job: "call-pbmm2_align_hifi-53", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "log_level": "INFO", "out_prefix": "m84036_250809_035451_s4.bc2150.mapped", "ref_fasta": "/meta/refs/hg38.fa", "unmapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0054_m84036_250809_035451_s4.bc2150.unmapped.bam", "sample_name": "m84036_250809_035451_s4.bc2150"}
2025-09-15 20:22:02.668 wdl.w:ptcp.t:call-pbmm2_align_hifi-40 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:22:02.668 wdl.w:ptcp.t:call-pbmm2_align_hifi-42 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:22:02.668 wdl.w:ptcp.t:call-pbmm2_align_hifi-44 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:22:02.670 wdl.w:ptcp.t:call-pbmm2_align_hifi-45 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 64, memory_reservation: 64000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:22:02.670 wdl.w:ptcp.t:call-pbmm2_align_hifi-29 NOTICE slurm_singularity run :: pid: 1197231, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-29/slurm_singularity.log.txt"
2025-09-15 20:22:02.670 wdl.w:ptcp.t:call-pbmm2_align_hifi-48 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:22:02.671 wdl.w:ptcp.t:call-pbmm2_align_hifi-30 NOTICE slurm_singularity run :: pid: 1197241, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-30/slurm_singularity.log.txt"
2025-09-15 20:22:02.671 wdl.w:ptcp.t:call-pbmm2_align_hifi-31 NOTICE slurm_singularity run :: pid: 1197240, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-31/slurm_singularity.log.txt"
2025-09-15 20:22:02.671 wdl.w:ptcp.t:call-pbmm2_align_hifi-32 NOTICE slurm_singularity run :: pid: 1197244, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-32/slurm_singularity.log.txt"
2025-09-15 20:22:02.672 wdl.w:ptcp.t:call-pbmm2_align_hifi-47 INFO input :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2144.mapped"
2025-09-15 20:22:02.673 wdl.w:ptcp.t:call-pbmm2_align_hifi-46 INFO eval :: name: "mem_gb", value: 64
2025-09-15 20:22:02.673 wdl.w:ptcp.t:call-pbmm2_align_hifi-52 NOTICE task setup :: name: "pbmm2_align_hifi", source: "./common.wdl", line: 170, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-52", thread: 140609838900800
2025-09-15 20:22:02.674 wdl.w:ptcp.t:call-pbmm2_align_hifi-41 INFO provisioned :: seconds_waited: 0, cpu: 64, mem_bytes: 64000000000
2025-09-15 20:22:02.675 wdl.w:ptcp.t:call-pbmm2_align_hifi-43 INFO provisioned :: seconds_waited: 0, cpu: 64, mem_bytes: 64000000000
2025-09-15 20:22:02.677 wdl.w:ptcp NOTICE ready :: job: "call-pbmm2_align_hifi-54", callee: "pbmm2_align_hifi"
2025-09-15 20:22:02.678 wdl.w:ptcp.t:call-pbmm2_align_hifi-45 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:22:02.679 wdl.w:ptcp.t:call-pbmm2_align_hifi-48 INFO input :: name: "log_level", value: "INFO"
2025-09-15 20:22:02.680 wdl.w:ptcp.t:call-pbmm2_align_hifi-44 INFO provisioned :: seconds_waited: 0, cpu: 64, mem_bytes: 64000000000
2025-09-15 20:22:02.680 wdl.w:ptcp.t:call-pbmm2_align_hifi-42 INFO provisioned :: seconds_waited: 0, cpu: 64, mem_bytes: 64000000000
2025-09-15 20:22:02.681 wdl.w:ptcp.t:call-pbmm2_align_hifi-47 INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:22:02.682 wdl.w:ptcp.t:call-pbmm2_align_hifi-46 INFO eval :: name: "disk_size", value: 30
2025-09-15 20:22:02.682 wdl.w:ptcp.t:call-pbmm2_align_hifi-41 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:22:02.682 wdl.w:ptcp.t:call-pbmm2_align_hifi-43 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:22:02.682 wdl.w:ptcp INFO input :: job: "call-pbmm2_align_hifi-54", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "log_level": "INFO", "out_prefix": "m84036_250809_035451_s4.bc2151.mapped", "ref_fasta": "/meta/refs/hg38.fa", "unmapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0055_m84036_250809_035451_s4.bc2151.unmapped.bam", "sample_name": "m84036_250809_035451_s4.bc2151"}
2025-09-15 20:22:02.683 wdl.w:ptcp.t:call-pbmm2_align_hifi-48 INFO input :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2145.mapped"
2025-09-15 20:22:02.684 wdl.w:ptcp.t:call-pbmm2_align_hifi-44 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:22:02.685 wdl.w:ptcp.t:call-pbmm2_align_hifi-49 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:22:02.684 wdl.w:ptcp.t:call-pbmm2_align_hifi-42 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:22:02.685 wdl.w:ptcp.t:call-pbmm2_align_hifi-47 INFO input :: name: "unmapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0048_m84036_250809_035451_s4.bc2144.unmapped.bam"
2025-09-15 20:22:02.685 wdl.w:ptcp.t:call-pbmm2_align_hifi-45 INFO provisioned :: seconds_waited: 0, cpu: 64, mem_bytes: 64000000000
2025-09-15 20:22:02.686 wdl.w:ptcp.t:call-pbmm2_align_hifi-53 NOTICE task setup :: name: "pbmm2_align_hifi", source: "./common.wdl", line: 170, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-53", thread: 140609830508096
2025-09-15 20:22:02.687 wdl.w:ptcp.t:call-pbmm2_align_hifi-46 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 64, memory_reservation: 64000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:22:02.687 wdl.w:ptcp.t:call-pbmm2_align_hifi-48 INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:22:02.688 wdl.w:ptcp.t:call-pbmm2_align_hifi-49 INFO input :: name: "log_level", value: "INFO"
2025-09-15 20:22:02.689 wdl.w:ptcp NOTICE ready :: job: "call-pbmm2_align_hifi-55", callee: "pbmm2_align_hifi"
2025-09-15 20:22:02.689 wdl.w:ptcp.t:call-pbmm2_align_hifi-47 INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2144"
2025-09-15 20:22:02.689 wdl.w:ptcp.t:call-pbmm2_align_hifi-45 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:22:02.690 wdl.w:ptcp.t:call-pbmm2_align_hifi-46 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:22:02.690 wdl.w:ptcp.t:call-pbmm2_align_hifi-48 INFO input :: name: "unmapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0049_m84036_250809_035451_s4.bc2145.unmapped.bam"
2025-09-15 20:22:02.690 wdl.w:ptcp.t:call-pbmm2_align_hifi-49 INFO input :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2146.mapped"
2025-09-15 20:22:02.690 wdl.w:ptcp INFO input :: job: "call-pbmm2_align_hifi-55", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "log_level": "INFO", "out_prefix": "m84036_250809_035451_s4.bc2152.mapped", "ref_fasta": "/meta/refs/hg38.fa", "unmapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0056_m84036_250809_035451_s4.bc2152.unmapped.bam", "sample_name": "m84036_250809_035451_s4.bc2152"}
2025-09-15 20:22:02.691 wdl.w:ptcp.t:call-pbmm2_align_hifi-47 INFO eval :: name: "threads", value: 64
2025-09-15 20:22:02.692 wdl.w:ptcp.t:call-pbmm2_align_hifi-48 INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2145"
2025-09-15 20:22:02.692 wdl.w:ptcp.t:call-pbmm2_align_hifi-49 INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:22:02.692 wdl.w:ptcp.t:call-pbmm2_align_hifi-47 INFO eval :: name: "mem_gb", value: 64
2025-09-15 20:22:02.693 wdl.w:ptcp.t:call-pbmm2_align_hifi-46 INFO provisioned :: seconds_waited: 0, cpu: 64, mem_bytes: 64000000000
2025-09-15 20:22:02.693 wdl.w:ptcp.t:call-pbmm2_align_hifi-48 INFO eval :: name: "threads", value: 64
2025-09-15 20:22:02.693 wdl.w:ptcp.t:call-pbmm2_align_hifi-49 INFO input :: name: "unmapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0050_m84036_250809_035451_s4.bc2146.unmapped.bam"
2025-09-15 20:22:02.694 wdl.w:ptcp.t:call-pbmm2_align_hifi-46 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:22:02.694 wdl.w:ptcp.t:call-pbmm2_align_hifi-47 INFO eval :: name: "disk_size", value: 30
2025-09-15 20:22:02.694 wdl.w:ptcp.t:call-pbmm2_align_hifi-48 INFO eval :: name: "mem_gb", value: 64
2025-09-15 20:22:02.694 wdl.w:ptcp.t:call-pbmm2_align_hifi-49 INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2146"
2025-09-15 20:22:02.695 wdl.w:ptcp.t:call-pbmm2_align_hifi-49 INFO eval :: name: "threads", value: 64
2025-09-15 20:22:02.696 wdl.w:ptcp.t:call-pbmm2_align_hifi-49 INFO eval :: name: "mem_gb", value: 64
2025-09-15 20:22:02.696 wdl.w:ptcp.t:call-pbmm2_align_hifi-48 INFO eval :: name: "disk_size", value: 30
2025-09-15 20:22:02.697 wdl.w:ptcp NOTICE ready :: job: "call-pbmm2_align_hifi-56", callee: "pbmm2_align_hifi"
2025-09-15 20:22:02.697 wdl.w:ptcp.t:call-pbmm2_align_hifi-47 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 64, memory_reservation: 64000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:22:02.698 wdl.w:ptcp.t:call-pbmm2_align_hifi-49 INFO eval :: name: "disk_size", value: 30
2025-09-15 20:22:02.698 wdl.w:ptcp INFO input :: job: "call-pbmm2_align_hifi-56", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "log_level": "INFO", "out_prefix": "m84036_250809_035451_s4.bc2153.mapped", "ref_fasta": "/meta/refs/hg38.fa", "unmapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0057_m84036_250809_035451_s4.bc2153.unmapped.bam", "sample_name": "m84036_250809_035451_s4.bc2153"}
2025-09-15 20:22:02.698 wdl.w:ptcp.t:call-pbmm2_align_hifi-48 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 64, memory_reservation: 64000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:22:02.699 wdl.w:ptcp.t:call-pbmm2_align_hifi-47 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:22:02.699 wdl.w:ptcp.t:call-pbmm2_align_hifi-48 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:22:02.700 wdl.w:ptcp.t:call-pbmm2_align_hifi-49 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 64, memory_reservation: 64000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:22:02.700 wdl.w:ptcp.t:call-pbmm2_align_hifi-49 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:22:02.701 wdl.w:ptcp.t:call-pbmm2_align_hifi-47 INFO provisioned :: seconds_waited: 0, cpu: 64, mem_bytes: 64000000000
2025-09-15 20:22:02.701 wdl.w:ptcp.t:call-pbmm2_align_hifi-54 NOTICE task setup :: name: "pbmm2_align_hifi", source: "./common.wdl", line: 170, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-54", thread: 140609822115392
2025-09-15 20:22:02.701 wdl.w:ptcp.t:call-pbmm2_align_hifi-33 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 8, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-33/_singularity_tmpdir_pfje8uzj"
2025-09-15 20:22:02.702 wdl.w:ptcp.t:call-pbmm2_align_hifi-50 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:22:02.702 wdl.w:ptcp.t:call-pbmm2_align_hifi-47 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:22:02.702 wdl.w:ptcp.t:call-pbmm2_align_hifi-48 INFO provisioned :: seconds_waited: 0, cpu: 64, mem_bytes: 64000000000
2025-09-15 20:22:02.703 wdl.w:ptcp.t:call-pbmm2_align_hifi-49 INFO provisioned :: seconds_waited: 0, cpu: 64, mem_bytes: 64000000000
2025-09-15 20:22:02.703 wdl.w:ptcp.t:call-pbmm2_align_hifi-33 INFO Slurm invocation: srun --job-name call-pbmm2_align_hifi-33 --partition compute,compute9 --cpus-per-task 64 --mem 61035M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-33/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-33/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-33/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-33/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0034_m84036_250809_035451_s4.bc2130.unmapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0034_m84036_250809_035451_s4.bc2130.unmapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-33/_singularity_tmpdir_pfje8uzj/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-33/_singularity_tmpdir_pfje8uzj/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:22:02.704 wdl.w:ptcp NOTICE ready :: job: "call-pbmm2_align_hifi-57", callee: "pbmm2_align_hifi"
2025-09-15 20:22:02.704 wdl.w:ptcp.t:call-pbmm2_align_hifi-50 INFO input :: name: "log_level", value: "INFO"
2025-09-15 20:22:02.704 wdl.w:ptcp.t:call-pbmm2_align_hifi-48 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:22:02.704 wdl.w:ptcp.t:call-pbmm2_align_hifi-34 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 8, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-34/_singularity_tmpdir_154hw54x"
2025-09-15 20:22:02.705 wdl.w:ptcp.t:call-pbmm2_align_hifi-49 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:22:02.705 wdl.w:ptcp INFO input :: job: "call-pbmm2_align_hifi-57", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "log_level": "INFO", "out_prefix": "m84036_250809_035451_s4.bc2154.mapped", "ref_fasta": "/meta/refs/hg38.fa", "unmapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0058_m84036_250809_035451_s4.bc2154.unmapped.bam", "sample_name": "m84036_250809_035451_s4.bc2154"}
2025-09-15 20:22:02.705 wdl.w:ptcp.t:call-pbmm2_align_hifi-50 INFO input :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2147.mapped"
2025-09-15 20:22:02.705 wdl.w:ptcp.t:call-pbmm2_align_hifi-34 INFO Slurm invocation: srun --job-name call-pbmm2_align_hifi-34 --partition compute,compute9 --cpus-per-task 64 --mem 61035M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-34/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-34/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-34/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-34/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0035_m84036_250809_035451_s4.bc2131.unmapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0035_m84036_250809_035451_s4.bc2131.unmapped.bam:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-34/_singularity_tmpdir_154hw54x/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-34/_singularity_tmpdir_154hw54x/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:22:02.707 wdl.w:ptcp.t:call-pbmm2_align_hifi-51 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:22:02.708 wdl.w:ptcp.t:call-pbmm2_align_hifi-50 INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:22:02.708 wdl.w:ptcp.t:call-pbmm2_align_hifi-51 INFO input :: name: "log_level", value: "INFO"
2025-09-15 20:22:02.708 wdl.w:ptcp.t:call-pbmm2_align_hifi-50 INFO input :: name: "unmapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0051_m84036_250809_035451_s4.bc2147.unmapped.bam"
2025-09-15 20:22:02.711 wdl.w:ptcp NOTICE ready :: job: "call-pbmm2_align_hifi-58", callee: "pbmm2_align_hifi"
2025-09-15 20:22:02.711 wdl.w:ptcp.t:call-pbmm2_align_hifi-51 INFO input :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2148.mapped"
2025-09-15 20:22:02.711 wdl.w:ptcp.t:call-pbmm2_align_hifi-50 INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2147"
2025-09-15 20:22:02.711 wdl.w:ptcp INFO input :: job: "call-pbmm2_align_hifi-58", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "log_level": "INFO", "out_prefix": "m84036_250809_035451_s4.bc2155.mapped", "ref_fasta": "/meta/refs/hg38.fa", "unmapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0059_m84036_250809_035451_s4.bc2155.unmapped.bam", "sample_name": "m84036_250809_035451_s4.bc2155"}
2025-09-15 20:22:02.711 wdl.w:ptcp.t:call-pbmm2_align_hifi-51 INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:22:02.712 wdl.w:ptcp.t:call-pbmm2_align_hifi-50 INFO eval :: name: "threads", value: 64
2025-09-15 20:22:02.712 wdl.w:ptcp.t:call-pbmm2_align_hifi-35 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 8, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-35/_singularity_tmpdir_5xl0vya0"
2025-09-15 20:22:02.712 wdl.w:ptcp.t:call-pbmm2_align_hifi-51 INFO input :: name: "unmapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0052_m84036_250809_035451_s4.bc2148.unmapped.bam"
2025-09-15 20:22:02.712 wdl.w:ptcp.t:call-pbmm2_align_hifi-50 INFO eval :: name: "mem_gb", value: 64
2025-09-15 20:22:02.712 wdl.w:ptcp.t:call-pbmm2_align_hifi-35 INFO Slurm invocation: srun --job-name call-pbmm2_align_hifi-35 --partition compute,compute9 --cpus-per-task 64 --mem 61035M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-35/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-35/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-35/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-35/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0036_m84036_250809_035451_s4.bc2132.unmapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0036_m84036_250809_035451_s4.bc2132.unmapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-35/_singularity_tmpdir_5xl0vya0/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-35/_singularity_tmpdir_5xl0vya0/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:22:02.713 wdl.w:ptcp.t:call-pbmm2_align_hifi-51 INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2148"
2025-09-15 20:22:02.714 wdl.w:ptcp.t:call-pbmm2_align_hifi-50 INFO eval :: name: "disk_size", value: 30
2025-09-15 20:22:02.714 wdl.w:ptcp.t:call-pbmm2_align_hifi-51 INFO eval :: name: "threads", value: 64
2025-09-15 20:22:02.715 wdl.w:ptcp.t:call-pbmm2_align_hifi-55 NOTICE task setup :: name: "pbmm2_align_hifi", source: "./common.wdl", line: 170, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-55", thread: 140609813722688
2025-09-15 20:22:02.717 wdl.w:ptcp.t:call-pbmm2_align_hifi-51 INFO eval :: name: "mem_gb", value: 64
2025-09-15 20:22:02.718 wdl.w:ptcp.t:call-pbmm2_align_hifi-50 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 64, memory_reservation: 64000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:22:02.718 wdl.w:ptcp.t:call-pbmm2_align_hifi-50 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:22:02.720 wdl.w:ptcp.t:call-pbmm2_align_hifi-51 INFO eval :: name: "disk_size", value: 30
2025-09-15 20:22:02.720 wdl.w:ptcp NOTICE ready :: job: "call-pbmm2_align_hifi-59", callee: "pbmm2_align_hifi"
2025-09-15 20:22:02.720 wdl.w:ptcp.t:call-pbmm2_align_hifi-52 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:22:02.721 wdl.w:ptcp INFO input :: job: "call-pbmm2_align_hifi-59", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "log_level": "INFO", "out_prefix": "m84036_250809_035451_s4.bc2156.mapped", "ref_fasta": "/meta/refs/hg38.fa", "unmapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0060_m84036_250809_035451_s4.bc2156.unmapped.bam", "sample_name": "m84036_250809_035451_s4.bc2156"}
2025-09-15 20:22:02.721 wdl.w:ptcp.t:call-pbmm2_align_hifi-52 INFO input :: name: "log_level", value: "INFO"
2025-09-15 20:22:02.721 wdl.w:ptcp.t:call-pbmm2_align_hifi-56 NOTICE task setup :: name: "pbmm2_align_hifi", source: "./common.wdl", line: 170, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-56", thread: 140609805329984
2025-09-15 20:22:02.722 wdl.w:ptcp.t:call-pbmm2_align_hifi-51 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 64, memory_reservation: 64000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:22:02.722 wdl.w:ptcp.t:call-pbmm2_align_hifi-50 INFO provisioned :: seconds_waited: 0, cpu: 64, mem_bytes: 64000000000
2025-09-15 20:22:02.723 wdl.w:ptcp.t:call-pbmm2_align_hifi-52 INFO input :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2149.mapped"
2025-09-15 20:22:02.723 wdl.w:ptcp.t:call-pbmm2_align_hifi-51 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:22:02.724 wdl.w:ptcp.t:call-pbmm2_align_hifi-50 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:22:02.724 wdl.w:ptcp.t:call-pbmm2_align_hifi-52 INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:22:02.724 wdl.w:ptcp.t:call-pbmm2_align_hifi-52 INFO input :: name: "unmapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0053_m84036_250809_035451_s4.bc2149.unmapped.bam"
2025-09-15 20:22:02.724 wdl.w:ptcp.t:call-pbmm2_align_hifi-51 INFO provisioned :: seconds_waited: 0, cpu: 64, mem_bytes: 64000000000
2025-09-15 20:22:02.725 wdl.w:ptcp.t:call-pbmm2_align_hifi-52 INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2149"
2025-09-15 20:22:02.725 wdl.w:ptcp.t:call-pbmm2_align_hifi-51 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:22:02.725 wdl.w:ptcp.t:call-pbmm2_align_hifi-52 INFO eval :: name: "threads", value: 64
2025-09-15 20:22:02.726 wdl.w:ptcp.t:call-pbmm2_align_hifi-52 INFO eval :: name: "mem_gb", value: 64
2025-09-15 20:22:02.726 wdl.w:ptcp.t:call-pbmm2_align_hifi-52 INFO eval :: name: "disk_size", value: 30
2025-09-15 20:22:02.727 wdl.w:ptcp.t:call-pbmm2_align_hifi-52 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 64, memory_reservation: 64000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:22:02.727 wdl.w:ptcp.t:call-pbmm2_align_hifi-52 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:22:02.727 wdl.w:ptcp.t:call-pbmm2_align_hifi-57 NOTICE task setup :: name: "pbmm2_align_hifi", source: "./common.wdl", line: 170, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-57", thread: 140609796937280
2025-09-15 20:22:02.729 wdl.w:ptcp NOTICE ready :: job: "call-pbmm2_align_hifi-60", callee: "pbmm2_align_hifi"
2025-09-15 20:22:02.729 wdl.w:ptcp.t:call-pbmm2_align_hifi-52 INFO provisioned :: seconds_waited: 0, cpu: 64, mem_bytes: 64000000000
2025-09-15 20:22:02.729 wdl.w:ptcp INFO input :: job: "call-pbmm2_align_hifi-60", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "log_level": "INFO", "out_prefix": "m84036_250809_035451_s4.bc2157.mapped", "ref_fasta": "/meta/refs/hg38.fa", "unmapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0061_m84036_250809_035451_s4.bc2157.unmapped.bam", "sample_name": "m84036_250809_035451_s4.bc2157"}
2025-09-15 20:22:02.730 wdl.w:ptcp.t:call-pbmm2_align_hifi-52 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:22:02.730 wdl.w:ptcp.t:call-pbmm2_align_hifi-53 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:22:02.730 wdl.w:ptcp.t:call-pbmm2_align_hifi-53 INFO input :: name: "log_level", value: "INFO"
2025-09-15 20:22:02.730 wdl.w:ptcp.t:call-pbmm2_align_hifi-53 INFO input :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2150.mapped"
2025-09-15 20:22:02.731 wdl.w:ptcp.t:call-pbmm2_align_hifi-53 INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:22:02.731 wdl.w:ptcp.t:call-pbmm2_align_hifi-53 INFO input :: name: "unmapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0054_m84036_250809_035451_s4.bc2150.unmapped.bam"
2025-09-15 20:22:02.731 wdl.w:ptcp.t:call-pbmm2_align_hifi-53 INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2150"
2025-09-15 20:22:02.731 wdl.w:ptcp.t:call-pbmm2_align_hifi-53 INFO eval :: name: "threads", value: 64
2025-09-15 20:22:02.731 wdl.w:ptcp.t:call-pbmm2_align_hifi-53 INFO eval :: name: "mem_gb", value: 64
2025-09-15 20:22:02.732 wdl.w:ptcp.t:call-pbmm2_align_hifi-53 INFO eval :: name: "disk_size", value: 30
2025-09-15 20:22:02.732 wdl.w:ptcp.t:call-pbmm2_align_hifi-53 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 64, memory_reservation: 64000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:22:02.732 wdl.w:ptcp.t:call-pbmm2_align_hifi-53 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:22:02.733 wdl.w:ptcp.t:call-pbmm2_align_hifi-53 INFO provisioned :: seconds_waited: 0, cpu: 64, mem_bytes: 64000000000
2025-09-15 20:22:02.733 wdl.w:ptcp.t:call-pbmm2_align_hifi-53 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:22:02.739 wdl.w:ptcp NOTICE ready :: job: "call-pbmm2_align_hifi-61", callee: "pbmm2_align_hifi"
2025-09-15 20:22:02.739 wdl.w:ptcp INFO input :: job: "call-pbmm2_align_hifi-61", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "log_level": "INFO", "out_prefix": "m84036_250809_035451_s4.bc2158.mapped", "ref_fasta": "/meta/refs/hg38.fa", "unmapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0062_m84036_250809_035451_s4.bc2158.unmapped.bam", "sample_name": "m84036_250809_035451_s4.bc2158"}
2025-09-15 20:22:02.740 wdl.w:ptcp.t:call-pbmm2_align_hifi-54 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:22:02.740 wdl.w:ptcp.t:call-pbmm2_align_hifi-54 INFO input :: name: "log_level", value: "INFO"
2025-09-15 20:22:02.740 wdl.w:ptcp.t:call-pbmm2_align_hifi-54 INFO input :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2151.mapped"
2025-09-15 20:22:02.740 wdl.w:ptcp.t:call-pbmm2_align_hifi-54 INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:22:02.740 wdl.w:ptcp.t:call-pbmm2_align_hifi-54 INFO input :: name: "unmapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0055_m84036_250809_035451_s4.bc2151.unmapped.bam"
2025-09-15 20:22:02.740 wdl.w:ptcp.t:call-pbmm2_align_hifi-54 INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2151"
2025-09-15 20:22:02.740 wdl.w:ptcp.t:call-pbmm2_align_hifi-54 INFO eval :: name: "threads", value: 64
2025-09-15 20:22:02.740 wdl.w:ptcp.t:call-pbmm2_align_hifi-54 INFO eval :: name: "mem_gb", value: 64
2025-09-15 20:22:02.741 wdl.w:ptcp.t:call-pbmm2_align_hifi-54 INFO eval :: name: "disk_size", value: 30
2025-09-15 20:22:02.742 wdl.w:ptcp.t:call-pbmm2_align_hifi-54 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 64, memory_reservation: 64000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:22:02.743 wdl.w:ptcp.t:call-pbmm2_align_hifi-54 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:22:02.744 wdl.w:ptcp.t:call-pbmm2_align_hifi-58 NOTICE task setup :: name: "pbmm2_align_hifi", source: "./common.wdl", line: 170, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-58", thread: 140609310422592
2025-09-15 20:22:02.746 wdl.w:ptcp.t:call-pbmm2_align_hifi-54 INFO provisioned :: seconds_waited: 0, cpu: 64, mem_bytes: 64000000000
2025-09-15 20:22:02.746 wdl.w:ptcp.t:call-pbmm2_align_hifi-54 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:22:02.756 wdl.w:ptcp NOTICE ready :: job: "call-pbmm2_align_hifi-62", callee: "pbmm2_align_hifi"
2025-09-15 20:22:02.756 wdl.w:ptcp INFO input :: job: "call-pbmm2_align_hifi-62", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "log_level": "INFO", "out_prefix": "m84036_250809_035451_s4.bc2159.mapped", "ref_fasta": "/meta/refs/hg38.fa", "unmapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0063_m84036_250809_035451_s4.bc2159.unmapped.bam", "sample_name": "m84036_250809_035451_s4.bc2159"}
2025-09-15 20:22:02.757 wdl.w:ptcp.t:call-pbmm2_align_hifi-59 NOTICE task setup :: name: "pbmm2_align_hifi", source: "./common.wdl", line: 170, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-59", thread: 140609302029888
2025-09-15 20:22:02.757 wdl.w:ptcp.t:call-pbmm2_align_hifi-55 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:22:02.757 wdl.w:ptcp.t:call-pbmm2_align_hifi-55 INFO input :: name: "log_level", value: "INFO"
2025-09-15 20:22:02.758 wdl.w:ptcp.t:call-pbmm2_align_hifi-55 INFO input :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2152.mapped"
2025-09-15 20:22:02.758 wdl.w:ptcp.t:call-pbmm2_align_hifi-55 INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:22:02.758 wdl.w:ptcp.t:call-pbmm2_align_hifi-55 INFO input :: name: "unmapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0056_m84036_250809_035451_s4.bc2152.unmapped.bam"
2025-09-15 20:22:02.758 wdl.w:ptcp.t:call-pbmm2_align_hifi-55 INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2152"
2025-09-15 20:22:02.758 wdl.w:ptcp.t:call-pbmm2_align_hifi-55 INFO eval :: name: "threads", value: 64
2025-09-15 20:22:02.758 wdl.w:ptcp.t:call-pbmm2_align_hifi-55 INFO eval :: name: "mem_gb", value: 64
2025-09-15 20:22:02.759 wdl.w:ptcp.t:call-pbmm2_align_hifi-55 INFO eval :: name: "disk_size", value: 30
2025-09-15 20:22:02.759 wdl.w:ptcp.t:call-pbmm2_align_hifi-36 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 8, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-36/_singularity_tmpdir_55n6kw6u"
2025-09-15 20:22:02.760 wdl.w:ptcp.t:call-pbmm2_align_hifi-55 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 64, memory_reservation: 64000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:22:02.760 wdl.w:ptcp.t:call-pbmm2_align_hifi-36 INFO Slurm invocation: srun --job-name call-pbmm2_align_hifi-36 --partition compute,compute9 --cpus-per-task 64 --mem 61035M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-36/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-36/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-36/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-36/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0037_m84036_250809_035451_s4.bc2133.unmapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0037_m84036_250809_035451_s4.bc2133.unmapped.bam:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-36/_singularity_tmpdir_55n6kw6u/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-36/_singularity_tmpdir_55n6kw6u/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:22:02.760 wdl.w:ptcp.t:call-pbmm2_align_hifi-55 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:22:02.761 wdl.w:ptcp.t:call-pbmm2_align_hifi-55 INFO provisioned :: seconds_waited: 0, cpu: 64, mem_bytes: 64000000000
2025-09-15 20:22:02.762 wdl.w:ptcp.t:call-pbmm2_align_hifi-56 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:22:02.763 wdl.w:ptcp.t:call-pbmm2_align_hifi-55 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:22:02.763 wdl.w:ptcp.t:call-pbmm2_align_hifi-56 INFO input :: name: "log_level", value: "INFO"
2025-09-15 20:22:02.763 wdl.w:ptcp.t:call-pbmm2_align_hifi-56 INFO input :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2153.mapped"
2025-09-15 20:22:02.763 wdl.w:ptcp.t:call-pbmm2_align_hifi-56 INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:22:02.763 wdl.w:ptcp.t:call-pbmm2_align_hifi-56 INFO input :: name: "unmapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0057_m84036_250809_035451_s4.bc2153.unmapped.bam"
2025-09-15 20:22:02.763 wdl.w:ptcp.t:call-pbmm2_align_hifi-56 INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2153"
2025-09-15 20:22:02.764 wdl.w:ptcp.t:call-pbmm2_align_hifi-56 INFO eval :: name: "threads", value: 64
2025-09-15 20:22:02.764 wdl.w:ptcp.t:call-pbmm2_align_hifi-56 INFO eval :: name: "mem_gb", value: 64
2025-09-15 20:22:02.764 wdl.w:ptcp.t:call-pbmm2_align_hifi-56 INFO eval :: name: "disk_size", value: 30
2025-09-15 20:22:02.764 wdl.w:ptcp.t:call-pbmm2_align_hifi-56 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 64, memory_reservation: 64000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:22:02.764 wdl.w:ptcp.t:call-pbmm2_align_hifi-56 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:22:02.765 wdl.w:ptcp.t:call-pbmm2_align_hifi-56 INFO provisioned :: seconds_waited: 0, cpu: 64, mem_bytes: 64000000000
2025-09-15 20:22:02.765 wdl.w:ptcp.t:call-pbmm2_align_hifi-56 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:22:02.766 wdl.w:ptcp.t:call-pbmm2_align_hifi-57 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:22:02.766 wdl.w:ptcp.t:call-pbmm2_align_hifi-57 INFO input :: name: "log_level", value: "INFO"
2025-09-15 20:22:02.766 wdl.w:ptcp.t:call-pbmm2_align_hifi-57 INFO input :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2154.mapped"
2025-09-15 20:22:02.766 wdl.w:ptcp.t:call-pbmm2_align_hifi-57 INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:22:02.766 wdl.w:ptcp.t:call-pbmm2_align_hifi-57 INFO input :: name: "unmapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0058_m84036_250809_035451_s4.bc2154.unmapped.bam"
2025-09-15 20:22:02.766 wdl.w:ptcp.t:call-pbmm2_align_hifi-57 INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2154"
2025-09-15 20:22:02.766 wdl.w:ptcp.t:call-pbmm2_align_hifi-57 INFO eval :: name: "threads", value: 64
2025-09-15 20:22:02.766 wdl.w:ptcp.t:call-pbmm2_align_hifi-57 INFO eval :: name: "mem_gb", value: 64
2025-09-15 20:22:02.767 wdl.w:ptcp.t:call-pbmm2_align_hifi-57 INFO eval :: name: "disk_size", value: 30
2025-09-15 20:22:02.767 wdl.w:ptcp.t:call-pbmm2_align_hifi-57 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 64, memory_reservation: 64000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:22:02.767 wdl.w:ptcp.t:call-pbmm2_align_hifi-57 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:22:02.767 wdl.w:ptcp.t:call-pbmm2_align_hifi-57 INFO provisioned :: seconds_waited: 0, cpu: 64, mem_bytes: 64000000000
2025-09-15 20:22:02.767 wdl.w:ptcp.t:call-pbmm2_align_hifi-57 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:22:02.769 wdl.w:ptcp.t:call-pbmm2_align_hifi-60 NOTICE task setup :: name: "pbmm2_align_hifi", source: "./common.wdl", line: 170, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-60", thread: 140609293637184
2025-09-15 20:22:02.770 wdl.w:ptcp.t:call-pbmm2_align_hifi-37 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 8, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-37/_singularity_tmpdir_k_6n80i7"
2025-09-15 20:22:02.770 wdl.w:ptcp.t:call-pbmm2_align_hifi-37 INFO Slurm invocation: srun --job-name call-pbmm2_align_hifi-37 --partition compute,compute9 --cpus-per-task 64 --mem 61035M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-37/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-37/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-37/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-37/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0038_m84036_250809_035451_s4.bc2134.unmapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0038_m84036_250809_035451_s4.bc2134.unmapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-37/_singularity_tmpdir_k_6n80i7/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-37/_singularity_tmpdir_k_6n80i7/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:22:02.771 wdl.w:ptcp NOTICE ready :: job: "call-pbmm2_align_hifi-63", callee: "pbmm2_align_hifi"
2025-09-15 20:22:02.775 wdl.w:ptcp INFO input :: job: "call-pbmm2_align_hifi-63", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "log_level": "INFO", "out_prefix": "m84036_250809_035451_s4.bc2160.mapped", "ref_fasta": "/meta/refs/hg38.fa", "unmapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0064_m84036_250809_035451_s4.bc2160.unmapped.bam", "sample_name": "m84036_250809_035451_s4.bc2160"}
2025-09-15 20:22:02.783 wdl.w:ptcp.t:call-pbmm2_align_hifi-58 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:22:02.783 wdl.w:ptcp.t:call-pbmm2_align_hifi-58 INFO input :: name: "log_level", value: "INFO"
2025-09-15 20:22:02.783 wdl.w:ptcp.t:call-pbmm2_align_hifi-58 INFO input :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2155.mapped"
2025-09-15 20:22:02.783 wdl.w:ptcp.t:call-pbmm2_align_hifi-58 INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:22:02.783 wdl.w:ptcp.t:call-pbmm2_align_hifi-58 INFO input :: name: "unmapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0059_m84036_250809_035451_s4.bc2155.unmapped.bam"
2025-09-15 20:22:02.783 wdl.w:ptcp.t:call-pbmm2_align_hifi-58 INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2155"
2025-09-15 20:22:02.783 wdl.w:ptcp.t:call-pbmm2_align_hifi-58 INFO eval :: name: "threads", value: 64
2025-09-15 20:22:02.783 wdl.w:ptcp.t:call-pbmm2_align_hifi-58 INFO eval :: name: "mem_gb", value: 64
2025-09-15 20:22:02.784 wdl.w:ptcp.t:call-pbmm2_align_hifi-58 INFO eval :: name: "disk_size", value: 30
2025-09-15 20:22:02.784 wdl.w:ptcp.t:call-pbmm2_align_hifi-58 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 64, memory_reservation: 64000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:22:02.784 wdl.w:ptcp.t:call-pbmm2_align_hifi-58 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:22:02.785 wdl.w:ptcp.t:call-pbmm2_align_hifi-58 INFO provisioned :: seconds_waited: 0, cpu: 64, mem_bytes: 64000000000
2025-09-15 20:22:02.785 wdl.w:ptcp.t:call-pbmm2_align_hifi-58 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:22:02.789 wdl.w:ptcp.t:call-pbmm2_align_hifi-38 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 8, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-38/_singularity_tmpdir_a5fbz2r2"
2025-09-15 20:22:02.789 wdl.w:ptcp.t:call-pbmm2_align_hifi-38 INFO Slurm invocation: srun --job-name call-pbmm2_align_hifi-38 --partition compute,compute9 --cpus-per-task 64 --mem 61035M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-38/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-38/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-38/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-38/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0039_m84036_250809_035451_s4.bc2135.unmapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0039_m84036_250809_035451_s4.bc2135.unmapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-38/_singularity_tmpdir_a5fbz2r2/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-38/_singularity_tmpdir_a5fbz2r2/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:22:02.790 wdl.w:ptcp.t:call-pbmm2_align_hifi-61 NOTICE task setup :: name: "pbmm2_align_hifi", source: "./common.wdl", line: 170, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-61", thread: 140609285244480
2025-09-15 20:22:02.794 wdl.w:ptcp.t:call-pbmm2_align_hifi-35 NOTICE slurm_singularity run :: pid: 1197258, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-35/slurm_singularity.log.txt"
2025-09-15 20:22:02.794 wdl.w:ptcp.t:call-pbmm2_align_hifi-40 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 8, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-40/_singularity_tmpdir_hhar7_ev"
2025-09-15 20:22:02.795 wdl.w:ptcp.t:call-pbmm2_align_hifi-40 INFO Slurm invocation: srun --job-name call-pbmm2_align_hifi-40 --partition compute,compute9 --cpus-per-task 64 --mem 61035M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-40/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-40/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-40/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-40/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0041_m84036_250809_035451_s4.bc2137.unmapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0041_m84036_250809_035451_s4.bc2137.unmapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-40/_singularity_tmpdir_hhar7_ev/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-40/_singularity_tmpdir_hhar7_ev/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:22:02.796 wdl.w:ptcp.t:call-pbmm2_align_hifi-59 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:22:02.797 wdl.w:ptcp NOTICE ready :: job: "call-pbmm2_align_hifi-64", callee: "pbmm2_align_hifi"
2025-09-15 20:22:02.797 wdl.w:ptcp.t:call-pbmm2_align_hifi-33 NOTICE slurm_singularity run :: pid: 1197255, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-33/slurm_singularity.log.txt"
2025-09-15 20:22:02.797 wdl.w:ptcp.t:call-pbmm2_align_hifi-34 NOTICE slurm_singularity run :: pid: 1197256, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-34/slurm_singularity.log.txt"
2025-09-15 20:22:02.797 wdl.w:ptcp.t:call-pbmm2_align_hifi-59 INFO input :: name: "log_level", value: "INFO"
2025-09-15 20:22:02.798 wdl.w:ptcp INFO input :: job: "call-pbmm2_align_hifi-64", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "log_level": "INFO", "out_prefix": "m84036_250809_035451_s4.bc2161.mapped", "ref_fasta": "/meta/refs/hg38.fa", "unmapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0065_m84036_250809_035451_s4.bc2161.unmapped.bam", "sample_name": "m84036_250809_035451_s4.bc2161"}
2025-09-15 20:22:02.798 wdl.w:ptcp.t:call-pbmm2_align_hifi-59 INFO input :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2156.mapped"
2025-09-15 20:22:02.798 wdl.w:ptcp.t:call-pbmm2_align_hifi-59 INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:22:02.799 wdl.w:ptcp.t:call-pbmm2_align_hifi-59 INFO input :: name: "unmapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0060_m84036_250809_035451_s4.bc2156.unmapped.bam"
2025-09-15 20:22:02.799 wdl.w:ptcp.t:call-pbmm2_align_hifi-59 INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2156"
2025-09-15 20:22:02.799 wdl.w:ptcp.t:call-pbmm2_align_hifi-59 INFO eval :: name: "threads", value: 64
2025-09-15 20:22:02.799 wdl.w:ptcp.t:call-pbmm2_align_hifi-59 INFO eval :: name: "mem_gb", value: 64
2025-09-15 20:22:02.799 wdl.w:ptcp.t:call-pbmm2_align_hifi-59 INFO eval :: name: "disk_size", value: 30
2025-09-15 20:22:02.800 wdl.w:ptcp.t:call-pbmm2_align_hifi-59 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 64, memory_reservation: 64000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:22:02.800 wdl.w:ptcp.t:call-pbmm2_align_hifi-59 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:22:02.802 wdl.w:ptcp.t:call-pbmm2_align_hifi-59 INFO provisioned :: seconds_waited: 0, cpu: 64, mem_bytes: 64000000000
2025-09-15 20:22:02.803 wdl.w:ptcp.t:call-pbmm2_align_hifi-59 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:22:02.806 wdl.w:ptcp.t:call-pbmm2_align_hifi-60 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:22:02.806 wdl.w:ptcp.t:call-pbmm2_align_hifi-60 INFO input :: name: "log_level", value: "INFO"
2025-09-15 20:22:02.806 wdl.w:ptcp.t:call-pbmm2_align_hifi-60 INFO input :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2157.mapped"
2025-09-15 20:22:02.806 wdl.w:ptcp.t:call-pbmm2_align_hifi-60 INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:22:02.806 wdl.w:ptcp.t:call-pbmm2_align_hifi-60 INFO input :: name: "unmapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0061_m84036_250809_035451_s4.bc2157.unmapped.bam"
2025-09-15 20:22:02.806 wdl.w:ptcp.t:call-pbmm2_align_hifi-60 INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2157"
2025-09-15 20:22:02.806 wdl.w:ptcp.t:call-pbmm2_align_hifi-60 INFO eval :: name: "threads", value: 64
2025-09-15 20:22:02.807 wdl.w:ptcp.t:call-pbmm2_align_hifi-60 INFO eval :: name: "mem_gb", value: 64
2025-09-15 20:22:02.808 wdl.w:ptcp.t:call-pbmm2_align_hifi-39 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 8, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-39/_singularity_tmpdir_klvn46py"
2025-09-15 20:22:02.808 wdl.w:ptcp.t:call-pbmm2_align_hifi-39 INFO Slurm invocation: srun --job-name call-pbmm2_align_hifi-39 --partition compute,compute9 --cpus-per-task 64 --mem 61035M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-39/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-39/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-39/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-39/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0040_m84036_250809_035451_s4.bc2136.unmapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0040_m84036_250809_035451_s4.bc2136.unmapped.bam:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-39/_singularity_tmpdir_klvn46py/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-39/_singularity_tmpdir_klvn46py/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:22:02.809 wdl.w:ptcp NOTICE ready :: job: "call-pbmm2_align_hifi-65", callee: "pbmm2_align_hifi"
2025-09-15 20:22:02.807 wdl.w:ptcp.t:call-pbmm2_align_hifi-60 INFO eval :: name: "disk_size", value: 30
2025-09-15 20:22:02.811 wdl.w:ptcp.t:call-pbmm2_align_hifi-62 NOTICE task setup :: name: "pbmm2_align_hifi", source: "./common.wdl", line: 170, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-62", thread: 140609276851776
2025-09-15 20:22:02.811 wdl.w:ptcp INFO input :: job: "call-pbmm2_align_hifi-65", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "log_level": "INFO", "out_prefix": "m84036_250809_035451_s4.bc2162.mapped", "ref_fasta": "/meta/refs/hg38.fa", "unmapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0066_m84036_250809_035451_s4.bc2162.unmapped.bam", "sample_name": "m84036_250809_035451_s4.bc2162"}
2025-09-15 20:22:02.812 wdl.w:ptcp.t:call-pbmm2_align_hifi-60 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 64, memory_reservation: 64000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:22:02.812 wdl.w:ptcp.t:call-pbmm2_align_hifi-60 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:22:02.813 wdl.w:ptcp.t:call-pbmm2_align_hifi-60 INFO provisioned :: seconds_waited: 0, cpu: 64, mem_bytes: 64000000000
2025-09-15 20:22:02.813 wdl.w:ptcp.t:call-pbmm2_align_hifi-60 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:22:02.814 wdl.w:ptcp.t:call-pbmm2_align_hifi-36 NOTICE slurm_singularity run :: pid: 1197263, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-36/slurm_singularity.log.txt"
2025-09-15 20:22:02.818 wdl.w:ptcp.t:call-pbmm2_align_hifi-38 NOTICE slurm_singularity run :: pid: 1197266, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-38/slurm_singularity.log.txt"
2025-09-15 20:22:02.818 wdl.w:ptcp.t:call-pbmm2_align_hifi-37 NOTICE slurm_singularity run :: pid: 1197264, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-37/slurm_singularity.log.txt"
2025-09-15 20:22:02.825 wdl.w:ptcp.t:call-pbmm2_align_hifi-61 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:22:02.825 wdl.w:ptcp.t:call-pbmm2_align_hifi-61 INFO input :: name: "log_level", value: "INFO"
2025-09-15 20:22:02.825 wdl.w:ptcp.t:call-pbmm2_align_hifi-61 INFO input :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2158.mapped"
2025-09-15 20:22:02.825 wdl.w:ptcp.t:call-pbmm2_align_hifi-61 INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:22:02.825 wdl.w:ptcp.t:call-pbmm2_align_hifi-61 INFO input :: name: "unmapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0062_m84036_250809_035451_s4.bc2158.unmapped.bam"
2025-09-15 20:22:02.825 wdl.w:ptcp.t:call-pbmm2_align_hifi-61 INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2158"
2025-09-15 20:22:02.825 wdl.w:ptcp.t:call-pbmm2_align_hifi-61 INFO eval :: name: "threads", value: 64
2025-09-15 20:22:02.825 wdl.w:ptcp.t:call-pbmm2_align_hifi-61 INFO eval :: name: "mem_gb", value: 64
2025-09-15 20:22:02.825 wdl.w:ptcp.t:call-pbmm2_align_hifi-61 INFO eval :: name: "disk_size", value: 30
2025-09-15 20:22:02.826 wdl.w:ptcp.t:call-pbmm2_align_hifi-61 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 64, memory_reservation: 64000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:22:02.826 wdl.w:ptcp.t:call-pbmm2_align_hifi-61 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:22:02.826 wdl.w:ptcp.t:call-pbmm2_align_hifi-61 INFO provisioned :: seconds_waited: 0, cpu: 64, mem_bytes: 64000000000
2025-09-15 20:22:02.826 wdl.w:ptcp.t:call-pbmm2_align_hifi-61 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:22:02.831 wdl.w:ptcp.t:call-pbmm2_align_hifi-63 NOTICE task setup :: name: "pbmm2_align_hifi", source: "./common.wdl", line: 170, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-63", thread: 140609268459072
2025-09-15 20:22:02.833 wdl.w:ptcp NOTICE ready :: job: "call-pbmm2_align_hifi-66", callee: "pbmm2_align_hifi"
2025-09-15 20:22:02.833 wdl.w:ptcp INFO input :: job: "call-pbmm2_align_hifi-66", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "log_level": "INFO", "out_prefix": "m84036_250809_035451_s4.bc2163.mapped", "ref_fasta": "/meta/refs/hg38.fa", "unmapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0067_m84036_250809_035451_s4.bc2163.unmapped.bam", "sample_name": "m84036_250809_035451_s4.bc2163"}
2025-09-15 20:22:02.841 wdl.w:ptcp.t:call-pbmm2_align_hifi-43 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 8, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-43/_singularity_tmpdir_7o57iac3"
2025-09-15 20:22:02.842 wdl.w:ptcp.t:call-pbmm2_align_hifi-43 INFO Slurm invocation: srun --job-name call-pbmm2_align_hifi-43 --partition compute,compute9 --cpus-per-task 64 --mem 61035M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-43/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-43/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-43/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-43/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0044_m84036_250809_035451_s4.bc2140.unmapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0044_m84036_250809_035451_s4.bc2140.unmapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-43/_singularity_tmpdir_7o57iac3/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-43/_singularity_tmpdir_7o57iac3/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:22:02.845 wdl.w:ptcp.t:call-pbmm2_align_hifi-40 NOTICE slurm_singularity run :: pid: 1197267, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-40/slurm_singularity.log.txt"
2025-09-15 20:22:02.846 wdl.w:ptcp.t:call-pbmm2_align_hifi-64 NOTICE task setup :: name: "pbmm2_align_hifi", source: "./common.wdl", line: 170, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-64", thread: 140609260066368
2025-09-15 20:22:02.846 wdl.w:ptcp.t:call-pbmm2_align_hifi-41 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 8, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-41/_singularity_tmpdir_8nic4qjx"
2025-09-15 20:22:02.846 wdl.w:ptcp.t:call-pbmm2_align_hifi-41 INFO Slurm invocation: srun --job-name call-pbmm2_align_hifi-41 --partition compute,compute9 --cpus-per-task 64 --mem 61035M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-41/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-41/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-41/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-41/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0042_m84036_250809_035451_s4.bc2138.unmapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0042_m84036_250809_035451_s4.bc2138.unmapped.bam:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-41/_singularity_tmpdir_8nic4qjx/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-41/_singularity_tmpdir_8nic4qjx/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:22:02.848 wdl.w:ptcp.t:call-pbmm2_align_hifi-46 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 8, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-46/_singularity_tmpdir_l671qv2l"
2025-09-15 20:22:02.850 wdl.w:ptcp.t:call-pbmm2_align_hifi-62 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:22:02.852 wdl.w:ptcp.t:call-pbmm2_align_hifi-46 INFO Slurm invocation: srun --job-name call-pbmm2_align_hifi-46 --partition compute,compute9 --cpus-per-task 64 --mem 61035M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-46/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-46/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-46/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-46/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0047_m84036_250809_035451_s4.bc2143.unmapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0047_m84036_250809_035451_s4.bc2143.unmapped.bam:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-46/_singularity_tmpdir_l671qv2l/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-46/_singularity_tmpdir_l671qv2l/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:22:02.852 wdl.w:ptcp.t:call-pbmm2_align_hifi-62 INFO input :: name: "log_level", value: "INFO"
2025-09-15 20:22:02.852 wdl.w:ptcp.t:call-pbmm2_align_hifi-62 INFO input :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2159.mapped"
2025-09-15 20:22:02.852 wdl.w:ptcp.t:call-pbmm2_align_hifi-62 INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:22:02.852 wdl.w:ptcp.t:call-pbmm2_align_hifi-62 INFO input :: name: "unmapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0063_m84036_250809_035451_s4.bc2159.unmapped.bam"
2025-09-15 20:22:02.852 wdl.w:ptcp.t:call-pbmm2_align_hifi-62 INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2159"
2025-09-15 20:22:02.855 wdl.w:ptcp NOTICE ready :: job: "call-pbmm2_align_hifi-67", callee: "pbmm2_align_hifi"
2025-09-15 20:22:02.856 wdl.w:ptcp.t:call-pbmm2_align_hifi-62 INFO eval :: name: "threads", value: 64
2025-09-15 20:22:02.856 wdl.w:ptcp INFO input :: job: "call-pbmm2_align_hifi-67", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "log_level": "INFO", "out_prefix": "m84036_250809_035451_s4.bc2164.mapped", "ref_fasta": "/meta/refs/hg38.fa", "unmapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0068_m84036_250809_035451_s4.bc2164.unmapped.bam", "sample_name": "m84036_250809_035451_s4.bc2164"}
2025-09-15 20:22:02.856 wdl.w:ptcp.t:call-pbmm2_align_hifi-44 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 8, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-44/_singularity_tmpdir_vekzl52c"
2025-09-15 20:22:02.856 wdl.w:ptcp.t:call-pbmm2_align_hifi-62 INFO eval :: name: "mem_gb", value: 64
2025-09-15 20:22:02.857 wdl.w:ptcp.t:call-pbmm2_align_hifi-44 INFO Slurm invocation: srun --job-name call-pbmm2_align_hifi-44 --partition compute,compute9 --cpus-per-task 64 --mem 61035M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-44/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-44/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-44/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-44/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0045_m84036_250809_035451_s4.bc2141.unmapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0045_m84036_250809_035451_s4.bc2141.unmapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-44/_singularity_tmpdir_vekzl52c/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-44/_singularity_tmpdir_vekzl52c/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:22:02.857 wdl.w:ptcp.t:call-pbmm2_align_hifi-62 INFO eval :: name: "disk_size", value: 30
2025-09-15 20:22:02.860 wdl.w:ptcp.t:call-pbmm2_align_hifi-62 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 64, memory_reservation: 64000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:22:02.860 wdl.w:ptcp.t:call-pbmm2_align_hifi-62 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:22:02.860 wdl.w:ptcp.t:call-pbmm2_align_hifi-62 INFO provisioned :: seconds_waited: 0, cpu: 64, mem_bytes: 64000000000
2025-09-15 20:22:02.861 wdl.w:ptcp.t:call-pbmm2_align_hifi-62 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:22:02.862 wdl.w:ptcp NOTICE ready :: job: "call-pbmm2_align_hifi-68", callee: "pbmm2_align_hifi"
2025-09-15 20:22:02.862 wdl.w:ptcp INFO input :: job: "call-pbmm2_align_hifi-68", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "log_level": "INFO", "out_prefix": "m84036_250809_035451_s4.bc2165.mapped", "ref_fasta": "/meta/refs/hg38.fa", "unmapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0069_m84036_250809_035451_s4.bc2165.unmapped.bam", "sample_name": "m84036_250809_035451_s4.bc2165"}
2025-09-15 20:22:02.863 wdl.w:ptcp.t:call-pbmm2_align_hifi-65 NOTICE task setup :: name: "pbmm2_align_hifi", source: "./common.wdl", line: 170, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-65", thread: 140608773551680
2025-09-15 20:22:02.863 wdl.w:ptcp.t:call-pbmm2_align_hifi-45 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 8, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-45/_singularity_tmpdir_4vlzf0jf"
2025-09-15 20:22:02.864 wdl.w:ptcp.t:call-pbmm2_align_hifi-45 INFO Slurm invocation: srun --job-name call-pbmm2_align_hifi-45 --partition compute,compute9 --cpus-per-task 64 --mem 61035M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-45/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-45/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-45/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-45/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0046_m84036_250809_035451_s4.bc2142.unmapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0046_m84036_250809_035451_s4.bc2142.unmapped.bam:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-45/_singularity_tmpdir_4vlzf0jf/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-45/_singularity_tmpdir_4vlzf0jf/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:22:02.865 wdl.w:ptcp.t:call-pbmm2_align_hifi-47 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 8, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-47/_singularity_tmpdir_fjmdb7dw"
2025-09-15 20:22:02.867 wdl.w:ptcp.t:call-pbmm2_align_hifi-47 INFO Slurm invocation: srun --job-name call-pbmm2_align_hifi-47 --partition compute,compute9 --cpus-per-task 64 --mem 61035M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-47/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-47/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-47/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-47/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0048_m84036_250809_035451_s4.bc2144.unmapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0048_m84036_250809_035451_s4.bc2144.unmapped.bam:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-47/_singularity_tmpdir_fjmdb7dw/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-47/_singularity_tmpdir_fjmdb7dw/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:22:02.868 wdl.w:ptcp.t:call-pbmm2_align_hifi-39 NOTICE slurm_singularity run :: pid: 1197272, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-39/slurm_singularity.log.txt"
2025-09-15 20:22:02.869 wdl.w:ptcp NOTICE ready :: job: "call-pbmm2_align_hifi-69", callee: "pbmm2_align_hifi"
2025-09-15 20:22:02.869 wdl.w:ptcp INFO input :: job: "call-pbmm2_align_hifi-69", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "log_level": "INFO", "out_prefix": "m84036_250809_035451_s4.bc2166.mapped", "ref_fasta": "/meta/refs/hg38.fa", "unmapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0070_m84036_250809_035451_s4.bc2166.unmapped.bam", "sample_name": "m84036_250809_035451_s4.bc2166"}
2025-09-15 20:22:02.873 wdl.w:ptcp.t:call-pbmm2_align_hifi-63 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:22:02.873 wdl.w:ptcp.t:call-pbmm2_align_hifi-63 INFO input :: name: "log_level", value: "INFO"
2025-09-15 20:22:02.873 wdl.w:ptcp.t:call-pbmm2_align_hifi-63 INFO input :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2160.mapped"
2025-09-15 20:22:02.873 wdl.w:ptcp.t:call-pbmm2_align_hifi-63 INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:22:02.873 wdl.w:ptcp.t:call-pbmm2_align_hifi-63 INFO input :: name: "unmapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0064_m84036_250809_035451_s4.bc2160.unmapped.bam"
2025-09-15 20:22:02.873 wdl.w:ptcp.t:call-pbmm2_align_hifi-63 INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2160"
2025-09-15 20:22:02.874 wdl.w:ptcp.t:call-pbmm2_align_hifi-63 INFO eval :: name: "threads", value: 64
2025-09-15 20:22:02.874 wdl.w:ptcp.t:call-pbmm2_align_hifi-63 INFO eval :: name: "mem_gb", value: 64
2025-09-15 20:22:02.874 wdl.w:ptcp.t:call-pbmm2_align_hifi-63 INFO eval :: name: "disk_size", value: 30
2025-09-15 20:22:02.875 wdl.w:ptcp.t:call-pbmm2_align_hifi-44 NOTICE slurm_singularity run :: pid: 1197284, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-44/slurm_singularity.log.txt"
2025-09-15 20:22:02.876 wdl.w:ptcp.t:call-pbmm2_align_hifi-46 NOTICE slurm_singularity run :: pid: 1197281, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-46/slurm_singularity.log.txt"
2025-09-15 20:22:02.876 wdl.w:ptcp.t:call-pbmm2_align_hifi-66 NOTICE task setup :: name: "pbmm2_align_hifi", source: "./common.wdl", line: 170, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-66", thread: 140608765158976
2025-09-15 20:22:02.876 wdl.w:ptcp.t:call-pbmm2_align_hifi-41 NOTICE slurm_singularity run :: pid: 1197280, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-41/slurm_singularity.log.txt"
2025-09-15 20:22:02.876 wdl.w:ptcp.t:call-pbmm2_align_hifi-43 NOTICE slurm_singularity run :: pid: 1197279, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-43/slurm_singularity.log.txt"
2025-09-15 20:22:02.876 wdl.w:ptcp.t:call-pbmm2_align_hifi-42 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 8, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-42/_singularity_tmpdir_caub76mu"
2025-09-15 20:22:02.877 wdl.w:ptcp.t:call-pbmm2_align_hifi-47 NOTICE slurm_singularity run :: pid: 1197287, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-47/slurm_singularity.log.txt"
2025-09-15 20:22:02.876 wdl.w:ptcp.t:call-pbmm2_align_hifi-45 NOTICE slurm_singularity run :: pid: 1197286, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-45/slurm_singularity.log.txt"
2025-09-15 20:22:02.877 wdl.w:ptcp.t:call-pbmm2_align_hifi-63 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 64, memory_reservation: 64000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:22:02.879 wdl.w:ptcp.t:call-pbmm2_align_hifi-42 INFO Slurm invocation: srun --job-name call-pbmm2_align_hifi-42 --partition compute,compute9 --cpus-per-task 64 --mem 61035M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-42/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-42/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-42/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-42/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0043_m84036_250809_035451_s4.bc2139.unmapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0043_m84036_250809_035451_s4.bc2139.unmapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-42/_singularity_tmpdir_caub76mu/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-42/_singularity_tmpdir_caub76mu/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:22:02.879 wdl.w:ptcp.t:call-pbmm2_align_hifi-63 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:22:02.880 wdl.w:ptcp.t:call-pbmm2_align_hifi-63 INFO provisioned :: seconds_waited: 0, cpu: 64, mem_bytes: 64000000000
2025-09-15 20:22:02.882 wdl.w:ptcp.t:call-pbmm2_align_hifi-63 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:22:02.884 wdl.w:ptcp.t:call-pbmm2_align_hifi-50 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 8, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-50/_singularity_tmpdir_0p3_98vq"
2025-09-15 20:22:02.884 wdl.w:ptcp.t:call-pbmm2_align_hifi-50 INFO Slurm invocation: srun --job-name call-pbmm2_align_hifi-50 --partition compute,compute9 --cpus-per-task 64 --mem 61035M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-50/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-50/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-50/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-50/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0051_m84036_250809_035451_s4.bc2147.unmapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0051_m84036_250809_035451_s4.bc2147.unmapped.bam:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-50/_singularity_tmpdir_0p3_98vq/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-50/_singularity_tmpdir_0p3_98vq/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:22:02.887 wdl.w:ptcp.t:call-pbmm2_align_hifi-49 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 8, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-49/_singularity_tmpdir_97popwyh"
2025-09-15 20:22:02.887 wdl.w:ptcp.t:call-pbmm2_align_hifi-67 NOTICE task setup :: name: "pbmm2_align_hifi", source: "./common.wdl", line: 170, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-67", thread: 140608756766272
2025-09-15 20:22:02.887 wdl.w:ptcp.t:call-pbmm2_align_hifi-49 INFO Slurm invocation: srun --job-name call-pbmm2_align_hifi-49 --partition compute,compute9 --cpus-per-task 64 --mem 61035M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-49/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-49/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-49/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-49/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0050_m84036_250809_035451_s4.bc2146.unmapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0050_m84036_250809_035451_s4.bc2146.unmapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-49/_singularity_tmpdir_97popwyh/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-49/_singularity_tmpdir_97popwyh/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:22:02.887 wdl.w:ptcp.t:call-pbmm2_align_hifi-51 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 8, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-51/_singularity_tmpdir_8loqdf2i"
2025-09-15 20:22:02.888 wdl.w:ptcp.t:call-pbmm2_align_hifi-51 INFO Slurm invocation: srun --job-name call-pbmm2_align_hifi-51 --partition compute,compute9 --cpus-per-task 64 --mem 61035M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-51/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-51/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-51/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-51/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0052_m84036_250809_035451_s4.bc2148.unmapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0052_m84036_250809_035451_s4.bc2148.unmapped.bam:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-51/_singularity_tmpdir_8loqdf2i/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-51/_singularity_tmpdir_8loqdf2i/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:22:02.890 wdl.w:ptcp NOTICE ready :: job: "call-pbmm2_align_hifi-70", callee: "pbmm2_align_hifi"
2025-09-15 20:22:02.890 wdl.w:ptcp.t:call-pbmm2_align_hifi-64 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:22:02.892 wdl.w:ptcp INFO input :: job: "call-pbmm2_align_hifi-70", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "log_level": "INFO", "out_prefix": "m84036_250809_035451_s4.bc2167.mapped", "ref_fasta": "/meta/refs/hg38.fa", "unmapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0071_m84036_250809_035451_s4.bc2167.unmapped.bam", "sample_name": "m84036_250809_035451_s4.bc2167"}
2025-09-15 20:22:02.894 wdl.w:ptcp.t:call-pbmm2_align_hifi-48 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 8, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-48/_singularity_tmpdir_tda3waxe"
2025-09-15 20:22:02.894 wdl.w:ptcp.t:call-pbmm2_align_hifi-64 INFO input :: name: "log_level", value: "INFO"
2025-09-15 20:22:02.894 wdl.w:ptcp.t:call-pbmm2_align_hifi-64 INFO input :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2161.mapped"
2025-09-15 20:22:02.895 wdl.w:ptcp.t:call-pbmm2_align_hifi-64 INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:22:02.895 wdl.w:ptcp.t:call-pbmm2_align_hifi-64 INFO input :: name: "unmapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0065_m84036_250809_035451_s4.bc2161.unmapped.bam"
2025-09-15 20:22:02.895 wdl.w:ptcp.t:call-pbmm2_align_hifi-64 INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2161"
2025-09-15 20:22:02.895 wdl.w:ptcp.t:call-pbmm2_align_hifi-64 INFO eval :: name: "threads", value: 64
2025-09-15 20:22:02.895 wdl.w:ptcp.t:call-pbmm2_align_hifi-64 INFO eval :: name: "mem_gb", value: 64
2025-09-15 20:22:02.895 wdl.w:ptcp.t:call-pbmm2_align_hifi-64 INFO eval :: name: "disk_size", value: 30
2025-09-15 20:22:02.896 wdl.w:ptcp.t:call-pbmm2_align_hifi-64 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 64, memory_reservation: 64000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:22:02.896 wdl.w:ptcp.t:call-pbmm2_align_hifi-64 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:22:02.894 wdl.w:ptcp.t:call-pbmm2_align_hifi-48 INFO Slurm invocation: srun --job-name call-pbmm2_align_hifi-48 --partition compute,compute9 --cpus-per-task 64 --mem 61035M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-48/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-48/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-48/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-48/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0049_m84036_250809_035451_s4.bc2145.unmapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0049_m84036_250809_035451_s4.bc2145.unmapped.bam:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-48/_singularity_tmpdir_tda3waxe/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-48/_singularity_tmpdir_tda3waxe/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:22:02.896 wdl.w:ptcp.t:call-pbmm2_align_hifi-64 INFO provisioned :: seconds_waited: 0, cpu: 64, mem_bytes: 64000000000
2025-09-15 20:22:02.897 wdl.w:ptcp NOTICE ready :: job: "call-pbmm2_align_hifi-71", callee: "pbmm2_align_hifi"
2025-09-15 20:22:02.897 wdl.w:ptcp.t:call-pbmm2_align_hifi-64 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:22:02.898 wdl.w:ptcp.t:call-pbmm2_align_hifi-65 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:22:02.899 wdl.w:ptcp INFO input :: job: "call-pbmm2_align_hifi-71", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "log_level": "INFO", "out_prefix": "m84036_250809_035451_s4.bc2168.mapped", "ref_fasta": "/meta/refs/hg38.fa", "unmapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0072_m84036_250809_035451_s4.bc2168.unmapped.bam", "sample_name": "m84036_250809_035451_s4.bc2168"}
2025-09-15 20:22:02.899 wdl.w:ptcp.t:call-pbmm2_align_hifi-65 INFO input :: name: "log_level", value: "INFO"
2025-09-15 20:22:02.899 wdl.w:ptcp.t:call-pbmm2_align_hifi-65 INFO input :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2162.mapped"
2025-09-15 20:22:02.899 wdl.w:ptcp.t:call-pbmm2_align_hifi-65 INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:22:02.899 wdl.w:ptcp.t:call-pbmm2_align_hifi-65 INFO input :: name: "unmapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0066_m84036_250809_035451_s4.bc2162.unmapped.bam"
2025-09-15 20:22:02.899 wdl.w:ptcp.t:call-pbmm2_align_hifi-65 INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2162"
2025-09-15 20:22:02.899 wdl.w:ptcp.t:call-pbmm2_align_hifi-65 INFO eval :: name: "threads", value: 64
2025-09-15 20:22:02.900 wdl.w:ptcp.t:call-pbmm2_align_hifi-65 INFO eval :: name: "mem_gb", value: 64
2025-09-15 20:22:02.900 wdl.w:ptcp.t:call-pbmm2_align_hifi-65 INFO eval :: name: "disk_size", value: 30
2025-09-15 20:22:02.900 wdl.w:ptcp.t:call-pbmm2_align_hifi-65 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 64, memory_reservation: 64000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:22:02.900 wdl.w:ptcp.t:call-pbmm2_align_hifi-65 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:22:02.900 wdl.w:ptcp.t:call-pbmm2_align_hifi-65 INFO provisioned :: seconds_waited: 0, cpu: 64, mem_bytes: 64000000000
2025-09-15 20:22:02.901 wdl.w:ptcp.t:call-pbmm2_align_hifi-65 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:22:02.901 wdl.w:ptcp.t:call-pbmm2_align_hifi-68 NOTICE task setup :: name: "pbmm2_align_hifi", source: "./common.wdl", line: 170, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-68", thread: 140608748373568
2025-09-15 20:22:02.901 wdl.w:ptcp.t:call-pbmm2_align_hifi-53 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 8, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-53/_singularity_tmpdir_11zylcn_"
2025-09-15 20:22:02.901 wdl.w:ptcp.t:call-pbmm2_align_hifi-53 INFO Slurm invocation: srun --job-name call-pbmm2_align_hifi-53 --partition compute,compute9 --cpus-per-task 64 --mem 61035M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-53/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-53/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-53/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-53/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0054_m84036_250809_035451_s4.bc2150.unmapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0054_m84036_250809_035451_s4.bc2150.unmapped.bam:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-53/_singularity_tmpdir_11zylcn_/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-53/_singularity_tmpdir_11zylcn_/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:22:02.905 wdl.w:ptcp NOTICE ready :: job: "call-pbmm2_align_hifi-72", callee: "pbmm2_align_hifi"
2025-09-15 20:22:02.905 wdl.w:ptcp INFO input :: job: "call-pbmm2_align_hifi-72", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "log_level": "INFO", "out_prefix": "m84036_250809_035451_s4.bc2169.mapped", "ref_fasta": "/meta/refs/hg38.fa", "unmapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0073_m84036_250809_035451_s4.bc2169.unmapped.bam", "sample_name": "m84036_250809_035451_s4.bc2169"}
2025-09-15 20:22:02.907 wdl.w:ptcp.t:call-pbmm2_align_hifi-52 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 8, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-52/_singularity_tmpdir_3uadnie1"
2025-09-15 20:22:02.907 wdl.w:ptcp NOTICE ready :: job: "call-pbmm2_align_hifi-73", callee: "pbmm2_align_hifi"
2025-09-15 20:22:02.907 wdl.w:ptcp.t:call-pbmm2_align_hifi-52 INFO Slurm invocation: srun --job-name call-pbmm2_align_hifi-52 --partition compute,compute9 --cpus-per-task 64 --mem 61035M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-52/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-52/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-52/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-52/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0053_m84036_250809_035451_s4.bc2149.unmapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0053_m84036_250809_035451_s4.bc2149.unmapped.bam:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-52/_singularity_tmpdir_3uadnie1/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-52/_singularity_tmpdir_3uadnie1/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:22:02.908 wdl.w:ptcp.t:call-pbmm2_align_hifi-69 NOTICE task setup :: name: "pbmm2_align_hifi", source: "./common.wdl", line: 170, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-69", thread: 140608739980864
2025-09-15 20:22:02.909 wdl.w:ptcp INFO input :: job: "call-pbmm2_align_hifi-73", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "log_level": "INFO", "out_prefix": "m84036_250809_035451_s4.bc2170.mapped", "ref_fasta": "/meta/refs/hg38.fa", "unmapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0074_m84036_250809_035451_s4.bc2170.unmapped.bam", "sample_name": "m84036_250809_035451_s4.bc2170"}
2025-09-15 20:22:02.916 wdl.w:ptcp NOTICE ready :: job: "call-pbmm2_align_hifi-74", callee: "pbmm2_align_hifi"
2025-09-15 20:22:02.916 wdl.w:ptcp INFO input :: job: "call-pbmm2_align_hifi-74", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "log_level": "INFO", "out_prefix": "m84036_250809_035451_s4.bc2171.mapped", "ref_fasta": "/meta/refs/hg38.fa", "unmapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0075_m84036_250809_035451_s4.bc2171.unmapped.bam", "sample_name": "m84036_250809_035451_s4.bc2171"}
2025-09-15 20:22:02.917 wdl.w:ptcp.t:call-pbmm2_align_hifi-70 NOTICE task setup :: name: "pbmm2_align_hifi", source: "./common.wdl", line: 170, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-70", thread: 140608731588160
2025-09-15 20:22:02.920 wdl.w:ptcp NOTICE ready :: job: "call-pbmm2_align_hifi-75", callee: "pbmm2_align_hifi"
2025-09-15 20:22:02.920 wdl.w:ptcp.t:call-pbmm2_align_hifi-56 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 8, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-56/_singularity_tmpdir_id4rrti1"
2025-09-15 20:22:02.920 wdl.w:ptcp INFO input :: job: "call-pbmm2_align_hifi-75", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "log_level": "INFO", "out_prefix": "m84036_250809_035451_s4.bc2172.mapped", "ref_fasta": "/meta/refs/hg38.fa", "unmapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0076_m84036_250809_035451_s4.bc2172.unmapped.bam", "sample_name": "m84036_250809_035451_s4.bc2172"}
2025-09-15 20:22:02.921 wdl.w:ptcp.t:call-pbmm2_align_hifi-56 INFO Slurm invocation: srun --job-name call-pbmm2_align_hifi-56 --partition compute,compute9 --cpus-per-task 64 --mem 61035M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-56/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-56/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-56/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-56/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0057_m84036_250809_035451_s4.bc2153.unmapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0057_m84036_250809_035451_s4.bc2153.unmapped.bam:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-56/_singularity_tmpdir_id4rrti1/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-56/_singularity_tmpdir_id4rrti1/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:22:02.922 wdl.w:ptcp.t:call-pbmm2_align_hifi-71 NOTICE task setup :: name: "pbmm2_align_hifi", source: "./common.wdl", line: 170, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-71", thread: 140608723195456
2025-09-15 20:22:02.922 wdl.w:ptcp.t:call-pbmm2_align_hifi-57 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 8, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-57/_singularity_tmpdir_s1_y_et2"
2025-09-15 20:22:02.924 wdl.w:ptcp.t:call-pbmm2_align_hifi-57 INFO Slurm invocation: srun --job-name call-pbmm2_align_hifi-57 --partition compute,compute9 --cpus-per-task 64 --mem 61035M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-57/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-57/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-57/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-57/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0058_m84036_250809_035451_s4.bc2154.unmapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0058_m84036_250809_035451_s4.bc2154.unmapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-57/_singularity_tmpdir_s1_y_et2/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-57/_singularity_tmpdir_s1_y_et2/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:22:02.927 wdl.w:ptcp.t:call-pbmm2_align_hifi-66 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:22:02.927 wdl.w:ptcp.t:call-pbmm2_align_hifi-66 INFO input :: name: "log_level", value: "INFO"
2025-09-15 20:22:02.927 wdl.w:ptcp.t:call-pbmm2_align_hifi-66 INFO input :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2163.mapped"
2025-09-15 20:22:02.927 wdl.w:ptcp.t:call-pbmm2_align_hifi-66 INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:22:02.927 wdl.w:ptcp.t:call-pbmm2_align_hifi-66 INFO input :: name: "unmapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0067_m84036_250809_035451_s4.bc2163.unmapped.bam"
2025-09-15 20:22:02.928 wdl.w:ptcp.t:call-pbmm2_align_hifi-66 INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2163"
2025-09-15 20:22:02.928 wdl.w:ptcp.t:call-pbmm2_align_hifi-66 INFO eval :: name: "threads", value: 64
2025-09-15 20:22:02.928 wdl.w:ptcp.t:call-pbmm2_align_hifi-66 INFO eval :: name: "mem_gb", value: 64
2025-09-15 20:22:02.928 wdl.w:ptcp.t:call-pbmm2_align_hifi-66 INFO eval :: name: "disk_size", value: 30
2025-09-15 20:22:02.929 wdl.w:ptcp.t:call-pbmm2_align_hifi-66 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 64, memory_reservation: 64000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:22:02.929 wdl.w:ptcp.t:call-pbmm2_align_hifi-66 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:22:02.929 wdl.w:ptcp.t:call-pbmm2_align_hifi-67 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:22:02.929 wdl.w:ptcp.t:call-pbmm2_align_hifi-67 INFO input :: name: "log_level", value: "INFO"
2025-09-15 20:22:02.929 wdl.w:ptcp.t:call-pbmm2_align_hifi-67 INFO input :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2164.mapped"
2025-09-15 20:22:02.930 wdl.w:ptcp.t:call-pbmm2_align_hifi-66 INFO provisioned :: seconds_waited: 0, cpu: 64, mem_bytes: 64000000000
2025-09-15 20:22:02.930 wdl.w:ptcp.t:call-pbmm2_align_hifi-54 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 8, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-54/_singularity_tmpdir_x4kxp8kn"
2025-09-15 20:22:02.930 wdl.w:ptcp.t:call-pbmm2_align_hifi-67 INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:22:02.930 wdl.w:ptcp.t:call-pbmm2_align_hifi-72 NOTICE task setup :: name: "pbmm2_align_hifi", source: "./common.wdl", line: 170, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-72", thread: 140608236680768
2025-09-15 20:22:02.930 wdl.w:ptcp.t:call-pbmm2_align_hifi-66 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:22:02.930 wdl.w:ptcp.t:call-pbmm2_align_hifi-54 INFO Slurm invocation: srun --job-name call-pbmm2_align_hifi-54 --partition compute,compute9 --cpus-per-task 64 --mem 61035M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-54/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-54/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-54/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-54/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0055_m84036_250809_035451_s4.bc2151.unmapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0055_m84036_250809_035451_s4.bc2151.unmapped.bam:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-54/_singularity_tmpdir_x4kxp8kn/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-54/_singularity_tmpdir_x4kxp8kn/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:22:02.931 wdl.w:ptcp.t:call-pbmm2_align_hifi-67 INFO input :: name: "unmapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0068_m84036_250809_035451_s4.bc2164.unmapped.bam"
2025-09-15 20:22:02.932 wdl.w:ptcp NOTICE ready :: job: "call-pbmm2_align_hifi-76", callee: "pbmm2_align_hifi"
2025-09-15 20:22:02.932 wdl.w:ptcp.t:call-pbmm2_align_hifi-67 INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2164"
2025-09-15 20:22:02.932 wdl.w:ptcp INFO input :: job: "call-pbmm2_align_hifi-76", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "log_level": "INFO", "out_prefix": "m84036_250809_035451_s4.bc2173.mapped", "ref_fasta": "/meta/refs/hg38.fa", "unmapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0077_m84036_250809_035451_s4.bc2173.unmapped.bam", "sample_name": "m84036_250809_035451_s4.bc2173"}
2025-09-15 20:22:02.933 wdl.w:ptcp.t:call-pbmm2_align_hifi-67 INFO eval :: name: "threads", value: 64
2025-09-15 20:22:02.935 wdl.w:ptcp.t:call-pbmm2_align_hifi-68 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:22:02.937 wdl.w:ptcp.t:call-pbmm2_align_hifi-67 INFO eval :: name: "mem_gb", value: 64
2025-09-15 20:22:02.937 wdl.w:ptcp.t:call-pbmm2_align_hifi-68 INFO input :: name: "log_level", value: "INFO"
2025-09-15 20:22:02.937 wdl.w:ptcp.t:call-pbmm2_align_hifi-68 INFO input :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2165.mapped"
2025-09-15 20:22:02.937 wdl.w:ptcp.t:call-pbmm2_align_hifi-68 INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:22:02.937 wdl.w:ptcp.t:call-pbmm2_align_hifi-67 INFO eval :: name: "disk_size", value: 30
2025-09-15 20:22:02.938 wdl.w:ptcp.t:call-pbmm2_align_hifi-68 INFO input :: name: "unmapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0069_m84036_250809_035451_s4.bc2165.unmapped.bam"
2025-09-15 20:22:02.939 wdl.w:ptcp.t:call-pbmm2_align_hifi-68 INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2165"
2025-09-15 20:22:02.939 wdl.w:ptcp.t:call-pbmm2_align_hifi-67 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 64, memory_reservation: 64000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:22:02.939 wdl.w:ptcp.t:call-pbmm2_align_hifi-68 INFO eval :: name: "threads", value: 64
2025-09-15 20:22:02.939 wdl.w:ptcp.t:call-pbmm2_align_hifi-67 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:22:02.940 wdl.w:ptcp.t:call-pbmm2_align_hifi-68 INFO eval :: name: "mem_gb", value: 64
2025-09-15 20:22:02.940 wdl.w:ptcp NOTICE ready :: job: "call-pbmm2_align_hifi-77", callee: "pbmm2_align_hifi"
2025-09-15 20:22:02.941 wdl.w:ptcp.t:call-pbmm2_align_hifi-73 NOTICE task setup :: name: "pbmm2_align_hifi", source: "./common.wdl", line: 170, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-73", thread: 140608228288064
2025-09-15 20:22:02.942 wdl.w:ptcp INFO input :: job: "call-pbmm2_align_hifi-77", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "log_level": "INFO", "out_prefix": "m84036_250809_035451_s4.bc2174.mapped", "ref_fasta": "/meta/refs/hg38.fa", "unmapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0078_m84036_250809_035451_s4.bc2174.unmapped.bam", "sample_name": "m84036_250809_035451_s4.bc2174"}
2025-09-15 20:22:02.942 wdl.w:ptcp.t:call-pbmm2_align_hifi-68 INFO eval :: name: "disk_size", value: 30
2025-09-15 20:22:02.943 wdl.w:ptcp.t:call-pbmm2_align_hifi-74 NOTICE task setup :: name: "pbmm2_align_hifi", source: "./common.wdl", line: 170, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-74", thread: 140608219895360
2025-09-15 20:22:02.943 wdl.w:ptcp.t:call-pbmm2_align_hifi-67 INFO provisioned :: seconds_waited: 0, cpu: 64, mem_bytes: 64000000000
2025-09-15 20:22:02.945 wdl.w:ptcp.t:call-pbmm2_align_hifi-68 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 64, memory_reservation: 64000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:22:02.945 wdl.w:ptcp.t:call-pbmm2_align_hifi-67 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:22:02.945 wdl.w:ptcp.t:call-pbmm2_align_hifi-68 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:22:02.946 wdl.w:ptcp.t:call-pbmm2_align_hifi-68 INFO provisioned :: seconds_waited: 0, cpu: 64, mem_bytes: 64000000000
2025-09-15 20:22:02.946 wdl.w:ptcp.t:call-pbmm2_align_hifi-68 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:22:02.946 wdl.w:ptcp.t:call-pbmm2_align_hifi-69 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:22:02.947 wdl.w:ptcp.t:call-pbmm2_align_hifi-69 INFO input :: name: "log_level", value: "INFO"
2025-09-15 20:22:02.947 wdl.w:ptcp.t:call-pbmm2_align_hifi-69 INFO input :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2166.mapped"
2025-09-15 20:22:02.947 wdl.w:ptcp.t:call-pbmm2_align_hifi-69 INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:22:02.947 wdl.w:ptcp.t:call-pbmm2_align_hifi-69 INFO input :: name: "unmapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0070_m84036_250809_035451_s4.bc2166.unmapped.bam"
2025-09-15 20:22:02.947 wdl.w:ptcp.t:call-pbmm2_align_hifi-69 INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2166"
2025-09-15 20:22:02.947 wdl.w:ptcp.t:call-pbmm2_align_hifi-69 INFO eval :: name: "threads", value: 64
2025-09-15 20:22:02.948 wdl.w:ptcp.t:call-pbmm2_align_hifi-69 INFO eval :: name: "mem_gb", value: 64
2025-09-15 20:22:02.948 wdl.w:ptcp.t:call-pbmm2_align_hifi-69 INFO eval :: name: "disk_size", value: 30
2025-09-15 20:22:02.949 wdl.w:ptcp NOTICE ready :: job: "call-pbmm2_align_hifi-78", callee: "pbmm2_align_hifi"
2025-09-15 20:22:02.950 wdl.w:ptcp.t:call-pbmm2_align_hifi-69 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 64, memory_reservation: 64000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:22:02.950 wdl.w:ptcp.t:call-pbmm2_align_hifi-58 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 8, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-58/_singularity_tmpdir_3x8j3e36"
2025-09-15 20:22:02.950 wdl.w:ptcp INFO input :: job: "call-pbmm2_align_hifi-78", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "log_level": "INFO", "out_prefix": "m84036_250809_035451_s4.bc2175.mapped", "ref_fasta": "/meta/refs/hg38.fa", "unmapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0079_m84036_250809_035451_s4.bc2175.unmapped.bam", "sample_name": "m84036_250809_035451_s4.bc2175"}
2025-09-15 20:22:02.950 wdl.w:ptcp.t:call-pbmm2_align_hifi-55 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 8, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-55/_singularity_tmpdir_5t3cztbd"
2025-09-15 20:22:02.951 wdl.w:ptcp.t:call-pbmm2_align_hifi-51 NOTICE slurm_singularity run :: pid: 1197298, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-51/slurm_singularity.log.txt"
2025-09-15 20:22:02.951 wdl.w:ptcp.t:call-pbmm2_align_hifi-69 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:22:02.951 wdl.w:ptcp.t:call-pbmm2_align_hifi-52 NOTICE slurm_singularity run :: pid: 1197305, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-52/slurm_singularity.log.txt"
2025-09-15 20:22:02.951 wdl.w:ptcp.t:call-pbmm2_align_hifi-58 INFO Slurm invocation: srun --job-name call-pbmm2_align_hifi-58 --partition compute,compute9 --cpus-per-task 64 --mem 61035M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-58/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-58/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-58/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-58/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0059_m84036_250809_035451_s4.bc2155.unmapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0059_m84036_250809_035451_s4.bc2155.unmapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-58/_singularity_tmpdir_3x8j3e36/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-58/_singularity_tmpdir_3x8j3e36/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:22:02.952 wdl.w:ptcp.t:call-pbmm2_align_hifi-55 INFO Slurm invocation: srun --job-name call-pbmm2_align_hifi-55 --partition compute,compute9 --cpus-per-task 64 --mem 61035M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-55/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-55/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-55/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-55/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0056_m84036_250809_035451_s4.bc2152.unmapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0056_m84036_250809_035451_s4.bc2152.unmapped.bam:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-55/_singularity_tmpdir_5t3cztbd/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-55/_singularity_tmpdir_5t3cztbd/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:22:02.953 wdl.w:ptcp.t:call-pbmm2_align_hifi-75 NOTICE task setup :: name: "pbmm2_align_hifi", source: "./common.wdl", line: 170, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-75", thread: 140608211502656
2025-09-15 20:22:02.956 wdl.w:ptcp.t:call-pbmm2_align_hifi-42 NOTICE slurm_singularity run :: pid: 1197293, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-42/slurm_singularity.log.txt"
2025-09-15 20:22:02.955 wdl.w:ptcp.t:call-pbmm2_align_hifi-50 NOTICE slurm_singularity run :: pid: 1197296, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-50/slurm_singularity.log.txt"
2025-09-15 20:22:02.956 wdl.w:ptcp NOTICE ready :: job: "call-pbmm2_align_hifi-79", callee: "pbmm2_align_hifi"
2025-09-15 20:22:02.956 wdl.w:ptcp.t:call-pbmm2_align_hifi-49 NOTICE slurm_singularity run :: pid: 1197297, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-49/slurm_singularity.log.txt"
2025-09-15 20:22:02.957 wdl.w:ptcp.t:call-pbmm2_align_hifi-69 INFO provisioned :: seconds_waited: 0, cpu: 64, mem_bytes: 64000000000
2025-09-15 20:22:02.957 wdl.w:ptcp.t:call-pbmm2_align_hifi-48 NOTICE slurm_singularity run :: pid: 1197301, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-48/slurm_singularity.log.txt"
2025-09-15 20:22:02.958 wdl.w:ptcp.t:call-pbmm2_align_hifi-59 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 8, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-59/_singularity_tmpdir_ydssp54n"
2025-09-15 20:22:02.960 wdl.w:ptcp INFO input :: job: "call-pbmm2_align_hifi-79", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "log_level": "INFO", "out_prefix": "m84036_250809_035451_s4.bc2176.mapped", "ref_fasta": "/meta/refs/hg38.fa", "unmapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0080_m84036_250809_035451_s4.bc2176.unmapped.bam", "sample_name": "m84036_250809_035451_s4.bc2176"}
2025-09-15 20:22:02.959 wdl.w:ptcp.t:call-pbmm2_align_hifi-53 NOTICE slurm_singularity run :: pid: 1197302, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-53/slurm_singularity.log.txt"
2025-09-15 20:22:02.960 wdl.w:ptcp.t:call-pbmm2_align_hifi-70 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:22:02.961 wdl.w:ptcp.t:call-pbmm2_align_hifi-76 NOTICE task setup :: name: "pbmm2_align_hifi", source: "./common.wdl", line: 170, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-76", thread: 140608203109952
2025-09-15 20:22:02.962 wdl.w:ptcp.t:call-pbmm2_align_hifi-69 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:22:02.962 wdl.w:ptcp.t:call-pbmm2_align_hifi-59 INFO Slurm invocation: srun --job-name call-pbmm2_align_hifi-59 --partition compute,compute9 --cpus-per-task 64 --mem 61035M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-59/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-59/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-59/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-59/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0060_m84036_250809_035451_s4.bc2156.unmapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0060_m84036_250809_035451_s4.bc2156.unmapped.bam:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-59/_singularity_tmpdir_ydssp54n/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-59/_singularity_tmpdir_ydssp54n/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:22:02.964 wdl.w:ptcp.t:call-pbmm2_align_hifi-77 NOTICE task setup :: name: "pbmm2_align_hifi", source: "./common.wdl", line: 170, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-77", thread: 140608194717248
2025-09-15 20:22:02.965 wdl.w:ptcp.t:call-pbmm2_align_hifi-70 INFO input :: name: "log_level", value: "INFO"
2025-09-15 20:22:02.968 wdl.w:ptcp.t:call-pbmm2_align_hifi-70 INFO input :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2167.mapped"
2025-09-15 20:22:02.970 wdl.w:ptcp.t:call-pbmm2_align_hifi-70 INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:22:02.970 wdl.w:ptcp.t:call-pbmm2_align_hifi-70 INFO input :: name: "unmapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0071_m84036_250809_035451_s4.bc2167.unmapped.bam"
2025-09-15 20:22:02.971 wdl.w:ptcp.t:call-pbmm2_align_hifi-70 INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2167"
2025-09-15 20:22:02.972 wdl.w:ptcp NOTICE ready :: job: "call-pbmm2_align_hifi-80", callee: "pbmm2_align_hifi"
2025-09-15 20:22:02.972 wdl.w:ptcp.t:call-pbmm2_align_hifi-70 INFO eval :: name: "threads", value: 64
2025-09-15 20:22:02.973 wdl.w:ptcp INFO input :: job: "call-pbmm2_align_hifi-80", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "log_level": "INFO", "out_prefix": "m84036_250809_035451_s4.bc2177.mapped", "ref_fasta": "/meta/refs/hg38.fa", "unmapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0081_m84036_250809_035451_s4.bc2177.unmapped.bam", "sample_name": "m84036_250809_035451_s4.bc2177"}
2025-09-15 20:22:02.972 wdl.w:ptcp.t:call-pbmm2_align_hifi-60 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 8, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-60/_singularity_tmpdir_ynzwraa3"
2025-09-15 20:22:02.974 wdl.w:ptcp.t:call-pbmm2_align_hifi-70 INFO eval :: name: "mem_gb", value: 64
2025-09-15 20:22:02.974 wdl.w:ptcp.t:call-pbmm2_align_hifi-71 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:22:02.974 wdl.w:ptcp.t:call-pbmm2_align_hifi-78 NOTICE task setup :: name: "pbmm2_align_hifi", source: "./common.wdl", line: 170, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-78", thread: 140608186324544
2025-09-15 20:22:02.975 wdl.w:ptcp.t:call-pbmm2_align_hifi-60 INFO Slurm invocation: srun --job-name call-pbmm2_align_hifi-60 --partition compute,compute9 --cpus-per-task 64 --mem 61035M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-60/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-60/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-60/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-60/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0061_m84036_250809_035451_s4.bc2157.unmapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0061_m84036_250809_035451_s4.bc2157.unmapped.bam:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-60/_singularity_tmpdir_ynzwraa3/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-60/_singularity_tmpdir_ynzwraa3/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:22:02.976 wdl.w:ptcp.t:call-pbmm2_align_hifi-71 INFO input :: name: "log_level", value: "INFO"
2025-09-15 20:22:02.976 wdl.w:ptcp.t:call-pbmm2_align_hifi-70 INFO eval :: name: "disk_size", value: 30
2025-09-15 20:22:02.978 wdl.w:ptcp.t:call-pbmm2_align_hifi-71 INFO input :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2168.mapped"
2025-09-15 20:22:02.979 wdl.w:ptcp.t:call-pbmm2_align_hifi-70 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 64, memory_reservation: 64000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:22:02.979 wdl.w:ptcp.t:call-pbmm2_align_hifi-61 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 8, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-61/_singularity_tmpdir_h9dj78u8"
2025-09-15 20:22:02.980 wdl.w:ptcp.t:call-pbmm2_align_hifi-71 INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:22:02.982 wdl.w:ptcp NOTICE ready :: job: "call-pbmm2_align_hifi-81", callee: "pbmm2_align_hifi"
2025-09-15 20:22:02.982 wdl.w:ptcp.t:call-pbmm2_align_hifi-70 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:22:02.983 wdl.w:ptcp.t:call-pbmm2_align_hifi-61 INFO Slurm invocation: srun --job-name call-pbmm2_align_hifi-61 --partition compute,compute9 --cpus-per-task 64 --mem 61035M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-61/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-61/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-61/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-61/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0062_m84036_250809_035451_s4.bc2158.unmapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0062_m84036_250809_035451_s4.bc2158.unmapped.bam:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-61/_singularity_tmpdir_h9dj78u8/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-61/_singularity_tmpdir_h9dj78u8/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:22:02.983 wdl.w:ptcp INFO input :: job: "call-pbmm2_align_hifi-81", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "log_level": "INFO", "out_prefix": "m84036_250809_035451_s4.bc2178.mapped", "ref_fasta": "/meta/refs/hg38.fa", "unmapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0082_m84036_250809_035451_s4.bc2178.unmapped.bam", "sample_name": "m84036_250809_035451_s4.bc2178"}
2025-09-15 20:22:02.983 wdl.w:ptcp.t:call-pbmm2_align_hifi-71 INFO input :: name: "unmapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0072_m84036_250809_035451_s4.bc2168.unmapped.bam"
2025-09-15 20:22:02.985 wdl.w:ptcp.t:call-pbmm2_align_hifi-79 NOTICE task setup :: name: "pbmm2_align_hifi", source: "./common.wdl", line: 170, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-79", thread: 140607699809856
2025-09-15 20:22:02.985 wdl.w:ptcp.t:call-pbmm2_align_hifi-71 INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2168"
2025-09-15 20:22:02.985 wdl.w:ptcp.t:call-pbmm2_align_hifi-70 INFO provisioned :: seconds_waited: 0, cpu: 64, mem_bytes: 64000000000
2025-09-15 20:22:02.987 wdl.w:ptcp.t:call-pbmm2_align_hifi-72 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:22:02.988 wdl.w:ptcp.t:call-pbmm2_align_hifi-71 INFO eval :: name: "threads", value: 64
2025-09-15 20:22:02.989 wdl.w:ptcp.t:call-pbmm2_align_hifi-70 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:22:02.990 wdl.w:ptcp.t:call-pbmm2_align_hifi-72 INFO input :: name: "log_level", value: "INFO"
2025-09-15 20:22:02.991 wdl.w:ptcp NOTICE ready :: job: "call-pbmm2_align_hifi-82", callee: "pbmm2_align_hifi"
2025-09-15 20:22:02.991 wdl.w:ptcp.t:call-pbmm2_align_hifi-71 INFO eval :: name: "mem_gb", value: 64
2025-09-15 20:22:02.993 wdl.w:ptcp.t:call-pbmm2_align_hifi-72 INFO input :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2169.mapped"
2025-09-15 20:22:02.993 wdl.w:ptcp INFO input :: job: "call-pbmm2_align_hifi-82", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "log_level": "INFO", "out_prefix": "m84036_250809_035451_s4.bc2179.mapped", "ref_fasta": "/meta/refs/hg38.fa", "unmapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0083_m84036_250809_035451_s4.bc2179.unmapped.bam", "sample_name": "m84036_250809_035451_s4.bc2179"}
2025-09-15 20:22:02.993 wdl.w:ptcp.t:call-pbmm2_align_hifi-72 INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:22:02.994 wdl.w:ptcp.t:call-pbmm2_align_hifi-71 INFO eval :: name: "disk_size", value: 30
2025-09-15 20:22:02.994 wdl.w:ptcp.t:call-pbmm2_align_hifi-62 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 8, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-62/_singularity_tmpdir_vlivqv6c"
2025-09-15 20:22:02.995 wdl.w:ptcp.t:call-pbmm2_align_hifi-72 INFO input :: name: "unmapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0073_m84036_250809_035451_s4.bc2169.unmapped.bam"
2025-09-15 20:22:02.995 wdl.w:ptcp.t:call-pbmm2_align_hifi-62 INFO Slurm invocation: srun --job-name call-pbmm2_align_hifi-62 --partition compute,compute9 --cpus-per-task 64 --mem 61035M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-62/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-62/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-62/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-62/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0063_m84036_250809_035451_s4.bc2159.unmapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0063_m84036_250809_035451_s4.bc2159.unmapped.bam:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-62/_singularity_tmpdir_vlivqv6c/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-62/_singularity_tmpdir_vlivqv6c/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:22:02.996 wdl.w:ptcp.t:call-pbmm2_align_hifi-72 INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2169"
2025-09-15 20:22:02.996 wdl.w:ptcp.t:call-pbmm2_align_hifi-71 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 64, memory_reservation: 64000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:22:02.997 wdl.w:ptcp.t:call-pbmm2_align_hifi-80 NOTICE task setup :: name: "pbmm2_align_hifi", source: "./common.wdl", line: 170, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-80", thread: 140607691417152
2025-09-15 20:22:02.997 wdl.w:ptcp.t:call-pbmm2_align_hifi-73 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:22:02.999 wdl.w:ptcp NOTICE ready :: job: "call-pbmm2_align_hifi-83", callee: "pbmm2_align_hifi"
2025-09-15 20:22:02.999 wdl.w:ptcp.t:call-pbmm2_align_hifi-72 INFO eval :: name: "threads", value: 64
2025-09-15 20:22:03.000 wdl.w:ptcp.t:call-pbmm2_align_hifi-71 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:22:03.001 wdl.w:ptcp.t:call-pbmm2_align_hifi-73 INFO input :: name: "log_level", value: "INFO"
2025-09-15 20:22:03.001 wdl.w:ptcp.t:call-pbmm2_align_hifi-74 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:22:03.002 wdl.w:ptcp INFO input :: job: "call-pbmm2_align_hifi-83", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "log_level": "INFO", "out_prefix": "m84036_250809_035451_s4.bc2180.mapped", "ref_fasta": "/meta/refs/hg38.fa", "unmapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0084_m84036_250809_035451_s4.bc2180.unmapped.bam", "sample_name": "m84036_250809_035451_s4.bc2180"}
2025-09-15 20:22:03.002 wdl.w:ptcp.t:call-pbmm2_align_hifi-81 NOTICE task setup :: name: "pbmm2_align_hifi", source: "./common.wdl", line: 170, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-81", thread: 140607683024448
2025-09-15 20:22:03.003 wdl.w:ptcp.t:call-pbmm2_align_hifi-72 INFO eval :: name: "mem_gb", value: 64
2025-09-15 20:22:03.004 wdl.w:ptcp.t:call-pbmm2_align_hifi-73 INFO input :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2170.mapped"
2025-09-15 20:22:03.005 wdl.w:ptcp.t:call-pbmm2_align_hifi-74 INFO input :: name: "log_level", value: "INFO"
2025-09-15 20:22:03.005 wdl.w:ptcp.t:call-pbmm2_align_hifi-63 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 8, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-63/_singularity_tmpdir_wq9_qhsq"
2025-09-15 20:22:03.005 wdl.w:ptcp.t:call-pbmm2_align_hifi-75 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:22:03.007 wdl.w:ptcp.t:call-pbmm2_align_hifi-71 INFO provisioned :: seconds_waited: 0, cpu: 64, mem_bytes: 64000000000
2025-09-15 20:22:03.009 wdl.w:ptcp NOTICE ready :: job: "call-pbmm2_align_hifi-84", callee: "pbmm2_align_hifi"
2025-09-15 20:22:03.009 wdl.w:ptcp.t:call-pbmm2_align_hifi-73 INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:22:03.009 wdl.w:ptcp.t:call-pbmm2_align_hifi-72 INFO eval :: name: "disk_size", value: 30
2025-09-15 20:22:03.009 wdl.w:ptcp.t:call-pbmm2_align_hifi-74 INFO input :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2171.mapped"
2025-09-15 20:22:03.010 wdl.w:ptcp.t:call-pbmm2_align_hifi-76 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:22:03.010 wdl.w:ptcp.t:call-pbmm2_align_hifi-63 INFO Slurm invocation: srun --job-name call-pbmm2_align_hifi-63 --partition compute,compute9 --cpus-per-task 64 --mem 61035M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-63/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-63/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-63/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-63/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0064_m84036_250809_035451_s4.bc2160.unmapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0064_m84036_250809_035451_s4.bc2160.unmapped.bam:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-63/_singularity_tmpdir_wq9_qhsq/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-63/_singularity_tmpdir_wq9_qhsq/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:22:03.010 wdl.w:ptcp.t:call-pbmm2_align_hifi-75 INFO input :: name: "log_level", value: "INFO"
2025-09-15 20:22:03.011 wdl.w:ptcp.t:call-pbmm2_align_hifi-71 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:22:03.011 wdl.w:ptcp INFO input :: job: "call-pbmm2_align_hifi-84", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "log_level": "INFO", "out_prefix": "m84036_250809_035451_s4.bc2181.mapped", "ref_fasta": "/meta/refs/hg38.fa", "unmapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0085_m84036_250809_035451_s4.bc2181.unmapped.bam", "sample_name": "m84036_250809_035451_s4.bc2181"}
2025-09-15 20:22:03.013 wdl.w:ptcp.t:call-pbmm2_align_hifi-74 INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:22:03.013 wdl.w:ptcp.t:call-pbmm2_align_hifi-82 NOTICE task setup :: name: "pbmm2_align_hifi", source: "./common.wdl", line: 170, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-82", thread: 140607674631744
2025-09-15 20:22:03.013 wdl.w:ptcp.t:call-pbmm2_align_hifi-76 INFO input :: name: "log_level", value: "INFO"
2025-09-15 20:22:03.012 wdl.w:ptcp.t:call-pbmm2_align_hifi-73 INFO input :: name: "unmapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0074_m84036_250809_035451_s4.bc2170.unmapped.bam"
2025-09-15 20:22:03.014 wdl.w:ptcp.t:call-pbmm2_align_hifi-72 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 64, memory_reservation: 64000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:22:03.015 wdl.w:ptcp.t:call-pbmm2_align_hifi-77 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:22:03.014 wdl.w:ptcp.t:call-pbmm2_align_hifi-75 INFO input :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2172.mapped"
2025-09-15 20:22:03.015 wdl.w:ptcp.t:call-pbmm2_align_hifi-74 INFO input :: name: "unmapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0075_m84036_250809_035451_s4.bc2171.unmapped.bam"
2025-09-15 20:22:03.017 wdl.w:ptcp.t:call-pbmm2_align_hifi-76 INFO input :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2173.mapped"
2025-09-15 20:22:03.017 wdl.w:ptcp NOTICE ready :: job: "call-pbmm2_align_hifi-85", callee: "pbmm2_align_hifi"
2025-09-15 20:22:03.017 wdl.w:ptcp.t:call-pbmm2_align_hifi-57 NOTICE slurm_singularity run :: pid: 1197309, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-57/slurm_singularity.log.txt"
2025-09-15 20:22:03.017 wdl.w:ptcp.t:call-pbmm2_align_hifi-56 NOTICE slurm_singularity run :: pid: 1197308, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-56/slurm_singularity.log.txt"
2025-09-15 20:22:03.017 wdl.w:ptcp.t:call-pbmm2_align_hifi-73 INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2170"
2025-09-15 20:22:03.018 wdl.w:ptcp.t:call-pbmm2_align_hifi-72 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:22:03.018 wdl.w:ptcp.t:call-pbmm2_align_hifi-77 INFO input :: name: "log_level", value: "INFO"
2025-09-15 20:22:03.019 wdl.w:ptcp.t:call-pbmm2_align_hifi-54 NOTICE slurm_singularity run :: pid: 1197311, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-54/slurm_singularity.log.txt"
2025-09-15 20:22:03.019 wdl.w:ptcp.t:call-pbmm2_align_hifi-74 INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2171"
2025-09-15 20:22:03.020 wdl.w:ptcp INFO input :: job: "call-pbmm2_align_hifi-85", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "log_level": "INFO", "out_prefix": "m84036_250809_035451_s4.bc2182.mapped", "ref_fasta": "/meta/refs/hg38.fa", "unmapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0086_m84036_250809_035451_s4.bc2182.unmapped.bam", "sample_name": "m84036_250809_035451_s4.bc2182"}
2025-09-15 20:22:03.020 wdl.w:ptcp.t:call-pbmm2_align_hifi-76 INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:22:03.021 wdl.w:ptcp.t:call-pbmm2_align_hifi-78 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:22:03.019 wdl.w:ptcp.t:call-pbmm2_align_hifi-75 INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:22:03.021 wdl.w:ptcp.t:call-pbmm2_align_hifi-73 INFO eval :: name: "threads", value: 64
2025-09-15 20:22:03.022 wdl.w:ptcp.t:call-pbmm2_align_hifi-83 NOTICE task setup :: name: "pbmm2_align_hifi", source: "./common.wdl", line: 170, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-83", thread: 140607666239040
2025-09-15 20:22:03.023 wdl.w:ptcp.t:call-pbmm2_align_hifi-77 INFO input :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2174.mapped"
2025-09-15 20:22:03.024 wdl.w:ptcp.t:call-pbmm2_align_hifi-74 INFO eval :: name: "threads", value: 64
2025-09-15 20:22:03.023 wdl.w:ptcp.t:call-pbmm2_align_hifi-72 INFO provisioned :: seconds_waited: 0, cpu: 64, mem_bytes: 64000000000
2025-09-15 20:22:03.024 wdl.w:ptcp.t:call-pbmm2_align_hifi-64 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 8, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-64/_singularity_tmpdir_fgl1z8qf"
2025-09-15 20:22:03.024 wdl.w:ptcp.t:call-pbmm2_align_hifi-76 INFO input :: name: "unmapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0077_m84036_250809_035451_s4.bc2173.unmapped.bam"
2025-09-15 20:22:03.025 wdl.w:ptcp.t:call-pbmm2_align_hifi-78 INFO input :: name: "log_level", value: "INFO"
2025-09-15 20:22:03.025 wdl.w:ptcp.t:call-pbmm2_align_hifi-75 INFO input :: name: "unmapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0076_m84036_250809_035451_s4.bc2172.unmapped.bam"
2025-09-15 20:22:03.025 wdl.w:ptcp.t:call-pbmm2_align_hifi-73 INFO eval :: name: "mem_gb", value: 64
2025-09-15 20:22:03.026 wdl.w:ptcp.t:call-pbmm2_align_hifi-72 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:22:03.026 wdl.w:ptcp.t:call-pbmm2_align_hifi-77 INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:22:03.026 wdl.w:ptcp.t:call-pbmm2_align_hifi-74 INFO eval :: name: "mem_gb", value: 64
2025-09-15 20:22:03.026 wdl.w:ptcp.t:call-pbmm2_align_hifi-55 NOTICE slurm_singularity run :: pid: 1197316, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-55/slurm_singularity.log.txt"
2025-09-15 20:22:03.026 wdl.w:ptcp.t:call-pbmm2_align_hifi-64 INFO Slurm invocation: srun --job-name call-pbmm2_align_hifi-64 --partition compute,compute9 --cpus-per-task 64 --mem 61035M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-64/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-64/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-64/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-64/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0065_m84036_250809_035451_s4.bc2161.unmapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0065_m84036_250809_035451_s4.bc2161.unmapped.bam:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-64/_singularity_tmpdir_fgl1z8qf/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-64/_singularity_tmpdir_fgl1z8qf/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:22:03.027 wdl.w:ptcp.t:call-pbmm2_align_hifi-58 NOTICE slurm_singularity run :: pid: 1197314, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-58/slurm_singularity.log.txt"
2025-09-15 20:22:03.027 wdl.w:ptcp NOTICE ready :: job: "call-pbmm2_align_hifi-86", callee: "pbmm2_align_hifi"
2025-09-15 20:22:03.028 wdl.w:ptcp.t:call-pbmm2_align_hifi-79 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:22:03.027 wdl.w:ptcp.t:call-pbmm2_align_hifi-76 INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2173"
2025-09-15 20:22:03.028 wdl.w:ptcp.t:call-pbmm2_align_hifi-78 INFO input :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2175.mapped"
2025-09-15 20:22:03.028 wdl.w:ptcp.t:call-pbmm2_align_hifi-75 INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2172"
2025-09-15 20:22:03.029 wdl.w:ptcp.t:call-pbmm2_align_hifi-61 NOTICE slurm_singularity run :: pid: 1197331, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-61/slurm_singularity.log.txt"
2025-09-15 20:22:03.029 wdl.w:ptcp.t:call-pbmm2_align_hifi-77 INFO input :: name: "unmapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0078_m84036_250809_035451_s4.bc2174.unmapped.bam"
2025-09-15 20:22:03.030 wdl.w:ptcp.t:call-pbmm2_align_hifi-74 INFO eval :: name: "disk_size", value: 30
2025-09-15 20:22:03.031 wdl.w:ptcp INFO input :: job: "call-pbmm2_align_hifi-86", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "log_level": "INFO", "out_prefix": "m84036_250809_035451_s4.bc2183.mapped", "ref_fasta": "/meta/refs/hg38.fa", "unmapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0087_m84036_250809_035451_s4.bc2183.unmapped.bam", "sample_name": "m84036_250809_035451_s4.bc2183"}
2025-09-15 20:22:03.030 wdl.w:ptcp.t:call-pbmm2_align_hifi-65 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 8, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-65/_singularity_tmpdir_1juy28fb"
2025-09-15 20:22:03.029 wdl.w:ptcp.t:call-pbmm2_align_hifi-73 INFO eval :: name: "disk_size", value: 30
2025-09-15 20:22:03.031 wdl.w:ptcp.t:call-pbmm2_align_hifi-79 INFO input :: name: "log_level", value: "INFO"
2025-09-15 20:22:03.032 wdl.w:ptcp.t:call-pbmm2_align_hifi-76 INFO eval :: name: "threads", value: 64
2025-09-15 20:22:03.032 wdl.w:ptcp.t:call-pbmm2_align_hifi-78 INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:22:03.033 wdl.w:ptcp.t:call-pbmm2_align_hifi-84 NOTICE task setup :: name: "pbmm2_align_hifi", source: "./common.wdl", line: 170, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-84", thread: 140607657846336
2025-09-15 20:22:03.033 wdl.w:ptcp.t:call-pbmm2_align_hifi-77 INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2174"
2025-09-15 20:22:03.032 wdl.w:ptcp.t:call-pbmm2_align_hifi-75 INFO eval :: name: "threads", value: 64
2025-09-15 20:22:03.034 wdl.w:ptcp.t:call-pbmm2_align_hifi-74 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 64, memory_reservation: 64000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:22:03.034 wdl.w:ptcp.t:call-pbmm2_align_hifi-65 INFO Slurm invocation: srun --job-name call-pbmm2_align_hifi-65 --partition compute,compute9 --cpus-per-task 64 --mem 61035M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-65/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-65/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-65/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-65/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0066_m84036_250809_035451_s4.bc2162.unmapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0066_m84036_250809_035451_s4.bc2162.unmapped.bam:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-65/_singularity_tmpdir_1juy28fb/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-65/_singularity_tmpdir_1juy28fb/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:22:03.035 wdl.w:ptcp.t:call-pbmm2_align_hifi-80 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:22:03.036 wdl.w:ptcp NOTICE ready :: job: "call-pbmm2_align_hifi-87", callee: "pbmm2_align_hifi"
2025-09-15 20:22:03.036 wdl.w:ptcp.t:call-pbmm2_align_hifi-79 INFO input :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2176.mapped"
2025-09-15 20:22:03.036 wdl.w:ptcp.t:call-pbmm2_align_hifi-59 NOTICE slurm_singularity run :: pid: 1197326, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-59/slurm_singularity.log.txt"
2025-09-15 20:22:03.037 wdl.w:ptcp.t:call-pbmm2_align_hifi-76 INFO eval :: name: "mem_gb", value: 64
2025-09-15 20:22:03.037 wdl.w:ptcp.t:call-pbmm2_align_hifi-78 INFO input :: name: "unmapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0079_m84036_250809_035451_s4.bc2175.unmapped.bam"
2025-09-15 20:22:03.037 wdl.w:ptcp.t:call-pbmm2_align_hifi-73 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 64, memory_reservation: 64000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:22:03.037 wdl.w:ptcp.t:call-pbmm2_align_hifi-60 NOTICE slurm_singularity run :: pid: 1197329, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-60/slurm_singularity.log.txt"
2025-09-15 20:22:03.038 wdl.w:ptcp.t:call-pbmm2_align_hifi-77 INFO eval :: name: "threads", value: 64
2025-09-15 20:22:03.038 wdl.w:ptcp.t:call-pbmm2_align_hifi-75 INFO eval :: name: "mem_gb", value: 64
2025-09-15 20:22:03.039 wdl.w:ptcp.t:call-pbmm2_align_hifi-74 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:22:03.039 wdl.w:ptcp.t:call-pbmm2_align_hifi-85 NOTICE task setup :: name: "pbmm2_align_hifi", source: "./common.wdl", line: 170, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-85", thread: 140607649453632
2025-09-15 20:22:03.039 wdl.w:ptcp.t:call-pbmm2_align_hifi-62 NOTICE slurm_singularity run :: pid: 1197334, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-62/slurm_singularity.log.txt"
2025-09-15 20:22:03.040 wdl.w:ptcp.t:call-pbmm2_align_hifi-80 INFO input :: name: "log_level", value: "INFO"
2025-09-15 20:22:03.040 wdl.w:ptcp INFO input :: job: "call-pbmm2_align_hifi-87", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "log_level": "INFO", "out_prefix": "m84036_250809_035451_s4.bc2184.mapped", "ref_fasta": "/meta/refs/hg38.fa", "unmapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0088_m84036_250809_035451_s4.bc2184.unmapped.bam", "sample_name": "m84036_250809_035451_s4.bc2184"}
2025-09-15 20:22:03.040 wdl.w:ptcp.t:call-pbmm2_align_hifi-79 INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:22:03.042 wdl.w:ptcp.t:call-pbmm2_align_hifi-78 INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2175"
2025-09-15 20:22:03.042 wdl.w:ptcp.t:call-pbmm2_align_hifi-76 INFO eval :: name: "disk_size", value: 30
2025-09-15 20:22:03.042 wdl.w:ptcp.t:call-pbmm2_align_hifi-73 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:22:03.043 wdl.w:ptcp.t:call-pbmm2_align_hifi-77 INFO eval :: name: "mem_gb", value: 64
2025-09-15 20:22:03.045 wdl.w:ptcp.t:call-pbmm2_align_hifi-75 INFO eval :: name: "disk_size", value: 30
2025-09-15 20:22:03.046 wdl.w:ptcp.t:call-pbmm2_align_hifi-80 INFO input :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2177.mapped"
2025-09-15 20:22:03.046 wdl.w:ptcp.t:call-pbmm2_align_hifi-74 INFO provisioned :: seconds_waited: 0, cpu: 64, mem_bytes: 64000000000
2025-09-15 20:22:03.047 wdl.w:ptcp.t:call-pbmm2_align_hifi-79 INFO input :: name: "unmapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0080_m84036_250809_035451_s4.bc2176.unmapped.bam"
2025-09-15 20:22:03.048 wdl.w:ptcp.t:call-pbmm2_align_hifi-78 INFO eval :: name: "threads", value: 64
2025-09-15 20:22:03.048 wdl.w:ptcp.t:call-pbmm2_align_hifi-86 NOTICE task setup :: name: "pbmm2_align_hifi", source: "./common.wdl", line: 170, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-86", thread: 140607162938944
2025-09-15 20:22:03.049 wdl.w:ptcp NOTICE ready :: job: "call-pbmm2_align_hifi-88", callee: "pbmm2_align_hifi"
2025-09-15 20:22:03.049 wdl.w:ptcp.t:call-pbmm2_align_hifi-67 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 8, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-67/_singularity_tmpdir_c_dmby1b"
2025-09-15 20:22:03.050 wdl.w:ptcp.t:call-pbmm2_align_hifi-76 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 64, memory_reservation: 64000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:22:03.052 wdl.w:ptcp.t:call-pbmm2_align_hifi-77 INFO eval :: name: "disk_size", value: 30
2025-09-15 20:22:03.051 wdl.w:ptcp.t:call-pbmm2_align_hifi-80 INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:22:03.052 wdl.w:ptcp.t:call-pbmm2_align_hifi-66 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 8, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-66/_singularity_tmpdir_v5ce3mr6"
2025-09-15 20:22:03.053 wdl.w:ptcp.t:call-pbmm2_align_hifi-75 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 64, memory_reservation: 64000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:22:03.053 wdl.w:ptcp.t:call-pbmm2_align_hifi-74 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:22:03.053 wdl.w:ptcp.t:call-pbmm2_align_hifi-81 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:22:03.053 wdl.w:ptcp.t:call-pbmm2_align_hifi-73 INFO provisioned :: seconds_waited: 0, cpu: 64, mem_bytes: 64000000000
2025-09-15 20:22:03.054 wdl.w:ptcp.t:call-pbmm2_align_hifi-79 INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2176"
2025-09-15 20:22:03.054 wdl.w:ptcp.t:call-pbmm2_align_hifi-78 INFO eval :: name: "mem_gb", value: 64
2025-09-15 20:22:03.055 wdl.w:ptcp INFO input :: job: "call-pbmm2_align_hifi-88", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "log_level": "INFO", "out_prefix": "m84036_250809_035451_s4.bc2185.mapped", "ref_fasta": "/meta/refs/hg38.fa", "unmapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0089_m84036_250809_035451_s4.bc2185.unmapped.bam", "sample_name": "m84036_250809_035451_s4.bc2185"}
2025-09-15 20:22:03.055 wdl.w:ptcp.t:call-pbmm2_align_hifi-67 INFO Slurm invocation: srun --job-name call-pbmm2_align_hifi-67 --partition compute,compute9 --cpus-per-task 64 --mem 61035M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-67/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-67/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-67/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-67/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0068_m84036_250809_035451_s4.bc2164.unmapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0068_m84036_250809_035451_s4.bc2164.unmapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-67/_singularity_tmpdir_c_dmby1b/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-67/_singularity_tmpdir_c_dmby1b/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:22:03.055 wdl.w:ptcp.t:call-pbmm2_align_hifi-76 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:22:03.057 wdl.w:ptcp.t:call-pbmm2_align_hifi-80 INFO input :: name: "unmapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0081_m84036_250809_035451_s4.bc2177.unmapped.bam"
2025-09-15 20:22:03.056 wdl.w:ptcp.t:call-pbmm2_align_hifi-77 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 64, memory_reservation: 64000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:22:03.057 wdl.w:ptcp.t:call-pbmm2_align_hifi-66 INFO Slurm invocation: srun --job-name call-pbmm2_align_hifi-66 --partition compute,compute9 --cpus-per-task 64 --mem 61035M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-66/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-66/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-66/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-66/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0067_m84036_250809_035451_s4.bc2163.unmapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0067_m84036_250809_035451_s4.bc2163.unmapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-66/_singularity_tmpdir_v5ce3mr6/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-66/_singularity_tmpdir_v5ce3mr6/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:22:03.057 wdl.w:ptcp.t:call-pbmm2_align_hifi-75 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:22:03.057 wdl.w:ptcp.t:call-pbmm2_align_hifi-87 NOTICE task setup :: name: "pbmm2_align_hifi", source: "./common.wdl", line: 170, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-87", thread: 140607154546240
2025-09-15 20:22:03.058 wdl.w:ptcp.t:call-pbmm2_align_hifi-81 INFO input :: name: "log_level", value: "INFO"
2025-09-15 20:22:03.058 wdl.w:ptcp.t:call-pbmm2_align_hifi-73 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:22:03.058 wdl.w:ptcp.t:call-pbmm2_align_hifi-79 INFO eval :: name: "threads", value: 64
2025-09-15 20:22:03.059 wdl.w:ptcp.t:call-pbmm2_align_hifi-68 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 8, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-68/_singularity_tmpdir_8t9ak82g"
2025-09-15 20:22:03.059 wdl.w:ptcp.t:call-pbmm2_align_hifi-78 INFO eval :: name: "disk_size", value: 30
2025-09-15 20:22:03.060 wdl.w:ptcp NOTICE ready :: job: "call-pbmm2_align_hifi-89", callee: "pbmm2_align_hifi"
2025-09-15 20:22:03.061 wdl.w:ptcp.t:call-pbmm2_align_hifi-80 INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2177"
2025-09-15 20:22:03.061 wdl.w:ptcp.t:call-pbmm2_align_hifi-77 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:22:03.063 wdl.w:ptcp.t:call-pbmm2_align_hifi-81 INFO input :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2178.mapped"
2025-09-15 20:22:03.063 wdl.w:ptcp.t:call-pbmm2_align_hifi-76 INFO provisioned :: seconds_waited: 0, cpu: 64, mem_bytes: 64000000000
2025-09-15 20:22:03.064 wdl.w:ptcp.t:call-pbmm2_align_hifi-79 INFO eval :: name: "mem_gb", value: 64
2025-09-15 20:22:03.064 wdl.w:ptcp.t:call-pbmm2_align_hifi-75 INFO provisioned :: seconds_waited: 0, cpu: 64, mem_bytes: 64000000000
2025-09-15 20:22:03.065 wdl.w:ptcp.t:call-pbmm2_align_hifi-68 INFO Slurm invocation: srun --job-name call-pbmm2_align_hifi-68 --partition compute,compute9 --cpus-per-task 64 --mem 61035M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-68/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-68/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-68/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-68/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0069_m84036_250809_035451_s4.bc2165.unmapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0069_m84036_250809_035451_s4.bc2165.unmapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-68/_singularity_tmpdir_8t9ak82g/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-68/_singularity_tmpdir_8t9ak82g/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:22:03.066 wdl.w:ptcp INFO input :: job: "call-pbmm2_align_hifi-89", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "log_level": "INFO", "out_prefix": "m84036_250809_035451_s4.bc2186.mapped", "ref_fasta": "/meta/refs/hg38.fa", "unmapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0090_m84036_250809_035451_s4.bc2186.unmapped.bam", "sample_name": "m84036_250809_035451_s4.bc2186"}
2025-09-15 20:22:03.066 wdl.w:ptcp.t:call-pbmm2_align_hifi-78 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 64, memory_reservation: 64000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:22:03.067 wdl.w:ptcp.t:call-pbmm2_align_hifi-80 INFO eval :: name: "threads", value: 64
2025-09-15 20:22:03.067 wdl.w:ptcp.t:call-pbmm2_align_hifi-81 INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:22:03.068 wdl.w:ptcp.t:call-pbmm2_align_hifi-82 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:22:03.068 wdl.w:ptcp.t:call-pbmm2_align_hifi-76 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:22:03.069 wdl.w:ptcp.t:call-pbmm2_align_hifi-69 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 8, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-69/_singularity_tmpdir_aqttfhgs"
2025-09-15 20:22:03.070 wdl.w:ptcp.t:call-pbmm2_align_hifi-79 INFO eval :: name: "disk_size", value: 30
2025-09-15 20:22:03.070 wdl.w:ptcp.t:call-pbmm2_align_hifi-77 INFO provisioned :: seconds_waited: 0, cpu: 64, mem_bytes: 64000000000
2025-09-15 20:22:03.071 wdl.w:ptcp.t:call-pbmm2_align_hifi-75 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:22:03.071 wdl.w:ptcp.t:call-pbmm2_align_hifi-78 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:22:03.072 wdl.w:ptcp.t:call-pbmm2_align_hifi-80 INFO eval :: name: "mem_gb", value: 64
2025-09-15 20:22:03.072 wdl.w:ptcp.t:call-pbmm2_align_hifi-81 INFO input :: name: "unmapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0082_m84036_250809_035451_s4.bc2178.unmapped.bam"
2025-09-15 20:22:03.072 wdl.w:ptcp.t:call-pbmm2_align_hifi-83 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:22:03.073 wdl.w:ptcp NOTICE ready :: job: "call-pbmm2_align_hifi-90", callee: "pbmm2_align_hifi"
2025-09-15 20:22:03.073 wdl.w:ptcp.t:call-pbmm2_align_hifi-82 INFO input :: name: "log_level", value: "INFO"
2025-09-15 20:22:03.075 wdl.w:ptcp.t:call-pbmm2_align_hifi-77 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:22:03.074 wdl.w:ptcp.t:call-pbmm2_align_hifi-69 INFO Slurm invocation: srun --job-name call-pbmm2_align_hifi-69 --partition compute,compute9 --cpus-per-task 64 --mem 61035M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-69/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-69/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-69/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-69/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0070_m84036_250809_035451_s4.bc2166.unmapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0070_m84036_250809_035451_s4.bc2166.unmapped.bam:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-69/_singularity_tmpdir_aqttfhgs/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-69/_singularity_tmpdir_aqttfhgs/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:22:03.076 wdl.w:ptcp.t:call-pbmm2_align_hifi-88 NOTICE task setup :: name: "pbmm2_align_hifi", source: "./common.wdl", line: 170, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-88", thread: 140607146153536
2025-09-15 20:22:03.077 wdl.w:ptcp.t:call-pbmm2_align_hifi-79 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 64, memory_reservation: 64000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:22:03.079 wdl.w:ptcp.t:call-pbmm2_align_hifi-81 INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2178"
2025-09-15 20:22:03.079 wdl.w:ptcp.t:call-pbmm2_align_hifi-80 INFO eval :: name: "disk_size", value: 30
2025-09-15 20:22:03.079 wdl.w:ptcp.t:call-pbmm2_align_hifi-83 INFO input :: name: "log_level", value: "INFO"
2025-09-15 20:22:03.080 wdl.w:ptcp INFO input :: job: "call-pbmm2_align_hifi-90", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "log_level": "INFO", "out_prefix": "m84036_250809_035451_s4.bc2187.mapped", "ref_fasta": "/meta/refs/hg38.fa", "unmapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0091_m84036_250809_035451_s4.bc2187.unmapped.bam", "sample_name": "m84036_250809_035451_s4.bc2187"}
2025-09-15 20:22:03.080 wdl.w:ptcp.t:call-pbmm2_align_hifi-78 INFO provisioned :: seconds_waited: 0, cpu: 64, mem_bytes: 64000000000
2025-09-15 20:22:03.080 wdl.w:ptcp.t:call-pbmm2_align_hifi-82 INFO input :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2179.mapped"
2025-09-15 20:22:03.084 wdl.w:ptcp.t:call-pbmm2_align_hifi-81 INFO eval :: name: "threads", value: 64
2025-09-15 20:22:03.085 wdl.w:ptcp.t:call-pbmm2_align_hifi-84 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:22:03.083 wdl.w:ptcp.t:call-pbmm2_align_hifi-79 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:22:03.085 wdl.w:ptcp.t:call-pbmm2_align_hifi-83 INFO input :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2180.mapped"
2025-09-15 20:22:03.086 wdl.w:ptcp.t:call-pbmm2_align_hifi-80 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 64, memory_reservation: 64000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:22:03.087 wdl.w:ptcp.t:call-pbmm2_align_hifi-82 INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:22:03.088 wdl.w:ptcp.t:call-pbmm2_align_hifi-81 INFO eval :: name: "mem_gb", value: 64
2025-09-15 20:22:03.088 wdl.w:ptcp NOTICE ready :: job: "call-pbmm2_align_hifi-91", callee: "pbmm2_align_hifi"
2025-09-15 20:22:03.086 wdl.w:ptcp.t:call-pbmm2_align_hifi-78 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:22:03.089 wdl.w:ptcp.t:call-pbmm2_align_hifi-85 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:22:03.089 wdl.w:ptcp.t:call-pbmm2_align_hifi-84 INFO input :: name: "log_level", value: "INFO"
2025-09-15 20:22:03.089 wdl.w:ptcp.t:call-pbmm2_align_hifi-83 INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:22:03.090 wdl.w:ptcp.t:call-pbmm2_align_hifi-82 INFO input :: name: "unmapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0083_m84036_250809_035451_s4.bc2179.unmapped.bam"
2025-09-15 20:22:03.090 wdl.w:ptcp.t:call-pbmm2_align_hifi-79 INFO provisioned :: seconds_waited: 0, cpu: 64, mem_bytes: 64000000000
2025-09-15 20:22:03.091 wdl.w:ptcp INFO input :: job: "call-pbmm2_align_hifi-91", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "log_level": "INFO", "out_prefix": "m84036_250809_035451_s4.bc2188.mapped", "ref_fasta": "/meta/refs/hg38.fa", "unmapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0092_m84036_250809_035451_s4.bc2188.unmapped.bam", "sample_name": "m84036_250809_035451_s4.bc2188"}
2025-09-15 20:22:03.089 wdl.w:ptcp.t:call-pbmm2_align_hifi-80 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:22:03.092 wdl.w:ptcp.t:call-pbmm2_align_hifi-89 NOTICE task setup :: name: "pbmm2_align_hifi", source: "./common.wdl", line: 170, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-89", thread: 140607137760832
2025-09-15 20:22:03.092 wdl.w:ptcp.t:call-pbmm2_align_hifi-85 INFO input :: name: "log_level", value: "INFO"
2025-09-15 20:22:03.091 wdl.w:ptcp.t:call-pbmm2_align_hifi-81 INFO eval :: name: "disk_size", value: 30
2025-09-15 20:22:03.093 wdl.w:ptcp.t:call-pbmm2_align_hifi-82 INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2179"
2025-09-15 20:22:03.093 wdl.w:ptcp.t:call-pbmm2_align_hifi-79 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:22:03.094 wdl.w:ptcp.t:call-pbmm2_align_hifi-85 INFO input :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2182.mapped"
2025-09-15 20:22:03.092 wdl.w:ptcp.t:call-pbmm2_align_hifi-83 INFO input :: name: "unmapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0084_m84036_250809_035451_s4.bc2180.unmapped.bam"
2025-09-15 20:22:03.092 wdl.w:ptcp.t:call-pbmm2_align_hifi-84 INFO input :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2181.mapped"
2025-09-15 20:22:03.095 wdl.w:ptcp.t:call-pbmm2_align_hifi-63 NOTICE slurm_singularity run :: pid: 1197336, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-63/slurm_singularity.log.txt"
2025-09-15 20:22:03.095 wdl.w:ptcp.t:call-pbmm2_align_hifi-80 INFO provisioned :: seconds_waited: 0, cpu: 64, mem_bytes: 64000000000
2025-09-15 20:22:03.095 wdl.w:ptcp.t:call-pbmm2_align_hifi-85 INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:22:03.096 wdl.w:ptcp.t:call-pbmm2_align_hifi-81 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 64, memory_reservation: 64000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:22:03.096 wdl.w:ptcp.t:call-pbmm2_align_hifi-83 INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2180"
2025-09-15 20:22:03.094 wdl.w:ptcp.t:call-pbmm2_align_hifi-82 INFO eval :: name: "threads", value: 64
2025-09-15 20:22:03.096 wdl.w:ptcp.t:call-pbmm2_align_hifi-84 INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:22:03.097 wdl.w:ptcp.t:call-pbmm2_align_hifi-86 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:22:03.098 wdl.w:ptcp NOTICE ready :: job: "call-pbmm2_align_hifi-92", callee: "pbmm2_align_hifi"
2025-09-15 20:22:03.098 wdl.w:ptcp.t:call-pbmm2_align_hifi-80 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:22:03.098 wdl.w:ptcp.t:call-pbmm2_align_hifi-85 INFO input :: name: "unmapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0086_m84036_250809_035451_s4.bc2182.unmapped.bam"
2025-09-15 20:22:03.098 wdl.w:ptcp.t:call-pbmm2_align_hifi-81 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:22:03.099 wdl.w:ptcp.t:call-pbmm2_align_hifi-83 INFO eval :: name: "threads", value: 64
2025-09-15 20:22:03.099 wdl.w:ptcp.t:call-pbmm2_align_hifi-82 INFO eval :: name: "mem_gb", value: 64
2025-09-15 20:22:03.099 wdl.w:ptcp.t:call-pbmm2_align_hifi-84 INFO input :: name: "unmapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0085_m84036_250809_035451_s4.bc2181.unmapped.bam"
2025-09-15 20:22:03.099 wdl.w:ptcp.t:call-pbmm2_align_hifi-86 INFO input :: name: "log_level", value: "INFO"
2025-09-15 20:22:03.099 wdl.w:ptcp INFO input :: job: "call-pbmm2_align_hifi-92", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "log_level": "INFO", "out_prefix": "m84036_250809_035451_s4.bc2189.mapped", "ref_fasta": "/meta/refs/hg38.fa", "unmapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0093_m84036_250809_035451_s4.bc2189.unmapped.bam", "sample_name": "m84036_250809_035451_s4.bc2189"}
2025-09-15 20:22:03.099 wdl.w:ptcp.t:call-pbmm2_align_hifi-85 INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2182"
2025-09-15 20:22:03.099 wdl.w:ptcp.t:call-pbmm2_align_hifi-83 INFO eval :: name: "mem_gb", value: 64
2025-09-15 20:22:03.100 wdl.w:ptcp.t:call-pbmm2_align_hifi-84 INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2181"
2025-09-15 20:22:03.100 wdl.w:ptcp.t:call-pbmm2_align_hifi-82 INFO eval :: name: "disk_size", value: 30
2025-09-15 20:22:03.100 wdl.w:ptcp.t:call-pbmm2_align_hifi-86 INFO input :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2183.mapped"
2025-09-15 20:22:03.101 wdl.w:ptcp.t:call-pbmm2_align_hifi-81 INFO provisioned :: seconds_waited: 0, cpu: 64, mem_bytes: 64000000000
2025-09-15 20:22:03.101 wdl.w:ptcp.t:call-pbmm2_align_hifi-85 INFO eval :: name: "threads", value: 64
2025-09-15 20:22:03.101 wdl.w:ptcp.t:call-pbmm2_align_hifi-87 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:22:03.102 wdl.w:ptcp.t:call-pbmm2_align_hifi-83 INFO eval :: name: "disk_size", value: 30
2025-09-15 20:22:03.102 wdl.w:ptcp.t:call-pbmm2_align_hifi-84 INFO eval :: name: "threads", value: 64
2025-09-15 20:22:03.103 wdl.w:ptcp.t:call-pbmm2_align_hifi-86 INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:22:03.103 wdl.w:ptcp.t:call-pbmm2_align_hifi-70 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 8, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-70/_singularity_tmpdir_e_tgs7qh"
2025-09-15 20:22:03.103 wdl.w:ptcp.t:call-pbmm2_align_hifi-82 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 64, memory_reservation: 64000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:22:03.103 wdl.w:ptcp.t:call-pbmm2_align_hifi-81 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:22:03.104 wdl.w:ptcp.t:call-pbmm2_align_hifi-85 INFO eval :: name: "mem_gb", value: 64
2025-09-15 20:22:03.104 wdl.w:ptcp.t:call-pbmm2_align_hifi-87 INFO input :: name: "log_level", value: "INFO"
2025-09-15 20:22:03.105 wdl.w:ptcp.t:call-pbmm2_align_hifi-90 NOTICE task setup :: name: "pbmm2_align_hifi", source: "./common.wdl", line: 170, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-90", thread: 140607129368128
2025-09-15 20:22:03.105 wdl.w:ptcp.t:call-pbmm2_align_hifi-84 INFO eval :: name: "mem_gb", value: 64
2025-09-15 20:22:03.105 wdl.w:ptcp.t:call-pbmm2_align_hifi-65 NOTICE slurm_singularity run :: pid: 1197347, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-65/slurm_singularity.log.txt"
2025-09-15 20:22:03.106 wdl.w:ptcp.t:call-pbmm2_align_hifi-86 INFO input :: name: "unmapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0087_m84036_250809_035451_s4.bc2183.unmapped.bam"
2025-09-15 20:22:03.105 wdl.w:ptcp.t:call-pbmm2_align_hifi-83 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 64, memory_reservation: 64000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:22:03.106 wdl.w:ptcp.t:call-pbmm2_align_hifi-70 INFO Slurm invocation: srun --job-name call-pbmm2_align_hifi-70 --partition compute,compute9 --cpus-per-task 64 --mem 61035M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-70/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-70/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-70/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-70/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0071_m84036_250809_035451_s4.bc2167.unmapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0071_m84036_250809_035451_s4.bc2167.unmapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-70/_singularity_tmpdir_e_tgs7qh/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-70/_singularity_tmpdir_e_tgs7qh/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:22:03.106 wdl.w:ptcp.t:call-pbmm2_align_hifi-82 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:22:03.108 wdl.w:ptcp NOTICE ready :: job: "call-pbmm2_align_hifi-93", callee: "pbmm2_align_hifi"
2025-09-15 20:22:03.108 wdl.w:ptcp.t:call-pbmm2_align_hifi-64 NOTICE slurm_singularity run :: pid: 1197343, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-64/slurm_singularity.log.txt"
2025-09-15 20:22:03.108 wdl.w:ptcp.t:call-pbmm2_align_hifi-87 INFO input :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2184.mapped"
2025-09-15 20:22:03.109 wdl.w:ptcp.t:call-pbmm2_align_hifi-85 INFO eval :: name: "disk_size", value: 30
2025-09-15 20:22:03.109 wdl.w:ptcp.t:call-pbmm2_align_hifi-66 NOTICE slurm_singularity run :: pid: 1197352, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-66/slurm_singularity.log.txt"
2025-09-15 20:22:03.109 wdl.w:ptcp.t:call-pbmm2_align_hifi-67 NOTICE slurm_singularity run :: pid: 1197350, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-67/slurm_singularity.log.txt"
2025-09-15 20:22:03.110 wdl.w:ptcp.t:call-pbmm2_align_hifi-84 INFO eval :: name: "disk_size", value: 30
2025-09-15 20:22:03.110 wdl.w:ptcp.t:call-pbmm2_align_hifi-86 INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2183"
2025-09-15 20:22:03.111 wdl.w:ptcp INFO input :: job: "call-pbmm2_align_hifi-93", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "log_level": "INFO", "out_prefix": "m84036_250809_035451_s4.bc2190.mapped", "ref_fasta": "/meta/refs/hg38.fa", "unmapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0094_m84036_250809_035451_s4.bc2190.unmapped.bam", "sample_name": "m84036_250809_035451_s4.bc2190"}
2025-09-15 20:22:03.110 wdl.w:ptcp.t:call-pbmm2_align_hifi-83 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:22:03.111 wdl.w:ptcp.t:call-pbmm2_align_hifi-71 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 8, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-71/_singularity_tmpdir_fdz9b3tc"
2025-09-15 20:22:03.112 wdl.w:ptcp.t:call-pbmm2_align_hifi-87 INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:22:03.113 wdl.w:ptcp.t:call-pbmm2_align_hifi-85 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 64, memory_reservation: 64000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:22:03.114 wdl.w:ptcp.t:call-pbmm2_align_hifi-86 INFO eval :: name: "threads", value: 64
2025-09-15 20:22:03.112 wdl.w:ptcp.t:call-pbmm2_align_hifi-82 INFO provisioned :: seconds_waited: 0, cpu: 64, mem_bytes: 64000000000
2025-09-15 20:22:03.114 wdl.w:ptcp.t:call-pbmm2_align_hifi-84 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 64, memory_reservation: 64000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:22:03.115 wdl.w:ptcp.t:call-pbmm2_align_hifi-71 INFO Slurm invocation: srun --job-name call-pbmm2_align_hifi-71 --partition compute,compute9 --cpus-per-task 64 --mem 61035M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-71/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-71/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-71/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-71/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0072_m84036_250809_035451_s4.bc2168.unmapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0072_m84036_250809_035451_s4.bc2168.unmapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-71/_singularity_tmpdir_fdz9b3tc/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-71/_singularity_tmpdir_fdz9b3tc/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:22:03.115 wdl.w:ptcp.t:call-pbmm2_align_hifi-87 INFO input :: name: "unmapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0088_m84036_250809_035451_s4.bc2184.unmapped.bam"
2025-09-15 20:22:03.115 wdl.w:ptcp.t:call-pbmm2_align_hifi-91 NOTICE task setup :: name: "pbmm2_align_hifi", source: "./common.wdl", line: 170, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-91", thread: 140607120975424
2025-09-15 20:22:03.116 wdl.w:ptcp.t:call-pbmm2_align_hifi-85 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:22:03.116 wdl.w:ptcp.t:call-pbmm2_align_hifi-86 INFO eval :: name: "mem_gb", value: 64
2025-09-15 20:22:03.116 wdl.w:ptcp.t:call-pbmm2_align_hifi-83 INFO provisioned :: seconds_waited: 0, cpu: 64, mem_bytes: 64000000000
2025-09-15 20:22:03.117 wdl.w:ptcp NOTICE ready :: job: "call-pbmm2_align_hifi-94", callee: "pbmm2_align_hifi"
2025-09-15 20:22:03.117 wdl.w:ptcp.t:call-pbmm2_align_hifi-82 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:22:03.118 wdl.w:ptcp.t:call-pbmm2_align_hifi-84 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:22:03.118 wdl.w:ptcp.t:call-pbmm2_align_hifi-87 INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2184"
2025-09-15 20:22:03.118 wdl.w:ptcp.t:call-pbmm2_align_hifi-68 NOTICE slurm_singularity run :: pid: 1197353, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-68/slurm_singularity.log.txt"
2025-09-15 20:22:03.120 wdl.w:ptcp.t:call-pbmm2_align_hifi-83 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:22:03.120 wdl.w:ptcp.t:call-pbmm2_align_hifi-86 INFO eval :: name: "disk_size", value: 30
2025-09-15 20:22:03.120 wdl.w:ptcp INFO input :: job: "call-pbmm2_align_hifi-94", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "log_level": "INFO", "out_prefix": "m84036_250809_035451_s4.bc2191.mapped", "ref_fasta": "/meta/refs/hg38.fa", "unmapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0095_m84036_250809_035451_s4.bc2191.unmapped.bam", "sample_name": "m84036_250809_035451_s4.bc2191"}
2025-09-15 20:22:03.120 wdl.w:ptcp.t:call-pbmm2_align_hifi-92 NOTICE task setup :: name: "pbmm2_align_hifi", source: "./common.wdl", line: 170, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-92", thread: 140607112582720
2025-09-15 20:22:03.121 wdl.w:ptcp.t:call-pbmm2_align_hifi-85 INFO provisioned :: seconds_waited: 0, cpu: 64, mem_bytes: 64000000000
2025-09-15 20:22:03.121 wdl.w:ptcp.t:call-pbmm2_align_hifi-88 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:22:03.122 wdl.w:ptcp.t:call-pbmm2_align_hifi-87 INFO eval :: name: "threads", value: 64
2025-09-15 20:22:03.123 wdl.w:ptcp.t:call-pbmm2_align_hifi-72 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 8, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-72/_singularity_tmpdir_qfez2q5r"
2025-09-15 20:22:03.124 wdl.w:ptcp.t:call-pbmm2_align_hifi-84 INFO provisioned :: seconds_waited: 0, cpu: 64, mem_bytes: 64000000000
2025-09-15 20:22:03.124 wdl.w:ptcp.t:call-pbmm2_align_hifi-86 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 64, memory_reservation: 64000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:22:03.125 wdl.w:ptcp.t:call-pbmm2_align_hifi-85 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:22:03.125 wdl.w:ptcp.t:call-pbmm2_align_hifi-88 INFO input :: name: "log_level", value: "INFO"
2025-09-15 20:22:03.125 wdl.w:ptcp.t:call-pbmm2_align_hifi-87 INFO eval :: name: "mem_gb", value: 64
2025-09-15 20:22:03.125 wdl.w:ptcp.t:call-pbmm2_align_hifi-72 INFO Slurm invocation: srun --job-name call-pbmm2_align_hifi-72 --partition compute,compute9 --cpus-per-task 64 --mem 61035M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-72/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-72/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-72/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-72/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0073_m84036_250809_035451_s4.bc2169.unmapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0073_m84036_250809_035451_s4.bc2169.unmapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-72/_singularity_tmpdir_qfez2q5r/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-72/_singularity_tmpdir_qfez2q5r/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:22:03.125 wdl.w:ptcp.t:call-pbmm2_align_hifi-84 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:22:03.125 wdl.w:ptcp.t:call-pbmm2_align_hifi-86 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:22:03.126 wdl.w:ptcp.t:call-pbmm2_align_hifi-88 INFO input :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2185.mapped"
2025-09-15 20:22:03.127 wdl.w:ptcp.t:call-pbmm2_align_hifi-87 INFO eval :: name: "disk_size", value: 30
2025-09-15 20:22:03.127 wdl.w:ptcp.t:call-pbmm2_align_hifi-88 INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:22:03.128 wdl.w:ptcp.t:call-pbmm2_align_hifi-86 INFO provisioned :: seconds_waited: 0, cpu: 64, mem_bytes: 64000000000
2025-09-15 20:22:03.128 wdl.w:ptcp.t:call-pbmm2_align_hifi-93 NOTICE task setup :: name: "pbmm2_align_hifi", source: "./common.wdl", line: 170, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-93", thread: 140606626068032
2025-09-15 20:22:03.129 wdl.w:ptcp NOTICE ready :: job: "call-pbmm2_align_hifi-95", callee: "pbmm2_align_hifi"
2025-09-15 20:22:03.130 wdl.w:ptcp.t:call-pbmm2_align_hifi-87 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 64, memory_reservation: 64000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:22:03.130 wdl.w:ptcp.t:call-pbmm2_align_hifi-86 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:22:03.131 wdl.w:ptcp INFO input :: job: "call-pbmm2_align_hifi-95", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "log_level": "INFO", "out_prefix": "m84036_250809_035451_s4.bc2192.mapped", "ref_fasta": "/meta/refs/hg38.fa", "unmapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0096_m84036_250809_035451_s4.bc2192.unmapped.bam", "sample_name": "m84036_250809_035451_s4.bc2192"}
2025-09-15 20:22:03.130 wdl.w:ptcp.t:call-pbmm2_align_hifi-88 INFO input :: name: "unmapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0089_m84036_250809_035451_s4.bc2185.unmapped.bam"
2025-09-15 20:22:03.132 wdl.w:ptcp.t:call-pbmm2_align_hifi-89 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:22:03.132 wdl.w:ptcp.t:call-pbmm2_align_hifi-88 INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2185"
2025-09-15 20:22:03.132 wdl.w:ptcp.t:call-pbmm2_align_hifi-89 INFO input :: name: "log_level", value: "INFO"
2025-09-15 20:22:03.133 wdl.w:ptcp.t:call-pbmm2_align_hifi-88 INFO eval :: name: "threads", value: 64
2025-09-15 20:22:03.131 wdl.w:ptcp.t:call-pbmm2_align_hifi-87 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:22:03.133 wdl.w:ptcp.t:call-pbmm2_align_hifi-89 INFO input :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2186.mapped"
2025-09-15 20:22:03.133 wdl.w:ptcp.t:call-pbmm2_align_hifi-88 INFO eval :: name: "mem_gb", value: 64
2025-09-15 20:22:03.133 wdl.w:ptcp.t:call-pbmm2_align_hifi-89 INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:22:03.134 wdl.w:ptcp.t:call-pbmm2_align_hifi-89 INFO input :: name: "unmapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0090_m84036_250809_035451_s4.bc2186.unmapped.bam"
2025-09-15 20:22:03.135 wdl.w:ptcp.t:call-pbmm2_align_hifi-87 INFO provisioned :: seconds_waited: 0, cpu: 64, mem_bytes: 64000000000
2025-09-15 20:22:03.135 wdl.w:ptcp.t:call-pbmm2_align_hifi-88 INFO eval :: name: "disk_size", value: 30
2025-09-15 20:22:03.135 wdl.w:ptcp.t:call-pbmm2_align_hifi-89 INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2186"
2025-09-15 20:22:03.135 wdl.w:ptcp.t:call-pbmm2_align_hifi-87 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:22:03.136 wdl.w:ptcp.t:call-pbmm2_align_hifi-89 INFO eval :: name: "threads", value: 64
2025-09-15 20:22:03.137 wdl.w:ptcp.t:call-pbmm2_align_hifi-88 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 64, memory_reservation: 64000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:22:03.137 wdl.w:ptcp.t:call-pbmm2_align_hifi-89 INFO eval :: name: "mem_gb", value: 64
2025-09-15 20:22:03.137 wdl.w:ptcp.t:call-pbmm2_align_hifi-88 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:22:03.138 wdl.w:ptcp.t:call-pbmm2_align_hifi-89 INFO eval :: name: "disk_size", value: 30
2025-09-15 20:22:03.139 wdl.w:ptcp.t:call-pbmm2_align_hifi-88 INFO provisioned :: seconds_waited: 0, cpu: 64, mem_bytes: 64000000000
2025-09-15 20:22:03.140 wdl.w:ptcp.t:call-pbmm2_align_hifi-89 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 64, memory_reservation: 64000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:22:03.140 wdl.w:ptcp.t:call-pbmm2_align_hifi-88 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:22:03.140 wdl.w:ptcp.t:call-pbmm2_align_hifi-89 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:22:03.142 wdl.w:ptcp.t:call-pbmm2_align_hifi-89 INFO provisioned :: seconds_waited: 0, cpu: 64, mem_bytes: 64000000000
2025-09-15 20:22:03.143 wdl.w:ptcp.t:call-pbmm2_align_hifi-89 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:22:03.144 wdl.w:ptcp INFO visit :: node: "gather-decl-unmapped_bam", values: "(((large)))"
2025-09-15 20:22:03.150 wdl.w:ptcp.t:call-pbmm2_align_hifi-94 NOTICE task setup :: name: "pbmm2_align_hifi", source: "./common.wdl", line: 170, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-94", thread: 140606617675328
2025-09-15 20:22:03.150 wdl.w:ptcp.t:call-pbmm2_align_hifi-90 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:22:03.151 wdl.w:ptcp.t:call-pbmm2_align_hifi-90 INFO input :: name: "log_level", value: "INFO"
2025-09-15 20:22:03.151 wdl.w:ptcp.t:call-pbmm2_align_hifi-90 INFO input :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2187.mapped"
2025-09-15 20:22:03.152 wdl.w:ptcp.t:call-pbmm2_align_hifi-90 INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:22:03.152 wdl.w:ptcp.t:call-pbmm2_align_hifi-90 INFO input :: name: "unmapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0091_m84036_250809_035451_s4.bc2187.unmapped.bam"
2025-09-15 20:22:03.152 wdl.w:ptcp.t:call-pbmm2_align_hifi-90 INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2187"
2025-09-15 20:22:03.153 wdl.w:ptcp.t:call-pbmm2_align_hifi-90 INFO eval :: name: "threads", value: 64
2025-09-15 20:22:03.153 wdl.w:ptcp.t:call-pbmm2_align_hifi-90 INFO eval :: name: "mem_gb", value: 64
2025-09-15 20:22:03.154 wdl.w:ptcp.t:call-pbmm2_align_hifi-90 INFO eval :: name: "disk_size", value: 30
2025-09-15 20:22:03.155 wdl.w:ptcp.t:call-pbmm2_align_hifi-90 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 64, memory_reservation: 64000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:22:03.156 wdl.w:ptcp.t:call-pbmm2_align_hifi-90 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:22:03.157 wdl.w:ptcp.t:call-pbmm2_align_hifi-90 INFO provisioned :: seconds_waited: 0, cpu: 64, mem_bytes: 64000000000
2025-09-15 20:22:03.157 wdl.w:ptcp.t:call-pbmm2_align_hifi-90 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:22:03.160 wdl.w:ptcp.t:call-pbmm2_align_hifi-91 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:22:03.160 wdl.w:ptcp.t:call-pbmm2_align_hifi-91 INFO input :: name: "log_level", value: "INFO"
2025-09-15 20:22:03.160 wdl.w:ptcp.t:call-pbmm2_align_hifi-74 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 8, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-74/_singularity_tmpdir_qvcgcfeo"
2025-09-15 20:22:03.161 wdl.w:ptcp.t:call-pbmm2_align_hifi-91 INFO input :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2188.mapped"
2025-09-15 20:22:03.161 wdl.w:ptcp.t:call-pbmm2_align_hifi-74 INFO Slurm invocation: srun --job-name call-pbmm2_align_hifi-74 --partition compute,compute9 --cpus-per-task 64 --mem 61035M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-74/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-74/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-74/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-74/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0075_m84036_250809_035451_s4.bc2171.unmapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0075_m84036_250809_035451_s4.bc2171.unmapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-74/_singularity_tmpdir_qvcgcfeo/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-74/_singularity_tmpdir_qvcgcfeo/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:22:03.161 wdl.w:ptcp.t:call-pbmm2_align_hifi-91 INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:22:03.161 wdl.w:ptcp.t:call-pbmm2_align_hifi-91 INFO input :: name: "unmapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0092_m84036_250809_035451_s4.bc2188.unmapped.bam"
2025-09-15 20:22:03.161 wdl.w:ptcp.t:call-pbmm2_align_hifi-91 INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2188"
2025-09-15 20:22:03.161 wdl.w:ptcp.t:call-pbmm2_align_hifi-91 INFO eval :: name: "threads", value: 64
2025-09-15 20:22:03.163 wdl.w:ptcp.t:call-pbmm2_align_hifi-91 INFO eval :: name: "mem_gb", value: 64
2025-09-15 20:22:03.164 wdl.w:ptcp.t:call-pbmm2_align_hifi-91 INFO eval :: name: "disk_size", value: 30
2025-09-15 20:22:03.165 wdl.w:ptcp.t:call-pbmm2_align_hifi-91 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 64, memory_reservation: 64000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:22:03.166 wdl.w:ptcp.t:call-pbmm2_align_hifi-92 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:22:03.167 wdl.w:ptcp.t:call-pbmm2_align_hifi-69 NOTICE slurm_singularity run :: pid: 1197355, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-69/slurm_singularity.log.txt"
2025-09-15 20:22:03.167 wdl.w:ptcp.t:call-pbmm2_align_hifi-91 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:22:03.168 wdl.w:ptcp.t:call-pbmm2_align_hifi-92 INFO input :: name: "log_level", value: "INFO"
2025-09-15 20:22:03.168 wdl.w:ptcp.t:call-pbmm2_align_hifi-92 INFO input :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2189.mapped"
2025-09-15 20:22:03.168 wdl.w:ptcp.t:call-pbmm2_align_hifi-92 INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:22:03.168 wdl.w:ptcp.t:call-pbmm2_align_hifi-92 INFO input :: name: "unmapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0093_m84036_250809_035451_s4.bc2189.unmapped.bam"
2025-09-15 20:22:03.168 wdl.w:ptcp.t:call-pbmm2_align_hifi-91 INFO provisioned :: seconds_waited: 0, cpu: 64, mem_bytes: 64000000000
2025-09-15 20:22:03.169 wdl.w:ptcp.t:call-pbmm2_align_hifi-92 INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2189"
2025-09-15 20:22:03.169 wdl.w:ptcp.t:call-pbmm2_align_hifi-91 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:22:03.169 wdl.w:ptcp.t:call-pbmm2_align_hifi-92 INFO eval :: name: "threads", value: 64
2025-09-15 20:22:03.169 wdl.w:ptcp.t:call-pbmm2_align_hifi-92 INFO eval :: name: "mem_gb", value: 64
2025-09-15 20:22:03.170 wdl.w:ptcp.t:call-pbmm2_align_hifi-92 INFO eval :: name: "disk_size", value: 30
2025-09-15 20:22:03.173 wdl.w:ptcp.t:call-pbmm2_align_hifi-92 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 64, memory_reservation: 64000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:22:03.173 wdl.w:ptcp.t:call-pbmm2_align_hifi-92 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:22:03.173 wdl.w:ptcp.t:call-pbmm2_align_hifi-92 INFO provisioned :: seconds_waited: 0, cpu: 64, mem_bytes: 64000000000
2025-09-15 20:22:03.173 wdl.w:ptcp.t:call-pbmm2_align_hifi-73 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 8, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-73/_singularity_tmpdir_g4imu2v0"
2025-09-15 20:22:03.174 wdl.w:ptcp.t:call-pbmm2_align_hifi-72 NOTICE slurm_singularity run :: pid: 1197367, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-72/slurm_singularity.log.txt"
2025-09-15 20:22:03.174 wdl.w:ptcp.t:call-pbmm2_align_hifi-71 NOTICE slurm_singularity run :: pid: 1197366, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-71/slurm_singularity.log.txt"
2025-09-15 20:22:03.174 wdl.w:ptcp.t:call-pbmm2_align_hifi-92 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:22:03.174 wdl.w:ptcp.t:call-pbmm2_align_hifi-70 NOTICE slurm_singularity run :: pid: 1197364, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-70/slurm_singularity.log.txt"
2025-09-15 20:22:03.174 wdl.w:ptcp.t:call-pbmm2_align_hifi-73 INFO Slurm invocation: srun --job-name call-pbmm2_align_hifi-73 --partition compute,compute9 --cpus-per-task 64 --mem 61035M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-73/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-73/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-73/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-73/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0074_m84036_250809_035451_s4.bc2170.unmapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0074_m84036_250809_035451_s4.bc2170.unmapped.bam:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-73/_singularity_tmpdir_g4imu2v0/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-73/_singularity_tmpdir_g4imu2v0/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:22:03.176 wdl.w:ptcp.t:call-pbmm2_align_hifi-95 NOTICE task setup :: name: "pbmm2_align_hifi", source: "./common.wdl", line: 170, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-95", thread: 140606609282624
2025-09-15 20:22:03.178 wdl.w:ptcp.t:call-pbmm2_align_hifi-93 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:22:03.178 wdl.w:ptcp.t:call-pbmm2_align_hifi-93 INFO input :: name: "log_level", value: "INFO"
2025-09-15 20:22:03.178 wdl.w:ptcp.t:call-pbmm2_align_hifi-93 INFO input :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2190.mapped"
2025-09-15 20:22:03.178 wdl.w:ptcp.t:call-pbmm2_align_hifi-93 INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:22:03.179 wdl.w:ptcp.t:call-pbmm2_align_hifi-93 INFO input :: name: "unmapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0094_m84036_250809_035451_s4.bc2190.unmapped.bam"
2025-09-15 20:22:03.179 wdl.w:ptcp.t:call-pbmm2_align_hifi-93 INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2190"
2025-09-15 20:22:03.179 wdl.w:ptcp.t:call-pbmm2_align_hifi-93 INFO eval :: name: "threads", value: 64
2025-09-15 20:22:03.179 wdl.w:ptcp.t:call-pbmm2_align_hifi-93 INFO eval :: name: "mem_gb", value: 64
2025-09-15 20:22:03.179 wdl.w:ptcp.t:call-pbmm2_align_hifi-93 INFO eval :: name: "disk_size", value: 30
2025-09-15 20:22:03.179 wdl.w:ptcp.t:call-pbmm2_align_hifi-93 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 64, memory_reservation: 64000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:22:03.180 wdl.w:ptcp.t:call-pbmm2_align_hifi-93 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:22:03.180 wdl.w:ptcp.t:call-pbmm2_align_hifi-93 INFO provisioned :: seconds_waited: 0, cpu: 64, mem_bytes: 64000000000
2025-09-15 20:22:03.180 wdl.w:ptcp.t:call-pbmm2_align_hifi-93 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:22:03.193 wdl.w:ptcp.t:call-pbmm2_align_hifi-75 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 8, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-75/_singularity_tmpdir_9cpgnwmh"
2025-09-15 20:22:03.194 wdl.w:ptcp.t:call-pbmm2_align_hifi-76 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 8, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-76/_singularity_tmpdir_sfup2783"
2025-09-15 20:22:03.194 wdl.w:ptcp.t:call-pbmm2_align_hifi-75 INFO Slurm invocation: srun --job-name call-pbmm2_align_hifi-75 --partition compute,compute9 --cpus-per-task 64 --mem 61035M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-75/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-75/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-75/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-75/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0076_m84036_250809_035451_s4.bc2172.unmapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0076_m84036_250809_035451_s4.bc2172.unmapped.bam:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-75/_singularity_tmpdir_9cpgnwmh/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-75/_singularity_tmpdir_9cpgnwmh/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:22:03.194 wdl.w:ptcp.t:call-pbmm2_align_hifi-76 INFO Slurm invocation: srun --job-name call-pbmm2_align_hifi-76 --partition compute,compute9 --cpus-per-task 64 --mem 61035M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-76/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-76/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-76/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-76/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0077_m84036_250809_035451_s4.bc2173.unmapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0077_m84036_250809_035451_s4.bc2173.unmapped.bam:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-76/_singularity_tmpdir_sfup2783/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-76/_singularity_tmpdir_sfup2783/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:22:03.197 wdl.w:ptcp.t:call-pbmm2_align_hifi-94 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:22:03.197 wdl.w:ptcp.t:call-pbmm2_align_hifi-94 INFO input :: name: "log_level", value: "INFO"
2025-09-15 20:22:03.197 wdl.w:ptcp.t:call-pbmm2_align_hifi-94 INFO input :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2191.mapped"
2025-09-15 20:22:03.197 wdl.w:ptcp.t:call-pbmm2_align_hifi-94 INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:22:03.198 wdl.w:ptcp.t:call-pbmm2_align_hifi-94 INFO input :: name: "unmapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0095_m84036_250809_035451_s4.bc2191.unmapped.bam"
2025-09-15 20:22:03.198 wdl.w:ptcp.t:call-pbmm2_align_hifi-94 INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2191"
2025-09-15 20:22:03.198 wdl.w:ptcp.t:call-pbmm2_align_hifi-94 INFO eval :: name: "threads", value: 64
2025-09-15 20:22:03.198 wdl.w:ptcp.t:call-pbmm2_align_hifi-94 INFO eval :: name: "mem_gb", value: 64
2025-09-15 20:22:03.198 wdl.w:ptcp.t:call-pbmm2_align_hifi-94 INFO eval :: name: "disk_size", value: 30
2025-09-15 20:22:03.198 wdl.w:ptcp.t:call-pbmm2_align_hifi-94 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 64, memory_reservation: 64000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:22:03.199 wdl.w:ptcp.t:call-pbmm2_align_hifi-94 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:22:03.199 wdl.w:ptcp.t:call-pbmm2_align_hifi-94 INFO provisioned :: seconds_waited: 0, cpu: 64, mem_bytes: 64000000000
2025-09-15 20:22:03.199 wdl.w:ptcp.t:call-pbmm2_align_hifi-94 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:22:03.207 wdl.w:ptcp.t:call-pbmm2_align_hifi-74 NOTICE slurm_singularity run :: pid: 1197405, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-74/slurm_singularity.log.txt"
2025-09-15 20:22:03.209 wdl.w:ptcp.t:call-pbmm2_align_hifi-77 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 8, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-77/_singularity_tmpdir_4spw7ra6"
2025-09-15 20:22:03.209 wdl.w:ptcp.t:call-pbmm2_align_hifi-77 INFO Slurm invocation: srun --job-name call-pbmm2_align_hifi-77 --partition compute,compute9 --cpus-per-task 64 --mem 61035M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-77/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-77/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-77/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-77/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0078_m84036_250809_035451_s4.bc2174.unmapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0078_m84036_250809_035451_s4.bc2174.unmapped.bam:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-77/_singularity_tmpdir_4spw7ra6/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-77/_singularity_tmpdir_4spw7ra6/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:22:03.212 wdl.w:ptcp.t:call-pbmm2_align_hifi-95 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:22:03.213 wdl.w:ptcp.t:call-pbmm2_align_hifi-95 INFO input :: name: "log_level", value: "INFO"
2025-09-15 20:22:03.213 wdl.w:ptcp.t:call-pbmm2_align_hifi-95 INFO input :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2192.mapped"
2025-09-15 20:22:03.213 wdl.w:ptcp.t:call-pbmm2_align_hifi-95 INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:22:03.213 wdl.w:ptcp.t:call-pbmm2_align_hifi-95 INFO input :: name: "unmapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0096_m84036_250809_035451_s4.bc2192.unmapped.bam"
2025-09-15 20:22:03.213 wdl.w:ptcp.t:call-pbmm2_align_hifi-95 INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2192"
2025-09-15 20:22:03.214 wdl.w:ptcp.t:call-pbmm2_align_hifi-95 INFO eval :: name: "threads", value: 64
2025-09-15 20:22:03.214 wdl.w:ptcp.t:call-pbmm2_align_hifi-95 INFO eval :: name: "mem_gb", value: 64
2025-09-15 20:22:03.214 wdl.w:ptcp.t:call-pbmm2_align_hifi-95 INFO eval :: name: "disk_size", value: 30
2025-09-15 20:22:03.214 wdl.w:ptcp.t:call-pbmm2_align_hifi-95 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 64, memory_reservation: 64000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:22:03.215 wdl.w:ptcp.t:call-pbmm2_align_hifi-95 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:22:03.215 wdl.w:ptcp.t:call-pbmm2_align_hifi-95 INFO provisioned :: seconds_waited: 0, cpu: 64, mem_bytes: 64000000000
2025-09-15 20:22:03.215 wdl.w:ptcp.t:call-pbmm2_align_hifi-95 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:22:03.227 wdl.w:ptcp.t:call-pbmm2_align_hifi-73 NOTICE slurm_singularity run :: pid: 1197413, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-73/slurm_singularity.log.txt"
2025-09-15 20:22:03.227 wdl.w:ptcp.t:call-pbmm2_align_hifi-75 NOTICE slurm_singularity run :: pid: 1197419, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-75/slurm_singularity.log.txt"
2025-09-15 20:22:03.232 wdl.w:ptcp.t:call-pbmm2_align_hifi-76 NOTICE slurm_singularity run :: pid: 1197420, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-76/slurm_singularity.log.txt"
2025-09-15 20:22:03.232 wdl.w:ptcp.t:call-pbmm2_align_hifi-77 NOTICE slurm_singularity run :: pid: 1197421, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-77/slurm_singularity.log.txt"
2025-09-15 20:22:03.233 wdl.w:ptcp.t:call-pbmm2_align_hifi-78 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 8, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-78/_singularity_tmpdir_jrn9vmq8"
2025-09-15 20:22:03.233 wdl.w:ptcp.t:call-pbmm2_align_hifi-78 INFO Slurm invocation: srun --job-name call-pbmm2_align_hifi-78 --partition compute,compute9 --cpus-per-task 64 --mem 61035M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-78/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-78/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-78/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-78/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0079_m84036_250809_035451_s4.bc2175.unmapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0079_m84036_250809_035451_s4.bc2175.unmapped.bam:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-78/_singularity_tmpdir_jrn9vmq8/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-78/_singularity_tmpdir_jrn9vmq8/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:22:03.243 wdl.w:ptcp.t:call-pbmm2_align_hifi-79 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 8, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-79/_singularity_tmpdir_bt_a23m1"
2025-09-15 20:22:03.243 wdl.w:ptcp.t:call-pbmm2_align_hifi-79 INFO Slurm invocation: srun --job-name call-pbmm2_align_hifi-79 --partition compute,compute9 --cpus-per-task 64 --mem 61035M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-79/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-79/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-79/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-79/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0080_m84036_250809_035451_s4.bc2176.unmapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0080_m84036_250809_035451_s4.bc2176.unmapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-79/_singularity_tmpdir_bt_a23m1/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-79/_singularity_tmpdir_bt_a23m1/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:22:03.250 wdl.w:ptcp.t:call-pbmm2_align_hifi-80 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 8, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-80/_singularity_tmpdir_xr_64p94"
2025-09-15 20:22:03.250 wdl.w:ptcp.t:call-pbmm2_align_hifi-80 INFO Slurm invocation: srun --job-name call-pbmm2_align_hifi-80 --partition compute,compute9 --cpus-per-task 64 --mem 61035M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-80/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-80/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-80/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-80/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0081_m84036_250809_035451_s4.bc2177.unmapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0081_m84036_250809_035451_s4.bc2177.unmapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-80/_singularity_tmpdir_xr_64p94/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-80/_singularity_tmpdir_xr_64p94/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:22:03.253 wdl.w:ptcp.t:call-pbmm2_align_hifi-82 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 8, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-82/_singularity_tmpdir_7mew3o7t"
2025-09-15 20:22:03.254 wdl.w:ptcp.t:call-pbmm2_align_hifi-82 INFO Slurm invocation: srun --job-name call-pbmm2_align_hifi-82 --partition compute,compute9 --cpus-per-task 64 --mem 61035M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-82/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-82/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-82/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-82/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0083_m84036_250809_035451_s4.bc2179.unmapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0083_m84036_250809_035451_s4.bc2179.unmapped.bam:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-82/_singularity_tmpdir_7mew3o7t/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-82/_singularity_tmpdir_7mew3o7t/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:22:03.255 wdl.w:ptcp.t:call-pbmm2_align_hifi-79 NOTICE slurm_singularity run :: pid: 1197427, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-79/slurm_singularity.log.txt"
2025-09-15 20:22:03.256 wdl.w:ptcp.t:call-pbmm2_align_hifi-81 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 8, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-81/_singularity_tmpdir_jefas279"
2025-09-15 20:22:03.257 wdl.w:ptcp.t:call-pbmm2_align_hifi-78 NOTICE slurm_singularity run :: pid: 1197425, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-78/slurm_singularity.log.txt"
2025-09-15 20:22:03.257 wdl.w:ptcp.t:call-pbmm2_align_hifi-81 INFO Slurm invocation: srun --job-name call-pbmm2_align_hifi-81 --partition compute,compute9 --cpus-per-task 64 --mem 61035M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-81/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-81/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-81/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-81/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0082_m84036_250809_035451_s4.bc2178.unmapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0082_m84036_250809_035451_s4.bc2178.unmapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-81/_singularity_tmpdir_jefas279/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-81/_singularity_tmpdir_jefas279/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:22:03.257 wdl.w:ptcp.t:call-pbmm2_align_hifi-85 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 8, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-85/_singularity_tmpdir_tjdpckrz"
2025-09-15 20:22:03.259 wdl.w:ptcp.t:call-pbmm2_align_hifi-84 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 8, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-84/_singularity_tmpdir_f0np8hoj"
2025-09-15 20:22:03.259 wdl.w:ptcp.t:call-pbmm2_align_hifi-85 INFO Slurm invocation: srun --job-name call-pbmm2_align_hifi-85 --partition compute,compute9 --cpus-per-task 64 --mem 61035M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-85/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-85/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-85/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-85/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0086_m84036_250809_035451_s4.bc2182.unmapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0086_m84036_250809_035451_s4.bc2182.unmapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-85/_singularity_tmpdir_tjdpckrz/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-85/_singularity_tmpdir_tjdpckrz/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:22:03.259 wdl.w:ptcp.t:call-pbmm2_align_hifi-84 INFO Slurm invocation: srun --job-name call-pbmm2_align_hifi-84 --partition compute,compute9 --cpus-per-task 64 --mem 61035M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-84/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-84/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-84/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-84/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0085_m84036_250809_035451_s4.bc2181.unmapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0085_m84036_250809_035451_s4.bc2181.unmapped.bam:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-84/_singularity_tmpdir_f0np8hoj/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-84/_singularity_tmpdir_f0np8hoj/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:22:03.264 wdl.w:ptcp.t:call-pbmm2_align_hifi-80 NOTICE slurm_singularity run :: pid: 1197428, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-80/slurm_singularity.log.txt"
2025-09-15 20:22:03.264 wdl.w:ptcp.t:call-pbmm2_align_hifi-84 NOTICE slurm_singularity run :: pid: 1197432, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-84/slurm_singularity.log.txt"
2025-09-15 20:22:03.264 wdl.w:ptcp.t:call-pbmm2_align_hifi-81 NOTICE slurm_singularity run :: pid: 1197430, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-81/slurm_singularity.log.txt"
2025-09-15 20:22:03.265 wdl.w:ptcp.t:call-pbmm2_align_hifi-82 NOTICE slurm_singularity run :: pid: 1197429, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-82/slurm_singularity.log.txt"
2025-09-15 20:22:03.265 wdl.w:ptcp.t:call-pbmm2_align_hifi-85 NOTICE slurm_singularity run :: pid: 1197431, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-85/slurm_singularity.log.txt"
2025-09-15 20:22:03.269 wdl.w:ptcp.t:call-pbmm2_align_hifi-83 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 8, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-83/_singularity_tmpdir_nteu_ico"
2025-09-15 20:22:03.269 wdl.w:ptcp.t:call-pbmm2_align_hifi-83 INFO Slurm invocation: srun --job-name call-pbmm2_align_hifi-83 --partition compute,compute9 --cpus-per-task 64 --mem 61035M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-83/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-83/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-83/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-83/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0084_m84036_250809_035451_s4.bc2180.unmapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0084_m84036_250809_035451_s4.bc2180.unmapped.bam:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-83/_singularity_tmpdir_nteu_ico/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-83/_singularity_tmpdir_nteu_ico/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:22:03.270 wdl.w:ptcp.t:call-pbmm2_align_hifi-86 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 8, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-86/_singularity_tmpdir__eublqqu"
2025-09-15 20:22:03.272 wdl.w:ptcp.t:call-pbmm2_align_hifi-86 INFO Slurm invocation: srun --job-name call-pbmm2_align_hifi-86 --partition compute,compute9 --cpus-per-task 64 --mem 61035M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-86/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-86/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-86/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-86/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0087_m84036_250809_035451_s4.bc2183.unmapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0087_m84036_250809_035451_s4.bc2183.unmapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-86/_singularity_tmpdir__eublqqu/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-86/_singularity_tmpdir__eublqqu/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:22:03.273 wdl.w:ptcp.t:call-pbmm2_align_hifi-87 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 8, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-87/_singularity_tmpdir_bqglmriv"
2025-09-15 20:22:03.275 wdl.w:ptcp.t:call-pbmm2_align_hifi-88 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 8, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-88/_singularity_tmpdir_exzg00fx"
2025-09-15 20:22:03.275 wdl.w:ptcp.t:call-pbmm2_align_hifi-89 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 8, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-89/_singularity_tmpdir_d91sct1d"
2025-09-15 20:22:03.276 wdl.w:ptcp.t:call-pbmm2_align_hifi-87 INFO Slurm invocation: srun --job-name call-pbmm2_align_hifi-87 --partition compute,compute9 --cpus-per-task 64 --mem 61035M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-87/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-87/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-87/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-87/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0088_m84036_250809_035451_s4.bc2184.unmapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0088_m84036_250809_035451_s4.bc2184.unmapped.bam:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-87/_singularity_tmpdir_bqglmriv/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-87/_singularity_tmpdir_bqglmriv/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:22:03.277 wdl.w:ptcp.t:call-pbmm2_align_hifi-88 INFO Slurm invocation: srun --job-name call-pbmm2_align_hifi-88 --partition compute,compute9 --cpus-per-task 64 --mem 61035M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-88/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-88/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-88/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-88/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0089_m84036_250809_035451_s4.bc2185.unmapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0089_m84036_250809_035451_s4.bc2185.unmapped.bam:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-88/_singularity_tmpdir_exzg00fx/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-88/_singularity_tmpdir_exzg00fx/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:22:03.277 wdl.w:ptcp.t:call-pbmm2_align_hifi-89 INFO Slurm invocation: srun --job-name call-pbmm2_align_hifi-89 --partition compute,compute9 --cpus-per-task 64 --mem 61035M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-89/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-89/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-89/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-89/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0090_m84036_250809_035451_s4.bc2186.unmapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0090_m84036_250809_035451_s4.bc2186.unmapped.bam:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-89/_singularity_tmpdir_d91sct1d/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-89/_singularity_tmpdir_d91sct1d/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:22:03.280 wdl.w:ptcp.t:call-pbmm2_align_hifi-90 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 8, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-90/_singularity_tmpdir_712hwfi8"
2025-09-15 20:22:03.280 wdl.w:ptcp.t:call-pbmm2_align_hifi-90 INFO Slurm invocation: srun --job-name call-pbmm2_align_hifi-90 --partition compute,compute9 --cpus-per-task 64 --mem 61035M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-90/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-90/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-90/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-90/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0091_m84036_250809_035451_s4.bc2187.unmapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0091_m84036_250809_035451_s4.bc2187.unmapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-90/_singularity_tmpdir_712hwfi8/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-90/_singularity_tmpdir_712hwfi8/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:22:03.286 wdl.w:ptcp.t:call-pbmm2_align_hifi-92 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 8, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-92/_singularity_tmpdir_1j11houd"
2025-09-15 20:22:03.286 wdl.w:ptcp.t:call-pbmm2_align_hifi-92 INFO Slurm invocation: srun --job-name call-pbmm2_align_hifi-92 --partition compute,compute9 --cpus-per-task 64 --mem 61035M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-92/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-92/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-92/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-92/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0093_m84036_250809_035451_s4.bc2189.unmapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0093_m84036_250809_035451_s4.bc2189.unmapped.bam:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-92/_singularity_tmpdir_1j11houd/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-92/_singularity_tmpdir_1j11houd/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:22:03.286 wdl.w:ptcp.t:call-pbmm2_align_hifi-93 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 8, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-93/_singularity_tmpdir_evn2im75"
2025-09-15 20:22:03.287 wdl.w:ptcp.t:call-pbmm2_align_hifi-93 INFO Slurm invocation: srun --job-name call-pbmm2_align_hifi-93 --partition compute,compute9 --cpus-per-task 64 --mem 61035M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-93/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-93/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-93/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-93/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0094_m84036_250809_035451_s4.bc2190.unmapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0094_m84036_250809_035451_s4.bc2190.unmapped.bam:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-93/_singularity_tmpdir_evn2im75/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-93/_singularity_tmpdir_evn2im75/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:22:03.291 wdl.w:ptcp.t:call-pbmm2_align_hifi-91 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 8, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-91/_singularity_tmpdir_lq8h_xjm"
2025-09-15 20:22:03.291 wdl.w:ptcp.t:call-pbmm2_align_hifi-91 INFO Slurm invocation: srun --job-name call-pbmm2_align_hifi-91 --partition compute,compute9 --cpus-per-task 64 --mem 61035M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-91/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-91/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-91/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-91/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0092_m84036_250809_035451_s4.bc2188.unmapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0092_m84036_250809_035451_s4.bc2188.unmapped.bam:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-91/_singularity_tmpdir_lq8h_xjm/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-91/_singularity_tmpdir_lq8h_xjm/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:22:03.300 wdl.w:ptcp.t:call-pbmm2_align_hifi-94 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 8, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-94/_singularity_tmpdir_i3w003dx"
2025-09-15 20:22:03.300 wdl.w:ptcp.t:call-pbmm2_align_hifi-94 INFO Slurm invocation: srun --job-name call-pbmm2_align_hifi-94 --partition compute,compute9 --cpus-per-task 64 --mem 61035M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-94/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-94/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-94/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-94/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0095_m84036_250809_035451_s4.bc2191.unmapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0095_m84036_250809_035451_s4.bc2191.unmapped.bam:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-94/_singularity_tmpdir_i3w003dx/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-94/_singularity_tmpdir_i3w003dx/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:22:03.301 wdl.w:ptcp.t:call-pbmm2_align_hifi-95 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 8, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-95/_singularity_tmpdir_cbv5pguf"
2025-09-15 20:22:03.302 wdl.w:ptcp.t:call-pbmm2_align_hifi-95 INFO Slurm invocation: srun --job-name call-pbmm2_align_hifi-95 --partition compute,compute9 --cpus-per-task 64 --mem 61035M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-95/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-95/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-95/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-95/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-collect_inputs/out/sample0096_m84036_250809_035451_s4.bc2192.unmapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0096_m84036_250809_035451_s4.bc2192.unmapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-95/_singularity_tmpdir_cbv5pguf/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-95/_singularity_tmpdir_cbv5pguf/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:22:03.312 wdl.w:ptcp.t:call-pbmm2_align_hifi-88 NOTICE slurm_singularity run :: pid: 1197463, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-88/slurm_singularity.log.txt"
2025-09-15 20:22:03.312 wdl.w:ptcp.t:call-pbmm2_align_hifi-92 NOTICE slurm_singularity run :: pid: 1197476, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-92/slurm_singularity.log.txt"
2025-09-15 20:22:03.312 wdl.w:ptcp.t:call-pbmm2_align_hifi-93 NOTICE slurm_singularity run :: pid: 1197477, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-93/slurm_singularity.log.txt"
2025-09-15 20:22:03.312 wdl.w:ptcp.t:call-pbmm2_align_hifi-89 NOTICE slurm_singularity run :: pid: 1197464, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-89/slurm_singularity.log.txt"
2025-09-15 20:22:03.312 wdl.w:ptcp.t:call-pbmm2_align_hifi-95 NOTICE slurm_singularity run :: pid: 1197495, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-95/slurm_singularity.log.txt"
2025-09-15 20:22:03.312 wdl.w:ptcp.t:call-pbmm2_align_hifi-87 NOTICE slurm_singularity run :: pid: 1197462, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-87/slurm_singularity.log.txt"
2025-09-15 20:22:03.313 wdl.w:ptcp.t:call-pbmm2_align_hifi-91 NOTICE slurm_singularity run :: pid: 1197483, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-91/slurm_singularity.log.txt"
2025-09-15 20:22:03.313 wdl.w:ptcp.t:call-pbmm2_align_hifi-86 NOTICE slurm_singularity run :: pid: 1197448, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-86/slurm_singularity.log.txt"
2025-09-15 20:22:03.313 wdl.w:ptcp.t:call-pbmm2_align_hifi-94 NOTICE slurm_singularity run :: pid: 1197492, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-94/slurm_singularity.log.txt"
2025-09-15 20:22:03.313 wdl.w:ptcp.t:call-pbmm2_align_hifi-83 NOTICE slurm_singularity run :: pid: 1197440, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-83/slurm_singularity.log.txt"
2025-09-15 20:22:03.313 wdl.w:ptcp.t:call-pbmm2_align_hifi-90 NOTICE slurm_singularity run :: pid: 1197468, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-90/slurm_singularity.log.txt"
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2025-09-15 20:22:04.495 wdl.w:ptcp.t:call-pbmm2_align_hifi-04.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:22:04.503 wdl.w:ptcp.t:call-pbmm2_align_hifi-05.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:22:04.503 wdl.w:ptcp.t:call-pbmm2_align_hifi-05.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:22:04.505 wdl.w:ptcp.t:call-pbmm2_align_hifi-06.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:22:04.505 wdl.w:ptcp.t:call-pbmm2_align_hifi-06.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:22:04.508 wdl.w:ptcp.t:call-pbmm2_align_hifi-09.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:22:04.508 wdl.w:ptcp.t:call-pbmm2_align_hifi-09.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:22:04.515 wdl.w:ptcp.t:call-pbmm2_align_hifi-07.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:22:04.515 wdl.w:ptcp.t:call-pbmm2_align_hifi-07.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:22:04.566 wdl.w:ptcp.t:call-pbmm2_align_hifi-08.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:22:04.571 wdl.w:ptcp.t:call-pbmm2_align_hifi-10.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:22:04.571 wdl.w:ptcp.t:call-pbmm2_align_hifi-10.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:22:04.571 wdl.w:ptcp.t:call-pbmm2_align_hifi-13.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:22:04.573 wdl.w:ptcp.t:call-pbmm2_align_hifi-12.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:22:04.578 wdl.w:ptcp.t:call-pbmm2_align_hifi-11.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:22:04.583 wdl.w:ptcp.t:call-pbmm2_align_hifi-14.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:22:04.583 wdl.w:ptcp.t:call-pbmm2_align_hifi-14.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:22:04.586 wdl.w:ptcp.t:call-pbmm2_align_hifi-15.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:22:04.586 wdl.w:ptcp.t:call-pbmm2_align_hifi-15.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:22:04.587 wdl.w:ptcp.t:call-pbmm2_align_hifi-18.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:22:04.587 wdl.w:ptcp.t:call-pbmm2_align_hifi-18.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:22:04.592 wdl.w:ptcp.t:call-pbmm2_align_hifi-19.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:22:04.592 wdl.w:ptcp.t:call-pbmm2_align_hifi-19.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:22:04.599 wdl.w:ptcp.t:call-pbmm2_align_hifi-16.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:22:04.599 wdl.w:ptcp.t:call-pbmm2_align_hifi-16.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:22:04.653 wdl.w:ptcp.t:call-pbmm2_align_hifi-17.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:22:04.653 wdl.w:ptcp.t:call-pbmm2_align_hifi-17.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:22:04.665 wdl.w:ptcp.t:call-pbmm2_align_hifi-20.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:22:04.665 wdl.w:ptcp.t:call-pbmm2_align_hifi-20.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:22:04.666 wdl.w:ptcp.t:call-pbmm2_align_hifi-21.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:22:04.666 wdl.w:ptcp.t:call-pbmm2_align_hifi-21.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:22:04.671 wdl.w:ptcp.t:call-pbmm2_align_hifi-25.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:22:04.671 wdl.w:ptcp.t:call-pbmm2_align_hifi-25.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:22:06.476 wdl.w:ptcp.t:call-pbmm2_align_hifi-00.stderr VERBOSE 
2025-09-15 20:22:06.476 wdl.w:ptcp.t:call-pbmm2_align_hifi-00.stderr VERBOSE pbmm2 \
2025-09-15 20:22:06.476 wdl.w:ptcp.t:call-pbmm2_align_hifi-00.stderr VERBOSE   align \
2025-09-15 20:22:06.476 wdl.w:ptcp.t:call-pbmm2_align_hifi-00.stderr VERBOSE   --log-level INFO \
2025-09-15 20:22:06.476 wdl.w:ptcp.t:call-pbmm2_align_hifi-00.stderr VERBOSE   --log-file pbmm2.log \
2025-09-15 20:22:06.477 wdl.w:ptcp.t:call-pbmm2_align_hifi-00.stderr VERBOSE   --alarms alarms.json \
2025-09-15 20:22:06.477 wdl.w:ptcp.t:call-pbmm2_align_hifi-00.stderr VERBOSE   --num-threads 64 \
2025-09-15 20:22:06.477 wdl.w:ptcp.t:call-pbmm2_align_hifi-00.stderr VERBOSE   --sort \
2025-09-15 20:22:06.477 wdl.w:ptcp.t:call-pbmm2_align_hifi-00.stderr VERBOSE   --preset HiFi \
2025-09-15 20:22:06.477 wdl.w:ptcp.t:call-pbmm2_align_hifi-00.stderr VERBOSE   --report-json mapping_stats.report.json \
2025-09-15 20:22:06.477 wdl.w:ptcp.t:call-pbmm2_align_hifi-00.stderr VERBOSE   --sample "m84036_250809_035451_s4.bc2097" \
2025-09-15 20:22:06.477 wdl.w:ptcp.t:call-pbmm2_align_hifi-00.stderr VERBOSE   --unmapped \
2025-09-15 20:22:06.477 wdl.w:ptcp.t:call-pbmm2_align_hifi-00.stderr VERBOSE   /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa \
2025-09-15 20:22:06.477 wdl.w:ptcp.t:call-pbmm2_align_hifi-00.stderr VERBOSE   /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0001_m84036_250809_035451_s4.bc2097.unmapped.bam \
2025-09-15 20:22:06.477 wdl.w:ptcp.t:call-pbmm2_align_hifi-00.stderr VERBOSE   m84036_250809_035451_s4.bc2097.mapped.bam
2025-09-15 20:22:06.477 wdl.w:ptcp.t:call-pbmm2_align_hifi-00.stderr VERBOSE + pbmm2 align --log-level INFO --log-file pbmm2.log --alarms alarms.json --num-threads 64 --sort --preset HiFi --report-json mapping_stats.report.json --sample m84036_250809_035451_s4.bc2097 --unmapped /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0001_m84036_250809_035451_s4.bc2097.unmapped.bam m84036_250809_035451_s4.bc2097.mapped.bam
2025-09-15 20:22:06.478 wdl.w:ptcp.t:call-pbmm2_align_hifi-02.stderr VERBOSE 
2025-09-15 20:22:06.479 wdl.w:ptcp.t:call-pbmm2_align_hifi-02.stderr VERBOSE pbmm2 \
2025-09-15 20:22:06.479 wdl.w:ptcp.t:call-pbmm2_align_hifi-02.stderr VERBOSE   align \
2025-09-15 20:22:06.479 wdl.w:ptcp.t:call-pbmm2_align_hifi-02.stderr VERBOSE   --log-level INFO \
2025-09-15 20:22:06.479 wdl.w:ptcp.t:call-pbmm2_align_hifi-02.stderr VERBOSE   --log-file pbmm2.log \
2025-09-15 20:22:06.479 wdl.w:ptcp.t:call-pbmm2_align_hifi-02.stderr VERBOSE   --alarms alarms.json \
2025-09-15 20:22:06.479 wdl.w:ptcp.t:call-pbmm2_align_hifi-02.stderr VERBOSE   --num-threads 64 \
2025-09-15 20:22:06.479 wdl.w:ptcp.t:call-pbmm2_align_hifi-02.stderr VERBOSE   --sort \
2025-09-15 20:22:06.479 wdl.w:ptcp.t:call-pbmm2_align_hifi-02.stderr VERBOSE   --preset HiFi \
2025-09-15 20:22:06.479 wdl.w:ptcp.t:call-pbmm2_align_hifi-02.stderr VERBOSE   --report-json mapping_stats.report.json \
2025-09-15 20:22:06.479 wdl.w:ptcp.t:call-pbmm2_align_hifi-02.stderr VERBOSE   --sample "m84036_250809_035451_s4.bc2099" \
2025-09-15 20:22:06.479 wdl.w:ptcp.t:call-pbmm2_align_hifi-02.stderr VERBOSE   --unmapped \
2025-09-15 20:22:06.479 wdl.w:ptcp.t:call-pbmm2_align_hifi-02.stderr VERBOSE   /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa \
2025-09-15 20:22:06.479 wdl.w:ptcp.t:call-pbmm2_align_hifi-02.stderr VERBOSE   /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0003_m84036_250809_035451_s4.bc2099.unmapped.bam \
2025-09-15 20:22:06.479 wdl.w:ptcp.t:call-pbmm2_align_hifi-02.stderr VERBOSE   m84036_250809_035451_s4.bc2099.mapped.bam
2025-09-15 20:22:06.479 wdl.w:ptcp.t:call-pbmm2_align_hifi-03.stderr VERBOSE 
2025-09-15 20:22:06.479 wdl.w:ptcp.t:call-pbmm2_align_hifi-02.stderr VERBOSE + pbmm2 align --log-level INFO --log-file pbmm2.log --alarms alarms.json --num-threads 64 --sort --preset HiFi --report-json mapping_stats.report.json --sample m84036_250809_035451_s4.bc2099 --unmapped /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0003_m84036_250809_035451_s4.bc2099.unmapped.bam m84036_250809_035451_s4.bc2099.mapped.bam
2025-09-15 20:22:06.480 wdl.w:ptcp.t:call-pbmm2_align_hifi-03.stderr VERBOSE pbmm2 \
2025-09-15 20:22:06.480 wdl.w:ptcp.t:call-pbmm2_align_hifi-03.stderr VERBOSE   align \
2025-09-15 20:22:06.480 wdl.w:ptcp.t:call-pbmm2_align_hifi-03.stderr VERBOSE   --log-level INFO \
2025-09-15 20:22:06.480 wdl.w:ptcp.t:call-pbmm2_align_hifi-03.stderr VERBOSE   --log-file pbmm2.log \
2025-09-15 20:22:06.480 wdl.w:ptcp.t:call-pbmm2_align_hifi-03.stderr VERBOSE   --alarms alarms.json \
2025-09-15 20:22:06.480 wdl.w:ptcp.t:call-pbmm2_align_hifi-03.stderr VERBOSE   --num-threads 64 \
2025-09-15 20:22:06.480 wdl.w:ptcp.t:call-pbmm2_align_hifi-03.stderr VERBOSE   --sort \
2025-09-15 20:22:06.480 wdl.w:ptcp.t:call-pbmm2_align_hifi-03.stderr VERBOSE   --preset HiFi \
2025-09-15 20:22:06.480 wdl.w:ptcp.t:call-pbmm2_align_hifi-03.stderr VERBOSE   --report-json mapping_stats.report.json \
2025-09-15 20:22:06.480 wdl.w:ptcp.t:call-pbmm2_align_hifi-03.stderr VERBOSE   --sample "m84036_250809_035451_s4.bc2100" \
2025-09-15 20:22:06.480 wdl.w:ptcp.t:call-pbmm2_align_hifi-03.stderr VERBOSE   --unmapped \
2025-09-15 20:22:06.480 wdl.w:ptcp.t:call-pbmm2_align_hifi-03.stderr VERBOSE   /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa \
2025-09-15 20:22:06.480 wdl.w:ptcp.t:call-pbmm2_align_hifi-03.stderr VERBOSE   /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0004_m84036_250809_035451_s4.bc2100.unmapped.bam \
2025-09-15 20:22:06.480 wdl.w:ptcp.t:call-pbmm2_align_hifi-03.stderr VERBOSE   m84036_250809_035451_s4.bc2100.mapped.bam
2025-09-15 20:22:06.480 wdl.w:ptcp.t:call-pbmm2_align_hifi-03.stderr VERBOSE + pbmm2 align --log-level INFO --log-file pbmm2.log --alarms alarms.json --num-threads 64 --sort --preset HiFi --report-json mapping_stats.report.json --sample m84036_250809_035451_s4.bc2100 --unmapped /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0004_m84036_250809_035451_s4.bc2100.unmapped.bam m84036_250809_035451_s4.bc2100.mapped.bam
2025-09-15 20:22:06.483 wdl.w:ptcp.t:call-pbmm2_align_hifi-01.stderr VERBOSE 
2025-09-15 20:22:06.483 wdl.w:ptcp.t:call-pbmm2_align_hifi-01.stderr VERBOSE pbmm2 \
2025-09-15 20:22:06.483 wdl.w:ptcp.t:call-pbmm2_align_hifi-01.stderr VERBOSE   align \
2025-09-15 20:22:06.483 wdl.w:ptcp.t:call-pbmm2_align_hifi-01.stderr VERBOSE   --log-level INFO \
2025-09-15 20:22:06.483 wdl.w:ptcp.t:call-pbmm2_align_hifi-01.stderr VERBOSE   --log-file pbmm2.log \
2025-09-15 20:22:06.483 wdl.w:ptcp.t:call-pbmm2_align_hifi-01.stderr VERBOSE   --alarms alarms.json \
2025-09-15 20:22:06.483 wdl.w:ptcp.t:call-pbmm2_align_hifi-01.stderr VERBOSE   --num-threads 64 \
2025-09-15 20:22:06.483 wdl.w:ptcp.t:call-pbmm2_align_hifi-01.stderr VERBOSE   --sort \
2025-09-15 20:22:06.483 wdl.w:ptcp.t:call-pbmm2_align_hifi-01.stderr VERBOSE   --preset HiFi \
2025-09-15 20:22:06.483 wdl.w:ptcp.t:call-pbmm2_align_hifi-01.stderr VERBOSE   --report-json mapping_stats.report.json \
2025-09-15 20:22:06.483 wdl.w:ptcp.t:call-pbmm2_align_hifi-01.stderr VERBOSE   --sample "m84036_250809_035451_s4.bc2098" \
2025-09-15 20:22:06.483 wdl.w:ptcp.t:call-pbmm2_align_hifi-01.stderr VERBOSE   --unmapped \
2025-09-15 20:22:06.484 wdl.w:ptcp.t:call-pbmm2_align_hifi-01.stderr VERBOSE   /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa \
2025-09-15 20:22:06.484 wdl.w:ptcp.t:call-pbmm2_align_hifi-01.stderr VERBOSE   /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0002_m84036_250809_035451_s4.bc2098.unmapped.bam \
2025-09-15 20:22:06.484 wdl.w:ptcp.t:call-pbmm2_align_hifi-01.stderr VERBOSE   m84036_250809_035451_s4.bc2098.mapped.bam
2025-09-15 20:22:06.484 wdl.w:ptcp.t:call-pbmm2_align_hifi-01.stderr VERBOSE + pbmm2 align --log-level INFO --log-file pbmm2.log --alarms alarms.json --num-threads 64 --sort --preset HiFi --report-json mapping_stats.report.json --sample m84036_250809_035451_s4.bc2098 --unmapped /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0002_m84036_250809_035451_s4.bc2098.unmapped.bam m84036_250809_035451_s4.bc2098.mapped.bam
2025-09-15 20:22:06.516 wdl.w:ptcp.t:call-pbmm2_align_hifi-04.stderr VERBOSE 
2025-09-15 20:22:06.516 wdl.w:ptcp.t:call-pbmm2_align_hifi-04.stderr VERBOSE pbmm2 \
2025-09-15 20:22:06.516 wdl.w:ptcp.t:call-pbmm2_align_hifi-04.stderr VERBOSE   align \
2025-09-15 20:22:06.516 wdl.w:ptcp.t:call-pbmm2_align_hifi-04.stderr VERBOSE   --log-level INFO \
2025-09-15 20:22:06.516 wdl.w:ptcp.t:call-pbmm2_align_hifi-04.stderr VERBOSE   --log-file pbmm2.log \
2025-09-15 20:22:06.516 wdl.w:ptcp.t:call-pbmm2_align_hifi-04.stderr VERBOSE   --alarms alarms.json \
2025-09-15 20:22:06.517 wdl.w:ptcp.t:call-pbmm2_align_hifi-04.stderr VERBOSE   --num-threads 64 \
2025-09-15 20:22:06.517 wdl.w:ptcp.t:call-pbmm2_align_hifi-04.stderr VERBOSE   --sort \
2025-09-15 20:22:06.517 wdl.w:ptcp.t:call-pbmm2_align_hifi-04.stderr VERBOSE   --preset HiFi \
2025-09-15 20:22:06.517 wdl.w:ptcp.t:call-pbmm2_align_hifi-04.stderr VERBOSE   --report-json mapping_stats.report.json \
2025-09-15 20:22:06.517 wdl.w:ptcp.t:call-pbmm2_align_hifi-04.stderr VERBOSE   --sample "m84036_250809_035451_s4.bc2101" \
2025-09-15 20:22:06.517 wdl.w:ptcp.t:call-pbmm2_align_hifi-04.stderr VERBOSE   --unmapped \
2025-09-15 20:22:06.517 wdl.w:ptcp.t:call-pbmm2_align_hifi-04.stderr VERBOSE   /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa \
2025-09-15 20:22:06.517 wdl.w:ptcp.t:call-pbmm2_align_hifi-04.stderr VERBOSE   /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0005_m84036_250809_035451_s4.bc2101.unmapped.bam \
2025-09-15 20:22:06.517 wdl.w:ptcp.t:call-pbmm2_align_hifi-04.stderr VERBOSE   m84036_250809_035451_s4.bc2101.mapped.bam
2025-09-15 20:22:06.517 wdl.w:ptcp.t:call-pbmm2_align_hifi-04.stderr VERBOSE + pbmm2 align --log-level INFO --log-file pbmm2.log --alarms alarms.json --num-threads 64 --sort --preset HiFi --report-json mapping_stats.report.json --sample m84036_250809_035451_s4.bc2101 --unmapped /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0005_m84036_250809_035451_s4.bc2101.unmapped.bam m84036_250809_035451_s4.bc2101.mapped.bam
2025-09-15 20:22:06.527 wdl.w:ptcp.t:call-pbmm2_align_hifi-06.stderr VERBOSE 
2025-09-15 20:22:06.527 wdl.w:ptcp.t:call-pbmm2_align_hifi-06.stderr VERBOSE pbmm2 \
2025-09-15 20:22:06.527 wdl.w:ptcp.t:call-pbmm2_align_hifi-06.stderr VERBOSE   align \
2025-09-15 20:22:06.527 wdl.w:ptcp.t:call-pbmm2_align_hifi-06.stderr VERBOSE   --log-level INFO \
2025-09-15 20:22:06.528 wdl.w:ptcp.t:call-pbmm2_align_hifi-06.stderr VERBOSE   --log-file pbmm2.log \
2025-09-15 20:22:06.528 wdl.w:ptcp.t:call-pbmm2_align_hifi-06.stderr VERBOSE   --alarms alarms.json \
2025-09-15 20:22:06.528 wdl.w:ptcp.t:call-pbmm2_align_hifi-06.stderr VERBOSE   --num-threads 64 \
2025-09-15 20:22:06.528 wdl.w:ptcp.t:call-pbmm2_align_hifi-06.stderr VERBOSE   --sort \
2025-09-15 20:22:06.528 wdl.w:ptcp.t:call-pbmm2_align_hifi-06.stderr VERBOSE   --preset HiFi \
2025-09-15 20:22:06.528 wdl.w:ptcp.t:call-pbmm2_align_hifi-06.stderr VERBOSE   --report-json mapping_stats.report.json \
2025-09-15 20:22:06.528 wdl.w:ptcp.t:call-pbmm2_align_hifi-06.stderr VERBOSE   --sample "m84036_250809_035451_s4.bc2103" \
2025-09-15 20:22:06.528 wdl.w:ptcp.t:call-pbmm2_align_hifi-06.stderr VERBOSE   --unmapped \
2025-09-15 20:22:06.528 wdl.w:ptcp.t:call-pbmm2_align_hifi-06.stderr VERBOSE   /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa \
2025-09-15 20:22:06.528 wdl.w:ptcp.t:call-pbmm2_align_hifi-06.stderr VERBOSE   /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0007_m84036_250809_035451_s4.bc2103.unmapped.bam \
2025-09-15 20:22:06.528 wdl.w:ptcp.t:call-pbmm2_align_hifi-06.stderr VERBOSE   m84036_250809_035451_s4.bc2103.mapped.bam
2025-09-15 20:22:06.528 wdl.w:ptcp.t:call-pbmm2_align_hifi-06.stderr VERBOSE + pbmm2 align --log-level INFO --log-file pbmm2.log --alarms alarms.json --num-threads 64 --sort --preset HiFi --report-json mapping_stats.report.json --sample m84036_250809_035451_s4.bc2103 --unmapped /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0007_m84036_250809_035451_s4.bc2103.unmapped.bam m84036_250809_035451_s4.bc2103.mapped.bam
2025-09-15 20:22:06.535 wdl.w:ptcp.t:call-pbmm2_align_hifi-05.stderr VERBOSE 
2025-09-15 20:22:06.536 wdl.w:ptcp.t:call-pbmm2_align_hifi-05.stderr VERBOSE pbmm2 \
2025-09-15 20:22:06.536 wdl.w:ptcp.t:call-pbmm2_align_hifi-05.stderr VERBOSE   align \
2025-09-15 20:22:06.536 wdl.w:ptcp.t:call-pbmm2_align_hifi-05.stderr VERBOSE   --log-level INFO \
2025-09-15 20:22:06.536 wdl.w:ptcp.t:call-pbmm2_align_hifi-05.stderr VERBOSE   --log-file pbmm2.log \
2025-09-15 20:22:06.536 wdl.w:ptcp.t:call-pbmm2_align_hifi-05.stderr VERBOSE   --alarms alarms.json \
2025-09-15 20:22:06.536 wdl.w:ptcp.t:call-pbmm2_align_hifi-05.stderr VERBOSE   --num-threads 64 \
2025-09-15 20:22:06.536 wdl.w:ptcp.t:call-pbmm2_align_hifi-05.stderr VERBOSE   --sort \
2025-09-15 20:22:06.536 wdl.w:ptcp.t:call-pbmm2_align_hifi-05.stderr VERBOSE   --preset HiFi \
2025-09-15 20:22:06.536 wdl.w:ptcp.t:call-pbmm2_align_hifi-05.stderr VERBOSE   --report-json mapping_stats.report.json \
2025-09-15 20:22:06.536 wdl.w:ptcp.t:call-pbmm2_align_hifi-05.stderr VERBOSE   --sample "m84036_250809_035451_s4.bc2102" \
2025-09-15 20:22:06.536 wdl.w:ptcp.t:call-pbmm2_align_hifi-05.stderr VERBOSE   --unmapped \
2025-09-15 20:22:06.536 wdl.w:ptcp.t:call-pbmm2_align_hifi-05.stderr VERBOSE   /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa \
2025-09-15 20:22:06.536 wdl.w:ptcp.t:call-pbmm2_align_hifi-05.stderr VERBOSE   /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0006_m84036_250809_035451_s4.bc2102.unmapped.bam \
2025-09-15 20:22:06.536 wdl.w:ptcp.t:call-pbmm2_align_hifi-05.stderr VERBOSE   m84036_250809_035451_s4.bc2102.mapped.bam
2025-09-15 20:22:06.536 wdl.w:ptcp.t:call-pbmm2_align_hifi-05.stderr VERBOSE + pbmm2 align --log-level INFO --log-file pbmm2.log --alarms alarms.json --num-threads 64 --sort --preset HiFi --report-json mapping_stats.report.json --sample m84036_250809_035451_s4.bc2102 --unmapped /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0006_m84036_250809_035451_s4.bc2102.unmapped.bam m84036_250809_035451_s4.bc2102.mapped.bam
2025-09-15 20:22:06.547 wdl.w:ptcp.t:call-pbmm2_align_hifi-09.stderr VERBOSE 
2025-09-15 20:22:06.547 wdl.w:ptcp.t:call-pbmm2_align_hifi-09.stderr VERBOSE pbmm2 \
2025-09-15 20:22:06.547 wdl.w:ptcp.t:call-pbmm2_align_hifi-09.stderr VERBOSE   align \
2025-09-15 20:22:06.547 wdl.w:ptcp.t:call-pbmm2_align_hifi-09.stderr VERBOSE   --log-level INFO \
2025-09-15 20:22:06.547 wdl.w:ptcp.t:call-pbmm2_align_hifi-09.stderr VERBOSE   --log-file pbmm2.log \
2025-09-15 20:22:06.547 wdl.w:ptcp.t:call-pbmm2_align_hifi-09.stderr VERBOSE   --alarms alarms.json \
2025-09-15 20:22:06.547 wdl.w:ptcp.t:call-pbmm2_align_hifi-09.stderr VERBOSE   --num-threads 64 \
2025-09-15 20:22:06.547 wdl.w:ptcp.t:call-pbmm2_align_hifi-09.stderr VERBOSE   --sort \
2025-09-15 20:22:06.547 wdl.w:ptcp.t:call-pbmm2_align_hifi-09.stderr VERBOSE   --preset HiFi \
2025-09-15 20:22:06.547 wdl.w:ptcp.t:call-pbmm2_align_hifi-09.stderr VERBOSE   --report-json mapping_stats.report.json \
2025-09-15 20:22:06.547 wdl.w:ptcp.t:call-pbmm2_align_hifi-09.stderr VERBOSE   --sample "m84036_250809_035451_s4.bc2106" \
2025-09-15 20:22:06.547 wdl.w:ptcp.t:call-pbmm2_align_hifi-09.stderr VERBOSE   --unmapped \
2025-09-15 20:22:06.548 wdl.w:ptcp.t:call-pbmm2_align_hifi-09.stderr VERBOSE   /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa \
2025-09-15 20:22:06.548 wdl.w:ptcp.t:call-pbmm2_align_hifi-09.stderr VERBOSE   /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0010_m84036_250809_035451_s4.bc2106.unmapped.bam \
2025-09-15 20:22:06.548 wdl.w:ptcp.t:call-pbmm2_align_hifi-09.stderr VERBOSE   m84036_250809_035451_s4.bc2106.mapped.bam
2025-09-15 20:22:06.548 wdl.w:ptcp.t:call-pbmm2_align_hifi-09.stderr VERBOSE + pbmm2 align --log-level INFO --log-file pbmm2.log --alarms alarms.json --num-threads 64 --sort --preset HiFi --report-json mapping_stats.report.json --sample m84036_250809_035451_s4.bc2106 --unmapped /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0010_m84036_250809_035451_s4.bc2106.unmapped.bam m84036_250809_035451_s4.bc2106.mapped.bam
2025-09-15 20:22:06.553 wdl.w:ptcp.t:call-pbmm2_align_hifi-07.stderr VERBOSE 
2025-09-15 20:22:06.553 wdl.w:ptcp.t:call-pbmm2_align_hifi-07.stderr VERBOSE pbmm2 \
2025-09-15 20:22:06.553 wdl.w:ptcp.t:call-pbmm2_align_hifi-07.stderr VERBOSE   align \
2025-09-15 20:22:06.553 wdl.w:ptcp.t:call-pbmm2_align_hifi-07.stderr VERBOSE   --log-level INFO \
2025-09-15 20:22:06.553 wdl.w:ptcp.t:call-pbmm2_align_hifi-07.stderr VERBOSE   --log-file pbmm2.log \
2025-09-15 20:22:06.553 wdl.w:ptcp.t:call-pbmm2_align_hifi-07.stderr VERBOSE   --alarms alarms.json \
2025-09-15 20:22:06.553 wdl.w:ptcp.t:call-pbmm2_align_hifi-07.stderr VERBOSE   --num-threads 64 \
2025-09-15 20:22:06.553 wdl.w:ptcp.t:call-pbmm2_align_hifi-07.stderr VERBOSE   --sort \
2025-09-15 20:22:06.553 wdl.w:ptcp.t:call-pbmm2_align_hifi-07.stderr VERBOSE   --preset HiFi \
2025-09-15 20:22:06.553 wdl.w:ptcp.t:call-pbmm2_align_hifi-07.stderr VERBOSE   --report-json mapping_stats.report.json \
2025-09-15 20:22:06.553 wdl.w:ptcp.t:call-pbmm2_align_hifi-07.stderr VERBOSE   --sample "m84036_250809_035451_s4.bc2104" \
2025-09-15 20:22:06.554 wdl.w:ptcp.t:call-pbmm2_align_hifi-07.stderr VERBOSE   --unmapped \
2025-09-15 20:22:06.554 wdl.w:ptcp.t:call-pbmm2_align_hifi-07.stderr VERBOSE   /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa \
2025-09-15 20:22:06.554 wdl.w:ptcp.t:call-pbmm2_align_hifi-07.stderr VERBOSE   /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0008_m84036_250809_035451_s4.bc2104.unmapped.bam \
2025-09-15 20:22:06.554 wdl.w:ptcp.t:call-pbmm2_align_hifi-07.stderr VERBOSE   m84036_250809_035451_s4.bc2104.mapped.bam
2025-09-15 20:22:06.554 wdl.w:ptcp.t:call-pbmm2_align_hifi-07.stderr VERBOSE + pbmm2 align --log-level INFO --log-file pbmm2.log --alarms alarms.json --num-threads 64 --sort --preset HiFi --report-json mapping_stats.report.json --sample m84036_250809_035451_s4.bc2104 --unmapped /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0008_m84036_250809_035451_s4.bc2104.unmapped.bam m84036_250809_035451_s4.bc2104.mapped.bam
2025-09-15 20:22:06.583 wdl.w:ptcp.t:call-pbmm2_align_hifi-08.stderr VERBOSE 
2025-09-15 20:22:06.583 wdl.w:ptcp.t:call-pbmm2_align_hifi-08.stderr VERBOSE pbmm2 \
2025-09-15 20:22:06.583 wdl.w:ptcp.t:call-pbmm2_align_hifi-08.stderr VERBOSE   align \
2025-09-15 20:22:06.583 wdl.w:ptcp.t:call-pbmm2_align_hifi-08.stderr VERBOSE   --log-level INFO \
2025-09-15 20:22:06.583 wdl.w:ptcp.t:call-pbmm2_align_hifi-08.stderr VERBOSE   --log-file pbmm2.log \
2025-09-15 20:22:06.583 wdl.w:ptcp.t:call-pbmm2_align_hifi-08.stderr VERBOSE   --alarms alarms.json \
2025-09-15 20:22:06.583 wdl.w:ptcp.t:call-pbmm2_align_hifi-08.stderr VERBOSE   --num-threads 64 \
2025-09-15 20:22:06.583 wdl.w:ptcp.t:call-pbmm2_align_hifi-08.stderr VERBOSE   --sort \
2025-09-15 20:22:06.583 wdl.w:ptcp.t:call-pbmm2_align_hifi-08.stderr VERBOSE   --preset HiFi \
2025-09-15 20:22:06.583 wdl.w:ptcp.t:call-pbmm2_align_hifi-08.stderr VERBOSE   --report-json mapping_stats.report.json \
2025-09-15 20:22:06.583 wdl.w:ptcp.t:call-pbmm2_align_hifi-08.stderr VERBOSE   --sample "m84036_250809_035451_s4.bc2105" \
2025-09-15 20:22:06.583 wdl.w:ptcp.t:call-pbmm2_align_hifi-08.stderr VERBOSE   --unmapped \
2025-09-15 20:22:06.584 wdl.w:ptcp.t:call-pbmm2_align_hifi-08.stderr VERBOSE   /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa \
2025-09-15 20:22:06.584 wdl.w:ptcp.t:call-pbmm2_align_hifi-08.stderr VERBOSE   /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0009_m84036_250809_035451_s4.bc2105.unmapped.bam \
2025-09-15 20:22:06.584 wdl.w:ptcp.t:call-pbmm2_align_hifi-08.stderr VERBOSE   m84036_250809_035451_s4.bc2105.mapped.bam
2025-09-15 20:22:06.584 wdl.w:ptcp.t:call-pbmm2_align_hifi-08.stderr VERBOSE + pbmm2 align --log-level INFO --log-file pbmm2.log --alarms alarms.json --num-threads 64 --sort --preset HiFi --report-json mapping_stats.report.json --sample m84036_250809_035451_s4.bc2105 --unmapped /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0009_m84036_250809_035451_s4.bc2105.unmapped.bam m84036_250809_035451_s4.bc2105.mapped.bam
2025-09-15 20:22:06.591 wdl.w:ptcp.t:call-pbmm2_align_hifi-10.stderr VERBOSE 
2025-09-15 20:22:06.592 wdl.w:ptcp.t:call-pbmm2_align_hifi-10.stderr VERBOSE pbmm2 \
2025-09-15 20:22:06.592 wdl.w:ptcp.t:call-pbmm2_align_hifi-10.stderr VERBOSE   align \
2025-09-15 20:22:06.592 wdl.w:ptcp.t:call-pbmm2_align_hifi-10.stderr VERBOSE   --log-level INFO \
2025-09-15 20:22:06.592 wdl.w:ptcp.t:call-pbmm2_align_hifi-10.stderr VERBOSE   --log-file pbmm2.log \
2025-09-15 20:22:06.592 wdl.w:ptcp.t:call-pbmm2_align_hifi-10.stderr VERBOSE   --alarms alarms.json \
2025-09-15 20:22:06.592 wdl.w:ptcp.t:call-pbmm2_align_hifi-10.stderr VERBOSE   --num-threads 64 \
2025-09-15 20:22:06.592 wdl.w:ptcp.t:call-pbmm2_align_hifi-10.stderr VERBOSE   --sort \
2025-09-15 20:22:06.592 wdl.w:ptcp.t:call-pbmm2_align_hifi-10.stderr VERBOSE   --preset HiFi \
2025-09-15 20:22:06.592 wdl.w:ptcp.t:call-pbmm2_align_hifi-10.stderr VERBOSE   --report-json mapping_stats.report.json \
2025-09-15 20:22:06.592 wdl.w:ptcp.t:call-pbmm2_align_hifi-10.stderr VERBOSE   --sample "m84036_250809_035451_s4.bc2107" \
2025-09-15 20:22:06.592 wdl.w:ptcp.t:call-pbmm2_align_hifi-10.stderr VERBOSE   --unmapped \
2025-09-15 20:22:06.592 wdl.w:ptcp.t:call-pbmm2_align_hifi-10.stderr VERBOSE   /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa \
2025-09-15 20:22:06.592 wdl.w:ptcp.t:call-pbmm2_align_hifi-10.stderr VERBOSE   /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0011_m84036_250809_035451_s4.bc2107.unmapped.bam \
2025-09-15 20:22:06.592 wdl.w:ptcp.t:call-pbmm2_align_hifi-10.stderr VERBOSE   m84036_250809_035451_s4.bc2107.mapped.bam
2025-09-15 20:22:06.592 wdl.w:ptcp.t:call-pbmm2_align_hifi-10.stderr VERBOSE + pbmm2 align --log-level INFO --log-file pbmm2.log --alarms alarms.json --num-threads 64 --sort --preset HiFi --report-json mapping_stats.report.json --sample m84036_250809_035451_s4.bc2107 --unmapped /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0011_m84036_250809_035451_s4.bc2107.unmapped.bam m84036_250809_035451_s4.bc2107.mapped.bam
2025-09-15 20:22:06.595 wdl.w:ptcp.t:call-pbmm2_align_hifi-13.stderr VERBOSE 
2025-09-15 20:22:06.595 wdl.w:ptcp.t:call-pbmm2_align_hifi-13.stderr VERBOSE pbmm2 \
2025-09-15 20:22:06.595 wdl.w:ptcp.t:call-pbmm2_align_hifi-13.stderr VERBOSE   align \
2025-09-15 20:22:06.595 wdl.w:ptcp.t:call-pbmm2_align_hifi-13.stderr VERBOSE   --log-level INFO \
2025-09-15 20:22:06.595 wdl.w:ptcp.t:call-pbmm2_align_hifi-13.stderr VERBOSE   --log-file pbmm2.log \
2025-09-15 20:22:06.595 wdl.w:ptcp.t:call-pbmm2_align_hifi-13.stderr VERBOSE   --alarms alarms.json \
2025-09-15 20:22:06.595 wdl.w:ptcp.t:call-pbmm2_align_hifi-13.stderr VERBOSE   --num-threads 64 \
2025-09-15 20:22:06.595 wdl.w:ptcp.t:call-pbmm2_align_hifi-13.stderr VERBOSE   --sort \
2025-09-15 20:22:06.595 wdl.w:ptcp.t:call-pbmm2_align_hifi-13.stderr VERBOSE   --preset HiFi \
2025-09-15 20:22:06.595 wdl.w:ptcp.t:call-pbmm2_align_hifi-13.stderr VERBOSE   --report-json mapping_stats.report.json \
2025-09-15 20:22:06.596 wdl.w:ptcp.t:call-pbmm2_align_hifi-13.stderr VERBOSE   --sample "m84036_250809_035451_s4.bc2110" \
2025-09-15 20:22:06.596 wdl.w:ptcp.t:call-pbmm2_align_hifi-13.stderr VERBOSE   --unmapped \
2025-09-15 20:22:06.596 wdl.w:ptcp.t:call-pbmm2_align_hifi-13.stderr VERBOSE   /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa \
2025-09-15 20:22:06.596 wdl.w:ptcp.t:call-pbmm2_align_hifi-13.stderr VERBOSE   /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0014_m84036_250809_035451_s4.bc2110.unmapped.bam \
2025-09-15 20:22:06.596 wdl.w:ptcp.t:call-pbmm2_align_hifi-13.stderr VERBOSE   m84036_250809_035451_s4.bc2110.mapped.bam
2025-09-15 20:22:06.596 wdl.w:ptcp.t:call-pbmm2_align_hifi-13.stderr VERBOSE + pbmm2 align --log-level INFO --log-file pbmm2.log --alarms alarms.json --num-threads 64 --sort --preset HiFi --report-json mapping_stats.report.json --sample m84036_250809_035451_s4.bc2110 --unmapped /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0014_m84036_250809_035451_s4.bc2110.unmapped.bam m84036_250809_035451_s4.bc2110.mapped.bam
2025-09-15 20:22:06.598 wdl.w:ptcp.t:call-pbmm2_align_hifi-12.stderr VERBOSE 
2025-09-15 20:22:06.599 wdl.w:ptcp.t:call-pbmm2_align_hifi-12.stderr VERBOSE pbmm2 \
2025-09-15 20:22:06.599 wdl.w:ptcp.t:call-pbmm2_align_hifi-12.stderr VERBOSE   align \
2025-09-15 20:22:06.599 wdl.w:ptcp.t:call-pbmm2_align_hifi-12.stderr VERBOSE   --log-level INFO \
2025-09-15 20:22:06.599 wdl.w:ptcp.t:call-pbmm2_align_hifi-12.stderr VERBOSE   --log-file pbmm2.log \
2025-09-15 20:22:06.599 wdl.w:ptcp.t:call-pbmm2_align_hifi-12.stderr VERBOSE   --alarms alarms.json \
2025-09-15 20:22:06.599 wdl.w:ptcp.t:call-pbmm2_align_hifi-12.stderr VERBOSE   --num-threads 64 \
2025-09-15 20:22:06.599 wdl.w:ptcp.t:call-pbmm2_align_hifi-12.stderr VERBOSE   --sort \
2025-09-15 20:22:06.599 wdl.w:ptcp.t:call-pbmm2_align_hifi-12.stderr VERBOSE   --preset HiFi \
2025-09-15 20:22:06.599 wdl.w:ptcp.t:call-pbmm2_align_hifi-12.stderr VERBOSE   --report-json mapping_stats.report.json \
2025-09-15 20:22:06.599 wdl.w:ptcp.t:call-pbmm2_align_hifi-12.stderr VERBOSE   --sample "m84036_250809_035451_s4.bc2109" \
2025-09-15 20:22:06.599 wdl.w:ptcp.t:call-pbmm2_align_hifi-12.stderr VERBOSE   --unmapped \
2025-09-15 20:22:06.599 wdl.w:ptcp.t:call-pbmm2_align_hifi-12.stderr VERBOSE   /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa \
2025-09-15 20:22:06.599 wdl.w:ptcp.t:call-pbmm2_align_hifi-12.stderr VERBOSE   /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0013_m84036_250809_035451_s4.bc2109.unmapped.bam \
2025-09-15 20:22:06.599 wdl.w:ptcp.t:call-pbmm2_align_hifi-12.stderr VERBOSE   m84036_250809_035451_s4.bc2109.mapped.bam
2025-09-15 20:22:06.599 wdl.w:ptcp.t:call-pbmm2_align_hifi-12.stderr VERBOSE + pbmm2 align --log-level INFO --log-file pbmm2.log --alarms alarms.json --num-threads 64 --sort --preset HiFi --report-json mapping_stats.report.json --sample m84036_250809_035451_s4.bc2109 --unmapped /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0013_m84036_250809_035451_s4.bc2109.unmapped.bam m84036_250809_035451_s4.bc2109.mapped.bam
2025-09-15 20:22:06.611 wdl.w:ptcp.t:call-pbmm2_align_hifi-11.stderr VERBOSE 
2025-09-15 20:22:06.612 wdl.w:ptcp.t:call-pbmm2_align_hifi-11.stderr VERBOSE pbmm2 \
2025-09-15 20:22:06.612 wdl.w:ptcp.t:call-pbmm2_align_hifi-11.stderr VERBOSE   align \
2025-09-15 20:22:06.612 wdl.w:ptcp.t:call-pbmm2_align_hifi-11.stderr VERBOSE   --log-level INFO \
2025-09-15 20:22:06.612 wdl.w:ptcp.t:call-pbmm2_align_hifi-11.stderr VERBOSE   --log-file pbmm2.log \
2025-09-15 20:22:06.612 wdl.w:ptcp.t:call-pbmm2_align_hifi-11.stderr VERBOSE   --alarms alarms.json \
2025-09-15 20:22:06.612 wdl.w:ptcp.t:call-pbmm2_align_hifi-11.stderr VERBOSE   --num-threads 64 \
2025-09-15 20:22:06.612 wdl.w:ptcp.t:call-pbmm2_align_hifi-11.stderr VERBOSE   --sort \
2025-09-15 20:22:06.612 wdl.w:ptcp.t:call-pbmm2_align_hifi-11.stderr VERBOSE   --preset HiFi \
2025-09-15 20:22:06.612 wdl.w:ptcp.t:call-pbmm2_align_hifi-11.stderr VERBOSE   --report-json mapping_stats.report.json \
2025-09-15 20:22:06.612 wdl.w:ptcp.t:call-pbmm2_align_hifi-11.stderr VERBOSE   --sample "m84036_250809_035451_s4.bc2108" \
2025-09-15 20:22:06.612 wdl.w:ptcp.t:call-pbmm2_align_hifi-11.stderr VERBOSE   --unmapped \
2025-09-15 20:22:06.612 wdl.w:ptcp.t:call-pbmm2_align_hifi-11.stderr VERBOSE   /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa \
2025-09-15 20:22:06.612 wdl.w:ptcp.t:call-pbmm2_align_hifi-11.stderr VERBOSE   /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0012_m84036_250809_035451_s4.bc2108.unmapped.bam \
2025-09-15 20:22:06.612 wdl.w:ptcp.t:call-pbmm2_align_hifi-11.stderr VERBOSE   m84036_250809_035451_s4.bc2108.mapped.bam
2025-09-15 20:22:06.612 wdl.w:ptcp.t:call-pbmm2_align_hifi-11.stderr VERBOSE + pbmm2 align --log-level INFO --log-file pbmm2.log --alarms alarms.json --num-threads 64 --sort --preset HiFi --report-json mapping_stats.report.json --sample m84036_250809_035451_s4.bc2108 --unmapped /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0012_m84036_250809_035451_s4.bc2108.unmapped.bam m84036_250809_035451_s4.bc2108.mapped.bam
2025-09-15 20:22:06.618 wdl.w:ptcp.t:call-pbmm2_align_hifi-14.stderr VERBOSE 
2025-09-15 20:22:06.619 wdl.w:ptcp.t:call-pbmm2_align_hifi-14.stderr VERBOSE pbmm2 \
2025-09-15 20:22:06.619 wdl.w:ptcp.t:call-pbmm2_align_hifi-14.stderr VERBOSE   align \
2025-09-15 20:22:06.619 wdl.w:ptcp.t:call-pbmm2_align_hifi-14.stderr VERBOSE   --log-level INFO \
2025-09-15 20:22:06.619 wdl.w:ptcp.t:call-pbmm2_align_hifi-14.stderr VERBOSE   --log-file pbmm2.log \
2025-09-15 20:22:06.619 wdl.w:ptcp.t:call-pbmm2_align_hifi-14.stderr VERBOSE   --alarms alarms.json \
2025-09-15 20:22:06.619 wdl.w:ptcp.t:call-pbmm2_align_hifi-14.stderr VERBOSE   --num-threads 64 \
2025-09-15 20:22:06.619 wdl.w:ptcp.t:call-pbmm2_align_hifi-14.stderr VERBOSE   --sort \
2025-09-15 20:22:06.619 wdl.w:ptcp.t:call-pbmm2_align_hifi-14.stderr VERBOSE   --preset HiFi \
2025-09-15 20:22:06.619 wdl.w:ptcp.t:call-pbmm2_align_hifi-14.stderr VERBOSE   --report-json mapping_stats.report.json \
2025-09-15 20:22:06.619 wdl.w:ptcp.t:call-pbmm2_align_hifi-14.stderr VERBOSE   --sample "m84036_250809_035451_s4.bc2111" \
2025-09-15 20:22:06.619 wdl.w:ptcp.t:call-pbmm2_align_hifi-14.stderr VERBOSE   --unmapped \
2025-09-15 20:22:06.619 wdl.w:ptcp.t:call-pbmm2_align_hifi-14.stderr VERBOSE   /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa \
2025-09-15 20:22:06.619 wdl.w:ptcp.t:call-pbmm2_align_hifi-14.stderr VERBOSE   /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0015_m84036_250809_035451_s4.bc2111.unmapped.bam \
2025-09-15 20:22:06.619 wdl.w:ptcp.t:call-pbmm2_align_hifi-14.stderr VERBOSE   m84036_250809_035451_s4.bc2111.mapped.bam
2025-09-15 20:22:06.619 wdl.w:ptcp.t:call-pbmm2_align_hifi-14.stderr VERBOSE + pbmm2 align --log-level INFO --log-file pbmm2.log --alarms alarms.json --num-threads 64 --sort --preset HiFi --report-json mapping_stats.report.json --sample m84036_250809_035451_s4.bc2111 --unmapped /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0015_m84036_250809_035451_s4.bc2111.unmapped.bam m84036_250809_035451_s4.bc2111.mapped.bam
2025-09-15 20:22:06.620 wdl.w:ptcp.t:call-pbmm2_align_hifi-18.stderr VERBOSE 
2025-09-15 20:22:06.620 wdl.w:ptcp.t:call-pbmm2_align_hifi-18.stderr VERBOSE pbmm2 \
2025-09-15 20:22:06.620 wdl.w:ptcp.t:call-pbmm2_align_hifi-18.stderr VERBOSE   align \
2025-09-15 20:22:06.620 wdl.w:ptcp.t:call-pbmm2_align_hifi-18.stderr VERBOSE   --log-level INFO \
2025-09-15 20:22:06.621 wdl.w:ptcp.t:call-pbmm2_align_hifi-18.stderr VERBOSE   --log-file pbmm2.log \
2025-09-15 20:22:06.621 wdl.w:ptcp.t:call-pbmm2_align_hifi-18.stderr VERBOSE   --alarms alarms.json \
2025-09-15 20:22:06.621 wdl.w:ptcp.t:call-pbmm2_align_hifi-18.stderr VERBOSE   --num-threads 64 \
2025-09-15 20:22:06.621 wdl.w:ptcp.t:call-pbmm2_align_hifi-18.stderr VERBOSE   --sort \
2025-09-15 20:22:06.621 wdl.w:ptcp.t:call-pbmm2_align_hifi-18.stderr VERBOSE   --preset HiFi \
2025-09-15 20:22:06.621 wdl.w:ptcp.t:call-pbmm2_align_hifi-18.stderr VERBOSE   --report-json mapping_stats.report.json \
2025-09-15 20:22:06.621 wdl.w:ptcp.t:call-pbmm2_align_hifi-18.stderr VERBOSE   --sample "m84036_250809_035451_s4.bc2115" \
2025-09-15 20:22:06.621 wdl.w:ptcp.t:call-pbmm2_align_hifi-18.stderr VERBOSE   --unmapped \
2025-09-15 20:22:06.621 wdl.w:ptcp.t:call-pbmm2_align_hifi-18.stderr VERBOSE   /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa \
2025-09-15 20:22:06.621 wdl.w:ptcp.t:call-pbmm2_align_hifi-18.stderr VERBOSE   /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0019_m84036_250809_035451_s4.bc2115.unmapped.bam \
2025-09-15 20:22:06.621 wdl.w:ptcp.t:call-pbmm2_align_hifi-18.stderr VERBOSE   m84036_250809_035451_s4.bc2115.mapped.bam
2025-09-15 20:22:06.621 wdl.w:ptcp.t:call-pbmm2_align_hifi-18.stderr VERBOSE + pbmm2 align --log-level INFO --log-file pbmm2.log --alarms alarms.json --num-threads 64 --sort --preset HiFi --report-json mapping_stats.report.json --sample m84036_250809_035451_s4.bc2115 --unmapped /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0019_m84036_250809_035451_s4.bc2115.unmapped.bam m84036_250809_035451_s4.bc2115.mapped.bam
2025-09-15 20:22:06.625 wdl.w:ptcp.t:call-pbmm2_align_hifi-15.stderr VERBOSE 
2025-09-15 20:22:06.626 wdl.w:ptcp.t:call-pbmm2_align_hifi-15.stderr VERBOSE pbmm2 \
2025-09-15 20:22:06.626 wdl.w:ptcp.t:call-pbmm2_align_hifi-15.stderr VERBOSE   align \
2025-09-15 20:22:06.626 wdl.w:ptcp.t:call-pbmm2_align_hifi-15.stderr VERBOSE   --log-level INFO \
2025-09-15 20:22:06.626 wdl.w:ptcp.t:call-pbmm2_align_hifi-15.stderr VERBOSE   --log-file pbmm2.log \
2025-09-15 20:22:06.626 wdl.w:ptcp.t:call-pbmm2_align_hifi-15.stderr VERBOSE   --alarms alarms.json \
2025-09-15 20:22:06.626 wdl.w:ptcp.t:call-pbmm2_align_hifi-15.stderr VERBOSE   --num-threads 64 \
2025-09-15 20:22:06.626 wdl.w:ptcp.t:call-pbmm2_align_hifi-15.stderr VERBOSE   --sort \
2025-09-15 20:22:06.626 wdl.w:ptcp.t:call-pbmm2_align_hifi-15.stderr VERBOSE   --preset HiFi \
2025-09-15 20:22:06.626 wdl.w:ptcp.t:call-pbmm2_align_hifi-15.stderr VERBOSE   --report-json mapping_stats.report.json \
2025-09-15 20:22:06.626 wdl.w:ptcp.t:call-pbmm2_align_hifi-15.stderr VERBOSE   --sample "m84036_250809_035451_s4.bc2112" \
2025-09-15 20:22:06.627 wdl.w:ptcp.t:call-pbmm2_align_hifi-15.stderr VERBOSE   --unmapped \
2025-09-15 20:22:06.627 wdl.w:ptcp.t:call-pbmm2_align_hifi-15.stderr VERBOSE   /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa \
2025-09-15 20:22:06.627 wdl.w:ptcp.t:call-pbmm2_align_hifi-15.stderr VERBOSE   /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0016_m84036_250809_035451_s4.bc2112.unmapped.bam \
2025-09-15 20:22:06.627 wdl.w:ptcp.t:call-pbmm2_align_hifi-15.stderr VERBOSE   m84036_250809_035451_s4.bc2112.mapped.bam
2025-09-15 20:22:06.627 wdl.w:ptcp.t:call-pbmm2_align_hifi-15.stderr VERBOSE + pbmm2 align --log-level INFO --log-file pbmm2.log --alarms alarms.json --num-threads 64 --sort --preset HiFi --report-json mapping_stats.report.json --sample m84036_250809_035451_s4.bc2112 --unmapped /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0016_m84036_250809_035451_s4.bc2112.unmapped.bam m84036_250809_035451_s4.bc2112.mapped.bam
2025-09-15 20:22:06.628 wdl.w:ptcp.t:call-pbmm2_align_hifi-16.stderr VERBOSE 
2025-09-15 20:22:06.628 wdl.w:ptcp.t:call-pbmm2_align_hifi-16.stderr VERBOSE pbmm2 \
2025-09-15 20:22:06.628 wdl.w:ptcp.t:call-pbmm2_align_hifi-16.stderr VERBOSE   align \
2025-09-15 20:22:06.628 wdl.w:ptcp.t:call-pbmm2_align_hifi-16.stderr VERBOSE   --log-level INFO \
2025-09-15 20:22:06.628 wdl.w:ptcp.t:call-pbmm2_align_hifi-16.stderr VERBOSE   --log-file pbmm2.log \
2025-09-15 20:22:06.628 wdl.w:ptcp.t:call-pbmm2_align_hifi-16.stderr VERBOSE   --alarms alarms.json \
2025-09-15 20:22:06.628 wdl.w:ptcp.t:call-pbmm2_align_hifi-16.stderr VERBOSE   --num-threads 64 \
2025-09-15 20:22:06.629 wdl.w:ptcp.t:call-pbmm2_align_hifi-16.stderr VERBOSE   --sort \
2025-09-15 20:22:06.629 wdl.w:ptcp.t:call-pbmm2_align_hifi-16.stderr VERBOSE   --preset HiFi \
2025-09-15 20:22:06.629 wdl.w:ptcp.t:call-pbmm2_align_hifi-16.stderr VERBOSE   --report-json mapping_stats.report.json \
2025-09-15 20:22:06.629 wdl.w:ptcp.t:call-pbmm2_align_hifi-16.stderr VERBOSE   --sample "m84036_250809_035451_s4.bc2113" \
2025-09-15 20:22:06.629 wdl.w:ptcp.t:call-pbmm2_align_hifi-16.stderr VERBOSE   --unmapped \
2025-09-15 20:22:06.629 wdl.w:ptcp.t:call-pbmm2_align_hifi-16.stderr VERBOSE   /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa \
2025-09-15 20:22:06.629 wdl.w:ptcp.t:call-pbmm2_align_hifi-16.stderr VERBOSE   /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0017_m84036_250809_035451_s4.bc2113.unmapped.bam \
2025-09-15 20:22:06.629 wdl.w:ptcp.t:call-pbmm2_align_hifi-16.stderr VERBOSE   m84036_250809_035451_s4.bc2113.mapped.bam
2025-09-15 20:22:06.629 wdl.w:ptcp.t:call-pbmm2_align_hifi-16.stderr VERBOSE + pbmm2 align --log-level INFO --log-file pbmm2.log --alarms alarms.json --num-threads 64 --sort --preset HiFi --report-json mapping_stats.report.json --sample m84036_250809_035451_s4.bc2113 --unmapped /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0017_m84036_250809_035451_s4.bc2113.unmapped.bam m84036_250809_035451_s4.bc2113.mapped.bam
2025-09-15 20:22:06.631 wdl.w:ptcp.t:call-pbmm2_align_hifi-19.stderr VERBOSE 
2025-09-15 20:22:06.632 wdl.w:ptcp.t:call-pbmm2_align_hifi-19.stderr VERBOSE pbmm2 \
2025-09-15 20:22:06.632 wdl.w:ptcp.t:call-pbmm2_align_hifi-19.stderr VERBOSE   align \
2025-09-15 20:22:06.632 wdl.w:ptcp.t:call-pbmm2_align_hifi-19.stderr VERBOSE   --log-level INFO \
2025-09-15 20:22:06.632 wdl.w:ptcp.t:call-pbmm2_align_hifi-19.stderr VERBOSE   --log-file pbmm2.log \
2025-09-15 20:22:06.632 wdl.w:ptcp.t:call-pbmm2_align_hifi-19.stderr VERBOSE   --alarms alarms.json \
2025-09-15 20:22:06.632 wdl.w:ptcp.t:call-pbmm2_align_hifi-19.stderr VERBOSE   --num-threads 64 \
2025-09-15 20:22:06.632 wdl.w:ptcp.t:call-pbmm2_align_hifi-19.stderr VERBOSE   --sort \
2025-09-15 20:22:06.632 wdl.w:ptcp.t:call-pbmm2_align_hifi-19.stderr VERBOSE   --preset HiFi \
2025-09-15 20:22:06.632 wdl.w:ptcp.t:call-pbmm2_align_hifi-19.stderr VERBOSE   --report-json mapping_stats.report.json \
2025-09-15 20:22:06.632 wdl.w:ptcp.t:call-pbmm2_align_hifi-19.stderr VERBOSE   --sample "m84036_250809_035451_s4.bc2116" \
2025-09-15 20:22:06.632 wdl.w:ptcp.t:call-pbmm2_align_hifi-19.stderr VERBOSE   --unmapped \
2025-09-15 20:22:06.632 wdl.w:ptcp.t:call-pbmm2_align_hifi-19.stderr VERBOSE   /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa \
2025-09-15 20:22:06.632 wdl.w:ptcp.t:call-pbmm2_align_hifi-19.stderr VERBOSE   /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0020_m84036_250809_035451_s4.bc2116.unmapped.bam \
2025-09-15 20:22:06.632 wdl.w:ptcp.t:call-pbmm2_align_hifi-19.stderr VERBOSE   m84036_250809_035451_s4.bc2116.mapped.bam
2025-09-15 20:22:06.633 wdl.w:ptcp.t:call-pbmm2_align_hifi-19.stderr VERBOSE + pbmm2 align --log-level INFO --log-file pbmm2.log --alarms alarms.json --num-threads 64 --sort --preset HiFi --report-json mapping_stats.report.json --sample m84036_250809_035451_s4.bc2116 --unmapped /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0020_m84036_250809_035451_s4.bc2116.unmapped.bam m84036_250809_035451_s4.bc2116.mapped.bam
2025-09-15 20:22:06.673 wdl.w:ptcp.t:call-pbmm2_align_hifi-22.slurm_singularity INFO srun: job 51797245 has been allocated resources
2025-09-15 20:22:06.673 wdl.w:ptcp.t:call-pbmm2_align_hifi-22.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:22:06.674 wdl.w:ptcp.t:call-pbmm2_align_hifi-22.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:22:06.674 wdl.w:ptcp.t:call-pbmm2_align_hifi-17.stderr VERBOSE 
2025-09-15 20:22:06.675 wdl.w:ptcp.t:call-pbmm2_align_hifi-17.stderr VERBOSE pbmm2 \
2025-09-15 20:22:06.675 wdl.w:ptcp.t:call-pbmm2_align_hifi-17.stderr VERBOSE   align \
2025-09-15 20:22:06.675 wdl.w:ptcp.t:call-pbmm2_align_hifi-17.stderr VERBOSE   --log-level INFO \
2025-09-15 20:22:06.675 wdl.w:ptcp.t:call-pbmm2_align_hifi-17.stderr VERBOSE   --log-file pbmm2.log \
2025-09-15 20:22:06.675 wdl.w:ptcp.t:call-pbmm2_align_hifi-17.stderr VERBOSE   --alarms alarms.json \
2025-09-15 20:22:06.675 wdl.w:ptcp.t:call-pbmm2_align_hifi-17.stderr VERBOSE   --num-threads 64 \
2025-09-15 20:22:06.675 wdl.w:ptcp.t:call-pbmm2_align_hifi-17.stderr VERBOSE   --sort \
2025-09-15 20:22:06.675 wdl.w:ptcp.t:call-pbmm2_align_hifi-17.stderr VERBOSE   --preset HiFi \
2025-09-15 20:22:06.675 wdl.w:ptcp.t:call-pbmm2_align_hifi-17.stderr VERBOSE   --report-json mapping_stats.report.json \
2025-09-15 20:22:06.675 wdl.w:ptcp.t:call-pbmm2_align_hifi-17.stderr VERBOSE   --sample "m84036_250809_035451_s4.bc2114" \
2025-09-15 20:22:06.675 wdl.w:ptcp.t:call-pbmm2_align_hifi-17.stderr VERBOSE   --unmapped \
2025-09-15 20:22:06.675 wdl.w:ptcp.t:call-pbmm2_align_hifi-17.stderr VERBOSE   /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa \
2025-09-15 20:22:06.675 wdl.w:ptcp.t:call-pbmm2_align_hifi-17.stderr VERBOSE   /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0018_m84036_250809_035451_s4.bc2114.unmapped.bam \
2025-09-15 20:22:06.675 wdl.w:ptcp.t:call-pbmm2_align_hifi-17.stderr VERBOSE   m84036_250809_035451_s4.bc2114.mapped.bam
2025-09-15 20:22:06.675 wdl.w:ptcp.t:call-pbmm2_align_hifi-17.stderr VERBOSE + pbmm2 align --log-level INFO --log-file pbmm2.log --alarms alarms.json --num-threads 64 --sort --preset HiFi --report-json mapping_stats.report.json --sample m84036_250809_035451_s4.bc2114 --unmapped /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0018_m84036_250809_035451_s4.bc2114.unmapped.bam m84036_250809_035451_s4.bc2114.mapped.bam
2025-09-15 20:22:06.680 wdl.w:ptcp.t:call-pbmm2_align_hifi-26.slurm_singularity INFO srun: job 51797247 has been allocated resources
2025-09-15 20:22:06.691 wdl.w:ptcp.t:call-pbmm2_align_hifi-20.stderr VERBOSE 
2025-09-15 20:22:06.692 wdl.w:ptcp.t:call-pbmm2_align_hifi-20.stderr VERBOSE pbmm2 \
2025-09-15 20:22:06.692 wdl.w:ptcp.t:call-pbmm2_align_hifi-20.stderr VERBOSE   align \
2025-09-15 20:22:06.692 wdl.w:ptcp.t:call-pbmm2_align_hifi-20.stderr VERBOSE   --log-level INFO \
2025-09-15 20:22:06.692 wdl.w:ptcp.t:call-pbmm2_align_hifi-20.stderr VERBOSE   --log-file pbmm2.log \
2025-09-15 20:22:06.692 wdl.w:ptcp.t:call-pbmm2_align_hifi-20.stderr VERBOSE   --alarms alarms.json \
2025-09-15 20:22:06.692 wdl.w:ptcp.t:call-pbmm2_align_hifi-20.stderr VERBOSE   --num-threads 64 \
2025-09-15 20:22:06.692 wdl.w:ptcp.t:call-pbmm2_align_hifi-20.stderr VERBOSE   --sort \
2025-09-15 20:22:06.692 wdl.w:ptcp.t:call-pbmm2_align_hifi-20.stderr VERBOSE   --preset HiFi \
2025-09-15 20:22:06.692 wdl.w:ptcp.t:call-pbmm2_align_hifi-20.stderr VERBOSE   --report-json mapping_stats.report.json \
2025-09-15 20:22:06.692 wdl.w:ptcp.t:call-pbmm2_align_hifi-20.stderr VERBOSE   --sample "m84036_250809_035451_s4.bc2117" \
2025-09-15 20:22:06.692 wdl.w:ptcp.t:call-pbmm2_align_hifi-20.stderr VERBOSE   --unmapped \
2025-09-15 20:22:06.692 wdl.w:ptcp.t:call-pbmm2_align_hifi-20.stderr VERBOSE   /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa \
2025-09-15 20:22:06.692 wdl.w:ptcp.t:call-pbmm2_align_hifi-20.stderr VERBOSE   /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0021_m84036_250809_035451_s4.bc2117.unmapped.bam \
2025-09-15 20:22:06.692 wdl.w:ptcp.t:call-pbmm2_align_hifi-20.stderr VERBOSE   m84036_250809_035451_s4.bc2117.mapped.bam
2025-09-15 20:22:06.693 wdl.w:ptcp.t:call-pbmm2_align_hifi-20.stderr VERBOSE + pbmm2 align --log-level INFO --log-file pbmm2.log --alarms alarms.json --num-threads 64 --sort --preset HiFi --report-json mapping_stats.report.json --sample m84036_250809_035451_s4.bc2117 --unmapped /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0021_m84036_250809_035451_s4.bc2117.unmapped.bam m84036_250809_035451_s4.bc2117.mapped.bam
2025-09-15 20:22:06.692 wdl.w:ptcp.t:call-pbmm2_align_hifi-21.stderr VERBOSE 
2025-09-15 20:22:06.693 wdl.w:ptcp.t:call-pbmm2_align_hifi-21.stderr VERBOSE pbmm2 \
2025-09-15 20:22:06.693 wdl.w:ptcp.t:call-pbmm2_align_hifi-21.stderr VERBOSE   align \
2025-09-15 20:22:06.693 wdl.w:ptcp.t:call-pbmm2_align_hifi-21.stderr VERBOSE   --log-level INFO \
2025-09-15 20:22:06.693 wdl.w:ptcp.t:call-pbmm2_align_hifi-21.stderr VERBOSE   --log-file pbmm2.log \
2025-09-15 20:22:06.693 wdl.w:ptcp.t:call-pbmm2_align_hifi-21.stderr VERBOSE   --alarms alarms.json \
2025-09-15 20:22:06.693 wdl.w:ptcp.t:call-pbmm2_align_hifi-21.stderr VERBOSE   --num-threads 64 \
2025-09-15 20:22:06.694 wdl.w:ptcp.t:call-pbmm2_align_hifi-21.stderr VERBOSE   --sort \
2025-09-15 20:22:06.694 wdl.w:ptcp.t:call-pbmm2_align_hifi-21.stderr VERBOSE   --preset HiFi \
2025-09-15 20:22:06.694 wdl.w:ptcp.t:call-pbmm2_align_hifi-21.stderr VERBOSE   --report-json mapping_stats.report.json \
2025-09-15 20:22:06.694 wdl.w:ptcp.t:call-pbmm2_align_hifi-21.stderr VERBOSE   --sample "m84036_250809_035451_s4.bc2118" \
2025-09-15 20:22:06.694 wdl.w:ptcp.t:call-pbmm2_align_hifi-21.stderr VERBOSE   --unmapped \
2025-09-15 20:22:06.694 wdl.w:ptcp.t:call-pbmm2_align_hifi-21.stderr VERBOSE   /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa \
2025-09-15 20:22:06.694 wdl.w:ptcp.t:call-pbmm2_align_hifi-21.stderr VERBOSE   /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0022_m84036_250809_035451_s4.bc2118.unmapped.bam \
2025-09-15 20:22:06.694 wdl.w:ptcp.t:call-pbmm2_align_hifi-21.stderr VERBOSE   m84036_250809_035451_s4.bc2118.mapped.bam
2025-09-15 20:22:06.694 wdl.w:ptcp.t:call-pbmm2_align_hifi-21.stderr VERBOSE + pbmm2 align --log-level INFO --log-file pbmm2.log --alarms alarms.json --num-threads 64 --sort --preset HiFi --report-json mapping_stats.report.json --sample m84036_250809_035451_s4.bc2118 --unmapped /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0022_m84036_250809_035451_s4.bc2118.unmapped.bam m84036_250809_035451_s4.bc2118.mapped.bam
2025-09-15 20:22:06.696 wdl.w:ptcp.t:call-pbmm2_align_hifi-25.stderr VERBOSE 
2025-09-15 20:22:06.696 wdl.w:ptcp.t:call-pbmm2_align_hifi-25.stderr VERBOSE pbmm2 \
2025-09-15 20:22:06.696 wdl.w:ptcp.t:call-pbmm2_align_hifi-25.stderr VERBOSE   align \
2025-09-15 20:22:06.696 wdl.w:ptcp.t:call-pbmm2_align_hifi-25.stderr VERBOSE   --log-level INFO \
2025-09-15 20:22:06.696 wdl.w:ptcp.t:call-pbmm2_align_hifi-25.stderr VERBOSE   --log-file pbmm2.log \
2025-09-15 20:22:06.696 wdl.w:ptcp.t:call-pbmm2_align_hifi-25.stderr VERBOSE   --alarms alarms.json \
2025-09-15 20:22:06.696 wdl.w:ptcp.t:call-pbmm2_align_hifi-25.stderr VERBOSE   --num-threads 64 \
2025-09-15 20:22:06.696 wdl.w:ptcp.t:call-pbmm2_align_hifi-25.stderr VERBOSE   --sort \
2025-09-15 20:22:06.697 wdl.w:ptcp.t:call-pbmm2_align_hifi-25.stderr VERBOSE   --preset HiFi \
2025-09-15 20:22:06.697 wdl.w:ptcp.t:call-pbmm2_align_hifi-25.stderr VERBOSE   --report-json mapping_stats.report.json \
2025-09-15 20:22:06.697 wdl.w:ptcp.t:call-pbmm2_align_hifi-25.stderr VERBOSE   --sample "m84036_250809_035451_s4.bc2122" \
2025-09-15 20:22:06.697 wdl.w:ptcp.t:call-pbmm2_align_hifi-25.stderr VERBOSE   --unmapped \
2025-09-15 20:22:06.697 wdl.w:ptcp.t:call-pbmm2_align_hifi-25.stderr VERBOSE   /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa \
2025-09-15 20:22:06.697 wdl.w:ptcp.t:call-pbmm2_align_hifi-25.stderr VERBOSE   /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0026_m84036_250809_035451_s4.bc2122.unmapped.bam \
2025-09-15 20:22:06.697 wdl.w:ptcp.t:call-pbmm2_align_hifi-25.stderr VERBOSE   m84036_250809_035451_s4.bc2122.mapped.bam
2025-09-15 20:22:06.696 wdl.w:ptcp.t:call-pbmm2_align_hifi-27.slurm_singularity INFO srun: job 51797248 has been allocated resources
2025-09-15 20:22:06.697 wdl.w:ptcp.t:call-pbmm2_align_hifi-25.stderr VERBOSE + pbmm2 align --log-level INFO --log-file pbmm2.log --alarms alarms.json --num-threads 64 --sort --preset HiFi --report-json mapping_stats.report.json --sample m84036_250809_035451_s4.bc2122 --unmapped /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0026_m84036_250809_035451_s4.bc2122.unmapped.bam m84036_250809_035451_s4.bc2122.mapped.bam
2025-09-15 20:22:06.700 wdl.w:ptcp.t:call-pbmm2_align_hifi-24.slurm_singularity INFO srun: job 51797246 has been allocated resources
2025-09-15 20:22:06.712 wdl.w:ptcp.t:call-pbmm2_align_hifi-23.slurm_singularity INFO srun: job 51797250 has been allocated resources
2025-09-15 20:22:06.715 wdl.w:ptcp.t:call-pbmm2_align_hifi-28.slurm_singularity INFO srun: job 51797249 has been allocated resources
2025-09-15 20:22:06.729 wdl.w:ptcp.t:call-pbmm2_align_hifi-29.slurm_singularity INFO srun: job 51797253 has been allocated resources
2025-09-15 20:22:06.733 wdl.w:ptcp.t:call-pbmm2_align_hifi-31.slurm_singularity INFO srun: job 51797252 has been allocated resources
2025-09-15 20:22:06.737 wdl.w:ptcp.t:call-pbmm2_align_hifi-30.slurm_singularity INFO srun: job 51797254 has been allocated resources
2025-09-15 20:22:06.737 wdl.w:ptcp.t:call-pbmm2_align_hifi-32.slurm_singularity INFO srun: job 51797251 has been allocated resources
2025-09-15 20:22:06.843 wdl.w:ptcp.t:call-pbmm2_align_hifi-35.slurm_singularity INFO srun: job 51797255 has been allocated resources
2025-09-15 20:22:06.843 wdl.w:ptcp.t:call-pbmm2_align_hifi-35.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:22:06.844 wdl.w:ptcp.t:call-pbmm2_align_hifi-35.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:22:06.846 wdl.w:ptcp.t:call-pbmm2_align_hifi-33.slurm_singularity INFO srun: job 51797256 has been allocated resources
2025-09-15 20:22:06.847 wdl.w:ptcp.t:call-pbmm2_align_hifi-33.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:22:06.847 wdl.w:ptcp.t:call-pbmm2_align_hifi-33.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:22:06.848 wdl.w:ptcp.t:call-pbmm2_align_hifi-34.slurm_singularity INFO srun: job 51797257 has been allocated resources
2025-09-15 20:22:06.849 wdl.w:ptcp.t:call-pbmm2_align_hifi-34.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:22:06.849 wdl.w:ptcp.t:call-pbmm2_align_hifi-34.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:22:07.695 wdl.w:ptcp.t:call-pbmm2_align_hifi-26.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:22:07.695 wdl.w:ptcp.t:call-pbmm2_align_hifi-26.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:22:07.715 wdl.w:ptcp.t:call-pbmm2_align_hifi-27.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:22:07.715 wdl.w:ptcp.t:call-pbmm2_align_hifi-27.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:22:07.715 wdl.w:ptcp.t:call-pbmm2_align_hifi-24.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:22:07.716 wdl.w:ptcp.t:call-pbmm2_align_hifi-24.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:22:07.726 wdl.w:ptcp.t:call-pbmm2_align_hifi-28.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:22:07.726 wdl.w:ptcp.t:call-pbmm2_align_hifi-28.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:22:07.728 wdl.w:ptcp.t:call-pbmm2_align_hifi-23.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:22:07.729 wdl.w:ptcp.t:call-pbmm2_align_hifi-23.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:22:07.741 wdl.w:ptcp.t:call-pbmm2_align_hifi-29.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:22:07.741 wdl.w:ptcp.t:call-pbmm2_align_hifi-29.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:22:07.748 wdl.w:ptcp.t:call-pbmm2_align_hifi-31.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:22:07.748 wdl.w:ptcp.t:call-pbmm2_align_hifi-31.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:22:07.750 wdl.w:ptcp.t:call-pbmm2_align_hifi-30.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:22:07.750 wdl.w:ptcp.t:call-pbmm2_align_hifi-30.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:22:07.750 wdl.w:ptcp.t:call-pbmm2_align_hifi-32.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:22:12.743 wdl.w:ptcp.t:call-pbmm2_align_hifi-22.stderr VERBOSE 
2025-09-15 20:22:12.744 wdl.w:ptcp.t:call-pbmm2_align_hifi-22.stderr VERBOSE pbmm2 \
2025-09-15 20:22:12.744 wdl.w:ptcp.t:call-pbmm2_align_hifi-22.stderr VERBOSE   align \
2025-09-15 20:22:12.744 wdl.w:ptcp.t:call-pbmm2_align_hifi-22.stderr VERBOSE   --log-level INFO \
2025-09-15 20:22:12.744 wdl.w:ptcp.t:call-pbmm2_align_hifi-22.stderr VERBOSE   --log-file pbmm2.log \
2025-09-15 20:22:12.744 wdl.w:ptcp.t:call-pbmm2_align_hifi-22.stderr VERBOSE   --alarms alarms.json \
2025-09-15 20:22:12.744 wdl.w:ptcp.t:call-pbmm2_align_hifi-22.stderr VERBOSE   --num-threads 64 \
2025-09-15 20:22:12.744 wdl.w:ptcp.t:call-pbmm2_align_hifi-22.stderr VERBOSE   --sort \
2025-09-15 20:22:12.744 wdl.w:ptcp.t:call-pbmm2_align_hifi-22.stderr VERBOSE   --preset HiFi \
2025-09-15 20:22:12.744 wdl.w:ptcp.t:call-pbmm2_align_hifi-22.stderr VERBOSE   --report-json mapping_stats.report.json \
2025-09-15 20:22:12.744 wdl.w:ptcp.t:call-pbmm2_align_hifi-22.stderr VERBOSE   --sample "m84036_250809_035451_s4.bc2119" \
2025-09-15 20:22:12.744 wdl.w:ptcp.t:call-pbmm2_align_hifi-22.stderr VERBOSE   --unmapped \
2025-09-15 20:22:12.744 wdl.w:ptcp.t:call-pbmm2_align_hifi-22.stderr VERBOSE   /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa \
2025-09-15 20:22:12.744 wdl.w:ptcp.t:call-pbmm2_align_hifi-22.stderr VERBOSE   /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0023_m84036_250809_035451_s4.bc2119.unmapped.bam \
2025-09-15 20:22:12.744 wdl.w:ptcp.t:call-pbmm2_align_hifi-22.stderr VERBOSE   m84036_250809_035451_s4.bc2119.mapped.bam
2025-09-15 20:22:12.744 wdl.w:ptcp.t:call-pbmm2_align_hifi-22.stderr VERBOSE + pbmm2 align --log-level INFO --log-file pbmm2.log --alarms alarms.json --num-threads 64 --sort --preset HiFi --report-json mapping_stats.report.json --sample m84036_250809_035451_s4.bc2119 --unmapped /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0023_m84036_250809_035451_s4.bc2119.unmapped.bam m84036_250809_035451_s4.bc2119.mapped.bam
2025-09-15 20:22:12.745 wdl.w:ptcp.t:call-pbmm2_align_hifi-26.stderr VERBOSE 
2025-09-15 20:22:12.747 wdl.w:ptcp.t:call-pbmm2_align_hifi-26.stderr VERBOSE pbmm2 \
2025-09-15 20:22:12.747 wdl.w:ptcp.t:call-pbmm2_align_hifi-26.stderr VERBOSE   align \
2025-09-15 20:22:12.747 wdl.w:ptcp.t:call-pbmm2_align_hifi-26.stderr VERBOSE   --log-level INFO \
2025-09-15 20:22:12.747 wdl.w:ptcp.t:call-pbmm2_align_hifi-26.stderr VERBOSE   --log-file pbmm2.log \
2025-09-15 20:22:12.747 wdl.w:ptcp.t:call-pbmm2_align_hifi-26.stderr VERBOSE   --alarms alarms.json \
2025-09-15 20:22:12.747 wdl.w:ptcp.t:call-pbmm2_align_hifi-26.stderr VERBOSE   --num-threads 64 \
2025-09-15 20:22:12.747 wdl.w:ptcp.t:call-pbmm2_align_hifi-26.stderr VERBOSE   --sort \
2025-09-15 20:22:12.747 wdl.w:ptcp.t:call-pbmm2_align_hifi-26.stderr VERBOSE   --preset HiFi \
2025-09-15 20:22:12.747 wdl.w:ptcp.t:call-pbmm2_align_hifi-26.stderr VERBOSE   --report-json mapping_stats.report.json \
2025-09-15 20:22:12.747 wdl.w:ptcp.t:call-pbmm2_align_hifi-26.stderr VERBOSE   --sample "m84036_250809_035451_s4.bc2123" \
2025-09-15 20:22:12.747 wdl.w:ptcp.t:call-pbmm2_align_hifi-26.stderr VERBOSE   --unmapped \
2025-09-15 20:22:12.747 wdl.w:ptcp.t:call-pbmm2_align_hifi-26.stderr VERBOSE   /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa \
2025-09-15 20:22:12.747 wdl.w:ptcp.t:call-pbmm2_align_hifi-26.stderr VERBOSE   /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0027_m84036_250809_035451_s4.bc2123.unmapped.bam \
2025-09-15 20:22:12.747 wdl.w:ptcp.t:call-pbmm2_align_hifi-26.stderr VERBOSE   m84036_250809_035451_s4.bc2123.mapped.bam
2025-09-15 20:22:12.747 wdl.w:ptcp.t:call-pbmm2_align_hifi-26.stderr VERBOSE + pbmm2 align --log-level INFO --log-file pbmm2.log --alarms alarms.json --num-threads 64 --sort --preset HiFi --report-json mapping_stats.report.json --sample m84036_250809_035451_s4.bc2123 --unmapped /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0027_m84036_250809_035451_s4.bc2123.unmapped.bam m84036_250809_035451_s4.bc2123.mapped.bam
2025-09-15 20:22:12.777 wdl.w:ptcp.t:call-pbmm2_align_hifi-24.stderr VERBOSE 
2025-09-15 20:22:12.778 wdl.w:ptcp.t:call-pbmm2_align_hifi-24.stderr VERBOSE pbmm2 \
2025-09-15 20:22:12.778 wdl.w:ptcp.t:call-pbmm2_align_hifi-24.stderr VERBOSE   align \
2025-09-15 20:22:12.778 wdl.w:ptcp.t:call-pbmm2_align_hifi-24.stderr VERBOSE   --log-level INFO \
2025-09-15 20:22:12.778 wdl.w:ptcp.t:call-pbmm2_align_hifi-24.stderr VERBOSE   --log-file pbmm2.log \
2025-09-15 20:22:12.778 wdl.w:ptcp.t:call-pbmm2_align_hifi-24.stderr VERBOSE   --alarms alarms.json \
2025-09-15 20:22:12.778 wdl.w:ptcp.t:call-pbmm2_align_hifi-24.stderr VERBOSE   --num-threads 64 \
2025-09-15 20:22:12.778 wdl.w:ptcp.t:call-pbmm2_align_hifi-24.stderr VERBOSE   --sort \
2025-09-15 20:22:12.778 wdl.w:ptcp.t:call-pbmm2_align_hifi-24.stderr VERBOSE   --preset HiFi \
2025-09-15 20:22:12.778 wdl.w:ptcp.t:call-pbmm2_align_hifi-24.stderr VERBOSE   --report-json mapping_stats.report.json \
2025-09-15 20:22:12.778 wdl.w:ptcp.t:call-pbmm2_align_hifi-24.stderr VERBOSE   --sample "m84036_250809_035451_s4.bc2121" \
2025-09-15 20:22:12.778 wdl.w:ptcp.t:call-pbmm2_align_hifi-24.stderr VERBOSE   --unmapped \
2025-09-15 20:22:12.778 wdl.w:ptcp.t:call-pbmm2_align_hifi-24.stderr VERBOSE   /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa \
2025-09-15 20:22:12.778 wdl.w:ptcp.t:call-pbmm2_align_hifi-24.stderr VERBOSE   /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0025_m84036_250809_035451_s4.bc2121.unmapped.bam \
2025-09-15 20:22:12.778 wdl.w:ptcp.t:call-pbmm2_align_hifi-24.stderr VERBOSE   m84036_250809_035451_s4.bc2121.mapped.bam
2025-09-15 20:22:12.778 wdl.w:ptcp.t:call-pbmm2_align_hifi-24.stderr VERBOSE + pbmm2 align --log-level INFO --log-file pbmm2.log --alarms alarms.json --num-threads 64 --sort --preset HiFi --report-json mapping_stats.report.json --sample m84036_250809_035451_s4.bc2121 --unmapped /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0025_m84036_250809_035451_s4.bc2121.unmapped.bam m84036_250809_035451_s4.bc2121.mapped.bam
2025-09-15 20:22:12.784 wdl.w:ptcp.t:call-pbmm2_align_hifi-23.stderr VERBOSE 
2025-09-15 20:22:12.784 wdl.w:ptcp.t:call-pbmm2_align_hifi-27.stderr VERBOSE 
2025-09-15 20:22:12.785 wdl.w:ptcp.t:call-pbmm2_align_hifi-23.stderr VERBOSE pbmm2 \
2025-09-15 20:22:12.785 wdl.w:ptcp.t:call-pbmm2_align_hifi-27.stderr VERBOSE pbmm2 \
2025-09-15 20:22:12.785 wdl.w:ptcp.t:call-pbmm2_align_hifi-23.stderr VERBOSE   align \
2025-09-15 20:22:12.785 wdl.w:ptcp.t:call-pbmm2_align_hifi-23.stderr VERBOSE   --log-level INFO \
2025-09-15 20:22:12.785 wdl.w:ptcp.t:call-pbmm2_align_hifi-27.stderr VERBOSE   align \
2025-09-15 20:22:12.785 wdl.w:ptcp.t:call-pbmm2_align_hifi-23.stderr VERBOSE   --log-file pbmm2.log \
2025-09-15 20:22:12.785 wdl.w:ptcp.t:call-pbmm2_align_hifi-27.stderr VERBOSE   --log-level INFO \
2025-09-15 20:22:12.786 wdl.w:ptcp.t:call-pbmm2_align_hifi-23.stderr VERBOSE   --alarms alarms.json \
2025-09-15 20:22:12.786 wdl.w:ptcp.t:call-pbmm2_align_hifi-27.stderr VERBOSE   --log-file pbmm2.log \
2025-09-15 20:22:12.786 wdl.w:ptcp.t:call-pbmm2_align_hifi-23.stderr VERBOSE   --num-threads 64 \
2025-09-15 20:22:12.786 wdl.w:ptcp.t:call-pbmm2_align_hifi-27.stderr VERBOSE   --alarms alarms.json \
2025-09-15 20:22:12.786 wdl.w:ptcp.t:call-pbmm2_align_hifi-23.stderr VERBOSE   --sort \
2025-09-15 20:22:12.786 wdl.w:ptcp.t:call-pbmm2_align_hifi-27.stderr VERBOSE   --num-threads 64 \
2025-09-15 20:22:12.786 wdl.w:ptcp.t:call-pbmm2_align_hifi-23.stderr VERBOSE   --preset HiFi \
2025-09-15 20:22:12.786 wdl.w:ptcp.t:call-pbmm2_align_hifi-27.stderr VERBOSE   --sort \
2025-09-15 20:22:12.786 wdl.w:ptcp.t:call-pbmm2_align_hifi-23.stderr VERBOSE   --report-json mapping_stats.report.json \
2025-09-15 20:22:12.786 wdl.w:ptcp.t:call-pbmm2_align_hifi-27.stderr VERBOSE   --preset HiFi \
2025-09-15 20:22:12.786 wdl.w:ptcp.t:call-pbmm2_align_hifi-23.stderr VERBOSE   --sample "m84036_250809_035451_s4.bc2120" \
2025-09-15 20:22:12.786 wdl.w:ptcp.t:call-pbmm2_align_hifi-27.stderr VERBOSE   --report-json mapping_stats.report.json \
2025-09-15 20:22:12.787 wdl.w:ptcp.t:call-pbmm2_align_hifi-23.stderr VERBOSE   --unmapped \
2025-09-15 20:22:12.787 wdl.w:ptcp.t:call-pbmm2_align_hifi-27.stderr VERBOSE   --sample "m84036_250809_035451_s4.bc2124" \
2025-09-15 20:22:12.787 wdl.w:ptcp.t:call-pbmm2_align_hifi-23.stderr VERBOSE   /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa \
2025-09-15 20:22:12.787 wdl.w:ptcp.t:call-pbmm2_align_hifi-27.stderr VERBOSE   --unmapped \
2025-09-15 20:22:12.787 wdl.w:ptcp.t:call-pbmm2_align_hifi-23.stderr VERBOSE   /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0024_m84036_250809_035451_s4.bc2120.unmapped.bam \
2025-09-15 20:22:12.787 wdl.w:ptcp.t:call-pbmm2_align_hifi-27.stderr VERBOSE   /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa \
2025-09-15 20:22:12.787 wdl.w:ptcp.t:call-pbmm2_align_hifi-23.stderr VERBOSE   m84036_250809_035451_s4.bc2120.mapped.bam
2025-09-15 20:22:12.787 wdl.w:ptcp.t:call-pbmm2_align_hifi-27.stderr VERBOSE   /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0028_m84036_250809_035451_s4.bc2124.unmapped.bam \
2025-09-15 20:22:12.787 wdl.w:ptcp.t:call-pbmm2_align_hifi-23.stderr VERBOSE + pbmm2 align --log-level INFO --log-file pbmm2.log --alarms alarms.json --num-threads 64 --sort --preset HiFi --report-json mapping_stats.report.json --sample m84036_250809_035451_s4.bc2120 --unmapped /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0024_m84036_250809_035451_s4.bc2120.unmapped.bam m84036_250809_035451_s4.bc2120.mapped.bam
2025-09-15 20:22:12.787 wdl.w:ptcp.t:call-pbmm2_align_hifi-27.stderr VERBOSE   m84036_250809_035451_s4.bc2124.mapped.bam
2025-09-15 20:22:12.788 wdl.w:ptcp.t:call-pbmm2_align_hifi-27.stderr VERBOSE + pbmm2 align --log-level INFO --log-file pbmm2.log --alarms alarms.json --num-threads 64 --sort --preset HiFi --report-json mapping_stats.report.json --sample m84036_250809_035451_s4.bc2124 --unmapped /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0028_m84036_250809_035451_s4.bc2124.unmapped.bam m84036_250809_035451_s4.bc2124.mapped.bam
2025-09-15 20:22:12.792 wdl.w:ptcp.t:call-pbmm2_align_hifi-28.stderr VERBOSE 
2025-09-15 20:22:12.793 wdl.w:ptcp.t:call-pbmm2_align_hifi-28.stderr VERBOSE pbmm2 \
2025-09-15 20:22:12.793 wdl.w:ptcp.t:call-pbmm2_align_hifi-28.stderr VERBOSE   align \
2025-09-15 20:22:12.792 wdl.w:ptcp.t:call-pbmm2_align_hifi-29.stderr VERBOSE 
2025-09-15 20:22:12.793 wdl.w:ptcp.t:call-pbmm2_align_hifi-28.stderr VERBOSE   --log-level INFO \
2025-09-15 20:22:12.793 wdl.w:ptcp.t:call-pbmm2_align_hifi-29.stderr VERBOSE pbmm2 \
2025-09-15 20:22:12.793 wdl.w:ptcp.t:call-pbmm2_align_hifi-28.stderr VERBOSE   --log-file pbmm2.log \
2025-09-15 20:22:12.793 wdl.w:ptcp.t:call-pbmm2_align_hifi-29.stderr VERBOSE   align \
2025-09-15 20:22:12.793 wdl.w:ptcp.t:call-pbmm2_align_hifi-28.stderr VERBOSE   --alarms alarms.json \
2025-09-15 20:22:12.793 wdl.w:ptcp.t:call-pbmm2_align_hifi-29.stderr VERBOSE   --log-level INFO \
2025-09-15 20:22:12.794 wdl.w:ptcp.t:call-pbmm2_align_hifi-28.stderr VERBOSE   --num-threads 64 \
2025-09-15 20:22:12.794 wdl.w:ptcp.t:call-pbmm2_align_hifi-29.stderr VERBOSE   --log-file pbmm2.log \
2025-09-15 20:22:12.794 wdl.w:ptcp.t:call-pbmm2_align_hifi-28.stderr VERBOSE   --sort \
2025-09-15 20:22:12.794 wdl.w:ptcp.t:call-pbmm2_align_hifi-29.stderr VERBOSE   --alarms alarms.json \
2025-09-15 20:22:12.794 wdl.w:ptcp.t:call-pbmm2_align_hifi-28.stderr VERBOSE   --preset HiFi \
2025-09-15 20:22:12.794 wdl.w:ptcp.t:call-pbmm2_align_hifi-29.stderr VERBOSE   --num-threads 64 \
2025-09-15 20:22:12.794 wdl.w:ptcp.t:call-pbmm2_align_hifi-28.stderr VERBOSE   --report-json mapping_stats.report.json \
2025-09-15 20:22:12.794 wdl.w:ptcp.t:call-pbmm2_align_hifi-29.stderr VERBOSE   --sort \
2025-09-15 20:22:12.794 wdl.w:ptcp.t:call-pbmm2_align_hifi-28.stderr VERBOSE   --sample "m84036_250809_035451_s4.bc2125" \
2025-09-15 20:22:12.794 wdl.w:ptcp.t:call-pbmm2_align_hifi-29.stderr VERBOSE   --preset HiFi \
2025-09-15 20:22:12.794 wdl.w:ptcp.t:call-pbmm2_align_hifi-28.stderr VERBOSE   --unmapped \
2025-09-15 20:22:12.794 wdl.w:ptcp.t:call-pbmm2_align_hifi-29.stderr VERBOSE   --report-json mapping_stats.report.json \
2025-09-15 20:22:12.795 wdl.w:ptcp.t:call-pbmm2_align_hifi-28.stderr VERBOSE   /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa \
2025-09-15 20:22:12.795 wdl.w:ptcp.t:call-pbmm2_align_hifi-29.stderr VERBOSE   --sample "m84036_250809_035451_s4.bc2126" \
2025-09-15 20:22:12.795 wdl.w:ptcp.t:call-pbmm2_align_hifi-28.stderr VERBOSE   /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0029_m84036_250809_035451_s4.bc2125.unmapped.bam \
2025-09-15 20:22:12.795 wdl.w:ptcp.t:call-pbmm2_align_hifi-29.stderr VERBOSE   --unmapped \
2025-09-15 20:22:12.795 wdl.w:ptcp.t:call-pbmm2_align_hifi-28.stderr VERBOSE   m84036_250809_035451_s4.bc2125.mapped.bam
2025-09-15 20:22:12.795 wdl.w:ptcp.t:call-pbmm2_align_hifi-29.stderr VERBOSE   /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa \
2025-09-15 20:22:12.795 wdl.w:ptcp.t:call-pbmm2_align_hifi-28.stderr VERBOSE + pbmm2 align --log-level INFO --log-file pbmm2.log --alarms alarms.json --num-threads 64 --sort --preset HiFi --report-json mapping_stats.report.json --sample m84036_250809_035451_s4.bc2125 --unmapped /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0029_m84036_250809_035451_s4.bc2125.unmapped.bam m84036_250809_035451_s4.bc2125.mapped.bam
2025-09-15 20:22:12.795 wdl.w:ptcp.t:call-pbmm2_align_hifi-29.stderr VERBOSE   /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0030_m84036_250809_035451_s4.bc2126.unmapped.bam \
2025-09-15 20:22:12.795 wdl.w:ptcp.t:call-pbmm2_align_hifi-29.stderr VERBOSE   m84036_250809_035451_s4.bc2126.mapped.bam
2025-09-15 20:22:12.796 wdl.w:ptcp.t:call-pbmm2_align_hifi-29.stderr VERBOSE + pbmm2 align --log-level INFO --log-file pbmm2.log --alarms alarms.json --num-threads 64 --sort --preset HiFi --report-json mapping_stats.report.json --sample m84036_250809_035451_s4.bc2126 --unmapped /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0030_m84036_250809_035451_s4.bc2126.unmapped.bam m84036_250809_035451_s4.bc2126.mapped.bam
2025-09-15 20:22:12.802 wdl.w:ptcp.t:call-pbmm2_align_hifi-32.stderr VERBOSE 
2025-09-15 20:22:12.802 wdl.w:ptcp.t:call-pbmm2_align_hifi-32.stderr VERBOSE pbmm2 \
2025-09-15 20:22:12.802 wdl.w:ptcp.t:call-pbmm2_align_hifi-32.stderr VERBOSE   align \
2025-09-15 20:22:12.802 wdl.w:ptcp.t:call-pbmm2_align_hifi-32.stderr VERBOSE   --log-level INFO \
2025-09-15 20:22:12.802 wdl.w:ptcp.t:call-pbmm2_align_hifi-32.stderr VERBOSE   --log-file pbmm2.log \
2025-09-15 20:22:12.802 wdl.w:ptcp.t:call-pbmm2_align_hifi-32.stderr VERBOSE   --alarms alarms.json \
2025-09-15 20:22:12.802 wdl.w:ptcp.t:call-pbmm2_align_hifi-32.stderr VERBOSE   --num-threads 64 \
2025-09-15 20:22:12.803 wdl.w:ptcp.t:call-pbmm2_align_hifi-32.stderr VERBOSE   --sort \
2025-09-15 20:22:12.803 wdl.w:ptcp.t:call-pbmm2_align_hifi-32.stderr VERBOSE   --preset HiFi \
2025-09-15 20:22:12.803 wdl.w:ptcp.t:call-pbmm2_align_hifi-32.stderr VERBOSE   --report-json mapping_stats.report.json \
2025-09-15 20:22:12.803 wdl.w:ptcp.t:call-pbmm2_align_hifi-32.stderr VERBOSE   --sample "m84036_250809_035451_s4.bc2129" \
2025-09-15 20:22:12.803 wdl.w:ptcp.t:call-pbmm2_align_hifi-32.stderr VERBOSE   --unmapped \
2025-09-15 20:22:12.803 wdl.w:ptcp.t:call-pbmm2_align_hifi-32.stderr VERBOSE   /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa \
2025-09-15 20:22:12.803 wdl.w:ptcp.t:call-pbmm2_align_hifi-32.stderr VERBOSE   /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0033_m84036_250809_035451_s4.bc2129.unmapped.bam \
2025-09-15 20:22:12.803 wdl.w:ptcp.t:call-pbmm2_align_hifi-32.stderr VERBOSE   m84036_250809_035451_s4.bc2129.mapped.bam
2025-09-15 20:22:12.803 wdl.w:ptcp.t:call-pbmm2_align_hifi-32.stderr VERBOSE + pbmm2 align --log-level INFO --log-file pbmm2.log --alarms alarms.json --num-threads 64 --sort --preset HiFi --report-json mapping_stats.report.json --sample m84036_250809_035451_s4.bc2129 --unmapped /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0033_m84036_250809_035451_s4.bc2129.unmapped.bam m84036_250809_035451_s4.bc2129.mapped.bam
2025-09-15 20:22:12.803 wdl.w:ptcp.t:call-pbmm2_align_hifi-30.stderr VERBOSE 
2025-09-15 20:22:12.803 wdl.w:ptcp.t:call-pbmm2_align_hifi-30.stderr VERBOSE pbmm2 \
2025-09-15 20:22:12.803 wdl.w:ptcp.t:call-pbmm2_align_hifi-30.stderr VERBOSE   align \
2025-09-15 20:22:12.803 wdl.w:ptcp.t:call-pbmm2_align_hifi-30.stderr VERBOSE   --log-level INFO \
2025-09-15 20:22:12.803 wdl.w:ptcp.t:call-pbmm2_align_hifi-30.stderr VERBOSE   --log-file pbmm2.log \
2025-09-15 20:22:12.804 wdl.w:ptcp.t:call-pbmm2_align_hifi-30.stderr VERBOSE   --alarms alarms.json \
2025-09-15 20:22:12.804 wdl.w:ptcp.t:call-pbmm2_align_hifi-30.stderr VERBOSE   --num-threads 64 \
2025-09-15 20:22:12.804 wdl.w:ptcp.t:call-pbmm2_align_hifi-30.stderr VERBOSE   --sort \
2025-09-15 20:22:12.804 wdl.w:ptcp.t:call-pbmm2_align_hifi-30.stderr VERBOSE   --preset HiFi \
2025-09-15 20:22:12.804 wdl.w:ptcp.t:call-pbmm2_align_hifi-30.stderr VERBOSE   --report-json mapping_stats.report.json \
2025-09-15 20:22:12.804 wdl.w:ptcp.t:call-pbmm2_align_hifi-30.stderr VERBOSE   --sample "m84036_250809_035451_s4.bc2127" \
2025-09-15 20:22:12.804 wdl.w:ptcp.t:call-pbmm2_align_hifi-30.stderr VERBOSE   --unmapped \
2025-09-15 20:22:12.804 wdl.w:ptcp.t:call-pbmm2_align_hifi-30.stderr VERBOSE   /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa \
2025-09-15 20:22:12.804 wdl.w:ptcp.t:call-pbmm2_align_hifi-30.stderr VERBOSE   /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0031_m84036_250809_035451_s4.bc2127.unmapped.bam \
2025-09-15 20:22:12.804 wdl.w:ptcp.t:call-pbmm2_align_hifi-30.stderr VERBOSE   m84036_250809_035451_s4.bc2127.mapped.bam
2025-09-15 20:22:12.804 wdl.w:ptcp.t:call-pbmm2_align_hifi-30.stderr VERBOSE + pbmm2 align --log-level INFO --log-file pbmm2.log --alarms alarms.json --num-threads 64 --sort --preset HiFi --report-json mapping_stats.report.json --sample m84036_250809_035451_s4.bc2127 --unmapped /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0031_m84036_250809_035451_s4.bc2127.unmapped.bam m84036_250809_035451_s4.bc2127.mapped.bam
2025-09-15 20:22:12.804 wdl.w:ptcp.t:call-pbmm2_align_hifi-31.stderr VERBOSE 
2025-09-15 20:22:12.804 wdl.w:ptcp.t:call-pbmm2_align_hifi-31.stderr VERBOSE pbmm2 \
2025-09-15 20:22:12.804 wdl.w:ptcp.t:call-pbmm2_align_hifi-31.stderr VERBOSE   align \
2025-09-15 20:22:12.804 wdl.w:ptcp.t:call-pbmm2_align_hifi-31.stderr VERBOSE   --log-level INFO \
2025-09-15 20:22:12.805 wdl.w:ptcp.t:call-pbmm2_align_hifi-31.stderr VERBOSE   --log-file pbmm2.log \
2025-09-15 20:22:12.805 wdl.w:ptcp.t:call-pbmm2_align_hifi-31.stderr VERBOSE   --alarms alarms.json \
2025-09-15 20:22:12.805 wdl.w:ptcp.t:call-pbmm2_align_hifi-31.stderr VERBOSE   --num-threads 64 \
2025-09-15 20:22:12.805 wdl.w:ptcp.t:call-pbmm2_align_hifi-31.stderr VERBOSE   --sort \
2025-09-15 20:22:12.805 wdl.w:ptcp.t:call-pbmm2_align_hifi-31.stderr VERBOSE   --preset HiFi \
2025-09-15 20:22:12.805 wdl.w:ptcp.t:call-pbmm2_align_hifi-31.stderr VERBOSE   --report-json mapping_stats.report.json \
2025-09-15 20:22:12.805 wdl.w:ptcp.t:call-pbmm2_align_hifi-31.stderr VERBOSE   --sample "m84036_250809_035451_s4.bc2128" \
2025-09-15 20:22:12.805 wdl.w:ptcp.t:call-pbmm2_align_hifi-31.stderr VERBOSE   --unmapped \
2025-09-15 20:22:12.805 wdl.w:ptcp.t:call-pbmm2_align_hifi-31.stderr VERBOSE   /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa \
2025-09-15 20:22:12.805 wdl.w:ptcp.t:call-pbmm2_align_hifi-31.stderr VERBOSE   /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0032_m84036_250809_035451_s4.bc2128.unmapped.bam \
2025-09-15 20:22:12.805 wdl.w:ptcp.t:call-pbmm2_align_hifi-31.stderr VERBOSE   m84036_250809_035451_s4.bc2128.mapped.bam
2025-09-15 20:22:12.805 wdl.w:ptcp.t:call-pbmm2_align_hifi-31.stderr VERBOSE + pbmm2 align --log-level INFO --log-file pbmm2.log --alarms alarms.json --num-threads 64 --sort --preset HiFi --report-json mapping_stats.report.json --sample m84036_250809_035451_s4.bc2128 --unmapped /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0032_m84036_250809_035451_s4.bc2128.unmapped.bam m84036_250809_035451_s4.bc2128.mapped.bam
2025-09-15 20:22:12.906 wdl.w:ptcp.t:call-pbmm2_align_hifi-35.stderr VERBOSE 
2025-09-15 20:22:12.907 wdl.w:ptcp.t:call-pbmm2_align_hifi-35.stderr VERBOSE pbmm2 \
2025-09-15 20:22:12.907 wdl.w:ptcp.t:call-pbmm2_align_hifi-35.stderr VERBOSE   align \
2025-09-15 20:22:12.907 wdl.w:ptcp.t:call-pbmm2_align_hifi-35.stderr VERBOSE   --log-level INFO \
2025-09-15 20:22:12.907 wdl.w:ptcp.t:call-pbmm2_align_hifi-35.stderr VERBOSE   --log-file pbmm2.log \
2025-09-15 20:22:12.907 wdl.w:ptcp.t:call-pbmm2_align_hifi-35.stderr VERBOSE   --alarms alarms.json \
2025-09-15 20:22:12.907 wdl.w:ptcp.t:call-pbmm2_align_hifi-35.stderr VERBOSE   --num-threads 64 \
2025-09-15 20:22:12.907 wdl.w:ptcp.t:call-pbmm2_align_hifi-35.stderr VERBOSE   --sort \
2025-09-15 20:22:12.907 wdl.w:ptcp.t:call-pbmm2_align_hifi-35.stderr VERBOSE   --preset HiFi \
2025-09-15 20:22:12.907 wdl.w:ptcp.t:call-pbmm2_align_hifi-35.stderr VERBOSE   --report-json mapping_stats.report.json \
2025-09-15 20:22:12.907 wdl.w:ptcp.t:call-pbmm2_align_hifi-35.stderr VERBOSE   --sample "m84036_250809_035451_s4.bc2132" \
2025-09-15 20:22:12.907 wdl.w:ptcp.t:call-pbmm2_align_hifi-35.stderr VERBOSE   --unmapped \
2025-09-15 20:22:12.907 wdl.w:ptcp.t:call-pbmm2_align_hifi-35.stderr VERBOSE   /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa \
2025-09-15 20:22:12.907 wdl.w:ptcp.t:call-pbmm2_align_hifi-35.stderr VERBOSE   /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0036_m84036_250809_035451_s4.bc2132.unmapped.bam \
2025-09-15 20:22:12.907 wdl.w:ptcp.t:call-pbmm2_align_hifi-35.stderr VERBOSE   m84036_250809_035451_s4.bc2132.mapped.bam
2025-09-15 20:22:12.907 wdl.w:ptcp.t:call-pbmm2_align_hifi-35.stderr VERBOSE + pbmm2 align --log-level INFO --log-file pbmm2.log --alarms alarms.json --num-threads 64 --sort --preset HiFi --report-json mapping_stats.report.json --sample m84036_250809_035451_s4.bc2132 --unmapped /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0036_m84036_250809_035451_s4.bc2132.unmapped.bam m84036_250809_035451_s4.bc2132.mapped.bam
2025-09-15 20:22:12.910 wdl.w:ptcp.t:call-pbmm2_align_hifi-34.stderr VERBOSE 
2025-09-15 20:22:12.910 wdl.w:ptcp.t:call-pbmm2_align_hifi-34.stderr VERBOSE pbmm2 \
2025-09-15 20:22:12.910 wdl.w:ptcp.t:call-pbmm2_align_hifi-34.stderr VERBOSE   align \
2025-09-15 20:22:12.910 wdl.w:ptcp.t:call-pbmm2_align_hifi-34.stderr VERBOSE   --log-level INFO \
2025-09-15 20:22:12.910 wdl.w:ptcp.t:call-pbmm2_align_hifi-34.stderr VERBOSE   --log-file pbmm2.log \
2025-09-15 20:22:12.910 wdl.w:ptcp.t:call-pbmm2_align_hifi-34.stderr VERBOSE   --alarms alarms.json \
2025-09-15 20:22:12.910 wdl.w:ptcp.t:call-pbmm2_align_hifi-34.stderr VERBOSE   --num-threads 64 \
2025-09-15 20:22:12.911 wdl.w:ptcp.t:call-pbmm2_align_hifi-34.stderr VERBOSE   --sort \
2025-09-15 20:22:12.911 wdl.w:ptcp.t:call-pbmm2_align_hifi-34.stderr VERBOSE   --preset HiFi \
2025-09-15 20:22:12.911 wdl.w:ptcp.t:call-pbmm2_align_hifi-34.stderr VERBOSE   --report-json mapping_stats.report.json \
2025-09-15 20:22:12.911 wdl.w:ptcp.t:call-pbmm2_align_hifi-34.stderr VERBOSE   --sample "m84036_250809_035451_s4.bc2131" \
2025-09-15 20:22:12.911 wdl.w:ptcp.t:call-pbmm2_align_hifi-34.stderr VERBOSE   --unmapped \
2025-09-15 20:22:12.911 wdl.w:ptcp.t:call-pbmm2_align_hifi-34.stderr VERBOSE   /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa \
2025-09-15 20:22:12.911 wdl.w:ptcp.t:call-pbmm2_align_hifi-34.stderr VERBOSE   /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0035_m84036_250809_035451_s4.bc2131.unmapped.bam \
2025-09-15 20:22:12.911 wdl.w:ptcp.t:call-pbmm2_align_hifi-34.stderr VERBOSE   m84036_250809_035451_s4.bc2131.mapped.bam
2025-09-15 20:22:12.911 wdl.w:ptcp.t:call-pbmm2_align_hifi-34.stderr VERBOSE + pbmm2 align --log-level INFO --log-file pbmm2.log --alarms alarms.json --num-threads 64 --sort --preset HiFi --report-json mapping_stats.report.json --sample m84036_250809_035451_s4.bc2131 --unmapped /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0035_m84036_250809_035451_s4.bc2131.unmapped.bam m84036_250809_035451_s4.bc2131.mapped.bam
2025-09-15 20:22:12.915 wdl.w:ptcp.t:call-pbmm2_align_hifi-33.stderr VERBOSE 
2025-09-15 20:22:12.915 wdl.w:ptcp.t:call-pbmm2_align_hifi-33.stderr VERBOSE pbmm2 \
2025-09-15 20:22:12.915 wdl.w:ptcp.t:call-pbmm2_align_hifi-33.stderr VERBOSE   align \
2025-09-15 20:22:12.915 wdl.w:ptcp.t:call-pbmm2_align_hifi-33.stderr VERBOSE   --log-level INFO \
2025-09-15 20:22:12.915 wdl.w:ptcp.t:call-pbmm2_align_hifi-33.stderr VERBOSE   --log-file pbmm2.log \
2025-09-15 20:22:12.915 wdl.w:ptcp.t:call-pbmm2_align_hifi-33.stderr VERBOSE   --alarms alarms.json \
2025-09-15 20:22:12.915 wdl.w:ptcp.t:call-pbmm2_align_hifi-33.stderr VERBOSE   --num-threads 64 \
2025-09-15 20:22:12.915 wdl.w:ptcp.t:call-pbmm2_align_hifi-33.stderr VERBOSE   --sort \
2025-09-15 20:22:12.915 wdl.w:ptcp.t:call-pbmm2_align_hifi-33.stderr VERBOSE   --preset HiFi \
2025-09-15 20:22:12.916 wdl.w:ptcp.t:call-pbmm2_align_hifi-33.stderr VERBOSE   --report-json mapping_stats.report.json \
2025-09-15 20:22:12.916 wdl.w:ptcp.t:call-pbmm2_align_hifi-33.stderr VERBOSE   --sample "m84036_250809_035451_s4.bc2130" \
2025-09-15 20:22:12.916 wdl.w:ptcp.t:call-pbmm2_align_hifi-33.stderr VERBOSE   --unmapped \
2025-09-15 20:22:12.916 wdl.w:ptcp.t:call-pbmm2_align_hifi-33.stderr VERBOSE   /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa \
2025-09-15 20:22:12.916 wdl.w:ptcp.t:call-pbmm2_align_hifi-33.stderr VERBOSE   /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0034_m84036_250809_035451_s4.bc2130.unmapped.bam \
2025-09-15 20:22:12.916 wdl.w:ptcp.t:call-pbmm2_align_hifi-33.stderr VERBOSE   m84036_250809_035451_s4.bc2130.mapped.bam
2025-09-15 20:22:12.916 wdl.w:ptcp.t:call-pbmm2_align_hifi-33.stderr VERBOSE + pbmm2 align --log-level INFO --log-file pbmm2.log --alarms alarms.json --num-threads 64 --sort --preset HiFi --report-json mapping_stats.report.json --sample m84036_250809_035451_s4.bc2130 --unmapped /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0034_m84036_250809_035451_s4.bc2130.unmapped.bam m84036_250809_035451_s4.bc2130.mapped.bam
2025-09-15 20:22:45.699 wdl.w:ptcp.t:call-pbmm2_align_hifi-14 INFO output :: name: "mapped_bam", value: "m84036_250809_035451_s4.bc2111.mapped.bam"
2025-09-15 20:22:45.702 wdl.w:ptcp.t:call-pbmm2_align_hifi-14 INFO output :: name: "mapped_bam_bai", value: "m84036_250809_035451_s4.bc2111.mapped.bam.bai"
2025-09-15 20:22:45.703 wdl.w:ptcp.t:call-pbmm2_align_hifi-14 INFO output :: name: "mapped_bam_pbi", value: "m84036_250809_035451_s4.bc2111.mapped.bam.pbi"
2025-09-15 20:22:45.704 wdl.w:ptcp.t:call-pbmm2_align_hifi-14 INFO output :: name: "report", value: "mapping_stats.report.json"
2025-09-15 20:22:45.781 wdl.w:ptcp.t:call-pbmm2_align_hifi-14 NOTICE done
2025-09-15 20:22:45.787 wdl.w:ptcp NOTICE finish :: job: "call-pbmm2_align_hifi-14"
2025-09-15 20:22:45.787 wdl.w:ptcp INFO output :: job: "call-pbmm2_align_hifi-14", values: {"report": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-14/out/mapping_stats.report.json", "mapped_bam_pbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-14/out/m84036_250809_035451_s4.bc2111.mapped.bam.pbi", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-14/out/m84036_250809_035451_s4.bc2111.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-14/out/m84036_250809_035451_s4.bc2111.mapped.bam"}
2025-09-15 20:22:45.788 wdl.w:ptcp NOTICE ready :: job: "call-paraphase-14", callee: "paraphase"
2025-09-15 20:22:45.788 wdl.w:ptcp INFO input :: job: "call-paraphase-14", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf", "genome_version": "38", "config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-14/out/m84036_250809_035451_s4.bc2111.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-14/out/m84036_250809_035451_s4.bc2111.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2111"}
2025-09-15 20:22:45.789 wdl.w:ptcp INFO subworkflow thread pool initialized :: subworkflow_concurrency: 128, call_depth: 0
2025-09-15 20:22:45.790 wdl.w:ptcp NOTICE ready :: job: "call-sawfish-14", callee: "sawfish"
2025-09-15 20:22:45.790 wdl.w:ptcp INFO input :: job: "call-sawfish-14", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-14/out/m84036_250809_035451_s4.bc2111.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-14/out/m84036_250809_035451_s4.bc2111.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2111"}
2025-09-15 20:22:45.793 wdl.w:ptcp NOTICE ready :: job: "call-trgt-14", callee: "trgt"
2025-09-15 20:22:45.793 wdl.w:ptcp INFO input :: job: "call-trgt-14", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-14/out/m84036_250809_035451_s4.bc2111.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-14/out/m84036_250809_035451_s4.bc2111.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2111"}
2025-09-15 20:22:45.797 wdl.w:ptcp.w:call-paraphase-14 NOTICE workflow start :: name: "paraphase", source: "./paraphase.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-14"
2025-09-15 20:22:45.799 wdl.w:ptcp.w:call-sawfish-14 NOTICE workflow start :: name: "sawfish", source: "./sawfish.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-14"
2025-09-15 20:22:45.803 wdl.w:ptcp.t:call-pbmm2_align_hifi-22 INFO output :: name: "mapped_bam", value: "m84036_250809_035451_s4.bc2119.mapped.bam"
2025-09-15 20:22:45.803 wdl.w:ptcp.w:call-trgt-14 NOTICE workflow start :: name: "trgt", source: "./trgt.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-14"
2025-09-15 20:22:45.807 wdl.w:ptcp.t:call-pbmm2_align_hifi-22 INFO output :: name: "mapped_bam_bai", value: "m84036_250809_035451_s4.bc2119.mapped.bam.bai"
2025-09-15 20:22:45.808 wdl.w:ptcp.t:call-pbmm2_align_hifi-22 INFO output :: name: "mapped_bam_pbi", value: "m84036_250809_035451_s4.bc2119.mapped.bam.pbi"
2025-09-15 20:22:45.810 wdl.w:ptcp.t:call-pbmm2_align_hifi-22 INFO output :: name: "report", value: "mapping_stats.report.json"
2025-09-15 20:22:45.812 wdl.w:ptcp.w:call-paraphase-14 INFO visit :: node: "decl-annotation_vcf", values: {"annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf"}
2025-09-15 20:22:45.812 wdl.w:ptcp.w:call-paraphase-14 INFO visit :: node: "decl-config_file", values: {"config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml"}
2025-09-15 20:22:45.813 wdl.w:ptcp.w:call-paraphase-14 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:22:45.814 wdl.w:ptcp.w:call-paraphase-14 INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:22:45.814 wdl.w:ptcp.w:call-paraphase-14 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-14/out/m84036_250809_035451_s4.bc2111.mapped.bam"}
2025-09-15 20:22:45.814 wdl.w:ptcp.w:call-paraphase-14 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-14/out/m84036_250809_035451_s4.bc2111.mapped.bam.bai"}
2025-09-15 20:22:45.814 wdl.w:ptcp.w:call-paraphase-14 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:22:45.815 wdl.w:ptcp.w:call-paraphase-14 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:22:45.815 wdl.w:ptcp.w:call-paraphase-14 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2111"}
2025-09-15 20:22:45.815 wdl.w:ptcp.w:call-paraphase-14 INFO visit :: node: "decl-sex", values: {"sex": "F"}
2025-09-15 20:22:45.816 wdl.w:ptcp.w:call-paraphase-14 NOTICE ready :: job: "call-run_paraphase", callee: "run_paraphase"
2025-09-15 20:22:45.816 wdl.w:ptcp.w:call-paraphase-14 INFO input :: job: "call-run_paraphase", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf", "genome_version": "38", "config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-14/out/m84036_250809_035451_s4.bc2111.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-14/out/m84036_250809_035451_s4.bc2111.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2111"}
2025-09-15 20:22:45.821 wdl.w:ptcp.w:call-sawfish-14 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:22:45.822 wdl.w:ptcp.w:call-sawfish-14 INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:22:45.822 wdl.w:ptcp.w:call-sawfish-14 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-14/out/m84036_250809_035451_s4.bc2111.mapped.bam"}
2025-09-15 20:22:45.822 wdl.w:ptcp.w:call-sawfish-14 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-14/out/m84036_250809_035451_s4.bc2111.mapped.bam.bai"}
2025-09-15 20:22:45.822 wdl.w:ptcp.w:call-sawfish-14 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:22:45.822 wdl.w:ptcp.w:call-sawfish-14 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:22:45.822 wdl.w:ptcp.w:call-sawfish-14 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2111"}
2025-09-15 20:22:45.822 wdl.w:ptcp.w:call-sawfish-14 NOTICE ready :: job: "call-run_sawfish", callee: "run_sawfish"
2025-09-15 20:22:45.823 wdl.w:ptcp.w:call-sawfish-14 INFO input :: job: "call-run_sawfish", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-14/out/m84036_250809_035451_s4.bc2111.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-14/out/m84036_250809_035451_s4.bc2111.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2111"}
2025-09-15 20:22:45.824 wdl.w:ptcp.w:call-trgt-14 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:22:45.824 wdl.w:ptcp.w:call-trgt-14 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-14/out/m84036_250809_035451_s4.bc2111.mapped.bam"}
2025-09-15 20:22:45.825 wdl.w:ptcp.w:call-trgt-14 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-14/out/m84036_250809_035451_s4.bc2111.mapped.bam.bai"}
2025-09-15 20:22:45.825 wdl.w:ptcp.w:call-trgt-14 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:22:45.825 wdl.w:ptcp.w:call-trgt-14 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:22:45.825 wdl.w:ptcp.w:call-trgt-14 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2111"}
2025-09-15 20:22:45.825 wdl.w:ptcp.w:call-trgt-14 INFO visit :: node: "decl-sex", values: {"sex": "F"}
2025-09-15 20:22:45.825 wdl.w:ptcp.w:call-trgt-14 INFO visit :: node: "decl-trgt_bed", values: {"trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"}
2025-09-15 20:22:45.825 wdl.w:ptcp.w:call-trgt-14 NOTICE ready :: job: "call-get_reads_overlapping_repeats", callee: "get_reads_overlapping_repeats"
2025-09-15 20:22:45.825 wdl.w:ptcp.w:call-trgt-14 INFO input :: job: "call-get_reads_overlapping_repeats", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-14/out/m84036_250809_035451_s4.bc2111.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-14/out/m84036_250809_035451_s4.bc2111.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2111"}
2025-09-15 20:22:45.826 wdl.w:ptcp.w:call-trgt-14 NOTICE ready :: job: "call-trgt_genotype", callee: "trgt_genotype"
2025-09-15 20:22:45.826 wdl.w:ptcp.w:call-trgt-14 INFO input :: job: "call-trgt_genotype", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-14/out/m84036_250809_035451_s4.bc2111.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-14/out/m84036_250809_035451_s4.bc2111.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2111"}
2025-09-15 20:22:45.827 wdl.w:ptcp.w:call-paraphase-14.t:call-run_paraphase NOTICE task setup :: name: "run_paraphase", source: "./paraphase.wdl", line: 127, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-14/call-run_paraphase", thread: 140613026555456
2025-09-15 20:22:45.835 wdl.w:ptcp.w:call-sawfish-14.t:call-run_sawfish NOTICE task setup :: name: "run_sawfish", source: "./sawfish.wdl", line: 83, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-14/call-run_sawfish", thread: 140606575711808
2025-09-15 20:22:45.837 wdl.w:ptcp.w:call-trgt-14.t:call-get_reads_overlapping_repeats NOTICE task setup :: name: "get_reads_overlapping_repeats", source: "./trgt.wdl", line: 182, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-14/call-get_reads_overlapping_repeats", thread: 140606089197120
2025-09-15 20:22:45.839 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_genotype NOTICE task setup :: name: "trgt_genotype", source: "./trgt.wdl", line: 272, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-14/call-trgt_genotype", thread: 140606080804416
2025-09-15 20:22:45.854 wdl.w:ptcp.w:call-paraphase-14.t:call-run_paraphase INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:22:45.855 wdl.w:ptcp.w:call-paraphase-14.t:call-run_paraphase INFO input :: name: "annotation_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf"
2025-09-15 20:22:45.856 wdl.w:ptcp.w:call-paraphase-14.t:call-run_paraphase INFO input :: name: "genome_version", value: "38"
2025-09-15 20:22:45.856 wdl.w:ptcp.w:call-paraphase-14.t:call-run_paraphase INFO input :: name: "config_file", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/paraphase_config.GRCh38.yaml"
2025-09-15 20:22:45.856 wdl.w:ptcp.w:call-paraphase-14.t:call-run_paraphase INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:22:45.856 wdl.w:ptcp.w:call-paraphase-14.t:call-run_paraphase INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:22:45.857 wdl.w:ptcp.w:call-paraphase-14.t:call-run_paraphase INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2111.mapped.bam.bai"
2025-09-15 20:22:45.857 wdl.w:ptcp.w:call-paraphase-14.t:call-run_paraphase INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2111.mapped.bam"
2025-09-15 20:22:45.857 wdl.w:ptcp.w:call-paraphase-14.t:call-run_paraphase INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2111"
2025-09-15 20:22:45.858 wdl.w:ptcp.w:call-paraphase-14.t:call-run_paraphase INFO eval :: name: "threads", value: 4
2025-09-15 20:22:45.859 wdl.w:ptcp.w:call-paraphase-14.t:call-run_paraphase INFO eval :: name: "mem_gb", value: 8
2025-09-15 20:22:45.860 wdl.w:ptcp.w:call-paraphase-14.t:call-run_paraphase INFO eval :: name: "disk_size", value: 27
2025-09-15 20:22:45.860 wdl.w:ptcp.w:call-paraphase-14.t:call-run_paraphase INFO eval :: name: "out_dir", value: "m84036_250809_035451_s4.bc2111_paraphase"
2025-09-15 20:22:45.861 wdl.w:ptcp.w:call-paraphase-14.t:call-run_paraphase INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 4, memory_reservation: 8000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:22:45.862 wdl.w:ptcp.w:call-paraphase-14.t:call-run_paraphase WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:22:45.863 wdl.w:ptcp.w:call-paraphase-14.t:call-run_paraphase INFO provisioned :: seconds_waited: 0, cpu: 4, mem_bytes: 8000000000
2025-09-15 20:22:45.864 wdl.w:ptcp.w:call-paraphase-14.t:call-run_paraphase INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:22:45.864 wdl.w:ptcp.w:call-sawfish-14.t:call-run_sawfish INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:22:45.865 wdl.w:ptcp.w:call-sawfish-14.t:call-run_sawfish INFO input :: name: "genome_version", value: "38"
2025-09-15 20:22:45.865 wdl.w:ptcp.w:call-sawfish-14.t:call-run_sawfish INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:22:45.865 wdl.w:ptcp.w:call-sawfish-14.t:call-run_sawfish INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:22:45.865 wdl.w:ptcp.w:call-sawfish-14.t:call-run_sawfish INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2111.mapped.bam.bai"
2025-09-15 20:22:45.865 wdl.w:ptcp.w:call-sawfish-14.t:call-run_sawfish INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2111.mapped.bam"
2025-09-15 20:22:45.866 wdl.w:ptcp.w:call-sawfish-14.t:call-run_sawfish INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2111"
2025-09-15 20:22:45.866 wdl.w:ptcp.w:call-sawfish-14.t:call-run_sawfish INFO eval :: name: "mem_gb", value: 32
2025-09-15 20:22:45.866 wdl.w:ptcp.w:call-sawfish-14.t:call-run_sawfish INFO eval :: name: "threads", value: 16
2025-09-15 20:22:45.866 wdl.w:ptcp.w:call-sawfish-14.t:call-run_sawfish INFO eval :: name: "disk_size", value: 30
2025-09-15 20:22:45.866 wdl.w:ptcp.w:call-sawfish-14.t:call-run_sawfish INFO eval :: name: "discover_dirname", value: "m84036_250809_035451_s4.bc2111_sawfish_discover"
2025-09-15 20:22:45.866 wdl.w:ptcp.w:call-sawfish-14.t:call-run_sawfish INFO eval :: name: "call_dirname", value: "m84036_250809_035451_s4.bc2111_sawfish"
2025-09-15 20:22:45.867 wdl.w:ptcp.w:call-sawfish-14.t:call-run_sawfish INFO eval :: name: "minimap2_bam_filename", value: "m84036_250809_035451_s4.bc2111.minimap2.bam"
2025-09-15 20:22:45.867 wdl.w:ptcp.w:call-sawfish-14.t:call-run_sawfish INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 16, memory_reservation: 32000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:22:45.867 wdl.w:ptcp.w:call-sawfish-14.t:call-run_sawfish WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:22:45.868 wdl.w:ptcp.w:call-sawfish-14.t:call-run_sawfish INFO provisioned :: seconds_waited: 0, cpu: 16, mem_bytes: 32000000000
2025-09-15 20:22:45.868 wdl.w:ptcp.w:call-sawfish-14.t:call-run_sawfish INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:22:45.868 wdl.w:ptcp.w:call-trgt-14.t:call-get_reads_overlapping_repeats INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:22:45.868 wdl.w:ptcp.w:call-trgt-14.t:call-get_reads_overlapping_repeats INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:22:45.868 wdl.w:ptcp.w:call-trgt-14.t:call-get_reads_overlapping_repeats INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2111.mapped.bam.bai"
2025-09-15 20:22:45.868 wdl.w:ptcp.w:call-trgt-14.t:call-get_reads_overlapping_repeats INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2111.mapped.bam"
2025-09-15 20:22:45.869 wdl.w:ptcp.w:call-trgt-14.t:call-get_reads_overlapping_repeats INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2111"
2025-09-15 20:22:45.869 wdl.w:ptcp.w:call-trgt-14.t:call-get_reads_overlapping_repeats INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:22:45.869 wdl.w:ptcp.w:call-trgt-14.t:call-get_reads_overlapping_repeats INFO eval :: name: "expand_size", value: 3000
2025-09-15 20:22:45.869 wdl.w:ptcp.w:call-trgt-14.t:call-get_reads_overlapping_repeats INFO eval :: name: "threads", value: 1
2025-09-15 20:22:45.869 wdl.w:ptcp.w:call-trgt-14.t:call-get_reads_overlapping_repeats INFO eval :: name: "expanded_bed_name", value: "m84036_250809_035451_s4.bc2111.expanded.bed"
2025-09-15 20:22:45.870 wdl.w:ptcp.w:call-trgt-14.t:call-get_reads_overlapping_repeats INFO eval :: name: "disk_size", value: 11
2025-09-15 20:22:45.870 wdl.w:ptcp.w:call-trgt-14.t:call-get_reads_overlapping_repeats INFO eval :: name: "output_name", value: "m84036_250809_035451_s4.bc2111.repeats.bam"
2025-09-15 20:22:45.870 wdl.w:ptcp.w:call-trgt-14.t:call-get_reads_overlapping_repeats INFO eval :: name: "index_name", value: "m84036_250809_035451_s4.bc2111.repeats.bam.bai"
2025-09-15 20:22:45.870 wdl.w:ptcp.w:call-trgt-14.t:call-get_reads_overlapping_repeats INFO eval :: name: "output_name_with_index", value: "m84036_250809_035451_s4.bc2111.repeats.bam##idx##m84036_250809_035451_s4.bc2111.repeats.bam.bai"
2025-09-15 20:22:45.870 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_genotype INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:22:45.871 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_genotype INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:22:45.871 wdl.w:ptcp.w:call-trgt-14.t:call-get_reads_overlapping_repeats INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:22:45.871 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_genotype INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:22:45.871 wdl.w:ptcp.w:call-trgt-14.t:call-get_reads_overlapping_repeats WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:22:45.871 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_genotype INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:22:45.872 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_genotype INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2111.mapped.bam.bai"
2025-09-15 20:22:45.872 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_genotype INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2111.mapped.bam"
2025-09-15 20:22:45.872 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_genotype INFO input :: name: "sex", value: "F"
2025-09-15 20:22:45.872 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_genotype INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2111"
2025-09-15 20:22:45.873 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_genotype INFO eval :: name: "mem_gb", value: 16
2025-09-15 20:22:45.873 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_genotype INFO eval :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2111.trgt"
2025-09-15 20:22:45.873 wdl.w:ptcp.w:call-trgt-14.t:call-get_reads_overlapping_repeats INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:22:45.873 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_genotype INFO eval :: name: "threads", value: 8
2025-09-15 20:22:45.873 wdl.w:ptcp.w:call-trgt-14.t:call-get_reads_overlapping_repeats INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:22:45.874 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_genotype INFO eval :: name: "disk_size", value: 27
2025-09-15 20:22:45.874 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_genotype INFO eval :: name: "karyotype", value: "XX"
2025-09-15 20:22:45.875 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_genotype INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 8, memory_reservation: 16000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:22:45.875 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_genotype WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:22:45.875 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_genotype INFO provisioned :: seconds_waited: 0, cpu: 8, mem_bytes: 16000000000
2025-09-15 20:22:45.875 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_genotype INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:22:45.937 wdl.w:ptcp.t:call-pbmm2_align_hifi-22 NOTICE done
2025-09-15 20:22:45.943 wdl.w:ptcp NOTICE finish :: job: "call-pbmm2_align_hifi-22"
2025-09-15 20:22:45.943 wdl.w:ptcp.w:call-trgt-14.t:call-get_reads_overlapping_repeats INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 9, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-14/call-get_reads_overlapping_repeats/_singularity_tmpdir_yrp7rii0"
2025-09-15 20:22:45.943 wdl.w:ptcp INFO output :: job: "call-pbmm2_align_hifi-22", values: {"report": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-22/out/mapping_stats.report.json", "mapped_bam_pbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-22/out/m84036_250809_035451_s4.bc2119.mapped.bam.pbi", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-22/out/m84036_250809_035451_s4.bc2119.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-22/out/m84036_250809_035451_s4.bc2119.mapped.bam"}
2025-09-15 20:22:45.943 wdl.w:ptcp.w:call-trgt-14.t:call-get_reads_overlapping_repeats INFO Slurm invocation: srun --job-name call-get_reads_overlapping_repeats --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-14/call-get_reads_overlapping_repeats/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-14/call-get_reads_overlapping_repeats/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-14/call-get_reads_overlapping_repeats/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-14/call-get_reads_overlapping_repeats/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-14/out/m84036_250809_035451_s4.bc2111.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2111.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-14/out/m84036_250809_035451_s4.bc2111.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2111.mapped.bam:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-14/call-get_reads_overlapping_repeats/_singularity_tmpdir_yrp7rii0/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-14/call-get_reads_overlapping_repeats/_singularity_tmpdir_yrp7rii0/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:22:45.944 wdl.w:ptcp NOTICE ready :: job: "call-paraphase-22", callee: "paraphase"
2025-09-15 20:22:45.945 wdl.w:ptcp INFO input :: job: "call-paraphase-22", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf", "genome_version": "38", "config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-22/out/m84036_250809_035451_s4.bc2119.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-22/out/m84036_250809_035451_s4.bc2119.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2119"}
2025-09-15 20:22:45.946 wdl.w:ptcp NOTICE ready :: job: "call-sawfish-22", callee: "sawfish"
2025-09-15 20:22:45.946 wdl.w:ptcp INFO input :: job: "call-sawfish-22", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-22/out/m84036_250809_035451_s4.bc2119.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-22/out/m84036_250809_035451_s4.bc2119.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2119"}
2025-09-15 20:22:45.949 wdl.w:ptcp NOTICE ready :: job: "call-trgt-22", callee: "trgt"
2025-09-15 20:22:45.949 wdl.w:ptcp INFO input :: job: "call-trgt-22", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-22/out/m84036_250809_035451_s4.bc2119.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-22/out/m84036_250809_035451_s4.bc2119.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2119"}
2025-09-15 20:22:45.955 wdl.w:ptcp.w:call-paraphase-22 NOTICE workflow start :: name: "paraphase", source: "./paraphase.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-22"
2025-09-15 20:22:45.955 wdl.w:ptcp.w:call-sawfish-14.t:call-run_sawfish INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 10, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-14/call-run_sawfish/_singularity_tmpdir_z8ctbd8u"
2025-09-15 20:22:45.956 wdl.w:ptcp.w:call-sawfish-14.t:call-run_sawfish INFO Slurm invocation: srun --job-name call-run_sawfish --partition compute,compute9 --cpus-per-task 16 --mem 30518M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-14/call-run_sawfish/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-14/call-run_sawfish/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-14/call-run_sawfish/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-14/call-run_sawfish/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-14/out/m84036_250809_035451_s4.bc2111.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2111.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-14/out/m84036_250809_035451_s4.bc2111.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2111.mapped.bam:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-14/call-run_sawfish/_singularity_tmpdir_z8ctbd8u/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-14/call-run_sawfish/_singularity_tmpdir_z8ctbd8u/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:22:45.959 wdl.w:ptcp.w:call-paraphase-14.t:call-run_paraphase INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-14/call-run_paraphase/_singularity_tmpdir_j5i0uge5"
2025-09-15 20:22:45.959 wdl.w:ptcp.w:call-paraphase-14.t:call-run_paraphase INFO Slurm invocation: srun --job-name call-run_paraphase --partition compute,compute9 --cpus-per-task 4 --mem 7629M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-14/call-run_paraphase/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-14/call-run_paraphase/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-14/call-run_paraphase/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-14/call-run_paraphase/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-14/out/m84036_250809_035451_s4.bc2111.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2111.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-14/out/m84036_250809_035451_s4.bc2111.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2111.mapped.bam:ro --bind /ptcp/meta/variant_list/variant_list.GRCh38.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf:ro --bind /ptcp/meta/paraphase/paraphase_config.GRCh38.yaml:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/paraphase_config.GRCh38.yaml:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-14/call-run_paraphase/_singularity_tmpdir_j5i0uge5/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-14/call-run_paraphase/_singularity_tmpdir_j5i0uge5/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:22:45.960 wdl.w:ptcp.w:call-sawfish-22 NOTICE workflow start :: name: "sawfish", source: "./sawfish.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-22"
2025-09-15 20:22:45.967 wdl.w:ptcp.w:call-trgt-14.t:call-get_reads_overlapping_repeats NOTICE slurm_singularity run :: pid: 1197984, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-14/call-get_reads_overlapping_repeats/slurm_singularity.log.txt"
2025-09-15 20:22:45.967 wdl.w:ptcp.w:call-sawfish-14.t:call-run_sawfish NOTICE slurm_singularity run :: pid: 1197988, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-14/call-run_sawfish/slurm_singularity.log.txt"
2025-09-15 20:22:45.967 wdl.w:ptcp.w:call-paraphase-14.t:call-run_paraphase NOTICE slurm_singularity run :: pid: 1197989, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-14/call-run_paraphase/slurm_singularity.log.txt"
2025-09-15 20:22:45.967 wdl.w:ptcp.w:call-trgt-22 NOTICE workflow start :: name: "trgt", source: "./trgt.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-22"
2025-09-15 20:22:45.972 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_genotype INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 11, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-14/call-trgt_genotype/_singularity_tmpdir_e_7w9t0x"
2025-09-15 20:22:45.973 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_genotype INFO Slurm invocation: srun --job-name call-trgt_genotype --partition compute,compute9 --cpus-per-task 8 --mem 15259M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-14/call-trgt_genotype/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-14/call-trgt_genotype/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-14/call-trgt_genotype/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-14/call-trgt_genotype/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-14/out/m84036_250809_035451_s4.bc2111.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2111.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-14/out/m84036_250809_035451_s4.bc2111.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2111.mapped.bam:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-14/call-trgt_genotype/_singularity_tmpdir_e_7w9t0x/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-14/call-trgt_genotype/_singularity_tmpdir_e_7w9t0x/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:22:45.978 wdl.w:ptcp.w:call-paraphase-22 INFO visit :: node: "decl-annotation_vcf", values: {"annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf"}
2025-09-15 20:22:45.979 wdl.w:ptcp.w:call-paraphase-22 INFO visit :: node: "decl-config_file", values: {"config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml"}
2025-09-15 20:22:45.979 wdl.w:ptcp.w:call-paraphase-22 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:22:45.979 wdl.w:ptcp.w:call-paraphase-22 INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:22:45.979 wdl.w:ptcp.w:call-paraphase-22 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-22/out/m84036_250809_035451_s4.bc2119.mapped.bam"}
2025-09-15 20:22:45.979 wdl.w:ptcp.w:call-paraphase-22 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-22/out/m84036_250809_035451_s4.bc2119.mapped.bam.bai"}
2025-09-15 20:22:45.979 wdl.w:ptcp.w:call-paraphase-22 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:22:45.980 wdl.w:ptcp.w:call-paraphase-22 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:22:45.980 wdl.w:ptcp.w:call-paraphase-22 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2119"}
2025-09-15 20:22:45.980 wdl.w:ptcp.w:call-paraphase-22 INFO visit :: node: "decl-sex", values: {"sex": "F"}
2025-09-15 20:22:45.981 wdl.w:ptcp.w:call-paraphase-22 NOTICE ready :: job: "call-run_paraphase", callee: "run_paraphase"
2025-09-15 20:22:45.981 wdl.w:ptcp.w:call-paraphase-22 INFO input :: job: "call-run_paraphase", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf", "genome_version": "38", "config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-22/out/m84036_250809_035451_s4.bc2119.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-22/out/m84036_250809_035451_s4.bc2119.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2119"}
2025-09-15 20:22:45.982 wdl.w:ptcp.w:call-sawfish-22 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:22:45.982 wdl.w:ptcp.w:call-sawfish-22 INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:22:45.983 wdl.w:ptcp.w:call-sawfish-22 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-22/out/m84036_250809_035451_s4.bc2119.mapped.bam"}
2025-09-15 20:22:45.983 wdl.w:ptcp.w:call-sawfish-22 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-22/out/m84036_250809_035451_s4.bc2119.mapped.bam.bai"}
2025-09-15 20:22:45.983 wdl.w:ptcp.w:call-sawfish-22 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:22:45.983 wdl.w:ptcp.w:call-sawfish-22 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:22:45.983 wdl.w:ptcp.w:call-sawfish-22 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2119"}
2025-09-15 20:22:45.983 wdl.w:ptcp.w:call-sawfish-22 NOTICE ready :: job: "call-run_sawfish", callee: "run_sawfish"
2025-09-15 20:22:45.983 wdl.w:ptcp.w:call-sawfish-22 INFO input :: job: "call-run_sawfish", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-22/out/m84036_250809_035451_s4.bc2119.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-22/out/m84036_250809_035451_s4.bc2119.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2119"}
2025-09-15 20:22:45.987 wdl.w:ptcp.w:call-trgt-22 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:22:45.987 wdl.w:ptcp.w:call-trgt-22 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-22/out/m84036_250809_035451_s4.bc2119.mapped.bam"}
2025-09-15 20:22:45.987 wdl.w:ptcp.w:call-trgt-22 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-22/out/m84036_250809_035451_s4.bc2119.mapped.bam.bai"}
2025-09-15 20:22:45.987 wdl.w:ptcp.w:call-trgt-22 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:22:45.988 wdl.w:ptcp.w:call-trgt-22 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:22:45.988 wdl.w:ptcp.w:call-trgt-22 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2119"}
2025-09-15 20:22:45.988 wdl.w:ptcp.w:call-trgt-22 INFO visit :: node: "decl-sex", values: {"sex": "F"}
2025-09-15 20:22:45.988 wdl.w:ptcp.w:call-trgt-22 INFO visit :: node: "decl-trgt_bed", values: {"trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"}
2025-09-15 20:22:45.989 wdl.w:ptcp.w:call-paraphase-22.t:call-run_paraphase NOTICE task setup :: name: "run_paraphase", source: "./paraphase.wdl", line: 127, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-22/call-run_paraphase", thread: 140612481291840
2025-09-15 20:22:45.988 wdl.w:ptcp.w:call-trgt-22 NOTICE ready :: job: "call-get_reads_overlapping_repeats", callee: "get_reads_overlapping_repeats"
2025-09-15 20:22:45.989 wdl.w:ptcp.w:call-trgt-22 INFO input :: job: "call-get_reads_overlapping_repeats", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-22/out/m84036_250809_035451_s4.bc2119.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-22/out/m84036_250809_035451_s4.bc2119.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2119"}
2025-09-15 20:22:45.989 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_genotype NOTICE slurm_singularity run :: pid: 1197992, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-14/call-trgt_genotype/slurm_singularity.log.txt"
2025-09-15 20:22:45.990 wdl.w:ptcp.w:call-trgt-22 NOTICE ready :: job: "call-trgt_genotype", callee: "trgt_genotype"
2025-09-15 20:22:45.990 wdl.w:ptcp.w:call-trgt-22 INFO input :: job: "call-trgt_genotype", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-22/out/m84036_250809_035451_s4.bc2119.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-22/out/m84036_250809_035451_s4.bc2119.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2119"}
2025-09-15 20:22:45.991 wdl.w:ptcp.w:call-sawfish-22.t:call-run_sawfish NOTICE task setup :: name: "run_sawfish", source: "./sawfish.wdl", line: 83, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-22/call-run_sawfish", thread: 140606047233600
2025-09-15 20:22:46.007 wdl.w:ptcp.w:call-paraphase-22.t:call-run_paraphase INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:22:46.007 wdl.w:ptcp.w:call-paraphase-22.t:call-run_paraphase INFO input :: name: "annotation_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf"
2025-09-15 20:22:46.008 wdl.w:ptcp.w:call-paraphase-22.t:call-run_paraphase INFO input :: name: "genome_version", value: "38"
2025-09-15 20:22:46.008 wdl.w:ptcp.w:call-paraphase-22.t:call-run_paraphase INFO input :: name: "config_file", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/paraphase_config.GRCh38.yaml"
2025-09-15 20:22:46.008 wdl.w:ptcp.w:call-paraphase-22.t:call-run_paraphase INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:22:46.008 wdl.w:ptcp.w:call-paraphase-22.t:call-run_paraphase INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:22:46.008 wdl.w:ptcp.w:call-paraphase-22.t:call-run_paraphase INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2119.mapped.bam.bai"
2025-09-15 20:22:46.008 wdl.w:ptcp.w:call-paraphase-22.t:call-run_paraphase INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2119.mapped.bam"
2025-09-15 20:22:46.008 wdl.w:ptcp.w:call-paraphase-22.t:call-run_paraphase INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2119"
2025-09-15 20:22:46.008 wdl.w:ptcp.w:call-paraphase-22.t:call-run_paraphase INFO eval :: name: "threads", value: 4
2025-09-15 20:22:46.008 wdl.w:ptcp.w:call-paraphase-22.t:call-run_paraphase INFO eval :: name: "mem_gb", value: 8
2025-09-15 20:22:46.009 wdl.w:ptcp.w:call-paraphase-22.t:call-run_paraphase INFO eval :: name: "disk_size", value: 27
2025-09-15 20:22:46.009 wdl.w:ptcp.w:call-paraphase-22.t:call-run_paraphase INFO eval :: name: "out_dir", value: "m84036_250809_035451_s4.bc2119_paraphase"
2025-09-15 20:22:46.009 wdl.w:ptcp.w:call-paraphase-22.t:call-run_paraphase INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 4, memory_reservation: 8000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:22:46.009 wdl.w:ptcp.w:call-paraphase-22.t:call-run_paraphase WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:22:46.010 wdl.w:ptcp.w:call-sawfish-22.t:call-run_sawfish INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:22:46.010 wdl.w:ptcp.w:call-paraphase-22.t:call-run_paraphase INFO provisioned :: seconds_waited: 0, cpu: 4, mem_bytes: 8000000000
2025-09-15 20:22:46.010 wdl.w:ptcp.w:call-sawfish-22.t:call-run_sawfish INFO input :: name: "genome_version", value: "38"
2025-09-15 20:22:46.010 wdl.w:ptcp.w:call-paraphase-22.t:call-run_paraphase INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:22:46.010 wdl.w:ptcp.w:call-sawfish-22.t:call-run_sawfish INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:22:46.011 wdl.w:ptcp.w:call-sawfish-22.t:call-run_sawfish INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:22:46.011 wdl.w:ptcp.w:call-sawfish-22.t:call-run_sawfish INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2119.mapped.bam.bai"
2025-09-15 20:22:46.011 wdl.w:ptcp.w:call-sawfish-22.t:call-run_sawfish INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2119.mapped.bam"
2025-09-15 20:22:46.011 wdl.w:ptcp.w:call-sawfish-22.t:call-run_sawfish INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2119"
2025-09-15 20:22:46.011 wdl.w:ptcp.w:call-sawfish-22.t:call-run_sawfish INFO eval :: name: "mem_gb", value: 32
2025-09-15 20:22:46.011 wdl.w:ptcp.w:call-sawfish-22.t:call-run_sawfish INFO eval :: name: "threads", value: 16
2025-09-15 20:22:46.011 wdl.w:ptcp.w:call-sawfish-22.t:call-run_sawfish INFO eval :: name: "disk_size", value: 30
2025-09-15 20:22:46.011 wdl.w:ptcp.w:call-sawfish-22.t:call-run_sawfish INFO eval :: name: "discover_dirname", value: "m84036_250809_035451_s4.bc2119_sawfish_discover"
2025-09-15 20:22:46.012 wdl.w:ptcp.w:call-sawfish-22.t:call-run_sawfish INFO eval :: name: "call_dirname", value: "m84036_250809_035451_s4.bc2119_sawfish"
2025-09-15 20:22:46.012 wdl.w:ptcp.w:call-sawfish-22.t:call-run_sawfish INFO eval :: name: "minimap2_bam_filename", value: "m84036_250809_035451_s4.bc2119.minimap2.bam"
2025-09-15 20:22:46.012 wdl.w:ptcp.w:call-sawfish-22.t:call-run_sawfish INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 16, memory_reservation: 32000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:22:46.012 wdl.w:ptcp.w:call-sawfish-22.t:call-run_sawfish WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:22:46.013 wdl.w:ptcp.w:call-sawfish-22.t:call-run_sawfish INFO provisioned :: seconds_waited: 0, cpu: 16, mem_bytes: 32000000000
2025-09-15 20:22:46.013 wdl.w:ptcp.w:call-sawfish-22.t:call-run_sawfish INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:22:46.067 wdl.w:ptcp.w:call-sawfish-22.t:call-run_sawfish INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 10, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-22/call-run_sawfish/_singularity_tmpdir_e5n_k2hu"
2025-09-15 20:22:46.068 wdl.w:ptcp.w:call-sawfish-22.t:call-run_sawfish INFO Slurm invocation: srun --job-name call-run_sawfish --partition compute,compute9 --cpus-per-task 16 --mem 30518M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-22/call-run_sawfish/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-22/call-run_sawfish/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-22/call-run_sawfish/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-22/call-run_sawfish/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-22/out/m84036_250809_035451_s4.bc2119.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2119.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-22/out/m84036_250809_035451_s4.bc2119.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2119.mapped.bam.bai:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-22/call-run_sawfish/_singularity_tmpdir_e5n_k2hu/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-22/call-run_sawfish/_singularity_tmpdir_e5n_k2hu/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:22:46.081 wdl.w:ptcp.w:call-paraphase-22.t:call-run_paraphase INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-22/call-run_paraphase/_singularity_tmpdir_4x6rp9ox"
2025-09-15 20:22:46.082 wdl.w:ptcp.w:call-paraphase-22.t:call-run_paraphase INFO Slurm invocation: srun --job-name call-run_paraphase --partition compute,compute9 --cpus-per-task 4 --mem 7629M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-22/call-run_paraphase/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-22/call-run_paraphase/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-22/call-run_paraphase/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-22/call-run_paraphase/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-22/out/m84036_250809_035451_s4.bc2119.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2119.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-22/out/m84036_250809_035451_s4.bc2119.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2119.mapped.bam.bai:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/variant_list/variant_list.GRCh38.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf:ro --bind /ptcp/meta/paraphase/paraphase_config.GRCh38.yaml:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/paraphase_config.GRCh38.yaml:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-22/call-run_paraphase/_singularity_tmpdir_4x6rp9ox/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-22/call-run_paraphase/_singularity_tmpdir_4x6rp9ox/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:22:46.086 wdl.w:ptcp.w:call-sawfish-22.t:call-run_sawfish NOTICE slurm_singularity run :: pid: 1197996, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-22/call-run_sawfish/slurm_singularity.log.txt"
2025-09-15 20:22:46.086 wdl.w:ptcp.w:call-paraphase-22.t:call-run_paraphase NOTICE slurm_singularity run :: pid: 1197997, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-22/call-run_paraphase/slurm_singularity.log.txt"
2025-09-15 20:22:46.346 wdl.w:ptcp.t:call-pbmm2_align_hifi-38.slurm_singularity INFO srun: job 51797259 has been allocated resources
2025-09-15 20:22:46.346 wdl.w:ptcp.t:call-pbmm2_align_hifi-38.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:22:46.346 wdl.w:ptcp.t:call-pbmm2_align_hifi-38.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:22:46.377 wdl.w:ptcp.t:call-pbmm2_align_hifi-37.slurm_singularity INFO srun: job 51797258 has been allocated resources
2025-09-15 20:22:46.377 wdl.w:ptcp.t:call-pbmm2_align_hifi-37.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:22:46.377 wdl.w:ptcp.t:call-pbmm2_align_hifi-37.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:22:46.982 wdl.w:ptcp.w:call-sawfish-14.t:call-run_sawfish.slurm_singularity INFO srun: job 51797320 queued and waiting for resources
2025-09-15 20:22:46.982 wdl.w:ptcp.w:call-paraphase-14.t:call-run_paraphase.slurm_singularity INFO srun: job 51797321 queued and waiting for resources
2025-09-15 20:22:46.983 wdl.w:ptcp.w:call-trgt-14.t:call-get_reads_overlapping_repeats.slurm_singularity INFO srun: job 51797319 queued and waiting for resources
2025-09-15 20:22:46.996 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_genotype.slurm_singularity INFO srun: job 51797322 queued and waiting for resources
2025-09-15 20:22:47.080 wdl.w:ptcp.t:call-pbmm2_align_hifi-15 INFO output :: name: "mapped_bam", value: "m84036_250809_035451_s4.bc2112.mapped.bam"
2025-09-15 20:22:47.084 wdl.w:ptcp.t:call-pbmm2_align_hifi-15 INFO output :: name: "mapped_bam_bai", value: "m84036_250809_035451_s4.bc2112.mapped.bam.bai"
2025-09-15 20:22:47.085 wdl.w:ptcp.t:call-pbmm2_align_hifi-15 INFO output :: name: "mapped_bam_pbi", value: "m84036_250809_035451_s4.bc2112.mapped.bam.pbi"
2025-09-15 20:22:47.087 wdl.w:ptcp.t:call-pbmm2_align_hifi-15 INFO output :: name: "report", value: "mapping_stats.report.json"
2025-09-15 20:22:47.097 wdl.w:ptcp.w:call-sawfish-22.t:call-run_sawfish.slurm_singularity INFO srun: job 51797323 queued and waiting for resources
2025-09-15 20:22:47.100 wdl.w:ptcp.w:call-paraphase-22.t:call-run_paraphase.slurm_singularity INFO srun: job 51797324 queued and waiting for resources
2025-09-15 20:22:47.168 wdl.w:ptcp.t:call-pbmm2_align_hifi-15 NOTICE done
2025-09-15 20:22:47.173 wdl.w:ptcp NOTICE finish :: job: "call-pbmm2_align_hifi-15"
2025-09-15 20:22:47.173 wdl.w:ptcp INFO output :: job: "call-pbmm2_align_hifi-15", values: {"report": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-15/out/mapping_stats.report.json", "mapped_bam_pbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-15/out/m84036_250809_035451_s4.bc2112.mapped.bam.pbi", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-15/out/m84036_250809_035451_s4.bc2112.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-15/out/m84036_250809_035451_s4.bc2112.mapped.bam"}
2025-09-15 20:22:47.174 wdl.w:ptcp NOTICE ready :: job: "call-paraphase-15", callee: "paraphase"
2025-09-15 20:22:47.174 wdl.w:ptcp INFO input :: job: "call-paraphase-15", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf", "genome_version": "38", "config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-15/out/m84036_250809_035451_s4.bc2112.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-15/out/m84036_250809_035451_s4.bc2112.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2112"}
2025-09-15 20:22:47.175 wdl.w:ptcp NOTICE ready :: job: "call-sawfish-15", callee: "sawfish"
2025-09-15 20:22:47.175 wdl.w:ptcp INFO input :: job: "call-sawfish-15", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-15/out/m84036_250809_035451_s4.bc2112.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-15/out/m84036_250809_035451_s4.bc2112.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2112"}
2025-09-15 20:22:47.180 wdl.w:ptcp NOTICE ready :: job: "call-trgt-15", callee: "trgt"
2025-09-15 20:22:47.181 wdl.w:ptcp.w:call-trgt-22.t:call-get_reads_overlapping_repeats NOTICE task setup :: name: "get_reads_overlapping_repeats", source: "./trgt.wdl", line: 182, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-22/call-get_reads_overlapping_repeats", thread: 140613018162752
2025-09-15 20:22:47.181 wdl.w:ptcp INFO input :: job: "call-trgt-15", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-15/out/m84036_250809_035451_s4.bc2112.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-15/out/m84036_250809_035451_s4.bc2112.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2112"}
2025-09-15 20:22:47.185 wdl.w:ptcp.w:call-paraphase-15 NOTICE workflow start :: name: "paraphase", source: "./paraphase.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-15"
2025-09-15 20:22:47.190 wdl.w:ptcp.w:call-sawfish-15 NOTICE workflow start :: name: "sawfish", source: "./sawfish.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-15"
2025-09-15 20:22:47.192 wdl.w:ptcp.w:call-trgt-15 NOTICE workflow start :: name: "trgt", source: "./trgt.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-15"
2025-09-15 20:22:47.206 wdl.w:ptcp.w:call-paraphase-15 INFO visit :: node: "decl-annotation_vcf", values: {"annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf"}
2025-09-15 20:22:47.207 wdl.w:ptcp.w:call-trgt-22.t:call-get_reads_overlapping_repeats INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:22:47.208 wdl.w:ptcp.w:call-paraphase-15 INFO visit :: node: "decl-config_file", values: {"config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml"}
2025-09-15 20:22:47.208 wdl.w:ptcp.w:call-trgt-22.t:call-get_reads_overlapping_repeats INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:22:47.209 wdl.w:ptcp.w:call-paraphase-15 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:22:47.209 wdl.w:ptcp.w:call-trgt-22.t:call-get_reads_overlapping_repeats INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2119.mapped.bam.bai"
2025-09-15 20:22:47.209 wdl.w:ptcp.w:call-paraphase-15 INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:22:47.209 wdl.w:ptcp.w:call-trgt-22.t:call-get_reads_overlapping_repeats INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2119.mapped.bam"
2025-09-15 20:22:47.210 wdl.w:ptcp.w:call-paraphase-15 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-15/out/m84036_250809_035451_s4.bc2112.mapped.bam"}
2025-09-15 20:22:47.210 wdl.w:ptcp.w:call-trgt-22.t:call-get_reads_overlapping_repeats INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2119"
2025-09-15 20:22:47.210 wdl.w:ptcp.w:call-paraphase-15 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-15/out/m84036_250809_035451_s4.bc2112.mapped.bam.bai"}
2025-09-15 20:22:47.211 wdl.w:ptcp.w:call-trgt-22.t:call-get_reads_overlapping_repeats INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:22:47.211 wdl.w:ptcp.w:call-paraphase-15 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:22:47.212 wdl.w:ptcp.w:call-trgt-22.t:call-get_reads_overlapping_repeats INFO eval :: name: "expand_size", value: 3000
2025-09-15 20:22:47.212 wdl.w:ptcp.w:call-paraphase-15 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:22:47.212 wdl.w:ptcp.t:call-pbmm2_align_hifi-20 INFO output :: name: "mapped_bam", value: "m84036_250809_035451_s4.bc2117.mapped.bam"
2025-09-15 20:22:47.212 wdl.w:ptcp.w:call-trgt-22.t:call-get_reads_overlapping_repeats INFO eval :: name: "threads", value: 1
2025-09-15 20:22:47.213 wdl.w:ptcp.w:call-paraphase-15 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2112"}
2025-09-15 20:22:47.213 wdl.w:ptcp.w:call-trgt-22.t:call-get_reads_overlapping_repeats INFO eval :: name: "expanded_bed_name", value: "m84036_250809_035451_s4.bc2119.expanded.bed"
2025-09-15 20:22:47.213 wdl.w:ptcp.w:call-paraphase-15 INFO visit :: node: "decl-sex", values: {"sex": "F"}
2025-09-15 20:22:47.213 wdl.w:ptcp.w:call-trgt-22.t:call-get_reads_overlapping_repeats INFO eval :: name: "disk_size", value: 11
2025-09-15 20:22:47.214 wdl.w:ptcp.w:call-paraphase-15 NOTICE ready :: job: "call-run_paraphase", callee: "run_paraphase"
2025-09-15 20:22:47.215 wdl.w:ptcp.w:call-trgt-22.t:call-get_reads_overlapping_repeats INFO eval :: name: "output_name", value: "m84036_250809_035451_s4.bc2119.repeats.bam"
2025-09-15 20:22:47.215 wdl.w:ptcp.w:call-paraphase-15 INFO input :: job: "call-run_paraphase", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf", "genome_version": "38", "config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-15/out/m84036_250809_035451_s4.bc2112.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-15/out/m84036_250809_035451_s4.bc2112.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2112"}
2025-09-15 20:22:47.215 wdl.w:ptcp.w:call-trgt-22.t:call-get_reads_overlapping_repeats INFO eval :: name: "index_name", value: "m84036_250809_035451_s4.bc2119.repeats.bam.bai"
2025-09-15 20:22:47.216 wdl.w:ptcp.w:call-trgt-22.t:call-get_reads_overlapping_repeats INFO eval :: name: "output_name_with_index", value: "m84036_250809_035451_s4.bc2119.repeats.bam##idx##m84036_250809_035451_s4.bc2119.repeats.bam.bai"
2025-09-15 20:22:47.216 wdl.w:ptcp.w:call-trgt-22.t:call-get_reads_overlapping_repeats INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:22:47.217 wdl.w:ptcp.w:call-trgt-15 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:22:47.218 wdl.w:ptcp.w:call-trgt-22.t:call-get_reads_overlapping_repeats WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:22:47.218 wdl.w:ptcp.w:call-trgt-15 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-15/out/m84036_250809_035451_s4.bc2112.mapped.bam"}
2025-09-15 20:22:47.219 wdl.w:ptcp.w:call-sawfish-15 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:22:47.219 wdl.w:ptcp.w:call-trgt-15 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-15/out/m84036_250809_035451_s4.bc2112.mapped.bam.bai"}
2025-09-15 20:22:47.219 wdl.w:ptcp.w:call-sawfish-15 INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:22:47.220 wdl.w:ptcp.w:call-trgt-15 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:22:47.220 wdl.w:ptcp.t:call-pbmm2_align_hifi-20 INFO output :: name: "mapped_bam_bai", value: "m84036_250809_035451_s4.bc2117.mapped.bam.bai"
2025-09-15 20:22:47.220 wdl.w:ptcp.w:call-sawfish-15 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-15/out/m84036_250809_035451_s4.bc2112.mapped.bam"}
2025-09-15 20:22:47.220 wdl.w:ptcp.w:call-trgt-15 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:22:47.220 wdl.w:ptcp.w:call-trgt-22.t:call-get_reads_overlapping_repeats INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:22:47.220 wdl.w:ptcp.w:call-sawfish-15 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-15/out/m84036_250809_035451_s4.bc2112.mapped.bam.bai"}
2025-09-15 20:22:47.221 wdl.w:ptcp.w:call-trgt-15 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2112"}
2025-09-15 20:22:47.221 wdl.w:ptcp.w:call-sawfish-15 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:22:47.221 wdl.w:ptcp.w:call-trgt-22.t:call-get_reads_overlapping_repeats INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:22:47.221 wdl.w:ptcp.w:call-trgt-15 INFO visit :: node: "decl-sex", values: {"sex": "F"}
2025-09-15 20:22:47.221 wdl.w:ptcp.w:call-sawfish-15 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:22:47.221 wdl.w:ptcp.w:call-trgt-15 INFO visit :: node: "decl-trgt_bed", values: {"trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"}
2025-09-15 20:22:47.222 wdl.w:ptcp.w:call-sawfish-15 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2112"}
2025-09-15 20:22:47.222 wdl.w:ptcp.w:call-trgt-15 NOTICE ready :: job: "call-get_reads_overlapping_repeats", callee: "get_reads_overlapping_repeats"
2025-09-15 20:22:47.222 wdl.w:ptcp.w:call-sawfish-15 NOTICE ready :: job: "call-run_sawfish", callee: "run_sawfish"
2025-09-15 20:22:47.223 wdl.w:ptcp.w:call-trgt-15 INFO input :: job: "call-get_reads_overlapping_repeats", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-15/out/m84036_250809_035451_s4.bc2112.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-15/out/m84036_250809_035451_s4.bc2112.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2112"}
2025-09-15 20:22:47.223 wdl.w:ptcp.t:call-pbmm2_align_hifi-20 INFO output :: name: "mapped_bam_pbi", value: "m84036_250809_035451_s4.bc2117.mapped.bam.pbi"
2025-09-15 20:22:47.223 wdl.w:ptcp.w:call-sawfish-15 INFO input :: job: "call-run_sawfish", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-15/out/m84036_250809_035451_s4.bc2112.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-15/out/m84036_250809_035451_s4.bc2112.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2112"}
2025-09-15 20:22:47.224 wdl.w:ptcp.w:call-trgt-15 NOTICE ready :: job: "call-trgt_genotype", callee: "trgt_genotype"
2025-09-15 20:22:47.224 wdl.w:ptcp.w:call-trgt-15 INFO input :: job: "call-trgt_genotype", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-15/out/m84036_250809_035451_s4.bc2112.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-15/out/m84036_250809_035451_s4.bc2112.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2112"}
2025-09-15 20:22:47.225 wdl.w:ptcp.t:call-pbmm2_align_hifi-20 INFO output :: name: "report", value: "mapping_stats.report.json"
2025-09-15 20:22:47.273 wdl.w:ptcp.w:call-trgt-22.t:call-get_reads_overlapping_repeats INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 9, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-22/call-get_reads_overlapping_repeats/_singularity_tmpdir_ains2mfi"
2025-09-15 20:22:47.273 wdl.w:ptcp.w:call-trgt-22.t:call-get_reads_overlapping_repeats INFO Slurm invocation: srun --job-name call-get_reads_overlapping_repeats --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-22/call-get_reads_overlapping_repeats/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-22/call-get_reads_overlapping_repeats/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-22/call-get_reads_overlapping_repeats/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-22/call-get_reads_overlapping_repeats/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-22/out/m84036_250809_035451_s4.bc2119.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2119.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-22/out/m84036_250809_035451_s4.bc2119.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2119.mapped.bam.bai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-22/call-get_reads_overlapping_repeats/_singularity_tmpdir_ains2mfi/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-22/call-get_reads_overlapping_repeats/_singularity_tmpdir_ains2mfi/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:22:47.286 wdl.w:ptcp.t:call-pbmm2_align_hifi-36.slurm_singularity INFO srun: job 51797260 has been allocated resources
2025-09-15 20:22:47.302 wdl.w:ptcp.t:call-pbmm2_align_hifi-20 NOTICE done
2025-09-15 20:22:47.306 wdl.w:ptcp.w:call-trgt-22.t:call-get_reads_overlapping_repeats NOTICE slurm_singularity run :: pid: 1198025, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-22/call-get_reads_overlapping_repeats/slurm_singularity.log.txt"
2025-09-15 20:22:47.308 wdl.w:ptcp NOTICE finish :: job: "call-pbmm2_align_hifi-20"
2025-09-15 20:22:47.308 wdl.w:ptcp INFO output :: job: "call-pbmm2_align_hifi-20", values: {"report": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-20/out/mapping_stats.report.json", "mapped_bam_pbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-20/out/m84036_250809_035451_s4.bc2117.mapped.bam.pbi", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-20/out/m84036_250809_035451_s4.bc2117.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-20/out/m84036_250809_035451_s4.bc2117.mapped.bam"}
2025-09-15 20:22:47.309 wdl.w:ptcp NOTICE ready :: job: "call-paraphase-20", callee: "paraphase"
2025-09-15 20:22:47.309 wdl.w:ptcp INFO input :: job: "call-paraphase-20", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf", "genome_version": "38", "config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-20/out/m84036_250809_035451_s4.bc2117.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-20/out/m84036_250809_035451_s4.bc2117.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2117"}
2025-09-15 20:22:47.310 wdl.w:ptcp NOTICE ready :: job: "call-sawfish-20", callee: "sawfish"
2025-09-15 20:22:47.310 wdl.w:ptcp INFO input :: job: "call-sawfish-20", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-20/out/m84036_250809_035451_s4.bc2117.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-20/out/m84036_250809_035451_s4.bc2117.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2117"}
2025-09-15 20:22:47.314 wdl.w:ptcp NOTICE ready :: job: "call-trgt-20", callee: "trgt"
2025-09-15 20:22:47.315 wdl.w:ptcp INFO input :: job: "call-trgt-20", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-20/out/m84036_250809_035451_s4.bc2117.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-20/out/m84036_250809_035451_s4.bc2117.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2117"}
2025-09-15 20:22:47.314 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_genotype NOTICE task setup :: name: "trgt_genotype", source: "./trgt.wdl", line: 272, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-22/call-trgt_genotype", thread: 140612498077248
2025-09-15 20:22:47.319 wdl.w:ptcp.w:call-paraphase-20 NOTICE workflow start :: name: "paraphase", source: "./paraphase.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-20"
2025-09-15 20:22:47.321 wdl.w:ptcp.w:call-sawfish-20 NOTICE workflow start :: name: "sawfish", source: "./sawfish.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-20"
2025-09-15 20:22:47.326 wdl.w:ptcp.w:call-trgt-20 NOTICE workflow start :: name: "trgt", source: "./trgt.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-20"
2025-09-15 20:22:47.327 wdl.w:ptcp.t:call-pbmm2_align_hifi-07 INFO output :: name: "mapped_bam", value: "m84036_250809_035451_s4.bc2104.mapped.bam"
2025-09-15 20:22:47.334 wdl.w:ptcp.t:call-pbmm2_align_hifi-07 INFO output :: name: "mapped_bam_bai", value: "m84036_250809_035451_s4.bc2104.mapped.bam.bai"
2025-09-15 20:22:47.338 wdl.w:ptcp.t:call-pbmm2_align_hifi-07 INFO output :: name: "mapped_bam_pbi", value: "m84036_250809_035451_s4.bc2104.mapped.bam.pbi"
2025-09-15 20:22:47.339 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_genotype INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:22:47.340 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_genotype INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:22:47.341 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_genotype INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:22:47.341 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_genotype INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:22:47.341 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_genotype INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2119.mapped.bam.bai"
2025-09-15 20:22:47.342 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_genotype INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2119.mapped.bam"
2025-09-15 20:22:47.343 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_genotype INFO input :: name: "sex", value: "F"
2025-09-15 20:22:47.344 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_genotype INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2119"
2025-09-15 20:22:47.344 wdl.w:ptcp.w:call-paraphase-20 INFO visit :: node: "decl-annotation_vcf", values: {"annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf"}
2025-09-15 20:22:47.345 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_genotype INFO eval :: name: "mem_gb", value: 16
2025-09-15 20:22:47.344 wdl.w:ptcp.t:call-pbmm2_align_hifi-07 INFO output :: name: "report", value: "mapping_stats.report.json"
2025-09-15 20:22:47.345 wdl.w:ptcp.w:call-paraphase-20 INFO visit :: node: "decl-config_file", values: {"config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml"}
2025-09-15 20:22:47.345 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_genotype INFO eval :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2119.trgt"
2025-09-15 20:22:47.346 wdl.w:ptcp.w:call-paraphase-20 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:22:47.346 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_genotype INFO eval :: name: "threads", value: 8
2025-09-15 20:22:47.347 wdl.w:ptcp.w:call-paraphase-20 INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:22:47.347 wdl.w:ptcp.w:call-sawfish-20 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:22:47.348 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_genotype INFO eval :: name: "disk_size", value: 27
2025-09-15 20:22:47.348 wdl.w:ptcp.w:call-paraphase-20 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-20/out/m84036_250809_035451_s4.bc2117.mapped.bam"}
2025-09-15 20:22:47.348 wdl.w:ptcp.w:call-sawfish-20 INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:22:47.349 wdl.w:ptcp.w:call-paraphase-20 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-20/out/m84036_250809_035451_s4.bc2117.mapped.bam.bai"}
2025-09-15 20:22:47.349 wdl.w:ptcp.w:call-sawfish-20 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-20/out/m84036_250809_035451_s4.bc2117.mapped.bam"}
2025-09-15 20:22:47.349 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_genotype INFO eval :: name: "karyotype", value: "XX"
2025-09-15 20:22:47.349 wdl.w:ptcp.w:call-paraphase-20 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:22:47.349 wdl.w:ptcp.w:call-sawfish-20 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-20/out/m84036_250809_035451_s4.bc2117.mapped.bam.bai"}
2025-09-15 20:22:47.350 wdl.w:ptcp.w:call-paraphase-20 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:22:47.350 wdl.w:ptcp.w:call-sawfish-20 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:22:47.351 wdl.w:ptcp.w:call-paraphase-20 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2117"}
2025-09-15 20:22:47.351 wdl.w:ptcp.w:call-sawfish-20 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:22:47.351 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_genotype INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 8, memory_reservation: 16000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:22:47.352 wdl.w:ptcp.w:call-trgt-20 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:22:47.352 wdl.w:ptcp.w:call-paraphase-20 INFO visit :: node: "decl-sex", values: {"sex": "F"}
2025-09-15 20:22:47.352 wdl.w:ptcp.w:call-sawfish-20 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2117"}
2025-09-15 20:22:47.352 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_genotype WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:22:47.353 wdl.w:ptcp.w:call-trgt-20 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-20/out/m84036_250809_035451_s4.bc2117.mapped.bam"}
2025-09-15 20:22:47.353 wdl.w:ptcp.w:call-paraphase-20 NOTICE ready :: job: "call-run_paraphase", callee: "run_paraphase"
2025-09-15 20:22:47.353 wdl.w:ptcp.w:call-sawfish-20 NOTICE ready :: job: "call-run_sawfish", callee: "run_sawfish"
2025-09-15 20:22:47.354 wdl.w:ptcp.w:call-trgt-20 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-20/out/m84036_250809_035451_s4.bc2117.mapped.bam.bai"}
2025-09-15 20:22:47.354 wdl.w:ptcp.w:call-paraphase-20 INFO input :: job: "call-run_paraphase", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf", "genome_version": "38", "config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-20/out/m84036_250809_035451_s4.bc2117.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-20/out/m84036_250809_035451_s4.bc2117.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2117"}
2025-09-15 20:22:47.354 wdl.w:ptcp.w:call-sawfish-20 INFO input :: job: "call-run_sawfish", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-20/out/m84036_250809_035451_s4.bc2117.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-20/out/m84036_250809_035451_s4.bc2117.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2117"}
2025-09-15 20:22:47.355 wdl.w:ptcp.w:call-trgt-20 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:22:47.355 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_genotype INFO provisioned :: seconds_waited: 0, cpu: 8, mem_bytes: 16000000000
2025-09-15 20:22:47.355 wdl.w:ptcp.w:call-trgt-20 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:22:47.355 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_genotype INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:22:47.355 wdl.w:ptcp.w:call-trgt-20 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2117"}
2025-09-15 20:22:47.356 wdl.w:ptcp.w:call-trgt-20 INFO visit :: node: "decl-sex", values: {"sex": "F"}
2025-09-15 20:22:47.356 wdl.w:ptcp.w:call-trgt-20 INFO visit :: node: "decl-trgt_bed", values: {"trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"}
2025-09-15 20:22:47.356 wdl.w:ptcp.w:call-trgt-20 NOTICE ready :: job: "call-get_reads_overlapping_repeats", callee: "get_reads_overlapping_repeats"
2025-09-15 20:22:47.356 wdl.w:ptcp.w:call-trgt-20 INFO input :: job: "call-get_reads_overlapping_repeats", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-20/out/m84036_250809_035451_s4.bc2117.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-20/out/m84036_250809_035451_s4.bc2117.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2117"}
2025-09-15 20:22:47.357 wdl.w:ptcp.w:call-trgt-20 NOTICE ready :: job: "call-trgt_genotype", callee: "trgt_genotype"
2025-09-15 20:22:47.357 wdl.w:ptcp.w:call-trgt-20 INFO input :: job: "call-trgt_genotype", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-20/out/m84036_250809_035451_s4.bc2117.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-20/out/m84036_250809_035451_s4.bc2117.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2117"}
2025-09-15 20:22:47.387 wdl.w:ptcp.t:call-pbmm2_align_hifi-39.slurm_singularity INFO srun: job 51797262 has been allocated resources
2025-09-15 20:22:47.392 wdl.w:ptcp.t:call-pbmm2_align_hifi-04 INFO output :: name: "mapped_bam", value: "m84036_250809_035451_s4.bc2101.mapped.bam"
2025-09-15 20:22:47.396 wdl.w:ptcp.t:call-pbmm2_align_hifi-04 INFO output :: name: "mapped_bam_bai", value: "m84036_250809_035451_s4.bc2101.mapped.bam.bai"
2025-09-15 20:22:47.397 wdl.w:ptcp.t:call-pbmm2_align_hifi-04 INFO output :: name: "mapped_bam_pbi", value: "m84036_250809_035451_s4.bc2101.mapped.bam.pbi"
2025-09-15 20:22:47.397 wdl.w:ptcp.t:call-pbmm2_align_hifi-43.slurm_singularity INFO srun: job 51797263 has been allocated resources
2025-09-15 20:22:47.399 wdl.w:ptcp.t:call-pbmm2_align_hifi-04 INFO output :: name: "report", value: "mapping_stats.report.json"
2025-09-15 20:22:47.400 wdl.w:ptcp.t:call-pbmm2_align_hifi-40.slurm_singularity INFO srun: job 51797261 has been allocated resources
2025-09-15 20:22:47.427 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_genotype INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 11, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-22/call-trgt_genotype/_singularity_tmpdir_umocv11j"
2025-09-15 20:22:47.427 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_genotype INFO Slurm invocation: srun --job-name call-trgt_genotype --partition compute,compute9 --cpus-per-task 8 --mem 15259M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-22/call-trgt_genotype/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-22/call-trgt_genotype/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-22/call-trgt_genotype/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-22/call-trgt_genotype/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-22/out/m84036_250809_035451_s4.bc2119.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2119.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-22/out/m84036_250809_035451_s4.bc2119.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2119.mapped.bam.bai:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-22/call-trgt_genotype/_singularity_tmpdir_umocv11j/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-22/call-trgt_genotype/_singularity_tmpdir_umocv11j/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:22:47.444 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_genotype NOTICE slurm_singularity run :: pid: 1198041, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-22/call-trgt_genotype/slurm_singularity.log.txt"
2025-09-15 20:22:47.447 wdl.w:ptcp.t:call-pbmm2_align_hifi-07 NOTICE done
2025-09-15 20:22:47.452 wdl.w:ptcp NOTICE finish :: job: "call-pbmm2_align_hifi-07"
2025-09-15 20:22:47.452 wdl.w:ptcp INFO output :: job: "call-pbmm2_align_hifi-07", values: {"report": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-07/out/mapping_stats.report.json", "mapped_bam_pbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-07/out/m84036_250809_035451_s4.bc2104.mapped.bam.pbi", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-07/out/m84036_250809_035451_s4.bc2104.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-07/out/m84036_250809_035451_s4.bc2104.mapped.bam"}
2025-09-15 20:22:47.453 wdl.w:ptcp NOTICE ready :: job: "call-paraphase-07", callee: "paraphase"
2025-09-15 20:22:47.454 wdl.w:ptcp INFO input :: job: "call-paraphase-07", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf", "genome_version": "38", "config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-07/out/m84036_250809_035451_s4.bc2104.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-07/out/m84036_250809_035451_s4.bc2104.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2104"}
2025-09-15 20:22:47.455 wdl.w:ptcp NOTICE ready :: job: "call-sawfish-07", callee: "sawfish"
2025-09-15 20:22:47.455 wdl.w:ptcp INFO input :: job: "call-sawfish-07", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-07/out/m84036_250809_035451_s4.bc2104.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-07/out/m84036_250809_035451_s4.bc2104.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2104"}
2025-09-15 20:22:47.459 wdl.w:ptcp NOTICE ready :: job: "call-trgt-07", callee: "trgt"
2025-09-15 20:22:47.459 wdl.w:ptcp INFO input :: job: "call-trgt-07", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-07/out/m84036_250809_035451_s4.bc2104.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-07/out/m84036_250809_035451_s4.bc2104.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2104"}
2025-09-15 20:22:47.461 wdl.w:ptcp.w:call-paraphase-15.t:call-run_paraphase NOTICE task setup :: name: "run_paraphase", source: "./paraphase.wdl", line: 127, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-15/call-run_paraphase", thread: 140613563426368
2025-09-15 20:22:47.467 wdl.w:ptcp.w:call-sawfish-07 NOTICE workflow start :: name: "sawfish", source: "./sawfish.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-07"
2025-09-15 20:22:47.468 wdl.w:ptcp.w:call-paraphase-07 NOTICE workflow start :: name: "paraphase", source: "./paraphase.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-07"
2025-09-15 20:22:47.471 wdl.w:ptcp.w:call-trgt-07 NOTICE workflow start :: name: "trgt", source: "./trgt.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-07"
2025-09-15 20:22:47.483 wdl.w:ptcp.w:call-paraphase-15.t:call-run_paraphase INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:22:47.483 wdl.w:ptcp.w:call-paraphase-15.t:call-run_paraphase INFO input :: name: "annotation_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf"
2025-09-15 20:22:47.484 wdl.w:ptcp.w:call-paraphase-15.t:call-run_paraphase INFO input :: name: "genome_version", value: "38"
2025-09-15 20:22:47.484 wdl.w:ptcp.w:call-paraphase-15.t:call-run_paraphase INFO input :: name: "config_file", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/paraphase_config.GRCh38.yaml"
2025-09-15 20:22:47.485 wdl.w:ptcp.w:call-paraphase-15.t:call-run_paraphase INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:22:47.485 wdl.w:ptcp.w:call-paraphase-15.t:call-run_paraphase INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:22:47.485 wdl.w:ptcp.w:call-paraphase-15.t:call-run_paraphase INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2112.mapped.bam.bai"
2025-09-15 20:22:47.486 wdl.w:ptcp.w:call-paraphase-15.t:call-run_paraphase INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2112.mapped.bam"
2025-09-15 20:22:47.486 wdl.w:ptcp.w:call-paraphase-15.t:call-run_paraphase INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2112"
2025-09-15 20:22:47.487 wdl.w:ptcp.w:call-paraphase-15.t:call-run_paraphase INFO eval :: name: "threads", value: 4
2025-09-15 20:22:47.488 wdl.w:ptcp.w:call-paraphase-15.t:call-run_paraphase INFO eval :: name: "mem_gb", value: 8
2025-09-15 20:22:47.490 wdl.w:ptcp.w:call-paraphase-15.t:call-run_paraphase INFO eval :: name: "disk_size", value: 27
2025-09-15 20:22:47.491 wdl.w:ptcp.w:call-paraphase-15.t:call-run_paraphase INFO eval :: name: "out_dir", value: "m84036_250809_035451_s4.bc2112_paraphase"
2025-09-15 20:22:47.493 wdl.w:ptcp.w:call-paraphase-15.t:call-run_paraphase INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 4, memory_reservation: 8000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:22:47.494 wdl.w:ptcp.w:call-paraphase-15.t:call-run_paraphase WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:22:47.498 wdl.w:ptcp.w:call-paraphase-15.t:call-run_paraphase INFO provisioned :: seconds_waited: 0, cpu: 4, mem_bytes: 8000000000
2025-09-15 20:22:47.499 wdl.w:ptcp.w:call-trgt-07 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:22:47.500 wdl.w:ptcp.w:call-paraphase-15.t:call-run_paraphase INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:22:47.500 wdl.w:ptcp.w:call-trgt-07 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-07/out/m84036_250809_035451_s4.bc2104.mapped.bam"}
2025-09-15 20:22:47.501 wdl.w:ptcp.w:call-sawfish-07 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:22:47.501 wdl.w:ptcp.w:call-trgt-07 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-07/out/m84036_250809_035451_s4.bc2104.mapped.bam.bai"}
2025-09-15 20:22:47.501 wdl.w:ptcp.w:call-sawfish-07 INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:22:47.501 wdl.w:ptcp.w:call-trgt-07 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:22:47.501 wdl.w:ptcp.w:call-sawfish-07 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-07/out/m84036_250809_035451_s4.bc2104.mapped.bam"}
2025-09-15 20:22:47.502 wdl.w:ptcp.w:call-trgt-07 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:22:47.502 wdl.w:ptcp.w:call-paraphase-07 INFO visit :: node: "decl-annotation_vcf", values: {"annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf"}
2025-09-15 20:22:47.503 wdl.w:ptcp.w:call-sawfish-07 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-07/out/m84036_250809_035451_s4.bc2104.mapped.bam.bai"}
2025-09-15 20:22:47.503 wdl.w:ptcp.w:call-trgt-07 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2104"}
2025-09-15 20:22:47.503 wdl.w:ptcp.w:call-paraphase-07 INFO visit :: node: "decl-config_file", values: {"config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml"}
2025-09-15 20:22:47.503 wdl.w:ptcp.w:call-sawfish-07 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:22:47.503 wdl.w:ptcp.w:call-trgt-07 INFO visit :: node: "decl-sex", values: {"sex": "F"}
2025-09-15 20:22:47.503 wdl.w:ptcp.w:call-paraphase-07 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:22:47.503 wdl.w:ptcp.w:call-sawfish-07 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:22:47.504 wdl.w:ptcp.w:call-trgt-07 INFO visit :: node: "decl-trgt_bed", values: {"trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"}
2025-09-15 20:22:47.504 wdl.w:ptcp.w:call-paraphase-07 INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:22:47.504 wdl.w:ptcp.w:call-sawfish-07 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2104"}
2025-09-15 20:22:47.504 wdl.w:ptcp.w:call-trgt-07 NOTICE ready :: job: "call-get_reads_overlapping_repeats", callee: "get_reads_overlapping_repeats"
2025-09-15 20:22:47.504 wdl.w:ptcp.w:call-paraphase-07 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-07/out/m84036_250809_035451_s4.bc2104.mapped.bam"}
2025-09-15 20:22:47.504 wdl.w:ptcp.w:call-sawfish-07 NOTICE ready :: job: "call-run_sawfish", callee: "run_sawfish"
2025-09-15 20:22:47.505 wdl.w:ptcp.w:call-trgt-07 INFO input :: job: "call-get_reads_overlapping_repeats", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-07/out/m84036_250809_035451_s4.bc2104.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-07/out/m84036_250809_035451_s4.bc2104.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2104"}
2025-09-15 20:22:47.505 wdl.w:ptcp.w:call-paraphase-07 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-07/out/m84036_250809_035451_s4.bc2104.mapped.bam.bai"}
2025-09-15 20:22:47.505 wdl.w:ptcp.w:call-sawfish-07 INFO input :: job: "call-run_sawfish", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-07/out/m84036_250809_035451_s4.bc2104.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-07/out/m84036_250809_035451_s4.bc2104.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2104"}
2025-09-15 20:22:47.505 wdl.w:ptcp.w:call-paraphase-07 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:22:47.505 wdl.w:ptcp.w:call-paraphase-07 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:22:47.505 wdl.w:ptcp.w:call-paraphase-07 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2104"}
2025-09-15 20:22:47.505 wdl.w:ptcp.w:call-paraphase-07 INFO visit :: node: "decl-sex", values: {"sex": "F"}
2025-09-15 20:22:47.507 wdl.w:ptcp.w:call-paraphase-07 NOTICE ready :: job: "call-run_paraphase", callee: "run_paraphase"
2025-09-15 20:22:47.507 wdl.w:ptcp.w:call-trgt-07 NOTICE ready :: job: "call-trgt_genotype", callee: "trgt_genotype"
2025-09-15 20:22:47.508 wdl.w:ptcp.w:call-paraphase-07 INFO input :: job: "call-run_paraphase", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf", "genome_version": "38", "config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-07/out/m84036_250809_035451_s4.bc2104.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-07/out/m84036_250809_035451_s4.bc2104.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2104"}
2025-09-15 20:22:47.508 wdl.w:ptcp.w:call-trgt-07 INFO input :: job: "call-trgt_genotype", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-07/out/m84036_250809_035451_s4.bc2104.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-07/out/m84036_250809_035451_s4.bc2104.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2104"}
2025-09-15 20:22:47.509 wdl.w:ptcp.t:call-pbmm2_align_hifi-04 NOTICE done
2025-09-15 20:22:47.514 wdl.w:ptcp NOTICE finish :: job: "call-pbmm2_align_hifi-04"
2025-09-15 20:22:47.514 wdl.w:ptcp INFO output :: job: "call-pbmm2_align_hifi-04", values: {"report": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-04/out/mapping_stats.report.json", "mapped_bam_pbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-04/out/m84036_250809_035451_s4.bc2101.mapped.bam.pbi", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-04/out/m84036_250809_035451_s4.bc2101.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-04/out/m84036_250809_035451_s4.bc2101.mapped.bam"}
2025-09-15 20:22:47.515 wdl.w:ptcp NOTICE ready :: job: "call-paraphase-04", callee: "paraphase"
2025-09-15 20:22:47.515 wdl.w:ptcp INFO input :: job: "call-paraphase-04", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf", "genome_version": "38", "config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-04/out/m84036_250809_035451_s4.bc2101.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-04/out/m84036_250809_035451_s4.bc2101.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2101"}
2025-09-15 20:22:47.516 wdl.w:ptcp NOTICE ready :: job: "call-sawfish-04", callee: "sawfish"
2025-09-15 20:22:47.516 wdl.w:ptcp INFO input :: job: "call-sawfish-04", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-04/out/m84036_250809_035451_s4.bc2101.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-04/out/m84036_250809_035451_s4.bc2101.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2101"}
2025-09-15 20:22:47.520 wdl.w:ptcp.w:call-trgt-15.t:call-get_reads_overlapping_repeats NOTICE task setup :: name: "get_reads_overlapping_repeats", source: "./trgt.wdl", line: 182, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-15/call-get_reads_overlapping_repeats", thread: 140613588604480
2025-09-15 20:22:47.521 wdl.w:ptcp NOTICE ready :: job: "call-trgt-04", callee: "trgt"
2025-09-15 20:22:47.521 wdl.w:ptcp INFO input :: job: "call-trgt-04", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-04/out/m84036_250809_035451_s4.bc2101.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-04/out/m84036_250809_035451_s4.bc2101.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2101"}
2025-09-15 20:22:47.524 wdl.w:ptcp.w:call-paraphase-04 NOTICE workflow start :: name: "paraphase", source: "./paraphase.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-04"
2025-09-15 20:22:47.531 wdl.w:ptcp.w:call-sawfish-04 NOTICE workflow start :: name: "sawfish", source: "./sawfish.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-04"
2025-09-15 20:22:47.533 wdl.w:ptcp.w:call-trgt-04 NOTICE workflow start :: name: "trgt", source: "./trgt.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-04"
2025-09-15 20:22:47.549 wdl.w:ptcp.w:call-paraphase-04 INFO visit :: node: "decl-annotation_vcf", values: {"annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf"}
2025-09-15 20:22:47.549 wdl.w:ptcp.w:call-paraphase-04 INFO visit :: node: "decl-config_file", values: {"config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml"}
2025-09-15 20:22:47.549 wdl.w:ptcp.w:call-paraphase-04 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:22:47.550 wdl.w:ptcp.w:call-paraphase-04 INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:22:47.551 wdl.w:ptcp.w:call-paraphase-04 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-04/out/m84036_250809_035451_s4.bc2101.mapped.bam"}
2025-09-15 20:22:47.551 wdl.w:ptcp.w:call-paraphase-04 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-04/out/m84036_250809_035451_s4.bc2101.mapped.bam.bai"}
2025-09-15 20:22:47.552 wdl.w:ptcp.w:call-paraphase-04 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:22:47.552 wdl.w:ptcp.w:call-paraphase-04 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:22:47.552 wdl.w:ptcp.w:call-paraphase-04 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2101"}
2025-09-15 20:22:47.553 wdl.w:ptcp.w:call-paraphase-04 INFO visit :: node: "decl-sex", values: {"sex": "F"}
2025-09-15 20:22:47.553 wdl.w:ptcp.w:call-paraphase-04 NOTICE ready :: job: "call-run_paraphase", callee: "run_paraphase"
2025-09-15 20:22:47.553 wdl.w:ptcp.w:call-paraphase-04 INFO input :: job: "call-run_paraphase", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf", "genome_version": "38", "config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-04/out/m84036_250809_035451_s4.bc2101.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-04/out/m84036_250809_035451_s4.bc2101.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2101"}
2025-09-15 20:22:47.554 wdl.w:ptcp.w:call-trgt-15.t:call-get_reads_overlapping_repeats INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:22:47.554 wdl.w:ptcp.w:call-trgt-15.t:call-get_reads_overlapping_repeats INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:22:47.555 wdl.w:ptcp.w:call-trgt-15.t:call-get_reads_overlapping_repeats INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2112.mapped.bam.bai"
2025-09-15 20:22:47.555 wdl.w:ptcp.w:call-trgt-15.t:call-get_reads_overlapping_repeats INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2112.mapped.bam"
2025-09-15 20:22:47.555 wdl.w:ptcp.w:call-trgt-15.t:call-get_reads_overlapping_repeats INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2112"
2025-09-15 20:22:47.555 wdl.w:ptcp.w:call-trgt-15.t:call-get_reads_overlapping_repeats INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:22:47.556 wdl.w:ptcp.w:call-trgt-15.t:call-get_reads_overlapping_repeats INFO eval :: name: "expand_size", value: 3000
2025-09-15 20:22:47.556 wdl.w:ptcp.w:call-sawfish-04 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:22:47.557 wdl.w:ptcp.w:call-trgt-04 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:22:47.557 wdl.w:ptcp.w:call-trgt-15.t:call-get_reads_overlapping_repeats INFO eval :: name: "threads", value: 1
2025-09-15 20:22:47.558 wdl.w:ptcp.w:call-sawfish-04 INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:22:47.558 wdl.w:ptcp.w:call-trgt-04 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-04/out/m84036_250809_035451_s4.bc2101.mapped.bam"}
2025-09-15 20:22:47.558 wdl.w:ptcp.w:call-trgt-15.t:call-get_reads_overlapping_repeats INFO eval :: name: "expanded_bed_name", value: "m84036_250809_035451_s4.bc2112.expanded.bed"
2025-09-15 20:22:47.558 wdl.w:ptcp.w:call-sawfish-04 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-04/out/m84036_250809_035451_s4.bc2101.mapped.bam"}
2025-09-15 20:22:47.558 wdl.w:ptcp.w:call-trgt-04 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-04/out/m84036_250809_035451_s4.bc2101.mapped.bam.bai"}
2025-09-15 20:22:47.559 wdl.w:ptcp.w:call-sawfish-04 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-04/out/m84036_250809_035451_s4.bc2101.mapped.bam.bai"}
2025-09-15 20:22:47.559 wdl.w:ptcp.w:call-trgt-15.t:call-get_reads_overlapping_repeats INFO eval :: name: "disk_size", value: 11
2025-09-15 20:22:47.559 wdl.w:ptcp.w:call-trgt-04 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:22:47.559 wdl.w:ptcp.w:call-sawfish-04 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:22:47.559 wdl.w:ptcp.w:call-trgt-15.t:call-get_reads_overlapping_repeats INFO eval :: name: "output_name", value: "m84036_250809_035451_s4.bc2112.repeats.bam"
2025-09-15 20:22:47.559 wdl.w:ptcp.w:call-trgt-04 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:22:47.559 wdl.w:ptcp.w:call-sawfish-04 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:22:47.560 wdl.w:ptcp.w:call-trgt-15.t:call-get_reads_overlapping_repeats INFO eval :: name: "index_name", value: "m84036_250809_035451_s4.bc2112.repeats.bam.bai"
2025-09-15 20:22:47.560 wdl.w:ptcp.w:call-trgt-04 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2101"}
2025-09-15 20:22:47.560 wdl.w:ptcp.w:call-sawfish-04 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2101"}
2025-09-15 20:22:47.560 wdl.w:ptcp.w:call-trgt-15.t:call-get_reads_overlapping_repeats INFO eval :: name: "output_name_with_index", value: "m84036_250809_035451_s4.bc2112.repeats.bam##idx##m84036_250809_035451_s4.bc2112.repeats.bam.bai"
2025-09-15 20:22:47.560 wdl.w:ptcp.w:call-trgt-04 INFO visit :: node: "decl-sex", values: {"sex": "F"}
2025-09-15 20:22:47.560 wdl.w:ptcp.w:call-sawfish-04 NOTICE ready :: job: "call-run_sawfish", callee: "run_sawfish"
2025-09-15 20:22:47.561 wdl.w:ptcp.w:call-trgt-04 INFO visit :: node: "decl-trgt_bed", values: {"trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"}
2025-09-15 20:22:47.561 wdl.w:ptcp.w:call-trgt-15.t:call-get_reads_overlapping_repeats INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:22:47.561 wdl.w:ptcp.w:call-sawfish-04 INFO input :: job: "call-run_sawfish", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-04/out/m84036_250809_035451_s4.bc2101.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-04/out/m84036_250809_035451_s4.bc2101.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2101"}
2025-09-15 20:22:47.562 wdl.w:ptcp.w:call-trgt-04 NOTICE ready :: job: "call-get_reads_overlapping_repeats", callee: "get_reads_overlapping_repeats"
2025-09-15 20:22:47.562 wdl.w:ptcp.w:call-trgt-15.t:call-get_reads_overlapping_repeats WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:22:47.562 wdl.w:ptcp.w:call-trgt-04 INFO input :: job: "call-get_reads_overlapping_repeats", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-04/out/m84036_250809_035451_s4.bc2101.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-04/out/m84036_250809_035451_s4.bc2101.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2101"}
2025-09-15 20:22:47.563 wdl.w:ptcp.w:call-trgt-15.t:call-get_reads_overlapping_repeats INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:22:47.563 wdl.w:ptcp.w:call-trgt-04 NOTICE ready :: job: "call-trgt_genotype", callee: "trgt_genotype"
2025-09-15 20:22:47.563 wdl.w:ptcp.w:call-trgt-15.t:call-get_reads_overlapping_repeats INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:22:47.563 wdl.w:ptcp.w:call-trgt-04 INFO input :: job: "call-trgt_genotype", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-04/out/m84036_250809_035451_s4.bc2101.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-04/out/m84036_250809_035451_s4.bc2101.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2101"}
2025-09-15 20:22:47.586 wdl.w:ptcp.w:call-paraphase-15.t:call-run_paraphase INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-15/call-run_paraphase/_singularity_tmpdir_2hmiaf62"
2025-09-15 20:22:47.586 wdl.w:ptcp.w:call-paraphase-15.t:call-run_paraphase INFO Slurm invocation: srun --job-name call-run_paraphase --partition compute,compute9 --cpus-per-task 4 --mem 7629M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-15/call-run_paraphase/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-15/call-run_paraphase/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-15/call-run_paraphase/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-15/call-run_paraphase/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-15/out/m84036_250809_035451_s4.bc2112.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2112.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-15/out/m84036_250809_035451_s4.bc2112.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2112.mapped.bam:ro --bind /ptcp/meta/variant_list/variant_list.GRCh38.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf:ro --bind /ptcp/meta/paraphase/paraphase_config.GRCh38.yaml:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/paraphase_config.GRCh38.yaml:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-15/call-run_paraphase/_singularity_tmpdir_2hmiaf62/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-15/call-run_paraphase/_singularity_tmpdir_2hmiaf62/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:22:47.604 wdl.w:ptcp.w:call-paraphase-15.t:call-run_paraphase NOTICE slurm_singularity run :: pid: 1198049, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-15/call-run_paraphase/slurm_singularity.log.txt"
2025-09-15 20:22:47.618 wdl.w:ptcp.w:call-trgt-15.t:call-get_reads_overlapping_repeats INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 9, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-15/call-get_reads_overlapping_repeats/_singularity_tmpdir_x0rz9qwk"
2025-09-15 20:22:47.618 wdl.w:ptcp.w:call-trgt-15.t:call-get_reads_overlapping_repeats INFO Slurm invocation: srun --job-name call-get_reads_overlapping_repeats --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-15/call-get_reads_overlapping_repeats/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-15/call-get_reads_overlapping_repeats/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-15/call-get_reads_overlapping_repeats/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-15/call-get_reads_overlapping_repeats/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-15/out/m84036_250809_035451_s4.bc2112.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2112.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-15/out/m84036_250809_035451_s4.bc2112.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2112.mapped.bam:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-15/call-get_reads_overlapping_repeats/_singularity_tmpdir_x0rz9qwk/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-15/call-get_reads_overlapping_repeats/_singularity_tmpdir_x0rz9qwk/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:22:47.629 wdl.w:ptcp.w:call-trgt-15.t:call-get_reads_overlapping_repeats NOTICE slurm_singularity run :: pid: 1198051, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-15/call-get_reads_overlapping_repeats/slurm_singularity.log.txt"
2025-09-15 20:22:47.755 wdl.w:ptcp.t:call-pbmm2_align_hifi-31 INFO output :: name: "mapped_bam", value: "m84036_250809_035451_s4.bc2128.mapped.bam"
2025-09-15 20:22:47.759 wdl.w:ptcp.t:call-pbmm2_align_hifi-31 INFO output :: name: "mapped_bam_bai", value: "m84036_250809_035451_s4.bc2128.mapped.bam.bai"
2025-09-15 20:22:47.761 wdl.w:ptcp.t:call-pbmm2_align_hifi-31 INFO output :: name: "mapped_bam_pbi", value: "m84036_250809_035451_s4.bc2128.mapped.bam.pbi"
2025-09-15 20:22:47.764 wdl.w:ptcp.t:call-pbmm2_align_hifi-31 INFO output :: name: "report", value: "mapping_stats.report.json"
2025-09-15 20:22:47.809 wdl.w:ptcp.t:call-pbmm2_align_hifi-34 INFO output :: name: "mapped_bam", value: "m84036_250809_035451_s4.bc2131.mapped.bam"
2025-09-15 20:22:47.814 wdl.w:ptcp.t:call-pbmm2_align_hifi-34 INFO output :: name: "mapped_bam_bai", value: "m84036_250809_035451_s4.bc2131.mapped.bam.bai"
2025-09-15 20:22:47.817 wdl.w:ptcp.t:call-pbmm2_align_hifi-34 INFO output :: name: "mapped_bam_pbi", value: "m84036_250809_035451_s4.bc2131.mapped.bam.pbi"
2025-09-15 20:22:47.820 wdl.w:ptcp.t:call-pbmm2_align_hifi-34 INFO output :: name: "report", value: "mapping_stats.report.json"
2025-09-15 20:22:47.920 wdl.w:ptcp.t:call-pbmm2_align_hifi-31 NOTICE done
2025-09-15 20:22:47.932 wdl.w:ptcp NOTICE finish :: job: "call-pbmm2_align_hifi-31"
2025-09-15 20:22:47.932 wdl.w:ptcp INFO output :: job: "call-pbmm2_align_hifi-31", values: {"report": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-31/out/mapping_stats.report.json", "mapped_bam_pbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-31/out/m84036_250809_035451_s4.bc2128.mapped.bam.pbi", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-31/out/m84036_250809_035451_s4.bc2128.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-31/out/m84036_250809_035451_s4.bc2128.mapped.bam"}
2025-09-15 20:22:47.933 wdl.w:ptcp NOTICE ready :: job: "call-paraphase-31", callee: "paraphase"
2025-09-15 20:22:47.933 wdl.w:ptcp INFO input :: job: "call-paraphase-31", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf", "genome_version": "38", "config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-31/out/m84036_250809_035451_s4.bc2128.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-31/out/m84036_250809_035451_s4.bc2128.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2128"}
2025-09-15 20:22:47.935 wdl.w:ptcp NOTICE ready :: job: "call-sawfish-31", callee: "sawfish"
2025-09-15 20:22:47.935 wdl.w:ptcp INFO input :: job: "call-sawfish-31", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-31/out/m84036_250809_035451_s4.bc2128.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-31/out/m84036_250809_035451_s4.bc2128.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2128"}
2025-09-15 20:22:47.941 wdl.w:ptcp NOTICE ready :: job: "call-trgt-31", callee: "trgt"
2025-09-15 20:22:47.941 wdl.w:ptcp INFO input :: job: "call-trgt-31", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-31/out/m84036_250809_035451_s4.bc2128.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-31/out/m84036_250809_035451_s4.bc2128.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2128"}
2025-09-15 20:22:47.944 wdl.w:ptcp.w:call-sawfish-15.t:call-run_sawfish NOTICE task setup :: name: "run_sawfish", source: "./sawfish.wdl", line: 83, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-15/call-run_sawfish", thread: 140611449513536
2025-09-15 20:22:47.947 wdl.w:ptcp.w:call-paraphase-31 NOTICE workflow start :: name: "paraphase", source: "./paraphase.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-31"
2025-09-15 20:22:47.950 wdl.w:ptcp.w:call-sawfish-31 NOTICE workflow start :: name: "sawfish", source: "./sawfish.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-31"
2025-09-15 20:22:47.956 wdl.w:ptcp.w:call-trgt-31 NOTICE workflow start :: name: "trgt", source: "./trgt.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-31"
2025-09-15 20:22:47.970 wdl.w:ptcp.w:call-sawfish-15.t:call-run_sawfish INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:22:47.970 wdl.w:ptcp.w:call-sawfish-15.t:call-run_sawfish INFO input :: name: "genome_version", value: "38"
2025-09-15 20:22:47.971 wdl.w:ptcp.w:call-sawfish-15.t:call-run_sawfish INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:22:47.971 wdl.w:ptcp.w:call-sawfish-15.t:call-run_sawfish INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:22:47.971 wdl.w:ptcp.w:call-sawfish-15.t:call-run_sawfish INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2112.mapped.bam.bai"
2025-09-15 20:22:47.971 wdl.w:ptcp.w:call-sawfish-15.t:call-run_sawfish INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2112.mapped.bam"
2025-09-15 20:22:47.971 wdl.w:ptcp.w:call-sawfish-15.t:call-run_sawfish INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2112"
2025-09-15 20:22:47.972 wdl.w:ptcp.w:call-sawfish-15.t:call-run_sawfish INFO eval :: name: "mem_gb", value: 32
2025-09-15 20:22:47.972 wdl.w:ptcp.w:call-sawfish-15.t:call-run_sawfish INFO eval :: name: "threads", value: 16
2025-09-15 20:22:47.972 wdl.w:ptcp.w:call-sawfish-15.t:call-run_sawfish INFO eval :: name: "disk_size", value: 30
2025-09-15 20:22:47.973 wdl.w:ptcp.w:call-sawfish-15.t:call-run_sawfish INFO eval :: name: "discover_dirname", value: "m84036_250809_035451_s4.bc2112_sawfish_discover"
2025-09-15 20:22:47.973 wdl.w:ptcp.w:call-sawfish-15.t:call-run_sawfish INFO eval :: name: "call_dirname", value: "m84036_250809_035451_s4.bc2112_sawfish"
2025-09-15 20:22:47.973 wdl.w:ptcp.w:call-sawfish-15.t:call-run_sawfish INFO eval :: name: "minimap2_bam_filename", value: "m84036_250809_035451_s4.bc2112.minimap2.bam"
2025-09-15 20:22:47.974 wdl.w:ptcp.w:call-sawfish-15.t:call-run_sawfish INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 16, memory_reservation: 32000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:22:47.975 wdl.w:ptcp.w:call-sawfish-15.t:call-run_sawfish WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:22:47.977 wdl.w:ptcp.w:call-sawfish-15.t:call-run_sawfish INFO provisioned :: seconds_waited: 0, cpu: 16, mem_bytes: 32000000000
2025-09-15 20:22:47.977 wdl.w:ptcp.w:call-sawfish-15.t:call-run_sawfish INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:22:47.979 wdl.w:ptcp.w:call-paraphase-31 INFO visit :: node: "decl-annotation_vcf", values: {"annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf"}
2025-09-15 20:22:47.979 wdl.w:ptcp.w:call-paraphase-31 INFO visit :: node: "decl-config_file", values: {"config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml"}
2025-09-15 20:22:47.980 wdl.w:ptcp.w:call-paraphase-31 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:22:47.980 wdl.w:ptcp.w:call-paraphase-31 INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:22:47.980 wdl.w:ptcp.w:call-paraphase-31 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-31/out/m84036_250809_035451_s4.bc2128.mapped.bam"}
2025-09-15 20:22:47.980 wdl.w:ptcp.w:call-paraphase-31 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-31/out/m84036_250809_035451_s4.bc2128.mapped.bam.bai"}
2025-09-15 20:22:47.980 wdl.w:ptcp.w:call-paraphase-31 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:22:47.981 wdl.w:ptcp.w:call-paraphase-31 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:22:47.981 wdl.w:ptcp.w:call-paraphase-31 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2128"}
2025-09-15 20:22:47.981 wdl.w:ptcp.w:call-paraphase-31 INFO visit :: node: "decl-sex", values: {"sex": "F"}
2025-09-15 20:22:47.982 wdl.w:ptcp.w:call-paraphase-31 NOTICE ready :: job: "call-run_paraphase", callee: "run_paraphase"
2025-09-15 20:22:47.982 wdl.w:ptcp.w:call-paraphase-31 INFO input :: job: "call-run_paraphase", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf", "genome_version": "38", "config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-31/out/m84036_250809_035451_s4.bc2128.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-31/out/m84036_250809_035451_s4.bc2128.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2128"}
2025-09-15 20:22:47.984 wdl.w:ptcp.t:call-pbmm2_align_hifi-34 NOTICE done
2025-09-15 20:22:47.987 wdl.w:ptcp.w:call-sawfish-31 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:22:47.987 wdl.w:ptcp.w:call-sawfish-31 INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:22:47.987 wdl.w:ptcp.w:call-sawfish-31 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-31/out/m84036_250809_035451_s4.bc2128.mapped.bam"}
2025-09-15 20:22:47.987 wdl.w:ptcp.w:call-sawfish-31 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-31/out/m84036_250809_035451_s4.bc2128.mapped.bam.bai"}
2025-09-15 20:22:47.988 wdl.w:ptcp.w:call-sawfish-31 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:22:47.988 wdl.w:ptcp.w:call-sawfish-31 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:22:47.988 wdl.w:ptcp.w:call-sawfish-31 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2128"}
2025-09-15 20:22:47.988 wdl.w:ptcp.w:call-sawfish-31 NOTICE ready :: job: "call-run_sawfish", callee: "run_sawfish"
2025-09-15 20:22:47.988 wdl.w:ptcp.w:call-sawfish-31 INFO input :: job: "call-run_sawfish", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-31/out/m84036_250809_035451_s4.bc2128.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-31/out/m84036_250809_035451_s4.bc2128.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2128"}
2025-09-15 20:22:47.990 wdl.w:ptcp.w:call-trgt-31 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:22:47.991 wdl.w:ptcp.w:call-trgt-31 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-31/out/m84036_250809_035451_s4.bc2128.mapped.bam"}
2025-09-15 20:22:47.991 wdl.w:ptcp.w:call-trgt-31 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-31/out/m84036_250809_035451_s4.bc2128.mapped.bam.bai"}
2025-09-15 20:22:47.991 wdl.w:ptcp.w:call-trgt-31 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:22:47.991 wdl.w:ptcp.w:call-trgt-31 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:22:47.991 wdl.w:ptcp.w:call-trgt-31 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2128"}
2025-09-15 20:22:47.991 wdl.w:ptcp.w:call-trgt-31 INFO visit :: node: "decl-sex", values: {"sex": "F"}
2025-09-15 20:22:47.991 wdl.w:ptcp.w:call-trgt-31 INFO visit :: node: "decl-trgt_bed", values: {"trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"}
2025-09-15 20:22:47.991 wdl.w:ptcp.w:call-trgt-31 NOTICE ready :: job: "call-get_reads_overlapping_repeats", callee: "get_reads_overlapping_repeats"
2025-09-15 20:22:47.991 wdl.w:ptcp.w:call-trgt-31 INFO input :: job: "call-get_reads_overlapping_repeats", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-31/out/m84036_250809_035451_s4.bc2128.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-31/out/m84036_250809_035451_s4.bc2128.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2128"}
2025-09-15 20:22:47.993 wdl.w:ptcp.w:call-trgt-31 NOTICE ready :: job: "call-trgt_genotype", callee: "trgt_genotype"
2025-09-15 20:22:47.993 wdl.w:ptcp.w:call-trgt-31 INFO input :: job: "call-trgt_genotype", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-31/out/m84036_250809_035451_s4.bc2128.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-31/out/m84036_250809_035451_s4.bc2128.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2128"}
2025-09-15 20:22:47.995 wdl.w:ptcp NOTICE finish :: job: "call-pbmm2_align_hifi-34"
2025-09-15 20:22:47.995 wdl.w:ptcp INFO output :: job: "call-pbmm2_align_hifi-34", values: {"report": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-34/out/mapping_stats.report.json", "mapped_bam_pbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-34/out/m84036_250809_035451_s4.bc2131.mapped.bam.pbi", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-34/out/m84036_250809_035451_s4.bc2131.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-34/out/m84036_250809_035451_s4.bc2131.mapped.bam"}
2025-09-15 20:22:47.996 wdl.w:ptcp NOTICE ready :: job: "call-paraphase-34", callee: "paraphase"
2025-09-15 20:22:47.996 wdl.w:ptcp INFO input :: job: "call-paraphase-34", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf", "genome_version": "38", "config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-34/out/m84036_250809_035451_s4.bc2131.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-34/out/m84036_250809_035451_s4.bc2131.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2131"}
2025-09-15 20:22:47.998 wdl.w:ptcp NOTICE ready :: job: "call-sawfish-34", callee: "sawfish"
2025-09-15 20:22:47.998 wdl.w:ptcp INFO input :: job: "call-sawfish-34", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-34/out/m84036_250809_035451_s4.bc2131.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-34/out/m84036_250809_035451_s4.bc2131.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2131"}
2025-09-15 20:22:48.002 wdl.w:ptcp NOTICE ready :: job: "call-trgt-34", callee: "trgt"
2025-09-15 20:22:48.003 wdl.w:ptcp INFO input :: job: "call-trgt-34", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-34/out/m84036_250809_035451_s4.bc2131.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-34/out/m84036_250809_035451_s4.bc2131.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2131"}
2025-09-15 20:22:48.009 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_genotype NOTICE task setup :: name: "trgt_genotype", source: "./trgt.wdl", line: 272, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-15/call-trgt_genotype", thread: 140611424335424
2025-09-15 20:22:48.011 wdl.w:ptcp.w:call-paraphase-34 NOTICE workflow start :: name: "paraphase", source: "./paraphase.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-34"
2025-09-15 20:22:48.020 wdl.w:ptcp.w:call-trgt-34 NOTICE workflow start :: name: "trgt", source: "./trgt.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-34"
2025-09-15 20:22:48.024 wdl.w:ptcp.w:call-sawfish-34 NOTICE workflow start :: name: "sawfish", source: "./sawfish.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-34"
2025-09-15 20:22:48.036 wdl.w:ptcp.w:call-paraphase-34 INFO visit :: node: "decl-annotation_vcf", values: {"annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf"}
2025-09-15 20:22:48.037 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_genotype INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:22:48.037 wdl.w:ptcp.w:call-paraphase-34 INFO visit :: node: "decl-config_file", values: {"config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml"}
2025-09-15 20:22:48.037 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_genotype INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:22:48.037 wdl.w:ptcp.w:call-paraphase-34 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:22:48.037 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_genotype INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:22:48.037 wdl.w:ptcp.w:call-paraphase-34 INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:22:48.038 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_genotype INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:22:48.038 wdl.w:ptcp.w:call-paraphase-34 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-34/out/m84036_250809_035451_s4.bc2131.mapped.bam"}
2025-09-15 20:22:48.038 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_genotype INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2112.mapped.bam.bai"
2025-09-15 20:22:48.038 wdl.w:ptcp.w:call-paraphase-34 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-34/out/m84036_250809_035451_s4.bc2131.mapped.bam.bai"}
2025-09-15 20:22:48.038 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_genotype INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2112.mapped.bam"
2025-09-15 20:22:48.038 wdl.w:ptcp.w:call-paraphase-34 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:22:48.039 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_genotype INFO input :: name: "sex", value: "F"
2025-09-15 20:22:48.039 wdl.w:ptcp.w:call-paraphase-34 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:22:48.039 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_genotype INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2112"
2025-09-15 20:22:48.039 wdl.w:ptcp.w:call-paraphase-34 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2131"}
2025-09-15 20:22:48.039 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_genotype INFO eval :: name: "mem_gb", value: 16
2025-09-15 20:22:48.040 wdl.w:ptcp.w:call-paraphase-34 INFO visit :: node: "decl-sex", values: {"sex": "F"}
2025-09-15 20:22:48.040 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_genotype INFO eval :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2112.trgt"
2025-09-15 20:22:48.042 wdl.w:ptcp.w:call-paraphase-34 NOTICE ready :: job: "call-run_paraphase", callee: "run_paraphase"
2025-09-15 20:22:48.042 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_genotype INFO eval :: name: "threads", value: 8
2025-09-15 20:22:48.043 wdl.w:ptcp.w:call-paraphase-34 INFO input :: job: "call-run_paraphase", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf", "genome_version": "38", "config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-34/out/m84036_250809_035451_s4.bc2131.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-34/out/m84036_250809_035451_s4.bc2131.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2131"}
2025-09-15 20:22:48.043 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_genotype INFO eval :: name: "disk_size", value: 27
2025-09-15 20:22:48.044 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_genotype INFO eval :: name: "karyotype", value: "XX"
2025-09-15 20:22:48.045 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_genotype INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 8, memory_reservation: 16000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:22:48.045 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_genotype WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:22:48.046 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_genotype INFO provisioned :: seconds_waited: 0, cpu: 8, mem_bytes: 16000000000
2025-09-15 20:22:48.046 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_genotype INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:22:48.047 wdl.w:ptcp.w:call-sawfish-34 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:22:48.048 wdl.w:ptcp.w:call-sawfish-34 INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:22:48.048 wdl.w:ptcp.w:call-sawfish-34 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-34/out/m84036_250809_035451_s4.bc2131.mapped.bam"}
2025-09-15 20:22:48.048 wdl.w:ptcp.w:call-sawfish-34 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-34/out/m84036_250809_035451_s4.bc2131.mapped.bam.bai"}
2025-09-15 20:22:48.048 wdl.w:ptcp.w:call-sawfish-34 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:22:48.048 wdl.w:ptcp.w:call-sawfish-34 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:22:48.048 wdl.w:ptcp.w:call-sawfish-34 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2131"}
2025-09-15 20:22:48.048 wdl.w:ptcp.w:call-sawfish-34 NOTICE ready :: job: "call-run_sawfish", callee: "run_sawfish"
2025-09-15 20:22:48.048 wdl.w:ptcp.w:call-sawfish-34 INFO input :: job: "call-run_sawfish", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-34/out/m84036_250809_035451_s4.bc2131.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-34/out/m84036_250809_035451_s4.bc2131.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2131"}
2025-09-15 20:22:48.068 wdl.w:ptcp.w:call-trgt-34 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:22:48.068 wdl.w:ptcp.w:call-trgt-34 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-34/out/m84036_250809_035451_s4.bc2131.mapped.bam"}
2025-09-15 20:22:48.068 wdl.w:ptcp.w:call-trgt-34 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-34/out/m84036_250809_035451_s4.bc2131.mapped.bam.bai"}
2025-09-15 20:22:48.069 wdl.w:ptcp.w:call-trgt-34 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:22:48.069 wdl.w:ptcp.w:call-trgt-34 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:22:48.069 wdl.w:ptcp.w:call-trgt-34 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2131"}
2025-09-15 20:22:48.069 wdl.w:ptcp.w:call-trgt-34 INFO visit :: node: "decl-sex", values: {"sex": "F"}
2025-09-15 20:22:48.069 wdl.w:ptcp.w:call-trgt-34 INFO visit :: node: "decl-trgt_bed", values: {"trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"}
2025-09-15 20:22:48.069 wdl.w:ptcp.w:call-trgt-34 NOTICE ready :: job: "call-get_reads_overlapping_repeats", callee: "get_reads_overlapping_repeats"
2025-09-15 20:22:48.069 wdl.w:ptcp.t:call-pbmm2_align_hifi-23 INFO output :: name: "mapped_bam", value: "m84036_250809_035451_s4.bc2120.mapped.bam"
2025-09-15 20:22:48.069 wdl.w:ptcp.w:call-trgt-34 INFO input :: job: "call-get_reads_overlapping_repeats", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-34/out/m84036_250809_035451_s4.bc2131.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-34/out/m84036_250809_035451_s4.bc2131.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2131"}
2025-09-15 20:22:48.070 wdl.w:ptcp.w:call-trgt-34 NOTICE ready :: job: "call-trgt_genotype", callee: "trgt_genotype"
2025-09-15 20:22:48.071 wdl.w:ptcp.w:call-trgt-34 INFO input :: job: "call-trgt_genotype", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-34/out/m84036_250809_035451_s4.bc2131.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-34/out/m84036_250809_035451_s4.bc2131.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2131"}
2025-09-15 20:22:48.075 wdl.w:ptcp.t:call-pbmm2_align_hifi-23 INFO output :: name: "mapped_bam_bai", value: "m84036_250809_035451_s4.bc2120.mapped.bam.bai"
2025-09-15 20:22:48.076 wdl.w:ptcp.t:call-pbmm2_align_hifi-23 INFO output :: name: "mapped_bam_pbi", value: "m84036_250809_035451_s4.bc2120.mapped.bam.pbi"
2025-09-15 20:22:48.079 wdl.w:ptcp.t:call-pbmm2_align_hifi-23 INFO output :: name: "report", value: "mapping_stats.report.json"
2025-09-15 20:22:48.092 wdl.w:ptcp.w:call-sawfish-15.t:call-run_sawfish INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 10, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-15/call-run_sawfish/_singularity_tmpdir_byoxfqfi"
2025-09-15 20:22:48.092 wdl.w:ptcp.w:call-sawfish-15.t:call-run_sawfish INFO Slurm invocation: srun --job-name call-run_sawfish --partition compute,compute9 --cpus-per-task 16 --mem 30518M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-15/call-run_sawfish/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-15/call-run_sawfish/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-15/call-run_sawfish/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-15/call-run_sawfish/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-15/out/m84036_250809_035451_s4.bc2112.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2112.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-15/out/m84036_250809_035451_s4.bc2112.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2112.mapped.bam:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-15/call-run_sawfish/_singularity_tmpdir_byoxfqfi/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-15/call-run_sawfish/_singularity_tmpdir_byoxfqfi/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:22:48.130 wdl.w:ptcp.w:call-sawfish-15.t:call-run_sawfish NOTICE slurm_singularity run :: pid: 1198082, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-15/call-run_sawfish/slurm_singularity.log.txt"
2025-09-15 20:22:48.144 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_genotype INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 11, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-15/call-trgt_genotype/_singularity_tmpdir_f_6kut47"
2025-09-15 20:22:48.144 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_genotype INFO Slurm invocation: srun --job-name call-trgt_genotype --partition compute,compute9 --cpus-per-task 8 --mem 15259M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-15/call-trgt_genotype/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-15/call-trgt_genotype/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-15/call-trgt_genotype/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-15/call-trgt_genotype/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-15/out/m84036_250809_035451_s4.bc2112.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2112.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-15/out/m84036_250809_035451_s4.bc2112.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2112.mapped.bam:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-15/call-trgt_genotype/_singularity_tmpdir_f_6kut47/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-15/call-trgt_genotype/_singularity_tmpdir_f_6kut47/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:22:48.156 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_genotype NOTICE slurm_singularity run :: pid: 1198095, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-15/call-trgt_genotype/slurm_singularity.log.txt"
2025-09-15 20:22:48.173 wdl.w:ptcp.t:call-pbmm2_align_hifi-35 INFO output :: name: "mapped_bam", value: "m84036_250809_035451_s4.bc2132.mapped.bam"
2025-09-15 20:22:48.174 wdl.w:ptcp.t:call-pbmm2_align_hifi-26 INFO output :: name: "mapped_bam", value: "m84036_250809_035451_s4.bc2123.mapped.bam"
2025-09-15 20:22:48.177 wdl.w:ptcp.t:call-pbmm2_align_hifi-35 INFO output :: name: "mapped_bam_bai", value: "m84036_250809_035451_s4.bc2132.mapped.bam.bai"
2025-09-15 20:22:48.177 wdl.w:ptcp.t:call-pbmm2_align_hifi-26 INFO output :: name: "mapped_bam_bai", value: "m84036_250809_035451_s4.bc2123.mapped.bam.bai"
2025-09-15 20:22:48.178 wdl.w:ptcp.t:call-pbmm2_align_hifi-35 INFO output :: name: "mapped_bam_pbi", value: "m84036_250809_035451_s4.bc2132.mapped.bam.pbi"
2025-09-15 20:22:48.178 wdl.w:ptcp.t:call-pbmm2_align_hifi-26 INFO output :: name: "mapped_bam_pbi", value: "m84036_250809_035451_s4.bc2123.mapped.bam.pbi"
2025-09-15 20:22:48.179 wdl.w:ptcp.t:call-pbmm2_align_hifi-35 INFO output :: name: "report", value: "mapping_stats.report.json"
2025-09-15 20:22:48.180 wdl.w:ptcp.t:call-pbmm2_align_hifi-26 INFO output :: name: "report", value: "mapping_stats.report.json"
2025-09-15 20:22:48.196 wdl.w:ptcp.t:call-pbmm2_align_hifi-23 NOTICE done
2025-09-15 20:22:48.202 wdl.w:ptcp NOTICE finish :: job: "call-pbmm2_align_hifi-23"
2025-09-15 20:22:48.202 wdl.w:ptcp INFO output :: job: "call-pbmm2_align_hifi-23", values: {"report": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-23/out/mapping_stats.report.json", "mapped_bam_pbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-23/out/m84036_250809_035451_s4.bc2120.mapped.bam.pbi", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-23/out/m84036_250809_035451_s4.bc2120.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-23/out/m84036_250809_035451_s4.bc2120.mapped.bam"}
2025-09-15 20:22:48.203 wdl.w:ptcp NOTICE ready :: job: "call-paraphase-23", callee: "paraphase"
2025-09-15 20:22:48.203 wdl.w:ptcp INFO input :: job: "call-paraphase-23", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf", "genome_version": "38", "config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-23/out/m84036_250809_035451_s4.bc2120.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-23/out/m84036_250809_035451_s4.bc2120.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2120"}
2025-09-15 20:22:48.204 wdl.w:ptcp NOTICE ready :: job: "call-sawfish-23", callee: "sawfish"
2025-09-15 20:22:48.204 wdl.w:ptcp INFO input :: job: "call-sawfish-23", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-23/out/m84036_250809_035451_s4.bc2120.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-23/out/m84036_250809_035451_s4.bc2120.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2120"}
2025-09-15 20:22:48.208 wdl.w:ptcp NOTICE ready :: job: "call-trgt-23", callee: "trgt"
2025-09-15 20:22:48.208 wdl.w:ptcp INFO input :: job: "call-trgt-23", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-23/out/m84036_250809_035451_s4.bc2120.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-23/out/m84036_250809_035451_s4.bc2120.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2120"}
2025-09-15 20:22:48.210 wdl.w:ptcp.w:call-paraphase-20.t:call-run_paraphase NOTICE task setup :: name: "run_paraphase", source: "./paraphase.wdl", line: 127, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-20/call-run_paraphase", thread: 140611994777152
2025-09-15 20:22:48.213 wdl.w:ptcp.w:call-paraphase-23 NOTICE workflow start :: name: "paraphase", source: "./paraphase.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-23"
2025-09-15 20:22:48.219 wdl.w:ptcp.w:call-sawfish-23 NOTICE workflow start :: name: "sawfish", source: "./sawfish.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-23"
2025-09-15 20:22:48.222 wdl.w:ptcp.w:call-trgt-23 NOTICE workflow start :: name: "trgt", source: "./trgt.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-23"
2025-09-15 20:22:48.235 wdl.w:ptcp.w:call-paraphase-23 INFO visit :: node: "decl-annotation_vcf", values: {"annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf"}
2025-09-15 20:22:48.235 wdl.w:ptcp.w:call-paraphase-23 INFO visit :: node: "decl-config_file", values: {"config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml"}
2025-09-15 20:22:48.236 wdl.w:ptcp.w:call-paraphase-23 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:22:48.236 wdl.w:ptcp.w:call-paraphase-23 INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:22:48.237 wdl.w:ptcp.w:call-paraphase-23 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-23/out/m84036_250809_035451_s4.bc2120.mapped.bam"}
2025-09-15 20:22:48.237 wdl.w:ptcp.w:call-paraphase-20.t:call-run_paraphase INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:22:48.237 wdl.w:ptcp.w:call-paraphase-23 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-23/out/m84036_250809_035451_s4.bc2120.mapped.bam.bai"}
2025-09-15 20:22:48.238 wdl.w:ptcp.w:call-paraphase-20.t:call-run_paraphase INFO input :: name: "annotation_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf"
2025-09-15 20:22:48.238 wdl.w:ptcp.w:call-paraphase-23 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:22:48.239 wdl.w:ptcp.w:call-paraphase-20.t:call-run_paraphase INFO input :: name: "genome_version", value: "38"
2025-09-15 20:22:48.239 wdl.w:ptcp.w:call-paraphase-23 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:22:48.240 wdl.w:ptcp.w:call-paraphase-20.t:call-run_paraphase INFO input :: name: "config_file", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/paraphase_config.GRCh38.yaml"
2025-09-15 20:22:48.240 wdl.w:ptcp.w:call-paraphase-23 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2120"}
2025-09-15 20:22:48.240 wdl.w:ptcp.w:call-paraphase-20.t:call-run_paraphase INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:22:48.241 wdl.w:ptcp.w:call-paraphase-23 INFO visit :: node: "decl-sex", values: {"sex": "F"}
2025-09-15 20:22:48.241 wdl.w:ptcp.w:call-paraphase-20.t:call-run_paraphase INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:22:48.242 wdl.w:ptcp.w:call-paraphase-23 NOTICE ready :: job: "call-run_paraphase", callee: "run_paraphase"
2025-09-15 20:22:48.242 wdl.w:ptcp.w:call-paraphase-20.t:call-run_paraphase INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2117.mapped.bam.bai"
2025-09-15 20:22:48.242 wdl.w:ptcp.w:call-paraphase-23 INFO input :: job: "call-run_paraphase", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf", "genome_version": "38", "config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-23/out/m84036_250809_035451_s4.bc2120.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-23/out/m84036_250809_035451_s4.bc2120.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2120"}
2025-09-15 20:22:48.243 wdl.w:ptcp.w:call-paraphase-20.t:call-run_paraphase INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2117.mapped.bam"
2025-09-15 20:22:48.244 wdl.w:ptcp.w:call-paraphase-20.t:call-run_paraphase INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2117"
2025-09-15 20:22:48.245 wdl.w:ptcp.w:call-sawfish-23 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:22:48.244 wdl.w:ptcp.w:call-paraphase-20.t:call-run_paraphase INFO eval :: name: "threads", value: 4
2025-09-15 20:22:48.245 wdl.w:ptcp.w:call-sawfish-23 INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:22:48.246 wdl.w:ptcp.w:call-paraphase-20.t:call-run_paraphase INFO eval :: name: "mem_gb", value: 8
2025-09-15 20:22:48.246 wdl.w:ptcp.w:call-sawfish-23 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-23/out/m84036_250809_035451_s4.bc2120.mapped.bam"}
2025-09-15 20:22:48.246 wdl.w:ptcp.w:call-sawfish-23 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-23/out/m84036_250809_035451_s4.bc2120.mapped.bam.bai"}
2025-09-15 20:22:48.246 wdl.w:ptcp.w:call-sawfish-23 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:22:48.247 wdl.w:ptcp.w:call-sawfish-23 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:22:48.247 wdl.w:ptcp.w:call-paraphase-20.t:call-run_paraphase INFO eval :: name: "disk_size", value: 27
2025-09-15 20:22:48.248 wdl.w:ptcp.w:call-trgt-23 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:22:48.248 wdl.w:ptcp.w:call-sawfish-23 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2120"}
2025-09-15 20:22:48.248 wdl.w:ptcp.w:call-paraphase-20.t:call-run_paraphase INFO eval :: name: "out_dir", value: "m84036_250809_035451_s4.bc2117_paraphase"
2025-09-15 20:22:48.249 wdl.w:ptcp.w:call-trgt-23 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-23/out/m84036_250809_035451_s4.bc2120.mapped.bam"}
2025-09-15 20:22:48.249 wdl.w:ptcp.w:call-sawfish-23 NOTICE ready :: job: "call-run_sawfish", callee: "run_sawfish"
2025-09-15 20:22:48.249 wdl.w:ptcp.w:call-trgt-23 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-23/out/m84036_250809_035451_s4.bc2120.mapped.bam.bai"}
2025-09-15 20:22:48.250 wdl.w:ptcp.w:call-sawfish-23 INFO input :: job: "call-run_sawfish", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-23/out/m84036_250809_035451_s4.bc2120.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-23/out/m84036_250809_035451_s4.bc2120.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2120"}
2025-09-15 20:22:48.250 wdl.w:ptcp.w:call-paraphase-20.t:call-run_paraphase INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 4, memory_reservation: 8000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:22:48.250 wdl.w:ptcp.w:call-trgt-23 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:22:48.250 wdl.w:ptcp.w:call-paraphase-20.t:call-run_paraphase WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:22:48.251 wdl.w:ptcp.w:call-trgt-23 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:22:48.251 wdl.w:ptcp.w:call-trgt-23 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2120"}
2025-09-15 20:22:48.251 wdl.w:ptcp.w:call-trgt-23 INFO visit :: node: "decl-sex", values: {"sex": "F"}
2025-09-15 20:22:48.251 wdl.w:ptcp.w:call-trgt-23 INFO visit :: node: "decl-trgt_bed", values: {"trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"}
2025-09-15 20:22:48.252 wdl.w:ptcp.w:call-trgt-23 NOTICE ready :: job: "call-get_reads_overlapping_repeats", callee: "get_reads_overlapping_repeats"
2025-09-15 20:22:48.252 wdl.w:ptcp.w:call-trgt-23 INFO input :: job: "call-get_reads_overlapping_repeats", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-23/out/m84036_250809_035451_s4.bc2120.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-23/out/m84036_250809_035451_s4.bc2120.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2120"}
2025-09-15 20:22:48.252 wdl.w:ptcp.w:call-paraphase-20.t:call-run_paraphase INFO provisioned :: seconds_waited: 0, cpu: 4, mem_bytes: 8000000000
2025-09-15 20:22:48.253 wdl.w:ptcp.w:call-paraphase-20.t:call-run_paraphase INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:22:48.253 wdl.w:ptcp.w:call-trgt-23 NOTICE ready :: job: "call-trgt_genotype", callee: "trgt_genotype"
2025-09-15 20:22:48.254 wdl.w:ptcp.w:call-trgt-23 INFO input :: job: "call-trgt_genotype", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-23/out/m84036_250809_035451_s4.bc2120.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-23/out/m84036_250809_035451_s4.bc2120.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2120"}
2025-09-15 20:22:48.290 wdl.w:ptcp.t:call-pbmm2_align_hifi-35 NOTICE done
2025-09-15 20:22:48.296 wdl.w:ptcp NOTICE finish :: job: "call-pbmm2_align_hifi-35"
2025-09-15 20:22:48.296 wdl.w:ptcp INFO output :: job: "call-pbmm2_align_hifi-35", values: {"report": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-35/out/mapping_stats.report.json", "mapped_bam_pbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-35/out/m84036_250809_035451_s4.bc2132.mapped.bam.pbi", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-35/out/m84036_250809_035451_s4.bc2132.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-35/out/m84036_250809_035451_s4.bc2132.mapped.bam"}
2025-09-15 20:22:48.297 wdl.w:ptcp NOTICE ready :: job: "call-paraphase-35", callee: "paraphase"
2025-09-15 20:22:48.297 wdl.w:ptcp INFO input :: job: "call-paraphase-35", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf", "genome_version": "38", "config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-35/out/m84036_250809_035451_s4.bc2132.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-35/out/m84036_250809_035451_s4.bc2132.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2132"}
2025-09-15 20:22:48.298 wdl.w:ptcp NOTICE ready :: job: "call-sawfish-35", callee: "sawfish"
2025-09-15 20:22:48.298 wdl.w:ptcp INFO input :: job: "call-sawfish-35", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-35/out/m84036_250809_035451_s4.bc2132.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-35/out/m84036_250809_035451_s4.bc2132.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2132"}
2025-09-15 20:22:48.302 wdl.w:ptcp NOTICE ready :: job: "call-trgt-35", callee: "trgt"
2025-09-15 20:22:48.302 wdl.w:ptcp INFO input :: job: "call-trgt-35", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-35/out/m84036_250809_035451_s4.bc2132.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-35/out/m84036_250809_035451_s4.bc2132.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2132"}
2025-09-15 20:22:48.304 wdl.w:ptcp.t:call-pbmm2_align_hifi-36.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:22:48.304 wdl.w:ptcp.t:call-pbmm2_align_hifi-36.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:22:48.305 wdl.w:ptcp.w:call-paraphase-35 NOTICE workflow start :: name: "paraphase", source: "./paraphase.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-35"
2025-09-15 20:22:48.307 wdl.w:ptcp.w:call-sawfish-20.t:call-run_sawfish NOTICE task setup :: name: "run_sawfish", source: "./sawfish.wdl", line: 83, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-20/call-run_sawfish", thread: 140611415942720
2025-09-15 20:22:48.310 wdl.w:ptcp.w:call-sawfish-35 NOTICE workflow start :: name: "sawfish", source: "./sawfish.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-35"
2025-09-15 20:22:48.314 wdl.w:ptcp.w:call-trgt-35 NOTICE workflow start :: name: "trgt", source: "./trgt.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-35"
2025-09-15 20:22:48.324 wdl.w:ptcp.w:call-trgt-22.t:call-get_reads_overlapping_repeats.slurm_singularity INFO srun: job 51797325 queued and waiting for resources
2025-09-15 20:22:48.326 wdl.w:ptcp.w:call-paraphase-35 INFO visit :: node: "decl-annotation_vcf", values: {"annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf"}
2025-09-15 20:22:48.327 wdl.w:ptcp.w:call-paraphase-35 INFO visit :: node: "decl-config_file", values: {"config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml"}
2025-09-15 20:22:48.328 wdl.w:ptcp.t:call-pbmm2_align_hifi-28 INFO output :: name: "mapped_bam", value: "m84036_250809_035451_s4.bc2125.mapped.bam"
2025-09-15 20:22:48.328 wdl.w:ptcp.w:call-paraphase-35 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:22:48.329 wdl.w:ptcp.t:call-pbmm2_align_hifi-26 NOTICE done
2025-09-15 20:22:48.330 wdl.w:ptcp.w:call-paraphase-35 INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:22:48.331 wdl.w:ptcp.w:call-paraphase-35 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-35/out/m84036_250809_035451_s4.bc2132.mapped.bam"}
2025-09-15 20:22:48.332 wdl.w:ptcp.w:call-paraphase-35 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-35/out/m84036_250809_035451_s4.bc2132.mapped.bam.bai"}
2025-09-15 20:22:48.333 wdl.w:ptcp.w:call-paraphase-35 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:22:48.334 wdl.w:ptcp.w:call-paraphase-35 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:22:48.334 wdl.w:ptcp.w:call-paraphase-35 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2132"}
2025-09-15 20:22:48.335 wdl.w:ptcp.w:call-paraphase-35 INFO visit :: node: "decl-sex", values: {"sex": "F"}
2025-09-15 20:22:48.337 wdl.w:ptcp.w:call-paraphase-35 NOTICE ready :: job: "call-run_paraphase", callee: "run_paraphase"
2025-09-15 20:22:48.337 wdl.w:ptcp.w:call-paraphase-35 INFO input :: job: "call-run_paraphase", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf", "genome_version": "38", "config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-35/out/m84036_250809_035451_s4.bc2132.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-35/out/m84036_250809_035451_s4.bc2132.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2132"}
2025-09-15 20:22:48.337 wdl.w:ptcp.t:call-pbmm2_align_hifi-28 INFO output :: name: "mapped_bam_bai", value: "m84036_250809_035451_s4.bc2125.mapped.bam.bai"
2025-09-15 20:22:48.339 wdl.w:ptcp NOTICE finish :: job: "call-pbmm2_align_hifi-26"
2025-09-15 20:22:48.340 wdl.w:ptcp INFO output :: job: "call-pbmm2_align_hifi-26", values: {"report": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-26/out/mapping_stats.report.json", "mapped_bam_pbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-26/out/m84036_250809_035451_s4.bc2123.mapped.bam.pbi", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-26/out/m84036_250809_035451_s4.bc2123.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-26/out/m84036_250809_035451_s4.bc2123.mapped.bam"}
2025-09-15 20:22:48.341 wdl.w:ptcp NOTICE ready :: job: "call-paraphase-26", callee: "paraphase"
2025-09-15 20:22:48.342 wdl.w:ptcp INFO input :: job: "call-paraphase-26", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf", "genome_version": "38", "config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-26/out/m84036_250809_035451_s4.bc2123.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-26/out/m84036_250809_035451_s4.bc2123.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2123"}
2025-09-15 20:22:48.343 wdl.w:ptcp.w:call-sawfish-35 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:22:48.344 wdl.w:ptcp NOTICE ready :: job: "call-sawfish-26", callee: "sawfish"
2025-09-15 20:22:48.344 wdl.w:ptcp.w:call-paraphase-20.t:call-run_paraphase INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-20/call-run_paraphase/_singularity_tmpdir_qkcmpbjo"
2025-09-15 20:22:48.344 wdl.w:ptcp.t:call-pbmm2_align_hifi-28 INFO output :: name: "mapped_bam_pbi", value: "m84036_250809_035451_s4.bc2125.mapped.bam.pbi"
2025-09-15 20:22:48.344 wdl.w:ptcp.w:call-trgt-20.t:call-get_reads_overlapping_repeats NOTICE task setup :: name: "get_reads_overlapping_repeats", source: "./trgt.wdl", line: 182, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-20/call-get_reads_overlapping_repeats", thread: 140611969599040
2025-09-15 20:22:48.345 wdl.w:ptcp.w:call-sawfish-35 INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:22:48.345 wdl.w:ptcp INFO input :: job: "call-sawfish-26", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-26/out/m84036_250809_035451_s4.bc2123.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-26/out/m84036_250809_035451_s4.bc2123.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2123"}
2025-09-15 20:22:48.345 wdl.w:ptcp.w:call-paraphase-20.t:call-run_paraphase INFO Slurm invocation: srun --job-name call-run_paraphase --partition compute,compute9 --cpus-per-task 4 --mem 7629M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-20/call-run_paraphase/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-20/call-run_paraphase/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-20/call-run_paraphase/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-20/call-run_paraphase/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-20/out/m84036_250809_035451_s4.bc2117.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2117.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-20/out/m84036_250809_035451_s4.bc2117.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2117.mapped.bam:ro --bind /ptcp/meta/variant_list/variant_list.GRCh38.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf:ro --bind /ptcp/meta/paraphase/paraphase_config.GRCh38.yaml:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/paraphase_config.GRCh38.yaml:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-20/call-run_paraphase/_singularity_tmpdir_qkcmpbjo/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-20/call-run_paraphase/_singularity_tmpdir_qkcmpbjo/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:22:48.346 wdl.w:ptcp.w:call-sawfish-35 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-35/out/m84036_250809_035451_s4.bc2132.mapped.bam"}
2025-09-15 20:22:48.347 wdl.w:ptcp.w:call-trgt-35 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:22:48.347 wdl.w:ptcp.w:call-sawfish-35 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-35/out/m84036_250809_035451_s4.bc2132.mapped.bam.bai"}
2025-09-15 20:22:48.347 wdl.w:ptcp.w:call-trgt-35 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-35/out/m84036_250809_035451_s4.bc2132.mapped.bam"}
2025-09-15 20:22:48.347 wdl.w:ptcp.w:call-sawfish-35 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:22:48.348 wdl.w:ptcp.w:call-sawfish-20.t:call-run_sawfish INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:22:48.349 wdl.w:ptcp NOTICE ready :: job: "call-trgt-26", callee: "trgt"
2025-09-15 20:22:48.350 wdl.w:ptcp.w:call-trgt-35 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-35/out/m84036_250809_035451_s4.bc2132.mapped.bam.bai"}
2025-09-15 20:22:48.350 wdl.w:ptcp.t:call-pbmm2_align_hifi-28 INFO output :: name: "report", value: "mapping_stats.report.json"
2025-09-15 20:22:48.351 wdl.w:ptcp.w:call-paraphase-26 NOTICE workflow start :: name: "paraphase", source: "./paraphase.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-26"
2025-09-15 20:22:48.351 wdl.w:ptcp.w:call-sawfish-35 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:22:48.351 wdl.w:ptcp.w:call-sawfish-20.t:call-run_sawfish INFO input :: name: "genome_version", value: "38"
2025-09-15 20:22:48.351 wdl.w:ptcp INFO input :: job: "call-trgt-26", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-26/out/m84036_250809_035451_s4.bc2123.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-26/out/m84036_250809_035451_s4.bc2123.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2123"}
2025-09-15 20:22:48.351 wdl.w:ptcp.w:call-trgt-35 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:22:48.352 wdl.w:ptcp.w:call-sawfish-35 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2132"}
2025-09-15 20:22:48.352 wdl.w:ptcp.w:call-sawfish-20.t:call-run_sawfish INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:22:48.352 wdl.w:ptcp.w:call-trgt-35 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:22:48.352 wdl.w:ptcp.w:call-sawfish-35 NOTICE ready :: job: "call-run_sawfish", callee: "run_sawfish"
2025-09-15 20:22:48.352 wdl.w:ptcp.w:call-sawfish-20.t:call-run_sawfish INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:22:48.353 wdl.w:ptcp.w:call-trgt-35 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2132"}
2025-09-15 20:22:48.353 wdl.w:ptcp.w:call-sawfish-35 INFO input :: job: "call-run_sawfish", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-35/out/m84036_250809_035451_s4.bc2132.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-35/out/m84036_250809_035451_s4.bc2132.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2132"}
2025-09-15 20:22:48.353 wdl.w:ptcp.w:call-sawfish-20.t:call-run_sawfish INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2117.mapped.bam.bai"
2025-09-15 20:22:48.353 wdl.w:ptcp.w:call-trgt-35 INFO visit :: node: "decl-sex", values: {"sex": "F"}
2025-09-15 20:22:48.354 wdl.w:ptcp.w:call-sawfish-20.t:call-run_sawfish INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2117.mapped.bam"
2025-09-15 20:22:48.354 wdl.w:ptcp.w:call-trgt-35 INFO visit :: node: "decl-trgt_bed", values: {"trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"}
2025-09-15 20:22:48.354 wdl.w:ptcp.w:call-sawfish-20.t:call-run_sawfish INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2117"
2025-09-15 20:22:48.355 wdl.w:ptcp.w:call-trgt-35 NOTICE ready :: job: "call-get_reads_overlapping_repeats", callee: "get_reads_overlapping_repeats"
2025-09-15 20:22:48.355 wdl.w:ptcp.w:call-sawfish-20.t:call-run_sawfish INFO eval :: name: "mem_gb", value: 32
2025-09-15 20:22:48.355 wdl.w:ptcp.w:call-trgt-35 INFO input :: job: "call-get_reads_overlapping_repeats", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-35/out/m84036_250809_035451_s4.bc2132.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-35/out/m84036_250809_035451_s4.bc2132.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2132"}
2025-09-15 20:22:48.355 wdl.w:ptcp.w:call-sawfish-20.t:call-run_sawfish INFO eval :: name: "threads", value: 16
2025-09-15 20:22:48.356 wdl.w:ptcp.w:call-sawfish-20.t:call-run_sawfish INFO eval :: name: "disk_size", value: 30
2025-09-15 20:22:48.356 wdl.w:ptcp.w:call-sawfish-20.t:call-run_sawfish INFO eval :: name: "discover_dirname", value: "m84036_250809_035451_s4.bc2117_sawfish_discover"
2025-09-15 20:22:48.356 wdl.w:ptcp.w:call-sawfish-20.t:call-run_sawfish INFO eval :: name: "call_dirname", value: "m84036_250809_035451_s4.bc2117_sawfish"
2025-09-15 20:22:48.356 wdl.w:ptcp.w:call-sawfish-20.t:call-run_sawfish INFO eval :: name: "minimap2_bam_filename", value: "m84036_250809_035451_s4.bc2117.minimap2.bam"
2025-09-15 20:22:48.356 wdl.w:ptcp.w:call-trgt-35 NOTICE ready :: job: "call-trgt_genotype", callee: "trgt_genotype"
2025-09-15 20:22:48.380 wdl.w:ptcp.w:call-trgt-26 NOTICE workflow start :: name: "trgt", source: "./trgt.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-26"
2025-09-15 20:22:48.381 wdl.w:ptcp.w:call-trgt-35 INFO input :: job: "call-trgt_genotype", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-35/out/m84036_250809_035451_s4.bc2132.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-35/out/m84036_250809_035451_s4.bc2132.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2132"}
2025-09-15 20:22:48.381 wdl.w:ptcp.w:call-sawfish-26 NOTICE workflow start :: name: "sawfish", source: "./sawfish.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-26"
2025-09-15 20:22:48.381 wdl.w:ptcp.w:call-paraphase-20.t:call-run_paraphase NOTICE slurm_singularity run :: pid: 1198110, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-20/call-run_paraphase/slurm_singularity.log.txt"
2025-09-15 20:22:48.382 wdl.w:ptcp.w:call-sawfish-20.t:call-run_sawfish INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 16, memory_reservation: 32000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:22:48.383 wdl.w:ptcp.w:call-sawfish-20.t:call-run_sawfish WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:22:48.385 wdl.w:ptcp.w:call-sawfish-20.t:call-run_sawfish INFO provisioned :: seconds_waited: 0, cpu: 16, mem_bytes: 32000000000
2025-09-15 20:22:48.385 wdl.w:ptcp.w:call-sawfish-20.t:call-run_sawfish INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:22:48.393 wdl.w:ptcp.w:call-trgt-20.t:call-get_reads_overlapping_repeats INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:22:48.393 wdl.w:ptcp.w:call-trgt-20.t:call-get_reads_overlapping_repeats INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:22:48.394 wdl.w:ptcp.w:call-trgt-20.t:call-get_reads_overlapping_repeats INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2117.mapped.bam.bai"
2025-09-15 20:22:48.394 wdl.w:ptcp.w:call-trgt-20.t:call-get_reads_overlapping_repeats INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2117.mapped.bam"
2025-09-15 20:22:48.395 wdl.w:ptcp.w:call-trgt-20.t:call-get_reads_overlapping_repeats INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2117"
2025-09-15 20:22:48.395 wdl.w:ptcp.w:call-trgt-20.t:call-get_reads_overlapping_repeats INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:22:48.395 wdl.w:ptcp.w:call-trgt-20.t:call-get_reads_overlapping_repeats INFO eval :: name: "expand_size", value: 3000
2025-09-15 20:22:48.396 wdl.w:ptcp.w:call-trgt-20.t:call-get_reads_overlapping_repeats INFO eval :: name: "threads", value: 1
2025-09-15 20:22:48.397 wdl.w:ptcp.w:call-paraphase-26 INFO visit :: node: "decl-annotation_vcf", values: {"annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf"}
2025-09-15 20:22:48.397 wdl.w:ptcp.w:call-trgt-20.t:call-get_reads_overlapping_repeats INFO eval :: name: "expanded_bed_name", value: "m84036_250809_035451_s4.bc2117.expanded.bed"
2025-09-15 20:22:48.397 wdl.w:ptcp.w:call-paraphase-26 INFO visit :: node: "decl-config_file", values: {"config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml"}
2025-09-15 20:22:48.398 wdl.w:ptcp.w:call-trgt-20.t:call-get_reads_overlapping_repeats INFO eval :: name: "disk_size", value: 11
2025-09-15 20:22:48.398 wdl.w:ptcp.w:call-paraphase-26 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:22:48.399 wdl.w:ptcp.w:call-paraphase-26 INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:22:48.399 wdl.w:ptcp.w:call-trgt-20.t:call-get_reads_overlapping_repeats INFO eval :: name: "output_name", value: "m84036_250809_035451_s4.bc2117.repeats.bam"
2025-09-15 20:22:48.399 wdl.w:ptcp.w:call-paraphase-26 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-26/out/m84036_250809_035451_s4.bc2123.mapped.bam"}
2025-09-15 20:22:48.400 wdl.w:ptcp.w:call-paraphase-26 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-26/out/m84036_250809_035451_s4.bc2123.mapped.bam.bai"}
2025-09-15 20:22:48.400 wdl.w:ptcp.w:call-trgt-20.t:call-get_reads_overlapping_repeats INFO eval :: name: "index_name", value: "m84036_250809_035451_s4.bc2117.repeats.bam.bai"
2025-09-15 20:22:48.400 wdl.w:ptcp.w:call-paraphase-26 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:22:48.401 wdl.w:ptcp.w:call-trgt-20.t:call-get_reads_overlapping_repeats INFO eval :: name: "output_name_with_index", value: "m84036_250809_035451_s4.bc2117.repeats.bam##idx##m84036_250809_035451_s4.bc2117.repeats.bam.bai"
2025-09-15 20:22:48.402 wdl.w:ptcp.w:call-paraphase-26 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:22:48.403 wdl.w:ptcp.w:call-paraphase-26 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2123"}
2025-09-15 20:22:48.403 wdl.w:ptcp.w:call-paraphase-26 INFO visit :: node: "decl-sex", values: {"sex": "F"}
2025-09-15 20:22:48.404 wdl.w:ptcp.w:call-trgt-20.t:call-get_reads_overlapping_repeats INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:22:48.403 wdl.w:ptcp.w:call-paraphase-26 NOTICE ready :: job: "call-run_paraphase", callee: "run_paraphase"
2025-09-15 20:22:48.404 wdl.w:ptcp.w:call-trgt-20.t:call-get_reads_overlapping_repeats WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:22:48.405 wdl.w:ptcp.t:call-pbmm2_align_hifi-39.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:22:48.405 wdl.w:ptcp.w:call-paraphase-26 INFO input :: job: "call-run_paraphase", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf", "genome_version": "38", "config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-26/out/m84036_250809_035451_s4.bc2123.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-26/out/m84036_250809_035451_s4.bc2123.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2123"}
2025-09-15 20:22:48.406 wdl.w:ptcp.w:call-trgt-26 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:22:48.406 wdl.w:ptcp.t:call-pbmm2_align_hifi-39.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:22:48.407 wdl.w:ptcp.w:call-trgt-26 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-26/out/m84036_250809_035451_s4.bc2123.mapped.bam"}
2025-09-15 20:22:48.407 wdl.w:ptcp.w:call-trgt-20.t:call-get_reads_overlapping_repeats INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:22:48.408 wdl.w:ptcp.w:call-trgt-26 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-26/out/m84036_250809_035451_s4.bc2123.mapped.bam.bai"}
2025-09-15 20:22:48.408 wdl.w:ptcp.w:call-trgt-20.t:call-get_reads_overlapping_repeats INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:22:48.408 wdl.w:ptcp.w:call-trgt-26 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:22:48.408 wdl.w:ptcp.w:call-trgt-26 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:22:48.408 wdl.w:ptcp.w:call-trgt-26 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2123"}
2025-09-15 20:22:48.408 wdl.w:ptcp.w:call-trgt-26 INFO visit :: node: "decl-sex", values: {"sex": "F"}
2025-09-15 20:22:48.409 wdl.w:ptcp.w:call-trgt-26 INFO visit :: node: "decl-trgt_bed", values: {"trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"}
2025-09-15 20:22:48.409 wdl.w:ptcp.w:call-trgt-26 NOTICE ready :: job: "call-get_reads_overlapping_repeats", callee: "get_reads_overlapping_repeats"
2025-09-15 20:22:48.409 wdl.w:ptcp.w:call-trgt-26 INFO input :: job: "call-get_reads_overlapping_repeats", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-26/out/m84036_250809_035451_s4.bc2123.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-26/out/m84036_250809_035451_s4.bc2123.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2123"}
2025-09-15 20:22:48.410 wdl.w:ptcp.w:call-sawfish-26 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:22:48.411 wdl.w:ptcp.w:call-trgt-26 NOTICE ready :: job: "call-trgt_genotype", callee: "trgt_genotype"
2025-09-15 20:22:48.411 wdl.w:ptcp.w:call-sawfish-26 INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:22:48.411 wdl.w:ptcp.w:call-trgt-26 INFO input :: job: "call-trgt_genotype", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-26/out/m84036_250809_035451_s4.bc2123.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-26/out/m84036_250809_035451_s4.bc2123.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2123"}
2025-09-15 20:22:48.411 wdl.w:ptcp.w:call-sawfish-26 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-26/out/m84036_250809_035451_s4.bc2123.mapped.bam"}
2025-09-15 20:22:48.412 wdl.w:ptcp.w:call-sawfish-26 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-26/out/m84036_250809_035451_s4.bc2123.mapped.bam.bai"}
2025-09-15 20:22:48.412 wdl.w:ptcp.w:call-sawfish-26 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:22:48.412 wdl.w:ptcp.w:call-sawfish-26 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:22:48.412 wdl.w:ptcp.w:call-sawfish-26 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2123"}
2025-09-15 20:22:48.412 wdl.w:ptcp.w:call-sawfish-26 NOTICE ready :: job: "call-run_sawfish", callee: "run_sawfish"
2025-09-15 20:22:48.413 wdl.w:ptcp.w:call-sawfish-26 INFO input :: job: "call-run_sawfish", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-26/out/m84036_250809_035451_s4.bc2123.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-26/out/m84036_250809_035451_s4.bc2123.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2123"}
2025-09-15 20:22:48.413 wdl.w:ptcp.t:call-pbmm2_align_hifi-41.slurm_singularity INFO srun: job 51797265 has been allocated resources
2025-09-15 20:22:48.413 wdl.w:ptcp.t:call-pbmm2_align_hifi-41.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:22:48.413 wdl.w:ptcp.t:call-pbmm2_align_hifi-41.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:22:48.420 wdl.w:ptcp.t:call-pbmm2_align_hifi-43.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:22:48.420 wdl.w:ptcp.t:call-pbmm2_align_hifi-43.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:22:48.420 wdl.w:ptcp.t:call-pbmm2_align_hifi-40.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:22:48.420 wdl.w:ptcp.t:call-pbmm2_align_hifi-40.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:22:48.424 wdl.w:ptcp.t:call-pbmm2_align_hifi-44.slurm_singularity INFO srun: job 51797266 has been allocated resources
2025-09-15 20:22:48.424 wdl.w:ptcp.t:call-pbmm2_align_hifi-44.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:22:48.425 wdl.w:ptcp.t:call-pbmm2_align_hifi-44.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:22:48.454 wdl.w:ptcp.w:call-sawfish-20.t:call-run_sawfish INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 10, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-20/call-run_sawfish/_singularity_tmpdir_8gdovn9b"
2025-09-15 20:22:48.455 wdl.w:ptcp.w:call-sawfish-20.t:call-run_sawfish INFO Slurm invocation: srun --job-name call-run_sawfish --partition compute,compute9 --cpus-per-task 16 --mem 30518M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-20/call-run_sawfish/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-20/call-run_sawfish/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-20/call-run_sawfish/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-20/call-run_sawfish/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-20/out/m84036_250809_035451_s4.bc2117.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2117.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-20/out/m84036_250809_035451_s4.bc2117.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2117.mapped.bam:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-20/call-run_sawfish/_singularity_tmpdir_8gdovn9b/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-20/call-run_sawfish/_singularity_tmpdir_8gdovn9b/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:22:48.457 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_genotype.slurm_singularity INFO srun: job 51797326 queued and waiting for resources
2025-09-15 20:22:48.479 wdl.w:ptcp.w:call-trgt-20.t:call-get_reads_overlapping_repeats INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 9, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-20/call-get_reads_overlapping_repeats/_singularity_tmpdir_27oh7pr5"
2025-09-15 20:22:48.479 wdl.w:ptcp.w:call-trgt-20.t:call-get_reads_overlapping_repeats INFO Slurm invocation: srun --job-name call-get_reads_overlapping_repeats --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-20/call-get_reads_overlapping_repeats/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-20/call-get_reads_overlapping_repeats/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-20/call-get_reads_overlapping_repeats/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-20/call-get_reads_overlapping_repeats/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-20/out/m84036_250809_035451_s4.bc2117.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2117.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-20/out/m84036_250809_035451_s4.bc2117.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2117.mapped.bam:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-20/call-get_reads_overlapping_repeats/_singularity_tmpdir_27oh7pr5/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-20/call-get_reads_overlapping_repeats/_singularity_tmpdir_27oh7pr5/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:22:48.479 wdl.w:ptcp.t:call-pbmm2_align_hifi-45.slurm_singularity INFO srun: job 51797268 has been allocated resources
2025-09-15 20:22:48.480 wdl.w:ptcp.t:call-pbmm2_align_hifi-28 NOTICE done
2025-09-15 20:22:48.481 wdl.w:ptcp.t:call-pbmm2_align_hifi-45.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:22:48.481 wdl.w:ptcp.t:call-pbmm2_align_hifi-45.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:22:48.483 wdl.w:ptcp.t:call-pbmm2_align_hifi-51.slurm_singularity INFO srun: job 51797269 has been allocated resources
2025-09-15 20:22:48.484 wdl.w:ptcp.t:call-pbmm2_align_hifi-51.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:22:48.484 wdl.w:ptcp.t:call-pbmm2_align_hifi-51.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:22:48.488 wdl.w:ptcp NOTICE finish :: job: "call-pbmm2_align_hifi-28"
2025-09-15 20:22:48.488 wdl.w:ptcp INFO output :: job: "call-pbmm2_align_hifi-28", values: {"report": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-28/out/mapping_stats.report.json", "mapped_bam_pbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-28/out/m84036_250809_035451_s4.bc2125.mapped.bam.pbi", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-28/out/m84036_250809_035451_s4.bc2125.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-28/out/m84036_250809_035451_s4.bc2125.mapped.bam"}
2025-09-15 20:22:48.489 wdl.w:ptcp NOTICE ready :: job: "call-paraphase-28", callee: "paraphase"
2025-09-15 20:22:48.489 wdl.w:ptcp INFO input :: job: "call-paraphase-28", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf", "genome_version": "38", "config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-28/out/m84036_250809_035451_s4.bc2125.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-28/out/m84036_250809_035451_s4.bc2125.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2125"}
2025-09-15 20:22:48.489 wdl.w:ptcp.w:call-sawfish-20.t:call-run_sawfish NOTICE slurm_singularity run :: pid: 1198114, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-20/call-run_sawfish/slurm_singularity.log.txt"
2025-09-15 20:22:48.489 wdl.w:ptcp.w:call-trgt-20.t:call-get_reads_overlapping_repeats NOTICE slurm_singularity run :: pid: 1198115, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-20/call-get_reads_overlapping_repeats/slurm_singularity.log.txt"
2025-09-15 20:22:48.490 wdl.w:ptcp NOTICE ready :: job: "call-sawfish-28", callee: "sawfish"
2025-09-15 20:22:48.491 wdl.w:ptcp INFO input :: job: "call-sawfish-28", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-28/out/m84036_250809_035451_s4.bc2125.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-28/out/m84036_250809_035451_s4.bc2125.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2125"}
2025-09-15 20:22:48.495 wdl.w:ptcp NOTICE ready :: job: "call-trgt-28", callee: "trgt"
2025-09-15 20:22:48.495 wdl.w:ptcp INFO input :: job: "call-trgt-28", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-28/out/m84036_250809_035451_s4.bc2125.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-28/out/m84036_250809_035451_s4.bc2125.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2125"}
2025-09-15 20:22:48.496 wdl.w:ptcp.w:call-trgt-20.t:call-trgt_genotype NOTICE task setup :: name: "trgt_genotype", source: "./trgt.wdl", line: 272, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-20/call-trgt_genotype", thread: 140611952813632
2025-09-15 20:22:48.498 wdl.w:ptcp.w:call-paraphase-28 NOTICE workflow start :: name: "paraphase", source: "./paraphase.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-28"
2025-09-15 20:22:48.499 wdl.w:ptcp.t:call-pbmm2_align_hifi-46.slurm_singularity INFO srun: job 51797264 has been allocated resources
2025-09-15 20:22:48.500 wdl.w:ptcp.t:call-pbmm2_align_hifi-46.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:22:48.500 wdl.w:ptcp.t:call-pbmm2_align_hifi-46.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:22:48.501 wdl.w:ptcp.t:call-pbmm2_align_hifi-47.slurm_singularity INFO srun: job 51797267 has been allocated resources
2025-09-15 20:22:48.502 wdl.w:ptcp.t:call-pbmm2_align_hifi-47.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:22:48.502 wdl.w:ptcp.t:call-pbmm2_align_hifi-47.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:22:48.505 wdl.w:ptcp.w:call-sawfish-28 NOTICE workflow start :: name: "sawfish", source: "./sawfish.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-28"
2025-09-15 20:22:48.509 wdl.w:ptcp.w:call-trgt-28 NOTICE workflow start :: name: "trgt", source: "./trgt.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-28"
2025-09-15 20:22:48.519 wdl.w:ptcp.w:call-paraphase-28 INFO visit :: node: "decl-annotation_vcf", values: {"annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf"}
2025-09-15 20:22:48.519 wdl.w:ptcp.w:call-paraphase-28 INFO visit :: node: "decl-config_file", values: {"config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml"}
2025-09-15 20:22:48.519 wdl.w:ptcp.w:call-paraphase-28 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:22:48.520 wdl.w:ptcp.w:call-paraphase-28 INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:22:48.520 wdl.w:ptcp.w:call-paraphase-28 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-28/out/m84036_250809_035451_s4.bc2125.mapped.bam"}
2025-09-15 20:22:48.521 wdl.w:ptcp.w:call-paraphase-28 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-28/out/m84036_250809_035451_s4.bc2125.mapped.bam.bai"}
2025-09-15 20:22:48.521 wdl.w:ptcp.w:call-paraphase-28 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:22:48.521 wdl.w:ptcp.w:call-paraphase-28 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:22:48.521 wdl.w:ptcp.w:call-paraphase-28 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2125"}
2025-09-15 20:22:48.522 wdl.w:ptcp.w:call-paraphase-28 INFO visit :: node: "decl-sex", values: {"sex": "F"}
2025-09-15 20:22:48.522 wdl.w:ptcp.w:call-paraphase-28 NOTICE ready :: job: "call-run_paraphase", callee: "run_paraphase"
2025-09-15 20:22:48.523 wdl.w:ptcp.w:call-paraphase-28 INFO input :: job: "call-run_paraphase", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf", "genome_version": "38", "config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-28/out/m84036_250809_035451_s4.bc2125.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-28/out/m84036_250809_035451_s4.bc2125.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2125"}
2025-09-15 20:22:48.523 wdl.w:ptcp.w:call-trgt-20.t:call-trgt_genotype INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:22:48.524 wdl.w:ptcp.w:call-trgt-20.t:call-trgt_genotype INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:22:48.524 wdl.w:ptcp.w:call-trgt-20.t:call-trgt_genotype INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:22:48.525 wdl.w:ptcp.w:call-trgt-20.t:call-trgt_genotype INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:22:48.525 wdl.w:ptcp.w:call-trgt-20.t:call-trgt_genotype INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2117.mapped.bam.bai"
2025-09-15 20:22:48.525 wdl.w:ptcp.w:call-trgt-20.t:call-trgt_genotype INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2117.mapped.bam"
2025-09-15 20:22:48.526 wdl.w:ptcp.w:call-trgt-20.t:call-trgt_genotype INFO input :: name: "sex", value: "F"
2025-09-15 20:22:48.526 wdl.w:ptcp.w:call-trgt-20.t:call-trgt_genotype INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2117"
2025-09-15 20:22:48.526 wdl.w:ptcp.w:call-trgt-20.t:call-trgt_genotype INFO eval :: name: "mem_gb", value: 16
2025-09-15 20:22:48.527 wdl.w:ptcp.w:call-trgt-20.t:call-trgt_genotype INFO eval :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2117.trgt"
2025-09-15 20:22:48.527 wdl.w:ptcp.w:call-trgt-20.t:call-trgt_genotype INFO eval :: name: "threads", value: 8
2025-09-15 20:22:48.528 wdl.w:ptcp.w:call-trgt-20.t:call-trgt_genotype INFO eval :: name: "disk_size", value: 27
2025-09-15 20:22:48.528 wdl.w:ptcp.w:call-trgt-20.t:call-trgt_genotype INFO eval :: name: "karyotype", value: "XX"
2025-09-15 20:22:48.529 wdl.w:ptcp.w:call-trgt-20.t:call-trgt_genotype INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 8, memory_reservation: 16000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:22:48.529 wdl.w:ptcp.w:call-trgt-20.t:call-trgt_genotype WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:22:48.531 wdl.w:ptcp.w:call-sawfish-28 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:22:48.531 wdl.w:ptcp.w:call-sawfish-28 INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:22:48.532 wdl.w:ptcp.w:call-sawfish-28 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-28/out/m84036_250809_035451_s4.bc2125.mapped.bam"}
2025-09-15 20:22:48.532 wdl.w:ptcp.w:call-sawfish-28 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-28/out/m84036_250809_035451_s4.bc2125.mapped.bam.bai"}
2025-09-15 20:22:48.532 wdl.w:ptcp.w:call-sawfish-28 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:22:48.532 wdl.w:ptcp.w:call-sawfish-28 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:22:48.533 wdl.w:ptcp.w:call-sawfish-28 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2125"}
2025-09-15 20:22:48.533 wdl.w:ptcp.w:call-trgt-28 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:22:48.533 wdl.w:ptcp.w:call-sawfish-28 NOTICE ready :: job: "call-run_sawfish", callee: "run_sawfish"
2025-09-15 20:22:48.534 wdl.w:ptcp.w:call-trgt-20.t:call-trgt_genotype INFO provisioned :: seconds_waited: 0, cpu: 8, mem_bytes: 16000000000
2025-09-15 20:22:48.534 wdl.w:ptcp.w:call-trgt-28 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-28/out/m84036_250809_035451_s4.bc2125.mapped.bam"}
2025-09-15 20:22:48.534 wdl.w:ptcp.w:call-sawfish-28 INFO input :: job: "call-run_sawfish", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-28/out/m84036_250809_035451_s4.bc2125.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-28/out/m84036_250809_035451_s4.bc2125.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2125"}
2025-09-15 20:22:48.534 wdl.w:ptcp.w:call-trgt-20.t:call-trgt_genotype INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:22:48.534 wdl.w:ptcp.w:call-trgt-28 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-28/out/m84036_250809_035451_s4.bc2125.mapped.bam.bai"}
2025-09-15 20:22:48.534 wdl.w:ptcp.w:call-trgt-28 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:22:48.535 wdl.w:ptcp.w:call-trgt-28 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:22:48.535 wdl.w:ptcp.w:call-trgt-28 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2125"}
2025-09-15 20:22:48.535 wdl.w:ptcp.w:call-trgt-28 INFO visit :: node: "decl-sex", values: {"sex": "F"}
2025-09-15 20:22:48.535 wdl.w:ptcp.w:call-trgt-28 INFO visit :: node: "decl-trgt_bed", values: {"trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"}
2025-09-15 20:22:48.535 wdl.w:ptcp.w:call-trgt-28 NOTICE ready :: job: "call-get_reads_overlapping_repeats", callee: "get_reads_overlapping_repeats"
2025-09-15 20:22:48.535 wdl.w:ptcp.w:call-trgt-28 INFO input :: job: "call-get_reads_overlapping_repeats", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-28/out/m84036_250809_035451_s4.bc2125.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-28/out/m84036_250809_035451_s4.bc2125.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2125"}
2025-09-15 20:22:48.536 wdl.w:ptcp.w:call-trgt-28 NOTICE ready :: job: "call-trgt_genotype", callee: "trgt_genotype"
2025-09-15 20:22:48.536 wdl.w:ptcp.w:call-trgt-28 INFO input :: job: "call-trgt_genotype", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-28/out/m84036_250809_035451_s4.bc2125.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-28/out/m84036_250809_035451_s4.bc2125.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2125"}
2025-09-15 20:22:48.601 wdl.w:ptcp.w:call-trgt-20.t:call-trgt_genotype INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 11, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-20/call-trgt_genotype/_singularity_tmpdir_4_aut44a"
2025-09-15 20:22:48.601 wdl.w:ptcp.w:call-trgt-20.t:call-trgt_genotype INFO Slurm invocation: srun --job-name call-trgt_genotype --partition compute,compute9 --cpus-per-task 8 --mem 15259M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-20/call-trgt_genotype/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-20/call-trgt_genotype/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-20/call-trgt_genotype/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-20/call-trgt_genotype/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-20/out/m84036_250809_035451_s4.bc2117.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2117.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-20/out/m84036_250809_035451_s4.bc2117.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2117.mapped.bam:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-20/call-trgt_genotype/_singularity_tmpdir_4_aut44a/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-20/call-trgt_genotype/_singularity_tmpdir_4_aut44a/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:22:48.612 wdl.w:ptcp.w:call-paraphase-15.t:call-run_paraphase.slurm_singularity INFO srun: job 51797327 queued and waiting for resources
2025-09-15 20:22:48.619 wdl.w:ptcp.w:call-trgt-20.t:call-trgt_genotype NOTICE slurm_singularity run :: pid: 1198122, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-20/call-trgt_genotype/slurm_singularity.log.txt"
2025-09-15 20:22:48.640 wdl.w:ptcp.w:call-trgt-15.t:call-get_reads_overlapping_repeats.slurm_singularity INFO srun: job 51797328 queued and waiting for resources
2025-09-15 20:22:48.675 wdl.w:ptcp.t:call-pbmm2_align_hifi-18 INFO output :: name: "mapped_bam", value: "m84036_250809_035451_s4.bc2115.mapped.bam"
2025-09-15 20:22:48.678 wdl.w:ptcp.t:call-pbmm2_align_hifi-10 INFO output :: name: "mapped_bam", value: "m84036_250809_035451_s4.bc2107.mapped.bam"
2025-09-15 20:22:48.679 wdl.w:ptcp.t:call-pbmm2_align_hifi-18 INFO output :: name: "mapped_bam_bai", value: "m84036_250809_035451_s4.bc2115.mapped.bam.bai"
2025-09-15 20:22:48.681 wdl.w:ptcp.t:call-pbmm2_align_hifi-18 INFO output :: name: "mapped_bam_pbi", value: "m84036_250809_035451_s4.bc2115.mapped.bam.pbi"
2025-09-15 20:22:48.682 wdl.w:ptcp.t:call-pbmm2_align_hifi-10 INFO output :: name: "mapped_bam_bai", value: "m84036_250809_035451_s4.bc2107.mapped.bam.bai"
2025-09-15 20:22:48.683 wdl.w:ptcp.t:call-pbmm2_align_hifi-18 INFO output :: name: "report", value: "mapping_stats.report.json"
2025-09-15 20:22:48.684 wdl.w:ptcp.t:call-pbmm2_align_hifi-10 INFO output :: name: "mapped_bam_pbi", value: "m84036_250809_035451_s4.bc2107.mapped.bam.pbi"
2025-09-15 20:22:48.685 wdl.w:ptcp.t:call-pbmm2_align_hifi-10 INFO output :: name: "report", value: "mapping_stats.report.json"
2025-09-15 20:22:48.766 wdl.w:ptcp.t:call-pbmm2_align_hifi-18 NOTICE done
2025-09-15 20:22:48.768 wdl.w:ptcp.t:call-pbmm2_align_hifi-10 NOTICE done
2025-09-15 20:22:48.768 wdl.w:ptcp.t:call-pbmm2_align_hifi-11 INFO output :: name: "mapped_bam", value: "m84036_250809_035451_s4.bc2108.mapped.bam"
2025-09-15 20:22:48.771 wdl.w:ptcp.t:call-pbmm2_align_hifi-11 INFO output :: name: "mapped_bam_bai", value: "m84036_250809_035451_s4.bc2108.mapped.bam.bai"
2025-09-15 20:22:48.772 wdl.w:ptcp.t:call-pbmm2_align_hifi-11 INFO output :: name: "mapped_bam_pbi", value: "m84036_250809_035451_s4.bc2108.mapped.bam.pbi"
2025-09-15 20:22:48.772 wdl.w:ptcp.t:call-pbmm2_align_hifi-11 INFO output :: name: "report", value: "mapping_stats.report.json"
2025-09-15 20:22:48.801 wdl.w:ptcp NOTICE finish :: job: "call-pbmm2_align_hifi-10"
2025-09-15 20:22:48.801 wdl.w:ptcp INFO output :: job: "call-pbmm2_align_hifi-10", values: {"report": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-10/out/mapping_stats.report.json", "mapped_bam_pbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-10/out/m84036_250809_035451_s4.bc2107.mapped.bam.pbi", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-10/out/m84036_250809_035451_s4.bc2107.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-10/out/m84036_250809_035451_s4.bc2107.mapped.bam"}
2025-09-15 20:22:48.802 wdl.w:ptcp NOTICE ready :: job: "call-paraphase-10", callee: "paraphase"
2025-09-15 20:22:48.802 wdl.w:ptcp INFO input :: job: "call-paraphase-10", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf", "genome_version": "38", "config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-10/out/m84036_250809_035451_s4.bc2107.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-10/out/m84036_250809_035451_s4.bc2107.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2107"}
2025-09-15 20:22:48.803 wdl.w:ptcp NOTICE ready :: job: "call-sawfish-10", callee: "sawfish"
2025-09-15 20:22:48.804 wdl.w:ptcp INFO input :: job: "call-sawfish-10", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-10/out/m84036_250809_035451_s4.bc2107.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-10/out/m84036_250809_035451_s4.bc2107.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2107"}
2025-09-15 20:22:48.807 wdl.w:ptcp NOTICE ready :: job: "call-trgt-10", callee: "trgt"
2025-09-15 20:22:48.807 wdl.w:ptcp INFO input :: job: "call-trgt-10", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-10/out/m84036_250809_035451_s4.bc2107.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-10/out/m84036_250809_035451_s4.bc2107.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2107"}
2025-09-15 20:22:48.810 wdl.w:ptcp NOTICE finish :: job: "call-pbmm2_align_hifi-18"
2025-09-15 20:22:48.810 wdl.w:ptcp INFO output :: job: "call-pbmm2_align_hifi-18", values: {"report": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-18/out/mapping_stats.report.json", "mapped_bam_pbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-18/out/m84036_250809_035451_s4.bc2115.mapped.bam.pbi", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-18/out/m84036_250809_035451_s4.bc2115.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-18/out/m84036_250809_035451_s4.bc2115.mapped.bam"}
2025-09-15 20:22:48.812 wdl.w:ptcp NOTICE ready :: job: "call-paraphase-18", callee: "paraphase"
2025-09-15 20:22:48.812 wdl.w:ptcp INFO input :: job: "call-paraphase-18", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf", "genome_version": "38", "config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-18/out/m84036_250809_035451_s4.bc2115.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-18/out/m84036_250809_035451_s4.bc2115.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2115"}
2025-09-15 20:22:48.812 wdl.w:ptcp.w:call-trgt-07.t:call-get_reads_overlapping_repeats NOTICE task setup :: name: "get_reads_overlapping_repeats", source: "./trgt.wdl", line: 182, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-07/call-get_reads_overlapping_repeats", thread: 140612514862656
2025-09-15 20:22:48.813 wdl.w:ptcp.w:call-sawfish-07.t:call-run_sawfish NOTICE task setup :: name: "run_sawfish", source: "./sawfish.wdl", line: 83, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-07/call-run_sawfish", thread: 140613060126272
2025-09-15 20:22:48.815 wdl.w:ptcp.w:call-paraphase-10 NOTICE workflow start :: name: "paraphase", source: "./paraphase.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-10"
2025-09-15 20:22:48.818 wdl.w:ptcp NOTICE ready :: job: "call-sawfish-18", callee: "sawfish"
2025-09-15 20:22:48.818 wdl.w:ptcp.w:call-sawfish-10 NOTICE workflow start :: name: "sawfish", source: "./sawfish.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-10"
2025-09-15 20:22:48.818 wdl.w:ptcp INFO input :: job: "call-sawfish-18", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-18/out/m84036_250809_035451_s4.bc2115.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-18/out/m84036_250809_035451_s4.bc2115.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2115"}
2025-09-15 20:22:48.822 wdl.w:ptcp NOTICE ready :: job: "call-trgt-18", callee: "trgt"
2025-09-15 20:22:48.822 wdl.w:ptcp INFO input :: job: "call-trgt-18", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-18/out/m84036_250809_035451_s4.bc2115.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-18/out/m84036_250809_035451_s4.bc2115.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2115"}
2025-09-15 20:22:48.824 wdl.w:ptcp.t:call-pbmm2_align_hifi-19 INFO output :: name: "mapped_bam", value: "m84036_250809_035451_s4.bc2116.mapped.bam"
2025-09-15 20:22:48.825 wdl.w:ptcp.w:call-trgt-10 NOTICE workflow start :: name: "trgt", source: "./trgt.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-10"
2025-09-15 20:22:48.828 wdl.w:ptcp.t:call-pbmm2_align_hifi-19 INFO output :: name: "mapped_bam_bai", value: "m84036_250809_035451_s4.bc2116.mapped.bam.bai"
2025-09-15 20:22:48.829 wdl.w:ptcp.w:call-paraphase-18 NOTICE workflow start :: name: "paraphase", source: "./paraphase.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-18"
2025-09-15 20:22:48.831 wdl.w:ptcp.w:call-sawfish-18 NOTICE workflow start :: name: "sawfish", source: "./sawfish.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-18"
2025-09-15 20:22:48.833 wdl.w:ptcp.t:call-pbmm2_align_hifi-19 INFO output :: name: "mapped_bam_pbi", value: "m84036_250809_035451_s4.bc2116.mapped.bam.pbi"
2025-09-15 20:22:48.835 wdl.w:ptcp.w:call-trgt-18 NOTICE workflow start :: name: "trgt", source: "./trgt.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-18"
2025-09-15 20:22:48.841 wdl.w:ptcp.t:call-pbmm2_align_hifi-19 INFO output :: name: "report", value: "mapping_stats.report.json"
2025-09-15 20:22:48.842 wdl.w:ptcp.w:call-trgt-07.t:call-get_reads_overlapping_repeats INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:22:48.843 wdl.w:ptcp.w:call-trgt-07.t:call-get_reads_overlapping_repeats INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:22:48.843 wdl.w:ptcp.w:call-trgt-07.t:call-get_reads_overlapping_repeats INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2104.mapped.bam.bai"
2025-09-15 20:22:48.843 wdl.w:ptcp.w:call-trgt-07.t:call-get_reads_overlapping_repeats INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2104.mapped.bam"
2025-09-15 20:22:48.843 wdl.w:ptcp.w:call-trgt-07.t:call-get_reads_overlapping_repeats INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2104"
2025-09-15 20:22:48.844 wdl.w:ptcp.w:call-trgt-07.t:call-get_reads_overlapping_repeats INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:22:48.847 wdl.w:ptcp.w:call-trgt-07.t:call-get_reads_overlapping_repeats INFO eval :: name: "expand_size", value: 3000
2025-09-15 20:22:48.849 wdl.w:ptcp.w:call-trgt-07.t:call-get_reads_overlapping_repeats INFO eval :: name: "threads", value: 1
2025-09-15 20:22:48.851 wdl.w:ptcp.w:call-trgt-07.t:call-get_reads_overlapping_repeats INFO eval :: name: "expanded_bed_name", value: "m84036_250809_035451_s4.bc2104.expanded.bed"
2025-09-15 20:22:48.853 wdl.w:ptcp.w:call-paraphase-10 INFO visit :: node: "decl-annotation_vcf", values: {"annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf"}
2025-09-15 20:22:48.857 wdl.w:ptcp.w:call-sawfish-10 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:22:48.856 wdl.w:ptcp.w:call-trgt-07.t:call-get_reads_overlapping_repeats INFO eval :: name: "disk_size", value: 11
2025-09-15 20:22:48.857 wdl.w:ptcp.w:call-paraphase-10 INFO visit :: node: "decl-config_file", values: {"config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml"}
2025-09-15 20:22:48.858 wdl.w:ptcp.w:call-sawfish-10 INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:22:48.859 wdl.w:ptcp.w:call-trgt-07.t:call-get_reads_overlapping_repeats INFO eval :: name: "output_name", value: "m84036_250809_035451_s4.bc2104.repeats.bam"
2025-09-15 20:22:48.859 wdl.w:ptcp.w:call-paraphase-10 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:22:48.861 wdl.w:ptcp.w:call-sawfish-10 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-10/out/m84036_250809_035451_s4.bc2107.mapped.bam"}
2025-09-15 20:22:48.862 wdl.w:ptcp.w:call-trgt-07.t:call-get_reads_overlapping_repeats INFO eval :: name: "index_name", value: "m84036_250809_035451_s4.bc2104.repeats.bam.bai"
2025-09-15 20:22:48.862 wdl.w:ptcp.w:call-paraphase-10 INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:22:48.864 wdl.w:ptcp.w:call-sawfish-10 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-10/out/m84036_250809_035451_s4.bc2107.mapped.bam.bai"}
2025-09-15 20:22:48.864 wdl.w:ptcp.w:call-sawfish-07.t:call-run_sawfish INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:22:48.865 wdl.w:ptcp.w:call-trgt-07.t:call-get_reads_overlapping_repeats INFO eval :: name: "output_name_with_index", value: "m84036_250809_035451_s4.bc2104.repeats.bam##idx##m84036_250809_035451_s4.bc2104.repeats.bam.bai"
2025-09-15 20:22:48.866 wdl.w:ptcp.w:call-sawfish-10 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:22:48.865 wdl.w:ptcp.w:call-paraphase-10 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-10/out/m84036_250809_035451_s4.bc2107.mapped.bam"}
2025-09-15 20:22:48.867 wdl.w:ptcp.w:call-sawfish-07.t:call-run_sawfish INFO input :: name: "genome_version", value: "38"
2025-09-15 20:22:48.869 wdl.w:ptcp.w:call-sawfish-10 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:22:48.870 wdl.w:ptcp.w:call-paraphase-10 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-10/out/m84036_250809_035451_s4.bc2107.mapped.bam.bai"}
2025-09-15 20:22:48.871 wdl.w:ptcp.w:call-sawfish-07.t:call-run_sawfish INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:22:48.870 wdl.w:ptcp.w:call-trgt-07.t:call-get_reads_overlapping_repeats INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:22:48.872 wdl.w:ptcp.w:call-sawfish-10 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2107"}
2025-09-15 20:22:48.872 wdl.w:ptcp.w:call-paraphase-18 INFO visit :: node: "decl-annotation_vcf", values: {"annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf"}
2025-09-15 20:22:48.873 wdl.w:ptcp.w:call-paraphase-10 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:22:48.873 wdl.w:ptcp.w:call-sawfish-18 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:22:48.874 wdl.w:ptcp.w:call-sawfish-07.t:call-run_sawfish INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:22:48.874 wdl.w:ptcp.w:call-trgt-07.t:call-get_reads_overlapping_repeats WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:22:48.875 wdl.w:ptcp.w:call-sawfish-10 NOTICE ready :: job: "call-run_sawfish", callee: "run_sawfish"
2025-09-15 20:22:48.875 wdl.w:ptcp.w:call-paraphase-18 INFO visit :: node: "decl-config_file", values: {"config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml"}
2025-09-15 20:22:48.876 wdl.w:ptcp.w:call-paraphase-10 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:22:48.877 wdl.w:ptcp.w:call-sawfish-18 INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:22:48.877 wdl.w:ptcp.w:call-trgt-18 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:22:48.877 wdl.w:ptcp.w:call-sawfish-07.t:call-run_sawfish INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2104.mapped.bam.bai"
2025-09-15 20:22:48.878 wdl.w:ptcp.w:call-trgt-10 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:22:48.879 wdl.w:ptcp.w:call-sawfish-10 INFO input :: job: "call-run_sawfish", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-10/out/m84036_250809_035451_s4.bc2107.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-10/out/m84036_250809_035451_s4.bc2107.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2107"}
2025-09-15 20:22:48.879 wdl.w:ptcp.w:call-paraphase-18 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:22:48.879 wdl.w:ptcp.w:call-paraphase-10 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2107"}
2025-09-15 20:22:48.879 wdl.w:ptcp.w:call-sawfish-18 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-18/out/m84036_250809_035451_s4.bc2115.mapped.bam"}
2025-09-15 20:22:48.879 wdl.w:ptcp.w:call-trgt-07.t:call-get_reads_overlapping_repeats INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:22:48.880 wdl.w:ptcp.w:call-trgt-18 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-18/out/m84036_250809_035451_s4.bc2115.mapped.bam"}
2025-09-15 20:22:48.880 wdl.w:ptcp.w:call-sawfish-07.t:call-run_sawfish INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2104.mapped.bam"
2025-09-15 20:22:48.880 wdl.w:ptcp.w:call-trgt-10 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-10/out/m84036_250809_035451_s4.bc2107.mapped.bam"}
2025-09-15 20:22:48.880 wdl.w:ptcp.w:call-paraphase-18 INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:22:48.880 wdl.w:ptcp.w:call-paraphase-10 INFO visit :: node: "decl-sex", values: {"sex": "F"}
2025-09-15 20:22:48.881 wdl.w:ptcp.w:call-sawfish-18 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-18/out/m84036_250809_035451_s4.bc2115.mapped.bam.bai"}
2025-09-15 20:22:48.881 wdl.w:ptcp.w:call-trgt-07.t:call-get_reads_overlapping_repeats INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:22:48.881 wdl.w:ptcp.w:call-trgt-18 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-18/out/m84036_250809_035451_s4.bc2115.mapped.bam.bai"}
2025-09-15 20:22:48.881 wdl.w:ptcp.w:call-sawfish-07.t:call-run_sawfish INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2104"
2025-09-15 20:22:48.881 wdl.w:ptcp.w:call-trgt-10 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-10/out/m84036_250809_035451_s4.bc2107.mapped.bam.bai"}
2025-09-15 20:22:48.882 wdl.w:ptcp.w:call-paraphase-18 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-18/out/m84036_250809_035451_s4.bc2115.mapped.bam"}
2025-09-15 20:22:48.882 wdl.w:ptcp.w:call-paraphase-10 NOTICE ready :: job: "call-run_paraphase", callee: "run_paraphase"
2025-09-15 20:22:48.882 wdl.w:ptcp.w:call-sawfish-18 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:22:48.883 wdl.w:ptcp.w:call-trgt-18 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:22:48.883 wdl.w:ptcp.w:call-sawfish-07.t:call-run_sawfish INFO eval :: name: "mem_gb", value: 32
2025-09-15 20:22:48.883 wdl.w:ptcp.w:call-trgt-10 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:22:48.883 wdl.w:ptcp.w:call-paraphase-18 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-18/out/m84036_250809_035451_s4.bc2115.mapped.bam.bai"}
2025-09-15 20:22:48.884 wdl.w:ptcp.w:call-paraphase-10 INFO input :: job: "call-run_paraphase", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf", "genome_version": "38", "config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-10/out/m84036_250809_035451_s4.bc2107.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-10/out/m84036_250809_035451_s4.bc2107.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2107"}
2025-09-15 20:22:48.884 wdl.w:ptcp.w:call-sawfish-18 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:22:48.884 wdl.w:ptcp.w:call-trgt-18 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:22:48.884 wdl.w:ptcp.w:call-sawfish-07.t:call-run_sawfish INFO eval :: name: "threads", value: 16
2025-09-15 20:22:48.884 wdl.w:ptcp.w:call-trgt-10 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:22:48.884 wdl.w:ptcp.w:call-paraphase-18 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:22:48.885 wdl.w:ptcp.w:call-sawfish-18 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2115"}
2025-09-15 20:22:48.885 wdl.w:ptcp.w:call-trgt-18 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2115"}
2025-09-15 20:22:48.885 wdl.w:ptcp.w:call-trgt-10 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2107"}
2025-09-15 20:22:48.885 wdl.w:ptcp.w:call-sawfish-07.t:call-run_sawfish INFO eval :: name: "disk_size", value: 30
2025-09-15 20:22:48.886 wdl.w:ptcp.w:call-paraphase-18 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:22:48.886 wdl.w:ptcp.w:call-sawfish-18 NOTICE ready :: job: "call-run_sawfish", callee: "run_sawfish"
2025-09-15 20:22:48.886 wdl.w:ptcp.w:call-trgt-18 INFO visit :: node: "decl-sex", values: {"sex": "F"}
2025-09-15 20:22:48.887 wdl.w:ptcp.w:call-trgt-10 INFO visit :: node: "decl-sex", values: {"sex": "F"}
2025-09-15 20:22:48.887 wdl.w:ptcp.w:call-sawfish-07.t:call-run_sawfish INFO eval :: name: "discover_dirname", value: "m84036_250809_035451_s4.bc2104_sawfish_discover"
2025-09-15 20:22:48.887 wdl.w:ptcp.w:call-paraphase-18 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2115"}
2025-09-15 20:22:48.887 wdl.w:ptcp.w:call-sawfish-18 INFO input :: job: "call-run_sawfish", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-18/out/m84036_250809_035451_s4.bc2115.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-18/out/m84036_250809_035451_s4.bc2115.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2115"}
2025-09-15 20:22:48.887 wdl.w:ptcp.w:call-trgt-18 INFO visit :: node: "decl-trgt_bed", values: {"trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"}
2025-09-15 20:22:48.888 wdl.w:ptcp.w:call-trgt-10 INFO visit :: node: "decl-trgt_bed", values: {"trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"}
2025-09-15 20:22:48.888 wdl.w:ptcp.w:call-sawfish-07.t:call-run_sawfish INFO eval :: name: "call_dirname", value: "m84036_250809_035451_s4.bc2104_sawfish"
2025-09-15 20:22:48.888 wdl.w:ptcp.w:call-paraphase-18 INFO visit :: node: "decl-sex", values: {"sex": "F"}
2025-09-15 20:22:48.888 wdl.w:ptcp.w:call-trgt-18 NOTICE ready :: job: "call-get_reads_overlapping_repeats", callee: "get_reads_overlapping_repeats"
2025-09-15 20:22:48.889 wdl.w:ptcp.w:call-trgt-10 NOTICE ready :: job: "call-get_reads_overlapping_repeats", callee: "get_reads_overlapping_repeats"
2025-09-15 20:22:48.889 wdl.w:ptcp.w:call-sawfish-07.t:call-run_sawfish INFO eval :: name: "minimap2_bam_filename", value: "m84036_250809_035451_s4.bc2104.minimap2.bam"
2025-09-15 20:22:48.889 wdl.w:ptcp.w:call-paraphase-18 NOTICE ready :: job: "call-run_paraphase", callee: "run_paraphase"
2025-09-15 20:22:48.890 wdl.w:ptcp.w:call-trgt-18 INFO input :: job: "call-get_reads_overlapping_repeats", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-18/out/m84036_250809_035451_s4.bc2115.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-18/out/m84036_250809_035451_s4.bc2115.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2115"}
2025-09-15 20:22:48.890 wdl.w:ptcp.w:call-trgt-10 INFO input :: job: "call-get_reads_overlapping_repeats", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-10/out/m84036_250809_035451_s4.bc2107.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-10/out/m84036_250809_035451_s4.bc2107.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2107"}
2025-09-15 20:22:48.891 wdl.w:ptcp.w:call-paraphase-18 INFO input :: job: "call-run_paraphase", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf", "genome_version": "38", "config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-18/out/m84036_250809_035451_s4.bc2115.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-18/out/m84036_250809_035451_s4.bc2115.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2115"}
2025-09-15 20:22:48.891 wdl.w:ptcp.w:call-sawfish-07.t:call-run_sawfish INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 16, memory_reservation: 32000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:22:48.891 wdl.w:ptcp.w:call-sawfish-07.t:call-run_sawfish WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:22:48.892 wdl.w:ptcp.w:call-trgt-18 NOTICE ready :: job: "call-trgt_genotype", callee: "trgt_genotype"
2025-09-15 20:22:48.892 wdl.w:ptcp.w:call-trgt-10 NOTICE ready :: job: "call-trgt_genotype", callee: "trgt_genotype"
2025-09-15 20:22:48.892 wdl.w:ptcp.w:call-trgt-18 INFO input :: job: "call-trgt_genotype", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-18/out/m84036_250809_035451_s4.bc2115.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-18/out/m84036_250809_035451_s4.bc2115.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2115"}
2025-09-15 20:22:48.892 wdl.w:ptcp.w:call-trgt-10 INFO input :: job: "call-trgt_genotype", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-10/out/m84036_250809_035451_s4.bc2107.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-10/out/m84036_250809_035451_s4.bc2107.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2107"}
2025-09-15 20:22:48.893 wdl.w:ptcp.w:call-sawfish-07.t:call-run_sawfish INFO provisioned :: seconds_waited: 0, cpu: 16, mem_bytes: 32000000000
2025-09-15 20:22:48.893 wdl.w:ptcp.w:call-sawfish-07.t:call-run_sawfish INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:22:48.907 wdl.w:ptcp.t:call-pbmm2_align_hifi-11 NOTICE done
2025-09-15 20:22:48.914 wdl.w:ptcp NOTICE finish :: job: "call-pbmm2_align_hifi-11"
2025-09-15 20:22:48.914 wdl.w:ptcp INFO output :: job: "call-pbmm2_align_hifi-11", values: {"report": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-11/out/mapping_stats.report.json", "mapped_bam_pbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-11/out/m84036_250809_035451_s4.bc2108.mapped.bam.pbi", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-11/out/m84036_250809_035451_s4.bc2108.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-11/out/m84036_250809_035451_s4.bc2108.mapped.bam"}
2025-09-15 20:22:48.915 wdl.w:ptcp NOTICE ready :: job: "call-paraphase-11", callee: "paraphase"
2025-09-15 20:22:48.915 wdl.w:ptcp INFO input :: job: "call-paraphase-11", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf", "genome_version": "38", "config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-11/out/m84036_250809_035451_s4.bc2108.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-11/out/m84036_250809_035451_s4.bc2108.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2108"}
2025-09-15 20:22:48.916 wdl.w:ptcp NOTICE ready :: job: "call-sawfish-11", callee: "sawfish"
2025-09-15 20:22:48.916 wdl.w:ptcp INFO input :: job: "call-sawfish-11", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-11/out/m84036_250809_035451_s4.bc2108.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-11/out/m84036_250809_035451_s4.bc2108.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2108"}
2025-09-15 20:22:48.920 wdl.w:ptcp NOTICE ready :: job: "call-trgt-11", callee: "trgt"
2025-09-15 20:22:48.920 wdl.w:ptcp INFO input :: job: "call-trgt-11", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-11/out/m84036_250809_035451_s4.bc2108.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-11/out/m84036_250809_035451_s4.bc2108.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2108"}
2025-09-15 20:22:48.924 wdl.w:ptcp.w:call-paraphase-11 NOTICE workflow start :: name: "paraphase", source: "./paraphase.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-11"
2025-09-15 20:22:48.925 wdl.w:ptcp.w:call-paraphase-07.t:call-run_paraphase NOTICE task setup :: name: "run_paraphase", source: "./paraphase.wdl", line: 127, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-07/call-run_paraphase", thread: 140613051733568
2025-09-15 20:22:48.928 wdl.w:ptcp.w:call-sawfish-11 NOTICE workflow start :: name: "sawfish", source: "./sawfish.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-11"
2025-09-15 20:22:48.937 wdl.w:ptcp.w:call-trgt-11 NOTICE workflow start :: name: "trgt", source: "./trgt.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-11"
2025-09-15 20:22:48.948 wdl.w:ptcp.w:call-paraphase-11 INFO visit :: node: "decl-annotation_vcf", values: {"annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf"}
2025-09-15 20:22:48.948 wdl.w:ptcp.w:call-paraphase-11 INFO visit :: node: "decl-config_file", values: {"config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml"}
2025-09-15 20:22:48.949 wdl.w:ptcp.w:call-paraphase-11 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:22:48.949 wdl.w:ptcp.w:call-paraphase-11 INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:22:48.949 wdl.w:ptcp.w:call-paraphase-11 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-11/out/m84036_250809_035451_s4.bc2108.mapped.bam"}
2025-09-15 20:22:48.950 wdl.w:ptcp.w:call-paraphase-11 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-11/out/m84036_250809_035451_s4.bc2108.mapped.bam.bai"}
2025-09-15 20:22:48.950 wdl.w:ptcp.w:call-paraphase-11 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:22:48.950 wdl.w:ptcp.w:call-paraphase-11 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:22:48.951 wdl.w:ptcp.w:call-paraphase-11 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2108"}
2025-09-15 20:22:48.951 wdl.w:ptcp.w:call-trgt-07.t:call-get_reads_overlapping_repeats INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 9, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-07/call-get_reads_overlapping_repeats/_singularity_tmpdir_he_lbarf"
2025-09-15 20:22:48.952 wdl.w:ptcp.w:call-paraphase-11 INFO visit :: node: "decl-sex", values: {"sex": "F"}
2025-09-15 20:22:48.952 wdl.w:ptcp.w:call-trgt-07.t:call-get_reads_overlapping_repeats INFO Slurm invocation: srun --job-name call-get_reads_overlapping_repeats --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-07/call-get_reads_overlapping_repeats/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-07/call-get_reads_overlapping_repeats/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-07/call-get_reads_overlapping_repeats/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-07/call-get_reads_overlapping_repeats/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-07/out/m84036_250809_035451_s4.bc2104.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2104.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-07/out/m84036_250809_035451_s4.bc2104.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2104.mapped.bam:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-07/call-get_reads_overlapping_repeats/_singularity_tmpdir_he_lbarf/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-07/call-get_reads_overlapping_repeats/_singularity_tmpdir_he_lbarf/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:22:48.953 wdl.w:ptcp.w:call-paraphase-11 NOTICE ready :: job: "call-run_paraphase", callee: "run_paraphase"
2025-09-15 20:22:48.953 wdl.w:ptcp.w:call-paraphase-11 INFO input :: job: "call-run_paraphase", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf", "genome_version": "38", "config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-11/out/m84036_250809_035451_s4.bc2108.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-11/out/m84036_250809_035451_s4.bc2108.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2108"}
2025-09-15 20:22:48.957 wdl.w:ptcp.w:call-sawfish-11 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:22:48.958 wdl.w:ptcp.w:call-sawfish-11 INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:22:48.958 wdl.w:ptcp.w:call-sawfish-11 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-11/out/m84036_250809_035451_s4.bc2108.mapped.bam"}
2025-09-15 20:22:48.958 wdl.w:ptcp.w:call-sawfish-11 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-11/out/m84036_250809_035451_s4.bc2108.mapped.bam.bai"}
2025-09-15 20:22:48.958 wdl.w:ptcp.w:call-sawfish-11 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:22:48.959 wdl.w:ptcp.w:call-sawfish-11 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:22:48.959 wdl.w:ptcp.w:call-sawfish-11 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2108"}
2025-09-15 20:22:48.959 wdl.w:ptcp.w:call-sawfish-11 NOTICE ready :: job: "call-run_sawfish", callee: "run_sawfish"
2025-09-15 20:22:48.959 wdl.w:ptcp.w:call-sawfish-11 INFO input :: job: "call-run_sawfish", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-11/out/m84036_250809_035451_s4.bc2108.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-11/out/m84036_250809_035451_s4.bc2108.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2108"}
2025-09-15 20:22:48.960 wdl.w:ptcp.w:call-paraphase-07.t:call-run_paraphase INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:22:48.960 wdl.w:ptcp.w:call-paraphase-07.t:call-run_paraphase INFO input :: name: "annotation_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf"
2025-09-15 20:22:48.960 wdl.w:ptcp.w:call-paraphase-07.t:call-run_paraphase INFO input :: name: "genome_version", value: "38"
2025-09-15 20:22:48.960 wdl.w:ptcp.w:call-paraphase-07.t:call-run_paraphase INFO input :: name: "config_file", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/paraphase_config.GRCh38.yaml"
2025-09-15 20:22:48.960 wdl.w:ptcp.w:call-paraphase-07.t:call-run_paraphase INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:22:48.960 wdl.w:ptcp.w:call-paraphase-07.t:call-run_paraphase INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:22:48.961 wdl.w:ptcp.w:call-paraphase-07.t:call-run_paraphase INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2104.mapped.bam.bai"
2025-09-15 20:22:48.961 wdl.w:ptcp.w:call-paraphase-07.t:call-run_paraphase INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2104.mapped.bam"
2025-09-15 20:22:48.961 wdl.w:ptcp.w:call-paraphase-07.t:call-run_paraphase INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2104"
2025-09-15 20:22:48.961 wdl.w:ptcp.w:call-paraphase-07.t:call-run_paraphase INFO eval :: name: "threads", value: 4
2025-09-15 20:22:48.961 wdl.w:ptcp.w:call-paraphase-07.t:call-run_paraphase INFO eval :: name: "mem_gb", value: 8
2025-09-15 20:22:48.962 wdl.w:ptcp.w:call-paraphase-07.t:call-run_paraphase INFO eval :: name: "disk_size", value: 27
2025-09-15 20:22:48.963 wdl.w:ptcp.w:call-trgt-11 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:22:48.963 wdl.w:ptcp.w:call-paraphase-07.t:call-run_paraphase INFO eval :: name: "out_dir", value: "m84036_250809_035451_s4.bc2104_paraphase"
2025-09-15 20:22:48.963 wdl.w:ptcp.w:call-trgt-11 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-11/out/m84036_250809_035451_s4.bc2108.mapped.bam"}
2025-09-15 20:22:48.964 wdl.w:ptcp.w:call-paraphase-07.t:call-run_paraphase INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 4, memory_reservation: 8000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:22:48.964 wdl.w:ptcp.w:call-trgt-11 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-11/out/m84036_250809_035451_s4.bc2108.mapped.bam.bai"}
2025-09-15 20:22:48.964 wdl.w:ptcp.w:call-paraphase-07.t:call-run_paraphase WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:22:48.964 wdl.w:ptcp.w:call-trgt-11 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:22:48.964 wdl.w:ptcp.w:call-trgt-11 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:22:48.964 wdl.w:ptcp.w:call-trgt-11 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2108"}
2025-09-15 20:22:48.965 wdl.w:ptcp.w:call-trgt-11 INFO visit :: node: "decl-sex", values: {"sex": "F"}
2025-09-15 20:22:48.965 wdl.w:ptcp.w:call-trgt-11 INFO visit :: node: "decl-trgt_bed", values: {"trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"}
2025-09-15 20:22:48.965 wdl.w:ptcp.w:call-trgt-11 NOTICE ready :: job: "call-get_reads_overlapping_repeats", callee: "get_reads_overlapping_repeats"
2025-09-15 20:22:48.965 wdl.w:ptcp.w:call-paraphase-07.t:call-run_paraphase INFO provisioned :: seconds_waited: 0, cpu: 4, mem_bytes: 8000000000
2025-09-15 20:22:48.966 wdl.w:ptcp.w:call-trgt-11 INFO input :: job: "call-get_reads_overlapping_repeats", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-11/out/m84036_250809_035451_s4.bc2108.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-11/out/m84036_250809_035451_s4.bc2108.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2108"}
2025-09-15 20:22:48.966 wdl.w:ptcp.w:call-paraphase-07.t:call-run_paraphase INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:22:48.966 wdl.w:ptcp.w:call-trgt-11 NOTICE ready :: job: "call-trgt_genotype", callee: "trgt_genotype"
2025-09-15 20:22:48.967 wdl.w:ptcp.w:call-trgt-11 INFO input :: job: "call-trgt_genotype", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-11/out/m84036_250809_035451_s4.bc2108.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-11/out/m84036_250809_035451_s4.bc2108.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2108"}
2025-09-15 20:22:48.972 wdl.w:ptcp.w:call-sawfish-07.t:call-run_sawfish INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 10, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-07/call-run_sawfish/_singularity_tmpdir_7xhffg1n"
2025-09-15 20:22:48.972 wdl.w:ptcp.w:call-sawfish-07.t:call-run_sawfish INFO Slurm invocation: srun --job-name call-run_sawfish --partition compute,compute9 --cpus-per-task 16 --mem 30518M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-07/call-run_sawfish/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-07/call-run_sawfish/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-07/call-run_sawfish/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-07/call-run_sawfish/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-07/out/m84036_250809_035451_s4.bc2104.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2104.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-07/out/m84036_250809_035451_s4.bc2104.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2104.mapped.bam:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-07/call-run_sawfish/_singularity_tmpdir_7xhffg1n/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-07/call-run_sawfish/_singularity_tmpdir_7xhffg1n/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:22:48.976 wdl.w:ptcp.t:call-pbmm2_align_hifi-19 NOTICE done
2025-09-15 20:22:48.984 wdl.w:ptcp NOTICE finish :: job: "call-pbmm2_align_hifi-19"
2025-09-15 20:22:48.985 wdl.w:ptcp INFO output :: job: "call-pbmm2_align_hifi-19", values: {"report": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-19/out/mapping_stats.report.json", "mapped_bam_pbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-19/out/m84036_250809_035451_s4.bc2116.mapped.bam.pbi", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-19/out/m84036_250809_035451_s4.bc2116.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-19/out/m84036_250809_035451_s4.bc2116.mapped.bam"}
2025-09-15 20:22:48.985 wdl.w:ptcp NOTICE ready :: job: "call-paraphase-19", callee: "paraphase"
2025-09-15 20:22:48.985 wdl.w:ptcp INFO input :: job: "call-paraphase-19", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf", "genome_version": "38", "config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-19/out/m84036_250809_035451_s4.bc2116.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-19/out/m84036_250809_035451_s4.bc2116.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2116"}
2025-09-15 20:22:48.987 wdl.w:ptcp NOTICE ready :: job: "call-sawfish-19", callee: "sawfish"
2025-09-15 20:22:48.987 wdl.w:ptcp INFO input :: job: "call-sawfish-19", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-19/out/m84036_250809_035451_s4.bc2116.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-19/out/m84036_250809_035451_s4.bc2116.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2116"}
2025-09-15 20:22:48.990 wdl.w:ptcp NOTICE ready :: job: "call-trgt-19", callee: "trgt"
2025-09-15 20:22:48.990 wdl.w:ptcp INFO input :: job: "call-trgt-19", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-19/out/m84036_250809_035451_s4.bc2116.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-19/out/m84036_250809_035451_s4.bc2116.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2116"}
2025-09-15 20:22:48.993 wdl.w:ptcp.w:call-sawfish-07.t:call-run_sawfish NOTICE slurm_singularity run :: pid: 1198163, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-07/call-run_sawfish/slurm_singularity.log.txt"
2025-09-15 20:22:48.993 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_genotype NOTICE task setup :: name: "trgt_genotype", source: "./trgt.wdl", line: 272, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-07/call-trgt_genotype", thread: 140612506469952
2025-09-15 20:22:48.993 wdl.w:ptcp.w:call-trgt-07.t:call-get_reads_overlapping_repeats NOTICE slurm_singularity run :: pid: 1198162, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-07/call-get_reads_overlapping_repeats/slurm_singularity.log.txt"
2025-09-15 20:22:48.994 wdl.w:ptcp.w:call-paraphase-19 NOTICE workflow start :: name: "paraphase", source: "./paraphase.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-19"
2025-09-15 20:22:48.997 wdl.w:ptcp.w:call-sawfish-19 NOTICE workflow start :: name: "sawfish", source: "./sawfish.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-19"
2025-09-15 20:22:49.002 wdl.w:ptcp.w:call-trgt-19 NOTICE workflow start :: name: "trgt", source: "./trgt.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-19"
2025-09-15 20:22:49.021 wdl.w:ptcp.w:call-paraphase-19 INFO visit :: node: "decl-annotation_vcf", values: {"annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf"}
2025-09-15 20:22:49.021 wdl.w:ptcp.w:call-paraphase-19 INFO visit :: node: "decl-config_file", values: {"config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml"}
2025-09-15 20:22:49.021 wdl.w:ptcp.w:call-paraphase-19 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:22:49.021 wdl.w:ptcp.w:call-paraphase-19 INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:22:49.022 wdl.w:ptcp.w:call-paraphase-19 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-19/out/m84036_250809_035451_s4.bc2116.mapped.bam"}
2025-09-15 20:22:49.022 wdl.w:ptcp.w:call-paraphase-19 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-19/out/m84036_250809_035451_s4.bc2116.mapped.bam.bai"}
2025-09-15 20:22:49.022 wdl.w:ptcp.w:call-paraphase-19 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:22:49.022 wdl.w:ptcp.w:call-paraphase-19 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:22:49.023 wdl.w:ptcp.w:call-paraphase-19 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2116"}
2025-09-15 20:22:49.023 wdl.w:ptcp.w:call-sawfish-19 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:22:49.023 wdl.w:ptcp.w:call-paraphase-19 INFO visit :: node: "decl-sex", values: {"sex": "F"}
2025-09-15 20:22:49.023 wdl.w:ptcp.w:call-sawfish-19 INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:22:49.024 wdl.w:ptcp.w:call-paraphase-19 NOTICE ready :: job: "call-run_paraphase", callee: "run_paraphase"
2025-09-15 20:22:49.024 wdl.w:ptcp.w:call-sawfish-19 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-19/out/m84036_250809_035451_s4.bc2116.mapped.bam"}
2025-09-15 20:22:49.024 wdl.w:ptcp.w:call-paraphase-19 INFO input :: job: "call-run_paraphase", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf", "genome_version": "38", "config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-19/out/m84036_250809_035451_s4.bc2116.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-19/out/m84036_250809_035451_s4.bc2116.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2116"}
2025-09-15 20:22:49.025 wdl.w:ptcp.w:call-sawfish-19 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-19/out/m84036_250809_035451_s4.bc2116.mapped.bam.bai"}
2025-09-15 20:22:49.025 wdl.w:ptcp.w:call-sawfish-19 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:22:49.026 wdl.w:ptcp.w:call-sawfish-19 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:22:49.025 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_genotype INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:22:49.026 wdl.w:ptcp.w:call-trgt-19 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:22:49.026 wdl.w:ptcp.w:call-sawfish-19 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2116"}
2025-09-15 20:22:49.027 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_genotype INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:22:49.027 wdl.w:ptcp.w:call-trgt-19 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-19/out/m84036_250809_035451_s4.bc2116.mapped.bam"}
2025-09-15 20:22:49.027 wdl.w:ptcp.w:call-sawfish-19 NOTICE ready :: job: "call-run_sawfish", callee: "run_sawfish"
2025-09-15 20:22:49.027 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_genotype INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:22:49.027 wdl.w:ptcp.w:call-trgt-19 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-19/out/m84036_250809_035451_s4.bc2116.mapped.bam.bai"}
2025-09-15 20:22:49.028 wdl.w:ptcp.w:call-sawfish-19 INFO input :: job: "call-run_sawfish", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-19/out/m84036_250809_035451_s4.bc2116.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-19/out/m84036_250809_035451_s4.bc2116.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2116"}
2025-09-15 20:22:49.028 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_genotype INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:22:49.028 wdl.w:ptcp.w:call-trgt-19 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:22:49.028 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_genotype INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2104.mapped.bam.bai"
2025-09-15 20:22:49.028 wdl.w:ptcp.w:call-trgt-19 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:22:49.028 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_genotype INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2104.mapped.bam"
2025-09-15 20:22:49.028 wdl.w:ptcp.w:call-trgt-19 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2116"}
2025-09-15 20:22:49.029 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_genotype INFO input :: name: "sex", value: "F"
2025-09-15 20:22:49.029 wdl.w:ptcp.w:call-trgt-19 INFO visit :: node: "decl-sex", values: {"sex": "F"}
2025-09-15 20:22:49.029 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_genotype INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2104"
2025-09-15 20:22:49.029 wdl.w:ptcp.w:call-trgt-19 INFO visit :: node: "decl-trgt_bed", values: {"trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"}
2025-09-15 20:22:49.029 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_genotype INFO eval :: name: "mem_gb", value: 16
2025-09-15 20:22:49.030 wdl.w:ptcp.w:call-trgt-19 NOTICE ready :: job: "call-get_reads_overlapping_repeats", callee: "get_reads_overlapping_repeats"
2025-09-15 20:22:49.030 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_genotype INFO eval :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2104.trgt"
2025-09-15 20:22:49.030 wdl.w:ptcp.w:call-trgt-19 INFO input :: job: "call-get_reads_overlapping_repeats", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-19/out/m84036_250809_035451_s4.bc2116.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-19/out/m84036_250809_035451_s4.bc2116.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2116"}
2025-09-15 20:22:49.030 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_genotype INFO eval :: name: "threads", value: 8
2025-09-15 20:22:49.030 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_genotype INFO eval :: name: "disk_size", value: 27
2025-09-15 20:22:49.031 wdl.w:ptcp.w:call-trgt-19 NOTICE ready :: job: "call-trgt_genotype", callee: "trgt_genotype"
2025-09-15 20:22:49.031 wdl.w:ptcp.w:call-trgt-19 INFO input :: job: "call-trgt_genotype", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-19/out/m84036_250809_035451_s4.bc2116.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-19/out/m84036_250809_035451_s4.bc2116.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2116"}
2025-09-15 20:22:49.031 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_genotype INFO eval :: name: "karyotype", value: "XX"
2025-09-15 20:22:49.032 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_genotype INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 8, memory_reservation: 16000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:22:49.032 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_genotype WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:22:49.032 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_genotype INFO provisioned :: seconds_waited: 0, cpu: 8, mem_bytes: 16000000000
2025-09-15 20:22:49.032 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_genotype INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:22:49.048 wdl.w:ptcp.w:call-paraphase-07.t:call-run_paraphase INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-07/call-run_paraphase/_singularity_tmpdir_br19ofto"
2025-09-15 20:22:49.048 wdl.w:ptcp.w:call-paraphase-07.t:call-run_paraphase INFO Slurm invocation: srun --job-name call-run_paraphase --partition compute,compute9 --cpus-per-task 4 --mem 7629M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-07/call-run_paraphase/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-07/call-run_paraphase/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-07/call-run_paraphase/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-07/call-run_paraphase/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/variant_list/variant_list.GRCh38.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-07/out/m84036_250809_035451_s4.bc2104.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2104.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-07/out/m84036_250809_035451_s4.bc2104.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2104.mapped.bam:ro --bind /ptcp/meta/paraphase/paraphase_config.GRCh38.yaml:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/paraphase_config.GRCh38.yaml:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-07/call-run_paraphase/_singularity_tmpdir_br19ofto/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-07/call-run_paraphase/_singularity_tmpdir_br19ofto/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:22:49.070 wdl.w:ptcp.w:call-paraphase-07.t:call-run_paraphase NOTICE slurm_singularity run :: pid: 1198171, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-07/call-run_paraphase/slurm_singularity.log.txt"
2025-09-15 20:22:49.088 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_genotype INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 11, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-07/call-trgt_genotype/_singularity_tmpdir_n3lrjczl"
2025-09-15 20:22:49.088 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_genotype INFO Slurm invocation: srun --job-name call-trgt_genotype --partition compute,compute9 --cpus-per-task 8 --mem 15259M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-07/call-trgt_genotype/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-07/call-trgt_genotype/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-07/call-trgt_genotype/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-07/call-trgt_genotype/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-07/out/m84036_250809_035451_s4.bc2104.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2104.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-07/out/m84036_250809_035451_s4.bc2104.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2104.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-07/call-trgt_genotype/_singularity_tmpdir_n3lrjczl/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-07/call-trgt_genotype/_singularity_tmpdir_n3lrjczl/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:22:49.095 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_genotype NOTICE slurm_singularity run :: pid: 1198183, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-07/call-trgt_genotype/slurm_singularity.log.txt"
2025-09-15 20:22:49.115 wdl.w:ptcp.t:call-pbmm2_align_hifi-17 INFO output :: name: "mapped_bam", value: "m84036_250809_035451_s4.bc2114.mapped.bam"
2025-09-15 20:22:49.119 wdl.w:ptcp.t:call-pbmm2_align_hifi-17 INFO output :: name: "mapped_bam_bai", value: "m84036_250809_035451_s4.bc2114.mapped.bam.bai"
2025-09-15 20:22:49.120 wdl.w:ptcp.t:call-pbmm2_align_hifi-17 INFO output :: name: "mapped_bam_pbi", value: "m84036_250809_035451_s4.bc2114.mapped.bam.pbi"
2025-09-15 20:22:49.121 wdl.w:ptcp.t:call-pbmm2_align_hifi-17 INFO output :: name: "report", value: "mapping_stats.report.json"
2025-09-15 20:22:49.130 wdl.w:ptcp.t:call-pbmm2_align_hifi-21 INFO output :: name: "mapped_bam", value: "m84036_250809_035451_s4.bc2118.mapped.bam"
2025-09-15 20:22:49.133 wdl.w:ptcp.t:call-pbmm2_align_hifi-21 INFO output :: name: "mapped_bam_bai", value: "m84036_250809_035451_s4.bc2118.mapped.bam.bai"
2025-09-15 20:22:49.134 wdl.w:ptcp.t:call-pbmm2_align_hifi-21 INFO output :: name: "mapped_bam_pbi", value: "m84036_250809_035451_s4.bc2118.mapped.bam.pbi"
2025-09-15 20:22:49.136 wdl.w:ptcp.t:call-pbmm2_align_hifi-21 INFO output :: name: "report", value: "mapping_stats.report.json"
2025-09-15 20:22:49.139 wdl.w:ptcp.w:call-sawfish-15.t:call-run_sawfish.slurm_singularity INFO srun: job 51797329 queued and waiting for resources
2025-09-15 20:22:49.164 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_genotype.slurm_singularity INFO srun: job 51797330 queued and waiting for resources
2025-09-15 20:22:49.203 wdl.w:ptcp.t:call-pbmm2_align_hifi-17 NOTICE done
2025-09-15 20:22:49.210 wdl.w:ptcp NOTICE finish :: job: "call-pbmm2_align_hifi-17"
2025-09-15 20:22:49.211 wdl.w:ptcp INFO output :: job: "call-pbmm2_align_hifi-17", values: {"report": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-17/out/mapping_stats.report.json", "mapped_bam_pbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-17/out/m84036_250809_035451_s4.bc2114.mapped.bam.pbi", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-17/out/m84036_250809_035451_s4.bc2114.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-17/out/m84036_250809_035451_s4.bc2114.mapped.bam"}
2025-09-15 20:22:49.211 wdl.w:ptcp NOTICE ready :: job: "call-paraphase-17", callee: "paraphase"
2025-09-15 20:22:49.212 wdl.w:ptcp INFO input :: job: "call-paraphase-17", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf", "genome_version": "38", "config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-17/out/m84036_250809_035451_s4.bc2114.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-17/out/m84036_250809_035451_s4.bc2114.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2114"}
2025-09-15 20:22:49.213 wdl.w:ptcp NOTICE ready :: job: "call-sawfish-17", callee: "sawfish"
2025-09-15 20:22:49.213 wdl.w:ptcp INFO input :: job: "call-sawfish-17", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-17/out/m84036_250809_035451_s4.bc2114.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-17/out/m84036_250809_035451_s4.bc2114.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2114"}
2025-09-15 20:22:49.217 wdl.w:ptcp NOTICE ready :: job: "call-trgt-17", callee: "trgt"
2025-09-15 20:22:49.217 wdl.w:ptcp INFO input :: job: "call-trgt-17", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-17/out/m84036_250809_035451_s4.bc2114.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-17/out/m84036_250809_035451_s4.bc2114.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2114"}
2025-09-15 20:22:49.220 wdl.w:ptcp.w:call-paraphase-04.t:call-run_paraphase NOTICE task setup :: name: "run_paraphase", source: "./paraphase.wdl", line: 127, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-04/call-run_paraphase", thread: 140612523255360
2025-09-15 20:22:49.221 wdl.w:ptcp.w:call-paraphase-17 NOTICE workflow start :: name: "paraphase", source: "./paraphase.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-17"
2025-09-15 20:22:49.221 wdl.w:ptcp.t:call-pbmm2_align_hifi-21 NOTICE done
2025-09-15 20:22:49.228 wdl.w:ptcp.w:call-sawfish-17 NOTICE workflow start :: name: "sawfish", source: "./sawfish.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-17"
2025-09-15 20:22:49.230 wdl.w:ptcp NOTICE finish :: job: "call-pbmm2_align_hifi-21"
2025-09-15 20:22:49.230 wdl.w:ptcp INFO output :: job: "call-pbmm2_align_hifi-21", values: {"report": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-21/out/mapping_stats.report.json", "mapped_bam_pbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-21/out/m84036_250809_035451_s4.bc2118.mapped.bam.pbi", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-21/out/m84036_250809_035451_s4.bc2118.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-21/out/m84036_250809_035451_s4.bc2118.mapped.bam"}
2025-09-15 20:22:49.230 wdl.w:ptcp NOTICE ready :: job: "call-paraphase-21", callee: "paraphase"
2025-09-15 20:22:49.230 wdl.w:ptcp INFO input :: job: "call-paraphase-21", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf", "genome_version": "38", "config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-21/out/m84036_250809_035451_s4.bc2118.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-21/out/m84036_250809_035451_s4.bc2118.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2118"}
2025-09-15 20:22:49.232 wdl.w:ptcp NOTICE ready :: job: "call-sawfish-21", callee: "sawfish"
2025-09-15 20:22:49.232 wdl.w:ptcp INFO input :: job: "call-sawfish-21", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-21/out/m84036_250809_035451_s4.bc2118.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-21/out/m84036_250809_035451_s4.bc2118.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2118"}
2025-09-15 20:22:49.232 wdl.w:ptcp.w:call-trgt-17 NOTICE workflow start :: name: "trgt", source: "./trgt.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-17"
2025-09-15 20:22:49.240 wdl.w:ptcp NOTICE ready :: job: "call-trgt-21", callee: "trgt"
2025-09-15 20:22:49.240 wdl.w:ptcp INFO input :: job: "call-trgt-21", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-21/out/m84036_250809_035451_s4.bc2118.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-21/out/m84036_250809_035451_s4.bc2118.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2118"}
2025-09-15 20:22:49.241 wdl.w:ptcp.w:call-sawfish-04.t:call-run_sawfish NOTICE task setup :: name: "run_sawfish", source: "./sawfish.wdl", line: 83, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-04/call-run_sawfish", thread: 140612489684544
2025-09-15 20:22:49.246 wdl.w:ptcp.w:call-paraphase-21 NOTICE workflow start :: name: "paraphase", source: "./paraphase.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-21"
2025-09-15 20:22:49.247 wdl.w:ptcp.w:call-paraphase-04.t:call-run_paraphase INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:22:49.247 wdl.w:ptcp.w:call-paraphase-04.t:call-run_paraphase INFO input :: name: "annotation_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf"
2025-09-15 20:22:49.248 wdl.w:ptcp.w:call-sawfish-21 NOTICE workflow start :: name: "sawfish", source: "./sawfish.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-21"
2025-09-15 20:22:49.248 wdl.w:ptcp.w:call-paraphase-04.t:call-run_paraphase INFO input :: name: "genome_version", value: "38"
2025-09-15 20:22:49.249 wdl.w:ptcp.w:call-paraphase-04.t:call-run_paraphase INFO input :: name: "config_file", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/paraphase_config.GRCh38.yaml"
2025-09-15 20:22:49.250 wdl.w:ptcp.w:call-paraphase-04.t:call-run_paraphase INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:22:49.250 wdl.w:ptcp.w:call-paraphase-04.t:call-run_paraphase INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:22:49.251 wdl.w:ptcp.w:call-paraphase-04.t:call-run_paraphase INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2101.mapped.bam.bai"
2025-09-15 20:22:49.251 wdl.w:ptcp.w:call-paraphase-04.t:call-run_paraphase INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2101.mapped.bam"
2025-09-15 20:22:49.252 wdl.w:ptcp.w:call-paraphase-04.t:call-run_paraphase INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2101"
2025-09-15 20:22:49.252 wdl.w:ptcp.w:call-paraphase-04.t:call-run_paraphase INFO eval :: name: "threads", value: 4
2025-09-15 20:22:49.253 wdl.w:ptcp.w:call-paraphase-04.t:call-run_paraphase INFO eval :: name: "mem_gb", value: 8
2025-09-15 20:22:49.253 wdl.w:ptcp.w:call-paraphase-17 INFO visit :: node: "decl-annotation_vcf", values: {"annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf"}
2025-09-15 20:22:49.254 wdl.w:ptcp.w:call-paraphase-17 INFO visit :: node: "decl-config_file", values: {"config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml"}
2025-09-15 20:22:49.255 wdl.w:ptcp.w:call-paraphase-17 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:22:49.255 wdl.w:ptcp.w:call-paraphase-04.t:call-run_paraphase INFO eval :: name: "disk_size", value: 27
2025-09-15 20:22:49.255 wdl.w:ptcp.w:call-paraphase-17 INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:22:49.256 wdl.w:ptcp.w:call-paraphase-17 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-17/out/m84036_250809_035451_s4.bc2114.mapped.bam"}
2025-09-15 20:22:49.257 wdl.w:ptcp.w:call-trgt-21 NOTICE workflow start :: name: "trgt", source: "./trgt.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-21"
2025-09-15 20:22:49.256 wdl.w:ptcp.w:call-paraphase-04.t:call-run_paraphase INFO eval :: name: "out_dir", value: "m84036_250809_035451_s4.bc2101_paraphase"
2025-09-15 20:22:49.257 wdl.w:ptcp.w:call-paraphase-17 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-17/out/m84036_250809_035451_s4.bc2114.mapped.bam.bai"}
2025-09-15 20:22:49.261 wdl.w:ptcp.w:call-paraphase-17 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:22:49.261 wdl.w:ptcp.w:call-sawfish-17 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:22:49.263 wdl.w:ptcp.w:call-paraphase-04.t:call-run_paraphase INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 4, memory_reservation: 8000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:22:49.263 wdl.w:ptcp.t:call-pbmm2_align_hifi-33 INFO output :: name: "mapped_bam", value: "m84036_250809_035451_s4.bc2130.mapped.bam"
2025-09-15 20:22:49.264 wdl.w:ptcp.w:call-paraphase-17 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:22:49.265 wdl.w:ptcp.w:call-sawfish-17 INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:22:49.266 wdl.w:ptcp.t:call-pbmm2_align_hifi-30 INFO output :: name: "mapped_bam", value: "m84036_250809_035451_s4.bc2127.mapped.bam"
2025-09-15 20:22:49.266 wdl.w:ptcp.w:call-paraphase-04.t:call-run_paraphase WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:22:49.268 wdl.w:ptcp.w:call-paraphase-17 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2114"}
2025-09-15 20:22:49.268 wdl.w:ptcp.w:call-sawfish-17 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-17/out/m84036_250809_035451_s4.bc2114.mapped.bam"}
2025-09-15 20:22:49.269 wdl.w:ptcp.w:call-trgt-17 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:22:49.270 wdl.w:ptcp.w:call-paraphase-17 INFO visit :: node: "decl-sex", values: {"sex": "F"}
2025-09-15 20:22:49.272 wdl.w:ptcp.w:call-sawfish-17 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-17/out/m84036_250809_035451_s4.bc2114.mapped.bam.bai"}
2025-09-15 20:22:49.273 wdl.w:ptcp.w:call-trgt-17 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-17/out/m84036_250809_035451_s4.bc2114.mapped.bam"}
2025-09-15 20:22:49.274 wdl.w:ptcp.w:call-paraphase-17 NOTICE ready :: job: "call-run_paraphase", callee: "run_paraphase"
2025-09-15 20:22:49.275 wdl.w:ptcp.w:call-sawfish-17 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:22:49.278 wdl.w:ptcp.w:call-trgt-17 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-17/out/m84036_250809_035451_s4.bc2114.mapped.bam.bai"}
2025-09-15 20:22:49.278 wdl.w:ptcp.t:call-pbmm2_align_hifi-33 INFO output :: name: "mapped_bam_bai", value: "m84036_250809_035451_s4.bc2130.mapped.bam.bai"
2025-09-15 20:22:49.280 wdl.w:ptcp.t:call-pbmm2_align_hifi-30 INFO output :: name: "mapped_bam_bai", value: "m84036_250809_035451_s4.bc2127.mapped.bam.bai"
2025-09-15 20:22:49.279 wdl.w:ptcp.w:call-paraphase-17 INFO input :: job: "call-run_paraphase", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf", "genome_version": "38", "config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-17/out/m84036_250809_035451_s4.bc2114.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-17/out/m84036_250809_035451_s4.bc2114.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2114"}
2025-09-15 20:22:49.280 wdl.w:ptcp.w:call-sawfish-17 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:22:49.281 wdl.w:ptcp.w:call-paraphase-04.t:call-run_paraphase INFO provisioned :: seconds_waited: 0, cpu: 4, mem_bytes: 8000000000
2025-09-15 20:22:49.281 wdl.w:ptcp.w:call-trgt-17 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:22:49.283 wdl.w:ptcp.w:call-sawfish-04.t:call-run_sawfish INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:22:49.284 wdl.w:ptcp.t:call-pbmm2_align_hifi-06 INFO output :: name: "mapped_bam", value: "m84036_250809_035451_s4.bc2103.mapped.bam"
2025-09-15 20:22:49.284 wdl.w:ptcp.w:call-sawfish-17 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2114"}
2025-09-15 20:22:49.285 wdl.w:ptcp.w:call-paraphase-04.t:call-run_paraphase INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:22:49.285 wdl.w:ptcp.w:call-trgt-17 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:22:49.286 wdl.w:ptcp.w:call-sawfish-04.t:call-run_sawfish INFO input :: name: "genome_version", value: "38"
2025-09-15 20:22:49.287 wdl.w:ptcp.w:call-sawfish-17 NOTICE ready :: job: "call-run_sawfish", callee: "run_sawfish"
2025-09-15 20:22:49.288 wdl.w:ptcp.w:call-paraphase-21 INFO visit :: node: "decl-annotation_vcf", values: {"annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf"}
2025-09-15 20:22:49.289 wdl.w:ptcp.t:call-pbmm2_align_hifi-33 INFO output :: name: "mapped_bam_pbi", value: "m84036_250809_035451_s4.bc2130.mapped.bam.pbi"
2025-09-15 20:22:49.289 wdl.w:ptcp.t:call-pbmm2_align_hifi-30 INFO output :: name: "mapped_bam_pbi", value: "m84036_250809_035451_s4.bc2127.mapped.bam.pbi"
2025-09-15 20:22:49.290 wdl.w:ptcp.w:call-trgt-17 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2114"}
2025-09-15 20:22:49.290 wdl.w:ptcp.w:call-trgt-21 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:22:49.291 wdl.w:ptcp.w:call-sawfish-04.t:call-run_sawfish INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:22:49.291 wdl.w:ptcp.w:call-sawfish-17 INFO input :: job: "call-run_sawfish", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-17/out/m84036_250809_035451_s4.bc2114.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-17/out/m84036_250809_035451_s4.bc2114.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2114"}
2025-09-15 20:22:49.291 wdl.w:ptcp.w:call-paraphase-21 INFO visit :: node: "decl-config_file", values: {"config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml"}
2025-09-15 20:22:49.292 wdl.w:ptcp.w:call-sawfish-21 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:22:49.292 wdl.w:ptcp.w:call-trgt-17 INFO visit :: node: "decl-sex", values: {"sex": "F"}
2025-09-15 20:22:49.293 wdl.w:ptcp.w:call-trgt-21 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-21/out/m84036_250809_035451_s4.bc2118.mapped.bam"}
2025-09-15 20:22:49.293 wdl.w:ptcp.w:call-sawfish-04.t:call-run_sawfish INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:22:49.293 wdl.w:ptcp.t:call-pbmm2_align_hifi-06 INFO output :: name: "mapped_bam_bai", value: "m84036_250809_035451_s4.bc2103.mapped.bam.bai"
2025-09-15 20:22:49.293 wdl.w:ptcp.w:call-paraphase-21 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:22:49.294 wdl.w:ptcp.w:call-sawfish-21 INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:22:49.294 wdl.w:ptcp.w:call-trgt-17 INFO visit :: node: "decl-trgt_bed", values: {"trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"}
2025-09-15 20:22:49.294 wdl.w:ptcp.w:call-trgt-21 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-21/out/m84036_250809_035451_s4.bc2118.mapped.bam.bai"}
2025-09-15 20:22:49.295 wdl.w:ptcp.t:call-pbmm2_align_hifi-33 INFO output :: name: "report", value: "mapping_stats.report.json"
2025-09-15 20:22:49.295 wdl.w:ptcp.w:call-sawfish-04.t:call-run_sawfish INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2101.mapped.bam.bai"
2025-09-15 20:22:49.295 wdl.w:ptcp.w:call-paraphase-21 INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:22:49.296 wdl.w:ptcp.t:call-pbmm2_align_hifi-30 INFO output :: name: "report", value: "mapping_stats.report.json"
2025-09-15 20:22:49.296 wdl.w:ptcp.w:call-sawfish-21 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-21/out/m84036_250809_035451_s4.bc2118.mapped.bam"}
2025-09-15 20:22:49.296 wdl.w:ptcp.w:call-trgt-17 NOTICE ready :: job: "call-get_reads_overlapping_repeats", callee: "get_reads_overlapping_repeats"
2025-09-15 20:22:49.296 wdl.w:ptcp.w:call-trgt-21 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:22:49.296 wdl.w:ptcp.w:call-sawfish-04.t:call-run_sawfish INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2101.mapped.bam"
2025-09-15 20:22:49.297 wdl.w:ptcp.w:call-paraphase-21 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-21/out/m84036_250809_035451_s4.bc2118.mapped.bam"}
2025-09-15 20:22:49.297 wdl.w:ptcp.w:call-sawfish-21 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-21/out/m84036_250809_035451_s4.bc2118.mapped.bam.bai"}
2025-09-15 20:22:49.297 wdl.w:ptcp.w:call-trgt-17 INFO input :: job: "call-get_reads_overlapping_repeats", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-17/out/m84036_250809_035451_s4.bc2114.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-17/out/m84036_250809_035451_s4.bc2114.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2114"}
2025-09-15 20:22:49.297 wdl.w:ptcp.w:call-trgt-21 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:22:49.297 wdl.w:ptcp.w:call-sawfish-04.t:call-run_sawfish INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2101"
2025-09-15 20:22:49.298 wdl.w:ptcp.w:call-paraphase-21 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-21/out/m84036_250809_035451_s4.bc2118.mapped.bam.bai"}
2025-09-15 20:22:49.298 wdl.w:ptcp.t:call-pbmm2_align_hifi-06 INFO output :: name: "mapped_bam_pbi", value: "m84036_250809_035451_s4.bc2103.mapped.bam.pbi"
2025-09-15 20:22:49.298 wdl.w:ptcp.w:call-sawfish-21 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:22:49.299 wdl.w:ptcp.w:call-trgt-21 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2118"}
2025-09-15 20:22:49.299 wdl.w:ptcp.w:call-sawfish-04.t:call-run_sawfish INFO eval :: name: "mem_gb", value: 32
2025-09-15 20:22:49.299 wdl.w:ptcp.w:call-trgt-17 NOTICE ready :: job: "call-trgt_genotype", callee: "trgt_genotype"
2025-09-15 20:22:49.300 wdl.w:ptcp.w:call-paraphase-21 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:22:49.300 wdl.w:ptcp.w:call-sawfish-21 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:22:49.300 wdl.w:ptcp.w:call-trgt-21 INFO visit :: node: "decl-sex", values: {"sex": "F"}
2025-09-15 20:22:49.301 wdl.w:ptcp.w:call-sawfish-04.t:call-run_sawfish INFO eval :: name: "threads", value: 16
2025-09-15 20:22:49.301 wdl.w:ptcp.w:call-trgt-17 INFO input :: job: "call-trgt_genotype", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-17/out/m84036_250809_035451_s4.bc2114.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-17/out/m84036_250809_035451_s4.bc2114.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2114"}
2025-09-15 20:22:49.300 wdl.w:ptcp.t:call-pbmm2_align_hifi-05 INFO output :: name: "mapped_bam", value: "m84036_250809_035451_s4.bc2102.mapped.bam"
2025-09-15 20:22:49.301 wdl.w:ptcp.w:call-paraphase-21 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:22:49.301 wdl.w:ptcp.w:call-sawfish-21 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2118"}
2025-09-15 20:22:49.301 wdl.w:ptcp.w:call-trgt-21 INFO visit :: node: "decl-trgt_bed", values: {"trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"}
2025-09-15 20:22:49.302 wdl.w:ptcp.w:call-sawfish-04.t:call-run_sawfish INFO eval :: name: "disk_size", value: 30
2025-09-15 20:22:49.302 wdl.w:ptcp.w:call-paraphase-21 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2118"}
2025-09-15 20:22:49.303 wdl.w:ptcp.w:call-sawfish-21 NOTICE ready :: job: "call-run_sawfish", callee: "run_sawfish"
2025-09-15 20:22:49.303 wdl.w:ptcp.t:call-pbmm2_align_hifi-06 INFO output :: name: "report", value: "mapping_stats.report.json"
2025-09-15 20:22:49.303 wdl.w:ptcp.w:call-trgt-21 NOTICE ready :: job: "call-get_reads_overlapping_repeats", callee: "get_reads_overlapping_repeats"
2025-09-15 20:22:49.304 wdl.w:ptcp.w:call-sawfish-04.t:call-run_sawfish INFO eval :: name: "discover_dirname", value: "m84036_250809_035451_s4.bc2101_sawfish_discover"
2025-09-15 20:22:49.304 wdl.w:ptcp.w:call-paraphase-21 INFO visit :: node: "decl-sex", values: {"sex": "F"}
2025-09-15 20:22:49.304 wdl.w:ptcp.w:call-sawfish-21 INFO input :: job: "call-run_sawfish", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-21/out/m84036_250809_035451_s4.bc2118.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-21/out/m84036_250809_035451_s4.bc2118.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2118"}
2025-09-15 20:22:49.304 wdl.w:ptcp.w:call-trgt-21 INFO input :: job: "call-get_reads_overlapping_repeats", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-21/out/m84036_250809_035451_s4.bc2118.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-21/out/m84036_250809_035451_s4.bc2118.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2118"}
2025-09-15 20:22:49.305 wdl.w:ptcp.w:call-sawfish-04.t:call-run_sawfish INFO eval :: name: "call_dirname", value: "m84036_250809_035451_s4.bc2101_sawfish"
2025-09-15 20:22:49.305 wdl.w:ptcp.w:call-paraphase-21 NOTICE ready :: job: "call-run_paraphase", callee: "run_paraphase"
2025-09-15 20:22:49.306 wdl.w:ptcp.w:call-sawfish-04.t:call-run_sawfish INFO eval :: name: "minimap2_bam_filename", value: "m84036_250809_035451_s4.bc2101.minimap2.bam"
2025-09-15 20:22:49.307 wdl.w:ptcp.w:call-trgt-21 NOTICE ready :: job: "call-trgt_genotype", callee: "trgt_genotype"
2025-09-15 20:22:49.307 wdl.w:ptcp.w:call-paraphase-21 INFO input :: job: "call-run_paraphase", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf", "genome_version": "38", "config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-21/out/m84036_250809_035451_s4.bc2118.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-21/out/m84036_250809_035451_s4.bc2118.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2118"}
2025-09-15 20:22:49.308 wdl.w:ptcp.w:call-trgt-21 INFO input :: job: "call-trgt_genotype", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-21/out/m84036_250809_035451_s4.bc2118.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-21/out/m84036_250809_035451_s4.bc2118.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2118"}
2025-09-15 20:22:49.308 wdl.w:ptcp.w:call-sawfish-04.t:call-run_sawfish INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 16, memory_reservation: 32000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:22:49.308 wdl.w:ptcp.t:call-pbmm2_align_hifi-05 INFO output :: name: "mapped_bam_bai", value: "m84036_250809_035451_s4.bc2102.mapped.bam.bai"
2025-09-15 20:22:49.309 wdl.w:ptcp.w:call-sawfish-04.t:call-run_sawfish WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:22:49.309 wdl.w:ptcp.w:call-sawfish-04.t:call-run_sawfish INFO provisioned :: seconds_waited: 0, cpu: 16, mem_bytes: 32000000000
2025-09-15 20:22:49.309 wdl.w:ptcp.w:call-sawfish-04.t:call-run_sawfish INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:22:49.310 wdl.w:ptcp.t:call-pbmm2_align_hifi-05 INFO output :: name: "mapped_bam_pbi", value: "m84036_250809_035451_s4.bc2102.mapped.bam.pbi"
2025-09-15 20:22:49.311 wdl.w:ptcp.t:call-pbmm2_align_hifi-05 INFO output :: name: "report", value: "mapping_stats.report.json"
2025-09-15 20:22:49.316 wdl.w:ptcp.t:call-pbmm2_align_hifi-36.stderr VERBOSE 
2025-09-15 20:22:49.316 wdl.w:ptcp.t:call-pbmm2_align_hifi-36.stderr VERBOSE pbmm2 \
2025-09-15 20:22:49.316 wdl.w:ptcp.t:call-pbmm2_align_hifi-36.stderr VERBOSE   align \
2025-09-15 20:22:49.316 wdl.w:ptcp.t:call-pbmm2_align_hifi-36.stderr VERBOSE   --log-level INFO \
2025-09-15 20:22:49.316 wdl.w:ptcp.t:call-pbmm2_align_hifi-36.stderr VERBOSE   --log-file pbmm2.log \
2025-09-15 20:22:49.316 wdl.w:ptcp.t:call-pbmm2_align_hifi-36.stderr VERBOSE   --alarms alarms.json \
2025-09-15 20:22:49.316 wdl.w:ptcp.t:call-pbmm2_align_hifi-36.stderr VERBOSE   --num-threads 64 \
2025-09-15 20:22:49.317 wdl.w:ptcp.t:call-pbmm2_align_hifi-36.stderr VERBOSE   --sort \
2025-09-15 20:22:49.317 wdl.w:ptcp.t:call-pbmm2_align_hifi-36.stderr VERBOSE   --preset HiFi \
2025-09-15 20:22:49.317 wdl.w:ptcp.t:call-pbmm2_align_hifi-36.stderr VERBOSE   --report-json mapping_stats.report.json \
2025-09-15 20:22:49.317 wdl.w:ptcp.t:call-pbmm2_align_hifi-36.stderr VERBOSE   --sample "m84036_250809_035451_s4.bc2133" \
2025-09-15 20:22:49.317 wdl.w:ptcp.t:call-pbmm2_align_hifi-36.stderr VERBOSE   --unmapped \
2025-09-15 20:22:49.317 wdl.w:ptcp.t:call-pbmm2_align_hifi-36.stderr VERBOSE   /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa \
2025-09-15 20:22:49.317 wdl.w:ptcp.t:call-pbmm2_align_hifi-36.stderr VERBOSE   /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0037_m84036_250809_035451_s4.bc2133.unmapped.bam \
2025-09-15 20:22:49.317 wdl.w:ptcp.t:call-pbmm2_align_hifi-36.stderr VERBOSE   m84036_250809_035451_s4.bc2133.mapped.bam
2025-09-15 20:22:49.317 wdl.w:ptcp.t:call-pbmm2_align_hifi-36.stderr VERBOSE + pbmm2 align --log-level INFO --log-file pbmm2.log --alarms alarms.json --num-threads 64 --sort --preset HiFi --report-json mapping_stats.report.json --sample m84036_250809_035451_s4.bc2133 --unmapped /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0037_m84036_250809_035451_s4.bc2133.unmapped.bam m84036_250809_035451_s4.bc2133.mapped.bam
2025-09-15 20:22:49.389 wdl.w:ptcp.w:call-sawfish-04.t:call-run_sawfish INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 10, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-04/call-run_sawfish/_singularity_tmpdir_wij2oyhf"
2025-09-15 20:22:49.389 wdl.w:ptcp.w:call-sawfish-04.t:call-run_sawfish INFO Slurm invocation: srun --job-name call-run_sawfish --partition compute,compute9 --cpus-per-task 16 --mem 30518M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-04/call-run_sawfish/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-04/call-run_sawfish/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-04/call-run_sawfish/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-04/call-run_sawfish/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-04/out/m84036_250809_035451_s4.bc2101.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2101.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-04/out/m84036_250809_035451_s4.bc2101.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2101.mapped.bam:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-04/call-run_sawfish/_singularity_tmpdir_wij2oyhf/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-04/call-run_sawfish/_singularity_tmpdir_wij2oyhf/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:22:49.391 wdl.w:ptcp.w:call-paraphase-04.t:call-run_paraphase INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-04/call-run_paraphase/_singularity_tmpdir_7zf_4kx5"
2025-09-15 20:22:49.393 wdl.w:ptcp.w:call-paraphase-04.t:call-run_paraphase INFO Slurm invocation: srun --job-name call-run_paraphase --partition compute,compute9 --cpus-per-task 4 --mem 7629M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-04/call-run_paraphase/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-04/call-run_paraphase/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-04/call-run_paraphase/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-04/call-run_paraphase/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-04/out/m84036_250809_035451_s4.bc2101.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2101.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-04/out/m84036_250809_035451_s4.bc2101.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2101.mapped.bam:ro --bind /ptcp/meta/variant_list/variant_list.GRCh38.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf:ro --bind /ptcp/meta/paraphase/paraphase_config.GRCh38.yaml:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/paraphase_config.GRCh38.yaml:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-04/call-run_paraphase/_singularity_tmpdir_7zf_4kx5/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-04/call-run_paraphase/_singularity_tmpdir_7zf_4kx5/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:22:49.396 wdl.w:ptcp.t:call-pbmm2_align_hifi-13 INFO output :: name: "mapped_bam", value: "m84036_250809_035451_s4.bc2110.mapped.bam"
2025-09-15 20:22:49.397 wdl.w:ptcp.w:call-paraphase-20.t:call-run_paraphase.slurm_singularity INFO srun: job 51797331 queued and waiting for resources
2025-09-15 20:22:49.398 wdl.w:ptcp.t:call-pbmm2_align_hifi-38.stderr VERBOSE 
2025-09-15 20:22:49.398 wdl.w:ptcp.t:call-pbmm2_align_hifi-38.stderr VERBOSE pbmm2 \
2025-09-15 20:22:49.399 wdl.w:ptcp.t:call-pbmm2_align_hifi-38.stderr VERBOSE   align \
2025-09-15 20:22:49.399 wdl.w:ptcp.t:call-pbmm2_align_hifi-38.stderr VERBOSE   --log-level INFO \
2025-09-15 20:22:49.399 wdl.w:ptcp.t:call-pbmm2_align_hifi-38.stderr VERBOSE   --log-file pbmm2.log \
2025-09-15 20:22:49.399 wdl.w:ptcp.t:call-pbmm2_align_hifi-38.stderr VERBOSE   --alarms alarms.json \
2025-09-15 20:22:49.399 wdl.w:ptcp.t:call-pbmm2_align_hifi-38.stderr VERBOSE   --num-threads 64 \
2025-09-15 20:22:49.399 wdl.w:ptcp.t:call-pbmm2_align_hifi-38.stderr VERBOSE   --sort \
2025-09-15 20:22:49.399 wdl.w:ptcp.t:call-pbmm2_align_hifi-38.stderr VERBOSE   --preset HiFi \
2025-09-15 20:22:49.399 wdl.w:ptcp.t:call-pbmm2_align_hifi-38.stderr VERBOSE   --report-json mapping_stats.report.json \
2025-09-15 20:22:49.399 wdl.w:ptcp.t:call-pbmm2_align_hifi-38.stderr VERBOSE   --sample "m84036_250809_035451_s4.bc2135" \
2025-09-15 20:22:49.399 wdl.w:ptcp.t:call-pbmm2_align_hifi-38.stderr VERBOSE   --unmapped \
2025-09-15 20:22:49.399 wdl.w:ptcp.t:call-pbmm2_align_hifi-38.stderr VERBOSE   /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa \
2025-09-15 20:22:49.399 wdl.w:ptcp.t:call-pbmm2_align_hifi-38.stderr VERBOSE   /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0039_m84036_250809_035451_s4.bc2135.unmapped.bam \
2025-09-15 20:22:49.399 wdl.w:ptcp.t:call-pbmm2_align_hifi-38.stderr VERBOSE   m84036_250809_035451_s4.bc2135.mapped.bam
2025-09-15 20:22:49.399 wdl.w:ptcp.t:call-pbmm2_align_hifi-38.stderr VERBOSE + pbmm2 align --log-level INFO --log-file pbmm2.log --alarms alarms.json --num-threads 64 --sort --preset HiFi --report-json mapping_stats.report.json --sample m84036_250809_035451_s4.bc2135 --unmapped /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0039_m84036_250809_035451_s4.bc2135.unmapped.bam m84036_250809_035451_s4.bc2135.mapped.bam
2025-09-15 20:22:49.400 wdl.w:ptcp.t:call-pbmm2_align_hifi-13 INFO output :: name: "mapped_bam_bai", value: "m84036_250809_035451_s4.bc2110.mapped.bam.bai"
2025-09-15 20:22:49.402 wdl.w:ptcp.t:call-pbmm2_align_hifi-13 INFO output :: name: "mapped_bam_pbi", value: "m84036_250809_035451_s4.bc2110.mapped.bam.pbi"
2025-09-15 20:22:49.405 wdl.w:ptcp.t:call-pbmm2_align_hifi-13 INFO output :: name: "report", value: "mapping_stats.report.json"
2025-09-15 20:22:49.419 wdl.w:ptcp.t:call-pbmm2_align_hifi-39.stderr VERBOSE 
2025-09-15 20:22:49.419 wdl.w:ptcp.t:call-pbmm2_align_hifi-39.stderr VERBOSE pbmm2 \
2025-09-15 20:22:49.419 wdl.w:ptcp.t:call-pbmm2_align_hifi-39.stderr VERBOSE   align \
2025-09-15 20:22:49.419 wdl.w:ptcp.t:call-pbmm2_align_hifi-39.stderr VERBOSE   --log-level INFO \
2025-09-15 20:22:49.419 wdl.w:ptcp.t:call-pbmm2_align_hifi-39.stderr VERBOSE   --log-file pbmm2.log \
2025-09-15 20:22:49.419 wdl.w:ptcp.t:call-pbmm2_align_hifi-39.stderr VERBOSE   --alarms alarms.json \
2025-09-15 20:22:49.419 wdl.w:ptcp.t:call-pbmm2_align_hifi-39.stderr VERBOSE   --num-threads 64 \
2025-09-15 20:22:49.420 wdl.w:ptcp.t:call-pbmm2_align_hifi-39.stderr VERBOSE   --sort \
2025-09-15 20:22:49.420 wdl.w:ptcp.t:call-pbmm2_align_hifi-39.stderr VERBOSE   --preset HiFi \
2025-09-15 20:22:49.420 wdl.w:ptcp.t:call-pbmm2_align_hifi-39.stderr VERBOSE   --report-json mapping_stats.report.json \
2025-09-15 20:22:49.420 wdl.w:ptcp.t:call-pbmm2_align_hifi-39.stderr VERBOSE   --sample "m84036_250809_035451_s4.bc2136" \
2025-09-15 20:22:49.420 wdl.w:ptcp.t:call-pbmm2_align_hifi-39.stderr VERBOSE   --unmapped \
2025-09-15 20:22:49.420 wdl.w:ptcp.t:call-pbmm2_align_hifi-39.stderr VERBOSE   /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa \
2025-09-15 20:22:49.420 wdl.w:ptcp.t:call-pbmm2_align_hifi-39.stderr VERBOSE   /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0040_m84036_250809_035451_s4.bc2136.unmapped.bam \
2025-09-15 20:22:49.420 wdl.w:ptcp.t:call-pbmm2_align_hifi-39.stderr VERBOSE   m84036_250809_035451_s4.bc2136.mapped.bam
2025-09-15 20:22:49.420 wdl.w:ptcp.t:call-pbmm2_align_hifi-39.stderr VERBOSE + pbmm2 align --log-level INFO --log-file pbmm2.log --alarms alarms.json --num-threads 64 --sort --preset HiFi --report-json mapping_stats.report.json --sample m84036_250809_035451_s4.bc2136 --unmapped /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0040_m84036_250809_035451_s4.bc2136.unmapped.bam m84036_250809_035451_s4.bc2136.mapped.bam
2025-09-15 20:22:49.421 wdl.w:ptcp.t:call-pbmm2_align_hifi-30 NOTICE done
2025-09-15 20:22:49.421 wdl.w:ptcp.t:call-pbmm2_align_hifi-06 NOTICE done
2025-09-15 20:22:49.422 wdl.w:ptcp.t:call-pbmm2_align_hifi-37.stderr VERBOSE 
2025-09-15 20:22:49.422 wdl.w:ptcp.t:call-pbmm2_align_hifi-37.stderr VERBOSE pbmm2 \
2025-09-15 20:22:49.422 wdl.w:ptcp.t:call-pbmm2_align_hifi-37.stderr VERBOSE   align \
2025-09-15 20:22:49.422 wdl.w:ptcp.t:call-pbmm2_align_hifi-37.stderr VERBOSE   --log-level INFO \
2025-09-15 20:22:49.422 wdl.w:ptcp.t:call-pbmm2_align_hifi-37.stderr VERBOSE   --log-file pbmm2.log \
2025-09-15 20:22:49.422 wdl.w:ptcp.t:call-pbmm2_align_hifi-37.stderr VERBOSE   --alarms alarms.json \
2025-09-15 20:22:49.423 wdl.w:ptcp.t:call-pbmm2_align_hifi-37.stderr VERBOSE   --num-threads 64 \
2025-09-15 20:22:49.423 wdl.w:ptcp.t:call-pbmm2_align_hifi-37.stderr VERBOSE   --sort \
2025-09-15 20:22:49.423 wdl.w:ptcp.t:call-pbmm2_align_hifi-37.stderr VERBOSE   --preset HiFi \
2025-09-15 20:22:49.423 wdl.w:ptcp.t:call-pbmm2_align_hifi-37.stderr VERBOSE   --report-json mapping_stats.report.json \
2025-09-15 20:22:49.423 wdl.w:ptcp.t:call-pbmm2_align_hifi-37.stderr VERBOSE   --sample "m84036_250809_035451_s4.bc2134" \
2025-09-15 20:22:49.423 wdl.w:ptcp.t:call-pbmm2_align_hifi-37.stderr VERBOSE   --unmapped \
2025-09-15 20:22:49.423 wdl.w:ptcp.t:call-pbmm2_align_hifi-37.stderr VERBOSE   /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa \
2025-09-15 20:22:49.423 wdl.w:ptcp.t:call-pbmm2_align_hifi-41.stderr VERBOSE 
2025-09-15 20:22:49.423 wdl.w:ptcp.t:call-pbmm2_align_hifi-37.stderr VERBOSE   /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0038_m84036_250809_035451_s4.bc2134.unmapped.bam \
2025-09-15 20:22:49.423 wdl.w:ptcp.t:call-pbmm2_align_hifi-41.stderr VERBOSE pbmm2 \
2025-09-15 20:22:49.424 wdl.w:ptcp.t:call-pbmm2_align_hifi-37.stderr VERBOSE   m84036_250809_035451_s4.bc2134.mapped.bam
2025-09-15 20:22:49.424 wdl.w:ptcp.t:call-pbmm2_align_hifi-41.stderr VERBOSE   align \
2025-09-15 20:22:49.424 wdl.w:ptcp.t:call-pbmm2_align_hifi-37.stderr VERBOSE + pbmm2 align --log-level INFO --log-file pbmm2.log --alarms alarms.json --num-threads 64 --sort --preset HiFi --report-json mapping_stats.report.json --sample m84036_250809_035451_s4.bc2134 --unmapped /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0038_m84036_250809_035451_s4.bc2134.unmapped.bam m84036_250809_035451_s4.bc2134.mapped.bam
2025-09-15 20:22:49.424 wdl.w:ptcp.t:call-pbmm2_align_hifi-41.stderr VERBOSE   --log-level INFO \
2025-09-15 20:22:49.424 wdl.w:ptcp.t:call-pbmm2_align_hifi-41.stderr VERBOSE   --log-file pbmm2.log \
2025-09-15 20:22:49.424 wdl.w:ptcp.t:call-pbmm2_align_hifi-41.stderr VERBOSE   --alarms alarms.json \
2025-09-15 20:22:49.424 wdl.w:ptcp.t:call-pbmm2_align_hifi-41.stderr VERBOSE   --num-threads 64 \
2025-09-15 20:22:49.424 wdl.w:ptcp.t:call-pbmm2_align_hifi-33 NOTICE done
2025-09-15 20:22:49.424 wdl.w:ptcp.t:call-pbmm2_align_hifi-41.stderr VERBOSE   --sort \
2025-09-15 20:22:49.425 wdl.w:ptcp.t:call-pbmm2_align_hifi-41.stderr VERBOSE   --preset HiFi \
2025-09-15 20:22:49.425 wdl.w:ptcp.t:call-pbmm2_align_hifi-41.stderr VERBOSE   --report-json mapping_stats.report.json \
2025-09-15 20:22:49.425 wdl.w:ptcp.t:call-pbmm2_align_hifi-41.stderr VERBOSE   --sample "m84036_250809_035451_s4.bc2138" \
2025-09-15 20:22:49.425 wdl.w:ptcp.t:call-pbmm2_align_hifi-41.stderr VERBOSE   --unmapped \
2025-09-15 20:22:49.425 wdl.w:ptcp.t:call-pbmm2_align_hifi-41.stderr VERBOSE   /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa \
2025-09-15 20:22:49.425 wdl.w:ptcp.t:call-pbmm2_align_hifi-41.stderr VERBOSE   /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0042_m84036_250809_035451_s4.bc2138.unmapped.bam \
2025-09-15 20:22:49.425 wdl.w:ptcp.t:call-pbmm2_align_hifi-41.stderr VERBOSE   m84036_250809_035451_s4.bc2138.mapped.bam
2025-09-15 20:22:49.426 wdl.w:ptcp.t:call-pbmm2_align_hifi-41.stderr VERBOSE + pbmm2 align --log-level INFO --log-file pbmm2.log --alarms alarms.json --num-threads 64 --sort --preset HiFi --report-json mapping_stats.report.json --sample m84036_250809_035451_s4.bc2138 --unmapped /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0042_m84036_250809_035451_s4.bc2138.unmapped.bam m84036_250809_035451_s4.bc2138.mapped.bam
2025-09-15 20:22:49.429 wdl.w:ptcp NOTICE finish :: job: "call-pbmm2_align_hifi-06"
2025-09-15 20:22:49.429 wdl.w:ptcp INFO output :: job: "call-pbmm2_align_hifi-06", values: {"report": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-06/out/mapping_stats.report.json", "mapped_bam_pbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-06/out/m84036_250809_035451_s4.bc2103.mapped.bam.pbi", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-06/out/m84036_250809_035451_s4.bc2103.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-06/out/m84036_250809_035451_s4.bc2103.mapped.bam"}
2025-09-15 20:22:49.430 wdl.w:ptcp NOTICE ready :: job: "call-paraphase-06", callee: "paraphase"
2025-09-15 20:22:49.430 wdl.w:ptcp INFO input :: job: "call-paraphase-06", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf", "genome_version": "38", "config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-06/out/m84036_250809_035451_s4.bc2103.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-06/out/m84036_250809_035451_s4.bc2103.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2103"}
2025-09-15 20:22:49.431 wdl.w:ptcp NOTICE ready :: job: "call-sawfish-06", callee: "sawfish"
2025-09-15 20:22:49.432 wdl.w:ptcp.t:call-pbmm2_align_hifi-43.stderr VERBOSE 
2025-09-15 20:22:49.432 wdl.w:ptcp.t:call-pbmm2_align_hifi-40.stderr VERBOSE 
2025-09-15 20:22:49.432 wdl.w:ptcp INFO input :: job: "call-sawfish-06", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-06/out/m84036_250809_035451_s4.bc2103.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-06/out/m84036_250809_035451_s4.bc2103.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2103"}
2025-09-15 20:22:49.432 wdl.w:ptcp.t:call-pbmm2_align_hifi-43.stderr VERBOSE pbmm2 \
2025-09-15 20:22:49.432 wdl.w:ptcp.t:call-pbmm2_align_hifi-40.stderr VERBOSE pbmm2 \
2025-09-15 20:22:49.432 wdl.w:ptcp.t:call-pbmm2_align_hifi-43.stderr VERBOSE   align \
2025-09-15 20:22:49.432 wdl.w:ptcp.t:call-pbmm2_align_hifi-40.stderr VERBOSE   align \
2025-09-15 20:22:49.433 wdl.w:ptcp.t:call-pbmm2_align_hifi-43.stderr VERBOSE   --log-level INFO \
2025-09-15 20:22:49.433 wdl.w:ptcp.t:call-pbmm2_align_hifi-40.stderr VERBOSE   --log-level INFO \
2025-09-15 20:22:49.433 wdl.w:ptcp.t:call-pbmm2_align_hifi-43.stderr VERBOSE   --log-file pbmm2.log \
2025-09-15 20:22:49.433 wdl.w:ptcp.t:call-pbmm2_align_hifi-40.stderr VERBOSE   --log-file pbmm2.log \
2025-09-15 20:22:49.433 wdl.w:ptcp.t:call-pbmm2_align_hifi-43.stderr VERBOSE   --alarms alarms.json \
2025-09-15 20:22:49.433 wdl.w:ptcp.t:call-pbmm2_align_hifi-40.stderr VERBOSE   --alarms alarms.json \
2025-09-15 20:22:49.433 wdl.w:ptcp.t:call-pbmm2_align_hifi-43.stderr VERBOSE   --num-threads 64 \
2025-09-15 20:22:49.433 wdl.w:ptcp.t:call-pbmm2_align_hifi-40.stderr VERBOSE   --num-threads 64 \
2025-09-15 20:22:49.433 wdl.w:ptcp.t:call-pbmm2_align_hifi-43.stderr VERBOSE   --sort \
2025-09-15 20:22:49.433 wdl.w:ptcp.t:call-pbmm2_align_hifi-40.stderr VERBOSE   --sort \
2025-09-15 20:22:49.434 wdl.w:ptcp.t:call-pbmm2_align_hifi-43.stderr VERBOSE   --preset HiFi \
2025-09-15 20:22:49.434 wdl.w:ptcp.t:call-pbmm2_align_hifi-40.stderr VERBOSE   --preset HiFi \
2025-09-15 20:22:49.434 wdl.w:ptcp.t:call-pbmm2_align_hifi-43.stderr VERBOSE   --report-json mapping_stats.report.json \
2025-09-15 20:22:49.434 wdl.w:ptcp.t:call-pbmm2_align_hifi-40.stderr VERBOSE   --report-json mapping_stats.report.json \
2025-09-15 20:22:49.434 wdl.w:ptcp.t:call-pbmm2_align_hifi-43.stderr VERBOSE   --sample "m84036_250809_035451_s4.bc2140" \
2025-09-15 20:22:49.434 wdl.w:ptcp.t:call-pbmm2_align_hifi-40.stderr VERBOSE   --sample "m84036_250809_035451_s4.bc2137" \
2025-09-15 20:22:49.434 wdl.w:ptcp.t:call-pbmm2_align_hifi-43.stderr VERBOSE   --unmapped \
2025-09-15 20:22:49.434 wdl.w:ptcp.t:call-pbmm2_align_hifi-44.stderr VERBOSE 
2025-09-15 20:22:49.434 wdl.w:ptcp.t:call-pbmm2_align_hifi-05 NOTICE done
2025-09-15 20:22:49.434 wdl.w:ptcp.t:call-pbmm2_align_hifi-40.stderr VERBOSE   --unmapped \
2025-09-15 20:22:49.435 wdl.w:ptcp.t:call-pbmm2_align_hifi-43.stderr VERBOSE   /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa \
2025-09-15 20:22:49.435 wdl.w:ptcp.t:call-pbmm2_align_hifi-44.stderr VERBOSE pbmm2 \
2025-09-15 20:22:49.435 wdl.w:ptcp.t:call-pbmm2_align_hifi-40.stderr VERBOSE   /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa \
2025-09-15 20:22:49.435 wdl.w:ptcp.t:call-pbmm2_align_hifi-43.stderr VERBOSE   /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0044_m84036_250809_035451_s4.bc2140.unmapped.bam \
2025-09-15 20:22:49.435 wdl.w:ptcp.t:call-pbmm2_align_hifi-44.stderr VERBOSE   align \
2025-09-15 20:22:49.435 wdl.w:ptcp.t:call-pbmm2_align_hifi-40.stderr VERBOSE   /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0041_m84036_250809_035451_s4.bc2137.unmapped.bam \
2025-09-15 20:22:49.435 wdl.w:ptcp.t:call-pbmm2_align_hifi-43.stderr VERBOSE   m84036_250809_035451_s4.bc2140.mapped.bam
2025-09-15 20:22:49.436 wdl.w:ptcp.t:call-pbmm2_align_hifi-44.stderr VERBOSE   --log-level INFO \
2025-09-15 20:22:49.436 wdl.w:ptcp.t:call-pbmm2_align_hifi-40.stderr VERBOSE   m84036_250809_035451_s4.bc2137.mapped.bam
2025-09-15 20:22:49.436 wdl.w:ptcp.t:call-pbmm2_align_hifi-43.stderr VERBOSE + pbmm2 align --log-level INFO --log-file pbmm2.log --alarms alarms.json --num-threads 64 --sort --preset HiFi --report-json mapping_stats.report.json --sample m84036_250809_035451_s4.bc2140 --unmapped /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0044_m84036_250809_035451_s4.bc2140.unmapped.bam m84036_250809_035451_s4.bc2140.mapped.bam
2025-09-15 20:22:49.436 wdl.w:ptcp.t:call-pbmm2_align_hifi-44.stderr VERBOSE   --log-file pbmm2.log \
2025-09-15 20:22:49.436 wdl.w:ptcp.t:call-pbmm2_align_hifi-40.stderr VERBOSE + pbmm2 align --log-level INFO --log-file pbmm2.log --alarms alarms.json --num-threads 64 --sort --preset HiFi --report-json mapping_stats.report.json --sample m84036_250809_035451_s4.bc2137 --unmapped /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0041_m84036_250809_035451_s4.bc2137.unmapped.bam m84036_250809_035451_s4.bc2137.mapped.bam
2025-09-15 20:22:49.436 wdl.w:ptcp.t:call-pbmm2_align_hifi-44.stderr VERBOSE   --alarms alarms.json \
2025-09-15 20:22:49.436 wdl.w:ptcp.t:call-pbmm2_align_hifi-44.stderr VERBOSE   --num-threads 64 \
2025-09-15 20:22:49.436 wdl.w:ptcp.t:call-pbmm2_align_hifi-44.stderr VERBOSE   --sort \
2025-09-15 20:22:49.436 wdl.w:ptcp.t:call-pbmm2_align_hifi-44.stderr VERBOSE   --preset HiFi \
2025-09-15 20:22:49.436 wdl.w:ptcp.t:call-pbmm2_align_hifi-44.stderr VERBOSE   --report-json mapping_stats.report.json \
2025-09-15 20:22:49.436 wdl.w:ptcp.t:call-pbmm2_align_hifi-44.stderr VERBOSE   --sample "m84036_250809_035451_s4.bc2141" \
2025-09-15 20:22:49.437 wdl.w:ptcp.t:call-pbmm2_align_hifi-44.stderr VERBOSE   --unmapped \
2025-09-15 20:22:49.437 wdl.w:ptcp.t:call-pbmm2_align_hifi-44.stderr VERBOSE   /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa \
2025-09-15 20:22:49.437 wdl.w:ptcp.t:call-pbmm2_align_hifi-44.stderr VERBOSE   /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0045_m84036_250809_035451_s4.bc2141.unmapped.bam \
2025-09-15 20:22:49.437 wdl.w:ptcp.t:call-pbmm2_align_hifi-44.stderr VERBOSE   m84036_250809_035451_s4.bc2141.mapped.bam
2025-09-15 20:22:49.437 wdl.w:ptcp.t:call-pbmm2_align_hifi-44.stderr VERBOSE + pbmm2 align --log-level INFO --log-file pbmm2.log --alarms alarms.json --num-threads 64 --sort --preset HiFi --report-json mapping_stats.report.json --sample m84036_250809_035451_s4.bc2141 --unmapped /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0045_m84036_250809_035451_s4.bc2141.unmapped.bam m84036_250809_035451_s4.bc2141.mapped.bam
2025-09-15 20:22:49.442 wdl.w:ptcp NOTICE ready :: job: "call-trgt-06", callee: "trgt"
2025-09-15 20:22:49.442 wdl.w:ptcp INFO input :: job: "call-trgt-06", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-06/out/m84036_250809_035451_s4.bc2103.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-06/out/m84036_250809_035451_s4.bc2103.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2103"}
2025-09-15 20:22:49.442 wdl.w:ptcp.w:call-trgt-04.t:call-trgt_genotype NOTICE task setup :: name: "trgt_genotype", source: "./trgt.wdl", line: 272, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-04/call-trgt_genotype", thread: 140611457906240
2025-09-15 20:22:49.443 wdl.w:ptcp.w:call-trgt-04.t:call-get_reads_overlapping_repeats NOTICE task setup :: name: "get_reads_overlapping_repeats", source: "./trgt.wdl", line: 182, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-04/call-get_reads_overlapping_repeats", thread: 140613571819072
2025-09-15 20:22:49.446 wdl.w:ptcp NOTICE finish :: job: "call-pbmm2_align_hifi-30"
2025-09-15 20:22:49.446 wdl.w:ptcp INFO output :: job: "call-pbmm2_align_hifi-30", values: {"report": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-30/out/mapping_stats.report.json", "mapped_bam_pbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-30/out/m84036_250809_035451_s4.bc2127.mapped.bam.pbi", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-30/out/m84036_250809_035451_s4.bc2127.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-30/out/m84036_250809_035451_s4.bc2127.mapped.bam"}
2025-09-15 20:22:49.447 wdl.w:ptcp NOTICE ready :: job: "call-paraphase-30", callee: "paraphase"
2025-09-15 20:22:49.447 wdl.w:ptcp INFO input :: job: "call-paraphase-30", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf", "genome_version": "38", "config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-30/out/m84036_250809_035451_s4.bc2127.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-30/out/m84036_250809_035451_s4.bc2127.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2127"}
2025-09-15 20:22:49.447 wdl.w:ptcp.w:call-paraphase-06 NOTICE workflow start :: name: "paraphase", source: "./paraphase.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-06"
2025-09-15 20:22:49.448 wdl.w:ptcp.w:call-paraphase-31.t:call-run_paraphase NOTICE task setup :: name: "run_paraphase", source: "./paraphase.wdl", line: 127, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-31/call-run_paraphase", thread: 140611432728128
2025-09-15 20:22:49.450 wdl.w:ptcp.w:call-sawfish-04.t:call-run_sawfish NOTICE slurm_singularity run :: pid: 1198221, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-04/call-run_sawfish/slurm_singularity.log.txt"
2025-09-15 20:22:49.450 wdl.w:ptcp.w:call-paraphase-04.t:call-run_paraphase NOTICE slurm_singularity run :: pid: 1198222, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-04/call-run_paraphase/slurm_singularity.log.txt"
2025-09-15 20:22:49.453 wdl.w:ptcp NOTICE ready :: job: "call-sawfish-30", callee: "sawfish"
2025-09-15 20:22:49.453 wdl.w:ptcp INFO input :: job: "call-sawfish-30", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-30/out/m84036_250809_035451_s4.bc2127.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-30/out/m84036_250809_035451_s4.bc2127.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2127"}
2025-09-15 20:22:49.454 wdl.w:ptcp.w:call-sawfish-06 NOTICE workflow start :: name: "sawfish", source: "./sawfish.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-06"
2025-09-15 20:22:49.454 wdl.w:ptcp NOTICE ready :: job: "call-trgt-30", callee: "trgt"
2025-09-15 20:22:49.455 wdl.w:ptcp INFO input :: job: "call-trgt-30", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-30/out/m84036_250809_035451_s4.bc2127.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-30/out/m84036_250809_035451_s4.bc2127.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2127"}
2025-09-15 20:22:49.456 wdl.w:ptcp.w:call-sawfish-31.t:call-run_sawfish NOTICE task setup :: name: "run_sawfish", source: "./sawfish.wdl", line: 83, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-31/call-run_sawfish", thread: 140613580211776
2025-09-15 20:22:49.460 wdl.w:ptcp NOTICE finish :: job: "call-pbmm2_align_hifi-33"
2025-09-15 20:22:49.461 wdl.w:ptcp.w:call-trgt-06 NOTICE workflow start :: name: "trgt", source: "./trgt.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-06"
2025-09-15 20:22:49.461 wdl.w:ptcp INFO output :: job: "call-pbmm2_align_hifi-33", values: {"report": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-33/out/mapping_stats.report.json", "mapped_bam_pbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-33/out/m84036_250809_035451_s4.bc2130.mapped.bam.pbi", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-33/out/m84036_250809_035451_s4.bc2130.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-33/out/m84036_250809_035451_s4.bc2130.mapped.bam"}
2025-09-15 20:22:49.462 wdl.w:ptcp NOTICE ready :: job: "call-paraphase-33", callee: "paraphase"
2025-09-15 20:22:49.462 wdl.w:ptcp INFO input :: job: "call-paraphase-33", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf", "genome_version": "38", "config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-33/out/m84036_250809_035451_s4.bc2130.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-33/out/m84036_250809_035451_s4.bc2130.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2130"}
2025-09-15 20:22:49.464 wdl.w:ptcp.w:call-paraphase-30 NOTICE workflow start :: name: "paraphase", source: "./paraphase.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-30"
2025-09-15 20:22:49.466 wdl.w:ptcp NOTICE ready :: job: "call-sawfish-33", callee: "sawfish"
2025-09-15 20:22:49.466 wdl.w:ptcp INFO input :: job: "call-sawfish-33", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-33/out/m84036_250809_035451_s4.bc2130.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-33/out/m84036_250809_035451_s4.bc2130.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2130"}
2025-09-15 20:22:49.467 wdl.w:ptcp.w:call-sawfish-30 NOTICE workflow start :: name: "sawfish", source: "./sawfish.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-30"
2025-09-15 20:22:49.472 wdl.w:ptcp NOTICE ready :: job: "call-trgt-33", callee: "trgt"
2025-09-15 20:22:49.472 wdl.w:ptcp.w:call-trgt-30 NOTICE workflow start :: name: "trgt", source: "./trgt.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-30"
2025-09-15 20:22:49.474 wdl.w:ptcp INFO input :: job: "call-trgt-33", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-33/out/m84036_250809_035451_s4.bc2130.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-33/out/m84036_250809_035451_s4.bc2130.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2130"}
2025-09-15 20:22:49.473 wdl.w:ptcp.t:call-pbmm2_align_hifi-48.stderr VERBOSE 
2025-09-15 20:22:49.476 wdl.w:ptcp.w:call-paraphase-33 NOTICE workflow start :: name: "paraphase", source: "./paraphase.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-33"
2025-09-15 20:22:49.478 wdl.w:ptcp.t:call-pbmm2_align_hifi-48.stderr VERBOSE pbmm2 \
2025-09-15 20:22:49.478 wdl.w:ptcp.w:call-trgt-04.t:call-get_reads_overlapping_repeats INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:22:49.479 wdl.w:ptcp NOTICE finish :: job: "call-pbmm2_align_hifi-05"
2025-09-15 20:22:49.483 wdl.w:ptcp.t:call-pbmm2_align_hifi-48.stderr VERBOSE   align \
2025-09-15 20:22:49.485 wdl.w:ptcp.w:call-sawfish-33 NOTICE workflow start :: name: "sawfish", source: "./sawfish.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-33"
2025-09-15 20:22:49.485 wdl.w:ptcp.w:call-trgt-04.t:call-get_reads_overlapping_repeats INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:22:49.486 wdl.w:ptcp INFO output :: job: "call-pbmm2_align_hifi-05", values: {"report": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-05/out/mapping_stats.report.json", "mapped_bam_pbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-05/out/m84036_250809_035451_s4.bc2102.mapped.bam.pbi", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-05/out/m84036_250809_035451_s4.bc2102.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-05/out/m84036_250809_035451_s4.bc2102.mapped.bam"}
2025-09-15 20:22:49.486 wdl.w:ptcp.w:call-trgt-33 NOTICE workflow start :: name: "trgt", source: "./trgt.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-33"
2025-09-15 20:22:49.488 wdl.w:ptcp.t:call-pbmm2_align_hifi-48.stderr VERBOSE   --log-level INFO \
2025-09-15 20:22:49.489 wdl.w:ptcp.w:call-trgt-04.t:call-trgt_genotype INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:22:49.492 wdl.w:ptcp.t:call-pbmm2_align_hifi-45.stderr VERBOSE 
2025-09-15 20:22:49.494 wdl.w:ptcp.w:call-trgt-04.t:call-get_reads_overlapping_repeats INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2101.mapped.bam.bai"
2025-09-15 20:22:49.495 wdl.w:ptcp NOTICE ready :: job: "call-paraphase-05", callee: "paraphase"
2025-09-15 20:22:49.496 wdl.w:ptcp.t:call-pbmm2_align_hifi-50.slurm_singularity INFO srun: job 51797276 has been allocated resources
2025-09-15 20:22:49.496 wdl.w:ptcp.t:call-pbmm2_align_hifi-51.stderr VERBOSE 
2025-09-15 20:22:49.499 wdl.w:ptcp.w:call-paraphase-06 INFO visit :: node: "decl-annotation_vcf", values: {"annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf"}
2025-09-15 20:22:49.499 wdl.w:ptcp.t:call-pbmm2_align_hifi-48.stderr VERBOSE   --log-file pbmm2.log \
2025-09-15 20:22:49.503 wdl.w:ptcp.w:call-trgt-04.t:call-trgt_genotype INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:22:49.503 wdl.w:ptcp.w:call-sawfish-20.t:call-run_sawfish.slurm_singularity INFO srun: job 51797332 queued and waiting for resources
2025-09-15 20:22:49.504 wdl.w:ptcp.w:call-trgt-20.t:call-get_reads_overlapping_repeats.slurm_singularity INFO srun: job 51797333 queued and waiting for resources
2025-09-15 20:22:49.506 wdl.w:ptcp.t:call-pbmm2_align_hifi-45.stderr VERBOSE pbmm2 \
2025-09-15 20:22:49.507 wdl.w:ptcp.w:call-trgt-04.t:call-get_reads_overlapping_repeats INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2101.mapped.bam"
2025-09-15 20:22:49.507 wdl.w:ptcp INFO input :: job: "call-paraphase-05", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf", "genome_version": "38", "config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-05/out/m84036_250809_035451_s4.bc2102.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-05/out/m84036_250809_035451_s4.bc2102.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2102"}
2025-09-15 20:22:49.509 wdl.w:ptcp.t:call-pbmm2_align_hifi-52.stderr VERBOSE 
2025-09-15 20:22:49.509 wdl.w:ptcp.t:call-pbmm2_align_hifi-50.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:22:49.510 wdl.w:ptcp.w:call-sawfish-31.t:call-run_sawfish INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:22:49.510 wdl.w:ptcp.t:call-pbmm2_align_hifi-46.stderr VERBOSE 
2025-09-15 20:22:49.511 wdl.w:ptcp.t:call-pbmm2_align_hifi-51.stderr VERBOSE pbmm2 \
2025-09-15 20:22:49.512 wdl.w:ptcp.w:call-sawfish-06 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:22:49.512 wdl.w:ptcp.w:call-paraphase-06 INFO visit :: node: "decl-config_file", values: {"config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml"}
2025-09-15 20:22:49.514 wdl.w:ptcp.t:call-pbmm2_align_hifi-53.stderr VERBOSE 
2025-09-15 20:22:49.514 wdl.w:ptcp.t:call-pbmm2_align_hifi-47.stderr VERBOSE 
2025-09-15 20:22:49.514 wdl.w:ptcp.t:call-pbmm2_align_hifi-48.stderr VERBOSE   --alarms alarms.json \
2025-09-15 20:22:49.516 wdl.w:ptcp.w:call-trgt-04.t:call-trgt_genotype INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:22:49.518 wdl.w:ptcp.w:call-trgt-06 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:22:49.519 wdl.w:ptcp.t:call-pbmm2_align_hifi-45.stderr VERBOSE   align \
2025-09-15 20:22:49.520 wdl.w:ptcp.w:call-paraphase-30 INFO visit :: node: "decl-annotation_vcf", values: {"annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf"}
2025-09-15 20:22:49.520 wdl.w:ptcp.w:call-trgt-04.t:call-get_reads_overlapping_repeats INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2101"
2025-09-15 20:22:49.523 wdl.w:ptcp NOTICE ready :: job: "call-sawfish-05", callee: "sawfish"
2025-09-15 20:22:49.522 wdl.w:ptcp.t:call-pbmm2_align_hifi-52.stderr VERBOSE pbmm2 \
2025-09-15 20:22:49.523 wdl.w:ptcp.w:call-paraphase-31.t:call-run_paraphase INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:22:49.524 wdl.w:ptcp.t:call-pbmm2_align_hifi-50.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:22:49.524 wdl.w:ptcp.w:call-sawfish-31.t:call-run_sawfish INFO input :: name: "genome_version", value: "38"
2025-09-15 20:22:49.525 wdl.w:ptcp.t:call-pbmm2_align_hifi-46.stderr VERBOSE pbmm2 \
2025-09-15 20:22:49.526 wdl.w:ptcp.t:call-pbmm2_align_hifi-51.stderr VERBOSE   align \
2025-09-15 20:22:49.527 wdl.w:ptcp.w:call-sawfish-06 INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:22:49.528 wdl.w:ptcp.w:call-sawfish-30 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:22:49.527 wdl.w:ptcp.t:call-pbmm2_align_hifi-42.stderr VERBOSE 
2025-09-15 20:22:49.529 wdl.w:ptcp.w:call-paraphase-06 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:22:49.529 wdl.w:ptcp.t:call-pbmm2_align_hifi-49.slurm_singularity INFO srun: job 51797274 has been allocated resources
2025-09-15 20:22:49.530 wdl.w:ptcp.t:call-pbmm2_align_hifi-53.stderr VERBOSE pbmm2 \
2025-09-15 20:22:49.530 wdl.w:ptcp.t:call-pbmm2_align_hifi-47.stderr VERBOSE pbmm2 \
2025-09-15 20:22:49.531 wdl.w:ptcp.w:call-trgt-30 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:22:49.532 wdl.w:ptcp.t:call-pbmm2_align_hifi-48.stderr VERBOSE   --num-threads 64 \
2025-09-15 20:22:49.532 wdl.w:ptcp.w:call-trgt-04.t:call-trgt_genotype INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:22:49.533 wdl.w:ptcp.w:call-trgt-06 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-06/out/m84036_250809_035451_s4.bc2103.mapped.bam"}
2025-09-15 20:22:49.533 wdl.w:ptcp.t:call-pbmm2_align_hifi-45.stderr VERBOSE   --log-level INFO \
2025-09-15 20:22:49.534 wdl.w:ptcp.w:call-paraphase-30 INFO visit :: node: "decl-config_file", values: {"config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml"}
2025-09-15 20:22:49.534 wdl.w:ptcp.w:call-trgt-04.t:call-get_reads_overlapping_repeats INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:22:49.535 wdl.w:ptcp INFO input :: job: "call-sawfish-05", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-05/out/m84036_250809_035451_s4.bc2102.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-05/out/m84036_250809_035451_s4.bc2102.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2102"}
2025-09-15 20:22:49.535 wdl.w:ptcp.w:call-paraphase-05 NOTICE workflow start :: name: "paraphase", source: "./paraphase.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-05"
2025-09-15 20:22:49.536 wdl.w:ptcp.t:call-pbmm2_align_hifi-52.stderr VERBOSE   align \
2025-09-15 20:22:49.537 wdl.w:ptcp.w:call-paraphase-33 INFO visit :: node: "decl-annotation_vcf", values: {"annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf"}
2025-09-15 20:22:49.537 wdl.w:ptcp.w:call-paraphase-31.t:call-run_paraphase INFO input :: name: "annotation_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf"
2025-09-15 20:22:49.537 wdl.w:ptcp.w:call-sawfish-31.t:call-run_sawfish INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:22:49.537 wdl.w:ptcp.t:call-pbmm2_align_hifi-46.stderr VERBOSE   align \
2025-09-15 20:22:49.538 wdl.w:ptcp.t:call-pbmm2_align_hifi-51.stderr VERBOSE   --log-level INFO \
2025-09-15 20:22:49.537 wdl.w:ptcp.t:call-pbmm2_align_hifi-54.slurm_singularity INFO srun: job 51797278 has been allocated resources
2025-09-15 20:22:49.538 wdl.w:ptcp.w:call-sawfish-06 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-06/out/m84036_250809_035451_s4.bc2103.mapped.bam"}
2025-09-15 20:22:49.538 wdl.w:ptcp.w:call-sawfish-30 INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:22:49.539 wdl.w:ptcp.w:call-sawfish-33 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:22:49.539 wdl.w:ptcp.t:call-pbmm2_align_hifi-42.stderr VERBOSE pbmm2 \
2025-09-15 20:22:49.540 wdl.w:ptcp.w:call-paraphase-06 INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:22:49.540 wdl.w:ptcp.t:call-pbmm2_align_hifi-49.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:22:49.540 wdl.w:ptcp.t:call-pbmm2_align_hifi-53.stderr VERBOSE   align \
2025-09-15 20:22:49.541 wdl.w:ptcp.w:call-trgt-33 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:22:49.541 wdl.w:ptcp.t:call-pbmm2_align_hifi-47.stderr VERBOSE   align \
2025-09-15 20:22:49.541 wdl.w:ptcp.w:call-trgt-30 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-30/out/m84036_250809_035451_s4.bc2127.mapped.bam"}
2025-09-15 20:22:49.541 wdl.w:ptcp.t:call-pbmm2_align_hifi-48.stderr VERBOSE   --sort \
2025-09-15 20:22:49.542 wdl.w:ptcp.w:call-trgt-04.t:call-trgt_genotype INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2101.mapped.bam.bai"
2025-09-15 20:22:49.542 wdl.w:ptcp.w:call-trgt-06 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-06/out/m84036_250809_035451_s4.bc2103.mapped.bam.bai"}
2025-09-15 20:22:49.542 wdl.w:ptcp.t:call-pbmm2_align_hifi-45.stderr VERBOSE   --log-file pbmm2.log \
2025-09-15 20:22:49.542 wdl.w:ptcp.w:call-paraphase-30 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:22:49.542 wdl.w:ptcp.w:call-trgt-04.t:call-get_reads_overlapping_repeats INFO eval :: name: "expand_size", value: 3000
2025-09-15 20:22:49.543 wdl.w:ptcp.t:call-pbmm2_align_hifi-52.stderr VERBOSE   --log-level INFO \
2025-09-15 20:22:49.543 wdl.w:ptcp.w:call-paraphase-33 INFO visit :: node: "decl-config_file", values: {"config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml"}
2025-09-15 20:22:49.543 wdl.w:ptcp.w:call-paraphase-31.t:call-run_paraphase INFO input :: name: "genome_version", value: "38"
2025-09-15 20:22:49.543 wdl.w:ptcp.w:call-sawfish-31.t:call-run_sawfish INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:22:49.544 wdl.w:ptcp NOTICE ready :: job: "call-trgt-05", callee: "trgt"
2025-09-15 20:22:49.543 wdl.w:ptcp.t:call-pbmm2_align_hifi-57.slurm_singularity INFO srun: job 51797277 has been allocated resources
2025-09-15 20:22:49.544 wdl.w:ptcp.t:call-pbmm2_align_hifi-46.stderr VERBOSE   --log-level INFO \
2025-09-15 20:22:49.544 wdl.w:ptcp.t:call-pbmm2_align_hifi-51.stderr VERBOSE   --log-file pbmm2.log \
2025-09-15 20:22:49.544 wdl.w:ptcp.t:call-pbmm2_align_hifi-54.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:22:49.544 wdl.w:ptcp.w:call-sawfish-06 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-06/out/m84036_250809_035451_s4.bc2103.mapped.bam.bai"}
2025-09-15 20:22:49.545 wdl.w:ptcp.w:call-sawfish-30 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-30/out/m84036_250809_035451_s4.bc2127.mapped.bam"}
2025-09-15 20:22:49.545 wdl.w:ptcp.w:call-sawfish-33 INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:22:49.545 wdl.w:ptcp.t:call-pbmm2_align_hifi-42.stderr VERBOSE   align \
2025-09-15 20:22:49.545 wdl.w:ptcp.w:call-paraphase-06 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-06/out/m84036_250809_035451_s4.bc2103.mapped.bam"}
2025-09-15 20:22:49.545 wdl.w:ptcp.t:call-pbmm2_align_hifi-49.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:22:49.545 wdl.w:ptcp.t:call-pbmm2_align_hifi-53.stderr VERBOSE   --log-level INFO \
2025-09-15 20:22:49.545 wdl.w:ptcp.w:call-trgt-33 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-33/out/m84036_250809_035451_s4.bc2130.mapped.bam"}
2025-09-15 20:22:49.546 wdl.w:ptcp.t:call-pbmm2_align_hifi-47.stderr VERBOSE   --log-level INFO \
2025-09-15 20:22:49.546 wdl.w:ptcp.w:call-trgt-30 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-30/out/m84036_250809_035451_s4.bc2127.mapped.bam.bai"}
2025-09-15 20:22:49.546 wdl.w:ptcp.t:call-pbmm2_align_hifi-48.stderr VERBOSE   --preset HiFi \
2025-09-15 20:22:49.546 wdl.w:ptcp.w:call-trgt-04.t:call-trgt_genotype INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2101.mapped.bam"
2025-09-15 20:22:49.546 wdl.w:ptcp.w:call-trgt-06 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:22:49.546 wdl.w:ptcp.t:call-pbmm2_align_hifi-45.stderr VERBOSE   --alarms alarms.json \
2025-09-15 20:22:49.546 wdl.w:ptcp.w:call-paraphase-30 INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:22:49.547 wdl.w:ptcp.w:call-trgt-04.t:call-get_reads_overlapping_repeats INFO eval :: name: "threads", value: 1
2025-09-15 20:22:49.547 wdl.w:ptcp.t:call-pbmm2_align_hifi-52.stderr VERBOSE   --log-file pbmm2.log \
2025-09-15 20:22:49.547 wdl.w:ptcp.w:call-paraphase-33 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:22:49.547 wdl.w:ptcp.w:call-paraphase-31.t:call-run_paraphase INFO input :: name: "config_file", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/paraphase_config.GRCh38.yaml"
2025-09-15 20:22:49.547 wdl.w:ptcp.w:call-sawfish-31.t:call-run_sawfish INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2128.mapped.bam.bai"
2025-09-15 20:22:49.547 wdl.w:ptcp INFO input :: job: "call-trgt-05", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-05/out/m84036_250809_035451_s4.bc2102.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-05/out/m84036_250809_035451_s4.bc2102.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2102"}
2025-09-15 20:22:49.547 wdl.w:ptcp.t:call-pbmm2_align_hifi-57.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:22:49.547 wdl.w:ptcp.t:call-pbmm2_align_hifi-46.stderr VERBOSE   --log-file pbmm2.log \
2025-09-15 20:22:49.547 wdl.w:ptcp.t:call-pbmm2_align_hifi-51.stderr VERBOSE   --alarms alarms.json \
2025-09-15 20:22:49.548 wdl.w:ptcp.t:call-pbmm2_align_hifi-54.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:22:49.548 wdl.w:ptcp.w:call-sawfish-06 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:22:49.548 wdl.w:ptcp.w:call-sawfish-30 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-30/out/m84036_250809_035451_s4.bc2127.mapped.bam.bai"}
2025-09-15 20:22:49.548 wdl.w:ptcp.w:call-sawfish-33 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-33/out/m84036_250809_035451_s4.bc2130.mapped.bam"}
2025-09-15 20:22:49.548 wdl.w:ptcp.t:call-pbmm2_align_hifi-42.stderr VERBOSE   --log-level INFO \
2025-09-15 20:22:49.548 wdl.w:ptcp.w:call-paraphase-06 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-06/out/m84036_250809_035451_s4.bc2103.mapped.bam.bai"}
2025-09-15 20:22:49.549 wdl.w:ptcp.t:call-pbmm2_align_hifi-53.stderr VERBOSE   --log-file pbmm2.log \
2025-09-15 20:22:49.549 wdl.w:ptcp.w:call-trgt-33 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-33/out/m84036_250809_035451_s4.bc2130.mapped.bam.bai"}
2025-09-15 20:22:49.549 wdl.w:ptcp.t:call-pbmm2_align_hifi-47.stderr VERBOSE   --log-file pbmm2.log \
2025-09-15 20:22:49.549 wdl.w:ptcp.w:call-trgt-30 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:22:49.549 wdl.w:ptcp.t:call-pbmm2_align_hifi-48.stderr VERBOSE   --report-json mapping_stats.report.json \
2025-09-15 20:22:49.549 wdl.w:ptcp.w:call-trgt-04.t:call-trgt_genotype INFO input :: name: "sex", value: "F"
2025-09-15 20:22:49.550 wdl.w:ptcp.w:call-trgt-06 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:22:49.550 wdl.w:ptcp.t:call-pbmm2_align_hifi-45.stderr VERBOSE   --num-threads 64 \
2025-09-15 20:22:49.550 wdl.w:ptcp.w:call-paraphase-30 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-30/out/m84036_250809_035451_s4.bc2127.mapped.bam"}
2025-09-15 20:22:49.550 wdl.w:ptcp.w:call-sawfish-05 NOTICE workflow start :: name: "sawfish", source: "./sawfish.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-05"
2025-09-15 20:22:49.550 wdl.w:ptcp.w:call-trgt-04.t:call-get_reads_overlapping_repeats INFO eval :: name: "expanded_bed_name", value: "m84036_250809_035451_s4.bc2101.expanded.bed"
2025-09-15 20:22:49.550 wdl.w:ptcp.t:call-pbmm2_align_hifi-52.stderr VERBOSE   --alarms alarms.json \
2025-09-15 20:22:49.550 wdl.w:ptcp.w:call-paraphase-33 INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:22:49.551 wdl.w:ptcp.w:call-paraphase-31.t:call-run_paraphase INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:22:49.551 wdl.w:ptcp.w:call-sawfish-31.t:call-run_sawfish INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2128.mapped.bam"
2025-09-15 20:22:49.551 wdl.w:ptcp.t:call-pbmm2_align_hifi-57.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:22:49.551 wdl.w:ptcp.t:call-pbmm2_align_hifi-46.stderr VERBOSE   --alarms alarms.json \
2025-09-15 20:22:49.551 wdl.w:ptcp.t:call-pbmm2_align_hifi-51.stderr VERBOSE   --num-threads 64 \
2025-09-15 20:22:49.551 wdl.w:ptcp.w:call-sawfish-06 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:22:49.552 wdl.w:ptcp.w:call-sawfish-30 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:22:49.552 wdl.w:ptcp.w:call-sawfish-33 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-33/out/m84036_250809_035451_s4.bc2130.mapped.bam.bai"}
2025-09-15 20:22:49.552 wdl.w:ptcp.t:call-pbmm2_align_hifi-42.stderr VERBOSE   --log-file pbmm2.log \
2025-09-15 20:22:49.552 wdl.w:ptcp.w:call-paraphase-06 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:22:49.553 wdl.w:ptcp.t:call-pbmm2_align_hifi-53.stderr VERBOSE   --alarms alarms.json \
2025-09-15 20:22:49.553 wdl.w:ptcp.w:call-trgt-33 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:22:49.553 wdl.w:ptcp.t:call-pbmm2_align_hifi-47.stderr VERBOSE   --alarms alarms.json \
2025-09-15 20:22:49.553 wdl.w:ptcp.w:call-trgt-30 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:22:49.553 wdl.w:ptcp.t:call-pbmm2_align_hifi-48.stderr VERBOSE   --sample "m84036_250809_035451_s4.bc2145" \
2025-09-15 20:22:49.553 wdl.w:ptcp.w:call-trgt-04.t:call-trgt_genotype INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2101"
2025-09-15 20:22:49.553 wdl.w:ptcp.w:call-trgt-06 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2103"}
2025-09-15 20:22:49.554 wdl.w:ptcp.t:call-pbmm2_align_hifi-45.stderr VERBOSE   --sort \
2025-09-15 20:22:49.554 wdl.w:ptcp.w:call-paraphase-30 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-30/out/m84036_250809_035451_s4.bc2127.mapped.bam.bai"}
2025-09-15 20:22:49.554 wdl.w:ptcp.t:call-pbmm2_align_hifi-52.stderr VERBOSE   --num-threads 64 \
2025-09-15 20:22:49.554 wdl.w:ptcp.w:call-trgt-04.t:call-get_reads_overlapping_repeats INFO eval :: name: "disk_size", value: 11
2025-09-15 20:22:49.554 wdl.w:ptcp.w:call-paraphase-33 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-33/out/m84036_250809_035451_s4.bc2130.mapped.bam"}
2025-09-15 20:22:49.555 wdl.w:ptcp.w:call-paraphase-31.t:call-run_paraphase INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:22:49.555 wdl.w:ptcp.w:call-sawfish-31.t:call-run_sawfish INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2128"
2025-09-15 20:22:49.555 wdl.w:ptcp.t:call-pbmm2_align_hifi-46.stderr VERBOSE   --num-threads 64 \
2025-09-15 20:22:49.555 wdl.w:ptcp.t:call-pbmm2_align_hifi-51.stderr VERBOSE   --sort \
2025-09-15 20:22:49.555 wdl.w:ptcp.w:call-sawfish-06 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2103"}
2025-09-15 20:22:49.555 wdl.w:ptcp.w:call-sawfish-30 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:22:49.555 wdl.w:ptcp.w:call-sawfish-33 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:22:49.556 wdl.w:ptcp.t:call-pbmm2_align_hifi-42.stderr VERBOSE   --alarms alarms.json \
2025-09-15 20:22:49.556 wdl.w:ptcp.w:call-paraphase-06 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:22:49.556 wdl.w:ptcp.t:call-pbmm2_align_hifi-53.stderr VERBOSE   --num-threads 64 \
2025-09-15 20:22:49.556 wdl.w:ptcp.w:call-trgt-33 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:22:49.556 wdl.w:ptcp.t:call-pbmm2_align_hifi-47.stderr VERBOSE   --num-threads 64 \
2025-09-15 20:22:49.556 wdl.w:ptcp.w:call-trgt-30 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2127"}
2025-09-15 20:22:49.557 wdl.w:ptcp.t:call-pbmm2_align_hifi-48.stderr VERBOSE   --unmapped \
2025-09-15 20:22:49.557 wdl.w:ptcp.w:call-trgt-04.t:call-trgt_genotype INFO eval :: name: "mem_gb", value: 16
2025-09-15 20:22:49.556 wdl.w:ptcp.t:call-pbmm2_align_hifi-56.slurm_singularity INFO srun: job 51797275 has been allocated resources
2025-09-15 20:22:49.557 wdl.w:ptcp.w:call-trgt-06 INFO visit :: node: "decl-sex", values: {"sex": "F"}
2025-09-15 20:22:49.557 wdl.w:ptcp.t:call-pbmm2_align_hifi-45.stderr VERBOSE   --preset HiFi \
2025-09-15 20:22:49.557 wdl.w:ptcp.w:call-paraphase-30 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:22:49.557 wdl.w:ptcp.t:call-pbmm2_align_hifi-52.stderr VERBOSE   --sort \
2025-09-15 20:22:49.558 wdl.w:ptcp.w:call-trgt-04.t:call-get_reads_overlapping_repeats INFO eval :: name: "output_name", value: "m84036_250809_035451_s4.bc2101.repeats.bam"
2025-09-15 20:22:49.558 wdl.w:ptcp.w:call-paraphase-33 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-33/out/m84036_250809_035451_s4.bc2130.mapped.bam.bai"}
2025-09-15 20:22:49.558 wdl.w:ptcp.w:call-paraphase-31.t:call-run_paraphase INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2128.mapped.bam.bai"
2025-09-15 20:22:49.558 wdl.w:ptcp.w:call-sawfish-31.t:call-run_sawfish INFO eval :: name: "mem_gb", value: 32
2025-09-15 20:22:49.558 wdl.w:ptcp.t:call-pbmm2_align_hifi-46.stderr VERBOSE   --sort \
2025-09-15 20:22:49.558 wdl.w:ptcp.t:call-pbmm2_align_hifi-51.stderr VERBOSE   --preset HiFi \
2025-09-15 20:22:49.559 wdl.w:ptcp.w:call-sawfish-06 NOTICE ready :: job: "call-run_sawfish", callee: "run_sawfish"
2025-09-15 20:22:49.559 wdl.w:ptcp.w:call-sawfish-30 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2127"}
2025-09-15 20:22:49.559 wdl.w:ptcp.w:call-sawfish-33 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:22:49.559 wdl.w:ptcp.t:call-pbmm2_align_hifi-42.stderr VERBOSE   --num-threads 64 \
2025-09-15 20:22:49.560 wdl.w:ptcp.w:call-paraphase-06 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2103"}
2025-09-15 20:22:49.560 wdl.w:ptcp.t:call-pbmm2_align_hifi-53.stderr VERBOSE   --sort \
2025-09-15 20:22:49.560 wdl.w:ptcp.w:call-trgt-33 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2130"}
2025-09-15 20:22:49.560 wdl.w:ptcp.t:call-pbmm2_align_hifi-47.stderr VERBOSE   --sort \
2025-09-15 20:22:49.560 wdl.w:ptcp.w:call-trgt-05 NOTICE workflow start :: name: "trgt", source: "./trgt.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-05"
2025-09-15 20:22:49.560 wdl.w:ptcp.w:call-trgt-30 INFO visit :: node: "decl-sex", values: {"sex": "F"}
2025-09-15 20:22:49.561 wdl.w:ptcp.t:call-pbmm2_align_hifi-48.stderr VERBOSE   /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa \
2025-09-15 20:22:49.561 wdl.w:ptcp.w:call-trgt-04.t:call-trgt_genotype INFO eval :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2101.trgt"
2025-09-15 20:22:49.561 wdl.w:ptcp.t:call-pbmm2_align_hifi-56.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:22:49.561 wdl.w:ptcp.w:call-trgt-06 INFO visit :: node: "decl-trgt_bed", values: {"trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"}
2025-09-15 20:22:49.561 wdl.w:ptcp.t:call-pbmm2_align_hifi-45.stderr VERBOSE   --report-json mapping_stats.report.json \
2025-09-15 20:22:49.561 wdl.w:ptcp.w:call-paraphase-30 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:22:49.562 wdl.w:ptcp.t:call-pbmm2_align_hifi-52.stderr VERBOSE   --preset HiFi \
2025-09-15 20:22:49.562 wdl.w:ptcp.w:call-trgt-04.t:call-get_reads_overlapping_repeats INFO eval :: name: "index_name", value: "m84036_250809_035451_s4.bc2101.repeats.bam.bai"
2025-09-15 20:22:49.562 wdl.w:ptcp.w:call-paraphase-33 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:22:49.562 wdl.w:ptcp.w:call-paraphase-31.t:call-run_paraphase INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2128.mapped.bam"
2025-09-15 20:22:49.562 wdl.w:ptcp.w:call-sawfish-31.t:call-run_sawfish INFO eval :: name: "threads", value: 16
2025-09-15 20:22:49.562 wdl.w:ptcp.t:call-pbmm2_align_hifi-46.stderr VERBOSE   --preset HiFi \
2025-09-15 20:22:49.562 wdl.w:ptcp.t:call-pbmm2_align_hifi-51.stderr VERBOSE   --report-json mapping_stats.report.json \
2025-09-15 20:22:49.562 wdl.w:ptcp.w:call-sawfish-06 INFO input :: job: "call-run_sawfish", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-06/out/m84036_250809_035451_s4.bc2103.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-06/out/m84036_250809_035451_s4.bc2103.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2103"}
2025-09-15 20:22:49.563 wdl.w:ptcp.w:call-sawfish-30 NOTICE ready :: job: "call-run_sawfish", callee: "run_sawfish"
2025-09-15 20:22:49.563 wdl.w:ptcp.w:call-sawfish-33 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2130"}
2025-09-15 20:22:49.563 wdl.w:ptcp.t:call-pbmm2_align_hifi-42.stderr VERBOSE   --sort \
2025-09-15 20:22:49.564 wdl.w:ptcp.w:call-paraphase-06 INFO visit :: node: "decl-sex", values: {"sex": "F"}
2025-09-15 20:22:49.564 wdl.w:ptcp.t:call-pbmm2_align_hifi-53.stderr VERBOSE   --preset HiFi \
2025-09-15 20:22:49.564 wdl.w:ptcp.w:call-trgt-33 INFO visit :: node: "decl-sex", values: {"sex": "F"}
2025-09-15 20:22:49.564 wdl.w:ptcp.t:call-pbmm2_align_hifi-47.stderr VERBOSE   --preset HiFi \
2025-09-15 20:22:49.565 wdl.w:ptcp.w:call-trgt-30 INFO visit :: node: "decl-trgt_bed", values: {"trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"}
2025-09-15 20:22:49.565 wdl.w:ptcp.t:call-pbmm2_align_hifi-48.stderr VERBOSE   /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0049_m84036_250809_035451_s4.bc2145.unmapped.bam \
2025-09-15 20:22:49.565 wdl.w:ptcp.w:call-trgt-04.t:call-trgt_genotype INFO eval :: name: "threads", value: 8
2025-09-15 20:22:49.566 wdl.w:ptcp.t:call-pbmm2_align_hifi-56.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:22:49.566 wdl.w:ptcp.w:call-trgt-06 NOTICE ready :: job: "call-get_reads_overlapping_repeats", callee: "get_reads_overlapping_repeats"
2025-09-15 20:22:49.567 wdl.w:ptcp.t:call-pbmm2_align_hifi-45.stderr VERBOSE   --sample "m84036_250809_035451_s4.bc2142" \
2025-09-15 20:22:49.567 wdl.w:ptcp.w:call-paraphase-30 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2127"}
2025-09-15 20:22:49.567 wdl.w:ptcp.t:call-pbmm2_align_hifi-52.stderr VERBOSE   --report-json mapping_stats.report.json \
2025-09-15 20:22:49.567 wdl.w:ptcp.w:call-trgt-04.t:call-get_reads_overlapping_repeats INFO eval :: name: "output_name_with_index", value: "m84036_250809_035451_s4.bc2101.repeats.bam##idx##m84036_250809_035451_s4.bc2101.repeats.bam.bai"
2025-09-15 20:22:49.567 wdl.w:ptcp.w:call-paraphase-33 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:22:49.568 wdl.w:ptcp.w:call-paraphase-31.t:call-run_paraphase INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2128"
2025-09-15 20:22:49.568 wdl.w:ptcp.w:call-sawfish-31.t:call-run_sawfish INFO eval :: name: "disk_size", value: 30
2025-09-15 20:22:49.568 wdl.w:ptcp.t:call-pbmm2_align_hifi-46.stderr VERBOSE   --report-json mapping_stats.report.json \
2025-09-15 20:22:49.569 wdl.w:ptcp.t:call-pbmm2_align_hifi-51.stderr VERBOSE   --sample "m84036_250809_035451_s4.bc2148" \
2025-09-15 20:22:49.569 wdl.w:ptcp.w:call-sawfish-30 INFO input :: job: "call-run_sawfish", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-30/out/m84036_250809_035451_s4.bc2127.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-30/out/m84036_250809_035451_s4.bc2127.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2127"}
2025-09-15 20:22:49.570 wdl.w:ptcp.w:call-sawfish-33 NOTICE ready :: job: "call-run_sawfish", callee: "run_sawfish"
2025-09-15 20:22:49.570 wdl.w:ptcp.t:call-pbmm2_align_hifi-42.stderr VERBOSE   --preset HiFi \
2025-09-15 20:22:49.571 wdl.w:ptcp.w:call-paraphase-06 NOTICE ready :: job: "call-run_paraphase", callee: "run_paraphase"
2025-09-15 20:22:49.571 wdl.w:ptcp.t:call-pbmm2_align_hifi-53.stderr VERBOSE   --report-json mapping_stats.report.json \
2025-09-15 20:22:49.571 wdl.w:ptcp.w:call-trgt-33 INFO visit :: node: "decl-trgt_bed", values: {"trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"}
2025-09-15 20:22:49.572 wdl.w:ptcp.t:call-pbmm2_align_hifi-47.stderr VERBOSE   --report-json mapping_stats.report.json \
2025-09-15 20:22:49.572 wdl.w:ptcp.w:call-trgt-30 NOTICE ready :: job: "call-get_reads_overlapping_repeats", callee: "get_reads_overlapping_repeats"
2025-09-15 20:22:49.573 wdl.w:ptcp.t:call-pbmm2_align_hifi-48.stderr VERBOSE   m84036_250809_035451_s4.bc2145.mapped.bam
2025-09-15 20:22:49.574 wdl.w:ptcp.w:call-trgt-06 INFO input :: job: "call-get_reads_overlapping_repeats", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-06/out/m84036_250809_035451_s4.bc2103.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-06/out/m84036_250809_035451_s4.bc2103.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2103"}
2025-09-15 20:22:49.574 wdl.w:ptcp.t:call-pbmm2_align_hifi-45.stderr VERBOSE   --unmapped \
2025-09-15 20:22:49.574 wdl.w:ptcp.w:call-trgt-04.t:call-trgt_genotype INFO eval :: name: "disk_size", value: 27
2025-09-15 20:22:49.575 wdl.w:ptcp.w:call-paraphase-30 INFO visit :: node: "decl-sex", values: {"sex": "F"}
2025-09-15 20:22:49.576 wdl.w:ptcp.w:call-paraphase-05 INFO visit :: node: "decl-annotation_vcf", values: {"annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf"}
2025-09-15 20:22:49.576 wdl.w:ptcp.t:call-pbmm2_align_hifi-52.stderr VERBOSE   --sample "m84036_250809_035451_s4.bc2149" \
2025-09-15 20:22:49.577 wdl.w:ptcp.w:call-paraphase-33 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2130"}
2025-09-15 20:22:49.577 wdl.w:ptcp.w:call-paraphase-31.t:call-run_paraphase INFO eval :: name: "threads", value: 4
2025-09-15 20:22:49.577 wdl.w:ptcp.w:call-trgt-04.t:call-get_reads_overlapping_repeats INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:22:49.578 wdl.w:ptcp.w:call-sawfish-31.t:call-run_sawfish INFO eval :: name: "discover_dirname", value: "m84036_250809_035451_s4.bc2128_sawfish_discover"
2025-09-15 20:22:49.578 wdl.w:ptcp.t:call-pbmm2_align_hifi-46.stderr VERBOSE   --sample "m84036_250809_035451_s4.bc2143" \
2025-09-15 20:22:49.578 wdl.w:ptcp.t:call-pbmm2_align_hifi-51.stderr VERBOSE   --unmapped \
2025-09-15 20:22:49.578 wdl.w:ptcp.w:call-sawfish-33 INFO input :: job: "call-run_sawfish", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-33/out/m84036_250809_035451_s4.bc2130.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-33/out/m84036_250809_035451_s4.bc2130.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2130"}
2025-09-15 20:22:49.579 wdl.w:ptcp.t:call-pbmm2_align_hifi-42.stderr VERBOSE   --report-json mapping_stats.report.json \
2025-09-15 20:22:49.579 wdl.w:ptcp.w:call-paraphase-06 INFO input :: job: "call-run_paraphase", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf", "genome_version": "38", "config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-06/out/m84036_250809_035451_s4.bc2103.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-06/out/m84036_250809_035451_s4.bc2103.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2103"}
2025-09-15 20:22:49.579 wdl.w:ptcp.t:call-pbmm2_align_hifi-53.stderr VERBOSE   --sample "m84036_250809_035451_s4.bc2150" \
2025-09-15 20:22:49.579 wdl.w:ptcp.t:call-pbmm2_align_hifi-58.slurm_singularity INFO srun: job 51797280 has been allocated resources
2025-09-15 20:22:49.580 wdl.w:ptcp.w:call-trgt-33 NOTICE ready :: job: "call-get_reads_overlapping_repeats", callee: "get_reads_overlapping_repeats"
2025-09-15 20:22:49.580 wdl.w:ptcp.t:call-pbmm2_align_hifi-47.stderr VERBOSE   --sample "m84036_250809_035451_s4.bc2144" \
2025-09-15 20:22:49.580 wdl.w:ptcp.w:call-trgt-30 INFO input :: job: "call-get_reads_overlapping_repeats", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-30/out/m84036_250809_035451_s4.bc2127.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-30/out/m84036_250809_035451_s4.bc2127.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2127"}
2025-09-15 20:22:49.580 wdl.w:ptcp.t:call-pbmm2_align_hifi-48.stderr VERBOSE + pbmm2 align --log-level INFO --log-file pbmm2.log --alarms alarms.json --num-threads 64 --sort --preset HiFi --report-json mapping_stats.report.json --sample m84036_250809_035451_s4.bc2145 --unmapped /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0049_m84036_250809_035451_s4.bc2145.unmapped.bam m84036_250809_035451_s4.bc2145.mapped.bam
2025-09-15 20:22:49.581 wdl.w:ptcp.t:call-pbmm2_align_hifi-45.stderr VERBOSE   /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa \
2025-09-15 20:22:49.582 wdl.w:ptcp.w:call-trgt-06 NOTICE ready :: job: "call-trgt_genotype", callee: "trgt_genotype"
2025-09-15 20:22:49.582 wdl.w:ptcp.w:call-paraphase-30 NOTICE ready :: job: "call-run_paraphase", callee: "run_paraphase"
2025-09-15 20:22:49.582 wdl.w:ptcp.w:call-trgt-04.t:call-trgt_genotype INFO eval :: name: "karyotype", value: "XX"
2025-09-15 20:22:49.583 wdl.w:ptcp.w:call-paraphase-05 INFO visit :: node: "decl-config_file", values: {"config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml"}
2025-09-15 20:22:49.583 wdl.w:ptcp.t:call-pbmm2_align_hifi-52.stderr VERBOSE   --unmapped \
2025-09-15 20:22:49.583 wdl.w:ptcp.w:call-paraphase-33 INFO visit :: node: "decl-sex", values: {"sex": "F"}
2025-09-15 20:22:49.583 wdl.w:ptcp.w:call-paraphase-31.t:call-run_paraphase INFO eval :: name: "mem_gb", value: 8
2025-09-15 20:22:49.584 wdl.w:ptcp.w:call-trgt-04.t:call-get_reads_overlapping_repeats WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:22:49.584 wdl.w:ptcp.t:call-pbmm2_align_hifi-13 NOTICE done
2025-09-15 20:22:49.585 wdl.w:ptcp.w:call-sawfish-05 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:22:49.585 wdl.w:ptcp.w:call-sawfish-31.t:call-run_sawfish INFO eval :: name: "call_dirname", value: "m84036_250809_035451_s4.bc2128_sawfish"
2025-09-15 20:22:49.585 wdl.w:ptcp.t:call-pbmm2_align_hifi-46.stderr VERBOSE   --unmapped \
2025-09-15 20:22:49.586 wdl.w:ptcp.t:call-pbmm2_align_hifi-51.stderr VERBOSE   /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa \
2025-09-15 20:22:49.586 wdl.w:ptcp.t:call-pbmm2_align_hifi-42.stderr VERBOSE   --sample "m84036_250809_035451_s4.bc2139" \
2025-09-15 20:22:49.587 wdl.w:ptcp.t:call-pbmm2_align_hifi-53.stderr VERBOSE   --unmapped \
2025-09-15 20:22:49.587 wdl.w:ptcp.t:call-pbmm2_align_hifi-58.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:22:49.587 wdl.w:ptcp.w:call-trgt-33 INFO input :: job: "call-get_reads_overlapping_repeats", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-33/out/m84036_250809_035451_s4.bc2130.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-33/out/m84036_250809_035451_s4.bc2130.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2130"}
2025-09-15 20:22:49.587 wdl.w:ptcp.t:call-pbmm2_align_hifi-47.stderr VERBOSE   --unmapped \
2025-09-15 20:22:49.588 wdl.w:ptcp.t:call-pbmm2_align_hifi-45.stderr VERBOSE   /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0046_m84036_250809_035451_s4.bc2142.unmapped.bam \
2025-09-15 20:22:49.588 wdl.w:ptcp.w:call-trgt-06 INFO input :: job: "call-trgt_genotype", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-06/out/m84036_250809_035451_s4.bc2103.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-06/out/m84036_250809_035451_s4.bc2103.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2103"}
2025-09-15 20:22:49.588 wdl.w:ptcp.w:call-trgt-30 NOTICE ready :: job: "call-trgt_genotype", callee: "trgt_genotype"
2025-09-15 20:22:49.589 wdl.w:ptcp.w:call-paraphase-30 INFO input :: job: "call-run_paraphase", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf", "genome_version": "38", "config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-30/out/m84036_250809_035451_s4.bc2127.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-30/out/m84036_250809_035451_s4.bc2127.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2127"}
2025-09-15 20:22:49.590 wdl.w:ptcp.w:call-paraphase-05 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:22:49.590 wdl.w:ptcp.w:call-trgt-04.t:call-trgt_genotype INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 8, memory_reservation: 16000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:22:49.590 wdl.w:ptcp.t:call-pbmm2_align_hifi-52.stderr VERBOSE   /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa \
2025-09-15 20:22:49.591 wdl.w:ptcp.w:call-paraphase-33 NOTICE ready :: job: "call-run_paraphase", callee: "run_paraphase"
2025-09-15 20:22:49.591 wdl.w:ptcp.w:call-paraphase-31.t:call-run_paraphase INFO eval :: name: "disk_size", value: 27
2025-09-15 20:22:49.592 wdl.w:ptcp.w:call-sawfish-05 INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:22:49.592 wdl.w:ptcp.w:call-sawfish-31.t:call-run_sawfish INFO eval :: name: "minimap2_bam_filename", value: "m84036_250809_035451_s4.bc2128.minimap2.bam"
2025-09-15 20:22:49.592 wdl.w:ptcp.t:call-pbmm2_align_hifi-46.stderr VERBOSE   /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa \
2025-09-15 20:22:49.592 wdl.w:ptcp.t:call-pbmm2_align_hifi-51.stderr VERBOSE   /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0052_m84036_250809_035451_s4.bc2148.unmapped.bam \
2025-09-15 20:22:49.592 wdl.w:ptcp.w:call-trgt-04.t:call-get_reads_overlapping_repeats INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:22:49.593 wdl.w:ptcp.t:call-pbmm2_align_hifi-42.stderr VERBOSE   --unmapped \
2025-09-15 20:22:49.593 wdl.w:ptcp.t:call-pbmm2_align_hifi-53.stderr VERBOSE   /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa \
2025-09-15 20:22:49.593 wdl.w:ptcp.t:call-pbmm2_align_hifi-47.stderr VERBOSE   /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa \
2025-09-15 20:22:49.594 wdl.w:ptcp.t:call-pbmm2_align_hifi-45.stderr VERBOSE   m84036_250809_035451_s4.bc2142.mapped.bam
2025-09-15 20:22:49.594 wdl.w:ptcp.w:call-trgt-05 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:22:49.595 wdl.w:ptcp.w:call-trgt-33 NOTICE ready :: job: "call-trgt_genotype", callee: "trgt_genotype"
2025-09-15 20:22:49.595 wdl.w:ptcp.w:call-trgt-30 INFO input :: job: "call-trgt_genotype", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-30/out/m84036_250809_035451_s4.bc2127.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-30/out/m84036_250809_035451_s4.bc2127.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2127"}
2025-09-15 20:22:49.595 wdl.w:ptcp.w:call-paraphase-05 INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:22:49.595 wdl.w:ptcp.w:call-trgt-04.t:call-trgt_genotype WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:22:49.596 wdl.w:ptcp.t:call-pbmm2_align_hifi-52.stderr VERBOSE   /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0053_m84036_250809_035451_s4.bc2149.unmapped.bam \
2025-09-15 20:22:49.596 wdl.w:ptcp.w:call-paraphase-33 INFO input :: job: "call-run_paraphase", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf", "genome_version": "38", "config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-33/out/m84036_250809_035451_s4.bc2130.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-33/out/m84036_250809_035451_s4.bc2130.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2130"}
2025-09-15 20:22:49.596 wdl.w:ptcp.w:call-paraphase-31.t:call-run_paraphase INFO eval :: name: "out_dir", value: "m84036_250809_035451_s4.bc2128_paraphase"
2025-09-15 20:22:49.596 wdl.w:ptcp.w:call-sawfish-05 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-05/out/m84036_250809_035451_s4.bc2102.mapped.bam"}
2025-09-15 20:22:49.597 wdl.w:ptcp.t:call-pbmm2_align_hifi-46.stderr VERBOSE   /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0047_m84036_250809_035451_s4.bc2143.unmapped.bam \
2025-09-15 20:22:49.597 wdl.w:ptcp.t:call-pbmm2_align_hifi-48.slurm_singularity INFO srun: job 51797271 has been allocated resources
2025-09-15 20:22:49.597 wdl.w:ptcp.w:call-sawfish-31.t:call-run_sawfish INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 16, memory_reservation: 32000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:22:49.597 wdl.w:ptcp.t:call-pbmm2_align_hifi-51.stderr VERBOSE   m84036_250809_035451_s4.bc2148.mapped.bam
2025-09-15 20:22:49.597 wdl.w:ptcp.t:call-pbmm2_align_hifi-55.slurm_singularity INFO srun: job 51797279 has been allocated resources
2025-09-15 20:22:49.597 wdl.w:ptcp.w:call-trgt-04.t:call-get_reads_overlapping_repeats INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:22:49.598 wdl.w:ptcp.t:call-pbmm2_align_hifi-42.stderr VERBOSE   /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa \
2025-09-15 20:22:49.598 wdl.w:ptcp.t:call-pbmm2_align_hifi-53.stderr VERBOSE   /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0054_m84036_250809_035451_s4.bc2150.unmapped.bam \
2025-09-15 20:22:49.598 wdl.w:ptcp.t:call-pbmm2_align_hifi-47.stderr VERBOSE   /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0048_m84036_250809_035451_s4.bc2144.unmapped.bam \
2025-09-15 20:22:49.598 wdl.w:ptcp.t:call-pbmm2_align_hifi-45.stderr VERBOSE + pbmm2 align --log-level INFO --log-file pbmm2.log --alarms alarms.json --num-threads 64 --sort --preset HiFi --report-json mapping_stats.report.json --sample m84036_250809_035451_s4.bc2142 --unmapped /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0046_m84036_250809_035451_s4.bc2142.unmapped.bam m84036_250809_035451_s4.bc2142.mapped.bam
2025-09-15 20:22:49.598 wdl.w:ptcp.w:call-trgt-05 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-05/out/m84036_250809_035451_s4.bc2102.mapped.bam"}
2025-09-15 20:22:49.598 wdl.w:ptcp.w:call-trgt-33 INFO input :: job: "call-trgt_genotype", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-33/out/m84036_250809_035451_s4.bc2130.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-33/out/m84036_250809_035451_s4.bc2130.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2130"}
2025-09-15 20:22:49.599 wdl.w:ptcp.w:call-paraphase-05 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-05/out/m84036_250809_035451_s4.bc2102.mapped.bam"}
2025-09-15 20:22:49.599 wdl.w:ptcp.t:call-pbmm2_align_hifi-52.stderr VERBOSE   m84036_250809_035451_s4.bc2149.mapped.bam
2025-09-15 20:22:49.600 wdl.w:ptcp.w:call-sawfish-05 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-05/out/m84036_250809_035451_s4.bc2102.mapped.bam.bai"}
2025-09-15 20:22:49.600 wdl.w:ptcp.t:call-pbmm2_align_hifi-46.stderr VERBOSE   m84036_250809_035451_s4.bc2143.mapped.bam
2025-09-15 20:22:49.600 wdl.w:ptcp.t:call-pbmm2_align_hifi-48.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:22:49.600 wdl.w:ptcp.w:call-sawfish-31.t:call-run_sawfish WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:22:49.600 wdl.w:ptcp.w:call-paraphase-31.t:call-run_paraphase INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 4, memory_reservation: 8000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:22:49.601 wdl.w:ptcp.w:call-trgt-04.t:call-trgt_genotype INFO provisioned :: seconds_waited: 0, cpu: 8, mem_bytes: 16000000000
2025-09-15 20:22:49.601 wdl.w:ptcp.t:call-pbmm2_align_hifi-51.stderr VERBOSE + pbmm2 align --log-level INFO --log-file pbmm2.log --alarms alarms.json --num-threads 64 --sort --preset HiFi --report-json mapping_stats.report.json --sample m84036_250809_035451_s4.bc2148 --unmapped /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0052_m84036_250809_035451_s4.bc2148.unmapped.bam m84036_250809_035451_s4.bc2148.mapped.bam
2025-09-15 20:22:49.601 wdl.w:ptcp.t:call-pbmm2_align_hifi-55.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:22:49.601 wdl.w:ptcp.t:call-pbmm2_align_hifi-42.stderr VERBOSE   /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0043_m84036_250809_035451_s4.bc2139.unmapped.bam \
2025-09-15 20:22:49.601 wdl.w:ptcp.t:call-pbmm2_align_hifi-53.stderr VERBOSE   m84036_250809_035451_s4.bc2150.mapped.bam
2025-09-15 20:22:49.602 wdl.w:ptcp.t:call-pbmm2_align_hifi-47.stderr VERBOSE   m84036_250809_035451_s4.bc2144.mapped.bam
2025-09-15 20:22:49.602 wdl.w:ptcp.w:call-trgt-05 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-05/out/m84036_250809_035451_s4.bc2102.mapped.bam.bai"}
2025-09-15 20:22:49.602 wdl.w:ptcp.w:call-paraphase-05 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-05/out/m84036_250809_035451_s4.bc2102.mapped.bam.bai"}
2025-09-15 20:22:49.602 wdl.w:ptcp.t:call-pbmm2_align_hifi-52.stderr VERBOSE + pbmm2 align --log-level INFO --log-file pbmm2.log --alarms alarms.json --num-threads 64 --sort --preset HiFi --report-json mapping_stats.report.json --sample m84036_250809_035451_s4.bc2149 --unmapped /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0053_m84036_250809_035451_s4.bc2149.unmapped.bam m84036_250809_035451_s4.bc2149.mapped.bam
2025-09-15 20:22:49.602 wdl.w:ptcp.w:call-sawfish-05 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:22:49.602 wdl.w:ptcp.t:call-pbmm2_align_hifi-46.stderr VERBOSE + pbmm2 align --log-level INFO --log-file pbmm2.log --alarms alarms.json --num-threads 64 --sort --preset HiFi --report-json mapping_stats.report.json --sample m84036_250809_035451_s4.bc2143 --unmapped /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0047_m84036_250809_035451_s4.bc2143.unmapped.bam m84036_250809_035451_s4.bc2143.mapped.bam
2025-09-15 20:22:49.602 wdl.w:ptcp.t:call-pbmm2_align_hifi-48.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:22:49.603 wdl.w:ptcp NOTICE finish :: job: "call-pbmm2_align_hifi-13"
2025-09-15 20:22:49.603 wdl.w:ptcp.w:call-paraphase-31.t:call-run_paraphase WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:22:49.603 wdl.w:ptcp.w:call-trgt-04.t:call-trgt_genotype INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:22:49.604 wdl.w:ptcp.t:call-pbmm2_align_hifi-55.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:22:49.604 wdl.w:ptcp.t:call-pbmm2_align_hifi-42.stderr VERBOSE   m84036_250809_035451_s4.bc2139.mapped.bam
2025-09-15 20:22:49.604 wdl.w:ptcp.t:call-pbmm2_align_hifi-53.stderr VERBOSE + pbmm2 align --log-level INFO --log-file pbmm2.log --alarms alarms.json --num-threads 64 --sort --preset HiFi --report-json mapping_stats.report.json --sample m84036_250809_035451_s4.bc2150 --unmapped /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0054_m84036_250809_035451_s4.bc2150.unmapped.bam m84036_250809_035451_s4.bc2150.mapped.bam
2025-09-15 20:22:49.604 wdl.w:ptcp.t:call-pbmm2_align_hifi-47.stderr VERBOSE + pbmm2 align --log-level INFO --log-file pbmm2.log --alarms alarms.json --num-threads 64 --sort --preset HiFi --report-json mapping_stats.report.json --sample m84036_250809_035451_s4.bc2144 --unmapped /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0048_m84036_250809_035451_s4.bc2144.unmapped.bam m84036_250809_035451_s4.bc2144.mapped.bam
2025-09-15 20:22:49.604 wdl.w:ptcp.w:call-sawfish-31.t:call-run_sawfish INFO provisioned :: seconds_waited: 0, cpu: 16, mem_bytes: 32000000000
2025-09-15 20:22:49.604 wdl.w:ptcp.w:call-trgt-05 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:22:49.605 wdl.w:ptcp.w:call-paraphase-05 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:22:49.605 wdl.w:ptcp.w:call-sawfish-05 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:22:49.605 wdl.w:ptcp INFO output :: job: "call-pbmm2_align_hifi-13", values: {"report": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-13/out/mapping_stats.report.json", "mapped_bam_pbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-13/out/m84036_250809_035451_s4.bc2110.mapped.bam.pbi", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-13/out/m84036_250809_035451_s4.bc2110.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-13/out/m84036_250809_035451_s4.bc2110.mapped.bam"}
2025-09-15 20:22:49.606 wdl.w:ptcp.t:call-pbmm2_align_hifi-42.stderr VERBOSE + pbmm2 align --log-level INFO --log-file pbmm2.log --alarms alarms.json --num-threads 64 --sort --preset HiFi --report-json mapping_stats.report.json --sample m84036_250809_035451_s4.bc2139 --unmapped /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0043_m84036_250809_035451_s4.bc2139.unmapped.bam m84036_250809_035451_s4.bc2139.mapped.bam
2025-09-15 20:22:49.606 wdl.w:ptcp.w:call-sawfish-31.t:call-run_sawfish INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:22:49.606 wdl.w:ptcp.w:call-trgt-05 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:22:49.606 wdl.w:ptcp.w:call-paraphase-31.t:call-run_paraphase INFO provisioned :: seconds_waited: 0, cpu: 4, mem_bytes: 8000000000
2025-09-15 20:22:49.607 wdl.w:ptcp.w:call-paraphase-05 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:22:49.607 wdl.w:ptcp.w:call-sawfish-05 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2102"}
2025-09-15 20:22:49.607 wdl.w:ptcp NOTICE ready :: job: "call-paraphase-13", callee: "paraphase"
2025-09-15 20:22:49.608 wdl.w:ptcp.w:call-trgt-05 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2102"}
2025-09-15 20:22:49.608 wdl.w:ptcp.w:call-paraphase-31.t:call-run_paraphase INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:22:49.608 wdl.w:ptcp.w:call-paraphase-05 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2102"}
2025-09-15 20:22:49.609 wdl.w:ptcp.w:call-sawfish-05 NOTICE ready :: job: "call-run_sawfish", callee: "run_sawfish"
2025-09-15 20:22:49.609 wdl.w:ptcp INFO input :: job: "call-paraphase-13", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf", "genome_version": "38", "config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-13/out/m84036_250809_035451_s4.bc2110.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-13/out/m84036_250809_035451_s4.bc2110.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2110"}
2025-09-15 20:22:49.609 wdl.w:ptcp.w:call-trgt-05 INFO visit :: node: "decl-sex", values: {"sex": "F"}
2025-09-15 20:22:49.609 wdl.w:ptcp.w:call-paraphase-05 INFO visit :: node: "decl-sex", values: {"sex": "F"}
2025-09-15 20:22:49.609 wdl.w:ptcp.w:call-sawfish-05 INFO input :: job: "call-run_sawfish", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-05/out/m84036_250809_035451_s4.bc2102.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-05/out/m84036_250809_035451_s4.bc2102.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2102"}
2025-09-15 20:22:49.609 wdl.w:ptcp.w:call-trgt-05 INFO visit :: node: "decl-trgt_bed", values: {"trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"}
2025-09-15 20:22:49.611 wdl.w:ptcp.w:call-paraphase-05 NOTICE ready :: job: "call-run_paraphase", callee: "run_paraphase"
2025-09-15 20:22:49.612 wdl.w:ptcp NOTICE ready :: job: "call-sawfish-13", callee: "sawfish"
2025-09-15 20:22:49.612 wdl.w:ptcp.w:call-trgt-05 NOTICE ready :: job: "call-get_reads_overlapping_repeats", callee: "get_reads_overlapping_repeats"
2025-09-15 20:22:49.612 wdl.w:ptcp.w:call-paraphase-05 INFO input :: job: "call-run_paraphase", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf", "genome_version": "38", "config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-05/out/m84036_250809_035451_s4.bc2102.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-05/out/m84036_250809_035451_s4.bc2102.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2102"}
2025-09-15 20:22:49.612 wdl.w:ptcp INFO input :: job: "call-sawfish-13", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-13/out/m84036_250809_035451_s4.bc2110.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-13/out/m84036_250809_035451_s4.bc2110.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2110"}
2025-09-15 20:22:49.613 wdl.w:ptcp.w:call-trgt-05 INFO input :: job: "call-get_reads_overlapping_repeats", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-05/out/m84036_250809_035451_s4.bc2102.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-05/out/m84036_250809_035451_s4.bc2102.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2102"}
2025-09-15 20:22:49.614 wdl.w:ptcp.w:call-trgt-05 NOTICE ready :: job: "call-trgt_genotype", callee: "trgt_genotype"
2025-09-15 20:22:49.615 wdl.w:ptcp.w:call-trgt-05 INFO input :: job: "call-trgt_genotype", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-05/out/m84036_250809_035451_s4.bc2102.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-05/out/m84036_250809_035451_s4.bc2102.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2102"}
2025-09-15 20:22:49.617 wdl.w:ptcp NOTICE ready :: job: "call-trgt-13", callee: "trgt"
2025-09-15 20:22:49.617 wdl.w:ptcp INFO input :: job: "call-trgt-13", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-13/out/m84036_250809_035451_s4.bc2110.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-13/out/m84036_250809_035451_s4.bc2110.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2110"}
2025-09-15 20:22:49.620 wdl.w:ptcp.t:call-pbmm2_align_hifi-52.slurm_singularity INFO srun: job 51797273 has been allocated resources
2025-09-15 20:22:49.621 wdl.w:ptcp.t:call-pbmm2_align_hifi-52.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:22:49.621 wdl.w:ptcp.t:call-pbmm2_align_hifi-52.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:22:49.626 wdl.w:ptcp.w:call-trgt-31.t:call-get_reads_overlapping_repeats NOTICE task setup :: name: "get_reads_overlapping_repeats", source: "./trgt.wdl", line: 182, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-31/call-get_reads_overlapping_repeats", thread: 140613034948160
2025-09-15 20:22:49.627 wdl.w:ptcp.t:call-pbmm2_align_hifi-53.slurm_singularity INFO srun: job 51797272 has been allocated resources
2025-09-15 20:22:49.628 wdl.w:ptcp.t:call-pbmm2_align_hifi-53.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:22:49.631 wdl.w:ptcp.w:call-paraphase-13 NOTICE workflow start :: name: "paraphase", source: "./paraphase.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-13"
2025-09-15 20:22:49.633 wdl.w:ptcp.t:call-pbmm2_align_hifi-42.slurm_singularity INFO srun: job 51797270 has been allocated resources
2025-09-15 20:22:49.633 wdl.w:ptcp.t:call-pbmm2_align_hifi-42.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:22:49.633 wdl.w:ptcp.t:call-pbmm2_align_hifi-42.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:22:49.636 wdl.w:ptcp.w:call-sawfish-13 NOTICE workflow start :: name: "sawfish", source: "./sawfish.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-13"
2025-09-15 20:22:49.639 wdl.w:ptcp.w:call-trgt-13 NOTICE workflow start :: name: "trgt", source: "./trgt.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-13"
2025-09-15 20:22:49.652 wdl.w:ptcp.w:call-trgt-20.t:call-trgt_genotype.slurm_singularity INFO srun: job 51797334 queued and waiting for resources
2025-09-15 20:22:49.661 wdl.w:ptcp.w:call-paraphase-13 INFO visit :: node: "decl-annotation_vcf", values: {"annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf"}
2025-09-15 20:22:49.661 wdl.w:ptcp.w:call-paraphase-13 INFO visit :: node: "decl-config_file", values: {"config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml"}
2025-09-15 20:22:49.662 wdl.w:ptcp.w:call-paraphase-13 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:22:49.662 wdl.w:ptcp.w:call-paraphase-13 INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:22:49.662 wdl.w:ptcp.w:call-paraphase-13 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-13/out/m84036_250809_035451_s4.bc2110.mapped.bam"}
2025-09-15 20:22:49.662 wdl.w:ptcp.w:call-paraphase-13 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-13/out/m84036_250809_035451_s4.bc2110.mapped.bam.bai"}
2025-09-15 20:22:49.662 wdl.w:ptcp.w:call-paraphase-13 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:22:49.662 wdl.w:ptcp.w:call-paraphase-13 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:22:49.662 wdl.w:ptcp.w:call-paraphase-13 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2110"}
2025-09-15 20:22:49.663 wdl.w:ptcp.w:call-paraphase-13 INFO visit :: node: "decl-sex", values: {"sex": "F"}
2025-09-15 20:22:49.663 wdl.w:ptcp.w:call-paraphase-13 NOTICE ready :: job: "call-run_paraphase", callee: "run_paraphase"
2025-09-15 20:22:49.663 wdl.w:ptcp.w:call-paraphase-13 INFO input :: job: "call-run_paraphase", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf", "genome_version": "38", "config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-13/out/m84036_250809_035451_s4.bc2110.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-13/out/m84036_250809_035451_s4.bc2110.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2110"}
2025-09-15 20:22:49.664 wdl.w:ptcp.w:call-sawfish-13 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:22:49.665 wdl.w:ptcp.w:call-sawfish-13 INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:22:49.665 wdl.w:ptcp.w:call-sawfish-13 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-13/out/m84036_250809_035451_s4.bc2110.mapped.bam"}
2025-09-15 20:22:49.665 wdl.w:ptcp.w:call-sawfish-13 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-13/out/m84036_250809_035451_s4.bc2110.mapped.bam.bai"}
2025-09-15 20:22:49.665 wdl.w:ptcp.w:call-sawfish-13 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:22:49.665 wdl.w:ptcp.w:call-sawfish-13 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:22:49.665 wdl.w:ptcp.w:call-sawfish-13 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2110"}
2025-09-15 20:22:49.665 wdl.w:ptcp.w:call-sawfish-13 NOTICE ready :: job: "call-run_sawfish", callee: "run_sawfish"
2025-09-15 20:22:49.665 wdl.w:ptcp.w:call-sawfish-13 INFO input :: job: "call-run_sawfish", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-13/out/m84036_250809_035451_s4.bc2110.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-13/out/m84036_250809_035451_s4.bc2110.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2110"}
2025-09-15 20:22:49.667 wdl.w:ptcp.w:call-trgt-31.t:call-get_reads_overlapping_repeats INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:22:49.668 wdl.w:ptcp.w:call-trgt-31.t:call-get_reads_overlapping_repeats INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:22:49.668 wdl.w:ptcp.w:call-trgt-31.t:call-get_reads_overlapping_repeats INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2128.mapped.bam.bai"
2025-09-15 20:22:49.668 wdl.w:ptcp.w:call-trgt-31.t:call-get_reads_overlapping_repeats INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2128.mapped.bam"
2025-09-15 20:22:49.668 wdl.w:ptcp.w:call-trgt-31.t:call-get_reads_overlapping_repeats INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2128"
2025-09-15 20:22:49.669 wdl.w:ptcp.w:call-trgt-31.t:call-get_reads_overlapping_repeats INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:22:49.669 wdl.w:ptcp.w:call-trgt-31.t:call-get_reads_overlapping_repeats INFO eval :: name: "expand_size", value: 3000
2025-09-15 20:22:49.669 wdl.w:ptcp.w:call-trgt-31.t:call-get_reads_overlapping_repeats INFO eval :: name: "threads", value: 1
2025-09-15 20:22:49.669 wdl.w:ptcp.w:call-trgt-31.t:call-get_reads_overlapping_repeats INFO eval :: name: "expanded_bed_name", value: "m84036_250809_035451_s4.bc2128.expanded.bed"
2025-09-15 20:22:49.669 wdl.w:ptcp.w:call-trgt-31.t:call-get_reads_overlapping_repeats INFO eval :: name: "disk_size", value: 11
2025-09-15 20:22:49.670 wdl.w:ptcp.w:call-trgt-31.t:call-get_reads_overlapping_repeats INFO eval :: name: "output_name", value: "m84036_250809_035451_s4.bc2128.repeats.bam"
2025-09-15 20:22:49.670 wdl.w:ptcp.w:call-trgt-31.t:call-get_reads_overlapping_repeats INFO eval :: name: "index_name", value: "m84036_250809_035451_s4.bc2128.repeats.bam.bai"
2025-09-15 20:22:49.670 wdl.w:ptcp.w:call-trgt-31.t:call-get_reads_overlapping_repeats INFO eval :: name: "output_name_with_index", value: "m84036_250809_035451_s4.bc2128.repeats.bam##idx##m84036_250809_035451_s4.bc2128.repeats.bam.bai"
2025-09-15 20:22:49.670 wdl.w:ptcp.w:call-trgt-31.t:call-get_reads_overlapping_repeats INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:22:49.671 wdl.w:ptcp.w:call-trgt-31.t:call-get_reads_overlapping_repeats WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:22:49.671 wdl.w:ptcp.w:call-trgt-31.t:call-get_reads_overlapping_repeats INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:22:49.671 wdl.w:ptcp.w:call-trgt-31.t:call-get_reads_overlapping_repeats INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:22:49.673 wdl.w:ptcp.w:call-trgt-13 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:22:49.673 wdl.w:ptcp.w:call-trgt-13 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-13/out/m84036_250809_035451_s4.bc2110.mapped.bam"}
2025-09-15 20:22:49.674 wdl.w:ptcp.w:call-trgt-13 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-13/out/m84036_250809_035451_s4.bc2110.mapped.bam.bai"}
2025-09-15 20:22:49.674 wdl.w:ptcp.w:call-trgt-13 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:22:49.674 wdl.w:ptcp.w:call-trgt-13 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:22:49.674 wdl.w:ptcp.w:call-trgt-13 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2110"}
2025-09-15 20:22:49.674 wdl.w:ptcp.w:call-trgt-13 INFO visit :: node: "decl-sex", values: {"sex": "F"}
2025-09-15 20:22:49.674 wdl.w:ptcp.w:call-trgt-13 INFO visit :: node: "decl-trgt_bed", values: {"trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"}
2025-09-15 20:22:49.674 wdl.w:ptcp.w:call-trgt-13 NOTICE ready :: job: "call-get_reads_overlapping_repeats", callee: "get_reads_overlapping_repeats"
2025-09-15 20:22:49.674 wdl.w:ptcp.w:call-trgt-13 INFO input :: job: "call-get_reads_overlapping_repeats", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-13/out/m84036_250809_035451_s4.bc2110.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-13/out/m84036_250809_035451_s4.bc2110.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2110"}
2025-09-15 20:22:49.675 wdl.w:ptcp.w:call-trgt-13 NOTICE ready :: job: "call-trgt_genotype", callee: "trgt_genotype"
2025-09-15 20:22:49.675 wdl.w:ptcp.w:call-trgt-13 INFO input :: job: "call-trgt_genotype", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-13/out/m84036_250809_035451_s4.bc2110.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-13/out/m84036_250809_035451_s4.bc2110.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2110"}
2025-09-15 20:22:49.701 wdl.w:ptcp.w:call-trgt-04.t:call-get_reads_overlapping_repeats INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 9, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-04/call-get_reads_overlapping_repeats/_singularity_tmpdir_ucfw54ho"
2025-09-15 20:22:49.701 wdl.w:ptcp.w:call-trgt-04.t:call-get_reads_overlapping_repeats INFO Slurm invocation: srun --job-name call-get_reads_overlapping_repeats --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-04/call-get_reads_overlapping_repeats/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-04/call-get_reads_overlapping_repeats/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-04/call-get_reads_overlapping_repeats/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-04/call-get_reads_overlapping_repeats/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-04/out/m84036_250809_035451_s4.bc2101.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2101.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-04/out/m84036_250809_035451_s4.bc2101.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2101.mapped.bam:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-04/call-get_reads_overlapping_repeats/_singularity_tmpdir_ucfw54ho/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-04/call-get_reads_overlapping_repeats/_singularity_tmpdir_ucfw54ho/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:22:49.722 wdl.w:ptcp.w:call-sawfish-31.t:call-run_sawfish INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 10, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-31/call-run_sawfish/_singularity_tmpdir_v8d64t8p"
2025-09-15 20:22:49.722 wdl.w:ptcp.w:call-sawfish-31.t:call-run_sawfish INFO Slurm invocation: srun --job-name call-run_sawfish --partition compute,compute9 --cpus-per-task 16 --mem 30518M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-31/call-run_sawfish/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-31/call-run_sawfish/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-31/call-run_sawfish/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-31/call-run_sawfish/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-31/out/m84036_250809_035451_s4.bc2128.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2128.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-31/out/m84036_250809_035451_s4.bc2128.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2128.mapped.bam:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-31/call-run_sawfish/_singularity_tmpdir_v8d64t8p/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-31/call-run_sawfish/_singularity_tmpdir_v8d64t8p/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:22:49.728 wdl.w:ptcp.w:call-trgt-04.t:call-trgt_genotype INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 11, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-04/call-trgt_genotype/_singularity_tmpdir_kzcjpywj"
2025-09-15 20:22:49.728 wdl.w:ptcp.w:call-trgt-04.t:call-trgt_genotype INFO Slurm invocation: srun --job-name call-trgt_genotype --partition compute,compute9 --cpus-per-task 8 --mem 15259M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-04/call-trgt_genotype/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-04/call-trgt_genotype/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-04/call-trgt_genotype/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-04/call-trgt_genotype/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-04/out/m84036_250809_035451_s4.bc2101.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2101.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-04/out/m84036_250809_035451_s4.bc2101.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2101.mapped.bam:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-04/call-trgt_genotype/_singularity_tmpdir_kzcjpywj/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-04/call-trgt_genotype/_singularity_tmpdir_kzcjpywj/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:22:49.740 wdl.w:ptcp.w:call-paraphase-31.t:call-run_paraphase INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-31/call-run_paraphase/_singularity_tmpdir__wo5h1xn"
2025-09-15 20:22:49.740 wdl.w:ptcp.w:call-paraphase-31.t:call-run_paraphase INFO Slurm invocation: srun --job-name call-run_paraphase --partition compute,compute9 --cpus-per-task 4 --mem 7629M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-31/call-run_paraphase/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-31/call-run_paraphase/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-31/call-run_paraphase/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-31/call-run_paraphase/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/variant_list/variant_list.GRCh38.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-31/out/m84036_250809_035451_s4.bc2128.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2128.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-31/out/m84036_250809_035451_s4.bc2128.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2128.mapped.bam.bai:ro --bind /ptcp/meta/paraphase/paraphase_config.GRCh38.yaml:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/paraphase_config.GRCh38.yaml:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-31/call-run_paraphase/_singularity_tmpdir__wo5h1xn/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-31/call-run_paraphase/_singularity_tmpdir__wo5h1xn/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:22:49.744 wdl.w:ptcp.w:call-trgt-31.t:call-get_reads_overlapping_repeats INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 9, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-31/call-get_reads_overlapping_repeats/_singularity_tmpdir_dh7tu_t2"
2025-09-15 20:22:49.744 wdl.w:ptcp.w:call-trgt-31.t:call-get_reads_overlapping_repeats INFO Slurm invocation: srun --job-name call-get_reads_overlapping_repeats --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-31/call-get_reads_overlapping_repeats/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-31/call-get_reads_overlapping_repeats/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-31/call-get_reads_overlapping_repeats/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-31/call-get_reads_overlapping_repeats/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-31/out/m84036_250809_035451_s4.bc2128.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2128.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-31/out/m84036_250809_035451_s4.bc2128.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2128.mapped.bam:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-31/call-get_reads_overlapping_repeats/_singularity_tmpdir_dh7tu_t2/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-31/call-get_reads_overlapping_repeats/_singularity_tmpdir_dh7tu_t2/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:22:49.781 wdl.w:ptcp.w:call-sawfish-31.t:call-run_sawfish NOTICE slurm_singularity run :: pid: 1198315, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-31/call-run_sawfish/slurm_singularity.log.txt"
2025-09-15 20:22:49.781 wdl.w:ptcp.w:call-paraphase-31.t:call-run_paraphase NOTICE slurm_singularity run :: pid: 1198317, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-31/call-run_paraphase/slurm_singularity.log.txt"
2025-09-15 20:22:49.781 wdl.w:ptcp.w:call-trgt-31.t:call-get_reads_overlapping_repeats NOTICE slurm_singularity run :: pid: 1198318, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-31/call-get_reads_overlapping_repeats/slurm_singularity.log.txt"
2025-09-15 20:22:49.781 wdl.w:ptcp.w:call-trgt-04.t:call-trgt_genotype NOTICE slurm_singularity run :: pid: 1198316, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-04/call-trgt_genotype/slurm_singularity.log.txt"
2025-09-15 20:22:49.781 wdl.w:ptcp.w:call-trgt-04.t:call-get_reads_overlapping_repeats NOTICE slurm_singularity run :: pid: 1198314, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-04/call-get_reads_overlapping_repeats/slurm_singularity.log.txt"
2025-09-15 20:22:49.798 wdl.w:ptcp.t:call-pbmm2_align_hifi-29 INFO output :: name: "mapped_bam", value: "m84036_250809_035451_s4.bc2126.mapped.bam"
2025-09-15 20:22:49.801 wdl.w:ptcp.t:call-pbmm2_align_hifi-29 INFO output :: name: "mapped_bam_bai", value: "m84036_250809_035451_s4.bc2126.mapped.bam.bai"
2025-09-15 20:22:49.802 wdl.w:ptcp.t:call-pbmm2_align_hifi-29 INFO output :: name: "mapped_bam_pbi", value: "m84036_250809_035451_s4.bc2126.mapped.bam.pbi"
2025-09-15 20:22:49.803 wdl.w:ptcp.t:call-pbmm2_align_hifi-29 INFO output :: name: "report", value: "mapping_stats.report.json"
2025-09-15 20:22:49.893 wdl.w:ptcp.t:call-pbmm2_align_hifi-29 NOTICE done
2025-09-15 20:22:49.901 wdl.w:ptcp NOTICE finish :: job: "call-pbmm2_align_hifi-29"
2025-09-15 20:22:49.901 wdl.w:ptcp INFO output :: job: "call-pbmm2_align_hifi-29", values: {"report": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-29/out/mapping_stats.report.json", "mapped_bam_pbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-29/out/m84036_250809_035451_s4.bc2126.mapped.bam.pbi", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-29/out/m84036_250809_035451_s4.bc2126.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-29/out/m84036_250809_035451_s4.bc2126.mapped.bam"}
2025-09-15 20:22:49.902 wdl.w:ptcp NOTICE ready :: job: "call-paraphase-29", callee: "paraphase"
2025-09-15 20:22:49.902 wdl.w:ptcp INFO input :: job: "call-paraphase-29", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf", "genome_version": "38", "config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-29/out/m84036_250809_035451_s4.bc2126.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-29/out/m84036_250809_035451_s4.bc2126.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2126"}
2025-09-15 20:22:49.904 wdl.w:ptcp NOTICE ready :: job: "call-sawfish-29", callee: "sawfish"
2025-09-15 20:22:49.904 wdl.w:ptcp INFO input :: job: "call-sawfish-29", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-29/out/m84036_250809_035451_s4.bc2126.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-29/out/m84036_250809_035451_s4.bc2126.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2126"}
2025-09-15 20:22:49.908 wdl.w:ptcp NOTICE ready :: job: "call-trgt-29", callee: "trgt"
2025-09-15 20:22:49.908 wdl.w:ptcp INFO input :: job: "call-trgt-29", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-29/out/m84036_250809_035451_s4.bc2126.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-29/out/m84036_250809_035451_s4.bc2126.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2126"}
2025-09-15 20:22:49.912 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_genotype NOTICE task setup :: name: "trgt_genotype", source: "./trgt.wdl", line: 272, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-31/call-trgt_genotype", thread: 140611944420928
2025-09-15 20:22:49.914 wdl.w:ptcp.w:call-paraphase-29 NOTICE workflow start :: name: "paraphase", source: "./paraphase.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-29"
2025-09-15 20:22:49.920 wdl.w:ptcp.w:call-sawfish-29 NOTICE workflow start :: name: "sawfish", source: "./sawfish.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-29"
2025-09-15 20:22:49.927 wdl.w:ptcp.w:call-trgt-29 NOTICE workflow start :: name: "trgt", source: "./trgt.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-29"
2025-09-15 20:22:49.934 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_genotype INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:22:49.935 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_genotype INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:22:49.935 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_genotype INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:22:49.935 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_genotype INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:22:49.935 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_genotype INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2128.mapped.bam.bai"
2025-09-15 20:22:49.935 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_genotype INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2128.mapped.bam"
2025-09-15 20:22:49.936 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_genotype INFO input :: name: "sex", value: "F"
2025-09-15 20:22:49.936 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_genotype INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2128"
2025-09-15 20:22:49.936 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_genotype INFO eval :: name: "mem_gb", value: 16
2025-09-15 20:22:49.937 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_genotype INFO eval :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2128.trgt"
2025-09-15 20:22:49.937 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_genotype INFO eval :: name: "threads", value: 8
2025-09-15 20:22:49.938 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_genotype INFO eval :: name: "disk_size", value: 27
2025-09-15 20:22:49.940 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_genotype INFO eval :: name: "karyotype", value: "XX"
2025-09-15 20:22:49.940 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_genotype INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 8, memory_reservation: 16000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:22:49.941 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_genotype WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:22:49.943 wdl.w:ptcp.w:call-sawfish-29 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:22:49.943 wdl.w:ptcp.w:call-sawfish-29 INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:22:49.943 wdl.w:ptcp.t:call-pbmm2_align_hifi-12 INFO output :: name: "mapped_bam", value: "m84036_250809_035451_s4.bc2109.mapped.bam"
2025-09-15 20:22:49.944 wdl.w:ptcp.w:call-sawfish-29 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-29/out/m84036_250809_035451_s4.bc2126.mapped.bam"}
2025-09-15 20:22:49.944 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_genotype INFO provisioned :: seconds_waited: 0, cpu: 8, mem_bytes: 16000000000
2025-09-15 20:22:49.945 wdl.w:ptcp.w:call-sawfish-29 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-29/out/m84036_250809_035451_s4.bc2126.mapped.bam.bai"}
2025-09-15 20:22:49.945 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_genotype INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:22:49.945 wdl.w:ptcp.w:call-sawfish-29 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:22:49.946 wdl.w:ptcp.w:call-paraphase-29 INFO visit :: node: "decl-annotation_vcf", values: {"annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf"}
2025-09-15 20:22:49.947 wdl.w:ptcp.w:call-sawfish-29 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:22:49.947 wdl.w:ptcp.w:call-paraphase-29 INFO visit :: node: "decl-config_file", values: {"config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml"}
2025-09-15 20:22:49.947 wdl.w:ptcp.w:call-sawfish-29 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2126"}
2025-09-15 20:22:49.947 wdl.w:ptcp.w:call-paraphase-29 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:22:49.948 wdl.w:ptcp.w:call-sawfish-29 NOTICE ready :: job: "call-run_sawfish", callee: "run_sawfish"
2025-09-15 20:22:49.948 wdl.w:ptcp.w:call-paraphase-29 INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:22:49.948 wdl.w:ptcp.w:call-sawfish-29 INFO input :: job: "call-run_sawfish", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-29/out/m84036_250809_035451_s4.bc2126.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-29/out/m84036_250809_035451_s4.bc2126.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2126"}
2025-09-15 20:22:49.948 wdl.w:ptcp.w:call-paraphase-29 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-29/out/m84036_250809_035451_s4.bc2126.mapped.bam"}
2025-09-15 20:22:49.949 wdl.w:ptcp.w:call-paraphase-29 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-29/out/m84036_250809_035451_s4.bc2126.mapped.bam.bai"}
2025-09-15 20:22:49.949 wdl.w:ptcp.w:call-paraphase-29 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:22:49.949 wdl.w:ptcp.t:call-pbmm2_align_hifi-12 INFO output :: name: "mapped_bam_bai", value: "m84036_250809_035451_s4.bc2109.mapped.bam.bai"
2025-09-15 20:22:49.949 wdl.w:ptcp.w:call-paraphase-29 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:22:49.950 wdl.w:ptcp.w:call-paraphase-29 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2126"}
2025-09-15 20:22:49.950 wdl.w:ptcp.w:call-paraphase-29 INFO visit :: node: "decl-sex", values: {"sex": "F"}
2025-09-15 20:22:49.950 wdl.w:ptcp.w:call-paraphase-29 NOTICE ready :: job: "call-run_paraphase", callee: "run_paraphase"
2025-09-15 20:22:49.950 wdl.w:ptcp.w:call-paraphase-29 INFO input :: job: "call-run_paraphase", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf", "genome_version": "38", "config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-29/out/m84036_250809_035451_s4.bc2126.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-29/out/m84036_250809_035451_s4.bc2126.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2126"}
2025-09-15 20:22:49.952 wdl.w:ptcp.w:call-trgt-29 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:22:49.952 wdl.w:ptcp.t:call-pbmm2_align_hifi-12 INFO output :: name: "mapped_bam_pbi", value: "m84036_250809_035451_s4.bc2109.mapped.bam.pbi"
2025-09-15 20:22:49.952 wdl.w:ptcp.w:call-trgt-29 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-29/out/m84036_250809_035451_s4.bc2126.mapped.bam"}
2025-09-15 20:22:49.953 wdl.w:ptcp.w:call-trgt-29 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-29/out/m84036_250809_035451_s4.bc2126.mapped.bam.bai"}
2025-09-15 20:22:49.953 wdl.w:ptcp.w:call-trgt-29 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:22:49.953 wdl.w:ptcp.w:call-trgt-29 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:22:49.953 wdl.w:ptcp.w:call-trgt-29 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2126"}
2025-09-15 20:22:49.953 wdl.w:ptcp.w:call-trgt-29 INFO visit :: node: "decl-sex", values: {"sex": "F"}
2025-09-15 20:22:49.953 wdl.w:ptcp.w:call-trgt-29 INFO visit :: node: "decl-trgt_bed", values: {"trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"}
2025-09-15 20:22:49.953 wdl.w:ptcp.w:call-trgt-29 NOTICE ready :: job: "call-get_reads_overlapping_repeats", callee: "get_reads_overlapping_repeats"
2025-09-15 20:22:49.953 wdl.w:ptcp.w:call-trgt-29 INFO input :: job: "call-get_reads_overlapping_repeats", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-29/out/m84036_250809_035451_s4.bc2126.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-29/out/m84036_250809_035451_s4.bc2126.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2126"}
2025-09-15 20:22:49.953 wdl.w:ptcp.t:call-pbmm2_align_hifi-12 INFO output :: name: "report", value: "mapping_stats.report.json"
2025-09-15 20:22:49.954 wdl.w:ptcp.w:call-trgt-29 NOTICE ready :: job: "call-trgt_genotype", callee: "trgt_genotype"
2025-09-15 20:22:49.954 wdl.w:ptcp.w:call-trgt-29 INFO input :: job: "call-trgt_genotype", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-29/out/m84036_250809_035451_s4.bc2126.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-29/out/m84036_250809_035451_s4.bc2126.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2126"}
2025-09-15 20:22:50.008 wdl.w:ptcp.w:call-trgt-07.t:call-get_reads_overlapping_repeats.slurm_singularity INFO srun: job 51797336 queued and waiting for resources
2025-09-15 20:22:50.010 wdl.w:ptcp.w:call-sawfish-07.t:call-run_sawfish.slurm_singularity INFO srun: job 51797335 queued and waiting for resources
2025-09-15 20:22:50.032 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_genotype INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 11, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-31/call-trgt_genotype/_singularity_tmpdir_6dg3wm_z"
2025-09-15 20:22:50.033 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_genotype INFO Slurm invocation: srun --job-name call-trgt_genotype --partition compute,compute9 --cpus-per-task 8 --mem 15259M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-31/call-trgt_genotype/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-31/call-trgt_genotype/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-31/call-trgt_genotype/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-31/call-trgt_genotype/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-31/out/m84036_250809_035451_s4.bc2128.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2128.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-31/out/m84036_250809_035451_s4.bc2128.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2128.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-31/call-trgt_genotype/_singularity_tmpdir_6dg3wm_z/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-31/call-trgt_genotype/_singularity_tmpdir_6dg3wm_z/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:22:50.048 wdl.w:ptcp.t:call-pbmm2_align_hifi-12 NOTICE done
2025-09-15 20:22:50.053 wdl.w:ptcp NOTICE finish :: job: "call-pbmm2_align_hifi-12"
2025-09-15 20:22:50.054 wdl.w:ptcp INFO output :: job: "call-pbmm2_align_hifi-12", values: {"report": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-12/out/mapping_stats.report.json", "mapped_bam_pbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-12/out/m84036_250809_035451_s4.bc2109.mapped.bam.pbi", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-12/out/m84036_250809_035451_s4.bc2109.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-12/out/m84036_250809_035451_s4.bc2109.mapped.bam"}
2025-09-15 20:22:50.054 wdl.w:ptcp NOTICE ready :: job: "call-paraphase-12", callee: "paraphase"
2025-09-15 20:22:50.055 wdl.w:ptcp INFO input :: job: "call-paraphase-12", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf", "genome_version": "38", "config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-12/out/m84036_250809_035451_s4.bc2109.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-12/out/m84036_250809_035451_s4.bc2109.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2109"}
2025-09-15 20:22:50.056 wdl.w:ptcp NOTICE ready :: job: "call-sawfish-12", callee: "sawfish"
2025-09-15 20:22:50.056 wdl.w:ptcp INFO input :: job: "call-sawfish-12", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-12/out/m84036_250809_035451_s4.bc2109.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-12/out/m84036_250809_035451_s4.bc2109.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2109"}
2025-09-15 20:22:50.059 wdl.w:ptcp NOTICE ready :: job: "call-trgt-12", callee: "trgt"
2025-09-15 20:22:50.059 wdl.w:ptcp INFO input :: job: "call-trgt-12", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-12/out/m84036_250809_035451_s4.bc2109.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-12/out/m84036_250809_035451_s4.bc2109.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2109"}
2025-09-15 20:22:50.060 wdl.w:ptcp.w:call-paraphase-34.t:call-run_paraphase NOTICE task setup :: name: "run_paraphase", source: "./paraphase.wdl", line: 127, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-34/call-run_paraphase", thread: 140613043340864
2025-09-15 20:22:50.063 wdl.w:ptcp.w:call-paraphase-12 NOTICE workflow start :: name: "paraphase", source: "./paraphase.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-12"
2025-09-15 20:22:50.067 wdl.w:ptcp.w:call-sawfish-12 NOTICE workflow start :: name: "sawfish", source: "./sawfish.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-12"
2025-09-15 20:22:50.070 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_genotype NOTICE slurm_singularity run :: pid: 1198339, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-31/call-trgt_genotype/slurm_singularity.log.txt"
2025-09-15 20:22:50.072 wdl.w:ptcp.w:call-trgt-12 NOTICE workflow start :: name: "trgt", source: "./trgt.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-12"
2025-09-15 20:22:50.079 wdl.w:ptcp.w:call-paraphase-07.t:call-run_paraphase.slurm_singularity INFO srun: job 51797337 queued and waiting for resources
2025-09-15 20:22:50.086 wdl.w:ptcp.w:call-paraphase-12 INFO visit :: node: "decl-annotation_vcf", values: {"annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf"}
2025-09-15 20:22:50.086 wdl.w:ptcp.w:call-paraphase-12 INFO visit :: node: "decl-config_file", values: {"config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml"}
2025-09-15 20:22:50.087 wdl.w:ptcp.w:call-paraphase-12 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:22:50.088 wdl.w:ptcp.w:call-paraphase-12 INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:22:50.088 wdl.w:ptcp.w:call-paraphase-34.t:call-run_paraphase INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:22:50.088 wdl.w:ptcp.w:call-paraphase-12 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-12/out/m84036_250809_035451_s4.bc2109.mapped.bam"}
2025-09-15 20:22:50.089 wdl.w:ptcp.w:call-paraphase-34.t:call-run_paraphase INFO input :: name: "annotation_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf"
2025-09-15 20:22:50.089 wdl.w:ptcp.w:call-paraphase-12 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-12/out/m84036_250809_035451_s4.bc2109.mapped.bam.bai"}
2025-09-15 20:22:50.090 wdl.w:ptcp.w:call-paraphase-34.t:call-run_paraphase INFO input :: name: "genome_version", value: "38"
2025-09-15 20:22:50.090 wdl.w:ptcp.w:call-sawfish-12 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:22:50.090 wdl.w:ptcp.w:call-paraphase-12 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:22:50.090 wdl.w:ptcp.w:call-paraphase-34.t:call-run_paraphase INFO input :: name: "config_file", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/paraphase_config.GRCh38.yaml"
2025-09-15 20:22:50.091 wdl.w:ptcp.w:call-sawfish-12 INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:22:50.091 wdl.w:ptcp.w:call-paraphase-12 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:22:50.091 wdl.w:ptcp.w:call-paraphase-34.t:call-run_paraphase INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:22:50.091 wdl.w:ptcp.w:call-sawfish-12 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-12/out/m84036_250809_035451_s4.bc2109.mapped.bam"}
2025-09-15 20:22:50.091 wdl.w:ptcp.w:call-paraphase-12 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2109"}
2025-09-15 20:22:50.091 wdl.w:ptcp.w:call-paraphase-34.t:call-run_paraphase INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:22:50.091 wdl.w:ptcp.w:call-sawfish-12 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-12/out/m84036_250809_035451_s4.bc2109.mapped.bam.bai"}
2025-09-15 20:22:50.092 wdl.w:ptcp.w:call-paraphase-12 INFO visit :: node: "decl-sex", values: {"sex": "F"}
2025-09-15 20:22:50.092 wdl.w:ptcp.w:call-paraphase-34.t:call-run_paraphase INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2131.mapped.bam.bai"
2025-09-15 20:22:50.092 wdl.w:ptcp.w:call-sawfish-12 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:22:50.092 wdl.w:ptcp.w:call-paraphase-12 NOTICE ready :: job: "call-run_paraphase", callee: "run_paraphase"
2025-09-15 20:22:50.093 wdl.w:ptcp.w:call-paraphase-34.t:call-run_paraphase INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2131.mapped.bam"
2025-09-15 20:22:50.093 wdl.w:ptcp.w:call-sawfish-12 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:22:50.093 wdl.w:ptcp.w:call-paraphase-12 INFO input :: job: "call-run_paraphase", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf", "genome_version": "38", "config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-12/out/m84036_250809_035451_s4.bc2109.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-12/out/m84036_250809_035451_s4.bc2109.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2109"}
2025-09-15 20:22:50.093 wdl.w:ptcp.w:call-paraphase-34.t:call-run_paraphase INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2131"
2025-09-15 20:22:50.093 wdl.w:ptcp.w:call-sawfish-12 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2109"}
2025-09-15 20:22:50.094 wdl.w:ptcp.w:call-paraphase-34.t:call-run_paraphase INFO eval :: name: "threads", value: 4
2025-09-15 20:22:50.094 wdl.w:ptcp.w:call-sawfish-12 NOTICE ready :: job: "call-run_sawfish", callee: "run_sawfish"
2025-09-15 20:22:50.095 wdl.w:ptcp.w:call-paraphase-34.t:call-run_paraphase INFO eval :: name: "mem_gb", value: 8
2025-09-15 20:22:50.095 wdl.w:ptcp.w:call-sawfish-12 INFO input :: job: "call-run_sawfish", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-12/out/m84036_250809_035451_s4.bc2109.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-12/out/m84036_250809_035451_s4.bc2109.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2109"}
2025-09-15 20:22:50.095 wdl.w:ptcp.w:call-paraphase-34.t:call-run_paraphase INFO eval :: name: "disk_size", value: 27
2025-09-15 20:22:50.096 wdl.w:ptcp.w:call-trgt-12 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:22:50.097 wdl.w:ptcp.w:call-paraphase-34.t:call-run_paraphase INFO eval :: name: "out_dir", value: "m84036_250809_035451_s4.bc2131_paraphase"
2025-09-15 20:22:50.097 wdl.w:ptcp.w:call-trgt-12 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-12/out/m84036_250809_035451_s4.bc2109.mapped.bam"}
2025-09-15 20:22:50.097 wdl.w:ptcp.w:call-trgt-12 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-12/out/m84036_250809_035451_s4.bc2109.mapped.bam.bai"}
2025-09-15 20:22:50.097 wdl.w:ptcp.w:call-trgt-12 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:22:50.097 wdl.w:ptcp.w:call-paraphase-34.t:call-run_paraphase INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 4, memory_reservation: 8000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:22:50.098 wdl.w:ptcp.w:call-trgt-12 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:22:50.098 wdl.w:ptcp.w:call-paraphase-34.t:call-run_paraphase WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:22:50.098 wdl.w:ptcp.w:call-trgt-12 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2109"}
2025-09-15 20:22:50.098 wdl.w:ptcp.w:call-trgt-12 INFO visit :: node: "decl-sex", values: {"sex": "F"}
2025-09-15 20:22:50.098 wdl.w:ptcp.w:call-trgt-12 INFO visit :: node: "decl-trgt_bed", values: {"trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"}
2025-09-15 20:22:50.098 wdl.w:ptcp.w:call-trgt-12 NOTICE ready :: job: "call-get_reads_overlapping_repeats", callee: "get_reads_overlapping_repeats"
2025-09-15 20:22:50.099 wdl.w:ptcp.w:call-trgt-12 INFO input :: job: "call-get_reads_overlapping_repeats", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-12/out/m84036_250809_035451_s4.bc2109.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-12/out/m84036_250809_035451_s4.bc2109.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2109"}
2025-09-15 20:22:50.099 wdl.w:ptcp.w:call-paraphase-34.t:call-run_paraphase INFO provisioned :: seconds_waited: 0, cpu: 4, mem_bytes: 8000000000
2025-09-15 20:22:50.099 wdl.w:ptcp.w:call-paraphase-34.t:call-run_paraphase INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:22:50.099 wdl.w:ptcp.w:call-trgt-12 NOTICE ready :: job: "call-trgt_genotype", callee: "trgt_genotype"
2025-09-15 20:22:50.100 wdl.w:ptcp.w:call-trgt-12 INFO input :: job: "call-trgt_genotype", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-12/out/m84036_250809_035451_s4.bc2109.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-12/out/m84036_250809_035451_s4.bc2109.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2109"}
2025-09-15 20:22:50.105 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_genotype.slurm_singularity INFO srun: job 51797338 queued and waiting for resources
2025-09-15 20:22:50.160 wdl.w:ptcp.w:call-paraphase-34.t:call-run_paraphase INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-34/call-run_paraphase/_singularity_tmpdir_3mhgv1uj"
2025-09-15 20:22:50.160 wdl.w:ptcp.w:call-paraphase-34.t:call-run_paraphase INFO Slurm invocation: srun --job-name call-run_paraphase --partition compute,compute9 --cpus-per-task 4 --mem 7629M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-34/call-run_paraphase/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-34/call-run_paraphase/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-34/call-run_paraphase/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-34/call-run_paraphase/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-34/out/m84036_250809_035451_s4.bc2131.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2131.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-34/out/m84036_250809_035451_s4.bc2131.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2131.mapped.bam:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/paraphase/paraphase_config.GRCh38.yaml:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/paraphase_config.GRCh38.yaml:ro --bind /ptcp/meta/variant_list/variant_list.GRCh38.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-34/call-run_paraphase/_singularity_tmpdir_3mhgv1uj/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-34/call-run_paraphase/_singularity_tmpdir_3mhgv1uj/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:22:50.175 wdl.w:ptcp.w:call-paraphase-34.t:call-run_paraphase NOTICE slurm_singularity run :: pid: 1198344, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-34/call-run_paraphase/slurm_singularity.log.txt"
2025-09-15 20:22:50.293 wdl.w:ptcp.t:call-pbmm2_align_hifi-09 INFO output :: name: "mapped_bam", value: "m84036_250809_035451_s4.bc2106.mapped.bam"
2025-09-15 20:22:50.296 wdl.w:ptcp.t:call-pbmm2_align_hifi-09 INFO output :: name: "mapped_bam_bai", value: "m84036_250809_035451_s4.bc2106.mapped.bam.bai"
2025-09-15 20:22:50.297 wdl.w:ptcp.t:call-pbmm2_align_hifi-09 INFO output :: name: "mapped_bam_pbi", value: "m84036_250809_035451_s4.bc2106.mapped.bam.pbi"
2025-09-15 20:22:50.298 wdl.w:ptcp.t:call-pbmm2_align_hifi-09 INFO output :: name: "report", value: "mapping_stats.report.json"
2025-09-15 20:22:50.362 wdl.w:ptcp.t:call-pbmm2_align_hifi-24 INFO output :: name: "mapped_bam", value: "m84036_250809_035451_s4.bc2121.mapped.bam"
2025-09-15 20:22:50.364 wdl.w:ptcp.t:call-pbmm2_align_hifi-24 INFO output :: name: "mapped_bam_bai", value: "m84036_250809_035451_s4.bc2121.mapped.bam.bai"
2025-09-15 20:22:50.366 wdl.w:ptcp.t:call-pbmm2_align_hifi-24 INFO output :: name: "mapped_bam_pbi", value: "m84036_250809_035451_s4.bc2121.mapped.bam.pbi"
2025-09-15 20:22:50.367 wdl.w:ptcp.t:call-pbmm2_align_hifi-24 INFO output :: name: "report", value: "mapping_stats.report.json"
2025-09-15 20:22:50.378 wdl.w:ptcp.t:call-pbmm2_align_hifi-09 NOTICE done
2025-09-15 20:22:50.384 wdl.w:ptcp NOTICE finish :: job: "call-pbmm2_align_hifi-09"
2025-09-15 20:22:50.384 wdl.w:ptcp INFO output :: job: "call-pbmm2_align_hifi-09", values: {"report": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-09/out/mapping_stats.report.json", "mapped_bam_pbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-09/out/m84036_250809_035451_s4.bc2106.mapped.bam.pbi", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-09/out/m84036_250809_035451_s4.bc2106.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-09/out/m84036_250809_035451_s4.bc2106.mapped.bam"}
2025-09-15 20:22:50.386 wdl.w:ptcp NOTICE ready :: job: "call-paraphase-09", callee: "paraphase"
2025-09-15 20:22:50.386 wdl.w:ptcp INFO input :: job: "call-paraphase-09", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf", "genome_version": "38", "config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-09/out/m84036_250809_035451_s4.bc2106.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-09/out/m84036_250809_035451_s4.bc2106.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2106"}
2025-09-15 20:22:50.387 wdl.w:ptcp NOTICE ready :: job: "call-sawfish-09", callee: "sawfish"
2025-09-15 20:22:50.387 wdl.w:ptcp INFO input :: job: "call-sawfish-09", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-09/out/m84036_250809_035451_s4.bc2106.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-09/out/m84036_250809_035451_s4.bc2106.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2106"}
2025-09-15 20:22:50.390 wdl.w:ptcp NOTICE ready :: job: "call-trgt-09", callee: "trgt"
2025-09-15 20:22:50.390 wdl.w:ptcp INFO input :: job: "call-trgt-09", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-09/out/m84036_250809_035451_s4.bc2106.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-09/out/m84036_250809_035451_s4.bc2106.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2106"}
2025-09-15 20:22:50.391 wdl.w:ptcp.w:call-sawfish-34.t:call-run_sawfish NOTICE task setup :: name: "run_sawfish", source: "./sawfish.wdl", line: 83, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-34/call-run_sawfish", thread: 140613068518976
2025-09-15 20:22:50.394 wdl.w:ptcp.w:call-paraphase-09 NOTICE workflow start :: name: "paraphase", source: "./paraphase.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-09"
2025-09-15 20:22:50.397 wdl.w:ptcp.w:call-sawfish-09 NOTICE workflow start :: name: "sawfish", source: "./sawfish.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-09"
2025-09-15 20:22:50.402 wdl.w:ptcp.w:call-trgt-09 NOTICE workflow start :: name: "trgt", source: "./trgt.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-09"
2025-09-15 20:22:50.414 wdl.w:ptcp.w:call-paraphase-09 INFO visit :: node: "decl-annotation_vcf", values: {"annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf"}
2025-09-15 20:22:50.415 wdl.w:ptcp.w:call-sawfish-34.t:call-run_sawfish INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:22:50.415 wdl.w:ptcp.w:call-paraphase-09 INFO visit :: node: "decl-config_file", values: {"config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml"}
2025-09-15 20:22:50.415 wdl.w:ptcp.w:call-sawfish-34.t:call-run_sawfish INFO input :: name: "genome_version", value: "38"
2025-09-15 20:22:50.416 wdl.w:ptcp.w:call-paraphase-09 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:22:50.416 wdl.w:ptcp.w:call-sawfish-34.t:call-run_sawfish INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:22:50.416 wdl.w:ptcp.w:call-paraphase-09 INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:22:50.417 wdl.w:ptcp.w:call-sawfish-34.t:call-run_sawfish INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:22:50.417 wdl.w:ptcp.w:call-paraphase-09 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-09/out/m84036_250809_035451_s4.bc2106.mapped.bam"}
2025-09-15 20:22:50.417 wdl.w:ptcp.w:call-sawfish-34.t:call-run_sawfish INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2131.mapped.bam.bai"
2025-09-15 20:22:50.418 wdl.w:ptcp.w:call-paraphase-09 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-09/out/m84036_250809_035451_s4.bc2106.mapped.bam.bai"}
2025-09-15 20:22:50.418 wdl.w:ptcp.w:call-sawfish-34.t:call-run_sawfish INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2131.mapped.bam"
2025-09-15 20:22:50.418 wdl.w:ptcp.w:call-paraphase-09 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:22:50.419 wdl.w:ptcp.w:call-sawfish-34.t:call-run_sawfish INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2131"
2025-09-15 20:22:50.419 wdl.w:ptcp.w:call-paraphase-09 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:22:50.419 wdl.w:ptcp.w:call-sawfish-34.t:call-run_sawfish INFO eval :: name: "mem_gb", value: 32
2025-09-15 20:22:50.420 wdl.w:ptcp.w:call-paraphase-09 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2106"}
2025-09-15 20:22:50.420 wdl.w:ptcp.w:call-sawfish-34.t:call-run_sawfish INFO eval :: name: "threads", value: 16
2025-09-15 20:22:50.420 wdl.w:ptcp.w:call-paraphase-09 INFO visit :: node: "decl-sex", values: {"sex": "F"}
2025-09-15 20:22:50.421 wdl.w:ptcp.w:call-sawfish-09 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:22:50.422 wdl.w:ptcp.w:call-paraphase-09 NOTICE ready :: job: "call-run_paraphase", callee: "run_paraphase"
2025-09-15 20:22:50.422 wdl.w:ptcp.w:call-sawfish-34.t:call-run_sawfish INFO eval :: name: "disk_size", value: 30
2025-09-15 20:22:50.422 wdl.w:ptcp.w:call-sawfish-09 INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:22:50.423 wdl.w:ptcp.w:call-paraphase-09 INFO input :: job: "call-run_paraphase", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf", "genome_version": "38", "config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-09/out/m84036_250809_035451_s4.bc2106.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-09/out/m84036_250809_035451_s4.bc2106.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2106"}
2025-09-15 20:22:50.423 wdl.w:ptcp.w:call-sawfish-34.t:call-run_sawfish INFO eval :: name: "discover_dirname", value: "m84036_250809_035451_s4.bc2131_sawfish_discover"
2025-09-15 20:22:50.423 wdl.w:ptcp.w:call-sawfish-09 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-09/out/m84036_250809_035451_s4.bc2106.mapped.bam"}
2025-09-15 20:22:50.424 wdl.w:ptcp.w:call-sawfish-34.t:call-run_sawfish INFO eval :: name: "call_dirname", value: "m84036_250809_035451_s4.bc2131_sawfish"
2025-09-15 20:22:50.424 wdl.w:ptcp.w:call-sawfish-09 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-09/out/m84036_250809_035451_s4.bc2106.mapped.bam.bai"}
2025-09-15 20:22:50.424 wdl.w:ptcp.w:call-sawfish-34.t:call-run_sawfish INFO eval :: name: "minimap2_bam_filename", value: "m84036_250809_035451_s4.bc2131.minimap2.bam"
2025-09-15 20:22:50.424 wdl.w:ptcp.w:call-sawfish-09 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:22:50.425 wdl.w:ptcp.w:call-sawfish-09 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:22:50.425 wdl.w:ptcp.w:call-sawfish-09 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2106"}
2025-09-15 20:22:50.425 wdl.w:ptcp.w:call-sawfish-09 NOTICE ready :: job: "call-run_sawfish", callee: "run_sawfish"
2025-09-15 20:22:50.426 wdl.w:ptcp.w:call-sawfish-34.t:call-run_sawfish INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 16, memory_reservation: 32000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:22:50.426 wdl.w:ptcp.w:call-sawfish-09 INFO input :: job: "call-run_sawfish", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-09/out/m84036_250809_035451_s4.bc2106.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-09/out/m84036_250809_035451_s4.bc2106.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2106"}
2025-09-15 20:22:50.426 wdl.w:ptcp.w:call-sawfish-34.t:call-run_sawfish WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:22:50.428 wdl.w:ptcp.w:call-trgt-09 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:22:50.428 wdl.w:ptcp.w:call-trgt-09 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-09/out/m84036_250809_035451_s4.bc2106.mapped.bam"}
2025-09-15 20:22:50.428 wdl.w:ptcp.w:call-trgt-09 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-09/out/m84036_250809_035451_s4.bc2106.mapped.bam.bai"}
2025-09-15 20:22:50.428 wdl.w:ptcp.w:call-sawfish-34.t:call-run_sawfish INFO provisioned :: seconds_waited: 0, cpu: 16, mem_bytes: 32000000000
2025-09-15 20:22:50.428 wdl.w:ptcp.w:call-trgt-09 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:22:50.429 wdl.w:ptcp.w:call-trgt-09 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:22:50.429 wdl.w:ptcp.w:call-sawfish-34.t:call-run_sawfish INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:22:50.429 wdl.w:ptcp.w:call-trgt-09 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2106"}
2025-09-15 20:22:50.429 wdl.w:ptcp.w:call-trgt-09 INFO visit :: node: "decl-sex", values: {"sex": "F"}
2025-09-15 20:22:50.429 wdl.w:ptcp.w:call-trgt-09 INFO visit :: node: "decl-trgt_bed", values: {"trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"}
2025-09-15 20:22:50.429 wdl.w:ptcp.w:call-trgt-09 NOTICE ready :: job: "call-get_reads_overlapping_repeats", callee: "get_reads_overlapping_repeats"
2025-09-15 20:22:50.429 wdl.w:ptcp.w:call-trgt-09 INFO input :: job: "call-get_reads_overlapping_repeats", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-09/out/m84036_250809_035451_s4.bc2106.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-09/out/m84036_250809_035451_s4.bc2106.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2106"}
2025-09-15 20:22:50.430 wdl.w:ptcp.w:call-trgt-09 NOTICE ready :: job: "call-trgt_genotype", callee: "trgt_genotype"
2025-09-15 20:22:50.430 wdl.w:ptcp.w:call-trgt-09 INFO input :: job: "call-trgt_genotype", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-09/out/m84036_250809_035451_s4.bc2106.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-09/out/m84036_250809_035451_s4.bc2106.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2106"}
2025-09-15 20:22:50.460 wdl.w:ptcp.t:call-pbmm2_align_hifi-24 NOTICE done
2025-09-15 20:22:50.465 wdl.w:ptcp.w:call-paraphase-04.t:call-run_paraphase.slurm_singularity INFO srun: job 51797339 queued and waiting for resources
2025-09-15 20:22:50.465 wdl.w:ptcp.w:call-sawfish-04.t:call-run_sawfish.slurm_singularity INFO srun: job 51797340 queued and waiting for resources
2025-09-15 20:22:50.498 wdl.w:ptcp.w:call-sawfish-34.t:call-run_sawfish INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 10, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-34/call-run_sawfish/_singularity_tmpdir_p5mvz7ch"
2025-09-15 20:22:50.499 wdl.w:ptcp.w:call-sawfish-34.t:call-run_sawfish INFO Slurm invocation: srun --job-name call-run_sawfish --partition compute,compute9 --cpus-per-task 16 --mem 30518M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-34/call-run_sawfish/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-34/call-run_sawfish/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-34/call-run_sawfish/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-34/call-run_sawfish/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-34/out/m84036_250809_035451_s4.bc2131.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2131.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-34/out/m84036_250809_035451_s4.bc2131.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2131.mapped.bam:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-34/call-run_sawfish/_singularity_tmpdir_p5mvz7ch/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-34/call-run_sawfish/_singularity_tmpdir_p5mvz7ch/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:22:50.516 wdl.w:ptcp.w:call-sawfish-34.t:call-run_sawfish NOTICE slurm_singularity run :: pid: 1198368, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-34/call-run_sawfish/slurm_singularity.log.txt"
2025-09-15 20:22:50.517 wdl.w:ptcp NOTICE finish :: job: "call-pbmm2_align_hifi-24"
2025-09-15 20:22:50.517 wdl.w:ptcp INFO output :: job: "call-pbmm2_align_hifi-24", values: {"report": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-24/out/mapping_stats.report.json", "mapped_bam_pbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-24/out/m84036_250809_035451_s4.bc2121.mapped.bam.pbi", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-24/out/m84036_250809_035451_s4.bc2121.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-24/out/m84036_250809_035451_s4.bc2121.mapped.bam"}
2025-09-15 20:22:50.518 wdl.w:ptcp NOTICE ready :: job: "call-paraphase-24", callee: "paraphase"
2025-09-15 20:22:50.518 wdl.w:ptcp INFO input :: job: "call-paraphase-24", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf", "genome_version": "38", "config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-24/out/m84036_250809_035451_s4.bc2121.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-24/out/m84036_250809_035451_s4.bc2121.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2121"}
2025-09-15 20:22:50.519 wdl.w:ptcp NOTICE ready :: job: "call-sawfish-24", callee: "sawfish"
2025-09-15 20:22:50.519 wdl.w:ptcp INFO input :: job: "call-sawfish-24", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-24/out/m84036_250809_035451_s4.bc2121.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-24/out/m84036_250809_035451_s4.bc2121.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2121"}
2025-09-15 20:22:50.523 wdl.w:ptcp.w:call-trgt-34.t:call-get_reads_overlapping_repeats NOTICE task setup :: name: "get_reads_overlapping_repeats", source: "./trgt.wdl", line: 182, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-34/call-get_reads_overlapping_repeats", thread: 140611986384448
2025-09-15 20:22:50.524 wdl.w:ptcp NOTICE ready :: job: "call-trgt-24", callee: "trgt"
2025-09-15 20:22:50.524 wdl.w:ptcp INFO input :: job: "call-trgt-24", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-24/out/m84036_250809_035451_s4.bc2121.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-24/out/m84036_250809_035451_s4.bc2121.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2121"}
2025-09-15 20:22:50.528 wdl.w:ptcp.w:call-paraphase-24 NOTICE workflow start :: name: "paraphase", source: "./paraphase.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-24"
2025-09-15 20:22:50.531 wdl.w:ptcp.w:call-sawfish-24 NOTICE workflow start :: name: "sawfish", source: "./sawfish.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-24"
2025-09-15 20:22:50.537 wdl.w:ptcp.w:call-trgt-24 NOTICE workflow start :: name: "trgt", source: "./trgt.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-24"
2025-09-15 20:22:50.547 wdl.w:ptcp.w:call-paraphase-24 INFO visit :: node: "decl-annotation_vcf", values: {"annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf"}
2025-09-15 20:22:50.547 wdl.w:ptcp.w:call-paraphase-24 INFO visit :: node: "decl-config_file", values: {"config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml"}
2025-09-15 20:22:50.548 wdl.w:ptcp.w:call-paraphase-24 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:22:50.548 wdl.w:ptcp.w:call-paraphase-24 INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:22:50.548 wdl.w:ptcp.w:call-paraphase-24 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-24/out/m84036_250809_035451_s4.bc2121.mapped.bam"}
2025-09-15 20:22:50.548 wdl.w:ptcp.w:call-paraphase-24 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-24/out/m84036_250809_035451_s4.bc2121.mapped.bam.bai"}
2025-09-15 20:22:50.548 wdl.w:ptcp.w:call-paraphase-24 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:22:50.549 wdl.w:ptcp.w:call-paraphase-24 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:22:50.549 wdl.w:ptcp.w:call-paraphase-24 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2121"}
2025-09-15 20:22:50.549 wdl.w:ptcp.w:call-paraphase-24 INFO visit :: node: "decl-sex", values: {"sex": "F"}
2025-09-15 20:22:50.549 wdl.w:ptcp.w:call-paraphase-24 NOTICE ready :: job: "call-run_paraphase", callee: "run_paraphase"
2025-09-15 20:22:50.549 wdl.w:ptcp.w:call-paraphase-24 INFO input :: job: "call-run_paraphase", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf", "genome_version": "38", "config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-24/out/m84036_250809_035451_s4.bc2121.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-24/out/m84036_250809_035451_s4.bc2121.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2121"}
2025-09-15 20:22:50.549 wdl.w:ptcp.w:call-trgt-34.t:call-get_reads_overlapping_repeats INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:22:50.550 wdl.w:ptcp.w:call-trgt-34.t:call-get_reads_overlapping_repeats INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:22:50.551 wdl.w:ptcp.w:call-trgt-34.t:call-get_reads_overlapping_repeats INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2131.mapped.bam.bai"
2025-09-15 20:22:50.551 wdl.w:ptcp.w:call-trgt-34.t:call-get_reads_overlapping_repeats INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2131.mapped.bam"
2025-09-15 20:22:50.551 wdl.w:ptcp.w:call-trgt-34.t:call-get_reads_overlapping_repeats INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2131"
2025-09-15 20:22:50.552 wdl.w:ptcp.w:call-trgt-34.t:call-get_reads_overlapping_repeats INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:22:50.552 wdl.w:ptcp.w:call-trgt-34.t:call-get_reads_overlapping_repeats INFO eval :: name: "expand_size", value: 3000
2025-09-15 20:22:50.552 wdl.w:ptcp.w:call-trgt-34.t:call-get_reads_overlapping_repeats INFO eval :: name: "threads", value: 1
2025-09-15 20:22:50.553 wdl.w:ptcp.w:call-trgt-34.t:call-get_reads_overlapping_repeats INFO eval :: name: "expanded_bed_name", value: "m84036_250809_035451_s4.bc2131.expanded.bed"
2025-09-15 20:22:50.553 wdl.w:ptcp.w:call-trgt-34.t:call-get_reads_overlapping_repeats INFO eval :: name: "disk_size", value: 11
2025-09-15 20:22:50.554 wdl.w:ptcp.w:call-trgt-34.t:call-get_reads_overlapping_repeats INFO eval :: name: "output_name", value: "m84036_250809_035451_s4.bc2131.repeats.bam"
2025-09-15 20:22:50.554 wdl.w:ptcp.w:call-trgt-34.t:call-get_reads_overlapping_repeats INFO eval :: name: "index_name", value: "m84036_250809_035451_s4.bc2131.repeats.bam.bai"
2025-09-15 20:22:50.554 wdl.w:ptcp.w:call-trgt-34.t:call-get_reads_overlapping_repeats INFO eval :: name: "output_name_with_index", value: "m84036_250809_035451_s4.bc2131.repeats.bam##idx##m84036_250809_035451_s4.bc2131.repeats.bam.bai"
2025-09-15 20:22:50.556 wdl.w:ptcp.w:call-sawfish-24 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:22:50.556 wdl.w:ptcp.w:call-trgt-34.t:call-get_reads_overlapping_repeats INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:22:50.556 wdl.w:ptcp.w:call-sawfish-24 INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:22:50.556 wdl.w:ptcp.w:call-trgt-34.t:call-get_reads_overlapping_repeats WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:22:50.556 wdl.w:ptcp.w:call-sawfish-24 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-24/out/m84036_250809_035451_s4.bc2121.mapped.bam"}
2025-09-15 20:22:50.557 wdl.w:ptcp.w:call-sawfish-24 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-24/out/m84036_250809_035451_s4.bc2121.mapped.bam.bai"}
2025-09-15 20:22:50.557 wdl.w:ptcp.w:call-sawfish-24 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:22:50.557 wdl.w:ptcp.w:call-sawfish-24 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:22:50.557 wdl.w:ptcp.w:call-trgt-34.t:call-get_reads_overlapping_repeats INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:22:50.557 wdl.w:ptcp.w:call-sawfish-24 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2121"}
2025-09-15 20:22:50.558 wdl.w:ptcp.w:call-trgt-34.t:call-get_reads_overlapping_repeats INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:22:50.558 wdl.w:ptcp.w:call-sawfish-24 NOTICE ready :: job: "call-run_sawfish", callee: "run_sawfish"
2025-09-15 20:22:50.558 wdl.w:ptcp.w:call-sawfish-24 INFO input :: job: "call-run_sawfish", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-24/out/m84036_250809_035451_s4.bc2121.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-24/out/m84036_250809_035451_s4.bc2121.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2121"}
2025-09-15 20:22:50.560 wdl.w:ptcp.w:call-trgt-24 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:22:50.561 wdl.w:ptcp.w:call-trgt-24 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-24/out/m84036_250809_035451_s4.bc2121.mapped.bam"}
2025-09-15 20:22:50.561 wdl.w:ptcp.w:call-trgt-24 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-24/out/m84036_250809_035451_s4.bc2121.mapped.bam.bai"}
2025-09-15 20:22:50.561 wdl.w:ptcp.w:call-trgt-24 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:22:50.561 wdl.w:ptcp.w:call-trgt-24 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:22:50.561 wdl.w:ptcp.w:call-trgt-24 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2121"}
2025-09-15 20:22:50.561 wdl.w:ptcp.w:call-trgt-24 INFO visit :: node: "decl-sex", values: {"sex": "F"}
2025-09-15 20:22:50.561 wdl.w:ptcp.w:call-trgt-24 INFO visit :: node: "decl-trgt_bed", values: {"trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"}
2025-09-15 20:22:50.561 wdl.w:ptcp.w:call-trgt-24 NOTICE ready :: job: "call-get_reads_overlapping_repeats", callee: "get_reads_overlapping_repeats"
2025-09-15 20:22:50.561 wdl.w:ptcp.w:call-trgt-24 INFO input :: job: "call-get_reads_overlapping_repeats", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-24/out/m84036_250809_035451_s4.bc2121.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-24/out/m84036_250809_035451_s4.bc2121.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2121"}
2025-09-15 20:22:50.562 wdl.w:ptcp.w:call-trgt-24 NOTICE ready :: job: "call-trgt_genotype", callee: "trgt_genotype"
2025-09-15 20:22:50.562 wdl.w:ptcp.w:call-trgt-24 INFO input :: job: "call-trgt_genotype", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-24/out/m84036_250809_035451_s4.bc2121.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-24/out/m84036_250809_035451_s4.bc2121.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2121"}
2025-09-15 20:22:50.604 wdl.w:ptcp.t:call-pbmm2_align_hifi-61.slurm_singularity INFO srun: job 51797283 has been allocated resources
2025-09-15 20:22:50.604 wdl.w:ptcp.t:call-pbmm2_align_hifi-61.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:22:50.604 wdl.w:ptcp.t:call-pbmm2_align_hifi-61.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:22:50.604 wdl.w:ptcp.t:call-pbmm2_align_hifi-62.slurm_singularity INFO srun: job 51797284 has been allocated resources
2025-09-15 20:22:50.604 wdl.w:ptcp.t:call-pbmm2_align_hifi-62.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:22:50.605 wdl.w:ptcp.t:call-pbmm2_align_hifi-62.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:22:50.611 wdl.w:ptcp.w:call-trgt-34.t:call-get_reads_overlapping_repeats INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 9, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-34/call-get_reads_overlapping_repeats/_singularity_tmpdir_3mqlg1ev"
2025-09-15 20:22:50.611 wdl.w:ptcp.w:call-trgt-34.t:call-get_reads_overlapping_repeats INFO Slurm invocation: srun --job-name call-get_reads_overlapping_repeats --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-34/call-get_reads_overlapping_repeats/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-34/call-get_reads_overlapping_repeats/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-34/call-get_reads_overlapping_repeats/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-34/call-get_reads_overlapping_repeats/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-34/out/m84036_250809_035451_s4.bc2131.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2131.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-34/out/m84036_250809_035451_s4.bc2131.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2131.mapped.bam:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-34/call-get_reads_overlapping_repeats/_singularity_tmpdir_3mqlg1ev/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-34/call-get_reads_overlapping_repeats/_singularity_tmpdir_3mqlg1ev/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:22:50.623 wdl.w:ptcp.t:call-pbmm2_align_hifi-59.slurm_singularity INFO srun: job 51797281 has been allocated resources
2025-09-15 20:22:50.624 wdl.w:ptcp.t:call-pbmm2_align_hifi-59.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:22:50.624 wdl.w:ptcp.t:call-pbmm2_align_hifi-59.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:22:50.628 wdl.w:ptcp.w:call-trgt-34.t:call-get_reads_overlapping_repeats NOTICE slurm_singularity run :: pid: 1198373, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-34/call-get_reads_overlapping_repeats/slurm_singularity.log.txt"
2025-09-15 20:22:50.631 wdl.w:ptcp.t:call-pbmm2_align_hifi-60.slurm_singularity INFO srun: job 51797282 has been allocated resources
2025-09-15 20:22:50.631 wdl.w:ptcp.t:call-pbmm2_align_hifi-60.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:22:50.790 wdl.w:ptcp.t:call-pbmm2_align_hifi-27 INFO output :: name: "mapped_bam", value: "m84036_250809_035451_s4.bc2124.mapped.bam"
2025-09-15 20:22:50.795 wdl.w:ptcp.w:call-sawfish-31.t:call-run_sawfish.slurm_singularity INFO srun: job 51797341 queued and waiting for resources
2025-09-15 20:22:50.796 wdl.w:ptcp.t:call-pbmm2_align_hifi-27 INFO output :: name: "mapped_bam_bai", value: "m84036_250809_035451_s4.bc2124.mapped.bam.bai"
2025-09-15 20:22:50.798 wdl.w:ptcp.t:call-pbmm2_align_hifi-27 INFO output :: name: "mapped_bam_pbi", value: "m84036_250809_035451_s4.bc2124.mapped.bam.pbi"
2025-09-15 20:22:50.800 wdl.w:ptcp.t:call-pbmm2_align_hifi-27 INFO output :: name: "report", value: "mapping_stats.report.json"
2025-09-15 20:22:50.801 wdl.w:ptcp.w:call-paraphase-31.t:call-run_paraphase.slurm_singularity INFO srun: job 51797345 queued and waiting for resources
2025-09-15 20:22:50.802 wdl.w:ptcp.w:call-trgt-04.t:call-get_reads_overlapping_repeats.slurm_singularity INFO srun: job 51797344 queued and waiting for resources
2025-09-15 20:22:50.803 wdl.w:ptcp.w:call-trgt-04.t:call-trgt_genotype.slurm_singularity INFO srun: job 51797343 queued and waiting for resources
2025-09-15 20:22:50.804 wdl.w:ptcp.w:call-trgt-31.t:call-get_reads_overlapping_repeats.slurm_singularity INFO srun: job 51797342 queued and waiting for resources
2025-09-15 20:22:50.882 wdl.w:ptcp.t:call-pbmm2_align_hifi-27 NOTICE done
2025-09-15 20:22:50.889 wdl.w:ptcp NOTICE finish :: job: "call-pbmm2_align_hifi-27"
2025-09-15 20:22:50.889 wdl.w:ptcp INFO output :: job: "call-pbmm2_align_hifi-27", values: {"report": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-27/out/mapping_stats.report.json", "mapped_bam_pbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-27/out/m84036_250809_035451_s4.bc2124.mapped.bam.pbi", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-27/out/m84036_250809_035451_s4.bc2124.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-27/out/m84036_250809_035451_s4.bc2124.mapped.bam"}
2025-09-15 20:22:50.891 wdl.w:ptcp NOTICE ready :: job: "call-paraphase-27", callee: "paraphase"
2025-09-15 20:22:50.892 wdl.w:ptcp INFO input :: job: "call-paraphase-27", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf", "genome_version": "38", "config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-27/out/m84036_250809_035451_s4.bc2124.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-27/out/m84036_250809_035451_s4.bc2124.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2124"}
2025-09-15 20:22:50.893 wdl.w:ptcp NOTICE ready :: job: "call-sawfish-27", callee: "sawfish"
2025-09-15 20:22:50.893 wdl.w:ptcp INFO input :: job: "call-sawfish-27", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-27/out/m84036_250809_035451_s4.bc2124.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-27/out/m84036_250809_035451_s4.bc2124.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2124"}
2025-09-15 20:22:50.895 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_genotype NOTICE task setup :: name: "trgt_genotype", source: "./trgt.wdl", line: 272, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-34/call-trgt_genotype", thread: 140611961206336
2025-09-15 20:22:50.896 wdl.w:ptcp NOTICE ready :: job: "call-trgt-27", callee: "trgt"
2025-09-15 20:22:50.896 wdl.w:ptcp INFO input :: job: "call-trgt-27", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-27/out/m84036_250809_035451_s4.bc2124.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-27/out/m84036_250809_035451_s4.bc2124.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2124"}
2025-09-15 20:22:50.899 wdl.w:ptcp.w:call-paraphase-27 NOTICE workflow start :: name: "paraphase", source: "./paraphase.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-27"
2025-09-15 20:22:50.905 wdl.w:ptcp.w:call-sawfish-27 NOTICE workflow start :: name: "sawfish", source: "./sawfish.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-27"
2025-09-15 20:22:50.908 wdl.w:ptcp.w:call-trgt-27 NOTICE workflow start :: name: "trgt", source: "./trgt.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-27"
2025-09-15 20:22:50.914 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_genotype INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:22:50.914 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_genotype INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:22:50.914 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_genotype INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:22:50.914 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_genotype INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:22:50.914 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_genotype INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2131.mapped.bam.bai"
2025-09-15 20:22:50.914 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_genotype INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2131.mapped.bam"
2025-09-15 20:22:50.914 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_genotype INFO input :: name: "sex", value: "F"
2025-09-15 20:22:50.914 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_genotype INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2131"
2025-09-15 20:22:50.915 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_genotype INFO eval :: name: "mem_gb", value: 16
2025-09-15 20:22:50.915 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_genotype INFO eval :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2131.trgt"
2025-09-15 20:22:50.915 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_genotype INFO eval :: name: "threads", value: 8
2025-09-15 20:22:50.915 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_genotype INFO eval :: name: "disk_size", value: 27
2025-09-15 20:22:50.916 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_genotype INFO eval :: name: "karyotype", value: "XX"
2025-09-15 20:22:50.916 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_genotype INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 8, memory_reservation: 16000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:22:50.917 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_genotype WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:22:50.917 wdl.w:ptcp.w:call-paraphase-27 INFO visit :: node: "decl-annotation_vcf", values: {"annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf"}
2025-09-15 20:22:50.918 wdl.w:ptcp.w:call-paraphase-27 INFO visit :: node: "decl-config_file", values: {"config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml"}
2025-09-15 20:22:50.918 wdl.w:ptcp.w:call-paraphase-27 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:22:50.918 wdl.w:ptcp.w:call-paraphase-27 INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:22:50.919 wdl.w:ptcp.w:call-paraphase-27 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-27/out/m84036_250809_035451_s4.bc2124.mapped.bam"}
2025-09-15 20:22:50.919 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_genotype INFO provisioned :: seconds_waited: 0, cpu: 8, mem_bytes: 16000000000
2025-09-15 20:22:50.919 wdl.w:ptcp.w:call-paraphase-27 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-27/out/m84036_250809_035451_s4.bc2124.mapped.bam.bai"}
2025-09-15 20:22:50.919 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_genotype INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:22:50.920 wdl.w:ptcp.w:call-paraphase-27 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:22:50.920 wdl.w:ptcp.w:call-paraphase-27 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:22:50.920 wdl.w:ptcp.w:call-paraphase-27 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2124"}
2025-09-15 20:22:50.920 wdl.w:ptcp.w:call-paraphase-27 INFO visit :: node: "decl-sex", values: {"sex": "F"}
2025-09-15 20:22:50.920 wdl.w:ptcp.w:call-paraphase-27 NOTICE ready :: job: "call-run_paraphase", callee: "run_paraphase"
2025-09-15 20:22:50.921 wdl.w:ptcp.w:call-paraphase-27 INFO input :: job: "call-run_paraphase", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf", "genome_version": "38", "config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-27/out/m84036_250809_035451_s4.bc2124.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-27/out/m84036_250809_035451_s4.bc2124.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2124"}
2025-09-15 20:22:50.926 wdl.w:ptcp.w:call-sawfish-27 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:22:50.927 wdl.w:ptcp.w:call-sawfish-27 INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:22:50.927 wdl.w:ptcp.w:call-sawfish-27 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-27/out/m84036_250809_035451_s4.bc2124.mapped.bam"}
2025-09-15 20:22:50.927 wdl.w:ptcp.w:call-sawfish-27 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-27/out/m84036_250809_035451_s4.bc2124.mapped.bam.bai"}
2025-09-15 20:22:50.927 wdl.w:ptcp.w:call-sawfish-27 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:22:50.927 wdl.w:ptcp.w:call-sawfish-27 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:22:50.927 wdl.w:ptcp.w:call-sawfish-27 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2124"}
2025-09-15 20:22:50.928 wdl.w:ptcp.w:call-sawfish-27 NOTICE ready :: job: "call-run_sawfish", callee: "run_sawfish"
2025-09-15 20:22:50.928 wdl.w:ptcp.w:call-sawfish-27 INFO input :: job: "call-run_sawfish", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-27/out/m84036_250809_035451_s4.bc2124.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-27/out/m84036_250809_035451_s4.bc2124.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2124"}
2025-09-15 20:22:50.932 wdl.w:ptcp.w:call-trgt-27 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:22:50.932 wdl.w:ptcp.w:call-trgt-27 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-27/out/m84036_250809_035451_s4.bc2124.mapped.bam"}
2025-09-15 20:22:50.932 wdl.w:ptcp.w:call-trgt-27 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-27/out/m84036_250809_035451_s4.bc2124.mapped.bam.bai"}
2025-09-15 20:22:50.932 wdl.w:ptcp.w:call-trgt-27 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:22:50.932 wdl.w:ptcp.w:call-trgt-27 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:22:50.932 wdl.w:ptcp.w:call-trgt-27 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2124"}
2025-09-15 20:22:50.932 wdl.w:ptcp.w:call-trgt-27 INFO visit :: node: "decl-sex", values: {"sex": "F"}
2025-09-15 20:22:50.932 wdl.w:ptcp.w:call-trgt-27 INFO visit :: node: "decl-trgt_bed", values: {"trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"}
2025-09-15 20:22:50.933 wdl.w:ptcp.w:call-trgt-27 NOTICE ready :: job: "call-get_reads_overlapping_repeats", callee: "get_reads_overlapping_repeats"
2025-09-15 20:22:50.933 wdl.w:ptcp.w:call-trgt-27 INFO input :: job: "call-get_reads_overlapping_repeats", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-27/out/m84036_250809_035451_s4.bc2124.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-27/out/m84036_250809_035451_s4.bc2124.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2124"}
2025-09-15 20:22:50.933 wdl.w:ptcp.w:call-trgt-27 NOTICE ready :: job: "call-trgt_genotype", callee: "trgt_genotype"
2025-09-15 20:22:50.934 wdl.w:ptcp.w:call-trgt-27 INFO input :: job: "call-trgt_genotype", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-27/out/m84036_250809_035451_s4.bc2124.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-27/out/m84036_250809_035451_s4.bc2124.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2124"}
2025-09-15 20:22:50.991 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_genotype INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 11, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-34/call-trgt_genotype/_singularity_tmpdir_19kfoplc"
2025-09-15 20:22:50.991 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_genotype INFO Slurm invocation: srun --job-name call-trgt_genotype --partition compute,compute9 --cpus-per-task 8 --mem 15259M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-34/call-trgt_genotype/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-34/call-trgt_genotype/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-34/call-trgt_genotype/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-34/call-trgt_genotype/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-34/out/m84036_250809_035451_s4.bc2131.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2131.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-34/out/m84036_250809_035451_s4.bc2131.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2131.mapped.bam:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-34/call-trgt_genotype/_singularity_tmpdir_19kfoplc/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-34/call-trgt_genotype/_singularity_tmpdir_19kfoplc/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:22:51.021 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_genotype NOTICE slurm_singularity run :: pid: 1198384, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-34/call-trgt_genotype/slurm_singularity.log.txt"
2025-09-15 20:22:51.079 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_genotype.slurm_singularity INFO srun: job 51797346 queued and waiting for resources
2025-09-15 20:22:51.181 wdl.w:ptcp.t:call-pbmm2_align_hifi-25 INFO output :: name: "mapped_bam", value: "m84036_250809_035451_s4.bc2122.mapped.bam"
2025-09-15 20:22:51.184 wdl.w:ptcp.t:call-pbmm2_align_hifi-25 INFO output :: name: "mapped_bam_bai", value: "m84036_250809_035451_s4.bc2122.mapped.bam.bai"
2025-09-15 20:22:51.186 wdl.w:ptcp.t:call-pbmm2_align_hifi-25 INFO output :: name: "mapped_bam_pbi", value: "m84036_250809_035451_s4.bc2122.mapped.bam.pbi"
2025-09-15 20:22:51.187 wdl.w:ptcp.t:call-pbmm2_align_hifi-25 INFO output :: name: "report", value: "mapping_stats.report.json"
2025-09-15 20:22:51.187 wdl.w:ptcp.w:call-paraphase-34.t:call-run_paraphase.slurm_singularity INFO srun: job 51797347 queued and waiting for resources
2025-09-15 20:22:51.278 wdl.w:ptcp.t:call-pbmm2_align_hifi-25 NOTICE done
2025-09-15 20:22:51.286 wdl.w:ptcp NOTICE finish :: job: "call-pbmm2_align_hifi-25"
2025-09-15 20:22:51.286 wdl.w:ptcp INFO output :: job: "call-pbmm2_align_hifi-25", values: {"report": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-25/out/mapping_stats.report.json", "mapped_bam_pbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-25/out/m84036_250809_035451_s4.bc2122.mapped.bam.pbi", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-25/out/m84036_250809_035451_s4.bc2122.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-25/out/m84036_250809_035451_s4.bc2122.mapped.bam"}
2025-09-15 20:22:51.287 wdl.w:ptcp NOTICE ready :: job: "call-paraphase-25", callee: "paraphase"
2025-09-15 20:22:51.287 wdl.w:ptcp INFO input :: job: "call-paraphase-25", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf", "genome_version": "38", "config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-25/out/m84036_250809_035451_s4.bc2122.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-25/out/m84036_250809_035451_s4.bc2122.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2122"}
2025-09-15 20:22:51.288 wdl.w:ptcp NOTICE ready :: job: "call-sawfish-25", callee: "sawfish"
2025-09-15 20:22:51.288 wdl.w:ptcp INFO input :: job: "call-sawfish-25", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-25/out/m84036_250809_035451_s4.bc2122.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-25/out/m84036_250809_035451_s4.bc2122.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2122"}
2025-09-15 20:22:51.292 wdl.w:ptcp NOTICE ready :: job: "call-trgt-25", callee: "trgt"
2025-09-15 20:22:51.292 wdl.w:ptcp INFO input :: job: "call-trgt-25", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-25/out/m84036_250809_035451_s4.bc2122.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-25/out/m84036_250809_035451_s4.bc2122.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2122"}
2025-09-15 20:22:51.295 wdl.w:ptcp.w:call-paraphase-23.t:call-run_paraphase NOTICE task setup :: name: "run_paraphase", source: "./paraphase.wdl", line: 127, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-23/call-run_paraphase", thread: 140611977991744
2025-09-15 20:22:51.296 wdl.w:ptcp.w:call-paraphase-25 NOTICE workflow start :: name: "paraphase", source: "./paraphase.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-25"
2025-09-15 20:22:51.303 wdl.w:ptcp.w:call-sawfish-25 NOTICE workflow start :: name: "sawfish", source: "./sawfish.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-25"
2025-09-15 20:22:51.307 wdl.w:ptcp.w:call-trgt-25 NOTICE workflow start :: name: "trgt", source: "./trgt.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-25"
2025-09-15 20:22:51.317 wdl.w:ptcp.w:call-paraphase-25 INFO visit :: node: "decl-annotation_vcf", values: {"annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf"}
2025-09-15 20:22:51.318 wdl.w:ptcp.w:call-paraphase-25 INFO visit :: node: "decl-config_file", values: {"config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml"}
2025-09-15 20:22:51.318 wdl.w:ptcp.w:call-paraphase-25 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:22:51.319 wdl.w:ptcp.w:call-paraphase-25 INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:22:51.319 wdl.w:ptcp.w:call-paraphase-25 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-25/out/m84036_250809_035451_s4.bc2122.mapped.bam"}
2025-09-15 20:22:51.320 wdl.w:ptcp.w:call-paraphase-25 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-25/out/m84036_250809_035451_s4.bc2122.mapped.bam.bai"}
2025-09-15 20:22:51.320 wdl.w:ptcp.w:call-paraphase-25 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:22:51.320 wdl.w:ptcp.w:call-paraphase-25 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:22:51.321 wdl.w:ptcp.w:call-paraphase-25 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2122"}
2025-09-15 20:22:51.321 wdl.w:ptcp.w:call-paraphase-25 INFO visit :: node: "decl-sex", values: {"sex": "F"}
2025-09-15 20:22:51.322 wdl.w:ptcp.w:call-paraphase-25 NOTICE ready :: job: "call-run_paraphase", callee: "run_paraphase"
2025-09-15 20:22:51.322 wdl.w:ptcp.w:call-paraphase-25 INFO input :: job: "call-run_paraphase", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf", "genome_version": "38", "config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-25/out/m84036_250809_035451_s4.bc2122.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-25/out/m84036_250809_035451_s4.bc2122.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2122"}
2025-09-15 20:22:51.327 wdl.w:ptcp.w:call-sawfish-25 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:22:51.327 wdl.w:ptcp.w:call-paraphase-23.t:call-run_paraphase INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:22:51.327 wdl.w:ptcp.w:call-sawfish-25 INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:22:51.327 wdl.w:ptcp.w:call-paraphase-23.t:call-run_paraphase INFO input :: name: "annotation_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf"
2025-09-15 20:22:51.327 wdl.w:ptcp.w:call-sawfish-25 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-25/out/m84036_250809_035451_s4.bc2122.mapped.bam"}
2025-09-15 20:22:51.328 wdl.w:ptcp.w:call-paraphase-23.t:call-run_paraphase INFO input :: name: "genome_version", value: "38"
2025-09-15 20:22:51.328 wdl.w:ptcp.w:call-sawfish-25 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-25/out/m84036_250809_035451_s4.bc2122.mapped.bam.bai"}
2025-09-15 20:22:51.328 wdl.w:ptcp.w:call-paraphase-23.t:call-run_paraphase INFO input :: name: "config_file", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/paraphase_config.GRCh38.yaml"
2025-09-15 20:22:51.328 wdl.w:ptcp.w:call-sawfish-25 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:22:51.328 wdl.w:ptcp.w:call-paraphase-23.t:call-run_paraphase INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:22:51.328 wdl.w:ptcp.w:call-sawfish-25 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:22:51.328 wdl.w:ptcp.w:call-paraphase-23.t:call-run_paraphase INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:22:51.329 wdl.w:ptcp.w:call-sawfish-25 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2122"}
2025-09-15 20:22:51.330 wdl.w:ptcp.w:call-paraphase-23.t:call-run_paraphase INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2120.mapped.bam.bai"
2025-09-15 20:22:51.329 wdl.w:ptcp.w:call-trgt-25 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:22:51.330 wdl.w:ptcp.w:call-sawfish-25 NOTICE ready :: job: "call-run_sawfish", callee: "run_sawfish"
2025-09-15 20:22:51.330 wdl.w:ptcp.w:call-paraphase-23.t:call-run_paraphase INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2120.mapped.bam"
2025-09-15 20:22:51.330 wdl.w:ptcp.w:call-trgt-25 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-25/out/m84036_250809_035451_s4.bc2122.mapped.bam"}
2025-09-15 20:22:51.330 wdl.w:ptcp.w:call-sawfish-25 INFO input :: job: "call-run_sawfish", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-25/out/m84036_250809_035451_s4.bc2122.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-25/out/m84036_250809_035451_s4.bc2122.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2122"}
2025-09-15 20:22:51.331 wdl.w:ptcp.w:call-paraphase-23.t:call-run_paraphase INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2120"
2025-09-15 20:22:51.331 wdl.w:ptcp.w:call-trgt-25 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-25/out/m84036_250809_035451_s4.bc2122.mapped.bam.bai"}
2025-09-15 20:22:51.331 wdl.w:ptcp.w:call-paraphase-23.t:call-run_paraphase INFO eval :: name: "threads", value: 4
2025-09-15 20:22:51.331 wdl.w:ptcp.w:call-trgt-25 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:22:51.331 wdl.w:ptcp.w:call-paraphase-23.t:call-run_paraphase INFO eval :: name: "mem_gb", value: 8
2025-09-15 20:22:51.331 wdl.w:ptcp.w:call-trgt-25 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:22:51.332 wdl.w:ptcp.w:call-trgt-25 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2122"}
2025-09-15 20:22:51.332 wdl.w:ptcp.w:call-trgt-25 INFO visit :: node: "decl-sex", values: {"sex": "F"}
2025-09-15 20:22:51.332 wdl.w:ptcp.w:call-paraphase-23.t:call-run_paraphase INFO eval :: name: "disk_size", value: 27
2025-09-15 20:22:51.332 wdl.w:ptcp.w:call-trgt-25 INFO visit :: node: "decl-trgt_bed", values: {"trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"}
2025-09-15 20:22:51.332 wdl.w:ptcp.w:call-paraphase-23.t:call-run_paraphase INFO eval :: name: "out_dir", value: "m84036_250809_035451_s4.bc2120_paraphase"
2025-09-15 20:22:51.332 wdl.w:ptcp.w:call-trgt-25 NOTICE ready :: job: "call-get_reads_overlapping_repeats", callee: "get_reads_overlapping_repeats"
2025-09-15 20:22:51.333 wdl.w:ptcp.w:call-trgt-25 INFO input :: job: "call-get_reads_overlapping_repeats", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-25/out/m84036_250809_035451_s4.bc2122.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-25/out/m84036_250809_035451_s4.bc2122.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2122"}
2025-09-15 20:22:51.333 wdl.w:ptcp.w:call-paraphase-23.t:call-run_paraphase INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 4, memory_reservation: 8000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:22:51.333 wdl.w:ptcp.w:call-paraphase-23.t:call-run_paraphase WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:22:51.334 wdl.w:ptcp.w:call-trgt-25 NOTICE ready :: job: "call-trgt_genotype", callee: "trgt_genotype"
2025-09-15 20:22:51.334 wdl.w:ptcp.w:call-trgt-25 INFO input :: job: "call-trgt_genotype", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-25/out/m84036_250809_035451_s4.bc2122.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-25/out/m84036_250809_035451_s4.bc2122.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2122"}
2025-09-15 20:22:51.334 wdl.w:ptcp.w:call-paraphase-23.t:call-run_paraphase INFO provisioned :: seconds_waited: 0, cpu: 4, mem_bytes: 8000000000
2025-09-15 20:22:51.335 wdl.w:ptcp.w:call-paraphase-23.t:call-run_paraphase INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:22:51.389 wdl.w:ptcp.w:call-paraphase-23.t:call-run_paraphase INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-23/call-run_paraphase/_singularity_tmpdir_xgyxg7sv"
2025-09-15 20:22:51.389 wdl.w:ptcp.w:call-paraphase-23.t:call-run_paraphase INFO Slurm invocation: srun --job-name call-run_paraphase --partition compute,compute9 --cpus-per-task 4 --mem 7629M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-23/call-run_paraphase/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-23/call-run_paraphase/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-23/call-run_paraphase/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-23/call-run_paraphase/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-23/out/m84036_250809_035451_s4.bc2120.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2120.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-23/out/m84036_250809_035451_s4.bc2120.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2120.mapped.bam:ro --bind /ptcp/meta/variant_list/variant_list.GRCh38.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf:ro --bind /ptcp/meta/paraphase/paraphase_config.GRCh38.yaml:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/paraphase_config.GRCh38.yaml:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-23/call-run_paraphase/_singularity_tmpdir_xgyxg7sv/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-23/call-run_paraphase/_singularity_tmpdir_xgyxg7sv/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:22:51.405 wdl.w:ptcp.w:call-paraphase-23.t:call-run_paraphase NOTICE slurm_singularity run :: pid: 1198398, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-23/call-run_paraphase/slurm_singularity.log.txt"
2025-09-15 20:22:51.525 wdl.w:ptcp.w:call-sawfish-34.t:call-run_sawfish.slurm_singularity INFO srun: job 51797348 queued and waiting for resources
2025-09-15 20:22:51.637 wdl.w:ptcp.w:call-trgt-34.t:call-get_reads_overlapping_repeats.slurm_singularity INFO srun: job 51797349 queued and waiting for resources
2025-09-15 20:22:51.657 wdl.w:ptcp.t:call-pbmm2_align_hifi-63.slurm_singularity INFO srun: job 51797285 has been allocated resources
2025-09-15 20:22:51.657 wdl.w:ptcp.t:call-pbmm2_align_hifi-63.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:22:51.657 wdl.w:ptcp.t:call-pbmm2_align_hifi-63.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:22:51.693 wdl.w:ptcp.t:call-pbmm2_align_hifi-65.slurm_singularity INFO srun: job 51797286 has been allocated resources
2025-09-15 20:22:51.693 wdl.w:ptcp.t:call-pbmm2_align_hifi-65.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:22:51.693 wdl.w:ptcp.t:call-pbmm2_align_hifi-65.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:22:52.031 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_genotype.slurm_singularity INFO srun: job 51797350 queued and waiting for resources
2025-09-15 20:22:52.156 wdl.w:ptcp.t:call-pbmm2_align_hifi-16.stderr VERBOSE 
2025-09-15 20:22:52.157 wdl.w:ptcp.t:call-pbmm2_align_hifi-16.stderr VERBOSE pbindex --num-threads 64 m84036_250809_035451_s4.bc2113.mapped.bam
2025-09-15 20:22:52.157 wdl.w:ptcp.t:call-pbmm2_align_hifi-16.stderr VERBOSE + pbindex --num-threads 64 m84036_250809_035451_s4.bc2113.mapped.bam
2025-09-15 20:22:52.413 wdl.w:ptcp.w:call-paraphase-23.t:call-run_paraphase.slurm_singularity INFO srun: job 51797351 queued and waiting for resources
2025-09-15 20:22:52.423 wdl.w:ptcp.t:call-pbmm2_align_hifi-16 INFO output :: name: "mapped_bam", value: "m84036_250809_035451_s4.bc2113.mapped.bam"
2025-09-15 20:22:52.426 wdl.w:ptcp.t:call-pbmm2_align_hifi-16 INFO output :: name: "mapped_bam_bai", value: "m84036_250809_035451_s4.bc2113.mapped.bam.bai"
2025-09-15 20:22:52.427 wdl.w:ptcp.t:call-pbmm2_align_hifi-16 INFO output :: name: "mapped_bam_pbi", value: "m84036_250809_035451_s4.bc2113.mapped.bam.pbi"
2025-09-15 20:22:52.428 wdl.w:ptcp.t:call-pbmm2_align_hifi-16 INFO output :: name: "report", value: "mapping_stats.report.json"
2025-09-15 20:22:52.512 wdl.w:ptcp.t:call-pbmm2_align_hifi-16 NOTICE done
2025-09-15 20:22:52.519 wdl.w:ptcp NOTICE finish :: job: "call-pbmm2_align_hifi-16"
2025-09-15 20:22:52.519 wdl.w:ptcp INFO output :: job: "call-pbmm2_align_hifi-16", values: {"report": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-16/out/mapping_stats.report.json", "mapped_bam_pbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-16/out/m84036_250809_035451_s4.bc2113.mapped.bam.pbi", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-16/out/m84036_250809_035451_s4.bc2113.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-16/out/m84036_250809_035451_s4.bc2113.mapped.bam"}
2025-09-15 20:22:52.520 wdl.w:ptcp NOTICE ready :: job: "call-paraphase-16", callee: "paraphase"
2025-09-15 20:22:52.520 wdl.w:ptcp INFO input :: job: "call-paraphase-16", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf", "genome_version": "38", "config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-16/out/m84036_250809_035451_s4.bc2113.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-16/out/m84036_250809_035451_s4.bc2113.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2113"}
2025-09-15 20:22:52.521 wdl.w:ptcp NOTICE ready :: job: "call-sawfish-16", callee: "sawfish"
2025-09-15 20:22:52.521 wdl.w:ptcp INFO input :: job: "call-sawfish-16", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-16/out/m84036_250809_035451_s4.bc2113.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-16/out/m84036_250809_035451_s4.bc2113.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2113"}
2025-09-15 20:22:52.524 wdl.w:ptcp NOTICE ready :: job: "call-trgt-16", callee: "trgt"
2025-09-15 20:22:52.525 wdl.w:ptcp INFO input :: job: "call-trgt-16", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-16/out/m84036_250809_035451_s4.bc2113.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-16/out/m84036_250809_035451_s4.bc2113.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2113"}
2025-09-15 20:22:52.525 wdl.w:ptcp.w:call-sawfish-23.t:call-run_sawfish NOTICE task setup :: name: "run_sawfish", source: "./sawfish.wdl", line: 83, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-23/call-run_sawfish", thread: 140612531648064
2025-09-15 20:22:52.528 wdl.w:ptcp.w:call-paraphase-16 NOTICE workflow start :: name: "paraphase", source: "./paraphase.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-16"
2025-09-15 20:22:52.531 wdl.w:ptcp.w:call-sawfish-16 NOTICE workflow start :: name: "sawfish", source: "./sawfish.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-16"
2025-09-15 20:22:52.535 wdl.w:ptcp.w:call-trgt-16 NOTICE workflow start :: name: "trgt", source: "./trgt.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-16"
2025-09-15 20:22:52.547 wdl.w:ptcp.w:call-sawfish-23.t:call-run_sawfish INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:22:52.547 wdl.w:ptcp.w:call-sawfish-23.t:call-run_sawfish INFO input :: name: "genome_version", value: "38"
2025-09-15 20:22:52.548 wdl.w:ptcp.w:call-sawfish-23.t:call-run_sawfish INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:22:52.548 wdl.w:ptcp.w:call-sawfish-23.t:call-run_sawfish INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:22:52.548 wdl.w:ptcp.w:call-sawfish-23.t:call-run_sawfish INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2120.mapped.bam.bai"
2025-09-15 20:22:52.548 wdl.w:ptcp.w:call-sawfish-23.t:call-run_sawfish INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2120.mapped.bam"
2025-09-15 20:22:52.549 wdl.w:ptcp.w:call-sawfish-23.t:call-run_sawfish INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2120"
2025-09-15 20:22:52.550 wdl.w:ptcp.w:call-sawfish-23.t:call-run_sawfish INFO eval :: name: "mem_gb", value: 32
2025-09-15 20:22:52.551 wdl.w:ptcp.w:call-sawfish-23.t:call-run_sawfish INFO eval :: name: "threads", value: 16
2025-09-15 20:22:52.552 wdl.w:ptcp.w:call-sawfish-23.t:call-run_sawfish INFO eval :: name: "disk_size", value: 30
2025-09-15 20:22:52.553 wdl.w:ptcp.w:call-sawfish-23.t:call-run_sawfish INFO eval :: name: "discover_dirname", value: "m84036_250809_035451_s4.bc2120_sawfish_discover"
2025-09-15 20:22:52.554 wdl.w:ptcp.w:call-sawfish-23.t:call-run_sawfish INFO eval :: name: "call_dirname", value: "m84036_250809_035451_s4.bc2120_sawfish"
2025-09-15 20:22:52.554 wdl.w:ptcp.w:call-sawfish-23.t:call-run_sawfish INFO eval :: name: "minimap2_bam_filename", value: "m84036_250809_035451_s4.bc2120.minimap2.bam"
2025-09-15 20:22:52.555 wdl.w:ptcp.w:call-sawfish-23.t:call-run_sawfish INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 16, memory_reservation: 32000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:22:52.556 wdl.w:ptcp.w:call-paraphase-16 INFO visit :: node: "decl-annotation_vcf", values: {"annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf"}
2025-09-15 20:22:52.557 wdl.w:ptcp.w:call-sawfish-23.t:call-run_sawfish WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:22:52.557 wdl.w:ptcp.w:call-paraphase-16 INFO visit :: node: "decl-config_file", values: {"config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml"}
2025-09-15 20:22:52.558 wdl.w:ptcp.w:call-sawfish-16 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:22:52.558 wdl.w:ptcp.w:call-paraphase-16 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:22:52.559 wdl.w:ptcp.w:call-sawfish-16 INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:22:52.559 wdl.w:ptcp.w:call-paraphase-16 INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:22:52.559 wdl.w:ptcp.w:call-sawfish-16 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-16/out/m84036_250809_035451_s4.bc2113.mapped.bam"}
2025-09-15 20:22:52.560 wdl.w:ptcp.w:call-paraphase-16 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-16/out/m84036_250809_035451_s4.bc2113.mapped.bam"}
2025-09-15 20:22:52.560 wdl.w:ptcp.w:call-sawfish-16 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-16/out/m84036_250809_035451_s4.bc2113.mapped.bam.bai"}
2025-09-15 20:22:52.560 wdl.w:ptcp.w:call-paraphase-16 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-16/out/m84036_250809_035451_s4.bc2113.mapped.bam.bai"}
2025-09-15 20:22:52.560 wdl.w:ptcp.w:call-sawfish-16 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:22:52.561 wdl.w:ptcp.w:call-paraphase-16 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:22:52.561 wdl.w:ptcp.w:call-sawfish-23.t:call-run_sawfish INFO provisioned :: seconds_waited: 0, cpu: 16, mem_bytes: 32000000000
2025-09-15 20:22:52.561 wdl.w:ptcp.w:call-sawfish-16 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:22:52.561 wdl.w:ptcp.w:call-paraphase-16 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:22:52.561 wdl.w:ptcp.w:call-sawfish-23.t:call-run_sawfish INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:22:52.561 wdl.w:ptcp.w:call-sawfish-16 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2113"}
2025-09-15 20:22:52.562 wdl.w:ptcp.w:call-trgt-16 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:22:52.562 wdl.w:ptcp.w:call-paraphase-16 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2113"}
2025-09-15 20:22:52.563 wdl.w:ptcp.w:call-sawfish-16 NOTICE ready :: job: "call-run_sawfish", callee: "run_sawfish"
2025-09-15 20:22:52.563 wdl.w:ptcp.w:call-trgt-16 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-16/out/m84036_250809_035451_s4.bc2113.mapped.bam"}
2025-09-15 20:22:52.563 wdl.w:ptcp.w:call-paraphase-16 INFO visit :: node: "decl-sex", values: {"sex": "F"}
2025-09-15 20:22:52.563 wdl.w:ptcp.w:call-sawfish-16 INFO input :: job: "call-run_sawfish", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-16/out/m84036_250809_035451_s4.bc2113.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-16/out/m84036_250809_035451_s4.bc2113.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2113"}
2025-09-15 20:22:52.563 wdl.w:ptcp.w:call-trgt-16 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-16/out/m84036_250809_035451_s4.bc2113.mapped.bam.bai"}
2025-09-15 20:22:52.564 wdl.w:ptcp.w:call-paraphase-16 NOTICE ready :: job: "call-run_paraphase", callee: "run_paraphase"
2025-09-15 20:22:52.564 wdl.w:ptcp.w:call-trgt-16 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:22:52.564 wdl.w:ptcp.w:call-paraphase-16 INFO input :: job: "call-run_paraphase", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf", "genome_version": "38", "config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-16/out/m84036_250809_035451_s4.bc2113.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-16/out/m84036_250809_035451_s4.bc2113.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2113"}
2025-09-15 20:22:52.564 wdl.w:ptcp.w:call-trgt-16 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:22:52.564 wdl.w:ptcp.w:call-trgt-16 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2113"}
2025-09-15 20:22:52.565 wdl.w:ptcp.w:call-trgt-16 INFO visit :: node: "decl-sex", values: {"sex": "F"}
2025-09-15 20:22:52.565 wdl.w:ptcp.w:call-trgt-16 INFO visit :: node: "decl-trgt_bed", values: {"trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"}
2025-09-15 20:22:52.565 wdl.w:ptcp.w:call-trgt-16 NOTICE ready :: job: "call-get_reads_overlapping_repeats", callee: "get_reads_overlapping_repeats"
2025-09-15 20:22:52.565 wdl.w:ptcp.w:call-trgt-16 INFO input :: job: "call-get_reads_overlapping_repeats", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-16/out/m84036_250809_035451_s4.bc2113.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-16/out/m84036_250809_035451_s4.bc2113.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2113"}
2025-09-15 20:22:52.566 wdl.w:ptcp.w:call-trgt-16 NOTICE ready :: job: "call-trgt_genotype", callee: "trgt_genotype"
2025-09-15 20:22:52.566 wdl.w:ptcp.w:call-trgt-16 INFO input :: job: "call-trgt_genotype", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-16/out/m84036_250809_035451_s4.bc2113.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-16/out/m84036_250809_035451_s4.bc2113.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2113"}
2025-09-15 20:22:52.610 wdl.w:ptcp.t:call-pbmm2_align_hifi-32 INFO output :: name: "mapped_bam", value: "m84036_250809_035451_s4.bc2129.mapped.bam"
2025-09-15 20:22:52.613 wdl.w:ptcp.t:call-pbmm2_align_hifi-32 INFO output :: name: "mapped_bam_bai", value: "m84036_250809_035451_s4.bc2129.mapped.bam.bai"
2025-09-15 20:22:52.615 wdl.w:ptcp.t:call-pbmm2_align_hifi-32 INFO output :: name: "mapped_bam_pbi", value: "m84036_250809_035451_s4.bc2129.mapped.bam.pbi"
2025-09-15 20:22:52.616 wdl.w:ptcp.t:call-pbmm2_align_hifi-32 INFO output :: name: "report", value: "mapping_stats.report.json"
2025-09-15 20:22:52.621 wdl.w:ptcp.w:call-sawfish-23.t:call-run_sawfish INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 10, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-23/call-run_sawfish/_singularity_tmpdir_osz0rf3z"
2025-09-15 20:22:52.622 wdl.w:ptcp.w:call-sawfish-23.t:call-run_sawfish INFO Slurm invocation: srun --job-name call-run_sawfish --partition compute,compute9 --cpus-per-task 16 --mem 30518M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-23/call-run_sawfish/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-23/call-run_sawfish/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-23/call-run_sawfish/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-23/call-run_sawfish/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-23/out/m84036_250809_035451_s4.bc2120.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2120.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-23/out/m84036_250809_035451_s4.bc2120.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2120.mapped.bam:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-23/call-run_sawfish/_singularity_tmpdir_osz0rf3z/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-23/call-run_sawfish/_singularity_tmpdir_osz0rf3z/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:22:52.660 wdl.w:ptcp.w:call-sawfish-23.t:call-run_sawfish NOTICE slurm_singularity run :: pid: 1198417, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-23/call-run_sawfish/slurm_singularity.log.txt"
2025-09-15 20:22:52.705 wdl.w:ptcp.t:call-pbmm2_align_hifi-67.slurm_singularity INFO srun: job 51797288 has been allocated resources
2025-09-15 20:22:52.714 wdl.w:ptcp.t:call-pbmm2_align_hifi-32 NOTICE done
2025-09-15 20:22:52.719 wdl.w:ptcp NOTICE finish :: job: "call-pbmm2_align_hifi-32"
2025-09-15 20:22:52.720 wdl.w:ptcp INFO output :: job: "call-pbmm2_align_hifi-32", values: {"report": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-32/out/mapping_stats.report.json", "mapped_bam_pbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-32/out/m84036_250809_035451_s4.bc2129.mapped.bam.pbi", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-32/out/m84036_250809_035451_s4.bc2129.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-32/out/m84036_250809_035451_s4.bc2129.mapped.bam"}
2025-09-15 20:22:52.720 wdl.w:ptcp NOTICE ready :: job: "call-paraphase-32", callee: "paraphase"
2025-09-15 20:22:52.720 wdl.w:ptcp INFO input :: job: "call-paraphase-32", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf", "genome_version": "38", "config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-32/out/m84036_250809_035451_s4.bc2129.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-32/out/m84036_250809_035451_s4.bc2129.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2129"}
2025-09-15 20:22:52.722 wdl.w:ptcp NOTICE ready :: job: "call-sawfish-32", callee: "sawfish"
2025-09-15 20:22:52.722 wdl.w:ptcp INFO input :: job: "call-sawfish-32", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-32/out/m84036_250809_035451_s4.bc2129.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-32/out/m84036_250809_035451_s4.bc2129.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2129"}
2025-09-15 20:22:52.725 wdl.w:ptcp NOTICE ready :: job: "call-trgt-32", callee: "trgt"
2025-09-15 20:22:52.725 wdl.w:ptcp INFO input :: job: "call-trgt-32", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-32/out/m84036_250809_035451_s4.bc2129.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-32/out/m84036_250809_035451_s4.bc2129.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2129"}
2025-09-15 20:22:52.730 wdl.w:ptcp.w:call-paraphase-32 NOTICE workflow start :: name: "paraphase", source: "./paraphase.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-32"
2025-09-15 20:22:52.732 wdl.w:ptcp.w:call-trgt-23.t:call-get_reads_overlapping_repeats NOTICE task setup :: name: "get_reads_overlapping_repeats", source: "./trgt.wdl", line: 182, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-23/call-get_reads_overlapping_repeats", thread: 140611441120832
2025-09-15 20:22:52.733 wdl.w:ptcp.w:call-sawfish-32 NOTICE workflow start :: name: "sawfish", source: "./sawfish.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-32"
2025-09-15 20:22:52.735 wdl.w:ptcp.t:call-pbmm2_align_hifi-64.slurm_singularity INFO srun: job 51797287 has been allocated resources
2025-09-15 20:22:52.736 wdl.w:ptcp.t:call-pbmm2_align_hifi-64.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:22:52.736 wdl.w:ptcp.t:call-pbmm2_align_hifi-64.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:22:52.738 wdl.w:ptcp.w:call-trgt-32 NOTICE workflow start :: name: "trgt", source: "./trgt.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-32"
2025-09-15 20:22:52.752 wdl.w:ptcp.w:call-paraphase-32 INFO visit :: node: "decl-annotation_vcf", values: {"annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf"}
2025-09-15 20:22:52.753 wdl.w:ptcp.w:call-paraphase-32 INFO visit :: node: "decl-config_file", values: {"config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml"}
2025-09-15 20:22:52.754 wdl.w:ptcp.w:call-paraphase-32 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:22:52.754 wdl.w:ptcp.w:call-paraphase-32 INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:22:52.755 wdl.w:ptcp.w:call-paraphase-32 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-32/out/m84036_250809_035451_s4.bc2129.mapped.bam"}
2025-09-15 20:22:52.755 wdl.w:ptcp.w:call-paraphase-32 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-32/out/m84036_250809_035451_s4.bc2129.mapped.bam.bai"}
2025-09-15 20:22:52.756 wdl.w:ptcp.w:call-paraphase-32 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:22:52.756 wdl.w:ptcp.w:call-paraphase-32 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:22:52.756 wdl.w:ptcp.w:call-paraphase-32 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2129"}
2025-09-15 20:22:52.757 wdl.w:ptcp.w:call-paraphase-32 INFO visit :: node: "decl-sex", values: {"sex": "F"}
2025-09-15 20:22:52.758 wdl.w:ptcp.w:call-paraphase-32 NOTICE ready :: job: "call-run_paraphase", callee: "run_paraphase"
2025-09-15 20:22:52.758 wdl.w:ptcp.w:call-paraphase-32 INFO input :: job: "call-run_paraphase", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf", "genome_version": "38", "config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-32/out/m84036_250809_035451_s4.bc2129.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-32/out/m84036_250809_035451_s4.bc2129.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2129"}
2025-09-15 20:22:52.761 wdl.w:ptcp.w:call-trgt-23.t:call-get_reads_overlapping_repeats INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:22:52.762 wdl.w:ptcp.w:call-trgt-23.t:call-get_reads_overlapping_repeats INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:22:52.762 wdl.w:ptcp.w:call-sawfish-32 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:22:52.762 wdl.w:ptcp.w:call-trgt-23.t:call-get_reads_overlapping_repeats INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2120.mapped.bam.bai"
2025-09-15 20:22:52.762 wdl.w:ptcp.w:call-sawfish-32 INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:22:52.763 wdl.w:ptcp.w:call-trgt-23.t:call-get_reads_overlapping_repeats INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2120.mapped.bam"
2025-09-15 20:22:52.763 wdl.w:ptcp.w:call-trgt-32 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:22:52.764 wdl.w:ptcp.w:call-sawfish-32 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-32/out/m84036_250809_035451_s4.bc2129.mapped.bam"}
2025-09-15 20:22:52.764 wdl.w:ptcp.w:call-trgt-23.t:call-get_reads_overlapping_repeats INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2120"
2025-09-15 20:22:52.764 wdl.w:ptcp.w:call-trgt-32 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-32/out/m84036_250809_035451_s4.bc2129.mapped.bam"}
2025-09-15 20:22:52.764 wdl.w:ptcp.w:call-sawfish-32 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-32/out/m84036_250809_035451_s4.bc2129.mapped.bam.bai"}
2025-09-15 20:22:52.764 wdl.w:ptcp.w:call-trgt-23.t:call-get_reads_overlapping_repeats INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:22:52.764 wdl.w:ptcp.w:call-trgt-32 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-32/out/m84036_250809_035451_s4.bc2129.mapped.bam.bai"}
2025-09-15 20:22:52.765 wdl.w:ptcp.w:call-sawfish-32 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:22:52.765 wdl.w:ptcp.w:call-trgt-23.t:call-get_reads_overlapping_repeats INFO eval :: name: "expand_size", value: 3000
2025-09-15 20:22:52.765 wdl.w:ptcp.w:call-trgt-32 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:22:52.765 wdl.w:ptcp.w:call-sawfish-32 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:22:52.765 wdl.w:ptcp.w:call-trgt-23.t:call-get_reads_overlapping_repeats INFO eval :: name: "threads", value: 1
2025-09-15 20:22:52.765 wdl.w:ptcp.w:call-trgt-32 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:22:52.765 wdl.w:ptcp.w:call-sawfish-32 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2129"}
2025-09-15 20:22:52.765 wdl.w:ptcp.w:call-trgt-23.t:call-get_reads_overlapping_repeats INFO eval :: name: "expanded_bed_name", value: "m84036_250809_035451_s4.bc2120.expanded.bed"
2025-09-15 20:22:52.766 wdl.w:ptcp.w:call-trgt-32 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2129"}
2025-09-15 20:22:52.766 wdl.w:ptcp.w:call-sawfish-32 NOTICE ready :: job: "call-run_sawfish", callee: "run_sawfish"
2025-09-15 20:22:52.766 wdl.w:ptcp.w:call-trgt-32 INFO visit :: node: "decl-sex", values: {"sex": "F"}
2025-09-15 20:22:52.766 wdl.w:ptcp.w:call-trgt-23.t:call-get_reads_overlapping_repeats INFO eval :: name: "disk_size", value: 11
2025-09-15 20:22:52.766 wdl.w:ptcp.w:call-sawfish-32 INFO input :: job: "call-run_sawfish", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-32/out/m84036_250809_035451_s4.bc2129.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-32/out/m84036_250809_035451_s4.bc2129.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2129"}
2025-09-15 20:22:52.766 wdl.w:ptcp.w:call-trgt-32 INFO visit :: node: "decl-trgt_bed", values: {"trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"}
2025-09-15 20:22:52.767 wdl.w:ptcp.w:call-trgt-23.t:call-get_reads_overlapping_repeats INFO eval :: name: "output_name", value: "m84036_250809_035451_s4.bc2120.repeats.bam"
2025-09-15 20:22:52.767 wdl.w:ptcp.w:call-trgt-32 NOTICE ready :: job: "call-get_reads_overlapping_repeats", callee: "get_reads_overlapping_repeats"
2025-09-15 20:22:52.767 wdl.w:ptcp.w:call-trgt-23.t:call-get_reads_overlapping_repeats INFO eval :: name: "index_name", value: "m84036_250809_035451_s4.bc2120.repeats.bam.bai"
2025-09-15 20:22:52.767 wdl.w:ptcp.w:call-trgt-32 INFO input :: job: "call-get_reads_overlapping_repeats", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-32/out/m84036_250809_035451_s4.bc2129.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-32/out/m84036_250809_035451_s4.bc2129.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2129"}
2025-09-15 20:22:52.767 wdl.w:ptcp.w:call-trgt-23.t:call-get_reads_overlapping_repeats INFO eval :: name: "output_name_with_index", value: "m84036_250809_035451_s4.bc2120.repeats.bam##idx##m84036_250809_035451_s4.bc2120.repeats.bam.bai"
2025-09-15 20:22:52.768 wdl.w:ptcp.w:call-trgt-32 NOTICE ready :: job: "call-trgt_genotype", callee: "trgt_genotype"
2025-09-15 20:22:52.768 wdl.w:ptcp.w:call-trgt-23.t:call-get_reads_overlapping_repeats INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:22:52.768 wdl.w:ptcp.w:call-trgt-32 INFO input :: job: "call-trgt_genotype", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-32/out/m84036_250809_035451_s4.bc2129.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-32/out/m84036_250809_035451_s4.bc2129.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2129"}
2025-09-15 20:22:52.769 wdl.w:ptcp.w:call-trgt-23.t:call-get_reads_overlapping_repeats WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:22:52.769 wdl.w:ptcp.w:call-trgt-23.t:call-get_reads_overlapping_repeats INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:22:52.769 wdl.w:ptcp.w:call-trgt-23.t:call-get_reads_overlapping_repeats INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:22:52.808 wdl.w:ptcp.w:call-trgt-23.t:call-get_reads_overlapping_repeats INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 9, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-23/call-get_reads_overlapping_repeats/_singularity_tmpdir_k9dhz7wx"
2025-09-15 20:22:52.808 wdl.w:ptcp.w:call-trgt-23.t:call-get_reads_overlapping_repeats INFO Slurm invocation: srun --job-name call-get_reads_overlapping_repeats --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-23/call-get_reads_overlapping_repeats/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-23/call-get_reads_overlapping_repeats/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-23/call-get_reads_overlapping_repeats/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-23/call-get_reads_overlapping_repeats/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-23/out/m84036_250809_035451_s4.bc2120.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2120.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-23/out/m84036_250809_035451_s4.bc2120.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2120.mapped.bam:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-23/call-get_reads_overlapping_repeats/_singularity_tmpdir_k9dhz7wx/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-23/call-get_reads_overlapping_repeats/_singularity_tmpdir_k9dhz7wx/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:22:52.825 wdl.w:ptcp.w:call-trgt-23.t:call-get_reads_overlapping_repeats NOTICE slurm_singularity run :: pid: 1198422, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-23/call-get_reads_overlapping_repeats/slurm_singularity.log.txt"
2025-09-15 20:22:53.228 wdl.w:ptcp.t:call-pbmm2_align_hifi-02 INFO output :: name: "mapped_bam", value: "m84036_250809_035451_s4.bc2099.mapped.bam"
2025-09-15 20:22:53.230 wdl.w:ptcp.t:call-pbmm2_align_hifi-02 INFO output :: name: "mapped_bam_bai", value: "m84036_250809_035451_s4.bc2099.mapped.bam.bai"
2025-09-15 20:22:53.231 wdl.w:ptcp.t:call-pbmm2_align_hifi-02 INFO output :: name: "mapped_bam_pbi", value: "m84036_250809_035451_s4.bc2099.mapped.bam.pbi"
2025-09-15 20:22:53.232 wdl.w:ptcp.t:call-pbmm2_align_hifi-02 INFO output :: name: "report", value: "mapping_stats.report.json"
2025-09-15 20:22:53.301 wdl.w:ptcp.t:call-pbmm2_align_hifi-02 NOTICE done
2025-09-15 20:22:53.306 wdl.w:ptcp NOTICE finish :: job: "call-pbmm2_align_hifi-02"
2025-09-15 20:22:53.306 wdl.w:ptcp INFO output :: job: "call-pbmm2_align_hifi-02", values: {"report": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-02/out/mapping_stats.report.json", "mapped_bam_pbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-02/out/m84036_250809_035451_s4.bc2099.mapped.bam.pbi", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-02/out/m84036_250809_035451_s4.bc2099.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-02/out/m84036_250809_035451_s4.bc2099.mapped.bam"}
2025-09-15 20:22:53.307 wdl.w:ptcp NOTICE ready :: job: "call-paraphase-02", callee: "paraphase"
2025-09-15 20:22:53.307 wdl.w:ptcp INFO input :: job: "call-paraphase-02", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf", "genome_version": "38", "config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-02/out/m84036_250809_035451_s4.bc2099.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-02/out/m84036_250809_035451_s4.bc2099.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2099"}
2025-09-15 20:22:53.308 wdl.w:ptcp NOTICE ready :: job: "call-sawfish-02", callee: "sawfish"
2025-09-15 20:22:53.309 wdl.w:ptcp INFO input :: job: "call-sawfish-02", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-02/out/m84036_250809_035451_s4.bc2099.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-02/out/m84036_250809_035451_s4.bc2099.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2099"}
2025-09-15 20:22:53.312 wdl.w:ptcp NOTICE ready :: job: "call-trgt-02", callee: "trgt"
2025-09-15 20:22:53.312 wdl.w:ptcp INFO input :: job: "call-trgt-02", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-02/out/m84036_250809_035451_s4.bc2099.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-02/out/m84036_250809_035451_s4.bc2099.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2099"}
2025-09-15 20:22:53.314 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_genotype NOTICE task setup :: name: "trgt_genotype", source: "./trgt.wdl", line: 272, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-23/call-trgt_genotype", thread: 140613605389888
2025-09-15 20:22:53.315 wdl.w:ptcp.w:call-paraphase-02 NOTICE workflow start :: name: "paraphase", source: "./paraphase.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-02"
2025-09-15 20:22:53.316 wdl.w:ptcp.t:call-pbmm2_align_hifi-03 INFO output :: name: "mapped_bam", value: "m84036_250809_035451_s4.bc2100.mapped.bam"
2025-09-15 20:22:53.321 wdl.w:ptcp.w:call-sawfish-02 NOTICE workflow start :: name: "sawfish", source: "./sawfish.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-02"
2025-09-15 20:22:53.321 wdl.w:ptcp.t:call-pbmm2_align_hifi-03 INFO output :: name: "mapped_bam_bai", value: "m84036_250809_035451_s4.bc2100.mapped.bam.bai"
2025-09-15 20:22:53.323 wdl.w:ptcp.t:call-pbmm2_align_hifi-03 INFO output :: name: "mapped_bam_pbi", value: "m84036_250809_035451_s4.bc2100.mapped.bam.pbi"
2025-09-15 20:22:53.324 wdl.w:ptcp.w:call-trgt-02 NOTICE workflow start :: name: "trgt", source: "./trgt.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-02"
2025-09-15 20:22:53.325 wdl.w:ptcp.t:call-pbmm2_align_hifi-03 INFO output :: name: "report", value: "mapping_stats.report.json"
2025-09-15 20:22:53.333 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_genotype INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:22:53.334 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_genotype INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:22:53.335 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_genotype INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:22:53.335 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_genotype INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:22:53.335 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_genotype INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2120.mapped.bam.bai"
2025-09-15 20:22:53.335 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_genotype INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2120.mapped.bam"
2025-09-15 20:22:53.336 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_genotype INFO input :: name: "sex", value: "F"
2025-09-15 20:22:53.336 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_genotype INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2120"
2025-09-15 20:22:53.337 wdl.w:ptcp.w:call-paraphase-02 INFO visit :: node: "decl-annotation_vcf", values: {"annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf"}
2025-09-15 20:22:53.337 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_genotype INFO eval :: name: "mem_gb", value: 16
2025-09-15 20:22:53.338 wdl.w:ptcp.w:call-paraphase-02 INFO visit :: node: "decl-config_file", values: {"config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml"}
2025-09-15 20:22:53.339 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_genotype INFO eval :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2120.trgt"
2025-09-15 20:22:53.339 wdl.w:ptcp.w:call-paraphase-02 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:22:53.339 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_genotype INFO eval :: name: "threads", value: 8
2025-09-15 20:22:53.340 wdl.w:ptcp.w:call-paraphase-02 INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:22:53.341 wdl.w:ptcp.w:call-paraphase-02 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-02/out/m84036_250809_035451_s4.bc2099.mapped.bam"}
2025-09-15 20:22:53.341 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_genotype INFO eval :: name: "disk_size", value: 27
2025-09-15 20:22:53.341 wdl.w:ptcp.w:call-paraphase-02 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-02/out/m84036_250809_035451_s4.bc2099.mapped.bam.bai"}
2025-09-15 20:22:53.342 wdl.w:ptcp.w:call-paraphase-02 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:22:53.342 wdl.w:ptcp.w:call-paraphase-02 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:22:53.342 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_genotype INFO eval :: name: "karyotype", value: "XX"
2025-09-15 20:22:53.342 wdl.w:ptcp.w:call-paraphase-02 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2099"}
2025-09-15 20:22:53.343 wdl.w:ptcp.w:call-paraphase-02 INFO visit :: node: "decl-sex", values: {"sex": "F"}
2025-09-15 20:22:53.344 wdl.w:ptcp.w:call-paraphase-02 NOTICE ready :: job: "call-run_paraphase", callee: "run_paraphase"
2025-09-15 20:22:53.344 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_genotype INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 8, memory_reservation: 16000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:22:53.345 wdl.w:ptcp.w:call-sawfish-02 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:22:53.345 wdl.w:ptcp.w:call-paraphase-02 INFO input :: job: "call-run_paraphase", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf", "genome_version": "38", "config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-02/out/m84036_250809_035451_s4.bc2099.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-02/out/m84036_250809_035451_s4.bc2099.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2099"}
2025-09-15 20:22:53.345 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_genotype WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:22:53.346 wdl.w:ptcp.w:call-sawfish-02 INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:22:53.346 wdl.w:ptcp.w:call-sawfish-02 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-02/out/m84036_250809_035451_s4.bc2099.mapped.bam"}
2025-09-15 20:22:53.347 wdl.w:ptcp.w:call-sawfish-02 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-02/out/m84036_250809_035451_s4.bc2099.mapped.bam.bai"}
2025-09-15 20:22:53.347 wdl.w:ptcp.w:call-sawfish-02 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:22:53.347 wdl.w:ptcp.w:call-sawfish-02 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:22:53.347 wdl.w:ptcp.w:call-sawfish-02 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2099"}
2025-09-15 20:22:53.348 wdl.w:ptcp.w:call-sawfish-02 NOTICE ready :: job: "call-run_sawfish", callee: "run_sawfish"
2025-09-15 20:22:53.348 wdl.w:ptcp.w:call-sawfish-02 INFO input :: job: "call-run_sawfish", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-02/out/m84036_250809_035451_s4.bc2099.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-02/out/m84036_250809_035451_s4.bc2099.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2099"}
2025-09-15 20:22:53.348 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_genotype INFO provisioned :: seconds_waited: 0, cpu: 8, mem_bytes: 16000000000
2025-09-15 20:22:53.349 wdl.w:ptcp.w:call-trgt-02 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:22:53.349 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_genotype INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:22:53.349 wdl.w:ptcp.w:call-trgt-02 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-02/out/m84036_250809_035451_s4.bc2099.mapped.bam"}
2025-09-15 20:22:53.349 wdl.w:ptcp.w:call-trgt-02 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-02/out/m84036_250809_035451_s4.bc2099.mapped.bam.bai"}
2025-09-15 20:22:53.349 wdl.w:ptcp.w:call-trgt-02 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:22:53.350 wdl.w:ptcp.w:call-trgt-02 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:22:53.350 wdl.w:ptcp.w:call-trgt-02 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2099"}
2025-09-15 20:22:53.350 wdl.w:ptcp.w:call-trgt-02 INFO visit :: node: "decl-sex", values: {"sex": "F"}
2025-09-15 20:22:53.350 wdl.w:ptcp.w:call-trgt-02 INFO visit :: node: "decl-trgt_bed", values: {"trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"}
2025-09-15 20:22:53.350 wdl.w:ptcp.w:call-trgt-02 NOTICE ready :: job: "call-get_reads_overlapping_repeats", callee: "get_reads_overlapping_repeats"
2025-09-15 20:22:53.350 wdl.w:ptcp.w:call-trgt-02 INFO input :: job: "call-get_reads_overlapping_repeats", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-02/out/m84036_250809_035451_s4.bc2099.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-02/out/m84036_250809_035451_s4.bc2099.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2099"}
2025-09-15 20:22:53.352 wdl.w:ptcp.w:call-trgt-02 NOTICE ready :: job: "call-trgt_genotype", callee: "trgt_genotype"
2025-09-15 20:22:53.352 wdl.w:ptcp.w:call-trgt-02 INFO input :: job: "call-trgt_genotype", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-02/out/m84036_250809_035451_s4.bc2099.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-02/out/m84036_250809_035451_s4.bc2099.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2099"}
2025-09-15 20:22:53.404 wdl.w:ptcp.t:call-pbmm2_align_hifi-03 NOTICE done
2025-09-15 20:22:53.409 wdl.w:ptcp NOTICE finish :: job: "call-pbmm2_align_hifi-03"
2025-09-15 20:22:53.409 wdl.w:ptcp INFO output :: job: "call-pbmm2_align_hifi-03", values: {"report": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-03/out/mapping_stats.report.json", "mapped_bam_pbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-03/out/m84036_250809_035451_s4.bc2100.mapped.bam.pbi", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-03/out/m84036_250809_035451_s4.bc2100.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-03/out/m84036_250809_035451_s4.bc2100.mapped.bam"}
2025-09-15 20:22:53.410 wdl.w:ptcp NOTICE ready :: job: "call-paraphase-03", callee: "paraphase"
2025-09-15 20:22:53.410 wdl.w:ptcp INFO input :: job: "call-paraphase-03", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf", "genome_version": "38", "config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-03/out/m84036_250809_035451_s4.bc2100.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-03/out/m84036_250809_035451_s4.bc2100.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2100"}
2025-09-15 20:22:53.410 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_genotype INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 11, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-23/call-trgt_genotype/_singularity_tmpdir_xh83gbd1"
2025-09-15 20:22:53.410 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_genotype INFO Slurm invocation: srun --job-name call-trgt_genotype --partition compute,compute9 --cpus-per-task 8 --mem 15259M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-23/call-trgt_genotype/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-23/call-trgt_genotype/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-23/call-trgt_genotype/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-23/call-trgt_genotype/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-23/out/m84036_250809_035451_s4.bc2120.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2120.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-23/out/m84036_250809_035451_s4.bc2120.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2120.mapped.bam:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-23/call-trgt_genotype/_singularity_tmpdir_xh83gbd1/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-23/call-trgt_genotype/_singularity_tmpdir_xh83gbd1/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:22:53.411 wdl.w:ptcp NOTICE ready :: job: "call-sawfish-03", callee: "sawfish"
2025-09-15 20:22:53.412 wdl.w:ptcp INFO input :: job: "call-sawfish-03", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-03/out/m84036_250809_035451_s4.bc2100.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-03/out/m84036_250809_035451_s4.bc2100.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2100"}
2025-09-15 20:22:53.415 wdl.w:ptcp NOTICE ready :: job: "call-trgt-03", callee: "trgt"
2025-09-15 20:22:53.415 wdl.w:ptcp INFO input :: job: "call-trgt-03", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-03/out/m84036_250809_035451_s4.bc2100.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-03/out/m84036_250809_035451_s4.bc2100.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2100"}
2025-09-15 20:22:53.415 wdl.w:ptcp.w:call-paraphase-35.t:call-run_paraphase NOTICE task setup :: name: "run_paraphase", source: "./paraphase.wdl", line: 127, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-35/call-run_paraphase", thread: 140613596997184
2025-09-15 20:22:53.418 wdl.w:ptcp.w:call-paraphase-03 NOTICE workflow start :: name: "paraphase", source: "./paraphase.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-03"
2025-09-15 20:22:53.423 wdl.w:ptcp.w:call-sawfish-03 NOTICE workflow start :: name: "sawfish", source: "./sawfish.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-03"
2025-09-15 20:22:53.428 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_genotype NOTICE slurm_singularity run :: pid: 1198439, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-23/call-trgt_genotype/slurm_singularity.log.txt"
2025-09-15 20:22:53.435 wdl.w:ptcp.w:call-paraphase-35.t:call-run_paraphase INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:22:53.436 wdl.w:ptcp.w:call-paraphase-35.t:call-run_paraphase INFO input :: name: "annotation_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf"
2025-09-15 20:22:53.436 wdl.w:ptcp.w:call-paraphase-35.t:call-run_paraphase INFO input :: name: "genome_version", value: "38"
2025-09-15 20:22:53.436 wdl.w:ptcp.w:call-paraphase-35.t:call-run_paraphase INFO input :: name: "config_file", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/paraphase_config.GRCh38.yaml"
2025-09-15 20:22:53.436 wdl.w:ptcp.w:call-paraphase-35.t:call-run_paraphase INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:22:53.436 wdl.w:ptcp.w:call-paraphase-35.t:call-run_paraphase INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:22:53.437 wdl.w:ptcp.w:call-paraphase-35.t:call-run_paraphase INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2132.mapped.bam.bai"
2025-09-15 20:22:53.437 wdl.w:ptcp.w:call-paraphase-35.t:call-run_paraphase INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2132.mapped.bam"
2025-09-15 20:22:53.437 wdl.w:ptcp.w:call-paraphase-35.t:call-run_paraphase INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2132"
2025-09-15 20:22:53.437 wdl.w:ptcp.w:call-paraphase-35.t:call-run_paraphase INFO eval :: name: "threads", value: 4
2025-09-15 20:22:53.438 wdl.w:ptcp.w:call-paraphase-35.t:call-run_paraphase INFO eval :: name: "mem_gb", value: 8
2025-09-15 20:22:53.438 wdl.w:ptcp.w:call-trgt-03 NOTICE workflow start :: name: "trgt", source: "./trgt.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-03"
2025-09-15 20:22:53.439 wdl.w:ptcp.w:call-paraphase-35.t:call-run_paraphase INFO eval :: name: "disk_size", value: 27
2025-09-15 20:22:53.440 wdl.w:ptcp.w:call-paraphase-35.t:call-run_paraphase INFO eval :: name: "out_dir", value: "m84036_250809_035451_s4.bc2132_paraphase"
2025-09-15 20:22:53.440 wdl.w:ptcp.w:call-paraphase-35.t:call-run_paraphase INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 4, memory_reservation: 8000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:22:53.440 wdl.w:ptcp.w:call-paraphase-35.t:call-run_paraphase WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:22:53.441 wdl.w:ptcp.w:call-paraphase-35.t:call-run_paraphase INFO provisioned :: seconds_waited: 0, cpu: 4, mem_bytes: 8000000000
2025-09-15 20:22:53.442 wdl.w:ptcp.w:call-paraphase-35.t:call-run_paraphase INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:22:53.442 wdl.w:ptcp.w:call-sawfish-03 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:22:53.443 wdl.w:ptcp.w:call-sawfish-03 INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:22:53.443 wdl.w:ptcp.w:call-sawfish-03 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-03/out/m84036_250809_035451_s4.bc2100.mapped.bam"}
2025-09-15 20:22:53.443 wdl.w:ptcp.w:call-sawfish-03 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-03/out/m84036_250809_035451_s4.bc2100.mapped.bam.bai"}
2025-09-15 20:22:53.444 wdl.w:ptcp.w:call-sawfish-03 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:22:53.444 wdl.w:ptcp.w:call-paraphase-03 INFO visit :: node: "decl-annotation_vcf", values: {"annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf"}
2025-09-15 20:22:53.444 wdl.w:ptcp.w:call-sawfish-03 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:22:53.444 wdl.w:ptcp.w:call-paraphase-03 INFO visit :: node: "decl-config_file", values: {"config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml"}
2025-09-15 20:22:53.444 wdl.w:ptcp.w:call-sawfish-03 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2100"}
2025-09-15 20:22:53.444 wdl.w:ptcp.w:call-paraphase-03 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:22:53.445 wdl.w:ptcp.w:call-sawfish-03 NOTICE ready :: job: "call-run_sawfish", callee: "run_sawfish"
2025-09-15 20:22:53.445 wdl.w:ptcp.w:call-paraphase-03 INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:22:53.445 wdl.w:ptcp.w:call-sawfish-03 INFO input :: job: "call-run_sawfish", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-03/out/m84036_250809_035451_s4.bc2100.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-03/out/m84036_250809_035451_s4.bc2100.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2100"}
2025-09-15 20:22:53.445 wdl.w:ptcp.w:call-paraphase-03 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-03/out/m84036_250809_035451_s4.bc2100.mapped.bam"}
2025-09-15 20:22:53.445 wdl.w:ptcp.w:call-paraphase-03 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-03/out/m84036_250809_035451_s4.bc2100.mapped.bam.bai"}
2025-09-15 20:22:53.445 wdl.w:ptcp.w:call-paraphase-03 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:22:53.445 wdl.w:ptcp.w:call-paraphase-03 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:22:53.445 wdl.w:ptcp.w:call-paraphase-03 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2100"}
2025-09-15 20:22:53.445 wdl.w:ptcp.w:call-paraphase-03 INFO visit :: node: "decl-sex", values: {"sex": "F"}
2025-09-15 20:22:53.446 wdl.w:ptcp.w:call-paraphase-03 NOTICE ready :: job: "call-run_paraphase", callee: "run_paraphase"
2025-09-15 20:22:53.446 wdl.w:ptcp.w:call-paraphase-03 INFO input :: job: "call-run_paraphase", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf", "genome_version": "38", "config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-03/out/m84036_250809_035451_s4.bc2100.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-03/out/m84036_250809_035451_s4.bc2100.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2100"}
2025-09-15 20:22:53.453 wdl.w:ptcp.w:call-trgt-03 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:22:53.454 wdl.w:ptcp.w:call-trgt-03 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-03/out/m84036_250809_035451_s4.bc2100.mapped.bam"}
2025-09-15 20:22:53.454 wdl.w:ptcp.w:call-trgt-03 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-03/out/m84036_250809_035451_s4.bc2100.mapped.bam.bai"}
2025-09-15 20:22:53.454 wdl.w:ptcp.w:call-trgt-03 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:22:53.454 wdl.w:ptcp.w:call-trgt-03 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:22:53.454 wdl.w:ptcp.w:call-trgt-03 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2100"}
2025-09-15 20:22:53.454 wdl.w:ptcp.w:call-trgt-03 INFO visit :: node: "decl-sex", values: {"sex": "F"}
2025-09-15 20:22:53.454 wdl.w:ptcp.w:call-trgt-03 INFO visit :: node: "decl-trgt_bed", values: {"trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"}
2025-09-15 20:22:53.454 wdl.w:ptcp.w:call-trgt-03 NOTICE ready :: job: "call-get_reads_overlapping_repeats", callee: "get_reads_overlapping_repeats"
2025-09-15 20:22:53.454 wdl.w:ptcp.w:call-trgt-03 INFO input :: job: "call-get_reads_overlapping_repeats", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-03/out/m84036_250809_035451_s4.bc2100.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-03/out/m84036_250809_035451_s4.bc2100.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2100"}
2025-09-15 20:22:53.455 wdl.w:ptcp.w:call-trgt-03 NOTICE ready :: job: "call-trgt_genotype", callee: "trgt_genotype"
2025-09-15 20:22:53.455 wdl.w:ptcp.w:call-trgt-03 INFO input :: job: "call-trgt_genotype", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-03/out/m84036_250809_035451_s4.bc2100.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-03/out/m84036_250809_035451_s4.bc2100.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2100"}
2025-09-15 20:22:53.505 wdl.w:ptcp.w:call-paraphase-35.t:call-run_paraphase INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-35/call-run_paraphase/_singularity_tmpdir_r1j5re3d"
2025-09-15 20:22:53.505 wdl.w:ptcp.w:call-paraphase-35.t:call-run_paraphase INFO Slurm invocation: srun --job-name call-run_paraphase --partition compute,compute9 --cpus-per-task 4 --mem 7629M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-35/call-run_paraphase/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-35/call-run_paraphase/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-35/call-run_paraphase/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-35/call-run_paraphase/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-35/out/m84036_250809_035451_s4.bc2132.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2132.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-35/out/m84036_250809_035451_s4.bc2132.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2132.mapped.bam.bai:ro --bind /ptcp/meta/variant_list/variant_list.GRCh38.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf:ro --bind /ptcp/meta/paraphase/paraphase_config.GRCh38.yaml:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/paraphase_config.GRCh38.yaml:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-35/call-run_paraphase/_singularity_tmpdir_r1j5re3d/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-35/call-run_paraphase/_singularity_tmpdir_r1j5re3d/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:22:53.523 wdl.w:ptcp.w:call-paraphase-35.t:call-run_paraphase NOTICE slurm_singularity run :: pid: 1198450, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-35/call-run_paraphase/slurm_singularity.log.txt"
2025-09-15 20:22:53.540 wdl.w:ptcp.t:call-pbmm2_align_hifi-08 INFO output :: name: "mapped_bam", value: "m84036_250809_035451_s4.bc2105.mapped.bam"
2025-09-15 20:22:53.543 wdl.w:ptcp.t:call-pbmm2_align_hifi-08 INFO output :: name: "mapped_bam_bai", value: "m84036_250809_035451_s4.bc2105.mapped.bam.bai"
2025-09-15 20:22:53.544 wdl.w:ptcp.t:call-pbmm2_align_hifi-08 INFO output :: name: "mapped_bam_pbi", value: "m84036_250809_035451_s4.bc2105.mapped.bam.pbi"
2025-09-15 20:22:53.545 wdl.w:ptcp.t:call-pbmm2_align_hifi-08 INFO output :: name: "report", value: "mapping_stats.report.json"
2025-09-15 20:22:53.615 wdl.w:ptcp.t:call-pbmm2_align_hifi-08 NOTICE done
2025-09-15 20:22:53.620 wdl.w:ptcp NOTICE finish :: job: "call-pbmm2_align_hifi-08"
2025-09-15 20:22:53.620 wdl.w:ptcp INFO output :: job: "call-pbmm2_align_hifi-08", values: {"report": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-08/out/mapping_stats.report.json", "mapped_bam_pbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-08/out/m84036_250809_035451_s4.bc2105.mapped.bam.pbi", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-08/out/m84036_250809_035451_s4.bc2105.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-08/out/m84036_250809_035451_s4.bc2105.mapped.bam"}
2025-09-15 20:22:53.621 wdl.w:ptcp NOTICE ready :: job: "call-paraphase-08", callee: "paraphase"
2025-09-15 20:22:53.621 wdl.w:ptcp INFO input :: job: "call-paraphase-08", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf", "genome_version": "38", "config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-08/out/m84036_250809_035451_s4.bc2105.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-08/out/m84036_250809_035451_s4.bc2105.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2105"}
2025-09-15 20:22:53.622 wdl.w:ptcp NOTICE ready :: job: "call-sawfish-08", callee: "sawfish"
2025-09-15 20:22:53.622 wdl.w:ptcp INFO input :: job: "call-sawfish-08", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-08/out/m84036_250809_035451_s4.bc2105.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-08/out/m84036_250809_035451_s4.bc2105.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2105"}
2025-09-15 20:22:53.626 wdl.w:ptcp NOTICE ready :: job: "call-trgt-08", callee: "trgt"
2025-09-15 20:22:53.626 wdl.w:ptcp INFO input :: job: "call-trgt-08", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-08/out/m84036_250809_035451_s4.bc2105.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-08/out/m84036_250809_035451_s4.bc2105.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2105"}
2025-09-15 20:22:53.628 wdl.w:ptcp.w:call-sawfish-35.t:call-run_sawfish NOTICE task setup :: name: "run_sawfish", source: "./sawfish.wdl", line: 83, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-35/call-run_sawfish", thread: 140613555033664
2025-09-15 20:22:53.630 wdl.w:ptcp.w:call-paraphase-08 NOTICE workflow start :: name: "paraphase", source: "./paraphase.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-08"
2025-09-15 20:22:53.634 wdl.w:ptcp.w:call-sawfish-08 NOTICE workflow start :: name: "sawfish", source: "./sawfish.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-08"
2025-09-15 20:22:53.636 wdl.w:ptcp.w:call-trgt-08 NOTICE workflow start :: name: "trgt", source: "./trgt.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-08"
2025-09-15 20:22:53.654 wdl.w:ptcp.w:call-paraphase-08 INFO visit :: node: "decl-annotation_vcf", values: {"annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf"}
2025-09-15 20:22:53.654 wdl.w:ptcp.w:call-paraphase-08 INFO visit :: node: "decl-config_file", values: {"config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml"}
2025-09-15 20:22:53.655 wdl.w:ptcp.w:call-paraphase-08 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:22:53.656 wdl.w:ptcp.w:call-paraphase-08 INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:22:53.656 wdl.w:ptcp.w:call-paraphase-08 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-08/out/m84036_250809_035451_s4.bc2105.mapped.bam"}
2025-09-15 20:22:53.656 wdl.w:ptcp.w:call-paraphase-08 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-08/out/m84036_250809_035451_s4.bc2105.mapped.bam.bai"}
2025-09-15 20:22:53.657 wdl.w:ptcp.w:call-paraphase-08 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:22:53.657 wdl.w:ptcp.w:call-paraphase-08 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:22:53.657 wdl.w:ptcp.w:call-paraphase-08 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2105"}
2025-09-15 20:22:53.658 wdl.w:ptcp.w:call-paraphase-08 INFO visit :: node: "decl-sex", values: {"sex": "F"}
2025-09-15 20:22:53.658 wdl.w:ptcp.w:call-paraphase-08 NOTICE ready :: job: "call-run_paraphase", callee: "run_paraphase"
2025-09-15 20:22:53.659 wdl.w:ptcp.w:call-paraphase-08 INFO input :: job: "call-run_paraphase", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf", "genome_version": "38", "config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-08/out/m84036_250809_035451_s4.bc2105.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-08/out/m84036_250809_035451_s4.bc2105.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2105"}
2025-09-15 20:22:53.659 wdl.w:ptcp.w:call-sawfish-35.t:call-run_sawfish INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:22:53.660 wdl.w:ptcp.w:call-sawfish-08 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:22:53.661 wdl.w:ptcp.w:call-sawfish-35.t:call-run_sawfish INFO input :: name: "genome_version", value: "38"
2025-09-15 20:22:53.661 wdl.w:ptcp.w:call-trgt-08 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:22:53.662 wdl.w:ptcp.w:call-sawfish-08 INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:22:53.662 wdl.w:ptcp.w:call-sawfish-35.t:call-run_sawfish INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:22:53.662 wdl.w:ptcp.w:call-trgt-08 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-08/out/m84036_250809_035451_s4.bc2105.mapped.bam"}
2025-09-15 20:22:53.662 wdl.w:ptcp.w:call-sawfish-08 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-08/out/m84036_250809_035451_s4.bc2105.mapped.bam"}
2025-09-15 20:22:53.662 wdl.w:ptcp.w:call-sawfish-35.t:call-run_sawfish INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:22:53.662 wdl.w:ptcp.w:call-trgt-08 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-08/out/m84036_250809_035451_s4.bc2105.mapped.bam.bai"}
2025-09-15 20:22:53.662 wdl.w:ptcp.w:call-sawfish-08 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-08/out/m84036_250809_035451_s4.bc2105.mapped.bam.bai"}
2025-09-15 20:22:53.662 wdl.w:ptcp.w:call-sawfish-35.t:call-run_sawfish INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2132.mapped.bam.bai"
2025-09-15 20:22:53.663 wdl.w:ptcp.w:call-trgt-08 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:22:53.663 wdl.w:ptcp.w:call-sawfish-08 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:22:53.663 wdl.w:ptcp.w:call-sawfish-35.t:call-run_sawfish INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2132.mapped.bam"
2025-09-15 20:22:53.663 wdl.w:ptcp.w:call-trgt-08 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:22:53.663 wdl.w:ptcp.w:call-sawfish-08 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:22:53.663 wdl.w:ptcp.w:call-sawfish-35.t:call-run_sawfish INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2132"
2025-09-15 20:22:53.663 wdl.w:ptcp.w:call-trgt-08 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2105"}
2025-09-15 20:22:53.664 wdl.w:ptcp.w:call-sawfish-08 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2105"}
2025-09-15 20:22:53.664 wdl.w:ptcp.w:call-sawfish-35.t:call-run_sawfish INFO eval :: name: "mem_gb", value: 32
2025-09-15 20:22:53.664 wdl.w:ptcp.w:call-trgt-08 INFO visit :: node: "decl-sex", values: {"sex": "F"}
2025-09-15 20:22:53.664 wdl.w:ptcp.w:call-sawfish-08 NOTICE ready :: job: "call-run_sawfish", callee: "run_sawfish"
2025-09-15 20:22:53.665 wdl.w:ptcp.w:call-sawfish-35.t:call-run_sawfish INFO eval :: name: "threads", value: 16
2025-09-15 20:22:53.665 wdl.w:ptcp.w:call-trgt-08 INFO visit :: node: "decl-trgt_bed", values: {"trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"}
2025-09-15 20:22:53.665 wdl.w:ptcp.w:call-sawfish-08 INFO input :: job: "call-run_sawfish", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-08/out/m84036_250809_035451_s4.bc2105.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-08/out/m84036_250809_035451_s4.bc2105.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2105"}
2025-09-15 20:22:53.665 wdl.w:ptcp.w:call-trgt-08 NOTICE ready :: job: "call-get_reads_overlapping_repeats", callee: "get_reads_overlapping_repeats"
2025-09-15 20:22:53.665 wdl.w:ptcp.w:call-sawfish-35.t:call-run_sawfish INFO eval :: name: "disk_size", value: 30
2025-09-15 20:22:53.666 wdl.w:ptcp.w:call-trgt-08 INFO input :: job: "call-get_reads_overlapping_repeats", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-08/out/m84036_250809_035451_s4.bc2105.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-08/out/m84036_250809_035451_s4.bc2105.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2105"}
2025-09-15 20:22:53.666 wdl.w:ptcp.w:call-sawfish-35.t:call-run_sawfish INFO eval :: name: "discover_dirname", value: "m84036_250809_035451_s4.bc2132_sawfish_discover"
2025-09-15 20:22:53.666 wdl.w:ptcp.w:call-sawfish-35.t:call-run_sawfish INFO eval :: name: "call_dirname", value: "m84036_250809_035451_s4.bc2132_sawfish"
2025-09-15 20:22:53.666 wdl.w:ptcp.w:call-sawfish-35.t:call-run_sawfish INFO eval :: name: "minimap2_bam_filename", value: "m84036_250809_035451_s4.bc2132.minimap2.bam"
2025-09-15 20:22:53.667 wdl.w:ptcp.w:call-trgt-08 NOTICE ready :: job: "call-trgt_genotype", callee: "trgt_genotype"
2025-09-15 20:22:53.667 wdl.w:ptcp.w:call-sawfish-35.t:call-run_sawfish INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 16, memory_reservation: 32000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:22:53.667 wdl.w:ptcp.w:call-trgt-08 INFO input :: job: "call-trgt_genotype", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-08/out/m84036_250809_035451_s4.bc2105.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-08/out/m84036_250809_035451_s4.bc2105.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2105"}
2025-09-15 20:22:53.667 wdl.w:ptcp.w:call-sawfish-35.t:call-run_sawfish WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:22:53.668 wdl.w:ptcp.w:call-sawfish-35.t:call-run_sawfish INFO provisioned :: seconds_waited: 0, cpu: 16, mem_bytes: 32000000000
2025-09-15 20:22:53.668 wdl.w:ptcp.w:call-sawfish-35.t:call-run_sawfish INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:22:53.672 wdl.w:ptcp.w:call-sawfish-23.t:call-run_sawfish.slurm_singularity INFO srun: job 51797352 queued and waiting for resources
2025-09-15 20:22:53.717 wdl.w:ptcp.t:call-pbmm2_align_hifi-68.slurm_singularity INFO srun: job 51797290 has been allocated resources
2025-09-15 20:22:53.719 wdl.w:ptcp.t:call-pbmm2_align_hifi-67.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:22:53.722 wdl.w:ptcp.t:call-pbmm2_align_hifi-66.slurm_singularity INFO srun: job 51797289 has been allocated resources
2025-09-15 20:22:53.722 wdl.w:ptcp.t:call-pbmm2_align_hifi-66.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:22:53.722 wdl.w:ptcp.t:call-pbmm2_align_hifi-66.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:22:53.736 wdl.w:ptcp.w:call-sawfish-35.t:call-run_sawfish INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 10, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-35/call-run_sawfish/_singularity_tmpdir_3roejhtz"
2025-09-15 20:22:53.736 wdl.w:ptcp.w:call-sawfish-35.t:call-run_sawfish INFO Slurm invocation: srun --job-name call-run_sawfish --partition compute,compute9 --cpus-per-task 16 --mem 30518M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-35/call-run_sawfish/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-35/call-run_sawfish/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-35/call-run_sawfish/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-35/call-run_sawfish/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-35/out/m84036_250809_035451_s4.bc2132.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2132.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-35/out/m84036_250809_035451_s4.bc2132.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2132.mapped.bam.bai:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-35/call-run_sawfish/_singularity_tmpdir_3roejhtz/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-35/call-run_sawfish/_singularity_tmpdir_3roejhtz/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:22:53.753 wdl.w:ptcp.t:call-pbmm2_align_hifi-69.slurm_singularity INFO srun: job 51797291 has been allocated resources
2025-09-15 20:22:53.753 wdl.w:ptcp.w:call-sawfish-35.t:call-run_sawfish NOTICE slurm_singularity run :: pid: 1198455, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-35/call-run_sawfish/slurm_singularity.log.txt"
2025-09-15 20:22:53.835 wdl.w:ptcp.w:call-trgt-23.t:call-get_reads_overlapping_repeats.slurm_singularity INFO srun: job 51797353 queued and waiting for resources
2025-09-15 20:22:54.140 wdl.w:ptcp.t:call-pbmm2_align_hifi-01 INFO output :: name: "mapped_bam", value: "m84036_250809_035451_s4.bc2098.mapped.bam"
2025-09-15 20:22:54.143 wdl.w:ptcp.t:call-pbmm2_align_hifi-01 INFO output :: name: "mapped_bam_bai", value: "m84036_250809_035451_s4.bc2098.mapped.bam.bai"
2025-09-15 20:22:54.144 wdl.w:ptcp.t:call-pbmm2_align_hifi-01 INFO output :: name: "mapped_bam_pbi", value: "m84036_250809_035451_s4.bc2098.mapped.bam.pbi"
2025-09-15 20:22:54.146 wdl.w:ptcp.t:call-pbmm2_align_hifi-01 INFO output :: name: "report", value: "mapping_stats.report.json"
2025-09-15 20:22:54.209 wdl.w:ptcp.t:call-pbmm2_align_hifi-01 NOTICE done
2025-09-15 20:22:54.214 wdl.w:ptcp NOTICE finish :: job: "call-pbmm2_align_hifi-01"
2025-09-15 20:22:54.215 wdl.w:ptcp INFO output :: job: "call-pbmm2_align_hifi-01", values: {"report": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-01/out/mapping_stats.report.json", "mapped_bam_pbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-01/out/m84036_250809_035451_s4.bc2098.mapped.bam.pbi", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-01/out/m84036_250809_035451_s4.bc2098.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-01/out/m84036_250809_035451_s4.bc2098.mapped.bam"}
2025-09-15 20:22:54.215 wdl.w:ptcp NOTICE ready :: job: "call-paraphase-01", callee: "paraphase"
2025-09-15 20:22:54.215 wdl.w:ptcp INFO input :: job: "call-paraphase-01", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf", "genome_version": "38", "config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-01/out/m84036_250809_035451_s4.bc2098.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-01/out/m84036_250809_035451_s4.bc2098.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2098"}
2025-09-15 20:22:54.216 wdl.w:ptcp NOTICE ready :: job: "call-sawfish-01", callee: "sawfish"
2025-09-15 20:22:54.217 wdl.w:ptcp INFO input :: job: "call-sawfish-01", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-01/out/m84036_250809_035451_s4.bc2098.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-01/out/m84036_250809_035451_s4.bc2098.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2098"}
2025-09-15 20:22:54.221 wdl.w:ptcp NOTICE ready :: job: "call-trgt-01", callee: "trgt"
2025-09-15 20:22:54.221 wdl.w:ptcp INFO input :: job: "call-trgt-01", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-01/out/m84036_250809_035451_s4.bc2098.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-01/out/m84036_250809_035451_s4.bc2098.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2098"}
2025-09-15 20:22:54.222 wdl.w:ptcp.w:call-trgt-35.t:call-get_reads_overlapping_repeats NOTICE task setup :: name: "get_reads_overlapping_repeats", source: "./trgt.wdl", line: 182, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-35/call-get_reads_overlapping_repeats", thread: 140613823374912
2025-09-15 20:22:54.227 wdl.w:ptcp.w:call-paraphase-01 NOTICE workflow start :: name: "paraphase", source: "./paraphase.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-01"
2025-09-15 20:22:54.229 wdl.w:ptcp.w:call-sawfish-01 NOTICE workflow start :: name: "sawfish", source: "./sawfish.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-01"
2025-09-15 20:22:54.231 wdl.w:ptcp.w:call-trgt-01 NOTICE workflow start :: name: "trgt", source: "./trgt.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-01"
2025-09-15 20:22:54.245 wdl.w:ptcp.w:call-trgt-35.t:call-get_reads_overlapping_repeats INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:22:54.246 wdl.w:ptcp.w:call-trgt-35.t:call-get_reads_overlapping_repeats INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:22:54.246 wdl.w:ptcp.w:call-trgt-35.t:call-get_reads_overlapping_repeats INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2132.mapped.bam.bai"
2025-09-15 20:22:54.247 wdl.w:ptcp.w:call-trgt-35.t:call-get_reads_overlapping_repeats INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2132.mapped.bam"
2025-09-15 20:22:54.247 wdl.w:ptcp.w:call-trgt-35.t:call-get_reads_overlapping_repeats INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2132"
2025-09-15 20:22:54.247 wdl.w:ptcp.w:call-trgt-35.t:call-get_reads_overlapping_repeats INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:22:54.248 wdl.w:ptcp.w:call-trgt-35.t:call-get_reads_overlapping_repeats INFO eval :: name: "expand_size", value: 3000
2025-09-15 20:22:54.249 wdl.w:ptcp.w:call-trgt-35.t:call-get_reads_overlapping_repeats INFO eval :: name: "threads", value: 1
2025-09-15 20:22:54.249 wdl.w:ptcp.w:call-trgt-35.t:call-get_reads_overlapping_repeats INFO eval :: name: "expanded_bed_name", value: "m84036_250809_035451_s4.bc2132.expanded.bed"
2025-09-15 20:22:54.252 wdl.w:ptcp.w:call-trgt-35.t:call-get_reads_overlapping_repeats INFO eval :: name: "disk_size", value: 11
2025-09-15 20:22:54.252 wdl.w:ptcp.w:call-trgt-35.t:call-get_reads_overlapping_repeats INFO eval :: name: "output_name", value: "m84036_250809_035451_s4.bc2132.repeats.bam"
2025-09-15 20:22:54.253 wdl.w:ptcp.w:call-trgt-35.t:call-get_reads_overlapping_repeats INFO eval :: name: "index_name", value: "m84036_250809_035451_s4.bc2132.repeats.bam.bai"
2025-09-15 20:22:54.253 wdl.w:ptcp.w:call-trgt-35.t:call-get_reads_overlapping_repeats INFO eval :: name: "output_name_with_index", value: "m84036_250809_035451_s4.bc2132.repeats.bam##idx##m84036_250809_035451_s4.bc2132.repeats.bam.bai"
2025-09-15 20:22:54.254 wdl.w:ptcp.w:call-trgt-35.t:call-get_reads_overlapping_repeats INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:22:54.254 wdl.w:ptcp.w:call-trgt-35.t:call-get_reads_overlapping_repeats WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:22:54.256 wdl.w:ptcp.w:call-paraphase-01 INFO visit :: node: "decl-annotation_vcf", values: {"annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf"}
2025-09-15 20:22:54.256 wdl.w:ptcp.w:call-sawfish-01 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:22:54.257 wdl.w:ptcp.w:call-paraphase-01 INFO visit :: node: "decl-config_file", values: {"config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml"}
2025-09-15 20:22:54.257 wdl.w:ptcp.w:call-sawfish-01 INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:22:54.258 wdl.w:ptcp.w:call-trgt-01 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:22:54.258 wdl.w:ptcp.w:call-trgt-35.t:call-get_reads_overlapping_repeats INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:22:54.258 wdl.w:ptcp.w:call-paraphase-01 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:22:54.258 wdl.w:ptcp.w:call-sawfish-01 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-01/out/m84036_250809_035451_s4.bc2098.mapped.bam"}
2025-09-15 20:22:54.258 wdl.w:ptcp.w:call-trgt-01 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-01/out/m84036_250809_035451_s4.bc2098.mapped.bam"}
2025-09-15 20:22:54.258 wdl.w:ptcp.w:call-trgt-35.t:call-get_reads_overlapping_repeats INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:22:54.259 wdl.w:ptcp.w:call-paraphase-01 INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:22:54.259 wdl.w:ptcp.w:call-sawfish-01 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-01/out/m84036_250809_035451_s4.bc2098.mapped.bam.bai"}
2025-09-15 20:22:54.259 wdl.w:ptcp.w:call-trgt-01 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-01/out/m84036_250809_035451_s4.bc2098.mapped.bam.bai"}
2025-09-15 20:22:54.259 wdl.w:ptcp.w:call-paraphase-01 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-01/out/m84036_250809_035451_s4.bc2098.mapped.bam"}
2025-09-15 20:22:54.259 wdl.w:ptcp.w:call-sawfish-01 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:22:54.259 wdl.w:ptcp.w:call-trgt-01 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:22:54.260 wdl.w:ptcp.w:call-paraphase-01 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-01/out/m84036_250809_035451_s4.bc2098.mapped.bam.bai"}
2025-09-15 20:22:54.260 wdl.w:ptcp.w:call-sawfish-01 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:22:54.260 wdl.w:ptcp.w:call-trgt-01 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:22:54.260 wdl.w:ptcp.w:call-paraphase-01 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:22:54.260 wdl.w:ptcp.w:call-sawfish-01 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2098"}
2025-09-15 20:22:54.260 wdl.w:ptcp.w:call-trgt-01 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2098"}
2025-09-15 20:22:54.260 wdl.w:ptcp.w:call-paraphase-01 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:22:54.260 wdl.w:ptcp.w:call-sawfish-01 NOTICE ready :: job: "call-run_sawfish", callee: "run_sawfish"
2025-09-15 20:22:54.261 wdl.w:ptcp.w:call-trgt-01 INFO visit :: node: "decl-sex", values: {"sex": "F"}
2025-09-15 20:22:54.261 wdl.w:ptcp.w:call-paraphase-01 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2098"}
2025-09-15 20:22:54.261 wdl.w:ptcp.w:call-sawfish-01 INFO input :: job: "call-run_sawfish", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-01/out/m84036_250809_035451_s4.bc2098.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-01/out/m84036_250809_035451_s4.bc2098.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2098"}
2025-09-15 20:22:54.261 wdl.w:ptcp.w:call-trgt-01 INFO visit :: node: "decl-trgt_bed", values: {"trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"}
2025-09-15 20:22:54.261 wdl.w:ptcp.w:call-paraphase-01 INFO visit :: node: "decl-sex", values: {"sex": "F"}
2025-09-15 20:22:54.261 wdl.w:ptcp.w:call-trgt-01 NOTICE ready :: job: "call-get_reads_overlapping_repeats", callee: "get_reads_overlapping_repeats"
2025-09-15 20:22:54.262 wdl.w:ptcp.w:call-paraphase-01 NOTICE ready :: job: "call-run_paraphase", callee: "run_paraphase"
2025-09-15 20:22:54.262 wdl.w:ptcp.w:call-trgt-01 INFO input :: job: "call-get_reads_overlapping_repeats", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-01/out/m84036_250809_035451_s4.bc2098.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-01/out/m84036_250809_035451_s4.bc2098.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2098"}
2025-09-15 20:22:54.262 wdl.w:ptcp.w:call-paraphase-01 INFO input :: job: "call-run_paraphase", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf", "genome_version": "38", "config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-01/out/m84036_250809_035451_s4.bc2098.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-01/out/m84036_250809_035451_s4.bc2098.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2098"}
2025-09-15 20:22:54.263 wdl.w:ptcp.w:call-trgt-01 NOTICE ready :: job: "call-trgt_genotype", callee: "trgt_genotype"
2025-09-15 20:22:54.263 wdl.w:ptcp.w:call-trgt-01 INFO input :: job: "call-trgt_genotype", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-01/out/m84036_250809_035451_s4.bc2098.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-01/out/m84036_250809_035451_s4.bc2098.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2098"}
2025-09-15 20:22:54.297 wdl.w:ptcp.w:call-trgt-35.t:call-get_reads_overlapping_repeats INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 9, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-35/call-get_reads_overlapping_repeats/_singularity_tmpdir_52wgtk5e"
2025-09-15 20:22:54.298 wdl.w:ptcp.w:call-trgt-35.t:call-get_reads_overlapping_repeats INFO Slurm invocation: srun --job-name call-get_reads_overlapping_repeats --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-35/call-get_reads_overlapping_repeats/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-35/call-get_reads_overlapping_repeats/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-35/call-get_reads_overlapping_repeats/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-35/call-get_reads_overlapping_repeats/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-35/out/m84036_250809_035451_s4.bc2132.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2132.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-35/out/m84036_250809_035451_s4.bc2132.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2132.mapped.bam.bai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-35/call-get_reads_overlapping_repeats/_singularity_tmpdir_52wgtk5e/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-35/call-get_reads_overlapping_repeats/_singularity_tmpdir_52wgtk5e/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:22:54.312 wdl.w:ptcp.w:call-trgt-35.t:call-get_reads_overlapping_repeats NOTICE slurm_singularity run :: pid: 1198466, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-35/call-get_reads_overlapping_repeats/slurm_singularity.log.txt"
2025-09-15 20:22:54.355 wdl.w:ptcp.t:call-pbmm2_align_hifi-00 INFO output :: name: "mapped_bam", value: "m84036_250809_035451_s4.bc2097.mapped.bam"
2025-09-15 20:22:54.358 wdl.w:ptcp.t:call-pbmm2_align_hifi-00 INFO output :: name: "mapped_bam_bai", value: "m84036_250809_035451_s4.bc2097.mapped.bam.bai"
2025-09-15 20:22:54.359 wdl.w:ptcp.t:call-pbmm2_align_hifi-00 INFO output :: name: "mapped_bam_pbi", value: "m84036_250809_035451_s4.bc2097.mapped.bam.pbi"
2025-09-15 20:22:54.360 wdl.w:ptcp.t:call-pbmm2_align_hifi-00 INFO output :: name: "report", value: "mapping_stats.report.json"
2025-09-15 20:22:54.425 wdl.w:ptcp.t:call-pbmm2_align_hifi-00 NOTICE done
2025-09-15 20:22:54.431 wdl.w:ptcp NOTICE finish :: job: "call-pbmm2_align_hifi-00"
2025-09-15 20:22:54.431 wdl.w:ptcp INFO output :: job: "call-pbmm2_align_hifi-00", values: {"report": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-00/out/mapping_stats.report.json", "mapped_bam_pbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-00/out/m84036_250809_035451_s4.bc2097.mapped.bam.pbi", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-00/out/m84036_250809_035451_s4.bc2097.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-00/out/m84036_250809_035451_s4.bc2097.mapped.bam"}
2025-09-15 20:22:54.432 wdl.w:ptcp NOTICE ready :: job: "call-paraphase-00", callee: "paraphase"
2025-09-15 20:22:54.433 wdl.w:ptcp INFO input :: job: "call-paraphase-00", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf", "genome_version": "38", "config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-00/out/m84036_250809_035451_s4.bc2097.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-00/out/m84036_250809_035451_s4.bc2097.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2097"}
2025-09-15 20:22:54.434 wdl.w:ptcp NOTICE ready :: job: "call-sawfish-00", callee: "sawfish"
2025-09-15 20:22:54.434 wdl.w:ptcp INFO input :: job: "call-sawfish-00", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-00/out/m84036_250809_035451_s4.bc2097.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-00/out/m84036_250809_035451_s4.bc2097.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2097"}
2025-09-15 20:22:54.438 wdl.w:ptcp NOTICE ready :: job: "call-trgt-00", callee: "trgt"
2025-09-15 20:22:54.438 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_genotype NOTICE task setup :: name: "trgt_genotype", source: "./trgt.wdl", line: 272, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-35/call-trgt_genotype", thread: 140613838284352
2025-09-15 20:22:54.438 wdl.w:ptcp INFO input :: job: "call-trgt-00", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-00/out/m84036_250809_035451_s4.bc2097.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-00/out/m84036_250809_035451_s4.bc2097.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2097"}
2025-09-15 20:22:54.442 wdl.w:ptcp.w:call-paraphase-00 NOTICE workflow start :: name: "paraphase", source: "./paraphase.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-00"
2025-09-15 20:22:54.445 wdl.w:ptcp.w:call-sawfish-00 NOTICE workflow start :: name: "sawfish", source: "./sawfish.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-00"
2025-09-15 20:22:54.446 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_genotype.slurm_singularity INFO srun: job 51797354 queued and waiting for resources
2025-09-15 20:22:54.450 wdl.w:ptcp.w:call-trgt-00 NOTICE workflow start :: name: "trgt", source: "./trgt.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-00"
2025-09-15 20:22:54.465 wdl.w:ptcp.w:call-paraphase-00 INFO visit :: node: "decl-annotation_vcf", values: {"annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf"}
2025-09-15 20:22:54.466 wdl.w:ptcp.w:call-paraphase-00 INFO visit :: node: "decl-config_file", values: {"config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml"}
2025-09-15 20:22:54.466 wdl.w:ptcp.w:call-paraphase-00 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:22:54.466 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_genotype INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:22:54.466 wdl.w:ptcp.w:call-paraphase-00 INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:22:54.467 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_genotype INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:22:54.467 wdl.w:ptcp.w:call-paraphase-00 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-00/out/m84036_250809_035451_s4.bc2097.mapped.bam"}
2025-09-15 20:22:54.467 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_genotype INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:22:54.468 wdl.w:ptcp.w:call-paraphase-00 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-00/out/m84036_250809_035451_s4.bc2097.mapped.bam.bai"}
2025-09-15 20:22:54.468 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_genotype INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:22:54.469 wdl.w:ptcp.w:call-paraphase-00 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:22:54.469 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_genotype INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2132.mapped.bam.bai"
2025-09-15 20:22:54.469 wdl.w:ptcp.w:call-sawfish-00 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:22:54.470 wdl.w:ptcp.w:call-paraphase-00 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:22:54.470 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_genotype INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2132.mapped.bam"
2025-09-15 20:22:54.470 wdl.w:ptcp.w:call-sawfish-00 INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:22:54.470 wdl.w:ptcp.w:call-paraphase-00 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2097"}
2025-09-15 20:22:54.470 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_genotype INFO input :: name: "sex", value: "F"
2025-09-15 20:22:54.471 wdl.w:ptcp.w:call-sawfish-00 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-00/out/m84036_250809_035451_s4.bc2097.mapped.bam"}
2025-09-15 20:22:54.471 wdl.w:ptcp.w:call-paraphase-00 INFO visit :: node: "decl-sex", values: {"sex": "F"}
2025-09-15 20:22:54.471 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_genotype INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2132"
2025-09-15 20:22:54.471 wdl.w:ptcp.w:call-sawfish-00 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-00/out/m84036_250809_035451_s4.bc2097.mapped.bam.bai"}
2025-09-15 20:22:54.472 wdl.w:ptcp.w:call-paraphase-00 NOTICE ready :: job: "call-run_paraphase", callee: "run_paraphase"
2025-09-15 20:22:54.472 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_genotype INFO eval :: name: "mem_gb", value: 16
2025-09-15 20:22:54.473 wdl.w:ptcp.w:call-sawfish-00 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:22:54.473 wdl.w:ptcp.w:call-trgt-00 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:22:54.473 wdl.w:ptcp.w:call-paraphase-00 INFO input :: job: "call-run_paraphase", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf", "genome_version": "38", "config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-00/out/m84036_250809_035451_s4.bc2097.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-00/out/m84036_250809_035451_s4.bc2097.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2097"}
2025-09-15 20:22:54.473 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_genotype INFO eval :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2132.trgt"
2025-09-15 20:22:54.473 wdl.w:ptcp.w:call-sawfish-00 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:22:54.474 wdl.w:ptcp.w:call-trgt-00 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-00/out/m84036_250809_035451_s4.bc2097.mapped.bam"}
2025-09-15 20:22:54.474 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_genotype INFO eval :: name: "threads", value: 8
2025-09-15 20:22:54.474 wdl.w:ptcp.w:call-sawfish-00 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2097"}
2025-09-15 20:22:54.474 wdl.w:ptcp.w:call-trgt-00 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-00/out/m84036_250809_035451_s4.bc2097.mapped.bam.bai"}
2025-09-15 20:22:54.475 wdl.w:ptcp.w:call-sawfish-00 NOTICE ready :: job: "call-run_sawfish", callee: "run_sawfish"
2025-09-15 20:22:54.475 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_genotype INFO eval :: name: "disk_size", value: 27
2025-09-15 20:22:54.475 wdl.w:ptcp.w:call-trgt-00 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:22:54.475 wdl.w:ptcp.w:call-sawfish-00 INFO input :: job: "call-run_sawfish", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-00/out/m84036_250809_035451_s4.bc2097.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-00/out/m84036_250809_035451_s4.bc2097.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2097"}
2025-09-15 20:22:54.475 wdl.w:ptcp.w:call-trgt-00 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:22:54.475 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_genotype INFO eval :: name: "karyotype", value: "XX"
2025-09-15 20:22:54.476 wdl.w:ptcp.w:call-trgt-00 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2097"}
2025-09-15 20:22:54.476 wdl.w:ptcp.w:call-trgt-00 INFO visit :: node: "decl-sex", values: {"sex": "F"}
2025-09-15 20:22:54.476 wdl.w:ptcp.w:call-trgt-00 INFO visit :: node: "decl-trgt_bed", values: {"trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"}
2025-09-15 20:22:54.476 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_genotype INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 8, memory_reservation: 16000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:22:54.477 wdl.w:ptcp.w:call-trgt-00 NOTICE ready :: job: "call-get_reads_overlapping_repeats", callee: "get_reads_overlapping_repeats"
2025-09-15 20:22:54.477 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_genotype WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:22:54.477 wdl.w:ptcp.w:call-trgt-00 INFO input :: job: "call-get_reads_overlapping_repeats", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-00/out/m84036_250809_035451_s4.bc2097.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-00/out/m84036_250809_035451_s4.bc2097.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2097"}
2025-09-15 20:22:54.478 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_genotype INFO provisioned :: seconds_waited: 0, cpu: 8, mem_bytes: 16000000000
2025-09-15 20:22:54.478 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_genotype INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:22:54.478 wdl.w:ptcp.w:call-trgt-00 NOTICE ready :: job: "call-trgt_genotype", callee: "trgt_genotype"
2025-09-15 20:22:54.478 wdl.w:ptcp.w:call-trgt-00 INFO input :: job: "call-trgt_genotype", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-00/out/m84036_250809_035451_s4.bc2097.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-00/out/m84036_250809_035451_s4.bc2097.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2097"}
2025-09-15 20:22:54.534 wdl.w:ptcp.w:call-paraphase-35.t:call-run_paraphase.slurm_singularity INFO srun: job 51797355 queued and waiting for resources
2025-09-15 20:22:54.542 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_genotype INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 11, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-35/call-trgt_genotype/_singularity_tmpdir_d5guoxxr"
2025-09-15 20:22:54.542 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_genotype INFO Slurm invocation: srun --job-name call-trgt_genotype --partition compute,compute9 --cpus-per-task 8 --mem 15259M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-35/call-trgt_genotype/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-35/call-trgt_genotype/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-35/call-trgt_genotype/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-35/call-trgt_genotype/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-35/out/m84036_250809_035451_s4.bc2132.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2132.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-35/out/m84036_250809_035451_s4.bc2132.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2132.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-35/call-trgt_genotype/_singularity_tmpdir_d5guoxxr/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-35/call-trgt_genotype/_singularity_tmpdir_d5guoxxr/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:22:54.562 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_genotype NOTICE slurm_singularity run :: pid: 1198477, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-35/call-trgt_genotype/slurm_singularity.log.txt"
2025-09-15 20:22:54.765 wdl.w:ptcp.w:call-sawfish-35.t:call-run_sawfish.slurm_singularity INFO srun: job 51797356 queued and waiting for resources
2025-09-15 20:22:54.768 wdl.w:ptcp.t:call-pbmm2_align_hifi-69.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:22:54.770 wdl.w:ptcp.t:call-pbmm2_align_hifi-70.slurm_singularity INFO srun: job 51797292 has been allocated resources
2025-09-15 20:22:54.770 wdl.w:ptcp.t:call-pbmm2_align_hifi-70.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:22:54.770 wdl.w:ptcp.t:call-pbmm2_align_hifi-70.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:22:54.773 wdl.w:ptcp.t:call-pbmm2_align_hifi-71.slurm_singularity INFO srun: job 51797293 has been allocated resources
2025-09-15 20:22:54.774 wdl.w:ptcp.t:call-pbmm2_align_hifi-71.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:22:54.774 wdl.w:ptcp.t:call-pbmm2_align_hifi-71.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:22:55.319 wdl.w:ptcp.w:call-trgt-35.t:call-get_reads_overlapping_repeats.slurm_singularity INFO srun: job 51797357 queued and waiting for resources
2025-09-15 20:22:55.573 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_genotype.slurm_singularity INFO srun: job 51797358 queued and waiting for resources
2025-09-15 20:23:00.123 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_genotype.slurm_singularity INFO srun: job 51797350 has been allocated resources
2025-09-15 20:23:00.130 wdl.w:ptcp.w:call-trgt-07.t:call-get_reads_overlapping_repeats.slurm_singularity INFO srun: job 51797336 has been allocated resources
2025-09-15 20:23:00.131 wdl.w:ptcp.w:call-sawfish-07.t:call-run_sawfish.slurm_singularity INFO srun: job 51797335 has been allocated resources
2025-09-15 20:23:00.178 wdl.w:ptcp.w:call-paraphase-14.t:call-run_paraphase.slurm_singularity INFO srun: job 51797321 has been allocated resources
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2025-09-15 20:23:00.271 wdl.w:ptcp.w:call-paraphase-22.t:call-run_paraphase.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:00.295 wdl.w:ptcp.w:call-paraphase-34.t:call-run_paraphase.slurm_singularity INFO srun: job 51797347 has been allocated resources
2025-09-15 20:23:00.297 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_genotype.slurm_singularity INFO srun: job 51797330 has been allocated resources
2025-09-15 20:23:00.364 wdl.w:ptcp.w:call-trgt-35.t:call-get_reads_overlapping_repeats.slurm_singularity INFO srun: job 51797357 has been allocated resources
2025-09-15 20:23:00.460 wdl.w:ptcp.w:call-trgt-22.t:call-get_reads_overlapping_repeats.slurm_singularity INFO srun: job 51797325 has been allocated resources
2025-09-15 20:23:00.461 wdl.w:ptcp.w:call-trgt-22.t:call-get_reads_overlapping_repeats.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:00.498 wdl.w:ptcp.w:call-paraphase-23.t:call-run_paraphase.slurm_singularity INFO srun: job 51797351 has been allocated resources
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2025-09-15 20:23:00.504 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_genotype.slurm_singularity INFO srun: job 51797354 has been allocated resources
2025-09-15 20:23:00.505 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_genotype.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:00.522 wdl.w:ptcp.w:call-paraphase-20.t:call-run_paraphase.slurm_singularity INFO srun: job 51797331 has been allocated resources
2025-09-15 20:23:00.523 wdl.w:ptcp.w:call-paraphase-20.t:call-run_paraphase.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:00.583 wdl.w:ptcp.w:call-sawfish-04.t:call-run_sawfish.slurm_singularity INFO srun: job 51797340 has been allocated resources
2025-09-15 20:23:00.583 wdl.w:ptcp.w:call-sawfish-04.t:call-run_sawfish.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:00.593 wdl.w:ptcp.w:call-paraphase-04.t:call-run_paraphase.slurm_singularity INFO srun: job 51797339 has been allocated resources
2025-09-15 20:23:00.594 wdl.w:ptcp.w:call-paraphase-04.t:call-run_paraphase.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:00.615 wdl.w:ptcp.w:call-paraphase-35.t:call-run_paraphase.slurm_singularity INFO srun: job 51797355 has been allocated resources
2025-09-15 20:23:00.615 wdl.w:ptcp.w:call-paraphase-35.t:call-run_paraphase.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:00.622 wdl.w:ptcp.w:call-sawfish-34.t:call-run_sawfish.slurm_singularity INFO srun: job 51797348 has been allocated resources
2025-09-15 20:23:00.622 wdl.w:ptcp.w:call-sawfish-34.t:call-run_sawfish.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:00.629 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_genotype.slurm_singularity INFO srun: job 51797358 has been allocated resources
2025-09-15 20:23:00.630 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_genotype.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:00.637 wdl.w:ptcp.w:call-sawfish-20.t:call-run_sawfish.slurm_singularity INFO srun: job 51797332 has been allocated resources
2025-09-15 20:23:00.637 wdl.w:ptcp.w:call-sawfish-20.t:call-run_sawfish.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:00.643 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_genotype.slurm_singularity INFO srun: job 51797326 has been allocated resources
2025-09-15 20:23:00.643 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_genotype.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:00.671 wdl.w:ptcp.w:call-trgt-20.t:call-get_reads_overlapping_repeats.slurm_singularity INFO srun: job 51797333 has been allocated resources
2025-09-15 20:23:00.672 wdl.w:ptcp.w:call-trgt-20.t:call-get_reads_overlapping_repeats.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:00.751 wdl.w:ptcp.w:call-trgt-34.t:call-get_reads_overlapping_repeats.slurm_singularity INFO srun: job 51797349 has been allocated resources
2025-09-15 20:23:00.752 wdl.w:ptcp.w:call-trgt-34.t:call-get_reads_overlapping_repeats.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:00.770 wdl.w:ptcp.w:call-sawfish-23.t:call-run_sawfish.slurm_singularity INFO srun: job 51797352 has been allocated resources
2025-09-15 20:23:00.770 wdl.w:ptcp.w:call-sawfish-23.t:call-run_sawfish.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:00.812 wdl.w:ptcp.w:call-trgt-20.t:call-trgt_genotype.slurm_singularity INFO srun: job 51797334 has been allocated resources
2025-09-15 20:23:00.812 wdl.w:ptcp.w:call-trgt-20.t:call-trgt_genotype.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:00.813 wdl.w:ptcp.w:call-paraphase-15.t:call-run_paraphase.slurm_singularity INFO srun: job 51797327 has been allocated resources
2025-09-15 20:23:00.814 wdl.w:ptcp.w:call-paraphase-15.t:call-run_paraphase.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:00.855 wdl.w:ptcp.w:call-trgt-15.t:call-get_reads_overlapping_repeats.slurm_singularity INFO srun: job 51797328 has been allocated resources
2025-09-15 20:23:00.855 wdl.w:ptcp.w:call-trgt-15.t:call-get_reads_overlapping_repeats.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:00.861 wdl.w:ptcp.w:call-sawfish-35.t:call-run_sawfish.slurm_singularity INFO srun: job 51797356 has been allocated resources
2025-09-15 20:23:00.862 wdl.w:ptcp.w:call-sawfish-35.t:call-run_sawfish.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:00.925 wdl.w:ptcp.w:call-trgt-23.t:call-get_reads_overlapping_repeats.slurm_singularity INFO srun: job 51797353 has been allocated resources
2025-09-15 20:23:00.925 wdl.w:ptcp.w:call-trgt-23.t:call-get_reads_overlapping_repeats.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:00.929 wdl.w:ptcp.w:call-sawfish-31.t:call-run_sawfish.slurm_singularity INFO srun: job 51797341 has been allocated resources
2025-09-15 20:23:00.929 wdl.w:ptcp.w:call-sawfish-31.t:call-run_sawfish.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:00.948 wdl.w:ptcp.w:call-trgt-31.t:call-get_reads_overlapping_repeats.slurm_singularity INFO srun: job 51797342 has been allocated resources
2025-09-15 20:23:00.948 wdl.w:ptcp.w:call-trgt-31.t:call-get_reads_overlapping_repeats.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:00.956 wdl.w:ptcp.w:call-trgt-04.t:call-trgt_genotype.slurm_singularity INFO srun: job 51797343 has been allocated resources
2025-09-15 20:23:00.957 wdl.w:ptcp.w:call-trgt-04.t:call-trgt_genotype.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:00.957 wdl.w:ptcp.w:call-paraphase-31.t:call-run_paraphase.slurm_singularity INFO srun: job 51797345 has been allocated resources
2025-09-15 20:23:00.958 wdl.w:ptcp.w:call-paraphase-31.t:call-run_paraphase.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:00.958 wdl.w:ptcp.w:call-trgt-04.t:call-get_reads_overlapping_repeats.slurm_singularity INFO srun: job 51797344 has been allocated resources
2025-09-15 20:23:00.959 wdl.w:ptcp.w:call-trgt-04.t:call-get_reads_overlapping_repeats.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:01.134 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_genotype.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:01.143 wdl.w:ptcp.w:call-trgt-07.t:call-get_reads_overlapping_repeats.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:01.143 wdl.w:ptcp.w:call-sawfish-07.t:call-run_sawfish.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:01.193 wdl.w:ptcp.w:call-paraphase-14.t:call-run_paraphase.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:01.194 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_genotype.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:01.198 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_genotype.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:01.204 wdl.w:ptcp.w:call-sawfish-14.t:call-run_sawfish.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:01.205 wdl.w:ptcp.w:call-trgt-14.t:call-get_reads_overlapping_repeats.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:01.205 wdl.w:ptcp.w:call-paraphase-07.t:call-run_paraphase.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:01.212 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_genotype.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:01.278 wdl.w:ptcp.w:call-trgt-14.t:call-get_reads_overlapping_repeats INFO output :: name: "reads_overlapping_repeats", value: "m84036_250809_035451_s4.bc2111.repeats.bam"
2025-09-15 20:23:01.280 wdl.w:ptcp.w:call-sawfish-22.t:call-run_sawfish.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:01.281 wdl.w:ptcp.w:call-sawfish-15.t:call-run_sawfish.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:01.281 wdl.w:ptcp.w:call-trgt-14.t:call-get_reads_overlapping_repeats INFO output :: name: "reads_overlapping_repeats_bai", value: "m84036_250809_035451_s4.bc2111.repeats.bam.bai"
2025-09-15 20:23:01.308 wdl.w:ptcp.w:call-paraphase-34.t:call-run_paraphase.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:01.309 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_genotype.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:01.335 wdl.w:ptcp.w:call-trgt-14.t:call-get_reads_overlapping_repeats NOTICE done
2025-09-15 20:23:01.361 wdl.w:ptcp.w:call-trgt-14 NOTICE finish :: job: "call-get_reads_overlapping_repeats"
2025-09-15 20:23:01.362 wdl.w:ptcp.w:call-trgt-14 INFO output :: job: "call-get_reads_overlapping_repeats", values: {"reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-14/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2111.repeats.bam.bai", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-14/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2111.repeats.bam"}
2025-09-15 20:23:01.362 wdl.w:ptcp.w:call-trgt-14 INFO visit :: node: "output-reads_overlapping_repeats", values: {"reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-14/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2111.repeats.bam"}
2025-09-15 20:23:01.362 wdl.w:ptcp.w:call-trgt-14 INFO visit :: node: "output-reads_overlapping_repeats_bai", values: {"reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-14/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2111.repeats.bam.bai"}
2025-09-15 20:23:01.367 wdl.w:ptcp.w:call-paraphase-26.t:call-run_paraphase NOTICE task setup :: name: "run_paraphase", source: "./paraphase.wdl", line: 127, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-26/call-run_paraphase", thread: 140606089197120
2025-09-15 20:23:01.376 wdl.w:ptcp.w:call-trgt-35.t:call-get_reads_overlapping_repeats.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:01.384 wdl.w:ptcp.w:call-paraphase-26.t:call-run_paraphase INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:23:01.384 wdl.w:ptcp.w:call-paraphase-26.t:call-run_paraphase INFO input :: name: "annotation_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf"
2025-09-15 20:23:01.384 wdl.w:ptcp.w:call-paraphase-26.t:call-run_paraphase INFO input :: name: "genome_version", value: "38"
2025-09-15 20:23:01.384 wdl.w:ptcp.w:call-paraphase-26.t:call-run_paraphase INFO input :: name: "config_file", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/paraphase_config.GRCh38.yaml"
2025-09-15 20:23:01.384 wdl.w:ptcp.w:call-paraphase-26.t:call-run_paraphase INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:23:01.384 wdl.w:ptcp.w:call-paraphase-26.t:call-run_paraphase INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:23:01.385 wdl.w:ptcp.w:call-paraphase-26.t:call-run_paraphase INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2123.mapped.bam.bai"
2025-09-15 20:23:01.385 wdl.w:ptcp.w:call-paraphase-26.t:call-run_paraphase INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2123.mapped.bam"
2025-09-15 20:23:01.385 wdl.w:ptcp.w:call-paraphase-26.t:call-run_paraphase INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2123"
2025-09-15 20:23:01.385 wdl.w:ptcp.w:call-paraphase-26.t:call-run_paraphase INFO eval :: name: "threads", value: 4
2025-09-15 20:23:01.385 wdl.w:ptcp.w:call-paraphase-26.t:call-run_paraphase INFO eval :: name: "mem_gb", value: 8
2025-09-15 20:23:01.385 wdl.w:ptcp.w:call-paraphase-26.t:call-run_paraphase INFO eval :: name: "disk_size", value: 27
2025-09-15 20:23:01.385 wdl.w:ptcp.w:call-paraphase-26.t:call-run_paraphase INFO eval :: name: "out_dir", value: "m84036_250809_035451_s4.bc2123_paraphase"
2025-09-15 20:23:01.386 wdl.w:ptcp.w:call-paraphase-26.t:call-run_paraphase INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 4, memory_reservation: 8000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:23:01.386 wdl.w:ptcp.w:call-paraphase-26.t:call-run_paraphase WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:23:01.386 wdl.w:ptcp.w:call-paraphase-26.t:call-run_paraphase INFO provisioned :: seconds_waited: 0, cpu: 4, mem_bytes: 8000000000
2025-09-15 20:23:01.386 wdl.w:ptcp.w:call-paraphase-26.t:call-run_paraphase INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:23:01.401 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_genotype INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2119.trgt.vcf"
2025-09-15 20:23:01.405 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_genotype INFO output :: name: "spanning_bam", value: "m84036_250809_035451_s4.bc2119.trgt.sorted.spanning.bam"
2025-09-15 20:23:01.406 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_genotype INFO output :: name: "spanning_bam_bai", value: "m84036_250809_035451_s4.bc2119.trgt.sorted.spanning.bam.bai"
2025-09-15 20:23:01.444 wdl.w:ptcp.w:call-paraphase-26.t:call-run_paraphase INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-26/call-run_paraphase/_singularity_tmpdir_caygneu4"
2025-09-15 20:23:01.444 wdl.w:ptcp.w:call-paraphase-26.t:call-run_paraphase INFO Slurm invocation: srun --job-name call-run_paraphase --partition compute,compute9 --cpus-per-task 4 --mem 7629M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-26/call-run_paraphase/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-26/call-run_paraphase/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-26/call-run_paraphase/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-26/call-run_paraphase/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-26/out/m84036_250809_035451_s4.bc2123.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2123.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-26/out/m84036_250809_035451_s4.bc2123.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2123.mapped.bam.bai:ro --bind /ptcp/meta/variant_list/variant_list.GRCh38.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf:ro --bind /ptcp/meta/paraphase/paraphase_config.GRCh38.yaml:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/paraphase_config.GRCh38.yaml:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-26/call-run_paraphase/_singularity_tmpdir_caygneu4/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-26/call-run_paraphase/_singularity_tmpdir_caygneu4/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:23:01.475 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_genotype NOTICE done
2025-09-15 20:23:01.482 wdl.w:ptcp.w:call-trgt-22 NOTICE finish :: job: "call-trgt_genotype"
2025-09-15 20:23:01.482 wdl.w:ptcp.w:call-trgt-22 INFO output :: job: "call-trgt_genotype", values: {"spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-22/call-trgt_genotype/out/m84036_250809_035451_s4.bc2119.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-22/call-trgt_genotype/out/m84036_250809_035451_s4.bc2119.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-22/call-trgt_genotype/out/m84036_250809_035451_s4.bc2119.trgt.vcf"}
2025-09-15 20:23:01.482 wdl.w:ptcp.w:call-trgt-22 NOTICE ready :: job: "call-trgt_plot_meth_allele", callee: "trgt_plot"
2025-09-15 20:23:01.483 wdl.w:ptcp.w:call-trgt-22 INFO input :: job: "call-trgt_plot_meth_allele", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": false, "methylation": true, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-22/call-trgt_genotype/out/m84036_250809_035451_s4.bc2119.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-22/call-trgt_genotype/out/m84036_250809_035451_s4.bc2119.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-22/call-trgt_genotype/out/m84036_250809_035451_s4.bc2119.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2119"}
2025-09-15 20:23:01.484 wdl.w:ptcp.w:call-trgt-22 NOTICE ready :: job: "call-trgt_plot_meth_waterfall", callee: "trgt_plot"
2025-09-15 20:23:01.484 wdl.w:ptcp.w:call-trgt-22 INFO input :: job: "call-trgt_plot_meth_waterfall", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": true, "methylation": true, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-22/call-trgt_genotype/out/m84036_250809_035451_s4.bc2119.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-22/call-trgt_genotype/out/m84036_250809_035451_s4.bc2119.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-22/call-trgt_genotype/out/m84036_250809_035451_s4.bc2119.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2119"}
2025-09-15 20:23:01.485 wdl.w:ptcp.w:call-trgt-22 NOTICE ready :: job: "call-trgt_plot_motifs_allele", callee: "trgt_plot"
2025-09-15 20:23:01.485 wdl.w:ptcp.w:call-trgt-22 INFO input :: job: "call-trgt_plot_motifs_allele", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": false, "methylation": false, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-22/call-trgt_genotype/out/m84036_250809_035451_s4.bc2119.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-22/call-trgt_genotype/out/m84036_250809_035451_s4.bc2119.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-22/call-trgt_genotype/out/m84036_250809_035451_s4.bc2119.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2119"}
2025-09-15 20:23:01.486 wdl.w:ptcp.w:call-trgt-22 NOTICE ready :: job: "call-trgt_plot_motifs_waterfall", callee: "trgt_plot"
2025-09-15 20:23:01.486 wdl.w:ptcp.w:call-trgt-22 INFO input :: job: "call-trgt_plot_motifs_waterfall", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": true, "methylation": false, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-22/call-trgt_genotype/out/m84036_250809_035451_s4.bc2119.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-22/call-trgt_genotype/out/m84036_250809_035451_s4.bc2119.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-22/call-trgt_genotype/out/m84036_250809_035451_s4.bc2119.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2119"}
2025-09-15 20:23:01.486 wdl.w:ptcp.w:call-trgt-22 INFO visit :: node: "output-spanning_bam", values: {"spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-22/call-trgt_genotype/out/m84036_250809_035451_s4.bc2119.trgt.sorted.spanning.bam"}
2025-09-15 20:23:01.486 wdl.w:ptcp.w:call-trgt-22 INFO visit :: node: "output-spanning_bam_bai", values: {"spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-22/call-trgt_genotype/out/m84036_250809_035451_s4.bc2119.trgt.sorted.spanning.bam.bai"}
2025-09-15 20:23:01.486 wdl.w:ptcp.w:call-trgt-22 INFO visit :: node: "output-vcf", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-22/call-trgt_genotype/out/m84036_250809_035451_s4.bc2119.trgt.vcf"}
2025-09-15 20:23:01.489 wdl.w:ptcp.w:call-trgt-26.t:call-get_reads_overlapping_repeats NOTICE task setup :: name: "get_reads_overlapping_repeats", source: "./trgt.wdl", line: 182, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-26/call-get_reads_overlapping_repeats", thread: 140612498077248
2025-09-15 20:23:01.506 wdl.w:ptcp.w:call-trgt-26.t:call-get_reads_overlapping_repeats INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:23:01.506 wdl.w:ptcp.w:call-trgt-26.t:call-get_reads_overlapping_repeats INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:23:01.506 wdl.w:ptcp.w:call-trgt-26.t:call-get_reads_overlapping_repeats INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2123.mapped.bam.bai"
2025-09-15 20:23:01.506 wdl.w:ptcp.w:call-trgt-26.t:call-get_reads_overlapping_repeats INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2123.mapped.bam"
2025-09-15 20:23:01.507 wdl.w:ptcp.w:call-trgt-26.t:call-get_reads_overlapping_repeats INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2123"
2025-09-15 20:23:01.507 wdl.w:ptcp.w:call-trgt-26.t:call-get_reads_overlapping_repeats INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:23:01.507 wdl.w:ptcp.w:call-trgt-26.t:call-get_reads_overlapping_repeats INFO eval :: name: "expand_size", value: 3000
2025-09-15 20:23:01.507 wdl.w:ptcp.w:call-trgt-26.t:call-get_reads_overlapping_repeats INFO eval :: name: "threads", value: 1
2025-09-15 20:23:01.507 wdl.w:ptcp.w:call-trgt-26.t:call-get_reads_overlapping_repeats INFO eval :: name: "expanded_bed_name", value: "m84036_250809_035451_s4.bc2123.expanded.bed"
2025-09-15 20:23:01.507 wdl.w:ptcp.w:call-trgt-26.t:call-get_reads_overlapping_repeats INFO eval :: name: "disk_size", value: 11
2025-09-15 20:23:01.507 wdl.w:ptcp.w:call-trgt-26.t:call-get_reads_overlapping_repeats INFO eval :: name: "output_name", value: "m84036_250809_035451_s4.bc2123.repeats.bam"
2025-09-15 20:23:01.507 wdl.w:ptcp.w:call-trgt-26.t:call-get_reads_overlapping_repeats INFO eval :: name: "index_name", value: "m84036_250809_035451_s4.bc2123.repeats.bam.bai"
2025-09-15 20:23:01.507 wdl.w:ptcp.w:call-trgt-26.t:call-get_reads_overlapping_repeats INFO eval :: name: "output_name_with_index", value: "m84036_250809_035451_s4.bc2123.repeats.bam##idx##m84036_250809_035451_s4.bc2123.repeats.bam.bai"
2025-09-15 20:23:01.508 wdl.w:ptcp.w:call-trgt-26.t:call-get_reads_overlapping_repeats INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:23:01.508 wdl.w:ptcp.w:call-trgt-26.t:call-get_reads_overlapping_repeats WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:23:01.508 wdl.w:ptcp.w:call-trgt-26.t:call-get_reads_overlapping_repeats INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:23:01.508 wdl.w:ptcp.w:call-trgt-26.t:call-get_reads_overlapping_repeats INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:23:01.511 wdl.w:ptcp.w:call-trgt-22.t:call-get_reads_overlapping_repeats INFO output :: name: "reads_overlapping_repeats", value: "m84036_250809_035451_s4.bc2119.repeats.bam"
2025-09-15 20:23:01.516 wdl.w:ptcp.w:call-trgt-22.t:call-get_reads_overlapping_repeats INFO output :: name: "reads_overlapping_repeats_bai", value: "m84036_250809_035451_s4.bc2119.repeats.bam.bai"
2025-09-15 20:23:01.524 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_genotype INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2112.trgt.vcf"
2025-09-15 20:23:01.528 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_genotype INFO output :: name: "spanning_bam", value: "m84036_250809_035451_s4.bc2112.trgt.sorted.spanning.bam"
2025-09-15 20:23:01.529 wdl.w:ptcp.w:call-trgt-15.t:call-get_reads_overlapping_repeats INFO output :: name: "reads_overlapping_repeats", value: "m84036_250809_035451_s4.bc2112.repeats.bam"
2025-09-15 20:23:01.529 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_genotype INFO output :: name: "spanning_bam_bai", value: "m84036_250809_035451_s4.bc2112.trgt.sorted.spanning.bam.bai"
2025-09-15 20:23:01.532 wdl.w:ptcp.w:call-trgt-15.t:call-get_reads_overlapping_repeats INFO output :: name: "reads_overlapping_repeats_bai", value: "m84036_250809_035451_s4.bc2112.repeats.bam.bai"
2025-09-15 20:23:01.557 wdl.w:ptcp.w:call-paraphase-26.t:call-run_paraphase NOTICE slurm_singularity run :: pid: 1198753, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-26/call-run_paraphase/slurm_singularity.log.txt"
2025-09-15 20:23:01.567 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_genotype INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2128.trgt.vcf"
2025-09-15 20:23:01.571 wdl.w:ptcp.w:call-trgt-31.t:call-get_reads_overlapping_repeats INFO output :: name: "reads_overlapping_repeats", value: "m84036_250809_035451_s4.bc2128.repeats.bam"
2025-09-15 20:23:01.572 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_genotype INFO output :: name: "spanning_bam", value: "m84036_250809_035451_s4.bc2128.trgt.sorted.spanning.bam"
2025-09-15 20:23:01.573 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_genotype INFO output :: name: "spanning_bam_bai", value: "m84036_250809_035451_s4.bc2128.trgt.sorted.spanning.bam.bai"
2025-09-15 20:23:01.575 wdl.w:ptcp.w:call-trgt-26.t:call-get_reads_overlapping_repeats INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 9, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-26/call-get_reads_overlapping_repeats/_singularity_tmpdir_hlpk9rwd"
2025-09-15 20:23:01.575 wdl.w:ptcp.w:call-trgt-26.t:call-get_reads_overlapping_repeats INFO Slurm invocation: srun --job-name call-get_reads_overlapping_repeats --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-26/call-get_reads_overlapping_repeats/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-26/call-get_reads_overlapping_repeats/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-26/call-get_reads_overlapping_repeats/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-26/call-get_reads_overlapping_repeats/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-26/out/m84036_250809_035451_s4.bc2123.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2123.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-26/out/m84036_250809_035451_s4.bc2123.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2123.mapped.bam.bai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-26/call-get_reads_overlapping_repeats/_singularity_tmpdir_hlpk9rwd/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-26/call-get_reads_overlapping_repeats/_singularity_tmpdir_hlpk9rwd/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:23:01.576 wdl.w:ptcp.w:call-trgt-31.t:call-get_reads_overlapping_repeats INFO output :: name: "reads_overlapping_repeats_bai", value: "m84036_250809_035451_s4.bc2128.repeats.bam.bai"
2025-09-15 20:23:01.597 wdl.w:ptcp.w:call-trgt-26.t:call-get_reads_overlapping_repeats NOTICE slurm_singularity run :: pid: 1198757, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-26/call-get_reads_overlapping_repeats/slurm_singularity.log.txt"
2025-09-15 20:23:01.597 wdl.w:ptcp.w:call-trgt-22.t:call-get_reads_overlapping_repeats NOTICE done
2025-09-15 20:23:01.602 wdl.w:ptcp.w:call-trgt-22 NOTICE finish :: job: "call-get_reads_overlapping_repeats"
2025-09-15 20:23:01.602 wdl.w:ptcp.w:call-trgt-22 INFO output :: job: "call-get_reads_overlapping_repeats", values: {"reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-22/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2119.repeats.bam.bai", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-22/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2119.repeats.bam"}
2025-09-15 20:23:01.603 wdl.w:ptcp.w:call-trgt-22 INFO visit :: node: "output-reads_overlapping_repeats", values: {"reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-22/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2119.repeats.bam"}
2025-09-15 20:23:01.603 wdl.w:ptcp.w:call-trgt-22 INFO visit :: node: "output-reads_overlapping_repeats_bai", values: {"reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-22/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2119.repeats.bam.bai"}
2025-09-15 20:23:01.608 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_genotype NOTICE task setup :: name: "trgt_genotype", source: "./trgt.wdl", line: 272, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-26/call-trgt_genotype", thread: 140613018162752
2025-09-15 20:23:01.620 wdl.w:ptcp.w:call-trgt-15.t:call-get_reads_overlapping_repeats NOTICE done
2025-09-15 20:23:01.623 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_genotype NOTICE done
2025-09-15 20:23:01.625 wdl.w:ptcp.w:call-trgt-15 NOTICE finish :: job: "call-get_reads_overlapping_repeats"
2025-09-15 20:23:01.625 wdl.w:ptcp.w:call-trgt-15 INFO output :: job: "call-get_reads_overlapping_repeats", values: {"reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-15/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2112.repeats.bam.bai", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-15/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2112.repeats.bam"}
2025-09-15 20:23:01.625 wdl.w:ptcp.w:call-trgt-15 INFO visit :: node: "output-reads_overlapping_repeats", values: {"reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-15/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2112.repeats.bam"}
2025-09-15 20:23:01.626 wdl.w:ptcp.w:call-trgt-15 INFO visit :: node: "output-reads_overlapping_repeats_bai", values: {"reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-15/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2112.repeats.bam.bai"}
2025-09-15 20:23:01.663 wdl.w:ptcp.w:call-trgt-15 NOTICE finish :: job: "call-trgt_genotype"
2025-09-15 20:23:01.664 wdl.w:ptcp.w:call-trgt-15 INFO output :: job: "call-trgt_genotype", values: {"spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-15/call-trgt_genotype/out/m84036_250809_035451_s4.bc2112.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-15/call-trgt_genotype/out/m84036_250809_035451_s4.bc2112.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-15/call-trgt_genotype/out/m84036_250809_035451_s4.bc2112.trgt.vcf"}
2025-09-15 20:23:01.662 wdl.w:ptcp.w:call-sawfish-26.t:call-run_sawfish NOTICE task setup :: name: "run_sawfish", source: "./sawfish.wdl", line: 83, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-26/call-run_sawfish", thread: 140613588604480
2025-09-15 20:23:01.664 wdl.w:ptcp.w:call-trgt-15 NOTICE ready :: job: "call-trgt_plot_meth_allele", callee: "trgt_plot"
2025-09-15 20:23:01.665 wdl.w:ptcp.w:call-trgt-15 INFO input :: job: "call-trgt_plot_meth_allele", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": false, "methylation": true, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-15/call-trgt_genotype/out/m84036_250809_035451_s4.bc2112.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-15/call-trgt_genotype/out/m84036_250809_035451_s4.bc2112.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-15/call-trgt_genotype/out/m84036_250809_035451_s4.bc2112.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2112"}
2025-09-15 20:23:01.667 wdl.w:ptcp.w:call-trgt-15 NOTICE ready :: job: "call-trgt_plot_meth_waterfall", callee: "trgt_plot"
2025-09-15 20:23:01.667 wdl.w:ptcp.w:call-trgt-15 INFO input :: job: "call-trgt_plot_meth_waterfall", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": true, "methylation": true, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-15/call-trgt_genotype/out/m84036_250809_035451_s4.bc2112.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-15/call-trgt_genotype/out/m84036_250809_035451_s4.bc2112.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-15/call-trgt_genotype/out/m84036_250809_035451_s4.bc2112.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2112"}
2025-09-15 20:23:01.668 wdl.w:ptcp.w:call-trgt-15 NOTICE ready :: job: "call-trgt_plot_motifs_allele", callee: "trgt_plot"
2025-09-15 20:23:01.668 wdl.w:ptcp.w:call-trgt-15 INFO input :: job: "call-trgt_plot_motifs_allele", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": false, "methylation": false, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-15/call-trgt_genotype/out/m84036_250809_035451_s4.bc2112.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-15/call-trgt_genotype/out/m84036_250809_035451_s4.bc2112.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-15/call-trgt_genotype/out/m84036_250809_035451_s4.bc2112.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2112"}
2025-09-15 20:23:01.669 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_genotype INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:23:01.670 wdl.w:ptcp.w:call-trgt-15 NOTICE ready :: job: "call-trgt_plot_motifs_waterfall", callee: "trgt_plot"
2025-09-15 20:23:01.670 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_genotype INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:23:01.670 wdl.w:ptcp.w:call-trgt-15 INFO input :: job: "call-trgt_plot_motifs_waterfall", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": true, "methylation": false, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-15/call-trgt_genotype/out/m84036_250809_035451_s4.bc2112.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-15/call-trgt_genotype/out/m84036_250809_035451_s4.bc2112.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-15/call-trgt_genotype/out/m84036_250809_035451_s4.bc2112.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2112"}
2025-09-15 20:23:01.670 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_genotype INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:23:01.670 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_genotype INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:23:01.670 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_genotype INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2123.mapped.bam.bai"
2025-09-15 20:23:01.671 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_genotype INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2123.mapped.bam"
2025-09-15 20:23:01.671 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_genotype INFO input :: name: "sex", value: "F"
2025-09-15 20:23:01.671 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_genotype INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2123"
2025-09-15 20:23:01.671 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_genotype INFO eval :: name: "mem_gb", value: 16
2025-09-15 20:23:01.671 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_genotype INFO eval :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2123.trgt"
2025-09-15 20:23:01.671 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_genotype INFO eval :: name: "threads", value: 8
2025-09-15 20:23:01.671 wdl.w:ptcp.w:call-trgt-15 INFO visit :: node: "output-spanning_bam", values: {"spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-15/call-trgt_genotype/out/m84036_250809_035451_s4.bc2112.trgt.sorted.spanning.bam"}
2025-09-15 20:23:01.671 wdl.w:ptcp.w:call-trgt-15 INFO visit :: node: "output-spanning_bam_bai", values: {"spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-15/call-trgt_genotype/out/m84036_250809_035451_s4.bc2112.trgt.sorted.spanning.bam.bai"}
2025-09-15 20:23:01.671 wdl.w:ptcp.w:call-trgt-15 INFO visit :: node: "output-vcf", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-15/call-trgt_genotype/out/m84036_250809_035451_s4.bc2112.trgt.vcf"}
2025-09-15 20:23:01.672 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_genotype INFO eval :: name: "disk_size", value: 27
2025-09-15 20:23:01.672 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_genotype INFO eval :: name: "karyotype", value: "XX"
2025-09-15 20:23:01.672 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_genotype INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 8, memory_reservation: 16000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:23:01.673 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_genotype WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:23:01.673 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_genotype INFO provisioned :: seconds_waited: 0, cpu: 8, mem_bytes: 16000000000
2025-09-15 20:23:01.673 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_genotype INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:23:01.675 wdl.w:ptcp.w:call-paraphase-28.t:call-run_paraphase NOTICE task setup :: name: "run_paraphase", source: "./paraphase.wdl", line: 127, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-28/call-run_paraphase", thread: 140611424335424
2025-09-15 20:23:01.697 wdl.w:ptcp.w:call-sawfish-26.t:call-run_sawfish INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:23:01.697 wdl.w:ptcp.w:call-sawfish-26.t:call-run_sawfish INFO input :: name: "genome_version", value: "38"
2025-09-15 20:23:01.697 wdl.w:ptcp.w:call-sawfish-26.t:call-run_sawfish INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:23:01.698 wdl.w:ptcp.w:call-sawfish-26.t:call-run_sawfish INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:23:01.698 wdl.w:ptcp.w:call-sawfish-26.t:call-run_sawfish INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2123.mapped.bam.bai"
2025-09-15 20:23:01.698 wdl.w:ptcp.w:call-sawfish-26.t:call-run_sawfish INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2123.mapped.bam"
2025-09-15 20:23:01.698 wdl.w:ptcp.w:call-sawfish-26.t:call-run_sawfish INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2123"
2025-09-15 20:23:01.698 wdl.w:ptcp.w:call-sawfish-26.t:call-run_sawfish INFO eval :: name: "mem_gb", value: 32
2025-09-15 20:23:01.698 wdl.w:ptcp.w:call-sawfish-26.t:call-run_sawfish INFO eval :: name: "threads", value: 16
2025-09-15 20:23:01.699 wdl.w:ptcp.w:call-sawfish-26.t:call-run_sawfish INFO eval :: name: "disk_size", value: 30
2025-09-15 20:23:01.699 wdl.w:ptcp.w:call-sawfish-26.t:call-run_sawfish INFO eval :: name: "discover_dirname", value: "m84036_250809_035451_s4.bc2123_sawfish_discover"
2025-09-15 20:23:01.699 wdl.w:ptcp.w:call-sawfish-26.t:call-run_sawfish INFO eval :: name: "call_dirname", value: "m84036_250809_035451_s4.bc2123_sawfish"
2025-09-15 20:23:01.699 wdl.w:ptcp.w:call-sawfish-26.t:call-run_sawfish INFO eval :: name: "minimap2_bam_filename", value: "m84036_250809_035451_s4.bc2123.minimap2.bam"
2025-09-15 20:23:01.700 wdl.w:ptcp.w:call-sawfish-26.t:call-run_sawfish INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 16, memory_reservation: 32000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:23:01.700 wdl.w:ptcp.w:call-sawfish-26.t:call-run_sawfish WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:23:01.701 wdl.w:ptcp.w:call-sawfish-26.t:call-run_sawfish INFO provisioned :: seconds_waited: 0, cpu: 16, mem_bytes: 32000000000
2025-09-15 20:23:01.701 wdl.w:ptcp.w:call-sawfish-26.t:call-run_sawfish INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:23:01.706 wdl.w:ptcp.w:call-paraphase-28.t:call-run_paraphase INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:23:01.706 wdl.w:ptcp.w:call-paraphase-28.t:call-run_paraphase INFO input :: name: "annotation_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf"
2025-09-15 20:23:01.706 wdl.w:ptcp.w:call-paraphase-28.t:call-run_paraphase INFO input :: name: "genome_version", value: "38"
2025-09-15 20:23:01.706 wdl.w:ptcp.w:call-paraphase-28.t:call-run_paraphase INFO input :: name: "config_file", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/paraphase_config.GRCh38.yaml"
2025-09-15 20:23:01.707 wdl.w:ptcp.w:call-paraphase-28.t:call-run_paraphase INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:23:01.707 wdl.w:ptcp.w:call-paraphase-28.t:call-run_paraphase INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:23:01.707 wdl.w:ptcp.w:call-paraphase-28.t:call-run_paraphase INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2125.mapped.bam.bai"
2025-09-15 20:23:01.707 wdl.w:ptcp.w:call-paraphase-28.t:call-run_paraphase INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2125.mapped.bam"
2025-09-15 20:23:01.707 wdl.w:ptcp.w:call-paraphase-28.t:call-run_paraphase INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2125"
2025-09-15 20:23:01.707 wdl.w:ptcp.w:call-paraphase-28.t:call-run_paraphase INFO eval :: name: "threads", value: 4
2025-09-15 20:23:01.707 wdl.w:ptcp.w:call-paraphase-28.t:call-run_paraphase INFO eval :: name: "mem_gb", value: 8
2025-09-15 20:23:01.708 wdl.w:ptcp.w:call-paraphase-28.t:call-run_paraphase INFO eval :: name: "disk_size", value: 27
2025-09-15 20:23:01.708 wdl.w:ptcp.w:call-paraphase-28.t:call-run_paraphase INFO eval :: name: "out_dir", value: "m84036_250809_035451_s4.bc2125_paraphase"
2025-09-15 20:23:01.708 wdl.w:ptcp.w:call-paraphase-28.t:call-run_paraphase INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 4, memory_reservation: 8000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:23:01.708 wdl.w:ptcp.w:call-paraphase-28.t:call-run_paraphase WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:23:01.709 wdl.w:ptcp.w:call-paraphase-28.t:call-run_paraphase INFO provisioned :: seconds_waited: 0, cpu: 4, mem_bytes: 8000000000
2025-09-15 20:23:01.709 wdl.w:ptcp.w:call-paraphase-28.t:call-run_paraphase INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:23:01.719 wdl.w:ptcp.w:call-trgt-31.t:call-get_reads_overlapping_repeats NOTICE done
2025-09-15 20:23:01.727 wdl.w:ptcp.w:call-trgt-35.t:call-get_reads_overlapping_repeats INFO output :: name: "reads_overlapping_repeats", value: "m84036_250809_035451_s4.bc2132.repeats.bam"
2025-09-15 20:23:01.728 wdl.w:ptcp.w:call-trgt-31 NOTICE finish :: job: "call-get_reads_overlapping_repeats"
2025-09-15 20:23:01.728 wdl.w:ptcp.w:call-trgt-31 INFO output :: job: "call-get_reads_overlapping_repeats", values: {"reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-31/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2128.repeats.bam.bai", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-31/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2128.repeats.bam"}
2025-09-15 20:23:01.728 wdl.w:ptcp.w:call-trgt-31 INFO visit :: node: "output-reads_overlapping_repeats", values: {"reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-31/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2128.repeats.bam"}
2025-09-15 20:23:01.728 wdl.w:ptcp.w:call-trgt-31 INFO visit :: node: "output-reads_overlapping_repeats_bai", values: {"reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-31/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2128.repeats.bam.bai"}
2025-09-15 20:23:01.731 wdl.w:ptcp.w:call-trgt-35.t:call-get_reads_overlapping_repeats INFO output :: name: "reads_overlapping_repeats_bai", value: "m84036_250809_035451_s4.bc2132.repeats.bam.bai"
2025-09-15 20:23:01.733 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_genotype NOTICE done
2025-09-15 20:23:01.740 wdl.w:ptcp.w:call-trgt-34.t:call-get_reads_overlapping_repeats INFO output :: name: "reads_overlapping_repeats", value: "m84036_250809_035451_s4.bc2131.repeats.bam"
2025-09-15 20:23:01.740 wdl.w:ptcp.w:call-trgt-23.t:call-get_reads_overlapping_repeats INFO output :: name: "reads_overlapping_repeats", value: "m84036_250809_035451_s4.bc2120.repeats.bam"
2025-09-15 20:23:01.740 wdl.w:ptcp.w:call-trgt-31 NOTICE finish :: job: "call-trgt_genotype"
2025-09-15 20:23:01.741 wdl.w:ptcp.w:call-trgt-31 INFO output :: job: "call-trgt_genotype", values: {"spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-31/call-trgt_genotype/out/m84036_250809_035451_s4.bc2128.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-31/call-trgt_genotype/out/m84036_250809_035451_s4.bc2128.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-31/call-trgt_genotype/out/m84036_250809_035451_s4.bc2128.trgt.vcf"}
2025-09-15 20:23:01.741 wdl.w:ptcp.w:call-trgt-31 NOTICE ready :: job: "call-trgt_plot_meth_allele", callee: "trgt_plot"
2025-09-15 20:23:01.741 wdl.w:ptcp.w:call-trgt-31 INFO input :: job: "call-trgt_plot_meth_allele", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": false, "methylation": true, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-31/call-trgt_genotype/out/m84036_250809_035451_s4.bc2128.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-31/call-trgt_genotype/out/m84036_250809_035451_s4.bc2128.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-31/call-trgt_genotype/out/m84036_250809_035451_s4.bc2128.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2128"}
2025-09-15 20:23:01.741 wdl.w:ptcp.w:call-sawfish-28.t:call-run_sawfish NOTICE task setup :: name: "run_sawfish", source: "./sawfish.wdl", line: 83, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-28/call-run_sawfish", thread: 140613034948160
2025-09-15 20:23:01.743 wdl.w:ptcp.w:call-trgt-31 NOTICE ready :: job: "call-trgt_plot_meth_waterfall", callee: "trgt_plot"
2025-09-15 20:23:01.743 wdl.w:ptcp.w:call-trgt-31 INFO input :: job: "call-trgt_plot_meth_waterfall", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": true, "methylation": true, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-31/call-trgt_genotype/out/m84036_250809_035451_s4.bc2128.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-31/call-trgt_genotype/out/m84036_250809_035451_s4.bc2128.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-31/call-trgt_genotype/out/m84036_250809_035451_s4.bc2128.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2128"}
2025-09-15 20:23:01.744 wdl.w:ptcp.w:call-trgt-31 NOTICE ready :: job: "call-trgt_plot_motifs_allele", callee: "trgt_plot"
2025-09-15 20:23:01.745 wdl.w:ptcp.w:call-trgt-31 INFO input :: job: "call-trgt_plot_motifs_allele", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": false, "methylation": false, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-31/call-trgt_genotype/out/m84036_250809_035451_s4.bc2128.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-31/call-trgt_genotype/out/m84036_250809_035451_s4.bc2128.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-31/call-trgt_genotype/out/m84036_250809_035451_s4.bc2128.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2128"}
2025-09-15 20:23:01.745 wdl.w:ptcp.w:call-trgt-34.t:call-get_reads_overlapping_repeats INFO output :: name: "reads_overlapping_repeats_bai", value: "m84036_250809_035451_s4.bc2131.repeats.bam.bai"
2025-09-15 20:23:01.745 wdl.w:ptcp.w:call-trgt-31 NOTICE ready :: job: "call-trgt_plot_motifs_waterfall", callee: "trgt_plot"
2025-09-15 20:23:01.746 wdl.w:ptcp.w:call-trgt-31 INFO input :: job: "call-trgt_plot_motifs_waterfall", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": true, "methylation": false, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-31/call-trgt_genotype/out/m84036_250809_035451_s4.bc2128.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-31/call-trgt_genotype/out/m84036_250809_035451_s4.bc2128.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-31/call-trgt_genotype/out/m84036_250809_035451_s4.bc2128.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2128"}
2025-09-15 20:23:01.748 wdl.w:ptcp.w:call-trgt-23.t:call-get_reads_overlapping_repeats INFO output :: name: "reads_overlapping_repeats_bai", value: "m84036_250809_035451_s4.bc2120.repeats.bam.bai"
2025-09-15 20:23:01.748 wdl.w:ptcp.w:call-trgt-31 INFO visit :: node: "output-spanning_bam", values: {"spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-31/call-trgt_genotype/out/m84036_250809_035451_s4.bc2128.trgt.sorted.spanning.bam"}
2025-09-15 20:23:01.748 wdl.w:ptcp.w:call-trgt-31 INFO visit :: node: "output-spanning_bam_bai", values: {"spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-31/call-trgt_genotype/out/m84036_250809_035451_s4.bc2128.trgt.sorted.spanning.bam.bai"}
2025-09-15 20:23:01.748 wdl.w:ptcp.w:call-trgt-31 INFO visit :: node: "output-vcf", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-31/call-trgt_genotype/out/m84036_250809_035451_s4.bc2128.trgt.vcf"}
2025-09-15 20:23:01.755 wdl.w:ptcp.w:call-trgt-28.t:call-get_reads_overlapping_repeats NOTICE task setup :: name: "get_reads_overlapping_repeats", source: "./trgt.wdl", line: 182, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-28/call-get_reads_overlapping_repeats", thread: 140611944420928
2025-09-15 20:23:01.763 wdl.w:ptcp.w:call-sawfish-28.t:call-run_sawfish INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:23:01.763 wdl.w:ptcp.w:call-sawfish-28.t:call-run_sawfish INFO input :: name: "genome_version", value: "38"
2025-09-15 20:23:01.763 wdl.w:ptcp.w:call-sawfish-28.t:call-run_sawfish INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:23:01.763 wdl.w:ptcp.w:call-sawfish-28.t:call-run_sawfish INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:23:01.763 wdl.w:ptcp.w:call-sawfish-28.t:call-run_sawfish INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2125.mapped.bam.bai"
2025-09-15 20:23:01.763 wdl.w:ptcp.w:call-sawfish-28.t:call-run_sawfish INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2125.mapped.bam"
2025-09-15 20:23:01.763 wdl.w:ptcp.w:call-sawfish-28.t:call-run_sawfish INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2125"
2025-09-15 20:23:01.764 wdl.w:ptcp.w:call-sawfish-28.t:call-run_sawfish INFO eval :: name: "mem_gb", value: 32
2025-09-15 20:23:01.764 wdl.w:ptcp.w:call-sawfish-28.t:call-run_sawfish INFO eval :: name: "threads", value: 16
2025-09-15 20:23:01.764 wdl.w:ptcp.w:call-sawfish-28.t:call-run_sawfish INFO eval :: name: "disk_size", value: 30
2025-09-15 20:23:01.765 wdl.w:ptcp.w:call-sawfish-28.t:call-run_sawfish INFO eval :: name: "discover_dirname", value: "m84036_250809_035451_s4.bc2125_sawfish_discover"
2025-09-15 20:23:01.765 wdl.w:ptcp.w:call-sawfish-28.t:call-run_sawfish INFO eval :: name: "call_dirname", value: "m84036_250809_035451_s4.bc2125_sawfish"
2025-09-15 20:23:01.765 wdl.w:ptcp.w:call-sawfish-28.t:call-run_sawfish INFO eval :: name: "minimap2_bam_filename", value: "m84036_250809_035451_s4.bc2125.minimap2.bam"
2025-09-15 20:23:01.766 wdl.w:ptcp.w:call-sawfish-28.t:call-run_sawfish INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 16, memory_reservation: 32000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:23:01.766 wdl.w:ptcp.w:call-sawfish-28.t:call-run_sawfish WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:23:01.766 wdl.w:ptcp.w:call-sawfish-28.t:call-run_sawfish INFO provisioned :: seconds_waited: 0, cpu: 16, mem_bytes: 32000000000
2025-09-15 20:23:01.767 wdl.w:ptcp.w:call-sawfish-28.t:call-run_sawfish INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:23:01.779 wdl.w:ptcp.w:call-trgt-28.t:call-get_reads_overlapping_repeats INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:23:01.779 wdl.w:ptcp.w:call-trgt-28.t:call-get_reads_overlapping_repeats INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:23:01.779 wdl.w:ptcp.w:call-trgt-28.t:call-get_reads_overlapping_repeats INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2125.mapped.bam.bai"
2025-09-15 20:23:01.779 wdl.w:ptcp.w:call-trgt-28.t:call-get_reads_overlapping_repeats INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2125.mapped.bam"
2025-09-15 20:23:01.779 wdl.w:ptcp.w:call-trgt-28.t:call-get_reads_overlapping_repeats INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2125"
2025-09-15 20:23:01.779 wdl.w:ptcp.w:call-trgt-28.t:call-get_reads_overlapping_repeats INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:23:01.780 wdl.w:ptcp.w:call-trgt-28.t:call-get_reads_overlapping_repeats INFO eval :: name: "expand_size", value: 3000
2025-09-15 20:23:01.780 wdl.w:ptcp.w:call-trgt-28.t:call-get_reads_overlapping_repeats INFO eval :: name: "threads", value: 1
2025-09-15 20:23:01.780 wdl.w:ptcp.w:call-trgt-28.t:call-get_reads_overlapping_repeats INFO eval :: name: "expanded_bed_name", value: "m84036_250809_035451_s4.bc2125.expanded.bed"
2025-09-15 20:23:01.780 wdl.w:ptcp.w:call-trgt-28.t:call-get_reads_overlapping_repeats INFO eval :: name: "disk_size", value: 11
2025-09-15 20:23:01.780 wdl.w:ptcp.w:call-trgt-28.t:call-get_reads_overlapping_repeats INFO eval :: name: "output_name", value: "m84036_250809_035451_s4.bc2125.repeats.bam"
2025-09-15 20:23:01.781 wdl.w:ptcp.w:call-trgt-28.t:call-get_reads_overlapping_repeats INFO eval :: name: "index_name", value: "m84036_250809_035451_s4.bc2125.repeats.bam.bai"
2025-09-15 20:23:01.781 wdl.w:ptcp.w:call-trgt-28.t:call-get_reads_overlapping_repeats INFO eval :: name: "output_name_with_index", value: "m84036_250809_035451_s4.bc2125.repeats.bam##idx##m84036_250809_035451_s4.bc2125.repeats.bam.bai"
2025-09-15 20:23:01.781 wdl.w:ptcp.w:call-trgt-28.t:call-get_reads_overlapping_repeats INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:23:01.781 wdl.w:ptcp.w:call-trgt-28.t:call-get_reads_overlapping_repeats WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:23:01.782 wdl.w:ptcp.w:call-trgt-28.t:call-get_reads_overlapping_repeats INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:23:01.782 wdl.w:ptcp.w:call-trgt-28.t:call-get_reads_overlapping_repeats INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:23:01.795 wdl.w:ptcp.w:call-trgt-07.t:call-get_reads_overlapping_repeats INFO output :: name: "reads_overlapping_repeats", value: "m84036_250809_035451_s4.bc2104.repeats.bam"
2025-09-15 20:23:01.802 wdl.w:ptcp.w:call-trgt-07.t:call-get_reads_overlapping_repeats INFO output :: name: "reads_overlapping_repeats_bai", value: "m84036_250809_035451_s4.bc2104.repeats.bam.bai"
2025-09-15 20:23:01.803 wdl.w:ptcp.w:call-sawfish-26.t:call-run_sawfish INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 10, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-26/call-run_sawfish/_singularity_tmpdir_k756092j"
2025-09-15 20:23:01.803 wdl.w:ptcp.w:call-sawfish-26.t:call-run_sawfish INFO Slurm invocation: srun --job-name call-run_sawfish --partition compute,compute9 --cpus-per-task 16 --mem 30518M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-26/call-run_sawfish/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-26/call-run_sawfish/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-26/call-run_sawfish/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-26/call-run_sawfish/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-26/out/m84036_250809_035451_s4.bc2123.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2123.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-26/out/m84036_250809_035451_s4.bc2123.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2123.mapped.bam.bai:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-26/call-run_sawfish/_singularity_tmpdir_k756092j/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-26/call-run_sawfish/_singularity_tmpdir_k756092j/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:23:01.805 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_genotype INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 11, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-26/call-trgt_genotype/_singularity_tmpdir_byvkctcm"
2025-09-15 20:23:01.805 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_genotype INFO Slurm invocation: srun --job-name call-trgt_genotype --partition compute,compute9 --cpus-per-task 8 --mem 15259M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-26/call-trgt_genotype/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-26/call-trgt_genotype/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-26/call-trgt_genotype/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-26/call-trgt_genotype/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-26/out/m84036_250809_035451_s4.bc2123.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2123.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-26/out/m84036_250809_035451_s4.bc2123.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2123.mapped.bam.bai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-26/call-trgt_genotype/_singularity_tmpdir_byvkctcm/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-26/call-trgt_genotype/_singularity_tmpdir_byvkctcm/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:23:01.844 wdl.w:ptcp.w:call-paraphase-28.t:call-run_paraphase INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-28/call-run_paraphase/_singularity_tmpdir_bf4pawx1"
2025-09-15 20:23:01.844 wdl.w:ptcp.w:call-paraphase-28.t:call-run_paraphase INFO Slurm invocation: srun --job-name call-run_paraphase --partition compute,compute9 --cpus-per-task 4 --mem 7629M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-28/call-run_paraphase/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-28/call-run_paraphase/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-28/call-run_paraphase/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-28/call-run_paraphase/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-28/out/m84036_250809_035451_s4.bc2125.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2125.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-28/out/m84036_250809_035451_s4.bc2125.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2125.mapped.bam.bai:ro --bind /ptcp/meta/variant_list/variant_list.GRCh38.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf:ro --bind /ptcp/meta/paraphase/paraphase_config.GRCh38.yaml:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/paraphase_config.GRCh38.yaml:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-28/call-run_paraphase/_singularity_tmpdir_bf4pawx1/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-28/call-run_paraphase/_singularity_tmpdir_bf4pawx1/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:23:01.849 wdl.w:ptcp.w:call-trgt-35.t:call-get_reads_overlapping_repeats NOTICE done
2025-09-15 20:23:01.855 wdl.w:ptcp.w:call-trgt-35 NOTICE finish :: job: "call-get_reads_overlapping_repeats"
2025-09-15 20:23:01.855 wdl.w:ptcp.w:call-trgt-35 INFO output :: job: "call-get_reads_overlapping_repeats", values: {"reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-35/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2132.repeats.bam.bai", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-35/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2132.repeats.bam"}
2025-09-15 20:23:01.855 wdl.w:ptcp.w:call-trgt-35 INFO visit :: node: "output-reads_overlapping_repeats", values: {"reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-35/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2132.repeats.bam"}
2025-09-15 20:23:01.856 wdl.w:ptcp.w:call-paraphase-28.t:call-run_paraphase NOTICE slurm_singularity run :: pid: 1198765, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-28/call-run_paraphase/slurm_singularity.log.txt"
2025-09-15 20:23:01.856 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_genotype NOTICE slurm_singularity run :: pid: 1198764, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-26/call-trgt_genotype/slurm_singularity.log.txt"
2025-09-15 20:23:01.856 wdl.w:ptcp.w:call-sawfish-26.t:call-run_sawfish NOTICE slurm_singularity run :: pid: 1198763, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-26/call-run_sawfish/slurm_singularity.log.txt"
2025-09-15 20:23:01.856 wdl.w:ptcp.w:call-trgt-35 INFO visit :: node: "output-reads_overlapping_repeats_bai", values: {"reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-35/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2132.repeats.bam.bai"}
2025-09-15 20:23:01.866 wdl.w:ptcp.w:call-trgt-28.t:call-trgt_genotype NOTICE task setup :: name: "trgt_genotype", source: "./trgt.wdl", line: 272, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-28/call-trgt_genotype", thread: 140613823374912
2025-09-15 20:23:01.868 wdl.w:ptcp.w:call-trgt-23.t:call-get_reads_overlapping_repeats NOTICE done
2025-09-15 20:23:01.869 wdl.w:ptcp.w:call-trgt-34.t:call-get_reads_overlapping_repeats NOTICE done
2025-09-15 20:23:01.875 wdl.w:ptcp.w:call-trgt-23 NOTICE finish :: job: "call-get_reads_overlapping_repeats"
2025-09-15 20:23:01.875 wdl.w:ptcp.w:call-trgt-23 INFO output :: job: "call-get_reads_overlapping_repeats", values: {"reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-23/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2120.repeats.bam.bai", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-23/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2120.repeats.bam"}
2025-09-15 20:23:01.875 wdl.w:ptcp.w:call-trgt-23 INFO visit :: node: "output-reads_overlapping_repeats", values: {"reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-23/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2120.repeats.bam"}
2025-09-15 20:23:01.876 wdl.w:ptcp.w:call-trgt-34 NOTICE finish :: job: "call-get_reads_overlapping_repeats"
2025-09-15 20:23:01.876 wdl.w:ptcp.w:call-trgt-23 INFO visit :: node: "output-reads_overlapping_repeats_bai", values: {"reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-23/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2120.repeats.bam.bai"}
2025-09-15 20:23:01.876 wdl.w:ptcp.w:call-trgt-34 INFO output :: job: "call-get_reads_overlapping_repeats", values: {"reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-34/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2131.repeats.bam.bai", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-34/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2131.repeats.bam"}
2025-09-15 20:23:01.876 wdl.w:ptcp.w:call-trgt-34 INFO visit :: node: "output-reads_overlapping_repeats", values: {"reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-34/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2131.repeats.bam"}
2025-09-15 20:23:01.877 wdl.w:ptcp.w:call-trgt-34 INFO visit :: node: "output-reads_overlapping_repeats_bai", values: {"reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-34/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2131.repeats.bam.bai"}
2025-09-15 20:23:01.882 wdl.w:ptcp.w:call-trgt-28.t:call-get_reads_overlapping_repeats INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 9, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-28/call-get_reads_overlapping_repeats/_singularity_tmpdir_22qag7dj"
2025-09-15 20:23:01.882 wdl.w:ptcp.w:call-trgt-28.t:call-get_reads_overlapping_repeats INFO Slurm invocation: srun --job-name call-get_reads_overlapping_repeats --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-28/call-get_reads_overlapping_repeats/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-28/call-get_reads_overlapping_repeats/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-28/call-get_reads_overlapping_repeats/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-28/call-get_reads_overlapping_repeats/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-28/out/m84036_250809_035451_s4.bc2125.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2125.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-28/out/m84036_250809_035451_s4.bc2125.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2125.mapped.bam.bai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-28/call-get_reads_overlapping_repeats/_singularity_tmpdir_22qag7dj/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-28/call-get_reads_overlapping_repeats/_singularity_tmpdir_22qag7dj/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:23:01.887 wdl.w:ptcp.w:call-paraphase-10.t:call-run_paraphase NOTICE task setup :: name: "run_paraphase", source: "./paraphase.wdl", line: 127, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-10/call-run_paraphase", thread: 140611986384448
2025-09-15 20:23:01.888 wdl.w:ptcp.w:call-sawfish-28.t:call-run_sawfish INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 10, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-28/call-run_sawfish/_singularity_tmpdir_n80bk0in"
2025-09-15 20:23:01.888 wdl.w:ptcp.w:call-sawfish-28.t:call-run_sawfish INFO Slurm invocation: srun --job-name call-run_sawfish --partition compute,compute9 --cpus-per-task 16 --mem 30518M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-28/call-run_sawfish/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-28/call-run_sawfish/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-28/call-run_sawfish/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-28/call-run_sawfish/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-28/out/m84036_250809_035451_s4.bc2125.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2125.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-28/out/m84036_250809_035451_s4.bc2125.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2125.mapped.bam.bai:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-28/call-run_sawfish/_singularity_tmpdir_n80bk0in/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-28/call-run_sawfish/_singularity_tmpdir_n80bk0in/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:23:01.889 wdl.w:ptcp.w:call-sawfish-10.t:call-run_sawfish NOTICE task setup :: name: "run_sawfish", source: "./sawfish.wdl", line: 83, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-10/call-run_sawfish", thread: 140611441120832
2025-09-15 20:23:01.891 wdl.w:ptcp.w:call-trgt-28.t:call-trgt_genotype INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:23:01.893 wdl.w:ptcp.w:call-trgt-28.t:call-trgt_genotype INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:23:01.893 wdl.w:ptcp.w:call-trgt-28.t:call-trgt_genotype INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:23:01.893 wdl.w:ptcp.w:call-trgt-28.t:call-trgt_genotype INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:23:01.893 wdl.w:ptcp.w:call-trgt-28.t:call-trgt_genotype INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2125.mapped.bam.bai"
2025-09-15 20:23:01.893 wdl.w:ptcp.w:call-trgt-28.t:call-trgt_genotype INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2125.mapped.bam"
2025-09-15 20:23:01.893 wdl.w:ptcp.w:call-trgt-28.t:call-trgt_genotype INFO input :: name: "sex", value: "F"
2025-09-15 20:23:01.893 wdl.w:ptcp.w:call-trgt-28.t:call-trgt_genotype INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2125"
2025-09-15 20:23:01.894 wdl.w:ptcp.w:call-trgt-28.t:call-trgt_genotype INFO eval :: name: "mem_gb", value: 16
2025-09-15 20:23:01.894 wdl.w:ptcp.w:call-trgt-28.t:call-trgt_genotype INFO eval :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2125.trgt"
2025-09-15 20:23:01.894 wdl.w:ptcp.w:call-trgt-28.t:call-trgt_genotype INFO eval :: name: "threads", value: 8
2025-09-15 20:23:01.894 wdl.w:ptcp.w:call-trgt-28.t:call-trgt_genotype INFO eval :: name: "disk_size", value: 27
2025-09-15 20:23:01.894 wdl.w:ptcp.w:call-trgt-28.t:call-trgt_genotype INFO eval :: name: "karyotype", value: "XX"
2025-09-15 20:23:01.895 wdl.w:ptcp.w:call-trgt-28.t:call-trgt_genotype INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 8, memory_reservation: 16000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:23:01.895 wdl.w:ptcp.w:call-trgt-28.t:call-trgt_genotype WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:23:01.895 wdl.w:ptcp.w:call-trgt-28.t:call-trgt_genotype INFO provisioned :: seconds_waited: 0, cpu: 8, mem_bytes: 16000000000
2025-09-15 20:23:01.896 wdl.w:ptcp.w:call-trgt-28.t:call-trgt_genotype INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:23:01.909 wdl.w:ptcp.w:call-sawfish-28.t:call-run_sawfish NOTICE slurm_singularity run :: pid: 1198770, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-28/call-run_sawfish/slurm_singularity.log.txt"
2025-09-15 20:23:01.909 wdl.w:ptcp.w:call-trgt-28.t:call-get_reads_overlapping_repeats NOTICE slurm_singularity run :: pid: 1198769, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-28/call-get_reads_overlapping_repeats/slurm_singularity.log.txt"
2025-09-15 20:23:01.912 wdl.w:ptcp.w:call-paraphase-10.t:call-run_paraphase INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:23:01.913 wdl.w:ptcp.w:call-paraphase-10.t:call-run_paraphase INFO input :: name: "annotation_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf"
2025-09-15 20:23:01.913 wdl.w:ptcp.w:call-paraphase-10.t:call-run_paraphase INFO input :: name: "genome_version", value: "38"
2025-09-15 20:23:01.913 wdl.w:ptcp.w:call-paraphase-10.t:call-run_paraphase INFO input :: name: "config_file", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/paraphase_config.GRCh38.yaml"
2025-09-15 20:23:01.913 wdl.w:ptcp.w:call-paraphase-10.t:call-run_paraphase INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:23:01.913 wdl.w:ptcp.w:call-paraphase-10.t:call-run_paraphase INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:23:01.913 wdl.w:ptcp.w:call-paraphase-10.t:call-run_paraphase INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2107.mapped.bam.bai"
2025-09-15 20:23:01.913 wdl.w:ptcp.w:call-paraphase-10.t:call-run_paraphase INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2107.mapped.bam"
2025-09-15 20:23:01.913 wdl.w:ptcp.w:call-paraphase-10.t:call-run_paraphase INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2107"
2025-09-15 20:23:01.914 wdl.w:ptcp.w:call-paraphase-10.t:call-run_paraphase INFO eval :: name: "threads", value: 4
2025-09-15 20:23:01.914 wdl.w:ptcp.w:call-paraphase-10.t:call-run_paraphase INFO eval :: name: "mem_gb", value: 8
2025-09-15 20:23:01.914 wdl.w:ptcp.w:call-paraphase-10.t:call-run_paraphase INFO eval :: name: "disk_size", value: 27
2025-09-15 20:23:01.915 wdl.w:ptcp.w:call-paraphase-10.t:call-run_paraphase INFO eval :: name: "out_dir", value: "m84036_250809_035451_s4.bc2107_paraphase"
2025-09-15 20:23:01.915 wdl.w:ptcp.w:call-trgt-07.t:call-get_reads_overlapping_repeats NOTICE done
2025-09-15 20:23:01.915 wdl.w:ptcp.w:call-paraphase-10.t:call-run_paraphase INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 4, memory_reservation: 8000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:23:01.916 wdl.w:ptcp.w:call-paraphase-10.t:call-run_paraphase WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:23:01.916 wdl.w:ptcp.w:call-paraphase-10.t:call-run_paraphase INFO provisioned :: seconds_waited: 0, cpu: 4, mem_bytes: 8000000000
2025-09-15 20:23:01.916 wdl.w:ptcp.w:call-paraphase-10.t:call-run_paraphase INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:23:01.918 wdl.w:ptcp.w:call-sawfish-10.t:call-run_sawfish INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:23:01.918 wdl.w:ptcp.w:call-sawfish-10.t:call-run_sawfish INFO input :: name: "genome_version", value: "38"
2025-09-15 20:23:01.918 wdl.w:ptcp.w:call-sawfish-10.t:call-run_sawfish INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:23:01.918 wdl.w:ptcp.w:call-sawfish-10.t:call-run_sawfish INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:23:01.918 wdl.w:ptcp.w:call-sawfish-10.t:call-run_sawfish INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2107.mapped.bam.bai"
2025-09-15 20:23:01.918 wdl.w:ptcp.w:call-sawfish-10.t:call-run_sawfish INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2107.mapped.bam"
2025-09-15 20:23:01.918 wdl.w:ptcp.w:call-sawfish-10.t:call-run_sawfish INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2107"
2025-09-15 20:23:01.918 wdl.w:ptcp.w:call-sawfish-10.t:call-run_sawfish INFO eval :: name: "mem_gb", value: 32
2025-09-15 20:23:01.918 wdl.w:ptcp.w:call-sawfish-10.t:call-run_sawfish INFO eval :: name: "threads", value: 16
2025-09-15 20:23:01.918 wdl.w:ptcp.w:call-sawfish-10.t:call-run_sawfish INFO eval :: name: "disk_size", value: 30
2025-09-15 20:23:01.919 wdl.w:ptcp.w:call-sawfish-10.t:call-run_sawfish INFO eval :: name: "discover_dirname", value: "m84036_250809_035451_s4.bc2107_sawfish_discover"
2025-09-15 20:23:01.919 wdl.w:ptcp.w:call-sawfish-10.t:call-run_sawfish INFO eval :: name: "call_dirname", value: "m84036_250809_035451_s4.bc2107_sawfish"
2025-09-15 20:23:01.919 wdl.w:ptcp.w:call-sawfish-10.t:call-run_sawfish INFO eval :: name: "minimap2_bam_filename", value: "m84036_250809_035451_s4.bc2107.minimap2.bam"
2025-09-15 20:23:01.919 wdl.w:ptcp.w:call-sawfish-10.t:call-run_sawfish INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 16, memory_reservation: 32000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:23:01.919 wdl.w:ptcp.w:call-sawfish-10.t:call-run_sawfish WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:23:01.920 wdl.w:ptcp.w:call-sawfish-10.t:call-run_sawfish INFO provisioned :: seconds_waited: 0, cpu: 16, mem_bytes: 32000000000
2025-09-15 20:23:01.920 wdl.w:ptcp.w:call-sawfish-10.t:call-run_sawfish INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:23:01.921 wdl.w:ptcp.w:call-trgt-07 NOTICE finish :: job: "call-get_reads_overlapping_repeats"
2025-09-15 20:23:01.921 wdl.w:ptcp.w:call-trgt-07 INFO output :: job: "call-get_reads_overlapping_repeats", values: {"reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-07/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2104.repeats.bam.bai", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-07/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2104.repeats.bam"}
2025-09-15 20:23:01.921 wdl.w:ptcp.w:call-trgt-07 INFO visit :: node: "output-reads_overlapping_repeats", values: {"reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-07/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2104.repeats.bam"}
2025-09-15 20:23:01.921 wdl.w:ptcp.w:call-trgt-07 INFO visit :: node: "output-reads_overlapping_repeats_bai", values: {"reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-07/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2104.repeats.bam.bai"}
2025-09-15 20:23:01.929 wdl.w:ptcp.w:call-sawfish-18.t:call-run_sawfish NOTICE task setup :: name: "run_sawfish", source: "./sawfish.wdl", line: 83, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-18/call-run_sawfish", thread: 140612514862656
2025-09-15 20:23:01.955 wdl.w:ptcp.w:call-sawfish-18.t:call-run_sawfish INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:23:01.955 wdl.w:ptcp.w:call-sawfish-18.t:call-run_sawfish INFO input :: name: "genome_version", value: "38"
2025-09-15 20:23:01.955 wdl.w:ptcp.w:call-sawfish-18.t:call-run_sawfish INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:23:01.955 wdl.w:ptcp.w:call-sawfish-18.t:call-run_sawfish INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:23:01.955 wdl.w:ptcp.w:call-sawfish-18.t:call-run_sawfish INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2115.mapped.bam.bai"
2025-09-15 20:23:01.955 wdl.w:ptcp.w:call-sawfish-18.t:call-run_sawfish INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2115.mapped.bam"
2025-09-15 20:23:01.955 wdl.w:ptcp.w:call-sawfish-18.t:call-run_sawfish INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2115"
2025-09-15 20:23:01.955 wdl.w:ptcp.w:call-sawfish-18.t:call-run_sawfish INFO eval :: name: "mem_gb", value: 32
2025-09-15 20:23:01.956 wdl.w:ptcp.w:call-sawfish-18.t:call-run_sawfish INFO eval :: name: "threads", value: 16
2025-09-15 20:23:01.956 wdl.w:ptcp.w:call-sawfish-18.t:call-run_sawfish INFO eval :: name: "disk_size", value: 30
2025-09-15 20:23:01.956 wdl.w:ptcp.w:call-sawfish-18.t:call-run_sawfish INFO eval :: name: "discover_dirname", value: "m84036_250809_035451_s4.bc2115_sawfish_discover"
2025-09-15 20:23:01.956 wdl.w:ptcp.w:call-sawfish-18.t:call-run_sawfish INFO eval :: name: "call_dirname", value: "m84036_250809_035451_s4.bc2115_sawfish"
2025-09-15 20:23:01.956 wdl.w:ptcp.w:call-sawfish-18.t:call-run_sawfish INFO eval :: name: "minimap2_bam_filename", value: "m84036_250809_035451_s4.bc2115.minimap2.bam"
2025-09-15 20:23:01.956 wdl.w:ptcp.w:call-sawfish-18.t:call-run_sawfish INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 16, memory_reservation: 32000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:23:01.957 wdl.w:ptcp.w:call-sawfish-18.t:call-run_sawfish WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:23:01.957 wdl.w:ptcp.w:call-sawfish-18.t:call-run_sawfish INFO provisioned :: seconds_waited: 0, cpu: 16, mem_bytes: 32000000000
2025-09-15 20:23:01.957 wdl.w:ptcp.w:call-sawfish-18.t:call-run_sawfish INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:23:01.977 wdl.w:ptcp.w:call-trgt-28.t:call-trgt_genotype INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 11, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-28/call-trgt_genotype/_singularity_tmpdir_28vvv39z"
2025-09-15 20:23:01.977 wdl.w:ptcp.w:call-trgt-28.t:call-trgt_genotype INFO Slurm invocation: srun --job-name call-trgt_genotype --partition compute,compute9 --cpus-per-task 8 --mem 15259M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-28/call-trgt_genotype/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-28/call-trgt_genotype/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-28/call-trgt_genotype/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-28/call-trgt_genotype/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-28/out/m84036_250809_035451_s4.bc2125.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2125.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-28/out/m84036_250809_035451_s4.bc2125.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2125.mapped.bam.bai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-28/call-trgt_genotype/_singularity_tmpdir_28vvv39z/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-28/call-trgt_genotype/_singularity_tmpdir_28vvv39z/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:23:02.008 wdl.w:ptcp.w:call-trgt-28.t:call-trgt_genotype NOTICE slurm_singularity run :: pid: 1198773, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-28/call-trgt_genotype/slurm_singularity.log.txt"
2025-09-15 20:23:02.012 wdl.w:ptcp.w:call-sawfish-10.t:call-run_sawfish INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 10, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-10/call-run_sawfish/_singularity_tmpdir_q3d5_6iw"
2025-09-15 20:23:02.012 wdl.w:ptcp.w:call-sawfish-10.t:call-run_sawfish INFO Slurm invocation: srun --job-name call-run_sawfish --partition compute,compute9 --cpus-per-task 16 --mem 30518M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-10/call-run_sawfish/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-10/call-run_sawfish/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-10/call-run_sawfish/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-10/call-run_sawfish/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-10/out/m84036_250809_035451_s4.bc2107.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2107.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-10/out/m84036_250809_035451_s4.bc2107.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2107.mapped.bam:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-10/call-run_sawfish/_singularity_tmpdir_q3d5_6iw/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-10/call-run_sawfish/_singularity_tmpdir_q3d5_6iw/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:23:02.020 wdl.w:ptcp.w:call-sawfish-10.t:call-run_sawfish NOTICE slurm_singularity run :: pid: 1198774, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-10/call-run_sawfish/slurm_singularity.log.txt"
2025-09-15 20:23:02.024 wdl.w:ptcp.w:call-paraphase-10.t:call-run_paraphase INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-10/call-run_paraphase/_singularity_tmpdir_h1aob4y0"
2025-09-15 20:23:02.024 wdl.w:ptcp.w:call-paraphase-10.t:call-run_paraphase INFO Slurm invocation: srun --job-name call-run_paraphase --partition compute,compute9 --cpus-per-task 4 --mem 7629M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-10/call-run_paraphase/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-10/call-run_paraphase/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-10/call-run_paraphase/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-10/call-run_paraphase/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/variant_list/variant_list.GRCh38.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-10/out/m84036_250809_035451_s4.bc2107.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2107.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-10/out/m84036_250809_035451_s4.bc2107.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2107.mapped.bam:ro --bind /ptcp/meta/paraphase/paraphase_config.GRCh38.yaml:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/paraphase_config.GRCh38.yaml:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-10/call-run_paraphase/_singularity_tmpdir_h1aob4y0/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-10/call-run_paraphase/_singularity_tmpdir_h1aob4y0/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:23:02.033 wdl.w:ptcp.w:call-paraphase-10.t:call-run_paraphase NOTICE slurm_singularity run :: pid: 1198776, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-10/call-run_paraphase/slurm_singularity.log.txt"
2025-09-15 20:23:02.038 wdl.w:ptcp.w:call-sawfish-18.t:call-run_sawfish INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 10, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-18/call-run_sawfish/_singularity_tmpdir_v7n4prci"
2025-09-15 20:23:02.038 wdl.w:ptcp.w:call-sawfish-18.t:call-run_sawfish INFO Slurm invocation: srun --job-name call-run_sawfish --partition compute,compute9 --cpus-per-task 16 --mem 30518M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-18/call-run_sawfish/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-18/call-run_sawfish/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-18/call-run_sawfish/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-18/call-run_sawfish/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-18/out/m84036_250809_035451_s4.bc2115.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2115.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-18/out/m84036_250809_035451_s4.bc2115.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2115.mapped.bam:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-18/call-run_sawfish/_singularity_tmpdir_v7n4prci/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-18/call-run_sawfish/_singularity_tmpdir_v7n4prci/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:23:02.047 wdl.w:ptcp.w:call-sawfish-18.t:call-run_sawfish NOTICE slurm_singularity run :: pid: 1198778, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-18/call-run_sawfish/slurm_singularity.log.txt"
2025-09-15 20:23:02.105 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_genotype INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2104.trgt.vcf"
2025-09-15 20:23:02.107 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_genotype INFO output :: name: "spanning_bam", value: "m84036_250809_035451_s4.bc2104.trgt.sorted.spanning.bam"
2025-09-15 20:23:02.108 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_genotype INFO output :: name: "spanning_bam_bai", value: "m84036_250809_035451_s4.bc2104.trgt.sorted.spanning.bam.bai"
2025-09-15 20:23:02.185 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_genotype NOTICE done
2025-09-15 20:23:02.189 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_genotype INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2131.trgt.vcf"
2025-09-15 20:23:02.192 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_genotype INFO output :: name: "spanning_bam", value: "m84036_250809_035451_s4.bc2131.trgt.sorted.spanning.bam"
2025-09-15 20:23:02.194 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_genotype INFO output :: name: "spanning_bam_bai", value: "m84036_250809_035451_s4.bc2131.trgt.sorted.spanning.bam.bai"
2025-09-15 20:23:02.196 wdl.w:ptcp.w:call-trgt-07 NOTICE finish :: job: "call-trgt_genotype"
2025-09-15 20:23:02.196 wdl.w:ptcp.w:call-trgt-07 INFO output :: job: "call-trgt_genotype", values: {"spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-07/call-trgt_genotype/out/m84036_250809_035451_s4.bc2104.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-07/call-trgt_genotype/out/m84036_250809_035451_s4.bc2104.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-07/call-trgt_genotype/out/m84036_250809_035451_s4.bc2104.trgt.vcf"}
2025-09-15 20:23:02.197 wdl.w:ptcp.w:call-trgt-07 NOTICE ready :: job: "call-trgt_plot_meth_allele", callee: "trgt_plot"
2025-09-15 20:23:02.197 wdl.w:ptcp.w:call-trgt-07 INFO input :: job: "call-trgt_plot_meth_allele", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": false, "methylation": true, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-07/call-trgt_genotype/out/m84036_250809_035451_s4.bc2104.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-07/call-trgt_genotype/out/m84036_250809_035451_s4.bc2104.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-07/call-trgt_genotype/out/m84036_250809_035451_s4.bc2104.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2104"}
2025-09-15 20:23:02.199 wdl.w:ptcp.w:call-trgt-07 NOTICE ready :: job: "call-trgt_plot_meth_waterfall", callee: "trgt_plot"
2025-09-15 20:23:02.199 wdl.w:ptcp.w:call-trgt-07 INFO input :: job: "call-trgt_plot_meth_waterfall", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": true, "methylation": true, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-07/call-trgt_genotype/out/m84036_250809_035451_s4.bc2104.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-07/call-trgt_genotype/out/m84036_250809_035451_s4.bc2104.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-07/call-trgt_genotype/out/m84036_250809_035451_s4.bc2104.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2104"}
2025-09-15 20:23:02.200 wdl.w:ptcp.w:call-trgt-07 NOTICE ready :: job: "call-trgt_plot_motifs_allele", callee: "trgt_plot"
2025-09-15 20:23:02.200 wdl.w:ptcp.w:call-trgt-07 INFO input :: job: "call-trgt_plot_motifs_allele", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": false, "methylation": false, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-07/call-trgt_genotype/out/m84036_250809_035451_s4.bc2104.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-07/call-trgt_genotype/out/m84036_250809_035451_s4.bc2104.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-07/call-trgt_genotype/out/m84036_250809_035451_s4.bc2104.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2104"}
2025-09-15 20:23:02.200 wdl.w:ptcp.w:call-trgt-07 NOTICE ready :: job: "call-trgt_plot_motifs_waterfall", callee: "trgt_plot"
2025-09-15 20:23:02.200 wdl.w:ptcp.w:call-trgt-07 INFO input :: job: "call-trgt_plot_motifs_waterfall", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": true, "methylation": false, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-07/call-trgt_genotype/out/m84036_250809_035451_s4.bc2104.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-07/call-trgt_genotype/out/m84036_250809_035451_s4.bc2104.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-07/call-trgt_genotype/out/m84036_250809_035451_s4.bc2104.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2104"}
2025-09-15 20:23:02.201 wdl.w:ptcp.w:call-trgt-07 INFO visit :: node: "output-spanning_bam", values: {"spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-07/call-trgt_genotype/out/m84036_250809_035451_s4.bc2104.trgt.sorted.spanning.bam"}
2025-09-15 20:23:02.201 wdl.w:ptcp.w:call-trgt-07 INFO visit :: node: "output-spanning_bam_bai", values: {"spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-07/call-trgt_genotype/out/m84036_250809_035451_s4.bc2104.trgt.sorted.spanning.bam.bai"}
2025-09-15 20:23:02.201 wdl.w:ptcp.w:call-trgt-07 INFO visit :: node: "output-vcf", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-07/call-trgt_genotype/out/m84036_250809_035451_s4.bc2104.trgt.vcf"}
2025-09-15 20:23:02.204 wdl.w:ptcp.w:call-trgt-10.t:call-get_reads_overlapping_repeats NOTICE task setup :: name: "get_reads_overlapping_repeats", source: "./trgt.wdl", line: 182, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-10/call-get_reads_overlapping_repeats", thread: 140612506469952
2025-09-15 20:23:02.212 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_genotype INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2120.trgt.vcf"
2025-09-15 20:23:02.217 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_genotype INFO output :: name: "spanning_bam", value: "m84036_250809_035451_s4.bc2120.trgt.sorted.spanning.bam"
2025-09-15 20:23:02.219 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_genotype INFO output :: name: "spanning_bam_bai", value: "m84036_250809_035451_s4.bc2120.trgt.sorted.spanning.bam.bai"
2025-09-15 20:23:02.232 wdl.w:ptcp.w:call-trgt-10.t:call-get_reads_overlapping_repeats INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:23:02.232 wdl.w:ptcp.w:call-trgt-10.t:call-get_reads_overlapping_repeats INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:23:02.232 wdl.w:ptcp.w:call-trgt-10.t:call-get_reads_overlapping_repeats INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2107.mapped.bam.bai"
2025-09-15 20:23:02.232 wdl.w:ptcp.w:call-trgt-10.t:call-get_reads_overlapping_repeats INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2107.mapped.bam"
2025-09-15 20:23:02.232 wdl.w:ptcp.w:call-trgt-10.t:call-get_reads_overlapping_repeats INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2107"
2025-09-15 20:23:02.232 wdl.w:ptcp.w:call-trgt-10.t:call-get_reads_overlapping_repeats INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:23:02.232 wdl.w:ptcp.w:call-trgt-10.t:call-get_reads_overlapping_repeats INFO eval :: name: "expand_size", value: 3000
2025-09-15 20:23:02.233 wdl.w:ptcp.w:call-trgt-10.t:call-get_reads_overlapping_repeats INFO eval :: name: "threads", value: 1
2025-09-15 20:23:02.233 wdl.w:ptcp.w:call-trgt-10.t:call-get_reads_overlapping_repeats INFO eval :: name: "expanded_bed_name", value: "m84036_250809_035451_s4.bc2107.expanded.bed"
2025-09-15 20:23:02.233 wdl.w:ptcp.w:call-trgt-10.t:call-get_reads_overlapping_repeats INFO eval :: name: "disk_size", value: 11
2025-09-15 20:23:02.233 wdl.w:ptcp.w:call-trgt-10.t:call-get_reads_overlapping_repeats INFO eval :: name: "output_name", value: "m84036_250809_035451_s4.bc2107.repeats.bam"
2025-09-15 20:23:02.233 wdl.w:ptcp.w:call-trgt-10.t:call-get_reads_overlapping_repeats INFO eval :: name: "index_name", value: "m84036_250809_035451_s4.bc2107.repeats.bam.bai"
2025-09-15 20:23:02.233 wdl.w:ptcp.w:call-trgt-10.t:call-get_reads_overlapping_repeats INFO eval :: name: "output_name_with_index", value: "m84036_250809_035451_s4.bc2107.repeats.bam##idx##m84036_250809_035451_s4.bc2107.repeats.bam.bai"
2025-09-15 20:23:02.233 wdl.w:ptcp.w:call-trgt-10.t:call-get_reads_overlapping_repeats INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:23:02.234 wdl.w:ptcp.w:call-trgt-10.t:call-get_reads_overlapping_repeats WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:23:02.234 wdl.w:ptcp.w:call-trgt-10.t:call-get_reads_overlapping_repeats INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:23:02.234 wdl.w:ptcp.w:call-trgt-10.t:call-get_reads_overlapping_repeats INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:23:02.285 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_genotype NOTICE done
2025-09-15 20:23:02.288 wdl.w:ptcp.w:call-trgt-10.t:call-get_reads_overlapping_repeats INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 9, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-10/call-get_reads_overlapping_repeats/_singularity_tmpdir_5bzr6eas"
2025-09-15 20:23:02.288 wdl.w:ptcp.w:call-trgt-10.t:call-get_reads_overlapping_repeats INFO Slurm invocation: srun --job-name call-get_reads_overlapping_repeats --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-10/call-get_reads_overlapping_repeats/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-10/call-get_reads_overlapping_repeats/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-10/call-get_reads_overlapping_repeats/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-10/call-get_reads_overlapping_repeats/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-10/out/m84036_250809_035451_s4.bc2107.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2107.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-10/out/m84036_250809_035451_s4.bc2107.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2107.mapped.bam:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-10/call-get_reads_overlapping_repeats/_singularity_tmpdir_5bzr6eas/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-10/call-get_reads_overlapping_repeats/_singularity_tmpdir_5bzr6eas/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:23:02.290 wdl.w:ptcp.w:call-trgt-34 NOTICE finish :: job: "call-trgt_genotype"
2025-09-15 20:23:02.297 wdl.w:ptcp.w:call-trgt-34 INFO output :: job: "call-trgt_genotype", values: {"spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-34/call-trgt_genotype/out/m84036_250809_035451_s4.bc2131.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-34/call-trgt_genotype/out/m84036_250809_035451_s4.bc2131.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-34/call-trgt_genotype/out/m84036_250809_035451_s4.bc2131.trgt.vcf"}
2025-09-15 20:23:02.298 wdl.w:ptcp.w:call-trgt-34 NOTICE ready :: job: "call-trgt_plot_meth_allele", callee: "trgt_plot"
2025-09-15 20:23:02.298 wdl.w:ptcp.w:call-trgt-34 INFO input :: job: "call-trgt_plot_meth_allele", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": false, "methylation": true, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-34/call-trgt_genotype/out/m84036_250809_035451_s4.bc2131.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-34/call-trgt_genotype/out/m84036_250809_035451_s4.bc2131.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-34/call-trgt_genotype/out/m84036_250809_035451_s4.bc2131.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2131"}
2025-09-15 20:23:02.298 wdl.w:ptcp.w:call-trgt-18.t:call-get_reads_overlapping_repeats NOTICE task setup :: name: "get_reads_overlapping_repeats", source: "./trgt.wdl", line: 182, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-18/call-get_reads_overlapping_repeats", thread: 140611961206336
2025-09-15 20:23:02.300 wdl.w:ptcp.w:call-trgt-34 NOTICE ready :: job: "call-trgt_plot_meth_waterfall", callee: "trgt_plot"
2025-09-15 20:23:02.300 wdl.w:ptcp.w:call-trgt-34 INFO input :: job: "call-trgt_plot_meth_waterfall", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": true, "methylation": true, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-34/call-trgt_genotype/out/m84036_250809_035451_s4.bc2131.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-34/call-trgt_genotype/out/m84036_250809_035451_s4.bc2131.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-34/call-trgt_genotype/out/m84036_250809_035451_s4.bc2131.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2131"}
2025-09-15 20:23:02.301 wdl.w:ptcp.w:call-trgt-34 NOTICE ready :: job: "call-trgt_plot_motifs_allele", callee: "trgt_plot"
2025-09-15 20:23:02.301 wdl.w:ptcp.w:call-trgt-34 INFO input :: job: "call-trgt_plot_motifs_allele", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": false, "methylation": false, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-34/call-trgt_genotype/out/m84036_250809_035451_s4.bc2131.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-34/call-trgt_genotype/out/m84036_250809_035451_s4.bc2131.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-34/call-trgt_genotype/out/m84036_250809_035451_s4.bc2131.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2131"}
2025-09-15 20:23:02.302 wdl.w:ptcp.w:call-trgt-34 NOTICE ready :: job: "call-trgt_plot_motifs_waterfall", callee: "trgt_plot"
2025-09-15 20:23:02.302 wdl.w:ptcp.w:call-trgt-34 INFO input :: job: "call-trgt_plot_motifs_waterfall", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": true, "methylation": false, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-34/call-trgt_genotype/out/m84036_250809_035451_s4.bc2131.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-34/call-trgt_genotype/out/m84036_250809_035451_s4.bc2131.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-34/call-trgt_genotype/out/m84036_250809_035451_s4.bc2131.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2131"}
2025-09-15 20:23:02.302 wdl.w:ptcp.w:call-trgt-34 INFO visit :: node: "output-spanning_bam", values: {"spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-34/call-trgt_genotype/out/m84036_250809_035451_s4.bc2131.trgt.sorted.spanning.bam"}
2025-09-15 20:23:02.302 wdl.w:ptcp.w:call-trgt-34 INFO visit :: node: "output-spanning_bam_bai", values: {"spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-34/call-trgt_genotype/out/m84036_250809_035451_s4.bc2131.trgt.sorted.spanning.bam.bai"}
2025-09-15 20:23:02.302 wdl.w:ptcp.w:call-trgt-34 INFO visit :: node: "output-vcf", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-34/call-trgt_genotype/out/m84036_250809_035451_s4.bc2131.trgt.vcf"}
2025-09-15 20:23:02.309 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_genotype NOTICE done
2025-09-15 20:23:02.312 wdl.w:ptcp.w:call-trgt-10.t:call-get_reads_overlapping_repeats NOTICE slurm_singularity run :: pid: 1198784, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-10/call-get_reads_overlapping_repeats/slurm_singularity.log.txt"
2025-09-15 20:23:02.315 wdl.w:ptcp.w:call-trgt-23 NOTICE finish :: job: "call-trgt_genotype"
2025-09-15 20:23:02.315 wdl.w:ptcp.w:call-trgt-23 INFO output :: job: "call-trgt_genotype", values: {"spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-23/call-trgt_genotype/out/m84036_250809_035451_s4.bc2120.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-23/call-trgt_genotype/out/m84036_250809_035451_s4.bc2120.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-23/call-trgt_genotype/out/m84036_250809_035451_s4.bc2120.trgt.vcf"}
2025-09-15 20:23:02.316 wdl.w:ptcp.w:call-trgt-23 NOTICE ready :: job: "call-trgt_plot_meth_allele", callee: "trgt_plot"
2025-09-15 20:23:02.316 wdl.w:ptcp.w:call-trgt-23 INFO input :: job: "call-trgt_plot_meth_allele", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": false, "methylation": true, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-23/call-trgt_genotype/out/m84036_250809_035451_s4.bc2120.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-23/call-trgt_genotype/out/m84036_250809_035451_s4.bc2120.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-23/call-trgt_genotype/out/m84036_250809_035451_s4.bc2120.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2120"}
2025-09-15 20:23:02.320 wdl.w:ptcp.w:call-trgt-23 NOTICE ready :: job: "call-trgt_plot_meth_waterfall", callee: "trgt_plot"
2025-09-15 20:23:02.320 wdl.w:ptcp.w:call-trgt-23 INFO input :: job: "call-trgt_plot_meth_waterfall", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": true, "methylation": true, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-23/call-trgt_genotype/out/m84036_250809_035451_s4.bc2120.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-23/call-trgt_genotype/out/m84036_250809_035451_s4.bc2120.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-23/call-trgt_genotype/out/m84036_250809_035451_s4.bc2120.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2120"}
2025-09-15 20:23:02.320 wdl.w:ptcp.w:call-trgt-23 NOTICE ready :: job: "call-trgt_plot_motifs_allele", callee: "trgt_plot"
2025-09-15 20:23:02.320 wdl.w:ptcp.w:call-trgt-23 INFO input :: job: "call-trgt_plot_motifs_allele", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": false, "methylation": false, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-23/call-trgt_genotype/out/m84036_250809_035451_s4.bc2120.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-23/call-trgt_genotype/out/m84036_250809_035451_s4.bc2120.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-23/call-trgt_genotype/out/m84036_250809_035451_s4.bc2120.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2120"}
2025-09-15 20:23:02.321 wdl.w:ptcp.w:call-trgt-23 NOTICE ready :: job: "call-trgt_plot_motifs_waterfall", callee: "trgt_plot"
2025-09-15 20:23:02.321 wdl.w:ptcp.w:call-trgt-18.t:call-get_reads_overlapping_repeats INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:23:02.321 wdl.w:ptcp.w:call-trgt-23 INFO input :: job: "call-trgt_plot_motifs_waterfall", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": true, "methylation": false, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-23/call-trgt_genotype/out/m84036_250809_035451_s4.bc2120.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-23/call-trgt_genotype/out/m84036_250809_035451_s4.bc2120.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-23/call-trgt_genotype/out/m84036_250809_035451_s4.bc2120.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2120"}
2025-09-15 20:23:02.322 wdl.w:ptcp.w:call-trgt-18.t:call-get_reads_overlapping_repeats INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:23:02.322 wdl.w:ptcp.w:call-trgt-18.t:call-get_reads_overlapping_repeats INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2115.mapped.bam.bai"
2025-09-15 20:23:02.322 wdl.w:ptcp.w:call-trgt-18.t:call-get_reads_overlapping_repeats INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2115.mapped.bam"
2025-09-15 20:23:02.322 wdl.w:ptcp.w:call-trgt-18.t:call-get_reads_overlapping_repeats INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2115"
2025-09-15 20:23:02.323 wdl.w:ptcp.w:call-trgt-18.t:call-get_reads_overlapping_repeats INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:23:02.323 wdl.w:ptcp.w:call-trgt-23 INFO visit :: node: "output-spanning_bam", values: {"spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-23/call-trgt_genotype/out/m84036_250809_035451_s4.bc2120.trgt.sorted.spanning.bam"}
2025-09-15 20:23:02.322 wdl.w:ptcp.w:call-paraphase-18.t:call-run_paraphase NOTICE task setup :: name: "run_paraphase", source: "./paraphase.wdl", line: 127, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-18/call-run_paraphase", thread: 140613605389888
2025-09-15 20:23:02.323 wdl.w:ptcp.w:call-trgt-18.t:call-get_reads_overlapping_repeats INFO eval :: name: "expand_size", value: 3000
2025-09-15 20:23:02.323 wdl.w:ptcp.w:call-trgt-23 INFO visit :: node: "output-spanning_bam_bai", values: {"spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-23/call-trgt_genotype/out/m84036_250809_035451_s4.bc2120.trgt.sorted.spanning.bam.bai"}
2025-09-15 20:23:02.323 wdl.w:ptcp.w:call-trgt-18.t:call-get_reads_overlapping_repeats INFO eval :: name: "threads", value: 1
2025-09-15 20:23:02.324 wdl.w:ptcp.w:call-trgt-23 INFO visit :: node: "output-vcf", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-23/call-trgt_genotype/out/m84036_250809_035451_s4.bc2120.trgt.vcf"}
2025-09-15 20:23:02.324 wdl.w:ptcp.w:call-trgt-18.t:call-get_reads_overlapping_repeats INFO eval :: name: "expanded_bed_name", value: "m84036_250809_035451_s4.bc2115.expanded.bed"
2025-09-15 20:23:02.324 wdl.w:ptcp.w:call-trgt-18.t:call-get_reads_overlapping_repeats INFO eval :: name: "disk_size", value: 11
2025-09-15 20:23:02.324 wdl.w:ptcp.w:call-trgt-18.t:call-get_reads_overlapping_repeats INFO eval :: name: "output_name", value: "m84036_250809_035451_s4.bc2115.repeats.bam"
2025-09-15 20:23:02.324 wdl.w:ptcp.w:call-trgt-18.t:call-get_reads_overlapping_repeats INFO eval :: name: "index_name", value: "m84036_250809_035451_s4.bc2115.repeats.bam.bai"
2025-09-15 20:23:02.324 wdl.w:ptcp.w:call-trgt-18.t:call-get_reads_overlapping_repeats INFO eval :: name: "output_name_with_index", value: "m84036_250809_035451_s4.bc2115.repeats.bam##idx##m84036_250809_035451_s4.bc2115.repeats.bam.bai"
2025-09-15 20:23:02.325 wdl.w:ptcp.w:call-trgt-18.t:call-get_reads_overlapping_repeats INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:23:02.325 wdl.w:ptcp.w:call-trgt-18.t:call-get_reads_overlapping_repeats WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:23:02.325 wdl.w:ptcp.w:call-trgt-18.t:call-get_reads_overlapping_repeats INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:23:02.326 wdl.w:ptcp.w:call-trgt-18.t:call-get_reads_overlapping_repeats INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:23:02.341 wdl.w:ptcp.w:call-paraphase-18.t:call-run_paraphase INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:23:02.341 wdl.w:ptcp.w:call-paraphase-18.t:call-run_paraphase INFO input :: name: "annotation_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf"
2025-09-15 20:23:02.341 wdl.w:ptcp.w:call-paraphase-18.t:call-run_paraphase INFO input :: name: "genome_version", value: "38"
2025-09-15 20:23:02.341 wdl.w:ptcp.w:call-paraphase-18.t:call-run_paraphase INFO input :: name: "config_file", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/paraphase_config.GRCh38.yaml"
2025-09-15 20:23:02.341 wdl.w:ptcp.w:call-paraphase-18.t:call-run_paraphase INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:23:02.341 wdl.w:ptcp.w:call-paraphase-18.t:call-run_paraphase INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:23:02.342 wdl.w:ptcp.w:call-paraphase-18.t:call-run_paraphase INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2115.mapped.bam.bai"
2025-09-15 20:23:02.342 wdl.w:ptcp.w:call-paraphase-18.t:call-run_paraphase INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2115.mapped.bam"
2025-09-15 20:23:02.342 wdl.w:ptcp.w:call-paraphase-18.t:call-run_paraphase INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2115"
2025-09-15 20:23:02.342 wdl.w:ptcp.w:call-paraphase-18.t:call-run_paraphase INFO eval :: name: "threads", value: 4
2025-09-15 20:23:02.342 wdl.w:ptcp.w:call-paraphase-18.t:call-run_paraphase INFO eval :: name: "mem_gb", value: 8
2025-09-15 20:23:02.342 wdl.w:ptcp.w:call-paraphase-18.t:call-run_paraphase INFO eval :: name: "disk_size", value: 27
2025-09-15 20:23:02.342 wdl.w:ptcp.w:call-paraphase-18.t:call-run_paraphase INFO eval :: name: "out_dir", value: "m84036_250809_035451_s4.bc2115_paraphase"
2025-09-15 20:23:02.343 wdl.w:ptcp.w:call-paraphase-18.t:call-run_paraphase INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 4, memory_reservation: 8000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:23:02.343 wdl.w:ptcp.w:call-paraphase-18.t:call-run_paraphase WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:23:02.343 wdl.w:ptcp.w:call-paraphase-18.t:call-run_paraphase INFO provisioned :: seconds_waited: 0, cpu: 4, mem_bytes: 8000000000
2025-09-15 20:23:02.343 wdl.w:ptcp.w:call-paraphase-18.t:call-run_paraphase INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:23:02.369 wdl.w:ptcp.w:call-trgt-18.t:call-get_reads_overlapping_repeats INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 9, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-18/call-get_reads_overlapping_repeats/_singularity_tmpdir_kedi2n_p"
2025-09-15 20:23:02.369 wdl.w:ptcp.w:call-trgt-18.t:call-get_reads_overlapping_repeats INFO Slurm invocation: srun --job-name call-get_reads_overlapping_repeats --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-18/call-get_reads_overlapping_repeats/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-18/call-get_reads_overlapping_repeats/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-18/call-get_reads_overlapping_repeats/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-18/call-get_reads_overlapping_repeats/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-18/out/m84036_250809_035451_s4.bc2115.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2115.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-18/out/m84036_250809_035451_s4.bc2115.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2115.mapped.bam:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-18/call-get_reads_overlapping_repeats/_singularity_tmpdir_kedi2n_p/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-18/call-get_reads_overlapping_repeats/_singularity_tmpdir_kedi2n_p/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:23:02.382 wdl.w:ptcp.w:call-trgt-18.t:call-get_reads_overlapping_repeats NOTICE slurm_singularity run :: pid: 1198799, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-18/call-get_reads_overlapping_repeats/slurm_singularity.log.txt"
2025-09-15 20:23:02.401 wdl.w:ptcp.w:call-paraphase-18.t:call-run_paraphase INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-18/call-run_paraphase/_singularity_tmpdir_agm_y6_k"
2025-09-15 20:23:02.401 wdl.w:ptcp.w:call-paraphase-18.t:call-run_paraphase INFO Slurm invocation: srun --job-name call-run_paraphase --partition compute,compute9 --cpus-per-task 4 --mem 7629M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-18/call-run_paraphase/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-18/call-run_paraphase/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-18/call-run_paraphase/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-18/call-run_paraphase/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-18/out/m84036_250809_035451_s4.bc2115.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2115.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-18/out/m84036_250809_035451_s4.bc2115.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2115.mapped.bam:ro --bind /ptcp/meta/variant_list/variant_list.GRCh38.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf:ro --bind /ptcp/meta/paraphase/paraphase_config.GRCh38.yaml:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/paraphase_config.GRCh38.yaml:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-18/call-run_paraphase/_singularity_tmpdir_agm_y6_k/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-18/call-run_paraphase/_singularity_tmpdir_agm_y6_k/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:23:02.411 wdl.w:ptcp.w:call-paraphase-18.t:call-run_paraphase NOTICE slurm_singularity run :: pid: 1198801, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-18/call-run_paraphase/slurm_singularity.log.txt"
2025-09-15 20:23:02.438 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_genotype INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2132.trgt.vcf"
2025-09-15 20:23:02.441 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_genotype INFO output :: name: "spanning_bam", value: "m84036_250809_035451_s4.bc2132.trgt.sorted.spanning.bam"
2025-09-15 20:23:02.442 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_genotype INFO output :: name: "spanning_bam_bai", value: "m84036_250809_035451_s4.bc2132.trgt.sorted.spanning.bam.bai"
2025-09-15 20:23:02.508 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_genotype NOTICE done
2025-09-15 20:23:02.521 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_genotype INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2111.trgt.vcf"
2025-09-15 20:23:02.524 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_genotype INFO output :: name: "spanning_bam", value: "m84036_250809_035451_s4.bc2111.trgt.sorted.spanning.bam"
2025-09-15 20:23:02.525 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_genotype INFO output :: name: "spanning_bam_bai", value: "m84036_250809_035451_s4.bc2111.trgt.sorted.spanning.bam.bai"
2025-09-15 20:23:02.567 wdl.w:ptcp.w:call-paraphase-26.t:call-run_paraphase.slurm_singularity INFO srun: job 51797359 queued and waiting for resources
2025-09-15 20:23:02.584 wdl.w:ptcp.w:call-trgt-35 NOTICE finish :: job: "call-trgt_genotype"
2025-09-15 20:23:02.585 wdl.w:ptcp.w:call-trgt-35 INFO output :: job: "call-trgt_genotype", values: {"spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-35/call-trgt_genotype/out/m84036_250809_035451_s4.bc2132.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-35/call-trgt_genotype/out/m84036_250809_035451_s4.bc2132.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-35/call-trgt_genotype/out/m84036_250809_035451_s4.bc2132.trgt.vcf"}
2025-09-15 20:23:02.585 wdl.w:ptcp.w:call-trgt-35 NOTICE ready :: job: "call-trgt_plot_meth_allele", callee: "trgt_plot"
2025-09-15 20:23:02.585 wdl.w:ptcp.w:call-trgt-35 INFO input :: job: "call-trgt_plot_meth_allele", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": false, "methylation": true, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-35/call-trgt_genotype/out/m84036_250809_035451_s4.bc2132.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-35/call-trgt_genotype/out/m84036_250809_035451_s4.bc2132.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-35/call-trgt_genotype/out/m84036_250809_035451_s4.bc2132.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2132"}
2025-09-15 20:23:02.586 wdl.w:ptcp.w:call-trgt-35 NOTICE ready :: job: "call-trgt_plot_meth_waterfall", callee: "trgt_plot"
2025-09-15 20:23:02.587 wdl.w:ptcp.w:call-trgt-35 INFO input :: job: "call-trgt_plot_meth_waterfall", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": true, "methylation": true, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-35/call-trgt_genotype/out/m84036_250809_035451_s4.bc2132.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-35/call-trgt_genotype/out/m84036_250809_035451_s4.bc2132.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-35/call-trgt_genotype/out/m84036_250809_035451_s4.bc2132.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2132"}
2025-09-15 20:23:02.587 wdl.w:ptcp.w:call-trgt-35 NOTICE ready :: job: "call-trgt_plot_motifs_allele", callee: "trgt_plot"
2025-09-15 20:23:02.587 wdl.w:ptcp.w:call-trgt-35 INFO input :: job: "call-trgt_plot_motifs_allele", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": false, "methylation": false, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-35/call-trgt_genotype/out/m84036_250809_035451_s4.bc2132.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-35/call-trgt_genotype/out/m84036_250809_035451_s4.bc2132.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-35/call-trgt_genotype/out/m84036_250809_035451_s4.bc2132.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2132"}
2025-09-15 20:23:02.588 wdl.w:ptcp.w:call-trgt-35 NOTICE ready :: job: "call-trgt_plot_motifs_waterfall", callee: "trgt_plot"
2025-09-15 20:23:02.588 wdl.w:ptcp.w:call-trgt-35 INFO input :: job: "call-trgt_plot_motifs_waterfall", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": true, "methylation": false, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-35/call-trgt_genotype/out/m84036_250809_035451_s4.bc2132.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-35/call-trgt_genotype/out/m84036_250809_035451_s4.bc2132.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-35/call-trgt_genotype/out/m84036_250809_035451_s4.bc2132.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2132"}
2025-09-15 20:23:02.589 wdl.w:ptcp.w:call-trgt-35 INFO visit :: node: "output-spanning_bam", values: {"spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-35/call-trgt_genotype/out/m84036_250809_035451_s4.bc2132.trgt.sorted.spanning.bam"}
2025-09-15 20:23:02.589 wdl.w:ptcp.w:call-trgt-35 INFO visit :: node: "output-spanning_bam_bai", values: {"spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-35/call-trgt_genotype/out/m84036_250809_035451_s4.bc2132.trgt.sorted.spanning.bam.bai"}
2025-09-15 20:23:02.589 wdl.w:ptcp.w:call-trgt-35 INFO visit :: node: "output-vcf", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-35/call-trgt_genotype/out/m84036_250809_035451_s4.bc2132.trgt.vcf"}
2025-09-15 20:23:02.590 wdl.w:ptcp.w:call-trgt-18.t:call-trgt_genotype NOTICE task setup :: name: "trgt_genotype", source: "./trgt.wdl", line: 272, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-18/call-trgt_genotype", thread: 140613838284352
2025-09-15 20:23:02.600 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_genotype NOTICE done
2025-09-15 20:23:02.606 wdl.w:ptcp.w:call-trgt-14 NOTICE finish :: job: "call-trgt_genotype"
2025-09-15 20:23:02.606 wdl.w:ptcp.w:call-trgt-14 INFO output :: job: "call-trgt_genotype", values: {"spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-14/call-trgt_genotype/out/m84036_250809_035451_s4.bc2111.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-14/call-trgt_genotype/out/m84036_250809_035451_s4.bc2111.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-14/call-trgt_genotype/out/m84036_250809_035451_s4.bc2111.trgt.vcf"}
2025-09-15 20:23:02.607 wdl.w:ptcp.w:call-trgt-14 NOTICE ready :: job: "call-trgt_plot_meth_allele", callee: "trgt_plot"
2025-09-15 20:23:02.607 wdl.w:ptcp.w:call-trgt-26.t:call-get_reads_overlapping_repeats.slurm_singularity INFO srun: job 51797360 queued and waiting for resources
2025-09-15 20:23:02.607 wdl.w:ptcp.w:call-trgt-14 INFO input :: job: "call-trgt_plot_meth_allele", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": false, "methylation": true, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-14/call-trgt_genotype/out/m84036_250809_035451_s4.bc2111.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-14/call-trgt_genotype/out/m84036_250809_035451_s4.bc2111.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-14/call-trgt_genotype/out/m84036_250809_035451_s4.bc2111.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2111"}
2025-09-15 20:23:02.608 wdl.w:ptcp.w:call-trgt-18.t:call-trgt_genotype INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:23:02.608 wdl.w:ptcp.w:call-trgt-18.t:call-trgt_genotype INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:23:02.608 wdl.w:ptcp.w:call-trgt-18.t:call-trgt_genotype INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:23:02.608 wdl.w:ptcp.w:call-trgt-18.t:call-trgt_genotype INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:23:02.608 wdl.w:ptcp.w:call-trgt-18.t:call-trgt_genotype INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2115.mapped.bam.bai"
2025-09-15 20:23:02.608 wdl.w:ptcp.w:call-trgt-18.t:call-trgt_genotype INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2115.mapped.bam"
2025-09-15 20:23:02.608 wdl.w:ptcp.w:call-trgt-18.t:call-trgt_genotype INFO input :: name: "sex", value: "F"
2025-09-15 20:23:02.608 wdl.w:ptcp.w:call-trgt-18.t:call-trgt_genotype INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2115"
2025-09-15 20:23:02.608 wdl.w:ptcp.w:call-trgt-18.t:call-trgt_genotype INFO eval :: name: "mem_gb", value: 16
2025-09-15 20:23:02.609 wdl.w:ptcp.w:call-trgt-18.t:call-trgt_genotype INFO eval :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2115.trgt"
2025-09-15 20:23:02.609 wdl.w:ptcp.w:call-trgt-18.t:call-trgt_genotype INFO eval :: name: "threads", value: 8
2025-09-15 20:23:02.609 wdl.w:ptcp.w:call-trgt-18.t:call-trgt_genotype INFO eval :: name: "disk_size", value: 27
2025-09-15 20:23:02.609 wdl.w:ptcp.w:call-trgt-18.t:call-trgt_genotype INFO eval :: name: "karyotype", value: "XX"
2025-09-15 20:23:02.610 wdl.w:ptcp.w:call-trgt-14 NOTICE ready :: job: "call-trgt_plot_meth_waterfall", callee: "trgt_plot"
2025-09-15 20:23:02.610 wdl.w:ptcp.w:call-trgt-14 INFO input :: job: "call-trgt_plot_meth_waterfall", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": true, "methylation": true, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-14/call-trgt_genotype/out/m84036_250809_035451_s4.bc2111.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-14/call-trgt_genotype/out/m84036_250809_035451_s4.bc2111.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-14/call-trgt_genotype/out/m84036_250809_035451_s4.bc2111.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2111"}
2025-09-15 20:23:02.610 wdl.w:ptcp.w:call-trgt-18.t:call-trgt_genotype INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 8, memory_reservation: 16000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:23:02.610 wdl.w:ptcp.w:call-trgt-18.t:call-trgt_genotype WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:23:02.611 wdl.w:ptcp.w:call-trgt-18.t:call-trgt_genotype INFO provisioned :: seconds_waited: 0, cpu: 8, mem_bytes: 16000000000
2025-09-15 20:23:02.611 wdl.w:ptcp.w:call-trgt-14 NOTICE ready :: job: "call-trgt_plot_motifs_allele", callee: "trgt_plot"
2025-09-15 20:23:02.611 wdl.w:ptcp.w:call-trgt-18.t:call-trgt_genotype INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:23:02.611 wdl.w:ptcp.w:call-trgt-14 INFO input :: job: "call-trgt_plot_motifs_allele", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": false, "methylation": false, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-14/call-trgt_genotype/out/m84036_250809_035451_s4.bc2111.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-14/call-trgt_genotype/out/m84036_250809_035451_s4.bc2111.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-14/call-trgt_genotype/out/m84036_250809_035451_s4.bc2111.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2111"}
2025-09-15 20:23:02.612 wdl.w:ptcp.w:call-trgt-14 NOTICE ready :: job: "call-trgt_plot_motifs_waterfall", callee: "trgt_plot"
2025-09-15 20:23:02.612 wdl.w:ptcp.w:call-trgt-14 INFO input :: job: "call-trgt_plot_motifs_waterfall", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": true, "methylation": false, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-14/call-trgt_genotype/out/m84036_250809_035451_s4.bc2111.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-14/call-trgt_genotype/out/m84036_250809_035451_s4.bc2111.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-14/call-trgt_genotype/out/m84036_250809_035451_s4.bc2111.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2111"}
2025-09-15 20:23:02.613 wdl.w:ptcp.w:call-trgt-14 INFO visit :: node: "output-spanning_bam", values: {"spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-14/call-trgt_genotype/out/m84036_250809_035451_s4.bc2111.trgt.sorted.spanning.bam"}
2025-09-15 20:23:02.613 wdl.w:ptcp.w:call-trgt-14 INFO visit :: node: "output-spanning_bam_bai", values: {"spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-14/call-trgt_genotype/out/m84036_250809_035451_s4.bc2111.trgt.sorted.spanning.bam.bai"}
2025-09-15 20:23:02.613 wdl.w:ptcp.w:call-trgt-14 INFO visit :: node: "output-vcf", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-14/call-trgt_genotype/out/m84036_250809_035451_s4.bc2111.trgt.vcf"}
2025-09-15 20:23:02.614 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_genotype NOTICE task setup :: name: "trgt_genotype", source: "./trgt.wdl", line: 272, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-10/call-trgt_genotype", thread: 140606080804416
2025-09-15 20:23:02.634 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_genotype INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:23:02.635 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_genotype INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:23:02.635 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_genotype INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:23:02.635 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_genotype INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:23:02.635 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_genotype INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2107.mapped.bam.bai"
2025-09-15 20:23:02.635 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_genotype INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2107.mapped.bam"
2025-09-15 20:23:02.635 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_genotype INFO input :: name: "sex", value: "F"
2025-09-15 20:23:02.635 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_genotype INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2107"
2025-09-15 20:23:02.635 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_genotype INFO eval :: name: "mem_gb", value: 16
2025-09-15 20:23:02.635 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_genotype INFO eval :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2107.trgt"
2025-09-15 20:23:02.635 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_genotype INFO eval :: name: "threads", value: 8
2025-09-15 20:23:02.636 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_genotype INFO eval :: name: "disk_size", value: 27
2025-09-15 20:23:02.636 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_genotype INFO eval :: name: "karyotype", value: "XX"
2025-09-15 20:23:02.636 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_genotype INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 8, memory_reservation: 16000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:23:02.636 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_genotype WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:23:02.636 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_genotype INFO provisioned :: seconds_waited: 0, cpu: 8, mem_bytes: 16000000000
2025-09-15 20:23:02.637 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_genotype INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:23:02.682 wdl.w:ptcp.w:call-trgt-18.t:call-trgt_genotype INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 11, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-18/call-trgt_genotype/_singularity_tmpdir_mb4nzj3z"
2025-09-15 20:23:02.682 wdl.w:ptcp.w:call-trgt-18.t:call-trgt_genotype INFO Slurm invocation: srun --job-name call-trgt_genotype --partition compute,compute9 --cpus-per-task 8 --mem 15259M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-18/call-trgt_genotype/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-18/call-trgt_genotype/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-18/call-trgt_genotype/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-18/call-trgt_genotype/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-18/out/m84036_250809_035451_s4.bc2115.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2115.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-18/out/m84036_250809_035451_s4.bc2115.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2115.mapped.bam:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-18/call-trgt_genotype/_singularity_tmpdir_mb4nzj3z/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-18/call-trgt_genotype/_singularity_tmpdir_mb4nzj3z/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:23:02.698 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_genotype INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 11, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-10/call-trgt_genotype/_singularity_tmpdir_9tg212m4"
2025-09-15 20:23:02.698 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_genotype INFO Slurm invocation: srun --job-name call-trgt_genotype --partition compute,compute9 --cpus-per-task 8 --mem 15259M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-10/call-trgt_genotype/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-10/call-trgt_genotype/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-10/call-trgt_genotype/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-10/call-trgt_genotype/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-10/out/m84036_250809_035451_s4.bc2107.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2107.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-10/out/m84036_250809_035451_s4.bc2107.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2107.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-10/call-trgt_genotype/_singularity_tmpdir_9tg212m4/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-10/call-trgt_genotype/_singularity_tmpdir_9tg212m4/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:23:02.703 wdl.w:ptcp.w:call-trgt-18.t:call-trgt_genotype NOTICE slurm_singularity run :: pid: 1198804, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-18/call-trgt_genotype/slurm_singularity.log.txt"
2025-09-15 20:23:02.704 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_genotype NOTICE slurm_singularity run :: pid: 1198805, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-10/call-trgt_genotype/slurm_singularity.log.txt"
2025-09-15 20:23:02.869 wdl.w:ptcp.w:call-paraphase-28.t:call-run_paraphase.slurm_singularity INFO srun: job 51797361 queued and waiting for resources
2025-09-15 20:23:02.869 wdl.w:ptcp.w:call-sawfish-26.t:call-run_sawfish.slurm_singularity INFO srun: job 51797363 queued and waiting for resources
2025-09-15 20:23:02.870 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_genotype.slurm_singularity INFO srun: job 51797362 queued and waiting for resources
2025-09-15 20:23:02.917 wdl.w:ptcp.w:call-trgt-28.t:call-get_reads_overlapping_repeats.slurm_singularity INFO srun: job 51797365 queued and waiting for resources
2025-09-15 20:23:02.921 wdl.w:ptcp.w:call-sawfish-28.t:call-run_sawfish.slurm_singularity INFO srun: job 51797364 queued and waiting for resources
2025-09-15 20:23:03.018 wdl.w:ptcp.w:call-trgt-28.t:call-trgt_genotype.slurm_singularity INFO srun: job 51797366 queued and waiting for resources
2025-09-15 20:23:03.027 wdl.w:ptcp.w:call-sawfish-10.t:call-run_sawfish.slurm_singularity INFO srun: job 51797367 queued and waiting for resources
2025-09-15 20:23:03.041 wdl.w:ptcp.w:call-paraphase-10.t:call-run_paraphase.slurm_singularity INFO srun: job 51797368 queued and waiting for resources
2025-09-15 20:23:03.054 wdl.w:ptcp.w:call-sawfish-18.t:call-run_sawfish.slurm_singularity INFO srun: job 51797369 queued and waiting for resources
2025-09-15 20:23:03.321 wdl.w:ptcp.w:call-trgt-10.t:call-get_reads_overlapping_repeats.slurm_singularity INFO srun: job 51797370 queued and waiting for resources
2025-09-15 20:23:03.354 wdl.w:ptcp.w:call-trgt-20.t:call-trgt_genotype INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2117.trgt.vcf"
2025-09-15 20:23:03.357 wdl.w:ptcp.w:call-trgt-20.t:call-trgt_genotype INFO output :: name: "spanning_bam", value: "m84036_250809_035451_s4.bc2117.trgt.sorted.spanning.bam"
2025-09-15 20:23:03.358 wdl.w:ptcp.w:call-trgt-20.t:call-trgt_genotype INFO output :: name: "spanning_bam_bai", value: "m84036_250809_035451_s4.bc2117.trgt.sorted.spanning.bam.bai"
2025-09-15 20:23:03.392 wdl.w:ptcp.w:call-trgt-18.t:call-get_reads_overlapping_repeats.slurm_singularity INFO srun: job 51797371 queued and waiting for resources
2025-09-15 20:23:03.420 wdl.w:ptcp.w:call-paraphase-18.t:call-run_paraphase.slurm_singularity INFO srun: job 51797372 queued and waiting for resources
2025-09-15 20:23:03.429 wdl.w:ptcp.w:call-trgt-20.t:call-trgt_genotype NOTICE done
2025-09-15 20:23:03.434 wdl.w:ptcp.w:call-trgt-20 NOTICE finish :: job: "call-trgt_genotype"
2025-09-15 20:23:03.434 wdl.w:ptcp.w:call-trgt-20 INFO output :: job: "call-trgt_genotype", values: {"spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-20/call-trgt_genotype/out/m84036_250809_035451_s4.bc2117.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-20/call-trgt_genotype/out/m84036_250809_035451_s4.bc2117.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-20/call-trgt_genotype/out/m84036_250809_035451_s4.bc2117.trgt.vcf"}
2025-09-15 20:23:03.435 wdl.w:ptcp.w:call-trgt-20 NOTICE ready :: job: "call-trgt_plot_meth_allele", callee: "trgt_plot"
2025-09-15 20:23:03.435 wdl.w:ptcp.w:call-trgt-20 INFO input :: job: "call-trgt_plot_meth_allele", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": false, "methylation": true, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-20/call-trgt_genotype/out/m84036_250809_035451_s4.bc2117.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-20/call-trgt_genotype/out/m84036_250809_035451_s4.bc2117.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-20/call-trgt_genotype/out/m84036_250809_035451_s4.bc2117.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2117"}
2025-09-15 20:23:03.436 wdl.w:ptcp.w:call-trgt-20 NOTICE ready :: job: "call-trgt_plot_meth_waterfall", callee: "trgt_plot"
2025-09-15 20:23:03.436 wdl.w:ptcp.w:call-trgt-20 INFO input :: job: "call-trgt_plot_meth_waterfall", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": true, "methylation": true, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-20/call-trgt_genotype/out/m84036_250809_035451_s4.bc2117.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-20/call-trgt_genotype/out/m84036_250809_035451_s4.bc2117.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-20/call-trgt_genotype/out/m84036_250809_035451_s4.bc2117.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2117"}
2025-09-15 20:23:03.437 wdl.w:ptcp.w:call-trgt-20 NOTICE ready :: job: "call-trgt_plot_motifs_allele", callee: "trgt_plot"
2025-09-15 20:23:03.437 wdl.w:ptcp.w:call-trgt-20 INFO input :: job: "call-trgt_plot_motifs_allele", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": false, "methylation": false, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-20/call-trgt_genotype/out/m84036_250809_035451_s4.bc2117.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-20/call-trgt_genotype/out/m84036_250809_035451_s4.bc2117.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-20/call-trgt_genotype/out/m84036_250809_035451_s4.bc2117.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2117"}
2025-09-15 20:23:03.438 wdl.w:ptcp.w:call-trgt-20 NOTICE ready :: job: "call-trgt_plot_motifs_waterfall", callee: "trgt_plot"
2025-09-15 20:23:03.438 wdl.w:ptcp.w:call-trgt-20 INFO input :: job: "call-trgt_plot_motifs_waterfall", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": true, "methylation": false, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-20/call-trgt_genotype/out/m84036_250809_035451_s4.bc2117.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-20/call-trgt_genotype/out/m84036_250809_035451_s4.bc2117.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-20/call-trgt_genotype/out/m84036_250809_035451_s4.bc2117.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2117"}
2025-09-15 20:23:03.438 wdl.w:ptcp.w:call-trgt-20 INFO visit :: node: "output-spanning_bam", values: {"spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-20/call-trgt_genotype/out/m84036_250809_035451_s4.bc2117.trgt.sorted.spanning.bam"}
2025-09-15 20:23:03.439 wdl.w:ptcp.w:call-trgt-20 INFO visit :: node: "output-spanning_bam_bai", values: {"spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-20/call-trgt_genotype/out/m84036_250809_035451_s4.bc2117.trgt.sorted.spanning.bam.bai"}
2025-09-15 20:23:03.439 wdl.w:ptcp.w:call-trgt-20 INFO visit :: node: "output-vcf", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-20/call-trgt_genotype/out/m84036_250809_035451_s4.bc2117.trgt.vcf"}
2025-09-15 20:23:03.440 wdl.w:ptcp.w:call-paraphase-11.t:call-run_paraphase NOTICE task setup :: name: "run_paraphase", source: "./paraphase.wdl", line: 127, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-11/call-run_paraphase", thread: 140611952813632
2025-09-15 20:23:03.457 wdl.w:ptcp.w:call-paraphase-11.t:call-run_paraphase INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:23:03.457 wdl.w:ptcp.w:call-paraphase-11.t:call-run_paraphase INFO input :: name: "annotation_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf"
2025-09-15 20:23:03.457 wdl.w:ptcp.w:call-paraphase-11.t:call-run_paraphase INFO input :: name: "genome_version", value: "38"
2025-09-15 20:23:03.457 wdl.w:ptcp.w:call-paraphase-11.t:call-run_paraphase INFO input :: name: "config_file", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/paraphase_config.GRCh38.yaml"
2025-09-15 20:23:03.457 wdl.w:ptcp.w:call-paraphase-11.t:call-run_paraphase INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:23:03.457 wdl.w:ptcp.w:call-paraphase-11.t:call-run_paraphase INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:23:03.457 wdl.w:ptcp.w:call-paraphase-11.t:call-run_paraphase INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2108.mapped.bam.bai"
2025-09-15 20:23:03.457 wdl.w:ptcp.w:call-paraphase-11.t:call-run_paraphase INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2108.mapped.bam"
2025-09-15 20:23:03.457 wdl.w:ptcp.w:call-paraphase-11.t:call-run_paraphase INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2108"
2025-09-15 20:23:03.458 wdl.w:ptcp.w:call-paraphase-11.t:call-run_paraphase INFO eval :: name: "threads", value: 4
2025-09-15 20:23:03.458 wdl.w:ptcp.w:call-paraphase-11.t:call-run_paraphase INFO eval :: name: "mem_gb", value: 8
2025-09-15 20:23:03.458 wdl.w:ptcp.w:call-paraphase-11.t:call-run_paraphase INFO eval :: name: "disk_size", value: 27
2025-09-15 20:23:03.458 wdl.w:ptcp.w:call-paraphase-11.t:call-run_paraphase INFO eval :: name: "out_dir", value: "m84036_250809_035451_s4.bc2108_paraphase"
2025-09-15 20:23:03.458 wdl.w:ptcp.w:call-paraphase-11.t:call-run_paraphase INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 4, memory_reservation: 8000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:23:03.458 wdl.w:ptcp.w:call-paraphase-11.t:call-run_paraphase WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:23:03.459 wdl.w:ptcp.w:call-paraphase-11.t:call-run_paraphase INFO provisioned :: seconds_waited: 0, cpu: 4, mem_bytes: 8000000000
2025-09-15 20:23:03.459 wdl.w:ptcp.w:call-paraphase-11.t:call-run_paraphase INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:23:03.517 wdl.w:ptcp.w:call-paraphase-11.t:call-run_paraphase INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-11/call-run_paraphase/_singularity_tmpdir_pimg0v5_"
2025-09-15 20:23:03.517 wdl.w:ptcp.w:call-paraphase-11.t:call-run_paraphase INFO Slurm invocation: srun --job-name call-run_paraphase --partition compute,compute9 --cpus-per-task 4 --mem 7629M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-11/call-run_paraphase/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-11/call-run_paraphase/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-11/call-run_paraphase/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-11/call-run_paraphase/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-11/out/m84036_250809_035451_s4.bc2108.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2108.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-11/out/m84036_250809_035451_s4.bc2108.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2108.mapped.bam:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/variant_list/variant_list.GRCh38.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf:ro --bind /ptcp/meta/paraphase/paraphase_config.GRCh38.yaml:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/paraphase_config.GRCh38.yaml:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-11/call-run_paraphase/_singularity_tmpdir_pimg0v5_/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-11/call-run_paraphase/_singularity_tmpdir_pimg0v5_/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:23:03.551 wdl.w:ptcp.w:call-paraphase-11.t:call-run_paraphase NOTICE slurm_singularity run :: pid: 1198813, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-11/call-run_paraphase/slurm_singularity.log.txt"
2025-09-15 20:23:03.717 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_genotype.slurm_singularity INFO srun: job 51797374 queued and waiting for resources
2025-09-15 20:23:03.720 wdl.w:ptcp.w:call-trgt-18.t:call-trgt_genotype.slurm_singularity INFO srun: job 51797373 queued and waiting for resources
2025-09-15 20:23:04.368 wdl.w:ptcp.w:call-trgt-20.t:call-get_reads_overlapping_repeats INFO output :: name: "reads_overlapping_repeats", value: "m84036_250809_035451_s4.bc2117.repeats.bam"
2025-09-15 20:23:04.370 wdl.w:ptcp.w:call-trgt-20.t:call-get_reads_overlapping_repeats INFO output :: name: "reads_overlapping_repeats_bai", value: "m84036_250809_035451_s4.bc2117.repeats.bam.bai"
2025-09-15 20:23:04.421 wdl.w:ptcp.w:call-trgt-20.t:call-get_reads_overlapping_repeats NOTICE done
2025-09-15 20:23:04.425 wdl.w:ptcp.w:call-trgt-20 NOTICE finish :: job: "call-get_reads_overlapping_repeats"
2025-09-15 20:23:04.425 wdl.w:ptcp.w:call-trgt-20 INFO output :: job: "call-get_reads_overlapping_repeats", values: {"reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-20/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2117.repeats.bam.bai", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-20/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2117.repeats.bam"}
2025-09-15 20:23:04.426 wdl.w:ptcp.w:call-trgt-20 INFO visit :: node: "output-reads_overlapping_repeats", values: {"reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-20/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2117.repeats.bam"}
2025-09-15 20:23:04.426 wdl.w:ptcp.w:call-trgt-20 INFO visit :: node: "output-reads_overlapping_repeats_bai", values: {"reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-20/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2117.repeats.bam.bai"}
2025-09-15 20:23:04.431 wdl.w:ptcp.w:call-sawfish-11.t:call-run_sawfish NOTICE task setup :: name: "run_sawfish", source: "./sawfish.wdl", line: 83, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-11/call-run_sawfish", thread: 140611969599040
2025-09-15 20:23:04.445 wdl.w:ptcp.w:call-sawfish-11.t:call-run_sawfish INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:23:04.446 wdl.w:ptcp.w:call-sawfish-11.t:call-run_sawfish INFO input :: name: "genome_version", value: "38"
2025-09-15 20:23:04.446 wdl.w:ptcp.w:call-sawfish-11.t:call-run_sawfish INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:23:04.446 wdl.w:ptcp.w:call-sawfish-11.t:call-run_sawfish INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:23:04.446 wdl.w:ptcp.w:call-sawfish-11.t:call-run_sawfish INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2108.mapped.bam.bai"
2025-09-15 20:23:04.446 wdl.w:ptcp.w:call-sawfish-11.t:call-run_sawfish INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2108.mapped.bam"
2025-09-15 20:23:04.446 wdl.w:ptcp.w:call-sawfish-11.t:call-run_sawfish INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2108"
2025-09-15 20:23:04.446 wdl.w:ptcp.w:call-sawfish-11.t:call-run_sawfish INFO eval :: name: "mem_gb", value: 32
2025-09-15 20:23:04.446 wdl.w:ptcp.w:call-sawfish-11.t:call-run_sawfish INFO eval :: name: "threads", value: 16
2025-09-15 20:23:04.446 wdl.w:ptcp.w:call-sawfish-11.t:call-run_sawfish INFO eval :: name: "disk_size", value: 30
2025-09-15 20:23:04.446 wdl.w:ptcp.w:call-sawfish-11.t:call-run_sawfish INFO eval :: name: "discover_dirname", value: "m84036_250809_035451_s4.bc2108_sawfish_discover"
2025-09-15 20:23:04.447 wdl.w:ptcp.w:call-sawfish-11.t:call-run_sawfish INFO eval :: name: "call_dirname", value: "m84036_250809_035451_s4.bc2108_sawfish"
2025-09-15 20:23:04.447 wdl.w:ptcp.w:call-sawfish-11.t:call-run_sawfish INFO eval :: name: "minimap2_bam_filename", value: "m84036_250809_035451_s4.bc2108.minimap2.bam"
2025-09-15 20:23:04.447 wdl.w:ptcp.w:call-sawfish-11.t:call-run_sawfish INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 16, memory_reservation: 32000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:23:04.447 wdl.w:ptcp.w:call-sawfish-11.t:call-run_sawfish WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:23:04.448 wdl.w:ptcp.w:call-sawfish-11.t:call-run_sawfish INFO provisioned :: seconds_waited: 0, cpu: 16, mem_bytes: 32000000000
2025-09-15 20:23:04.448 wdl.w:ptcp.w:call-sawfish-11.t:call-run_sawfish INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:23:04.488 wdl.w:ptcp.w:call-sawfish-11.t:call-run_sawfish INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 10, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-11/call-run_sawfish/_singularity_tmpdir_gfra5el_"
2025-09-15 20:23:04.488 wdl.w:ptcp.w:call-sawfish-11.t:call-run_sawfish INFO Slurm invocation: srun --job-name call-run_sawfish --partition compute,compute9 --cpus-per-task 16 --mem 30518M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-11/call-run_sawfish/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-11/call-run_sawfish/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-11/call-run_sawfish/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-11/call-run_sawfish/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-11/out/m84036_250809_035451_s4.bc2108.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2108.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-11/out/m84036_250809_035451_s4.bc2108.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2108.mapped.bam:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-11/call-run_sawfish/_singularity_tmpdir_gfra5el_/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-11/call-run_sawfish/_singularity_tmpdir_gfra5el_/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:23:04.501 wdl.w:ptcp.w:call-sawfish-11.t:call-run_sawfish NOTICE slurm_singularity run :: pid: 1198817, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-11/call-run_sawfish/slurm_singularity.log.txt"
2025-09-15 20:23:04.558 wdl.w:ptcp.w:call-paraphase-11.t:call-run_paraphase.slurm_singularity INFO srun: job 51797375 queued and waiting for resources
2025-09-15 20:23:05.509 wdl.w:ptcp.w:call-sawfish-11.t:call-run_sawfish.slurm_singularity INFO srun: job 51797376 queued and waiting for resources
2025-09-15 20:23:06.363 wdl.w:ptcp.w:call-trgt-04.t:call-trgt_genotype INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2101.trgt.vcf"
2025-09-15 20:23:06.366 wdl.w:ptcp.w:call-trgt-04.t:call-get_reads_overlapping_repeats INFO output :: name: "reads_overlapping_repeats", value: "m84036_250809_035451_s4.bc2101.repeats.bam"
2025-09-15 20:23:06.370 wdl.w:ptcp.w:call-trgt-04.t:call-trgt_genotype INFO output :: name: "spanning_bam", value: "m84036_250809_035451_s4.bc2101.trgt.sorted.spanning.bam"
2025-09-15 20:23:06.371 wdl.w:ptcp.w:call-trgt-04.t:call-get_reads_overlapping_repeats INFO output :: name: "reads_overlapping_repeats_bai", value: "m84036_250809_035451_s4.bc2101.repeats.bam.bai"
2025-09-15 20:23:06.372 wdl.w:ptcp.w:call-trgt-04.t:call-trgt_genotype INFO output :: name: "spanning_bam_bai", value: "m84036_250809_035451_s4.bc2101.trgt.sorted.spanning.bam.bai"
2025-09-15 20:23:06.467 wdl.w:ptcp.w:call-trgt-04.t:call-get_reads_overlapping_repeats NOTICE done
2025-09-15 20:23:06.472 wdl.w:ptcp.w:call-trgt-04 NOTICE finish :: job: "call-get_reads_overlapping_repeats"
2025-09-15 20:23:06.472 wdl.w:ptcp.w:call-trgt-04 INFO output :: job: "call-get_reads_overlapping_repeats", values: {"reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-04/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2101.repeats.bam.bai", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-04/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2101.repeats.bam"}
2025-09-15 20:23:06.473 wdl.w:ptcp.w:call-trgt-04 INFO visit :: node: "output-reads_overlapping_repeats", values: {"reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-04/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2101.repeats.bam"}
2025-09-15 20:23:06.473 wdl.w:ptcp.w:call-trgt-04 INFO visit :: node: "output-reads_overlapping_repeats_bai", values: {"reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-04/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2101.repeats.bam.bai"}
2025-09-15 20:23:06.476 wdl.w:ptcp.w:call-trgt-04.t:call-trgt_genotype NOTICE done
2025-09-15 20:23:06.478 wdl.w:ptcp.w:call-trgt-11.t:call-get_reads_overlapping_repeats NOTICE task setup :: name: "get_reads_overlapping_repeats", source: "./trgt.wdl", line: 182, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-11/call-get_reads_overlapping_repeats", thread: 140613571819072
2025-09-15 20:23:06.481 wdl.w:ptcp.w:call-trgt-04 NOTICE finish :: job: "call-trgt_genotype"
2025-09-15 20:23:06.481 wdl.w:ptcp.w:call-trgt-04 INFO output :: job: "call-trgt_genotype", values: {"spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-04/call-trgt_genotype/out/m84036_250809_035451_s4.bc2101.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-04/call-trgt_genotype/out/m84036_250809_035451_s4.bc2101.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-04/call-trgt_genotype/out/m84036_250809_035451_s4.bc2101.trgt.vcf"}
2025-09-15 20:23:06.482 wdl.w:ptcp.w:call-trgt-04 NOTICE ready :: job: "call-trgt_plot_meth_allele", callee: "trgt_plot"
2025-09-15 20:23:06.482 wdl.w:ptcp.w:call-trgt-04 INFO input :: job: "call-trgt_plot_meth_allele", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": false, "methylation": true, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-04/call-trgt_genotype/out/m84036_250809_035451_s4.bc2101.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-04/call-trgt_genotype/out/m84036_250809_035451_s4.bc2101.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-04/call-trgt_genotype/out/m84036_250809_035451_s4.bc2101.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2101"}
2025-09-15 20:23:06.483 wdl.w:ptcp.w:call-trgt-04 NOTICE ready :: job: "call-trgt_plot_meth_waterfall", callee: "trgt_plot"
2025-09-15 20:23:06.483 wdl.w:ptcp.w:call-trgt-04 INFO input :: job: "call-trgt_plot_meth_waterfall", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": true, "methylation": true, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-04/call-trgt_genotype/out/m84036_250809_035451_s4.bc2101.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-04/call-trgt_genotype/out/m84036_250809_035451_s4.bc2101.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-04/call-trgt_genotype/out/m84036_250809_035451_s4.bc2101.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2101"}
2025-09-15 20:23:06.484 wdl.w:ptcp.w:call-trgt-04 NOTICE ready :: job: "call-trgt_plot_motifs_allele", callee: "trgt_plot"
2025-09-15 20:23:06.484 wdl.w:ptcp.w:call-trgt-04 INFO input :: job: "call-trgt_plot_motifs_allele", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": false, "methylation": false, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-04/call-trgt_genotype/out/m84036_250809_035451_s4.bc2101.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-04/call-trgt_genotype/out/m84036_250809_035451_s4.bc2101.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-04/call-trgt_genotype/out/m84036_250809_035451_s4.bc2101.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2101"}
2025-09-15 20:23:06.484 wdl.w:ptcp.w:call-trgt-04 NOTICE ready :: job: "call-trgt_plot_motifs_waterfall", callee: "trgt_plot"
2025-09-15 20:23:06.485 wdl.w:ptcp.w:call-trgt-04 INFO input :: job: "call-trgt_plot_motifs_waterfall", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": true, "methylation": false, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-04/call-trgt_genotype/out/m84036_250809_035451_s4.bc2101.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-04/call-trgt_genotype/out/m84036_250809_035451_s4.bc2101.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-04/call-trgt_genotype/out/m84036_250809_035451_s4.bc2101.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2101"}
2025-09-15 20:23:06.485 wdl.w:ptcp.w:call-trgt-04 INFO visit :: node: "output-spanning_bam", values: {"spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-04/call-trgt_genotype/out/m84036_250809_035451_s4.bc2101.trgt.sorted.spanning.bam"}
2025-09-15 20:23:06.485 wdl.w:ptcp.w:call-trgt-04 INFO visit :: node: "output-spanning_bam_bai", values: {"spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-04/call-trgt_genotype/out/m84036_250809_035451_s4.bc2101.trgt.sorted.spanning.bam.bai"}
2025-09-15 20:23:06.485 wdl.w:ptcp.w:call-trgt-04 INFO visit :: node: "output-vcf", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-04/call-trgt_genotype/out/m84036_250809_035451_s4.bc2101.trgt.vcf"}
2025-09-15 20:23:06.487 wdl.w:ptcp.w:call-trgt-11.t:call-trgt_genotype NOTICE task setup :: name: "trgt_genotype", source: "./trgt.wdl", line: 272, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-11/call-trgt_genotype", thread: 140611457906240
2025-09-15 20:23:06.498 wdl.w:ptcp.w:call-trgt-11.t:call-get_reads_overlapping_repeats INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:23:06.498 wdl.w:ptcp.w:call-trgt-11.t:call-get_reads_overlapping_repeats INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:23:06.498 wdl.w:ptcp.w:call-trgt-11.t:call-get_reads_overlapping_repeats INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2108.mapped.bam.bai"
2025-09-15 20:23:06.499 wdl.w:ptcp.w:call-trgt-11.t:call-get_reads_overlapping_repeats INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2108.mapped.bam"
2025-09-15 20:23:06.499 wdl.w:ptcp.w:call-trgt-11.t:call-get_reads_overlapping_repeats INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2108"
2025-09-15 20:23:06.499 wdl.w:ptcp.w:call-trgt-11.t:call-get_reads_overlapping_repeats INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:23:06.499 wdl.w:ptcp.w:call-trgt-11.t:call-get_reads_overlapping_repeats INFO eval :: name: "expand_size", value: 3000
2025-09-15 20:23:06.499 wdl.w:ptcp.w:call-trgt-11.t:call-get_reads_overlapping_repeats INFO eval :: name: "threads", value: 1
2025-09-15 20:23:06.499 wdl.w:ptcp.w:call-trgt-11.t:call-get_reads_overlapping_repeats INFO eval :: name: "expanded_bed_name", value: "m84036_250809_035451_s4.bc2108.expanded.bed"
2025-09-15 20:23:06.500 wdl.w:ptcp.w:call-trgt-11.t:call-get_reads_overlapping_repeats INFO eval :: name: "disk_size", value: 11
2025-09-15 20:23:06.500 wdl.w:ptcp.w:call-trgt-11.t:call-get_reads_overlapping_repeats INFO eval :: name: "output_name", value: "m84036_250809_035451_s4.bc2108.repeats.bam"
2025-09-15 20:23:06.500 wdl.w:ptcp.w:call-trgt-11.t:call-get_reads_overlapping_repeats INFO eval :: name: "index_name", value: "m84036_250809_035451_s4.bc2108.repeats.bam.bai"
2025-09-15 20:23:06.500 wdl.w:ptcp.w:call-trgt-11.t:call-get_reads_overlapping_repeats INFO eval :: name: "output_name_with_index", value: "m84036_250809_035451_s4.bc2108.repeats.bam##idx##m84036_250809_035451_s4.bc2108.repeats.bam.bai"
2025-09-15 20:23:06.501 wdl.w:ptcp.w:call-trgt-11.t:call-get_reads_overlapping_repeats INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:23:06.501 wdl.w:ptcp.w:call-trgt-11.t:call-get_reads_overlapping_repeats WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:23:06.501 wdl.w:ptcp.w:call-trgt-11.t:call-get_reads_overlapping_repeats INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:23:06.502 wdl.w:ptcp.w:call-trgt-11.t:call-get_reads_overlapping_repeats INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:23:06.505 wdl.w:ptcp.w:call-trgt-11.t:call-trgt_genotype INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:23:06.505 wdl.w:ptcp.w:call-trgt-11.t:call-trgt_genotype INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:23:06.505 wdl.w:ptcp.w:call-trgt-11.t:call-trgt_genotype INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:23:06.506 wdl.w:ptcp.w:call-trgt-11.t:call-trgt_genotype INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:23:06.506 wdl.w:ptcp.w:call-trgt-11.t:call-trgt_genotype INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2108.mapped.bam.bai"
2025-09-15 20:23:06.506 wdl.w:ptcp.w:call-trgt-11.t:call-trgt_genotype INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2108.mapped.bam"
2025-09-15 20:23:06.506 wdl.w:ptcp.w:call-trgt-11.t:call-trgt_genotype INFO input :: name: "sex", value: "F"
2025-09-15 20:23:06.506 wdl.w:ptcp.w:call-trgt-11.t:call-trgt_genotype INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2108"
2025-09-15 20:23:06.506 wdl.w:ptcp.w:call-trgt-11.t:call-trgt_genotype INFO eval :: name: "mem_gb", value: 16
2025-09-15 20:23:06.506 wdl.w:ptcp.w:call-trgt-11.t:call-trgt_genotype INFO eval :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2108.trgt"
2025-09-15 20:23:06.506 wdl.w:ptcp.w:call-trgt-11.t:call-trgt_genotype INFO eval :: name: "threads", value: 8
2025-09-15 20:23:06.507 wdl.w:ptcp.w:call-trgt-11.t:call-trgt_genotype INFO eval :: name: "disk_size", value: 27
2025-09-15 20:23:06.507 wdl.w:ptcp.w:call-trgt-11.t:call-trgt_genotype INFO eval :: name: "karyotype", value: "XX"
2025-09-15 20:23:06.507 wdl.w:ptcp.w:call-trgt-11.t:call-trgt_genotype INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 8, memory_reservation: 16000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:23:06.507 wdl.w:ptcp.w:call-trgt-11.t:call-trgt_genotype WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:23:06.507 wdl.w:ptcp.w:call-trgt-11.t:call-trgt_genotype INFO provisioned :: seconds_waited: 0, cpu: 8, mem_bytes: 16000000000
2025-09-15 20:23:06.508 wdl.w:ptcp.w:call-trgt-11.t:call-trgt_genotype INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:23:06.551 wdl.w:ptcp.w:call-trgt-11.t:call-get_reads_overlapping_repeats INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 9, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-11/call-get_reads_overlapping_repeats/_singularity_tmpdir_vx5pcluh"
2025-09-15 20:23:06.551 wdl.w:ptcp.w:call-trgt-11.t:call-get_reads_overlapping_repeats INFO Slurm invocation: srun --job-name call-get_reads_overlapping_repeats --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-11/call-get_reads_overlapping_repeats/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-11/call-get_reads_overlapping_repeats/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-11/call-get_reads_overlapping_repeats/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-11/call-get_reads_overlapping_repeats/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-11/out/m84036_250809_035451_s4.bc2108.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2108.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-11/out/m84036_250809_035451_s4.bc2108.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2108.mapped.bam:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-11/call-get_reads_overlapping_repeats/_singularity_tmpdir_vx5pcluh/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-11/call-get_reads_overlapping_repeats/_singularity_tmpdir_vx5pcluh/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:23:06.567 wdl.w:ptcp.w:call-trgt-11.t:call-get_reads_overlapping_repeats NOTICE slurm_singularity run :: pid: 1198822, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-11/call-get_reads_overlapping_repeats/slurm_singularity.log.txt"
2025-09-15 20:23:06.575 wdl.w:ptcp.w:call-trgt-11.t:call-trgt_genotype INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 11, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-11/call-trgt_genotype/_singularity_tmpdir_4sh_7_a5"
2025-09-15 20:23:06.575 wdl.w:ptcp.w:call-trgt-11.t:call-trgt_genotype INFO Slurm invocation: srun --job-name call-trgt_genotype --partition compute,compute9 --cpus-per-task 8 --mem 15259M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-11/call-trgt_genotype/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-11/call-trgt_genotype/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-11/call-trgt_genotype/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-11/call-trgt_genotype/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-11/out/m84036_250809_035451_s4.bc2108.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2108.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-11/out/m84036_250809_035451_s4.bc2108.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2108.mapped.bam:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-11/call-trgt_genotype/_singularity_tmpdir_4sh_7_a5/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-11/call-trgt_genotype/_singularity_tmpdir_4sh_7_a5/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:23:06.583 wdl.w:ptcp.w:call-trgt-11.t:call-trgt_genotype NOTICE slurm_singularity run :: pid: 1198824, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-11/call-trgt_genotype/slurm_singularity.log.txt"
2025-09-15 20:23:07.135 wdl.w:ptcp.w:call-paraphase-20.t:call-run_paraphase INFO output :: name: "paraphase_bam", value: "m84036_250809_035451_s4.bc2117_paraphase/m84036_250809_035451_s4.bc2117.paraphase.bam"
2025-09-15 20:23:07.139 wdl.w:ptcp.w:call-paraphase-20.t:call-run_paraphase INFO output :: name: "paraphase_bam_bai", value: "m84036_250809_035451_s4.bc2117_paraphase/m84036_250809_035451_s4.bc2117.paraphase.bam.bai"
2025-09-15 20:23:07.141 wdl.w:ptcp.w:call-paraphase-20.t:call-run_paraphase INFO output :: name: "paraphase_json", value: "m84036_250809_035451_s4.bc2117_paraphase/m84036_250809_035451_s4.bc2117.paraphase.json"
2025-09-15 20:23:07.142 wdl.w:ptcp.w:call-paraphase-20.t:call-run_paraphase INFO output :: name: "paraphase_vcfs", value: []
2025-09-15 20:23:07.142 wdl.w:ptcp.w:call-paraphase-20.t:call-run_paraphase INFO output :: name: "havanno_json", value: "m84036_250809_035451_s4.bc2117.havanno.json"
2025-09-15 20:23:07.231 wdl.w:ptcp.w:call-paraphase-20.t:call-run_paraphase NOTICE done
2025-09-15 20:23:07.256 wdl.w:ptcp.w:call-paraphase-20 NOTICE finish :: job: "call-run_paraphase"
2025-09-15 20:23:07.257 wdl.w:ptcp.w:call-paraphase-20 INFO output :: job: "call-run_paraphase", values: {"havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-20/call-run_paraphase/out/m84036_250809_035451_s4.bc2117.havanno.json", "paraphase_vcfs": [], "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-20/call-run_paraphase/out/m84036_250809_035451_s4.bc2117_paraphase/m84036_250809_035451_s4.bc2117.paraphase.json", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-20/call-run_paraphase/out/m84036_250809_035451_s4.bc2117_paraphase/m84036_250809_035451_s4.bc2117.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-20/call-run_paraphase/out/m84036_250809_035451_s4.bc2117_paraphase/m84036_250809_035451_s4.bc2117.paraphase.bam"}
2025-09-15 20:23:07.258 wdl.w:ptcp.w:call-paraphase-20 NOTICE ready :: job: "call-call_f8", callee: "call_f8"
2025-09-15 20:23:07.258 wdl.w:ptcp.w:call-paraphase-20 INFO input :: job: "call-call_f8", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "out_prefix": "m84036_250809_035451_s4.bc2117", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-20/call-run_paraphase/out/m84036_250809_035451_s4.bc2117_paraphase/m84036_250809_035451_s4.bc2117.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-20/call-run_paraphase/out/m84036_250809_035451_s4.bc2117_paraphase/m84036_250809_035451_s4.bc2117.paraphase.bam", "sex": "F"}
2025-09-15 20:23:07.260 wdl.w:ptcp.w:call-paraphase-20 INFO visit :: node: "output-havanno_json", values: {"havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-20/call-run_paraphase/out/m84036_250809_035451_s4.bc2117.havanno.json"}
2025-09-15 20:23:07.261 wdl.w:ptcp.w:call-paraphase-20 INFO visit :: node: "output-paraphase_bam", values: {"paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-20/call-run_paraphase/out/m84036_250809_035451_s4.bc2117_paraphase/m84036_250809_035451_s4.bc2117.paraphase.bam"}
2025-09-15 20:23:07.261 wdl.w:ptcp.w:call-paraphase-20 INFO visit :: node: "output-paraphase_bam_bai", values: {"paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-20/call-run_paraphase/out/m84036_250809_035451_s4.bc2117_paraphase/m84036_250809_035451_s4.bc2117.paraphase.bam.bai"}
2025-09-15 20:23:07.261 wdl.w:ptcp.w:call-paraphase-20 INFO visit :: node: "output-paraphase_json", values: {"paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-20/call-run_paraphase/out/m84036_250809_035451_s4.bc2117_paraphase/m84036_250809_035451_s4.bc2117.paraphase.json"}
2025-09-15 20:23:07.261 wdl.w:ptcp.w:call-paraphase-20 INFO visit :: node: "output-paraphase_vcfs", values: {"paraphase_vcfs": []}
2025-09-15 20:23:07.262 wdl.w:ptcp.w:call-paraphase-19.t:call-run_paraphase NOTICE task setup :: name: "run_paraphase", source: "./paraphase.wdl", line: 127, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-19/call-run_paraphase", thread: 140611994777152
2025-09-15 20:23:07.280 wdl.w:ptcp.w:call-paraphase-19.t:call-run_paraphase INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:23:07.280 wdl.w:ptcp.w:call-paraphase-19.t:call-run_paraphase INFO input :: name: "annotation_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf"
2025-09-15 20:23:07.280 wdl.w:ptcp.w:call-paraphase-19.t:call-run_paraphase INFO input :: name: "genome_version", value: "38"
2025-09-15 20:23:07.280 wdl.w:ptcp.w:call-paraphase-19.t:call-run_paraphase INFO input :: name: "config_file", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/paraphase_config.GRCh38.yaml"
2025-09-15 20:23:07.280 wdl.w:ptcp.w:call-paraphase-19.t:call-run_paraphase INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:23:07.280 wdl.w:ptcp.w:call-paraphase-19.t:call-run_paraphase INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:23:07.281 wdl.w:ptcp.w:call-paraphase-19.t:call-run_paraphase INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2116.mapped.bam.bai"
2025-09-15 20:23:07.281 wdl.w:ptcp.w:call-paraphase-19.t:call-run_paraphase INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2116.mapped.bam"
2025-09-15 20:23:07.281 wdl.w:ptcp.w:call-paraphase-19.t:call-run_paraphase INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2116"
2025-09-15 20:23:07.281 wdl.w:ptcp.w:call-paraphase-19.t:call-run_paraphase INFO eval :: name: "threads", value: 4
2025-09-15 20:23:07.281 wdl.w:ptcp.w:call-paraphase-19.t:call-run_paraphase INFO eval :: name: "mem_gb", value: 8
2025-09-15 20:23:07.281 wdl.w:ptcp.w:call-paraphase-19.t:call-run_paraphase INFO eval :: name: "disk_size", value: 27
2025-09-15 20:23:07.281 wdl.w:ptcp.w:call-paraphase-19.t:call-run_paraphase INFO eval :: name: "out_dir", value: "m84036_250809_035451_s4.bc2116_paraphase"
2025-09-15 20:23:07.282 wdl.w:ptcp.w:call-paraphase-19.t:call-run_paraphase INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 4, memory_reservation: 8000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:23:07.282 wdl.w:ptcp.w:call-paraphase-19.t:call-run_paraphase WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:23:07.282 wdl.w:ptcp.w:call-paraphase-19.t:call-run_paraphase INFO provisioned :: seconds_waited: 0, cpu: 4, mem_bytes: 8000000000
2025-09-15 20:23:07.282 wdl.w:ptcp.w:call-paraphase-19.t:call-run_paraphase INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:23:07.331 wdl.w:ptcp.w:call-paraphase-19.t:call-run_paraphase INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-19/call-run_paraphase/_singularity_tmpdir_ovs9_q9d"
2025-09-15 20:23:07.332 wdl.w:ptcp.w:call-paraphase-19.t:call-run_paraphase INFO Slurm invocation: srun --job-name call-run_paraphase --partition compute,compute9 --cpus-per-task 4 --mem 7629M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-19/call-run_paraphase/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-19/call-run_paraphase/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-19/call-run_paraphase/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-19/call-run_paraphase/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-19/out/m84036_250809_035451_s4.bc2116.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2116.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-19/out/m84036_250809_035451_s4.bc2116.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2116.mapped.bam.bai:ro --bind /ptcp/meta/variant_list/variant_list.GRCh38.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf:ro --bind /ptcp/meta/paraphase/paraphase_config.GRCh38.yaml:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/paraphase_config.GRCh38.yaml:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-19/call-run_paraphase/_singularity_tmpdir_ovs9_q9d/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-19/call-run_paraphase/_singularity_tmpdir_ovs9_q9d/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:23:07.341 wdl.w:ptcp.w:call-paraphase-19.t:call-run_paraphase NOTICE slurm_singularity run :: pid: 1198829, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-19/call-run_paraphase/slurm_singularity.log.txt"
2025-09-15 20:23:07.574 wdl.w:ptcp.w:call-trgt-11.t:call-get_reads_overlapping_repeats.slurm_singularity INFO srun: job 51797377 queued and waiting for resources
2025-09-15 20:23:07.591 wdl.w:ptcp.w:call-trgt-11.t:call-trgt_genotype.slurm_singularity INFO srun: job 51797378 queued and waiting for resources
2025-09-15 20:23:07.957 wdl.w:ptcp.w:call-paraphase-04.t:call-run_paraphase INFO output :: name: "paraphase_bam", value: "m84036_250809_035451_s4.bc2101_paraphase/m84036_250809_035451_s4.bc2101.paraphase.bam"
2025-09-15 20:23:07.965 wdl.w:ptcp.w:call-paraphase-04.t:call-run_paraphase INFO output :: name: "paraphase_bam_bai", value: "m84036_250809_035451_s4.bc2101_paraphase/m84036_250809_035451_s4.bc2101.paraphase.bam.bai"
2025-09-15 20:23:07.966 wdl.w:ptcp.w:call-paraphase-04.t:call-run_paraphase INFO output :: name: "paraphase_json", value: "m84036_250809_035451_s4.bc2101_paraphase/m84036_250809_035451_s4.bc2101.paraphase.json"
2025-09-15 20:23:07.970 wdl.w:ptcp.w:call-paraphase-04.t:call-run_paraphase INFO output :: name: "paraphase_vcfs", value: []
2025-09-15 20:23:07.970 wdl.w:ptcp.w:call-paraphase-04.t:call-run_paraphase INFO output :: name: "havanno_json", value: "m84036_250809_035451_s4.bc2101.havanno.json"
2025-09-15 20:23:08.081 wdl.w:ptcp.w:call-paraphase-04.t:call-run_paraphase NOTICE done
2025-09-15 20:23:08.086 wdl.w:ptcp.w:call-paraphase-04 NOTICE finish :: job: "call-run_paraphase"
2025-09-15 20:23:08.086 wdl.w:ptcp.w:call-paraphase-04 INFO output :: job: "call-run_paraphase", values: {"havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-04/call-run_paraphase/out/m84036_250809_035451_s4.bc2101.havanno.json", "paraphase_vcfs": [], "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-04/call-run_paraphase/out/m84036_250809_035451_s4.bc2101_paraphase/m84036_250809_035451_s4.bc2101.paraphase.json", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-04/call-run_paraphase/out/m84036_250809_035451_s4.bc2101_paraphase/m84036_250809_035451_s4.bc2101.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-04/call-run_paraphase/out/m84036_250809_035451_s4.bc2101_paraphase/m84036_250809_035451_s4.bc2101.paraphase.bam"}
2025-09-15 20:23:08.087 wdl.w:ptcp.w:call-paraphase-04 NOTICE ready :: job: "call-call_f8", callee: "call_f8"
2025-09-15 20:23:08.087 wdl.w:ptcp.w:call-paraphase-04 INFO input :: job: "call-call_f8", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "out_prefix": "m84036_250809_035451_s4.bc2101", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-04/call-run_paraphase/out/m84036_250809_035451_s4.bc2101_paraphase/m84036_250809_035451_s4.bc2101.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-04/call-run_paraphase/out/m84036_250809_035451_s4.bc2101_paraphase/m84036_250809_035451_s4.bc2101.paraphase.bam", "sex": "F"}
2025-09-15 20:23:08.088 wdl.w:ptcp.w:call-paraphase-04 INFO visit :: node: "output-havanno_json", values: {"havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-04/call-run_paraphase/out/m84036_250809_035451_s4.bc2101.havanno.json"}
2025-09-15 20:23:08.088 wdl.w:ptcp.w:call-paraphase-04 INFO visit :: node: "output-paraphase_bam", values: {"paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-04/call-run_paraphase/out/m84036_250809_035451_s4.bc2101_paraphase/m84036_250809_035451_s4.bc2101.paraphase.bam"}
2025-09-15 20:23:08.089 wdl.w:ptcp.w:call-paraphase-04 INFO visit :: node: "output-paraphase_bam_bai", values: {"paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-04/call-run_paraphase/out/m84036_250809_035451_s4.bc2101_paraphase/m84036_250809_035451_s4.bc2101.paraphase.bam.bai"}
2025-09-15 20:23:08.089 wdl.w:ptcp.w:call-paraphase-04 INFO visit :: node: "output-paraphase_json", values: {"paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-04/call-run_paraphase/out/m84036_250809_035451_s4.bc2101_paraphase/m84036_250809_035451_s4.bc2101.paraphase.json"}
2025-09-15 20:23:08.089 wdl.w:ptcp.w:call-paraphase-04 INFO visit :: node: "output-paraphase_vcfs", values: {"paraphase_vcfs": []}
2025-09-15 20:23:08.098 wdl.w:ptcp.w:call-sawfish-19.t:call-run_sawfish NOTICE task setup :: name: "run_sawfish", source: "./sawfish.wdl", line: 83, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-19/call-run_sawfish", thread: 140612523255360
2025-09-15 20:23:08.115 wdl.w:ptcp.w:call-sawfish-19.t:call-run_sawfish INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:23:08.115 wdl.w:ptcp.w:call-sawfish-19.t:call-run_sawfish INFO input :: name: "genome_version", value: "38"
2025-09-15 20:23:08.115 wdl.w:ptcp.w:call-sawfish-19.t:call-run_sawfish INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:23:08.115 wdl.w:ptcp.w:call-sawfish-19.t:call-run_sawfish INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:23:08.115 wdl.w:ptcp.w:call-sawfish-19.t:call-run_sawfish INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2116.mapped.bam.bai"
2025-09-15 20:23:08.115 wdl.w:ptcp.w:call-sawfish-19.t:call-run_sawfish INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2116.mapped.bam"
2025-09-15 20:23:08.115 wdl.w:ptcp.w:call-sawfish-19.t:call-run_sawfish INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2116"
2025-09-15 20:23:08.116 wdl.w:ptcp.w:call-sawfish-19.t:call-run_sawfish INFO eval :: name: "mem_gb", value: 32
2025-09-15 20:23:08.116 wdl.w:ptcp.w:call-sawfish-19.t:call-run_sawfish INFO eval :: name: "threads", value: 16
2025-09-15 20:23:08.116 wdl.w:ptcp.w:call-sawfish-19.t:call-run_sawfish INFO eval :: name: "disk_size", value: 30
2025-09-15 20:23:08.116 wdl.w:ptcp.w:call-sawfish-19.t:call-run_sawfish INFO eval :: name: "discover_dirname", value: "m84036_250809_035451_s4.bc2116_sawfish_discover"
2025-09-15 20:23:08.116 wdl.w:ptcp.w:call-sawfish-19.t:call-run_sawfish INFO eval :: name: "call_dirname", value: "m84036_250809_035451_s4.bc2116_sawfish"
2025-09-15 20:23:08.116 wdl.w:ptcp.w:call-sawfish-19.t:call-run_sawfish INFO eval :: name: "minimap2_bam_filename", value: "m84036_250809_035451_s4.bc2116.minimap2.bam"
2025-09-15 20:23:08.117 wdl.w:ptcp.w:call-sawfish-19.t:call-run_sawfish INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 16, memory_reservation: 32000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:23:08.117 wdl.w:ptcp.w:call-sawfish-19.t:call-run_sawfish WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:23:08.117 wdl.w:ptcp.w:call-sawfish-19.t:call-run_sawfish INFO provisioned :: seconds_waited: 0, cpu: 16, mem_bytes: 32000000000
2025-09-15 20:23:08.117 wdl.w:ptcp.w:call-sawfish-19.t:call-run_sawfish INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:23:08.168 wdl.w:ptcp.w:call-sawfish-19.t:call-run_sawfish INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 10, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-19/call-run_sawfish/_singularity_tmpdir_x3xgrdo9"
2025-09-15 20:23:08.168 wdl.w:ptcp.w:call-sawfish-19.t:call-run_sawfish INFO Slurm invocation: srun --job-name call-run_sawfish --partition compute,compute9 --cpus-per-task 16 --mem 30518M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-19/call-run_sawfish/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-19/call-run_sawfish/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-19/call-run_sawfish/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-19/call-run_sawfish/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-19/out/m84036_250809_035451_s4.bc2116.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2116.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-19/out/m84036_250809_035451_s4.bc2116.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2116.mapped.bam.bai:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-19/call-run_sawfish/_singularity_tmpdir_x3xgrdo9/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-19/call-run_sawfish/_singularity_tmpdir_x3xgrdo9/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:23:08.182 wdl.w:ptcp.w:call-sawfish-19.t:call-run_sawfish NOTICE slurm_singularity run :: pid: 1198833, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-19/call-run_sawfish/slurm_singularity.log.txt"
2025-09-15 20:23:08.266 wdl.w:ptcp.w:call-paraphase-14.t:call-run_paraphase.stderr VERBOSE INFO:root:Processing sample m84036_250809_035451_s4.bc2111 at 2025-09-15 20:23:05.573835...
2025-09-15 20:23:08.267 wdl.w:ptcp.w:call-paraphase-14.t:call-run_paraphase.stderr VERBOSE INFO:root:Checking sample sex at 2025-09-15 20:23:05.574721...
2025-09-15 20:23:08.267 wdl.w:ptcp.w:call-paraphase-14.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for cyp21 for sample m84036_250809_035451_s4.bc2111 at 2025-09-15 20:23:05.613029...
2025-09-15 20:23:08.267 wdl.w:ptcp.w:call-paraphase-14.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for cyp21 for sample m84036_250809_035451_s4.bc2111 at 2025-09-15 20:23:05.613620...
2025-09-15 20:23:08.267 wdl.w:ptcp.w:call-paraphase-14.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for smn1 for sample m84036_250809_035451_s4.bc2111 at 2025-09-15 20:23:05.613220...
2025-09-15 20:23:08.267 wdl.w:ptcp.w:call-paraphase-14.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for smn1 for sample m84036_250809_035451_s4.bc2111 at 2025-09-15 20:23:05.613737...
2025-09-15 20:23:08.267 wdl.w:ptcp.w:call-paraphase-14.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for gba for sample m84036_250809_035451_s4.bc2111 at 2025-09-15 20:23:05.613318...
2025-09-15 20:23:08.267 wdl.w:ptcp.w:call-paraphase-14.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for gba for sample m84036_250809_035451_s4.bc2111 at 2025-09-15 20:23:05.613818...
2025-09-15 20:23:08.267 wdl.w:ptcp.w:call-paraphase-14.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for hba for sample m84036_250809_035451_s4.bc2111 at 2025-09-15 20:23:05.614703...
2025-09-15 20:23:08.267 wdl.w:ptcp.w:call-paraphase-14.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for hba for sample m84036_250809_035451_s4.bc2111 at 2025-09-15 20:23:05.615162...
2025-09-15 20:23:08.348 wdl.w:ptcp.w:call-paraphase-19.t:call-run_paraphase.slurm_singularity INFO srun: job 51797379 queued and waiting for resources
2025-09-15 20:23:08.376 wdl.w:ptcp.w:call-paraphase-22.t:call-run_paraphase.stderr VERBOSE INFO:root:Processing sample m84036_250809_035451_s4.bc2119 at 2025-09-15 20:23:04.671186...
2025-09-15 20:23:08.377 wdl.w:ptcp.w:call-paraphase-22.t:call-run_paraphase.stderr VERBOSE INFO:root:Checking sample sex at 2025-09-15 20:23:04.671797...
2025-09-15 20:23:08.378 wdl.w:ptcp.w:call-paraphase-22.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for cyp21 for sample m84036_250809_035451_s4.bc2119 at 2025-09-15 20:23:04.701181...
2025-09-15 20:23:08.378 wdl.w:ptcp.w:call-paraphase-22.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for cyp21 for sample m84036_250809_035451_s4.bc2119 at 2025-09-15 20:23:04.701545...
2025-09-15 20:23:08.378 wdl.w:ptcp.w:call-paraphase-22.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for smn1 for sample m84036_250809_035451_s4.bc2119 at 2025-09-15 20:23:04.701254...
2025-09-15 20:23:08.378 wdl.w:ptcp.w:call-paraphase-22.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for smn1 for sample m84036_250809_035451_s4.bc2119 at 2025-09-15 20:23:04.701599...
2025-09-15 20:23:08.378 wdl.w:ptcp.w:call-paraphase-22.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for gba for sample m84036_250809_035451_s4.bc2119 at 2025-09-15 20:23:04.702454...
2025-09-15 20:23:08.378 wdl.w:ptcp.w:call-paraphase-22.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for hba for sample m84036_250809_035451_s4.bc2119 at 2025-09-15 20:23:04.702467...
2025-09-15 20:23:08.378 wdl.w:ptcp.w:call-paraphase-22.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for gba for sample m84036_250809_035451_s4.bc2119 at 2025-09-15 20:23:04.702809...
2025-09-15 20:23:08.378 wdl.w:ptcp.w:call-paraphase-22.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for hba for sample m84036_250809_035451_s4.bc2119 at 2025-09-15 20:23:04.702827...
2025-09-15 20:23:09.194 wdl.w:ptcp.w:call-sawfish-19.t:call-run_sawfish.slurm_singularity INFO srun: job 51797380 queued and waiting for resources
2025-09-15 20:23:09.925 wdl.w:ptcp.w:call-paraphase-15.t:call-run_paraphase.stderr VERBOSE INFO:root:Processing sample m84036_250809_035451_s4.bc2112 at 2025-09-15 20:23:05.108760...
2025-09-15 20:23:09.926 wdl.w:ptcp.w:call-paraphase-15.t:call-run_paraphase.stderr VERBOSE INFO:root:Checking sample sex at 2025-09-15 20:23:05.109430...
2025-09-15 20:23:09.926 wdl.w:ptcp.w:call-paraphase-15.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for gba for sample m84036_250809_035451_s4.bc2112 at 2025-09-15 20:23:05.156445...
2025-09-15 20:23:09.926 wdl.w:ptcp.w:call-paraphase-15.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for gba for sample m84036_250809_035451_s4.bc2112 at 2025-09-15 20:23:05.156888...
2025-09-15 20:23:09.926 wdl.w:ptcp.w:call-paraphase-15.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for cyp21 for sample m84036_250809_035451_s4.bc2112 at 2025-09-15 20:23:05.156416...
2025-09-15 20:23:09.926 wdl.w:ptcp.w:call-paraphase-15.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for smn1 for sample m84036_250809_035451_s4.bc2112 at 2025-09-15 20:23:05.156538...
2025-09-15 20:23:09.926 wdl.w:ptcp.w:call-paraphase-15.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for cyp21 for sample m84036_250809_035451_s4.bc2112 at 2025-09-15 20:23:05.156999...
2025-09-15 20:23:09.926 wdl.w:ptcp.w:call-paraphase-15.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for smn1 for sample m84036_250809_035451_s4.bc2112 at 2025-09-15 20:23:05.157059...
2025-09-15 20:23:09.927 wdl.w:ptcp.w:call-paraphase-15.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for hba for sample m84036_250809_035451_s4.bc2112 at 2025-09-15 20:23:05.157880...
2025-09-15 20:23:09.927 wdl.w:ptcp.w:call-paraphase-15.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for hba for sample m84036_250809_035451_s4.bc2112 at 2025-09-15 20:23:05.158296...
2025-09-15 20:23:10.802 wdl.w:ptcp.w:call-sawfish-20.t:call-run_sawfish.stderr VERBOSE [M::bam2fq_mainloop] discarded 0 singletons
2025-09-15 20:23:10.803 wdl.w:ptcp.w:call-sawfish-20.t:call-run_sawfish.stderr VERBOSE [M::bam2fq_mainloop] processed 1 reads
2025-09-15 20:23:11.315 wdl.w:ptcp.w:call-paraphase-07.t:call-run_paraphase.stderr VERBOSE INFO:root:Processing sample m84036_250809_035451_s4.bc2104 at 2025-09-15 20:23:05.560276...
2025-09-15 20:23:11.316 wdl.w:ptcp.w:call-paraphase-07.t:call-run_paraphase.stderr VERBOSE INFO:root:Checking sample sex at 2025-09-15 20:23:05.561045...
2025-09-15 20:23:11.316 wdl.w:ptcp.w:call-paraphase-07.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for cyp21 for sample m84036_250809_035451_s4.bc2104 at 2025-09-15 20:23:05.595903...
2025-09-15 20:23:11.316 wdl.w:ptcp.w:call-paraphase-07.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for cyp21 for sample m84036_250809_035451_s4.bc2104 at 2025-09-15 20:23:05.596566...
2025-09-15 20:23:11.316 wdl.w:ptcp.w:call-paraphase-07.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for smn1 for sample m84036_250809_035451_s4.bc2104 at 2025-09-15 20:23:05.596128...
2025-09-15 20:23:11.317 wdl.w:ptcp.w:call-paraphase-07.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for gba for sample m84036_250809_035451_s4.bc2104 at 2025-09-15 20:23:05.596206...
2025-09-15 20:23:11.317 wdl.w:ptcp.w:call-paraphase-07.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for hba for sample m84036_250809_035451_s4.bc2104 at 2025-09-15 20:23:05.596263...
2025-09-15 20:23:11.317 wdl.w:ptcp.w:call-paraphase-07.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for smn1 for sample m84036_250809_035451_s4.bc2104 at 2025-09-15 20:23:05.596766...
2025-09-15 20:23:11.317 wdl.w:ptcp.w:call-paraphase-07.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for gba for sample m84036_250809_035451_s4.bc2104 at 2025-09-15 20:23:05.596780...
2025-09-15 20:23:11.317 wdl.w:ptcp.w:call-paraphase-07.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for hba for sample m84036_250809_035451_s4.bc2104 at 2025-09-15 20:23:05.596825...
2025-09-15 20:23:11.717 wdl.w:ptcp.w:call-sawfish-04.t:call-run_sawfish.stderr VERBOSE [M::bam2fq_mainloop] discarded 0 singletons
2025-09-15 20:23:11.719 wdl.w:ptcp.w:call-sawfish-04.t:call-run_sawfish.stderr VERBOSE [M::bam2fq_mainloop] processed 0 reads
2025-09-15 20:23:12.114 wdl.w:ptcp.w:call-paraphase-31.t:call-run_paraphase.stderr VERBOSE INFO:root:Processing sample m84036_250809_035451_s4.bc2128 at 2025-09-15 20:23:05.604064...
2025-09-15 20:23:12.115 wdl.w:ptcp.w:call-paraphase-31.t:call-run_paraphase.stderr VERBOSE INFO:root:Checking sample sex at 2025-09-15 20:23:05.604927...
2025-09-15 20:23:12.115 wdl.w:ptcp.w:call-paraphase-31.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for gba for sample m84036_250809_035451_s4.bc2128 at 2025-09-15 20:23:05.639336...
2025-09-15 20:23:12.115 wdl.w:ptcp.w:call-paraphase-31.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for gba for sample m84036_250809_035451_s4.bc2128 at 2025-09-15 20:23:05.639798...
2025-09-15 20:23:12.115 wdl.w:ptcp.w:call-paraphase-31.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for cyp21 for sample m84036_250809_035451_s4.bc2128 at 2025-09-15 20:23:05.639258...
2025-09-15 20:23:12.115 wdl.w:ptcp.w:call-paraphase-31.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for cyp21 for sample m84036_250809_035451_s4.bc2128 at 2025-09-15 20:23:05.639888...
2025-09-15 20:23:12.115 wdl.w:ptcp.w:call-paraphase-31.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for smn1 for sample m84036_250809_035451_s4.bc2128 at 2025-09-15 20:23:05.639484...
2025-09-15 20:23:12.115 wdl.w:ptcp.w:call-paraphase-31.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for smn1 for sample m84036_250809_035451_s4.bc2128 at 2025-09-15 20:23:05.640035...
2025-09-15 20:23:12.116 wdl.w:ptcp.w:call-paraphase-31.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for hba for sample m84036_250809_035451_s4.bc2128 at 2025-09-15 20:23:05.640792...
2025-09-15 20:23:12.116 wdl.w:ptcp.w:call-paraphase-31.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for hba for sample m84036_250809_035451_s4.bc2128 at 2025-09-15 20:23:05.641174...
2025-09-15 20:23:12.432 wdl.w:ptcp.w:call-paraphase-34.t:call-run_paraphase.stderr VERBOSE INFO:root:Processing sample m84036_250809_035451_s4.bc2131 at 2025-09-15 20:23:07.015362...
2025-09-15 20:23:12.433 wdl.w:ptcp.w:call-paraphase-34.t:call-run_paraphase.stderr VERBOSE INFO:root:Checking sample sex at 2025-09-15 20:23:07.016753...
2025-09-15 20:23:12.433 wdl.w:ptcp.w:call-paraphase-34.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for cyp21 for sample m84036_250809_035451_s4.bc2131 at 2025-09-15 20:23:07.063591...
2025-09-15 20:23:12.433 wdl.w:ptcp.w:call-paraphase-34.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for cyp21 for sample m84036_250809_035451_s4.bc2131 at 2025-09-15 20:23:07.064053...
2025-09-15 20:23:12.433 wdl.w:ptcp.w:call-paraphase-34.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for smn1 for sample m84036_250809_035451_s4.bc2131 at 2025-09-15 20:23:07.063725...
2025-09-15 20:23:12.433 wdl.w:ptcp.w:call-paraphase-34.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for smn1 for sample m84036_250809_035451_s4.bc2131 at 2025-09-15 20:23:07.064112...
2025-09-15 20:23:12.433 wdl.w:ptcp.w:call-paraphase-34.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for gba for sample m84036_250809_035451_s4.bc2131 at 2025-09-15 20:23:07.063845...
2025-09-15 20:23:12.433 wdl.w:ptcp.w:call-paraphase-34.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for hba for sample m84036_250809_035451_s4.bc2131 at 2025-09-15 20:23:07.063878...
2025-09-15 20:23:12.433 wdl.w:ptcp.w:call-paraphase-34.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for gba for sample m84036_250809_035451_s4.bc2131 at 2025-09-15 20:23:07.064208...
2025-09-15 20:23:12.433 wdl.w:ptcp.w:call-paraphase-34.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for hba for sample m84036_250809_035451_s4.bc2131 at 2025-09-15 20:23:07.064232...
2025-09-15 20:23:13.638 wdl.w:ptcp.w:call-paraphase-23.t:call-run_paraphase.stderr VERBOSE INFO:root:Processing sample m84036_250809_035451_s4.bc2120 at 2025-09-15 20:23:06.967698...
2025-09-15 20:23:13.639 wdl.w:ptcp.w:call-paraphase-23.t:call-run_paraphase.stderr VERBOSE INFO:root:Checking sample sex at 2025-09-15 20:23:06.968698...
2025-09-15 20:23:13.639 wdl.w:ptcp.w:call-paraphase-23.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for cyp21 for sample m84036_250809_035451_s4.bc2120 at 2025-09-15 20:23:07.004888...
2025-09-15 20:23:13.639 wdl.w:ptcp.w:call-paraphase-23.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for smn1 for sample m84036_250809_035451_s4.bc2120 at 2025-09-15 20:23:07.004926...
2025-09-15 20:23:13.639 wdl.w:ptcp.w:call-paraphase-23.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for cyp21 for sample m84036_250809_035451_s4.bc2120 at 2025-09-15 20:23:07.005296...
2025-09-15 20:23:13.639 wdl.w:ptcp.w:call-paraphase-23.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for smn1 for sample m84036_250809_035451_s4.bc2120 at 2025-09-15 20:23:07.005302...
2025-09-15 20:23:13.639 wdl.w:ptcp.w:call-paraphase-23.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for gba for sample m84036_250809_035451_s4.bc2120 at 2025-09-15 20:23:07.006186...
2025-09-15 20:23:13.639 wdl.w:ptcp.w:call-paraphase-23.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for hba for sample m84036_250809_035451_s4.bc2120 at 2025-09-15 20:23:07.006189...
2025-09-15 20:23:13.639 wdl.w:ptcp.w:call-paraphase-23.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for hba for sample m84036_250809_035451_s4.bc2120 at 2025-09-15 20:23:07.006645...
2025-09-15 20:23:13.639 wdl.w:ptcp.w:call-paraphase-23.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for gba for sample m84036_250809_035451_s4.bc2120 at 2025-09-15 20:23:07.006643...
2025-09-15 20:23:15.826 wdl.w:ptcp.w:call-paraphase-35.t:call-run_paraphase.stderr VERBOSE INFO:root:Processing sample m84036_250809_035451_s4.bc2132 at 2025-09-15 20:23:06.295863...
2025-09-15 20:23:15.827 wdl.w:ptcp.w:call-paraphase-35.t:call-run_paraphase.stderr VERBOSE INFO:root:Checking sample sex at 2025-09-15 20:23:06.296619...
2025-09-15 20:23:15.827 wdl.w:ptcp.w:call-paraphase-35.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for cyp21 for sample m84036_250809_035451_s4.bc2132 at 2025-09-15 20:23:06.346836...
2025-09-15 20:23:15.827 wdl.w:ptcp.w:call-paraphase-35.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for cyp21 for sample m84036_250809_035451_s4.bc2132 at 2025-09-15 20:23:06.347556...
2025-09-15 20:23:15.827 wdl.w:ptcp.w:call-paraphase-35.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for smn1 for sample m84036_250809_035451_s4.bc2132 at 2025-09-15 20:23:06.347035...
2025-09-15 20:23:15.827 wdl.w:ptcp.w:call-paraphase-35.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for smn1 for sample m84036_250809_035451_s4.bc2132 at 2025-09-15 20:23:06.347687...
2025-09-15 20:23:15.827 wdl.w:ptcp.w:call-paraphase-35.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for gba for sample m84036_250809_035451_s4.bc2132 at 2025-09-15 20:23:06.347167...
2025-09-15 20:23:15.827 wdl.w:ptcp.w:call-paraphase-35.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for hba for sample m84036_250809_035451_s4.bc2132 at 2025-09-15 20:23:06.347167...
2025-09-15 20:23:15.827 wdl.w:ptcp.w:call-paraphase-35.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for gba for sample m84036_250809_035451_s4.bc2132 at 2025-09-15 20:23:06.347839...
2025-09-15 20:23:15.827 wdl.w:ptcp.w:call-paraphase-35.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for hba for sample m84036_250809_035451_s4.bc2132 at 2025-09-15 20:23:06.347842...
2025-09-15 20:23:17.360 wdl.w:ptcp.w:call-paraphase-14.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for smn1 for sample m84036_250809_035451_s4.bc2111 at 2025-09-15 20:23:07.494857...
2025-09-15 20:23:17.360 wdl.w:ptcp.w:call-paraphase-14.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for hba for sample m84036_250809_035451_s4.bc2111 at 2025-09-15 20:23:07.826854...
2025-09-15 20:23:17.360 wdl.w:ptcp.w:call-paraphase-14.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for gba for sample m84036_250809_035451_s4.bc2111 at 2025-09-15 20:23:08.562070...
2025-09-15 20:23:17.360 wdl.w:ptcp.w:call-paraphase-14.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for cyp21 for sample m84036_250809_035451_s4.bc2111 at 2025-09-15 20:23:08.907167...
2025-09-15 20:23:17.361 wdl.w:ptcp.w:call-paraphase-14.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for smn1 for sample m84036_250809_035451_s4.bc2111 at 2025-09-15 20:23:16.547333...
2025-09-15 20:23:17.361 wdl.w:ptcp.w:call-paraphase-14.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning to gene2 region for smn1 for sample m84036_250809_035451_s4.bc2111 at 2025-09-15 20:23:16.784813...
2025-09-15 20:23:17.485 wdl.w:ptcp.w:call-paraphase-22.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for smn1 for sample m84036_250809_035451_s4.bc2119 at 2025-09-15 20:23:05.736412...
2025-09-15 20:23:17.485 wdl.w:ptcp.w:call-paraphase-22.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for hba for sample m84036_250809_035451_s4.bc2119 at 2025-09-15 20:23:06.129599...
2025-09-15 20:23:17.485 wdl.w:ptcp.w:call-paraphase-22.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for gba for sample m84036_250809_035451_s4.bc2119 at 2025-09-15 20:23:07.537368...
2025-09-15 20:23:17.485 wdl.w:ptcp.w:call-paraphase-22.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for cyp21 for sample m84036_250809_035451_s4.bc2119 at 2025-09-15 20:23:08.971879...
2025-09-15 20:23:17.485 wdl.w:ptcp.w:call-paraphase-22.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for smn1 for sample m84036_250809_035451_s4.bc2119 at 2025-09-15 20:23:12.895403...
2025-09-15 20:23:17.485 wdl.w:ptcp.w:call-paraphase-22.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning to gene2 region for smn1 for sample m84036_250809_035451_s4.bc2119 at 2025-09-15 20:23:13.045021...
2025-09-15 20:23:19.037 wdl.w:ptcp.w:call-paraphase-15.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for smn1 for sample m84036_250809_035451_s4.bc2112 at 2025-09-15 20:23:06.686779...
2025-09-15 20:23:19.038 wdl.w:ptcp.w:call-paraphase-15.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for hba for sample m84036_250809_035451_s4.bc2112 at 2025-09-15 20:23:07.870025...
2025-09-15 20:23:19.038 wdl.w:ptcp.w:call-paraphase-15.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for gba for sample m84036_250809_035451_s4.bc2112 at 2025-09-15 20:23:08.050759...
2025-09-15 20:23:19.038 wdl.w:ptcp.w:call-paraphase-15.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for cyp21 for sample m84036_250809_035451_s4.bc2112 at 2025-09-15 20:23:08.320520...
2025-09-15 20:23:19.038 wdl.w:ptcp.w:call-paraphase-15.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for smn1 for sample m84036_250809_035451_s4.bc2112 at 2025-09-15 20:23:16.374723...
2025-09-15 20:23:19.038 wdl.w:ptcp.w:call-paraphase-15.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning to gene2 region for smn1 for sample m84036_250809_035451_s4.bc2112 at 2025-09-15 20:23:16.516720...
2025-09-15 20:23:20.520 wdl.w:ptcp.w:call-paraphase-22.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for smn1 for sample m84036_250809_035451_s4.bc2119 at 2025-09-15 20:23:13.765185...
2025-09-15 20:23:20.520 wdl.w:ptcp.w:call-paraphase-22.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for f8inv1 for sample m84036_250809_035451_s4.bc2119 at 2025-09-15 20:23:19.820004...
2025-09-15 20:23:20.520 wdl.w:ptcp.w:call-paraphase-22.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for f8inv1 for sample m84036_250809_035451_s4.bc2119 at 2025-09-15 20:23:19.820714...
2025-09-15 20:23:21.260 wdl.w:ptcp.w:call-paraphase-31.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for smn1 for sample m84036_250809_035451_s4.bc2128 at 2025-09-15 20:23:07.532081...
2025-09-15 20:23:21.261 wdl.w:ptcp.w:call-paraphase-31.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for hba for sample m84036_250809_035451_s4.bc2128 at 2025-09-15 20:23:07.819186...
2025-09-15 20:23:21.261 wdl.w:ptcp.w:call-paraphase-31.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for gba for sample m84036_250809_035451_s4.bc2128 at 2025-09-15 20:23:08.261051...
2025-09-15 20:23:21.261 wdl.w:ptcp.w:call-paraphase-31.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for cyp21 for sample m84036_250809_035451_s4.bc2128 at 2025-09-15 20:23:08.966325...
2025-09-15 20:23:21.261 wdl.w:ptcp.w:call-paraphase-31.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for smn1 for sample m84036_250809_035451_s4.bc2128 at 2025-09-15 20:23:15.261506...
2025-09-15 20:23:21.261 wdl.w:ptcp.w:call-paraphase-31.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning to gene2 region for smn1 for sample m84036_250809_035451_s4.bc2128 at 2025-09-15 20:23:15.477479...
2025-09-15 20:23:21.537 wdl.w:ptcp.w:call-paraphase-34.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for hba for sample m84036_250809_035451_s4.bc2131 at 2025-09-15 20:23:08.156343...
2025-09-15 20:23:21.538 wdl.w:ptcp.w:call-paraphase-34.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for smn1 for sample m84036_250809_035451_s4.bc2131 at 2025-09-15 20:23:08.199525...
2025-09-15 20:23:21.538 wdl.w:ptcp.w:call-paraphase-34.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for gba for sample m84036_250809_035451_s4.bc2131 at 2025-09-15 20:23:08.544948...
2025-09-15 20:23:21.538 wdl.w:ptcp.w:call-paraphase-34.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for cyp21 for sample m84036_250809_035451_s4.bc2131 at 2025-09-15 20:23:09.151486...
2025-09-15 20:23:21.538 wdl.w:ptcp.w:call-paraphase-34.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for smn1 for sample m84036_250809_035451_s4.bc2131 at 2025-09-15 20:23:18.898990...
2025-09-15 20:23:21.538 wdl.w:ptcp.w:call-paraphase-34.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning to gene2 region for smn1 for sample m84036_250809_035451_s4.bc2131 at 2025-09-15 20:23:19.306337...
2025-09-15 20:23:22.742 wdl.w:ptcp.w:call-paraphase-23.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for smn1 for sample m84036_250809_035451_s4.bc2120 at 2025-09-15 20:23:08.976489...
2025-09-15 20:23:22.742 wdl.w:ptcp.w:call-paraphase-23.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for hba for sample m84036_250809_035451_s4.bc2120 at 2025-09-15 20:23:09.358920...
2025-09-15 20:23:22.742 wdl.w:ptcp.w:call-paraphase-23.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for gba for sample m84036_250809_035451_s4.bc2120 at 2025-09-15 20:23:09.821488...
2025-09-15 20:23:22.742 wdl.w:ptcp.w:call-paraphase-23.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for cyp21 for sample m84036_250809_035451_s4.bc2120 at 2025-09-15 20:23:10.715618...
2025-09-15 20:23:22.742 wdl.w:ptcp.w:call-paraphase-23.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for smn1 for sample m84036_250809_035451_s4.bc2120 at 2025-09-15 20:23:20.241022...
2025-09-15 20:23:22.742 wdl.w:ptcp.w:call-paraphase-23.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning to gene2 region for smn1 for sample m84036_250809_035451_s4.bc2120 at 2025-09-15 20:23:20.609689...
2025-09-15 20:23:25.832 wdl.w:ptcp.t:call-pbmm2_align_hifi-36 INFO output :: name: "mapped_bam", value: "m84036_250809_035451_s4.bc2133.mapped.bam"
2025-09-15 20:23:25.835 wdl.w:ptcp.t:call-pbmm2_align_hifi-36 INFO output :: name: "mapped_bam_bai", value: "m84036_250809_035451_s4.bc2133.mapped.bam.bai"
2025-09-15 20:23:25.836 wdl.w:ptcp.t:call-pbmm2_align_hifi-36 INFO output :: name: "mapped_bam_pbi", value: "m84036_250809_035451_s4.bc2133.mapped.bam.pbi"
2025-09-15 20:23:25.837 wdl.w:ptcp.t:call-pbmm2_align_hifi-36 INFO output :: name: "report", value: "mapping_stats.report.json"
2025-09-15 20:23:25.908 wdl.w:ptcp.t:call-pbmm2_align_hifi-36 NOTICE done
2025-09-15 20:23:25.914 wdl.w:ptcp NOTICE finish :: job: "call-pbmm2_align_hifi-36"
2025-09-15 20:23:25.915 wdl.w:ptcp INFO output :: job: "call-pbmm2_align_hifi-36", values: {"report": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-36/out/mapping_stats.report.json", "mapped_bam_pbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-36/out/m84036_250809_035451_s4.bc2133.mapped.bam.pbi", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-36/out/m84036_250809_035451_s4.bc2133.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-36/out/m84036_250809_035451_s4.bc2133.mapped.bam"}
2025-09-15 20:23:25.916 wdl.w:ptcp NOTICE ready :: job: "call-paraphase-36", callee: "paraphase"
2025-09-15 20:23:25.916 wdl.w:ptcp INFO input :: job: "call-paraphase-36", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf", "genome_version": "38", "config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-36/out/m84036_250809_035451_s4.bc2133.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-36/out/m84036_250809_035451_s4.bc2133.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2133"}
2025-09-15 20:23:25.917 wdl.w:ptcp NOTICE ready :: job: "call-sawfish-36", callee: "sawfish"
2025-09-15 20:23:25.917 wdl.w:ptcp INFO input :: job: "call-sawfish-36", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-36/out/m84036_250809_035451_s4.bc2133.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-36/out/m84036_250809_035451_s4.bc2133.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2133"}
2025-09-15 20:23:25.920 wdl.w:ptcp NOTICE ready :: job: "call-trgt-36", callee: "trgt"
2025-09-15 20:23:25.919 wdl.w:ptcp.w:call-trgt-19.t:call-get_reads_overlapping_repeats NOTICE task setup :: name: "get_reads_overlapping_repeats", source: "./trgt.wdl", line: 182, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-19/call-get_reads_overlapping_repeats", thread: 140611407550016
2025-09-15 20:23:25.920 wdl.w:ptcp INFO input :: job: "call-trgt-36", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-36/out/m84036_250809_035451_s4.bc2133.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-36/out/m84036_250809_035451_s4.bc2133.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2133"}
2025-09-15 20:23:25.922 wdl.w:ptcp.w:call-paraphase-36 NOTICE workflow start :: name: "paraphase", source: "./paraphase.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-36"
2025-09-15 20:23:25.928 wdl.w:ptcp.w:call-sawfish-36 NOTICE workflow start :: name: "sawfish", source: "./sawfish.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-36"
2025-09-15 20:23:25.931 wdl.w:ptcp.w:call-trgt-36 NOTICE workflow start :: name: "trgt", source: "./trgt.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-36"
2025-09-15 20:23:25.943 wdl.w:ptcp.w:call-paraphase-36 INFO visit :: node: "decl-annotation_vcf", values: {"annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf"}
2025-09-15 20:23:25.943 wdl.w:ptcp.w:call-paraphase-36 INFO visit :: node: "decl-config_file", values: {"config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml"}
2025-09-15 20:23:25.943 wdl.w:ptcp.w:call-trgt-19.t:call-get_reads_overlapping_repeats INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:23:25.944 wdl.w:ptcp.w:call-paraphase-36 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:23:25.944 wdl.w:ptcp.w:call-trgt-19.t:call-get_reads_overlapping_repeats INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:23:25.945 wdl.w:ptcp.w:call-paraphase-36 INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:23:25.945 wdl.w:ptcp.w:call-trgt-19.t:call-get_reads_overlapping_repeats INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2116.mapped.bam.bai"
2025-09-15 20:23:25.945 wdl.w:ptcp.w:call-paraphase-36 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-36/out/m84036_250809_035451_s4.bc2133.mapped.bam"}
2025-09-15 20:23:25.946 wdl.w:ptcp.w:call-trgt-19.t:call-get_reads_overlapping_repeats INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2116.mapped.bam"
2025-09-15 20:23:25.946 wdl.w:ptcp.w:call-paraphase-36 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-36/out/m84036_250809_035451_s4.bc2133.mapped.bam.bai"}
2025-09-15 20:23:25.946 wdl.w:ptcp.w:call-trgt-19.t:call-get_reads_overlapping_repeats INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2116"
2025-09-15 20:23:25.946 wdl.w:ptcp.w:call-paraphase-36 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:23:25.947 wdl.w:ptcp.w:call-paraphase-36 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:23:25.947 wdl.w:ptcp.w:call-trgt-19.t:call-get_reads_overlapping_repeats INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:23:25.947 wdl.w:ptcp.w:call-paraphase-36 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2133"}
2025-09-15 20:23:25.948 wdl.w:ptcp.w:call-trgt-19.t:call-get_reads_overlapping_repeats INFO eval :: name: "expand_size", value: 3000
2025-09-15 20:23:25.948 wdl.w:ptcp.w:call-paraphase-36 INFO visit :: node: "decl-sex", values: {"sex": "F"}
2025-09-15 20:23:25.948 wdl.w:ptcp.w:call-trgt-19.t:call-get_reads_overlapping_repeats INFO eval :: name: "threads", value: 1
2025-09-15 20:23:25.949 wdl.w:ptcp.w:call-paraphase-36 NOTICE ready :: job: "call-run_paraphase", callee: "run_paraphase"
2025-09-15 20:23:25.949 wdl.w:ptcp.w:call-trgt-19.t:call-get_reads_overlapping_repeats INFO eval :: name: "expanded_bed_name", value: "m84036_250809_035451_s4.bc2116.expanded.bed"
2025-09-15 20:23:25.949 wdl.w:ptcp.w:call-paraphase-36 INFO input :: job: "call-run_paraphase", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf", "genome_version": "38", "config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-36/out/m84036_250809_035451_s4.bc2133.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-36/out/m84036_250809_035451_s4.bc2133.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2133"}
2025-09-15 20:23:25.950 wdl.w:ptcp.w:call-trgt-19.t:call-get_reads_overlapping_repeats INFO eval :: name: "disk_size", value: 11
2025-09-15 20:23:25.950 wdl.w:ptcp.w:call-trgt-19.t:call-get_reads_overlapping_repeats INFO eval :: name: "output_name", value: "m84036_250809_035451_s4.bc2116.repeats.bam"
2025-09-15 20:23:25.950 wdl.w:ptcp.w:call-trgt-19.t:call-get_reads_overlapping_repeats INFO eval :: name: "index_name", value: "m84036_250809_035451_s4.bc2116.repeats.bam.bai"
2025-09-15 20:23:25.951 wdl.w:ptcp.w:call-trgt-19.t:call-get_reads_overlapping_repeats INFO eval :: name: "output_name_with_index", value: "m84036_250809_035451_s4.bc2116.repeats.bam##idx##m84036_250809_035451_s4.bc2116.repeats.bam.bai"
2025-09-15 20:23:25.951 wdl.w:ptcp.w:call-trgt-19.t:call-get_reads_overlapping_repeats INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:23:25.952 wdl.w:ptcp.w:call-trgt-19.t:call-get_reads_overlapping_repeats WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:23:25.952 wdl.w:ptcp.w:call-sawfish-36 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:23:25.953 wdl.w:ptcp.w:call-sawfish-36 INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:23:25.953 wdl.w:ptcp.w:call-sawfish-36 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-36/out/m84036_250809_035451_s4.bc2133.mapped.bam"}
2025-09-15 20:23:25.953 wdl.w:ptcp.w:call-sawfish-36 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-36/out/m84036_250809_035451_s4.bc2133.mapped.bam.bai"}
2025-09-15 20:23:25.953 wdl.w:ptcp.w:call-sawfish-36 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:23:25.953 wdl.w:ptcp.w:call-trgt-19.t:call-get_reads_overlapping_repeats INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:23:25.953 wdl.w:ptcp.w:call-sawfish-36 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:23:25.954 wdl.w:ptcp.w:call-sawfish-36 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2133"}
2025-09-15 20:23:25.954 wdl.w:ptcp.w:call-trgt-19.t:call-get_reads_overlapping_repeats INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:23:25.954 wdl.w:ptcp.w:call-sawfish-36 NOTICE ready :: job: "call-run_sawfish", callee: "run_sawfish"
2025-09-15 20:23:25.955 wdl.w:ptcp.w:call-trgt-36 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:23:25.955 wdl.w:ptcp.w:call-sawfish-36 INFO input :: job: "call-run_sawfish", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-36/out/m84036_250809_035451_s4.bc2133.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-36/out/m84036_250809_035451_s4.bc2133.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2133"}
2025-09-15 20:23:25.955 wdl.w:ptcp.w:call-trgt-36 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-36/out/m84036_250809_035451_s4.bc2133.mapped.bam"}
2025-09-15 20:23:25.956 wdl.w:ptcp.w:call-trgt-36 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-36/out/m84036_250809_035451_s4.bc2133.mapped.bam.bai"}
2025-09-15 20:23:25.956 wdl.w:ptcp.w:call-trgt-36 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:23:25.956 wdl.w:ptcp.w:call-trgt-36 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:23:25.956 wdl.w:ptcp.w:call-trgt-36 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2133"}
2025-09-15 20:23:25.956 wdl.w:ptcp.w:call-trgt-36 INFO visit :: node: "decl-sex", values: {"sex": "F"}
2025-09-15 20:23:25.956 wdl.w:ptcp.w:call-trgt-36 INFO visit :: node: "decl-trgt_bed", values: {"trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"}
2025-09-15 20:23:25.956 wdl.w:ptcp.w:call-trgt-36 NOTICE ready :: job: "call-get_reads_overlapping_repeats", callee: "get_reads_overlapping_repeats"
2025-09-15 20:23:25.956 wdl.w:ptcp.w:call-trgt-36 INFO input :: job: "call-get_reads_overlapping_repeats", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-36/out/m84036_250809_035451_s4.bc2133.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-36/out/m84036_250809_035451_s4.bc2133.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2133"}
2025-09-15 20:23:25.957 wdl.w:ptcp.w:call-trgt-36 NOTICE ready :: job: "call-trgt_genotype", callee: "trgt_genotype"
2025-09-15 20:23:25.957 wdl.w:ptcp.w:call-trgt-36 INFO input :: job: "call-trgt_genotype", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-36/out/m84036_250809_035451_s4.bc2133.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-36/out/m84036_250809_035451_s4.bc2133.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2133"}
2025-09-15 20:23:26.005 wdl.w:ptcp.w:call-trgt-19.t:call-get_reads_overlapping_repeats INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 9, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-19/call-get_reads_overlapping_repeats/_singularity_tmpdir_r3j6f6ut"
2025-09-15 20:23:26.005 wdl.w:ptcp.w:call-trgt-19.t:call-get_reads_overlapping_repeats INFO Slurm invocation: srun --job-name call-get_reads_overlapping_repeats --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-19/call-get_reads_overlapping_repeats/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-19/call-get_reads_overlapping_repeats/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-19/call-get_reads_overlapping_repeats/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-19/call-get_reads_overlapping_repeats/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-19/out/m84036_250809_035451_s4.bc2116.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2116.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-19/out/m84036_250809_035451_s4.bc2116.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2116.mapped.bam.bai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-19/call-get_reads_overlapping_repeats/_singularity_tmpdir_r3j6f6ut/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-19/call-get_reads_overlapping_repeats/_singularity_tmpdir_r3j6f6ut/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:23:26.023 wdl.w:ptcp.w:call-trgt-19.t:call-get_reads_overlapping_repeats NOTICE slurm_singularity run :: pid: 1198989, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-19/call-get_reads_overlapping_repeats/slurm_singularity.log.txt"
2025-09-15 20:23:26.054 wdl.w:ptcp.t:call-pbmm2_align_hifi-38 INFO output :: name: "mapped_bam", value: "m84036_250809_035451_s4.bc2135.mapped.bam"
2025-09-15 20:23:26.057 wdl.w:ptcp.t:call-pbmm2_align_hifi-38 INFO output :: name: "mapped_bam_bai", value: "m84036_250809_035451_s4.bc2135.mapped.bam.bai"
2025-09-15 20:23:26.059 wdl.w:ptcp.t:call-pbmm2_align_hifi-38 INFO output :: name: "mapped_bam_pbi", value: "m84036_250809_035451_s4.bc2135.mapped.bam.pbi"
2025-09-15 20:23:26.060 wdl.w:ptcp.t:call-pbmm2_align_hifi-38 INFO output :: name: "report", value: "mapping_stats.report.json"
2025-09-15 20:23:26.139 wdl.w:ptcp.t:call-pbmm2_align_hifi-38 NOTICE done
2025-09-15 20:23:26.145 wdl.w:ptcp NOTICE finish :: job: "call-pbmm2_align_hifi-38"
2025-09-15 20:23:26.145 wdl.w:ptcp INFO output :: job: "call-pbmm2_align_hifi-38", values: {"report": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-38/out/mapping_stats.report.json", "mapped_bam_pbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-38/out/m84036_250809_035451_s4.bc2135.mapped.bam.pbi", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-38/out/m84036_250809_035451_s4.bc2135.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-38/out/m84036_250809_035451_s4.bc2135.mapped.bam"}
2025-09-15 20:23:26.146 wdl.w:ptcp NOTICE ready :: job: "call-paraphase-38", callee: "paraphase"
2025-09-15 20:23:26.146 wdl.w:ptcp INFO input :: job: "call-paraphase-38", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf", "genome_version": "38", "config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-38/out/m84036_250809_035451_s4.bc2135.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-38/out/m84036_250809_035451_s4.bc2135.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2135"}
2025-09-15 20:23:26.147 wdl.w:ptcp NOTICE ready :: job: "call-sawfish-38", callee: "sawfish"
2025-09-15 20:23:26.148 wdl.w:ptcp INFO input :: job: "call-sawfish-38", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-38/out/m84036_250809_035451_s4.bc2135.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-38/out/m84036_250809_035451_s4.bc2135.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2135"}
2025-09-15 20:23:26.150 wdl.w:ptcp NOTICE ready :: job: "call-trgt-38", callee: "trgt"
2025-09-15 20:23:26.151 wdl.w:ptcp INFO input :: job: "call-trgt-38", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-38/out/m84036_250809_035451_s4.bc2135.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-38/out/m84036_250809_035451_s4.bc2135.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2135"}
2025-09-15 20:23:26.152 wdl.w:ptcp.w:call-trgt-19.t:call-trgt_genotype NOTICE task setup :: name: "trgt_genotype", source: "./trgt.wdl", line: 272, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-19/call-trgt_genotype", thread: 140610912642624
2025-09-15 20:23:26.153 wdl.w:ptcp.w:call-paraphase-38 NOTICE workflow start :: name: "paraphase", source: "./paraphase.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-38"
2025-09-15 20:23:26.157 wdl.w:ptcp.w:call-sawfish-38 NOTICE workflow start :: name: "sawfish", source: "./sawfish.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-38"
2025-09-15 20:23:26.160 wdl.w:ptcp.w:call-trgt-38 NOTICE workflow start :: name: "trgt", source: "./trgt.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-38"
2025-09-15 20:23:26.176 wdl.w:ptcp.w:call-paraphase-38 INFO visit :: node: "decl-annotation_vcf", values: {"annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf"}
2025-09-15 20:23:26.177 wdl.w:ptcp.w:call-paraphase-38 INFO visit :: node: "decl-config_file", values: {"config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml"}
2025-09-15 20:23:26.177 wdl.w:ptcp.w:call-paraphase-38 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:23:26.177 wdl.w:ptcp.w:call-paraphase-38 INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:23:26.178 wdl.w:ptcp.w:call-paraphase-38 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-38/out/m84036_250809_035451_s4.bc2135.mapped.bam"}
2025-09-15 20:23:26.178 wdl.w:ptcp.w:call-paraphase-38 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-38/out/m84036_250809_035451_s4.bc2135.mapped.bam.bai"}
2025-09-15 20:23:26.178 wdl.w:ptcp.w:call-paraphase-38 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:23:26.179 wdl.w:ptcp.w:call-paraphase-38 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:23:26.179 wdl.w:ptcp.w:call-paraphase-38 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2135"}
2025-09-15 20:23:26.179 wdl.w:ptcp.w:call-paraphase-38 INFO visit :: node: "decl-sex", values: {"sex": "F"}
2025-09-15 20:23:26.180 wdl.w:ptcp.w:call-paraphase-38 NOTICE ready :: job: "call-run_paraphase", callee: "run_paraphase"
2025-09-15 20:23:26.180 wdl.w:ptcp.w:call-paraphase-38 INFO input :: job: "call-run_paraphase", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf", "genome_version": "38", "config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-38/out/m84036_250809_035451_s4.bc2135.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-38/out/m84036_250809_035451_s4.bc2135.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2135"}
2025-09-15 20:23:26.181 wdl.w:ptcp.w:call-sawfish-38 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:23:26.182 wdl.w:ptcp.w:call-sawfish-38 INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:23:26.182 wdl.w:ptcp.w:call-sawfish-38 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-38/out/m84036_250809_035451_s4.bc2135.mapped.bam"}
2025-09-15 20:23:26.182 wdl.w:ptcp.w:call-trgt-19.t:call-trgt_genotype INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:23:26.182 wdl.w:ptcp.w:call-sawfish-38 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-38/out/m84036_250809_035451_s4.bc2135.mapped.bam.bai"}
2025-09-15 20:23:26.182 wdl.w:ptcp.w:call-trgt-19.t:call-trgt_genotype INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:23:26.182 wdl.w:ptcp.w:call-sawfish-38 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:23:26.183 wdl.w:ptcp.w:call-trgt-19.t:call-trgt_genotype INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:23:26.184 wdl.w:ptcp.w:call-sawfish-38 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:23:26.183 wdl.w:ptcp.w:call-trgt-38 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:23:26.184 wdl.w:ptcp.w:call-trgt-19.t:call-trgt_genotype INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:23:26.184 wdl.w:ptcp.w:call-sawfish-38 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2135"}
2025-09-15 20:23:26.184 wdl.w:ptcp.w:call-trgt-38 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-38/out/m84036_250809_035451_s4.bc2135.mapped.bam"}
2025-09-15 20:23:26.184 wdl.w:ptcp.w:call-trgt-19.t:call-trgt_genotype INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2116.mapped.bam.bai"
2025-09-15 20:23:26.185 wdl.w:ptcp.w:call-sawfish-38 NOTICE ready :: job: "call-run_sawfish", callee: "run_sawfish"
2025-09-15 20:23:26.186 wdl.w:ptcp.w:call-trgt-38 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-38/out/m84036_250809_035451_s4.bc2135.mapped.bam.bai"}
2025-09-15 20:23:26.186 wdl.w:ptcp.w:call-trgt-19.t:call-trgt_genotype INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2116.mapped.bam"
2025-09-15 20:23:26.186 wdl.w:ptcp.w:call-sawfish-38 INFO input :: job: "call-run_sawfish", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-38/out/m84036_250809_035451_s4.bc2135.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-38/out/m84036_250809_035451_s4.bc2135.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2135"}
2025-09-15 20:23:26.186 wdl.w:ptcp.w:call-trgt-38 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:23:26.186 wdl.w:ptcp.w:call-trgt-19.t:call-trgt_genotype INFO input :: name: "sex", value: "F"
2025-09-15 20:23:26.186 wdl.w:ptcp.w:call-trgt-38 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:23:26.186 wdl.w:ptcp.w:call-trgt-19.t:call-trgt_genotype INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2116"
2025-09-15 20:23:26.186 wdl.w:ptcp.w:call-trgt-38 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2135"}
2025-09-15 20:23:26.187 wdl.w:ptcp.w:call-trgt-19.t:call-trgt_genotype INFO eval :: name: "mem_gb", value: 16
2025-09-15 20:23:26.187 wdl.w:ptcp.w:call-trgt-38 INFO visit :: node: "decl-sex", values: {"sex": "F"}
2025-09-15 20:23:26.187 wdl.w:ptcp.w:call-trgt-19.t:call-trgt_genotype INFO eval :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2116.trgt"
2025-09-15 20:23:26.187 wdl.w:ptcp.w:call-trgt-38 INFO visit :: node: "decl-trgt_bed", values: {"trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"}
2025-09-15 20:23:26.187 wdl.w:ptcp.w:call-trgt-19.t:call-trgt_genotype INFO eval :: name: "threads", value: 8
2025-09-15 20:23:26.187 wdl.w:ptcp.w:call-trgt-38 NOTICE ready :: job: "call-get_reads_overlapping_repeats", callee: "get_reads_overlapping_repeats"
2025-09-15 20:23:26.188 wdl.w:ptcp.w:call-trgt-38 INFO input :: job: "call-get_reads_overlapping_repeats", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-38/out/m84036_250809_035451_s4.bc2135.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-38/out/m84036_250809_035451_s4.bc2135.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2135"}
2025-09-15 20:23:26.188 wdl.w:ptcp.w:call-trgt-19.t:call-trgt_genotype INFO eval :: name: "disk_size", value: 27
2025-09-15 20:23:26.188 wdl.w:ptcp.w:call-trgt-19.t:call-trgt_genotype INFO eval :: name: "karyotype", value: "XX"
2025-09-15 20:23:26.189 wdl.w:ptcp.w:call-trgt-38 NOTICE ready :: job: "call-trgt_genotype", callee: "trgt_genotype"
2025-09-15 20:23:26.189 wdl.w:ptcp.w:call-trgt-19.t:call-trgt_genotype INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 8, memory_reservation: 16000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:23:26.189 wdl.w:ptcp.w:call-trgt-38 INFO input :: job: "call-trgt_genotype", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-38/out/m84036_250809_035451_s4.bc2135.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-38/out/m84036_250809_035451_s4.bc2135.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2135"}
2025-09-15 20:23:26.189 wdl.w:ptcp.w:call-trgt-19.t:call-trgt_genotype WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:23:26.190 wdl.w:ptcp.w:call-trgt-19.t:call-trgt_genotype INFO provisioned :: seconds_waited: 0, cpu: 8, mem_bytes: 16000000000
2025-09-15 20:23:26.190 wdl.w:ptcp.w:call-trgt-19.t:call-trgt_genotype INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:23:26.241 wdl.w:ptcp.w:call-trgt-19.t:call-trgt_genotype INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 11, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-19/call-trgt_genotype/_singularity_tmpdir_p74gbdmg"
2025-09-15 20:23:26.241 wdl.w:ptcp.w:call-trgt-19.t:call-trgt_genotype INFO Slurm invocation: srun --job-name call-trgt_genotype --partition compute,compute9 --cpus-per-task 8 --mem 15259M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-19/call-trgt_genotype/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-19/call-trgt_genotype/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-19/call-trgt_genotype/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-19/call-trgt_genotype/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-19/out/m84036_250809_035451_s4.bc2116.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2116.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-19/out/m84036_250809_035451_s4.bc2116.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2116.mapped.bam.bai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-19/call-trgt_genotype/_singularity_tmpdir_p74gbdmg/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-19/call-trgt_genotype/_singularity_tmpdir_p74gbdmg/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:23:26.252 wdl.w:ptcp.w:call-trgt-19.t:call-trgt_genotype NOTICE slurm_singularity run :: pid: 1198997, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-19/call-trgt_genotype/slurm_singularity.log.txt"
2025-09-15 20:23:26.270 wdl.w:ptcp.t:call-pbmm2_align_hifi-74.slurm_singularity INFO srun: job 51797295 has been allocated resources
2025-09-15 20:23:26.271 wdl.w:ptcp.t:call-pbmm2_align_hifi-74.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:26.271 wdl.w:ptcp.t:call-pbmm2_align_hifi-74.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:23:26.339 wdl.w:ptcp.t:call-pbmm2_align_hifi-72.slurm_singularity INFO srun: job 51797294 has been allocated resources
2025-09-15 20:23:26.342 wdl.w:ptcp.t:call-pbmm2_align_hifi-72.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:26.342 wdl.w:ptcp.t:call-pbmm2_align_hifi-72.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:23:26.448 wdl.w:ptcp.t:call-pbmm2_align_hifi-37 INFO output :: name: "mapped_bam", value: "m84036_250809_035451_s4.bc2134.mapped.bam"
2025-09-15 20:23:26.452 wdl.w:ptcp.t:call-pbmm2_align_hifi-37 INFO output :: name: "mapped_bam_bai", value: "m84036_250809_035451_s4.bc2134.mapped.bam.bai"
2025-09-15 20:23:26.453 wdl.w:ptcp.t:call-pbmm2_align_hifi-37 INFO output :: name: "mapped_bam_pbi", value: "m84036_250809_035451_s4.bc2134.mapped.bam.pbi"
2025-09-15 20:23:26.454 wdl.w:ptcp.t:call-pbmm2_align_hifi-37 INFO output :: name: "report", value: "mapping_stats.report.json"
2025-09-15 20:23:26.496 wdl.w:ptcp.w:call-paraphase-14.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for smn1 for sample m84036_250809_035451_s4.bc2111 at 2025-09-15 20:23:17.798231...
2025-09-15 20:23:26.497 wdl.w:ptcp.w:call-paraphase-14.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for f8inv1 for sample m84036_250809_035451_s4.bc2111 at 2025-09-15 20:23:25.006267...
2025-09-15 20:23:26.497 wdl.w:ptcp.w:call-paraphase-14.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for f8inv1 for sample m84036_250809_035451_s4.bc2111 at 2025-09-15 20:23:25.024804...
2025-09-15 20:23:26.579 wdl.w:ptcp.t:call-pbmm2_align_hifi-37 NOTICE done
2025-09-15 20:23:26.587 wdl.w:ptcp NOTICE finish :: job: "call-pbmm2_align_hifi-37"
2025-09-15 20:23:26.587 wdl.w:ptcp INFO output :: job: "call-pbmm2_align_hifi-37", values: {"report": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-37/out/mapping_stats.report.json", "mapped_bam_pbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-37/out/m84036_250809_035451_s4.bc2134.mapped.bam.pbi", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-37/out/m84036_250809_035451_s4.bc2134.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-37/out/m84036_250809_035451_s4.bc2134.mapped.bam"}
2025-09-15 20:23:26.588 wdl.w:ptcp NOTICE ready :: job: "call-paraphase-37", callee: "paraphase"
2025-09-15 20:23:26.588 wdl.w:ptcp INFO input :: job: "call-paraphase-37", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf", "genome_version": "38", "config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-37/out/m84036_250809_035451_s4.bc2134.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-37/out/m84036_250809_035451_s4.bc2134.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2134"}
2025-09-15 20:23:26.589 wdl.w:ptcp NOTICE ready :: job: "call-sawfish-37", callee: "sawfish"
2025-09-15 20:23:26.589 wdl.w:ptcp INFO input :: job: "call-sawfish-37", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-37/out/m84036_250809_035451_s4.bc2134.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-37/out/m84036_250809_035451_s4.bc2134.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2134"}
2025-09-15 20:23:26.593 wdl.w:ptcp NOTICE ready :: job: "call-trgt-37", callee: "trgt"
2025-09-15 20:23:26.593 wdl.w:ptcp INFO input :: job: "call-trgt-37", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-37/out/m84036_250809_035451_s4.bc2134.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-37/out/m84036_250809_035451_s4.bc2134.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2134"}
2025-09-15 20:23:26.593 wdl.w:ptcp.w:call-paraphase-17.t:call-run_paraphase NOTICE task setup :: name: "run_paraphase", source: "./paraphase.wdl", line: 127, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-17/call-run_paraphase", thread: 140610921035328
2025-09-15 20:23:26.595 wdl.w:ptcp.w:call-paraphase-37 NOTICE workflow start :: name: "paraphase", source: "./paraphase.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-37"
2025-09-15 20:23:26.599 wdl.w:ptcp.w:call-sawfish-37 NOTICE workflow start :: name: "sawfish", source: "./sawfish.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-37"
2025-09-15 20:23:26.606 wdl.w:ptcp.w:call-trgt-37 NOTICE workflow start :: name: "trgt", source: "./trgt.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-37"
2025-09-15 20:23:26.616 wdl.w:ptcp.w:call-paraphase-37 INFO visit :: node: "decl-annotation_vcf", values: {"annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf"}
2025-09-15 20:23:26.617 wdl.w:ptcp.w:call-paraphase-37 INFO visit :: node: "decl-config_file", values: {"config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml"}
2025-09-15 20:23:26.617 wdl.w:ptcp.w:call-paraphase-37 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:23:26.617 wdl.w:ptcp.w:call-paraphase-37 INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:23:26.618 wdl.w:ptcp.w:call-paraphase-37 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-37/out/m84036_250809_035451_s4.bc2134.mapped.bam"}
2025-09-15 20:23:26.618 wdl.w:ptcp.w:call-paraphase-37 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-37/out/m84036_250809_035451_s4.bc2134.mapped.bam.bai"}
2025-09-15 20:23:26.618 wdl.w:ptcp.w:call-paraphase-37 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:23:26.618 wdl.w:ptcp.w:call-paraphase-37 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:23:26.618 wdl.w:ptcp.w:call-paraphase-37 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2134"}
2025-09-15 20:23:26.618 wdl.w:ptcp.w:call-paraphase-37 INFO visit :: node: "decl-sex", values: {"sex": "F"}
2025-09-15 20:23:26.619 wdl.w:ptcp.w:call-paraphase-37 NOTICE ready :: job: "call-run_paraphase", callee: "run_paraphase"
2025-09-15 20:23:26.619 wdl.w:ptcp.w:call-paraphase-37 INFO input :: job: "call-run_paraphase", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf", "genome_version": "38", "config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-37/out/m84036_250809_035451_s4.bc2134.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-37/out/m84036_250809_035451_s4.bc2134.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2134"}
2025-09-15 20:23:26.623 wdl.w:ptcp.w:call-sawfish-37 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:23:26.624 wdl.w:ptcp.w:call-paraphase-17.t:call-run_paraphase INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:23:26.624 wdl.w:ptcp.w:call-sawfish-37 INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:23:26.624 wdl.w:ptcp.w:call-paraphase-17.t:call-run_paraphase INFO input :: name: "annotation_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf"
2025-09-15 20:23:26.624 wdl.w:ptcp.w:call-sawfish-37 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-37/out/m84036_250809_035451_s4.bc2134.mapped.bam"}
2025-09-15 20:23:26.624 wdl.w:ptcp.w:call-paraphase-17.t:call-run_paraphase INFO input :: name: "genome_version", value: "38"
2025-09-15 20:23:26.624 wdl.w:ptcp.w:call-sawfish-37 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-37/out/m84036_250809_035451_s4.bc2134.mapped.bam.bai"}
2025-09-15 20:23:26.624 wdl.w:ptcp.w:call-paraphase-17.t:call-run_paraphase INFO input :: name: "config_file", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/paraphase_config.GRCh38.yaml"
2025-09-15 20:23:26.625 wdl.w:ptcp.w:call-sawfish-37 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:23:26.625 wdl.w:ptcp.w:call-paraphase-17.t:call-run_paraphase INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:23:26.625 wdl.w:ptcp.w:call-sawfish-37 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:23:26.625 wdl.w:ptcp.w:call-paraphase-17.t:call-run_paraphase INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:23:26.625 wdl.w:ptcp.w:call-sawfish-37 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2134"}
2025-09-15 20:23:26.625 wdl.w:ptcp.w:call-paraphase-17.t:call-run_paraphase INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2114.mapped.bam.bai"
2025-09-15 20:23:26.625 wdl.w:ptcp.w:call-sawfish-37 NOTICE ready :: job: "call-run_sawfish", callee: "run_sawfish"
2025-09-15 20:23:26.626 wdl.w:ptcp.w:call-paraphase-17.t:call-run_paraphase INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2114.mapped.bam"
2025-09-15 20:23:26.626 wdl.w:ptcp.w:call-sawfish-37 INFO input :: job: "call-run_sawfish", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-37/out/m84036_250809_035451_s4.bc2134.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-37/out/m84036_250809_035451_s4.bc2134.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2134"}
2025-09-15 20:23:26.626 wdl.w:ptcp.w:call-paraphase-17.t:call-run_paraphase INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2114"
2025-09-15 20:23:26.626 wdl.w:ptcp.w:call-paraphase-17.t:call-run_paraphase INFO eval :: name: "threads", value: 4
2025-09-15 20:23:26.626 wdl.w:ptcp.w:call-paraphase-17.t:call-run_paraphase INFO eval :: name: "mem_gb", value: 8
2025-09-15 20:23:26.626 wdl.w:ptcp.w:call-paraphase-17.t:call-run_paraphase INFO eval :: name: "disk_size", value: 27
2025-09-15 20:23:26.627 wdl.w:ptcp.w:call-paraphase-17.t:call-run_paraphase INFO eval :: name: "out_dir", value: "m84036_250809_035451_s4.bc2114_paraphase"
2025-09-15 20:23:26.627 wdl.w:ptcp.w:call-paraphase-17.t:call-run_paraphase INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 4, memory_reservation: 8000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:23:26.627 wdl.w:ptcp.w:call-paraphase-17.t:call-run_paraphase WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:23:26.628 wdl.w:ptcp.w:call-paraphase-17.t:call-run_paraphase INFO provisioned :: seconds_waited: 0, cpu: 4, mem_bytes: 8000000000
2025-09-15 20:23:26.628 wdl.w:ptcp.w:call-paraphase-17.t:call-run_paraphase INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:23:26.660 wdl.w:ptcp.w:call-trgt-37 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:23:26.660 wdl.w:ptcp.w:call-trgt-37 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-37/out/m84036_250809_035451_s4.bc2134.mapped.bam"}
2025-09-15 20:23:26.660 wdl.w:ptcp.w:call-trgt-37 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-37/out/m84036_250809_035451_s4.bc2134.mapped.bam.bai"}
2025-09-15 20:23:26.660 wdl.w:ptcp.w:call-trgt-37 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:23:26.660 wdl.w:ptcp.w:call-trgt-37 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:23:26.660 wdl.w:ptcp.w:call-trgt-37 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2134"}
2025-09-15 20:23:26.660 wdl.w:ptcp.w:call-trgt-37 INFO visit :: node: "decl-sex", values: {"sex": "F"}
2025-09-15 20:23:26.660 wdl.w:ptcp.w:call-trgt-37 INFO visit :: node: "decl-trgt_bed", values: {"trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"}
2025-09-15 20:23:26.661 wdl.w:ptcp.w:call-trgt-37 NOTICE ready :: job: "call-get_reads_overlapping_repeats", callee: "get_reads_overlapping_repeats"
2025-09-15 20:23:26.661 wdl.w:ptcp.w:call-trgt-37 INFO input :: job: "call-get_reads_overlapping_repeats", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-37/out/m84036_250809_035451_s4.bc2134.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-37/out/m84036_250809_035451_s4.bc2134.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2134"}
2025-09-15 20:23:26.662 wdl.w:ptcp.w:call-trgt-37 NOTICE ready :: job: "call-trgt_genotype", callee: "trgt_genotype"
2025-09-15 20:23:26.662 wdl.w:ptcp.w:call-trgt-37 INFO input :: job: "call-trgt_genotype", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-37/out/m84036_250809_035451_s4.bc2134.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-37/out/m84036_250809_035451_s4.bc2134.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2134"}
2025-09-15 20:23:26.706 wdl.w:ptcp.w:call-paraphase-17.t:call-run_paraphase INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-17/call-run_paraphase/_singularity_tmpdir_wi3npdik"
2025-09-15 20:23:26.706 wdl.w:ptcp.w:call-paraphase-17.t:call-run_paraphase INFO Slurm invocation: srun --job-name call-run_paraphase --partition compute,compute9 --cpus-per-task 4 --mem 7629M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-17/call-run_paraphase/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-17/call-run_paraphase/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-17/call-run_paraphase/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-17/call-run_paraphase/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-17/out/m84036_250809_035451_s4.bc2114.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2114.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-17/out/m84036_250809_035451_s4.bc2114.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2114.mapped.bam:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/variant_list/variant_list.GRCh38.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf:ro --bind /ptcp/meta/paraphase/paraphase_config.GRCh38.yaml:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/paraphase_config.GRCh38.yaml:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-17/call-run_paraphase/_singularity_tmpdir_wi3npdik/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-17/call-run_paraphase/_singularity_tmpdir_wi3npdik/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:23:26.724 wdl.w:ptcp.w:call-paraphase-17.t:call-run_paraphase NOTICE slurm_singularity run :: pid: 1199013, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-17/call-run_paraphase/slurm_singularity.log.txt"
2025-09-15 20:23:27.032 wdl.w:ptcp.w:call-trgt-19.t:call-get_reads_overlapping_repeats.slurm_singularity INFO srun: job 51797381 queued and waiting for resources
2025-09-15 20:23:27.263 wdl.w:ptcp.w:call-trgt-19.t:call-trgt_genotype.slurm_singularity INFO srun: job 51797382 queued and waiting for resources
2025-09-15 20:23:27.345 wdl.w:ptcp.t:call-pbmm2_align_hifi-73.slurm_singularity INFO srun: job 51797296 has been allocated resources
2025-09-15 20:23:27.345 wdl.w:ptcp.t:call-pbmm2_align_hifi-73.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:27.345 wdl.w:ptcp.t:call-pbmm2_align_hifi-73.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:23:27.732 wdl.w:ptcp.w:call-paraphase-17.t:call-run_paraphase.slurm_singularity INFO srun: job 51797383 queued and waiting for resources
2025-09-15 20:23:27.770 wdl.w:ptcp.t:call-pbmm2_align_hifi-45 INFO output :: name: "mapped_bam", value: "m84036_250809_035451_s4.bc2142.mapped.bam"
2025-09-15 20:23:27.775 wdl.w:ptcp.t:call-pbmm2_align_hifi-45 INFO output :: name: "mapped_bam_bai", value: "m84036_250809_035451_s4.bc2142.mapped.bam.bai"
2025-09-15 20:23:27.776 wdl.w:ptcp.t:call-pbmm2_align_hifi-45 INFO output :: name: "mapped_bam_pbi", value: "m84036_250809_035451_s4.bc2142.mapped.bam.pbi"
2025-09-15 20:23:27.778 wdl.w:ptcp.t:call-pbmm2_align_hifi-45 INFO output :: name: "report", value: "mapping_stats.report.json"
2025-09-15 20:23:27.877 wdl.w:ptcp.t:call-pbmm2_align_hifi-45 NOTICE done
2025-09-15 20:23:27.883 wdl.w:ptcp NOTICE finish :: job: "call-pbmm2_align_hifi-45"
2025-09-15 20:23:27.884 wdl.w:ptcp INFO output :: job: "call-pbmm2_align_hifi-45", values: {"report": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-45/out/mapping_stats.report.json", "mapped_bam_pbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-45/out/m84036_250809_035451_s4.bc2142.mapped.bam.pbi", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-45/out/m84036_250809_035451_s4.bc2142.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-45/out/m84036_250809_035451_s4.bc2142.mapped.bam"}
2025-09-15 20:23:27.884 wdl.w:ptcp NOTICE ready :: job: "call-paraphase-45", callee: "paraphase"
2025-09-15 20:23:27.884 wdl.w:ptcp INFO input :: job: "call-paraphase-45", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf", "genome_version": "38", "config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-45/out/m84036_250809_035451_s4.bc2142.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-45/out/m84036_250809_035451_s4.bc2142.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2142"}
2025-09-15 20:23:27.886 wdl.w:ptcp NOTICE ready :: job: "call-sawfish-45", callee: "sawfish"
2025-09-15 20:23:27.886 wdl.w:ptcp INFO input :: job: "call-sawfish-45", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-45/out/m84036_250809_035451_s4.bc2142.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-45/out/m84036_250809_035451_s4.bc2142.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2142"}
2025-09-15 20:23:27.890 wdl.w:ptcp NOTICE ready :: job: "call-trgt-45", callee: "trgt"
2025-09-15 20:23:27.890 wdl.w:ptcp INFO input :: job: "call-trgt-45", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-45/out/m84036_250809_035451_s4.bc2142.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-45/out/m84036_250809_035451_s4.bc2142.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2142"}
2025-09-15 20:23:27.895 wdl.w:ptcp.w:call-paraphase-45 NOTICE workflow start :: name: "paraphase", source: "./paraphase.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-45"
2025-09-15 20:23:27.895 wdl.w:ptcp.w:call-sawfish-17.t:call-run_sawfish NOTICE task setup :: name: "run_sawfish", source: "./sawfish.wdl", line: 83, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-17/call-run_sawfish", thread: 140610375771712
2025-09-15 20:23:27.899 wdl.w:ptcp.w:call-sawfish-45 NOTICE workflow start :: name: "sawfish", source: "./sawfish.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-45"
2025-09-15 20:23:27.905 wdl.w:ptcp.w:call-trgt-45 NOTICE workflow start :: name: "trgt", source: "./trgt.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-45"
2025-09-15 20:23:27.906 wdl.w:ptcp.t:call-pbmm2_align_hifi-51 INFO output :: name: "mapped_bam", value: "m84036_250809_035451_s4.bc2148.mapped.bam"
2025-09-15 20:23:27.923 wdl.w:ptcp.t:call-pbmm2_align_hifi-51 INFO output :: name: "mapped_bam_bai", value: "m84036_250809_035451_s4.bc2148.mapped.bam.bai"
2025-09-15 20:23:27.928 wdl.w:ptcp.w:call-sawfish-45 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:23:27.928 wdl.w:ptcp.w:call-sawfish-45 INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:23:27.929 wdl.w:ptcp.w:call-sawfish-45 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-45/out/m84036_250809_035451_s4.bc2142.mapped.bam"}
2025-09-15 20:23:27.929 wdl.w:ptcp.t:call-pbmm2_align_hifi-51 INFO output :: name: "mapped_bam_pbi", value: "m84036_250809_035451_s4.bc2148.mapped.bam.pbi"
2025-09-15 20:23:27.929 wdl.w:ptcp.w:call-sawfish-45 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-45/out/m84036_250809_035451_s4.bc2142.mapped.bam.bai"}
2025-09-15 20:23:27.930 wdl.w:ptcp.w:call-sawfish-45 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:23:27.930 wdl.w:ptcp.w:call-sawfish-45 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:23:27.930 wdl.w:ptcp.w:call-sawfish-45 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2142"}
2025-09-15 20:23:27.930 wdl.w:ptcp.w:call-sawfish-45 NOTICE ready :: job: "call-run_sawfish", callee: "run_sawfish"
2025-09-15 20:23:27.930 wdl.w:ptcp.w:call-sawfish-45 INFO input :: job: "call-run_sawfish", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-45/out/m84036_250809_035451_s4.bc2142.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-45/out/m84036_250809_035451_s4.bc2142.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2142"}
2025-09-15 20:23:27.932 wdl.w:ptcp.w:call-paraphase-45 INFO visit :: node: "decl-annotation_vcf", values: {"annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf"}
2025-09-15 20:23:27.933 wdl.w:ptcp.t:call-pbmm2_align_hifi-51 INFO output :: name: "report", value: "mapping_stats.report.json"
2025-09-15 20:23:27.933 wdl.w:ptcp.w:call-sawfish-17.t:call-run_sawfish INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:23:27.933 wdl.w:ptcp.w:call-paraphase-45 INFO visit :: node: "decl-config_file", values: {"config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml"}
2025-09-15 20:23:27.933 wdl.w:ptcp.w:call-sawfish-17.t:call-run_sawfish INFO input :: name: "genome_version", value: "38"
2025-09-15 20:23:27.933 wdl.w:ptcp.w:call-paraphase-45 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:23:27.933 wdl.w:ptcp.w:call-sawfish-17.t:call-run_sawfish INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:23:27.933 wdl.w:ptcp.w:call-paraphase-45 INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:23:27.934 wdl.w:ptcp.w:call-sawfish-17.t:call-run_sawfish INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:23:27.934 wdl.w:ptcp.w:call-paraphase-45 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-45/out/m84036_250809_035451_s4.bc2142.mapped.bam"}
2025-09-15 20:23:27.934 wdl.w:ptcp.w:call-sawfish-17.t:call-run_sawfish INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2114.mapped.bam.bai"
2025-09-15 20:23:27.934 wdl.w:ptcp.w:call-paraphase-45 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-45/out/m84036_250809_035451_s4.bc2142.mapped.bam.bai"}
2025-09-15 20:23:27.934 wdl.w:ptcp.w:call-sawfish-17.t:call-run_sawfish INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2114.mapped.bam"
2025-09-15 20:23:27.934 wdl.w:ptcp.w:call-paraphase-45 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:23:27.935 wdl.w:ptcp.w:call-sawfish-17.t:call-run_sawfish INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2114"
2025-09-15 20:23:27.935 wdl.w:ptcp.w:call-paraphase-45 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:23:27.935 wdl.w:ptcp.w:call-trgt-45 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:23:27.936 wdl.w:ptcp.w:call-sawfish-17.t:call-run_sawfish INFO eval :: name: "mem_gb", value: 32
2025-09-15 20:23:27.936 wdl.w:ptcp.w:call-paraphase-45 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2142"}
2025-09-15 20:23:27.936 wdl.w:ptcp.w:call-trgt-45 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-45/out/m84036_250809_035451_s4.bc2142.mapped.bam"}
2025-09-15 20:23:27.937 wdl.w:ptcp.w:call-sawfish-17.t:call-run_sawfish INFO eval :: name: "threads", value: 16
2025-09-15 20:23:27.937 wdl.w:ptcp.w:call-paraphase-45 INFO visit :: node: "decl-sex", values: {"sex": "F"}
2025-09-15 20:23:27.937 wdl.w:ptcp.w:call-trgt-45 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-45/out/m84036_250809_035451_s4.bc2142.mapped.bam.bai"}
2025-09-15 20:23:27.937 wdl.w:ptcp.w:call-paraphase-45 NOTICE ready :: job: "call-run_paraphase", callee: "run_paraphase"
2025-09-15 20:23:27.938 wdl.w:ptcp.w:call-sawfish-17.t:call-run_sawfish INFO eval :: name: "disk_size", value: 30
2025-09-15 20:23:27.938 wdl.w:ptcp.w:call-trgt-45 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:23:27.938 wdl.w:ptcp.w:call-paraphase-45 INFO input :: job: "call-run_paraphase", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf", "genome_version": "38", "config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-45/out/m84036_250809_035451_s4.bc2142.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-45/out/m84036_250809_035451_s4.bc2142.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2142"}
2025-09-15 20:23:27.938 wdl.w:ptcp.w:call-trgt-45 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:23:27.938 wdl.w:ptcp.w:call-sawfish-17.t:call-run_sawfish INFO eval :: name: "discover_dirname", value: "m84036_250809_035451_s4.bc2114_sawfish_discover"
2025-09-15 20:23:27.938 wdl.w:ptcp.w:call-trgt-45 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2142"}
2025-09-15 20:23:27.939 wdl.w:ptcp.w:call-sawfish-17.t:call-run_sawfish INFO eval :: name: "call_dirname", value: "m84036_250809_035451_s4.bc2114_sawfish"
2025-09-15 20:23:27.939 wdl.w:ptcp.w:call-trgt-45 INFO visit :: node: "decl-sex", values: {"sex": "F"}
2025-09-15 20:23:27.939 wdl.w:ptcp.w:call-trgt-45 INFO visit :: node: "decl-trgt_bed", values: {"trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"}
2025-09-15 20:23:27.939 wdl.w:ptcp.w:call-sawfish-17.t:call-run_sawfish INFO eval :: name: "minimap2_bam_filename", value: "m84036_250809_035451_s4.bc2114.minimap2.bam"
2025-09-15 20:23:27.939 wdl.w:ptcp.w:call-trgt-45 NOTICE ready :: job: "call-get_reads_overlapping_repeats", callee: "get_reads_overlapping_repeats"
2025-09-15 20:23:27.940 wdl.w:ptcp.w:call-trgt-45 INFO input :: job: "call-get_reads_overlapping_repeats", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-45/out/m84036_250809_035451_s4.bc2142.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-45/out/m84036_250809_035451_s4.bc2142.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2142"}
2025-09-15 20:23:27.940 wdl.w:ptcp.w:call-sawfish-17.t:call-run_sawfish INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 16, memory_reservation: 32000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:23:27.940 wdl.w:ptcp.w:call-sawfish-17.t:call-run_sawfish WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:23:27.941 wdl.w:ptcp.w:call-trgt-45 NOTICE ready :: job: "call-trgt_genotype", callee: "trgt_genotype"
2025-09-15 20:23:27.941 wdl.w:ptcp.w:call-sawfish-17.t:call-run_sawfish INFO provisioned :: seconds_waited: 0, cpu: 16, mem_bytes: 32000000000
2025-09-15 20:23:27.941 wdl.w:ptcp.w:call-trgt-45 INFO input :: job: "call-trgt_genotype", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-45/out/m84036_250809_035451_s4.bc2142.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-45/out/m84036_250809_035451_s4.bc2142.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2142"}
2025-09-15 20:23:27.942 wdl.w:ptcp.w:call-sawfish-17.t:call-run_sawfish INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:23:28.028 wdl.w:ptcp.w:call-sawfish-17.t:call-run_sawfish INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 10, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-17/call-run_sawfish/_singularity_tmpdir_fh1uix_r"
2025-09-15 20:23:28.029 wdl.w:ptcp.w:call-sawfish-17.t:call-run_sawfish INFO Slurm invocation: srun --job-name call-run_sawfish --partition compute,compute9 --cpus-per-task 16 --mem 30518M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-17/call-run_sawfish/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-17/call-run_sawfish/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-17/call-run_sawfish/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-17/call-run_sawfish/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-17/out/m84036_250809_035451_s4.bc2114.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2114.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-17/out/m84036_250809_035451_s4.bc2114.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2114.mapped.bam:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-17/call-run_sawfish/_singularity_tmpdir_fh1uix_r/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-17/call-run_sawfish/_singularity_tmpdir_fh1uix_r/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:23:28.045 wdl.w:ptcp.t:call-pbmm2_align_hifi-51 NOTICE done
2025-09-15 20:23:28.070 wdl.w:ptcp.w:call-sawfish-17.t:call-run_sawfish NOTICE slurm_singularity run :: pid: 1199031, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-17/call-run_sawfish/slurm_singularity.log.txt"
2025-09-15 20:23:28.130 wdl.w:ptcp.w:call-paraphase-15.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for smn1 for sample m84036_250809_035451_s4.bc2112 at 2025-09-15 20:23:17.218301...
2025-09-15 20:23:28.130 wdl.w:ptcp.w:call-paraphase-15.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for f8inv1 for sample m84036_250809_035451_s4.bc2112 at 2025-09-15 20:23:22.266749...
2025-09-15 20:23:28.130 wdl.w:ptcp.w:call-paraphase-15.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for f8inv1 for sample m84036_250809_035451_s4.bc2112 at 2025-09-15 20:23:22.267435...
2025-09-15 20:23:28.135 wdl.w:ptcp NOTICE finish :: job: "call-pbmm2_align_hifi-51"
2025-09-15 20:23:28.135 wdl.w:ptcp INFO output :: job: "call-pbmm2_align_hifi-51", values: {"report": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-51/out/mapping_stats.report.json", "mapped_bam_pbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-51/out/m84036_250809_035451_s4.bc2148.mapped.bam.pbi", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-51/out/m84036_250809_035451_s4.bc2148.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-51/out/m84036_250809_035451_s4.bc2148.mapped.bam"}
2025-09-15 20:23:28.136 wdl.w:ptcp NOTICE ready :: job: "call-paraphase-51", callee: "paraphase"
2025-09-15 20:23:28.136 wdl.w:ptcp INFO input :: job: "call-paraphase-51", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf", "genome_version": "38", "config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-51/out/m84036_250809_035451_s4.bc2148.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-51/out/m84036_250809_035451_s4.bc2148.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2148"}
2025-09-15 20:23:28.137 wdl.w:ptcp NOTICE ready :: job: "call-sawfish-51", callee: "sawfish"
2025-09-15 20:23:28.137 wdl.w:ptcp INFO input :: job: "call-sawfish-51", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-51/out/m84036_250809_035451_s4.bc2148.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-51/out/m84036_250809_035451_s4.bc2148.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2148"}
2025-09-15 20:23:28.140 wdl.w:ptcp NOTICE ready :: job: "call-trgt-51", callee: "trgt"
2025-09-15 20:23:28.141 wdl.w:ptcp INFO input :: job: "call-trgt-51", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-51/out/m84036_250809_035451_s4.bc2148.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-51/out/m84036_250809_035451_s4.bc2148.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2148"}
2025-09-15 20:23:28.142 wdl.w:ptcp.w:call-trgt-17.t:call-get_reads_overlapping_repeats NOTICE task setup :: name: "get_reads_overlapping_repeats", source: "./trgt.wdl", line: 182, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-17/call-get_reads_overlapping_repeats", thread: 140609847293504
2025-09-15 20:23:28.144 wdl.w:ptcp.w:call-paraphase-51 NOTICE workflow start :: name: "paraphase", source: "./paraphase.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-51"
2025-09-15 20:23:28.154 wdl.w:ptcp.w:call-sawfish-51 NOTICE workflow start :: name: "sawfish", source: "./sawfish.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-51"
2025-09-15 20:23:28.155 wdl.w:ptcp.w:call-trgt-51 NOTICE workflow start :: name: "trgt", source: "./trgt.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-51"
2025-09-15 20:23:28.165 wdl.w:ptcp.w:call-paraphase-51 INFO visit :: node: "decl-annotation_vcf", values: {"annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf"}
2025-09-15 20:23:28.165 wdl.w:ptcp.w:call-trgt-17.t:call-get_reads_overlapping_repeats INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:23:28.165 wdl.w:ptcp.w:call-paraphase-51 INFO visit :: node: "decl-config_file", values: {"config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml"}
2025-09-15 20:23:28.166 wdl.w:ptcp.w:call-trgt-17.t:call-get_reads_overlapping_repeats INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:23:28.166 wdl.w:ptcp.w:call-paraphase-51 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:23:28.166 wdl.w:ptcp.w:call-trgt-17.t:call-get_reads_overlapping_repeats INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2114.mapped.bam.bai"
2025-09-15 20:23:28.167 wdl.w:ptcp.w:call-paraphase-51 INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:23:28.167 wdl.w:ptcp.w:call-trgt-17.t:call-get_reads_overlapping_repeats INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2114.mapped.bam"
2025-09-15 20:23:28.167 wdl.w:ptcp.w:call-paraphase-51 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-51/out/m84036_250809_035451_s4.bc2148.mapped.bam"}
2025-09-15 20:23:28.167 wdl.w:ptcp.w:call-trgt-17.t:call-get_reads_overlapping_repeats INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2114"
2025-09-15 20:23:28.168 wdl.w:ptcp.w:call-paraphase-51 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-51/out/m84036_250809_035451_s4.bc2148.mapped.bam.bai"}
2025-09-15 20:23:28.168 wdl.w:ptcp.w:call-trgt-17.t:call-get_reads_overlapping_repeats INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:23:28.168 wdl.w:ptcp.w:call-paraphase-51 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:23:28.169 wdl.w:ptcp.w:call-trgt-17.t:call-get_reads_overlapping_repeats INFO eval :: name: "expand_size", value: 3000
2025-09-15 20:23:28.169 wdl.w:ptcp.w:call-paraphase-51 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:23:28.170 wdl.w:ptcp.w:call-trgt-17.t:call-get_reads_overlapping_repeats INFO eval :: name: "threads", value: 1
2025-09-15 20:23:28.170 wdl.w:ptcp.w:call-paraphase-51 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2148"}
2025-09-15 20:23:28.170 wdl.w:ptcp.w:call-trgt-17.t:call-get_reads_overlapping_repeats INFO eval :: name: "expanded_bed_name", value: "m84036_250809_035451_s4.bc2114.expanded.bed"
2025-09-15 20:23:28.171 wdl.w:ptcp.w:call-paraphase-51 INFO visit :: node: "decl-sex", values: {"sex": "F"}
2025-09-15 20:23:28.172 wdl.w:ptcp.w:call-paraphase-51 NOTICE ready :: job: "call-run_paraphase", callee: "run_paraphase"
2025-09-15 20:23:28.172 wdl.w:ptcp.w:call-trgt-17.t:call-get_reads_overlapping_repeats INFO eval :: name: "disk_size", value: 11
2025-09-15 20:23:28.173 wdl.w:ptcp.w:call-paraphase-51 INFO input :: job: "call-run_paraphase", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf", "genome_version": "38", "config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-51/out/m84036_250809_035451_s4.bc2148.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-51/out/m84036_250809_035451_s4.bc2148.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2148"}
2025-09-15 20:23:28.173 wdl.w:ptcp.w:call-trgt-17.t:call-get_reads_overlapping_repeats INFO eval :: name: "output_name", value: "m84036_250809_035451_s4.bc2114.repeats.bam"
2025-09-15 20:23:28.174 wdl.w:ptcp.w:call-trgt-17.t:call-get_reads_overlapping_repeats INFO eval :: name: "index_name", value: "m84036_250809_035451_s4.bc2114.repeats.bam.bai"
2025-09-15 20:23:28.174 wdl.w:ptcp.w:call-trgt-17.t:call-get_reads_overlapping_repeats INFO eval :: name: "output_name_with_index", value: "m84036_250809_035451_s4.bc2114.repeats.bam##idx##m84036_250809_035451_s4.bc2114.repeats.bam.bai"
2025-09-15 20:23:28.175 wdl.w:ptcp.w:call-sawfish-51 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:23:28.176 wdl.w:ptcp.w:call-sawfish-51 INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:23:28.176 wdl.w:ptcp.w:call-sawfish-51 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-51/out/m84036_250809_035451_s4.bc2148.mapped.bam"}
2025-09-15 20:23:28.176 wdl.w:ptcp.w:call-sawfish-51 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-51/out/m84036_250809_035451_s4.bc2148.mapped.bam.bai"}
2025-09-15 20:23:28.176 wdl.w:ptcp.w:call-trgt-17.t:call-get_reads_overlapping_repeats INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:23:28.176 wdl.w:ptcp.w:call-sawfish-51 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:23:28.177 wdl.w:ptcp.w:call-trgt-17.t:call-get_reads_overlapping_repeats WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:23:28.177 wdl.w:ptcp.w:call-sawfish-51 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:23:28.177 wdl.w:ptcp.w:call-sawfish-51 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2148"}
2025-09-15 20:23:28.178 wdl.w:ptcp.w:call-sawfish-51 NOTICE ready :: job: "call-run_sawfish", callee: "run_sawfish"
2025-09-15 20:23:28.178 wdl.w:ptcp.w:call-sawfish-51 INFO input :: job: "call-run_sawfish", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-51/out/m84036_250809_035451_s4.bc2148.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-51/out/m84036_250809_035451_s4.bc2148.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2148"}
2025-09-15 20:23:28.178 wdl.w:ptcp.w:call-trgt-17.t:call-get_reads_overlapping_repeats INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:23:28.179 wdl.w:ptcp.w:call-trgt-17.t:call-get_reads_overlapping_repeats INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:23:28.180 wdl.w:ptcp.w:call-trgt-51 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:23:28.180 wdl.w:ptcp.w:call-trgt-51 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-51/out/m84036_250809_035451_s4.bc2148.mapped.bam"}
2025-09-15 20:23:28.180 wdl.w:ptcp.w:call-trgt-51 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-51/out/m84036_250809_035451_s4.bc2148.mapped.bam.bai"}
2025-09-15 20:23:28.180 wdl.w:ptcp.w:call-trgt-51 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:23:28.180 wdl.w:ptcp.w:call-trgt-51 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:23:28.180 wdl.w:ptcp.w:call-trgt-51 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2148"}
2025-09-15 20:23:28.180 wdl.w:ptcp.w:call-trgt-51 INFO visit :: node: "decl-sex", values: {"sex": "F"}
2025-09-15 20:23:28.180 wdl.w:ptcp.w:call-trgt-51 INFO visit :: node: "decl-trgt_bed", values: {"trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"}
2025-09-15 20:23:28.181 wdl.w:ptcp.w:call-trgt-51 NOTICE ready :: job: "call-get_reads_overlapping_repeats", callee: "get_reads_overlapping_repeats"
2025-09-15 20:23:28.181 wdl.w:ptcp.w:call-trgt-51 INFO input :: job: "call-get_reads_overlapping_repeats", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-51/out/m84036_250809_035451_s4.bc2148.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-51/out/m84036_250809_035451_s4.bc2148.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2148"}
2025-09-15 20:23:28.181 wdl.w:ptcp.w:call-trgt-51 NOTICE ready :: job: "call-trgt_genotype", callee: "trgt_genotype"
2025-09-15 20:23:28.182 wdl.w:ptcp.w:call-trgt-51 INFO input :: job: "call-trgt_genotype", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-51/out/m84036_250809_035451_s4.bc2148.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-51/out/m84036_250809_035451_s4.bc2148.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2148"}
2025-09-15 20:23:28.215 wdl.w:ptcp.t:call-pbmm2_align_hifi-46 INFO output :: name: "mapped_bam", value: "m84036_250809_035451_s4.bc2143.mapped.bam"
2025-09-15 20:23:28.219 wdl.w:ptcp.t:call-pbmm2_align_hifi-46 INFO output :: name: "mapped_bam_bai", value: "m84036_250809_035451_s4.bc2143.mapped.bam.bai"
2025-09-15 20:23:28.220 wdl.w:ptcp.t:call-pbmm2_align_hifi-46 INFO output :: name: "mapped_bam_pbi", value: "m84036_250809_035451_s4.bc2143.mapped.bam.pbi"
2025-09-15 20:23:28.221 wdl.w:ptcp.t:call-pbmm2_align_hifi-46 INFO output :: name: "report", value: "mapping_stats.report.json"
2025-09-15 20:23:28.226 wdl.w:ptcp.w:call-trgt-17.t:call-get_reads_overlapping_repeats INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 9, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-17/call-get_reads_overlapping_repeats/_singularity_tmpdir_cy1buzom"
2025-09-15 20:23:28.227 wdl.w:ptcp.w:call-trgt-17.t:call-get_reads_overlapping_repeats INFO Slurm invocation: srun --job-name call-get_reads_overlapping_repeats --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-17/call-get_reads_overlapping_repeats/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-17/call-get_reads_overlapping_repeats/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-17/call-get_reads_overlapping_repeats/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-17/call-get_reads_overlapping_repeats/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-17/out/m84036_250809_035451_s4.bc2114.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2114.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-17/out/m84036_250809_035451_s4.bc2114.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2114.mapped.bam:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-17/call-get_reads_overlapping_repeats/_singularity_tmpdir_cy1buzom/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-17/call-get_reads_overlapping_repeats/_singularity_tmpdir_cy1buzom/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:23:28.244 wdl.w:ptcp.w:call-trgt-17.t:call-get_reads_overlapping_repeats NOTICE slurm_singularity run :: pid: 1199042, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-17/call-get_reads_overlapping_repeats/slurm_singularity.log.txt"
2025-09-15 20:23:28.294 wdl.w:ptcp.t:call-pbmm2_align_hifi-46 NOTICE done
2025-09-15 20:23:28.299 wdl.w:ptcp NOTICE finish :: job: "call-pbmm2_align_hifi-46"
2025-09-15 20:23:28.300 wdl.w:ptcp INFO output :: job: "call-pbmm2_align_hifi-46", values: {"report": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-46/out/mapping_stats.report.json", "mapped_bam_pbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-46/out/m84036_250809_035451_s4.bc2143.mapped.bam.pbi", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-46/out/m84036_250809_035451_s4.bc2143.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-46/out/m84036_250809_035451_s4.bc2143.mapped.bam"}
2025-09-15 20:23:28.300 wdl.w:ptcp NOTICE ready :: job: "call-paraphase-46", callee: "paraphase"
2025-09-15 20:23:28.301 wdl.w:ptcp INFO input :: job: "call-paraphase-46", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf", "genome_version": "38", "config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-46/out/m84036_250809_035451_s4.bc2143.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-46/out/m84036_250809_035451_s4.bc2143.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2143"}
2025-09-15 20:23:28.301 wdl.w:ptcp.t:call-pbmm2_align_hifi-44 INFO output :: name: "mapped_bam", value: "m84036_250809_035451_s4.bc2141.mapped.bam"
2025-09-15 20:23:28.302 wdl.w:ptcp NOTICE ready :: job: "call-sawfish-46", callee: "sawfish"
2025-09-15 20:23:28.303 wdl.w:ptcp INFO input :: job: "call-sawfish-46", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-46/out/m84036_250809_035451_s4.bc2143.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-46/out/m84036_250809_035451_s4.bc2143.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2143"}
2025-09-15 20:23:28.306 wdl.w:ptcp NOTICE ready :: job: "call-trgt-46", callee: "trgt"
2025-09-15 20:23:28.306 wdl.w:ptcp INFO input :: job: "call-trgt-46", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-46/out/m84036_250809_035451_s4.bc2143.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-46/out/m84036_250809_035451_s4.bc2143.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2143"}
2025-09-15 20:23:28.306 wdl.w:ptcp.t:call-pbmm2_align_hifi-44 INFO output :: name: "mapped_bam_bai", value: "m84036_250809_035451_s4.bc2141.mapped.bam.bai"
2025-09-15 20:23:28.308 wdl.w:ptcp.w:call-trgt-17.t:call-trgt_genotype NOTICE task setup :: name: "trgt_genotype", source: "./trgt.wdl", line: 272, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-17/call-trgt_genotype", thread: 140610367379008
2025-09-15 20:23:28.308 wdl.w:ptcp.t:call-pbmm2_align_hifi-44 INFO output :: name: "mapped_bam_pbi", value: "m84036_250809_035451_s4.bc2141.mapped.bam.pbi"
2025-09-15 20:23:28.309 wdl.w:ptcp.w:call-paraphase-46 NOTICE workflow start :: name: "paraphase", source: "./paraphase.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-46"
2025-09-15 20:23:28.311 wdl.w:ptcp.t:call-pbmm2_align_hifi-44 INFO output :: name: "report", value: "mapping_stats.report.json"
2025-09-15 20:23:28.316 wdl.w:ptcp.w:call-sawfish-46 NOTICE workflow start :: name: "sawfish", source: "./sawfish.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-46"
2025-09-15 20:23:28.321 wdl.w:ptcp.w:call-trgt-46 NOTICE workflow start :: name: "trgt", source: "./trgt.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-46"
2025-09-15 20:23:28.333 wdl.w:ptcp.w:call-paraphase-46 INFO visit :: node: "decl-annotation_vcf", values: {"annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf"}
2025-09-15 20:23:28.333 wdl.w:ptcp.w:call-paraphase-46 INFO visit :: node: "decl-config_file", values: {"config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml"}
2025-09-15 20:23:28.334 wdl.w:ptcp.w:call-paraphase-46 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:23:28.335 wdl.w:ptcp.w:call-paraphase-46 INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:23:28.335 wdl.w:ptcp.w:call-paraphase-46 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-46/out/m84036_250809_035451_s4.bc2143.mapped.bam"}
2025-09-15 20:23:28.336 wdl.w:ptcp.w:call-paraphase-46 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-46/out/m84036_250809_035451_s4.bc2143.mapped.bam.bai"}
2025-09-15 20:23:28.337 wdl.w:ptcp.w:call-paraphase-46 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:23:28.337 wdl.w:ptcp.w:call-paraphase-46 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:23:28.337 wdl.w:ptcp.w:call-paraphase-46 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2143"}
2025-09-15 20:23:28.337 wdl.w:ptcp.w:call-paraphase-46 INFO visit :: node: "decl-sex", values: {"sex": "F"}
2025-09-15 20:23:28.338 wdl.w:ptcp.w:call-paraphase-46 NOTICE ready :: job: "call-run_paraphase", callee: "run_paraphase"
2025-09-15 20:23:28.338 wdl.w:ptcp.w:call-paraphase-46 INFO input :: job: "call-run_paraphase", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf", "genome_version": "38", "config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-46/out/m84036_250809_035451_s4.bc2143.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-46/out/m84036_250809_035451_s4.bc2143.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2143"}
2025-09-15 20:23:28.339 wdl.w:ptcp.w:call-trgt-17.t:call-trgt_genotype INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:23:28.340 wdl.w:ptcp.w:call-trgt-17.t:call-trgt_genotype INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:23:28.340 wdl.w:ptcp.t:call-pbmm2_align_hifi-77.slurm_singularity INFO srun: job 51797299 has been allocated resources
2025-09-15 20:23:28.341 wdl.w:ptcp.w:call-trgt-17.t:call-trgt_genotype INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:23:28.341 wdl.w:ptcp.w:call-trgt-17.t:call-trgt_genotype INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:23:28.342 wdl.w:ptcp.w:call-trgt-17.t:call-trgt_genotype INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2114.mapped.bam.bai"
2025-09-15 20:23:28.342 wdl.w:ptcp.w:call-trgt-17.t:call-trgt_genotype INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2114.mapped.bam"
2025-09-15 20:23:28.342 wdl.w:ptcp.w:call-trgt-17.t:call-trgt_genotype INFO input :: name: "sex", value: "F"
2025-09-15 20:23:28.342 wdl.w:ptcp.w:call-trgt-17.t:call-trgt_genotype INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2114"
2025-09-15 20:23:28.343 wdl.w:ptcp.w:call-trgt-17.t:call-trgt_genotype INFO eval :: name: "mem_gb", value: 16
2025-09-15 20:23:28.343 wdl.w:ptcp.w:call-trgt-17.t:call-trgt_genotype INFO eval :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2114.trgt"
2025-09-15 20:23:28.344 wdl.w:ptcp.w:call-trgt-17.t:call-trgt_genotype INFO eval :: name: "threads", value: 8
2025-09-15 20:23:28.345 wdl.w:ptcp.w:call-sawfish-46 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:23:28.345 wdl.w:ptcp.w:call-sawfish-46 INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:23:28.345 wdl.w:ptcp.w:call-trgt-17.t:call-trgt_genotype INFO eval :: name: "disk_size", value: 27
2025-09-15 20:23:28.346 wdl.w:ptcp.w:call-sawfish-46 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-46/out/m84036_250809_035451_s4.bc2143.mapped.bam"}
2025-09-15 20:23:28.346 wdl.w:ptcp.w:call-sawfish-46 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-46/out/m84036_250809_035451_s4.bc2143.mapped.bam.bai"}
2025-09-15 20:23:28.346 wdl.w:ptcp.w:call-trgt-17.t:call-trgt_genotype INFO eval :: name: "karyotype", value: "XX"
2025-09-15 20:23:28.347 wdl.w:ptcp.w:call-sawfish-46 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:23:28.347 wdl.w:ptcp.w:call-sawfish-46 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:23:28.347 wdl.w:ptcp.w:call-sawfish-46 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2143"}
2025-09-15 20:23:28.347 wdl.w:ptcp.w:call-trgt-17.t:call-trgt_genotype INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 8, memory_reservation: 16000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:23:28.348 wdl.w:ptcp.w:call-sawfish-46 NOTICE ready :: job: "call-run_sawfish", callee: "run_sawfish"
2025-09-15 20:23:28.348 wdl.w:ptcp.w:call-trgt-17.t:call-trgt_genotype WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:23:28.348 wdl.w:ptcp.w:call-sawfish-46 INFO input :: job: "call-run_sawfish", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-46/out/m84036_250809_035451_s4.bc2143.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-46/out/m84036_250809_035451_s4.bc2143.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2143"}
2025-09-15 20:23:28.349 wdl.w:ptcp.w:call-trgt-46 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:23:28.350 wdl.w:ptcp.w:call-trgt-46 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-46/out/m84036_250809_035451_s4.bc2143.mapped.bam"}
2025-09-15 20:23:28.350 wdl.w:ptcp.w:call-trgt-46 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-46/out/m84036_250809_035451_s4.bc2143.mapped.bam.bai"}
2025-09-15 20:23:28.350 wdl.w:ptcp.w:call-trgt-46 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:23:28.350 wdl.w:ptcp.w:call-trgt-46 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:23:28.351 wdl.w:ptcp.w:call-trgt-17.t:call-trgt_genotype INFO provisioned :: seconds_waited: 0, cpu: 8, mem_bytes: 16000000000
2025-09-15 20:23:28.351 wdl.w:ptcp.w:call-trgt-46 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2143"}
2025-09-15 20:23:28.351 wdl.w:ptcp.w:call-trgt-17.t:call-trgt_genotype INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:23:28.351 wdl.w:ptcp.w:call-trgt-46 INFO visit :: node: "decl-sex", values: {"sex": "F"}
2025-09-15 20:23:28.351 wdl.w:ptcp.w:call-trgt-46 INFO visit :: node: "decl-trgt_bed", values: {"trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"}
2025-09-15 20:23:28.351 wdl.w:ptcp.w:call-trgt-46 NOTICE ready :: job: "call-get_reads_overlapping_repeats", callee: "get_reads_overlapping_repeats"
2025-09-15 20:23:28.352 wdl.w:ptcp.w:call-trgt-46 INFO input :: job: "call-get_reads_overlapping_repeats", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-46/out/m84036_250809_035451_s4.bc2143.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-46/out/m84036_250809_035451_s4.bc2143.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2143"}
2025-09-15 20:23:28.352 wdl.w:ptcp.w:call-trgt-46 NOTICE ready :: job: "call-trgt_genotype", callee: "trgt_genotype"
2025-09-15 20:23:28.353 wdl.w:ptcp.w:call-trgt-46 INFO input :: job: "call-trgt_genotype", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-46/out/m84036_250809_035451_s4.bc2143.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-46/out/m84036_250809_035451_s4.bc2143.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2143"}
2025-09-15 20:23:28.360 wdl.w:ptcp.t:call-pbmm2_align_hifi-76.slurm_singularity INFO srun: job 51797298 has been allocated resources
2025-09-15 20:23:28.360 wdl.w:ptcp.t:call-pbmm2_align_hifi-76.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:28.361 wdl.w:ptcp.t:call-pbmm2_align_hifi-76.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:23:28.405 wdl.w:ptcp.t:call-pbmm2_align_hifi-44 NOTICE done
2025-09-15 20:23:28.411 wdl.w:ptcp NOTICE finish :: job: "call-pbmm2_align_hifi-44"
2025-09-15 20:23:28.411 wdl.w:ptcp INFO output :: job: "call-pbmm2_align_hifi-44", values: {"report": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-44/out/mapping_stats.report.json", "mapped_bam_pbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-44/out/m84036_250809_035451_s4.bc2141.mapped.bam.pbi", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-44/out/m84036_250809_035451_s4.bc2141.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-44/out/m84036_250809_035451_s4.bc2141.mapped.bam"}
2025-09-15 20:23:28.412 wdl.w:ptcp NOTICE ready :: job: "call-paraphase-44", callee: "paraphase"
2025-09-15 20:23:28.412 wdl.w:ptcp INFO input :: job: "call-paraphase-44", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf", "genome_version": "38", "config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-44/out/m84036_250809_035451_s4.bc2141.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-44/out/m84036_250809_035451_s4.bc2141.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2141"}
2025-09-15 20:23:28.413 wdl.w:ptcp NOTICE ready :: job: "call-sawfish-44", callee: "sawfish"
2025-09-15 20:23:28.413 wdl.w:ptcp.w:call-trgt-17.t:call-trgt_genotype INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 11, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-17/call-trgt_genotype/_singularity_tmpdir_tqdfptfb"
2025-09-15 20:23:28.414 wdl.w:ptcp INFO input :: job: "call-sawfish-44", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-44/out/m84036_250809_035451_s4.bc2141.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-44/out/m84036_250809_035451_s4.bc2141.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2141"}
2025-09-15 20:23:28.414 wdl.w:ptcp.w:call-trgt-17.t:call-trgt_genotype INFO Slurm invocation: srun --job-name call-trgt_genotype --partition compute,compute9 --cpus-per-task 8 --mem 15259M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-17/call-trgt_genotype/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-17/call-trgt_genotype/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-17/call-trgt_genotype/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-17/call-trgt_genotype/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-17/out/m84036_250809_035451_s4.bc2114.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2114.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-17/out/m84036_250809_035451_s4.bc2114.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2114.mapped.bam:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-17/call-trgt_genotype/_singularity_tmpdir_tqdfptfb/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-17/call-trgt_genotype/_singularity_tmpdir_tqdfptfb/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:23:28.418 wdl.w:ptcp NOTICE ready :: job: "call-trgt-44", callee: "trgt"
2025-09-15 20:23:28.418 wdl.w:ptcp INFO input :: job: "call-trgt-44", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-44/out/m84036_250809_035451_s4.bc2141.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-44/out/m84036_250809_035451_s4.bc2141.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2141"}
2025-09-15 20:23:28.419 wdl.w:ptcp.w:call-sawfish-21.t:call-run_sawfish NOTICE task setup :: name: "run_sawfish", source: "./sawfish.wdl", line: 83, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-21/call-run_sawfish", thread: 140610384164416
2025-09-15 20:23:28.422 wdl.w:ptcp.w:call-paraphase-44 NOTICE workflow start :: name: "paraphase", source: "./paraphase.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-44"
2025-09-15 20:23:28.425 wdl.w:ptcp.w:call-sawfish-44 NOTICE workflow start :: name: "sawfish", source: "./sawfish.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-44"
2025-09-15 20:23:28.439 wdl.w:ptcp.w:call-paraphase-44 INFO visit :: node: "decl-annotation_vcf", values: {"annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf"}
2025-09-15 20:23:28.439 wdl.w:ptcp.w:call-paraphase-44 INFO visit :: node: "decl-config_file", values: {"config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml"}
2025-09-15 20:23:28.439 wdl.w:ptcp.w:call-trgt-17.t:call-trgt_genotype NOTICE slurm_singularity run :: pid: 1199054, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-17/call-trgt_genotype/slurm_singularity.log.txt"
2025-09-15 20:23:28.439 wdl.w:ptcp.w:call-paraphase-44 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:23:28.440 wdl.w:ptcp.w:call-paraphase-44 INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:23:28.440 wdl.w:ptcp.w:call-paraphase-44 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-44/out/m84036_250809_035451_s4.bc2141.mapped.bam"}
2025-09-15 20:23:28.440 wdl.w:ptcp.w:call-paraphase-44 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-44/out/m84036_250809_035451_s4.bc2141.mapped.bam.bai"}
2025-09-15 20:23:28.440 wdl.w:ptcp.w:call-paraphase-44 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:23:28.440 wdl.w:ptcp.w:call-paraphase-44 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:23:28.440 wdl.w:ptcp.w:call-paraphase-44 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2141"}
2025-09-15 20:23:28.440 wdl.w:ptcp.w:call-paraphase-44 INFO visit :: node: "decl-sex", values: {"sex": "F"}
2025-09-15 20:23:28.440 wdl.w:ptcp.w:call-paraphase-44 NOTICE ready :: job: "call-run_paraphase", callee: "run_paraphase"
2025-09-15 20:23:28.441 wdl.w:ptcp.w:call-sawfish-21.t:call-run_sawfish INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:23:28.441 wdl.w:ptcp.w:call-paraphase-44 INFO input :: job: "call-run_paraphase", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf", "genome_version": "38", "config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-44/out/m84036_250809_035451_s4.bc2141.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-44/out/m84036_250809_035451_s4.bc2141.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2141"}
2025-09-15 20:23:28.441 wdl.w:ptcp.w:call-sawfish-21.t:call-run_sawfish INFO input :: name: "genome_version", value: "38"
2025-09-15 20:23:28.442 wdl.w:ptcp.w:call-sawfish-21.t:call-run_sawfish INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:23:28.442 wdl.w:ptcp.w:call-sawfish-21.t:call-run_sawfish INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:23:28.441 wdl.w:ptcp.t:call-pbmm2_align_hifi-75.slurm_singularity INFO srun: job 51797297 has been allocated resources
2025-09-15 20:23:28.442 wdl.w:ptcp.w:call-sawfish-21.t:call-run_sawfish INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2118.mapped.bam.bai"
2025-09-15 20:23:28.442 wdl.w:ptcp.t:call-pbmm2_align_hifi-75.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:28.443 wdl.w:ptcp.w:call-sawfish-21.t:call-run_sawfish INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2118.mapped.bam"
2025-09-15 20:23:28.443 wdl.w:ptcp.t:call-pbmm2_align_hifi-75.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:23:28.443 wdl.w:ptcp.w:call-sawfish-21.t:call-run_sawfish INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2118"
2025-09-15 20:23:28.443 wdl.w:ptcp.w:call-sawfish-21.t:call-run_sawfish INFO eval :: name: "mem_gb", value: 32
2025-09-15 20:23:28.444 wdl.w:ptcp.w:call-sawfish-21.t:call-run_sawfish INFO eval :: name: "threads", value: 16
2025-09-15 20:23:28.444 wdl.w:ptcp.w:call-sawfish-21.t:call-run_sawfish INFO eval :: name: "disk_size", value: 30
2025-09-15 20:23:28.445 wdl.w:ptcp.w:call-sawfish-21.t:call-run_sawfish INFO eval :: name: "discover_dirname", value: "m84036_250809_035451_s4.bc2118_sawfish_discover"
2025-09-15 20:23:28.445 wdl.w:ptcp.w:call-sawfish-21.t:call-run_sawfish INFO eval :: name: "call_dirname", value: "m84036_250809_035451_s4.bc2118_sawfish"
2025-09-15 20:23:28.445 wdl.w:ptcp.w:call-sawfish-21.t:call-run_sawfish INFO eval :: name: "minimap2_bam_filename", value: "m84036_250809_035451_s4.bc2118.minimap2.bam"
2025-09-15 20:23:28.446 wdl.w:ptcp.w:call-sawfish-21.t:call-run_sawfish INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 16, memory_reservation: 32000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:23:28.446 wdl.w:ptcp.w:call-sawfish-21.t:call-run_sawfish WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:23:28.447 wdl.w:ptcp.w:call-sawfish-21.t:call-run_sawfish INFO provisioned :: seconds_waited: 0, cpu: 16, mem_bytes: 32000000000
2025-09-15 20:23:28.448 wdl.w:ptcp.w:call-sawfish-21.t:call-run_sawfish INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:23:28.450 wdl.w:ptcp.w:call-sawfish-44 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:23:28.450 wdl.w:ptcp.w:call-sawfish-44 INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:23:28.450 wdl.w:ptcp.w:call-sawfish-44 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-44/out/m84036_250809_035451_s4.bc2141.mapped.bam"}
2025-09-15 20:23:28.450 wdl.w:ptcp.w:call-sawfish-44 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-44/out/m84036_250809_035451_s4.bc2141.mapped.bam.bai"}
2025-09-15 20:23:28.450 wdl.w:ptcp.w:call-sawfish-44 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:23:28.451 wdl.w:ptcp.w:call-sawfish-44 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:23:28.451 wdl.w:ptcp.w:call-sawfish-44 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2141"}
2025-09-15 20:23:28.451 wdl.w:ptcp.w:call-sawfish-44 NOTICE ready :: job: "call-run_sawfish", callee: "run_sawfish"
2025-09-15 20:23:28.451 wdl.w:ptcp.w:call-sawfish-44 INFO input :: job: "call-run_sawfish", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-44/out/m84036_250809_035451_s4.bc2141.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-44/out/m84036_250809_035451_s4.bc2141.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2141"}
2025-09-15 20:23:28.464 wdl.w:ptcp.t:call-pbmm2_align_hifi-79.slurm_singularity INFO srun: job 51797300 has been allocated resources
2025-09-15 20:23:28.500 wdl.w:ptcp.t:call-pbmm2_align_hifi-78.slurm_singularity INFO srun: job 51797301 has been allocated resources
2025-09-15 20:23:28.510 wdl.w:ptcp.w:call-sawfish-21.t:call-run_sawfish INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 10, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-21/call-run_sawfish/_singularity_tmpdir_8gtc5_9m"
2025-09-15 20:23:28.510 wdl.w:ptcp.w:call-sawfish-21.t:call-run_sawfish INFO Slurm invocation: srun --job-name call-run_sawfish --partition compute,compute9 --cpus-per-task 16 --mem 30518M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-21/call-run_sawfish/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-21/call-run_sawfish/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-21/call-run_sawfish/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-21/call-run_sawfish/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-21/out/m84036_250809_035451_s4.bc2118.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2118.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-21/out/m84036_250809_035451_s4.bc2118.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2118.mapped.bam:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-21/call-run_sawfish/_singularity_tmpdir_8gtc5_9m/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-21/call-run_sawfish/_singularity_tmpdir_8gtc5_9m/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:23:28.523 wdl.w:ptcp.t:call-pbmm2_align_hifi-52 INFO output :: name: "mapped_bam", value: "m84036_250809_035451_s4.bc2149.mapped.bam"
2025-09-15 20:23:28.526 wdl.w:ptcp.t:call-pbmm2_align_hifi-52 INFO output :: name: "mapped_bam_bai", value: "m84036_250809_035451_s4.bc2149.mapped.bam.bai"
2025-09-15 20:23:28.527 wdl.w:ptcp.t:call-pbmm2_align_hifi-52 INFO output :: name: "mapped_bam_pbi", value: "m84036_250809_035451_s4.bc2149.mapped.bam.pbi"
2025-09-15 20:23:28.528 wdl.w:ptcp.t:call-pbmm2_align_hifi-52 INFO output :: name: "report", value: "mapping_stats.report.json"
2025-09-15 20:23:28.532 wdl.w:ptcp.w:call-sawfish-21.t:call-run_sawfish NOTICE slurm_singularity run :: pid: 1199063, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-21/call-run_sawfish/slurm_singularity.log.txt"
2025-09-15 20:23:28.609 wdl.w:ptcp.t:call-pbmm2_align_hifi-52 NOTICE done
2025-09-15 20:23:28.615 wdl.w:ptcp NOTICE finish :: job: "call-pbmm2_align_hifi-52"
2025-09-15 20:23:28.615 wdl.w:ptcp INFO output :: job: "call-pbmm2_align_hifi-52", values: {"report": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-52/out/mapping_stats.report.json", "mapped_bam_pbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-52/out/m84036_250809_035451_s4.bc2149.mapped.bam.pbi", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-52/out/m84036_250809_035451_s4.bc2149.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-52/out/m84036_250809_035451_s4.bc2149.mapped.bam"}
2025-09-15 20:23:28.616 wdl.w:ptcp NOTICE ready :: job: "call-paraphase-52", callee: "paraphase"
2025-09-15 20:23:28.616 wdl.w:ptcp INFO input :: job: "call-paraphase-52", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf", "genome_version": "38", "config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-52/out/m84036_250809_035451_s4.bc2149.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-52/out/m84036_250809_035451_s4.bc2149.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2149"}
2025-09-15 20:23:28.617 wdl.w:ptcp NOTICE ready :: job: "call-sawfish-52", callee: "sawfish"
2025-09-15 20:23:28.617 wdl.w:ptcp INFO input :: job: "call-sawfish-52", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-52/out/m84036_250809_035451_s4.bc2149.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-52/out/m84036_250809_035451_s4.bc2149.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2149"}
2025-09-15 20:23:28.618 wdl.w:ptcp NOTICE ready :: job: "call-trgt-52", callee: "trgt"
2025-09-15 20:23:28.618 wdl.w:ptcp INFO input :: job: "call-trgt-52", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-52/out/m84036_250809_035451_s4.bc2149.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-52/out/m84036_250809_035451_s4.bc2149.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2149"}
2025-09-15 20:23:28.623 wdl.w:ptcp.w:call-trgt-21.t:call-get_reads_overlapping_repeats NOTICE task setup :: name: "get_reads_overlapping_repeats", source: "./trgt.wdl", line: 182, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-21/call-get_reads_overlapping_repeats", thread: 140609838900800
2025-09-15 20:23:28.639 wdl.w:ptcp.w:call-trgt-21.t:call-get_reads_overlapping_repeats INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:23:28.639 wdl.w:ptcp.w:call-trgt-21.t:call-get_reads_overlapping_repeats INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:23:28.639 wdl.w:ptcp.w:call-trgt-21.t:call-get_reads_overlapping_repeats INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2118.mapped.bam.bai"
2025-09-15 20:23:28.640 wdl.w:ptcp.w:call-trgt-21.t:call-get_reads_overlapping_repeats INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2118.mapped.bam"
2025-09-15 20:23:28.640 wdl.w:ptcp.w:call-trgt-21.t:call-get_reads_overlapping_repeats INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2118"
2025-09-15 20:23:28.640 wdl.w:ptcp.w:call-trgt-21.t:call-get_reads_overlapping_repeats INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:23:28.640 wdl.w:ptcp.w:call-trgt-21.t:call-get_reads_overlapping_repeats INFO eval :: name: "expand_size", value: 3000
2025-09-15 20:23:28.640 wdl.w:ptcp.w:call-trgt-21.t:call-get_reads_overlapping_repeats INFO eval :: name: "threads", value: 1
2025-09-15 20:23:28.640 wdl.w:ptcp.w:call-trgt-21.t:call-get_reads_overlapping_repeats INFO eval :: name: "expanded_bed_name", value: "m84036_250809_035451_s4.bc2118.expanded.bed"
2025-09-15 20:23:28.640 wdl.w:ptcp.w:call-trgt-21.t:call-get_reads_overlapping_repeats INFO eval :: name: "disk_size", value: 11
2025-09-15 20:23:28.640 wdl.w:ptcp.w:call-trgt-21.t:call-get_reads_overlapping_repeats INFO eval :: name: "output_name", value: "m84036_250809_035451_s4.bc2118.repeats.bam"
2025-09-15 20:23:28.640 wdl.w:ptcp.w:call-trgt-21.t:call-get_reads_overlapping_repeats INFO eval :: name: "index_name", value: "m84036_250809_035451_s4.bc2118.repeats.bam.bai"
2025-09-15 20:23:28.641 wdl.w:ptcp.w:call-trgt-21.t:call-get_reads_overlapping_repeats INFO eval :: name: "output_name_with_index", value: "m84036_250809_035451_s4.bc2118.repeats.bam##idx##m84036_250809_035451_s4.bc2118.repeats.bam.bai"
2025-09-15 20:23:28.641 wdl.w:ptcp.w:call-trgt-21.t:call-get_reads_overlapping_repeats INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:23:28.641 wdl.w:ptcp.w:call-trgt-21.t:call-get_reads_overlapping_repeats WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:23:28.641 wdl.w:ptcp.w:call-trgt-21.t:call-get_reads_overlapping_repeats INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:23:28.642 wdl.w:ptcp.w:call-trgt-21.t:call-get_reads_overlapping_repeats INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:23:28.689 wdl.w:ptcp.w:call-trgt-21.t:call-get_reads_overlapping_repeats INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 9, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-21/call-get_reads_overlapping_repeats/_singularity_tmpdir_32_tm5bb"
2025-09-15 20:23:28.689 wdl.w:ptcp.w:call-trgt-21.t:call-get_reads_overlapping_repeats INFO Slurm invocation: srun --job-name call-get_reads_overlapping_repeats --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-21/call-get_reads_overlapping_repeats/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-21/call-get_reads_overlapping_repeats/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-21/call-get_reads_overlapping_repeats/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-21/call-get_reads_overlapping_repeats/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-21/out/m84036_250809_035451_s4.bc2118.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2118.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-21/out/m84036_250809_035451_s4.bc2118.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2118.mapped.bam:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-21/call-get_reads_overlapping_repeats/_singularity_tmpdir_32_tm5bb/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-21/call-get_reads_overlapping_repeats/_singularity_tmpdir_32_tm5bb/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:23:28.699 wdl.w:ptcp.w:call-trgt-21.t:call-get_reads_overlapping_repeats NOTICE slurm_singularity run :: pid: 1199065, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-21/call-get_reads_overlapping_repeats/slurm_singularity.log.txt"
2025-09-15 20:23:29.028 wdl.w:ptcp.t:call-pbmm2_align_hifi-47 INFO output :: name: "mapped_bam", value: "m84036_250809_035451_s4.bc2144.mapped.bam"
2025-09-15 20:23:29.033 wdl.w:ptcp.t:call-pbmm2_align_hifi-47 INFO output :: name: "mapped_bam_bai", value: "m84036_250809_035451_s4.bc2144.mapped.bam.bai"
2025-09-15 20:23:29.034 wdl.w:ptcp.t:call-pbmm2_align_hifi-47 INFO output :: name: "mapped_bam_pbi", value: "m84036_250809_035451_s4.bc2144.mapped.bam.pbi"
2025-09-15 20:23:29.035 wdl.w:ptcp.t:call-pbmm2_align_hifi-47 INFO output :: name: "report", value: "mapping_stats.report.json"
2025-09-15 20:23:29.046 wdl.w:ptcp.t:call-pbmm2_align_hifi-50 INFO output :: name: "mapped_bam", value: "m84036_250809_035451_s4.bc2147.mapped.bam"
2025-09-15 20:23:29.049 wdl.w:ptcp.t:call-pbmm2_align_hifi-50 INFO output :: name: "mapped_bam_bai", value: "m84036_250809_035451_s4.bc2147.mapped.bam.bai"
2025-09-15 20:23:29.050 wdl.w:ptcp.t:call-pbmm2_align_hifi-50 INFO output :: name: "mapped_bam_pbi", value: "m84036_250809_035451_s4.bc2147.mapped.bam.pbi"
2025-09-15 20:23:29.051 wdl.w:ptcp.t:call-pbmm2_align_hifi-50 INFO output :: name: "report", value: "mapping_stats.report.json"
2025-09-15 20:23:29.085 wdl.w:ptcp.w:call-sawfish-17.t:call-run_sawfish.slurm_singularity INFO srun: job 51797384 queued and waiting for resources
2025-09-15 20:23:29.145 wdl.w:ptcp.t:call-pbmm2_align_hifi-47 NOTICE done
2025-09-15 20:23:29.152 wdl.w:ptcp NOTICE finish :: job: "call-pbmm2_align_hifi-47"
2025-09-15 20:23:29.152 wdl.w:ptcp INFO output :: job: "call-pbmm2_align_hifi-47", values: {"report": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-47/out/mapping_stats.report.json", "mapped_bam_pbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-47/out/m84036_250809_035451_s4.bc2144.mapped.bam.pbi", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-47/out/m84036_250809_035451_s4.bc2144.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-47/out/m84036_250809_035451_s4.bc2144.mapped.bam"}
2025-09-15 20:23:29.153 wdl.w:ptcp NOTICE ready :: job: "call-paraphase-47", callee: "paraphase"
2025-09-15 20:23:29.153 wdl.w:ptcp INFO input :: job: "call-paraphase-47", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf", "genome_version": "38", "config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-47/out/m84036_250809_035451_s4.bc2144.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-47/out/m84036_250809_035451_s4.bc2144.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2144"}
2025-09-15 20:23:29.154 wdl.w:ptcp NOTICE ready :: job: "call-sawfish-47", callee: "sawfish"
2025-09-15 20:23:29.155 wdl.w:ptcp INFO input :: job: "call-sawfish-47", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-47/out/m84036_250809_035451_s4.bc2144.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-47/out/m84036_250809_035451_s4.bc2144.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2144"}
2025-09-15 20:23:29.156 wdl.w:ptcp NOTICE ready :: job: "call-trgt-47", callee: "trgt"
2025-09-15 20:23:29.156 wdl.w:ptcp INFO input :: job: "call-trgt-47", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-47/out/m84036_250809_035451_s4.bc2144.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-47/out/m84036_250809_035451_s4.bc2144.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2144"}
2025-09-15 20:23:29.163 wdl.w:ptcp.w:call-paraphase-21.t:call-run_paraphase NOTICE task setup :: name: "run_paraphase", source: "./paraphase.wdl", line: 127, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-21/call-run_paraphase", thread: 140610358986304
2025-09-15 20:23:29.169 wdl.w:ptcp.t:call-pbmm2_align_hifi-50 NOTICE done
2025-09-15 20:23:29.175 wdl.w:ptcp NOTICE finish :: job: "call-pbmm2_align_hifi-50"
2025-09-15 20:23:29.176 wdl.w:ptcp INFO output :: job: "call-pbmm2_align_hifi-50", values: {"report": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-50/out/mapping_stats.report.json", "mapped_bam_pbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-50/out/m84036_250809_035451_s4.bc2147.mapped.bam.pbi", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-50/out/m84036_250809_035451_s4.bc2147.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-50/out/m84036_250809_035451_s4.bc2147.mapped.bam"}
2025-09-15 20:23:29.176 wdl.w:ptcp NOTICE ready :: job: "call-paraphase-50", callee: "paraphase"
2025-09-15 20:23:29.177 wdl.w:ptcp INFO input :: job: "call-paraphase-50", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf", "genome_version": "38", "config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-50/out/m84036_250809_035451_s4.bc2147.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-50/out/m84036_250809_035451_s4.bc2147.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2147"}
2025-09-15 20:23:29.178 wdl.w:ptcp NOTICE ready :: job: "call-sawfish-50", callee: "sawfish"
2025-09-15 20:23:29.178 wdl.w:ptcp INFO input :: job: "call-sawfish-50", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-50/out/m84036_250809_035451_s4.bc2147.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-50/out/m84036_250809_035451_s4.bc2147.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2147"}
2025-09-15 20:23:29.180 wdl.w:ptcp NOTICE ready :: job: "call-trgt-50", callee: "trgt"
2025-09-15 20:23:29.180 wdl.w:ptcp INFO input :: job: "call-trgt-50", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-50/out/m84036_250809_035451_s4.bc2147.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-50/out/m84036_250809_035451_s4.bc2147.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2147"}
2025-09-15 20:23:29.182 wdl.w:ptcp.w:call-trgt-21.t:call-trgt_genotype NOTICE task setup :: name: "trgt_genotype", source: "./trgt.wdl", line: 272, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-21/call-trgt_genotype", thread: 140610333808192
2025-09-15 20:23:29.185 wdl.w:ptcp.w:call-paraphase-21.t:call-run_paraphase INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:23:29.186 wdl.w:ptcp.w:call-paraphase-21.t:call-run_paraphase INFO input :: name: "annotation_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf"
2025-09-15 20:23:29.186 wdl.w:ptcp.w:call-paraphase-21.t:call-run_paraphase INFO input :: name: "genome_version", value: "38"
2025-09-15 20:23:29.186 wdl.w:ptcp.w:call-paraphase-21.t:call-run_paraphase INFO input :: name: "config_file", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/paraphase_config.GRCh38.yaml"
2025-09-15 20:23:29.186 wdl.w:ptcp.w:call-paraphase-21.t:call-run_paraphase INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:23:29.186 wdl.w:ptcp.w:call-paraphase-21.t:call-run_paraphase INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:23:29.186 wdl.w:ptcp.w:call-paraphase-21.t:call-run_paraphase INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2118.mapped.bam.bai"
2025-09-15 20:23:29.186 wdl.w:ptcp.w:call-paraphase-21.t:call-run_paraphase INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2118.mapped.bam"
2025-09-15 20:23:29.186 wdl.w:ptcp.w:call-paraphase-21.t:call-run_paraphase INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2118"
2025-09-15 20:23:29.186 wdl.w:ptcp.w:call-paraphase-21.t:call-run_paraphase INFO eval :: name: "threads", value: 4
2025-09-15 20:23:29.186 wdl.w:ptcp.w:call-paraphase-21.t:call-run_paraphase INFO eval :: name: "mem_gb", value: 8
2025-09-15 20:23:29.186 wdl.w:ptcp.w:call-paraphase-21.t:call-run_paraphase INFO eval :: name: "disk_size", value: 27
2025-09-15 20:23:29.187 wdl.w:ptcp.w:call-paraphase-21.t:call-run_paraphase INFO eval :: name: "out_dir", value: "m84036_250809_035451_s4.bc2118_paraphase"
2025-09-15 20:23:29.187 wdl.w:ptcp.w:call-paraphase-21.t:call-run_paraphase INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 4, memory_reservation: 8000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:23:29.187 wdl.w:ptcp.w:call-paraphase-21.t:call-run_paraphase WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:23:29.188 wdl.w:ptcp.w:call-paraphase-21.t:call-run_paraphase INFO provisioned :: seconds_waited: 0, cpu: 4, mem_bytes: 8000000000
2025-09-15 20:23:29.188 wdl.w:ptcp.w:call-paraphase-21.t:call-run_paraphase INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:23:29.202 wdl.w:ptcp.w:call-trgt-21.t:call-trgt_genotype INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:23:29.202 wdl.w:ptcp.w:call-trgt-21.t:call-trgt_genotype INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:23:29.202 wdl.w:ptcp.w:call-trgt-21.t:call-trgt_genotype INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:23:29.202 wdl.w:ptcp.w:call-trgt-21.t:call-trgt_genotype INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:23:29.202 wdl.w:ptcp.w:call-trgt-21.t:call-trgt_genotype INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2118.mapped.bam.bai"
2025-09-15 20:23:29.202 wdl.w:ptcp.w:call-trgt-21.t:call-trgt_genotype INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2118.mapped.bam"
2025-09-15 20:23:29.202 wdl.w:ptcp.w:call-trgt-21.t:call-trgt_genotype INFO input :: name: "sex", value: "F"
2025-09-15 20:23:29.202 wdl.w:ptcp.w:call-trgt-21.t:call-trgt_genotype INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2118"
2025-09-15 20:23:29.203 wdl.w:ptcp.w:call-trgt-21.t:call-trgt_genotype INFO eval :: name: "mem_gb", value: 16
2025-09-15 20:23:29.203 wdl.w:ptcp.w:call-trgt-21.t:call-trgt_genotype INFO eval :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2118.trgt"
2025-09-15 20:23:29.203 wdl.w:ptcp.w:call-trgt-21.t:call-trgt_genotype INFO eval :: name: "threads", value: 8
2025-09-15 20:23:29.203 wdl.w:ptcp.w:call-trgt-21.t:call-trgt_genotype INFO eval :: name: "disk_size", value: 27
2025-09-15 20:23:29.203 wdl.w:ptcp.w:call-trgt-21.t:call-trgt_genotype INFO eval :: name: "karyotype", value: "XX"
2025-09-15 20:23:29.203 wdl.w:ptcp.w:call-trgt-21.t:call-trgt_genotype INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 8, memory_reservation: 16000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:23:29.204 wdl.w:ptcp.w:call-trgt-21.t:call-trgt_genotype WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:23:29.204 wdl.w:ptcp.w:call-trgt-21.t:call-trgt_genotype INFO provisioned :: seconds_waited: 0, cpu: 8, mem_bytes: 16000000000
2025-09-15 20:23:29.204 wdl.w:ptcp.w:call-trgt-21.t:call-trgt_genotype INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:23:29.257 wdl.w:ptcp.w:call-trgt-17.t:call-get_reads_overlapping_repeats.slurm_singularity INFO srun: job 51797385 queued and waiting for resources
2025-09-15 20:23:29.274 wdl.w:ptcp.w:call-paraphase-21.t:call-run_paraphase INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-21/call-run_paraphase/_singularity_tmpdir_p2fhhn1e"
2025-09-15 20:23:29.274 wdl.w:ptcp.w:call-paraphase-21.t:call-run_paraphase INFO Slurm invocation: srun --job-name call-run_paraphase --partition compute,compute9 --cpus-per-task 4 --mem 7629M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-21/call-run_paraphase/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-21/call-run_paraphase/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-21/call-run_paraphase/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-21/call-run_paraphase/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-21/out/m84036_250809_035451_s4.bc2118.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2118.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-21/out/m84036_250809_035451_s4.bc2118.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2118.mapped.bam:ro --bind /ptcp/meta/variant_list/variant_list.GRCh38.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf:ro --bind /ptcp/meta/paraphase/paraphase_config.GRCh38.yaml:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/paraphase_config.GRCh38.yaml:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-21/call-run_paraphase/_singularity_tmpdir_p2fhhn1e/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-21/call-run_paraphase/_singularity_tmpdir_p2fhhn1e/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:23:29.280 wdl.w:ptcp.w:call-trgt-21.t:call-trgt_genotype INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 11, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-21/call-trgt_genotype/_singularity_tmpdir_4wbgjlm8"
2025-09-15 20:23:29.280 wdl.w:ptcp.w:call-trgt-21.t:call-trgt_genotype INFO Slurm invocation: srun --job-name call-trgt_genotype --partition compute,compute9 --cpus-per-task 8 --mem 15259M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-21/call-trgt_genotype/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-21/call-trgt_genotype/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-21/call-trgt_genotype/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-21/call-trgt_genotype/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-21/out/m84036_250809_035451_s4.bc2118.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2118.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-21/out/m84036_250809_035451_s4.bc2118.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2118.mapped.bam:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-21/call-trgt_genotype/_singularity_tmpdir_4wbgjlm8/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-21/call-trgt_genotype/_singularity_tmpdir_4wbgjlm8/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:23:29.294 wdl.w:ptcp.w:call-trgt-21.t:call-trgt_genotype NOTICE slurm_singularity run :: pid: 1199085, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-21/call-trgt_genotype/slurm_singularity.log.txt"
2025-09-15 20:23:29.294 wdl.w:ptcp.w:call-paraphase-21.t:call-run_paraphase NOTICE slurm_singularity run :: pid: 1199084, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-21/call-run_paraphase/slurm_singularity.log.txt"
2025-09-15 20:23:29.355 wdl.w:ptcp.t:call-pbmm2_align_hifi-77.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:29.356 wdl.w:ptcp.t:call-pbmm2_align_hifi-77.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:23:29.454 wdl.w:ptcp.w:call-trgt-17.t:call-trgt_genotype.slurm_singularity INFO srun: job 51797386 queued and waiting for resources
2025-09-15 20:23:29.469 wdl.w:ptcp.t:call-pbmm2_align_hifi-81.slurm_singularity INFO srun: job 51797303 has been allocated resources
2025-09-15 20:23:29.470 wdl.w:ptcp.t:call-pbmm2_align_hifi-81.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:29.470 wdl.w:ptcp.t:call-pbmm2_align_hifi-81.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:23:29.478 wdl.w:ptcp.t:call-pbmm2_align_hifi-79.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:29.478 wdl.w:ptcp.t:call-pbmm2_align_hifi-79.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:23:29.481 wdl.w:ptcp.t:call-pbmm2_align_hifi-80.slurm_singularity INFO srun: job 51797302 has been allocated resources
2025-09-15 20:23:29.482 wdl.w:ptcp.t:call-pbmm2_align_hifi-80.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:29.482 wdl.w:ptcp.t:call-pbmm2_align_hifi-80.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:23:29.514 wdl.w:ptcp.t:call-pbmm2_align_hifi-78.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:29.514 wdl.w:ptcp.t:call-pbmm2_align_hifi-78.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:23:29.539 wdl.w:ptcp.w:call-sawfish-21.t:call-run_sawfish.slurm_singularity INFO srun: job 51797387 queued and waiting for resources
2025-09-15 20:23:29.706 wdl.w:ptcp.w:call-trgt-21.t:call-get_reads_overlapping_repeats.slurm_singularity INFO srun: job 51797388 queued and waiting for resources
2025-09-15 20:23:29.904 wdl.w:ptcp.t:call-pbmm2_align_hifi-63 INFO output :: name: "mapped_bam", value: "m84036_250809_035451_s4.bc2160.mapped.bam"
2025-09-15 20:23:29.906 wdl.w:ptcp.t:call-pbmm2_align_hifi-63 INFO output :: name: "mapped_bam_bai", value: "m84036_250809_035451_s4.bc2160.mapped.bam.bai"
2025-09-15 20:23:29.907 wdl.w:ptcp.t:call-pbmm2_align_hifi-63 INFO output :: name: "mapped_bam_pbi", value: "m84036_250809_035451_s4.bc2160.mapped.bam.pbi"
2025-09-15 20:23:29.908 wdl.w:ptcp.t:call-pbmm2_align_hifi-63 INFO output :: name: "report", value: "mapping_stats.report.json"
2025-09-15 20:23:29.986 wdl.w:ptcp.t:call-pbmm2_align_hifi-63 NOTICE done
2025-09-15 20:23:29.992 wdl.w:ptcp NOTICE finish :: job: "call-pbmm2_align_hifi-63"
2025-09-15 20:23:29.992 wdl.w:ptcp INFO output :: job: "call-pbmm2_align_hifi-63", values: {"report": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-63/out/mapping_stats.report.json", "mapped_bam_pbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-63/out/m84036_250809_035451_s4.bc2160.mapped.bam.pbi", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-63/out/m84036_250809_035451_s4.bc2160.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-63/out/m84036_250809_035451_s4.bc2160.mapped.bam"}
2025-09-15 20:23:29.993 wdl.w:ptcp NOTICE ready :: job: "call-paraphase-63", callee: "paraphase"
2025-09-15 20:23:29.993 wdl.w:ptcp INFO input :: job: "call-paraphase-63", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf", "genome_version": "38", "config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-63/out/m84036_250809_035451_s4.bc2160.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-63/out/m84036_250809_035451_s4.bc2160.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2160"}
2025-09-15 20:23:29.994 wdl.w:ptcp NOTICE ready :: job: "call-sawfish-63", callee: "sawfish"
2025-09-15 20:23:29.994 wdl.w:ptcp INFO input :: job: "call-sawfish-63", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-63/out/m84036_250809_035451_s4.bc2160.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-63/out/m84036_250809_035451_s4.bc2160.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2160"}
2025-09-15 20:23:29.995 wdl.w:ptcp NOTICE ready :: job: "call-trgt-63", callee: "trgt"
2025-09-15 20:23:29.995 wdl.w:ptcp INFO input :: job: "call-trgt-63", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-63/out/m84036_250809_035451_s4.bc2160.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-63/out/m84036_250809_035451_s4.bc2160.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2160"}
2025-09-15 20:23:29.997 wdl.w:ptcp.w:call-sawfish-06.t:call-run_sawfish NOTICE task setup :: name: "run_sawfish", source: "./sawfish.wdl", line: 83, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-06/call-run_sawfish", thread: 140609268459072
2025-09-15 20:23:30.013 wdl.w:ptcp.w:call-sawfish-06.t:call-run_sawfish INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:23:30.013 wdl.w:ptcp.w:call-sawfish-06.t:call-run_sawfish INFO input :: name: "genome_version", value: "38"
2025-09-15 20:23:30.013 wdl.w:ptcp.w:call-sawfish-06.t:call-run_sawfish INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:23:30.013 wdl.w:ptcp.w:call-sawfish-06.t:call-run_sawfish INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:23:30.013 wdl.w:ptcp.w:call-sawfish-06.t:call-run_sawfish INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2103.mapped.bam.bai"
2025-09-15 20:23:30.013 wdl.w:ptcp.w:call-sawfish-06.t:call-run_sawfish INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2103.mapped.bam"
2025-09-15 20:23:30.013 wdl.w:ptcp.w:call-sawfish-06.t:call-run_sawfish INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2103"
2025-09-15 20:23:30.014 wdl.w:ptcp.w:call-sawfish-06.t:call-run_sawfish INFO eval :: name: "mem_gb", value: 32
2025-09-15 20:23:30.014 wdl.w:ptcp.w:call-sawfish-06.t:call-run_sawfish INFO eval :: name: "threads", value: 16
2025-09-15 20:23:30.014 wdl.w:ptcp.w:call-sawfish-06.t:call-run_sawfish INFO eval :: name: "disk_size", value: 30
2025-09-15 20:23:30.014 wdl.w:ptcp.w:call-sawfish-06.t:call-run_sawfish INFO eval :: name: "discover_dirname", value: "m84036_250809_035451_s4.bc2103_sawfish_discover"
2025-09-15 20:23:30.014 wdl.w:ptcp.w:call-sawfish-06.t:call-run_sawfish INFO eval :: name: "call_dirname", value: "m84036_250809_035451_s4.bc2103_sawfish"
2025-09-15 20:23:30.014 wdl.w:ptcp.w:call-sawfish-06.t:call-run_sawfish INFO eval :: name: "minimap2_bam_filename", value: "m84036_250809_035451_s4.bc2103.minimap2.bam"
2025-09-15 20:23:30.015 wdl.w:ptcp.w:call-sawfish-06.t:call-run_sawfish INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 16, memory_reservation: 32000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:23:30.015 wdl.w:ptcp.w:call-sawfish-06.t:call-run_sawfish WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:23:30.015 wdl.w:ptcp.w:call-sawfish-06.t:call-run_sawfish INFO provisioned :: seconds_waited: 0, cpu: 16, mem_bytes: 32000000000
2025-09-15 20:23:30.015 wdl.w:ptcp.w:call-sawfish-06.t:call-run_sawfish INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:23:30.045 wdl.w:ptcp.w:call-trgt-18.t:call-trgt_genotype.slurm_singularity INFO srun: job 51797373 has been allocated resources
2025-09-15 20:23:30.049 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_genotype.slurm_singularity INFO srun: job 51797374 has been allocated resources
2025-09-15 20:23:30.067 wdl.w:ptcp.w:call-trgt-19.t:call-get_reads_overlapping_repeats.slurm_singularity INFO srun: job 51797381 has been allocated resources
2025-09-15 20:23:30.072 wdl.w:ptcp.w:call-sawfish-06.t:call-run_sawfish INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 10, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-06/call-run_sawfish/_singularity_tmpdir_3tgatuti"
2025-09-15 20:23:30.072 wdl.w:ptcp.w:call-sawfish-06.t:call-run_sawfish INFO Slurm invocation: srun --job-name call-run_sawfish --partition compute,compute9 --cpus-per-task 16 --mem 30518M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-06/call-run_sawfish/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-06/call-run_sawfish/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-06/call-run_sawfish/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-06/call-run_sawfish/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-06/out/m84036_250809_035451_s4.bc2103.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2103.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-06/out/m84036_250809_035451_s4.bc2103.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2103.mapped.bam:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-06/call-run_sawfish/_singularity_tmpdir_3tgatuti/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-06/call-run_sawfish/_singularity_tmpdir_3tgatuti/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:23:30.104 wdl.w:ptcp.w:call-sawfish-17.t:call-run_sawfish.slurm_singularity INFO srun: job 51797384 has been allocated resources
2025-09-15 20:23:30.138 wdl.w:ptcp.w:call-sawfish-06.t:call-run_sawfish NOTICE slurm_singularity run :: pid: 1199323, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-06/call-run_sawfish/slurm_singularity.log.txt"
2025-09-15 20:23:30.189 wdl.w:ptcp.t:call-pbmm2_align_hifi-39 INFO output :: name: "mapped_bam", value: "m84036_250809_035451_s4.bc2136.mapped.bam"
2025-09-15 20:23:30.192 wdl.w:ptcp.t:call-pbmm2_align_hifi-39 INFO output :: name: "mapped_bam_bai", value: "m84036_250809_035451_s4.bc2136.mapped.bam.bai"
2025-09-15 20:23:30.192 wdl.w:ptcp.w:call-sawfish-26.t:call-run_sawfish.slurm_singularity INFO srun: job 51797363 has been allocated resources
2025-09-15 20:23:30.193 wdl.w:ptcp.w:call-sawfish-26.t:call-run_sawfish.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:30.193 wdl.w:ptcp.t:call-pbmm2_align_hifi-39 INFO output :: name: "mapped_bam_pbi", value: "m84036_250809_035451_s4.bc2136.mapped.bam.pbi"
2025-09-15 20:23:30.194 wdl.w:ptcp.t:call-pbmm2_align_hifi-39 INFO output :: name: "report", value: "mapping_stats.report.json"
2025-09-15 20:23:30.261 wdl.w:ptcp.t:call-pbmm2_align_hifi-39 NOTICE done
2025-09-15 20:23:30.267 wdl.w:ptcp NOTICE finish :: job: "call-pbmm2_align_hifi-39"
2025-09-15 20:23:30.267 wdl.w:ptcp INFO output :: job: "call-pbmm2_align_hifi-39", values: {"report": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-39/out/mapping_stats.report.json", "mapped_bam_pbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-39/out/m84036_250809_035451_s4.bc2136.mapped.bam.pbi", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-39/out/m84036_250809_035451_s4.bc2136.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-39/out/m84036_250809_035451_s4.bc2136.mapped.bam"}
2025-09-15 20:23:30.268 wdl.w:ptcp NOTICE ready :: job: "call-paraphase-39", callee: "paraphase"
2025-09-15 20:23:30.268 wdl.w:ptcp INFO input :: job: "call-paraphase-39", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf", "genome_version": "38", "config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-39/out/m84036_250809_035451_s4.bc2136.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-39/out/m84036_250809_035451_s4.bc2136.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2136"}
2025-09-15 20:23:30.269 wdl.w:ptcp NOTICE ready :: job: "call-sawfish-39", callee: "sawfish"
2025-09-15 20:23:30.269 wdl.w:ptcp INFO input :: job: "call-sawfish-39", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-39/out/m84036_250809_035451_s4.bc2136.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-39/out/m84036_250809_035451_s4.bc2136.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2136"}
2025-09-15 20:23:30.270 wdl.w:ptcp NOTICE ready :: job: "call-trgt-39", callee: "trgt"
2025-09-15 20:23:30.270 wdl.w:ptcp INFO input :: job: "call-trgt-39", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-39/out/m84036_250809_035451_s4.bc2136.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-39/out/m84036_250809_035451_s4.bc2136.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2136"}
2025-09-15 20:23:30.273 wdl.w:ptcp.w:call-trgt-17.t:call-get_reads_overlapping_repeats.slurm_singularity INFO srun: job 51797385 has been allocated resources
2025-09-15 20:23:30.273 wdl.w:ptcp.w:call-trgt-17.t:call-get_reads_overlapping_repeats.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:30.272 wdl.w:ptcp.w:call-sawfish-30.t:call-run_sawfish NOTICE task setup :: name: "run_sawfish", source: "./sawfish.wdl", line: 83, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-30/call-run_sawfish", thread: 140610904249920
2025-09-15 20:23:30.289 wdl.w:ptcp.w:call-sawfish-30.t:call-run_sawfish INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:23:30.290 wdl.w:ptcp.w:call-sawfish-30.t:call-run_sawfish INFO input :: name: "genome_version", value: "38"
2025-09-15 20:23:30.290 wdl.w:ptcp.w:call-sawfish-30.t:call-run_sawfish INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:23:30.290 wdl.w:ptcp.w:call-sawfish-30.t:call-run_sawfish INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:23:30.290 wdl.w:ptcp.w:call-sawfish-30.t:call-run_sawfish INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2127.mapped.bam.bai"
2025-09-15 20:23:30.290 wdl.w:ptcp.w:call-sawfish-30.t:call-run_sawfish INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2127.mapped.bam"
2025-09-15 20:23:30.290 wdl.w:ptcp.w:call-sawfish-30.t:call-run_sawfish INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2127"
2025-09-15 20:23:30.290 wdl.w:ptcp.w:call-sawfish-30.t:call-run_sawfish INFO eval :: name: "mem_gb", value: 32
2025-09-15 20:23:30.290 wdl.w:ptcp.w:call-sawfish-30.t:call-run_sawfish INFO eval :: name: "threads", value: 16
2025-09-15 20:23:30.290 wdl.w:ptcp.w:call-sawfish-30.t:call-run_sawfish INFO eval :: name: "disk_size", value: 30
2025-09-15 20:23:30.291 wdl.w:ptcp.w:call-sawfish-30.t:call-run_sawfish INFO eval :: name: "discover_dirname", value: "m84036_250809_035451_s4.bc2127_sawfish_discover"
2025-09-15 20:23:30.291 wdl.w:ptcp.w:call-sawfish-30.t:call-run_sawfish INFO eval :: name: "call_dirname", value: "m84036_250809_035451_s4.bc2127_sawfish"
2025-09-15 20:23:30.291 wdl.w:ptcp.w:call-sawfish-30.t:call-run_sawfish INFO eval :: name: "minimap2_bam_filename", value: "m84036_250809_035451_s4.bc2127.minimap2.bam"
2025-09-15 20:23:30.291 wdl.w:ptcp.w:call-sawfish-30.t:call-run_sawfish INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 16, memory_reservation: 32000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:23:30.291 wdl.w:ptcp.w:call-sawfish-30.t:call-run_sawfish WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:23:30.292 wdl.w:ptcp.w:call-sawfish-30.t:call-run_sawfish INFO provisioned :: seconds_waited: 0, cpu: 16, mem_bytes: 32000000000
2025-09-15 20:23:30.292 wdl.w:ptcp.w:call-sawfish-30.t:call-run_sawfish INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:23:30.299 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_genotype.slurm_singularity INFO srun: job 51797362 has been allocated resources
2025-09-15 20:23:30.300 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_genotype.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:30.309 wdl.w:ptcp.w:call-trgt-21.t:call-trgt_genotype.slurm_singularity INFO srun: job 51797390 queued and waiting for resources
2025-09-15 20:23:30.310 wdl.w:ptcp.w:call-trgt-19.t:call-trgt_genotype.slurm_singularity INFO srun: job 51797382 has been allocated resources
2025-09-15 20:23:30.310 wdl.w:ptcp.w:call-trgt-21.t:call-trgt_genotype.slurm_singularity INFO srun: job 51797390 has been allocated resources
2025-09-15 20:23:30.310 wdl.w:ptcp.w:call-trgt-19.t:call-trgt_genotype.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:30.310 wdl.w:ptcp.w:call-paraphase-21.t:call-run_paraphase.slurm_singularity INFO srun: job 51797389 queued and waiting for resources
2025-09-15 20:23:30.310 wdl.w:ptcp.w:call-paraphase-21.t:call-run_paraphase.slurm_singularity INFO srun: job 51797389 has been allocated resources
2025-09-15 20:23:30.346 wdl.w:ptcp.w:call-paraphase-28.t:call-run_paraphase.slurm_singularity INFO srun: job 51797361 has been allocated resources
2025-09-15 20:23:30.347 wdl.w:ptcp.w:call-paraphase-28.t:call-run_paraphase.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:30.356 wdl.w:ptcp.w:call-sawfish-28.t:call-run_sawfish.slurm_singularity INFO srun: job 51797364 has been allocated resources
2025-09-15 20:23:30.359 wdl.w:ptcp.w:call-sawfish-30.t:call-run_sawfish INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 10, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-30/call-run_sawfish/_singularity_tmpdir_37ujmesq"
2025-09-15 20:23:30.359 wdl.w:ptcp.w:call-sawfish-30.t:call-run_sawfish INFO Slurm invocation: srun --job-name call-run_sawfish --partition compute,compute9 --cpus-per-task 16 --mem 30518M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-30/call-run_sawfish/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-30/call-run_sawfish/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-30/call-run_sawfish/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-30/call-run_sawfish/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-30/out/m84036_250809_035451_s4.bc2127.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2127.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-30/out/m84036_250809_035451_s4.bc2127.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2127.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-30/call-run_sawfish/_singularity_tmpdir_37ujmesq/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-30/call-run_sawfish/_singularity_tmpdir_37ujmesq/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:23:30.366 wdl.w:ptcp.w:call-trgt-28.t:call-get_reads_overlapping_repeats.slurm_singularity INFO srun: job 51797365 has been allocated resources
2025-09-15 20:23:30.366 wdl.w:ptcp.w:call-trgt-28.t:call-get_reads_overlapping_repeats.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:30.416 wdl.w:ptcp.w:call-sawfish-30.t:call-run_sawfish NOTICE slurm_singularity run :: pid: 1199331, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-30/call-run_sawfish/slurm_singularity.log.txt"
2025-09-15 20:23:30.429 wdl.w:ptcp.w:call-paraphase-31.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for smn1 for sample m84036_250809_035451_s4.bc2128 at 2025-09-15 20:23:16.372290...
2025-09-15 20:23:30.429 wdl.w:ptcp.w:call-paraphase-31.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for f8inv1 for sample m84036_250809_035451_s4.bc2128 at 2025-09-15 20:23:25.217148...
2025-09-15 20:23:30.429 wdl.w:ptcp.w:call-paraphase-31.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for f8inv1 for sample m84036_250809_035451_s4.bc2128 at 2025-09-15 20:23:25.217866...
2025-09-15 20:23:30.440 wdl.w:ptcp.t:call-pbmm2_align_hifi-84.slurm_singularity INFO srun: job 51797304 has been allocated resources
2025-09-15 20:23:30.440 wdl.w:ptcp.t:call-pbmm2_align_hifi-84.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:30.440 wdl.w:ptcp.t:call-pbmm2_align_hifi-84.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:23:30.469 wdl.w:ptcp.w:call-trgt-28.t:call-trgt_genotype.slurm_singularity INFO srun: job 51797366 has been allocated resources
2025-09-15 20:23:30.469 wdl.w:ptcp.w:call-trgt-28.t:call-trgt_genotype.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:30.470 wdl.w:ptcp.w:call-trgt-17.t:call-trgt_genotype.slurm_singularity INFO srun: job 51797386 has been allocated resources
2025-09-15 20:23:30.470 wdl.w:ptcp.w:call-trgt-17.t:call-trgt_genotype.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:30.470 wdl.w:ptcp.w:call-trgt-17.t:call-trgt_genotype.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:23:30.473 wdl.w:ptcp.w:call-paraphase-10.t:call-run_paraphase.slurm_singularity INFO srun: job 51797368 has been allocated resources
2025-09-15 20:23:30.474 wdl.w:ptcp.w:call-paraphase-10.t:call-run_paraphase.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:30.482 wdl.w:ptcp.w:call-sawfish-18.t:call-run_sawfish.slurm_singularity INFO srun: job 51797369 has been allocated resources
2025-09-15 20:23:30.483 wdl.w:ptcp.w:call-sawfish-18.t:call-run_sawfish.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:30.500 wdl.w:ptcp.w:call-sawfish-10.t:call-run_sawfish.slurm_singularity INFO srun: job 51797367 has been allocated resources
2025-09-15 20:23:30.501 wdl.w:ptcp.w:call-sawfish-10.t:call-run_sawfish.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:30.511 wdl.w:ptcp.t:call-pbmm2_align_hifi-82.slurm_singularity INFO srun: job 51797305 has been allocated resources
2025-09-15 20:23:30.511 wdl.w:ptcp.t:call-pbmm2_align_hifi-82.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:30.511 wdl.w:ptcp.t:call-pbmm2_align_hifi-82.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:23:30.533 wdl.w:ptcp.t:call-pbmm2_align_hifi-41 INFO output :: name: "mapped_bam", value: "m84036_250809_035451_s4.bc2138.mapped.bam"
2025-09-15 20:23:30.536 wdl.w:ptcp.t:call-pbmm2_align_hifi-41 INFO output :: name: "mapped_bam_bai", value: "m84036_250809_035451_s4.bc2138.mapped.bam.bai"
2025-09-15 20:23:30.537 wdl.w:ptcp.t:call-pbmm2_align_hifi-41 INFO output :: name: "mapped_bam_pbi", value: "m84036_250809_035451_s4.bc2138.mapped.bam.pbi"
2025-09-15 20:23:30.538 wdl.w:ptcp.t:call-pbmm2_align_hifi-41 INFO output :: name: "report", value: "mapping_stats.report.json"
2025-09-15 20:23:30.550 wdl.w:ptcp.w:call-sawfish-21.t:call-run_sawfish.slurm_singularity INFO srun: job 51797387 has been allocated resources
2025-09-15 20:23:30.550 wdl.w:ptcp.w:call-sawfish-21.t:call-run_sawfish.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:30.550 wdl.w:ptcp.w:call-sawfish-21.t:call-run_sawfish.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:23:30.574 wdl.w:ptcp.t:call-pbmm2_align_hifi-85.slurm_singularity INFO srun: job 51797306 has been allocated resources
2025-09-15 20:23:30.577 wdl.w:ptcp.t:call-pbmm2_align_hifi-40 INFO output :: name: "mapped_bam", value: "m84036_250809_035451_s4.bc2137.mapped.bam"
2025-09-15 20:23:30.580 wdl.w:ptcp.t:call-pbmm2_align_hifi-40 INFO output :: name: "mapped_bam_bai", value: "m84036_250809_035451_s4.bc2137.mapped.bam.bai"
2025-09-15 20:23:30.582 wdl.w:ptcp.t:call-pbmm2_align_hifi-40 INFO output :: name: "mapped_bam_pbi", value: "m84036_250809_035451_s4.bc2137.mapped.bam.pbi"
2025-09-15 20:23:30.583 wdl.w:ptcp.t:call-pbmm2_align_hifi-40 INFO output :: name: "report", value: "mapping_stats.report.json"
2025-09-15 20:23:30.636 wdl.w:ptcp.t:call-pbmm2_align_hifi-41 NOTICE done
2025-09-15 20:23:30.644 wdl.w:ptcp NOTICE finish :: job: "call-pbmm2_align_hifi-41"
2025-09-15 20:23:30.644 wdl.w:ptcp INFO output :: job: "call-pbmm2_align_hifi-41", values: {"report": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-41/out/mapping_stats.report.json", "mapped_bam_pbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-41/out/m84036_250809_035451_s4.bc2138.mapped.bam.pbi", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-41/out/m84036_250809_035451_s4.bc2138.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-41/out/m84036_250809_035451_s4.bc2138.mapped.bam"}
2025-09-15 20:23:30.645 wdl.w:ptcp NOTICE ready :: job: "call-paraphase-41", callee: "paraphase"
2025-09-15 20:23:30.645 wdl.w:ptcp.w:call-sawfish-19.t:call-run_sawfish.slurm_singularity INFO srun: job 51797380 has been allocated resources
2025-09-15 20:23:30.645 wdl.w:ptcp INFO input :: job: "call-paraphase-41", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf", "genome_version": "38", "config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-41/out/m84036_250809_035451_s4.bc2138.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-41/out/m84036_250809_035451_s4.bc2138.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2138"}
2025-09-15 20:23:30.645 wdl.w:ptcp.w:call-sawfish-19.t:call-run_sawfish.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:30.647 wdl.w:ptcp NOTICE ready :: job: "call-sawfish-41", callee: "sawfish"
2025-09-15 20:23:30.647 wdl.w:ptcp INFO input :: job: "call-sawfish-41", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-41/out/m84036_250809_035451_s4.bc2138.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-41/out/m84036_250809_035451_s4.bc2138.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2138"}
2025-09-15 20:23:30.648 wdl.w:ptcp NOTICE ready :: job: "call-trgt-41", callee: "trgt"
2025-09-15 20:23:30.648 wdl.w:ptcp INFO input :: job: "call-trgt-41", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-41/out/m84036_250809_035451_s4.bc2138.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-41/out/m84036_250809_035451_s4.bc2138.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2138"}
2025-09-15 20:23:30.649 wdl.w:ptcp.w:call-paraphase-19.t:call-run_paraphase.slurm_singularity INFO srun: job 51797379 has been allocated resources
2025-09-15 20:23:30.649 wdl.w:ptcp.w:call-paraphase-19.t:call-run_paraphase.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:30.655 wdl.w:ptcp.w:call-trgt-06.t:call-get_reads_overlapping_repeats NOTICE task setup :: name: "get_reads_overlapping_repeats", source: "./trgt.wdl", line: 182, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-06/call-get_reads_overlapping_repeats", thread: 140610887464512
2025-09-15 20:23:30.673 wdl.w:ptcp.t:call-pbmm2_align_hifi-40 NOTICE done
2025-09-15 20:23:30.680 wdl.w:ptcp.w:call-trgt-06.t:call-get_reads_overlapping_repeats INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:23:30.680 wdl.w:ptcp.w:call-trgt-06.t:call-get_reads_overlapping_repeats INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:23:30.680 wdl.w:ptcp.w:call-trgt-06.t:call-get_reads_overlapping_repeats INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2103.mapped.bam.bai"
2025-09-15 20:23:30.680 wdl.w:ptcp.w:call-trgt-06.t:call-get_reads_overlapping_repeats INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2103.mapped.bam"
2025-09-15 20:23:30.680 wdl.w:ptcp.w:call-trgt-06.t:call-get_reads_overlapping_repeats INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2103"
2025-09-15 20:23:30.681 wdl.w:ptcp.w:call-trgt-06.t:call-get_reads_overlapping_repeats INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:23:30.681 wdl.w:ptcp.w:call-trgt-06.t:call-get_reads_overlapping_repeats INFO eval :: name: "expand_size", value: 3000
2025-09-15 20:23:30.681 wdl.w:ptcp.w:call-trgt-06.t:call-get_reads_overlapping_repeats INFO eval :: name: "threads", value: 1
2025-09-15 20:23:30.681 wdl.w:ptcp.w:call-trgt-06.t:call-get_reads_overlapping_repeats INFO eval :: name: "expanded_bed_name", value: "m84036_250809_035451_s4.bc2103.expanded.bed"
2025-09-15 20:23:30.681 wdl.w:ptcp.w:call-trgt-06.t:call-get_reads_overlapping_repeats INFO eval :: name: "disk_size", value: 11
2025-09-15 20:23:30.681 wdl.w:ptcp.w:call-trgt-06.t:call-get_reads_overlapping_repeats INFO eval :: name: "output_name", value: "m84036_250809_035451_s4.bc2103.repeats.bam"
2025-09-15 20:23:30.681 wdl.w:ptcp.w:call-trgt-06.t:call-get_reads_overlapping_repeats INFO eval :: name: "index_name", value: "m84036_250809_035451_s4.bc2103.repeats.bam.bai"
2025-09-15 20:23:30.681 wdl.w:ptcp.w:call-trgt-06.t:call-get_reads_overlapping_repeats INFO eval :: name: "output_name_with_index", value: "m84036_250809_035451_s4.bc2103.repeats.bam##idx##m84036_250809_035451_s4.bc2103.repeats.bam.bai"
2025-09-15 20:23:30.682 wdl.w:ptcp.w:call-trgt-06.t:call-get_reads_overlapping_repeats INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:23:30.682 wdl.w:ptcp.w:call-trgt-06.t:call-get_reads_overlapping_repeats WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:23:30.682 wdl.w:ptcp.w:call-trgt-10.t:call-get_reads_overlapping_repeats.slurm_singularity INFO srun: job 51797370 has been allocated resources
2025-09-15 20:23:30.682 wdl.w:ptcp.w:call-trgt-06.t:call-get_reads_overlapping_repeats INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:23:30.682 wdl.w:ptcp.w:call-trgt-10.t:call-get_reads_overlapping_repeats.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:30.683 wdl.w:ptcp.w:call-trgt-06.t:call-get_reads_overlapping_repeats INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:23:30.683 wdl.w:ptcp NOTICE finish :: job: "call-pbmm2_align_hifi-40"
2025-09-15 20:23:30.683 wdl.w:ptcp INFO output :: job: "call-pbmm2_align_hifi-40", values: {"report": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-40/out/mapping_stats.report.json", "mapped_bam_pbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-40/out/m84036_250809_035451_s4.bc2137.mapped.bam.pbi", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-40/out/m84036_250809_035451_s4.bc2137.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-40/out/m84036_250809_035451_s4.bc2137.mapped.bam"}
2025-09-15 20:23:30.684 wdl.w:ptcp NOTICE ready :: job: "call-paraphase-40", callee: "paraphase"
2025-09-15 20:23:30.684 wdl.w:ptcp INFO input :: job: "call-paraphase-40", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf", "genome_version": "38", "config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-40/out/m84036_250809_035451_s4.bc2137.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-40/out/m84036_250809_035451_s4.bc2137.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2137"}
2025-09-15 20:23:30.685 wdl.w:ptcp NOTICE ready :: job: "call-sawfish-40", callee: "sawfish"
2025-09-15 20:23:30.685 wdl.w:ptcp INFO input :: job: "call-sawfish-40", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-40/out/m84036_250809_035451_s4.bc2137.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-40/out/m84036_250809_035451_s4.bc2137.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2137"}
2025-09-15 20:23:30.686 wdl.w:ptcp NOTICE ready :: job: "call-trgt-40", callee: "trgt"
2025-09-15 20:23:30.686 wdl.w:ptcp INFO input :: job: "call-trgt-40", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-40/out/m84036_250809_035451_s4.bc2137.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-40/out/m84036_250809_035451_s4.bc2137.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2137"}
2025-09-15 20:23:30.688 wdl.w:ptcp.w:call-trgt-18.t:call-get_reads_overlapping_repeats.slurm_singularity INFO srun: job 51797371 has been allocated resources
2025-09-15 20:23:30.689 wdl.w:ptcp.w:call-trgt-18.t:call-get_reads_overlapping_repeats.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:30.693 wdl.w:ptcp.w:call-sawfish-33.t:call-run_sawfish NOTICE task setup :: name: "run_sawfish", source: "./sawfish.wdl", line: 83, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-33/call-run_sawfish", thread: 140610895857216
2025-09-15 20:23:30.704 wdl.w:ptcp.w:call-paraphase-18.t:call-run_paraphase.slurm_singularity INFO srun: job 51797372 has been allocated resources
2025-09-15 20:23:30.705 wdl.w:ptcp.w:call-paraphase-18.t:call-run_paraphase.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:30.716 wdl.w:ptcp.w:call-trgt-21.t:call-get_reads_overlapping_repeats.slurm_singularity INFO srun: job 51797388 has been allocated resources
2025-09-15 20:23:30.717 wdl.w:ptcp.w:call-trgt-21.t:call-get_reads_overlapping_repeats.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:30.718 wdl.w:ptcp.w:call-sawfish-33.t:call-run_sawfish INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:23:30.718 wdl.w:ptcp.w:call-sawfish-33.t:call-run_sawfish INFO input :: name: "genome_version", value: "38"
2025-09-15 20:23:30.718 wdl.w:ptcp.w:call-sawfish-33.t:call-run_sawfish INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:23:30.718 wdl.w:ptcp.w:call-sawfish-33.t:call-run_sawfish INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:23:30.719 wdl.w:ptcp.w:call-sawfish-33.t:call-run_sawfish INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2130.mapped.bam.bai"
2025-09-15 20:23:30.719 wdl.w:ptcp.w:call-sawfish-33.t:call-run_sawfish INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2130.mapped.bam"
2025-09-15 20:23:30.719 wdl.w:ptcp.w:call-sawfish-33.t:call-run_sawfish INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2130"
2025-09-15 20:23:30.719 wdl.w:ptcp.w:call-sawfish-33.t:call-run_sawfish INFO eval :: name: "mem_gb", value: 32
2025-09-15 20:23:30.719 wdl.w:ptcp.w:call-sawfish-33.t:call-run_sawfish INFO eval :: name: "threads", value: 16
2025-09-15 20:23:30.719 wdl.w:ptcp.w:call-sawfish-33.t:call-run_sawfish INFO eval :: name: "disk_size", value: 30
2025-09-15 20:23:30.719 wdl.w:ptcp.w:call-sawfish-33.t:call-run_sawfish INFO eval :: name: "discover_dirname", value: "m84036_250809_035451_s4.bc2130_sawfish_discover"
2025-09-15 20:23:30.719 wdl.w:ptcp.w:call-sawfish-33.t:call-run_sawfish INFO eval :: name: "call_dirname", value: "m84036_250809_035451_s4.bc2130_sawfish"
2025-09-15 20:23:30.720 wdl.w:ptcp.w:call-sawfish-33.t:call-run_sawfish INFO eval :: name: "minimap2_bam_filename", value: "m84036_250809_035451_s4.bc2130.minimap2.bam"
2025-09-15 20:23:30.720 wdl.w:ptcp.w:call-sawfish-33.t:call-run_sawfish INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 16, memory_reservation: 32000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:23:30.720 wdl.w:ptcp.w:call-sawfish-33.t:call-run_sawfish WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:23:30.720 wdl.w:ptcp.w:call-sawfish-33.t:call-run_sawfish INFO provisioned :: seconds_waited: 0, cpu: 16, mem_bytes: 32000000000
2025-09-15 20:23:30.721 wdl.w:ptcp.w:call-sawfish-33.t:call-run_sawfish INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:23:30.741 wdl.w:ptcp.w:call-trgt-06.t:call-get_reads_overlapping_repeats INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 9, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-06/call-get_reads_overlapping_repeats/_singularity_tmpdir_3s_vvu1b"
2025-09-15 20:23:30.741 wdl.w:ptcp.w:call-trgt-06.t:call-get_reads_overlapping_repeats INFO Slurm invocation: srun --job-name call-get_reads_overlapping_repeats --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-06/call-get_reads_overlapping_repeats/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-06/call-get_reads_overlapping_repeats/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-06/call-get_reads_overlapping_repeats/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-06/call-get_reads_overlapping_repeats/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-06/out/m84036_250809_035451_s4.bc2103.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2103.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-06/out/m84036_250809_035451_s4.bc2103.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2103.mapped.bam:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-06/call-get_reads_overlapping_repeats/_singularity_tmpdir_3s_vvu1b/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-06/call-get_reads_overlapping_repeats/_singularity_tmpdir_3s_vvu1b/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:23:30.758 wdl.w:ptcp.w:call-sawfish-11.t:call-run_sawfish.slurm_singularity INFO srun: job 51797376 has been allocated resources
2025-09-15 20:23:30.759 wdl.w:ptcp.w:call-sawfish-11.t:call-run_sawfish.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:30.771 wdl.w:ptcp.w:call-paraphase-17.t:call-run_paraphase.slurm_singularity INFO srun: job 51797383 has been allocated resources
2025-09-15 20:23:30.771 wdl.w:ptcp.w:call-paraphase-17.t:call-run_paraphase.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:30.783 wdl.w:ptcp.w:call-sawfish-33.t:call-run_sawfish INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 10, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-33/call-run_sawfish/_singularity_tmpdir_wo6n7o62"
2025-09-15 20:23:30.783 wdl.w:ptcp.w:call-sawfish-33.t:call-run_sawfish INFO Slurm invocation: srun --job-name call-run_sawfish --partition compute,compute9 --cpus-per-task 16 --mem 30518M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-33/call-run_sawfish/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-33/call-run_sawfish/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-33/call-run_sawfish/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-33/call-run_sawfish/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-33/out/m84036_250809_035451_s4.bc2130.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2130.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-33/out/m84036_250809_035451_s4.bc2130.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2130.mapped.bam:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-33/call-run_sawfish/_singularity_tmpdir_wo6n7o62/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-33/call-run_sawfish/_singularity_tmpdir_wo6n7o62/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:23:30.804 wdl.w:ptcp.w:call-sawfish-33.t:call-run_sawfish NOTICE slurm_singularity run :: pid: 1199347, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-33/call-run_sawfish/slurm_singularity.log.txt"
2025-09-15 20:23:30.804 wdl.w:ptcp.w:call-trgt-06.t:call-get_reads_overlapping_repeats NOTICE slurm_singularity run :: pid: 1199346, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-06/call-get_reads_overlapping_repeats/slurm_singularity.log.txt"
2025-09-15 20:23:30.843 wdl.w:ptcp.w:call-trgt-11.t:call-get_reads_overlapping_repeats.slurm_singularity INFO srun: job 51797377 has been allocated resources
2025-09-15 20:23:30.844 wdl.w:ptcp.w:call-trgt-11.t:call-get_reads_overlapping_repeats.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:30.850 wdl.w:ptcp.w:call-paraphase-11.t:call-run_paraphase.slurm_singularity INFO srun: job 51797375 has been allocated resources
2025-09-15 20:23:30.850 wdl.w:ptcp.w:call-paraphase-11.t:call-run_paraphase.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:30.865 wdl.w:ptcp.w:call-paraphase-26.t:call-run_paraphase.slurm_singularity INFO srun: job 51797359 has been allocated resources
2025-09-15 20:23:30.866 wdl.w:ptcp.w:call-paraphase-26.t:call-run_paraphase.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:30.866 wdl.w:ptcp.w:call-trgt-11.t:call-trgt_genotype.slurm_singularity INFO srun: job 51797378 has been allocated resources
2025-09-15 20:23:30.867 wdl.w:ptcp.w:call-trgt-11.t:call-trgt_genotype.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:30.928 wdl.w:ptcp.w:call-trgt-26.t:call-get_reads_overlapping_repeats.slurm_singularity INFO srun: job 51797360 has been allocated resources
2025-09-15 20:23:30.928 wdl.w:ptcp.w:call-trgt-26.t:call-get_reads_overlapping_repeats.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:31.065 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_genotype.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:31.065 wdl.w:ptcp.w:call-trgt-18.t:call-trgt_genotype.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:31.080 wdl.w:ptcp.w:call-trgt-19.t:call-get_reads_overlapping_repeats.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:31.098 wdl.w:ptcp.w:call-trgt-26.t:call-get_reads_overlapping_repeats INFO output :: name: "reads_overlapping_repeats", value: "m84036_250809_035451_s4.bc2123.repeats.bam"
2025-09-15 20:23:31.103 wdl.w:ptcp.w:call-trgt-26.t:call-get_reads_overlapping_repeats INFO output :: name: "reads_overlapping_repeats_bai", value: "m84036_250809_035451_s4.bc2123.repeats.bam.bai"
2025-09-15 20:23:31.104 wdl.w:ptcp.t:call-pbmm2_align_hifi-62 INFO output :: name: "mapped_bam", value: "m84036_250809_035451_s4.bc2159.mapped.bam"
2025-09-15 20:23:31.108 wdl.w:ptcp.t:call-pbmm2_align_hifi-62 INFO output :: name: "mapped_bam_bai", value: "m84036_250809_035451_s4.bc2159.mapped.bam.bai"
2025-09-15 20:23:31.109 wdl.w:ptcp.t:call-pbmm2_align_hifi-62 INFO output :: name: "mapped_bam_pbi", value: "m84036_250809_035451_s4.bc2159.mapped.bam.pbi"
2025-09-15 20:23:31.111 wdl.w:ptcp.t:call-pbmm2_align_hifi-62 INFO output :: name: "report", value: "mapping_stats.report.json"
2025-09-15 20:23:31.116 wdl.w:ptcp.w:call-sawfish-17.t:call-run_sawfish.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:31.129 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_genotype INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2123.trgt.vcf"
2025-09-15 20:23:31.134 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_genotype INFO output :: name: "spanning_bam", value: "m84036_250809_035451_s4.bc2123.trgt.sorted.spanning.bam"
2025-09-15 20:23:31.136 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_genotype INFO output :: name: "spanning_bam_bai", value: "m84036_250809_035451_s4.bc2123.trgt.sorted.spanning.bam.bai"
2025-09-15 20:23:31.151 wdl.w:ptcp.t:call-pbmm2_align_hifi-48 INFO output :: name: "mapped_bam", value: "m84036_250809_035451_s4.bc2145.mapped.bam"
2025-09-15 20:23:31.152 wdl.w:ptcp.w:call-sawfish-06.t:call-run_sawfish.slurm_singularity INFO srun: job 51797391 queued and waiting for resources
2025-09-15 20:23:31.157 wdl.w:ptcp.t:call-pbmm2_align_hifi-48 INFO output :: name: "mapped_bam_bai", value: "m84036_250809_035451_s4.bc2145.mapped.bam.bai"
2025-09-15 20:23:31.158 wdl.w:ptcp.t:call-pbmm2_align_hifi-48 INFO output :: name: "mapped_bam_pbi", value: "m84036_250809_035451_s4.bc2145.mapped.bam.pbi"
2025-09-15 20:23:31.159 wdl.w:ptcp.t:call-pbmm2_align_hifi-48 INFO output :: name: "report", value: "mapping_stats.report.json"
2025-09-15 20:23:31.172 wdl.w:ptcp.w:call-trgt-18.t:call-get_reads_overlapping_repeats INFO output :: name: "reads_overlapping_repeats", value: "m84036_250809_035451_s4.bc2115.repeats.bam"
2025-09-15 20:23:31.175 wdl.w:ptcp.w:call-paraphase-15.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for f8inv1 for sample m84036_250809_035451_s4.bc2112 at 2025-09-15 20:23:23.650492...
2025-09-15 20:23:31.175 wdl.w:ptcp.w:call-paraphase-15.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for f8inv1 for sample m84036_250809_035451_s4.bc2112 at 2025-09-15 20:23:27.744267...
2025-09-15 20:23:31.175 wdl.w:ptcp.w:call-paraphase-15.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for f8inv1 for sample m84036_250809_035451_s4.bc2112 at 2025-09-15 20:23:28.019914...
2025-09-15 20:23:31.177 wdl.w:ptcp.w:call-trgt-18.t:call-get_reads_overlapping_repeats INFO output :: name: "reads_overlapping_repeats_bai", value: "m84036_250809_035451_s4.bc2115.repeats.bam.bai"
2025-09-15 20:23:31.196 wdl.w:ptcp.w:call-trgt-18.t:call-trgt_genotype INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2115.trgt.vcf"
2025-09-15 20:23:31.199 wdl.w:ptcp.w:call-trgt-11.t:call-trgt_genotype INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2108.trgt.vcf"
2025-09-15 20:23:31.201 wdl.w:ptcp.w:call-trgt-18.t:call-trgt_genotype INFO output :: name: "spanning_bam", value: "m84036_250809_035451_s4.bc2115.trgt.sorted.spanning.bam"
2025-09-15 20:23:31.203 wdl.w:ptcp.w:call-trgt-18.t:call-trgt_genotype INFO output :: name: "spanning_bam_bai", value: "m84036_250809_035451_s4.bc2115.trgt.sorted.spanning.bam.bai"
2025-09-15 20:23:31.204 wdl.w:ptcp.w:call-trgt-11.t:call-trgt_genotype INFO output :: name: "spanning_bam", value: "m84036_250809_035451_s4.bc2108.trgt.sorted.spanning.bam"
2025-09-15 20:23:31.206 wdl.w:ptcp.w:call-trgt-11.t:call-trgt_genotype INFO output :: name: "spanning_bam_bai", value: "m84036_250809_035451_s4.bc2108.trgt.sorted.spanning.bam.bai"
2025-09-15 20:23:31.212 wdl.w:ptcp.w:call-trgt-26.t:call-get_reads_overlapping_repeats NOTICE done
2025-09-15 20:23:31.218 wdl.w:ptcp.w:call-trgt-26 NOTICE finish :: job: "call-get_reads_overlapping_repeats"
2025-09-15 20:23:31.218 wdl.w:ptcp.w:call-trgt-26 INFO output :: job: "call-get_reads_overlapping_repeats", values: {"reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-26/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2123.repeats.bam.bai", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-26/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2123.repeats.bam"}
2025-09-15 20:23:31.218 wdl.w:ptcp.w:call-trgt-26 INFO visit :: node: "output-reads_overlapping_repeats", values: {"reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-26/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2123.repeats.bam"}
2025-09-15 20:23:31.219 wdl.w:ptcp.w:call-trgt-26 INFO visit :: node: "output-reads_overlapping_repeats_bai", values: {"reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-26/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2123.repeats.bam.bai"}
2025-09-15 20:23:31.227 wdl.w:ptcp.w:call-paraphase-06.t:call-run_paraphase NOTICE task setup :: name: "run_paraphase", source: "./paraphase.wdl", line: 127, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-06/call-run_paraphase", thread: 140612498077248
2025-09-15 20:23:31.234 wdl.w:ptcp.w:call-trgt-19.t:call-get_reads_overlapping_repeats INFO output :: name: "reads_overlapping_repeats", value: "m84036_250809_035451_s4.bc2116.repeats.bam"
2025-09-15 20:23:31.239 wdl.w:ptcp.w:call-trgt-19.t:call-get_reads_overlapping_repeats INFO output :: name: "reads_overlapping_repeats_bai", value: "m84036_250809_035451_s4.bc2116.repeats.bam.bai"
2025-09-15 20:23:31.247 wdl.w:ptcp.t:call-pbmm2_align_hifi-62 NOTICE done
2025-09-15 20:23:31.251 wdl.w:ptcp.w:call-paraphase-06.t:call-run_paraphase INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:23:31.252 wdl.w:ptcp.w:call-paraphase-06.t:call-run_paraphase INFO input :: name: "annotation_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf"
2025-09-15 20:23:31.252 wdl.w:ptcp.w:call-paraphase-06.t:call-run_paraphase INFO input :: name: "genome_version", value: "38"
2025-09-15 20:23:31.252 wdl.w:ptcp.w:call-paraphase-06.t:call-run_paraphase INFO input :: name: "config_file", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/paraphase_config.GRCh38.yaml"
2025-09-15 20:23:31.252 wdl.w:ptcp.w:call-paraphase-06.t:call-run_paraphase INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:23:31.252 wdl.w:ptcp.w:call-paraphase-06.t:call-run_paraphase INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:23:31.253 wdl.w:ptcp.w:call-paraphase-06.t:call-run_paraphase INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2103.mapped.bam.bai"
2025-09-15 20:23:31.253 wdl.w:ptcp NOTICE finish :: job: "call-pbmm2_align_hifi-62"
2025-09-15 20:23:31.253 wdl.w:ptcp.w:call-paraphase-06.t:call-run_paraphase INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2103.mapped.bam"
2025-09-15 20:23:31.253 wdl.w:ptcp INFO output :: job: "call-pbmm2_align_hifi-62", values: {"report": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-62/out/mapping_stats.report.json", "mapped_bam_pbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-62/out/m84036_250809_035451_s4.bc2159.mapped.bam.pbi", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-62/out/m84036_250809_035451_s4.bc2159.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-62/out/m84036_250809_035451_s4.bc2159.mapped.bam"}
2025-09-15 20:23:31.254 wdl.w:ptcp.w:call-paraphase-06.t:call-run_paraphase INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2103"
2025-09-15 20:23:31.255 wdl.w:ptcp NOTICE ready :: job: "call-paraphase-62", callee: "paraphase"
2025-09-15 20:23:31.255 wdl.w:ptcp.w:call-paraphase-06.t:call-run_paraphase INFO eval :: name: "threads", value: 4
2025-09-15 20:23:31.256 wdl.w:ptcp INFO input :: job: "call-paraphase-62", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf", "genome_version": "38", "config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-62/out/m84036_250809_035451_s4.bc2159.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-62/out/m84036_250809_035451_s4.bc2159.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2159"}
2025-09-15 20:23:31.256 wdl.w:ptcp.w:call-paraphase-06.t:call-run_paraphase INFO eval :: name: "mem_gb", value: 8
2025-09-15 20:23:31.258 wdl.w:ptcp NOTICE ready :: job: "call-sawfish-62", callee: "sawfish"
2025-09-15 20:23:31.257 wdl.w:ptcp.w:call-paraphase-06.t:call-run_paraphase INFO eval :: name: "disk_size", value: 27
2025-09-15 20:23:31.258 wdl.w:ptcp INFO input :: job: "call-sawfish-62", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-62/out/m84036_250809_035451_s4.bc2159.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-62/out/m84036_250809_035451_s4.bc2159.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2159"}
2025-09-15 20:23:31.259 wdl.w:ptcp.w:call-paraphase-06.t:call-run_paraphase INFO eval :: name: "out_dir", value: "m84036_250809_035451_s4.bc2103_paraphase"
2025-09-15 20:23:31.260 wdl.w:ptcp NOTICE ready :: job: "call-trgt-62", callee: "trgt"
2025-09-15 20:23:31.260 wdl.w:ptcp.w:call-paraphase-06.t:call-run_paraphase INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 4, memory_reservation: 8000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:23:31.260 wdl.w:ptcp INFO input :: job: "call-trgt-62", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-62/out/m84036_250809_035451_s4.bc2159.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-62/out/m84036_250809_035451_s4.bc2159.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2159"}
2025-09-15 20:23:31.261 wdl.w:ptcp.w:call-paraphase-06.t:call-run_paraphase WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:23:31.262 wdl.w:ptcp.w:call-paraphase-06.t:call-run_paraphase INFO provisioned :: seconds_waited: 0, cpu: 4, mem_bytes: 8000000000
2025-09-15 20:23:31.262 wdl.w:ptcp.w:call-paraphase-06.t:call-run_paraphase INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:23:31.262 wdl.w:ptcp.w:call-trgt-30.t:call-get_reads_overlapping_repeats NOTICE task setup :: name: "get_reads_overlapping_repeats", source: "./trgt.wdl", line: 182, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-30/call-get_reads_overlapping_repeats", thread: 140609276851776
2025-09-15 20:23:31.263 wdl.w:ptcp.t:call-pbmm2_align_hifi-57 INFO output :: name: "mapped_bam", value: "m84036_250809_035451_s4.bc2154.mapped.bam"
2025-09-15 20:23:31.269 wdl.w:ptcp.t:call-pbmm2_align_hifi-57 INFO output :: name: "mapped_bam_bai", value: "m84036_250809_035451_s4.bc2154.mapped.bam.bai"
2025-09-15 20:23:31.271 wdl.w:ptcp.t:call-pbmm2_align_hifi-57 INFO output :: name: "mapped_bam_pbi", value: "m84036_250809_035451_s4.bc2154.mapped.bam.pbi"
2025-09-15 20:23:31.273 wdl.w:ptcp.t:call-pbmm2_align_hifi-57 INFO output :: name: "report", value: "mapping_stats.report.json"
2025-09-15 20:23:31.276 wdl.w:ptcp.w:call-trgt-18.t:call-get_reads_overlapping_repeats NOTICE done
2025-09-15 20:23:31.279 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_genotype NOTICE done
2025-09-15 20:23:31.284 wdl.w:ptcp.w:call-trgt-18 NOTICE finish :: job: "call-get_reads_overlapping_repeats"
2025-09-15 20:23:31.284 wdl.w:ptcp.w:call-trgt-18 INFO output :: job: "call-get_reads_overlapping_repeats", values: {"reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-18/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2115.repeats.bam.bai", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-18/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2115.repeats.bam"}
2025-09-15 20:23:31.285 wdl.w:ptcp.w:call-trgt-18 INFO visit :: node: "output-reads_overlapping_repeats", values: {"reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-18/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2115.repeats.bam"}
2025-09-15 20:23:31.285 wdl.w:ptcp.w:call-trgt-11.t:call-get_reads_overlapping_repeats INFO output :: name: "reads_overlapping_repeats", value: "m84036_250809_035451_s4.bc2108.repeats.bam"
2025-09-15 20:23:31.286 wdl.w:ptcp.w:call-trgt-18 INFO visit :: node: "output-reads_overlapping_repeats_bai", values: {"reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-18/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2115.repeats.bam.bai"}
2025-09-15 20:23:31.287 wdl.w:ptcp.w:call-trgt-26 NOTICE finish :: job: "call-trgt_genotype"
2025-09-15 20:23:31.287 wdl.w:ptcp.w:call-trgt-26 INFO output :: job: "call-trgt_genotype", values: {"spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-26/call-trgt_genotype/out/m84036_250809_035451_s4.bc2123.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-26/call-trgt_genotype/out/m84036_250809_035451_s4.bc2123.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-26/call-trgt_genotype/out/m84036_250809_035451_s4.bc2123.trgt.vcf"}
2025-09-15 20:23:31.287 wdl.w:ptcp.t:call-pbmm2_align_hifi-48 NOTICE done
2025-09-15 20:23:31.288 wdl.w:ptcp.w:call-trgt-26 NOTICE ready :: job: "call-trgt_plot_meth_allele", callee: "trgt_plot"
2025-09-15 20:23:31.288 wdl.w:ptcp.w:call-trgt-26 INFO input :: job: "call-trgt_plot_meth_allele", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": false, "methylation": true, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-26/call-trgt_genotype/out/m84036_250809_035451_s4.bc2123.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-26/call-trgt_genotype/out/m84036_250809_035451_s4.bc2123.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-26/call-trgt_genotype/out/m84036_250809_035451_s4.bc2123.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2123"}
2025-09-15 20:23:31.290 wdl.w:ptcp.w:call-trgt-26 NOTICE ready :: job: "call-trgt_plot_meth_waterfall", callee: "trgt_plot"
2025-09-15 20:23:31.290 wdl.w:ptcp.w:call-trgt-26 INFO input :: job: "call-trgt_plot_meth_waterfall", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": true, "methylation": true, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-26/call-trgt_genotype/out/m84036_250809_035451_s4.bc2123.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-26/call-trgt_genotype/out/m84036_250809_035451_s4.bc2123.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-26/call-trgt_genotype/out/m84036_250809_035451_s4.bc2123.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2123"}
2025-09-15 20:23:31.291 wdl.w:ptcp.w:call-trgt-26 NOTICE ready :: job: "call-trgt_plot_motifs_allele", callee: "trgt_plot"
2025-09-15 20:23:31.291 wdl.w:ptcp.w:call-trgt-26 INFO input :: job: "call-trgt_plot_motifs_allele", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": false, "methylation": false, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-26/call-trgt_genotype/out/m84036_250809_035451_s4.bc2123.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-26/call-trgt_genotype/out/m84036_250809_035451_s4.bc2123.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-26/call-trgt_genotype/out/m84036_250809_035451_s4.bc2123.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2123"}
2025-09-15 20:23:31.292 wdl.w:ptcp.w:call-trgt-26 NOTICE ready :: job: "call-trgt_plot_motifs_waterfall", callee: "trgt_plot"
2025-09-15 20:23:31.292 wdl.w:ptcp.w:call-trgt-11.t:call-get_reads_overlapping_repeats INFO output :: name: "reads_overlapping_repeats_bai", value: "m84036_250809_035451_s4.bc2108.repeats.bam.bai"
2025-09-15 20:23:31.292 wdl.w:ptcp.w:call-trgt-26 INFO input :: job: "call-trgt_plot_motifs_waterfall", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": true, "methylation": false, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-26/call-trgt_genotype/out/m84036_250809_035451_s4.bc2123.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-26/call-trgt_genotype/out/m84036_250809_035451_s4.bc2123.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-26/call-trgt_genotype/out/m84036_250809_035451_s4.bc2123.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2123"}
2025-09-15 20:23:31.293 wdl.w:ptcp.w:call-trgt-30.t:call-get_reads_overlapping_repeats INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:23:31.293 wdl.w:ptcp.w:call-trgt-30.t:call-get_reads_overlapping_repeats INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:23:31.293 wdl.w:ptcp.w:call-trgt-30.t:call-get_reads_overlapping_repeats INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2127.mapped.bam.bai"
2025-09-15 20:23:31.294 wdl.w:ptcp.w:call-trgt-30.t:call-get_reads_overlapping_repeats INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2127.mapped.bam"
2025-09-15 20:23:31.294 wdl.w:ptcp.w:call-trgt-26 INFO visit :: node: "output-spanning_bam", values: {"spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-26/call-trgt_genotype/out/m84036_250809_035451_s4.bc2123.trgt.sorted.spanning.bam"}
2025-09-15 20:23:31.294 wdl.w:ptcp.w:call-trgt-30.t:call-get_reads_overlapping_repeats INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2127"
2025-09-15 20:23:31.294 wdl.w:ptcp.w:call-trgt-26 INFO visit :: node: "output-spanning_bam_bai", values: {"spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-26/call-trgt_genotype/out/m84036_250809_035451_s4.bc2123.trgt.sorted.spanning.bam.bai"}
2025-09-15 20:23:31.294 wdl.w:ptcp.w:call-trgt-30.t:call-get_reads_overlapping_repeats INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:23:31.295 wdl.w:ptcp NOTICE finish :: job: "call-pbmm2_align_hifi-48"
2025-09-15 20:23:31.295 wdl.w:ptcp.w:call-trgt-26 INFO visit :: node: "output-vcf", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-26/call-trgt_genotype/out/m84036_250809_035451_s4.bc2123.trgt.vcf"}
2025-09-15 20:23:31.295 wdl.w:ptcp.w:call-trgt-30.t:call-get_reads_overlapping_repeats INFO eval :: name: "expand_size", value: 3000
2025-09-15 20:23:31.296 wdl.w:ptcp INFO output :: job: "call-pbmm2_align_hifi-48", values: {"report": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-48/out/mapping_stats.report.json", "mapped_bam_pbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-48/out/m84036_250809_035451_s4.bc2145.mapped.bam.pbi", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-48/out/m84036_250809_035451_s4.bc2145.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-48/out/m84036_250809_035451_s4.bc2145.mapped.bam"}
2025-09-15 20:23:31.296 wdl.w:ptcp.w:call-trgt-30.t:call-get_reads_overlapping_repeats INFO eval :: name: "threads", value: 1
2025-09-15 20:23:31.297 wdl.w:ptcp NOTICE ready :: job: "call-paraphase-48", callee: "paraphase"
2025-09-15 20:23:31.297 wdl.w:ptcp INFO input :: job: "call-paraphase-48", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf", "genome_version": "38", "config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-48/out/m84036_250809_035451_s4.bc2145.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-48/out/m84036_250809_035451_s4.bc2145.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2145"}
2025-09-15 20:23:31.297 wdl.w:ptcp.w:call-trgt-30.t:call-get_reads_overlapping_repeats INFO eval :: name: "expanded_bed_name", value: "m84036_250809_035451_s4.bc2127.expanded.bed"
2025-09-15 20:23:31.298 wdl.w:ptcp.w:call-trgt-30.t:call-get_reads_overlapping_repeats INFO eval :: name: "disk_size", value: 11
2025-09-15 20:23:31.298 wdl.w:ptcp.w:call-trgt-30.t:call-get_reads_overlapping_repeats INFO eval :: name: "output_name", value: "m84036_250809_035451_s4.bc2127.repeats.bam"
2025-09-15 20:23:31.298 wdl.w:ptcp.w:call-trgt-30.t:call-get_reads_overlapping_repeats INFO eval :: name: "index_name", value: "m84036_250809_035451_s4.bc2127.repeats.bam.bai"
2025-09-15 20:23:31.297 wdl.w:ptcp.w:call-trgt-33.t:call-get_reads_overlapping_repeats NOTICE task setup :: name: "get_reads_overlapping_repeats", source: "./trgt.wdl", line: 182, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-33/call-get_reads_overlapping_repeats", thread: 140611961206336
2025-09-15 20:23:31.299 wdl.w:ptcp NOTICE ready :: job: "call-sawfish-48", callee: "sawfish"
2025-09-15 20:23:31.299 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_genotype NOTICE task setup :: name: "trgt_genotype", source: "./trgt.wdl", line: 272, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-06/call-trgt_genotype", thread: 140613018162752
2025-09-15 20:23:31.299 wdl.w:ptcp.w:call-trgt-30.t:call-get_reads_overlapping_repeats INFO eval :: name: "output_name_with_index", value: "m84036_250809_035451_s4.bc2127.repeats.bam##idx##m84036_250809_035451_s4.bc2127.repeats.bam.bai"
2025-09-15 20:23:31.300 wdl.w:ptcp INFO input :: job: "call-sawfish-48", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-48/out/m84036_250809_035451_s4.bc2145.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-48/out/m84036_250809_035451_s4.bc2145.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2145"}
2025-09-15 20:23:31.301 wdl.w:ptcp.w:call-trgt-30.t:call-get_reads_overlapping_repeats INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:23:31.301 wdl.w:ptcp NOTICE ready :: job: "call-trgt-48", callee: "trgt"
2025-09-15 20:23:31.301 wdl.w:ptcp.w:call-trgt-30.t:call-get_reads_overlapping_repeats WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:23:31.302 wdl.w:ptcp INFO input :: job: "call-trgt-48", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-48/out/m84036_250809_035451_s4.bc2145.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-48/out/m84036_250809_035451_s4.bc2145.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2145"}
2025-09-15 20:23:31.302 wdl.w:ptcp.w:call-trgt-30.t:call-get_reads_overlapping_repeats INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:23:31.302 wdl.w:ptcp.w:call-trgt-30.t:call-get_reads_overlapping_repeats INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:23:31.311 wdl.w:ptcp.w:call-paraphase-30.t:call-run_paraphase NOTICE task setup :: name: "run_paraphase", source: "./paraphase.wdl", line: 127, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-30/call-run_paraphase", thread: 140610350593600
2025-09-15 20:23:31.332 wdl.w:ptcp.w:call-trgt-21.t:call-trgt_genotype.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:31.332 wdl.w:ptcp.w:call-trgt-21.t:call-trgt_genotype.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:23:31.336 wdl.w:ptcp.w:call-paraphase-21.t:call-run_paraphase.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:31.336 wdl.w:ptcp.w:call-paraphase-21.t:call-run_paraphase.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:23:31.339 wdl.w:ptcp.w:call-trgt-33.t:call-get_reads_overlapping_repeats INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:23:31.339 wdl.w:ptcp.w:call-trgt-33.t:call-get_reads_overlapping_repeats INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:23:31.339 wdl.w:ptcp.w:call-trgt-33.t:call-get_reads_overlapping_repeats INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2130.mapped.bam.bai"
2025-09-15 20:23:31.339 wdl.w:ptcp.w:call-trgt-33.t:call-get_reads_overlapping_repeats INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2130.mapped.bam"
2025-09-15 20:23:31.339 wdl.w:ptcp.w:call-trgt-33.t:call-get_reads_overlapping_repeats INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2130"
2025-09-15 20:23:31.340 wdl.w:ptcp.w:call-trgt-33.t:call-get_reads_overlapping_repeats INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:23:31.340 wdl.w:ptcp.w:call-trgt-33.t:call-get_reads_overlapping_repeats INFO eval :: name: "expand_size", value: 3000
2025-09-15 20:23:31.340 wdl.w:ptcp.w:call-trgt-33.t:call-get_reads_overlapping_repeats INFO eval :: name: "threads", value: 1
2025-09-15 20:23:31.340 wdl.w:ptcp.w:call-trgt-33.t:call-get_reads_overlapping_repeats INFO eval :: name: "expanded_bed_name", value: "m84036_250809_035451_s4.bc2130.expanded.bed"
2025-09-15 20:23:31.340 wdl.w:ptcp.w:call-trgt-33.t:call-get_reads_overlapping_repeats INFO eval :: name: "disk_size", value: 11
2025-09-15 20:23:31.340 wdl.w:ptcp.w:call-trgt-33.t:call-get_reads_overlapping_repeats INFO eval :: name: "output_name", value: "m84036_250809_035451_s4.bc2130.repeats.bam"
2025-09-15 20:23:31.340 wdl.w:ptcp.w:call-trgt-33.t:call-get_reads_overlapping_repeats INFO eval :: name: "index_name", value: "m84036_250809_035451_s4.bc2130.repeats.bam.bai"
2025-09-15 20:23:31.340 wdl.w:ptcp.w:call-trgt-33.t:call-get_reads_overlapping_repeats INFO eval :: name: "output_name_with_index", value: "m84036_250809_035451_s4.bc2130.repeats.bam##idx##m84036_250809_035451_s4.bc2130.repeats.bam.bai"
2025-09-15 20:23:31.342 wdl.w:ptcp.w:call-trgt-33.t:call-get_reads_overlapping_repeats INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:23:31.343 wdl.w:ptcp.w:call-trgt-33.t:call-get_reads_overlapping_repeats WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:23:31.343 wdl.w:ptcp.w:call-trgt-33.t:call-get_reads_overlapping_repeats INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:23:31.343 wdl.w:ptcp.w:call-trgt-33.t:call-get_reads_overlapping_repeats INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:23:31.344 wdl.w:ptcp.w:call-trgt-18.t:call-trgt_genotype NOTICE done
2025-09-15 20:23:31.345 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_genotype INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:23:31.346 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_genotype INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:23:31.346 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_genotype INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:23:31.346 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_genotype INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:23:31.346 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_genotype INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2103.mapped.bam.bai"
2025-09-15 20:23:31.346 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_genotype INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2103.mapped.bam"
2025-09-15 20:23:31.346 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_genotype INFO input :: name: "sex", value: "F"
2025-09-15 20:23:31.346 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_genotype INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2103"
2025-09-15 20:23:31.347 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_genotype INFO eval :: name: "mem_gb", value: 16
2025-09-15 20:23:31.347 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_genotype INFO eval :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2103.trgt"
2025-09-15 20:23:31.347 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_genotype INFO eval :: name: "threads", value: 8
2025-09-15 20:23:31.348 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_genotype INFO eval :: name: "disk_size", value: 27
2025-09-15 20:23:31.348 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_genotype INFO eval :: name: "karyotype", value: "XX"
2025-09-15 20:23:31.349 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_genotype INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 8, memory_reservation: 16000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:23:31.349 wdl.w:ptcp.w:call-paraphase-30.t:call-run_paraphase INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:23:31.349 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_genotype WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:23:31.349 wdl.w:ptcp.w:call-paraphase-30.t:call-run_paraphase INFO input :: name: "annotation_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf"
2025-09-15 20:23:31.350 wdl.w:ptcp.w:call-paraphase-30.t:call-run_paraphase INFO input :: name: "genome_version", value: "38"
2025-09-15 20:23:31.350 wdl.w:ptcp.w:call-paraphase-30.t:call-run_paraphase INFO input :: name: "config_file", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/paraphase_config.GRCh38.yaml"
2025-09-15 20:23:31.350 wdl.w:ptcp.w:call-paraphase-30.t:call-run_paraphase INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:23:31.350 wdl.w:ptcp.w:call-paraphase-30.t:call-run_paraphase INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:23:31.351 wdl.w:ptcp.w:call-paraphase-30.t:call-run_paraphase INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2127.mapped.bam.bai"
2025-09-15 20:23:31.351 wdl.w:ptcp.w:call-paraphase-30.t:call-run_paraphase INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2127.mapped.bam"
2025-09-15 20:23:31.351 wdl.w:ptcp.w:call-paraphase-30.t:call-run_paraphase INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2127"
2025-09-15 20:23:31.351 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_genotype INFO provisioned :: seconds_waited: 0, cpu: 8, mem_bytes: 16000000000
2025-09-15 20:23:31.352 wdl.w:ptcp.w:call-paraphase-30.t:call-run_paraphase INFO eval :: name: "threads", value: 4
2025-09-15 20:23:31.352 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_genotype INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:23:31.352 wdl.w:ptcp.w:call-paraphase-30.t:call-run_paraphase INFO eval :: name: "mem_gb", value: 8
2025-09-15 20:23:31.353 wdl.w:ptcp.w:call-paraphase-30.t:call-run_paraphase INFO eval :: name: "disk_size", value: 27
2025-09-15 20:23:31.353 wdl.w:ptcp.w:call-paraphase-30.t:call-run_paraphase INFO eval :: name: "out_dir", value: "m84036_250809_035451_s4.bc2127_paraphase"
2025-09-15 20:23:31.354 wdl.w:ptcp.w:call-paraphase-30.t:call-run_paraphase INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 4, memory_reservation: 8000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:23:31.354 wdl.w:ptcp.w:call-paraphase-30.t:call-run_paraphase WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:23:31.354 wdl.w:ptcp.w:call-paraphase-30.t:call-run_paraphase INFO provisioned :: seconds_waited: 0, cpu: 4, mem_bytes: 8000000000
2025-09-15 20:23:31.354 wdl.w:ptcp.w:call-paraphase-30.t:call-run_paraphase INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:23:31.356 wdl.w:ptcp.w:call-trgt-19.t:call-trgt_genotype INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2116.trgt.vcf"
2025-09-15 20:23:31.363 wdl.w:ptcp.w:call-trgt-19.t:call-trgt_genotype INFO output :: name: "spanning_bam", value: "m84036_250809_035451_s4.bc2116.trgt.sorted.spanning.bam"
2025-09-15 20:23:31.366 wdl.w:ptcp.w:call-trgt-19.t:call-trgt_genotype INFO output :: name: "spanning_bam_bai", value: "m84036_250809_035451_s4.bc2116.trgt.sorted.spanning.bam.bai"
2025-09-15 20:23:31.366 wdl.w:ptcp.w:call-trgt-19.t:call-get_reads_overlapping_repeats NOTICE done
2025-09-15 20:23:31.372 wdl.w:ptcp.w:call-trgt-19 NOTICE finish :: job: "call-get_reads_overlapping_repeats"
2025-09-15 20:23:31.372 wdl.w:ptcp.w:call-trgt-19 INFO output :: job: "call-get_reads_overlapping_repeats", values: {"reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-19/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2116.repeats.bam.bai", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-19/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2116.repeats.bam"}
2025-09-15 20:23:31.372 wdl.w:ptcp.w:call-trgt-19 INFO visit :: node: "output-reads_overlapping_repeats", values: {"reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-19/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2116.repeats.bam"}
2025-09-15 20:23:31.373 wdl.w:ptcp.w:call-trgt-19 INFO visit :: node: "output-reads_overlapping_repeats_bai", values: {"reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-19/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2116.repeats.bam.bai"}
2025-09-15 20:23:31.374 wdl.w:ptcp.w:call-sawfish-28.t:call-run_sawfish.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:31.383 wdl.w:ptcp.w:call-trgt-10.t:call-get_reads_overlapping_repeats INFO output :: name: "reads_overlapping_repeats", value: "m84036_250809_035451_s4.bc2107.repeats.bam"
2025-09-15 20:23:31.387 wdl.w:ptcp.w:call-trgt-18 NOTICE finish :: job: "call-trgt_genotype"
2025-09-15 20:23:31.387 wdl.w:ptcp.w:call-trgt-18 INFO output :: job: "call-trgt_genotype", values: {"spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-18/call-trgt_genotype/out/m84036_250809_035451_s4.bc2115.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-18/call-trgt_genotype/out/m84036_250809_035451_s4.bc2115.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-18/call-trgt_genotype/out/m84036_250809_035451_s4.bc2115.trgt.vcf"}
2025-09-15 20:23:31.388 wdl.w:ptcp.w:call-trgt-18 NOTICE ready :: job: "call-trgt_plot_meth_allele", callee: "trgt_plot"
2025-09-15 20:23:31.388 wdl.w:ptcp.w:call-trgt-18 INFO input :: job: "call-trgt_plot_meth_allele", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": false, "methylation": true, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-18/call-trgt_genotype/out/m84036_250809_035451_s4.bc2115.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-18/call-trgt_genotype/out/m84036_250809_035451_s4.bc2115.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-18/call-trgt_genotype/out/m84036_250809_035451_s4.bc2115.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2115"}
2025-09-15 20:23:31.390 wdl.w:ptcp.w:call-trgt-18 NOTICE ready :: job: "call-trgt_plot_meth_waterfall", callee: "trgt_plot"
2025-09-15 20:23:31.391 wdl.w:ptcp.w:call-trgt-18 INFO input :: job: "call-trgt_plot_meth_waterfall", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": true, "methylation": true, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-18/call-trgt_genotype/out/m84036_250809_035451_s4.bc2115.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-18/call-trgt_genotype/out/m84036_250809_035451_s4.bc2115.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-18/call-trgt_genotype/out/m84036_250809_035451_s4.bc2115.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2115"}
2025-09-15 20:23:31.391 wdl.w:ptcp.w:call-trgt-10.t:call-get_reads_overlapping_repeats INFO output :: name: "reads_overlapping_repeats_bai", value: "m84036_250809_035451_s4.bc2107.repeats.bam.bai"
2025-09-15 20:23:31.389 wdl.w:ptcp.w:call-paraphase-33.t:call-run_paraphase NOTICE task setup :: name: "run_paraphase", source: "./paraphase.wdl", line: 127, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-33/call-run_paraphase", thread: 140611407550016
2025-09-15 20:23:31.392 wdl.w:ptcp.w:call-trgt-18 NOTICE ready :: job: "call-trgt_plot_motifs_allele", callee: "trgt_plot"
2025-09-15 20:23:31.392 wdl.w:ptcp.w:call-trgt-18 INFO input :: job: "call-trgt_plot_motifs_allele", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": false, "methylation": false, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-18/call-trgt_genotype/out/m84036_250809_035451_s4.bc2115.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-18/call-trgt_genotype/out/m84036_250809_035451_s4.bc2115.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-18/call-trgt_genotype/out/m84036_250809_035451_s4.bc2115.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2115"}
2025-09-15 20:23:31.394 wdl.w:ptcp.w:call-trgt-18 NOTICE ready :: job: "call-trgt_plot_motifs_waterfall", callee: "trgt_plot"
2025-09-15 20:23:31.394 wdl.w:ptcp.w:call-trgt-18 INFO input :: job: "call-trgt_plot_motifs_waterfall", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": true, "methylation": false, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-18/call-trgt_genotype/out/m84036_250809_035451_s4.bc2115.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-18/call-trgt_genotype/out/m84036_250809_035451_s4.bc2115.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-18/call-trgt_genotype/out/m84036_250809_035451_s4.bc2115.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2115"}
2025-09-15 20:23:31.394 wdl.w:ptcp.w:call-trgt-11.t:call-trgt_genotype NOTICE done
2025-09-15 20:23:31.396 wdl.w:ptcp.w:call-trgt-18 INFO visit :: node: "output-spanning_bam", values: {"spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-18/call-trgt_genotype/out/m84036_250809_035451_s4.bc2115.trgt.sorted.spanning.bam"}
2025-09-15 20:23:31.396 wdl.w:ptcp.w:call-trgt-18 INFO visit :: node: "output-spanning_bam_bai", values: {"spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-18/call-trgt_genotype/out/m84036_250809_035451_s4.bc2115.trgt.sorted.spanning.bam.bai"}
2025-09-15 20:23:31.396 wdl.w:ptcp.w:call-trgt-18 INFO visit :: node: "output-vcf", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-18/call-trgt_genotype/out/m84036_250809_035451_s4.bc2115.trgt.vcf"}
2025-09-15 20:23:31.401 wdl.w:ptcp.w:call-trgt-30.t:call-trgt_genotype NOTICE task setup :: name: "trgt_genotype", source: "./trgt.wdl", line: 272, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-30/call-trgt_genotype", thread: 140613838284352
2025-09-15 20:23:31.406 wdl.w:ptcp.w:call-trgt-11 NOTICE finish :: job: "call-trgt_genotype"
2025-09-15 20:23:31.407 wdl.w:ptcp.w:call-trgt-11 INFO output :: job: "call-trgt_genotype", values: {"spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-11/call-trgt_genotype/out/m84036_250809_035451_s4.bc2108.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-11/call-trgt_genotype/out/m84036_250809_035451_s4.bc2108.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-11/call-trgt_genotype/out/m84036_250809_035451_s4.bc2108.trgt.vcf"}
2025-09-15 20:23:31.407 wdl.w:ptcp.w:call-trgt-11 NOTICE ready :: job: "call-trgt_plot_meth_allele", callee: "trgt_plot"
2025-09-15 20:23:31.407 wdl.w:ptcp.w:call-trgt-11 INFO input :: job: "call-trgt_plot_meth_allele", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": false, "methylation": true, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-11/call-trgt_genotype/out/m84036_250809_035451_s4.bc2108.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-11/call-trgt_genotype/out/m84036_250809_035451_s4.bc2108.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-11/call-trgt_genotype/out/m84036_250809_035451_s4.bc2108.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2108"}
2025-09-15 20:23:31.410 wdl.w:ptcp.w:call-trgt-11 NOTICE ready :: job: "call-trgt_plot_meth_waterfall", callee: "trgt_plot"
2025-09-15 20:23:31.410 wdl.w:ptcp.w:call-trgt-11 INFO input :: job: "call-trgt_plot_meth_waterfall", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": true, "methylation": true, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-11/call-trgt_genotype/out/m84036_250809_035451_s4.bc2108.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-11/call-trgt_genotype/out/m84036_250809_035451_s4.bc2108.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-11/call-trgt_genotype/out/m84036_250809_035451_s4.bc2108.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2108"}
2025-09-15 20:23:31.411 wdl.w:ptcp.w:call-trgt-11 NOTICE ready :: job: "call-trgt_plot_motifs_allele", callee: "trgt_plot"
2025-09-15 20:23:31.412 wdl.w:ptcp.w:call-trgt-11 INFO input :: job: "call-trgt_plot_motifs_allele", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": false, "methylation": false, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-11/call-trgt_genotype/out/m84036_250809_035451_s4.bc2108.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-11/call-trgt_genotype/out/m84036_250809_035451_s4.bc2108.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-11/call-trgt_genotype/out/m84036_250809_035451_s4.bc2108.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2108"}
2025-09-15 20:23:31.413 wdl.w:ptcp.w:call-trgt-11 NOTICE ready :: job: "call-trgt_plot_motifs_waterfall", callee: "trgt_plot"
2025-09-15 20:23:31.413 wdl.w:ptcp.w:call-trgt-11 INFO input :: job: "call-trgt_plot_motifs_waterfall", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": true, "methylation": false, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-11/call-trgt_genotype/out/m84036_250809_035451_s4.bc2108.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-11/call-trgt_genotype/out/m84036_250809_035451_s4.bc2108.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-11/call-trgt_genotype/out/m84036_250809_035451_s4.bc2108.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2108"}
2025-09-15 20:23:31.414 wdl.w:ptcp.w:call-trgt-11 INFO visit :: node: "output-spanning_bam", values: {"spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-11/call-trgt_genotype/out/m84036_250809_035451_s4.bc2108.trgt.sorted.spanning.bam"}
2025-09-15 20:23:31.414 wdl.w:ptcp.w:call-trgt-11 INFO visit :: node: "output-spanning_bam_bai", values: {"spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-11/call-trgt_genotype/out/m84036_250809_035451_s4.bc2108.trgt.sorted.spanning.bam.bai"}
2025-09-15 20:23:31.414 wdl.w:ptcp.w:call-trgt-11 INFO visit :: node: "output-vcf", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-11/call-trgt_genotype/out/m84036_250809_035451_s4.bc2108.trgt.vcf"}
2025-09-15 20:23:31.420 wdl.w:ptcp.w:call-trgt-30.t:call-get_reads_overlapping_repeats INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 9, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-30/call-get_reads_overlapping_repeats/_singularity_tmpdir_htytp9u5"
2025-09-15 20:23:31.420 wdl.w:ptcp.w:call-trgt-30.t:call-get_reads_overlapping_repeats INFO Slurm invocation: srun --job-name call-get_reads_overlapping_repeats --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-30/call-get_reads_overlapping_repeats/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-30/call-get_reads_overlapping_repeats/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-30/call-get_reads_overlapping_repeats/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-30/call-get_reads_overlapping_repeats/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-30/out/m84036_250809_035451_s4.bc2127.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2127.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-30/out/m84036_250809_035451_s4.bc2127.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2127.mapped.bam.bai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-30/call-get_reads_overlapping_repeats/_singularity_tmpdir_htytp9u5/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-30/call-get_reads_overlapping_repeats/_singularity_tmpdir_htytp9u5/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:23:31.421 wdl.w:ptcp.w:call-trgt-33.t:call-trgt_genotype NOTICE task setup :: name: "trgt_genotype", source: "./trgt.wdl", line: 272, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-33/call-trgt_genotype", thread: 140611457906240
2025-09-15 20:23:31.425 wdl.w:ptcp.w:call-paraphase-06.t:call-run_paraphase INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-06/call-run_paraphase/_singularity_tmpdir__5nn8s2f"
2025-09-15 20:23:31.426 wdl.w:ptcp.w:call-paraphase-06.t:call-run_paraphase INFO Slurm invocation: srun --job-name call-run_paraphase --partition compute,compute9 --cpus-per-task 4 --mem 7629M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-06/call-run_paraphase/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-06/call-run_paraphase/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-06/call-run_paraphase/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-06/call-run_paraphase/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-06/out/m84036_250809_035451_s4.bc2103.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2103.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-06/out/m84036_250809_035451_s4.bc2103.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2103.mapped.bam:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/variant_list/variant_list.GRCh38.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf:ro --bind /ptcp/meta/paraphase/paraphase_config.GRCh38.yaml:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/paraphase_config.GRCh38.yaml:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-06/call-run_paraphase/_singularity_tmpdir__5nn8s2f/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-06/call-run_paraphase/_singularity_tmpdir__5nn8s2f/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:23:31.430 wdl.w:ptcp.w:call-paraphase-33.t:call-run_paraphase INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:23:31.430 wdl.w:ptcp.w:call-paraphase-33.t:call-run_paraphase INFO input :: name: "annotation_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf"
2025-09-15 20:23:31.430 wdl.w:ptcp.w:call-paraphase-33.t:call-run_paraphase INFO input :: name: "genome_version", value: "38"
2025-09-15 20:23:31.430 wdl.w:ptcp.w:call-paraphase-33.t:call-run_paraphase INFO input :: name: "config_file", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/paraphase_config.GRCh38.yaml"
2025-09-15 20:23:31.430 wdl.w:ptcp.w:call-paraphase-33.t:call-run_paraphase INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:23:31.431 wdl.w:ptcp.w:call-paraphase-33.t:call-run_paraphase INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:23:31.431 wdl.w:ptcp.w:call-paraphase-33.t:call-run_paraphase INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2130.mapped.bam.bai"
2025-09-15 20:23:31.431 wdl.w:ptcp.w:call-paraphase-33.t:call-run_paraphase INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2130.mapped.bam"
2025-09-15 20:23:31.431 wdl.w:ptcp.w:call-paraphase-33.t:call-run_paraphase INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2130"
2025-09-15 20:23:31.431 wdl.w:ptcp.w:call-paraphase-33.t:call-run_paraphase INFO eval :: name: "threads", value: 4
2025-09-15 20:23:31.431 wdl.w:ptcp.w:call-paraphase-33.t:call-run_paraphase INFO eval :: name: "mem_gb", value: 8
2025-09-15 20:23:31.432 wdl.w:ptcp.w:call-paraphase-33.t:call-run_paraphase INFO eval :: name: "disk_size", value: 27
2025-09-15 20:23:31.432 wdl.w:ptcp.w:call-paraphase-33.t:call-run_paraphase INFO eval :: name: "out_dir", value: "m84036_250809_035451_s4.bc2130_paraphase"
2025-09-15 20:23:31.432 wdl.w:ptcp.w:call-paraphase-33.t:call-run_paraphase INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 4, memory_reservation: 8000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:23:31.433 wdl.w:ptcp.w:call-paraphase-33.t:call-run_paraphase WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:23:31.433 wdl.w:ptcp.w:call-paraphase-33.t:call-run_paraphase INFO provisioned :: seconds_waited: 0, cpu: 4, mem_bytes: 8000000000
2025-09-15 20:23:31.433 wdl.w:ptcp.w:call-paraphase-33.t:call-run_paraphase INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:23:31.437 wdl.w:ptcp.w:call-trgt-30.t:call-trgt_genotype INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:23:31.437 wdl.w:ptcp.w:call-trgt-30.t:call-trgt_genotype INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:23:31.437 wdl.w:ptcp.w:call-trgt-30.t:call-trgt_genotype INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:23:31.437 wdl.w:ptcp.w:call-trgt-30.t:call-trgt_genotype INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:23:31.438 wdl.w:ptcp.w:call-trgt-30.t:call-trgt_genotype INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2127.mapped.bam.bai"
2025-09-15 20:23:31.438 wdl.w:ptcp.w:call-trgt-30.t:call-trgt_genotype INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2127.mapped.bam"
2025-09-15 20:23:31.438 wdl.w:ptcp.w:call-trgt-30.t:call-trgt_genotype INFO input :: name: "sex", value: "F"
2025-09-15 20:23:31.438 wdl.w:ptcp.w:call-trgt-30.t:call-trgt_genotype INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2127"
2025-09-15 20:23:31.438 wdl.w:ptcp.w:call-trgt-30.t:call-trgt_genotype INFO eval :: name: "mem_gb", value: 16
2025-09-15 20:23:31.438 wdl.w:ptcp.w:call-trgt-30.t:call-trgt_genotype INFO eval :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2127.trgt"
2025-09-15 20:23:31.439 wdl.w:ptcp.w:call-trgt-30.t:call-trgt_genotype INFO eval :: name: "threads", value: 8
2025-09-15 20:23:31.439 wdl.w:ptcp.w:call-trgt-30.t:call-trgt_genotype INFO eval :: name: "disk_size", value: 27
2025-09-15 20:23:31.439 wdl.w:ptcp.w:call-trgt-30.t:call-trgt_genotype INFO eval :: name: "karyotype", value: "XX"
2025-09-15 20:23:31.440 wdl.w:ptcp.w:call-trgt-11.t:call-get_reads_overlapping_repeats NOTICE done
2025-09-15 20:23:31.441 wdl.w:ptcp.w:call-trgt-30.t:call-trgt_genotype INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 8, memory_reservation: 16000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:23:31.441 wdl.w:ptcp.w:call-trgt-30.t:call-trgt_genotype WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:23:31.442 wdl.w:ptcp.w:call-trgt-30.t:call-trgt_genotype INFO provisioned :: seconds_waited: 0, cpu: 8, mem_bytes: 16000000000
2025-09-15 20:23:31.443 wdl.w:ptcp.w:call-trgt-30.t:call-trgt_genotype INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:23:31.444 wdl.w:ptcp.w:call-sawfish-30.t:call-run_sawfish.slurm_singularity INFO srun: job 51797392 queued and waiting for resources
2025-09-15 20:23:31.445 wdl.w:ptcp.w:call-trgt-11 NOTICE finish :: job: "call-get_reads_overlapping_repeats"
2025-09-15 20:23:31.445 wdl.w:ptcp.w:call-trgt-11 INFO output :: job: "call-get_reads_overlapping_repeats", values: {"reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-11/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2108.repeats.bam.bai", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-11/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2108.repeats.bam"}
2025-09-15 20:23:31.446 wdl.w:ptcp.w:call-trgt-11 INFO visit :: node: "output-reads_overlapping_repeats", values: {"reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-11/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2108.repeats.bam"}
2025-09-15 20:23:31.446 wdl.w:ptcp.w:call-trgt-11 INFO visit :: node: "output-reads_overlapping_repeats_bai", values: {"reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-11/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2108.repeats.bam.bai"}
2025-09-15 20:23:31.454 wdl.w:ptcp.w:call-trgt-33.t:call-trgt_genotype INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:23:31.454 wdl.w:ptcp.w:call-trgt-33.t:call-trgt_genotype INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:23:31.454 wdl.w:ptcp.w:call-trgt-33.t:call-trgt_genotype INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:23:31.454 wdl.w:ptcp.w:call-trgt-33.t:call-trgt_genotype INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:23:31.454 wdl.w:ptcp.w:call-trgt-33.t:call-trgt_genotype INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2130.mapped.bam.bai"
2025-09-15 20:23:31.454 wdl.w:ptcp.w:call-trgt-33.t:call-trgt_genotype INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2130.mapped.bam"
2025-09-15 20:23:31.455 wdl.w:ptcp.w:call-trgt-33.t:call-trgt_genotype INFO input :: name: "sex", value: "F"
2025-09-15 20:23:31.455 wdl.w:ptcp.w:call-trgt-33.t:call-trgt_genotype INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2130"
2025-09-15 20:23:31.455 wdl.w:ptcp.w:call-trgt-33.t:call-trgt_genotype INFO eval :: name: "mem_gb", value: 16
2025-09-15 20:23:31.455 wdl.w:ptcp.w:call-trgt-33.t:call-trgt_genotype INFO eval :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2130.trgt"
2025-09-15 20:23:31.455 wdl.w:ptcp.w:call-trgt-33.t:call-trgt_genotype INFO eval :: name: "threads", value: 8
2025-09-15 20:23:31.455 wdl.w:ptcp.w:call-trgt-33.t:call-trgt_genotype INFO eval :: name: "disk_size", value: 27
2025-09-15 20:23:31.455 wdl.w:ptcp.w:call-trgt-33.t:call-trgt_genotype INFO eval :: name: "karyotype", value: "XX"
2025-09-15 20:23:31.456 wdl.w:ptcp.w:call-trgt-33.t:call-trgt_genotype INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 8, memory_reservation: 16000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:23:31.456 wdl.w:ptcp.w:call-trgt-33.t:call-trgt_genotype WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:23:31.456 wdl.w:ptcp.t:call-pbmm2_align_hifi-57 NOTICE done
2025-09-15 20:23:31.457 wdl.w:ptcp.w:call-trgt-33.t:call-trgt_genotype INFO provisioned :: seconds_waited: 0, cpu: 8, mem_bytes: 16000000000
2025-09-15 20:23:31.457 wdl.w:ptcp.w:call-trgt-33.t:call-trgt_genotype INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:23:31.463 wdl.w:ptcp NOTICE finish :: job: "call-pbmm2_align_hifi-57"
2025-09-15 20:23:31.463 wdl.w:ptcp INFO output :: job: "call-pbmm2_align_hifi-57", values: {"report": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-57/out/mapping_stats.report.json", "mapped_bam_pbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-57/out/m84036_250809_035451_s4.bc2154.mapped.bam.pbi", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-57/out/m84036_250809_035451_s4.bc2154.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-57/out/m84036_250809_035451_s4.bc2154.mapped.bam"}
2025-09-15 20:23:31.463 wdl.w:ptcp NOTICE ready :: job: "call-paraphase-57", callee: "paraphase"
2025-09-15 20:23:31.464 wdl.w:ptcp INFO input :: job: "call-paraphase-57", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf", "genome_version": "38", "config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-57/out/m84036_250809_035451_s4.bc2154.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-57/out/m84036_250809_035451_s4.bc2154.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2154"}
2025-09-15 20:23:31.465 wdl.w:ptcp NOTICE ready :: job: "call-sawfish-57", callee: "sawfish"
2025-09-15 20:23:31.465 wdl.w:ptcp INFO input :: job: "call-sawfish-57", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-57/out/m84036_250809_035451_s4.bc2154.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-57/out/m84036_250809_035451_s4.bc2154.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2154"}
2025-09-15 20:23:31.466 wdl.w:ptcp NOTICE ready :: job: "call-trgt-57", callee: "trgt"
2025-09-15 20:23:31.466 wdl.w:ptcp INFO input :: job: "call-trgt-57", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-57/out/m84036_250809_035451_s4.bc2154.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-57/out/m84036_250809_035451_s4.bc2154.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2154"}
2025-09-15 20:23:31.469 wdl.w:ptcp.w:call-trgt-33.t:call-get_reads_overlapping_repeats INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 9, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-33/call-get_reads_overlapping_repeats/_singularity_tmpdir_i3bd0hre"
2025-09-15 20:23:31.469 wdl.w:ptcp.w:call-trgt-33.t:call-get_reads_overlapping_repeats INFO Slurm invocation: srun --job-name call-get_reads_overlapping_repeats --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-33/call-get_reads_overlapping_repeats/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-33/call-get_reads_overlapping_repeats/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-33/call-get_reads_overlapping_repeats/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-33/call-get_reads_overlapping_repeats/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-33/out/m84036_250809_035451_s4.bc2130.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2130.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-33/out/m84036_250809_035451_s4.bc2130.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2130.mapped.bam:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-33/call-get_reads_overlapping_repeats/_singularity_tmpdir_i3bd0hre/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-33/call-get_reads_overlapping_repeats/_singularity_tmpdir_i3bd0hre/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:23:31.478 wdl.w:ptcp.w:call-trgt-05.t:call-get_reads_overlapping_repeats NOTICE task setup :: name: "get_reads_overlapping_repeats", source: "./trgt.wdl", line: 182, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-05/call-get_reads_overlapping_repeats", thread: 140609796937280
2025-09-15 20:23:31.481 wdl.w:ptcp.w:call-sawfish-05.t:call-run_sawfish NOTICE task setup :: name: "run_sawfish", source: "./sawfish.wdl", line: 83, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-05/call-run_sawfish", thread: 140613571819072
2025-09-15 20:23:31.508 wdl.w:ptcp.t:call-pbmm2_align_hifi-88.slurm_singularity INFO srun: job 51797307 has been allocated resources
2025-09-15 20:23:31.509 wdl.w:ptcp.t:call-pbmm2_align_hifi-88.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:31.509 wdl.w:ptcp.t:call-pbmm2_align_hifi-88.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:23:31.512 wdl.w:ptcp.w:call-paraphase-30.t:call-run_paraphase INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-30/call-run_paraphase/_singularity_tmpdir_t2ixp9wd"
2025-09-15 20:23:31.512 wdl.w:ptcp.w:call-paraphase-30.t:call-run_paraphase INFO Slurm invocation: srun --job-name call-run_paraphase --partition compute,compute9 --cpus-per-task 4 --mem 7629M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-30/call-run_paraphase/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-30/call-run_paraphase/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-30/call-run_paraphase/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-30/call-run_paraphase/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/variant_list/variant_list.GRCh38.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-30/out/m84036_250809_035451_s4.bc2127.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2127.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-30/out/m84036_250809_035451_s4.bc2127.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2127.mapped.bam.bai:ro --bind /ptcp/meta/paraphase/paraphase_config.GRCh38.yaml:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/paraphase_config.GRCh38.yaml:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-30/call-run_paraphase/_singularity_tmpdir_t2ixp9wd/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-30/call-run_paraphase/_singularity_tmpdir_t2ixp9wd/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:23:31.513 wdl.w:ptcp.w:call-trgt-05.t:call-get_reads_overlapping_repeats INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:23:31.517 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_genotype INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 11, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-06/call-trgt_genotype/_singularity_tmpdir_if77xa2m"
2025-09-15 20:23:31.520 wdl.w:ptcp.t:call-pbmm2_align_hifi-92.slurm_singularity INFO srun: job 51797308 has been allocated resources
2025-09-15 20:23:31.526 wdl.w:ptcp.w:call-trgt-05.t:call-get_reads_overlapping_repeats INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:23:31.526 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_genotype INFO Slurm invocation: srun --job-name call-trgt_genotype --partition compute,compute9 --cpus-per-task 8 --mem 15259M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-06/call-trgt_genotype/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-06/call-trgt_genotype/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-06/call-trgt_genotype/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-06/call-trgt_genotype/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-06/out/m84036_250809_035451_s4.bc2103.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2103.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-06/out/m84036_250809_035451_s4.bc2103.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2103.mapped.bam:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-06/call-trgt_genotype/_singularity_tmpdir_if77xa2m/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-06/call-trgt_genotype/_singularity_tmpdir_if77xa2m/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:23:31.526 wdl.w:ptcp.t:call-pbmm2_align_hifi-92.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:31.526 wdl.w:ptcp.w:call-trgt-05.t:call-get_reads_overlapping_repeats INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2102.mapped.bam.bai"
2025-09-15 20:23:31.526 wdl.w:ptcp.t:call-pbmm2_align_hifi-92.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:23:31.526 wdl.w:ptcp.w:call-trgt-05.t:call-get_reads_overlapping_repeats INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2102.mapped.bam"
2025-09-15 20:23:31.526 wdl.w:ptcp.w:call-trgt-05.t:call-get_reads_overlapping_repeats INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2102"
2025-09-15 20:23:31.528 wdl.w:ptcp.w:call-trgt-19.t:call-trgt_genotype NOTICE done
2025-09-15 20:23:31.529 wdl.w:ptcp.w:call-trgt-05.t:call-get_reads_overlapping_repeats INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:23:31.529 wdl.w:ptcp.w:call-trgt-05.t:call-get_reads_overlapping_repeats INFO eval :: name: "expand_size", value: 3000
2025-09-15 20:23:31.527 wdl.w:ptcp.t:call-pbmm2_align_hifi-87.slurm_singularity INFO srun: job 51797309 has been allocated resources
2025-09-15 20:23:31.529 wdl.w:ptcp.w:call-trgt-05.t:call-get_reads_overlapping_repeats INFO eval :: name: "threads", value: 1
2025-09-15 20:23:31.530 wdl.w:ptcp.t:call-pbmm2_align_hifi-87.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:31.530 wdl.w:ptcp.w:call-trgt-05.t:call-get_reads_overlapping_repeats INFO eval :: name: "expanded_bed_name", value: "m84036_250809_035451_s4.bc2102.expanded.bed"
2025-09-15 20:23:31.530 wdl.w:ptcp.t:call-pbmm2_align_hifi-87.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:23:31.530 wdl.w:ptcp.w:call-trgt-05.t:call-get_reads_overlapping_repeats INFO eval :: name: "disk_size", value: 11
2025-09-15 20:23:31.530 wdl.w:ptcp.w:call-trgt-05.t:call-get_reads_overlapping_repeats INFO eval :: name: "output_name", value: "m84036_250809_035451_s4.bc2102.repeats.bam"
2025-09-15 20:23:31.530 wdl.w:ptcp.w:call-trgt-05.t:call-get_reads_overlapping_repeats INFO eval :: name: "index_name", value: "m84036_250809_035451_s4.bc2102.repeats.bam.bai"
2025-09-15 20:23:31.530 wdl.w:ptcp.w:call-trgt-05.t:call-get_reads_overlapping_repeats INFO eval :: name: "output_name_with_index", value: "m84036_250809_035451_s4.bc2102.repeats.bam##idx##m84036_250809_035451_s4.bc2102.repeats.bam.bai"
2025-09-15 20:23:31.531 wdl.w:ptcp.w:call-trgt-05.t:call-get_reads_overlapping_repeats INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:23:31.531 wdl.w:ptcp.w:call-trgt-05.t:call-get_reads_overlapping_repeats WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:23:31.531 wdl.w:ptcp.w:call-trgt-05.t:call-get_reads_overlapping_repeats INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:23:31.531 wdl.w:ptcp.w:call-trgt-05.t:call-get_reads_overlapping_repeats INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:23:31.532 wdl.w:ptcp.w:call-trgt-10.t:call-get_reads_overlapping_repeats NOTICE done
2025-09-15 20:23:31.534 wdl.w:ptcp.w:call-trgt-19 NOTICE finish :: job: "call-trgt_genotype"
2025-09-15 20:23:31.535 wdl.w:ptcp.w:call-trgt-19 INFO output :: job: "call-trgt_genotype", values: {"spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-19/call-trgt_genotype/out/m84036_250809_035451_s4.bc2116.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-19/call-trgt_genotype/out/m84036_250809_035451_s4.bc2116.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-19/call-trgt_genotype/out/m84036_250809_035451_s4.bc2116.trgt.vcf"}
2025-09-15 20:23:31.535 wdl.w:ptcp.w:call-trgt-19 NOTICE ready :: job: "call-trgt_plot_meth_allele", callee: "trgt_plot"
2025-09-15 20:23:31.536 wdl.w:ptcp.w:call-trgt-19 INFO input :: job: "call-trgt_plot_meth_allele", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": false, "methylation": true, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-19/call-trgt_genotype/out/m84036_250809_035451_s4.bc2116.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-19/call-trgt_genotype/out/m84036_250809_035451_s4.bc2116.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-19/call-trgt_genotype/out/m84036_250809_035451_s4.bc2116.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2116"}
2025-09-15 20:23:31.537 wdl.w:ptcp.w:call-trgt-19 NOTICE ready :: job: "call-trgt_plot_meth_waterfall", callee: "trgt_plot"
2025-09-15 20:23:31.538 wdl.w:ptcp.w:call-trgt-19 INFO input :: job: "call-trgt_plot_meth_waterfall", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": true, "methylation": true, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-19/call-trgt_genotype/out/m84036_250809_035451_s4.bc2116.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-19/call-trgt_genotype/out/m84036_250809_035451_s4.bc2116.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-19/call-trgt_genotype/out/m84036_250809_035451_s4.bc2116.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2116"}
2025-09-15 20:23:31.539 wdl.w:ptcp.w:call-trgt-19 NOTICE ready :: job: "call-trgt_plot_motifs_allele", callee: "trgt_plot"
2025-09-15 20:23:31.539 wdl.w:ptcp.w:call-trgt-19 INFO input :: job: "call-trgt_plot_motifs_allele", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": false, "methylation": false, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-19/call-trgt_genotype/out/m84036_250809_035451_s4.bc2116.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-19/call-trgt_genotype/out/m84036_250809_035451_s4.bc2116.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-19/call-trgt_genotype/out/m84036_250809_035451_s4.bc2116.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2116"}
2025-09-15 20:23:31.540 wdl.w:ptcp.w:call-trgt-19 NOTICE ready :: job: "call-trgt_plot_motifs_waterfall", callee: "trgt_plot"
2025-09-15 20:23:31.541 wdl.w:ptcp.w:call-trgt-19 INFO input :: job: "call-trgt_plot_motifs_waterfall", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": true, "methylation": false, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-19/call-trgt_genotype/out/m84036_250809_035451_s4.bc2116.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-19/call-trgt_genotype/out/m84036_250809_035451_s4.bc2116.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-19/call-trgt_genotype/out/m84036_250809_035451_s4.bc2116.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2116"}
2025-09-15 20:23:31.542 wdl.w:ptcp.w:call-trgt-19 INFO visit :: node: "output-spanning_bam", values: {"spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-19/call-trgt_genotype/out/m84036_250809_035451_s4.bc2116.trgt.sorted.spanning.bam"}
2025-09-15 20:23:31.542 wdl.w:ptcp.w:call-trgt-19 INFO visit :: node: "output-spanning_bam_bai", values: {"spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-19/call-trgt_genotype/out/m84036_250809_035451_s4.bc2116.trgt.sorted.spanning.bam.bai"}
2025-09-15 20:23:31.542 wdl.w:ptcp.w:call-trgt-19 INFO visit :: node: "output-vcf", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-19/call-trgt_genotype/out/m84036_250809_035451_s4.bc2116.trgt.vcf"}
2025-09-15 20:23:31.544 wdl.w:ptcp.t:call-pbmm2_align_hifi-89.slurm_singularity INFO srun: job 51797310 has been allocated resources
2025-09-15 20:23:31.544 wdl.w:ptcp.t:call-pbmm2_align_hifi-89.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:31.544 wdl.w:ptcp.t:call-pbmm2_align_hifi-89.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:23:31.547 wdl.w:ptcp.w:call-sawfish-05.t:call-run_sawfish INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:23:31.547 wdl.w:ptcp.w:call-sawfish-05.t:call-run_sawfish INFO input :: name: "genome_version", value: "38"
2025-09-15 20:23:31.547 wdl.w:ptcp.w:call-sawfish-05.t:call-run_sawfish INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:23:31.547 wdl.w:ptcp.w:call-sawfish-05.t:call-run_sawfish INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:23:31.547 wdl.w:ptcp.w:call-sawfish-05.t:call-run_sawfish INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2102.mapped.bam.bai"
2025-09-15 20:23:31.547 wdl.w:ptcp.w:call-sawfish-05.t:call-run_sawfish INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2102.mapped.bam"
2025-09-15 20:23:31.547 wdl.w:ptcp.w:call-sawfish-05.t:call-run_sawfish INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2102"
2025-09-15 20:23:31.548 wdl.w:ptcp.w:call-sawfish-05.t:call-run_sawfish INFO eval :: name: "mem_gb", value: 32
2025-09-15 20:23:31.548 wdl.w:ptcp.w:call-sawfish-05.t:call-run_sawfish INFO eval :: name: "threads", value: 16
2025-09-15 20:23:31.548 wdl.w:ptcp.w:call-sawfish-05.t:call-run_sawfish INFO eval :: name: "disk_size", value: 30
2025-09-15 20:23:31.548 wdl.w:ptcp.w:call-sawfish-05.t:call-run_sawfish INFO eval :: name: "discover_dirname", value: "m84036_250809_035451_s4.bc2102_sawfish_discover"
2025-09-15 20:23:31.549 wdl.w:ptcp.w:call-sawfish-05.t:call-run_sawfish INFO eval :: name: "call_dirname", value: "m84036_250809_035451_s4.bc2102_sawfish"
2025-09-15 20:23:31.549 wdl.w:ptcp.w:call-sawfish-05.t:call-run_sawfish INFO eval :: name: "minimap2_bam_filename", value: "m84036_250809_035451_s4.bc2102.minimap2.bam"
2025-09-15 20:23:31.549 wdl.w:ptcp.w:call-sawfish-05.t:call-run_sawfish INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 16, memory_reservation: 32000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:23:31.549 wdl.w:ptcp.w:call-sawfish-05.t:call-run_sawfish WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:23:31.548 wdl.w:ptcp.w:call-paraphase-05.t:call-run_paraphase NOTICE task setup :: name: "run_paraphase", source: "./paraphase.wdl", line: 127, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-05/call-run_paraphase", thread: 140610912642624
2025-09-15 20:23:31.550 wdl.w:ptcp.w:call-sawfish-05.t:call-run_sawfish INFO provisioned :: seconds_waited: 0, cpu: 16, mem_bytes: 32000000000
2025-09-15 20:23:31.550 wdl.w:ptcp.w:call-sawfish-05.t:call-run_sawfish INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:23:31.560 wdl.w:ptcp.t:call-pbmm2_align_hifi-95.slurm_singularity INFO srun: job 51797311 has been allocated resources
2025-09-15 20:23:31.575 wdl.w:ptcp.w:call-paraphase-05.t:call-run_paraphase INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:23:31.575 wdl.w:ptcp.w:call-paraphase-05.t:call-run_paraphase INFO input :: name: "annotation_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf"
2025-09-15 20:23:31.575 wdl.w:ptcp.w:call-paraphase-05.t:call-run_paraphase INFO input :: name: "genome_version", value: "38"
2025-09-15 20:23:31.575 wdl.w:ptcp.w:call-paraphase-05.t:call-run_paraphase INFO input :: name: "config_file", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/paraphase_config.GRCh38.yaml"
2025-09-15 20:23:31.576 wdl.w:ptcp.w:call-paraphase-05.t:call-run_paraphase INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:23:31.576 wdl.w:ptcp.w:call-paraphase-05.t:call-run_paraphase INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:23:31.576 wdl.w:ptcp.w:call-paraphase-05.t:call-run_paraphase INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2102.mapped.bam.bai"
2025-09-15 20:23:31.576 wdl.w:ptcp.w:call-paraphase-05.t:call-run_paraphase INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2102.mapped.bam"
2025-09-15 20:23:31.576 wdl.w:ptcp.w:call-paraphase-05.t:call-run_paraphase INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2102"
2025-09-15 20:23:31.576 wdl.w:ptcp.w:call-paraphase-05.t:call-run_paraphase INFO eval :: name: "threads", value: 4
2025-09-15 20:23:31.576 wdl.w:ptcp.w:call-paraphase-05.t:call-run_paraphase INFO eval :: name: "mem_gb", value: 8
2025-09-15 20:23:31.576 wdl.w:ptcp.w:call-paraphase-05.t:call-run_paraphase INFO eval :: name: "disk_size", value: 27
2025-09-15 20:23:31.576 wdl.w:ptcp.w:call-paraphase-05.t:call-run_paraphase INFO eval :: name: "out_dir", value: "m84036_250809_035451_s4.bc2102_paraphase"
2025-09-15 20:23:31.577 wdl.w:ptcp.w:call-paraphase-05.t:call-run_paraphase INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 4, memory_reservation: 8000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:23:31.577 wdl.w:ptcp.w:call-paraphase-05.t:call-run_paraphase WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:23:31.578 wdl.w:ptcp.w:call-paraphase-05.t:call-run_paraphase INFO provisioned :: seconds_waited: 0, cpu: 4, mem_bytes: 8000000000
2025-09-15 20:23:31.578 wdl.w:ptcp.w:call-paraphase-05.t:call-run_paraphase INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:23:31.595 wdl.w:ptcp.t:call-pbmm2_align_hifi-85.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:31.595 wdl.w:ptcp.t:call-pbmm2_align_hifi-85.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:23:31.597 wdl.w:ptcp.w:call-paraphase-06.t:call-run_paraphase NOTICE slurm_singularity run :: pid: 1199381, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-06/call-run_paraphase/slurm_singularity.log.txt"
2025-09-15 20:23:31.597 wdl.w:ptcp.w:call-paraphase-30.t:call-run_paraphase NOTICE slurm_singularity run :: pid: 1199383, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-30/call-run_paraphase/slurm_singularity.log.txt"
2025-09-15 20:23:31.597 wdl.w:ptcp.w:call-trgt-30.t:call-get_reads_overlapping_repeats NOTICE slurm_singularity run :: pid: 1199380, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-30/call-get_reads_overlapping_repeats/slurm_singularity.log.txt"
2025-09-15 20:23:31.597 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_genotype NOTICE slurm_singularity run :: pid: 1199385, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-06/call-trgt_genotype/slurm_singularity.log.txt"
2025-09-15 20:23:31.598 wdl.w:ptcp.w:call-paraphase-33.t:call-run_paraphase INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-33/call-run_paraphase/_singularity_tmpdir_e7phoje7"
2025-09-15 20:23:31.598 wdl.w:ptcp.w:call-trgt-33.t:call-get_reads_overlapping_repeats NOTICE slurm_singularity run :: pid: 1199382, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-33/call-get_reads_overlapping_repeats/slurm_singularity.log.txt"
2025-09-15 20:23:31.598 wdl.w:ptcp.w:call-trgt-30.t:call-trgt_genotype INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 11, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-30/call-trgt_genotype/_singularity_tmpdir_xen3stvv"
2025-09-15 20:23:31.599 wdl.w:ptcp.w:call-paraphase-33.t:call-run_paraphase INFO Slurm invocation: srun --job-name call-run_paraphase --partition compute,compute9 --cpus-per-task 4 --mem 7629M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-33/call-run_paraphase/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-33/call-run_paraphase/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-33/call-run_paraphase/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-33/call-run_paraphase/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/variant_list/variant_list.GRCh38.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-33/out/m84036_250809_035451_s4.bc2130.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2130.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-33/out/m84036_250809_035451_s4.bc2130.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2130.mapped.bam:ro --bind /ptcp/meta/paraphase/paraphase_config.GRCh38.yaml:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/paraphase_config.GRCh38.yaml:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-33/call-run_paraphase/_singularity_tmpdir_e7phoje7/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-33/call-run_paraphase/_singularity_tmpdir_e7phoje7/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:23:31.599 wdl.w:ptcp.w:call-trgt-30.t:call-trgt_genotype INFO Slurm invocation: srun --job-name call-trgt_genotype --partition compute,compute9 --cpus-per-task 8 --mem 15259M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-30/call-trgt_genotype/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-30/call-trgt_genotype/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-30/call-trgt_genotype/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-30/call-trgt_genotype/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-30/out/m84036_250809_035451_s4.bc2127.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2127.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-30/out/m84036_250809_035451_s4.bc2127.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2127.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-30/call-trgt_genotype/_singularity_tmpdir_xen3stvv/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-30/call-trgt_genotype/_singularity_tmpdir_xen3stvv/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:23:31.607 wdl.w:ptcp.w:call-trgt-33.t:call-trgt_genotype INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 11, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-33/call-trgt_genotype/_singularity_tmpdir_3a3bzevu"
2025-09-15 20:23:31.607 wdl.w:ptcp.w:call-trgt-33.t:call-trgt_genotype INFO Slurm invocation: srun --job-name call-trgt_genotype --partition compute,compute9 --cpus-per-task 8 --mem 15259M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-33/call-trgt_genotype/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-33/call-trgt_genotype/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-33/call-trgt_genotype/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-33/call-trgt_genotype/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-33/out/m84036_250809_035451_s4.bc2130.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2130.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-33/out/m84036_250809_035451_s4.bc2130.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2130.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-33/call-trgt_genotype/_singularity_tmpdir_3a3bzevu/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-33/call-trgt_genotype/_singularity_tmpdir_3a3bzevu/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:23:31.615 wdl.w:ptcp.w:call-trgt-10 NOTICE finish :: job: "call-get_reads_overlapping_repeats"
2025-09-15 20:23:31.615 wdl.w:ptcp.w:call-trgt-10 INFO output :: job: "call-get_reads_overlapping_repeats", values: {"reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-10/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2107.repeats.bam.bai", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-10/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2107.repeats.bam"}
2025-09-15 20:23:31.615 wdl.w:ptcp.w:call-trgt-10 INFO visit :: node: "output-reads_overlapping_repeats", values: {"reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-10/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2107.repeats.bam"}
2025-09-15 20:23:31.615 wdl.w:ptcp.w:call-trgt-10 INFO visit :: node: "output-reads_overlapping_repeats_bai", values: {"reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-10/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2107.repeats.bam.bai"}
2025-09-15 20:23:31.618 wdl.w:ptcp.t:call-pbmm2_align_hifi-49 INFO output :: name: "mapped_bam", value: "m84036_250809_035451_s4.bc2146.mapped.bam"
2025-09-15 20:23:31.623 wdl.w:ptcp.t:call-pbmm2_align_hifi-49 INFO output :: name: "mapped_bam_bai", value: "m84036_250809_035451_s4.bc2146.mapped.bam.bai"
2025-09-15 20:23:31.626 wdl.w:ptcp.w:call-trgt-05.t:call-trgt_genotype NOTICE task setup :: name: "trgt_genotype", source: "./trgt.wdl", line: 272, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-05/call-trgt_genotype", thread: 140612506469952
2025-09-15 20:23:31.626 wdl.w:ptcp.t:call-pbmm2_align_hifi-49 INFO output :: name: "mapped_bam_pbi", value: "m84036_250809_035451_s4.bc2146.mapped.bam.pbi"
2025-09-15 20:23:31.629 wdl.w:ptcp.t:call-pbmm2_align_hifi-49 INFO output :: name: "report", value: "mapping_stats.report.json"
2025-09-15 20:23:31.644 wdl.w:ptcp.w:call-trgt-05.t:call-get_reads_overlapping_repeats INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 9, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-05/call-get_reads_overlapping_repeats/_singularity_tmpdir_xm_xd1ue"
2025-09-15 20:23:31.644 wdl.w:ptcp.w:call-trgt-05.t:call-get_reads_overlapping_repeats INFO Slurm invocation: srun --job-name call-get_reads_overlapping_repeats --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-05/call-get_reads_overlapping_repeats/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-05/call-get_reads_overlapping_repeats/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-05/call-get_reads_overlapping_repeats/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-05/call-get_reads_overlapping_repeats/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-05/out/m84036_250809_035451_s4.bc2102.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2102.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-05/out/m84036_250809_035451_s4.bc2102.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2102.mapped.bam:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-05/call-get_reads_overlapping_repeats/_singularity_tmpdir_xm_xd1ue/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-05/call-get_reads_overlapping_repeats/_singularity_tmpdir_xm_xd1ue/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:23:31.649 wdl.w:ptcp.w:call-trgt-05.t:call-trgt_genotype INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:23:31.651 wdl.w:ptcp.w:call-sawfish-05.t:call-run_sawfish INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 10, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-05/call-run_sawfish/_singularity_tmpdir_30uof5_m"
2025-09-15 20:23:31.651 wdl.w:ptcp.w:call-sawfish-05.t:call-run_sawfish INFO Slurm invocation: srun --job-name call-run_sawfish --partition compute,compute9 --cpus-per-task 16 --mem 30518M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-05/call-run_sawfish/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-05/call-run_sawfish/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-05/call-run_sawfish/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-05/call-run_sawfish/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-05/out/m84036_250809_035451_s4.bc2102.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2102.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-05/out/m84036_250809_035451_s4.bc2102.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2102.mapped.bam:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-05/call-run_sawfish/_singularity_tmpdir_30uof5_m/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-05/call-run_sawfish/_singularity_tmpdir_30uof5_m/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:23:31.650 wdl.w:ptcp.w:call-trgt-05.t:call-trgt_genotype INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:23:31.653 wdl.w:ptcp.w:call-trgt-05.t:call-trgt_genotype INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:23:31.653 wdl.w:ptcp.w:call-trgt-05.t:call-trgt_genotype INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:23:31.653 wdl.w:ptcp.w:call-trgt-05.t:call-trgt_genotype INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2102.mapped.bam.bai"
2025-09-15 20:23:31.653 wdl.w:ptcp.w:call-trgt-05.t:call-trgt_genotype INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2102.mapped.bam"
2025-09-15 20:23:31.654 wdl.w:ptcp.w:call-trgt-05.t:call-trgt_genotype INFO input :: name: "sex", value: "F"
2025-09-15 20:23:31.654 wdl.w:ptcp.w:call-trgt-05.t:call-trgt_genotype INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2102"
2025-09-15 20:23:31.654 wdl.w:ptcp.w:call-trgt-05.t:call-trgt_genotype INFO eval :: name: "mem_gb", value: 16
2025-09-15 20:23:31.654 wdl.w:ptcp.w:call-trgt-05.t:call-trgt_genotype INFO eval :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2102.trgt"
2025-09-15 20:23:31.654 wdl.w:ptcp.w:call-trgt-05.t:call-trgt_genotype INFO eval :: name: "threads", value: 8
2025-09-15 20:23:31.655 wdl.w:ptcp.w:call-trgt-05.t:call-trgt_genotype INFO eval :: name: "disk_size", value: 27
2025-09-15 20:23:31.655 wdl.w:ptcp.w:call-trgt-05.t:call-trgt_genotype INFO eval :: name: "karyotype", value: "XX"
2025-09-15 20:23:31.655 wdl.w:ptcp.w:call-trgt-05.t:call-trgt_genotype INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 8, memory_reservation: 16000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:23:31.655 wdl.w:ptcp.w:call-trgt-05.t:call-trgt_genotype WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:23:31.656 wdl.w:ptcp.w:call-trgt-05.t:call-trgt_genotype INFO provisioned :: seconds_waited: 0, cpu: 8, mem_bytes: 16000000000
2025-09-15 20:23:31.656 wdl.w:ptcp.w:call-trgt-05.t:call-trgt_genotype INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:23:31.661 wdl.w:ptcp.w:call-trgt-05.t:call-get_reads_overlapping_repeats NOTICE slurm_singularity run :: pid: 1199400, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-05/call-get_reads_overlapping_repeats/slurm_singularity.log.txt"
2025-09-15 20:23:31.663 wdl.w:ptcp.w:call-paraphase-33.t:call-run_paraphase NOTICE slurm_singularity run :: pid: 1199392, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-33/call-run_paraphase/slurm_singularity.log.txt"
2025-09-15 20:23:31.663 wdl.w:ptcp.w:call-trgt-30.t:call-trgt_genotype NOTICE slurm_singularity run :: pid: 1199393, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-30/call-trgt_genotype/slurm_singularity.log.txt"
2025-09-15 20:23:31.664 wdl.w:ptcp.w:call-sawfish-05.t:call-run_sawfish NOTICE slurm_singularity run :: pid: 1199401, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-05/call-run_sawfish/slurm_singularity.log.txt"
2025-09-15 20:23:31.666 wdl.w:ptcp.w:call-trgt-33.t:call-trgt_genotype NOTICE slurm_singularity run :: pid: 1199399, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-33/call-trgt_genotype/slurm_singularity.log.txt"
2025-09-15 20:23:31.679 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_genotype INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2107.trgt.vcf"
2025-09-15 20:23:31.684 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_genotype INFO output :: name: "spanning_bam", value: "m84036_250809_035451_s4.bc2107.trgt.sorted.spanning.bam"
2025-09-15 20:23:31.685 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_genotype INFO output :: name: "spanning_bam_bai", value: "m84036_250809_035451_s4.bc2107.trgt.sorted.spanning.bam.bai"
2025-09-15 20:23:31.693 wdl.w:ptcp.w:call-paraphase-05.t:call-run_paraphase INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-05/call-run_paraphase/_singularity_tmpdir_pqo1zek0"
2025-09-15 20:23:31.693 wdl.w:ptcp.w:call-paraphase-05.t:call-run_paraphase INFO Slurm invocation: srun --job-name call-run_paraphase --partition compute,compute9 --cpus-per-task 4 --mem 7629M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-05/call-run_paraphase/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-05/call-run_paraphase/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-05/call-run_paraphase/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-05/call-run_paraphase/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/variant_list/variant_list.GRCh38.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-05/out/m84036_250809_035451_s4.bc2102.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2102.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-05/out/m84036_250809_035451_s4.bc2102.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2102.mapped.bam:ro --bind /ptcp/meta/paraphase/paraphase_config.GRCh38.yaml:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/paraphase_config.GRCh38.yaml:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-05/call-run_paraphase/_singularity_tmpdir_pqo1zek0/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-05/call-run_paraphase/_singularity_tmpdir_pqo1zek0/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:23:31.729 wdl.w:ptcp.t:call-pbmm2_align_hifi-49 NOTICE done
2025-09-15 20:23:31.732 wdl.w:ptcp.w:call-paraphase-05.t:call-run_paraphase NOTICE slurm_singularity run :: pid: 1199407, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-05/call-run_paraphase/slurm_singularity.log.txt"
2025-09-15 20:23:31.738 wdl.w:ptcp NOTICE finish :: job: "call-pbmm2_align_hifi-49"
2025-09-15 20:23:31.738 wdl.w:ptcp INFO output :: job: "call-pbmm2_align_hifi-49", values: {"report": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-49/out/mapping_stats.report.json", "mapped_bam_pbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-49/out/m84036_250809_035451_s4.bc2146.mapped.bam.pbi", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-49/out/m84036_250809_035451_s4.bc2146.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-49/out/m84036_250809_035451_s4.bc2146.mapped.bam"}
2025-09-15 20:23:31.739 wdl.w:ptcp NOTICE ready :: job: "call-paraphase-49", callee: "paraphase"
2025-09-15 20:23:31.739 wdl.w:ptcp INFO input :: job: "call-paraphase-49", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf", "genome_version": "38", "config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-49/out/m84036_250809_035451_s4.bc2146.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-49/out/m84036_250809_035451_s4.bc2146.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2146"}
2025-09-15 20:23:31.740 wdl.w:ptcp NOTICE ready :: job: "call-sawfish-49", callee: "sawfish"
2025-09-15 20:23:31.740 wdl.w:ptcp INFO input :: job: "call-sawfish-49", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-49/out/m84036_250809_035451_s4.bc2146.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-49/out/m84036_250809_035451_s4.bc2146.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2146"}
2025-09-15 20:23:31.741 wdl.w:ptcp NOTICE ready :: job: "call-trgt-49", callee: "trgt"
2025-09-15 20:23:31.742 wdl.w:ptcp INFO input :: job: "call-trgt-49", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-49/out/m84036_250809_035451_s4.bc2146.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-49/out/m84036_250809_035451_s4.bc2146.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2146"}
2025-09-15 20:23:31.747 wdl.w:ptcp.w:call-paraphase-13.t:call-run_paraphase NOTICE task setup :: name: "run_paraphase", source: "./paraphase.wdl", line: 127, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-13/call-run_paraphase", thread: 140610342200896
2025-09-15 20:23:31.758 wdl.w:ptcp.w:call-trgt-05.t:call-trgt_genotype INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 11, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-05/call-trgt_genotype/_singularity_tmpdir_7jandj_f"
2025-09-15 20:23:31.758 wdl.w:ptcp.w:call-trgt-05.t:call-trgt_genotype INFO Slurm invocation: srun --job-name call-trgt_genotype --partition compute,compute9 --cpus-per-task 8 --mem 15259M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-05/call-trgt_genotype/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-05/call-trgt_genotype/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-05/call-trgt_genotype/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-05/call-trgt_genotype/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-05/out/m84036_250809_035451_s4.bc2102.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2102.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-05/out/m84036_250809_035451_s4.bc2102.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2102.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-05/call-trgt_genotype/_singularity_tmpdir_7jandj_f/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-05/call-trgt_genotype/_singularity_tmpdir_7jandj_f/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:23:31.767 wdl.w:ptcp.w:call-paraphase-13.t:call-run_paraphase INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:23:31.769 wdl.w:ptcp.w:call-paraphase-13.t:call-run_paraphase INFO input :: name: "annotation_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf"
2025-09-15 20:23:31.769 wdl.w:ptcp.w:call-paraphase-13.t:call-run_paraphase INFO input :: name: "genome_version", value: "38"
2025-09-15 20:23:31.769 wdl.w:ptcp.w:call-paraphase-13.t:call-run_paraphase INFO input :: name: "config_file", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/paraphase_config.GRCh38.yaml"
2025-09-15 20:23:31.769 wdl.w:ptcp.w:call-paraphase-13.t:call-run_paraphase INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:23:31.769 wdl.w:ptcp.w:call-paraphase-13.t:call-run_paraphase INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:23:31.769 wdl.w:ptcp.w:call-paraphase-13.t:call-run_paraphase INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2110.mapped.bam.bai"
2025-09-15 20:23:31.769 wdl.w:ptcp.w:call-paraphase-13.t:call-run_paraphase INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2110.mapped.bam"
2025-09-15 20:23:31.769 wdl.w:ptcp.w:call-paraphase-13.t:call-run_paraphase INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2110"
2025-09-15 20:23:31.770 wdl.w:ptcp.w:call-paraphase-13.t:call-run_paraphase INFO eval :: name: "threads", value: 4
2025-09-15 20:23:31.770 wdl.w:ptcp.w:call-trgt-05.t:call-trgt_genotype NOTICE slurm_singularity run :: pid: 1199410, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-05/call-trgt_genotype/slurm_singularity.log.txt"
2025-09-15 20:23:31.770 wdl.w:ptcp.w:call-paraphase-13.t:call-run_paraphase INFO eval :: name: "mem_gb", value: 8
2025-09-15 20:23:31.770 wdl.w:ptcp.w:call-paraphase-13.t:call-run_paraphase INFO eval :: name: "disk_size", value: 27
2025-09-15 20:23:31.770 wdl.w:ptcp.w:call-paraphase-13.t:call-run_paraphase INFO eval :: name: "out_dir", value: "m84036_250809_035451_s4.bc2110_paraphase"
2025-09-15 20:23:31.771 wdl.w:ptcp.w:call-paraphase-13.t:call-run_paraphase INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 4, memory_reservation: 8000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:23:31.771 wdl.w:ptcp.w:call-paraphase-13.t:call-run_paraphase WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:23:31.771 wdl.w:ptcp.w:call-paraphase-13.t:call-run_paraphase INFO provisioned :: seconds_waited: 0, cpu: 4, mem_bytes: 8000000000
2025-09-15 20:23:31.771 wdl.w:ptcp.w:call-paraphase-13.t:call-run_paraphase INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:23:31.788 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_genotype NOTICE done
2025-09-15 20:23:31.794 wdl.w:ptcp.w:call-trgt-10 NOTICE finish :: job: "call-trgt_genotype"
2025-09-15 20:23:31.794 wdl.w:ptcp.w:call-trgt-10 INFO output :: job: "call-trgt_genotype", values: {"spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-10/call-trgt_genotype/out/m84036_250809_035451_s4.bc2107.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-10/call-trgt_genotype/out/m84036_250809_035451_s4.bc2107.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-10/call-trgt_genotype/out/m84036_250809_035451_s4.bc2107.trgt.vcf"}
2025-09-15 20:23:31.795 wdl.w:ptcp.w:call-trgt-10 NOTICE ready :: job: "call-trgt_plot_meth_allele", callee: "trgt_plot"
2025-09-15 20:23:31.795 wdl.w:ptcp.w:call-trgt-10 INFO input :: job: "call-trgt_plot_meth_allele", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": false, "methylation": true, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-10/call-trgt_genotype/out/m84036_250809_035451_s4.bc2107.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-10/call-trgt_genotype/out/m84036_250809_035451_s4.bc2107.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-10/call-trgt_genotype/out/m84036_250809_035451_s4.bc2107.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2107"}
2025-09-15 20:23:31.797 wdl.w:ptcp.w:call-trgt-10 NOTICE ready :: job: "call-trgt_plot_meth_waterfall", callee: "trgt_plot"
2025-09-15 20:23:31.797 wdl.w:ptcp.w:call-trgt-21.t:call-trgt_genotype INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2118.trgt.vcf"
2025-09-15 20:23:31.797 wdl.w:ptcp.w:call-trgt-10 INFO input :: job: "call-trgt_plot_meth_waterfall", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": true, "methylation": true, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-10/call-trgt_genotype/out/m84036_250809_035451_s4.bc2107.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-10/call-trgt_genotype/out/m84036_250809_035451_s4.bc2107.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-10/call-trgt_genotype/out/m84036_250809_035451_s4.bc2107.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2107"}
2025-09-15 20:23:31.798 wdl.w:ptcp.w:call-trgt-10 NOTICE ready :: job: "call-trgt_plot_motifs_allele", callee: "trgt_plot"
2025-09-15 20:23:31.798 wdl.w:ptcp.w:call-trgt-10 INFO input :: job: "call-trgt_plot_motifs_allele", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": false, "methylation": false, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-10/call-trgt_genotype/out/m84036_250809_035451_s4.bc2107.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-10/call-trgt_genotype/out/m84036_250809_035451_s4.bc2107.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-10/call-trgt_genotype/out/m84036_250809_035451_s4.bc2107.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2107"}
2025-09-15 20:23:31.799 wdl.w:ptcp.w:call-trgt-10 NOTICE ready :: job: "call-trgt_plot_motifs_waterfall", callee: "trgt_plot"
2025-09-15 20:23:31.799 wdl.w:ptcp.w:call-trgt-10 INFO input :: job: "call-trgt_plot_motifs_waterfall", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": true, "methylation": false, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-10/call-trgt_genotype/out/m84036_250809_035451_s4.bc2107.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-10/call-trgt_genotype/out/m84036_250809_035451_s4.bc2107.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-10/call-trgt_genotype/out/m84036_250809_035451_s4.bc2107.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2107"}
2025-09-15 20:23:31.800 wdl.w:ptcp.w:call-trgt-10 INFO visit :: node: "output-spanning_bam", values: {"spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-10/call-trgt_genotype/out/m84036_250809_035451_s4.bc2107.trgt.sorted.spanning.bam"}
2025-09-15 20:23:31.800 wdl.w:ptcp.w:call-trgt-10 INFO visit :: node: "output-spanning_bam_bai", values: {"spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-10/call-trgt_genotype/out/m84036_250809_035451_s4.bc2107.trgt.sorted.spanning.bam.bai"}
2025-09-15 20:23:31.800 wdl.w:ptcp.w:call-trgt-10 INFO visit :: node: "output-vcf", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-10/call-trgt_genotype/out/m84036_250809_035451_s4.bc2107.trgt.vcf"}
2025-09-15 20:23:31.801 wdl.w:ptcp.w:call-trgt-21.t:call-trgt_genotype INFO output :: name: "spanning_bam", value: "m84036_250809_035451_s4.bc2118.trgt.sorted.spanning.bam"
2025-09-15 20:23:31.801 wdl.w:ptcp.w:call-sawfish-13.t:call-run_sawfish NOTICE task setup :: name: "run_sawfish", source: "./sawfish.wdl", line: 83, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-13/call-run_sawfish", thread: 140606080804416
2025-09-15 20:23:31.807 wdl.w:ptcp.w:call-trgt-21.t:call-trgt_genotype INFO output :: name: "spanning_bam_bai", value: "m84036_250809_035451_s4.bc2118.trgt.sorted.spanning.bam.bai"
2025-09-15 20:23:31.814 wdl.w:ptcp.w:call-sawfish-33.t:call-run_sawfish.slurm_singularity INFO srun: job 51797393 queued and waiting for resources
2025-09-15 20:23:31.817 wdl.w:ptcp.w:call-trgt-06.t:call-get_reads_overlapping_repeats.slurm_singularity INFO srun: job 51797394 queued and waiting for resources
2025-09-15 20:23:31.835 wdl.w:ptcp.w:call-sawfish-13.t:call-run_sawfish INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:23:31.835 wdl.w:ptcp.w:call-sawfish-13.t:call-run_sawfish INFO input :: name: "genome_version", value: "38"
2025-09-15 20:23:31.835 wdl.w:ptcp.w:call-sawfish-13.t:call-run_sawfish INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:23:31.835 wdl.w:ptcp.w:call-sawfish-13.t:call-run_sawfish INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:23:31.836 wdl.w:ptcp.w:call-sawfish-13.t:call-run_sawfish INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2110.mapped.bam.bai"
2025-09-15 20:23:31.836 wdl.w:ptcp.w:call-sawfish-13.t:call-run_sawfish INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2110.mapped.bam"
2025-09-15 20:23:31.836 wdl.w:ptcp.w:call-sawfish-13.t:call-run_sawfish INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2110"
2025-09-15 20:23:31.836 wdl.w:ptcp.w:call-sawfish-13.t:call-run_sawfish INFO eval :: name: "mem_gb", value: 32
2025-09-15 20:23:31.836 wdl.w:ptcp.w:call-sawfish-13.t:call-run_sawfish INFO eval :: name: "threads", value: 16
2025-09-15 20:23:31.836 wdl.w:ptcp.w:call-sawfish-13.t:call-run_sawfish INFO eval :: name: "disk_size", value: 30
2025-09-15 20:23:31.836 wdl.w:ptcp.w:call-sawfish-13.t:call-run_sawfish INFO eval :: name: "discover_dirname", value: "m84036_250809_035451_s4.bc2110_sawfish_discover"
2025-09-15 20:23:31.837 wdl.w:ptcp.w:call-sawfish-13.t:call-run_sawfish INFO eval :: name: "call_dirname", value: "m84036_250809_035451_s4.bc2110_sawfish"
2025-09-15 20:23:31.837 wdl.w:ptcp.w:call-sawfish-13.t:call-run_sawfish INFO eval :: name: "minimap2_bam_filename", value: "m84036_250809_035451_s4.bc2110.minimap2.bam"
2025-09-15 20:23:31.837 wdl.w:ptcp.w:call-sawfish-13.t:call-run_sawfish INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 16, memory_reservation: 32000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:23:31.837 wdl.w:ptcp.w:call-sawfish-13.t:call-run_sawfish WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:23:31.838 wdl.w:ptcp.w:call-sawfish-13.t:call-run_sawfish INFO provisioned :: seconds_waited: 0, cpu: 16, mem_bytes: 32000000000
2025-09-15 20:23:31.838 wdl.w:ptcp.w:call-sawfish-13.t:call-run_sawfish INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:23:31.842 wdl.w:ptcp.w:call-paraphase-23.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for smn1 for sample m84036_250809_035451_s4.bc2120 at 2025-09-15 20:23:22.340659...
2025-09-15 20:23:31.874 wdl.w:ptcp.w:call-paraphase-13.t:call-run_paraphase INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-13/call-run_paraphase/_singularity_tmpdir_tq5cruiw"
2025-09-15 20:23:31.874 wdl.w:ptcp.w:call-paraphase-13.t:call-run_paraphase INFO Slurm invocation: srun --job-name call-run_paraphase --partition compute,compute9 --cpus-per-task 4 --mem 7629M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-13/call-run_paraphase/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-13/call-run_paraphase/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-13/call-run_paraphase/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-13/call-run_paraphase/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-13/out/m84036_250809_035451_s4.bc2110.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2110.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-13/out/m84036_250809_035451_s4.bc2110.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2110.mapped.bam.bai:ro --bind /ptcp/meta/variant_list/variant_list.GRCh38.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf:ro --bind /ptcp/meta/paraphase/paraphase_config.GRCh38.yaml:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/paraphase_config.GRCh38.yaml:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-13/call-run_paraphase/_singularity_tmpdir_tq5cruiw/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-13/call-run_paraphase/_singularity_tmpdir_tq5cruiw/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:23:31.896 wdl.w:ptcp.w:call-trgt-21.t:call-trgt_genotype NOTICE done
2025-09-15 20:23:31.898 wdl.w:ptcp.w:call-paraphase-13.t:call-run_paraphase NOTICE slurm_singularity run :: pid: 1199412, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-13/call-run_paraphase/slurm_singularity.log.txt"
2025-09-15 20:23:31.901 wdl.w:ptcp.w:call-trgt-21 NOTICE finish :: job: "call-trgt_genotype"
2025-09-15 20:23:31.901 wdl.w:ptcp.w:call-trgt-21 INFO output :: job: "call-trgt_genotype", values: {"spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-21/call-trgt_genotype/out/m84036_250809_035451_s4.bc2118.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-21/call-trgt_genotype/out/m84036_250809_035451_s4.bc2118.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-21/call-trgt_genotype/out/m84036_250809_035451_s4.bc2118.trgt.vcf"}
2025-09-15 20:23:31.902 wdl.w:ptcp.w:call-trgt-21 NOTICE ready :: job: "call-trgt_plot_meth_allele", callee: "trgt_plot"
2025-09-15 20:23:31.902 wdl.w:ptcp.w:call-trgt-21 INFO input :: job: "call-trgt_plot_meth_allele", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": false, "methylation": true, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-21/call-trgt_genotype/out/m84036_250809_035451_s4.bc2118.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-21/call-trgt_genotype/out/m84036_250809_035451_s4.bc2118.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-21/call-trgt_genotype/out/m84036_250809_035451_s4.bc2118.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2118"}
2025-09-15 20:23:31.902 wdl.w:ptcp.w:call-trgt-21 NOTICE ready :: job: "call-trgt_plot_meth_waterfall", callee: "trgt_plot"
2025-09-15 20:23:31.903 wdl.w:ptcp.w:call-trgt-21 INFO input :: job: "call-trgt_plot_meth_waterfall", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": true, "methylation": true, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-21/call-trgt_genotype/out/m84036_250809_035451_s4.bc2118.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-21/call-trgt_genotype/out/m84036_250809_035451_s4.bc2118.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-21/call-trgt_genotype/out/m84036_250809_035451_s4.bc2118.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2118"}
2025-09-15 20:23:31.903 wdl.w:ptcp.w:call-trgt-21 NOTICE ready :: job: "call-trgt_plot_motifs_allele", callee: "trgt_plot"
2025-09-15 20:23:31.903 wdl.w:ptcp.w:call-trgt-21 INFO input :: job: "call-trgt_plot_motifs_allele", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": false, "methylation": false, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-21/call-trgt_genotype/out/m84036_250809_035451_s4.bc2118.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-21/call-trgt_genotype/out/m84036_250809_035451_s4.bc2118.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-21/call-trgt_genotype/out/m84036_250809_035451_s4.bc2118.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2118"}
2025-09-15 20:23:31.904 wdl.w:ptcp.w:call-trgt-21 NOTICE ready :: job: "call-trgt_plot_motifs_waterfall", callee: "trgt_plot"
2025-09-15 20:23:31.904 wdl.w:ptcp.w:call-trgt-21 INFO input :: job: "call-trgt_plot_motifs_waterfall", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": true, "methylation": false, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-21/call-trgt_genotype/out/m84036_250809_035451_s4.bc2118.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-21/call-trgt_genotype/out/m84036_250809_035451_s4.bc2118.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-21/call-trgt_genotype/out/m84036_250809_035451_s4.bc2118.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2118"}
2025-09-15 20:23:31.905 wdl.w:ptcp.w:call-trgt-21 INFO visit :: node: "output-spanning_bam", values: {"spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-21/call-trgt_genotype/out/m84036_250809_035451_s4.bc2118.trgt.sorted.spanning.bam"}
2025-09-15 20:23:31.905 wdl.w:ptcp.w:call-trgt-21 INFO visit :: node: "output-spanning_bam_bai", values: {"spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-21/call-trgt_genotype/out/m84036_250809_035451_s4.bc2118.trgt.sorted.spanning.bam.bai"}
2025-09-15 20:23:31.905 wdl.w:ptcp.w:call-trgt-21 INFO visit :: node: "output-vcf", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-21/call-trgt_genotype/out/m84036_250809_035451_s4.bc2118.trgt.vcf"}
2025-09-15 20:23:31.906 wdl.w:ptcp.w:call-trgt-13.t:call-get_reads_overlapping_repeats NOTICE task setup :: name: "get_reads_overlapping_repeats", source: "./trgt.wdl", line: 182, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-13/call-get_reads_overlapping_repeats", thread: 140610333808192
2025-09-15 20:23:31.920 wdl.w:ptcp.w:call-sawfish-13.t:call-run_sawfish INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 10, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-13/call-run_sawfish/_singularity_tmpdir_jikfpzgh"
2025-09-15 20:23:31.921 wdl.w:ptcp.w:call-sawfish-13.t:call-run_sawfish INFO Slurm invocation: srun --job-name call-run_sawfish --partition compute,compute9 --cpus-per-task 16 --mem 30518M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-13/call-run_sawfish/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-13/call-run_sawfish/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-13/call-run_sawfish/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-13/call-run_sawfish/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-13/out/m84036_250809_035451_s4.bc2110.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2110.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-13/out/m84036_250809_035451_s4.bc2110.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2110.mapped.bam.bai:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-13/call-run_sawfish/_singularity_tmpdir_jikfpzgh/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-13/call-run_sawfish/_singularity_tmpdir_jikfpzgh/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:23:31.922 wdl.w:ptcp.w:call-trgt-13.t:call-get_reads_overlapping_repeats INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:23:31.922 wdl.w:ptcp.w:call-trgt-13.t:call-get_reads_overlapping_repeats INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:23:31.922 wdl.w:ptcp.w:call-trgt-13.t:call-get_reads_overlapping_repeats INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2110.mapped.bam.bai"
2025-09-15 20:23:31.922 wdl.w:ptcp.w:call-trgt-13.t:call-get_reads_overlapping_repeats INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2110.mapped.bam"
2025-09-15 20:23:31.922 wdl.w:ptcp.w:call-trgt-13.t:call-get_reads_overlapping_repeats INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2110"
2025-09-15 20:23:31.923 wdl.w:ptcp.w:call-trgt-13.t:call-get_reads_overlapping_repeats INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:23:31.923 wdl.w:ptcp.w:call-trgt-13.t:call-get_reads_overlapping_repeats INFO eval :: name: "expand_size", value: 3000
2025-09-15 20:23:31.924 wdl.w:ptcp.w:call-trgt-13.t:call-get_reads_overlapping_repeats INFO eval :: name: "threads", value: 1
2025-09-15 20:23:31.924 wdl.w:ptcp.w:call-trgt-13.t:call-get_reads_overlapping_repeats INFO eval :: name: "expanded_bed_name", value: "m84036_250809_035451_s4.bc2110.expanded.bed"
2025-09-15 20:23:31.924 wdl.w:ptcp.w:call-trgt-13.t:call-get_reads_overlapping_repeats INFO eval :: name: "disk_size", value: 11
2025-09-15 20:23:31.924 wdl.w:ptcp.w:call-trgt-13.t:call-get_reads_overlapping_repeats INFO eval :: name: "output_name", value: "m84036_250809_035451_s4.bc2110.repeats.bam"
2025-09-15 20:23:31.924 wdl.w:ptcp.w:call-trgt-13.t:call-get_reads_overlapping_repeats INFO eval :: name: "index_name", value: "m84036_250809_035451_s4.bc2110.repeats.bam.bai"
2025-09-15 20:23:31.924 wdl.w:ptcp.w:call-trgt-13.t:call-get_reads_overlapping_repeats INFO eval :: name: "output_name_with_index", value: "m84036_250809_035451_s4.bc2110.repeats.bam##idx##m84036_250809_035451_s4.bc2110.repeats.bam.bai"
2025-09-15 20:23:31.924 wdl.w:ptcp.w:call-trgt-13.t:call-get_reads_overlapping_repeats INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:23:31.925 wdl.w:ptcp.w:call-trgt-13.t:call-get_reads_overlapping_repeats WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:23:31.925 wdl.w:ptcp.w:call-trgt-13.t:call-get_reads_overlapping_repeats INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:23:31.925 wdl.w:ptcp.w:call-trgt-13.t:call-get_reads_overlapping_repeats INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:23:31.932 wdl.w:ptcp.w:call-sawfish-13.t:call-run_sawfish NOTICE slurm_singularity run :: pid: 1199414, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-13/call-run_sawfish/slurm_singularity.log.txt"
2025-09-15 20:23:31.965 wdl.w:ptcp.w:call-trgt-13.t:call-get_reads_overlapping_repeats INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 9, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-13/call-get_reads_overlapping_repeats/_singularity_tmpdir_xoce6ogo"
2025-09-15 20:23:31.965 wdl.w:ptcp.w:call-trgt-13.t:call-get_reads_overlapping_repeats INFO Slurm invocation: srun --job-name call-get_reads_overlapping_repeats --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-13/call-get_reads_overlapping_repeats/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-13/call-get_reads_overlapping_repeats/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-13/call-get_reads_overlapping_repeats/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-13/call-get_reads_overlapping_repeats/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-13/out/m84036_250809_035451_s4.bc2110.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2110.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-13/out/m84036_250809_035451_s4.bc2110.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2110.mapped.bam.bai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-13/call-get_reads_overlapping_repeats/_singularity_tmpdir_xoce6ogo/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-13/call-get_reads_overlapping_repeats/_singularity_tmpdir_xoce6ogo/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:23:31.977 wdl.w:ptcp.w:call-trgt-13.t:call-get_reads_overlapping_repeats NOTICE slurm_singularity run :: pid: 1199434, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-13/call-get_reads_overlapping_repeats/slurm_singularity.log.txt"
2025-09-15 20:23:32.019 wdl.w:ptcp.t:call-pbmm2_align_hifi-54 INFO output :: name: "mapped_bam", value: "m84036_250809_035451_s4.bc2151.mapped.bam"
2025-09-15 20:23:32.021 wdl.w:ptcp.t:call-pbmm2_align_hifi-54 INFO output :: name: "mapped_bam_bai", value: "m84036_250809_035451_s4.bc2151.mapped.bam.bai"
2025-09-15 20:23:32.022 wdl.w:ptcp.t:call-pbmm2_align_hifi-54 INFO output :: name: "mapped_bam_pbi", value: "m84036_250809_035451_s4.bc2151.mapped.bam.pbi"
2025-09-15 20:23:32.023 wdl.w:ptcp.t:call-pbmm2_align_hifi-54 INFO output :: name: "report", value: "mapping_stats.report.json"
2025-09-15 20:23:32.099 wdl.w:ptcp.t:call-pbmm2_align_hifi-54 NOTICE done
2025-09-15 20:23:32.124 wdl.w:ptcp.w:call-sawfish-17.t:call-run_sawfish.stderr VERBOSE [M::bam2fq_mainloop] discarded 0 singletons
2025-09-15 20:23:32.124 wdl.w:ptcp.w:call-sawfish-17.t:call-run_sawfish.stderr VERBOSE [M::bam2fq_mainloop] processed 0 reads
2025-09-15 20:23:32.127 wdl.w:ptcp NOTICE finish :: job: "call-pbmm2_align_hifi-54"
2025-09-15 20:23:32.127 wdl.w:ptcp INFO output :: job: "call-pbmm2_align_hifi-54", values: {"report": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-54/out/mapping_stats.report.json", "mapped_bam_pbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-54/out/m84036_250809_035451_s4.bc2151.mapped.bam.pbi", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-54/out/m84036_250809_035451_s4.bc2151.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-54/out/m84036_250809_035451_s4.bc2151.mapped.bam"}
2025-09-15 20:23:32.128 wdl.w:ptcp NOTICE ready :: job: "call-paraphase-54", callee: "paraphase"
2025-09-15 20:23:32.128 wdl.w:ptcp INFO input :: job: "call-paraphase-54", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf", "genome_version": "38", "config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-54/out/m84036_250809_035451_s4.bc2151.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-54/out/m84036_250809_035451_s4.bc2151.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2151"}
2025-09-15 20:23:32.129 wdl.w:ptcp NOTICE ready :: job: "call-sawfish-54", callee: "sawfish"
2025-09-15 20:23:32.129 wdl.w:ptcp INFO input :: job: "call-sawfish-54", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-54/out/m84036_250809_035451_s4.bc2151.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-54/out/m84036_250809_035451_s4.bc2151.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2151"}
2025-09-15 20:23:32.130 wdl.w:ptcp NOTICE ready :: job: "call-trgt-54", callee: "trgt"
2025-09-15 20:23:32.130 wdl.w:ptcp INFO input :: job: "call-trgt-54", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-54/out/m84036_250809_035451_s4.bc2151.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-54/out/m84036_250809_035451_s4.bc2151.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2151"}
2025-09-15 20:23:32.133 wdl.w:ptcp.w:call-trgt-13.t:call-trgt_genotype NOTICE task setup :: name: "trgt_genotype", source: "./trgt.wdl", line: 272, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-13/call-trgt_genotype", thread: 140609822115392
2025-09-15 20:23:32.150 wdl.w:ptcp.w:call-trgt-13.t:call-trgt_genotype INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:23:32.150 wdl.w:ptcp.w:call-trgt-13.t:call-trgt_genotype INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:23:32.150 wdl.w:ptcp.w:call-trgt-13.t:call-trgt_genotype INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:23:32.150 wdl.w:ptcp.w:call-trgt-13.t:call-trgt_genotype INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:23:32.150 wdl.w:ptcp.w:call-trgt-13.t:call-trgt_genotype INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2110.mapped.bam.bai"
2025-09-15 20:23:32.150 wdl.w:ptcp.w:call-trgt-13.t:call-trgt_genotype INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2110.mapped.bam"
2025-09-15 20:23:32.150 wdl.w:ptcp.w:call-trgt-13.t:call-trgt_genotype INFO input :: name: "sex", value: "F"
2025-09-15 20:23:32.150 wdl.w:ptcp.w:call-trgt-13.t:call-trgt_genotype INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2110"
2025-09-15 20:23:32.151 wdl.w:ptcp.w:call-trgt-13.t:call-trgt_genotype INFO eval :: name: "mem_gb", value: 16
2025-09-15 20:23:32.151 wdl.w:ptcp.w:call-trgt-13.t:call-trgt_genotype INFO eval :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2110.trgt"
2025-09-15 20:23:32.151 wdl.w:ptcp.w:call-trgt-13.t:call-trgt_genotype INFO eval :: name: "threads", value: 8
2025-09-15 20:23:32.151 wdl.w:ptcp.w:call-trgt-13.t:call-trgt_genotype INFO eval :: name: "disk_size", value: 27
2025-09-15 20:23:32.151 wdl.w:ptcp.w:call-trgt-13.t:call-trgt_genotype INFO eval :: name: "karyotype", value: "XX"
2025-09-15 20:23:32.151 wdl.w:ptcp.w:call-trgt-13.t:call-trgt_genotype INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 8, memory_reservation: 16000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:23:32.152 wdl.w:ptcp.w:call-trgt-13.t:call-trgt_genotype WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:23:32.152 wdl.w:ptcp.w:call-trgt-13.t:call-trgt_genotype INFO provisioned :: seconds_waited: 0, cpu: 8, mem_bytes: 16000000000
2025-09-15 20:23:32.152 wdl.w:ptcp.w:call-trgt-13.t:call-trgt_genotype INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:23:32.204 wdl.w:ptcp.w:call-trgt-13.t:call-trgt_genotype INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 11, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-13/call-trgt_genotype/_singularity_tmpdir_oxuhkmtv"
2025-09-15 20:23:32.204 wdl.w:ptcp.w:call-trgt-13.t:call-trgt_genotype INFO Slurm invocation: srun --job-name call-trgt_genotype --partition compute,compute9 --cpus-per-task 8 --mem 15259M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-13/call-trgt_genotype/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-13/call-trgt_genotype/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-13/call-trgt_genotype/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-13/call-trgt_genotype/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-13/out/m84036_250809_035451_s4.bc2110.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2110.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-13/out/m84036_250809_035451_s4.bc2110.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2110.mapped.bam.bai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-13/call-trgt_genotype/_singularity_tmpdir_oxuhkmtv/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-13/call-trgt_genotype/_singularity_tmpdir_oxuhkmtv/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:23:32.213 wdl.w:ptcp.w:call-trgt-13.t:call-trgt_genotype NOTICE slurm_singularity run :: pid: 1199436, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-13/call-trgt_genotype/slurm_singularity.log.txt"
2025-09-15 20:23:32.295 wdl.w:ptcp.t:call-pbmm2_align_hifi-59 INFO output :: name: "mapped_bam", value: "m84036_250809_035451_s4.bc2156.mapped.bam"
2025-09-15 20:23:32.297 wdl.w:ptcp.t:call-pbmm2_align_hifi-59 INFO output :: name: "mapped_bam_bai", value: "m84036_250809_035451_s4.bc2156.mapped.bam.bai"
2025-09-15 20:23:32.298 wdl.w:ptcp.t:call-pbmm2_align_hifi-59 INFO output :: name: "mapped_bam_pbi", value: "m84036_250809_035451_s4.bc2156.mapped.bam.pbi"
2025-09-15 20:23:32.299 wdl.w:ptcp.t:call-pbmm2_align_hifi-59 INFO output :: name: "report", value: "mapping_stats.report.json"
2025-09-15 20:23:32.368 wdl.w:ptcp.t:call-pbmm2_align_hifi-59 NOTICE done
2025-09-15 20:23:32.374 wdl.w:ptcp NOTICE finish :: job: "call-pbmm2_align_hifi-59"
2025-09-15 20:23:32.374 wdl.w:ptcp INFO output :: job: "call-pbmm2_align_hifi-59", values: {"report": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-59/out/mapping_stats.report.json", "mapped_bam_pbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-59/out/m84036_250809_035451_s4.bc2156.mapped.bam.pbi", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-59/out/m84036_250809_035451_s4.bc2156.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-59/out/m84036_250809_035451_s4.bc2156.mapped.bam"}
2025-09-15 20:23:32.375 wdl.w:ptcp NOTICE ready :: job: "call-paraphase-59", callee: "paraphase"
2025-09-15 20:23:32.375 wdl.w:ptcp INFO input :: job: "call-paraphase-59", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf", "genome_version": "38", "config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-59/out/m84036_250809_035451_s4.bc2156.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-59/out/m84036_250809_035451_s4.bc2156.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2156"}
2025-09-15 20:23:32.376 wdl.w:ptcp NOTICE ready :: job: "call-sawfish-59", callee: "sawfish"
2025-09-15 20:23:32.376 wdl.w:ptcp INFO input :: job: "call-sawfish-59", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-59/out/m84036_250809_035451_s4.bc2156.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-59/out/m84036_250809_035451_s4.bc2156.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2156"}
2025-09-15 20:23:32.377 wdl.w:ptcp NOTICE ready :: job: "call-trgt-59", callee: "trgt"
2025-09-15 20:23:32.377 wdl.w:ptcp INFO input :: job: "call-trgt-59", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-59/out/m84036_250809_035451_s4.bc2156.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-59/out/m84036_250809_035451_s4.bc2156.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2156"}
2025-09-15 20:23:32.381 wdl.w:ptcp.w:call-sawfish-29.t:call-run_sawfish NOTICE task setup :: name: "run_sawfish", source: "./sawfish.wdl", line: 83, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-29/call-run_sawfish", thread: 140609302029888
2025-09-15 20:23:32.402 wdl.w:ptcp.w:call-sawfish-29.t:call-run_sawfish INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:23:32.402 wdl.w:ptcp.w:call-sawfish-29.t:call-run_sawfish INFO input :: name: "genome_version", value: "38"
2025-09-15 20:23:32.402 wdl.w:ptcp.w:call-sawfish-29.t:call-run_sawfish INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:23:32.402 wdl.w:ptcp.w:call-sawfish-29.t:call-run_sawfish INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:23:32.402 wdl.w:ptcp.w:call-sawfish-29.t:call-run_sawfish INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2126.mapped.bam.bai"
2025-09-15 20:23:32.402 wdl.w:ptcp.w:call-sawfish-29.t:call-run_sawfish INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2126.mapped.bam"
2025-09-15 20:23:32.402 wdl.w:ptcp.w:call-sawfish-29.t:call-run_sawfish INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2126"
2025-09-15 20:23:32.403 wdl.w:ptcp.w:call-sawfish-29.t:call-run_sawfish INFO eval :: name: "mem_gb", value: 32
2025-09-15 20:23:32.403 wdl.w:ptcp.w:call-sawfish-29.t:call-run_sawfish INFO eval :: name: "threads", value: 16
2025-09-15 20:23:32.403 wdl.w:ptcp.w:call-sawfish-29.t:call-run_sawfish INFO eval :: name: "disk_size", value: 30
2025-09-15 20:23:32.403 wdl.w:ptcp.w:call-sawfish-29.t:call-run_sawfish INFO eval :: name: "discover_dirname", value: "m84036_250809_035451_s4.bc2126_sawfish_discover"
2025-09-15 20:23:32.403 wdl.w:ptcp.w:call-sawfish-29.t:call-run_sawfish INFO eval :: name: "call_dirname", value: "m84036_250809_035451_s4.bc2126_sawfish"
2025-09-15 20:23:32.403 wdl.w:ptcp.w:call-sawfish-29.t:call-run_sawfish INFO eval :: name: "minimap2_bam_filename", value: "m84036_250809_035451_s4.bc2126.minimap2.bam"
2025-09-15 20:23:32.404 wdl.w:ptcp.w:call-sawfish-29.t:call-run_sawfish INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 16, memory_reservation: 32000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:23:32.404 wdl.w:ptcp.w:call-sawfish-29.t:call-run_sawfish WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:23:32.404 wdl.w:ptcp.w:call-sawfish-29.t:call-run_sawfish INFO provisioned :: seconds_waited: 0, cpu: 16, mem_bytes: 32000000000
2025-09-15 20:23:32.404 wdl.w:ptcp.w:call-sawfish-29.t:call-run_sawfish INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:23:32.472 wdl.w:ptcp.w:call-sawfish-29.t:call-run_sawfish INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 10, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-29/call-run_sawfish/_singularity_tmpdir_6qqmv2qi"
2025-09-15 20:23:32.472 wdl.w:ptcp.w:call-sawfish-29.t:call-run_sawfish INFO Slurm invocation: srun --job-name call-run_sawfish --partition compute,compute9 --cpus-per-task 16 --mem 30518M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-29/call-run_sawfish/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-29/call-run_sawfish/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-29/call-run_sawfish/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-29/call-run_sawfish/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-29/out/m84036_250809_035451_s4.bc2126.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2126.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-29/out/m84036_250809_035451_s4.bc2126.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2126.mapped.bam:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-29/call-run_sawfish/_singularity_tmpdir_6qqmv2qi/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-29/call-run_sawfish/_singularity_tmpdir_6qqmv2qi/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:23:32.482 wdl.w:ptcp.w:call-sawfish-29.t:call-run_sawfish NOTICE slurm_singularity run :: pid: 1199444, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-29/call-run_sawfish/slurm_singularity.log.txt"
2025-09-15 20:23:32.506 wdl.w:ptcp.w:call-trgt-17.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:31 [INFO] - Running trgt-4.0.0-429afcd [genotype]
2025-09-15 20:23:32.507 wdl.w:ptcp.w:call-trgt-17.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:31 [WARN] - OPDM_ABCD3: Filtered out 5 impure reads
2025-09-15 20:23:32.507 wdl.w:ptcp.w:call-trgt-17.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:31 [WARN] - SCA2_ATXN2: Filtered out 6 impure reads
2025-09-15 20:23:32.507 wdl.w:ptcp.w:call-trgt-17.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:31 [WARN] - NIID_NOTCH2NLC: Filtered out 17 impure reads
2025-09-15 20:23:32.507 wdl.w:ptcp.w:call-trgt-17.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:31 [WARN] - DRPLA_ATN1: Filtered out 21 impure reads
2025-09-15 20:23:32.507 wdl.w:ptcp.w:call-trgt-17.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:31 [WARN] - OPDM4_RILPL1: Filtered out 4 impure reads
2025-09-15 20:23:32.507 wdl.w:ptcp.w:call-trgt-17.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:31 [WARN] - SCA37_DAB1: Filtered out 12 impure reads
2025-09-15 20:23:32.507 wdl.w:ptcp.w:call-trgt-17.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:31 [WARN] - SCA8_ATXN8OS: Filtered out 12 impure reads
2025-09-15 20:23:32.507 wdl.w:ptcp.w:call-trgt-17.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:31 [WARN] - SCA27B_FGF14: Filtered out 15 impure reads
2025-09-15 20:23:32.507 wdl.w:ptcp.w:call-trgt-17.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:31 [WARN] - SCA31_BEAN1: Filtered out 4 impure reads
2025-09-15 20:23:32.507 wdl.w:ptcp.w:call-trgt-17.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:31 [WARN] - OPMD_PABPN1: Filtered out 10 impure reads
2025-09-15 20:23:32.507 wdl.w:ptcp.w:call-trgt-17.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:31 [WARN] - SCA3_ATXN3: Filtered out 15 impure reads
2025-09-15 20:23:32.507 wdl.w:ptcp.w:call-trgt-17.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:31 [WARN] - SCA4_ZFHX3: Filtered out 21 impure reads
2025-09-15 20:23:32.507 wdl.w:ptcp.w:call-trgt-17.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:31 [WARN] - HDL2_JPH3: Filtered out 11 impure reads
2025-09-15 20:23:32.507 wdl.w:ptcp.w:call-trgt-17.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:31 [WARN] - FECD3_TCF4: Filtered out 12 impure reads
2025-09-15 20:23:32.507 wdl.w:ptcp.w:call-trgt-17.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:31 [WARN] - SCA6_CACNA1A: Filtered out 10 impure reads
2025-09-15 20:23:32.507 wdl.w:ptcp.w:call-trgt-17.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:31 [WARN] - DM1_DMPK: Filtered out 13 impure reads
2025-09-15 20:23:32.507 wdl.w:ptcp.w:call-trgt-17.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:31 [WARN] - OPDM2_GIPC1: Filtered out 7 impure reads
2025-09-15 20:23:32.508 wdl.w:ptcp.w:call-trgt-17.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:31 [WARN] - CJD_PRNP: Filtered out 7 impure reads
2025-09-15 20:23:32.508 wdl.w:ptcp.w:call-trgt-17.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:31 [WARN] - SD5_HOXD13: Filtered out 12 impure reads
2025-09-15 20:23:32.508 wdl.w:ptcp.w:call-trgt-17.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:31 [WARN] - EPM1_CSTB: Filtered out 10 impure reads
2025-09-15 20:23:32.508 wdl.w:ptcp.w:call-trgt-17.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:31 [WARN] - SCA10_ATXN10: Filtered out 12 impure reads
2025-09-15 20:23:32.508 wdl.w:ptcp.w:call-trgt-17.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:31 [WARN] - SCA36_NOP56: Filtered out 12 impure reads
2025-09-15 20:23:32.508 wdl.w:ptcp.w:call-trgt-17.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:31 [WARN] - DM2_CNBP: Filtered out 1 impure reads
2025-09-15 20:23:32.508 wdl.w:ptcp.w:call-trgt-17.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:31 [WARN] - FRA2A_AFF3: Filtered out 16 impure reads
2025-09-15 20:23:32.508 wdl.w:ptcp.w:call-trgt-17.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:31 [WARN] - SCA7_ATXN7: Filtered out 19 impure reads
2025-09-15 20:23:32.508 wdl.w:ptcp.w:call-trgt-17.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:32 [WARN] - SCA12_PPP2R2B: Filtered out 5 impure reads
2025-09-15 20:23:32.508 wdl.w:ptcp.w:call-trgt-17.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:32 [WARN] - SCA17_TBP: Filtered out 6 impure reads
2025-09-15 20:23:32.508 wdl.w:ptcp.w:call-trgt-17.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:32 [WARN] - CANVAS_RFC1: Filtered out 6 impure reads
2025-09-15 20:23:32.508 wdl.w:ptcp.w:call-trgt-17.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:32 [WARN] - SCA1_ATXN1: Filtered out 18 impure reads
2025-09-15 20:23:32.508 wdl.w:ptcp.w:call-trgt-17.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:32 [WARN] - FAME1_SAMD12: Filtered out 10 impure reads
2025-09-15 20:23:32.508 wdl.w:ptcp.w:call-trgt-17.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:32 [WARN] - HD_HTT: Filtered out 17 impure reads
2025-09-15 20:23:32.508 wdl.w:ptcp.w:call-trgt-17.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:32 [WARN] - OPDM1_LRP12: Filtered out 11 impure reads
2025-09-15 20:23:32.508 wdl.w:ptcp.w:call-trgt-17.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:32 [WARN] - FTDALS1_C9orf72: Filtered out 9 impure reads
2025-09-15 20:23:32.508 wdl.w:ptcp.w:call-trgt-17.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:32 [WARN] - FXS_FMR1: Filtered out 1 impure reads
2025-09-15 20:23:32.509 wdl.w:ptcp.w:call-trgt-17.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:32 [WARN] - FRDA_FXN: Filtered out 3 impure reads
2025-09-15 20:23:32.509 wdl.w:ptcp.w:call-trgt-17.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:32 [WARN] - FRAXE_AFF2: Filtered out 8 impure reads
2025-09-15 20:23:32.509 wdl.w:ptcp.w:call-trgt-17.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:32 [WARN] - SBMA_AR: Filtered out 9 impure reads
2025-09-15 20:23:32.509 wdl.w:ptcp.w:call-trgt-17.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:32 [INFO] - Total execution time: 1.02s
2025-09-15 20:23:32.509 wdl.w:ptcp.w:call-trgt-17.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:32 [INFO] - trgt end
2025-09-15 20:23:32.509 wdl.w:ptcp.t:call-pbmm2_align_hifi-91.slurm_singularity INFO srun: job 51797313 has been allocated resources
2025-09-15 20:23:32.510 wdl.w:ptcp.t:call-pbmm2_align_hifi-91.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:32.510 wdl.w:ptcp.t:call-pbmm2_align_hifi-91.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:23:32.572 wdl.w:ptcp.t:call-pbmm2_align_hifi-94.slurm_singularity INFO srun: job 51797312 has been allocated resources
2025-09-15 20:23:32.572 wdl.w:ptcp.t:call-pbmm2_align_hifi-94.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:32.572 wdl.w:ptcp.t:call-pbmm2_align_hifi-94.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:23:32.576 wdl.w:ptcp.w:call-sawfish-21.t:call-run_sawfish.stderr VERBOSE [M::bam2fq_mainloop] discarded 0 singletons
2025-09-15 20:23:32.577 wdl.w:ptcp.w:call-sawfish-21.t:call-run_sawfish.stderr VERBOSE [M::bam2fq_mainloop] processed 0 reads
2025-09-15 20:23:32.582 wdl.w:ptcp.t:call-pbmm2_align_hifi-95.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:32.582 wdl.w:ptcp.t:call-pbmm2_align_hifi-95.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:23:32.611 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_genotype.slurm_singularity INFO srun: job 51797396 queued and waiting for resources
2025-09-15 20:23:32.611 wdl.w:ptcp.w:call-paraphase-06.t:call-run_paraphase.slurm_singularity INFO srun: job 51797399 queued and waiting for resources
2025-09-15 20:23:32.612 wdl.w:ptcp.w:call-paraphase-30.t:call-run_paraphase.slurm_singularity INFO srun: job 51797395 queued and waiting for resources
2025-09-15 20:23:32.614 wdl.w:ptcp.w:call-trgt-33.t:call-get_reads_overlapping_repeats.slurm_singularity INFO srun: job 51797397 queued and waiting for resources
2025-09-15 20:23:32.614 wdl.w:ptcp.w:call-trgt-30.t:call-get_reads_overlapping_repeats.slurm_singularity INFO srun: job 51797398 queued and waiting for resources
2025-09-15 20:23:32.673 wdl.w:ptcp.w:call-trgt-05.t:call-get_reads_overlapping_repeats.slurm_singularity INFO srun: job 51797400 queued and waiting for resources
2025-09-15 20:23:32.676 wdl.w:ptcp.w:call-trgt-30.t:call-trgt_genotype.slurm_singularity INFO srun: job 51797402 queued and waiting for resources
2025-09-15 20:23:32.678 wdl.w:ptcp.w:call-sawfish-05.t:call-run_sawfish.slurm_singularity INFO srun: job 51797403 queued and waiting for resources
2025-09-15 20:23:32.679 wdl.w:ptcp.w:call-paraphase-33.t:call-run_paraphase.slurm_singularity INFO srun: job 51797401 queued and waiting for resources
2025-09-15 20:23:32.680 wdl.w:ptcp.w:call-trgt-33.t:call-trgt_genotype.slurm_singularity INFO srun: job 51797404 queued and waiting for resources
2025-09-15 20:23:32.684 wdl.w:ptcp.w:call-paraphase-07.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for smn1 for sample m84036_250809_035451_s4.bc2104 at 2025-09-15 20:23:09.870853...
2025-09-15 20:23:32.685 wdl.w:ptcp.w:call-paraphase-07.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for hba for sample m84036_250809_035451_s4.bc2104 at 2025-09-15 20:23:10.797018...
2025-09-15 20:23:32.685 wdl.w:ptcp.w:call-paraphase-07.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for gba for sample m84036_250809_035451_s4.bc2104 at 2025-09-15 20:23:12.097737...
2025-09-15 20:23:32.685 wdl.w:ptcp.w:call-paraphase-07.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for cyp21 for sample m84036_250809_035451_s4.bc2104 at 2025-09-15 20:23:13.300103...
2025-09-15 20:23:32.686 wdl.w:ptcp.w:call-paraphase-07.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for smn1 for sample m84036_250809_035451_s4.bc2104 at 2025-09-15 20:23:28.570919...
2025-09-15 20:23:32.686 wdl.w:ptcp.w:call-paraphase-07.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning to gene2 region for smn1 for sample m84036_250809_035451_s4.bc2104 at 2025-09-15 20:23:29.022452...
2025-09-15 20:23:32.739 wdl.w:ptcp.w:call-paraphase-05.t:call-run_paraphase.slurm_singularity INFO srun: job 51797405 queued and waiting for resources
2025-09-15 20:23:32.777 wdl.w:ptcp.w:call-trgt-05.t:call-trgt_genotype.slurm_singularity INFO srun: job 51797406 queued and waiting for resources
2025-09-15 20:23:32.822 wdl.w:ptcp.w:call-trgt-17.t:call-trgt_genotype INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2114.trgt.vcf"
2025-09-15 20:23:32.826 wdl.w:ptcp.w:call-trgt-17.t:call-trgt_genotype INFO output :: name: "spanning_bam", value: "m84036_250809_035451_s4.bc2114.trgt.sorted.spanning.bam"
2025-09-15 20:23:32.827 wdl.w:ptcp.w:call-trgt-17.t:call-trgt_genotype INFO output :: name: "spanning_bam_bai", value: "m84036_250809_035451_s4.bc2114.trgt.sorted.spanning.bam.bai"
2025-09-15 20:23:32.897 wdl.w:ptcp.w:call-trgt-17.t:call-trgt_genotype NOTICE done
2025-09-15 20:23:32.902 wdl.w:ptcp.w:call-trgt-17 NOTICE finish :: job: "call-trgt_genotype"
2025-09-15 20:23:32.903 wdl.w:ptcp.w:call-trgt-17 INFO output :: job: "call-trgt_genotype", values: {"spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-17/call-trgt_genotype/out/m84036_250809_035451_s4.bc2114.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-17/call-trgt_genotype/out/m84036_250809_035451_s4.bc2114.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-17/call-trgt_genotype/out/m84036_250809_035451_s4.bc2114.trgt.vcf"}
2025-09-15 20:23:32.903 wdl.w:ptcp.w:call-trgt-17 NOTICE ready :: job: "call-trgt_plot_meth_allele", callee: "trgt_plot"
2025-09-15 20:23:32.903 wdl.w:ptcp.w:call-trgt-17 INFO input :: job: "call-trgt_plot_meth_allele", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": false, "methylation": true, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-17/call-trgt_genotype/out/m84036_250809_035451_s4.bc2114.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-17/call-trgt_genotype/out/m84036_250809_035451_s4.bc2114.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-17/call-trgt_genotype/out/m84036_250809_035451_s4.bc2114.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2114"}
2025-09-15 20:23:32.904 wdl.w:ptcp.w:call-trgt-17 NOTICE ready :: job: "call-trgt_plot_meth_waterfall", callee: "trgt_plot"
2025-09-15 20:23:32.904 wdl.w:ptcp.w:call-trgt-17 INFO input :: job: "call-trgt_plot_meth_waterfall", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": true, "methylation": true, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-17/call-trgt_genotype/out/m84036_250809_035451_s4.bc2114.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-17/call-trgt_genotype/out/m84036_250809_035451_s4.bc2114.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-17/call-trgt_genotype/out/m84036_250809_035451_s4.bc2114.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2114"}
2025-09-15 20:23:32.906 wdl.w:ptcp.w:call-trgt-17 NOTICE ready :: job: "call-trgt_plot_motifs_allele", callee: "trgt_plot"
2025-09-15 20:23:32.906 wdl.w:ptcp.w:call-trgt-17 INFO input :: job: "call-trgt_plot_motifs_allele", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": false, "methylation": false, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-17/call-trgt_genotype/out/m84036_250809_035451_s4.bc2114.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-17/call-trgt_genotype/out/m84036_250809_035451_s4.bc2114.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-17/call-trgt_genotype/out/m84036_250809_035451_s4.bc2114.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2114"}
2025-09-15 20:23:32.906 wdl.w:ptcp.w:call-trgt-17 NOTICE ready :: job: "call-trgt_plot_motifs_waterfall", callee: "trgt_plot"
2025-09-15 20:23:32.906 wdl.w:ptcp.w:call-trgt-17 INFO input :: job: "call-trgt_plot_motifs_waterfall", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": true, "methylation": false, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-17/call-trgt_genotype/out/m84036_250809_035451_s4.bc2114.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-17/call-trgt_genotype/out/m84036_250809_035451_s4.bc2114.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-17/call-trgt_genotype/out/m84036_250809_035451_s4.bc2114.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2114"}
2025-09-15 20:23:32.907 wdl.w:ptcp.w:call-trgt-17 INFO visit :: node: "output-spanning_bam", values: {"spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-17/call-trgt_genotype/out/m84036_250809_035451_s4.bc2114.trgt.sorted.spanning.bam"}
2025-09-15 20:23:32.907 wdl.w:ptcp.w:call-trgt-17 INFO visit :: node: "output-spanning_bam_bai", values: {"spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-17/call-trgt_genotype/out/m84036_250809_035451_s4.bc2114.trgt.sorted.spanning.bam.bai"}
2025-09-15 20:23:32.907 wdl.w:ptcp.w:call-trgt-17 INFO visit :: node: "output-vcf", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-17/call-trgt_genotype/out/m84036_250809_035451_s4.bc2114.trgt.vcf"}
2025-09-15 20:23:32.908 wdl.w:ptcp.w:call-paraphase-13.t:call-run_paraphase.slurm_singularity INFO srun: job 51797407 queued and waiting for resources
2025-09-15 20:23:32.910 wdl.w:ptcp.w:call-paraphase-29.t:call-run_paraphase NOTICE task setup :: name: "run_paraphase", source: "./paraphase.wdl", line: 127, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-29/call-run_paraphase", thread: 140610367379008
2025-09-15 20:23:32.927 wdl.w:ptcp.w:call-paraphase-29.t:call-run_paraphase INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:23:32.927 wdl.w:ptcp.w:call-paraphase-29.t:call-run_paraphase INFO input :: name: "annotation_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf"
2025-09-15 20:23:32.927 wdl.w:ptcp.w:call-paraphase-29.t:call-run_paraphase INFO input :: name: "genome_version", value: "38"
2025-09-15 20:23:32.927 wdl.w:ptcp.w:call-paraphase-29.t:call-run_paraphase INFO input :: name: "config_file", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/paraphase_config.GRCh38.yaml"
2025-09-15 20:23:32.927 wdl.w:ptcp.w:call-paraphase-29.t:call-run_paraphase INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:23:32.927 wdl.w:ptcp.w:call-paraphase-29.t:call-run_paraphase INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:23:32.927 wdl.w:ptcp.w:call-paraphase-29.t:call-run_paraphase INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2126.mapped.bam.bai"
2025-09-15 20:23:32.927 wdl.w:ptcp.w:call-paraphase-29.t:call-run_paraphase INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2126.mapped.bam"
2025-09-15 20:23:32.927 wdl.w:ptcp.w:call-paraphase-29.t:call-run_paraphase INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2126"
2025-09-15 20:23:32.928 wdl.w:ptcp.w:call-paraphase-29.t:call-run_paraphase INFO eval :: name: "threads", value: 4
2025-09-15 20:23:32.928 wdl.w:ptcp.w:call-paraphase-29.t:call-run_paraphase INFO eval :: name: "mem_gb", value: 8
2025-09-15 20:23:32.928 wdl.w:ptcp.w:call-paraphase-29.t:call-run_paraphase INFO eval :: name: "disk_size", value: 27
2025-09-15 20:23:32.928 wdl.w:ptcp.w:call-paraphase-29.t:call-run_paraphase INFO eval :: name: "out_dir", value: "m84036_250809_035451_s4.bc2126_paraphase"
2025-09-15 20:23:32.928 wdl.w:ptcp.w:call-paraphase-29.t:call-run_paraphase INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 4, memory_reservation: 8000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:23:32.929 wdl.w:ptcp.w:call-paraphase-29.t:call-run_paraphase WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:23:32.929 wdl.w:ptcp.w:call-paraphase-29.t:call-run_paraphase INFO provisioned :: seconds_waited: 0, cpu: 4, mem_bytes: 8000000000
2025-09-15 20:23:32.929 wdl.w:ptcp.w:call-paraphase-29.t:call-run_paraphase INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:23:32.942 wdl.w:ptcp.w:call-sawfish-13.t:call-run_sawfish.slurm_singularity INFO srun: job 51797408 queued and waiting for resources
2025-09-15 20:23:32.988 wdl.w:ptcp.w:call-trgt-13.t:call-get_reads_overlapping_repeats.slurm_singularity INFO srun: job 51797409 queued and waiting for resources
2025-09-15 20:23:33.013 wdl.w:ptcp.w:call-paraphase-29.t:call-run_paraphase INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-29/call-run_paraphase/_singularity_tmpdir_saou_kgj"
2025-09-15 20:23:33.013 wdl.w:ptcp.w:call-paraphase-29.t:call-run_paraphase INFO Slurm invocation: srun --job-name call-run_paraphase --partition compute,compute9 --cpus-per-task 4 --mem 7629M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-29/call-run_paraphase/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-29/call-run_paraphase/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-29/call-run_paraphase/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-29/call-run_paraphase/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/variant_list/variant_list.GRCh38.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf:ro --bind /ptcp/meta/paraphase/paraphase_config.GRCh38.yaml:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/paraphase_config.GRCh38.yaml:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-29/out/m84036_250809_035451_s4.bc2126.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2126.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-29/out/m84036_250809_035451_s4.bc2126.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2126.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-29/call-run_paraphase/_singularity_tmpdir_saou_kgj/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-29/call-run_paraphase/_singularity_tmpdir_saou_kgj/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:23:33.075 wdl.w:ptcp.w:call-paraphase-29.t:call-run_paraphase NOTICE slurm_singularity run :: pid: 1199450, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-29/call-run_paraphase/slurm_singularity.log.txt"
2025-09-15 20:23:33.221 wdl.w:ptcp.w:call-trgt-13.t:call-trgt_genotype.slurm_singularity INFO srun: job 51797410 queued and waiting for resources
2025-09-15 20:23:33.366 wdl.w:ptcp.w:call-trgt-28.t:call-trgt_genotype INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2125.trgt.vcf"
2025-09-15 20:23:33.368 wdl.w:ptcp.w:call-trgt-28.t:call-trgt_genotype INFO output :: name: "spanning_bam", value: "m84036_250809_035451_s4.bc2125.trgt.sorted.spanning.bam"
2025-09-15 20:23:33.369 wdl.w:ptcp.w:call-trgt-28.t:call-trgt_genotype INFO output :: name: "spanning_bam_bai", value: "m84036_250809_035451_s4.bc2125.trgt.sorted.spanning.bam.bai"
2025-09-15 20:23:33.454 wdl.w:ptcp.w:call-trgt-28.t:call-trgt_genotype NOTICE done
2025-09-15 20:23:33.462 wdl.w:ptcp.w:call-trgt-28 NOTICE finish :: job: "call-trgt_genotype"
2025-09-15 20:23:33.463 wdl.w:ptcp.w:call-trgt-28 INFO output :: job: "call-trgt_genotype", values: {"spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-28/call-trgt_genotype/out/m84036_250809_035451_s4.bc2125.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-28/call-trgt_genotype/out/m84036_250809_035451_s4.bc2125.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-28/call-trgt_genotype/out/m84036_250809_035451_s4.bc2125.trgt.vcf"}
2025-09-15 20:23:33.463 wdl.w:ptcp.w:call-trgt-28 NOTICE ready :: job: "call-trgt_plot_meth_allele", callee: "trgt_plot"
2025-09-15 20:23:33.463 wdl.w:ptcp.w:call-trgt-28 INFO input :: job: "call-trgt_plot_meth_allele", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": false, "methylation": true, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-28/call-trgt_genotype/out/m84036_250809_035451_s4.bc2125.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-28/call-trgt_genotype/out/m84036_250809_035451_s4.bc2125.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-28/call-trgt_genotype/out/m84036_250809_035451_s4.bc2125.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2125"}
2025-09-15 20:23:33.464 wdl.w:ptcp.w:call-trgt-28 NOTICE ready :: job: "call-trgt_plot_meth_waterfall", callee: "trgt_plot"
2025-09-15 20:23:33.464 wdl.w:ptcp.w:call-trgt-28 INFO input :: job: "call-trgt_plot_meth_waterfall", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": true, "methylation": true, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-28/call-trgt_genotype/out/m84036_250809_035451_s4.bc2125.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-28/call-trgt_genotype/out/m84036_250809_035451_s4.bc2125.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-28/call-trgt_genotype/out/m84036_250809_035451_s4.bc2125.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2125"}
2025-09-15 20:23:33.465 wdl.w:ptcp.w:call-trgt-28 NOTICE ready :: job: "call-trgt_plot_motifs_allele", callee: "trgt_plot"
2025-09-15 20:23:33.465 wdl.w:ptcp.w:call-trgt-28 INFO input :: job: "call-trgt_plot_motifs_allele", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": false, "methylation": false, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-28/call-trgt_genotype/out/m84036_250809_035451_s4.bc2125.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-28/call-trgt_genotype/out/m84036_250809_035451_s4.bc2125.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-28/call-trgt_genotype/out/m84036_250809_035451_s4.bc2125.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2125"}
2025-09-15 20:23:33.466 wdl.w:ptcp.w:call-trgt-28 NOTICE ready :: job: "call-trgt_plot_motifs_waterfall", callee: "trgt_plot"
2025-09-15 20:23:33.466 wdl.w:ptcp.w:call-trgt-28 INFO input :: job: "call-trgt_plot_motifs_waterfall", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": true, "methylation": false, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-28/call-trgt_genotype/out/m84036_250809_035451_s4.bc2125.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-28/call-trgt_genotype/out/m84036_250809_035451_s4.bc2125.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-28/call-trgt_genotype/out/m84036_250809_035451_s4.bc2125.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2125"}
2025-09-15 20:23:33.466 wdl.w:ptcp.w:call-trgt-28 INFO visit :: node: "output-spanning_bam", values: {"spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-28/call-trgt_genotype/out/m84036_250809_035451_s4.bc2125.trgt.sorted.spanning.bam"}
2025-09-15 20:23:33.466 wdl.w:ptcp.w:call-trgt-28 INFO visit :: node: "output-spanning_bam_bai", values: {"spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-28/call-trgt_genotype/out/m84036_250809_035451_s4.bc2125.trgt.sorted.spanning.bam.bai"}
2025-09-15 20:23:33.467 wdl.w:ptcp.w:call-trgt-28 INFO visit :: node: "output-vcf", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-28/call-trgt_genotype/out/m84036_250809_035451_s4.bc2125.trgt.vcf"}
2025-09-15 20:23:33.469 wdl.w:ptcp.w:call-trgt-29.t:call-get_reads_overlapping_repeats NOTICE task setup :: name: "get_reads_overlapping_repeats", source: "./trgt.wdl", line: 182, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-29/call-get_reads_overlapping_repeats", thread: 140613823374912
2025-09-15 20:23:33.485 wdl.w:ptcp.w:call-trgt-29.t:call-get_reads_overlapping_repeats INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:23:33.485 wdl.w:ptcp.w:call-trgt-29.t:call-get_reads_overlapping_repeats INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:23:33.485 wdl.w:ptcp.w:call-trgt-29.t:call-get_reads_overlapping_repeats INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2126.mapped.bam.bai"
2025-09-15 20:23:33.485 wdl.w:ptcp.w:call-trgt-29.t:call-get_reads_overlapping_repeats INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2126.mapped.bam"
2025-09-15 20:23:33.486 wdl.w:ptcp.w:call-trgt-29.t:call-get_reads_overlapping_repeats INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2126"
2025-09-15 20:23:33.486 wdl.w:ptcp.w:call-trgt-29.t:call-get_reads_overlapping_repeats INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:23:33.486 wdl.w:ptcp.w:call-trgt-29.t:call-get_reads_overlapping_repeats INFO eval :: name: "expand_size", value: 3000
2025-09-15 20:23:33.486 wdl.w:ptcp.w:call-trgt-29.t:call-get_reads_overlapping_repeats INFO eval :: name: "threads", value: 1
2025-09-15 20:23:33.486 wdl.w:ptcp.w:call-trgt-29.t:call-get_reads_overlapping_repeats INFO eval :: name: "expanded_bed_name", value: "m84036_250809_035451_s4.bc2126.expanded.bed"
2025-09-15 20:23:33.486 wdl.w:ptcp.w:call-trgt-29.t:call-get_reads_overlapping_repeats INFO eval :: name: "disk_size", value: 11
2025-09-15 20:23:33.486 wdl.w:ptcp.w:call-trgt-29.t:call-get_reads_overlapping_repeats INFO eval :: name: "output_name", value: "m84036_250809_035451_s4.bc2126.repeats.bam"
2025-09-15 20:23:33.486 wdl.w:ptcp.w:call-trgt-29.t:call-get_reads_overlapping_repeats INFO eval :: name: "index_name", value: "m84036_250809_035451_s4.bc2126.repeats.bam.bai"
2025-09-15 20:23:33.487 wdl.w:ptcp.w:call-trgt-29.t:call-get_reads_overlapping_repeats INFO eval :: name: "output_name_with_index", value: "m84036_250809_035451_s4.bc2126.repeats.bam##idx##m84036_250809_035451_s4.bc2126.repeats.bam.bai"
2025-09-15 20:23:33.487 wdl.w:ptcp.w:call-trgt-29.t:call-get_reads_overlapping_repeats INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:23:33.487 wdl.w:ptcp.w:call-trgt-29.t:call-get_reads_overlapping_repeats WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:23:33.487 wdl.w:ptcp.w:call-trgt-29.t:call-get_reads_overlapping_repeats INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:23:33.488 wdl.w:ptcp.w:call-trgt-29.t:call-get_reads_overlapping_repeats INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:23:33.490 wdl.w:ptcp.w:call-sawfish-29.t:call-run_sawfish.slurm_singularity INFO srun: job 51797411 queued and waiting for resources
2025-09-15 20:23:33.531 wdl.w:ptcp.w:call-trgt-29.t:call-get_reads_overlapping_repeats INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 9, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-29/call-get_reads_overlapping_repeats/_singularity_tmpdir_xhbw5cp9"
2025-09-15 20:23:33.531 wdl.w:ptcp.w:call-trgt-29.t:call-get_reads_overlapping_repeats INFO Slurm invocation: srun --job-name call-get_reads_overlapping_repeats --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-29/call-get_reads_overlapping_repeats/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-29/call-get_reads_overlapping_repeats/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-29/call-get_reads_overlapping_repeats/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-29/call-get_reads_overlapping_repeats/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-29/out/m84036_250809_035451_s4.bc2126.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2126.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-29/out/m84036_250809_035451_s4.bc2126.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2126.mapped.bam:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-29/call-get_reads_overlapping_repeats/_singularity_tmpdir_xhbw5cp9/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-29/call-get_reads_overlapping_repeats/_singularity_tmpdir_xhbw5cp9/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:23:33.552 wdl.w:ptcp.w:call-trgt-29.t:call-get_reads_overlapping_repeats NOTICE slurm_singularity run :: pid: 1199453, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-29/call-get_reads_overlapping_repeats/slurm_singularity.log.txt"
2025-09-15 20:23:33.702 wdl.w:ptcp.t:call-pbmm2_align_hifi-53 INFO output :: name: "mapped_bam", value: "m84036_250809_035451_s4.bc2150.mapped.bam"
2025-09-15 20:23:33.706 wdl.w:ptcp.t:call-pbmm2_align_hifi-53 INFO output :: name: "mapped_bam_bai", value: "m84036_250809_035451_s4.bc2150.mapped.bam.bai"
2025-09-15 20:23:33.706 wdl.w:ptcp.t:call-pbmm2_align_hifi-53 INFO output :: name: "mapped_bam_pbi", value: "m84036_250809_035451_s4.bc2150.mapped.bam.pbi"
2025-09-15 20:23:33.708 wdl.w:ptcp.t:call-pbmm2_align_hifi-53 INFO output :: name: "report", value: "mapping_stats.report.json"
2025-09-15 20:23:33.782 wdl.w:ptcp.t:call-pbmm2_align_hifi-53 NOTICE done
2025-09-15 20:23:33.787 wdl.w:ptcp NOTICE finish :: job: "call-pbmm2_align_hifi-53"
2025-09-15 20:23:33.788 wdl.w:ptcp INFO output :: job: "call-pbmm2_align_hifi-53", values: {"report": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-53/out/mapping_stats.report.json", "mapped_bam_pbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-53/out/m84036_250809_035451_s4.bc2150.mapped.bam.pbi", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-53/out/m84036_250809_035451_s4.bc2150.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-53/out/m84036_250809_035451_s4.bc2150.mapped.bam"}
2025-09-15 20:23:33.788 wdl.w:ptcp NOTICE ready :: job: "call-paraphase-53", callee: "paraphase"
2025-09-15 20:23:33.788 wdl.w:ptcp INFO input :: job: "call-paraphase-53", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf", "genome_version": "38", "config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-53/out/m84036_250809_035451_s4.bc2150.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-53/out/m84036_250809_035451_s4.bc2150.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2150"}
2025-09-15 20:23:33.789 wdl.w:ptcp NOTICE ready :: job: "call-sawfish-53", callee: "sawfish"
2025-09-15 20:23:33.789 wdl.w:ptcp INFO input :: job: "call-sawfish-53", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-53/out/m84036_250809_035451_s4.bc2150.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-53/out/m84036_250809_035451_s4.bc2150.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2150"}
2025-09-15 20:23:33.791 wdl.w:ptcp NOTICE ready :: job: "call-trgt-53", callee: "trgt"
2025-09-15 20:23:33.791 wdl.w:ptcp INFO input :: job: "call-trgt-53", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-53/out/m84036_250809_035451_s4.bc2150.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-53/out/m84036_250809_035451_s4.bc2150.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2150"}
2025-09-15 20:23:33.793 wdl.w:ptcp.w:call-trgt-29.t:call-trgt_genotype NOTICE task setup :: name: "trgt_genotype", source: "./trgt.wdl", line: 272, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-29/call-trgt_genotype", thread: 140609830508096
2025-09-15 20:23:33.803 wdl.w:ptcp.t:call-pbmm2_align_hifi-56 INFO output :: name: "mapped_bam", value: "m84036_250809_035451_s4.bc2153.mapped.bam"
2025-09-15 20:23:33.806 wdl.w:ptcp.t:call-pbmm2_align_hifi-56 INFO output :: name: "mapped_bam_bai", value: "m84036_250809_035451_s4.bc2153.mapped.bam.bai"
2025-09-15 20:23:33.808 wdl.w:ptcp.t:call-pbmm2_align_hifi-56 INFO output :: name: "mapped_bam_pbi", value: "m84036_250809_035451_s4.bc2153.mapped.bam.pbi"
2025-09-15 20:23:33.809 wdl.w:ptcp.t:call-pbmm2_align_hifi-56 INFO output :: name: "report", value: "mapping_stats.report.json"
2025-09-15 20:23:33.812 wdl.w:ptcp.w:call-trgt-29.t:call-trgt_genotype INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:23:33.812 wdl.w:ptcp.w:call-trgt-29.t:call-trgt_genotype INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:23:33.812 wdl.w:ptcp.w:call-trgt-29.t:call-trgt_genotype INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:23:33.812 wdl.w:ptcp.w:call-trgt-29.t:call-trgt_genotype INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:23:33.812 wdl.w:ptcp.w:call-trgt-29.t:call-trgt_genotype INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2126.mapped.bam.bai"
2025-09-15 20:23:33.812 wdl.w:ptcp.w:call-trgt-29.t:call-trgt_genotype INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2126.mapped.bam"
2025-09-15 20:23:33.812 wdl.w:ptcp.w:call-trgt-29.t:call-trgt_genotype INFO input :: name: "sex", value: "F"
2025-09-15 20:23:33.812 wdl.w:ptcp.w:call-trgt-29.t:call-trgt_genotype INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2126"
2025-09-15 20:23:33.812 wdl.w:ptcp.w:call-trgt-29.t:call-trgt_genotype INFO eval :: name: "mem_gb", value: 16
2025-09-15 20:23:33.813 wdl.w:ptcp.w:call-trgt-29.t:call-trgt_genotype INFO eval :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2126.trgt"
2025-09-15 20:23:33.813 wdl.w:ptcp.w:call-trgt-29.t:call-trgt_genotype INFO eval :: name: "threads", value: 8
2025-09-15 20:23:33.813 wdl.w:ptcp.w:call-trgt-29.t:call-trgt_genotype INFO eval :: name: "disk_size", value: 27
2025-09-15 20:23:33.813 wdl.w:ptcp.w:call-trgt-29.t:call-trgt_genotype INFO eval :: name: "karyotype", value: "XX"
2025-09-15 20:23:33.813 wdl.w:ptcp.w:call-trgt-29.t:call-trgt_genotype INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 8, memory_reservation: 16000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:23:33.814 wdl.w:ptcp.w:call-trgt-29.t:call-trgt_genotype WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:23:33.814 wdl.w:ptcp.w:call-trgt-29.t:call-trgt_genotype INFO provisioned :: seconds_waited: 0, cpu: 8, mem_bytes: 16000000000
2025-09-15 20:23:33.814 wdl.w:ptcp.w:call-trgt-29.t:call-trgt_genotype INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:23:33.878 wdl.w:ptcp.w:call-trgt-29.t:call-trgt_genotype INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 11, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-29/call-trgt_genotype/_singularity_tmpdir_5231fr3y"
2025-09-15 20:23:33.879 wdl.w:ptcp.w:call-trgt-29.t:call-trgt_genotype INFO Slurm invocation: srun --job-name call-trgt_genotype --partition compute,compute9 --cpus-per-task 8 --mem 15259M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-29/call-trgt_genotype/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-29/call-trgt_genotype/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-29/call-trgt_genotype/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-29/call-trgt_genotype/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-29/out/m84036_250809_035451_s4.bc2126.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2126.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-29/out/m84036_250809_035451_s4.bc2126.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2126.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-29/call-trgt_genotype/_singularity_tmpdir_5231fr3y/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-29/call-trgt_genotype/_singularity_tmpdir_5231fr3y/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:23:33.889 wdl.w:ptcp.w:call-trgt-29.t:call-trgt_genotype NOTICE slurm_singularity run :: pid: 1199469, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-29/call-trgt_genotype/slurm_singularity.log.txt"
2025-09-15 20:23:33.890 wdl.w:ptcp.t:call-pbmm2_align_hifi-56 NOTICE done
2025-09-15 20:23:33.897 wdl.w:ptcp NOTICE finish :: job: "call-pbmm2_align_hifi-56"
2025-09-15 20:23:33.897 wdl.w:ptcp INFO output :: job: "call-pbmm2_align_hifi-56", values: {"report": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-56/out/mapping_stats.report.json", "mapped_bam_pbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-56/out/m84036_250809_035451_s4.bc2153.mapped.bam.pbi", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-56/out/m84036_250809_035451_s4.bc2153.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-56/out/m84036_250809_035451_s4.bc2153.mapped.bam"}
2025-09-15 20:23:33.898 wdl.w:ptcp NOTICE ready :: job: "call-paraphase-56", callee: "paraphase"
2025-09-15 20:23:33.898 wdl.w:ptcp INFO input :: job: "call-paraphase-56", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf", "genome_version": "38", "config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-56/out/m84036_250809_035451_s4.bc2153.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-56/out/m84036_250809_035451_s4.bc2153.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2153"}
2025-09-15 20:23:33.899 wdl.w:ptcp NOTICE ready :: job: "call-sawfish-56", callee: "sawfish"
2025-09-15 20:23:33.899 wdl.w:ptcp INFO input :: job: "call-sawfish-56", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-56/out/m84036_250809_035451_s4.bc2153.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-56/out/m84036_250809_035451_s4.bc2153.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2153"}
2025-09-15 20:23:33.900 wdl.w:ptcp NOTICE ready :: job: "call-trgt-56", callee: "trgt"
2025-09-15 20:23:33.900 wdl.w:ptcp INFO input :: job: "call-trgt-56", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-56/out/m84036_250809_035451_s4.bc2153.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-56/out/m84036_250809_035451_s4.bc2153.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2153"}
2025-09-15 20:23:33.903 wdl.w:ptcp.w:call-paraphase-12.t:call-run_paraphase NOTICE task setup :: name: "run_paraphase", source: "./paraphase.wdl", line: 127, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-12/call-run_paraphase", thread: 140609805329984
2025-09-15 20:23:33.923 wdl.w:ptcp.w:call-paraphase-12.t:call-run_paraphase INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:23:33.923 wdl.w:ptcp.w:call-paraphase-12.t:call-run_paraphase INFO input :: name: "annotation_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf"
2025-09-15 20:23:33.923 wdl.w:ptcp.w:call-paraphase-12.t:call-run_paraphase INFO input :: name: "genome_version", value: "38"
2025-09-15 20:23:33.923 wdl.w:ptcp.w:call-paraphase-12.t:call-run_paraphase INFO input :: name: "config_file", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/paraphase_config.GRCh38.yaml"
2025-09-15 20:23:33.923 wdl.w:ptcp.w:call-paraphase-12.t:call-run_paraphase INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:23:33.923 wdl.w:ptcp.w:call-paraphase-12.t:call-run_paraphase INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:23:33.923 wdl.w:ptcp.w:call-paraphase-12.t:call-run_paraphase INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2109.mapped.bam.bai"
2025-09-15 20:23:33.923 wdl.w:ptcp.w:call-paraphase-12.t:call-run_paraphase INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2109.mapped.bam"
2025-09-15 20:23:33.923 wdl.w:ptcp.w:call-paraphase-12.t:call-run_paraphase INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2109"
2025-09-15 20:23:33.924 wdl.w:ptcp.w:call-paraphase-12.t:call-run_paraphase INFO eval :: name: "threads", value: 4
2025-09-15 20:23:33.924 wdl.w:ptcp.w:call-paraphase-12.t:call-run_paraphase INFO eval :: name: "mem_gb", value: 8
2025-09-15 20:23:33.924 wdl.w:ptcp.w:call-paraphase-12.t:call-run_paraphase INFO eval :: name: "disk_size", value: 27
2025-09-15 20:23:33.924 wdl.w:ptcp.w:call-paraphase-12.t:call-run_paraphase INFO eval :: name: "out_dir", value: "m84036_250809_035451_s4.bc2109_paraphase"
2025-09-15 20:23:33.924 wdl.w:ptcp.w:call-paraphase-12.t:call-run_paraphase INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 4, memory_reservation: 8000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:23:33.925 wdl.w:ptcp.w:call-paraphase-12.t:call-run_paraphase WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:23:33.925 wdl.w:ptcp.w:call-paraphase-12.t:call-run_paraphase INFO provisioned :: seconds_waited: 0, cpu: 4, mem_bytes: 8000000000
2025-09-15 20:23:33.925 wdl.w:ptcp.w:call-paraphase-12.t:call-run_paraphase INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:23:33.934 wdl.w:ptcp.w:call-trgt-28.t:call-get_reads_overlapping_repeats INFO output :: name: "reads_overlapping_repeats", value: "m84036_250809_035451_s4.bc2125.repeats.bam"
2025-09-15 20:23:33.936 wdl.w:ptcp.w:call-trgt-28.t:call-get_reads_overlapping_repeats INFO output :: name: "reads_overlapping_repeats_bai", value: "m84036_250809_035451_s4.bc2125.repeats.bam.bai"
2025-09-15 20:23:34.002 wdl.w:ptcp.w:call-paraphase-12.t:call-run_paraphase INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-12/call-run_paraphase/_singularity_tmpdir_i2x1q6bx"
2025-09-15 20:23:34.002 wdl.w:ptcp.w:call-paraphase-12.t:call-run_paraphase INFO Slurm invocation: srun --job-name call-run_paraphase --partition compute,compute9 --cpus-per-task 4 --mem 7629M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-12/call-run_paraphase/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-12/call-run_paraphase/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-12/call-run_paraphase/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-12/call-run_paraphase/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-12/out/m84036_250809_035451_s4.bc2109.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2109.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-12/out/m84036_250809_035451_s4.bc2109.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2109.mapped.bam:ro --bind /ptcp/meta/variant_list/variant_list.GRCh38.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf:ro --bind /ptcp/meta/paraphase/paraphase_config.GRCh38.yaml:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/paraphase_config.GRCh38.yaml:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-12/call-run_paraphase/_singularity_tmpdir_i2x1q6bx/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-12/call-run_paraphase/_singularity_tmpdir_i2x1q6bx/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:23:34.002 wdl.w:ptcp.w:call-trgt-28.t:call-get_reads_overlapping_repeats NOTICE done
2025-09-15 20:23:34.009 wdl.w:ptcp.w:call-trgt-28 NOTICE finish :: job: "call-get_reads_overlapping_repeats"
2025-09-15 20:23:34.009 wdl.w:ptcp.w:call-trgt-28 INFO output :: job: "call-get_reads_overlapping_repeats", values: {"reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-28/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2125.repeats.bam.bai", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-28/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2125.repeats.bam"}
2025-09-15 20:23:34.009 wdl.w:ptcp.w:call-trgt-28 INFO visit :: node: "output-reads_overlapping_repeats", values: {"reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-28/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2125.repeats.bam"}
2025-09-15 20:23:34.009 wdl.w:ptcp.w:call-trgt-28 INFO visit :: node: "output-reads_overlapping_repeats_bai", values: {"reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-28/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2125.repeats.bam.bai"}
2025-09-15 20:23:34.020 wdl.w:ptcp.w:call-paraphase-12.t:call-run_paraphase NOTICE slurm_singularity run :: pid: 1199472, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-12/call-run_paraphase/slurm_singularity.log.txt"
2025-09-15 20:23:34.021 wdl.w:ptcp.w:call-sawfish-12.t:call-run_sawfish NOTICE task setup :: name: "run_sawfish", source: "./sawfish.wdl", line: 83, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-12/call-run_sawfish", thread: 140611944420928
2025-09-15 20:23:34.041 wdl.w:ptcp.w:call-sawfish-12.t:call-run_sawfish INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:23:34.041 wdl.w:ptcp.w:call-sawfish-12.t:call-run_sawfish INFO input :: name: "genome_version", value: "38"
2025-09-15 20:23:34.041 wdl.w:ptcp.w:call-sawfish-12.t:call-run_sawfish INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:23:34.041 wdl.w:ptcp.w:call-sawfish-12.t:call-run_sawfish INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:23:34.041 wdl.w:ptcp.w:call-sawfish-12.t:call-run_sawfish INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2109.mapped.bam.bai"
2025-09-15 20:23:34.041 wdl.w:ptcp.w:call-sawfish-12.t:call-run_sawfish INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2109.mapped.bam"
2025-09-15 20:23:34.041 wdl.w:ptcp.w:call-sawfish-12.t:call-run_sawfish INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2109"
2025-09-15 20:23:34.042 wdl.w:ptcp.w:call-sawfish-12.t:call-run_sawfish INFO eval :: name: "mem_gb", value: 32
2025-09-15 20:23:34.042 wdl.w:ptcp.w:call-sawfish-12.t:call-run_sawfish INFO eval :: name: "threads", value: 16
2025-09-15 20:23:34.042 wdl.w:ptcp.w:call-sawfish-12.t:call-run_sawfish INFO eval :: name: "disk_size", value: 30
2025-09-15 20:23:34.042 wdl.w:ptcp.w:call-sawfish-12.t:call-run_sawfish INFO eval :: name: "discover_dirname", value: "m84036_250809_035451_s4.bc2109_sawfish_discover"
2025-09-15 20:23:34.042 wdl.w:ptcp.w:call-sawfish-12.t:call-run_sawfish INFO eval :: name: "call_dirname", value: "m84036_250809_035451_s4.bc2109_sawfish"
2025-09-15 20:23:34.042 wdl.w:ptcp.w:call-sawfish-12.t:call-run_sawfish INFO eval :: name: "minimap2_bam_filename", value: "m84036_250809_035451_s4.bc2109.minimap2.bam"
2025-09-15 20:23:34.043 wdl.w:ptcp.w:call-sawfish-12.t:call-run_sawfish INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 16, memory_reservation: 32000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:23:34.043 wdl.w:ptcp.w:call-sawfish-12.t:call-run_sawfish WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:23:34.043 wdl.w:ptcp.w:call-sawfish-12.t:call-run_sawfish INFO provisioned :: seconds_waited: 0, cpu: 16, mem_bytes: 32000000000
2025-09-15 20:23:34.043 wdl.w:ptcp.w:call-sawfish-12.t:call-run_sawfish INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:23:34.055 wdl.w:ptcp.t:call-pbmm2_align_hifi-43 INFO output :: name: "mapped_bam", value: "m84036_250809_035451_s4.bc2140.mapped.bam"
2025-09-15 20:23:34.057 wdl.w:ptcp.t:call-pbmm2_align_hifi-43 INFO output :: name: "mapped_bam_bai", value: "m84036_250809_035451_s4.bc2140.mapped.bam.bai"
2025-09-15 20:23:34.058 wdl.w:ptcp.t:call-pbmm2_align_hifi-43 INFO output :: name: "mapped_bam_pbi", value: "m84036_250809_035451_s4.bc2140.mapped.bam.pbi"
2025-09-15 20:23:34.059 wdl.w:ptcp.t:call-pbmm2_align_hifi-43 INFO output :: name: "report", value: "mapping_stats.report.json"
2025-09-15 20:23:34.085 wdl.w:ptcp.w:call-paraphase-29.t:call-run_paraphase.slurm_singularity INFO srun: job 51797412 queued and waiting for resources
2025-09-15 20:23:34.100 wdl.w:ptcp.w:call-sawfish-12.t:call-run_sawfish INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 10, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-12/call-run_sawfish/_singularity_tmpdir_azw7_jzb"
2025-09-15 20:23:34.100 wdl.w:ptcp.w:call-sawfish-12.t:call-run_sawfish INFO Slurm invocation: srun --job-name call-run_sawfish --partition compute,compute9 --cpus-per-task 16 --mem 30518M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-12/call-run_sawfish/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-12/call-run_sawfish/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-12/call-run_sawfish/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-12/call-run_sawfish/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-12/out/m84036_250809_035451_s4.bc2109.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2109.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-12/out/m84036_250809_035451_s4.bc2109.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2109.mapped.bam:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-12/call-run_sawfish/_singularity_tmpdir_azw7_jzb/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-12/call-run_sawfish/_singularity_tmpdir_azw7_jzb/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:23:34.115 wdl.w:ptcp.w:call-sawfish-12.t:call-run_sawfish NOTICE slurm_singularity run :: pid: 1199479, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-12/call-run_sawfish/slurm_singularity.log.txt"
2025-09-15 20:23:34.138 wdl.w:ptcp.t:call-pbmm2_align_hifi-43 NOTICE done
2025-09-15 20:23:34.157 wdl.w:ptcp NOTICE finish :: job: "call-pbmm2_align_hifi-43"
2025-09-15 20:23:34.157 wdl.w:ptcp INFO output :: job: "call-pbmm2_align_hifi-43", values: {"report": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-43/out/mapping_stats.report.json", "mapped_bam_pbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-43/out/m84036_250809_035451_s4.bc2140.mapped.bam.pbi", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-43/out/m84036_250809_035451_s4.bc2140.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-43/out/m84036_250809_035451_s4.bc2140.mapped.bam"}
2025-09-15 20:23:34.158 wdl.w:ptcp NOTICE ready :: job: "call-paraphase-43", callee: "paraphase"
2025-09-15 20:23:34.158 wdl.w:ptcp INFO input :: job: "call-paraphase-43", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf", "genome_version": "38", "config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-43/out/m84036_250809_035451_s4.bc2140.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-43/out/m84036_250809_035451_s4.bc2140.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2140"}
2025-09-15 20:23:34.159 wdl.w:ptcp NOTICE ready :: job: "call-sawfish-43", callee: "sawfish"
2025-09-15 20:23:34.159 wdl.w:ptcp INFO input :: job: "call-sawfish-43", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-43/out/m84036_250809_035451_s4.bc2140.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-43/out/m84036_250809_035451_s4.bc2140.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2140"}
2025-09-15 20:23:34.160 wdl.w:ptcp NOTICE ready :: job: "call-trgt-43", callee: "trgt"
2025-09-15 20:23:34.160 wdl.w:ptcp INFO input :: job: "call-trgt-43", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-43/out/m84036_250809_035451_s4.bc2140.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-43/out/m84036_250809_035451_s4.bc2140.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2140"}
2025-09-15 20:23:34.162 wdl.w:ptcp.w:call-trgt-12.t:call-get_reads_overlapping_repeats NOTICE task setup :: name: "get_reads_overlapping_repeats", source: "./trgt.wdl", line: 182, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-12/call-get_reads_overlapping_repeats", thread: 140610870679104
2025-09-15 20:23:34.225 wdl.w:ptcp.w:call-trgt-12.t:call-get_reads_overlapping_repeats INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:23:34.225 wdl.w:ptcp.w:call-trgt-12.t:call-get_reads_overlapping_repeats INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:23:34.225 wdl.w:ptcp.w:call-trgt-12.t:call-get_reads_overlapping_repeats INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2109.mapped.bam.bai"
2025-09-15 20:23:34.225 wdl.w:ptcp.w:call-trgt-12.t:call-get_reads_overlapping_repeats INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2109.mapped.bam"
2025-09-15 20:23:34.225 wdl.w:ptcp.w:call-trgt-12.t:call-get_reads_overlapping_repeats INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2109"
2025-09-15 20:23:34.225 wdl.w:ptcp.w:call-trgt-12.t:call-get_reads_overlapping_repeats INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:23:34.225 wdl.w:ptcp.w:call-trgt-12.t:call-get_reads_overlapping_repeats INFO eval :: name: "expand_size", value: 3000
2025-09-15 20:23:34.225 wdl.w:ptcp.w:call-trgt-12.t:call-get_reads_overlapping_repeats INFO eval :: name: "threads", value: 1
2025-09-15 20:23:34.225 wdl.w:ptcp.w:call-trgt-12.t:call-get_reads_overlapping_repeats INFO eval :: name: "expanded_bed_name", value: "m84036_250809_035451_s4.bc2109.expanded.bed"
2025-09-15 20:23:34.226 wdl.w:ptcp.w:call-trgt-12.t:call-get_reads_overlapping_repeats INFO eval :: name: "disk_size", value: 11
2025-09-15 20:23:34.226 wdl.w:ptcp.w:call-trgt-12.t:call-get_reads_overlapping_repeats INFO eval :: name: "output_name", value: "m84036_250809_035451_s4.bc2109.repeats.bam"
2025-09-15 20:23:34.226 wdl.w:ptcp.w:call-trgt-12.t:call-get_reads_overlapping_repeats INFO eval :: name: "index_name", value: "m84036_250809_035451_s4.bc2109.repeats.bam.bai"
2025-09-15 20:23:34.226 wdl.w:ptcp.w:call-trgt-12.t:call-get_reads_overlapping_repeats INFO eval :: name: "output_name_with_index", value: "m84036_250809_035451_s4.bc2109.repeats.bam##idx##m84036_250809_035451_s4.bc2109.repeats.bam.bai"
2025-09-15 20:23:34.226 wdl.w:ptcp.w:call-trgt-12.t:call-get_reads_overlapping_repeats INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:23:34.226 wdl.w:ptcp.w:call-trgt-12.t:call-get_reads_overlapping_repeats WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:23:34.227 wdl.w:ptcp.w:call-trgt-12.t:call-get_reads_overlapping_repeats INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:23:34.227 wdl.w:ptcp.w:call-trgt-12.t:call-get_reads_overlapping_repeats INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:23:34.273 wdl.w:ptcp.w:call-trgt-12.t:call-get_reads_overlapping_repeats INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 9, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-12/call-get_reads_overlapping_repeats/_singularity_tmpdir_roe6t0pq"
2025-09-15 20:23:34.273 wdl.w:ptcp.w:call-trgt-12.t:call-get_reads_overlapping_repeats INFO Slurm invocation: srun --job-name call-get_reads_overlapping_repeats --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-12/call-get_reads_overlapping_repeats/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-12/call-get_reads_overlapping_repeats/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-12/call-get_reads_overlapping_repeats/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-12/call-get_reads_overlapping_repeats/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-12/out/m84036_250809_035451_s4.bc2109.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2109.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-12/out/m84036_250809_035451_s4.bc2109.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2109.mapped.bam:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-12/call-get_reads_overlapping_repeats/_singularity_tmpdir_roe6t0pq/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-12/call-get_reads_overlapping_repeats/_singularity_tmpdir_roe6t0pq/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:23:34.284 wdl.w:ptcp.w:call-trgt-12.t:call-get_reads_overlapping_repeats NOTICE slurm_singularity run :: pid: 1199481, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-12/call-get_reads_overlapping_repeats/slurm_singularity.log.txt"
2025-09-15 20:23:34.464 wdl.w:ptcp.t:call-pbmm2_align_hifi-55 INFO output :: name: "mapped_bam", value: "m84036_250809_035451_s4.bc2152.mapped.bam"
2025-09-15 20:23:34.467 wdl.w:ptcp.t:call-pbmm2_align_hifi-55 INFO output :: name: "mapped_bam_bai", value: "m84036_250809_035451_s4.bc2152.mapped.bam.bai"
2025-09-15 20:23:34.469 wdl.w:ptcp.t:call-pbmm2_align_hifi-55 INFO output :: name: "mapped_bam_pbi", value: "m84036_250809_035451_s4.bc2152.mapped.bam.pbi"
2025-09-15 20:23:34.471 wdl.w:ptcp.t:call-pbmm2_align_hifi-55 INFO output :: name: "report", value: "mapping_stats.report.json"
2025-09-15 20:23:34.486 wdl.w:ptcp.w:call-sawfish-30.t:call-run_sawfish.slurm_singularity INFO srun: job 51797392 has been allocated resources
2025-09-15 20:23:34.503 wdl.w:ptcp.w:call-sawfish-29.t:call-run_sawfish.slurm_singularity INFO srun: job 51797411 has been allocated resources
2025-09-15 20:23:34.565 wdl.w:ptcp.w:call-trgt-29.t:call-get_reads_overlapping_repeats.slurm_singularity INFO srun: job 51797413 queued and waiting for resources
2025-09-15 20:23:34.565 wdl.w:ptcp.w:call-trgt-29.t:call-get_reads_overlapping_repeats.slurm_singularity INFO srun: job 51797413 has been allocated resources
2025-09-15 20:23:34.567 wdl.w:ptcp.t:call-pbmm2_align_hifi-55 NOTICE done
2025-09-15 20:23:34.567 wdl.w:ptcp.t:call-pbmm2_align_hifi-86.slurm_singularity INFO srun: job 51797316 has been allocated resources
2025-09-15 20:23:34.567 wdl.w:ptcp.t:call-pbmm2_align_hifi-86.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:34.567 wdl.w:ptcp.t:call-pbmm2_align_hifi-86.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:23:34.574 wdl.w:ptcp NOTICE finish :: job: "call-pbmm2_align_hifi-55"
2025-09-15 20:23:34.574 wdl.w:ptcp INFO output :: job: "call-pbmm2_align_hifi-55", values: {"report": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-55/out/mapping_stats.report.json", "mapped_bam_pbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-55/out/m84036_250809_035451_s4.bc2152.mapped.bam.pbi", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-55/out/m84036_250809_035451_s4.bc2152.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-55/out/m84036_250809_035451_s4.bc2152.mapped.bam"}
2025-09-15 20:23:34.575 wdl.w:ptcp NOTICE ready :: job: "call-paraphase-55", callee: "paraphase"
2025-09-15 20:23:34.575 wdl.w:ptcp INFO input :: job: "call-paraphase-55", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf", "genome_version": "38", "config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-55/out/m84036_250809_035451_s4.bc2152.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-55/out/m84036_250809_035451_s4.bc2152.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2152"}
2025-09-15 20:23:34.576 wdl.w:ptcp NOTICE ready :: job: "call-sawfish-55", callee: "sawfish"
2025-09-15 20:23:34.576 wdl.w:ptcp INFO input :: job: "call-sawfish-55", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-55/out/m84036_250809_035451_s4.bc2152.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-55/out/m84036_250809_035451_s4.bc2152.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2152"}
2025-09-15 20:23:34.577 wdl.w:ptcp NOTICE ready :: job: "call-trgt-55", callee: "trgt"
2025-09-15 20:23:34.577 wdl.w:ptcp INFO input :: job: "call-trgt-55", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-55/out/m84036_250809_035451_s4.bc2152.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-55/out/m84036_250809_035451_s4.bc2152.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2152"}
2025-09-15 20:23:34.583 wdl.w:ptcp.t:call-pbmm2_align_hifi-90.slurm_singularity INFO srun: job 51797314 has been allocated resources
2025-09-15 20:23:34.584 wdl.w:ptcp.t:call-pbmm2_align_hifi-90.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:34.590 wdl.w:ptcp.w:call-trgt-12.t:call-trgt_genotype NOTICE task setup :: name: "trgt_genotype", source: "./trgt.wdl", line: 272, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-12/call-trgt_genotype", thread: 140609813722688
2025-09-15 20:23:34.592 wdl.w:ptcp.t:call-pbmm2_align_hifi-93.slurm_singularity INFO srun: job 51797315 has been allocated resources
2025-09-15 20:23:34.593 wdl.w:ptcp.t:call-pbmm2_align_hifi-93.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:34.593 wdl.w:ptcp.t:call-pbmm2_align_hifi-93.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:23:34.616 wdl.w:ptcp.w:call-trgt-12.t:call-trgt_genotype INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:23:34.616 wdl.w:ptcp.w:call-trgt-12.t:call-trgt_genotype INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:23:34.616 wdl.w:ptcp.w:call-trgt-12.t:call-trgt_genotype INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:23:34.616 wdl.w:ptcp.w:call-trgt-12.t:call-trgt_genotype INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:23:34.616 wdl.w:ptcp.w:call-trgt-12.t:call-trgt_genotype INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2109.mapped.bam.bai"
2025-09-15 20:23:34.616 wdl.w:ptcp.w:call-trgt-12.t:call-trgt_genotype INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2109.mapped.bam"
2025-09-15 20:23:34.616 wdl.w:ptcp.w:call-trgt-12.t:call-trgt_genotype INFO input :: name: "sex", value: "F"
2025-09-15 20:23:34.616 wdl.w:ptcp.w:call-trgt-12.t:call-trgt_genotype INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2109"
2025-09-15 20:23:34.616 wdl.w:ptcp.w:call-trgt-12.t:call-trgt_genotype INFO eval :: name: "mem_gb", value: 16
2025-09-15 20:23:34.617 wdl.w:ptcp.w:call-trgt-12.t:call-trgt_genotype INFO eval :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2109.trgt"
2025-09-15 20:23:34.617 wdl.w:ptcp.w:call-trgt-12.t:call-trgt_genotype INFO eval :: name: "threads", value: 8
2025-09-15 20:23:34.617 wdl.w:ptcp.w:call-trgt-12.t:call-trgt_genotype INFO eval :: name: "disk_size", value: 27
2025-09-15 20:23:34.617 wdl.w:ptcp.w:call-trgt-12.t:call-trgt_genotype INFO eval :: name: "karyotype", value: "XX"
2025-09-15 20:23:34.617 wdl.w:ptcp.w:call-trgt-12.t:call-trgt_genotype INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 8, memory_reservation: 16000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:23:34.618 wdl.w:ptcp.w:call-trgt-12.t:call-trgt_genotype WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:23:34.618 wdl.w:ptcp.w:call-trgt-12.t:call-trgt_genotype INFO provisioned :: seconds_waited: 0, cpu: 8, mem_bytes: 16000000000
2025-09-15 20:23:34.618 wdl.w:ptcp.w:call-trgt-12.t:call-trgt_genotype INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:23:34.640 wdl.w:ptcp.w:call-paraphase-06.t:call-run_paraphase.slurm_singularity INFO srun: job 51797399 has been allocated resources
2025-09-15 20:23:34.640 wdl.w:ptcp.w:call-paraphase-06.t:call-run_paraphase.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:34.640 wdl.w:ptcp.w:call-paraphase-06.t:call-run_paraphase.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:23:34.645 wdl.w:ptcp.w:call-trgt-33.t:call-get_reads_overlapping_repeats.slurm_singularity INFO srun: job 51797397 has been allocated resources
2025-09-15 20:23:34.646 wdl.w:ptcp.w:call-paraphase-30.t:call-run_paraphase.slurm_singularity INFO srun: job 51797395 has been allocated resources
2025-09-15 20:23:34.648 wdl.w:ptcp.w:call-trgt-30.t:call-get_reads_overlapping_repeats.slurm_singularity INFO srun: job 51797398 has been allocated resources
2025-09-15 20:23:34.648 wdl.w:ptcp.w:call-trgt-30.t:call-get_reads_overlapping_repeats.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:34.648 wdl.w:ptcp.w:call-trgt-30.t:call-get_reads_overlapping_repeats.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:23:34.655 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_genotype.slurm_singularity INFO srun: job 51797396 has been allocated resources
2025-09-15 20:23:34.676 wdl.w:ptcp.t:call-pbmm2_align_hifi-83.slurm_singularity INFO srun: job 51797317 has been allocated resources
2025-09-15 20:23:34.677 wdl.w:ptcp.t:call-pbmm2_align_hifi-83.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:34.677 wdl.w:ptcp.t:call-pbmm2_align_hifi-83.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:23:34.688 wdl.w:ptcp.t:call-pbmm2_align_hifi-42 INFO output :: name: "mapped_bam", value: "m84036_250809_035451_s4.bc2139.mapped.bam"
2025-09-15 20:23:34.692 wdl.w:ptcp.t:call-pbmm2_align_hifi-42 INFO output :: name: "mapped_bam_bai", value: "m84036_250809_035451_s4.bc2139.mapped.bam.bai"
2025-09-15 20:23:34.692 wdl.w:ptcp.w:call-trgt-12.t:call-trgt_genotype INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 11, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-12/call-trgt_genotype/_singularity_tmpdir_x7l86cde"
2025-09-15 20:23:34.693 wdl.w:ptcp.w:call-trgt-12.t:call-trgt_genotype INFO Slurm invocation: srun --job-name call-trgt_genotype --partition compute,compute9 --cpus-per-task 8 --mem 15259M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-12/call-trgt_genotype/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-12/call-trgt_genotype/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-12/call-trgt_genotype/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-12/call-trgt_genotype/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-12/out/m84036_250809_035451_s4.bc2109.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2109.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-12/out/m84036_250809_035451_s4.bc2109.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2109.mapped.bam:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-12/call-trgt_genotype/_singularity_tmpdir_x7l86cde/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-12/call-trgt_genotype/_singularity_tmpdir_x7l86cde/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:23:34.693 wdl.w:ptcp.t:call-pbmm2_align_hifi-42 INFO output :: name: "mapped_bam_pbi", value: "m84036_250809_035451_s4.bc2139.mapped.bam.pbi"
2025-09-15 20:23:34.696 wdl.w:ptcp.t:call-pbmm2_align_hifi-42 INFO output :: name: "report", value: "mapping_stats.report.json"
2025-09-15 20:23:34.704 wdl.w:ptcp.w:call-sawfish-05.t:call-run_sawfish.slurm_singularity INFO srun: job 51797403 has been allocated resources
2025-09-15 20:23:34.704 wdl.w:ptcp.w:call-sawfish-05.t:call-run_sawfish.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:34.704 wdl.w:ptcp.w:call-sawfish-05.t:call-run_sawfish.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:23:34.706 wdl.w:ptcp.w:call-paraphase-33.t:call-run_paraphase.slurm_singularity INFO srun: job 51797401 has been allocated resources
2025-09-15 20:23:34.706 wdl.w:ptcp.w:call-paraphase-33.t:call-run_paraphase.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:34.706 wdl.w:ptcp.w:call-paraphase-33.t:call-run_paraphase.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:23:34.708 wdl.w:ptcp.w:call-trgt-05.t:call-get_reads_overlapping_repeats.slurm_singularity INFO srun: job 51797400 has been allocated resources
2025-09-15 20:23:34.708 wdl.w:ptcp.w:call-trgt-05.t:call-get_reads_overlapping_repeats.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:34.708 wdl.w:ptcp.w:call-trgt-05.t:call-get_reads_overlapping_repeats.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:23:34.711 wdl.w:ptcp.w:call-trgt-33.t:call-trgt_genotype.slurm_singularity INFO srun: job 51797404 has been allocated resources
2025-09-15 20:23:34.712 wdl.w:ptcp.w:call-trgt-33.t:call-trgt_genotype.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:34.712 wdl.w:ptcp.w:call-trgt-33.t:call-trgt_genotype.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:23:34.724 wdl.w:ptcp.w:call-trgt-30.t:call-trgt_genotype.slurm_singularity INFO srun: job 51797402 has been allocated resources
2025-09-15 20:23:34.760 wdl.w:ptcp.w:call-paraphase-05.t:call-run_paraphase.slurm_singularity INFO srun: job 51797405 has been allocated resources
2025-09-15 20:23:34.760 wdl.w:ptcp.w:call-paraphase-05.t:call-run_paraphase.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:34.760 wdl.w:ptcp.w:call-paraphase-05.t:call-run_paraphase.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:23:34.796 wdl.w:ptcp.w:call-trgt-12.t:call-trgt_genotype NOTICE slurm_singularity run :: pid: 1199625, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-12/call-trgt_genotype/slurm_singularity.log.txt"
2025-09-15 20:23:34.803 wdl.w:ptcp.w:call-trgt-05.t:call-trgt_genotype.slurm_singularity INFO srun: job 51797406 has been allocated resources
2025-09-15 20:23:34.803 wdl.w:ptcp.w:call-trgt-05.t:call-trgt_genotype.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:34.803 wdl.w:ptcp.w:call-trgt-05.t:call-trgt_genotype.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:23:34.807 wdl.w:ptcp.t:call-pbmm2_align_hifi-42 NOTICE done
2025-09-15 20:23:34.814 wdl.w:ptcp NOTICE finish :: job: "call-pbmm2_align_hifi-42"
2025-09-15 20:23:34.815 wdl.w:ptcp INFO output :: job: "call-pbmm2_align_hifi-42", values: {"report": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-42/out/mapping_stats.report.json", "mapped_bam_pbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-42/out/m84036_250809_035451_s4.bc2139.mapped.bam.pbi", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-42/out/m84036_250809_035451_s4.bc2139.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-42/out/m84036_250809_035451_s4.bc2139.mapped.bam"}
2025-09-15 20:23:34.816 wdl.w:ptcp NOTICE ready :: job: "call-paraphase-42", callee: "paraphase"
2025-09-15 20:23:34.816 wdl.w:ptcp INFO input :: job: "call-paraphase-42", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf", "genome_version": "38", "config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-42/out/m84036_250809_035451_s4.bc2139.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-42/out/m84036_250809_035451_s4.bc2139.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2139"}
2025-09-15 20:23:34.817 wdl.w:ptcp NOTICE ready :: job: "call-sawfish-42", callee: "sawfish"
2025-09-15 20:23:34.817 wdl.w:ptcp INFO input :: job: "call-sawfish-42", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-42/out/m84036_250809_035451_s4.bc2139.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-42/out/m84036_250809_035451_s4.bc2139.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2139"}
2025-09-15 20:23:34.818 wdl.w:ptcp NOTICE ready :: job: "call-trgt-42", callee: "trgt"
2025-09-15 20:23:34.818 wdl.w:ptcp INFO input :: job: "call-trgt-42", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-42/out/m84036_250809_035451_s4.bc2139.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-42/out/m84036_250809_035451_s4.bc2139.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2139"}
2025-09-15 20:23:34.824 wdl.w:ptcp.w:call-paraphase-09.t:call-run_paraphase NOTICE task setup :: name: "run_paraphase", source: "./paraphase.wdl", line: 127, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-09/call-run_paraphase", thread: 140610879071808
2025-09-15 20:23:34.843 wdl.w:ptcp.w:call-paraphase-09.t:call-run_paraphase INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:23:34.843 wdl.w:ptcp.w:call-paraphase-09.t:call-run_paraphase INFO input :: name: "annotation_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf"
2025-09-15 20:23:34.843 wdl.w:ptcp.w:call-paraphase-09.t:call-run_paraphase INFO input :: name: "genome_version", value: "38"
2025-09-15 20:23:34.843 wdl.w:ptcp.w:call-paraphase-09.t:call-run_paraphase INFO input :: name: "config_file", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/paraphase_config.GRCh38.yaml"
2025-09-15 20:23:34.843 wdl.w:ptcp.w:call-paraphase-09.t:call-run_paraphase INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:23:34.843 wdl.w:ptcp.w:call-paraphase-09.t:call-run_paraphase INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:23:34.843 wdl.w:ptcp.w:call-paraphase-09.t:call-run_paraphase INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2106.mapped.bam.bai"
2025-09-15 20:23:34.843 wdl.w:ptcp.w:call-paraphase-09.t:call-run_paraphase INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2106.mapped.bam"
2025-09-15 20:23:34.843 wdl.w:ptcp.w:call-paraphase-09.t:call-run_paraphase INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2106"
2025-09-15 20:23:34.844 wdl.w:ptcp.w:call-paraphase-09.t:call-run_paraphase INFO eval :: name: "threads", value: 4
2025-09-15 20:23:34.844 wdl.w:ptcp.w:call-paraphase-09.t:call-run_paraphase INFO eval :: name: "mem_gb", value: 8
2025-09-15 20:23:34.844 wdl.w:ptcp.w:call-paraphase-09.t:call-run_paraphase INFO eval :: name: "disk_size", value: 27
2025-09-15 20:23:34.844 wdl.w:ptcp.w:call-paraphase-09.t:call-run_paraphase INFO eval :: name: "out_dir", value: "m84036_250809_035451_s4.bc2106_paraphase"
2025-09-15 20:23:34.844 wdl.w:ptcp.w:call-paraphase-09.t:call-run_paraphase INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 4, memory_reservation: 8000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:23:34.844 wdl.w:ptcp.w:call-paraphase-09.t:call-run_paraphase WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:23:34.845 wdl.w:ptcp.w:call-paraphase-09.t:call-run_paraphase INFO provisioned :: seconds_waited: 0, cpu: 4, mem_bytes: 8000000000
2025-09-15 20:23:34.845 wdl.w:ptcp.w:call-paraphase-09.t:call-run_paraphase INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:23:34.853 wdl.w:ptcp.w:call-sawfish-33.t:call-run_sawfish.slurm_singularity INFO srun: job 51797393 has been allocated resources
2025-09-15 20:23:34.854 wdl.w:ptcp.w:call-sawfish-33.t:call-run_sawfish.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:34.862 wdl.w:ptcp.w:call-trgt-06.t:call-get_reads_overlapping_repeats.slurm_singularity INFO srun: job 51797394 has been allocated resources
2025-09-15 20:23:34.862 wdl.w:ptcp.w:call-trgt-06.t:call-get_reads_overlapping_repeats.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:34.862 wdl.w:ptcp.w:call-trgt-06.t:call-get_reads_overlapping_repeats.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:23:34.881 wdl.w:ptcp.w:call-paraphase-23.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for f8inv1 for sample m84036_250809_035451_s4.bc2120 at 2025-09-15 20:23:32.645000...
2025-09-15 20:23:34.881 wdl.w:ptcp.w:call-paraphase-23.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for f8inv1 for sample m84036_250809_035451_s4.bc2120 at 2025-09-15 20:23:32.645150...
2025-09-15 20:23:34.898 wdl.w:ptcp.w:call-trgt-29.t:call-trgt_genotype.slurm_singularity INFO srun: job 51797414 queued and waiting for resources
2025-09-15 20:23:34.898 wdl.w:ptcp.w:call-trgt-29.t:call-trgt_genotype.slurm_singularity INFO srun: job 51797414 has been allocated resources
2025-09-15 20:23:34.898 wdl.w:ptcp.w:call-trgt-29.t:call-trgt_genotype.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:34.917 wdl.w:ptcp.w:call-paraphase-09.t:call-run_paraphase INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-09/call-run_paraphase/_singularity_tmpdir_iiueifi7"
2025-09-15 20:23:34.917 wdl.w:ptcp.w:call-paraphase-09.t:call-run_paraphase INFO Slurm invocation: srun --job-name call-run_paraphase --partition compute,compute9 --cpus-per-task 4 --mem 7629M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-09/call-run_paraphase/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-09/call-run_paraphase/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-09/call-run_paraphase/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-09/call-run_paraphase/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-09/out/m84036_250809_035451_s4.bc2106.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2106.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-09/out/m84036_250809_035451_s4.bc2106.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2106.mapped.bam.bai:ro --bind /ptcp/meta/variant_list/variant_list.GRCh38.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf:ro --bind /ptcp/meta/paraphase/paraphase_config.GRCh38.yaml:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/paraphase_config.GRCh38.yaml:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-09/call-run_paraphase/_singularity_tmpdir_iiueifi7/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-09/call-run_paraphase/_singularity_tmpdir_iiueifi7/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:23:34.931 wdl.w:ptcp.w:call-paraphase-13.t:call-run_paraphase.slurm_singularity INFO srun: job 51797407 has been allocated resources
2025-09-15 20:23:34.931 wdl.w:ptcp.w:call-paraphase-13.t:call-run_paraphase.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:34.931 wdl.w:ptcp.w:call-paraphase-13.t:call-run_paraphase.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:23:34.945 wdl.w:ptcp.w:call-paraphase-09.t:call-run_paraphase NOTICE slurm_singularity run :: pid: 1199627, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-09/call-run_paraphase/slurm_singularity.log.txt"
2025-09-15 20:23:34.966 wdl.w:ptcp.w:call-sawfish-13.t:call-run_sawfish.slurm_singularity INFO srun: job 51797408 has been allocated resources
2025-09-15 20:23:34.967 wdl.w:ptcp.w:call-sawfish-13.t:call-run_sawfish.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:34.967 wdl.w:ptcp.w:call-sawfish-13.t:call-run_sawfish.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:23:35.014 wdl.w:ptcp.w:call-trgt-13.t:call-get_reads_overlapping_repeats.slurm_singularity INFO srun: job 51797409 has been allocated resources
2025-09-15 20:23:35.014 wdl.w:ptcp.w:call-trgt-13.t:call-get_reads_overlapping_repeats.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:35.014 wdl.w:ptcp.w:call-trgt-13.t:call-get_reads_overlapping_repeats.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:23:35.029 wdl.w:ptcp.w:call-paraphase-12.t:call-run_paraphase.slurm_singularity INFO srun: job 51797415 queued and waiting for resources
2025-09-15 20:23:35.030 wdl.w:ptcp.w:call-paraphase-12.t:call-run_paraphase.slurm_singularity INFO srun: job 51797415 has been allocated resources
2025-09-15 20:23:35.030 wdl.w:ptcp.w:call-paraphase-12.t:call-run_paraphase.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:35.052 wdl.w:ptcp.w:call-trgt-17.t:call-get_reads_overlapping_repeats INFO output :: name: "reads_overlapping_repeats", value: "m84036_250809_035451_s4.bc2114.repeats.bam"
2025-09-15 20:23:35.055 wdl.w:ptcp.w:call-trgt-17.t:call-get_reads_overlapping_repeats INFO output :: name: "reads_overlapping_repeats_bai", value: "m84036_250809_035451_s4.bc2114.repeats.bam.bai"
2025-09-15 20:23:35.098 wdl.w:ptcp.w:call-paraphase-29.t:call-run_paraphase.slurm_singularity INFO srun: job 51797412 has been allocated resources
2025-09-15 20:23:35.098 wdl.w:ptcp.w:call-paraphase-29.t:call-run_paraphase.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:35.098 wdl.w:ptcp.w:call-paraphase-29.t:call-run_paraphase.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:23:35.113 wdl.w:ptcp.w:call-trgt-17.t:call-get_reads_overlapping_repeats NOTICE done
2025-09-15 20:23:35.117 wdl.w:ptcp.w:call-sawfish-12.t:call-run_sawfish.stderr VERBOSE [M::bam2fq_mainloop] discarded 0 singletons
2025-09-15 20:23:35.117 wdl.w:ptcp.w:call-sawfish-12.t:call-run_sawfish.stderr VERBOSE [M::bam2fq_mainloop] processed 0 reads
2025-09-15 20:23:35.119 wdl.w:ptcp.w:call-trgt-17 NOTICE finish :: job: "call-get_reads_overlapping_repeats"
2025-09-15 20:23:35.119 wdl.w:ptcp.w:call-trgt-17 INFO output :: job: "call-get_reads_overlapping_repeats", values: {"reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-17/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2114.repeats.bam.bai", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-17/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2114.repeats.bam"}
2025-09-15 20:23:35.119 wdl.w:ptcp.w:call-trgt-17 INFO visit :: node: "output-reads_overlapping_repeats", values: {"reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-17/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2114.repeats.bam"}
2025-09-15 20:23:35.119 wdl.w:ptcp.w:call-trgt-17 INFO visit :: node: "output-reads_overlapping_repeats_bai", values: {"reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-17/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2114.repeats.bam.bai"}
2025-09-15 20:23:35.125 wdl.w:ptcp.w:call-sawfish-09.t:call-run_sawfish NOTICE task setup :: name: "run_sawfish", source: "./sawfish.wdl", line: 83, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-09/call-run_sawfish", thread: 140609847293504
2025-09-15 20:23:35.127 wdl.w:ptcp.w:call-sawfish-12.t:call-run_sawfish.slurm_singularity INFO srun: job 51797416 queued and waiting for resources
2025-09-15 20:23:35.127 wdl.w:ptcp.w:call-sawfish-12.t:call-run_sawfish.slurm_singularity INFO srun: job 51797416 has been allocated resources
2025-09-15 20:23:35.127 wdl.w:ptcp.w:call-sawfish-12.t:call-run_sawfish.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:35.127 wdl.w:ptcp.w:call-sawfish-12.t:call-run_sawfish.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:23:35.142 wdl.w:ptcp.w:call-sawfish-09.t:call-run_sawfish INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:23:35.143 wdl.w:ptcp.w:call-sawfish-09.t:call-run_sawfish INFO input :: name: "genome_version", value: "38"
2025-09-15 20:23:35.143 wdl.w:ptcp.w:call-sawfish-09.t:call-run_sawfish INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:23:35.143 wdl.w:ptcp.w:call-sawfish-09.t:call-run_sawfish INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:23:35.143 wdl.w:ptcp.w:call-sawfish-09.t:call-run_sawfish INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2106.mapped.bam.bai"
2025-09-15 20:23:35.143 wdl.w:ptcp.w:call-sawfish-09.t:call-run_sawfish INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2106.mapped.bam"
2025-09-15 20:23:35.143 wdl.w:ptcp.w:call-sawfish-09.t:call-run_sawfish INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2106"
2025-09-15 20:23:35.143 wdl.w:ptcp.w:call-sawfish-09.t:call-run_sawfish INFO eval :: name: "mem_gb", value: 32
2025-09-15 20:23:35.143 wdl.w:ptcp.w:call-sawfish-09.t:call-run_sawfish INFO eval :: name: "threads", value: 16
2025-09-15 20:23:35.143 wdl.w:ptcp.w:call-sawfish-09.t:call-run_sawfish INFO eval :: name: "disk_size", value: 30
2025-09-15 20:23:35.143 wdl.w:ptcp.w:call-sawfish-09.t:call-run_sawfish INFO eval :: name: "discover_dirname", value: "m84036_250809_035451_s4.bc2106_sawfish_discover"
2025-09-15 20:23:35.144 wdl.w:ptcp.w:call-sawfish-09.t:call-run_sawfish INFO eval :: name: "call_dirname", value: "m84036_250809_035451_s4.bc2106_sawfish"
2025-09-15 20:23:35.144 wdl.w:ptcp.w:call-sawfish-09.t:call-run_sawfish INFO eval :: name: "minimap2_bam_filename", value: "m84036_250809_035451_s4.bc2106.minimap2.bam"
2025-09-15 20:23:35.144 wdl.w:ptcp.w:call-sawfish-09.t:call-run_sawfish INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 16, memory_reservation: 32000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:23:35.144 wdl.w:ptcp.w:call-sawfish-09.t:call-run_sawfish WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:23:35.144 wdl.w:ptcp.w:call-sawfish-09.t:call-run_sawfish INFO provisioned :: seconds_waited: 0, cpu: 16, mem_bytes: 32000000000
2025-09-15 20:23:35.145 wdl.w:ptcp.w:call-sawfish-09.t:call-run_sawfish INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:23:35.206 wdl.w:ptcp.w:call-sawfish-09.t:call-run_sawfish INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 10, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-09/call-run_sawfish/_singularity_tmpdir_p5uopcs5"
2025-09-15 20:23:35.206 wdl.w:ptcp.w:call-sawfish-09.t:call-run_sawfish INFO Slurm invocation: srun --job-name call-run_sawfish --partition compute,compute9 --cpus-per-task 16 --mem 30518M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-09/call-run_sawfish/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-09/call-run_sawfish/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-09/call-run_sawfish/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-09/call-run_sawfish/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-09/out/m84036_250809_035451_s4.bc2106.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2106.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-09/out/m84036_250809_035451_s4.bc2106.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2106.mapped.bam.bai:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-09/call-run_sawfish/_singularity_tmpdir_p5uopcs5/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-09/call-run_sawfish/_singularity_tmpdir_p5uopcs5/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:23:35.231 wdl.w:ptcp.w:call-sawfish-09.t:call-run_sawfish NOTICE slurm_singularity run :: pid: 1199640, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-09/call-run_sawfish/slurm_singularity.log.txt"
2025-09-15 20:23:35.247 wdl.w:ptcp.w:call-trgt-13.t:call-trgt_genotype.slurm_singularity INFO srun: job 51797410 has been allocated resources
2025-09-15 20:23:35.247 wdl.w:ptcp.w:call-trgt-13.t:call-trgt_genotype.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:35.247 wdl.w:ptcp.w:call-trgt-13.t:call-trgt_genotype.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:23:35.251 wdl.w:ptcp.w:call-sawfish-06.t:call-run_sawfish.slurm_singularity INFO srun: job 51797391 has been allocated resources
2025-09-15 20:23:35.252 wdl.w:ptcp.w:call-sawfish-06.t:call-run_sawfish.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:35.292 wdl.w:ptcp.w:call-trgt-12.t:call-get_reads_overlapping_repeats.slurm_singularity INFO srun: job 51797417 queued and waiting for resources
2025-09-15 20:23:35.292 wdl.w:ptcp.w:call-trgt-12.t:call-get_reads_overlapping_repeats.slurm_singularity INFO srun: job 51797417 has been allocated resources
2025-09-15 20:23:35.293 wdl.w:ptcp.w:call-trgt-12.t:call-get_reads_overlapping_repeats.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:35.293 wdl.w:ptcp.w:call-trgt-12.t:call-get_reads_overlapping_repeats.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:23:35.344 wdl.w:ptcp.t:call-pbmm2_align_hifi-58 INFO output :: name: "mapped_bam", value: "m84036_250809_035451_s4.bc2155.mapped.bam"
2025-09-15 20:23:35.346 wdl.w:ptcp.t:call-pbmm2_align_hifi-58 INFO output :: name: "mapped_bam_bai", value: "m84036_250809_035451_s4.bc2155.mapped.bam.bai"
2025-09-15 20:23:35.347 wdl.w:ptcp.t:call-pbmm2_align_hifi-58 INFO output :: name: "mapped_bam_pbi", value: "m84036_250809_035451_s4.bc2155.mapped.bam.pbi"
2025-09-15 20:23:35.348 wdl.w:ptcp.t:call-pbmm2_align_hifi-58 INFO output :: name: "report", value: "mapping_stats.report.json"
2025-09-15 20:23:35.442 wdl.w:ptcp.t:call-pbmm2_align_hifi-58 NOTICE done
2025-09-15 20:23:35.450 wdl.w:ptcp NOTICE finish :: job: "call-pbmm2_align_hifi-58"
2025-09-15 20:23:35.450 wdl.w:ptcp INFO output :: job: "call-pbmm2_align_hifi-58", values: {"report": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-58/out/mapping_stats.report.json", "mapped_bam_pbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-58/out/m84036_250809_035451_s4.bc2155.mapped.bam.pbi", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-58/out/m84036_250809_035451_s4.bc2155.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-58/out/m84036_250809_035451_s4.bc2155.mapped.bam"}
2025-09-15 20:23:35.451 wdl.w:ptcp NOTICE ready :: job: "call-paraphase-58", callee: "paraphase"
2025-09-15 20:23:35.451 wdl.w:ptcp INFO input :: job: "call-paraphase-58", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf", "genome_version": "38", "config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-58/out/m84036_250809_035451_s4.bc2155.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-58/out/m84036_250809_035451_s4.bc2155.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2155"}
2025-09-15 20:23:35.452 wdl.w:ptcp NOTICE ready :: job: "call-sawfish-58", callee: "sawfish"
2025-09-15 20:23:35.452 wdl.w:ptcp INFO input :: job: "call-sawfish-58", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-58/out/m84036_250809_035451_s4.bc2155.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-58/out/m84036_250809_035451_s4.bc2155.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2155"}
2025-09-15 20:23:35.453 wdl.w:ptcp NOTICE ready :: job: "call-trgt-58", callee: "trgt"
2025-09-15 20:23:35.453 wdl.w:ptcp INFO input :: job: "call-trgt-58", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-58/out/m84036_250809_035451_s4.bc2155.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-58/out/m84036_250809_035451_s4.bc2155.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2155"}
2025-09-15 20:23:35.455 wdl.w:ptcp.w:call-trgt-30.t:call-trgt_genotype.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:35.455 wdl.w:ptcp.w:call-trgt-30.t:call-trgt_genotype.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:23:35.464 wdl.w:ptcp.w:call-trgt-09.t:call-get_reads_overlapping_repeats NOTICE task setup :: name: "get_reads_overlapping_repeats", source: "./trgt.wdl", line: 182, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-09/call-get_reads_overlapping_repeats", thread: 140609310422592
2025-09-15 20:23:35.496 wdl.w:ptcp.w:call-trgt-30.t:call-trgt_genotype INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2127.trgt.vcf"
2025-09-15 20:23:35.500 wdl.w:ptcp.w:call-trgt-30.t:call-trgt_genotype INFO output :: name: "spanning_bam", value: "m84036_250809_035451_s4.bc2127.trgt.sorted.spanning.bam"
2025-09-15 20:23:35.501 wdl.w:ptcp.w:call-trgt-30.t:call-trgt_genotype INFO output :: name: "spanning_bam_bai", value: "m84036_250809_035451_s4.bc2127.trgt.sorted.spanning.bam.bai"
2025-09-15 20:23:35.504 wdl.w:ptcp.w:call-sawfish-30.t:call-run_sawfish.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:35.509 wdl.w:ptcp.w:call-trgt-09.t:call-get_reads_overlapping_repeats INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:23:35.509 wdl.w:ptcp.w:call-trgt-09.t:call-get_reads_overlapping_repeats INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:23:35.509 wdl.w:ptcp.w:call-trgt-09.t:call-get_reads_overlapping_repeats INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2106.mapped.bam.bai"
2025-09-15 20:23:35.509 wdl.w:ptcp.w:call-trgt-09.t:call-get_reads_overlapping_repeats INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2106.mapped.bam"
2025-09-15 20:23:35.509 wdl.w:ptcp.w:call-trgt-09.t:call-get_reads_overlapping_repeats INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2106"
2025-09-15 20:23:35.510 wdl.w:ptcp.w:call-trgt-09.t:call-get_reads_overlapping_repeats INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:23:35.510 wdl.w:ptcp.w:call-trgt-09.t:call-get_reads_overlapping_repeats INFO eval :: name: "expand_size", value: 3000
2025-09-15 20:23:35.510 wdl.w:ptcp.w:call-trgt-09.t:call-get_reads_overlapping_repeats INFO eval :: name: "threads", value: 1
2025-09-15 20:23:35.510 wdl.w:ptcp.w:call-trgt-09.t:call-get_reads_overlapping_repeats INFO eval :: name: "expanded_bed_name", value: "m84036_250809_035451_s4.bc2106.expanded.bed"
2025-09-15 20:23:35.510 wdl.w:ptcp.w:call-trgt-09.t:call-get_reads_overlapping_repeats INFO eval :: name: "disk_size", value: 11
2025-09-15 20:23:35.510 wdl.w:ptcp.w:call-trgt-09.t:call-get_reads_overlapping_repeats INFO eval :: name: "output_name", value: "m84036_250809_035451_s4.bc2106.repeats.bam"
2025-09-15 20:23:35.510 wdl.w:ptcp.w:call-trgt-09.t:call-get_reads_overlapping_repeats INFO eval :: name: "index_name", value: "m84036_250809_035451_s4.bc2106.repeats.bam.bai"
2025-09-15 20:23:35.511 wdl.w:ptcp.w:call-trgt-09.t:call-get_reads_overlapping_repeats INFO eval :: name: "output_name_with_index", value: "m84036_250809_035451_s4.bc2106.repeats.bam##idx##m84036_250809_035451_s4.bc2106.repeats.bam.bai"
2025-09-15 20:23:35.511 wdl.w:ptcp.w:call-trgt-09.t:call-get_reads_overlapping_repeats INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:23:35.511 wdl.w:ptcp.w:call-trgt-09.t:call-get_reads_overlapping_repeats WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:23:35.512 wdl.w:ptcp.w:call-trgt-09.t:call-get_reads_overlapping_repeats INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:23:35.512 wdl.w:ptcp.w:call-trgt-09.t:call-get_reads_overlapping_repeats INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:23:35.516 wdl.w:ptcp.w:call-sawfish-29.t:call-run_sawfish.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:35.516 wdl.w:ptcp.w:call-sawfish-29.t:call-run_sawfish.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:23:35.578 wdl.w:ptcp.w:call-trgt-29.t:call-get_reads_overlapping_repeats.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:35.578 wdl.w:ptcp.w:call-trgt-29.t:call-get_reads_overlapping_repeats.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:23:35.603 wdl.w:ptcp.w:call-trgt-09.t:call-get_reads_overlapping_repeats INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 9, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-09/call-get_reads_overlapping_repeats/_singularity_tmpdir_a6cl5qq_"
2025-09-15 20:23:35.603 wdl.w:ptcp.w:call-trgt-09.t:call-get_reads_overlapping_repeats INFO Slurm invocation: srun --job-name call-get_reads_overlapping_repeats --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-09/call-get_reads_overlapping_repeats/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-09/call-get_reads_overlapping_repeats/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-09/call-get_reads_overlapping_repeats/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-09/call-get_reads_overlapping_repeats/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-09/out/m84036_250809_035451_s4.bc2106.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2106.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-09/out/m84036_250809_035451_s4.bc2106.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2106.mapped.bam.bai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-09/call-get_reads_overlapping_repeats/_singularity_tmpdir_a6cl5qq_/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-09/call-get_reads_overlapping_repeats/_singularity_tmpdir_a6cl5qq_/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:23:35.605 wdl.w:ptcp.w:call-trgt-21.t:call-get_reads_overlapping_repeats INFO output :: name: "reads_overlapping_repeats", value: "m84036_250809_035451_s4.bc2118.repeats.bam"
2025-09-15 20:23:35.614 wdl.w:ptcp.w:call-trgt-21.t:call-get_reads_overlapping_repeats INFO output :: name: "reads_overlapping_repeats_bai", value: "m84036_250809_035451_s4.bc2118.repeats.bam.bai"
2025-09-15 20:23:35.634 wdl.w:ptcp.w:call-trgt-30.t:call-trgt_genotype NOTICE done
2025-09-15 20:23:35.638 wdl.w:ptcp.w:call-trgt-30 NOTICE finish :: job: "call-trgt_genotype"
2025-09-15 20:23:35.639 wdl.w:ptcp.w:call-trgt-30 INFO output :: job: "call-trgt_genotype", values: {"spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-30/call-trgt_genotype/out/m84036_250809_035451_s4.bc2127.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-30/call-trgt_genotype/out/m84036_250809_035451_s4.bc2127.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-30/call-trgt_genotype/out/m84036_250809_035451_s4.bc2127.trgt.vcf"}
2025-09-15 20:23:35.639 wdl.w:ptcp.w:call-trgt-30 NOTICE ready :: job: "call-trgt_plot_meth_allele", callee: "trgt_plot"
2025-09-15 20:23:35.639 wdl.w:ptcp.w:call-trgt-30 INFO input :: job: "call-trgt_plot_meth_allele", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": false, "methylation": true, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-30/call-trgt_genotype/out/m84036_250809_035451_s4.bc2127.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-30/call-trgt_genotype/out/m84036_250809_035451_s4.bc2127.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-30/call-trgt_genotype/out/m84036_250809_035451_s4.bc2127.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2127"}
2025-09-15 20:23:35.640 wdl.w:ptcp.w:call-trgt-30 NOTICE ready :: job: "call-trgt_plot_meth_waterfall", callee: "trgt_plot"
2025-09-15 20:23:35.640 wdl.w:ptcp.w:call-trgt-30 INFO input :: job: "call-trgt_plot_meth_waterfall", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": true, "methylation": true, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-30/call-trgt_genotype/out/m84036_250809_035451_s4.bc2127.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-30/call-trgt_genotype/out/m84036_250809_035451_s4.bc2127.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-30/call-trgt_genotype/out/m84036_250809_035451_s4.bc2127.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2127"}
2025-09-15 20:23:35.641 wdl.w:ptcp.w:call-trgt-30 NOTICE ready :: job: "call-trgt_plot_motifs_allele", callee: "trgt_plot"
2025-09-15 20:23:35.644 wdl.w:ptcp.w:call-trgt-30 INFO input :: job: "call-trgt_plot_motifs_allele", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": false, "methylation": false, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-30/call-trgt_genotype/out/m84036_250809_035451_s4.bc2127.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-30/call-trgt_genotype/out/m84036_250809_035451_s4.bc2127.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-30/call-trgt_genotype/out/m84036_250809_035451_s4.bc2127.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2127"}
2025-09-15 20:23:35.645 wdl.w:ptcp.w:call-trgt-30 NOTICE ready :: job: "call-trgt_plot_motifs_waterfall", callee: "trgt_plot"
2025-09-15 20:23:35.645 wdl.w:ptcp.w:call-trgt-30 INFO input :: job: "call-trgt_plot_motifs_waterfall", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": true, "methylation": false, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-30/call-trgt_genotype/out/m84036_250809_035451_s4.bc2127.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-30/call-trgt_genotype/out/m84036_250809_035451_s4.bc2127.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-30/call-trgt_genotype/out/m84036_250809_035451_s4.bc2127.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2127"}
2025-09-15 20:23:35.645 wdl.w:ptcp.w:call-trgt-30 INFO visit :: node: "output-spanning_bam", values: {"spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-30/call-trgt_genotype/out/m84036_250809_035451_s4.bc2127.trgt.sorted.spanning.bam"}
2025-09-15 20:23:35.646 wdl.w:ptcp.w:call-trgt-30 INFO visit :: node: "output-spanning_bam_bai", values: {"spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-30/call-trgt_genotype/out/m84036_250809_035451_s4.bc2127.trgt.sorted.spanning.bam.bai"}
2025-09-15 20:23:35.646 wdl.w:ptcp.w:call-trgt-30 INFO visit :: node: "output-vcf", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-30/call-trgt_genotype/out/m84036_250809_035451_s4.bc2127.trgt.vcf"}
2025-09-15 20:23:35.649 wdl.w:ptcp.w:call-trgt-09.t:call-trgt_genotype NOTICE task setup :: name: "trgt_genotype", source: "./trgt.wdl", line: 272, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-09/call-trgt_genotype", thread: 140613838284352
2025-09-15 20:23:35.655 wdl.w:ptcp.w:call-trgt-09.t:call-get_reads_overlapping_repeats NOTICE slurm_singularity run :: pid: 1199650, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-09/call-get_reads_overlapping_repeats/slurm_singularity.log.txt"
2025-09-15 20:23:35.661 wdl.w:ptcp.w:call-trgt-33.t:call-get_reads_overlapping_repeats.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:35.662 wdl.w:ptcp.w:call-trgt-33.t:call-get_reads_overlapping_repeats.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:23:35.671 wdl.w:ptcp.w:call-trgt-09.t:call-trgt_genotype INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:23:35.671 wdl.w:ptcp.w:call-trgt-09.t:call-trgt_genotype INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:23:35.671 wdl.w:ptcp.w:call-trgt-09.t:call-trgt_genotype INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:23:35.671 wdl.w:ptcp.w:call-trgt-09.t:call-trgt_genotype INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:23:35.671 wdl.w:ptcp.w:call-trgt-09.t:call-trgt_genotype INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2106.mapped.bam.bai"
2025-09-15 20:23:35.672 wdl.w:ptcp.w:call-trgt-09.t:call-trgt_genotype INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2106.mapped.bam"
2025-09-15 20:23:35.672 wdl.w:ptcp.w:call-trgt-09.t:call-trgt_genotype INFO input :: name: "sex", value: "F"
2025-09-15 20:23:35.672 wdl.w:ptcp.w:call-trgt-09.t:call-trgt_genotype INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2106"
2025-09-15 20:23:35.673 wdl.w:ptcp.w:call-trgt-09.t:call-trgt_genotype INFO eval :: name: "mem_gb", value: 16
2025-09-15 20:23:35.673 wdl.w:ptcp.w:call-trgt-09.t:call-trgt_genotype INFO eval :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2106.trgt"
2025-09-15 20:23:35.673 wdl.w:ptcp.w:call-trgt-09.t:call-trgt_genotype INFO eval :: name: "threads", value: 8
2025-09-15 20:23:35.674 wdl.w:ptcp.w:call-trgt-09.t:call-trgt_genotype INFO eval :: name: "disk_size", value: 27
2025-09-15 20:23:35.674 wdl.w:ptcp.w:call-trgt-09.t:call-trgt_genotype INFO eval :: name: "karyotype", value: "XX"
2025-09-15 20:23:35.674 wdl.w:ptcp.w:call-trgt-09.t:call-trgt_genotype INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 8, memory_reservation: 16000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:23:35.674 wdl.w:ptcp.w:call-trgt-09.t:call-trgt_genotype WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:23:35.675 wdl.w:ptcp.w:call-trgt-09.t:call-trgt_genotype INFO provisioned :: seconds_waited: 0, cpu: 8, mem_bytes: 16000000000
2025-09-15 20:23:35.675 wdl.w:ptcp.w:call-trgt-09.t:call-trgt_genotype INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:23:35.676 wdl.w:ptcp.w:call-paraphase-14.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for f8inv1 for sample m84036_250809_035451_s4.bc2111 at 2025-09-15 20:23:26.680274...
2025-09-15 20:23:35.678 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_genotype.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:35.680 wdl.w:ptcp.w:call-paraphase-30.t:call-run_paraphase.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:35.681 wdl.w:ptcp.w:call-paraphase-30.t:call-run_paraphase.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:23:35.699 wdl.w:ptcp.w:call-trgt-30.t:call-get_reads_overlapping_repeats INFO output :: name: "reads_overlapping_repeats", value: "m84036_250809_035451_s4.bc2127.repeats.bam"
2025-09-15 20:23:35.705 wdl.w:ptcp.w:call-trgt-30.t:call-get_reads_overlapping_repeats INFO output :: name: "reads_overlapping_repeats_bai", value: "m84036_250809_035451_s4.bc2127.repeats.bam.bai"
2025-09-15 20:23:35.716 wdl.w:ptcp.w:call-sawfish-05.t:call-run_sawfish.stderr VERBOSE [M::bam2fq_mainloop] discarded 0 singletons
2025-09-15 20:23:35.716 wdl.w:ptcp.w:call-sawfish-05.t:call-run_sawfish.stderr VERBOSE [M::bam2fq_mainloop] processed 0 reads
2025-09-15 20:23:35.721 wdl.w:ptcp.w:call-trgt-21.t:call-get_reads_overlapping_repeats NOTICE done
2025-09-15 20:23:35.727 wdl.w:ptcp.w:call-trgt-21 NOTICE finish :: job: "call-get_reads_overlapping_repeats"
2025-09-15 20:23:35.727 wdl.w:ptcp.w:call-trgt-21 INFO output :: job: "call-get_reads_overlapping_repeats", values: {"reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-21/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2118.repeats.bam.bai", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-21/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2118.repeats.bam"}
2025-09-15 20:23:35.727 wdl.w:ptcp.w:call-trgt-21 INFO visit :: node: "output-reads_overlapping_repeats", values: {"reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-21/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2118.repeats.bam"}
2025-09-15 20:23:35.727 wdl.w:ptcp.w:call-trgt-21 INFO visit :: node: "output-reads_overlapping_repeats_bai", values: {"reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-21/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2118.repeats.bam.bai"}
2025-09-15 20:23:35.747 wdl.w:ptcp.w:call-paraphase-24.t:call-run_paraphase NOTICE task setup :: name: "run_paraphase", source: "./paraphase.wdl", line: 127, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-24/call-run_paraphase", thread: 140609838900800
2025-09-15 20:23:35.759 wdl.w:ptcp.t:call-pbmm2_align_hifi-61 INFO output :: name: "mapped_bam", value: "m84036_250809_035451_s4.bc2158.mapped.bam"
2025-09-15 20:23:35.763 wdl.w:ptcp.t:call-pbmm2_align_hifi-61 INFO output :: name: "mapped_bam_bai", value: "m84036_250809_035451_s4.bc2158.mapped.bam.bai"
2025-09-15 20:23:35.764 wdl.w:ptcp.t:call-pbmm2_align_hifi-61 INFO output :: name: "mapped_bam_pbi", value: "m84036_250809_035451_s4.bc2158.mapped.bam.pbi"
2025-09-15 20:23:35.766 wdl.w:ptcp.t:call-pbmm2_align_hifi-61 INFO output :: name: "report", value: "mapping_stats.report.json"
2025-09-15 20:23:35.772 wdl.w:ptcp.w:call-paraphase-24.t:call-run_paraphase INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:23:35.772 wdl.w:ptcp.w:call-paraphase-24.t:call-run_paraphase INFO input :: name: "annotation_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf"
2025-09-15 20:23:35.773 wdl.w:ptcp.w:call-paraphase-24.t:call-run_paraphase INFO input :: name: "genome_version", value: "38"
2025-09-15 20:23:35.773 wdl.w:ptcp.w:call-paraphase-24.t:call-run_paraphase INFO input :: name: "config_file", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/paraphase_config.GRCh38.yaml"
2025-09-15 20:23:35.773 wdl.w:ptcp.w:call-paraphase-24.t:call-run_paraphase INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:23:35.773 wdl.w:ptcp.w:call-paraphase-24.t:call-run_paraphase INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:23:35.773 wdl.w:ptcp.w:call-paraphase-24.t:call-run_paraphase INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2121.mapped.bam.bai"
2025-09-15 20:23:35.773 wdl.w:ptcp.w:call-paraphase-24.t:call-run_paraphase INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2121.mapped.bam"
2025-09-15 20:23:35.773 wdl.w:ptcp.w:call-paraphase-24.t:call-run_paraphase INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2121"
2025-09-15 20:23:35.773 wdl.w:ptcp.w:call-paraphase-24.t:call-run_paraphase INFO eval :: name: "threads", value: 4
2025-09-15 20:23:35.773 wdl.w:ptcp.w:call-paraphase-24.t:call-run_paraphase INFO eval :: name: "mem_gb", value: 8
2025-09-15 20:23:35.773 wdl.w:ptcp.w:call-paraphase-24.t:call-run_paraphase INFO eval :: name: "disk_size", value: 27
2025-09-15 20:23:35.774 wdl.w:ptcp.w:call-paraphase-24.t:call-run_paraphase INFO eval :: name: "out_dir", value: "m84036_250809_035451_s4.bc2121_paraphase"
2025-09-15 20:23:35.774 wdl.w:ptcp.w:call-paraphase-24.t:call-run_paraphase INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 4, memory_reservation: 8000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:23:35.774 wdl.w:ptcp.w:call-paraphase-24.t:call-run_paraphase WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:23:35.775 wdl.w:ptcp.w:call-paraphase-24.t:call-run_paraphase INFO provisioned :: seconds_waited: 0, cpu: 4, mem_bytes: 8000000000
2025-09-15 20:23:35.775 wdl.w:ptcp.w:call-paraphase-24.t:call-run_paraphase INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:23:35.779 wdl.w:ptcp.w:call-trgt-09.t:call-trgt_genotype INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 11, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-09/call-trgt_genotype/_singularity_tmpdir_dtj3xfz5"
2025-09-15 20:23:35.780 wdl.w:ptcp.w:call-trgt-09.t:call-trgt_genotype INFO Slurm invocation: srun --job-name call-trgt_genotype --partition compute,compute9 --cpus-per-task 8 --mem 15259M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-09/call-trgt_genotype/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-09/call-trgt_genotype/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-09/call-trgt_genotype/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-09/call-trgt_genotype/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-09/out/m84036_250809_035451_s4.bc2106.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2106.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-09/out/m84036_250809_035451_s4.bc2106.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2106.mapped.bam.bai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-09/call-trgt_genotype/_singularity_tmpdir_dtj3xfz5/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-09/call-trgt_genotype/_singularity_tmpdir_dtj3xfz5/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:23:35.805 wdl.w:ptcp.w:call-trgt-30.t:call-get_reads_overlapping_repeats NOTICE done
2025-09-15 20:23:35.811 wdl.w:ptcp.w:call-trgt-30 NOTICE finish :: job: "call-get_reads_overlapping_repeats"
2025-09-15 20:23:35.811 wdl.w:ptcp.w:call-trgt-12.t:call-trgt_genotype.slurm_singularity INFO srun: job 51797418 queued and waiting for resources
2025-09-15 20:23:35.811 wdl.w:ptcp.w:call-trgt-30 INFO output :: job: "call-get_reads_overlapping_repeats", values: {"reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-30/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2127.repeats.bam.bai", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-30/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2127.repeats.bam"}
2025-09-15 20:23:35.812 wdl.w:ptcp.w:call-trgt-12.t:call-trgt_genotype.slurm_singularity INFO srun: job 51797418 has been allocated resources
2025-09-15 20:23:35.812 wdl.w:ptcp.w:call-trgt-30 INFO visit :: node: "output-reads_overlapping_repeats", values: {"reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-30/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2127.repeats.bam"}
2025-09-15 20:23:35.812 wdl.w:ptcp.w:call-trgt-12.t:call-trgt_genotype.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:35.812 wdl.w:ptcp.w:call-trgt-30 INFO visit :: node: "output-reads_overlapping_repeats_bai", values: {"reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-30/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2127.repeats.bam.bai"}
2025-09-15 20:23:35.813 wdl.w:ptcp.w:call-trgt-09.t:call-trgt_genotype NOTICE slurm_singularity run :: pid: 1199659, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-09/call-trgt_genotype/slurm_singularity.log.txt"
2025-09-15 20:23:35.820 wdl.w:ptcp.w:call-sawfish-24.t:call-run_sawfish NOTICE task setup :: name: "run_sawfish", source: "./sawfish.wdl", line: 83, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-24/call-run_sawfish", thread: 140609276851776
2025-09-15 20:23:35.844 wdl.w:ptcp.w:call-sawfish-24.t:call-run_sawfish INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:23:35.844 wdl.w:ptcp.w:call-sawfish-24.t:call-run_sawfish INFO input :: name: "genome_version", value: "38"
2025-09-15 20:23:35.844 wdl.w:ptcp.w:call-sawfish-24.t:call-run_sawfish INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:23:35.844 wdl.w:ptcp.w:call-sawfish-24.t:call-run_sawfish INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:23:35.844 wdl.w:ptcp.w:call-sawfish-24.t:call-run_sawfish INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2121.mapped.bam.bai"
2025-09-15 20:23:35.844 wdl.w:ptcp.w:call-sawfish-24.t:call-run_sawfish INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2121.mapped.bam"
2025-09-15 20:23:35.844 wdl.w:ptcp.w:call-sawfish-24.t:call-run_sawfish INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2121"
2025-09-15 20:23:35.845 wdl.w:ptcp.w:call-sawfish-24.t:call-run_sawfish INFO eval :: name: "mem_gb", value: 32
2025-09-15 20:23:35.845 wdl.w:ptcp.w:call-sawfish-24.t:call-run_sawfish INFO eval :: name: "threads", value: 16
2025-09-15 20:23:35.845 wdl.w:ptcp.w:call-sawfish-24.t:call-run_sawfish INFO eval :: name: "disk_size", value: 30
2025-09-15 20:23:35.845 wdl.w:ptcp.w:call-sawfish-24.t:call-run_sawfish INFO eval :: name: "discover_dirname", value: "m84036_250809_035451_s4.bc2121_sawfish_discover"
2025-09-15 20:23:35.845 wdl.w:ptcp.w:call-sawfish-24.t:call-run_sawfish INFO eval :: name: "call_dirname", value: "m84036_250809_035451_s4.bc2121_sawfish"
2025-09-15 20:23:35.845 wdl.w:ptcp.w:call-sawfish-24.t:call-run_sawfish INFO eval :: name: "minimap2_bam_filename", value: "m84036_250809_035451_s4.bc2121.minimap2.bam"
2025-09-15 20:23:35.846 wdl.w:ptcp.w:call-sawfish-24.t:call-run_sawfish INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 16, memory_reservation: 32000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:23:35.846 wdl.w:ptcp.w:call-sawfish-24.t:call-run_sawfish WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:23:35.846 wdl.w:ptcp.w:call-sawfish-24.t:call-run_sawfish INFO provisioned :: seconds_waited: 0, cpu: 16, mem_bytes: 32000000000
2025-09-15 20:23:35.846 wdl.w:ptcp.w:call-sawfish-24.t:call-run_sawfish INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:23:35.864 wdl.w:ptcp.w:call-paraphase-24.t:call-run_paraphase INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-24/call-run_paraphase/_singularity_tmpdir_vxxjfxyi"
2025-09-15 20:23:35.865 wdl.w:ptcp.w:call-paraphase-24.t:call-run_paraphase INFO Slurm invocation: srun --job-name call-run_paraphase --partition compute,compute9 --cpus-per-task 4 --mem 7629M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-24/call-run_paraphase/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-24/call-run_paraphase/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-24/call-run_paraphase/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-24/call-run_paraphase/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/variant_list/variant_list.GRCh38.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-24/out/m84036_250809_035451_s4.bc2121.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2121.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-24/out/m84036_250809_035451_s4.bc2121.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2121.mapped.bam:ro --bind /ptcp/meta/paraphase/paraphase_config.GRCh38.yaml:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/paraphase_config.GRCh38.yaml:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-24/call-run_paraphase/_singularity_tmpdir_vxxjfxyi/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-24/call-run_paraphase/_singularity_tmpdir_vxxjfxyi/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:23:35.868 wdl.w:ptcp.t:call-pbmm2_align_hifi-61 NOTICE done
2025-09-15 20:23:35.871 wdl.w:ptcp NOTICE finish :: job: "call-pbmm2_align_hifi-61"
2025-09-15 20:23:35.872 wdl.w:ptcp INFO output :: job: "call-pbmm2_align_hifi-61", values: {"report": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-61/out/mapping_stats.report.json", "mapped_bam_pbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-61/out/m84036_250809_035451_s4.bc2158.mapped.bam.pbi", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-61/out/m84036_250809_035451_s4.bc2158.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-61/out/m84036_250809_035451_s4.bc2158.mapped.bam"}
2025-09-15 20:23:35.872 wdl.w:ptcp NOTICE ready :: job: "call-paraphase-61", callee: "paraphase"
2025-09-15 20:23:35.872 wdl.w:ptcp INFO input :: job: "call-paraphase-61", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf", "genome_version": "38", "config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-61/out/m84036_250809_035451_s4.bc2158.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-61/out/m84036_250809_035451_s4.bc2158.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2158"}
2025-09-15 20:23:35.873 wdl.w:ptcp NOTICE ready :: job: "call-sawfish-61", callee: "sawfish"
2025-09-15 20:23:35.873 wdl.w:ptcp INFO input :: job: "call-sawfish-61", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-61/out/m84036_250809_035451_s4.bc2158.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-61/out/m84036_250809_035451_s4.bc2158.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2158"}
2025-09-15 20:23:35.874 wdl.w:ptcp NOTICE ready :: job: "call-trgt-61", callee: "trgt"
2025-09-15 20:23:35.874 wdl.w:ptcp INFO input :: job: "call-trgt-61", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-61/out/m84036_250809_035451_s4.bc2158.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-61/out/m84036_250809_035451_s4.bc2158.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2158"}
2025-09-15 20:23:35.879 wdl.w:ptcp.w:call-trgt-24.t:call-get_reads_overlapping_repeats NOTICE task setup :: name: "get_reads_overlapping_repeats", source: "./trgt.wdl", line: 182, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-24/call-get_reads_overlapping_repeats", thread: 140609285244480
2025-09-15 20:23:35.890 wdl.w:ptcp.w:call-paraphase-24.t:call-run_paraphase NOTICE slurm_singularity run :: pid: 1199661, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-24/call-run_paraphase/slurm_singularity.log.txt"
2025-09-15 20:23:35.899 wdl.w:ptcp.w:call-trgt-24.t:call-get_reads_overlapping_repeats INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:23:35.899 wdl.w:ptcp.w:call-trgt-24.t:call-get_reads_overlapping_repeats INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:23:35.899 wdl.w:ptcp.w:call-trgt-24.t:call-get_reads_overlapping_repeats INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2121.mapped.bam.bai"
2025-09-15 20:23:35.899 wdl.w:ptcp.w:call-trgt-24.t:call-get_reads_overlapping_repeats INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2121.mapped.bam"
2025-09-15 20:23:35.899 wdl.w:ptcp.w:call-trgt-24.t:call-get_reads_overlapping_repeats INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2121"
2025-09-15 20:23:35.900 wdl.w:ptcp.w:call-trgt-24.t:call-get_reads_overlapping_repeats INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:23:35.900 wdl.w:ptcp.w:call-trgt-24.t:call-get_reads_overlapping_repeats INFO eval :: name: "expand_size", value: 3000
2025-09-15 20:23:35.900 wdl.w:ptcp.w:call-trgt-24.t:call-get_reads_overlapping_repeats INFO eval :: name: "threads", value: 1
2025-09-15 20:23:35.900 wdl.w:ptcp.w:call-trgt-24.t:call-get_reads_overlapping_repeats INFO eval :: name: "expanded_bed_name", value: "m84036_250809_035451_s4.bc2121.expanded.bed"
2025-09-15 20:23:35.900 wdl.w:ptcp.w:call-trgt-24.t:call-get_reads_overlapping_repeats INFO eval :: name: "disk_size", value: 11
2025-09-15 20:23:35.900 wdl.w:ptcp.w:call-trgt-24.t:call-get_reads_overlapping_repeats INFO eval :: name: "output_name", value: "m84036_250809_035451_s4.bc2121.repeats.bam"
2025-09-15 20:23:35.900 wdl.w:ptcp.w:call-trgt-24.t:call-get_reads_overlapping_repeats INFO eval :: name: "index_name", value: "m84036_250809_035451_s4.bc2121.repeats.bam.bai"
2025-09-15 20:23:35.900 wdl.w:ptcp.w:call-trgt-24.t:call-get_reads_overlapping_repeats INFO eval :: name: "output_name_with_index", value: "m84036_250809_035451_s4.bc2121.repeats.bam##idx##m84036_250809_035451_s4.bc2121.repeats.bam.bai"
2025-09-15 20:23:35.901 wdl.w:ptcp.w:call-trgt-24.t:call-get_reads_overlapping_repeats INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:23:35.901 wdl.w:ptcp.w:call-trgt-24.t:call-get_reads_overlapping_repeats WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:23:35.901 wdl.w:ptcp.w:call-trgt-24.t:call-get_reads_overlapping_repeats INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:23:35.901 wdl.w:ptcp.w:call-trgt-24.t:call-get_reads_overlapping_repeats INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:23:35.909 wdl.w:ptcp.w:call-sawfish-24.t:call-run_sawfish INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 10, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-24/call-run_sawfish/_singularity_tmpdir_kudq2ueh"
2025-09-15 20:23:35.909 wdl.w:ptcp.w:call-sawfish-24.t:call-run_sawfish INFO Slurm invocation: srun --job-name call-run_sawfish --partition compute,compute9 --cpus-per-task 16 --mem 30518M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-24/call-run_sawfish/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-24/call-run_sawfish/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-24/call-run_sawfish/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-24/call-run_sawfish/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-24/out/m84036_250809_035451_s4.bc2121.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2121.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-24/out/m84036_250809_035451_s4.bc2121.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2121.mapped.bam:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-24/call-run_sawfish/_singularity_tmpdir_kudq2ueh/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-24/call-run_sawfish/_singularity_tmpdir_kudq2ueh/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:23:35.922 wdl.w:ptcp.w:call-sawfish-24.t:call-run_sawfish NOTICE slurm_singularity run :: pid: 1199663, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-24/call-run_sawfish/slurm_singularity.log.txt"
2025-09-15 20:23:35.954 wdl.w:ptcp.w:call-trgt-24.t:call-get_reads_overlapping_repeats INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 9, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-24/call-get_reads_overlapping_repeats/_singularity_tmpdir_rfp5fcvs"
2025-09-15 20:23:35.955 wdl.w:ptcp.w:call-paraphase-09.t:call-run_paraphase.slurm_singularity INFO srun: job 51797419 queued and waiting for resources
2025-09-15 20:23:35.955 wdl.w:ptcp.w:call-trgt-24.t:call-get_reads_overlapping_repeats INFO Slurm invocation: srun --job-name call-get_reads_overlapping_repeats --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-24/call-get_reads_overlapping_repeats/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-24/call-get_reads_overlapping_repeats/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-24/call-get_reads_overlapping_repeats/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-24/call-get_reads_overlapping_repeats/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-24/out/m84036_250809_035451_s4.bc2121.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2121.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-24/out/m84036_250809_035451_s4.bc2121.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2121.mapped.bam:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-24/call-get_reads_overlapping_repeats/_singularity_tmpdir_rfp5fcvs/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-24/call-get_reads_overlapping_repeats/_singularity_tmpdir_rfp5fcvs/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:23:35.955 wdl.w:ptcp.w:call-paraphase-09.t:call-run_paraphase.slurm_singularity INFO srun: job 51797419 has been allocated resources
2025-09-15 20:23:35.955 wdl.w:ptcp.w:call-paraphase-09.t:call-run_paraphase.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:35.965 wdl.w:ptcp.w:call-trgt-24.t:call-get_reads_overlapping_repeats NOTICE slurm_singularity run :: pid: 1199665, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-24/call-get_reads_overlapping_repeats/slurm_singularity.log.txt"
2025-09-15 20:23:35.972 wdl.w:ptcp.w:call-sawfish-13.t:call-run_sawfish.stderr VERBOSE [M::bam2fq_mainloop] discarded 0 singletons
2025-09-15 20:23:35.973 wdl.w:ptcp.w:call-sawfish-13.t:call-run_sawfish.stderr VERBOSE [M::bam2fq_mainloop] processed 0 reads
2025-09-15 20:23:36.039 wdl.w:ptcp.w:call-trgt-06.t:call-get_reads_overlapping_repeats INFO output :: name: "reads_overlapping_repeats", value: "m84036_250809_035451_s4.bc2103.repeats.bam"
2025-09-15 20:23:36.042 wdl.w:ptcp.w:call-trgt-06.t:call-get_reads_overlapping_repeats INFO output :: name: "reads_overlapping_repeats_bai", value: "m84036_250809_035451_s4.bc2103.repeats.bam.bai"
2025-09-15 20:23:36.103 wdl.w:ptcp.w:call-trgt-06.t:call-get_reads_overlapping_repeats NOTICE done
2025-09-15 20:23:36.108 wdl.w:ptcp.w:call-trgt-06 NOTICE finish :: job: "call-get_reads_overlapping_repeats"
2025-09-15 20:23:36.108 wdl.w:ptcp.w:call-trgt-06 INFO output :: job: "call-get_reads_overlapping_repeats", values: {"reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-06/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2103.repeats.bam.bai", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-06/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2103.repeats.bam"}
2025-09-15 20:23:36.108 wdl.w:ptcp.w:call-trgt-06 INFO visit :: node: "output-reads_overlapping_repeats", values: {"reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-06/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2103.repeats.bam"}
2025-09-15 20:23:36.108 wdl.w:ptcp.w:call-trgt-06 INFO visit :: node: "output-reads_overlapping_repeats_bai", values: {"reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-06/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2103.repeats.bam.bai"}
2025-09-15 20:23:36.117 wdl.w:ptcp.w:call-trgt-24.t:call-trgt_genotype NOTICE task setup :: name: "trgt_genotype", source: "./trgt.wdl", line: 272, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-24/call-trgt_genotype", thread: 140610887464512
2025-09-15 20:23:36.123 wdl.w:ptcp.t:call-pbmm2_align_hifi-67 INFO output :: name: "mapped_bam", value: "m84036_250809_035451_s4.bc2164.mapped.bam"
2025-09-15 20:23:36.126 wdl.w:ptcp.t:call-pbmm2_align_hifi-67 INFO output :: name: "mapped_bam_bai", value: "m84036_250809_035451_s4.bc2164.mapped.bam.bai"
2025-09-15 20:23:36.128 wdl.w:ptcp.t:call-pbmm2_align_hifi-67 INFO output :: name: "mapped_bam_pbi", value: "m84036_250809_035451_s4.bc2164.mapped.bam.pbi"
2025-09-15 20:23:36.130 wdl.w:ptcp.t:call-pbmm2_align_hifi-67 INFO output :: name: "report", value: "mapping_stats.report.json"
2025-09-15 20:23:36.135 wdl.w:ptcp.w:call-trgt-24.t:call-trgt_genotype INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:23:36.135 wdl.w:ptcp.w:call-trgt-24.t:call-trgt_genotype INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:23:36.135 wdl.w:ptcp.w:call-trgt-24.t:call-trgt_genotype INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:23:36.135 wdl.w:ptcp.w:call-trgt-24.t:call-trgt_genotype INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:23:36.135 wdl.w:ptcp.w:call-trgt-24.t:call-trgt_genotype INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2121.mapped.bam.bai"
2025-09-15 20:23:36.136 wdl.w:ptcp.w:call-trgt-24.t:call-trgt_genotype INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2121.mapped.bam"
2025-09-15 20:23:36.136 wdl.w:ptcp.w:call-trgt-24.t:call-trgt_genotype INFO input :: name: "sex", value: "F"
2025-09-15 20:23:36.136 wdl.w:ptcp.w:call-trgt-24.t:call-trgt_genotype INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2121"
2025-09-15 20:23:36.136 wdl.w:ptcp.w:call-trgt-24.t:call-trgt_genotype INFO eval :: name: "mem_gb", value: 16
2025-09-15 20:23:36.136 wdl.w:ptcp.w:call-trgt-24.t:call-trgt_genotype INFO eval :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2121.trgt"
2025-09-15 20:23:36.136 wdl.w:ptcp.w:call-trgt-24.t:call-trgt_genotype INFO eval :: name: "threads", value: 8
2025-09-15 20:23:36.136 wdl.w:ptcp.w:call-trgt-24.t:call-trgt_genotype INFO eval :: name: "disk_size", value: 27
2025-09-15 20:23:36.136 wdl.w:ptcp.w:call-trgt-24.t:call-trgt_genotype INFO eval :: name: "karyotype", value: "XX"
2025-09-15 20:23:36.137 wdl.w:ptcp.w:call-trgt-24.t:call-trgt_genotype INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 8, memory_reservation: 16000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:23:36.137 wdl.w:ptcp.w:call-trgt-24.t:call-trgt_genotype WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:23:36.137 wdl.w:ptcp.w:call-trgt-24.t:call-trgt_genotype INFO provisioned :: seconds_waited: 0, cpu: 8, mem_bytes: 16000000000
2025-09-15 20:23:36.137 wdl.w:ptcp.w:call-trgt-24.t:call-trgt_genotype INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:23:36.149 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_genotype INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2103.trgt.vcf"
2025-09-15 20:23:36.152 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_genotype INFO output :: name: "spanning_bam", value: "m84036_250809_035451_s4.bc2103.trgt.sorted.spanning.bam"
2025-09-15 20:23:36.153 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_genotype INFO output :: name: "spanning_bam_bai", value: "m84036_250809_035451_s4.bc2103.trgt.sorted.spanning.bam.bai"
2025-09-15 20:23:36.203 wdl.w:ptcp.w:call-trgt-24.t:call-trgt_genotype INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 11, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-24/call-trgt_genotype/_singularity_tmpdir_uuyxwel5"
2025-09-15 20:23:36.203 wdl.w:ptcp.w:call-trgt-24.t:call-trgt_genotype INFO Slurm invocation: srun --job-name call-trgt_genotype --partition compute,compute9 --cpus-per-task 8 --mem 15259M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-24/call-trgt_genotype/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-24/call-trgt_genotype/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-24/call-trgt_genotype/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-24/call-trgt_genotype/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-24/out/m84036_250809_035451_s4.bc2121.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2121.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-24/out/m84036_250809_035451_s4.bc2121.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2121.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-24/call-trgt_genotype/_singularity_tmpdir_uuyxwel5/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-24/call-trgt_genotype/_singularity_tmpdir_uuyxwel5/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:23:36.211 wdl.w:ptcp.t:call-pbmm2_align_hifi-67 NOTICE done
2025-09-15 20:23:36.218 wdl.w:ptcp NOTICE finish :: job: "call-pbmm2_align_hifi-67"
2025-09-15 20:23:36.218 wdl.w:ptcp INFO output :: job: "call-pbmm2_align_hifi-67", values: {"report": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-67/out/mapping_stats.report.json", "mapped_bam_pbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-67/out/m84036_250809_035451_s4.bc2164.mapped.bam.pbi", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-67/out/m84036_250809_035451_s4.bc2164.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-67/out/m84036_250809_035451_s4.bc2164.mapped.bam"}
2025-09-15 20:23:36.218 wdl.w:ptcp.w:call-trgt-24.t:call-trgt_genotype NOTICE slurm_singularity run :: pid: 1199690, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-24/call-trgt_genotype/slurm_singularity.log.txt"
2025-09-15 20:23:36.219 wdl.w:ptcp NOTICE ready :: job: "call-paraphase-67", callee: "paraphase"
2025-09-15 20:23:36.219 wdl.w:ptcp INFO input :: job: "call-paraphase-67", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf", "genome_version": "38", "config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-67/out/m84036_250809_035451_s4.bc2164.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-67/out/m84036_250809_035451_s4.bc2164.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2164"}
2025-09-15 20:23:36.220 wdl.w:ptcp NOTICE ready :: job: "call-sawfish-67", callee: "sawfish"
2025-09-15 20:23:36.220 wdl.w:ptcp INFO input :: job: "call-sawfish-67", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-67/out/m84036_250809_035451_s4.bc2164.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-67/out/m84036_250809_035451_s4.bc2164.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2164"}
2025-09-15 20:23:36.221 wdl.w:ptcp NOTICE ready :: job: "call-trgt-67", callee: "trgt"
2025-09-15 20:23:36.221 wdl.w:ptcp INFO input :: job: "call-trgt-67", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-67/out/m84036_250809_035451_s4.bc2164.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-67/out/m84036_250809_035451_s4.bc2164.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2164"}
2025-09-15 20:23:36.225 wdl.w:ptcp.w:call-paraphase-27.t:call-run_paraphase NOTICE task setup :: name: "run_paraphase", source: "./paraphase.wdl", line: 127, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-27/call-run_paraphase", thread: 140608756766272
2025-09-15 20:23:36.231 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_genotype NOTICE done
2025-09-15 20:23:36.233 wdl.w:ptcp.w:call-sawfish-09.t:call-run_sawfish.stderr VERBOSE [M::bam2fq_mainloop] discarded 0 singletons
2025-09-15 20:23:36.233 wdl.w:ptcp.w:call-sawfish-09.t:call-run_sawfish.stderr VERBOSE [M::bam2fq_mainloop] processed 0 reads
2025-09-15 20:23:36.239 wdl.w:ptcp.w:call-sawfish-09.t:call-run_sawfish.slurm_singularity INFO srun: job 51797420 queued and waiting for resources
2025-09-15 20:23:36.239 wdl.w:ptcp.w:call-sawfish-09.t:call-run_sawfish.slurm_singularity INFO srun: job 51797420 has been allocated resources
2025-09-15 20:23:36.240 wdl.w:ptcp.w:call-sawfish-09.t:call-run_sawfish.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:36.240 wdl.w:ptcp.w:call-sawfish-09.t:call-run_sawfish.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:23:36.246 wdl.w:ptcp.w:call-paraphase-27.t:call-run_paraphase INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:23:36.246 wdl.w:ptcp.w:call-paraphase-27.t:call-run_paraphase INFO input :: name: "annotation_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf"
2025-09-15 20:23:36.246 wdl.w:ptcp.w:call-paraphase-27.t:call-run_paraphase INFO input :: name: "genome_version", value: "38"
2025-09-15 20:23:36.246 wdl.w:ptcp.w:call-paraphase-27.t:call-run_paraphase INFO input :: name: "config_file", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/paraphase_config.GRCh38.yaml"
2025-09-15 20:23:36.247 wdl.w:ptcp.w:call-paraphase-27.t:call-run_paraphase INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:23:36.247 wdl.w:ptcp.w:call-paraphase-27.t:call-run_paraphase INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:23:36.247 wdl.w:ptcp.w:call-paraphase-27.t:call-run_paraphase INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2124.mapped.bam.bai"
2025-09-15 20:23:36.247 wdl.w:ptcp.w:call-paraphase-27.t:call-run_paraphase INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2124.mapped.bam"
2025-09-15 20:23:36.247 wdl.w:ptcp.w:call-paraphase-27.t:call-run_paraphase INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2124"
2025-09-15 20:23:36.247 wdl.w:ptcp.w:call-paraphase-27.t:call-run_paraphase INFO eval :: name: "threads", value: 4
2025-09-15 20:23:36.247 wdl.w:ptcp.w:call-paraphase-27.t:call-run_paraphase INFO eval :: name: "mem_gb", value: 8
2025-09-15 20:23:36.247 wdl.w:ptcp.w:call-paraphase-27.t:call-run_paraphase INFO eval :: name: "disk_size", value: 27
2025-09-15 20:23:36.248 wdl.w:ptcp.w:call-paraphase-27.t:call-run_paraphase INFO eval :: name: "out_dir", value: "m84036_250809_035451_s4.bc2124_paraphase"
2025-09-15 20:23:36.248 wdl.w:ptcp.w:call-paraphase-27.t:call-run_paraphase INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 4, memory_reservation: 8000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:23:36.248 wdl.w:ptcp.w:call-paraphase-27.t:call-run_paraphase WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:23:36.249 wdl.w:ptcp.w:call-paraphase-27.t:call-run_paraphase INFO provisioned :: seconds_waited: 0, cpu: 4, mem_bytes: 8000000000
2025-09-15 20:23:36.249 wdl.w:ptcp.w:call-paraphase-27.t:call-run_paraphase INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:23:36.256 wdl.w:ptcp.w:call-trgt-13.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:35 [INFO] - Running trgt-4.0.0-429afcd [genotype]
2025-09-15 20:23:36.256 wdl.w:ptcp.w:call-trgt-13.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:35 [WARN] - OPDM_ABCD3: Filtered out 4 impure reads
2025-09-15 20:23:36.256 wdl.w:ptcp.w:call-trgt-13.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:35 [WARN] - SCA37_DAB1: Filtered out 9 impure reads
2025-09-15 20:23:36.256 wdl.w:ptcp.w:call-trgt-13.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:35 [WARN] - SCA2_ATXN2: Filtered out 7 impure reads
2025-09-15 20:23:36.256 wdl.w:ptcp.w:call-trgt-13.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:35 [WARN] - NIID_NOTCH2NLC: Filtered out 21 impure reads
2025-09-15 20:23:36.256 wdl.w:ptcp.w:call-trgt-13.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:35 [WARN] - OPDM4_RILPL1: Filtered out 5 impure reads
2025-09-15 20:23:36.256 wdl.w:ptcp.w:call-trgt-13.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:35 [WARN] - DRPLA_ATN1: Filtered out 24 impure reads
2025-09-15 20:23:36.256 wdl.w:ptcp.w:call-trgt-13.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:35 [WARN] - SCA31_BEAN1: Filtered out 9 impure reads
2025-09-15 20:23:36.256 wdl.w:ptcp.w:call-trgt-13.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:35 [WARN] - SCA3_ATXN3: Filtered out 18 impure reads
2025-09-15 20:23:36.256 wdl.w:ptcp.w:call-trgt-13.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:35 [WARN] - SCA8_ATXN8OS: Filtered out 19 impure reads
2025-09-15 20:23:36.256 wdl.w:ptcp.w:call-trgt-13.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:35 [WARN] - OPMD_PABPN1: Filtered out 15 impure reads
2025-09-15 20:23:36.257 wdl.w:ptcp.w:call-trgt-13.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:35 [WARN] - SCA27B_FGF14: Filtered out 20 impure reads
2025-09-15 20:23:36.257 wdl.w:ptcp.w:call-trgt-13.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:35 [WARN] - HDL2_JPH3: Filtered out 12 impure reads
2025-09-15 20:23:36.257 wdl.w:ptcp.w:call-trgt-13.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:35 [WARN] - SCA6_CACNA1A: Filtered out 10 impure reads
2025-09-15 20:23:36.257 wdl.w:ptcp.w:call-trgt-13.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:35 [WARN] - FECD3_TCF4: Filtered out 15 impure reads
2025-09-15 20:23:36.257 wdl.w:ptcp.w:call-trgt-13.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:35 [WARN] - OPDM2_GIPC1: Filtered out 16 impure reads
2025-09-15 20:23:36.257 wdl.w:ptcp.w:call-trgt-13.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:35 [WARN] - CJD_PRNP: Filtered out 8 impure reads
2025-09-15 20:23:36.257 wdl.w:ptcp.w:call-trgt-13.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:35 [WARN] - SCA36_NOP56: Filtered out 26 impure reads
2025-09-15 20:23:36.257 wdl.w:ptcp.w:call-trgt-13.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:35 [WARN] - SCA4_ZFHX3: Filtered out 23 impure reads
2025-09-15 20:23:36.257 wdl.w:ptcp.w:call-trgt-06 NOTICE finish :: job: "call-trgt_genotype"
2025-09-15 20:23:36.257 wdl.w:ptcp.w:call-trgt-13.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:35 [WARN] - DM1_DMPK: Filtered out 18 impure reads
2025-09-15 20:23:36.258 wdl.w:ptcp.w:call-trgt-06 INFO output :: job: "call-trgt_genotype", values: {"spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-06/call-trgt_genotype/out/m84036_250809_035451_s4.bc2103.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-06/call-trgt_genotype/out/m84036_250809_035451_s4.bc2103.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-06/call-trgt_genotype/out/m84036_250809_035451_s4.bc2103.trgt.vcf"}
2025-09-15 20:23:36.258 wdl.w:ptcp.w:call-trgt-13.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:35 [WARN] - SCA10_ATXN10: Filtered out 9 impure reads
2025-09-15 20:23:36.258 wdl.w:ptcp.w:call-trgt-06 NOTICE ready :: job: "call-trgt_plot_meth_allele", callee: "trgt_plot"
2025-09-15 20:23:36.259 wdl.w:ptcp.w:call-trgt-13.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:35 [WARN] - SD5_HOXD13: Filtered out 10 impure reads
2025-09-15 20:23:36.259 wdl.w:ptcp.w:call-trgt-06 INFO input :: job: "call-trgt_plot_meth_allele", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": false, "methylation": true, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-06/call-trgt_genotype/out/m84036_250809_035451_s4.bc2103.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-06/call-trgt_genotype/out/m84036_250809_035451_s4.bc2103.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-06/call-trgt_genotype/out/m84036_250809_035451_s4.bc2103.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2103"}
2025-09-15 20:23:36.259 wdl.w:ptcp.w:call-trgt-13.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:35 [WARN] - EPM1_CSTB: Filtered out 16 impure reads
2025-09-15 20:23:36.259 wdl.w:ptcp.w:call-trgt-13.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:35 [WARN] - DM2_CNBP: Filtered out 2 impure reads
2025-09-15 20:23:36.259 wdl.w:ptcp.w:call-trgt-13.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:35 [WARN] - FRA2A_AFF3: Filtered out 22 impure reads
2025-09-15 20:23:36.259 wdl.w:ptcp.w:call-trgt-13.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:35 [WARN] - CCHS_PHOX2B: Filtered out 4 impure reads
2025-09-15 20:23:36.259 wdl.w:ptcp.w:call-trgt-13.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:35 [WARN] - SCA17_TBP: Filtered out 3 impure reads
2025-09-15 20:23:36.259 wdl.w:ptcp.w:call-trgt-13.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:35 [WARN] - HD_HTT: Filtered out 22 impure reads
2025-09-15 20:23:36.259 wdl.w:ptcp.w:call-trgt-13.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:35 [WARN] - SCA7_ATXN7: Filtered out 16 impure reads
2025-09-15 20:23:36.259 wdl.w:ptcp.w:call-trgt-13.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:35 [WARN] - SCA12_PPP2R2B: Filtered out 14 impure reads
2025-09-15 20:23:36.259 wdl.w:ptcp.w:call-trgt-13.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:35 [WARN] - CANVAS_RFC1: Filtered out 10 impure reads
2025-09-15 20:23:36.259 wdl.w:ptcp.w:call-trgt-13.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:35 [WARN] - SCA1_ATXN1: Filtered out 22 impure reads
2025-09-15 20:23:36.260 wdl.w:ptcp.w:call-trgt-13.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:36 [WARN] - FAME1_SAMD12: Filtered out 17 impure reads
2025-09-15 20:23:36.260 wdl.w:ptcp.w:call-trgt-13.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:36 [WARN] - FTDALS1_C9orf72: Filtered out 16 impure reads
2025-09-15 20:23:36.260 wdl.w:ptcp.w:call-trgt-13.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:36 [WARN] - OPDM1_LRP12: Filtered out 23 impure reads
2025-09-15 20:23:36.260 wdl.w:ptcp.w:call-trgt-13.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:36 [WARN] - FXS_FMR1: Filtered out 4 impure reads
2025-09-15 20:23:36.260 wdl.w:ptcp.w:call-trgt-13.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:36 [WARN] - SBMA_AR: Filtered out 19 impure reads
2025-09-15 20:23:36.260 wdl.w:ptcp.w:call-trgt-13.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:36 [WARN] - FRDA_FXN: Filtered out 2 impure reads
2025-09-15 20:23:36.260 wdl.w:ptcp.w:call-trgt-13.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:36 [WARN] - FRAXE_AFF2: Filtered out 21 impure reads
2025-09-15 20:23:36.260 wdl.w:ptcp.w:call-trgt-13.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:36 [INFO] - Total execution time: 1.03s
2025-09-15 20:23:36.260 wdl.w:ptcp.w:call-trgt-06 NOTICE ready :: job: "call-trgt_plot_meth_waterfall", callee: "trgt_plot"
2025-09-15 20:23:36.260 wdl.w:ptcp.w:call-trgt-13.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:36 [INFO] - trgt end
2025-09-15 20:23:36.260 wdl.w:ptcp.w:call-trgt-06 INFO input :: job: "call-trgt_plot_meth_waterfall", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": true, "methylation": true, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-06/call-trgt_genotype/out/m84036_250809_035451_s4.bc2103.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-06/call-trgt_genotype/out/m84036_250809_035451_s4.bc2103.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-06/call-trgt_genotype/out/m84036_250809_035451_s4.bc2103.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2103"}
2025-09-15 20:23:36.262 wdl.w:ptcp.w:call-trgt-06 NOTICE ready :: job: "call-trgt_plot_motifs_allele", callee: "trgt_plot"
2025-09-15 20:23:36.262 wdl.w:ptcp.w:call-trgt-06 INFO input :: job: "call-trgt_plot_motifs_allele", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": false, "methylation": false, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-06/call-trgt_genotype/out/m84036_250809_035451_s4.bc2103.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-06/call-trgt_genotype/out/m84036_250809_035451_s4.bc2103.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-06/call-trgt_genotype/out/m84036_250809_035451_s4.bc2103.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2103"}
2025-09-15 20:23:36.263 wdl.w:ptcp.w:call-trgt-06 NOTICE ready :: job: "call-trgt_plot_motifs_waterfall", callee: "trgt_plot"
2025-09-15 20:23:36.263 wdl.w:ptcp.w:call-trgt-06 INFO input :: job: "call-trgt_plot_motifs_waterfall", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": true, "methylation": false, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-06/call-trgt_genotype/out/m84036_250809_035451_s4.bc2103.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-06/call-trgt_genotype/out/m84036_250809_035451_s4.bc2103.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-06/call-trgt_genotype/out/m84036_250809_035451_s4.bc2103.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2103"}
2025-09-15 20:23:36.264 wdl.w:ptcp.w:call-trgt-06 INFO visit :: node: "output-spanning_bam", values: {"spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-06/call-trgt_genotype/out/m84036_250809_035451_s4.bc2103.trgt.sorted.spanning.bam"}
2025-09-15 20:23:36.264 wdl.w:ptcp.w:call-trgt-06 INFO visit :: node: "output-spanning_bam_bai", values: {"spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-06/call-trgt_genotype/out/m84036_250809_035451_s4.bc2103.trgt.sorted.spanning.bam.bai"}
2025-09-15 20:23:36.264 wdl.w:ptcp.w:call-trgt-06 INFO visit :: node: "output-vcf", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-06/call-trgt_genotype/out/m84036_250809_035451_s4.bc2103.trgt.vcf"}
2025-09-15 20:23:36.270 wdl.w:ptcp.w:call-sawfish-27.t:call-run_sawfish NOTICE task setup :: name: "run_sawfish", source: "./sawfish.wdl", line: 83, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-27/call-run_sawfish", thread: 140613018162752
2025-09-15 20:23:36.288 wdl.w:ptcp.w:call-sawfish-27.t:call-run_sawfish INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:23:36.289 wdl.w:ptcp.w:call-sawfish-27.t:call-run_sawfish INFO input :: name: "genome_version", value: "38"
2025-09-15 20:23:36.289 wdl.w:ptcp.w:call-sawfish-27.t:call-run_sawfish INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:23:36.289 wdl.w:ptcp.w:call-sawfish-27.t:call-run_sawfish INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:23:36.289 wdl.w:ptcp.w:call-sawfish-27.t:call-run_sawfish INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2124.mapped.bam.bai"
2025-09-15 20:23:36.289 wdl.w:ptcp.w:call-sawfish-27.t:call-run_sawfish INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2124.mapped.bam"
2025-09-15 20:23:36.289 wdl.w:ptcp.w:call-sawfish-27.t:call-run_sawfish INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2124"
2025-09-15 20:23:36.289 wdl.w:ptcp.w:call-sawfish-27.t:call-run_sawfish INFO eval :: name: "mem_gb", value: 32
2025-09-15 20:23:36.289 wdl.w:ptcp.w:call-sawfish-27.t:call-run_sawfish INFO eval :: name: "threads", value: 16
2025-09-15 20:23:36.291 wdl.w:ptcp.w:call-sawfish-27.t:call-run_sawfish INFO eval :: name: "disk_size", value: 30
2025-09-15 20:23:36.291 wdl.w:ptcp.w:call-sawfish-27.t:call-run_sawfish INFO eval :: name: "discover_dirname", value: "m84036_250809_035451_s4.bc2124_sawfish_discover"
2025-09-15 20:23:36.291 wdl.w:ptcp.w:call-sawfish-27.t:call-run_sawfish INFO eval :: name: "call_dirname", value: "m84036_250809_035451_s4.bc2124_sawfish"
2025-09-15 20:23:36.291 wdl.w:ptcp.w:call-sawfish-27.t:call-run_sawfish INFO eval :: name: "minimap2_bam_filename", value: "m84036_250809_035451_s4.bc2124.minimap2.bam"
2025-09-15 20:23:36.291 wdl.w:ptcp.w:call-sawfish-27.t:call-run_sawfish INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 16, memory_reservation: 32000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:23:36.291 wdl.w:ptcp.w:call-sawfish-27.t:call-run_sawfish WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:23:36.292 wdl.w:ptcp.w:call-sawfish-27.t:call-run_sawfish INFO provisioned :: seconds_waited: 0, cpu: 16, mem_bytes: 32000000000
2025-09-15 20:23:36.292 wdl.w:ptcp.w:call-sawfish-27.t:call-run_sawfish INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:23:36.306 wdl.w:ptcp.w:call-trgt-33.t:call-trgt_genotype INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2130.trgt.vcf"
2025-09-15 20:23:36.309 wdl.w:ptcp.w:call-trgt-33.t:call-trgt_genotype INFO output :: name: "spanning_bam", value: "m84036_250809_035451_s4.bc2130.trgt.sorted.spanning.bam"
2025-09-15 20:23:36.310 wdl.w:ptcp.w:call-trgt-33.t:call-trgt_genotype INFO output :: name: "spanning_bam_bai", value: "m84036_250809_035451_s4.bc2130.trgt.sorted.spanning.bam.bai"
2025-09-15 20:23:36.345 wdl.w:ptcp.w:call-paraphase-27.t:call-run_paraphase INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-27/call-run_paraphase/_singularity_tmpdir_i_wjlfby"
2025-09-15 20:23:36.345 wdl.w:ptcp.w:call-paraphase-27.t:call-run_paraphase INFO Slurm invocation: srun --job-name call-run_paraphase --partition compute,compute9 --cpus-per-task 4 --mem 7629M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-27/call-run_paraphase/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-27/call-run_paraphase/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-27/call-run_paraphase/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-27/call-run_paraphase/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-27/out/m84036_250809_035451_s4.bc2124.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2124.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-27/out/m84036_250809_035451_s4.bc2124.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2124.mapped.bam.bai:ro --bind /ptcp/meta/variant_list/variant_list.GRCh38.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf:ro --bind /ptcp/meta/paraphase/paraphase_config.GRCh38.yaml:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/paraphase_config.GRCh38.yaml:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-27/call-run_paraphase/_singularity_tmpdir_i_wjlfby/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-27/call-run_paraphase/_singularity_tmpdir_i_wjlfby/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:23:36.358 wdl.w:ptcp.w:call-sawfish-27.t:call-run_sawfish INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 10, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-27/call-run_sawfish/_singularity_tmpdir_2kdpzpln"
2025-09-15 20:23:36.358 wdl.w:ptcp.w:call-sawfish-27.t:call-run_sawfish INFO Slurm invocation: srun --job-name call-run_sawfish --partition compute,compute9 --cpus-per-task 16 --mem 30518M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-27/call-run_sawfish/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-27/call-run_sawfish/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-27/call-run_sawfish/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-27/call-run_sawfish/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-27/out/m84036_250809_035451_s4.bc2124.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2124.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-27/out/m84036_250809_035451_s4.bc2124.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2124.mapped.bam.bai:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-27/call-run_sawfish/_singularity_tmpdir_2kdpzpln/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-27/call-run_sawfish/_singularity_tmpdir_2kdpzpln/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:23:36.362 wdl.w:ptcp.w:call-paraphase-27.t:call-run_paraphase NOTICE slurm_singularity run :: pid: 1199693, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-27/call-run_paraphase/slurm_singularity.log.txt"
2025-09-15 20:23:36.363 wdl.w:ptcp.w:call-sawfish-27.t:call-run_sawfish NOTICE slurm_singularity run :: pid: 1199694, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-27/call-run_sawfish/slurm_singularity.log.txt"
2025-09-15 20:23:36.390 wdl.w:ptcp.w:call-trgt-33.t:call-trgt_genotype NOTICE done
2025-09-15 20:23:36.396 wdl.w:ptcp.w:call-trgt-33 NOTICE finish :: job: "call-trgt_genotype"
2025-09-15 20:23:36.396 wdl.w:ptcp.w:call-trgt-33 INFO output :: job: "call-trgt_genotype", values: {"spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-33/call-trgt_genotype/out/m84036_250809_035451_s4.bc2130.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-33/call-trgt_genotype/out/m84036_250809_035451_s4.bc2130.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-33/call-trgt_genotype/out/m84036_250809_035451_s4.bc2130.trgt.vcf"}
2025-09-15 20:23:36.397 wdl.w:ptcp.w:call-trgt-33 NOTICE ready :: job: "call-trgt_plot_meth_allele", callee: "trgt_plot"
2025-09-15 20:23:36.397 wdl.w:ptcp.w:call-trgt-33 INFO input :: job: "call-trgt_plot_meth_allele", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": false, "methylation": true, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-33/call-trgt_genotype/out/m84036_250809_035451_s4.bc2130.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-33/call-trgt_genotype/out/m84036_250809_035451_s4.bc2130.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-33/call-trgt_genotype/out/m84036_250809_035451_s4.bc2130.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2130"}
2025-09-15 20:23:36.398 wdl.w:ptcp.w:call-trgt-33 NOTICE ready :: job: "call-trgt_plot_meth_waterfall", callee: "trgt_plot"
2025-09-15 20:23:36.398 wdl.w:ptcp.w:call-trgt-33 INFO input :: job: "call-trgt_plot_meth_waterfall", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": true, "methylation": true, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-33/call-trgt_genotype/out/m84036_250809_035451_s4.bc2130.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-33/call-trgt_genotype/out/m84036_250809_035451_s4.bc2130.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-33/call-trgt_genotype/out/m84036_250809_035451_s4.bc2130.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2130"}
2025-09-15 20:23:36.399 wdl.w:ptcp.w:call-trgt-33 NOTICE ready :: job: "call-trgt_plot_motifs_allele", callee: "trgt_plot"
2025-09-15 20:23:36.399 wdl.w:ptcp.w:call-trgt-33 INFO input :: job: "call-trgt_plot_motifs_allele", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": false, "methylation": false, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-33/call-trgt_genotype/out/m84036_250809_035451_s4.bc2130.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-33/call-trgt_genotype/out/m84036_250809_035451_s4.bc2130.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-33/call-trgt_genotype/out/m84036_250809_035451_s4.bc2130.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2130"}
2025-09-15 20:23:36.399 wdl.w:ptcp.w:call-trgt-33 NOTICE ready :: job: "call-trgt_plot_motifs_waterfall", callee: "trgt_plot"
2025-09-15 20:23:36.400 wdl.w:ptcp.w:call-trgt-33 INFO input :: job: "call-trgt_plot_motifs_waterfall", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": true, "methylation": false, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-33/call-trgt_genotype/out/m84036_250809_035451_s4.bc2130.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-33/call-trgt_genotype/out/m84036_250809_035451_s4.bc2130.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-33/call-trgt_genotype/out/m84036_250809_035451_s4.bc2130.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2130"}
2025-09-15 20:23:36.400 wdl.w:ptcp.w:call-trgt-33 INFO visit :: node: "output-spanning_bam", values: {"spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-33/call-trgt_genotype/out/m84036_250809_035451_s4.bc2130.trgt.sorted.spanning.bam"}
2025-09-15 20:23:36.400 wdl.w:ptcp.w:call-trgt-33 INFO visit :: node: "output-spanning_bam_bai", values: {"spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-33/call-trgt_genotype/out/m84036_250809_035451_s4.bc2130.trgt.sorted.spanning.bam.bai"}
2025-09-15 20:23:36.400 wdl.w:ptcp.w:call-trgt-33 INFO visit :: node: "output-vcf", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-33/call-trgt_genotype/out/m84036_250809_035451_s4.bc2130.trgt.vcf"}
2025-09-15 20:23:36.401 wdl.w:ptcp.w:call-trgt-27.t:call-get_reads_overlapping_repeats NOTICE task setup :: name: "get_reads_overlapping_repeats", source: "./trgt.wdl", line: 182, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-27/call-get_reads_overlapping_repeats", thread: 140611457906240
2025-09-15 20:23:36.415 wdl.w:ptcp.w:call-trgt-27.t:call-get_reads_overlapping_repeats INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:23:36.415 wdl.w:ptcp.w:call-trgt-27.t:call-get_reads_overlapping_repeats INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:23:36.415 wdl.w:ptcp.w:call-trgt-27.t:call-get_reads_overlapping_repeats INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2124.mapped.bam.bai"
2025-09-15 20:23:36.415 wdl.w:ptcp.w:call-trgt-27.t:call-get_reads_overlapping_repeats INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2124.mapped.bam"
2025-09-15 20:23:36.415 wdl.w:ptcp.w:call-trgt-27.t:call-get_reads_overlapping_repeats INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2124"
2025-09-15 20:23:36.416 wdl.w:ptcp.w:call-trgt-27.t:call-get_reads_overlapping_repeats INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:23:36.416 wdl.w:ptcp.w:call-trgt-27.t:call-get_reads_overlapping_repeats INFO eval :: name: "expand_size", value: 3000
2025-09-15 20:23:36.416 wdl.w:ptcp.w:call-trgt-27.t:call-get_reads_overlapping_repeats INFO eval :: name: "threads", value: 1
2025-09-15 20:23:36.416 wdl.w:ptcp.w:call-trgt-27.t:call-get_reads_overlapping_repeats INFO eval :: name: "expanded_bed_name", value: "m84036_250809_035451_s4.bc2124.expanded.bed"
2025-09-15 20:23:36.416 wdl.w:ptcp.w:call-trgt-27.t:call-get_reads_overlapping_repeats INFO eval :: name: "disk_size", value: 11
2025-09-15 20:23:36.416 wdl.w:ptcp.w:call-trgt-27.t:call-get_reads_overlapping_repeats INFO eval :: name: "output_name", value: "m84036_250809_035451_s4.bc2124.repeats.bam"
2025-09-15 20:23:36.416 wdl.w:ptcp.w:call-trgt-27.t:call-get_reads_overlapping_repeats INFO eval :: name: "index_name", value: "m84036_250809_035451_s4.bc2124.repeats.bam.bai"
2025-09-15 20:23:36.416 wdl.w:ptcp.w:call-trgt-27.t:call-get_reads_overlapping_repeats INFO eval :: name: "output_name_with_index", value: "m84036_250809_035451_s4.bc2124.repeats.bam##idx##m84036_250809_035451_s4.bc2124.repeats.bam.bai"
2025-09-15 20:23:36.417 wdl.w:ptcp.w:call-trgt-27.t:call-get_reads_overlapping_repeats INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:23:36.417 wdl.w:ptcp.w:call-trgt-27.t:call-get_reads_overlapping_repeats WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:23:36.417 wdl.w:ptcp.w:call-trgt-27.t:call-get_reads_overlapping_repeats INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:23:36.417 wdl.w:ptcp.w:call-trgt-27.t:call-get_reads_overlapping_repeats INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:23:36.466 wdl.w:ptcp.w:call-trgt-27.t:call-get_reads_overlapping_repeats INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 9, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-27/call-get_reads_overlapping_repeats/_singularity_tmpdir_cccwr3fx"
2025-09-15 20:23:36.466 wdl.w:ptcp.w:call-trgt-27.t:call-get_reads_overlapping_repeats INFO Slurm invocation: srun --job-name call-get_reads_overlapping_repeats --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-27/call-get_reads_overlapping_repeats/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-27/call-get_reads_overlapping_repeats/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-27/call-get_reads_overlapping_repeats/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-27/call-get_reads_overlapping_repeats/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-27/out/m84036_250809_035451_s4.bc2124.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2124.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-27/out/m84036_250809_035451_s4.bc2124.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2124.mapped.bam.bai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-27/call-get_reads_overlapping_repeats/_singularity_tmpdir_cccwr3fx/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-27/call-get_reads_overlapping_repeats/_singularity_tmpdir_cccwr3fx/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:23:36.486 wdl.w:ptcp.w:call-trgt-27.t:call-get_reads_overlapping_repeats NOTICE slurm_singularity run :: pid: 1199697, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-27/call-get_reads_overlapping_repeats/slurm_singularity.log.txt"
2025-09-15 20:23:36.531 wdl.w:ptcp.w:call-sawfish-29.t:call-run_sawfish.stderr VERBOSE [M::bam2fq_mainloop] discarded 0 singletons
2025-09-15 20:23:36.531 wdl.w:ptcp.w:call-sawfish-29.t:call-run_sawfish.stderr VERBOSE [M::bam2fq_mainloop] processed 1 reads
2025-09-15 20:23:36.574 wdl.w:ptcp.w:call-trgt-13.t:call-trgt_genotype INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2110.trgt.vcf"
2025-09-15 20:23:36.577 wdl.w:ptcp.w:call-trgt-13.t:call-trgt_genotype INFO output :: name: "spanning_bam", value: "m84036_250809_035451_s4.bc2110.trgt.sorted.spanning.bam"
2025-09-15 20:23:36.578 wdl.w:ptcp.w:call-trgt-13.t:call-trgt_genotype INFO output :: name: "spanning_bam_bai", value: "m84036_250809_035451_s4.bc2110.trgt.sorted.spanning.bam.bai"
2025-09-15 20:23:36.670 wdl.w:ptcp.w:call-trgt-09.t:call-get_reads_overlapping_repeats.slurm_singularity INFO srun: job 51797421 queued and waiting for resources
2025-09-15 20:23:36.671 wdl.w:ptcp.w:call-trgt-09.t:call-get_reads_overlapping_repeats.slurm_singularity INFO srun: job 51797421 has been allocated resources
2025-09-15 20:23:36.671 wdl.w:ptcp.w:call-trgt-09.t:call-get_reads_overlapping_repeats.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:36.676 wdl.w:ptcp.w:call-trgt-13.t:call-trgt_genotype NOTICE done
2025-09-15 20:23:36.681 wdl.w:ptcp.w:call-trgt-13 NOTICE finish :: job: "call-trgt_genotype"
2025-09-15 20:23:36.682 wdl.w:ptcp.w:call-trgt-13 INFO output :: job: "call-trgt_genotype", values: {"spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-13/call-trgt_genotype/out/m84036_250809_035451_s4.bc2110.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-13/call-trgt_genotype/out/m84036_250809_035451_s4.bc2110.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-13/call-trgt_genotype/out/m84036_250809_035451_s4.bc2110.trgt.vcf"}
2025-09-15 20:23:36.682 wdl.w:ptcp.w:call-trgt-13 NOTICE ready :: job: "call-trgt_plot_meth_allele", callee: "trgt_plot"
2025-09-15 20:23:36.682 wdl.w:ptcp.w:call-trgt-13 INFO input :: job: "call-trgt_plot_meth_allele", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": false, "methylation": true, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-13/call-trgt_genotype/out/m84036_250809_035451_s4.bc2110.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-13/call-trgt_genotype/out/m84036_250809_035451_s4.bc2110.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-13/call-trgt_genotype/out/m84036_250809_035451_s4.bc2110.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2110"}
2025-09-15 20:23:36.684 wdl.w:ptcp.w:call-trgt-13 NOTICE ready :: job: "call-trgt_plot_meth_waterfall", callee: "trgt_plot"
2025-09-15 20:23:36.684 wdl.w:ptcp.w:call-trgt-13 INFO input :: job: "call-trgt_plot_meth_waterfall", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": true, "methylation": true, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-13/call-trgt_genotype/out/m84036_250809_035451_s4.bc2110.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-13/call-trgt_genotype/out/m84036_250809_035451_s4.bc2110.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-13/call-trgt_genotype/out/m84036_250809_035451_s4.bc2110.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2110"}
2025-09-15 20:23:36.685 wdl.w:ptcp.w:call-trgt-13 NOTICE ready :: job: "call-trgt_plot_motifs_allele", callee: "trgt_plot"
2025-09-15 20:23:36.685 wdl.w:ptcp.w:call-trgt-13 INFO input :: job: "call-trgt_plot_motifs_allele", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": false, "methylation": false, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-13/call-trgt_genotype/out/m84036_250809_035451_s4.bc2110.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-13/call-trgt_genotype/out/m84036_250809_035451_s4.bc2110.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-13/call-trgt_genotype/out/m84036_250809_035451_s4.bc2110.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2110"}
2025-09-15 20:23:36.686 wdl.w:ptcp.w:call-trgt-13 NOTICE ready :: job: "call-trgt_plot_motifs_waterfall", callee: "trgt_plot"
2025-09-15 20:23:36.686 wdl.w:ptcp.w:call-trgt-13 INFO input :: job: "call-trgt_plot_motifs_waterfall", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": true, "methylation": false, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-13/call-trgt_genotype/out/m84036_250809_035451_s4.bc2110.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-13/call-trgt_genotype/out/m84036_250809_035451_s4.bc2110.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-13/call-trgt_genotype/out/m84036_250809_035451_s4.bc2110.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2110"}
2025-09-15 20:23:36.687 wdl.w:ptcp.w:call-trgt-13 INFO visit :: node: "output-spanning_bam", values: {"spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-13/call-trgt_genotype/out/m84036_250809_035451_s4.bc2110.trgt.sorted.spanning.bam"}
2025-09-15 20:23:36.687 wdl.w:ptcp.w:call-trgt-13 INFO visit :: node: "output-spanning_bam_bai", values: {"spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-13/call-trgt_genotype/out/m84036_250809_035451_s4.bc2110.trgt.sorted.spanning.bam.bai"}
2025-09-15 20:23:36.687 wdl.w:ptcp.w:call-trgt-13 INFO visit :: node: "output-vcf", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-13/call-trgt_genotype/out/m84036_250809_035451_s4.bc2110.trgt.vcf"}
2025-09-15 20:23:36.693 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_genotype NOTICE task setup :: name: "trgt_genotype", source: "./trgt.wdl", line: 272, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-27/call-trgt_genotype", thread: 140609822115392
2025-09-15 20:23:36.720 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_genotype INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:23:36.720 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_genotype INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:23:36.720 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_genotype INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:23:36.720 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_genotype INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:23:36.720 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_genotype INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2124.mapped.bam.bai"
2025-09-15 20:23:36.720 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_genotype INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2124.mapped.bam"
2025-09-15 20:23:36.720 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_genotype INFO input :: name: "sex", value: "F"
2025-09-15 20:23:36.720 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_genotype INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2124"
2025-09-15 20:23:36.720 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_genotype INFO eval :: name: "mem_gb", value: 16
2025-09-15 20:23:36.721 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_genotype INFO eval :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2124.trgt"
2025-09-15 20:23:36.721 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_genotype INFO eval :: name: "threads", value: 8
2025-09-15 20:23:36.721 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_genotype INFO eval :: name: "disk_size", value: 27
2025-09-15 20:23:36.721 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_genotype INFO eval :: name: "karyotype", value: "XX"
2025-09-15 20:23:36.721 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_genotype INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 8, memory_reservation: 16000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:23:36.722 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_genotype WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:23:36.722 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_genotype INFO provisioned :: seconds_waited: 0, cpu: 8, mem_bytes: 16000000000
2025-09-15 20:23:36.722 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_genotype INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:23:36.818 wdl.w:ptcp.t:call-pbmm2_align_hifi-64 INFO output :: name: "mapped_bam", value: "m84036_250809_035451_s4.bc2161.mapped.bam"
2025-09-15 20:23:36.824 wdl.w:ptcp.t:call-pbmm2_align_hifi-64 INFO output :: name: "mapped_bam_bai", value: "m84036_250809_035451_s4.bc2161.mapped.bam.bai"
2025-09-15 20:23:36.825 wdl.w:ptcp.t:call-pbmm2_align_hifi-64 INFO output :: name: "mapped_bam_pbi", value: "m84036_250809_035451_s4.bc2161.mapped.bam.pbi"
2025-09-15 20:23:36.828 wdl.w:ptcp.t:call-pbmm2_align_hifi-64 INFO output :: name: "report", value: "mapping_stats.report.json"
2025-09-15 20:23:36.829 wdl.w:ptcp.w:call-trgt-09.t:call-trgt_genotype.slurm_singularity INFO srun: job 51797422 queued and waiting for resources
2025-09-15 20:23:36.829 wdl.w:ptcp.w:call-trgt-09.t:call-trgt_genotype.slurm_singularity INFO srun: job 51797422 has been allocated resources
2025-09-15 20:23:36.829 wdl.w:ptcp.w:call-trgt-09.t:call-trgt_genotype.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:36.830 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_genotype INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 11, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-27/call-trgt_genotype/_singularity_tmpdir_rtiskh84"
2025-09-15 20:23:36.830 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_genotype INFO Slurm invocation: srun --job-name call-trgt_genotype --partition compute,compute9 --cpus-per-task 8 --mem 15259M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-27/call-trgt_genotype/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-27/call-trgt_genotype/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-27/call-trgt_genotype/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-27/call-trgt_genotype/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-27/out/m84036_250809_035451_s4.bc2124.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2124.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-27/out/m84036_250809_035451_s4.bc2124.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2124.mapped.bam.bai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-27/call-trgt_genotype/_singularity_tmpdir_rtiskh84/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-27/call-trgt_genotype/_singularity_tmpdir_rtiskh84/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:23:36.843 wdl.w:ptcp.w:call-paraphase-17.t:call-run_paraphase.stderr VERBOSE INFO:root:Processing sample m84036_250809_035451_s4.bc2114 at 2025-09-15 20:23:35.768360...
2025-09-15 20:23:36.844 wdl.w:ptcp.w:call-paraphase-17.t:call-run_paraphase.stderr VERBOSE INFO:root:Checking sample sex at 2025-09-15 20:23:35.769325...
2025-09-15 20:23:36.844 wdl.w:ptcp.w:call-paraphase-17.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for cyp21 for sample m84036_250809_035451_s4.bc2114 at 2025-09-15 20:23:35.808692...
2025-09-15 20:23:36.844 wdl.w:ptcp.w:call-paraphase-17.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for cyp21 for sample m84036_250809_035451_s4.bc2114 at 2025-09-15 20:23:35.809221...
2025-09-15 20:23:36.844 wdl.w:ptcp.w:call-paraphase-17.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for smn1 for sample m84036_250809_035451_s4.bc2114 at 2025-09-15 20:23:35.809056...
2025-09-15 20:23:36.844 wdl.w:ptcp.w:call-paraphase-17.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for gba for sample m84036_250809_035451_s4.bc2114 at 2025-09-15 20:23:35.809157...
2025-09-15 20:23:36.844 wdl.w:ptcp.w:call-paraphase-17.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for smn1 for sample m84036_250809_035451_s4.bc2114 at 2025-09-15 20:23:35.809762...
2025-09-15 20:23:36.844 wdl.w:ptcp.w:call-trgt-29.t:call-trgt_genotype INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2126.trgt.vcf"
2025-09-15 20:23:36.844 wdl.w:ptcp.w:call-paraphase-17.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for gba for sample m84036_250809_035451_s4.bc2114 at 2025-09-15 20:23:35.809816...
2025-09-15 20:23:36.845 wdl.w:ptcp.w:call-paraphase-17.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for hba for sample m84036_250809_035451_s4.bc2114 at 2025-09-15 20:23:35.811018...
2025-09-15 20:23:36.845 wdl.w:ptcp.w:call-paraphase-17.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for hba for sample m84036_250809_035451_s4.bc2114 at 2025-09-15 20:23:35.811495...
2025-09-15 20:23:36.845 wdl.w:ptcp.w:call-paraphase-17.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for hba for sample m84036_250809_035451_s4.bc2114 at 2025-09-15 20:23:36.121988...
2025-09-15 20:23:36.845 wdl.w:ptcp.w:call-paraphase-17.t:call-run_paraphase.stderr VERBOSE WARNING:root:This region does not appear to have coverage. Will not attempt to phase haplotypes.
2025-09-15 20:23:36.845 wdl.w:ptcp.w:call-paraphase-17.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for hba for sample m84036_250809_035451_s4.bc2114 at 2025-09-15 20:23:36.147095...
2025-09-15 20:23:36.845 wdl.w:ptcp.w:call-paraphase-17.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for cyp21 for sample m84036_250809_035451_s4.bc2114 at 2025-09-15 20:23:36.152432...
2025-09-15 20:23:36.845 wdl.w:ptcp.w:call-paraphase-17.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for gba for sample m84036_250809_035451_s4.bc2114 at 2025-09-15 20:23:36.163397...
2025-09-15 20:23:36.845 wdl.w:ptcp.w:call-paraphase-17.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for smn1 for sample m84036_250809_035451_s4.bc2114 at 2025-09-15 20:23:36.173925...
2025-09-15 20:23:36.845 wdl.w:ptcp.w:call-paraphase-17.t:call-run_paraphase.stderr VERBOSE WARNING:root:This region does not appear to have coverage. Will not attempt to phase haplotypes.
2025-09-15 20:23:36.845 wdl.w:ptcp.w:call-paraphase-17.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for cyp21 for sample m84036_250809_035451_s4.bc2114 at 2025-09-15 20:23:36.183589...
2025-09-15 20:23:36.845 wdl.w:ptcp.w:call-paraphase-17.t:call-run_paraphase.stderr VERBOSE WARNING:root:This region does not appear to have coverage. Will not attempt to phase haplotypes.
2025-09-15 20:23:36.845 wdl.w:ptcp.w:call-paraphase-17.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for gba for sample m84036_250809_035451_s4.bc2114 at 2025-09-15 20:23:36.196828...
2025-09-15 20:23:36.845 wdl.w:ptcp.w:call-paraphase-17.t:call-run_paraphase.stderr VERBOSE WARNING:root:This region does not appear to have coverage. Will not attempt to phase haplotypes.
2025-09-15 20:23:36.845 wdl.w:ptcp.w:call-paraphase-17.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for smn1 for sample m84036_250809_035451_s4.bc2114 at 2025-09-15 20:23:36.250658...
2025-09-15 20:23:36.845 wdl.w:ptcp.w:call-paraphase-17.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for hba for sample m84036_250809_035451_s4.bc2114 at 2025-09-15 20:23:36.287700...
2025-09-15 20:23:36.845 wdl.w:ptcp.w:call-paraphase-17.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for hbb for sample m84036_250809_035451_s4.bc2114 at 2025-09-15 20:23:36.290808...
2025-09-15 20:23:36.846 wdl.w:ptcp.w:call-paraphase-17.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for hbb for sample m84036_250809_035451_s4.bc2114 at 2025-09-15 20:23:36.290882...
2025-09-15 20:23:36.846 wdl.w:ptcp.w:call-paraphase-17.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for cyp21 for sample m84036_250809_035451_s4.bc2114 at 2025-09-15 20:23:36.315870...
2025-09-15 20:23:36.846 wdl.w:ptcp.w:call-paraphase-17.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for f8inv22 for sample m84036_250809_035451_s4.bc2114 at 2025-09-15 20:23:36.321977...
2025-09-15 20:23:36.846 wdl.w:ptcp.w:call-paraphase-17.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for f8inv22 for sample m84036_250809_035451_s4.bc2114 at 2025-09-15 20:23:36.322100...
2025-09-15 20:23:36.846 wdl.w:ptcp.w:call-paraphase-17.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for gba for sample m84036_250809_035451_s4.bc2114 at 2025-09-15 20:23:36.379719...
2025-09-15 20:23:36.846 wdl.w:ptcp.w:call-paraphase-17.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for rpgr for sample m84036_250809_035451_s4.bc2114 at 2025-09-15 20:23:36.387880...
2025-09-15 20:23:36.846 wdl.w:ptcp.w:call-paraphase-17.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for rpgr for sample m84036_250809_035451_s4.bc2114 at 2025-09-15 20:23:36.388001...
2025-09-15 20:23:36.846 wdl.w:ptcp.w:call-paraphase-17.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning to gene2 region for smn1 for sample m84036_250809_035451_s4.bc2114 at 2025-09-15 20:23:36.406090...
2025-09-15 20:23:36.848 wdl.w:ptcp.w:call-trgt-29.t:call-trgt_genotype INFO output :: name: "spanning_bam", value: "m84036_250809_035451_s4.bc2126.trgt.sorted.spanning.bam"
2025-09-15 20:23:36.849 wdl.w:ptcp.w:call-trgt-29.t:call-trgt_genotype INFO output :: name: "spanning_bam_bai", value: "m84036_250809_035451_s4.bc2126.trgt.sorted.spanning.bam.bai"
2025-09-15 20:23:36.857 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_genotype NOTICE slurm_singularity run :: pid: 1199722, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-27/call-trgt_genotype/slurm_singularity.log.txt"
2025-09-15 20:23:36.901 wdl.w:ptcp.w:call-paraphase-24.t:call-run_paraphase.slurm_singularity INFO srun: job 51797423 queued and waiting for resources
2025-09-15 20:23:36.901 wdl.w:ptcp.w:call-paraphase-24.t:call-run_paraphase.slurm_singularity INFO srun: job 51797423 has been allocated resources
2025-09-15 20:23:36.901 wdl.w:ptcp.w:call-paraphase-24.t:call-run_paraphase.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:36.912 wdl.w:ptcp.t:call-pbmm2_align_hifi-64 NOTICE done
2025-09-15 20:23:36.918 wdl.w:ptcp NOTICE finish :: job: "call-pbmm2_align_hifi-64"
2025-09-15 20:23:36.918 wdl.w:ptcp INFO output :: job: "call-pbmm2_align_hifi-64", values: {"report": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-64/out/mapping_stats.report.json", "mapped_bam_pbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-64/out/m84036_250809_035451_s4.bc2161.mapped.bam.pbi", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-64/out/m84036_250809_035451_s4.bc2161.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-64/out/m84036_250809_035451_s4.bc2161.mapped.bam"}
2025-09-15 20:23:36.919 wdl.w:ptcp NOTICE ready :: job: "call-paraphase-64", callee: "paraphase"
2025-09-15 20:23:36.919 wdl.w:ptcp.w:call-trgt-29.t:call-trgt_genotype NOTICE done
2025-09-15 20:23:36.919 wdl.w:ptcp INFO input :: job: "call-paraphase-64", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf", "genome_version": "38", "config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-64/out/m84036_250809_035451_s4.bc2161.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-64/out/m84036_250809_035451_s4.bc2161.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2161"}
2025-09-15 20:23:36.920 wdl.w:ptcp NOTICE ready :: job: "call-sawfish-64", callee: "sawfish"
2025-09-15 20:23:36.920 wdl.w:ptcp INFO input :: job: "call-sawfish-64", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-64/out/m84036_250809_035451_s4.bc2161.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-64/out/m84036_250809_035451_s4.bc2161.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2161"}
2025-09-15 20:23:36.921 wdl.w:ptcp NOTICE ready :: job: "call-trgt-64", callee: "trgt"
2025-09-15 20:23:36.921 wdl.w:ptcp INFO input :: job: "call-trgt-64", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-64/out/m84036_250809_035451_s4.bc2161.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-64/out/m84036_250809_035451_s4.bc2161.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2161"}
2025-09-15 20:23:36.924 wdl.w:ptcp.w:call-trgt-29 NOTICE finish :: job: "call-trgt_genotype"
2025-09-15 20:23:36.925 wdl.w:ptcp.w:call-trgt-29 INFO output :: job: "call-trgt_genotype", values: {"spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-29/call-trgt_genotype/out/m84036_250809_035451_s4.bc2126.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-29/call-trgt_genotype/out/m84036_250809_035451_s4.bc2126.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-29/call-trgt_genotype/out/m84036_250809_035451_s4.bc2126.trgt.vcf"}
2025-09-15 20:23:36.925 wdl.w:ptcp.w:call-trgt-29 NOTICE ready :: job: "call-trgt_plot_meth_allele", callee: "trgt_plot"
2025-09-15 20:23:36.925 wdl.w:ptcp.w:call-trgt-29 INFO input :: job: "call-trgt_plot_meth_allele", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": false, "methylation": true, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-29/call-trgt_genotype/out/m84036_250809_035451_s4.bc2126.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-29/call-trgt_genotype/out/m84036_250809_035451_s4.bc2126.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-29/call-trgt_genotype/out/m84036_250809_035451_s4.bc2126.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2126"}
2025-09-15 20:23:36.925 wdl.w:ptcp.w:call-paraphase-25.t:call-run_paraphase NOTICE task setup :: name: "run_paraphase", source: "./paraphase.wdl", line: 127, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-25/call-run_paraphase", thread: 140609260066368
2025-09-15 20:23:36.926 wdl.w:ptcp.w:call-trgt-29 NOTICE ready :: job: "call-trgt_plot_meth_waterfall", callee: "trgt_plot"
2025-09-15 20:23:36.926 wdl.w:ptcp.w:call-trgt-29 INFO input :: job: "call-trgt_plot_meth_waterfall", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": true, "methylation": true, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-29/call-trgt_genotype/out/m84036_250809_035451_s4.bc2126.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-29/call-trgt_genotype/out/m84036_250809_035451_s4.bc2126.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-29/call-trgt_genotype/out/m84036_250809_035451_s4.bc2126.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2126"}
2025-09-15 20:23:36.927 wdl.w:ptcp.w:call-trgt-29 NOTICE ready :: job: "call-trgt_plot_motifs_allele", callee: "trgt_plot"
2025-09-15 20:23:36.927 wdl.w:ptcp.w:call-trgt-29 INFO input :: job: "call-trgt_plot_motifs_allele", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": false, "methylation": false, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-29/call-trgt_genotype/out/m84036_250809_035451_s4.bc2126.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-29/call-trgt_genotype/out/m84036_250809_035451_s4.bc2126.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-29/call-trgt_genotype/out/m84036_250809_035451_s4.bc2126.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2126"}
2025-09-15 20:23:36.928 wdl.w:ptcp.w:call-trgt-29 NOTICE ready :: job: "call-trgt_plot_motifs_waterfall", callee: "trgt_plot"
2025-09-15 20:23:36.928 wdl.w:ptcp.w:call-trgt-29 INFO input :: job: "call-trgt_plot_motifs_waterfall", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": true, "methylation": false, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-29/call-trgt_genotype/out/m84036_250809_035451_s4.bc2126.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-29/call-trgt_genotype/out/m84036_250809_035451_s4.bc2126.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-29/call-trgt_genotype/out/m84036_250809_035451_s4.bc2126.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2126"}
2025-09-15 20:23:36.929 wdl.w:ptcp.w:call-trgt-29 INFO visit :: node: "output-spanning_bam", values: {"spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-29/call-trgt_genotype/out/m84036_250809_035451_s4.bc2126.trgt.sorted.spanning.bam"}
2025-09-15 20:23:36.929 wdl.w:ptcp.w:call-trgt-29 INFO visit :: node: "output-spanning_bam_bai", values: {"spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-29/call-trgt_genotype/out/m84036_250809_035451_s4.bc2126.trgt.sorted.spanning.bam.bai"}
2025-09-15 20:23:36.929 wdl.w:ptcp.w:call-trgt-29 INFO visit :: node: "output-vcf", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-29/call-trgt_genotype/out/m84036_250809_035451_s4.bc2126.trgt.vcf"}
2025-09-15 20:23:36.932 wdl.w:ptcp.w:call-sawfish-24.t:call-run_sawfish.slurm_singularity INFO srun: job 51797424 queued and waiting for resources
2025-09-15 20:23:36.932 wdl.w:ptcp.w:call-sawfish-24.t:call-run_sawfish.slurm_singularity INFO srun: job 51797424 has been allocated resources
2025-09-15 20:23:36.932 wdl.w:ptcp.w:call-sawfish-24.t:call-run_sawfish.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:36.932 wdl.w:ptcp.w:call-sawfish-24.t:call-run_sawfish.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:23:36.933 wdl.w:ptcp.w:call-sawfish-25.t:call-run_sawfish NOTICE task setup :: name: "run_sawfish", source: "./sawfish.wdl", line: 83, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-25/call-run_sawfish", thread: 140609830508096
2025-09-15 20:23:36.945 wdl.w:ptcp.w:call-paraphase-25.t:call-run_paraphase INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:23:36.945 wdl.w:ptcp.w:call-paraphase-25.t:call-run_paraphase INFO input :: name: "annotation_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf"
2025-09-15 20:23:36.945 wdl.w:ptcp.w:call-paraphase-25.t:call-run_paraphase INFO input :: name: "genome_version", value: "38"
2025-09-15 20:23:36.945 wdl.w:ptcp.w:call-paraphase-25.t:call-run_paraphase INFO input :: name: "config_file", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/paraphase_config.GRCh38.yaml"
2025-09-15 20:23:36.945 wdl.w:ptcp.w:call-paraphase-25.t:call-run_paraphase INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:23:36.945 wdl.w:ptcp.w:call-paraphase-25.t:call-run_paraphase INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:23:36.945 wdl.w:ptcp.w:call-paraphase-25.t:call-run_paraphase INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2122.mapped.bam.bai"
2025-09-15 20:23:36.946 wdl.w:ptcp.w:call-paraphase-25.t:call-run_paraphase INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2122.mapped.bam"
2025-09-15 20:23:36.946 wdl.w:ptcp.w:call-paraphase-25.t:call-run_paraphase INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2122"
2025-09-15 20:23:36.946 wdl.w:ptcp.w:call-paraphase-25.t:call-run_paraphase INFO eval :: name: "threads", value: 4
2025-09-15 20:23:36.946 wdl.w:ptcp.w:call-paraphase-25.t:call-run_paraphase INFO eval :: name: "mem_gb", value: 8
2025-09-15 20:23:36.946 wdl.w:ptcp.w:call-paraphase-25.t:call-run_paraphase INFO eval :: name: "disk_size", value: 27
2025-09-15 20:23:36.947 wdl.w:ptcp.w:call-paraphase-25.t:call-run_paraphase INFO eval :: name: "out_dir", value: "m84036_250809_035451_s4.bc2122_paraphase"
2025-09-15 20:23:36.947 wdl.w:ptcp.w:call-paraphase-25.t:call-run_paraphase INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 4, memory_reservation: 8000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:23:36.947 wdl.w:ptcp.w:call-paraphase-25.t:call-run_paraphase WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:23:36.948 wdl.w:ptcp.w:call-paraphase-25.t:call-run_paraphase INFO provisioned :: seconds_waited: 0, cpu: 4, mem_bytes: 8000000000
2025-09-15 20:23:36.948 wdl.w:ptcp.w:call-paraphase-25.t:call-run_paraphase INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:23:36.952 wdl.w:ptcp.w:call-sawfish-25.t:call-run_sawfish INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:23:36.952 wdl.w:ptcp.w:call-sawfish-25.t:call-run_sawfish INFO input :: name: "genome_version", value: "38"
2025-09-15 20:23:36.952 wdl.w:ptcp.w:call-sawfish-25.t:call-run_sawfish INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:23:36.952 wdl.w:ptcp.w:call-sawfish-25.t:call-run_sawfish INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:23:36.952 wdl.w:ptcp.w:call-sawfish-25.t:call-run_sawfish INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2122.mapped.bam.bai"
2025-09-15 20:23:36.952 wdl.w:ptcp.w:call-sawfish-25.t:call-run_sawfish INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2122.mapped.bam"
2025-09-15 20:23:36.952 wdl.w:ptcp.w:call-sawfish-25.t:call-run_sawfish INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2122"
2025-09-15 20:23:36.953 wdl.w:ptcp.w:call-sawfish-25.t:call-run_sawfish INFO eval :: name: "mem_gb", value: 32
2025-09-15 20:23:36.953 wdl.w:ptcp.w:call-sawfish-25.t:call-run_sawfish INFO eval :: name: "threads", value: 16
2025-09-15 20:23:36.953 wdl.w:ptcp.w:call-sawfish-25.t:call-run_sawfish INFO eval :: name: "disk_size", value: 30
2025-09-15 20:23:36.953 wdl.w:ptcp.w:call-sawfish-25.t:call-run_sawfish INFO eval :: name: "discover_dirname", value: "m84036_250809_035451_s4.bc2122_sawfish_discover"
2025-09-15 20:23:36.953 wdl.w:ptcp.w:call-sawfish-25.t:call-run_sawfish INFO eval :: name: "call_dirname", value: "m84036_250809_035451_s4.bc2122_sawfish"
2025-09-15 20:23:36.953 wdl.w:ptcp.w:call-sawfish-25.t:call-run_sawfish INFO eval :: name: "minimap2_bam_filename", value: "m84036_250809_035451_s4.bc2122.minimap2.bam"
2025-09-15 20:23:36.954 wdl.w:ptcp.w:call-sawfish-25.t:call-run_sawfish INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 16, memory_reservation: 32000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:23:36.954 wdl.w:ptcp.w:call-sawfish-25.t:call-run_sawfish WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:23:36.954 wdl.w:ptcp.w:call-sawfish-25.t:call-run_sawfish INFO provisioned :: seconds_waited: 0, cpu: 16, mem_bytes: 32000000000
2025-09-15 20:23:36.954 wdl.w:ptcp.w:call-sawfish-25.t:call-run_sawfish INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:23:36.977 wdl.w:ptcp.w:call-trgt-24.t:call-get_reads_overlapping_repeats.slurm_singularity INFO srun: job 51797425 queued and waiting for resources
2025-09-15 20:23:36.977 wdl.w:ptcp.w:call-trgt-24.t:call-get_reads_overlapping_repeats.slurm_singularity INFO srun: job 51797425 has been allocated resources
2025-09-15 20:23:36.977 wdl.w:ptcp.w:call-trgt-24.t:call-get_reads_overlapping_repeats.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:36.977 wdl.w:ptcp.w:call-trgt-24.t:call-get_reads_overlapping_repeats.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:23:37.008 wdl.w:ptcp.w:call-sawfish-25.t:call-run_sawfish INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 10, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-25/call-run_sawfish/_singularity_tmpdir_mc0t1acm"
2025-09-15 20:23:37.009 wdl.w:ptcp.w:call-sawfish-25.t:call-run_sawfish INFO Slurm invocation: srun --job-name call-run_sawfish --partition compute,compute9 --cpus-per-task 16 --mem 30518M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-25/call-run_sawfish/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-25/call-run_sawfish/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-25/call-run_sawfish/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-25/call-run_sawfish/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-25/out/m84036_250809_035451_s4.bc2122.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2122.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-25/out/m84036_250809_035451_s4.bc2122.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2122.mapped.bam:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-25/call-run_sawfish/_singularity_tmpdir_mc0t1acm/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-25/call-run_sawfish/_singularity_tmpdir_mc0t1acm/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:23:37.016 wdl.w:ptcp.w:call-paraphase-25.t:call-run_paraphase INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-25/call-run_paraphase/_singularity_tmpdir_b4ryvwng"
2025-09-15 20:23:37.016 wdl.w:ptcp.w:call-paraphase-25.t:call-run_paraphase INFO Slurm invocation: srun --job-name call-run_paraphase --partition compute,compute9 --cpus-per-task 4 --mem 7629M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-25/call-run_paraphase/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-25/call-run_paraphase/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-25/call-run_paraphase/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-25/call-run_paraphase/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-25/out/m84036_250809_035451_s4.bc2122.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2122.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-25/out/m84036_250809_035451_s4.bc2122.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2122.mapped.bam:ro --bind /ptcp/meta/variant_list/variant_list.GRCh38.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf:ro --bind /ptcp/meta/paraphase/paraphase_config.GRCh38.yaml:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/paraphase_config.GRCh38.yaml:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-25/call-run_paraphase/_singularity_tmpdir_b4ryvwng/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-25/call-run_paraphase/_singularity_tmpdir_b4ryvwng/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:23:37.028 wdl.w:ptcp.w:call-paraphase-25.t:call-run_paraphase NOTICE slurm_singularity run :: pid: 1199725, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-25/call-run_paraphase/slurm_singularity.log.txt"
2025-09-15 20:23:37.028 wdl.w:ptcp.w:call-sawfish-25.t:call-run_sawfish NOTICE slurm_singularity run :: pid: 1199724, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-25/call-run_sawfish/slurm_singularity.log.txt"
2025-09-15 20:23:37.054 wdl.w:ptcp.w:call-paraphase-35.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for hba for sample m84036_250809_035451_s4.bc2132 at 2025-09-15 20:23:09.361185...
2025-09-15 20:23:37.055 wdl.w:ptcp.w:call-paraphase-35.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for smn1 for sample m84036_250809_035451_s4.bc2132 at 2025-09-15 20:23:09.861450...
2025-09-15 20:23:37.055 wdl.w:ptcp.w:call-paraphase-35.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for gba for sample m84036_250809_035451_s4.bc2132 at 2025-09-15 20:23:11.187218...
2025-09-15 20:23:37.055 wdl.w:ptcp.w:call-paraphase-35.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for cyp21 for sample m84036_250809_035451_s4.bc2132 at 2025-09-15 20:23:13.033411...
2025-09-15 20:23:37.055 wdl.w:ptcp.w:call-paraphase-35.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for smn1 for sample m84036_250809_035451_s4.bc2132 at 2025-09-15 20:23:36.039889...
2025-09-15 20:23:37.055 wdl.w:ptcp.w:call-paraphase-35.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning to gene2 region for smn1 for sample m84036_250809_035451_s4.bc2132 at 2025-09-15 20:23:36.625020...
2025-09-15 20:23:37.226 wdl.w:ptcp.w:call-trgt-24.t:call-trgt_genotype.slurm_singularity INFO srun: job 51797426 queued and waiting for resources
2025-09-15 20:23:37.226 wdl.w:ptcp.w:call-trgt-24.t:call-trgt_genotype.slurm_singularity INFO srun: job 51797426 has been allocated resources
2025-09-15 20:23:37.226 wdl.w:ptcp.w:call-trgt-24.t:call-trgt_genotype.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:37.285 wdl.w:ptcp.t:call-pbmm2_align_hifi-69 INFO output :: name: "mapped_bam", value: "m84036_250809_035451_s4.bc2166.mapped.bam"
2025-09-15 20:23:37.289 wdl.w:ptcp.t:call-pbmm2_align_hifi-69 INFO output :: name: "mapped_bam_bai", value: "m84036_250809_035451_s4.bc2166.mapped.bam.bai"
2025-09-15 20:23:37.291 wdl.w:ptcp.t:call-pbmm2_align_hifi-69 INFO output :: name: "mapped_bam_pbi", value: "m84036_250809_035451_s4.bc2166.mapped.bam.pbi"
2025-09-15 20:23:37.292 wdl.w:ptcp.t:call-pbmm2_align_hifi-69 INFO output :: name: "report", value: "mapping_stats.report.json"
2025-09-15 20:23:37.362 wdl.w:ptcp.t:call-pbmm2_align_hifi-69 NOTICE done
2025-09-15 20:23:37.368 wdl.w:ptcp NOTICE finish :: job: "call-pbmm2_align_hifi-69"
2025-09-15 20:23:37.368 wdl.w:ptcp INFO output :: job: "call-pbmm2_align_hifi-69", values: {"report": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-69/out/mapping_stats.report.json", "mapped_bam_pbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-69/out/m84036_250809_035451_s4.bc2166.mapped.bam.pbi", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-69/out/m84036_250809_035451_s4.bc2166.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-69/out/m84036_250809_035451_s4.bc2166.mapped.bam"}
2025-09-15 20:23:37.369 wdl.w:ptcp NOTICE ready :: job: "call-paraphase-69", callee: "paraphase"
2025-09-15 20:23:37.369 wdl.w:ptcp INFO input :: job: "call-paraphase-69", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf", "genome_version": "38", "config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-69/out/m84036_250809_035451_s4.bc2166.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-69/out/m84036_250809_035451_s4.bc2166.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2166"}
2025-09-15 20:23:37.370 wdl.w:ptcp NOTICE ready :: job: "call-sawfish-69", callee: "sawfish"
2025-09-15 20:23:37.370 wdl.w:ptcp INFO input :: job: "call-sawfish-69", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-69/out/m84036_250809_035451_s4.bc2166.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-69/out/m84036_250809_035451_s4.bc2166.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2166"}
2025-09-15 20:23:37.371 wdl.w:ptcp NOTICE ready :: job: "call-trgt-69", callee: "trgt"
2025-09-15 20:23:37.371 wdl.w:ptcp INFO input :: job: "call-trgt-69", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-69/out/m84036_250809_035451_s4.bc2166.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-69/out/m84036_250809_035451_s4.bc2166.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2166"}
2025-09-15 20:23:37.373 wdl.w:ptcp.w:call-paraphase-27.t:call-run_paraphase.slurm_singularity INFO srun: job 51797427 queued and waiting for resources
2025-09-15 20:23:37.373 wdl.w:ptcp.w:call-paraphase-27.t:call-run_paraphase.slurm_singularity INFO srun: job 51797427 has been allocated resources
2025-09-15 20:23:37.373 wdl.w:ptcp.w:call-paraphase-27.t:call-run_paraphase.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:37.373 wdl.w:ptcp.w:call-sawfish-27.t:call-run_sawfish.slurm_singularity INFO srun: job 51797428 queued and waiting for resources
2025-09-15 20:23:37.373 wdl.w:ptcp.w:call-sawfish-27.t:call-run_sawfish.slurm_singularity INFO srun: job 51797428 has been allocated resources
2025-09-15 20:23:37.374 wdl.w:ptcp.w:call-sawfish-27.t:call-run_sawfish.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:37.374 wdl.w:ptcp.w:call-sawfish-27.t:call-run_sawfish.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:23:37.380 wdl.w:ptcp.w:call-trgt-25.t:call-get_reads_overlapping_repeats NOTICE task setup :: name: "get_reads_overlapping_repeats", source: "./trgt.wdl", line: 182, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-25/call-get_reads_overlapping_repeats", thread: 140608739980864
2025-09-15 20:23:37.397 wdl.w:ptcp.w:call-trgt-25.t:call-get_reads_overlapping_repeats INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:23:37.397 wdl.w:ptcp.w:call-trgt-25.t:call-get_reads_overlapping_repeats INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:23:37.397 wdl.w:ptcp.w:call-trgt-25.t:call-get_reads_overlapping_repeats INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2122.mapped.bam.bai"
2025-09-15 20:23:37.397 wdl.w:ptcp.w:call-trgt-25.t:call-get_reads_overlapping_repeats INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2122.mapped.bam"
2025-09-15 20:23:37.397 wdl.w:ptcp.w:call-trgt-25.t:call-get_reads_overlapping_repeats INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2122"
2025-09-15 20:23:37.397 wdl.w:ptcp.w:call-trgt-25.t:call-get_reads_overlapping_repeats INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:23:37.398 wdl.w:ptcp.w:call-trgt-25.t:call-get_reads_overlapping_repeats INFO eval :: name: "expand_size", value: 3000
2025-09-15 20:23:37.398 wdl.w:ptcp.w:call-trgt-25.t:call-get_reads_overlapping_repeats INFO eval :: name: "threads", value: 1
2025-09-15 20:23:37.398 wdl.w:ptcp.w:call-trgt-25.t:call-get_reads_overlapping_repeats INFO eval :: name: "expanded_bed_name", value: "m84036_250809_035451_s4.bc2122.expanded.bed"
2025-09-15 20:23:37.398 wdl.w:ptcp.w:call-trgt-25.t:call-get_reads_overlapping_repeats INFO eval :: name: "disk_size", value: 11
2025-09-15 20:23:37.398 wdl.w:ptcp.w:call-trgt-25.t:call-get_reads_overlapping_repeats INFO eval :: name: "output_name", value: "m84036_250809_035451_s4.bc2122.repeats.bam"
2025-09-15 20:23:37.398 wdl.w:ptcp.w:call-trgt-25.t:call-get_reads_overlapping_repeats INFO eval :: name: "index_name", value: "m84036_250809_035451_s4.bc2122.repeats.bam.bai"
2025-09-15 20:23:37.398 wdl.w:ptcp.w:call-trgt-25.t:call-get_reads_overlapping_repeats INFO eval :: name: "output_name_with_index", value: "m84036_250809_035451_s4.bc2122.repeats.bam##idx##m84036_250809_035451_s4.bc2122.repeats.bam.bai"
2025-09-15 20:23:37.399 wdl.w:ptcp.w:call-trgt-25.t:call-get_reads_overlapping_repeats INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:23:37.399 wdl.w:ptcp.w:call-trgt-25.t:call-get_reads_overlapping_repeats WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:23:37.399 wdl.w:ptcp.w:call-trgt-25.t:call-get_reads_overlapping_repeats INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:23:37.399 wdl.w:ptcp.w:call-trgt-25.t:call-get_reads_overlapping_repeats INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:23:37.414 wdl.w:ptcp.w:call-trgt-05.t:call-trgt_genotype INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2102.trgt.vcf"
2025-09-15 20:23:37.417 wdl.w:ptcp.w:call-trgt-05.t:call-trgt_genotype INFO output :: name: "spanning_bam", value: "m84036_250809_035451_s4.bc2102.trgt.sorted.spanning.bam"
2025-09-15 20:23:37.418 wdl.w:ptcp.w:call-trgt-05.t:call-trgt_genotype INFO output :: name: "spanning_bam_bai", value: "m84036_250809_035451_s4.bc2102.trgt.sorted.spanning.bam.bai"
2025-09-15 20:23:37.449 wdl.w:ptcp.w:call-trgt-25.t:call-get_reads_overlapping_repeats INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 9, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-25/call-get_reads_overlapping_repeats/_singularity_tmpdir_ffhujc9z"
2025-09-15 20:23:37.449 wdl.w:ptcp.w:call-trgt-25.t:call-get_reads_overlapping_repeats INFO Slurm invocation: srun --job-name call-get_reads_overlapping_repeats --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-25/call-get_reads_overlapping_repeats/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-25/call-get_reads_overlapping_repeats/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-25/call-get_reads_overlapping_repeats/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-25/call-get_reads_overlapping_repeats/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-25/out/m84036_250809_035451_s4.bc2122.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2122.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-25/out/m84036_250809_035451_s4.bc2122.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2122.mapped.bam:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-25/call-get_reads_overlapping_repeats/_singularity_tmpdir_ffhujc9z/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-25/call-get_reads_overlapping_repeats/_singularity_tmpdir_ffhujc9z/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:23:37.473 wdl.w:ptcp.w:call-trgt-25.t:call-get_reads_overlapping_repeats NOTICE slurm_singularity run :: pid: 1199745, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-25/call-get_reads_overlapping_repeats/slurm_singularity.log.txt"
2025-09-15 20:23:37.490 wdl.w:ptcp.w:call-trgt-05.t:call-trgt_genotype NOTICE done
2025-09-15 20:23:37.495 wdl.w:ptcp.w:call-trgt-05 NOTICE finish :: job: "call-trgt_genotype"
2025-09-15 20:23:37.496 wdl.w:ptcp.w:call-trgt-05 INFO output :: job: "call-trgt_genotype", values: {"spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-05/call-trgt_genotype/out/m84036_250809_035451_s4.bc2102.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-05/call-trgt_genotype/out/m84036_250809_035451_s4.bc2102.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-05/call-trgt_genotype/out/m84036_250809_035451_s4.bc2102.trgt.vcf"}
2025-09-15 20:23:37.496 wdl.w:ptcp.w:call-trgt-05 NOTICE ready :: job: "call-trgt_plot_meth_allele", callee: "trgt_plot"
2025-09-15 20:23:37.496 wdl.w:ptcp.w:call-trgt-05 INFO input :: job: "call-trgt_plot_meth_allele", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": false, "methylation": true, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-05/call-trgt_genotype/out/m84036_250809_035451_s4.bc2102.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-05/call-trgt_genotype/out/m84036_250809_035451_s4.bc2102.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-05/call-trgt_genotype/out/m84036_250809_035451_s4.bc2102.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2102"}
2025-09-15 20:23:37.496 wdl.w:ptcp.w:call-trgt-27.t:call-get_reads_overlapping_repeats.slurm_singularity INFO srun: job 51797429 queued and waiting for resources
2025-09-15 20:23:37.497 wdl.w:ptcp.w:call-trgt-27.t:call-get_reads_overlapping_repeats.slurm_singularity INFO srun: job 51797429 has been allocated resources
2025-09-15 20:23:37.497 wdl.w:ptcp.w:call-trgt-27.t:call-get_reads_overlapping_repeats.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:37.497 wdl.w:ptcp.w:call-trgt-27.t:call-get_reads_overlapping_repeats.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:23:37.498 wdl.w:ptcp.w:call-trgt-05 NOTICE ready :: job: "call-trgt_plot_meth_waterfall", callee: "trgt_plot"
2025-09-15 20:23:37.498 wdl.w:ptcp.w:call-trgt-05 INFO input :: job: "call-trgt_plot_meth_waterfall", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": true, "methylation": true, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-05/call-trgt_genotype/out/m84036_250809_035451_s4.bc2102.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-05/call-trgt_genotype/out/m84036_250809_035451_s4.bc2102.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-05/call-trgt_genotype/out/m84036_250809_035451_s4.bc2102.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2102"}
2025-09-15 20:23:37.499 wdl.w:ptcp.w:call-trgt-05 NOTICE ready :: job: "call-trgt_plot_motifs_allele", callee: "trgt_plot"
2025-09-15 20:23:37.499 wdl.w:ptcp.w:call-trgt-05 INFO input :: job: "call-trgt_plot_motifs_allele", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": false, "methylation": false, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-05/call-trgt_genotype/out/m84036_250809_035451_s4.bc2102.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-05/call-trgt_genotype/out/m84036_250809_035451_s4.bc2102.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-05/call-trgt_genotype/out/m84036_250809_035451_s4.bc2102.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2102"}
2025-09-15 20:23:37.500 wdl.w:ptcp.w:call-trgt-05 NOTICE ready :: job: "call-trgt_plot_motifs_waterfall", callee: "trgt_plot"
2025-09-15 20:23:37.500 wdl.w:ptcp.w:call-trgt-05 INFO input :: job: "call-trgt_plot_motifs_waterfall", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": true, "methylation": false, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-05/call-trgt_genotype/out/m84036_250809_035451_s4.bc2102.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-05/call-trgt_genotype/out/m84036_250809_035451_s4.bc2102.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-05/call-trgt_genotype/out/m84036_250809_035451_s4.bc2102.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2102"}
2025-09-15 20:23:37.500 wdl.w:ptcp.w:call-trgt-05 INFO visit :: node: "output-spanning_bam", values: {"spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-05/call-trgt_genotype/out/m84036_250809_035451_s4.bc2102.trgt.sorted.spanning.bam"}
2025-09-15 20:23:37.500 wdl.w:ptcp.w:call-trgt-05 INFO visit :: node: "output-spanning_bam_bai", values: {"spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-05/call-trgt_genotype/out/m84036_250809_035451_s4.bc2102.trgt.sorted.spanning.bam.bai"}
2025-09-15 20:23:37.501 wdl.w:ptcp.w:call-trgt-05 INFO visit :: node: "output-vcf", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-05/call-trgt_genotype/out/m84036_250809_035451_s4.bc2102.trgt.vcf"}
2025-09-15 20:23:37.505 wdl.w:ptcp.w:call-trgt-25.t:call-trgt_genotype NOTICE task setup :: name: "trgt_genotype", source: "./trgt.wdl", line: 272, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-25/call-trgt_genotype", thread: 140612506469952
2025-09-15 20:23:37.527 wdl.w:ptcp.w:call-trgt-25.t:call-trgt_genotype INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:23:37.527 wdl.w:ptcp.w:call-trgt-25.t:call-trgt_genotype INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:23:37.527 wdl.w:ptcp.w:call-trgt-25.t:call-trgt_genotype INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:23:37.527 wdl.w:ptcp.w:call-trgt-25.t:call-trgt_genotype INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:23:37.527 wdl.w:ptcp.w:call-trgt-25.t:call-trgt_genotype INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2122.mapped.bam.bai"
2025-09-15 20:23:37.527 wdl.w:ptcp.w:call-trgt-25.t:call-trgt_genotype INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2122.mapped.bam"
2025-09-15 20:23:37.527 wdl.w:ptcp.w:call-trgt-25.t:call-trgt_genotype INFO input :: name: "sex", value: "F"
2025-09-15 20:23:37.527 wdl.w:ptcp.w:call-trgt-25.t:call-trgt_genotype INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2122"
2025-09-15 20:23:37.527 wdl.w:ptcp.w:call-trgt-25.t:call-trgt_genotype INFO eval :: name: "mem_gb", value: 16
2025-09-15 20:23:37.528 wdl.w:ptcp.w:call-trgt-25.t:call-trgt_genotype INFO eval :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2122.trgt"
2025-09-15 20:23:37.528 wdl.w:ptcp.w:call-trgt-25.t:call-trgt_genotype INFO eval :: name: "threads", value: 8
2025-09-15 20:23:37.528 wdl.w:ptcp.w:call-trgt-25.t:call-trgt_genotype INFO eval :: name: "disk_size", value: 27
2025-09-15 20:23:37.528 wdl.w:ptcp.w:call-trgt-25.t:call-trgt_genotype INFO eval :: name: "karyotype", value: "XX"
2025-09-15 20:23:37.528 wdl.w:ptcp.w:call-trgt-25.t:call-trgt_genotype INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 8, memory_reservation: 16000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:23:37.529 wdl.w:ptcp.w:call-trgt-25.t:call-trgt_genotype WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:23:37.529 wdl.w:ptcp.w:call-trgt-25.t:call-trgt_genotype INFO provisioned :: seconds_waited: 0, cpu: 8, mem_bytes: 16000000000
2025-09-15 20:23:37.529 wdl.w:ptcp.w:call-trgt-25.t:call-trgt_genotype INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:23:37.549 wdl.w:ptcp.w:call-trgt-27.t:call-get_reads_overlapping_repeats INFO output :: name: "reads_overlapping_repeats", value: "m84036_250809_035451_s4.bc2124.repeats.bam"
2025-09-15 20:23:37.554 wdl.w:ptcp.w:call-trgt-27.t:call-get_reads_overlapping_repeats INFO output :: name: "reads_overlapping_repeats_bai", value: "m84036_250809_035451_s4.bc2124.repeats.bam.bai"
2025-09-15 20:23:37.622 wdl.w:ptcp.w:call-trgt-25.t:call-trgt_genotype INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 11, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-25/call-trgt_genotype/_singularity_tmpdir_7ytfor2l"
2025-09-15 20:23:37.623 wdl.w:ptcp.w:call-trgt-25.t:call-trgt_genotype INFO Slurm invocation: srun --job-name call-trgt_genotype --partition compute,compute9 --cpus-per-task 8 --mem 15259M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-25/call-trgt_genotype/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-25/call-trgt_genotype/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-25/call-trgt_genotype/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-25/call-trgt_genotype/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-25/out/m84036_250809_035451_s4.bc2122.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2122.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-25/out/m84036_250809_035451_s4.bc2122.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2122.mapped.bam:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-25/call-trgt_genotype/_singularity_tmpdir_7ytfor2l/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-25/call-trgt_genotype/_singularity_tmpdir_7ytfor2l/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:23:37.644 wdl.w:ptcp.t:call-pbmm2_align_hifi-60.stderr VERBOSE 
2025-09-15 20:23:37.645 wdl.w:ptcp.t:call-pbmm2_align_hifi-60.stderr VERBOSE pbmm2 \
2025-09-15 20:23:37.645 wdl.w:ptcp.t:call-pbmm2_align_hifi-60.stderr VERBOSE   align \
2025-09-15 20:23:37.645 wdl.w:ptcp.t:call-pbmm2_align_hifi-60.stderr VERBOSE   --log-level INFO \
2025-09-15 20:23:37.645 wdl.w:ptcp.t:call-pbmm2_align_hifi-60.stderr VERBOSE   --log-file pbmm2.log \
2025-09-15 20:23:37.645 wdl.w:ptcp.t:call-pbmm2_align_hifi-60.stderr VERBOSE   --alarms alarms.json \
2025-09-15 20:23:37.645 wdl.w:ptcp.t:call-pbmm2_align_hifi-60.stderr VERBOSE   --num-threads 64 \
2025-09-15 20:23:37.645 wdl.w:ptcp.t:call-pbmm2_align_hifi-60.stderr VERBOSE   --sort \
2025-09-15 20:23:37.645 wdl.w:ptcp.t:call-pbmm2_align_hifi-60.stderr VERBOSE   --preset HiFi \
2025-09-15 20:23:37.645 wdl.w:ptcp.t:call-pbmm2_align_hifi-60.stderr VERBOSE   --report-json mapping_stats.report.json \
2025-09-15 20:23:37.645 wdl.w:ptcp.t:call-pbmm2_align_hifi-60.stderr VERBOSE   --sample "m84036_250809_035451_s4.bc2157" \
2025-09-15 20:23:37.646 wdl.w:ptcp.t:call-pbmm2_align_hifi-60.stderr VERBOSE   --unmapped \
2025-09-15 20:23:37.646 wdl.w:ptcp.t:call-pbmm2_align_hifi-60.stderr VERBOSE   /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa \
2025-09-15 20:23:37.646 wdl.w:ptcp.t:call-pbmm2_align_hifi-60.stderr VERBOSE   /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0061_m84036_250809_035451_s4.bc2157.unmapped.bam \
2025-09-15 20:23:37.646 wdl.w:ptcp.t:call-pbmm2_align_hifi-60.stderr VERBOSE   m84036_250809_035451_s4.bc2157.mapped.bam
2025-09-15 20:23:37.646 wdl.w:ptcp.t:call-pbmm2_align_hifi-60.stderr VERBOSE + pbmm2 align --log-level INFO --log-file pbmm2.log --alarms alarms.json --num-threads 64 --sort --preset HiFi --report-json mapping_stats.report.json --sample m84036_250809_035451_s4.bc2157 --unmapped /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0061_m84036_250809_035451_s4.bc2157.unmapped.bam m84036_250809_035451_s4.bc2157.mapped.bam
2025-09-15 20:23:37.646 wdl.w:ptcp.t:call-pbmm2_align_hifi-60.stderr VERBOSE 
2025-09-15 20:23:37.646 wdl.w:ptcp.t:call-pbmm2_align_hifi-60.stderr VERBOSE pbindex --num-threads 64 m84036_250809_035451_s4.bc2157.mapped.bam
2025-09-15 20:23:37.646 wdl.w:ptcp.t:call-pbmm2_align_hifi-60.stderr VERBOSE + pbindex --num-threads 64 m84036_250809_035451_s4.bc2157.mapped.bam
2025-09-15 20:23:37.646 wdl.w:ptcp.t:call-pbmm2_align_hifi-60.stderr VERBOSE 
2025-09-15 20:23:37.649 wdl.w:ptcp.w:call-trgt-25.t:call-trgt_genotype NOTICE slurm_singularity run :: pid: 1199753, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-25/call-trgt_genotype/slurm_singularity.log.txt"
2025-09-15 20:23:37.649 wdl.w:ptcp.w:call-trgt-27.t:call-get_reads_overlapping_repeats NOTICE done
2025-09-15 20:23:37.661 wdl.w:ptcp.w:call-trgt-27 NOTICE finish :: job: "call-get_reads_overlapping_repeats"
2025-09-15 20:23:37.661 wdl.w:ptcp.w:call-trgt-27 INFO output :: job: "call-get_reads_overlapping_repeats", values: {"reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-27/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2124.repeats.bam.bai", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-27/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2124.repeats.bam"}
2025-09-15 20:23:37.661 wdl.w:ptcp.w:call-trgt-27 INFO visit :: node: "output-reads_overlapping_repeats", values: {"reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-27/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2124.repeats.bam"}
2025-09-15 20:23:37.661 wdl.w:ptcp.w:call-trgt-27 INFO visit :: node: "output-reads_overlapping_repeats_bai", values: {"reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-27/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2124.repeats.bam.bai"}
2025-09-15 20:23:37.669 wdl.w:ptcp.t:call-pbmm2_align_hifi-65.stderr VERBOSE 
2025-09-15 20:23:37.670 wdl.w:ptcp.t:call-pbmm2_align_hifi-65.stderr VERBOSE pbmm2 \
2025-09-15 20:23:37.670 wdl.w:ptcp.t:call-pbmm2_align_hifi-65.stderr VERBOSE   align \
2025-09-15 20:23:37.670 wdl.w:ptcp.t:call-pbmm2_align_hifi-65.stderr VERBOSE   --log-level INFO \
2025-09-15 20:23:37.670 wdl.w:ptcp.t:call-pbmm2_align_hifi-65.stderr VERBOSE   --log-file pbmm2.log \
2025-09-15 20:23:37.670 wdl.w:ptcp.t:call-pbmm2_align_hifi-65.stderr VERBOSE   --alarms alarms.json \
2025-09-15 20:23:37.670 wdl.w:ptcp.t:call-pbmm2_align_hifi-65.stderr VERBOSE   --num-threads 64 \
2025-09-15 20:23:37.670 wdl.w:ptcp.t:call-pbmm2_align_hifi-65.stderr VERBOSE   --sort \
2025-09-15 20:23:37.670 wdl.w:ptcp.t:call-pbmm2_align_hifi-65.stderr VERBOSE   --preset HiFi \
2025-09-15 20:23:37.670 wdl.w:ptcp.t:call-pbmm2_align_hifi-65.stderr VERBOSE   --report-json mapping_stats.report.json \
2025-09-15 20:23:37.670 wdl.w:ptcp.t:call-pbmm2_align_hifi-65.stderr VERBOSE   --sample "m84036_250809_035451_s4.bc2162" \
2025-09-15 20:23:37.670 wdl.w:ptcp.t:call-pbmm2_align_hifi-65.stderr VERBOSE   --unmapped \
2025-09-15 20:23:37.671 wdl.w:ptcp.t:call-pbmm2_align_hifi-65.stderr VERBOSE   /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa \
2025-09-15 20:23:37.671 wdl.w:ptcp.t:call-pbmm2_align_hifi-65.stderr VERBOSE   /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0066_m84036_250809_035451_s4.bc2162.unmapped.bam \
2025-09-15 20:23:37.671 wdl.w:ptcp.t:call-pbmm2_align_hifi-65.stderr VERBOSE   m84036_250809_035451_s4.bc2162.mapped.bam
2025-09-15 20:23:37.671 wdl.w:ptcp.t:call-pbmm2_align_hifi-65.stderr VERBOSE + pbmm2 align --log-level INFO --log-file pbmm2.log --alarms alarms.json --num-threads 64 --sort --preset HiFi --report-json mapping_stats.report.json --sample m84036_250809_035451_s4.bc2162 --unmapped /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0066_m84036_250809_035451_s4.bc2162.unmapped.bam m84036_250809_035451_s4.bc2162.mapped.bam
2025-09-15 20:23:37.671 wdl.w:ptcp.t:call-pbmm2_align_hifi-65.stderr VERBOSE 
2025-09-15 20:23:37.671 wdl.w:ptcp.t:call-pbmm2_align_hifi-65.stderr VERBOSE pbindex --num-threads 64 m84036_250809_035451_s4.bc2162.mapped.bam
2025-09-15 20:23:37.671 wdl.w:ptcp.t:call-pbmm2_align_hifi-65.stderr VERBOSE + pbindex --num-threads 64 m84036_250809_035451_s4.bc2162.mapped.bam
2025-09-15 20:23:37.671 wdl.w:ptcp.t:call-pbmm2_align_hifi-65.stderr VERBOSE 
2025-09-15 20:23:37.672 wdl.w:ptcp.w:call-sawfish-16.t:call-run_sawfish NOTICE task setup :: name: "run_sawfish", source: "./sawfish.wdl", line: 83, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-16/call-run_sawfish", thread: 140611457906240
2025-09-15 20:23:37.698 wdl.w:ptcp.w:call-sawfish-16.t:call-run_sawfish INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:23:37.698 wdl.w:ptcp.w:call-sawfish-16.t:call-run_sawfish INFO input :: name: "genome_version", value: "38"
2025-09-15 20:23:37.698 wdl.w:ptcp.w:call-sawfish-16.t:call-run_sawfish INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:23:37.698 wdl.w:ptcp.w:call-sawfish-16.t:call-run_sawfish INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:23:37.698 wdl.w:ptcp.w:call-sawfish-16.t:call-run_sawfish INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2113.mapped.bam.bai"
2025-09-15 20:23:37.699 wdl.w:ptcp.w:call-sawfish-16.t:call-run_sawfish INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2113.mapped.bam"
2025-09-15 20:23:37.699 wdl.w:ptcp.w:call-sawfish-16.t:call-run_sawfish INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2113"
2025-09-15 20:23:37.699 wdl.w:ptcp.w:call-sawfish-16.t:call-run_sawfish INFO eval :: name: "mem_gb", value: 32
2025-09-15 20:23:37.699 wdl.w:ptcp.w:call-sawfish-16.t:call-run_sawfish INFO eval :: name: "threads", value: 16
2025-09-15 20:23:37.699 wdl.w:ptcp.w:call-sawfish-16.t:call-run_sawfish INFO eval :: name: "disk_size", value: 30
2025-09-15 20:23:37.699 wdl.w:ptcp.w:call-sawfish-16.t:call-run_sawfish INFO eval :: name: "discover_dirname", value: "m84036_250809_035451_s4.bc2113_sawfish_discover"
2025-09-15 20:23:37.699 wdl.w:ptcp.w:call-sawfish-16.t:call-run_sawfish INFO eval :: name: "call_dirname", value: "m84036_250809_035451_s4.bc2113_sawfish"
2025-09-15 20:23:37.699 wdl.w:ptcp.w:call-sawfish-16.t:call-run_sawfish INFO eval :: name: "minimap2_bam_filename", value: "m84036_250809_035451_s4.bc2113.minimap2.bam"
2025-09-15 20:23:37.700 wdl.w:ptcp.w:call-sawfish-16.t:call-run_sawfish INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 16, memory_reservation: 32000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:23:37.700 wdl.w:ptcp.w:call-sawfish-16.t:call-run_sawfish WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:23:37.700 wdl.w:ptcp.w:call-sawfish-16.t:call-run_sawfish INFO provisioned :: seconds_waited: 0, cpu: 16, mem_bytes: 32000000000
2025-09-15 20:23:37.700 wdl.w:ptcp.w:call-sawfish-16.t:call-run_sawfish INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:23:37.720 wdl.w:ptcp.t:call-pbmm2_align_hifi-60 INFO output :: name: "mapped_bam", value: "m84036_250809_035451_s4.bc2157.mapped.bam"
2025-09-15 20:23:37.724 wdl.w:ptcp.t:call-pbmm2_align_hifi-60 INFO output :: name: "mapped_bam_bai", value: "m84036_250809_035451_s4.bc2157.mapped.bam.bai"
2025-09-15 20:23:37.725 wdl.w:ptcp.t:call-pbmm2_align_hifi-60 INFO output :: name: "mapped_bam_pbi", value: "m84036_250809_035451_s4.bc2157.mapped.bam.pbi"
2025-09-15 20:23:37.727 wdl.w:ptcp.t:call-pbmm2_align_hifi-60 INFO output :: name: "report", value: "mapping_stats.report.json"
2025-09-15 20:23:37.734 wdl.w:ptcp.t:call-pbmm2_align_hifi-65 INFO output :: name: "mapped_bam", value: "m84036_250809_035451_s4.bc2162.mapped.bam"
2025-09-15 20:23:37.738 wdl.w:ptcp.t:call-pbmm2_align_hifi-65 INFO output :: name: "mapped_bam_bai", value: "m84036_250809_035451_s4.bc2162.mapped.bam.bai"
2025-09-15 20:23:37.740 wdl.w:ptcp.t:call-pbmm2_align_hifi-65 INFO output :: name: "mapped_bam_pbi", value: "m84036_250809_035451_s4.bc2162.mapped.bam.pbi"
2025-09-15 20:23:37.743 wdl.w:ptcp.t:call-pbmm2_align_hifi-65 INFO output :: name: "report", value: "mapping_stats.report.json"
2025-09-15 20:23:37.783 wdl.w:ptcp.w:call-sawfish-16.t:call-run_sawfish INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 10, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-16/call-run_sawfish/_singularity_tmpdir_cllqgi5d"
2025-09-15 20:23:37.783 wdl.w:ptcp.w:call-sawfish-16.t:call-run_sawfish INFO Slurm invocation: srun --job-name call-run_sawfish --partition compute,compute9 --cpus-per-task 16 --mem 30518M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-16/call-run_sawfish/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-16/call-run_sawfish/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-16/call-run_sawfish/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-16/call-run_sawfish/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-16/out/m84036_250809_035451_s4.bc2113.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2113.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-16/out/m84036_250809_035451_s4.bc2113.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2113.mapped.bam.bai:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-16/call-run_sawfish/_singularity_tmpdir_cllqgi5d/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-16/call-run_sawfish/_singularity_tmpdir_cllqgi5d/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:23:37.815 wdl.w:ptcp.w:call-sawfish-16.t:call-run_sawfish NOTICE slurm_singularity run :: pid: 1199762, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-16/call-run_sawfish/slurm_singularity.log.txt"
2025-09-15 20:23:37.851 wdl.w:ptcp.t:call-pbmm2_align_hifi-60 NOTICE done
2025-09-15 20:23:37.860 wdl.w:ptcp NOTICE finish :: job: "call-pbmm2_align_hifi-60"
2025-09-15 20:23:37.860 wdl.w:ptcp INFO output :: job: "call-pbmm2_align_hifi-60", values: {"report": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-60/out/mapping_stats.report.json", "mapped_bam_pbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-60/out/m84036_250809_035451_s4.bc2157.mapped.bam.pbi", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-60/out/m84036_250809_035451_s4.bc2157.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-60/out/m84036_250809_035451_s4.bc2157.mapped.bam"}
2025-09-15 20:23:37.861 wdl.w:ptcp NOTICE ready :: job: "call-paraphase-60", callee: "paraphase"
2025-09-15 20:23:37.861 wdl.w:ptcp INFO input :: job: "call-paraphase-60", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf", "genome_version": "38", "config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-60/out/m84036_250809_035451_s4.bc2157.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-60/out/m84036_250809_035451_s4.bc2157.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2157"}
2025-09-15 20:23:37.862 wdl.w:ptcp NOTICE ready :: job: "call-sawfish-60", callee: "sawfish"
2025-09-15 20:23:37.863 wdl.w:ptcp INFO input :: job: "call-sawfish-60", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-60/out/m84036_250809_035451_s4.bc2157.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-60/out/m84036_250809_035451_s4.bc2157.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2157"}
2025-09-15 20:23:37.864 wdl.w:ptcp NOTICE ready :: job: "call-trgt-60", callee: "trgt"
2025-09-15 20:23:37.864 wdl.w:ptcp INFO input :: job: "call-trgt-60", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-60/out/m84036_250809_035451_s4.bc2157.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-60/out/m84036_250809_035451_s4.bc2157.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2157"}
2025-09-15 20:23:37.872 wdl.w:ptcp.w:call-paraphase-16.t:call-run_paraphase NOTICE task setup :: name: "run_paraphase", source: "./paraphase.wdl", line: 127, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-16/call-run_paraphase", thread: 140609293637184
2025-09-15 20:23:37.875 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_genotype.slurm_singularity INFO srun: job 51797430 queued and waiting for resources
2025-09-15 20:23:37.875 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_genotype.slurm_singularity INFO srun: job 51797430 has been allocated resources
2025-09-15 20:23:37.875 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_genotype.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:37.880 wdl.w:ptcp.t:call-pbmm2_align_hifi-65 NOTICE done
2025-09-15 20:23:37.892 wdl.w:ptcp NOTICE finish :: job: "call-pbmm2_align_hifi-65"
2025-09-15 20:23:37.892 wdl.w:ptcp INFO output :: job: "call-pbmm2_align_hifi-65", values: {"report": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-65/out/mapping_stats.report.json", "mapped_bam_pbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-65/out/m84036_250809_035451_s4.bc2162.mapped.bam.pbi", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-65/out/m84036_250809_035451_s4.bc2162.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-65/out/m84036_250809_035451_s4.bc2162.mapped.bam"}
2025-09-15 20:23:37.893 wdl.w:ptcp NOTICE ready :: job: "call-paraphase-65", callee: "paraphase"
2025-09-15 20:23:37.893 wdl.w:ptcp INFO input :: job: "call-paraphase-65", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf", "genome_version": "38", "config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-65/out/m84036_250809_035451_s4.bc2162.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-65/out/m84036_250809_035451_s4.bc2162.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2162"}
2025-09-15 20:23:37.894 wdl.w:ptcp NOTICE ready :: job: "call-sawfish-65", callee: "sawfish"
2025-09-15 20:23:37.894 wdl.w:ptcp INFO input :: job: "call-sawfish-65", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-65/out/m84036_250809_035451_s4.bc2162.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-65/out/m84036_250809_035451_s4.bc2162.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2162"}
2025-09-15 20:23:37.895 wdl.w:ptcp NOTICE ready :: job: "call-trgt-65", callee: "trgt"
2025-09-15 20:23:37.895 wdl.w:ptcp INFO input :: job: "call-trgt-65", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-65/out/m84036_250809_035451_s4.bc2162.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-65/out/m84036_250809_035451_s4.bc2162.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2162"}
2025-09-15 20:23:37.900 wdl.w:ptcp.w:call-trgt-16.t:call-get_reads_overlapping_repeats NOTICE task setup :: name: "get_reads_overlapping_repeats", source: "./trgt.wdl", line: 182, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-16/call-get_reads_overlapping_repeats", thread: 140608773551680
2025-09-15 20:23:37.904 wdl.w:ptcp.w:call-paraphase-16.t:call-run_paraphase INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:23:37.905 wdl.w:ptcp.w:call-paraphase-16.t:call-run_paraphase INFO input :: name: "annotation_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf"
2025-09-15 20:23:37.905 wdl.w:ptcp.w:call-paraphase-16.t:call-run_paraphase INFO input :: name: "genome_version", value: "38"
2025-09-15 20:23:37.905 wdl.w:ptcp.w:call-paraphase-16.t:call-run_paraphase INFO input :: name: "config_file", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/paraphase_config.GRCh38.yaml"
2025-09-15 20:23:37.905 wdl.w:ptcp.w:call-paraphase-16.t:call-run_paraphase INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:23:37.905 wdl.w:ptcp.w:call-paraphase-16.t:call-run_paraphase INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:23:37.905 wdl.w:ptcp.w:call-paraphase-16.t:call-run_paraphase INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2113.mapped.bam.bai"
2025-09-15 20:23:37.905 wdl.w:ptcp.w:call-paraphase-16.t:call-run_paraphase INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2113.mapped.bam"
2025-09-15 20:23:37.905 wdl.w:ptcp.w:call-paraphase-16.t:call-run_paraphase INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2113"
2025-09-15 20:23:37.905 wdl.w:ptcp.w:call-paraphase-16.t:call-run_paraphase INFO eval :: name: "threads", value: 4
2025-09-15 20:23:37.905 wdl.w:ptcp.w:call-paraphase-16.t:call-run_paraphase INFO eval :: name: "mem_gb", value: 8
2025-09-15 20:23:37.906 wdl.w:ptcp.w:call-paraphase-16.t:call-run_paraphase INFO eval :: name: "disk_size", value: 27
2025-09-15 20:23:37.906 wdl.w:ptcp.w:call-paraphase-16.t:call-run_paraphase INFO eval :: name: "out_dir", value: "m84036_250809_035451_s4.bc2113_paraphase"
2025-09-15 20:23:37.906 wdl.w:ptcp.w:call-paraphase-16.t:call-run_paraphase INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 4, memory_reservation: 8000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:23:37.906 wdl.w:ptcp.w:call-paraphase-16.t:call-run_paraphase WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:23:37.907 wdl.w:ptcp.w:call-paraphase-16.t:call-run_paraphase INFO provisioned :: seconds_waited: 0, cpu: 4, mem_bytes: 8000000000
2025-09-15 20:23:37.907 wdl.w:ptcp.w:call-paraphase-16.t:call-run_paraphase INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:23:37.925 wdl.w:ptcp.w:call-trgt-16.t:call-get_reads_overlapping_repeats INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:23:37.925 wdl.w:ptcp.w:call-trgt-16.t:call-get_reads_overlapping_repeats INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:23:37.925 wdl.w:ptcp.w:call-trgt-16.t:call-get_reads_overlapping_repeats INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2113.mapped.bam.bai"
2025-09-15 20:23:37.925 wdl.w:ptcp.w:call-trgt-16.t:call-get_reads_overlapping_repeats INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2113.mapped.bam"
2025-09-15 20:23:37.926 wdl.w:ptcp.w:call-trgt-16.t:call-get_reads_overlapping_repeats INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2113"
2025-09-15 20:23:37.926 wdl.w:ptcp.w:call-trgt-16.t:call-get_reads_overlapping_repeats INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:23:37.926 wdl.w:ptcp.w:call-trgt-16.t:call-get_reads_overlapping_repeats INFO eval :: name: "expand_size", value: 3000
2025-09-15 20:23:37.926 wdl.w:ptcp.w:call-trgt-16.t:call-get_reads_overlapping_repeats INFO eval :: name: "threads", value: 1
2025-09-15 20:23:37.926 wdl.w:ptcp.w:call-trgt-16.t:call-get_reads_overlapping_repeats INFO eval :: name: "expanded_bed_name", value: "m84036_250809_035451_s4.bc2113.expanded.bed"
2025-09-15 20:23:37.926 wdl.w:ptcp.w:call-trgt-16.t:call-get_reads_overlapping_repeats INFO eval :: name: "disk_size", value: 11
2025-09-15 20:23:37.926 wdl.w:ptcp.w:call-trgt-16.t:call-get_reads_overlapping_repeats INFO eval :: name: "output_name", value: "m84036_250809_035451_s4.bc2113.repeats.bam"
2025-09-15 20:23:37.927 wdl.w:ptcp.w:call-trgt-16.t:call-get_reads_overlapping_repeats INFO eval :: name: "index_name", value: "m84036_250809_035451_s4.bc2113.repeats.bam.bai"
2025-09-15 20:23:37.927 wdl.w:ptcp.w:call-trgt-16.t:call-get_reads_overlapping_repeats INFO eval :: name: "output_name_with_index", value: "m84036_250809_035451_s4.bc2113.repeats.bam##idx##m84036_250809_035451_s4.bc2113.repeats.bam.bai"
2025-09-15 20:23:37.927 wdl.w:ptcp.w:call-trgt-16.t:call-get_reads_overlapping_repeats INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:23:37.927 wdl.w:ptcp.w:call-trgt-16.t:call-get_reads_overlapping_repeats WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:23:37.927 wdl.w:ptcp.w:call-trgt-16.t:call-get_reads_overlapping_repeats INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:23:37.928 wdl.w:ptcp.w:call-trgt-16.t:call-get_reads_overlapping_repeats INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:23:38.010 wdl.w:ptcp.w:call-trgt-16.t:call-get_reads_overlapping_repeats INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 9, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-16/call-get_reads_overlapping_repeats/_singularity_tmpdir_k2wdpuka"
2025-09-15 20:23:38.011 wdl.w:ptcp.w:call-trgt-16.t:call-get_reads_overlapping_repeats INFO Slurm invocation: srun --job-name call-get_reads_overlapping_repeats --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-16/call-get_reads_overlapping_repeats/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-16/call-get_reads_overlapping_repeats/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-16/call-get_reads_overlapping_repeats/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-16/call-get_reads_overlapping_repeats/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-16/out/m84036_250809_035451_s4.bc2113.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2113.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-16/out/m84036_250809_035451_s4.bc2113.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2113.mapped.bam.bai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-16/call-get_reads_overlapping_repeats/_singularity_tmpdir_k2wdpuka/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-16/call-get_reads_overlapping_repeats/_singularity_tmpdir_k2wdpuka/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:23:38.020 wdl.w:ptcp.w:call-paraphase-16.t:call-run_paraphase INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-16/call-run_paraphase/_singularity_tmpdir_k1sl4vxv"
2025-09-15 20:23:38.021 wdl.w:ptcp.w:call-paraphase-16.t:call-run_paraphase INFO Slurm invocation: srun --job-name call-run_paraphase --partition compute,compute9 --cpus-per-task 4 --mem 7629M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-16/call-run_paraphase/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-16/call-run_paraphase/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-16/call-run_paraphase/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-16/call-run_paraphase/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-16/out/m84036_250809_035451_s4.bc2113.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2113.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-16/out/m84036_250809_035451_s4.bc2113.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2113.mapped.bam.bai:ro --bind /ptcp/meta/variant_list/variant_list.GRCh38.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf:ro --bind /ptcp/meta/paraphase/paraphase_config.GRCh38.yaml:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/paraphase_config.GRCh38.yaml:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-16/call-run_paraphase/_singularity_tmpdir_k1sl4vxv/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-16/call-run_paraphase/_singularity_tmpdir_k1sl4vxv/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:23:38.038 wdl.w:ptcp.w:call-sawfish-25.t:call-run_sawfish.stderr VERBOSE [M::bam2fq_mainloop] discarded 0 singletons
2025-09-15 20:23:38.038 wdl.w:ptcp.w:call-sawfish-25.t:call-run_sawfish.stderr VERBOSE [M::bam2fq_mainloop] processed 1 reads
2025-09-15 20:23:38.042 wdl.w:ptcp.w:call-trgt-12.t:call-get_reads_overlapping_repeats INFO output :: name: "reads_overlapping_repeats", value: "m84036_250809_035451_s4.bc2109.repeats.bam"
2025-09-15 20:23:38.046 wdl.w:ptcp.w:call-paraphase-25.t:call-run_paraphase.slurm_singularity INFO srun: job 51797431 queued and waiting for resources
2025-09-15 20:23:38.046 wdl.w:ptcp.w:call-paraphase-25.t:call-run_paraphase.slurm_singularity INFO srun: job 51797431 has been allocated resources
2025-09-15 20:23:38.046 wdl.w:ptcp.w:call-paraphase-25.t:call-run_paraphase.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:38.049 wdl.w:ptcp.w:call-trgt-12.t:call-get_reads_overlapping_repeats INFO output :: name: "reads_overlapping_repeats_bai", value: "m84036_250809_035451_s4.bc2109.repeats.bam.bai"
2025-09-15 20:23:38.053 wdl.w:ptcp.w:call-paraphase-16.t:call-run_paraphase NOTICE slurm_singularity run :: pid: 1199771, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-16/call-run_paraphase/slurm_singularity.log.txt"
2025-09-15 20:23:38.056 wdl.w:ptcp.w:call-trgt-16.t:call-get_reads_overlapping_repeats NOTICE slurm_singularity run :: pid: 1199770, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-16/call-get_reads_overlapping_repeats/slurm_singularity.log.txt"
2025-09-15 20:23:38.059 wdl.w:ptcp.w:call-sawfish-25.t:call-run_sawfish.slurm_singularity INFO srun: job 51797432 queued and waiting for resources
2025-09-15 20:23:38.059 wdl.w:ptcp.w:call-sawfish-25.t:call-run_sawfish.slurm_singularity INFO srun: job 51797432 has been allocated resources
2025-09-15 20:23:38.059 wdl.w:ptcp.w:call-sawfish-25.t:call-run_sawfish.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:38.059 wdl.w:ptcp.w:call-sawfish-25.t:call-run_sawfish.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:23:38.130 wdl.w:ptcp.w:call-trgt-12.t:call-get_reads_overlapping_repeats NOTICE done
2025-09-15 20:23:38.135 wdl.w:ptcp.w:call-trgt-12 NOTICE finish :: job: "call-get_reads_overlapping_repeats"
2025-09-15 20:23:38.135 wdl.w:ptcp.w:call-trgt-12 INFO output :: job: "call-get_reads_overlapping_repeats", values: {"reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-12/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2109.repeats.bam.bai", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-12/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2109.repeats.bam"}
2025-09-15 20:23:38.135 wdl.w:ptcp.w:call-trgt-12 INFO visit :: node: "output-reads_overlapping_repeats", values: {"reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-12/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2109.repeats.bam"}
2025-09-15 20:23:38.135 wdl.w:ptcp.w:call-trgt-12 INFO visit :: node: "output-reads_overlapping_repeats_bai", values: {"reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-12/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2109.repeats.bam.bai"}
2025-09-15 20:23:38.142 wdl.w:ptcp.w:call-trgt-16.t:call-trgt_genotype NOTICE task setup :: name: "trgt_genotype", source: "./trgt.wdl", line: 272, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-16/call-trgt_genotype", thread: 140610870679104
2025-09-15 20:23:38.162 wdl.w:ptcp.w:call-trgt-16.t:call-trgt_genotype INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:23:38.162 wdl.w:ptcp.w:call-trgt-16.t:call-trgt_genotype INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:23:38.162 wdl.w:ptcp.w:call-trgt-16.t:call-trgt_genotype INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:23:38.163 wdl.w:ptcp.w:call-trgt-16.t:call-trgt_genotype INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:23:38.163 wdl.w:ptcp.w:call-trgt-16.t:call-trgt_genotype INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2113.mapped.bam.bai"
2025-09-15 20:23:38.163 wdl.w:ptcp.w:call-trgt-16.t:call-trgt_genotype INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2113.mapped.bam"
2025-09-15 20:23:38.163 wdl.w:ptcp.w:call-trgt-16.t:call-trgt_genotype INFO input :: name: "sex", value: "F"
2025-09-15 20:23:38.163 wdl.w:ptcp.w:call-trgt-16.t:call-trgt_genotype INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2113"
2025-09-15 20:23:38.163 wdl.w:ptcp.w:call-trgt-16.t:call-trgt_genotype INFO eval :: name: "mem_gb", value: 16
2025-09-15 20:23:38.163 wdl.w:ptcp.w:call-trgt-16.t:call-trgt_genotype INFO eval :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2113.trgt"
2025-09-15 20:23:38.163 wdl.w:ptcp.w:call-trgt-16.t:call-trgt_genotype INFO eval :: name: "threads", value: 8
2025-09-15 20:23:38.163 wdl.w:ptcp.w:call-trgt-16.t:call-trgt_genotype INFO eval :: name: "disk_size", value: 27
2025-09-15 20:23:38.164 wdl.w:ptcp.w:call-trgt-16.t:call-trgt_genotype INFO eval :: name: "karyotype", value: "XX"
2025-09-15 20:23:38.164 wdl.w:ptcp.w:call-trgt-16.t:call-trgt_genotype INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 8, memory_reservation: 16000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:23:38.164 wdl.w:ptcp.w:call-trgt-16.t:call-trgt_genotype WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:23:38.164 wdl.w:ptcp.w:call-trgt-16.t:call-trgt_genotype INFO provisioned :: seconds_waited: 0, cpu: 8, mem_bytes: 16000000000
2025-09-15 20:23:38.165 wdl.w:ptcp.w:call-trgt-16.t:call-trgt_genotype INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:23:38.230 wdl.w:ptcp.w:call-trgt-12.t:call-trgt_genotype INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2109.trgt.vcf"
2025-09-15 20:23:38.235 wdl.w:ptcp.w:call-trgt-12.t:call-trgt_genotype INFO output :: name: "spanning_bam", value: "m84036_250809_035451_s4.bc2109.trgt.sorted.spanning.bam"
2025-09-15 20:23:38.236 wdl.w:ptcp.w:call-trgt-12.t:call-trgt_genotype INFO output :: name: "spanning_bam_bai", value: "m84036_250809_035451_s4.bc2109.trgt.sorted.spanning.bam.bai"
2025-09-15 20:23:38.252 wdl.w:ptcp.w:call-trgt-16.t:call-trgt_genotype INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 11, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-16/call-trgt_genotype/_singularity_tmpdir_zf5jkiu7"
2025-09-15 20:23:38.252 wdl.w:ptcp.w:call-trgt-16.t:call-trgt_genotype INFO Slurm invocation: srun --job-name call-trgt_genotype --partition compute,compute9 --cpus-per-task 8 --mem 15259M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-16/call-trgt_genotype/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-16/call-trgt_genotype/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-16/call-trgt_genotype/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-16/call-trgt_genotype/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-16/out/m84036_250809_035451_s4.bc2113.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2113.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-16/out/m84036_250809_035451_s4.bc2113.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2113.mapped.bam.bai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-16/call-trgt_genotype/_singularity_tmpdir_zf5jkiu7/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-16/call-trgt_genotype/_singularity_tmpdir_zf5jkiu7/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:23:38.279 wdl.w:ptcp.w:call-trgt-16.t:call-trgt_genotype NOTICE slurm_singularity run :: pid: 1199786, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-16/call-trgt_genotype/slurm_singularity.log.txt"
2025-09-15 20:23:38.338 wdl.w:ptcp.w:call-trgt-12.t:call-trgt_genotype NOTICE done
2025-09-15 20:23:38.346 wdl.w:ptcp.w:call-trgt-12 NOTICE finish :: job: "call-trgt_genotype"
2025-09-15 20:23:38.346 wdl.w:ptcp.w:call-trgt-12 INFO output :: job: "call-trgt_genotype", values: {"spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-12/call-trgt_genotype/out/m84036_250809_035451_s4.bc2109.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-12/call-trgt_genotype/out/m84036_250809_035451_s4.bc2109.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-12/call-trgt_genotype/out/m84036_250809_035451_s4.bc2109.trgt.vcf"}
2025-09-15 20:23:38.346 wdl.w:ptcp.w:call-trgt-12 NOTICE ready :: job: "call-trgt_plot_meth_allele", callee: "trgt_plot"
2025-09-15 20:23:38.347 wdl.w:ptcp.w:call-trgt-12 INFO input :: job: "call-trgt_plot_meth_allele", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": false, "methylation": true, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-12/call-trgt_genotype/out/m84036_250809_035451_s4.bc2109.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-12/call-trgt_genotype/out/m84036_250809_035451_s4.bc2109.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-12/call-trgt_genotype/out/m84036_250809_035451_s4.bc2109.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2109"}
2025-09-15 20:23:38.348 wdl.w:ptcp.w:call-trgt-12 NOTICE ready :: job: "call-trgt_plot_meth_waterfall", callee: "trgt_plot"
2025-09-15 20:23:38.348 wdl.w:ptcp.w:call-trgt-12 INFO input :: job: "call-trgt_plot_meth_waterfall", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": true, "methylation": true, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-12/call-trgt_genotype/out/m84036_250809_035451_s4.bc2109.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-12/call-trgt_genotype/out/m84036_250809_035451_s4.bc2109.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-12/call-trgt_genotype/out/m84036_250809_035451_s4.bc2109.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2109"}
2025-09-15 20:23:38.350 wdl.w:ptcp.w:call-trgt-12 NOTICE ready :: job: "call-trgt_plot_motifs_allele", callee: "trgt_plot"
2025-09-15 20:23:38.350 wdl.w:ptcp.w:call-trgt-12 INFO input :: job: "call-trgt_plot_motifs_allele", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": false, "methylation": false, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-12/call-trgt_genotype/out/m84036_250809_035451_s4.bc2109.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-12/call-trgt_genotype/out/m84036_250809_035451_s4.bc2109.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-12/call-trgt_genotype/out/m84036_250809_035451_s4.bc2109.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2109"}
2025-09-15 20:23:38.351 wdl.w:ptcp.w:call-trgt-12 NOTICE ready :: job: "call-trgt_plot_motifs_waterfall", callee: "trgt_plot"
2025-09-15 20:23:38.351 wdl.w:ptcp.w:call-trgt-12 INFO input :: job: "call-trgt_plot_motifs_waterfall", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": true, "methylation": false, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-12/call-trgt_genotype/out/m84036_250809_035451_s4.bc2109.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-12/call-trgt_genotype/out/m84036_250809_035451_s4.bc2109.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-12/call-trgt_genotype/out/m84036_250809_035451_s4.bc2109.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2109"}
2025-09-15 20:23:38.352 wdl.w:ptcp.w:call-trgt-12 INFO visit :: node: "output-spanning_bam", values: {"spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-12/call-trgt_genotype/out/m84036_250809_035451_s4.bc2109.trgt.sorted.spanning.bam"}
2025-09-15 20:23:38.352 wdl.w:ptcp.w:call-trgt-12 INFO visit :: node: "output-spanning_bam_bai", values: {"spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-12/call-trgt_genotype/out/m84036_250809_035451_s4.bc2109.trgt.sorted.spanning.bam.bai"}
2025-09-15 20:23:38.352 wdl.w:ptcp.w:call-trgt-12 INFO visit :: node: "output-vcf", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-12/call-trgt_genotype/out/m84036_250809_035451_s4.bc2109.trgt.vcf"}
2025-09-15 20:23:38.358 wdl.w:ptcp.w:call-paraphase-32.t:call-run_paraphase NOTICE task setup :: name: "run_paraphase", source: "./paraphase.wdl", line: 127, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-32/call-run_paraphase", thread: 140609813722688
2025-09-15 20:23:38.399 wdl.w:ptcp.w:call-paraphase-32.t:call-run_paraphase INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:23:38.399 wdl.w:ptcp.w:call-paraphase-32.t:call-run_paraphase INFO input :: name: "annotation_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf"
2025-09-15 20:23:38.399 wdl.w:ptcp.w:call-paraphase-32.t:call-run_paraphase INFO input :: name: "genome_version", value: "38"
2025-09-15 20:23:38.399 wdl.w:ptcp.w:call-paraphase-32.t:call-run_paraphase INFO input :: name: "config_file", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/paraphase_config.GRCh38.yaml"
2025-09-15 20:23:38.399 wdl.w:ptcp.w:call-paraphase-32.t:call-run_paraphase INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:23:38.399 wdl.w:ptcp.w:call-paraphase-32.t:call-run_paraphase INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:23:38.399 wdl.w:ptcp.w:call-paraphase-32.t:call-run_paraphase INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2129.mapped.bam.bai"
2025-09-15 20:23:38.399 wdl.w:ptcp.w:call-paraphase-32.t:call-run_paraphase INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2129.mapped.bam"
2025-09-15 20:23:38.399 wdl.w:ptcp.w:call-paraphase-32.t:call-run_paraphase INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2129"
2025-09-15 20:23:38.399 wdl.w:ptcp.w:call-paraphase-32.t:call-run_paraphase INFO eval :: name: "threads", value: 4
2025-09-15 20:23:38.400 wdl.w:ptcp.w:call-paraphase-32.t:call-run_paraphase INFO eval :: name: "mem_gb", value: 8
2025-09-15 20:23:38.400 wdl.w:ptcp.w:call-paraphase-32.t:call-run_paraphase INFO eval :: name: "disk_size", value: 27
2025-09-15 20:23:38.400 wdl.w:ptcp.w:call-paraphase-32.t:call-run_paraphase INFO eval :: name: "out_dir", value: "m84036_250809_035451_s4.bc2129_paraphase"
2025-09-15 20:23:38.401 wdl.w:ptcp.w:call-paraphase-32.t:call-run_paraphase INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 4, memory_reservation: 8000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:23:38.401 wdl.w:ptcp.w:call-paraphase-32.t:call-run_paraphase WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:23:38.402 wdl.w:ptcp.w:call-paraphase-32.t:call-run_paraphase INFO provisioned :: seconds_waited: 0, cpu: 4, mem_bytes: 8000000000
2025-09-15 20:23:38.402 wdl.w:ptcp.w:call-paraphase-32.t:call-run_paraphase INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:23:38.410 wdl.w:ptcp.t:call-pbmm2_align_hifi-66.stderr VERBOSE 
2025-09-15 20:23:38.411 wdl.w:ptcp.t:call-pbmm2_align_hifi-66.stderr VERBOSE pbmm2 \
2025-09-15 20:23:38.411 wdl.w:ptcp.t:call-pbmm2_align_hifi-66.stderr VERBOSE   align \
2025-09-15 20:23:38.411 wdl.w:ptcp.t:call-pbmm2_align_hifi-66.stderr VERBOSE   --log-level INFO \
2025-09-15 20:23:38.411 wdl.w:ptcp.t:call-pbmm2_align_hifi-66.stderr VERBOSE   --log-file pbmm2.log \
2025-09-15 20:23:38.411 wdl.w:ptcp.t:call-pbmm2_align_hifi-66.stderr VERBOSE   --alarms alarms.json \
2025-09-15 20:23:38.411 wdl.w:ptcp.t:call-pbmm2_align_hifi-66.stderr VERBOSE   --num-threads 64 \
2025-09-15 20:23:38.411 wdl.w:ptcp.t:call-pbmm2_align_hifi-66.stderr VERBOSE   --sort \
2025-09-15 20:23:38.411 wdl.w:ptcp.t:call-pbmm2_align_hifi-66.stderr VERBOSE   --preset HiFi \
2025-09-15 20:23:38.411 wdl.w:ptcp.t:call-pbmm2_align_hifi-66.stderr VERBOSE   --report-json mapping_stats.report.json \
2025-09-15 20:23:38.411 wdl.w:ptcp.t:call-pbmm2_align_hifi-66.stderr VERBOSE   --sample "m84036_250809_035451_s4.bc2163" \
2025-09-15 20:23:38.411 wdl.w:ptcp.t:call-pbmm2_align_hifi-66.stderr VERBOSE   --unmapped \
2025-09-15 20:23:38.411 wdl.w:ptcp.t:call-pbmm2_align_hifi-66.stderr VERBOSE   /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa \
2025-09-15 20:23:38.412 wdl.w:ptcp.t:call-pbmm2_align_hifi-66.stderr VERBOSE   /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0067_m84036_250809_035451_s4.bc2163.unmapped.bam \
2025-09-15 20:23:38.412 wdl.w:ptcp.t:call-pbmm2_align_hifi-66.stderr VERBOSE   m84036_250809_035451_s4.bc2163.mapped.bam
2025-09-15 20:23:38.412 wdl.w:ptcp.t:call-pbmm2_align_hifi-66.stderr VERBOSE + pbmm2 align --log-level INFO --log-file pbmm2.log --alarms alarms.json --num-threads 64 --sort --preset HiFi --report-json mapping_stats.report.json --sample m84036_250809_035451_s4.bc2163 --unmapped /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0067_m84036_250809_035451_s4.bc2163.unmapped.bam m84036_250809_035451_s4.bc2163.mapped.bam
2025-09-15 20:23:38.425 wdl.w:ptcp.w:call-paraphase-17.t:call-run_paraphase INFO output :: name: "paraphase_bam", value: "m84036_250809_035451_s4.bc2114_paraphase/m84036_250809_035451_s4.bc2114.paraphase.bam"
2025-09-15 20:23:38.430 wdl.w:ptcp.w:call-paraphase-17.t:call-run_paraphase INFO output :: name: "paraphase_bam_bai", value: "m84036_250809_035451_s4.bc2114_paraphase/m84036_250809_035451_s4.bc2114.paraphase.bam.bai"
2025-09-15 20:23:38.431 wdl.w:ptcp.w:call-paraphase-17.t:call-run_paraphase INFO output :: name: "paraphase_json", value: "m84036_250809_035451_s4.bc2114_paraphase/m84036_250809_035451_s4.bc2114.paraphase.json"
2025-09-15 20:23:38.434 wdl.w:ptcp.w:call-paraphase-17.t:call-run_paraphase INFO output :: name: "paraphase_vcfs", value: []
2025-09-15 20:23:38.434 wdl.w:ptcp.w:call-paraphase-17.t:call-run_paraphase INFO output :: name: "havanno_json", value: "m84036_250809_035451_s4.bc2114.havanno.json"
2025-09-15 20:23:38.496 wdl.w:ptcp.w:call-trgt-25.t:call-get_reads_overlapping_repeats.slurm_singularity INFO srun: job 51797433 queued and waiting for resources
2025-09-15 20:23:38.496 wdl.w:ptcp.w:call-trgt-25.t:call-get_reads_overlapping_repeats.slurm_singularity INFO srun: job 51797433 has been allocated resources
2025-09-15 20:23:38.496 wdl.w:ptcp.w:call-trgt-25.t:call-get_reads_overlapping_repeats.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:38.505 wdl.w:ptcp.t:call-pbmm2_align_hifi-74.stderr VERBOSE 
2025-09-15 20:23:38.506 wdl.w:ptcp.t:call-pbmm2_align_hifi-74.stderr VERBOSE pbmm2 \
2025-09-15 20:23:38.506 wdl.w:ptcp.t:call-pbmm2_align_hifi-74.stderr VERBOSE   align \
2025-09-15 20:23:38.506 wdl.w:ptcp.t:call-pbmm2_align_hifi-74.stderr VERBOSE   --log-level INFO \
2025-09-15 20:23:38.506 wdl.w:ptcp.t:call-pbmm2_align_hifi-74.stderr VERBOSE   --log-file pbmm2.log \
2025-09-15 20:23:38.506 wdl.w:ptcp.t:call-pbmm2_align_hifi-74.stderr VERBOSE   --alarms alarms.json \
2025-09-15 20:23:38.506 wdl.w:ptcp.t:call-pbmm2_align_hifi-74.stderr VERBOSE   --num-threads 64 \
2025-09-15 20:23:38.506 wdl.w:ptcp.t:call-pbmm2_align_hifi-74.stderr VERBOSE   --sort \
2025-09-15 20:23:38.506 wdl.w:ptcp.t:call-pbmm2_align_hifi-74.stderr VERBOSE   --preset HiFi \
2025-09-15 20:23:38.506 wdl.w:ptcp.t:call-pbmm2_align_hifi-74.stderr VERBOSE   --report-json mapping_stats.report.json \
2025-09-15 20:23:38.506 wdl.w:ptcp.t:call-pbmm2_align_hifi-74.stderr VERBOSE   --sample "m84036_250809_035451_s4.bc2171" \
2025-09-15 20:23:38.506 wdl.w:ptcp.t:call-pbmm2_align_hifi-74.stderr VERBOSE   --unmapped \
2025-09-15 20:23:38.506 wdl.w:ptcp.t:call-pbmm2_align_hifi-74.stderr VERBOSE   /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa \
2025-09-15 20:23:38.506 wdl.w:ptcp.t:call-pbmm2_align_hifi-74.stderr VERBOSE   /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0075_m84036_250809_035451_s4.bc2171.unmapped.bam \
2025-09-15 20:23:38.506 wdl.w:ptcp.t:call-pbmm2_align_hifi-74.stderr VERBOSE   m84036_250809_035451_s4.bc2171.mapped.bam
2025-09-15 20:23:38.506 wdl.w:ptcp.t:call-pbmm2_align_hifi-74.stderr VERBOSE + pbmm2 align --log-level INFO --log-file pbmm2.log --alarms alarms.json --num-threads 64 --sort --preset HiFi --report-json mapping_stats.report.json --sample m84036_250809_035451_s4.bc2171 --unmapped /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0075_m84036_250809_035451_s4.bc2171.unmapped.bam m84036_250809_035451_s4.bc2171.mapped.bam
2025-09-15 20:23:38.513 wdl.w:ptcp.w:call-paraphase-32.t:call-run_paraphase INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-32/call-run_paraphase/_singularity_tmpdir_xot3_p6m"
2025-09-15 20:23:38.514 wdl.w:ptcp.w:call-paraphase-32.t:call-run_paraphase INFO Slurm invocation: srun --job-name call-run_paraphase --partition compute,compute9 --cpus-per-task 4 --mem 7629M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-32/call-run_paraphase/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-32/call-run_paraphase/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-32/call-run_paraphase/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-32/call-run_paraphase/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-32/out/m84036_250809_035451_s4.bc2129.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2129.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-32/out/m84036_250809_035451_s4.bc2129.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2129.mapped.bam:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/variant_list/variant_list.GRCh38.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf:ro --bind /ptcp/meta/paraphase/paraphase_config.GRCh38.yaml:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/paraphase_config.GRCh38.yaml:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-32/call-run_paraphase/_singularity_tmpdir_xot3_p6m/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-32/call-run_paraphase/_singularity_tmpdir_xot3_p6m/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:23:38.517 wdl.w:ptcp.t:call-pbmm2_align_hifi-76.stderr VERBOSE 
2025-09-15 20:23:38.517 wdl.w:ptcp.t:call-pbmm2_align_hifi-76.stderr VERBOSE pbmm2 \
2025-09-15 20:23:38.518 wdl.w:ptcp.t:call-pbmm2_align_hifi-76.stderr VERBOSE   align \
2025-09-15 20:23:38.518 wdl.w:ptcp.t:call-pbmm2_align_hifi-76.stderr VERBOSE   --log-level INFO \
2025-09-15 20:23:38.518 wdl.w:ptcp.t:call-pbmm2_align_hifi-76.stderr VERBOSE   --log-file pbmm2.log \
2025-09-15 20:23:38.518 wdl.w:ptcp.t:call-pbmm2_align_hifi-76.stderr VERBOSE   --alarms alarms.json \
2025-09-15 20:23:38.518 wdl.w:ptcp.t:call-pbmm2_align_hifi-76.stderr VERBOSE   --num-threads 64 \
2025-09-15 20:23:38.518 wdl.w:ptcp.t:call-pbmm2_align_hifi-76.stderr VERBOSE   --sort \
2025-09-15 20:23:38.518 wdl.w:ptcp.t:call-pbmm2_align_hifi-76.stderr VERBOSE   --preset HiFi \
2025-09-15 20:23:38.518 wdl.w:ptcp.t:call-pbmm2_align_hifi-76.stderr VERBOSE   --report-json mapping_stats.report.json \
2025-09-15 20:23:38.518 wdl.w:ptcp.t:call-pbmm2_align_hifi-76.stderr VERBOSE   --sample "m84036_250809_035451_s4.bc2173" \
2025-09-15 20:23:38.518 wdl.w:ptcp.t:call-pbmm2_align_hifi-76.stderr VERBOSE   --unmapped \
2025-09-15 20:23:38.518 wdl.w:ptcp.t:call-pbmm2_align_hifi-76.stderr VERBOSE   /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa \
2025-09-15 20:23:38.518 wdl.w:ptcp.t:call-pbmm2_align_hifi-76.stderr VERBOSE   /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0077_m84036_250809_035451_s4.bc2173.unmapped.bam \
2025-09-15 20:23:38.518 wdl.w:ptcp.t:call-pbmm2_align_hifi-76.stderr VERBOSE   m84036_250809_035451_s4.bc2173.mapped.bam
2025-09-15 20:23:38.518 wdl.w:ptcp.t:call-pbmm2_align_hifi-76.stderr VERBOSE + pbmm2 align --log-level INFO --log-file pbmm2.log --alarms alarms.json --num-threads 64 --sort --preset HiFi --report-json mapping_stats.report.json --sample m84036_250809_035451_s4.bc2173 --unmapped /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0077_m84036_250809_035451_s4.bc2173.unmapped.bam m84036_250809_035451_s4.bc2173.mapped.bam
2025-09-15 20:23:38.519 wdl.w:ptcp.t:call-pbmm2_align_hifi-70.stderr VERBOSE 
2025-09-15 20:23:38.520 wdl.w:ptcp.t:call-pbmm2_align_hifi-70.stderr VERBOSE pbmm2 \
2025-09-15 20:23:38.520 wdl.w:ptcp.t:call-pbmm2_align_hifi-70.stderr VERBOSE   align \
2025-09-15 20:23:38.520 wdl.w:ptcp.t:call-pbmm2_align_hifi-70.stderr VERBOSE   --log-level INFO \
2025-09-15 20:23:38.520 wdl.w:ptcp.t:call-pbmm2_align_hifi-70.stderr VERBOSE   --log-file pbmm2.log \
2025-09-15 20:23:38.520 wdl.w:ptcp.t:call-pbmm2_align_hifi-70.stderr VERBOSE   --alarms alarms.json \
2025-09-15 20:23:38.520 wdl.w:ptcp.t:call-pbmm2_align_hifi-70.stderr VERBOSE   --num-threads 64 \
2025-09-15 20:23:38.520 wdl.w:ptcp.t:call-pbmm2_align_hifi-70.stderr VERBOSE   --sort \
2025-09-15 20:23:38.520 wdl.w:ptcp.t:call-pbmm2_align_hifi-70.stderr VERBOSE   --preset HiFi \
2025-09-15 20:23:38.520 wdl.w:ptcp.t:call-pbmm2_align_hifi-70.stderr VERBOSE   --report-json mapping_stats.report.json \
2025-09-15 20:23:38.520 wdl.w:ptcp.t:call-pbmm2_align_hifi-72.stderr VERBOSE 
2025-09-15 20:23:38.521 wdl.w:ptcp.t:call-pbmm2_align_hifi-70.stderr VERBOSE   --sample "m84036_250809_035451_s4.bc2167" \
2025-09-15 20:23:38.521 wdl.w:ptcp.t:call-pbmm2_align_hifi-72.stderr VERBOSE pbmm2 \
2025-09-15 20:23:38.521 wdl.w:ptcp.t:call-pbmm2_align_hifi-70.stderr VERBOSE   --unmapped \
2025-09-15 20:23:38.521 wdl.w:ptcp.t:call-pbmm2_align_hifi-72.stderr VERBOSE   align \
2025-09-15 20:23:38.521 wdl.w:ptcp.t:call-pbmm2_align_hifi-70.stderr VERBOSE   /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa \
2025-09-15 20:23:38.521 wdl.w:ptcp.t:call-pbmm2_align_hifi-72.stderr VERBOSE   --log-level INFO \
2025-09-15 20:23:38.521 wdl.w:ptcp.t:call-pbmm2_align_hifi-70.stderr VERBOSE   /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0071_m84036_250809_035451_s4.bc2167.unmapped.bam \
2025-09-15 20:23:38.521 wdl.w:ptcp.t:call-pbmm2_align_hifi-72.stderr VERBOSE   --log-file pbmm2.log \
2025-09-15 20:23:38.521 wdl.w:ptcp.t:call-pbmm2_align_hifi-70.stderr VERBOSE   m84036_250809_035451_s4.bc2167.mapped.bam
2025-09-15 20:23:38.521 wdl.w:ptcp.t:call-pbmm2_align_hifi-72.stderr VERBOSE   --alarms alarms.json \
2025-09-15 20:23:38.522 wdl.w:ptcp.t:call-pbmm2_align_hifi-70.stderr VERBOSE + pbmm2 align --log-level INFO --log-file pbmm2.log --alarms alarms.json --num-threads 64 --sort --preset HiFi --report-json mapping_stats.report.json --sample m84036_250809_035451_s4.bc2167 --unmapped /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0071_m84036_250809_035451_s4.bc2167.unmapped.bam m84036_250809_035451_s4.bc2167.mapped.bam
2025-09-15 20:23:38.522 wdl.w:ptcp.t:call-pbmm2_align_hifi-72.stderr VERBOSE   --num-threads 64 \
2025-09-15 20:23:38.522 wdl.w:ptcp.t:call-pbmm2_align_hifi-72.stderr VERBOSE   --sort \
2025-09-15 20:23:38.522 wdl.w:ptcp.t:call-pbmm2_align_hifi-72.stderr VERBOSE   --preset HiFi \
2025-09-15 20:23:38.522 wdl.w:ptcp.t:call-pbmm2_align_hifi-72.stderr VERBOSE   --report-json mapping_stats.report.json \
2025-09-15 20:23:38.522 wdl.w:ptcp.t:call-pbmm2_align_hifi-72.stderr VERBOSE   --sample "m84036_250809_035451_s4.bc2169" \
2025-09-15 20:23:38.522 wdl.w:ptcp.t:call-pbmm2_align_hifi-72.stderr VERBOSE   --unmapped \
2025-09-15 20:23:38.522 wdl.w:ptcp.t:call-pbmm2_align_hifi-72.stderr VERBOSE   /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa \
2025-09-15 20:23:38.522 wdl.w:ptcp.t:call-pbmm2_align_hifi-72.stderr VERBOSE   /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0073_m84036_250809_035451_s4.bc2169.unmapped.bam \
2025-09-15 20:23:38.522 wdl.w:ptcp.t:call-pbmm2_align_hifi-72.stderr VERBOSE   m84036_250809_035451_s4.bc2169.mapped.bam
2025-09-15 20:23:38.522 wdl.w:ptcp.t:call-pbmm2_align_hifi-72.stderr VERBOSE + pbmm2 align --log-level INFO --log-file pbmm2.log --alarms alarms.json --num-threads 64 --sort --preset HiFi --report-json mapping_stats.report.json --sample m84036_250809_035451_s4.bc2169 --unmapped /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0073_m84036_250809_035451_s4.bc2169.unmapped.bam m84036_250809_035451_s4.bc2169.mapped.bam
2025-09-15 20:23:38.524 wdl.w:ptcp.t:call-pbmm2_align_hifi-77.stderr VERBOSE 
2025-09-15 20:23:38.524 wdl.w:ptcp.t:call-pbmm2_align_hifi-77.stderr VERBOSE pbmm2 \
2025-09-15 20:23:38.525 wdl.w:ptcp.t:call-pbmm2_align_hifi-77.stderr VERBOSE   align \
2025-09-15 20:23:38.525 wdl.w:ptcp.t:call-pbmm2_align_hifi-77.stderr VERBOSE   --log-level INFO \
2025-09-15 20:23:38.525 wdl.w:ptcp.t:call-pbmm2_align_hifi-77.stderr VERBOSE   --log-file pbmm2.log \
2025-09-15 20:23:38.525 wdl.w:ptcp.t:call-pbmm2_align_hifi-77.stderr VERBOSE   --alarms alarms.json \
2025-09-15 20:23:38.525 wdl.w:ptcp.t:call-pbmm2_align_hifi-77.stderr VERBOSE   --num-threads 64 \
2025-09-15 20:23:38.525 wdl.w:ptcp.t:call-pbmm2_align_hifi-77.stderr VERBOSE   --sort \
2025-09-15 20:23:38.525 wdl.w:ptcp.t:call-pbmm2_align_hifi-77.stderr VERBOSE   --preset HiFi \
2025-09-15 20:23:38.525 wdl.w:ptcp.t:call-pbmm2_align_hifi-77.stderr VERBOSE   --report-json mapping_stats.report.json \
2025-09-15 20:23:38.525 wdl.w:ptcp.t:call-pbmm2_align_hifi-77.stderr VERBOSE   --sample "m84036_250809_035451_s4.bc2174" \
2025-09-15 20:23:38.525 wdl.w:ptcp.t:call-pbmm2_align_hifi-77.stderr VERBOSE   --unmapped \
2025-09-15 20:23:38.525 wdl.w:ptcp.t:call-pbmm2_align_hifi-77.stderr VERBOSE   /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa \
2025-09-15 20:23:38.525 wdl.w:ptcp.t:call-pbmm2_align_hifi-77.stderr VERBOSE   /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0078_m84036_250809_035451_s4.bc2174.unmapped.bam \
2025-09-15 20:23:38.525 wdl.w:ptcp.t:call-pbmm2_align_hifi-77.stderr VERBOSE   m84036_250809_035451_s4.bc2174.mapped.bam
2025-09-15 20:23:38.525 wdl.w:ptcp.t:call-pbmm2_align_hifi-77.stderr VERBOSE + pbmm2 align --log-level INFO --log-file pbmm2.log --alarms alarms.json --num-threads 64 --sort --preset HiFi --report-json mapping_stats.report.json --sample m84036_250809_035451_s4.bc2174 --unmapped /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0078_m84036_250809_035451_s4.bc2174.unmapped.bam m84036_250809_035451_s4.bc2174.mapped.bam
2025-09-15 20:23:38.527 wdl.w:ptcp.t:call-pbmm2_align_hifi-73.stderr VERBOSE 
2025-09-15 20:23:38.527 wdl.w:ptcp.t:call-pbmm2_align_hifi-73.stderr VERBOSE pbmm2 \
2025-09-15 20:23:38.527 wdl.w:ptcp.t:call-pbmm2_align_hifi-73.stderr VERBOSE   align \
2025-09-15 20:23:38.527 wdl.w:ptcp.t:call-pbmm2_align_hifi-73.stderr VERBOSE   --log-level INFO \
2025-09-15 20:23:38.527 wdl.w:ptcp.t:call-pbmm2_align_hifi-73.stderr VERBOSE   --log-file pbmm2.log \
2025-09-15 20:23:38.527 wdl.w:ptcp.t:call-pbmm2_align_hifi-73.stderr VERBOSE   --alarms alarms.json \
2025-09-15 20:23:38.527 wdl.w:ptcp.t:call-pbmm2_align_hifi-73.stderr VERBOSE   --num-threads 64 \
2025-09-15 20:23:38.527 wdl.w:ptcp.t:call-pbmm2_align_hifi-73.stderr VERBOSE   --sort \
2025-09-15 20:23:38.527 wdl.w:ptcp.t:call-pbmm2_align_hifi-73.stderr VERBOSE   --preset HiFi \
2025-09-15 20:23:38.527 wdl.w:ptcp.t:call-pbmm2_align_hifi-73.stderr VERBOSE   --report-json mapping_stats.report.json \
2025-09-15 20:23:38.527 wdl.w:ptcp.t:call-pbmm2_align_hifi-73.stderr VERBOSE   --sample "m84036_250809_035451_s4.bc2170" \
2025-09-15 20:23:38.527 wdl.w:ptcp.t:call-pbmm2_align_hifi-73.stderr VERBOSE   --unmapped \
2025-09-15 20:23:38.528 wdl.w:ptcp.t:call-pbmm2_align_hifi-73.stderr VERBOSE   /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa \
2025-09-15 20:23:38.528 wdl.w:ptcp.t:call-pbmm2_align_hifi-73.stderr VERBOSE   /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0074_m84036_250809_035451_s4.bc2170.unmapped.bam \
2025-09-15 20:23:38.528 wdl.w:ptcp.t:call-pbmm2_align_hifi-73.stderr VERBOSE   m84036_250809_035451_s4.bc2170.mapped.bam
2025-09-15 20:23:38.528 wdl.w:ptcp.t:call-pbmm2_align_hifi-73.stderr VERBOSE + pbmm2 align --log-level INFO --log-file pbmm2.log --alarms alarms.json --num-threads 64 --sort --preset HiFi --report-json mapping_stats.report.json --sample m84036_250809_035451_s4.bc2170 --unmapped /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0074_m84036_250809_035451_s4.bc2170.unmapped.bam m84036_250809_035451_s4.bc2170.mapped.bam
2025-09-15 20:23:38.547 wdl.w:ptcp.w:call-paraphase-32.t:call-run_paraphase NOTICE slurm_singularity run :: pid: 1199794, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-32/call-run_paraphase/slurm_singularity.log.txt"
2025-09-15 20:23:38.562 wdl.w:ptcp.w:call-paraphase-17.t:call-run_paraphase NOTICE done
2025-09-15 20:23:38.564 wdl.w:ptcp.t:call-pbmm2_align_hifi-84.stderr VERBOSE 
2025-09-15 20:23:38.564 wdl.w:ptcp.t:call-pbmm2_align_hifi-84.stderr VERBOSE pbmm2 \
2025-09-15 20:23:38.564 wdl.w:ptcp.t:call-pbmm2_align_hifi-84.stderr VERBOSE   align \
2025-09-15 20:23:38.564 wdl.w:ptcp.t:call-pbmm2_align_hifi-84.stderr VERBOSE   --log-level INFO \
2025-09-15 20:23:38.564 wdl.w:ptcp.t:call-pbmm2_align_hifi-84.stderr VERBOSE   --log-file pbmm2.log \
2025-09-15 20:23:38.564 wdl.w:ptcp.t:call-pbmm2_align_hifi-84.stderr VERBOSE   --alarms alarms.json \
2025-09-15 20:23:38.564 wdl.w:ptcp.t:call-pbmm2_align_hifi-84.stderr VERBOSE   --num-threads 64 \
2025-09-15 20:23:38.564 wdl.w:ptcp.t:call-pbmm2_align_hifi-84.stderr VERBOSE   --sort \
2025-09-15 20:23:38.564 wdl.w:ptcp.t:call-pbmm2_align_hifi-84.stderr VERBOSE   --preset HiFi \
2025-09-15 20:23:38.564 wdl.w:ptcp.t:call-pbmm2_align_hifi-84.stderr VERBOSE   --report-json mapping_stats.report.json \
2025-09-15 20:23:38.564 wdl.w:ptcp.t:call-pbmm2_align_hifi-84.stderr VERBOSE   --sample "m84036_250809_035451_s4.bc2181" \
2025-09-15 20:23:38.564 wdl.w:ptcp.t:call-pbmm2_align_hifi-84.stderr VERBOSE   --unmapped \
2025-09-15 20:23:38.565 wdl.w:ptcp.t:call-pbmm2_align_hifi-84.stderr VERBOSE   /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa \
2025-09-15 20:23:38.565 wdl.w:ptcp.t:call-pbmm2_align_hifi-84.stderr VERBOSE   /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0085_m84036_250809_035451_s4.bc2181.unmapped.bam \
2025-09-15 20:23:38.565 wdl.w:ptcp.t:call-pbmm2_align_hifi-84.stderr VERBOSE   m84036_250809_035451_s4.bc2181.mapped.bam
2025-09-15 20:23:38.565 wdl.w:ptcp.t:call-pbmm2_align_hifi-84.stderr VERBOSE + pbmm2 align --log-level INFO --log-file pbmm2.log --alarms alarms.json --num-threads 64 --sort --preset HiFi --report-json mapping_stats.report.json --sample m84036_250809_035451_s4.bc2181 --unmapped /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0085_m84036_250809_035451_s4.bc2181.unmapped.bam m84036_250809_035451_s4.bc2181.mapped.bam
2025-09-15 20:23:38.568 wdl.w:ptcp.w:call-paraphase-17 NOTICE finish :: job: "call-run_paraphase"
2025-09-15 20:23:38.569 wdl.w:ptcp.w:call-paraphase-17 INFO output :: job: "call-run_paraphase", values: {"havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-17/call-run_paraphase/out/m84036_250809_035451_s4.bc2114.havanno.json", "paraphase_vcfs": [], "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-17/call-run_paraphase/out/m84036_250809_035451_s4.bc2114_paraphase/m84036_250809_035451_s4.bc2114.paraphase.json", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-17/call-run_paraphase/out/m84036_250809_035451_s4.bc2114_paraphase/m84036_250809_035451_s4.bc2114.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-17/call-run_paraphase/out/m84036_250809_035451_s4.bc2114_paraphase/m84036_250809_035451_s4.bc2114.paraphase.bam"}
2025-09-15 20:23:38.569 wdl.w:ptcp.w:call-paraphase-17 NOTICE ready :: job: "call-call_f8", callee: "call_f8"
2025-09-15 20:23:38.569 wdl.w:ptcp.w:call-paraphase-17 INFO input :: job: "call-call_f8", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "out_prefix": "m84036_250809_035451_s4.bc2114", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-17/call-run_paraphase/out/m84036_250809_035451_s4.bc2114_paraphase/m84036_250809_035451_s4.bc2114.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-17/call-run_paraphase/out/m84036_250809_035451_s4.bc2114_paraphase/m84036_250809_035451_s4.bc2114.paraphase.bam", "sex": "F"}
2025-09-15 20:23:38.571 wdl.w:ptcp.w:call-paraphase-17 INFO visit :: node: "output-havanno_json", values: {"havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-17/call-run_paraphase/out/m84036_250809_035451_s4.bc2114.havanno.json"}
2025-09-15 20:23:38.571 wdl.w:ptcp.w:call-paraphase-17 INFO visit :: node: "output-paraphase_bam", values: {"paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-17/call-run_paraphase/out/m84036_250809_035451_s4.bc2114_paraphase/m84036_250809_035451_s4.bc2114.paraphase.bam"}
2025-09-15 20:23:38.571 wdl.w:ptcp.w:call-paraphase-17 INFO visit :: node: "output-paraphase_bam_bai", values: {"paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-17/call-run_paraphase/out/m84036_250809_035451_s4.bc2114_paraphase/m84036_250809_035451_s4.bc2114.paraphase.bam.bai"}
2025-09-15 20:23:38.571 wdl.w:ptcp.w:call-paraphase-17 INFO visit :: node: "output-paraphase_json", values: {"paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-17/call-run_paraphase/out/m84036_250809_035451_s4.bc2114_paraphase/m84036_250809_035451_s4.bc2114.paraphase.json"}
2025-09-15 20:23:38.571 wdl.w:ptcp.w:call-paraphase-17 INFO visit :: node: "output-paraphase_vcfs", values: {"paraphase_vcfs": []}
2025-09-15 20:23:38.577 wdl.w:ptcp.w:call-sawfish-32.t:call-run_sawfish NOTICE task setup :: name: "run_sawfish", source: "./sawfish.wdl", line: 83, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-32/call-run_sawfish", thread: 140610921035328
2025-09-15 20:23:38.592 wdl.w:ptcp.t:call-pbmm2_align_hifi-91.stderr VERBOSE 
2025-09-15 20:23:38.592 wdl.w:ptcp.t:call-pbmm2_align_hifi-91.stderr VERBOSE pbmm2 \
2025-09-15 20:23:38.592 wdl.w:ptcp.t:call-pbmm2_align_hifi-91.stderr VERBOSE   align \
2025-09-15 20:23:38.592 wdl.w:ptcp.t:call-pbmm2_align_hifi-91.stderr VERBOSE   --log-level INFO \
2025-09-15 20:23:38.592 wdl.w:ptcp.t:call-pbmm2_align_hifi-91.stderr VERBOSE   --log-file pbmm2.log \
2025-09-15 20:23:38.592 wdl.w:ptcp.t:call-pbmm2_align_hifi-91.stderr VERBOSE   --alarms alarms.json \
2025-09-15 20:23:38.592 wdl.w:ptcp.t:call-pbmm2_align_hifi-91.stderr VERBOSE   --num-threads 64 \
2025-09-15 20:23:38.592 wdl.w:ptcp.t:call-pbmm2_align_hifi-91.stderr VERBOSE   --sort \
2025-09-15 20:23:38.592 wdl.w:ptcp.t:call-pbmm2_align_hifi-91.stderr VERBOSE   --preset HiFi \
2025-09-15 20:23:38.592 wdl.w:ptcp.t:call-pbmm2_align_hifi-91.stderr VERBOSE   --report-json mapping_stats.report.json \
2025-09-15 20:23:38.592 wdl.w:ptcp.t:call-pbmm2_align_hifi-91.stderr VERBOSE   --sample "m84036_250809_035451_s4.bc2188" \
2025-09-15 20:23:38.592 wdl.w:ptcp.t:call-pbmm2_align_hifi-91.stderr VERBOSE   --unmapped \
2025-09-15 20:23:38.592 wdl.w:ptcp.t:call-pbmm2_align_hifi-91.stderr VERBOSE   /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa \
2025-09-15 20:23:38.592 wdl.w:ptcp.t:call-pbmm2_align_hifi-91.stderr VERBOSE   /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0092_m84036_250809_035451_s4.bc2188.unmapped.bam \
2025-09-15 20:23:38.592 wdl.w:ptcp.t:call-pbmm2_align_hifi-91.stderr VERBOSE   m84036_250809_035451_s4.bc2188.mapped.bam
2025-09-15 20:23:38.593 wdl.w:ptcp.t:call-pbmm2_align_hifi-91.stderr VERBOSE + pbmm2 align --log-level INFO --log-file pbmm2.log --alarms alarms.json --num-threads 64 --sort --preset HiFi --report-json mapping_stats.report.json --sample m84036_250809_035451_s4.bc2188 --unmapped /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0092_m84036_250809_035451_s4.bc2188.unmapped.bam m84036_250809_035451_s4.bc2188.mapped.bam
2025-09-15 20:23:38.596 wdl.w:ptcp.w:call-sawfish-32.t:call-run_sawfish INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:23:38.596 wdl.w:ptcp.w:call-sawfish-32.t:call-run_sawfish INFO input :: name: "genome_version", value: "38"
2025-09-15 20:23:38.596 wdl.w:ptcp.w:call-sawfish-32.t:call-run_sawfish INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:23:38.596 wdl.w:ptcp.w:call-sawfish-32.t:call-run_sawfish INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:23:38.596 wdl.w:ptcp.w:call-sawfish-32.t:call-run_sawfish INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2129.mapped.bam.bai"
2025-09-15 20:23:38.596 wdl.w:ptcp.w:call-sawfish-32.t:call-run_sawfish INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2129.mapped.bam"
2025-09-15 20:23:38.596 wdl.w:ptcp.w:call-sawfish-32.t:call-run_sawfish INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2129"
2025-09-15 20:23:38.596 wdl.w:ptcp.w:call-sawfish-32.t:call-run_sawfish INFO eval :: name: "mem_gb", value: 32
2025-09-15 20:23:38.596 wdl.w:ptcp.w:call-sawfish-32.t:call-run_sawfish INFO eval :: name: "threads", value: 16
2025-09-15 20:23:38.597 wdl.w:ptcp.w:call-sawfish-32.t:call-run_sawfish INFO eval :: name: "disk_size", value: 30
2025-09-15 20:23:38.597 wdl.w:ptcp.w:call-sawfish-32.t:call-run_sawfish INFO eval :: name: "discover_dirname", value: "m84036_250809_035451_s4.bc2129_sawfish_discover"
2025-09-15 20:23:38.597 wdl.w:ptcp.w:call-sawfish-32.t:call-run_sawfish INFO eval :: name: "call_dirname", value: "m84036_250809_035451_s4.bc2129_sawfish"
2025-09-15 20:23:38.597 wdl.w:ptcp.w:call-sawfish-32.t:call-run_sawfish INFO eval :: name: "minimap2_bam_filename", value: "m84036_250809_035451_s4.bc2129.minimap2.bam"
2025-09-15 20:23:38.597 wdl.w:ptcp.w:call-sawfish-32.t:call-run_sawfish INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 16, memory_reservation: 32000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:23:38.597 wdl.w:ptcp.w:call-sawfish-32.t:call-run_sawfish WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:23:38.598 wdl.w:ptcp.w:call-sawfish-32.t:call-run_sawfish INFO provisioned :: seconds_waited: 0, cpu: 16, mem_bytes: 32000000000
2025-09-15 20:23:38.598 wdl.w:ptcp.w:call-sawfish-32.t:call-run_sawfish INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:23:38.601 wdl.w:ptcp.t:call-pbmm2_align_hifi-68.stderr VERBOSE 
2025-09-15 20:23:38.602 wdl.w:ptcp.t:call-pbmm2_align_hifi-68.stderr VERBOSE pbmm2 \
2025-09-15 20:23:38.602 wdl.w:ptcp.t:call-pbmm2_align_hifi-68.stderr VERBOSE   align \
2025-09-15 20:23:38.602 wdl.w:ptcp.t:call-pbmm2_align_hifi-68.stderr VERBOSE   --log-level INFO \
2025-09-15 20:23:38.602 wdl.w:ptcp.t:call-pbmm2_align_hifi-68.stderr VERBOSE   --log-file pbmm2.log \
2025-09-15 20:23:38.602 wdl.w:ptcp.t:call-pbmm2_align_hifi-68.stderr VERBOSE   --alarms alarms.json \
2025-09-15 20:23:38.602 wdl.w:ptcp.t:call-pbmm2_align_hifi-68.stderr VERBOSE   --num-threads 64 \
2025-09-15 20:23:38.602 wdl.w:ptcp.t:call-pbmm2_align_hifi-68.stderr VERBOSE   --sort \
2025-09-15 20:23:38.602 wdl.w:ptcp.t:call-pbmm2_align_hifi-68.stderr VERBOSE   --preset HiFi \
2025-09-15 20:23:38.602 wdl.w:ptcp.t:call-pbmm2_align_hifi-68.stderr VERBOSE   --report-json mapping_stats.report.json \
2025-09-15 20:23:38.602 wdl.w:ptcp.t:call-pbmm2_align_hifi-68.stderr VERBOSE   --sample "m84036_250809_035451_s4.bc2165" \
2025-09-15 20:23:38.602 wdl.w:ptcp.t:call-pbmm2_align_hifi-68.stderr VERBOSE   --unmapped \
2025-09-15 20:23:38.602 wdl.w:ptcp.t:call-pbmm2_align_hifi-68.stderr VERBOSE   /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa \
2025-09-15 20:23:38.602 wdl.w:ptcp.t:call-pbmm2_align_hifi-68.stderr VERBOSE   /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0069_m84036_250809_035451_s4.bc2165.unmapped.bam \
2025-09-15 20:23:38.602 wdl.w:ptcp.t:call-pbmm2_align_hifi-68.stderr VERBOSE   m84036_250809_035451_s4.bc2165.mapped.bam
2025-09-15 20:23:38.602 wdl.w:ptcp.t:call-pbmm2_align_hifi-68.stderr VERBOSE + pbmm2 align --log-level INFO --log-file pbmm2.log --alarms alarms.json --num-threads 64 --sort --preset HiFi --report-json mapping_stats.report.json --sample m84036_250809_035451_s4.bc2165 --unmapped /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0069_m84036_250809_035451_s4.bc2165.unmapped.bam m84036_250809_035451_s4.bc2165.mapped.bam
2025-09-15 20:23:38.611 wdl.w:ptcp.t:call-pbmm2_align_hifi-88.stderr VERBOSE 
2025-09-15 20:23:38.611 wdl.w:ptcp.t:call-pbmm2_align_hifi-88.stderr VERBOSE pbmm2 \
2025-09-15 20:23:38.611 wdl.w:ptcp.t:call-pbmm2_align_hifi-88.stderr VERBOSE   align \
2025-09-15 20:23:38.611 wdl.w:ptcp.t:call-pbmm2_align_hifi-88.stderr VERBOSE   --log-level INFO \
2025-09-15 20:23:38.611 wdl.w:ptcp.t:call-pbmm2_align_hifi-88.stderr VERBOSE   --log-file pbmm2.log \
2025-09-15 20:23:38.611 wdl.w:ptcp.t:call-pbmm2_align_hifi-88.stderr VERBOSE   --alarms alarms.json \
2025-09-15 20:23:38.611 wdl.w:ptcp.t:call-pbmm2_align_hifi-88.stderr VERBOSE   --num-threads 64 \
2025-09-15 20:23:38.611 wdl.w:ptcp.t:call-pbmm2_align_hifi-88.stderr VERBOSE   --sort \
2025-09-15 20:23:38.611 wdl.w:ptcp.t:call-pbmm2_align_hifi-88.stderr VERBOSE   --preset HiFi \
2025-09-15 20:23:38.611 wdl.w:ptcp.t:call-pbmm2_align_hifi-75.stderr VERBOSE 
2025-09-15 20:23:38.611 wdl.w:ptcp.t:call-pbmm2_align_hifi-88.stderr VERBOSE   --report-json mapping_stats.report.json \
2025-09-15 20:23:38.611 wdl.w:ptcp.t:call-pbmm2_align_hifi-75.stderr VERBOSE pbmm2 \
2025-09-15 20:23:38.611 wdl.w:ptcp.t:call-pbmm2_align_hifi-88.stderr VERBOSE   --sample "m84036_250809_035451_s4.bc2185" \
2025-09-15 20:23:38.611 wdl.w:ptcp.t:call-pbmm2_align_hifi-75.stderr VERBOSE   align \
2025-09-15 20:23:38.611 wdl.w:ptcp.t:call-pbmm2_align_hifi-88.stderr VERBOSE   --unmapped \
2025-09-15 20:23:38.611 wdl.w:ptcp.t:call-pbmm2_align_hifi-75.stderr VERBOSE   --log-level INFO \
2025-09-15 20:23:38.612 wdl.w:ptcp.t:call-pbmm2_align_hifi-88.stderr VERBOSE   /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa \
2025-09-15 20:23:38.612 wdl.w:ptcp.t:call-pbmm2_align_hifi-75.stderr VERBOSE   --log-file pbmm2.log \
2025-09-15 20:23:38.612 wdl.w:ptcp.t:call-pbmm2_align_hifi-88.stderr VERBOSE   /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0089_m84036_250809_035451_s4.bc2185.unmapped.bam \
2025-09-15 20:23:38.612 wdl.w:ptcp.t:call-pbmm2_align_hifi-75.stderr VERBOSE   --alarms alarms.json \
2025-09-15 20:23:38.612 wdl.w:ptcp.t:call-pbmm2_align_hifi-88.stderr VERBOSE   m84036_250809_035451_s4.bc2185.mapped.bam
2025-09-15 20:23:38.612 wdl.w:ptcp.t:call-pbmm2_align_hifi-75.stderr VERBOSE   --num-threads 64 \
2025-09-15 20:23:38.612 wdl.w:ptcp.t:call-pbmm2_align_hifi-88.stderr VERBOSE + pbmm2 align --log-level INFO --log-file pbmm2.log --alarms alarms.json --num-threads 64 --sort --preset HiFi --report-json mapping_stats.report.json --sample m84036_250809_035451_s4.bc2185 --unmapped /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0089_m84036_250809_035451_s4.bc2185.unmapped.bam m84036_250809_035451_s4.bc2185.mapped.bam
2025-09-15 20:23:38.612 wdl.w:ptcp.t:call-pbmm2_align_hifi-75.stderr VERBOSE   --sort \
2025-09-15 20:23:38.612 wdl.w:ptcp.t:call-pbmm2_align_hifi-75.stderr VERBOSE   --preset HiFi \
2025-09-15 20:23:38.612 wdl.w:ptcp.t:call-pbmm2_align_hifi-75.stderr VERBOSE   --report-json mapping_stats.report.json \
2025-09-15 20:23:38.612 wdl.w:ptcp.t:call-pbmm2_align_hifi-75.stderr VERBOSE   --sample "m84036_250809_035451_s4.bc2172" \
2025-09-15 20:23:38.612 wdl.w:ptcp.t:call-pbmm2_align_hifi-75.stderr VERBOSE   --unmapped \
2025-09-15 20:23:38.612 wdl.w:ptcp.t:call-pbmm2_align_hifi-75.stderr VERBOSE   /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa \
2025-09-15 20:23:38.612 wdl.w:ptcp.t:call-pbmm2_align_hifi-75.stderr VERBOSE   /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0076_m84036_250809_035451_s4.bc2172.unmapped.bam \
2025-09-15 20:23:38.613 wdl.w:ptcp.t:call-pbmm2_align_hifi-75.stderr VERBOSE   m84036_250809_035451_s4.bc2172.mapped.bam
2025-09-15 20:23:38.613 wdl.w:ptcp.t:call-pbmm2_align_hifi-75.stderr VERBOSE + pbmm2 align --log-level INFO --log-file pbmm2.log --alarms alarms.json --num-threads 64 --sort --preset HiFi --report-json mapping_stats.report.json --sample m84036_250809_035451_s4.bc2172 --unmapped /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0076_m84036_250809_035451_s4.bc2172.unmapped.bam m84036_250809_035451_s4.bc2172.mapped.bam
2025-09-15 20:23:38.621 wdl.w:ptcp.t:call-pbmm2_align_hifi-86.stderr VERBOSE 
2025-09-15 20:23:38.621 wdl.w:ptcp.t:call-pbmm2_align_hifi-86.stderr VERBOSE pbmm2 \
2025-09-15 20:23:38.621 wdl.w:ptcp.t:call-pbmm2_align_hifi-86.stderr VERBOSE   align \
2025-09-15 20:23:38.621 wdl.w:ptcp.t:call-pbmm2_align_hifi-86.stderr VERBOSE   --log-level INFO \
2025-09-15 20:23:38.621 wdl.w:ptcp.t:call-pbmm2_align_hifi-86.stderr VERBOSE   --log-file pbmm2.log \
2025-09-15 20:23:38.621 wdl.w:ptcp.t:call-pbmm2_align_hifi-86.stderr VERBOSE   --alarms alarms.json \
2025-09-15 20:23:38.621 wdl.w:ptcp.t:call-pbmm2_align_hifi-86.stderr VERBOSE   --num-threads 64 \
2025-09-15 20:23:38.621 wdl.w:ptcp.t:call-pbmm2_align_hifi-86.stderr VERBOSE   --sort \
2025-09-15 20:23:38.621 wdl.w:ptcp.t:call-pbmm2_align_hifi-86.stderr VERBOSE   --preset HiFi \
2025-09-15 20:23:38.621 wdl.w:ptcp.t:call-pbmm2_align_hifi-86.stderr VERBOSE   --report-json mapping_stats.report.json \
2025-09-15 20:23:38.621 wdl.w:ptcp.t:call-pbmm2_align_hifi-86.stderr VERBOSE   --sample "m84036_250809_035451_s4.bc2183" \
2025-09-15 20:23:38.621 wdl.w:ptcp.t:call-pbmm2_align_hifi-86.stderr VERBOSE   --unmapped \
2025-09-15 20:23:38.621 wdl.w:ptcp.t:call-pbmm2_align_hifi-86.stderr VERBOSE   /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa \
2025-09-15 20:23:38.621 wdl.w:ptcp.t:call-pbmm2_align_hifi-86.stderr VERBOSE   /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0087_m84036_250809_035451_s4.bc2183.unmapped.bam \
2025-09-15 20:23:38.621 wdl.w:ptcp.t:call-pbmm2_align_hifi-86.stderr VERBOSE   m84036_250809_035451_s4.bc2183.mapped.bam
2025-09-15 20:23:38.621 wdl.w:ptcp.t:call-pbmm2_align_hifi-86.stderr VERBOSE + pbmm2 align --log-level INFO --log-file pbmm2.log --alarms alarms.json --num-threads 64 --sort --preset HiFi --report-json mapping_stats.report.json --sample m84036_250809_035451_s4.bc2183 --unmapped /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0087_m84036_250809_035451_s4.bc2183.unmapped.bam m84036_250809_035451_s4.bc2183.mapped.bam
2025-09-15 20:23:38.633 wdl.w:ptcp.t:call-pbmm2_align_hifi-81.stderr VERBOSE 
2025-09-15 20:23:38.633 wdl.w:ptcp.t:call-pbmm2_align_hifi-81.stderr VERBOSE pbmm2 \
2025-09-15 20:23:38.633 wdl.w:ptcp.t:call-pbmm2_align_hifi-81.stderr VERBOSE   align \
2025-09-15 20:23:38.633 wdl.w:ptcp.t:call-pbmm2_align_hifi-81.stderr VERBOSE   --log-level INFO \
2025-09-15 20:23:38.633 wdl.w:ptcp.t:call-pbmm2_align_hifi-81.stderr VERBOSE   --log-file pbmm2.log \
2025-09-15 20:23:38.634 wdl.w:ptcp.t:call-pbmm2_align_hifi-81.stderr VERBOSE   --alarms alarms.json \
2025-09-15 20:23:38.634 wdl.w:ptcp.t:call-pbmm2_align_hifi-81.stderr VERBOSE   --num-threads 64 \
2025-09-15 20:23:38.634 wdl.w:ptcp.t:call-pbmm2_align_hifi-81.stderr VERBOSE   --sort \
2025-09-15 20:23:38.634 wdl.w:ptcp.t:call-pbmm2_align_hifi-81.stderr VERBOSE   --preset HiFi \
2025-09-15 20:23:38.634 wdl.w:ptcp.t:call-pbmm2_align_hifi-81.stderr VERBOSE   --report-json mapping_stats.report.json \
2025-09-15 20:23:38.634 wdl.w:ptcp.t:call-pbmm2_align_hifi-81.stderr VERBOSE   --sample "m84036_250809_035451_s4.bc2178" \
2025-09-15 20:23:38.634 wdl.w:ptcp.t:call-pbmm2_align_hifi-81.stderr VERBOSE   --unmapped \
2025-09-15 20:23:38.634 wdl.w:ptcp.t:call-pbmm2_align_hifi-81.stderr VERBOSE   /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa \
2025-09-15 20:23:38.634 wdl.w:ptcp.t:call-pbmm2_align_hifi-81.stderr VERBOSE   /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0082_m84036_250809_035451_s4.bc2178.unmapped.bam \
2025-09-15 20:23:38.634 wdl.w:ptcp.t:call-pbmm2_align_hifi-81.stderr VERBOSE   m84036_250809_035451_s4.bc2178.mapped.bam
2025-09-15 20:23:38.634 wdl.w:ptcp.t:call-pbmm2_align_hifi-81.stderr VERBOSE + pbmm2 align --log-level INFO --log-file pbmm2.log --alarms alarms.json --num-threads 64 --sort --preset HiFi --report-json mapping_stats.report.json --sample m84036_250809_035451_s4.bc2178 --unmapped /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0082_m84036_250809_035451_s4.bc2178.unmapped.bam m84036_250809_035451_s4.bc2178.mapped.bam
2025-09-15 20:23:38.644 wdl.w:ptcp.t:call-pbmm2_align_hifi-92.stderr VERBOSE 
2025-09-15 20:23:38.644 wdl.w:ptcp.t:call-pbmm2_align_hifi-92.stderr VERBOSE pbmm2 \
2025-09-15 20:23:38.644 wdl.w:ptcp.t:call-pbmm2_align_hifi-92.stderr VERBOSE   align \
2025-09-15 20:23:38.644 wdl.w:ptcp.t:call-pbmm2_align_hifi-92.stderr VERBOSE   --log-level INFO \
2025-09-15 20:23:38.644 wdl.w:ptcp.t:call-pbmm2_align_hifi-92.stderr VERBOSE   --log-file pbmm2.log \
2025-09-15 20:23:38.644 wdl.w:ptcp.t:call-pbmm2_align_hifi-92.stderr VERBOSE   --alarms alarms.json \
2025-09-15 20:23:38.644 wdl.w:ptcp.t:call-pbmm2_align_hifi-92.stderr VERBOSE   --num-threads 64 \
2025-09-15 20:23:38.644 wdl.w:ptcp.t:call-pbmm2_align_hifi-92.stderr VERBOSE   --sort \
2025-09-15 20:23:38.644 wdl.w:ptcp.t:call-pbmm2_align_hifi-92.stderr VERBOSE   --preset HiFi \
2025-09-15 20:23:38.644 wdl.w:ptcp.t:call-pbmm2_align_hifi-92.stderr VERBOSE   --report-json mapping_stats.report.json \
2025-09-15 20:23:38.644 wdl.w:ptcp.t:call-pbmm2_align_hifi-92.stderr VERBOSE   --sample "m84036_250809_035451_s4.bc2189" \
2025-09-15 20:23:38.644 wdl.w:ptcp.t:call-pbmm2_align_hifi-92.stderr VERBOSE   --unmapped \
2025-09-15 20:23:38.644 wdl.w:ptcp.t:call-pbmm2_align_hifi-92.stderr VERBOSE   /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa \
2025-09-15 20:23:38.644 wdl.w:ptcp.t:call-pbmm2_align_hifi-92.stderr VERBOSE   /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0093_m84036_250809_035451_s4.bc2189.unmapped.bam \
2025-09-15 20:23:38.645 wdl.w:ptcp.t:call-pbmm2_align_hifi-92.stderr VERBOSE   m84036_250809_035451_s4.bc2189.mapped.bam
2025-09-15 20:23:38.645 wdl.w:ptcp.t:call-pbmm2_align_hifi-92.stderr VERBOSE + pbmm2 align --log-level INFO --log-file pbmm2.log --alarms alarms.json --num-threads 64 --sort --preset HiFi --report-json mapping_stats.report.json --sample m84036_250809_035451_s4.bc2189 --unmapped /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0093_m84036_250809_035451_s4.bc2189.unmapped.bam m84036_250809_035451_s4.bc2189.mapped.bam
2025-09-15 20:23:38.654 wdl.w:ptcp.t:call-pbmm2_align_hifi-90.stderr VERBOSE 
2025-09-15 20:23:38.655 wdl.w:ptcp.t:call-pbmm2_align_hifi-90.stderr VERBOSE pbmm2 \
2025-09-15 20:23:38.655 wdl.w:ptcp.t:call-pbmm2_align_hifi-90.stderr VERBOSE   align \
2025-09-15 20:23:38.655 wdl.w:ptcp.t:call-pbmm2_align_hifi-90.stderr VERBOSE   --log-level INFO \
2025-09-15 20:23:38.655 wdl.w:ptcp.t:call-pbmm2_align_hifi-90.stderr VERBOSE   --log-file pbmm2.log \
2025-09-15 20:23:38.655 wdl.w:ptcp.t:call-pbmm2_align_hifi-90.stderr VERBOSE   --alarms alarms.json \
2025-09-15 20:23:38.655 wdl.w:ptcp.t:call-pbmm2_align_hifi-90.stderr VERBOSE   --num-threads 64 \
2025-09-15 20:23:38.655 wdl.w:ptcp.t:call-pbmm2_align_hifi-90.stderr VERBOSE   --sort \
2025-09-15 20:23:38.655 wdl.w:ptcp.t:call-pbmm2_align_hifi-90.stderr VERBOSE   --preset HiFi \
2025-09-15 20:23:38.655 wdl.w:ptcp.t:call-pbmm2_align_hifi-90.stderr VERBOSE   --report-json mapping_stats.report.json \
2025-09-15 20:23:38.655 wdl.w:ptcp.t:call-pbmm2_align_hifi-90.stderr VERBOSE   --sample "m84036_250809_035451_s4.bc2187" \
2025-09-15 20:23:38.655 wdl.w:ptcp.t:call-pbmm2_align_hifi-90.stderr VERBOSE   --unmapped \
2025-09-15 20:23:38.655 wdl.w:ptcp.t:call-pbmm2_align_hifi-90.stderr VERBOSE   /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa \
2025-09-15 20:23:38.655 wdl.w:ptcp.t:call-pbmm2_align_hifi-90.stderr VERBOSE   /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0091_m84036_250809_035451_s4.bc2187.unmapped.bam \
2025-09-15 20:23:38.655 wdl.w:ptcp.t:call-pbmm2_align_hifi-90.stderr VERBOSE   m84036_250809_035451_s4.bc2187.mapped.bam
2025-09-15 20:23:38.656 wdl.w:ptcp.t:call-pbmm2_align_hifi-90.stderr VERBOSE + pbmm2 align --log-level INFO --log-file pbmm2.log --alarms alarms.json --num-threads 64 --sort --preset HiFi --report-json mapping_stats.report.json --sample m84036_250809_035451_s4.bc2187 --unmapped /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0091_m84036_250809_035451_s4.bc2187.unmapped.bam m84036_250809_035451_s4.bc2187.mapped.bam
2025-09-15 20:23:38.659 wdl.w:ptcp.w:call-trgt-25.t:call-trgt_genotype.slurm_singularity INFO srun: job 51797434 queued and waiting for resources
2025-09-15 20:23:38.659 wdl.w:ptcp.w:call-trgt-25.t:call-trgt_genotype.slurm_singularity INFO srun: job 51797434 has been allocated resources
2025-09-15 20:23:38.659 wdl.w:ptcp.w:call-trgt-25.t:call-trgt_genotype.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:38.668 wdl.w:ptcp.t:call-pbmm2_align_hifi-79.stderr VERBOSE 
2025-09-15 20:23:38.668 wdl.w:ptcp.t:call-pbmm2_align_hifi-79.stderr VERBOSE pbmm2 \
2025-09-15 20:23:38.668 wdl.w:ptcp.t:call-pbmm2_align_hifi-79.stderr VERBOSE   align \
2025-09-15 20:23:38.668 wdl.w:ptcp.t:call-pbmm2_align_hifi-79.stderr VERBOSE   --log-level INFO \
2025-09-15 20:23:38.668 wdl.w:ptcp.t:call-pbmm2_align_hifi-79.stderr VERBOSE   --log-file pbmm2.log \
2025-09-15 20:23:38.668 wdl.w:ptcp.t:call-pbmm2_align_hifi-79.stderr VERBOSE   --alarms alarms.json \
2025-09-15 20:23:38.668 wdl.w:ptcp.t:call-pbmm2_align_hifi-79.stderr VERBOSE   --num-threads 64 \
2025-09-15 20:23:38.668 wdl.w:ptcp.t:call-pbmm2_align_hifi-79.stderr VERBOSE   --sort \
2025-09-15 20:23:38.668 wdl.w:ptcp.t:call-pbmm2_align_hifi-79.stderr VERBOSE   --preset HiFi \
2025-09-15 20:23:38.668 wdl.w:ptcp.t:call-pbmm2_align_hifi-79.stderr VERBOSE   --report-json mapping_stats.report.json \
2025-09-15 20:23:38.668 wdl.w:ptcp.t:call-pbmm2_align_hifi-79.stderr VERBOSE   --sample "m84036_250809_035451_s4.bc2176" \
2025-09-15 20:23:38.668 wdl.w:ptcp.t:call-pbmm2_align_hifi-79.stderr VERBOSE   --unmapped \
2025-09-15 20:23:38.668 wdl.w:ptcp.t:call-pbmm2_align_hifi-79.stderr VERBOSE   /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa \
2025-09-15 20:23:38.669 wdl.w:ptcp.t:call-pbmm2_align_hifi-79.stderr VERBOSE   /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0080_m84036_250809_035451_s4.bc2176.unmapped.bam \
2025-09-15 20:23:38.669 wdl.w:ptcp.t:call-pbmm2_align_hifi-79.stderr VERBOSE   m84036_250809_035451_s4.bc2176.mapped.bam
2025-09-15 20:23:38.669 wdl.w:ptcp.t:call-pbmm2_align_hifi-79.stderr VERBOSE + pbmm2 align --log-level INFO --log-file pbmm2.log --alarms alarms.json --num-threads 64 --sort --preset HiFi --report-json mapping_stats.report.json --sample m84036_250809_035451_s4.bc2176 --unmapped /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0080_m84036_250809_035451_s4.bc2176.unmapped.bam m84036_250809_035451_s4.bc2176.mapped.bam
2025-09-15 20:23:38.670 wdl.w:ptcp.t:call-pbmm2_align_hifi-82.stderr VERBOSE 
2025-09-15 20:23:38.671 wdl.w:ptcp.t:call-pbmm2_align_hifi-82.stderr VERBOSE pbmm2 \
2025-09-15 20:23:38.671 wdl.w:ptcp.t:call-pbmm2_align_hifi-82.stderr VERBOSE   align \
2025-09-15 20:23:38.671 wdl.w:ptcp.t:call-pbmm2_align_hifi-82.stderr VERBOSE   --log-level INFO \
2025-09-15 20:23:38.671 wdl.w:ptcp.t:call-pbmm2_align_hifi-82.stderr VERBOSE   --log-file pbmm2.log \
2025-09-15 20:23:38.671 wdl.w:ptcp.t:call-pbmm2_align_hifi-82.stderr VERBOSE   --alarms alarms.json \
2025-09-15 20:23:38.671 wdl.w:ptcp.t:call-pbmm2_align_hifi-82.stderr VERBOSE   --num-threads 64 \
2025-09-15 20:23:38.671 wdl.w:ptcp.t:call-pbmm2_align_hifi-82.stderr VERBOSE   --sort \
2025-09-15 20:23:38.671 wdl.w:ptcp.t:call-pbmm2_align_hifi-82.stderr VERBOSE   --preset HiFi \
2025-09-15 20:23:38.671 wdl.w:ptcp.t:call-pbmm2_align_hifi-82.stderr VERBOSE   --report-json mapping_stats.report.json \
2025-09-15 20:23:38.671 wdl.w:ptcp.t:call-pbmm2_align_hifi-82.stderr VERBOSE   --sample "m84036_250809_035451_s4.bc2179" \
2025-09-15 20:23:38.671 wdl.w:ptcp.t:call-pbmm2_align_hifi-82.stderr VERBOSE   --unmapped \
2025-09-15 20:23:38.671 wdl.w:ptcp.t:call-pbmm2_align_hifi-82.stderr VERBOSE   /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa \
2025-09-15 20:23:38.671 wdl.w:ptcp.t:call-pbmm2_align_hifi-82.stderr VERBOSE   /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0083_m84036_250809_035451_s4.bc2179.unmapped.bam \
2025-09-15 20:23:38.671 wdl.w:ptcp.t:call-pbmm2_align_hifi-82.stderr VERBOSE   m84036_250809_035451_s4.bc2179.mapped.bam
2025-09-15 20:23:38.671 wdl.w:ptcp.t:call-pbmm2_align_hifi-82.stderr VERBOSE + pbmm2 align --log-level INFO --log-file pbmm2.log --alarms alarms.json --num-threads 64 --sort --preset HiFi --report-json mapping_stats.report.json --sample m84036_250809_035451_s4.bc2179 --unmapped /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0083_m84036_250809_035451_s4.bc2179.unmapped.bam m84036_250809_035451_s4.bc2179.mapped.bam
2025-09-15 20:23:38.674 wdl.w:ptcp.t:call-pbmm2_align_hifi-78.stderr VERBOSE 
2025-09-15 20:23:38.675 wdl.w:ptcp.t:call-pbmm2_align_hifi-78.stderr VERBOSE pbmm2 \
2025-09-15 20:23:38.675 wdl.w:ptcp.t:call-pbmm2_align_hifi-78.stderr VERBOSE   align \
2025-09-15 20:23:38.675 wdl.w:ptcp.t:call-pbmm2_align_hifi-78.stderr VERBOSE   --log-level INFO \
2025-09-15 20:23:38.675 wdl.w:ptcp.t:call-pbmm2_align_hifi-78.stderr VERBOSE   --log-file pbmm2.log \
2025-09-15 20:23:38.675 wdl.w:ptcp.t:call-pbmm2_align_hifi-78.stderr VERBOSE   --alarms alarms.json \
2025-09-15 20:23:38.675 wdl.w:ptcp.t:call-pbmm2_align_hifi-78.stderr VERBOSE   --num-threads 64 \
2025-09-15 20:23:38.675 wdl.w:ptcp.t:call-pbmm2_align_hifi-78.stderr VERBOSE   --sort \
2025-09-15 20:23:38.675 wdl.w:ptcp.t:call-pbmm2_align_hifi-78.stderr VERBOSE   --preset HiFi \
2025-09-15 20:23:38.675 wdl.w:ptcp.t:call-pbmm2_align_hifi-78.stderr VERBOSE   --report-json mapping_stats.report.json \
2025-09-15 20:23:38.675 wdl.w:ptcp.t:call-pbmm2_align_hifi-78.stderr VERBOSE   --sample "m84036_250809_035451_s4.bc2175" \
2025-09-15 20:23:38.675 wdl.w:ptcp.t:call-pbmm2_align_hifi-78.stderr VERBOSE   --unmapped \
2025-09-15 20:23:38.675 wdl.w:ptcp.t:call-pbmm2_align_hifi-78.stderr VERBOSE   /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa \
2025-09-15 20:23:38.675 wdl.w:ptcp.t:call-pbmm2_align_hifi-78.stderr VERBOSE   /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0079_m84036_250809_035451_s4.bc2175.unmapped.bam \
2025-09-15 20:23:38.675 wdl.w:ptcp.t:call-pbmm2_align_hifi-78.stderr VERBOSE   m84036_250809_035451_s4.bc2175.mapped.bam
2025-09-15 20:23:38.675 wdl.w:ptcp.t:call-pbmm2_align_hifi-78.stderr VERBOSE + pbmm2 align --log-level INFO --log-file pbmm2.log --alarms alarms.json --num-threads 64 --sort --preset HiFi --report-json mapping_stats.report.json --sample m84036_250809_035451_s4.bc2175 --unmapped /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0079_m84036_250809_035451_s4.bc2175.unmapped.bam m84036_250809_035451_s4.bc2175.mapped.bam
2025-09-15 20:23:38.677 wdl.w:ptcp.t:call-pbmm2_align_hifi-87.stderr VERBOSE 
2025-09-15 20:23:38.677 wdl.w:ptcp.t:call-pbmm2_align_hifi-87.stderr VERBOSE pbmm2 \
2025-09-15 20:23:38.677 wdl.w:ptcp.t:call-pbmm2_align_hifi-87.stderr VERBOSE   align \
2025-09-15 20:23:38.677 wdl.w:ptcp.t:call-pbmm2_align_hifi-87.stderr VERBOSE   --log-level INFO \
2025-09-15 20:23:38.678 wdl.w:ptcp.t:call-pbmm2_align_hifi-87.stderr VERBOSE   --log-file pbmm2.log \
2025-09-15 20:23:38.678 wdl.w:ptcp.t:call-pbmm2_align_hifi-87.stderr VERBOSE   --alarms alarms.json \
2025-09-15 20:23:38.678 wdl.w:ptcp.t:call-pbmm2_align_hifi-87.stderr VERBOSE   --num-threads 64 \
2025-09-15 20:23:38.678 wdl.w:ptcp.t:call-pbmm2_align_hifi-87.stderr VERBOSE   --sort \
2025-09-15 20:23:38.678 wdl.w:ptcp.t:call-pbmm2_align_hifi-87.stderr VERBOSE   --preset HiFi \
2025-09-15 20:23:38.678 wdl.w:ptcp.t:call-pbmm2_align_hifi-87.stderr VERBOSE   --report-json mapping_stats.report.json \
2025-09-15 20:23:38.678 wdl.w:ptcp.t:call-pbmm2_align_hifi-87.stderr VERBOSE   --sample "m84036_250809_035451_s4.bc2184" \
2025-09-15 20:23:38.678 wdl.w:ptcp.t:call-pbmm2_align_hifi-87.stderr VERBOSE   --unmapped \
2025-09-15 20:23:38.678 wdl.w:ptcp.t:call-pbmm2_align_hifi-87.stderr VERBOSE   /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa \
2025-09-15 20:23:38.678 wdl.w:ptcp.t:call-pbmm2_align_hifi-87.stderr VERBOSE   /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0088_m84036_250809_035451_s4.bc2184.unmapped.bam \
2025-09-15 20:23:38.678 wdl.w:ptcp.t:call-pbmm2_align_hifi-87.stderr VERBOSE   m84036_250809_035451_s4.bc2184.mapped.bam
2025-09-15 20:23:38.678 wdl.w:ptcp.t:call-pbmm2_align_hifi-87.stderr VERBOSE + pbmm2 align --log-level INFO --log-file pbmm2.log --alarms alarms.json --num-threads 64 --sort --preset HiFi --report-json mapping_stats.report.json --sample m84036_250809_035451_s4.bc2184 --unmapped /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0088_m84036_250809_035451_s4.bc2184.unmapped.bam m84036_250809_035451_s4.bc2184.mapped.bam
2025-09-15 20:23:38.683 wdl.w:ptcp.t:call-pbmm2_align_hifi-89.stderr VERBOSE 
2025-09-15 20:23:38.683 wdl.w:ptcp.t:call-pbmm2_align_hifi-89.stderr VERBOSE pbmm2 \
2025-09-15 20:23:38.683 wdl.w:ptcp.t:call-pbmm2_align_hifi-89.stderr VERBOSE   align \
2025-09-15 20:23:38.683 wdl.w:ptcp.t:call-pbmm2_align_hifi-89.stderr VERBOSE   --log-level INFO \
2025-09-15 20:23:38.683 wdl.w:ptcp.t:call-pbmm2_align_hifi-89.stderr VERBOSE   --log-file pbmm2.log \
2025-09-15 20:23:38.683 wdl.w:ptcp.t:call-pbmm2_align_hifi-89.stderr VERBOSE   --alarms alarms.json \
2025-09-15 20:23:38.683 wdl.w:ptcp.t:call-pbmm2_align_hifi-89.stderr VERBOSE   --num-threads 64 \
2025-09-15 20:23:38.683 wdl.w:ptcp.t:call-pbmm2_align_hifi-89.stderr VERBOSE   --sort \
2025-09-15 20:23:38.683 wdl.w:ptcp.t:call-pbmm2_align_hifi-89.stderr VERBOSE   --preset HiFi \
2025-09-15 20:23:38.683 wdl.w:ptcp.t:call-pbmm2_align_hifi-89.stderr VERBOSE   --report-json mapping_stats.report.json \
2025-09-15 20:23:38.683 wdl.w:ptcp.t:call-pbmm2_align_hifi-89.stderr VERBOSE   --sample "m84036_250809_035451_s4.bc2186" \
2025-09-15 20:23:38.683 wdl.w:ptcp.t:call-pbmm2_align_hifi-89.stderr VERBOSE   --unmapped \
2025-09-15 20:23:38.683 wdl.w:ptcp.t:call-pbmm2_align_hifi-89.stderr VERBOSE   /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa \
2025-09-15 20:23:38.683 wdl.w:ptcp.t:call-pbmm2_align_hifi-89.stderr VERBOSE   /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0090_m84036_250809_035451_s4.bc2186.unmapped.bam \
2025-09-15 20:23:38.683 wdl.w:ptcp.t:call-pbmm2_align_hifi-89.stderr VERBOSE   m84036_250809_035451_s4.bc2186.mapped.bam
2025-09-15 20:23:38.683 wdl.w:ptcp.t:call-pbmm2_align_hifi-89.stderr VERBOSE + pbmm2 align --log-level INFO --log-file pbmm2.log --alarms alarms.json --num-threads 64 --sort --preset HiFi --report-json mapping_stats.report.json --sample m84036_250809_035451_s4.bc2186 --unmapped /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0090_m84036_250809_035451_s4.bc2186.unmapped.bam m84036_250809_035451_s4.bc2186.mapped.bam
2025-09-15 20:23:38.687 wdl.w:ptcp.w:call-sawfish-32.t:call-run_sawfish INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 10, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-32/call-run_sawfish/_singularity_tmpdir_42e45q21"
2025-09-15 20:23:38.688 wdl.w:ptcp.w:call-sawfish-32.t:call-run_sawfish INFO Slurm invocation: srun --job-name call-run_sawfish --partition compute,compute9 --cpus-per-task 16 --mem 30518M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-32/call-run_sawfish/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-32/call-run_sawfish/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-32/call-run_sawfish/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-32/call-run_sawfish/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-32/out/m84036_250809_035451_s4.bc2129.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2129.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-32/out/m84036_250809_035451_s4.bc2129.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2129.mapped.bam:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-32/call-run_sawfish/_singularity_tmpdir_42e45q21/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-32/call-run_sawfish/_singularity_tmpdir_42e45q21/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:23:38.690 wdl.w:ptcp.t:call-pbmm2_align_hifi-80.stderr VERBOSE 
2025-09-15 20:23:38.691 wdl.w:ptcp.t:call-pbmm2_align_hifi-94.stderr VERBOSE 
2025-09-15 20:23:38.691 wdl.w:ptcp.t:call-pbmm2_align_hifi-80.stderr VERBOSE pbmm2 \
2025-09-15 20:23:38.691 wdl.w:ptcp.t:call-pbmm2_align_hifi-94.stderr VERBOSE pbmm2 \
2025-09-15 20:23:38.691 wdl.w:ptcp.t:call-pbmm2_align_hifi-80.stderr VERBOSE   align \
2025-09-15 20:23:38.691 wdl.w:ptcp.t:call-pbmm2_align_hifi-94.stderr VERBOSE   align \
2025-09-15 20:23:38.692 wdl.w:ptcp.t:call-pbmm2_align_hifi-80.stderr VERBOSE   --log-level INFO \
2025-09-15 20:23:38.692 wdl.w:ptcp.t:call-pbmm2_align_hifi-94.stderr VERBOSE   --log-level INFO \
2025-09-15 20:23:38.692 wdl.w:ptcp.t:call-pbmm2_align_hifi-80.stderr VERBOSE   --log-file pbmm2.log \
2025-09-15 20:23:38.692 wdl.w:ptcp.t:call-pbmm2_align_hifi-94.stderr VERBOSE   --log-file pbmm2.log \
2025-09-15 20:23:38.692 wdl.w:ptcp.t:call-pbmm2_align_hifi-80.stderr VERBOSE   --alarms alarms.json \
2025-09-15 20:23:38.692 wdl.w:ptcp.t:call-pbmm2_align_hifi-94.stderr VERBOSE   --alarms alarms.json \
2025-09-15 20:23:38.692 wdl.w:ptcp.t:call-pbmm2_align_hifi-80.stderr VERBOSE   --num-threads 64 \
2025-09-15 20:23:38.692 wdl.w:ptcp.t:call-pbmm2_align_hifi-94.stderr VERBOSE   --num-threads 64 \
2025-09-15 20:23:38.692 wdl.w:ptcp.t:call-pbmm2_align_hifi-80.stderr VERBOSE   --sort \
2025-09-15 20:23:38.692 wdl.w:ptcp.t:call-pbmm2_align_hifi-94.stderr VERBOSE   --sort \
2025-09-15 20:23:38.693 wdl.w:ptcp.t:call-pbmm2_align_hifi-80.stderr VERBOSE   --preset HiFi \
2025-09-15 20:23:38.693 wdl.w:ptcp.t:call-pbmm2_align_hifi-94.stderr VERBOSE   --preset HiFi \
2025-09-15 20:23:38.693 wdl.w:ptcp.t:call-pbmm2_align_hifi-80.stderr VERBOSE   --report-json mapping_stats.report.json \
2025-09-15 20:23:38.693 wdl.w:ptcp.t:call-pbmm2_align_hifi-94.stderr VERBOSE   --report-json mapping_stats.report.json \
2025-09-15 20:23:38.693 wdl.w:ptcp.t:call-pbmm2_align_hifi-80.stderr VERBOSE   --sample "m84036_250809_035451_s4.bc2177" \
2025-09-15 20:23:38.693 wdl.w:ptcp.t:call-pbmm2_align_hifi-94.stderr VERBOSE   --sample "m84036_250809_035451_s4.bc2191" \
2025-09-15 20:23:38.693 wdl.w:ptcp.t:call-pbmm2_align_hifi-80.stderr VERBOSE   --unmapped \
2025-09-15 20:23:38.693 wdl.w:ptcp.t:call-pbmm2_align_hifi-94.stderr VERBOSE   --unmapped \
2025-09-15 20:23:38.693 wdl.w:ptcp.t:call-pbmm2_align_hifi-80.stderr VERBOSE   /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa \
2025-09-15 20:23:38.693 wdl.w:ptcp.t:call-pbmm2_align_hifi-94.stderr VERBOSE   /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa \
2025-09-15 20:23:38.693 wdl.w:ptcp.t:call-pbmm2_align_hifi-80.stderr VERBOSE   /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0081_m84036_250809_035451_s4.bc2177.unmapped.bam \
2025-09-15 20:23:38.694 wdl.w:ptcp.t:call-pbmm2_align_hifi-94.stderr VERBOSE   /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0095_m84036_250809_035451_s4.bc2191.unmapped.bam \
2025-09-15 20:23:38.694 wdl.w:ptcp.t:call-pbmm2_align_hifi-80.stderr VERBOSE   m84036_250809_035451_s4.bc2177.mapped.bam
2025-09-15 20:23:38.694 wdl.w:ptcp.t:call-pbmm2_align_hifi-94.stderr VERBOSE   m84036_250809_035451_s4.bc2191.mapped.bam
2025-09-15 20:23:38.694 wdl.w:ptcp.t:call-pbmm2_align_hifi-80.stderr VERBOSE + pbmm2 align --log-level INFO --log-file pbmm2.log --alarms alarms.json --num-threads 64 --sort --preset HiFi --report-json mapping_stats.report.json --sample m84036_250809_035451_s4.bc2177 --unmapped /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0081_m84036_250809_035451_s4.bc2177.unmapped.bam m84036_250809_035451_s4.bc2177.mapped.bam
2025-09-15 20:23:38.694 wdl.w:ptcp.t:call-pbmm2_align_hifi-94.stderr VERBOSE + pbmm2 align --log-level INFO --log-file pbmm2.log --alarms alarms.json --num-threads 64 --sort --preset HiFi --report-json mapping_stats.report.json --sample m84036_250809_035451_s4.bc2191 --unmapped /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0095_m84036_250809_035451_s4.bc2191.unmapped.bam m84036_250809_035451_s4.bc2191.mapped.bam
2025-09-15 20:23:38.694 wdl.w:ptcp.t:call-pbmm2_align_hifi-71.stderr VERBOSE 
2025-09-15 20:23:38.695 wdl.w:ptcp.t:call-pbmm2_align_hifi-71.stderr VERBOSE pbmm2 \
2025-09-15 20:23:38.695 wdl.w:ptcp.t:call-pbmm2_align_hifi-71.stderr VERBOSE   align \
2025-09-15 20:23:38.695 wdl.w:ptcp.t:call-pbmm2_align_hifi-71.stderr VERBOSE   --log-level INFO \
2025-09-15 20:23:38.695 wdl.w:ptcp.t:call-pbmm2_align_hifi-71.stderr VERBOSE   --log-file pbmm2.log \
2025-09-15 20:23:38.695 wdl.w:ptcp.t:call-pbmm2_align_hifi-71.stderr VERBOSE   --alarms alarms.json \
2025-09-15 20:23:38.695 wdl.w:ptcp.t:call-pbmm2_align_hifi-71.stderr VERBOSE   --num-threads 64 \
2025-09-15 20:23:38.695 wdl.w:ptcp.t:call-pbmm2_align_hifi-71.stderr VERBOSE   --sort \
2025-09-15 20:23:38.695 wdl.w:ptcp.t:call-pbmm2_align_hifi-71.stderr VERBOSE   --preset HiFi \
2025-09-15 20:23:38.695 wdl.w:ptcp.t:call-pbmm2_align_hifi-71.stderr VERBOSE   --report-json mapping_stats.report.json \
2025-09-15 20:23:38.696 wdl.w:ptcp.t:call-pbmm2_align_hifi-71.stderr VERBOSE   --sample "m84036_250809_035451_s4.bc2168" \
2025-09-15 20:23:38.696 wdl.w:ptcp.t:call-pbmm2_align_hifi-71.stderr VERBOSE   --unmapped \
2025-09-15 20:23:38.696 wdl.w:ptcp.t:call-pbmm2_align_hifi-71.stderr VERBOSE   /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa \
2025-09-15 20:23:38.696 wdl.w:ptcp.t:call-pbmm2_align_hifi-71.stderr VERBOSE   /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0072_m84036_250809_035451_s4.bc2168.unmapped.bam \
2025-09-15 20:23:38.696 wdl.w:ptcp.t:call-pbmm2_align_hifi-71.stderr VERBOSE   m84036_250809_035451_s4.bc2168.mapped.bam
2025-09-15 20:23:38.696 wdl.w:ptcp.t:call-pbmm2_align_hifi-71.stderr VERBOSE + pbmm2 align --log-level INFO --log-file pbmm2.log --alarms alarms.json --num-threads 64 --sort --preset HiFi --report-json mapping_stats.report.json --sample m84036_250809_035451_s4.bc2168 --unmapped /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0072_m84036_250809_035451_s4.bc2168.unmapped.bam m84036_250809_035451_s4.bc2168.mapped.bam
2025-09-15 20:23:38.696 wdl.w:ptcp.t:call-pbmm2_align_hifi-95.stderr VERBOSE 
2025-09-15 20:23:38.696 wdl.w:ptcp.t:call-pbmm2_align_hifi-95.stderr VERBOSE pbmm2 \
2025-09-15 20:23:38.696 wdl.w:ptcp.t:call-pbmm2_align_hifi-95.stderr VERBOSE   align \
2025-09-15 20:23:38.696 wdl.w:ptcp.t:call-pbmm2_align_hifi-95.stderr VERBOSE   --log-level INFO \
2025-09-15 20:23:38.696 wdl.w:ptcp.t:call-pbmm2_align_hifi-95.stderr VERBOSE   --log-file pbmm2.log \
2025-09-15 20:23:38.696 wdl.w:ptcp.t:call-pbmm2_align_hifi-95.stderr VERBOSE   --alarms alarms.json \
2025-09-15 20:23:38.696 wdl.w:ptcp.t:call-pbmm2_align_hifi-95.stderr VERBOSE   --num-threads 64 \
2025-09-15 20:23:38.696 wdl.w:ptcp.t:call-pbmm2_align_hifi-95.stderr VERBOSE   --sort \
2025-09-15 20:23:38.697 wdl.w:ptcp.t:call-pbmm2_align_hifi-95.stderr VERBOSE   --preset HiFi \
2025-09-15 20:23:38.697 wdl.w:ptcp.t:call-pbmm2_align_hifi-95.stderr VERBOSE   --report-json mapping_stats.report.json \
2025-09-15 20:23:38.697 wdl.w:ptcp.t:call-pbmm2_align_hifi-95.stderr VERBOSE   --sample "m84036_250809_035451_s4.bc2192" \
2025-09-15 20:23:38.697 wdl.w:ptcp.t:call-pbmm2_align_hifi-95.stderr VERBOSE   --unmapped \
2025-09-15 20:23:38.697 wdl.w:ptcp.t:call-pbmm2_align_hifi-95.stderr VERBOSE   /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa \
2025-09-15 20:23:38.697 wdl.w:ptcp.t:call-pbmm2_align_hifi-95.stderr VERBOSE   /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0096_m84036_250809_035451_s4.bc2192.unmapped.bam \
2025-09-15 20:23:38.697 wdl.w:ptcp.t:call-pbmm2_align_hifi-95.stderr VERBOSE   m84036_250809_035451_s4.bc2192.mapped.bam
2025-09-15 20:23:38.697 wdl.w:ptcp.t:call-pbmm2_align_hifi-95.stderr VERBOSE + pbmm2 align --log-level INFO --log-file pbmm2.log --alarms alarms.json --num-threads 64 --sort --preset HiFi --report-json mapping_stats.report.json --sample m84036_250809_035451_s4.bc2192 --unmapped /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0096_m84036_250809_035451_s4.bc2192.unmapped.bam m84036_250809_035451_s4.bc2192.mapped.bam
2025-09-15 20:23:38.706 wdl.w:ptcp.t:call-pbmm2_align_hifi-93.stderr VERBOSE 
2025-09-15 20:23:38.706 wdl.w:ptcp.t:call-pbmm2_align_hifi-93.stderr VERBOSE pbmm2 \
2025-09-15 20:23:38.706 wdl.w:ptcp.t:call-pbmm2_align_hifi-93.stderr VERBOSE   align \
2025-09-15 20:23:38.706 wdl.w:ptcp.t:call-pbmm2_align_hifi-93.stderr VERBOSE   --log-level INFO \
2025-09-15 20:23:38.706 wdl.w:ptcp.t:call-pbmm2_align_hifi-93.stderr VERBOSE   --log-file pbmm2.log \
2025-09-15 20:23:38.707 wdl.w:ptcp.t:call-pbmm2_align_hifi-93.stderr VERBOSE   --alarms alarms.json \
2025-09-15 20:23:38.707 wdl.w:ptcp.t:call-pbmm2_align_hifi-93.stderr VERBOSE   --num-threads 64 \
2025-09-15 20:23:38.707 wdl.w:ptcp.t:call-pbmm2_align_hifi-93.stderr VERBOSE   --sort \
2025-09-15 20:23:38.707 wdl.w:ptcp.t:call-pbmm2_align_hifi-93.stderr VERBOSE   --preset HiFi \
2025-09-15 20:23:38.707 wdl.w:ptcp.t:call-pbmm2_align_hifi-93.stderr VERBOSE   --report-json mapping_stats.report.json \
2025-09-15 20:23:38.707 wdl.w:ptcp.t:call-pbmm2_align_hifi-93.stderr VERBOSE   --sample "m84036_250809_035451_s4.bc2190" \
2025-09-15 20:23:38.707 wdl.w:ptcp.t:call-pbmm2_align_hifi-93.stderr VERBOSE   --unmapped \
2025-09-15 20:23:38.707 wdl.w:ptcp.t:call-pbmm2_align_hifi-93.stderr VERBOSE   /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa \
2025-09-15 20:23:38.707 wdl.w:ptcp.t:call-pbmm2_align_hifi-93.stderr VERBOSE   /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0094_m84036_250809_035451_s4.bc2190.unmapped.bam \
2025-09-15 20:23:38.707 wdl.w:ptcp.t:call-pbmm2_align_hifi-93.stderr VERBOSE   m84036_250809_035451_s4.bc2190.mapped.bam
2025-09-15 20:23:38.707 wdl.w:ptcp.t:call-pbmm2_align_hifi-93.stderr VERBOSE + pbmm2 align --log-level INFO --log-file pbmm2.log --alarms alarms.json --num-threads 64 --sort --preset HiFi --report-json mapping_stats.report.json --sample m84036_250809_035451_s4.bc2190 --unmapped /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0094_m84036_250809_035451_s4.bc2190.unmapped.bam m84036_250809_035451_s4.bc2190.mapped.bam
2025-09-15 20:23:38.718 wdl.w:ptcp.t:call-pbmm2_align_hifi-85.stderr VERBOSE 
2025-09-15 20:23:38.718 wdl.w:ptcp.t:call-pbmm2_align_hifi-85.stderr VERBOSE pbmm2 \
2025-09-15 20:23:38.719 wdl.w:ptcp.t:call-pbmm2_align_hifi-85.stderr VERBOSE   align \
2025-09-15 20:23:38.719 wdl.w:ptcp.t:call-pbmm2_align_hifi-85.stderr VERBOSE   --log-level INFO \
2025-09-15 20:23:38.719 wdl.w:ptcp.t:call-pbmm2_align_hifi-85.stderr VERBOSE   --log-file pbmm2.log \
2025-09-15 20:23:38.719 wdl.w:ptcp.t:call-pbmm2_align_hifi-85.stderr VERBOSE   --alarms alarms.json \
2025-09-15 20:23:38.719 wdl.w:ptcp.t:call-pbmm2_align_hifi-85.stderr VERBOSE   --num-threads 64 \
2025-09-15 20:23:38.719 wdl.w:ptcp.t:call-pbmm2_align_hifi-85.stderr VERBOSE   --sort \
2025-09-15 20:23:38.719 wdl.w:ptcp.t:call-pbmm2_align_hifi-85.stderr VERBOSE   --preset HiFi \
2025-09-15 20:23:38.719 wdl.w:ptcp.t:call-pbmm2_align_hifi-85.stderr VERBOSE   --report-json mapping_stats.report.json \
2025-09-15 20:23:38.719 wdl.w:ptcp.t:call-pbmm2_align_hifi-85.stderr VERBOSE   --sample "m84036_250809_035451_s4.bc2182" \
2025-09-15 20:23:38.719 wdl.w:ptcp.t:call-pbmm2_align_hifi-85.stderr VERBOSE   --unmapped \
2025-09-15 20:23:38.719 wdl.w:ptcp.t:call-pbmm2_align_hifi-85.stderr VERBOSE   /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa \
2025-09-15 20:23:38.719 wdl.w:ptcp.t:call-pbmm2_align_hifi-85.stderr VERBOSE   /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0086_m84036_250809_035451_s4.bc2182.unmapped.bam \
2025-09-15 20:23:38.719 wdl.w:ptcp.t:call-pbmm2_align_hifi-85.stderr VERBOSE   m84036_250809_035451_s4.bc2182.mapped.bam
2025-09-15 20:23:38.719 wdl.w:ptcp.t:call-pbmm2_align_hifi-85.stderr VERBOSE + pbmm2 align --log-level INFO --log-file pbmm2.log --alarms alarms.json --num-threads 64 --sort --preset HiFi --report-json mapping_stats.report.json --sample m84036_250809_035451_s4.bc2182 --unmapped /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0086_m84036_250809_035451_s4.bc2182.unmapped.bam m84036_250809_035451_s4.bc2182.mapped.bam
2025-09-15 20:23:38.743 wdl.w:ptcp.t:call-pbmm2_align_hifi-83.stderr VERBOSE 
2025-09-15 20:23:38.743 wdl.w:ptcp.t:call-pbmm2_align_hifi-83.stderr VERBOSE pbmm2 \
2025-09-15 20:23:38.743 wdl.w:ptcp.t:call-pbmm2_align_hifi-83.stderr VERBOSE   align \
2025-09-15 20:23:38.743 wdl.w:ptcp.t:call-pbmm2_align_hifi-83.stderr VERBOSE   --log-level INFO \
2025-09-15 20:23:38.743 wdl.w:ptcp.t:call-pbmm2_align_hifi-83.stderr VERBOSE   --log-file pbmm2.log \
2025-09-15 20:23:38.743 wdl.w:ptcp.t:call-pbmm2_align_hifi-83.stderr VERBOSE   --alarms alarms.json \
2025-09-15 20:23:38.743 wdl.w:ptcp.t:call-pbmm2_align_hifi-83.stderr VERBOSE   --num-threads 64 \
2025-09-15 20:23:38.743 wdl.w:ptcp.t:call-pbmm2_align_hifi-83.stderr VERBOSE   --sort \
2025-09-15 20:23:38.743 wdl.w:ptcp.t:call-pbmm2_align_hifi-83.stderr VERBOSE   --preset HiFi \
2025-09-15 20:23:38.743 wdl.w:ptcp.t:call-pbmm2_align_hifi-83.stderr VERBOSE   --report-json mapping_stats.report.json \
2025-09-15 20:23:38.744 wdl.w:ptcp.t:call-pbmm2_align_hifi-83.stderr VERBOSE   --sample "m84036_250809_035451_s4.bc2180" \
2025-09-15 20:23:38.744 wdl.w:ptcp.t:call-pbmm2_align_hifi-83.stderr VERBOSE   --unmapped \
2025-09-15 20:23:38.744 wdl.w:ptcp.t:call-pbmm2_align_hifi-83.stderr VERBOSE   /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa \
2025-09-15 20:23:38.744 wdl.w:ptcp.t:call-pbmm2_align_hifi-83.stderr VERBOSE   /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0084_m84036_250809_035451_s4.bc2180.unmapped.bam \
2025-09-15 20:23:38.744 wdl.w:ptcp.t:call-pbmm2_align_hifi-83.stderr VERBOSE   m84036_250809_035451_s4.bc2180.mapped.bam
2025-09-15 20:23:38.744 wdl.w:ptcp.t:call-pbmm2_align_hifi-83.stderr VERBOSE + pbmm2 align --log-level INFO --log-file pbmm2.log --alarms alarms.json --num-threads 64 --sort --preset HiFi --report-json mapping_stats.report.json --sample m84036_250809_035451_s4.bc2180 --unmapped /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/sample0084_m84036_250809_035451_s4.bc2180.unmapped.bam m84036_250809_035451_s4.bc2180.mapped.bam
2025-09-15 20:23:38.761 wdl.w:ptcp.w:call-sawfish-32.t:call-run_sawfish NOTICE slurm_singularity run :: pid: 1199796, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-32/call-run_sawfish/slurm_singularity.log.txt"
2025-09-15 20:23:38.818 wdl.w:ptcp.w:call-sawfish-16.t:call-run_sawfish.stderr VERBOSE [M::bam2fq_mainloop] discarded 0 singletons
2025-09-15 20:23:38.818 wdl.w:ptcp.w:call-sawfish-16.t:call-run_sawfish.stderr VERBOSE [M::bam2fq_mainloop] processed 0 reads
2025-09-15 20:23:38.830 wdl.w:ptcp.w:call-sawfish-16.t:call-run_sawfish.slurm_singularity INFO srun: job 51797435 queued and waiting for resources
2025-09-15 20:23:38.830 wdl.w:ptcp.w:call-sawfish-16.t:call-run_sawfish.slurm_singularity INFO srun: job 51797435 has been allocated resources
2025-09-15 20:23:38.830 wdl.w:ptcp.w:call-sawfish-16.t:call-run_sawfish.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:38.830 wdl.w:ptcp.w:call-sawfish-16.t:call-run_sawfish.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:23:38.941 wdl.w:ptcp.w:call-trgt-29.t:call-get_reads_overlapping_repeats INFO output :: name: "reads_overlapping_repeats", value: "m84036_250809_035451_s4.bc2126.repeats.bam"
2025-09-15 20:23:38.944 wdl.w:ptcp.w:call-trgt-29.t:call-get_reads_overlapping_repeats INFO output :: name: "reads_overlapping_repeats_bai", value: "m84036_250809_035451_s4.bc2126.repeats.bam.bai"
2025-09-15 20:23:39.014 wdl.w:ptcp.w:call-trgt-29.t:call-get_reads_overlapping_repeats NOTICE done
2025-09-15 20:23:39.022 wdl.w:ptcp.w:call-trgt-29 NOTICE finish :: job: "call-get_reads_overlapping_repeats"
2025-09-15 20:23:39.022 wdl.w:ptcp.w:call-trgt-29 INFO output :: job: "call-get_reads_overlapping_repeats", values: {"reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-29/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2126.repeats.bam.bai", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-29/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2126.repeats.bam"}
2025-09-15 20:23:39.023 wdl.w:ptcp.w:call-trgt-29 INFO visit :: node: "output-reads_overlapping_repeats", values: {"reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-29/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2126.repeats.bam"}
2025-09-15 20:23:39.023 wdl.w:ptcp.w:call-trgt-29 INFO visit :: node: "output-reads_overlapping_repeats_bai", values: {"reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-29/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2126.repeats.bam.bai"}
2025-09-15 20:23:39.028 wdl.w:ptcp.w:call-trgt-32.t:call-get_reads_overlapping_repeats NOTICE task setup :: name: "get_reads_overlapping_repeats", source: "./trgt.wdl", line: 182, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-32/call-get_reads_overlapping_repeats", thread: 140613823374912
2025-09-15 20:23:39.045 wdl.w:ptcp.w:call-trgt-32.t:call-get_reads_overlapping_repeats INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:23:39.045 wdl.w:ptcp.w:call-trgt-32.t:call-get_reads_overlapping_repeats INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:23:39.045 wdl.w:ptcp.w:call-trgt-32.t:call-get_reads_overlapping_repeats INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2129.mapped.bam.bai"
2025-09-15 20:23:39.045 wdl.w:ptcp.w:call-trgt-32.t:call-get_reads_overlapping_repeats INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2129.mapped.bam"
2025-09-15 20:23:39.045 wdl.w:ptcp.w:call-trgt-32.t:call-get_reads_overlapping_repeats INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2129"
2025-09-15 20:23:39.045 wdl.w:ptcp.w:call-trgt-32.t:call-get_reads_overlapping_repeats INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:23:39.045 wdl.w:ptcp.w:call-trgt-32.t:call-get_reads_overlapping_repeats INFO eval :: name: "expand_size", value: 3000
2025-09-15 20:23:39.046 wdl.w:ptcp.w:call-trgt-32.t:call-get_reads_overlapping_repeats INFO eval :: name: "threads", value: 1
2025-09-15 20:23:39.046 wdl.w:ptcp.w:call-trgt-32.t:call-get_reads_overlapping_repeats INFO eval :: name: "expanded_bed_name", value: "m84036_250809_035451_s4.bc2129.expanded.bed"
2025-09-15 20:23:39.046 wdl.w:ptcp.w:call-trgt-32.t:call-get_reads_overlapping_repeats INFO eval :: name: "disk_size", value: 11
2025-09-15 20:23:39.046 wdl.w:ptcp.w:call-trgt-32.t:call-get_reads_overlapping_repeats INFO eval :: name: "output_name", value: "m84036_250809_035451_s4.bc2129.repeats.bam"
2025-09-15 20:23:39.046 wdl.w:ptcp.w:call-trgt-32.t:call-get_reads_overlapping_repeats INFO eval :: name: "index_name", value: "m84036_250809_035451_s4.bc2129.repeats.bam.bai"
2025-09-15 20:23:39.046 wdl.w:ptcp.w:call-trgt-32.t:call-get_reads_overlapping_repeats INFO eval :: name: "output_name_with_index", value: "m84036_250809_035451_s4.bc2129.repeats.bam##idx##m84036_250809_035451_s4.bc2129.repeats.bam.bai"
2025-09-15 20:23:39.046 wdl.w:ptcp.w:call-trgt-32.t:call-get_reads_overlapping_repeats INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:23:39.047 wdl.w:ptcp.w:call-trgt-32.t:call-get_reads_overlapping_repeats WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:23:39.047 wdl.w:ptcp.w:call-trgt-32.t:call-get_reads_overlapping_repeats INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:23:39.047 wdl.w:ptcp.w:call-trgt-32.t:call-get_reads_overlapping_repeats INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:23:39.067 wdl.w:ptcp.w:call-paraphase-16.t:call-run_paraphase.slurm_singularity INFO srun: job 51797436 queued and waiting for resources
2025-09-15 20:23:39.067 wdl.w:ptcp.w:call-paraphase-16.t:call-run_paraphase.slurm_singularity INFO srun: job 51797436 has been allocated resources
2025-09-15 20:23:39.067 wdl.w:ptcp.w:call-paraphase-16.t:call-run_paraphase.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:39.072 wdl.w:ptcp.w:call-trgt-16.t:call-get_reads_overlapping_repeats.slurm_singularity INFO srun: job 51797437 queued and waiting for resources
2025-09-15 20:23:39.072 wdl.w:ptcp.w:call-trgt-16.t:call-get_reads_overlapping_repeats.slurm_singularity INFO srun: job 51797437 has been allocated resources
2025-09-15 20:23:39.072 wdl.w:ptcp.w:call-trgt-16.t:call-get_reads_overlapping_repeats.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:39.111 wdl.w:ptcp.w:call-trgt-32.t:call-get_reads_overlapping_repeats INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 9, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-32/call-get_reads_overlapping_repeats/_singularity_tmpdir_b1e6qjnb"
2025-09-15 20:23:39.111 wdl.w:ptcp.w:call-trgt-32.t:call-get_reads_overlapping_repeats INFO Slurm invocation: srun --job-name call-get_reads_overlapping_repeats --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-32/call-get_reads_overlapping_repeats/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-32/call-get_reads_overlapping_repeats/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-32/call-get_reads_overlapping_repeats/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-32/call-get_reads_overlapping_repeats/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-32/out/m84036_250809_035451_s4.bc2129.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2129.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-32/out/m84036_250809_035451_s4.bc2129.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2129.mapped.bam:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-32/call-get_reads_overlapping_repeats/_singularity_tmpdir_b1e6qjnb/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-32/call-get_reads_overlapping_repeats/_singularity_tmpdir_b1e6qjnb/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:23:39.134 wdl.w:ptcp.w:call-trgt-32.t:call-get_reads_overlapping_repeats NOTICE slurm_singularity run :: pid: 1199881, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-32/call-get_reads_overlapping_repeats/slurm_singularity.log.txt"
2025-09-15 20:23:39.140 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_genotype INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2124.trgt.vcf"
2025-09-15 20:23:39.143 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_genotype INFO output :: name: "spanning_bam", value: "m84036_250809_035451_s4.bc2124.trgt.sorted.spanning.bam"
2025-09-15 20:23:39.145 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_genotype INFO output :: name: "spanning_bam_bai", value: "m84036_250809_035451_s4.bc2124.trgt.sorted.spanning.bam.bai"
2025-09-15 20:23:39.236 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_genotype NOTICE done
2025-09-15 20:23:39.277 wdl.w:ptcp.w:call-trgt-27 NOTICE finish :: job: "call-trgt_genotype"
2025-09-15 20:23:39.277 wdl.w:ptcp.w:call-trgt-27 INFO output :: job: "call-trgt_genotype", values: {"spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-27/call-trgt_genotype/out/m84036_250809_035451_s4.bc2124.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-27/call-trgt_genotype/out/m84036_250809_035451_s4.bc2124.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-27/call-trgt_genotype/out/m84036_250809_035451_s4.bc2124.trgt.vcf"}
2025-09-15 20:23:39.278 wdl.w:ptcp.w:call-trgt-27 NOTICE ready :: job: "call-trgt_plot_meth_allele", callee: "trgt_plot"
2025-09-15 20:23:39.278 wdl.w:ptcp.w:call-trgt-27 INFO input :: job: "call-trgt_plot_meth_allele", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": false, "methylation": true, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-27/call-trgt_genotype/out/m84036_250809_035451_s4.bc2124.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-27/call-trgt_genotype/out/m84036_250809_035451_s4.bc2124.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-27/call-trgt_genotype/out/m84036_250809_035451_s4.bc2124.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2124"}
2025-09-15 20:23:39.279 wdl.w:ptcp.w:call-trgt-27 NOTICE ready :: job: "call-trgt_plot_meth_waterfall", callee: "trgt_plot"
2025-09-15 20:23:39.279 wdl.w:ptcp.w:call-trgt-27 INFO input :: job: "call-trgt_plot_meth_waterfall", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": true, "methylation": true, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-27/call-trgt_genotype/out/m84036_250809_035451_s4.bc2124.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-27/call-trgt_genotype/out/m84036_250809_035451_s4.bc2124.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-27/call-trgt_genotype/out/m84036_250809_035451_s4.bc2124.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2124"}
2025-09-15 20:23:39.280 wdl.w:ptcp.w:call-trgt-27 NOTICE ready :: job: "call-trgt_plot_motifs_allele", callee: "trgt_plot"
2025-09-15 20:23:39.280 wdl.w:ptcp.w:call-trgt-27 INFO input :: job: "call-trgt_plot_motifs_allele", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": false, "methylation": false, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-27/call-trgt_genotype/out/m84036_250809_035451_s4.bc2124.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-27/call-trgt_genotype/out/m84036_250809_035451_s4.bc2124.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-27/call-trgt_genotype/out/m84036_250809_035451_s4.bc2124.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2124"}
2025-09-15 20:23:39.281 wdl.w:ptcp.w:call-trgt-27 NOTICE ready :: job: "call-trgt_plot_motifs_waterfall", callee: "trgt_plot"
2025-09-15 20:23:39.281 wdl.w:ptcp.w:call-trgt-27 INFO input :: job: "call-trgt_plot_motifs_waterfall", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": true, "methylation": false, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-27/call-trgt_genotype/out/m84036_250809_035451_s4.bc2124.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-27/call-trgt_genotype/out/m84036_250809_035451_s4.bc2124.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-27/call-trgt_genotype/out/m84036_250809_035451_s4.bc2124.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2124"}
2025-09-15 20:23:39.282 wdl.w:ptcp.w:call-trgt-27 INFO visit :: node: "output-spanning_bam", values: {"spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-27/call-trgt_genotype/out/m84036_250809_035451_s4.bc2124.trgt.sorted.spanning.bam"}
2025-09-15 20:23:39.282 wdl.w:ptcp.w:call-trgt-27 INFO visit :: node: "output-spanning_bam_bai", values: {"spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-27/call-trgt_genotype/out/m84036_250809_035451_s4.bc2124.trgt.sorted.spanning.bam.bai"}
2025-09-15 20:23:39.282 wdl.w:ptcp.w:call-trgt-27 INFO visit :: node: "output-vcf", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-27/call-trgt_genotype/out/m84036_250809_035451_s4.bc2124.trgt.vcf"}
2025-09-15 20:23:39.284 wdl.w:ptcp.w:call-trgt-32.t:call-trgt_genotype NOTICE task setup :: name: "trgt_genotype", source: "./trgt.wdl", line: 272, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-32/call-trgt_genotype", thread: 140609822115392
2025-09-15 20:23:39.291 wdl.w:ptcp.w:call-trgt-16.t:call-trgt_genotype.slurm_singularity INFO srun: job 51797438 queued and waiting for resources
2025-09-15 20:23:39.291 wdl.w:ptcp.w:call-trgt-16.t:call-trgt_genotype.slurm_singularity INFO srun: job 51797438 has been allocated resources
2025-09-15 20:23:39.291 wdl.w:ptcp.w:call-trgt-16.t:call-trgt_genotype.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:39.291 wdl.w:ptcp.w:call-trgt-16.t:call-trgt_genotype.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:23:39.292 wdl.w:ptcp.w:call-trgt-13.t:call-get_reads_overlapping_repeats INFO output :: name: "reads_overlapping_repeats", value: "m84036_250809_035451_s4.bc2110.repeats.bam"
2025-09-15 20:23:39.298 wdl.w:ptcp.w:call-trgt-13.t:call-get_reads_overlapping_repeats INFO output :: name: "reads_overlapping_repeats_bai", value: "m84036_250809_035451_s4.bc2110.repeats.bam.bai"
2025-09-15 20:23:39.308 wdl.w:ptcp.w:call-trgt-32.t:call-trgt_genotype INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:23:39.308 wdl.w:ptcp.w:call-trgt-32.t:call-trgt_genotype INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:23:39.308 wdl.w:ptcp.w:call-trgt-32.t:call-trgt_genotype INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:23:39.308 wdl.w:ptcp.w:call-trgt-32.t:call-trgt_genotype INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:23:39.308 wdl.w:ptcp.w:call-trgt-32.t:call-trgt_genotype INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2129.mapped.bam.bai"
2025-09-15 20:23:39.308 wdl.w:ptcp.w:call-trgt-32.t:call-trgt_genotype INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2129.mapped.bam"
2025-09-15 20:23:39.308 wdl.w:ptcp.w:call-trgt-32.t:call-trgt_genotype INFO input :: name: "sex", value: "F"
2025-09-15 20:23:39.308 wdl.w:ptcp.w:call-trgt-32.t:call-trgt_genotype INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2129"
2025-09-15 20:23:39.309 wdl.w:ptcp.w:call-trgt-32.t:call-trgt_genotype INFO eval :: name: "mem_gb", value: 16
2025-09-15 20:23:39.309 wdl.w:ptcp.w:call-trgt-32.t:call-trgt_genotype INFO eval :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2129.trgt"
2025-09-15 20:23:39.309 wdl.w:ptcp.w:call-trgt-32.t:call-trgt_genotype INFO eval :: name: "threads", value: 8
2025-09-15 20:23:39.309 wdl.w:ptcp.w:call-trgt-32.t:call-trgt_genotype INFO eval :: name: "disk_size", value: 27
2025-09-15 20:23:39.309 wdl.w:ptcp.w:call-trgt-32.t:call-trgt_genotype INFO eval :: name: "karyotype", value: "XX"
2025-09-15 20:23:39.310 wdl.w:ptcp.w:call-trgt-32.t:call-trgt_genotype INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 8, memory_reservation: 16000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:23:39.310 wdl.w:ptcp.w:call-trgt-32.t:call-trgt_genotype WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:23:39.310 wdl.w:ptcp.w:call-trgt-32.t:call-trgt_genotype INFO provisioned :: seconds_waited: 0, cpu: 8, mem_bytes: 16000000000
2025-09-15 20:23:39.310 wdl.w:ptcp.w:call-trgt-32.t:call-trgt_genotype INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:23:39.345 wdl.w:ptcp.w:call-trgt-33.t:call-get_reads_overlapping_repeats INFO output :: name: "reads_overlapping_repeats", value: "m84036_250809_035451_s4.bc2130.repeats.bam"
2025-09-15 20:23:39.350 wdl.w:ptcp.w:call-trgt-33.t:call-get_reads_overlapping_repeats INFO output :: name: "reads_overlapping_repeats_bai", value: "m84036_250809_035451_s4.bc2130.repeats.bam.bai"
2025-09-15 20:23:39.367 wdl.w:ptcp.w:call-paraphase-28.t:call-run_paraphase INFO output :: name: "paraphase_bam", value: "m84036_250809_035451_s4.bc2125_paraphase/m84036_250809_035451_s4.bc2125.paraphase.bam"
2025-09-15 20:23:39.371 wdl.w:ptcp.w:call-paraphase-28.t:call-run_paraphase INFO output :: name: "paraphase_bam_bai", value: "m84036_250809_035451_s4.bc2125_paraphase/m84036_250809_035451_s4.bc2125.paraphase.bam.bai"
2025-09-15 20:23:39.372 wdl.w:ptcp.w:call-paraphase-28.t:call-run_paraphase INFO output :: name: "paraphase_json", value: "m84036_250809_035451_s4.bc2125_paraphase/m84036_250809_035451_s4.bc2125.paraphase.json"
2025-09-15 20:23:39.374 wdl.w:ptcp.w:call-paraphase-28.t:call-run_paraphase INFO output :: name: "paraphase_vcfs", value: []
2025-09-15 20:23:39.374 wdl.w:ptcp.w:call-paraphase-28.t:call-run_paraphase INFO output :: name: "havanno_json", value: "m84036_250809_035451_s4.bc2125.havanno.json"
2025-09-15 20:23:39.395 wdl.w:ptcp.w:call-trgt-13.t:call-get_reads_overlapping_repeats NOTICE done
2025-09-15 20:23:39.402 wdl.w:ptcp.w:call-trgt-13 NOTICE finish :: job: "call-get_reads_overlapping_repeats"
2025-09-15 20:23:39.402 wdl.w:ptcp.w:call-trgt-13 INFO output :: job: "call-get_reads_overlapping_repeats", values: {"reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-13/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2110.repeats.bam.bai", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-13/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2110.repeats.bam"}
2025-09-15 20:23:39.403 wdl.w:ptcp.w:call-trgt-13 INFO visit :: node: "output-reads_overlapping_repeats", values: {"reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-13/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2110.repeats.bam"}
2025-09-15 20:23:39.403 wdl.w:ptcp.w:call-trgt-13 INFO visit :: node: "output-reads_overlapping_repeats_bai", values: {"reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-13/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2110.repeats.bam.bai"}
2025-09-15 20:23:39.410 wdl.w:ptcp.w:call-paraphase-02.t:call-run_paraphase NOTICE task setup :: name: "run_paraphase", source: "./paraphase.wdl", line: 127, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-02/call-run_paraphase", thread: 140610333808192
2025-09-15 20:23:39.413 wdl.w:ptcp.w:call-trgt-32.t:call-trgt_genotype INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 11, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-32/call-trgt_genotype/_singularity_tmpdir_0o95vlj0"
2025-09-15 20:23:39.413 wdl.w:ptcp.w:call-trgt-32.t:call-trgt_genotype INFO Slurm invocation: srun --job-name call-trgt_genotype --partition compute,compute9 --cpus-per-task 8 --mem 15259M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-32/call-trgt_genotype/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-32/call-trgt_genotype/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-32/call-trgt_genotype/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-32/call-trgt_genotype/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-32/out/m84036_250809_035451_s4.bc2129.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2129.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-32/out/m84036_250809_035451_s4.bc2129.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2129.mapped.bam:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-32/call-trgt_genotype/_singularity_tmpdir_0o95vlj0/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-32/call-trgt_genotype/_singularity_tmpdir_0o95vlj0/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:23:39.432 wdl.w:ptcp.w:call-paraphase-02.t:call-run_paraphase INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:23:39.433 wdl.w:ptcp.w:call-paraphase-02.t:call-run_paraphase INFO input :: name: "annotation_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf"
2025-09-15 20:23:39.433 wdl.w:ptcp.w:call-paraphase-02.t:call-run_paraphase INFO input :: name: "genome_version", value: "38"
2025-09-15 20:23:39.433 wdl.w:ptcp.w:call-paraphase-02.t:call-run_paraphase INFO input :: name: "config_file", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/paraphase_config.GRCh38.yaml"
2025-09-15 20:23:39.433 wdl.w:ptcp.w:call-paraphase-02.t:call-run_paraphase INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:23:39.433 wdl.w:ptcp.w:call-paraphase-02.t:call-run_paraphase INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:23:39.433 wdl.w:ptcp.w:call-paraphase-02.t:call-run_paraphase INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2099.mapped.bam.bai"
2025-09-15 20:23:39.433 wdl.w:ptcp.w:call-paraphase-02.t:call-run_paraphase INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2099.mapped.bam"
2025-09-15 20:23:39.433 wdl.w:ptcp.w:call-paraphase-02.t:call-run_paraphase INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2099"
2025-09-15 20:23:39.433 wdl.w:ptcp.w:call-paraphase-02.t:call-run_paraphase INFO eval :: name: "threads", value: 4
2025-09-15 20:23:39.433 wdl.w:ptcp.w:call-paraphase-02.t:call-run_paraphase INFO eval :: name: "mem_gb", value: 8
2025-09-15 20:23:39.434 wdl.w:ptcp.w:call-paraphase-02.t:call-run_paraphase INFO eval :: name: "disk_size", value: 27
2025-09-15 20:23:39.434 wdl.w:ptcp.w:call-paraphase-02.t:call-run_paraphase INFO eval :: name: "out_dir", value: "m84036_250809_035451_s4.bc2099_paraphase"
2025-09-15 20:23:39.434 wdl.w:ptcp.w:call-paraphase-02.t:call-run_paraphase INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 4, memory_reservation: 8000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:23:39.434 wdl.w:ptcp.w:call-paraphase-02.t:call-run_paraphase WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:23:39.435 wdl.w:ptcp.w:call-paraphase-02.t:call-run_paraphase INFO provisioned :: seconds_waited: 0, cpu: 4, mem_bytes: 8000000000
2025-09-15 20:23:39.435 wdl.w:ptcp.w:call-paraphase-02.t:call-run_paraphase INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:23:39.444 wdl.w:ptcp.w:call-trgt-32.t:call-trgt_genotype NOTICE slurm_singularity run :: pid: 1199903, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-32/call-trgt_genotype/slurm_singularity.log.txt"
2025-09-15 20:23:39.455 wdl.w:ptcp.w:call-trgt-33.t:call-get_reads_overlapping_repeats NOTICE done
2025-09-15 20:23:39.460 wdl.w:ptcp.w:call-trgt-33 NOTICE finish :: job: "call-get_reads_overlapping_repeats"
2025-09-15 20:23:39.460 wdl.w:ptcp.w:call-trgt-33 INFO output :: job: "call-get_reads_overlapping_repeats", values: {"reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-33/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2130.repeats.bam.bai", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-33/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2130.repeats.bam"}
2025-09-15 20:23:39.461 wdl.w:ptcp.w:call-trgt-33 INFO visit :: node: "output-reads_overlapping_repeats", values: {"reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-33/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2130.repeats.bam"}
2025-09-15 20:23:39.461 wdl.w:ptcp.w:call-trgt-33 INFO visit :: node: "output-reads_overlapping_repeats_bai", values: {"reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-33/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2130.repeats.bam.bai"}
2025-09-15 20:23:39.468 wdl.w:ptcp.w:call-sawfish-02.t:call-run_sawfish NOTICE task setup :: name: "run_sawfish", source: "./sawfish.wdl", line: 83, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-02/call-run_sawfish", thread: 140611961206336
2025-09-15 20:23:39.471 wdl.w:ptcp.w:call-paraphase-21.t:call-run_paraphase.stderr VERBOSE INFO:root:Processing sample m84036_250809_035451_s4.bc2118 at 2025-09-15 20:23:37.761735...
2025-09-15 20:23:39.473 wdl.w:ptcp.w:call-paraphase-21.t:call-run_paraphase.stderr VERBOSE INFO:root:Checking sample sex at 2025-09-15 20:23:37.762814...
2025-09-15 20:23:39.473 wdl.w:ptcp.w:call-paraphase-21.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for cyp21 for sample m84036_250809_035451_s4.bc2118 at 2025-09-15 20:23:37.805951...
2025-09-15 20:23:39.473 wdl.w:ptcp.w:call-paraphase-21.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for cyp21 for sample m84036_250809_035451_s4.bc2118 at 2025-09-15 20:23:37.806405...
2025-09-15 20:23:39.473 wdl.w:ptcp.w:call-paraphase-21.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for smn1 for sample m84036_250809_035451_s4.bc2118 at 2025-09-15 20:23:37.806077...
2025-09-15 20:23:39.473 wdl.w:ptcp.w:call-paraphase-21.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for smn1 for sample m84036_250809_035451_s4.bc2118 at 2025-09-15 20:23:37.806473...
2025-09-15 20:23:39.473 wdl.w:ptcp.w:call-paraphase-21.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for hba for sample m84036_250809_035451_s4.bc2118 at 2025-09-15 20:23:37.806187...
2025-09-15 20:23:39.473 wdl.w:ptcp.w:call-paraphase-21.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for gba for sample m84036_250809_035451_s4.bc2118 at 2025-09-15 20:23:37.806176...
2025-09-15 20:23:39.474 wdl.w:ptcp.w:call-paraphase-21.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for hba for sample m84036_250809_035451_s4.bc2118 at 2025-09-15 20:23:37.806564...
2025-09-15 20:23:39.474 wdl.w:ptcp.w:call-paraphase-21.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for gba for sample m84036_250809_035451_s4.bc2118 at 2025-09-15 20:23:37.806583...
2025-09-15 20:23:39.474 wdl.w:ptcp.w:call-paraphase-21.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for hba for sample m84036_250809_035451_s4.bc2118 at 2025-09-15 20:23:38.348749...
2025-09-15 20:23:39.474 wdl.w:ptcp.w:call-paraphase-21.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for cyp21 for sample m84036_250809_035451_s4.bc2118 at 2025-09-15 20:23:38.369666...
2025-09-15 20:23:39.474 wdl.w:ptcp.w:call-paraphase-21.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for smn1 for sample m84036_250809_035451_s4.bc2118 at 2025-09-15 20:23:38.402742...
2025-09-15 20:23:39.474 wdl.w:ptcp.w:call-paraphase-21.t:call-run_paraphase.stderr VERBOSE WARNING:root:This region does not appear to have coverage. Will not attempt to phase haplotypes.
2025-09-15 20:23:39.474 wdl.w:ptcp.w:call-paraphase-21.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for hba for sample m84036_250809_035451_s4.bc2118 at 2025-09-15 20:23:38.456307...
2025-09-15 20:23:39.474 wdl.w:ptcp.w:call-paraphase-21.t:call-run_paraphase.stderr VERBOSE WARNING:root:This region does not appear to have coverage. Will not attempt to phase haplotypes.
2025-09-15 20:23:39.474 wdl.w:ptcp.w:call-paraphase-21.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for cyp21 for sample m84036_250809_035451_s4.bc2118 at 2025-09-15 20:23:38.470414...
2025-09-15 20:23:39.474 wdl.w:ptcp.w:call-paraphase-21.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for gba for sample m84036_250809_035451_s4.bc2118 at 2025-09-15 20:23:38.484076...
2025-09-15 20:23:39.474 wdl.w:ptcp.w:call-paraphase-21.t:call-run_paraphase.stderr VERBOSE WARNING:root:This region does not appear to have coverage. Will not attempt to phase haplotypes.
2025-09-15 20:23:39.474 wdl.w:ptcp.w:call-paraphase-21.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for smn1 for sample m84036_250809_035451_s4.bc2118 at 2025-09-15 20:23:38.548549...
2025-09-15 20:23:39.474 wdl.w:ptcp.w:call-paraphase-21.t:call-run_paraphase.stderr VERBOSE WARNING:root:This region does not appear to have coverage. Will not attempt to phase haplotypes.
2025-09-15 20:23:39.474 wdl.w:ptcp.w:call-paraphase-21.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for gba for sample m84036_250809_035451_s4.bc2118 at 2025-09-15 20:23:38.591401...
2025-09-15 20:23:39.474 wdl.w:ptcp.w:call-paraphase-21.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for hba for sample m84036_250809_035451_s4.bc2118 at 2025-09-15 20:23:38.912509...
2025-09-15 20:23:39.474 wdl.w:ptcp.w:call-paraphase-21.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for hbb for sample m84036_250809_035451_s4.bc2118 at 2025-09-15 20:23:38.922065...
2025-09-15 20:23:39.474 wdl.w:ptcp.w:call-paraphase-21.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for hbb for sample m84036_250809_035451_s4.bc2118 at 2025-09-15 20:23:38.922180...
2025-09-15 20:23:39.474 wdl.w:ptcp.w:call-paraphase-21.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for cyp21 for sample m84036_250809_035451_s4.bc2118 at 2025-09-15 20:23:38.970357...
2025-09-15 20:23:39.474 wdl.w:ptcp.w:call-paraphase-21.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for f8inv22 for sample m84036_250809_035451_s4.bc2118 at 2025-09-15 20:23:38.976173...
2025-09-15 20:23:39.474 wdl.w:ptcp.w:call-paraphase-21.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for f8inv22 for sample m84036_250809_035451_s4.bc2118 at 2025-09-15 20:23:38.976335...
2025-09-15 20:23:39.475 wdl.w:ptcp.w:call-paraphase-21.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning to gene2 region for smn1 for sample m84036_250809_035451_s4.bc2118 at 2025-09-15 20:23:39.008340...
2025-09-15 20:23:39.475 wdl.w:ptcp.w:call-paraphase-21.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for gba for sample m84036_250809_035451_s4.bc2118 at 2025-09-15 20:23:39.031515...
2025-09-15 20:23:39.475 wdl.w:ptcp.w:call-paraphase-21.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for rpgr for sample m84036_250809_035451_s4.bc2118 at 2025-09-15 20:23:39.068622...
2025-09-15 20:23:39.475 wdl.w:ptcp.w:call-paraphase-21.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for rpgr for sample m84036_250809_035451_s4.bc2118 at 2025-09-15 20:23:39.068802...
2025-09-15 20:23:39.490 wdl.w:ptcp.w:call-sawfish-02.t:call-run_sawfish INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:23:39.490 wdl.w:ptcp.w:call-sawfish-02.t:call-run_sawfish INFO input :: name: "genome_version", value: "38"
2025-09-15 20:23:39.490 wdl.w:ptcp.w:call-sawfish-02.t:call-run_sawfish INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:23:39.490 wdl.w:ptcp.w:call-sawfish-02.t:call-run_sawfish INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:23:39.490 wdl.w:ptcp.w:call-sawfish-02.t:call-run_sawfish INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2099.mapped.bam.bai"
2025-09-15 20:23:39.490 wdl.w:ptcp.w:call-sawfish-02.t:call-run_sawfish INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2099.mapped.bam"
2025-09-15 20:23:39.490 wdl.w:ptcp.w:call-sawfish-02.t:call-run_sawfish INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2099"
2025-09-15 20:23:39.491 wdl.w:ptcp.w:call-sawfish-02.t:call-run_sawfish INFO eval :: name: "mem_gb", value: 32
2025-09-15 20:23:39.491 wdl.w:ptcp.w:call-sawfish-02.t:call-run_sawfish INFO eval :: name: "threads", value: 16
2025-09-15 20:23:39.491 wdl.w:ptcp.w:call-sawfish-02.t:call-run_sawfish INFO eval :: name: "disk_size", value: 30
2025-09-15 20:23:39.491 wdl.w:ptcp.w:call-sawfish-02.t:call-run_sawfish INFO eval :: name: "discover_dirname", value: "m84036_250809_035451_s4.bc2099_sawfish_discover"
2025-09-15 20:23:39.491 wdl.w:ptcp.w:call-sawfish-02.t:call-run_sawfish INFO eval :: name: "call_dirname", value: "m84036_250809_035451_s4.bc2099_sawfish"
2025-09-15 20:23:39.491 wdl.w:ptcp.w:call-sawfish-02.t:call-run_sawfish INFO eval :: name: "minimap2_bam_filename", value: "m84036_250809_035451_s4.bc2099.minimap2.bam"
2025-09-15 20:23:39.492 wdl.w:ptcp.w:call-sawfish-02.t:call-run_sawfish INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 16, memory_reservation: 32000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:23:39.492 wdl.w:ptcp.w:call-sawfish-02.t:call-run_sawfish WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:23:39.493 wdl.w:ptcp.w:call-sawfish-02.t:call-run_sawfish INFO provisioned :: seconds_waited: 0, cpu: 16, mem_bytes: 32000000000
2025-09-15 20:23:39.493 wdl.w:ptcp.w:call-sawfish-02.t:call-run_sawfish INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:23:39.539 wdl.w:ptcp.w:call-paraphase-02.t:call-run_paraphase INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-02/call-run_paraphase/_singularity_tmpdir_gnd5jgyo"
2025-09-15 20:23:39.539 wdl.w:ptcp.w:call-paraphase-02.t:call-run_paraphase INFO Slurm invocation: srun --job-name call-run_paraphase --partition compute,compute9 --cpus-per-task 4 --mem 7629M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-02/call-run_paraphase/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-02/call-run_paraphase/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-02/call-run_paraphase/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-02/call-run_paraphase/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-02/out/m84036_250809_035451_s4.bc2099.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2099.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-02/out/m84036_250809_035451_s4.bc2099.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2099.mapped.bam:ro --bind /ptcp/meta/variant_list/variant_list.GRCh38.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf:ro --bind /ptcp/meta/paraphase/paraphase_config.GRCh38.yaml:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/paraphase_config.GRCh38.yaml:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-02/call-run_paraphase/_singularity_tmpdir_gnd5jgyo/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-02/call-run_paraphase/_singularity_tmpdir_gnd5jgyo/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:23:39.563 wdl.w:ptcp.w:call-paraphase-28.t:call-run_paraphase NOTICE done
2025-09-15 20:23:39.563 wdl.w:ptcp.w:call-paraphase-32.t:call-run_paraphase.slurm_singularity INFO srun: job 51797439 queued and waiting for resources
2025-09-15 20:23:39.563 wdl.w:ptcp.w:call-paraphase-32.t:call-run_paraphase.slurm_singularity INFO srun: job 51797439 has been allocated resources
2025-09-15 20:23:39.563 wdl.w:ptcp.w:call-paraphase-32.t:call-run_paraphase.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:39.570 wdl.w:ptcp.w:call-paraphase-28 NOTICE finish :: job: "call-run_paraphase"
2025-09-15 20:23:39.570 wdl.w:ptcp.w:call-paraphase-28 INFO output :: job: "call-run_paraphase", values: {"havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-28/call-run_paraphase/out/m84036_250809_035451_s4.bc2125.havanno.json", "paraphase_vcfs": [], "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-28/call-run_paraphase/out/m84036_250809_035451_s4.bc2125_paraphase/m84036_250809_035451_s4.bc2125.paraphase.json", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-28/call-run_paraphase/out/m84036_250809_035451_s4.bc2125_paraphase/m84036_250809_035451_s4.bc2125.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-28/call-run_paraphase/out/m84036_250809_035451_s4.bc2125_paraphase/m84036_250809_035451_s4.bc2125.paraphase.bam"}
2025-09-15 20:23:39.571 wdl.w:ptcp.w:call-paraphase-28 NOTICE ready :: job: "call-call_f8", callee: "call_f8"
2025-09-15 20:23:39.571 wdl.w:ptcp.w:call-paraphase-28 INFO input :: job: "call-call_f8", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "out_prefix": "m84036_250809_035451_s4.bc2125", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-28/call-run_paraphase/out/m84036_250809_035451_s4.bc2125_paraphase/m84036_250809_035451_s4.bc2125.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-28/call-run_paraphase/out/m84036_250809_035451_s4.bc2125_paraphase/m84036_250809_035451_s4.bc2125.paraphase.bam", "sex": "F"}
2025-09-15 20:23:39.571 wdl.w:ptcp.w:call-paraphase-28 INFO visit :: node: "output-havanno_json", values: {"havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-28/call-run_paraphase/out/m84036_250809_035451_s4.bc2125.havanno.json"}
2025-09-15 20:23:39.571 wdl.w:ptcp.w:call-paraphase-28 INFO visit :: node: "output-paraphase_bam", values: {"paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-28/call-run_paraphase/out/m84036_250809_035451_s4.bc2125_paraphase/m84036_250809_035451_s4.bc2125.paraphase.bam"}
2025-09-15 20:23:39.572 wdl.w:ptcp.w:call-paraphase-28 INFO visit :: node: "output-paraphase_bam_bai", values: {"paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-28/call-run_paraphase/out/m84036_250809_035451_s4.bc2125_paraphase/m84036_250809_035451_s4.bc2125.paraphase.bam.bai"}
2025-09-15 20:23:39.572 wdl.w:ptcp.w:call-paraphase-28 INFO visit :: node: "output-paraphase_json", values: {"paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-28/call-run_paraphase/out/m84036_250809_035451_s4.bc2125_paraphase/m84036_250809_035451_s4.bc2125.paraphase.json"}
2025-09-15 20:23:39.572 wdl.w:ptcp.w:call-paraphase-28 INFO visit :: node: "output-paraphase_vcfs", values: {"paraphase_vcfs": []}
2025-09-15 20:23:39.576 wdl.w:ptcp.w:call-paraphase-02.t:call-run_paraphase NOTICE slurm_singularity run :: pid: 1199905, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-02/call-run_paraphase/slurm_singularity.log.txt"
2025-09-15 20:23:39.577 wdl.w:ptcp.w:call-trgt-02.t:call-get_reads_overlapping_repeats NOTICE task setup :: name: "get_reads_overlapping_repeats", source: "./trgt.wdl", line: 182, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-02/call-get_reads_overlapping_repeats", thread: 140611424335424
2025-09-15 20:23:39.582 wdl.w:ptcp.w:call-paraphase-31.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for f8inv1 for sample m84036_250809_035451_s4.bc2128 at 2025-09-15 20:23:26.498624...
2025-09-15 20:23:39.582 wdl.w:ptcp.w:call-paraphase-31.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for f8inv1 for sample m84036_250809_035451_s4.bc2128 at 2025-09-15 20:23:30.751577...
2025-09-15 20:23:39.582 wdl.w:ptcp.w:call-paraphase-31.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for f8inv1 for sample m84036_250809_035451_s4.bc2128 at 2025-09-15 20:23:31.113347...
2025-09-15 20:23:39.599 wdl.w:ptcp.w:call-sawfish-02.t:call-run_sawfish INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 10, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-02/call-run_sawfish/_singularity_tmpdir__afowfwk"
2025-09-15 20:23:39.599 wdl.w:ptcp.w:call-sawfish-02.t:call-run_sawfish INFO Slurm invocation: srun --job-name call-run_sawfish --partition compute,compute9 --cpus-per-task 16 --mem 30518M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-02/call-run_sawfish/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-02/call-run_sawfish/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-02/call-run_sawfish/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-02/call-run_sawfish/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-02/out/m84036_250809_035451_s4.bc2099.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2099.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-02/out/m84036_250809_035451_s4.bc2099.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2099.mapped.bam:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-02/call-run_sawfish/_singularity_tmpdir__afowfwk/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-02/call-run_sawfish/_singularity_tmpdir__afowfwk/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:23:39.603 wdl.w:ptcp.w:call-trgt-02.t:call-get_reads_overlapping_repeats INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:23:39.603 wdl.w:ptcp.w:call-trgt-02.t:call-get_reads_overlapping_repeats INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:23:39.603 wdl.w:ptcp.w:call-trgt-02.t:call-get_reads_overlapping_repeats INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2099.mapped.bam.bai"
2025-09-15 20:23:39.603 wdl.w:ptcp.w:call-trgt-02.t:call-get_reads_overlapping_repeats INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2099.mapped.bam"
2025-09-15 20:23:39.603 wdl.w:ptcp.w:call-trgt-02.t:call-get_reads_overlapping_repeats INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2099"
2025-09-15 20:23:39.604 wdl.w:ptcp.w:call-trgt-02.t:call-get_reads_overlapping_repeats INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:23:39.604 wdl.w:ptcp.w:call-trgt-02.t:call-get_reads_overlapping_repeats INFO eval :: name: "expand_size", value: 3000
2025-09-15 20:23:39.604 wdl.w:ptcp.w:call-trgt-02.t:call-get_reads_overlapping_repeats INFO eval :: name: "threads", value: 1
2025-09-15 20:23:39.604 wdl.w:ptcp.w:call-trgt-02.t:call-get_reads_overlapping_repeats INFO eval :: name: "expanded_bed_name", value: "m84036_250809_035451_s4.bc2099.expanded.bed"
2025-09-15 20:23:39.604 wdl.w:ptcp.w:call-trgt-02.t:call-get_reads_overlapping_repeats INFO eval :: name: "disk_size", value: 11
2025-09-15 20:23:39.606 wdl.w:ptcp.w:call-trgt-02.t:call-get_reads_overlapping_repeats INFO eval :: name: "output_name", value: "m84036_250809_035451_s4.bc2099.repeats.bam"
2025-09-15 20:23:39.606 wdl.w:ptcp.w:call-trgt-02.t:call-get_reads_overlapping_repeats INFO eval :: name: "index_name", value: "m84036_250809_035451_s4.bc2099.repeats.bam.bai"
2025-09-15 20:23:39.606 wdl.w:ptcp.w:call-trgt-02.t:call-get_reads_overlapping_repeats INFO eval :: name: "output_name_with_index", value: "m84036_250809_035451_s4.bc2099.repeats.bam##idx##m84036_250809_035451_s4.bc2099.repeats.bam.bai"
2025-09-15 20:23:39.607 wdl.w:ptcp.w:call-trgt-02.t:call-get_reads_overlapping_repeats INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:23:39.607 wdl.w:ptcp.w:call-trgt-02.t:call-get_reads_overlapping_repeats WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:23:39.607 wdl.w:ptcp.w:call-trgt-02.t:call-get_reads_overlapping_repeats INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:23:39.607 wdl.w:ptcp.w:call-trgt-02.t:call-get_reads_overlapping_repeats INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:23:39.628 wdl.w:ptcp.w:call-sawfish-02.t:call-run_sawfish NOTICE slurm_singularity run :: pid: 1199907, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-02/call-run_sawfish/slurm_singularity.log.txt"
2025-09-15 20:23:39.676 wdl.w:ptcp.w:call-trgt-02.t:call-get_reads_overlapping_repeats INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 9, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-02/call-get_reads_overlapping_repeats/_singularity_tmpdir_o24ukj2o"
2025-09-15 20:23:39.676 wdl.w:ptcp.w:call-trgt-02.t:call-get_reads_overlapping_repeats INFO Slurm invocation: srun --job-name call-get_reads_overlapping_repeats --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-02/call-get_reads_overlapping_repeats/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-02/call-get_reads_overlapping_repeats/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-02/call-get_reads_overlapping_repeats/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-02/call-get_reads_overlapping_repeats/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-02/out/m84036_250809_035451_s4.bc2099.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2099.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-02/out/m84036_250809_035451_s4.bc2099.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2099.mapped.bam:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-02/call-get_reads_overlapping_repeats/_singularity_tmpdir_o24ukj2o/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-02/call-get_reads_overlapping_repeats/_singularity_tmpdir_o24ukj2o/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:23:39.692 wdl.w:ptcp.w:call-trgt-02.t:call-get_reads_overlapping_repeats NOTICE slurm_singularity run :: pid: 1199909, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-02/call-get_reads_overlapping_repeats/slurm_singularity.log.txt"
2025-09-15 20:23:39.781 wdl.w:ptcp.w:call-sawfish-32.t:call-run_sawfish.slurm_singularity INFO srun: job 51797440 queued and waiting for resources
2025-09-15 20:23:39.781 wdl.w:ptcp.w:call-sawfish-32.t:call-run_sawfish.slurm_singularity INFO srun: job 51797440 has been allocated resources
2025-09-15 20:23:39.781 wdl.w:ptcp.w:call-sawfish-32.t:call-run_sawfish.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:39.781 wdl.w:ptcp.w:call-sawfish-32.t:call-run_sawfish.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:23:39.899 wdl.w:ptcp.w:call-trgt-24.t:call-trgt_genotype INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2121.trgt.vcf"
2025-09-15 20:23:39.902 wdl.w:ptcp.w:call-trgt-24.t:call-trgt_genotype INFO output :: name: "spanning_bam", value: "m84036_250809_035451_s4.bc2121.trgt.sorted.spanning.bam"
2025-09-15 20:23:39.904 wdl.w:ptcp.w:call-trgt-24.t:call-trgt_genotype INFO output :: name: "spanning_bam_bai", value: "m84036_250809_035451_s4.bc2121.trgt.sorted.spanning.bam.bai"
2025-09-15 20:23:39.984 wdl.w:ptcp.w:call-sawfish-24.t:call-run_sawfish.stderr VERBOSE [M::bam2fq_mainloop] discarded 0 singletons
2025-09-15 20:23:39.984 wdl.w:ptcp.w:call-sawfish-24.t:call-run_sawfish.stderr VERBOSE [M::bam2fq_mainloop] processed 1 reads
2025-09-15 20:23:40.038 wdl.w:ptcp.w:call-trgt-24.t:call-trgt_genotype NOTICE done
2025-09-15 20:23:40.044 wdl.w:ptcp.w:call-trgt-24 NOTICE finish :: job: "call-trgt_genotype"
2025-09-15 20:23:40.045 wdl.w:ptcp.w:call-trgt-24 INFO output :: job: "call-trgt_genotype", values: {"spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-24/call-trgt_genotype/out/m84036_250809_035451_s4.bc2121.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-24/call-trgt_genotype/out/m84036_250809_035451_s4.bc2121.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-24/call-trgt_genotype/out/m84036_250809_035451_s4.bc2121.trgt.vcf"}
2025-09-15 20:23:40.045 wdl.w:ptcp.w:call-trgt-24 NOTICE ready :: job: "call-trgt_plot_meth_allele", callee: "trgt_plot"
2025-09-15 20:23:40.045 wdl.w:ptcp.w:call-trgt-24 INFO input :: job: "call-trgt_plot_meth_allele", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": false, "methylation": true, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-24/call-trgt_genotype/out/m84036_250809_035451_s4.bc2121.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-24/call-trgt_genotype/out/m84036_250809_035451_s4.bc2121.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-24/call-trgt_genotype/out/m84036_250809_035451_s4.bc2121.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2121"}
2025-09-15 20:23:40.047 wdl.w:ptcp.w:call-trgt-24 NOTICE ready :: job: "call-trgt_plot_meth_waterfall", callee: "trgt_plot"
2025-09-15 20:23:40.047 wdl.w:ptcp.w:call-trgt-24 INFO input :: job: "call-trgt_plot_meth_waterfall", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": true, "methylation": true, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-24/call-trgt_genotype/out/m84036_250809_035451_s4.bc2121.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-24/call-trgt_genotype/out/m84036_250809_035451_s4.bc2121.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-24/call-trgt_genotype/out/m84036_250809_035451_s4.bc2121.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2121"}
2025-09-15 20:23:40.049 wdl.w:ptcp.w:call-trgt-24 NOTICE ready :: job: "call-trgt_plot_motifs_allele", callee: "trgt_plot"
2025-09-15 20:23:40.049 wdl.w:ptcp.w:call-trgt-24 INFO input :: job: "call-trgt_plot_motifs_allele", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": false, "methylation": false, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-24/call-trgt_genotype/out/m84036_250809_035451_s4.bc2121.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-24/call-trgt_genotype/out/m84036_250809_035451_s4.bc2121.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-24/call-trgt_genotype/out/m84036_250809_035451_s4.bc2121.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2121"}
2025-09-15 20:23:40.050 wdl.w:ptcp.w:call-trgt-24 NOTICE ready :: job: "call-trgt_plot_motifs_waterfall", callee: "trgt_plot"
2025-09-15 20:23:40.050 wdl.w:ptcp.w:call-trgt-24 INFO input :: job: "call-trgt_plot_motifs_waterfall", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": true, "methylation": false, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-24/call-trgt_genotype/out/m84036_250809_035451_s4.bc2121.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-24/call-trgt_genotype/out/m84036_250809_035451_s4.bc2121.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-24/call-trgt_genotype/out/m84036_250809_035451_s4.bc2121.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2121"}
2025-09-15 20:23:40.050 wdl.w:ptcp.w:call-trgt-24 INFO visit :: node: "output-spanning_bam", values: {"spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-24/call-trgt_genotype/out/m84036_250809_035451_s4.bc2121.trgt.sorted.spanning.bam"}
2025-09-15 20:23:40.050 wdl.w:ptcp.w:call-trgt-24 INFO visit :: node: "output-spanning_bam_bai", values: {"spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-24/call-trgt_genotype/out/m84036_250809_035451_s4.bc2121.trgt.sorted.spanning.bam.bai"}
2025-09-15 20:23:40.050 wdl.w:ptcp.w:call-trgt-24 INFO visit :: node: "output-vcf", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-24/call-trgt_genotype/out/m84036_250809_035451_s4.bc2121.trgt.vcf"}
2025-09-15 20:23:40.054 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_genotype NOTICE task setup :: name: "trgt_genotype", source: "./trgt.wdl", line: 272, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-02/call-trgt_genotype", thread: 140610887464512
2025-09-15 20:23:40.074 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_genotype INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:23:40.074 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_genotype INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:23:40.074 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_genotype INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:23:40.075 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_genotype INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:23:40.075 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_genotype INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2099.mapped.bam.bai"
2025-09-15 20:23:40.075 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_genotype INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2099.mapped.bam"
2025-09-15 20:23:40.075 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_genotype INFO input :: name: "sex", value: "F"
2025-09-15 20:23:40.075 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_genotype INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2099"
2025-09-15 20:23:40.075 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_genotype INFO eval :: name: "mem_gb", value: 16
2025-09-15 20:23:40.075 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_genotype INFO eval :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2099.trgt"
2025-09-15 20:23:40.075 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_genotype INFO eval :: name: "threads", value: 8
2025-09-15 20:23:40.075 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_genotype INFO eval :: name: "disk_size", value: 27
2025-09-15 20:23:40.076 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_genotype INFO eval :: name: "karyotype", value: "XX"
2025-09-15 20:23:40.076 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_genotype INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 8, memory_reservation: 16000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:23:40.076 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_genotype WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:23:40.077 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_genotype INFO provisioned :: seconds_waited: 0, cpu: 8, mem_bytes: 16000000000
2025-09-15 20:23:40.077 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_genotype INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:23:40.101 wdl.w:ptcp.w:call-paraphase-35.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for smn1 for sample m84036_250809_035451_s4.bc2132 at 2025-09-15 20:23:39.576829...
2025-09-15 20:23:40.147 wdl.w:ptcp.w:call-trgt-32.t:call-get_reads_overlapping_repeats.slurm_singularity INFO srun: job 51797441 queued and waiting for resources
2025-09-15 20:23:40.148 wdl.w:ptcp.w:call-trgt-32.t:call-get_reads_overlapping_repeats.slurm_singularity INFO srun: job 51797441 has been allocated resources
2025-09-15 20:23:40.148 wdl.w:ptcp.w:call-trgt-32.t:call-get_reads_overlapping_repeats.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:40.155 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_genotype INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 11, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-02/call-trgt_genotype/_singularity_tmpdir_vg07z2a7"
2025-09-15 20:23:40.155 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_genotype INFO Slurm invocation: srun --job-name call-trgt_genotype --partition compute,compute9 --cpus-per-task 8 --mem 15259M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-02/call-trgt_genotype/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-02/call-trgt_genotype/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-02/call-trgt_genotype/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-02/call-trgt_genotype/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-02/out/m84036_250809_035451_s4.bc2099.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2099.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-02/out/m84036_250809_035451_s4.bc2099.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2099.mapped.bam:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-02/call-trgt_genotype/_singularity_tmpdir_vg07z2a7/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-02/call-trgt_genotype/_singularity_tmpdir_vg07z2a7/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:23:40.206 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_genotype NOTICE slurm_singularity run :: pid: 1199932, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-02/call-trgt_genotype/slurm_singularity.log.txt"
2025-09-15 20:23:40.452 wdl.w:ptcp.w:call-trgt-32.t:call-trgt_genotype.slurm_singularity INFO srun: job 51797442 queued and waiting for resources
2025-09-15 20:23:40.453 wdl.w:ptcp.w:call-trgt-32.t:call-trgt_genotype.slurm_singularity INFO srun: job 51797442 has been allocated resources
2025-09-15 20:23:40.453 wdl.w:ptcp.w:call-trgt-32.t:call-trgt_genotype.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:40.585 wdl.w:ptcp.w:call-paraphase-02.t:call-run_paraphase.slurm_singularity INFO srun: job 51797443 queued and waiting for resources
2025-09-15 20:23:40.585 wdl.w:ptcp.w:call-paraphase-02.t:call-run_paraphase.slurm_singularity INFO srun: job 51797443 has been allocated resources
2025-09-15 20:23:40.585 wdl.w:ptcp.w:call-paraphase-02.t:call-run_paraphase.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:40.637 wdl.w:ptcp.w:call-sawfish-02.t:call-run_sawfish.slurm_singularity INFO srun: job 51797444 queued and waiting for resources
2025-09-15 20:23:40.637 wdl.w:ptcp.w:call-sawfish-02.t:call-run_sawfish.slurm_singularity INFO srun: job 51797444 has been allocated resources
2025-09-15 20:23:40.637 wdl.w:ptcp.w:call-sawfish-02.t:call-run_sawfish.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:40.637 wdl.w:ptcp.w:call-sawfish-02.t:call-run_sawfish.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:23:40.701 wdl.w:ptcp.w:call-trgt-02.t:call-get_reads_overlapping_repeats.slurm_singularity INFO srun: job 51797445 queued and waiting for resources
2025-09-15 20:23:40.701 wdl.w:ptcp.w:call-trgt-02.t:call-get_reads_overlapping_repeats.slurm_singularity INFO srun: job 51797445 has been allocated resources
2025-09-15 20:23:40.701 wdl.w:ptcp.w:call-trgt-02.t:call-get_reads_overlapping_repeats.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:40.701 wdl.w:ptcp.w:call-trgt-02.t:call-get_reads_overlapping_repeats.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:23:40.857 wdl.w:ptcp.w:call-trgt-24.t:call-get_reads_overlapping_repeats INFO output :: name: "reads_overlapping_repeats", value: "m84036_250809_035451_s4.bc2121.repeats.bam"
2025-09-15 20:23:40.862 wdl.w:ptcp.w:call-trgt-24.t:call-get_reads_overlapping_repeats INFO output :: name: "reads_overlapping_repeats_bai", value: "m84036_250809_035451_s4.bc2121.repeats.bam.bai"
2025-09-15 20:23:40.866 wdl.w:ptcp.w:call-trgt-09.t:call-trgt_genotype INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2106.trgt.vcf"
2025-09-15 20:23:40.872 wdl.w:ptcp.w:call-trgt-09.t:call-trgt_genotype INFO output :: name: "spanning_bam", value: "m84036_250809_035451_s4.bc2106.trgt.sorted.spanning.bam"
2025-09-15 20:23:40.875 wdl.w:ptcp.w:call-trgt-09.t:call-trgt_genotype INFO output :: name: "spanning_bam_bai", value: "m84036_250809_035451_s4.bc2106.trgt.sorted.spanning.bam.bai"
2025-09-15 20:23:40.935 wdl.w:ptcp.w:call-sawfish-33.t:call-run_sawfish.stderr VERBOSE [M::bam2fq_mainloop] discarded 0 singletons
2025-09-15 20:23:40.936 wdl.w:ptcp.w:call-sawfish-33.t:call-run_sawfish.stderr VERBOSE [M::bam2fq_mainloop] processed 2 reads
2025-09-15 20:23:40.946 wdl.w:ptcp.w:call-trgt-24.t:call-get_reads_overlapping_repeats NOTICE done
2025-09-15 20:23:40.947 wdl.w:ptcp.w:call-trgt-02.t:call-get_reads_overlapping_repeats INFO output :: name: "reads_overlapping_repeats", value: "m84036_250809_035451_s4.bc2099.repeats.bam"
2025-09-15 20:23:40.951 wdl.w:ptcp.w:call-trgt-02.t:call-get_reads_overlapping_repeats INFO output :: name: "reads_overlapping_repeats_bai", value: "m84036_250809_035451_s4.bc2099.repeats.bam.bai"
2025-09-15 20:23:40.952 wdl.w:ptcp.w:call-trgt-24 NOTICE finish :: job: "call-get_reads_overlapping_repeats"
2025-09-15 20:23:40.953 wdl.w:ptcp.w:call-trgt-24 INFO output :: job: "call-get_reads_overlapping_repeats", values: {"reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-24/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2121.repeats.bam.bai", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-24/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2121.repeats.bam"}
2025-09-15 20:23:40.953 wdl.w:ptcp.w:call-trgt-24 INFO visit :: node: "output-reads_overlapping_repeats", values: {"reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-24/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2121.repeats.bam"}
2025-09-15 20:23:40.953 wdl.w:ptcp.w:call-trgt-24 INFO visit :: node: "output-reads_overlapping_repeats_bai", values: {"reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-24/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2121.repeats.bam.bai"}
2025-09-15 20:23:40.962 wdl.w:ptcp.w:call-sawfish-03.t:call-run_sawfish NOTICE task setup :: name: "run_sawfish", source: "./sawfish.wdl", line: 83, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-03/call-run_sawfish", thread: 140609285244480
2025-09-15 20:23:40.975 wdl.w:ptcp.w:call-trgt-09.t:call-trgt_genotype NOTICE done
2025-09-15 20:23:40.974 wdl.w:ptcp.w:call-paraphase-13.t:call-run_paraphase INFO output :: name: "paraphase_bam", value: "m84036_250809_035451_s4.bc2110_paraphase/m84036_250809_035451_s4.bc2110.paraphase.bam"
2025-09-15 20:23:40.983 wdl.w:ptcp.w:call-paraphase-13.t:call-run_paraphase INFO output :: name: "paraphase_bam_bai", value: "m84036_250809_035451_s4.bc2110_paraphase/m84036_250809_035451_s4.bc2110.paraphase.bam.bai"
2025-09-15 20:23:40.983 wdl.w:ptcp.w:call-trgt-09 NOTICE finish :: job: "call-trgt_genotype"
2025-09-15 20:23:40.983 wdl.w:ptcp.w:call-trgt-09 INFO output :: job: "call-trgt_genotype", values: {"spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-09/call-trgt_genotype/out/m84036_250809_035451_s4.bc2106.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-09/call-trgt_genotype/out/m84036_250809_035451_s4.bc2106.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-09/call-trgt_genotype/out/m84036_250809_035451_s4.bc2106.trgt.vcf"}
2025-09-15 20:23:40.984 wdl.w:ptcp.w:call-trgt-09 NOTICE ready :: job: "call-trgt_plot_meth_allele", callee: "trgt_plot"
2025-09-15 20:23:40.985 wdl.w:ptcp.w:call-trgt-09 INFO input :: job: "call-trgt_plot_meth_allele", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": false, "methylation": true, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-09/call-trgt_genotype/out/m84036_250809_035451_s4.bc2106.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-09/call-trgt_genotype/out/m84036_250809_035451_s4.bc2106.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-09/call-trgt_genotype/out/m84036_250809_035451_s4.bc2106.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2106"}
2025-09-15 20:23:40.985 wdl.w:ptcp.w:call-paraphase-13.t:call-run_paraphase INFO output :: name: "paraphase_json", value: "m84036_250809_035451_s4.bc2110_paraphase/m84036_250809_035451_s4.bc2110.paraphase.json"
2025-09-15 20:23:40.987 wdl.w:ptcp.w:call-trgt-09 NOTICE ready :: job: "call-trgt_plot_meth_waterfall", callee: "trgt_plot"
2025-09-15 20:23:40.987 wdl.w:ptcp.w:call-trgt-09 INFO input :: job: "call-trgt_plot_meth_waterfall", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": true, "methylation": true, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-09/call-trgt_genotype/out/m84036_250809_035451_s4.bc2106.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-09/call-trgt_genotype/out/m84036_250809_035451_s4.bc2106.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-09/call-trgt_genotype/out/m84036_250809_035451_s4.bc2106.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2106"}
2025-09-15 20:23:40.988 wdl.w:ptcp.w:call-paraphase-13.t:call-run_paraphase INFO output :: name: "paraphase_vcfs", value: []
2025-09-15 20:23:40.989 wdl.w:ptcp.w:call-trgt-09 NOTICE ready :: job: "call-trgt_plot_motifs_allele", callee: "trgt_plot"
2025-09-15 20:23:40.989 wdl.w:ptcp.w:call-paraphase-13.t:call-run_paraphase INFO output :: name: "havanno_json", value: "m84036_250809_035451_s4.bc2110.havanno.json"
2025-09-15 20:23:40.989 wdl.w:ptcp.w:call-trgt-09 INFO input :: job: "call-trgt_plot_motifs_allele", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": false, "methylation": false, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-09/call-trgt_genotype/out/m84036_250809_035451_s4.bc2106.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-09/call-trgt_genotype/out/m84036_250809_035451_s4.bc2106.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-09/call-trgt_genotype/out/m84036_250809_035451_s4.bc2106.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2106"}
2025-09-15 20:23:40.990 wdl.w:ptcp.w:call-trgt-09 NOTICE ready :: job: "call-trgt_plot_motifs_waterfall", callee: "trgt_plot"
2025-09-15 20:23:40.990 wdl.w:ptcp.w:call-trgt-09 INFO input :: job: "call-trgt_plot_motifs_waterfall", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": true, "methylation": false, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-09/call-trgt_genotype/out/m84036_250809_035451_s4.bc2106.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-09/call-trgt_genotype/out/m84036_250809_035451_s4.bc2106.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-09/call-trgt_genotype/out/m84036_250809_035451_s4.bc2106.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2106"}
2025-09-15 20:23:40.991 wdl.w:ptcp.w:call-trgt-09 INFO visit :: node: "output-spanning_bam", values: {"spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-09/call-trgt_genotype/out/m84036_250809_035451_s4.bc2106.trgt.sorted.spanning.bam"}
2025-09-15 20:23:40.991 wdl.w:ptcp.w:call-trgt-09 INFO visit :: node: "output-spanning_bam_bai", values: {"spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-09/call-trgt_genotype/out/m84036_250809_035451_s4.bc2106.trgt.sorted.spanning.bam.bai"}
2025-09-15 20:23:40.991 wdl.w:ptcp.w:call-trgt-09 INFO visit :: node: "output-vcf", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-09/call-trgt_genotype/out/m84036_250809_035451_s4.bc2106.trgt.vcf"}
2025-09-15 20:23:40.992 wdl.w:ptcp.w:call-paraphase-03.t:call-run_paraphase NOTICE task setup :: name: "run_paraphase", source: "./paraphase.wdl", line: 127, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-03/call-run_paraphase", thread: 140613838284352
2025-09-15 20:23:40.994 wdl.w:ptcp.w:call-sawfish-03.t:call-run_sawfish INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:23:40.994 wdl.w:ptcp.w:call-sawfish-03.t:call-run_sawfish INFO input :: name: "genome_version", value: "38"
2025-09-15 20:23:40.994 wdl.w:ptcp.w:call-sawfish-03.t:call-run_sawfish INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:23:40.994 wdl.w:ptcp.w:call-sawfish-03.t:call-run_sawfish INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:23:40.995 wdl.w:ptcp.w:call-sawfish-03.t:call-run_sawfish INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2100.mapped.bam.bai"
2025-09-15 20:23:40.995 wdl.w:ptcp.w:call-sawfish-03.t:call-run_sawfish INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2100.mapped.bam"
2025-09-15 20:23:40.995 wdl.w:ptcp.w:call-sawfish-03.t:call-run_sawfish INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2100"
2025-09-15 20:23:40.995 wdl.w:ptcp.w:call-sawfish-03.t:call-run_sawfish INFO eval :: name: "mem_gb", value: 32
2025-09-15 20:23:40.995 wdl.w:ptcp.w:call-sawfish-03.t:call-run_sawfish INFO eval :: name: "threads", value: 16
2025-09-15 20:23:40.996 wdl.w:ptcp.w:call-sawfish-03.t:call-run_sawfish INFO eval :: name: "disk_size", value: 30
2025-09-15 20:23:40.996 wdl.w:ptcp.w:call-sawfish-03.t:call-run_sawfish INFO eval :: name: "discover_dirname", value: "m84036_250809_035451_s4.bc2100_sawfish_discover"
2025-09-15 20:23:40.996 wdl.w:ptcp.w:call-sawfish-03.t:call-run_sawfish INFO eval :: name: "call_dirname", value: "m84036_250809_035451_s4.bc2100_sawfish"
2025-09-15 20:23:40.996 wdl.w:ptcp.w:call-sawfish-03.t:call-run_sawfish INFO eval :: name: "minimap2_bam_filename", value: "m84036_250809_035451_s4.bc2100.minimap2.bam"
2025-09-15 20:23:40.996 wdl.w:ptcp.w:call-sawfish-03.t:call-run_sawfish INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 16, memory_reservation: 32000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:23:40.996 wdl.w:ptcp.w:call-sawfish-03.t:call-run_sawfish WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:23:40.997 wdl.w:ptcp.w:call-sawfish-03.t:call-run_sawfish INFO provisioned :: seconds_waited: 0, cpu: 16, mem_bytes: 32000000000
2025-09-15 20:23:40.997 wdl.w:ptcp.w:call-sawfish-03.t:call-run_sawfish INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:23:41.020 wdl.w:ptcp.w:call-paraphase-03.t:call-run_paraphase INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:23:41.020 wdl.w:ptcp.w:call-paraphase-03.t:call-run_paraphase INFO input :: name: "annotation_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf"
2025-09-15 20:23:41.020 wdl.w:ptcp.w:call-paraphase-03.t:call-run_paraphase INFO input :: name: "genome_version", value: "38"
2025-09-15 20:23:41.020 wdl.w:ptcp.w:call-paraphase-03.t:call-run_paraphase INFO input :: name: "config_file", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/paraphase_config.GRCh38.yaml"
2025-09-15 20:23:41.021 wdl.w:ptcp.w:call-paraphase-03.t:call-run_paraphase INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:23:41.021 wdl.w:ptcp.w:call-paraphase-03.t:call-run_paraphase INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:23:41.021 wdl.w:ptcp.w:call-paraphase-03.t:call-run_paraphase INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2100.mapped.bam.bai"
2025-09-15 20:23:41.021 wdl.w:ptcp.w:call-paraphase-03.t:call-run_paraphase INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2100.mapped.bam"
2025-09-15 20:23:41.021 wdl.w:ptcp.w:call-paraphase-03.t:call-run_paraphase INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2100"
2025-09-15 20:23:41.021 wdl.w:ptcp.w:call-paraphase-03.t:call-run_paraphase INFO eval :: name: "threads", value: 4
2025-09-15 20:23:41.021 wdl.w:ptcp.w:call-paraphase-03.t:call-run_paraphase INFO eval :: name: "mem_gb", value: 8
2025-09-15 20:23:41.022 wdl.w:ptcp.w:call-paraphase-03.t:call-run_paraphase INFO eval :: name: "disk_size", value: 27
2025-09-15 20:23:41.022 wdl.w:ptcp.w:call-paraphase-03.t:call-run_paraphase INFO eval :: name: "out_dir", value: "m84036_250809_035451_s4.bc2100_paraphase"
2025-09-15 20:23:41.023 wdl.w:ptcp.w:call-paraphase-03.t:call-run_paraphase INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 4, memory_reservation: 8000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:23:41.023 wdl.w:ptcp.w:call-paraphase-03.t:call-run_paraphase WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:23:41.023 wdl.w:ptcp.w:call-paraphase-03.t:call-run_paraphase INFO provisioned :: seconds_waited: 0, cpu: 4, mem_bytes: 8000000000
2025-09-15 20:23:41.023 wdl.w:ptcp.w:call-paraphase-03.t:call-run_paraphase INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:23:41.030 wdl.w:ptcp.w:call-trgt-16.t:call-trgt_genotype INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2113.trgt.vcf"
2025-09-15 20:23:41.035 wdl.w:ptcp.w:call-trgt-16.t:call-trgt_genotype INFO output :: name: "spanning_bam", value: "m84036_250809_035451_s4.bc2113.trgt.sorted.spanning.bam"
2025-09-15 20:23:41.037 wdl.w:ptcp.w:call-trgt-16.t:call-trgt_genotype INFO output :: name: "spanning_bam_bai", value: "m84036_250809_035451_s4.bc2113.trgt.sorted.spanning.bam.bai"
2025-09-15 20:23:41.044 wdl.w:ptcp.w:call-trgt-02.t:call-get_reads_overlapping_repeats NOTICE done
2025-09-15 20:23:41.049 wdl.w:ptcp.w:call-trgt-02 NOTICE finish :: job: "call-get_reads_overlapping_repeats"
2025-09-15 20:23:41.049 wdl.w:ptcp.w:call-trgt-02 INFO output :: job: "call-get_reads_overlapping_repeats", values: {"reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-02/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2099.repeats.bam.bai", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-02/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2099.repeats.bam"}
2025-09-15 20:23:41.049 wdl.w:ptcp.w:call-trgt-02 INFO visit :: node: "output-reads_overlapping_repeats", values: {"reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-02/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2099.repeats.bam"}
2025-09-15 20:23:41.050 wdl.w:ptcp.w:call-trgt-02 INFO visit :: node: "output-reads_overlapping_repeats_bai", values: {"reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-02/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2099.repeats.bam.bai"}
2025-09-15 20:23:41.057 wdl.w:ptcp.w:call-trgt-03.t:call-get_reads_overlapping_repeats NOTICE task setup :: name: "get_reads_overlapping_repeats", source: "./trgt.wdl", line: 182, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-03/call-get_reads_overlapping_repeats", thread: 140611424335424
2025-09-15 20:23:41.079 wdl.w:ptcp.w:call-sawfish-03.t:call-run_sawfish INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 10, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-03/call-run_sawfish/_singularity_tmpdir_8x5u6ie3"
2025-09-15 20:23:41.079 wdl.w:ptcp.w:call-sawfish-03.t:call-run_sawfish INFO Slurm invocation: srun --job-name call-run_sawfish --partition compute,compute9 --cpus-per-task 16 --mem 30518M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-03/call-run_sawfish/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-03/call-run_sawfish/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-03/call-run_sawfish/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-03/call-run_sawfish/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-03/out/m84036_250809_035451_s4.bc2100.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2100.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-03/out/m84036_250809_035451_s4.bc2100.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2100.mapped.bam.bai:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-03/call-run_sawfish/_singularity_tmpdir_8x5u6ie3/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-03/call-run_sawfish/_singularity_tmpdir_8x5u6ie3/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:23:41.084 wdl.w:ptcp.w:call-trgt-03.t:call-get_reads_overlapping_repeats INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:23:41.087 wdl.w:ptcp.w:call-trgt-03.t:call-get_reads_overlapping_repeats INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:23:41.089 wdl.w:ptcp.w:call-trgt-03.t:call-get_reads_overlapping_repeats INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2100.mapped.bam.bai"
2025-09-15 20:23:41.090 wdl.w:ptcp.w:call-trgt-03.t:call-get_reads_overlapping_repeats INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2100.mapped.bam"
2025-09-15 20:23:41.090 wdl.w:ptcp.w:call-trgt-03.t:call-get_reads_overlapping_repeats INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2100"
2025-09-15 20:23:41.091 wdl.w:ptcp.w:call-trgt-03.t:call-get_reads_overlapping_repeats INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:23:41.091 wdl.w:ptcp.w:call-trgt-03.t:call-get_reads_overlapping_repeats INFO eval :: name: "expand_size", value: 3000
2025-09-15 20:23:41.091 wdl.w:ptcp.w:call-trgt-03.t:call-get_reads_overlapping_repeats INFO eval :: name: "threads", value: 1
2025-09-15 20:23:41.091 wdl.w:ptcp.w:call-trgt-03.t:call-get_reads_overlapping_repeats INFO eval :: name: "expanded_bed_name", value: "m84036_250809_035451_s4.bc2100.expanded.bed"
2025-09-15 20:23:41.091 wdl.w:ptcp.w:call-trgt-03.t:call-get_reads_overlapping_repeats INFO eval :: name: "disk_size", value: 11
2025-09-15 20:23:41.092 wdl.w:ptcp.w:call-trgt-03.t:call-get_reads_overlapping_repeats INFO eval :: name: "output_name", value: "m84036_250809_035451_s4.bc2100.repeats.bam"
2025-09-15 20:23:41.092 wdl.w:ptcp.w:call-trgt-03.t:call-get_reads_overlapping_repeats INFO eval :: name: "index_name", value: "m84036_250809_035451_s4.bc2100.repeats.bam.bai"
2025-09-15 20:23:41.092 wdl.w:ptcp.w:call-trgt-03.t:call-get_reads_overlapping_repeats INFO eval :: name: "output_name_with_index", value: "m84036_250809_035451_s4.bc2100.repeats.bam##idx##m84036_250809_035451_s4.bc2100.repeats.bam.bai"
2025-09-15 20:23:41.092 wdl.w:ptcp.w:call-trgt-03.t:call-get_reads_overlapping_repeats INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:23:41.092 wdl.w:ptcp.w:call-trgt-03.t:call-get_reads_overlapping_repeats WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:23:41.092 wdl.w:ptcp.w:call-trgt-03.t:call-get_reads_overlapping_repeats INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:23:41.093 wdl.w:ptcp.w:call-trgt-03.t:call-get_reads_overlapping_repeats INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:23:41.120 wdl.w:ptcp.w:call-paraphase-03.t:call-run_paraphase INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-03/call-run_paraphase/_singularity_tmpdir_y_foi2w7"
2025-09-15 20:23:41.120 wdl.w:ptcp.w:call-paraphase-03.t:call-run_paraphase INFO Slurm invocation: srun --job-name call-run_paraphase --partition compute,compute9 --cpus-per-task 4 --mem 7629M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-03/call-run_paraphase/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-03/call-run_paraphase/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-03/call-run_paraphase/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-03/call-run_paraphase/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-03/out/m84036_250809_035451_s4.bc2100.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2100.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-03/out/m84036_250809_035451_s4.bc2100.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2100.mapped.bam.bai:ro --bind /ptcp/meta/variant_list/variant_list.GRCh38.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf:ro --bind /ptcp/meta/paraphase/paraphase_config.GRCh38.yaml:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/paraphase_config.GRCh38.yaml:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-03/call-run_paraphase/_singularity_tmpdir_y_foi2w7/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-03/call-run_paraphase/_singularity_tmpdir_y_foi2w7/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:23:41.131 wdl.w:ptcp.w:call-sawfish-03.t:call-run_sawfish NOTICE slurm_singularity run :: pid: 1199945, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-03/call-run_sawfish/slurm_singularity.log.txt"
2025-09-15 20:23:41.135 wdl.w:ptcp.w:call-paraphase-03.t:call-run_paraphase NOTICE slurm_singularity run :: pid: 1199946, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-03/call-run_paraphase/slurm_singularity.log.txt"
2025-09-15 20:23:41.141 wdl.w:ptcp.w:call-paraphase-13.t:call-run_paraphase NOTICE done
2025-09-15 20:23:41.143 wdl.w:ptcp.w:call-trgt-16.t:call-trgt_genotype NOTICE done
2025-09-15 20:23:41.148 wdl.w:ptcp.w:call-trgt-16 NOTICE finish :: job: "call-trgt_genotype"
2025-09-15 20:23:41.148 wdl.w:ptcp.w:call-trgt-16 INFO output :: job: "call-trgt_genotype", values: {"spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-16/call-trgt_genotype/out/m84036_250809_035451_s4.bc2113.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-16/call-trgt_genotype/out/m84036_250809_035451_s4.bc2113.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-16/call-trgt_genotype/out/m84036_250809_035451_s4.bc2113.trgt.vcf"}
2025-09-15 20:23:41.149 wdl.w:ptcp.w:call-trgt-16 NOTICE ready :: job: "call-trgt_plot_meth_allele", callee: "trgt_plot"
2025-09-15 20:23:41.149 wdl.w:ptcp.w:call-paraphase-13 NOTICE finish :: job: "call-run_paraphase"
2025-09-15 20:23:41.149 wdl.w:ptcp.w:call-trgt-16 INFO input :: job: "call-trgt_plot_meth_allele", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": false, "methylation": true, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-16/call-trgt_genotype/out/m84036_250809_035451_s4.bc2113.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-16/call-trgt_genotype/out/m84036_250809_035451_s4.bc2113.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-16/call-trgt_genotype/out/m84036_250809_035451_s4.bc2113.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2113"}
2025-09-15 20:23:41.150 wdl.w:ptcp.t:call-pbmm2_align_hifi-71 INFO output :: name: "mapped_bam", value: "m84036_250809_035451_s4.bc2168.mapped.bam"
2025-09-15 20:23:41.150 wdl.w:ptcp.w:call-paraphase-13 INFO output :: job: "call-run_paraphase", values: {"havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-13/call-run_paraphase/out/m84036_250809_035451_s4.bc2110.havanno.json", "paraphase_vcfs": [], "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-13/call-run_paraphase/out/m84036_250809_035451_s4.bc2110_paraphase/m84036_250809_035451_s4.bc2110.paraphase.json", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-13/call-run_paraphase/out/m84036_250809_035451_s4.bc2110_paraphase/m84036_250809_035451_s4.bc2110.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-13/call-run_paraphase/out/m84036_250809_035451_s4.bc2110_paraphase/m84036_250809_035451_s4.bc2110.paraphase.bam"}
2025-09-15 20:23:41.150 wdl.w:ptcp.w:call-paraphase-13 NOTICE ready :: job: "call-call_f8", callee: "call_f8"
2025-09-15 20:23:41.151 wdl.w:ptcp.w:call-paraphase-13 INFO input :: job: "call-call_f8", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "out_prefix": "m84036_250809_035451_s4.bc2110", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-13/call-run_paraphase/out/m84036_250809_035451_s4.bc2110_paraphase/m84036_250809_035451_s4.bc2110.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-13/call-run_paraphase/out/m84036_250809_035451_s4.bc2110_paraphase/m84036_250809_035451_s4.bc2110.paraphase.bam", "sex": "F"}
2025-09-15 20:23:41.151 wdl.w:ptcp.w:call-trgt-16 NOTICE ready :: job: "call-trgt_plot_meth_waterfall", callee: "trgt_plot"
2025-09-15 20:23:41.151 wdl.w:ptcp.w:call-paraphase-13 INFO visit :: node: "output-havanno_json", values: {"havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-13/call-run_paraphase/out/m84036_250809_035451_s4.bc2110.havanno.json"}
2025-09-15 20:23:41.152 wdl.w:ptcp.w:call-trgt-16 INFO input :: job: "call-trgt_plot_meth_waterfall", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": true, "methylation": true, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-16/call-trgt_genotype/out/m84036_250809_035451_s4.bc2113.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-16/call-trgt_genotype/out/m84036_250809_035451_s4.bc2113.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-16/call-trgt_genotype/out/m84036_250809_035451_s4.bc2113.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2113"}
2025-09-15 20:23:41.152 wdl.w:ptcp.w:call-paraphase-13 INFO visit :: node: "output-paraphase_bam", values: {"paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-13/call-run_paraphase/out/m84036_250809_035451_s4.bc2110_paraphase/m84036_250809_035451_s4.bc2110.paraphase.bam"}
2025-09-15 20:23:41.152 wdl.w:ptcp.w:call-paraphase-13 INFO visit :: node: "output-paraphase_bam_bai", values: {"paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-13/call-run_paraphase/out/m84036_250809_035451_s4.bc2110_paraphase/m84036_250809_035451_s4.bc2110.paraphase.bam.bai"}
2025-09-15 20:23:41.152 wdl.w:ptcp.w:call-paraphase-13 INFO visit :: node: "output-paraphase_json", values: {"paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-13/call-run_paraphase/out/m84036_250809_035451_s4.bc2110_paraphase/m84036_250809_035451_s4.bc2110.paraphase.json"}
2025-09-15 20:23:41.152 wdl.w:ptcp.w:call-paraphase-13 INFO visit :: node: "output-paraphase_vcfs", values: {"paraphase_vcfs": []}
2025-09-15 20:23:41.153 wdl.w:ptcp.w:call-trgt-16 NOTICE ready :: job: "call-trgt_plot_motifs_allele", callee: "trgt_plot"
2025-09-15 20:23:41.153 wdl.w:ptcp.w:call-trgt-16 INFO input :: job: "call-trgt_plot_motifs_allele", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": false, "methylation": false, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-16/call-trgt_genotype/out/m84036_250809_035451_s4.bc2113.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-16/call-trgt_genotype/out/m84036_250809_035451_s4.bc2113.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-16/call-trgt_genotype/out/m84036_250809_035451_s4.bc2113.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2113"}
2025-09-15 20:23:41.154 wdl.w:ptcp.w:call-trgt-16 NOTICE ready :: job: "call-trgt_plot_motifs_waterfall", callee: "trgt_plot"
2025-09-15 20:23:41.154 wdl.w:ptcp.w:call-trgt-16 INFO input :: job: "call-trgt_plot_motifs_waterfall", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": true, "methylation": false, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-16/call-trgt_genotype/out/m84036_250809_035451_s4.bc2113.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-16/call-trgt_genotype/out/m84036_250809_035451_s4.bc2113.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-16/call-trgt_genotype/out/m84036_250809_035451_s4.bc2113.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2113"}
2025-09-15 20:23:41.155 wdl.w:ptcp.w:call-trgt-16 INFO visit :: node: "output-spanning_bam", values: {"spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-16/call-trgt_genotype/out/m84036_250809_035451_s4.bc2113.trgt.sorted.spanning.bam"}
2025-09-15 20:23:41.155 wdl.w:ptcp.w:call-trgt-16 INFO visit :: node: "output-spanning_bam_bai", values: {"spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-16/call-trgt_genotype/out/m84036_250809_035451_s4.bc2113.trgt.sorted.spanning.bam.bai"}
2025-09-15 20:23:41.155 wdl.w:ptcp.w:call-trgt-16 INFO visit :: node: "output-vcf", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-16/call-trgt_genotype/out/m84036_250809_035451_s4.bc2113.trgt.vcf"}
2025-09-15 20:23:41.155 wdl.w:ptcp.t:call-pbmm2_align_hifi-71 INFO output :: name: "mapped_bam_bai", value: "m84036_250809_035451_s4.bc2168.mapped.bam.bai"
2025-09-15 20:23:41.157 wdl.w:ptcp.t:call-pbmm2_align_hifi-71 INFO output :: name: "mapped_bam_pbi", value: "m84036_250809_035451_s4.bc2168.mapped.bam.pbi"
2025-09-15 20:23:41.159 wdl.w:ptcp.t:call-pbmm2_align_hifi-71 INFO output :: name: "report", value: "mapping_stats.report.json"
2025-09-15 20:23:41.159 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_genotype NOTICE task setup :: name: "trgt_genotype", source: "./trgt.wdl", line: 272, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-03/call-trgt_genotype", thread: 140610870679104
2025-09-15 20:23:41.160 wdl.w:ptcp.w:call-paraphase-08.t:call-run_paraphase NOTICE task setup :: name: "run_paraphase", source: "./paraphase.wdl", line: 127, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-08/call-run_paraphase", thread: 140610342200896
2025-09-15 20:23:41.173 wdl.w:ptcp.w:call-trgt-03.t:call-get_reads_overlapping_repeats INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 9, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-03/call-get_reads_overlapping_repeats/_singularity_tmpdir_a7ex2hab"
2025-09-15 20:23:41.174 wdl.w:ptcp.w:call-trgt-03.t:call-get_reads_overlapping_repeats INFO Slurm invocation: srun --job-name call-get_reads_overlapping_repeats --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-03/call-get_reads_overlapping_repeats/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-03/call-get_reads_overlapping_repeats/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-03/call-get_reads_overlapping_repeats/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-03/call-get_reads_overlapping_repeats/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-03/out/m84036_250809_035451_s4.bc2100.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2100.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-03/out/m84036_250809_035451_s4.bc2100.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2100.mapped.bam.bai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-03/call-get_reads_overlapping_repeats/_singularity_tmpdir_a7ex2hab/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-03/call-get_reads_overlapping_repeats/_singularity_tmpdir_a7ex2hab/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:23:41.183 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_genotype INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:23:41.183 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_genotype INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:23:41.183 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_genotype INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:23:41.183 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_genotype INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:23:41.183 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_genotype INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2100.mapped.bam.bai"
2025-09-15 20:23:41.183 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_genotype INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2100.mapped.bam"
2025-09-15 20:23:41.183 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_genotype INFO input :: name: "sex", value: "F"
2025-09-15 20:23:41.183 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_genotype INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2100"
2025-09-15 20:23:41.184 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_genotype INFO eval :: name: "mem_gb", value: 16
2025-09-15 20:23:41.184 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_genotype INFO eval :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2100.trgt"
2025-09-15 20:23:41.184 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_genotype INFO eval :: name: "threads", value: 8
2025-09-15 20:23:41.184 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_genotype INFO eval :: name: "disk_size", value: 27
2025-09-15 20:23:41.184 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_genotype INFO eval :: name: "karyotype", value: "XX"
2025-09-15 20:23:41.185 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_genotype INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 8, memory_reservation: 16000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:23:41.185 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_genotype WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:23:41.185 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_genotype INFO provisioned :: seconds_waited: 0, cpu: 8, mem_bytes: 16000000000
2025-09-15 20:23:41.185 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_genotype INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:23:41.191 wdl.w:ptcp.w:call-paraphase-08.t:call-run_paraphase INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:23:41.191 wdl.w:ptcp.w:call-paraphase-08.t:call-run_paraphase INFO input :: name: "annotation_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf"
2025-09-15 20:23:41.191 wdl.w:ptcp.w:call-paraphase-08.t:call-run_paraphase INFO input :: name: "genome_version", value: "38"
2025-09-15 20:23:41.192 wdl.w:ptcp.w:call-paraphase-08.t:call-run_paraphase INFO input :: name: "config_file", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/paraphase_config.GRCh38.yaml"
2025-09-15 20:23:41.192 wdl.w:ptcp.w:call-paraphase-08.t:call-run_paraphase INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:23:41.192 wdl.w:ptcp.w:call-paraphase-08.t:call-run_paraphase INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:23:41.192 wdl.w:ptcp.w:call-paraphase-08.t:call-run_paraphase INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2105.mapped.bam.bai"
2025-09-15 20:23:41.192 wdl.w:ptcp.w:call-paraphase-08.t:call-run_paraphase INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2105.mapped.bam"
2025-09-15 20:23:41.192 wdl.w:ptcp.w:call-paraphase-08.t:call-run_paraphase INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2105"
2025-09-15 20:23:41.192 wdl.w:ptcp.w:call-paraphase-08.t:call-run_paraphase INFO eval :: name: "threads", value: 4
2025-09-15 20:23:41.192 wdl.w:ptcp.w:call-paraphase-08.t:call-run_paraphase INFO eval :: name: "mem_gb", value: 8
2025-09-15 20:23:41.193 wdl.w:ptcp.w:call-paraphase-08.t:call-run_paraphase INFO eval :: name: "disk_size", value: 27
2025-09-15 20:23:41.193 wdl.w:ptcp.w:call-paraphase-08.t:call-run_paraphase INFO eval :: name: "out_dir", value: "m84036_250809_035451_s4.bc2105_paraphase"
2025-09-15 20:23:41.193 wdl.w:ptcp.w:call-paraphase-08.t:call-run_paraphase INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 4, memory_reservation: 8000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:23:41.194 wdl.w:ptcp.w:call-paraphase-08.t:call-run_paraphase WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:23:41.194 wdl.w:ptcp.w:call-paraphase-08.t:call-run_paraphase INFO provisioned :: seconds_waited: 0, cpu: 4, mem_bytes: 8000000000
2025-09-15 20:23:41.194 wdl.w:ptcp.w:call-paraphase-08.t:call-run_paraphase INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:23:41.195 wdl.w:ptcp.w:call-trgt-03.t:call-get_reads_overlapping_repeats NOTICE slurm_singularity run :: pid: 1199949, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-03/call-get_reads_overlapping_repeats/slurm_singularity.log.txt"
2025-09-15 20:23:41.223 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_genotype.slurm_singularity INFO srun: job 51797446 queued and waiting for resources
2025-09-15 20:23:41.223 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_genotype.slurm_singularity INFO srun: job 51797446 has been allocated resources
2025-09-15 20:23:41.223 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_genotype.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:41.268 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_genotype INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 11, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-03/call-trgt_genotype/_singularity_tmpdir_dncef67r"
2025-09-15 20:23:41.269 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_genotype INFO Slurm invocation: srun --job-name call-trgt_genotype --partition compute,compute9 --cpus-per-task 8 --mem 15259M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-03/call-trgt_genotype/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-03/call-trgt_genotype/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-03/call-trgt_genotype/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-03/call-trgt_genotype/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-03/out/m84036_250809_035451_s4.bc2100.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2100.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-03/out/m84036_250809_035451_s4.bc2100.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2100.mapped.bam.bai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-03/call-trgt_genotype/_singularity_tmpdir_dncef67r/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-03/call-trgt_genotype/_singularity_tmpdir_dncef67r/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:23:41.273 wdl.w:ptcp.t:call-pbmm2_align_hifi-71 NOTICE done
2025-09-15 20:23:41.284 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_genotype NOTICE slurm_singularity run :: pid: 1199952, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-03/call-trgt_genotype/slurm_singularity.log.txt"
2025-09-15 20:23:41.287 wdl.w:ptcp.w:call-paraphase-08.t:call-run_paraphase INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-08/call-run_paraphase/_singularity_tmpdir_tr6ix3c2"
2025-09-15 20:23:41.287 wdl.w:ptcp.w:call-paraphase-08.t:call-run_paraphase INFO Slurm invocation: srun --job-name call-run_paraphase --partition compute,compute9 --cpus-per-task 4 --mem 7629M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-08/call-run_paraphase/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-08/call-run_paraphase/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-08/call-run_paraphase/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-08/call-run_paraphase/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-08/out/m84036_250809_035451_s4.bc2105.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2105.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-08/out/m84036_250809_035451_s4.bc2105.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2105.mapped.bam:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/variant_list/variant_list.GRCh38.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf:ro --bind /ptcp/meta/paraphase/paraphase_config.GRCh38.yaml:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/paraphase_config.GRCh38.yaml:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-08/call-run_paraphase/_singularity_tmpdir_tr6ix3c2/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-08/call-run_paraphase/_singularity_tmpdir_tr6ix3c2/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:23:41.295 wdl.w:ptcp.w:call-paraphase-08.t:call-run_paraphase NOTICE slurm_singularity run :: pid: 1199953, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-08/call-run_paraphase/slurm_singularity.log.txt"
2025-09-15 20:23:41.299 wdl.w:ptcp NOTICE finish :: job: "call-pbmm2_align_hifi-71"
2025-09-15 20:23:41.299 wdl.w:ptcp INFO output :: job: "call-pbmm2_align_hifi-71", values: {"report": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-71/out/mapping_stats.report.json", "mapped_bam_pbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-71/out/m84036_250809_035451_s4.bc2168.mapped.bam.pbi", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-71/out/m84036_250809_035451_s4.bc2168.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-71/out/m84036_250809_035451_s4.bc2168.mapped.bam"}
2025-09-15 20:23:41.301 wdl.w:ptcp NOTICE ready :: job: "call-paraphase-71", callee: "paraphase"
2025-09-15 20:23:41.301 wdl.w:ptcp INFO input :: job: "call-paraphase-71", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf", "genome_version": "38", "config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-71/out/m84036_250809_035451_s4.bc2168.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-71/out/m84036_250809_035451_s4.bc2168.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2168"}
2025-09-15 20:23:41.302 wdl.w:ptcp NOTICE ready :: job: "call-sawfish-71", callee: "sawfish"
2025-09-15 20:23:41.302 wdl.w:ptcp INFO input :: job: "call-sawfish-71", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-71/out/m84036_250809_035451_s4.bc2168.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-71/out/m84036_250809_035451_s4.bc2168.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2168"}
2025-09-15 20:23:41.304 wdl.w:ptcp NOTICE ready :: job: "call-trgt-71", callee: "trgt"
2025-09-15 20:23:41.304 wdl.w:ptcp INFO input :: job: "call-trgt-71", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-71/out/m84036_250809_035451_s4.bc2168.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-71/out/m84036_250809_035451_s4.bc2168.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2168"}
2025-09-15 20:23:41.304 wdl.w:ptcp.w:call-sawfish-08.t:call-run_sawfish NOTICE task setup :: name: "run_sawfish", source: "./sawfish.wdl", line: 83, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-08/call-run_sawfish", thread: 140608723195456
2025-09-15 20:23:41.319 wdl.w:ptcp.w:call-sawfish-08.t:call-run_sawfish INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:23:41.319 wdl.w:ptcp.w:call-sawfish-08.t:call-run_sawfish INFO input :: name: "genome_version", value: "38"
2025-09-15 20:23:41.319 wdl.w:ptcp.w:call-sawfish-08.t:call-run_sawfish INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:23:41.319 wdl.w:ptcp.w:call-sawfish-08.t:call-run_sawfish INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:23:41.320 wdl.w:ptcp.w:call-sawfish-08.t:call-run_sawfish INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2105.mapped.bam.bai"
2025-09-15 20:23:41.320 wdl.w:ptcp.w:call-sawfish-08.t:call-run_sawfish INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2105.mapped.bam"
2025-09-15 20:23:41.320 wdl.w:ptcp.w:call-sawfish-08.t:call-run_sawfish INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2105"
2025-09-15 20:23:41.320 wdl.w:ptcp.w:call-sawfish-08.t:call-run_sawfish INFO eval :: name: "mem_gb", value: 32
2025-09-15 20:23:41.320 wdl.w:ptcp.w:call-sawfish-08.t:call-run_sawfish INFO eval :: name: "threads", value: 16
2025-09-15 20:23:41.320 wdl.w:ptcp.w:call-sawfish-08.t:call-run_sawfish INFO eval :: name: "disk_size", value: 30
2025-09-15 20:23:41.320 wdl.w:ptcp.w:call-sawfish-08.t:call-run_sawfish INFO eval :: name: "discover_dirname", value: "m84036_250809_035451_s4.bc2105_sawfish_discover"
2025-09-15 20:23:41.320 wdl.w:ptcp.w:call-sawfish-08.t:call-run_sawfish INFO eval :: name: "call_dirname", value: "m84036_250809_035451_s4.bc2105_sawfish"
2025-09-15 20:23:41.321 wdl.w:ptcp.w:call-sawfish-08.t:call-run_sawfish INFO eval :: name: "minimap2_bam_filename", value: "m84036_250809_035451_s4.bc2105.minimap2.bam"
2025-09-15 20:23:41.321 wdl.w:ptcp.w:call-sawfish-08.t:call-run_sawfish INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 16, memory_reservation: 32000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:23:41.321 wdl.w:ptcp.w:call-sawfish-08.t:call-run_sawfish WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:23:41.321 wdl.w:ptcp.w:call-sawfish-08.t:call-run_sawfish INFO provisioned :: seconds_waited: 0, cpu: 16, mem_bytes: 32000000000
2025-09-15 20:23:41.322 wdl.w:ptcp.w:call-sawfish-08.t:call-run_sawfish INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:23:41.360 wdl.w:ptcp.w:call-trgt-05.t:call-get_reads_overlapping_repeats INFO output :: name: "reads_overlapping_repeats", value: "m84036_250809_035451_s4.bc2102.repeats.bam"
2025-09-15 20:23:41.364 wdl.w:ptcp.w:call-trgt-05.t:call-get_reads_overlapping_repeats INFO output :: name: "reads_overlapping_repeats_bai", value: "m84036_250809_035451_s4.bc2102.repeats.bam.bai"
2025-09-15 20:23:41.388 wdl.w:ptcp.w:call-sawfish-08.t:call-run_sawfish INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 10, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-08/call-run_sawfish/_singularity_tmpdir_ehfso4zz"
2025-09-15 20:23:41.388 wdl.w:ptcp.w:call-sawfish-08.t:call-run_sawfish INFO Slurm invocation: srun --job-name call-run_sawfish --partition compute,compute9 --cpus-per-task 16 --mem 30518M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-08/call-run_sawfish/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-08/call-run_sawfish/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-08/call-run_sawfish/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-08/call-run_sawfish/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-08/out/m84036_250809_035451_s4.bc2105.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2105.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-08/out/m84036_250809_035451_s4.bc2105.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2105.mapped.bam:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-08/call-run_sawfish/_singularity_tmpdir_ehfso4zz/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-08/call-run_sawfish/_singularity_tmpdir_ehfso4zz/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:23:41.407 wdl.w:ptcp.w:call-sawfish-08.t:call-run_sawfish NOTICE slurm_singularity run :: pid: 1199976, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-08/call-run_sawfish/slurm_singularity.log.txt"
2025-09-15 20:23:41.428 wdl.w:ptcp.w:call-trgt-05.t:call-get_reads_overlapping_repeats NOTICE done
2025-09-15 20:23:41.433 wdl.w:ptcp.w:call-trgt-05 NOTICE finish :: job: "call-get_reads_overlapping_repeats"
2025-09-15 20:23:41.433 wdl.w:ptcp.w:call-trgt-05 INFO output :: job: "call-get_reads_overlapping_repeats", values: {"reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-05/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2102.repeats.bam.bai", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-05/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2102.repeats.bam"}
2025-09-15 20:23:41.434 wdl.w:ptcp.w:call-trgt-05 INFO visit :: node: "output-reads_overlapping_repeats", values: {"reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-05/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2102.repeats.bam"}
2025-09-15 20:23:41.434 wdl.w:ptcp.w:call-trgt-05 INFO visit :: node: "output-reads_overlapping_repeats_bai", values: {"reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-05/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2102.repeats.bam.bai"}
2025-09-15 20:23:41.441 wdl.w:ptcp.w:call-trgt-08.t:call-get_reads_overlapping_repeats NOTICE task setup :: name: "get_reads_overlapping_repeats", source: "./trgt.wdl", line: 182, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-08/call-get_reads_overlapping_repeats", thread: 140609796937280
2025-09-15 20:23:41.457 wdl.w:ptcp.w:call-trgt-08.t:call-get_reads_overlapping_repeats INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:23:41.457 wdl.w:ptcp.w:call-trgt-08.t:call-get_reads_overlapping_repeats INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:23:41.457 wdl.w:ptcp.w:call-trgt-08.t:call-get_reads_overlapping_repeats INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2105.mapped.bam.bai"
2025-09-15 20:23:41.458 wdl.w:ptcp.w:call-trgt-08.t:call-get_reads_overlapping_repeats INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2105.mapped.bam"
2025-09-15 20:23:41.458 wdl.w:ptcp.w:call-trgt-08.t:call-get_reads_overlapping_repeats INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2105"
2025-09-15 20:23:41.458 wdl.w:ptcp.w:call-trgt-08.t:call-get_reads_overlapping_repeats INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:23:41.458 wdl.w:ptcp.w:call-trgt-08.t:call-get_reads_overlapping_repeats INFO eval :: name: "expand_size", value: 3000
2025-09-15 20:23:41.458 wdl.w:ptcp.w:call-trgt-08.t:call-get_reads_overlapping_repeats INFO eval :: name: "threads", value: 1
2025-09-15 20:23:41.458 wdl.w:ptcp.w:call-trgt-08.t:call-get_reads_overlapping_repeats INFO eval :: name: "expanded_bed_name", value: "m84036_250809_035451_s4.bc2105.expanded.bed"
2025-09-15 20:23:41.458 wdl.w:ptcp.w:call-trgt-08.t:call-get_reads_overlapping_repeats INFO eval :: name: "disk_size", value: 11
2025-09-15 20:23:41.458 wdl.w:ptcp.w:call-trgt-08.t:call-get_reads_overlapping_repeats INFO eval :: name: "output_name", value: "m84036_250809_035451_s4.bc2105.repeats.bam"
2025-09-15 20:23:41.458 wdl.w:ptcp.w:call-trgt-08.t:call-get_reads_overlapping_repeats INFO eval :: name: "index_name", value: "m84036_250809_035451_s4.bc2105.repeats.bam.bai"
2025-09-15 20:23:41.459 wdl.w:ptcp.w:call-trgt-08.t:call-get_reads_overlapping_repeats INFO eval :: name: "output_name_with_index", value: "m84036_250809_035451_s4.bc2105.repeats.bam##idx##m84036_250809_035451_s4.bc2105.repeats.bam.bai"
2025-09-15 20:23:41.459 wdl.w:ptcp.w:call-trgt-08.t:call-get_reads_overlapping_repeats INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:23:41.459 wdl.w:ptcp.w:call-trgt-08.t:call-get_reads_overlapping_repeats WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:23:41.459 wdl.w:ptcp.w:call-trgt-08.t:call-get_reads_overlapping_repeats INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:23:41.459 wdl.w:ptcp.w:call-trgt-08.t:call-get_reads_overlapping_repeats INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:23:41.512 wdl.w:ptcp.w:call-trgt-08.t:call-get_reads_overlapping_repeats INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 9, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-08/call-get_reads_overlapping_repeats/_singularity_tmpdir_1buqdeqz"
2025-09-15 20:23:41.512 wdl.w:ptcp.w:call-trgt-08.t:call-get_reads_overlapping_repeats INFO Slurm invocation: srun --job-name call-get_reads_overlapping_repeats --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-08/call-get_reads_overlapping_repeats/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-08/call-get_reads_overlapping_repeats/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-08/call-get_reads_overlapping_repeats/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-08/call-get_reads_overlapping_repeats/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-08/out/m84036_250809_035451_s4.bc2105.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2105.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-08/out/m84036_250809_035451_s4.bc2105.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2105.mapped.bam:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-08/call-get_reads_overlapping_repeats/_singularity_tmpdir_1buqdeqz/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-08/call-get_reads_overlapping_repeats/_singularity_tmpdir_1buqdeqz/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:23:41.530 wdl.w:ptcp.w:call-trgt-08.t:call-get_reads_overlapping_repeats NOTICE slurm_singularity run :: pid: 1199988, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-08/call-get_reads_overlapping_repeats/slurm_singularity.log.txt"
2025-09-15 20:23:41.698 wdl.w:ptcp.w:call-trgt-25.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:38 [INFO] - Running trgt-4.0.0-429afcd [genotype]
2025-09-15 20:23:41.698 wdl.w:ptcp.w:call-trgt-25.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:38 [WARN] - OPDM_ABCD3: Filtered out 8 impure reads
2025-09-15 20:23:41.698 wdl.w:ptcp.w:call-trgt-25.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:38 [WARN] - SCA37_DAB1: Filtered out 14 impure reads
2025-09-15 20:23:41.698 wdl.w:ptcp.w:call-trgt-25.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:38 [WARN] - NIID_NOTCH2NLC: Filtered out 23 impure reads
2025-09-15 20:23:41.698 wdl.w:ptcp.w:call-trgt-25.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:38 [WARN] - SCA2_ATXN2: Filtered out 14 impure reads
2025-09-15 20:23:41.698 wdl.w:ptcp.w:call-trgt-25.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:38 [WARN] - OPDM4_RILPL1: Filtered out 9 impure reads
2025-09-15 20:23:41.699 wdl.w:ptcp.w:call-trgt-25.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:38 [WARN] - DRPLA_ATN1: Filtered out 20 impure reads
2025-09-15 20:23:41.699 wdl.w:ptcp.w:call-trgt-25.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:38 [WARN] - SCA3_ATXN3: Filtered out 20 impure reads
2025-09-15 20:23:41.699 wdl.w:ptcp.w:call-trgt-25.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:38 [WARN] - SCA8_ATXN8OS: Filtered out 5 impure reads
2025-09-15 20:23:41.699 wdl.w:ptcp.w:call-trgt-25.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:38 [WARN] - SCA27B_FGF14: Filtered out 9 impure reads
2025-09-15 20:23:41.699 wdl.w:ptcp.w:call-trgt-25.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:38 [WARN] - OPMD_PABPN1: Filtered out 18 impure reads
2025-09-15 20:23:41.699 wdl.w:ptcp.w:call-trgt-25.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:39 [WARN] - SCA31_BEAN1: Filtered out 7 impure reads
2025-09-15 20:23:41.699 wdl.w:ptcp.w:call-trgt-25.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:39 [WARN] - FECD3_TCF4: Filtered out 15 impure reads
2025-09-15 20:23:41.699 wdl.w:ptcp.w:call-trgt-25.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:39 [WARN] - HDL2_JPH3: Filtered out 10 impure reads
2025-09-15 20:23:41.699 wdl.w:ptcp.w:call-trgt-25.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:39 [WARN] - SCA4_ZFHX3: Filtered out 26 impure reads
2025-09-15 20:23:41.699 wdl.w:ptcp.w:call-trgt-25.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:39 [WARN] - SD5_HOXD13: Filtered out 5 impure reads
2025-09-15 20:23:41.699 wdl.w:ptcp.w:call-trgt-25.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:39 [WARN] - SCA6_CACNA1A: Filtered out 23 impure reads
2025-09-15 20:23:41.699 wdl.w:ptcp.w:call-trgt-25.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:39 [WARN] - OPDM2_GIPC1: Filtered out 17 impure reads
2025-09-15 20:23:41.699 wdl.w:ptcp.w:call-trgt-25.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:39 [WARN] - SCA36_NOP56: Filtered out 13 impure reads
2025-09-15 20:23:41.699 wdl.w:ptcp.w:call-trgt-25.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:39 [WARN] - CJD_PRNP: Filtered out 19 impure reads
2025-09-15 20:23:41.699 wdl.w:ptcp.w:call-trgt-25.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:40 [WARN] - DM1_DMPK: Filtered out 17 impure reads
2025-09-15 20:23:41.700 wdl.w:ptcp.w:call-trgt-25.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:40 [WARN] - EPM1_CSTB: Filtered out 15 impure reads
2025-09-15 20:23:41.700 wdl.w:ptcp.w:call-trgt-25.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:40 [WARN] - FRA2A_AFF3: Filtered out 13 impure reads
2025-09-15 20:23:41.700 wdl.w:ptcp.w:call-trgt-25.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:40 [WARN] - SCA10_ATXN10: Filtered out 8 impure reads
2025-09-15 20:23:41.700 wdl.w:ptcp.w:call-trgt-25.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:40 [WARN] - HD_HTT: Filtered out 16 impure reads
2025-09-15 20:23:41.700 wdl.w:ptcp.w:call-trgt-25.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:40 [WARN] - CCHS_PHOX2B: Filtered out 3 impure reads
2025-09-15 20:23:41.700 wdl.w:ptcp.w:call-trgt-25.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:40 [WARN] - SCA12_PPP2R2B: Filtered out 8 impure reads
2025-09-15 20:23:41.700 wdl.w:ptcp.w:call-trgt-25.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:40 [WARN] - SCA7_ATXN7: Filtered out 16 impure reads
2025-09-15 20:23:41.700 wdl.w:ptcp.w:call-trgt-25.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:40 [WARN] - SCA1_ATXN1: Filtered out 19 impure reads
2025-09-15 20:23:41.700 wdl.w:ptcp.w:call-trgt-25.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:40 [WARN] - DM2_CNBP: Filtered out 2 impure reads
2025-09-15 20:23:41.700 wdl.w:ptcp.w:call-trgt-25.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:40 [WARN] - SCA17_TBP: Filtered out 9 impure reads
2025-09-15 20:23:41.700 wdl.w:ptcp.w:call-trgt-25.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:40 [WARN] - OPDM1_LRP12: Filtered out 18 impure reads
2025-09-15 20:23:41.700 wdl.w:ptcp.w:call-trgt-25.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:40 [WARN] - FAME1_SAMD12: Filtered out 8 impure reads
2025-09-15 20:23:41.700 wdl.w:ptcp.w:call-trgt-25.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:40 [WARN] - CANVAS_RFC1: Filtered out 8 impure reads
2025-09-15 20:23:41.700 wdl.w:ptcp.w:call-trgt-25.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:40 [WARN] - SBMA_AR: Filtered out 17 impure reads
2025-09-15 20:23:41.700 wdl.w:ptcp.w:call-trgt-25.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:40 [WARN] - FXS_FMR1: Filtered out 3 impure reads
2025-09-15 20:23:41.700 wdl.w:ptcp.w:call-trgt-25.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:40 [WARN] - FRDA_FXN: Filtered out 3 impure reads
2025-09-15 20:23:41.701 wdl.w:ptcp.w:call-trgt-25.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:40 [WARN] - FRAXE_AFF2: Filtered out 16 impure reads
2025-09-15 20:23:41.701 wdl.w:ptcp.w:call-trgt-25.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:40 [WARN] - FTDALS1_C9orf72: Filtered out 32 impure reads
2025-09-15 20:23:41.701 wdl.w:ptcp.w:call-trgt-25.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:41 [INFO] - Total execution time: 3.18s
2025-09-15 20:23:41.701 wdl.w:ptcp.w:call-trgt-25.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:41 [INFO] - trgt end
2025-09-15 20:23:41.768 wdl.w:ptcp.w:call-paraphase-06.t:call-run_paraphase.stderr VERBOSE INFO:root:Processing sample m84036_250809_035451_s4.bc2103 at 2025-09-15 20:23:39.102451...
2025-09-15 20:23:41.769 wdl.w:ptcp.w:call-paraphase-06.t:call-run_paraphase.stderr VERBOSE INFO:root:Checking sample sex at 2025-09-15 20:23:39.103493...
2025-09-15 20:23:41.769 wdl.w:ptcp.w:call-paraphase-06.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for cyp21 for sample m84036_250809_035451_s4.bc2103 at 2025-09-15 20:23:39.139546...
2025-09-15 20:23:41.769 wdl.w:ptcp.w:call-paraphase-06.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for cyp21 for sample m84036_250809_035451_s4.bc2103 at 2025-09-15 20:23:39.139853...
2025-09-15 20:23:41.769 wdl.w:ptcp.w:call-paraphase-06.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for smn1 for sample m84036_250809_035451_s4.bc2103 at 2025-09-15 20:23:39.139648...
2025-09-15 20:23:41.769 wdl.w:ptcp.w:call-paraphase-06.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for smn1 for sample m84036_250809_035451_s4.bc2103 at 2025-09-15 20:23:39.139932...
2025-09-15 20:23:41.769 wdl.w:ptcp.w:call-paraphase-06.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for gba for sample m84036_250809_035451_s4.bc2103 at 2025-09-15 20:23:39.139705...
2025-09-15 20:23:41.769 wdl.w:ptcp.w:call-paraphase-06.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for hba for sample m84036_250809_035451_s4.bc2103 at 2025-09-15 20:23:39.139728...
2025-09-15 20:23:41.769 wdl.w:ptcp.w:call-paraphase-06.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for gba for sample m84036_250809_035451_s4.bc2103 at 2025-09-15 20:23:39.139977...
2025-09-15 20:23:41.769 wdl.w:ptcp.w:call-paraphase-06.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for hba for sample m84036_250809_035451_s4.bc2103 at 2025-09-15 20:23:39.139983...
2025-09-15 20:23:41.798 wdl.w:ptcp.w:call-paraphase-33.t:call-run_paraphase.stderr VERBOSE INFO:root:Processing sample m84036_250809_035451_s4.bc2130 at 2025-09-15 20:23:39.084817...
2025-09-15 20:23:41.799 wdl.w:ptcp.w:call-paraphase-33.t:call-run_paraphase.stderr VERBOSE INFO:root:Checking sample sex at 2025-09-15 20:23:39.085886...
2025-09-15 20:23:41.799 wdl.w:ptcp.w:call-paraphase-33.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for cyp21 for sample m84036_250809_035451_s4.bc2130 at 2025-09-15 20:23:39.122603...
2025-09-15 20:23:41.799 wdl.w:ptcp.w:call-paraphase-33.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for cyp21 for sample m84036_250809_035451_s4.bc2130 at 2025-09-15 20:23:39.122953...
2025-09-15 20:23:41.799 wdl.w:ptcp.w:call-paraphase-33.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for smn1 for sample m84036_250809_035451_s4.bc2130 at 2025-09-15 20:23:39.122826...
2025-09-15 20:23:41.800 wdl.w:ptcp.w:call-paraphase-33.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for gba for sample m84036_250809_035451_s4.bc2130 at 2025-09-15 20:23:39.122864...
2025-09-15 20:23:41.800 wdl.w:ptcp.w:call-paraphase-33.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for hba for sample m84036_250809_035451_s4.bc2130 at 2025-09-15 20:23:39.122868...
2025-09-15 20:23:41.800 wdl.w:ptcp.w:call-paraphase-33.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for smn1 for sample m84036_250809_035451_s4.bc2130 at 2025-09-15 20:23:39.123125...
2025-09-15 20:23:41.800 wdl.w:ptcp.w:call-paraphase-33.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for gba for sample m84036_250809_035451_s4.bc2130 at 2025-09-15 20:23:39.123150...
2025-09-15 20:23:41.800 wdl.w:ptcp.w:call-paraphase-33.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for hba for sample m84036_250809_035451_s4.bc2130 at 2025-09-15 20:23:39.123158...
2025-09-15 20:23:41.800 wdl.w:ptcp.w:call-paraphase-33.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for cyp21 for sample m84036_250809_035451_s4.bc2130 at 2025-09-15 20:23:39.503906...
2025-09-15 20:23:41.800 wdl.w:ptcp.w:call-paraphase-33.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for gba for sample m84036_250809_035451_s4.bc2130 at 2025-09-15 20:23:39.513553...
2025-09-15 20:23:41.800 wdl.w:ptcp.w:call-paraphase-33.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for hba for sample m84036_250809_035451_s4.bc2130 at 2025-09-15 20:23:39.535334...
2025-09-15 20:23:41.800 wdl.w:ptcp.w:call-paraphase-33.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for smn1 for sample m84036_250809_035451_s4.bc2130 at 2025-09-15 20:23:39.540441...
2025-09-15 20:23:41.800 wdl.w:ptcp.w:call-paraphase-33.t:call-run_paraphase.stderr VERBOSE WARNING:root:This region does not appear to have coverage. Will not attempt to phase haplotypes.
2025-09-15 20:23:41.800 wdl.w:ptcp.w:call-paraphase-33.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for cyp21 for sample m84036_250809_035451_s4.bc2130 at 2025-09-15 20:23:39.542281...
2025-09-15 20:23:41.800 wdl.w:ptcp.w:call-paraphase-33.t:call-run_paraphase.stderr VERBOSE WARNING:root:This region does not appear to have coverage. Will not attempt to phase haplotypes.
2025-09-15 20:23:41.800 wdl.w:ptcp.w:call-paraphase-33.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for gba for sample m84036_250809_035451_s4.bc2130 at 2025-09-15 20:23:39.565897...
2025-09-15 20:23:41.800 wdl.w:ptcp.w:call-paraphase-33.t:call-run_paraphase.stderr VERBOSE WARNING:root:This region does not appear to have coverage. Will not attempt to phase haplotypes.
2025-09-15 20:23:41.800 wdl.w:ptcp.w:call-paraphase-33.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for hba for sample m84036_250809_035451_s4.bc2130 at 2025-09-15 20:23:39.571096...
2025-09-15 20:23:41.800 wdl.w:ptcp.w:call-paraphase-33.t:call-run_paraphase.stderr VERBOSE WARNING:root:This region does not appear to have coverage. Will not attempt to phase haplotypes.
2025-09-15 20:23:41.801 wdl.w:ptcp.w:call-paraphase-33.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for smn1 for sample m84036_250809_035451_s4.bc2130 at 2025-09-15 20:23:39.621109...
2025-09-15 20:23:41.801 wdl.w:ptcp.w:call-paraphase-33.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for cyp21 for sample m84036_250809_035451_s4.bc2130 at 2025-09-15 20:23:39.853810...
2025-09-15 20:23:41.801 wdl.w:ptcp.w:call-paraphase-33.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for f8inv22 for sample m84036_250809_035451_s4.bc2130 at 2025-09-15 20:23:39.856874...
2025-09-15 20:23:41.801 wdl.w:ptcp.w:call-paraphase-33.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for f8inv22 for sample m84036_250809_035451_s4.bc2130 at 2025-09-15 20:23:39.856930...
2025-09-15 20:23:41.801 wdl.w:ptcp.w:call-paraphase-33.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for gba for sample m84036_250809_035451_s4.bc2130 at 2025-09-15 20:23:39.893914...
2025-09-15 20:23:41.801 wdl.w:ptcp.w:call-paraphase-33.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for rpgr for sample m84036_250809_035451_s4.bc2130 at 2025-09-15 20:23:39.904938...
2025-09-15 20:23:41.801 wdl.w:ptcp.w:call-paraphase-33.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for rpgr for sample m84036_250809_035451_s4.bc2130 at 2025-09-15 20:23:39.905014...
2025-09-15 20:23:41.801 wdl.w:ptcp.w:call-paraphase-33.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for hba for sample m84036_250809_035451_s4.bc2130 at 2025-09-15 20:23:39.930462...
2025-09-15 20:23:41.801 wdl.w:ptcp.w:call-paraphase-33.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for hbb for sample m84036_250809_035451_s4.bc2130 at 2025-09-15 20:23:39.936134...
2025-09-15 20:23:41.801 wdl.w:ptcp.w:call-paraphase-33.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for hbb for sample m84036_250809_035451_s4.bc2130 at 2025-09-15 20:23:39.936203...
2025-09-15 20:23:41.801 wdl.w:ptcp.w:call-paraphase-33.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning to gene2 region for smn1 for sample m84036_250809_035451_s4.bc2130 at 2025-09-15 20:23:39.947106...
2025-09-15 20:23:41.801 wdl.w:ptcp.w:call-paraphase-33.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for f8inv22 for sample m84036_250809_035451_s4.bc2130 at 2025-09-15 20:23:40.236693...
2025-09-15 20:23:41.801 wdl.w:ptcp.w:call-paraphase-33.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for rpgr for sample m84036_250809_035451_s4.bc2130 at 2025-09-15 20:23:40.269461...
2025-09-15 20:23:41.801 wdl.w:ptcp.w:call-paraphase-33.t:call-run_paraphase.stderr VERBOSE WARNING:root:This region does not appear to have coverage. Will not attempt to phase haplotypes.
2025-09-15 20:23:41.801 wdl.w:ptcp.w:call-paraphase-33.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for f8inv22 for sample m84036_250809_035451_s4.bc2130 at 2025-09-15 20:23:40.276884...
2025-09-15 20:23:41.801 wdl.w:ptcp.w:call-paraphase-33.t:call-run_paraphase.stderr VERBOSE WARNING:root:This region does not appear to have coverage. Will not attempt to phase haplotypes.
2025-09-15 20:23:41.801 wdl.w:ptcp.w:call-paraphase-33.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for rpgr for sample m84036_250809_035451_s4.bc2130 at 2025-09-15 20:23:40.309176...
2025-09-15 20:23:41.801 wdl.w:ptcp.w:call-paraphase-33.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for hbb for sample m84036_250809_035451_s4.bc2130 at 2025-09-15 20:23:40.315906...
2025-09-15 20:23:41.801 wdl.w:ptcp.w:call-paraphase-33.t:call-run_paraphase.stderr VERBOSE WARNING:root:This region does not appear to have coverage. Will not attempt to phase haplotypes.
2025-09-15 20:23:41.802 wdl.w:ptcp.w:call-paraphase-33.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for hbb for sample m84036_250809_035451_s4.bc2130 at 2025-09-15 20:23:40.355437...
2025-09-15 20:23:41.802 wdl.w:ptcp.w:call-paraphase-33.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for f8inv22 for sample m84036_250809_035451_s4.bc2130 at 2025-09-15 20:23:40.501989...
2025-09-15 20:23:41.802 wdl.w:ptcp.w:call-paraphase-33.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for rpgr for sample m84036_250809_035451_s4.bc2130 at 2025-09-15 20:23:40.518118...
2025-09-15 20:23:41.802 wdl.w:ptcp.w:call-paraphase-33.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for hbb for sample m84036_250809_035451_s4.bc2130 at 2025-09-15 20:23:40.531292...
2025-09-15 20:23:41.802 wdl.w:ptcp.w:call-paraphase-33.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for smn1 for sample m84036_250809_035451_s4.bc2130 at 2025-09-15 20:23:40.545799...
2025-09-15 20:23:41.802 wdl.w:ptcp.w:call-paraphase-33.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for f8inv1 for sample m84036_250809_035451_s4.bc2130 at 2025-09-15 20:23:40.582112...
2025-09-15 20:23:41.802 wdl.w:ptcp.w:call-paraphase-33.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for f8inv1 for sample m84036_250809_035451_s4.bc2130 at 2025-09-15 20:23:40.582222...
2025-09-15 20:23:41.802 wdl.w:ptcp.w:call-paraphase-33.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for f8inv1 for sample m84036_250809_035451_s4.bc2130 at 2025-09-15 20:23:40.798695...
2025-09-15 20:23:41.802 wdl.w:ptcp.w:call-paraphase-33.t:call-run_paraphase.stderr VERBOSE WARNING:root:This region does not appear to have coverage. Will not attempt to phase haplotypes.
2025-09-15 20:23:41.802 wdl.w:ptcp.w:call-paraphase-33.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for f8inv1 for sample m84036_250809_035451_s4.bc2130 at 2025-09-15 20:23:40.828509...
2025-09-15 20:23:41.802 wdl.w:ptcp.w:call-paraphase-33.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for f8inv1 for sample m84036_250809_035451_s4.bc2130 at 2025-09-15 20:23:40.941137...
2025-09-15 20:23:41.800 wdl.w:ptcp.w:call-paraphase-05.t:call-run_paraphase.stderr VERBOSE INFO:root:Processing sample m84036_250809_035451_s4.bc2102 at 2025-09-15 20:23:39.033337...
2025-09-15 20:23:41.802 wdl.w:ptcp.w:call-paraphase-33.t:call-run_paraphase.stderr VERBOSE INFO:root:Merging all bams for sample m84036_250809_035451_s4.bc2130 at 2025-09-15 20:23:40.955527...
2025-09-15 20:23:41.802 wdl.w:ptcp.w:call-paraphase-05.t:call-run_paraphase.stderr VERBOSE INFO:root:Checking sample sex at 2025-09-15 20:23:39.034277...
2025-09-15 20:23:41.802 wdl.w:ptcp.w:call-paraphase-33.t:call-run_paraphase.stderr VERBOSE INFO:root:Writing to json for sample m84036_250809_035451_s4.bc2130 at 2025-09-15 20:23:41.150621...
2025-09-15 20:23:41.803 wdl.w:ptcp.w:call-paraphase-05.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for cyp21 for sample m84036_250809_035451_s4.bc2102 at 2025-09-15 20:23:39.072504...
2025-09-15 20:23:41.803 wdl.w:ptcp.w:call-paraphase-33.t:call-run_paraphase.stderr VERBOSE INFO:root:Completed Paraphase analysis at 2025-09-15 20:23:41.351130...
2025-09-15 20:23:41.803 wdl.w:ptcp.w:call-paraphase-05.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for smn1 for sample m84036_250809_035451_s4.bc2102 at 2025-09-15 20:23:39.072704...
2025-09-15 20:23:41.803 wdl.w:ptcp.w:call-paraphase-33.t:call-run_paraphase.stderr VERBOSE [2025-09-15 20:23:41,640] INFO - reading variant list from /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf
2025-09-15 20:23:41.803 wdl.w:ptcp.w:call-paraphase-05.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for cyp21 for sample m84036_250809_035451_s4.bc2102 at 2025-09-15 20:23:39.072947...
2025-09-15 20:23:41.803 wdl.w:ptcp.w:call-paraphase-05.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for gba for sample m84036_250809_035451_s4.bc2102 at 2025-09-15 20:23:39.072702...
2025-09-15 20:23:41.803 wdl.w:ptcp.w:call-paraphase-05.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for hba for sample m84036_250809_035451_s4.bc2102 at 2025-09-15 20:23:39.072730...
2025-09-15 20:23:41.803 wdl.w:ptcp.w:call-paraphase-05.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for smn1 for sample m84036_250809_035451_s4.bc2102 at 2025-09-15 20:23:39.072984...
2025-09-15 20:23:41.803 wdl.w:ptcp.w:call-paraphase-05.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for gba for sample m84036_250809_035451_s4.bc2102 at 2025-09-15 20:23:39.072995...
2025-09-15 20:23:41.803 wdl.w:ptcp.w:call-paraphase-05.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for hba for sample m84036_250809_035451_s4.bc2102 at 2025-09-15 20:23:39.073005...
2025-09-15 20:23:41.804 wdl.w:ptcp.w:call-paraphase-05.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for smn1 for sample m84036_250809_035451_s4.bc2102 at 2025-09-15 20:23:39.427557...
2025-09-15 20:23:41.804 wdl.w:ptcp.w:call-paraphase-05.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for gba for sample m84036_250809_035451_s4.bc2102 at 2025-09-15 20:23:39.432882...
2025-09-15 20:23:41.804 wdl.w:ptcp.w:call-paraphase-05.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for hba for sample m84036_250809_035451_s4.bc2102 at 2025-09-15 20:23:39.444143...
2025-09-15 20:23:41.804 wdl.w:ptcp.w:call-paraphase-05.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for cyp21 for sample m84036_250809_035451_s4.bc2102 at 2025-09-15 20:23:39.452094...
2025-09-15 20:23:41.804 wdl.w:ptcp.w:call-paraphase-05.t:call-run_paraphase.stderr VERBOSE WARNING:root:This region does not appear to have coverage. Will not attempt to phase haplotypes.
2025-09-15 20:23:41.804 wdl.w:ptcp.w:call-paraphase-05.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for hba for sample m84036_250809_035451_s4.bc2102 at 2025-09-15 20:23:39.483478...
2025-09-15 20:23:41.804 wdl.w:ptcp.w:call-paraphase-05.t:call-run_paraphase.stderr VERBOSE WARNING:root:This region does not appear to have coverage. Will not attempt to phase haplotypes.
2025-09-15 20:23:41.804 wdl.w:ptcp.w:call-paraphase-05.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for gba for sample m84036_250809_035451_s4.bc2102 at 2025-09-15 20:23:39.486196...
2025-09-15 20:23:41.804 wdl.w:ptcp.w:call-paraphase-05.t:call-run_paraphase.stderr VERBOSE WARNING:root:This region does not appear to have coverage. Will not attempt to phase haplotypes.
2025-09-15 20:23:41.804 wdl.w:ptcp.w:call-paraphase-05.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for cyp21 for sample m84036_250809_035451_s4.bc2102 at 2025-09-15 20:23:39.487161...
2025-09-15 20:23:41.804 wdl.w:ptcp.w:call-paraphase-05.t:call-run_paraphase.stderr VERBOSE WARNING:root:This region does not appear to have coverage. Will not attempt to phase haplotypes.
2025-09-15 20:23:41.804 wdl.w:ptcp.w:call-paraphase-05.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for smn1 for sample m84036_250809_035451_s4.bc2102 at 2025-09-15 20:23:39.499933...
2025-09-15 20:23:41.804 wdl.w:ptcp.w:call-paraphase-05.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for hba for sample m84036_250809_035451_s4.bc2102 at 2025-09-15 20:23:39.750276...
2025-09-15 20:23:41.804 wdl.w:ptcp.w:call-paraphase-05.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for hbb for sample m84036_250809_035451_s4.bc2102 at 2025-09-15 20:23:39.755890...
2025-09-15 20:23:41.804 wdl.w:ptcp.w:call-paraphase-05.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for hbb for sample m84036_250809_035451_s4.bc2102 at 2025-09-15 20:23:39.755934...
2025-09-15 20:23:41.804 wdl.w:ptcp.w:call-paraphase-05.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for cyp21 for sample m84036_250809_035451_s4.bc2102 at 2025-09-15 20:23:39.799324...
2025-09-15 20:23:41.804 wdl.w:ptcp.w:call-paraphase-05.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for f8inv22 for sample m84036_250809_035451_s4.bc2102 at 2025-09-15 20:23:39.804038...
2025-09-15 20:23:41.805 wdl.w:ptcp.w:call-paraphase-05.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for f8inv22 for sample m84036_250809_035451_s4.bc2102 at 2025-09-15 20:23:39.804092...
2025-09-15 20:23:41.805 wdl.w:ptcp.w:call-paraphase-05.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for gba for sample m84036_250809_035451_s4.bc2102 at 2025-09-15 20:23:39.810212...
2025-09-15 20:23:41.805 wdl.w:ptcp.w:call-paraphase-05.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for rpgr for sample m84036_250809_035451_s4.bc2102 at 2025-09-15 20:23:39.817517...
2025-09-15 20:23:41.805 wdl.w:ptcp.w:call-paraphase-05.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for rpgr for sample m84036_250809_035451_s4.bc2102 at 2025-09-15 20:23:39.817566...
2025-09-15 20:23:41.805 wdl.w:ptcp.w:call-paraphase-05.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning to gene2 region for smn1 for sample m84036_250809_035451_s4.bc2102 at 2025-09-15 20:23:39.841726...
2025-09-15 20:23:41.805 wdl.w:ptcp.w:call-paraphase-05.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for hbb for sample m84036_250809_035451_s4.bc2102 at 2025-09-15 20:23:40.109784...
2025-09-15 20:23:41.805 wdl.w:ptcp.w:call-paraphase-05.t:call-run_paraphase.stderr VERBOSE WARNING:root:This region does not appear to have coverage. Will not attempt to phase haplotypes.
2025-09-15 20:23:41.805 wdl.w:ptcp.w:call-paraphase-05.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for hbb for sample m84036_250809_035451_s4.bc2102 at 2025-09-15 20:23:40.146522...
2025-09-15 20:23:41.805 wdl.w:ptcp.w:call-paraphase-05.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for rpgr for sample m84036_250809_035451_s4.bc2102 at 2025-09-15 20:23:40.187795...
2025-09-15 20:23:41.805 wdl.w:ptcp.w:call-paraphase-05.t:call-run_paraphase.stderr VERBOSE WARNING:root:This region does not appear to have coverage. Will not attempt to phase haplotypes.
2025-09-15 20:23:41.805 wdl.w:ptcp.w:call-paraphase-05.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for rpgr for sample m84036_250809_035451_s4.bc2102 at 2025-09-15 20:23:40.220344...
2025-09-15 20:23:41.805 wdl.w:ptcp.w:call-paraphase-05.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for f8inv22 for sample m84036_250809_035451_s4.bc2102 at 2025-09-15 20:23:40.233547...
2025-09-15 20:23:41.805 wdl.w:ptcp.w:call-paraphase-05.t:call-run_paraphase.stderr VERBOSE WARNING:root:This region does not appear to have coverage. Will not attempt to phase haplotypes.
2025-09-15 20:23:41.805 wdl.w:ptcp.w:call-paraphase-05.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for f8inv22 for sample m84036_250809_035451_s4.bc2102 at 2025-09-15 20:23:40.281891...
2025-09-15 20:23:41.806 wdl.w:ptcp.w:call-paraphase-05.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for hbb for sample m84036_250809_035451_s4.bc2102 at 2025-09-15 20:23:40.396607...
2025-09-15 20:23:41.806 wdl.w:ptcp.w:call-paraphase-05.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for rpgr for sample m84036_250809_035451_s4.bc2102 at 2025-09-15 20:23:40.467881...
2025-09-15 20:23:41.806 wdl.w:ptcp.w:call-paraphase-05.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for smn1 for sample m84036_250809_035451_s4.bc2102 at 2025-09-15 20:23:40.496564...
2025-09-15 20:23:41.806 wdl.w:ptcp.w:call-paraphase-05.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for f8inv22 for sample m84036_250809_035451_s4.bc2102 at 2025-09-15 20:23:40.504655...
2025-09-15 20:23:41.806 wdl.w:ptcp.w:call-paraphase-05.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for f8inv1 for sample m84036_250809_035451_s4.bc2102 at 2025-09-15 20:23:40.532403...
2025-09-15 20:23:41.806 wdl.w:ptcp.w:call-paraphase-05.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for f8inv1 for sample m84036_250809_035451_s4.bc2102 at 2025-09-15 20:23:40.532475...
2025-09-15 20:23:41.806 wdl.w:ptcp.w:call-paraphase-05.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for f8inv1 for sample m84036_250809_035451_s4.bc2102 at 2025-09-15 20:23:40.713866...
2025-09-15 20:23:41.806 wdl.w:ptcp.w:call-paraphase-05.t:call-run_paraphase.stderr VERBOSE WARNING:root:This region does not appear to have coverage. Will not attempt to phase haplotypes.
2025-09-15 20:23:41.806 wdl.w:ptcp.w:call-paraphase-05.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for f8inv1 for sample m84036_250809_035451_s4.bc2102 at 2025-09-15 20:23:40.732655...
2025-09-15 20:23:41.806 wdl.w:ptcp.w:call-paraphase-05.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for f8inv1 for sample m84036_250809_035451_s4.bc2102 at 2025-09-15 20:23:40.853651...
2025-09-15 20:23:41.806 wdl.w:ptcp.w:call-paraphase-05.t:call-run_paraphase.stderr VERBOSE INFO:root:Merging all bams for sample m84036_250809_035451_s4.bc2102 at 2025-09-15 20:23:40.867909...
2025-09-15 20:23:41.806 wdl.w:ptcp.w:call-paraphase-05.t:call-run_paraphase.stderr VERBOSE INFO:root:Writing to json for sample m84036_250809_035451_s4.bc2102 at 2025-09-15 20:23:41.058215...
2025-09-15 20:23:41.806 wdl.w:ptcp.w:call-paraphase-05.t:call-run_paraphase.stderr VERBOSE INFO:root:Completed Paraphase analysis at 2025-09-15 20:23:41.234106...
2025-09-15 20:23:41.806 wdl.w:ptcp.w:call-paraphase-05.t:call-run_paraphase.stderr VERBOSE [2025-09-15 20:23:41,640] INFO - reading variant list from /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf
2025-09-15 20:23:41.849 wdl.w:ptcp.w:call-paraphase-33.t:call-run_paraphase INFO output :: name: "paraphase_bam", value: "m84036_250809_035451_s4.bc2130_paraphase/m84036_250809_035451_s4.bc2130.paraphase.bam"
2025-09-15 20:23:41.854 wdl.w:ptcp.w:call-paraphase-33.t:call-run_paraphase INFO output :: name: "paraphase_bam_bai", value: "m84036_250809_035451_s4.bc2130_paraphase/m84036_250809_035451_s4.bc2130.paraphase.bam.bai"
2025-09-15 20:23:41.855 wdl.w:ptcp.w:call-paraphase-33.t:call-run_paraphase INFO output :: name: "paraphase_json", value: "m84036_250809_035451_s4.bc2130_paraphase/m84036_250809_035451_s4.bc2130.paraphase.json"
2025-09-15 20:23:41.857 wdl.w:ptcp.w:call-paraphase-05.t:call-run_paraphase INFO output :: name: "paraphase_bam", value: "m84036_250809_035451_s4.bc2102_paraphase/m84036_250809_035451_s4.bc2102.paraphase.bam"
2025-09-15 20:23:41.858 wdl.w:ptcp.w:call-paraphase-33.t:call-run_paraphase INFO output :: name: "paraphase_vcfs", value: []
2025-09-15 20:23:41.858 wdl.w:ptcp.w:call-paraphase-33.t:call-run_paraphase INFO output :: name: "havanno_json", value: "m84036_250809_035451_s4.bc2130.havanno.json"
2025-09-15 20:23:41.864 wdl.w:ptcp.w:call-paraphase-05.t:call-run_paraphase INFO output :: name: "paraphase_bam_bai", value: "m84036_250809_035451_s4.bc2102_paraphase/m84036_250809_035451_s4.bc2102.paraphase.bam.bai"
2025-09-15 20:23:41.865 wdl.w:ptcp.w:call-paraphase-05.t:call-run_paraphase INFO output :: name: "paraphase_json", value: "m84036_250809_035451_s4.bc2102_paraphase/m84036_250809_035451_s4.bc2102.paraphase.json"
2025-09-15 20:23:41.867 wdl.w:ptcp.w:call-paraphase-05.t:call-run_paraphase INFO output :: name: "paraphase_vcfs", value: []
2025-09-15 20:23:41.868 wdl.w:ptcp.w:call-paraphase-05.t:call-run_paraphase INFO output :: name: "havanno_json", value: "m84036_250809_035451_s4.bc2102.havanno.json"
2025-09-15 20:23:41.893 wdl.w:ptcp.w:call-paraphase-22.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for f8inv1 for sample m84036_250809_035451_s4.bc2119 at 2025-09-15 20:23:21.102211...
2025-09-15 20:23:41.894 wdl.w:ptcp.w:call-paraphase-22.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for f8inv1 for sample m84036_250809_035451_s4.bc2119 at 2025-09-15 20:23:25.049197...
2025-09-15 20:23:41.894 wdl.w:ptcp.w:call-paraphase-22.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for f8inv1 for sample m84036_250809_035451_s4.bc2119 at 2025-09-15 20:23:25.321117...
2025-09-15 20:23:41.985 wdl.w:ptcp.w:call-paraphase-05.t:call-run_paraphase NOTICE done
2025-09-15 20:23:41.989 wdl.w:ptcp.w:call-paraphase-33.t:call-run_paraphase NOTICE done
2025-09-15 20:23:41.994 wdl.w:ptcp.w:call-paraphase-33 NOTICE finish :: job: "call-run_paraphase"
2025-09-15 20:23:41.995 wdl.w:ptcp.w:call-paraphase-33 INFO output :: job: "call-run_paraphase", values: {"havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-33/call-run_paraphase/out/m84036_250809_035451_s4.bc2130.havanno.json", "paraphase_vcfs": [], "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-33/call-run_paraphase/out/m84036_250809_035451_s4.bc2130_paraphase/m84036_250809_035451_s4.bc2130.paraphase.json", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-33/call-run_paraphase/out/m84036_250809_035451_s4.bc2130_paraphase/m84036_250809_035451_s4.bc2130.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-33/call-run_paraphase/out/m84036_250809_035451_s4.bc2130_paraphase/m84036_250809_035451_s4.bc2130.paraphase.bam"}
2025-09-15 20:23:41.996 wdl.w:ptcp.w:call-paraphase-33 NOTICE ready :: job: "call-call_f8", callee: "call_f8"
2025-09-15 20:23:41.995 wdl.w:ptcp.w:call-paraphase-05 NOTICE finish :: job: "call-run_paraphase"
2025-09-15 20:23:41.996 wdl.w:ptcp.w:call-paraphase-33 INFO input :: job: "call-call_f8", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "out_prefix": "m84036_250809_035451_s4.bc2130", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-33/call-run_paraphase/out/m84036_250809_035451_s4.bc2130_paraphase/m84036_250809_035451_s4.bc2130.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-33/call-run_paraphase/out/m84036_250809_035451_s4.bc2130_paraphase/m84036_250809_035451_s4.bc2130.paraphase.bam", "sex": "F"}
2025-09-15 20:23:41.996 wdl.w:ptcp.w:call-paraphase-05 INFO output :: job: "call-run_paraphase", values: {"havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-05/call-run_paraphase/out/m84036_250809_035451_s4.bc2102.havanno.json", "paraphase_vcfs": [], "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-05/call-run_paraphase/out/m84036_250809_035451_s4.bc2102_paraphase/m84036_250809_035451_s4.bc2102.paraphase.json", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-05/call-run_paraphase/out/m84036_250809_035451_s4.bc2102_paraphase/m84036_250809_035451_s4.bc2102.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-05/call-run_paraphase/out/m84036_250809_035451_s4.bc2102_paraphase/m84036_250809_035451_s4.bc2102.paraphase.bam"}
2025-09-15 20:23:41.997 wdl.w:ptcp.w:call-paraphase-05 NOTICE ready :: job: "call-call_f8", callee: "call_f8"
2025-09-15 20:23:41.997 wdl.w:ptcp.w:call-paraphase-33 INFO visit :: node: "output-havanno_json", values: {"havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-33/call-run_paraphase/out/m84036_250809_035451_s4.bc2130.havanno.json"}
2025-09-15 20:23:41.997 wdl.w:ptcp.w:call-paraphase-05 INFO input :: job: "call-call_f8", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "out_prefix": "m84036_250809_035451_s4.bc2102", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-05/call-run_paraphase/out/m84036_250809_035451_s4.bc2102_paraphase/m84036_250809_035451_s4.bc2102.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-05/call-run_paraphase/out/m84036_250809_035451_s4.bc2102_paraphase/m84036_250809_035451_s4.bc2102.paraphase.bam", "sex": "F"}
2025-09-15 20:23:41.997 wdl.w:ptcp.w:call-paraphase-33 INFO visit :: node: "output-paraphase_bam", values: {"paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-33/call-run_paraphase/out/m84036_250809_035451_s4.bc2130_paraphase/m84036_250809_035451_s4.bc2130.paraphase.bam"}
2025-09-15 20:23:41.997 wdl.w:ptcp.w:call-paraphase-33 INFO visit :: node: "output-paraphase_bam_bai", values: {"paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-33/call-run_paraphase/out/m84036_250809_035451_s4.bc2130_paraphase/m84036_250809_035451_s4.bc2130.paraphase.bam.bai"}
2025-09-15 20:23:41.997 wdl.w:ptcp.w:call-paraphase-33 INFO visit :: node: "output-paraphase_json", values: {"paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-33/call-run_paraphase/out/m84036_250809_035451_s4.bc2130_paraphase/m84036_250809_035451_s4.bc2130.paraphase.json"}
2025-09-15 20:23:41.998 wdl.w:ptcp.w:call-paraphase-33 INFO visit :: node: "output-paraphase_vcfs", values: {"paraphase_vcfs": []}
2025-09-15 20:23:41.998 wdl.w:ptcp.w:call-paraphase-05 INFO visit :: node: "output-havanno_json", values: {"havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-05/call-run_paraphase/out/m84036_250809_035451_s4.bc2102.havanno.json"}
2025-09-15 20:23:41.998 wdl.w:ptcp.w:call-paraphase-05 INFO visit :: node: "output-paraphase_bam", values: {"paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-05/call-run_paraphase/out/m84036_250809_035451_s4.bc2102_paraphase/m84036_250809_035451_s4.bc2102.paraphase.bam"}
2025-09-15 20:23:41.998 wdl.w:ptcp.w:call-paraphase-05 INFO visit :: node: "output-paraphase_bam_bai", values: {"paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-05/call-run_paraphase/out/m84036_250809_035451_s4.bc2102_paraphase/m84036_250809_035451_s4.bc2102.paraphase.bam.bai"}
2025-09-15 20:23:41.998 wdl.w:ptcp.w:call-paraphase-05 INFO visit :: node: "output-paraphase_json", values: {"paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-05/call-run_paraphase/out/m84036_250809_035451_s4.bc2102_paraphase/m84036_250809_035451_s4.bc2102.paraphase.json"}
2025-09-15 20:23:41.998 wdl.w:ptcp.w:call-paraphase-05 INFO visit :: node: "output-paraphase_vcfs", values: {"paraphase_vcfs": []}
2025-09-15 20:23:42.003 wdl.w:ptcp.w:call-sawfish-01.t:call-run_sawfish NOTICE task setup :: name: "run_sawfish", source: "./sawfish.wdl", line: 83, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-01/call-run_sawfish", thread: 140610912642624
2025-09-15 20:23:42.007 wdl.w:ptcp.w:call-trgt-08.t:call-trgt_genotype NOTICE task setup :: name: "trgt_genotype", source: "./trgt.wdl", line: 272, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-08/call-trgt_genotype", thread: 140611407550016
2025-09-15 20:23:42.017 wdl.w:ptcp.w:call-trgt-09.t:call-get_reads_overlapping_repeats INFO output :: name: "reads_overlapping_repeats", value: "m84036_250809_035451_s4.bc2106.repeats.bam"
2025-09-15 20:23:42.023 wdl.w:ptcp.w:call-trgt-09.t:call-get_reads_overlapping_repeats INFO output :: name: "reads_overlapping_repeats_bai", value: "m84036_250809_035451_s4.bc2106.repeats.bam.bai"
2025-09-15 20:23:42.031 wdl.w:ptcp.w:call-sawfish-01.t:call-run_sawfish INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:23:42.031 wdl.w:ptcp.w:call-sawfish-01.t:call-run_sawfish INFO input :: name: "genome_version", value: "38"
2025-09-15 20:23:42.031 wdl.w:ptcp.w:call-sawfish-01.t:call-run_sawfish INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:23:42.031 wdl.w:ptcp.w:call-sawfish-01.t:call-run_sawfish INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:23:42.031 wdl.w:ptcp.w:call-sawfish-01.t:call-run_sawfish INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2098.mapped.bam.bai"
2025-09-15 20:23:42.031 wdl.w:ptcp.w:call-sawfish-01.t:call-run_sawfish INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2098.mapped.bam"
2025-09-15 20:23:42.031 wdl.w:ptcp.w:call-sawfish-01.t:call-run_sawfish INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2098"
2025-09-15 20:23:42.031 wdl.w:ptcp.w:call-sawfish-01.t:call-run_sawfish INFO eval :: name: "mem_gb", value: 32
2025-09-15 20:23:42.032 wdl.w:ptcp.w:call-sawfish-01.t:call-run_sawfish INFO eval :: name: "threads", value: 16
2025-09-15 20:23:42.032 wdl.w:ptcp.w:call-sawfish-01.t:call-run_sawfish INFO eval :: name: "disk_size", value: 30
2025-09-15 20:23:42.032 wdl.w:ptcp.w:call-sawfish-01.t:call-run_sawfish INFO eval :: name: "discover_dirname", value: "m84036_250809_035451_s4.bc2098_sawfish_discover"
2025-09-15 20:23:42.032 wdl.w:ptcp.w:call-sawfish-01.t:call-run_sawfish INFO eval :: name: "call_dirname", value: "m84036_250809_035451_s4.bc2098_sawfish"
2025-09-15 20:23:42.032 wdl.w:ptcp.w:call-sawfish-01.t:call-run_sawfish INFO eval :: name: "minimap2_bam_filename", value: "m84036_250809_035451_s4.bc2098.minimap2.bam"
2025-09-15 20:23:42.033 wdl.w:ptcp.w:call-sawfish-01.t:call-run_sawfish INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 16, memory_reservation: 32000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:23:42.033 wdl.w:ptcp.w:call-sawfish-01.t:call-run_sawfish WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:23:42.033 wdl.w:ptcp.w:call-sawfish-01.t:call-run_sawfish INFO provisioned :: seconds_waited: 0, cpu: 16, mem_bytes: 32000000000
2025-09-15 20:23:42.034 wdl.w:ptcp.w:call-sawfish-01.t:call-run_sawfish INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:23:42.040 wdl.w:ptcp.w:call-trgt-08.t:call-trgt_genotype INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:23:42.040 wdl.w:ptcp.w:call-trgt-08.t:call-trgt_genotype INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:23:42.040 wdl.w:ptcp.w:call-trgt-08.t:call-trgt_genotype INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:23:42.040 wdl.w:ptcp.w:call-trgt-08.t:call-trgt_genotype INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:23:42.040 wdl.w:ptcp.w:call-trgt-08.t:call-trgt_genotype INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2105.mapped.bam.bai"
2025-09-15 20:23:42.040 wdl.w:ptcp.w:call-trgt-08.t:call-trgt_genotype INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2105.mapped.bam"
2025-09-15 20:23:42.040 wdl.w:ptcp.w:call-trgt-08.t:call-trgt_genotype INFO input :: name: "sex", value: "F"
2025-09-15 20:23:42.040 wdl.w:ptcp.w:call-trgt-08.t:call-trgt_genotype INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2105"
2025-09-15 20:23:42.041 wdl.w:ptcp.w:call-trgt-08.t:call-trgt_genotype INFO eval :: name: "mem_gb", value: 16
2025-09-15 20:23:42.041 wdl.w:ptcp.w:call-trgt-08.t:call-trgt_genotype INFO eval :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2105.trgt"
2025-09-15 20:23:42.041 wdl.w:ptcp.w:call-trgt-08.t:call-trgt_genotype INFO eval :: name: "threads", value: 8
2025-09-15 20:23:42.041 wdl.w:ptcp.w:call-trgt-08.t:call-trgt_genotype INFO eval :: name: "disk_size", value: 27
2025-09-15 20:23:42.041 wdl.w:ptcp.w:call-trgt-08.t:call-trgt_genotype INFO eval :: name: "karyotype", value: "XX"
2025-09-15 20:23:42.042 wdl.w:ptcp.w:call-trgt-08.t:call-trgt_genotype INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 8, memory_reservation: 16000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:23:42.042 wdl.w:ptcp.w:call-trgt-08.t:call-trgt_genotype WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:23:42.042 wdl.w:ptcp.w:call-trgt-08.t:call-trgt_genotype INFO provisioned :: seconds_waited: 0, cpu: 8, mem_bytes: 16000000000
2025-09-15 20:23:42.042 wdl.w:ptcp.w:call-trgt-08.t:call-trgt_genotype INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:23:42.047 wdl.w:ptcp.w:call-trgt-25.t:call-trgt_genotype INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2122.trgt.vcf"
2025-09-15 20:23:42.054 wdl.w:ptcp.w:call-trgt-25.t:call-trgt_genotype INFO output :: name: "spanning_bam", value: "m84036_250809_035451_s4.bc2122.trgt.sorted.spanning.bam"
2025-09-15 20:23:42.056 wdl.w:ptcp.w:call-trgt-25.t:call-trgt_genotype INFO output :: name: "spanning_bam_bai", value: "m84036_250809_035451_s4.bc2122.trgt.sorted.spanning.bam.bai"
2025-09-15 20:23:42.111 wdl.w:ptcp.w:call-sawfish-01.t:call-run_sawfish INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 10, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-01/call-run_sawfish/_singularity_tmpdir_3cvq07iy"
2025-09-15 20:23:42.111 wdl.w:ptcp.w:call-sawfish-01.t:call-run_sawfish INFO Slurm invocation: srun --job-name call-run_sawfish --partition compute,compute9 --cpus-per-task 16 --mem 30518M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-01/call-run_sawfish/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-01/call-run_sawfish/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-01/call-run_sawfish/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-01/call-run_sawfish/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-01/out/m84036_250809_035451_s4.bc2098.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2098.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-01/out/m84036_250809_035451_s4.bc2098.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2098.mapped.bam.bai:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-01/call-run_sawfish/_singularity_tmpdir_3cvq07iy/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-01/call-run_sawfish/_singularity_tmpdir_3cvq07iy/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:23:42.114 wdl.w:ptcp.w:call-trgt-09.t:call-get_reads_overlapping_repeats NOTICE done
2025-09-15 20:23:42.146 wdl.w:ptcp.w:call-trgt-08.t:call-trgt_genotype INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 11, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-08/call-trgt_genotype/_singularity_tmpdir_2dhm1hlv"
2025-09-15 20:23:42.146 wdl.w:ptcp.w:call-trgt-08.t:call-trgt_genotype INFO Slurm invocation: srun --job-name call-trgt_genotype --partition compute,compute9 --cpus-per-task 8 --mem 15259M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-08/call-trgt_genotype/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-08/call-trgt_genotype/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-08/call-trgt_genotype/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-08/call-trgt_genotype/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-08/out/m84036_250809_035451_s4.bc2105.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2105.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-08/out/m84036_250809_035451_s4.bc2105.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2105.mapped.bam:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-08/call-trgt_genotype/_singularity_tmpdir_2dhm1hlv/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-08/call-trgt_genotype/_singularity_tmpdir_2dhm1hlv/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:23:42.150 wdl.w:ptcp.w:call-trgt-09 NOTICE finish :: job: "call-get_reads_overlapping_repeats"
2025-09-15 20:23:42.150 wdl.w:ptcp.w:call-sawfish-03.t:call-run_sawfish.slurm_singularity INFO srun: job 51797447 queued and waiting for resources
2025-09-15 20:23:42.150 wdl.w:ptcp.w:call-trgt-09 INFO output :: job: "call-get_reads_overlapping_repeats", values: {"reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-09/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2106.repeats.bam.bai", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-09/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2106.repeats.bam"}
2025-09-15 20:23:42.151 wdl.w:ptcp.w:call-sawfish-03.t:call-run_sawfish.slurm_singularity INFO srun: job 51797447 has been allocated resources
2025-09-15 20:23:42.151 wdl.w:ptcp.w:call-trgt-09 INFO visit :: node: "output-reads_overlapping_repeats", values: {"reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-09/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2106.repeats.bam"}
2025-09-15 20:23:42.151 wdl.w:ptcp.w:call-sawfish-03.t:call-run_sawfish.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:42.151 wdl.w:ptcp.w:call-trgt-09 INFO visit :: node: "output-reads_overlapping_repeats_bai", values: {"reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-09/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2106.repeats.bam.bai"}
2025-09-15 20:23:42.151 wdl.w:ptcp.w:call-sawfish-03.t:call-run_sawfish.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:23:42.153 wdl.w:ptcp.w:call-paraphase-03.t:call-run_paraphase.slurm_singularity INFO srun: job 51797448 queued and waiting for resources
2025-09-15 20:23:42.154 wdl.w:ptcp.w:call-paraphase-03.t:call-run_paraphase.slurm_singularity INFO srun: job 51797448 has been allocated resources
2025-09-15 20:23:42.154 wdl.w:ptcp.w:call-paraphase-03.t:call-run_paraphase.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:42.154 wdl.w:ptcp.w:call-paraphase-03.t:call-run_paraphase.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:23:42.159 wdl.w:ptcp.w:call-sawfish-01.t:call-run_sawfish NOTICE slurm_singularity run :: pid: 1199999, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-01/call-run_sawfish/slurm_singularity.log.txt"
2025-09-15 20:23:42.158 wdl.w:ptcp.w:call-trgt-01.t:call-get_reads_overlapping_repeats NOTICE task setup :: name: "get_reads_overlapping_repeats", source: "./trgt.wdl", line: 182, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-01/call-get_reads_overlapping_repeats", thread: 140609310422592
2025-09-15 20:23:42.161 wdl.w:ptcp.w:call-trgt-08.t:call-trgt_genotype NOTICE slurm_singularity run :: pid: 1200001, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-08/call-trgt_genotype/slurm_singularity.log.txt"
2025-09-15 20:23:42.181 wdl.w:ptcp.w:call-trgt-01.t:call-get_reads_overlapping_repeats INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:23:42.181 wdl.w:ptcp.w:call-trgt-01.t:call-get_reads_overlapping_repeats INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:23:42.181 wdl.w:ptcp.w:call-trgt-01.t:call-get_reads_overlapping_repeats INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2098.mapped.bam.bai"
2025-09-15 20:23:42.181 wdl.w:ptcp.w:call-trgt-01.t:call-get_reads_overlapping_repeats INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2098.mapped.bam"
2025-09-15 20:23:42.181 wdl.w:ptcp.w:call-trgt-01.t:call-get_reads_overlapping_repeats INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2098"
2025-09-15 20:23:42.182 wdl.w:ptcp.w:call-trgt-01.t:call-get_reads_overlapping_repeats INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:23:42.182 wdl.w:ptcp.w:call-trgt-01.t:call-get_reads_overlapping_repeats INFO eval :: name: "expand_size", value: 3000
2025-09-15 20:23:42.182 wdl.w:ptcp.w:call-trgt-01.t:call-get_reads_overlapping_repeats INFO eval :: name: "threads", value: 1
2025-09-15 20:23:42.182 wdl.w:ptcp.w:call-trgt-01.t:call-get_reads_overlapping_repeats INFO eval :: name: "expanded_bed_name", value: "m84036_250809_035451_s4.bc2098.expanded.bed"
2025-09-15 20:23:42.182 wdl.w:ptcp.w:call-trgt-01.t:call-get_reads_overlapping_repeats INFO eval :: name: "disk_size", value: 11
2025-09-15 20:23:42.182 wdl.w:ptcp.w:call-trgt-01.t:call-get_reads_overlapping_repeats INFO eval :: name: "output_name", value: "m84036_250809_035451_s4.bc2098.repeats.bam"
2025-09-15 20:23:42.182 wdl.w:ptcp.w:call-trgt-01.t:call-get_reads_overlapping_repeats INFO eval :: name: "index_name", value: "m84036_250809_035451_s4.bc2098.repeats.bam.bai"
2025-09-15 20:23:42.182 wdl.w:ptcp.w:call-trgt-01.t:call-get_reads_overlapping_repeats INFO eval :: name: "output_name_with_index", value: "m84036_250809_035451_s4.bc2098.repeats.bam##idx##m84036_250809_035451_s4.bc2098.repeats.bam.bai"
2025-09-15 20:23:42.182 wdl.w:ptcp.w:call-trgt-25.t:call-trgt_genotype NOTICE done
2025-09-15 20:23:42.183 wdl.w:ptcp.w:call-trgt-01.t:call-get_reads_overlapping_repeats INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:23:42.183 wdl.w:ptcp.w:call-trgt-01.t:call-get_reads_overlapping_repeats WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:23:42.183 wdl.w:ptcp.w:call-trgt-01.t:call-get_reads_overlapping_repeats INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:23:42.183 wdl.w:ptcp.w:call-trgt-01.t:call-get_reads_overlapping_repeats INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:23:42.191 wdl.w:ptcp.w:call-trgt-25 NOTICE finish :: job: "call-trgt_genotype"
2025-09-15 20:23:42.191 wdl.w:ptcp.w:call-trgt-25 INFO output :: job: "call-trgt_genotype", values: {"spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-25/call-trgt_genotype/out/m84036_250809_035451_s4.bc2122.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-25/call-trgt_genotype/out/m84036_250809_035451_s4.bc2122.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-25/call-trgt_genotype/out/m84036_250809_035451_s4.bc2122.trgt.vcf"}
2025-09-15 20:23:42.192 wdl.w:ptcp.w:call-trgt-25 NOTICE ready :: job: "call-trgt_plot_meth_allele", callee: "trgt_plot"
2025-09-15 20:23:42.192 wdl.w:ptcp.w:call-trgt-25 INFO input :: job: "call-trgt_plot_meth_allele", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": false, "methylation": true, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-25/call-trgt_genotype/out/m84036_250809_035451_s4.bc2122.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-25/call-trgt_genotype/out/m84036_250809_035451_s4.bc2122.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-25/call-trgt_genotype/out/m84036_250809_035451_s4.bc2122.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2122"}
2025-09-15 20:23:42.193 wdl.w:ptcp.w:call-trgt-25 NOTICE ready :: job: "call-trgt_plot_meth_waterfall", callee: "trgt_plot"
2025-09-15 20:23:42.193 wdl.w:ptcp.w:call-trgt-25 INFO input :: job: "call-trgt_plot_meth_waterfall", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": true, "methylation": true, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-25/call-trgt_genotype/out/m84036_250809_035451_s4.bc2122.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-25/call-trgt_genotype/out/m84036_250809_035451_s4.bc2122.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-25/call-trgt_genotype/out/m84036_250809_035451_s4.bc2122.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2122"}
2025-09-15 20:23:42.194 wdl.w:ptcp.w:call-trgt-25 NOTICE ready :: job: "call-trgt_plot_motifs_allele", callee: "trgt_plot"
2025-09-15 20:23:42.194 wdl.w:ptcp.w:call-trgt-25 INFO input :: job: "call-trgt_plot_motifs_allele", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": false, "methylation": false, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-25/call-trgt_genotype/out/m84036_250809_035451_s4.bc2122.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-25/call-trgt_genotype/out/m84036_250809_035451_s4.bc2122.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-25/call-trgt_genotype/out/m84036_250809_035451_s4.bc2122.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2122"}
2025-09-15 20:23:42.195 wdl.w:ptcp.w:call-trgt-25 NOTICE ready :: job: "call-trgt_plot_motifs_waterfall", callee: "trgt_plot"
2025-09-15 20:23:42.195 wdl.w:ptcp.w:call-trgt-25 INFO input :: job: "call-trgt_plot_motifs_waterfall", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": true, "methylation": false, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-25/call-trgt_genotype/out/m84036_250809_035451_s4.bc2122.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-25/call-trgt_genotype/out/m84036_250809_035451_s4.bc2122.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-25/call-trgt_genotype/out/m84036_250809_035451_s4.bc2122.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2122"}
2025-09-15 20:23:42.195 wdl.w:ptcp.w:call-trgt-25 INFO visit :: node: "output-spanning_bam", values: {"spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-25/call-trgt_genotype/out/m84036_250809_035451_s4.bc2122.trgt.sorted.spanning.bam"}
2025-09-15 20:23:42.195 wdl.w:ptcp.w:call-trgt-25 INFO visit :: node: "output-spanning_bam_bai", values: {"spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-25/call-trgt_genotype/out/m84036_250809_035451_s4.bc2122.trgt.sorted.spanning.bam.bai"}
2025-09-15 20:23:42.195 wdl.w:ptcp.w:call-trgt-25 INFO visit :: node: "output-vcf", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-25/call-trgt_genotype/out/m84036_250809_035451_s4.bc2122.trgt.vcf"}
2025-09-15 20:23:42.199 wdl.w:ptcp.w:call-paraphase-01.t:call-run_paraphase NOTICE task setup :: name: "run_paraphase", source: "./paraphase.wdl", line: 127, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-01/call-run_paraphase", thread: 140612506469952
2025-09-15 20:23:42.212 wdl.w:ptcp.w:call-trgt-03.t:call-get_reads_overlapping_repeats.slurm_singularity INFO srun: job 51797449 queued and waiting for resources
2025-09-15 20:23:42.212 wdl.w:ptcp.w:call-trgt-03.t:call-get_reads_overlapping_repeats.slurm_singularity INFO srun: job 51797449 has been allocated resources
2025-09-15 20:23:42.212 wdl.w:ptcp.w:call-trgt-03.t:call-get_reads_overlapping_repeats.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:42.212 wdl.w:ptcp.w:call-trgt-03.t:call-get_reads_overlapping_repeats.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:23:42.227 wdl.w:ptcp.w:call-paraphase-01.t:call-run_paraphase INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:23:42.227 wdl.w:ptcp.w:call-paraphase-01.t:call-run_paraphase INFO input :: name: "annotation_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf"
2025-09-15 20:23:42.227 wdl.w:ptcp.w:call-paraphase-01.t:call-run_paraphase INFO input :: name: "genome_version", value: "38"
2025-09-15 20:23:42.227 wdl.w:ptcp.w:call-paraphase-01.t:call-run_paraphase INFO input :: name: "config_file", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/paraphase_config.GRCh38.yaml"
2025-09-15 20:23:42.227 wdl.w:ptcp.w:call-paraphase-01.t:call-run_paraphase INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:23:42.227 wdl.w:ptcp.w:call-paraphase-01.t:call-run_paraphase INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:23:42.227 wdl.w:ptcp.w:call-paraphase-01.t:call-run_paraphase INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2098.mapped.bam.bai"
2025-09-15 20:23:42.228 wdl.w:ptcp.w:call-paraphase-01.t:call-run_paraphase INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2098.mapped.bam"
2025-09-15 20:23:42.228 wdl.w:ptcp.w:call-paraphase-01.t:call-run_paraphase INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2098"
2025-09-15 20:23:42.228 wdl.w:ptcp.w:call-paraphase-01.t:call-run_paraphase INFO eval :: name: "threads", value: 4
2025-09-15 20:23:42.228 wdl.w:ptcp.w:call-paraphase-01.t:call-run_paraphase INFO eval :: name: "mem_gb", value: 8
2025-09-15 20:23:42.228 wdl.w:ptcp.w:call-paraphase-01.t:call-run_paraphase INFO eval :: name: "disk_size", value: 27
2025-09-15 20:23:42.228 wdl.w:ptcp.w:call-paraphase-01.t:call-run_paraphase INFO eval :: name: "out_dir", value: "m84036_250809_035451_s4.bc2098_paraphase"
2025-09-15 20:23:42.229 wdl.w:ptcp.w:call-paraphase-01.t:call-run_paraphase INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 4, memory_reservation: 8000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:23:42.229 wdl.w:ptcp.w:call-paraphase-01.t:call-run_paraphase WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:23:42.229 wdl.w:ptcp.w:call-paraphase-01.t:call-run_paraphase INFO provisioned :: seconds_waited: 0, cpu: 4, mem_bytes: 8000000000
2025-09-15 20:23:42.229 wdl.w:ptcp.w:call-paraphase-01.t:call-run_paraphase INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:23:42.250 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_genotype INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2099.trgt.vcf"
2025-09-15 20:23:42.254 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_genotype INFO output :: name: "spanning_bam", value: "m84036_250809_035451_s4.bc2099.trgt.sorted.spanning.bam"
2025-09-15 20:23:42.255 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_genotype INFO output :: name: "spanning_bam_bai", value: "m84036_250809_035451_s4.bc2099.trgt.sorted.spanning.bam.bai"
2025-09-15 20:23:42.258 wdl.w:ptcp.w:call-trgt-01.t:call-get_reads_overlapping_repeats INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 9, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-01/call-get_reads_overlapping_repeats/_singularity_tmpdir_cdwmoc38"
2025-09-15 20:23:42.258 wdl.w:ptcp.w:call-trgt-01.t:call-get_reads_overlapping_repeats INFO Slurm invocation: srun --job-name call-get_reads_overlapping_repeats --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-01/call-get_reads_overlapping_repeats/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-01/call-get_reads_overlapping_repeats/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-01/call-get_reads_overlapping_repeats/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-01/call-get_reads_overlapping_repeats/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-01/out/m84036_250809_035451_s4.bc2098.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2098.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-01/out/m84036_250809_035451_s4.bc2098.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2098.mapped.bam.bai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-01/call-get_reads_overlapping_repeats/_singularity_tmpdir_cdwmoc38/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-01/call-get_reads_overlapping_repeats/_singularity_tmpdir_cdwmoc38/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:23:42.287 wdl.w:ptcp.w:call-trgt-01.t:call-get_reads_overlapping_repeats NOTICE slurm_singularity run :: pid: 1200004, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-01/call-get_reads_overlapping_repeats/slurm_singularity.log.txt"
2025-09-15 20:23:42.294 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_genotype.slurm_singularity INFO srun: job 51797450 queued and waiting for resources
2025-09-15 20:23:42.294 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_genotype.slurm_singularity INFO srun: job 51797450 has been allocated resources
2025-09-15 20:23:42.294 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_genotype.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:42.294 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_genotype.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:23:42.306 wdl.w:ptcp.w:call-paraphase-08.t:call-run_paraphase.slurm_singularity INFO srun: job 51797451 queued and waiting for resources
2025-09-15 20:23:42.306 wdl.w:ptcp.w:call-paraphase-08.t:call-run_paraphase.slurm_singularity INFO srun: job 51797451 has been allocated resources
2025-09-15 20:23:42.306 wdl.w:ptcp.w:call-paraphase-08.t:call-run_paraphase.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:42.317 wdl.w:ptcp.w:call-paraphase-01.t:call-run_paraphase INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-01/call-run_paraphase/_singularity_tmpdir_mi2z6qk5"
2025-09-15 20:23:42.318 wdl.w:ptcp.w:call-paraphase-01.t:call-run_paraphase INFO Slurm invocation: srun --job-name call-run_paraphase --partition compute,compute9 --cpus-per-task 4 --mem 7629M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-01/call-run_paraphase/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-01/call-run_paraphase/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-01/call-run_paraphase/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-01/call-run_paraphase/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/variant_list/variant_list.GRCh38.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-01/out/m84036_250809_035451_s4.bc2098.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2098.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-01/out/m84036_250809_035451_s4.bc2098.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2098.mapped.bam.bai:ro --bind /ptcp/meta/paraphase/paraphase_config.GRCh38.yaml:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/paraphase_config.GRCh38.yaml:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-01/call-run_paraphase/_singularity_tmpdir_mi2z6qk5/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-01/call-run_paraphase/_singularity_tmpdir_mi2z6qk5/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:23:42.332 wdl.w:ptcp.w:call-paraphase-01.t:call-run_paraphase NOTICE slurm_singularity run :: pid: 1200007, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-01/call-run_paraphase/slurm_singularity.log.txt"
2025-09-15 20:23:42.340 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_genotype NOTICE done
2025-09-15 20:23:42.359 wdl.w:ptcp.w:call-trgt-02 NOTICE finish :: job: "call-trgt_genotype"
2025-09-15 20:23:42.359 wdl.w:ptcp.w:call-trgt-02 INFO output :: job: "call-trgt_genotype", values: {"spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-02/call-trgt_genotype/out/m84036_250809_035451_s4.bc2099.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-02/call-trgt_genotype/out/m84036_250809_035451_s4.bc2099.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-02/call-trgt_genotype/out/m84036_250809_035451_s4.bc2099.trgt.vcf"}
2025-09-15 20:23:42.360 wdl.w:ptcp.w:call-trgt-02 NOTICE ready :: job: "call-trgt_plot_meth_allele", callee: "trgt_plot"
2025-09-15 20:23:42.360 wdl.w:ptcp.w:call-trgt-02 INFO input :: job: "call-trgt_plot_meth_allele", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": false, "methylation": true, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-02/call-trgt_genotype/out/m84036_250809_035451_s4.bc2099.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-02/call-trgt_genotype/out/m84036_250809_035451_s4.bc2099.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-02/call-trgt_genotype/out/m84036_250809_035451_s4.bc2099.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2099"}
2025-09-15 20:23:42.361 wdl.w:ptcp.w:call-trgt-02 NOTICE ready :: job: "call-trgt_plot_meth_waterfall", callee: "trgt_plot"
2025-09-15 20:23:42.361 wdl.w:ptcp.w:call-trgt-02 INFO input :: job: "call-trgt_plot_meth_waterfall", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": true, "methylation": true, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-02/call-trgt_genotype/out/m84036_250809_035451_s4.bc2099.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-02/call-trgt_genotype/out/m84036_250809_035451_s4.bc2099.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-02/call-trgt_genotype/out/m84036_250809_035451_s4.bc2099.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2099"}
2025-09-15 20:23:42.362 wdl.w:ptcp.w:call-trgt-02 NOTICE ready :: job: "call-trgt_plot_motifs_allele", callee: "trgt_plot"
2025-09-15 20:23:42.362 wdl.w:ptcp.w:call-trgt-02 INFO input :: job: "call-trgt_plot_motifs_allele", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": false, "methylation": false, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-02/call-trgt_genotype/out/m84036_250809_035451_s4.bc2099.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-02/call-trgt_genotype/out/m84036_250809_035451_s4.bc2099.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-02/call-trgt_genotype/out/m84036_250809_035451_s4.bc2099.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2099"}
2025-09-15 20:23:42.364 wdl.w:ptcp.w:call-trgt-02 NOTICE ready :: job: "call-trgt_plot_motifs_waterfall", callee: "trgt_plot"
2025-09-15 20:23:42.364 wdl.w:ptcp.w:call-trgt-02 INFO input :: job: "call-trgt_plot_motifs_waterfall", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": true, "methylation": false, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-02/call-trgt_genotype/out/m84036_250809_035451_s4.bc2099.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-02/call-trgt_genotype/out/m84036_250809_035451_s4.bc2099.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-02/call-trgt_genotype/out/m84036_250809_035451_s4.bc2099.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2099"}
2025-09-15 20:23:42.365 wdl.w:ptcp.w:call-trgt-02 INFO visit :: node: "output-spanning_bam", values: {"spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-02/call-trgt_genotype/out/m84036_250809_035451_s4.bc2099.trgt.sorted.spanning.bam"}
2025-09-15 20:23:42.365 wdl.w:ptcp.w:call-trgt-02 INFO visit :: node: "output-spanning_bam_bai", values: {"spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-02/call-trgt_genotype/out/m84036_250809_035451_s4.bc2099.trgt.sorted.spanning.bam.bai"}
2025-09-15 20:23:42.365 wdl.w:ptcp.w:call-trgt-02 INFO visit :: node: "output-vcf", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-02/call-trgt_genotype/out/m84036_250809_035451_s4.bc2099.trgt.vcf"}
2025-09-15 20:23:42.368 wdl.w:ptcp.w:call-trgt-01.t:call-trgt_genotype NOTICE task setup :: name: "trgt_genotype", source: "./trgt.wdl", line: 272, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-01/call-trgt_genotype", thread: 140610887464512
2025-09-15 20:23:42.376 wdl.w:ptcp.w:call-trgt-03.t:call-get_reads_overlapping_repeats INFO output :: name: "reads_overlapping_repeats", value: "m84036_250809_035451_s4.bc2100.repeats.bam"
2025-09-15 20:23:42.379 wdl.w:ptcp.w:call-trgt-03.t:call-get_reads_overlapping_repeats INFO output :: name: "reads_overlapping_repeats_bai", value: "m84036_250809_035451_s4.bc2100.repeats.bam.bai"
2025-09-15 20:23:42.388 wdl.w:ptcp.w:call-trgt-01.t:call-trgt_genotype INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:23:42.388 wdl.w:ptcp.w:call-trgt-01.t:call-trgt_genotype INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:23:42.388 wdl.w:ptcp.w:call-trgt-01.t:call-trgt_genotype INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:23:42.388 wdl.w:ptcp.w:call-trgt-01.t:call-trgt_genotype INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:23:42.388 wdl.w:ptcp.w:call-trgt-01.t:call-trgt_genotype INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2098.mapped.bam.bai"
2025-09-15 20:23:42.388 wdl.w:ptcp.w:call-trgt-01.t:call-trgt_genotype INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2098.mapped.bam"
2025-09-15 20:23:42.388 wdl.w:ptcp.w:call-trgt-01.t:call-trgt_genotype INFO input :: name: "sex", value: "F"
2025-09-15 20:23:42.388 wdl.w:ptcp.w:call-trgt-01.t:call-trgt_genotype INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2098"
2025-09-15 20:23:42.388 wdl.w:ptcp.w:call-trgt-01.t:call-trgt_genotype INFO eval :: name: "mem_gb", value: 16
2025-09-15 20:23:42.389 wdl.w:ptcp.w:call-trgt-01.t:call-trgt_genotype INFO eval :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2098.trgt"
2025-09-15 20:23:42.389 wdl.w:ptcp.w:call-trgt-01.t:call-trgt_genotype INFO eval :: name: "threads", value: 8
2025-09-15 20:23:42.389 wdl.w:ptcp.w:call-trgt-01.t:call-trgt_genotype INFO eval :: name: "disk_size", value: 27
2025-09-15 20:23:42.389 wdl.w:ptcp.w:call-trgt-01.t:call-trgt_genotype INFO eval :: name: "karyotype", value: "XX"
2025-09-15 20:23:42.389 wdl.w:ptcp.w:call-trgt-01.t:call-trgt_genotype INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 8, memory_reservation: 16000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:23:42.389 wdl.w:ptcp.w:call-trgt-01.t:call-trgt_genotype WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:23:42.390 wdl.w:ptcp.w:call-trgt-01.t:call-trgt_genotype INFO provisioned :: seconds_waited: 0, cpu: 8, mem_bytes: 16000000000
2025-09-15 20:23:42.390 wdl.w:ptcp.w:call-trgt-01.t:call-trgt_genotype INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:23:42.410 wdl.w:ptcp.w:call-sawfish-08.t:call-run_sawfish.stderr VERBOSE [M::bam2fq_mainloop] discarded 0 singletons
2025-09-15 20:23:42.410 wdl.w:ptcp.w:call-sawfish-08.t:call-run_sawfish.stderr VERBOSE [M::bam2fq_mainloop] processed 0 reads
2025-09-15 20:23:42.421 wdl.w:ptcp.w:call-sawfish-08.t:call-run_sawfish.slurm_singularity INFO srun: job 51797452 queued and waiting for resources
2025-09-15 20:23:42.421 wdl.w:ptcp.w:call-sawfish-08.t:call-run_sawfish.slurm_singularity INFO srun: job 51797452 has been allocated resources
2025-09-15 20:23:42.421 wdl.w:ptcp.w:call-sawfish-08.t:call-run_sawfish.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:42.421 wdl.w:ptcp.w:call-sawfish-08.t:call-run_sawfish.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:23:42.448 wdl.w:ptcp.w:call-trgt-03.t:call-get_reads_overlapping_repeats NOTICE done
2025-09-15 20:23:42.452 wdl.w:ptcp.w:call-trgt-03 NOTICE finish :: job: "call-get_reads_overlapping_repeats"
2025-09-15 20:23:42.453 wdl.w:ptcp.w:call-trgt-03 INFO output :: job: "call-get_reads_overlapping_repeats", values: {"reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-03/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2100.repeats.bam.bai", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-03/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2100.repeats.bam"}
2025-09-15 20:23:42.453 wdl.w:ptcp.w:call-trgt-03 INFO visit :: node: "output-reads_overlapping_repeats", values: {"reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-03/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2100.repeats.bam"}
2025-09-15 20:23:42.453 wdl.w:ptcp.w:call-trgt-03 INFO visit :: node: "output-reads_overlapping_repeats_bai", values: {"reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-03/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2100.repeats.bam.bai"}
2025-09-15 20:23:42.462 wdl.w:ptcp.w:call-paraphase-00.t:call-run_paraphase NOTICE task setup :: name: "run_paraphase", source: "./paraphase.wdl", line: 127, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-00/call-run_paraphase", thread: 140611424335424
2025-09-15 20:23:42.463 wdl.w:ptcp.w:call-trgt-01.t:call-trgt_genotype INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 11, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-01/call-trgt_genotype/_singularity_tmpdir_l4sbdzrj"
2025-09-15 20:23:42.463 wdl.w:ptcp.w:call-trgt-01.t:call-trgt_genotype INFO Slurm invocation: srun --job-name call-trgt_genotype --partition compute,compute9 --cpus-per-task 8 --mem 15259M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-01/call-trgt_genotype/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-01/call-trgt_genotype/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-01/call-trgt_genotype/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-01/call-trgt_genotype/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-01/out/m84036_250809_035451_s4.bc2098.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2098.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-01/out/m84036_250809_035451_s4.bc2098.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2098.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-01/call-trgt_genotype/_singularity_tmpdir_l4sbdzrj/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-01/call-trgt_genotype/_singularity_tmpdir_l4sbdzrj/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:23:42.482 wdl.w:ptcp.w:call-trgt-01.t:call-trgt_genotype NOTICE slurm_singularity run :: pid: 1200024, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-01/call-trgt_genotype/slurm_singularity.log.txt"
2025-09-15 20:23:42.485 wdl.w:ptcp.w:call-paraphase-00.t:call-run_paraphase INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:23:42.485 wdl.w:ptcp.w:call-paraphase-00.t:call-run_paraphase INFO input :: name: "annotation_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf"
2025-09-15 20:23:42.486 wdl.w:ptcp.w:call-paraphase-00.t:call-run_paraphase INFO input :: name: "genome_version", value: "38"
2025-09-15 20:23:42.486 wdl.w:ptcp.w:call-paraphase-00.t:call-run_paraphase INFO input :: name: "config_file", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/paraphase_config.GRCh38.yaml"
2025-09-15 20:23:42.486 wdl.w:ptcp.w:call-paraphase-00.t:call-run_paraphase INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:23:42.486 wdl.w:ptcp.w:call-paraphase-00.t:call-run_paraphase INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:23:42.486 wdl.w:ptcp.w:call-paraphase-00.t:call-run_paraphase INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2097.mapped.bam.bai"
2025-09-15 20:23:42.486 wdl.w:ptcp.w:call-paraphase-00.t:call-run_paraphase INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2097.mapped.bam"
2025-09-15 20:23:42.486 wdl.w:ptcp.w:call-paraphase-00.t:call-run_paraphase INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2097"
2025-09-15 20:23:42.486 wdl.w:ptcp.w:call-paraphase-00.t:call-run_paraphase INFO eval :: name: "threads", value: 4
2025-09-15 20:23:42.486 wdl.w:ptcp.w:call-paraphase-00.t:call-run_paraphase INFO eval :: name: "mem_gb", value: 8
2025-09-15 20:23:42.486 wdl.w:ptcp.w:call-paraphase-00.t:call-run_paraphase INFO eval :: name: "disk_size", value: 27
2025-09-15 20:23:42.487 wdl.w:ptcp.w:call-paraphase-00.t:call-run_paraphase INFO eval :: name: "out_dir", value: "m84036_250809_035451_s4.bc2097_paraphase"
2025-09-15 20:23:42.487 wdl.w:ptcp.w:call-paraphase-00.t:call-run_paraphase INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 4, memory_reservation: 8000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:23:42.487 wdl.w:ptcp.w:call-paraphase-00.t:call-run_paraphase WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:23:42.487 wdl.w:ptcp.w:call-paraphase-00.t:call-run_paraphase INFO provisioned :: seconds_waited: 0, cpu: 4, mem_bytes: 8000000000
2025-09-15 20:23:42.488 wdl.w:ptcp.w:call-paraphase-00.t:call-run_paraphase INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:23:42.522 wdl.w:ptcp.w:call-paraphase-21.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for hbb for sample m84036_250809_035451_s4.bc2118 at 2025-09-15 20:23:39.776016...
2025-09-15 20:23:42.523 wdl.w:ptcp.w:call-paraphase-21.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for f8inv22 for sample m84036_250809_035451_s4.bc2118 at 2025-09-15 20:23:39.782477...
2025-09-15 20:23:42.523 wdl.w:ptcp.w:call-paraphase-21.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for rpgr for sample m84036_250809_035451_s4.bc2118 at 2025-09-15 20:23:39.913283...
2025-09-15 20:23:42.523 wdl.w:ptcp.w:call-paraphase-21.t:call-run_paraphase.stderr VERBOSE WARNING:root:This region does not appear to have coverage. Will not attempt to phase haplotypes.
2025-09-15 20:23:42.523 wdl.w:ptcp.w:call-paraphase-21.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for f8inv22 for sample m84036_250809_035451_s4.bc2118 at 2025-09-15 20:23:39.924970...
2025-09-15 20:23:42.523 wdl.w:ptcp.w:call-paraphase-21.t:call-run_paraphase.stderr VERBOSE WARNING:root:This region does not appear to have coverage. Will not attempt to phase haplotypes.
2025-09-15 20:23:42.523 wdl.w:ptcp.w:call-paraphase-21.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for hbb for sample m84036_250809_035451_s4.bc2118 at 2025-09-15 20:23:39.936733...
2025-09-15 20:23:42.523 wdl.w:ptcp.w:call-paraphase-21.t:call-run_paraphase.stderr VERBOSE WARNING:root:This region does not appear to have coverage. Will not attempt to phase haplotypes.
2025-09-15 20:23:42.523 wdl.w:ptcp.w:call-paraphase-21.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for rpgr for sample m84036_250809_035451_s4.bc2118 at 2025-09-15 20:23:40.049805...
2025-09-15 20:23:42.523 wdl.w:ptcp.w:call-paraphase-21.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for smn1 for sample m84036_250809_035451_s4.bc2118 at 2025-09-15 20:23:40.599209...
2025-09-15 20:23:42.523 wdl.w:ptcp.w:call-paraphase-21.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for f8inv1 for sample m84036_250809_035451_s4.bc2118 at 2025-09-15 20:23:40.696295...
2025-09-15 20:23:42.523 wdl.w:ptcp.w:call-paraphase-21.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for f8inv1 for sample m84036_250809_035451_s4.bc2118 at 2025-09-15 20:23:40.696479...
2025-09-15 20:23:42.523 wdl.w:ptcp.w:call-paraphase-21.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for f8inv22 for sample m84036_250809_035451_s4.bc2118 at 2025-09-15 20:23:40.826058...
2025-09-15 20:23:42.523 wdl.w:ptcp.w:call-paraphase-21.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for hbb for sample m84036_250809_035451_s4.bc2118 at 2025-09-15 20:23:40.846138...
2025-09-15 20:23:42.523 wdl.w:ptcp.w:call-paraphase-21.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for rpgr for sample m84036_250809_035451_s4.bc2118 at 2025-09-15 20:23:40.927511...
2025-09-15 20:23:42.523 wdl.w:ptcp.w:call-paraphase-21.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for f8inv1 for sample m84036_250809_035451_s4.bc2118 at 2025-09-15 20:23:41.517972...
2025-09-15 20:23:42.523 wdl.w:ptcp.w:call-paraphase-21.t:call-run_paraphase.stderr VERBOSE WARNING:root:This region does not appear to have coverage. Will not attempt to phase haplotypes.
2025-09-15 20:23:42.523 wdl.w:ptcp.w:call-paraphase-21.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for f8inv1 for sample m84036_250809_035451_s4.bc2118 at 2025-09-15 20:23:41.652703...
2025-09-15 20:23:42.524 wdl.w:ptcp.w:call-paraphase-21.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for f8inv1 for sample m84036_250809_035451_s4.bc2118 at 2025-09-15 20:23:42.247414...
2025-09-15 20:23:42.540 wdl.w:ptcp.w:call-trgt-08.t:call-get_reads_overlapping_repeats.slurm_singularity INFO srun: job 51797453 queued and waiting for resources
2025-09-15 20:23:42.540 wdl.w:ptcp.w:call-trgt-08.t:call-get_reads_overlapping_repeats.slurm_singularity INFO srun: job 51797453 has been allocated resources
2025-09-15 20:23:42.541 wdl.w:ptcp.w:call-trgt-08.t:call-get_reads_overlapping_repeats.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:42.555 wdl.w:ptcp.w:call-paraphase-00.t:call-run_paraphase INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-00/call-run_paraphase/_singularity_tmpdir_6iput19v"
2025-09-15 20:23:42.556 wdl.w:ptcp.w:call-paraphase-00.t:call-run_paraphase INFO Slurm invocation: srun --job-name call-run_paraphase --partition compute,compute9 --cpus-per-task 4 --mem 7629M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-00/call-run_paraphase/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-00/call-run_paraphase/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-00/call-run_paraphase/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-00/call-run_paraphase/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-00/out/m84036_250809_035451_s4.bc2097.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2097.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-00/out/m84036_250809_035451_s4.bc2097.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2097.mapped.bam:ro --bind /ptcp/meta/variant_list/variant_list.GRCh38.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf:ro --bind /ptcp/meta/paraphase/paraphase_config.GRCh38.yaml:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/paraphase_config.GRCh38.yaml:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-00/call-run_paraphase/_singularity_tmpdir_6iput19v/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-00/call-run_paraphase/_singularity_tmpdir_6iput19v/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:23:42.573 wdl.w:ptcp.w:call-paraphase-00.t:call-run_paraphase NOTICE slurm_singularity run :: pid: 1200037, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-00/call-run_paraphase/slurm_singularity.log.txt"
2025-09-15 20:23:42.616 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_genotype INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2100.trgt.vcf"
2025-09-15 20:23:42.620 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_genotype INFO output :: name: "spanning_bam", value: "m84036_250809_035451_s4.bc2100.trgt.sorted.spanning.bam"
2025-09-15 20:23:42.621 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_genotype INFO output :: name: "spanning_bam_bai", value: "m84036_250809_035451_s4.bc2100.trgt.sorted.spanning.bam.bai"
2025-09-15 20:23:42.705 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_genotype NOTICE done
2025-09-15 20:23:42.717 wdl.w:ptcp.w:call-trgt-03 NOTICE finish :: job: "call-trgt_genotype"
2025-09-15 20:23:42.718 wdl.w:ptcp.w:call-trgt-03 INFO output :: job: "call-trgt_genotype", values: {"spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-03/call-trgt_genotype/out/m84036_250809_035451_s4.bc2100.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-03/call-trgt_genotype/out/m84036_250809_035451_s4.bc2100.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-03/call-trgt_genotype/out/m84036_250809_035451_s4.bc2100.trgt.vcf"}
2025-09-15 20:23:42.718 wdl.w:ptcp.w:call-trgt-03 NOTICE ready :: job: "call-trgt_plot_meth_allele", callee: "trgt_plot"
2025-09-15 20:23:42.718 wdl.w:ptcp.w:call-trgt-03 INFO input :: job: "call-trgt_plot_meth_allele", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": false, "methylation": true, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-03/call-trgt_genotype/out/m84036_250809_035451_s4.bc2100.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-03/call-trgt_genotype/out/m84036_250809_035451_s4.bc2100.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-03/call-trgt_genotype/out/m84036_250809_035451_s4.bc2100.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2100"}
2025-09-15 20:23:42.719 wdl.w:ptcp.w:call-trgt-03 NOTICE ready :: job: "call-trgt_plot_meth_waterfall", callee: "trgt_plot"
2025-09-15 20:23:42.719 wdl.w:ptcp.w:call-trgt-03 INFO input :: job: "call-trgt_plot_meth_waterfall", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": true, "methylation": true, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-03/call-trgt_genotype/out/m84036_250809_035451_s4.bc2100.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-03/call-trgt_genotype/out/m84036_250809_035451_s4.bc2100.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-03/call-trgt_genotype/out/m84036_250809_035451_s4.bc2100.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2100"}
2025-09-15 20:23:42.720 wdl.w:ptcp.w:call-trgt-03 NOTICE ready :: job: "call-trgt_plot_motifs_allele", callee: "trgt_plot"
2025-09-15 20:23:42.720 wdl.w:ptcp.w:call-trgt-03 INFO input :: job: "call-trgt_plot_motifs_allele", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": false, "methylation": false, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-03/call-trgt_genotype/out/m84036_250809_035451_s4.bc2100.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-03/call-trgt_genotype/out/m84036_250809_035451_s4.bc2100.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-03/call-trgt_genotype/out/m84036_250809_035451_s4.bc2100.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2100"}
2025-09-15 20:23:42.721 wdl.w:ptcp.w:call-trgt-03 NOTICE ready :: job: "call-trgt_plot_motifs_waterfall", callee: "trgt_plot"
2025-09-15 20:23:42.721 wdl.w:ptcp.w:call-trgt-03 INFO input :: job: "call-trgt_plot_motifs_waterfall", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": true, "methylation": false, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-03/call-trgt_genotype/out/m84036_250809_035451_s4.bc2100.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-03/call-trgt_genotype/out/m84036_250809_035451_s4.bc2100.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-03/call-trgt_genotype/out/m84036_250809_035451_s4.bc2100.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2100"}
2025-09-15 20:23:42.722 wdl.w:ptcp.w:call-trgt-03 INFO visit :: node: "output-spanning_bam", values: {"spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-03/call-trgt_genotype/out/m84036_250809_035451_s4.bc2100.trgt.sorted.spanning.bam"}
2025-09-15 20:23:42.722 wdl.w:ptcp.w:call-trgt-03 INFO visit :: node: "output-spanning_bam_bai", values: {"spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-03/call-trgt_genotype/out/m84036_250809_035451_s4.bc2100.trgt.sorted.spanning.bam.bai"}
2025-09-15 20:23:42.722 wdl.w:ptcp.w:call-trgt-03 INFO visit :: node: "output-vcf", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-03/call-trgt_genotype/out/m84036_250809_035451_s4.bc2100.trgt.vcf"}
2025-09-15 20:23:42.722 wdl.w:ptcp.w:call-trgt-25.t:call-get_reads_overlapping_repeats INFO output :: name: "reads_overlapping_repeats", value: "m84036_250809_035451_s4.bc2122.repeats.bam"
2025-09-15 20:23:42.725 wdl.w:ptcp.w:call-sawfish-00.t:call-run_sawfish NOTICE task setup :: name: "run_sawfish", source: "./sawfish.wdl", line: 83, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-00/call-run_sawfish", thread: 140610870679104
2025-09-15 20:23:42.726 wdl.w:ptcp.w:call-trgt-25.t:call-get_reads_overlapping_repeats INFO output :: name: "reads_overlapping_repeats_bai", value: "m84036_250809_035451_s4.bc2122.repeats.bam.bai"
2025-09-15 20:23:42.745 wdl.w:ptcp.w:call-sawfish-00.t:call-run_sawfish INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:23:42.746 wdl.w:ptcp.w:call-sawfish-00.t:call-run_sawfish INFO input :: name: "genome_version", value: "38"
2025-09-15 20:23:42.746 wdl.w:ptcp.w:call-sawfish-00.t:call-run_sawfish INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:23:42.746 wdl.w:ptcp.w:call-sawfish-00.t:call-run_sawfish INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:23:42.746 wdl.w:ptcp.w:call-sawfish-00.t:call-run_sawfish INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2097.mapped.bam.bai"
2025-09-15 20:23:42.746 wdl.w:ptcp.w:call-sawfish-00.t:call-run_sawfish INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2097.mapped.bam"
2025-09-15 20:23:42.746 wdl.w:ptcp.w:call-sawfish-00.t:call-run_sawfish INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2097"
2025-09-15 20:23:42.746 wdl.w:ptcp.w:call-sawfish-00.t:call-run_sawfish INFO eval :: name: "mem_gb", value: 32
2025-09-15 20:23:42.746 wdl.w:ptcp.w:call-sawfish-00.t:call-run_sawfish INFO eval :: name: "threads", value: 16
2025-09-15 20:23:42.746 wdl.w:ptcp.w:call-sawfish-00.t:call-run_sawfish INFO eval :: name: "disk_size", value: 30
2025-09-15 20:23:42.747 wdl.w:ptcp.w:call-sawfish-00.t:call-run_sawfish INFO eval :: name: "discover_dirname", value: "m84036_250809_035451_s4.bc2097_sawfish_discover"
2025-09-15 20:23:42.747 wdl.w:ptcp.w:call-sawfish-00.t:call-run_sawfish INFO eval :: name: "call_dirname", value: "m84036_250809_035451_s4.bc2097_sawfish"
2025-09-15 20:23:42.747 wdl.w:ptcp.w:call-sawfish-00.t:call-run_sawfish INFO eval :: name: "minimap2_bam_filename", value: "m84036_250809_035451_s4.bc2097.minimap2.bam"
2025-09-15 20:23:42.747 wdl.w:ptcp.w:call-sawfish-00.t:call-run_sawfish INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 16, memory_reservation: 32000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:23:42.747 wdl.w:ptcp.w:call-sawfish-00.t:call-run_sawfish WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:23:42.748 wdl.w:ptcp.w:call-sawfish-00.t:call-run_sawfish INFO provisioned :: seconds_waited: 0, cpu: 16, mem_bytes: 32000000000
2025-09-15 20:23:42.748 wdl.w:ptcp.w:call-sawfish-00.t:call-run_sawfish INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:23:42.795 wdl.w:ptcp.w:call-trgt-25.t:call-get_reads_overlapping_repeats NOTICE done
2025-09-15 20:23:42.799 wdl.w:ptcp.w:call-trgt-25 NOTICE finish :: job: "call-get_reads_overlapping_repeats"
2025-09-15 20:23:42.800 wdl.w:ptcp.w:call-trgt-25 INFO output :: job: "call-get_reads_overlapping_repeats", values: {"reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-25/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2122.repeats.bam.bai", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-25/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2122.repeats.bam"}
2025-09-15 20:23:42.800 wdl.w:ptcp.w:call-trgt-25 INFO visit :: node: "output-reads_overlapping_repeats", values: {"reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-25/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2122.repeats.bam"}
2025-09-15 20:23:42.800 wdl.w:ptcp.w:call-trgt-25 INFO visit :: node: "output-reads_overlapping_repeats_bai", values: {"reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-25/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2122.repeats.bam.bai"}
2025-09-15 20:23:42.807 wdl.w:ptcp.w:call-trgt-00.t:call-get_reads_overlapping_repeats NOTICE task setup :: name: "get_reads_overlapping_repeats", source: "./trgt.wdl", line: 182, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-00/call-get_reads_overlapping_repeats", thread: 140608739980864
2025-09-15 20:23:42.826 wdl.w:ptcp.w:call-trgt-00.t:call-get_reads_overlapping_repeats INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:23:42.826 wdl.w:ptcp.w:call-trgt-00.t:call-get_reads_overlapping_repeats INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:23:42.826 wdl.w:ptcp.w:call-trgt-00.t:call-get_reads_overlapping_repeats INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2097.mapped.bam.bai"
2025-09-15 20:23:42.826 wdl.w:ptcp.w:call-trgt-00.t:call-get_reads_overlapping_repeats INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2097.mapped.bam"
2025-09-15 20:23:42.826 wdl.w:ptcp.w:call-trgt-00.t:call-get_reads_overlapping_repeats INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2097"
2025-09-15 20:23:42.826 wdl.w:ptcp.w:call-trgt-00.t:call-get_reads_overlapping_repeats INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:23:42.827 wdl.w:ptcp.w:call-trgt-00.t:call-get_reads_overlapping_repeats INFO eval :: name: "expand_size", value: 3000
2025-09-15 20:23:42.827 wdl.w:ptcp.w:call-trgt-00.t:call-get_reads_overlapping_repeats INFO eval :: name: "threads", value: 1
2025-09-15 20:23:42.827 wdl.w:ptcp.w:call-trgt-00.t:call-get_reads_overlapping_repeats INFO eval :: name: "expanded_bed_name", value: "m84036_250809_035451_s4.bc2097.expanded.bed"
2025-09-15 20:23:42.827 wdl.w:ptcp.w:call-trgt-00.t:call-get_reads_overlapping_repeats INFO eval :: name: "disk_size", value: 11
2025-09-15 20:23:42.827 wdl.w:ptcp.w:call-trgt-00.t:call-get_reads_overlapping_repeats INFO eval :: name: "output_name", value: "m84036_250809_035451_s4.bc2097.repeats.bam"
2025-09-15 20:23:42.827 wdl.w:ptcp.w:call-trgt-00.t:call-get_reads_overlapping_repeats INFO eval :: name: "index_name", value: "m84036_250809_035451_s4.bc2097.repeats.bam.bai"
2025-09-15 20:23:42.827 wdl.w:ptcp.w:call-trgt-00.t:call-get_reads_overlapping_repeats INFO eval :: name: "output_name_with_index", value: "m84036_250809_035451_s4.bc2097.repeats.bam##idx##m84036_250809_035451_s4.bc2097.repeats.bam.bai"
2025-09-15 20:23:42.828 wdl.w:ptcp.w:call-trgt-00.t:call-get_reads_overlapping_repeats INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:23:42.828 wdl.w:ptcp.w:call-trgt-00.t:call-get_reads_overlapping_repeats WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:23:42.828 wdl.w:ptcp.w:call-trgt-00.t:call-get_reads_overlapping_repeats INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:23:42.828 wdl.w:ptcp.w:call-trgt-00.t:call-get_reads_overlapping_repeats INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:23:42.833 wdl.w:ptcp.w:call-sawfish-32.t:call-run_sawfish.stderr VERBOSE [M::bam2fq_mainloop] discarded 0 singletons
2025-09-15 20:23:42.833 wdl.w:ptcp.w:call-sawfish-32.t:call-run_sawfish.stderr VERBOSE [M::bam2fq_mainloop] processed 1 reads
2025-09-15 20:23:42.843 wdl.w:ptcp.w:call-sawfish-00.t:call-run_sawfish INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 10, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-00/call-run_sawfish/_singularity_tmpdir_lx5cl_nj"
2025-09-15 20:23:42.843 wdl.w:ptcp.w:call-sawfish-00.t:call-run_sawfish INFO Slurm invocation: srun --job-name call-run_sawfish --partition compute,compute9 --cpus-per-task 16 --mem 30518M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-00/call-run_sawfish/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-00/call-run_sawfish/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-00/call-run_sawfish/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-00/call-run_sawfish/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-00/out/m84036_250809_035451_s4.bc2097.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2097.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-00/out/m84036_250809_035451_s4.bc2097.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2097.mapped.bam:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-00/call-run_sawfish/_singularity_tmpdir_lx5cl_nj/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-00/call-run_sawfish/_singularity_tmpdir_lx5cl_nj/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:23:42.866 wdl.w:ptcp.w:call-sawfish-00.t:call-run_sawfish NOTICE slurm_singularity run :: pid: 1200045, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-00/call-run_sawfish/slurm_singularity.log.txt"
2025-09-15 20:23:42.878 wdl.w:ptcp.w:call-trgt-00.t:call-get_reads_overlapping_repeats INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 9, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-00/call-get_reads_overlapping_repeats/_singularity_tmpdir_yus4pp4f"
2025-09-15 20:23:42.879 wdl.w:ptcp.w:call-trgt-00.t:call-get_reads_overlapping_repeats INFO Slurm invocation: srun --job-name call-get_reads_overlapping_repeats --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-00/call-get_reads_overlapping_repeats/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-00/call-get_reads_overlapping_repeats/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-00/call-get_reads_overlapping_repeats/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-00/call-get_reads_overlapping_repeats/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-00/out/m84036_250809_035451_s4.bc2097.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2097.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-00/out/m84036_250809_035451_s4.bc2097.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2097.mapped.bam:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-00/call-get_reads_overlapping_repeats/_singularity_tmpdir_yus4pp4f/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-00/call-get_reads_overlapping_repeats/_singularity_tmpdir_yus4pp4f/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:23:42.888 wdl.w:ptcp.w:call-trgt-00.t:call-get_reads_overlapping_repeats NOTICE slurm_singularity run :: pid: 1200047, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-00/call-get_reads_overlapping_repeats/slurm_singularity.log.txt"
2025-09-15 20:23:42.901 wdl.w:ptcp.w:call-paraphase-34.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for smn1 for sample m84036_250809_035451_s4.bc2131 at 2025-09-15 20:23:20.988594...
2025-09-15 20:23:43.163 wdl.w:ptcp.w:call-sawfish-01.t:call-run_sawfish.stderr VERBOSE [M::bam2fq_mainloop] discarded 0 singletons
2025-09-15 20:23:43.163 wdl.w:ptcp.w:call-sawfish-01.t:call-run_sawfish.stderr VERBOSE [M::bam2fq_mainloop] processed 0 reads
2025-09-15 20:23:43.172 wdl.w:ptcp.w:call-sawfish-01.t:call-run_sawfish.slurm_singularity INFO srun: job 51797454 queued and waiting for resources
2025-09-15 20:23:43.172 wdl.w:ptcp.w:call-sawfish-01.t:call-run_sawfish.slurm_singularity INFO srun: job 51797454 has been allocated resources
2025-09-15 20:23:43.172 wdl.w:ptcp.w:call-sawfish-01.t:call-run_sawfish.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:43.172 wdl.w:ptcp.w:call-sawfish-01.t:call-run_sawfish.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:23:43.173 wdl.w:ptcp.w:call-trgt-08.t:call-trgt_genotype.slurm_singularity INFO srun: job 51797455 queued and waiting for resources
2025-09-15 20:23:43.174 wdl.w:ptcp.w:call-trgt-08.t:call-trgt_genotype.slurm_singularity INFO srun: job 51797455 has been allocated resources
2025-09-15 20:23:43.174 wdl.w:ptcp.w:call-trgt-08.t:call-trgt_genotype.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:43.209 wdl.w:ptcp.w:call-paraphase-29.t:call-run_paraphase.stderr VERBOSE INFO:root:Processing sample m84036_250809_035451_s4.bc2126 at 2025-09-15 20:23:39.891378...
2025-09-15 20:23:43.211 wdl.w:ptcp.w:call-paraphase-29.t:call-run_paraphase.stderr VERBOSE INFO:root:Checking sample sex at 2025-09-15 20:23:39.892199...
2025-09-15 20:23:43.211 wdl.w:ptcp.w:call-paraphase-29.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for cyp21 for sample m84036_250809_035451_s4.bc2126 at 2025-09-15 20:23:39.925232...
2025-09-15 20:23:43.211 wdl.w:ptcp.w:call-paraphase-29.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for cyp21 for sample m84036_250809_035451_s4.bc2126 at 2025-09-15 20:23:39.925491...
2025-09-15 20:23:43.211 wdl.w:ptcp.w:call-paraphase-29.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for smn1 for sample m84036_250809_035451_s4.bc2126 at 2025-09-15 20:23:39.925334...
2025-09-15 20:23:43.211 wdl.w:ptcp.w:call-paraphase-29.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for gba for sample m84036_250809_035451_s4.bc2126 at 2025-09-15 20:23:39.925372...
2025-09-15 20:23:43.211 wdl.w:ptcp.w:call-paraphase-29.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for smn1 for sample m84036_250809_035451_s4.bc2126 at 2025-09-15 20:23:39.925587...
2025-09-15 20:23:43.211 wdl.w:ptcp.w:call-paraphase-29.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for hba for sample m84036_250809_035451_s4.bc2126 at 2025-09-15 20:23:39.925392...
2025-09-15 20:23:43.211 wdl.w:ptcp.w:call-paraphase-29.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for gba for sample m84036_250809_035451_s4.bc2126 at 2025-09-15 20:23:39.925620...
2025-09-15 20:23:43.211 wdl.w:ptcp.w:call-paraphase-29.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for hba for sample m84036_250809_035451_s4.bc2126 at 2025-09-15 20:23:39.925648...
2025-09-15 20:23:43.211 wdl.w:ptcp.w:call-paraphase-29.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for cyp21 for sample m84036_250809_035451_s4.bc2126 at 2025-09-15 20:23:40.357553...
2025-09-15 20:23:43.211 wdl.w:ptcp.w:call-paraphase-29.t:call-run_paraphase.stderr VERBOSE WARNING:root:This region does not appear to have coverage. Will not attempt to phase haplotypes.
2025-09-15 20:23:43.211 wdl.w:ptcp.w:call-paraphase-29.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for cyp21 for sample m84036_250809_035451_s4.bc2126 at 2025-09-15 20:23:40.433037...
2025-09-15 20:23:43.211 wdl.w:ptcp.w:call-paraphase-29.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for hba for sample m84036_250809_035451_s4.bc2126 at 2025-09-15 20:23:40.437914...
2025-09-15 20:23:43.211 wdl.w:ptcp.w:call-paraphase-29.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for gba for sample m84036_250809_035451_s4.bc2126 at 2025-09-15 20:23:40.474661...
2025-09-15 20:23:43.212 wdl.w:ptcp.w:call-paraphase-29.t:call-run_paraphase.stderr VERBOSE WARNING:root:This region does not appear to have coverage. Will not attempt to phase haplotypes.
2025-09-15 20:23:43.212 wdl.w:ptcp.w:call-paraphase-29.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for hba for sample m84036_250809_035451_s4.bc2126 at 2025-09-15 20:23:40.476775...
2025-09-15 20:23:43.212 wdl.w:ptcp.w:call-paraphase-29.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for smn1 for sample m84036_250809_035451_s4.bc2126 at 2025-09-15 20:23:40.477826...
2025-09-15 20:23:43.212 wdl.w:ptcp.w:call-paraphase-29.t:call-run_paraphase.stderr VERBOSE WARNING:root:This region does not appear to have coverage. Will not attempt to phase haplotypes.
2025-09-15 20:23:43.212 wdl.w:ptcp.w:call-paraphase-29.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for gba for sample m84036_250809_035451_s4.bc2126 at 2025-09-15 20:23:40.525972...
2025-09-15 20:23:43.212 wdl.w:ptcp.w:call-paraphase-29.t:call-run_paraphase.stderr VERBOSE WARNING:root:This region does not appear to have coverage. Will not attempt to phase haplotypes.
2025-09-15 20:23:43.212 wdl.w:ptcp.w:call-paraphase-29.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for smn1 for sample m84036_250809_035451_s4.bc2126 at 2025-09-15 20:23:40.563939...
2025-09-15 20:23:43.212 wdl.w:ptcp.w:call-paraphase-29.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for cyp21 for sample m84036_250809_035451_s4.bc2126 at 2025-09-15 20:23:40.701809...
2025-09-15 20:23:43.212 wdl.w:ptcp.w:call-paraphase-29.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for f8inv22 for sample m84036_250809_035451_s4.bc2126 at 2025-09-15 20:23:40.708172...
2025-09-15 20:23:43.212 wdl.w:ptcp.w:call-paraphase-29.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for f8inv22 for sample m84036_250809_035451_s4.bc2126 at 2025-09-15 20:23:40.708222...
2025-09-15 20:23:43.212 wdl.w:ptcp.w:call-paraphase-29.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for hba for sample m84036_250809_035451_s4.bc2126 at 2025-09-15 20:23:40.741576...
2025-09-15 20:23:43.212 wdl.w:ptcp.w:call-paraphase-29.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for hbb for sample m84036_250809_035451_s4.bc2126 at 2025-09-15 20:23:40.749063...
2025-09-15 20:23:43.212 wdl.w:ptcp.w:call-paraphase-29.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for hbb for sample m84036_250809_035451_s4.bc2126 at 2025-09-15 20:23:40.749116...
2025-09-15 20:23:43.212 wdl.w:ptcp.w:call-paraphase-29.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for gba for sample m84036_250809_035451_s4.bc2126 at 2025-09-15 20:23:40.809988...
2025-09-15 20:23:43.212 wdl.w:ptcp.w:call-paraphase-29.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for rpgr for sample m84036_250809_035451_s4.bc2126 at 2025-09-15 20:23:40.820517...
2025-09-15 20:23:43.212 wdl.w:ptcp.w:call-paraphase-29.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for rpgr for sample m84036_250809_035451_s4.bc2126 at 2025-09-15 20:23:40.820649...
2025-09-15 20:23:43.212 wdl.w:ptcp.w:call-paraphase-29.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning to gene2 region for smn1 for sample m84036_250809_035451_s4.bc2126 at 2025-09-15 20:23:40.831472...
2025-09-15 20:23:43.212 wdl.w:ptcp.w:call-paraphase-29.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for f8inv22 for sample m84036_250809_035451_s4.bc2126 at 2025-09-15 20:23:41.076723...
2025-09-15 20:23:43.212 wdl.w:ptcp.w:call-paraphase-29.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for hbb for sample m84036_250809_035451_s4.bc2126 at 2025-09-15 20:23:41.108760...
2025-09-15 20:23:43.212 wdl.w:ptcp.w:call-paraphase-29.t:call-run_paraphase.stderr VERBOSE WARNING:root:This region does not appear to have coverage. Will not attempt to phase haplotypes.
2025-09-15 20:23:43.213 wdl.w:ptcp.w:call-paraphase-29.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for f8inv22 for sample m84036_250809_035451_s4.bc2126 at 2025-09-15 20:23:41.158166...
2025-09-15 20:23:43.213 wdl.w:ptcp.w:call-paraphase-29.t:call-run_paraphase.stderr VERBOSE WARNING:root:This region does not appear to have coverage. Will not attempt to phase haplotypes.
2025-09-15 20:23:43.213 wdl.w:ptcp.w:call-paraphase-29.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for hbb for sample m84036_250809_035451_s4.bc2126 at 2025-09-15 20:23:41.169240...
2025-09-15 20:23:43.213 wdl.w:ptcp.w:call-paraphase-29.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for rpgr for sample m84036_250809_035451_s4.bc2126 at 2025-09-15 20:23:41.170339...
2025-09-15 20:23:43.213 wdl.w:ptcp.w:call-paraphase-29.t:call-run_paraphase.stderr VERBOSE WARNING:root:This region does not appear to have coverage. Will not attempt to phase haplotypes.
2025-09-15 20:23:43.213 wdl.w:ptcp.w:call-paraphase-29.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for rpgr for sample m84036_250809_035451_s4.bc2126 at 2025-09-15 20:23:41.237127...
2025-09-15 20:23:43.213 wdl.w:ptcp.w:call-paraphase-29.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for smn1 for sample m84036_250809_035451_s4.bc2126 at 2025-09-15 20:23:41.463062...
2025-09-15 20:23:43.213 wdl.w:ptcp.w:call-paraphase-29.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for f8inv1 for sample m84036_250809_035451_s4.bc2126 at 2025-09-15 20:23:41.511673...
2025-09-15 20:23:43.213 wdl.w:ptcp.w:call-paraphase-29.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for f8inv1 for sample m84036_250809_035451_s4.bc2126 at 2025-09-15 20:23:41.511740...
2025-09-15 20:23:43.213 wdl.w:ptcp.w:call-paraphase-29.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for f8inv22 for sample m84036_250809_035451_s4.bc2126 at 2025-09-15 20:23:41.531001...
2025-09-15 20:23:43.213 wdl.w:ptcp.w:call-paraphase-29.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for hbb for sample m84036_250809_035451_s4.bc2126 at 2025-09-15 20:23:41.571765...
2025-09-15 20:23:43.213 wdl.w:ptcp.w:call-paraphase-29.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for rpgr for sample m84036_250809_035451_s4.bc2126 at 2025-09-15 20:23:41.613173...
2025-09-15 20:23:43.213 wdl.w:ptcp.w:call-paraphase-29.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for f8inv1 for sample m84036_250809_035451_s4.bc2126 at 2025-09-15 20:23:41.782775...
2025-09-15 20:23:43.213 wdl.w:ptcp.w:call-paraphase-29.t:call-run_paraphase.stderr VERBOSE WARNING:root:This region does not appear to have coverage. Will not attempt to phase haplotypes.
2025-09-15 20:23:43.213 wdl.w:ptcp.w:call-paraphase-29.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for f8inv1 for sample m84036_250809_035451_s4.bc2126 at 2025-09-15 20:23:41.808449...
2025-09-15 20:23:43.213 wdl.w:ptcp.w:call-paraphase-29.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for f8inv1 for sample m84036_250809_035451_s4.bc2126 at 2025-09-15 20:23:41.949320...
2025-09-15 20:23:43.213 wdl.w:ptcp.w:call-paraphase-29.t:call-run_paraphase.stderr VERBOSE INFO:root:Merging all bams for sample m84036_250809_035451_s4.bc2126 at 2025-09-15 20:23:41.962348...
2025-09-15 20:23:43.213 wdl.w:ptcp.w:call-paraphase-29.t:call-run_paraphase.stderr VERBOSE INFO:root:Writing to json for sample m84036_250809_035451_s4.bc2126 at 2025-09-15 20:23:42.224435...
2025-09-15 20:23:43.213 wdl.w:ptcp.w:call-paraphase-29.t:call-run_paraphase.stderr VERBOSE INFO:root:Completed Paraphase analysis at 2025-09-15 20:23:42.583737...
2025-09-15 20:23:43.295 wdl.w:ptcp.w:call-trgt-01.t:call-get_reads_overlapping_repeats.slurm_singularity INFO srun: job 51797456 queued and waiting for resources
2025-09-15 20:23:43.295 wdl.w:ptcp.w:call-trgt-01.t:call-get_reads_overlapping_repeats.slurm_singularity INFO srun: job 51797456 has been allocated resources
2025-09-15 20:23:43.295 wdl.w:ptcp.w:call-trgt-01.t:call-get_reads_overlapping_repeats.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:43.295 wdl.w:ptcp.w:call-trgt-01.t:call-get_reads_overlapping_repeats.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:23:43.339 wdl.w:ptcp.w:call-paraphase-01.t:call-run_paraphase.slurm_singularity INFO srun: job 51797457 queued and waiting for resources
2025-09-15 20:23:43.339 wdl.w:ptcp.w:call-paraphase-01.t:call-run_paraphase.slurm_singularity INFO srun: job 51797457 has been allocated resources
2025-09-15 20:23:43.339 wdl.w:ptcp.w:call-paraphase-01.t:call-run_paraphase.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:43.485 wdl.w:ptcp.w:call-trgt-32.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:40 [INFO] - Running trgt-4.0.0-429afcd [genotype]
2025-09-15 20:23:43.486 wdl.w:ptcp.w:call-trgt-32.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:41 [WARN] - SCA37_DAB1: Filtered out 14 impure reads
2025-09-15 20:23:43.486 wdl.w:ptcp.w:call-trgt-32.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:41 [WARN] - OPDM_ABCD3: Filtered out 11 impure reads
2025-09-15 20:23:43.486 wdl.w:ptcp.w:call-trgt-32.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:41 [WARN] - NIID_NOTCH2NLC: Filtered out 23 impure reads
2025-09-15 20:23:43.486 wdl.w:ptcp.w:call-trgt-32.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:41 [WARN] - DRPLA_ATN1: Filtered out 35 impure reads
2025-09-15 20:23:43.486 wdl.w:ptcp.w:call-trgt-32.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:41 [WARN] - SCA8_ATXN8OS: Filtered out 10 impure reads
2025-09-15 20:23:43.486 wdl.w:ptcp.w:call-trgt-32.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:41 [WARN] - SCA2_ATXN2: Filtered out 25 impure reads
2025-09-15 20:23:43.486 wdl.w:ptcp.w:call-trgt-32.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:41 [WARN] - OPMD_PABPN1: Filtered out 18 impure reads
2025-09-15 20:23:43.486 wdl.w:ptcp.w:call-trgt-32.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:41 [WARN] - OPDM4_RILPL1: Filtered out 12 impure reads
2025-09-15 20:23:43.486 wdl.w:ptcp.w:call-trgt-32.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:41 [WARN] - SCA27B_FGF14: Filtered out 33 impure reads
2025-09-15 20:23:43.486 wdl.w:ptcp.w:call-trgt-32.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:41 [WARN] - SCA31_BEAN1: Filtered out 12 impure reads
2025-09-15 20:23:43.486 wdl.w:ptcp.w:call-trgt-32.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:42 [WARN] - HDL2_JPH3: Filtered out 14 impure reads
2025-09-15 20:23:43.486 wdl.w:ptcp.w:call-trgt-32.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:42 [WARN] - FECD3_TCF4: Filtered out 14 impure reads
2025-09-15 20:23:43.486 wdl.w:ptcp.w:call-trgt-32.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:42 [WARN] - SCA3_ATXN3: Filtered out 23 impure reads
2025-09-15 20:23:43.486 wdl.w:ptcp.w:call-trgt-32.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:42 [WARN] - SCA6_CACNA1A: Filtered out 24 impure reads
2025-09-15 20:23:43.486 wdl.w:ptcp.w:call-trgt-32.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:42 [WARN] - SCA4_ZFHX3: Filtered out 31 impure reads
2025-09-15 20:23:43.486 wdl.w:ptcp.w:call-trgt-32.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:42 [WARN] - OPDM2_GIPC1: Filtered out 11 impure reads
2025-09-15 20:23:43.487 wdl.w:ptcp.w:call-trgt-32.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:42 [WARN] - FRA2A_AFF3: Filtered out 23 impure reads
2025-09-15 20:23:43.487 wdl.w:ptcp.w:call-trgt-32.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:42 [WARN] - SD5_HOXD13: Filtered out 10 impure reads
2025-09-15 20:23:43.487 wdl.w:ptcp.w:call-trgt-32.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:42 [WARN] - SCA36_NOP56: Filtered out 25 impure reads
2025-09-15 20:23:43.487 wdl.w:ptcp.w:call-trgt-32.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:42 [WARN] - CJD_PRNP: Filtered out 16 impure reads
2025-09-15 20:23:43.487 wdl.w:ptcp.w:call-trgt-32.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:43 [WARN] - SCA7_ATXN7: Filtered out 26 impure reads
2025-09-15 20:23:43.492 wdl.w:ptcp.w:call-trgt-01.t:call-trgt_genotype.slurm_singularity INFO srun: job 51797458 queued and waiting for resources
2025-09-15 20:23:43.492 wdl.w:ptcp.w:call-trgt-01.t:call-trgt_genotype.slurm_singularity INFO srun: job 51797458 has been allocated resources
2025-09-15 20:23:43.492 wdl.w:ptcp.w:call-trgt-01.t:call-trgt_genotype.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:43.583 wdl.w:ptcp.w:call-paraphase-00.t:call-run_paraphase.slurm_singularity INFO srun: job 51797459 queued and waiting for resources
2025-09-15 20:23:43.583 wdl.w:ptcp.w:call-paraphase-00.t:call-run_paraphase.slurm_singularity INFO srun: job 51797459 has been allocated resources
2025-09-15 20:23:43.583 wdl.w:ptcp.w:call-paraphase-00.t:call-run_paraphase.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:43.801 wdl.w:ptcp.w:call-paraphase-29.t:call-run_paraphase INFO output :: name: "paraphase_bam", value: "m84036_250809_035451_s4.bc2126_paraphase/m84036_250809_035451_s4.bc2126.paraphase.bam"
2025-09-15 20:23:43.807 wdl.w:ptcp.w:call-paraphase-29.t:call-run_paraphase INFO output :: name: "paraphase_bam_bai", value: "m84036_250809_035451_s4.bc2126_paraphase/m84036_250809_035451_s4.bc2126.paraphase.bam.bai"
2025-09-15 20:23:43.811 wdl.w:ptcp.w:call-paraphase-29.t:call-run_paraphase INFO output :: name: "paraphase_json", value: "m84036_250809_035451_s4.bc2126_paraphase/m84036_250809_035451_s4.bc2126.paraphase.json"
2025-09-15 20:23:43.815 wdl.w:ptcp.w:call-paraphase-29.t:call-run_paraphase INFO output :: name: "paraphase_vcfs", value: []
2025-09-15 20:23:43.815 wdl.w:ptcp.w:call-paraphase-29.t:call-run_paraphase INFO output :: name: "havanno_json", value: "m84036_250809_035451_s4.bc2126.havanno.json"
2025-09-15 20:23:43.880 wdl.w:ptcp.w:call-sawfish-00.t:call-run_sawfish.slurm_singularity INFO srun: job 51797460 queued and waiting for resources
2025-09-15 20:23:43.880 wdl.w:ptcp.w:call-sawfish-00.t:call-run_sawfish.slurm_singularity INFO srun: job 51797460 has been allocated resources
2025-09-15 20:23:43.887 wdl.w:ptcp.t:call-pbmm2_align_hifi-68 INFO output :: name: "mapped_bam", value: "m84036_250809_035451_s4.bc2165.mapped.bam"
2025-09-15 20:23:43.891 wdl.w:ptcp.t:call-pbmm2_align_hifi-68 INFO output :: name: "mapped_bam_bai", value: "m84036_250809_035451_s4.bc2165.mapped.bam.bai"
2025-09-15 20:23:43.892 wdl.w:ptcp.t:call-pbmm2_align_hifi-68 INFO output :: name: "mapped_bam_pbi", value: "m84036_250809_035451_s4.bc2165.mapped.bam.pbi"
2025-09-15 20:23:43.895 wdl.w:ptcp.t:call-pbmm2_align_hifi-68 INFO output :: name: "report", value: "mapping_stats.report.json"
2025-09-15 20:23:43.905 wdl.w:ptcp.w:call-trgt-00.t:call-get_reads_overlapping_repeats.slurm_singularity INFO srun: job 51797461 queued and waiting for resources
2025-09-15 20:23:43.905 wdl.w:ptcp.w:call-trgt-00.t:call-get_reads_overlapping_repeats.slurm_singularity INFO srun: job 51797461 has been allocated resources
2025-09-15 20:23:43.905 wdl.w:ptcp.w:call-trgt-00.t:call-get_reads_overlapping_repeats.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:43.905 wdl.w:ptcp.w:call-trgt-00.t:call-get_reads_overlapping_repeats.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:23:43.934 wdl.w:ptcp.w:call-trgt-16.t:call-get_reads_overlapping_repeats INFO output :: name: "reads_overlapping_repeats", value: "m84036_250809_035451_s4.bc2113.repeats.bam"
2025-09-15 20:23:43.941 wdl.w:ptcp.w:call-trgt-16.t:call-get_reads_overlapping_repeats INFO output :: name: "reads_overlapping_repeats_bai", value: "m84036_250809_035451_s4.bc2113.repeats.bam.bai"
2025-09-15 20:23:43.951 wdl.w:ptcp.w:call-paraphase-29.t:call-run_paraphase NOTICE done
2025-09-15 20:23:43.957 wdl.w:ptcp.w:call-paraphase-29 NOTICE finish :: job: "call-run_paraphase"
2025-09-15 20:23:43.957 wdl.w:ptcp.w:call-paraphase-29 INFO output :: job: "call-run_paraphase", values: {"havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-29/call-run_paraphase/out/m84036_250809_035451_s4.bc2126.havanno.json", "paraphase_vcfs": [], "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-29/call-run_paraphase/out/m84036_250809_035451_s4.bc2126_paraphase/m84036_250809_035451_s4.bc2126.paraphase.json", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-29/call-run_paraphase/out/m84036_250809_035451_s4.bc2126_paraphase/m84036_250809_035451_s4.bc2126.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-29/call-run_paraphase/out/m84036_250809_035451_s4.bc2126_paraphase/m84036_250809_035451_s4.bc2126.paraphase.bam"}
2025-09-15 20:23:43.958 wdl.w:ptcp.w:call-paraphase-29 NOTICE ready :: job: "call-call_f8", callee: "call_f8"
2025-09-15 20:23:43.958 wdl.w:ptcp.w:call-paraphase-29 INFO input :: job: "call-call_f8", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "out_prefix": "m84036_250809_035451_s4.bc2126", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-29/call-run_paraphase/out/m84036_250809_035451_s4.bc2126_paraphase/m84036_250809_035451_s4.bc2126.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-29/call-run_paraphase/out/m84036_250809_035451_s4.bc2126_paraphase/m84036_250809_035451_s4.bc2126.paraphase.bam", "sex": "F"}
2025-09-15 20:23:43.960 wdl.w:ptcp.w:call-paraphase-29 INFO visit :: node: "output-havanno_json", values: {"havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-29/call-run_paraphase/out/m84036_250809_035451_s4.bc2126.havanno.json"}
2025-09-15 20:23:43.960 wdl.w:ptcp.w:call-paraphase-29 INFO visit :: node: "output-paraphase_bam", values: {"paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-29/call-run_paraphase/out/m84036_250809_035451_s4.bc2126_paraphase/m84036_250809_035451_s4.bc2126.paraphase.bam"}
2025-09-15 20:23:43.960 wdl.w:ptcp.w:call-paraphase-29 INFO visit :: node: "output-paraphase_bam_bai", values: {"paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-29/call-run_paraphase/out/m84036_250809_035451_s4.bc2126_paraphase/m84036_250809_035451_s4.bc2126.paraphase.bam.bai"}
2025-09-15 20:23:43.960 wdl.w:ptcp.w:call-paraphase-29 INFO visit :: node: "output-paraphase_json", values: {"paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-29/call-run_paraphase/out/m84036_250809_035451_s4.bc2126_paraphase/m84036_250809_035451_s4.bc2126.paraphase.json"}
2025-09-15 20:23:43.960 wdl.w:ptcp.w:call-paraphase-29 INFO visit :: node: "output-paraphase_vcfs", values: {"paraphase_vcfs": []}
2025-09-15 20:23:43.964 wdl.w:ptcp.w:call-trgt-00.t:call-trgt_genotype NOTICE task setup :: name: "trgt_genotype", source: "./trgt.wdl", line: 272, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-00/call-trgt_genotype", thread: 140610367379008
2025-09-15 20:23:43.982 wdl.w:ptcp.w:call-trgt-00.t:call-trgt_genotype INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:23:43.982 wdl.w:ptcp.w:call-trgt-00.t:call-trgt_genotype INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:23:43.982 wdl.w:ptcp.w:call-trgt-00.t:call-trgt_genotype INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:23:43.982 wdl.w:ptcp.w:call-trgt-00.t:call-trgt_genotype INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:23:43.982 wdl.w:ptcp.w:call-trgt-00.t:call-trgt_genotype INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2097.mapped.bam.bai"
2025-09-15 20:23:43.982 wdl.w:ptcp.w:call-trgt-00.t:call-trgt_genotype INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2097.mapped.bam"
2025-09-15 20:23:43.982 wdl.w:ptcp.w:call-trgt-00.t:call-trgt_genotype INFO input :: name: "sex", value: "F"
2025-09-15 20:23:43.982 wdl.w:ptcp.w:call-trgt-00.t:call-trgt_genotype INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2097"
2025-09-15 20:23:43.983 wdl.w:ptcp.w:call-trgt-00.t:call-trgt_genotype INFO eval :: name: "mem_gb", value: 16
2025-09-15 20:23:43.983 wdl.w:ptcp.w:call-trgt-00.t:call-trgt_genotype INFO eval :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2097.trgt"
2025-09-15 20:23:43.983 wdl.w:ptcp.w:call-trgt-00.t:call-trgt_genotype INFO eval :: name: "threads", value: 8
2025-09-15 20:23:43.983 wdl.w:ptcp.w:call-trgt-00.t:call-trgt_genotype INFO eval :: name: "disk_size", value: 27
2025-09-15 20:23:43.983 wdl.w:ptcp.w:call-trgt-00.t:call-trgt_genotype INFO eval :: name: "karyotype", value: "XX"
2025-09-15 20:23:43.984 wdl.w:ptcp.w:call-trgt-00.t:call-trgt_genotype INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 8, memory_reservation: 16000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:23:43.984 wdl.w:ptcp.w:call-trgt-00.t:call-trgt_genotype WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:23:43.984 wdl.w:ptcp.w:call-trgt-00.t:call-trgt_genotype INFO provisioned :: seconds_waited: 0, cpu: 8, mem_bytes: 16000000000
2025-09-15 20:23:43.984 wdl.w:ptcp.w:call-trgt-00.t:call-trgt_genotype INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:23:43.998 wdl.w:ptcp.t:call-pbmm2_align_hifi-68 NOTICE done
2025-09-15 20:23:44.006 wdl.w:ptcp NOTICE finish :: job: "call-pbmm2_align_hifi-68"
2025-09-15 20:23:44.006 wdl.w:ptcp INFO output :: job: "call-pbmm2_align_hifi-68", values: {"report": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-68/out/mapping_stats.report.json", "mapped_bam_pbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-68/out/m84036_250809_035451_s4.bc2165.mapped.bam.pbi", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-68/out/m84036_250809_035451_s4.bc2165.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-68/out/m84036_250809_035451_s4.bc2165.mapped.bam"}
2025-09-15 20:23:44.007 wdl.w:ptcp NOTICE ready :: job: "call-paraphase-68", callee: "paraphase"
2025-09-15 20:23:44.007 wdl.w:ptcp INFO input :: job: "call-paraphase-68", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf", "genome_version": "38", "config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-68/out/m84036_250809_035451_s4.bc2165.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-68/out/m84036_250809_035451_s4.bc2165.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2165"}
2025-09-15 20:23:44.008 wdl.w:ptcp NOTICE ready :: job: "call-sawfish-68", callee: "sawfish"
2025-09-15 20:23:44.008 wdl.w:ptcp INFO input :: job: "call-sawfish-68", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-68/out/m84036_250809_035451_s4.bc2165.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-68/out/m84036_250809_035451_s4.bc2165.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2165"}
2025-09-15 20:23:44.009 wdl.w:ptcp NOTICE ready :: job: "call-trgt-68", callee: "trgt"
2025-09-15 20:23:44.009 wdl.w:ptcp INFO input :: job: "call-trgt-68", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-68/out/m84036_250809_035451_s4.bc2165.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-68/out/m84036_250809_035451_s4.bc2165.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2165"}
2025-09-15 20:23:44.012 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_plot_meth_allele NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-22/call-trgt_plot_meth_allele", thread: 140608748373568
2025-09-15 20:23:44.019 wdl.w:ptcp.w:call-trgt-16.t:call-get_reads_overlapping_repeats NOTICE done
2025-09-15 20:23:44.026 wdl.w:ptcp.w:call-trgt-16 NOTICE finish :: job: "call-get_reads_overlapping_repeats"
2025-09-15 20:23:44.026 wdl.w:ptcp.w:call-trgt-16 INFO output :: job: "call-get_reads_overlapping_repeats", values: {"reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-16/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2113.repeats.bam.bai", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-16/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2113.repeats.bam"}
2025-09-15 20:23:44.027 wdl.w:ptcp.w:call-trgt-16 INFO visit :: node: "output-reads_overlapping_repeats", values: {"reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-16/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2113.repeats.bam"}
2025-09-15 20:23:44.027 wdl.w:ptcp.w:call-trgt-16 INFO visit :: node: "output-reads_overlapping_repeats_bai", values: {"reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-16/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2113.repeats.bam.bai"}
2025-09-15 20:23:44.034 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_plot_meth_waterfall NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-22/call-trgt_plot_meth_waterfall", thread: 140608773551680
2025-09-15 20:23:44.037 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_plot_meth_allele INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:23:44.038 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_plot_meth_allele INFO input :: name: "waterfall", value: false
2025-09-15 20:23:44.038 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_plot_meth_allele INFO input :: name: "methylation", value: true
2025-09-15 20:23:44.038 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_plot_meth_allele INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:23:44.038 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_plot_meth_allele INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:23:44.038 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_plot_meth_allele INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:23:44.038 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_plot_meth_allele INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2119.trgt.sorted.spanning.bam.bai"
2025-09-15 20:23:44.038 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_plot_meth_allele INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2119.trgt.sorted.spanning.bam"
2025-09-15 20:23:44.038 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_plot_meth_allele INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2119.trgt.vcf"
2025-09-15 20:23:44.038 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_plot_meth_allele INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2119"
2025-09-15 20:23:44.038 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_plot_meth_allele INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:23:44.039 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_plot_meth_allele INFO eval :: name: "plot_type", value: "allele"
2025-09-15 20:23:44.039 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_plot_meth_allele INFO eval :: name: "show", value: "meth"
2025-09-15 20:23:44.039 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_plot_meth_allele INFO eval :: name: "threads", value: 1
2025-09-15 20:23:44.039 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_plot_meth_allele INFO eval :: name: "disk_size", value: 27
2025-09-15 20:23:44.039 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_plot_meth_allele INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2119.meth_allele"
2025-09-15 20:23:44.040 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_plot_meth_allele INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:23:44.040 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_plot_meth_allele WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:23:44.040 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_plot_meth_allele INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:23:44.040 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_plot_meth_allele INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:23:44.056 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_plot_meth_waterfall INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:23:44.056 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_plot_meth_waterfall INFO input :: name: "waterfall", value: true
2025-09-15 20:23:44.056 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_plot_meth_waterfall INFO input :: name: "methylation", value: true
2025-09-15 20:23:44.056 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_plot_meth_waterfall INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:23:44.056 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_plot_meth_waterfall INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:23:44.056 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_plot_meth_waterfall INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:23:44.056 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_plot_meth_waterfall INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2119.trgt.sorted.spanning.bam.bai"
2025-09-15 20:23:44.056 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_plot_meth_waterfall INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2119.trgt.sorted.spanning.bam"
2025-09-15 20:23:44.057 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_plot_meth_waterfall INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2119.trgt.vcf"
2025-09-15 20:23:44.057 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_plot_meth_waterfall INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2119"
2025-09-15 20:23:44.058 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_plot_meth_waterfall INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:23:44.058 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_plot_meth_waterfall INFO eval :: name: "plot_type", value: "waterfall"
2025-09-15 20:23:44.058 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_plot_meth_waterfall INFO eval :: name: "show", value: "meth"
2025-09-15 20:23:44.058 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_plot_meth_waterfall INFO eval :: name: "threads", value: 1
2025-09-15 20:23:44.059 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_plot_meth_waterfall INFO eval :: name: "disk_size", value: 27
2025-09-15 20:23:44.059 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_plot_meth_waterfall INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2119.meth_waterfall"
2025-09-15 20:23:44.059 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_plot_meth_waterfall INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:23:44.059 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_plot_meth_waterfall WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:23:44.059 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_plot_meth_waterfall INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:23:44.060 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_plot_meth_waterfall INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:23:44.063 wdl.w:ptcp.w:call-trgt-00.t:call-trgt_genotype INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 11, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-00/call-trgt_genotype/_singularity_tmpdir_0wb7owvr"
2025-09-15 20:23:44.063 wdl.w:ptcp.w:call-trgt-00.t:call-trgt_genotype INFO Slurm invocation: srun --job-name call-trgt_genotype --partition compute,compute9 --cpus-per-task 8 --mem 15259M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-00/call-trgt_genotype/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-00/call-trgt_genotype/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-00/call-trgt_genotype/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-00/call-trgt_genotype/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-00/out/m84036_250809_035451_s4.bc2097.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2097.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-00/out/m84036_250809_035451_s4.bc2097.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2097.mapped.bam:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-00/call-trgt_genotype/_singularity_tmpdir_0wb7owvr/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-00/call-trgt_genotype/_singularity_tmpdir_0wb7owvr/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:23:44.106 wdl.w:ptcp.w:call-trgt-00.t:call-trgt_genotype NOTICE slurm_singularity run :: pid: 1200062, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-00/call-trgt_genotype/slurm_singularity.log.txt"
2025-09-15 20:23:44.130 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_plot_meth_allele INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-22/call-trgt_plot_meth_allele/_singularity_tmpdir_g5gwjkqc"
2025-09-15 20:23:44.131 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_plot_meth_allele INFO Slurm invocation: srun --job-name call-trgt_plot_meth_allele --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-22/call-trgt_plot_meth_allele/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-22/call-trgt_plot_meth_allele/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-22/call-trgt_plot_meth_allele/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-22/call-trgt_plot_meth_allele/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-22/call-trgt_genotype/out/m84036_250809_035451_s4.bc2119.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2119.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-22/call-trgt_genotype/out/m84036_250809_035451_s4.bc2119.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2119.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-22/call-trgt_genotype/out/m84036_250809_035451_s4.bc2119.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2119.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-22/call-trgt_plot_meth_allele/_singularity_tmpdir_g5gwjkqc/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-22/call-trgt_plot_meth_allele/_singularity_tmpdir_g5gwjkqc/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:23:44.139 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_plot_meth_waterfall INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-22/call-trgt_plot_meth_waterfall/_singularity_tmpdir_8ntwtzvi"
2025-09-15 20:23:44.139 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_plot_meth_waterfall INFO Slurm invocation: srun --job-name call-trgt_plot_meth_waterfall --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-22/call-trgt_plot_meth_waterfall/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-22/call-trgt_plot_meth_waterfall/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-22/call-trgt_plot_meth_waterfall/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-22/call-trgt_plot_meth_waterfall/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-22/call-trgt_genotype/out/m84036_250809_035451_s4.bc2119.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2119.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-22/call-trgt_genotype/out/m84036_250809_035451_s4.bc2119.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2119.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-22/call-trgt_genotype/out/m84036_250809_035451_s4.bc2119.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2119.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-22/call-trgt_plot_meth_waterfall/_singularity_tmpdir_8ntwtzvi/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-22/call-trgt_plot_meth_waterfall/_singularity_tmpdir_8ntwtzvi/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:23:44.139 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_plot_meth_allele NOTICE slurm_singularity run :: pid: 1200064, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-22/call-trgt_plot_meth_allele/slurm_singularity.log.txt"
2025-09-15 20:23:44.145 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_plot_meth_waterfall NOTICE slurm_singularity run :: pid: 1200065, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-22/call-trgt_plot_meth_waterfall/slurm_singularity.log.txt"
2025-09-15 20:23:44.167 wdl.w:ptcp.w:call-paraphase-12.t:call-run_paraphase.stderr VERBOSE INFO:root:Processing sample m84036_250809_035451_s4.bc2109 at 2025-09-15 20:23:41.292299...
2025-09-15 20:23:44.168 wdl.w:ptcp.w:call-paraphase-12.t:call-run_paraphase.stderr VERBOSE INFO:root:Checking sample sex at 2025-09-15 20:23:41.293674...
2025-09-15 20:23:44.168 wdl.w:ptcp.w:call-paraphase-12.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for cyp21 for sample m84036_250809_035451_s4.bc2109 at 2025-09-15 20:23:41.331795...
2025-09-15 20:23:44.168 wdl.w:ptcp.w:call-paraphase-12.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for cyp21 for sample m84036_250809_035451_s4.bc2109 at 2025-09-15 20:23:41.332062...
2025-09-15 20:23:44.168 wdl.w:ptcp.w:call-paraphase-12.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for smn1 for sample m84036_250809_035451_s4.bc2109 at 2025-09-15 20:23:41.331918...
2025-09-15 20:23:44.168 wdl.w:ptcp.w:call-paraphase-12.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for smn1 for sample m84036_250809_035451_s4.bc2109 at 2025-09-15 20:23:41.332154...
2025-09-15 20:23:44.168 wdl.w:ptcp.w:call-paraphase-12.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for gba for sample m84036_250809_035451_s4.bc2109 at 2025-09-15 20:23:41.331993...
2025-09-15 20:23:44.168 wdl.w:ptcp.w:call-paraphase-12.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for hba for sample m84036_250809_035451_s4.bc2109 at 2025-09-15 20:23:41.331999...
2025-09-15 20:23:44.168 wdl.w:ptcp.w:call-paraphase-12.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for gba for sample m84036_250809_035451_s4.bc2109 at 2025-09-15 20:23:41.332231...
2025-09-15 20:23:44.168 wdl.w:ptcp.w:call-paraphase-12.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for hba for sample m84036_250809_035451_s4.bc2109 at 2025-09-15 20:23:41.332237...
2025-09-15 20:23:44.168 wdl.w:ptcp.w:call-paraphase-12.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for cyp21 for sample m84036_250809_035451_s4.bc2109 at 2025-09-15 20:23:42.104957...
2025-09-15 20:23:44.168 wdl.w:ptcp.w:call-paraphase-12.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for smn1 for sample m84036_250809_035451_s4.bc2109 at 2025-09-15 20:23:42.112504...
2025-09-15 20:23:44.168 wdl.w:ptcp.w:call-paraphase-12.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for hba for sample m84036_250809_035451_s4.bc2109 at 2025-09-15 20:23:42.144942...
2025-09-15 20:23:44.168 wdl.w:ptcp.w:call-paraphase-12.t:call-run_paraphase.stderr VERBOSE WARNING:root:This region does not appear to have coverage. Will not attempt to phase haplotypes.
2025-09-15 20:23:44.168 wdl.w:ptcp.w:call-paraphase-12.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for cyp21 for sample m84036_250809_035451_s4.bc2109 at 2025-09-15 20:23:42.177731...
2025-09-15 20:23:44.168 wdl.w:ptcp.w:call-paraphase-12.t:call-run_paraphase.stderr VERBOSE WARNING:root:This region does not appear to have coverage. Will not attempt to phase haplotypes.
2025-09-15 20:23:44.169 wdl.w:ptcp.w:call-paraphase-12.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for hba for sample m84036_250809_035451_s4.bc2109 at 2025-09-15 20:23:42.202640...
2025-09-15 20:23:44.169 wdl.w:ptcp.w:call-paraphase-12.t:call-run_paraphase.stderr VERBOSE WARNING:root:This region does not appear to have coverage. Will not attempt to phase haplotypes.
2025-09-15 20:23:44.169 wdl.w:ptcp.w:call-paraphase-12.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for smn1 for sample m84036_250809_035451_s4.bc2109 at 2025-09-15 20:23:42.213043...
2025-09-15 20:23:44.169 wdl.w:ptcp.w:call-paraphase-12.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for gba for sample m84036_250809_035451_s4.bc2109 at 2025-09-15 20:23:42.218540...
2025-09-15 20:23:44.169 wdl.w:ptcp.w:call-paraphase-12.t:call-run_paraphase.stderr VERBOSE WARNING:root:This region does not appear to have coverage. Will not attempt to phase haplotypes.
2025-09-15 20:23:44.169 wdl.w:ptcp.w:call-paraphase-12.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for gba for sample m84036_250809_035451_s4.bc2109 at 2025-09-15 20:23:42.318900...
2025-09-15 20:23:44.169 wdl.w:ptcp.w:call-paraphase-12.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for cyp21 for sample m84036_250809_035451_s4.bc2109 at 2025-09-15 20:23:42.679542...
2025-09-15 20:23:44.169 wdl.w:ptcp.w:call-paraphase-12.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for f8inv22 for sample m84036_250809_035451_s4.bc2109 at 2025-09-15 20:23:42.686469...
2025-09-15 20:23:44.169 wdl.w:ptcp.w:call-paraphase-12.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for f8inv22 for sample m84036_250809_035451_s4.bc2109 at 2025-09-15 20:23:42.686515...
2025-09-15 20:23:44.169 wdl.w:ptcp.w:call-paraphase-12.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for hba for sample m84036_250809_035451_s4.bc2109 at 2025-09-15 20:23:42.746494...
2025-09-15 20:23:44.169 wdl.w:ptcp.w:call-paraphase-12.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for hbb for sample m84036_250809_035451_s4.bc2109 at 2025-09-15 20:23:42.754330...
2025-09-15 20:23:44.169 wdl.w:ptcp.w:call-paraphase-12.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for hbb for sample m84036_250809_035451_s4.bc2109 at 2025-09-15 20:23:42.754385...
2025-09-15 20:23:44.169 wdl.w:ptcp.w:call-paraphase-12.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning to gene2 region for smn1 for sample m84036_250809_035451_s4.bc2109 at 2025-09-15 20:23:42.807955...
2025-09-15 20:23:44.169 wdl.w:ptcp.w:call-paraphase-12.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for gba for sample m84036_250809_035451_s4.bc2109 at 2025-09-15 20:23:42.884878...
2025-09-15 20:23:44.169 wdl.w:ptcp.w:call-paraphase-12.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for rpgr for sample m84036_250809_035451_s4.bc2109 at 2025-09-15 20:23:42.891921...
2025-09-15 20:23:44.169 wdl.w:ptcp.w:call-paraphase-12.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for rpgr for sample m84036_250809_035451_s4.bc2109 at 2025-09-15 20:23:42.891976...
2025-09-15 20:23:44.169 wdl.w:ptcp.w:call-paraphase-12.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for f8inv22 for sample m84036_250809_035451_s4.bc2109 at 2025-09-15 20:23:43.300788...
2025-09-15 20:23:44.170 wdl.w:ptcp.w:call-paraphase-12.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for hbb for sample m84036_250809_035451_s4.bc2109 at 2025-09-15 20:23:43.335704...
2025-09-15 20:23:44.170 wdl.w:ptcp.w:call-paraphase-12.t:call-run_paraphase.stderr VERBOSE WARNING:root:This region does not appear to have coverage. Will not attempt to phase haplotypes.
2025-09-15 20:23:44.170 wdl.w:ptcp.w:call-paraphase-12.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for f8inv22 for sample m84036_250809_035451_s4.bc2109 at 2025-09-15 20:23:43.342952...
2025-09-15 20:23:44.170 wdl.w:ptcp.w:call-paraphase-12.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for rpgr for sample m84036_250809_035451_s4.bc2109 at 2025-09-15 20:23:43.385357...
2025-09-15 20:23:44.170 wdl.w:ptcp.w:call-paraphase-12.t:call-run_paraphase.stderr VERBOSE WARNING:root:This region does not appear to have coverage. Will not attempt to phase haplotypes.
2025-09-15 20:23:44.170 wdl.w:ptcp.w:call-paraphase-12.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for hbb for sample m84036_250809_035451_s4.bc2109 at 2025-09-15 20:23:43.387038...
2025-09-15 20:23:44.170 wdl.w:ptcp.w:call-paraphase-12.t:call-run_paraphase.stderr VERBOSE WARNING:root:This region does not appear to have coverage. Will not attempt to phase haplotypes.
2025-09-15 20:23:44.170 wdl.w:ptcp.w:call-paraphase-12.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for rpgr for sample m84036_250809_035451_s4.bc2109 at 2025-09-15 20:23:43.419531...
2025-09-15 20:23:44.170 wdl.w:ptcp.w:call-paraphase-12.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for f8inv22 for sample m84036_250809_035451_s4.bc2109 at 2025-09-15 20:23:43.755548...
2025-09-15 20:23:44.170 wdl.w:ptcp.w:call-paraphase-12.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for smn1 for sample m84036_250809_035451_s4.bc2109 at 2025-09-15 20:23:43.795474...
2025-09-15 20:23:44.170 wdl.w:ptcp.w:call-paraphase-12.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for f8inv1 for sample m84036_250809_035451_s4.bc2109 at 2025-09-15 20:23:43.844583...
2025-09-15 20:23:44.170 wdl.w:ptcp.w:call-paraphase-12.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for f8inv1 for sample m84036_250809_035451_s4.bc2109 at 2025-09-15 20:23:43.844672...
2025-09-15 20:23:44.897 wdl.w:ptcp.w:call-sawfish-00.t:call-run_sawfish.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:44.897 wdl.w:ptcp.w:call-sawfish-00.t:call-run_sawfish.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:23:45.007 wdl.w:ptcp.w:call-paraphase-21.t:call-run_paraphase INFO output :: name: "paraphase_bam", value: "m84036_250809_035451_s4.bc2118_paraphase/m84036_250809_035451_s4.bc2118.paraphase.bam"
2025-09-15 20:23:45.011 wdl.w:ptcp.w:call-paraphase-21.t:call-run_paraphase INFO output :: name: "paraphase_bam_bai", value: "m84036_250809_035451_s4.bc2118_paraphase/m84036_250809_035451_s4.bc2118.paraphase.bam.bai"
2025-09-15 20:23:45.013 wdl.w:ptcp.w:call-paraphase-21.t:call-run_paraphase INFO output :: name: "paraphase_json", value: "m84036_250809_035451_s4.bc2118_paraphase/m84036_250809_035451_s4.bc2118.paraphase.json"
2025-09-15 20:23:45.015 wdl.w:ptcp.w:call-paraphase-21.t:call-run_paraphase INFO output :: name: "paraphase_vcfs", value: []
2025-09-15 20:23:45.015 wdl.w:ptcp.w:call-paraphase-21.t:call-run_paraphase INFO output :: name: "havanno_json", value: "m84036_250809_035451_s4.bc2118.havanno.json"
2025-09-15 20:23:45.104 wdl.w:ptcp.w:call-paraphase-09.t:call-run_paraphase.stderr VERBOSE INFO:root:Processing sample m84036_250809_035451_s4.bc2106 at 2025-09-15 20:23:40.700980...
2025-09-15 20:23:45.105 wdl.w:ptcp.w:call-paraphase-09.t:call-run_paraphase.stderr VERBOSE INFO:root:Checking sample sex at 2025-09-15 20:23:40.702285...
2025-09-15 20:23:45.105 wdl.w:ptcp.w:call-paraphase-09.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for cyp21 for sample m84036_250809_035451_s4.bc2106 at 2025-09-15 20:23:40.761926...
2025-09-15 20:23:45.105 wdl.w:ptcp.w:call-paraphase-09.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for smn1 for sample m84036_250809_035451_s4.bc2106 at 2025-09-15 20:23:40.762086...
2025-09-15 20:23:45.105 wdl.w:ptcp.w:call-paraphase-09.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for gba for sample m84036_250809_035451_s4.bc2106 at 2025-09-15 20:23:40.762128...
2025-09-15 20:23:45.105 wdl.w:ptcp.w:call-paraphase-09.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for cyp21 for sample m84036_250809_035451_s4.bc2106 at 2025-09-15 20:23:40.762671...
2025-09-15 20:23:45.105 wdl.w:ptcp.w:call-paraphase-09.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for hba for sample m84036_250809_035451_s4.bc2106 at 2025-09-15 20:23:40.762156...
2025-09-15 20:23:45.105 wdl.w:ptcp.w:call-paraphase-09.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for smn1 for sample m84036_250809_035451_s4.bc2106 at 2025-09-15 20:23:40.762745...
2025-09-15 20:23:45.105 wdl.w:ptcp.w:call-paraphase-09.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for gba for sample m84036_250809_035451_s4.bc2106 at 2025-09-15 20:23:40.762747...
2025-09-15 20:23:45.105 wdl.w:ptcp.w:call-paraphase-09.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for hba for sample m84036_250809_035451_s4.bc2106 at 2025-09-15 20:23:40.762768...
2025-09-15 20:23:45.105 wdl.w:ptcp.w:call-paraphase-09.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for smn1 for sample m84036_250809_035451_s4.bc2106 at 2025-09-15 20:23:41.341869...
2025-09-15 20:23:45.105 wdl.w:ptcp.w:call-paraphase-09.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for cyp21 for sample m84036_250809_035451_s4.bc2106 at 2025-09-15 20:23:41.390847...
2025-09-15 20:23:45.105 wdl.w:ptcp.w:call-paraphase-09.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for hba for sample m84036_250809_035451_s4.bc2106 at 2025-09-15 20:23:41.420669...
2025-09-15 20:23:45.105 wdl.w:ptcp.w:call-paraphase-09.t:call-run_paraphase.stderr VERBOSE WARNING:root:This region does not appear to have coverage. Will not attempt to phase haplotypes.
2025-09-15 20:23:45.105 wdl.w:ptcp.w:call-paraphase-09.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for cyp21 for sample m84036_250809_035451_s4.bc2106 at 2025-09-15 20:23:41.488396...
2025-09-15 20:23:45.105 wdl.w:ptcp.w:call-paraphase-09.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for gba for sample m84036_250809_035451_s4.bc2106 at 2025-09-15 20:23:41.498996...
2025-09-15 20:23:45.105 wdl.w:ptcp.w:call-paraphase-09.t:call-run_paraphase.stderr VERBOSE WARNING:root:This region does not appear to have coverage. Will not attempt to phase haplotypes.
2025-09-15 20:23:45.105 wdl.w:ptcp.w:call-paraphase-09.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for hba for sample m84036_250809_035451_s4.bc2106 at 2025-09-15 20:23:41.505103...
2025-09-15 20:23:45.106 wdl.w:ptcp.w:call-paraphase-09.t:call-run_paraphase.stderr VERBOSE WARNING:root:This region does not appear to have coverage. Will not attempt to phase haplotypes.
2025-09-15 20:23:45.106 wdl.w:ptcp.w:call-paraphase-09.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for smn1 for sample m84036_250809_035451_s4.bc2106 at 2025-09-15 20:23:41.526275...
2025-09-15 20:23:45.106 wdl.w:ptcp.w:call-paraphase-09.t:call-run_paraphase.stderr VERBOSE WARNING:root:This region does not appear to have coverage. Will not attempt to phase haplotypes.
2025-09-15 20:23:45.106 wdl.w:ptcp.w:call-paraphase-09.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for gba for sample m84036_250809_035451_s4.bc2106 at 2025-09-15 20:23:41.617981...
2025-09-15 20:23:45.106 wdl.w:ptcp.w:call-paraphase-09.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for cyp21 for sample m84036_250809_035451_s4.bc2106 at 2025-09-15 20:23:41.899908...
2025-09-15 20:23:45.106 wdl.w:ptcp.w:call-paraphase-09.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for f8inv22 for sample m84036_250809_035451_s4.bc2106 at 2025-09-15 20:23:41.905257...
2025-09-15 20:23:45.106 wdl.w:ptcp.w:call-paraphase-09.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for f8inv22 for sample m84036_250809_035451_s4.bc2106 at 2025-09-15 20:23:41.905321...
2025-09-15 20:23:45.106 wdl.w:ptcp.w:call-paraphase-09.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for hba for sample m84036_250809_035451_s4.bc2106 at 2025-09-15 20:23:42.024336...
2025-09-15 20:23:45.106 wdl.w:ptcp.w:call-paraphase-09.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for hbb for sample m84036_250809_035451_s4.bc2106 at 2025-09-15 20:23:42.033684...
2025-09-15 20:23:45.106 wdl.w:ptcp.w:call-paraphase-09.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for hbb for sample m84036_250809_035451_s4.bc2106 at 2025-09-15 20:23:42.033749...
2025-09-15 20:23:45.106 wdl.w:ptcp.w:call-paraphase-09.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning to gene2 region for smn1 for sample m84036_250809_035451_s4.bc2106 at 2025-09-15 20:23:42.050411...
2025-09-15 20:23:45.106 wdl.w:ptcp.w:call-paraphase-09.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for gba for sample m84036_250809_035451_s4.bc2106 at 2025-09-15 20:23:42.128455...
2025-09-15 20:23:45.106 wdl.w:ptcp.w:call-paraphase-09.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for rpgr for sample m84036_250809_035451_s4.bc2106 at 2025-09-15 20:23:42.141201...
2025-09-15 20:23:45.106 wdl.w:ptcp.w:call-paraphase-09.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for rpgr for sample m84036_250809_035451_s4.bc2106 at 2025-09-15 20:23:42.141297...
2025-09-15 20:23:45.106 wdl.w:ptcp.w:call-paraphase-09.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for f8inv22 for sample m84036_250809_035451_s4.bc2106 at 2025-09-15 20:23:42.384800...
2025-09-15 20:23:45.106 wdl.w:ptcp.w:call-paraphase-09.t:call-run_paraphase.stderr VERBOSE WARNING:root:This region does not appear to have coverage. Will not attempt to phase haplotypes.
2025-09-15 20:23:45.106 wdl.w:ptcp.w:call-paraphase-09.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for f8inv22 for sample m84036_250809_035451_s4.bc2106 at 2025-09-15 20:23:42.462512...
2025-09-15 20:23:45.107 wdl.w:ptcp.w:call-paraphase-09.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for hbb for sample m84036_250809_035451_s4.bc2106 at 2025-09-15 20:23:42.528137...
2025-09-15 20:23:45.107 wdl.w:ptcp.w:call-paraphase-09.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for rpgr for sample m84036_250809_035451_s4.bc2106 at 2025-09-15 20:23:42.592479...
2025-09-15 20:23:45.107 wdl.w:ptcp.w:call-paraphase-09.t:call-run_paraphase.stderr VERBOSE WARNING:root:This region does not appear to have coverage. Will not attempt to phase haplotypes.
2025-09-15 20:23:45.107 wdl.w:ptcp.w:call-paraphase-09.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for hbb for sample m84036_250809_035451_s4.bc2106 at 2025-09-15 20:23:42.607104...
2025-09-15 20:23:45.107 wdl.w:ptcp.w:call-paraphase-09.t:call-run_paraphase.stderr VERBOSE WARNING:root:This region does not appear to have coverage. Will not attempt to phase haplotypes.
2025-09-15 20:23:45.107 wdl.w:ptcp.w:call-paraphase-09.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for rpgr for sample m84036_250809_035451_s4.bc2106 at 2025-09-15 20:23:42.661878...
2025-09-15 20:23:45.107 wdl.w:ptcp.w:call-paraphase-09.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for f8inv22 for sample m84036_250809_035451_s4.bc2106 at 2025-09-15 20:23:42.935369...
2025-09-15 20:23:45.107 wdl.w:ptcp.w:call-paraphase-09.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for smn1 for sample m84036_250809_035451_s4.bc2106 at 2025-09-15 20:23:42.997050...
2025-09-15 20:23:45.107 wdl.w:ptcp.w:call-paraphase-09.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for hbb for sample m84036_250809_035451_s4.bc2106 at 2025-09-15 20:23:43.025171...
2025-09-15 20:23:45.107 wdl.w:ptcp.w:call-paraphase-09.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for f8inv1 for sample m84036_250809_035451_s4.bc2106 at 2025-09-15 20:23:43.060040...
2025-09-15 20:23:45.107 wdl.w:ptcp.w:call-paraphase-09.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for f8inv1 for sample m84036_250809_035451_s4.bc2106 at 2025-09-15 20:23:43.060194...
2025-09-15 20:23:45.107 wdl.w:ptcp.w:call-paraphase-09.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for rpgr for sample m84036_250809_035451_s4.bc2106 at 2025-09-15 20:23:43.075817...
2025-09-15 20:23:45.107 wdl.w:ptcp.w:call-paraphase-09.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for f8inv1 for sample m84036_250809_035451_s4.bc2106 at 2025-09-15 20:23:43.543442...
2025-09-15 20:23:45.107 wdl.w:ptcp.w:call-paraphase-21.t:call-run_paraphase NOTICE done
2025-09-15 20:23:45.107 wdl.w:ptcp.w:call-paraphase-09.t:call-run_paraphase.stderr VERBOSE WARNING:root:This region does not appear to have coverage. Will not attempt to phase haplotypes.
2025-09-15 20:23:45.108 wdl.w:ptcp.w:call-paraphase-09.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for f8inv1 for sample m84036_250809_035451_s4.bc2106 at 2025-09-15 20:23:43.591773...
2025-09-15 20:23:45.108 wdl.w:ptcp.w:call-paraphase-09.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for f8inv1 for sample m84036_250809_035451_s4.bc2106 at 2025-09-15 20:23:43.867207...
2025-09-15 20:23:45.108 wdl.w:ptcp.w:call-paraphase-09.t:call-run_paraphase.stderr VERBOSE INFO:root:Merging all bams for sample m84036_250809_035451_s4.bc2106 at 2025-09-15 20:23:43.887545...
2025-09-15 20:23:45.108 wdl.w:ptcp.w:call-paraphase-09.t:call-run_paraphase.stderr VERBOSE INFO:root:Writing to json for sample m84036_250809_035451_s4.bc2106 at 2025-09-15 20:23:44.341542...
2025-09-15 20:23:45.108 wdl.w:ptcp.w:call-paraphase-09.t:call-run_paraphase.stderr VERBOSE INFO:root:Completed Paraphase analysis at 2025-09-15 20:23:44.700383...
2025-09-15 20:23:45.114 wdl.w:ptcp.w:call-paraphase-21 NOTICE finish :: job: "call-run_paraphase"
2025-09-15 20:23:45.114 wdl.w:ptcp.w:call-paraphase-21 INFO output :: job: "call-run_paraphase", values: {"havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-21/call-run_paraphase/out/m84036_250809_035451_s4.bc2118.havanno.json", "paraphase_vcfs": [], "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-21/call-run_paraphase/out/m84036_250809_035451_s4.bc2118_paraphase/m84036_250809_035451_s4.bc2118.paraphase.json", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-21/call-run_paraphase/out/m84036_250809_035451_s4.bc2118_paraphase/m84036_250809_035451_s4.bc2118.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-21/call-run_paraphase/out/m84036_250809_035451_s4.bc2118_paraphase/m84036_250809_035451_s4.bc2118.paraphase.bam"}
2025-09-15 20:23:45.115 wdl.w:ptcp.w:call-paraphase-21 NOTICE ready :: job: "call-call_f8", callee: "call_f8"
2025-09-15 20:23:45.115 wdl.w:ptcp.w:call-paraphase-21 INFO input :: job: "call-call_f8", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "out_prefix": "m84036_250809_035451_s4.bc2118", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-21/call-run_paraphase/out/m84036_250809_035451_s4.bc2118_paraphase/m84036_250809_035451_s4.bc2118.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-21/call-run_paraphase/out/m84036_250809_035451_s4.bc2118_paraphase/m84036_250809_035451_s4.bc2118.paraphase.bam", "sex": "F"}
2025-09-15 20:23:45.116 wdl.w:ptcp.w:call-paraphase-21 INFO visit :: node: "output-havanno_json", values: {"havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-21/call-run_paraphase/out/m84036_250809_035451_s4.bc2118.havanno.json"}
2025-09-15 20:23:45.116 wdl.w:ptcp.w:call-paraphase-21 INFO visit :: node: "output-paraphase_bam", values: {"paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-21/call-run_paraphase/out/m84036_250809_035451_s4.bc2118_paraphase/m84036_250809_035451_s4.bc2118.paraphase.bam"}
2025-09-15 20:23:45.116 wdl.w:ptcp.w:call-paraphase-21 INFO visit :: node: "output-paraphase_bam_bai", values: {"paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-21/call-run_paraphase/out/m84036_250809_035451_s4.bc2118_paraphase/m84036_250809_035451_s4.bc2118.paraphase.bam.bai"}
2025-09-15 20:23:45.116 wdl.w:ptcp.w:call-paraphase-21 INFO visit :: node: "output-paraphase_json", values: {"paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-21/call-run_paraphase/out/m84036_250809_035451_s4.bc2118_paraphase/m84036_250809_035451_s4.bc2118.paraphase.json"}
2025-09-15 20:23:45.116 wdl.w:ptcp.w:call-paraphase-21 INFO visit :: node: "output-paraphase_vcfs", values: {"paraphase_vcfs": []}
2025-09-15 20:23:45.118 wdl.w:ptcp.w:call-trgt-00.t:call-trgt_genotype.slurm_singularity INFO srun: job 51797462 queued and waiting for resources
2025-09-15 20:23:45.119 wdl.w:ptcp.w:call-trgt-00.t:call-trgt_genotype.slurm_singularity INFO srun: job 51797462 has been allocated resources
2025-09-15 20:23:45.119 wdl.w:ptcp.w:call-trgt-00.t:call-trgt_genotype.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:45.119 wdl.w:ptcp.w:call-trgt-00.t:call-trgt_genotype.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:23:45.121 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_plot_motifs_allele NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-22/call-trgt_plot_motifs_allele", thread: 140610358986304
2025-09-15 20:23:45.139 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_plot_motifs_allele INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:23:45.139 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_plot_motifs_allele INFO input :: name: "waterfall", value: false
2025-09-15 20:23:45.139 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_plot_motifs_allele INFO input :: name: "methylation", value: false
2025-09-15 20:23:45.139 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_plot_motifs_allele INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:23:45.140 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_plot_motifs_allele INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:23:45.140 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_plot_motifs_allele INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:23:45.140 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_plot_motifs_allele INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2119.trgt.sorted.spanning.bam.bai"
2025-09-15 20:23:45.140 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_plot_motifs_allele INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2119.trgt.sorted.spanning.bam"
2025-09-15 20:23:45.140 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_plot_motifs_allele INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2119.trgt.vcf"
2025-09-15 20:23:45.140 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_plot_motifs_allele INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2119"
2025-09-15 20:23:45.140 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_plot_motifs_allele INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:23:45.140 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_plot_motifs_allele INFO eval :: name: "plot_type", value: "allele"
2025-09-15 20:23:45.140 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_plot_motifs_allele INFO eval :: name: "show", value: "motifs"
2025-09-15 20:23:45.140 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_plot_motifs_allele INFO eval :: name: "threads", value: 1
2025-09-15 20:23:45.141 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_plot_motifs_allele INFO eval :: name: "disk_size", value: 27
2025-09-15 20:23:45.141 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_plot_motifs_allele INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2119.motifs_allele"
2025-09-15 20:23:45.141 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_plot_motifs_allele INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:23:45.141 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_plot_motifs_allele WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:23:45.142 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_plot_motifs_allele INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:23:45.142 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_plot_motifs_allele INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:23:45.150 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_plot_meth_allele.slurm_singularity INFO srun: job 51797463 queued and waiting for resources
2025-09-15 20:23:45.150 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_plot_meth_allele.slurm_singularity INFO srun: job 51797463 has been allocated resources
2025-09-15 20:23:45.150 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_plot_meth_allele.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:45.150 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_plot_meth_allele.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:23:45.157 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO srun: job 51797464 queued and waiting for resources
2025-09-15 20:23:45.157 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO srun: job 51797464 has been allocated resources
2025-09-15 20:23:45.157 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:45.157 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:23:45.228 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_plot_motifs_allele INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-22/call-trgt_plot_motifs_allele/_singularity_tmpdir_pr0v1cs9"
2025-09-15 20:23:45.229 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_plot_motifs_allele INFO Slurm invocation: srun --job-name call-trgt_plot_motifs_allele --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-22/call-trgt_plot_motifs_allele/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-22/call-trgt_plot_motifs_allele/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-22/call-trgt_plot_motifs_allele/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-22/call-trgt_plot_motifs_allele/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-22/call-trgt_genotype/out/m84036_250809_035451_s4.bc2119.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2119.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-22/call-trgt_genotype/out/m84036_250809_035451_s4.bc2119.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2119.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-22/call-trgt_genotype/out/m84036_250809_035451_s4.bc2119.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2119.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-22/call-trgt_plot_motifs_allele/_singularity_tmpdir_pr0v1cs9/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-22/call-trgt_plot_motifs_allele/_singularity_tmpdir_pr0v1cs9/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:23:45.247 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_plot_motifs_allele NOTICE slurm_singularity run :: pid: 1200084, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-22/call-trgt_plot_motifs_allele/slurm_singularity.log.txt"
2025-09-15 20:23:45.377 wdl.w:ptcp.w:call-paraphase-09.t:call-run_paraphase INFO output :: name: "paraphase_bam", value: "m84036_250809_035451_s4.bc2106_paraphase/m84036_250809_035451_s4.bc2106.paraphase.bam"
2025-09-15 20:23:45.382 wdl.w:ptcp.w:call-paraphase-09.t:call-run_paraphase INFO output :: name: "paraphase_bam_bai", value: "m84036_250809_035451_s4.bc2106_paraphase/m84036_250809_035451_s4.bc2106.paraphase.bam.bai"
2025-09-15 20:23:45.383 wdl.w:ptcp.w:call-paraphase-09.t:call-run_paraphase INFO output :: name: "paraphase_json", value: "m84036_250809_035451_s4.bc2106_paraphase/m84036_250809_035451_s4.bc2106.paraphase.json"
2025-09-15 20:23:45.386 wdl.w:ptcp.w:call-paraphase-09.t:call-run_paraphase INFO output :: name: "paraphase_vcfs", value: []
2025-09-15 20:23:45.387 wdl.w:ptcp.w:call-paraphase-09.t:call-run_paraphase INFO output :: name: "havanno_json", value: "m84036_250809_035451_s4.bc2106.havanno.json"
2025-09-15 20:23:45.479 wdl.w:ptcp.w:call-paraphase-09.t:call-run_paraphase NOTICE done
2025-09-15 20:23:45.484 wdl.w:ptcp.w:call-paraphase-09 NOTICE finish :: job: "call-run_paraphase"
2025-09-15 20:23:45.485 wdl.w:ptcp.w:call-paraphase-09 INFO output :: job: "call-run_paraphase", values: {"havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-09/call-run_paraphase/out/m84036_250809_035451_s4.bc2106.havanno.json", "paraphase_vcfs": [], "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-09/call-run_paraphase/out/m84036_250809_035451_s4.bc2106_paraphase/m84036_250809_035451_s4.bc2106.paraphase.json", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-09/call-run_paraphase/out/m84036_250809_035451_s4.bc2106_paraphase/m84036_250809_035451_s4.bc2106.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-09/call-run_paraphase/out/m84036_250809_035451_s4.bc2106_paraphase/m84036_250809_035451_s4.bc2106.paraphase.bam"}
2025-09-15 20:23:45.485 wdl.w:ptcp.w:call-paraphase-09 NOTICE ready :: job: "call-call_f8", callee: "call_f8"
2025-09-15 20:23:45.486 wdl.w:ptcp.w:call-paraphase-09 INFO input :: job: "call-call_f8", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "out_prefix": "m84036_250809_035451_s4.bc2106", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-09/call-run_paraphase/out/m84036_250809_035451_s4.bc2106_paraphase/m84036_250809_035451_s4.bc2106.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-09/call-run_paraphase/out/m84036_250809_035451_s4.bc2106_paraphase/m84036_250809_035451_s4.bc2106.paraphase.bam", "sex": "F"}
2025-09-15 20:23:45.487 wdl.w:ptcp.w:call-paraphase-09 INFO visit :: node: "output-havanno_json", values: {"havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-09/call-run_paraphase/out/m84036_250809_035451_s4.bc2106.havanno.json"}
2025-09-15 20:23:45.487 wdl.w:ptcp.w:call-paraphase-09 INFO visit :: node: "output-paraphase_bam", values: {"paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-09/call-run_paraphase/out/m84036_250809_035451_s4.bc2106_paraphase/m84036_250809_035451_s4.bc2106.paraphase.bam"}
2025-09-15 20:23:45.487 wdl.w:ptcp.w:call-paraphase-09 INFO visit :: node: "output-paraphase_bam_bai", values: {"paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-09/call-run_paraphase/out/m84036_250809_035451_s4.bc2106_paraphase/m84036_250809_035451_s4.bc2106.paraphase.bam.bai"}
2025-09-15 20:23:45.487 wdl.w:ptcp.w:call-paraphase-09 INFO visit :: node: "output-paraphase_json", values: {"paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-09/call-run_paraphase/out/m84036_250809_035451_s4.bc2106_paraphase/m84036_250809_035451_s4.bc2106.paraphase.json"}
2025-09-15 20:23:45.487 wdl.w:ptcp.w:call-paraphase-09 INFO visit :: node: "output-paraphase_vcfs", values: {"paraphase_vcfs": []}
2025-09-15 20:23:45.492 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_plot_motifs_waterfall NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-22/call-trgt_plot_motifs_waterfall", thread: 140610879071808
2025-09-15 20:23:45.510 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_plot_motifs_waterfall INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:23:45.510 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_plot_motifs_waterfall INFO input :: name: "waterfall", value: true
2025-09-15 20:23:45.510 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_plot_motifs_waterfall INFO input :: name: "methylation", value: false
2025-09-15 20:23:45.510 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_plot_motifs_waterfall INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:23:45.510 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_plot_motifs_waterfall INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:23:45.511 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_plot_motifs_waterfall INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:23:45.511 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_plot_motifs_waterfall INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2119.trgt.sorted.spanning.bam.bai"
2025-09-15 20:23:45.511 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_plot_motifs_waterfall INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2119.trgt.sorted.spanning.bam"
2025-09-15 20:23:45.511 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_plot_motifs_waterfall INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2119.trgt.vcf"
2025-09-15 20:23:45.511 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_plot_motifs_waterfall INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2119"
2025-09-15 20:23:45.511 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:23:45.511 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "plot_type", value: "waterfall"
2025-09-15 20:23:45.511 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "show", value: "motifs"
2025-09-15 20:23:45.511 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "threads", value: 1
2025-09-15 20:23:45.512 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "disk_size", value: 27
2025-09-15 20:23:45.512 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2119.motifs_waterfall"
2025-09-15 20:23:45.512 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_plot_motifs_waterfall INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:23:45.512 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_plot_motifs_waterfall WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:23:45.513 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_plot_motifs_waterfall INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:23:45.513 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_plot_motifs_waterfall INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:23:45.598 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_plot_motifs_waterfall INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-22/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_8d9uc0r_"
2025-09-15 20:23:45.599 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_plot_motifs_waterfall INFO Slurm invocation: srun --job-name call-trgt_plot_motifs_waterfall --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-22/call-trgt_plot_motifs_waterfall/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-22/call-trgt_plot_motifs_waterfall/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-22/call-trgt_plot_motifs_waterfall/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-22/call-trgt_plot_motifs_waterfall/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-22/call-trgt_genotype/out/m84036_250809_035451_s4.bc2119.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2119.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-22/call-trgt_genotype/out/m84036_250809_035451_s4.bc2119.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2119.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-22/call-trgt_genotype/out/m84036_250809_035451_s4.bc2119.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2119.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-22/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_8d9uc0r_/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-22/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_8d9uc0r_/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:23:45.605 wdl.w:ptcp.w:call-trgt-32.t:call-trgt_genotype INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2129.trgt.vcf"
2025-09-15 20:23:45.609 wdl.w:ptcp.w:call-trgt-32.t:call-trgt_genotype INFO output :: name: "spanning_bam", value: "m84036_250809_035451_s4.bc2129.trgt.sorted.spanning.bam"
2025-09-15 20:23:45.612 wdl.w:ptcp.w:call-trgt-32.t:call-trgt_genotype INFO output :: name: "spanning_bam_bai", value: "m84036_250809_035451_s4.bc2129.trgt.sorted.spanning.bam.bai"
2025-09-15 20:23:45.613 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_plot_motifs_waterfall NOTICE slurm_singularity run :: pid: 1200093, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-22/call-trgt_plot_motifs_waterfall/slurm_singularity.log.txt"
2025-09-15 20:23:45.699 wdl.w:ptcp.w:call-trgt-32.t:call-trgt_genotype NOTICE done
2025-09-15 20:23:45.704 wdl.w:ptcp.w:call-trgt-32 NOTICE finish :: job: "call-trgt_genotype"
2025-09-15 20:23:45.704 wdl.w:ptcp.w:call-trgt-32 INFO output :: job: "call-trgt_genotype", values: {"spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-32/call-trgt_genotype/out/m84036_250809_035451_s4.bc2129.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-32/call-trgt_genotype/out/m84036_250809_035451_s4.bc2129.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-32/call-trgt_genotype/out/m84036_250809_035451_s4.bc2129.trgt.vcf"}
2025-09-15 20:23:45.705 wdl.w:ptcp.w:call-trgt-32 NOTICE ready :: job: "call-trgt_plot_meth_allele", callee: "trgt_plot"
2025-09-15 20:23:45.705 wdl.w:ptcp.w:call-trgt-32 INFO input :: job: "call-trgt_plot_meth_allele", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": false, "methylation": true, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-32/call-trgt_genotype/out/m84036_250809_035451_s4.bc2129.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-32/call-trgt_genotype/out/m84036_250809_035451_s4.bc2129.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-32/call-trgt_genotype/out/m84036_250809_035451_s4.bc2129.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2129"}
2025-09-15 20:23:45.706 wdl.w:ptcp.w:call-trgt-32 NOTICE ready :: job: "call-trgt_plot_meth_waterfall", callee: "trgt_plot"
2025-09-15 20:23:45.706 wdl.w:ptcp.w:call-trgt-32 INFO input :: job: "call-trgt_plot_meth_waterfall", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": true, "methylation": true, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-32/call-trgt_genotype/out/m84036_250809_035451_s4.bc2129.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-32/call-trgt_genotype/out/m84036_250809_035451_s4.bc2129.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-32/call-trgt_genotype/out/m84036_250809_035451_s4.bc2129.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2129"}
2025-09-15 20:23:45.707 wdl.w:ptcp.w:call-trgt-32 NOTICE ready :: job: "call-trgt_plot_motifs_allele", callee: "trgt_plot"
2025-09-15 20:23:45.707 wdl.w:ptcp.w:call-trgt-32 INFO input :: job: "call-trgt_plot_motifs_allele", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": false, "methylation": false, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-32/call-trgt_genotype/out/m84036_250809_035451_s4.bc2129.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-32/call-trgt_genotype/out/m84036_250809_035451_s4.bc2129.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-32/call-trgt_genotype/out/m84036_250809_035451_s4.bc2129.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2129"}
2025-09-15 20:23:45.708 wdl.w:ptcp.w:call-trgt-32 NOTICE ready :: job: "call-trgt_plot_motifs_waterfall", callee: "trgt_plot"
2025-09-15 20:23:45.708 wdl.w:ptcp.w:call-trgt-32 INFO input :: job: "call-trgt_plot_motifs_waterfall", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": true, "methylation": false, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-32/call-trgt_genotype/out/m84036_250809_035451_s4.bc2129.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-32/call-trgt_genotype/out/m84036_250809_035451_s4.bc2129.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-32/call-trgt_genotype/out/m84036_250809_035451_s4.bc2129.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2129"}
2025-09-15 20:23:45.709 wdl.w:ptcp.w:call-trgt-32 INFO visit :: node: "output-spanning_bam", values: {"spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-32/call-trgt_genotype/out/m84036_250809_035451_s4.bc2129.trgt.sorted.spanning.bam"}
2025-09-15 20:23:45.709 wdl.w:ptcp.w:call-trgt-32 INFO visit :: node: "output-spanning_bam_bai", values: {"spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-32/call-trgt_genotype/out/m84036_250809_035451_s4.bc2129.trgt.sorted.spanning.bam.bai"}
2025-09-15 20:23:45.709 wdl.w:ptcp.w:call-trgt-32 INFO visit :: node: "output-vcf", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-32/call-trgt_genotype/out/m84036_250809_035451_s4.bc2129.trgt.vcf"}
2025-09-15 20:23:45.710 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_plot_meth_allele NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-15/call-trgt_plot_meth_allele", thread: 140609822115392
2025-09-15 20:23:45.729 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_plot_meth_allele INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:23:45.729 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_plot_meth_allele INFO input :: name: "waterfall", value: false
2025-09-15 20:23:45.729 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_plot_meth_allele INFO input :: name: "methylation", value: true
2025-09-15 20:23:45.729 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_plot_meth_allele INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:23:45.729 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_plot_meth_allele INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:23:45.730 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_plot_meth_allele INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:23:45.730 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_plot_meth_allele INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2112.trgt.sorted.spanning.bam.bai"
2025-09-15 20:23:45.730 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_plot_meth_allele INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2112.trgt.sorted.spanning.bam"
2025-09-15 20:23:45.730 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_plot_meth_allele INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2112.trgt.vcf"
2025-09-15 20:23:45.730 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_plot_meth_allele INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2112"
2025-09-15 20:23:45.730 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_plot_meth_allele INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:23:45.730 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_plot_meth_allele INFO eval :: name: "plot_type", value: "allele"
2025-09-15 20:23:45.730 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_plot_meth_allele INFO eval :: name: "show", value: "meth"
2025-09-15 20:23:45.730 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_plot_meth_allele INFO eval :: name: "threads", value: 1
2025-09-15 20:23:45.731 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_plot_meth_allele INFO eval :: name: "disk_size", value: 27
2025-09-15 20:23:45.731 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_plot_meth_allele INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2112.meth_allele"
2025-09-15 20:23:45.731 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_plot_meth_allele INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:23:45.731 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_plot_meth_allele WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:23:45.731 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_plot_meth_allele INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:23:45.732 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_plot_meth_allele INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:23:45.825 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_plot_meth_allele INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-15/call-trgt_plot_meth_allele/_singularity_tmpdir_bp1hcpfs"
2025-09-15 20:23:45.825 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_plot_meth_allele INFO Slurm invocation: srun --job-name call-trgt_plot_meth_allele --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-15/call-trgt_plot_meth_allele/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-15/call-trgt_plot_meth_allele/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-15/call-trgt_plot_meth_allele/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-15/call-trgt_plot_meth_allele/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-15/call-trgt_genotype/out/m84036_250809_035451_s4.bc2112.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2112.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-15/call-trgt_genotype/out/m84036_250809_035451_s4.bc2112.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2112.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-15/call-trgt_genotype/out/m84036_250809_035451_s4.bc2112.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2112.trgt.vcf:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-15/call-trgt_plot_meth_allele/_singularity_tmpdir_bp1hcpfs/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-15/call-trgt_plot_meth_allele/_singularity_tmpdir_bp1hcpfs/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:23:45.839 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_plot_meth_allele NOTICE slurm_singularity run :: pid: 1200095, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-15/call-trgt_plot_meth_allele/slurm_singularity.log.txt"
2025-09-15 20:23:45.965 wdl.w:ptcp.w:call-paraphase-34.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for cyp21 for sample m84036_250809_035451_s4.bc2131 at 2025-09-15 20:23:35.806870...
2025-09-15 20:23:45.965 wdl.w:ptcp.w:call-paraphase-34.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for hba for sample m84036_250809_035451_s4.bc2131 at 2025-09-15 20:23:36.549546...
2025-09-15 20:23:45.965 wdl.w:ptcp.w:call-paraphase-34.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for cyp21 for sample m84036_250809_035451_s4.bc2131 at 2025-09-15 20:23:36.596484...
2025-09-15 20:23:45.965 wdl.w:ptcp.w:call-paraphase-34.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for hba for sample m84036_250809_035451_s4.bc2131 at 2025-09-15 20:23:36.963935...
2025-09-15 20:23:45.966 wdl.w:ptcp.w:call-paraphase-34.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for gba for sample m84036_250809_035451_s4.bc2131 at 2025-09-15 20:23:43.441388...
2025-09-15 20:23:45.966 wdl.w:ptcp.w:call-paraphase-34.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for gba for sample m84036_250809_035451_s4.bc2131 at 2025-09-15 20:23:43.967626...
2025-09-15 20:23:45.966 wdl.w:ptcp.w:call-paraphase-34.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for f8inv1 for sample m84036_250809_035451_s4.bc2131 at 2025-09-15 20:23:44.824712...
2025-09-15 20:23:45.966 wdl.w:ptcp.w:call-paraphase-34.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for f8inv1 for sample m84036_250809_035451_s4.bc2131 at 2025-09-15 20:23:44.824894...
2025-09-15 20:23:46.027 wdl.w:ptcp.w:call-paraphase-24.t:call-run_paraphase.stderr VERBOSE INFO:root:Processing sample m84036_250809_035451_s4.bc2121 at 2025-09-15 20:23:42.457950...
2025-09-15 20:23:46.027 wdl.w:ptcp.w:call-paraphase-24.t:call-run_paraphase.stderr VERBOSE INFO:root:Checking sample sex at 2025-09-15 20:23:42.459508...
2025-09-15 20:23:46.027 wdl.w:ptcp.w:call-paraphase-24.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for smn1 for sample m84036_250809_035451_s4.bc2121 at 2025-09-15 20:23:42.527185...
2025-09-15 20:23:46.028 wdl.w:ptcp.w:call-paraphase-24.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for cyp21 for sample m84036_250809_035451_s4.bc2121 at 2025-09-15 20:23:42.527111...
2025-09-15 20:23:46.028 wdl.w:ptcp.w:call-paraphase-24.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for smn1 for sample m84036_250809_035451_s4.bc2121 at 2025-09-15 20:23:42.527658...
2025-09-15 20:23:46.028 wdl.w:ptcp.w:call-paraphase-24.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for cyp21 for sample m84036_250809_035451_s4.bc2121 at 2025-09-15 20:23:42.527683...
2025-09-15 20:23:46.028 wdl.w:ptcp.w:call-paraphase-24.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for gba for sample m84036_250809_035451_s4.bc2121 at 2025-09-15 20:23:42.528427...
2025-09-15 20:23:46.028 wdl.w:ptcp.w:call-paraphase-24.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for gba for sample m84036_250809_035451_s4.bc2121 at 2025-09-15 20:23:42.529018...
2025-09-15 20:23:46.028 wdl.w:ptcp.w:call-paraphase-24.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for hba for sample m84036_250809_035451_s4.bc2121 at 2025-09-15 20:23:42.528992...
2025-09-15 20:23:46.028 wdl.w:ptcp.w:call-paraphase-24.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for hba for sample m84036_250809_035451_s4.bc2121 at 2025-09-15 20:23:42.529547...
2025-09-15 20:23:46.028 wdl.w:ptcp.w:call-paraphase-24.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for smn1 for sample m84036_250809_035451_s4.bc2121 at 2025-09-15 20:23:43.144937...
2025-09-15 20:23:46.028 wdl.w:ptcp.w:call-paraphase-24.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for cyp21 for sample m84036_250809_035451_s4.bc2121 at 2025-09-15 20:23:43.188631...
2025-09-15 20:23:46.028 wdl.w:ptcp.w:call-paraphase-24.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for hba for sample m84036_250809_035451_s4.bc2121 at 2025-09-15 20:23:43.250664...
2025-09-15 20:23:46.028 wdl.w:ptcp.w:call-paraphase-24.t:call-run_paraphase.stderr VERBOSE WARNING:root:This region does not appear to have coverage. Will not attempt to phase haplotypes.
2025-09-15 20:23:46.028 wdl.w:ptcp.w:call-paraphase-24.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for smn1 for sample m84036_250809_035451_s4.bc2121 at 2025-09-15 20:23:43.278755...
2025-09-15 20:23:46.028 wdl.w:ptcp.w:call-paraphase-24.t:call-run_paraphase.stderr VERBOSE WARNING:root:This region does not appear to have coverage. Will not attempt to phase haplotypes.
2025-09-15 20:23:46.028 wdl.w:ptcp.w:call-paraphase-24.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for cyp21 for sample m84036_250809_035451_s4.bc2121 at 2025-09-15 20:23:43.284154...
2025-09-15 20:23:46.028 wdl.w:ptcp.w:call-paraphase-24.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for gba for sample m84036_250809_035451_s4.bc2121 at 2025-09-15 20:23:43.351478...
2025-09-15 20:23:46.028 wdl.w:ptcp.w:call-paraphase-24.t:call-run_paraphase.stderr VERBOSE WARNING:root:This region does not appear to have coverage. Will not attempt to phase haplotypes.
2025-09-15 20:23:46.028 wdl.w:ptcp.w:call-paraphase-24.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for hba for sample m84036_250809_035451_s4.bc2121 at 2025-09-15 20:23:43.362955...
2025-09-15 20:23:46.028 wdl.w:ptcp.w:call-paraphase-24.t:call-run_paraphase.stderr VERBOSE WARNING:root:This region does not appear to have coverage. Will not attempt to phase haplotypes.
2025-09-15 20:23:46.028 wdl.w:ptcp.w:call-paraphase-24.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for gba for sample m84036_250809_035451_s4.bc2121 at 2025-09-15 20:23:43.432670...
2025-09-15 20:23:46.029 wdl.w:ptcp.w:call-paraphase-24.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning to gene2 region for smn1 for sample m84036_250809_035451_s4.bc2121 at 2025-09-15 20:23:43.671274...
2025-09-15 20:23:46.029 wdl.w:ptcp.w:call-paraphase-24.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for cyp21 for sample m84036_250809_035451_s4.bc2121 at 2025-09-15 20:23:43.743167...
2025-09-15 20:23:46.029 wdl.w:ptcp.w:call-paraphase-24.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for f8inv22 for sample m84036_250809_035451_s4.bc2121 at 2025-09-15 20:23:43.749964...
2025-09-15 20:23:46.029 wdl.w:ptcp.w:call-paraphase-24.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for f8inv22 for sample m84036_250809_035451_s4.bc2121 at 2025-09-15 20:23:43.750036...
2025-09-15 20:23:46.029 wdl.w:ptcp.w:call-paraphase-24.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for hba for sample m84036_250809_035451_s4.bc2121 at 2025-09-15 20:23:43.767918...
2025-09-15 20:23:46.029 wdl.w:ptcp.w:call-paraphase-24.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for hbb for sample m84036_250809_035451_s4.bc2121 at 2025-09-15 20:23:43.778181...
2025-09-15 20:23:46.029 wdl.w:ptcp.w:call-paraphase-24.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for hbb for sample m84036_250809_035451_s4.bc2121 at 2025-09-15 20:23:43.778261...
2025-09-15 20:23:46.029 wdl.w:ptcp.w:call-paraphase-24.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for gba for sample m84036_250809_035451_s4.bc2121 at 2025-09-15 20:23:43.810713...
2025-09-15 20:23:46.029 wdl.w:ptcp.w:call-paraphase-24.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for rpgr for sample m84036_250809_035451_s4.bc2121 at 2025-09-15 20:23:43.818507...
2025-09-15 20:23:46.029 wdl.w:ptcp.w:call-paraphase-24.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for rpgr for sample m84036_250809_035451_s4.bc2121 at 2025-09-15 20:23:43.818666...
2025-09-15 20:23:46.029 wdl.w:ptcp.w:call-paraphase-24.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for f8inv22 for sample m84036_250809_035451_s4.bc2121 at 2025-09-15 20:23:44.190824...
2025-09-15 20:23:46.029 wdl.w:ptcp.w:call-paraphase-24.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for hbb for sample m84036_250809_035451_s4.bc2121 at 2025-09-15 20:23:44.217121...
2025-09-15 20:23:46.029 wdl.w:ptcp.w:call-paraphase-24.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for rpgr for sample m84036_250809_035451_s4.bc2121 at 2025-09-15 20:23:44.230740...
2025-09-15 20:23:46.029 wdl.w:ptcp.w:call-paraphase-24.t:call-run_paraphase.stderr VERBOSE WARNING:root:This region does not appear to have coverage. Will not attempt to phase haplotypes.
2025-09-15 20:23:46.029 wdl.w:ptcp.w:call-paraphase-24.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for f8inv22 for sample m84036_250809_035451_s4.bc2121 at 2025-09-15 20:23:44.261638...
2025-09-15 20:23:46.029 wdl.w:ptcp.w:call-paraphase-24.t:call-run_paraphase.stderr VERBOSE WARNING:root:This region does not appear to have coverage. Will not attempt to phase haplotypes.
2025-09-15 20:23:46.029 wdl.w:ptcp.w:call-paraphase-24.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for rpgr for sample m84036_250809_035451_s4.bc2121 at 2025-09-15 20:23:44.300800...
2025-09-15 20:23:46.029 wdl.w:ptcp.w:call-paraphase-24.t:call-run_paraphase.stderr VERBOSE WARNING:root:This region does not appear to have coverage. Will not attempt to phase haplotypes.
2025-09-15 20:23:46.029 wdl.w:ptcp.w:call-paraphase-24.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for hbb for sample m84036_250809_035451_s4.bc2121 at 2025-09-15 20:23:44.302261...
2025-09-15 20:23:46.029 wdl.w:ptcp.w:call-paraphase-24.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for smn1 for sample m84036_250809_035451_s4.bc2121 at 2025-09-15 20:23:44.440386...
2025-09-15 20:23:46.030 wdl.w:ptcp.w:call-paraphase-24.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for f8inv1 for sample m84036_250809_035451_s4.bc2121 at 2025-09-15 20:23:44.498372...
2025-09-15 20:23:46.030 wdl.w:ptcp.w:call-paraphase-24.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for f8inv1 for sample m84036_250809_035451_s4.bc2121 at 2025-09-15 20:23:44.498587...
2025-09-15 20:23:46.030 wdl.w:ptcp.w:call-paraphase-24.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for f8inv22 for sample m84036_250809_035451_s4.bc2121 at 2025-09-15 20:23:44.599278...
2025-09-15 20:23:46.030 wdl.w:ptcp.w:call-paraphase-24.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for hbb for sample m84036_250809_035451_s4.bc2121 at 2025-09-15 20:23:44.624036...
2025-09-15 20:23:46.030 wdl.w:ptcp.w:call-paraphase-24.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for rpgr for sample m84036_250809_035451_s4.bc2121 at 2025-09-15 20:23:44.674251...
2025-09-15 20:23:46.030 wdl.w:ptcp.w:call-paraphase-24.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for f8inv1 for sample m84036_250809_035451_s4.bc2121 at 2025-09-15 20:23:44.833711...
2025-09-15 20:23:46.030 wdl.w:ptcp.w:call-paraphase-24.t:call-run_paraphase.stderr VERBOSE WARNING:root:This region does not appear to have coverage. Will not attempt to phase haplotypes.
2025-09-15 20:23:46.030 wdl.w:ptcp.w:call-paraphase-24.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for f8inv1 for sample m84036_250809_035451_s4.bc2121 at 2025-09-15 20:23:44.870968...
2025-09-15 20:23:46.030 wdl.w:ptcp.w:call-paraphase-24.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for f8inv1 for sample m84036_250809_035451_s4.bc2121 at 2025-09-15 20:23:45.043339...
2025-09-15 20:23:46.030 wdl.w:ptcp.w:call-paraphase-24.t:call-run_paraphase.stderr VERBOSE INFO:root:Merging all bams for sample m84036_250809_035451_s4.bc2121 at 2025-09-15 20:23:45.063620...
2025-09-15 20:23:46.030 wdl.w:ptcp.w:call-paraphase-24.t:call-run_paraphase.stderr VERBOSE INFO:root:Writing to json for sample m84036_250809_035451_s4.bc2121 at 2025-09-15 20:23:45.393271...
2025-09-15 20:23:46.030 wdl.w:ptcp.w:call-paraphase-24.t:call-run_paraphase.stderr VERBOSE INFO:root:Completed Paraphase analysis at 2025-09-15 20:23:45.657940...
2025-09-15 20:23:46.091 wdl.w:ptcp.w:call-trgt-32.t:call-get_reads_overlapping_repeats INFO output :: name: "reads_overlapping_repeats", value: "m84036_250809_035451_s4.bc2129.repeats.bam"
2025-09-15 20:23:46.094 wdl.w:ptcp.w:call-trgt-32.t:call-get_reads_overlapping_repeats INFO output :: name: "reads_overlapping_repeats_bai", value: "m84036_250809_035451_s4.bc2129.repeats.bam.bai"
2025-09-15 20:23:46.099 wdl.w:ptcp.w:call-paraphase-16.t:call-run_paraphase INFO output :: name: "paraphase_bam", value: "m84036_250809_035451_s4.bc2113_paraphase/m84036_250809_035451_s4.bc2113.paraphase.bam"
2025-09-15 20:23:46.104 wdl.w:ptcp.w:call-paraphase-16.t:call-run_paraphase INFO output :: name: "paraphase_bam_bai", value: "m84036_250809_035451_s4.bc2113_paraphase/m84036_250809_035451_s4.bc2113.paraphase.bam.bai"
2025-09-15 20:23:46.105 wdl.w:ptcp.w:call-paraphase-16.t:call-run_paraphase INFO output :: name: "paraphase_json", value: "m84036_250809_035451_s4.bc2113_paraphase/m84036_250809_035451_s4.bc2113.paraphase.json"
2025-09-15 20:23:46.107 wdl.w:ptcp.w:call-paraphase-16.t:call-run_paraphase INFO output :: name: "paraphase_vcfs", value: []
2025-09-15 20:23:46.107 wdl.w:ptcp.w:call-paraphase-16.t:call-run_paraphase INFO output :: name: "havanno_json", value: "m84036_250809_035451_s4.bc2113.havanno.json"
2025-09-15 20:23:46.174 wdl.w:ptcp.w:call-trgt-32.t:call-get_reads_overlapping_repeats NOTICE done
2025-09-15 20:23:46.179 wdl.w:ptcp.w:call-trgt-32 NOTICE finish :: job: "call-get_reads_overlapping_repeats"
2025-09-15 20:23:46.179 wdl.w:ptcp.w:call-trgt-32 INFO output :: job: "call-get_reads_overlapping_repeats", values: {"reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-32/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2129.repeats.bam.bai", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-32/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2129.repeats.bam"}
2025-09-15 20:23:46.180 wdl.w:ptcp.w:call-trgt-32 INFO visit :: node: "output-reads_overlapping_repeats", values: {"reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-32/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2129.repeats.bam"}
2025-09-15 20:23:46.180 wdl.w:ptcp.w:call-trgt-32 INFO visit :: node: "output-reads_overlapping_repeats_bai", values: {"reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-32/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2129.repeats.bam.bai"}
2025-09-15 20:23:46.186 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_plot_meth_waterfall NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-15/call-trgt_plot_meth_waterfall", thread: 140613823374912
2025-09-15 20:23:46.202 wdl.w:ptcp.w:call-paraphase-16.t:call-run_paraphase NOTICE done
2025-09-15 20:23:46.207 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_plot_meth_waterfall INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:23:46.207 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_plot_meth_waterfall INFO input :: name: "waterfall", value: true
2025-09-15 20:23:46.207 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_plot_meth_waterfall INFO input :: name: "methylation", value: true
2025-09-15 20:23:46.207 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_plot_meth_waterfall INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:23:46.207 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_plot_meth_waterfall INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:23:46.207 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_plot_meth_waterfall INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:23:46.207 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_plot_meth_waterfall INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2112.trgt.sorted.spanning.bam.bai"
2025-09-15 20:23:46.207 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_plot_meth_waterfall INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2112.trgt.sorted.spanning.bam"
2025-09-15 20:23:46.207 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_plot_meth_waterfall INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2112.trgt.vcf"
2025-09-15 20:23:46.207 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_plot_meth_waterfall INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2112"
2025-09-15 20:23:46.207 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_plot_meth_waterfall INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:23:46.208 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_plot_meth_waterfall INFO eval :: name: "plot_type", value: "waterfall"
2025-09-15 20:23:46.208 wdl.w:ptcp.w:call-paraphase-16 NOTICE finish :: job: "call-run_paraphase"
2025-09-15 20:23:46.208 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_plot_meth_waterfall INFO eval :: name: "show", value: "meth"
2025-09-15 20:23:46.208 wdl.w:ptcp.w:call-paraphase-16 INFO output :: job: "call-run_paraphase", values: {"havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-16/call-run_paraphase/out/m84036_250809_035451_s4.bc2113.havanno.json", "paraphase_vcfs": [], "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-16/call-run_paraphase/out/m84036_250809_035451_s4.bc2113_paraphase/m84036_250809_035451_s4.bc2113.paraphase.json", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-16/call-run_paraphase/out/m84036_250809_035451_s4.bc2113_paraphase/m84036_250809_035451_s4.bc2113.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-16/call-run_paraphase/out/m84036_250809_035451_s4.bc2113_paraphase/m84036_250809_035451_s4.bc2113.paraphase.bam"}
2025-09-15 20:23:46.208 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_plot_meth_waterfall INFO eval :: name: "threads", value: 1
2025-09-15 20:23:46.209 wdl.w:ptcp.w:call-paraphase-16 NOTICE ready :: job: "call-call_f8", callee: "call_f8"
2025-09-15 20:23:46.209 wdl.w:ptcp.w:call-paraphase-16 INFO input :: job: "call-call_f8", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "out_prefix": "m84036_250809_035451_s4.bc2113", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-16/call-run_paraphase/out/m84036_250809_035451_s4.bc2113_paraphase/m84036_250809_035451_s4.bc2113.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-16/call-run_paraphase/out/m84036_250809_035451_s4.bc2113_paraphase/m84036_250809_035451_s4.bc2113.paraphase.bam", "sex": "F"}
2025-09-15 20:23:46.209 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_plot_meth_waterfall INFO eval :: name: "disk_size", value: 27
2025-09-15 20:23:46.209 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_plot_meth_waterfall INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2112.meth_waterfall"
2025-09-15 20:23:46.210 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_plot_meth_waterfall INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:23:46.210 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_plot_meth_waterfall WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:23:46.210 wdl.w:ptcp.w:call-paraphase-16 INFO visit :: node: "output-havanno_json", values: {"havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-16/call-run_paraphase/out/m84036_250809_035451_s4.bc2113.havanno.json"}
2025-09-15 20:23:46.211 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_plot_meth_waterfall INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:23:46.211 wdl.w:ptcp.w:call-paraphase-16 INFO visit :: node: "output-paraphase_bam", values: {"paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-16/call-run_paraphase/out/m84036_250809_035451_s4.bc2113_paraphase/m84036_250809_035451_s4.bc2113.paraphase.bam"}
2025-09-15 20:23:46.211 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_plot_meth_waterfall INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:23:46.211 wdl.w:ptcp.w:call-paraphase-16 INFO visit :: node: "output-paraphase_bam_bai", values: {"paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-16/call-run_paraphase/out/m84036_250809_035451_s4.bc2113_paraphase/m84036_250809_035451_s4.bc2113.paraphase.bam.bai"}
2025-09-15 20:23:46.211 wdl.w:ptcp.w:call-paraphase-16 INFO visit :: node: "output-paraphase_json", values: {"paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-16/call-run_paraphase/out/m84036_250809_035451_s4.bc2113_paraphase/m84036_250809_035451_s4.bc2113.paraphase.json"}
2025-09-15 20:23:46.211 wdl.w:ptcp.w:call-paraphase-16 INFO visit :: node: "output-paraphase_vcfs", values: {"paraphase_vcfs": []}
2025-09-15 20:23:46.214 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_plot_motifs_allele NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-15/call-trgt_plot_motifs_allele", thread: 140609293637184
2025-09-15 20:23:46.216 wdl.w:ptcp.w:call-trgt-08.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:43 [INFO] - Running trgt-4.0.0-429afcd [genotype]
2025-09-15 20:23:46.216 wdl.w:ptcp.w:call-trgt-08.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:43 [WARN] - OPDM_ABCD3: Filtered out 14 impure reads
2025-09-15 20:23:46.216 wdl.w:ptcp.w:call-trgt-08.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:43 [WARN] - NIID_NOTCH2NLC: Filtered out 33 impure reads
2025-09-15 20:23:46.216 wdl.w:ptcp.w:call-trgt-08.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:43 [WARN] - SCA37_DAB1: Filtered out 21 impure reads
2025-09-15 20:23:46.216 wdl.w:ptcp.w:call-trgt-08.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:43 [WARN] - DRPLA_ATN1: Filtered out 48 impure reads
2025-09-15 20:23:46.216 wdl.w:ptcp.w:call-trgt-08.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:43 [WARN] - SCA8_ATXN8OS: Filtered out 18 impure reads
2025-09-15 20:23:46.216 wdl.w:ptcp.w:call-trgt-08.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:43 [WARN] - SCA2_ATXN2: Filtered out 26 impure reads
2025-09-15 20:23:46.216 wdl.w:ptcp.w:call-trgt-08.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:43 [WARN] - SCA27B_FGF14: Filtered out 31 impure reads
2025-09-15 20:23:46.216 wdl.w:ptcp.w:call-trgt-08.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:43 [WARN] - OPDM4_RILPL1: Filtered out 32 impure reads
2025-09-15 20:23:46.216 wdl.w:ptcp.w:call-trgt-08.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:44 [WARN] - SCA3_ATXN3: Filtered out 28 impure reads
2025-09-15 20:23:46.216 wdl.w:ptcp.w:call-trgt-08.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:44 [WARN] - SCA31_BEAN1: Filtered out 13 impure reads
2025-09-15 20:23:46.216 wdl.w:ptcp.w:call-trgt-08.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:44 [WARN] - OPMD_PABPN1: Filtered out 28 impure reads
2025-09-15 20:23:46.217 wdl.w:ptcp.w:call-trgt-08.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:44 [WARN] - SCA4_ZFHX3: Filtered out 36 impure reads
2025-09-15 20:23:46.217 wdl.w:ptcp.w:call-trgt-08.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:44 [WARN] - HDL2_JPH3: Filtered out 42 impure reads
2025-09-15 20:23:46.217 wdl.w:ptcp.w:call-trgt-08.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:44 [WARN] - FECD3_TCF4: Filtered out 21 impure reads
2025-09-15 20:23:46.217 wdl.w:ptcp.w:call-trgt-08.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:44 [WARN] - OPDM2_GIPC1: Filtered out 19 impure reads
2025-09-15 20:23:46.217 wdl.w:ptcp.w:call-trgt-08.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:44 [WARN] - SCA6_CACNA1A: Filtered out 23 impure reads
2025-09-15 20:23:46.217 wdl.w:ptcp.w:call-trgt-08.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:44 [WARN] - DM1_DMPK: Filtered out 30 impure reads
2025-09-15 20:23:46.217 wdl.w:ptcp.w:call-trgt-08.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:44 [WARN] - CJD_PRNP: Filtered out 22 impure reads
2025-09-15 20:23:46.217 wdl.w:ptcp.w:call-trgt-08.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:44 [WARN] - EPM1_CSTB: Filtered out 24 impure reads
2025-09-15 20:23:46.217 wdl.w:ptcp.w:call-trgt-08.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:44 [WARN] - SD5_HOXD13: Filtered out 22 impure reads
2025-09-15 20:23:46.217 wdl.w:ptcp.w:call-trgt-08.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:44 [WARN] - SCA36_NOP56: Filtered out 28 impure reads
2025-09-15 20:23:46.217 wdl.w:ptcp.w:call-trgt-08.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:44 [WARN] - FRA2A_AFF3: Filtered out 22 impure reads
2025-09-15 20:23:46.217 wdl.w:ptcp.w:call-trgt-08.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:45 [WARN] - DM2_CNBP: Filtered out 7 impure reads
2025-09-15 20:23:46.217 wdl.w:ptcp.w:call-trgt-08.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:45 [WARN] - HD_HTT: Filtered out 27 impure reads
2025-09-15 20:23:46.217 wdl.w:ptcp.w:call-trgt-08.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:45 [WARN] - SCA10_ATXN10: Filtered out 15 impure reads
2025-09-15 20:23:46.217 wdl.w:ptcp.w:call-trgt-08.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:45 [WARN] - CANVAS_RFC1: Filtered out 14 impure reads
2025-09-15 20:23:46.217 wdl.w:ptcp.w:call-trgt-08.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:45 [WARN] - SCA7_ATXN7: Filtered out 25 impure reads
2025-09-15 20:23:46.217 wdl.w:ptcp.w:call-trgt-08.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:45 [WARN] - CCHS_PHOX2B: Filtered out 12 impure reads
2025-09-15 20:23:46.217 wdl.w:ptcp.w:call-trgt-08.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:45 [WARN] - SCA1_ATXN1: Filtered out 32 impure reads
2025-09-15 20:23:46.217 wdl.w:ptcp.w:call-trgt-08.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:45 [WARN] - SCA17_TBP: Filtered out 16 impure reads
2025-09-15 20:23:46.218 wdl.w:ptcp.w:call-trgt-08.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:45 [WARN] - OPDM1_LRP12: Filtered out 22 impure reads
2025-09-15 20:23:46.218 wdl.w:ptcp.w:call-trgt-08.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:45 [WARN] - FAME1_SAMD12: Filtered out 10 impure reads
2025-09-15 20:23:46.218 wdl.w:ptcp.w:call-trgt-08.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:45 [WARN] - SCA12_PPP2R2B: Filtered out 27 impure reads
2025-09-15 20:23:46.218 wdl.w:ptcp.w:call-trgt-08.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:45 [WARN] - FXS_FMR1: Filtered out 7 impure reads
2025-09-15 20:23:46.218 wdl.w:ptcp.w:call-trgt-08.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:45 [WARN] - FRDA_FXN: Filtered out 7 impure reads
2025-09-15 20:23:46.218 wdl.w:ptcp.w:call-trgt-08.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:45 [WARN] - SBMA_AR: Filtered out 33 impure reads
2025-09-15 20:23:46.218 wdl.w:ptcp.w:call-trgt-08.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:45 [WARN] - FTDALS1_C9orf72: Filtered out 49 impure reads
2025-09-15 20:23:46.218 wdl.w:ptcp.w:call-trgt-08.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:45 [WARN] - FRAXE_AFF2: Filtered out 21 impure reads
2025-09-15 20:23:46.218 wdl.w:ptcp.w:call-trgt-08.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:45 [INFO] - Total execution time: 2.77s
2025-09-15 20:23:46.218 wdl.w:ptcp.w:call-trgt-08.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:45 [INFO] - trgt end
2025-09-15 20:23:46.238 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_plot_motifs_allele INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:23:46.238 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_plot_motifs_allele INFO input :: name: "waterfall", value: false
2025-09-15 20:23:46.238 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_plot_motifs_allele INFO input :: name: "methylation", value: false
2025-09-15 20:23:46.238 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_plot_motifs_allele INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:23:46.238 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_plot_motifs_allele INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:23:46.239 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_plot_motifs_allele INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:23:46.239 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_plot_motifs_allele INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2112.trgt.sorted.spanning.bam.bai"
2025-09-15 20:23:46.239 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_plot_motifs_allele INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2112.trgt.sorted.spanning.bam"
2025-09-15 20:23:46.239 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_plot_motifs_allele INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2112.trgt.vcf"
2025-09-15 20:23:46.239 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_plot_motifs_allele INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2112"
2025-09-15 20:23:46.239 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_plot_motifs_allele INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:23:46.239 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_plot_motifs_allele INFO eval :: name: "plot_type", value: "allele"
2025-09-15 20:23:46.239 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_plot_motifs_allele INFO eval :: name: "show", value: "motifs"
2025-09-15 20:23:46.239 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_plot_motifs_allele INFO eval :: name: "threads", value: 1
2025-09-15 20:23:46.240 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_plot_motifs_allele INFO eval :: name: "disk_size", value: 27
2025-09-15 20:23:46.240 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_plot_motifs_allele INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2112.motifs_allele"
2025-09-15 20:23:46.240 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_plot_motifs_allele INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:23:46.240 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_plot_motifs_allele WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:23:46.240 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_plot_motifs_allele INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:23:46.241 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_plot_motifs_allele INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:23:46.251 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:46 [ERROR] - No reads found for TRID=NIID_NOTCH2NLC
2025-09-15 20:23:46.251 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:46 [ERROR] - No reads found for TRID=OPDM_ABCD3
2025-09-15 20:23:46.251 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:46 [ERROR] - No reads found for TRID=SCA2_ATXN2
2025-09-15 20:23:46.251 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:46 [ERROR] - No reads found for TRID=SCA37_DAB1
2025-09-15 20:23:46.251 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:46 [ERROR] - No reads found for TRID=OPDM4_RILPL1
2025-09-15 20:23:46.251 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:46 [ERROR] - No reads found for TRID=SCA3_ATXN3
2025-09-15 20:23:46.251 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:46 [ERROR] - No reads found for TRID=SCA31_BEAN1
2025-09-15 20:23:46.251 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:46 [ERROR] - No reads found for TRID=SCA4_ZFHX3
2025-09-15 20:23:46.261 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_plot_motifs_allele.slurm_singularity INFO srun: job 51797466 queued and waiting for resources
2025-09-15 20:23:46.261 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_plot_motifs_allele.slurm_singularity INFO srun: job 51797466 has been allocated resources
2025-09-15 20:23:46.261 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_plot_motifs_allele.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:46.300 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_plot_meth_waterfall INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-15/call-trgt_plot_meth_waterfall/_singularity_tmpdir_4ktvxi4j"
2025-09-15 20:23:46.300 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_plot_meth_waterfall INFO Slurm invocation: srun --job-name call-trgt_plot_meth_waterfall --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-15/call-trgt_plot_meth_waterfall/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-15/call-trgt_plot_meth_waterfall/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-15/call-trgt_plot_meth_waterfall/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-15/call-trgt_plot_meth_waterfall/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-15/call-trgt_genotype/out/m84036_250809_035451_s4.bc2112.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2112.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-15/call-trgt_genotype/out/m84036_250809_035451_s4.bc2112.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2112.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-15/call-trgt_genotype/out/m84036_250809_035451_s4.bc2112.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2112.trgt.vcf:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-15/call-trgt_plot_meth_waterfall/_singularity_tmpdir_4ktvxi4j/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-15/call-trgt_plot_meth_waterfall/_singularity_tmpdir_4ktvxi4j/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:23:46.313 wdl.w:ptcp.w:call-paraphase-24.t:call-run_paraphase INFO output :: name: "paraphase_bam", value: "m84036_250809_035451_s4.bc2121_paraphase/m84036_250809_035451_s4.bc2121.paraphase.bam"
2025-09-15 20:23:46.317 wdl.w:ptcp.w:call-paraphase-24.t:call-run_paraphase INFO output :: name: "paraphase_bam_bai", value: "m84036_250809_035451_s4.bc2121_paraphase/m84036_250809_035451_s4.bc2121.paraphase.bam.bai"
2025-09-15 20:23:46.319 wdl.w:ptcp.w:call-paraphase-24.t:call-run_paraphase INFO output :: name: "paraphase_json", value: "m84036_250809_035451_s4.bc2121_paraphase/m84036_250809_035451_s4.bc2121.paraphase.json"
2025-09-15 20:23:46.320 wdl.w:ptcp.w:call-paraphase-24.t:call-run_paraphase INFO output :: name: "paraphase_vcfs", value: []
2025-09-15 20:23:46.321 wdl.w:ptcp.w:call-paraphase-24.t:call-run_paraphase INFO output :: name: "havanno_json", value: "m84036_250809_035451_s4.bc2121.havanno.json"
2025-09-15 20:23:46.320 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_plot_motifs_allele INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-15/call-trgt_plot_motifs_allele/_singularity_tmpdir_elwaebfs"
2025-09-15 20:23:46.321 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_plot_motifs_allele INFO Slurm invocation: srun --job-name call-trgt_plot_motifs_allele --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-15/call-trgt_plot_motifs_allele/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-15/call-trgt_plot_motifs_allele/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-15/call-trgt_plot_motifs_allele/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-15/call-trgt_plot_motifs_allele/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-15/call-trgt_genotype/out/m84036_250809_035451_s4.bc2112.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2112.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-15/call-trgt_genotype/out/m84036_250809_035451_s4.bc2112.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2112.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-15/call-trgt_genotype/out/m84036_250809_035451_s4.bc2112.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2112.trgt.vcf:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-15/call-trgt_plot_motifs_allele/_singularity_tmpdir_elwaebfs/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-15/call-trgt_plot_motifs_allele/_singularity_tmpdir_elwaebfs/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:23:46.326 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_plot_meth_waterfall NOTICE slurm_singularity run :: pid: 1200110, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-15/call-trgt_plot_meth_waterfall/slurm_singularity.log.txt"
2025-09-15 20:23:46.328 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_plot_motifs_allele NOTICE slurm_singularity run :: pid: 1200112, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-15/call-trgt_plot_motifs_allele/slurm_singularity.log.txt"
2025-09-15 20:23:46.368 wdl.w:ptcp.w:call-paraphase-12.t:call-run_paraphase INFO output :: name: "paraphase_bam", value: "m84036_250809_035451_s4.bc2109_paraphase/m84036_250809_035451_s4.bc2109.paraphase.bam"
2025-09-15 20:23:46.372 wdl.w:ptcp.w:call-paraphase-12.t:call-run_paraphase INFO output :: name: "paraphase_bam_bai", value: "m84036_250809_035451_s4.bc2109_paraphase/m84036_250809_035451_s4.bc2109.paraphase.bam.bai"
2025-09-15 20:23:46.373 wdl.w:ptcp.w:call-paraphase-12.t:call-run_paraphase INFO output :: name: "paraphase_json", value: "m84036_250809_035451_s4.bc2109_paraphase/m84036_250809_035451_s4.bc2109.paraphase.json"
2025-09-15 20:23:46.374 wdl.w:ptcp.w:call-paraphase-12.t:call-run_paraphase INFO output :: name: "paraphase_vcfs", value: []
2025-09-15 20:23:46.374 wdl.w:ptcp.w:call-paraphase-12.t:call-run_paraphase INFO output :: name: "havanno_json", value: "m84036_250809_035451_s4.bc2109.havanno.json"
2025-09-15 20:23:46.422 wdl.w:ptcp.w:call-paraphase-24.t:call-run_paraphase NOTICE done
2025-09-15 20:23:46.427 wdl.w:ptcp.w:call-paraphase-24 NOTICE finish :: job: "call-run_paraphase"
2025-09-15 20:23:46.427 wdl.w:ptcp.w:call-paraphase-24 INFO output :: job: "call-run_paraphase", values: {"havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-24/call-run_paraphase/out/m84036_250809_035451_s4.bc2121.havanno.json", "paraphase_vcfs": [], "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-24/call-run_paraphase/out/m84036_250809_035451_s4.bc2121_paraphase/m84036_250809_035451_s4.bc2121.paraphase.json", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-24/call-run_paraphase/out/m84036_250809_035451_s4.bc2121_paraphase/m84036_250809_035451_s4.bc2121.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-24/call-run_paraphase/out/m84036_250809_035451_s4.bc2121_paraphase/m84036_250809_035451_s4.bc2121.paraphase.bam"}
2025-09-15 20:23:46.428 wdl.w:ptcp.w:call-paraphase-24 NOTICE ready :: job: "call-call_f8", callee: "call_f8"
2025-09-15 20:23:46.428 wdl.w:ptcp.w:call-paraphase-24 INFO input :: job: "call-call_f8", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "out_prefix": "m84036_250809_035451_s4.bc2121", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-24/call-run_paraphase/out/m84036_250809_035451_s4.bc2121_paraphase/m84036_250809_035451_s4.bc2121.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-24/call-run_paraphase/out/m84036_250809_035451_s4.bc2121_paraphase/m84036_250809_035451_s4.bc2121.paraphase.bam", "sex": "F"}
2025-09-15 20:23:46.429 wdl.w:ptcp.w:call-paraphase-24 INFO visit :: node: "output-havanno_json", values: {"havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-24/call-run_paraphase/out/m84036_250809_035451_s4.bc2121.havanno.json"}
2025-09-15 20:23:46.429 wdl.w:ptcp.w:call-paraphase-24 INFO visit :: node: "output-paraphase_bam", values: {"paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-24/call-run_paraphase/out/m84036_250809_035451_s4.bc2121_paraphase/m84036_250809_035451_s4.bc2121.paraphase.bam"}
2025-09-15 20:23:46.429 wdl.w:ptcp.w:call-paraphase-24 INFO visit :: node: "output-paraphase_bam_bai", values: {"paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-24/call-run_paraphase/out/m84036_250809_035451_s4.bc2121_paraphase/m84036_250809_035451_s4.bc2121.paraphase.bam.bai"}
2025-09-15 20:23:46.429 wdl.w:ptcp.w:call-paraphase-24 INFO visit :: node: "output-paraphase_json", values: {"paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-24/call-run_paraphase/out/m84036_250809_035451_s4.bc2121_paraphase/m84036_250809_035451_s4.bc2121.paraphase.json"}
2025-09-15 20:23:46.429 wdl.w:ptcp.w:call-paraphase-24 INFO visit :: node: "output-paraphase_vcfs", values: {"paraphase_vcfs": []}
2025-09-15 20:23:46.433 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_plot_motifs_waterfall NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-15/call-trgt_plot_motifs_waterfall", thread: 140609838900800
2025-09-15 20:23:46.451 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_plot_motifs_waterfall INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:23:46.451 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_plot_motifs_waterfall INFO input :: name: "waterfall", value: true
2025-09-15 20:23:46.452 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_plot_motifs_waterfall INFO input :: name: "methylation", value: false
2025-09-15 20:23:46.452 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_plot_motifs_waterfall INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:23:46.452 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_plot_motifs_waterfall INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:23:46.452 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_plot_motifs_waterfall INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:23:46.452 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_plot_motifs_waterfall INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2112.trgt.sorted.spanning.bam.bai"
2025-09-15 20:23:46.452 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_plot_motifs_waterfall INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2112.trgt.sorted.spanning.bam"
2025-09-15 20:23:46.452 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_plot_motifs_waterfall INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2112.trgt.vcf"
2025-09-15 20:23:46.452 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_plot_motifs_waterfall INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2112"
2025-09-15 20:23:46.452 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:23:46.452 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "plot_type", value: "waterfall"
2025-09-15 20:23:46.452 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "show", value: "motifs"
2025-09-15 20:23:46.453 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "threads", value: 1
2025-09-15 20:23:46.453 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "disk_size", value: 27
2025-09-15 20:23:46.453 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2112.motifs_waterfall"
2025-09-15 20:23:46.453 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_plot_motifs_waterfall INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:23:46.453 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_plot_motifs_waterfall WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:23:46.454 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_plot_motifs_waterfall INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:23:46.454 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_plot_motifs_waterfall INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:23:46.474 wdl.w:ptcp.w:call-paraphase-12.t:call-run_paraphase NOTICE done
2025-09-15 20:23:46.479 wdl.w:ptcp.w:call-paraphase-12 NOTICE finish :: job: "call-run_paraphase"
2025-09-15 20:23:46.480 wdl.w:ptcp.w:call-paraphase-12 INFO output :: job: "call-run_paraphase", values: {"havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-12/call-run_paraphase/out/m84036_250809_035451_s4.bc2109.havanno.json", "paraphase_vcfs": [], "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-12/call-run_paraphase/out/m84036_250809_035451_s4.bc2109_paraphase/m84036_250809_035451_s4.bc2109.paraphase.json", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-12/call-run_paraphase/out/m84036_250809_035451_s4.bc2109_paraphase/m84036_250809_035451_s4.bc2109.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-12/call-run_paraphase/out/m84036_250809_035451_s4.bc2109_paraphase/m84036_250809_035451_s4.bc2109.paraphase.bam"}
2025-09-15 20:23:46.480 wdl.w:ptcp.w:call-paraphase-12 NOTICE ready :: job: "call-call_f8", callee: "call_f8"
2025-09-15 20:23:46.480 wdl.w:ptcp.w:call-paraphase-12 INFO input :: job: "call-call_f8", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "out_prefix": "m84036_250809_035451_s4.bc2109", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-12/call-run_paraphase/out/m84036_250809_035451_s4.bc2109_paraphase/m84036_250809_035451_s4.bc2109.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-12/call-run_paraphase/out/m84036_250809_035451_s4.bc2109_paraphase/m84036_250809_035451_s4.bc2109.paraphase.bam", "sex": "F"}
2025-09-15 20:23:46.481 wdl.w:ptcp.w:call-paraphase-12 INFO visit :: node: "output-havanno_json", values: {"havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-12/call-run_paraphase/out/m84036_250809_035451_s4.bc2109.havanno.json"}
2025-09-15 20:23:46.481 wdl.w:ptcp.w:call-paraphase-12 INFO visit :: node: "output-paraphase_bam", values: {"paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-12/call-run_paraphase/out/m84036_250809_035451_s4.bc2109_paraphase/m84036_250809_035451_s4.bc2109.paraphase.bam"}
2025-09-15 20:23:46.481 wdl.w:ptcp.w:call-paraphase-12 INFO visit :: node: "output-paraphase_bam_bai", values: {"paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-12/call-run_paraphase/out/m84036_250809_035451_s4.bc2109_paraphase/m84036_250809_035451_s4.bc2109.paraphase.bam.bai"}
2025-09-15 20:23:46.481 wdl.w:ptcp.w:call-paraphase-12 INFO visit :: node: "output-paraphase_json", values: {"paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-12/call-run_paraphase/out/m84036_250809_035451_s4.bc2109_paraphase/m84036_250809_035451_s4.bc2109.paraphase.json"}
2025-09-15 20:23:46.482 wdl.w:ptcp.w:call-paraphase-12 INFO visit :: node: "output-paraphase_vcfs", values: {"paraphase_vcfs": []}
2025-09-15 20:23:46.484 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_meth_allele NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-31/call-trgt_plot_meth_allele", thread: 140609805329984
2025-09-15 20:23:46.503 wdl.w:ptcp.w:call-paraphase-27.t:call-run_paraphase.stderr VERBOSE INFO:root:Processing sample m84036_250809_035451_s4.bc2124 at 2025-09-15 20:23:41.033254...
2025-09-15 20:23:46.504 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_meth_allele INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:23:46.504 wdl.w:ptcp.w:call-paraphase-27.t:call-run_paraphase.stderr VERBOSE INFO:root:Checking sample sex at 2025-09-15 20:23:41.034037...
2025-09-15 20:23:46.505 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_meth_allele INFO input :: name: "waterfall", value: false
2025-09-15 20:23:46.505 wdl.w:ptcp.w:call-paraphase-27.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for gba for sample m84036_250809_035451_s4.bc2124 at 2025-09-15 20:23:41.069896...
2025-09-15 20:23:46.505 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_meth_allele INFO input :: name: "methylation", value: true
2025-09-15 20:23:46.505 wdl.w:ptcp.w:call-paraphase-27.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for cyp21 for sample m84036_250809_035451_s4.bc2124 at 2025-09-15 20:23:41.069827...
2025-09-15 20:23:46.505 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_meth_allele INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:23:46.505 wdl.w:ptcp.w:call-paraphase-27.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for gba for sample m84036_250809_035451_s4.bc2124 at 2025-09-15 20:23:41.070292...
2025-09-15 20:23:46.505 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_meth_allele INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:23:46.505 wdl.w:ptcp.w:call-paraphase-27.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for smn1 for sample m84036_250809_035451_s4.bc2124 at 2025-09-15 20:23:41.069938...
2025-09-15 20:23:46.505 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_meth_allele INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:23:46.506 wdl.w:ptcp.w:call-paraphase-27.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for cyp21 for sample m84036_250809_035451_s4.bc2124 at 2025-09-15 20:23:41.070331...
2025-09-15 20:23:46.506 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_meth_allele INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2128.trgt.sorted.spanning.bam.bai"
2025-09-15 20:23:46.506 wdl.w:ptcp.w:call-paraphase-27.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for smn1 for sample m84036_250809_035451_s4.bc2124 at 2025-09-15 20:23:41.070388...
2025-09-15 20:23:46.506 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_meth_allele INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2128.trgt.sorted.spanning.bam"
2025-09-15 20:23:46.506 wdl.w:ptcp.w:call-paraphase-27.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for hba for sample m84036_250809_035451_s4.bc2124 at 2025-09-15 20:23:41.071210...
2025-09-15 20:23:46.506 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_meth_allele INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2128.trgt.vcf"
2025-09-15 20:23:46.506 wdl.w:ptcp.w:call-paraphase-27.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for hba for sample m84036_250809_035451_s4.bc2124 at 2025-09-15 20:23:41.071611...
2025-09-15 20:23:46.506 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_meth_allele INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2128"
2025-09-15 20:23:46.507 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_meth_allele INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:23:46.507 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_meth_allele INFO eval :: name: "plot_type", value: "allele"
2025-09-15 20:23:46.507 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_meth_allele INFO eval :: name: "show", value: "meth"
2025-09-15 20:23:46.507 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_meth_allele INFO eval :: name: "threads", value: 1
2025-09-15 20:23:46.507 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_meth_allele INFO eval :: name: "disk_size", value: 27
2025-09-15 20:23:46.507 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_meth_allele INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2128.meth_allele"
2025-09-15 20:23:46.508 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_meth_allele INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:23:46.508 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_meth_allele WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:23:46.508 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_meth_allele INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:23:46.508 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_meth_allele INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:23:46.527 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_plot_motifs_waterfall INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-15/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_j9z0smvn"
2025-09-15 20:23:46.528 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_plot_motifs_waterfall INFO Slurm invocation: srun --job-name call-trgt_plot_motifs_waterfall --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-15/call-trgt_plot_motifs_waterfall/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-15/call-trgt_plot_motifs_waterfall/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-15/call-trgt_plot_motifs_waterfall/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-15/call-trgt_plot_motifs_waterfall/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-15/call-trgt_genotype/out/m84036_250809_035451_s4.bc2112.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2112.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-15/call-trgt_genotype/out/m84036_250809_035451_s4.bc2112.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2112.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-15/call-trgt_genotype/out/m84036_250809_035451_s4.bc2112.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2112.trgt.vcf:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-15/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_j9z0smvn/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-15/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_j9z0smvn/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:23:46.552 wdl.w:ptcp.w:call-trgt-08.t:call-trgt_genotype INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2105.trgt.vcf"
2025-09-15 20:23:46.556 wdl.w:ptcp.w:call-trgt-08.t:call-trgt_genotype INFO output :: name: "spanning_bam", value: "m84036_250809_035451_s4.bc2105.trgt.sorted.spanning.bam"
2025-09-15 20:23:46.558 wdl.w:ptcp.w:call-trgt-08.t:call-trgt_genotype INFO output :: name: "spanning_bam_bai", value: "m84036_250809_035451_s4.bc2105.trgt.sorted.spanning.bam.bai"
2025-09-15 20:23:46.559 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_plot_motifs_waterfall NOTICE slurm_singularity run :: pid: 1200126, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-15/call-trgt_plot_motifs_waterfall/slurm_singularity.log.txt"
2025-09-15 20:23:46.587 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_meth_allele INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-31/call-trgt_plot_meth_allele/_singularity_tmpdir_w0aw11zj"
2025-09-15 20:23:46.587 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_meth_allele INFO Slurm invocation: srun --job-name call-trgt_plot_meth_allele --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-31/call-trgt_plot_meth_allele/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-31/call-trgt_plot_meth_allele/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-31/call-trgt_plot_meth_allele/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-31/call-trgt_plot_meth_allele/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-31/call-trgt_genotype/out/m84036_250809_035451_s4.bc2128.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2128.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-31/call-trgt_genotype/out/m84036_250809_035451_s4.bc2128.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2128.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-31/call-trgt_genotype/out/m84036_250809_035451_s4.bc2128.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2128.trgt.sorted.spanning.bam:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-31/call-trgt_plot_meth_allele/_singularity_tmpdir_w0aw11zj/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-31/call-trgt_plot_meth_allele/_singularity_tmpdir_w0aw11zj/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:23:46.601 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_meth_allele NOTICE slurm_singularity run :: pid: 1200128, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-31/call-trgt_plot_meth_allele/slurm_singularity.log.txt"
2025-09-15 20:23:46.625 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO srun: job 51797467 queued and waiting for resources
2025-09-15 20:23:46.625 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO srun: job 51797467 has been allocated resources
2025-09-15 20:23:46.625 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:46.645 wdl.w:ptcp.w:call-trgt-08.t:call-trgt_genotype NOTICE done
2025-09-15 20:23:46.680 wdl.w:ptcp.w:call-trgt-08 NOTICE finish :: job: "call-trgt_genotype"
2025-09-15 20:23:46.680 wdl.w:ptcp.w:call-trgt-08 INFO output :: job: "call-trgt_genotype", values: {"spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-08/call-trgt_genotype/out/m84036_250809_035451_s4.bc2105.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-08/call-trgt_genotype/out/m84036_250809_035451_s4.bc2105.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-08/call-trgt_genotype/out/m84036_250809_035451_s4.bc2105.trgt.vcf"}
2025-09-15 20:23:46.681 wdl.w:ptcp.w:call-trgt-08 NOTICE ready :: job: "call-trgt_plot_meth_allele", callee: "trgt_plot"
2025-09-15 20:23:46.681 wdl.w:ptcp.w:call-trgt-08 INFO input :: job: "call-trgt_plot_meth_allele", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": false, "methylation": true, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-08/call-trgt_genotype/out/m84036_250809_035451_s4.bc2105.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-08/call-trgt_genotype/out/m84036_250809_035451_s4.bc2105.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-08/call-trgt_genotype/out/m84036_250809_035451_s4.bc2105.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2105"}
2025-09-15 20:23:46.686 wdl.w:ptcp.w:call-trgt-08 NOTICE ready :: job: "call-trgt_plot_meth_waterfall", callee: "trgt_plot"
2025-09-15 20:23:46.686 wdl.w:ptcp.w:call-trgt-08 INFO input :: job: "call-trgt_plot_meth_waterfall", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": true, "methylation": true, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-08/call-trgt_genotype/out/m84036_250809_035451_s4.bc2105.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-08/call-trgt_genotype/out/m84036_250809_035451_s4.bc2105.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-08/call-trgt_genotype/out/m84036_250809_035451_s4.bc2105.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2105"}
2025-09-15 20:23:46.686 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_meth_waterfall NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-31/call-trgt_plot_meth_waterfall", thread: 140611407550016
2025-09-15 20:23:46.687 wdl.w:ptcp.w:call-trgt-08 NOTICE ready :: job: "call-trgt_plot_motifs_allele", callee: "trgt_plot"
2025-09-15 20:23:46.687 wdl.w:ptcp.w:call-trgt-08 INFO input :: job: "call-trgt_plot_motifs_allele", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": false, "methylation": false, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-08/call-trgt_genotype/out/m84036_250809_035451_s4.bc2105.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-08/call-trgt_genotype/out/m84036_250809_035451_s4.bc2105.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-08/call-trgt_genotype/out/m84036_250809_035451_s4.bc2105.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2105"}
2025-09-15 20:23:46.688 wdl.w:ptcp.w:call-trgt-08 NOTICE ready :: job: "call-trgt_plot_motifs_waterfall", callee: "trgt_plot"
2025-09-15 20:23:46.688 wdl.w:ptcp.w:call-trgt-08 INFO input :: job: "call-trgt_plot_motifs_waterfall", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": true, "methylation": false, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-08/call-trgt_genotype/out/m84036_250809_035451_s4.bc2105.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-08/call-trgt_genotype/out/m84036_250809_035451_s4.bc2105.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-08/call-trgt_genotype/out/m84036_250809_035451_s4.bc2105.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2105"}
2025-09-15 20:23:46.689 wdl.w:ptcp.w:call-trgt-08 INFO visit :: node: "output-spanning_bam", values: {"spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-08/call-trgt_genotype/out/m84036_250809_035451_s4.bc2105.trgt.sorted.spanning.bam"}
2025-09-15 20:23:46.689 wdl.w:ptcp.w:call-trgt-08 INFO visit :: node: "output-spanning_bam_bai", values: {"spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-08/call-trgt_genotype/out/m84036_250809_035451_s4.bc2105.trgt.sorted.spanning.bam.bai"}
2025-09-15 20:23:46.689 wdl.w:ptcp.w:call-trgt-08 INFO visit :: node: "output-vcf", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-08/call-trgt_genotype/out/m84036_250809_035451_s4.bc2105.trgt.vcf"}
2025-09-15 20:23:46.710 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_meth_waterfall INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:23:46.710 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_meth_waterfall INFO input :: name: "waterfall", value: true
2025-09-15 20:23:46.710 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_meth_waterfall INFO input :: name: "methylation", value: true
2025-09-15 20:23:46.710 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_meth_waterfall INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:23:46.710 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_meth_waterfall INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:23:46.710 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_meth_waterfall INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:23:46.710 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_meth_waterfall INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2128.trgt.sorted.spanning.bam.bai"
2025-09-15 20:23:46.710 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_meth_waterfall INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2128.trgt.sorted.spanning.bam"
2025-09-15 20:23:46.710 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_meth_waterfall INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2128.trgt.vcf"
2025-09-15 20:23:46.710 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_meth_waterfall INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2128"
2025-09-15 20:23:46.711 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_meth_waterfall INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:23:46.711 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_meth_waterfall INFO eval :: name: "plot_type", value: "waterfall"
2025-09-15 20:23:46.711 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_meth_waterfall INFO eval :: name: "show", value: "meth"
2025-09-15 20:23:46.711 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_meth_waterfall INFO eval :: name: "threads", value: 1
2025-09-15 20:23:46.711 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_meth_waterfall INFO eval :: name: "disk_size", value: 27
2025-09-15 20:23:46.711 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_meth_waterfall INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2128.meth_waterfall"
2025-09-15 20:23:46.712 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_meth_waterfall INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:23:46.712 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_meth_waterfall WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:23:46.712 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_meth_waterfall INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:23:46.712 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_meth_waterfall INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:23:46.759 wdl.w:ptcp.w:call-paraphase-25.t:call-run_paraphase INFO output :: name: "paraphase_bam", value: "m84036_250809_035451_s4.bc2122_paraphase/m84036_250809_035451_s4.bc2122.paraphase.bam"
2025-09-15 20:23:46.767 wdl.w:ptcp.w:call-paraphase-25.t:call-run_paraphase INFO output :: name: "paraphase_bam_bai", value: "m84036_250809_035451_s4.bc2122_paraphase/m84036_250809_035451_s4.bc2122.paraphase.bam.bai"
2025-09-15 20:23:46.768 wdl.w:ptcp.w:call-paraphase-25.t:call-run_paraphase INFO output :: name: "paraphase_json", value: "m84036_250809_035451_s4.bc2122_paraphase/m84036_250809_035451_s4.bc2122.paraphase.json"
2025-09-15 20:23:46.772 wdl.w:ptcp.w:call-paraphase-25.t:call-run_paraphase INFO output :: name: "paraphase_vcfs", value: []
2025-09-15 20:23:46.772 wdl.w:ptcp.w:call-paraphase-25.t:call-run_paraphase INFO output :: name: "havanno_json", value: "m84036_250809_035451_s4.bc2122.havanno.json"
2025-09-15 20:23:46.799 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_meth_waterfall INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-31/call-trgt_plot_meth_waterfall/_singularity_tmpdir_8cqps9vm"
2025-09-15 20:23:46.799 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_meth_waterfall INFO Slurm invocation: srun --job-name call-trgt_plot_meth_waterfall --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-31/call-trgt_plot_meth_waterfall/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-31/call-trgt_plot_meth_waterfall/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-31/call-trgt_plot_meth_waterfall/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-31/call-trgt_plot_meth_waterfall/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-31/call-trgt_genotype/out/m84036_250809_035451_s4.bc2128.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2128.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-31/call-trgt_genotype/out/m84036_250809_035451_s4.bc2128.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2128.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-31/call-trgt_genotype/out/m84036_250809_035451_s4.bc2128.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2128.trgt.sorted.spanning.bam:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-31/call-trgt_plot_meth_waterfall/_singularity_tmpdir_8cqps9vm/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-31/call-trgt_plot_meth_waterfall/_singularity_tmpdir_8cqps9vm/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:23:46.834 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_meth_waterfall NOTICE slurm_singularity run :: pid: 1200141, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-31/call-trgt_plot_meth_waterfall/slurm_singularity.log.txt"
2025-09-15 20:23:46.844 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:23:46 [ERROR] - No reads found for TRID=NIID_NOTCH2NLC
2025-09-15 20:23:46.844 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:23:46 [ERROR] - No reads found for TRID=OPDM_ABCD3
2025-09-15 20:23:46.844 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:23:46 [ERROR] - No reads found for TRID=SCA37_DAB1
2025-09-15 20:23:46.844 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:23:46 [ERROR] - No reads found for TRID=DRPLA_ATN1
2025-09-15 20:23:46.844 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:23:46 [ERROR] - No reads found for TRID=SCA2_ATXN2
2025-09-15 20:23:46.844 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:23:46 [ERROR] - No reads found for TRID=OPDM4_RILPL1
2025-09-15 20:23:46.859 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_plot_meth_allele.slurm_singularity INFO srun: job 51797468 queued and waiting for resources
2025-09-15 20:23:46.859 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_plot_meth_allele.slurm_singularity INFO srun: job 51797468 has been allocated resources
2025-09-15 20:23:46.859 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_plot_meth_allele.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:46.903 wdl.w:ptcp.w:call-paraphase-25.t:call-run_paraphase NOTICE done
2025-09-15 20:23:46.914 wdl.w:ptcp.w:call-sawfish-00.t:call-run_sawfish.stderr VERBOSE [M::bam2fq_mainloop] discarded 0 singletons
2025-09-15 20:23:46.914 wdl.w:ptcp.w:call-sawfish-00.t:call-run_sawfish.stderr VERBOSE [M::bam2fq_mainloop] processed 1 reads
2025-09-15 20:23:46.914 wdl.w:ptcp.w:call-paraphase-25 NOTICE finish :: job: "call-run_paraphase"
2025-09-15 20:23:46.914 wdl.w:ptcp.w:call-paraphase-25 INFO output :: job: "call-run_paraphase", values: {"havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-25/call-run_paraphase/out/m84036_250809_035451_s4.bc2122.havanno.json", "paraphase_vcfs": [], "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-25/call-run_paraphase/out/m84036_250809_035451_s4.bc2122_paraphase/m84036_250809_035451_s4.bc2122.paraphase.json", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-25/call-run_paraphase/out/m84036_250809_035451_s4.bc2122_paraphase/m84036_250809_035451_s4.bc2122.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-25/call-run_paraphase/out/m84036_250809_035451_s4.bc2122_paraphase/m84036_250809_035451_s4.bc2122.paraphase.bam"}
2025-09-15 20:23:46.915 wdl.w:ptcp.w:call-paraphase-25 NOTICE ready :: job: "call-call_f8", callee: "call_f8"
2025-09-15 20:23:46.915 wdl.w:ptcp.w:call-paraphase-25 INFO input :: job: "call-call_f8", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "out_prefix": "m84036_250809_035451_s4.bc2122", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-25/call-run_paraphase/out/m84036_250809_035451_s4.bc2122_paraphase/m84036_250809_035451_s4.bc2122.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-25/call-run_paraphase/out/m84036_250809_035451_s4.bc2122_paraphase/m84036_250809_035451_s4.bc2122.paraphase.bam", "sex": "F"}
2025-09-15 20:23:46.916 wdl.w:ptcp.w:call-paraphase-25 INFO visit :: node: "output-havanno_json", values: {"havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-25/call-run_paraphase/out/m84036_250809_035451_s4.bc2122.havanno.json"}
2025-09-15 20:23:46.916 wdl.w:ptcp.w:call-paraphase-25 INFO visit :: node: "output-paraphase_bam", values: {"paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-25/call-run_paraphase/out/m84036_250809_035451_s4.bc2122_paraphase/m84036_250809_035451_s4.bc2122.paraphase.bam"}
2025-09-15 20:23:46.916 wdl.w:ptcp.w:call-paraphase-25 INFO visit :: node: "output-paraphase_bam_bai", values: {"paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-25/call-run_paraphase/out/m84036_250809_035451_s4.bc2122_paraphase/m84036_250809_035451_s4.bc2122.paraphase.bam.bai"}
2025-09-15 20:23:46.916 wdl.w:ptcp.w:call-paraphase-25 INFO visit :: node: "output-paraphase_json", values: {"paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-25/call-run_paraphase/out/m84036_250809_035451_s4.bc2122_paraphase/m84036_250809_035451_s4.bc2122.paraphase.json"}
2025-09-15 20:23:46.916 wdl.w:ptcp.w:call-paraphase-25 INFO visit :: node: "output-paraphase_vcfs", values: {"paraphase_vcfs": []}
2025-09-15 20:23:46.923 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_motifs_allele NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-31/call-trgt_plot_motifs_allele", thread: 140609260066368
2025-09-15 20:23:46.940 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_motifs_allele INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:23:46.940 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_motifs_allele INFO input :: name: "waterfall", value: false
2025-09-15 20:23:46.940 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_motifs_allele INFO input :: name: "methylation", value: false
2025-09-15 20:23:46.941 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_motifs_allele INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:23:46.941 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_motifs_allele INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:23:46.941 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_motifs_allele INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:23:46.941 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_motifs_allele INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2128.trgt.sorted.spanning.bam.bai"
2025-09-15 20:23:46.941 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_motifs_allele INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2128.trgt.sorted.spanning.bam"
2025-09-15 20:23:46.941 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_motifs_allele INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2128.trgt.vcf"
2025-09-15 20:23:46.941 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_motifs_allele INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2128"
2025-09-15 20:23:46.941 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_motifs_allele INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:23:46.941 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_motifs_allele INFO eval :: name: "plot_type", value: "allele"
2025-09-15 20:23:46.941 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_motifs_allele INFO eval :: name: "show", value: "motifs"
2025-09-15 20:23:46.941 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_motifs_allele INFO eval :: name: "threads", value: 1
2025-09-15 20:23:46.942 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_motifs_allele INFO eval :: name: "disk_size", value: 27
2025-09-15 20:23:46.942 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_motifs_allele INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2128.motifs_allele"
2025-09-15 20:23:46.942 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_motifs_allele INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:23:46.942 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_motifs_allele WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:23:46.943 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_motifs_allele INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:23:46.943 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_motifs_allele INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:23:47.027 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_motifs_allele INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-31/call-trgt_plot_motifs_allele/_singularity_tmpdir_6xdq7du7"
2025-09-15 20:23:47.028 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_motifs_allele INFO Slurm invocation: srun --job-name call-trgt_plot_motifs_allele --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-31/call-trgt_plot_motifs_allele/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-31/call-trgt_plot_motifs_allele/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-31/call-trgt_plot_motifs_allele/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-31/call-trgt_plot_motifs_allele/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-31/call-trgt_genotype/out/m84036_250809_035451_s4.bc2128.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2128.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-31/call-trgt_genotype/out/m84036_250809_035451_s4.bc2128.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2128.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-31/call-trgt_genotype/out/m84036_250809_035451_s4.bc2128.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2128.trgt.sorted.spanning.bam:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-31/call-trgt_plot_motifs_allele/_singularity_tmpdir_6xdq7du7/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-31/call-trgt_plot_motifs_allele/_singularity_tmpdir_6xdq7du7/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:23:47.041 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_motifs_allele NOTICE slurm_singularity run :: pid: 1200144, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-31/call-trgt_plot_motifs_allele/slurm_singularity.log.txt"
2025-09-15 20:23:47.102 wdl.w:ptcp.w:call-paraphase-32.t:call-run_paraphase INFO output :: name: "paraphase_bam", value: "m84036_250809_035451_s4.bc2129_paraphase/m84036_250809_035451_s4.bc2129.paraphase.bam"
2025-09-15 20:23:47.108 wdl.w:ptcp.w:call-paraphase-32.t:call-run_paraphase INFO output :: name: "paraphase_bam_bai", value: "m84036_250809_035451_s4.bc2129_paraphase/m84036_250809_035451_s4.bc2129.paraphase.bam.bai"
2025-09-15 20:23:47.109 wdl.w:ptcp.w:call-paraphase-32.t:call-run_paraphase INFO output :: name: "paraphase_json", value: "m84036_250809_035451_s4.bc2129_paraphase/m84036_250809_035451_s4.bc2129.paraphase.json"
2025-09-15 20:23:47.111 wdl.w:ptcp.w:call-paraphase-32.t:call-run_paraphase INFO output :: name: "paraphase_vcfs", value: []
2025-09-15 20:23:47.111 wdl.w:ptcp.w:call-paraphase-32.t:call-run_paraphase INFO output :: name: "havanno_json", value: "m84036_250809_035451_s4.bc2129.havanno.json"
2025-09-15 20:23:47.223 wdl.w:ptcp.w:call-paraphase-32.t:call-run_paraphase NOTICE done
2025-09-15 20:23:47.261 wdl.w:ptcp.w:call-paraphase-32 NOTICE finish :: job: "call-run_paraphase"
2025-09-15 20:23:47.261 wdl.w:ptcp.w:call-paraphase-32 INFO output :: job: "call-run_paraphase", values: {"havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-32/call-run_paraphase/out/m84036_250809_035451_s4.bc2129.havanno.json", "paraphase_vcfs": [], "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-32/call-run_paraphase/out/m84036_250809_035451_s4.bc2129_paraphase/m84036_250809_035451_s4.bc2129.paraphase.json", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-32/call-run_paraphase/out/m84036_250809_035451_s4.bc2129_paraphase/m84036_250809_035451_s4.bc2129.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-32/call-run_paraphase/out/m84036_250809_035451_s4.bc2129_paraphase/m84036_250809_035451_s4.bc2129.paraphase.bam"}
2025-09-15 20:23:47.262 wdl.w:ptcp.w:call-paraphase-32 NOTICE ready :: job: "call-call_f8", callee: "call_f8"
2025-09-15 20:23:47.262 wdl.w:ptcp.w:call-paraphase-32 INFO input :: job: "call-call_f8", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "out_prefix": "m84036_250809_035451_s4.bc2129", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-32/call-run_paraphase/out/m84036_250809_035451_s4.bc2129_paraphase/m84036_250809_035451_s4.bc2129.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-32/call-run_paraphase/out/m84036_250809_035451_s4.bc2129_paraphase/m84036_250809_035451_s4.bc2129.paraphase.bam", "sex": "F"}
2025-09-15 20:23:47.263 wdl.w:ptcp.w:call-paraphase-32 INFO visit :: node: "output-havanno_json", values: {"havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-32/call-run_paraphase/out/m84036_250809_035451_s4.bc2129.havanno.json"}
2025-09-15 20:23:47.263 wdl.w:ptcp.w:call-paraphase-32 INFO visit :: node: "output-paraphase_bam", values: {"paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-32/call-run_paraphase/out/m84036_250809_035451_s4.bc2129_paraphase/m84036_250809_035451_s4.bc2129.paraphase.bam"}
2025-09-15 20:23:47.263 wdl.w:ptcp.w:call-paraphase-32 INFO visit :: node: "output-paraphase_bam_bai", values: {"paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-32/call-run_paraphase/out/m84036_250809_035451_s4.bc2129_paraphase/m84036_250809_035451_s4.bc2129.paraphase.bam.bai"}
2025-09-15 20:23:47.263 wdl.w:ptcp.w:call-paraphase-32 INFO visit :: node: "output-paraphase_json", values: {"paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-32/call-run_paraphase/out/m84036_250809_035451_s4.bc2129_paraphase/m84036_250809_035451_s4.bc2129.paraphase.json"}
2025-09-15 20:23:47.263 wdl.w:ptcp.w:call-paraphase-32 INFO visit :: node: "output-paraphase_vcfs", values: {"paraphase_vcfs": []}
2025-09-15 20:23:47.266 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_motifs_waterfall NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-31/call-trgt_plot_motifs_waterfall", thread: 140609813722688
2025-09-15 20:23:47.283 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_motifs_waterfall INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:23:47.283 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_motifs_waterfall INFO input :: name: "waterfall", value: true
2025-09-15 20:23:47.283 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_motifs_waterfall INFO input :: name: "methylation", value: false
2025-09-15 20:23:47.283 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_motifs_waterfall INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:23:47.283 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_motifs_waterfall INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:23:47.283 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_motifs_waterfall INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:23:47.283 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_motifs_waterfall INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2128.trgt.sorted.spanning.bam.bai"
2025-09-15 20:23:47.283 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_motifs_waterfall INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2128.trgt.sorted.spanning.bam"
2025-09-15 20:23:47.283 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_motifs_waterfall INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2128.trgt.vcf"
2025-09-15 20:23:47.283 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_motifs_waterfall INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2128"
2025-09-15 20:23:47.283 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:23:47.284 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "plot_type", value: "waterfall"
2025-09-15 20:23:47.284 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "show", value: "motifs"
2025-09-15 20:23:47.284 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "threads", value: 1
2025-09-15 20:23:47.284 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "disk_size", value: 27
2025-09-15 20:23:47.284 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2128.motifs_waterfall"
2025-09-15 20:23:47.284 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_motifs_waterfall INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:23:47.285 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_motifs_waterfall WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:23:47.285 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_motifs_waterfall INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:23:47.285 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_motifs_waterfall INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:23:47.329 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:47 [ERROR] - No reads found for TRID=NIID_NOTCH2NLC
2025-09-15 20:23:47.330 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:47 [ERROR] - No reads found for TRID=NIID_NOTCH2NLC
2025-09-15 20:23:47.339 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO srun: job 51797469 queued and waiting for resources
2025-09-15 20:23:47.339 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO srun: job 51797469 has been allocated resources
2025-09-15 20:23:47.339 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:47.340 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_plot_motifs_allele.slurm_singularity INFO srun: job 51797470 queued and waiting for resources
2025-09-15 20:23:47.340 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_plot_motifs_allele.slurm_singularity INFO srun: job 51797470 has been allocated resources
2025-09-15 20:23:47.340 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_plot_motifs_allele.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:47.351 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_motifs_waterfall INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-31/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_uvvwb8nr"
2025-09-15 20:23:47.351 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_motifs_waterfall INFO Slurm invocation: srun --job-name call-trgt_plot_motifs_waterfall --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-31/call-trgt_plot_motifs_waterfall/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-31/call-trgt_plot_motifs_waterfall/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-31/call-trgt_plot_motifs_waterfall/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-31/call-trgt_plot_motifs_waterfall/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-31/call-trgt_genotype/out/m84036_250809_035451_s4.bc2128.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2128.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-31/call-trgt_genotype/out/m84036_250809_035451_s4.bc2128.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2128.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-31/call-trgt_genotype/out/m84036_250809_035451_s4.bc2128.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2128.trgt.sorted.spanning.bam:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-31/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_uvvwb8nr/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-31/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_uvvwb8nr/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:23:47.364 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_motifs_waterfall NOTICE slurm_singularity run :: pid: 1200151, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-31/call-trgt_plot_motifs_waterfall/slurm_singularity.log.txt"
2025-09-15 20:23:47.560 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:23:47 [ERROR] - No reads found for TRID=NIID_NOTCH2NLC
2025-09-15 20:23:47.561 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:23:47 [ERROR] - No reads found for TRID=OPDM_ABCD3
2025-09-15 20:23:47.561 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:23:47 [ERROR] - No reads found for TRID=SCA37_DAB1
2025-09-15 20:23:47.561 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:23:47 [ERROR] - No reads found for TRID=DRPLA_ATN1
2025-09-15 20:23:47.568 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO srun: job 51797471 queued and waiting for resources
2025-09-15 20:23:47.568 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO srun: job 51797471 has been allocated resources
2025-09-15 20:23:47.568 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:47.603 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:23:47 [ERROR] - No reads found for TRID=DRPLA_ATN1
2025-09-15 20:23:47.603 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:23:47 [ERROR] - No reads found for TRID=OPDM_ABCD3
2025-09-15 20:23:47.603 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:23:47 [ERROR] - No reads found for TRID=SCA37_DAB1
2025-09-15 20:23:47.603 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:23:47 [ERROR] - No reads found for TRID=NIID_NOTCH2NLC
2025-09-15 20:23:47.611 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_meth_allele.slurm_singularity INFO srun: job 51797472 queued and waiting for resources
2025-09-15 20:23:47.611 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_meth_allele.slurm_singularity INFO srun: job 51797472 has been allocated resources
2025-09-15 20:23:47.611 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_meth_allele.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:47.839 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:47 [ERROR] - No reads found for TRID=DRPLA_ATN1
2025-09-15 20:23:47.839 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:47 [ERROR] - No reads found for TRID=OPDM_ABCD3
2025-09-15 20:23:47.839 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:47 [ERROR] - No reads found for TRID=SCA37_DAB1
2025-09-15 20:23:47.851 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO srun: job 51797473 queued and waiting for resources
2025-09-15 20:23:47.851 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO srun: job 51797473 has been allocated resources
2025-09-15 20:23:47.851 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:47.882 wdl.w:ptcp.w:call-trgt-01.t:call-get_reads_overlapping_repeats INFO output :: name: "reads_overlapping_repeats", value: "m84036_250809_035451_s4.bc2098.repeats.bam"
2025-09-15 20:23:47.889 wdl.w:ptcp.w:call-trgt-01.t:call-get_reads_overlapping_repeats INFO output :: name: "reads_overlapping_repeats_bai", value: "m84036_250809_035451_s4.bc2098.repeats.bam.bai"
2025-09-15 20:23:47.916 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_plot_motifs_allele INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2119.motifs_allele.trgt_plots.zip"
2025-09-15 20:23:47.993 wdl.w:ptcp.w:call-trgt-01.t:call-get_reads_overlapping_repeats NOTICE done
2025-09-15 20:23:47.998 wdl.w:ptcp.w:call-trgt-01 NOTICE finish :: job: "call-get_reads_overlapping_repeats"
2025-09-15 20:23:47.998 wdl.w:ptcp.w:call-trgt-01 INFO output :: job: "call-get_reads_overlapping_repeats", values: {"reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-01/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2098.repeats.bam.bai", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-01/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2098.repeats.bam"}
2025-09-15 20:23:47.999 wdl.w:ptcp.w:call-trgt-01 INFO visit :: node: "output-reads_overlapping_repeats", values: {"reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-01/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2098.repeats.bam"}
2025-09-15 20:23:47.999 wdl.w:ptcp.w:call-trgt-01 INFO visit :: node: "output-reads_overlapping_repeats_bai", values: {"reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-01/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2098.repeats.bam.bai"}
2025-09-15 20:23:48.009 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_plot_meth_allele NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-07/call-trgt_plot_meth_allele", thread: 140609310422592
2025-09-15 20:23:48.016 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_plot_motifs_allele NOTICE done
2025-09-15 20:23:48.033 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_plot_meth_allele INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:23:48.033 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_plot_meth_allele INFO input :: name: "waterfall", value: false
2025-09-15 20:23:48.033 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_plot_meth_allele INFO input :: name: "methylation", value: true
2025-09-15 20:23:48.033 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_plot_meth_allele INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:23:48.033 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_plot_meth_allele INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:23:48.033 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_plot_meth_allele INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:23:48.033 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_plot_meth_allele INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2104.trgt.sorted.spanning.bam.bai"
2025-09-15 20:23:48.033 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_plot_meth_allele INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2104.trgt.sorted.spanning.bam"
2025-09-15 20:23:48.033 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_plot_meth_allele INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2104.trgt.vcf"
2025-09-15 20:23:48.033 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_plot_meth_allele INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2104"
2025-09-15 20:23:48.034 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_plot_meth_allele INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:23:48.034 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_plot_meth_allele INFO eval :: name: "plot_type", value: "allele"
2025-09-15 20:23:48.034 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_plot_meth_allele INFO eval :: name: "show", value: "meth"
2025-09-15 20:23:48.034 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_plot_meth_allele INFO eval :: name: "threads", value: 1
2025-09-15 20:23:48.034 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_plot_meth_allele INFO eval :: name: "disk_size", value: 27
2025-09-15 20:23:48.034 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_plot_meth_allele INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2104.meth_allele"
2025-09-15 20:23:48.035 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_plot_meth_allele INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:23:48.035 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_plot_meth_allele WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:23:48.035 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_plot_meth_allele INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:23:48.035 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_plot_meth_allele INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:23:48.046 wdl.w:ptcp.w:call-trgt-22 NOTICE finish :: job: "call-trgt_plot_motifs_allele"
2025-09-15 20:23:48.047 wdl.w:ptcp.w:call-trgt-22 INFO output :: job: "call-trgt_plot_motifs_allele", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-22/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2119.motifs_allele.trgt_plots.zip"}
2025-09-15 20:23:48.047 wdl.w:ptcp.w:call-trgt-22 INFO visit :: node: "output-images_motifs_allele", values: {"images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-22/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2119.motifs_allele.trgt_plots.zip"}
2025-09-15 20:23:48.057 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_plot_meth_waterfall NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-07/call-trgt_plot_meth_waterfall", thread: 140610358986304
2025-09-15 20:23:48.058 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_motifs_allele.slurm_singularity INFO srun: job 51797474 queued and waiting for resources
2025-09-15 20:23:48.058 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_motifs_allele.slurm_singularity INFO srun: job 51797474 has been allocated resources
2025-09-15 20:23:48.058 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_motifs_allele.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:48.082 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_plot_meth_waterfall INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:23:48.082 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_plot_meth_waterfall INFO input :: name: "waterfall", value: true
2025-09-15 20:23:48.082 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_plot_meth_waterfall INFO input :: name: "methylation", value: true
2025-09-15 20:23:48.082 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_plot_meth_waterfall INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:23:48.082 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_plot_meth_waterfall INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:23:48.082 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_plot_meth_waterfall INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:23:48.082 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_plot_meth_waterfall INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2104.trgt.sorted.spanning.bam.bai"
2025-09-15 20:23:48.083 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_plot_meth_waterfall INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2104.trgt.sorted.spanning.bam"
2025-09-15 20:23:48.083 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_plot_meth_waterfall INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2104.trgt.vcf"
2025-09-15 20:23:48.083 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_plot_meth_waterfall INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2104"
2025-09-15 20:23:48.083 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_plot_meth_waterfall INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:23:48.083 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_plot_meth_waterfall INFO eval :: name: "plot_type", value: "waterfall"
2025-09-15 20:23:48.083 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_plot_meth_waterfall INFO eval :: name: "show", value: "meth"
2025-09-15 20:23:48.083 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_plot_meth_waterfall INFO eval :: name: "threads", value: 1
2025-09-15 20:23:48.084 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_plot_meth_waterfall INFO eval :: name: "disk_size", value: 27
2025-09-15 20:23:48.084 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_plot_meth_waterfall INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2104.meth_waterfall"
2025-09-15 20:23:48.084 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_plot_meth_waterfall INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:23:48.084 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_plot_meth_waterfall WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:23:48.084 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_plot_meth_waterfall INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:23:48.085 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_plot_meth_waterfall INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:23:48.097 wdl.w:ptcp.w:call-paraphase-26.t:call-run_paraphase.stderr VERBOSE INFO:root:Processing sample m84036_250809_035451_s4.bc2123 at 2025-09-15 20:23:36.037518...
2025-09-15 20:23:48.098 wdl.w:ptcp.w:call-paraphase-26.t:call-run_paraphase.stderr VERBOSE INFO:root:Checking sample sex at 2025-09-15 20:23:36.038574...
2025-09-15 20:23:48.098 wdl.w:ptcp.w:call-paraphase-26.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for cyp21 for sample m84036_250809_035451_s4.bc2123 at 2025-09-15 20:23:36.110138...
2025-09-15 20:23:48.098 wdl.w:ptcp.w:call-paraphase-26.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for cyp21 for sample m84036_250809_035451_s4.bc2123 at 2025-09-15 20:23:36.110719...
2025-09-15 20:23:48.098 wdl.w:ptcp.w:call-paraphase-26.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for smn1 for sample m84036_250809_035451_s4.bc2123 at 2025-09-15 20:23:36.112057...
2025-09-15 20:23:48.099 wdl.w:ptcp.w:call-paraphase-26.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for smn1 for sample m84036_250809_035451_s4.bc2123 at 2025-09-15 20:23:36.112785...
2025-09-15 20:23:48.099 wdl.w:ptcp.w:call-paraphase-26.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for hba for sample m84036_250809_035451_s4.bc2123 at 2025-09-15 20:23:36.112496...
2025-09-15 20:23:48.099 wdl.w:ptcp.w:call-paraphase-26.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for gba for sample m84036_250809_035451_s4.bc2123 at 2025-09-15 20:23:36.112468...
2025-09-15 20:23:48.099 wdl.w:ptcp.w:call-paraphase-26.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for hba for sample m84036_250809_035451_s4.bc2123 at 2025-09-15 20:23:36.113121...
2025-09-15 20:23:48.099 wdl.w:ptcp.w:call-paraphase-26.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for gba for sample m84036_250809_035451_s4.bc2123 at 2025-09-15 20:23:36.113130...
2025-09-15 20:23:48.131 wdl.w:ptcp.w:call-trgt-00.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:44 [INFO] - Running trgt-4.0.0-429afcd [genotype]
2025-09-15 20:23:48.131 wdl.w:ptcp.w:call-trgt-00.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:45 [WARN] - SCA37_DAB1: Filtered out 20 impure reads
2025-09-15 20:23:48.131 wdl.w:ptcp.w:call-trgt-00.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:45 [WARN] - OPDM_ABCD3: Filtered out 21 impure reads
2025-09-15 20:23:48.131 wdl.w:ptcp.w:call-trgt-00.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:45 [WARN] - DRPLA_ATN1: Filtered out 32 impure reads
2025-09-15 20:23:48.131 wdl.w:ptcp.w:call-trgt-00.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:45 [WARN] - NIID_NOTCH2NLC: Filtered out 43 impure reads
2025-09-15 20:23:48.131 wdl.w:ptcp.w:call-trgt-00.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:45 [WARN] - OPDM4_RILPL1: Filtered out 18 impure reads
2025-09-15 20:23:48.132 wdl.w:ptcp.w:call-trgt-00.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:45 [WARN] - SCA27B_FGF14: Filtered out 13 impure reads
2025-09-15 20:23:48.132 wdl.w:ptcp.w:call-trgt-00.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:45 [WARN] - SCA2_ATXN2: Filtered out 30 impure reads
2025-09-15 20:23:48.132 wdl.w:ptcp.w:call-trgt-00.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:45 [WARN] - SCA8_ATXN8OS: Filtered out 26 impure reads
2025-09-15 20:23:48.132 wdl.w:ptcp.w:call-trgt-00.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:45 [WARN] - SCA3_ATXN3: Filtered out 23 impure reads
2025-09-15 20:23:48.132 wdl.w:ptcp.w:call-trgt-00.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:45 [WARN] - SCA31_BEAN1: Filtered out 18 impure reads
2025-09-15 20:23:48.132 wdl.w:ptcp.w:call-trgt-00.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:46 [WARN] - OPMD_PABPN1: Filtered out 22 impure reads
2025-09-15 20:23:48.132 wdl.w:ptcp.w:call-trgt-00.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:46 [WARN] - SCA4_ZFHX3: Filtered out 41 impure reads
2025-09-15 20:23:48.132 wdl.w:ptcp.w:call-trgt-00.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:46 [WARN] - FECD3_TCF4: Filtered out 21 impure reads
2025-09-15 20:23:48.132 wdl.w:ptcp.w:call-trgt-00.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:46 [WARN] - HDL2_JPH3: Filtered out 16 impure reads
2025-09-15 20:23:48.132 wdl.w:ptcp.w:call-trgt-00.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:46 [WARN] - OPDM2_GIPC1: Filtered out 23 impure reads
2025-09-15 20:23:48.132 wdl.w:ptcp.w:call-trgt-00.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:46 [WARN] - DM1_DMPK: Filtered out 33 impure reads
2025-09-15 20:23:48.132 wdl.w:ptcp.w:call-trgt-00.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:46 [WARN] - SCA6_CACNA1A: Filtered out 26 impure reads
2025-09-15 20:23:48.132 wdl.w:ptcp.w:call-trgt-00.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:46 [WARN] - FRA2A_AFF3: Filtered out 35 impure reads
2025-09-15 20:23:48.132 wdl.w:ptcp.w:call-trgt-00.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:46 [WARN] - CJD_PRNP: Filtered out 26 impure reads
2025-09-15 20:23:48.132 wdl.w:ptcp.w:call-trgt-00.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:46 [WARN] - EPM1_CSTB: Filtered out 23 impure reads
2025-09-15 20:23:48.132 wdl.w:ptcp.w:call-trgt-00.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:46 [WARN] - SCA36_NOP56: Filtered out 29 impure reads
2025-09-15 20:23:48.133 wdl.w:ptcp.w:call-trgt-00.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:46 [WARN] - DM2_CNBP: Filtered out 10 impure reads
2025-09-15 20:23:48.133 wdl.w:ptcp.w:call-trgt-00.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:46 [WARN] - SCA10_ATXN10: Filtered out 14 impure reads
2025-09-15 20:23:48.133 wdl.w:ptcp.w:call-trgt-00.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:46 [WARN] - SD5_HOXD13: Filtered out 18 impure reads
2025-09-15 20:23:48.133 wdl.w:ptcp.w:call-trgt-00.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:46 [WARN] - CCHS_PHOX2B: Filtered out 7 impure reads
2025-09-15 20:23:48.133 wdl.w:ptcp.w:call-trgt-00.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:46 [WARN] - SCA7_ATXN7: Filtered out 26 impure reads
2025-09-15 20:23:48.133 wdl.w:ptcp.w:call-trgt-00.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:46 [WARN] - HD_HTT: Filtered out 29 impure reads
2025-09-15 20:23:48.133 wdl.w:ptcp.w:call-trgt-00.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:46 [WARN] - SCA17_TBP: Filtered out 23 impure reads
2025-09-15 20:23:48.133 wdl.w:ptcp.w:call-trgt-00.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:46 [WARN] - CANVAS_RFC1: Filtered out 4 impure reads
2025-09-15 20:23:48.133 wdl.w:ptcp.w:call-trgt-00.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:46 [WARN] - SCA1_ATXN1: Filtered out 31 impure reads
2025-09-15 20:23:48.133 wdl.w:ptcp.w:call-trgt-00.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:46 [WARN] - OPDM1_LRP12: Filtered out 16 impure reads
2025-09-15 20:23:48.133 wdl.w:ptcp.w:call-trgt-00.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:46 [WARN] - FAME1_SAMD12: Filtered out 16 impure reads
2025-09-15 20:23:48.133 wdl.w:ptcp.w:call-trgt-00.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:46 [WARN] - FTDALS1_C9orf72: Filtered out 32 impure reads
2025-09-15 20:23:48.133 wdl.w:ptcp.w:call-trgt-00.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:46 [WARN] - SCA12_PPP2R2B: Filtered out 28 impure reads
2025-09-15 20:23:48.133 wdl.w:ptcp.w:call-trgt-00.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:46 [WARN] - SBMA_AR: Filtered out 35 impure reads
2025-09-15 20:23:48.133 wdl.w:ptcp.w:call-trgt-00.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:47 [WARN] - FXS_FMR1: Filtered out 5 impure reads
2025-09-15 20:23:48.133 wdl.w:ptcp.w:call-trgt-00.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:47 [WARN] - FRAXE_AFF2: Filtered out 29 impure reads
2025-09-15 20:23:48.133 wdl.w:ptcp.w:call-trgt-00.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:47 [WARN] - FRDA_FXN: Filtered out 11 impure reads
2025-09-15 20:23:48.133 wdl.w:ptcp.w:call-trgt-00.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:47 [INFO] - Total execution time: 2.55s
2025-09-15 20:23:48.134 wdl.w:ptcp.w:call-trgt-00.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:47 [INFO] - trgt end
2025-09-15 20:23:48.146 wdl.w:ptcp.w:call-trgt-00.t:call-trgt_genotype INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2097.trgt.vcf"
2025-09-15 20:23:48.151 wdl.w:ptcp.w:call-trgt-00.t:call-trgt_genotype INFO output :: name: "spanning_bam", value: "m84036_250809_035451_s4.bc2097.trgt.sorted.spanning.bam"
2025-09-15 20:23:48.152 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_plot_meth_allele INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-07/call-trgt_plot_meth_allele/_singularity_tmpdir__2eaveet"
2025-09-15 20:23:48.152 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_plot_meth_allele INFO Slurm invocation: srun --job-name call-trgt_plot_meth_allele --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-07/call-trgt_plot_meth_allele/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-07/call-trgt_plot_meth_allele/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-07/call-trgt_plot_meth_allele/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-07/call-trgt_plot_meth_allele/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-07/call-trgt_genotype/out/m84036_250809_035451_s4.bc2104.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2104.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-07/call-trgt_genotype/out/m84036_250809_035451_s4.bc2104.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2104.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-07/call-trgt_genotype/out/m84036_250809_035451_s4.bc2104.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2104.trgt.sorted.spanning.bam.bai:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-07/call-trgt_plot_meth_allele/_singularity_tmpdir__2eaveet/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-07/call-trgt_plot_meth_allele/_singularity_tmpdir__2eaveet/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:23:48.153 wdl.w:ptcp.w:call-trgt-00.t:call-trgt_genotype INFO output :: name: "spanning_bam_bai", value: "m84036_250809_035451_s4.bc2097.trgt.sorted.spanning.bam.bai"
2025-09-15 20:23:48.182 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:23:45 [ERROR] - No reads found for TRID=NIID_NOTCH2NLC
2025-09-15 20:23:48.182 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:23:45 [ERROR] - No reads found for TRID=OPDM_ABCD3
2025-09-15 20:23:48.182 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:23:45 [ERROR] - No reads found for TRID=SCA2_ATXN2
2025-09-15 20:23:48.182 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:23:45 [ERROR] - No reads found for TRID=SCA37_DAB1
2025-09-15 20:23:48.182 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:23:46 [ERROR] - No reads found for TRID=OPDM4_RILPL1
2025-09-15 20:23:48.182 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:23:46 [ERROR] - No reads found for TRID=SCA3_ATXN3
2025-09-15 20:23:48.182 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:23:46 [ERROR] - No reads found for TRID=SCA31_BEAN1
2025-09-15 20:23:48.182 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:23:46 [ERROR] - No reads found for TRID=SCA4_ZFHX3
2025-09-15 20:23:48.183 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:23:46 [ERROR] - No reads found for TRID=HDL2_JPH3
2025-09-15 20:23:48.183 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:23:46 [ERROR] - No reads found for TRID=OPMD_PABPN1
2025-09-15 20:23:48.183 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:23:46 [ERROR] - No reads found for TRID=FECD3_TCF4
2025-09-15 20:23:48.183 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:23:46 [ERROR] - No reads found for TRID=SCA6_CACNA1A
2025-09-15 20:23:48.183 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:23:46 [ERROR] - No reads found for TRID=OPDM2_GIPC1
2025-09-15 20:23:48.183 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:23:46 [ERROR] - No reads found for TRID=DM1_DMPK
2025-09-15 20:23:48.183 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:23:46 [ERROR] - No reads found for TRID=SD5_HOXD13
2025-09-15 20:23:48.183 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:23:46 [ERROR] - No reads found for TRID=SCA36_NOP56
2025-09-15 20:23:48.183 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:23:47 [ERROR] - No reads found for TRID=SCA8_ATXN8OS
2025-09-15 20:23:48.183 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:23:47 [ERROR] - No reads found for TRID=EPM1_CSTB
2025-09-15 20:23:48.183 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:23:47 [ERROR] - No reads found for TRID=DRPLA_ATN1
2025-09-15 20:23:48.183 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:23:47 [ERROR] - No reads found for TRID=FRA2A_AFF3
2025-09-15 20:23:48.183 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:23:47 [ERROR] - No reads found for TRID=DM2_CNBP
2025-09-15 20:23:48.183 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:23:47 [ERROR] - No reads found for TRID=SCA7_ATXN7
2025-09-15 20:23:48.183 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:23:47 [ERROR] - No reads found for TRID=CJD_PRNP
2025-09-15 20:23:48.183 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:23:47 [ERROR] - No reads found for TRID=SCA27B_FGF14
2025-09-15 20:23:48.183 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:23:47 [ERROR] - No reads found for TRID=CCHS_PHOX2B
2025-09-15 20:23:48.183 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:23:47 [ERROR] - No reads found for TRID=SCA12_PPP2R2B
2025-09-15 20:23:48.183 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:23:47 [ERROR] - No reads found for TRID=SCA1_ATXN1
2025-09-15 20:23:48.183 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:23:47 [ERROR] - No reads found for TRID=SCA10_ATXN10
2025-09-15 20:23:48.184 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:23:47 [ERROR] - No reads found for TRID=FAME1_SAMD12
2025-09-15 20:23:48.184 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:23:47 [ERROR] - No reads found for TRID=OPDM1_LRP12
2025-09-15 20:23:48.184 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:23:48 [ERROR] - No reads found for TRID=HD_HTT
2025-09-15 20:23:48.184 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:23:48 [ERROR] - No reads found for TRID=FTDALS1_C9orf72
2025-09-15 20:23:48.186 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_plot_meth_waterfall INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-07/call-trgt_plot_meth_waterfall/_singularity_tmpdir_7la_99ey"
2025-09-15 20:23:48.187 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_plot_meth_waterfall INFO Slurm invocation: srun --job-name call-trgt_plot_meth_waterfall --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-07/call-trgt_plot_meth_waterfall/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-07/call-trgt_plot_meth_waterfall/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-07/call-trgt_plot_meth_waterfall/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-07/call-trgt_plot_meth_waterfall/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-07/call-trgt_genotype/out/m84036_250809_035451_s4.bc2104.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2104.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-07/call-trgt_genotype/out/m84036_250809_035451_s4.bc2104.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2104.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-07/call-trgt_genotype/out/m84036_250809_035451_s4.bc2104.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2104.trgt.sorted.spanning.bam.bai:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-07/call-trgt_plot_meth_waterfall/_singularity_tmpdir_7la_99ey/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-07/call-trgt_plot_meth_waterfall/_singularity_tmpdir_7la_99ey/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:23:48.196 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:45 [ERROR] - No reads found for TRID=NIID_NOTCH2NLC
2025-09-15 20:23:48.196 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:45 [ERROR] - No reads found for TRID=OPDM_ABCD3
2025-09-15 20:23:48.196 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:45 [ERROR] - No reads found for TRID=SCA2_ATXN2
2025-09-15 20:23:48.196 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:46 [ERROR] - No reads found for TRID=SCA37_DAB1
2025-09-15 20:23:48.196 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:46 [ERROR] - No reads found for TRID=OPDM4_RILPL1
2025-09-15 20:23:48.196 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:46 [ERROR] - No reads found for TRID=SCA3_ATXN3
2025-09-15 20:23:48.196 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:46 [ERROR] - No reads found for TRID=SCA31_BEAN1
2025-09-15 20:23:48.196 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:46 [ERROR] - No reads found for TRID=SCA4_ZFHX3
2025-09-15 20:23:48.196 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:46 [ERROR] - No reads found for TRID=HDL2_JPH3
2025-09-15 20:23:48.197 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:46 [ERROR] - No reads found for TRID=OPMD_PABPN1
2025-09-15 20:23:48.197 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:46 [ERROR] - No reads found for TRID=FECD3_TCF4
2025-09-15 20:23:48.197 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:46 [ERROR] - No reads found for TRID=SCA6_CACNA1A
2025-09-15 20:23:48.198 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_plot_meth_allele NOTICE slurm_singularity run :: pid: 1200166, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-07/call-trgt_plot_meth_allele/slurm_singularity.log.txt"
2025-09-15 20:23:48.197 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:46 [ERROR] - No reads found for TRID=OPDM2_GIPC1
2025-09-15 20:23:48.199 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:46 [ERROR] - No reads found for TRID=DM1_DMPK
2025-09-15 20:23:48.199 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:46 [ERROR] - No reads found for TRID=SD5_HOXD13
2025-09-15 20:23:48.200 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:46 [ERROR] - No reads found for TRID=SCA36_NOP56
2025-09-15 20:23:48.200 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:47 [ERROR] - No reads found for TRID=SCA8_ATXN8OS
2025-09-15 20:23:48.200 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:47 [ERROR] - No reads found for TRID=EPM1_CSTB
2025-09-15 20:23:48.200 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:47 [ERROR] - No reads found for TRID=DRPLA_ATN1
2025-09-15 20:23:48.200 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:47 [ERROR] - No reads found for TRID=FRA2A_AFF3
2025-09-15 20:23:48.200 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:47 [ERROR] - No reads found for TRID=DM2_CNBP
2025-09-15 20:23:48.200 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:47 [ERROR] - No reads found for TRID=SCA7_ATXN7
2025-09-15 20:23:48.200 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:47 [ERROR] - No reads found for TRID=CJD_PRNP
2025-09-15 20:23:48.200 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:47 [ERROR] - No reads found for TRID=SCA27B_FGF14
2025-09-15 20:23:48.200 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:47 [ERROR] - No reads found for TRID=CCHS_PHOX2B
2025-09-15 20:23:48.200 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:47 [ERROR] - No reads found for TRID=SCA12_PPP2R2B
2025-09-15 20:23:48.200 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_plot_meth_waterfall NOTICE slurm_singularity run :: pid: 1200167, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-07/call-trgt_plot_meth_waterfall/slurm_singularity.log.txt"
2025-09-15 20:23:48.201 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:47 [ERROR] - No reads found for TRID=SCA1_ATXN1
2025-09-15 20:23:48.201 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:47 [ERROR] - No reads found for TRID=SCA10_ATXN10
2025-09-15 20:23:48.201 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:47 [ERROR] - No reads found for TRID=FAME1_SAMD12
2025-09-15 20:23:48.201 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:47 [ERROR] - No reads found for TRID=OPDM1_LRP12
2025-09-15 20:23:48.201 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:48 [ERROR] - No reads found for TRID=HD_HTT
2025-09-15 20:23:48.201 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:48 [ERROR] - No reads found for TRID=FTDALS1_C9orf72
2025-09-15 20:23:48.252 wdl.w:ptcp.w:call-trgt-00.t:call-trgt_genotype NOTICE done
2025-09-15 20:23:48.258 wdl.w:ptcp.w:call-trgt-00 NOTICE finish :: job: "call-trgt_genotype"
2025-09-15 20:23:48.259 wdl.w:ptcp.w:call-trgt-00 INFO output :: job: "call-trgt_genotype", values: {"spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-00/call-trgt_genotype/out/m84036_250809_035451_s4.bc2097.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-00/call-trgt_genotype/out/m84036_250809_035451_s4.bc2097.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-00/call-trgt_genotype/out/m84036_250809_035451_s4.bc2097.trgt.vcf"}
2025-09-15 20:23:48.260 wdl.w:ptcp.w:call-trgt-00 NOTICE ready :: job: "call-trgt_plot_meth_allele", callee: "trgt_plot"
2025-09-15 20:23:48.260 wdl.w:ptcp.w:call-trgt-00 INFO input :: job: "call-trgt_plot_meth_allele", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": false, "methylation": true, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-00/call-trgt_genotype/out/m84036_250809_035451_s4.bc2097.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-00/call-trgt_genotype/out/m84036_250809_035451_s4.bc2097.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-00/call-trgt_genotype/out/m84036_250809_035451_s4.bc2097.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2097"}
2025-09-15 20:23:48.262 wdl.w:ptcp.w:call-trgt-00 NOTICE ready :: job: "call-trgt_plot_meth_waterfall", callee: "trgt_plot"
2025-09-15 20:23:48.262 wdl.w:ptcp.w:call-trgt-00 INFO input :: job: "call-trgt_plot_meth_waterfall", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": true, "methylation": true, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-00/call-trgt_genotype/out/m84036_250809_035451_s4.bc2097.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-00/call-trgt_genotype/out/m84036_250809_035451_s4.bc2097.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-00/call-trgt_genotype/out/m84036_250809_035451_s4.bc2097.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2097"}
2025-09-15 20:23:48.262 wdl.w:ptcp.w:call-trgt-00 NOTICE ready :: job: "call-trgt_plot_motifs_allele", callee: "trgt_plot"
2025-09-15 20:23:48.263 wdl.w:ptcp.w:call-trgt-00 INFO input :: job: "call-trgt_plot_motifs_allele", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": false, "methylation": false, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-00/call-trgt_genotype/out/m84036_250809_035451_s4.bc2097.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-00/call-trgt_genotype/out/m84036_250809_035451_s4.bc2097.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-00/call-trgt_genotype/out/m84036_250809_035451_s4.bc2097.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2097"}
2025-09-15 20:23:48.264 wdl.w:ptcp.w:call-trgt-00 NOTICE ready :: job: "call-trgt_plot_motifs_waterfall", callee: "trgt_plot"
2025-09-15 20:23:48.264 wdl.w:ptcp.w:call-trgt-00 INFO input :: job: "call-trgt_plot_motifs_waterfall", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": true, "methylation": false, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-00/call-trgt_genotype/out/m84036_250809_035451_s4.bc2097.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-00/call-trgt_genotype/out/m84036_250809_035451_s4.bc2097.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-00/call-trgt_genotype/out/m84036_250809_035451_s4.bc2097.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2097"}
2025-09-15 20:23:48.265 wdl.w:ptcp.w:call-trgt-00 INFO visit :: node: "output-spanning_bam", values: {"spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-00/call-trgt_genotype/out/m84036_250809_035451_s4.bc2097.trgt.sorted.spanning.bam"}
2025-09-15 20:23:48.265 wdl.w:ptcp.w:call-trgt-00 INFO visit :: node: "output-spanning_bam_bai", values: {"spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-00/call-trgt_genotype/out/m84036_250809_035451_s4.bc2097.trgt.sorted.spanning.bam.bai"}
2025-09-15 20:23:48.265 wdl.w:ptcp.w:call-trgt-00 INFO visit :: node: "output-vcf", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-00/call-trgt_genotype/out/m84036_250809_035451_s4.bc2097.trgt.vcf"}
2025-09-15 20:23:48.270 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_plot_motifs_allele NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-07/call-trgt_plot_motifs_allele", thread: 140610367379008
2025-09-15 20:23:48.289 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_plot_motifs_allele INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:23:48.289 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_plot_motifs_allele INFO input :: name: "waterfall", value: false
2025-09-15 20:23:48.289 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_plot_motifs_allele INFO input :: name: "methylation", value: false
2025-09-15 20:23:48.290 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_plot_motifs_allele INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:23:48.290 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_plot_motifs_allele INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:23:48.290 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_plot_motifs_allele INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:23:48.290 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_plot_motifs_allele INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2104.trgt.sorted.spanning.bam.bai"
2025-09-15 20:23:48.290 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_plot_motifs_allele INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2104.trgt.sorted.spanning.bam"
2025-09-15 20:23:48.290 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_plot_motifs_allele INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2104.trgt.vcf"
2025-09-15 20:23:48.290 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_plot_motifs_allele INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2104"
2025-09-15 20:23:48.290 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_plot_motifs_allele INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:23:48.290 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_plot_motifs_allele INFO eval :: name: "plot_type", value: "allele"
2025-09-15 20:23:48.290 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_plot_motifs_allele INFO eval :: name: "show", value: "motifs"
2025-09-15 20:23:48.290 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_plot_motifs_allele INFO eval :: name: "threads", value: 1
2025-09-15 20:23:48.291 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_plot_motifs_allele INFO eval :: name: "disk_size", value: 27
2025-09-15 20:23:48.291 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_plot_motifs_allele INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2104.motifs_allele"
2025-09-15 20:23:48.291 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_plot_motifs_allele INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:23:48.291 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_plot_motifs_allele WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:23:48.292 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_plot_motifs_allele INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:23:48.292 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_plot_motifs_allele INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:23:48.368 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:23:48 [ERROR] - No reads found for TRID=DRPLA_ATN1
2025-09-15 20:23:48.368 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:23:48 [ERROR] - No reads found for TRID=OPDM_ABCD3
2025-09-15 20:23:48.380 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_plot_motifs_allele INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-07/call-trgt_plot_motifs_allele/_singularity_tmpdir_814wrfpt"
2025-09-15 20:23:48.381 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_plot_motifs_allele INFO Slurm invocation: srun --job-name call-trgt_plot_motifs_allele --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-07/call-trgt_plot_motifs_allele/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-07/call-trgt_plot_motifs_allele/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-07/call-trgt_plot_motifs_allele/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-07/call-trgt_plot_motifs_allele/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-07/call-trgt_genotype/out/m84036_250809_035451_s4.bc2104.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2104.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-07/call-trgt_genotype/out/m84036_250809_035451_s4.bc2104.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2104.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-07/call-trgt_genotype/out/m84036_250809_035451_s4.bc2104.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2104.trgt.sorted.spanning.bam.bai:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-07/call-trgt_plot_motifs_allele/_singularity_tmpdir_814wrfpt/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-07/call-trgt_plot_motifs_allele/_singularity_tmpdir_814wrfpt/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:23:48.382 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO srun: job 51797475 queued and waiting for resources
2025-09-15 20:23:48.384 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO srun: job 51797475 has been allocated resources
2025-09-15 20:23:48.384 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:48.402 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_plot_motifs_allele NOTICE slurm_singularity run :: pid: 1200170, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-07/call-trgt_plot_motifs_allele/slurm_singularity.log.txt"
2025-09-15 20:23:48.501 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_plot_motifs_waterfall INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2119.motifs_waterfall.trgt_plots.zip"
2025-09-15 20:23:48.592 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_plot_motifs_waterfall NOTICE done
2025-09-15 20:23:48.600 wdl.w:ptcp.w:call-trgt-22 NOTICE finish :: job: "call-trgt_plot_motifs_waterfall"
2025-09-15 20:23:48.600 wdl.w:ptcp.w:call-trgt-22 INFO output :: job: "call-trgt_plot_motifs_waterfall", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-22/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2119.motifs_waterfall.trgt_plots.zip"}
2025-09-15 20:23:48.600 wdl.w:ptcp.w:call-trgt-22 INFO visit :: node: "output-images_motifs_waterfall", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-22/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2119.motifs_waterfall.trgt_plots.zip"}
2025-09-15 20:23:48.607 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_plot_motifs_waterfall NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-07/call-trgt_plot_motifs_waterfall", thread: 140610879071808
2025-09-15 20:23:48.615 wdl.w:ptcp.w:call-sawfish-28.t:call-run_sawfish.stderr VERBOSE [M::bam2fq_mainloop] discarded 0 singletons
2025-09-15 20:23:48.616 wdl.w:ptcp.w:call-sawfish-28.t:call-run_sawfish.stderr VERBOSE [M::bam2fq_mainloop] processed 0 reads
2025-09-15 20:23:48.627 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_plot_motifs_waterfall INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:23:48.627 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_plot_motifs_waterfall INFO input :: name: "waterfall", value: true
2025-09-15 20:23:48.627 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_plot_motifs_waterfall INFO input :: name: "methylation", value: false
2025-09-15 20:23:48.627 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_plot_motifs_waterfall INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:23:48.627 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_plot_motifs_waterfall INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:23:48.628 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_plot_motifs_waterfall INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:23:48.628 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_plot_motifs_waterfall INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2104.trgt.sorted.spanning.bam.bai"
2025-09-15 20:23:48.628 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_plot_motifs_waterfall INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2104.trgt.sorted.spanning.bam"
2025-09-15 20:23:48.628 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_plot_motifs_waterfall INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2104.trgt.vcf"
2025-09-15 20:23:48.628 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_plot_motifs_waterfall INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2104"
2025-09-15 20:23:48.628 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:23:48.628 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "plot_type", value: "waterfall"
2025-09-15 20:23:48.628 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "show", value: "motifs"
2025-09-15 20:23:48.628 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "threads", value: 1
2025-09-15 20:23:48.629 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "disk_size", value: 27
2025-09-15 20:23:48.629 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2104.motifs_waterfall"
2025-09-15 20:23:48.629 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_plot_motifs_waterfall INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:23:48.629 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_plot_motifs_waterfall WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:23:48.630 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_plot_motifs_waterfall INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:23:48.630 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_plot_motifs_waterfall INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:23:48.660 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_plot_meth_allele INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2112.meth_allele.trgt_plots.zip"
2025-09-15 20:23:48.731 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_plot_motifs_waterfall INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-07/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_aughaf87"
2025-09-15 20:23:48.732 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_plot_motifs_waterfall INFO Slurm invocation: srun --job-name call-trgt_plot_motifs_waterfall --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-07/call-trgt_plot_motifs_waterfall/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-07/call-trgt_plot_motifs_waterfall/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-07/call-trgt_plot_motifs_waterfall/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-07/call-trgt_plot_motifs_waterfall/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-07/call-trgt_genotype/out/m84036_250809_035451_s4.bc2104.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2104.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-07/call-trgt_genotype/out/m84036_250809_035451_s4.bc2104.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2104.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-07/call-trgt_genotype/out/m84036_250809_035451_s4.bc2104.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2104.trgt.sorted.spanning.bam.bai:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-07/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_aughaf87/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-07/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_aughaf87/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:23:48.749 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_plot_motifs_waterfall NOTICE slurm_singularity run :: pid: 1200189, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-07/call-trgt_plot_motifs_waterfall/slurm_singularity.log.txt"
2025-09-15 20:23:48.757 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_plot_meth_allele NOTICE done
2025-09-15 20:23:48.761 wdl.w:ptcp.w:call-paraphase-10.t:call-run_paraphase.stderr VERBOSE INFO:root:Processing sample m84036_250809_035451_s4.bc2107 at 2025-09-15 20:23:35.655403...
2025-09-15 20:23:48.762 wdl.w:ptcp.w:call-trgt-15 NOTICE finish :: job: "call-trgt_plot_meth_allele"
2025-09-15 20:23:48.762 wdl.w:ptcp.w:call-paraphase-10.t:call-run_paraphase.stderr VERBOSE INFO:root:Checking sample sex at 2025-09-15 20:23:35.656348...
2025-09-15 20:23:48.762 wdl.w:ptcp.w:call-trgt-15 INFO output :: job: "call-trgt_plot_meth_allele", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-15/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2112.meth_allele.trgt_plots.zip"}
2025-09-15 20:23:48.762 wdl.w:ptcp.w:call-paraphase-10.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for smn1 for sample m84036_250809_035451_s4.bc2107 at 2025-09-15 20:23:35.712042...
2025-09-15 20:23:48.762 wdl.w:ptcp.w:call-trgt-15 INFO visit :: node: "output-images_meth_allele", values: {"images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-15/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2112.meth_allele.trgt_plots.zip"}
2025-09-15 20:23:48.763 wdl.w:ptcp.w:call-paraphase-10.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for smn1 for sample m84036_250809_035451_s4.bc2107 at 2025-09-15 20:23:35.712446...
2025-09-15 20:23:48.763 wdl.w:ptcp.w:call-paraphase-10.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for cyp21 for sample m84036_250809_035451_s4.bc2107 at 2025-09-15 20:23:35.712056...
2025-09-15 20:23:48.763 wdl.w:ptcp.w:call-paraphase-10.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for cyp21 for sample m84036_250809_035451_s4.bc2107 at 2025-09-15 20:23:35.712538...
2025-09-15 20:23:48.763 wdl.w:ptcp.w:call-paraphase-10.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for gba for sample m84036_250809_035451_s4.bc2107 at 2025-09-15 20:23:35.712393...
2025-09-15 20:23:48.763 wdl.w:ptcp.w:call-paraphase-10.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for gba for sample m84036_250809_035451_s4.bc2107 at 2025-09-15 20:23:35.712835...
2025-09-15 20:23:48.763 wdl.w:ptcp.w:call-paraphase-10.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for hba for sample m84036_250809_035451_s4.bc2107 at 2025-09-15 20:23:35.713485...
2025-09-15 20:23:48.763 wdl.w:ptcp.w:call-paraphase-10.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for hba for sample m84036_250809_035451_s4.bc2107 at 2025-09-15 20:23:35.713842...
2025-09-15 20:23:48.767 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_meth_allele NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-34/call-trgt_plot_meth_allele", thread: 140609822115392
2025-09-15 20:23:48.785 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_meth_allele INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:23:48.786 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_meth_allele INFO input :: name: "waterfall", value: false
2025-09-15 20:23:48.786 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_meth_allele INFO input :: name: "methylation", value: true
2025-09-15 20:23:48.786 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_meth_allele INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:23:48.786 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_meth_allele INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:23:48.786 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_meth_allele INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:23:48.786 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_meth_allele INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2131.trgt.sorted.spanning.bam.bai"
2025-09-15 20:23:48.786 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_meth_allele INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2131.trgt.sorted.spanning.bam"
2025-09-15 20:23:48.786 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_meth_allele INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2131.trgt.vcf"
2025-09-15 20:23:48.786 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_meth_allele INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2131"
2025-09-15 20:23:48.786 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_meth_allele INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:23:48.786 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_meth_allele INFO eval :: name: "plot_type", value: "allele"
2025-09-15 20:23:48.787 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_meth_allele INFO eval :: name: "show", value: "meth"
2025-09-15 20:23:48.787 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_meth_allele INFO eval :: name: "threads", value: 1
2025-09-15 20:23:48.787 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_meth_allele INFO eval :: name: "disk_size", value: 27
2025-09-15 20:23:48.787 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_meth_allele INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2131.meth_allele"
2025-09-15 20:23:48.787 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_meth_allele INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:23:48.787 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_meth_allele WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:23:48.788 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_meth_allele INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:23:48.788 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_meth_allele INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:23:48.874 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_meth_allele INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-34/call-trgt_plot_meth_allele/_singularity_tmpdir_5u_ieax2"
2025-09-15 20:23:48.874 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_meth_allele INFO Slurm invocation: srun --job-name call-trgt_plot_meth_allele --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-34/call-trgt_plot_meth_allele/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-34/call-trgt_plot_meth_allele/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-34/call-trgt_plot_meth_allele/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-34/call-trgt_plot_meth_allele/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-34/call-trgt_genotype/out/m84036_250809_035451_s4.bc2131.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2131.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-34/call-trgt_genotype/out/m84036_250809_035451_s4.bc2131.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2131.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-34/call-trgt_genotype/out/m84036_250809_035451_s4.bc2131.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2131.trgt.sorted.spanning.bam.bai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-34/call-trgt_plot_meth_allele/_singularity_tmpdir_5u_ieax2/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-34/call-trgt_plot_meth_allele/_singularity_tmpdir_5u_ieax2/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:23:48.891 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_meth_allele NOTICE slurm_singularity run :: pid: 1200191, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-34/call-trgt_plot_meth_allele/slurm_singularity.log.txt"
2025-09-15 20:23:49.003 wdl.w:ptcp.w:call-paraphase-18.t:call-run_paraphase.stderr VERBOSE INFO:root:Processing sample m84036_250809_035451_s4.bc2115 at 2025-09-15 20:23:35.217676...
2025-09-15 20:23:49.004 wdl.w:ptcp.w:call-paraphase-18.t:call-run_paraphase.stderr VERBOSE INFO:root:Checking sample sex at 2025-09-15 20:23:35.218635...
2025-09-15 20:23:49.004 wdl.w:ptcp.w:call-paraphase-18.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for cyp21 for sample m84036_250809_035451_s4.bc2115 at 2025-09-15 20:23:35.262936...
2025-09-15 20:23:49.004 wdl.w:ptcp.w:call-paraphase-18.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for cyp21 for sample m84036_250809_035451_s4.bc2115 at 2025-09-15 20:23:35.263608...
2025-09-15 20:23:49.005 wdl.w:ptcp.w:call-paraphase-18.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for smn1 for sample m84036_250809_035451_s4.bc2115 at 2025-09-15 20:23:35.263129...
2025-09-15 20:23:49.005 wdl.w:ptcp.w:call-paraphase-18.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for gba for sample m84036_250809_035451_s4.bc2115 at 2025-09-15 20:23:35.263222...
2025-09-15 20:23:49.005 wdl.w:ptcp.w:call-paraphase-18.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for smn1 for sample m84036_250809_035451_s4.bc2115 at 2025-09-15 20:23:35.263799...
2025-09-15 20:23:49.005 wdl.w:ptcp.w:call-paraphase-18.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for hba for sample m84036_250809_035451_s4.bc2115 at 2025-09-15 20:23:35.263284...
2025-09-15 20:23:49.005 wdl.w:ptcp.w:call-paraphase-18.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for gba for sample m84036_250809_035451_s4.bc2115 at 2025-09-15 20:23:35.263833...
2025-09-15 20:23:49.005 wdl.w:ptcp.w:call-paraphase-18.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for hba for sample m84036_250809_035451_s4.bc2115 at 2025-09-15 20:23:35.263903...
2025-09-15 20:23:49.064 wdl.w:ptcp.w:call-trgt-01.t:call-trgt_genotype INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2098.trgt.vcf"
2025-09-15 20:23:49.067 wdl.w:ptcp.w:call-trgt-01.t:call-trgt_genotype INFO output :: name: "spanning_bam", value: "m84036_250809_035451_s4.bc2098.trgt.sorted.spanning.bam"
2025-09-15 20:23:49.068 wdl.w:ptcp.w:call-trgt-01.t:call-trgt_genotype INFO output :: name: "spanning_bam_bai", value: "m84036_250809_035451_s4.bc2098.trgt.sorted.spanning.bam.bai"
2025-09-15 20:23:49.146 wdl.w:ptcp.w:call-trgt-01.t:call-trgt_genotype NOTICE done
2025-09-15 20:23:49.154 wdl.w:ptcp.w:call-trgt-01 NOTICE finish :: job: "call-trgt_genotype"
2025-09-15 20:23:49.155 wdl.w:ptcp.w:call-trgt-01 INFO output :: job: "call-trgt_genotype", values: {"spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-01/call-trgt_genotype/out/m84036_250809_035451_s4.bc2098.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-01/call-trgt_genotype/out/m84036_250809_035451_s4.bc2098.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-01/call-trgt_genotype/out/m84036_250809_035451_s4.bc2098.trgt.vcf"}
2025-09-15 20:23:49.155 wdl.w:ptcp.w:call-trgt-01 NOTICE ready :: job: "call-trgt_plot_meth_allele", callee: "trgt_plot"
2025-09-15 20:23:49.155 wdl.w:ptcp.w:call-trgt-01 INFO input :: job: "call-trgt_plot_meth_allele", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": false, "methylation": true, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-01/call-trgt_genotype/out/m84036_250809_035451_s4.bc2098.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-01/call-trgt_genotype/out/m84036_250809_035451_s4.bc2098.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-01/call-trgt_genotype/out/m84036_250809_035451_s4.bc2098.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2098"}
2025-09-15 20:23:49.156 wdl.w:ptcp.w:call-trgt-01 NOTICE ready :: job: "call-trgt_plot_meth_waterfall", callee: "trgt_plot"
2025-09-15 20:23:49.156 wdl.w:ptcp.w:call-trgt-01 INFO input :: job: "call-trgt_plot_meth_waterfall", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": true, "methylation": true, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-01/call-trgt_genotype/out/m84036_250809_035451_s4.bc2098.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-01/call-trgt_genotype/out/m84036_250809_035451_s4.bc2098.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-01/call-trgt_genotype/out/m84036_250809_035451_s4.bc2098.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2098"}
2025-09-15 20:23:49.157 wdl.w:ptcp.w:call-trgt-01 NOTICE ready :: job: "call-trgt_plot_motifs_allele", callee: "trgt_plot"
2025-09-15 20:23:49.157 wdl.w:ptcp.w:call-trgt-01 INFO input :: job: "call-trgt_plot_motifs_allele", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": false, "methylation": false, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-01/call-trgt_genotype/out/m84036_250809_035451_s4.bc2098.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-01/call-trgt_genotype/out/m84036_250809_035451_s4.bc2098.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-01/call-trgt_genotype/out/m84036_250809_035451_s4.bc2098.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2098"}
2025-09-15 20:23:49.158 wdl.w:ptcp.w:call-trgt-01 NOTICE ready :: job: "call-trgt_plot_motifs_waterfall", callee: "trgt_plot"
2025-09-15 20:23:49.158 wdl.w:ptcp.w:call-trgt-01 INFO input :: job: "call-trgt_plot_motifs_waterfall", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": true, "methylation": false, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-01/call-trgt_genotype/out/m84036_250809_035451_s4.bc2098.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-01/call-trgt_genotype/out/m84036_250809_035451_s4.bc2098.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-01/call-trgt_genotype/out/m84036_250809_035451_s4.bc2098.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2098"}
2025-09-15 20:23:49.159 wdl.w:ptcp.w:call-trgt-01 INFO visit :: node: "output-spanning_bam", values: {"spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-01/call-trgt_genotype/out/m84036_250809_035451_s4.bc2098.trgt.sorted.spanning.bam"}
2025-09-15 20:23:49.159 wdl.w:ptcp.w:call-trgt-01 INFO visit :: node: "output-spanning_bam_bai", values: {"spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-01/call-trgt_genotype/out/m84036_250809_035451_s4.bc2098.trgt.sorted.spanning.bam.bai"}
2025-09-15 20:23:49.159 wdl.w:ptcp.w:call-trgt-01 INFO visit :: node: "output-vcf", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-01/call-trgt_genotype/out/m84036_250809_035451_s4.bc2098.trgt.vcf"}
2025-09-15 20:23:49.162 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_meth_waterfall NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-34/call-trgt_plot_meth_waterfall", thread: 140610887464512
2025-09-15 20:23:49.178 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_meth_waterfall INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:23:49.178 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_meth_waterfall INFO input :: name: "waterfall", value: true
2025-09-15 20:23:49.178 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_meth_waterfall INFO input :: name: "methylation", value: true
2025-09-15 20:23:49.178 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_meth_waterfall INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:23:49.178 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_meth_waterfall INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:23:49.178 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_meth_waterfall INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:23:49.178 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_meth_waterfall INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2131.trgt.sorted.spanning.bam.bai"
2025-09-15 20:23:49.178 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_meth_waterfall INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2131.trgt.sorted.spanning.bam"
2025-09-15 20:23:49.178 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_meth_waterfall INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2131.trgt.vcf"
2025-09-15 20:23:49.178 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_meth_waterfall INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2131"
2025-09-15 20:23:49.179 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_meth_waterfall INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:23:49.179 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_meth_waterfall INFO eval :: name: "plot_type", value: "waterfall"
2025-09-15 20:23:49.179 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_meth_waterfall INFO eval :: name: "show", value: "meth"
2025-09-15 20:23:49.179 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_meth_waterfall INFO eval :: name: "threads", value: 1
2025-09-15 20:23:49.179 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_meth_waterfall INFO eval :: name: "disk_size", value: 27
2025-09-15 20:23:49.179 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_meth_waterfall INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2131.meth_waterfall"
2025-09-15 20:23:49.180 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_meth_waterfall INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:23:49.180 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_meth_waterfall WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:23:49.180 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_meth_waterfall INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:23:49.180 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_meth_waterfall INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:23:49.200 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:23:48 [ERROR] - No reads found for TRID=SCA37_DAB1
2025-09-15 20:23:49.201 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:23:48 [ERROR] - No reads found for TRID=NIID_NOTCH2NLC
2025-09-15 20:23:49.201 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:23:49 [ERROR] - No reads found for TRID=OPDM_ABCD3
2025-09-15 20:23:49.201 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:23:49 [ERROR] - No reads found for TRID=SCA2_ATXN2
2025-09-15 20:23:49.201 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:23:49 [ERROR] - No reads found for TRID=OPDM4_RILPL1
2025-09-15 20:23:49.203 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:49 [ERROR] - No reads found for TRID=SCA37_DAB1
2025-09-15 20:23:49.211 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_plot_meth_allele.slurm_singularity INFO srun: job 51797476 queued and waiting for resources
2025-09-15 20:23:49.211 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_plot_meth_allele.slurm_singularity INFO srun: job 51797476 has been allocated resources
2025-09-15 20:23:49.212 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_plot_meth_allele.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:49.213 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO srun: job 51797477 queued and waiting for resources
2025-09-15 20:23:49.213 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO srun: job 51797477 has been allocated resources
2025-09-15 20:23:49.213 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:49.244 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_meth_waterfall INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-34/call-trgt_plot_meth_waterfall/_singularity_tmpdir_ttt1ji12"
2025-09-15 20:23:49.244 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_meth_waterfall INFO Slurm invocation: srun --job-name call-trgt_plot_meth_waterfall --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-34/call-trgt_plot_meth_waterfall/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-34/call-trgt_plot_meth_waterfall/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-34/call-trgt_plot_meth_waterfall/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-34/call-trgt_plot_meth_waterfall/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-34/call-trgt_genotype/out/m84036_250809_035451_s4.bc2131.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2131.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-34/call-trgt_genotype/out/m84036_250809_035451_s4.bc2131.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2131.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-34/call-trgt_genotype/out/m84036_250809_035451_s4.bc2131.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2131.trgt.sorted.spanning.bam.bai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-34/call-trgt_plot_meth_waterfall/_singularity_tmpdir_ttt1ji12/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-34/call-trgt_plot_meth_waterfall/_singularity_tmpdir_ttt1ji12/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:23:49.264 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_meth_waterfall NOTICE slurm_singularity run :: pid: 1200204, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-34/call-trgt_plot_meth_waterfall/slurm_singularity.log.txt"
2025-09-15 20:23:49.406 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:49 [ERROR] - No reads found for TRID=SCA37_DAB1
2025-09-15 20:23:49.406 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:49 [ERROR] - No reads found for TRID=NIID_NOTCH2NLC
2025-09-15 20:23:49.416 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_plot_motifs_allele.slurm_singularity INFO srun: job 51797478 queued and waiting for resources
2025-09-15 20:23:49.416 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_plot_motifs_allele.slurm_singularity INFO srun: job 51797478 has been allocated resources
2025-09-15 20:23:49.417 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_plot_motifs_allele.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:49.478 wdl.w:ptcp.w:call-paraphase-08.t:call-run_paraphase INFO output :: name: "paraphase_bam", value: "m84036_250809_035451_s4.bc2105_paraphase/m84036_250809_035451_s4.bc2105.paraphase.bam"
2025-09-15 20:23:49.483 wdl.w:ptcp.w:call-paraphase-08.t:call-run_paraphase INFO output :: name: "paraphase_bam_bai", value: "m84036_250809_035451_s4.bc2105_paraphase/m84036_250809_035451_s4.bc2105.paraphase.bam.bai"
2025-09-15 20:23:49.484 wdl.w:ptcp.w:call-paraphase-08.t:call-run_paraphase INFO output :: name: "paraphase_json", value: "m84036_250809_035451_s4.bc2105_paraphase/m84036_250809_035451_s4.bc2105.paraphase.json"
2025-09-15 20:23:49.487 wdl.w:ptcp.w:call-paraphase-08.t:call-run_paraphase INFO output :: name: "paraphase_vcfs", value: []
2025-09-15 20:23:49.487 wdl.w:ptcp.w:call-paraphase-08.t:call-run_paraphase INFO output :: name: "havanno_json", value: "m84036_250809_035451_s4.bc2105.havanno.json"
2025-09-15 20:23:49.580 wdl.w:ptcp.w:call-paraphase-08.t:call-run_paraphase NOTICE done
2025-09-15 20:23:49.586 wdl.w:ptcp.w:call-paraphase-08 NOTICE finish :: job: "call-run_paraphase"
2025-09-15 20:23:49.586 wdl.w:ptcp.w:call-paraphase-08 INFO output :: job: "call-run_paraphase", values: {"havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-08/call-run_paraphase/out/m84036_250809_035451_s4.bc2105.havanno.json", "paraphase_vcfs": [], "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-08/call-run_paraphase/out/m84036_250809_035451_s4.bc2105_paraphase/m84036_250809_035451_s4.bc2105.paraphase.json", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-08/call-run_paraphase/out/m84036_250809_035451_s4.bc2105_paraphase/m84036_250809_035451_s4.bc2105.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-08/call-run_paraphase/out/m84036_250809_035451_s4.bc2105_paraphase/m84036_250809_035451_s4.bc2105.paraphase.bam"}
2025-09-15 20:23:49.587 wdl.w:ptcp.w:call-paraphase-08 NOTICE ready :: job: "call-call_f8", callee: "call_f8"
2025-09-15 20:23:49.587 wdl.w:ptcp.w:call-paraphase-08 INFO input :: job: "call-call_f8", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "out_prefix": "m84036_250809_035451_s4.bc2105", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-08/call-run_paraphase/out/m84036_250809_035451_s4.bc2105_paraphase/m84036_250809_035451_s4.bc2105.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-08/call-run_paraphase/out/m84036_250809_035451_s4.bc2105_paraphase/m84036_250809_035451_s4.bc2105.paraphase.bam", "sex": "F"}
2025-09-15 20:23:49.590 wdl.w:ptcp.w:call-paraphase-08 INFO visit :: node: "output-havanno_json", values: {"havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-08/call-run_paraphase/out/m84036_250809_035451_s4.bc2105.havanno.json"}
2025-09-15 20:23:49.591 wdl.w:ptcp.w:call-paraphase-08 INFO visit :: node: "output-paraphase_bam", values: {"paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-08/call-run_paraphase/out/m84036_250809_035451_s4.bc2105_paraphase/m84036_250809_035451_s4.bc2105.paraphase.bam"}
2025-09-15 20:23:49.591 wdl.w:ptcp.w:call-paraphase-08 INFO visit :: node: "output-paraphase_bam_bai", values: {"paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-08/call-run_paraphase/out/m84036_250809_035451_s4.bc2105_paraphase/m84036_250809_035451_s4.bc2105.paraphase.bam.bai"}
2025-09-15 20:23:49.591 wdl.w:ptcp.w:call-paraphase-08 INFO visit :: node: "output-paraphase_json", values: {"paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-08/call-run_paraphase/out/m84036_250809_035451_s4.bc2105_paraphase/m84036_250809_035451_s4.bc2105.paraphase.json"}
2025-09-15 20:23:49.591 wdl.w:ptcp.w:call-paraphase-08 INFO visit :: node: "output-paraphase_vcfs", values: {"paraphase_vcfs": []}
2025-09-15 20:23:49.594 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_motifs_allele NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-34/call-trgt_plot_motifs_allele", thread: 140610342200896
2025-09-15 20:23:49.609 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_motifs_allele INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:23:49.609 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_motifs_allele INFO input :: name: "waterfall", value: false
2025-09-15 20:23:49.609 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_motifs_allele INFO input :: name: "methylation", value: false
2025-09-15 20:23:49.609 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_motifs_allele INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:23:49.609 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_motifs_allele INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:23:49.609 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_motifs_allele INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:23:49.609 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_motifs_allele INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2131.trgt.sorted.spanning.bam.bai"
2025-09-15 20:23:49.609 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_motifs_allele INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2131.trgt.sorted.spanning.bam"
2025-09-15 20:23:49.610 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_motifs_allele INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2131.trgt.vcf"
2025-09-15 20:23:49.610 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_motifs_allele INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2131"
2025-09-15 20:23:49.610 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_motifs_allele INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:23:49.610 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_motifs_allele INFO eval :: name: "plot_type", value: "allele"
2025-09-15 20:23:49.610 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_motifs_allele INFO eval :: name: "show", value: "motifs"
2025-09-15 20:23:49.610 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_motifs_allele INFO eval :: name: "threads", value: 1
2025-09-15 20:23:49.610 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_motifs_allele INFO eval :: name: "disk_size", value: 27
2025-09-15 20:23:49.611 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_motifs_allele INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2131.motifs_allele"
2025-09-15 20:23:49.611 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_motifs_allele INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:23:49.611 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_motifs_allele WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:23:49.611 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_motifs_allele INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:23:49.611 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_motifs_allele INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:23:49.687 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_motifs_allele INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-34/call-trgt_plot_motifs_allele/_singularity_tmpdir_y03cnie1"
2025-09-15 20:23:49.688 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_motifs_allele INFO Slurm invocation: srun --job-name call-trgt_plot_motifs_allele --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-34/call-trgt_plot_motifs_allele/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-34/call-trgt_plot_motifs_allele/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-34/call-trgt_plot_motifs_allele/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-34/call-trgt_plot_motifs_allele/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-34/call-trgt_genotype/out/m84036_250809_035451_s4.bc2131.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2131.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-34/call-trgt_genotype/out/m84036_250809_035451_s4.bc2131.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2131.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-34/call-trgt_genotype/out/m84036_250809_035451_s4.bc2131.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2131.trgt.sorted.spanning.bam.bai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-34/call-trgt_plot_motifs_allele/_singularity_tmpdir_y03cnie1/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-34/call-trgt_plot_motifs_allele/_singularity_tmpdir_y03cnie1/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:23:49.705 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_motifs_allele NOTICE slurm_singularity run :: pid: 1200276, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-34/call-trgt_plot_motifs_allele/slurm_singularity.log.txt"
2025-09-15 20:23:49.736 wdl.w:ptcp.w:call-paraphase-02.t:call-run_paraphase.stderr VERBOSE INFO:root:Processing sample m84036_250809_035451_s4.bc2099 at 2025-09-15 20:23:45.336989...
2025-09-15 20:23:49.737 wdl.w:ptcp.w:call-paraphase-02.t:call-run_paraphase.stderr VERBOSE INFO:root:Checking sample sex at 2025-09-15 20:23:45.338375...
2025-09-15 20:23:49.737 wdl.w:ptcp.w:call-paraphase-02.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for smn1 for sample m84036_250809_035451_s4.bc2099 at 2025-09-15 20:23:45.381352...
2025-09-15 20:23:49.737 wdl.w:ptcp.w:call-paraphase-02.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for smn1 for sample m84036_250809_035451_s4.bc2099 at 2025-09-15 20:23:45.381741...
2025-09-15 20:23:49.737 wdl.w:ptcp.w:call-paraphase-02.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for cyp21 for sample m84036_250809_035451_s4.bc2099 at 2025-09-15 20:23:45.381357...
2025-09-15 20:23:49.737 wdl.w:ptcp.w:call-paraphase-02.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for cyp21 for sample m84036_250809_035451_s4.bc2099 at 2025-09-15 20:23:45.381862...
2025-09-15 20:23:49.737 wdl.w:ptcp.w:call-paraphase-02.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for gba for sample m84036_250809_035451_s4.bc2099 at 2025-09-15 20:23:45.381728...
2025-09-15 20:23:49.737 wdl.w:ptcp.w:call-paraphase-02.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for gba for sample m84036_250809_035451_s4.bc2099 at 2025-09-15 20:23:45.382157...
2025-09-15 20:23:49.737 wdl.w:ptcp.w:call-paraphase-02.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for hba for sample m84036_250809_035451_s4.bc2099 at 2025-09-15 20:23:45.382779...
2025-09-15 20:23:49.737 wdl.w:ptcp.w:call-paraphase-02.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for hba for sample m84036_250809_035451_s4.bc2099 at 2025-09-15 20:23:45.383136...
2025-09-15 20:23:49.752 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:23:49 [ERROR] - No reads found for TRID=SCA37_DAB1
2025-09-15 20:23:49.752 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:23:49 [ERROR] - No reads found for TRID=NIID_NOTCH2NLC
2025-09-15 20:23:49.752 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:23:49 [ERROR] - No reads found for TRID=OPDM_ABCD3
2025-09-15 20:23:49.752 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:23:49 [ERROR] - No reads found for TRID=SCA2_ATXN2
2025-09-15 20:23:49.752 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:23:49 [ERROR] - No reads found for TRID=OPDM4_RILPL1
2025-09-15 20:23:49.760 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO srun: job 51797479 queued and waiting for resources
2025-09-15 20:23:49.760 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO srun: job 51797479 has been allocated resources
2025-09-15 20:23:49.760 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:49.830 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_plot_meth_allele INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2119.meth_allele.trgt_plots.zip"
2025-09-15 20:23:49.854 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_plot_meth_waterfall INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2119.meth_waterfall.trgt_plots.zip"
2025-09-15 20:23:49.894 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:23:49 [ERROR] - No reads found for TRID=SCA37_DAB1
2025-09-15 20:23:49.894 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:23:49 [ERROR] - No reads found for TRID=DRPLA_ATN1
2025-09-15 20:23:49.894 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:23:49 [ERROR] - No reads found for TRID=NIID_NOTCH2NLC
2025-09-15 20:23:49.894 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:23:49 [ERROR] - No reads found for TRID=OPDM4_RILPL1
2025-09-15 20:23:49.894 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:23:49 [ERROR] - No reads found for TRID=SCA27B_FGF14
2025-09-15 20:23:49.894 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:23:49 [ERROR] - No reads found for TRID=OPDM_ABCD3
2025-09-15 20:23:49.896 wdl.w:ptcp.w:call-trgt-08.t:call-get_reads_overlapping_repeats INFO output :: name: "reads_overlapping_repeats", value: "m84036_250809_035451_s4.bc2105.repeats.bam"
2025-09-15 20:23:49.904 wdl.w:ptcp.w:call-trgt-08.t:call-get_reads_overlapping_repeats INFO output :: name: "reads_overlapping_repeats_bai", value: "m84036_250809_035451_s4.bc2105.repeats.bam.bai"
2025-09-15 20:23:49.910 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_meth_allele.slurm_singularity INFO srun: job 51797480 queued and waiting for resources
2025-09-15 20:23:49.910 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_meth_allele.slurm_singularity INFO srun: job 51797480 has been allocated resources
2025-09-15 20:23:49.910 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_meth_allele.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:49.930 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_plot_meth_allele NOTICE done
2025-09-15 20:23:49.935 wdl.w:ptcp.w:call-trgt-22 NOTICE finish :: job: "call-trgt_plot_meth_allele"
2025-09-15 20:23:49.936 wdl.w:ptcp.w:call-trgt-22 INFO output :: job: "call-trgt_plot_meth_allele", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-22/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2119.meth_allele.trgt_plots.zip"}
2025-09-15 20:23:49.936 wdl.w:ptcp.w:call-trgt-22 INFO visit :: node: "output-images_meth_allele", values: {"images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-22/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2119.meth_allele.trgt_plots.zip"}
2025-09-15 20:23:49.939 wdl.w:ptcp.w:call-trgt-00.t:call-get_reads_overlapping_repeats INFO output :: name: "reads_overlapping_repeats", value: "m84036_250809_035451_s4.bc2097.repeats.bam"
2025-09-15 20:23:49.947 wdl.w:ptcp.w:call-trgt-00.t:call-get_reads_overlapping_repeats INFO output :: name: "reads_overlapping_repeats_bai", value: "m84036_250809_035451_s4.bc2097.repeats.bam.bai"
2025-09-15 20:23:49.949 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_motifs_waterfall NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-34/call-trgt_plot_motifs_waterfall", thread: 140608748373568
2025-09-15 20:23:49.961 wdl.w:ptcp.w:call-trgt-22.t:call-trgt_plot_meth_waterfall NOTICE done
2025-09-15 20:23:49.969 wdl.w:ptcp.w:call-trgt-22 NOTICE finish :: job: "call-trgt_plot_meth_waterfall"
2025-09-15 20:23:49.970 wdl.w:ptcp.w:call-trgt-22 INFO output :: job: "call-trgt_plot_meth_waterfall", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-22/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2119.meth_waterfall.trgt_plots.zip"}
2025-09-15 20:23:49.970 wdl.w:ptcp.w:call-trgt-22 INFO visit :: node: "output-images_meth_waterfall", values: {"images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-22/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2119.meth_waterfall.trgt_plots.zip"}
2025-09-15 20:23:49.970 wdl.w:ptcp.w:call-trgt-22 INFO visit :: node: "outputs", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-22/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2119.motifs_waterfall.trgt_plots.zip", "images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-22/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2119.meth_allele.trgt_plots.zip", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-22/call-trgt_genotype/out/m84036_250809_035451_s4.bc2119.trgt.sorted.spanning.bam.bai", "images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-22/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2119.motifs_allele.trgt_plots.zip", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-22/call-trgt_genotype/out/m84036_250809_035451_s4.bc2119.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-22/call-trgt_genotype/out/m84036_250809_035451_s4.bc2119.trgt.vcf", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-22/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2119.repeats.bam", "images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-22/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2119.meth_waterfall.trgt_plots.zip", "reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-22/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2119.repeats.bam.bai"}
2025-09-15 20:23:49.979 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_motifs_waterfall INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:23:49.979 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_motifs_waterfall INFO input :: name: "waterfall", value: true
2025-09-15 20:23:49.979 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_motifs_waterfall INFO input :: name: "methylation", value: false
2025-09-15 20:23:49.979 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_motifs_waterfall INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:23:49.979 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_motifs_waterfall INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:23:49.979 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_motifs_waterfall INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:23:49.979 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_motifs_waterfall INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2131.trgt.sorted.spanning.bam.bai"
2025-09-15 20:23:49.979 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_motifs_waterfall INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2131.trgt.sorted.spanning.bam"
2025-09-15 20:23:49.979 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_motifs_waterfall INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2131.trgt.vcf"
2025-09-15 20:23:49.979 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_motifs_waterfall INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2131"
2025-09-15 20:23:49.980 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:23:49.981 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "plot_type", value: "waterfall"
2025-09-15 20:23:49.981 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_meth_allele NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-23/call-trgt_plot_meth_allele", thread: 140608773551680
2025-09-15 20:23:49.981 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "show", value: "motifs"
2025-09-15 20:23:49.982 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "threads", value: 1
2025-09-15 20:23:49.982 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "disk_size", value: 27
2025-09-15 20:23:49.982 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2131.motifs_waterfall"
2025-09-15 20:23:49.983 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_motifs_waterfall INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:23:49.983 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_motifs_waterfall WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:23:49.983 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_motifs_waterfall INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:23:49.983 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_motifs_waterfall INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:23:50.009 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_meth_allele INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:23:50.010 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_meth_allele INFO input :: name: "waterfall", value: false
2025-09-15 20:23:50.010 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_meth_allele INFO input :: name: "methylation", value: true
2025-09-15 20:23:50.010 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_meth_allele INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:23:50.010 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_meth_allele INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:23:50.010 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_meth_allele INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:23:50.010 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_meth_allele INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2120.trgt.sorted.spanning.bam.bai"
2025-09-15 20:23:50.010 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_meth_allele INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2120.trgt.sorted.spanning.bam"
2025-09-15 20:23:50.010 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_meth_allele INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2120.trgt.vcf"
2025-09-15 20:23:50.010 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_meth_allele INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2120"
2025-09-15 20:23:50.060 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_meth_allele INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:23:50.061 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_meth_allele INFO eval :: name: "plot_type", value: "allele"
2025-09-15 20:23:50.061 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_meth_allele INFO eval :: name: "show", value: "meth"
2025-09-15 20:23:50.061 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_meth_allele INFO eval :: name: "threads", value: 1
2025-09-15 20:23:50.061 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_meth_allele INFO eval :: name: "disk_size", value: 27
2025-09-15 20:23:50.061 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_meth_allele INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2120.meth_allele"
2025-09-15 20:23:50.062 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_meth_allele INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:23:50.062 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_meth_allele WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:23:50.063 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_meth_allele INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:23:50.063 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_meth_allele INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:23:50.072 wdl.w:ptcp.w:call-trgt-08.t:call-get_reads_overlapping_repeats NOTICE done
2025-09-15 20:23:50.080 wdl.w:ptcp.w:call-trgt-08 NOTICE finish :: job: "call-get_reads_overlapping_repeats"
2025-09-15 20:23:50.080 wdl.w:ptcp.w:call-trgt-08 INFO output :: job: "call-get_reads_overlapping_repeats", values: {"reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-08/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2105.repeats.bam.bai", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-08/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2105.repeats.bam"}
2025-09-15 20:23:50.080 wdl.w:ptcp.w:call-trgt-08 INFO visit :: node: "output-reads_overlapping_repeats", values: {"reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-08/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2105.repeats.bam"}
2025-09-15 20:23:50.080 wdl.w:ptcp.w:call-trgt-08 INFO visit :: node: "output-reads_overlapping_repeats_bai", values: {"reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-08/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2105.repeats.bam.bai"}
2025-09-15 20:23:50.088 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_meth_waterfall NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-23/call-trgt_plot_meth_waterfall", thread: 140609796937280
2025-09-15 20:23:50.097 wdl.w:ptcp.w:call-trgt-00.t:call-get_reads_overlapping_repeats NOTICE done
2025-09-15 20:23:50.101 wdl.w:ptcp.w:call-trgt-00 NOTICE finish :: job: "call-get_reads_overlapping_repeats"
2025-09-15 20:23:50.102 wdl.w:ptcp.w:call-trgt-00 INFO output :: job: "call-get_reads_overlapping_repeats", values: {"reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-00/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2097.repeats.bam.bai", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-00/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2097.repeats.bam"}
2025-09-15 20:23:50.102 wdl.w:ptcp.w:call-trgt-00 INFO visit :: node: "output-reads_overlapping_repeats", values: {"reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-00/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2097.repeats.bam"}
2025-09-15 20:23:50.103 wdl.w:ptcp.w:call-trgt-00 INFO visit :: node: "output-reads_overlapping_repeats_bai", values: {"reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-00/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2097.repeats.bam.bai"}
2025-09-15 20:23:50.109 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_motifs_allele NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-23/call-trgt_plot_motifs_allele", thread: 140608739980864
2025-09-15 20:23:50.113 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_meth_waterfall INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:23:50.113 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_meth_waterfall INFO input :: name: "waterfall", value: true
2025-09-15 20:23:50.113 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_meth_waterfall INFO input :: name: "methylation", value: true
2025-09-15 20:23:50.113 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_meth_waterfall INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:23:50.113 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_meth_waterfall INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:23:50.113 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_meth_waterfall INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:23:50.113 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_meth_waterfall INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2120.trgt.sorted.spanning.bam.bai"
2025-09-15 20:23:50.113 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_meth_waterfall INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2120.trgt.sorted.spanning.bam"
2025-09-15 20:23:50.113 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_meth_waterfall INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2120.trgt.vcf"
2025-09-15 20:23:50.113 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_meth_waterfall INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2120"
2025-09-15 20:23:50.113 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_meth_waterfall INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:23:50.114 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_meth_waterfall INFO eval :: name: "plot_type", value: "waterfall"
2025-09-15 20:23:50.114 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_meth_waterfall INFO eval :: name: "show", value: "meth"
2025-09-15 20:23:50.114 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_meth_waterfall INFO eval :: name: "threads", value: 1
2025-09-15 20:23:50.114 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_meth_waterfall INFO eval :: name: "disk_size", value: 27
2025-09-15 20:23:50.114 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_meth_waterfall INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2120.meth_waterfall"
2025-09-15 20:23:50.114 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_meth_waterfall INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:23:50.115 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_meth_waterfall WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:23:50.115 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_meth_waterfall INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:23:50.115 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_meth_waterfall INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:23:50.132 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_motifs_waterfall INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-34/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_o6zs9e7w"
2025-09-15 20:23:50.132 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_motifs_waterfall INFO Slurm invocation: srun --job-name call-trgt_plot_motifs_waterfall --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-34/call-trgt_plot_motifs_waterfall/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-34/call-trgt_plot_motifs_waterfall/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-34/call-trgt_plot_motifs_waterfall/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-34/call-trgt_plot_motifs_waterfall/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-34/call-trgt_genotype/out/m84036_250809_035451_s4.bc2131.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2131.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-34/call-trgt_genotype/out/m84036_250809_035451_s4.bc2131.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2131.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-34/call-trgt_genotype/out/m84036_250809_035451_s4.bc2131.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2131.trgt.sorted.spanning.bam.bai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-34/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_o6zs9e7w/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-34/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_o6zs9e7w/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:23:50.135 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_motifs_allele INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:23:50.135 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_motifs_allele INFO input :: name: "waterfall", value: false
2025-09-15 20:23:50.135 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_motifs_allele INFO input :: name: "methylation", value: false
2025-09-15 20:23:50.135 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_motifs_allele INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:23:50.136 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_motifs_allele INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:23:50.136 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_motifs_allele INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:23:50.136 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_motifs_allele INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2120.trgt.sorted.spanning.bam.bai"
2025-09-15 20:23:50.136 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_motifs_allele INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2120.trgt.sorted.spanning.bam"
2025-09-15 20:23:50.136 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_motifs_allele INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2120.trgt.vcf"
2025-09-15 20:23:50.136 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_motifs_allele INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2120"
2025-09-15 20:23:50.136 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_motifs_allele INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:23:50.136 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_motifs_allele INFO eval :: name: "plot_type", value: "allele"
2025-09-15 20:23:50.136 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_motifs_allele INFO eval :: name: "show", value: "motifs"
2025-09-15 20:23:50.136 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_motifs_allele INFO eval :: name: "threads", value: 1
2025-09-15 20:23:50.137 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_motifs_allele INFO eval :: name: "disk_size", value: 27
2025-09-15 20:23:50.137 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_motifs_allele INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2120.motifs_allele"
2025-09-15 20:23:50.137 wdl.w:ptcp.w:call-trgt-22 NOTICE done
2025-09-15 20:23:50.137 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_motifs_allele INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:23:50.138 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_motifs_allele WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:23:50.139 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_motifs_allele INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:23:50.139 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_motifs_allele INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:23:50.141 wdl.w:ptcp NOTICE finish :: job: "call-trgt-22"
2025-09-15 20:23:50.142 wdl.w:ptcp INFO output :: job: "call-trgt-22", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-22/out/m84036_250809_035451_s4.bc2119.motifs_waterfall.trgt_plots.zip", "images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-22/out/m84036_250809_035451_s4.bc2119.meth_allele.trgt_plots.zip", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-22/out/m84036_250809_035451_s4.bc2119.trgt.sorted.spanning.bam.bai", "images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-22/out/m84036_250809_035451_s4.bc2119.motifs_allele.trgt_plots.zip", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-22/out/m84036_250809_035451_s4.bc2119.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-22/out/m84036_250809_035451_s4.bc2119.trgt.vcf", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-22/out/m84036_250809_035451_s4.bc2119.repeats.bam", "images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-22/out/m84036_250809_035451_s4.bc2119.meth_waterfall.trgt_plots.zip", "reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-22/out/m84036_250809_035451_s4.bc2119.repeats.bam.bai"}
2025-09-15 20:23:50.148 wdl.w:ptcp.w:call-trgt-44 NOTICE workflow start :: name: "trgt", source: "./trgt.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-44"
2025-09-15 20:23:50.148 wdl.w:ptcp.w:call-paraphase-11.t:call-run_paraphase.stderr VERBOSE INFO:root:Processing sample m84036_250809_035451_s4.bc2108 at 2025-09-15 20:23:35.413080...
2025-09-15 20:23:50.149 wdl.w:ptcp.w:call-paraphase-11.t:call-run_paraphase.stderr VERBOSE INFO:root:Checking sample sex at 2025-09-15 20:23:35.413955...
2025-09-15 20:23:50.149 wdl.w:ptcp.w:call-paraphase-11.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for cyp21 for sample m84036_250809_035451_s4.bc2108 at 2025-09-15 20:23:35.454158...
2025-09-15 20:23:50.149 wdl.w:ptcp.w:call-paraphase-11.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for cyp21 for sample m84036_250809_035451_s4.bc2108 at 2025-09-15 20:23:35.454846...
2025-09-15 20:23:50.149 wdl.w:ptcp.w:call-paraphase-11.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for smn1 for sample m84036_250809_035451_s4.bc2108 at 2025-09-15 20:23:35.454340...
2025-09-15 20:23:50.149 wdl.w:ptcp.w:call-paraphase-11.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for smn1 for sample m84036_250809_035451_s4.bc2108 at 2025-09-15 20:23:35.454944...
2025-09-15 20:23:50.149 wdl.w:ptcp.w:call-paraphase-11.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for gba for sample m84036_250809_035451_s4.bc2108 at 2025-09-15 20:23:35.454438...
2025-09-15 20:23:50.149 wdl.w:ptcp.w:call-paraphase-11.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for hba for sample m84036_250809_035451_s4.bc2108 at 2025-09-15 20:23:35.454461...
2025-09-15 20:23:50.149 wdl.w:ptcp.w:call-paraphase-11.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for hba for sample m84036_250809_035451_s4.bc2108 at 2025-09-15 20:23:35.455062...
2025-09-15 20:23:50.149 wdl.w:ptcp.w:call-paraphase-11.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for gba for sample m84036_250809_035451_s4.bc2108 at 2025-09-15 20:23:35.455060...
2025-09-15 20:23:50.163 wdl.w:ptcp.w:call-trgt-44 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:23:50.163 wdl.w:ptcp.w:call-trgt-44 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-44/out/m84036_250809_035451_s4.bc2141.mapped.bam"}
2025-09-15 20:23:50.163 wdl.w:ptcp.w:call-trgt-44 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-44/out/m84036_250809_035451_s4.bc2141.mapped.bam.bai"}
2025-09-15 20:23:50.163 wdl.w:ptcp.w:call-trgt-44 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:23:50.164 wdl.w:ptcp.w:call-trgt-44 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:23:50.164 wdl.w:ptcp.w:call-trgt-44 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2141"}
2025-09-15 20:23:50.164 wdl.w:ptcp.w:call-trgt-44 INFO visit :: node: "decl-sex", values: {"sex": "F"}
2025-09-15 20:23:50.164 wdl.w:ptcp.w:call-trgt-44 INFO visit :: node: "decl-trgt_bed", values: {"trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"}
2025-09-15 20:23:50.164 wdl.w:ptcp.w:call-trgt-44 NOTICE ready :: job: "call-get_reads_overlapping_repeats", callee: "get_reads_overlapping_repeats"
2025-09-15 20:23:50.164 wdl.w:ptcp.w:call-trgt-44 INFO input :: job: "call-get_reads_overlapping_repeats", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-44/out/m84036_250809_035451_s4.bc2141.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-44/out/m84036_250809_035451_s4.bc2141.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2141"}
2025-09-15 20:23:50.165 wdl.w:ptcp.w:call-trgt-44 NOTICE ready :: job: "call-trgt_genotype", callee: "trgt_genotype"
2025-09-15 20:23:50.165 wdl.w:ptcp.w:call-trgt-44 INFO input :: job: "call-trgt_genotype", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-44/out/m84036_250809_035451_s4.bc2141.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-44/out/m84036_250809_035451_s4.bc2141.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2141"}
2025-09-15 20:23:50.173 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_meth_allele INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-23/call-trgt_plot_meth_allele/_singularity_tmpdir_xrw9w67t"
2025-09-15 20:23:50.174 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_meth_allele INFO Slurm invocation: srun --job-name call-trgt_plot_meth_allele --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-23/call-trgt_plot_meth_allele/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-23/call-trgt_plot_meth_allele/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-23/call-trgt_plot_meth_allele/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-23/call-trgt_plot_meth_allele/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-23/call-trgt_genotype/out/m84036_250809_035451_s4.bc2120.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2120.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-23/call-trgt_genotype/out/m84036_250809_035451_s4.bc2120.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2120.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-23/call-trgt_genotype/out/m84036_250809_035451_s4.bc2120.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2120.trgt.sorted.spanning.bam.bai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-23/call-trgt_plot_meth_allele/_singularity_tmpdir_xrw9w67t/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-23/call-trgt_plot_meth_allele/_singularity_tmpdir_xrw9w67t/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:23:50.174 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_motifs_waterfall NOTICE slurm_singularity run :: pid: 1200290, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-34/call-trgt_plot_motifs_waterfall/slurm_singularity.log.txt"
2025-09-15 20:23:50.186 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_meth_allele NOTICE slurm_singularity run :: pid: 1200291, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-23/call-trgt_plot_meth_allele/slurm_singularity.log.txt"
2025-09-15 20:23:50.205 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_meth_waterfall INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-23/call-trgt_plot_meth_waterfall/_singularity_tmpdir_dgpklqxt"
2025-09-15 20:23:50.206 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_meth_waterfall INFO Slurm invocation: srun --job-name call-trgt_plot_meth_waterfall --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-23/call-trgt_plot_meth_waterfall/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-23/call-trgt_plot_meth_waterfall/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-23/call-trgt_plot_meth_waterfall/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-23/call-trgt_plot_meth_waterfall/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-23/call-trgt_genotype/out/m84036_250809_035451_s4.bc2120.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2120.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-23/call-trgt_genotype/out/m84036_250809_035451_s4.bc2120.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2120.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-23/call-trgt_genotype/out/m84036_250809_035451_s4.bc2120.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2120.trgt.sorted.spanning.bam.bai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-23/call-trgt_plot_meth_waterfall/_singularity_tmpdir_dgpklqxt/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-23/call-trgt_plot_meth_waterfall/_singularity_tmpdir_dgpklqxt/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:23:50.217 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_meth_waterfall NOTICE slurm_singularity run :: pid: 1200294, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-23/call-trgt_plot_meth_waterfall/slurm_singularity.log.txt"
2025-09-15 20:23:50.222 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_motifs_allele INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-23/call-trgt_plot_motifs_allele/_singularity_tmpdir_l1jglsj_"
2025-09-15 20:23:50.222 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_motifs_allele INFO Slurm invocation: srun --job-name call-trgt_plot_motifs_allele --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-23/call-trgt_plot_motifs_allele/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-23/call-trgt_plot_motifs_allele/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-23/call-trgt_plot_motifs_allele/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-23/call-trgt_plot_motifs_allele/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-23/call-trgt_genotype/out/m84036_250809_035451_s4.bc2120.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2120.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-23/call-trgt_genotype/out/m84036_250809_035451_s4.bc2120.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2120.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-23/call-trgt_genotype/out/m84036_250809_035451_s4.bc2120.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2120.trgt.sorted.spanning.bam.bai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-23/call-trgt_plot_motifs_allele/_singularity_tmpdir_l1jglsj_/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-23/call-trgt_plot_motifs_allele/_singularity_tmpdir_l1jglsj_/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:23:50.229 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_motifs_allele NOTICE slurm_singularity run :: pid: 1200296, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-23/call-trgt_plot_motifs_allele/slurm_singularity.log.txt"
2025-09-15 20:23:50.266 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:50 [ERROR] - No reads found for TRID=SCA37_DAB1
2025-09-15 20:23:50.266 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:50 [ERROR] - No reads found for TRID=DRPLA_ATN1
2025-09-15 20:23:50.266 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:50 [ERROR] - No reads found for TRID=NIID_NOTCH2NLC
2025-09-15 20:23:50.266 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:50 [ERROR] - No reads found for TRID=OPDM4_RILPL1
2025-09-15 20:23:50.278 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO srun: job 51797481 queued and waiting for resources
2025-09-15 20:23:50.278 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO srun: job 51797481 has been allocated resources
2025-09-15 20:23:50.278 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:50.305 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_plot_motifs_waterfall INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2112.motifs_waterfall.trgt_plots.zip"
2025-09-15 20:23:50.380 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_plot_motifs_waterfall NOTICE done
2025-09-15 20:23:50.383 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:47 [ERROR] - No reads found for TRID=OPDM_ABCD3
2025-09-15 20:23:50.383 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:47 [ERROR] - No reads found for TRID=SCA37_DAB1
2025-09-15 20:23:50.384 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:47 [ERROR] - No reads found for TRID=DRPLA_ATN1
2025-09-15 20:23:50.384 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:47 [ERROR] - No reads found for TRID=SCA2_ATXN2
2025-09-15 20:23:50.384 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:47 [ERROR] - No reads found for TRID=OPDM4_RILPL1
2025-09-15 20:23:50.384 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:47 [ERROR] - No reads found for TRID=SCA8_ATXN8OS
2025-09-15 20:23:50.384 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:47 [ERROR] - No reads found for TRID=OPMD_PABPN1
2025-09-15 20:23:50.384 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:47 [ERROR] - No reads found for TRID=SCA3_ATXN3
2025-09-15 20:23:50.384 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:47 [ERROR] - No reads found for TRID=SCA31_BEAN1
2025-09-15 20:23:50.384 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:47 [ERROR] - No reads found for TRID=SCA27B_FGF14
2025-09-15 20:23:50.384 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:47 [ERROR] - No reads found for TRID=HDL2_JPH3
2025-09-15 20:23:50.384 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:48 [ERROR] - No reads found for TRID=SCA6_CACNA1A
2025-09-15 20:23:50.384 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:48 [ERROR] - No reads found for TRID=DM1_DMPK
2025-09-15 20:23:50.384 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:48 [ERROR] - No reads found for TRID=OPDM2_GIPC1
2025-09-15 20:23:50.384 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:48 [ERROR] - No reads found for TRID=SCA4_ZFHX3
2025-09-15 20:23:50.384 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:48 [ERROR] - No reads found for TRID=SD5_HOXD13
2025-09-15 20:23:50.384 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:48 [ERROR] - No reads found for TRID=SCA36_NOP56
2025-09-15 20:23:50.384 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:48 [ERROR] - No reads found for TRID=CJD_PRNP
2025-09-15 20:23:50.384 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:48 [ERROR] - No reads found for TRID=EPM1_CSTB
2025-09-15 20:23:50.384 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:48 [ERROR] - No reads found for TRID=SCA10_ATXN10
2025-09-15 20:23:50.384 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:48 [ERROR] - No reads found for TRID=SCA7_ATXN7
2025-09-15 20:23:50.385 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:48 [ERROR] - No reads found for TRID=FRA2A_AFF3
2025-09-15 20:23:50.385 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:48 [ERROR] - No reads found for TRID=HD_HTT
2025-09-15 20:23:50.385 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:48 [ERROR] - No reads found for TRID=SCA1_ATXN1
2025-09-15 20:23:50.385 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:49 [ERROR] - No reads found for TRID=SCA12_PPP2R2B
2025-09-15 20:23:50.385 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:49 [ERROR] - No reads found for TRID=OPDM1_LRP12
2025-09-15 20:23:50.385 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:49 [ERROR] - No reads found for TRID=FTDALS1_C9orf72
2025-09-15 20:23:50.385 wdl.w:ptcp.w:call-trgt-15 NOTICE finish :: job: "call-trgt_plot_motifs_waterfall"
2025-09-15 20:23:50.385 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:49 [ERROR] - No reads found for TRID=CCHS_PHOX2B
2025-09-15 20:23:50.385 wdl.w:ptcp.w:call-trgt-15 INFO output :: job: "call-trgt_plot_motifs_waterfall", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-15/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2112.motifs_waterfall.trgt_plots.zip"}
2025-09-15 20:23:50.385 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:49 [ERROR] - No reads found for TRID=FAME1_SAMD12
2025-09-15 20:23:50.386 wdl.w:ptcp.w:call-trgt-15 INFO visit :: node: "output-images_motifs_waterfall", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-15/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2112.motifs_waterfall.trgt_plots.zip"}
2025-09-15 20:23:50.392 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_motifs_waterfall NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-23/call-trgt_plot_motifs_waterfall", thread: 140609838900800
2025-09-15 20:23:50.392 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:47 [ERROR] - No reads found for TRID=OPDM_ABCD3
2025-09-15 20:23:50.393 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:47 [ERROR] - No reads found for TRID=SCA37_DAB1
2025-09-15 20:23:50.393 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:47 [ERROR] - No reads found for TRID=DRPLA_ATN1
2025-09-15 20:23:50.393 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:47 [ERROR] - No reads found for TRID=SCA2_ATXN2
2025-09-15 20:23:50.393 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:47 [ERROR] - No reads found for TRID=OPDM4_RILPL1
2025-09-15 20:23:50.393 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:47 [ERROR] - No reads found for TRID=SCA8_ATXN8OS
2025-09-15 20:23:50.393 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:47 [ERROR] - No reads found for TRID=OPMD_PABPN1
2025-09-15 20:23:50.393 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:47 [ERROR] - No reads found for TRID=SCA3_ATXN3
2025-09-15 20:23:50.393 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:47 [ERROR] - No reads found for TRID=SCA31_BEAN1
2025-09-15 20:23:50.393 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:47 [ERROR] - No reads found for TRID=SCA27B_FGF14
2025-09-15 20:23:50.393 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:47 [ERROR] - No reads found for TRID=HDL2_JPH3
2025-09-15 20:23:50.393 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:48 [ERROR] - No reads found for TRID=SCA6_CACNA1A
2025-09-15 20:23:50.393 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:48 [ERROR] - No reads found for TRID=DM1_DMPK
2025-09-15 20:23:50.394 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:48 [ERROR] - No reads found for TRID=OPDM2_GIPC1
2025-09-15 20:23:50.394 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:48 [ERROR] - No reads found for TRID=SCA4_ZFHX3
2025-09-15 20:23:50.394 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:48 [ERROR] - No reads found for TRID=SD5_HOXD13
2025-09-15 20:23:50.394 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:48 [ERROR] - No reads found for TRID=SCA36_NOP56
2025-09-15 20:23:50.394 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:48 [ERROR] - No reads found for TRID=CJD_PRNP
2025-09-15 20:23:50.394 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:48 [ERROR] - No reads found for TRID=EPM1_CSTB
2025-09-15 20:23:50.394 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:48 [ERROR] - No reads found for TRID=SCA10_ATXN10
2025-09-15 20:23:50.394 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:48 [ERROR] - No reads found for TRID=SCA7_ATXN7
2025-09-15 20:23:50.394 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:48 [ERROR] - No reads found for TRID=FRA2A_AFF3
2025-09-15 20:23:50.394 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:48 [ERROR] - No reads found for TRID=HD_HTT
2025-09-15 20:23:50.394 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:48 [ERROR] - No reads found for TRID=SCA1_ATXN1
2025-09-15 20:23:50.394 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:48 [ERROR] - No reads found for TRID=SCA12_PPP2R2B
2025-09-15 20:23:50.394 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:49 [ERROR] - No reads found for TRID=OPDM1_LRP12
2025-09-15 20:23:50.394 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:49 [ERROR] - No reads found for TRID=FTDALS1_C9orf72
2025-09-15 20:23:50.394 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:49 [ERROR] - No reads found for TRID=CCHS_PHOX2B
2025-09-15 20:23:50.394 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:49 [ERROR] - No reads found for TRID=FAME1_SAMD12
2025-09-15 20:23:50.412 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_motifs_waterfall INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:23:50.412 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_motifs_waterfall INFO input :: name: "waterfall", value: true
2025-09-15 20:23:50.412 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_motifs_waterfall INFO input :: name: "methylation", value: false
2025-09-15 20:23:50.412 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_motifs_waterfall INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:23:50.412 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_motifs_waterfall INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:23:50.412 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_motifs_waterfall INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:23:50.413 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_motifs_waterfall INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2120.trgt.sorted.spanning.bam.bai"
2025-09-15 20:23:50.413 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_motifs_waterfall INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2120.trgt.sorted.spanning.bam"
2025-09-15 20:23:50.413 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_motifs_waterfall INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2120.trgt.vcf"
2025-09-15 20:23:50.413 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_motifs_waterfall INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2120"
2025-09-15 20:23:50.413 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:23:50.413 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "plot_type", value: "waterfall"
2025-09-15 20:23:50.413 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "show", value: "motifs"
2025-09-15 20:23:50.413 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "threads", value: 1
2025-09-15 20:23:50.413 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "disk_size", value: 27
2025-09-15 20:23:50.414 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2120.motifs_waterfall"
2025-09-15 20:23:50.414 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_motifs_waterfall INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:23:50.414 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_motifs_waterfall WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:23:50.414 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_motifs_waterfall INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:23:50.414 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_motifs_waterfall INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:23:50.485 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_motifs_waterfall INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-23/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_yh3lp4ae"
2025-09-15 20:23:50.485 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_motifs_waterfall INFO Slurm invocation: srun --job-name call-trgt_plot_motifs_waterfall --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-23/call-trgt_plot_motifs_waterfall/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-23/call-trgt_plot_motifs_waterfall/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-23/call-trgt_plot_motifs_waterfall/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-23/call-trgt_plot_motifs_waterfall/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-23/call-trgt_genotype/out/m84036_250809_035451_s4.bc2120.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2120.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-23/call-trgt_genotype/out/m84036_250809_035451_s4.bc2120.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2120.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-23/call-trgt_genotype/out/m84036_250809_035451_s4.bc2120.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2120.trgt.sorted.spanning.bam.bai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-23/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_yh3lp4ae/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-23/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_yh3lp4ae/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:23:50.505 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_motifs_waterfall NOTICE slurm_singularity run :: pid: 1200315, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-23/call-trgt_plot_motifs_waterfall/slurm_singularity.log.txt"
2025-09-15 20:23:50.612 wdl.w:ptcp.w:call-paraphase-01.t:call-run_paraphase INFO output :: name: "paraphase_bam", value: "m84036_250809_035451_s4.bc2098_paraphase/m84036_250809_035451_s4.bc2098.paraphase.bam"
2025-09-15 20:23:50.619 wdl.w:ptcp.w:call-paraphase-01.t:call-run_paraphase INFO output :: name: "paraphase_bam_bai", value: "m84036_250809_035451_s4.bc2098_paraphase/m84036_250809_035451_s4.bc2098.paraphase.bam.bai"
2025-09-15 20:23:50.620 wdl.w:ptcp.w:call-paraphase-01.t:call-run_paraphase INFO output :: name: "paraphase_json", value: "m84036_250809_035451_s4.bc2098_paraphase/m84036_250809_035451_s4.bc2098.paraphase.json"
2025-09-15 20:23:50.621 wdl.w:ptcp.w:call-paraphase-01.t:call-run_paraphase INFO output :: name: "paraphase_vcfs", value: []
2025-09-15 20:23:50.622 wdl.w:ptcp.w:call-paraphase-01.t:call-run_paraphase INFO output :: name: "havanno_json", value: "m84036_250809_035451_s4.bc2098.havanno.json"
2025-09-15 20:23:50.661 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:23:47 [ERROR] - No reads found for TRID=OPDM4_RILPL1
2025-09-15 20:23:50.661 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:23:47 [ERROR] - No reads found for TRID=SCA4_ZFHX3
2025-09-15 20:23:50.662 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:23:47 [ERROR] - No reads found for TRID=HDL2_JPH3
2025-09-15 20:23:50.662 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:23:47 [ERROR] - No reads found for TRID=SCA31_BEAN1
2025-09-15 20:23:50.662 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:23:47 [ERROR] - No reads found for TRID=SCA27B_FGF14
2025-09-15 20:23:50.662 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:23:47 [ERROR] - No reads found for TRID=OPDM2_GIPC1
2025-09-15 20:23:50.662 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:23:47 [ERROR] - No reads found for TRID=FRA2A_AFF3
2025-09-15 20:23:50.662 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:23:48 [ERROR] - No reads found for TRID=SD5_HOXD13
2025-09-15 20:23:50.662 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:23:48 [ERROR] - No reads found for TRID=DM1_DMPK
2025-09-15 20:23:50.662 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:23:48 [ERROR] - No reads found for TRID=SCA36_NOP56
2025-09-15 20:23:50.662 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:23:48 [ERROR] - No reads found for TRID=CJD_PRNP
2025-09-15 20:23:50.662 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:23:48 [ERROR] - No reads found for TRID=EPM1_CSTB
2025-09-15 20:23:50.662 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:23:48 [ERROR] - No reads found for TRID=SCA10_ATXN10
2025-09-15 20:23:50.662 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:23:48 [ERROR] - No reads found for TRID=SCA7_ATXN7
2025-09-15 20:23:50.662 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:23:48 [ERROR] - No reads found for TRID=SCA3_ATXN3
2025-09-15 20:23:50.662 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:23:48 [ERROR] - No reads found for TRID=FECD3_TCF4
2025-09-15 20:23:50.662 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:23:48 [ERROR] - No reads found for TRID=SCA6_CACNA1A
2025-09-15 20:23:50.662 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:23:48 [ERROR] - No reads found for TRID=CCHS_PHOX2B
2025-09-15 20:23:50.662 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:23:48 [ERROR] - No reads found for TRID=SCA1_ATXN1
2025-09-15 20:23:50.662 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:23:49 [ERROR] - No reads found for TRID=OPDM1_LRP12
2025-09-15 20:23:50.662 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:23:49 [ERROR] - No reads found for TRID=FAME1_SAMD12
2025-09-15 20:23:50.662 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:23:49 [ERROR] - No reads found for TRID=FTDALS1_C9orf72
2025-09-15 20:23:50.707 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_meth_allele INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2128.meth_allele.trgt_plots.zip"
2025-09-15 20:23:50.709 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:50 [ERROR] - No reads found for TRID=SCA37_DAB1
2025-09-15 20:23:50.709 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:50 [ERROR] - No reads found for TRID=DRPLA_ATN1
2025-09-15 20:23:50.709 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:50 [ERROR] - No reads found for TRID=NIID_NOTCH2NLC
2025-09-15 20:23:50.709 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:50 [ERROR] - No reads found for TRID=OPDM4_RILPL1
2025-09-15 20:23:50.709 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:50 [ERROR] - No reads found for TRID=SCA27B_FGF14
2025-09-15 20:23:50.709 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:50 [ERROR] - No reads found for TRID=OPDM_ABCD3
2025-09-15 20:23:50.709 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:50 [ERROR] - No reads found for TRID=SCA31_BEAN1
2025-09-15 20:23:50.719 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_motifs_allele.slurm_singularity INFO srun: job 51797482 queued and waiting for resources
2025-09-15 20:23:50.719 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_motifs_allele.slurm_singularity INFO srun: job 51797482 has been allocated resources
2025-09-15 20:23:50.719 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_motifs_allele.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:50.743 wdl.w:ptcp.w:call-paraphase-01.t:call-run_paraphase NOTICE done
2025-09-15 20:23:50.750 wdl.w:ptcp.w:call-paraphase-01 NOTICE finish :: job: "call-run_paraphase"
2025-09-15 20:23:50.750 wdl.w:ptcp.w:call-paraphase-01 INFO output :: job: "call-run_paraphase", values: {"havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-01/call-run_paraphase/out/m84036_250809_035451_s4.bc2098.havanno.json", "paraphase_vcfs": [], "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-01/call-run_paraphase/out/m84036_250809_035451_s4.bc2098_paraphase/m84036_250809_035451_s4.bc2098.paraphase.json", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-01/call-run_paraphase/out/m84036_250809_035451_s4.bc2098_paraphase/m84036_250809_035451_s4.bc2098.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-01/call-run_paraphase/out/m84036_250809_035451_s4.bc2098_paraphase/m84036_250809_035451_s4.bc2098.paraphase.bam"}
2025-09-15 20:23:50.750 wdl.w:ptcp.w:call-paraphase-01 NOTICE ready :: job: "call-call_f8", callee: "call_f8"
2025-09-15 20:23:50.750 wdl.w:ptcp.w:call-paraphase-01 INFO input :: job: "call-call_f8", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "out_prefix": "m84036_250809_035451_s4.bc2098", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-01/call-run_paraphase/out/m84036_250809_035451_s4.bc2098_paraphase/m84036_250809_035451_s4.bc2098.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-01/call-run_paraphase/out/m84036_250809_035451_s4.bc2098_paraphase/m84036_250809_035451_s4.bc2098.paraphase.bam", "sex": "F"}
2025-09-15 20:23:50.752 wdl.w:ptcp.w:call-paraphase-01 INFO visit :: node: "output-havanno_json", values: {"havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-01/call-run_paraphase/out/m84036_250809_035451_s4.bc2098.havanno.json"}
2025-09-15 20:23:50.753 wdl.w:ptcp.w:call-paraphase-01 INFO visit :: node: "output-paraphase_bam", values: {"paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-01/call-run_paraphase/out/m84036_250809_035451_s4.bc2098_paraphase/m84036_250809_035451_s4.bc2098.paraphase.bam"}
2025-09-15 20:23:50.753 wdl.w:ptcp.w:call-paraphase-01 INFO visit :: node: "output-paraphase_bam_bai", values: {"paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-01/call-run_paraphase/out/m84036_250809_035451_s4.bc2098_paraphase/m84036_250809_035451_s4.bc2098.paraphase.bam.bai"}
2025-09-15 20:23:50.753 wdl.w:ptcp.w:call-paraphase-01 INFO visit :: node: "output-paraphase_json", values: {"paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-01/call-run_paraphase/out/m84036_250809_035451_s4.bc2098_paraphase/m84036_250809_035451_s4.bc2098.paraphase.json"}
2025-09-15 20:23:50.753 wdl.w:ptcp.w:call-paraphase-01 INFO visit :: node: "output-paraphase_vcfs", values: {"paraphase_vcfs": []}
2025-09-15 20:23:50.761 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_meth_allele NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-35/call-trgt_plot_meth_allele", thread: 140612506469952
2025-09-15 20:23:50.787 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_meth_allele INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:23:50.787 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_meth_allele INFO input :: name: "waterfall", value: false
2025-09-15 20:23:50.787 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_meth_allele INFO input :: name: "methylation", value: true
2025-09-15 20:23:50.787 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_meth_allele INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:23:50.787 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_meth_allele INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:23:50.787 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_meth_allele INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:23:50.787 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_meth_allele INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2132.trgt.sorted.spanning.bam.bai"
2025-09-15 20:23:50.787 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_meth_allele INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2132.trgt.sorted.spanning.bam"
2025-09-15 20:23:50.787 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_meth_allele INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2132.trgt.vcf"
2025-09-15 20:23:50.787 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_meth_allele INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2132"
2025-09-15 20:23:50.788 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_meth_allele INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:23:50.788 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_meth_allele INFO eval :: name: "plot_type", value: "allele"
2025-09-15 20:23:50.788 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_meth_allele INFO eval :: name: "show", value: "meth"
2025-09-15 20:23:50.788 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_meth_allele INFO eval :: name: "threads", value: 1
2025-09-15 20:23:50.788 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_meth_allele INFO eval :: name: "disk_size", value: 27
2025-09-15 20:23:50.788 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_meth_allele INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2132.meth_allele"
2025-09-15 20:23:50.789 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_meth_allele INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:23:50.789 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_meth_allele WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:23:50.789 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_meth_allele INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:23:50.789 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_meth_allele INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:23:50.814 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_meth_allele NOTICE done
2025-09-15 20:23:50.857 wdl.w:ptcp.w:call-trgt-31 NOTICE finish :: job: "call-trgt_plot_meth_allele"
2025-09-15 20:23:50.858 wdl.w:ptcp.w:call-trgt-31 INFO output :: job: "call-trgt_plot_meth_allele", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-31/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2128.meth_allele.trgt_plots.zip"}
2025-09-15 20:23:50.858 wdl.w:ptcp.w:call-trgt-31 INFO visit :: node: "output-images_meth_allele", values: {"images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-31/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2128.meth_allele.trgt_plots.zip"}
2025-09-15 20:23:50.869 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_meth_waterfall NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-35/call-trgt_plot_meth_waterfall", thread: 140609805329984
2025-09-15 20:23:50.875 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_meth_allele INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-35/call-trgt_plot_meth_allele/_singularity_tmpdir_771rph0g"
2025-09-15 20:23:50.875 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_meth_allele INFO Slurm invocation: srun --job-name call-trgt_plot_meth_allele --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-35/call-trgt_plot_meth_allele/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-35/call-trgt_plot_meth_allele/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-35/call-trgt_plot_meth_allele/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-35/call-trgt_plot_meth_allele/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-35/call-trgt_genotype/out/m84036_250809_035451_s4.bc2132.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2132.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-35/call-trgt_genotype/out/m84036_250809_035451_s4.bc2132.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2132.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-35/call-trgt_genotype/out/m84036_250809_035451_s4.bc2132.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2132.trgt.vcf:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-35/call-trgt_plot_meth_allele/_singularity_tmpdir_771rph0g/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-35/call-trgt_plot_meth_allele/_singularity_tmpdir_771rph0g/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:23:50.888 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_meth_waterfall INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:23:50.888 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_meth_waterfall INFO input :: name: "waterfall", value: true
2025-09-15 20:23:50.888 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_meth_waterfall INFO input :: name: "methylation", value: true
2025-09-15 20:23:50.888 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_meth_waterfall INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:23:50.888 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_meth_waterfall INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:23:50.888 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_meth_waterfall INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:23:50.890 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_meth_waterfall INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2132.trgt.sorted.spanning.bam.bai"
2025-09-15 20:23:50.890 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_meth_waterfall INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2132.trgt.sorted.spanning.bam"
2025-09-15 20:23:50.890 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_meth_waterfall INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2132.trgt.vcf"
2025-09-15 20:23:50.890 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_meth_waterfall INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2132"
2025-09-15 20:23:50.890 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_meth_waterfall INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:23:50.890 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_meth_waterfall INFO eval :: name: "plot_type", value: "waterfall"
2025-09-15 20:23:50.890 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_meth_waterfall INFO eval :: name: "show", value: "meth"
2025-09-15 20:23:50.891 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_meth_waterfall INFO eval :: name: "threads", value: 1
2025-09-15 20:23:50.891 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_meth_waterfall INFO eval :: name: "disk_size", value: 27
2025-09-15 20:23:50.892 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_meth_waterfall INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2132.meth_waterfall"
2025-09-15 20:23:50.892 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_meth_waterfall INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:23:50.892 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_meth_waterfall WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:23:50.892 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_meth_waterfall INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:23:50.893 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_meth_waterfall INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:23:50.894 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:47 [ERROR] - No reads found for TRID=NIID_NOTCH2NLC
2025-09-15 20:23:50.895 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:47 [ERROR] - No reads found for TRID=OPDM4_RILPL1
2025-09-15 20:23:50.895 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:48 [ERROR] - No reads found for TRID=SCA4_ZFHX3
2025-09-15 20:23:50.895 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:48 [ERROR] - No reads found for TRID=HDL2_JPH3
2025-09-15 20:23:50.895 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:48 [ERROR] - No reads found for TRID=SCA31_BEAN1
2025-09-15 20:23:50.895 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:48 [ERROR] - No reads found for TRID=SCA27B_FGF14
2025-09-15 20:23:50.895 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:48 [ERROR] - No reads found for TRID=OPDM2_GIPC1
2025-09-15 20:23:50.895 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:48 [ERROR] - No reads found for TRID=FRA2A_AFF3
2025-09-15 20:23:50.895 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:48 [ERROR] - No reads found for TRID=SD5_HOXD13
2025-09-15 20:23:50.896 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:48 [ERROR] - No reads found for TRID=DM1_DMPK
2025-09-15 20:23:50.896 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:48 [ERROR] - No reads found for TRID=SCA36_NOP56
2025-09-15 20:23:50.896 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:48 [ERROR] - No reads found for TRID=CJD_PRNP
2025-09-15 20:23:50.896 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:48 [ERROR] - No reads found for TRID=EPM1_CSTB
2025-09-15 20:23:50.896 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:48 [ERROR] - No reads found for TRID=SCA10_ATXN10
2025-09-15 20:23:50.896 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:48 [ERROR] - No reads found for TRID=SCA7_ATXN7
2025-09-15 20:23:50.896 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:48 [ERROR] - No reads found for TRID=SCA3_ATXN3
2025-09-15 20:23:50.896 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:48 [ERROR] - No reads found for TRID=FECD3_TCF4
2025-09-15 20:23:50.896 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:48 [ERROR] - No reads found for TRID=SCA6_CACNA1A
2025-09-15 20:23:50.896 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:48 [ERROR] - No reads found for TRID=CCHS_PHOX2B
2025-09-15 20:23:50.896 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:49 [ERROR] - No reads found for TRID=SCA1_ATXN1
2025-09-15 20:23:50.896 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:49 [ERROR] - No reads found for TRID=OPDM1_LRP12
2025-09-15 20:23:50.896 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:49 [ERROR] - No reads found for TRID=FAME1_SAMD12
2025-09-15 20:23:50.896 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:49 [ERROR] - No reads found for TRID=FTDALS1_C9orf72
2025-09-15 20:23:50.899 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_meth_allele NOTICE slurm_singularity run :: pid: 1200329, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-35/call-trgt_plot_meth_allele/slurm_singularity.log.txt"
2025-09-15 20:23:50.921 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:23:49 [ERROR] - No reads found for TRID=SCA31_BEAN1
2025-09-15 20:23:50.933 wdl.w:ptcp.w:call-paraphase-06.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for smn1 for sample m84036_250809_035451_s4.bc2103 at 2025-09-15 20:23:41.364106...
2025-09-15 20:23:50.934 wdl.w:ptcp.w:call-paraphase-06.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for hba for sample m84036_250809_035451_s4.bc2103 at 2025-09-15 20:23:41.664998...
2025-09-15 20:23:50.934 wdl.w:ptcp.w:call-paraphase-06.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for gba for sample m84036_250809_035451_s4.bc2103 at 2025-09-15 20:23:42.296388...
2025-09-15 20:23:50.934 wdl.w:ptcp.w:call-paraphase-06.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for cyp21 for sample m84036_250809_035451_s4.bc2103 at 2025-09-15 20:23:43.726855...
2025-09-15 20:23:50.934 wdl.w:ptcp.w:call-paraphase-06.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for smn1 for sample m84036_250809_035451_s4.bc2103 at 2025-09-15 20:23:49.309068...
2025-09-15 20:23:50.934 wdl.w:ptcp.w:call-paraphase-06.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning to gene2 region for smn1 for sample m84036_250809_035451_s4.bc2103 at 2025-09-15 20:23:49.759843...
2025-09-15 20:23:50.993 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_meth_waterfall INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-35/call-trgt_plot_meth_waterfall/_singularity_tmpdir_urpagwhz"
2025-09-15 20:23:50.993 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_meth_waterfall INFO Slurm invocation: srun --job-name call-trgt_plot_meth_waterfall --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-35/call-trgt_plot_meth_waterfall/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-35/call-trgt_plot_meth_waterfall/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-35/call-trgt_plot_meth_waterfall/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-35/call-trgt_plot_meth_waterfall/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-35/call-trgt_genotype/out/m84036_250809_035451_s4.bc2132.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2132.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-35/call-trgt_genotype/out/m84036_250809_035451_s4.bc2132.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2132.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-35/call-trgt_genotype/out/m84036_250809_035451_s4.bc2132.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2132.trgt.vcf:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-35/call-trgt_plot_meth_waterfall/_singularity_tmpdir_urpagwhz/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-35/call-trgt_plot_meth_waterfall/_singularity_tmpdir_urpagwhz/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:23:51.004 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_meth_waterfall INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2128.meth_waterfall.trgt_plots.zip"
2025-09-15 20:23:51.013 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_meth_waterfall NOTICE slurm_singularity run :: pid: 1200337, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-35/call-trgt_plot_meth_waterfall/slurm_singularity.log.txt"
2025-09-15 20:23:51.077 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_meth_waterfall NOTICE done
2025-09-15 20:23:51.084 wdl.w:ptcp.w:call-trgt-31 NOTICE finish :: job: "call-trgt_plot_meth_waterfall"
2025-09-15 20:23:51.084 wdl.w:ptcp.w:call-trgt-31 INFO output :: job: "call-trgt_plot_meth_waterfall", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-31/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2128.meth_waterfall.trgt_plots.zip"}
2025-09-15 20:23:51.084 wdl.w:ptcp.w:call-trgt-31 INFO visit :: node: "output-images_meth_waterfall", values: {"images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-31/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2128.meth_waterfall.trgt_plots.zip"}
2025-09-15 20:23:51.093 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_motifs_allele NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-35/call-trgt_plot_motifs_allele", thread: 140611407550016
2025-09-15 20:23:51.104 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:48 [ERROR] - No reads found for TRID=DRPLA_ATN1
2025-09-15 20:23:51.105 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:48 [ERROR] - No reads found for TRID=OPDM_ABCD3
2025-09-15 20:23:51.105 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:48 [ERROR] - No reads found for TRID=SCA37_DAB1
2025-09-15 20:23:51.105 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:48 [ERROR] - No reads found for TRID=NIID_NOTCH2NLC
2025-09-15 20:23:51.105 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:48 [ERROR] - No reads found for TRID=OPDM4_RILPL1
2025-09-15 20:23:51.105 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:48 [ERROR] - No reads found for TRID=SCA4_ZFHX3
2025-09-15 20:23:51.105 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:48 [ERROR] - No reads found for TRID=HDL2_JPH3
2025-09-15 20:23:51.105 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:48 [ERROR] - No reads found for TRID=SCA31_BEAN1
2025-09-15 20:23:51.105 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:48 [ERROR] - No reads found for TRID=SCA27B_FGF14
2025-09-15 20:23:51.105 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:48 [ERROR] - No reads found for TRID=OPDM2_GIPC1
2025-09-15 20:23:51.105 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:48 [ERROR] - No reads found for TRID=FRA2A_AFF3
2025-09-15 20:23:51.105 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:48 [ERROR] - No reads found for TRID=SD5_HOXD13
2025-09-15 20:23:51.105 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:49 [ERROR] - No reads found for TRID=DM1_DMPK
2025-09-15 20:23:51.105 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:49 [ERROR] - No reads found for TRID=SCA36_NOP56
2025-09-15 20:23:51.105 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:49 [ERROR] - No reads found for TRID=CJD_PRNP
2025-09-15 20:23:51.105 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:49 [ERROR] - No reads found for TRID=EPM1_CSTB
2025-09-15 20:23:51.106 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:49 [ERROR] - No reads found for TRID=SCA10_ATXN10
2025-09-15 20:23:51.106 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:49 [ERROR] - No reads found for TRID=SCA7_ATXN7
2025-09-15 20:23:51.106 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:49 [ERROR] - No reads found for TRID=SCA3_ATXN3
2025-09-15 20:23:51.106 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:49 [ERROR] - No reads found for TRID=FECD3_TCF4
2025-09-15 20:23:51.106 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:49 [ERROR] - No reads found for TRID=SCA6_CACNA1A
2025-09-15 20:23:51.106 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:49 [ERROR] - No reads found for TRID=CCHS_PHOX2B
2025-09-15 20:23:51.106 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:49 [ERROR] - No reads found for TRID=SCA1_ATXN1
2025-09-15 20:23:51.106 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:50 [ERROR] - No reads found for TRID=OPDM1_LRP12
2025-09-15 20:23:51.106 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:50 [ERROR] - No reads found for TRID=FAME1_SAMD12
2025-09-15 20:23:51.106 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:50 [ERROR] - No reads found for TRID=FTDALS1_C9orf72
2025-09-15 20:23:51.122 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_motifs_allele INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:23:51.122 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_motifs_allele INFO input :: name: "waterfall", value: false
2025-09-15 20:23:51.122 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_motifs_allele INFO input :: name: "methylation", value: false
2025-09-15 20:23:51.122 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_motifs_allele INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:23:51.122 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_motifs_allele INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:23:51.122 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_motifs_allele INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:23:51.122 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_motifs_allele INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2132.trgt.sorted.spanning.bam.bai"
2025-09-15 20:23:51.122 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_motifs_allele INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2132.trgt.sorted.spanning.bam"
2025-09-15 20:23:51.122 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_motifs_allele INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2132.trgt.vcf"
2025-09-15 20:23:51.122 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_motifs_allele INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2132"
2025-09-15 20:23:51.123 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_motifs_allele INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:23:51.123 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_motifs_allele INFO eval :: name: "plot_type", value: "allele"
2025-09-15 20:23:51.123 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_motifs_allele INFO eval :: name: "show", value: "motifs"
2025-09-15 20:23:51.123 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_motifs_allele INFO eval :: name: "threads", value: 1
2025-09-15 20:23:51.123 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_motifs_allele INFO eval :: name: "disk_size", value: 27
2025-09-15 20:23:51.123 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_motifs_allele INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2132.motifs_allele"
2025-09-15 20:23:51.124 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_motifs_allele INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:23:51.124 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_motifs_allele WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:23:51.124 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_motifs_allele INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:23:51.124 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_motifs_allele INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:23:51.162 wdl.w:ptcp.t:call-pbmm2_align_hifi-66 INFO output :: name: "mapped_bam", value: "m84036_250809_035451_s4.bc2163.mapped.bam"
2025-09-15 20:23:51.165 wdl.w:ptcp.t:call-pbmm2_align_hifi-66 INFO output :: name: "mapped_bam_bai", value: "m84036_250809_035451_s4.bc2163.mapped.bam.bai"
2025-09-15 20:23:51.166 wdl.w:ptcp.t:call-pbmm2_align_hifi-66 INFO output :: name: "mapped_bam_pbi", value: "m84036_250809_035451_s4.bc2163.mapped.bam.pbi"
2025-09-15 20:23:51.167 wdl.w:ptcp.t:call-pbmm2_align_hifi-66 INFO output :: name: "report", value: "mapping_stats.report.json"
2025-09-15 20:23:51.178 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:23:50 [ERROR] - No reads found for TRID=SCA37_DAB1
2025-09-15 20:23:51.178 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:23:51 [ERROR] - No reads found for TRID=DRPLA_ATN1
2025-09-15 20:23:51.178 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:23:51 [ERROR] - No reads found for TRID=NIID_NOTCH2NLC
2025-09-15 20:23:51.178 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:23:51 [ERROR] - No reads found for TRID=OPDM4_RILPL1
2025-09-15 20:23:51.178 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:23:51 [ERROR] - No reads found for TRID=SCA27B_FGF14
2025-09-15 20:23:51.189 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:23:50 [ERROR] - No reads found for TRID=SCA37_DAB1
2025-09-15 20:23:51.189 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:23:51 [ERROR] - No reads found for TRID=OPDM_ABCD3
2025-09-15 20:23:51.189 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:23:51 [ERROR] - No reads found for TRID=NIID_NOTCH2NLC
2025-09-15 20:23:51.189 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:23:51 [ERROR] - No reads found for TRID=SCA2_ATXN2
2025-09-15 20:23:51.189 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:23:51 [ERROR] - No reads found for TRID=SCA8_ATXN8OS
2025-09-15 20:23:51.190 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO srun: job 51797483 queued and waiting for resources
2025-09-15 20:23:51.191 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO srun: job 51797483 has been allocated resources
2025-09-15 20:23:51.191 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:51.194 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_plot_meth_allele INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2104.meth_allele.trgt_plots.zip"
2025-09-15 20:23:51.202 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_meth_allele.slurm_singularity INFO srun: job 51797484 queued and waiting for resources
2025-09-15 20:23:51.202 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_meth_allele.slurm_singularity INFO srun: job 51797484 has been allocated resources
2025-09-15 20:23:51.203 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_meth_allele.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:51.212 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_motifs_allele INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-35/call-trgt_plot_motifs_allele/_singularity_tmpdir_7yovo8bq"
2025-09-15 20:23:51.212 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_motifs_allele INFO Slurm invocation: srun --job-name call-trgt_plot_motifs_allele --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-35/call-trgt_plot_motifs_allele/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-35/call-trgt_plot_motifs_allele/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-35/call-trgt_plot_motifs_allele/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-35/call-trgt_plot_motifs_allele/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-35/call-trgt_genotype/out/m84036_250809_035451_s4.bc2132.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2132.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-35/call-trgt_genotype/out/m84036_250809_035451_s4.bc2132.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2132.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-35/call-trgt_genotype/out/m84036_250809_035451_s4.bc2132.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2132.trgt.vcf:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-35/call-trgt_plot_motifs_allele/_singularity_tmpdir_7yovo8bq/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-35/call-trgt_plot_motifs_allele/_singularity_tmpdir_7yovo8bq/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:23:51.221 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:50 [ERROR] - No reads found for TRID=SCA37_DAB1
2025-09-15 20:23:51.221 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:50 [ERROR] - No reads found for TRID=OPDM_ABCD3
2025-09-15 20:23:51.221 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:51 [ERROR] - No reads found for TRID=NIID_NOTCH2NLC
2025-09-15 20:23:51.221 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:51 [ERROR] - No reads found for TRID=SCA2_ATXN2
2025-09-15 20:23:51.221 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:51 [ERROR] - No reads found for TRID=SCA8_ATXN8OS
2025-09-15 20:23:51.221 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:51 [ERROR] - No reads found for TRID=SCA27B_FGF14
2025-09-15 20:23:51.231 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO srun: job 51797485 queued and waiting for resources
2025-09-15 20:23:51.231 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO srun: job 51797485 has been allocated resources
2025-09-15 20:23:51.231 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:51.240 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_motifs_allele NOTICE slurm_singularity run :: pid: 1200346, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-35/call-trgt_plot_motifs_allele/slurm_singularity.log.txt"
2025-09-15 20:23:51.241 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_motifs_allele.slurm_singularity INFO srun: job 51797486 queued and waiting for resources
2025-09-15 20:23:51.241 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_motifs_allele.slurm_singularity INFO srun: job 51797486 has been allocated resources
2025-09-15 20:23:51.241 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_motifs_allele.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:51.267 wdl.w:ptcp.t:call-pbmm2_align_hifi-66 NOTICE done
2025-09-15 20:23:51.273 wdl.w:ptcp NOTICE finish :: job: "call-pbmm2_align_hifi-66"
2025-09-15 20:23:51.273 wdl.w:ptcp INFO output :: job: "call-pbmm2_align_hifi-66", values: {"report": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-66/out/mapping_stats.report.json", "mapped_bam_pbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-66/out/m84036_250809_035451_s4.bc2163.mapped.bam.pbi", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-66/out/m84036_250809_035451_s4.bc2163.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-66/out/m84036_250809_035451_s4.bc2163.mapped.bam"}
2025-09-15 20:23:51.274 wdl.w:ptcp NOTICE ready :: job: "call-paraphase-66", callee: "paraphase"
2025-09-15 20:23:51.274 wdl.w:ptcp INFO input :: job: "call-paraphase-66", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf", "genome_version": "38", "config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-66/out/m84036_250809_035451_s4.bc2163.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-66/out/m84036_250809_035451_s4.bc2163.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2163"}
2025-09-15 20:23:51.276 wdl.w:ptcp NOTICE ready :: job: "call-sawfish-66", callee: "sawfish"
2025-09-15 20:23:51.276 wdl.w:ptcp INFO input :: job: "call-sawfish-66", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-66/out/m84036_250809_035451_s4.bc2163.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-66/out/m84036_250809_035451_s4.bc2163.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2163"}
2025-09-15 20:23:51.277 wdl.w:ptcp NOTICE ready :: job: "call-trgt-66", callee: "trgt"
2025-09-15 20:23:51.277 wdl.w:ptcp INFO input :: job: "call-trgt-66", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-66/out/m84036_250809_035451_s4.bc2163.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-66/out/m84036_250809_035451_s4.bc2163.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2163"}
2025-09-15 20:23:51.281 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_motifs_waterfall NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-35/call-trgt_plot_motifs_waterfall", thread: 140608765158976
2025-09-15 20:23:51.290 wdl.w:ptcp.w:call-paraphase-03.t:call-run_paraphase.stderr VERBOSE INFO:root:Processing sample m84036_250809_035451_s4.bc2100 at 2025-09-15 20:23:47.722604...
2025-09-15 20:23:51.291 wdl.w:ptcp.w:call-paraphase-03.t:call-run_paraphase.stderr VERBOSE INFO:root:Checking sample sex at 2025-09-15 20:23:47.723666...
2025-09-15 20:23:51.291 wdl.w:ptcp.w:call-paraphase-03.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for cyp21 for sample m84036_250809_035451_s4.bc2100 at 2025-09-15 20:23:47.780135...
2025-09-15 20:23:51.291 wdl.w:ptcp.w:call-paraphase-03.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for cyp21 for sample m84036_250809_035451_s4.bc2100 at 2025-09-15 20:23:47.780604...
2025-09-15 20:23:51.292 wdl.w:ptcp.w:call-paraphase-03.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for smn1 for sample m84036_250809_035451_s4.bc2100 at 2025-09-15 20:23:47.780259...
2025-09-15 20:23:51.292 wdl.w:ptcp.w:call-paraphase-03.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for smn1 for sample m84036_250809_035451_s4.bc2100 at 2025-09-15 20:23:47.780674...
2025-09-15 20:23:51.292 wdl.w:ptcp.w:call-paraphase-03.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for gba for sample m84036_250809_035451_s4.bc2100 at 2025-09-15 20:23:47.780333...
2025-09-15 20:23:51.292 wdl.w:ptcp.w:call-paraphase-03.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for gba for sample m84036_250809_035451_s4.bc2100 at 2025-09-15 20:23:47.780740...
2025-09-15 20:23:51.292 wdl.w:ptcp.w:call-paraphase-03.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for hba for sample m84036_250809_035451_s4.bc2100 at 2025-09-15 20:23:47.780387...
2025-09-15 20:23:51.292 wdl.w:ptcp.w:call-paraphase-03.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for hba for sample m84036_250809_035451_s4.bc2100 at 2025-09-15 20:23:47.780809...
2025-09-15 20:23:51.292 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_plot_meth_allele NOTICE done
2025-09-15 20:23:51.299 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_motifs_waterfall INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:23:51.300 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_motifs_waterfall INFO input :: name: "waterfall", value: true
2025-09-15 20:23:51.299 wdl.w:ptcp.w:call-trgt-07 NOTICE finish :: job: "call-trgt_plot_meth_allele"
2025-09-15 20:23:51.300 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_motifs_waterfall INFO input :: name: "methylation", value: false
2025-09-15 20:23:51.300 wdl.w:ptcp.w:call-trgt-07 INFO output :: job: "call-trgt_plot_meth_allele", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-07/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2104.meth_allele.trgt_plots.zip"}
2025-09-15 20:23:51.300 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_motifs_waterfall INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:23:51.300 wdl.w:ptcp.w:call-trgt-07 INFO visit :: node: "output-images_meth_allele", values: {"images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-07/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2104.meth_allele.trgt_plots.zip"}
2025-09-15 20:23:51.301 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_motifs_waterfall INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:23:51.301 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_motifs_waterfall INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:23:51.301 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_motifs_waterfall INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2132.trgt.sorted.spanning.bam.bai"
2025-09-15 20:23:51.301 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_motifs_waterfall INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2132.trgt.sorted.spanning.bam"
2025-09-15 20:23:51.301 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_motifs_waterfall INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2132.trgt.vcf"
2025-09-15 20:23:51.301 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_motifs_waterfall INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2132"
2025-09-15 20:23:51.301 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:23:51.301 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "plot_type", value: "waterfall"
2025-09-15 20:23:51.302 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "show", value: "motifs"
2025-09-15 20:23:51.302 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "threads", value: 1
2025-09-15 20:23:51.302 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "disk_size", value: 27
2025-09-15 20:23:51.302 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2132.motifs_waterfall"
2025-09-15 20:23:51.302 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_motifs_waterfall INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:23:51.302 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_motifs_waterfall WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:23:51.303 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_motifs_waterfall INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:23:51.303 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_motifs_waterfall INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:23:51.311 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_meth_allele NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-14/call-trgt_plot_meth_allele", thread: 140609310422592
2025-09-15 20:23:51.333 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_motifs_allele INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2128.motifs_allele.trgt_plots.zip"
2025-09-15 20:23:51.335 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_meth_allele INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:23:51.335 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_meth_allele INFO input :: name: "waterfall", value: false
2025-09-15 20:23:51.335 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_meth_allele INFO input :: name: "methylation", value: true
2025-09-15 20:23:51.335 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_meth_allele INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:23:51.335 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_meth_allele INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:23:51.335 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_meth_allele INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:23:51.335 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_meth_allele INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2111.trgt.sorted.spanning.bam.bai"
2025-09-15 20:23:51.335 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_meth_allele INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2111.trgt.sorted.spanning.bam"
2025-09-15 20:23:51.335 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_meth_allele INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2111.trgt.vcf"
2025-09-15 20:23:51.335 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_meth_allele INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2111"
2025-09-15 20:23:51.336 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_meth_allele INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:23:51.336 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_meth_allele INFO eval :: name: "plot_type", value: "allele"
2025-09-15 20:23:51.336 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_meth_allele INFO eval :: name: "show", value: "meth"
2025-09-15 20:23:51.336 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_meth_allele INFO eval :: name: "threads", value: 1
2025-09-15 20:23:51.336 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_meth_allele INFO eval :: name: "disk_size", value: 27
2025-09-15 20:23:51.336 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_meth_allele INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2111.meth_allele"
2025-09-15 20:23:51.337 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_meth_allele INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:23:51.337 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_meth_allele WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:23:51.337 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_meth_allele INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:23:51.338 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_meth_allele INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:23:51.389 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_motifs_waterfall INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-35/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_bhhac81z"
2025-09-15 20:23:51.389 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_motifs_waterfall INFO Slurm invocation: srun --job-name call-trgt_plot_motifs_waterfall --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-35/call-trgt_plot_motifs_waterfall/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-35/call-trgt_plot_motifs_waterfall/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-35/call-trgt_plot_motifs_waterfall/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-35/call-trgt_plot_motifs_waterfall/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-35/call-trgt_genotype/out/m84036_250809_035451_s4.bc2132.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2132.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-35/call-trgt_genotype/out/m84036_250809_035451_s4.bc2132.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2132.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-35/call-trgt_genotype/out/m84036_250809_035451_s4.bc2132.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2132.trgt.vcf:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-35/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_bhhac81z/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-35/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_bhhac81z/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:23:51.416 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_motifs_waterfall NOTICE slurm_singularity run :: pid: 1200354, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-35/call-trgt_plot_motifs_waterfall/slurm_singularity.log.txt"
2025-09-15 20:23:51.418 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:23:48 [ERROR] - No reads found for TRID=SCA37_DAB1
2025-09-15 20:23:51.419 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:23:48 [ERROR] - No reads found for TRID=NIID_NOTCH2NLC
2025-09-15 20:23:51.419 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:23:48 [ERROR] - No reads found for TRID=OPDM4_RILPL1
2025-09-15 20:23:51.419 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:23:48 [ERROR] - No reads found for TRID=SCA4_ZFHX3
2025-09-15 20:23:51.419 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:23:48 [ERROR] - No reads found for TRID=HDL2_JPH3
2025-09-15 20:23:51.419 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:23:48 [ERROR] - No reads found for TRID=SCA31_BEAN1
2025-09-15 20:23:51.419 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:23:48 [ERROR] - No reads found for TRID=SCA27B_FGF14
2025-09-15 20:23:51.419 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:23:48 [ERROR] - No reads found for TRID=OPDM2_GIPC1
2025-09-15 20:23:51.419 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:23:48 [ERROR] - No reads found for TRID=FRA2A_AFF3
2025-09-15 20:23:51.419 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:23:48 [ERROR] - No reads found for TRID=SD5_HOXD13
2025-09-15 20:23:51.420 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:23:49 [ERROR] - No reads found for TRID=DM1_DMPK
2025-09-15 20:23:51.420 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:23:49 [ERROR] - No reads found for TRID=SCA36_NOP56
2025-09-15 20:23:51.420 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:23:49 [ERROR] - No reads found for TRID=CJD_PRNP
2025-09-15 20:23:51.420 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:23:49 [ERROR] - No reads found for TRID=EPM1_CSTB
2025-09-15 20:23:51.420 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:23:49 [ERROR] - No reads found for TRID=SCA10_ATXN10
2025-09-15 20:23:51.420 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:23:49 [ERROR] - No reads found for TRID=SCA7_ATXN7
2025-09-15 20:23:51.420 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:23:49 [ERROR] - No reads found for TRID=SCA3_ATXN3
2025-09-15 20:23:51.420 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:23:49 [ERROR] - No reads found for TRID=FECD3_TCF4
2025-09-15 20:23:51.420 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:23:49 [ERROR] - No reads found for TRID=SCA6_CACNA1A
2025-09-15 20:23:51.420 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:23:49 [ERROR] - No reads found for TRID=CCHS_PHOX2B
2025-09-15 20:23:51.420 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:23:49 [ERROR] - No reads found for TRID=SCA1_ATXN1
2025-09-15 20:23:51.420 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:23:50 [ERROR] - No reads found for TRID=OPDM1_LRP12
2025-09-15 20:23:51.420 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:23:50 [ERROR] - No reads found for TRID=FAME1_SAMD12
2025-09-15 20:23:51.420 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:23:50 [ERROR] - No reads found for TRID=FTDALS1_C9orf72
2025-09-15 20:23:51.425 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_meth_allele INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-14/call-trgt_plot_meth_allele/_singularity_tmpdir_sjgmi532"
2025-09-15 20:23:51.426 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_meth_allele INFO Slurm invocation: srun --job-name call-trgt_plot_meth_allele --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-14/call-trgt_plot_meth_allele/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-14/call-trgt_plot_meth_allele/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-14/call-trgt_plot_meth_allele/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-14/call-trgt_plot_meth_allele/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-14/call-trgt_genotype/out/m84036_250809_035451_s4.bc2111.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2111.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-14/call-trgt_genotype/out/m84036_250809_035451_s4.bc2111.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2111.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-14/call-trgt_genotype/out/m84036_250809_035451_s4.bc2111.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2111.trgt.sorted.spanning.bam.bai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-14/call-trgt_plot_meth_allele/_singularity_tmpdir_sjgmi532/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-14/call-trgt_plot_meth_allele/_singularity_tmpdir_sjgmi532/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:23:51.432 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_motifs_allele NOTICE done
2025-09-15 20:23:51.437 wdl.w:ptcp.w:call-trgt-31 NOTICE finish :: job: "call-trgt_plot_motifs_allele"
2025-09-15 20:23:51.437 wdl.w:ptcp.w:call-trgt-31 INFO output :: job: "call-trgt_plot_motifs_allele", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-31/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2128.motifs_allele.trgt_plots.zip"}
2025-09-15 20:23:51.437 wdl.w:ptcp.w:call-trgt-31 INFO visit :: node: "output-images_motifs_allele", values: {"images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-31/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2128.motifs_allele.trgt_plots.zip"}
2025-09-15 20:23:51.443 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_meth_waterfall NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-14/call-trgt_plot_meth_waterfall", thread: 140609260066368
2025-09-15 20:23:51.449 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_meth_allele NOTICE slurm_singularity run :: pid: 1200357, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-14/call-trgt_plot_meth_allele/slurm_singularity.log.txt"
2025-09-15 20:23:51.460 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_meth_waterfall INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:23:51.460 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_meth_waterfall INFO input :: name: "waterfall", value: true
2025-09-15 20:23:51.460 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_meth_waterfall INFO input :: name: "methylation", value: true
2025-09-15 20:23:51.460 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_meth_waterfall INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:23:51.460 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_meth_waterfall INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:23:51.460 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_meth_waterfall INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:23:51.460 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_meth_waterfall INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2111.trgt.sorted.spanning.bam.bai"
2025-09-15 20:23:51.460 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_meth_waterfall INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2111.trgt.sorted.spanning.bam"
2025-09-15 20:23:51.460 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_meth_waterfall INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2111.trgt.vcf"
2025-09-15 20:23:51.460 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_meth_waterfall INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2111"
2025-09-15 20:23:51.461 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_meth_waterfall INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:23:51.461 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_motifs_waterfall INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2128.motifs_waterfall.trgt_plots.zip"
2025-09-15 20:23:51.462 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_meth_waterfall INFO eval :: name: "plot_type", value: "waterfall"
2025-09-15 20:23:51.462 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_meth_waterfall INFO eval :: name: "show", value: "meth"
2025-09-15 20:23:51.462 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_meth_waterfall INFO eval :: name: "threads", value: 1
2025-09-15 20:23:51.462 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_meth_waterfall INFO eval :: name: "disk_size", value: 27
2025-09-15 20:23:51.462 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_meth_waterfall INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2111.meth_waterfall"
2025-09-15 20:23:51.462 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_meth_waterfall INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:23:51.463 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_meth_waterfall WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:23:51.463 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_meth_waterfall INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:23:51.463 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_meth_waterfall INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:23:51.509 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:23:51 [ERROR] - No reads found for TRID=SCA37_DAB1
2025-09-15 20:23:51.509 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:23:51 [ERROR] - No reads found for TRID=OPDM_ABCD3
2025-09-15 20:23:51.509 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:23:51 [ERROR] - No reads found for TRID=NIID_NOTCH2NLC
2025-09-15 20:23:51.517 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO srun: job 51797487 queued and waiting for resources
2025-09-15 20:23:51.518 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO srun: job 51797487 has been allocated resources
2025-09-15 20:23:51.518 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:51.544 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_meth_waterfall INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-14/call-trgt_plot_meth_waterfall/_singularity_tmpdir_3m_4rwcq"
2025-09-15 20:23:51.544 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_meth_waterfall INFO Slurm invocation: srun --job-name call-trgt_plot_meth_waterfall --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-14/call-trgt_plot_meth_waterfall/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-14/call-trgt_plot_meth_waterfall/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-14/call-trgt_plot_meth_waterfall/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-14/call-trgt_plot_meth_waterfall/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-14/call-trgt_genotype/out/m84036_250809_035451_s4.bc2111.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2111.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-14/call-trgt_genotype/out/m84036_250809_035451_s4.bc2111.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2111.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-14/call-trgt_genotype/out/m84036_250809_035451_s4.bc2111.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2111.trgt.sorted.spanning.bam.bai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-14/call-trgt_plot_meth_waterfall/_singularity_tmpdir_3m_4rwcq/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-14/call-trgt_plot_meth_waterfall/_singularity_tmpdir_3m_4rwcq/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:23:51.545 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_plot_meth_waterfall INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2112.meth_waterfall.trgt_plots.zip"
2025-09-15 20:23:51.548 wdl.w:ptcp.w:call-trgt-31.t:call-trgt_plot_motifs_waterfall NOTICE done
2025-09-15 20:23:51.554 wdl.w:ptcp.w:call-trgt-31 NOTICE finish :: job: "call-trgt_plot_motifs_waterfall"
2025-09-15 20:23:51.554 wdl.w:ptcp.w:call-trgt-31 INFO output :: job: "call-trgt_plot_motifs_waterfall", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-31/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2128.motifs_waterfall.trgt_plots.zip"}
2025-09-15 20:23:51.554 wdl.w:ptcp.w:call-trgt-31 INFO visit :: node: "output-images_motifs_waterfall", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-31/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2128.motifs_waterfall.trgt_plots.zip"}
2025-09-15 20:23:51.554 wdl.w:ptcp.w:call-trgt-31 INFO visit :: node: "outputs", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-31/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2128.motifs_waterfall.trgt_plots.zip", "images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-31/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2128.meth_allele.trgt_plots.zip", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-31/call-trgt_genotype/out/m84036_250809_035451_s4.bc2128.trgt.sorted.spanning.bam.bai", "images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-31/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2128.motifs_allele.trgt_plots.zip", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-31/call-trgt_genotype/out/m84036_250809_035451_s4.bc2128.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-31/call-trgt_genotype/out/m84036_250809_035451_s4.bc2128.trgt.vcf", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-31/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2128.repeats.bam", "images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-31/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2128.meth_waterfall.trgt_plots.zip", "reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-31/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2128.repeats.bam.bai"}
2025-09-15 20:23:51.560 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_motifs_allele NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-14/call-trgt_plot_motifs_allele", thread: 140609813722688
2025-09-15 20:23:51.566 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_meth_waterfall NOTICE slurm_singularity run :: pid: 1200371, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-14/call-trgt_plot_meth_waterfall/slurm_singularity.log.txt"
2025-09-15 20:23:51.583 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_motifs_allele INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:23:51.583 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_motifs_allele INFO input :: name: "waterfall", value: false
2025-09-15 20:23:51.583 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_motifs_allele INFO input :: name: "methylation", value: false
2025-09-15 20:23:51.583 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_motifs_allele INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:23:51.583 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_motifs_allele INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:23:51.583 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_motifs_allele INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:23:51.583 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_motifs_allele INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2111.trgt.sorted.spanning.bam.bai"
2025-09-15 20:23:51.583 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_motifs_allele INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2111.trgt.sorted.spanning.bam"
2025-09-15 20:23:51.584 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_motifs_allele INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2111.trgt.vcf"
2025-09-15 20:23:51.584 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_motifs_allele INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2111"
2025-09-15 20:23:51.584 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_motifs_allele INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:23:51.584 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_motifs_allele INFO eval :: name: "plot_type", value: "allele"
2025-09-15 20:23:51.584 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_motifs_allele INFO eval :: name: "show", value: "motifs"
2025-09-15 20:23:51.584 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_motifs_allele INFO eval :: name: "threads", value: 1
2025-09-15 20:23:51.584 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_motifs_allele INFO eval :: name: "disk_size", value: 27
2025-09-15 20:23:51.585 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_motifs_allele INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2111.motifs_allele"
2025-09-15 20:23:51.585 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_motifs_allele INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:23:51.586 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_motifs_allele WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:23:51.586 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_motifs_allele INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:23:51.586 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_motifs_allele INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:23:51.629 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_plot_motifs_allele INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2112.motifs_allele.trgt_plots.zip"
2025-09-15 20:23:51.633 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_plot_meth_waterfall NOTICE done
2025-09-15 20:23:51.638 wdl.w:ptcp.w:call-trgt-15 NOTICE finish :: job: "call-trgt_plot_meth_waterfall"
2025-09-15 20:23:51.638 wdl.w:ptcp.w:call-trgt-15 INFO output :: job: "call-trgt_plot_meth_waterfall", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-15/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2112.meth_waterfall.trgt_plots.zip"}
2025-09-15 20:23:51.638 wdl.w:ptcp.w:call-trgt-15 INFO visit :: node: "output-images_meth_waterfall", values: {"images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-15/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2112.meth_waterfall.trgt_plots.zip"}
2025-09-15 20:23:51.643 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_plot_motifs_waterfall INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2104.motifs_waterfall.trgt_plots.zip"
2025-09-15 20:23:51.644 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_motifs_waterfall NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-14/call-trgt_plot_motifs_waterfall", thread: 140613823374912
2025-09-15 20:23:51.665 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_motifs_waterfall INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:23:51.665 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_motifs_waterfall INFO input :: name: "waterfall", value: true
2025-09-15 20:23:51.665 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_motifs_waterfall INFO input :: name: "methylation", value: false
2025-09-15 20:23:51.665 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_motifs_waterfall INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:23:51.665 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_motifs_waterfall INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:23:51.665 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_motifs_waterfall INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:23:51.666 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_motifs_waterfall INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2111.trgt.sorted.spanning.bam.bai"
2025-09-15 20:23:51.666 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_motifs_waterfall INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2111.trgt.sorted.spanning.bam"
2025-09-15 20:23:51.666 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_motifs_waterfall INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2111.trgt.vcf"
2025-09-15 20:23:51.666 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_motifs_waterfall INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2111"
2025-09-15 20:23:51.666 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:23:51.666 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "plot_type", value: "waterfall"
2025-09-15 20:23:51.666 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "show", value: "motifs"
2025-09-15 20:23:51.667 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "threads", value: 1
2025-09-15 20:23:51.667 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "disk_size", value: 27
2025-09-15 20:23:51.667 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2111.motifs_waterfall"
2025-09-15 20:23:51.667 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_motifs_waterfall INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:23:51.667 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_motifs_waterfall WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:23:51.668 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_motifs_waterfall INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:23:51.668 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_motifs_waterfall INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:23:51.672 wdl.w:ptcp.w:call-trgt-31 NOTICE done
2025-09-15 20:23:51.675 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_motifs_allele INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-14/call-trgt_plot_motifs_allele/_singularity_tmpdir_1vmap979"
2025-09-15 20:23:51.675 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_motifs_allele INFO Slurm invocation: srun --job-name call-trgt_plot_motifs_allele --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-14/call-trgt_plot_motifs_allele/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-14/call-trgt_plot_motifs_allele/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-14/call-trgt_plot_motifs_allele/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-14/call-trgt_plot_motifs_allele/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-14/call-trgt_genotype/out/m84036_250809_035451_s4.bc2111.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2111.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-14/call-trgt_genotype/out/m84036_250809_035451_s4.bc2111.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2111.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-14/call-trgt_genotype/out/m84036_250809_035451_s4.bc2111.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2111.trgt.sorted.spanning.bam.bai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-14/call-trgt_plot_motifs_allele/_singularity_tmpdir_1vmap979/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-14/call-trgt_plot_motifs_allele/_singularity_tmpdir_1vmap979/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:23:51.678 wdl.w:ptcp NOTICE finish :: job: "call-trgt-31"
2025-09-15 20:23:51.678 wdl.w:ptcp INFO output :: job: "call-trgt-31", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-31/out/m84036_250809_035451_s4.bc2128.motifs_waterfall.trgt_plots.zip", "images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-31/out/m84036_250809_035451_s4.bc2128.meth_allele.trgt_plots.zip", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-31/out/m84036_250809_035451_s4.bc2128.trgt.sorted.spanning.bam.bai", "images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-31/out/m84036_250809_035451_s4.bc2128.motifs_allele.trgt_plots.zip", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-31/out/m84036_250809_035451_s4.bc2128.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-31/out/m84036_250809_035451_s4.bc2128.trgt.vcf", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-31/out/m84036_250809_035451_s4.bc2128.repeats.bam", "images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-31/out/m84036_250809_035451_s4.bc2128.meth_waterfall.trgt_plots.zip", "reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-31/out/m84036_250809_035451_s4.bc2128.repeats.bam.bai"}
2025-09-15 20:23:51.687 wdl.w:ptcp.w:call-paraphase-52 NOTICE workflow start :: name: "paraphase", source: "./paraphase.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-52"
2025-09-15 20:23:51.693 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_motifs_allele NOTICE slurm_singularity run :: pid: 1200379, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-14/call-trgt_plot_motifs_allele/slurm_singularity.log.txt"
2025-09-15 20:23:51.705 wdl.w:ptcp.w:call-paraphase-52 INFO visit :: node: "decl-annotation_vcf", values: {"annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf"}
2025-09-15 20:23:51.705 wdl.w:ptcp.w:call-paraphase-52 INFO visit :: node: "decl-config_file", values: {"config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml"}
2025-09-15 20:23:51.705 wdl.w:ptcp.w:call-paraphase-52 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:23:51.705 wdl.w:ptcp.w:call-paraphase-52 INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:23:51.705 wdl.w:ptcp.w:call-paraphase-52 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-52/out/m84036_250809_035451_s4.bc2149.mapped.bam"}
2025-09-15 20:23:51.705 wdl.w:ptcp.w:call-paraphase-52 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-52/out/m84036_250809_035451_s4.bc2149.mapped.bam.bai"}
2025-09-15 20:23:51.706 wdl.w:ptcp.w:call-paraphase-52 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:23:51.706 wdl.w:ptcp.w:call-paraphase-52 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:23:51.706 wdl.w:ptcp.w:call-paraphase-52 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2149"}
2025-09-15 20:23:51.706 wdl.w:ptcp.w:call-paraphase-52 INFO visit :: node: "decl-sex", values: {"sex": "F"}
2025-09-15 20:23:51.706 wdl.w:ptcp.w:call-paraphase-52 NOTICE ready :: job: "call-run_paraphase", callee: "run_paraphase"
2025-09-15 20:23:51.706 wdl.w:ptcp.w:call-paraphase-52 INFO input :: job: "call-run_paraphase", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf", "genome_version": "38", "config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-52/out/m84036_250809_035451_s4.bc2149.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-52/out/m84036_250809_035451_s4.bc2149.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2149"}
2025-09-15 20:23:51.722 wdl.w:ptcp.w:call-trgt-15.t:call-trgt_plot_motifs_allele NOTICE done
2025-09-15 20:23:51.727 wdl.w:ptcp.w:call-trgt-15 NOTICE finish :: job: "call-trgt_plot_motifs_allele"
2025-09-15 20:23:51.727 wdl.w:ptcp.w:call-trgt-15 INFO output :: job: "call-trgt_plot_motifs_allele", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-15/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2112.motifs_allele.trgt_plots.zip"}
2025-09-15 20:23:51.728 wdl.w:ptcp.w:call-trgt-15 INFO visit :: node: "output-images_motifs_allele", values: {"images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-15/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2112.motifs_allele.trgt_plots.zip"}
2025-09-15 20:23:51.728 wdl.w:ptcp.w:call-trgt-15 INFO visit :: node: "outputs", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-15/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2112.motifs_waterfall.trgt_plots.zip", "images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-15/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2112.meth_allele.trgt_plots.zip", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-15/call-trgt_genotype/out/m84036_250809_035451_s4.bc2112.trgt.sorted.spanning.bam.bai", "images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-15/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2112.motifs_allele.trgt_plots.zip", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-15/call-trgt_genotype/out/m84036_250809_035451_s4.bc2112.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-15/call-trgt_genotype/out/m84036_250809_035451_s4.bc2112.trgt.vcf", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-15/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2112.repeats.bam", "images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-15/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2112.meth_waterfall.trgt_plots.zip", "reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-15/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2112.repeats.bam.bai"}
2025-09-15 20:23:51.734 wdl.w:ptcp.w:call-trgt-20.t:call-trgt_plot_meth_allele NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-20/call-trgt_plot_meth_allele", thread: 140609293637184
2025-09-15 20:23:51.762 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_motifs_waterfall INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-14/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_yh_84xr7"
2025-09-15 20:23:51.763 wdl.w:ptcp.w:call-trgt-20.t:call-trgt_plot_meth_allele INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:23:51.763 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_motifs_waterfall INFO Slurm invocation: srun --job-name call-trgt_plot_motifs_waterfall --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-14/call-trgt_plot_motifs_waterfall/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-14/call-trgt_plot_motifs_waterfall/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-14/call-trgt_plot_motifs_waterfall/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-14/call-trgt_plot_motifs_waterfall/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-14/call-trgt_genotype/out/m84036_250809_035451_s4.bc2111.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2111.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-14/call-trgt_genotype/out/m84036_250809_035451_s4.bc2111.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2111.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-14/call-trgt_genotype/out/m84036_250809_035451_s4.bc2111.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2111.trgt.sorted.spanning.bam.bai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-14/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_yh_84xr7/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-14/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_yh_84xr7/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:23:51.763 wdl.w:ptcp.w:call-trgt-20.t:call-trgt_plot_meth_allele INFO input :: name: "waterfall", value: false
2025-09-15 20:23:51.763 wdl.w:ptcp.w:call-trgt-20.t:call-trgt_plot_meth_allele INFO input :: name: "methylation", value: true
2025-09-15 20:23:51.763 wdl.w:ptcp.w:call-trgt-20.t:call-trgt_plot_meth_allele INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:23:51.763 wdl.w:ptcp.w:call-trgt-20.t:call-trgt_plot_meth_allele INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:23:51.764 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_plot_motifs_waterfall NOTICE done
2025-09-15 20:23:51.765 wdl.w:ptcp.w:call-trgt-20.t:call-trgt_plot_meth_allele INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:23:51.767 wdl.w:ptcp.w:call-trgt-20.t:call-trgt_plot_meth_allele INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2117.trgt.sorted.spanning.bam.bai"
2025-09-15 20:23:51.767 wdl.w:ptcp.w:call-trgt-20.t:call-trgt_plot_meth_allele INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2117.trgt.sorted.spanning.bam"
2025-09-15 20:23:51.767 wdl.w:ptcp.w:call-trgt-20.t:call-trgt_plot_meth_allele INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2117.trgt.vcf"
2025-09-15 20:23:51.767 wdl.w:ptcp.w:call-trgt-20.t:call-trgt_plot_meth_allele INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2117"
2025-09-15 20:23:51.767 wdl.w:ptcp.w:call-trgt-20.t:call-trgt_plot_meth_allele INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:23:51.767 wdl.w:ptcp.w:call-trgt-20.t:call-trgt_plot_meth_allele INFO eval :: name: "plot_type", value: "allele"
2025-09-15 20:23:51.767 wdl.w:ptcp.w:call-trgt-20.t:call-trgt_plot_meth_allele INFO eval :: name: "show", value: "meth"
2025-09-15 20:23:51.767 wdl.w:ptcp.w:call-trgt-20.t:call-trgt_plot_meth_allele INFO eval :: name: "threads", value: 1
2025-09-15 20:23:51.768 wdl.w:ptcp.w:call-trgt-20.t:call-trgt_plot_meth_allele INFO eval :: name: "disk_size", value: 27
2025-09-15 20:23:51.768 wdl.w:ptcp.w:call-trgt-20.t:call-trgt_plot_meth_allele INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2117.meth_allele"
2025-09-15 20:23:51.768 wdl.w:ptcp.w:call-trgt-20.t:call-trgt_plot_meth_allele INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:23:51.768 wdl.w:ptcp.w:call-trgt-20.t:call-trgt_plot_meth_allele WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:23:51.769 wdl.w:ptcp.w:call-trgt-20.t:call-trgt_plot_meth_allele INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:23:51.769 wdl.w:ptcp.w:call-trgt-20.t:call-trgt_plot_meth_allele INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:23:51.771 wdl.w:ptcp.w:call-trgt-07 NOTICE finish :: job: "call-trgt_plot_motifs_waterfall"
2025-09-15 20:23:51.771 wdl.w:ptcp.w:call-trgt-07 INFO output :: job: "call-trgt_plot_motifs_waterfall", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-07/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2104.motifs_waterfall.trgt_plots.zip"}
2025-09-15 20:23:51.772 wdl.w:ptcp.w:call-trgt-07 INFO visit :: node: "output-images_motifs_waterfall", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-07/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2104.motifs_waterfall.trgt_plots.zip"}
2025-09-15 20:23:51.783 wdl.w:ptcp.w:call-trgt-20.t:call-trgt_plot_meth_waterfall NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-20/call-trgt_plot_meth_waterfall", thread: 140610879071808
2025-09-15 20:23:51.790 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_motifs_waterfall NOTICE slurm_singularity run :: pid: 1200381, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-14/call-trgt_plot_motifs_waterfall/slurm_singularity.log.txt"
2025-09-15 20:23:51.803 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:23:49 [ERROR] - No reads found for TRID=SCA3_ATXN3
2025-09-15 20:23:51.803 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:23:49 [ERROR] - No reads found for TRID=HDL2_JPH3
2025-09-15 20:23:51.803 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:23:49 [ERROR] - No reads found for TRID=SCA8_ATXN8OS
2025-09-15 20:23:51.803 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:23:50 [ERROR] - No reads found for TRID=OPDM2_GIPC1
2025-09-15 20:23:51.803 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:23:50 [ERROR] - No reads found for TRID=SCA6_CACNA1A
2025-09-15 20:23:51.803 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:23:50 [ERROR] - No reads found for TRID=SCA2_ATXN2
2025-09-15 20:23:51.803 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:23:50 [ERROR] - No reads found for TRID=SCA4_ZFHX3
2025-09-15 20:23:51.803 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:23:50 [ERROR] - No reads found for TRID=SCA36_NOP56
2025-09-15 20:23:51.803 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:23:50 [ERROR] - No reads found for TRID=CJD_PRNP
2025-09-15 20:23:51.803 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:23:50 [ERROR] - No reads found for TRID=SD5_HOXD13
2025-09-15 20:23:51.803 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:23:50 [ERROR] - No reads found for TRID=DM1_DMPK
2025-09-15 20:23:51.803 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:23:50 [ERROR] - No reads found for TRID=FRA2A_AFF3
2025-09-15 20:23:51.803 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:23:50 [ERROR] - No reads found for TRID=EPM1_CSTB
2025-09-15 20:23:51.803 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:23:50 [ERROR] - No reads found for TRID=SCA7_ATXN7
2025-09-15 20:23:51.803 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:23:50 [ERROR] - No reads found for TRID=HD_HTT
2025-09-15 20:23:51.804 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:23:50 [ERROR] - No reads found for TRID=SCA12_PPP2R2B
2025-09-15 20:23:51.804 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:23:50 [ERROR] - No reads found for TRID=SCA1_ATXN1
2025-09-15 20:23:51.804 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:23:50 [ERROR] - No reads found for TRID=OPDM1_LRP12
2025-09-15 20:23:51.804 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:23:50 [ERROR] - No reads found for TRID=FAME1_SAMD12
2025-09-15 20:23:51.804 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:23:50 [ERROR] - No reads found for TRID=FTDALS1_C9orf72
2025-09-15 20:23:51.804 wdl.w:ptcp.w:call-trgt-20.t:call-trgt_plot_meth_waterfall INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:23:51.804 wdl.w:ptcp.w:call-trgt-20.t:call-trgt_plot_meth_waterfall INFO input :: name: "waterfall", value: true
2025-09-15 20:23:51.804 wdl.w:ptcp.w:call-trgt-20.t:call-trgt_plot_meth_waterfall INFO input :: name: "methylation", value: true
2025-09-15 20:23:51.804 wdl.w:ptcp.w:call-trgt-20.t:call-trgt_plot_meth_waterfall INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:23:51.805 wdl.w:ptcp.w:call-trgt-20.t:call-trgt_plot_meth_waterfall INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:23:51.805 wdl.w:ptcp.w:call-trgt-20.t:call-trgt_plot_meth_waterfall INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:23:51.805 wdl.w:ptcp.w:call-trgt-20.t:call-trgt_plot_meth_waterfall INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2117.trgt.sorted.spanning.bam.bai"
2025-09-15 20:23:51.805 wdl.w:ptcp.w:call-trgt-20.t:call-trgt_plot_meth_waterfall INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2117.trgt.sorted.spanning.bam"
2025-09-15 20:23:51.805 wdl.w:ptcp.w:call-trgt-20.t:call-trgt_plot_meth_waterfall INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2117.trgt.vcf"
2025-09-15 20:23:51.805 wdl.w:ptcp.w:call-trgt-20.t:call-trgt_plot_meth_waterfall INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2117"
2025-09-15 20:23:51.805 wdl.w:ptcp.w:call-trgt-20.t:call-trgt_plot_meth_waterfall INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:23:51.805 wdl.w:ptcp.w:call-trgt-20.t:call-trgt_plot_meth_waterfall INFO eval :: name: "plot_type", value: "waterfall"
2025-09-15 20:23:51.806 wdl.w:ptcp.w:call-trgt-20.t:call-trgt_plot_meth_waterfall INFO eval :: name: "show", value: "meth"
2025-09-15 20:23:51.806 wdl.w:ptcp.w:call-trgt-20.t:call-trgt_plot_meth_waterfall INFO eval :: name: "threads", value: 1
2025-09-15 20:23:51.806 wdl.w:ptcp.w:call-trgt-20.t:call-trgt_plot_meth_waterfall INFO eval :: name: "disk_size", value: 27
2025-09-15 20:23:51.806 wdl.w:ptcp.w:call-trgt-20.t:call-trgt_plot_meth_waterfall INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2117.meth_waterfall"
2025-09-15 20:23:51.807 wdl.w:ptcp.w:call-trgt-20.t:call-trgt_plot_meth_waterfall INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:23:51.807 wdl.w:ptcp.w:call-trgt-20.t:call-trgt_plot_meth_waterfall WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:23:51.807 wdl.w:ptcp.w:call-trgt-20.t:call-trgt_plot_meth_waterfall INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:23:51.807 wdl.w:ptcp.w:call-trgt-20.t:call-trgt_plot_meth_waterfall INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:23:51.840 wdl.w:ptcp.w:call-trgt-15 NOTICE done
2025-09-15 20:23:51.846 wdl.w:ptcp NOTICE finish :: job: "call-trgt-15"
2025-09-15 20:23:51.846 wdl.w:ptcp INFO output :: job: "call-trgt-15", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-15/out/m84036_250809_035451_s4.bc2112.motifs_waterfall.trgt_plots.zip", "images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-15/out/m84036_250809_035451_s4.bc2112.meth_allele.trgt_plots.zip", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-15/out/m84036_250809_035451_s4.bc2112.trgt.sorted.spanning.bam.bai", "images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-15/out/m84036_250809_035451_s4.bc2112.motifs_allele.trgt_plots.zip", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-15/out/m84036_250809_035451_s4.bc2112.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-15/out/m84036_250809_035451_s4.bc2112.trgt.vcf", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-15/out/m84036_250809_035451_s4.bc2112.repeats.bam", "images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-15/out/m84036_250809_035451_s4.bc2112.meth_waterfall.trgt_plots.zip", "reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-15/out/m84036_250809_035451_s4.bc2112.repeats.bam.bai"}
2025-09-15 20:23:51.856 wdl.w:ptcp.w:call-sawfish-52 NOTICE workflow start :: name: "sawfish", source: "./sawfish.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-52"
2025-09-15 20:23:51.876 wdl.w:ptcp.w:call-sawfish-52 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:23:51.876 wdl.w:ptcp.w:call-sawfish-52 INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:23:51.876 wdl.w:ptcp.w:call-sawfish-52 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-52/out/m84036_250809_035451_s4.bc2149.mapped.bam"}
2025-09-15 20:23:51.876 wdl.w:ptcp.w:call-sawfish-52 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-52/out/m84036_250809_035451_s4.bc2149.mapped.bam.bai"}
2025-09-15 20:23:51.876 wdl.w:ptcp.w:call-sawfish-52 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:23:51.876 wdl.w:ptcp.w:call-sawfish-52 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:23:51.876 wdl.w:ptcp.w:call-sawfish-52 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2149"}
2025-09-15 20:23:51.876 wdl.w:ptcp.w:call-sawfish-52 NOTICE ready :: job: "call-run_sawfish", callee: "run_sawfish"
2025-09-15 20:23:51.876 wdl.w:ptcp.w:call-sawfish-52 INFO input :: job: "call-run_sawfish", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-52/out/m84036_250809_035451_s4.bc2149.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-52/out/m84036_250809_035451_s4.bc2149.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2149"}
2025-09-15 20:23:51.895 wdl.w:ptcp.w:call-trgt-20.t:call-trgt_plot_meth_allele INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-20/call-trgt_plot_meth_allele/_singularity_tmpdir_4o1qkm3s"
2025-09-15 20:23:51.896 wdl.w:ptcp.w:call-trgt-20.t:call-trgt_plot_meth_allele INFO Slurm invocation: srun --job-name call-trgt_plot_meth_allele --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-20/call-trgt_plot_meth_allele/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-20/call-trgt_plot_meth_allele/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-20/call-trgt_plot_meth_allele/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-20/call-trgt_plot_meth_allele/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-20/call-trgt_genotype/out/m84036_250809_035451_s4.bc2117.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2117.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-20/call-trgt_genotype/out/m84036_250809_035451_s4.bc2117.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2117.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-20/call-trgt_genotype/out/m84036_250809_035451_s4.bc2117.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2117.trgt.sorted.spanning.bam:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-20/call-trgt_plot_meth_allele/_singularity_tmpdir_4o1qkm3s/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-20/call-trgt_plot_meth_allele/_singularity_tmpdir_4o1qkm3s/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:23:51.898 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_meth_allele INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2131.meth_allele.trgt_plots.zip"
2025-09-15 20:23:51.905 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:23:51 [ERROR] - No reads found for TRID=SCA37_DAB1
2025-09-15 20:23:51.905 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:23:51 [ERROR] - No reads found for TRID=DRPLA_ATN1
2025-09-15 20:23:51.905 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:23:51 [ERROR] - No reads found for TRID=NIID_NOTCH2NLC
2025-09-15 20:23:51.905 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:23:51 [ERROR] - No reads found for TRID=OPDM_ABCD3
2025-09-15 20:23:51.920 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_meth_allele.slurm_singularity INFO srun: job 51797488 queued and waiting for resources
2025-09-15 20:23:51.921 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_meth_allele.slurm_singularity INFO srun: job 51797488 has been allocated resources
2025-09-15 20:23:51.921 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_meth_allele.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:51.934 wdl.w:ptcp.w:call-trgt-20.t:call-trgt_plot_meth_allele NOTICE slurm_singularity run :: pid: 1200389, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-20/call-trgt_plot_meth_allele/slurm_singularity.log.txt"
2025-09-15 20:23:51.971 wdl.w:ptcp.w:call-trgt-20.t:call-trgt_plot_meth_waterfall INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-20/call-trgt_plot_meth_waterfall/_singularity_tmpdir_2d_r_9q4"
2025-09-15 20:23:51.971 wdl.w:ptcp.w:call-trgt-20.t:call-trgt_plot_meth_waterfall INFO Slurm invocation: srun --job-name call-trgt_plot_meth_waterfall --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-20/call-trgt_plot_meth_waterfall/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-20/call-trgt_plot_meth_waterfall/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-20/call-trgt_plot_meth_waterfall/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-20/call-trgt_plot_meth_waterfall/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-20/call-trgt_genotype/out/m84036_250809_035451_s4.bc2117.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2117.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-20/call-trgt_genotype/out/m84036_250809_035451_s4.bc2117.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2117.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-20/call-trgt_genotype/out/m84036_250809_035451_s4.bc2117.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2117.trgt.sorted.spanning.bam:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-20/call-trgt_plot_meth_waterfall/_singularity_tmpdir_2d_r_9q4/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-20/call-trgt_plot_meth_waterfall/_singularity_tmpdir_2d_r_9q4/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:23:51.992 wdl.w:ptcp.w:call-trgt-20.t:call-trgt_plot_meth_waterfall NOTICE slurm_singularity run :: pid: 1200391, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-20/call-trgt_plot_meth_waterfall/slurm_singularity.log.txt"
2025-09-15 20:23:52.019 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:51 [ERROR] - No reads found for TRID=SCA37_DAB1
2025-09-15 20:23:52.019 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:51 [ERROR] - No reads found for TRID=DRPLA_ATN1
2025-09-15 20:23:52.019 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:51 [ERROR] - No reads found for TRID=NIID_NOTCH2NLC
2025-09-15 20:23:52.033 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO srun: job 51797489 queued and waiting for resources
2025-09-15 20:23:52.033 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO srun: job 51797489 has been allocated resources
2025-09-15 20:23:52.033 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:52.053 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_meth_allele NOTICE done
2025-09-15 20:23:52.057 wdl.w:ptcp.w:call-trgt-34 NOTICE finish :: job: "call-trgt_plot_meth_allele"
2025-09-15 20:23:52.058 wdl.w:ptcp.w:call-trgt-34 INFO output :: job: "call-trgt_plot_meth_allele", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-34/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2131.meth_allele.trgt_plots.zip"}
2025-09-15 20:23:52.058 wdl.w:ptcp.w:call-trgt-34 INFO visit :: node: "output-images_meth_allele", values: {"images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-34/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2131.meth_allele.trgt_plots.zip"}
2025-09-15 20:23:52.062 wdl.w:ptcp.w:call-trgt-20.t:call-trgt_plot_motifs_allele NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-20/call-trgt_plot_motifs_allele", thread: 140609822115392
2025-09-15 20:23:52.077 wdl.w:ptcp.w:call-trgt-20.t:call-trgt_plot_motifs_allele INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:23:52.077 wdl.w:ptcp.w:call-trgt-20.t:call-trgt_plot_motifs_allele INFO input :: name: "waterfall", value: false
2025-09-15 20:23:52.077 wdl.w:ptcp.w:call-trgt-20.t:call-trgt_plot_motifs_allele INFO input :: name: "methylation", value: false
2025-09-15 20:23:52.077 wdl.w:ptcp.w:call-trgt-20.t:call-trgt_plot_motifs_allele INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:23:52.078 wdl.w:ptcp.w:call-trgt-20.t:call-trgt_plot_motifs_allele INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:23:52.078 wdl.w:ptcp.w:call-trgt-20.t:call-trgt_plot_motifs_allele INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:23:52.078 wdl.w:ptcp.w:call-trgt-20.t:call-trgt_plot_motifs_allele INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2117.trgt.sorted.spanning.bam.bai"
2025-09-15 20:23:52.078 wdl.w:ptcp.w:call-trgt-20.t:call-trgt_plot_motifs_allele INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2117.trgt.sorted.spanning.bam"
2025-09-15 20:23:52.078 wdl.w:ptcp.w:call-trgt-20.t:call-trgt_plot_motifs_allele INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2117.trgt.vcf"
2025-09-15 20:23:52.078 wdl.w:ptcp.w:call-trgt-20.t:call-trgt_plot_motifs_allele INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2117"
2025-09-15 20:23:52.078 wdl.w:ptcp.w:call-trgt-20.t:call-trgt_plot_motifs_allele INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:23:52.078 wdl.w:ptcp.w:call-trgt-20.t:call-trgt_plot_motifs_allele INFO eval :: name: "plot_type", value: "allele"
2025-09-15 20:23:52.078 wdl.w:ptcp.w:call-trgt-20.t:call-trgt_plot_motifs_allele INFO eval :: name: "show", value: "motifs"
2025-09-15 20:23:52.078 wdl.w:ptcp.w:call-trgt-20.t:call-trgt_plot_motifs_allele INFO eval :: name: "threads", value: 1
2025-09-15 20:23:52.078 wdl.w:ptcp.w:call-trgt-20.t:call-trgt_plot_motifs_allele INFO eval :: name: "disk_size", value: 27
2025-09-15 20:23:52.079 wdl.w:ptcp.w:call-trgt-20.t:call-trgt_plot_motifs_allele INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2117.motifs_allele"
2025-09-15 20:23:52.079 wdl.w:ptcp.w:call-trgt-20.t:call-trgt_plot_motifs_allele INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:23:52.079 wdl.w:ptcp.w:call-trgt-20.t:call-trgt_plot_motifs_allele WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:23:52.079 wdl.w:ptcp.w:call-trgt-20.t:call-trgt_plot_motifs_allele INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:23:52.080 wdl.w:ptcp.w:call-trgt-20.t:call-trgt_plot_motifs_allele INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:23:52.154 wdl.w:ptcp.w:call-trgt-20.t:call-trgt_plot_motifs_allele INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-20/call-trgt_plot_motifs_allele/_singularity_tmpdir_vyyb557t"
2025-09-15 20:23:52.154 wdl.w:ptcp.w:call-trgt-20.t:call-trgt_plot_motifs_allele INFO Slurm invocation: srun --job-name call-trgt_plot_motifs_allele --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-20/call-trgt_plot_motifs_allele/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-20/call-trgt_plot_motifs_allele/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-20/call-trgt_plot_motifs_allele/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-20/call-trgt_plot_motifs_allele/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-20/call-trgt_genotype/out/m84036_250809_035451_s4.bc2117.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2117.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-20/call-trgt_genotype/out/m84036_250809_035451_s4.bc2117.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2117.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-20/call-trgt_genotype/out/m84036_250809_035451_s4.bc2117.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2117.trgt.sorted.spanning.bam:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-20/call-trgt_plot_motifs_allele/_singularity_tmpdir_vyyb557t/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-20/call-trgt_plot_motifs_allele/_singularity_tmpdir_vyyb557t/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:23:52.165 wdl.w:ptcp.w:call-trgt-20.t:call-trgt_plot_motifs_allele NOTICE slurm_singularity run :: pid: 1200393, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-20/call-trgt_plot_motifs_allele/slurm_singularity.log.txt"
2025-09-15 20:23:52.243 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:52 [ERROR] - No reads found for TRID=SCA37_DAB1
2025-09-15 20:23:52.243 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:52 [ERROR] - No reads found for TRID=DRPLA_ATN1
2025-09-15 20:23:52.243 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:52 [ERROR] - No reads found for TRID=NIID_NOTCH2NLC
2025-09-15 20:23:52.250 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_motifs_allele.slurm_singularity INFO srun: job 51797490 queued and waiting for resources
2025-09-15 20:23:52.250 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_motifs_allele.slurm_singularity INFO srun: job 51797490 has been allocated resources
2025-09-15 20:23:52.250 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_motifs_allele.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:52.255 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:49 [ERROR] - No reads found for TRID=NIID_NOTCH2NLC
2025-09-15 20:23:52.256 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:49 [ERROR] - No reads found for TRID=OPDM_ABCD3
2025-09-15 20:23:52.256 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:49 [ERROR] - No reads found for TRID=SCA2_ATXN2
2025-09-15 20:23:52.256 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:49 [ERROR] - No reads found for TRID=OPDM4_RILPL1
2025-09-15 20:23:52.256 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:49 [ERROR] - No reads found for TRID=SCA27B_FGF14
2025-09-15 20:23:52.256 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:49 [ERROR] - No reads found for TRID=SCA4_ZFHX3
2025-09-15 20:23:52.256 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:49 [ERROR] - No reads found for TRID=HDL2_JPH3
2025-09-15 20:23:52.256 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:49 [ERROR] - No reads found for TRID=SCA6_CACNA1A
2025-09-15 20:23:52.256 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:49 [ERROR] - No reads found for TRID=DM1_DMPK
2025-09-15 20:23:52.256 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:50 [ERROR] - No reads found for TRID=FRA2A_AFF3
2025-09-15 20:23:52.256 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:50 [ERROR] - No reads found for TRID=SD5_HOXD13
2025-09-15 20:23:52.256 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:50 [ERROR] - No reads found for TRID=OPDM2_GIPC1
2025-09-15 20:23:52.256 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:50 [ERROR] - No reads found for TRID=CJD_PRNP
2025-09-15 20:23:52.256 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:50 [ERROR] - No reads found for TRID=EPM1_CSTB
2025-09-15 20:23:52.256 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:50 [ERROR] - No reads found for TRID=SCA31_BEAN1
2025-09-15 20:23:52.256 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:50 [ERROR] - No reads found for TRID=SCA36_NOP56
2025-09-15 20:23:52.256 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:50 [ERROR] - No reads found for TRID=SCA7_ATXN7
2025-09-15 20:23:52.256 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:50 [ERROR] - No reads found for TRID=CCHS_PHOX2B
2025-09-15 20:23:52.256 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:50 [ERROR] - No reads found for TRID=SCA12_PPP2R2B
2025-09-15 20:23:52.257 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:50 [ERROR] - No reads found for TRID=OPDM1_LRP12
2025-09-15 20:23:52.257 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:50 [ERROR] - No reads found for TRID=FTDALS1_C9orf72
2025-09-15 20:23:52.257 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:50 [ERROR] - No reads found for TRID=FAME1_SAMD12
2025-09-15 20:23:52.425 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO srun: job 51797491 queued and waiting for resources
2025-09-15 20:23:52.425 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO srun: job 51797491 has been allocated resources
2025-09-15 20:23:52.425 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:52.452 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:49 [ERROR] - No reads found for TRID=OPDM_ABCD3
2025-09-15 20:23:52.452 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:49 [ERROR] - No reads found for TRID=SCA2_ATXN2
2025-09-15 20:23:52.452 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:49 [ERROR] - No reads found for TRID=OPDM4_RILPL1
2025-09-15 20:23:52.452 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:49 [ERROR] - No reads found for TRID=SCA27B_FGF14
2025-09-15 20:23:52.452 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:49 [ERROR] - No reads found for TRID=SCA4_ZFHX3
2025-09-15 20:23:52.452 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:50 [ERROR] - No reads found for TRID=HDL2_JPH3
2025-09-15 20:23:52.452 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:50 [ERROR] - No reads found for TRID=SCA6_CACNA1A
2025-09-15 20:23:52.452 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:50 [ERROR] - No reads found for TRID=DM1_DMPK
2025-09-15 20:23:52.453 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:50 [ERROR] - No reads found for TRID=FRA2A_AFF3
2025-09-15 20:23:52.453 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:50 [ERROR] - No reads found for TRID=SD5_HOXD13
2025-09-15 20:23:52.453 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:50 [ERROR] - No reads found for TRID=OPDM2_GIPC1
2025-09-15 20:23:52.453 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:50 [ERROR] - No reads found for TRID=CJD_PRNP
2025-09-15 20:23:52.453 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:50 [ERROR] - No reads found for TRID=EPM1_CSTB
2025-09-15 20:23:52.453 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:50 [ERROR] - No reads found for TRID=SCA31_BEAN1
2025-09-15 20:23:52.453 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:50 [ERROR] - No reads found for TRID=SCA36_NOP56
2025-09-15 20:23:52.453 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:50 [ERROR] - No reads found for TRID=SCA7_ATXN7
2025-09-15 20:23:52.453 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:50 [ERROR] - No reads found for TRID=CCHS_PHOX2B
2025-09-15 20:23:52.453 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:50 [ERROR] - No reads found for TRID=SCA12_PPP2R2B
2025-09-15 20:23:52.453 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:50 [ERROR] - No reads found for TRID=OPDM1_LRP12
2025-09-15 20:23:52.453 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:51 [ERROR] - No reads found for TRID=FTDALS1_C9orf72
2025-09-15 20:23:52.453 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:51 [ERROR] - No reads found for TRID=FAME1_SAMD12
2025-09-15 20:23:52.456 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:23:52 [ERROR] - No reads found for TRID=NIID_NOTCH2NLC
2025-09-15 20:23:52.456 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:23:52 [ERROR] - No reads found for TRID=DRPLA_ATN1
2025-09-15 20:23:52.456 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:23:52 [ERROR] - No reads found for TRID=OPDM_ABCD3
2025-09-15 20:23:52.456 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:23:52 [ERROR] - No reads found for TRID=OPDM4_RILPL1
2025-09-15 20:23:52.456 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:23:52 [ERROR] - No reads found for TRID=SCA37_DAB1
2025-09-15 20:23:52.456 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:23:52 [ERROR] - No reads found for TRID=OPMD_PABPN1
2025-09-15 20:23:52.456 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:23:52 [ERROR] - No reads found for TRID=SCA27B_FGF14
2025-09-15 20:23:52.456 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:23:52 [ERROR] - No reads found for TRID=SCA8_ATXN8OS
2025-09-15 20:23:52.457 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:23:52 [ERROR] - No reads found for TRID=SCA4_ZFHX3
2025-09-15 20:23:52.457 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:23:52 [ERROR] - No reads found for TRID=HDL2_JPH3
2025-09-15 20:23:52.457 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:23:52 [ERROR] - No reads found for TRID=SCA31_BEAN1
2025-09-15 20:23:52.464 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_meth_allele.slurm_singularity INFO srun: job 51797492 queued and waiting for resources
2025-09-15 20:23:52.464 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_meth_allele.slurm_singularity INFO srun: job 51797492 has been allocated resources
2025-09-15 20:23:52.464 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_meth_allele.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:52.568 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:52 [ERROR] - No reads found for TRID=NIID_NOTCH2NLC
2025-09-15 20:23:52.568 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_plot_motifs_allele INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2104.motifs_allele.trgt_plots.zip"
2025-09-15 20:23:52.568 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:52 [ERROR] - No reads found for TRID=DRPLA_ATN1
2025-09-15 20:23:52.568 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:52 [ERROR] - No reads found for TRID=OPDM_ABCD3
2025-09-15 20:23:52.568 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:52 [ERROR] - No reads found for TRID=OPDM4_RILPL1
2025-09-15 20:23:52.568 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:52 [ERROR] - No reads found for TRID=SCA37_DAB1
2025-09-15 20:23:52.568 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:52 [ERROR] - No reads found for TRID=OPMD_PABPN1
2025-09-15 20:23:52.568 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:52 [ERROR] - No reads found for TRID=SCA27B_FGF14
2025-09-15 20:23:52.569 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:52 [ERROR] - No reads found for TRID=SCA8_ATXN8OS
2025-09-15 20:23:52.569 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:52 [ERROR] - No reads found for TRID=SCA4_ZFHX3
2025-09-15 20:23:52.569 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:52 [ERROR] - No reads found for TRID=HDL2_JPH3
2025-09-15 20:23:52.569 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:52 [ERROR] - No reads found for TRID=SCA31_BEAN1
2025-09-15 20:23:52.569 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:52 [ERROR] - No reads found for TRID=SCA6_CACNA1A
2025-09-15 20:23:52.569 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:52 [ERROR] - No reads found for TRID=DM1_DMPK
2025-09-15 20:23:52.578 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO srun: job 51797493 queued and waiting for resources
2025-09-15 20:23:52.578 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO srun: job 51797493 has been allocated resources
2025-09-15 20:23:52.578 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:52.646 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_plot_motifs_allele NOTICE done
2025-09-15 20:23:52.651 wdl.w:ptcp.w:call-trgt-07 NOTICE finish :: job: "call-trgt_plot_motifs_allele"
2025-09-15 20:23:52.651 wdl.w:ptcp.w:call-trgt-07 INFO output :: job: "call-trgt_plot_motifs_allele", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-07/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2104.motifs_allele.trgt_plots.zip"}
2025-09-15 20:23:52.651 wdl.w:ptcp.w:call-trgt-07 INFO visit :: node: "output-images_motifs_allele", values: {"images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-07/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2104.motifs_allele.trgt_plots.zip"}
2025-09-15 20:23:52.655 wdl.w:ptcp.w:call-trgt-20.t:call-trgt_plot_motifs_waterfall NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-20/call-trgt_plot_motifs_waterfall", thread: 140610367379008
2025-09-15 20:23:52.678 wdl.w:ptcp.w:call-trgt-20.t:call-trgt_plot_motifs_waterfall INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:23:52.678 wdl.w:ptcp.w:call-trgt-20.t:call-trgt_plot_motifs_waterfall INFO input :: name: "waterfall", value: true
2025-09-15 20:23:52.678 wdl.w:ptcp.w:call-trgt-20.t:call-trgt_plot_motifs_waterfall INFO input :: name: "methylation", value: false
2025-09-15 20:23:52.678 wdl.w:ptcp.w:call-trgt-20.t:call-trgt_plot_motifs_waterfall INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:23:52.678 wdl.w:ptcp.w:call-trgt-20.t:call-trgt_plot_motifs_waterfall INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:23:52.678 wdl.w:ptcp.w:call-trgt-20.t:call-trgt_plot_motifs_waterfall INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:23:52.678 wdl.w:ptcp.w:call-trgt-20.t:call-trgt_plot_motifs_waterfall INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2117.trgt.sorted.spanning.bam.bai"
2025-09-15 20:23:52.678 wdl.w:ptcp.w:call-trgt-20.t:call-trgt_plot_motifs_waterfall INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2117.trgt.sorted.spanning.bam"
2025-09-15 20:23:52.678 wdl.w:ptcp.w:call-trgt-20.t:call-trgt_plot_motifs_waterfall INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2117.trgt.vcf"
2025-09-15 20:23:52.678 wdl.w:ptcp.w:call-trgt-20.t:call-trgt_plot_motifs_waterfall INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2117"
2025-09-15 20:23:52.678 wdl.w:ptcp.w:call-trgt-20.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:23:52.678 wdl.w:ptcp.w:call-trgt-20.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "plot_type", value: "waterfall"
2025-09-15 20:23:52.679 wdl.w:ptcp.w:call-trgt-20.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "show", value: "motifs"
2025-09-15 20:23:52.679 wdl.w:ptcp.w:call-trgt-20.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "threads", value: 1
2025-09-15 20:23:52.679 wdl.w:ptcp.w:call-trgt-20.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "disk_size", value: 27
2025-09-15 20:23:52.679 wdl.w:ptcp.w:call-trgt-20.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2117.motifs_waterfall"
2025-09-15 20:23:52.679 wdl.w:ptcp.w:call-trgt-20.t:call-trgt_plot_motifs_waterfall INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:23:52.679 wdl.w:ptcp.w:call-trgt-20.t:call-trgt_plot_motifs_waterfall WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:23:52.680 wdl.w:ptcp.w:call-trgt-20.t:call-trgt_plot_motifs_waterfall INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:23:52.680 wdl.w:ptcp.w:call-trgt-20.t:call-trgt_plot_motifs_waterfall INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:23:52.702 wdl.w:ptcp.w:call-paraphase-00.t:call-run_paraphase.stderr VERBOSE INFO:root:Processing sample m84036_250809_035451_s4.bc2097 at 2025-09-15 20:23:49.373727...
2025-09-15 20:23:52.703 wdl.w:ptcp.w:call-paraphase-00.t:call-run_paraphase.stderr VERBOSE INFO:root:Checking sample sex at 2025-09-15 20:23:49.376369...
2025-09-15 20:23:52.703 wdl.w:ptcp.w:call-paraphase-00.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for gba for sample m84036_250809_035451_s4.bc2097 at 2025-09-15 20:23:49.429056...
2025-09-15 20:23:52.703 wdl.w:ptcp.w:call-paraphase-00.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for gba for sample m84036_250809_035451_s4.bc2097 at 2025-09-15 20:23:49.429436...
2025-09-15 20:23:52.703 wdl.w:ptcp.w:call-paraphase-00.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for cyp21 for sample m84036_250809_035451_s4.bc2097 at 2025-09-15 20:23:49.429012...
2025-09-15 20:23:52.703 wdl.w:ptcp.w:call-paraphase-00.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for smn1 for sample m84036_250809_035451_s4.bc2097 at 2025-09-15 20:23:49.429125...
2025-09-15 20:23:52.703 wdl.w:ptcp.w:call-paraphase-00.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for cyp21 for sample m84036_250809_035451_s4.bc2097 at 2025-09-15 20:23:49.429498...
2025-09-15 20:23:52.703 wdl.w:ptcp.w:call-paraphase-00.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for smn1 for sample m84036_250809_035451_s4.bc2097 at 2025-09-15 20:23:49.429561...
2025-09-15 20:23:52.703 wdl.w:ptcp.w:call-paraphase-00.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for hba for sample m84036_250809_035451_s4.bc2097 at 2025-09-15 20:23:49.430334...
2025-09-15 20:23:52.703 wdl.w:ptcp.w:call-paraphase-00.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for hba for sample m84036_250809_035451_s4.bc2097 at 2025-09-15 20:23:49.430668...
2025-09-15 20:23:52.704 wdl.w:ptcp.w:call-paraphase-00.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for gba for sample m84036_250809_035451_s4.bc2097 at 2025-09-15 20:23:50.031934...
2025-09-15 20:23:52.704 wdl.w:ptcp.w:call-paraphase-00.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for cyp21 for sample m84036_250809_035451_s4.bc2097 at 2025-09-15 20:23:50.049276...
2025-09-15 20:23:52.704 wdl.w:ptcp.w:call-paraphase-00.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for smn1 for sample m84036_250809_035451_s4.bc2097 at 2025-09-15 20:23:50.104608...
2025-09-15 20:23:52.704 wdl.w:ptcp.w:call-paraphase-00.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for hba for sample m84036_250809_035451_s4.bc2097 at 2025-09-15 20:23:50.125849...
2025-09-15 20:23:52.704 wdl.w:ptcp.w:call-paraphase-00.t:call-run_paraphase.stderr VERBOSE WARNING:root:This region does not appear to have coverage. Will not attempt to phase haplotypes.
2025-09-15 20:23:52.704 wdl.w:ptcp.w:call-paraphase-00.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for cyp21 for sample m84036_250809_035451_s4.bc2097 at 2025-09-15 20:23:50.130915...
2025-09-15 20:23:52.704 wdl.w:ptcp.w:call-paraphase-00.t:call-run_paraphase.stderr VERBOSE WARNING:root:This region does not appear to have coverage. Will not attempt to phase haplotypes.
2025-09-15 20:23:52.704 wdl.w:ptcp.w:call-paraphase-00.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for gba for sample m84036_250809_035451_s4.bc2097 at 2025-09-15 20:23:50.142907...
2025-09-15 20:23:52.704 wdl.w:ptcp.w:call-paraphase-00.t:call-run_paraphase.stderr VERBOSE WARNING:root:This region does not appear to have coverage. Will not attempt to phase haplotypes.
2025-09-15 20:23:52.704 wdl.w:ptcp.w:call-paraphase-00.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for hba for sample m84036_250809_035451_s4.bc2097 at 2025-09-15 20:23:50.198680...
2025-09-15 20:23:52.704 wdl.w:ptcp.w:call-paraphase-00.t:call-run_paraphase.stderr VERBOSE WARNING:root:This region does not appear to have coverage. Will not attempt to phase haplotypes.
2025-09-15 20:23:52.704 wdl.w:ptcp.w:call-paraphase-00.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for smn1 for sample m84036_250809_035451_s4.bc2097 at 2025-09-15 20:23:50.276384...
2025-09-15 20:23:52.704 wdl.w:ptcp.w:call-paraphase-00.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for cyp21 for sample m84036_250809_035451_s4.bc2097 at 2025-09-15 20:23:50.599315...
2025-09-15 20:23:52.704 wdl.w:ptcp.w:call-paraphase-00.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for f8inv22 for sample m84036_250809_035451_s4.bc2097 at 2025-09-15 20:23:50.607186...
2025-09-15 20:23:52.704 wdl.w:ptcp.w:call-paraphase-00.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for f8inv22 for sample m84036_250809_035451_s4.bc2097 at 2025-09-15 20:23:50.607296...
2025-09-15 20:23:52.704 wdl.w:ptcp.w:call-paraphase-00.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for gba for sample m84036_250809_035451_s4.bc2097 at 2025-09-15 20:23:50.719532...
2025-09-15 20:23:52.704 wdl.w:ptcp.w:call-paraphase-00.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for rpgr for sample m84036_250809_035451_s4.bc2097 at 2025-09-15 20:23:50.724571...
2025-09-15 20:23:52.704 wdl.w:ptcp.w:call-paraphase-00.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for rpgr for sample m84036_250809_035451_s4.bc2097 at 2025-09-15 20:23:50.724652...
2025-09-15 20:23:52.704 wdl.w:ptcp.w:call-paraphase-00.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for hba for sample m84036_250809_035451_s4.bc2097 at 2025-09-15 20:23:50.748517...
2025-09-15 20:23:52.705 wdl.w:ptcp.w:call-paraphase-00.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for hbb for sample m84036_250809_035451_s4.bc2097 at 2025-09-15 20:23:50.756215...
2025-09-15 20:23:52.705 wdl.w:ptcp.w:call-paraphase-00.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for hbb for sample m84036_250809_035451_s4.bc2097 at 2025-09-15 20:23:50.756323...
2025-09-15 20:23:52.705 wdl.w:ptcp.w:call-paraphase-00.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning to gene2 region for smn1 for sample m84036_250809_035451_s4.bc2097 at 2025-09-15 20:23:50.787378...
2025-09-15 20:23:52.705 wdl.w:ptcp.w:call-paraphase-00.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for f8inv22 for sample m84036_250809_035451_s4.bc2097 at 2025-09-15 20:23:51.079888...
2025-09-15 20:23:52.705 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_motifs_allele.slurm_singularity INFO srun: job 51797494 queued and waiting for resources
2025-09-15 20:23:52.705 wdl.w:ptcp.w:call-paraphase-00.t:call-run_paraphase.stderr VERBOSE WARNING:root:This region does not appear to have coverage. Will not attempt to phase haplotypes.
2025-09-15 20:23:52.705 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_motifs_allele.slurm_singularity INFO srun: job 51797494 has been allocated resources
2025-09-15 20:23:52.705 wdl.w:ptcp.w:call-paraphase-00.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for f8inv22 for sample m84036_250809_035451_s4.bc2097 at 2025-09-15 20:23:51.158287...
2025-09-15 20:23:52.705 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_motifs_allele.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:52.705 wdl.w:ptcp.w:call-paraphase-00.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for rpgr for sample m84036_250809_035451_s4.bc2097 at 2025-09-15 20:23:51.228213...
2025-09-15 20:23:52.706 wdl.w:ptcp.w:call-paraphase-00.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for hbb for sample m84036_250809_035451_s4.bc2097 at 2025-09-15 20:23:51.253983...
2025-09-15 20:23:52.706 wdl.w:ptcp.w:call-paraphase-00.t:call-run_paraphase.stderr VERBOSE WARNING:root:This region does not appear to have coverage. Will not attempt to phase haplotypes.
2025-09-15 20:23:52.706 wdl.w:ptcp.w:call-paraphase-00.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for rpgr for sample m84036_250809_035451_s4.bc2097 at 2025-09-15 20:23:51.304146...
2025-09-15 20:23:52.706 wdl.w:ptcp.w:call-paraphase-00.t:call-run_paraphase.stderr VERBOSE WARNING:root:This region does not appear to have coverage. Will not attempt to phase haplotypes.
2025-09-15 20:23:52.706 wdl.w:ptcp.w:call-paraphase-00.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for hbb for sample m84036_250809_035451_s4.bc2097 at 2025-09-15 20:23:51.316099...
2025-09-15 20:23:52.706 wdl.w:ptcp.w:call-paraphase-00.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for f8inv22 for sample m84036_250809_035451_s4.bc2097 at 2025-09-15 20:23:51.596756...
2025-09-15 20:23:52.706 wdl.w:ptcp.w:call-paraphase-00.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for rpgr for sample m84036_250809_035451_s4.bc2097 at 2025-09-15 20:23:51.697516...
2025-09-15 20:23:52.706 wdl.w:ptcp.w:call-paraphase-00.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for hbb for sample m84036_250809_035451_s4.bc2097 at 2025-09-15 20:23:51.733298...
2025-09-15 20:23:52.706 wdl.w:ptcp.w:call-paraphase-00.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for smn1 for sample m84036_250809_035451_s4.bc2097 at 2025-09-15 20:23:51.788533...
2025-09-15 20:23:52.706 wdl.w:ptcp.w:call-paraphase-00.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for f8inv1 for sample m84036_250809_035451_s4.bc2097 at 2025-09-15 20:23:51.847498...
2025-09-15 20:23:52.706 wdl.w:ptcp.w:call-paraphase-00.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for f8inv1 for sample m84036_250809_035451_s4.bc2097 at 2025-09-15 20:23:51.847647...
2025-09-15 20:23:52.706 wdl.w:ptcp.w:call-paraphase-00.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for f8inv1 for sample m84036_250809_035451_s4.bc2097 at 2025-09-15 20:23:52.206178...
2025-09-15 20:23:52.706 wdl.w:ptcp.w:call-paraphase-00.t:call-run_paraphase.stderr VERBOSE WARNING:root:This region does not appear to have coverage. Will not attempt to phase haplotypes.
2025-09-15 20:23:52.706 wdl.w:ptcp.w:call-paraphase-00.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for f8inv1 for sample m84036_250809_035451_s4.bc2097 at 2025-09-15 20:23:52.237613...
2025-09-15 20:23:52.706 wdl.w:ptcp.w:call-paraphase-00.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for f8inv1 for sample m84036_250809_035451_s4.bc2097 at 2025-09-15 20:23:52.561860...
2025-09-15 20:23:52.746 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_plot_meth_waterfall INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2104.meth_waterfall.trgt_plots.zip"
2025-09-15 20:23:52.774 wdl.w:ptcp.w:call-trgt-20.t:call-trgt_plot_motifs_waterfall INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-20/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_4fd93r8f"
2025-09-15 20:23:52.774 wdl.w:ptcp.w:call-trgt-20.t:call-trgt_plot_motifs_waterfall INFO Slurm invocation: srun --job-name call-trgt_plot_motifs_waterfall --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-20/call-trgt_plot_motifs_waterfall/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-20/call-trgt_plot_motifs_waterfall/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-20/call-trgt_plot_motifs_waterfall/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-20/call-trgt_plot_motifs_waterfall/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-20/call-trgt_genotype/out/m84036_250809_035451_s4.bc2117.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2117.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-20/call-trgt_genotype/out/m84036_250809_035451_s4.bc2117.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2117.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-20/call-trgt_genotype/out/m84036_250809_035451_s4.bc2117.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2117.trgt.sorted.spanning.bam:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-20/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_4fd93r8f/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-20/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_4fd93r8f/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:23:52.804 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO srun: job 51797495 queued and waiting for resources
2025-09-15 20:23:52.804 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO srun: job 51797495 has been allocated resources
2025-09-15 20:23:52.805 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:52.806 wdl.w:ptcp.w:call-trgt-20.t:call-trgt_plot_motifs_waterfall NOTICE slurm_singularity run :: pid: 1200417, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-20/call-trgt_plot_motifs_waterfall/slurm_singularity.log.txt"
2025-09-15 20:23:52.844 wdl.w:ptcp.w:call-trgt-07.t:call-trgt_plot_meth_waterfall NOTICE done
2025-09-15 20:23:52.849 wdl.w:ptcp.w:call-trgt-07 NOTICE finish :: job: "call-trgt_plot_meth_waterfall"
2025-09-15 20:23:52.849 wdl.w:ptcp.w:call-trgt-07 INFO output :: job: "call-trgt_plot_meth_waterfall", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-07/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2104.meth_waterfall.trgt_plots.zip"}
2025-09-15 20:23:52.849 wdl.w:ptcp.w:call-trgt-07 INFO visit :: node: "output-images_meth_waterfall", values: {"images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-07/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2104.meth_waterfall.trgt_plots.zip"}
2025-09-15 20:23:52.849 wdl.w:ptcp.w:call-trgt-07 INFO visit :: node: "outputs", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-07/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2104.motifs_waterfall.trgt_plots.zip", "images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-07/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2104.meth_allele.trgt_plots.zip", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-07/call-trgt_genotype/out/m84036_250809_035451_s4.bc2104.trgt.sorted.spanning.bam.bai", "images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-07/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2104.motifs_allele.trgt_plots.zip", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-07/call-trgt_genotype/out/m84036_250809_035451_s4.bc2104.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-07/call-trgt_genotype/out/m84036_250809_035451_s4.bc2104.trgt.vcf", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-07/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2104.repeats.bam", "images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-07/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2104.meth_waterfall.trgt_plots.zip", "reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-07/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2104.repeats.bam.bai"}
2025-09-15 20:23:52.856 wdl.w:ptcp.w:call-trgt-04.t:call-trgt_plot_meth_allele NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-04/call-trgt_plot_meth_allele", thread: 140610358986304
2025-09-15 20:23:52.881 wdl.w:ptcp.w:call-trgt-04.t:call-trgt_plot_meth_allele INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:23:52.881 wdl.w:ptcp.w:call-trgt-04.t:call-trgt_plot_meth_allele INFO input :: name: "waterfall", value: false
2025-09-15 20:23:52.881 wdl.w:ptcp.w:call-trgt-04.t:call-trgt_plot_meth_allele INFO input :: name: "methylation", value: true
2025-09-15 20:23:52.881 wdl.w:ptcp.w:call-trgt-04.t:call-trgt_plot_meth_allele INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:23:52.881 wdl.w:ptcp.w:call-trgt-04.t:call-trgt_plot_meth_allele INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:23:52.881 wdl.w:ptcp.w:call-trgt-04.t:call-trgt_plot_meth_allele INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:23:52.881 wdl.w:ptcp.w:call-trgt-04.t:call-trgt_plot_meth_allele INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2101.trgt.sorted.spanning.bam.bai"
2025-09-15 20:23:52.881 wdl.w:ptcp.w:call-trgt-04.t:call-trgt_plot_meth_allele INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2101.trgt.sorted.spanning.bam"
2025-09-15 20:23:52.881 wdl.w:ptcp.w:call-trgt-04.t:call-trgt_plot_meth_allele INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2101.trgt.vcf"
2025-09-15 20:23:52.882 wdl.w:ptcp.w:call-trgt-04.t:call-trgt_plot_meth_allele INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2101"
2025-09-15 20:23:52.882 wdl.w:ptcp.w:call-trgt-04.t:call-trgt_plot_meth_allele INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:23:52.882 wdl.w:ptcp.w:call-trgt-04.t:call-trgt_plot_meth_allele INFO eval :: name: "plot_type", value: "allele"
2025-09-15 20:23:52.882 wdl.w:ptcp.w:call-trgt-04.t:call-trgt_plot_meth_allele INFO eval :: name: "show", value: "meth"
2025-09-15 20:23:52.882 wdl.w:ptcp.w:call-trgt-04.t:call-trgt_plot_meth_allele INFO eval :: name: "threads", value: 1
2025-09-15 20:23:52.882 wdl.w:ptcp.w:call-trgt-04.t:call-trgt_plot_meth_allele INFO eval :: name: "disk_size", value: 27
2025-09-15 20:23:52.882 wdl.w:ptcp.w:call-trgt-04.t:call-trgt_plot_meth_allele INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2101.meth_allele"
2025-09-15 20:23:52.883 wdl.w:ptcp.w:call-trgt-04.t:call-trgt_plot_meth_allele INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:23:52.883 wdl.w:ptcp.w:call-trgt-04.t:call-trgt_plot_meth_allele WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:23:52.883 wdl.w:ptcp.w:call-trgt-04.t:call-trgt_plot_meth_allele INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:23:52.883 wdl.w:ptcp.w:call-trgt-04.t:call-trgt_plot_meth_allele INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:23:52.946 wdl.w:ptcp.w:call-trgt-20.t:call-trgt_plot_meth_allele.slurm_singularity INFO srun: job 51797496 queued and waiting for resources
2025-09-15 20:23:52.946 wdl.w:ptcp.w:call-trgt-20.t:call-trgt_plot_meth_allele.slurm_singularity INFO srun: job 51797496 has been allocated resources
2025-09-15 20:23:52.946 wdl.w:ptcp.w:call-trgt-20.t:call-trgt_plot_meth_allele.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:52.954 wdl.w:ptcp.w:call-trgt-07 NOTICE done
2025-09-15 20:23:52.961 wdl.w:ptcp NOTICE finish :: job: "call-trgt-07"
2025-09-15 20:23:52.961 wdl.w:ptcp INFO output :: job: "call-trgt-07", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-07/out/m84036_250809_035451_s4.bc2104.motifs_waterfall.trgt_plots.zip", "images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-07/out/m84036_250809_035451_s4.bc2104.meth_allele.trgt_plots.zip", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-07/out/m84036_250809_035451_s4.bc2104.trgt.sorted.spanning.bam.bai", "images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-07/out/m84036_250809_035451_s4.bc2104.motifs_allele.trgt_plots.zip", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-07/out/m84036_250809_035451_s4.bc2104.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-07/out/m84036_250809_035451_s4.bc2104.trgt.vcf", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-07/out/m84036_250809_035451_s4.bc2104.repeats.bam", "images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-07/out/m84036_250809_035451_s4.bc2104.meth_waterfall.trgt_plots.zip", "reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-07/out/m84036_250809_035451_s4.bc2104.repeats.bam.bai"}
2025-09-15 20:23:52.967 wdl.w:ptcp.w:call-trgt-04.t:call-trgt_plot_meth_allele INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-04/call-trgt_plot_meth_allele/_singularity_tmpdir_h5emzkj7"
2025-09-15 20:23:52.967 wdl.w:ptcp.w:call-trgt-04.t:call-trgt_plot_meth_allele INFO Slurm invocation: srun --job-name call-trgt_plot_meth_allele --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-04/call-trgt_plot_meth_allele/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-04/call-trgt_plot_meth_allele/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-04/call-trgt_plot_meth_allele/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-04/call-trgt_plot_meth_allele/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-04/call-trgt_genotype/out/m84036_250809_035451_s4.bc2101.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2101.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-04/call-trgt_genotype/out/m84036_250809_035451_s4.bc2101.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2101.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-04/call-trgt_genotype/out/m84036_250809_035451_s4.bc2101.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2101.trgt.sorted.spanning.bam.bai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-04/call-trgt_plot_meth_allele/_singularity_tmpdir_h5emzkj7/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-04/call-trgt_plot_meth_allele/_singularity_tmpdir_h5emzkj7/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:23:52.968 wdl.w:ptcp.w:call-trgt-52 NOTICE workflow start :: name: "trgt", source: "./trgt.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-52"
2025-09-15 20:23:52.988 wdl.w:ptcp.w:call-trgt-52 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:23:52.988 wdl.w:ptcp.w:call-trgt-52 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-52/out/m84036_250809_035451_s4.bc2149.mapped.bam"}
2025-09-15 20:23:52.988 wdl.w:ptcp.w:call-trgt-52 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-52/out/m84036_250809_035451_s4.bc2149.mapped.bam.bai"}
2025-09-15 20:23:52.988 wdl.w:ptcp.w:call-trgt-52 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:23:52.988 wdl.w:ptcp.w:call-trgt-52 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:23:52.988 wdl.w:ptcp.w:call-trgt-52 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2149"}
2025-09-15 20:23:52.988 wdl.w:ptcp.w:call-trgt-52 INFO visit :: node: "decl-sex", values: {"sex": "F"}
2025-09-15 20:23:52.988 wdl.w:ptcp.w:call-trgt-52 INFO visit :: node: "decl-trgt_bed", values: {"trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"}
2025-09-15 20:23:52.988 wdl.w:ptcp.w:call-trgt-52 NOTICE ready :: job: "call-get_reads_overlapping_repeats", callee: "get_reads_overlapping_repeats"
2025-09-15 20:23:52.989 wdl.w:ptcp.w:call-trgt-52 INFO input :: job: "call-get_reads_overlapping_repeats", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-52/out/m84036_250809_035451_s4.bc2149.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-52/out/m84036_250809_035451_s4.bc2149.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2149"}
2025-09-15 20:23:52.989 wdl.w:ptcp.w:call-trgt-52 NOTICE ready :: job: "call-trgt_genotype", callee: "trgt_genotype"
2025-09-15 20:23:52.989 wdl.w:ptcp.w:call-trgt-52 INFO input :: job: "call-trgt_genotype", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-52/out/m84036_250809_035451_s4.bc2149.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-52/out/m84036_250809_035451_s4.bc2149.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2149"}
2025-09-15 20:23:52.991 wdl.w:ptcp.w:call-trgt-04.t:call-trgt_plot_meth_allele NOTICE slurm_singularity run :: pid: 1200419, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-04/call-trgt_plot_meth_allele/slurm_singularity.log.txt"
2025-09-15 20:23:53.002 wdl.w:ptcp.w:call-trgt-20.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO srun: job 51797497 queued and waiting for resources
2025-09-15 20:23:53.002 wdl.w:ptcp.w:call-trgt-20.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO srun: job 51797497 has been allocated resources
2025-09-15 20:23:53.002 wdl.w:ptcp.w:call-trgt-20.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:53.172 wdl.w:ptcp.w:call-trgt-20.t:call-trgt_plot_motifs_allele.slurm_singularity INFO srun: job 51797498 queued and waiting for resources
2025-09-15 20:23:53.172 wdl.w:ptcp.w:call-trgt-20.t:call-trgt_plot_motifs_allele.slurm_singularity INFO srun: job 51797498 has been allocated resources
2025-09-15 20:23:53.172 wdl.w:ptcp.w:call-trgt-20.t:call-trgt_plot_motifs_allele.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:53.202 wdl.w:ptcp.w:call-paraphase-11.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for smn1 for sample m84036_250809_035451_s4.bc2108 at 2025-09-15 20:23:37.097956...
2025-09-15 20:23:53.202 wdl.w:ptcp.w:call-paraphase-11.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for hba for sample m84036_250809_035451_s4.bc2108 at 2025-09-15 20:23:38.347076...
2025-09-15 20:23:53.202 wdl.w:ptcp.w:call-paraphase-11.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for gba for sample m84036_250809_035451_s4.bc2108 at 2025-09-15 20:23:38.479704...
2025-09-15 20:23:53.202 wdl.w:ptcp.w:call-paraphase-11.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for cyp21 for sample m84036_250809_035451_s4.bc2108 at 2025-09-15 20:23:39.087286...
2025-09-15 20:23:53.202 wdl.w:ptcp.w:call-paraphase-11.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for smn1 for sample m84036_250809_035451_s4.bc2108 at 2025-09-15 20:23:51.464580...
2025-09-15 20:23:53.202 wdl.w:ptcp.w:call-paraphase-11.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning to gene2 region for smn1 for sample m84036_250809_035451_s4.bc2108 at 2025-09-15 20:23:51.713109...
2025-09-15 20:23:53.317 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:50 [ERROR] - No reads found for TRID=SCA27B_FGF14
2025-09-15 20:23:53.317 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:50 [ERROR] - No reads found for TRID=OPDM_ABCD3
2025-09-15 20:23:53.317 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:50 [ERROR] - No reads found for TRID=SCA31_BEAN1
2025-09-15 20:23:53.317 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:50 [ERROR] - No reads found for TRID=SCA3_ATXN3
2025-09-15 20:23:53.318 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:50 [ERROR] - No reads found for TRID=HDL2_JPH3
2025-09-15 20:23:53.318 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:50 [ERROR] - No reads found for TRID=SCA8_ATXN8OS
2025-09-15 20:23:53.318 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:50 [ERROR] - No reads found for TRID=OPDM2_GIPC1
2025-09-15 20:23:53.318 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:50 [ERROR] - No reads found for TRID=SCA6_CACNA1A
2025-09-15 20:23:53.318 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:50 [ERROR] - No reads found for TRID=SCA2_ATXN2
2025-09-15 20:23:53.318 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:50 [ERROR] - No reads found for TRID=SCA4_ZFHX3
2025-09-15 20:23:53.318 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:50 [ERROR] - No reads found for TRID=SCA36_NOP56
2025-09-15 20:23:53.318 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:50 [ERROR] - No reads found for TRID=CJD_PRNP
2025-09-15 20:23:53.318 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:50 [ERROR] - No reads found for TRID=SD5_HOXD13
2025-09-15 20:23:53.318 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:50 [ERROR] - No reads found for TRID=DM1_DMPK
2025-09-15 20:23:53.318 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:51 [ERROR] - No reads found for TRID=FRA2A_AFF3
2025-09-15 20:23:53.318 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:51 [ERROR] - No reads found for TRID=EPM1_CSTB
2025-09-15 20:23:53.318 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:51 [ERROR] - No reads found for TRID=SCA7_ATXN7
2025-09-15 20:23:53.318 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:51 [ERROR] - No reads found for TRID=HD_HTT
2025-09-15 20:23:53.318 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:51 [ERROR] - No reads found for TRID=SCA12_PPP2R2B
2025-09-15 20:23:53.318 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:51 [ERROR] - No reads found for TRID=SCA1_ATXN1
2025-09-15 20:23:53.318 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:51 [ERROR] - No reads found for TRID=OPDM1_LRP12
2025-09-15 20:23:53.318 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:51 [ERROR] - No reads found for TRID=FAME1_SAMD12
2025-09-15 20:23:53.318 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:51 [ERROR] - No reads found for TRID=FTDALS1_C9orf72
2025-09-15 20:23:53.772 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:50 [ERROR] - No reads found for TRID=SCA3_ATXN3
2025-09-15 20:23:53.773 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:50 [ERROR] - No reads found for TRID=HDL2_JPH3
2025-09-15 20:23:53.773 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:50 [ERROR] - No reads found for TRID=SCA8_ATXN8OS
2025-09-15 20:23:53.773 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:50 [ERROR] - No reads found for TRID=OPDM2_GIPC1
2025-09-15 20:23:53.773 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:51 [ERROR] - No reads found for TRID=SCA6_CACNA1A
2025-09-15 20:23:53.773 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:51 [ERROR] - No reads found for TRID=SCA2_ATXN2
2025-09-15 20:23:53.773 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:51 [ERROR] - No reads found for TRID=SCA4_ZFHX3
2025-09-15 20:23:53.773 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:51 [ERROR] - No reads found for TRID=SCA36_NOP56
2025-09-15 20:23:53.773 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:51 [ERROR] - No reads found for TRID=CJD_PRNP
2025-09-15 20:23:53.773 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:51 [ERROR] - No reads found for TRID=SD5_HOXD13
2025-09-15 20:23:53.773 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:51 [ERROR] - No reads found for TRID=DM1_DMPK
2025-09-15 20:23:53.773 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:51 [ERROR] - No reads found for TRID=FRA2A_AFF3
2025-09-15 20:23:53.773 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:51 [ERROR] - No reads found for TRID=EPM1_CSTB
2025-09-15 20:23:53.774 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:51 [ERROR] - No reads found for TRID=SCA7_ATXN7
2025-09-15 20:23:53.774 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:51 [ERROR] - No reads found for TRID=HD_HTT
2025-09-15 20:23:53.774 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:52 [ERROR] - No reads found for TRID=SCA12_PPP2R2B
2025-09-15 20:23:53.774 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:52 [ERROR] - No reads found for TRID=SCA1_ATXN1
2025-09-15 20:23:53.774 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:52 [ERROR] - No reads found for TRID=OPDM1_LRP12
2025-09-15 20:23:53.774 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:52 [ERROR] - No reads found for TRID=FAME1_SAMD12
2025-09-15 20:23:53.774 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:52 [ERROR] - No reads found for TRID=FTDALS1_C9orf72
2025-09-15 20:23:53.826 wdl.w:ptcp.w:call-trgt-20.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO srun: job 51797499 queued and waiting for resources
2025-09-15 20:23:53.826 wdl.w:ptcp.w:call-trgt-20.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO srun: job 51797499 has been allocated resources
2025-09-15 20:23:53.826 wdl.w:ptcp.w:call-trgt-20.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:53.989 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_meth_waterfall INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2131.meth_waterfall.trgt_plots.zip"
2025-09-15 20:23:54.005 wdl.w:ptcp.w:call-trgt-04.t:call-trgt_plot_meth_allele.slurm_singularity INFO srun: job 51797500 queued and waiting for resources
2025-09-15 20:23:54.005 wdl.w:ptcp.w:call-trgt-04.t:call-trgt_plot_meth_allele.slurm_singularity INFO srun: job 51797500 has been allocated resources
2025-09-15 20:23:54.005 wdl.w:ptcp.w:call-trgt-04.t:call-trgt_plot_meth_allele.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:54.013 wdl.w:ptcp.w:call-paraphase-30.t:call-run_paraphase.stderr VERBOSE INFO:root:Processing sample m84036_250809_035451_s4.bc2127 at 2025-09-15 20:23:42.349777...
2025-09-15 20:23:54.015 wdl.w:ptcp.w:call-paraphase-30.t:call-run_paraphase.stderr VERBOSE INFO:root:Checking sample sex at 2025-09-15 20:23:42.353927...
2025-09-15 20:23:54.015 wdl.w:ptcp.w:call-paraphase-30.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for cyp21 for sample m84036_250809_035451_s4.bc2127 at 2025-09-15 20:23:42.459458...
2025-09-15 20:23:54.015 wdl.w:ptcp.w:call-paraphase-30.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for cyp21 for sample m84036_250809_035451_s4.bc2127 at 2025-09-15 20:23:42.459921...
2025-09-15 20:23:54.015 wdl.w:ptcp.w:call-paraphase-30.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for smn1 for sample m84036_250809_035451_s4.bc2127 at 2025-09-15 20:23:42.459613...
2025-09-15 20:23:54.015 wdl.w:ptcp.w:call-paraphase-30.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for smn1 for sample m84036_250809_035451_s4.bc2127 at 2025-09-15 20:23:42.460022...
2025-09-15 20:23:54.015 wdl.w:ptcp.w:call-paraphase-30.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for gba for sample m84036_250809_035451_s4.bc2127 at 2025-09-15 20:23:42.459682...
2025-09-15 20:23:54.015 wdl.w:ptcp.w:call-paraphase-30.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for hba for sample m84036_250809_035451_s4.bc2127 at 2025-09-15 20:23:42.459726...
2025-09-15 20:23:54.015 wdl.w:ptcp.w:call-paraphase-30.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for gba for sample m84036_250809_035451_s4.bc2127 at 2025-09-15 20:23:42.460079...
2025-09-15 20:23:54.015 wdl.w:ptcp.w:call-paraphase-30.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for hba for sample m84036_250809_035451_s4.bc2127 at 2025-09-15 20:23:42.460094...
2025-09-15 20:23:54.015 wdl.w:ptcp.w:call-paraphase-30.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for smn1 for sample m84036_250809_035451_s4.bc2127 at 2025-09-15 20:23:43.842206...
2025-09-15 20:23:54.015 wdl.w:ptcp.w:call-paraphase-30.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for hba for sample m84036_250809_035451_s4.bc2127 at 2025-09-15 20:23:44.194147...
2025-09-15 20:23:54.015 wdl.w:ptcp.w:call-paraphase-30.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for gba for sample m84036_250809_035451_s4.bc2127 at 2025-09-15 20:23:44.561340...
2025-09-15 20:23:54.015 wdl.w:ptcp.w:call-paraphase-30.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for cyp21 for sample m84036_250809_035451_s4.bc2127 at 2025-09-15 20:23:45.074316...
2025-09-15 20:23:54.015 wdl.w:ptcp.w:call-paraphase-30.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for smn1 for sample m84036_250809_035451_s4.bc2127 at 2025-09-15 20:23:50.535667...
2025-09-15 20:23:54.015 wdl.w:ptcp.w:call-paraphase-30.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning to gene2 region for smn1 for sample m84036_250809_035451_s4.bc2127 at 2025-09-15 20:23:50.898377...
2025-09-15 20:23:54.087 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_meth_waterfall NOTICE done
2025-09-15 20:23:54.091 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_meth_allele INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2111.meth_allele.trgt_plots.zip"
2025-09-15 20:23:54.092 wdl.w:ptcp.w:call-trgt-34 NOTICE finish :: job: "call-trgt_plot_meth_waterfall"
2025-09-15 20:23:54.093 wdl.w:ptcp.w:call-trgt-34 INFO output :: job: "call-trgt_plot_meth_waterfall", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-34/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2131.meth_waterfall.trgt_plots.zip"}
2025-09-15 20:23:54.094 wdl.w:ptcp.w:call-trgt-34 INFO visit :: node: "output-images_meth_waterfall", values: {"images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-34/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2131.meth_waterfall.trgt_plots.zip"}
2025-09-15 20:23:54.099 wdl.w:ptcp.w:call-trgt-04.t:call-trgt_plot_meth_waterfall NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-04/call-trgt_plot_meth_waterfall", thread: 140610887464512
2025-09-15 20:23:54.119 wdl.w:ptcp.w:call-trgt-04.t:call-trgt_plot_meth_waterfall INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:23:54.119 wdl.w:ptcp.w:call-trgt-04.t:call-trgt_plot_meth_waterfall INFO input :: name: "waterfall", value: true
2025-09-15 20:23:54.119 wdl.w:ptcp.w:call-trgt-04.t:call-trgt_plot_meth_waterfall INFO input :: name: "methylation", value: true
2025-09-15 20:23:54.119 wdl.w:ptcp.w:call-trgt-04.t:call-trgt_plot_meth_waterfall INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:23:54.119 wdl.w:ptcp.w:call-trgt-04.t:call-trgt_plot_meth_waterfall INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:23:54.119 wdl.w:ptcp.w:call-trgt-04.t:call-trgt_plot_meth_waterfall INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:23:54.120 wdl.w:ptcp.w:call-trgt-04.t:call-trgt_plot_meth_waterfall INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2101.trgt.sorted.spanning.bam.bai"
2025-09-15 20:23:54.120 wdl.w:ptcp.w:call-trgt-04.t:call-trgt_plot_meth_waterfall INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2101.trgt.sorted.spanning.bam"
2025-09-15 20:23:54.120 wdl.w:ptcp.w:call-trgt-04.t:call-trgt_plot_meth_waterfall INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2101.trgt.vcf"
2025-09-15 20:23:54.120 wdl.w:ptcp.w:call-trgt-04.t:call-trgt_plot_meth_waterfall INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2101"
2025-09-15 20:23:54.120 wdl.w:ptcp.w:call-trgt-04.t:call-trgt_plot_meth_waterfall INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:23:54.120 wdl.w:ptcp.w:call-trgt-04.t:call-trgt_plot_meth_waterfall INFO eval :: name: "plot_type", value: "waterfall"
2025-09-15 20:23:54.120 wdl.w:ptcp.w:call-trgt-04.t:call-trgt_plot_meth_waterfall INFO eval :: name: "show", value: "meth"
2025-09-15 20:23:54.120 wdl.w:ptcp.w:call-trgt-04.t:call-trgt_plot_meth_waterfall INFO eval :: name: "threads", value: 1
2025-09-15 20:23:54.120 wdl.w:ptcp.w:call-trgt-04.t:call-trgt_plot_meth_waterfall INFO eval :: name: "disk_size", value: 27
2025-09-15 20:23:54.120 wdl.w:ptcp.w:call-trgt-04.t:call-trgt_plot_meth_waterfall INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2101.meth_waterfall"
2025-09-15 20:23:54.121 wdl.w:ptcp.w:call-trgt-04.t:call-trgt_plot_meth_waterfall INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:23:54.121 wdl.w:ptcp.w:call-trgt-04.t:call-trgt_plot_meth_waterfall WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:23:54.121 wdl.w:ptcp.w:call-trgt-04.t:call-trgt_plot_meth_waterfall INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:23:54.121 wdl.w:ptcp.w:call-trgt-04.t:call-trgt_plot_meth_waterfall INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:23:54.135 wdl.w:ptcp.w:call-paraphase-19.t:call-run_paraphase.stderr VERBOSE INFO:root:Processing sample m84036_250809_035451_s4.bc2116 at 2025-09-15 20:23:35.323772...
2025-09-15 20:23:54.137 wdl.w:ptcp.w:call-paraphase-19.t:call-run_paraphase.stderr VERBOSE INFO:root:Checking sample sex at 2025-09-15 20:23:35.324675...
2025-09-15 20:23:54.137 wdl.w:ptcp.w:call-paraphase-19.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for gba for sample m84036_250809_035451_s4.bc2116 at 2025-09-15 20:23:35.372967...
2025-09-15 20:23:54.137 wdl.w:ptcp.w:call-paraphase-19.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for gba for sample m84036_250809_035451_s4.bc2116 at 2025-09-15 20:23:35.373463...
2025-09-15 20:23:54.137 wdl.w:ptcp.w:call-paraphase-19.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for cyp21 for sample m84036_250809_035451_s4.bc2116 at 2025-09-15 20:23:35.372870...
2025-09-15 20:23:54.137 wdl.w:ptcp.w:call-paraphase-19.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for cyp21 for sample m84036_250809_035451_s4.bc2116 at 2025-09-15 20:23:35.373547...
2025-09-15 20:23:54.137 wdl.w:ptcp.w:call-paraphase-19.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for smn1 for sample m84036_250809_035451_s4.bc2116 at 2025-09-15 20:23:35.373106...
2025-09-15 20:23:54.137 wdl.w:ptcp.w:call-paraphase-19.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for smn1 for sample m84036_250809_035451_s4.bc2116 at 2025-09-15 20:23:35.373723...
2025-09-15 20:23:54.137 wdl.w:ptcp.w:call-paraphase-19.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for hba for sample m84036_250809_035451_s4.bc2116 at 2025-09-15 20:23:35.374727...
2025-09-15 20:23:54.137 wdl.w:ptcp.w:call-paraphase-19.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for hba for sample m84036_250809_035451_s4.bc2116 at 2025-09-15 20:23:35.375154...
2025-09-15 20:23:54.137 wdl.w:ptcp.w:call-paraphase-19.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for smn1 for sample m84036_250809_035451_s4.bc2116 at 2025-09-15 20:23:37.421518...
2025-09-15 20:23:54.138 wdl.w:ptcp.w:call-paraphase-19.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for hba for sample m84036_250809_035451_s4.bc2116 at 2025-09-15 20:23:38.166423...
2025-09-15 20:23:54.138 wdl.w:ptcp.w:call-paraphase-19.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for gba for sample m84036_250809_035451_s4.bc2116 at 2025-09-15 20:23:39.109185...
2025-09-15 20:23:54.138 wdl.w:ptcp.w:call-paraphase-19.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for cyp21 for sample m84036_250809_035451_s4.bc2116 at 2025-09-15 20:23:39.381059...
2025-09-15 20:23:54.138 wdl.w:ptcp.w:call-paraphase-19.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for smn1 for sample m84036_250809_035451_s4.bc2116 at 2025-09-15 20:23:52.104396...
2025-09-15 20:23:54.138 wdl.w:ptcp.w:call-paraphase-19.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning to gene2 region for smn1 for sample m84036_250809_035451_s4.bc2116 at 2025-09-15 20:23:52.370860...
2025-09-15 20:23:54.148 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_motifs_waterfall INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2131.motifs_waterfall.trgt_plots.zip"
2025-09-15 20:23:54.157 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_meth_allele INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2120.meth_allele.trgt_plots.zip"
2025-09-15 20:23:54.189 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_meth_allele NOTICE done
2025-09-15 20:23:54.194 wdl.w:ptcp.w:call-trgt-14 NOTICE finish :: job: "call-trgt_plot_meth_allele"
2025-09-15 20:23:54.194 wdl.w:ptcp.w:call-trgt-14 INFO output :: job: "call-trgt_plot_meth_allele", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-14/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2111.meth_allele.trgt_plots.zip"}
2025-09-15 20:23:54.194 wdl.w:ptcp.w:call-trgt-14 INFO visit :: node: "output-images_meth_allele", values: {"images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-14/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2111.meth_allele.trgt_plots.zip"}
2025-09-15 20:23:54.204 wdl.w:ptcp.w:call-trgt-04.t:call-trgt_plot_motifs_allele NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-04/call-trgt_plot_motifs_allele", thread: 140609310422592
2025-09-15 20:23:54.221 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_meth_waterfall INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2111.meth_waterfall.trgt_plots.zip"
2025-09-15 20:23:54.228 wdl.w:ptcp.w:call-trgt-04.t:call-trgt_plot_meth_waterfall INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-04/call-trgt_plot_meth_waterfall/_singularity_tmpdir_w_onrx61"
2025-09-15 20:23:54.228 wdl.w:ptcp.w:call-trgt-04.t:call-trgt_plot_meth_waterfall INFO Slurm invocation: srun --job-name call-trgt_plot_meth_waterfall --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-04/call-trgt_plot_meth_waterfall/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-04/call-trgt_plot_meth_waterfall/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-04/call-trgt_plot_meth_waterfall/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-04/call-trgt_plot_meth_waterfall/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-04/call-trgt_genotype/out/m84036_250809_035451_s4.bc2101.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2101.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-04/call-trgt_genotype/out/m84036_250809_035451_s4.bc2101.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2101.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-04/call-trgt_genotype/out/m84036_250809_035451_s4.bc2101.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2101.trgt.sorted.spanning.bam.bai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-04/call-trgt_plot_meth_waterfall/_singularity_tmpdir_w_onrx61/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-04/call-trgt_plot_meth_waterfall/_singularity_tmpdir_w_onrx61/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:23:54.230 wdl.w:ptcp.w:call-trgt-04.t:call-trgt_plot_motifs_allele INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:23:54.230 wdl.w:ptcp.w:call-trgt-04.t:call-trgt_plot_motifs_allele INFO input :: name: "waterfall", value: false
2025-09-15 20:23:54.232 wdl.w:ptcp.w:call-trgt-04.t:call-trgt_plot_motifs_allele INFO input :: name: "methylation", value: false
2025-09-15 20:23:54.234 wdl.w:ptcp.w:call-trgt-04.t:call-trgt_plot_motifs_allele INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:23:54.234 wdl.w:ptcp.w:call-trgt-04.t:call-trgt_plot_motifs_allele INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:23:54.234 wdl.w:ptcp.w:call-trgt-04.t:call-trgt_plot_motifs_allele INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:23:54.234 wdl.w:ptcp.w:call-trgt-04.t:call-trgt_plot_motifs_allele INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2101.trgt.sorted.spanning.bam.bai"
2025-09-15 20:23:54.234 wdl.w:ptcp.w:call-trgt-04.t:call-trgt_plot_motifs_allele INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2101.trgt.sorted.spanning.bam"
2025-09-15 20:23:54.234 wdl.w:ptcp.w:call-trgt-04.t:call-trgt_plot_motifs_allele INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2101.trgt.vcf"
2025-09-15 20:23:54.234 wdl.w:ptcp.w:call-trgt-04.t:call-trgt_plot_motifs_allele INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2101"
2025-09-15 20:23:54.234 wdl.w:ptcp.w:call-trgt-04.t:call-trgt_plot_motifs_allele INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:23:54.234 wdl.w:ptcp.w:call-trgt-04.t:call-trgt_plot_motifs_allele INFO eval :: name: "plot_type", value: "allele"
2025-09-15 20:23:54.235 wdl.w:ptcp.w:call-trgt-04.t:call-trgt_plot_motifs_allele INFO eval :: name: "show", value: "motifs"
2025-09-15 20:23:54.235 wdl.w:ptcp.w:call-trgt-04.t:call-trgt_plot_motifs_allele INFO eval :: name: "threads", value: 1
2025-09-15 20:23:54.235 wdl.w:ptcp.w:call-trgt-04.t:call-trgt_plot_motifs_allele INFO eval :: name: "disk_size", value: 27
2025-09-15 20:23:54.235 wdl.w:ptcp.w:call-trgt-04.t:call-trgt_plot_motifs_allele INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2101.motifs_allele"
2025-09-15 20:23:54.236 wdl.w:ptcp.w:call-trgt-04.t:call-trgt_plot_motifs_allele INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:23:54.236 wdl.w:ptcp.w:call-trgt-04.t:call-trgt_plot_motifs_allele WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:23:54.236 wdl.w:ptcp.w:call-trgt-04.t:call-trgt_plot_motifs_allele INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:23:54.236 wdl.w:ptcp.w:call-trgt-04.t:call-trgt_plot_motifs_allele INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:23:54.259 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_motifs_waterfall NOTICE done
2025-09-15 20:23:54.265 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:51 [ERROR] - No reads found for TRID=OPMD_PABPN1
2025-09-15 20:23:54.265 wdl.w:ptcp.w:call-trgt-34 NOTICE finish :: job: "call-trgt_plot_motifs_waterfall"
2025-09-15 20:23:54.266 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:51 [ERROR] - No reads found for TRID=SCA3_ATXN3
2025-09-15 20:23:54.266 wdl.w:ptcp.w:call-trgt-34 INFO output :: job: "call-trgt_plot_motifs_waterfall", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-34/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2131.motifs_waterfall.trgt_plots.zip"}
2025-09-15 20:23:54.266 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:51 [ERROR] - No reads found for TRID=SCA31_BEAN1
2025-09-15 20:23:54.266 wdl.w:ptcp.w:call-trgt-34 INFO visit :: node: "output-images_motifs_waterfall", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-34/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2131.motifs_waterfall.trgt_plots.zip"}
2025-09-15 20:23:54.266 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:51 [ERROR] - No reads found for TRID=SCA4_ZFHX3
2025-09-15 20:23:54.266 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:51 [ERROR] - No reads found for TRID=HDL2_JPH3
2025-09-15 20:23:54.267 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:51 [ERROR] - No reads found for TRID=OPDM4_RILPL1
2025-09-15 20:23:54.267 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:51 [ERROR] - No reads found for TRID=OPDM2_GIPC1
2025-09-15 20:23:54.267 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:51 [ERROR] - No reads found for TRID=FRA2A_AFF3
2025-09-15 20:23:54.267 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:52 [ERROR] - No reads found for TRID=SD5_HOXD13
2025-09-15 20:23:54.267 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:52 [ERROR] - No reads found for TRID=SCA6_CACNA1A
2025-09-15 20:23:54.267 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:52 [ERROR] - No reads found for TRID=CJD_PRNP
2025-09-15 20:23:54.267 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:52 [ERROR] - No reads found for TRID=SCA10_ATXN10
2025-09-15 20:23:54.267 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:52 [ERROR] - No reads found for TRID=SCA7_ATXN7
2025-09-15 20:23:54.267 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:52 [ERROR] - No reads found for TRID=DM2_CNBP
2025-09-15 20:23:54.267 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:52 [ERROR] - No reads found for TRID=DM1_DMPK
2025-09-15 20:23:54.267 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:52 [ERROR] - No reads found for TRID=EPM1_CSTB
2025-09-15 20:23:54.267 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:53 [ERROR] - No reads found for TRID=SCA36_NOP56
2025-09-15 20:23:54.267 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:53 [ERROR] - No reads found for TRID=SCA1_ATXN1
2025-09-15 20:23:54.267 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:53 [ERROR] - No reads found for TRID=SCA17_TBP
2025-09-15 20:23:54.267 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:53 [ERROR] - No reads found for TRID=OPDM1_LRP12
2025-09-15 20:23:54.267 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:53 [ERROR] - No reads found for TRID=SCA12_PPP2R2B
2025-09-15 20:23:54.267 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:53 [ERROR] - No reads found for TRID=HD_HTT
2025-09-15 20:23:54.267 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:53 [ERROR] - No reads found for TRID=CCHS_PHOX2B
2025-09-15 20:23:54.268 wdl.w:ptcp.w:call-trgt-04.t:call-trgt_plot_meth_waterfall NOTICE slurm_singularity run :: pid: 1200436, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-04/call-trgt_plot_meth_waterfall/slurm_singularity.log.txt"
2025-09-15 20:23:54.269 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_meth_allele NOTICE done
2025-09-15 20:23:54.272 wdl.w:ptcp.w:call-trgt-04.t:call-trgt_plot_motifs_waterfall NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-04/call-trgt_plot_motifs_waterfall", thread: 140608748373568
2025-09-15 20:23:54.279 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:51 [ERROR] - No reads found for TRID=SCA37_DAB1
2025-09-15 20:23:54.280 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:51 [ERROR] - No reads found for TRID=OPDM_ABCD3
2025-09-15 20:23:54.280 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:51 [ERROR] - No reads found for TRID=NIID_NOTCH2NLC
2025-09-15 20:23:54.280 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:51 [ERROR] - No reads found for TRID=SCA2_ATXN2
2025-09-15 20:23:54.280 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:51 [ERROR] - No reads found for TRID=SCA8_ATXN8OS
2025-09-15 20:23:54.280 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:51 [ERROR] - No reads found for TRID=SCA27B_FGF14
2025-09-15 20:23:54.280 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:51 [ERROR] - No reads found for TRID=OPMD_PABPN1
2025-09-15 20:23:54.280 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:51 [ERROR] - No reads found for TRID=SCA3_ATXN3
2025-09-15 20:23:54.280 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:51 [ERROR] - No reads found for TRID=SCA31_BEAN1
2025-09-15 20:23:54.280 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:52 [ERROR] - No reads found for TRID=SCA4_ZFHX3
2025-09-15 20:23:54.280 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:52 [ERROR] - No reads found for TRID=HDL2_JPH3
2025-09-15 20:23:54.280 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:52 [ERROR] - No reads found for TRID=OPDM4_RILPL1
2025-09-15 20:23:54.281 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:52 [ERROR] - No reads found for TRID=OPDM2_GIPC1
2025-09-15 20:23:54.281 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:52 [ERROR] - No reads found for TRID=FRA2A_AFF3
2025-09-15 20:23:54.281 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:52 [ERROR] - No reads found for TRID=SD5_HOXD13
2025-09-15 20:23:54.281 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:52 [ERROR] - No reads found for TRID=SCA6_CACNA1A
2025-09-15 20:23:54.281 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:52 [ERROR] - No reads found for TRID=CJD_PRNP
2025-09-15 20:23:54.281 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:52 [ERROR] - No reads found for TRID=SCA10_ATXN10
2025-09-15 20:23:54.281 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:53 [ERROR] - No reads found for TRID=SCA7_ATXN7
2025-09-15 20:23:54.281 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:53 [ERROR] - No reads found for TRID=DM2_CNBP
2025-09-15 20:23:54.281 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:53 [ERROR] - No reads found for TRID=DM1_DMPK
2025-09-15 20:23:54.281 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:53 [ERROR] - No reads found for TRID=EPM1_CSTB
2025-09-15 20:23:54.281 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:53 [ERROR] - No reads found for TRID=SCA36_NOP56
2025-09-15 20:23:54.281 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:53 [ERROR] - No reads found for TRID=SCA1_ATXN1
2025-09-15 20:23:54.281 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:53 [ERROR] - No reads found for TRID=SCA17_TBP
2025-09-15 20:23:54.281 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:53 [ERROR] - No reads found for TRID=OPDM1_LRP12
2025-09-15 20:23:54.281 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:53 [ERROR] - No reads found for TRID=SCA12_PPP2R2B
2025-09-15 20:23:54.281 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:54 [ERROR] - No reads found for TRID=HD_HTT
2025-09-15 20:23:54.281 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:54 [ERROR] - No reads found for TRID=CCHS_PHOX2B
2025-09-15 20:23:54.301 wdl.w:ptcp.w:call-trgt-23 NOTICE finish :: job: "call-trgt_plot_meth_allele"
2025-09-15 20:23:54.302 wdl.w:ptcp.w:call-trgt-23 INFO output :: job: "call-trgt_plot_meth_allele", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-23/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2120.meth_allele.trgt_plots.zip"}
2025-09-15 20:23:54.302 wdl.w:ptcp.w:call-trgt-23 INFO visit :: node: "output-images_meth_allele", values: {"images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-23/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2120.meth_allele.trgt_plots.zip"}
2025-09-15 20:23:54.309 wdl.w:ptcp.w:call-paraphase-20.t:call-call_f8 NOTICE task setup :: name: "call_f8", source: "./paraphase.wdl", line: 232, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-20/call-call_f8", thread: 140608773551680
2025-09-15 20:23:54.310 wdl.w:ptcp.w:call-trgt-04.t:call-trgt_plot_motifs_waterfall INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:23:54.310 wdl.w:ptcp.w:call-trgt-04.t:call-trgt_plot_motifs_waterfall INFO input :: name: "waterfall", value: true
2025-09-15 20:23:54.310 wdl.w:ptcp.w:call-trgt-04.t:call-trgt_plot_motifs_waterfall INFO input :: name: "methylation", value: false
2025-09-15 20:23:54.310 wdl.w:ptcp.w:call-trgt-04.t:call-trgt_plot_motifs_waterfall INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:23:54.310 wdl.w:ptcp.w:call-trgt-04.t:call-trgt_plot_motifs_waterfall INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:23:54.310 wdl.w:ptcp.w:call-trgt-04.t:call-trgt_plot_motifs_waterfall INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:23:54.310 wdl.w:ptcp.w:call-trgt-04.t:call-trgt_plot_motifs_waterfall INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2101.trgt.sorted.spanning.bam.bai"
2025-09-15 20:23:54.310 wdl.w:ptcp.w:call-trgt-04.t:call-trgt_plot_motifs_waterfall INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2101.trgt.sorted.spanning.bam"
2025-09-15 20:23:54.311 wdl.w:ptcp.w:call-trgt-04.t:call-trgt_plot_motifs_waterfall INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2101.trgt.vcf"
2025-09-15 20:23:54.311 wdl.w:ptcp.w:call-trgt-04.t:call-trgt_plot_motifs_waterfall INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2101"
2025-09-15 20:23:54.311 wdl.w:ptcp.w:call-trgt-04.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:23:54.311 wdl.w:ptcp.w:call-trgt-04.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "plot_type", value: "waterfall"
2025-09-15 20:23:54.312 wdl.w:ptcp.w:call-trgt-04.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "show", value: "motifs"
2025-09-15 20:23:54.312 wdl.w:ptcp.w:call-trgt-04.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "threads", value: 1
2025-09-15 20:23:54.312 wdl.w:ptcp.w:call-trgt-04.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "disk_size", value: 27
2025-09-15 20:23:54.312 wdl.w:ptcp.w:call-trgt-04.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2101.motifs_waterfall"
2025-09-15 20:23:54.312 wdl.w:ptcp.w:call-trgt-04.t:call-trgt_plot_motifs_waterfall INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:23:54.313 wdl.w:ptcp.w:call-trgt-04.t:call-trgt_plot_motifs_waterfall WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:23:54.313 wdl.w:ptcp.w:call-trgt-04.t:call-trgt_plot_motifs_waterfall INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:23:54.313 wdl.w:ptcp.w:call-trgt-04.t:call-trgt_plot_motifs_waterfall INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:23:54.322 wdl.w:ptcp.w:call-trgt-04.t:call-trgt_plot_motifs_allele INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-04/call-trgt_plot_motifs_allele/_singularity_tmpdir_3pinebtu"
2025-09-15 20:23:54.322 wdl.w:ptcp.w:call-trgt-04.t:call-trgt_plot_motifs_allele INFO Slurm invocation: srun --job-name call-trgt_plot_motifs_allele --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-04/call-trgt_plot_motifs_allele/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-04/call-trgt_plot_motifs_allele/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-04/call-trgt_plot_motifs_allele/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-04/call-trgt_plot_motifs_allele/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-04/call-trgt_genotype/out/m84036_250809_035451_s4.bc2101.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2101.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-04/call-trgt_genotype/out/m84036_250809_035451_s4.bc2101.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2101.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-04/call-trgt_genotype/out/m84036_250809_035451_s4.bc2101.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2101.trgt.sorted.spanning.bam.bai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-04/call-trgt_plot_motifs_allele/_singularity_tmpdir_3pinebtu/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-04/call-trgt_plot_motifs_allele/_singularity_tmpdir_3pinebtu/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:23:54.331 wdl.w:ptcp.w:call-paraphase-20.t:call-call_f8 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:23:54.331 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_meth_waterfall NOTICE done
2025-09-15 20:23:54.331 wdl.w:ptcp.w:call-paraphase-20.t:call-call_f8 INFO input :: name: "genome_version", value: "38"
2025-09-15 20:23:54.332 wdl.w:ptcp.w:call-paraphase-20.t:call-call_f8 INFO input :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2117"
2025-09-15 20:23:54.332 wdl.w:ptcp.w:call-paraphase-20.t:call-call_f8 INFO input :: name: "paraphase_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2117.paraphase.bam.bai"
2025-09-15 20:23:54.332 wdl.w:ptcp.w:call-paraphase-20.t:call-call_f8 INFO input :: name: "paraphase_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2117.paraphase.bam"
2025-09-15 20:23:54.332 wdl.w:ptcp.w:call-paraphase-20.t:call-call_f8 INFO input :: name: "sex", value: "F"
2025-09-15 20:23:54.332 wdl.w:ptcp.w:call-paraphase-20.t:call-call_f8 INFO eval :: name: "threads", value: 1
2025-09-15 20:23:54.332 wdl.w:ptcp.w:call-paraphase-20.t:call-call_f8 INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:23:54.333 wdl.w:ptcp.w:call-paraphase-20.t:call-call_f8 INFO eval :: name: "disk_size", value: 11
2025-09-15 20:23:54.333 wdl.w:ptcp.w:call-paraphase-20.t:call-call_f8 INFO eval :: name: "sample_sex", value: "F"
2025-09-15 20:23:54.333 wdl.w:ptcp.w:call-paraphase-20.t:call-call_f8 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:23:54.333 wdl.w:ptcp.w:call-paraphase-20.t:call-call_f8 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:23:54.334 wdl.w:ptcp.w:call-paraphase-20.t:call-call_f8 INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:23:54.334 wdl.w:ptcp.w:call-paraphase-20.t:call-call_f8 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:23:54.336 wdl.w:ptcp.w:call-trgt-14 NOTICE finish :: job: "call-trgt_plot_meth_waterfall"
2025-09-15 20:23:54.336 wdl.w:ptcp.w:call-trgt-14 INFO output :: job: "call-trgt_plot_meth_waterfall", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-14/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2111.meth_waterfall.trgt_plots.zip"}
2025-09-15 20:23:54.336 wdl.w:ptcp.w:call-trgt-14 INFO visit :: node: "output-images_meth_waterfall", values: {"images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-14/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2111.meth_waterfall.trgt_plots.zip"}
2025-09-15 20:23:54.344 wdl.w:ptcp.w:call-paraphase-04.t:call-call_f8 NOTICE task setup :: name: "call_f8", source: "./paraphase.wdl", line: 232, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-04/call-call_f8", thread: 140609260066368
2025-09-15 20:23:54.351 wdl.w:ptcp.w:call-trgt-04.t:call-trgt_plot_motifs_allele NOTICE slurm_singularity run :: pid: 1200438, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-04/call-trgt_plot_motifs_allele/slurm_singularity.log.txt"
2025-09-15 20:23:54.372 wdl.w:ptcp.w:call-paraphase-04.t:call-call_f8 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:23:54.373 wdl.w:ptcp.w:call-paraphase-04.t:call-call_f8 INFO input :: name: "genome_version", value: "38"
2025-09-15 20:23:54.373 wdl.w:ptcp.w:call-paraphase-04.t:call-call_f8 INFO input :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2101"
2025-09-15 20:23:54.373 wdl.w:ptcp.w:call-paraphase-04.t:call-call_f8 INFO input :: name: "paraphase_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2101.paraphase.bam.bai"
2025-09-15 20:23:54.373 wdl.w:ptcp.w:call-paraphase-04.t:call-call_f8 INFO input :: name: "paraphase_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2101.paraphase.bam"
2025-09-15 20:23:54.373 wdl.w:ptcp.w:call-paraphase-04.t:call-call_f8 INFO input :: name: "sex", value: "F"
2025-09-15 20:23:54.373 wdl.w:ptcp.w:call-paraphase-04.t:call-call_f8 INFO eval :: name: "threads", value: 1
2025-09-15 20:23:54.373 wdl.w:ptcp.w:call-paraphase-04.t:call-call_f8 INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:23:54.373 wdl.w:ptcp.w:call-paraphase-04.t:call-call_f8 INFO eval :: name: "disk_size", value: 11
2025-09-15 20:23:54.373 wdl.w:ptcp.w:call-paraphase-04.t:call-call_f8 INFO eval :: name: "sample_sex", value: "F"
2025-09-15 20:23:54.374 wdl.w:ptcp.w:call-paraphase-04.t:call-call_f8 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:23:54.374 wdl.w:ptcp.w:call-paraphase-04.t:call-call_f8 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:23:54.374 wdl.w:ptcp.w:call-paraphase-04.t:call-call_f8 INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:23:54.374 wdl.w:ptcp.w:call-paraphase-04.t:call-call_f8 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:23:54.409 wdl.w:ptcp.w:call-trgt-04.t:call-trgt_plot_motifs_waterfall INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-04/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_hb_mcjzx"
2025-09-15 20:23:54.409 wdl.w:ptcp.w:call-trgt-04.t:call-trgt_plot_motifs_waterfall INFO Slurm invocation: srun --job-name call-trgt_plot_motifs_waterfall --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-04/call-trgt_plot_motifs_waterfall/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-04/call-trgt_plot_motifs_waterfall/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-04/call-trgt_plot_motifs_waterfall/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-04/call-trgt_plot_motifs_waterfall/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-04/call-trgt_genotype/out/m84036_250809_035451_s4.bc2101.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2101.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-04/call-trgt_genotype/out/m84036_250809_035451_s4.bc2101.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2101.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-04/call-trgt_genotype/out/m84036_250809_035451_s4.bc2101.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2101.trgt.sorted.spanning.bam.bai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-04/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_hb_mcjzx/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-04/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_hb_mcjzx/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:23:54.423 wdl.w:ptcp.w:call-trgt-04.t:call-trgt_plot_motifs_waterfall NOTICE slurm_singularity run :: pid: 1200440, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-04/call-trgt_plot_motifs_waterfall/slurm_singularity.log.txt"
2025-09-15 20:23:54.426 wdl.w:ptcp.w:call-paraphase-20.t:call-call_f8 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 8, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-20/call-call_f8/_singularity_tmpdir_6577t1ot"
2025-09-15 20:23:54.426 wdl.w:ptcp.w:call-paraphase-20.t:call-call_f8 INFO Slurm invocation: srun --job-name call-call_f8 --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-20/call-call_f8/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-20/call-call_f8/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-20/call-call_f8/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-20/call-call_f8/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-20/call-run_paraphase/out/m84036_250809_035451_s4.bc2117_paraphase/m84036_250809_035451_s4.bc2117.paraphase.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2117.paraphase.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-20/call-run_paraphase/out/m84036_250809_035451_s4.bc2117_paraphase/m84036_250809_035451_s4.bc2117.paraphase.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2117.paraphase.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-20/call-call_f8/_singularity_tmpdir_6577t1ot/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-20/call-call_f8/_singularity_tmpdir_6577t1ot/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:23:54.426 wdl.w:ptcp.w:call-paraphase-04.t:call-call_f8 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 8, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-04/call-call_f8/_singularity_tmpdir__rpis7s6"
2025-09-15 20:23:54.427 wdl.w:ptcp.w:call-paraphase-04.t:call-call_f8 INFO Slurm invocation: srun --job-name call-call_f8 --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-04/call-call_f8/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-04/call-call_f8/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-04/call-call_f8/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-04/call-call_f8/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-04/call-run_paraphase/out/m84036_250809_035451_s4.bc2101_paraphase/m84036_250809_035451_s4.bc2101.paraphase.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2101.paraphase.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-04/call-run_paraphase/out/m84036_250809_035451_s4.bc2101_paraphase/m84036_250809_035451_s4.bc2101.paraphase.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2101.paraphase.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-04/call-call_f8/_singularity_tmpdir__rpis7s6/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-04/call-call_f8/_singularity_tmpdir__rpis7s6/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:23:54.436 wdl.w:ptcp.w:call-paraphase-04.t:call-call_f8 NOTICE slurm_singularity run :: pid: 1200442, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-04/call-call_f8/slurm_singularity.log.txt"
2025-09-15 20:23:54.437 wdl.w:ptcp.w:call-paraphase-20.t:call-call_f8 NOTICE slurm_singularity run :: pid: 1200441, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-20/call-call_f8/slurm_singularity.log.txt"
2025-09-15 20:23:54.550 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:23:51 [ERROR] - No reads found for TRID=SCA2_ATXN2
2025-09-15 20:23:54.550 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:23:51 [ERROR] - No reads found for TRID=SCA8_ATXN8OS
2025-09-15 20:23:54.550 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:23:51 [ERROR] - No reads found for TRID=SCA27B_FGF14
2025-09-15 20:23:54.550 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:23:51 [ERROR] - No reads found for TRID=OPMD_PABPN1
2025-09-15 20:23:54.550 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:23:51 [ERROR] - No reads found for TRID=SCA3_ATXN3
2025-09-15 20:23:54.550 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:23:51 [ERROR] - No reads found for TRID=SCA31_BEAN1
2025-09-15 20:23:54.550 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:23:52 [ERROR] - No reads found for TRID=SCA4_ZFHX3
2025-09-15 20:23:54.551 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:23:52 [ERROR] - No reads found for TRID=HDL2_JPH3
2025-09-15 20:23:54.551 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:23:52 [ERROR] - No reads found for TRID=OPDM4_RILPL1
2025-09-15 20:23:54.551 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:23:52 [ERROR] - No reads found for TRID=OPDM2_GIPC1
2025-09-15 20:23:54.551 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:23:52 [ERROR] - No reads found for TRID=FRA2A_AFF3
2025-09-15 20:23:54.551 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:23:52 [ERROR] - No reads found for TRID=SD5_HOXD13
2025-09-15 20:23:54.551 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:23:52 [ERROR] - No reads found for TRID=SCA6_CACNA1A
2025-09-15 20:23:54.551 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:23:52 [ERROR] - No reads found for TRID=CJD_PRNP
2025-09-15 20:23:54.551 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:23:53 [ERROR] - No reads found for TRID=SCA10_ATXN10
2025-09-15 20:23:54.551 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:23:53 [ERROR] - No reads found for TRID=SCA7_ATXN7
2025-09-15 20:23:54.551 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:23:53 [ERROR] - No reads found for TRID=DM2_CNBP
2025-09-15 20:23:54.551 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:23:53 [ERROR] - No reads found for TRID=DM1_DMPK
2025-09-15 20:23:54.551 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:23:53 [ERROR] - No reads found for TRID=EPM1_CSTB
2025-09-15 20:23:54.551 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:23:53 [ERROR] - No reads found for TRID=SCA36_NOP56
2025-09-15 20:23:54.551 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:23:53 [ERROR] - No reads found for TRID=SCA1_ATXN1
2025-09-15 20:23:54.551 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:23:53 [ERROR] - No reads found for TRID=SCA17_TBP
2025-09-15 20:23:54.551 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:23:53 [ERROR] - No reads found for TRID=OPDM1_LRP12
2025-09-15 20:23:54.551 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:23:53 [ERROR] - No reads found for TRID=SCA12_PPP2R2B
2025-09-15 20:23:54.551 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:23:54 [ERROR] - No reads found for TRID=HD_HTT
2025-09-15 20:23:54.551 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:23:54 [ERROR] - No reads found for TRID=CCHS_PHOX2B
2025-09-15 20:23:54.600 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_motifs_allele INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2131.motifs_allele.trgt_plots.zip"
2025-09-15 20:23:54.603 wdl.w:ptcp.w:call-paraphase-00.t:call-run_paraphase INFO output :: name: "paraphase_bam", value: "m84036_250809_035451_s4.bc2097_paraphase/m84036_250809_035451_s4.bc2097.paraphase.bam"
2025-09-15 20:23:54.607 wdl.w:ptcp.w:call-paraphase-00.t:call-run_paraphase INFO output :: name: "paraphase_bam_bai", value: "m84036_250809_035451_s4.bc2097_paraphase/m84036_250809_035451_s4.bc2097.paraphase.bam.bai"
2025-09-15 20:23:54.609 wdl.w:ptcp.w:call-paraphase-00.t:call-run_paraphase INFO output :: name: "paraphase_json", value: "m84036_250809_035451_s4.bc2097_paraphase/m84036_250809_035451_s4.bc2097.paraphase.json"
2025-09-15 20:23:54.611 wdl.w:ptcp.w:call-paraphase-00.t:call-run_paraphase INFO output :: name: "paraphase_vcfs", value: []
2025-09-15 20:23:54.611 wdl.w:ptcp.w:call-paraphase-00.t:call-run_paraphase INFO output :: name: "havanno_json", value: "m84036_250809_035451_s4.bc2097.havanno.json"
2025-09-15 20:23:54.683 wdl.w:ptcp.w:call-trgt-34.t:call-trgt_plot_motifs_allele NOTICE done
2025-09-15 20:23:54.688 wdl.w:ptcp.w:call-trgt-34 NOTICE finish :: job: "call-trgt_plot_motifs_allele"
2025-09-15 20:23:54.688 wdl.w:ptcp.w:call-trgt-34 INFO output :: job: "call-trgt_plot_motifs_allele", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-34/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2131.motifs_allele.trgt_plots.zip"}
2025-09-15 20:23:54.689 wdl.w:ptcp.w:call-trgt-34 INFO visit :: node: "output-images_motifs_allele", values: {"images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-34/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2131.motifs_allele.trgt_plots.zip"}
2025-09-15 20:23:54.689 wdl.w:ptcp.w:call-trgt-34 INFO visit :: node: "outputs", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-34/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2131.motifs_waterfall.trgt_plots.zip", "images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-34/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2131.meth_allele.trgt_plots.zip", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-34/call-trgt_genotype/out/m84036_250809_035451_s4.bc2131.trgt.sorted.spanning.bam.bai", "images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-34/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2131.motifs_allele.trgt_plots.zip", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-34/call-trgt_genotype/out/m84036_250809_035451_s4.bc2131.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-34/call-trgt_genotype/out/m84036_250809_035451_s4.bc2131.trgt.vcf", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-34/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2131.repeats.bam", "images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-34/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2131.meth_waterfall.trgt_plots.zip", "reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-34/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2131.repeats.bam.bai"}
2025-09-15 20:23:54.699 wdl.w:ptcp.w:call-paraphase-36.t:call-run_paraphase NOTICE task setup :: name: "run_paraphase", source: "./paraphase.wdl", line: 127, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-36/call-run_paraphase", thread: 140610342200896
2025-09-15 20:23:54.708 wdl.w:ptcp.w:call-paraphase-00.t:call-run_paraphase NOTICE done
2025-09-15 20:23:54.714 wdl.w:ptcp.w:call-paraphase-00 NOTICE finish :: job: "call-run_paraphase"
2025-09-15 20:23:54.714 wdl.w:ptcp.w:call-paraphase-00 INFO output :: job: "call-run_paraphase", values: {"havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-00/call-run_paraphase/out/m84036_250809_035451_s4.bc2097.havanno.json", "paraphase_vcfs": [], "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-00/call-run_paraphase/out/m84036_250809_035451_s4.bc2097_paraphase/m84036_250809_035451_s4.bc2097.paraphase.json", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-00/call-run_paraphase/out/m84036_250809_035451_s4.bc2097_paraphase/m84036_250809_035451_s4.bc2097.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-00/call-run_paraphase/out/m84036_250809_035451_s4.bc2097_paraphase/m84036_250809_035451_s4.bc2097.paraphase.bam"}
2025-09-15 20:23:54.715 wdl.w:ptcp.w:call-paraphase-00 NOTICE ready :: job: "call-call_f8", callee: "call_f8"
2025-09-15 20:23:54.715 wdl.w:ptcp.w:call-paraphase-00 INFO input :: job: "call-call_f8", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "out_prefix": "m84036_250809_035451_s4.bc2097", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-00/call-run_paraphase/out/m84036_250809_035451_s4.bc2097_paraphase/m84036_250809_035451_s4.bc2097.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-00/call-run_paraphase/out/m84036_250809_035451_s4.bc2097_paraphase/m84036_250809_035451_s4.bc2097.paraphase.bam", "sex": "F"}
2025-09-15 20:23:54.716 wdl.w:ptcp.w:call-paraphase-00 INFO visit :: node: "output-havanno_json", values: {"havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-00/call-run_paraphase/out/m84036_250809_035451_s4.bc2097.havanno.json"}
2025-09-15 20:23:54.716 wdl.w:ptcp.w:call-paraphase-00 INFO visit :: node: "output-paraphase_bam", values: {"paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-00/call-run_paraphase/out/m84036_250809_035451_s4.bc2097_paraphase/m84036_250809_035451_s4.bc2097.paraphase.bam"}
2025-09-15 20:23:54.716 wdl.w:ptcp.w:call-paraphase-00 INFO visit :: node: "output-paraphase_bam_bai", values: {"paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-00/call-run_paraphase/out/m84036_250809_035451_s4.bc2097_paraphase/m84036_250809_035451_s4.bc2097.paraphase.bam.bai"}
2025-09-15 20:23:54.716 wdl.w:ptcp.w:call-paraphase-00 INFO visit :: node: "output-paraphase_json", values: {"paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-00/call-run_paraphase/out/m84036_250809_035451_s4.bc2097_paraphase/m84036_250809_035451_s4.bc2097.paraphase.json"}
2025-09-15 20:23:54.716 wdl.w:ptcp.w:call-paraphase-00 INFO visit :: node: "output-paraphase_vcfs", values: {"paraphase_vcfs": []}
2025-09-15 20:23:54.726 wdl.w:ptcp.w:call-sawfish-36.t:call-run_sawfish NOTICE task setup :: name: "run_sawfish", source: "./sawfish.wdl", line: 83, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-36/call-run_sawfish", thread: 140611424335424
2025-09-15 20:23:54.730 wdl.w:ptcp.w:call-paraphase-36.t:call-run_paraphase INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:23:54.730 wdl.w:ptcp.w:call-paraphase-36.t:call-run_paraphase INFO input :: name: "annotation_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf"
2025-09-15 20:23:54.730 wdl.w:ptcp.w:call-paraphase-36.t:call-run_paraphase INFO input :: name: "genome_version", value: "38"
2025-09-15 20:23:54.730 wdl.w:ptcp.w:call-paraphase-36.t:call-run_paraphase INFO input :: name: "config_file", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/paraphase_config.GRCh38.yaml"
2025-09-15 20:23:54.730 wdl.w:ptcp.w:call-paraphase-36.t:call-run_paraphase INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:23:54.730 wdl.w:ptcp.w:call-paraphase-36.t:call-run_paraphase INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:23:54.730 wdl.w:ptcp.w:call-paraphase-36.t:call-run_paraphase INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2133.mapped.bam.bai"
2025-09-15 20:23:54.730 wdl.w:ptcp.w:call-paraphase-36.t:call-run_paraphase INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2133.mapped.bam"
2025-09-15 20:23:54.731 wdl.w:ptcp.w:call-paraphase-36.t:call-run_paraphase INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2133"
2025-09-15 20:23:54.731 wdl.w:ptcp.w:call-paraphase-36.t:call-run_paraphase INFO eval :: name: "threads", value: 4
2025-09-15 20:23:54.731 wdl.w:ptcp.w:call-paraphase-36.t:call-run_paraphase INFO eval :: name: "mem_gb", value: 8
2025-09-15 20:23:54.731 wdl.w:ptcp.w:call-paraphase-36.t:call-run_paraphase INFO eval :: name: "disk_size", value: 27
2025-09-15 20:23:54.731 wdl.w:ptcp.w:call-paraphase-36.t:call-run_paraphase INFO eval :: name: "out_dir", value: "m84036_250809_035451_s4.bc2133_paraphase"
2025-09-15 20:23:54.732 wdl.w:ptcp.w:call-paraphase-36.t:call-run_paraphase INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 4, memory_reservation: 8000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:23:54.732 wdl.w:ptcp.w:call-paraphase-36.t:call-run_paraphase WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:23:54.732 wdl.w:ptcp.w:call-paraphase-36.t:call-run_paraphase INFO provisioned :: seconds_waited: 0, cpu: 4, mem_bytes: 8000000000
2025-09-15 20:23:54.733 wdl.w:ptcp.w:call-paraphase-36.t:call-run_paraphase INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:23:54.750 wdl.w:ptcp.w:call-sawfish-36.t:call-run_sawfish INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:23:54.750 wdl.w:ptcp.w:call-sawfish-36.t:call-run_sawfish INFO input :: name: "genome_version", value: "38"
2025-09-15 20:23:54.750 wdl.w:ptcp.w:call-sawfish-36.t:call-run_sawfish INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:23:54.750 wdl.w:ptcp.w:call-sawfish-36.t:call-run_sawfish INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:23:54.750 wdl.w:ptcp.w:call-sawfish-36.t:call-run_sawfish INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2133.mapped.bam.bai"
2025-09-15 20:23:54.750 wdl.w:ptcp.w:call-sawfish-36.t:call-run_sawfish INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2133.mapped.bam"
2025-09-15 20:23:54.750 wdl.w:ptcp.w:call-sawfish-36.t:call-run_sawfish INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2133"
2025-09-15 20:23:54.751 wdl.w:ptcp.w:call-sawfish-36.t:call-run_sawfish INFO eval :: name: "mem_gb", value: 32
2025-09-15 20:23:54.751 wdl.w:ptcp.w:call-sawfish-36.t:call-run_sawfish INFO eval :: name: "threads", value: 16
2025-09-15 20:23:54.751 wdl.w:ptcp.w:call-sawfish-36.t:call-run_sawfish INFO eval :: name: "disk_size", value: 30
2025-09-15 20:23:54.751 wdl.w:ptcp.w:call-sawfish-36.t:call-run_sawfish INFO eval :: name: "discover_dirname", value: "m84036_250809_035451_s4.bc2133_sawfish_discover"
2025-09-15 20:23:54.751 wdl.w:ptcp.w:call-sawfish-36.t:call-run_sawfish INFO eval :: name: "call_dirname", value: "m84036_250809_035451_s4.bc2133_sawfish"
2025-09-15 20:23:54.751 wdl.w:ptcp.w:call-sawfish-36.t:call-run_sawfish INFO eval :: name: "minimap2_bam_filename", value: "m84036_250809_035451_s4.bc2133.minimap2.bam"
2025-09-15 20:23:54.752 wdl.w:ptcp.w:call-sawfish-36.t:call-run_sawfish INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 16, memory_reservation: 32000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:23:54.752 wdl.w:ptcp.w:call-sawfish-36.t:call-run_sawfish WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:23:54.752 wdl.w:ptcp.w:call-sawfish-36.t:call-run_sawfish INFO provisioned :: seconds_waited: 0, cpu: 16, mem_bytes: 32000000000
2025-09-15 20:23:54.753 wdl.w:ptcp.w:call-sawfish-36.t:call-run_sawfish INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:23:54.821 wdl.w:ptcp.w:call-trgt-34 NOTICE done
2025-09-15 20:23:54.824 wdl.w:ptcp.w:call-paraphase-36.t:call-run_paraphase INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-36/call-run_paraphase/_singularity_tmpdir_e585ae03"
2025-09-15 20:23:54.824 wdl.w:ptcp.w:call-paraphase-36.t:call-run_paraphase INFO Slurm invocation: srun --job-name call-run_paraphase --partition compute,compute9 --cpus-per-task 4 --mem 7629M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-36/call-run_paraphase/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-36/call-run_paraphase/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-36/call-run_paraphase/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-36/call-run_paraphase/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-36/out/m84036_250809_035451_s4.bc2133.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2133.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-36/out/m84036_250809_035451_s4.bc2133.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2133.mapped.bam:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/variant_list/variant_list.GRCh38.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf:ro --bind /ptcp/meta/paraphase/paraphase_config.GRCh38.yaml:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/paraphase_config.GRCh38.yaml:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-36/call-run_paraphase/_singularity_tmpdir_e585ae03/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-36/call-run_paraphase/_singularity_tmpdir_e585ae03/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:23:54.829 wdl.w:ptcp NOTICE finish :: job: "call-trgt-34"
2025-09-15 20:23:54.829 wdl.w:ptcp INFO output :: job: "call-trgt-34", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-34/out/m84036_250809_035451_s4.bc2131.motifs_waterfall.trgt_plots.zip", "images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-34/out/m84036_250809_035451_s4.bc2131.meth_allele.trgt_plots.zip", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-34/out/m84036_250809_035451_s4.bc2131.trgt.sorted.spanning.bam.bai", "images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-34/out/m84036_250809_035451_s4.bc2131.motifs_allele.trgt_plots.zip", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-34/out/m84036_250809_035451_s4.bc2131.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-34/out/m84036_250809_035451_s4.bc2131.trgt.vcf", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-34/out/m84036_250809_035451_s4.bc2131.repeats.bam", "images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-34/out/m84036_250809_035451_s4.bc2131.meth_waterfall.trgt_plots.zip", "reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-34/out/m84036_250809_035451_s4.bc2131.repeats.bam.bai"}
2025-09-15 20:23:54.839 wdl.w:ptcp.w:call-paraphase-47 NOTICE workflow start :: name: "paraphase", source: "./paraphase.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-47"
2025-09-15 20:23:54.852 wdl.w:ptcp.w:call-sawfish-36.t:call-run_sawfish INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 10, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-36/call-run_sawfish/_singularity_tmpdir_pd5l7svy"
2025-09-15 20:23:54.853 wdl.w:ptcp.w:call-sawfish-36.t:call-run_sawfish INFO Slurm invocation: srun --job-name call-run_sawfish --partition compute,compute9 --cpus-per-task 16 --mem 30518M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-36/call-run_sawfish/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-36/call-run_sawfish/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-36/call-run_sawfish/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-36/call-run_sawfish/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-36/out/m84036_250809_035451_s4.bc2133.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2133.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-36/out/m84036_250809_035451_s4.bc2133.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2133.mapped.bam:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-36/call-run_sawfish/_singularity_tmpdir_pd5l7svy/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-36/call-run_sawfish/_singularity_tmpdir_pd5l7svy/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:23:54.858 wdl.w:ptcp.w:call-paraphase-47 INFO visit :: node: "decl-annotation_vcf", values: {"annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf"}
2025-09-15 20:23:54.858 wdl.w:ptcp.w:call-paraphase-47 INFO visit :: node: "decl-config_file", values: {"config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml"}
2025-09-15 20:23:54.858 wdl.w:ptcp.w:call-paraphase-47 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:23:54.858 wdl.w:ptcp.w:call-paraphase-47 INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:23:54.858 wdl.w:ptcp.w:call-paraphase-47 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-47/out/m84036_250809_035451_s4.bc2144.mapped.bam"}
2025-09-15 20:23:54.858 wdl.w:ptcp.w:call-paraphase-47 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-47/out/m84036_250809_035451_s4.bc2144.mapped.bam.bai"}
2025-09-15 20:23:54.858 wdl.w:ptcp.w:call-paraphase-47 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:23:54.858 wdl.w:ptcp.w:call-paraphase-47 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:23:54.858 wdl.w:ptcp.w:call-paraphase-47 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2144"}
2025-09-15 20:23:54.858 wdl.w:ptcp.w:call-paraphase-47 INFO visit :: node: "decl-sex", values: {"sex": "F"}
2025-09-15 20:23:54.859 wdl.w:ptcp.w:call-paraphase-47 NOTICE ready :: job: "call-run_paraphase", callee: "run_paraphase"
2025-09-15 20:23:54.859 wdl.w:ptcp.w:call-paraphase-36.t:call-run_paraphase NOTICE slurm_singularity run :: pid: 1200474, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-36/call-run_paraphase/slurm_singularity.log.txt"
2025-09-15 20:23:54.859 wdl.w:ptcp.w:call-paraphase-47 INFO input :: job: "call-run_paraphase", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf", "genome_version": "38", "config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-47/out/m84036_250809_035451_s4.bc2144.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-47/out/m84036_250809_035451_s4.bc2144.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2144"}
2025-09-15 20:23:54.861 wdl.w:ptcp.w:call-sawfish-36.t:call-run_sawfish NOTICE slurm_singularity run :: pid: 1200475, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-36/call-run_sawfish/slurm_singularity.log.txt"
2025-09-15 20:23:54.878 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_meth_allele INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2132.meth_allele.trgt_plots.zip"
2025-09-15 20:23:54.958 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_meth_allele NOTICE done
2025-09-15 20:23:54.965 wdl.w:ptcp.w:call-trgt-35 NOTICE finish :: job: "call-trgt_plot_meth_allele"
2025-09-15 20:23:54.966 wdl.w:ptcp.w:call-trgt-35 INFO output :: job: "call-trgt_plot_meth_allele", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-35/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2132.meth_allele.trgt_plots.zip"}
2025-09-15 20:23:54.966 wdl.w:ptcp.w:call-trgt-35 INFO visit :: node: "output-images_meth_allele", values: {"images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-35/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2132.meth_allele.trgt_plots.zip"}
2025-09-15 20:23:54.972 wdl.w:ptcp.w:call-trgt-36.t:call-get_reads_overlapping_repeats NOTICE task setup :: name: "get_reads_overlapping_repeats", source: "./trgt.wdl", line: 182, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-36/call-get_reads_overlapping_repeats", thread: 140612506469952
2025-09-15 20:23:54.989 wdl.w:ptcp.w:call-trgt-36.t:call-get_reads_overlapping_repeats INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:23:54.989 wdl.w:ptcp.w:call-trgt-36.t:call-get_reads_overlapping_repeats INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:23:54.989 wdl.w:ptcp.w:call-trgt-36.t:call-get_reads_overlapping_repeats INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2133.mapped.bam.bai"
2025-09-15 20:23:54.989 wdl.w:ptcp.w:call-trgt-36.t:call-get_reads_overlapping_repeats INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2133.mapped.bam"
2025-09-15 20:23:54.989 wdl.w:ptcp.w:call-trgt-36.t:call-get_reads_overlapping_repeats INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2133"
2025-09-15 20:23:54.990 wdl.w:ptcp.w:call-trgt-36.t:call-get_reads_overlapping_repeats INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:23:54.990 wdl.w:ptcp.w:call-trgt-36.t:call-get_reads_overlapping_repeats INFO eval :: name: "expand_size", value: 3000
2025-09-15 20:23:54.990 wdl.w:ptcp.w:call-trgt-36.t:call-get_reads_overlapping_repeats INFO eval :: name: "threads", value: 1
2025-09-15 20:23:54.990 wdl.w:ptcp.w:call-trgt-36.t:call-get_reads_overlapping_repeats INFO eval :: name: "expanded_bed_name", value: "m84036_250809_035451_s4.bc2133.expanded.bed"
2025-09-15 20:23:54.990 wdl.w:ptcp.w:call-trgt-36.t:call-get_reads_overlapping_repeats INFO eval :: name: "disk_size", value: 11
2025-09-15 20:23:54.990 wdl.w:ptcp.w:call-trgt-36.t:call-get_reads_overlapping_repeats INFO eval :: name: "output_name", value: "m84036_250809_035451_s4.bc2133.repeats.bam"
2025-09-15 20:23:54.990 wdl.w:ptcp.w:call-trgt-36.t:call-get_reads_overlapping_repeats INFO eval :: name: "index_name", value: "m84036_250809_035451_s4.bc2133.repeats.bam.bai"
2025-09-15 20:23:54.990 wdl.w:ptcp.w:call-trgt-36.t:call-get_reads_overlapping_repeats INFO eval :: name: "output_name_with_index", value: "m84036_250809_035451_s4.bc2133.repeats.bam##idx##m84036_250809_035451_s4.bc2133.repeats.bam.bai"
2025-09-15 20:23:54.991 wdl.w:ptcp.w:call-trgt-36.t:call-get_reads_overlapping_repeats INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:23:54.991 wdl.w:ptcp.w:call-trgt-36.t:call-get_reads_overlapping_repeats WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:23:54.991 wdl.w:ptcp.w:call-trgt-36.t:call-get_reads_overlapping_repeats INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:23:54.991 wdl.w:ptcp.w:call-trgt-36.t:call-get_reads_overlapping_repeats INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:23:55.054 wdl.w:ptcp.w:call-trgt-36.t:call-get_reads_overlapping_repeats INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 9, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-36/call-get_reads_overlapping_repeats/_singularity_tmpdir_oml1qhon"
2025-09-15 20:23:55.054 wdl.w:ptcp.w:call-trgt-36.t:call-get_reads_overlapping_repeats INFO Slurm invocation: srun --job-name call-get_reads_overlapping_repeats --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-36/call-get_reads_overlapping_repeats/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-36/call-get_reads_overlapping_repeats/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-36/call-get_reads_overlapping_repeats/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-36/call-get_reads_overlapping_repeats/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-36/out/m84036_250809_035451_s4.bc2133.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2133.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-36/out/m84036_250809_035451_s4.bc2133.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2133.mapped.bam:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-36/call-get_reads_overlapping_repeats/_singularity_tmpdir_oml1qhon/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-36/call-get_reads_overlapping_repeats/_singularity_tmpdir_oml1qhon/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:23:55.069 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:52 [ERROR] - No reads found for TRID=OPDM_ABCD3
2025-09-15 20:23:55.069 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:52 [ERROR] - No reads found for TRID=OPDM4_RILPL1
2025-09-15 20:23:55.070 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:52 [ERROR] - No reads found for TRID=SCA2_ATXN2
2025-09-15 20:23:55.070 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:52 [ERROR] - No reads found for TRID=SCA27B_FGF14
2025-09-15 20:23:55.070 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:52 [ERROR] - No reads found for TRID=OPMD_PABPN1
2025-09-15 20:23:55.070 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:52 [ERROR] - No reads found for TRID=SCA31_BEAN1
2025-09-15 20:23:55.070 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:52 [ERROR] - No reads found for TRID=SCA4_ZFHX3
2025-09-15 20:23:55.070 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:52 [ERROR] - No reads found for TRID=HDL2_JPH3
2025-09-15 20:23:55.070 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:52 [ERROR] - No reads found for TRID=FECD3_TCF4
2025-09-15 20:23:55.070 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:52 [ERROR] - No reads found for TRID=SCA6_CACNA1A
2025-09-15 20:23:55.070 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:52 [ERROR] - No reads found for TRID=OPDM2_GIPC1
2025-09-15 20:23:55.070 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:52 [ERROR] - No reads found for TRID=DM1_DMPK
2025-09-15 20:23:55.070 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:52 [ERROR] - No reads found for TRID=SD5_HOXD13
2025-09-15 20:23:55.070 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:52 [ERROR] - No reads found for TRID=CJD_PRNP
2025-09-15 20:23:55.070 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:52 [ERROR] - No reads found for TRID=EPM1_CSTB
2025-09-15 20:23:55.070 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:52 [ERROR] - No reads found for TRID=SCA36_NOP56
2025-09-15 20:23:55.070 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:53 [ERROR] - No reads found for TRID=SCA10_ATXN10
2025-09-15 20:23:55.070 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:53 [ERROR] - No reads found for TRID=SCA7_ATXN7
2025-09-15 20:23:55.070 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:53 [ERROR] - No reads found for TRID=FRA2A_AFF3
2025-09-15 20:23:55.071 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:53 [ERROR] - No reads found for TRID=SCA1_ATXN1
2025-09-15 20:23:55.071 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:53 [ERROR] - No reads found for TRID=SCA12_PPP2R2B
2025-09-15 20:23:55.071 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:53 [ERROR] - No reads found for TRID=OPDM1_LRP12
2025-09-15 20:23:55.071 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:53 [ERROR] - No reads found for TRID=FAME1_SAMD12
2025-09-15 20:23:55.071 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:53 [ERROR] - No reads found for TRID=CCHS_PHOX2B
2025-09-15 20:23:55.071 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:23:53 [ERROR] - No reads found for TRID=FTDALS1_C9orf72
2025-09-15 20:23:55.075 wdl.w:ptcp.w:call-trgt-36.t:call-get_reads_overlapping_repeats NOTICE slurm_singularity run :: pid: 1200478, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-36/call-get_reads_overlapping_repeats/slurm_singularity.log.txt"
2025-09-15 20:23:55.163 wdl.w:ptcp.w:call-paraphase-34.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for f8inv1 for sample m84036_250809_035451_s4.bc2131 at 2025-09-15 20:23:45.797439...
2025-09-15 20:23:55.163 wdl.w:ptcp.w:call-paraphase-34.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for f8inv1 for sample m84036_250809_035451_s4.bc2131 at 2025-09-15 20:23:49.081099...
2025-09-15 20:23:55.164 wdl.w:ptcp.w:call-paraphase-34.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for f8inv1 for sample m84036_250809_035451_s4.bc2131 at 2025-09-15 20:23:49.409741...
2025-09-15 20:23:55.164 wdl.w:ptcp.w:call-paraphase-34.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for hbb for sample m84036_250809_035451_s4.bc2131 at 2025-09-15 20:23:50.859320...
2025-09-15 20:23:55.164 wdl.w:ptcp.w:call-paraphase-34.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for hbb for sample m84036_250809_035451_s4.bc2131 at 2025-09-15 20:23:50.859540...
2025-09-15 20:23:55.243 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_meth_waterfall INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2132.meth_waterfall.trgt_plots.zip"
2025-09-15 20:23:55.247 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:52 [ERROR] - No reads found for TRID=OPDM_ABCD3
2025-09-15 20:23:55.247 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:52 [ERROR] - No reads found for TRID=OPDM4_RILPL1
2025-09-15 20:23:55.247 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:52 [ERROR] - No reads found for TRID=SCA2_ATXN2
2025-09-15 20:23:55.247 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:52 [ERROR] - No reads found for TRID=SCA27B_FGF14
2025-09-15 20:23:55.247 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:52 [ERROR] - No reads found for TRID=OPMD_PABPN1
2025-09-15 20:23:55.247 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:52 [ERROR] - No reads found for TRID=SCA31_BEAN1
2025-09-15 20:23:55.247 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:52 [ERROR] - No reads found for TRID=SCA4_ZFHX3
2025-09-15 20:23:55.247 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:52 [ERROR] - No reads found for TRID=HDL2_JPH3
2025-09-15 20:23:55.247 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:52 [ERROR] - No reads found for TRID=FECD3_TCF4
2025-09-15 20:23:55.247 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:52 [ERROR] - No reads found for TRID=SCA6_CACNA1A
2025-09-15 20:23:55.247 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:52 [ERROR] - No reads found for TRID=OPDM2_GIPC1
2025-09-15 20:23:55.247 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:52 [ERROR] - No reads found for TRID=DM1_DMPK
2025-09-15 20:23:55.247 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:52 [ERROR] - No reads found for TRID=SD5_HOXD13
2025-09-15 20:23:55.248 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:53 [ERROR] - No reads found for TRID=CJD_PRNP
2025-09-15 20:23:55.248 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:53 [ERROR] - No reads found for TRID=EPM1_CSTB
2025-09-15 20:23:55.248 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:53 [ERROR] - No reads found for TRID=SCA36_NOP56
2025-09-15 20:23:55.248 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:53 [ERROR] - No reads found for TRID=SCA10_ATXN10
2025-09-15 20:23:55.248 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:53 [ERROR] - No reads found for TRID=SCA7_ATXN7
2025-09-15 20:23:55.248 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:53 [ERROR] - No reads found for TRID=FRA2A_AFF3
2025-09-15 20:23:55.248 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:53 [ERROR] - No reads found for TRID=SCA1_ATXN1
2025-09-15 20:23:55.248 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:53 [ERROR] - No reads found for TRID=SCA12_PPP2R2B
2025-09-15 20:23:55.248 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:53 [ERROR] - No reads found for TRID=OPDM1_LRP12
2025-09-15 20:23:55.248 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:53 [ERROR] - No reads found for TRID=FAME1_SAMD12
2025-09-15 20:23:55.248 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:53 [ERROR] - No reads found for TRID=CCHS_PHOX2B
2025-09-15 20:23:55.248 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:54 [ERROR] - No reads found for TRID=FTDALS1_C9orf72
2025-09-15 20:23:55.259 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_motifs_allele INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2132.motifs_allele.trgt_plots.zip"
2025-09-15 20:23:55.276 wdl.w:ptcp.w:call-trgt-04.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO srun: job 51797501 queued and waiting for resources
2025-09-15 20:23:55.277 wdl.w:ptcp.w:call-trgt-04.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO srun: job 51797501 has been allocated resources
2025-09-15 20:23:55.277 wdl.w:ptcp.w:call-trgt-04.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:55.333 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_meth_waterfall NOTICE done
2025-09-15 20:23:55.339 wdl.w:ptcp.w:call-trgt-35 NOTICE finish :: job: "call-trgt_plot_meth_waterfall"
2025-09-15 20:23:55.339 wdl.w:ptcp.w:call-trgt-35 INFO output :: job: "call-trgt_plot_meth_waterfall", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-35/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2132.meth_waterfall.trgt_plots.zip"}
2025-09-15 20:23:55.340 wdl.w:ptcp.w:call-trgt-35 INFO visit :: node: "output-images_meth_waterfall", values: {"images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-35/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2132.meth_waterfall.trgt_plots.zip"}
2025-09-15 20:23:55.345 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_motifs_allele NOTICE done
2025-09-15 20:23:55.348 wdl.w:ptcp.w:call-trgt-36.t:call-trgt_genotype NOTICE task setup :: name: "trgt_genotype", source: "./trgt.wdl", line: 272, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-36/call-trgt_genotype", thread: 140609805329984
2025-09-15 20:23:55.350 wdl.w:ptcp.w:call-trgt-35 NOTICE finish :: job: "call-trgt_plot_motifs_allele"
2025-09-15 20:23:55.350 wdl.w:ptcp.w:call-trgt-35 INFO output :: job: "call-trgt_plot_motifs_allele", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-35/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2132.motifs_allele.trgt_plots.zip"}
2025-09-15 20:23:55.350 wdl.w:ptcp.w:call-trgt-35 INFO visit :: node: "output-images_motifs_allele", values: {"images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-35/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2132.motifs_allele.trgt_plots.zip"}
2025-09-15 20:23:55.359 wdl.w:ptcp.w:call-paraphase-38.t:call-run_paraphase NOTICE task setup :: name: "run_paraphase", source: "./paraphase.wdl", line: 127, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-38/call-run_paraphase", thread: 140611407550016
2025-09-15 20:23:55.367 wdl.w:ptcp.w:call-trgt-04.t:call-trgt_plot_motifs_allele.slurm_singularity INFO srun: job 51797502 queued and waiting for resources
2025-09-15 20:23:55.367 wdl.w:ptcp.w:call-trgt-04.t:call-trgt_plot_motifs_allele.slurm_singularity INFO srun: job 51797502 has been allocated resources
2025-09-15 20:23:55.367 wdl.w:ptcp.w:call-trgt-04.t:call-trgt_plot_motifs_allele.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:55.369 wdl.w:ptcp.w:call-trgt-36.t:call-trgt_genotype INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:23:55.369 wdl.w:ptcp.w:call-trgt-36.t:call-trgt_genotype INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:23:55.369 wdl.w:ptcp.w:call-trgt-36.t:call-trgt_genotype INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:23:55.369 wdl.w:ptcp.w:call-trgt-36.t:call-trgt_genotype INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:23:55.369 wdl.w:ptcp.w:call-trgt-36.t:call-trgt_genotype INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2133.mapped.bam.bai"
2025-09-15 20:23:55.369 wdl.w:ptcp.w:call-trgt-36.t:call-trgt_genotype INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2133.mapped.bam"
2025-09-15 20:23:55.369 wdl.w:ptcp.w:call-trgt-36.t:call-trgt_genotype INFO input :: name: "sex", value: "F"
2025-09-15 20:23:55.369 wdl.w:ptcp.w:call-trgt-36.t:call-trgt_genotype INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2133"
2025-09-15 20:23:55.369 wdl.w:ptcp.w:call-trgt-36.t:call-trgt_genotype INFO eval :: name: "mem_gb", value: 16
2025-09-15 20:23:55.370 wdl.w:ptcp.w:call-trgt-36.t:call-trgt_genotype INFO eval :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2133.trgt"
2025-09-15 20:23:55.370 wdl.w:ptcp.w:call-trgt-36.t:call-trgt_genotype INFO eval :: name: "threads", value: 8
2025-09-15 20:23:55.370 wdl.w:ptcp.w:call-trgt-36.t:call-trgt_genotype INFO eval :: name: "disk_size", value: 27
2025-09-15 20:23:55.370 wdl.w:ptcp.w:call-trgt-36.t:call-trgt_genotype INFO eval :: name: "karyotype", value: "XX"
2025-09-15 20:23:55.371 wdl.w:ptcp.w:call-trgt-36.t:call-trgt_genotype INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 8, memory_reservation: 16000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:23:55.371 wdl.w:ptcp.w:call-trgt-36.t:call-trgt_genotype WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:23:55.372 wdl.w:ptcp.w:call-trgt-36.t:call-trgt_genotype INFO provisioned :: seconds_waited: 0, cpu: 8, mem_bytes: 16000000000
2025-09-15 20:23:55.372 wdl.w:ptcp.w:call-trgt-36.t:call-trgt_genotype INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:23:55.381 wdl.w:ptcp.w:call-paraphase-38.t:call-run_paraphase INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:23:55.381 wdl.w:ptcp.w:call-paraphase-38.t:call-run_paraphase INFO input :: name: "annotation_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf"
2025-09-15 20:23:55.382 wdl.w:ptcp.w:call-paraphase-38.t:call-run_paraphase INFO input :: name: "genome_version", value: "38"
2025-09-15 20:23:55.382 wdl.w:ptcp.w:call-paraphase-38.t:call-run_paraphase INFO input :: name: "config_file", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/paraphase_config.GRCh38.yaml"
2025-09-15 20:23:55.382 wdl.w:ptcp.w:call-paraphase-38.t:call-run_paraphase INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:23:55.382 wdl.w:ptcp.w:call-paraphase-38.t:call-run_paraphase INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:23:55.382 wdl.w:ptcp.w:call-paraphase-38.t:call-run_paraphase INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2135.mapped.bam.bai"
2025-09-15 20:23:55.382 wdl.w:ptcp.w:call-paraphase-38.t:call-run_paraphase INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2135.mapped.bam"
2025-09-15 20:23:55.382 wdl.w:ptcp.w:call-paraphase-38.t:call-run_paraphase INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2135"
2025-09-15 20:23:55.382 wdl.w:ptcp.w:call-paraphase-38.t:call-run_paraphase INFO eval :: name: "threads", value: 4
2025-09-15 20:23:55.382 wdl.w:ptcp.w:call-paraphase-38.t:call-run_paraphase INFO eval :: name: "mem_gb", value: 8
2025-09-15 20:23:55.383 wdl.w:ptcp.w:call-paraphase-38.t:call-run_paraphase INFO eval :: name: "disk_size", value: 27
2025-09-15 20:23:55.383 wdl.w:ptcp.w:call-paraphase-38.t:call-run_paraphase INFO eval :: name: "out_dir", value: "m84036_250809_035451_s4.bc2135_paraphase"
2025-09-15 20:23:55.383 wdl.w:ptcp.w:call-paraphase-38.t:call-run_paraphase INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 4, memory_reservation: 8000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:23:55.383 wdl.w:ptcp.w:call-paraphase-38.t:call-run_paraphase WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:23:55.384 wdl.w:ptcp.w:call-paraphase-38.t:call-run_paraphase INFO provisioned :: seconds_waited: 0, cpu: 4, mem_bytes: 8000000000
2025-09-15 20:23:55.384 wdl.w:ptcp.w:call-paraphase-38.t:call-run_paraphase INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:23:55.438 wdl.w:ptcp.w:call-trgt-04.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO srun: job 51797503 queued and waiting for resources
2025-09-15 20:23:55.438 wdl.w:ptcp.w:call-trgt-04.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO srun: job 51797503 has been allocated resources
2025-09-15 20:23:55.438 wdl.w:ptcp.w:call-trgt-04.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:55.450 wdl.w:ptcp.w:call-paraphase-04.t:call-call_f8.slurm_singularity INFO srun: job 51797505 queued and waiting for resources
2025-09-15 20:23:55.450 wdl.w:ptcp.w:call-paraphase-04.t:call-call_f8.slurm_singularity INFO srun: job 51797505 has been allocated resources
2025-09-15 20:23:55.450 wdl.w:ptcp.w:call-paraphase-04.t:call-call_f8.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:55.453 wdl.w:ptcp.w:call-paraphase-20.t:call-call_f8.slurm_singularity INFO srun: job 51797504 queued and waiting for resources
2025-09-15 20:23:55.453 wdl.w:ptcp.w:call-paraphase-20.t:call-call_f8.slurm_singularity INFO srun: job 51797504 has been allocated resources
2025-09-15 20:23:55.453 wdl.w:ptcp.w:call-paraphase-20.t:call-call_f8.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:55.454 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:23:52 [ERROR] - No reads found for TRID=SCA37_DAB1
2025-09-15 20:23:55.454 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:23:52 [ERROR] - No reads found for TRID=DRPLA_ATN1
2025-09-15 20:23:55.454 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:23:52 [ERROR] - No reads found for TRID=NIID_NOTCH2NLC
2025-09-15 20:23:55.455 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:23:52 [ERROR] - No reads found for TRID=OPDM_ABCD3
2025-09-15 20:23:55.455 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:23:52 [ERROR] - No reads found for TRID=OPDM4_RILPL1
2025-09-15 20:23:55.455 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:23:52 [ERROR] - No reads found for TRID=SCA2_ATXN2
2025-09-15 20:23:55.455 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:23:52 [ERROR] - No reads found for TRID=SCA27B_FGF14
2025-09-15 20:23:55.455 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:23:52 [ERROR] - No reads found for TRID=OPMD_PABPN1
2025-09-15 20:23:55.455 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:23:52 [ERROR] - No reads found for TRID=SCA31_BEAN1
2025-09-15 20:23:55.455 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:23:52 [ERROR] - No reads found for TRID=SCA4_ZFHX3
2025-09-15 20:23:55.455 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:23:53 [ERROR] - No reads found for TRID=HDL2_JPH3
2025-09-15 20:23:55.455 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:23:53 [ERROR] - No reads found for TRID=FECD3_TCF4
2025-09-15 20:23:55.455 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:23:53 [ERROR] - No reads found for TRID=SCA6_CACNA1A
2025-09-15 20:23:55.455 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:23:53 [ERROR] - No reads found for TRID=OPDM2_GIPC1
2025-09-15 20:23:55.455 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:23:53 [ERROR] - No reads found for TRID=DM1_DMPK
2025-09-15 20:23:55.455 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:23:53 [ERROR] - No reads found for TRID=SD5_HOXD13
2025-09-15 20:23:55.455 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:23:53 [ERROR] - No reads found for TRID=CJD_PRNP
2025-09-15 20:23:55.455 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:23:53 [ERROR] - No reads found for TRID=EPM1_CSTB
2025-09-15 20:23:55.455 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:23:53 [ERROR] - No reads found for TRID=SCA36_NOP56
2025-09-15 20:23:55.455 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:23:53 [ERROR] - No reads found for TRID=SCA10_ATXN10
2025-09-15 20:23:55.455 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:23:53 [ERROR] - No reads found for TRID=SCA7_ATXN7
2025-09-15 20:23:55.455 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:23:53 [ERROR] - No reads found for TRID=FRA2A_AFF3
2025-09-15 20:23:55.455 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:23:53 [ERROR] - No reads found for TRID=SCA1_ATXN1
2025-09-15 20:23:55.456 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:23:53 [ERROR] - No reads found for TRID=SCA12_PPP2R2B
2025-09-15 20:23:55.456 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:23:53 [ERROR] - No reads found for TRID=OPDM1_LRP12
2025-09-15 20:23:55.456 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:23:53 [ERROR] - No reads found for TRID=FAME1_SAMD12
2025-09-15 20:23:55.456 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:23:54 [ERROR] - No reads found for TRID=CCHS_PHOX2B
2025-09-15 20:23:55.456 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:23:54 [ERROR] - No reads found for TRID=FTDALS1_C9orf72
2025-09-15 20:23:55.457 wdl.w:ptcp.w:call-trgt-36.t:call-trgt_genotype INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 11, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-36/call-trgt_genotype/_singularity_tmpdir_9b7i_mus"
2025-09-15 20:23:55.457 wdl.w:ptcp.w:call-trgt-36.t:call-trgt_genotype INFO Slurm invocation: srun --job-name call-trgt_genotype --partition compute,compute9 --cpus-per-task 8 --mem 15259M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-36/call-trgt_genotype/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-36/call-trgt_genotype/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-36/call-trgt_genotype/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-36/call-trgt_genotype/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-36/out/m84036_250809_035451_s4.bc2133.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2133.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-36/out/m84036_250809_035451_s4.bc2133.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2133.mapped.bam:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-36/call-trgt_genotype/_singularity_tmpdir_9b7i_mus/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-36/call-trgt_genotype/_singularity_tmpdir_9b7i_mus/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:23:55.465 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_meth_waterfall INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2120.meth_waterfall.trgt_plots.zip"
2025-09-15 20:23:55.476 wdl.w:ptcp.w:call-paraphase-38.t:call-run_paraphase INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-38/call-run_paraphase/_singularity_tmpdir_qr7ymhts"
2025-09-15 20:23:55.476 wdl.w:ptcp.w:call-paraphase-38.t:call-run_paraphase INFO Slurm invocation: srun --job-name call-run_paraphase --partition compute,compute9 --cpus-per-task 4 --mem 7629M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-38/call-run_paraphase/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-38/call-run_paraphase/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-38/call-run_paraphase/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-38/call-run_paraphase/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-38/out/m84036_250809_035451_s4.bc2135.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2135.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-38/out/m84036_250809_035451_s4.bc2135.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2135.mapped.bam.bai:ro --bind /ptcp/meta/variant_list/variant_list.GRCh38.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf:ro --bind /ptcp/meta/paraphase/paraphase_config.GRCh38.yaml:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/paraphase_config.GRCh38.yaml:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-38/call-run_paraphase/_singularity_tmpdir_qr7ymhts/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-38/call-run_paraphase/_singularity_tmpdir_qr7ymhts/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:23:55.488 wdl.w:ptcp.w:call-paraphase-38.t:call-run_paraphase NOTICE slurm_singularity run :: pid: 1200499, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-38/call-run_paraphase/slurm_singularity.log.txt"
2025-09-15 20:23:55.488 wdl.w:ptcp.w:call-trgt-36.t:call-trgt_genotype NOTICE slurm_singularity run :: pid: 1200498, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-36/call-trgt_genotype/slurm_singularity.log.txt"
2025-09-15 20:23:55.529 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_motifs_waterfall INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2132.motifs_waterfall.trgt_plots.zip"
2025-09-15 20:23:55.541 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_meth_waterfall NOTICE done
2025-09-15 20:23:55.545 wdl.w:ptcp.w:call-trgt-23 NOTICE finish :: job: "call-trgt_plot_meth_waterfall"
2025-09-15 20:23:55.546 wdl.w:ptcp.w:call-trgt-23 INFO output :: job: "call-trgt_plot_meth_waterfall", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-23/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2120.meth_waterfall.trgt_plots.zip"}
2025-09-15 20:23:55.546 wdl.w:ptcp.w:call-trgt-23 INFO visit :: node: "output-images_meth_waterfall", values: {"images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-23/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2120.meth_waterfall.trgt_plots.zip"}
2025-09-15 20:23:55.552 wdl.w:ptcp.w:call-sawfish-38.t:call-run_sawfish NOTICE task setup :: name: "run_sawfish", source: "./sawfish.wdl", line: 83, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-38/call-run_sawfish", thread: 140609796937280
2025-09-15 20:23:55.572 wdl.w:ptcp.w:call-sawfish-38.t:call-run_sawfish INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:23:55.572 wdl.w:ptcp.w:call-sawfish-38.t:call-run_sawfish INFO input :: name: "genome_version", value: "38"
2025-09-15 20:23:55.573 wdl.w:ptcp.w:call-sawfish-38.t:call-run_sawfish INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:23:55.573 wdl.w:ptcp.w:call-sawfish-38.t:call-run_sawfish INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:23:55.573 wdl.w:ptcp.w:call-sawfish-38.t:call-run_sawfish INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2135.mapped.bam.bai"
2025-09-15 20:23:55.573 wdl.w:ptcp.w:call-sawfish-38.t:call-run_sawfish INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2135.mapped.bam"
2025-09-15 20:23:55.573 wdl.w:ptcp.w:call-sawfish-38.t:call-run_sawfish INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2135"
2025-09-15 20:23:55.573 wdl.w:ptcp.w:call-sawfish-38.t:call-run_sawfish INFO eval :: name: "mem_gb", value: 32
2025-09-15 20:23:55.573 wdl.w:ptcp.w:call-sawfish-38.t:call-run_sawfish INFO eval :: name: "threads", value: 16
2025-09-15 20:23:55.573 wdl.w:ptcp.w:call-sawfish-38.t:call-run_sawfish INFO eval :: name: "disk_size", value: 30
2025-09-15 20:23:55.574 wdl.w:ptcp.w:call-sawfish-38.t:call-run_sawfish INFO eval :: name: "discover_dirname", value: "m84036_250809_035451_s4.bc2135_sawfish_discover"
2025-09-15 20:23:55.574 wdl.w:ptcp.w:call-sawfish-38.t:call-run_sawfish INFO eval :: name: "call_dirname", value: "m84036_250809_035451_s4.bc2135_sawfish"
2025-09-15 20:23:55.574 wdl.w:ptcp.w:call-sawfish-38.t:call-run_sawfish INFO eval :: name: "minimap2_bam_filename", value: "m84036_250809_035451_s4.bc2135.minimap2.bam"
2025-09-15 20:23:55.574 wdl.w:ptcp.w:call-sawfish-38.t:call-run_sawfish INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 16, memory_reservation: 32000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:23:55.574 wdl.w:ptcp.w:call-sawfish-38.t:call-run_sawfish WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:23:55.575 wdl.w:ptcp.w:call-sawfish-38.t:call-run_sawfish INFO provisioned :: seconds_waited: 0, cpu: 16, mem_bytes: 32000000000
2025-09-15 20:23:55.575 wdl.w:ptcp.w:call-sawfish-38.t:call-run_sawfish INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:23:55.609 wdl.w:ptcp.w:call-trgt-35.t:call-trgt_plot_motifs_waterfall NOTICE done
2025-09-15 20:23:55.614 wdl.w:ptcp.w:call-trgt-35 NOTICE finish :: job: "call-trgt_plot_motifs_waterfall"
2025-09-15 20:23:55.614 wdl.w:ptcp.w:call-trgt-35 INFO output :: job: "call-trgt_plot_motifs_waterfall", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-35/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2132.motifs_waterfall.trgt_plots.zip"}
2025-09-15 20:23:55.615 wdl.w:ptcp.w:call-trgt-35 INFO visit :: node: "output-images_motifs_waterfall", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-35/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2132.motifs_waterfall.trgt_plots.zip"}
2025-09-15 20:23:55.615 wdl.w:ptcp.w:call-trgt-35 INFO visit :: node: "outputs", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-35/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2132.motifs_waterfall.trgt_plots.zip", "images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-35/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2132.meth_allele.trgt_plots.zip", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-35/call-trgt_genotype/out/m84036_250809_035451_s4.bc2132.trgt.sorted.spanning.bam.bai", "images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-35/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2132.motifs_allele.trgt_plots.zip", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-35/call-trgt_genotype/out/m84036_250809_035451_s4.bc2132.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-35/call-trgt_genotype/out/m84036_250809_035451_s4.bc2132.trgt.vcf", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-35/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2132.repeats.bam", "images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-35/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2132.meth_waterfall.trgt_plots.zip", "reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-35/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2132.repeats.bam.bai"}
2025-09-15 20:23:55.622 wdl.w:ptcp.w:call-trgt-38.t:call-get_reads_overlapping_repeats NOTICE task setup :: name: "get_reads_overlapping_repeats", source: "./trgt.wdl", line: 182, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-38/call-get_reads_overlapping_repeats", thread: 140608765158976
2025-09-15 20:23:55.634 wdl.w:ptcp.w:call-sawfish-38.t:call-run_sawfish INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 10, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-38/call-run_sawfish/_singularity_tmpdir_d8cu9yy2"
2025-09-15 20:23:55.634 wdl.w:ptcp.w:call-sawfish-38.t:call-run_sawfish INFO Slurm invocation: srun --job-name call-run_sawfish --partition compute,compute9 --cpus-per-task 16 --mem 30518M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-38/call-run_sawfish/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-38/call-run_sawfish/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-38/call-run_sawfish/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-38/call-run_sawfish/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-38/out/m84036_250809_035451_s4.bc2135.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2135.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-38/out/m84036_250809_035451_s4.bc2135.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2135.mapped.bam.bai:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-38/call-run_sawfish/_singularity_tmpdir_d8cu9yy2/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-38/call-run_sawfish/_singularity_tmpdir_d8cu9yy2/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:23:55.640 wdl.w:ptcp.w:call-trgt-38.t:call-get_reads_overlapping_repeats INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:23:55.640 wdl.w:ptcp.w:call-trgt-38.t:call-get_reads_overlapping_repeats INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:23:55.640 wdl.w:ptcp.w:call-trgt-38.t:call-get_reads_overlapping_repeats INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2135.mapped.bam.bai"
2025-09-15 20:23:55.641 wdl.w:ptcp.w:call-trgt-38.t:call-get_reads_overlapping_repeats INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2135.mapped.bam"
2025-09-15 20:23:55.641 wdl.w:ptcp.w:call-trgt-38.t:call-get_reads_overlapping_repeats INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2135"
2025-09-15 20:23:55.641 wdl.w:ptcp.w:call-trgt-38.t:call-get_reads_overlapping_repeats INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:23:55.641 wdl.w:ptcp.w:call-trgt-38.t:call-get_reads_overlapping_repeats INFO eval :: name: "expand_size", value: 3000
2025-09-15 20:23:55.641 wdl.w:ptcp.w:call-trgt-38.t:call-get_reads_overlapping_repeats INFO eval :: name: "threads", value: 1
2025-09-15 20:23:55.641 wdl.w:ptcp.w:call-trgt-38.t:call-get_reads_overlapping_repeats INFO eval :: name: "expanded_bed_name", value: "m84036_250809_035451_s4.bc2135.expanded.bed"
2025-09-15 20:23:55.641 wdl.w:ptcp.w:call-trgt-38.t:call-get_reads_overlapping_repeats INFO eval :: name: "disk_size", value: 11
2025-09-15 20:23:55.641 wdl.w:ptcp.w:call-trgt-38.t:call-get_reads_overlapping_repeats INFO eval :: name: "output_name", value: "m84036_250809_035451_s4.bc2135.repeats.bam"
2025-09-15 20:23:55.641 wdl.w:ptcp.w:call-trgt-38.t:call-get_reads_overlapping_repeats INFO eval :: name: "index_name", value: "m84036_250809_035451_s4.bc2135.repeats.bam.bai"
2025-09-15 20:23:55.641 wdl.w:ptcp.w:call-trgt-38.t:call-get_reads_overlapping_repeats INFO eval :: name: "output_name_with_index", value: "m84036_250809_035451_s4.bc2135.repeats.bam##idx##m84036_250809_035451_s4.bc2135.repeats.bam.bai"
2025-09-15 20:23:55.642 wdl.w:ptcp.w:call-trgt-38.t:call-get_reads_overlapping_repeats INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:23:55.642 wdl.w:ptcp.w:call-trgt-38.t:call-get_reads_overlapping_repeats WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:23:55.642 wdl.w:ptcp.w:call-trgt-38.t:call-get_reads_overlapping_repeats INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:23:55.643 wdl.w:ptcp.w:call-trgt-38.t:call-get_reads_overlapping_repeats INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:23:55.656 wdl.w:ptcp.w:call-sawfish-38.t:call-run_sawfish NOTICE slurm_singularity run :: pid: 1200503, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-38/call-run_sawfish/slurm_singularity.log.txt"
2025-09-15 20:23:55.669 wdl.w:ptcp.w:call-paraphase-27.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for smn1 for sample m84036_250809_035451_s4.bc2124 at 2025-09-15 20:23:42.991238...
2025-09-15 20:23:55.670 wdl.w:ptcp.w:call-paraphase-27.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for hba for sample m84036_250809_035451_s4.bc2124 at 2025-09-15 20:23:43.833829...
2025-09-15 20:23:55.670 wdl.w:ptcp.w:call-paraphase-27.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for gba for sample m84036_250809_035451_s4.bc2124 at 2025-09-15 20:23:44.201578...
2025-09-15 20:23:55.670 wdl.w:ptcp.w:call-paraphase-27.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for cyp21 for sample m84036_250809_035451_s4.bc2124 at 2025-09-15 20:23:45.996187...
2025-09-15 20:23:55.670 wdl.w:ptcp.w:call-paraphase-27.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for smn1 for sample m84036_250809_035451_s4.bc2124 at 2025-09-15 20:23:55.350620...
2025-09-15 20:23:55.670 wdl.w:ptcp.w:call-paraphase-27.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning to gene2 region for smn1 for sample m84036_250809_035451_s4.bc2124 at 2025-09-15 20:23:55.552732...
2025-09-15 20:23:55.703 wdl.w:ptcp.w:call-trgt-35 NOTICE done
2025-09-15 20:23:55.707 wdl.w:ptcp NOTICE finish :: job: "call-trgt-35"
2025-09-15 20:23:55.708 wdl.w:ptcp INFO output :: job: "call-trgt-35", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-35/out/m84036_250809_035451_s4.bc2132.motifs_waterfall.trgt_plots.zip", "images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-35/out/m84036_250809_035451_s4.bc2132.meth_allele.trgt_plots.zip", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-35/out/m84036_250809_035451_s4.bc2132.trgt.sorted.spanning.bam.bai", "images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-35/out/m84036_250809_035451_s4.bc2132.motifs_allele.trgt_plots.zip", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-35/out/m84036_250809_035451_s4.bc2132.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-35/out/m84036_250809_035451_s4.bc2132.trgt.vcf", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-35/out/m84036_250809_035451_s4.bc2132.repeats.bam", "images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-35/out/m84036_250809_035451_s4.bc2132.meth_waterfall.trgt_plots.zip", "reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-35/out/m84036_250809_035451_s4.bc2132.repeats.bam.bai"}
2025-09-15 20:23:55.708 wdl.w:ptcp.w:call-trgt-38.t:call-get_reads_overlapping_repeats INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 9, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-38/call-get_reads_overlapping_repeats/_singularity_tmpdir_ct3601v3"
2025-09-15 20:23:55.709 wdl.w:ptcp.w:call-trgt-38.t:call-get_reads_overlapping_repeats INFO Slurm invocation: srun --job-name call-get_reads_overlapping_repeats --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-38/call-get_reads_overlapping_repeats/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-38/call-get_reads_overlapping_repeats/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-38/call-get_reads_overlapping_repeats/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-38/call-get_reads_overlapping_repeats/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-38/out/m84036_250809_035451_s4.bc2135.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2135.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-38/out/m84036_250809_035451_s4.bc2135.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2135.mapped.bam.bai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-38/call-get_reads_overlapping_repeats/_singularity_tmpdir_ct3601v3/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-38/call-get_reads_overlapping_repeats/_singularity_tmpdir_ct3601v3/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:23:55.710 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_motifs_allele INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2120.motifs_allele.trgt_plots.zip"
2025-09-15 20:23:55.716 wdl.w:ptcp.w:call-sawfish-47 NOTICE workflow start :: name: "sawfish", source: "./sawfish.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-47"
2025-09-15 20:23:55.734 wdl.w:ptcp.w:call-sawfish-47 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:23:55.735 wdl.w:ptcp.w:call-sawfish-47 INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:23:55.735 wdl.w:ptcp.w:call-sawfish-47 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-47/out/m84036_250809_035451_s4.bc2144.mapped.bam"}
2025-09-15 20:23:55.735 wdl.w:ptcp.w:call-sawfish-47 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-47/out/m84036_250809_035451_s4.bc2144.mapped.bam.bai"}
2025-09-15 20:23:55.735 wdl.w:ptcp.w:call-sawfish-47 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:23:55.735 wdl.w:ptcp.w:call-sawfish-47 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:23:55.735 wdl.w:ptcp.w:call-sawfish-47 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2144"}
2025-09-15 20:23:55.735 wdl.w:ptcp.w:call-sawfish-47 NOTICE ready :: job: "call-run_sawfish", callee: "run_sawfish"
2025-09-15 20:23:55.735 wdl.w:ptcp.w:call-sawfish-47 INFO input :: job: "call-run_sawfish", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-47/out/m84036_250809_035451_s4.bc2144.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-47/out/m84036_250809_035451_s4.bc2144.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2144"}
2025-09-15 20:23:55.741 wdl.w:ptcp.w:call-trgt-38.t:call-get_reads_overlapping_repeats NOTICE slurm_singularity run :: pid: 1200522, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-38/call-get_reads_overlapping_repeats/slurm_singularity.log.txt"
2025-09-15 20:23:55.743 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:52 [ERROR] - No reads found for TRID=NIID_NOTCH2NLC
2025-09-15 20:23:55.743 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:52 [ERROR] - No reads found for TRID=DRPLA_ATN1
2025-09-15 20:23:55.743 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:52 [ERROR] - No reads found for TRID=OPDM_ABCD3
2025-09-15 20:23:55.744 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:53 [ERROR] - No reads found for TRID=OPDM4_RILPL1
2025-09-15 20:23:55.744 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:53 [ERROR] - No reads found for TRID=SCA37_DAB1
2025-09-15 20:23:55.744 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:53 [ERROR] - No reads found for TRID=OPMD_PABPN1
2025-09-15 20:23:55.744 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:53 [ERROR] - No reads found for TRID=SCA27B_FGF14
2025-09-15 20:23:55.744 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:53 [ERROR] - No reads found for TRID=SCA8_ATXN8OS
2025-09-15 20:23:55.744 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:53 [ERROR] - No reads found for TRID=SCA4_ZFHX3
2025-09-15 20:23:55.744 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:53 [ERROR] - No reads found for TRID=HDL2_JPH3
2025-09-15 20:23:55.744 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:53 [ERROR] - No reads found for TRID=SCA31_BEAN1
2025-09-15 20:23:55.744 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:53 [ERROR] - No reads found for TRID=SCA6_CACNA1A
2025-09-15 20:23:55.744 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:53 [ERROR] - No reads found for TRID=DM1_DMPK
2025-09-15 20:23:55.744 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:54 [ERROR] - No reads found for TRID=OPDM2_GIPC1
2025-09-15 20:23:55.744 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:54 [ERROR] - No reads found for TRID=SD5_HOXD13
2025-09-15 20:23:55.744 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:54 [ERROR] - No reads found for TRID=SCA36_NOP56
2025-09-15 20:23:55.744 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:54 [ERROR] - No reads found for TRID=CJD_PRNP
2025-09-15 20:23:55.744 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:54 [ERROR] - No reads found for TRID=EPM1_CSTB
2025-09-15 20:23:55.744 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:54 [ERROR] - No reads found for TRID=SCA7_ATXN7
2025-09-15 20:23:55.745 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:54 [ERROR] - No reads found for TRID=FRA2A_AFF3
2025-09-15 20:23:55.745 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:54 [ERROR] - No reads found for TRID=SCA10_ATXN10
2025-09-15 20:23:55.745 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:54 [ERROR] - No reads found for TRID=FECD3_TCF4
2025-09-15 20:23:55.745 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:55 [ERROR] - No reads found for TRID=SCA12_PPP2R2B
2025-09-15 20:23:55.745 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:55 [ERROR] - No reads found for TRID=SCA1_ATXN1
2025-09-15 20:23:55.745 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:55 [ERROR] - No reads found for TRID=CCHS_PHOX2B
2025-09-15 20:23:55.745 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:55 [ERROR] - No reads found for TRID=FAME1_SAMD12
2025-09-15 20:23:55.745 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:55 [ERROR] - No reads found for TRID=OPDM1_LRP12
2025-09-15 20:23:55.745 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:55 [ERROR] - No reads found for TRID=SBMA_AR
2025-09-15 20:23:55.770 wdl.w:ptcp.w:call-paraphase-20.t:call-call_f8 INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2117.f8inversion.vcf"
2025-09-15 20:23:55.774 wdl.w:ptcp.w:call-paraphase-20.t:call-call_f8 INFO output :: name: "json", value: "m84036_250809_035451_s4.bc2117.f8inversion.json"
2025-09-15 20:23:55.791 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_motifs_allele NOTICE done
2025-09-15 20:23:55.795 wdl.w:ptcp.w:call-trgt-23 NOTICE finish :: job: "call-trgt_plot_motifs_allele"
2025-09-15 20:23:55.796 wdl.w:ptcp.w:call-trgt-23 INFO output :: job: "call-trgt_plot_motifs_allele", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-23/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2120.motifs_allele.trgt_plots.zip"}
2025-09-15 20:23:55.796 wdl.w:ptcp.w:call-trgt-23 INFO visit :: node: "output-images_motifs_allele", values: {"images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-23/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2120.motifs_allele.trgt_plots.zip"}
2025-09-15 20:23:55.804 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_genotype NOTICE task setup :: name: "trgt_genotype", source: "./trgt.wdl", line: 272, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-38/call-trgt_genotype", thread: 140608739980864
2025-09-15 20:23:55.822 wdl.w:ptcp.w:call-paraphase-04.t:call-call_f8 INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2101.f8inversion.vcf"
2025-09-15 20:23:55.824 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_genotype INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:23:55.824 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_genotype INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:23:55.824 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_genotype INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:23:55.824 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_genotype INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:23:55.824 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_genotype INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2135.mapped.bam.bai"
2025-09-15 20:23:55.824 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_genotype INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2135.mapped.bam"
2025-09-15 20:23:55.824 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_genotype INFO input :: name: "sex", value: "F"
2025-09-15 20:23:55.824 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_genotype INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2135"
2025-09-15 20:23:55.825 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_genotype INFO eval :: name: "mem_gb", value: 16
2025-09-15 20:23:55.825 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_genotype INFO eval :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2135.trgt"
2025-09-15 20:23:55.825 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_genotype INFO eval :: name: "threads", value: 8
2025-09-15 20:23:55.825 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_genotype INFO eval :: name: "disk_size", value: 27
2025-09-15 20:23:55.825 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_genotype INFO eval :: name: "karyotype", value: "XX"
2025-09-15 20:23:55.826 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_genotype INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 8, memory_reservation: 16000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:23:55.826 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_genotype WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:23:55.826 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_genotype INFO provisioned :: seconds_waited: 0, cpu: 8, mem_bytes: 16000000000
2025-09-15 20:23:55.827 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_genotype INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:23:55.827 wdl.w:ptcp.w:call-paraphase-04.t:call-call_f8 INFO output :: name: "json", value: "m84036_250809_035451_s4.bc2101.f8inversion.json"
2025-09-15 20:23:55.835 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_motifs_waterfall INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2120.motifs_waterfall.trgt_plots.zip"
2025-09-15 20:23:55.847 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:23:53 [ERROR] - No reads found for TRID=NIID_NOTCH2NLC
2025-09-15 20:23:55.847 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:23:53 [ERROR] - No reads found for TRID=DRPLA_ATN1
2025-09-15 20:23:55.847 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:23:53 [ERROR] - No reads found for TRID=OPDM_ABCD3
2025-09-15 20:23:55.847 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:23:53 [ERROR] - No reads found for TRID=OPDM4_RILPL1
2025-09-15 20:23:55.847 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:23:53 [ERROR] - No reads found for TRID=SCA37_DAB1
2025-09-15 20:23:55.847 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:23:53 [ERROR] - No reads found for TRID=OPMD_PABPN1
2025-09-15 20:23:55.847 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:23:53 [ERROR] - No reads found for TRID=SCA27B_FGF14
2025-09-15 20:23:55.847 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:23:53 [ERROR] - No reads found for TRID=SCA8_ATXN8OS
2025-09-15 20:23:55.847 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:23:53 [ERROR] - No reads found for TRID=SCA4_ZFHX3
2025-09-15 20:23:55.848 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:23:53 [ERROR] - No reads found for TRID=HDL2_JPH3
2025-09-15 20:23:55.848 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:23:53 [ERROR] - No reads found for TRID=SCA31_BEAN1
2025-09-15 20:23:55.848 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:23:53 [ERROR] - No reads found for TRID=SCA6_CACNA1A
2025-09-15 20:23:55.848 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:23:54 [ERROR] - No reads found for TRID=DM1_DMPK
2025-09-15 20:23:55.848 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:23:54 [ERROR] - No reads found for TRID=OPDM2_GIPC1
2025-09-15 20:23:55.848 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:23:54 [ERROR] - No reads found for TRID=SD5_HOXD13
2025-09-15 20:23:55.848 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:23:54 [ERROR] - No reads found for TRID=SCA36_NOP56
2025-09-15 20:23:55.848 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:23:54 [ERROR] - No reads found for TRID=CJD_PRNP
2025-09-15 20:23:55.848 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:23:54 [ERROR] - No reads found for TRID=EPM1_CSTB
2025-09-15 20:23:55.848 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:23:54 [ERROR] - No reads found for TRID=SCA7_ATXN7
2025-09-15 20:23:55.848 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:23:54 [ERROR] - No reads found for TRID=FRA2A_AFF3
2025-09-15 20:23:55.848 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:23:54 [ERROR] - No reads found for TRID=SCA10_ATXN10
2025-09-15 20:23:55.848 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:23:54 [ERROR] - No reads found for TRID=FECD3_TCF4
2025-09-15 20:23:55.848 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:23:54 [ERROR] - No reads found for TRID=SCA12_PPP2R2B
2025-09-15 20:23:55.848 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:23:54 [ERROR] - No reads found for TRID=SCA1_ATXN1
2025-09-15 20:23:55.848 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:23:54 [ERROR] - No reads found for TRID=CCHS_PHOX2B
2025-09-15 20:23:55.848 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:23:54 [ERROR] - No reads found for TRID=FAME1_SAMD12
2025-09-15 20:23:55.848 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:23:54 [ERROR] - No reads found for TRID=OPDM1_LRP12
2025-09-15 20:23:55.848 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:23:54 [ERROR] - No reads found for TRID=SBMA_AR
2025-09-15 20:23:55.849 wdl.w:ptcp.w:call-paraphase-20.t:call-call_f8 NOTICE done
2025-09-15 20:23:55.855 wdl.w:ptcp.w:call-paraphase-20 NOTICE finish :: job: "call-call_f8"
2025-09-15 20:23:55.856 wdl.w:ptcp.w:call-paraphase-20 INFO output :: job: "call-call_f8", values: {"json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-20/call-call_f8/out/m84036_250809_035451_s4.bc2117.f8inversion.json", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-20/call-call_f8/out/m84036_250809_035451_s4.bc2117.f8inversion.vcf"}
2025-09-15 20:23:55.856 wdl.w:ptcp.w:call-paraphase-20 INFO visit :: node: "output-f8_json", values: {"f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-20/call-call_f8/out/m84036_250809_035451_s4.bc2117.f8inversion.json"}
2025-09-15 20:23:55.856 wdl.w:ptcp.w:call-paraphase-20 INFO visit :: node: "output-f8_vcf", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-20/call-call_f8/out/m84036_250809_035451_s4.bc2117.f8inversion.vcf"}
2025-09-15 20:23:55.856 wdl.w:ptcp.w:call-paraphase-20 INFO visit :: node: "outputs", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-20/call-call_f8/out/m84036_250809_035451_s4.bc2117.f8inversion.vcf", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-20/call-run_paraphase/out/m84036_250809_035451_s4.bc2117_paraphase/m84036_250809_035451_s4.bc2117.paraphase.json", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-20/call-run_paraphase/out/m84036_250809_035451_s4.bc2117_paraphase/m84036_250809_035451_s4.bc2117.paraphase.bam", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-20/call-run_paraphase/out/m84036_250809_035451_s4.bc2117_paraphase/m84036_250809_035451_s4.bc2117.paraphase.bam.bai", "paraphase_vcfs": [], "havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-20/call-run_paraphase/out/m84036_250809_035451_s4.bc2117.havanno.json", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-20/call-call_f8/out/m84036_250809_035451_s4.bc2117.f8inversion.json"}
2025-09-15 20:23:55.869 wdl.w:ptcp.w:call-sawfish-36.t:call-run_sawfish.stderr VERBOSE [M::bam2fq_mainloop] discarded 0 singletons
2025-09-15 20:23:55.869 wdl.w:ptcp.w:call-sawfish-36.t:call-run_sawfish.stderr VERBOSE [M::bam2fq_mainloop] processed 0 reads
2025-09-15 20:23:55.872 wdl.w:ptcp.w:call-paraphase-37.t:call-run_paraphase NOTICE task setup :: name: "run_paraphase", source: "./paraphase.wdl", line: 127, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-37/call-run_paraphase", thread: 140608773551680
2025-09-15 20:23:55.883 wdl.w:ptcp.w:call-paraphase-36.t:call-run_paraphase.slurm_singularity INFO srun: job 51797506 queued and waiting for resources
2025-09-15 20:23:55.883 wdl.w:ptcp.w:call-paraphase-36.t:call-run_paraphase.slurm_singularity INFO srun: job 51797506 has been allocated resources
2025-09-15 20:23:55.883 wdl.w:ptcp.w:call-paraphase-36.t:call-run_paraphase.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:55.884 wdl.w:ptcp.w:call-sawfish-36.t:call-run_sawfish.slurm_singularity INFO srun: job 51797507 queued and waiting for resources
2025-09-15 20:23:55.884 wdl.w:ptcp.w:call-sawfish-36.t:call-run_sawfish.slurm_singularity INFO srun: job 51797507 has been allocated resources
2025-09-15 20:23:55.884 wdl.w:ptcp.w:call-sawfish-36.t:call-run_sawfish.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:55.884 wdl.w:ptcp.w:call-sawfish-36.t:call-run_sawfish.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:23:55.898 wdl.w:ptcp.w:call-paraphase-37.t:call-run_paraphase INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:23:55.898 wdl.w:ptcp.w:call-paraphase-37.t:call-run_paraphase INFO input :: name: "annotation_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf"
2025-09-15 20:23:55.898 wdl.w:ptcp.w:call-paraphase-37.t:call-run_paraphase INFO input :: name: "genome_version", value: "38"
2025-09-15 20:23:55.898 wdl.w:ptcp.w:call-paraphase-37.t:call-run_paraphase INFO input :: name: "config_file", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/paraphase_config.GRCh38.yaml"
2025-09-15 20:23:55.898 wdl.w:ptcp.w:call-paraphase-37.t:call-run_paraphase INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:23:55.899 wdl.w:ptcp.w:call-paraphase-37.t:call-run_paraphase INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:23:55.899 wdl.w:ptcp.w:call-paraphase-37.t:call-run_paraphase INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2134.mapped.bam.bai"
2025-09-15 20:23:55.899 wdl.w:ptcp.w:call-paraphase-37.t:call-run_paraphase INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2134.mapped.bam"
2025-09-15 20:23:55.899 wdl.w:ptcp.w:call-paraphase-37.t:call-run_paraphase INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2134"
2025-09-15 20:23:55.899 wdl.w:ptcp.w:call-paraphase-37.t:call-run_paraphase INFO eval :: name: "threads", value: 4
2025-09-15 20:23:55.899 wdl.w:ptcp.w:call-paraphase-37.t:call-run_paraphase INFO eval :: name: "mem_gb", value: 8
2025-09-15 20:23:55.900 wdl.w:ptcp.w:call-paraphase-37.t:call-run_paraphase INFO eval :: name: "disk_size", value: 27
2025-09-15 20:23:55.900 wdl.w:ptcp.w:call-paraphase-37.t:call-run_paraphase INFO eval :: name: "out_dir", value: "m84036_250809_035451_s4.bc2134_paraphase"
2025-09-15 20:23:55.900 wdl.w:ptcp.w:call-paraphase-37.t:call-run_paraphase INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 4, memory_reservation: 8000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:23:55.901 wdl.w:ptcp.w:call-paraphase-37.t:call-run_paraphase WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:23:55.901 wdl.w:ptcp.w:call-paraphase-37.t:call-run_paraphase INFO provisioned :: seconds_waited: 0, cpu: 4, mem_bytes: 8000000000
2025-09-15 20:23:55.901 wdl.w:ptcp.w:call-paraphase-37.t:call-run_paraphase INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:23:55.928 wdl.w:ptcp.w:call-paraphase-04.t:call-call_f8 NOTICE done
2025-09-15 20:23:55.935 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_genotype INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 11, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-38/call-trgt_genotype/_singularity_tmpdir_ffo5pfy3"
2025-09-15 20:23:55.935 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_genotype INFO Slurm invocation: srun --job-name call-trgt_genotype --partition compute,compute9 --cpus-per-task 8 --mem 15259M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-38/call-trgt_genotype/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-38/call-trgt_genotype/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-38/call-trgt_genotype/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-38/call-trgt_genotype/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-38/out/m84036_250809_035451_s4.bc2135.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2135.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-38/out/m84036_250809_035451_s4.bc2135.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2135.mapped.bam.bai:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-38/call-trgt_genotype/_singularity_tmpdir_ffo5pfy3/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-38/call-trgt_genotype/_singularity_tmpdir_ffo5pfy3/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:23:55.938 wdl.w:ptcp.w:call-paraphase-04 NOTICE finish :: job: "call-call_f8"
2025-09-15 20:23:55.938 wdl.w:ptcp.w:call-paraphase-04 INFO output :: job: "call-call_f8", values: {"json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-04/call-call_f8/out/m84036_250809_035451_s4.bc2101.f8inversion.json", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-04/call-call_f8/out/m84036_250809_035451_s4.bc2101.f8inversion.vcf"}
2025-09-15 20:23:55.938 wdl.w:ptcp.w:call-paraphase-04 INFO visit :: node: "output-f8_json", values: {"f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-04/call-call_f8/out/m84036_250809_035451_s4.bc2101.f8inversion.json"}
2025-09-15 20:23:55.939 wdl.w:ptcp.w:call-paraphase-04 INFO visit :: node: "output-f8_vcf", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-04/call-call_f8/out/m84036_250809_035451_s4.bc2101.f8inversion.vcf"}
2025-09-15 20:23:55.939 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_motifs_waterfall INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2111.motifs_waterfall.trgt_plots.zip"
2025-09-15 20:23:55.939 wdl.w:ptcp.w:call-paraphase-04 INFO visit :: node: "outputs", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-04/call-call_f8/out/m84036_250809_035451_s4.bc2101.f8inversion.vcf", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-04/call-run_paraphase/out/m84036_250809_035451_s4.bc2101_paraphase/m84036_250809_035451_s4.bc2101.paraphase.json", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-04/call-run_paraphase/out/m84036_250809_035451_s4.bc2101_paraphase/m84036_250809_035451_s4.bc2101.paraphase.bam", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-04/call-run_paraphase/out/m84036_250809_035451_s4.bc2101_paraphase/m84036_250809_035451_s4.bc2101.paraphase.bam.bai", "paraphase_vcfs": [], "havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-04/call-run_paraphase/out/m84036_250809_035451_s4.bc2101.havanno.json", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-04/call-call_f8/out/m84036_250809_035451_s4.bc2101.f8inversion.json"}
2025-09-15 20:23:55.946 wdl.w:ptcp.w:call-sawfish-37.t:call-run_sawfish NOTICE task setup :: name: "run_sawfish", source: "./sawfish.wdl", line: 83, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-37/call-run_sawfish", thread: 140609260066368
2025-09-15 20:23:55.975 wdl.w:ptcp.w:call-paraphase-20 NOTICE done
2025-09-15 20:23:55.975 wdl.w:ptcp.w:call-sawfish-37.t:call-run_sawfish INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:23:55.975 wdl.w:ptcp.w:call-sawfish-37.t:call-run_sawfish INFO input :: name: "genome_version", value: "38"
2025-09-15 20:23:55.975 wdl.w:ptcp.w:call-sawfish-37.t:call-run_sawfish INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:23:55.975 wdl.w:ptcp.w:call-sawfish-37.t:call-run_sawfish INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:23:55.976 wdl.w:ptcp.w:call-sawfish-37.t:call-run_sawfish INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2134.mapped.bam.bai"
2025-09-15 20:23:55.976 wdl.w:ptcp.w:call-sawfish-37.t:call-run_sawfish INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2134.mapped.bam"
2025-09-15 20:23:55.976 wdl.w:ptcp.w:call-sawfish-37.t:call-run_sawfish INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2134"
2025-09-15 20:23:55.976 wdl.w:ptcp.w:call-sawfish-37.t:call-run_sawfish INFO eval :: name: "mem_gb", value: 32
2025-09-15 20:23:55.976 wdl.w:ptcp.w:call-sawfish-37.t:call-run_sawfish INFO eval :: name: "threads", value: 16
2025-09-15 20:23:55.976 wdl.w:ptcp.w:call-sawfish-37.t:call-run_sawfish INFO eval :: name: "disk_size", value: 30
2025-09-15 20:23:55.977 wdl.w:ptcp.w:call-sawfish-37.t:call-run_sawfish INFO eval :: name: "discover_dirname", value: "m84036_250809_035451_s4.bc2134_sawfish_discover"
2025-09-15 20:23:55.977 wdl.w:ptcp.w:call-sawfish-37.t:call-run_sawfish INFO eval :: name: "call_dirname", value: "m84036_250809_035451_s4.bc2134_sawfish"
2025-09-15 20:23:55.977 wdl.w:ptcp.w:call-sawfish-37.t:call-run_sawfish INFO eval :: name: "minimap2_bam_filename", value: "m84036_250809_035451_s4.bc2134.minimap2.bam"
2025-09-15 20:23:55.977 wdl.w:ptcp.w:call-sawfish-37.t:call-run_sawfish INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 16, memory_reservation: 32000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:23:55.977 wdl.w:ptcp.w:call-sawfish-37.t:call-run_sawfish WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:23:55.978 wdl.w:ptcp.w:call-sawfish-37.t:call-run_sawfish INFO provisioned :: seconds_waited: 0, cpu: 16, mem_bytes: 32000000000
2025-09-15 20:23:55.978 wdl.w:ptcp.w:call-sawfish-37.t:call-run_sawfish INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:23:55.979 wdl.w:ptcp.w:call-trgt-23.t:call-trgt_plot_motifs_waterfall NOTICE done
2025-09-15 20:23:55.985 wdl.w:ptcp NOTICE finish :: job: "call-paraphase-20"
2025-09-15 20:23:55.985 wdl.w:ptcp INFO output :: job: "call-paraphase-20", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-20/out/m84036_250809_035451_s4.bc2117.f8inversion.vcf", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-20/out/m84036_250809_035451_s4.bc2117_paraphase/m84036_250809_035451_s4.bc2117.paraphase.json", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-20/out/m84036_250809_035451_s4.bc2117_paraphase/m84036_250809_035451_s4.bc2117.paraphase.bam", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-20/out/m84036_250809_035451_s4.bc2117_paraphase/m84036_250809_035451_s4.bc2117.paraphase.bam.bai", "paraphase_vcfs": [], "havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-20/out/m84036_250809_035451_s4.bc2117.havanno.json", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-20/out/m84036_250809_035451_s4.bc2117.f8inversion.json"}
2025-09-15 20:23:55.988 wdl.w:ptcp.w:call-trgt-23 NOTICE finish :: job: "call-trgt_plot_motifs_waterfall"
2025-09-15 20:23:55.988 wdl.w:ptcp.w:call-trgt-23 INFO output :: job: "call-trgt_plot_motifs_waterfall", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-23/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2120.motifs_waterfall.trgt_plots.zip"}
2025-09-15 20:23:55.988 wdl.w:ptcp.w:call-trgt-23 INFO visit :: node: "output-images_motifs_waterfall", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-23/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2120.motifs_waterfall.trgt_plots.zip"}
2025-09-15 20:23:55.988 wdl.w:ptcp.w:call-trgt-23 INFO visit :: node: "outputs", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-23/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2120.motifs_waterfall.trgt_plots.zip", "images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-23/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2120.meth_allele.trgt_plots.zip", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-23/call-trgt_genotype/out/m84036_250809_035451_s4.bc2120.trgt.sorted.spanning.bam.bai", "images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-23/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2120.motifs_allele.trgt_plots.zip", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-23/call-trgt_genotype/out/m84036_250809_035451_s4.bc2120.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-23/call-trgt_genotype/out/m84036_250809_035451_s4.bc2120.trgt.vcf", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-23/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2120.repeats.bam", "images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-23/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2120.meth_waterfall.trgt_plots.zip", "reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-23/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2120.repeats.bam.bai"}
2025-09-15 20:23:55.994 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_genotype NOTICE slurm_singularity run :: pid: 1200532, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-38/call-trgt_genotype/slurm_singularity.log.txt"
2025-09-15 20:23:55.995 wdl.w:ptcp.w:call-trgt-47 NOTICE workflow start :: name: "trgt", source: "./trgt.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-47"
2025-09-15 20:23:55.997 wdl.w:ptcp.w:call-trgt-37.t:call-get_reads_overlapping_repeats NOTICE task setup :: name: "get_reads_overlapping_repeats", source: "./trgt.wdl", line: 182, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-37/call-get_reads_overlapping_repeats", thread: 140609838900800
2025-09-15 20:23:56.017 wdl.w:ptcp.w:call-trgt-47 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:23:56.017 wdl.w:ptcp.w:call-paraphase-37.t:call-run_paraphase INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-37/call-run_paraphase/_singularity_tmpdir_w59dmxyn"
2025-09-15 20:23:56.018 wdl.w:ptcp.w:call-trgt-47 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-47/out/m84036_250809_035451_s4.bc2144.mapped.bam"}
2025-09-15 20:23:56.018 wdl.w:ptcp.w:call-paraphase-37.t:call-run_paraphase INFO Slurm invocation: srun --job-name call-run_paraphase --partition compute,compute9 --cpus-per-task 4 --mem 7629M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-37/call-run_paraphase/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-37/call-run_paraphase/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-37/call-run_paraphase/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-37/call-run_paraphase/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-37/out/m84036_250809_035451_s4.bc2134.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2134.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-37/out/m84036_250809_035451_s4.bc2134.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2134.mapped.bam:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/variant_list/variant_list.GRCh38.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf:ro --bind /ptcp/meta/paraphase/paraphase_config.GRCh38.yaml:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/paraphase_config.GRCh38.yaml:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-37/call-run_paraphase/_singularity_tmpdir_w59dmxyn/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-37/call-run_paraphase/_singularity_tmpdir_w59dmxyn/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:23:56.018 wdl.w:ptcp.w:call-trgt-47 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-47/out/m84036_250809_035451_s4.bc2144.mapped.bam.bai"}
2025-09-15 20:23:56.018 wdl.w:ptcp.w:call-trgt-47 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:23:56.019 wdl.w:ptcp.w:call-trgt-47 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:23:56.019 wdl.w:ptcp.w:call-trgt-47 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2144"}
2025-09-15 20:23:56.020 wdl.w:ptcp.w:call-trgt-47 INFO visit :: node: "decl-sex", values: {"sex": "F"}
2025-09-15 20:23:56.021 wdl.w:ptcp.w:call-trgt-47 INFO visit :: node: "decl-trgt_bed", values: {"trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"}
2025-09-15 20:23:56.021 wdl.w:ptcp.w:call-trgt-47 NOTICE ready :: job: "call-get_reads_overlapping_repeats", callee: "get_reads_overlapping_repeats"
2025-09-15 20:23:56.022 wdl.w:ptcp.w:call-trgt-47 INFO input :: job: "call-get_reads_overlapping_repeats", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-47/out/m84036_250809_035451_s4.bc2144.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-47/out/m84036_250809_035451_s4.bc2144.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2144"}
2025-09-15 20:23:56.023 wdl.w:ptcp.w:call-trgt-47 NOTICE ready :: job: "call-trgt_genotype", callee: "trgt_genotype"
2025-09-15 20:23:56.023 wdl.w:ptcp.w:call-trgt-47 INFO input :: job: "call-trgt_genotype", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-47/out/m84036_250809_035451_s4.bc2144.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-47/out/m84036_250809_035451_s4.bc2144.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2144"}
2025-09-15 20:23:56.032 wdl.w:ptcp.w:call-trgt-37.t:call-get_reads_overlapping_repeats INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:23:56.032 wdl.w:ptcp.w:call-trgt-37.t:call-get_reads_overlapping_repeats INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:23:56.032 wdl.w:ptcp.w:call-trgt-37.t:call-get_reads_overlapping_repeats INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2134.mapped.bam.bai"
2025-09-15 20:23:56.032 wdl.w:ptcp.w:call-trgt-37.t:call-get_reads_overlapping_repeats INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2134.mapped.bam"
2025-09-15 20:23:56.032 wdl.w:ptcp.w:call-trgt-37.t:call-get_reads_overlapping_repeats INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2134"
2025-09-15 20:23:56.032 wdl.w:ptcp.w:call-trgt-37.t:call-get_reads_overlapping_repeats INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:23:56.033 wdl.w:ptcp.w:call-trgt-37.t:call-get_reads_overlapping_repeats INFO eval :: name: "expand_size", value: 3000
2025-09-15 20:23:56.033 wdl.w:ptcp.w:call-trgt-37.t:call-get_reads_overlapping_repeats INFO eval :: name: "threads", value: 1
2025-09-15 20:23:56.033 wdl.w:ptcp.w:call-trgt-37.t:call-get_reads_overlapping_repeats INFO eval :: name: "expanded_bed_name", value: "m84036_250809_035451_s4.bc2134.expanded.bed"
2025-09-15 20:23:56.033 wdl.w:ptcp.w:call-trgt-37.t:call-get_reads_overlapping_repeats INFO eval :: name: "disk_size", value: 11
2025-09-15 20:23:56.034 wdl.w:ptcp.w:call-trgt-37.t:call-get_reads_overlapping_repeats INFO eval :: name: "output_name", value: "m84036_250809_035451_s4.bc2134.repeats.bam"
2025-09-15 20:23:56.034 wdl.w:ptcp.w:call-trgt-37.t:call-get_reads_overlapping_repeats INFO eval :: name: "index_name", value: "m84036_250809_035451_s4.bc2134.repeats.bam.bai"
2025-09-15 20:23:56.034 wdl.w:ptcp.w:call-trgt-37.t:call-get_reads_overlapping_repeats INFO eval :: name: "output_name_with_index", value: "m84036_250809_035451_s4.bc2134.repeats.bam##idx##m84036_250809_035451_s4.bc2134.repeats.bam.bai"
2025-09-15 20:23:56.034 wdl.w:ptcp.w:call-trgt-37.t:call-get_reads_overlapping_repeats INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:23:56.034 wdl.w:ptcp.w:call-trgt-37.t:call-get_reads_overlapping_repeats WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:23:56.035 wdl.w:ptcp.w:call-trgt-37.t:call-get_reads_overlapping_repeats INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:23:56.035 wdl.w:ptcp.w:call-trgt-37.t:call-get_reads_overlapping_repeats INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:23:56.045 wdl.w:ptcp.w:call-paraphase-37.t:call-run_paraphase NOTICE slurm_singularity run :: pid: 1200534, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-37/call-run_paraphase/slurm_singularity.log.txt"
2025-09-15 20:23:56.078 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_motifs_waterfall NOTICE done
2025-09-15 20:23:56.081 wdl.w:ptcp.w:call-paraphase-04 NOTICE done
2025-09-15 20:23:56.086 wdl.w:ptcp.w:call-trgt-14 NOTICE finish :: job: "call-trgt_plot_motifs_waterfall"
2025-09-15 20:23:56.086 wdl.w:ptcp.w:call-trgt-14 INFO output :: job: "call-trgt_plot_motifs_waterfall", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-14/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2111.motifs_waterfall.trgt_plots.zip"}
2025-09-15 20:23:56.086 wdl.w:ptcp.w:call-trgt-14 INFO visit :: node: "output-images_motifs_waterfall", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-14/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2111.motifs_waterfall.trgt_plots.zip"}
2025-09-15 20:23:56.087 wdl.w:ptcp.w:call-sawfish-37.t:call-run_sawfish INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 10, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-37/call-run_sawfish/_singularity_tmpdir_t3_i9e6g"
2025-09-15 20:23:56.087 wdl.w:ptcp.w:call-sawfish-37.t:call-run_sawfish INFO Slurm invocation: srun --job-name call-run_sawfish --partition compute,compute9 --cpus-per-task 16 --mem 30518M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-37/call-run_sawfish/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-37/call-run_sawfish/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-37/call-run_sawfish/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-37/call-run_sawfish/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-37/out/m84036_250809_035451_s4.bc2134.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2134.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-37/out/m84036_250809_035451_s4.bc2134.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2134.mapped.bam:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-37/call-run_sawfish/_singularity_tmpdir_t3_i9e6g/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-37/call-run_sawfish/_singularity_tmpdir_t3_i9e6g/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:23:56.088 wdl.w:ptcp NOTICE finish :: job: "call-paraphase-04"
2025-09-15 20:23:56.089 wdl.w:ptcp INFO output :: job: "call-paraphase-04", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-04/out/m84036_250809_035451_s4.bc2101.f8inversion.vcf", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-04/out/m84036_250809_035451_s4.bc2101_paraphase/m84036_250809_035451_s4.bc2101.paraphase.json", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-04/out/m84036_250809_035451_s4.bc2101_paraphase/m84036_250809_035451_s4.bc2101.paraphase.bam", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-04/out/m84036_250809_035451_s4.bc2101_paraphase/m84036_250809_035451_s4.bc2101.paraphase.bam.bai", "paraphase_vcfs": [], "havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-04/out/m84036_250809_035451_s4.bc2101.havanno.json", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-04/out/m84036_250809_035451_s4.bc2101.f8inversion.json"}
2025-09-15 20:23:56.096 wdl.w:ptcp.w:call-trgt-36.t:call-get_reads_overlapping_repeats.slurm_singularity INFO srun: job 51797508 queued and waiting for resources
2025-09-15 20:23:56.096 wdl.w:ptcp.w:call-trgt-36.t:call-get_reads_overlapping_repeats.slurm_singularity INFO srun: job 51797508 has been allocated resources
2025-09-15 20:23:56.096 wdl.w:ptcp.w:call-trgt-36.t:call-get_reads_overlapping_repeats.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:56.096 wdl.w:ptcp.w:call-trgt-36.t:call-get_reads_overlapping_repeats.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:23:56.098 wdl.w:ptcp.w:call-trgt-37.t:call-trgt_genotype NOTICE task setup :: name: "trgt_genotype", source: "./trgt.wdl", line: 272, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-37/call-trgt_genotype", thread: 140613823374912
2025-09-15 20:23:56.103 wdl.w:ptcp.w:call-paraphase-50 NOTICE workflow start :: name: "paraphase", source: "./paraphase.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-50"
2025-09-15 20:23:56.115 wdl.w:ptcp.w:call-sawfish-37.t:call-run_sawfish NOTICE slurm_singularity run :: pid: 1200536, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-37/call-run_sawfish/slurm_singularity.log.txt"
2025-09-15 20:23:56.124 wdl.w:ptcp.w:call-paraphase-50 INFO visit :: node: "decl-annotation_vcf", values: {"annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf"}
2025-09-15 20:23:56.124 wdl.w:ptcp.w:call-paraphase-50 INFO visit :: node: "decl-config_file", values: {"config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml"}
2025-09-15 20:23:56.124 wdl.w:ptcp.w:call-paraphase-50 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:23:56.124 wdl.w:ptcp.w:call-paraphase-50 INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:23:56.125 wdl.w:ptcp.w:call-paraphase-50 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-50/out/m84036_250809_035451_s4.bc2147.mapped.bam"}
2025-09-15 20:23:56.125 wdl.w:ptcp.w:call-paraphase-50 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-50/out/m84036_250809_035451_s4.bc2147.mapped.bam.bai"}
2025-09-15 20:23:56.125 wdl.w:ptcp.w:call-paraphase-50 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:23:56.125 wdl.w:ptcp.w:call-paraphase-50 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:23:56.125 wdl.w:ptcp.w:call-paraphase-50 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2147"}
2025-09-15 20:23:56.125 wdl.w:ptcp.w:call-paraphase-50 INFO visit :: node: "decl-sex", values: {"sex": "F"}
2025-09-15 20:23:56.126 wdl.w:ptcp.w:call-paraphase-50 NOTICE ready :: job: "call-run_paraphase", callee: "run_paraphase"
2025-09-15 20:23:56.126 wdl.w:ptcp.w:call-paraphase-50 INFO input :: job: "call-run_paraphase", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf", "genome_version": "38", "config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-50/out/m84036_250809_035451_s4.bc2147.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-50/out/m84036_250809_035451_s4.bc2147.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2147"}
2025-09-15 20:23:56.128 wdl.w:ptcp.w:call-trgt-37.t:call-get_reads_overlapping_repeats INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 9, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-37/call-get_reads_overlapping_repeats/_singularity_tmpdir_mvp7qksj"
2025-09-15 20:23:56.128 wdl.w:ptcp.w:call-trgt-37.t:call-get_reads_overlapping_repeats INFO Slurm invocation: srun --job-name call-get_reads_overlapping_repeats --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-37/call-get_reads_overlapping_repeats/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-37/call-get_reads_overlapping_repeats/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-37/call-get_reads_overlapping_repeats/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-37/call-get_reads_overlapping_repeats/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-37/out/m84036_250809_035451_s4.bc2134.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2134.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-37/out/m84036_250809_035451_s4.bc2134.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2134.mapped.bam:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-37/call-get_reads_overlapping_repeats/_singularity_tmpdir_mvp7qksj/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-37/call-get_reads_overlapping_repeats/_singularity_tmpdir_mvp7qksj/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:23:56.129 wdl.w:ptcp.w:call-trgt-37.t:call-trgt_genotype INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:23:56.132 wdl.w:ptcp.w:call-trgt-37.t:call-trgt_genotype INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:23:56.132 wdl.w:ptcp.w:call-trgt-37.t:call-trgt_genotype INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:23:56.132 wdl.w:ptcp.w:call-trgt-37.t:call-trgt_genotype INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:23:56.132 wdl.w:ptcp.w:call-trgt-37.t:call-trgt_genotype INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2134.mapped.bam.bai"
2025-09-15 20:23:56.132 wdl.w:ptcp.w:call-trgt-37.t:call-trgt_genotype INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2134.mapped.bam"
2025-09-15 20:23:56.132 wdl.w:ptcp.w:call-trgt-37.t:call-trgt_genotype INFO input :: name: "sex", value: "F"
2025-09-15 20:23:56.132 wdl.w:ptcp.w:call-trgt-37.t:call-trgt_genotype INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2134"
2025-09-15 20:23:56.132 wdl.w:ptcp.w:call-trgt-37.t:call-trgt_genotype INFO eval :: name: "mem_gb", value: 16
2025-09-15 20:23:56.132 wdl.w:ptcp.w:call-trgt-37.t:call-trgt_genotype INFO eval :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2134.trgt"
2025-09-15 20:23:56.132 wdl.w:ptcp.w:call-trgt-37.t:call-trgt_genotype INFO eval :: name: "threads", value: 8
2025-09-15 20:23:56.133 wdl.w:ptcp.w:call-trgt-37.t:call-trgt_genotype INFO eval :: name: "disk_size", value: 27
2025-09-15 20:23:56.133 wdl.w:ptcp.w:call-trgt-37.t:call-trgt_genotype INFO eval :: name: "karyotype", value: "XX"
2025-09-15 20:23:56.133 wdl.w:ptcp.w:call-trgt-37.t:call-trgt_genotype INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 8, memory_reservation: 16000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:23:56.133 wdl.w:ptcp.w:call-trgt-37.t:call-trgt_genotype WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:23:56.134 wdl.w:ptcp.w:call-trgt-37.t:call-trgt_genotype INFO provisioned :: seconds_waited: 0, cpu: 8, mem_bytes: 16000000000
2025-09-15 20:23:56.134 wdl.w:ptcp.w:call-trgt-37.t:call-trgt_genotype INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:23:56.144 wdl.w:ptcp.w:call-trgt-23 NOTICE done
2025-09-15 20:23:56.144 wdl.w:ptcp.w:call-trgt-37.t:call-get_reads_overlapping_repeats NOTICE slurm_singularity run :: pid: 1200538, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-37/call-get_reads_overlapping_repeats/slurm_singularity.log.txt"
2025-09-15 20:23:56.150 wdl.w:ptcp NOTICE finish :: job: "call-trgt-23"
2025-09-15 20:23:56.151 wdl.w:ptcp INFO output :: job: "call-trgt-23", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-23/out/m84036_250809_035451_s4.bc2120.motifs_waterfall.trgt_plots.zip", "images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-23/out/m84036_250809_035451_s4.bc2120.meth_allele.trgt_plots.zip", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-23/out/m84036_250809_035451_s4.bc2120.trgt.sorted.spanning.bam.bai", "images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-23/out/m84036_250809_035451_s4.bc2120.motifs_allele.trgt_plots.zip", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-23/out/m84036_250809_035451_s4.bc2120.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-23/out/m84036_250809_035451_s4.bc2120.trgt.vcf", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-23/out/m84036_250809_035451_s4.bc2120.repeats.bam", "images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-23/out/m84036_250809_035451_s4.bc2120.meth_waterfall.trgt_plots.zip", "reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-23/out/m84036_250809_035451_s4.bc2120.repeats.bam.bai"}
2025-09-15 20:23:56.156 wdl.w:ptcp.w:call-sawfish-50 NOTICE workflow start :: name: "sawfish", source: "./sawfish.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-50"
2025-09-15 20:23:56.171 wdl.w:ptcp.w:call-sawfish-50 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:23:56.171 wdl.w:ptcp.w:call-sawfish-50 INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:23:56.172 wdl.w:ptcp.w:call-sawfish-50 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-50/out/m84036_250809_035451_s4.bc2147.mapped.bam"}
2025-09-15 20:23:56.172 wdl.w:ptcp.w:call-sawfish-50 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-50/out/m84036_250809_035451_s4.bc2147.mapped.bam.bai"}
2025-09-15 20:23:56.172 wdl.w:ptcp.w:call-sawfish-50 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:23:56.172 wdl.w:ptcp.w:call-sawfish-50 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:23:56.172 wdl.w:ptcp.w:call-sawfish-50 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2147"}
2025-09-15 20:23:56.172 wdl.w:ptcp.w:call-sawfish-50 NOTICE ready :: job: "call-run_sawfish", callee: "run_sawfish"
2025-09-15 20:23:56.172 wdl.w:ptcp.w:call-sawfish-50 INFO input :: job: "call-run_sawfish", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-50/out/m84036_250809_035451_s4.bc2147.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-50/out/m84036_250809_035451_s4.bc2147.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2147"}
2025-09-15 20:23:56.207 wdl.w:ptcp.w:call-trgt-37.t:call-trgt_genotype INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 11, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-37/call-trgt_genotype/_singularity_tmpdir_d4_6nbsg"
2025-09-15 20:23:56.207 wdl.w:ptcp.w:call-trgt-37.t:call-trgt_genotype INFO Slurm invocation: srun --job-name call-trgt_genotype --partition compute,compute9 --cpus-per-task 8 --mem 15259M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-37/call-trgt_genotype/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-37/call-trgt_genotype/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-37/call-trgt_genotype/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-37/call-trgt_genotype/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-37/out/m84036_250809_035451_s4.bc2134.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2134.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-37/out/m84036_250809_035451_s4.bc2134.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2134.mapped.bam:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-37/call-trgt_genotype/_singularity_tmpdir_d4_6nbsg/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-37/call-trgt_genotype/_singularity_tmpdir_d4_6nbsg/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:23:56.218 wdl.w:ptcp.w:call-trgt-37.t:call-trgt_genotype NOTICE slurm_singularity run :: pid: 1200540, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-37/call-trgt_genotype/slurm_singularity.log.txt"
2025-09-15 20:23:56.240 wdl.w:ptcp.w:call-trgt-20.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:54 [ERROR] - No reads found for TRID=PRTS_ARX
2025-09-15 20:23:56.240 wdl.w:ptcp.w:call-trgt-20.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:54 [ERROR] - No reads found for TRID=EIEE1_ARX
2025-09-15 20:23:56.497 wdl.w:ptcp.w:call-trgt-36.t:call-trgt_genotype.slurm_singularity INFO srun: job 51797510 queued and waiting for resources
2025-09-15 20:23:56.497 wdl.w:ptcp.w:call-trgt-36.t:call-trgt_genotype.slurm_singularity INFO srun: job 51797510 has been allocated resources
2025-09-15 20:23:56.497 wdl.w:ptcp.w:call-trgt-36.t:call-trgt_genotype.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:56.499 wdl.w:ptcp.w:call-paraphase-38.t:call-run_paraphase.slurm_singularity INFO srun: job 51797509 queued and waiting for resources
2025-09-15 20:23:56.499 wdl.w:ptcp.w:call-paraphase-38.t:call-run_paraphase.slurm_singularity INFO srun: job 51797509 has been allocated resources
2025-09-15 20:23:56.499 wdl.w:ptcp.w:call-paraphase-38.t:call-run_paraphase.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:56.565 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_motifs_allele INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2111.motifs_allele.trgt_plots.zip"
2025-09-15 20:23:56.634 wdl.w:ptcp.w:call-trgt-14.t:call-trgt_plot_motifs_allele NOTICE done
2025-09-15 20:23:56.640 wdl.w:ptcp.w:call-trgt-14 NOTICE finish :: job: "call-trgt_plot_motifs_allele"
2025-09-15 20:23:56.640 wdl.w:ptcp.w:call-trgt-14 INFO output :: job: "call-trgt_plot_motifs_allele", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-14/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2111.motifs_allele.trgt_plots.zip"}
2025-09-15 20:23:56.640 wdl.w:ptcp.w:call-trgt-14 INFO visit :: node: "output-images_motifs_allele", values: {"images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-14/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2111.motifs_allele.trgt_plots.zip"}
2025-09-15 20:23:56.640 wdl.w:ptcp.w:call-trgt-14 INFO visit :: node: "outputs", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-14/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2111.motifs_waterfall.trgt_plots.zip", "images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-14/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2111.meth_allele.trgt_plots.zip", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-14/call-trgt_genotype/out/m84036_250809_035451_s4.bc2111.trgt.sorted.spanning.bam.bai", "images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-14/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2111.motifs_allele.trgt_plots.zip", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-14/call-trgt_genotype/out/m84036_250809_035451_s4.bc2111.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-14/call-trgt_genotype/out/m84036_250809_035451_s4.bc2111.trgt.vcf", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-14/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2111.repeats.bam", "images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-14/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2111.meth_waterfall.trgt_plots.zip", "reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-14/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2111.repeats.bam.bai"}
2025-09-15 20:23:56.646 wdl.w:ptcp.w:call-sawfish-45.t:call-run_sawfish NOTICE task setup :: name: "run_sawfish", source: "./sawfish.wdl", line: 83, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-45/call-run_sawfish", thread: 140609813722688
2025-09-15 20:23:56.664 wdl.w:ptcp.w:call-sawfish-45.t:call-run_sawfish INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:23:56.664 wdl.w:ptcp.w:call-sawfish-45.t:call-run_sawfish INFO input :: name: "genome_version", value: "38"
2025-09-15 20:23:56.664 wdl.w:ptcp.w:call-sawfish-45.t:call-run_sawfish INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:23:56.664 wdl.w:ptcp.w:call-sawfish-45.t:call-run_sawfish INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:23:56.664 wdl.w:ptcp.w:call-sawfish-45.t:call-run_sawfish INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2142.mapped.bam.bai"
2025-09-15 20:23:56.664 wdl.w:ptcp.w:call-sawfish-45.t:call-run_sawfish INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2142.mapped.bam"
2025-09-15 20:23:56.664 wdl.w:ptcp.w:call-sawfish-45.t:call-run_sawfish INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2142"
2025-09-15 20:23:56.664 wdl.w:ptcp.w:call-sawfish-45.t:call-run_sawfish INFO eval :: name: "mem_gb", value: 32
2025-09-15 20:23:56.664 wdl.w:ptcp.w:call-sawfish-45.t:call-run_sawfish INFO eval :: name: "threads", value: 16
2025-09-15 20:23:56.664 wdl.w:ptcp.w:call-sawfish-45.t:call-run_sawfish INFO eval :: name: "disk_size", value: 30
2025-09-15 20:23:56.665 wdl.w:ptcp.w:call-sawfish-45.t:call-run_sawfish INFO eval :: name: "discover_dirname", value: "m84036_250809_035451_s4.bc2142_sawfish_discover"
2025-09-15 20:23:56.665 wdl.w:ptcp.w:call-sawfish-45.t:call-run_sawfish INFO eval :: name: "call_dirname", value: "m84036_250809_035451_s4.bc2142_sawfish"
2025-09-15 20:23:56.665 wdl.w:ptcp.w:call-sawfish-45.t:call-run_sawfish INFO eval :: name: "minimap2_bam_filename", value: "m84036_250809_035451_s4.bc2142.minimap2.bam"
2025-09-15 20:23:56.665 wdl.w:ptcp.w:call-sawfish-45.t:call-run_sawfish INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 16, memory_reservation: 32000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:23:56.665 wdl.w:ptcp.w:call-sawfish-45.t:call-run_sawfish WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:23:56.666 wdl.w:ptcp.w:call-sawfish-45.t:call-run_sawfish INFO provisioned :: seconds_waited: 0, cpu: 16, mem_bytes: 32000000000
2025-09-15 20:23:56.666 wdl.w:ptcp.w:call-sawfish-45.t:call-run_sawfish INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:23:56.666 wdl.w:ptcp.w:call-sawfish-38.t:call-run_sawfish.slurm_singularity INFO srun: job 51797511 queued and waiting for resources
2025-09-15 20:23:56.666 wdl.w:ptcp.w:call-sawfish-38.t:call-run_sawfish.slurm_singularity INFO srun: job 51797511 has been allocated resources
2025-09-15 20:23:56.666 wdl.w:ptcp.w:call-sawfish-38.t:call-run_sawfish.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:56.666 wdl.w:ptcp.w:call-sawfish-38.t:call-run_sawfish.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:23:56.733 wdl.w:ptcp.w:call-sawfish-45.t:call-run_sawfish INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 10, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-45/call-run_sawfish/_singularity_tmpdir_y15k2c86"
2025-09-15 20:23:56.734 wdl.w:ptcp.w:call-sawfish-45.t:call-run_sawfish INFO Slurm invocation: srun --job-name call-run_sawfish --partition compute,compute9 --cpus-per-task 16 --mem 30518M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-45/call-run_sawfish/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-45/call-run_sawfish/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-45/call-run_sawfish/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-45/call-run_sawfish/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-45/out/m84036_250809_035451_s4.bc2142.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2142.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-45/out/m84036_250809_035451_s4.bc2142.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2142.mapped.bam:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-45/call-run_sawfish/_singularity_tmpdir_y15k2c86/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-45/call-run_sawfish/_singularity_tmpdir_y15k2c86/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:23:56.735 wdl.w:ptcp.w:call-trgt-14 NOTICE done
2025-09-15 20:23:56.739 wdl.w:ptcp NOTICE finish :: job: "call-trgt-14"
2025-09-15 20:23:56.739 wdl.w:ptcp INFO output :: job: "call-trgt-14", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-14/out/m84036_250809_035451_s4.bc2111.motifs_waterfall.trgt_plots.zip", "images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-14/out/m84036_250809_035451_s4.bc2111.meth_allele.trgt_plots.zip", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-14/out/m84036_250809_035451_s4.bc2111.trgt.sorted.spanning.bam.bai", "images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-14/out/m84036_250809_035451_s4.bc2111.motifs_allele.trgt_plots.zip", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-14/out/m84036_250809_035451_s4.bc2111.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-14/out/m84036_250809_035451_s4.bc2111.trgt.vcf", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-14/out/m84036_250809_035451_s4.bc2111.repeats.bam", "images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-14/out/m84036_250809_035451_s4.bc2111.meth_waterfall.trgt_plots.zip", "reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-14/out/m84036_250809_035451_s4.bc2111.repeats.bam.bai"}
2025-09-15 20:23:56.747 wdl.w:ptcp.w:call-trgt-50 NOTICE workflow start :: name: "trgt", source: "./trgt.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-50"
2025-09-15 20:23:56.753 wdl.w:ptcp.w:call-trgt-38.t:call-get_reads_overlapping_repeats.slurm_singularity INFO srun: job 51797512 queued and waiting for resources
2025-09-15 20:23:56.753 wdl.w:ptcp.w:call-trgt-38.t:call-get_reads_overlapping_repeats.slurm_singularity INFO srun: job 51797512 has been allocated resources
2025-09-15 20:23:56.754 wdl.w:ptcp.w:call-trgt-38.t:call-get_reads_overlapping_repeats.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:56.768 wdl.w:ptcp.w:call-sawfish-45.t:call-run_sawfish NOTICE slurm_singularity run :: pid: 1200568, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-45/call-run_sawfish/slurm_singularity.log.txt"
2025-09-15 20:23:56.772 wdl.w:ptcp.w:call-trgt-50 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:23:56.772 wdl.w:ptcp.w:call-trgt-50 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-50/out/m84036_250809_035451_s4.bc2147.mapped.bam"}
2025-09-15 20:23:56.772 wdl.w:ptcp.w:call-trgt-50 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-50/out/m84036_250809_035451_s4.bc2147.mapped.bam.bai"}
2025-09-15 20:23:56.772 wdl.w:ptcp.w:call-trgt-50 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:23:56.773 wdl.w:ptcp.w:call-trgt-50 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:23:56.773 wdl.w:ptcp.w:call-trgt-50 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2147"}
2025-09-15 20:23:56.773 wdl.w:ptcp.w:call-trgt-50 INFO visit :: node: "decl-sex", values: {"sex": "F"}
2025-09-15 20:23:56.773 wdl.w:ptcp.w:call-trgt-50 INFO visit :: node: "decl-trgt_bed", values: {"trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"}
2025-09-15 20:23:56.773 wdl.w:ptcp.w:call-trgt-50 NOTICE ready :: job: "call-get_reads_overlapping_repeats", callee: "get_reads_overlapping_repeats"
2025-09-15 20:23:56.773 wdl.w:ptcp.w:call-trgt-50 INFO input :: job: "call-get_reads_overlapping_repeats", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-50/out/m84036_250809_035451_s4.bc2147.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-50/out/m84036_250809_035451_s4.bc2147.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2147"}
2025-09-15 20:23:56.774 wdl.w:ptcp.w:call-trgt-50 NOTICE ready :: job: "call-trgt_genotype", callee: "trgt_genotype"
2025-09-15 20:23:56.774 wdl.w:ptcp.w:call-trgt-50 INFO input :: job: "call-trgt_genotype", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-50/out/m84036_250809_035451_s4.bc2147.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-50/out/m84036_250809_035451_s4.bc2147.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2147"}
2025-09-15 20:23:57.012 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_genotype.slurm_singularity INFO srun: job 51797513 queued and waiting for resources
2025-09-15 20:23:57.012 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_genotype.slurm_singularity INFO srun: job 51797513 has been allocated resources
2025-09-15 20:23:57.012 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_genotype.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:57.053 wdl.w:ptcp.w:call-paraphase-37.t:call-run_paraphase.slurm_singularity INFO srun: job 51797514 queued and waiting for resources
2025-09-15 20:23:57.053 wdl.w:ptcp.w:call-paraphase-37.t:call-run_paraphase.slurm_singularity INFO srun: job 51797514 has been allocated resources
2025-09-15 20:23:57.053 wdl.w:ptcp.w:call-paraphase-37.t:call-run_paraphase.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:57.070 wdl.w:ptcp.w:call-paraphase-14.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for f8inv1 for sample m84036_250809_035451_s4.bc2111 at 2025-09-15 20:23:32.863585...
2025-09-15 20:23:57.071 wdl.w:ptcp.w:call-paraphase-14.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for f8inv1 for sample m84036_250809_035451_s4.bc2111 at 2025-09-15 20:23:33.237640...
2025-09-15 20:23:57.071 wdl.w:ptcp.w:call-paraphase-14.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for hba for sample m84036_250809_035451_s4.bc2111 at 2025-09-15 20:23:40.108033...
2025-09-15 20:23:57.071 wdl.w:ptcp.w:call-paraphase-14.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for hba for sample m84036_250809_035451_s4.bc2111 at 2025-09-15 20:23:40.480468...
2025-09-15 20:23:57.071 wdl.w:ptcp.w:call-paraphase-14.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for cyp21 for sample m84036_250809_035451_s4.bc2111 at 2025-09-15 20:23:43.990777...
2025-09-15 20:23:57.071 wdl.w:ptcp.w:call-paraphase-14.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for cyp21 for sample m84036_250809_035451_s4.bc2111 at 2025-09-15 20:23:44.806174...
2025-09-15 20:23:57.076 wdl.w:ptcp.w:call-paraphase-30.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for smn1 for sample m84036_250809_035451_s4.bc2127 at 2025-09-15 20:23:52.023028...
2025-09-15 20:23:57.076 wdl.w:ptcp.w:call-paraphase-30.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for f8inv1 for sample m84036_250809_035451_s4.bc2127 at 2025-09-15 20:23:56.882053...
2025-09-15 20:23:57.076 wdl.w:ptcp.w:call-paraphase-30.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for f8inv1 for sample m84036_250809_035451_s4.bc2127 at 2025-09-15 20:23:56.882252...
2025-09-15 20:23:57.117 wdl.w:ptcp.w:call-sawfish-37.t:call-run_sawfish.stderr VERBOSE [M::bam2fq_mainloop] discarded 0 singletons
2025-09-15 20:23:57.118 wdl.w:ptcp.w:call-sawfish-37.t:call-run_sawfish.stderr VERBOSE [M::bam2fq_mainloop] processed 1 reads
2025-09-15 20:23:57.130 wdl.w:ptcp.w:call-sawfish-37.t:call-run_sawfish.slurm_singularity INFO srun: job 51797515 queued and waiting for resources
2025-09-15 20:23:57.130 wdl.w:ptcp.w:call-sawfish-37.t:call-run_sawfish.slurm_singularity INFO srun: job 51797515 has been allocated resources
2025-09-15 20:23:57.130 wdl.w:ptcp.w:call-sawfish-37.t:call-run_sawfish.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:57.130 wdl.w:ptcp.w:call-sawfish-37.t:call-run_sawfish.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:23:57.153 wdl.w:ptcp.w:call-trgt-37.t:call-get_reads_overlapping_repeats.slurm_singularity INFO srun: job 51797516 queued and waiting for resources
2025-09-15 20:23:57.154 wdl.w:ptcp.w:call-trgt-37.t:call-get_reads_overlapping_repeats.slurm_singularity INFO srun: job 51797516 has been allocated resources
2025-09-15 20:23:57.154 wdl.w:ptcp.w:call-trgt-37.t:call-get_reads_overlapping_repeats.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:57.154 wdl.w:ptcp.w:call-trgt-37.t:call-get_reads_overlapping_repeats.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:23:57.158 wdl.w:ptcp.w:call-trgt-20.t:call-trgt_plot_motifs_allele INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2117.motifs_allele.trgt_plots.zip"
2025-09-15 20:23:57.230 wdl.w:ptcp.w:call-trgt-37.t:call-trgt_genotype.slurm_singularity INFO srun: job 51797517 queued and waiting for resources
2025-09-15 20:23:57.231 wdl.w:ptcp.w:call-trgt-37.t:call-trgt_genotype.slurm_singularity INFO srun: job 51797517 has been allocated resources
2025-09-15 20:23:57.231 wdl.w:ptcp.w:call-trgt-37.t:call-trgt_genotype.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:57.231 wdl.w:ptcp.w:call-trgt-37.t:call-trgt_genotype.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:23:57.232 wdl.w:ptcp.w:call-trgt-38.t:call-get_reads_overlapping_repeats INFO output :: name: "reads_overlapping_repeats", value: "m84036_250809_035451_s4.bc2135.repeats.bam"
2025-09-15 20:23:57.235 wdl.w:ptcp.w:call-trgt-38.t:call-get_reads_overlapping_repeats INFO output :: name: "reads_overlapping_repeats_bai", value: "m84036_250809_035451_s4.bc2135.repeats.bam.bai"
2025-09-15 20:23:57.271 wdl.w:ptcp.w:call-paraphase-26.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for smn1 for sample m84036_250809_035451_s4.bc2123 at 2025-09-15 20:23:38.077869...
2025-09-15 20:23:57.271 wdl.w:ptcp.w:call-paraphase-26.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for hba for sample m84036_250809_035451_s4.bc2123 at 2025-09-15 20:23:38.519961...
2025-09-15 20:23:57.271 wdl.w:ptcp.w:call-paraphase-26.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for gba for sample m84036_250809_035451_s4.bc2123 at 2025-09-15 20:23:39.423783...
2025-09-15 20:23:57.271 wdl.w:ptcp.w:call-paraphase-26.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for cyp21 for sample m84036_250809_035451_s4.bc2123 at 2025-09-15 20:23:40.275393...
2025-09-15 20:23:57.271 wdl.w:ptcp.w:call-paraphase-26.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for smn1 for sample m84036_250809_035451_s4.bc2123 at 2025-09-15 20:23:52.951379...
2025-09-15 20:23:57.271 wdl.w:ptcp.w:call-paraphase-26.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning to gene2 region for smn1 for sample m84036_250809_035451_s4.bc2123 at 2025-09-15 20:23:53.139656...
2025-09-15 20:23:57.287 wdl.w:ptcp.w:call-trgt-20.t:call-trgt_plot_motifs_allele NOTICE done
2025-09-15 20:23:57.292 wdl.w:ptcp.w:call-trgt-20 NOTICE finish :: job: "call-trgt_plot_motifs_allele"
2025-09-15 20:23:57.292 wdl.w:ptcp.w:call-trgt-20 INFO output :: job: "call-trgt_plot_motifs_allele", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-20/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2117.motifs_allele.trgt_plots.zip"}
2025-09-15 20:23:57.292 wdl.w:ptcp.w:call-trgt-20 INFO visit :: node: "output-images_motifs_allele", values: {"images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-20/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2117.motifs_allele.trgt_plots.zip"}
2025-09-15 20:23:57.297 wdl.w:ptcp.t:call-pbmm2_align_hifi-70 INFO output :: name: "mapped_bam", value: "m84036_250809_035451_s4.bc2167.mapped.bam"
2025-09-15 20:23:57.301 wdl.w:ptcp.t:call-pbmm2_align_hifi-70 INFO output :: name: "mapped_bam_bai", value: "m84036_250809_035451_s4.bc2167.mapped.bam.bai"
2025-09-15 20:23:57.302 wdl.w:ptcp.t:call-pbmm2_align_hifi-70 INFO output :: name: "mapped_bam_pbi", value: "m84036_250809_035451_s4.bc2167.mapped.bam.pbi"
2025-09-15 20:23:57.304 wdl.w:ptcp.t:call-pbmm2_align_hifi-70 INFO output :: name: "report", value: "mapping_stats.report.json"
2025-09-15 20:23:57.303 wdl.w:ptcp.w:call-paraphase-45.t:call-run_paraphase NOTICE task setup :: name: "run_paraphase", source: "./paraphase.wdl", line: 127, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-45/call-run_paraphase", thread: 140609822115392
2025-09-15 20:23:57.315 wdl.w:ptcp.w:call-trgt-38.t:call-get_reads_overlapping_repeats NOTICE done
2025-09-15 20:23:57.321 wdl.w:ptcp.w:call-trgt-38 NOTICE finish :: job: "call-get_reads_overlapping_repeats"
2025-09-15 20:23:57.321 wdl.w:ptcp.w:call-trgt-38 INFO output :: job: "call-get_reads_overlapping_repeats", values: {"reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-38/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2135.repeats.bam.bai", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-38/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2135.repeats.bam"}
2025-09-15 20:23:57.321 wdl.w:ptcp.w:call-trgt-38 INFO visit :: node: "output-reads_overlapping_repeats", values: {"reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-38/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2135.repeats.bam"}
2025-09-15 20:23:57.321 wdl.w:ptcp.w:call-trgt-38 INFO visit :: node: "output-reads_overlapping_repeats_bai", values: {"reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-38/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2135.repeats.bam.bai"}
2025-09-15 20:23:57.322 wdl.w:ptcp.w:call-paraphase-45.t:call-run_paraphase INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:23:57.322 wdl.w:ptcp.w:call-paraphase-45.t:call-run_paraphase INFO input :: name: "annotation_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf"
2025-09-15 20:23:57.323 wdl.w:ptcp.w:call-paraphase-45.t:call-run_paraphase INFO input :: name: "genome_version", value: "38"
2025-09-15 20:23:57.323 wdl.w:ptcp.w:call-paraphase-45.t:call-run_paraphase INFO input :: name: "config_file", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/paraphase_config.GRCh38.yaml"
2025-09-15 20:23:57.323 wdl.w:ptcp.w:call-paraphase-45.t:call-run_paraphase INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:23:57.323 wdl.w:ptcp.w:call-paraphase-45.t:call-run_paraphase INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:23:57.323 wdl.w:ptcp.w:call-paraphase-45.t:call-run_paraphase INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2142.mapped.bam.bai"
2025-09-15 20:23:57.323 wdl.w:ptcp.w:call-paraphase-45.t:call-run_paraphase INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2142.mapped.bam"
2025-09-15 20:23:57.323 wdl.w:ptcp.w:call-paraphase-45.t:call-run_paraphase INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2142"
2025-09-15 20:23:57.323 wdl.w:ptcp.w:call-paraphase-45.t:call-run_paraphase INFO eval :: name: "threads", value: 4
2025-09-15 20:23:57.323 wdl.w:ptcp.w:call-paraphase-45.t:call-run_paraphase INFO eval :: name: "mem_gb", value: 8
2025-09-15 20:23:57.324 wdl.w:ptcp.w:call-paraphase-45.t:call-run_paraphase INFO eval :: name: "disk_size", value: 27
2025-09-15 20:23:57.324 wdl.w:ptcp.w:call-paraphase-45.t:call-run_paraphase INFO eval :: name: "out_dir", value: "m84036_250809_035451_s4.bc2142_paraphase"
2025-09-15 20:23:57.324 wdl.w:ptcp.w:call-paraphase-45.t:call-run_paraphase INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 4, memory_reservation: 8000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:23:57.324 wdl.w:ptcp.w:call-paraphase-45.t:call-run_paraphase WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:23:57.325 wdl.w:ptcp.w:call-paraphase-45.t:call-run_paraphase INFO provisioned :: seconds_waited: 0, cpu: 4, mem_bytes: 8000000000
2025-09-15 20:23:57.325 wdl.w:ptcp.w:call-paraphase-45.t:call-run_paraphase INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:23:57.327 wdl.w:ptcp.w:call-trgt-45.t:call-get_reads_overlapping_repeats NOTICE task setup :: name: "get_reads_overlapping_repeats", source: "./trgt.wdl", line: 182, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-45/call-get_reads_overlapping_repeats", thread: 140608765158976
2025-09-15 20:23:57.352 wdl.w:ptcp.w:call-trgt-45.t:call-get_reads_overlapping_repeats INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:23:57.352 wdl.w:ptcp.w:call-trgt-45.t:call-get_reads_overlapping_repeats INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:23:57.352 wdl.w:ptcp.w:call-trgt-45.t:call-get_reads_overlapping_repeats INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2142.mapped.bam.bai"
2025-09-15 20:23:57.352 wdl.w:ptcp.w:call-trgt-45.t:call-get_reads_overlapping_repeats INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2142.mapped.bam"
2025-09-15 20:23:57.352 wdl.w:ptcp.w:call-trgt-45.t:call-get_reads_overlapping_repeats INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2142"
2025-09-15 20:23:57.353 wdl.w:ptcp.w:call-trgt-45.t:call-get_reads_overlapping_repeats INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:23:57.353 wdl.w:ptcp.w:call-trgt-45.t:call-get_reads_overlapping_repeats INFO eval :: name: "expand_size", value: 3000
2025-09-15 20:23:57.353 wdl.w:ptcp.w:call-trgt-45.t:call-get_reads_overlapping_repeats INFO eval :: name: "threads", value: 1
2025-09-15 20:23:57.353 wdl.w:ptcp.w:call-trgt-45.t:call-get_reads_overlapping_repeats INFO eval :: name: "expanded_bed_name", value: "m84036_250809_035451_s4.bc2142.expanded.bed"
2025-09-15 20:23:57.353 wdl.w:ptcp.w:call-trgt-45.t:call-get_reads_overlapping_repeats INFO eval :: name: "disk_size", value: 11
2025-09-15 20:23:57.353 wdl.w:ptcp.w:call-trgt-45.t:call-get_reads_overlapping_repeats INFO eval :: name: "output_name", value: "m84036_250809_035451_s4.bc2142.repeats.bam"
2025-09-15 20:23:57.353 wdl.w:ptcp.w:call-trgt-45.t:call-get_reads_overlapping_repeats INFO eval :: name: "index_name", value: "m84036_250809_035451_s4.bc2142.repeats.bam.bai"
2025-09-15 20:23:57.354 wdl.w:ptcp.w:call-trgt-45.t:call-get_reads_overlapping_repeats INFO eval :: name: "output_name_with_index", value: "m84036_250809_035451_s4.bc2142.repeats.bam##idx##m84036_250809_035451_s4.bc2142.repeats.bam.bai"
2025-09-15 20:23:57.354 wdl.w:ptcp.w:call-trgt-45.t:call-get_reads_overlapping_repeats INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:23:57.354 wdl.w:ptcp.w:call-trgt-45.t:call-get_reads_overlapping_repeats WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:23:57.354 wdl.w:ptcp.w:call-trgt-45.t:call-get_reads_overlapping_repeats INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:23:57.354 wdl.w:ptcp.w:call-trgt-45.t:call-get_reads_overlapping_repeats INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:23:57.400 wdl.w:ptcp.t:call-pbmm2_align_hifi-70 NOTICE done
2025-09-15 20:23:57.405 wdl.w:ptcp.w:call-paraphase-45.t:call-run_paraphase INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-45/call-run_paraphase/_singularity_tmpdir_zx87k0ce"
2025-09-15 20:23:57.406 wdl.w:ptcp.w:call-paraphase-45.t:call-run_paraphase INFO Slurm invocation: srun --job-name call-run_paraphase --partition compute,compute9 --cpus-per-task 4 --mem 7629M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-45/call-run_paraphase/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-45/call-run_paraphase/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-45/call-run_paraphase/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-45/call-run_paraphase/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-45/out/m84036_250809_035451_s4.bc2142.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2142.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-45/out/m84036_250809_035451_s4.bc2142.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2142.mapped.bam:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/variant_list/variant_list.GRCh38.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf:ro --bind /ptcp/meta/paraphase/paraphase_config.GRCh38.yaml:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/paraphase_config.GRCh38.yaml:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-45/call-run_paraphase/_singularity_tmpdir_zx87k0ce/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-45/call-run_paraphase/_singularity_tmpdir_zx87k0ce/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:23:57.407 wdl.w:ptcp NOTICE finish :: job: "call-pbmm2_align_hifi-70"
2025-09-15 20:23:57.408 wdl.w:ptcp INFO output :: job: "call-pbmm2_align_hifi-70", values: {"report": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-70/out/mapping_stats.report.json", "mapped_bam_pbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-70/out/m84036_250809_035451_s4.bc2167.mapped.bam.pbi", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-70/out/m84036_250809_035451_s4.bc2167.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-70/out/m84036_250809_035451_s4.bc2167.mapped.bam"}
2025-09-15 20:23:57.408 wdl.w:ptcp NOTICE ready :: job: "call-paraphase-70", callee: "paraphase"
2025-09-15 20:23:57.409 wdl.w:ptcp INFO input :: job: "call-paraphase-70", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf", "genome_version": "38", "config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-70/out/m84036_250809_035451_s4.bc2167.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-70/out/m84036_250809_035451_s4.bc2167.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2167"}
2025-09-15 20:23:57.411 wdl.w:ptcp NOTICE ready :: job: "call-sawfish-70", callee: "sawfish"
2025-09-15 20:23:57.411 wdl.w:ptcp INFO input :: job: "call-sawfish-70", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-70/out/m84036_250809_035451_s4.bc2167.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-70/out/m84036_250809_035451_s4.bc2167.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2167"}
2025-09-15 20:23:57.412 wdl.w:ptcp NOTICE ready :: job: "call-trgt-70", callee: "trgt"
2025-09-15 20:23:57.412 wdl.w:ptcp INFO input :: job: "call-trgt-70", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-70/out/m84036_250809_035451_s4.bc2167.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-70/out/m84036_250809_035451_s4.bc2167.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2167"}
2025-09-15 20:23:57.414 wdl.w:ptcp.w:call-trgt-45.t:call-trgt_genotype NOTICE task setup :: name: "trgt_genotype", source: "./trgt.wdl", line: 272, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-45/call-trgt_genotype", thread: 140608731588160
2025-09-15 20:23:57.424 wdl.w:ptcp.w:call-trgt-45.t:call-get_reads_overlapping_repeats INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 9, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-45/call-get_reads_overlapping_repeats/_singularity_tmpdir_lts2la6l"
2025-09-15 20:23:57.425 wdl.w:ptcp.w:call-trgt-45.t:call-get_reads_overlapping_repeats INFO Slurm invocation: srun --job-name call-get_reads_overlapping_repeats --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-45/call-get_reads_overlapping_repeats/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-45/call-get_reads_overlapping_repeats/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-45/call-get_reads_overlapping_repeats/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-45/call-get_reads_overlapping_repeats/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-45/out/m84036_250809_035451_s4.bc2142.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2142.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-45/out/m84036_250809_035451_s4.bc2142.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2142.mapped.bam:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-45/call-get_reads_overlapping_repeats/_singularity_tmpdir_lts2la6l/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-45/call-get_reads_overlapping_repeats/_singularity_tmpdir_lts2la6l/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:23:57.437 wdl.w:ptcp.w:call-trgt-45.t:call-trgt_genotype INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:23:57.437 wdl.w:ptcp.w:call-trgt-45.t:call-trgt_genotype INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:23:57.437 wdl.w:ptcp.w:call-trgt-45.t:call-trgt_genotype INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:23:57.437 wdl.w:ptcp.w:call-trgt-45.t:call-trgt_genotype INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:23:57.437 wdl.w:ptcp.w:call-trgt-45.t:call-trgt_genotype INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2142.mapped.bam.bai"
2025-09-15 20:23:57.437 wdl.w:ptcp.w:call-trgt-45.t:call-trgt_genotype INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2142.mapped.bam"
2025-09-15 20:23:57.437 wdl.w:ptcp.w:call-trgt-45.t:call-trgt_genotype INFO input :: name: "sex", value: "F"
2025-09-15 20:23:57.437 wdl.w:ptcp.w:call-trgt-45.t:call-trgt_genotype INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2142"
2025-09-15 20:23:57.438 wdl.w:ptcp.w:call-trgt-45.t:call-trgt_genotype INFO eval :: name: "mem_gb", value: 16
2025-09-15 20:23:57.438 wdl.w:ptcp.w:call-trgt-45.t:call-trgt_genotype INFO eval :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2142.trgt"
2025-09-15 20:23:57.438 wdl.w:ptcp.w:call-trgt-45.t:call-trgt_genotype INFO eval :: name: "threads", value: 8
2025-09-15 20:23:57.438 wdl.w:ptcp.w:call-trgt-45.t:call-trgt_genotype INFO eval :: name: "disk_size", value: 27
2025-09-15 20:23:57.438 wdl.w:ptcp.w:call-trgt-45.t:call-trgt_genotype INFO eval :: name: "karyotype", value: "XX"
2025-09-15 20:23:57.439 wdl.w:ptcp.w:call-trgt-45.t:call-trgt_genotype INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 8, memory_reservation: 16000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:23:57.439 wdl.w:ptcp.w:call-trgt-45.t:call-trgt_genotype WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:23:57.439 wdl.w:ptcp.w:call-trgt-45.t:call-trgt_genotype INFO provisioned :: seconds_waited: 0, cpu: 8, mem_bytes: 16000000000
2025-09-15 20:23:57.439 wdl.w:ptcp.w:call-trgt-45.t:call-trgt_genotype INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:23:57.443 wdl.w:ptcp.w:call-trgt-45.t:call-get_reads_overlapping_repeats NOTICE slurm_singularity run :: pid: 1200579, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-45/call-get_reads_overlapping_repeats/slurm_singularity.log.txt"
2025-09-15 20:23:57.443 wdl.w:ptcp.w:call-paraphase-45.t:call-run_paraphase NOTICE slurm_singularity run :: pid: 1200578, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-45/call-run_paraphase/slurm_singularity.log.txt"
2025-09-15 20:23:57.496 wdl.w:ptcp.w:call-trgt-45.t:call-trgt_genotype INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 11, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-45/call-trgt_genotype/_singularity_tmpdir_6ztrhrtn"
2025-09-15 20:23:57.496 wdl.w:ptcp.w:call-trgt-45.t:call-trgt_genotype INFO Slurm invocation: srun --job-name call-trgt_genotype --partition compute,compute9 --cpus-per-task 8 --mem 15259M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-45/call-trgt_genotype/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-45/call-trgt_genotype/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-45/call-trgt_genotype/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-45/call-trgt_genotype/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-45/out/m84036_250809_035451_s4.bc2142.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2142.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-45/out/m84036_250809_035451_s4.bc2142.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2142.mapped.bam:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-45/call-trgt_genotype/_singularity_tmpdir_6ztrhrtn/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-45/call-trgt_genotype/_singularity_tmpdir_6ztrhrtn/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:23:57.506 wdl.w:ptcp.w:call-trgt-45.t:call-trgt_genotype NOTICE slurm_singularity run :: pid: 1200582, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-45/call-trgt_genotype/slurm_singularity.log.txt"
2025-09-15 20:23:57.773 wdl.w:ptcp.w:call-sawfish-45.t:call-run_sawfish.stderr VERBOSE [M::bam2fq_mainloop] discarded 0 singletons
2025-09-15 20:23:57.773 wdl.w:ptcp.w:call-sawfish-45.t:call-run_sawfish.stderr VERBOSE [M::bam2fq_mainloop] processed 0 reads
2025-09-15 20:23:57.784 wdl.w:ptcp.w:call-sawfish-45.t:call-run_sawfish.slurm_singularity INFO srun: job 51797518 queued and waiting for resources
2025-09-15 20:23:57.784 wdl.w:ptcp.w:call-sawfish-45.t:call-run_sawfish.slurm_singularity INFO srun: job 51797518 has been allocated resources
2025-09-15 20:23:57.909 wdl.w:ptcp.w:call-paraphase-10.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for smn1 for sample m84036_250809_035451_s4.bc2107 at 2025-09-15 20:23:39.270140...
2025-09-15 20:23:57.910 wdl.w:ptcp.w:call-paraphase-10.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for hba for sample m84036_250809_035451_s4.bc2107 at 2025-09-15 20:23:39.853428...
2025-09-15 20:23:57.910 wdl.w:ptcp.w:call-paraphase-10.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for gba for sample m84036_250809_035451_s4.bc2107 at 2025-09-15 20:23:40.430846...
2025-09-15 20:23:57.910 wdl.w:ptcp.w:call-paraphase-10.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for cyp21 for sample m84036_250809_035451_s4.bc2107 at 2025-09-15 20:23:42.028430...
2025-09-15 20:23:57.910 wdl.w:ptcp.w:call-paraphase-10.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for smn1 for sample m84036_250809_035451_s4.bc2107 at 2025-09-15 20:23:54.129866...
2025-09-15 20:23:57.910 wdl.w:ptcp.w:call-paraphase-10.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning to gene2 region for smn1 for sample m84036_250809_035451_s4.bc2107 at 2025-09-15 20:23:54.638951...
2025-09-15 20:23:58.093 wdl.w:ptcp.w:call-trgt-36.t:call-trgt_genotype INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2133.trgt.vcf"
2025-09-15 20:23:58.098 wdl.w:ptcp.w:call-trgt-36.t:call-trgt_genotype INFO output :: name: "spanning_bam", value: "m84036_250809_035451_s4.bc2133.trgt.sorted.spanning.bam"
2025-09-15 20:23:58.099 wdl.w:ptcp.w:call-trgt-36.t:call-trgt_genotype INFO output :: name: "spanning_bam_bai", value: "m84036_250809_035451_s4.bc2133.trgt.sorted.spanning.bam.bai"
2025-09-15 20:23:58.168 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_genotype INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2135.trgt.vcf"
2025-09-15 20:23:58.173 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_genotype INFO output :: name: "spanning_bam", value: "m84036_250809_035451_s4.bc2135.trgt.sorted.spanning.bam"
2025-09-15 20:23:58.174 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_genotype INFO output :: name: "spanning_bam_bai", value: "m84036_250809_035451_s4.bc2135.trgt.sorted.spanning.bam.bai"
2025-09-15 20:23:58.204 wdl.w:ptcp.w:call-trgt-36.t:call-trgt_genotype NOTICE done
2025-09-15 20:23:58.207 wdl.w:ptcp.w:call-paraphase-18.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for smn1 for sample m84036_250809_035451_s4.bc2115 at 2025-09-15 20:23:37.555507...
2025-09-15 20:23:58.207 wdl.w:ptcp.w:call-paraphase-18.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for hba for sample m84036_250809_035451_s4.bc2115 at 2025-09-15 20:23:38.186899...
2025-09-15 20:23:58.207 wdl.w:ptcp.w:call-paraphase-18.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for gba for sample m84036_250809_035451_s4.bc2115 at 2025-09-15 20:23:38.915054...
2025-09-15 20:23:58.207 wdl.w:ptcp.w:call-paraphase-18.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for cyp21 for sample m84036_250809_035451_s4.bc2115 at 2025-09-15 20:23:39.664004...
2025-09-15 20:23:58.207 wdl.w:ptcp.w:call-paraphase-18.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for smn1 for sample m84036_250809_035451_s4.bc2115 at 2025-09-15 20:23:53.144172...
2025-09-15 20:23:58.207 wdl.w:ptcp.w:call-paraphase-18.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning to gene2 region for smn1 for sample m84036_250809_035451_s4.bc2115 at 2025-09-15 20:23:53.424684...
2025-09-15 20:23:58.209 wdl.w:ptcp.w:call-trgt-36 NOTICE finish :: job: "call-trgt_genotype"
2025-09-15 20:23:58.210 wdl.w:ptcp.w:call-trgt-36 INFO output :: job: "call-trgt_genotype", values: {"spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-36/call-trgt_genotype/out/m84036_250809_035451_s4.bc2133.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-36/call-trgt_genotype/out/m84036_250809_035451_s4.bc2133.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-36/call-trgt_genotype/out/m84036_250809_035451_s4.bc2133.trgt.vcf"}
2025-09-15 20:23:58.210 wdl.w:ptcp.w:call-trgt-36 NOTICE ready :: job: "call-trgt_plot_meth_allele", callee: "trgt_plot"
2025-09-15 20:23:58.210 wdl.w:ptcp.w:call-trgt-36 INFO input :: job: "call-trgt_plot_meth_allele", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": false, "methylation": true, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-36/call-trgt_genotype/out/m84036_250809_035451_s4.bc2133.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-36/call-trgt_genotype/out/m84036_250809_035451_s4.bc2133.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-36/call-trgt_genotype/out/m84036_250809_035451_s4.bc2133.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2133"}
2025-09-15 20:23:58.212 wdl.w:ptcp.w:call-trgt-36 NOTICE ready :: job: "call-trgt_plot_meth_waterfall", callee: "trgt_plot"
2025-09-15 20:23:58.212 wdl.w:ptcp.w:call-trgt-36 INFO input :: job: "call-trgt_plot_meth_waterfall", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": true, "methylation": true, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-36/call-trgt_genotype/out/m84036_250809_035451_s4.bc2133.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-36/call-trgt_genotype/out/m84036_250809_035451_s4.bc2133.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-36/call-trgt_genotype/out/m84036_250809_035451_s4.bc2133.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2133"}
2025-09-15 20:23:58.213 wdl.w:ptcp.w:call-trgt-36 NOTICE ready :: job: "call-trgt_plot_motifs_allele", callee: "trgt_plot"
2025-09-15 20:23:58.213 wdl.w:ptcp.w:call-trgt-36 INFO input :: job: "call-trgt_plot_motifs_allele", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": false, "methylation": false, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-36/call-trgt_genotype/out/m84036_250809_035451_s4.bc2133.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-36/call-trgt_genotype/out/m84036_250809_035451_s4.bc2133.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-36/call-trgt_genotype/out/m84036_250809_035451_s4.bc2133.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2133"}
2025-09-15 20:23:58.214 wdl.w:ptcp.w:call-trgt-36 NOTICE ready :: job: "call-trgt_plot_motifs_waterfall", callee: "trgt_plot"
2025-09-15 20:23:58.214 wdl.w:ptcp.w:call-trgt-36 INFO input :: job: "call-trgt_plot_motifs_waterfall", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": true, "methylation": false, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-36/call-trgt_genotype/out/m84036_250809_035451_s4.bc2133.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-36/call-trgt_genotype/out/m84036_250809_035451_s4.bc2133.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-36/call-trgt_genotype/out/m84036_250809_035451_s4.bc2133.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2133"}
2025-09-15 20:23:58.215 wdl.w:ptcp.w:call-trgt-36 INFO visit :: node: "output-spanning_bam", values: {"spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-36/call-trgt_genotype/out/m84036_250809_035451_s4.bc2133.trgt.sorted.spanning.bam"}
2025-09-15 20:23:58.215 wdl.w:ptcp.w:call-trgt-36 INFO visit :: node: "output-spanning_bam_bai", values: {"spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-36/call-trgt_genotype/out/m84036_250809_035451_s4.bc2133.trgt.sorted.spanning.bam.bai"}
2025-09-15 20:23:58.215 wdl.w:ptcp.w:call-trgt-36 INFO visit :: node: "output-vcf", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-36/call-trgt_genotype/out/m84036_250809_035451_s4.bc2133.trgt.vcf"}
2025-09-15 20:23:58.216 wdl.w:ptcp.w:call-trgt-36.t:call-get_reads_overlapping_repeats INFO output :: name: "reads_overlapping_repeats", value: "m84036_250809_035451_s4.bc2133.repeats.bam"
2025-09-15 20:23:58.219 wdl.w:ptcp.w:call-paraphase-51.t:call-run_paraphase NOTICE task setup :: name: "run_paraphase", source: "./paraphase.wdl", line: 127, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-51/call-run_paraphase", thread: 140609805329984
2025-09-15 20:23:58.222 wdl.w:ptcp.w:call-trgt-36.t:call-get_reads_overlapping_repeats INFO output :: name: "reads_overlapping_repeats_bai", value: "m84036_250809_035451_s4.bc2133.repeats.bam.bai"
2025-09-15 20:23:58.250 wdl.w:ptcp.w:call-paraphase-51.t:call-run_paraphase INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:23:58.250 wdl.w:ptcp.w:call-paraphase-51.t:call-run_paraphase INFO input :: name: "annotation_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf"
2025-09-15 20:23:58.250 wdl.w:ptcp.w:call-paraphase-51.t:call-run_paraphase INFO input :: name: "genome_version", value: "38"
2025-09-15 20:23:58.250 wdl.w:ptcp.w:call-paraphase-51.t:call-run_paraphase INFO input :: name: "config_file", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/paraphase_config.GRCh38.yaml"
2025-09-15 20:23:58.250 wdl.w:ptcp.w:call-paraphase-51.t:call-run_paraphase INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:23:58.250 wdl.w:ptcp.w:call-paraphase-51.t:call-run_paraphase INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:23:58.251 wdl.w:ptcp.w:call-paraphase-51.t:call-run_paraphase INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2148.mapped.bam.bai"
2025-09-15 20:23:58.251 wdl.w:ptcp.w:call-paraphase-51.t:call-run_paraphase INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2148.mapped.bam"
2025-09-15 20:23:58.251 wdl.w:ptcp.w:call-paraphase-51.t:call-run_paraphase INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2148"
2025-09-15 20:23:58.251 wdl.w:ptcp.w:call-paraphase-51.t:call-run_paraphase INFO eval :: name: "threads", value: 4
2025-09-15 20:23:58.251 wdl.w:ptcp.w:call-paraphase-51.t:call-run_paraphase INFO eval :: name: "mem_gb", value: 8
2025-09-15 20:23:58.251 wdl.w:ptcp.w:call-paraphase-51.t:call-run_paraphase INFO eval :: name: "disk_size", value: 27
2025-09-15 20:23:58.251 wdl.w:ptcp.w:call-paraphase-51.t:call-run_paraphase INFO eval :: name: "out_dir", value: "m84036_250809_035451_s4.bc2148_paraphase"
2025-09-15 20:23:58.252 wdl.w:ptcp.w:call-paraphase-51.t:call-run_paraphase INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 4, memory_reservation: 8000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:23:58.252 wdl.w:ptcp.w:call-paraphase-51.t:call-run_paraphase WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:23:58.252 wdl.w:ptcp.w:call-paraphase-51.t:call-run_paraphase INFO provisioned :: seconds_waited: 0, cpu: 4, mem_bytes: 8000000000
2025-09-15 20:23:58.252 wdl.w:ptcp.w:call-paraphase-51.t:call-run_paraphase INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:23:58.298 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_genotype NOTICE done
2025-09-15 20:23:58.304 wdl.w:ptcp.w:call-trgt-38 NOTICE finish :: job: "call-trgt_genotype"
2025-09-15 20:23:58.304 wdl.w:ptcp.w:call-trgt-38 INFO output :: job: "call-trgt_genotype", values: {"spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-38/call-trgt_genotype/out/m84036_250809_035451_s4.bc2135.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-38/call-trgt_genotype/out/m84036_250809_035451_s4.bc2135.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-38/call-trgt_genotype/out/m84036_250809_035451_s4.bc2135.trgt.vcf"}
2025-09-15 20:23:58.305 wdl.w:ptcp.w:call-trgt-38 NOTICE ready :: job: "call-trgt_plot_meth_allele", callee: "trgt_plot"
2025-09-15 20:23:58.305 wdl.w:ptcp.w:call-trgt-38 INFO input :: job: "call-trgt_plot_meth_allele", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": false, "methylation": true, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-38/call-trgt_genotype/out/m84036_250809_035451_s4.bc2135.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-38/call-trgt_genotype/out/m84036_250809_035451_s4.bc2135.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-38/call-trgt_genotype/out/m84036_250809_035451_s4.bc2135.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2135"}
2025-09-15 20:23:58.306 wdl.w:ptcp.w:call-trgt-38 NOTICE ready :: job: "call-trgt_plot_meth_waterfall", callee: "trgt_plot"
2025-09-15 20:23:58.307 wdl.w:ptcp.w:call-trgt-38 INFO input :: job: "call-trgt_plot_meth_waterfall", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": true, "methylation": true, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-38/call-trgt_genotype/out/m84036_250809_035451_s4.bc2135.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-38/call-trgt_genotype/out/m84036_250809_035451_s4.bc2135.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-38/call-trgt_genotype/out/m84036_250809_035451_s4.bc2135.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2135"}
2025-09-15 20:23:58.308 wdl.w:ptcp.w:call-trgt-38 NOTICE ready :: job: "call-trgt_plot_motifs_allele", callee: "trgt_plot"
2025-09-15 20:23:58.308 wdl.w:ptcp.w:call-trgt-38 INFO input :: job: "call-trgt_plot_motifs_allele", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": false, "methylation": false, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-38/call-trgt_genotype/out/m84036_250809_035451_s4.bc2135.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-38/call-trgt_genotype/out/m84036_250809_035451_s4.bc2135.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-38/call-trgt_genotype/out/m84036_250809_035451_s4.bc2135.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2135"}
2025-09-15 20:23:58.309 wdl.w:ptcp.w:call-trgt-38 NOTICE ready :: job: "call-trgt_plot_motifs_waterfall", callee: "trgt_plot"
2025-09-15 20:23:58.309 wdl.w:ptcp.w:call-trgt-38 INFO input :: job: "call-trgt_plot_motifs_waterfall", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": true, "methylation": false, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-38/call-trgt_genotype/out/m84036_250809_035451_s4.bc2135.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-38/call-trgt_genotype/out/m84036_250809_035451_s4.bc2135.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-38/call-trgt_genotype/out/m84036_250809_035451_s4.bc2135.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2135"}
2025-09-15 20:23:58.310 wdl.w:ptcp.w:call-trgt-38 INFO visit :: node: "output-spanning_bam", values: {"spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-38/call-trgt_genotype/out/m84036_250809_035451_s4.bc2135.trgt.sorted.spanning.bam"}
2025-09-15 20:23:58.310 wdl.w:ptcp.w:call-trgt-38 INFO visit :: node: "output-spanning_bam_bai", values: {"spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-38/call-trgt_genotype/out/m84036_250809_035451_s4.bc2135.trgt.sorted.spanning.bam.bai"}
2025-09-15 20:23:58.310 wdl.w:ptcp.w:call-trgt-38 INFO visit :: node: "output-vcf", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-38/call-trgt_genotype/out/m84036_250809_035451_s4.bc2135.trgt.vcf"}
2025-09-15 20:23:58.317 wdl.w:ptcp.w:call-sawfish-51.t:call-run_sawfish NOTICE task setup :: name: "run_sawfish", source: "./sawfish.wdl", line: 83, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-51/call-run_sawfish", thread: 140608739980864
2025-09-15 20:23:58.325 wdl.w:ptcp.w:call-trgt-36.t:call-get_reads_overlapping_repeats NOTICE done
2025-09-15 20:23:58.331 wdl.w:ptcp.w:call-trgt-36 NOTICE finish :: job: "call-get_reads_overlapping_repeats"
2025-09-15 20:23:58.331 wdl.w:ptcp.w:call-trgt-36 INFO output :: job: "call-get_reads_overlapping_repeats", values: {"reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-36/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2133.repeats.bam.bai", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-36/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2133.repeats.bam"}
2025-09-15 20:23:58.331 wdl.w:ptcp.w:call-trgt-36 INFO visit :: node: "output-reads_overlapping_repeats", values: {"reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-36/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2133.repeats.bam"}
2025-09-15 20:23:58.331 wdl.w:ptcp.w:call-trgt-36 INFO visit :: node: "output-reads_overlapping_repeats_bai", values: {"reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-36/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2133.repeats.bam.bai"}
2025-09-15 20:23:58.342 wdl.w:ptcp.w:call-trgt-51.t:call-get_reads_overlapping_repeats NOTICE task setup :: name: "get_reads_overlapping_repeats", source: "./trgt.wdl", line: 182, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-51/call-get_reads_overlapping_repeats", thread: 140612506469952
2025-09-15 20:23:58.343 wdl.w:ptcp.w:call-sawfish-51.t:call-run_sawfish INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:23:58.343 wdl.w:ptcp.w:call-sawfish-51.t:call-run_sawfish INFO input :: name: "genome_version", value: "38"
2025-09-15 20:23:58.343 wdl.w:ptcp.w:call-sawfish-51.t:call-run_sawfish INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:23:58.344 wdl.w:ptcp.w:call-sawfish-51.t:call-run_sawfish INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:23:58.344 wdl.w:ptcp.w:call-sawfish-51.t:call-run_sawfish INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2148.mapped.bam.bai"
2025-09-15 20:23:58.344 wdl.w:ptcp.w:call-sawfish-51.t:call-run_sawfish INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2148.mapped.bam"
2025-09-15 20:23:58.344 wdl.w:ptcp.w:call-sawfish-51.t:call-run_sawfish INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2148"
2025-09-15 20:23:58.344 wdl.w:ptcp.w:call-sawfish-51.t:call-run_sawfish INFO eval :: name: "mem_gb", value: 32
2025-09-15 20:23:58.344 wdl.w:ptcp.w:call-sawfish-51.t:call-run_sawfish INFO eval :: name: "threads", value: 16
2025-09-15 20:23:58.344 wdl.w:ptcp.w:call-sawfish-51.t:call-run_sawfish INFO eval :: name: "disk_size", value: 30
2025-09-15 20:23:58.345 wdl.w:ptcp.w:call-sawfish-51.t:call-run_sawfish INFO eval :: name: "discover_dirname", value: "m84036_250809_035451_s4.bc2148_sawfish_discover"
2025-09-15 20:23:58.345 wdl.w:ptcp.w:call-sawfish-51.t:call-run_sawfish INFO eval :: name: "call_dirname", value: "m84036_250809_035451_s4.bc2148_sawfish"
2025-09-15 20:23:58.345 wdl.w:ptcp.w:call-sawfish-51.t:call-run_sawfish INFO eval :: name: "minimap2_bam_filename", value: "m84036_250809_035451_s4.bc2148.minimap2.bam"
2025-09-15 20:23:58.345 wdl.w:ptcp.w:call-sawfish-51.t:call-run_sawfish INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 16, memory_reservation: 32000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:23:58.345 wdl.w:ptcp.w:call-sawfish-51.t:call-run_sawfish WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:23:58.346 wdl.w:ptcp.w:call-sawfish-51.t:call-run_sawfish INFO provisioned :: seconds_waited: 0, cpu: 16, mem_bytes: 32000000000
2025-09-15 20:23:58.346 wdl.w:ptcp.w:call-sawfish-51.t:call-run_sawfish INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:23:58.347 wdl.w:ptcp.w:call-paraphase-51.t:call-run_paraphase INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-51/call-run_paraphase/_singularity_tmpdir_69c3kcik"
2025-09-15 20:23:58.347 wdl.w:ptcp.w:call-paraphase-51.t:call-run_paraphase INFO Slurm invocation: srun --job-name call-run_paraphase --partition compute,compute9 --cpus-per-task 4 --mem 7629M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-51/call-run_paraphase/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-51/call-run_paraphase/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-51/call-run_paraphase/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-51/call-run_paraphase/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-51/out/m84036_250809_035451_s4.bc2148.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2148.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-51/out/m84036_250809_035451_s4.bc2148.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2148.mapped.bam:ro --bind /ptcp/meta/variant_list/variant_list.GRCh38.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf:ro --bind /ptcp/meta/paraphase/paraphase_config.GRCh38.yaml:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/paraphase_config.GRCh38.yaml:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-51/call-run_paraphase/_singularity_tmpdir_69c3kcik/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-51/call-run_paraphase/_singularity_tmpdir_69c3kcik/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:23:58.361 wdl.w:ptcp.w:call-trgt-51.t:call-get_reads_overlapping_repeats INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:23:58.361 wdl.w:ptcp.w:call-trgt-51.t:call-get_reads_overlapping_repeats INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:23:58.361 wdl.w:ptcp.w:call-trgt-51.t:call-get_reads_overlapping_repeats INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2148.mapped.bam.bai"
2025-09-15 20:23:58.361 wdl.w:ptcp.w:call-trgt-51.t:call-get_reads_overlapping_repeats INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2148.mapped.bam"
2025-09-15 20:23:58.361 wdl.w:ptcp.w:call-trgt-51.t:call-get_reads_overlapping_repeats INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2148"
2025-09-15 20:23:58.361 wdl.w:ptcp.w:call-trgt-51.t:call-get_reads_overlapping_repeats INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:23:58.361 wdl.w:ptcp.w:call-trgt-51.t:call-get_reads_overlapping_repeats INFO eval :: name: "expand_size", value: 3000
2025-09-15 20:23:58.361 wdl.w:ptcp.w:call-trgt-51.t:call-get_reads_overlapping_repeats INFO eval :: name: "threads", value: 1
2025-09-15 20:23:58.361 wdl.w:ptcp.w:call-trgt-51.t:call-get_reads_overlapping_repeats INFO eval :: name: "expanded_bed_name", value: "m84036_250809_035451_s4.bc2148.expanded.bed"
2025-09-15 20:23:58.362 wdl.w:ptcp.w:call-trgt-51.t:call-get_reads_overlapping_repeats INFO eval :: name: "disk_size", value: 11
2025-09-15 20:23:58.362 wdl.w:ptcp.w:call-trgt-51.t:call-get_reads_overlapping_repeats INFO eval :: name: "output_name", value: "m84036_250809_035451_s4.bc2148.repeats.bam"
2025-09-15 20:23:58.362 wdl.w:ptcp.w:call-trgt-51.t:call-get_reads_overlapping_repeats INFO eval :: name: "index_name", value: "m84036_250809_035451_s4.bc2148.repeats.bam.bai"
2025-09-15 20:23:58.362 wdl.w:ptcp.w:call-trgt-51.t:call-get_reads_overlapping_repeats INFO eval :: name: "output_name_with_index", value: "m84036_250809_035451_s4.bc2148.repeats.bam##idx##m84036_250809_035451_s4.bc2148.repeats.bam.bai"
2025-09-15 20:23:58.362 wdl.w:ptcp.w:call-trgt-51.t:call-get_reads_overlapping_repeats INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:23:58.362 wdl.w:ptcp.w:call-trgt-51.t:call-get_reads_overlapping_repeats WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:23:58.362 wdl.w:ptcp.w:call-trgt-51.t:call-get_reads_overlapping_repeats INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:23:58.363 wdl.w:ptcp.w:call-trgt-51.t:call-get_reads_overlapping_repeats INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:23:58.388 wdl.w:ptcp.w:call-paraphase-51.t:call-run_paraphase NOTICE slurm_singularity run :: pid: 1200602, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-51/call-run_paraphase/slurm_singularity.log.txt"
2025-09-15 20:23:58.428 wdl.w:ptcp.w:call-trgt-04.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:57 [ERROR] - No reads found for TRID=PRTS_ARX
2025-09-15 20:23:58.429 wdl.w:ptcp.w:call-trgt-04.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:23:57 [ERROR] - No reads found for TRID=EIEE1_ARX
2025-09-15 20:23:58.440 wdl.w:ptcp.w:call-sawfish-51.t:call-run_sawfish INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 10, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-51/call-run_sawfish/_singularity_tmpdir_6m546br1"
2025-09-15 20:23:58.440 wdl.w:ptcp.w:call-sawfish-51.t:call-run_sawfish INFO Slurm invocation: srun --job-name call-run_sawfish --partition compute,compute9 --cpus-per-task 16 --mem 30518M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-51/call-run_sawfish/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-51/call-run_sawfish/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-51/call-run_sawfish/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-51/call-run_sawfish/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-51/out/m84036_250809_035451_s4.bc2148.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2148.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-51/out/m84036_250809_035451_s4.bc2148.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2148.mapped.bam:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-51/call-run_sawfish/_singularity_tmpdir_6m546br1/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-51/call-run_sawfish/_singularity_tmpdir_6m546br1/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:23:58.446 wdl.w:ptcp.w:call-trgt-51.t:call-get_reads_overlapping_repeats INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 9, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-51/call-get_reads_overlapping_repeats/_singularity_tmpdir_8kapadyz"
2025-09-15 20:23:58.447 wdl.w:ptcp.w:call-trgt-51.t:call-get_reads_overlapping_repeats INFO Slurm invocation: srun --job-name call-get_reads_overlapping_repeats --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-51/call-get_reads_overlapping_repeats/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-51/call-get_reads_overlapping_repeats/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-51/call-get_reads_overlapping_repeats/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-51/call-get_reads_overlapping_repeats/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-51/out/m84036_250809_035451_s4.bc2148.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2148.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-51/out/m84036_250809_035451_s4.bc2148.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2148.mapped.bam:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-51/call-get_reads_overlapping_repeats/_singularity_tmpdir_8kapadyz/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-51/call-get_reads_overlapping_repeats/_singularity_tmpdir_8kapadyz/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:23:58.456 wdl.w:ptcp.w:call-trgt-45.t:call-get_reads_overlapping_repeats.slurm_singularity INFO srun: job 51797519 queued and waiting for resources
2025-09-15 20:23:58.456 wdl.w:ptcp.w:call-trgt-45.t:call-get_reads_overlapping_repeats.slurm_singularity INFO srun: job 51797519 has been allocated resources
2025-09-15 20:23:58.456 wdl.w:ptcp.w:call-paraphase-45.t:call-run_paraphase.slurm_singularity INFO srun: job 51797520 queued and waiting for resources
2025-09-15 20:23:58.457 wdl.w:ptcp.w:call-trgt-45.t:call-get_reads_overlapping_repeats.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:58.457 wdl.w:ptcp.w:call-paraphase-45.t:call-run_paraphase.slurm_singularity INFO srun: job 51797520 has been allocated resources
2025-09-15 20:23:58.457 wdl.w:ptcp.w:call-paraphase-45.t:call-run_paraphase.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:58.471 wdl.w:ptcp.w:call-sawfish-51.t:call-run_sawfish NOTICE slurm_singularity run :: pid: 1200604, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-51/call-run_sawfish/slurm_singularity.log.txt"
2025-09-15 20:23:58.471 wdl.w:ptcp.w:call-trgt-51.t:call-get_reads_overlapping_repeats NOTICE slurm_singularity run :: pid: 1200605, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-51/call-get_reads_overlapping_repeats/slurm_singularity.log.txt"
2025-09-15 20:23:58.471 wdl.w:ptcp.w:call-trgt-04.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:23:58 [ERROR] - No reads found for TRID=PRTS_ARX
2025-09-15 20:23:58.472 wdl.w:ptcp.w:call-trgt-04.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:23:58 [ERROR] - No reads found for TRID=EIEE1_ARX
2025-09-15 20:23:58.522 wdl.w:ptcp.w:call-trgt-45.t:call-trgt_genotype.slurm_singularity INFO srun: job 51797521 queued and waiting for resources
2025-09-15 20:23:58.522 wdl.w:ptcp.w:call-trgt-45.t:call-trgt_genotype.slurm_singularity INFO srun: job 51797521 has been allocated resources
2025-09-15 20:23:58.522 wdl.w:ptcp.w:call-trgt-45.t:call-trgt_genotype.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:58.553 wdl.w:ptcp.w:call-trgt-37.t:call-trgt_genotype INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2134.trgt.vcf"
2025-09-15 20:23:58.558 wdl.w:ptcp.w:call-trgt-37.t:call-trgt_genotype INFO output :: name: "spanning_bam", value: "m84036_250809_035451_s4.bc2134.trgt.sorted.spanning.bam"
2025-09-15 20:23:58.562 wdl.w:ptcp.w:call-trgt-37.t:call-trgt_genotype INFO output :: name: "spanning_bam_bai", value: "m84036_250809_035451_s4.bc2134.trgt.sorted.spanning.bam.bai"
2025-09-15 20:23:58.658 wdl.w:ptcp.w:call-trgt-37.t:call-trgt_genotype NOTICE done
2025-09-15 20:23:58.663 wdl.w:ptcp.w:call-trgt-37 NOTICE finish :: job: "call-trgt_genotype"
2025-09-15 20:23:58.664 wdl.w:ptcp.w:call-trgt-37 INFO output :: job: "call-trgt_genotype", values: {"spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-37/call-trgt_genotype/out/m84036_250809_035451_s4.bc2134.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-37/call-trgt_genotype/out/m84036_250809_035451_s4.bc2134.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-37/call-trgt_genotype/out/m84036_250809_035451_s4.bc2134.trgt.vcf"}
2025-09-15 20:23:58.664 wdl.w:ptcp.w:call-trgt-37 NOTICE ready :: job: "call-trgt_plot_meth_allele", callee: "trgt_plot"
2025-09-15 20:23:58.664 wdl.w:ptcp.w:call-trgt-37 INFO input :: job: "call-trgt_plot_meth_allele", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": false, "methylation": true, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-37/call-trgt_genotype/out/m84036_250809_035451_s4.bc2134.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-37/call-trgt_genotype/out/m84036_250809_035451_s4.bc2134.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-37/call-trgt_genotype/out/m84036_250809_035451_s4.bc2134.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2134"}
2025-09-15 20:23:58.667 wdl.w:ptcp.w:call-trgt-37 NOTICE ready :: job: "call-trgt_plot_meth_waterfall", callee: "trgt_plot"
2025-09-15 20:23:58.667 wdl.w:ptcp.w:call-trgt-37 INFO input :: job: "call-trgt_plot_meth_waterfall", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": true, "methylation": true, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-37/call-trgt_genotype/out/m84036_250809_035451_s4.bc2134.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-37/call-trgt_genotype/out/m84036_250809_035451_s4.bc2134.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-37/call-trgt_genotype/out/m84036_250809_035451_s4.bc2134.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2134"}
2025-09-15 20:23:58.667 wdl.w:ptcp.w:call-trgt-37 NOTICE ready :: job: "call-trgt_plot_motifs_allele", callee: "trgt_plot"
2025-09-15 20:23:58.668 wdl.w:ptcp.w:call-trgt-37 INFO input :: job: "call-trgt_plot_motifs_allele", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": false, "methylation": false, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-37/call-trgt_genotype/out/m84036_250809_035451_s4.bc2134.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-37/call-trgt_genotype/out/m84036_250809_035451_s4.bc2134.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-37/call-trgt_genotype/out/m84036_250809_035451_s4.bc2134.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2134"}
2025-09-15 20:23:58.668 wdl.w:ptcp.w:call-trgt-37 NOTICE ready :: job: "call-trgt_plot_motifs_waterfall", callee: "trgt_plot"
2025-09-15 20:23:58.668 wdl.w:ptcp.w:call-trgt-37 INFO input :: job: "call-trgt_plot_motifs_waterfall", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": true, "methylation": false, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-37/call-trgt_genotype/out/m84036_250809_035451_s4.bc2134.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-37/call-trgt_genotype/out/m84036_250809_035451_s4.bc2134.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-37/call-trgt_genotype/out/m84036_250809_035451_s4.bc2134.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2134"}
2025-09-15 20:23:58.669 wdl.w:ptcp.w:call-trgt-37 INFO visit :: node: "output-spanning_bam", values: {"spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-37/call-trgt_genotype/out/m84036_250809_035451_s4.bc2134.trgt.sorted.spanning.bam"}
2025-09-15 20:23:58.669 wdl.w:ptcp.w:call-trgt-37 INFO visit :: node: "output-spanning_bam_bai", values: {"spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-37/call-trgt_genotype/out/m84036_250809_035451_s4.bc2134.trgt.sorted.spanning.bam.bai"}
2025-09-15 20:23:58.669 wdl.w:ptcp.w:call-trgt-37 INFO visit :: node: "output-vcf", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-37/call-trgt_genotype/out/m84036_250809_035451_s4.bc2134.trgt.vcf"}
2025-09-15 20:23:58.670 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_genotype NOTICE task setup :: name: "trgt_genotype", source: "./trgt.wdl", line: 272, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-51/call-trgt_genotype", thread: 140613823374912
2025-09-15 20:23:58.684 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_genotype INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:23:58.684 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_genotype INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:23:58.684 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_genotype INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:23:58.685 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_genotype INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:23:58.685 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_genotype INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2148.mapped.bam.bai"
2025-09-15 20:23:58.685 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_genotype INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2148.mapped.bam"
2025-09-15 20:23:58.685 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_genotype INFO input :: name: "sex", value: "F"
2025-09-15 20:23:58.685 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_genotype INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2148"
2025-09-15 20:23:58.685 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_genotype INFO eval :: name: "mem_gb", value: 16
2025-09-15 20:23:58.685 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_genotype INFO eval :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2148.trgt"
2025-09-15 20:23:58.685 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_genotype INFO eval :: name: "threads", value: 8
2025-09-15 20:23:58.685 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_genotype INFO eval :: name: "disk_size", value: 27
2025-09-15 20:23:58.686 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_genotype INFO eval :: name: "karyotype", value: "XX"
2025-09-15 20:23:58.686 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_genotype INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 8, memory_reservation: 16000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:23:58.686 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_genotype WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:23:58.686 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_genotype INFO provisioned :: seconds_waited: 0, cpu: 8, mem_bytes: 16000000000
2025-09-15 20:23:58.686 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_genotype INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:23:58.740 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_genotype INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 11, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-51/call-trgt_genotype/_singularity_tmpdir_92nhlo4y"
2025-09-15 20:23:58.741 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_genotype INFO Slurm invocation: srun --job-name call-trgt_genotype --partition compute,compute9 --cpus-per-task 8 --mem 15259M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-51/call-trgt_genotype/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-51/call-trgt_genotype/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-51/call-trgt_genotype/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-51/call-trgt_genotype/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-51/out/m84036_250809_035451_s4.bc2148.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2148.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-51/out/m84036_250809_035451_s4.bc2148.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2148.mapped.bam:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-51/call-trgt_genotype/_singularity_tmpdir_92nhlo4y/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-51/call-trgt_genotype/_singularity_tmpdir_92nhlo4y/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:23:58.765 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_genotype NOTICE slurm_singularity run :: pid: 1200624, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-51/call-trgt_genotype/slurm_singularity.log.txt"
2025-09-15 20:23:59.064 wdl.w:ptcp.w:call-trgt-20.t:call-trgt_plot_meth_allele INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2117.meth_allele.trgt_plots.zip"
2025-09-15 20:23:59.203 wdl.w:ptcp.w:call-trgt-20.t:call-trgt_plot_meth_allele NOTICE done
2025-09-15 20:23:59.208 wdl.w:ptcp.w:call-trgt-20 NOTICE finish :: job: "call-trgt_plot_meth_allele"
2025-09-15 20:23:59.208 wdl.w:ptcp.w:call-trgt-20 INFO output :: job: "call-trgt_plot_meth_allele", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-20/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2117.meth_allele.trgt_plots.zip"}
2025-09-15 20:23:59.209 wdl.w:ptcp.w:call-trgt-20 INFO visit :: node: "output-images_meth_allele", values: {"images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-20/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2117.meth_allele.trgt_plots.zip"}
2025-09-15 20:23:59.213 wdl.w:ptcp.w:call-paraphase-46.t:call-run_paraphase NOTICE task setup :: name: "run_paraphase", source: "./paraphase.wdl", line: 127, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-46/call-run_paraphase", thread: 140609293637184
2025-09-15 20:23:59.230 wdl.w:ptcp.w:call-paraphase-46.t:call-run_paraphase INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:23:59.230 wdl.w:ptcp.w:call-paraphase-46.t:call-run_paraphase INFO input :: name: "annotation_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf"
2025-09-15 20:23:59.230 wdl.w:ptcp.w:call-paraphase-46.t:call-run_paraphase INFO input :: name: "genome_version", value: "38"
2025-09-15 20:23:59.230 wdl.w:ptcp.w:call-paraphase-46.t:call-run_paraphase INFO input :: name: "config_file", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/paraphase_config.GRCh38.yaml"
2025-09-15 20:23:59.230 wdl.w:ptcp.w:call-paraphase-46.t:call-run_paraphase INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:23:59.230 wdl.w:ptcp.w:call-paraphase-46.t:call-run_paraphase INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:23:59.231 wdl.w:ptcp.w:call-paraphase-46.t:call-run_paraphase INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2143.mapped.bam.bai"
2025-09-15 20:23:59.231 wdl.w:ptcp.w:call-paraphase-46.t:call-run_paraphase INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2143.mapped.bam"
2025-09-15 20:23:59.231 wdl.w:ptcp.w:call-paraphase-46.t:call-run_paraphase INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2143"
2025-09-15 20:23:59.231 wdl.w:ptcp.w:call-paraphase-46.t:call-run_paraphase INFO eval :: name: "threads", value: 4
2025-09-15 20:23:59.231 wdl.w:ptcp.w:call-paraphase-46.t:call-run_paraphase INFO eval :: name: "mem_gb", value: 8
2025-09-15 20:23:59.231 wdl.w:ptcp.w:call-paraphase-46.t:call-run_paraphase INFO eval :: name: "disk_size", value: 27
2025-09-15 20:23:59.231 wdl.w:ptcp.w:call-paraphase-46.t:call-run_paraphase INFO eval :: name: "out_dir", value: "m84036_250809_035451_s4.bc2143_paraphase"
2025-09-15 20:23:59.232 wdl.w:ptcp.w:call-paraphase-46.t:call-run_paraphase INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 4, memory_reservation: 8000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:23:59.232 wdl.w:ptcp.w:call-paraphase-46.t:call-run_paraphase WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:23:59.233 wdl.w:ptcp.w:call-paraphase-46.t:call-run_paraphase INFO provisioned :: seconds_waited: 0, cpu: 4, mem_bytes: 8000000000
2025-09-15 20:23:59.233 wdl.w:ptcp.w:call-paraphase-46.t:call-run_paraphase INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:23:59.301 wdl.w:ptcp.w:call-paraphase-46.t:call-run_paraphase INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-46/call-run_paraphase/_singularity_tmpdir_5d4342zu"
2025-09-15 20:23:59.301 wdl.w:ptcp.w:call-paraphase-46.t:call-run_paraphase INFO Slurm invocation: srun --job-name call-run_paraphase --partition compute,compute9 --cpus-per-task 4 --mem 7629M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-46/call-run_paraphase/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-46/call-run_paraphase/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-46/call-run_paraphase/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-46/call-run_paraphase/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-46/out/m84036_250809_035451_s4.bc2143.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2143.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-46/out/m84036_250809_035451_s4.bc2143.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2143.mapped.bam.bai:ro --bind /ptcp/meta/variant_list/variant_list.GRCh38.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf:ro --bind /ptcp/meta/paraphase/paraphase_config.GRCh38.yaml:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/paraphase_config.GRCh38.yaml:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-46/call-run_paraphase/_singularity_tmpdir_5d4342zu/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-46/call-run_paraphase/_singularity_tmpdir_5d4342zu/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:23:59.313 wdl.w:ptcp.w:call-paraphase-46.t:call-run_paraphase NOTICE slurm_singularity run :: pid: 1200632, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-46/call-run_paraphase/slurm_singularity.log.txt"
2025-09-15 20:23:59.398 wdl.w:ptcp.w:call-paraphase-51.t:call-run_paraphase.slurm_singularity INFO srun: job 51797522 queued and waiting for resources
2025-09-15 20:23:59.398 wdl.w:ptcp.w:call-paraphase-51.t:call-run_paraphase.slurm_singularity INFO srun: job 51797522 has been allocated resources
2025-09-15 20:23:59.398 wdl.w:ptcp.w:call-paraphase-51.t:call-run_paraphase.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:59.489 wdl.w:ptcp.w:call-trgt-51.t:call-get_reads_overlapping_repeats.slurm_singularity INFO srun: job 51797523 queued and waiting for resources
2025-09-15 20:23:59.489 wdl.w:ptcp.w:call-trgt-51.t:call-get_reads_overlapping_repeats.slurm_singularity INFO srun: job 51797523 has been allocated resources
2025-09-15 20:23:59.489 wdl.w:ptcp.w:call-trgt-51.t:call-get_reads_overlapping_repeats.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:59.490 wdl.w:ptcp.w:call-sawfish-51.t:call-run_sawfish.slurm_singularity INFO srun: job 51797524 queued and waiting for resources
2025-09-15 20:23:59.490 wdl.w:ptcp.w:call-sawfish-51.t:call-run_sawfish.slurm_singularity INFO srun: job 51797524 has been allocated resources
2025-09-15 20:23:59.603 wdl.w:ptcp.w:call-trgt-51.t:call-get_reads_overlapping_repeats INFO output :: name: "reads_overlapping_repeats", value: "m84036_250809_035451_s4.bc2148.repeats.bam"
2025-09-15 20:23:59.607 wdl.w:ptcp.w:call-trgt-51.t:call-get_reads_overlapping_repeats INFO output :: name: "reads_overlapping_repeats_bai", value: "m84036_250809_035451_s4.bc2148.repeats.bam.bai"
2025-09-15 20:23:59.671 wdl.w:ptcp.w:call-trgt-51.t:call-get_reads_overlapping_repeats NOTICE done
2025-09-15 20:23:59.675 wdl.w:ptcp.w:call-trgt-51 NOTICE finish :: job: "call-get_reads_overlapping_repeats"
2025-09-15 20:23:59.675 wdl.w:ptcp.w:call-trgt-51 INFO output :: job: "call-get_reads_overlapping_repeats", values: {"reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-51/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2148.repeats.bam.bai", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-51/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2148.repeats.bam"}
2025-09-15 20:23:59.675 wdl.w:ptcp.w:call-trgt-51 INFO visit :: node: "output-reads_overlapping_repeats", values: {"reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-51/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2148.repeats.bam"}
2025-09-15 20:23:59.675 wdl.w:ptcp.w:call-trgt-51 INFO visit :: node: "output-reads_overlapping_repeats_bai", values: {"reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-51/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2148.repeats.bam.bai"}
2025-09-15 20:23:59.681 wdl.w:ptcp.w:call-sawfish-46.t:call-run_sawfish NOTICE task setup :: name: "run_sawfish", source: "./sawfish.wdl", line: 83, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-46/call-run_sawfish", thread: 140612506469952
2025-09-15 20:23:59.683 wdl.w:ptcp.w:call-trgt-20.t:call-trgt_plot_motifs_waterfall INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2117.motifs_waterfall.trgt_plots.zip"
2025-09-15 20:23:59.699 wdl.w:ptcp.w:call-sawfish-46.t:call-run_sawfish INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:23:59.700 wdl.w:ptcp.w:call-sawfish-46.t:call-run_sawfish INFO input :: name: "genome_version", value: "38"
2025-09-15 20:23:59.700 wdl.w:ptcp.w:call-sawfish-46.t:call-run_sawfish INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:23:59.700 wdl.w:ptcp.w:call-sawfish-46.t:call-run_sawfish INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:23:59.700 wdl.w:ptcp.w:call-sawfish-46.t:call-run_sawfish INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2143.mapped.bam.bai"
2025-09-15 20:23:59.700 wdl.w:ptcp.w:call-sawfish-46.t:call-run_sawfish INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2143.mapped.bam"
2025-09-15 20:23:59.700 wdl.w:ptcp.w:call-sawfish-46.t:call-run_sawfish INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2143"
2025-09-15 20:23:59.700 wdl.w:ptcp.w:call-sawfish-46.t:call-run_sawfish INFO eval :: name: "mem_gb", value: 32
2025-09-15 20:23:59.700 wdl.w:ptcp.w:call-sawfish-46.t:call-run_sawfish INFO eval :: name: "threads", value: 16
2025-09-15 20:23:59.700 wdl.w:ptcp.w:call-sawfish-46.t:call-run_sawfish INFO eval :: name: "disk_size", value: 30
2025-09-15 20:23:59.701 wdl.w:ptcp.w:call-sawfish-46.t:call-run_sawfish INFO eval :: name: "discover_dirname", value: "m84036_250809_035451_s4.bc2143_sawfish_discover"
2025-09-15 20:23:59.701 wdl.w:ptcp.w:call-sawfish-46.t:call-run_sawfish INFO eval :: name: "call_dirname", value: "m84036_250809_035451_s4.bc2143_sawfish"
2025-09-15 20:23:59.701 wdl.w:ptcp.w:call-sawfish-46.t:call-run_sawfish INFO eval :: name: "minimap2_bam_filename", value: "m84036_250809_035451_s4.bc2143.minimap2.bam"
2025-09-15 20:23:59.701 wdl.w:ptcp.w:call-sawfish-46.t:call-run_sawfish INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 16, memory_reservation: 32000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:23:59.701 wdl.w:ptcp.w:call-sawfish-46.t:call-run_sawfish WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:23:59.702 wdl.w:ptcp.w:call-sawfish-46.t:call-run_sawfish INFO provisioned :: seconds_waited: 0, cpu: 16, mem_bytes: 32000000000
2025-09-15 20:23:59.702 wdl.w:ptcp.w:call-sawfish-46.t:call-run_sawfish INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:23:59.776 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_genotype.slurm_singularity INFO srun: job 51797525 queued and waiting for resources
2025-09-15 20:23:59.776 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_genotype.slurm_singularity INFO srun: job 51797525 has been allocated resources
2025-09-15 20:23:59.776 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_genotype.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:23:59.790 wdl.w:ptcp.w:call-sawfish-46.t:call-run_sawfish INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 10, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-46/call-run_sawfish/_singularity_tmpdir__hjin5cy"
2025-09-15 20:23:59.790 wdl.w:ptcp.w:call-sawfish-46.t:call-run_sawfish INFO Slurm invocation: srun --job-name call-run_sawfish --partition compute,compute9 --cpus-per-task 16 --mem 30518M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-46/call-run_sawfish/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-46/call-run_sawfish/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-46/call-run_sawfish/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-46/call-run_sawfish/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-46/out/m84036_250809_035451_s4.bc2143.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2143.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-46/out/m84036_250809_035451_s4.bc2143.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2143.mapped.bam.bai:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-46/call-run_sawfish/_singularity_tmpdir__hjin5cy/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-46/call-run_sawfish/_singularity_tmpdir__hjin5cy/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:23:59.802 wdl.w:ptcp.w:call-trgt-20.t:call-trgt_plot_motifs_waterfall NOTICE done
2025-09-15 20:23:59.808 wdl.w:ptcp.w:call-sawfish-46.t:call-run_sawfish NOTICE slurm_singularity run :: pid: 1200708, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-46/call-run_sawfish/slurm_singularity.log.txt"
2025-09-15 20:23:59.844 wdl.w:ptcp.w:call-trgt-20 NOTICE finish :: job: "call-trgt_plot_motifs_waterfall"
2025-09-15 20:23:59.844 wdl.w:ptcp.w:call-trgt-20 INFO output :: job: "call-trgt_plot_motifs_waterfall", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-20/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2117.motifs_waterfall.trgt_plots.zip"}
2025-09-15 20:23:59.844 wdl.w:ptcp.w:call-trgt-20 INFO visit :: node: "output-images_motifs_waterfall", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-20/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2117.motifs_waterfall.trgt_plots.zip"}
2025-09-15 20:23:59.850 wdl.w:ptcp.w:call-trgt-46.t:call-get_reads_overlapping_repeats NOTICE task setup :: name: "get_reads_overlapping_repeats", source: "./trgt.wdl", line: 182, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-46/call-get_reads_overlapping_repeats", thread: 140610367379008
2025-09-15 20:23:59.868 wdl.w:ptcp.w:call-trgt-04.t:call-trgt_plot_motifs_allele INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2101.motifs_allele.trgt_plots.zip"
2025-09-15 20:23:59.868 wdl.w:ptcp.w:call-trgt-46.t:call-get_reads_overlapping_repeats INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:23:59.868 wdl.w:ptcp.w:call-trgt-46.t:call-get_reads_overlapping_repeats INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:23:59.868 wdl.w:ptcp.w:call-trgt-46.t:call-get_reads_overlapping_repeats INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2143.mapped.bam.bai"
2025-09-15 20:23:59.868 wdl.w:ptcp.w:call-trgt-46.t:call-get_reads_overlapping_repeats INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2143.mapped.bam"
2025-09-15 20:23:59.868 wdl.w:ptcp.w:call-trgt-46.t:call-get_reads_overlapping_repeats INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2143"
2025-09-15 20:23:59.868 wdl.w:ptcp.w:call-trgt-46.t:call-get_reads_overlapping_repeats INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:23:59.868 wdl.w:ptcp.w:call-trgt-46.t:call-get_reads_overlapping_repeats INFO eval :: name: "expand_size", value: 3000
2025-09-15 20:23:59.868 wdl.w:ptcp.w:call-trgt-46.t:call-get_reads_overlapping_repeats INFO eval :: name: "threads", value: 1
2025-09-15 20:23:59.869 wdl.w:ptcp.w:call-trgt-46.t:call-get_reads_overlapping_repeats INFO eval :: name: "expanded_bed_name", value: "m84036_250809_035451_s4.bc2143.expanded.bed"
2025-09-15 20:23:59.869 wdl.w:ptcp.w:call-trgt-46.t:call-get_reads_overlapping_repeats INFO eval :: name: "disk_size", value: 11
2025-09-15 20:23:59.869 wdl.w:ptcp.w:call-trgt-46.t:call-get_reads_overlapping_repeats INFO eval :: name: "output_name", value: "m84036_250809_035451_s4.bc2143.repeats.bam"
2025-09-15 20:23:59.869 wdl.w:ptcp.w:call-trgt-46.t:call-get_reads_overlapping_repeats INFO eval :: name: "index_name", value: "m84036_250809_035451_s4.bc2143.repeats.bam.bai"
2025-09-15 20:23:59.869 wdl.w:ptcp.w:call-trgt-46.t:call-get_reads_overlapping_repeats INFO eval :: name: "output_name_with_index", value: "m84036_250809_035451_s4.bc2143.repeats.bam##idx##m84036_250809_035451_s4.bc2143.repeats.bam.bai"
2025-09-15 20:23:59.870 wdl.w:ptcp.w:call-trgt-46.t:call-get_reads_overlapping_repeats INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:23:59.870 wdl.w:ptcp.w:call-trgt-46.t:call-get_reads_overlapping_repeats WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:23:59.870 wdl.w:ptcp.w:call-trgt-46.t:call-get_reads_overlapping_repeats INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:23:59.870 wdl.w:ptcp.w:call-trgt-46.t:call-get_reads_overlapping_repeats INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:23:59.929 wdl.w:ptcp.w:call-trgt-46.t:call-get_reads_overlapping_repeats INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 9, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-46/call-get_reads_overlapping_repeats/_singularity_tmpdir_bp59rquq"
2025-09-15 20:23:59.929 wdl.w:ptcp.w:call-trgt-46.t:call-get_reads_overlapping_repeats INFO Slurm invocation: srun --job-name call-get_reads_overlapping_repeats --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-46/call-get_reads_overlapping_repeats/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-46/call-get_reads_overlapping_repeats/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-46/call-get_reads_overlapping_repeats/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-46/call-get_reads_overlapping_repeats/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-46/out/m84036_250809_035451_s4.bc2143.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2143.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-46/out/m84036_250809_035451_s4.bc2143.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2143.mapped.bam.bai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-46/call-get_reads_overlapping_repeats/_singularity_tmpdir_bp59rquq/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-46/call-get_reads_overlapping_repeats/_singularity_tmpdir_bp59rquq/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:23:59.955 wdl.w:ptcp.w:call-trgt-46.t:call-get_reads_overlapping_repeats NOTICE slurm_singularity run :: pid: 1200716, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-46/call-get_reads_overlapping_repeats/slurm_singularity.log.txt"
2025-09-15 20:23:59.984 wdl.w:ptcp.w:call-trgt-04.t:call-trgt_plot_motifs_allele NOTICE done
2025-09-15 20:23:59.989 wdl.w:ptcp.w:call-trgt-04 NOTICE finish :: job: "call-trgt_plot_motifs_allele"
2025-09-15 20:23:59.989 wdl.w:ptcp.w:call-trgt-04 INFO output :: job: "call-trgt_plot_motifs_allele", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-04/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2101.motifs_allele.trgt_plots.zip"}
2025-09-15 20:23:59.990 wdl.w:ptcp.w:call-trgt-04 INFO visit :: node: "output-images_motifs_allele", values: {"images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-04/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2101.motifs_allele.trgt_plots.zip"}
2025-09-15 20:23:59.996 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_genotype NOTICE task setup :: name: "trgt_genotype", source: "./trgt.wdl", line: 272, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-46/call-trgt_genotype", thread: 140609310422592
2025-09-15 20:24:00.012 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_genotype INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:00.012 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_genotype INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:00.012 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_genotype INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:00.012 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_genotype INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:00.012 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_genotype INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2143.mapped.bam.bai"
2025-09-15 20:24:00.012 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_genotype INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2143.mapped.bam"
2025-09-15 20:24:00.012 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_genotype INFO input :: name: "sex", value: "F"
2025-09-15 20:24:00.012 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_genotype INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2143"
2025-09-15 20:24:00.013 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_genotype INFO eval :: name: "mem_gb", value: 16
2025-09-15 20:24:00.013 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_genotype INFO eval :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2143.trgt"
2025-09-15 20:24:00.013 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_genotype INFO eval :: name: "threads", value: 8
2025-09-15 20:24:00.013 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_genotype INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:00.013 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_genotype INFO eval :: name: "karyotype", value: "XX"
2025-09-15 20:24:00.014 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_genotype INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 8, memory_reservation: 16000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:00.014 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_genotype WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:00.014 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_genotype INFO provisioned :: seconds_waited: 0, cpu: 8, mem_bytes: 16000000000
2025-09-15 20:24:00.014 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_genotype INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:00.098 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_genotype INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 11, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-46/call-trgt_genotype/_singularity_tmpdir_czxtyo4p"
2025-09-15 20:24:00.098 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_genotype INFO Slurm invocation: srun --job-name call-trgt_genotype --partition compute,compute9 --cpus-per-task 8 --mem 15259M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-46/call-trgt_genotype/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-46/call-trgt_genotype/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-46/call-trgt_genotype/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-46/call-trgt_genotype/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-46/out/m84036_250809_035451_s4.bc2143.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2143.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-46/out/m84036_250809_035451_s4.bc2143.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2143.mapped.bam.bai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-46/call-trgt_genotype/_singularity_tmpdir_czxtyo4p/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-46/call-trgt_genotype/_singularity_tmpdir_czxtyo4p/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:00.109 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_genotype NOTICE slurm_singularity run :: pid: 1200726, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-46/call-trgt_genotype/slurm_singularity.log.txt"
2025-09-15 20:24:00.136 wdl.w:ptcp.w:call-trgt-04.t:call-trgt_plot_meth_allele INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2101.meth_allele.trgt_plots.zip"
2025-09-15 20:24:00.155 wdl.w:ptcp.w:call-trgt-37.t:call-get_reads_overlapping_repeats INFO output :: name: "reads_overlapping_repeats", value: "m84036_250809_035451_s4.bc2134.repeats.bam"
2025-09-15 20:24:00.160 wdl.w:ptcp.w:call-trgt-37.t:call-get_reads_overlapping_repeats INFO output :: name: "reads_overlapping_repeats_bai", value: "m84036_250809_035451_s4.bc2134.repeats.bam.bai"
2025-09-15 20:24:00.224 wdl.w:ptcp.w:call-trgt-20.t:call-trgt_plot_meth_waterfall INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2117.meth_waterfall.trgt_plots.zip"
2025-09-15 20:24:00.235 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_genotype INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2148.trgt.vcf"
2025-09-15 20:24:00.239 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_genotype INFO output :: name: "spanning_bam", value: "m84036_250809_035451_s4.bc2148.trgt.sorted.spanning.bam"
2025-09-15 20:24:00.241 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_genotype INFO output :: name: "spanning_bam_bai", value: "m84036_250809_035451_s4.bc2148.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:00.244 wdl.w:ptcp.w:call-trgt-37.t:call-get_reads_overlapping_repeats NOTICE done
2025-09-15 20:24:00.249 wdl.w:ptcp.w:call-trgt-37 NOTICE finish :: job: "call-get_reads_overlapping_repeats"
2025-09-15 20:24:00.250 wdl.w:ptcp.w:call-trgt-37 INFO output :: job: "call-get_reads_overlapping_repeats", values: {"reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-37/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2134.repeats.bam.bai", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-37/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2134.repeats.bam"}
2025-09-15 20:24:00.250 wdl.w:ptcp.w:call-trgt-37 INFO visit :: node: "output-reads_overlapping_repeats", values: {"reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-37/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2134.repeats.bam"}
2025-09-15 20:24:00.250 wdl.w:ptcp.w:call-trgt-37 INFO visit :: node: "output-reads_overlapping_repeats_bai", values: {"reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-37/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2134.repeats.bam.bai"}
2025-09-15 20:24:00.260 wdl.w:ptcp.w:call-paraphase-44.t:call-run_paraphase NOTICE task setup :: name: "run_paraphase", source: "./paraphase.wdl", line: 127, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-44/call-run_paraphase", thread: 140609838900800
2025-09-15 20:24:00.286 wdl.w:ptcp.w:call-paraphase-44.t:call-run_paraphase INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:00.286 wdl.w:ptcp.w:call-paraphase-44.t:call-run_paraphase INFO input :: name: "annotation_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf"
2025-09-15 20:24:00.286 wdl.w:ptcp.w:call-paraphase-44.t:call-run_paraphase INFO input :: name: "genome_version", value: "38"
2025-09-15 20:24:00.286 wdl.w:ptcp.w:call-paraphase-44.t:call-run_paraphase INFO input :: name: "config_file", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/paraphase_config.GRCh38.yaml"
2025-09-15 20:24:00.286 wdl.w:ptcp.w:call-paraphase-44.t:call-run_paraphase INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:00.287 wdl.w:ptcp.w:call-paraphase-44.t:call-run_paraphase INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:00.287 wdl.w:ptcp.w:call-paraphase-44.t:call-run_paraphase INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2141.mapped.bam.bai"
2025-09-15 20:24:00.287 wdl.w:ptcp.w:call-paraphase-44.t:call-run_paraphase INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2141.mapped.bam"
2025-09-15 20:24:00.287 wdl.w:ptcp.w:call-paraphase-44.t:call-run_paraphase INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2141"
2025-09-15 20:24:00.287 wdl.w:ptcp.w:call-paraphase-44.t:call-run_paraphase INFO eval :: name: "threads", value: 4
2025-09-15 20:24:00.287 wdl.w:ptcp.w:call-paraphase-44.t:call-run_paraphase INFO eval :: name: "mem_gb", value: 8
2025-09-15 20:24:00.287 wdl.w:ptcp.w:call-paraphase-44.t:call-run_paraphase INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:00.287 wdl.w:ptcp.w:call-paraphase-44.t:call-run_paraphase INFO eval :: name: "out_dir", value: "m84036_250809_035451_s4.bc2141_paraphase"
2025-09-15 20:24:00.288 wdl.w:ptcp.w:call-paraphase-44.t:call-run_paraphase INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 4, memory_reservation: 8000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:00.288 wdl.w:ptcp.w:call-paraphase-44.t:call-run_paraphase WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:00.289 wdl.w:ptcp.w:call-paraphase-44.t:call-run_paraphase INFO provisioned :: seconds_waited: 0, cpu: 4, mem_bytes: 8000000000
2025-09-15 20:24:00.289 wdl.w:ptcp.w:call-paraphase-44.t:call-run_paraphase INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:00.293 wdl.w:ptcp.w:call-trgt-04.t:call-trgt_plot_meth_allele NOTICE done
2025-09-15 20:24:00.298 wdl.w:ptcp.w:call-trgt-04 NOTICE finish :: job: "call-trgt_plot_meth_allele"
2025-09-15 20:24:00.298 wdl.w:ptcp.w:call-trgt-04 INFO output :: job: "call-trgt_plot_meth_allele", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-04/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2101.meth_allele.trgt_plots.zip"}
2025-09-15 20:24:00.298 wdl.w:ptcp.w:call-trgt-04 INFO visit :: node: "output-images_meth_allele", values: {"images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-04/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2101.meth_allele.trgt_plots.zip"}
2025-09-15 20:24:00.309 wdl.w:ptcp.w:call-sawfish-44.t:call-run_sawfish NOTICE task setup :: name: "run_sawfish", source: "./sawfish.wdl", line: 83, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-44/call-run_sawfish", thread: 140610358986304
2025-09-15 20:24:00.328 wdl.w:ptcp.w:call-paraphase-46.t:call-run_paraphase.slurm_singularity INFO srun: job 51797526 queued and waiting for resources
2025-09-15 20:24:00.329 wdl.w:ptcp.w:call-paraphase-46.t:call-run_paraphase.slurm_singularity INFO srun: job 51797526 has been allocated resources
2025-09-15 20:24:00.329 wdl.w:ptcp.w:call-paraphase-46.t:call-run_paraphase.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:00.330 wdl.w:ptcp.w:call-sawfish-44.t:call-run_sawfish INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:00.330 wdl.w:ptcp.w:call-sawfish-44.t:call-run_sawfish INFO input :: name: "genome_version", value: "38"
2025-09-15 20:24:00.330 wdl.w:ptcp.w:call-sawfish-44.t:call-run_sawfish INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:00.330 wdl.w:ptcp.w:call-sawfish-44.t:call-run_sawfish INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:00.330 wdl.w:ptcp.w:call-sawfish-44.t:call-run_sawfish INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2141.mapped.bam.bai"
2025-09-15 20:24:00.331 wdl.w:ptcp.w:call-sawfish-44.t:call-run_sawfish INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2141.mapped.bam"
2025-09-15 20:24:00.331 wdl.w:ptcp.w:call-sawfish-44.t:call-run_sawfish INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2141"
2025-09-15 20:24:00.332 wdl.w:ptcp.w:call-sawfish-44.t:call-run_sawfish INFO eval :: name: "mem_gb", value: 32
2025-09-15 20:24:00.333 wdl.w:ptcp.w:call-sawfish-44.t:call-run_sawfish INFO eval :: name: "threads", value: 16
2025-09-15 20:24:00.333 wdl.w:ptcp.w:call-sawfish-44.t:call-run_sawfish INFO eval :: name: "disk_size", value: 30
2025-09-15 20:24:00.333 wdl.w:ptcp.w:call-sawfish-44.t:call-run_sawfish INFO eval :: name: "discover_dirname", value: "m84036_250809_035451_s4.bc2141_sawfish_discover"
2025-09-15 20:24:00.334 wdl.w:ptcp.w:call-sawfish-44.t:call-run_sawfish INFO eval :: name: "call_dirname", value: "m84036_250809_035451_s4.bc2141_sawfish"
2025-09-15 20:24:00.334 wdl.w:ptcp.w:call-paraphase-26.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for smn1 for sample m84036_250809_035451_s4.bc2123 at 2025-09-15 20:23:54.094446...
2025-09-15 20:24:00.334 wdl.w:ptcp.w:call-sawfish-44.t:call-run_sawfish INFO eval :: name: "minimap2_bam_filename", value: "m84036_250809_035451_s4.bc2141.minimap2.bam"
2025-09-15 20:24:00.334 wdl.w:ptcp.w:call-sawfish-44.t:call-run_sawfish INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 16, memory_reservation: 32000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:00.335 wdl.w:ptcp.w:call-sawfish-44.t:call-run_sawfish WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:00.335 wdl.w:ptcp.w:call-sawfish-44.t:call-run_sawfish INFO provisioned :: seconds_waited: 0, cpu: 16, mem_bytes: 32000000000
2025-09-15 20:24:00.336 wdl.w:ptcp.w:call-sawfish-44.t:call-run_sawfish INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:00.357 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_genotype NOTICE done
2025-09-15 20:24:00.376 wdl.w:ptcp.w:call-trgt-51 NOTICE finish :: job: "call-trgt_genotype"
2025-09-15 20:24:00.377 wdl.w:ptcp.w:call-trgt-51 INFO output :: job: "call-trgt_genotype", values: {"spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-51/call-trgt_genotype/out/m84036_250809_035451_s4.bc2148.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-51/call-trgt_genotype/out/m84036_250809_035451_s4.bc2148.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-51/call-trgt_genotype/out/m84036_250809_035451_s4.bc2148.trgt.vcf"}
2025-09-15 20:24:00.377 wdl.w:ptcp.w:call-trgt-20.t:call-trgt_plot_meth_waterfall NOTICE done
2025-09-15 20:24:00.377 wdl.w:ptcp.w:call-trgt-51 NOTICE ready :: job: "call-trgt_plot_meth_allele", callee: "trgt_plot"
2025-09-15 20:24:00.378 wdl.w:ptcp.w:call-trgt-51 INFO input :: job: "call-trgt_plot_meth_allele", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": false, "methylation": true, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-51/call-trgt_genotype/out/m84036_250809_035451_s4.bc2148.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-51/call-trgt_genotype/out/m84036_250809_035451_s4.bc2148.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-51/call-trgt_genotype/out/m84036_250809_035451_s4.bc2148.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2148"}
2025-09-15 20:24:00.378 wdl.w:ptcp.w:call-paraphase-44.t:call-run_paraphase INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-44/call-run_paraphase/_singularity_tmpdir_z81vlnt0"
2025-09-15 20:24:00.378 wdl.w:ptcp.w:call-paraphase-44.t:call-run_paraphase INFO Slurm invocation: srun --job-name call-run_paraphase --partition compute,compute9 --cpus-per-task 4 --mem 7629M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-44/call-run_paraphase/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-44/call-run_paraphase/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-44/call-run_paraphase/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-44/call-run_paraphase/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-44/out/m84036_250809_035451_s4.bc2141.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2141.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-44/out/m84036_250809_035451_s4.bc2141.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2141.mapped.bam:ro --bind /ptcp/meta/variant_list/variant_list.GRCh38.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf:ro --bind /ptcp/meta/paraphase/paraphase_config.GRCh38.yaml:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/paraphase_config.GRCh38.yaml:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-44/call-run_paraphase/_singularity_tmpdir_z81vlnt0/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-44/call-run_paraphase/_singularity_tmpdir_z81vlnt0/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:00.379 wdl.w:ptcp.w:call-trgt-51 NOTICE ready :: job: "call-trgt_plot_meth_waterfall", callee: "trgt_plot"
2025-09-15 20:24:00.380 wdl.w:ptcp.w:call-trgt-51 INFO input :: job: "call-trgt_plot_meth_waterfall", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": true, "methylation": true, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-51/call-trgt_genotype/out/m84036_250809_035451_s4.bc2148.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-51/call-trgt_genotype/out/m84036_250809_035451_s4.bc2148.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-51/call-trgt_genotype/out/m84036_250809_035451_s4.bc2148.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2148"}
2025-09-15 20:24:00.381 wdl.w:ptcp.w:call-trgt-51 NOTICE ready :: job: "call-trgt_plot_motifs_allele", callee: "trgt_plot"
2025-09-15 20:24:00.382 wdl.w:ptcp.w:call-trgt-20 NOTICE finish :: job: "call-trgt_plot_meth_waterfall"
2025-09-15 20:24:00.382 wdl.w:ptcp.w:call-trgt-51 INFO input :: job: "call-trgt_plot_motifs_allele", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": false, "methylation": false, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-51/call-trgt_genotype/out/m84036_250809_035451_s4.bc2148.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-51/call-trgt_genotype/out/m84036_250809_035451_s4.bc2148.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-51/call-trgt_genotype/out/m84036_250809_035451_s4.bc2148.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2148"}
2025-09-15 20:24:00.382 wdl.w:ptcp.w:call-trgt-20 INFO output :: job: "call-trgt_plot_meth_waterfall", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-20/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2117.meth_waterfall.trgt_plots.zip"}
2025-09-15 20:24:00.382 wdl.w:ptcp.w:call-trgt-20 INFO visit :: node: "output-images_meth_waterfall", values: {"images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-20/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2117.meth_waterfall.trgt_plots.zip"}
2025-09-15 20:24:00.383 wdl.w:ptcp.w:call-trgt-20 INFO visit :: node: "outputs", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-20/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2117.motifs_waterfall.trgt_plots.zip", "images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-20/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2117.meth_allele.trgt_plots.zip", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-20/call-trgt_genotype/out/m84036_250809_035451_s4.bc2117.trgt.sorted.spanning.bam.bai", "images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-20/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2117.motifs_allele.trgt_plots.zip", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-20/call-trgt_genotype/out/m84036_250809_035451_s4.bc2117.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-20/call-trgt_genotype/out/m84036_250809_035451_s4.bc2117.trgt.vcf", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-20/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2117.repeats.bam", "images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-20/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2117.meth_waterfall.trgt_plots.zip", "reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-20/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2117.repeats.bam.bai"}
2025-09-15 20:24:00.383 wdl.w:ptcp.w:call-trgt-51 NOTICE ready :: job: "call-trgt_plot_motifs_waterfall", callee: "trgt_plot"
2025-09-15 20:24:00.383 wdl.w:ptcp.w:call-trgt-51 INFO input :: job: "call-trgt_plot_motifs_waterfall", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": true, "methylation": false, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-51/call-trgt_genotype/out/m84036_250809_035451_s4.bc2148.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-51/call-trgt_genotype/out/m84036_250809_035451_s4.bc2148.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-51/call-trgt_genotype/out/m84036_250809_035451_s4.bc2148.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2148"}
2025-09-15 20:24:00.384 wdl.w:ptcp.w:call-trgt-51 INFO visit :: node: "output-spanning_bam", values: {"spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-51/call-trgt_genotype/out/m84036_250809_035451_s4.bc2148.trgt.sorted.spanning.bam"}
2025-09-15 20:24:00.384 wdl.w:ptcp.w:call-trgt-51 INFO visit :: node: "output-spanning_bam_bai", values: {"spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-51/call-trgt_genotype/out/m84036_250809_035451_s4.bc2148.trgt.sorted.spanning.bam.bai"}
2025-09-15 20:24:00.384 wdl.w:ptcp.w:call-trgt-51 INFO visit :: node: "output-vcf", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-51/call-trgt_genotype/out/m84036_250809_035451_s4.bc2148.trgt.vcf"}
2025-09-15 20:24:00.386 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_meth_allele NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-26/call-trgt_plot_meth_allele", thread: 140613823374912
2025-09-15 20:24:00.392 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_meth_waterfall NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-26/call-trgt_plot_meth_waterfall", thread: 140610879071808
2025-09-15 20:24:00.409 wdl.w:ptcp.w:call-paraphase-44.t:call-run_paraphase NOTICE slurm_singularity run :: pid: 1200734, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-44/call-run_paraphase/slurm_singularity.log.txt"
2025-09-15 20:24:00.412 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_meth_waterfall INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:00.413 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_meth_allele INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:00.413 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_meth_waterfall INFO input :: name: "waterfall", value: true
2025-09-15 20:24:00.413 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_meth_allele INFO input :: name: "waterfall", value: false
2025-09-15 20:24:00.413 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_meth_waterfall INFO input :: name: "methylation", value: true
2025-09-15 20:24:00.413 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_meth_allele INFO input :: name: "methylation", value: true
2025-09-15 20:24:00.413 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_meth_waterfall INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:00.413 wdl.w:ptcp.w:call-sawfish-44.t:call-run_sawfish INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 10, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-44/call-run_sawfish/_singularity_tmpdir_cuwfw8rt"
2025-09-15 20:24:00.413 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_meth_allele INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:00.414 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_meth_waterfall INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:00.414 wdl.w:ptcp.w:call-sawfish-44.t:call-run_sawfish INFO Slurm invocation: srun --job-name call-run_sawfish --partition compute,compute9 --cpus-per-task 16 --mem 30518M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-44/call-run_sawfish/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-44/call-run_sawfish/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-44/call-run_sawfish/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-44/call-run_sawfish/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-44/out/m84036_250809_035451_s4.bc2141.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2141.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-44/out/m84036_250809_035451_s4.bc2141.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2141.mapped.bam:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-44/call-run_sawfish/_singularity_tmpdir_cuwfw8rt/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-44/call-run_sawfish/_singularity_tmpdir_cuwfw8rt/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:00.414 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_meth_allele INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:00.414 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_meth_waterfall INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:00.414 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_meth_allele INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:00.414 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_meth_waterfall INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2123.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:00.415 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_meth_allele INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2123.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:00.416 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_meth_waterfall INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2123.trgt.sorted.spanning.bam"
2025-09-15 20:24:00.416 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_meth_allele INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2123.trgt.sorted.spanning.bam"
2025-09-15 20:24:00.416 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_meth_waterfall INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2123.trgt.vcf"
2025-09-15 20:24:00.416 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_meth_allele INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2123.trgt.vcf"
2025-09-15 20:24:00.416 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_meth_waterfall INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2123"
2025-09-15 20:24:00.416 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_meth_allele INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2123"
2025-09-15 20:24:00.416 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_meth_waterfall INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:00.417 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_meth_allele INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:00.417 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_meth_waterfall INFO eval :: name: "plot_type", value: "waterfall"
2025-09-15 20:24:00.417 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_meth_allele INFO eval :: name: "plot_type", value: "allele"
2025-09-15 20:24:00.417 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_meth_waterfall INFO eval :: name: "show", value: "meth"
2025-09-15 20:24:00.417 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_meth_allele INFO eval :: name: "show", value: "meth"
2025-09-15 20:24:00.417 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_meth_waterfall INFO eval :: name: "threads", value: 1
2025-09-15 20:24:00.417 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_meth_allele INFO eval :: name: "threads", value: 1
2025-09-15 20:24:00.418 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_meth_waterfall INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:00.418 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_meth_allele INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:00.418 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_meth_waterfall INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2123.meth_waterfall"
2025-09-15 20:24:00.418 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_meth_allele INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2123.meth_allele"
2025-09-15 20:24:00.419 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_meth_waterfall INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:00.419 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_meth_waterfall WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:00.419 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_meth_allele INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:00.419 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_meth_waterfall INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:00.419 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_meth_allele WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:00.420 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_meth_waterfall INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:00.420 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_meth_allele INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:00.420 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_meth_allele INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:00.426 wdl.w:ptcp.w:call-sawfish-44.t:call-run_sawfish NOTICE slurm_singularity run :: pid: 1200735, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-44/call-run_sawfish/slurm_singularity.log.txt"
2025-09-15 20:24:00.487 wdl.w:ptcp.w:call-trgt-20 NOTICE done
2025-09-15 20:24:00.494 wdl.w:ptcp NOTICE finish :: job: "call-trgt-20"
2025-09-15 20:24:00.494 wdl.w:ptcp INFO output :: job: "call-trgt-20", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-20/out/m84036_250809_035451_s4.bc2117.motifs_waterfall.trgt_plots.zip", "images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-20/out/m84036_250809_035451_s4.bc2117.meth_allele.trgt_plots.zip", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-20/out/m84036_250809_035451_s4.bc2117.trgt.sorted.spanning.bam.bai", "images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-20/out/m84036_250809_035451_s4.bc2117.motifs_allele.trgt_plots.zip", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-20/out/m84036_250809_035451_s4.bc2117.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-20/out/m84036_250809_035451_s4.bc2117.trgt.vcf", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-20/out/m84036_250809_035451_s4.bc2117.repeats.bam", "images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-20/out/m84036_250809_035451_s4.bc2117.meth_waterfall.trgt_plots.zip", "reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-20/out/m84036_250809_035451_s4.bc2117.repeats.bam.bai"}
2025-09-15 20:24:00.501 wdl.w:ptcp.w:call-paraphase-63 NOTICE workflow start :: name: "paraphase", source: "./paraphase.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-63"
2025-09-15 20:24:00.507 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_meth_allele INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-26/call-trgt_plot_meth_allele/_singularity_tmpdir_t6s1rt3d"
2025-09-15 20:24:00.508 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_meth_allele INFO Slurm invocation: srun --job-name call-trgt_plot_meth_allele --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-26/call-trgt_plot_meth_allele/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-26/call-trgt_plot_meth_allele/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-26/call-trgt_plot_meth_allele/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-26/call-trgt_plot_meth_allele/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-26/call-trgt_genotype/out/m84036_250809_035451_s4.bc2123.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2123.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-26/call-trgt_genotype/out/m84036_250809_035451_s4.bc2123.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2123.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-26/call-trgt_genotype/out/m84036_250809_035451_s4.bc2123.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2123.trgt.sorted.spanning.bam:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-26/call-trgt_plot_meth_allele/_singularity_tmpdir_t6s1rt3d/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-26/call-trgt_plot_meth_allele/_singularity_tmpdir_t6s1rt3d/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:00.508 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_meth_waterfall INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-26/call-trgt_plot_meth_waterfall/_singularity_tmpdir_pb5buw10"
2025-09-15 20:24:00.509 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_meth_waterfall INFO Slurm invocation: srun --job-name call-trgt_plot_meth_waterfall --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-26/call-trgt_plot_meth_waterfall/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-26/call-trgt_plot_meth_waterfall/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-26/call-trgt_plot_meth_waterfall/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-26/call-trgt_plot_meth_waterfall/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-26/call-trgt_genotype/out/m84036_250809_035451_s4.bc2123.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2123.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-26/call-trgt_genotype/out/m84036_250809_035451_s4.bc2123.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2123.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-26/call-trgt_genotype/out/m84036_250809_035451_s4.bc2123.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2123.trgt.sorted.spanning.bam:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-26/call-trgt_plot_meth_waterfall/_singularity_tmpdir_pb5buw10/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-26/call-trgt_plot_meth_waterfall/_singularity_tmpdir_pb5buw10/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:00.520 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_meth_waterfall NOTICE slurm_singularity run :: pid: 1200739, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-26/call-trgt_plot_meth_waterfall/slurm_singularity.log.txt"
2025-09-15 20:24:00.520 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_meth_allele NOTICE slurm_singularity run :: pid: 1200738, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-26/call-trgt_plot_meth_allele/slurm_singularity.log.txt"
2025-09-15 20:24:00.526 wdl.w:ptcp.w:call-paraphase-63 INFO visit :: node: "decl-annotation_vcf", values: {"annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf"}
2025-09-15 20:24:00.526 wdl.w:ptcp.w:call-paraphase-63 INFO visit :: node: "decl-config_file", values: {"config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml"}
2025-09-15 20:24:00.526 wdl.w:ptcp.w:call-paraphase-63 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:24:00.526 wdl.w:ptcp.w:call-paraphase-63 INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:24:00.526 wdl.w:ptcp.w:call-paraphase-63 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-63/out/m84036_250809_035451_s4.bc2160.mapped.bam"}
2025-09-15 20:24:00.526 wdl.w:ptcp.w:call-paraphase-63 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-63/out/m84036_250809_035451_s4.bc2160.mapped.bam.bai"}
2025-09-15 20:24:00.526 wdl.w:ptcp.w:call-paraphase-63 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:24:00.526 wdl.w:ptcp.w:call-paraphase-63 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:24:00.526 wdl.w:ptcp.w:call-paraphase-63 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2160"}
2025-09-15 20:24:00.527 wdl.w:ptcp.w:call-paraphase-63 INFO visit :: node: "decl-sex", values: {"sex": "F"}
2025-09-15 20:24:00.527 wdl.w:ptcp.w:call-paraphase-63 NOTICE ready :: job: "call-run_paraphase", callee: "run_paraphase"
2025-09-15 20:24:00.527 wdl.w:ptcp.w:call-paraphase-63 INFO input :: job: "call-run_paraphase", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf", "genome_version": "38", "config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-63/out/m84036_250809_035451_s4.bc2160.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-63/out/m84036_250809_035451_s4.bc2160.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2160"}
2025-09-15 20:24:00.812 wdl.w:ptcp.w:call-trgt-04.t:call-trgt_plot_motifs_waterfall INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2101.motifs_waterfall.trgt_plots.zip"
2025-09-15 20:24:00.821 wdl.w:ptcp.w:call-sawfish-46.t:call-run_sawfish.slurm_singularity INFO srun: job 51797527 queued and waiting for resources
2025-09-15 20:24:00.821 wdl.w:ptcp.w:call-sawfish-46.t:call-run_sawfish.slurm_singularity INFO srun: job 51797527 has been allocated resources
2025-09-15 20:24:00.821 wdl.w:ptcp.w:call-sawfish-46.t:call-run_sawfish.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:00.822 wdl.w:ptcp.w:call-sawfish-46.t:call-run_sawfish.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:24:00.914 wdl.w:ptcp.w:call-trgt-04.t:call-trgt_plot_motifs_waterfall NOTICE done
2025-09-15 20:24:00.920 wdl.w:ptcp.w:call-trgt-04 NOTICE finish :: job: "call-trgt_plot_motifs_waterfall"
2025-09-15 20:24:00.920 wdl.w:ptcp.w:call-trgt-04 INFO output :: job: "call-trgt_plot_motifs_waterfall", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-04/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2101.motifs_waterfall.trgt_plots.zip"}
2025-09-15 20:24:00.920 wdl.w:ptcp.w:call-trgt-04 INFO visit :: node: "output-images_motifs_waterfall", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-04/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2101.motifs_waterfall.trgt_plots.zip"}
2025-09-15 20:24:00.925 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_motifs_allele NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-26/call-trgt_plot_motifs_allele", thread: 140608748373568
2025-09-15 20:24:00.941 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_motifs_allele INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:00.941 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_motifs_allele INFO input :: name: "waterfall", value: false
2025-09-15 20:24:00.941 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_motifs_allele INFO input :: name: "methylation", value: false
2025-09-15 20:24:00.941 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_motifs_allele INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:00.941 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_motifs_allele INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:00.941 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_motifs_allele INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:00.941 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_motifs_allele INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2123.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:00.942 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_motifs_allele INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2123.trgt.sorted.spanning.bam"
2025-09-15 20:24:00.942 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_motifs_allele INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2123.trgt.vcf"
2025-09-15 20:24:00.942 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_motifs_allele INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2123"
2025-09-15 20:24:00.942 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_motifs_allele INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:00.942 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_motifs_allele INFO eval :: name: "plot_type", value: "allele"
2025-09-15 20:24:00.942 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_motifs_allele INFO eval :: name: "show", value: "motifs"
2025-09-15 20:24:00.942 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_motifs_allele INFO eval :: name: "threads", value: 1
2025-09-15 20:24:00.943 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_motifs_allele INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:00.943 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_motifs_allele INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2123.motifs_allele"
2025-09-15 20:24:00.943 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_motifs_allele INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:00.943 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_motifs_allele WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:00.943 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_motifs_allele INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:00.944 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_motifs_allele INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:00.967 wdl.w:ptcp.w:call-trgt-46.t:call-get_reads_overlapping_repeats.slurm_singularity INFO srun: job 51797528 queued and waiting for resources
2025-09-15 20:24:00.967 wdl.w:ptcp.w:call-trgt-46.t:call-get_reads_overlapping_repeats.slurm_singularity INFO srun: job 51797528 has been allocated resources
2025-09-15 20:24:00.967 wdl.w:ptcp.w:call-trgt-46.t:call-get_reads_overlapping_repeats.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:01.004 wdl.w:ptcp.w:call-trgt-46.t:call-get_reads_overlapping_repeats INFO output :: name: "reads_overlapping_repeats", value: "m84036_250809_035451_s4.bc2143.repeats.bam"
2025-09-15 20:24:01.007 wdl.w:ptcp.w:call-trgt-46.t:call-get_reads_overlapping_repeats INFO output :: name: "reads_overlapping_repeats_bai", value: "m84036_250809_035451_s4.bc2143.repeats.bam.bai"
2025-09-15 20:24:01.057 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_motifs_allele INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-26/call-trgt_plot_motifs_allele/_singularity_tmpdir_r7wvv9yr"
2025-09-15 20:24:01.057 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_motifs_allele INFO Slurm invocation: srun --job-name call-trgt_plot_motifs_allele --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-26/call-trgt_plot_motifs_allele/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-26/call-trgt_plot_motifs_allele/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-26/call-trgt_plot_motifs_allele/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-26/call-trgt_plot_motifs_allele/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-26/call-trgt_genotype/out/m84036_250809_035451_s4.bc2123.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2123.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-26/call-trgt_genotype/out/m84036_250809_035451_s4.bc2123.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2123.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-26/call-trgt_genotype/out/m84036_250809_035451_s4.bc2123.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2123.trgt.sorted.spanning.bam:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-26/call-trgt_plot_motifs_allele/_singularity_tmpdir_r7wvv9yr/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-26/call-trgt_plot_motifs_allele/_singularity_tmpdir_r7wvv9yr/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:01.084 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_motifs_allele NOTICE slurm_singularity run :: pid: 1200764, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-26/call-trgt_plot_motifs_allele/slurm_singularity.log.txt"
2025-09-15 20:24:01.085 wdl.w:ptcp.w:call-trgt-46.t:call-get_reads_overlapping_repeats NOTICE done
2025-09-15 20:24:01.090 wdl.w:ptcp.w:call-trgt-46 NOTICE finish :: job: "call-get_reads_overlapping_repeats"
2025-09-15 20:24:01.090 wdl.w:ptcp.w:call-trgt-46 INFO output :: job: "call-get_reads_overlapping_repeats", values: {"reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-46/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2143.repeats.bam.bai", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-46/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2143.repeats.bam"}
2025-09-15 20:24:01.090 wdl.w:ptcp.w:call-trgt-46 INFO visit :: node: "output-reads_overlapping_repeats", values: {"reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-46/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2143.repeats.bam"}
2025-09-15 20:24:01.090 wdl.w:ptcp.w:call-trgt-46 INFO visit :: node: "output-reads_overlapping_repeats_bai", values: {"reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-46/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2143.repeats.bam.bai"}
2025-09-15 20:24:01.096 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_motifs_waterfall NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-26/call-trgt_plot_motifs_waterfall", thread: 140610367379008
2025-09-15 20:24:01.113 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_motifs_waterfall INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:01.113 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:24:00 [INFO] - Running trgt-4.0.0-429afcd [genotype]
2025-09-15 20:24:01.113 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_motifs_waterfall INFO input :: name: "waterfall", value: true
2025-09-15 20:24:01.113 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:24:00 [WARN] - PRTS_ARX: Filtered out 5 impure reads
2025-09-15 20:24:01.113 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_motifs_waterfall INFO input :: name: "methylation", value: false
2025-09-15 20:24:01.113 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:24:00 [WARN] - FXS_FMR1: Filtered out 2 impure reads
2025-09-15 20:24:01.113 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_motifs_waterfall INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:01.113 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:24:00 [WARN] - FRAXE_AFF2: Filtered out 13 impure reads
2025-09-15 20:24:01.113 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_motifs_waterfall INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:01.114 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:24:00 [WARN] - FRDA_FXN: Filtered out 2 impure reads
2025-09-15 20:24:01.114 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_motifs_waterfall INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:01.114 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:24:00 [INFO] - Total execution time: 199.92ms
2025-09-15 20:24:01.114 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_motifs_waterfall INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2123.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:01.114 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:24:00 [INFO] - trgt end
2025-09-15 20:24:01.114 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_motifs_waterfall INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2123.trgt.sorted.spanning.bam"
2025-09-15 20:24:01.114 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_motifs_waterfall INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2123.trgt.vcf"
2025-09-15 20:24:01.114 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_motifs_waterfall INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2123"
2025-09-15 20:24:01.114 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:01.114 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "plot_type", value: "waterfall"
2025-09-15 20:24:01.115 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "show", value: "motifs"
2025-09-15 20:24:01.115 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "threads", value: 1
2025-09-15 20:24:01.115 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:01.115 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2123.motifs_waterfall"
2025-09-15 20:24:01.115 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_motifs_waterfall INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:01.116 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_motifs_waterfall WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:01.116 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_motifs_waterfall INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:01.116 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_motifs_waterfall INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:01.124 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_genotype.slurm_singularity INFO srun: job 51797529 queued and waiting for resources
2025-09-15 20:24:01.124 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_genotype.slurm_singularity INFO srun: job 51797529 has been allocated resources
2025-09-15 20:24:01.124 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_genotype.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:01.196 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_motifs_waterfall INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-26/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_ki2ndhd1"
2025-09-15 20:24:01.196 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_motifs_waterfall INFO Slurm invocation: srun --job-name call-trgt_plot_motifs_waterfall --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-26/call-trgt_plot_motifs_waterfall/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-26/call-trgt_plot_motifs_waterfall/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-26/call-trgt_plot_motifs_waterfall/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-26/call-trgt_plot_motifs_waterfall/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-26/call-trgt_genotype/out/m84036_250809_035451_s4.bc2123.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2123.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-26/call-trgt_genotype/out/m84036_250809_035451_s4.bc2123.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2123.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-26/call-trgt_genotype/out/m84036_250809_035451_s4.bc2123.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2123.trgt.sorted.spanning.bam:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-26/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_ki2ndhd1/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-26/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_ki2ndhd1/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:01.209 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_motifs_waterfall NOTICE slurm_singularity run :: pid: 1200766, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-26/call-trgt_plot_motifs_waterfall/slurm_singularity.log.txt"
2025-09-15 20:24:01.291 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_genotype INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2143.trgt.vcf"
2025-09-15 20:24:01.296 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_genotype INFO output :: name: "spanning_bam", value: "m84036_250809_035451_s4.bc2143.trgt.sorted.spanning.bam"
2025-09-15 20:24:01.298 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_genotype INFO output :: name: "spanning_bam_bai", value: "m84036_250809_035451_s4.bc2143.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:01.368 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_genotype NOTICE done
2025-09-15 20:24:01.375 wdl.w:ptcp.w:call-trgt-46 NOTICE finish :: job: "call-trgt_genotype"
2025-09-15 20:24:01.375 wdl.w:ptcp.w:call-trgt-46 INFO output :: job: "call-trgt_genotype", values: {"spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-46/call-trgt_genotype/out/m84036_250809_035451_s4.bc2143.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-46/call-trgt_genotype/out/m84036_250809_035451_s4.bc2143.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-46/call-trgt_genotype/out/m84036_250809_035451_s4.bc2143.trgt.vcf"}
2025-09-15 20:24:01.375 wdl.w:ptcp.w:call-trgt-46 NOTICE ready :: job: "call-trgt_plot_meth_allele", callee: "trgt_plot"
2025-09-15 20:24:01.376 wdl.w:ptcp.w:call-trgt-46 INFO input :: job: "call-trgt_plot_meth_allele", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": false, "methylation": true, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-46/call-trgt_genotype/out/m84036_250809_035451_s4.bc2143.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-46/call-trgt_genotype/out/m84036_250809_035451_s4.bc2143.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-46/call-trgt_genotype/out/m84036_250809_035451_s4.bc2143.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2143"}
2025-09-15 20:24:01.377 wdl.w:ptcp.w:call-trgt-46 NOTICE ready :: job: "call-trgt_plot_meth_waterfall", callee: "trgt_plot"
2025-09-15 20:24:01.377 wdl.w:ptcp.w:call-trgt-46 INFO input :: job: "call-trgt_plot_meth_waterfall", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": true, "methylation": true, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-46/call-trgt_genotype/out/m84036_250809_035451_s4.bc2143.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-46/call-trgt_genotype/out/m84036_250809_035451_s4.bc2143.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-46/call-trgt_genotype/out/m84036_250809_035451_s4.bc2143.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2143"}
2025-09-15 20:24:01.378 wdl.w:ptcp.w:call-trgt-46 NOTICE ready :: job: "call-trgt_plot_motifs_allele", callee: "trgt_plot"
2025-09-15 20:24:01.378 wdl.w:ptcp.w:call-trgt-46 INFO input :: job: "call-trgt_plot_motifs_allele", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": false, "methylation": false, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-46/call-trgt_genotype/out/m84036_250809_035451_s4.bc2143.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-46/call-trgt_genotype/out/m84036_250809_035451_s4.bc2143.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-46/call-trgt_genotype/out/m84036_250809_035451_s4.bc2143.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2143"}
2025-09-15 20:24:01.379 wdl.w:ptcp.w:call-trgt-46 NOTICE ready :: job: "call-trgt_plot_motifs_waterfall", callee: "trgt_plot"
2025-09-15 20:24:01.379 wdl.w:ptcp.w:call-trgt-46 INFO input :: job: "call-trgt_plot_motifs_waterfall", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": true, "methylation": false, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-46/call-trgt_genotype/out/m84036_250809_035451_s4.bc2143.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-46/call-trgt_genotype/out/m84036_250809_035451_s4.bc2143.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-46/call-trgt_genotype/out/m84036_250809_035451_s4.bc2143.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2143"}
2025-09-15 20:24:01.379 wdl.w:ptcp.w:call-trgt-46 INFO visit :: node: "output-spanning_bam", values: {"spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-46/call-trgt_genotype/out/m84036_250809_035451_s4.bc2143.trgt.sorted.spanning.bam"}
2025-09-15 20:24:01.379 wdl.w:ptcp.w:call-trgt-46 INFO visit :: node: "output-spanning_bam_bai", values: {"spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-46/call-trgt_genotype/out/m84036_250809_035451_s4.bc2143.trgt.sorted.spanning.bam.bai"}
2025-09-15 20:24:01.380 wdl.w:ptcp.w:call-trgt-46 INFO visit :: node: "output-vcf", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-46/call-trgt_genotype/out/m84036_250809_035451_s4.bc2143.trgt.vcf"}
2025-09-15 20:24:01.381 wdl.w:ptcp.w:call-trgt-18.t:call-trgt_plot_meth_allele NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-18/call-trgt_plot_meth_allele", thread: 140609310422592
2025-09-15 20:24:01.399 wdl.w:ptcp.w:call-trgt-18.t:call-trgt_plot_meth_allele INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:01.399 wdl.w:ptcp.w:call-trgt-18.t:call-trgt_plot_meth_allele INFO input :: name: "waterfall", value: false
2025-09-15 20:24:01.399 wdl.w:ptcp.w:call-trgt-18.t:call-trgt_plot_meth_allele INFO input :: name: "methylation", value: true
2025-09-15 20:24:01.399 wdl.w:ptcp.w:call-trgt-18.t:call-trgt_plot_meth_allele INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:01.399 wdl.w:ptcp.w:call-trgt-18.t:call-trgt_plot_meth_allele INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:01.399 wdl.w:ptcp.w:call-trgt-18.t:call-trgt_plot_meth_allele INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:01.399 wdl.w:ptcp.w:call-trgt-18.t:call-trgt_plot_meth_allele INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2115.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:01.399 wdl.w:ptcp.w:call-trgt-18.t:call-trgt_plot_meth_allele INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2115.trgt.sorted.spanning.bam"
2025-09-15 20:24:01.399 wdl.w:ptcp.w:call-trgt-18.t:call-trgt_plot_meth_allele INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2115.trgt.vcf"
2025-09-15 20:24:01.399 wdl.w:ptcp.w:call-trgt-18.t:call-trgt_plot_meth_allele INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2115"
2025-09-15 20:24:01.399 wdl.w:ptcp.w:call-trgt-18.t:call-trgt_plot_meth_allele INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:01.400 wdl.w:ptcp.w:call-trgt-18.t:call-trgt_plot_meth_allele INFO eval :: name: "plot_type", value: "allele"
2025-09-15 20:24:01.400 wdl.w:ptcp.w:call-trgt-18.t:call-trgt_plot_meth_allele INFO eval :: name: "show", value: "meth"
2025-09-15 20:24:01.400 wdl.w:ptcp.w:call-trgt-18.t:call-trgt_plot_meth_allele INFO eval :: name: "threads", value: 1
2025-09-15 20:24:01.400 wdl.w:ptcp.w:call-trgt-18.t:call-trgt_plot_meth_allele INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:01.400 wdl.w:ptcp.w:call-trgt-18.t:call-trgt_plot_meth_allele INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2115.meth_allele"
2025-09-15 20:24:01.400 wdl.w:ptcp.w:call-trgt-18.t:call-trgt_plot_meth_allele INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:01.401 wdl.w:ptcp.w:call-trgt-18.t:call-trgt_plot_meth_allele WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:01.401 wdl.w:ptcp.w:call-trgt-18.t:call-trgt_plot_meth_allele INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:01.401 wdl.w:ptcp.w:call-trgt-18.t:call-trgt_plot_meth_allele INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:01.418 wdl.w:ptcp.w:call-paraphase-44.t:call-run_paraphase.slurm_singularity INFO srun: job 51797530 queued and waiting for resources
2025-09-15 20:24:01.418 wdl.w:ptcp.w:call-paraphase-44.t:call-run_paraphase.slurm_singularity INFO srun: job 51797530 has been allocated resources
2025-09-15 20:24:01.418 wdl.w:ptcp.w:call-paraphase-44.t:call-run_paraphase.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:01.437 wdl.w:ptcp.w:call-sawfish-44.t:call-run_sawfish.slurm_singularity INFO srun: job 51797531 queued and waiting for resources
2025-09-15 20:24:01.437 wdl.w:ptcp.w:call-sawfish-44.t:call-run_sawfish.slurm_singularity INFO srun: job 51797531 has been allocated resources
2025-09-15 20:24:01.437 wdl.w:ptcp.w:call-sawfish-44.t:call-run_sawfish.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:01.437 wdl.w:ptcp.w:call-sawfish-44.t:call-run_sawfish.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:24:01.467 wdl.w:ptcp.w:call-trgt-18.t:call-trgt_plot_meth_allele INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-18/call-trgt_plot_meth_allele/_singularity_tmpdir_iodw3t2q"
2025-09-15 20:24:01.467 wdl.w:ptcp.w:call-trgt-18.t:call-trgt_plot_meth_allele INFO Slurm invocation: srun --job-name call-trgt_plot_meth_allele --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-18/call-trgt_plot_meth_allele/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-18/call-trgt_plot_meth_allele/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-18/call-trgt_plot_meth_allele/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-18/call-trgt_plot_meth_allele/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-18/call-trgt_genotype/out/m84036_250809_035451_s4.bc2115.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2115.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-18/call-trgt_genotype/out/m84036_250809_035451_s4.bc2115.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2115.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-18/call-trgt_genotype/out/m84036_250809_035451_s4.bc2115.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2115.trgt.sorted.spanning.bam:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-18/call-trgt_plot_meth_allele/_singularity_tmpdir_iodw3t2q/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-18/call-trgt_plot_meth_allele/_singularity_tmpdir_iodw3t2q/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:01.485 wdl.w:ptcp.w:call-trgt-18.t:call-trgt_plot_meth_allele NOTICE slurm_singularity run :: pid: 1200779, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-18/call-trgt_plot_meth_allele/slurm_singularity.log.txt"
2025-09-15 20:24:01.523 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:01 [ERROR] - No reads found for TRID=SCA37_DAB1
2025-09-15 20:24:01.523 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:01 [ERROR] - No reads found for TRID=NIID_NOTCH2NLC
2025-09-15 20:24:01.523 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:01 [ERROR] - No reads found for TRID=DRPLA_ATN1
2025-09-15 20:24:01.523 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:01 [ERROR] - No reads found for TRID=SCA2_ATXN2
2025-09-15 20:24:01.523 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:01 [ERROR] - No reads found for TRID=SCA37_DAB1
2025-09-15 20:24:01.524 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:01 [ERROR] - No reads found for TRID=OPDM4_RILPL1
2025-09-15 20:24:01.524 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:01 [ERROR] - No reads found for TRID=NIID_NOTCH2NLC
2025-09-15 20:24:01.524 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:01 [ERROR] - No reads found for TRID=OPDM_ABCD3
2025-09-15 20:24:01.524 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:01 [ERROR] - No reads found for TRID=DRPLA_ATN1
2025-09-15 20:24:01.524 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:01 [ERROR] - No reads found for TRID=OPMD_PABPN1
2025-09-15 20:24:01.524 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:01 [ERROR] - No reads found for TRID=SCA2_ATXN2
2025-09-15 20:24:01.524 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:01 [ERROR] - No reads found for TRID=SCA3_ATXN3
2025-09-15 20:24:01.524 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:01 [ERROR] - No reads found for TRID=OPDM4_RILPL1
2025-09-15 20:24:01.524 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:01 [ERROR] - No reads found for TRID=SCA31_BEAN1
2025-09-15 20:24:01.524 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:01 [ERROR] - No reads found for TRID=OPDM_ABCD3
2025-09-15 20:24:01.524 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:01 [ERROR] - No reads found for TRID=SCA27B_FGF14
2025-09-15 20:24:01.524 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:01 [ERROR] - No reads found for TRID=OPMD_PABPN1
2025-09-15 20:24:01.524 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:01 [ERROR] - No reads found for TRID=OPDM2_GIPC1
2025-09-15 20:24:01.524 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:01 [ERROR] - No reads found for TRID=SCA3_ATXN3
2025-09-15 20:24:01.525 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:01 [ERROR] - No reads found for TRID=HDL2_JPH3
2025-09-15 20:24:01.525 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:01 [ERROR] - No reads found for TRID=SCA31_BEAN1
2025-09-15 20:24:01.525 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:01 [ERROR] - No reads found for TRID=FRA2A_AFF3
2025-09-15 20:24:01.525 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:01 [ERROR] - No reads found for TRID=SCA27B_FGF14
2025-09-15 20:24:01.525 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:01 [ERROR] - No reads found for TRID=SD5_HOXD13
2025-09-15 20:24:01.525 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:01 [ERROR] - No reads found for TRID=OPDM2_GIPC1
2025-09-15 20:24:01.525 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:01 [ERROR] - No reads found for TRID=HDL2_JPH3
2025-09-15 20:24:01.525 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:01 [ERROR] - No reads found for TRID=FRA2A_AFF3
2025-09-15 20:24:01.533 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO srun: job 51797532 queued and waiting for resources
2025-09-15 20:24:01.533 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO srun: job 51797532 has been allocated resources
2025-09-15 20:24:01.533 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:01.534 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:24:01.535 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_meth_allele.slurm_singularity INFO srun: job 51797533 queued and waiting for resources
2025-09-15 20:24:01.535 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_meth_allele.slurm_singularity INFO srun: job 51797533 has been allocated resources
2025-09-15 20:24:01.535 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_meth_allele.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:01.535 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_meth_allele.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:24:01.569 wdl.w:ptcp.w:call-trgt-45.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:58 [INFO] - Running trgt-4.0.0-429afcd [genotype]
2025-09-15 20:24:01.569 wdl.w:ptcp.w:call-trgt-45.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:58 [WARN] - OPDM_ABCD3: Filtered out 7 impure reads
2025-09-15 20:24:01.569 wdl.w:ptcp.w:call-trgt-45.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:58 [WARN] - SCA37_DAB1: Filtered out 6 impure reads
2025-09-15 20:24:01.569 wdl.w:ptcp.w:call-trgt-45.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:58 [WARN] - DRPLA_ATN1: Filtered out 21 impure reads
2025-09-15 20:24:01.569 wdl.w:ptcp.w:call-trgt-45.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:58 [WARN] - SCA2_ATXN2: Filtered out 17 impure reads
2025-09-15 20:24:01.569 wdl.w:ptcp.w:call-trgt-45.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:58 [WARN] - NIID_NOTCH2NLC: Filtered out 19 impure reads
2025-09-15 20:24:01.569 wdl.w:ptcp.w:call-trgt-45.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:58 [WARN] - OPDM4_RILPL1: Filtered out 10 impure reads
2025-09-15 20:24:01.569 wdl.w:ptcp.w:call-trgt-45.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:58 [WARN] - SCA8_ATXN8OS: Filtered out 18 impure reads
2025-09-15 20:24:01.569 wdl.w:ptcp.w:call-trgt-45.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:59 [WARN] - SCA27B_FGF14: Filtered out 17 impure reads
2025-09-15 20:24:01.569 wdl.w:ptcp.w:call-trgt-45.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:59 [WARN] - OPMD_PABPN1: Filtered out 14 impure reads
2025-09-15 20:24:01.569 wdl.w:ptcp.w:call-trgt-45.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:59 [WARN] - SCA3_ATXN3: Filtered out 21 impure reads
2025-09-15 20:24:01.569 wdl.w:ptcp.w:call-trgt-45.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:59 [WARN] - SCA4_ZFHX3: Filtered out 31 impure reads
2025-09-15 20:24:01.570 wdl.w:ptcp.w:call-trgt-45.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:59 [WARN] - HDL2_JPH3: Filtered out 20 impure reads
2025-09-15 20:24:01.570 wdl.w:ptcp.w:call-trgt-45.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:59 [WARN] - SCA31_BEAN1: Filtered out 12 impure reads
2025-09-15 20:24:01.570 wdl.w:ptcp.w:call-trgt-45.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:59 [WARN] - FECD3_TCF4: Filtered out 20 impure reads
2025-09-15 20:24:01.570 wdl.w:ptcp.w:call-trgt-45.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:59 [WARN] - SCA6_CACNA1A: Filtered out 12 impure reads
2025-09-15 20:24:01.570 wdl.w:ptcp.w:call-trgt-45.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:23:59 [WARN] - FRA2A_AFF3: Filtered out 17 impure reads
2025-09-15 20:24:01.570 wdl.w:ptcp.w:call-trgt-45.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:24:00 [WARN] - DM1_DMPK: Filtered out 18 impure reads
2025-09-15 20:24:01.570 wdl.w:ptcp.w:call-trgt-45.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:24:00 [WARN] - OPDM2_GIPC1: Filtered out 8 impure reads
2025-09-15 20:24:01.570 wdl.w:ptcp.w:call-trgt-45.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:24:00 [WARN] - CJD_PRNP: Filtered out 11 impure reads
2025-09-15 20:24:01.570 wdl.w:ptcp.w:call-trgt-45.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:24:00 [WARN] - SCA10_ATXN10: Filtered out 8 impure reads
2025-09-15 20:24:01.570 wdl.w:ptcp.w:call-trgt-45.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:24:00 [WARN] - SD5_HOXD13: Filtered out 8 impure reads
2025-09-15 20:24:01.570 wdl.w:ptcp.w:call-trgt-45.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:24:00 [WARN] - EPM1_CSTB: Filtered out 7 impure reads
2025-09-15 20:24:01.570 wdl.w:ptcp.w:call-trgt-45.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:24:00 [WARN] - SCA36_NOP56: Filtered out 20 impure reads
2025-09-15 20:24:01.570 wdl.w:ptcp.w:call-trgt-45.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:24:00 [WARN] - DM2_CNBP: Filtered out 3 impure reads
2025-09-15 20:24:01.570 wdl.w:ptcp.w:call-trgt-45.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:24:00 [WARN] - CCHS_PHOX2B: Filtered out 2 impure reads
2025-09-15 20:24:01.570 wdl.w:ptcp.w:call-trgt-45.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:24:00 [WARN] - HD_HTT: Filtered out 16 impure reads
2025-09-15 20:24:01.570 wdl.w:ptcp.w:call-trgt-45.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:24:00 [WARN] - SCA17_TBP: Filtered out 9 impure reads
2025-09-15 20:24:01.570 wdl.w:ptcp.w:call-trgt-45.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:24:00 [WARN] - OPDM1_LRP12: Filtered out 11 impure reads
2025-09-15 20:24:01.570 wdl.w:ptcp.w:call-trgt-45.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:24:00 [WARN] - FAME1_SAMD12: Filtered out 11 impure reads
2025-09-15 20:24:01.570 wdl.w:ptcp.w:call-trgt-45.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:24:00 [WARN] - SCA7_ATXN7: Filtered out 16 impure reads
2025-09-15 20:24:01.570 wdl.w:ptcp.w:call-trgt-45.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:24:00 [WARN] - SCA12_PPP2R2B: Filtered out 19 impure reads
2025-09-15 20:24:01.570 wdl.w:ptcp.w:call-trgt-45.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:24:00 [WARN] - CANVAS_RFC1: Filtered out 6 impure reads
2025-09-15 20:24:01.571 wdl.w:ptcp.w:call-trgt-45.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:24:00 [WARN] - SCA1_ATXN1: Filtered out 30 impure reads
2025-09-15 20:24:01.571 wdl.w:ptcp.w:call-trgt-45.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:24:00 [WARN] - FTDALS1_C9orf72: Filtered out 15 impure reads
2025-09-15 20:24:01.571 wdl.w:ptcp.w:call-trgt-45.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:24:00 [WARN] - FXS_FMR1: Filtered out 6 impure reads
2025-09-15 20:24:01.571 wdl.w:ptcp.w:call-trgt-45.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:24:00 [WARN] - SBMA_AR: Filtered out 19 impure reads
2025-09-15 20:24:01.571 wdl.w:ptcp.w:call-trgt-45.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:24:00 [WARN] - FRAXE_AFF2: Filtered out 6 impure reads
2025-09-15 20:24:01.571 wdl.w:ptcp.w:call-trgt-45.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:24:01 [INFO] - Total execution time: 2.49s
2025-09-15 20:24:01.571 wdl.w:ptcp.w:call-trgt-45.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:24:01 [INFO] - trgt end
2025-09-15 20:24:01.676 wdl.w:ptcp.w:call-trgt-45.t:call-trgt_genotype INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2142.trgt.vcf"
2025-09-15 20:24:01.678 wdl.w:ptcp.w:call-trgt-45.t:call-trgt_genotype INFO output :: name: "spanning_bam", value: "m84036_250809_035451_s4.bc2142.trgt.sorted.spanning.bam"
2025-09-15 20:24:01.679 wdl.w:ptcp.w:call-trgt-45.t:call-trgt_genotype INFO output :: name: "spanning_bam_bai", value: "m84036_250809_035451_s4.bc2142.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:01.746 wdl.w:ptcp.w:call-trgt-45.t:call-trgt_genotype NOTICE done
2025-09-15 20:24:01.752 wdl.w:ptcp.w:call-trgt-45 NOTICE finish :: job: "call-trgt_genotype"
2025-09-15 20:24:01.752 wdl.w:ptcp.w:call-trgt-45 INFO output :: job: "call-trgt_genotype", values: {"spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-45/call-trgt_genotype/out/m84036_250809_035451_s4.bc2142.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-45/call-trgt_genotype/out/m84036_250809_035451_s4.bc2142.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-45/call-trgt_genotype/out/m84036_250809_035451_s4.bc2142.trgt.vcf"}
2025-09-15 20:24:01.752 wdl.w:ptcp.w:call-trgt-45 NOTICE ready :: job: "call-trgt_plot_meth_allele", callee: "trgt_plot"
2025-09-15 20:24:01.753 wdl.w:ptcp.w:call-trgt-45 INFO input :: job: "call-trgt_plot_meth_allele", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": false, "methylation": true, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-45/call-trgt_genotype/out/m84036_250809_035451_s4.bc2142.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-45/call-trgt_genotype/out/m84036_250809_035451_s4.bc2142.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-45/call-trgt_genotype/out/m84036_250809_035451_s4.bc2142.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2142"}
2025-09-15 20:24:01.754 wdl.w:ptcp.w:call-trgt-45 NOTICE ready :: job: "call-trgt_plot_meth_waterfall", callee: "trgt_plot"
2025-09-15 20:24:01.754 wdl.w:ptcp.w:call-trgt-45 INFO input :: job: "call-trgt_plot_meth_waterfall", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": true, "methylation": true, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-45/call-trgt_genotype/out/m84036_250809_035451_s4.bc2142.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-45/call-trgt_genotype/out/m84036_250809_035451_s4.bc2142.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-45/call-trgt_genotype/out/m84036_250809_035451_s4.bc2142.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2142"}
2025-09-15 20:24:01.756 wdl.w:ptcp.w:call-trgt-45 NOTICE ready :: job: "call-trgt_plot_motifs_allele", callee: "trgt_plot"
2025-09-15 20:24:01.756 wdl.w:ptcp.w:call-trgt-45 INFO input :: job: "call-trgt_plot_motifs_allele", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": false, "methylation": false, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-45/call-trgt_genotype/out/m84036_250809_035451_s4.bc2142.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-45/call-trgt_genotype/out/m84036_250809_035451_s4.bc2142.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-45/call-trgt_genotype/out/m84036_250809_035451_s4.bc2142.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2142"}
2025-09-15 20:24:01.757 wdl.w:ptcp.w:call-trgt-45 NOTICE ready :: job: "call-trgt_plot_motifs_waterfall", callee: "trgt_plot"
2025-09-15 20:24:01.757 wdl.w:ptcp.w:call-trgt-18.t:call-trgt_plot_meth_waterfall NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-18/call-trgt_plot_meth_waterfall", thread: 140608731588160
2025-09-15 20:24:01.757 wdl.w:ptcp.w:call-trgt-45 INFO input :: job: "call-trgt_plot_motifs_waterfall", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": true, "methylation": false, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-45/call-trgt_genotype/out/m84036_250809_035451_s4.bc2142.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-45/call-trgt_genotype/out/m84036_250809_035451_s4.bc2142.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-45/call-trgt_genotype/out/m84036_250809_035451_s4.bc2142.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2142"}
2025-09-15 20:24:01.758 wdl.w:ptcp.w:call-trgt-45 INFO visit :: node: "output-spanning_bam", values: {"spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-45/call-trgt_genotype/out/m84036_250809_035451_s4.bc2142.trgt.sorted.spanning.bam"}
2025-09-15 20:24:01.758 wdl.w:ptcp.w:call-trgt-45 INFO visit :: node: "output-spanning_bam_bai", values: {"spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-45/call-trgt_genotype/out/m84036_250809_035451_s4.bc2142.trgt.sorted.spanning.bam.bai"}
2025-09-15 20:24:01.758 wdl.w:ptcp.w:call-trgt-45 INFO visit :: node: "output-vcf", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-45/call-trgt_genotype/out/m84036_250809_035451_s4.bc2142.trgt.vcf"}
2025-09-15 20:24:01.775 wdl.w:ptcp.w:call-trgt-18.t:call-trgt_plot_meth_waterfall INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:01.775 wdl.w:ptcp.w:call-trgt-18.t:call-trgt_plot_meth_waterfall INFO input :: name: "waterfall", value: true
2025-09-15 20:24:01.775 wdl.w:ptcp.w:call-trgt-18.t:call-trgt_plot_meth_waterfall INFO input :: name: "methylation", value: true
2025-09-15 20:24:01.776 wdl.w:ptcp.w:call-trgt-18.t:call-trgt_plot_meth_waterfall INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:01.776 wdl.w:ptcp.w:call-trgt-18.t:call-trgt_plot_meth_waterfall INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:01.776 wdl.w:ptcp.w:call-trgt-18.t:call-trgt_plot_meth_waterfall INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:01.776 wdl.w:ptcp.w:call-trgt-18.t:call-trgt_plot_meth_waterfall INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2115.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:01.776 wdl.w:ptcp.w:call-trgt-18.t:call-trgt_plot_meth_waterfall INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2115.trgt.sorted.spanning.bam"
2025-09-15 20:24:01.776 wdl.w:ptcp.w:call-trgt-18.t:call-trgt_plot_meth_waterfall INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2115.trgt.vcf"
2025-09-15 20:24:01.776 wdl.w:ptcp.w:call-trgt-18.t:call-trgt_plot_meth_waterfall INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2115"
2025-09-15 20:24:01.776 wdl.w:ptcp.w:call-trgt-18.t:call-trgt_plot_meth_waterfall INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:01.776 wdl.w:ptcp.w:call-trgt-18.t:call-trgt_plot_meth_waterfall INFO eval :: name: "plot_type", value: "waterfall"
2025-09-15 20:24:01.776 wdl.w:ptcp.w:call-trgt-18.t:call-trgt_plot_meth_waterfall INFO eval :: name: "show", value: "meth"
2025-09-15 20:24:01.776 wdl.w:ptcp.w:call-trgt-18.t:call-trgt_plot_meth_waterfall INFO eval :: name: "threads", value: 1
2025-09-15 20:24:01.777 wdl.w:ptcp.w:call-trgt-18.t:call-trgt_plot_meth_waterfall INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:01.777 wdl.w:ptcp.w:call-trgt-18.t:call-trgt_plot_meth_waterfall INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2115.meth_waterfall"
2025-09-15 20:24:01.777 wdl.w:ptcp.w:call-trgt-18.t:call-trgt_plot_meth_waterfall INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:01.777 wdl.w:ptcp.w:call-trgt-18.t:call-trgt_plot_meth_waterfall WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:01.778 wdl.w:ptcp.w:call-trgt-18.t:call-trgt_plot_meth_waterfall INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:01.778 wdl.w:ptcp.w:call-trgt-18.t:call-trgt_plot_meth_waterfall INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:01.839 wdl.w:ptcp.w:call-trgt-18.t:call-trgt_plot_meth_waterfall INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-18/call-trgt_plot_meth_waterfall/_singularity_tmpdir_9z2yttm2"
2025-09-15 20:24:01.839 wdl.w:ptcp.w:call-trgt-18.t:call-trgt_plot_meth_waterfall INFO Slurm invocation: srun --job-name call-trgt_plot_meth_waterfall --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-18/call-trgt_plot_meth_waterfall/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-18/call-trgt_plot_meth_waterfall/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-18/call-trgt_plot_meth_waterfall/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-18/call-trgt_plot_meth_waterfall/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-18/call-trgt_genotype/out/m84036_250809_035451_s4.bc2115.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2115.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-18/call-trgt_genotype/out/m84036_250809_035451_s4.bc2115.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2115.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-18/call-trgt_genotype/out/m84036_250809_035451_s4.bc2115.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2115.trgt.sorted.spanning.bam:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-18/call-trgt_plot_meth_waterfall/_singularity_tmpdir_9z2yttm2/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-18/call-trgt_plot_meth_waterfall/_singularity_tmpdir_9z2yttm2/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:01.853 wdl.w:ptcp.w:call-trgt-18.t:call-trgt_plot_meth_waterfall NOTICE slurm_singularity run :: pid: 1200787, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-18/call-trgt_plot_meth_waterfall/slurm_singularity.log.txt"
2025-09-15 20:24:02.086 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:01 [ERROR] - No reads found for TRID=SCA37_DAB1
2025-09-15 20:24:02.087 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:01 [ERROR] - No reads found for TRID=NIID_NOTCH2NLC
2025-09-15 20:24:02.087 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:02 [ERROR] - No reads found for TRID=DRPLA_ATN1
2025-09-15 20:24:02.087 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:02 [ERROR] - No reads found for TRID=SCA2_ATXN2
2025-09-15 20:24:02.099 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_motifs_allele.slurm_singularity INFO srun: job 51797534 queued and waiting for resources
2025-09-15 20:24:02.100 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_motifs_allele.slurm_singularity INFO srun: job 51797534 has been allocated resources
2025-09-15 20:24:02.100 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_motifs_allele.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:02.211 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:02 [ERROR] - No reads found for TRID=SCA37_DAB1
2025-09-15 20:24:02.212 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:02 [ERROR] - No reads found for TRID=NIID_NOTCH2NLC
2025-09-15 20:24:02.212 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:02 [ERROR] - No reads found for TRID=DRPLA_ATN1
2025-09-15 20:24:02.212 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:02 [ERROR] - No reads found for TRID=SCA2_ATXN2
2025-09-15 20:24:02.222 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO srun: job 51797535 queued and waiting for resources
2025-09-15 20:24:02.222 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO srun: job 51797535 has been allocated resources
2025-09-15 20:24:02.223 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:02.344 wdl.w:ptcp.w:call-paraphase-11.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for smn1 for sample m84036_250809_035451_s4.bc2108 at 2025-09-15 20:23:52.691957...
2025-09-15 20:24:02.344 wdl.w:ptcp.w:call-paraphase-11.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for f8inv1 for sample m84036_250809_035451_s4.bc2108 at 2025-09-15 20:23:59.928121...
2025-09-15 20:24:02.345 wdl.w:ptcp.w:call-paraphase-11.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for f8inv1 for sample m84036_250809_035451_s4.bc2108 at 2025-09-15 20:23:59.928708...
2025-09-15 20:24:02.486 wdl.w:ptcp.w:call-trgt-18.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:02 [ERROR] - No reads found for TRID=OPDM_ABCD3
2025-09-15 20:24:02.487 wdl.w:ptcp.w:call-trgt-18.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:02 [ERROR] - No reads found for TRID=SCA37_DAB1
2025-09-15 20:24:02.487 wdl.w:ptcp.w:call-trgt-18.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:02 [ERROR] - No reads found for TRID=DRPLA_ATN1
2025-09-15 20:24:02.487 wdl.w:ptcp.w:call-trgt-18.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:02 [ERROR] - No reads found for TRID=NIID_NOTCH2NLC
2025-09-15 20:24:02.487 wdl.w:ptcp.w:call-trgt-18.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:02 [ERROR] - No reads found for TRID=OPDM4_RILPL1
2025-09-15 20:24:02.487 wdl.w:ptcp.w:call-trgt-18.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:02 [ERROR] - No reads found for TRID=SCA27B_FGF14
2025-09-15 20:24:02.487 wdl.w:ptcp.w:call-trgt-18.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:02 [ERROR] - No reads found for TRID=SCA8_ATXN8OS
2025-09-15 20:24:02.487 wdl.w:ptcp.w:call-trgt-18.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:02 [ERROR] - No reads found for TRID=SCA31_BEAN1
2025-09-15 20:24:02.487 wdl.w:ptcp.w:call-trgt-18.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:02 [ERROR] - No reads found for TRID=HDL2_JPH3
2025-09-15 20:24:02.487 wdl.w:ptcp.w:call-trgt-18.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:02 [ERROR] - No reads found for TRID=SCA4_ZFHX3
2025-09-15 20:24:02.487 wdl.w:ptcp.w:call-trgt-18.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:02 [ERROR] - No reads found for TRID=SCA3_ATXN3
2025-09-15 20:24:02.487 wdl.w:ptcp.w:call-trgt-18.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:02 [ERROR] - No reads found for TRID=SCA6_CACNA1A
2025-09-15 20:24:02.495 wdl.w:ptcp.w:call-trgt-18.t:call-trgt_plot_meth_allele.slurm_singularity INFO srun: job 51797536 queued and waiting for resources
2025-09-15 20:24:02.495 wdl.w:ptcp.w:call-trgt-18.t:call-trgt_plot_meth_allele.slurm_singularity INFO srun: job 51797536 has been allocated resources
2025-09-15 20:24:02.495 wdl.w:ptcp.w:call-trgt-18.t:call-trgt_plot_meth_allele.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:02.548 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:01 [ERROR] - No reads found for TRID=SD5_HOXD13
2025-09-15 20:24:02.867 wdl.w:ptcp.w:call-trgt-18.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO srun: job 51797537 queued and waiting for resources
2025-09-15 20:24:02.867 wdl.w:ptcp.w:call-trgt-18.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO srun: job 51797537 has been allocated resources
2025-09-15 20:24:02.867 wdl.w:ptcp.w:call-trgt-18.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:03.026 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:01 [ERROR] - No reads found for TRID=CJD_PRNP
2025-09-15 20:24:03.026 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:01 [ERROR] - No reads found for TRID=SCA36_NOP56
2025-09-15 20:24:03.026 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:01 [ERROR] - No reads found for TRID=EPM1_CSTB
2025-09-15 20:24:03.026 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:01 [ERROR] - No reads found for TRID=SCA10_ATXN10
2025-09-15 20:24:03.026 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:01 [ERROR] - No reads found for TRID=SCA7_ATXN7
2025-09-15 20:24:03.026 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:01 [ERROR] - No reads found for TRID=DM2_CNBP
2025-09-15 20:24:03.026 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:01 [ERROR] - No reads found for TRID=HD_HTT
2025-09-15 20:24:03.026 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:01 [ERROR] - No reads found for TRID=SCA6_CACNA1A
2025-09-15 20:24:03.027 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:01 [ERROR] - No reads found for TRID=SCA12_PPP2R2B
2025-09-15 20:24:03.027 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:01 [ERROR] - No reads found for TRID=SCA1_ATXN1
2025-09-15 20:24:03.027 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:02 [ERROR] - No reads found for TRID=CANVAS_RFC1
2025-09-15 20:24:03.027 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:02 [ERROR] - No reads found for TRID=FECD3_TCF4
2025-09-15 20:24:03.027 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:02 [ERROR] - No reads found for TRID=DM1_DMPK
2025-09-15 20:24:03.027 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:02 [ERROR] - No reads found for TRID=FAME1_SAMD12
2025-09-15 20:24:03.027 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:02 [ERROR] - No reads found for TRID=CCHS_PHOX2B
2025-09-15 20:24:03.027 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:02 [ERROR] - No reads found for TRID=FTDALS1_C9orf72
2025-09-15 20:24:03.027 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:02 [ERROR] - No reads found for TRID=OPDM1_LRP12
2025-09-15 20:24:03.027 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:02 [ERROR] - No reads found for TRID=SBMA_AR
2025-09-15 20:24:03.056 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_meth_waterfall INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2123.meth_waterfall.trgt_plots.zip"
2025-09-15 20:24:03.066 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_meth_allele INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2123.meth_allele.trgt_plots.zip"
2025-09-15 20:24:03.138 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_meth_waterfall NOTICE done
2025-09-15 20:24:03.166 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_meth_allele NOTICE done
2025-09-15 20:24:03.183 wdl.w:ptcp.w:call-trgt-26 NOTICE finish :: job: "call-trgt_plot_meth_allele"
2025-09-15 20:24:03.183 wdl.w:ptcp.w:call-trgt-26 INFO output :: job: "call-trgt_plot_meth_allele", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-26/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2123.meth_allele.trgt_plots.zip"}
2025-09-15 20:24:03.184 wdl.w:ptcp.w:call-trgt-26 INFO visit :: node: "output-images_meth_allele", values: {"images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-26/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2123.meth_allele.trgt_plots.zip"}
2025-09-15 20:24:03.184 wdl.w:ptcp.w:call-trgt-26 NOTICE finish :: job: "call-trgt_plot_meth_waterfall"
2025-09-15 20:24:03.184 wdl.w:ptcp.w:call-trgt-26 INFO output :: job: "call-trgt_plot_meth_waterfall", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-26/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2123.meth_waterfall.trgt_plots.zip"}
2025-09-15 20:24:03.184 wdl.w:ptcp.w:call-trgt-26 INFO visit :: node: "output-images_meth_waterfall", values: {"images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-26/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2123.meth_waterfall.trgt_plots.zip"}
2025-09-15 20:24:03.194 wdl.w:ptcp.w:call-trgt-18.t:call-trgt_plot_motifs_allele NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-18/call-trgt_plot_motifs_allele", thread: 140613823374912
2025-09-15 20:24:03.197 wdl.w:ptcp.w:call-trgt-18.t:call-trgt_plot_motifs_waterfall NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-18/call-trgt_plot_motifs_waterfall", thread: 140610879071808
2025-09-15 20:24:03.227 wdl.w:ptcp.w:call-trgt-18.t:call-trgt_plot_motifs_waterfall INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:03.227 wdl.w:ptcp.w:call-trgt-18.t:call-trgt_plot_motifs_waterfall INFO input :: name: "waterfall", value: true
2025-09-15 20:24:03.227 wdl.w:ptcp.w:call-trgt-18.t:call-trgt_plot_motifs_waterfall INFO input :: name: "methylation", value: false
2025-09-15 20:24:03.227 wdl.w:ptcp.w:call-trgt-18.t:call-trgt_plot_motifs_waterfall INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:03.228 wdl.w:ptcp.w:call-trgt-18.t:call-trgt_plot_motifs_waterfall INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:03.228 wdl.w:ptcp.w:call-trgt-18.t:call-trgt_plot_motifs_waterfall INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:03.228 wdl.w:ptcp.w:call-trgt-18.t:call-trgt_plot_motifs_waterfall INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2115.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:03.228 wdl.w:ptcp.w:call-trgt-18.t:call-trgt_plot_motifs_waterfall INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2115.trgt.sorted.spanning.bam"
2025-09-15 20:24:03.228 wdl.w:ptcp.w:call-trgt-18.t:call-trgt_plot_motifs_waterfall INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2115.trgt.vcf"
2025-09-15 20:24:03.228 wdl.w:ptcp.w:call-trgt-18.t:call-trgt_plot_motifs_waterfall INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2115"
2025-09-15 20:24:03.228 wdl.w:ptcp.w:call-trgt-18.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:03.228 wdl.w:ptcp.w:call-trgt-18.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "plot_type", value: "waterfall"
2025-09-15 20:24:03.228 wdl.w:ptcp.w:call-trgt-18.t:call-trgt_plot_motifs_allele INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:03.229 wdl.w:ptcp.w:call-trgt-18.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "show", value: "motifs"
2025-09-15 20:24:03.229 wdl.w:ptcp.w:call-trgt-18.t:call-trgt_plot_motifs_allele INFO input :: name: "waterfall", value: false
2025-09-15 20:24:03.229 wdl.w:ptcp.w:call-trgt-18.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "threads", value: 1
2025-09-15 20:24:03.229 wdl.w:ptcp.w:call-trgt-18.t:call-trgt_plot_motifs_allele INFO input :: name: "methylation", value: false
2025-09-15 20:24:03.229 wdl.w:ptcp.w:call-trgt-18.t:call-trgt_plot_motifs_allele INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:03.229 wdl.w:ptcp.w:call-trgt-18.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:03.229 wdl.w:ptcp.w:call-trgt-18.t:call-trgt_plot_motifs_allele INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:03.229 wdl.w:ptcp.w:call-trgt-18.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2115.motifs_waterfall"
2025-09-15 20:24:03.230 wdl.w:ptcp.w:call-trgt-18.t:call-trgt_plot_motifs_allele INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:03.230 wdl.w:ptcp.w:call-trgt-18.t:call-trgt_plot_motifs_allele INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2115.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:03.230 wdl.w:ptcp.w:call-trgt-18.t:call-trgt_plot_motifs_waterfall INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:03.230 wdl.w:ptcp.w:call-trgt-18.t:call-trgt_plot_motifs_allele INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2115.trgt.sorted.spanning.bam"
2025-09-15 20:24:03.231 wdl.w:ptcp.w:call-trgt-18.t:call-trgt_plot_motifs_waterfall WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:03.231 wdl.w:ptcp.w:call-trgt-18.t:call-trgt_plot_motifs_allele INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2115.trgt.vcf"
2025-09-15 20:24:03.231 wdl.w:ptcp.w:call-trgt-18.t:call-trgt_plot_motifs_allele INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2115"
2025-09-15 20:24:03.231 wdl.w:ptcp.w:call-trgt-18.t:call-trgt_plot_motifs_allele INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:03.231 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:02 [ERROR] - No reads found for TRID=OPDM4_RILPL1
2025-09-15 20:24:03.231 wdl.w:ptcp.w:call-trgt-18.t:call-trgt_plot_motifs_allele INFO eval :: name: "plot_type", value: "allele"
2025-09-15 20:24:03.232 wdl.w:ptcp.w:call-trgt-18.t:call-trgt_plot_motifs_waterfall INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:03.232 wdl.w:ptcp.w:call-trgt-18.t:call-trgt_plot_motifs_allele INFO eval :: name: "show", value: "motifs"
2025-09-15 20:24:03.232 wdl.w:ptcp.w:call-trgt-18.t:call-trgt_plot_motifs_allele INFO eval :: name: "threads", value: 1
2025-09-15 20:24:03.232 wdl.w:ptcp.w:call-trgt-18.t:call-trgt_plot_motifs_allele INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:03.232 wdl.w:ptcp.w:call-trgt-18.t:call-trgt_plot_motifs_allele INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2115.motifs_allele"
2025-09-15 20:24:03.233 wdl.w:ptcp.w:call-trgt-18.t:call-trgt_plot_motifs_allele INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:03.233 wdl.w:ptcp.w:call-trgt-18.t:call-trgt_plot_motifs_allele WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:03.233 wdl.w:ptcp.w:call-trgt-18.t:call-trgt_plot_motifs_allele INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:03.233 wdl.w:ptcp.w:call-trgt-18.t:call-trgt_plot_motifs_waterfall INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:03.234 wdl.w:ptcp.w:call-trgt-18.t:call-trgt_plot_motifs_allele INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:03.244 wdl.w:ptcp.w:call-trgt-45.t:call-get_reads_overlapping_repeats INFO output :: name: "reads_overlapping_repeats", value: "m84036_250809_035451_s4.bc2142.repeats.bam"
2025-09-15 20:24:03.249 wdl.w:ptcp.w:call-trgt-45.t:call-get_reads_overlapping_repeats INFO output :: name: "reads_overlapping_repeats_bai", value: "m84036_250809_035451_s4.bc2142.repeats.bam.bai"
2025-09-15 20:24:03.317 wdl.w:ptcp.w:call-paraphase-22.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for cyp21 for sample m84036_250809_035451_s4.bc2119 at 2025-09-15 20:23:31.296823...
2025-09-15 20:24:03.318 wdl.w:ptcp.w:call-paraphase-22.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for cyp21 for sample m84036_250809_035451_s4.bc2119 at 2025-09-15 20:23:31.902234...
2025-09-15 20:24:03.318 wdl.w:ptcp.w:call-paraphase-22.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for gba for sample m84036_250809_035451_s4.bc2119 at 2025-09-15 20:23:34.205226...
2025-09-15 20:24:03.318 wdl.w:ptcp.w:call-paraphase-22.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for gba for sample m84036_250809_035451_s4.bc2119 at 2025-09-15 20:23:34.481450...
2025-09-15 20:24:03.318 wdl.w:ptcp.w:call-paraphase-22.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for hba for sample m84036_250809_035451_s4.bc2119 at 2025-09-15 20:23:35.324295...
2025-09-15 20:24:03.318 wdl.w:ptcp.w:call-paraphase-22.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for hba for sample m84036_250809_035451_s4.bc2119 at 2025-09-15 20:23:35.580404...
2025-09-15 20:24:03.318 wdl.w:ptcp.w:call-paraphase-22.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for hbb for sample m84036_250809_035451_s4.bc2119 at 2025-09-15 20:23:54.632744...
2025-09-15 20:24:03.318 wdl.w:ptcp.w:call-paraphase-22.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for hbb for sample m84036_250809_035451_s4.bc2119 at 2025-09-15 20:23:54.633313...
2025-09-15 20:24:03.318 wdl.w:ptcp.w:call-trgt-18.t:call-trgt_plot_motifs_waterfall INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-18/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_7uig9kr5"
2025-09-15 20:24:03.318 wdl.w:ptcp.w:call-trgt-18.t:call-trgt_plot_motifs_waterfall INFO Slurm invocation: srun --job-name call-trgt_plot_motifs_waterfall --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-18/call-trgt_plot_motifs_waterfall/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-18/call-trgt_plot_motifs_waterfall/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-18/call-trgt_plot_motifs_waterfall/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-18/call-trgt_plot_motifs_waterfall/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-18/call-trgt_genotype/out/m84036_250809_035451_s4.bc2115.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2115.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-18/call-trgt_genotype/out/m84036_250809_035451_s4.bc2115.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2115.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-18/call-trgt_genotype/out/m84036_250809_035451_s4.bc2115.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2115.trgt.sorted.spanning.bam:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-18/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_7uig9kr5/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-18/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_7uig9kr5/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:03.321 wdl.w:ptcp.w:call-trgt-45.t:call-get_reads_overlapping_repeats NOTICE done
2025-09-15 20:24:03.327 wdl.w:ptcp.w:call-trgt-45 NOTICE finish :: job: "call-get_reads_overlapping_repeats"
2025-09-15 20:24:03.327 wdl.w:ptcp.w:call-trgt-45 INFO output :: job: "call-get_reads_overlapping_repeats", values: {"reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-45/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2142.repeats.bam.bai", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-45/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2142.repeats.bam"}
2025-09-15 20:24:03.327 wdl.w:ptcp.w:call-trgt-45 INFO visit :: node: "output-reads_overlapping_repeats", values: {"reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-45/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2142.repeats.bam"}
2025-09-15 20:24:03.327 wdl.w:ptcp.w:call-trgt-45 INFO visit :: node: "output-reads_overlapping_repeats_bai", values: {"reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-45/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2142.repeats.bam.bai"}
2025-09-15 20:24:03.336 wdl.w:ptcp.w:call-trgt-11.t:call-trgt_plot_meth_allele NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-11/call-trgt_plot_meth_allele", thread: 140608765158976
2025-09-15 20:24:03.345 wdl.w:ptcp.w:call-trgt-18.t:call-trgt_plot_motifs_allele INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-18/call-trgt_plot_motifs_allele/_singularity_tmpdir_v7izpq1f"
2025-09-15 20:24:03.346 wdl.w:ptcp.w:call-trgt-18.t:call-trgt_plot_motifs_allele INFO Slurm invocation: srun --job-name call-trgt_plot_motifs_allele --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-18/call-trgt_plot_motifs_allele/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-18/call-trgt_plot_motifs_allele/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-18/call-trgt_plot_motifs_allele/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-18/call-trgt_plot_motifs_allele/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-18/call-trgt_genotype/out/m84036_250809_035451_s4.bc2115.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2115.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-18/call-trgt_genotype/out/m84036_250809_035451_s4.bc2115.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2115.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-18/call-trgt_genotype/out/m84036_250809_035451_s4.bc2115.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2115.trgt.sorted.spanning.bam:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-18/call-trgt_plot_motifs_allele/_singularity_tmpdir_v7izpq1f/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-18/call-trgt_plot_motifs_allele/_singularity_tmpdir_v7izpq1f/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:03.354 wdl.w:ptcp.w:call-trgt-18.t:call-trgt_plot_motifs_waterfall NOTICE slurm_singularity run :: pid: 1200797, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-18/call-trgt_plot_motifs_waterfall/slurm_singularity.log.txt"
2025-09-15 20:24:03.356 wdl.w:ptcp.w:call-trgt-18.t:call-trgt_plot_motifs_allele NOTICE slurm_singularity run :: pid: 1200798, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-18/call-trgt_plot_motifs_allele/slurm_singularity.log.txt"
2025-09-15 20:24:03.361 wdl.w:ptcp.w:call-trgt-11.t:call-trgt_plot_meth_allele INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:03.361 wdl.w:ptcp.w:call-trgt-11.t:call-trgt_plot_meth_allele INFO input :: name: "waterfall", value: false
2025-09-15 20:24:03.361 wdl.w:ptcp.w:call-trgt-11.t:call-trgt_plot_meth_allele INFO input :: name: "methylation", value: true
2025-09-15 20:24:03.361 wdl.w:ptcp.w:call-trgt-11.t:call-trgt_plot_meth_allele INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:03.361 wdl.w:ptcp.w:call-trgt-11.t:call-trgt_plot_meth_allele INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:03.361 wdl.w:ptcp.w:call-trgt-11.t:call-trgt_plot_meth_allele INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:03.361 wdl.w:ptcp.w:call-trgt-11.t:call-trgt_plot_meth_allele INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2108.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:03.361 wdl.w:ptcp.w:call-trgt-11.t:call-trgt_plot_meth_allele INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2108.trgt.sorted.spanning.bam"
2025-09-15 20:24:03.362 wdl.w:ptcp.w:call-trgt-11.t:call-trgt_plot_meth_allele INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2108.trgt.vcf"
2025-09-15 20:24:03.362 wdl.w:ptcp.w:call-trgt-11.t:call-trgt_plot_meth_allele INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2108"
2025-09-15 20:24:03.362 wdl.w:ptcp.w:call-trgt-11.t:call-trgt_plot_meth_allele INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:03.362 wdl.w:ptcp.w:call-trgt-11.t:call-trgt_plot_meth_allele INFO eval :: name: "plot_type", value: "allele"
2025-09-15 20:24:03.362 wdl.w:ptcp.w:call-trgt-11.t:call-trgt_plot_meth_allele INFO eval :: name: "show", value: "meth"
2025-09-15 20:24:03.362 wdl.w:ptcp.w:call-trgt-11.t:call-trgt_plot_meth_allele INFO eval :: name: "threads", value: 1
2025-09-15 20:24:03.362 wdl.w:ptcp.w:call-trgt-11.t:call-trgt_plot_meth_allele INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:03.363 wdl.w:ptcp.w:call-trgt-11.t:call-trgt_plot_meth_allele INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2108.meth_allele"
2025-09-15 20:24:03.363 wdl.w:ptcp.w:call-trgt-11.t:call-trgt_plot_meth_allele INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:03.363 wdl.w:ptcp.w:call-trgt-11.t:call-trgt_plot_meth_allele WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:03.363 wdl.w:ptcp.w:call-trgt-11.t:call-trgt_plot_meth_allele INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:03.363 wdl.w:ptcp.w:call-trgt-11.t:call-trgt_plot_meth_allele INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:03.425 wdl.w:ptcp.w:call-trgt-11.t:call-trgt_plot_meth_allele INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-11/call-trgt_plot_meth_allele/_singularity_tmpdir_1x94_hpz"
2025-09-15 20:24:03.425 wdl.w:ptcp.w:call-trgt-11.t:call-trgt_plot_meth_allele INFO Slurm invocation: srun --job-name call-trgt_plot_meth_allele --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-11/call-trgt_plot_meth_allele/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-11/call-trgt_plot_meth_allele/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-11/call-trgt_plot_meth_allele/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-11/call-trgt_plot_meth_allele/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-11/call-trgt_genotype/out/m84036_250809_035451_s4.bc2108.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2108.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-11/call-trgt_genotype/out/m84036_250809_035451_s4.bc2108.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2108.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-11/call-trgt_genotype/out/m84036_250809_035451_s4.bc2108.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2108.trgt.sorted.spanning.bam:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-11/call-trgt_plot_meth_allele/_singularity_tmpdir_1x94_hpz/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-11/call-trgt_plot_meth_allele/_singularity_tmpdir_1x94_hpz/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:03.437 wdl.w:ptcp.w:call-trgt-11.t:call-trgt_plot_meth_allele NOTICE slurm_singularity run :: pid: 1200801, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-11/call-trgt_plot_meth_allele/slurm_singularity.log.txt"
2025-09-15 20:24:03.550 wdl.w:ptcp.w:call-trgt-04.t:call-trgt_plot_meth_waterfall INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2101.meth_waterfall.trgt_plots.zip"
2025-09-15 20:24:03.653 wdl.w:ptcp.w:call-trgt-04.t:call-trgt_plot_meth_waterfall NOTICE done
2025-09-15 20:24:03.657 wdl.w:ptcp.w:call-trgt-04 NOTICE finish :: job: "call-trgt_plot_meth_waterfall"
2025-09-15 20:24:03.658 wdl.w:ptcp.w:call-trgt-04 INFO output :: job: "call-trgt_plot_meth_waterfall", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-04/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2101.meth_waterfall.trgt_plots.zip"}
2025-09-15 20:24:03.658 wdl.w:ptcp.w:call-trgt-04 INFO visit :: node: "output-images_meth_waterfall", values: {"images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-04/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2101.meth_waterfall.trgt_plots.zip"}
2025-09-15 20:24:03.658 wdl.w:ptcp.w:call-trgt-04 INFO visit :: node: "outputs", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-04/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2101.motifs_waterfall.trgt_plots.zip", "images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-04/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2101.meth_allele.trgt_plots.zip", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-04/call-trgt_genotype/out/m84036_250809_035451_s4.bc2101.trgt.sorted.spanning.bam.bai", "images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-04/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2101.motifs_allele.trgt_plots.zip", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-04/call-trgt_genotype/out/m84036_250809_035451_s4.bc2101.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-04/call-trgt_genotype/out/m84036_250809_035451_s4.bc2101.trgt.vcf", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-04/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2101.repeats.bam", "images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-04/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2101.meth_waterfall.trgt_plots.zip", "reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-04/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2101.repeats.bam.bai"}
2025-09-15 20:24:03.663 wdl.w:ptcp.w:call-trgt-11.t:call-trgt_plot_meth_waterfall NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-11/call-trgt_plot_meth_waterfall", thread: 140610887464512
2025-09-15 20:24:03.681 wdl.w:ptcp.w:call-trgt-11.t:call-trgt_plot_meth_waterfall INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:03.681 wdl.w:ptcp.w:call-trgt-11.t:call-trgt_plot_meth_waterfall INFO input :: name: "waterfall", value: true
2025-09-15 20:24:03.681 wdl.w:ptcp.w:call-trgt-11.t:call-trgt_plot_meth_waterfall INFO input :: name: "methylation", value: true
2025-09-15 20:24:03.681 wdl.w:ptcp.w:call-trgt-11.t:call-trgt_plot_meth_waterfall INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:03.681 wdl.w:ptcp.w:call-trgt-11.t:call-trgt_plot_meth_waterfall INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:03.681 wdl.w:ptcp.w:call-trgt-11.t:call-trgt_plot_meth_waterfall INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:03.681 wdl.w:ptcp.w:call-trgt-11.t:call-trgt_plot_meth_waterfall INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2108.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:03.681 wdl.w:ptcp.w:call-trgt-11.t:call-trgt_plot_meth_waterfall INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2108.trgt.sorted.spanning.bam"
2025-09-15 20:24:03.681 wdl.w:ptcp.w:call-trgt-11.t:call-trgt_plot_meth_waterfall INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2108.trgt.vcf"
2025-09-15 20:24:03.681 wdl.w:ptcp.w:call-trgt-11.t:call-trgt_plot_meth_waterfall INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2108"
2025-09-15 20:24:03.682 wdl.w:ptcp.w:call-trgt-11.t:call-trgt_plot_meth_waterfall INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:03.682 wdl.w:ptcp.w:call-trgt-11.t:call-trgt_plot_meth_waterfall INFO eval :: name: "plot_type", value: "waterfall"
2025-09-15 20:24:03.682 wdl.w:ptcp.w:call-trgt-11.t:call-trgt_plot_meth_waterfall INFO eval :: name: "show", value: "meth"
2025-09-15 20:24:03.682 wdl.w:ptcp.w:call-trgt-11.t:call-trgt_plot_meth_waterfall INFO eval :: name: "threads", value: 1
2025-09-15 20:24:03.682 wdl.w:ptcp.w:call-trgt-11.t:call-trgt_plot_meth_waterfall INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:03.682 wdl.w:ptcp.w:call-trgt-11.t:call-trgt_plot_meth_waterfall INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2108.meth_waterfall"
2025-09-15 20:24:03.683 wdl.w:ptcp.w:call-trgt-11.t:call-trgt_plot_meth_waterfall INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:03.683 wdl.w:ptcp.w:call-trgt-11.t:call-trgt_plot_meth_waterfall WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:03.683 wdl.w:ptcp.w:call-trgt-11.t:call-trgt_plot_meth_waterfall INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:03.683 wdl.w:ptcp.w:call-trgt-11.t:call-trgt_plot_meth_waterfall INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:03.747 wdl.w:ptcp.w:call-trgt-04 NOTICE done
2025-09-15 20:24:03.751 wdl.w:ptcp NOTICE finish :: job: "call-trgt-04"
2025-09-15 20:24:03.752 wdl.w:ptcp INFO output :: job: "call-trgt-04", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-04/out/m84036_250809_035451_s4.bc2101.motifs_waterfall.trgt_plots.zip", "images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-04/out/m84036_250809_035451_s4.bc2101.meth_allele.trgt_plots.zip", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-04/out/m84036_250809_035451_s4.bc2101.trgt.sorted.spanning.bam.bai", "images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-04/out/m84036_250809_035451_s4.bc2101.motifs_allele.trgt_plots.zip", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-04/out/m84036_250809_035451_s4.bc2101.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-04/out/m84036_250809_035451_s4.bc2101.trgt.vcf", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-04/out/m84036_250809_035451_s4.bc2101.repeats.bam", "images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-04/out/m84036_250809_035451_s4.bc2101.meth_waterfall.trgt_plots.zip", "reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-04/out/m84036_250809_035451_s4.bc2101.repeats.bam.bai"}
2025-09-15 20:24:03.758 wdl.w:ptcp.w:call-sawfish-63 NOTICE workflow start :: name: "sawfish", source: "./sawfish.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-63"
2025-09-15 20:24:03.758 wdl.w:ptcp.w:call-trgt-11.t:call-trgt_plot_meth_waterfall INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-11/call-trgt_plot_meth_waterfall/_singularity_tmpdir_tphk4is5"
2025-09-15 20:24:03.758 wdl.w:ptcp.w:call-trgt-11.t:call-trgt_plot_meth_waterfall INFO Slurm invocation: srun --job-name call-trgt_plot_meth_waterfall --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-11/call-trgt_plot_meth_waterfall/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-11/call-trgt_plot_meth_waterfall/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-11/call-trgt_plot_meth_waterfall/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-11/call-trgt_plot_meth_waterfall/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-11/call-trgt_genotype/out/m84036_250809_035451_s4.bc2108.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2108.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-11/call-trgt_genotype/out/m84036_250809_035451_s4.bc2108.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2108.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-11/call-trgt_genotype/out/m84036_250809_035451_s4.bc2108.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2108.trgt.sorted.spanning.bam:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-11/call-trgt_plot_meth_waterfall/_singularity_tmpdir_tphk4is5/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-11/call-trgt_plot_meth_waterfall/_singularity_tmpdir_tphk4is5/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:03.770 wdl.w:ptcp.w:call-trgt-11.t:call-trgt_plot_meth_waterfall NOTICE slurm_singularity run :: pid: 1200819, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-11/call-trgt_plot_meth_waterfall/slurm_singularity.log.txt"
2025-09-15 20:24:03.773 wdl.w:ptcp.w:call-sawfish-63 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:24:03.773 wdl.w:ptcp.w:call-sawfish-63 INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:24:03.773 wdl.w:ptcp.w:call-sawfish-63 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-63/out/m84036_250809_035451_s4.bc2160.mapped.bam"}
2025-09-15 20:24:03.773 wdl.w:ptcp.w:call-sawfish-63 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-63/out/m84036_250809_035451_s4.bc2160.mapped.bam.bai"}
2025-09-15 20:24:03.773 wdl.w:ptcp.w:call-sawfish-63 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:24:03.773 wdl.w:ptcp.w:call-sawfish-63 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:24:03.773 wdl.w:ptcp.w:call-sawfish-63 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2160"}
2025-09-15 20:24:03.773 wdl.w:ptcp.w:call-sawfish-63 NOTICE ready :: job: "call-run_sawfish", callee: "run_sawfish"
2025-09-15 20:24:03.774 wdl.w:ptcp.w:call-sawfish-63 INFO input :: job: "call-run_sawfish", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-63/out/m84036_250809_035451_s4.bc2160.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-63/out/m84036_250809_035451_s4.bc2160.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2160"}
2025-09-15 20:24:03.917 wdl.w:ptcp.w:call-trgt-18.t:call-trgt_plot_meth_allele INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2115.meth_allele.trgt_plots.zip"
2025-09-15 20:24:03.997 wdl.w:ptcp.w:call-trgt-18.t:call-trgt_plot_meth_allele NOTICE done
2025-09-15 20:24:04.003 wdl.w:ptcp.w:call-trgt-18 NOTICE finish :: job: "call-trgt_plot_meth_allele"
2025-09-15 20:24:04.003 wdl.w:ptcp.w:call-trgt-18 INFO output :: job: "call-trgt_plot_meth_allele", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-18/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2115.meth_allele.trgt_plots.zip"}
2025-09-15 20:24:04.004 wdl.w:ptcp.w:call-trgt-18 INFO visit :: node: "output-images_meth_allele", values: {"images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-18/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2115.meth_allele.trgt_plots.zip"}
2025-09-15 20:24:04.011 wdl.w:ptcp.w:call-trgt-11.t:call-trgt_plot_motifs_allele NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-11/call-trgt_plot_motifs_allele", thread: 140609310422592
2025-09-15 20:24:04.028 wdl.w:ptcp.w:call-trgt-11.t:call-trgt_plot_motifs_allele INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:04.028 wdl.w:ptcp.w:call-trgt-11.t:call-trgt_plot_motifs_allele INFO input :: name: "waterfall", value: false
2025-09-15 20:24:04.028 wdl.w:ptcp.w:call-trgt-11.t:call-trgt_plot_motifs_allele INFO input :: name: "methylation", value: false
2025-09-15 20:24:04.028 wdl.w:ptcp.w:call-trgt-11.t:call-trgt_plot_motifs_allele INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:04.028 wdl.w:ptcp.w:call-trgt-11.t:call-trgt_plot_motifs_allele INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:04.028 wdl.w:ptcp.w:call-trgt-11.t:call-trgt_plot_motifs_allele INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:04.028 wdl.w:ptcp.w:call-trgt-11.t:call-trgt_plot_motifs_allele INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2108.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:04.028 wdl.w:ptcp.w:call-trgt-11.t:call-trgt_plot_motifs_allele INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2108.trgt.sorted.spanning.bam"
2025-09-15 20:24:04.028 wdl.w:ptcp.w:call-trgt-11.t:call-trgt_plot_motifs_allele INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2108.trgt.vcf"
2025-09-15 20:24:04.028 wdl.w:ptcp.w:call-trgt-11.t:call-trgt_plot_motifs_allele INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2108"
2025-09-15 20:24:04.029 wdl.w:ptcp.w:call-trgt-11.t:call-trgt_plot_motifs_allele INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:04.029 wdl.w:ptcp.w:call-trgt-11.t:call-trgt_plot_motifs_allele INFO eval :: name: "plot_type", value: "allele"
2025-09-15 20:24:04.029 wdl.w:ptcp.w:call-trgt-11.t:call-trgt_plot_motifs_allele INFO eval :: name: "show", value: "motifs"
2025-09-15 20:24:04.029 wdl.w:ptcp.w:call-trgt-11.t:call-trgt_plot_motifs_allele INFO eval :: name: "threads", value: 1
2025-09-15 20:24:04.029 wdl.w:ptcp.w:call-trgt-11.t:call-trgt_plot_motifs_allele INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:04.029 wdl.w:ptcp.w:call-trgt-11.t:call-trgt_plot_motifs_allele INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2108.motifs_allele"
2025-09-15 20:24:04.030 wdl.w:ptcp.w:call-trgt-11.t:call-trgt_plot_motifs_allele INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:04.030 wdl.w:ptcp.w:call-trgt-11.t:call-trgt_plot_motifs_allele WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:04.030 wdl.w:ptcp.w:call-trgt-11.t:call-trgt_plot_motifs_allele INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:04.030 wdl.w:ptcp.w:call-trgt-11.t:call-trgt_plot_motifs_allele INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:04.096 wdl.w:ptcp.w:call-trgt-11.t:call-trgt_plot_motifs_allele INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-11/call-trgt_plot_motifs_allele/_singularity_tmpdir_2ufw6hy7"
2025-09-15 20:24:04.096 wdl.w:ptcp.w:call-trgt-11.t:call-trgt_plot_motifs_allele INFO Slurm invocation: srun --job-name call-trgt_plot_motifs_allele --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-11/call-trgt_plot_motifs_allele/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-11/call-trgt_plot_motifs_allele/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-11/call-trgt_plot_motifs_allele/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-11/call-trgt_plot_motifs_allele/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-11/call-trgt_genotype/out/m84036_250809_035451_s4.bc2108.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2108.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-11/call-trgt_genotype/out/m84036_250809_035451_s4.bc2108.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2108.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-11/call-trgt_genotype/out/m84036_250809_035451_s4.bc2108.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2108.trgt.sorted.spanning.bam:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-11/call-trgt_plot_motifs_allele/_singularity_tmpdir_2ufw6hy7/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-11/call-trgt_plot_motifs_allele/_singularity_tmpdir_2ufw6hy7/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:04.107 wdl.w:ptcp.w:call-trgt-11.t:call-trgt_plot_motifs_allele NOTICE slurm_singularity run :: pid: 1200827, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-11/call-trgt_plot_motifs_allele/slurm_singularity.log.txt"
2025-09-15 20:24:04.249 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:02 [ERROR] - No reads found for TRID=OPDM_ABCD3
2025-09-15 20:24:04.249 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:02 [ERROR] - No reads found for TRID=OPMD_PABPN1
2025-09-15 20:24:04.249 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:02 [ERROR] - No reads found for TRID=SCA3_ATXN3
2025-09-15 20:24:04.249 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:02 [ERROR] - No reads found for TRID=SCA31_BEAN1
2025-09-15 20:24:04.249 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:02 [ERROR] - No reads found for TRID=SCA27B_FGF14
2025-09-15 20:24:04.250 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:02 [ERROR] - No reads found for TRID=OPDM2_GIPC1
2025-09-15 20:24:04.250 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:02 [ERROR] - No reads found for TRID=HDL2_JPH3
2025-09-15 20:24:04.250 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:02 [ERROR] - No reads found for TRID=FRA2A_AFF3
2025-09-15 20:24:04.250 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:02 [ERROR] - No reads found for TRID=SD5_HOXD13
2025-09-15 20:24:04.250 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:02 [ERROR] - No reads found for TRID=CJD_PRNP
2025-09-15 20:24:04.250 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:02 [ERROR] - No reads found for TRID=SCA36_NOP56
2025-09-15 20:24:04.250 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:02 [ERROR] - No reads found for TRID=EPM1_CSTB
2025-09-15 20:24:04.250 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:02 [ERROR] - No reads found for TRID=SCA10_ATXN10
2025-09-15 20:24:04.250 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:02 [ERROR] - No reads found for TRID=SCA7_ATXN7
2025-09-15 20:24:04.250 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:02 [ERROR] - No reads found for TRID=DM2_CNBP
2025-09-15 20:24:04.250 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:02 [ERROR] - No reads found for TRID=HD_HTT
2025-09-15 20:24:04.250 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:02 [ERROR] - No reads found for TRID=SCA6_CACNA1A
2025-09-15 20:24:04.250 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:03 [ERROR] - No reads found for TRID=SCA12_PPP2R2B
2025-09-15 20:24:04.250 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:03 [ERROR] - No reads found for TRID=SCA1_ATXN1
2025-09-15 20:24:04.250 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:03 [ERROR] - No reads found for TRID=CANVAS_RFC1
2025-09-15 20:24:04.250 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:03 [ERROR] - No reads found for TRID=FECD3_TCF4
2025-09-15 20:24:04.250 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:03 [ERROR] - No reads found for TRID=DM1_DMPK
2025-09-15 20:24:04.251 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:03 [ERROR] - No reads found for TRID=FAME1_SAMD12
2025-09-15 20:24:04.337 wdl.w:ptcp.w:call-paraphase-34.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for hbb for sample m84036_250809_035451_s4.bc2131 at 2025-09-15 20:23:51.680111...
2025-09-15 20:24:04.337 wdl.w:ptcp.w:call-paraphase-34.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for hbb for sample m84036_250809_035451_s4.bc2131 at 2025-09-15 20:23:54.344691...
2025-09-15 20:24:04.338 wdl.w:ptcp.w:call-paraphase-34.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for hbb for sample m84036_250809_035451_s4.bc2131 at 2025-09-15 20:23:54.721896...
2025-09-15 20:24:04.356 wdl.w:ptcp.w:call-trgt-18.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:04 [ERROR] - No reads found for TRID=OPDM_ABCD3
2025-09-15 20:24:04.356 wdl.w:ptcp.w:call-trgt-18.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:04 [ERROR] - No reads found for TRID=SCA37_DAB1
2025-09-15 20:24:04.356 wdl.w:ptcp.w:call-trgt-18.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:04 [ERROR] - No reads found for TRID=DRPLA_ATN1
2025-09-15 20:24:04.356 wdl.w:ptcp.w:call-trgt-18.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:04 [ERROR] - No reads found for TRID=NIID_NOTCH2NLC
2025-09-15 20:24:04.359 wdl.w:ptcp.w:call-trgt-18.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:04 [ERROR] - No reads found for TRID=OPDM_ABCD3
2025-09-15 20:24:04.359 wdl.w:ptcp.w:call-trgt-18.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:04 [ERROR] - No reads found for TRID=SCA37_DAB1
2025-09-15 20:24:04.359 wdl.w:ptcp.w:call-trgt-18.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:04 [ERROR] - No reads found for TRID=DRPLA_ATN1
2025-09-15 20:24:04.359 wdl.w:ptcp.w:call-trgt-18.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:04 [ERROR] - No reads found for TRID=NIID_NOTCH2NLC
2025-09-15 20:24:04.359 wdl.w:ptcp.w:call-trgt-18.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:04 [ERROR] - No reads found for TRID=OPDM4_RILPL1
2025-09-15 20:24:04.359 wdl.w:ptcp.w:call-trgt-18.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:04 [ERROR] - No reads found for TRID=SCA27B_FGF14
2025-09-15 20:24:04.366 wdl.w:ptcp.w:call-trgt-18.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO srun: job 51797538 queued and waiting for resources
2025-09-15 20:24:04.366 wdl.w:ptcp.w:call-trgt-18.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO srun: job 51797538 has been allocated resources
2025-09-15 20:24:04.366 wdl.w:ptcp.w:call-trgt-18.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:04.366 wdl.w:ptcp.w:call-trgt-18.t:call-trgt_plot_motifs_allele.slurm_singularity INFO srun: job 51797539 queued and waiting for resources
2025-09-15 20:24:04.366 wdl.w:ptcp.w:call-trgt-18.t:call-trgt_plot_motifs_allele.slurm_singularity INFO srun: job 51797539 has been allocated resources
2025-09-15 20:24:04.366 wdl.w:ptcp.w:call-trgt-18.t:call-trgt_plot_motifs_allele.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:04.378 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:03 [ERROR] - No reads found for TRID=CCHS_PHOX2B
2025-09-15 20:24:04.378 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:03 [ERROR] - No reads found for TRID=FTDALS1_C9orf72
2025-09-15 20:24:04.378 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:03 [ERROR] - No reads found for TRID=OPDM1_LRP12
2025-09-15 20:24:04.378 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:03 [ERROR] - No reads found for TRID=SBMA_AR
2025-09-15 20:24:04.413 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_motifs_allele INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2123.motifs_allele.trgt_plots.zip"
2025-09-15 20:24:04.418 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_motifs_waterfall INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2123.motifs_waterfall.trgt_plots.zip"
2025-09-15 20:24:04.440 wdl.w:ptcp.w:call-trgt-11.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:04 [ERROR] - No reads found for TRID=NIID_NOTCH2NLC
2025-09-15 20:24:04.440 wdl.w:ptcp.w:call-trgt-11.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:04 [ERROR] - No reads found for TRID=DRPLA_ATN1
2025-09-15 20:24:04.440 wdl.w:ptcp.w:call-trgt-11.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:04 [ERROR] - No reads found for TRID=SCA37_DAB1
2025-09-15 20:24:04.440 wdl.w:ptcp.w:call-trgt-11.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:04 [ERROR] - No reads found for TRID=OPDM4_RILPL1
2025-09-15 20:24:04.440 wdl.w:ptcp.w:call-trgt-11.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:04 [ERROR] - No reads found for TRID=SCA8_ATXN8OS
2025-09-15 20:24:04.440 wdl.w:ptcp.w:call-trgt-11.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:04 [ERROR] - No reads found for TRID=SCA2_ATXN2
2025-09-15 20:24:04.440 wdl.w:ptcp.w:call-trgt-11.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:04 [ERROR] - No reads found for TRID=OPMD_PABPN1
2025-09-15 20:24:04.451 wdl.w:ptcp.w:call-trgt-11.t:call-trgt_plot_meth_allele.slurm_singularity INFO srun: job 51797540 queued and waiting for resources
2025-09-15 20:24:04.451 wdl.w:ptcp.w:call-trgt-11.t:call-trgt_plot_meth_allele.slurm_singularity INFO srun: job 51797540 has been allocated resources
2025-09-15 20:24:04.451 wdl.w:ptcp.w:call-trgt-11.t:call-trgt_plot_meth_allele.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:04.467 wdl.w:ptcp.w:call-sawfish-44.t:call-run_sawfish.stderr VERBOSE [M::bam2fq_mainloop] discarded 0 singletons
2025-09-15 20:24:04.467 wdl.w:ptcp.w:call-sawfish-44.t:call-run_sawfish.stderr VERBOSE [M::bam2fq_mainloop] processed 0 reads
2025-09-15 20:24:04.487 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_motifs_allele NOTICE done
2025-09-15 20:24:04.487 wdl.w:ptcp.w:call-trgt-26.t:call-trgt_plot_motifs_waterfall NOTICE done
2025-09-15 20:24:04.493 wdl.w:ptcp.w:call-trgt-26 NOTICE finish :: job: "call-trgt_plot_motifs_allele"
2025-09-15 20:24:04.493 wdl.w:ptcp.w:call-trgt-26 INFO output :: job: "call-trgt_plot_motifs_allele", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-26/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2123.motifs_allele.trgt_plots.zip"}
2025-09-15 20:24:04.493 wdl.w:ptcp.w:call-trgt-26 INFO visit :: node: "output-images_motifs_allele", values: {"images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-26/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2123.motifs_allele.trgt_plots.zip"}
2025-09-15 20:24:04.493 wdl.w:ptcp.w:call-trgt-26 NOTICE finish :: job: "call-trgt_plot_motifs_waterfall"
2025-09-15 20:24:04.494 wdl.w:ptcp.w:call-trgt-26 INFO output :: job: "call-trgt_plot_motifs_waterfall", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-26/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2123.motifs_waterfall.trgt_plots.zip"}
2025-09-15 20:24:04.495 wdl.w:ptcp.w:call-trgt-26 INFO visit :: node: "output-images_motifs_waterfall", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-26/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2123.motifs_waterfall.trgt_plots.zip"}
2025-09-15 20:24:04.495 wdl.w:ptcp.w:call-trgt-26 INFO visit :: node: "outputs", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-26/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2123.motifs_waterfall.trgt_plots.zip", "images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-26/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2123.meth_allele.trgt_plots.zip", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-26/call-trgt_genotype/out/m84036_250809_035451_s4.bc2123.trgt.sorted.spanning.bam.bai", "images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-26/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2123.motifs_allele.trgt_plots.zip", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-26/call-trgt_genotype/out/m84036_250809_035451_s4.bc2123.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-26/call-trgt_genotype/out/m84036_250809_035451_s4.bc2123.trgt.vcf", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-26/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2123.repeats.bam", "images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-26/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2123.meth_waterfall.trgt_plots.zip", "reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-26/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2123.repeats.bam.bai"}
2025-09-15 20:24:04.500 wdl.w:ptcp.w:call-trgt-11.t:call-trgt_plot_motifs_waterfall NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-11/call-trgt_plot_motifs_waterfall", thread: 140608748373568
2025-09-15 20:24:04.501 wdl.w:ptcp.w:call-trgt-19.t:call-trgt_plot_meth_allele NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-19/call-trgt_plot_meth_allele", thread: 140610367379008
2025-09-15 20:24:04.519 wdl.w:ptcp.w:call-trgt-11.t:call-trgt_plot_motifs_waterfall INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:04.519 wdl.w:ptcp.w:call-trgt-11.t:call-trgt_plot_motifs_waterfall INFO input :: name: "waterfall", value: true
2025-09-15 20:24:04.519 wdl.w:ptcp.w:call-trgt-11.t:call-trgt_plot_motifs_waterfall INFO input :: name: "methylation", value: false
2025-09-15 20:24:04.519 wdl.w:ptcp.w:call-trgt-11.t:call-trgt_plot_motifs_waterfall INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:04.520 wdl.w:ptcp.w:call-trgt-11.t:call-trgt_plot_motifs_waterfall INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:04.520 wdl.w:ptcp.w:call-trgt-11.t:call-trgt_plot_motifs_waterfall INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:04.520 wdl.w:ptcp.w:call-trgt-11.t:call-trgt_plot_motifs_waterfall INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2108.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:04.520 wdl.w:ptcp.w:call-trgt-11.t:call-trgt_plot_motifs_waterfall INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2108.trgt.sorted.spanning.bam"
2025-09-15 20:24:04.520 wdl.w:ptcp.w:call-trgt-11.t:call-trgt_plot_motifs_waterfall INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2108.trgt.vcf"
2025-09-15 20:24:04.520 wdl.w:ptcp.w:call-trgt-11.t:call-trgt_plot_motifs_waterfall INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2108"
2025-09-15 20:24:04.520 wdl.w:ptcp.w:call-trgt-11.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:04.520 wdl.w:ptcp.w:call-trgt-11.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "plot_type", value: "waterfall"
2025-09-15 20:24:04.520 wdl.w:ptcp.w:call-trgt-11.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "show", value: "motifs"
2025-09-15 20:24:04.521 wdl.w:ptcp.w:call-trgt-11.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "threads", value: 1
2025-09-15 20:24:04.521 wdl.w:ptcp.w:call-trgt-11.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:04.521 wdl.w:ptcp.w:call-trgt-11.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2108.motifs_waterfall"
2025-09-15 20:24:04.521 wdl.w:ptcp.w:call-trgt-11.t:call-trgt_plot_motifs_waterfall INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:04.521 wdl.w:ptcp.w:call-trgt-11.t:call-trgt_plot_motifs_waterfall WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:04.522 wdl.w:ptcp.w:call-trgt-11.t:call-trgt_plot_motifs_waterfall INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:04.522 wdl.w:ptcp.w:call-trgt-11.t:call-trgt_plot_motifs_waterfall INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:04.526 wdl.w:ptcp.w:call-trgt-19.t:call-trgt_plot_meth_allele INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:04.526 wdl.w:ptcp.w:call-trgt-19.t:call-trgt_plot_meth_allele INFO input :: name: "waterfall", value: false
2025-09-15 20:24:04.526 wdl.w:ptcp.w:call-trgt-19.t:call-trgt_plot_meth_allele INFO input :: name: "methylation", value: true
2025-09-15 20:24:04.526 wdl.w:ptcp.w:call-trgt-19.t:call-trgt_plot_meth_allele INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:04.526 wdl.w:ptcp.w:call-trgt-19.t:call-trgt_plot_meth_allele INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:04.526 wdl.w:ptcp.w:call-trgt-19.t:call-trgt_plot_meth_allele INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:04.526 wdl.w:ptcp.w:call-trgt-19.t:call-trgt_plot_meth_allele INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2116.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:04.526 wdl.w:ptcp.w:call-trgt-19.t:call-trgt_plot_meth_allele INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2116.trgt.sorted.spanning.bam"
2025-09-15 20:24:04.526 wdl.w:ptcp.w:call-trgt-19.t:call-trgt_plot_meth_allele INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2116.trgt.vcf"
2025-09-15 20:24:04.526 wdl.w:ptcp.w:call-trgt-19.t:call-trgt_plot_meth_allele INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2116"
2025-09-15 20:24:04.527 wdl.w:ptcp.w:call-trgt-19.t:call-trgt_plot_meth_allele INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:04.527 wdl.w:ptcp.w:call-trgt-19.t:call-trgt_plot_meth_allele INFO eval :: name: "plot_type", value: "allele"
2025-09-15 20:24:04.527 wdl.w:ptcp.w:call-trgt-19.t:call-trgt_plot_meth_allele INFO eval :: name: "show", value: "meth"
2025-09-15 20:24:04.527 wdl.w:ptcp.w:call-trgt-19.t:call-trgt_plot_meth_allele INFO eval :: name: "threads", value: 1
2025-09-15 20:24:04.528 wdl.w:ptcp.w:call-trgt-19.t:call-trgt_plot_meth_allele INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:04.528 wdl.w:ptcp.w:call-trgt-19.t:call-trgt_plot_meth_allele INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2116.meth_allele"
2025-09-15 20:24:04.528 wdl.w:ptcp.w:call-trgt-19.t:call-trgt_plot_meth_allele INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:04.528 wdl.w:ptcp.w:call-trgt-19.t:call-trgt_plot_meth_allele WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:04.529 wdl.w:ptcp.w:call-trgt-19.t:call-trgt_plot_meth_allele INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:04.529 wdl.w:ptcp.w:call-trgt-19.t:call-trgt_plot_meth_allele INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:04.599 wdl.w:ptcp.w:call-trgt-26 NOTICE done
2025-09-15 20:24:04.603 wdl.w:ptcp.w:call-trgt-11.t:call-trgt_plot_motifs_waterfall INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-11/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_k4se2zql"
2025-09-15 20:24:04.603 wdl.w:ptcp.w:call-trgt-11.t:call-trgt_plot_motifs_waterfall INFO Slurm invocation: srun --job-name call-trgt_plot_motifs_waterfall --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-11/call-trgt_plot_motifs_waterfall/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-11/call-trgt_plot_motifs_waterfall/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-11/call-trgt_plot_motifs_waterfall/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-11/call-trgt_plot_motifs_waterfall/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-11/call-trgt_genotype/out/m84036_250809_035451_s4.bc2108.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2108.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-11/call-trgt_genotype/out/m84036_250809_035451_s4.bc2108.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2108.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-11/call-trgt_genotype/out/m84036_250809_035451_s4.bc2108.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2108.trgt.sorted.spanning.bam:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-11/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_k4se2zql/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-11/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_k4se2zql/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:04.604 wdl.w:ptcp.w:call-trgt-19.t:call-trgt_plot_meth_allele INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-19/call-trgt_plot_meth_allele/_singularity_tmpdir_z5ikp6u0"
2025-09-15 20:24:04.605 wdl.w:ptcp NOTICE finish :: job: "call-trgt-26"
2025-09-15 20:24:04.605 wdl.w:ptcp.w:call-trgt-19.t:call-trgt_plot_meth_allele INFO Slurm invocation: srun --job-name call-trgt_plot_meth_allele --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-19/call-trgt_plot_meth_allele/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-19/call-trgt_plot_meth_allele/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-19/call-trgt_plot_meth_allele/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-19/call-trgt_plot_meth_allele/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-19/call-trgt_genotype/out/m84036_250809_035451_s4.bc2116.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2116.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-19/call-trgt_genotype/out/m84036_250809_035451_s4.bc2116.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2116.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-19/call-trgt_genotype/out/m84036_250809_035451_s4.bc2116.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2116.trgt.vcf:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-19/call-trgt_plot_meth_allele/_singularity_tmpdir_z5ikp6u0/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-19/call-trgt_plot_meth_allele/_singularity_tmpdir_z5ikp6u0/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:04.605 wdl.w:ptcp INFO output :: job: "call-trgt-26", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-26/out/m84036_250809_035451_s4.bc2123.motifs_waterfall.trgt_plots.zip", "images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-26/out/m84036_250809_035451_s4.bc2123.meth_allele.trgt_plots.zip", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-26/out/m84036_250809_035451_s4.bc2123.trgt.sorted.spanning.bam.bai", "images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-26/out/m84036_250809_035451_s4.bc2123.motifs_allele.trgt_plots.zip", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-26/out/m84036_250809_035451_s4.bc2123.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-26/out/m84036_250809_035451_s4.bc2123.trgt.vcf", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-26/out/m84036_250809_035451_s4.bc2123.repeats.bam", "images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-26/out/m84036_250809_035451_s4.bc2123.meth_waterfall.trgt_plots.zip", "reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-26/out/m84036_250809_035451_s4.bc2123.repeats.bam.bai"}
2025-09-15 20:24:04.611 wdl.w:ptcp.w:call-trgt-63 NOTICE workflow start :: name: "trgt", source: "./trgt.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-63"
2025-09-15 20:24:04.625 wdl.w:ptcp.w:call-trgt-63 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:24:04.625 wdl.w:ptcp.w:call-trgt-63 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-63/out/m84036_250809_035451_s4.bc2160.mapped.bam"}
2025-09-15 20:24:04.625 wdl.w:ptcp.w:call-trgt-63 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-63/out/m84036_250809_035451_s4.bc2160.mapped.bam.bai"}
2025-09-15 20:24:04.625 wdl.w:ptcp.w:call-trgt-63 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:24:04.625 wdl.w:ptcp.w:call-trgt-63 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:24:04.626 wdl.w:ptcp.w:call-trgt-63 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2160"}
2025-09-15 20:24:04.626 wdl.w:ptcp.w:call-trgt-63 INFO visit :: node: "decl-sex", values: {"sex": "F"}
2025-09-15 20:24:04.626 wdl.w:ptcp.w:call-trgt-63 INFO visit :: node: "decl-trgt_bed", values: {"trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"}
2025-09-15 20:24:04.626 wdl.w:ptcp.w:call-trgt-63 NOTICE ready :: job: "call-get_reads_overlapping_repeats", callee: "get_reads_overlapping_repeats"
2025-09-15 20:24:04.626 wdl.w:ptcp.w:call-trgt-63 INFO input :: job: "call-get_reads_overlapping_repeats", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-63/out/m84036_250809_035451_s4.bc2160.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-63/out/m84036_250809_035451_s4.bc2160.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2160"}
2025-09-15 20:24:04.627 wdl.w:ptcp.w:call-trgt-63 NOTICE ready :: job: "call-trgt_genotype", callee: "trgt_genotype"
2025-09-15 20:24:04.627 wdl.w:ptcp.w:call-trgt-63 INFO input :: job: "call-trgt_genotype", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-63/out/m84036_250809_035451_s4.bc2160.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-63/out/m84036_250809_035451_s4.bc2160.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2160"}
2025-09-15 20:24:04.627 wdl.w:ptcp.w:call-trgt-11.t:call-trgt_plot_motifs_waterfall NOTICE slurm_singularity run :: pid: 1200836, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-11/call-trgt_plot_motifs_waterfall/slurm_singularity.log.txt"
2025-09-15 20:24:04.627 wdl.w:ptcp.w:call-trgt-19.t:call-trgt_plot_meth_allele NOTICE slurm_singularity run :: pid: 1200837, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-19/call-trgt_plot_meth_allele/slurm_singularity.log.txt"
2025-09-15 20:24:04.760 wdl.w:ptcp.w:call-paraphase-36.t:call-run_paraphase INFO output :: name: "paraphase_bam", value: "m84036_250809_035451_s4.bc2133_paraphase/m84036_250809_035451_s4.bc2133.paraphase.bam"
2025-09-15 20:24:04.764 wdl.w:ptcp.w:call-paraphase-36.t:call-run_paraphase INFO output :: name: "paraphase_bam_bai", value: "m84036_250809_035451_s4.bc2133_paraphase/m84036_250809_035451_s4.bc2133.paraphase.bam.bai"
2025-09-15 20:24:04.765 wdl.w:ptcp.w:call-paraphase-36.t:call-run_paraphase INFO output :: name: "paraphase_json", value: "m84036_250809_035451_s4.bc2133_paraphase/m84036_250809_035451_s4.bc2133.paraphase.json"
2025-09-15 20:24:04.767 wdl.w:ptcp.w:call-paraphase-36.t:call-run_paraphase INFO output :: name: "paraphase_vcfs", value: []
2025-09-15 20:24:04.767 wdl.w:ptcp.w:call-paraphase-36.t:call-run_paraphase INFO output :: name: "havanno_json", value: "m84036_250809_035451_s4.bc2133.havanno.json"
2025-09-15 20:24:04.772 wdl.w:ptcp.w:call-trgt-11.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:04 [ERROR] - No reads found for TRID=NIID_NOTCH2NLC
2025-09-15 20:24:04.772 wdl.w:ptcp.w:call-trgt-11.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:04 [ERROR] - No reads found for TRID=DRPLA_ATN1
2025-09-15 20:24:04.772 wdl.w:ptcp.w:call-paraphase-27.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for smn1 for sample m84036_250809_035451_s4.bc2124 at 2025-09-15 20:23:56.551462...
2025-09-15 20:24:04.772 wdl.w:ptcp.w:call-trgt-11.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:04 [ERROR] - No reads found for TRID=SCA37_DAB1
2025-09-15 20:24:04.772 wdl.w:ptcp.w:call-trgt-11.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:04 [ERROR] - No reads found for TRID=OPDM4_RILPL1
2025-09-15 20:24:04.772 wdl.w:ptcp.w:call-trgt-11.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:04 [ERROR] - No reads found for TRID=SCA8_ATXN8OS
2025-09-15 20:24:04.773 wdl.w:ptcp.w:call-trgt-11.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:04 [ERROR] - No reads found for TRID=SCA2_ATXN2
2025-09-15 20:24:04.773 wdl.w:ptcp.w:call-trgt-11.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:04 [ERROR] - No reads found for TRID=OPMD_PABPN1
2025-09-15 20:24:04.773 wdl.w:ptcp.w:call-trgt-11.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:04 [ERROR] - No reads found for TRID=OPDM_ABCD3
2025-09-15 20:24:04.773 wdl.w:ptcp.w:call-trgt-11.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:04 [ERROR] - No reads found for TRID=SCA27B_FGF14
2025-09-15 20:24:04.773 wdl.w:ptcp.w:call-trgt-11.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:04 [ERROR] - No reads found for TRID=SCA4_ZFHX3
2025-09-15 20:24:04.773 wdl.w:ptcp.w:call-trgt-11.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:04 [ERROR] - No reads found for TRID=FECD3_TCF4
2025-09-15 20:24:04.782 wdl.w:ptcp.w:call-trgt-11.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO srun: job 51797541 queued and waiting for resources
2025-09-15 20:24:04.782 wdl.w:ptcp.w:call-trgt-11.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO srun: job 51797541 has been allocated resources
2025-09-15 20:24:04.782 wdl.w:ptcp.w:call-trgt-11.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:04.849 wdl.w:ptcp.w:call-paraphase-36.t:call-run_paraphase NOTICE done
2025-09-15 20:24:04.855 wdl.w:ptcp.w:call-paraphase-36 NOTICE finish :: job: "call-run_paraphase"
2025-09-15 20:24:04.855 wdl.w:ptcp.w:call-paraphase-36 INFO output :: job: "call-run_paraphase", values: {"havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-36/call-run_paraphase/out/m84036_250809_035451_s4.bc2133.havanno.json", "paraphase_vcfs": [], "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-36/call-run_paraphase/out/m84036_250809_035451_s4.bc2133_paraphase/m84036_250809_035451_s4.bc2133.paraphase.json", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-36/call-run_paraphase/out/m84036_250809_035451_s4.bc2133_paraphase/m84036_250809_035451_s4.bc2133.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-36/call-run_paraphase/out/m84036_250809_035451_s4.bc2133_paraphase/m84036_250809_035451_s4.bc2133.paraphase.bam"}
2025-09-15 20:24:04.856 wdl.w:ptcp.w:call-paraphase-36 NOTICE ready :: job: "call-call_f8", callee: "call_f8"
2025-09-15 20:24:04.856 wdl.w:ptcp.w:call-paraphase-36 INFO input :: job: "call-call_f8", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "out_prefix": "m84036_250809_035451_s4.bc2133", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-36/call-run_paraphase/out/m84036_250809_035451_s4.bc2133_paraphase/m84036_250809_035451_s4.bc2133.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-36/call-run_paraphase/out/m84036_250809_035451_s4.bc2133_paraphase/m84036_250809_035451_s4.bc2133.paraphase.bam", "sex": "F"}
2025-09-15 20:24:04.857 wdl.w:ptcp.w:call-paraphase-36 INFO visit :: node: "output-havanno_json", values: {"havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-36/call-run_paraphase/out/m84036_250809_035451_s4.bc2133.havanno.json"}
2025-09-15 20:24:04.857 wdl.w:ptcp.w:call-paraphase-36 INFO visit :: node: "output-paraphase_bam", values: {"paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-36/call-run_paraphase/out/m84036_250809_035451_s4.bc2133_paraphase/m84036_250809_035451_s4.bc2133.paraphase.bam"}
2025-09-15 20:24:04.857 wdl.w:ptcp.w:call-paraphase-36 INFO visit :: node: "output-paraphase_bam_bai", values: {"paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-36/call-run_paraphase/out/m84036_250809_035451_s4.bc2133_paraphase/m84036_250809_035451_s4.bc2133.paraphase.bam.bai"}
2025-09-15 20:24:04.857 wdl.w:ptcp.w:call-paraphase-36 INFO visit :: node: "output-paraphase_json", values: {"paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-36/call-run_paraphase/out/m84036_250809_035451_s4.bc2133_paraphase/m84036_250809_035451_s4.bc2133.paraphase.json"}
2025-09-15 20:24:04.857 wdl.w:ptcp.w:call-paraphase-36 INFO visit :: node: "output-paraphase_vcfs", values: {"paraphase_vcfs": []}
2025-09-15 20:24:04.860 wdl.w:ptcp.w:call-trgt-19.t:call-trgt_plot_meth_waterfall NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-19/call-trgt_plot_meth_waterfall", thread: 140610342200896
2025-09-15 20:24:04.875 wdl.w:ptcp.w:call-trgt-19.t:call-trgt_plot_meth_waterfall INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:04.875 wdl.w:ptcp.w:call-trgt-19.t:call-trgt_plot_meth_waterfall INFO input :: name: "waterfall", value: true
2025-09-15 20:24:04.875 wdl.w:ptcp.w:call-trgt-19.t:call-trgt_plot_meth_waterfall INFO input :: name: "methylation", value: true
2025-09-15 20:24:04.875 wdl.w:ptcp.w:call-trgt-19.t:call-trgt_plot_meth_waterfall INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:04.875 wdl.w:ptcp.w:call-trgt-19.t:call-trgt_plot_meth_waterfall INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:04.875 wdl.w:ptcp.w:call-trgt-19.t:call-trgt_plot_meth_waterfall INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:04.875 wdl.w:ptcp.w:call-trgt-19.t:call-trgt_plot_meth_waterfall INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2116.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:04.875 wdl.w:ptcp.w:call-trgt-19.t:call-trgt_plot_meth_waterfall INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2116.trgt.sorted.spanning.bam"
2025-09-15 20:24:04.875 wdl.w:ptcp.w:call-trgt-19.t:call-trgt_plot_meth_waterfall INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2116.trgt.vcf"
2025-09-15 20:24:04.875 wdl.w:ptcp.w:call-trgt-19.t:call-trgt_plot_meth_waterfall INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2116"
2025-09-15 20:24:04.875 wdl.w:ptcp.w:call-trgt-19.t:call-trgt_plot_meth_waterfall INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:04.876 wdl.w:ptcp.w:call-trgt-19.t:call-trgt_plot_meth_waterfall INFO eval :: name: "plot_type", value: "waterfall"
2025-09-15 20:24:04.876 wdl.w:ptcp.w:call-trgt-19.t:call-trgt_plot_meth_waterfall INFO eval :: name: "show", value: "meth"
2025-09-15 20:24:04.876 wdl.w:ptcp.w:call-trgt-19.t:call-trgt_plot_meth_waterfall INFO eval :: name: "threads", value: 1
2025-09-15 20:24:04.876 wdl.w:ptcp.w:call-trgt-19.t:call-trgt_plot_meth_waterfall INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:04.876 wdl.w:ptcp.w:call-trgt-19.t:call-trgt_plot_meth_waterfall INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2116.meth_waterfall"
2025-09-15 20:24:04.876 wdl.w:ptcp.w:call-trgt-19.t:call-trgt_plot_meth_waterfall INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:04.877 wdl.w:ptcp.w:call-trgt-19.t:call-trgt_plot_meth_waterfall WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:04.877 wdl.w:ptcp.w:call-trgt-19.t:call-trgt_plot_meth_waterfall INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:04.877 wdl.w:ptcp.w:call-trgt-19.t:call-trgt_plot_meth_waterfall INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:04.945 wdl.w:ptcp.w:call-trgt-19.t:call-trgt_plot_meth_waterfall INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-19/call-trgt_plot_meth_waterfall/_singularity_tmpdir_2tspykqa"
2025-09-15 20:24:04.945 wdl.w:ptcp.w:call-trgt-19.t:call-trgt_plot_meth_waterfall INFO Slurm invocation: srun --job-name call-trgt_plot_meth_waterfall --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-19/call-trgt_plot_meth_waterfall/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-19/call-trgt_plot_meth_waterfall/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-19/call-trgt_plot_meth_waterfall/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-19/call-trgt_plot_meth_waterfall/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-19/call-trgt_genotype/out/m84036_250809_035451_s4.bc2116.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2116.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-19/call-trgt_genotype/out/m84036_250809_035451_s4.bc2116.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2116.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-19/call-trgt_genotype/out/m84036_250809_035451_s4.bc2116.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2116.trgt.vcf:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-19/call-trgt_plot_meth_waterfall/_singularity_tmpdir_2tspykqa/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-19/call-trgt_plot_meth_waterfall/_singularity_tmpdir_2tspykqa/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:04.962 wdl.w:ptcp.w:call-trgt-19.t:call-trgt_plot_meth_waterfall NOTICE slurm_singularity run :: pid: 1200851, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-19/call-trgt_plot_meth_waterfall/slurm_singularity.log.txt"
2025-09-15 20:24:05.110 wdl.w:ptcp.w:call-trgt-11.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:05 [ERROR] - No reads found for TRID=NIID_NOTCH2NLC
2025-09-15 20:24:05.110 wdl.w:ptcp.w:call-trgt-11.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:05 [ERROR] - No reads found for TRID=DRPLA_ATN1
2025-09-15 20:24:05.119 wdl.w:ptcp.w:call-trgt-11.t:call-trgt_plot_motifs_allele.slurm_singularity INFO srun: job 51797542 queued and waiting for resources
2025-09-15 20:24:05.119 wdl.w:ptcp.w:call-trgt-11.t:call-trgt_plot_motifs_allele.slurm_singularity INFO srun: job 51797542 has been allocated resources
2025-09-15 20:24:05.119 wdl.w:ptcp.w:call-trgt-11.t:call-trgt_plot_motifs_allele.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:05.120 wdl.w:ptcp.w:call-trgt-18.t:call-trgt_plot_meth_waterfall INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2115.meth_waterfall.trgt_plots.zip"
2025-09-15 20:24:05.208 wdl.w:ptcp.w:call-trgt-18.t:call-trgt_plot_meth_waterfall NOTICE done
2025-09-15 20:24:05.221 wdl.w:ptcp.w:call-trgt-18 NOTICE finish :: job: "call-trgt_plot_meth_waterfall"
2025-09-15 20:24:05.221 wdl.w:ptcp.w:call-trgt-18 INFO output :: job: "call-trgt_plot_meth_waterfall", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-18/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2115.meth_waterfall.trgt_plots.zip"}
2025-09-15 20:24:05.222 wdl.w:ptcp.w:call-trgt-18 INFO visit :: node: "output-images_meth_waterfall", values: {"images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-18/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2115.meth_waterfall.trgt_plots.zip"}
2025-09-15 20:24:05.227 wdl.w:ptcp.w:call-trgt-19.t:call-trgt_plot_motifs_allele NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-19/call-trgt_plot_motifs_allele", thread: 140608731588160
2025-09-15 20:24:05.254 wdl.w:ptcp.w:call-trgt-19.t:call-trgt_plot_motifs_allele INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:05.254 wdl.w:ptcp.w:call-trgt-19.t:call-trgt_plot_motifs_allele INFO input :: name: "waterfall", value: false
2025-09-15 20:24:05.254 wdl.w:ptcp.w:call-trgt-19.t:call-trgt_plot_motifs_allele INFO input :: name: "methylation", value: false
2025-09-15 20:24:05.254 wdl.w:ptcp.w:call-trgt-19.t:call-trgt_plot_motifs_allele INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:05.254 wdl.w:ptcp.w:call-trgt-19.t:call-trgt_plot_motifs_allele INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:05.254 wdl.w:ptcp.w:call-trgt-19.t:call-trgt_plot_motifs_allele INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:05.254 wdl.w:ptcp.w:call-trgt-19.t:call-trgt_plot_motifs_allele INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2116.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:05.254 wdl.w:ptcp.w:call-trgt-19.t:call-trgt_plot_motifs_allele INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2116.trgt.sorted.spanning.bam"
2025-09-15 20:24:05.254 wdl.w:ptcp.w:call-trgt-19.t:call-trgt_plot_motifs_allele INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2116.trgt.vcf"
2025-09-15 20:24:05.254 wdl.w:ptcp.w:call-trgt-19.t:call-trgt_plot_motifs_allele INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2116"
2025-09-15 20:24:05.254 wdl.w:ptcp.w:call-trgt-19.t:call-trgt_plot_motifs_allele INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:05.255 wdl.w:ptcp.w:call-trgt-19.t:call-trgt_plot_motifs_allele INFO eval :: name: "plot_type", value: "allele"
2025-09-15 20:24:05.255 wdl.w:ptcp.w:call-trgt-19.t:call-trgt_plot_motifs_allele INFO eval :: name: "show", value: "motifs"
2025-09-15 20:24:05.255 wdl.w:ptcp.w:call-trgt-19.t:call-trgt_plot_motifs_allele INFO eval :: name: "threads", value: 1
2025-09-15 20:24:05.255 wdl.w:ptcp.w:call-trgt-19.t:call-trgt_plot_motifs_allele INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:05.255 wdl.w:ptcp.w:call-trgt-19.t:call-trgt_plot_motifs_allele INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2116.motifs_allele"
2025-09-15 20:24:05.255 wdl.w:ptcp.w:call-trgt-19.t:call-trgt_plot_motifs_allele INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:05.256 wdl.w:ptcp.w:call-trgt-19.t:call-trgt_plot_motifs_allele WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:05.256 wdl.w:ptcp.w:call-trgt-19.t:call-trgt_plot_motifs_allele INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:05.256 wdl.w:ptcp.w:call-trgt-19.t:call-trgt_plot_motifs_allele INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:05.316 wdl.w:ptcp.w:call-trgt-19.t:call-trgt_plot_motifs_allele INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-19/call-trgt_plot_motifs_allele/_singularity_tmpdir_6846_8lp"
2025-09-15 20:24:05.316 wdl.w:ptcp.w:call-trgt-19.t:call-trgt_plot_motifs_allele INFO Slurm invocation: srun --job-name call-trgt_plot_motifs_allele --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-19/call-trgt_plot_motifs_allele/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-19/call-trgt_plot_motifs_allele/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-19/call-trgt_plot_motifs_allele/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-19/call-trgt_plot_motifs_allele/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-19/call-trgt_genotype/out/m84036_250809_035451_s4.bc2116.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2116.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-19/call-trgt_genotype/out/m84036_250809_035451_s4.bc2116.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2116.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-19/call-trgt_genotype/out/m84036_250809_035451_s4.bc2116.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2116.trgt.vcf:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-19/call-trgt_plot_motifs_allele/_singularity_tmpdir_6846_8lp/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-19/call-trgt_plot_motifs_allele/_singularity_tmpdir_6846_8lp/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:05.326 wdl.w:ptcp.w:call-trgt-19.t:call-trgt_plot_motifs_allele NOTICE slurm_singularity run :: pid: 1200859, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-19/call-trgt_plot_motifs_allele/slurm_singularity.log.txt"
2025-09-15 20:24:05.452 wdl.w:ptcp.w:call-paraphase-45.t:call-run_paraphase INFO output :: name: "paraphase_bam", value: "m84036_250809_035451_s4.bc2142_paraphase/m84036_250809_035451_s4.bc2142.paraphase.bam"
2025-09-15 20:24:05.457 wdl.w:ptcp.w:call-paraphase-45.t:call-run_paraphase INFO output :: name: "paraphase_bam_bai", value: "m84036_250809_035451_s4.bc2142_paraphase/m84036_250809_035451_s4.bc2142.paraphase.bam.bai"
2025-09-15 20:24:05.459 wdl.w:ptcp.w:call-paraphase-45.t:call-run_paraphase INFO output :: name: "paraphase_json", value: "m84036_250809_035451_s4.bc2142_paraphase/m84036_250809_035451_s4.bc2142.paraphase.json"
2025-09-15 20:24:05.461 wdl.w:ptcp.w:call-paraphase-45.t:call-run_paraphase INFO output :: name: "paraphase_vcfs", value: []
2025-09-15 20:24:05.461 wdl.w:ptcp.w:call-paraphase-45.t:call-run_paraphase INFO output :: name: "havanno_json", value: "m84036_250809_035451_s4.bc2142.havanno.json"
2025-09-15 20:24:05.551 wdl.w:ptcp.w:call-paraphase-45.t:call-run_paraphase NOTICE done
2025-09-15 20:24:05.556 wdl.w:ptcp.w:call-paraphase-45 NOTICE finish :: job: "call-run_paraphase"
2025-09-15 20:24:05.556 wdl.w:ptcp.w:call-paraphase-45 INFO output :: job: "call-run_paraphase", values: {"havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-45/call-run_paraphase/out/m84036_250809_035451_s4.bc2142.havanno.json", "paraphase_vcfs": [], "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-45/call-run_paraphase/out/m84036_250809_035451_s4.bc2142_paraphase/m84036_250809_035451_s4.bc2142.paraphase.json", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-45/call-run_paraphase/out/m84036_250809_035451_s4.bc2142_paraphase/m84036_250809_035451_s4.bc2142.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-45/call-run_paraphase/out/m84036_250809_035451_s4.bc2142_paraphase/m84036_250809_035451_s4.bc2142.paraphase.bam"}
2025-09-15 20:24:05.557 wdl.w:ptcp.w:call-paraphase-45 NOTICE ready :: job: "call-call_f8", callee: "call_f8"
2025-09-15 20:24:05.557 wdl.w:ptcp.w:call-paraphase-45 INFO input :: job: "call-call_f8", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "out_prefix": "m84036_250809_035451_s4.bc2142", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-45/call-run_paraphase/out/m84036_250809_035451_s4.bc2142_paraphase/m84036_250809_035451_s4.bc2142.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-45/call-run_paraphase/out/m84036_250809_035451_s4.bc2142_paraphase/m84036_250809_035451_s4.bc2142.paraphase.bam", "sex": "F"}
2025-09-15 20:24:05.558 wdl.w:ptcp.w:call-paraphase-45 INFO visit :: node: "output-havanno_json", values: {"havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-45/call-run_paraphase/out/m84036_250809_035451_s4.bc2142.havanno.json"}
2025-09-15 20:24:05.558 wdl.w:ptcp.w:call-paraphase-45 INFO visit :: node: "output-paraphase_bam", values: {"paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-45/call-run_paraphase/out/m84036_250809_035451_s4.bc2142_paraphase/m84036_250809_035451_s4.bc2142.paraphase.bam"}
2025-09-15 20:24:05.558 wdl.w:ptcp.w:call-paraphase-45 INFO visit :: node: "output-paraphase_bam_bai", values: {"paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-45/call-run_paraphase/out/m84036_250809_035451_s4.bc2142_paraphase/m84036_250809_035451_s4.bc2142.paraphase.bam.bai"}
2025-09-15 20:24:05.558 wdl.w:ptcp.w:call-paraphase-45 INFO visit :: node: "output-paraphase_json", values: {"paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-45/call-run_paraphase/out/m84036_250809_035451_s4.bc2142_paraphase/m84036_250809_035451_s4.bc2142.paraphase.json"}
2025-09-15 20:24:05.558 wdl.w:ptcp.w:call-paraphase-45 INFO visit :: node: "output-paraphase_vcfs", values: {"paraphase_vcfs": []}
2025-09-15 20:24:05.561 wdl.w:ptcp.w:call-trgt-19.t:call-trgt_plot_motifs_waterfall NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-19/call-trgt_plot_motifs_waterfall", thread: 140609822115392
2025-09-15 20:24:05.578 wdl.w:ptcp.w:call-trgt-19.t:call-trgt_plot_motifs_waterfall INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:05.578 wdl.w:ptcp.w:call-trgt-19.t:call-trgt_plot_motifs_waterfall INFO input :: name: "waterfall", value: true
2025-09-15 20:24:05.578 wdl.w:ptcp.w:call-trgt-19.t:call-trgt_plot_motifs_waterfall INFO input :: name: "methylation", value: false
2025-09-15 20:24:05.578 wdl.w:ptcp.w:call-trgt-19.t:call-trgt_plot_motifs_waterfall INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:05.578 wdl.w:ptcp.w:call-trgt-19.t:call-trgt_plot_motifs_waterfall INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:05.578 wdl.w:ptcp.w:call-trgt-19.t:call-trgt_plot_motifs_waterfall INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:05.578 wdl.w:ptcp.w:call-trgt-19.t:call-trgt_plot_motifs_waterfall INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2116.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:05.578 wdl.w:ptcp.w:call-trgt-19.t:call-trgt_plot_motifs_waterfall INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2116.trgt.sorted.spanning.bam"
2025-09-15 20:24:05.578 wdl.w:ptcp.w:call-trgt-19.t:call-trgt_plot_motifs_waterfall INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2116.trgt.vcf"
2025-09-15 20:24:05.578 wdl.w:ptcp.w:call-trgt-19.t:call-trgt_plot_motifs_waterfall INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2116"
2025-09-15 20:24:05.579 wdl.w:ptcp.w:call-trgt-19.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:05.579 wdl.w:ptcp.w:call-trgt-19.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "plot_type", value: "waterfall"
2025-09-15 20:24:05.579 wdl.w:ptcp.w:call-trgt-19.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "show", value: "motifs"
2025-09-15 20:24:05.579 wdl.w:ptcp.w:call-trgt-19.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "threads", value: 1
2025-09-15 20:24:05.579 wdl.w:ptcp.w:call-trgt-19.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:05.579 wdl.w:ptcp.w:call-trgt-19.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2116.motifs_waterfall"
2025-09-15 20:24:05.580 wdl.w:ptcp.w:call-trgt-19.t:call-trgt_plot_motifs_waterfall INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:05.580 wdl.w:ptcp.w:call-trgt-19.t:call-trgt_plot_motifs_waterfall WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:05.580 wdl.w:ptcp.w:call-trgt-19.t:call-trgt_plot_motifs_waterfall INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:05.580 wdl.w:ptcp.w:call-trgt-19.t:call-trgt_plot_motifs_waterfall INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:05.611 wdl.w:ptcp.w:call-paraphase-38.t:call-run_paraphase.stderr VERBOSE INFO:root:Processing sample m84036_250809_035451_s4.bc2135 at 2025-09-15 20:24:01.704696...
2025-09-15 20:24:05.612 wdl.w:ptcp.w:call-paraphase-38.t:call-run_paraphase.stderr VERBOSE INFO:root:Checking sample sex at 2025-09-15 20:24:01.705468...
2025-09-15 20:24:05.612 wdl.w:ptcp.w:call-paraphase-38.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for cyp21 for sample m84036_250809_035451_s4.bc2135 at 2025-09-15 20:24:01.747474...
2025-09-15 20:24:05.612 wdl.w:ptcp.w:call-paraphase-38.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for cyp21 for sample m84036_250809_035451_s4.bc2135 at 2025-09-15 20:24:01.748146...
2025-09-15 20:24:05.612 wdl.w:ptcp.w:call-paraphase-38.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for gba for sample m84036_250809_035451_s4.bc2135 at 2025-09-15 20:24:01.747932...
2025-09-15 20:24:05.613 wdl.w:ptcp.w:call-paraphase-38.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for gba for sample m84036_250809_035451_s4.bc2135 at 2025-09-15 20:24:01.748373...
2025-09-15 20:24:05.613 wdl.w:ptcp.w:call-paraphase-38.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for smn1 for sample m84036_250809_035451_s4.bc2135 at 2025-09-15 20:24:01.747856...
2025-09-15 20:24:05.613 wdl.w:ptcp.w:call-paraphase-38.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for smn1 for sample m84036_250809_035451_s4.bc2135 at 2025-09-15 20:24:01.748478...
2025-09-15 20:24:05.613 wdl.w:ptcp.w:call-paraphase-38.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for hba for sample m84036_250809_035451_s4.bc2135 at 2025-09-15 20:24:01.749691...
2025-09-15 20:24:05.613 wdl.w:ptcp.w:call-paraphase-38.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for hba for sample m84036_250809_035451_s4.bc2135 at 2025-09-15 20:24:01.750227...
2025-09-15 20:24:05.630 wdl.w:ptcp.w:call-trgt-11.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:05 [ERROR] - No reads found for TRID=NIID_NOTCH2NLC
2025-09-15 20:24:05.630 wdl.w:ptcp.w:call-trgt-19.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:05 [ERROR] - No reads found for TRID=SCA37_DAB1
2025-09-15 20:24:05.630 wdl.w:ptcp.w:call-trgt-11.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:05 [ERROR] - No reads found for TRID=DRPLA_ATN1
2025-09-15 20:24:05.631 wdl.w:ptcp.w:call-trgt-19.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:05 [ERROR] - No reads found for TRID=OPDM_ABCD3
2025-09-15 20:24:05.631 wdl.w:ptcp.w:call-trgt-11.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:05 [ERROR] - No reads found for TRID=SCA37_DAB1
2025-09-15 20:24:05.631 wdl.w:ptcp.w:call-trgt-19.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:05 [ERROR] - No reads found for TRID=OPDM4_RILPL1
2025-09-15 20:24:05.631 wdl.w:ptcp.w:call-trgt-11.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:05 [ERROR] - No reads found for TRID=OPDM4_RILPL1
2025-09-15 20:24:05.631 wdl.w:ptcp.w:call-trgt-19.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:05 [ERROR] - No reads found for TRID=SCA27B_FGF14
2025-09-15 20:24:05.631 wdl.w:ptcp.w:call-trgt-11.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:05 [ERROR] - No reads found for TRID=SCA8_ATXN8OS
2025-09-15 20:24:05.631 wdl.w:ptcp.w:call-trgt-19.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:05 [ERROR] - No reads found for TRID=OPMD_PABPN1
2025-09-15 20:24:05.631 wdl.w:ptcp.w:call-trgt-11.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:05 [ERROR] - No reads found for TRID=SCA2_ATXN2
2025-09-15 20:24:05.631 wdl.w:ptcp.w:call-trgt-11.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:05 [ERROR] - No reads found for TRID=OPMD_PABPN1
2025-09-15 20:24:05.641 wdl.w:ptcp.w:call-trgt-11.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO srun: job 51797544 queued and waiting for resources
2025-09-15 20:24:05.641 wdl.w:ptcp.w:call-trgt-11.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO srun: job 51797544 has been allocated resources
2025-09-15 20:24:05.641 wdl.w:ptcp.w:call-trgt-11.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:05.642 wdl.w:ptcp.w:call-trgt-19.t:call-trgt_plot_meth_allele.slurm_singularity INFO srun: job 51797543 queued and waiting for resources
2025-09-15 20:24:05.642 wdl.w:ptcp.w:call-trgt-19.t:call-trgt_plot_meth_allele.slurm_singularity INFO srun: job 51797543 has been allocated resources
2025-09-15 20:24:05.642 wdl.w:ptcp.w:call-trgt-19.t:call-trgt_plot_meth_allele.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:05.647 wdl.w:ptcp.w:call-trgt-19.t:call-trgt_plot_motifs_waterfall INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-19/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_iqzkrvs7"
2025-09-15 20:24:05.647 wdl.w:ptcp.w:call-trgt-19.t:call-trgt_plot_motifs_waterfall INFO Slurm invocation: srun --job-name call-trgt_plot_motifs_waterfall --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-19/call-trgt_plot_motifs_waterfall/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-19/call-trgt_plot_motifs_waterfall/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-19/call-trgt_plot_motifs_waterfall/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-19/call-trgt_plot_motifs_waterfall/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-19/call-trgt_genotype/out/m84036_250809_035451_s4.bc2116.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2116.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-19/call-trgt_genotype/out/m84036_250809_035451_s4.bc2116.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2116.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-19/call-trgt_genotype/out/m84036_250809_035451_s4.bc2116.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2116.trgt.vcf:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-19/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_iqzkrvs7/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-19/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_iqzkrvs7/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:05.665 wdl.w:ptcp.w:call-trgt-19.t:call-trgt_plot_motifs_waterfall NOTICE slurm_singularity run :: pid: 1200867, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-19/call-trgt_plot_motifs_waterfall/slurm_singularity.log.txt"
2025-09-15 20:24:05.964 wdl.w:ptcp.w:call-trgt-19.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:05 [ERROR] - No reads found for TRID=SCA37_DAB1
2025-09-15 20:24:05.965 wdl.w:ptcp.w:call-trgt-19.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:05 [ERROR] - No reads found for TRID=OPDM_ABCD3
2025-09-15 20:24:05.965 wdl.w:ptcp.w:call-trgt-19.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:05 [ERROR] - No reads found for TRID=OPDM4_RILPL1
2025-09-15 20:24:05.965 wdl.w:ptcp.w:call-trgt-19.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:05 [ERROR] - No reads found for TRID=SCA27B_FGF14
2025-09-15 20:24:05.965 wdl.w:ptcp.w:call-trgt-19.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:05 [ERROR] - No reads found for TRID=OPMD_PABPN1
2025-09-15 20:24:05.965 wdl.w:ptcp.w:call-trgt-19.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:05 [ERROR] - No reads found for TRID=DRPLA_ATN1
2025-09-15 20:24:05.965 wdl.w:ptcp.w:call-trgt-19.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:05 [ERROR] - No reads found for TRID=SCA31_BEAN1
2025-09-15 20:24:05.965 wdl.w:ptcp.w:call-trgt-19.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:05 [ERROR] - No reads found for TRID=SCA8_ATXN8OS
2025-09-15 20:24:05.972 wdl.w:ptcp.w:call-trgt-19.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO srun: job 51797545 queued and waiting for resources
2025-09-15 20:24:05.972 wdl.w:ptcp.w:call-trgt-19.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO srun: job 51797545 has been allocated resources
2025-09-15 20:24:05.972 wdl.w:ptcp.w:call-trgt-19.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:06.088 wdl.w:ptcp.w:call-paraphase-37.t:call-run_paraphase INFO output :: name: "paraphase_bam", value: "m84036_250809_035451_s4.bc2134_paraphase/m84036_250809_035451_s4.bc2134.paraphase.bam"
2025-09-15 20:24:06.092 wdl.w:ptcp.w:call-paraphase-37.t:call-run_paraphase INFO output :: name: "paraphase_bam_bai", value: "m84036_250809_035451_s4.bc2134_paraphase/m84036_250809_035451_s4.bc2134.paraphase.bam.bai"
2025-09-15 20:24:06.093 wdl.w:ptcp.w:call-paraphase-37.t:call-run_paraphase INFO output :: name: "paraphase_json", value: "m84036_250809_035451_s4.bc2134_paraphase/m84036_250809_035451_s4.bc2134.paraphase.json"
2025-09-15 20:24:06.095 wdl.w:ptcp.w:call-paraphase-37.t:call-run_paraphase INFO output :: name: "paraphase_vcfs", value: []
2025-09-15 20:24:06.095 wdl.w:ptcp.w:call-paraphase-37.t:call-run_paraphase INFO output :: name: "havanno_json", value: "m84036_250809_035451_s4.bc2134.havanno.json"
2025-09-15 20:24:06.197 wdl.w:ptcp.w:call-paraphase-37.t:call-run_paraphase NOTICE done
2025-09-15 20:24:06.203 wdl.w:ptcp.w:call-paraphase-37 NOTICE finish :: job: "call-run_paraphase"
2025-09-15 20:24:06.203 wdl.w:ptcp.w:call-paraphase-37 INFO output :: job: "call-run_paraphase", values: {"havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-37/call-run_paraphase/out/m84036_250809_035451_s4.bc2134.havanno.json", "paraphase_vcfs": [], "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-37/call-run_paraphase/out/m84036_250809_035451_s4.bc2134_paraphase/m84036_250809_035451_s4.bc2134.paraphase.json", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-37/call-run_paraphase/out/m84036_250809_035451_s4.bc2134_paraphase/m84036_250809_035451_s4.bc2134.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-37/call-run_paraphase/out/m84036_250809_035451_s4.bc2134_paraphase/m84036_250809_035451_s4.bc2134.paraphase.bam"}
2025-09-15 20:24:06.204 wdl.w:ptcp.w:call-paraphase-37 NOTICE ready :: job: "call-call_f8", callee: "call_f8"
2025-09-15 20:24:06.204 wdl.w:ptcp.w:call-paraphase-37 INFO input :: job: "call-call_f8", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "out_prefix": "m84036_250809_035451_s4.bc2134", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-37/call-run_paraphase/out/m84036_250809_035451_s4.bc2134_paraphase/m84036_250809_035451_s4.bc2134.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-37/call-run_paraphase/out/m84036_250809_035451_s4.bc2134_paraphase/m84036_250809_035451_s4.bc2134.paraphase.bam", "sex": "F"}
2025-09-15 20:24:06.205 wdl.w:ptcp.w:call-paraphase-37 INFO visit :: node: "output-havanno_json", values: {"havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-37/call-run_paraphase/out/m84036_250809_035451_s4.bc2134.havanno.json"}
2025-09-15 20:24:06.205 wdl.w:ptcp.w:call-paraphase-37 INFO visit :: node: "output-paraphase_bam", values: {"paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-37/call-run_paraphase/out/m84036_250809_035451_s4.bc2134_paraphase/m84036_250809_035451_s4.bc2134.paraphase.bam"}
2025-09-15 20:24:06.205 wdl.w:ptcp.w:call-paraphase-37 INFO visit :: node: "output-paraphase_bam_bai", values: {"paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-37/call-run_paraphase/out/m84036_250809_035451_s4.bc2134_paraphase/m84036_250809_035451_s4.bc2134.paraphase.bam.bai"}
2025-09-15 20:24:06.205 wdl.w:ptcp.w:call-paraphase-37 INFO visit :: node: "output-paraphase_json", values: {"paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-37/call-run_paraphase/out/m84036_250809_035451_s4.bc2134_paraphase/m84036_250809_035451_s4.bc2134.paraphase.json"}
2025-09-15 20:24:06.205 wdl.w:ptcp.w:call-paraphase-37 INFO visit :: node: "output-paraphase_vcfs", values: {"paraphase_vcfs": []}
2025-09-15 20:24:06.210 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_plot_meth_allele NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-10/call-trgt_plot_meth_allele", thread: 140608773551680
2025-09-15 20:24:06.230 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_plot_meth_allele INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:06.230 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_plot_meth_allele INFO input :: name: "waterfall", value: false
2025-09-15 20:24:06.230 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_plot_meth_allele INFO input :: name: "methylation", value: true
2025-09-15 20:24:06.230 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_plot_meth_allele INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:06.230 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_plot_meth_allele INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:06.230 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_plot_meth_allele INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:06.230 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_plot_meth_allele INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2107.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:06.230 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_plot_meth_allele INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2107.trgt.sorted.spanning.bam"
2025-09-15 20:24:06.230 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_plot_meth_allele INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2107.trgt.vcf"
2025-09-15 20:24:06.230 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_plot_meth_allele INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2107"
2025-09-15 20:24:06.231 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_plot_meth_allele INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:06.231 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_plot_meth_allele INFO eval :: name: "plot_type", value: "allele"
2025-09-15 20:24:06.231 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_plot_meth_allele INFO eval :: name: "show", value: "meth"
2025-09-15 20:24:06.231 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_plot_meth_allele INFO eval :: name: "threads", value: 1
2025-09-15 20:24:06.231 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_plot_meth_allele INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:06.231 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_plot_meth_allele INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2107.meth_allele"
2025-09-15 20:24:06.232 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_plot_meth_allele INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:06.232 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_plot_meth_allele WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:06.232 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_plot_meth_allele INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:06.232 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_plot_meth_allele INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:06.308 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_plot_meth_allele INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-10/call-trgt_plot_meth_allele/_singularity_tmpdir_vsadrzx0"
2025-09-15 20:24:06.308 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_plot_meth_allele INFO Slurm invocation: srun --job-name call-trgt_plot_meth_allele --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-10/call-trgt_plot_meth_allele/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-10/call-trgt_plot_meth_allele/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-10/call-trgt_plot_meth_allele/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-10/call-trgt_plot_meth_allele/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-10/call-trgt_genotype/out/m84036_250809_035451_s4.bc2107.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2107.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-10/call-trgt_genotype/out/m84036_250809_035451_s4.bc2107.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2107.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-10/call-trgt_genotype/out/m84036_250809_035451_s4.bc2107.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2107.trgt.sorted.spanning.bam.bai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-10/call-trgt_plot_meth_allele/_singularity_tmpdir_vsadrzx0/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-10/call-trgt_plot_meth_allele/_singularity_tmpdir_vsadrzx0/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:06.320 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_plot_meth_allele NOTICE slurm_singularity run :: pid: 1200875, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-10/call-trgt_plot_meth_allele/slurm_singularity.log.txt"
2025-09-15 20:24:06.328 wdl.w:ptcp.w:call-trgt-19.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:06 [ERROR] - No reads found for TRID=SCA37_DAB1
2025-09-15 20:24:06.328 wdl.w:ptcp.w:call-trgt-19.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:06 [ERROR] - No reads found for TRID=OPDM_ABCD3
2025-09-15 20:24:06.328 wdl.w:ptcp.w:call-trgt-19.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:06 [ERROR] - No reads found for TRID=OPDM4_RILPL1
2025-09-15 20:24:06.328 wdl.w:ptcp.w:call-trgt-19.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:06 [ERROR] - No reads found for TRID=SCA27B_FGF14
2025-09-15 20:24:06.335 wdl.w:ptcp.w:call-trgt-19.t:call-trgt_plot_motifs_allele.slurm_singularity INFO srun: job 51797546 queued and waiting for resources
2025-09-15 20:24:06.335 wdl.w:ptcp.w:call-trgt-19.t:call-trgt_plot_motifs_allele.slurm_singularity INFO srun: job 51797546 has been allocated resources
2025-09-15 20:24:06.336 wdl.w:ptcp.w:call-trgt-19.t:call-trgt_plot_motifs_allele.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:06.362 wdl.w:ptcp.w:call-paraphase-22.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for hbb for sample m84036_250809_035451_s4.bc2119 at 2025-09-15 20:23:55.891490...
2025-09-15 20:24:06.363 wdl.w:ptcp.w:call-paraphase-22.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for hbb for sample m84036_250809_035451_s4.bc2119 at 2025-09-15 20:23:59.430141...
2025-09-15 20:24:06.363 wdl.w:ptcp.w:call-paraphase-22.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for hbb for sample m84036_250809_035451_s4.bc2119 at 2025-09-15 20:23:59.635956...
2025-09-15 20:24:06.398 wdl.w:ptcp.w:call-trgt-18.t:call-trgt_plot_motifs_allele INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2115.motifs_allele.trgt_plots.zip"
2025-09-15 20:24:06.463 wdl.w:ptcp.w:call-trgt-11.t:call-trgt_plot_meth_waterfall INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2108.meth_waterfall.trgt_plots.zip"
2025-09-15 20:24:06.472 wdl.w:ptcp.w:call-trgt-18.t:call-trgt_plot_motifs_allele NOTICE done
2025-09-15 20:24:06.477 wdl.w:ptcp.w:call-trgt-18 NOTICE finish :: job: "call-trgt_plot_motifs_allele"
2025-09-15 20:24:06.477 wdl.w:ptcp.w:call-trgt-18 INFO output :: job: "call-trgt_plot_motifs_allele", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-18/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2115.motifs_allele.trgt_plots.zip"}
2025-09-15 20:24:06.478 wdl.w:ptcp.w:call-trgt-18 INFO visit :: node: "output-images_motifs_allele", values: {"images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-18/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2115.motifs_allele.trgt_plots.zip"}
2025-09-15 20:24:06.484 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_plot_meth_waterfall NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-10/call-trgt_plot_meth_waterfall", thread: 140613823374912
2025-09-15 20:24:06.504 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_plot_meth_waterfall INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:06.504 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_plot_meth_waterfall INFO input :: name: "waterfall", value: true
2025-09-15 20:24:06.504 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_plot_meth_waterfall INFO input :: name: "methylation", value: true
2025-09-15 20:24:06.504 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_plot_meth_waterfall INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:06.504 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_plot_meth_waterfall INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:06.504 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_plot_meth_waterfall INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:06.505 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_plot_meth_waterfall INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2107.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:06.505 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_plot_meth_waterfall INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2107.trgt.sorted.spanning.bam"
2025-09-15 20:24:06.505 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_plot_meth_waterfall INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2107.trgt.vcf"
2025-09-15 20:24:06.505 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_plot_meth_waterfall INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2107"
2025-09-15 20:24:06.505 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_plot_meth_waterfall INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:06.505 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_plot_meth_waterfall INFO eval :: name: "plot_type", value: "waterfall"
2025-09-15 20:24:06.505 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_plot_meth_waterfall INFO eval :: name: "show", value: "meth"
2025-09-15 20:24:06.505 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_plot_meth_waterfall INFO eval :: name: "threads", value: 1
2025-09-15 20:24:06.506 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_plot_meth_waterfall INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:06.506 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_plot_meth_waterfall INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2107.meth_waterfall"
2025-09-15 20:24:06.506 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_plot_meth_waterfall INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:06.506 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_plot_meth_waterfall WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:06.506 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_plot_meth_waterfall INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:06.507 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_plot_meth_waterfall INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:06.582 wdl.w:ptcp.w:call-trgt-11.t:call-trgt_plot_meth_allele INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2108.meth_allele.trgt_plots.zip"
2025-09-15 20:24:06.603 wdl.w:ptcp.w:call-trgt-11.t:call-trgt_plot_meth_waterfall NOTICE done
2025-09-15 20:24:06.607 wdl.w:ptcp.w:call-trgt-11 NOTICE finish :: job: "call-trgt_plot_meth_waterfall"
2025-09-15 20:24:06.608 wdl.w:ptcp.w:call-trgt-11 INFO output :: job: "call-trgt_plot_meth_waterfall", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-11/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2108.meth_waterfall.trgt_plots.zip"}
2025-09-15 20:24:06.608 wdl.w:ptcp.w:call-trgt-11 INFO visit :: node: "output-images_meth_waterfall", values: {"images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-11/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2108.meth_waterfall.trgt_plots.zip"}
2025-09-15 20:24:06.615 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_plot_motifs_allele NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-10/call-trgt_plot_motifs_allele", thread: 140610887464512
2025-09-15 20:24:06.634 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_plot_motifs_allele INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:06.635 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_plot_motifs_allele INFO input :: name: "waterfall", value: false
2025-09-15 20:24:06.635 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_plot_motifs_allele INFO input :: name: "methylation", value: false
2025-09-15 20:24:06.635 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_plot_motifs_allele INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:06.635 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_plot_motifs_allele INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:06.635 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_plot_motifs_allele INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:06.635 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_plot_motifs_allele INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2107.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:06.635 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_plot_motifs_allele INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2107.trgt.sorted.spanning.bam"
2025-09-15 20:24:06.635 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_plot_motifs_allele INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2107.trgt.vcf"
2025-09-15 20:24:06.635 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_plot_motifs_allele INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2107"
2025-09-15 20:24:06.635 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_plot_motifs_allele INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:06.636 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_plot_motifs_allele INFO eval :: name: "plot_type", value: "allele"
2025-09-15 20:24:06.636 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_plot_motifs_allele INFO eval :: name: "show", value: "motifs"
2025-09-15 20:24:06.636 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_plot_motifs_allele INFO eval :: name: "threads", value: 1
2025-09-15 20:24:06.636 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_plot_motifs_allele INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:06.636 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_plot_motifs_allele INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2107.motifs_allele"
2025-09-15 20:24:06.636 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_plot_motifs_allele INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:06.636 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_plot_motifs_allele WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:06.637 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_plot_motifs_allele INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:06.637 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_plot_motifs_allele INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:06.660 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_plot_meth_waterfall INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-10/call-trgt_plot_meth_waterfall/_singularity_tmpdir_yoyoqfeu"
2025-09-15 20:24:06.661 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_plot_meth_waterfall INFO Slurm invocation: srun --job-name call-trgt_plot_meth_waterfall --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-10/call-trgt_plot_meth_waterfall/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-10/call-trgt_plot_meth_waterfall/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-10/call-trgt_plot_meth_waterfall/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-10/call-trgt_plot_meth_waterfall/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-10/call-trgt_genotype/out/m84036_250809_035451_s4.bc2107.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2107.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-10/call-trgt_genotype/out/m84036_250809_035451_s4.bc2107.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2107.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-10/call-trgt_genotype/out/m84036_250809_035451_s4.bc2107.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2107.trgt.sorted.spanning.bam.bai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-10/call-trgt_plot_meth_waterfall/_singularity_tmpdir_yoyoqfeu/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-10/call-trgt_plot_meth_waterfall/_singularity_tmpdir_yoyoqfeu/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:06.668 wdl.w:ptcp.w:call-trgt-19.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:06 [ERROR] - No reads found for TRID=SCA37_DAB1
2025-09-15 20:24:06.680 wdl.w:ptcp.w:call-trgt-18.t:call-trgt_plot_motifs_waterfall INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2115.motifs_waterfall.trgt_plots.zip"
2025-09-15 20:24:06.682 wdl.w:ptcp.w:call-trgt-19.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO srun: job 51797547 queued and waiting for resources
2025-09-15 20:24:06.682 wdl.w:ptcp.w:call-trgt-19.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO srun: job 51797547 has been allocated resources
2025-09-15 20:24:06.682 wdl.w:ptcp.w:call-trgt-19.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:06.696 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_plot_meth_waterfall NOTICE slurm_singularity run :: pid: 1200886, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-10/call-trgt_plot_meth_waterfall/slurm_singularity.log.txt"
2025-09-15 20:24:06.699 wdl.w:ptcp.w:call-trgt-11.t:call-trgt_plot_meth_allele NOTICE done
2025-09-15 20:24:06.704 wdl.w:ptcp.w:call-trgt-11 NOTICE finish :: job: "call-trgt_plot_meth_allele"
2025-09-15 20:24:06.704 wdl.w:ptcp.w:call-trgt-11 INFO output :: job: "call-trgt_plot_meth_allele", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-11/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2108.meth_allele.trgt_plots.zip"}
2025-09-15 20:24:06.705 wdl.w:ptcp.w:call-trgt-11 INFO visit :: node: "output-images_meth_allele", values: {"images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-11/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2108.meth_allele.trgt_plots.zip"}
2025-09-15 20:24:06.711 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_plot_motifs_waterfall NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-10/call-trgt_plot_motifs_waterfall", thread: 140608765158976
2025-09-15 20:24:06.725 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_plot_motifs_allele INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-10/call-trgt_plot_motifs_allele/_singularity_tmpdir_e9zulawo"
2025-09-15 20:24:06.725 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_plot_motifs_allele INFO Slurm invocation: srun --job-name call-trgt_plot_motifs_allele --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-10/call-trgt_plot_motifs_allele/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-10/call-trgt_plot_motifs_allele/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-10/call-trgt_plot_motifs_allele/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-10/call-trgt_plot_motifs_allele/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-10/call-trgt_genotype/out/m84036_250809_035451_s4.bc2107.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2107.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-10/call-trgt_genotype/out/m84036_250809_035451_s4.bc2107.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2107.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-10/call-trgt_genotype/out/m84036_250809_035451_s4.bc2107.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2107.trgt.sorted.spanning.bam.bai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-10/call-trgt_plot_motifs_allele/_singularity_tmpdir_e9zulawo/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-10/call-trgt_plot_motifs_allele/_singularity_tmpdir_e9zulawo/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:06.727 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_plot_motifs_waterfall INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:06.728 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_plot_motifs_waterfall INFO input :: name: "waterfall", value: true
2025-09-15 20:24:06.728 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_plot_motifs_waterfall INFO input :: name: "methylation", value: false
2025-09-15 20:24:06.728 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_plot_motifs_waterfall INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:06.728 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_plot_motifs_waterfall INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:06.728 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_plot_motifs_waterfall INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:06.728 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_plot_motifs_waterfall INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2107.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:06.728 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_plot_motifs_waterfall INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2107.trgt.sorted.spanning.bam"
2025-09-15 20:24:06.728 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_plot_motifs_waterfall INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2107.trgt.vcf"
2025-09-15 20:24:06.728 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_plot_motifs_waterfall INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2107"
2025-09-15 20:24:06.728 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:06.728 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "plot_type", value: "waterfall"
2025-09-15 20:24:06.729 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "show", value: "motifs"
2025-09-15 20:24:06.729 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "threads", value: 1
2025-09-15 20:24:06.729 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:06.729 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2107.motifs_waterfall"
2025-09-15 20:24:06.729 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_plot_motifs_waterfall INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:06.729 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_plot_motifs_waterfall WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:06.730 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_plot_motifs_waterfall INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:06.733 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_plot_motifs_waterfall INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:06.739 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_plot_motifs_allele NOTICE slurm_singularity run :: pid: 1200888, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-10/call-trgt_plot_motifs_allele/slurm_singularity.log.txt"
2025-09-15 20:24:06.765 wdl.w:ptcp.w:call-trgt-18.t:call-trgt_plot_motifs_waterfall NOTICE done
2025-09-15 20:24:06.770 wdl.w:ptcp.w:call-trgt-18 NOTICE finish :: job: "call-trgt_plot_motifs_waterfall"
2025-09-15 20:24:06.770 wdl.w:ptcp.w:call-trgt-18 INFO output :: job: "call-trgt_plot_motifs_waterfall", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-18/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2115.motifs_waterfall.trgt_plots.zip"}
2025-09-15 20:24:06.771 wdl.w:ptcp.w:call-trgt-18 INFO visit :: node: "output-images_motifs_waterfall", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-18/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2115.motifs_waterfall.trgt_plots.zip"}
2025-09-15 20:24:06.771 wdl.w:ptcp.w:call-trgt-18 INFO visit :: node: "outputs", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-18/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2115.motifs_waterfall.trgt_plots.zip", "images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-18/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2115.meth_allele.trgt_plots.zip", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-18/call-trgt_genotype/out/m84036_250809_035451_s4.bc2115.trgt.sorted.spanning.bam.bai", "images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-18/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2115.motifs_allele.trgt_plots.zip", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-18/call-trgt_genotype/out/m84036_250809_035451_s4.bc2115.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-18/call-trgt_genotype/out/m84036_250809_035451_s4.bc2115.trgt.vcf", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-18/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2115.repeats.bam", "images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-18/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2115.meth_waterfall.trgt_plots.zip", "reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-18/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2115.repeats.bam.bai"}
2025-09-15 20:24:06.777 wdl.w:ptcp.w:call-trgt-21.t:call-trgt_plot_meth_allele NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-21/call-trgt_plot_meth_allele", thread: 140610879071808
2025-09-15 20:24:06.799 wdl.w:ptcp.w:call-trgt-21.t:call-trgt_plot_meth_allele INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:06.799 wdl.w:ptcp.w:call-trgt-21.t:call-trgt_plot_meth_allele INFO input :: name: "waterfall", value: false
2025-09-15 20:24:06.799 wdl.w:ptcp.w:call-trgt-21.t:call-trgt_plot_meth_allele INFO input :: name: "methylation", value: true
2025-09-15 20:24:06.799 wdl.w:ptcp.w:call-trgt-21.t:call-trgt_plot_meth_allele INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:06.799 wdl.w:ptcp.w:call-trgt-21.t:call-trgt_plot_meth_allele INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:06.799 wdl.w:ptcp.w:call-trgt-21.t:call-trgt_plot_meth_allele INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:06.799 wdl.w:ptcp.w:call-trgt-21.t:call-trgt_plot_meth_allele INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2118.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:06.800 wdl.w:ptcp.w:call-trgt-21.t:call-trgt_plot_meth_allele INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2118.trgt.sorted.spanning.bam"
2025-09-15 20:24:06.800 wdl.w:ptcp.w:call-trgt-21.t:call-trgt_plot_meth_allele INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2118.trgt.vcf"
2025-09-15 20:24:06.800 wdl.w:ptcp.w:call-trgt-21.t:call-trgt_plot_meth_allele INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2118"
2025-09-15 20:24:06.800 wdl.w:ptcp.w:call-trgt-21.t:call-trgt_plot_meth_allele INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:06.800 wdl.w:ptcp.w:call-trgt-21.t:call-trgt_plot_meth_allele INFO eval :: name: "plot_type", value: "allele"
2025-09-15 20:24:06.800 wdl.w:ptcp.w:call-trgt-21.t:call-trgt_plot_meth_allele INFO eval :: name: "show", value: "meth"
2025-09-15 20:24:06.800 wdl.w:ptcp.w:call-trgt-21.t:call-trgt_plot_meth_allele INFO eval :: name: "threads", value: 1
2025-09-15 20:24:06.801 wdl.w:ptcp.w:call-trgt-21.t:call-trgt_plot_meth_allele INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:06.801 wdl.w:ptcp.w:call-trgt-21.t:call-trgt_plot_meth_allele INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2118.meth_allele"
2025-09-15 20:24:06.801 wdl.w:ptcp.w:call-trgt-21.t:call-trgt_plot_meth_allele INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:06.801 wdl.w:ptcp.w:call-trgt-21.t:call-trgt_plot_meth_allele WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:06.802 wdl.w:ptcp.w:call-trgt-21.t:call-trgt_plot_meth_allele INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:06.802 wdl.w:ptcp.w:call-trgt-21.t:call-trgt_plot_meth_allele INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:06.804 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_plot_motifs_waterfall INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-10/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_r3qen8hm"
2025-09-15 20:24:06.804 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_plot_motifs_waterfall INFO Slurm invocation: srun --job-name call-trgt_plot_motifs_waterfall --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-10/call-trgt_plot_motifs_waterfall/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-10/call-trgt_plot_motifs_waterfall/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-10/call-trgt_plot_motifs_waterfall/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-10/call-trgt_plot_motifs_waterfall/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-10/call-trgt_genotype/out/m84036_250809_035451_s4.bc2107.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2107.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-10/call-trgt_genotype/out/m84036_250809_035451_s4.bc2107.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2107.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-10/call-trgt_genotype/out/m84036_250809_035451_s4.bc2107.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2107.trgt.sorted.spanning.bam.bai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-10/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_r3qen8hm/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-10/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_r3qen8hm/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:06.819 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_plot_motifs_waterfall NOTICE slurm_singularity run :: pid: 1200890, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-10/call-trgt_plot_motifs_waterfall/slurm_singularity.log.txt"
2025-09-15 20:24:06.859 wdl.w:ptcp.w:call-trgt-18 NOTICE done
2025-09-15 20:24:06.875 wdl.w:ptcp.w:call-trgt-21.t:call-trgt_plot_meth_allele INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-21/call-trgt_plot_meth_allele/_singularity_tmpdir_d4ttwdn3"
2025-09-15 20:24:06.875 wdl.w:ptcp.w:call-trgt-21.t:call-trgt_plot_meth_allele INFO Slurm invocation: srun --job-name call-trgt_plot_meth_allele --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-21/call-trgt_plot_meth_allele/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-21/call-trgt_plot_meth_allele/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-21/call-trgt_plot_meth_allele/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-21/call-trgt_plot_meth_allele/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-21/call-trgt_genotype/out/m84036_250809_035451_s4.bc2118.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2118.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-21/call-trgt_genotype/out/m84036_250809_035451_s4.bc2118.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2118.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-21/call-trgt_genotype/out/m84036_250809_035451_s4.bc2118.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2118.trgt.sorted.spanning.bam:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-21/call-trgt_plot_meth_allele/_singularity_tmpdir_d4ttwdn3/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-21/call-trgt_plot_meth_allele/_singularity_tmpdir_d4ttwdn3/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:06.884 wdl.w:ptcp.w:call-trgt-21.t:call-trgt_plot_meth_allele NOTICE slurm_singularity run :: pid: 1200892, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-21/call-trgt_plot_meth_allele/slurm_singularity.log.txt"
2025-09-15 20:24:06.891 wdl.w:ptcp NOTICE finish :: job: "call-trgt-18"
2025-09-15 20:24:06.891 wdl.w:ptcp INFO output :: job: "call-trgt-18", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-18/out/m84036_250809_035451_s4.bc2115.motifs_waterfall.trgt_plots.zip", "images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-18/out/m84036_250809_035451_s4.bc2115.meth_allele.trgt_plots.zip", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-18/out/m84036_250809_035451_s4.bc2115.trgt.sorted.spanning.bam.bai", "images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-18/out/m84036_250809_035451_s4.bc2115.motifs_allele.trgt_plots.zip", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-18/out/m84036_250809_035451_s4.bc2115.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-18/out/m84036_250809_035451_s4.bc2115.trgt.vcf", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-18/out/m84036_250809_035451_s4.bc2115.repeats.bam", "images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-18/out/m84036_250809_035451_s4.bc2115.meth_waterfall.trgt_plots.zip", "reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-18/out/m84036_250809_035451_s4.bc2115.repeats.bam.bai"}
2025-09-15 20:24:06.896 wdl.w:ptcp.w:call-paraphase-39 NOTICE workflow start :: name: "paraphase", source: "./paraphase.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-39"
2025-09-15 20:24:06.909 wdl.w:ptcp.w:call-paraphase-39 INFO visit :: node: "decl-annotation_vcf", values: {"annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf"}
2025-09-15 20:24:06.909 wdl.w:ptcp.w:call-paraphase-39 INFO visit :: node: "decl-config_file", values: {"config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml"}
2025-09-15 20:24:06.909 wdl.w:ptcp.w:call-paraphase-39 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:24:06.909 wdl.w:ptcp.w:call-paraphase-39 INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:24:06.910 wdl.w:ptcp.w:call-paraphase-39 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-39/out/m84036_250809_035451_s4.bc2136.mapped.bam"}
2025-09-15 20:24:06.910 wdl.w:ptcp.w:call-paraphase-39 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-39/out/m84036_250809_035451_s4.bc2136.mapped.bam.bai"}
2025-09-15 20:24:06.910 wdl.w:ptcp.w:call-paraphase-39 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:24:06.910 wdl.w:ptcp.w:call-paraphase-39 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:24:06.910 wdl.w:ptcp.w:call-paraphase-39 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2136"}
2025-09-15 20:24:06.910 wdl.w:ptcp.w:call-paraphase-39 INFO visit :: node: "decl-sex", values: {"sex": "F"}
2025-09-15 20:24:06.910 wdl.w:ptcp.w:call-paraphase-39 NOTICE ready :: job: "call-run_paraphase", callee: "run_paraphase"
2025-09-15 20:24:06.910 wdl.w:ptcp.w:call-paraphase-39 INFO input :: job: "call-run_paraphase", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf", "genome_version": "38", "config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-39/out/m84036_250809_035451_s4.bc2136.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-39/out/m84036_250809_035451_s4.bc2136.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2136"}
2025-09-15 20:24:07.322 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:07 [ERROR] - No reads found for TRID=SCA37_DAB1
2025-09-15 20:24:07.322 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:07 [ERROR] - No reads found for TRID=OPDM_ABCD3
2025-09-15 20:24:07.322 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:07 [ERROR] - No reads found for TRID=DRPLA_ATN1
2025-09-15 20:24:07.322 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:07 [ERROR] - No reads found for TRID=SCA2_ATXN2
2025-09-15 20:24:07.322 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:07 [ERROR] - No reads found for TRID=OPDM4_RILPL1
2025-09-15 20:24:07.322 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:07 [ERROR] - No reads found for TRID=NIID_NOTCH2NLC
2025-09-15 20:24:07.322 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:07 [ERROR] - No reads found for TRID=SCA3_ATXN3
2025-09-15 20:24:07.322 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:07 [ERROR] - No reads found for TRID=OPMD_PABPN1
2025-09-15 20:24:07.328 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_plot_meth_allele.slurm_singularity INFO srun: job 51797548 queued and waiting for resources
2025-09-15 20:24:07.328 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_plot_meth_allele.slurm_singularity INFO srun: job 51797548 has been allocated resources
2025-09-15 20:24:07.328 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_plot_meth_allele.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:07.389 wdl.w:ptcp.w:call-paraphase-18.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for smn1 for sample m84036_250809_035451_s4.bc2115 at 2025-09-15 20:23:54.757581...
2025-09-15 20:24:07.389 wdl.w:ptcp.w:call-paraphase-18.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for f8inv1 for sample m84036_250809_035451_s4.bc2115 at 2025-09-15 20:24:07.234218...
2025-09-15 20:24:07.389 wdl.w:ptcp.w:call-paraphase-18.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for f8inv1 for sample m84036_250809_035451_s4.bc2115 at 2025-09-15 20:24:07.235003...
2025-09-15 20:24:07.397 wdl.w:ptcp.w:call-trgt-11.t:call-trgt_plot_motifs_allele INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2108.motifs_allele.trgt_plots.zip"
2025-09-15 20:24:07.468 wdl.w:ptcp.w:call-trgt-11.t:call-trgt_plot_motifs_allele NOTICE done
2025-09-15 20:24:07.472 wdl.w:ptcp.w:call-trgt-11 NOTICE finish :: job: "call-trgt_plot_motifs_allele"
2025-09-15 20:24:07.473 wdl.w:ptcp.w:call-trgt-11 INFO output :: job: "call-trgt_plot_motifs_allele", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-11/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2108.motifs_allele.trgt_plots.zip"}
2025-09-15 20:24:07.473 wdl.w:ptcp.w:call-trgt-11 INFO visit :: node: "output-images_motifs_allele", values: {"images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-11/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2108.motifs_allele.trgt_plots.zip"}
2025-09-15 20:24:07.479 wdl.w:ptcp.w:call-trgt-21.t:call-trgt_plot_meth_waterfall NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-21/call-trgt_plot_meth_waterfall", thread: 140609310422592
2025-09-15 20:24:07.492 wdl.w:ptcp.w:call-trgt-19.t:call-trgt_plot_meth_waterfall INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2116.meth_waterfall.trgt_plots.zip"
2025-09-15 20:24:07.496 wdl.w:ptcp.w:call-trgt-21.t:call-trgt_plot_meth_waterfall INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:07.496 wdl.w:ptcp.w:call-trgt-21.t:call-trgt_plot_meth_waterfall INFO input :: name: "waterfall", value: true
2025-09-15 20:24:07.496 wdl.w:ptcp.w:call-trgt-21.t:call-trgt_plot_meth_waterfall INFO input :: name: "methylation", value: true
2025-09-15 20:24:07.497 wdl.w:ptcp.w:call-trgt-21.t:call-trgt_plot_meth_waterfall INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:07.497 wdl.w:ptcp.w:call-trgt-21.t:call-trgt_plot_meth_waterfall INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:07.497 wdl.w:ptcp.w:call-trgt-21.t:call-trgt_plot_meth_waterfall INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:07.497 wdl.w:ptcp.w:call-trgt-21.t:call-trgt_plot_meth_waterfall INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2118.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:07.497 wdl.w:ptcp.w:call-trgt-21.t:call-trgt_plot_meth_waterfall INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2118.trgt.sorted.spanning.bam"
2025-09-15 20:24:07.497 wdl.w:ptcp.w:call-trgt-21.t:call-trgt_plot_meth_waterfall INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2118.trgt.vcf"
2025-09-15 20:24:07.497 wdl.w:ptcp.w:call-trgt-21.t:call-trgt_plot_meth_waterfall INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2118"
2025-09-15 20:24:07.497 wdl.w:ptcp.w:call-trgt-21.t:call-trgt_plot_meth_waterfall INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:07.497 wdl.w:ptcp.w:call-trgt-21.t:call-trgt_plot_meth_waterfall INFO eval :: name: "plot_type", value: "waterfall"
2025-09-15 20:24:07.497 wdl.w:ptcp.w:call-trgt-21.t:call-trgt_plot_meth_waterfall INFO eval :: name: "show", value: "meth"
2025-09-15 20:24:07.497 wdl.w:ptcp.w:call-trgt-21.t:call-trgt_plot_meth_waterfall INFO eval :: name: "threads", value: 1
2025-09-15 20:24:07.498 wdl.w:ptcp.w:call-trgt-21.t:call-trgt_plot_meth_waterfall INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:07.498 wdl.w:ptcp.w:call-trgt-21.t:call-trgt_plot_meth_waterfall INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2118.meth_waterfall"
2025-09-15 20:24:07.498 wdl.w:ptcp.w:call-trgt-21.t:call-trgt_plot_meth_waterfall INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:07.498 wdl.w:ptcp.w:call-trgt-21.t:call-trgt_plot_meth_waterfall WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:07.498 wdl.w:ptcp.w:call-trgt-21.t:call-trgt_plot_meth_waterfall INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:07.499 wdl.w:ptcp.w:call-trgt-21.t:call-trgt_plot_meth_waterfall INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:07.576 wdl.w:ptcp.w:call-trgt-11.t:call-trgt_plot_motifs_waterfall INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2108.motifs_waterfall.trgt_plots.zip"
2025-09-15 20:24:07.580 wdl.w:ptcp.w:call-trgt-21.t:call-trgt_plot_meth_waterfall INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-21/call-trgt_plot_meth_waterfall/_singularity_tmpdir_6o1f78si"
2025-09-15 20:24:07.580 wdl.w:ptcp.w:call-trgt-21.t:call-trgt_plot_meth_waterfall INFO Slurm invocation: srun --job-name call-trgt_plot_meth_waterfall --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-21/call-trgt_plot_meth_waterfall/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-21/call-trgt_plot_meth_waterfall/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-21/call-trgt_plot_meth_waterfall/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-21/call-trgt_plot_meth_waterfall/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-21/call-trgt_genotype/out/m84036_250809_035451_s4.bc2118.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2118.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-21/call-trgt_genotype/out/m84036_250809_035451_s4.bc2118.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2118.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-21/call-trgt_genotype/out/m84036_250809_035451_s4.bc2118.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2118.trgt.sorted.spanning.bam:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-21/call-trgt_plot_meth_waterfall/_singularity_tmpdir_6o1f78si/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-21/call-trgt_plot_meth_waterfall/_singularity_tmpdir_6o1f78si/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:07.584 wdl.w:ptcp.w:call-trgt-19.t:call-trgt_plot_meth_waterfall NOTICE done
2025-09-15 20:24:07.588 wdl.w:ptcp.w:call-trgt-19 NOTICE finish :: job: "call-trgt_plot_meth_waterfall"
2025-09-15 20:24:07.588 wdl.w:ptcp.w:call-trgt-19 INFO output :: job: "call-trgt_plot_meth_waterfall", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-19/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2116.meth_waterfall.trgt_plots.zip"}
2025-09-15 20:24:07.588 wdl.w:ptcp.w:call-trgt-19 INFO visit :: node: "output-images_meth_waterfall", values: {"images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-19/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2116.meth_waterfall.trgt_plots.zip"}
2025-09-15 20:24:07.595 wdl.w:ptcp.w:call-trgt-21.t:call-trgt_plot_motifs_allele NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-21/call-trgt_plot_motifs_allele", thread: 140610342200896
2025-09-15 20:24:07.604 wdl.w:ptcp.w:call-trgt-21.t:call-trgt_plot_meth_waterfall NOTICE slurm_singularity run :: pid: 1200918, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-21/call-trgt_plot_meth_waterfall/slurm_singularity.log.txt"
2025-09-15 20:24:07.618 wdl.w:ptcp.w:call-trgt-21.t:call-trgt_plot_motifs_allele INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:07.618 wdl.w:ptcp.w:call-trgt-21.t:call-trgt_plot_motifs_allele INFO input :: name: "waterfall", value: false
2025-09-15 20:24:07.618 wdl.w:ptcp.w:call-trgt-21.t:call-trgt_plot_motifs_allele INFO input :: name: "methylation", value: false
2025-09-15 20:24:07.618 wdl.w:ptcp.w:call-trgt-21.t:call-trgt_plot_motifs_allele INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:07.618 wdl.w:ptcp.w:call-trgt-21.t:call-trgt_plot_motifs_allele INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:07.618 wdl.w:ptcp.w:call-trgt-21.t:call-trgt_plot_motifs_allele INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:07.619 wdl.w:ptcp.w:call-trgt-21.t:call-trgt_plot_motifs_allele INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2118.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:07.619 wdl.w:ptcp.w:call-trgt-21.t:call-trgt_plot_motifs_allele INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2118.trgt.sorted.spanning.bam"
2025-09-15 20:24:07.619 wdl.w:ptcp.w:call-trgt-21.t:call-trgt_plot_motifs_allele INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2118.trgt.vcf"
2025-09-15 20:24:07.619 wdl.w:ptcp.w:call-trgt-21.t:call-trgt_plot_motifs_allele INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2118"
2025-09-15 20:24:07.619 wdl.w:ptcp.w:call-trgt-21.t:call-trgt_plot_motifs_allele INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:07.619 wdl.w:ptcp.w:call-trgt-21.t:call-trgt_plot_motifs_allele INFO eval :: name: "plot_type", value: "allele"
2025-09-15 20:24:07.619 wdl.w:ptcp.w:call-trgt-21.t:call-trgt_plot_motifs_allele INFO eval :: name: "show", value: "motifs"
2025-09-15 20:24:07.619 wdl.w:ptcp.w:call-trgt-21.t:call-trgt_plot_motifs_allele INFO eval :: name: "threads", value: 1
2025-09-15 20:24:07.620 wdl.w:ptcp.w:call-trgt-21.t:call-trgt_plot_motifs_allele INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:07.620 wdl.w:ptcp.w:call-trgt-21.t:call-trgt_plot_motifs_allele INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2118.motifs_allele"
2025-09-15 20:24:07.620 wdl.w:ptcp.w:call-trgt-21.t:call-trgt_plot_motifs_allele INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:07.621 wdl.w:ptcp.w:call-trgt-21.t:call-trgt_plot_motifs_allele WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:07.621 wdl.w:ptcp.w:call-trgt-21.t:call-trgt_plot_motifs_allele INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:07.621 wdl.w:ptcp.w:call-trgt-21.t:call-trgt_plot_motifs_allele INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:07.651 wdl.w:ptcp.t:call-pbmm2_align_hifi-79 INFO output :: name: "mapped_bam", value: "m84036_250809_035451_s4.bc2176.mapped.bam"
2025-09-15 20:24:07.654 wdl.w:ptcp.t:call-pbmm2_align_hifi-79 INFO output :: name: "mapped_bam_bai", value: "m84036_250809_035451_s4.bc2176.mapped.bam.bai"
2025-09-15 20:24:07.656 wdl.w:ptcp.t:call-pbmm2_align_hifi-79 INFO output :: name: "mapped_bam_pbi", value: "m84036_250809_035451_s4.bc2176.mapped.bam.pbi"
2025-09-15 20:24:07.658 wdl.w:ptcp.t:call-pbmm2_align_hifi-79 INFO output :: name: "report", value: "mapping_stats.report.json"
2025-09-15 20:24:07.664 wdl.w:ptcp.w:call-trgt-11.t:call-trgt_plot_motifs_waterfall NOTICE done
2025-09-15 20:24:07.668 wdl.w:ptcp.w:call-trgt-11 NOTICE finish :: job: "call-trgt_plot_motifs_waterfall"
2025-09-15 20:24:07.669 wdl.w:ptcp.w:call-trgt-11 INFO output :: job: "call-trgt_plot_motifs_waterfall", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-11/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2108.motifs_waterfall.trgt_plots.zip"}
2025-09-15 20:24:07.669 wdl.w:ptcp.w:call-trgt-11 INFO visit :: node: "output-images_motifs_waterfall", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-11/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2108.motifs_waterfall.trgt_plots.zip"}
2025-09-15 20:24:07.669 wdl.w:ptcp.w:call-trgt-11 INFO visit :: node: "outputs", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-11/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2108.motifs_waterfall.trgt_plots.zip", "images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-11/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2108.meth_allele.trgt_plots.zip", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-11/call-trgt_genotype/out/m84036_250809_035451_s4.bc2108.trgt.sorted.spanning.bam.bai", "images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-11/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2108.motifs_allele.trgt_plots.zip", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-11/call-trgt_genotype/out/m84036_250809_035451_s4.bc2108.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-11/call-trgt_genotype/out/m84036_250809_035451_s4.bc2108.trgt.vcf", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-11/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2108.repeats.bam", "images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-11/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2108.meth_waterfall.trgt_plots.zip", "reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-11/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2108.repeats.bam.bai"}
2025-09-15 20:24:07.678 wdl.w:ptcp.w:call-trgt-21.t:call-trgt_plot_motifs_waterfall NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-21/call-trgt_plot_motifs_waterfall", thread: 140608748373568
2025-09-15 20:24:07.702 wdl.w:ptcp.w:call-trgt-21.t:call-trgt_plot_motifs_waterfall INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:07.702 wdl.w:ptcp.w:call-trgt-21.t:call-trgt_plot_motifs_waterfall INFO input :: name: "waterfall", value: true
2025-09-15 20:24:07.702 wdl.w:ptcp.w:call-trgt-21.t:call-trgt_plot_motifs_waterfall INFO input :: name: "methylation", value: false
2025-09-15 20:24:07.702 wdl.w:ptcp.w:call-trgt-21.t:call-trgt_plot_motifs_waterfall INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:07.702 wdl.w:ptcp.w:call-trgt-21.t:call-trgt_plot_motifs_waterfall INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:07.702 wdl.w:ptcp.w:call-trgt-21.t:call-trgt_plot_motifs_waterfall INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:07.702 wdl.w:ptcp.w:call-trgt-21.t:call-trgt_plot_motifs_waterfall INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2118.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:07.702 wdl.w:ptcp.w:call-trgt-21.t:call-trgt_plot_motifs_waterfall INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2118.trgt.sorted.spanning.bam"
2025-09-15 20:24:07.702 wdl.w:ptcp.w:call-trgt-21.t:call-trgt_plot_motifs_waterfall INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2118.trgt.vcf"
2025-09-15 20:24:07.702 wdl.w:ptcp.w:call-trgt-21.t:call-trgt_plot_motifs_waterfall INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2118"
2025-09-15 20:24:07.703 wdl.w:ptcp.w:call-trgt-21.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:07.703 wdl.w:ptcp.w:call-trgt-21.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "plot_type", value: "waterfall"
2025-09-15 20:24:07.703 wdl.w:ptcp.w:call-trgt-21.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "show", value: "motifs"
2025-09-15 20:24:07.703 wdl.w:ptcp.w:call-trgt-21.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "threads", value: 1
2025-09-15 20:24:07.703 wdl.w:ptcp.w:call-trgt-21.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:07.703 wdl.w:ptcp.w:call-trgt-21.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2118.motifs_waterfall"
2025-09-15 20:24:07.704 wdl.w:ptcp.w:call-trgt-21.t:call-trgt_plot_motifs_waterfall INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:07.704 wdl.w:ptcp.w:call-trgt-21.t:call-trgt_plot_motifs_waterfall WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:07.704 wdl.w:ptcp.w:call-trgt-21.t:call-trgt_plot_motifs_waterfall INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:07.704 wdl.w:ptcp.w:call-trgt-21.t:call-trgt_plot_motifs_waterfall INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:07.710 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO srun: job 51797549 queued and waiting for resources
2025-09-15 20:24:07.710 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO srun: job 51797549 has been allocated resources
2025-09-15 20:24:07.710 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:07.721 wdl.w:ptcp.w:call-trgt-21.t:call-trgt_plot_motifs_allele INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-21/call-trgt_plot_motifs_allele/_singularity_tmpdir___snbr6a"
2025-09-15 20:24:07.722 wdl.w:ptcp.w:call-trgt-21.t:call-trgt_plot_motifs_allele INFO Slurm invocation: srun --job-name call-trgt_plot_motifs_allele --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-21/call-trgt_plot_motifs_allele/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-21/call-trgt_plot_motifs_allele/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-21/call-trgt_plot_motifs_allele/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-21/call-trgt_plot_motifs_allele/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-21/call-trgt_genotype/out/m84036_250809_035451_s4.bc2118.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2118.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-21/call-trgt_genotype/out/m84036_250809_035451_s4.bc2118.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2118.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-21/call-trgt_genotype/out/m84036_250809_035451_s4.bc2118.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2118.trgt.sorted.spanning.bam:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-21/call-trgt_plot_motifs_allele/_singularity_tmpdir___snbr6a/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-21/call-trgt_plot_motifs_allele/_singularity_tmpdir___snbr6a/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:07.737 wdl.w:ptcp.w:call-trgt-21.t:call-trgt_plot_motifs_allele NOTICE slurm_singularity run :: pid: 1200926, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-21/call-trgt_plot_motifs_allele/slurm_singularity.log.txt"
2025-09-15 20:24:07.761 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_plot_motifs_allele.slurm_singularity INFO srun: job 51797550 queued and waiting for resources
2025-09-15 20:24:07.761 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_plot_motifs_allele.slurm_singularity INFO srun: job 51797550 has been allocated resources
2025-09-15 20:24:07.761 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_plot_motifs_allele.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:07.766 wdl.w:ptcp.w:call-trgt-19.t:call-trgt_plot_meth_allele INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2116.meth_allele.trgt_plots.zip"
2025-09-15 20:24:07.780 wdl.w:ptcp.w:call-trgt-11 NOTICE done
2025-09-15 20:24:07.787 wdl.w:ptcp NOTICE finish :: job: "call-trgt-11"
2025-09-15 20:24:07.787 wdl.w:ptcp INFO output :: job: "call-trgt-11", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-11/out/m84036_250809_035451_s4.bc2108.motifs_waterfall.trgt_plots.zip", "images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-11/out/m84036_250809_035451_s4.bc2108.meth_allele.trgt_plots.zip", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-11/out/m84036_250809_035451_s4.bc2108.trgt.sorted.spanning.bam.bai", "images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-11/out/m84036_250809_035451_s4.bc2108.motifs_allele.trgt_plots.zip", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-11/out/m84036_250809_035451_s4.bc2108.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-11/out/m84036_250809_035451_s4.bc2108.trgt.vcf", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-11/out/m84036_250809_035451_s4.bc2108.repeats.bam", "images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-11/out/m84036_250809_035451_s4.bc2108.meth_waterfall.trgt_plots.zip", "reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-11/out/m84036_250809_035451_s4.bc2108.repeats.bam.bai"}
2025-09-15 20:24:07.788 wdl.w:ptcp.t:call-pbmm2_align_hifi-79 NOTICE done
2025-09-15 20:24:07.794 wdl.w:ptcp NOTICE finish :: job: "call-pbmm2_align_hifi-79"
2025-09-15 20:24:07.794 wdl.w:ptcp INFO output :: job: "call-pbmm2_align_hifi-79", values: {"report": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-79/out/mapping_stats.report.json", "mapped_bam_pbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-79/out/m84036_250809_035451_s4.bc2176.mapped.bam.pbi", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-79/out/m84036_250809_035451_s4.bc2176.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-79/out/m84036_250809_035451_s4.bc2176.mapped.bam"}
2025-09-15 20:24:07.794 wdl.w:ptcp NOTICE ready :: job: "call-paraphase-79", callee: "paraphase"
2025-09-15 20:24:07.795 wdl.w:ptcp INFO input :: job: "call-paraphase-79", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf", "genome_version": "38", "config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-79/out/m84036_250809_035451_s4.bc2176.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-79/out/m84036_250809_035451_s4.bc2176.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2176"}
2025-09-15 20:24:07.794 wdl.w:ptcp.w:call-sawfish-39 NOTICE workflow start :: name: "sawfish", source: "./sawfish.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-39"
2025-09-15 20:24:07.796 wdl.w:ptcp NOTICE ready :: job: "call-sawfish-79", callee: "sawfish"
2025-09-15 20:24:07.796 wdl.w:ptcp INFO input :: job: "call-sawfish-79", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-79/out/m84036_250809_035451_s4.bc2176.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-79/out/m84036_250809_035451_s4.bc2176.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2176"}
2025-09-15 20:24:07.797 wdl.w:ptcp NOTICE ready :: job: "call-trgt-79", callee: "trgt"
2025-09-15 20:24:07.797 wdl.w:ptcp INFO input :: job: "call-trgt-79", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-79/out/m84036_250809_035451_s4.bc2176.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-79/out/m84036_250809_035451_s4.bc2176.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2176"}
2025-09-15 20:24:07.802 wdl.w:ptcp.w:call-trgt-17.t:call-trgt_plot_meth_allele NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-17/call-trgt_plot_meth_allele", thread: 140607699809856
2025-09-15 20:24:07.804 wdl.w:ptcp.w:call-trgt-21.t:call-trgt_plot_motifs_waterfall INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-21/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_08k5l9bu"
2025-09-15 20:24:07.805 wdl.w:ptcp.w:call-trgt-21.t:call-trgt_plot_motifs_waterfall INFO Slurm invocation: srun --job-name call-trgt_plot_motifs_waterfall --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-21/call-trgt_plot_motifs_waterfall/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-21/call-trgt_plot_motifs_waterfall/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-21/call-trgt_plot_motifs_waterfall/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-21/call-trgt_plot_motifs_waterfall/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-21/call-trgt_genotype/out/m84036_250809_035451_s4.bc2118.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2118.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-21/call-trgt_genotype/out/m84036_250809_035451_s4.bc2118.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2118.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-21/call-trgt_genotype/out/m84036_250809_035451_s4.bc2118.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2118.trgt.sorted.spanning.bam:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-21/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_08k5l9bu/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-21/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_08k5l9bu/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:07.809 wdl.w:ptcp.w:call-sawfish-39 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:24:07.809 wdl.w:ptcp.w:call-paraphase-27.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for f8inv1 for sample m84036_250809_035451_s4.bc2124 at 2025-09-15 20:24:07.077437...
2025-09-15 20:24:07.810 wdl.w:ptcp.w:call-sawfish-39 INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:24:07.810 wdl.w:ptcp.w:call-paraphase-27.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for f8inv1 for sample m84036_250809_035451_s4.bc2124 at 2025-09-15 20:24:07.078179...
2025-09-15 20:24:07.810 wdl.w:ptcp.w:call-sawfish-39 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-39/out/m84036_250809_035451_s4.bc2136.mapped.bam"}
2025-09-15 20:24:07.810 wdl.w:ptcp.w:call-sawfish-39 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-39/out/m84036_250809_035451_s4.bc2136.mapped.bam.bai"}
2025-09-15 20:24:07.810 wdl.w:ptcp.w:call-sawfish-39 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:24:07.810 wdl.w:ptcp.w:call-sawfish-39 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:24:07.810 wdl.w:ptcp.w:call-sawfish-39 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2136"}
2025-09-15 20:24:07.810 wdl.w:ptcp.w:call-sawfish-39 NOTICE ready :: job: "call-run_sawfish", callee: "run_sawfish"
2025-09-15 20:24:07.811 wdl.w:ptcp.w:call-sawfish-39 INFO input :: job: "call-run_sawfish", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-39/out/m84036_250809_035451_s4.bc2136.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-39/out/m84036_250809_035451_s4.bc2136.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2136"}
2025-09-15 20:24:07.823 wdl.w:ptcp.w:call-trgt-21.t:call-trgt_plot_motifs_waterfall NOTICE slurm_singularity run :: pid: 1200928, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-21/call-trgt_plot_motifs_waterfall/slurm_singularity.log.txt"
2025-09-15 20:24:07.824 wdl.w:ptcp.w:call-trgt-17.t:call-trgt_plot_meth_allele INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:07.824 wdl.w:ptcp.w:call-trgt-17.t:call-trgt_plot_meth_allele INFO input :: name: "waterfall", value: false
2025-09-15 20:24:07.824 wdl.w:ptcp.w:call-trgt-17.t:call-trgt_plot_meth_allele INFO input :: name: "methylation", value: true
2025-09-15 20:24:07.824 wdl.w:ptcp.w:call-trgt-17.t:call-trgt_plot_meth_allele INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:07.824 wdl.w:ptcp.w:call-trgt-17.t:call-trgt_plot_meth_allele INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:07.824 wdl.w:ptcp.w:call-trgt-17.t:call-trgt_plot_meth_allele INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:07.824 wdl.w:ptcp.w:call-trgt-17.t:call-trgt_plot_meth_allele INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2114.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:07.824 wdl.w:ptcp.w:call-trgt-17.t:call-trgt_plot_meth_allele INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2114.trgt.sorted.spanning.bam"
2025-09-15 20:24:07.825 wdl.w:ptcp.w:call-trgt-17.t:call-trgt_plot_meth_allele INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2114.trgt.vcf"
2025-09-15 20:24:07.825 wdl.w:ptcp.w:call-trgt-17.t:call-trgt_plot_meth_allele INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2114"
2025-09-15 20:24:07.825 wdl.w:ptcp.w:call-trgt-17.t:call-trgt_plot_meth_allele INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:07.825 wdl.w:ptcp.w:call-trgt-17.t:call-trgt_plot_meth_allele INFO eval :: name: "plot_type", value: "allele"
2025-09-15 20:24:07.825 wdl.w:ptcp.w:call-trgt-17.t:call-trgt_plot_meth_allele INFO eval :: name: "show", value: "meth"
2025-09-15 20:24:07.825 wdl.w:ptcp.w:call-trgt-17.t:call-trgt_plot_meth_allele INFO eval :: name: "threads", value: 1
2025-09-15 20:24:07.825 wdl.w:ptcp.w:call-trgt-17.t:call-trgt_plot_meth_allele INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:07.825 wdl.w:ptcp.w:call-trgt-17.t:call-trgt_plot_meth_allele INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2114.meth_allele"
2025-09-15 20:24:07.826 wdl.w:ptcp.w:call-trgt-17.t:call-trgt_plot_meth_allele INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:07.826 wdl.w:ptcp.w:call-trgt-17.t:call-trgt_plot_meth_allele WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:07.826 wdl.w:ptcp.w:call-trgt-17.t:call-trgt_plot_meth_allele INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:07.826 wdl.w:ptcp.w:call-trgt-17.t:call-trgt_plot_meth_allele INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:07.827 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO srun: job 51797551 queued and waiting for resources
2025-09-15 20:24:07.828 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO srun: job 51797551 has been allocated resources
2025-09-15 20:24:07.828 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:07.862 wdl.w:ptcp.w:call-trgt-19.t:call-trgt_plot_meth_allele NOTICE done
2025-09-15 20:24:07.890 wdl.w:ptcp.w:call-trgt-17.t:call-trgt_plot_meth_allele INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-17/call-trgt_plot_meth_allele/_singularity_tmpdir_94r7jzzt"
2025-09-15 20:24:07.891 wdl.w:ptcp.w:call-trgt-17.t:call-trgt_plot_meth_allele INFO Slurm invocation: srun --job-name call-trgt_plot_meth_allele --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-17/call-trgt_plot_meth_allele/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-17/call-trgt_plot_meth_allele/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-17/call-trgt_plot_meth_allele/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-17/call-trgt_plot_meth_allele/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-17/call-trgt_genotype/out/m84036_250809_035451_s4.bc2114.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2114.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-17/call-trgt_genotype/out/m84036_250809_035451_s4.bc2114.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2114.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-17/call-trgt_genotype/out/m84036_250809_035451_s4.bc2114.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2114.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-17/call-trgt_plot_meth_allele/_singularity_tmpdir_94r7jzzt/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-17/call-trgt_plot_meth_allele/_singularity_tmpdir_94r7jzzt/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:07.892 wdl.w:ptcp.w:call-trgt-19 NOTICE finish :: job: "call-trgt_plot_meth_allele"
2025-09-15 20:24:07.893 wdl.w:ptcp.w:call-trgt-21.t:call-trgt_plot_meth_allele.slurm_singularity INFO srun: job 51797552 queued and waiting for resources
2025-09-15 20:24:07.893 wdl.w:ptcp.w:call-trgt-19 INFO output :: job: "call-trgt_plot_meth_allele", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-19/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2116.meth_allele.trgt_plots.zip"}
2025-09-15 20:24:07.893 wdl.w:ptcp.w:call-trgt-21.t:call-trgt_plot_meth_allele.slurm_singularity INFO srun: job 51797552 has been allocated resources
2025-09-15 20:24:07.894 wdl.w:ptcp.w:call-trgt-19 INFO visit :: node: "output-images_meth_allele", values: {"images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-19/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2116.meth_allele.trgt_plots.zip"}
2025-09-15 20:24:07.894 wdl.w:ptcp.w:call-trgt-21.t:call-trgt_plot_meth_allele.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:07.898 wdl.w:ptcp.w:call-trgt-17.t:call-trgt_plot_meth_waterfall NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-17/call-trgt_plot_meth_waterfall", thread: 140610367379008
2025-09-15 20:24:07.916 wdl.w:ptcp.w:call-trgt-17.t:call-trgt_plot_meth_allele NOTICE slurm_singularity run :: pid: 1200930, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-17/call-trgt_plot_meth_allele/slurm_singularity.log.txt"
2025-09-15 20:24:07.921 wdl.w:ptcp.w:call-trgt-17.t:call-trgt_plot_meth_waterfall INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:07.921 wdl.w:ptcp.w:call-trgt-17.t:call-trgt_plot_meth_waterfall INFO input :: name: "waterfall", value: true
2025-09-15 20:24:07.922 wdl.w:ptcp.w:call-trgt-17.t:call-trgt_plot_meth_waterfall INFO input :: name: "methylation", value: true
2025-09-15 20:24:07.922 wdl.w:ptcp.w:call-trgt-17.t:call-trgt_plot_meth_waterfall INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:07.922 wdl.w:ptcp.w:call-trgt-17.t:call-trgt_plot_meth_waterfall INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:07.922 wdl.w:ptcp.w:call-trgt-17.t:call-trgt_plot_meth_waterfall INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:07.922 wdl.w:ptcp.w:call-trgt-17.t:call-trgt_plot_meth_waterfall INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2114.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:07.922 wdl.w:ptcp.w:call-trgt-17.t:call-trgt_plot_meth_waterfall INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2114.trgt.sorted.spanning.bam"
2025-09-15 20:24:07.922 wdl.w:ptcp.w:call-trgt-17.t:call-trgt_plot_meth_waterfall INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2114.trgt.vcf"
2025-09-15 20:24:07.922 wdl.w:ptcp.w:call-trgt-17.t:call-trgt_plot_meth_waterfall INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2114"
2025-09-15 20:24:07.922 wdl.w:ptcp.w:call-trgt-17.t:call-trgt_plot_meth_waterfall INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:07.923 wdl.w:ptcp.w:call-trgt-17.t:call-trgt_plot_meth_waterfall INFO eval :: name: "plot_type", value: "waterfall"
2025-09-15 20:24:07.923 wdl.w:ptcp.w:call-trgt-17.t:call-trgt_plot_meth_waterfall INFO eval :: name: "show", value: "meth"
2025-09-15 20:24:07.923 wdl.w:ptcp.w:call-trgt-17.t:call-trgt_plot_meth_waterfall INFO eval :: name: "threads", value: 1
2025-09-15 20:24:07.923 wdl.w:ptcp.w:call-trgt-17.t:call-trgt_plot_meth_waterfall INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:07.923 wdl.w:ptcp.w:call-trgt-17.t:call-trgt_plot_meth_waterfall INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2114.meth_waterfall"
2025-09-15 20:24:07.924 wdl.w:ptcp.w:call-trgt-17.t:call-trgt_plot_meth_waterfall INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:07.924 wdl.w:ptcp.w:call-trgt-17.t:call-trgt_plot_meth_waterfall WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:07.924 wdl.w:ptcp.w:call-trgt-17.t:call-trgt_plot_meth_waterfall INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:07.924 wdl.w:ptcp.w:call-trgt-17.t:call-trgt_plot_meth_waterfall INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:08.031 wdl.w:ptcp.w:call-trgt-17.t:call-trgt_plot_meth_waterfall INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-17/call-trgt_plot_meth_waterfall/_singularity_tmpdir_ek7hldd5"
2025-09-15 20:24:08.031 wdl.w:ptcp.w:call-trgt-17.t:call-trgt_plot_meth_waterfall INFO Slurm invocation: srun --job-name call-trgt_plot_meth_waterfall --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-17/call-trgt_plot_meth_waterfall/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-17/call-trgt_plot_meth_waterfall/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-17/call-trgt_plot_meth_waterfall/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-17/call-trgt_plot_meth_waterfall/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-17/call-trgt_genotype/out/m84036_250809_035451_s4.bc2114.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2114.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-17/call-trgt_genotype/out/m84036_250809_035451_s4.bc2114.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2114.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-17/call-trgt_genotype/out/m84036_250809_035451_s4.bc2114.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2114.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-17/call-trgt_plot_meth_waterfall/_singularity_tmpdir_ek7hldd5/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-17/call-trgt_plot_meth_waterfall/_singularity_tmpdir_ek7hldd5/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:08.042 wdl.w:ptcp.w:call-trgt-17.t:call-trgt_plot_meth_waterfall NOTICE slurm_singularity run :: pid: 1200932, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-17/call-trgt_plot_meth_waterfall/slurm_singularity.log.txt"
2025-09-15 20:24:08.333 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:07 [ERROR] - No reads found for TRID=HDL2_JPH3
2025-09-15 20:24:08.516 wdl.w:ptcp.w:call-paraphase-51.t:call-run_paraphase.stderr VERBOSE INFO:root:Processing sample m84036_250809_035451_s4.bc2148 at 2025-09-15 20:24:06.015569...
2025-09-15 20:24:08.517 wdl.w:ptcp.w:call-paraphase-51.t:call-run_paraphase.stderr VERBOSE INFO:root:Checking sample sex at 2025-09-15 20:24:06.016840...
2025-09-15 20:24:08.517 wdl.w:ptcp.w:call-paraphase-51.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for cyp21 for sample m84036_250809_035451_s4.bc2148 at 2025-09-15 20:24:06.077541...
2025-09-15 20:24:08.517 wdl.w:ptcp.w:call-paraphase-51.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for cyp21 for sample m84036_250809_035451_s4.bc2148 at 2025-09-15 20:24:06.078399...
2025-09-15 20:24:08.517 wdl.w:ptcp.w:call-paraphase-51.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for smn1 for sample m84036_250809_035451_s4.bc2148 at 2025-09-15 20:24:06.077851...
2025-09-15 20:24:08.517 wdl.w:ptcp.w:call-paraphase-51.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for hba for sample m84036_250809_035451_s4.bc2148 at 2025-09-15 20:24:06.077997...
2025-09-15 20:24:08.517 wdl.w:ptcp.w:call-paraphase-51.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for gba for sample m84036_250809_035451_s4.bc2148 at 2025-09-15 20:24:06.077980...
2025-09-15 20:24:08.518 wdl.w:ptcp.w:call-paraphase-51.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for smn1 for sample m84036_250809_035451_s4.bc2148 at 2025-09-15 20:24:06.078641...
2025-09-15 20:24:08.518 wdl.w:ptcp.w:call-paraphase-51.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for hba for sample m84036_250809_035451_s4.bc2148 at 2025-09-15 20:24:06.078710...
2025-09-15 20:24:08.518 wdl.w:ptcp.w:call-paraphase-51.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for gba for sample m84036_250809_035451_s4.bc2148 at 2025-09-15 20:24:06.078719...
2025-09-15 20:24:08.614 wdl.w:ptcp.w:call-trgt-21.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO srun: job 51797553 queued and waiting for resources
2025-09-15 20:24:08.614 wdl.w:ptcp.w:call-trgt-21.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO srun: job 51797553 has been allocated resources
2025-09-15 20:24:08.614 wdl.w:ptcp.w:call-trgt-21.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:08.740 wdl.w:ptcp.t:call-pbmm2_align_hifi-73 INFO output :: name: "mapped_bam", value: "m84036_250809_035451_s4.bc2170.mapped.bam"
2025-09-15 20:24:08.743 wdl.w:ptcp.t:call-pbmm2_align_hifi-73 INFO output :: name: "mapped_bam_bai", value: "m84036_250809_035451_s4.bc2170.mapped.bam.bai"
2025-09-15 20:24:08.744 wdl.w:ptcp.t:call-pbmm2_align_hifi-73 INFO output :: name: "mapped_bam_pbi", value: "m84036_250809_035451_s4.bc2170.mapped.bam.pbi"
2025-09-15 20:24:08.746 wdl.w:ptcp.t:call-pbmm2_align_hifi-73 INFO output :: name: "report", value: "mapping_stats.report.json"
2025-09-15 20:24:08.750 wdl.w:ptcp.w:call-trgt-21.t:call-trgt_plot_motifs_allele.slurm_singularity INFO srun: job 51797554 queued and waiting for resources
2025-09-15 20:24:08.750 wdl.w:ptcp.w:call-trgt-21.t:call-trgt_plot_motifs_allele.slurm_singularity INFO srun: job 51797554 has been allocated resources
2025-09-15 20:24:08.762 wdl.w:ptcp.w:call-paraphase-44.t:call-run_paraphase INFO output :: name: "paraphase_bam", value: "m84036_250809_035451_s4.bc2141_paraphase/m84036_250809_035451_s4.bc2141.paraphase.bam"
2025-09-15 20:24:08.768 wdl.w:ptcp.w:call-paraphase-44.t:call-run_paraphase INFO output :: name: "paraphase_bam_bai", value: "m84036_250809_035451_s4.bc2141_paraphase/m84036_250809_035451_s4.bc2141.paraphase.bam.bai"
2025-09-15 20:24:08.769 wdl.w:ptcp.w:call-paraphase-44.t:call-run_paraphase INFO output :: name: "paraphase_json", value: "m84036_250809_035451_s4.bc2141_paraphase/m84036_250809_035451_s4.bc2141.paraphase.json"
2025-09-15 20:24:08.770 wdl.w:ptcp.w:call-paraphase-44.t:call-run_paraphase INFO output :: name: "paraphase_vcfs", value: []
2025-09-15 20:24:08.771 wdl.w:ptcp.w:call-paraphase-44.t:call-run_paraphase INFO output :: name: "havanno_json", value: "m84036_250809_035451_s4.bc2141.havanno.json"
2025-09-15 20:24:08.826 wdl.w:ptcp.t:call-pbmm2_align_hifi-73 NOTICE done
2025-09-15 20:24:08.833 wdl.w:ptcp NOTICE finish :: job: "call-pbmm2_align_hifi-73"
2025-09-15 20:24:08.833 wdl.w:ptcp INFO output :: job: "call-pbmm2_align_hifi-73", values: {"report": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-73/out/mapping_stats.report.json", "mapped_bam_pbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-73/out/m84036_250809_035451_s4.bc2170.mapped.bam.pbi", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-73/out/m84036_250809_035451_s4.bc2170.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-73/out/m84036_250809_035451_s4.bc2170.mapped.bam"}
2025-09-15 20:24:08.834 wdl.w:ptcp NOTICE ready :: job: "call-paraphase-73", callee: "paraphase"
2025-09-15 20:24:08.834 wdl.w:ptcp INFO input :: job: "call-paraphase-73", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf", "genome_version": "38", "config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-73/out/m84036_250809_035451_s4.bc2170.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-73/out/m84036_250809_035451_s4.bc2170.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2170"}
2025-09-15 20:24:08.837 wdl.w:ptcp NOTICE ready :: job: "call-sawfish-73", callee: "sawfish"
2025-09-15 20:24:08.837 wdl.w:ptcp INFO input :: job: "call-sawfish-73", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-73/out/m84036_250809_035451_s4.bc2170.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-73/out/m84036_250809_035451_s4.bc2170.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2170"}
2025-09-15 20:24:08.838 wdl.w:ptcp NOTICE ready :: job: "call-trgt-73", callee: "trgt"
2025-09-15 20:24:08.838 wdl.w:ptcp INFO input :: job: "call-trgt-73", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-73/out/m84036_250809_035451_s4.bc2170.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-73/out/m84036_250809_035451_s4.bc2170.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2170"}
2025-09-15 20:24:08.838 wdl.w:ptcp.w:call-trgt-21.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO srun: job 51797555 queued and waiting for resources
2025-09-15 20:24:08.839 wdl.w:ptcp.w:call-trgt-21.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO srun: job 51797555 has been allocated resources
2025-09-15 20:24:08.839 wdl.w:ptcp.w:call-trgt-21.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:08.844 wdl.w:ptcp.w:call-trgt-17.t:call-trgt_plot_motifs_allele NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-17/call-trgt_plot_motifs_allele", thread: 140608228288064
2025-09-15 20:24:08.861 wdl.w:ptcp.w:call-trgt-17.t:call-trgt_plot_motifs_allele INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:08.861 wdl.w:ptcp.w:call-trgt-17.t:call-trgt_plot_motifs_allele INFO input :: name: "waterfall", value: false
2025-09-15 20:24:08.861 wdl.w:ptcp.w:call-trgt-17.t:call-trgt_plot_motifs_allele INFO input :: name: "methylation", value: false
2025-09-15 20:24:08.861 wdl.w:ptcp.w:call-trgt-17.t:call-trgt_plot_motifs_allele INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:08.861 wdl.w:ptcp.w:call-trgt-17.t:call-trgt_plot_motifs_allele INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:08.861 wdl.w:ptcp.w:call-trgt-17.t:call-trgt_plot_motifs_allele INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:08.861 wdl.w:ptcp.w:call-trgt-17.t:call-trgt_plot_motifs_allele INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2114.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:08.861 wdl.w:ptcp.w:call-trgt-17.t:call-trgt_plot_motifs_allele INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2114.trgt.sorted.spanning.bam"
2025-09-15 20:24:08.861 wdl.w:ptcp.w:call-trgt-17.t:call-trgt_plot_motifs_allele INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2114.trgt.vcf"
2025-09-15 20:24:08.862 wdl.w:ptcp.w:call-trgt-17.t:call-trgt_plot_motifs_allele INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2114"
2025-09-15 20:24:08.862 wdl.w:ptcp.w:call-trgt-17.t:call-trgt_plot_motifs_allele INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:08.862 wdl.w:ptcp.w:call-trgt-17.t:call-trgt_plot_motifs_allele INFO eval :: name: "plot_type", value: "allele"
2025-09-15 20:24:08.862 wdl.w:ptcp.w:call-trgt-17.t:call-trgt_plot_motifs_allele INFO eval :: name: "show", value: "motifs"
2025-09-15 20:24:08.862 wdl.w:ptcp.w:call-trgt-17.t:call-trgt_plot_motifs_allele INFO eval :: name: "threads", value: 1
2025-09-15 20:24:08.862 wdl.w:ptcp.w:call-trgt-17.t:call-trgt_plot_motifs_allele INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:08.863 wdl.w:ptcp.w:call-trgt-17.t:call-trgt_plot_motifs_allele INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2114.motifs_allele"
2025-09-15 20:24:08.863 wdl.w:ptcp.w:call-trgt-17.t:call-trgt_plot_motifs_allele INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:08.863 wdl.w:ptcp.w:call-trgt-17.t:call-trgt_plot_motifs_allele WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:08.863 wdl.w:ptcp.w:call-trgt-17.t:call-trgt_plot_motifs_allele INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:08.864 wdl.w:ptcp.w:call-trgt-17.t:call-trgt_plot_motifs_allele INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:08.874 wdl.w:ptcp.w:call-paraphase-44.t:call-run_paraphase NOTICE done
2025-09-15 20:24:08.880 wdl.w:ptcp.w:call-paraphase-44 NOTICE finish :: job: "call-run_paraphase"
2025-09-15 20:24:08.880 wdl.w:ptcp.w:call-paraphase-44 INFO output :: job: "call-run_paraphase", values: {"havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-44/call-run_paraphase/out/m84036_250809_035451_s4.bc2141.havanno.json", "paraphase_vcfs": [], "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-44/call-run_paraphase/out/m84036_250809_035451_s4.bc2141_paraphase/m84036_250809_035451_s4.bc2141.paraphase.json", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-44/call-run_paraphase/out/m84036_250809_035451_s4.bc2141_paraphase/m84036_250809_035451_s4.bc2141.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-44/call-run_paraphase/out/m84036_250809_035451_s4.bc2141_paraphase/m84036_250809_035451_s4.bc2141.paraphase.bam"}
2025-09-15 20:24:08.881 wdl.w:ptcp.w:call-paraphase-44 NOTICE ready :: job: "call-call_f8", callee: "call_f8"
2025-09-15 20:24:08.881 wdl.w:ptcp.w:call-paraphase-44 INFO input :: job: "call-call_f8", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "out_prefix": "m84036_250809_035451_s4.bc2141", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-44/call-run_paraphase/out/m84036_250809_035451_s4.bc2141_paraphase/m84036_250809_035451_s4.bc2141.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-44/call-run_paraphase/out/m84036_250809_035451_s4.bc2141_paraphase/m84036_250809_035451_s4.bc2141.paraphase.bam", "sex": "F"}
2025-09-15 20:24:08.882 wdl.w:ptcp.w:call-paraphase-44 INFO visit :: node: "output-havanno_json", values: {"havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-44/call-run_paraphase/out/m84036_250809_035451_s4.bc2141.havanno.json"}
2025-09-15 20:24:08.882 wdl.w:ptcp.w:call-paraphase-44 INFO visit :: node: "output-paraphase_bam", values: {"paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-44/call-run_paraphase/out/m84036_250809_035451_s4.bc2141_paraphase/m84036_250809_035451_s4.bc2141.paraphase.bam"}
2025-09-15 20:24:08.882 wdl.w:ptcp.w:call-paraphase-44 INFO visit :: node: "output-paraphase_bam_bai", values: {"paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-44/call-run_paraphase/out/m84036_250809_035451_s4.bc2141_paraphase/m84036_250809_035451_s4.bc2141.paraphase.bam.bai"}
2025-09-15 20:24:08.882 wdl.w:ptcp.w:call-paraphase-44 INFO visit :: node: "output-paraphase_json", values: {"paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-44/call-run_paraphase/out/m84036_250809_035451_s4.bc2141_paraphase/m84036_250809_035451_s4.bc2141.paraphase.json"}
2025-09-15 20:24:08.882 wdl.w:ptcp.w:call-paraphase-44 INFO visit :: node: "output-paraphase_vcfs", values: {"paraphase_vcfs": []}
2025-09-15 20:24:08.886 wdl.w:ptcp.w:call-trgt-17.t:call-trgt_plot_motifs_waterfall NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-17/call-trgt_plot_motifs_waterfall", thread: 140609838900800
2025-09-15 20:24:08.904 wdl.w:ptcp.w:call-trgt-17.t:call-trgt_plot_motifs_waterfall INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:08.904 wdl.w:ptcp.w:call-trgt-17.t:call-trgt_plot_motifs_waterfall INFO input :: name: "waterfall", value: true
2025-09-15 20:24:08.904 wdl.w:ptcp.w:call-trgt-17.t:call-trgt_plot_motifs_waterfall INFO input :: name: "methylation", value: false
2025-09-15 20:24:08.904 wdl.w:ptcp.w:call-trgt-17.t:call-trgt_plot_motifs_waterfall INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:08.904 wdl.w:ptcp.w:call-trgt-17.t:call-trgt_plot_motifs_waterfall INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:08.904 wdl.w:ptcp.w:call-trgt-17.t:call-trgt_plot_motifs_waterfall INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:08.904 wdl.w:ptcp.w:call-trgt-17.t:call-trgt_plot_motifs_waterfall INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2114.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:08.905 wdl.w:ptcp.w:call-trgt-17.t:call-trgt_plot_motifs_waterfall INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2114.trgt.sorted.spanning.bam"
2025-09-15 20:24:08.905 wdl.w:ptcp.w:call-trgt-17.t:call-trgt_plot_motifs_waterfall INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2114.trgt.vcf"
2025-09-15 20:24:08.905 wdl.w:ptcp.w:call-trgt-17.t:call-trgt_plot_motifs_waterfall INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2114"
2025-09-15 20:24:08.905 wdl.w:ptcp.w:call-trgt-17.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:08.905 wdl.w:ptcp.w:call-trgt-17.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "plot_type", value: "waterfall"
2025-09-15 20:24:08.905 wdl.w:ptcp.w:call-trgt-17.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "show", value: "motifs"
2025-09-15 20:24:08.905 wdl.w:ptcp.w:call-trgt-17.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "threads", value: 1
2025-09-15 20:24:08.905 wdl.w:ptcp.w:call-trgt-17.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:08.905 wdl.w:ptcp.w:call-trgt-17.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2114.motifs_waterfall"
2025-09-15 20:24:08.906 wdl.w:ptcp.w:call-trgt-17.t:call-trgt_plot_motifs_waterfall INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:08.906 wdl.w:ptcp.w:call-trgt-17.t:call-trgt_plot_motifs_waterfall WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:08.906 wdl.w:ptcp.w:call-trgt-17.t:call-trgt_plot_motifs_waterfall INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:08.906 wdl.w:ptcp.w:call-trgt-17.t:call-trgt_plot_motifs_waterfall INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:08.931 wdl.w:ptcp.w:call-trgt-17.t:call-trgt_plot_meth_allele.slurm_singularity INFO srun: job 51797556 queued and waiting for resources
2025-09-15 20:24:08.931 wdl.w:ptcp.w:call-trgt-17.t:call-trgt_plot_meth_allele.slurm_singularity INFO srun: job 51797556 has been allocated resources
2025-09-15 20:24:08.931 wdl.w:ptcp.w:call-trgt-17.t:call-trgt_plot_meth_allele.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:08.936 wdl.w:ptcp.w:call-trgt-19.t:call-trgt_plot_motifs_allele INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2116.motifs_allele.trgt_plots.zip"
2025-09-15 20:24:08.942 wdl.w:ptcp.w:call-trgt-17.t:call-trgt_plot_motifs_allele INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-17/call-trgt_plot_motifs_allele/_singularity_tmpdir_vv_uawp0"
2025-09-15 20:24:08.942 wdl.w:ptcp.w:call-trgt-17.t:call-trgt_plot_motifs_allele INFO Slurm invocation: srun --job-name call-trgt_plot_motifs_allele --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-17/call-trgt_plot_motifs_allele/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-17/call-trgt_plot_motifs_allele/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-17/call-trgt_plot_motifs_allele/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-17/call-trgt_plot_motifs_allele/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-17/call-trgt_genotype/out/m84036_250809_035451_s4.bc2114.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2114.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-17/call-trgt_genotype/out/m84036_250809_035451_s4.bc2114.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2114.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-17/call-trgt_genotype/out/m84036_250809_035451_s4.bc2114.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2114.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-17/call-trgt_plot_motifs_allele/_singularity_tmpdir_vv_uawp0/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-17/call-trgt_plot_motifs_allele/_singularity_tmpdir_vv_uawp0/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:08.977 wdl.w:ptcp.w:call-trgt-17.t:call-trgt_plot_motifs_allele NOTICE slurm_singularity run :: pid: 1200958, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-17/call-trgt_plot_motifs_allele/slurm_singularity.log.txt"
2025-09-15 20:24:08.990 wdl.w:ptcp.w:call-trgt-19.t:call-trgt_plot_motifs_waterfall INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2116.motifs_waterfall.trgt_plots.zip"
2025-09-15 20:24:08.995 wdl.w:ptcp.w:call-trgt-17.t:call-trgt_plot_motifs_waterfall INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-17/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_7sbp1128"
2025-09-15 20:24:08.995 wdl.w:ptcp.w:call-trgt-17.t:call-trgt_plot_motifs_waterfall INFO Slurm invocation: srun --job-name call-trgt_plot_motifs_waterfall --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-17/call-trgt_plot_motifs_waterfall/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-17/call-trgt_plot_motifs_waterfall/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-17/call-trgt_plot_motifs_waterfall/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-17/call-trgt_plot_motifs_waterfall/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-17/call-trgt_genotype/out/m84036_250809_035451_s4.bc2114.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2114.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-17/call-trgt_genotype/out/m84036_250809_035451_s4.bc2114.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2114.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-17/call-trgt_genotype/out/m84036_250809_035451_s4.bc2114.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2114.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-17/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_7sbp1128/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-17/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_7sbp1128/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:09.006 wdl.w:ptcp.w:call-trgt-17.t:call-trgt_plot_motifs_waterfall NOTICE slurm_singularity run :: pid: 1200960, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-17/call-trgt_plot_motifs_waterfall/slurm_singularity.log.txt"
2025-09-15 20:24:09.019 wdl.w:ptcp.w:call-trgt-19.t:call-trgt_plot_motifs_allele NOTICE done
2025-09-15 20:24:09.024 wdl.w:ptcp.w:call-trgt-19 NOTICE finish :: job: "call-trgt_plot_motifs_allele"
2025-09-15 20:24:09.025 wdl.w:ptcp.w:call-trgt-19 INFO output :: job: "call-trgt_plot_motifs_allele", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-19/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2116.motifs_allele.trgt_plots.zip"}
2025-09-15 20:24:09.025 wdl.w:ptcp.w:call-trgt-19 INFO visit :: node: "output-images_motifs_allele", values: {"images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-19/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2116.motifs_allele.trgt_plots.zip"}
2025-09-15 20:24:09.033 wdl.w:ptcp.w:call-trgt-28.t:call-trgt_plot_meth_allele NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-28/call-trgt_plot_meth_allele", thread: 140608731588160
2025-09-15 20:24:09.056 wdl.w:ptcp.w:call-trgt-28.t:call-trgt_plot_meth_allele INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:09.056 wdl.w:ptcp.w:call-trgt-28.t:call-trgt_plot_meth_allele INFO input :: name: "waterfall", value: false
2025-09-15 20:24:09.056 wdl.w:ptcp.w:call-trgt-28.t:call-trgt_plot_meth_allele INFO input :: name: "methylation", value: true
2025-09-15 20:24:09.056 wdl.w:ptcp.w:call-trgt-28.t:call-trgt_plot_meth_allele INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:09.056 wdl.w:ptcp.w:call-trgt-28.t:call-trgt_plot_meth_allele INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:09.056 wdl.w:ptcp.w:call-trgt-28.t:call-trgt_plot_meth_allele INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:09.056 wdl.w:ptcp.w:call-trgt-28.t:call-trgt_plot_meth_allele INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2125.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:09.056 wdl.w:ptcp.w:call-trgt-28.t:call-trgt_plot_meth_allele INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2125.trgt.sorted.spanning.bam"
2025-09-15 20:24:09.056 wdl.w:ptcp.w:call-trgt-28.t:call-trgt_plot_meth_allele INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2125.trgt.vcf"
2025-09-15 20:24:09.057 wdl.w:ptcp.w:call-trgt-28.t:call-trgt_plot_meth_allele INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2125"
2025-09-15 20:24:09.057 wdl.w:ptcp.w:call-trgt-28.t:call-trgt_plot_meth_allele INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:09.057 wdl.w:ptcp.w:call-trgt-28.t:call-trgt_plot_meth_allele INFO eval :: name: "plot_type", value: "allele"
2025-09-15 20:24:09.057 wdl.w:ptcp.w:call-trgt-28.t:call-trgt_plot_meth_allele INFO eval :: name: "show", value: "meth"
2025-09-15 20:24:09.057 wdl.w:ptcp.w:call-trgt-28.t:call-trgt_plot_meth_allele INFO eval :: name: "threads", value: 1
2025-09-15 20:24:09.057 wdl.w:ptcp.w:call-trgt-28.t:call-trgt_plot_meth_allele INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:09.057 wdl.w:ptcp.w:call-trgt-28.t:call-trgt_plot_meth_allele INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2125.meth_allele"
2025-09-15 20:24:09.059 wdl.w:ptcp.w:call-trgt-28.t:call-trgt_plot_meth_allele INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:09.059 wdl.w:ptcp.w:call-trgt-28.t:call-trgt_plot_meth_allele WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:09.059 wdl.w:ptcp.w:call-trgt-17.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO srun: job 51797557 queued and waiting for resources
2025-09-15 20:24:09.059 wdl.w:ptcp.w:call-trgt-17.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO srun: job 51797557 has been allocated resources
2025-09-15 20:24:09.060 wdl.w:ptcp.w:call-trgt-17.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:09.060 wdl.w:ptcp.w:call-trgt-28.t:call-trgt_plot_meth_allele INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:09.060 wdl.w:ptcp.w:call-trgt-28.t:call-trgt_plot_meth_allele INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:09.083 wdl.w:ptcp.w:call-trgt-19.t:call-trgt_plot_motifs_waterfall NOTICE done
2025-09-15 20:24:09.088 wdl.w:ptcp.w:call-trgt-19 NOTICE finish :: job: "call-trgt_plot_motifs_waterfall"
2025-09-15 20:24:09.088 wdl.w:ptcp.w:call-trgt-19 INFO output :: job: "call-trgt_plot_motifs_waterfall", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-19/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2116.motifs_waterfall.trgt_plots.zip"}
2025-09-15 20:24:09.088 wdl.w:ptcp.w:call-trgt-19 INFO visit :: node: "output-images_motifs_waterfall", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-19/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2116.motifs_waterfall.trgt_plots.zip"}
2025-09-15 20:24:09.089 wdl.w:ptcp.w:call-trgt-19 INFO visit :: node: "outputs", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-19/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2116.motifs_waterfall.trgt_plots.zip", "images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-19/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2116.meth_allele.trgt_plots.zip", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-19/call-trgt_genotype/out/m84036_250809_035451_s4.bc2116.trgt.sorted.spanning.bam.bai", "images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-19/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2116.motifs_allele.trgt_plots.zip", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-19/call-trgt_genotype/out/m84036_250809_035451_s4.bc2116.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-19/call-trgt_genotype/out/m84036_250809_035451_s4.bc2116.trgt.vcf", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-19/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2116.repeats.bam", "images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-19/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2116.meth_waterfall.trgt_plots.zip", "reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-19/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2116.repeats.bam.bai"}
2025-09-15 20:24:09.091 wdl.w:ptcp.t:call-pbmm2_align_hifi-74 INFO output :: name: "mapped_bam", value: "m84036_250809_035451_s4.bc2171.mapped.bam"
2025-09-15 20:24:09.095 wdl.w:ptcp.t:call-pbmm2_align_hifi-74 INFO output :: name: "mapped_bam_bai", value: "m84036_250809_035451_s4.bc2171.mapped.bam.bai"
2025-09-15 20:24:09.096 wdl.w:ptcp.w:call-trgt-28.t:call-trgt_plot_meth_waterfall NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-28/call-trgt_plot_meth_waterfall", thread: 140609822115392
2025-09-15 20:24:09.096 wdl.w:ptcp.t:call-pbmm2_align_hifi-74 INFO output :: name: "mapped_bam_pbi", value: "m84036_250809_035451_s4.bc2171.mapped.bam.pbi"
2025-09-15 20:24:09.097 wdl.w:ptcp.t:call-pbmm2_align_hifi-74 INFO output :: name: "report", value: "mapping_stats.report.json"
2025-09-15 20:24:09.116 wdl.w:ptcp.w:call-trgt-28.t:call-trgt_plot_meth_waterfall INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:09.116 wdl.w:ptcp.w:call-trgt-28.t:call-trgt_plot_meth_waterfall INFO input :: name: "waterfall", value: true
2025-09-15 20:24:09.116 wdl.w:ptcp.w:call-trgt-28.t:call-trgt_plot_meth_waterfall INFO input :: name: "methylation", value: true
2025-09-15 20:24:09.116 wdl.w:ptcp.w:call-trgt-28.t:call-trgt_plot_meth_waterfall INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:09.116 wdl.w:ptcp.w:call-trgt-28.t:call-trgt_plot_meth_waterfall INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:09.116 wdl.w:ptcp.w:call-trgt-28.t:call-trgt_plot_meth_waterfall INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:09.116 wdl.w:ptcp.w:call-trgt-28.t:call-trgt_plot_meth_waterfall INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2125.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:09.116 wdl.w:ptcp.w:call-trgt-28.t:call-trgt_plot_meth_waterfall INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2125.trgt.sorted.spanning.bam"
2025-09-15 20:24:09.116 wdl.w:ptcp.w:call-trgt-28.t:call-trgt_plot_meth_waterfall INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2125.trgt.vcf"
2025-09-15 20:24:09.116 wdl.w:ptcp.w:call-trgt-28.t:call-trgt_plot_meth_waterfall INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2125"
2025-09-15 20:24:09.116 wdl.w:ptcp.w:call-trgt-28.t:call-trgt_plot_meth_waterfall INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:09.117 wdl.w:ptcp.w:call-trgt-28.t:call-trgt_plot_meth_waterfall INFO eval :: name: "plot_type", value: "waterfall"
2025-09-15 20:24:09.117 wdl.w:ptcp.w:call-trgt-28.t:call-trgt_plot_meth_waterfall INFO eval :: name: "show", value: "meth"
2025-09-15 20:24:09.117 wdl.w:ptcp.w:call-trgt-28.t:call-trgt_plot_meth_waterfall INFO eval :: name: "threads", value: 1
2025-09-15 20:24:09.117 wdl.w:ptcp.w:call-trgt-28.t:call-trgt_plot_meth_waterfall INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:09.117 wdl.w:ptcp.w:call-trgt-28.t:call-trgt_plot_meth_waterfall INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2125.meth_waterfall"
2025-09-15 20:24:09.118 wdl.w:ptcp.w:call-trgt-28.t:call-trgt_plot_meth_waterfall INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:09.118 wdl.w:ptcp.w:call-trgt-28.t:call-trgt_plot_meth_waterfall WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:09.119 wdl.w:ptcp.w:call-trgt-28.t:call-trgt_plot_meth_waterfall INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:09.119 wdl.w:ptcp.w:call-trgt-28.t:call-trgt_plot_meth_waterfall INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:09.155 wdl.w:ptcp.w:call-trgt-28.t:call-trgt_plot_meth_allele INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-28/call-trgt_plot_meth_allele/_singularity_tmpdir_0n0bl7u9"
2025-09-15 20:24:09.156 wdl.w:ptcp.w:call-trgt-28.t:call-trgt_plot_meth_allele INFO Slurm invocation: srun --job-name call-trgt_plot_meth_allele --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-28/call-trgt_plot_meth_allele/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-28/call-trgt_plot_meth_allele/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-28/call-trgt_plot_meth_allele/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-28/call-trgt_plot_meth_allele/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-28/call-trgt_genotype/out/m84036_250809_035451_s4.bc2125.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2125.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-28/call-trgt_genotype/out/m84036_250809_035451_s4.bc2125.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2125.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-28/call-trgt_genotype/out/m84036_250809_035451_s4.bc2125.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2125.trgt.sorted.spanning.bam:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-28/call-trgt_plot_meth_allele/_singularity_tmpdir_0n0bl7u9/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-28/call-trgt_plot_meth_allele/_singularity_tmpdir_0n0bl7u9/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:09.175 wdl.w:ptcp.w:call-trgt-28.t:call-trgt_plot_meth_allele NOTICE slurm_singularity run :: pid: 1200973, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-28/call-trgt_plot_meth_allele/slurm_singularity.log.txt"
2025-09-15 20:24:09.195 wdl.w:ptcp.t:call-pbmm2_align_hifi-74 NOTICE done
2025-09-15 20:24:09.195 wdl.w:ptcp.w:call-trgt-19 NOTICE done
2025-09-15 20:24:09.199 wdl.w:ptcp.w:call-trgt-28.t:call-trgt_plot_meth_waterfall INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-28/call-trgt_plot_meth_waterfall/_singularity_tmpdir_zyq6grny"
2025-09-15 20:24:09.199 wdl.w:ptcp.w:call-trgt-28.t:call-trgt_plot_meth_waterfall INFO Slurm invocation: srun --job-name call-trgt_plot_meth_waterfall --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-28/call-trgt_plot_meth_waterfall/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-28/call-trgt_plot_meth_waterfall/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-28/call-trgt_plot_meth_waterfall/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-28/call-trgt_plot_meth_waterfall/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-28/call-trgt_genotype/out/m84036_250809_035451_s4.bc2125.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2125.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-28/call-trgt_genotype/out/m84036_250809_035451_s4.bc2125.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2125.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-28/call-trgt_genotype/out/m84036_250809_035451_s4.bc2125.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2125.trgt.sorted.spanning.bam:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-28/call-trgt_plot_meth_waterfall/_singularity_tmpdir_zyq6grny/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-28/call-trgt_plot_meth_waterfall/_singularity_tmpdir_zyq6grny/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:09.201 wdl.w:ptcp NOTICE finish :: job: "call-trgt-19"
2025-09-15 20:24:09.201 wdl.w:ptcp INFO output :: job: "call-trgt-19", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-19/out/m84036_250809_035451_s4.bc2116.motifs_waterfall.trgt_plots.zip", "images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-19/out/m84036_250809_035451_s4.bc2116.meth_allele.trgt_plots.zip", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-19/out/m84036_250809_035451_s4.bc2116.trgt.sorted.spanning.bam.bai", "images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-19/out/m84036_250809_035451_s4.bc2116.motifs_allele.trgt_plots.zip", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-19/out/m84036_250809_035451_s4.bc2116.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-19/out/m84036_250809_035451_s4.bc2116.trgt.vcf", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-19/out/m84036_250809_035451_s4.bc2116.repeats.bam", "images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-19/out/m84036_250809_035451_s4.bc2116.meth_waterfall.trgt_plots.zip", "reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-19/out/m84036_250809_035451_s4.bc2116.repeats.bam.bai"}
2025-09-15 20:24:09.203 wdl.w:ptcp NOTICE finish :: job: "call-pbmm2_align_hifi-74"
2025-09-15 20:24:09.203 wdl.w:ptcp INFO output :: job: "call-pbmm2_align_hifi-74", values: {"report": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-74/out/mapping_stats.report.json", "mapped_bam_pbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-74/out/m84036_250809_035451_s4.bc2171.mapped.bam.pbi", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-74/out/m84036_250809_035451_s4.bc2171.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-74/out/m84036_250809_035451_s4.bc2171.mapped.bam"}
2025-09-15 20:24:09.203 wdl.w:ptcp NOTICE ready :: job: "call-paraphase-74", callee: "paraphase"
2025-09-15 20:24:09.203 wdl.w:ptcp INFO input :: job: "call-paraphase-74", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf", "genome_version": "38", "config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-74/out/m84036_250809_035451_s4.bc2171.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-74/out/m84036_250809_035451_s4.bc2171.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2171"}
2025-09-15 20:24:09.205 wdl.w:ptcp NOTICE ready :: job: "call-sawfish-74", callee: "sawfish"
2025-09-15 20:24:09.205 wdl.w:ptcp INFO input :: job: "call-sawfish-74", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-74/out/m84036_250809_035451_s4.bc2171.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-74/out/m84036_250809_035451_s4.bc2171.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2171"}
2025-09-15 20:24:09.206 wdl.w:ptcp NOTICE ready :: job: "call-trgt-74", callee: "trgt"
2025-09-15 20:24:09.206 wdl.w:ptcp INFO input :: job: "call-trgt-74", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-74/out/m84036_250809_035451_s4.bc2171.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-74/out/m84036_250809_035451_s4.bc2171.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2171"}
2025-09-15 20:24:09.209 wdl.w:ptcp.w:call-trgt-39 NOTICE workflow start :: name: "trgt", source: "./trgt.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-39"
2025-09-15 20:24:09.209 wdl.w:ptcp.w:call-trgt-28.t:call-trgt_plot_motifs_allele NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-28/call-trgt_plot_motifs_allele", thread: 140608219895360
2025-09-15 20:24:09.214 wdl.w:ptcp.w:call-trgt-28.t:call-trgt_plot_meth_waterfall NOTICE slurm_singularity run :: pid: 1200975, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-28/call-trgt_plot_meth_waterfall/slurm_singularity.log.txt"
2025-09-15 20:24:09.230 wdl.w:ptcp.w:call-trgt-39 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:24:09.230 wdl.w:ptcp.w:call-trgt-39 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-39/out/m84036_250809_035451_s4.bc2136.mapped.bam"}
2025-09-15 20:24:09.230 wdl.w:ptcp.w:call-trgt-39 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-39/out/m84036_250809_035451_s4.bc2136.mapped.bam.bai"}
2025-09-15 20:24:09.230 wdl.w:ptcp.w:call-trgt-39 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:24:09.230 wdl.w:ptcp.w:call-trgt-39 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:24:09.230 wdl.w:ptcp.w:call-trgt-39 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2136"}
2025-09-15 20:24:09.230 wdl.w:ptcp.w:call-trgt-39 INFO visit :: node: "decl-sex", values: {"sex": "F"}
2025-09-15 20:24:09.231 wdl.w:ptcp.w:call-trgt-39 INFO visit :: node: "decl-trgt_bed", values: {"trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"}
2025-09-15 20:24:09.231 wdl.w:ptcp.w:call-trgt-39 NOTICE ready :: job: "call-get_reads_overlapping_repeats", callee: "get_reads_overlapping_repeats"
2025-09-15 20:24:09.231 wdl.w:ptcp.w:call-trgt-39 INFO input :: job: "call-get_reads_overlapping_repeats", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-39/out/m84036_250809_035451_s4.bc2136.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-39/out/m84036_250809_035451_s4.bc2136.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2136"}
2025-09-15 20:24:09.232 wdl.w:ptcp.w:call-trgt-39 NOTICE ready :: job: "call-trgt_genotype", callee: "trgt_genotype"
2025-09-15 20:24:09.232 wdl.w:ptcp.w:call-trgt-39 INFO input :: job: "call-trgt_genotype", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-39/out/m84036_250809_035451_s4.bc2136.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-39/out/m84036_250809_035451_s4.bc2136.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2136"}
2025-09-15 20:24:09.234 wdl.w:ptcp.w:call-trgt-28.t:call-trgt_plot_motifs_allele INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:09.234 wdl.w:ptcp.w:call-trgt-28.t:call-trgt_plot_motifs_allele INFO input :: name: "waterfall", value: false
2025-09-15 20:24:09.234 wdl.w:ptcp.w:call-trgt-28.t:call-trgt_plot_motifs_allele INFO input :: name: "methylation", value: false
2025-09-15 20:24:09.234 wdl.w:ptcp.w:call-trgt-28.t:call-trgt_plot_motifs_allele INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:09.234 wdl.w:ptcp.w:call-trgt-28.t:call-trgt_plot_motifs_allele INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:09.235 wdl.w:ptcp.w:call-trgt-28.t:call-trgt_plot_motifs_allele INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:09.235 wdl.w:ptcp.w:call-trgt-28.t:call-trgt_plot_motifs_allele INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2125.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:09.235 wdl.w:ptcp.w:call-trgt-28.t:call-trgt_plot_motifs_allele INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2125.trgt.sorted.spanning.bam"
2025-09-15 20:24:09.235 wdl.w:ptcp.w:call-trgt-28.t:call-trgt_plot_motifs_allele INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2125.trgt.vcf"
2025-09-15 20:24:09.235 wdl.w:ptcp.w:call-trgt-28.t:call-trgt_plot_motifs_allele INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2125"
2025-09-15 20:24:09.235 wdl.w:ptcp.w:call-trgt-28.t:call-trgt_plot_motifs_allele INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:09.235 wdl.w:ptcp.w:call-trgt-28.t:call-trgt_plot_motifs_allele INFO eval :: name: "plot_type", value: "allele"
2025-09-15 20:24:09.235 wdl.w:ptcp.w:call-trgt-28.t:call-trgt_plot_motifs_allele INFO eval :: name: "show", value: "motifs"
2025-09-15 20:24:09.235 wdl.w:ptcp.w:call-trgt-28.t:call-trgt_plot_motifs_allele INFO eval :: name: "threads", value: 1
2025-09-15 20:24:09.236 wdl.w:ptcp.w:call-trgt-28.t:call-trgt_plot_motifs_allele INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:09.236 wdl.w:ptcp.w:call-trgt-28.t:call-trgt_plot_motifs_allele INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2125.motifs_allele"
2025-09-15 20:24:09.236 wdl.w:ptcp.w:call-trgt-28.t:call-trgt_plot_motifs_allele INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:09.236 wdl.w:ptcp.w:call-trgt-28.t:call-trgt_plot_motifs_allele WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:09.237 wdl.w:ptcp.w:call-trgt-28.t:call-trgt_plot_motifs_allele INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:09.237 wdl.w:ptcp.w:call-trgt-28.t:call-trgt_plot_motifs_allele INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:09.291 wdl.w:ptcp.t:call-pbmm2_align_hifi-78 INFO output :: name: "mapped_bam", value: "m84036_250809_035451_s4.bc2175.mapped.bam"
2025-09-15 20:24:09.297 wdl.w:ptcp.t:call-pbmm2_align_hifi-78 INFO output :: name: "mapped_bam_bai", value: "m84036_250809_035451_s4.bc2175.mapped.bam.bai"
2025-09-15 20:24:09.299 wdl.w:ptcp.t:call-pbmm2_align_hifi-78 INFO output :: name: "mapped_bam_pbi", value: "m84036_250809_035451_s4.bc2175.mapped.bam.pbi"
2025-09-15 20:24:09.302 wdl.w:ptcp.t:call-pbmm2_align_hifi-78 INFO output :: name: "report", value: "mapping_stats.report.json"
2025-09-15 20:24:09.330 wdl.w:ptcp.w:call-trgt-28.t:call-trgt_plot_motifs_allele INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-28/call-trgt_plot_motifs_allele/_singularity_tmpdir_mpm9nlxg"
2025-09-15 20:24:09.330 wdl.w:ptcp.w:call-trgt-28.t:call-trgt_plot_motifs_allele INFO Slurm invocation: srun --job-name call-trgt_plot_motifs_allele --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-28/call-trgt_plot_motifs_allele/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-28/call-trgt_plot_motifs_allele/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-28/call-trgt_plot_motifs_allele/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-28/call-trgt_plot_motifs_allele/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-28/call-trgt_genotype/out/m84036_250809_035451_s4.bc2125.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2125.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-28/call-trgt_genotype/out/m84036_250809_035451_s4.bc2125.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2125.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-28/call-trgt_genotype/out/m84036_250809_035451_s4.bc2125.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2125.trgt.sorted.spanning.bam:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-28/call-trgt_plot_motifs_allele/_singularity_tmpdir_mpm9nlxg/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-28/call-trgt_plot_motifs_allele/_singularity_tmpdir_mpm9nlxg/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:09.331 wdl.w:ptcp.t:call-pbmm2_align_hifi-84 INFO output :: name: "mapped_bam", value: "m84036_250809_035451_s4.bc2181.mapped.bam"
2025-09-15 20:24:09.337 wdl.w:ptcp.t:call-pbmm2_align_hifi-84 INFO output :: name: "mapped_bam_bai", value: "m84036_250809_035451_s4.bc2181.mapped.bam.bai"
2025-09-15 20:24:09.339 wdl.w:ptcp.t:call-pbmm2_align_hifi-84 INFO output :: name: "mapped_bam_pbi", value: "m84036_250809_035451_s4.bc2181.mapped.bam.pbi"
2025-09-15 20:24:09.341 wdl.w:ptcp.t:call-pbmm2_align_hifi-84 INFO output :: name: "report", value: "mapping_stats.report.json"
2025-09-15 20:24:09.348 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:07 [ERROR] - No reads found for TRID=FECD3_TCF4
2025-09-15 20:24:09.349 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:07 [ERROR] - No reads found for TRID=OPDM2_GIPC1
2025-09-15 20:24:09.349 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:07 [ERROR] - No reads found for TRID=SCA4_ZFHX3
2025-09-15 20:24:09.349 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:07 [ERROR] - No reads found for TRID=FRA2A_AFF3
2025-09-15 20:24:09.349 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:07 [ERROR] - No reads found for TRID=SCA6_CACNA1A
2025-09-15 20:24:09.349 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:07 [ERROR] - No reads found for TRID=CJD_PRNP
2025-09-15 20:24:09.349 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:07 [ERROR] - No reads found for TRID=EPM1_CSTB
2025-09-15 20:24:09.349 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:07 [ERROR] - No reads found for TRID=SCA36_NOP56
2025-09-15 20:24:09.349 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:07 [ERROR] - No reads found for TRID=SCA7_ATXN7
2025-09-15 20:24:09.352 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:07 [ERROR] - No reads found for TRID=SCA31_BEAN1
2025-09-15 20:24:09.352 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:07 [ERROR] - No reads found for TRID=CCHS_PHOX2B
2025-09-15 20:24:09.352 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:07 [ERROR] - No reads found for TRID=SCA12_PPP2R2B
2025-09-15 20:24:09.352 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:08 [ERROR] - No reads found for TRID=OPDM1_LRP12
2025-09-15 20:24:09.352 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:08 [ERROR] - No reads found for TRID=SCA1_ATXN1
2025-09-15 20:24:09.352 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:08 [ERROR] - No reads found for TRID=FAME1_SAMD12
2025-09-15 20:24:09.353 wdl.w:ptcp.w:call-trgt-28.t:call-trgt_plot_motifs_allele NOTICE slurm_singularity run :: pid: 1200989, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-28/call-trgt_plot_motifs_allele/slurm_singularity.log.txt"
2025-09-15 20:24:09.388 wdl.w:ptcp.t:call-pbmm2_align_hifi-78 NOTICE done
2025-09-15 20:24:09.394 wdl.w:ptcp NOTICE finish :: job: "call-pbmm2_align_hifi-78"
2025-09-15 20:24:09.395 wdl.w:ptcp INFO output :: job: "call-pbmm2_align_hifi-78", values: {"report": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-78/out/mapping_stats.report.json", "mapped_bam_pbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-78/out/m84036_250809_035451_s4.bc2175.mapped.bam.pbi", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-78/out/m84036_250809_035451_s4.bc2175.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-78/out/m84036_250809_035451_s4.bc2175.mapped.bam"}
2025-09-15 20:24:09.395 wdl.w:ptcp NOTICE ready :: job: "call-paraphase-78", callee: "paraphase"
2025-09-15 20:24:09.395 wdl.w:ptcp INFO input :: job: "call-paraphase-78", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf", "genome_version": "38", "config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-78/out/m84036_250809_035451_s4.bc2175.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-78/out/m84036_250809_035451_s4.bc2175.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2175"}
2025-09-15 20:24:09.396 wdl.w:ptcp NOTICE ready :: job: "call-sawfish-78", callee: "sawfish"
2025-09-15 20:24:09.396 wdl.w:ptcp INFO input :: job: "call-sawfish-78", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-78/out/m84036_250809_035451_s4.bc2175.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-78/out/m84036_250809_035451_s4.bc2175.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2175"}
2025-09-15 20:24:09.398 wdl.w:ptcp NOTICE ready :: job: "call-trgt-78", callee: "trgt"
2025-09-15 20:24:09.398 wdl.w:ptcp INFO input :: job: "call-trgt-78", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-78/out/m84036_250809_035451_s4.bc2175.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-78/out/m84036_250809_035451_s4.bc2175.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2175"}
2025-09-15 20:24:09.402 wdl.w:ptcp.w:call-trgt-28.t:call-trgt_plot_motifs_waterfall NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-28/call-trgt_plot_motifs_waterfall", thread: 140608186324544
2025-09-15 20:24:09.424 wdl.w:ptcp.w:call-trgt-28.t:call-trgt_plot_motifs_waterfall INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:09.424 wdl.w:ptcp.w:call-trgt-28.t:call-trgt_plot_motifs_waterfall INFO input :: name: "waterfall", value: true
2025-09-15 20:24:09.424 wdl.w:ptcp.w:call-trgt-28.t:call-trgt_plot_motifs_waterfall INFO input :: name: "methylation", value: false
2025-09-15 20:24:09.425 wdl.w:ptcp.w:call-trgt-28.t:call-trgt_plot_motifs_waterfall INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:09.425 wdl.w:ptcp.w:call-trgt-28.t:call-trgt_plot_motifs_waterfall INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:09.425 wdl.w:ptcp.w:call-trgt-28.t:call-trgt_plot_motifs_waterfall INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:09.425 wdl.w:ptcp.w:call-trgt-28.t:call-trgt_plot_motifs_waterfall INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2125.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:09.425 wdl.w:ptcp.w:call-trgt-28.t:call-trgt_plot_motifs_waterfall INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2125.trgt.sorted.spanning.bam"
2025-09-15 20:24:09.425 wdl.w:ptcp.w:call-trgt-28.t:call-trgt_plot_motifs_waterfall INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2125.trgt.vcf"
2025-09-15 20:24:09.425 wdl.w:ptcp.w:call-trgt-28.t:call-trgt_plot_motifs_waterfall INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2125"
2025-09-15 20:24:09.425 wdl.w:ptcp.w:call-trgt-28.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:09.425 wdl.w:ptcp.w:call-trgt-28.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "plot_type", value: "waterfall"
2025-09-15 20:24:09.425 wdl.w:ptcp.w:call-trgt-28.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "show", value: "motifs"
2025-09-15 20:24:09.425 wdl.w:ptcp.w:call-trgt-28.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "threads", value: 1
2025-09-15 20:24:09.426 wdl.w:ptcp.w:call-trgt-28.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:09.426 wdl.w:ptcp.w:call-trgt-28.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2125.motifs_waterfall"
2025-09-15 20:24:09.426 wdl.w:ptcp.w:call-trgt-28.t:call-trgt_plot_motifs_waterfall INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:09.426 wdl.w:ptcp.w:call-trgt-28.t:call-trgt_plot_motifs_waterfall WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:09.427 wdl.w:ptcp.w:call-trgt-28.t:call-trgt_plot_motifs_waterfall INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:09.427 wdl.w:ptcp.w:call-trgt-28.t:call-trgt_plot_motifs_waterfall INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:09.437 wdl.w:ptcp.w:call-paraphase-46.t:call-run_paraphase.stderr VERBOSE INFO:root:Processing sample m84036_250809_035451_s4.bc2143 at 2025-09-15 20:24:07.259674...
2025-09-15 20:24:09.438 wdl.w:ptcp.w:call-paraphase-46.t:call-run_paraphase.stderr VERBOSE INFO:root:Checking sample sex at 2025-09-15 20:24:07.262756...
2025-09-15 20:24:09.439 wdl.w:ptcp.w:call-paraphase-46.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for gba for sample m84036_250809_035451_s4.bc2143 at 2025-09-15 20:24:07.327472...
2025-09-15 20:24:09.439 wdl.w:ptcp.w:call-paraphase-46.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for gba for sample m84036_250809_035451_s4.bc2143 at 2025-09-15 20:24:07.328056...
2025-09-15 20:24:09.439 wdl.w:ptcp.w:call-paraphase-46.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for cyp21 for sample m84036_250809_035451_s4.bc2143 at 2025-09-15 20:24:07.327460...
2025-09-15 20:24:09.439 wdl.w:ptcp.w:call-paraphase-46.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for cyp21 for sample m84036_250809_035451_s4.bc2143 at 2025-09-15 20:24:07.328239...
2025-09-15 20:24:09.439 wdl.w:ptcp.w:call-paraphase-46.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for smn1 for sample m84036_250809_035451_s4.bc2143 at 2025-09-15 20:24:07.327671...
2025-09-15 20:24:09.439 wdl.w:ptcp.w:call-paraphase-46.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for smn1 for sample m84036_250809_035451_s4.bc2143 at 2025-09-15 20:24:07.328369...
2025-09-15 20:24:09.439 wdl.w:ptcp.w:call-paraphase-46.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for hba for sample m84036_250809_035451_s4.bc2143 at 2025-09-15 20:24:07.329567...
2025-09-15 20:24:09.439 wdl.w:ptcp.w:call-paraphase-46.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for hba for sample m84036_250809_035451_s4.bc2143 at 2025-09-15 20:24:07.330049...
2025-09-15 20:24:09.441 wdl.w:ptcp.t:call-pbmm2_align_hifi-84 NOTICE done
2025-09-15 20:24:09.447 wdl.w:ptcp NOTICE finish :: job: "call-pbmm2_align_hifi-84"
2025-09-15 20:24:09.447 wdl.w:ptcp INFO output :: job: "call-pbmm2_align_hifi-84", values: {"report": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-84/out/mapping_stats.report.json", "mapped_bam_pbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-84/out/m84036_250809_035451_s4.bc2181.mapped.bam.pbi", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-84/out/m84036_250809_035451_s4.bc2181.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-84/out/m84036_250809_035451_s4.bc2181.mapped.bam"}
2025-09-15 20:24:09.448 wdl.w:ptcp NOTICE ready :: job: "call-paraphase-84", callee: "paraphase"
2025-09-15 20:24:09.448 wdl.w:ptcp INFO input :: job: "call-paraphase-84", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf", "genome_version": "38", "config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-84/out/m84036_250809_035451_s4.bc2181.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-84/out/m84036_250809_035451_s4.bc2181.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2181"}
2025-09-15 20:24:09.449 wdl.w:ptcp NOTICE ready :: job: "call-sawfish-84", callee: "sawfish"
2025-09-15 20:24:09.449 wdl.w:ptcp INFO input :: job: "call-sawfish-84", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-84/out/m84036_250809_035451_s4.bc2181.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-84/out/m84036_250809_035451_s4.bc2181.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2181"}
2025-09-15 20:24:09.450 wdl.w:ptcp NOTICE ready :: job: "call-trgt-84", callee: "trgt"
2025-09-15 20:24:09.450 wdl.w:ptcp INFO input :: job: "call-trgt-84", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-84/out/m84036_250809_035451_s4.bc2181.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-84/out/m84036_250809_035451_s4.bc2181.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2181"}
2025-09-15 20:24:09.453 wdl.w:ptcp.w:call-trgt-30.t:call-trgt_plot_meth_allele NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-30/call-trgt_plot_meth_allele", thread: 140607657846336
2025-09-15 20:24:09.460 wdl.w:ptcp.w:call-paraphase-26.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for f8inv1 for sample m84036_250809_035451_s4.bc2123 at 2025-09-15 20:24:04.147126...
2025-09-15 20:24:09.460 wdl.w:ptcp.w:call-paraphase-26.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for f8inv1 for sample m84036_250809_035451_s4.bc2123 at 2025-09-15 20:24:04.148342...
2025-09-15 20:24:09.472 wdl.w:ptcp.w:call-trgt-30.t:call-trgt_plot_meth_allele INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:09.472 wdl.w:ptcp.w:call-trgt-30.t:call-trgt_plot_meth_allele INFO input :: name: "waterfall", value: false
2025-09-15 20:24:09.472 wdl.w:ptcp.w:call-trgt-30.t:call-trgt_plot_meth_allele INFO input :: name: "methylation", value: true
2025-09-15 20:24:09.472 wdl.w:ptcp.w:call-trgt-30.t:call-trgt_plot_meth_allele INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:09.473 wdl.w:ptcp.w:call-trgt-30.t:call-trgt_plot_meth_allele INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:09.473 wdl.w:ptcp.w:call-trgt-30.t:call-trgt_plot_meth_allele INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:09.473 wdl.w:ptcp.w:call-trgt-30.t:call-trgt_plot_meth_allele INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2127.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:09.473 wdl.w:ptcp.w:call-trgt-30.t:call-trgt_plot_meth_allele INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2127.trgt.sorted.spanning.bam"
2025-09-15 20:24:09.473 wdl.w:ptcp.w:call-trgt-30.t:call-trgt_plot_meth_allele INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2127.trgt.vcf"
2025-09-15 20:24:09.473 wdl.w:ptcp.w:call-trgt-30.t:call-trgt_plot_meth_allele INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2127"
2025-09-15 20:24:09.473 wdl.w:ptcp.w:call-trgt-30.t:call-trgt_plot_meth_allele INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:09.473 wdl.w:ptcp.w:call-trgt-30.t:call-trgt_plot_meth_allele INFO eval :: name: "plot_type", value: "allele"
2025-09-15 20:24:09.473 wdl.w:ptcp.w:call-trgt-30.t:call-trgt_plot_meth_allele INFO eval :: name: "show", value: "meth"
2025-09-15 20:24:09.473 wdl.w:ptcp.w:call-trgt-30.t:call-trgt_plot_meth_allele INFO eval :: name: "threads", value: 1
2025-09-15 20:24:09.474 wdl.w:ptcp.w:call-trgt-30.t:call-trgt_plot_meth_allele INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:09.474 wdl.w:ptcp.w:call-trgt-30.t:call-trgt_plot_meth_allele INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2127.meth_allele"
2025-09-15 20:24:09.474 wdl.w:ptcp.w:call-trgt-30.t:call-trgt_plot_meth_allele INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:09.474 wdl.w:ptcp.w:call-trgt-30.t:call-trgt_plot_meth_allele WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:09.475 wdl.w:ptcp.w:call-trgt-30.t:call-trgt_plot_meth_allele INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:09.475 wdl.w:ptcp.w:call-trgt-30.t:call-trgt_plot_meth_allele INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:09.502 wdl.w:ptcp.w:call-trgt-28.t:call-trgt_plot_motifs_waterfall INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-28/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_8snf93ti"
2025-09-15 20:24:09.502 wdl.w:ptcp.w:call-trgt-28.t:call-trgt_plot_motifs_waterfall INFO Slurm invocation: srun --job-name call-trgt_plot_motifs_waterfall --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-28/call-trgt_plot_motifs_waterfall/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-28/call-trgt_plot_motifs_waterfall/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-28/call-trgt_plot_motifs_waterfall/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-28/call-trgt_plot_motifs_waterfall/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-28/call-trgt_genotype/out/m84036_250809_035451_s4.bc2125.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2125.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-28/call-trgt_genotype/out/m84036_250809_035451_s4.bc2125.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2125.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-28/call-trgt_genotype/out/m84036_250809_035451_s4.bc2125.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2125.trgt.sorted.spanning.bam:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-28/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_8snf93ti/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-28/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_8snf93ti/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:09.524 wdl.w:ptcp.w:call-trgt-28.t:call-trgt_plot_motifs_waterfall NOTICE slurm_singularity run :: pid: 1200991, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-28/call-trgt_plot_motifs_waterfall/slurm_singularity.log.txt"
2025-09-15 20:24:09.540 wdl.w:ptcp.w:call-trgt-30.t:call-trgt_plot_meth_allele INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-30/call-trgt_plot_meth_allele/_singularity_tmpdir_6ivfsnbl"
2025-09-15 20:24:09.540 wdl.w:ptcp.w:call-trgt-30.t:call-trgt_plot_meth_allele INFO Slurm invocation: srun --job-name call-trgt_plot_meth_allele --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-30/call-trgt_plot_meth_allele/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-30/call-trgt_plot_meth_allele/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-30/call-trgt_plot_meth_allele/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-30/call-trgt_plot_meth_allele/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-30/call-trgt_genotype/out/m84036_250809_035451_s4.bc2127.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2127.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-30/call-trgt_genotype/out/m84036_250809_035451_s4.bc2127.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2127.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-30/call-trgt_genotype/out/m84036_250809_035451_s4.bc2127.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2127.trgt.vcf:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-30/call-trgt_plot_meth_allele/_singularity_tmpdir_6ivfsnbl/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-30/call-trgt_plot_meth_allele/_singularity_tmpdir_6ivfsnbl/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:09.549 wdl.w:ptcp.w:call-trgt-30.t:call-trgt_plot_meth_allele NOTICE slurm_singularity run :: pid: 1200993, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-30/call-trgt_plot_meth_allele/slurm_singularity.log.txt"
2025-09-15 20:24:09.628 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:08 [ERROR] - No reads found for TRID=SBMA_AR
2025-09-15 20:24:09.676 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_plot_meth_allele INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2107.meth_allele.trgt_plots.zip"
2025-09-15 20:24:09.752 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_plot_meth_allele NOTICE done
2025-09-15 20:24:09.757 wdl.w:ptcp.w:call-trgt-10 NOTICE finish :: job: "call-trgt_plot_meth_allele"
2025-09-15 20:24:09.757 wdl.w:ptcp.w:call-trgt-10 INFO output :: job: "call-trgt_plot_meth_allele", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-10/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2107.meth_allele.trgt_plots.zip"}
2025-09-15 20:24:09.758 wdl.w:ptcp.w:call-trgt-10 INFO visit :: node: "output-images_meth_allele", values: {"images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-10/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2107.meth_allele.trgt_plots.zip"}
2025-09-15 20:24:09.762 wdl.w:ptcp.w:call-trgt-30.t:call-trgt_plot_meth_waterfall NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-30/call-trgt_plot_meth_waterfall", thread: 140608773551680
2025-09-15 20:24:09.765 wdl.w:ptcp.w:call-trgt-21.t:call-trgt_plot_motifs_allele.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:09.779 wdl.w:ptcp.w:call-trgt-30.t:call-trgt_plot_meth_waterfall INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:09.779 wdl.w:ptcp.w:call-trgt-30.t:call-trgt_plot_meth_waterfall INFO input :: name: "waterfall", value: true
2025-09-15 20:24:09.779 wdl.w:ptcp.w:call-trgt-30.t:call-trgt_plot_meth_waterfall INFO input :: name: "methylation", value: true
2025-09-15 20:24:09.780 wdl.w:ptcp.w:call-trgt-30.t:call-trgt_plot_meth_waterfall INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:09.780 wdl.w:ptcp.w:call-trgt-30.t:call-trgt_plot_meth_waterfall INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:09.780 wdl.w:ptcp.w:call-trgt-30.t:call-trgt_plot_meth_waterfall INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:09.780 wdl.w:ptcp.w:call-trgt-30.t:call-trgt_plot_meth_waterfall INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2127.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:09.780 wdl.w:ptcp.w:call-trgt-30.t:call-trgt_plot_meth_waterfall INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2127.trgt.sorted.spanning.bam"
2025-09-15 20:24:09.780 wdl.w:ptcp.w:call-trgt-30.t:call-trgt_plot_meth_waterfall INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2127.trgt.vcf"
2025-09-15 20:24:09.780 wdl.w:ptcp.w:call-trgt-30.t:call-trgt_plot_meth_waterfall INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2127"
2025-09-15 20:24:09.780 wdl.w:ptcp.w:call-trgt-30.t:call-trgt_plot_meth_waterfall INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:09.780 wdl.w:ptcp.w:call-trgt-30.t:call-trgt_plot_meth_waterfall INFO eval :: name: "plot_type", value: "waterfall"
2025-09-15 20:24:09.780 wdl.w:ptcp.w:call-trgt-30.t:call-trgt_plot_meth_waterfall INFO eval :: name: "show", value: "meth"
2025-09-15 20:24:09.780 wdl.w:ptcp.w:call-trgt-30.t:call-trgt_plot_meth_waterfall INFO eval :: name: "threads", value: 1
2025-09-15 20:24:09.781 wdl.w:ptcp.w:call-trgt-30.t:call-trgt_plot_meth_waterfall INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:09.781 wdl.w:ptcp.w:call-trgt-30.t:call-trgt_plot_meth_waterfall INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2127.meth_waterfall"
2025-09-15 20:24:09.781 wdl.w:ptcp.w:call-trgt-30.t:call-trgt_plot_meth_waterfall INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:09.781 wdl.w:ptcp.w:call-trgt-30.t:call-trgt_plot_meth_waterfall WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:09.782 wdl.w:ptcp.w:call-trgt-30.t:call-trgt_plot_meth_waterfall INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:09.782 wdl.w:ptcp.w:call-trgt-30.t:call-trgt_plot_meth_waterfall INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:09.839 wdl.w:ptcp.w:call-trgt-30.t:call-trgt_plot_meth_waterfall INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-30/call-trgt_plot_meth_waterfall/_singularity_tmpdir_lrvtmbwi"
2025-09-15 20:24:09.840 wdl.w:ptcp.w:call-trgt-30.t:call-trgt_plot_meth_waterfall INFO Slurm invocation: srun --job-name call-trgt_plot_meth_waterfall --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-30/call-trgt_plot_meth_waterfall/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-30/call-trgt_plot_meth_waterfall/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-30/call-trgt_plot_meth_waterfall/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-30/call-trgt_plot_meth_waterfall/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-30/call-trgt_genotype/out/m84036_250809_035451_s4.bc2127.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2127.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-30/call-trgt_genotype/out/m84036_250809_035451_s4.bc2127.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2127.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-30/call-trgt_genotype/out/m84036_250809_035451_s4.bc2127.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2127.trgt.vcf:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-30/call-trgt_plot_meth_waterfall/_singularity_tmpdir_lrvtmbwi/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-30/call-trgt_plot_meth_waterfall/_singularity_tmpdir_lrvtmbwi/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:09.855 wdl.w:ptcp.w:call-trgt-30.t:call-trgt_plot_meth_waterfall NOTICE slurm_singularity run :: pid: 1201080, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-30/call-trgt_plot_meth_waterfall/slurm_singularity.log.txt"
2025-09-15 20:24:09.987 wdl.w:ptcp.w:call-trgt-17.t:call-trgt_plot_motifs_allele.slurm_singularity INFO srun: job 51797558 queued and waiting for resources
2025-09-15 20:24:09.987 wdl.w:ptcp.w:call-trgt-17.t:call-trgt_plot_motifs_allele.slurm_singularity INFO srun: job 51797558 has been allocated resources
2025-09-15 20:24:09.987 wdl.w:ptcp.w:call-trgt-17.t:call-trgt_plot_motifs_allele.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:10.017 wdl.w:ptcp.w:call-trgt-17.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO srun: job 51797559 queued and waiting for resources
2025-09-15 20:24:10.018 wdl.w:ptcp.w:call-trgt-17.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO srun: job 51797559 has been allocated resources
2025-09-15 20:24:10.018 wdl.w:ptcp.w:call-trgt-17.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:10.035 wdl.w:ptcp.t:call-pbmm2_align_hifi-76 INFO output :: name: "mapped_bam", value: "m84036_250809_035451_s4.bc2173.mapped.bam"
2025-09-15 20:24:10.038 wdl.w:ptcp.t:call-pbmm2_align_hifi-76 INFO output :: name: "mapped_bam_bai", value: "m84036_250809_035451_s4.bc2173.mapped.bam.bai"
2025-09-15 20:24:10.039 wdl.w:ptcp.t:call-pbmm2_align_hifi-76 INFO output :: name: "mapped_bam_pbi", value: "m84036_250809_035451_s4.bc2173.mapped.bam.pbi"
2025-09-15 20:24:10.041 wdl.w:ptcp.t:call-pbmm2_align_hifi-76 INFO output :: name: "report", value: "mapping_stats.report.json"
2025-09-15 20:24:10.050 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_plot_meth_waterfall INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2107.meth_waterfall.trgt_plots.zip"
2025-09-15 20:24:10.125 wdl.w:ptcp.t:call-pbmm2_align_hifi-76 NOTICE done
2025-09-15 20:24:10.131 wdl.w:ptcp NOTICE finish :: job: "call-pbmm2_align_hifi-76"
2025-09-15 20:24:10.131 wdl.w:ptcp INFO output :: job: "call-pbmm2_align_hifi-76", values: {"report": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-76/out/mapping_stats.report.json", "mapped_bam_pbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-76/out/m84036_250809_035451_s4.bc2173.mapped.bam.pbi", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-76/out/m84036_250809_035451_s4.bc2173.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-76/out/m84036_250809_035451_s4.bc2173.mapped.bam"}
2025-09-15 20:24:10.132 wdl.w:ptcp NOTICE ready :: job: "call-paraphase-76", callee: "paraphase"
2025-09-15 20:24:10.132 wdl.w:ptcp INFO input :: job: "call-paraphase-76", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf", "genome_version": "38", "config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-76/out/m84036_250809_035451_s4.bc2173.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-76/out/m84036_250809_035451_s4.bc2173.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2173"}
2025-09-15 20:24:10.133 wdl.w:ptcp NOTICE ready :: job: "call-sawfish-76", callee: "sawfish"
2025-09-15 20:24:10.133 wdl.w:ptcp INFO input :: job: "call-sawfish-76", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-76/out/m84036_250809_035451_s4.bc2173.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-76/out/m84036_250809_035451_s4.bc2173.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2173"}
2025-09-15 20:24:10.134 wdl.w:ptcp NOTICE ready :: job: "call-trgt-76", callee: "trgt"
2025-09-15 20:24:10.135 wdl.w:ptcp INFO input :: job: "call-trgt-76", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-76/out/m84036_250809_035451_s4.bc2173.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-76/out/m84036_250809_035451_s4.bc2173.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2173"}
2025-09-15 20:24:10.137 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_plot_meth_waterfall NOTICE done
2025-09-15 20:24:10.138 wdl.w:ptcp.w:call-trgt-30.t:call-trgt_plot_motifs_allele NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-30/call-trgt_plot_motifs_allele", thread: 140608203109952
2025-09-15 20:24:10.143 wdl.w:ptcp.w:call-trgt-10 NOTICE finish :: job: "call-trgt_plot_meth_waterfall"
2025-09-15 20:24:10.144 wdl.w:ptcp.w:call-trgt-10 INFO output :: job: "call-trgt_plot_meth_waterfall", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-10/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2107.meth_waterfall.trgt_plots.zip"}
2025-09-15 20:24:10.144 wdl.w:ptcp.w:call-trgt-10 INFO visit :: node: "output-images_meth_waterfall", values: {"images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-10/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2107.meth_waterfall.trgt_plots.zip"}
2025-09-15 20:24:10.149 wdl.w:ptcp.w:call-trgt-30.t:call-trgt_plot_motifs_waterfall NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-30/call-trgt_plot_motifs_waterfall", thread: 140613823374912
2025-09-15 20:24:10.155 wdl.w:ptcp.w:call-trgt-30.t:call-trgt_plot_motifs_allele INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:10.156 wdl.w:ptcp.w:call-trgt-30.t:call-trgt_plot_motifs_allele INFO input :: name: "waterfall", value: false
2025-09-15 20:24:10.156 wdl.w:ptcp.w:call-trgt-30.t:call-trgt_plot_motifs_allele INFO input :: name: "methylation", value: false
2025-09-15 20:24:10.156 wdl.w:ptcp.w:call-trgt-30.t:call-trgt_plot_motifs_allele INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:10.156 wdl.w:ptcp.w:call-trgt-30.t:call-trgt_plot_motifs_allele INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:10.156 wdl.w:ptcp.w:call-trgt-30.t:call-trgt_plot_motifs_allele INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:10.156 wdl.w:ptcp.w:call-trgt-30.t:call-trgt_plot_motifs_allele INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2127.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:10.156 wdl.w:ptcp.w:call-trgt-30.t:call-trgt_plot_motifs_allele INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2127.trgt.sorted.spanning.bam"
2025-09-15 20:24:10.156 wdl.w:ptcp.w:call-trgt-30.t:call-trgt_plot_motifs_allele INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2127.trgt.vcf"
2025-09-15 20:24:10.156 wdl.w:ptcp.w:call-trgt-30.t:call-trgt_plot_motifs_allele INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2127"
2025-09-15 20:24:10.157 wdl.w:ptcp.w:call-trgt-30.t:call-trgt_plot_motifs_allele INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:10.157 wdl.w:ptcp.w:call-trgt-30.t:call-trgt_plot_motifs_allele INFO eval :: name: "plot_type", value: "allele"
2025-09-15 20:24:10.157 wdl.w:ptcp.w:call-trgt-30.t:call-trgt_plot_motifs_allele INFO eval :: name: "show", value: "motifs"
2025-09-15 20:24:10.157 wdl.w:ptcp.w:call-trgt-30.t:call-trgt_plot_motifs_allele INFO eval :: name: "threads", value: 1
2025-09-15 20:24:10.158 wdl.w:ptcp.w:call-trgt-30.t:call-trgt_plot_motifs_allele INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:10.158 wdl.w:ptcp.w:call-trgt-30.t:call-trgt_plot_motifs_allele INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2127.motifs_allele"
2025-09-15 20:24:10.159 wdl.w:ptcp.w:call-trgt-30.t:call-trgt_plot_motifs_allele INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:10.159 wdl.w:ptcp.w:call-trgt-30.t:call-trgt_plot_motifs_allele WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:10.159 wdl.w:ptcp.w:call-trgt-30.t:call-trgt_plot_motifs_allele INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:10.159 wdl.w:ptcp.w:call-trgt-30.t:call-trgt_plot_motifs_allele INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:10.165 wdl.w:ptcp.w:call-trgt-30.t:call-trgt_plot_motifs_waterfall INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:10.165 wdl.w:ptcp.w:call-trgt-30.t:call-trgt_plot_motifs_waterfall INFO input :: name: "waterfall", value: true
2025-09-15 20:24:10.165 wdl.w:ptcp.w:call-trgt-30.t:call-trgt_plot_motifs_waterfall INFO input :: name: "methylation", value: false
2025-09-15 20:24:10.165 wdl.w:ptcp.w:call-trgt-30.t:call-trgt_plot_motifs_waterfall INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:10.165 wdl.w:ptcp.w:call-trgt-30.t:call-trgt_plot_motifs_waterfall INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:10.165 wdl.w:ptcp.w:call-trgt-30.t:call-trgt_plot_motifs_waterfall INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:10.165 wdl.w:ptcp.w:call-trgt-30.t:call-trgt_plot_motifs_waterfall INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2127.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:10.165 wdl.w:ptcp.w:call-trgt-30.t:call-trgt_plot_motifs_waterfall INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2127.trgt.sorted.spanning.bam"
2025-09-15 20:24:10.165 wdl.w:ptcp.w:call-trgt-30.t:call-trgt_plot_motifs_waterfall INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2127.trgt.vcf"
2025-09-15 20:24:10.165 wdl.w:ptcp.w:call-trgt-30.t:call-trgt_plot_motifs_waterfall INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2127"
2025-09-15 20:24:10.166 wdl.w:ptcp.w:call-trgt-30.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:10.166 wdl.w:ptcp.w:call-trgt-30.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "plot_type", value: "waterfall"
2025-09-15 20:24:10.166 wdl.w:ptcp.w:call-trgt-30.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "show", value: "motifs"
2025-09-15 20:24:10.166 wdl.w:ptcp.w:call-trgt-30.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "threads", value: 1
2025-09-15 20:24:10.166 wdl.w:ptcp.w:call-trgt-30.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:10.166 wdl.w:ptcp.w:call-trgt-30.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2127.motifs_waterfall"
2025-09-15 20:24:10.167 wdl.w:ptcp.w:call-trgt-30.t:call-trgt_plot_motifs_waterfall INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:10.167 wdl.w:ptcp.w:call-trgt-30.t:call-trgt_plot_motifs_waterfall WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:10.167 wdl.w:ptcp.w:call-trgt-30.t:call-trgt_plot_motifs_waterfall INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:10.167 wdl.w:ptcp.w:call-trgt-30.t:call-trgt_plot_motifs_waterfall INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:10.187 wdl.w:ptcp.w:call-trgt-28.t:call-trgt_plot_meth_allele.slurm_singularity INFO srun: job 51797560 queued and waiting for resources
2025-09-15 20:24:10.187 wdl.w:ptcp.w:call-trgt-28.t:call-trgt_plot_meth_allele.slurm_singularity INFO srun: job 51797560 has been allocated resources
2025-09-15 20:24:10.187 wdl.w:ptcp.w:call-trgt-28.t:call-trgt_plot_meth_allele.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:10.225 wdl.w:ptcp.w:call-trgt-28.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO srun: job 51797561 queued and waiting for resources
2025-09-15 20:24:10.225 wdl.w:ptcp.w:call-trgt-28.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO srun: job 51797561 has been allocated resources
2025-09-15 20:24:10.225 wdl.w:ptcp.w:call-trgt-28.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:10.238 wdl.w:ptcp.w:call-trgt-30.t:call-trgt_plot_motifs_allele INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-30/call-trgt_plot_motifs_allele/_singularity_tmpdir_1jst63ln"
2025-09-15 20:24:10.238 wdl.w:ptcp.w:call-trgt-30.t:call-trgt_plot_motifs_allele INFO Slurm invocation: srun --job-name call-trgt_plot_motifs_allele --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-30/call-trgt_plot_motifs_allele/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-30/call-trgt_plot_motifs_allele/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-30/call-trgt_plot_motifs_allele/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-30/call-trgt_plot_motifs_allele/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-30/call-trgt_genotype/out/m84036_250809_035451_s4.bc2127.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2127.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-30/call-trgt_genotype/out/m84036_250809_035451_s4.bc2127.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2127.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-30/call-trgt_genotype/out/m84036_250809_035451_s4.bc2127.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2127.trgt.vcf:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-30/call-trgt_plot_motifs_allele/_singularity_tmpdir_1jst63ln/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-30/call-trgt_plot_motifs_allele/_singularity_tmpdir_1jst63ln/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:10.245 wdl.w:ptcp.w:call-trgt-30.t:call-trgt_plot_motifs_waterfall INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-30/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_iwdzjybm"
2025-09-15 20:24:10.246 wdl.w:ptcp.w:call-trgt-30.t:call-trgt_plot_motifs_waterfall INFO Slurm invocation: srun --job-name call-trgt_plot_motifs_waterfall --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-30/call-trgt_plot_motifs_waterfall/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-30/call-trgt_plot_motifs_waterfall/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-30/call-trgt_plot_motifs_waterfall/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-30/call-trgt_plot_motifs_waterfall/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-30/call-trgt_genotype/out/m84036_250809_035451_s4.bc2127.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2127.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-30/call-trgt_genotype/out/m84036_250809_035451_s4.bc2127.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2127.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-30/call-trgt_genotype/out/m84036_250809_035451_s4.bc2127.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2127.trgt.vcf:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-30/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_iwdzjybm/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-30/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_iwdzjybm/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:10.260 wdl.w:ptcp.w:call-trgt-30.t:call-trgt_plot_motifs_waterfall NOTICE slurm_singularity run :: pid: 1201092, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-30/call-trgt_plot_motifs_waterfall/slurm_singularity.log.txt"
2025-09-15 20:24:10.260 wdl.w:ptcp.w:call-trgt-30.t:call-trgt_plot_motifs_allele NOTICE slurm_singularity run :: pid: 1201091, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-30/call-trgt_plot_motifs_allele/slurm_singularity.log.txt"
2025-09-15 20:24:10.362 wdl.w:ptcp.w:call-trgt-28.t:call-trgt_plot_motifs_allele.slurm_singularity INFO srun: job 51797562 queued and waiting for resources
2025-09-15 20:24:10.362 wdl.w:ptcp.w:call-trgt-28.t:call-trgt_plot_motifs_allele.slurm_singularity INFO srun: job 51797562 has been allocated resources
2025-09-15 20:24:10.362 wdl.w:ptcp.w:call-trgt-28.t:call-trgt_plot_motifs_allele.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:10.431 wdl.w:ptcp.t:call-pbmm2_align_hifi-77 INFO output :: name: "mapped_bam", value: "m84036_250809_035451_s4.bc2174.mapped.bam"
2025-09-15 20:24:10.435 wdl.w:ptcp.t:call-pbmm2_align_hifi-77 INFO output :: name: "mapped_bam_bai", value: "m84036_250809_035451_s4.bc2174.mapped.bam.bai"
2025-09-15 20:24:10.436 wdl.w:ptcp.t:call-pbmm2_align_hifi-77 INFO output :: name: "mapped_bam_pbi", value: "m84036_250809_035451_s4.bc2174.mapped.bam.pbi"
2025-09-15 20:24:10.438 wdl.w:ptcp.t:call-pbmm2_align_hifi-77 INFO output :: name: "report", value: "mapping_stats.report.json"
2025-09-15 20:24:10.517 wdl.w:ptcp.t:call-pbmm2_align_hifi-77 NOTICE done
2025-09-15 20:24:10.524 wdl.w:ptcp NOTICE finish :: job: "call-pbmm2_align_hifi-77"
2025-09-15 20:24:10.524 wdl.w:ptcp INFO output :: job: "call-pbmm2_align_hifi-77", values: {"report": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-77/out/mapping_stats.report.json", "mapped_bam_pbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-77/out/m84036_250809_035451_s4.bc2174.mapped.bam.pbi", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-77/out/m84036_250809_035451_s4.bc2174.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-77/out/m84036_250809_035451_s4.bc2174.mapped.bam"}
2025-09-15 20:24:10.525 wdl.w:ptcp NOTICE ready :: job: "call-paraphase-77", callee: "paraphase"
2025-09-15 20:24:10.525 wdl.w:ptcp INFO input :: job: "call-paraphase-77", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf", "genome_version": "38", "config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-77/out/m84036_250809_035451_s4.bc2174.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-77/out/m84036_250809_035451_s4.bc2174.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2174"}
2025-09-15 20:24:10.526 wdl.w:ptcp NOTICE ready :: job: "call-sawfish-77", callee: "sawfish"
2025-09-15 20:24:10.526 wdl.w:ptcp INFO input :: job: "call-sawfish-77", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-77/out/m84036_250809_035451_s4.bc2174.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-77/out/m84036_250809_035451_s4.bc2174.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2174"}
2025-09-15 20:24:10.527 wdl.w:ptcp NOTICE ready :: job: "call-trgt-77", callee: "trgt"
2025-09-15 20:24:10.527 wdl.w:ptcp INFO input :: job: "call-trgt-77", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-77/out/m84036_250809_035451_s4.bc2174.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-77/out/m84036_250809_035451_s4.bc2174.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2174"}
2025-09-15 20:24:10.530 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_plot_meth_allele NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-06/call-trgt_plot_meth_allele", thread: 140608194717248
2025-09-15 20:24:10.534 wdl.w:ptcp.w:call-trgt-28.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO srun: job 51797563 queued and waiting for resources
2025-09-15 20:24:10.534 wdl.w:ptcp.w:call-trgt-28.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO srun: job 51797563 has been allocated resources
2025-09-15 20:24:10.534 wdl.w:ptcp.w:call-trgt-28.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:10.548 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_plot_meth_allele INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:10.548 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_plot_meth_allele INFO input :: name: "waterfall", value: false
2025-09-15 20:24:10.548 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_plot_meth_allele INFO input :: name: "methylation", value: true
2025-09-15 20:24:10.548 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_plot_meth_allele INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:10.548 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_plot_meth_allele INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:10.548 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_plot_meth_allele INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:10.548 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_plot_meth_allele INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2103.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:10.548 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_plot_meth_allele INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2103.trgt.sorted.spanning.bam"
2025-09-15 20:24:10.548 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_plot_meth_allele INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2103.trgt.vcf"
2025-09-15 20:24:10.548 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_plot_meth_allele INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2103"
2025-09-15 20:24:10.549 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_plot_meth_allele INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:10.549 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_plot_meth_allele INFO eval :: name: "plot_type", value: "allele"
2025-09-15 20:24:10.549 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_plot_meth_allele INFO eval :: name: "show", value: "meth"
2025-09-15 20:24:10.549 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_plot_meth_allele INFO eval :: name: "threads", value: 1
2025-09-15 20:24:10.549 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_plot_meth_allele INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:10.549 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_plot_meth_allele INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2103.meth_allele"
2025-09-15 20:24:10.550 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_plot_meth_allele INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:10.550 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_plot_meth_allele WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:10.550 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_plot_meth_allele INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:10.550 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_plot_meth_allele INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:10.551 wdl.w:ptcp.w:call-trgt-30.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:10 [ERROR] - No reads found for TRID=SCA37_DAB1
2025-09-15 20:24:10.551 wdl.w:ptcp.w:call-trgt-30.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:10 [ERROR] - No reads found for TRID=OPDM_ABCD3
2025-09-15 20:24:10.551 wdl.w:ptcp.w:call-trgt-30.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:10 [ERROR] - No reads found for TRID=NIID_NOTCH2NLC
2025-09-15 20:24:10.561 wdl.w:ptcp.w:call-trgt-30.t:call-trgt_plot_meth_allele.slurm_singularity INFO srun: job 51797564 queued and waiting for resources
2025-09-15 20:24:10.561 wdl.w:ptcp.w:call-trgt-30.t:call-trgt_plot_meth_allele.slurm_singularity INFO srun: job 51797564 has been allocated resources
2025-09-15 20:24:10.562 wdl.w:ptcp.w:call-trgt-30.t:call-trgt_plot_meth_allele.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:10.611 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_plot_meth_allele INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-06/call-trgt_plot_meth_allele/_singularity_tmpdir_5s0lt562"
2025-09-15 20:24:10.612 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_plot_meth_allele INFO Slurm invocation: srun --job-name call-trgt_plot_meth_allele --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-06/call-trgt_plot_meth_allele/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-06/call-trgt_plot_meth_allele/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-06/call-trgt_plot_meth_allele/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-06/call-trgt_plot_meth_allele/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-06/call-trgt_genotype/out/m84036_250809_035451_s4.bc2103.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2103.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-06/call-trgt_genotype/out/m84036_250809_035451_s4.bc2103.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2103.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-06/call-trgt_genotype/out/m84036_250809_035451_s4.bc2103.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2103.trgt.sorted.spanning.bam:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-06/call-trgt_plot_meth_allele/_singularity_tmpdir_5s0lt562/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-06/call-trgt_plot_meth_allele/_singularity_tmpdir_5s0lt562/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:10.627 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_plot_meth_allele NOTICE slurm_singularity run :: pid: 1201109, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-06/call-trgt_plot_meth_allele/slurm_singularity.log.txt"
2025-09-15 20:24:10.663 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_plot_motifs_allele INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2107.motifs_allele.trgt_plots.zip"
2025-09-15 20:24:10.743 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_plot_motifs_allele NOTICE done
2025-09-15 20:24:10.748 wdl.w:ptcp.w:call-trgt-10 NOTICE finish :: job: "call-trgt_plot_motifs_allele"
2025-09-15 20:24:10.748 wdl.w:ptcp.w:call-trgt-10 INFO output :: job: "call-trgt_plot_motifs_allele", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-10/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2107.motifs_allele.trgt_plots.zip"}
2025-09-15 20:24:10.748 wdl.w:ptcp.w:call-trgt-10 INFO visit :: node: "output-images_motifs_allele", values: {"images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-10/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2107.motifs_allele.trgt_plots.zip"}
2025-09-15 20:24:10.754 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_plot_meth_waterfall NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-06/call-trgt_plot_meth_waterfall", thread: 140610887464512
2025-09-15 20:24:10.772 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_plot_meth_waterfall INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:10.772 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_plot_meth_waterfall INFO input :: name: "waterfall", value: true
2025-09-15 20:24:10.772 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_plot_meth_waterfall INFO input :: name: "methylation", value: true
2025-09-15 20:24:10.773 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_plot_meth_waterfall INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:10.773 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_plot_meth_waterfall INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:10.773 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_plot_meth_waterfall INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:10.773 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_plot_meth_waterfall INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2103.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:10.773 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_plot_meth_waterfall INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2103.trgt.sorted.spanning.bam"
2025-09-15 20:24:10.773 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_plot_meth_waterfall INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2103.trgt.vcf"
2025-09-15 20:24:10.773 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_plot_meth_waterfall INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2103"
2025-09-15 20:24:10.773 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_plot_meth_waterfall INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:10.773 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_plot_meth_waterfall INFO eval :: name: "plot_type", value: "waterfall"
2025-09-15 20:24:10.773 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_plot_meth_waterfall INFO eval :: name: "show", value: "meth"
2025-09-15 20:24:10.774 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_plot_meth_waterfall INFO eval :: name: "threads", value: 1
2025-09-15 20:24:10.774 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_plot_meth_waterfall INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:10.774 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_plot_meth_waterfall INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2103.meth_waterfall"
2025-09-15 20:24:10.774 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_plot_meth_waterfall INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:10.774 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_plot_meth_waterfall WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:10.775 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_plot_meth_waterfall INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:10.775 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_plot_meth_waterfall INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:10.838 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_plot_meth_waterfall INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-06/call-trgt_plot_meth_waterfall/_singularity_tmpdir_gn4r_lh3"
2025-09-15 20:24:10.838 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_plot_meth_waterfall INFO Slurm invocation: srun --job-name call-trgt_plot_meth_waterfall --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-06/call-trgt_plot_meth_waterfall/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-06/call-trgt_plot_meth_waterfall/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-06/call-trgt_plot_meth_waterfall/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-06/call-trgt_plot_meth_waterfall/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-06/call-trgt_genotype/out/m84036_250809_035451_s4.bc2103.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2103.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-06/call-trgt_genotype/out/m84036_250809_035451_s4.bc2103.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2103.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-06/call-trgt_genotype/out/m84036_250809_035451_s4.bc2103.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2103.trgt.sorted.spanning.bam:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-06/call-trgt_plot_meth_waterfall/_singularity_tmpdir_gn4r_lh3/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-06/call-trgt_plot_meth_waterfall/_singularity_tmpdir_gn4r_lh3/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:10.847 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_plot_meth_waterfall NOTICE slurm_singularity run :: pid: 1201111, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-06/call-trgt_plot_meth_waterfall/slurm_singularity.log.txt"
2025-09-15 20:24:10.857 wdl.w:ptcp.w:call-trgt-30.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:10 [ERROR] - No reads found for TRID=SCA37_DAB1
2025-09-15 20:24:10.857 wdl.w:ptcp.w:call-trgt-30.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:10 [ERROR] - No reads found for TRID=OPDM_ABCD3
2025-09-15 20:24:10.857 wdl.w:ptcp.w:call-trgt-30.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:10 [ERROR] - No reads found for TRID=NIID_NOTCH2NLC
2025-09-15 20:24:10.857 wdl.w:ptcp.w:call-trgt-30.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:10 [ERROR] - No reads found for TRID=SCA2_ATXN2
2025-09-15 20:24:10.859 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:08 [ERROR] - No reads found for TRID=SCA37_DAB1
2025-09-15 20:24:10.859 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:08 [ERROR] - No reads found for TRID=OPDM_ABCD3
2025-09-15 20:24:10.859 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:08 [ERROR] - No reads found for TRID=DRPLA_ATN1
2025-09-15 20:24:10.859 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:08 [ERROR] - No reads found for TRID=SCA2_ATXN2
2025-09-15 20:24:10.859 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:08 [ERROR] - No reads found for TRID=OPDM4_RILPL1
2025-09-15 20:24:10.859 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:08 [ERROR] - No reads found for TRID=NIID_NOTCH2NLC
2025-09-15 20:24:10.859 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:08 [ERROR] - No reads found for TRID=SCA3_ATXN3
2025-09-15 20:24:10.859 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:08 [ERROR] - No reads found for TRID=OPMD_PABPN1
2025-09-15 20:24:10.859 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:08 [ERROR] - No reads found for TRID=HDL2_JPH3
2025-09-15 20:24:10.860 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:08 [ERROR] - No reads found for TRID=FECD3_TCF4
2025-09-15 20:24:10.860 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:08 [ERROR] - No reads found for TRID=OPDM2_GIPC1
2025-09-15 20:24:10.860 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:08 [ERROR] - No reads found for TRID=SCA4_ZFHX3
2025-09-15 20:24:10.860 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:08 [ERROR] - No reads found for TRID=FRA2A_AFF3
2025-09-15 20:24:10.860 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:08 [ERROR] - No reads found for TRID=SCA6_CACNA1A
2025-09-15 20:24:10.860 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:08 [ERROR] - No reads found for TRID=CJD_PRNP
2025-09-15 20:24:10.860 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:08 [ERROR] - No reads found for TRID=EPM1_CSTB
2025-09-15 20:24:10.860 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:08 [ERROR] - No reads found for TRID=SCA36_NOP56
2025-09-15 20:24:10.860 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:08 [ERROR] - No reads found for TRID=SCA7_ATXN7
2025-09-15 20:24:10.860 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:08 [ERROR] - No reads found for TRID=SCA31_BEAN1
2025-09-15 20:24:10.860 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:09 [ERROR] - No reads found for TRID=CCHS_PHOX2B
2025-09-15 20:24:10.860 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:09 [ERROR] - No reads found for TRID=SCA12_PPP2R2B
2025-09-15 20:24:10.860 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:09 [ERROR] - No reads found for TRID=OPDM1_LRP12
2025-09-15 20:24:10.860 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:09 [ERROR] - No reads found for TRID=SCA1_ATXN1
2025-09-15 20:24:10.860 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:09 [ERROR] - No reads found for TRID=FAME1_SAMD12
2025-09-15 20:24:10.860 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:09 [ERROR] - No reads found for TRID=SBMA_AR
2025-09-15 20:24:10.870 wdl.w:ptcp.w:call-trgt-30.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO srun: job 51797565 queued and waiting for resources
2025-09-15 20:24:10.870 wdl.w:ptcp.w:call-trgt-30.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO srun: job 51797565 has been allocated resources
2025-09-15 20:24:10.870 wdl.w:ptcp.w:call-trgt-30.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:10.923 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_plot_motifs_waterfall INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2107.motifs_waterfall.trgt_plots.zip"
2025-09-15 20:24:10.934 wdl.w:ptcp.w:call-trgt-21.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:10 [ERROR] - No reads found for TRID=PRTS_ARX
2025-09-15 20:24:10.935 wdl.w:ptcp.w:call-trgt-21.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:10 [ERROR] - No reads found for TRID=EIEE1_ARX
2025-09-15 20:24:10.956 wdl.w:ptcp.t:call-pbmm2_align_hifi-75 INFO output :: name: "mapped_bam", value: "m84036_250809_035451_s4.bc2172.mapped.bam"
2025-09-15 20:24:10.960 wdl.w:ptcp.t:call-pbmm2_align_hifi-75 INFO output :: name: "mapped_bam_bai", value: "m84036_250809_035451_s4.bc2172.mapped.bam.bai"
2025-09-15 20:24:10.961 wdl.w:ptcp.t:call-pbmm2_align_hifi-75 INFO output :: name: "mapped_bam_pbi", value: "m84036_250809_035451_s4.bc2172.mapped.bam.pbi"
2025-09-15 20:24:10.962 wdl.w:ptcp.t:call-pbmm2_align_hifi-75 INFO output :: name: "report", value: "mapping_stats.report.json"
2025-09-15 20:24:11.004 wdl.w:ptcp.w:call-trgt-10.t:call-trgt_plot_motifs_waterfall NOTICE done
2025-09-15 20:24:11.010 wdl.w:ptcp.w:call-trgt-10 NOTICE finish :: job: "call-trgt_plot_motifs_waterfall"
2025-09-15 20:24:11.010 wdl.w:ptcp.w:call-trgt-10 INFO output :: job: "call-trgt_plot_motifs_waterfall", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-10/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2107.motifs_waterfall.trgt_plots.zip"}
2025-09-15 20:24:11.010 wdl.w:ptcp.w:call-trgt-10 INFO visit :: node: "output-images_motifs_waterfall", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-10/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2107.motifs_waterfall.trgt_plots.zip"}
2025-09-15 20:24:11.011 wdl.w:ptcp.w:call-trgt-10 INFO visit :: node: "outputs", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-10/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2107.motifs_waterfall.trgt_plots.zip", "images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-10/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2107.meth_allele.trgt_plots.zip", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-10/call-trgt_genotype/out/m84036_250809_035451_s4.bc2107.trgt.sorted.spanning.bam.bai", "images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-10/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2107.motifs_allele.trgt_plots.zip", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-10/call-trgt_genotype/out/m84036_250809_035451_s4.bc2107.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-10/call-trgt_genotype/out/m84036_250809_035451_s4.bc2107.trgt.vcf", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-10/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2107.repeats.bam", "images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-10/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2107.meth_waterfall.trgt_plots.zip", "reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-10/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2107.repeats.bam.bai"}
2025-09-15 20:24:11.017 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_plot_motifs_allele NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-06/call-trgt_plot_motifs_allele", thread: 140608765158976
2025-09-15 20:24:11.035 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_plot_motifs_allele INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:11.035 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_plot_motifs_allele INFO input :: name: "waterfall", value: false
2025-09-15 20:24:11.035 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_plot_motifs_allele INFO input :: name: "methylation", value: false
2025-09-15 20:24:11.035 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_plot_motifs_allele INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:11.035 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_plot_motifs_allele INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:11.035 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_plot_motifs_allele INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:11.035 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_plot_motifs_allele INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2103.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:11.035 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_plot_motifs_allele INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2103.trgt.sorted.spanning.bam"
2025-09-15 20:24:11.035 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_plot_motifs_allele INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2103.trgt.vcf"
2025-09-15 20:24:11.035 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_plot_motifs_allele INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2103"
2025-09-15 20:24:11.036 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_plot_motifs_allele INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:11.036 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_plot_motifs_allele INFO eval :: name: "plot_type", value: "allele"
2025-09-15 20:24:11.036 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_plot_motifs_allele INFO eval :: name: "show", value: "motifs"
2025-09-15 20:24:11.036 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_plot_motifs_allele INFO eval :: name: "threads", value: 1
2025-09-15 20:24:11.036 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_plot_motifs_allele INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:11.037 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_plot_motifs_allele INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2103.motifs_allele"
2025-09-15 20:24:11.037 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_plot_motifs_allele INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:11.037 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_plot_motifs_allele WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:11.037 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_plot_motifs_allele INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:11.038 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_plot_motifs_allele INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:11.048 wdl.w:ptcp.t:call-pbmm2_align_hifi-75 NOTICE done
2025-09-15 20:24:11.055 wdl.w:ptcp NOTICE finish :: job: "call-pbmm2_align_hifi-75"
2025-09-15 20:24:11.055 wdl.w:ptcp INFO output :: job: "call-pbmm2_align_hifi-75", values: {"report": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-75/out/mapping_stats.report.json", "mapped_bam_pbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-75/out/m84036_250809_035451_s4.bc2172.mapped.bam.pbi", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-75/out/m84036_250809_035451_s4.bc2172.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-75/out/m84036_250809_035451_s4.bc2172.mapped.bam"}
2025-09-15 20:24:11.056 wdl.w:ptcp NOTICE ready :: job: "call-paraphase-75", callee: "paraphase"
2025-09-15 20:24:11.056 wdl.w:ptcp INFO input :: job: "call-paraphase-75", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf", "genome_version": "38", "config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-75/out/m84036_250809_035451_s4.bc2172.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-75/out/m84036_250809_035451_s4.bc2172.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2172"}
2025-09-15 20:24:11.057 wdl.w:ptcp NOTICE ready :: job: "call-sawfish-75", callee: "sawfish"
2025-09-15 20:24:11.057 wdl.w:ptcp INFO input :: job: "call-sawfish-75", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-75/out/m84036_250809_035451_s4.bc2172.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-75/out/m84036_250809_035451_s4.bc2172.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2172"}
2025-09-15 20:24:11.058 wdl.w:ptcp NOTICE ready :: job: "call-trgt-75", callee: "trgt"
2025-09-15 20:24:11.058 wdl.w:ptcp INFO input :: job: "call-trgt-75", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-75/out/m84036_250809_035451_s4.bc2172.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-75/out/m84036_250809_035451_s4.bc2172.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2172"}
2025-09-15 20:24:11.062 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_plot_motifs_waterfall NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-06/call-trgt_plot_motifs_waterfall", thread: 140608211502656
2025-09-15 20:24:11.062 wdl.w:ptcp.w:call-paraphase-02.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for smn1 for sample m84036_250809_035451_s4.bc2099 at 2025-09-15 20:23:48.347483...
2025-09-15 20:24:11.063 wdl.w:ptcp.w:call-paraphase-02.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for hba for sample m84036_250809_035451_s4.bc2099 at 2025-09-15 20:23:49.351152...
2025-09-15 20:24:11.063 wdl.w:ptcp.w:call-paraphase-02.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for gba for sample m84036_250809_035451_s4.bc2099 at 2025-09-15 20:23:50.430870...
2025-09-15 20:24:11.063 wdl.w:ptcp.w:call-paraphase-02.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for cyp21 for sample m84036_250809_035451_s4.bc2099 at 2025-09-15 20:23:52.135752...
2025-09-15 20:24:11.063 wdl.w:ptcp.w:call-paraphase-02.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for smn1 for sample m84036_250809_035451_s4.bc2099 at 2025-09-15 20:24:03.574552...
2025-09-15 20:24:11.063 wdl.w:ptcp.w:call-paraphase-02.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning to gene2 region for smn1 for sample m84036_250809_035451_s4.bc2099 at 2025-09-15 20:24:04.055372...
2025-09-15 20:24:11.083 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_plot_motifs_waterfall INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:11.083 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_plot_motifs_waterfall INFO input :: name: "waterfall", value: true
2025-09-15 20:24:11.083 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_plot_motifs_waterfall INFO input :: name: "methylation", value: false
2025-09-15 20:24:11.083 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_plot_motifs_waterfall INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:11.083 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_plot_motifs_waterfall INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:11.083 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_plot_motifs_waterfall INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:11.084 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_plot_motifs_waterfall INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2103.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:11.084 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_plot_motifs_waterfall INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2103.trgt.sorted.spanning.bam"
2025-09-15 20:24:11.084 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_plot_motifs_waterfall INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2103.trgt.vcf"
2025-09-15 20:24:11.084 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_plot_motifs_waterfall INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2103"
2025-09-15 20:24:11.084 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:11.084 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "plot_type", value: "waterfall"
2025-09-15 20:24:11.084 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "show", value: "motifs"
2025-09-15 20:24:11.084 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "threads", value: 1
2025-09-15 20:24:11.085 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:11.085 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2103.motifs_waterfall"
2025-09-15 20:24:11.085 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_plot_motifs_waterfall INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:11.085 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_plot_motifs_waterfall WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:11.085 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_plot_motifs_waterfall INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:11.086 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_plot_motifs_waterfall INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:11.114 wdl.w:ptcp.w:call-trgt-10 NOTICE done
2025-09-15 20:24:11.119 wdl.w:ptcp NOTICE finish :: job: "call-trgt-10"
2025-09-15 20:24:11.119 wdl.w:ptcp INFO output :: job: "call-trgt-10", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-10/out/m84036_250809_035451_s4.bc2107.motifs_waterfall.trgt_plots.zip", "images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-10/out/m84036_250809_035451_s4.bc2107.meth_allele.trgt_plots.zip", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-10/out/m84036_250809_035451_s4.bc2107.trgt.sorted.spanning.bam.bai", "images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-10/out/m84036_250809_035451_s4.bc2107.motifs_allele.trgt_plots.zip", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-10/out/m84036_250809_035451_s4.bc2107.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-10/out/m84036_250809_035451_s4.bc2107.trgt.vcf", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-10/out/m84036_250809_035451_s4.bc2107.repeats.bam", "images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-10/out/m84036_250809_035451_s4.bc2107.meth_waterfall.trgt_plots.zip", "reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-10/out/m84036_250809_035451_s4.bc2107.repeats.bam.bai"}
2025-09-15 20:24:11.124 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_plot_motifs_allele INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-06/call-trgt_plot_motifs_allele/_singularity_tmpdir_abnfxxqk"
2025-09-15 20:24:11.124 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_plot_motifs_allele INFO Slurm invocation: srun --job-name call-trgt_plot_motifs_allele --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-06/call-trgt_plot_motifs_allele/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-06/call-trgt_plot_motifs_allele/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-06/call-trgt_plot_motifs_allele/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-06/call-trgt_plot_motifs_allele/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-06/call-trgt_genotype/out/m84036_250809_035451_s4.bc2103.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2103.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-06/call-trgt_genotype/out/m84036_250809_035451_s4.bc2103.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2103.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-06/call-trgt_genotype/out/m84036_250809_035451_s4.bc2103.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2103.trgt.sorted.spanning.bam:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-06/call-trgt_plot_motifs_allele/_singularity_tmpdir_abnfxxqk/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-06/call-trgt_plot_motifs_allele/_singularity_tmpdir_abnfxxqk/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:11.127 wdl.w:ptcp.w:call-paraphase-41 NOTICE workflow start :: name: "paraphase", source: "./paraphase.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-41"
2025-09-15 20:24:11.145 wdl.w:ptcp.w:call-paraphase-41 INFO visit :: node: "decl-annotation_vcf", values: {"annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf"}
2025-09-15 20:24:11.145 wdl.w:ptcp.w:call-paraphase-41 INFO visit :: node: "decl-config_file", values: {"config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml"}
2025-09-15 20:24:11.146 wdl.w:ptcp.w:call-paraphase-41 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:24:11.146 wdl.w:ptcp.w:call-paraphase-41 INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:24:11.146 wdl.w:ptcp.w:call-paraphase-41 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-41/out/m84036_250809_035451_s4.bc2138.mapped.bam"}
2025-09-15 20:24:11.146 wdl.w:ptcp.w:call-paraphase-41 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-41/out/m84036_250809_035451_s4.bc2138.mapped.bam.bai"}
2025-09-15 20:24:11.146 wdl.w:ptcp.w:call-paraphase-41 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:24:11.146 wdl.w:ptcp.w:call-paraphase-41 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:24:11.146 wdl.w:ptcp.w:call-paraphase-41 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2138"}
2025-09-15 20:24:11.146 wdl.w:ptcp.w:call-paraphase-41 INFO visit :: node: "decl-sex", values: {"sex": "F"}
2025-09-15 20:24:11.146 wdl.w:ptcp.w:call-paraphase-41 NOTICE ready :: job: "call-run_paraphase", callee: "run_paraphase"
2025-09-15 20:24:11.146 wdl.w:ptcp.w:call-paraphase-41 INFO input :: job: "call-run_paraphase", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf", "genome_version": "38", "config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-41/out/m84036_250809_035451_s4.bc2138.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-41/out/m84036_250809_035451_s4.bc2138.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2138"}
2025-09-15 20:24:11.153 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_plot_motifs_allele NOTICE slurm_singularity run :: pid: 1201125, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-06/call-trgt_plot_motifs_allele/slurm_singularity.log.txt"
2025-09-15 20:24:11.164 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_plot_motifs_waterfall INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-06/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_jf32oree"
2025-09-15 20:24:11.164 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_plot_motifs_waterfall INFO Slurm invocation: srun --job-name call-trgt_plot_motifs_waterfall --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-06/call-trgt_plot_motifs_waterfall/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-06/call-trgt_plot_motifs_waterfall/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-06/call-trgt_plot_motifs_waterfall/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-06/call-trgt_plot_motifs_waterfall/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-06/call-trgt_genotype/out/m84036_250809_035451_s4.bc2103.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2103.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-06/call-trgt_genotype/out/m84036_250809_035451_s4.bc2103.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2103.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-06/call-trgt_genotype/out/m84036_250809_035451_s4.bc2103.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2103.trgt.sorted.spanning.bam:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-06/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_jf32oree/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-06/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_jf32oree/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:11.172 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_plot_motifs_waterfall NOTICE slurm_singularity run :: pid: 1201127, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-06/call-trgt_plot_motifs_waterfall/slurm_singularity.log.txt"
2025-09-15 20:24:11.264 wdl.w:ptcp.w:call-trgt-30.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:11 [ERROR] - No reads found for TRID=SCA37_DAB1
2025-09-15 20:24:11.264 wdl.w:ptcp.w:call-trgt-30.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:11 [ERROR] - No reads found for TRID=OPDM_ABCD3
2025-09-15 20:24:11.264 wdl.w:ptcp.w:call-trgt-30.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:11 [ERROR] - No reads found for TRID=NIID_NOTCH2NLC
2025-09-15 20:24:11.264 wdl.w:ptcp.w:call-trgt-30.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:11 [ERROR] - No reads found for TRID=SCA2_ATXN2
2025-09-15 20:24:11.266 wdl.w:ptcp.w:call-trgt-30.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:10 [ERROR] - No reads found for TRID=SCA37_DAB1
2025-09-15 20:24:11.266 wdl.w:ptcp.w:call-trgt-30.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:11 [ERROR] - No reads found for TRID=OPDM_ABCD3
2025-09-15 20:24:11.266 wdl.w:ptcp.w:call-trgt-30.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:11 [ERROR] - No reads found for TRID=NIID_NOTCH2NLC
2025-09-15 20:24:11.266 wdl.w:ptcp.w:call-trgt-30.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:11 [ERROR] - No reads found for TRID=SCA2_ATXN2
2025-09-15 20:24:11.266 wdl.w:ptcp.w:call-trgt-30.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:11 [ERROR] - No reads found for TRID=OPDM4_RILPL1
2025-09-15 20:24:11.266 wdl.w:ptcp.w:call-trgt-30.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:11 [ERROR] - No reads found for TRID=SCA8_ATXN8OS
2025-09-15 20:24:11.266 wdl.w:ptcp.w:call-trgt-30.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:11 [ERROR] - No reads found for TRID=SCA27B_FGF14
2025-09-15 20:24:11.266 wdl.w:ptcp.w:call-trgt-30.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:11 [ERROR] - No reads found for TRID=SCA3_ATXN3
2025-09-15 20:24:11.266 wdl.w:ptcp.w:call-trgt-30.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:11 [ERROR] - No reads found for TRID=SCA31_BEAN1
2025-09-15 20:24:11.275 wdl.w:ptcp.w:call-trgt-30.t:call-trgt_plot_motifs_allele.slurm_singularity INFO srun: job 51797567 queued and waiting for resources
2025-09-15 20:24:11.275 wdl.w:ptcp.w:call-trgt-30.t:call-trgt_plot_motifs_allele.slurm_singularity INFO srun: job 51797567 has been allocated resources
2025-09-15 20:24:11.275 wdl.w:ptcp.w:call-trgt-30.t:call-trgt_plot_motifs_allele.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:11.276 wdl.w:ptcp.w:call-trgt-30.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO srun: job 51797566 queued and waiting for resources
2025-09-15 20:24:11.276 wdl.w:ptcp.w:call-trgt-30.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO srun: job 51797566 has been allocated resources
2025-09-15 20:24:11.276 wdl.w:ptcp.w:call-trgt-30.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:11.463 wdl.w:ptcp.w:call-paraphase-11.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for f8inv1 for sample m84036_250809_035451_s4.bc2108 at 2025-09-15 20:24:01.505362...
2025-09-15 20:24:11.463 wdl.w:ptcp.w:call-paraphase-11.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for f8inv1 for sample m84036_250809_035451_s4.bc2108 at 2025-09-15 20:24:06.664957...
2025-09-15 20:24:11.463 wdl.w:ptcp.w:call-paraphase-11.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for f8inv1 for sample m84036_250809_035451_s4.bc2108 at 2025-09-15 20:24:07.013317...
2025-09-15 20:24:11.608 wdl.w:ptcp.t:call-pbmm2_align_hifi-81 INFO output :: name: "mapped_bam", value: "m84036_250809_035451_s4.bc2178.mapped.bam"
2025-09-15 20:24:11.611 wdl.w:ptcp.t:call-pbmm2_align_hifi-81 INFO output :: name: "mapped_bam_bai", value: "m84036_250809_035451_s4.bc2178.mapped.bam.bai"
2025-09-15 20:24:11.612 wdl.w:ptcp.t:call-pbmm2_align_hifi-81 INFO output :: name: "mapped_bam_pbi", value: "m84036_250809_035451_s4.bc2178.mapped.bam.pbi"
2025-09-15 20:24:11.613 wdl.w:ptcp.t:call-pbmm2_align_hifi-81 INFO output :: name: "report", value: "mapping_stats.report.json"
2025-09-15 20:24:11.629 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:11 [ERROR] - No reads found for TRID=SCA37_DAB1
2025-09-15 20:24:11.636 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_plot_meth_allele.slurm_singularity INFO srun: job 51797568 queued and waiting for resources
2025-09-15 20:24:11.636 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_plot_meth_allele.slurm_singularity INFO srun: job 51797568 has been allocated resources
2025-09-15 20:24:11.637 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_plot_meth_allele.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:11.699 wdl.w:ptcp.t:call-pbmm2_align_hifi-81 NOTICE done
2025-09-15 20:24:11.704 wdl.w:ptcp NOTICE finish :: job: "call-pbmm2_align_hifi-81"
2025-09-15 20:24:11.704 wdl.w:ptcp INFO output :: job: "call-pbmm2_align_hifi-81", values: {"report": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-81/out/mapping_stats.report.json", "mapped_bam_pbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-81/out/m84036_250809_035451_s4.bc2178.mapped.bam.pbi", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-81/out/m84036_250809_035451_s4.bc2178.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-81/out/m84036_250809_035451_s4.bc2178.mapped.bam"}
2025-09-15 20:24:11.705 wdl.w:ptcp NOTICE ready :: job: "call-paraphase-81", callee: "paraphase"
2025-09-15 20:24:11.705 wdl.w:ptcp INFO input :: job: "call-paraphase-81", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf", "genome_version": "38", "config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-81/out/m84036_250809_035451_s4.bc2178.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-81/out/m84036_250809_035451_s4.bc2178.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2178"}
2025-09-15 20:24:11.707 wdl.w:ptcp NOTICE ready :: job: "call-sawfish-81", callee: "sawfish"
2025-09-15 20:24:11.707 wdl.w:ptcp INFO input :: job: "call-sawfish-81", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-81/out/m84036_250809_035451_s4.bc2178.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-81/out/m84036_250809_035451_s4.bc2178.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2178"}
2025-09-15 20:24:11.708 wdl.w:ptcp NOTICE ready :: job: "call-trgt-81", callee: "trgt"
2025-09-15 20:24:11.708 wdl.w:ptcp INFO input :: job: "call-trgt-81", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-81/out/m84036_250809_035451_s4.bc2178.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-81/out/m84036_250809_035451_s4.bc2178.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2178"}
2025-09-15 20:24:11.709 wdl.w:ptcp.w:call-trgt-33.t:call-trgt_plot_meth_allele NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-33/call-trgt_plot_meth_allele", thread: 140607683024448
2025-09-15 20:24:11.726 wdl.w:ptcp.w:call-trgt-33.t:call-trgt_plot_meth_allele INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:11.726 wdl.w:ptcp.w:call-trgt-33.t:call-trgt_plot_meth_allele INFO input :: name: "waterfall", value: false
2025-09-15 20:24:11.726 wdl.w:ptcp.w:call-trgt-33.t:call-trgt_plot_meth_allele INFO input :: name: "methylation", value: true
2025-09-15 20:24:11.726 wdl.w:ptcp.w:call-trgt-33.t:call-trgt_plot_meth_allele INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:11.727 wdl.w:ptcp.w:call-trgt-33.t:call-trgt_plot_meth_allele INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:11.727 wdl.w:ptcp.w:call-trgt-33.t:call-trgt_plot_meth_allele INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:11.727 wdl.w:ptcp.w:call-trgt-33.t:call-trgt_plot_meth_allele INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2130.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:11.727 wdl.w:ptcp.w:call-trgt-33.t:call-trgt_plot_meth_allele INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2130.trgt.sorted.spanning.bam"
2025-09-15 20:24:11.727 wdl.w:ptcp.w:call-trgt-33.t:call-trgt_plot_meth_allele INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2130.trgt.vcf"
2025-09-15 20:24:11.727 wdl.w:ptcp.w:call-trgt-33.t:call-trgt_plot_meth_allele INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2130"
2025-09-15 20:24:11.727 wdl.w:ptcp.w:call-trgt-33.t:call-trgt_plot_meth_allele INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:11.727 wdl.w:ptcp.w:call-trgt-33.t:call-trgt_plot_meth_allele INFO eval :: name: "plot_type", value: "allele"
2025-09-15 20:24:11.727 wdl.w:ptcp.w:call-trgt-33.t:call-trgt_plot_meth_allele INFO eval :: name: "show", value: "meth"
2025-09-15 20:24:11.727 wdl.w:ptcp.w:call-trgt-33.t:call-trgt_plot_meth_allele INFO eval :: name: "threads", value: 1
2025-09-15 20:24:11.728 wdl.w:ptcp.w:call-trgt-33.t:call-trgt_plot_meth_allele INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:11.728 wdl.w:ptcp.w:call-trgt-33.t:call-trgt_plot_meth_allele INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2130.meth_allele"
2025-09-15 20:24:11.728 wdl.w:ptcp.w:call-trgt-33.t:call-trgt_plot_meth_allele INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:11.728 wdl.w:ptcp.w:call-trgt-33.t:call-trgt_plot_meth_allele WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:11.728 wdl.w:ptcp.w:call-trgt-33.t:call-trgt_plot_meth_allele INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:11.729 wdl.w:ptcp.w:call-trgt-33.t:call-trgt_plot_meth_allele INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:11.783 wdl.w:ptcp.w:call-trgt-21.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:10 [ERROR] - No reads found for TRID=PRTS_ARX
2025-09-15 20:24:11.783 wdl.w:ptcp.w:call-trgt-21.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:10 [ERROR] - No reads found for TRID=EIEE1_ARX
2025-09-15 20:24:11.791 wdl.w:ptcp.w:call-trgt-33.t:call-trgt_plot_meth_allele INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-33/call-trgt_plot_meth_allele/_singularity_tmpdir_i7totvap"
2025-09-15 20:24:11.792 wdl.w:ptcp.w:call-trgt-33.t:call-trgt_plot_meth_allele INFO Slurm invocation: srun --job-name call-trgt_plot_meth_allele --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-33/call-trgt_plot_meth_allele/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-33/call-trgt_plot_meth_allele/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-33/call-trgt_plot_meth_allele/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-33/call-trgt_plot_meth_allele/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-33/call-trgt_genotype/out/m84036_250809_035451_s4.bc2130.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2130.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-33/call-trgt_genotype/out/m84036_250809_035451_s4.bc2130.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2130.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-33/call-trgt_genotype/out/m84036_250809_035451_s4.bc2130.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2130.trgt.sorted.spanning.bam.bai:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-33/call-trgt_plot_meth_allele/_singularity_tmpdir_i7totvap/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-33/call-trgt_plot_meth_allele/_singularity_tmpdir_i7totvap/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:11.810 wdl.w:ptcp.w:call-trgt-33.t:call-trgt_plot_meth_allele NOTICE slurm_singularity run :: pid: 1201140, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-33/call-trgt_plot_meth_allele/slurm_singularity.log.txt"
2025-09-15 20:24:11.849 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:11 [ERROR] - No reads found for TRID=SCA37_DAB1
2025-09-15 20:24:11.849 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:11 [ERROR] - No reads found for TRID=OPDM_ABCD3
2025-09-15 20:24:11.849 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:11 [ERROR] - No reads found for TRID=NIID_NOTCH2NLC
2025-09-15 20:24:11.855 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO srun: job 51797569 queued and waiting for resources
2025-09-15 20:24:11.855 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO srun: job 51797569 has been allocated resources
2025-09-15 20:24:11.855 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:12.074 wdl.w:ptcp.t:call-pbmm2_align_hifi-72 INFO output :: name: "mapped_bam", value: "m84036_250809_035451_s4.bc2169.mapped.bam"
2025-09-15 20:24:12.076 wdl.w:ptcp.t:call-pbmm2_align_hifi-72 INFO output :: name: "mapped_bam_bai", value: "m84036_250809_035451_s4.bc2169.mapped.bam.bai"
2025-09-15 20:24:12.078 wdl.w:ptcp.t:call-pbmm2_align_hifi-72 INFO output :: name: "mapped_bam_pbi", value: "m84036_250809_035451_s4.bc2169.mapped.bam.pbi"
2025-09-15 20:24:12.079 wdl.w:ptcp.t:call-pbmm2_align_hifi-72 INFO output :: name: "report", value: "mapping_stats.report.json"
2025-09-15 20:24:12.164 wdl.w:ptcp.t:call-pbmm2_align_hifi-72 NOTICE done
2025-09-15 20:24:12.166 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_plot_motifs_allele.slurm_singularity INFO srun: job 51797570 queued and waiting for resources
2025-09-15 20:24:12.166 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_plot_motifs_allele.slurm_singularity INFO srun: job 51797570 has been allocated resources
2025-09-15 20:24:12.166 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_plot_motifs_allele.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:12.171 wdl.w:ptcp NOTICE finish :: job: "call-pbmm2_align_hifi-72"
2025-09-15 20:24:12.171 wdl.w:ptcp INFO output :: job: "call-pbmm2_align_hifi-72", values: {"report": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-72/out/mapping_stats.report.json", "mapped_bam_pbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-72/out/m84036_250809_035451_s4.bc2169.mapped.bam.pbi", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-72/out/m84036_250809_035451_s4.bc2169.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-72/out/m84036_250809_035451_s4.bc2169.mapped.bam"}
2025-09-15 20:24:12.172 wdl.w:ptcp NOTICE ready :: job: "call-paraphase-72", callee: "paraphase"
2025-09-15 20:24:12.172 wdl.w:ptcp INFO input :: job: "call-paraphase-72", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf", "genome_version": "38", "config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-72/out/m84036_250809_035451_s4.bc2169.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-72/out/m84036_250809_035451_s4.bc2169.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2169"}
2025-09-15 20:24:12.173 wdl.w:ptcp NOTICE ready :: job: "call-sawfish-72", callee: "sawfish"
2025-09-15 20:24:12.173 wdl.w:ptcp INFO input :: job: "call-sawfish-72", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-72/out/m84036_250809_035451_s4.bc2169.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-72/out/m84036_250809_035451_s4.bc2169.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2169"}
2025-09-15 20:24:12.174 wdl.w:ptcp NOTICE ready :: job: "call-trgt-72", callee: "trgt"
2025-09-15 20:24:12.174 wdl.w:ptcp INFO input :: job: "call-trgt-72", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-72/out/m84036_250809_035451_s4.bc2169.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-72/out/m84036_250809_035451_s4.bc2169.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2169"}
2025-09-15 20:24:12.177 wdl.w:ptcp.w:call-trgt-33.t:call-trgt_plot_meth_waterfall NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-33/call-trgt_plot_meth_waterfall", thread: 140608236680768
2025-09-15 20:24:12.181 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO srun: job 51797571 queued and waiting for resources
2025-09-15 20:24:12.181 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO srun: job 51797571 has been allocated resources
2025-09-15 20:24:12.181 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:12.191 wdl.w:ptcp.w:call-trgt-33.t:call-trgt_plot_meth_waterfall INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:12.192 wdl.w:ptcp.w:call-trgt-33.t:call-trgt_plot_meth_waterfall INFO input :: name: "waterfall", value: true
2025-09-15 20:24:12.192 wdl.w:ptcp.w:call-trgt-33.t:call-trgt_plot_meth_waterfall INFO input :: name: "methylation", value: true
2025-09-15 20:24:12.192 wdl.w:ptcp.w:call-trgt-33.t:call-trgt_plot_meth_waterfall INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:12.192 wdl.w:ptcp.w:call-trgt-33.t:call-trgt_plot_meth_waterfall INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:12.192 wdl.w:ptcp.w:call-trgt-33.t:call-trgt_plot_meth_waterfall INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:12.192 wdl.w:ptcp.w:call-trgt-33.t:call-trgt_plot_meth_waterfall INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2130.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:12.192 wdl.w:ptcp.w:call-trgt-33.t:call-trgt_plot_meth_waterfall INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2130.trgt.sorted.spanning.bam"
2025-09-15 20:24:12.192 wdl.w:ptcp.w:call-trgt-33.t:call-trgt_plot_meth_waterfall INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2130.trgt.vcf"
2025-09-15 20:24:12.192 wdl.w:ptcp.w:call-trgt-33.t:call-trgt_plot_meth_waterfall INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2130"
2025-09-15 20:24:12.192 wdl.w:ptcp.w:call-trgt-33.t:call-trgt_plot_meth_waterfall INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:12.192 wdl.w:ptcp.w:call-trgt-33.t:call-trgt_plot_meth_waterfall INFO eval :: name: "plot_type", value: "waterfall"
2025-09-15 20:24:12.193 wdl.w:ptcp.w:call-trgt-33.t:call-trgt_plot_meth_waterfall INFO eval :: name: "show", value: "meth"
2025-09-15 20:24:12.193 wdl.w:ptcp.w:call-trgt-33.t:call-trgt_plot_meth_waterfall INFO eval :: name: "threads", value: 1
2025-09-15 20:24:12.193 wdl.w:ptcp.w:call-trgt-33.t:call-trgt_plot_meth_waterfall INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:12.193 wdl.w:ptcp.w:call-trgt-33.t:call-trgt_plot_meth_waterfall INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2130.meth_waterfall"
2025-09-15 20:24:12.193 wdl.w:ptcp.w:call-trgt-33.t:call-trgt_plot_meth_waterfall INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:12.193 wdl.w:ptcp.w:call-trgt-33.t:call-trgt_plot_meth_waterfall WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:12.194 wdl.w:ptcp.w:call-trgt-33.t:call-trgt_plot_meth_waterfall INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:12.194 wdl.w:ptcp.w:call-trgt-33.t:call-trgt_plot_meth_waterfall INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:12.269 wdl.w:ptcp.w:call-trgt-33.t:call-trgt_plot_meth_waterfall INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-33/call-trgt_plot_meth_waterfall/_singularity_tmpdir___ob_2nh"
2025-09-15 20:24:12.269 wdl.w:ptcp.w:call-trgt-33.t:call-trgt_plot_meth_waterfall INFO Slurm invocation: srun --job-name call-trgt_plot_meth_waterfall --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-33/call-trgt_plot_meth_waterfall/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-33/call-trgt_plot_meth_waterfall/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-33/call-trgt_plot_meth_waterfall/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-33/call-trgt_plot_meth_waterfall/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-33/call-trgt_genotype/out/m84036_250809_035451_s4.bc2130.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2130.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-33/call-trgt_genotype/out/m84036_250809_035451_s4.bc2130.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2130.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-33/call-trgt_genotype/out/m84036_250809_035451_s4.bc2130.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2130.trgt.sorted.spanning.bam.bai:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-33/call-trgt_plot_meth_waterfall/_singularity_tmpdir___ob_2nh/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-33/call-trgt_plot_meth_waterfall/_singularity_tmpdir___ob_2nh/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:12.269 wdl.w:ptcp.t:call-pbmm2_align_hifi-80 INFO output :: name: "mapped_bam", value: "m84036_250809_035451_s4.bc2177.mapped.bam"
2025-09-15 20:24:12.272 wdl.w:ptcp.t:call-pbmm2_align_hifi-80 INFO output :: name: "mapped_bam_bai", value: "m84036_250809_035451_s4.bc2177.mapped.bam.bai"
2025-09-15 20:24:12.274 wdl.w:ptcp.t:call-pbmm2_align_hifi-80 INFO output :: name: "mapped_bam_pbi", value: "m84036_250809_035451_s4.bc2177.mapped.bam.pbi"
2025-09-15 20:24:12.275 wdl.w:ptcp.t:call-pbmm2_align_hifi-80 INFO output :: name: "report", value: "mapping_stats.report.json"
2025-09-15 20:24:12.291 wdl.w:ptcp.w:call-trgt-33.t:call-trgt_plot_meth_waterfall NOTICE slurm_singularity run :: pid: 1201150, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-33/call-trgt_plot_meth_waterfall/slurm_singularity.log.txt"
2025-09-15 20:24:12.301 wdl.w:ptcp.w:call-paraphase-06.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for smn1 for sample m84036_250809_035451_s4.bc2103 at 2025-09-15 20:23:51.492367...
2025-09-15 20:24:12.303 wdl.w:ptcp.w:call-paraphase-06.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for f8inv1 for sample m84036_250809_035451_s4.bc2103 at 2025-09-15 20:24:07.175182...
2025-09-15 20:24:12.303 wdl.w:ptcp.w:call-paraphase-06.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for f8inv1 for sample m84036_250809_035451_s4.bc2103 at 2025-09-15 20:24:07.175334...
2025-09-15 20:24:12.303 wdl.w:ptcp.w:call-paraphase-06.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for f8inv1 for sample m84036_250809_035451_s4.bc2103 at 2025-09-15 20:24:08.691943...
2025-09-15 20:24:12.320 wdl.w:ptcp.w:call-trgt-21.t:call-trgt_plot_motifs_allele INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2118.motifs_allele.trgt_plots.zip"
2025-09-15 20:24:12.375 wdl.w:ptcp.t:call-pbmm2_align_hifi-80 NOTICE done
2025-09-15 20:24:12.420 wdl.w:ptcp NOTICE finish :: job: "call-pbmm2_align_hifi-80"
2025-09-15 20:24:12.420 wdl.w:ptcp INFO output :: job: "call-pbmm2_align_hifi-80", values: {"report": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-80/out/mapping_stats.report.json", "mapped_bam_pbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-80/out/m84036_250809_035451_s4.bc2177.mapped.bam.pbi", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-80/out/m84036_250809_035451_s4.bc2177.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-80/out/m84036_250809_035451_s4.bc2177.mapped.bam"}
2025-09-15 20:24:12.421 wdl.w:ptcp NOTICE ready :: job: "call-paraphase-80", callee: "paraphase"
2025-09-15 20:24:12.421 wdl.w:ptcp INFO input :: job: "call-paraphase-80", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf", "genome_version": "38", "config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-80/out/m84036_250809_035451_s4.bc2177.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-80/out/m84036_250809_035451_s4.bc2177.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2177"}
2025-09-15 20:24:12.423 wdl.w:ptcp NOTICE ready :: job: "call-sawfish-80", callee: "sawfish"
2025-09-15 20:24:12.423 wdl.w:ptcp INFO input :: job: "call-sawfish-80", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-80/out/m84036_250809_035451_s4.bc2177.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-80/out/m84036_250809_035451_s4.bc2177.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2177"}
2025-09-15 20:24:12.424 wdl.w:ptcp NOTICE ready :: job: "call-trgt-80", callee: "trgt"
2025-09-15 20:24:12.424 wdl.w:ptcp INFO input :: job: "call-trgt-80", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-80/out/m84036_250809_035451_s4.bc2177.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-80/out/m84036_250809_035451_s4.bc2177.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2177"}
2025-09-15 20:24:12.427 wdl.w:ptcp.w:call-trgt-33.t:call-trgt_plot_motifs_allele NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-33/call-trgt_plot_motifs_allele", thread: 140607691417152
2025-09-15 20:24:12.437 wdl.w:ptcp.w:call-trgt-21.t:call-trgt_plot_motifs_allele NOTICE done
2025-09-15 20:24:12.442 wdl.w:ptcp.w:call-trgt-21 NOTICE finish :: job: "call-trgt_plot_motifs_allele"
2025-09-15 20:24:12.442 wdl.w:ptcp.w:call-trgt-21 INFO output :: job: "call-trgt_plot_motifs_allele", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-21/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2118.motifs_allele.trgt_plots.zip"}
2025-09-15 20:24:12.442 wdl.w:ptcp.w:call-trgt-21 INFO visit :: node: "output-images_motifs_allele", values: {"images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-21/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2118.motifs_allele.trgt_plots.zip"}
2025-09-15 20:24:12.447 wdl.w:ptcp.w:call-trgt-33.t:call-trgt_plot_motifs_waterfall NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-33/call-trgt_plot_motifs_waterfall", thread: 140610342200896
2025-09-15 20:24:12.448 wdl.w:ptcp.w:call-trgt-33.t:call-trgt_plot_motifs_allele INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:12.448 wdl.w:ptcp.w:call-trgt-33.t:call-trgt_plot_motifs_allele INFO input :: name: "waterfall", value: false
2025-09-15 20:24:12.448 wdl.w:ptcp.w:call-trgt-33.t:call-trgt_plot_motifs_allele INFO input :: name: "methylation", value: false
2025-09-15 20:24:12.448 wdl.w:ptcp.w:call-trgt-33.t:call-trgt_plot_motifs_allele INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:12.448 wdl.w:ptcp.w:call-trgt-33.t:call-trgt_plot_motifs_allele INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:12.448 wdl.w:ptcp.w:call-trgt-33.t:call-trgt_plot_motifs_allele INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:12.448 wdl.w:ptcp.w:call-trgt-33.t:call-trgt_plot_motifs_allele INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2130.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:12.448 wdl.w:ptcp.w:call-trgt-33.t:call-trgt_plot_motifs_allele INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2130.trgt.sorted.spanning.bam"
2025-09-15 20:24:12.448 wdl.w:ptcp.w:call-trgt-33.t:call-trgt_plot_motifs_allele INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2130.trgt.vcf"
2025-09-15 20:24:12.448 wdl.w:ptcp.w:call-trgt-33.t:call-trgt_plot_motifs_allele INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2130"
2025-09-15 20:24:12.448 wdl.w:ptcp.w:call-trgt-33.t:call-trgt_plot_motifs_allele INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:12.449 wdl.w:ptcp.w:call-trgt-33.t:call-trgt_plot_motifs_allele INFO eval :: name: "plot_type", value: "allele"
2025-09-15 20:24:12.449 wdl.w:ptcp.w:call-trgt-33.t:call-trgt_plot_motifs_allele INFO eval :: name: "show", value: "motifs"
2025-09-15 20:24:12.449 wdl.w:ptcp.w:call-trgt-33.t:call-trgt_plot_motifs_allele INFO eval :: name: "threads", value: 1
2025-09-15 20:24:12.449 wdl.w:ptcp.w:call-trgt-33.t:call-trgt_plot_motifs_allele INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:12.449 wdl.w:ptcp.w:call-trgt-33.t:call-trgt_plot_motifs_allele INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2130.motifs_allele"
2025-09-15 20:24:12.449 wdl.w:ptcp.w:call-trgt-33.t:call-trgt_plot_motifs_allele INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:12.450 wdl.w:ptcp.w:call-trgt-33.t:call-trgt_plot_motifs_allele WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:12.450 wdl.w:ptcp.w:call-trgt-33.t:call-trgt_plot_motifs_allele INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:12.450 wdl.w:ptcp.w:call-trgt-33.t:call-trgt_plot_motifs_allele INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:12.470 wdl.w:ptcp.w:call-trgt-33.t:call-trgt_plot_motifs_waterfall INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:12.470 wdl.w:ptcp.w:call-trgt-33.t:call-trgt_plot_motifs_waterfall INFO input :: name: "waterfall", value: true
2025-09-15 20:24:12.470 wdl.w:ptcp.w:call-trgt-33.t:call-trgt_plot_motifs_waterfall INFO input :: name: "methylation", value: false
2025-09-15 20:24:12.470 wdl.w:ptcp.w:call-trgt-33.t:call-trgt_plot_motifs_waterfall INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:12.470 wdl.w:ptcp.w:call-trgt-33.t:call-trgt_plot_motifs_waterfall INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:12.470 wdl.w:ptcp.w:call-trgt-33.t:call-trgt_plot_motifs_waterfall INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:12.470 wdl.w:ptcp.w:call-trgt-33.t:call-trgt_plot_motifs_waterfall INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2130.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:12.471 wdl.w:ptcp.w:call-trgt-33.t:call-trgt_plot_motifs_waterfall INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2130.trgt.sorted.spanning.bam"
2025-09-15 20:24:12.471 wdl.w:ptcp.w:call-trgt-33.t:call-trgt_plot_motifs_waterfall INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2130.trgt.vcf"
2025-09-15 20:24:12.471 wdl.w:ptcp.w:call-trgt-33.t:call-trgt_plot_motifs_waterfall INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2130"
2025-09-15 20:24:12.471 wdl.w:ptcp.w:call-trgt-33.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:12.471 wdl.w:ptcp.w:call-trgt-33.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "plot_type", value: "waterfall"
2025-09-15 20:24:12.471 wdl.w:ptcp.w:call-trgt-33.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "show", value: "motifs"
2025-09-15 20:24:12.471 wdl.w:ptcp.w:call-trgt-33.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "threads", value: 1
2025-09-15 20:24:12.472 wdl.w:ptcp.w:call-trgt-33.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:12.472 wdl.w:ptcp.w:call-trgt-33.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2130.motifs_waterfall"
2025-09-15 20:24:12.472 wdl.w:ptcp.w:call-trgt-33.t:call-trgt_plot_motifs_waterfall INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:12.472 wdl.w:ptcp.w:call-trgt-33.t:call-trgt_plot_motifs_waterfall WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:12.473 wdl.w:ptcp.w:call-trgt-33.t:call-trgt_plot_motifs_waterfall INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:12.473 wdl.w:ptcp.w:call-trgt-33.t:call-trgt_plot_motifs_waterfall INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:12.537 wdl.w:ptcp.w:call-trgt-33.t:call-trgt_plot_motifs_allele INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-33/call-trgt_plot_motifs_allele/_singularity_tmpdir_s6ngotd1"
2025-09-15 20:24:12.538 wdl.w:ptcp.w:call-trgt-33.t:call-trgt_plot_motifs_allele INFO Slurm invocation: srun --job-name call-trgt_plot_motifs_allele --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-33/call-trgt_plot_motifs_allele/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-33/call-trgt_plot_motifs_allele/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-33/call-trgt_plot_motifs_allele/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-33/call-trgt_plot_motifs_allele/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-33/call-trgt_genotype/out/m84036_250809_035451_s4.bc2130.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2130.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-33/call-trgt_genotype/out/m84036_250809_035451_s4.bc2130.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2130.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-33/call-trgt_genotype/out/m84036_250809_035451_s4.bc2130.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2130.trgt.sorted.spanning.bam.bai:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-33/call-trgt_plot_motifs_allele/_singularity_tmpdir_s6ngotd1/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-33/call-trgt_plot_motifs_allele/_singularity_tmpdir_s6ngotd1/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:12.547 wdl.w:ptcp.w:call-trgt-33.t:call-trgt_plot_motifs_waterfall INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-33/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_t4fsxrt8"
2025-09-15 20:24:12.547 wdl.w:ptcp.w:call-trgt-33.t:call-trgt_plot_motifs_waterfall INFO Slurm invocation: srun --job-name call-trgt_plot_motifs_waterfall --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-33/call-trgt_plot_motifs_waterfall/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-33/call-trgt_plot_motifs_waterfall/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-33/call-trgt_plot_motifs_waterfall/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-33/call-trgt_plot_motifs_waterfall/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-33/call-trgt_genotype/out/m84036_250809_035451_s4.bc2130.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2130.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-33/call-trgt_genotype/out/m84036_250809_035451_s4.bc2130.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2130.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-33/call-trgt_genotype/out/m84036_250809_035451_s4.bc2130.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2130.trgt.sorted.spanning.bam.bai:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-33/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_t4fsxrt8/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-33/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_t4fsxrt8/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:12.557 wdl.w:ptcp.w:call-trgt-33.t:call-trgt_plot_motifs_allele NOTICE slurm_singularity run :: pid: 1201152, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-33/call-trgt_plot_motifs_allele/slurm_singularity.log.txt"
2025-09-15 20:24:12.557 wdl.w:ptcp.w:call-trgt-33.t:call-trgt_plot_motifs_waterfall NOTICE slurm_singularity run :: pid: 1201153, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-33/call-trgt_plot_motifs_waterfall/slurm_singularity.log.txt"
2025-09-15 20:24:12.570 wdl.w:ptcp.w:call-paraphase-03.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for smn1 for sample m84036_250809_035451_s4.bc2100 at 2025-09-15 20:23:50.392302...
2025-09-15 20:24:12.571 wdl.w:ptcp.w:call-paraphase-03.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for hba for sample m84036_250809_035451_s4.bc2100 at 2025-09-15 20:23:50.808705...
2025-09-15 20:24:12.571 wdl.w:ptcp.w:call-paraphase-03.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for gba for sample m84036_250809_035451_s4.bc2100 at 2025-09-15 20:23:51.193374...
2025-09-15 20:24:12.571 wdl.w:ptcp.w:call-paraphase-03.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for cyp21 for sample m84036_250809_035451_s4.bc2100 at 2025-09-15 20:23:52.548790...
2025-09-15 20:24:12.571 wdl.w:ptcp.w:call-paraphase-03.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for smn1 for sample m84036_250809_035451_s4.bc2100 at 2025-09-15 20:24:00.453807...
2025-09-15 20:24:12.571 wdl.w:ptcp.w:call-paraphase-03.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning to gene2 region for smn1 for sample m84036_250809_035451_s4.bc2100 at 2025-09-15 20:24:01.015075...
2025-09-15 20:24:12.744 wdl.w:ptcp.w:call-trgt-30.t:call-trgt_plot_motifs_waterfall INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2127.motifs_waterfall.trgt_plots.zip"
2025-09-15 20:24:12.809 wdl.w:ptcp.w:call-trgt-30.t:call-trgt_plot_motifs_waterfall NOTICE done
2025-09-15 20:24:12.815 wdl.w:ptcp.w:call-trgt-30 NOTICE finish :: job: "call-trgt_plot_motifs_waterfall"
2025-09-15 20:24:12.815 wdl.w:ptcp.w:call-trgt-30 INFO output :: job: "call-trgt_plot_motifs_waterfall", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-30/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2127.motifs_waterfall.trgt_plots.zip"}
2025-09-15 20:24:12.815 wdl.w:ptcp.w:call-trgt-30 INFO visit :: node: "output-images_motifs_waterfall", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-30/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2127.motifs_waterfall.trgt_plots.zip"}
2025-09-15 20:24:12.819 wdl.w:ptcp.w:call-trgt-33.t:call-trgt_plot_meth_allele.slurm_singularity INFO srun: job 51797572 queued and waiting for resources
2025-09-15 20:24:12.819 wdl.w:ptcp.w:call-trgt-33.t:call-trgt_plot_meth_allele.slurm_singularity INFO srun: job 51797572 has been allocated resources
2025-09-15 20:24:12.819 wdl.w:ptcp.w:call-trgt-33.t:call-trgt_plot_meth_allele.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:12.822 wdl.w:ptcp.w:call-trgt-13.t:call-trgt_plot_meth_allele NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-13/call-trgt_plot_meth_allele", thread: 140613823374912
2025-09-15 20:24:12.840 wdl.w:ptcp.w:call-trgt-13.t:call-trgt_plot_meth_allele INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:12.841 wdl.w:ptcp.w:call-trgt-13.t:call-trgt_plot_meth_allele INFO input :: name: "waterfall", value: false
2025-09-15 20:24:12.841 wdl.w:ptcp.w:call-trgt-13.t:call-trgt_plot_meth_allele INFO input :: name: "methylation", value: true
2025-09-15 20:24:12.841 wdl.w:ptcp.w:call-trgt-13.t:call-trgt_plot_meth_allele INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:12.841 wdl.w:ptcp.w:call-trgt-13.t:call-trgt_plot_meth_allele INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:12.841 wdl.w:ptcp.w:call-trgt-13.t:call-trgt_plot_meth_allele INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:12.841 wdl.w:ptcp.w:call-trgt-13.t:call-trgt_plot_meth_allele INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2110.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:12.841 wdl.w:ptcp.w:call-trgt-13.t:call-trgt_plot_meth_allele INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2110.trgt.sorted.spanning.bam"
2025-09-15 20:24:12.841 wdl.w:ptcp.w:call-trgt-13.t:call-trgt_plot_meth_allele INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2110.trgt.vcf"
2025-09-15 20:24:12.841 wdl.w:ptcp.w:call-trgt-13.t:call-trgt_plot_meth_allele INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2110"
2025-09-15 20:24:12.842 wdl.w:ptcp.w:call-trgt-13.t:call-trgt_plot_meth_allele INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:12.842 wdl.w:ptcp.w:call-trgt-13.t:call-trgt_plot_meth_allele INFO eval :: name: "plot_type", value: "allele"
2025-09-15 20:24:12.842 wdl.w:ptcp.w:call-trgt-13.t:call-trgt_plot_meth_allele INFO eval :: name: "show", value: "meth"
2025-09-15 20:24:12.842 wdl.w:ptcp.w:call-trgt-13.t:call-trgt_plot_meth_allele INFO eval :: name: "threads", value: 1
2025-09-15 20:24:12.842 wdl.w:ptcp.w:call-trgt-13.t:call-trgt_plot_meth_allele INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:12.842 wdl.w:ptcp.w:call-trgt-13.t:call-trgt_plot_meth_allele INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2110.meth_allele"
2025-09-15 20:24:12.842 wdl.w:ptcp.w:call-trgt-13.t:call-trgt_plot_meth_allele INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:12.843 wdl.w:ptcp.w:call-trgt-13.t:call-trgt_plot_meth_allele WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:12.843 wdl.w:ptcp.w:call-trgt-13.t:call-trgt_plot_meth_allele INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:12.843 wdl.w:ptcp.w:call-trgt-13.t:call-trgt_plot_meth_allele INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:12.914 wdl.w:ptcp.w:call-trgt-13.t:call-trgt_plot_meth_allele INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-13/call-trgt_plot_meth_allele/_singularity_tmpdir__41vhuth"
2025-09-15 20:24:12.914 wdl.w:ptcp.w:call-trgt-13.t:call-trgt_plot_meth_allele INFO Slurm invocation: srun --job-name call-trgt_plot_meth_allele --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-13/call-trgt_plot_meth_allele/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-13/call-trgt_plot_meth_allele/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-13/call-trgt_plot_meth_allele/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-13/call-trgt_plot_meth_allele/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-13/call-trgt_genotype/out/m84036_250809_035451_s4.bc2110.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2110.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-13/call-trgt_genotype/out/m84036_250809_035451_s4.bc2110.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2110.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-13/call-trgt_genotype/out/m84036_250809_035451_s4.bc2110.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2110.trgt.sorted.spanning.bam.bai:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-13/call-trgt_plot_meth_allele/_singularity_tmpdir__41vhuth/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-13/call-trgt_plot_meth_allele/_singularity_tmpdir__41vhuth/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:12.935 wdl.w:ptcp.w:call-trgt-13.t:call-trgt_plot_meth_allele NOTICE slurm_singularity run :: pid: 1201174, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-13/call-trgt_plot_meth_allele/slurm_singularity.log.txt"
2025-09-15 20:24:12.949 wdl.w:ptcp.t:call-pbmm2_align_hifi-85 INFO output :: name: "mapped_bam", value: "m84036_250809_035451_s4.bc2182.mapped.bam"
2025-09-15 20:24:12.952 wdl.w:ptcp.t:call-pbmm2_align_hifi-85 INFO output :: name: "mapped_bam_bai", value: "m84036_250809_035451_s4.bc2182.mapped.bam.bai"
2025-09-15 20:24:12.953 wdl.w:ptcp.t:call-pbmm2_align_hifi-85 INFO output :: name: "mapped_bam_pbi", value: "m84036_250809_035451_s4.bc2182.mapped.bam.pbi"
2025-09-15 20:24:12.954 wdl.w:ptcp.t:call-pbmm2_align_hifi-85 INFO output :: name: "report", value: "mapping_stats.report.json"
2025-09-15 20:24:12.958 wdl.w:ptcp.t:call-pbmm2_align_hifi-92 INFO output :: name: "mapped_bam", value: "m84036_250809_035451_s4.bc2189.mapped.bam"
2025-09-15 20:24:12.961 wdl.w:ptcp.t:call-pbmm2_align_hifi-92 INFO output :: name: "mapped_bam_bai", value: "m84036_250809_035451_s4.bc2189.mapped.bam.bai"
2025-09-15 20:24:12.962 wdl.w:ptcp.t:call-pbmm2_align_hifi-92 INFO output :: name: "mapped_bam_pbi", value: "m84036_250809_035451_s4.bc2189.mapped.bam.pbi"
2025-09-15 20:24:12.963 wdl.w:ptcp.t:call-pbmm2_align_hifi-92 INFO output :: name: "report", value: "mapping_stats.report.json"
2025-09-15 20:24:13.034 wdl.w:ptcp.t:call-pbmm2_align_hifi-85 NOTICE done
2025-09-15 20:24:13.041 wdl.w:ptcp NOTICE finish :: job: "call-pbmm2_align_hifi-85"
2025-09-15 20:24:13.041 wdl.w:ptcp INFO output :: job: "call-pbmm2_align_hifi-85", values: {"report": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-85/out/mapping_stats.report.json", "mapped_bam_pbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-85/out/m84036_250809_035451_s4.bc2182.mapped.bam.pbi", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-85/out/m84036_250809_035451_s4.bc2182.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-85/out/m84036_250809_035451_s4.bc2182.mapped.bam"}
2025-09-15 20:24:13.041 wdl.w:ptcp NOTICE ready :: job: "call-paraphase-85", callee: "paraphase"
2025-09-15 20:24:13.042 wdl.w:ptcp INFO input :: job: "call-paraphase-85", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf", "genome_version": "38", "config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-85/out/m84036_250809_035451_s4.bc2182.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-85/out/m84036_250809_035451_s4.bc2182.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2182"}
2025-09-15 20:24:13.042 wdl.w:ptcp NOTICE ready :: job: "call-sawfish-85", callee: "sawfish"
2025-09-15 20:24:13.042 wdl.w:ptcp INFO input :: job: "call-sawfish-85", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-85/out/m84036_250809_035451_s4.bc2182.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-85/out/m84036_250809_035451_s4.bc2182.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2182"}
2025-09-15 20:24:13.044 wdl.w:ptcp NOTICE ready :: job: "call-trgt-85", callee: "trgt"
2025-09-15 20:24:13.044 wdl.w:ptcp INFO input :: job: "call-trgt-85", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-85/out/m84036_250809_035451_s4.bc2182.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-85/out/m84036_250809_035451_s4.bc2182.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2182"}
2025-09-15 20:24:13.044 wdl.w:ptcp.t:call-pbmm2_align_hifi-92 NOTICE done
2025-09-15 20:24:13.050 wdl.w:ptcp NOTICE finish :: job: "call-pbmm2_align_hifi-92"
2025-09-15 20:24:13.050 wdl.w:ptcp INFO output :: job: "call-pbmm2_align_hifi-92", values: {"report": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-92/out/mapping_stats.report.json", "mapped_bam_pbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-92/out/m84036_250809_035451_s4.bc2189.mapped.bam.pbi", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-92/out/m84036_250809_035451_s4.bc2189.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-92/out/m84036_250809_035451_s4.bc2189.mapped.bam"}
2025-09-15 20:24:13.052 wdl.w:ptcp NOTICE ready :: job: "call-paraphase-92", callee: "paraphase"
2025-09-15 20:24:13.052 wdl.w:ptcp INFO input :: job: "call-paraphase-92", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf", "genome_version": "38", "config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-92/out/m84036_250809_035451_s4.bc2189.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-92/out/m84036_250809_035451_s4.bc2189.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2189"}
2025-09-15 20:24:13.052 wdl.w:ptcp.w:call-trgt-13.t:call-trgt_plot_meth_waterfall NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-13/call-trgt_plot_meth_waterfall", thread: 140607649453632
2025-09-15 20:24:13.053 wdl.w:ptcp NOTICE ready :: job: "call-sawfish-92", callee: "sawfish"
2025-09-15 20:24:13.053 wdl.w:ptcp INFO input :: job: "call-sawfish-92", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-92/out/m84036_250809_035451_s4.bc2189.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-92/out/m84036_250809_035451_s4.bc2189.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2189"}
2025-09-15 20:24:13.054 wdl.w:ptcp NOTICE ready :: job: "call-trgt-92", callee: "trgt"
2025-09-15 20:24:13.054 wdl.w:ptcp INFO input :: job: "call-trgt-92", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-92/out/m84036_250809_035451_s4.bc2189.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-92/out/m84036_250809_035451_s4.bc2189.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2189"}
2025-09-15 20:24:13.058 wdl.w:ptcp.w:call-trgt-13.t:call-trgt_plot_motifs_allele NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-13/call-trgt_plot_motifs_allele", thread: 140607112582720
2025-09-15 20:24:13.074 wdl.w:ptcp.w:call-trgt-13.t:call-trgt_plot_motifs_allele INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:13.074 wdl.w:ptcp.w:call-trgt-13.t:call-trgt_plot_motifs_allele INFO input :: name: "waterfall", value: false
2025-09-15 20:24:13.075 wdl.w:ptcp.w:call-trgt-13.t:call-trgt_plot_motifs_allele INFO input :: name: "methylation", value: false
2025-09-15 20:24:13.075 wdl.w:ptcp.w:call-trgt-13.t:call-trgt_plot_motifs_allele INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:13.075 wdl.w:ptcp.w:call-trgt-13.t:call-trgt_plot_motifs_allele INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:13.075 wdl.w:ptcp.w:call-trgt-13.t:call-trgt_plot_motifs_allele INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:13.075 wdl.w:ptcp.w:call-trgt-13.t:call-trgt_plot_motifs_allele INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2110.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:13.075 wdl.w:ptcp.w:call-trgt-13.t:call-trgt_plot_motifs_allele INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2110.trgt.sorted.spanning.bam"
2025-09-15 20:24:13.075 wdl.w:ptcp.w:call-trgt-13.t:call-trgt_plot_motifs_allele INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2110.trgt.vcf"
2025-09-15 20:24:13.075 wdl.w:ptcp.w:call-trgt-13.t:call-trgt_plot_motifs_allele INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2110"
2025-09-15 20:24:13.075 wdl.w:ptcp.w:call-trgt-13.t:call-trgt_plot_motifs_allele INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:13.076 wdl.w:ptcp.w:call-trgt-13.t:call-trgt_plot_motifs_allele INFO eval :: name: "plot_type", value: "allele"
2025-09-15 20:24:13.076 wdl.w:ptcp.w:call-trgt-13.t:call-trgt_plot_motifs_allele INFO eval :: name: "show", value: "motifs"
2025-09-15 20:24:13.076 wdl.w:ptcp.w:call-trgt-13.t:call-trgt_plot_motifs_allele INFO eval :: name: "threads", value: 1
2025-09-15 20:24:13.076 wdl.w:ptcp.w:call-trgt-13.t:call-trgt_plot_motifs_allele INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:13.076 wdl.w:ptcp.w:call-trgt-13.t:call-trgt_plot_motifs_allele INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2110.motifs_allele"
2025-09-15 20:24:13.076 wdl.w:ptcp.w:call-trgt-13.t:call-trgt_plot_motifs_allele INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:13.077 wdl.w:ptcp.w:call-trgt-13.t:call-trgt_plot_motifs_allele WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:13.077 wdl.w:ptcp.w:call-trgt-13.t:call-trgt_plot_motifs_allele INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:13.077 wdl.w:ptcp.w:call-trgt-13.t:call-trgt_plot_motifs_allele INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:13.079 wdl.w:ptcp.w:call-trgt-13.t:call-trgt_plot_meth_waterfall INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:13.079 wdl.w:ptcp.w:call-trgt-13.t:call-trgt_plot_meth_waterfall INFO input :: name: "waterfall", value: true
2025-09-15 20:24:13.079 wdl.w:ptcp.w:call-trgt-13.t:call-trgt_plot_meth_waterfall INFO input :: name: "methylation", value: true
2025-09-15 20:24:13.079 wdl.w:ptcp.w:call-trgt-13.t:call-trgt_plot_meth_waterfall INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:13.079 wdl.w:ptcp.w:call-trgt-13.t:call-trgt_plot_meth_waterfall INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:13.079 wdl.w:ptcp.w:call-trgt-13.t:call-trgt_plot_meth_waterfall INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:13.079 wdl.w:ptcp.w:call-trgt-13.t:call-trgt_plot_meth_waterfall INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2110.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:13.079 wdl.w:ptcp.w:call-trgt-13.t:call-trgt_plot_meth_waterfall INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2110.trgt.sorted.spanning.bam"
2025-09-15 20:24:13.079 wdl.w:ptcp.w:call-trgt-13.t:call-trgt_plot_meth_waterfall INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2110.trgt.vcf"
2025-09-15 20:24:13.079 wdl.w:ptcp.w:call-trgt-13.t:call-trgt_plot_meth_waterfall INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2110"
2025-09-15 20:24:13.080 wdl.w:ptcp.w:call-trgt-13.t:call-trgt_plot_meth_waterfall INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:13.080 wdl.w:ptcp.w:call-trgt-13.t:call-trgt_plot_meth_waterfall INFO eval :: name: "plot_type", value: "waterfall"
2025-09-15 20:24:13.080 wdl.w:ptcp.w:call-trgt-13.t:call-trgt_plot_meth_waterfall INFO eval :: name: "show", value: "meth"
2025-09-15 20:24:13.080 wdl.w:ptcp.w:call-trgt-13.t:call-trgt_plot_meth_waterfall INFO eval :: name: "threads", value: 1
2025-09-15 20:24:13.080 wdl.w:ptcp.w:call-trgt-13.t:call-trgt_plot_meth_waterfall INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:13.080 wdl.w:ptcp.w:call-trgt-13.t:call-trgt_plot_meth_waterfall INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2110.meth_waterfall"
2025-09-15 20:24:13.081 wdl.w:ptcp.w:call-trgt-13.t:call-trgt_plot_meth_waterfall INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:13.081 wdl.w:ptcp.w:call-trgt-13.t:call-trgt_plot_meth_waterfall WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:13.081 wdl.w:ptcp.w:call-trgt-13.t:call-trgt_plot_meth_waterfall INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:13.082 wdl.w:ptcp.w:call-trgt-13.t:call-trgt_plot_meth_waterfall INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:13.153 wdl.w:ptcp.w:call-trgt-13.t:call-trgt_plot_motifs_allele INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-13/call-trgt_plot_motifs_allele/_singularity_tmpdir_yfb06d7d"
2025-09-15 20:24:13.153 wdl.w:ptcp.w:call-trgt-13.t:call-trgt_plot_motifs_allele INFO Slurm invocation: srun --job-name call-trgt_plot_motifs_allele --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-13/call-trgt_plot_motifs_allele/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-13/call-trgt_plot_motifs_allele/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-13/call-trgt_plot_motifs_allele/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-13/call-trgt_plot_motifs_allele/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-13/call-trgt_genotype/out/m84036_250809_035451_s4.bc2110.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2110.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-13/call-trgt_genotype/out/m84036_250809_035451_s4.bc2110.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2110.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-13/call-trgt_genotype/out/m84036_250809_035451_s4.bc2110.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2110.trgt.sorted.spanning.bam.bai:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-13/call-trgt_plot_motifs_allele/_singularity_tmpdir_yfb06d7d/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-13/call-trgt_plot_motifs_allele/_singularity_tmpdir_yfb06d7d/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:13.157 wdl.w:ptcp.t:call-pbmm2_align_hifi-91 INFO output :: name: "mapped_bam", value: "m84036_250809_035451_s4.bc2188.mapped.bam"
2025-09-15 20:24:13.161 wdl.w:ptcp.w:call-trgt-13.t:call-trgt_plot_meth_waterfall INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-13/call-trgt_plot_meth_waterfall/_singularity_tmpdir_gxasrne4"
2025-09-15 20:24:13.161 wdl.w:ptcp.w:call-trgt-13.t:call-trgt_plot_meth_waterfall INFO Slurm invocation: srun --job-name call-trgt_plot_meth_waterfall --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-13/call-trgt_plot_meth_waterfall/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-13/call-trgt_plot_meth_waterfall/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-13/call-trgt_plot_meth_waterfall/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-13/call-trgt_plot_meth_waterfall/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-13/call-trgt_genotype/out/m84036_250809_035451_s4.bc2110.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2110.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-13/call-trgt_genotype/out/m84036_250809_035451_s4.bc2110.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2110.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-13/call-trgt_genotype/out/m84036_250809_035451_s4.bc2110.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2110.trgt.sorted.spanning.bam.bai:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-13/call-trgt_plot_meth_waterfall/_singularity_tmpdir_gxasrne4/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-13/call-trgt_plot_meth_waterfall/_singularity_tmpdir_gxasrne4/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:13.162 wdl.w:ptcp.t:call-pbmm2_align_hifi-91 INFO output :: name: "mapped_bam_bai", value: "m84036_250809_035451_s4.bc2188.mapped.bam.bai"
2025-09-15 20:24:13.163 wdl.w:ptcp.t:call-pbmm2_align_hifi-91 INFO output :: name: "mapped_bam_pbi", value: "m84036_250809_035451_s4.bc2188.mapped.bam.pbi"
2025-09-15 20:24:13.164 wdl.w:ptcp.t:call-pbmm2_align_hifi-91 INFO output :: name: "report", value: "mapping_stats.report.json"
2025-09-15 20:24:13.168 wdl.w:ptcp.w:call-trgt-13.t:call-trgt_plot_meth_waterfall NOTICE slurm_singularity run :: pid: 1201183, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-13/call-trgt_plot_meth_waterfall/slurm_singularity.log.txt"
2025-09-15 20:24:13.168 wdl.w:ptcp.w:call-trgt-13.t:call-trgt_plot_motifs_allele NOTICE slurm_singularity run :: pid: 1201182, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-13/call-trgt_plot_motifs_allele/slurm_singularity.log.txt"
2025-09-15 20:24:13.252 wdl.w:ptcp.t:call-pbmm2_align_hifi-91 NOTICE done
2025-09-15 20:24:13.257 wdl.w:ptcp NOTICE finish :: job: "call-pbmm2_align_hifi-91"
2025-09-15 20:24:13.257 wdl.w:ptcp INFO output :: job: "call-pbmm2_align_hifi-91", values: {"report": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-91/out/mapping_stats.report.json", "mapped_bam_pbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-91/out/m84036_250809_035451_s4.bc2188.mapped.bam.pbi", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-91/out/m84036_250809_035451_s4.bc2188.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-91/out/m84036_250809_035451_s4.bc2188.mapped.bam"}
2025-09-15 20:24:13.258 wdl.w:ptcp NOTICE ready :: job: "call-paraphase-91", callee: "paraphase"
2025-09-15 20:24:13.258 wdl.w:ptcp INFO input :: job: "call-paraphase-91", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf", "genome_version": "38", "config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-91/out/m84036_250809_035451_s4.bc2188.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-91/out/m84036_250809_035451_s4.bc2188.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2188"}
2025-09-15 20:24:13.259 wdl.w:ptcp NOTICE ready :: job: "call-sawfish-91", callee: "sawfish"
2025-09-15 20:24:13.259 wdl.w:ptcp INFO input :: job: "call-sawfish-91", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-91/out/m84036_250809_035451_s4.bc2188.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-91/out/m84036_250809_035451_s4.bc2188.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2188"}
2025-09-15 20:24:13.260 wdl.w:ptcp NOTICE ready :: job: "call-trgt-91", callee: "trgt"
2025-09-15 20:24:13.260 wdl.w:ptcp INFO input :: job: "call-trgt-91", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-91/out/m84036_250809_035451_s4.bc2188.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-91/out/m84036_250809_035451_s4.bc2188.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2188"}
2025-09-15 20:24:13.263 wdl.w:ptcp.w:call-trgt-13.t:call-trgt_plot_motifs_waterfall NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-13/call-trgt_plot_motifs_waterfall", thread: 140607120975424
2025-09-15 20:24:13.282 wdl.w:ptcp.w:call-trgt-13.t:call-trgt_plot_motifs_waterfall INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:13.282 wdl.w:ptcp.w:call-trgt-13.t:call-trgt_plot_motifs_waterfall INFO input :: name: "waterfall", value: true
2025-09-15 20:24:13.282 wdl.w:ptcp.w:call-trgt-13.t:call-trgt_plot_motifs_waterfall INFO input :: name: "methylation", value: false
2025-09-15 20:24:13.282 wdl.w:ptcp.w:call-trgt-13.t:call-trgt_plot_motifs_waterfall INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:13.282 wdl.w:ptcp.w:call-trgt-13.t:call-trgt_plot_motifs_waterfall INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:13.282 wdl.w:ptcp.w:call-trgt-13.t:call-trgt_plot_motifs_waterfall INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:13.282 wdl.w:ptcp.w:call-trgt-13.t:call-trgt_plot_motifs_waterfall INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2110.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:13.282 wdl.w:ptcp.w:call-trgt-13.t:call-trgt_plot_motifs_waterfall INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2110.trgt.sorted.spanning.bam"
2025-09-15 20:24:13.282 wdl.w:ptcp.w:call-trgt-13.t:call-trgt_plot_motifs_waterfall INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2110.trgt.vcf"
2025-09-15 20:24:13.282 wdl.w:ptcp.w:call-trgt-13.t:call-trgt_plot_motifs_waterfall INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2110"
2025-09-15 20:24:13.283 wdl.w:ptcp.w:call-trgt-13.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:13.283 wdl.w:ptcp.w:call-trgt-13.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "plot_type", value: "waterfall"
2025-09-15 20:24:13.283 wdl.w:ptcp.w:call-trgt-13.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "show", value: "motifs"
2025-09-15 20:24:13.283 wdl.w:ptcp.w:call-trgt-13.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "threads", value: 1
2025-09-15 20:24:13.283 wdl.w:ptcp.w:call-trgt-13.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:13.283 wdl.w:ptcp.w:call-trgt-13.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2110.motifs_waterfall"
2025-09-15 20:24:13.284 wdl.w:ptcp.w:call-trgt-13.t:call-trgt_plot_motifs_waterfall INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:13.284 wdl.w:ptcp.w:call-trgt-13.t:call-trgt_plot_motifs_waterfall WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:13.284 wdl.w:ptcp.w:call-trgt-13.t:call-trgt_plot_motifs_waterfall INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:13.284 wdl.w:ptcp.w:call-trgt-13.t:call-trgt_plot_motifs_waterfall INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:13.306 wdl.w:ptcp.t:call-pbmm2_align_hifi-87 INFO output :: name: "mapped_bam", value: "m84036_250809_035451_s4.bc2184.mapped.bam"
2025-09-15 20:24:13.308 wdl.w:ptcp.t:call-pbmm2_align_hifi-87 INFO output :: name: "mapped_bam_bai", value: "m84036_250809_035451_s4.bc2184.mapped.bam.bai"
2025-09-15 20:24:13.310 wdl.w:ptcp.t:call-pbmm2_align_hifi-87 INFO output :: name: "mapped_bam_pbi", value: "m84036_250809_035451_s4.bc2184.mapped.bam.pbi"
2025-09-15 20:24:13.311 wdl.w:ptcp.t:call-pbmm2_align_hifi-87 INFO output :: name: "report", value: "mapping_stats.report.json"
2025-09-15 20:24:13.313 wdl.w:ptcp.w:call-trgt-33.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO srun: job 51797573 queued and waiting for resources
2025-09-15 20:24:13.313 wdl.w:ptcp.w:call-trgt-33.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO srun: job 51797573 has been allocated resources
2025-09-15 20:24:13.313 wdl.w:ptcp.w:call-trgt-33.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:13.372 wdl.w:ptcp.w:call-trgt-30.t:call-trgt_plot_meth_allele INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2127.meth_allele.trgt_plots.zip"
2025-09-15 20:24:13.395 wdl.w:ptcp.w:call-trgt-28.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:12 [ERROR] - No reads found for TRID=PRTS_ARX
2025-09-15 20:24:13.395 wdl.w:ptcp.w:call-trgt-28.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:12 [ERROR] - No reads found for TRID=EIEE1_ARX
2025-09-15 20:24:13.404 wdl.w:ptcp.w:call-trgt-13.t:call-trgt_plot_motifs_waterfall INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-13/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_xxd9pf_w"
2025-09-15 20:24:13.405 wdl.w:ptcp.w:call-trgt-13.t:call-trgt_plot_motifs_waterfall INFO Slurm invocation: srun --job-name call-trgt_plot_motifs_waterfall --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-13/call-trgt_plot_motifs_waterfall/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-13/call-trgt_plot_motifs_waterfall/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-13/call-trgt_plot_motifs_waterfall/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-13/call-trgt_plot_motifs_waterfall/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-13/call-trgt_genotype/out/m84036_250809_035451_s4.bc2110.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2110.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-13/call-trgt_genotype/out/m84036_250809_035451_s4.bc2110.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2110.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-13/call-trgt_genotype/out/m84036_250809_035451_s4.bc2110.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2110.trgt.sorted.spanning.bam.bai:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-13/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_xxd9pf_w/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-13/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_xxd9pf_w/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:13.424 wdl.w:ptcp.w:call-trgt-13.t:call-trgt_plot_motifs_waterfall NOTICE slurm_singularity run :: pid: 1201198, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-13/call-trgt_plot_motifs_waterfall/slurm_singularity.log.txt"
2025-09-15 20:24:13.425 wdl.w:ptcp.t:call-pbmm2_align_hifi-87 NOTICE done
2025-09-15 20:24:13.435 wdl.w:ptcp NOTICE finish :: job: "call-pbmm2_align_hifi-87"
2025-09-15 20:24:13.436 wdl.w:ptcp INFO output :: job: "call-pbmm2_align_hifi-87", values: {"report": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-87/out/mapping_stats.report.json", "mapped_bam_pbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-87/out/m84036_250809_035451_s4.bc2184.mapped.bam.pbi", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-87/out/m84036_250809_035451_s4.bc2184.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-87/out/m84036_250809_035451_s4.bc2184.mapped.bam"}
2025-09-15 20:24:13.436 wdl.w:ptcp NOTICE ready :: job: "call-paraphase-87", callee: "paraphase"
2025-09-15 20:24:13.436 wdl.w:ptcp INFO input :: job: "call-paraphase-87", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf", "genome_version": "38", "config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-87/out/m84036_250809_035451_s4.bc2184.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-87/out/m84036_250809_035451_s4.bc2184.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2184"}
2025-09-15 20:24:13.438 wdl.w:ptcp NOTICE ready :: job: "call-sawfish-87", callee: "sawfish"
2025-09-15 20:24:13.438 wdl.w:ptcp INFO input :: job: "call-sawfish-87", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-87/out/m84036_250809_035451_s4.bc2184.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-87/out/m84036_250809_035451_s4.bc2184.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2184"}
2025-09-15 20:24:13.439 wdl.w:ptcp NOTICE ready :: job: "call-trgt-87", callee: "trgt"
2025-09-15 20:24:13.439 wdl.w:ptcp INFO input :: job: "call-trgt-87", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-87/out/m84036_250809_035451_s4.bc2184.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-87/out/m84036_250809_035451_s4.bc2184.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2184"}
2025-09-15 20:24:13.442 wdl.w:ptcp.w:call-trgt-29.t:call-trgt_plot_meth_allele NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-29/call-trgt_plot_meth_allele", thread: 140607154546240
2025-09-15 20:24:13.454 wdl.w:ptcp.w:call-trgt-30.t:call-trgt_plot_meth_allele NOTICE done
2025-09-15 20:24:13.459 wdl.w:ptcp.w:call-trgt-30 NOTICE finish :: job: "call-trgt_plot_meth_allele"
2025-09-15 20:24:13.459 wdl.w:ptcp.w:call-trgt-30 INFO output :: job: "call-trgt_plot_meth_allele", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-30/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2127.meth_allele.trgt_plots.zip"}
2025-09-15 20:24:13.459 wdl.w:ptcp.w:call-trgt-30 INFO visit :: node: "output-images_meth_allele", values: {"images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-30/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2127.meth_allele.trgt_plots.zip"}
2025-09-15 20:24:13.463 wdl.w:ptcp.w:call-trgt-29.t:call-trgt_plot_meth_allele INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:13.463 wdl.w:ptcp.w:call-trgt-29.t:call-trgt_plot_meth_allele INFO input :: name: "waterfall", value: false
2025-09-15 20:24:13.464 wdl.w:ptcp.w:call-trgt-29.t:call-trgt_plot_meth_allele INFO input :: name: "methylation", value: true
2025-09-15 20:24:13.464 wdl.w:ptcp.w:call-trgt-29.t:call-trgt_plot_meth_allele INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:13.464 wdl.w:ptcp.w:call-trgt-29.t:call-trgt_plot_meth_allele INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:13.464 wdl.w:ptcp.w:call-trgt-29.t:call-trgt_plot_meth_allele INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:13.464 wdl.w:ptcp.w:call-trgt-29.t:call-trgt_plot_meth_allele INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2126.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:13.464 wdl.w:ptcp.w:call-trgt-29.t:call-trgt_plot_meth_allele INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2126.trgt.sorted.spanning.bam"
2025-09-15 20:24:13.464 wdl.w:ptcp.w:call-trgt-29.t:call-trgt_plot_meth_allele INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2126.trgt.vcf"
2025-09-15 20:24:13.464 wdl.w:ptcp.w:call-trgt-29.t:call-trgt_plot_meth_allele INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2126"
2025-09-15 20:24:13.464 wdl.w:ptcp.w:call-trgt-29.t:call-trgt_plot_meth_waterfall NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-29/call-trgt_plot_meth_waterfall", thread: 140607657846336
2025-09-15 20:24:13.465 wdl.w:ptcp.w:call-trgt-29.t:call-trgt_plot_meth_allele INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:13.465 wdl.w:ptcp.w:call-trgt-29.t:call-trgt_plot_meth_allele INFO eval :: name: "plot_type", value: "allele"
2025-09-15 20:24:13.465 wdl.w:ptcp.w:call-trgt-29.t:call-trgt_plot_meth_allele INFO eval :: name: "show", value: "meth"
2025-09-15 20:24:13.465 wdl.w:ptcp.w:call-trgt-29.t:call-trgt_plot_meth_allele INFO eval :: name: "threads", value: 1
2025-09-15 20:24:13.465 wdl.w:ptcp.w:call-trgt-29.t:call-trgt_plot_meth_allele INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:13.465 wdl.w:ptcp.w:call-trgt-29.t:call-trgt_plot_meth_allele INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2126.meth_allele"
2025-09-15 20:24:13.466 wdl.w:ptcp.w:call-trgt-29.t:call-trgt_plot_meth_allele INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:13.466 wdl.w:ptcp.w:call-trgt-29.t:call-trgt_plot_meth_allele WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:13.466 wdl.w:ptcp.w:call-trgt-29.t:call-trgt_plot_meth_allele INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:13.467 wdl.w:ptcp.w:call-trgt-29.t:call-trgt_plot_meth_allele INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:13.482 wdl.w:ptcp.w:call-trgt-29.t:call-trgt_plot_meth_waterfall INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:13.482 wdl.w:ptcp.w:call-trgt-29.t:call-trgt_plot_meth_waterfall INFO input :: name: "waterfall", value: true
2025-09-15 20:24:13.482 wdl.w:ptcp.w:call-trgt-29.t:call-trgt_plot_meth_waterfall INFO input :: name: "methylation", value: true
2025-09-15 20:24:13.482 wdl.w:ptcp.w:call-trgt-29.t:call-trgt_plot_meth_waterfall INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:13.482 wdl.w:ptcp.w:call-trgt-29.t:call-trgt_plot_meth_waterfall INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:13.482 wdl.w:ptcp.w:call-trgt-29.t:call-trgt_plot_meth_waterfall INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:13.483 wdl.w:ptcp.w:call-trgt-29.t:call-trgt_plot_meth_waterfall INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2126.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:13.483 wdl.w:ptcp.w:call-trgt-29.t:call-trgt_plot_meth_waterfall INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2126.trgt.sorted.spanning.bam"
2025-09-15 20:24:13.483 wdl.w:ptcp.w:call-trgt-29.t:call-trgt_plot_meth_waterfall INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2126.trgt.vcf"
2025-09-15 20:24:13.483 wdl.w:ptcp.w:call-trgt-29.t:call-trgt_plot_meth_waterfall INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2126"
2025-09-15 20:24:13.483 wdl.w:ptcp.w:call-trgt-29.t:call-trgt_plot_meth_waterfall INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:13.483 wdl.w:ptcp.w:call-trgt-29.t:call-trgt_plot_meth_waterfall INFO eval :: name: "plot_type", value: "waterfall"
2025-09-15 20:24:13.483 wdl.w:ptcp.w:call-trgt-29.t:call-trgt_plot_meth_waterfall INFO eval :: name: "show", value: "meth"
2025-09-15 20:24:13.484 wdl.w:ptcp.w:call-trgt-29.t:call-trgt_plot_meth_waterfall INFO eval :: name: "threads", value: 1
2025-09-15 20:24:13.484 wdl.w:ptcp.w:call-trgt-29.t:call-trgt_plot_meth_waterfall INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:13.484 wdl.w:ptcp.w:call-trgt-29.t:call-trgt_plot_meth_waterfall INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2126.meth_waterfall"
2025-09-15 20:24:13.484 wdl.w:ptcp.w:call-trgt-29.t:call-trgt_plot_meth_waterfall INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:13.484 wdl.w:ptcp.w:call-trgt-29.t:call-trgt_plot_meth_waterfall WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:13.485 wdl.w:ptcp.w:call-trgt-29.t:call-trgt_plot_meth_waterfall INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:13.485 wdl.w:ptcp.w:call-trgt-29.t:call-trgt_plot_meth_waterfall INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:13.527 wdl.w:ptcp.w:call-trgt-30.t:call-trgt_plot_meth_waterfall INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2127.meth_waterfall.trgt_plots.zip"
2025-09-15 20:24:13.559 wdl.w:ptcp.w:call-trgt-29.t:call-trgt_plot_meth_allele INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-29/call-trgt_plot_meth_allele/_singularity_tmpdir_lp3wx4hj"
2025-09-15 20:24:13.560 wdl.w:ptcp.w:call-trgt-29.t:call-trgt_plot_meth_allele INFO Slurm invocation: srun --job-name call-trgt_plot_meth_allele --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-29/call-trgt_plot_meth_allele/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-29/call-trgt_plot_meth_allele/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-29/call-trgt_plot_meth_allele/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-29/call-trgt_plot_meth_allele/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-29/call-trgt_genotype/out/m84036_250809_035451_s4.bc2126.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2126.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-29/call-trgt_genotype/out/m84036_250809_035451_s4.bc2126.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2126.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-29/call-trgt_genotype/out/m84036_250809_035451_s4.bc2126.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2126.trgt.vcf:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-29/call-trgt_plot_meth_allele/_singularity_tmpdir_lp3wx4hj/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-29/call-trgt_plot_meth_allele/_singularity_tmpdir_lp3wx4hj/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:13.570 wdl.w:ptcp.w:call-trgt-33.t:call-trgt_plot_motifs_allele.slurm_singularity INFO srun: job 51797574 queued and waiting for resources
2025-09-15 20:24:13.570 wdl.w:ptcp.w:call-trgt-33.t:call-trgt_plot_motifs_allele.slurm_singularity INFO srun: job 51797574 has been allocated resources
2025-09-15 20:24:13.570 wdl.w:ptcp.w:call-trgt-33.t:call-trgt_plot_motifs_allele.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:13.574 wdl.w:ptcp.w:call-trgt-33.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO srun: job 51797575 queued and waiting for resources
2025-09-15 20:24:13.574 wdl.w:ptcp.w:call-trgt-33.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO srun: job 51797575 has been allocated resources
2025-09-15 20:24:13.574 wdl.w:ptcp.w:call-trgt-33.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:13.578 wdl.w:ptcp.w:call-trgt-29.t:call-trgt_plot_meth_waterfall INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-29/call-trgt_plot_meth_waterfall/_singularity_tmpdir_7jaqpt7r"
2025-09-15 20:24:13.578 wdl.w:ptcp.w:call-trgt-29.t:call-trgt_plot_meth_waterfall INFO Slurm invocation: srun --job-name call-trgt_plot_meth_waterfall --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-29/call-trgt_plot_meth_waterfall/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-29/call-trgt_plot_meth_waterfall/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-29/call-trgt_plot_meth_waterfall/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-29/call-trgt_plot_meth_waterfall/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-29/call-trgt_genotype/out/m84036_250809_035451_s4.bc2126.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2126.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-29/call-trgt_genotype/out/m84036_250809_035451_s4.bc2126.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2126.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-29/call-trgt_genotype/out/m84036_250809_035451_s4.bc2126.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2126.trgt.vcf:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-29/call-trgt_plot_meth_waterfall/_singularity_tmpdir_7jaqpt7r/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-29/call-trgt_plot_meth_waterfall/_singularity_tmpdir_7jaqpt7r/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:13.590 wdl.w:ptcp.w:call-trgt-29.t:call-trgt_plot_meth_allele NOTICE slurm_singularity run :: pid: 1201206, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-29/call-trgt_plot_meth_allele/slurm_singularity.log.txt"
2025-09-15 20:24:13.590 wdl.w:ptcp.w:call-trgt-29.t:call-trgt_plot_meth_waterfall NOTICE slurm_singularity run :: pid: 1201207, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-29/call-trgt_plot_meth_waterfall/slurm_singularity.log.txt"
2025-09-15 20:24:13.613 wdl.w:ptcp.w:call-trgt-30.t:call-trgt_plot_meth_waterfall NOTICE done
2025-09-15 20:24:13.617 wdl.w:ptcp.w:call-trgt-30 NOTICE finish :: job: "call-trgt_plot_meth_waterfall"
2025-09-15 20:24:13.617 wdl.w:ptcp.w:call-trgt-30 INFO output :: job: "call-trgt_plot_meth_waterfall", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-30/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2127.meth_waterfall.trgt_plots.zip"}
2025-09-15 20:24:13.618 wdl.w:ptcp.w:call-trgt-30 INFO visit :: node: "output-images_meth_waterfall", values: {"images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-30/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2127.meth_waterfall.trgt_plots.zip"}
2025-09-15 20:24:13.622 wdl.w:ptcp.w:call-trgt-29.t:call-trgt_plot_motifs_allele NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-29/call-trgt_plot_motifs_allele", thread: 140608773551680
2025-09-15 20:24:13.640 wdl.w:ptcp.w:call-trgt-29.t:call-trgt_plot_motifs_allele INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:13.641 wdl.w:ptcp.w:call-trgt-29.t:call-trgt_plot_motifs_allele INFO input :: name: "waterfall", value: false
2025-09-15 20:24:13.641 wdl.w:ptcp.w:call-trgt-29.t:call-trgt_plot_motifs_allele INFO input :: name: "methylation", value: false
2025-09-15 20:24:13.641 wdl.w:ptcp.w:call-trgt-29.t:call-trgt_plot_motifs_allele INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:13.641 wdl.w:ptcp.w:call-trgt-29.t:call-trgt_plot_motifs_allele INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:13.641 wdl.w:ptcp.w:call-trgt-29.t:call-trgt_plot_motifs_allele INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:13.641 wdl.w:ptcp.w:call-trgt-29.t:call-trgt_plot_motifs_allele INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2126.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:13.641 wdl.w:ptcp.w:call-trgt-29.t:call-trgt_plot_motifs_allele INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2126.trgt.sorted.spanning.bam"
2025-09-15 20:24:13.641 wdl.w:ptcp.w:call-trgt-29.t:call-trgt_plot_motifs_allele INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2126.trgt.vcf"
2025-09-15 20:24:13.641 wdl.w:ptcp.w:call-trgt-29.t:call-trgt_plot_motifs_allele INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2126"
2025-09-15 20:24:13.641 wdl.w:ptcp.w:call-trgt-29.t:call-trgt_plot_motifs_allele INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:13.641 wdl.w:ptcp.w:call-trgt-29.t:call-trgt_plot_motifs_allele INFO eval :: name: "plot_type", value: "allele"
2025-09-15 20:24:13.642 wdl.w:ptcp.w:call-trgt-29.t:call-trgt_plot_motifs_allele INFO eval :: name: "show", value: "motifs"
2025-09-15 20:24:13.642 wdl.w:ptcp.w:call-trgt-29.t:call-trgt_plot_motifs_allele INFO eval :: name: "threads", value: 1
2025-09-15 20:24:13.642 wdl.w:ptcp.w:call-trgt-29.t:call-trgt_plot_motifs_allele INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:13.642 wdl.w:ptcp.w:call-trgt-29.t:call-trgt_plot_motifs_allele INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2126.motifs_allele"
2025-09-15 20:24:13.642 wdl.w:ptcp.w:call-trgt-29.t:call-trgt_plot_motifs_allele INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:13.643 wdl.w:ptcp.w:call-trgt-29.t:call-trgt_plot_motifs_allele WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:13.643 wdl.w:ptcp.w:call-trgt-29.t:call-trgt_plot_motifs_allele INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:13.643 wdl.w:ptcp.w:call-trgt-29.t:call-trgt_plot_motifs_allele INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:13.666 wdl.w:ptcp.w:call-trgt-30.t:call-trgt_plot_motifs_allele INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2127.motifs_allele.trgt_plots.zip"
2025-09-15 20:24:13.719 wdl.w:ptcp.w:call-trgt-29.t:call-trgt_plot_motifs_allele INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-29/call-trgt_plot_motifs_allele/_singularity_tmpdir_i9tz52kt"
2025-09-15 20:24:13.719 wdl.w:ptcp.w:call-trgt-29.t:call-trgt_plot_motifs_allele INFO Slurm invocation: srun --job-name call-trgt_plot_motifs_allele --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-29/call-trgt_plot_motifs_allele/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-29/call-trgt_plot_motifs_allele/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-29/call-trgt_plot_motifs_allele/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-29/call-trgt_plot_motifs_allele/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-29/call-trgt_genotype/out/m84036_250809_035451_s4.bc2126.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2126.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-29/call-trgt_genotype/out/m84036_250809_035451_s4.bc2126.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2126.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-29/call-trgt_genotype/out/m84036_250809_035451_s4.bc2126.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2126.trgt.vcf:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-29/call-trgt_plot_motifs_allele/_singularity_tmpdir_i9tz52kt/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-29/call-trgt_plot_motifs_allele/_singularity_tmpdir_i9tz52kt/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:13.736 wdl.w:ptcp.w:call-trgt-29.t:call-trgt_plot_motifs_allele NOTICE slurm_singularity run :: pid: 1201222, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-29/call-trgt_plot_motifs_allele/slurm_singularity.log.txt"
2025-09-15 20:24:13.738 wdl.w:ptcp.w:call-trgt-30.t:call-trgt_plot_motifs_allele NOTICE done
2025-09-15 20:24:13.743 wdl.w:ptcp.w:call-trgt-30 NOTICE finish :: job: "call-trgt_plot_motifs_allele"
2025-09-15 20:24:13.743 wdl.w:ptcp.w:call-trgt-30 INFO output :: job: "call-trgt_plot_motifs_allele", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-30/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2127.motifs_allele.trgt_plots.zip"}
2025-09-15 20:24:13.743 wdl.w:ptcp.w:call-trgt-30 INFO visit :: node: "output-images_motifs_allele", values: {"images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-30/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2127.motifs_allele.trgt_plots.zip"}
2025-09-15 20:24:13.743 wdl.w:ptcp.w:call-trgt-30 INFO visit :: node: "outputs", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-30/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2127.motifs_waterfall.trgt_plots.zip", "images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-30/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2127.meth_allele.trgt_plots.zip", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-30/call-trgt_genotype/out/m84036_250809_035451_s4.bc2127.trgt.sorted.spanning.bam.bai", "images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-30/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2127.motifs_allele.trgt_plots.zip", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-30/call-trgt_genotype/out/m84036_250809_035451_s4.bc2127.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-30/call-trgt_genotype/out/m84036_250809_035451_s4.bc2127.trgt.vcf", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-30/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2127.repeats.bam", "images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-30/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2127.meth_waterfall.trgt_plots.zip", "reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-30/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2127.repeats.bam.bai"}
2025-09-15 20:24:13.750 wdl.w:ptcp.w:call-trgt-29.t:call-trgt_plot_motifs_waterfall NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-29/call-trgt_plot_motifs_waterfall", thread: 140608203109952
2025-09-15 20:24:13.778 wdl.w:ptcp.t:call-pbmm2_align_hifi-89 INFO output :: name: "mapped_bam", value: "m84036_250809_035451_s4.bc2186.mapped.bam"
2025-09-15 20:24:13.783 wdl.w:ptcp.t:call-pbmm2_align_hifi-89 INFO output :: name: "mapped_bam_bai", value: "m84036_250809_035451_s4.bc2186.mapped.bam.bai"
2025-09-15 20:24:13.784 wdl.w:ptcp.t:call-pbmm2_align_hifi-89 INFO output :: name: "mapped_bam_pbi", value: "m84036_250809_035451_s4.bc2186.mapped.bam.pbi"
2025-09-15 20:24:13.786 wdl.w:ptcp.t:call-pbmm2_align_hifi-89 INFO output :: name: "report", value: "mapping_stats.report.json"
2025-09-15 20:24:13.791 wdl.w:ptcp.w:call-trgt-29.t:call-trgt_plot_motifs_waterfall INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:13.791 wdl.w:ptcp.w:call-trgt-29.t:call-trgt_plot_motifs_waterfall INFO input :: name: "waterfall", value: true
2025-09-15 20:24:13.792 wdl.w:ptcp.w:call-trgt-29.t:call-trgt_plot_motifs_waterfall INFO input :: name: "methylation", value: false
2025-09-15 20:24:13.792 wdl.w:ptcp.w:call-trgt-29.t:call-trgt_plot_motifs_waterfall INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:13.792 wdl.w:ptcp.w:call-trgt-29.t:call-trgt_plot_motifs_waterfall INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:13.792 wdl.w:ptcp.w:call-trgt-29.t:call-trgt_plot_motifs_waterfall INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:13.792 wdl.w:ptcp.w:call-trgt-29.t:call-trgt_plot_motifs_waterfall INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2126.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:13.792 wdl.w:ptcp.w:call-trgt-29.t:call-trgt_plot_motifs_waterfall INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2126.trgt.sorted.spanning.bam"
2025-09-15 20:24:13.792 wdl.w:ptcp.w:call-trgt-29.t:call-trgt_plot_motifs_waterfall INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2126.trgt.vcf"
2025-09-15 20:24:13.792 wdl.w:ptcp.w:call-trgt-29.t:call-trgt_plot_motifs_waterfall INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2126"
2025-09-15 20:24:13.794 wdl.w:ptcp.w:call-trgt-29.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:13.794 wdl.w:ptcp.w:call-trgt-29.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "plot_type", value: "waterfall"
2025-09-15 20:24:13.794 wdl.w:ptcp.w:call-trgt-29.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "show", value: "motifs"
2025-09-15 20:24:13.794 wdl.w:ptcp.w:call-trgt-29.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "threads", value: 1
2025-09-15 20:24:13.794 wdl.w:ptcp.w:call-trgt-29.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:13.794 wdl.w:ptcp.w:call-trgt-29.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2126.motifs_waterfall"
2025-09-15 20:24:13.795 wdl.w:ptcp.w:call-trgt-29.t:call-trgt_plot_motifs_waterfall INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:13.795 wdl.w:ptcp.w:call-trgt-29.t:call-trgt_plot_motifs_waterfall WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:13.795 wdl.w:ptcp.w:call-trgt-29.t:call-trgt_plot_motifs_waterfall INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:13.795 wdl.w:ptcp.w:call-trgt-29.t:call-trgt_plot_motifs_waterfall INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:13.829 wdl.w:ptcp.w:call-trgt-30 NOTICE done
2025-09-15 20:24:13.834 wdl.w:ptcp NOTICE finish :: job: "call-trgt-30"
2025-09-15 20:24:13.834 wdl.w:ptcp INFO output :: job: "call-trgt-30", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-30/out/m84036_250809_035451_s4.bc2127.motifs_waterfall.trgt_plots.zip", "images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-30/out/m84036_250809_035451_s4.bc2127.meth_allele.trgt_plots.zip", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-30/out/m84036_250809_035451_s4.bc2127.trgt.sorted.spanning.bam.bai", "images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-30/out/m84036_250809_035451_s4.bc2127.motifs_allele.trgt_plots.zip", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-30/out/m84036_250809_035451_s4.bc2127.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-30/out/m84036_250809_035451_s4.bc2127.trgt.vcf", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-30/out/m84036_250809_035451_s4.bc2127.repeats.bam", "images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-30/out/m84036_250809_035451_s4.bc2127.meth_waterfall.trgt_plots.zip", "reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-30/out/m84036_250809_035451_s4.bc2127.repeats.bam.bai"}
2025-09-15 20:24:13.841 wdl.w:ptcp.w:call-sawfish-41 NOTICE workflow start :: name: "sawfish", source: "./sawfish.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-41"
2025-09-15 20:24:13.855 wdl.w:ptcp.w:call-sawfish-41 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:24:13.856 wdl.w:ptcp.w:call-sawfish-41 INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:24:13.856 wdl.w:ptcp.w:call-sawfish-41 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-41/out/m84036_250809_035451_s4.bc2138.mapped.bam"}
2025-09-15 20:24:13.856 wdl.w:ptcp.w:call-sawfish-41 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-41/out/m84036_250809_035451_s4.bc2138.mapped.bam.bai"}
2025-09-15 20:24:13.856 wdl.w:ptcp.w:call-sawfish-41 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:24:13.856 wdl.w:ptcp.w:call-sawfish-41 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:24:13.856 wdl.w:ptcp.w:call-sawfish-41 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2138"}
2025-09-15 20:24:13.856 wdl.w:ptcp.w:call-sawfish-41 NOTICE ready :: job: "call-run_sawfish", callee: "run_sawfish"
2025-09-15 20:24:13.856 wdl.w:ptcp.w:call-sawfish-41 INFO input :: job: "call-run_sawfish", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-41/out/m84036_250809_035451_s4.bc2138.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-41/out/m84036_250809_035451_s4.bc2138.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2138"}
2025-09-15 20:24:13.870 wdl.w:ptcp.w:call-trgt-29.t:call-trgt_plot_motifs_waterfall INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-29/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_yr_casoz"
2025-09-15 20:24:13.870 wdl.w:ptcp.w:call-trgt-29.t:call-trgt_plot_motifs_waterfall INFO Slurm invocation: srun --job-name call-trgt_plot_motifs_waterfall --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-29/call-trgt_plot_motifs_waterfall/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-29/call-trgt_plot_motifs_waterfall/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-29/call-trgt_plot_motifs_waterfall/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-29/call-trgt_plot_motifs_waterfall/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-29/call-trgt_genotype/out/m84036_250809_035451_s4.bc2126.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2126.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-29/call-trgt_genotype/out/m84036_250809_035451_s4.bc2126.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2126.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-29/call-trgt_genotype/out/m84036_250809_035451_s4.bc2126.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2126.trgt.vcf:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-29/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_yr_casoz/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-29/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_yr_casoz/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:13.871 wdl.w:ptcp.t:call-pbmm2_align_hifi-89 NOTICE done
2025-09-15 20:24:13.876 wdl.w:ptcp NOTICE finish :: job: "call-pbmm2_align_hifi-89"
2025-09-15 20:24:13.876 wdl.w:ptcp INFO output :: job: "call-pbmm2_align_hifi-89", values: {"report": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-89/out/mapping_stats.report.json", "mapped_bam_pbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-89/out/m84036_250809_035451_s4.bc2186.mapped.bam.pbi", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-89/out/m84036_250809_035451_s4.bc2186.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-89/out/m84036_250809_035451_s4.bc2186.mapped.bam"}
2025-09-15 20:24:13.877 wdl.w:ptcp NOTICE ready :: job: "call-paraphase-89", callee: "paraphase"
2025-09-15 20:24:13.877 wdl.w:ptcp INFO input :: job: "call-paraphase-89", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf", "genome_version": "38", "config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-89/out/m84036_250809_035451_s4.bc2186.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-89/out/m84036_250809_035451_s4.bc2186.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2186"}
2025-09-15 20:24:13.878 wdl.w:ptcp NOTICE ready :: job: "call-sawfish-89", callee: "sawfish"
2025-09-15 20:24:13.878 wdl.w:ptcp INFO input :: job: "call-sawfish-89", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-89/out/m84036_250809_035451_s4.bc2186.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-89/out/m84036_250809_035451_s4.bc2186.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2186"}
2025-09-15 20:24:13.879 wdl.w:ptcp NOTICE ready :: job: "call-trgt-89", callee: "trgt"
2025-09-15 20:24:13.879 wdl.w:ptcp INFO input :: job: "call-trgt-89", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-89/out/m84036_250809_035451_s4.bc2186.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-89/out/m84036_250809_035451_s4.bc2186.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2186"}
2025-09-15 20:24:13.883 wdl.w:ptcp.w:call-trgt-05.t:call-trgt_plot_meth_allele NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-05/call-trgt_plot_meth_allele", thread: 140607137760832
2025-09-15 20:24:13.894 wdl.w:ptcp.w:call-trgt-29.t:call-trgt_plot_motifs_waterfall NOTICE slurm_singularity run :: pid: 1201224, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-29/call-trgt_plot_motifs_waterfall/slurm_singularity.log.txt"
2025-09-15 20:24:13.902 wdl.w:ptcp.w:call-trgt-05.t:call-trgt_plot_meth_allele INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:13.902 wdl.w:ptcp.w:call-trgt-05.t:call-trgt_plot_meth_allele INFO input :: name: "waterfall", value: false
2025-09-15 20:24:13.902 wdl.w:ptcp.w:call-trgt-05.t:call-trgt_plot_meth_allele INFO input :: name: "methylation", value: true
2025-09-15 20:24:13.903 wdl.w:ptcp.w:call-trgt-05.t:call-trgt_plot_meth_allele INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:13.903 wdl.w:ptcp.w:call-trgt-05.t:call-trgt_plot_meth_allele INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:13.903 wdl.w:ptcp.w:call-trgt-05.t:call-trgt_plot_meth_allele INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:13.903 wdl.w:ptcp.w:call-trgt-05.t:call-trgt_plot_meth_allele INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2102.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:13.903 wdl.w:ptcp.w:call-trgt-05.t:call-trgt_plot_meth_allele INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2102.trgt.sorted.spanning.bam"
2025-09-15 20:24:13.903 wdl.w:ptcp.w:call-trgt-05.t:call-trgt_plot_meth_allele INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2102.trgt.vcf"
2025-09-15 20:24:13.903 wdl.w:ptcp.w:call-trgt-05.t:call-trgt_plot_meth_allele INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2102"
2025-09-15 20:24:13.903 wdl.w:ptcp.w:call-trgt-05.t:call-trgt_plot_meth_allele INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:13.903 wdl.w:ptcp.w:call-trgt-05.t:call-trgt_plot_meth_allele INFO eval :: name: "plot_type", value: "allele"
2025-09-15 20:24:13.903 wdl.w:ptcp.w:call-trgt-05.t:call-trgt_plot_meth_allele INFO eval :: name: "show", value: "meth"
2025-09-15 20:24:13.904 wdl.w:ptcp.w:call-trgt-05.t:call-trgt_plot_meth_allele INFO eval :: name: "threads", value: 1
2025-09-15 20:24:13.904 wdl.w:ptcp.w:call-trgt-05.t:call-trgt_plot_meth_allele INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:13.904 wdl.w:ptcp.w:call-trgt-05.t:call-trgt_plot_meth_allele INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2102.meth_allele"
2025-09-15 20:24:13.904 wdl.w:ptcp.w:call-trgt-05.t:call-trgt_plot_meth_allele INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:13.904 wdl.w:ptcp.w:call-trgt-05.t:call-trgt_plot_meth_allele WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:13.905 wdl.w:ptcp.w:call-trgt-05.t:call-trgt_plot_meth_allele INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:13.905 wdl.w:ptcp.w:call-trgt-05.t:call-trgt_plot_meth_allele INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:13.945 wdl.w:ptcp.w:call-trgt-13.t:call-trgt_plot_meth_allele.slurm_singularity INFO srun: job 51797576 queued and waiting for resources
2025-09-15 20:24:13.946 wdl.w:ptcp.w:call-trgt-13.t:call-trgt_plot_meth_allele.slurm_singularity INFO srun: job 51797576 has been allocated resources
2025-09-15 20:24:13.946 wdl.w:ptcp.w:call-trgt-13.t:call-trgt_plot_meth_allele.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:13.968 wdl.w:ptcp.w:call-trgt-05.t:call-trgt_plot_meth_allele INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-05/call-trgt_plot_meth_allele/_singularity_tmpdir_6a82vzc6"
2025-09-15 20:24:13.969 wdl.w:ptcp.w:call-trgt-05.t:call-trgt_plot_meth_allele INFO Slurm invocation: srun --job-name call-trgt_plot_meth_allele --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-05/call-trgt_plot_meth_allele/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-05/call-trgt_plot_meth_allele/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-05/call-trgt_plot_meth_allele/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-05/call-trgt_plot_meth_allele/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-05/call-trgt_genotype/out/m84036_250809_035451_s4.bc2102.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2102.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-05/call-trgt_genotype/out/m84036_250809_035451_s4.bc2102.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2102.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-05/call-trgt_genotype/out/m84036_250809_035451_s4.bc2102.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2102.trgt.sorted.spanning.bam.bai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-05/call-trgt_plot_meth_allele/_singularity_tmpdir_6a82vzc6/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-05/call-trgt_plot_meth_allele/_singularity_tmpdir_6a82vzc6/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:13.978 wdl.w:ptcp.w:call-trgt-05.t:call-trgt_plot_meth_allele NOTICE slurm_singularity run :: pid: 1201226, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-05/call-trgt_plot_meth_allele/slurm_singularity.log.txt"
2025-09-15 20:24:14.177 wdl.w:ptcp.w:call-trgt-13.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO srun: job 51797577 queued and waiting for resources
2025-09-15 20:24:14.178 wdl.w:ptcp.w:call-trgt-13.t:call-trgt_plot_motifs_allele.slurm_singularity INFO srun: job 51797578 queued and waiting for resources
2025-09-15 20:24:14.178 wdl.w:ptcp.w:call-trgt-13.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO srun: job 51797577 has been allocated resources
2025-09-15 20:24:14.178 wdl.w:ptcp.w:call-trgt-13.t:call-trgt_plot_motifs_allele.slurm_singularity INFO srun: job 51797578 has been allocated resources
2025-09-15 20:24:14.178 wdl.w:ptcp.w:call-trgt-13.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:14.178 wdl.w:ptcp.w:call-trgt-13.t:call-trgt_plot_motifs_allele.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:14.335 wdl.w:ptcp.w:call-trgt-21.t:call-trgt_plot_meth_allele INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2118.meth_allele.trgt_plots.zip"
2025-09-15 20:24:14.434 wdl.w:ptcp.w:call-trgt-13.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO srun: job 51797579 queued and waiting for resources
2025-09-15 20:24:14.434 wdl.w:ptcp.w:call-trgt-13.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO srun: job 51797579 has been allocated resources
2025-09-15 20:24:14.434 wdl.w:ptcp.w:call-trgt-13.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:14.451 wdl.w:ptcp.w:call-trgt-21.t:call-trgt_plot_meth_allele NOTICE done
2025-09-15 20:24:14.457 wdl.w:ptcp.w:call-trgt-21 NOTICE finish :: job: "call-trgt_plot_meth_allele"
2025-09-15 20:24:14.457 wdl.w:ptcp.w:call-trgt-21 INFO output :: job: "call-trgt_plot_meth_allele", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-21/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2118.meth_allele.trgt_plots.zip"}
2025-09-15 20:24:14.458 wdl.w:ptcp.w:call-trgt-21 INFO visit :: node: "output-images_meth_allele", values: {"images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-21/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2118.meth_allele.trgt_plots.zip"}
2025-09-15 20:24:14.463 wdl.w:ptcp.w:call-trgt-05.t:call-trgt_plot_meth_waterfall NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-05/call-trgt_plot_meth_waterfall", thread: 140610879071808
2025-09-15 20:24:14.479 wdl.w:ptcp.w:call-trgt-05.t:call-trgt_plot_meth_waterfall INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:14.479 wdl.w:ptcp.w:call-trgt-05.t:call-trgt_plot_meth_waterfall INFO input :: name: "waterfall", value: true
2025-09-15 20:24:14.479 wdl.w:ptcp.w:call-trgt-05.t:call-trgt_plot_meth_waterfall INFO input :: name: "methylation", value: true
2025-09-15 20:24:14.479 wdl.w:ptcp.w:call-trgt-05.t:call-trgt_plot_meth_waterfall INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:14.479 wdl.w:ptcp.w:call-trgt-05.t:call-trgt_plot_meth_waterfall INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:14.479 wdl.w:ptcp.w:call-trgt-05.t:call-trgt_plot_meth_waterfall INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:14.479 wdl.w:ptcp.w:call-trgt-05.t:call-trgt_plot_meth_waterfall INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2102.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:14.479 wdl.w:ptcp.w:call-trgt-05.t:call-trgt_plot_meth_waterfall INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2102.trgt.sorted.spanning.bam"
2025-09-15 20:24:14.479 wdl.w:ptcp.w:call-trgt-05.t:call-trgt_plot_meth_waterfall INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2102.trgt.vcf"
2025-09-15 20:24:14.479 wdl.w:ptcp.w:call-trgt-05.t:call-trgt_plot_meth_waterfall INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2102"
2025-09-15 20:24:14.479 wdl.w:ptcp.w:call-trgt-05.t:call-trgt_plot_meth_waterfall INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:14.480 wdl.w:ptcp.w:call-trgt-05.t:call-trgt_plot_meth_waterfall INFO eval :: name: "plot_type", value: "waterfall"
2025-09-15 20:24:14.480 wdl.w:ptcp.w:call-trgt-05.t:call-trgt_plot_meth_waterfall INFO eval :: name: "show", value: "meth"
2025-09-15 20:24:14.480 wdl.w:ptcp.w:call-trgt-05.t:call-trgt_plot_meth_waterfall INFO eval :: name: "threads", value: 1
2025-09-15 20:24:14.480 wdl.w:ptcp.w:call-trgt-05.t:call-trgt_plot_meth_waterfall INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:14.480 wdl.w:ptcp.w:call-trgt-05.t:call-trgt_plot_meth_waterfall INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2102.meth_waterfall"
2025-09-15 20:24:14.480 wdl.w:ptcp.w:call-trgt-05.t:call-trgt_plot_meth_waterfall INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:14.480 wdl.w:ptcp.w:call-trgt-05.t:call-trgt_plot_meth_waterfall WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:14.481 wdl.w:ptcp.w:call-trgt-05.t:call-trgt_plot_meth_waterfall INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:14.481 wdl.w:ptcp.w:call-trgt-05.t:call-trgt_plot_meth_waterfall INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:14.552 wdl.w:ptcp.w:call-trgt-05.t:call-trgt_plot_meth_waterfall INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-05/call-trgt_plot_meth_waterfall/_singularity_tmpdir_uowsbvcx"
2025-09-15 20:24:14.552 wdl.w:ptcp.w:call-trgt-05.t:call-trgt_plot_meth_waterfall INFO Slurm invocation: srun --job-name call-trgt_plot_meth_waterfall --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-05/call-trgt_plot_meth_waterfall/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-05/call-trgt_plot_meth_waterfall/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-05/call-trgt_plot_meth_waterfall/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-05/call-trgt_plot_meth_waterfall/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-05/call-trgt_genotype/out/m84036_250809_035451_s4.bc2102.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2102.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-05/call-trgt_genotype/out/m84036_250809_035451_s4.bc2102.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2102.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-05/call-trgt_genotype/out/m84036_250809_035451_s4.bc2102.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2102.trgt.sorted.spanning.bam.bai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-05/call-trgt_plot_meth_waterfall/_singularity_tmpdir_uowsbvcx/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-05/call-trgt_plot_meth_waterfall/_singularity_tmpdir_uowsbvcx/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:14.567 wdl.w:ptcp.w:call-trgt-05.t:call-trgt_plot_meth_waterfall NOTICE slurm_singularity run :: pid: 1201245, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-05/call-trgt_plot_meth_waterfall/slurm_singularity.log.txt"
2025-09-15 20:24:14.600 wdl.w:ptcp.w:call-trgt-29.t:call-trgt_plot_meth_allele.slurm_singularity INFO srun: job 51797580 queued and waiting for resources
2025-09-15 20:24:14.600 wdl.w:ptcp.w:call-trgt-29.t:call-trgt_plot_meth_allele.slurm_singularity INFO srun: job 51797580 has been allocated resources
2025-09-15 20:24:14.600 wdl.w:ptcp.w:call-trgt-29.t:call-trgt_plot_meth_allele.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:14.601 wdl.w:ptcp.w:call-trgt-29.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO srun: job 51797581 queued and waiting for resources
2025-09-15 20:24:14.602 wdl.w:ptcp.w:call-trgt-29.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO srun: job 51797581 has been allocated resources
2025-09-15 20:24:14.602 wdl.w:ptcp.w:call-trgt-29.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:14.671 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:11 [ERROR] - No reads found for TRID=OPDM_ABCD3
2025-09-15 20:24:14.671 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:11 [ERROR] - No reads found for TRID=NIID_NOTCH2NLC
2025-09-15 20:24:14.671 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:11 [ERROR] - No reads found for TRID=OPDM4_RILPL1
2025-09-15 20:24:14.671 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:11 [ERROR] - No reads found for TRID=SCA27B_FGF14
2025-09-15 20:24:14.672 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:12 [ERROR] - No reads found for TRID=SCA3_ATXN3
2025-09-15 20:24:14.672 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:12 [ERROR] - No reads found for TRID=SCA31_BEAN1
2025-09-15 20:24:14.672 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:12 [ERROR] - No reads found for TRID=SCA4_ZFHX3
2025-09-15 20:24:14.672 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:12 [ERROR] - No reads found for TRID=HDL2_JPH3
2025-09-15 20:24:14.672 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:12 [ERROR] - No reads found for TRID=SCA6_CACNA1A
2025-09-15 20:24:14.672 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:12 [ERROR] - No reads found for TRID=OPDM2_GIPC1
2025-09-15 20:24:14.672 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:12 [ERROR] - No reads found for TRID=DM1_DMPK
2025-09-15 20:24:14.672 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:12 [ERROR] - No reads found for TRID=FRA2A_AFF3
2025-09-15 20:24:14.672 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:12 [ERROR] - No reads found for TRID=SD5_HOXD13
2025-09-15 20:24:14.672 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:12 [ERROR] - No reads found for TRID=SCA36_NOP56
2025-09-15 20:24:14.672 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:12 [ERROR] - No reads found for TRID=EPM1_CSTB
2025-09-15 20:24:14.672 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:12 [ERROR] - No reads found for TRID=CJD_PRNP
2025-09-15 20:24:14.672 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:12 [ERROR] - No reads found for TRID=SCA7_ATXN7
2025-09-15 20:24:14.672 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:12 [ERROR] - No reads found for TRID=HD_HTT
2025-09-15 20:24:14.672 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:13 [ERROR] - No reads found for TRID=CCHS_PHOX2B
2025-09-15 20:24:14.672 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:13 [ERROR] - No reads found for TRID=SCA12_PPP2R2B
2025-09-15 20:24:14.673 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:13 [ERROR] - No reads found for TRID=SCA1_ATXN1
2025-09-15 20:24:14.673 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:13 [ERROR] - No reads found for TRID=OPDM1_LRP12
2025-09-15 20:24:14.673 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:13 [ERROR] - No reads found for TRID=FAME1_SAMD12
2025-09-15 20:24:14.747 wdl.w:ptcp.w:call-trgt-29.t:call-trgt_plot_motifs_allele.slurm_singularity INFO srun: job 51797582 queued and waiting for resources
2025-09-15 20:24:14.747 wdl.w:ptcp.w:call-trgt-29.t:call-trgt_plot_motifs_allele.slurm_singularity INFO srun: job 51797582 has been allocated resources
2025-09-15 20:24:14.747 wdl.w:ptcp.w:call-trgt-29.t:call-trgt_plot_motifs_allele.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:14.821 wdl.w:ptcp.w:call-trgt-28.t:call-trgt_plot_motifs_allele INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2125.motifs_allele.trgt_plots.zip"
2025-09-15 20:24:14.885 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:11 [ERROR] - No reads found for TRID=OPDM4_RILPL1
2025-09-15 20:24:14.885 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:12 [ERROR] - No reads found for TRID=SCA27B_FGF14
2025-09-15 20:24:14.885 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:12 [ERROR] - No reads found for TRID=SCA3_ATXN3
2025-09-15 20:24:14.885 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:12 [ERROR] - No reads found for TRID=SCA31_BEAN1
2025-09-15 20:24:14.885 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:12 [ERROR] - No reads found for TRID=SCA4_ZFHX3
2025-09-15 20:24:14.885 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:12 [ERROR] - No reads found for TRID=HDL2_JPH3
2025-09-15 20:24:14.885 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:12 [ERROR] - No reads found for TRID=SCA6_CACNA1A
2025-09-15 20:24:14.885 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:12 [ERROR] - No reads found for TRID=OPDM2_GIPC1
2025-09-15 20:24:14.885 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:12 [ERROR] - No reads found for TRID=DM1_DMPK
2025-09-15 20:24:14.885 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:12 [ERROR] - No reads found for TRID=FRA2A_AFF3
2025-09-15 20:24:14.885 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:12 [ERROR] - No reads found for TRID=SD5_HOXD13
2025-09-15 20:24:14.885 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:12 [ERROR] - No reads found for TRID=SCA36_NOP56
2025-09-15 20:24:14.885 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:13 [ERROR] - No reads found for TRID=EPM1_CSTB
2025-09-15 20:24:14.885 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:13 [ERROR] - No reads found for TRID=CJD_PRNP
2025-09-15 20:24:14.886 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:13 [ERROR] - No reads found for TRID=SCA7_ATXN7
2025-09-15 20:24:14.886 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:13 [ERROR] - No reads found for TRID=HD_HTT
2025-09-15 20:24:14.886 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:13 [ERROR] - No reads found for TRID=CCHS_PHOX2B
2025-09-15 20:24:14.886 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:13 [ERROR] - No reads found for TRID=SCA12_PPP2R2B
2025-09-15 20:24:14.886 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:13 [ERROR] - No reads found for TRID=SCA1_ATXN1
2025-09-15 20:24:14.886 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:14 [ERROR] - No reads found for TRID=OPDM1_LRP12
2025-09-15 20:24:14.886 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:14 [ERROR] - No reads found for TRID=FAME1_SAMD12
2025-09-15 20:24:14.895 wdl.w:ptcp.t:call-pbmm2_align_hifi-82 INFO output :: name: "mapped_bam", value: "m84036_250809_035451_s4.bc2179.mapped.bam"
2025-09-15 20:24:14.898 wdl.w:ptcp.t:call-pbmm2_align_hifi-82 INFO output :: name: "mapped_bam_bai", value: "m84036_250809_035451_s4.bc2179.mapped.bam.bai"
2025-09-15 20:24:14.899 wdl.w:ptcp.t:call-pbmm2_align_hifi-82 INFO output :: name: "mapped_bam_pbi", value: "m84036_250809_035451_s4.bc2179.mapped.bam.pbi"
2025-09-15 20:24:14.902 wdl.w:ptcp.t:call-pbmm2_align_hifi-82 INFO output :: name: "report", value: "mapping_stats.report.json"
2025-09-15 20:24:14.904 wdl.w:ptcp.w:call-trgt-29.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO srun: job 51797583 queued and waiting for resources
2025-09-15 20:24:14.904 wdl.w:ptcp.w:call-trgt-29.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO srun: job 51797583 has been allocated resources
2025-09-15 20:24:14.904 wdl.w:ptcp.w:call-trgt-29.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:14.935 wdl.w:ptcp.w:call-trgt-28.t:call-trgt_plot_motifs_allele NOTICE done
2025-09-15 20:24:14.940 wdl.w:ptcp.w:call-trgt-28 NOTICE finish :: job: "call-trgt_plot_motifs_allele"
2025-09-15 20:24:14.940 wdl.w:ptcp.w:call-trgt-28 INFO output :: job: "call-trgt_plot_motifs_allele", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-28/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2125.motifs_allele.trgt_plots.zip"}
2025-09-15 20:24:14.940 wdl.w:ptcp.w:call-trgt-28 INFO visit :: node: "output-images_motifs_allele", values: {"images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-28/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2125.motifs_allele.trgt_plots.zip"}
2025-09-15 20:24:14.945 wdl.w:ptcp.w:call-trgt-05.t:call-trgt_plot_motifs_allele NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-05/call-trgt_plot_motifs_allele", thread: 140608219895360
2025-09-15 20:24:14.947 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_plot_meth_allele INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2103.meth_allele.trgt_plots.zip"
2025-09-15 20:24:14.963 wdl.w:ptcp.w:call-trgt-05.t:call-trgt_plot_motifs_allele INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:14.963 wdl.w:ptcp.w:call-trgt-05.t:call-trgt_plot_motifs_allele INFO input :: name: "waterfall", value: false
2025-09-15 20:24:14.963 wdl.w:ptcp.w:call-trgt-05.t:call-trgt_plot_motifs_allele INFO input :: name: "methylation", value: false
2025-09-15 20:24:14.963 wdl.w:ptcp.w:call-trgt-05.t:call-trgt_plot_motifs_allele INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:14.963 wdl.w:ptcp.w:call-trgt-05.t:call-trgt_plot_motifs_allele INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:14.963 wdl.w:ptcp.w:call-trgt-05.t:call-trgt_plot_motifs_allele INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:14.963 wdl.w:ptcp.w:call-trgt-05.t:call-trgt_plot_motifs_allele INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2102.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:14.963 wdl.w:ptcp.w:call-trgt-05.t:call-trgt_plot_motifs_allele INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2102.trgt.sorted.spanning.bam"
2025-09-15 20:24:14.963 wdl.w:ptcp.w:call-trgt-05.t:call-trgt_plot_motifs_allele INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2102.trgt.vcf"
2025-09-15 20:24:14.963 wdl.w:ptcp.w:call-trgt-05.t:call-trgt_plot_motifs_allele INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2102"
2025-09-15 20:24:14.963 wdl.w:ptcp.w:call-trgt-05.t:call-trgt_plot_motifs_allele INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:14.964 wdl.w:ptcp.w:call-trgt-05.t:call-trgt_plot_motifs_allele INFO eval :: name: "plot_type", value: "allele"
2025-09-15 20:24:14.964 wdl.w:ptcp.w:call-trgt-05.t:call-trgt_plot_motifs_allele INFO eval :: name: "show", value: "motifs"
2025-09-15 20:24:14.964 wdl.w:ptcp.w:call-trgt-05.t:call-trgt_plot_motifs_allele INFO eval :: name: "threads", value: 1
2025-09-15 20:24:14.964 wdl.w:ptcp.w:call-trgt-05.t:call-trgt_plot_motifs_allele INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:14.964 wdl.w:ptcp.w:call-trgt-05.t:call-trgt_plot_motifs_allele INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2102.motifs_allele"
2025-09-15 20:24:14.965 wdl.w:ptcp.w:call-trgt-05.t:call-trgt_plot_motifs_allele INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:14.965 wdl.w:ptcp.w:call-trgt-05.t:call-trgt_plot_motifs_allele WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:14.965 wdl.w:ptcp.w:call-trgt-05.t:call-trgt_plot_motifs_allele INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:14.965 wdl.w:ptcp.w:call-trgt-05.t:call-trgt_plot_motifs_allele INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:14.990 wdl.w:ptcp.w:call-trgt-05.t:call-trgt_plot_meth_allele.slurm_singularity INFO srun: job 51797584 queued and waiting for resources
2025-09-15 20:24:14.990 wdl.w:ptcp.w:call-trgt-05.t:call-trgt_plot_meth_allele.slurm_singularity INFO srun: job 51797584 has been allocated resources
2025-09-15 20:24:14.990 wdl.w:ptcp.w:call-trgt-05.t:call-trgt_plot_meth_allele.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:14.993 wdl.w:ptcp.t:call-pbmm2_align_hifi-82 NOTICE done
2025-09-15 20:24:15.002 wdl.w:ptcp NOTICE finish :: job: "call-pbmm2_align_hifi-82"
2025-09-15 20:24:15.002 wdl.w:ptcp INFO output :: job: "call-pbmm2_align_hifi-82", values: {"report": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-82/out/mapping_stats.report.json", "mapped_bam_pbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-82/out/m84036_250809_035451_s4.bc2179.mapped.bam.pbi", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-82/out/m84036_250809_035451_s4.bc2179.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-82/out/m84036_250809_035451_s4.bc2179.mapped.bam"}
2025-09-15 20:24:15.002 wdl.w:ptcp NOTICE ready :: job: "call-paraphase-82", callee: "paraphase"
2025-09-15 20:24:15.003 wdl.w:ptcp INFO input :: job: "call-paraphase-82", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf", "genome_version": "38", "config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-82/out/m84036_250809_035451_s4.bc2179.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-82/out/m84036_250809_035451_s4.bc2179.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2179"}
2025-09-15 20:24:15.004 wdl.w:ptcp NOTICE ready :: job: "call-sawfish-82", callee: "sawfish"
2025-09-15 20:24:15.004 wdl.w:ptcp INFO input :: job: "call-sawfish-82", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-82/out/m84036_250809_035451_s4.bc2179.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-82/out/m84036_250809_035451_s4.bc2179.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2179"}
2025-09-15 20:24:15.005 wdl.w:ptcp NOTICE ready :: job: "call-trgt-82", callee: "trgt"
2025-09-15 20:24:15.005 wdl.w:ptcp INFO input :: job: "call-trgt-82", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-82/out/m84036_250809_035451_s4.bc2179.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-82/out/m84036_250809_035451_s4.bc2179.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2179"}
2025-09-15 20:24:15.010 wdl.w:ptcp.w:call-trgt-05.t:call-trgt_plot_motifs_waterfall NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-05/call-trgt_plot_motifs_waterfall", thread: 140607674631744
2025-09-15 20:24:15.036 wdl.w:ptcp.w:call-trgt-05.t:call-trgt_plot_motifs_waterfall INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:15.037 wdl.w:ptcp.w:call-trgt-05.t:call-trgt_plot_motifs_waterfall INFO input :: name: "waterfall", value: true
2025-09-15 20:24:15.037 wdl.w:ptcp.w:call-trgt-05.t:call-trgt_plot_motifs_waterfall INFO input :: name: "methylation", value: false
2025-09-15 20:24:15.037 wdl.w:ptcp.w:call-trgt-05.t:call-trgt_plot_motifs_waterfall INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:15.037 wdl.w:ptcp.w:call-trgt-05.t:call-trgt_plot_motifs_waterfall INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:15.037 wdl.w:ptcp.w:call-trgt-05.t:call-trgt_plot_motifs_waterfall INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:15.037 wdl.w:ptcp.w:call-trgt-05.t:call-trgt_plot_motifs_waterfall INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2102.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:15.037 wdl.w:ptcp.w:call-trgt-05.t:call-trgt_plot_motifs_waterfall INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2102.trgt.sorted.spanning.bam"
2025-09-15 20:24:15.037 wdl.w:ptcp.w:call-trgt-05.t:call-trgt_plot_motifs_waterfall INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2102.trgt.vcf"
2025-09-15 20:24:15.037 wdl.w:ptcp.w:call-trgt-05.t:call-trgt_plot_motifs_waterfall INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2102"
2025-09-15 20:24:15.037 wdl.w:ptcp.w:call-trgt-05.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:15.038 wdl.w:ptcp.w:call-trgt-05.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "plot_type", value: "waterfall"
2025-09-15 20:24:15.038 wdl.w:ptcp.w:call-trgt-05.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "show", value: "motifs"
2025-09-15 20:24:15.038 wdl.w:ptcp.w:call-trgt-05.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "threads", value: 1
2025-09-15 20:24:15.038 wdl.w:ptcp.w:call-trgt-05.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:15.038 wdl.w:ptcp.w:call-trgt-05.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2102.motifs_waterfall"
2025-09-15 20:24:15.039 wdl.w:ptcp.w:call-trgt-05.t:call-trgt_plot_motifs_waterfall INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:15.039 wdl.w:ptcp.w:call-trgt-05.t:call-trgt_plot_motifs_waterfall WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:15.039 wdl.w:ptcp.w:call-trgt-05.t:call-trgt_plot_motifs_waterfall INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:15.039 wdl.w:ptcp.w:call-trgt-05.t:call-trgt_plot_motifs_waterfall INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:15.043 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_plot_meth_allele NOTICE done
2025-09-15 20:24:15.055 wdl.w:ptcp.w:call-trgt-05.t:call-trgt_plot_motifs_allele INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-05/call-trgt_plot_motifs_allele/_singularity_tmpdir_mxfthc4h"
2025-09-15 20:24:15.055 wdl.w:ptcp.w:call-trgt-05.t:call-trgt_plot_motifs_allele INFO Slurm invocation: srun --job-name call-trgt_plot_motifs_allele --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-05/call-trgt_plot_motifs_allele/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-05/call-trgt_plot_motifs_allele/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-05/call-trgt_plot_motifs_allele/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-05/call-trgt_plot_motifs_allele/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-05/call-trgt_genotype/out/m84036_250809_035451_s4.bc2102.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2102.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-05/call-trgt_genotype/out/m84036_250809_035451_s4.bc2102.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2102.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-05/call-trgt_genotype/out/m84036_250809_035451_s4.bc2102.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2102.trgt.sorted.spanning.bam.bai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-05/call-trgt_plot_motifs_allele/_singularity_tmpdir_mxfthc4h/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-05/call-trgt_plot_motifs_allele/_singularity_tmpdir_mxfthc4h/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:15.058 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_plot_motifs_allele INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2103.motifs_allele.trgt_plots.zip"
2025-09-15 20:24:15.073 wdl.w:ptcp.w:call-trgt-06 NOTICE finish :: job: "call-trgt_plot_meth_allele"
2025-09-15 20:24:15.073 wdl.w:ptcp.w:call-trgt-06 INFO output :: job: "call-trgt_plot_meth_allele", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-06/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2103.meth_allele.trgt_plots.zip"}
2025-09-15 20:24:15.073 wdl.w:ptcp.w:call-trgt-06 INFO visit :: node: "output-images_meth_allele", values: {"images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-06/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2103.meth_allele.trgt_plots.zip"}
2025-09-15 20:24:15.080 wdl.w:ptcp.w:call-trgt-12.t:call-trgt_plot_meth_allele NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-12/call-trgt_plot_meth_allele", thread: 140608194717248
2025-09-15 20:24:15.087 wdl.w:ptcp.w:call-trgt-05.t:call-trgt_plot_motifs_allele NOTICE slurm_singularity run :: pid: 1201257, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-05/call-trgt_plot_motifs_allele/slurm_singularity.log.txt"
2025-09-15 20:24:15.103 wdl.w:ptcp.w:call-trgt-12.t:call-trgt_plot_meth_allele INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:15.104 wdl.w:ptcp.w:call-trgt-12.t:call-trgt_plot_meth_allele INFO input :: name: "waterfall", value: false
2025-09-15 20:24:15.104 wdl.w:ptcp.w:call-trgt-12.t:call-trgt_plot_meth_allele INFO input :: name: "methylation", value: true
2025-09-15 20:24:15.104 wdl.w:ptcp.w:call-trgt-12.t:call-trgt_plot_meth_allele INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:15.104 wdl.w:ptcp.w:call-trgt-12.t:call-trgt_plot_meth_allele INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:15.104 wdl.w:ptcp.w:call-trgt-12.t:call-trgt_plot_meth_allele INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:15.104 wdl.w:ptcp.w:call-trgt-12.t:call-trgt_plot_meth_allele INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2109.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:15.104 wdl.w:ptcp.w:call-trgt-12.t:call-trgt_plot_meth_allele INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2109.trgt.sorted.spanning.bam"
2025-09-15 20:24:15.104 wdl.w:ptcp.w:call-trgt-12.t:call-trgt_plot_meth_allele INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2109.trgt.vcf"
2025-09-15 20:24:15.104 wdl.w:ptcp.w:call-trgt-12.t:call-trgt_plot_meth_allele INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2109"
2025-09-15 20:24:15.105 wdl.w:ptcp.w:call-trgt-12.t:call-trgt_plot_meth_allele INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:15.105 wdl.w:ptcp.w:call-trgt-12.t:call-trgt_plot_meth_allele INFO eval :: name: "plot_type", value: "allele"
2025-09-15 20:24:15.105 wdl.w:ptcp.w:call-trgt-12.t:call-trgt_plot_meth_allele INFO eval :: name: "show", value: "meth"
2025-09-15 20:24:15.105 wdl.w:ptcp.w:call-trgt-12.t:call-trgt_plot_meth_allele INFO eval :: name: "threads", value: 1
2025-09-15 20:24:15.105 wdl.w:ptcp.w:call-trgt-12.t:call-trgt_plot_meth_allele INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:15.106 wdl.w:ptcp.w:call-trgt-12.t:call-trgt_plot_meth_allele INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2109.meth_allele"
2025-09-15 20:24:15.106 wdl.w:ptcp.w:call-trgt-12.t:call-trgt_plot_meth_allele INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:15.106 wdl.w:ptcp.w:call-trgt-12.t:call-trgt_plot_meth_allele WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:15.106 wdl.w:ptcp.w:call-trgt-12.t:call-trgt_plot_meth_allele INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:15.107 wdl.w:ptcp.w:call-trgt-12.t:call-trgt_plot_meth_allele INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:15.122 wdl.w:ptcp.w:call-trgt-05.t:call-trgt_plot_motifs_waterfall INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-05/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_c5cziuac"
2025-09-15 20:24:15.122 wdl.w:ptcp.w:call-trgt-05.t:call-trgt_plot_motifs_waterfall INFO Slurm invocation: srun --job-name call-trgt_plot_motifs_waterfall --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-05/call-trgt_plot_motifs_waterfall/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-05/call-trgt_plot_motifs_waterfall/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-05/call-trgt_plot_motifs_waterfall/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-05/call-trgt_plot_motifs_waterfall/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-05/call-trgt_genotype/out/m84036_250809_035451_s4.bc2102.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2102.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-05/call-trgt_genotype/out/m84036_250809_035451_s4.bc2102.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2102.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-05/call-trgt_genotype/out/m84036_250809_035451_s4.bc2102.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2102.trgt.sorted.spanning.bam.bai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-05/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_c5cziuac/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-05/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_c5cziuac/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:15.139 wdl.w:ptcp.w:call-trgt-05.t:call-trgt_plot_motifs_waterfall NOTICE slurm_singularity run :: pid: 1201259, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-05/call-trgt_plot_motifs_waterfall/slurm_singularity.log.txt"
2025-09-15 20:24:15.156 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_plot_motifs_allele NOTICE done
2025-09-15 20:24:15.161 wdl.w:ptcp.w:call-trgt-06 NOTICE finish :: job: "call-trgt_plot_motifs_allele"
2025-09-15 20:24:15.161 wdl.w:ptcp.w:call-trgt-06 INFO output :: job: "call-trgt_plot_motifs_allele", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-06/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2103.motifs_allele.trgt_plots.zip"}
2025-09-15 20:24:15.162 wdl.w:ptcp.w:call-trgt-06 INFO visit :: node: "output-images_motifs_allele", values: {"images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-06/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2103.motifs_allele.trgt_plots.zip"}
2025-09-15 20:24:15.167 wdl.w:ptcp.w:call-trgt-12.t:call-trgt_plot_meth_waterfall NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-12/call-trgt_plot_meth_waterfall", thread: 140608765158976
2025-09-15 20:24:15.182 wdl.w:ptcp.w:call-trgt-12.t:call-trgt_plot_meth_allele INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-12/call-trgt_plot_meth_allele/_singularity_tmpdir_pxekq6eo"
2025-09-15 20:24:15.182 wdl.w:ptcp.w:call-trgt-12.t:call-trgt_plot_meth_allele INFO Slurm invocation: srun --job-name call-trgt_plot_meth_allele --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-12/call-trgt_plot_meth_allele/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-12/call-trgt_plot_meth_allele/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-12/call-trgt_plot_meth_allele/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-12/call-trgt_plot_meth_allele/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-12/call-trgt_genotype/out/m84036_250809_035451_s4.bc2109.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2109.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-12/call-trgt_genotype/out/m84036_250809_035451_s4.bc2109.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2109.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-12/call-trgt_genotype/out/m84036_250809_035451_s4.bc2109.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2109.trgt.vcf:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-12/call-trgt_plot_meth_allele/_singularity_tmpdir_pxekq6eo/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-12/call-trgt_plot_meth_allele/_singularity_tmpdir_pxekq6eo/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:15.184 wdl.w:ptcp.w:call-trgt-12.t:call-trgt_plot_meth_waterfall INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:15.185 wdl.w:ptcp.w:call-trgt-12.t:call-trgt_plot_meth_waterfall INFO input :: name: "waterfall", value: true
2025-09-15 20:24:15.185 wdl.w:ptcp.w:call-trgt-12.t:call-trgt_plot_meth_waterfall INFO input :: name: "methylation", value: true
2025-09-15 20:24:15.185 wdl.w:ptcp.w:call-trgt-12.t:call-trgt_plot_meth_waterfall INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:15.185 wdl.w:ptcp.w:call-trgt-12.t:call-trgt_plot_meth_waterfall INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:15.185 wdl.w:ptcp.w:call-trgt-12.t:call-trgt_plot_meth_waterfall INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:15.185 wdl.w:ptcp.w:call-trgt-12.t:call-trgt_plot_meth_waterfall INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2109.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:15.185 wdl.w:ptcp.w:call-trgt-12.t:call-trgt_plot_meth_waterfall INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2109.trgt.sorted.spanning.bam"
2025-09-15 20:24:15.185 wdl.w:ptcp.w:call-trgt-12.t:call-trgt_plot_meth_waterfall INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2109.trgt.vcf"
2025-09-15 20:24:15.185 wdl.w:ptcp.w:call-trgt-12.t:call-trgt_plot_meth_waterfall INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2109"
2025-09-15 20:24:15.185 wdl.w:ptcp.w:call-trgt-12.t:call-trgt_plot_meth_waterfall INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:15.186 wdl.w:ptcp.w:call-trgt-12.t:call-trgt_plot_meth_waterfall INFO eval :: name: "plot_type", value: "waterfall"
2025-09-15 20:24:15.186 wdl.w:ptcp.w:call-trgt-12.t:call-trgt_plot_meth_waterfall INFO eval :: name: "show", value: "meth"
2025-09-15 20:24:15.186 wdl.w:ptcp.w:call-trgt-12.t:call-trgt_plot_meth_waterfall INFO eval :: name: "threads", value: 1
2025-09-15 20:24:15.186 wdl.w:ptcp.w:call-trgt-12.t:call-trgt_plot_meth_waterfall INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:15.186 wdl.w:ptcp.w:call-trgt-12.t:call-trgt_plot_meth_waterfall INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2109.meth_waterfall"
2025-09-15 20:24:15.186 wdl.w:ptcp.w:call-trgt-12.t:call-trgt_plot_meth_waterfall INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:15.187 wdl.w:ptcp.w:call-trgt-12.t:call-trgt_plot_meth_waterfall WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:15.187 wdl.w:ptcp.w:call-trgt-12.t:call-trgt_plot_meth_waterfall INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:15.187 wdl.w:ptcp.w:call-trgt-12.t:call-trgt_plot_meth_waterfall INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:15.195 wdl.w:ptcp.w:call-trgt-12.t:call-trgt_plot_meth_allele NOTICE slurm_singularity run :: pid: 1201261, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-12/call-trgt_plot_meth_allele/slurm_singularity.log.txt"
2025-09-15 20:24:15.207 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:12 [ERROR] - No reads found for TRID=SCA37_DAB1
2025-09-15 20:24:15.207 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:12 [ERROR] - No reads found for TRID=OPDM_ABCD3
2025-09-15 20:24:15.207 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:12 [ERROR] - No reads found for TRID=NIID_NOTCH2NLC
2025-09-15 20:24:15.207 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:12 [ERROR] - No reads found for TRID=OPDM4_RILPL1
2025-09-15 20:24:15.207 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:12 [ERROR] - No reads found for TRID=SCA27B_FGF14
2025-09-15 20:24:15.207 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:12 [ERROR] - No reads found for TRID=SCA3_ATXN3
2025-09-15 20:24:15.207 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:12 [ERROR] - No reads found for TRID=SCA31_BEAN1
2025-09-15 20:24:15.207 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:13 [ERROR] - No reads found for TRID=SCA4_ZFHX3
2025-09-15 20:24:15.207 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:13 [ERROR] - No reads found for TRID=HDL2_JPH3
2025-09-15 20:24:15.207 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:13 [ERROR] - No reads found for TRID=SCA6_CACNA1A
2025-09-15 20:24:15.207 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:13 [ERROR] - No reads found for TRID=OPDM2_GIPC1
2025-09-15 20:24:15.207 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:13 [ERROR] - No reads found for TRID=DM1_DMPK
2025-09-15 20:24:15.208 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:13 [ERROR] - No reads found for TRID=FRA2A_AFF3
2025-09-15 20:24:15.208 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:13 [ERROR] - No reads found for TRID=SD5_HOXD13
2025-09-15 20:24:15.208 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:13 [ERROR] - No reads found for TRID=SCA36_NOP56
2025-09-15 20:24:15.208 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:14 [ERROR] - No reads found for TRID=EPM1_CSTB
2025-09-15 20:24:15.208 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:14 [ERROR] - No reads found for TRID=CJD_PRNP
2025-09-15 20:24:15.208 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:14 [ERROR] - No reads found for TRID=SCA7_ATXN7
2025-09-15 20:24:15.208 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:14 [ERROR] - No reads found for TRID=HD_HTT
2025-09-15 20:24:15.208 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:14 [ERROR] - No reads found for TRID=CCHS_PHOX2B
2025-09-15 20:24:15.208 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:14 [ERROR] - No reads found for TRID=SCA12_PPP2R2B
2025-09-15 20:24:15.208 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:15 [ERROR] - No reads found for TRID=SCA1_ATXN1
2025-09-15 20:24:15.251 wdl.w:ptcp.w:call-trgt-12.t:call-trgt_plot_meth_waterfall INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-12/call-trgt_plot_meth_waterfall/_singularity_tmpdir_5eqafh1v"
2025-09-15 20:24:15.252 wdl.w:ptcp.w:call-trgt-12.t:call-trgt_plot_meth_waterfall INFO Slurm invocation: srun --job-name call-trgt_plot_meth_waterfall --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-12/call-trgt_plot_meth_waterfall/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-12/call-trgt_plot_meth_waterfall/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-12/call-trgt_plot_meth_waterfall/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-12/call-trgt_plot_meth_waterfall/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-12/call-trgt_genotype/out/m84036_250809_035451_s4.bc2109.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2109.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-12/call-trgt_genotype/out/m84036_250809_035451_s4.bc2109.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2109.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-12/call-trgt_genotype/out/m84036_250809_035451_s4.bc2109.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2109.trgt.vcf:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-12/call-trgt_plot_meth_waterfall/_singularity_tmpdir_5eqafh1v/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-12/call-trgt_plot_meth_waterfall/_singularity_tmpdir_5eqafh1v/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:15.261 wdl.w:ptcp.w:call-trgt-12.t:call-trgt_plot_meth_waterfall NOTICE slurm_singularity run :: pid: 1201263, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-12/call-trgt_plot_meth_waterfall/slurm_singularity.log.txt"
2025-09-15 20:24:15.444 wdl.w:ptcp.w:call-paraphase-19.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for smn1 for sample m84036_250809_035451_s4.bc2116 at 2025-09-15 20:23:53.498443...
2025-09-15 20:24:15.445 wdl.w:ptcp.w:call-paraphase-19.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for f8inv1 for sample m84036_250809_035451_s4.bc2116 at 2025-09-15 20:24:05.774686...
2025-09-15 20:24:15.445 wdl.w:ptcp.w:call-paraphase-19.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for f8inv1 for sample m84036_250809_035451_s4.bc2116 at 2025-09-15 20:24:05.774923...
2025-09-15 20:24:15.445 wdl.w:ptcp.w:call-paraphase-19.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for f8inv1 for sample m84036_250809_035451_s4.bc2116 at 2025-09-15 20:24:07.651769...
2025-09-15 20:24:15.487 wdl.w:ptcp.w:call-trgt-21.t:call-trgt_plot_meth_waterfall INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2118.meth_waterfall.trgt_plots.zip"
2025-09-15 20:24:15.499 wdl.w:ptcp.w:call-paraphase-22.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for rpgr for sample m84036_250809_035451_s4.bc2119 at 2025-09-15 20:24:12.366267...
2025-09-15 20:24:15.499 wdl.w:ptcp.w:call-paraphase-22.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for rpgr for sample m84036_250809_035451_s4.bc2119 at 2025-09-15 20:24:12.366773...
2025-09-15 20:24:15.578 wdl.w:ptcp.w:call-trgt-05.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO srun: job 51797585 queued and waiting for resources
2025-09-15 20:24:15.578 wdl.w:ptcp.w:call-trgt-05.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO srun: job 51797585 has been allocated resources
2025-09-15 20:24:15.578 wdl.w:ptcp.w:call-trgt-05.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:15.610 wdl.w:ptcp.w:call-trgt-21.t:call-trgt_plot_meth_waterfall NOTICE done
2025-09-15 20:24:15.611 wdl.w:ptcp.t:call-pbmm2_align_hifi-93 INFO output :: name: "mapped_bam", value: "m84036_250809_035451_s4.bc2190.mapped.bam"
2025-09-15 20:24:15.615 wdl.w:ptcp.t:call-pbmm2_align_hifi-93 INFO output :: name: "mapped_bam_bai", value: "m84036_250809_035451_s4.bc2190.mapped.bam.bai"
2025-09-15 20:24:15.615 wdl.w:ptcp.w:call-trgt-21 NOTICE finish :: job: "call-trgt_plot_meth_waterfall"
2025-09-15 20:24:15.616 wdl.w:ptcp.w:call-trgt-21 INFO output :: job: "call-trgt_plot_meth_waterfall", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-21/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2118.meth_waterfall.trgt_plots.zip"}
2025-09-15 20:24:15.616 wdl.w:ptcp.w:call-trgt-21 INFO visit :: node: "output-images_meth_waterfall", values: {"images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-21/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2118.meth_waterfall.trgt_plots.zip"}
2025-09-15 20:24:15.616 wdl.w:ptcp.t:call-pbmm2_align_hifi-93 INFO output :: name: "mapped_bam_pbi", value: "m84036_250809_035451_s4.bc2190.mapped.bam.pbi"
2025-09-15 20:24:15.618 wdl.w:ptcp.t:call-pbmm2_align_hifi-93 INFO output :: name: "report", value: "mapping_stats.report.json"
2025-09-15 20:24:15.622 wdl.w:ptcp.w:call-trgt-12.t:call-trgt_plot_motifs_allele NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-12/call-trgt_plot_motifs_allele", thread: 140609310422592
2025-09-15 20:24:15.642 wdl.w:ptcp.w:call-trgt-12.t:call-trgt_plot_motifs_allele INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:15.642 wdl.w:ptcp.w:call-trgt-12.t:call-trgt_plot_motifs_allele INFO input :: name: "waterfall", value: false
2025-09-15 20:24:15.642 wdl.w:ptcp.w:call-trgt-12.t:call-trgt_plot_motifs_allele INFO input :: name: "methylation", value: false
2025-09-15 20:24:15.642 wdl.w:ptcp.w:call-trgt-12.t:call-trgt_plot_motifs_allele INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:15.642 wdl.w:ptcp.w:call-trgt-12.t:call-trgt_plot_motifs_allele INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:15.642 wdl.w:ptcp.w:call-trgt-12.t:call-trgt_plot_motifs_allele INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:15.642 wdl.w:ptcp.w:call-trgt-12.t:call-trgt_plot_motifs_allele INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2109.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:15.642 wdl.w:ptcp.w:call-trgt-12.t:call-trgt_plot_motifs_allele INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2109.trgt.sorted.spanning.bam"
2025-09-15 20:24:15.642 wdl.w:ptcp.w:call-trgt-12.t:call-trgt_plot_motifs_allele INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2109.trgt.vcf"
2025-09-15 20:24:15.642 wdl.w:ptcp.w:call-trgt-12.t:call-trgt_plot_motifs_allele INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2109"
2025-09-15 20:24:15.643 wdl.w:ptcp.w:call-trgt-12.t:call-trgt_plot_motifs_allele INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:15.643 wdl.w:ptcp.w:call-trgt-12.t:call-trgt_plot_motifs_allele INFO eval :: name: "plot_type", value: "allele"
2025-09-15 20:24:15.643 wdl.w:ptcp.w:call-trgt-12.t:call-trgt_plot_motifs_allele INFO eval :: name: "show", value: "motifs"
2025-09-15 20:24:15.643 wdl.w:ptcp.w:call-trgt-12.t:call-trgt_plot_motifs_allele INFO eval :: name: "threads", value: 1
2025-09-15 20:24:15.643 wdl.w:ptcp.w:call-trgt-12.t:call-trgt_plot_motifs_allele INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:15.643 wdl.w:ptcp.w:call-trgt-12.t:call-trgt_plot_motifs_allele INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2109.motifs_allele"
2025-09-15 20:24:15.643 wdl.w:ptcp.w:call-trgt-12.t:call-trgt_plot_motifs_allele INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:15.644 wdl.w:ptcp.w:call-trgt-12.t:call-trgt_plot_motifs_allele WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:15.644 wdl.w:ptcp.w:call-trgt-12.t:call-trgt_plot_motifs_allele INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:15.644 wdl.w:ptcp.w:call-trgt-12.t:call-trgt_plot_motifs_allele INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:15.699 wdl.w:ptcp.t:call-pbmm2_align_hifi-93 NOTICE done
2025-09-15 20:24:15.705 wdl.w:ptcp NOTICE finish :: job: "call-pbmm2_align_hifi-93"
2025-09-15 20:24:15.706 wdl.w:ptcp INFO output :: job: "call-pbmm2_align_hifi-93", values: {"report": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-93/out/mapping_stats.report.json", "mapped_bam_pbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-93/out/m84036_250809_035451_s4.bc2190.mapped.bam.pbi", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-93/out/m84036_250809_035451_s4.bc2190.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-93/out/m84036_250809_035451_s4.bc2190.mapped.bam"}
2025-09-15 20:24:15.706 wdl.w:ptcp NOTICE ready :: job: "call-paraphase-93", callee: "paraphase"
2025-09-15 20:24:15.706 wdl.w:ptcp INFO input :: job: "call-paraphase-93", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf", "genome_version": "38", "config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-93/out/m84036_250809_035451_s4.bc2190.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-93/out/m84036_250809_035451_s4.bc2190.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2190"}
2025-09-15 20:24:15.707 wdl.w:ptcp NOTICE ready :: job: "call-sawfish-93", callee: "sawfish"
2025-09-15 20:24:15.707 wdl.w:ptcp.w:call-trgt-12.t:call-trgt_plot_motifs_allele INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-12/call-trgt_plot_motifs_allele/_singularity_tmpdir_fd_ic37k"
2025-09-15 20:24:15.707 wdl.w:ptcp INFO input :: job: "call-sawfish-93", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-93/out/m84036_250809_035451_s4.bc2190.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-93/out/m84036_250809_035451_s4.bc2190.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2190"}
2025-09-15 20:24:15.707 wdl.w:ptcp.w:call-trgt-12.t:call-trgt_plot_motifs_allele INFO Slurm invocation: srun --job-name call-trgt_plot_motifs_allele --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-12/call-trgt_plot_motifs_allele/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-12/call-trgt_plot_motifs_allele/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-12/call-trgt_plot_motifs_allele/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-12/call-trgt_plot_motifs_allele/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-12/call-trgt_genotype/out/m84036_250809_035451_s4.bc2109.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2109.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-12/call-trgt_genotype/out/m84036_250809_035451_s4.bc2109.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2109.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-12/call-trgt_genotype/out/m84036_250809_035451_s4.bc2109.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2109.trgt.vcf:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-12/call-trgt_plot_motifs_allele/_singularity_tmpdir_fd_ic37k/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-12/call-trgt_plot_motifs_allele/_singularity_tmpdir_fd_ic37k/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:15.708 wdl.w:ptcp NOTICE ready :: job: "call-trgt-93", callee: "trgt"
2025-09-15 20:24:15.709 wdl.w:ptcp INFO input :: job: "call-trgt-93", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-93/out/m84036_250809_035451_s4.bc2190.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-93/out/m84036_250809_035451_s4.bc2190.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2190"}
2025-09-15 20:24:15.713 wdl.w:ptcp.w:call-trgt-12.t:call-trgt_plot_motifs_waterfall NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-12/call-trgt_plot_motifs_waterfall", thread: 140606626068032
2025-09-15 20:24:15.727 wdl.w:ptcp.w:call-trgt-12.t:call-trgt_plot_motifs_allele NOTICE slurm_singularity run :: pid: 1201287, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-12/call-trgt_plot_motifs_allele/slurm_singularity.log.txt"
2025-09-15 20:24:15.729 wdl.w:ptcp.w:call-trgt-12.t:call-trgt_plot_motifs_waterfall INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:15.729 wdl.w:ptcp.w:call-trgt-12.t:call-trgt_plot_motifs_waterfall INFO input :: name: "waterfall", value: true
2025-09-15 20:24:15.730 wdl.w:ptcp.w:call-trgt-12.t:call-trgt_plot_motifs_waterfall INFO input :: name: "methylation", value: false
2025-09-15 20:24:15.730 wdl.w:ptcp.w:call-trgt-12.t:call-trgt_plot_motifs_waterfall INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:15.730 wdl.w:ptcp.w:call-trgt-12.t:call-trgt_plot_motifs_waterfall INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:15.730 wdl.w:ptcp.w:call-trgt-12.t:call-trgt_plot_motifs_waterfall INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:15.730 wdl.w:ptcp.w:call-trgt-12.t:call-trgt_plot_motifs_waterfall INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2109.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:15.730 wdl.w:ptcp.w:call-trgt-12.t:call-trgt_plot_motifs_waterfall INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2109.trgt.sorted.spanning.bam"
2025-09-15 20:24:15.730 wdl.w:ptcp.w:call-trgt-12.t:call-trgt_plot_motifs_waterfall INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2109.trgt.vcf"
2025-09-15 20:24:15.730 wdl.w:ptcp.w:call-trgt-12.t:call-trgt_plot_motifs_waterfall INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2109"
2025-09-15 20:24:15.730 wdl.w:ptcp.w:call-trgt-12.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:15.730 wdl.w:ptcp.w:call-trgt-12.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "plot_type", value: "waterfall"
2025-09-15 20:24:15.730 wdl.w:ptcp.w:call-trgt-12.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "show", value: "motifs"
2025-09-15 20:24:15.730 wdl.w:ptcp.w:call-trgt-12.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "threads", value: 1
2025-09-15 20:24:15.731 wdl.w:ptcp.w:call-trgt-12.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:15.731 wdl.w:ptcp.w:call-trgt-12.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2109.motifs_waterfall"
2025-09-15 20:24:15.731 wdl.w:ptcp.w:call-trgt-12.t:call-trgt_plot_motifs_waterfall INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:15.731 wdl.w:ptcp.w:call-trgt-12.t:call-trgt_plot_motifs_waterfall WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:15.732 wdl.w:ptcp.w:call-trgt-12.t:call-trgt_plot_motifs_waterfall INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:15.732 wdl.w:ptcp.w:call-trgt-12.t:call-trgt_plot_motifs_waterfall INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:15.798 wdl.w:ptcp.w:call-trgt-12.t:call-trgt_plot_motifs_waterfall INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-12/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_pij7j82v"
2025-09-15 20:24:15.798 wdl.w:ptcp.w:call-trgt-12.t:call-trgt_plot_motifs_waterfall INFO Slurm invocation: srun --job-name call-trgt_plot_motifs_waterfall --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-12/call-trgt_plot_motifs_waterfall/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-12/call-trgt_plot_motifs_waterfall/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-12/call-trgt_plot_motifs_waterfall/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-12/call-trgt_plot_motifs_waterfall/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-12/call-trgt_genotype/out/m84036_250809_035451_s4.bc2109.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2109.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-12/call-trgt_genotype/out/m84036_250809_035451_s4.bc2109.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2109.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-12/call-trgt_genotype/out/m84036_250809_035451_s4.bc2109.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2109.trgt.vcf:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-12/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_pij7j82v/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-12/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_pij7j82v/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:15.807 wdl.w:ptcp.w:call-trgt-12.t:call-trgt_plot_motifs_waterfall NOTICE slurm_singularity run :: pid: 1201290, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-12/call-trgt_plot_motifs_waterfall/slurm_singularity.log.txt"
2025-09-15 20:24:15.875 wdl.w:ptcp.w:call-trgt-17.t:call-trgt_plot_meth_allele INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2114.meth_allele.trgt_plots.zip"
2025-09-15 20:24:15.977 wdl.w:ptcp.w:call-trgt-17.t:call-trgt_plot_meth_allele NOTICE done
2025-09-15 20:24:15.983 wdl.w:ptcp.w:call-trgt-17 NOTICE finish :: job: "call-trgt_plot_meth_allele"
2025-09-15 20:24:15.983 wdl.w:ptcp.w:call-trgt-17 INFO output :: job: "call-trgt_plot_meth_allele", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-17/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2114.meth_allele.trgt_plots.zip"}
2025-09-15 20:24:15.983 wdl.w:ptcp.w:call-trgt-17 INFO visit :: node: "output-images_meth_allele", values: {"images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-17/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2114.meth_allele.trgt_plots.zip"}
2025-09-15 20:24:15.987 wdl.w:ptcp.w:call-paraphase-17.t:call-call_f8 NOTICE task setup :: name: "call_f8", source: "./paraphase.wdl", line: 232, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-17/call-call_f8", thread: 140607699809856
2025-09-15 20:24:16.007 wdl.w:ptcp.w:call-paraphase-17.t:call-call_f8 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:16.007 wdl.w:ptcp.w:call-paraphase-17.t:call-call_f8 INFO input :: name: "genome_version", value: "38"
2025-09-15 20:24:16.007 wdl.w:ptcp.w:call-paraphase-17.t:call-call_f8 INFO input :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2114"
2025-09-15 20:24:16.007 wdl.w:ptcp.w:call-paraphase-17.t:call-call_f8 INFO input :: name: "paraphase_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2114.paraphase.bam.bai"
2025-09-15 20:24:16.007 wdl.w:ptcp.w:call-paraphase-17.t:call-call_f8 INFO input :: name: "paraphase_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2114.paraphase.bam"
2025-09-15 20:24:16.007 wdl.w:ptcp.w:call-paraphase-17.t:call-call_f8 INFO input :: name: "sex", value: "F"
2025-09-15 20:24:16.007 wdl.w:ptcp.w:call-paraphase-17.t:call-call_f8 INFO eval :: name: "threads", value: 1
2025-09-15 20:24:16.007 wdl.w:ptcp.w:call-paraphase-17.t:call-call_f8 INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:16.008 wdl.w:ptcp.w:call-paraphase-17.t:call-call_f8 INFO eval :: name: "disk_size", value: 11
2025-09-15 20:24:16.008 wdl.w:ptcp.w:call-paraphase-17.t:call-call_f8 INFO eval :: name: "sample_sex", value: "F"
2025-09-15 20:24:16.008 wdl.w:ptcp.w:call-paraphase-17.t:call-call_f8 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:16.008 wdl.w:ptcp.w:call-paraphase-17.t:call-call_f8 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:16.008 wdl.w:ptcp.w:call-paraphase-17.t:call-call_f8 INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:16.008 wdl.w:ptcp.w:call-paraphase-17.t:call-call_f8 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:16.047 wdl.w:ptcp.w:call-paraphase-17.t:call-call_f8 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 8, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-17/call-call_f8/_singularity_tmpdir_ut9__l7y"
2025-09-15 20:24:16.047 wdl.w:ptcp.w:call-paraphase-17.t:call-call_f8 INFO Slurm invocation: srun --job-name call-call_f8 --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-17/call-call_f8/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-17/call-call_f8/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-17/call-call_f8/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-17/call-call_f8/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-17/call-run_paraphase/out/m84036_250809_035451_s4.bc2114_paraphase/m84036_250809_035451_s4.bc2114.paraphase.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2114.paraphase.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-17/call-run_paraphase/out/m84036_250809_035451_s4.bc2114_paraphase/m84036_250809_035451_s4.bc2114.paraphase.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2114.paraphase.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-17/call-call_f8/_singularity_tmpdir_ut9__l7y/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-17/call-call_f8/_singularity_tmpdir_ut9__l7y/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:16.059 wdl.w:ptcp.w:call-paraphase-17.t:call-call_f8 NOTICE slurm_singularity run :: pid: 1201297, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-17/call-call_f8/slurm_singularity.log.txt"
2025-09-15 20:24:16.098 wdl.w:ptcp.w:call-trgt-05.t:call-trgt_plot_motifs_allele.slurm_singularity INFO srun: job 51797586 queued and waiting for resources
2025-09-15 20:24:16.098 wdl.w:ptcp.w:call-trgt-05.t:call-trgt_plot_motifs_allele.slurm_singularity INFO srun: job 51797586 has been allocated resources
2025-09-15 20:24:16.098 wdl.w:ptcp.w:call-trgt-05.t:call-trgt_plot_motifs_allele.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:16.115 wdl.w:ptcp.w:call-trgt-17.t:call-trgt_plot_motifs_allele INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2114.motifs_allele.trgt_plots.zip"
2025-09-15 20:24:16.151 wdl.w:ptcp.w:call-trgt-05.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO srun: job 51797587 queued and waiting for resources
2025-09-15 20:24:16.151 wdl.w:ptcp.w:call-trgt-05.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO srun: job 51797587 has been allocated resources
2025-09-15 20:24:16.151 wdl.w:ptcp.w:call-trgt-05.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:16.206 wdl.w:ptcp.w:call-trgt-12.t:call-trgt_plot_meth_allele.slurm_singularity INFO srun: job 51797588 queued and waiting for resources
2025-09-15 20:24:16.206 wdl.w:ptcp.w:call-trgt-12.t:call-trgt_plot_meth_allele.slurm_singularity INFO srun: job 51797588 has been allocated resources
2025-09-15 20:24:16.206 wdl.w:ptcp.w:call-trgt-12.t:call-trgt_plot_meth_allele.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:16.223 wdl.w:ptcp.w:call-trgt-17.t:call-trgt_plot_motifs_allele NOTICE done
2025-09-15 20:24:16.228 wdl.w:ptcp.w:call-trgt-17 NOTICE finish :: job: "call-trgt_plot_motifs_allele"
2025-09-15 20:24:16.229 wdl.w:ptcp.w:call-trgt-17 INFO output :: job: "call-trgt_plot_motifs_allele", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-17/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2114.motifs_allele.trgt_plots.zip"}
2025-09-15 20:24:16.229 wdl.w:ptcp.w:call-trgt-17 INFO visit :: node: "output-images_motifs_allele", values: {"images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-17/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2114.motifs_allele.trgt_plots.zip"}
2025-09-15 20:24:16.235 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_meth_allele NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-27/call-trgt_plot_meth_allele", thread: 140608228288064
2025-09-15 20:24:16.254 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_meth_allele INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:16.255 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_meth_allele INFO input :: name: "waterfall", value: false
2025-09-15 20:24:16.255 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_meth_allele INFO input :: name: "methylation", value: true
2025-09-15 20:24:16.255 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_meth_allele INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:16.255 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_meth_allele INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:16.255 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_meth_allele INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:16.255 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_meth_allele INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2124.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:16.255 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_meth_allele INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2124.trgt.sorted.spanning.bam"
2025-09-15 20:24:16.255 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_meth_allele INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2124.trgt.vcf"
2025-09-15 20:24:16.255 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_meth_allele INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2124"
2025-09-15 20:24:16.255 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_meth_allele INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:16.255 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_meth_allele INFO eval :: name: "plot_type", value: "allele"
2025-09-15 20:24:16.256 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_meth_allele INFO eval :: name: "show", value: "meth"
2025-09-15 20:24:16.256 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_meth_allele INFO eval :: name: "threads", value: 1
2025-09-15 20:24:16.256 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_meth_allele INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:16.256 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_meth_allele INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2124.meth_allele"
2025-09-15 20:24:16.256 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_meth_allele INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:16.256 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_meth_allele WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:16.257 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_meth_allele INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:16.257 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_meth_allele INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:16.271 wdl.w:ptcp.w:call-trgt-12.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO srun: job 51797589 queued and waiting for resources
2025-09-15 20:24:16.271 wdl.w:ptcp.w:call-trgt-12.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO srun: job 51797589 has been allocated resources
2025-09-15 20:24:16.271 wdl.w:ptcp.w:call-trgt-12.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:16.327 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_meth_allele INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-27/call-trgt_plot_meth_allele/_singularity_tmpdir_i90dl6uj"
2025-09-15 20:24:16.327 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_meth_allele INFO Slurm invocation: srun --job-name call-trgt_plot_meth_allele --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-27/call-trgt_plot_meth_allele/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-27/call-trgt_plot_meth_allele/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-27/call-trgt_plot_meth_allele/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-27/call-trgt_plot_meth_allele/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-27/call-trgt_genotype/out/m84036_250809_035451_s4.bc2124.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2124.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-27/call-trgt_genotype/out/m84036_250809_035451_s4.bc2124.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2124.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-27/call-trgt_genotype/out/m84036_250809_035451_s4.bc2124.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2124.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-27/call-trgt_plot_meth_allele/_singularity_tmpdir_i90dl6uj/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-27/call-trgt_plot_meth_allele/_singularity_tmpdir_i90dl6uj/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:16.331 wdl.w:ptcp.w:call-trgt-21.t:call-trgt_plot_motifs_waterfall INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2118.motifs_waterfall.trgt_plots.zip"
2025-09-15 20:24:16.349 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_meth_allele NOTICE slurm_singularity run :: pid: 1201311, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-27/call-trgt_plot_meth_allele/slurm_singularity.log.txt"
2025-09-15 20:24:16.460 wdl.w:ptcp.w:call-trgt-21.t:call-trgt_plot_motifs_waterfall NOTICE done
2025-09-15 20:24:16.465 wdl.w:ptcp.w:call-trgt-21 NOTICE finish :: job: "call-trgt_plot_motifs_waterfall"
2025-09-15 20:24:16.465 wdl.w:ptcp.w:call-trgt-21 INFO output :: job: "call-trgt_plot_motifs_waterfall", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-21/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2118.motifs_waterfall.trgt_plots.zip"}
2025-09-15 20:24:16.466 wdl.w:ptcp.w:call-trgt-21 INFO visit :: node: "output-images_motifs_waterfall", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-21/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2118.motifs_waterfall.trgt_plots.zip"}
2025-09-15 20:24:16.466 wdl.w:ptcp.w:call-trgt-21 INFO visit :: node: "outputs", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-21/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2118.motifs_waterfall.trgt_plots.zip", "images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-21/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2118.meth_allele.trgt_plots.zip", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-21/call-trgt_genotype/out/m84036_250809_035451_s4.bc2118.trgt.sorted.spanning.bam.bai", "images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-21/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2118.motifs_allele.trgt_plots.zip", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-21/call-trgt_genotype/out/m84036_250809_035451_s4.bc2118.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-21/call-trgt_genotype/out/m84036_250809_035451_s4.bc2118.trgt.vcf", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-21/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2118.repeats.bam", "images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-21/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2118.meth_waterfall.trgt_plots.zip", "reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-21/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2118.repeats.bam.bai"}
2025-09-15 20:24:16.472 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_meth_waterfall NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-27/call-trgt_plot_meth_waterfall", thread: 140608748373568
2025-09-15 20:24:16.491 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_meth_waterfall INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:16.491 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_meth_waterfall INFO input :: name: "waterfall", value: true
2025-09-15 20:24:16.491 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_meth_waterfall INFO input :: name: "methylation", value: true
2025-09-15 20:24:16.491 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_meth_waterfall INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:16.492 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_meth_waterfall INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:16.492 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_meth_waterfall INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:16.492 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_meth_waterfall INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2124.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:16.492 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_meth_waterfall INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2124.trgt.sorted.spanning.bam"
2025-09-15 20:24:16.492 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_meth_waterfall INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2124.trgt.vcf"
2025-09-15 20:24:16.492 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_meth_waterfall INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2124"
2025-09-15 20:24:16.492 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_meth_waterfall INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:16.492 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_meth_waterfall INFO eval :: name: "plot_type", value: "waterfall"
2025-09-15 20:24:16.493 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_meth_waterfall INFO eval :: name: "show", value: "meth"
2025-09-15 20:24:16.493 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_meth_waterfall INFO eval :: name: "threads", value: 1
2025-09-15 20:24:16.493 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_meth_waterfall INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:16.493 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_meth_waterfall INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2124.meth_waterfall"
2025-09-15 20:24:16.494 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_meth_waterfall INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:16.494 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_meth_waterfall WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:16.494 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_meth_waterfall INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:16.494 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_meth_waterfall INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:16.528 wdl.w:ptcp.w:call-paraphase-18.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for f8inv1 for sample m84036_250809_035451_s4.bc2115 at 2025-09-15 20:24:09.061373...
2025-09-15 20:24:16.573 wdl.w:ptcp.w:call-trgt-21 NOTICE done
2025-09-15 20:24:16.574 wdl.w:ptcp.t:call-pbmm2_align_hifi-95 INFO output :: name: "mapped_bam", value: "m84036_250809_035451_s4.bc2192.mapped.bam"
2025-09-15 20:24:16.578 wdl.w:ptcp.t:call-pbmm2_align_hifi-95 INFO output :: name: "mapped_bam_bai", value: "m84036_250809_035451_s4.bc2192.mapped.bam.bai"
2025-09-15 20:24:16.578 wdl.w:ptcp NOTICE finish :: job: "call-trgt-21"
2025-09-15 20:24:16.578 wdl.w:ptcp INFO output :: job: "call-trgt-21", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-21/out/m84036_250809_035451_s4.bc2118.motifs_waterfall.trgt_plots.zip", "images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-21/out/m84036_250809_035451_s4.bc2118.meth_allele.trgt_plots.zip", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-21/out/m84036_250809_035451_s4.bc2118.trgt.sorted.spanning.bam.bai", "images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-21/out/m84036_250809_035451_s4.bc2118.motifs_allele.trgt_plots.zip", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-21/out/m84036_250809_035451_s4.bc2118.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-21/out/m84036_250809_035451_s4.bc2118.trgt.vcf", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-21/out/m84036_250809_035451_s4.bc2118.repeats.bam", "images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-21/out/m84036_250809_035451_s4.bc2118.meth_waterfall.trgt_plots.zip", "reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-21/out/m84036_250809_035451_s4.bc2118.repeats.bam.bai"}
2025-09-15 20:24:16.579 wdl.w:ptcp.t:call-pbmm2_align_hifi-95 INFO output :: name: "mapped_bam_pbi", value: "m84036_250809_035451_s4.bc2192.mapped.bam.pbi"
2025-09-15 20:24:16.581 wdl.w:ptcp.t:call-pbmm2_align_hifi-95 INFO output :: name: "report", value: "mapping_stats.report.json"
2025-09-15 20:24:16.584 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_meth_waterfall INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-27/call-trgt_plot_meth_waterfall/_singularity_tmpdir_bu1tzexa"
2025-09-15 20:24:16.585 wdl.w:ptcp.w:call-trgt-41 NOTICE workflow start :: name: "trgt", source: "./trgt.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-41"
2025-09-15 20:24:16.585 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_meth_waterfall INFO Slurm invocation: srun --job-name call-trgt_plot_meth_waterfall --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-27/call-trgt_plot_meth_waterfall/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-27/call-trgt_plot_meth_waterfall/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-27/call-trgt_plot_meth_waterfall/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-27/call-trgt_plot_meth_waterfall/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-27/call-trgt_genotype/out/m84036_250809_035451_s4.bc2124.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2124.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-27/call-trgt_genotype/out/m84036_250809_035451_s4.bc2124.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2124.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-27/call-trgt_genotype/out/m84036_250809_035451_s4.bc2124.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2124.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-27/call-trgt_plot_meth_waterfall/_singularity_tmpdir_bu1tzexa/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-27/call-trgt_plot_meth_waterfall/_singularity_tmpdir_bu1tzexa/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:16.588 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_plot_meth_waterfall INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2103.meth_waterfall.trgt_plots.zip"
2025-09-15 20:24:16.601 wdl.w:ptcp.w:call-trgt-41 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:24:16.601 wdl.w:ptcp.w:call-trgt-41 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-41/out/m84036_250809_035451_s4.bc2138.mapped.bam"}
2025-09-15 20:24:16.602 wdl.w:ptcp.w:call-trgt-41 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-41/out/m84036_250809_035451_s4.bc2138.mapped.bam.bai"}
2025-09-15 20:24:16.602 wdl.w:ptcp.w:call-trgt-41 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:24:16.602 wdl.w:ptcp.w:call-trgt-41 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:24:16.602 wdl.w:ptcp.w:call-trgt-41 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2138"}
2025-09-15 20:24:16.602 wdl.w:ptcp.w:call-trgt-41 INFO visit :: node: "decl-sex", values: {"sex": "F"}
2025-09-15 20:24:16.602 wdl.w:ptcp.w:call-trgt-41 INFO visit :: node: "decl-trgt_bed", values: {"trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"}
2025-09-15 20:24:16.602 wdl.w:ptcp.w:call-trgt-41 NOTICE ready :: job: "call-get_reads_overlapping_repeats", callee: "get_reads_overlapping_repeats"
2025-09-15 20:24:16.602 wdl.w:ptcp.w:call-trgt-41 INFO input :: job: "call-get_reads_overlapping_repeats", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-41/out/m84036_250809_035451_s4.bc2138.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-41/out/m84036_250809_035451_s4.bc2138.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2138"}
2025-09-15 20:24:16.603 wdl.w:ptcp.w:call-trgt-41 NOTICE ready :: job: "call-trgt_genotype", callee: "trgt_genotype"
2025-09-15 20:24:16.603 wdl.w:ptcp.w:call-trgt-41 INFO input :: job: "call-trgt_genotype", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-41/out/m84036_250809_035451_s4.bc2138.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-41/out/m84036_250809_035451_s4.bc2138.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2138"}
2025-09-15 20:24:16.604 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_meth_waterfall NOTICE slurm_singularity run :: pid: 1201321, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-27/call-trgt_plot_meth_waterfall/slurm_singularity.log.txt"
2025-09-15 20:24:16.605 wdl.w:ptcp.w:call-trgt-33.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:14 [ERROR] - No reads found for TRID=PRTS_ARX
2025-09-15 20:24:16.606 wdl.w:ptcp.w:call-trgt-33.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:14 [ERROR] - No reads found for TRID=EIEE1_ARX
2025-09-15 20:24:16.669 wdl.w:ptcp.w:call-trgt-28.t:call-trgt_plot_motifs_waterfall INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2125.motifs_waterfall.trgt_plots.zip"
2025-09-15 20:24:16.673 wdl.w:ptcp.w:call-trgt-17.t:call-trgt_plot_motifs_waterfall INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2114.motifs_waterfall.trgt_plots.zip"
2025-09-15 20:24:16.690 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_plot_meth_waterfall NOTICE done
2025-09-15 20:24:16.695 wdl.w:ptcp.w:call-trgt-06 NOTICE finish :: job: "call-trgt_plot_meth_waterfall"
2025-09-15 20:24:16.696 wdl.w:ptcp.w:call-trgt-06 INFO output :: job: "call-trgt_plot_meth_waterfall", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-06/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2103.meth_waterfall.trgt_plots.zip"}
2025-09-15 20:24:16.696 wdl.w:ptcp.w:call-trgt-06 INFO visit :: node: "output-images_meth_waterfall", values: {"images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-06/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2103.meth_waterfall.trgt_plots.zip"}
2025-09-15 20:24:16.696 wdl.w:ptcp.t:call-pbmm2_align_hifi-95 NOTICE done
2025-09-15 20:24:16.701 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_motifs_allele NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-27/call-trgt_plot_motifs_allele", thread: 140610887464512
2025-09-15 20:24:16.702 wdl.w:ptcp NOTICE finish :: job: "call-pbmm2_align_hifi-95"
2025-09-15 20:24:16.703 wdl.w:ptcp INFO output :: job: "call-pbmm2_align_hifi-95", values: {"report": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-95/out/mapping_stats.report.json", "mapped_bam_pbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-95/out/m84036_250809_035451_s4.bc2192.mapped.bam.pbi", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-95/out/m84036_250809_035451_s4.bc2192.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-95/out/m84036_250809_035451_s4.bc2192.mapped.bam"}
2025-09-15 20:24:16.703 wdl.w:ptcp NOTICE ready :: job: "call-paraphase-95", callee: "paraphase"
2025-09-15 20:24:16.703 wdl.w:ptcp INFO input :: job: "call-paraphase-95", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf", "genome_version": "38", "config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-95/out/m84036_250809_035451_s4.bc2192.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-95/out/m84036_250809_035451_s4.bc2192.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2192"}
2025-09-15 20:24:16.704 wdl.w:ptcp NOTICE ready :: job: "call-sawfish-95", callee: "sawfish"
2025-09-15 20:24:16.704 wdl.w:ptcp INFO input :: job: "call-sawfish-95", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-95/out/m84036_250809_035451_s4.bc2192.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-95/out/m84036_250809_035451_s4.bc2192.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2192"}
2025-09-15 20:24:16.707 wdl.w:ptcp NOTICE ready :: job: "call-trgt-95", callee: "trgt"
2025-09-15 20:24:16.707 wdl.w:ptcp INFO input :: job: "call-trgt-95", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-95/out/m84036_250809_035451_s4.bc2192.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-95/out/m84036_250809_035451_s4.bc2192.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2192"}
2025-09-15 20:24:16.709 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_motifs_waterfall NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-27/call-trgt_plot_motifs_waterfall", thread: 140606609282624
2025-09-15 20:24:16.721 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_motifs_allele INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:16.722 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_motifs_allele INFO input :: name: "waterfall", value: false
2025-09-15 20:24:16.722 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_motifs_allele INFO input :: name: "methylation", value: false
2025-09-15 20:24:16.722 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_motifs_allele INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:16.722 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_motifs_allele INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:16.722 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_motifs_allele INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:16.723 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_motifs_allele INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2124.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:16.723 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_motifs_allele INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2124.trgt.sorted.spanning.bam"
2025-09-15 20:24:16.723 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_motifs_allele INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2124.trgt.vcf"
2025-09-15 20:24:16.723 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_motifs_allele INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2124"
2025-09-15 20:24:16.723 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_motifs_allele INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:16.724 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_motifs_allele INFO eval :: name: "plot_type", value: "allele"
2025-09-15 20:24:16.724 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_motifs_allele INFO eval :: name: "show", value: "motifs"
2025-09-15 20:24:16.724 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_motifs_allele INFO eval :: name: "threads", value: 1
2025-09-15 20:24:16.725 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_motifs_allele INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:16.725 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_motifs_allele INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2124.motifs_allele"
2025-09-15 20:24:16.725 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_motifs_allele INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:16.726 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_motifs_allele WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:16.726 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_motifs_allele INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:16.727 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_motifs_allele INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:16.730 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_motifs_waterfall INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:16.730 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_motifs_waterfall INFO input :: name: "waterfall", value: true
2025-09-15 20:24:16.730 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_motifs_waterfall INFO input :: name: "methylation", value: false
2025-09-15 20:24:16.730 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_motifs_waterfall INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:16.730 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_motifs_waterfall INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:16.730 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_motifs_waterfall INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:16.730 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_motifs_waterfall INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2124.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:16.730 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_motifs_waterfall INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2124.trgt.sorted.spanning.bam"
2025-09-15 20:24:16.730 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_motifs_waterfall INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2124.trgt.vcf"
2025-09-15 20:24:16.730 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_motifs_waterfall INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2124"
2025-09-15 20:24:16.731 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:16.731 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "plot_type", value: "waterfall"
2025-09-15 20:24:16.731 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "show", value: "motifs"
2025-09-15 20:24:16.731 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "threads", value: 1
2025-09-15 20:24:16.731 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:16.732 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2124.motifs_waterfall"
2025-09-15 20:24:16.732 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_motifs_waterfall INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:16.732 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_motifs_waterfall WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:16.732 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_motifs_waterfall INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:16.733 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_motifs_waterfall INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:16.740 wdl.w:ptcp.w:call-trgt-12.t:call-trgt_plot_motifs_allele.slurm_singularity INFO srun: job 51797590 queued and waiting for resources
2025-09-15 20:24:16.740 wdl.w:ptcp.w:call-trgt-12.t:call-trgt_plot_motifs_allele.slurm_singularity INFO srun: job 51797590 has been allocated resources
2025-09-15 20:24:16.740 wdl.w:ptcp.w:call-trgt-12.t:call-trgt_plot_motifs_allele.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:16.808 wdl.w:ptcp.w:call-paraphase-15.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for hba for sample m84036_250809_035451_s4.bc2112 at 2025-09-15 20:23:35.902841...
2025-09-15 20:24:16.810 wdl.w:ptcp.w:call-paraphase-15.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for hba for sample m84036_250809_035451_s4.bc2112 at 2025-09-15 20:23:36.174471...
2025-09-15 20:24:16.810 wdl.w:ptcp.w:call-paraphase-15.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for cyp21 for sample m84036_250809_035451_s4.bc2112 at 2025-09-15 20:23:41.922045...
2025-09-15 20:24:16.810 wdl.w:ptcp.w:call-paraphase-15.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for cyp21 for sample m84036_250809_035451_s4.bc2112 at 2025-09-15 20:23:42.698396...
2025-09-15 20:24:16.810 wdl.w:ptcp.w:call-paraphase-15.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for gba for sample m84036_250809_035451_s4.bc2112 at 2025-09-15 20:23:50.797154...
2025-09-15 20:24:16.810 wdl.w:ptcp.w:call-paraphase-15.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for gba for sample m84036_250809_035451_s4.bc2112 at 2025-09-15 20:23:51.240570...
2025-09-15 20:24:16.810 wdl.w:ptcp.w:call-paraphase-15.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for hbb for sample m84036_250809_035451_s4.bc2112 at 2025-09-15 20:23:56.391710...
2025-09-15 20:24:16.810 wdl.w:ptcp.w:call-paraphase-15.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for hbb for sample m84036_250809_035451_s4.bc2112 at 2025-09-15 20:23:56.392355...
2025-09-15 20:24:16.810 wdl.w:ptcp.w:call-paraphase-15.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for hbb for sample m84036_250809_035451_s4.bc2112 at 2025-09-15 20:23:57.288977...
2025-09-15 20:24:16.810 wdl.w:ptcp.w:call-paraphase-15.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for hbb for sample m84036_250809_035451_s4.bc2112 at 2025-09-15 20:24:01.143831...
2025-09-15 20:24:16.810 wdl.w:ptcp.w:call-paraphase-15.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for hbb for sample m84036_250809_035451_s4.bc2112 at 2025-09-15 20:24:01.375623...
2025-09-15 20:24:16.828 wdl.w:ptcp.w:call-trgt-12.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO srun: job 51797591 queued and waiting for resources
2025-09-15 20:24:16.828 wdl.w:ptcp.w:call-trgt-12.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO srun: job 51797591 has been allocated resources
2025-09-15 20:24:16.828 wdl.w:ptcp.w:call-trgt-12.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:16.829 wdl.w:ptcp.w:call-trgt-28.t:call-trgt_plot_motifs_waterfall NOTICE done
2025-09-15 20:24:16.834 wdl.w:ptcp.w:call-trgt-28 NOTICE finish :: job: "call-trgt_plot_motifs_waterfall"
2025-09-15 20:24:16.835 wdl.w:ptcp.w:call-trgt-28 INFO output :: job: "call-trgt_plot_motifs_waterfall", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-28/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2125.motifs_waterfall.trgt_plots.zip"}
2025-09-15 20:24:16.835 wdl.w:ptcp.w:call-trgt-28 INFO visit :: node: "output-images_motifs_waterfall", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-28/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2125.motifs_waterfall.trgt_plots.zip"}
2025-09-15 20:24:16.838 wdl.w:ptcp.w:call-trgt-17.t:call-trgt_plot_motifs_waterfall NOTICE done
2025-09-15 20:24:16.843 wdl.w:ptcp.w:call-trgt-17 NOTICE finish :: job: "call-trgt_plot_motifs_waterfall"
2025-09-15 20:24:16.843 wdl.w:ptcp.w:call-trgt-17 INFO output :: job: "call-trgt_plot_motifs_waterfall", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-17/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2114.motifs_waterfall.trgt_plots.zip"}
2025-09-15 20:24:16.843 wdl.w:ptcp.w:call-paraphase-28.t:call-call_f8 NOTICE task setup :: name: "call_f8", source: "./paraphase.wdl", line: 232, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-28/call-call_f8", thread: 140608186324544
2025-09-15 20:24:16.843 wdl.w:ptcp.w:call-trgt-17 INFO visit :: node: "output-images_motifs_waterfall", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-17/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2114.motifs_waterfall.trgt_plots.zip"}
2025-09-15 20:24:16.850 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_motifs_allele INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-27/call-trgt_plot_motifs_allele/_singularity_tmpdir_65q_p_2g"
2025-09-15 20:24:16.850 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_motifs_allele INFO Slurm invocation: srun --job-name call-trgt_plot_motifs_allele --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-27/call-trgt_plot_motifs_allele/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-27/call-trgt_plot_motifs_allele/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-27/call-trgt_plot_motifs_allele/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-27/call-trgt_plot_motifs_allele/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-27/call-trgt_genotype/out/m84036_250809_035451_s4.bc2124.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2124.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-27/call-trgt_genotype/out/m84036_250809_035451_s4.bc2124.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2124.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-27/call-trgt_genotype/out/m84036_250809_035451_s4.bc2124.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2124.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-27/call-trgt_plot_motifs_allele/_singularity_tmpdir_65q_p_2g/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-27/call-trgt_plot_motifs_allele/_singularity_tmpdir_65q_p_2g/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:16.851 wdl.w:ptcp.w:call-trgt-24.t:call-trgt_plot_meth_allele NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-24/call-trgt_plot_meth_allele", thread: 140609838900800
2025-09-15 20:24:16.860 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_motifs_waterfall INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-27/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_5gwg4k6w"
2025-09-15 20:24:16.861 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_motifs_waterfall INFO Slurm invocation: srun --job-name call-trgt_plot_motifs_waterfall --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-27/call-trgt_plot_motifs_waterfall/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-27/call-trgt_plot_motifs_waterfall/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-27/call-trgt_plot_motifs_waterfall/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-27/call-trgt_plot_motifs_waterfall/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-27/call-trgt_genotype/out/m84036_250809_035451_s4.bc2124.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2124.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-27/call-trgt_genotype/out/m84036_250809_035451_s4.bc2124.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2124.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-27/call-trgt_genotype/out/m84036_250809_035451_s4.bc2124.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2124.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-27/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_5gwg4k6w/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-27/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_5gwg4k6w/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:16.867 wdl.w:ptcp.w:call-paraphase-28.t:call-call_f8 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:16.867 wdl.w:ptcp.w:call-paraphase-28.t:call-call_f8 INFO input :: name: "genome_version", value: "38"
2025-09-15 20:24:16.867 wdl.w:ptcp.w:call-paraphase-28.t:call-call_f8 INFO input :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2125"
2025-09-15 20:24:16.867 wdl.w:ptcp.w:call-paraphase-28.t:call-call_f8 INFO input :: name: "paraphase_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2125.paraphase.bam.bai"
2025-09-15 20:24:16.867 wdl.w:ptcp.w:call-paraphase-28.t:call-call_f8 INFO input :: name: "paraphase_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2125.paraphase.bam"
2025-09-15 20:24:16.867 wdl.w:ptcp.w:call-paraphase-28.t:call-call_f8 INFO input :: name: "sex", value: "F"
2025-09-15 20:24:16.868 wdl.w:ptcp.w:call-paraphase-28.t:call-call_f8 INFO eval :: name: "threads", value: 1
2025-09-15 20:24:16.868 wdl.w:ptcp.w:call-paraphase-28.t:call-call_f8 INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:16.868 wdl.w:ptcp.w:call-paraphase-28.t:call-call_f8 INFO eval :: name: "disk_size", value: 11
2025-09-15 20:24:16.868 wdl.w:ptcp.w:call-paraphase-28.t:call-call_f8 INFO eval :: name: "sample_sex", value: "F"
2025-09-15 20:24:16.868 wdl.w:ptcp.w:call-paraphase-28.t:call-call_f8 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:16.869 wdl.w:ptcp.w:call-paraphase-28.t:call-call_f8 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:16.869 wdl.w:ptcp.w:call-paraphase-28.t:call-call_f8 INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:16.869 wdl.w:ptcp.w:call-paraphase-28.t:call-call_f8 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:16.874 wdl.w:ptcp.w:call-trgt-24.t:call-trgt_plot_meth_allele INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:16.874 wdl.w:ptcp.w:call-trgt-24.t:call-trgt_plot_meth_allele INFO input :: name: "waterfall", value: false
2025-09-15 20:24:16.874 wdl.w:ptcp.w:call-trgt-24.t:call-trgt_plot_meth_allele INFO input :: name: "methylation", value: true
2025-09-15 20:24:16.874 wdl.w:ptcp.w:call-trgt-24.t:call-trgt_plot_meth_allele INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:16.874 wdl.w:ptcp.w:call-trgt-24.t:call-trgt_plot_meth_allele INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:16.874 wdl.w:ptcp.w:call-trgt-24.t:call-trgt_plot_meth_allele INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:16.874 wdl.w:ptcp.w:call-trgt-24.t:call-trgt_plot_meth_allele INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2121.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:16.874 wdl.w:ptcp.w:call-trgt-24.t:call-trgt_plot_meth_allele INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2121.trgt.sorted.spanning.bam"
2025-09-15 20:24:16.874 wdl.w:ptcp.w:call-trgt-24.t:call-trgt_plot_meth_allele INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2121.trgt.vcf"
2025-09-15 20:24:16.874 wdl.w:ptcp.w:call-trgt-24.t:call-trgt_plot_meth_allele INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2121"
2025-09-15 20:24:16.874 wdl.w:ptcp.w:call-trgt-24.t:call-trgt_plot_meth_allele INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:16.875 wdl.w:ptcp.w:call-trgt-24.t:call-trgt_plot_meth_allele INFO eval :: name: "plot_type", value: "allele"
2025-09-15 20:24:16.875 wdl.w:ptcp.w:call-trgt-24.t:call-trgt_plot_meth_allele INFO eval :: name: "show", value: "meth"
2025-09-15 20:24:16.875 wdl.w:ptcp.w:call-trgt-24.t:call-trgt_plot_meth_allele INFO eval :: name: "threads", value: 1
2025-09-15 20:24:16.875 wdl.w:ptcp.w:call-trgt-24.t:call-trgt_plot_meth_allele INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:16.875 wdl.w:ptcp.w:call-trgt-24.t:call-trgt_plot_meth_allele INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2121.meth_allele"
2025-09-15 20:24:16.875 wdl.w:ptcp.w:call-trgt-24.t:call-trgt_plot_meth_allele INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:16.875 wdl.w:ptcp.w:call-trgt-24.t:call-trgt_plot_meth_allele WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:16.876 wdl.w:ptcp.w:call-trgt-24.t:call-trgt_plot_meth_allele INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:16.876 wdl.w:ptcp.w:call-trgt-24.t:call-trgt_plot_meth_allele INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:16.883 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_motifs_waterfall NOTICE slurm_singularity run :: pid: 1201325, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-27/call-trgt_plot_motifs_waterfall/slurm_singularity.log.txt"
2025-09-15 20:24:16.884 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_motifs_allele NOTICE slurm_singularity run :: pid: 1201324, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-27/call-trgt_plot_motifs_allele/slurm_singularity.log.txt"
2025-09-15 20:24:16.917 wdl.w:ptcp.w:call-paraphase-28.t:call-call_f8 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 8, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-28/call-call_f8/_singularity_tmpdir_ioy16v48"
2025-09-15 20:24:16.917 wdl.w:ptcp.w:call-paraphase-28.t:call-call_f8 INFO Slurm invocation: srun --job-name call-call_f8 --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-28/call-call_f8/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-28/call-call_f8/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-28/call-call_f8/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-28/call-call_f8/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-28/call-run_paraphase/out/m84036_250809_035451_s4.bc2125_paraphase/m84036_250809_035451_s4.bc2125.paraphase.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2125.paraphase.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-28/call-run_paraphase/out/m84036_250809_035451_s4.bc2125_paraphase/m84036_250809_035451_s4.bc2125.paraphase.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2125.paraphase.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-28/call-call_f8/_singularity_tmpdir_ioy16v48/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-28/call-call_f8/_singularity_tmpdir_ioy16v48/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:16.927 wdl.w:ptcp.w:call-paraphase-27.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for f8inv1 for sample m84036_250809_035451_s4.bc2124 at 2025-09-15 20:24:09.279335...
2025-09-15 20:24:16.939 wdl.w:ptcp.w:call-paraphase-28.t:call-call_f8 NOTICE slurm_singularity run :: pid: 1201344, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-28/call-call_f8/slurm_singularity.log.txt"
2025-09-15 20:24:16.945 wdl.w:ptcp.w:call-trgt-24.t:call-trgt_plot_meth_allele INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-24/call-trgt_plot_meth_allele/_singularity_tmpdir_r52fvve7"
2025-09-15 20:24:16.945 wdl.w:ptcp.w:call-trgt-24.t:call-trgt_plot_meth_allele INFO Slurm invocation: srun --job-name call-trgt_plot_meth_allele --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-24/call-trgt_plot_meth_allele/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-24/call-trgt_plot_meth_allele/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-24/call-trgt_plot_meth_allele/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-24/call-trgt_plot_meth_allele/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-24/call-trgt_genotype/out/m84036_250809_035451_s4.bc2121.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2121.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-24/call-trgt_genotype/out/m84036_250809_035451_s4.bc2121.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2121.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-24/call-trgt_genotype/out/m84036_250809_035451_s4.bc2121.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2121.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-24/call-trgt_plot_meth_allele/_singularity_tmpdir_r52fvve7/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-24/call-trgt_plot_meth_allele/_singularity_tmpdir_r52fvve7/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:16.957 wdl.w:ptcp.w:call-trgt-24.t:call-trgt_plot_meth_allele NOTICE slurm_singularity run :: pid: 1201346, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-24/call-trgt_plot_meth_allele/slurm_singularity.log.txt"
2025-09-15 20:24:16.974 wdl.w:ptcp.w:call-trgt-17.t:call-trgt_plot_meth_waterfall INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2114.meth_waterfall.trgt_plots.zip"
2025-09-15 20:24:17.034 wdl.w:ptcp.w:call-trgt-33.t:call-trgt_plot_motifs_allele INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2130.motifs_allele.trgt_plots.zip"
2025-09-15 20:24:17.071 wdl.w:ptcp.w:call-paraphase-17.t:call-call_f8.slurm_singularity INFO srun: job 51797592 queued and waiting for resources
2025-09-15 20:24:17.071 wdl.w:ptcp.w:call-paraphase-17.t:call-call_f8.slurm_singularity INFO srun: job 51797592 has been allocated resources
2025-09-15 20:24:17.071 wdl.w:ptcp.w:call-paraphase-17.t:call-call_f8.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:17.085 wdl.w:ptcp.w:call-trgt-17.t:call-trgt_plot_meth_waterfall NOTICE done
2025-09-15 20:24:17.091 wdl.w:ptcp.w:call-trgt-17 NOTICE finish :: job: "call-trgt_plot_meth_waterfall"
2025-09-15 20:24:17.091 wdl.w:ptcp.w:call-trgt-17 INFO output :: job: "call-trgt_plot_meth_waterfall", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-17/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2114.meth_waterfall.trgt_plots.zip"}
2025-09-15 20:24:17.092 wdl.w:ptcp.w:call-trgt-17 INFO visit :: node: "output-images_meth_waterfall", values: {"images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-17/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2114.meth_waterfall.trgt_plots.zip"}
2025-09-15 20:24:17.092 wdl.w:ptcp.w:call-trgt-17 INFO visit :: node: "outputs", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-17/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2114.motifs_waterfall.trgt_plots.zip", "images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-17/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2114.meth_allele.trgt_plots.zip", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-17/call-trgt_genotype/out/m84036_250809_035451_s4.bc2114.trgt.sorted.spanning.bam.bai", "images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-17/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2114.motifs_allele.trgt_plots.zip", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-17/call-trgt_genotype/out/m84036_250809_035451_s4.bc2114.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-17/call-trgt_genotype/out/m84036_250809_035451_s4.bc2114.trgt.vcf", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-17/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2114.repeats.bam", "images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-17/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2114.meth_waterfall.trgt_plots.zip", "reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-17/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2114.repeats.bam.bai"}
2025-09-15 20:24:17.098 wdl.w:ptcp.w:call-trgt-24.t:call-trgt_plot_meth_waterfall NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-24/call-trgt_plot_meth_waterfall", thread: 140610367379008
2025-09-15 20:24:17.115 wdl.w:ptcp.w:call-trgt-24.t:call-trgt_plot_meth_waterfall INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:17.115 wdl.w:ptcp.w:call-trgt-24.t:call-trgt_plot_meth_waterfall INFO input :: name: "waterfall", value: true
2025-09-15 20:24:17.115 wdl.w:ptcp.w:call-trgt-24.t:call-trgt_plot_meth_waterfall INFO input :: name: "methylation", value: true
2025-09-15 20:24:17.115 wdl.w:ptcp.w:call-trgt-24.t:call-trgt_plot_meth_waterfall INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:17.115 wdl.w:ptcp.w:call-trgt-24.t:call-trgt_plot_meth_waterfall INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:17.115 wdl.w:ptcp.w:call-trgt-24.t:call-trgt_plot_meth_waterfall INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:17.115 wdl.w:ptcp.w:call-trgt-24.t:call-trgt_plot_meth_waterfall INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2121.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:17.115 wdl.w:ptcp.w:call-trgt-24.t:call-trgt_plot_meth_waterfall INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2121.trgt.sorted.spanning.bam"
2025-09-15 20:24:17.115 wdl.w:ptcp.w:call-trgt-24.t:call-trgt_plot_meth_waterfall INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2121.trgt.vcf"
2025-09-15 20:24:17.115 wdl.w:ptcp.w:call-trgt-24.t:call-trgt_plot_meth_waterfall INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2121"
2025-09-15 20:24:17.116 wdl.w:ptcp.w:call-trgt-24.t:call-trgt_plot_meth_waterfall INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:17.116 wdl.w:ptcp.w:call-trgt-24.t:call-trgt_plot_meth_waterfall INFO eval :: name: "plot_type", value: "waterfall"
2025-09-15 20:24:17.116 wdl.w:ptcp.w:call-trgt-24.t:call-trgt_plot_meth_waterfall INFO eval :: name: "show", value: "meth"
2025-09-15 20:24:17.116 wdl.w:ptcp.w:call-trgt-24.t:call-trgt_plot_meth_waterfall INFO eval :: name: "threads", value: 1
2025-09-15 20:24:17.116 wdl.w:ptcp.w:call-trgt-24.t:call-trgt_plot_meth_waterfall INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:17.116 wdl.w:ptcp.w:call-trgt-24.t:call-trgt_plot_meth_waterfall INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2121.meth_waterfall"
2025-09-15 20:24:17.117 wdl.w:ptcp.w:call-trgt-24.t:call-trgt_plot_meth_waterfall INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:17.117 wdl.w:ptcp.w:call-trgt-24.t:call-trgt_plot_meth_waterfall WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:17.118 wdl.w:ptcp.w:call-trgt-24.t:call-trgt_plot_meth_waterfall INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:17.118 wdl.w:ptcp.w:call-trgt-24.t:call-trgt_plot_meth_waterfall INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:17.155 wdl.w:ptcp.w:call-trgt-33.t:call-trgt_plot_motifs_allele NOTICE done
2025-09-15 20:24:17.160 wdl.w:ptcp.w:call-trgt-33 NOTICE finish :: job: "call-trgt_plot_motifs_allele"
2025-09-15 20:24:17.160 wdl.w:ptcp.w:call-trgt-33 INFO output :: job: "call-trgt_plot_motifs_allele", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-33/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2130.motifs_allele.trgt_plots.zip"}
2025-09-15 20:24:17.161 wdl.w:ptcp.w:call-trgt-33 INFO visit :: node: "output-images_motifs_allele", values: {"images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-33/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2130.motifs_allele.trgt_plots.zip"}
2025-09-15 20:24:17.169 wdl.w:ptcp.w:call-trgt-24.t:call-trgt_plot_motifs_allele NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-24/call-trgt_plot_motifs_allele", thread: 140607691417152
2025-09-15 20:24:17.188 wdl.w:ptcp.w:call-trgt-24.t:call-trgt_plot_motifs_allele INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:17.189 wdl.w:ptcp.w:call-trgt-24.t:call-trgt_plot_motifs_allele INFO input :: name: "waterfall", value: false
2025-09-15 20:24:17.189 wdl.w:ptcp.w:call-trgt-24.t:call-trgt_plot_motifs_allele INFO input :: name: "methylation", value: false
2025-09-15 20:24:17.189 wdl.w:ptcp.w:call-trgt-24.t:call-trgt_plot_motifs_allele INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:17.189 wdl.w:ptcp.w:call-trgt-24.t:call-trgt_plot_motifs_allele INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:17.189 wdl.w:ptcp.w:call-trgt-24.t:call-trgt_plot_motifs_allele INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:17.189 wdl.w:ptcp.w:call-trgt-24.t:call-trgt_plot_motifs_allele INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2121.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:17.189 wdl.w:ptcp.w:call-trgt-24.t:call-trgt_plot_motifs_allele INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2121.trgt.sorted.spanning.bam"
2025-09-15 20:24:17.189 wdl.w:ptcp.w:call-trgt-24.t:call-trgt_plot_motifs_allele INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2121.trgt.vcf"
2025-09-15 20:24:17.189 wdl.w:ptcp.w:call-trgt-24.t:call-trgt_plot_motifs_allele INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2121"
2025-09-15 20:24:17.189 wdl.w:ptcp.w:call-trgt-24.t:call-trgt_plot_motifs_allele INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:17.190 wdl.w:ptcp.w:call-trgt-24.t:call-trgt_plot_motifs_allele INFO eval :: name: "plot_type", value: "allele"
2025-09-15 20:24:17.190 wdl.w:ptcp.w:call-trgt-24.t:call-trgt_plot_motifs_allele INFO eval :: name: "show", value: "motifs"
2025-09-15 20:24:17.190 wdl.w:ptcp.w:call-trgt-24.t:call-trgt_plot_motifs_allele INFO eval :: name: "threads", value: 1
2025-09-15 20:24:17.190 wdl.w:ptcp.w:call-trgt-24.t:call-trgt_plot_motifs_allele INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:17.190 wdl.w:ptcp.w:call-trgt-24.t:call-trgt_plot_motifs_allele INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2121.motifs_allele"
2025-09-15 20:24:17.190 wdl.w:ptcp.w:call-trgt-24.t:call-trgt_plot_motifs_allele INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:17.191 wdl.w:ptcp.w:call-trgt-24.t:call-trgt_plot_motifs_allele WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:17.191 wdl.w:ptcp.w:call-trgt-24.t:call-trgt_plot_motifs_allele INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:17.191 wdl.w:ptcp.w:call-trgt-24.t:call-trgt_plot_motifs_allele INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:17.212 wdl.w:ptcp.w:call-trgt-17 NOTICE done
2025-09-15 20:24:17.213 wdl.w:ptcp.w:call-trgt-24.t:call-trgt_plot_meth_waterfall INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-24/call-trgt_plot_meth_waterfall/_singularity_tmpdir_rt_bk8ec"
2025-09-15 20:24:17.213 wdl.w:ptcp.w:call-trgt-24.t:call-trgt_plot_meth_waterfall INFO Slurm invocation: srun --job-name call-trgt_plot_meth_waterfall --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-24/call-trgt_plot_meth_waterfall/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-24/call-trgt_plot_meth_waterfall/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-24/call-trgt_plot_meth_waterfall/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-24/call-trgt_plot_meth_waterfall/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-24/call-trgt_genotype/out/m84036_250809_035451_s4.bc2121.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2121.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-24/call-trgt_genotype/out/m84036_250809_035451_s4.bc2121.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2121.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-24/call-trgt_genotype/out/m84036_250809_035451_s4.bc2121.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2121.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-24/call-trgt_plot_meth_waterfall/_singularity_tmpdir_rt_bk8ec/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-24/call-trgt_plot_meth_waterfall/_singularity_tmpdir_rt_bk8ec/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:17.219 wdl.w:ptcp NOTICE finish :: job: "call-trgt-17"
2025-09-15 20:24:17.220 wdl.w:ptcp INFO output :: job: "call-trgt-17", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-17/out/m84036_250809_035451_s4.bc2114.motifs_waterfall.trgt_plots.zip", "images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-17/out/m84036_250809_035451_s4.bc2114.meth_allele.trgt_plots.zip", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-17/out/m84036_250809_035451_s4.bc2114.trgt.sorted.spanning.bam.bai", "images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-17/out/m84036_250809_035451_s4.bc2114.motifs_allele.trgt_plots.zip", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-17/out/m84036_250809_035451_s4.bc2114.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-17/out/m84036_250809_035451_s4.bc2114.trgt.vcf", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-17/out/m84036_250809_035451_s4.bc2114.repeats.bam", "images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-17/out/m84036_250809_035451_s4.bc2114.meth_waterfall.trgt_plots.zip", "reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-17/out/m84036_250809_035451_s4.bc2114.repeats.bam.bai"}
2025-09-15 20:24:17.227 wdl.w:ptcp.w:call-paraphase-40 NOTICE workflow start :: name: "paraphase", source: "./paraphase.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-40"
2025-09-15 20:24:17.236 wdl.w:ptcp.w:call-trgt-24.t:call-trgt_plot_meth_waterfall NOTICE slurm_singularity run :: pid: 1201354, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-24/call-trgt_plot_meth_waterfall/slurm_singularity.log.txt"
2025-09-15 20:24:17.245 wdl.w:ptcp.w:call-paraphase-40 INFO visit :: node: "decl-annotation_vcf", values: {"annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf"}
2025-09-15 20:24:17.245 wdl.w:ptcp.w:call-paraphase-40 INFO visit :: node: "decl-config_file", values: {"config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml"}
2025-09-15 20:24:17.245 wdl.w:ptcp.w:call-paraphase-40 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:24:17.245 wdl.w:ptcp.w:call-paraphase-40 INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:24:17.245 wdl.w:ptcp.w:call-paraphase-40 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-40/out/m84036_250809_035451_s4.bc2137.mapped.bam"}
2025-09-15 20:24:17.245 wdl.w:ptcp.w:call-paraphase-40 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-40/out/m84036_250809_035451_s4.bc2137.mapped.bam.bai"}
2025-09-15 20:24:17.245 wdl.w:ptcp.w:call-paraphase-40 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:24:17.245 wdl.w:ptcp.w:call-paraphase-40 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:24:17.245 wdl.w:ptcp.w:call-paraphase-40 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2137"}
2025-09-15 20:24:17.245 wdl.w:ptcp.w:call-paraphase-40 INFO visit :: node: "decl-sex", values: {"sex": "F"}
2025-09-15 20:24:17.246 wdl.w:ptcp.w:call-paraphase-40 NOTICE ready :: job: "call-run_paraphase", callee: "run_paraphase"
2025-09-15 20:24:17.246 wdl.w:ptcp.w:call-paraphase-40 INFO input :: job: "call-run_paraphase", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf", "genome_version": "38", "config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-40/out/m84036_250809_035451_s4.bc2137.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-40/out/m84036_250809_035451_s4.bc2137.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2137"}
2025-09-15 20:24:17.264 wdl.w:ptcp.w:call-trgt-24.t:call-trgt_plot_motifs_allele INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-24/call-trgt_plot_motifs_allele/_singularity_tmpdir_l9yp_0_c"
2025-09-15 20:24:17.265 wdl.w:ptcp.w:call-trgt-24.t:call-trgt_plot_motifs_allele INFO Slurm invocation: srun --job-name call-trgt_plot_motifs_allele --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-24/call-trgt_plot_motifs_allele/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-24/call-trgt_plot_motifs_allele/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-24/call-trgt_plot_motifs_allele/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-24/call-trgt_plot_motifs_allele/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-24/call-trgt_genotype/out/m84036_250809_035451_s4.bc2121.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2121.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-24/call-trgt_genotype/out/m84036_250809_035451_s4.bc2121.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2121.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-24/call-trgt_genotype/out/m84036_250809_035451_s4.bc2121.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2121.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-24/call-trgt_plot_motifs_allele/_singularity_tmpdir_l9yp_0_c/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-24/call-trgt_plot_motifs_allele/_singularity_tmpdir_l9yp_0_c/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:17.276 wdl.w:ptcp.w:call-trgt-24.t:call-trgt_plot_motifs_allele NOTICE slurm_singularity run :: pid: 1201356, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-24/call-trgt_plot_motifs_allele/slurm_singularity.log.txt"
2025-09-15 20:24:17.351 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:17 [ERROR] - No reads found for TRID=NIID_NOTCH2NLC
2025-09-15 20:24:17.357 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_meth_allele.slurm_singularity INFO srun: job 51797593 queued and waiting for resources
2025-09-15 20:24:17.357 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_meth_allele.slurm_singularity INFO srun: job 51797593 has been allocated resources
2025-09-15 20:24:17.357 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_meth_allele.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:17.439 wdl.w:ptcp.w:call-paraphase-17.t:call-call_f8 INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2114.f8inversion.vcf"
2025-09-15 20:24:17.444 wdl.w:ptcp.w:call-paraphase-17.t:call-call_f8 INFO output :: name: "json", value: "m84036_250809_035451_s4.bc2114.f8inversion.json"
2025-09-15 20:24:17.453 wdl.w:ptcp.w:call-trgt-28.t:call-trgt_plot_meth_allele INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2125.meth_allele.trgt_plots.zip"
2025-09-15 20:24:17.499 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_plot_motifs_waterfall INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2103.motifs_waterfall.trgt_plots.zip"
2025-09-15 20:24:17.522 wdl.w:ptcp.w:call-paraphase-17.t:call-call_f8 NOTICE done
2025-09-15 20:24:17.528 wdl.w:ptcp.w:call-paraphase-17 NOTICE finish :: job: "call-call_f8"
2025-09-15 20:24:17.528 wdl.w:ptcp.w:call-paraphase-17 INFO output :: job: "call-call_f8", values: {"json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-17/call-call_f8/out/m84036_250809_035451_s4.bc2114.f8inversion.json", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-17/call-call_f8/out/m84036_250809_035451_s4.bc2114.f8inversion.vcf"}
2025-09-15 20:24:17.528 wdl.w:ptcp.w:call-paraphase-17 INFO visit :: node: "output-f8_json", values: {"f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-17/call-call_f8/out/m84036_250809_035451_s4.bc2114.f8inversion.json"}
2025-09-15 20:24:17.528 wdl.w:ptcp.w:call-paraphase-17 INFO visit :: node: "output-f8_vcf", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-17/call-call_f8/out/m84036_250809_035451_s4.bc2114.f8inversion.vcf"}
2025-09-15 20:24:17.529 wdl.w:ptcp.w:call-paraphase-17 INFO visit :: node: "outputs", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-17/call-call_f8/out/m84036_250809_035451_s4.bc2114.f8inversion.vcf", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-17/call-run_paraphase/out/m84036_250809_035451_s4.bc2114_paraphase/m84036_250809_035451_s4.bc2114.paraphase.json", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-17/call-run_paraphase/out/m84036_250809_035451_s4.bc2114_paraphase/m84036_250809_035451_s4.bc2114.paraphase.bam", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-17/call-run_paraphase/out/m84036_250809_035451_s4.bc2114_paraphase/m84036_250809_035451_s4.bc2114.paraphase.bam.bai", "paraphase_vcfs": [], "havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-17/call-run_paraphase/out/m84036_250809_035451_s4.bc2114.havanno.json", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-17/call-call_f8/out/m84036_250809_035451_s4.bc2114.f8inversion.json"}
2025-09-15 20:24:17.534 wdl.w:ptcp.w:call-trgt-24.t:call-trgt_plot_motifs_waterfall NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-24/call-trgt_plot_motifs_waterfall", thread: 140607699809856
2025-09-15 20:24:17.555 wdl.w:ptcp.w:call-trgt-24.t:call-trgt_plot_motifs_waterfall INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:17.555 wdl.w:ptcp.w:call-trgt-24.t:call-trgt_plot_motifs_waterfall INFO input :: name: "waterfall", value: true
2025-09-15 20:24:17.555 wdl.w:ptcp.w:call-trgt-24.t:call-trgt_plot_motifs_waterfall INFO input :: name: "methylation", value: false
2025-09-15 20:24:17.556 wdl.w:ptcp.w:call-trgt-24.t:call-trgt_plot_motifs_waterfall INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:17.556 wdl.w:ptcp.w:call-trgt-24.t:call-trgt_plot_motifs_waterfall INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:17.556 wdl.w:ptcp.w:call-trgt-24.t:call-trgt_plot_motifs_waterfall INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:17.556 wdl.w:ptcp.w:call-trgt-24.t:call-trgt_plot_motifs_waterfall INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2121.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:17.556 wdl.w:ptcp.w:call-trgt-24.t:call-trgt_plot_motifs_waterfall INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2121.trgt.sorted.spanning.bam"
2025-09-15 20:24:17.556 wdl.w:ptcp.w:call-trgt-24.t:call-trgt_plot_motifs_waterfall INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2121.trgt.vcf"
2025-09-15 20:24:17.556 wdl.w:ptcp.w:call-trgt-24.t:call-trgt_plot_motifs_waterfall INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2121"
2025-09-15 20:24:17.556 wdl.w:ptcp.w:call-trgt-24.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:17.557 wdl.w:ptcp.w:call-trgt-24.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "plot_type", value: "waterfall"
2025-09-15 20:24:17.557 wdl.w:ptcp.w:call-trgt-24.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "show", value: "motifs"
2025-09-15 20:24:17.557 wdl.w:ptcp.w:call-trgt-24.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "threads", value: 1
2025-09-15 20:24:17.557 wdl.w:ptcp.w:call-trgt-24.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:17.557 wdl.w:ptcp.w:call-trgt-24.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2121.motifs_waterfall"
2025-09-15 20:24:17.558 wdl.w:ptcp.w:call-trgt-24.t:call-trgt_plot_motifs_waterfall INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:17.558 wdl.w:ptcp.w:call-trgt-24.t:call-trgt_plot_motifs_waterfall WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:17.560 wdl.w:ptcp.w:call-trgt-24.t:call-trgt_plot_motifs_waterfall INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:17.560 wdl.w:ptcp.w:call-trgt-24.t:call-trgt_plot_motifs_waterfall INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:17.602 wdl.w:ptcp.w:call-trgt-06.t:call-trgt_plot_motifs_waterfall NOTICE done
2025-09-15 20:24:17.604 wdl.w:ptcp.w:call-trgt-28.t:call-trgt_plot_meth_allele NOTICE done
2025-09-15 20:24:17.609 wdl.w:ptcp.w:call-trgt-06 NOTICE finish :: job: "call-trgt_plot_motifs_waterfall"
2025-09-15 20:24:17.609 wdl.w:ptcp.w:call-trgt-06 INFO output :: job: "call-trgt_plot_motifs_waterfall", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-06/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2103.motifs_waterfall.trgt_plots.zip"}
2025-09-15 20:24:17.609 wdl.w:ptcp.w:call-trgt-06 INFO visit :: node: "output-images_motifs_waterfall", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-06/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2103.motifs_waterfall.trgt_plots.zip"}
2025-09-15 20:24:17.609 wdl.w:ptcp.w:call-trgt-06 INFO visit :: node: "outputs", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-06/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2103.motifs_waterfall.trgt_plots.zip", "images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-06/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2103.meth_allele.trgt_plots.zip", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-06/call-trgt_genotype/out/m84036_250809_035451_s4.bc2103.trgt.sorted.spanning.bam.bai", "images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-06/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2103.motifs_allele.trgt_plots.zip", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-06/call-trgt_genotype/out/m84036_250809_035451_s4.bc2103.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-06/call-trgt_genotype/out/m84036_250809_035451_s4.bc2103.trgt.vcf", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-06/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2103.repeats.bam", "images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-06/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2103.meth_waterfall.trgt_plots.zip", "reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-06/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2103.repeats.bam.bai"}
2025-09-15 20:24:17.610 wdl.w:ptcp.w:call-trgt-28 NOTICE finish :: job: "call-trgt_plot_meth_allele"
2025-09-15 20:24:17.610 wdl.w:ptcp.w:call-trgt-28 INFO output :: job: "call-trgt_plot_meth_allele", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-28/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2125.meth_allele.trgt_plots.zip"}
2025-09-15 20:24:17.611 wdl.w:ptcp.w:call-trgt-28 INFO visit :: node: "output-images_meth_allele", values: {"images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-28/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2125.meth_allele.trgt_plots.zip"}
2025-09-15 20:24:17.615 wdl.w:ptcp.w:call-trgt-09.t:call-trgt_plot_meth_allele NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-09/call-trgt_plot_meth_allele", thread: 140608211502656
2025-09-15 20:24:17.617 wdl.w:ptcp.w:call-paraphase-17 NOTICE done
2025-09-15 20:24:17.619 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO srun: job 51797594 queued and waiting for resources
2025-09-15 20:24:17.619 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO srun: job 51797594 has been allocated resources
2025-09-15 20:24:17.619 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:17.620 wdl.w:ptcp.w:call-trgt-09.t:call-trgt_plot_meth_waterfall NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-09/call-trgt_plot_meth_waterfall", thread: 140608731588160
2025-09-15 20:24:17.623 wdl.w:ptcp NOTICE finish :: job: "call-paraphase-17"
2025-09-15 20:24:17.623 wdl.w:ptcp INFO output :: job: "call-paraphase-17", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-17/out/m84036_250809_035451_s4.bc2114.f8inversion.vcf", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-17/out/m84036_250809_035451_s4.bc2114_paraphase/m84036_250809_035451_s4.bc2114.paraphase.json", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-17/out/m84036_250809_035451_s4.bc2114_paraphase/m84036_250809_035451_s4.bc2114.paraphase.bam", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-17/out/m84036_250809_035451_s4.bc2114_paraphase/m84036_250809_035451_s4.bc2114.paraphase.bam.bai", "paraphase_vcfs": [], "havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-17/out/m84036_250809_035451_s4.bc2114.havanno.json", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-17/out/m84036_250809_035451_s4.bc2114.f8inversion.json"}
2025-09-15 20:24:17.629 wdl.w:ptcp.w:call-sawfish-40 NOTICE workflow start :: name: "sawfish", source: "./sawfish.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-40"
2025-09-15 20:24:17.641 wdl.w:ptcp.w:call-trgt-29.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:16 [ERROR] - No reads found for TRID=PRTS_ARX
2025-09-15 20:24:17.641 wdl.w:ptcp.w:call-trgt-29.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:16 [ERROR] - No reads found for TRID=EIEE1_ARX
2025-09-15 20:24:17.644 wdl.w:ptcp.w:call-trgt-09.t:call-trgt_plot_meth_allele INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:17.644 wdl.w:ptcp.w:call-trgt-09.t:call-trgt_plot_meth_waterfall INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:17.644 wdl.w:ptcp.w:call-trgt-09.t:call-trgt_plot_meth_allele INFO input :: name: "waterfall", value: false
2025-09-15 20:24:17.645 wdl.w:ptcp.w:call-trgt-09.t:call-trgt_plot_meth_waterfall INFO input :: name: "waterfall", value: true
2025-09-15 20:24:17.645 wdl.w:ptcp.w:call-trgt-09.t:call-trgt_plot_meth_allele INFO input :: name: "methylation", value: true
2025-09-15 20:24:17.645 wdl.w:ptcp.w:call-trgt-09.t:call-trgt_plot_meth_waterfall INFO input :: name: "methylation", value: true
2025-09-15 20:24:17.645 wdl.w:ptcp.w:call-trgt-09.t:call-trgt_plot_meth_allele INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:17.645 wdl.w:ptcp.w:call-trgt-09.t:call-trgt_plot_meth_waterfall INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:17.646 wdl.w:ptcp.w:call-trgt-09.t:call-trgt_plot_meth_allele INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:17.646 wdl.w:ptcp.w:call-trgt-09.t:call-trgt_plot_meth_waterfall INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:17.646 wdl.w:ptcp.w:call-trgt-09.t:call-trgt_plot_meth_allele INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:17.646 wdl.w:ptcp.w:call-trgt-09.t:call-trgt_plot_meth_waterfall INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:17.646 wdl.w:ptcp.w:call-sawfish-40 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:24:17.647 wdl.w:ptcp.w:call-trgt-09.t:call-trgt_plot_meth_allele INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2106.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:17.647 wdl.w:ptcp.w:call-trgt-09.t:call-trgt_plot_meth_waterfall INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2106.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:17.647 wdl.w:ptcp.w:call-sawfish-40 INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:24:17.647 wdl.w:ptcp.w:call-trgt-09.t:call-trgt_plot_meth_allele INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2106.trgt.sorted.spanning.bam"
2025-09-15 20:24:17.647 wdl.w:ptcp.w:call-trgt-09.t:call-trgt_plot_meth_waterfall INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2106.trgt.sorted.spanning.bam"
2025-09-15 20:24:17.647 wdl.w:ptcp.w:call-sawfish-40 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-40/out/m84036_250809_035451_s4.bc2137.mapped.bam"}
2025-09-15 20:24:17.647 wdl.w:ptcp.w:call-trgt-09.t:call-trgt_plot_meth_allele INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2106.trgt.vcf"
2025-09-15 20:24:17.647 wdl.w:ptcp.w:call-trgt-24.t:call-trgt_plot_motifs_waterfall INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-24/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_0bazzw3c"
2025-09-15 20:24:17.648 wdl.w:ptcp.w:call-trgt-09.t:call-trgt_plot_meth_waterfall INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2106.trgt.vcf"
2025-09-15 20:24:17.648 wdl.w:ptcp.w:call-sawfish-40 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-40/out/m84036_250809_035451_s4.bc2137.mapped.bam.bai"}
2025-09-15 20:24:17.648 wdl.w:ptcp.w:call-trgt-09.t:call-trgt_plot_meth_allele INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2106"
2025-09-15 20:24:17.648 wdl.w:ptcp.w:call-trgt-24.t:call-trgt_plot_motifs_waterfall INFO Slurm invocation: srun --job-name call-trgt_plot_motifs_waterfall --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-24/call-trgt_plot_motifs_waterfall/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-24/call-trgt_plot_motifs_waterfall/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-24/call-trgt_plot_motifs_waterfall/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-24/call-trgt_plot_motifs_waterfall/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-24/call-trgt_genotype/out/m84036_250809_035451_s4.bc2121.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2121.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-24/call-trgt_genotype/out/m84036_250809_035451_s4.bc2121.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2121.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-24/call-trgt_genotype/out/m84036_250809_035451_s4.bc2121.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2121.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-24/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_0bazzw3c/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-24/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_0bazzw3c/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:17.648 wdl.w:ptcp.w:call-trgt-09.t:call-trgt_plot_meth_waterfall INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2106"
2025-09-15 20:24:17.648 wdl.w:ptcp.w:call-sawfish-40 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:24:17.649 wdl.w:ptcp.w:call-trgt-09.t:call-trgt_plot_meth_allele INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:17.649 wdl.w:ptcp.w:call-trgt-09.t:call-trgt_plot_meth_waterfall INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:17.650 wdl.w:ptcp.w:call-sawfish-40 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:24:17.650 wdl.w:ptcp.w:call-trgt-09.t:call-trgt_plot_meth_allele INFO eval :: name: "plot_type", value: "allele"
2025-09-15 20:24:17.651 wdl.w:ptcp.w:call-trgt-09.t:call-trgt_plot_meth_waterfall INFO eval :: name: "plot_type", value: "waterfall"
2025-09-15 20:24:17.651 wdl.w:ptcp.w:call-sawfish-40 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2137"}
2025-09-15 20:24:17.651 wdl.w:ptcp.w:call-trgt-09.t:call-trgt_plot_meth_allele INFO eval :: name: "show", value: "meth"
2025-09-15 20:24:17.651 wdl.w:ptcp.w:call-trgt-09.t:call-trgt_plot_meth_waterfall INFO eval :: name: "show", value: "meth"
2025-09-15 20:24:17.652 wdl.w:ptcp.w:call-sawfish-40 NOTICE ready :: job: "call-run_sawfish", callee: "run_sawfish"
2025-09-15 20:24:17.652 wdl.w:ptcp.w:call-trgt-09.t:call-trgt_plot_meth_allele INFO eval :: name: "threads", value: 1
2025-09-15 20:24:17.652 wdl.w:ptcp.w:call-trgt-09.t:call-trgt_plot_meth_waterfall INFO eval :: name: "threads", value: 1
2025-09-15 20:24:17.652 wdl.w:ptcp.w:call-sawfish-40 INFO input :: job: "call-run_sawfish", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-40/out/m84036_250809_035451_s4.bc2137.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-40/out/m84036_250809_035451_s4.bc2137.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2137"}
2025-09-15 20:24:17.652 wdl.w:ptcp.w:call-trgt-09.t:call-trgt_plot_meth_allele INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:17.653 wdl.w:ptcp.w:call-trgt-09.t:call-trgt_plot_meth_allele INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2106.meth_allele"
2025-09-15 20:24:17.653 wdl.w:ptcp.w:call-trgt-09.t:call-trgt_plot_meth_waterfall INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:17.654 wdl.w:ptcp.w:call-trgt-09.t:call-trgt_plot_meth_waterfall INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2106.meth_waterfall"
2025-09-15 20:24:17.654 wdl.w:ptcp.w:call-trgt-09.t:call-trgt_plot_meth_waterfall INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:17.654 wdl.w:ptcp.w:call-trgt-09.t:call-trgt_plot_meth_waterfall WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:17.655 wdl.w:ptcp.w:call-trgt-09.t:call-trgt_plot_meth_waterfall INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:17.655 wdl.w:ptcp.w:call-trgt-09.t:call-trgt_plot_meth_waterfall INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:17.654 wdl.w:ptcp.w:call-trgt-09.t:call-trgt_plot_meth_allele INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:17.655 wdl.w:ptcp.w:call-trgt-09.t:call-trgt_plot_meth_allele WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:17.656 wdl.w:ptcp.w:call-trgt-09.t:call-trgt_plot_meth_allele INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:17.656 wdl.w:ptcp.w:call-trgt-09.t:call-trgt_plot_meth_allele INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:17.675 wdl.w:ptcp.w:call-trgt-24.t:call-trgt_plot_motifs_waterfall NOTICE slurm_singularity run :: pid: 1201376, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-24/call-trgt_plot_motifs_waterfall/slurm_singularity.log.txt"
2025-09-15 20:24:17.719 wdl.w:ptcp.w:call-trgt-06 NOTICE done
2025-09-15 20:24:17.723 wdl.w:ptcp NOTICE finish :: job: "call-trgt-06"
2025-09-15 20:24:17.723 wdl.w:ptcp INFO output :: job: "call-trgt-06", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-06/out/m84036_250809_035451_s4.bc2103.motifs_waterfall.trgt_plots.zip", "images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-06/out/m84036_250809_035451_s4.bc2103.meth_allele.trgt_plots.zip", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-06/out/m84036_250809_035451_s4.bc2103.trgt.sorted.spanning.bam.bai", "images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-06/out/m84036_250809_035451_s4.bc2103.motifs_allele.trgt_plots.zip", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-06/out/m84036_250809_035451_s4.bc2103.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-06/out/m84036_250809_035451_s4.bc2103.trgt.vcf", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-06/out/m84036_250809_035451_s4.bc2103.repeats.bam", "images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-06/out/m84036_250809_035451_s4.bc2103.meth_waterfall.trgt_plots.zip", "reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-06/out/m84036_250809_035451_s4.bc2103.repeats.bam.bai"}
2025-09-15 20:24:17.728 wdl.w:ptcp.w:call-trgt-40 NOTICE workflow start :: name: "trgt", source: "./trgt.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-40"
2025-09-15 20:24:17.734 wdl.w:ptcp.w:call-trgt-09.t:call-trgt_plot_meth_allele INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-09/call-trgt_plot_meth_allele/_singularity_tmpdir_ec798mpr"
2025-09-15 20:24:17.735 wdl.w:ptcp.w:call-trgt-09.t:call-trgt_plot_meth_allele INFO Slurm invocation: srun --job-name call-trgt_plot_meth_allele --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-09/call-trgt_plot_meth_allele/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-09/call-trgt_plot_meth_allele/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-09/call-trgt_plot_meth_allele/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-09/call-trgt_plot_meth_allele/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-09/call-trgt_genotype/out/m84036_250809_035451_s4.bc2106.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2106.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-09/call-trgt_genotype/out/m84036_250809_035451_s4.bc2106.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2106.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-09/call-trgt_genotype/out/m84036_250809_035451_s4.bc2106.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2106.trgt.vcf:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-09/call-trgt_plot_meth_allele/_singularity_tmpdir_ec798mpr/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-09/call-trgt_plot_meth_allele/_singularity_tmpdir_ec798mpr/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:17.736 wdl.w:ptcp.w:call-trgt-09.t:call-trgt_plot_meth_waterfall INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-09/call-trgt_plot_meth_waterfall/_singularity_tmpdir_i6vq2ulu"
2025-09-15 20:24:17.736 wdl.w:ptcp.w:call-trgt-09.t:call-trgt_plot_meth_waterfall INFO Slurm invocation: srun --job-name call-trgt_plot_meth_waterfall --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-09/call-trgt_plot_meth_waterfall/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-09/call-trgt_plot_meth_waterfall/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-09/call-trgt_plot_meth_waterfall/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-09/call-trgt_plot_meth_waterfall/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-09/call-trgt_genotype/out/m84036_250809_035451_s4.bc2106.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2106.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-09/call-trgt_genotype/out/m84036_250809_035451_s4.bc2106.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2106.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-09/call-trgt_genotype/out/m84036_250809_035451_s4.bc2106.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2106.trgt.vcf:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-09/call-trgt_plot_meth_waterfall/_singularity_tmpdir_i6vq2ulu/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-09/call-trgt_plot_meth_waterfall/_singularity_tmpdir_i6vq2ulu/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:17.744 wdl.w:ptcp.w:call-trgt-40 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:24:17.744 wdl.w:ptcp.w:call-trgt-40 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-40/out/m84036_250809_035451_s4.bc2137.mapped.bam"}
2025-09-15 20:24:17.744 wdl.w:ptcp.w:call-trgt-40 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-40/out/m84036_250809_035451_s4.bc2137.mapped.bam.bai"}
2025-09-15 20:24:17.744 wdl.w:ptcp.w:call-trgt-40 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:24:17.745 wdl.w:ptcp.w:call-trgt-40 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:24:17.745 wdl.w:ptcp.w:call-trgt-40 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2137"}
2025-09-15 20:24:17.745 wdl.w:ptcp.w:call-trgt-40 INFO visit :: node: "decl-sex", values: {"sex": "F"}
2025-09-15 20:24:17.745 wdl.w:ptcp.w:call-trgt-40 INFO visit :: node: "decl-trgt_bed", values: {"trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"}
2025-09-15 20:24:17.745 wdl.w:ptcp.w:call-trgt-40 NOTICE ready :: job: "call-get_reads_overlapping_repeats", callee: "get_reads_overlapping_repeats"
2025-09-15 20:24:17.745 wdl.w:ptcp.w:call-trgt-09.t:call-trgt_plot_meth_waterfall NOTICE slurm_singularity run :: pid: 1201384, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-09/call-trgt_plot_meth_waterfall/slurm_singularity.log.txt"
2025-09-15 20:24:17.745 wdl.w:ptcp.w:call-trgt-09.t:call-trgt_plot_meth_allele NOTICE slurm_singularity run :: pid: 1201383, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-09/call-trgt_plot_meth_allele/slurm_singularity.log.txt"
2025-09-15 20:24:17.745 wdl.w:ptcp.w:call-trgt-40 INFO input :: job: "call-get_reads_overlapping_repeats", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-40/out/m84036_250809_035451_s4.bc2137.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-40/out/m84036_250809_035451_s4.bc2137.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2137"}
2025-09-15 20:24:17.746 wdl.w:ptcp.w:call-trgt-40 NOTICE ready :: job: "call-trgt_genotype", callee: "trgt_genotype"
2025-09-15 20:24:17.747 wdl.w:ptcp.w:call-trgt-40 INFO input :: job: "call-trgt_genotype", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-40/out/m84036_250809_035451_s4.bc2137.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-40/out/m84036_250809_035451_s4.bc2137.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2137"}
2025-09-15 20:24:17.785 wdl.w:ptcp.w:call-trgt-29.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:17 [ERROR] - No reads found for TRID=PRTS_ARX
2025-09-15 20:24:17.786 wdl.w:ptcp.w:call-trgt-29.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:17 [ERROR] - No reads found for TRID=EIEE1_ARX
2025-09-15 20:24:17.886 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:17 [ERROR] - No reads found for TRID=NIID_NOTCH2NLC
2025-09-15 20:24:17.886 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:17 [ERROR] - No reads found for TRID=SCA37_DAB1
2025-09-15 20:24:17.886 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:17 [ERROR] - No reads found for TRID=OPDM4_RILPL1
2025-09-15 20:24:17.887 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:17 [ERROR] - No reads found for TRID=OPDM_ABCD3
2025-09-15 20:24:17.887 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:17 [ERROR] - No reads found for TRID=SCA8_ATXN8OS
2025-09-15 20:24:17.887 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:17 [ERROR] - No reads found for TRID=SCA27B_FGF14
2025-09-15 20:24:17.887 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:17 [ERROR] - No reads found for TRID=OPMD_PABPN1
2025-09-15 20:24:17.887 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:17 [ERROR] - No reads found for TRID=SCA2_ATXN2
2025-09-15 20:24:17.887 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:17 [ERROR] - No reads found for TRID=NIID_NOTCH2NLC
2025-09-15 20:24:17.888 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:17 [ERROR] - No reads found for TRID=SCA37_DAB1
2025-09-15 20:24:17.888 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:17 [ERROR] - No reads found for TRID=OPDM4_RILPL1
2025-09-15 20:24:17.888 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:17 [ERROR] - No reads found for TRID=OPDM_ABCD3
2025-09-15 20:24:17.898 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_motifs_allele.slurm_singularity INFO srun: job 51797596 queued and waiting for resources
2025-09-15 20:24:17.898 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_motifs_allele.slurm_singularity INFO srun: job 51797596 has been allocated resources
2025-09-15 20:24:17.898 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_motifs_allele.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:17.900 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO srun: job 51797595 queued and waiting for resources
2025-09-15 20:24:17.901 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO srun: job 51797595 has been allocated resources
2025-09-15 20:24:17.901 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:17.953 wdl.w:ptcp.w:call-paraphase-28.t:call-call_f8.slurm_singularity INFO srun: job 51797597 queued and waiting for resources
2025-09-15 20:24:17.954 wdl.w:ptcp.w:call-paraphase-28.t:call-call_f8.slurm_singularity INFO srun: job 51797597 has been allocated resources
2025-09-15 20:24:17.954 wdl.w:ptcp.w:call-paraphase-28.t:call-call_f8.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:17.967 wdl.w:ptcp.w:call-trgt-24.t:call-trgt_plot_meth_allele.slurm_singularity INFO srun: job 51797598 queued and waiting for resources
2025-09-15 20:24:17.967 wdl.w:ptcp.w:call-trgt-24.t:call-trgt_plot_meth_allele.slurm_singularity INFO srun: job 51797598 has been allocated resources
2025-09-15 20:24:17.968 wdl.w:ptcp.w:call-trgt-24.t:call-trgt_plot_meth_allele.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:18.235 wdl.w:ptcp.w:call-paraphase-28.t:call-call_f8 INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2125.f8inversion.vcf"
2025-09-15 20:24:18.239 wdl.w:ptcp.w:call-trgt-28.t:call-trgt_plot_meth_waterfall INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2125.meth_waterfall.trgt_plots.zip"
2025-09-15 20:24:18.242 wdl.w:ptcp.w:call-paraphase-28.t:call-call_f8 INFO output :: name: "json", value: "m84036_250809_035451_s4.bc2125.f8inversion.json"
2025-09-15 20:24:18.254 wdl.w:ptcp.w:call-trgt-24.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO srun: job 51797599 queued and waiting for resources
2025-09-15 20:24:18.255 wdl.w:ptcp.w:call-trgt-24.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO srun: job 51797599 has been allocated resources
2025-09-15 20:24:18.255 wdl.w:ptcp.w:call-trgt-24.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:18.296 wdl.w:ptcp.w:call-trgt-24.t:call-trgt_plot_motifs_allele.slurm_singularity INFO srun: job 51797600 queued and waiting for resources
2025-09-15 20:24:18.297 wdl.w:ptcp.w:call-trgt-24.t:call-trgt_plot_motifs_allele.slurm_singularity INFO srun: job 51797600 has been allocated resources
2025-09-15 20:24:18.297 wdl.w:ptcp.w:call-trgt-24.t:call-trgt_plot_motifs_allele.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:18.318 wdl.w:ptcp.t:call-pbmm2_align_hifi-94 INFO output :: name: "mapped_bam", value: "m84036_250809_035451_s4.bc2191.mapped.bam"
2025-09-15 20:24:18.321 wdl.w:ptcp.t:call-pbmm2_align_hifi-94 INFO output :: name: "mapped_bam_bai", value: "m84036_250809_035451_s4.bc2191.mapped.bam.bai"
2025-09-15 20:24:18.323 wdl.w:ptcp.t:call-pbmm2_align_hifi-94 INFO output :: name: "mapped_bam_pbi", value: "m84036_250809_035451_s4.bc2191.mapped.bam.pbi"
2025-09-15 20:24:18.324 wdl.w:ptcp.t:call-pbmm2_align_hifi-94 INFO output :: name: "report", value: "mapping_stats.report.json"
2025-09-15 20:24:18.343 wdl.w:ptcp.w:call-paraphase-28.t:call-call_f8 NOTICE done
2025-09-15 20:24:18.352 wdl.w:ptcp.w:call-paraphase-28 NOTICE finish :: job: "call-call_f8"
2025-09-15 20:24:18.353 wdl.w:ptcp.w:call-paraphase-28 INFO output :: job: "call-call_f8", values: {"json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-28/call-call_f8/out/m84036_250809_035451_s4.bc2125.f8inversion.json", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-28/call-call_f8/out/m84036_250809_035451_s4.bc2125.f8inversion.vcf"}
2025-09-15 20:24:18.353 wdl.w:ptcp.w:call-paraphase-28 INFO visit :: node: "output-f8_json", values: {"f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-28/call-call_f8/out/m84036_250809_035451_s4.bc2125.f8inversion.json"}
2025-09-15 20:24:18.353 wdl.w:ptcp.w:call-paraphase-28 INFO visit :: node: "output-f8_vcf", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-28/call-call_f8/out/m84036_250809_035451_s4.bc2125.f8inversion.vcf"}
2025-09-15 20:24:18.354 wdl.w:ptcp.w:call-paraphase-28 INFO visit :: node: "outputs", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-28/call-call_f8/out/m84036_250809_035451_s4.bc2125.f8inversion.vcf", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-28/call-run_paraphase/out/m84036_250809_035451_s4.bc2125_paraphase/m84036_250809_035451_s4.bc2125.paraphase.json", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-28/call-run_paraphase/out/m84036_250809_035451_s4.bc2125_paraphase/m84036_250809_035451_s4.bc2125.paraphase.bam", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-28/call-run_paraphase/out/m84036_250809_035451_s4.bc2125_paraphase/m84036_250809_035451_s4.bc2125.paraphase.bam.bai", "paraphase_vcfs": [], "havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-28/call-run_paraphase/out/m84036_250809_035451_s4.bc2125.havanno.json", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-28/call-call_f8/out/m84036_250809_035451_s4.bc2125.f8inversion.json"}
2025-09-15 20:24:18.362 wdl.w:ptcp.w:call-trgt-09.t:call-trgt_plot_motifs_allele NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-09/call-trgt_plot_motifs_allele", thread: 140608186324544
2025-09-15 20:24:18.372 wdl.w:ptcp.w:call-paraphase-30.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for f8inv1 for sample m84036_250809_035451_s4.bc2127 at 2025-09-15 20:23:58.671404...
2025-09-15 20:24:18.374 wdl.w:ptcp.w:call-paraphase-30.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for f8inv1 for sample m84036_250809_035451_s4.bc2127 at 2025-09-15 20:24:02.210834...
2025-09-15 20:24:18.374 wdl.w:ptcp.w:call-paraphase-30.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for f8inv1 for sample m84036_250809_035451_s4.bc2127 at 2025-09-15 20:24:02.638071...
2025-09-15 20:24:18.374 wdl.w:ptcp.w:call-paraphase-30.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for cyp21 for sample m84036_250809_035451_s4.bc2127 at 2025-09-15 20:24:07.141441...
2025-09-15 20:24:18.374 wdl.w:ptcp.w:call-paraphase-30.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for cyp21 for sample m84036_250809_035451_s4.bc2127 at 2025-09-15 20:24:07.803048...
2025-09-15 20:24:18.375 wdl.w:ptcp.w:call-paraphase-30.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for hba for sample m84036_250809_035451_s4.bc2127 at 2025-09-15 20:24:12.167693...
2025-09-15 20:24:18.375 wdl.w:ptcp.w:call-paraphase-30.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for hba for sample m84036_250809_035451_s4.bc2127 at 2025-09-15 20:24:12.538040...
2025-09-15 20:24:18.381 wdl.w:ptcp.w:call-trgt-09.t:call-trgt_plot_motifs_allele INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:18.381 wdl.w:ptcp.w:call-trgt-09.t:call-trgt_plot_motifs_allele INFO input :: name: "waterfall", value: false
2025-09-15 20:24:18.381 wdl.w:ptcp.w:call-trgt-09.t:call-trgt_plot_motifs_allele INFO input :: name: "methylation", value: false
2025-09-15 20:24:18.381 wdl.w:ptcp.w:call-trgt-09.t:call-trgt_plot_motifs_allele INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:18.382 wdl.w:ptcp.w:call-trgt-09.t:call-trgt_plot_motifs_allele INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:18.382 wdl.w:ptcp.w:call-trgt-09.t:call-trgt_plot_motifs_allele INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:18.382 wdl.w:ptcp.w:call-trgt-09.t:call-trgt_plot_motifs_allele INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2106.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:18.382 wdl.w:ptcp.w:call-trgt-09.t:call-trgt_plot_motifs_allele INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2106.trgt.sorted.spanning.bam"
2025-09-15 20:24:18.382 wdl.w:ptcp.w:call-trgt-09.t:call-trgt_plot_motifs_allele INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2106.trgt.vcf"
2025-09-15 20:24:18.382 wdl.w:ptcp.w:call-trgt-09.t:call-trgt_plot_motifs_allele INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2106"
2025-09-15 20:24:18.382 wdl.w:ptcp.w:call-trgt-09.t:call-trgt_plot_motifs_allele INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:18.382 wdl.w:ptcp.w:call-trgt-09.t:call-trgt_plot_motifs_allele INFO eval :: name: "plot_type", value: "allele"
2025-09-15 20:24:18.382 wdl.w:ptcp.w:call-trgt-09.t:call-trgt_plot_motifs_allele INFO eval :: name: "show", value: "motifs"
2025-09-15 20:24:18.383 wdl.w:ptcp.w:call-trgt-09.t:call-trgt_plot_motifs_allele INFO eval :: name: "threads", value: 1
2025-09-15 20:24:18.383 wdl.w:ptcp.w:call-trgt-09.t:call-trgt_plot_motifs_allele INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:18.383 wdl.w:ptcp.w:call-trgt-09.t:call-trgt_plot_motifs_allele INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2106.motifs_allele"
2025-09-15 20:24:18.383 wdl.w:ptcp.w:call-trgt-09.t:call-trgt_plot_motifs_allele INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:18.383 wdl.w:ptcp.w:call-trgt-09.t:call-trgt_plot_motifs_allele WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:18.384 wdl.w:ptcp.w:call-trgt-09.t:call-trgt_plot_motifs_allele INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:18.384 wdl.w:ptcp.w:call-trgt-09.t:call-trgt_plot_motifs_allele INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:18.418 wdl.w:ptcp.w:call-trgt-28.t:call-trgt_plot_meth_waterfall NOTICE done
2025-09-15 20:24:18.417 wdl.w:ptcp.w:call-sawfish-21.t:call-run_sawfish.stderr VERBOSE [M::mm_idx_gen::35.657*1.43] collected minimizers
2025-09-15 20:24:18.419 wdl.w:ptcp.w:call-paraphase-14.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for gba for sample m84036_250809_035451_s4.bc2111 at 2025-09-15 20:24:06.223464...
2025-09-15 20:24:18.419 wdl.w:ptcp.w:call-paraphase-14.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for gba for sample m84036_250809_035451_s4.bc2111 at 2025-09-15 20:24:06.659266...
2025-09-15 20:24:18.419 wdl.w:ptcp.w:call-paraphase-14.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for hbb for sample m84036_250809_035451_s4.bc2111 at 2025-09-15 20:24:11.907615...
2025-09-15 20:24:18.419 wdl.w:ptcp.w:call-paraphase-14.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for hbb for sample m84036_250809_035451_s4.bc2111 at 2025-09-15 20:24:11.907994...
2025-09-15 20:24:18.424 wdl.w:ptcp.w:call-trgt-28 NOTICE finish :: job: "call-trgt_plot_meth_waterfall"
2025-09-15 20:24:18.424 wdl.w:ptcp.w:call-trgt-28 INFO output :: job: "call-trgt_plot_meth_waterfall", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-28/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2125.meth_waterfall.trgt_plots.zip"}
2025-09-15 20:24:18.424 wdl.w:ptcp.w:call-trgt-28 INFO visit :: node: "output-images_meth_waterfall", values: {"images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-28/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2125.meth_waterfall.trgt_plots.zip"}
2025-09-15 20:24:18.425 wdl.w:ptcp.w:call-trgt-28 INFO visit :: node: "outputs", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-28/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2125.motifs_waterfall.trgt_plots.zip", "images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-28/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2125.meth_allele.trgt_plots.zip", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-28/call-trgt_genotype/out/m84036_250809_035451_s4.bc2125.trgt.sorted.spanning.bam.bai", "images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-28/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2125.motifs_allele.trgt_plots.zip", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-28/call-trgt_genotype/out/m84036_250809_035451_s4.bc2125.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-28/call-trgt_genotype/out/m84036_250809_035451_s4.bc2125.trgt.vcf", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-28/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2125.repeats.bam", "images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-28/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2125.meth_waterfall.trgt_plots.zip", "reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-28/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2125.repeats.bam.bai"}
2025-09-15 20:24:18.440 wdl.w:ptcp.w:call-trgt-09.t:call-trgt_plot_motifs_waterfall NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-09/call-trgt_plot_motifs_waterfall", thread: 140609822115392
2025-09-15 20:24:18.445 wdl.w:ptcp.w:call-paraphase-28 NOTICE done
2025-09-15 20:24:18.459 wdl.w:ptcp.t:call-pbmm2_align_hifi-94 NOTICE done
2025-09-15 20:24:18.463 wdl.w:ptcp.w:call-paraphase-07.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for smn1 for sample m84036_250809_035451_s4.bc2104 at 2025-09-15 20:23:31.467545...
2025-09-15 20:24:18.465 wdl.w:ptcp.w:call-paraphase-07.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for f8inv1 for sample m84036_250809_035451_s4.bc2104 at 2025-09-15 20:24:02.202273...
2025-09-15 20:24:18.465 wdl.w:ptcp.w:call-paraphase-07.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for f8inv1 for sample m84036_250809_035451_s4.bc2104 at 2025-09-15 20:24:02.203103...
2025-09-15 20:24:18.467 wdl.w:ptcp NOTICE finish :: job: "call-paraphase-28"
2025-09-15 20:24:18.467 wdl.w:ptcp INFO output :: job: "call-paraphase-28", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-28/out/m84036_250809_035451_s4.bc2125.f8inversion.vcf", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-28/out/m84036_250809_035451_s4.bc2125_paraphase/m84036_250809_035451_s4.bc2125.paraphase.json", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-28/out/m84036_250809_035451_s4.bc2125_paraphase/m84036_250809_035451_s4.bc2125.paraphase.bam", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-28/out/m84036_250809_035451_s4.bc2125_paraphase/m84036_250809_035451_s4.bc2125.paraphase.bam.bai", "paraphase_vcfs": [], "havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-28/out/m84036_250809_035451_s4.bc2125.havanno.json", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-28/out/m84036_250809_035451_s4.bc2125.f8inversion.json"}
2025-09-15 20:24:18.467 wdl.w:ptcp.w:call-trgt-09.t:call-trgt_plot_motifs_waterfall INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:18.468 wdl.w:ptcp.w:call-trgt-09.t:call-trgt_plot_motifs_waterfall INFO input :: name: "waterfall", value: true
2025-09-15 20:24:18.468 wdl.w:ptcp NOTICE finish :: job: "call-pbmm2_align_hifi-94"
2025-09-15 20:24:18.468 wdl.w:ptcp.w:call-trgt-09.t:call-trgt_plot_motifs_waterfall INFO input :: name: "methylation", value: false
2025-09-15 20:24:18.468 wdl.w:ptcp INFO output :: job: "call-pbmm2_align_hifi-94", values: {"report": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-94/out/mapping_stats.report.json", "mapped_bam_pbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-94/out/m84036_250809_035451_s4.bc2191.mapped.bam.pbi", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-94/out/m84036_250809_035451_s4.bc2191.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-94/out/m84036_250809_035451_s4.bc2191.mapped.bam"}
2025-09-15 20:24:18.468 wdl.w:ptcp.w:call-trgt-09.t:call-trgt_plot_motifs_waterfall INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:18.469 wdl.w:ptcp NOTICE ready :: job: "call-paraphase-94", callee: "paraphase"
2025-09-15 20:24:18.469 wdl.w:ptcp.w:call-trgt-09.t:call-trgt_plot_motifs_waterfall INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:18.469 wdl.w:ptcp INFO input :: job: "call-paraphase-94", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf", "genome_version": "38", "config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-94/out/m84036_250809_035451_s4.bc2191.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-94/out/m84036_250809_035451_s4.bc2191.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2191"}
2025-09-15 20:24:18.469 wdl.w:ptcp.w:call-trgt-09.t:call-trgt_plot_motifs_waterfall INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:18.469 wdl.w:ptcp.w:call-trgt-09.t:call-trgt_plot_motifs_waterfall INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2106.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:18.469 wdl.w:ptcp.w:call-trgt-09.t:call-trgt_plot_motifs_waterfall INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2106.trgt.sorted.spanning.bam"
2025-09-15 20:24:18.469 wdl.w:ptcp.w:call-trgt-09.t:call-trgt_plot_motifs_waterfall INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2106.trgt.vcf"
2025-09-15 20:24:18.470 wdl.w:ptcp.w:call-trgt-09.t:call-trgt_plot_motifs_waterfall INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2106"
2025-09-15 20:24:18.470 wdl.w:ptcp.w:call-trgt-09.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:18.470 wdl.w:ptcp.w:call-trgt-09.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "plot_type", value: "waterfall"
2025-09-15 20:24:18.470 wdl.w:ptcp.w:call-trgt-09.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "show", value: "motifs"
2025-09-15 20:24:18.470 wdl.w:ptcp.w:call-trgt-09.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "threads", value: 1
2025-09-15 20:24:18.471 wdl.w:ptcp.w:call-trgt-09.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:18.471 wdl.w:ptcp.w:call-trgt-09.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2106.motifs_waterfall"
2025-09-15 20:24:18.472 wdl.w:ptcp NOTICE ready :: job: "call-sawfish-94", callee: "sawfish"
2025-09-15 20:24:18.472 wdl.w:ptcp INFO input :: job: "call-sawfish-94", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-94/out/m84036_250809_035451_s4.bc2191.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-94/out/m84036_250809_035451_s4.bc2191.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2191"}
2025-09-15 20:24:18.472 wdl.w:ptcp.w:call-trgt-09.t:call-trgt_plot_motifs_waterfall INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:18.472 wdl.w:ptcp.w:call-trgt-09.t:call-trgt_plot_motifs_waterfall WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:18.472 wdl.w:ptcp.w:call-trgt-09.t:call-trgt_plot_motifs_waterfall INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:18.473 wdl.w:ptcp.w:call-trgt-09.t:call-trgt_plot_motifs_waterfall INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:18.473 wdl.w:ptcp NOTICE ready :: job: "call-trgt-94", callee: "trgt"
2025-09-15 20:24:18.473 wdl.w:ptcp INFO input :: job: "call-trgt-94", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-94/out/m84036_250809_035451_s4.bc2191.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-94/out/m84036_250809_035451_s4.bc2191.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2191"}
2025-09-15 20:24:18.477 wdl.w:ptcp.w:call-trgt-16.t:call-trgt_plot_meth_allele NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-16/call-trgt_plot_meth_allele", thread: 140606617675328
2025-09-15 20:24:18.479 wdl.w:ptcp.w:call-paraphase-62 NOTICE workflow start :: name: "paraphase", source: "./paraphase.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-62"
2025-09-15 20:24:18.498 wdl.w:ptcp.w:call-paraphase-62 INFO visit :: node: "decl-annotation_vcf", values: {"annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf"}
2025-09-15 20:24:18.498 wdl.w:ptcp.w:call-paraphase-62 INFO visit :: node: "decl-config_file", values: {"config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml"}
2025-09-15 20:24:18.499 wdl.w:ptcp.w:call-paraphase-62 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:24:18.499 wdl.w:ptcp.w:call-paraphase-62 INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:24:18.499 wdl.w:ptcp.w:call-paraphase-62 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-62/out/m84036_250809_035451_s4.bc2159.mapped.bam"}
2025-09-15 20:24:18.499 wdl.w:ptcp.w:call-paraphase-62 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-62/out/m84036_250809_035451_s4.bc2159.mapped.bam.bai"}
2025-09-15 20:24:18.499 wdl.w:ptcp.w:call-paraphase-62 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:24:18.499 wdl.w:ptcp.w:call-paraphase-62 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:24:18.499 wdl.w:ptcp.w:call-paraphase-62 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2159"}
2025-09-15 20:24:18.499 wdl.w:ptcp.w:call-paraphase-62 INFO visit :: node: "decl-sex", values: {"sex": "F"}
2025-09-15 20:24:18.500 wdl.w:ptcp.w:call-paraphase-62 NOTICE ready :: job: "call-run_paraphase", callee: "run_paraphase"
2025-09-15 20:24:18.500 wdl.w:ptcp.w:call-paraphase-62 INFO input :: job: "call-run_paraphase", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf", "genome_version": "38", "config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-62/out/m84036_250809_035451_s4.bc2159.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-62/out/m84036_250809_035451_s4.bc2159.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2159"}
2025-09-15 20:24:18.507 wdl.w:ptcp.w:call-trgt-09.t:call-trgt_plot_motifs_allele INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-09/call-trgt_plot_motifs_allele/_singularity_tmpdir_e5ehzk0j"
2025-09-15 20:24:18.507 wdl.w:ptcp.w:call-trgt-09.t:call-trgt_plot_motifs_allele INFO Slurm invocation: srun --job-name call-trgt_plot_motifs_allele --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-09/call-trgt_plot_motifs_allele/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-09/call-trgt_plot_motifs_allele/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-09/call-trgt_plot_motifs_allele/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-09/call-trgt_plot_motifs_allele/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-09/call-trgt_genotype/out/m84036_250809_035451_s4.bc2106.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2106.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-09/call-trgt_genotype/out/m84036_250809_035451_s4.bc2106.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2106.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-09/call-trgt_genotype/out/m84036_250809_035451_s4.bc2106.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2106.trgt.vcf:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-09/call-trgt_plot_motifs_allele/_singularity_tmpdir_e5ehzk0j/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-09/call-trgt_plot_motifs_allele/_singularity_tmpdir_e5ehzk0j/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:18.511 wdl.w:ptcp.w:call-trgt-16.t:call-trgt_plot_meth_allele INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:18.511 wdl.w:ptcp.w:call-trgt-16.t:call-trgt_plot_meth_allele INFO input :: name: "waterfall", value: false
2025-09-15 20:24:18.511 wdl.w:ptcp.w:call-trgt-16.t:call-trgt_plot_meth_allele INFO input :: name: "methylation", value: true
2025-09-15 20:24:18.511 wdl.w:ptcp.w:call-trgt-16.t:call-trgt_plot_meth_allele INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:18.511 wdl.w:ptcp.w:call-trgt-16.t:call-trgt_plot_meth_allele INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:18.511 wdl.w:ptcp.w:call-trgt-16.t:call-trgt_plot_meth_allele INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:18.512 wdl.w:ptcp.w:call-trgt-16.t:call-trgt_plot_meth_allele INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2113.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:18.512 wdl.w:ptcp.w:call-trgt-16.t:call-trgt_plot_meth_allele INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2113.trgt.sorted.spanning.bam"
2025-09-15 20:24:18.512 wdl.w:ptcp.w:call-trgt-16.t:call-trgt_plot_meth_allele INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2113.trgt.vcf"
2025-09-15 20:24:18.512 wdl.w:ptcp.w:call-trgt-16.t:call-trgt_plot_meth_allele INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2113"
2025-09-15 20:24:18.513 wdl.w:ptcp.w:call-trgt-16.t:call-trgt_plot_meth_allele INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:18.514 wdl.w:ptcp.w:call-trgt-16.t:call-trgt_plot_meth_allele INFO eval :: name: "plot_type", value: "allele"
2025-09-15 20:24:18.514 wdl.w:ptcp.w:call-trgt-16.t:call-trgt_plot_meth_allele INFO eval :: name: "show", value: "meth"
2025-09-15 20:24:18.514 wdl.w:ptcp.w:call-trgt-16.t:call-trgt_plot_meth_allele INFO eval :: name: "threads", value: 1
2025-09-15 20:24:18.514 wdl.w:ptcp.w:call-trgt-16.t:call-trgt_plot_meth_allele INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:18.514 wdl.w:ptcp.w:call-trgt-16.t:call-trgt_plot_meth_allele INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2113.meth_allele"
2025-09-15 20:24:18.515 wdl.w:ptcp.w:call-trgt-16.t:call-trgt_plot_meth_allele INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:18.515 wdl.w:ptcp.w:call-trgt-16.t:call-trgt_plot_meth_allele WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:18.515 wdl.w:ptcp.w:call-trgt-16.t:call-trgt_plot_meth_allele INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:18.515 wdl.w:ptcp.w:call-trgt-16.t:call-trgt_plot_meth_allele INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:18.560 wdl.w:ptcp.w:call-trgt-28 NOTICE done
2025-09-15 20:24:18.564 wdl.w:ptcp NOTICE finish :: job: "call-trgt-28"
2025-09-15 20:24:18.564 wdl.w:ptcp INFO output :: job: "call-trgt-28", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-28/out/m84036_250809_035451_s4.bc2125.motifs_waterfall.trgt_plots.zip", "images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-28/out/m84036_250809_035451_s4.bc2125.meth_allele.trgt_plots.zip", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-28/out/m84036_250809_035451_s4.bc2125.trgt.sorted.spanning.bam.bai", "images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-28/out/m84036_250809_035451_s4.bc2125.motifs_allele.trgt_plots.zip", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-28/out/m84036_250809_035451_s4.bc2125.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-28/out/m84036_250809_035451_s4.bc2125.trgt.vcf", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-28/out/m84036_250809_035451_s4.bc2125.repeats.bam", "images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-28/out/m84036_250809_035451_s4.bc2125.meth_waterfall.trgt_plots.zip", "reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-28/out/m84036_250809_035451_s4.bc2125.repeats.bam.bai"}
2025-09-15 20:24:18.571 wdl.w:ptcp.w:call-trgt-09.t:call-trgt_plot_motifs_allele NOTICE slurm_singularity run :: pid: 1201400, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-09/call-trgt_plot_motifs_allele/slurm_singularity.log.txt"
2025-09-15 20:24:18.574 wdl.w:ptcp.w:call-sawfish-62 NOTICE workflow start :: name: "sawfish", source: "./sawfish.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-62"
2025-09-15 20:24:18.582 wdl.w:ptcp.w:call-trgt-09.t:call-trgt_plot_motifs_waterfall INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-09/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_q7l15jhl"
2025-09-15 20:24:18.582 wdl.w:ptcp.w:call-trgt-09.t:call-trgt_plot_motifs_waterfall INFO Slurm invocation: srun --job-name call-trgt_plot_motifs_waterfall --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-09/call-trgt_plot_motifs_waterfall/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-09/call-trgt_plot_motifs_waterfall/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-09/call-trgt_plot_motifs_waterfall/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-09/call-trgt_plot_motifs_waterfall/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-09/call-trgt_genotype/out/m84036_250809_035451_s4.bc2106.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2106.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-09/call-trgt_genotype/out/m84036_250809_035451_s4.bc2106.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2106.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-09/call-trgt_genotype/out/m84036_250809_035451_s4.bc2106.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2106.trgt.vcf:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-09/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_q7l15jhl/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-09/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_q7l15jhl/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:18.591 wdl.w:ptcp.w:call-trgt-09.t:call-trgt_plot_motifs_waterfall NOTICE slurm_singularity run :: pid: 1201402, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-09/call-trgt_plot_motifs_waterfall/slurm_singularity.log.txt"
2025-09-15 20:24:18.594 wdl.w:ptcp.w:call-sawfish-62 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:24:18.595 wdl.w:ptcp.w:call-sawfish-62 INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:24:18.595 wdl.w:ptcp.w:call-sawfish-62 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-62/out/m84036_250809_035451_s4.bc2159.mapped.bam"}
2025-09-15 20:24:18.595 wdl.w:ptcp.w:call-sawfish-62 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-62/out/m84036_250809_035451_s4.bc2159.mapped.bam.bai"}
2025-09-15 20:24:18.595 wdl.w:ptcp.w:call-sawfish-62 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:24:18.595 wdl.w:ptcp.w:call-sawfish-62 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:24:18.595 wdl.w:ptcp.w:call-sawfish-62 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2159"}
2025-09-15 20:24:18.595 wdl.w:ptcp.w:call-sawfish-62 NOTICE ready :: job: "call-run_sawfish", callee: "run_sawfish"
2025-09-15 20:24:18.595 wdl.w:ptcp.w:call-sawfish-62 INFO input :: job: "call-run_sawfish", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-62/out/m84036_250809_035451_s4.bc2159.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-62/out/m84036_250809_035451_s4.bc2159.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2159"}
2025-09-15 20:24:18.618 wdl.w:ptcp.w:call-trgt-16.t:call-trgt_plot_meth_allele INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-16/call-trgt_plot_meth_allele/_singularity_tmpdir_a7lvi0ay"
2025-09-15 20:24:18.618 wdl.w:ptcp.w:call-trgt-16.t:call-trgt_plot_meth_allele INFO Slurm invocation: srun --job-name call-trgt_plot_meth_allele --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-16/call-trgt_plot_meth_allele/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-16/call-trgt_plot_meth_allele/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-16/call-trgt_plot_meth_allele/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-16/call-trgt_plot_meth_allele/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-16/call-trgt_genotype/out/m84036_250809_035451_s4.bc2113.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2113.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-16/call-trgt_genotype/out/m84036_250809_035451_s4.bc2113.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2113.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-16/call-trgt_genotype/out/m84036_250809_035451_s4.bc2113.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2113.trgt.vcf:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-16/call-trgt_plot_meth_allele/_singularity_tmpdir_a7lvi0ay/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-16/call-trgt_plot_meth_allele/_singularity_tmpdir_a7lvi0ay/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:18.631 wdl.w:ptcp.w:call-trgt-16.t:call-trgt_plot_meth_allele NOTICE slurm_singularity run :: pid: 1201415, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-16/call-trgt_plot_meth_allele/slurm_singularity.log.txt"
2025-09-15 20:24:18.652 wdl.w:ptcp.t:call-pbmm2_align_hifi-90 INFO output :: name: "mapped_bam", value: "m84036_250809_035451_s4.bc2187.mapped.bam"
2025-09-15 20:24:18.655 wdl.w:ptcp.t:call-pbmm2_align_hifi-90 INFO output :: name: "mapped_bam_bai", value: "m84036_250809_035451_s4.bc2187.mapped.bam.bai"
2025-09-15 20:24:18.656 wdl.w:ptcp.t:call-pbmm2_align_hifi-90 INFO output :: name: "mapped_bam_pbi", value: "m84036_250809_035451_s4.bc2187.mapped.bam.pbi"
2025-09-15 20:24:18.657 wdl.w:ptcp.t:call-pbmm2_align_hifi-90 INFO output :: name: "report", value: "mapping_stats.report.json"
2025-09-15 20:24:18.685 wdl.w:ptcp.w:call-trgt-24.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO srun: job 51797601 queued and waiting for resources
2025-09-15 20:24:18.686 wdl.w:ptcp.w:call-trgt-24.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO srun: job 51797601 has been allocated resources
2025-09-15 20:24:18.686 wdl.w:ptcp.w:call-trgt-24.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:18.735 wdl.w:ptcp.t:call-pbmm2_align_hifi-86 INFO output :: name: "mapped_bam", value: "m84036_250809_035451_s4.bc2183.mapped.bam"
2025-09-15 20:24:18.735 wdl.w:ptcp.t:call-pbmm2_align_hifi-90 NOTICE done
2025-09-15 20:24:18.738 wdl.w:ptcp.t:call-pbmm2_align_hifi-86 INFO output :: name: "mapped_bam_bai", value: "m84036_250809_035451_s4.bc2183.mapped.bam.bai"
2025-09-15 20:24:18.739 wdl.w:ptcp.t:call-pbmm2_align_hifi-86 INFO output :: name: "mapped_bam_pbi", value: "m84036_250809_035451_s4.bc2183.mapped.bam.pbi"
2025-09-15 20:24:18.740 wdl.w:ptcp.t:call-pbmm2_align_hifi-86 INFO output :: name: "report", value: "mapping_stats.report.json"
2025-09-15 20:24:18.741 wdl.w:ptcp NOTICE finish :: job: "call-pbmm2_align_hifi-90"
2025-09-15 20:24:18.741 wdl.w:ptcp INFO output :: job: "call-pbmm2_align_hifi-90", values: {"report": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-90/out/mapping_stats.report.json", "mapped_bam_pbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-90/out/m84036_250809_035451_s4.bc2187.mapped.bam.pbi", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-90/out/m84036_250809_035451_s4.bc2187.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-90/out/m84036_250809_035451_s4.bc2187.mapped.bam"}
2025-09-15 20:24:18.742 wdl.w:ptcp NOTICE ready :: job: "call-paraphase-90", callee: "paraphase"
2025-09-15 20:24:18.742 wdl.w:ptcp INFO input :: job: "call-paraphase-90", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf", "genome_version": "38", "config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-90/out/m84036_250809_035451_s4.bc2187.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-90/out/m84036_250809_035451_s4.bc2187.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2187"}
2025-09-15 20:24:18.743 wdl.w:ptcp NOTICE ready :: job: "call-sawfish-90", callee: "sawfish"
2025-09-15 20:24:18.743 wdl.w:ptcp INFO input :: job: "call-sawfish-90", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-90/out/m84036_250809_035451_s4.bc2187.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-90/out/m84036_250809_035451_s4.bc2187.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2187"}
2025-09-15 20:24:18.744 wdl.w:ptcp NOTICE ready :: job: "call-trgt-90", callee: "trgt"
2025-09-15 20:24:18.744 wdl.w:ptcp INFO input :: job: "call-trgt-90", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-90/out/m84036_250809_035451_s4.bc2187.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-90/out/m84036_250809_035451_s4.bc2187.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2187"}
2025-09-15 20:24:18.747 wdl.w:ptcp.w:call-paraphase-13.t:call-call_f8 NOTICE task setup :: name: "call_f8", source: "./paraphase.wdl", line: 232, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-13/call-call_f8", thread: 140607129368128
2025-09-15 20:24:18.757 wdl.w:ptcp.w:call-trgt-09.t:call-trgt_plot_meth_allele.slurm_singularity INFO srun: job 51797602 queued and waiting for resources
2025-09-15 20:24:18.757 wdl.w:ptcp.w:call-trgt-09.t:call-trgt_plot_meth_allele.slurm_singularity INFO srun: job 51797602 has been allocated resources
2025-09-15 20:24:18.757 wdl.w:ptcp.w:call-trgt-09.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO srun: job 51797603 queued and waiting for resources
2025-09-15 20:24:18.758 wdl.w:ptcp.w:call-trgt-09.t:call-trgt_plot_meth_allele.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:18.758 wdl.w:ptcp.w:call-trgt-09.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO srun: job 51797603 has been allocated resources
2025-09-15 20:24:18.758 wdl.w:ptcp.w:call-trgt-09.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:18.769 wdl.w:ptcp.w:call-paraphase-13.t:call-call_f8 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:18.770 wdl.w:ptcp.w:call-paraphase-13.t:call-call_f8 INFO input :: name: "genome_version", value: "38"
2025-09-15 20:24:18.770 wdl.w:ptcp.w:call-paraphase-13.t:call-call_f8 INFO input :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2110"
2025-09-15 20:24:18.770 wdl.w:ptcp.w:call-paraphase-13.t:call-call_f8 INFO input :: name: "paraphase_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2110.paraphase.bam.bai"
2025-09-15 20:24:18.770 wdl.w:ptcp.w:call-paraphase-13.t:call-call_f8 INFO input :: name: "paraphase_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2110.paraphase.bam"
2025-09-15 20:24:18.770 wdl.w:ptcp.w:call-paraphase-13.t:call-call_f8 INFO input :: name: "sex", value: "F"
2025-09-15 20:24:18.770 wdl.w:ptcp.w:call-paraphase-13.t:call-call_f8 INFO eval :: name: "threads", value: 1
2025-09-15 20:24:18.770 wdl.w:ptcp.w:call-paraphase-13.t:call-call_f8 INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:18.771 wdl.w:ptcp.w:call-paraphase-13.t:call-call_f8 INFO eval :: name: "disk_size", value: 11
2025-09-15 20:24:18.771 wdl.w:ptcp.w:call-paraphase-13.t:call-call_f8 INFO eval :: name: "sample_sex", value: "F"
2025-09-15 20:24:18.771 wdl.w:ptcp.w:call-paraphase-13.t:call-call_f8 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:18.771 wdl.w:ptcp.w:call-paraphase-13.t:call-call_f8 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:18.771 wdl.w:ptcp.w:call-paraphase-13.t:call-call_f8 INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:18.772 wdl.w:ptcp.w:call-paraphase-13.t:call-call_f8 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:18.827 wdl.w:ptcp.w:call-paraphase-13.t:call-call_f8 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 8, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-13/call-call_f8/_singularity_tmpdir_yhwlnqio"
2025-09-15 20:24:18.827 wdl.w:ptcp.w:call-paraphase-13.t:call-call_f8 INFO Slurm invocation: srun --job-name call-call_f8 --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-13/call-call_f8/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-13/call-call_f8/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-13/call-call_f8/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-13/call-call_f8/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-13/call-run_paraphase/out/m84036_250809_035451_s4.bc2110_paraphase/m84036_250809_035451_s4.bc2110.paraphase.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2110.paraphase.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-13/call-run_paraphase/out/m84036_250809_035451_s4.bc2110_paraphase/m84036_250809_035451_s4.bc2110.paraphase.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2110.paraphase.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-13/call-call_f8/_singularity_tmpdir_yhwlnqio/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-13/call-call_f8/_singularity_tmpdir_yhwlnqio/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:18.842 wdl.w:ptcp.t:call-pbmm2_align_hifi-86 NOTICE done
2025-09-15 20:24:18.846 wdl.w:ptcp.w:call-paraphase-13.t:call-call_f8 NOTICE slurm_singularity run :: pid: 1201423, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-13/call-call_f8/slurm_singularity.log.txt"
2025-09-15 20:24:18.848 wdl.w:ptcp NOTICE finish :: job: "call-pbmm2_align_hifi-86"
2025-09-15 20:24:18.848 wdl.w:ptcp INFO output :: job: "call-pbmm2_align_hifi-86", values: {"report": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-86/out/mapping_stats.report.json", "mapped_bam_pbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-86/out/m84036_250809_035451_s4.bc2183.mapped.bam.pbi", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-86/out/m84036_250809_035451_s4.bc2183.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-86/out/m84036_250809_035451_s4.bc2183.mapped.bam"}
2025-09-15 20:24:18.849 wdl.w:ptcp NOTICE ready :: job: "call-paraphase-86", callee: "paraphase"
2025-09-15 20:24:18.849 wdl.w:ptcp INFO input :: job: "call-paraphase-86", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf", "genome_version": "38", "config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-86/out/m84036_250809_035451_s4.bc2183.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-86/out/m84036_250809_035451_s4.bc2183.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2183"}
2025-09-15 20:24:18.850 wdl.w:ptcp NOTICE ready :: job: "call-sawfish-86", callee: "sawfish"
2025-09-15 20:24:18.850 wdl.w:ptcp INFO input :: job: "call-sawfish-86", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-86/out/m84036_250809_035451_s4.bc2183.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-86/out/m84036_250809_035451_s4.bc2183.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2183"}
2025-09-15 20:24:18.851 wdl.w:ptcp NOTICE ready :: job: "call-trgt-86", callee: "trgt"
2025-09-15 20:24:18.851 wdl.w:ptcp INFO input :: job: "call-trgt-86", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-86/out/m84036_250809_035451_s4.bc2183.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-86/out/m84036_250809_035451_s4.bc2183.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2183"}
2025-09-15 20:24:18.856 wdl.w:ptcp.w:call-trgt-16.t:call-trgt_plot_meth_waterfall NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-16/call-trgt_plot_meth_waterfall", thread: 140607162938944
2025-09-15 20:24:18.874 wdl.w:ptcp.w:call-trgt-16.t:call-trgt_plot_meth_waterfall INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:18.874 wdl.w:ptcp.w:call-trgt-16.t:call-trgt_plot_meth_waterfall INFO input :: name: "waterfall", value: true
2025-09-15 20:24:18.874 wdl.w:ptcp.w:call-trgt-16.t:call-trgt_plot_meth_waterfall INFO input :: name: "methylation", value: true
2025-09-15 20:24:18.874 wdl.w:ptcp.w:call-trgt-16.t:call-trgt_plot_meth_waterfall INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:18.875 wdl.w:ptcp.w:call-trgt-16.t:call-trgt_plot_meth_waterfall INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:18.875 wdl.w:ptcp.w:call-trgt-16.t:call-trgt_plot_meth_waterfall INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:18.875 wdl.w:ptcp.w:call-trgt-16.t:call-trgt_plot_meth_waterfall INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2113.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:18.875 wdl.w:ptcp.w:call-trgt-16.t:call-trgt_plot_meth_waterfall INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2113.trgt.sorted.spanning.bam"
2025-09-15 20:24:18.875 wdl.w:ptcp.w:call-trgt-16.t:call-trgt_plot_meth_waterfall INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2113.trgt.vcf"
2025-09-15 20:24:18.875 wdl.w:ptcp.w:call-trgt-16.t:call-trgt_plot_meth_waterfall INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2113"
2025-09-15 20:24:18.875 wdl.w:ptcp.w:call-trgt-16.t:call-trgt_plot_meth_waterfall INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:18.875 wdl.w:ptcp.w:call-trgt-16.t:call-trgt_plot_meth_waterfall INFO eval :: name: "plot_type", value: "waterfall"
2025-09-15 20:24:18.875 wdl.w:ptcp.w:call-trgt-16.t:call-trgt_plot_meth_waterfall INFO eval :: name: "show", value: "meth"
2025-09-15 20:24:18.875 wdl.w:ptcp.w:call-trgt-16.t:call-trgt_plot_meth_waterfall INFO eval :: name: "threads", value: 1
2025-09-15 20:24:18.875 wdl.w:ptcp.w:call-trgt-16.t:call-trgt_plot_meth_waterfall INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:18.876 wdl.w:ptcp.w:call-trgt-16.t:call-trgt_plot_meth_waterfall INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2113.meth_waterfall"
2025-09-15 20:24:18.876 wdl.w:ptcp.w:call-trgt-16.t:call-trgt_plot_meth_waterfall INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:18.876 wdl.w:ptcp.w:call-trgt-16.t:call-trgt_plot_meth_waterfall WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:18.876 wdl.w:ptcp.w:call-trgt-16.t:call-trgt_plot_meth_waterfall INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:18.876 wdl.w:ptcp.w:call-trgt-16.t:call-trgt_plot_meth_waterfall INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:18.941 wdl.w:ptcp.w:call-trgt-16.t:call-trgt_plot_meth_waterfall INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-16/call-trgt_plot_meth_waterfall/_singularity_tmpdir_a1xgvm9b"
2025-09-15 20:24:18.941 wdl.w:ptcp.w:call-trgt-16.t:call-trgt_plot_meth_waterfall INFO Slurm invocation: srun --job-name call-trgt_plot_meth_waterfall --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-16/call-trgt_plot_meth_waterfall/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-16/call-trgt_plot_meth_waterfall/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-16/call-trgt_plot_meth_waterfall/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-16/call-trgt_plot_meth_waterfall/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-16/call-trgt_genotype/out/m84036_250809_035451_s4.bc2113.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2113.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-16/call-trgt_genotype/out/m84036_250809_035451_s4.bc2113.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2113.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-16/call-trgt_genotype/out/m84036_250809_035451_s4.bc2113.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2113.trgt.vcf:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-16/call-trgt_plot_meth_waterfall/_singularity_tmpdir_a1xgvm9b/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-16/call-trgt_plot_meth_waterfall/_singularity_tmpdir_a1xgvm9b/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:18.949 wdl.w:ptcp.w:call-trgt-16.t:call-trgt_plot_meth_waterfall NOTICE slurm_singularity run :: pid: 1201425, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-16/call-trgt_plot_meth_waterfall/slurm_singularity.log.txt"
2025-09-15 20:24:19.132 wdl.w:ptcp.w:call-trgt-05.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:18 [ERROR] - No reads found for TRID=PRTS_ARX
2025-09-15 20:24:19.133 wdl.w:ptcp.w:call-trgt-05.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:18 [ERROR] - No reads found for TRID=EIEE1_ARX
2025-09-15 20:24:19.216 wdl.w:ptcp.w:call-paraphase-10.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for smn1 for sample m84036_250809_035451_s4.bc2107 at 2025-09-15 20:23:56.746170...
2025-09-15 20:24:19.217 wdl.w:ptcp.w:call-paraphase-10.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for f8inv1 for sample m84036_250809_035451_s4.bc2107 at 2025-09-15 20:24:18.218758...
2025-09-15 20:24:19.217 wdl.w:ptcp.w:call-paraphase-10.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for f8inv1 for sample m84036_250809_035451_s4.bc2107 at 2025-09-15 20:24:18.219564...
2025-09-15 20:24:19.246 wdl.w:ptcp.w:call-trgt-12.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:18 [ERROR] - No reads found for TRID=PRTS_ARX
2025-09-15 20:24:19.246 wdl.w:ptcp.w:call-trgt-12.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:18 [ERROR] - No reads found for TRID=EIEE1_ARX
2025-09-15 20:24:19.361 wdl.w:ptcp.w:call-trgt-29.t:call-trgt_plot_motifs_allele INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2126.motifs_allele.trgt_plots.zip"
2025-09-15 20:24:19.461 wdl.w:ptcp.w:call-trgt-29.t:call-trgt_plot_motifs_allele NOTICE done
2025-09-15 20:24:19.497 wdl.w:ptcp.w:call-trgt-29 NOTICE finish :: job: "call-trgt_plot_motifs_allele"
2025-09-15 20:24:19.497 wdl.w:ptcp.w:call-trgt-29 INFO output :: job: "call-trgt_plot_motifs_allele", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-29/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2126.motifs_allele.trgt_plots.zip"}
2025-09-15 20:24:19.497 wdl.w:ptcp.w:call-trgt-29 INFO visit :: node: "output-images_motifs_allele", values: {"images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-29/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2126.motifs_allele.trgt_plots.zip"}
2025-09-15 20:24:19.503 wdl.w:ptcp.w:call-trgt-16.t:call-trgt_plot_motifs_allele NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-16/call-trgt_plot_motifs_allele", thread: 140608773551680
2025-09-15 20:24:19.520 wdl.w:ptcp.w:call-trgt-16.t:call-trgt_plot_motifs_allele INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:19.520 wdl.w:ptcp.w:call-trgt-16.t:call-trgt_plot_motifs_allele INFO input :: name: "waterfall", value: false
2025-09-15 20:24:19.520 wdl.w:ptcp.w:call-trgt-16.t:call-trgt_plot_motifs_allele INFO input :: name: "methylation", value: false
2025-09-15 20:24:19.520 wdl.w:ptcp.w:call-trgt-16.t:call-trgt_plot_motifs_allele INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:19.520 wdl.w:ptcp.w:call-trgt-16.t:call-trgt_plot_motifs_allele INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:19.520 wdl.w:ptcp.w:call-trgt-16.t:call-trgt_plot_motifs_allele INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:19.520 wdl.w:ptcp.w:call-trgt-16.t:call-trgt_plot_motifs_allele INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2113.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:19.520 wdl.w:ptcp.w:call-trgt-16.t:call-trgt_plot_motifs_allele INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2113.trgt.sorted.spanning.bam"
2025-09-15 20:24:19.520 wdl.w:ptcp.w:call-trgt-16.t:call-trgt_plot_motifs_allele INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2113.trgt.vcf"
2025-09-15 20:24:19.520 wdl.w:ptcp.w:call-trgt-16.t:call-trgt_plot_motifs_allele INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2113"
2025-09-15 20:24:19.521 wdl.w:ptcp.w:call-trgt-16.t:call-trgt_plot_motifs_allele INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:19.521 wdl.w:ptcp.w:call-trgt-16.t:call-trgt_plot_motifs_allele INFO eval :: name: "plot_type", value: "allele"
2025-09-15 20:24:19.521 wdl.w:ptcp.w:call-trgt-16.t:call-trgt_plot_motifs_allele INFO eval :: name: "show", value: "motifs"
2025-09-15 20:24:19.521 wdl.w:ptcp.w:call-trgt-16.t:call-trgt_plot_motifs_allele INFO eval :: name: "threads", value: 1
2025-09-15 20:24:19.521 wdl.w:ptcp.w:call-trgt-16.t:call-trgt_plot_motifs_allele INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:19.522 wdl.w:ptcp.w:call-trgt-16.t:call-trgt_plot_motifs_allele INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2113.motifs_allele"
2025-09-15 20:24:19.522 wdl.w:ptcp.w:call-trgt-16.t:call-trgt_plot_motifs_allele INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:19.522 wdl.w:ptcp.w:call-trgt-16.t:call-trgt_plot_motifs_allele WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:19.522 wdl.w:ptcp.w:call-trgt-16.t:call-trgt_plot_motifs_allele INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:19.522 wdl.w:ptcp.w:call-trgt-16.t:call-trgt_plot_motifs_allele INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:19.582 wdl.w:ptcp.w:call-trgt-09.t:call-trgt_plot_motifs_allele.slurm_singularity INFO srun: job 51797604 queued and waiting for resources
2025-09-15 20:24:19.582 wdl.w:ptcp.w:call-trgt-09.t:call-trgt_plot_motifs_allele.slurm_singularity INFO srun: job 51797604 has been allocated resources
2025-09-15 20:24:19.582 wdl.w:ptcp.w:call-trgt-09.t:call-trgt_plot_motifs_allele.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:19.584 wdl.w:ptcp.w:call-trgt-16.t:call-trgt_plot_motifs_allele INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-16/call-trgt_plot_motifs_allele/_singularity_tmpdir_z03f67op"
2025-09-15 20:24:19.585 wdl.w:ptcp.w:call-trgt-16.t:call-trgt_plot_motifs_allele INFO Slurm invocation: srun --job-name call-trgt_plot_motifs_allele --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-16/call-trgt_plot_motifs_allele/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-16/call-trgt_plot_motifs_allele/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-16/call-trgt_plot_motifs_allele/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-16/call-trgt_plot_motifs_allele/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-16/call-trgt_genotype/out/m84036_250809_035451_s4.bc2113.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2113.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-16/call-trgt_genotype/out/m84036_250809_035451_s4.bc2113.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2113.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-16/call-trgt_genotype/out/m84036_250809_035451_s4.bc2113.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2113.trgt.vcf:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-16/call-trgt_plot_motifs_allele/_singularity_tmpdir_z03f67op/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-16/call-trgt_plot_motifs_allele/_singularity_tmpdir_z03f67op/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:19.606 wdl.w:ptcp.w:call-trgt-09.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO srun: job 51797605 queued and waiting for resources
2025-09-15 20:24:19.607 wdl.w:ptcp.w:call-trgt-09.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO srun: job 51797605 has been allocated resources
2025-09-15 20:24:19.607 wdl.w:ptcp.w:call-trgt-09.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:19.611 wdl.w:ptcp.w:call-trgt-16.t:call-trgt_plot_motifs_allele NOTICE slurm_singularity run :: pid: 1201465, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-16/call-trgt_plot_motifs_allele/slurm_singularity.log.txt"
2025-09-15 20:24:19.638 wdl.w:ptcp.w:call-trgt-16.t:call-trgt_plot_meth_allele.slurm_singularity INFO srun: job 51797606 queued and waiting for resources
2025-09-15 20:24:19.638 wdl.w:ptcp.w:call-trgt-16.t:call-trgt_plot_meth_allele.slurm_singularity INFO srun: job 51797606 has been allocated resources
2025-09-15 20:24:19.639 wdl.w:ptcp.w:call-trgt-16.t:call-trgt_plot_meth_allele.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:19.770 wdl.w:ptcp.w:call-trgt-12.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:19 [ERROR] - No reads found for TRID=PRTS_ARX
2025-09-15 20:24:19.770 wdl.w:ptcp.w:call-trgt-12.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:19 [ERROR] - No reads found for TRID=EIEE1_ARX
2025-09-15 20:24:19.855 wdl.w:ptcp.w:call-paraphase-13.t:call-call_f8.slurm_singularity INFO srun: job 51797607 queued and waiting for resources
2025-09-15 20:24:19.856 wdl.w:ptcp.w:call-paraphase-13.t:call-call_f8.slurm_singularity INFO srun: job 51797607 has been allocated resources
2025-09-15 20:24:19.856 wdl.w:ptcp.w:call-paraphase-13.t:call-call_f8.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:19.891 wdl.w:ptcp.w:call-trgt-29.t:call-trgt_plot_meth_allele INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2126.meth_allele.trgt_plots.zip"
2025-09-15 20:24:19.958 wdl.w:ptcp.w:call-trgt-16.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO srun: job 51797608 queued and waiting for resources
2025-09-15 20:24:19.959 wdl.w:ptcp.w:call-trgt-16.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO srun: job 51797608 has been allocated resources
2025-09-15 20:24:19.959 wdl.w:ptcp.w:call-trgt-16.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:19.969 wdl.w:ptcp.w:call-paraphase-27.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for f8inv1 for sample m84036_250809_035451_s4.bc2124 at 2025-09-15 20:24:14.928407...
2025-09-15 20:24:19.969 wdl.w:ptcp.w:call-paraphase-27.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for hba for sample m84036_250809_035451_s4.bc2124 at 2025-09-15 20:24:15.137349...
2025-09-15 20:24:19.969 wdl.w:ptcp.w:call-paraphase-27.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for f8inv1 for sample m84036_250809_035451_s4.bc2124 at 2025-09-15 20:24:15.262960...
2025-09-15 20:24:19.969 wdl.w:ptcp.w:call-paraphase-27.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for hba for sample m84036_250809_035451_s4.bc2124 at 2025-09-15 20:24:15.465015...
2025-09-15 20:24:19.999 wdl.w:ptcp.w:call-trgt-29.t:call-trgt_plot_meth_allele NOTICE done
2025-09-15 20:24:20.003 wdl.w:ptcp.w:call-trgt-29 NOTICE finish :: job: "call-trgt_plot_meth_allele"
2025-09-15 20:24:20.004 wdl.w:ptcp.w:call-trgt-29 INFO output :: job: "call-trgt_plot_meth_allele", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-29/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2126.meth_allele.trgt_plots.zip"}
2025-09-15 20:24:20.004 wdl.w:ptcp.w:call-trgt-29 INFO visit :: node: "output-images_meth_allele", values: {"images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-29/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2126.meth_allele.trgt_plots.zip"}
2025-09-15 20:24:20.008 wdl.w:ptcp.w:call-trgt-16.t:call-trgt_plot_motifs_waterfall NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-16/call-trgt_plot_motifs_waterfall", thread: 140607154546240
2025-09-15 20:24:20.024 wdl.w:ptcp.w:call-trgt-16.t:call-trgt_plot_motifs_waterfall INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:20.024 wdl.w:ptcp.w:call-trgt-16.t:call-trgt_plot_motifs_waterfall INFO input :: name: "waterfall", value: true
2025-09-15 20:24:20.024 wdl.w:ptcp.w:call-trgt-16.t:call-trgt_plot_motifs_waterfall INFO input :: name: "methylation", value: false
2025-09-15 20:24:20.024 wdl.w:ptcp.w:call-trgt-16.t:call-trgt_plot_motifs_waterfall INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:20.024 wdl.w:ptcp.w:call-trgt-16.t:call-trgt_plot_motifs_waterfall INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:20.024 wdl.w:ptcp.w:call-trgt-16.t:call-trgt_plot_motifs_waterfall INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:20.024 wdl.w:ptcp.w:call-trgt-16.t:call-trgt_plot_motifs_waterfall INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2113.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:20.024 wdl.w:ptcp.w:call-trgt-16.t:call-trgt_plot_motifs_waterfall INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2113.trgt.sorted.spanning.bam"
2025-09-15 20:24:20.024 wdl.w:ptcp.w:call-trgt-16.t:call-trgt_plot_motifs_waterfall INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2113.trgt.vcf"
2025-09-15 20:24:20.024 wdl.w:ptcp.w:call-trgt-16.t:call-trgt_plot_motifs_waterfall INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2113"
2025-09-15 20:24:20.025 wdl.w:ptcp.w:call-trgt-16.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:20.025 wdl.w:ptcp.w:call-trgt-16.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "plot_type", value: "waterfall"
2025-09-15 20:24:20.025 wdl.w:ptcp.w:call-trgt-16.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "show", value: "motifs"
2025-09-15 20:24:20.025 wdl.w:ptcp.w:call-trgt-16.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "threads", value: 1
2025-09-15 20:24:20.025 wdl.w:ptcp.w:call-trgt-16.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:20.025 wdl.w:ptcp.w:call-trgt-16.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2113.motifs_waterfall"
2025-09-15 20:24:20.026 wdl.w:ptcp.w:call-trgt-16.t:call-trgt_plot_motifs_waterfall INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:20.026 wdl.w:ptcp.w:call-trgt-16.t:call-trgt_plot_motifs_waterfall WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:20.026 wdl.w:ptcp.w:call-trgt-16.t:call-trgt_plot_motifs_waterfall INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:20.026 wdl.w:ptcp.w:call-trgt-16.t:call-trgt_plot_motifs_waterfall INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:20.088 wdl.w:ptcp.w:call-trgt-16.t:call-trgt_plot_motifs_waterfall INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-16/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_g1_mhjrf"
2025-09-15 20:24:20.088 wdl.w:ptcp.w:call-trgt-16.t:call-trgt_plot_motifs_waterfall INFO Slurm invocation: srun --job-name call-trgt_plot_motifs_waterfall --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-16/call-trgt_plot_motifs_waterfall/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-16/call-trgt_plot_motifs_waterfall/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-16/call-trgt_plot_motifs_waterfall/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-16/call-trgt_plot_motifs_waterfall/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-16/call-trgt_genotype/out/m84036_250809_035451_s4.bc2113.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2113.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-16/call-trgt_genotype/out/m84036_250809_035451_s4.bc2113.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2113.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-16/call-trgt_genotype/out/m84036_250809_035451_s4.bc2113.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2113.trgt.vcf:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-16/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_g1_mhjrf/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-16/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_g1_mhjrf/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:20.089 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_motifs_waterfall INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2124.motifs_waterfall.trgt_plots.zip"
2025-09-15 20:24:20.114 wdl.w:ptcp.w:call-trgt-16.t:call-trgt_plot_motifs_waterfall NOTICE slurm_singularity run :: pid: 1201514, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-16/call-trgt_plot_motifs_waterfall/slurm_singularity.log.txt"
2025-09-15 20:24:20.151 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_motifs_waterfall NOTICE done
2025-09-15 20:24:20.157 wdl.w:ptcp.w:call-trgt-27 NOTICE finish :: job: "call-trgt_plot_motifs_waterfall"
2025-09-15 20:24:20.157 wdl.w:ptcp.w:call-trgt-27 INFO output :: job: "call-trgt_plot_motifs_waterfall", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-27/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2124.motifs_waterfall.trgt_plots.zip"}
2025-09-15 20:24:20.157 wdl.w:ptcp.w:call-trgt-27 INFO visit :: node: "output-images_motifs_waterfall", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-27/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2124.motifs_waterfall.trgt_plots.zip"}
2025-09-15 20:24:20.162 wdl.w:ptcp.w:call-paraphase-33.t:call-call_f8 NOTICE task setup :: name: "call_f8", source: "./paraphase.wdl", line: 232, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-33/call-call_f8", thread: 140606609282624
2025-09-15 20:24:20.179 wdl.w:ptcp.w:call-paraphase-33.t:call-call_f8 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:20.179 wdl.w:ptcp.w:call-paraphase-33.t:call-call_f8 INFO input :: name: "genome_version", value: "38"
2025-09-15 20:24:20.179 wdl.w:ptcp.w:call-paraphase-33.t:call-call_f8 INFO input :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2130"
2025-09-15 20:24:20.179 wdl.w:ptcp.w:call-paraphase-33.t:call-call_f8 INFO input :: name: "paraphase_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2130.paraphase.bam.bai"
2025-09-15 20:24:20.179 wdl.w:ptcp.w:call-paraphase-33.t:call-call_f8 INFO input :: name: "paraphase_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2130.paraphase.bam"
2025-09-15 20:24:20.179 wdl.w:ptcp.w:call-paraphase-33.t:call-call_f8 INFO input :: name: "sex", value: "F"
2025-09-15 20:24:20.179 wdl.w:ptcp.w:call-paraphase-33.t:call-call_f8 INFO eval :: name: "threads", value: 1
2025-09-15 20:24:20.179 wdl.w:ptcp.w:call-paraphase-33.t:call-call_f8 INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:20.179 wdl.w:ptcp.w:call-paraphase-33.t:call-call_f8 INFO eval :: name: "disk_size", value: 11
2025-09-15 20:24:20.180 wdl.w:ptcp.w:call-paraphase-33.t:call-call_f8 INFO eval :: name: "sample_sex", value: "F"
2025-09-15 20:24:20.180 wdl.w:ptcp.w:call-paraphase-33.t:call-call_f8 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:20.180 wdl.w:ptcp.w:call-paraphase-33.t:call-call_f8 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:20.180 wdl.w:ptcp.w:call-paraphase-33.t:call-call_f8 INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:20.180 wdl.w:ptcp.w:call-paraphase-33.t:call-call_f8 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:20.190 wdl.w:ptcp.w:call-paraphase-02.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for smn1 for sample m84036_250809_035451_s4.bc2099 at 2025-09-15 20:24:06.142971...
2025-09-15 20:24:20.220 wdl.w:ptcp.w:call-paraphase-33.t:call-call_f8 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 8, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-33/call-call_f8/_singularity_tmpdir_0u64rekg"
2025-09-15 20:24:20.220 wdl.w:ptcp.w:call-paraphase-33.t:call-call_f8 INFO Slurm invocation: srun --job-name call-call_f8 --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-33/call-call_f8/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-33/call-call_f8/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-33/call-call_f8/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-33/call-call_f8/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-33/call-run_paraphase/out/m84036_250809_035451_s4.bc2130_paraphase/m84036_250809_035451_s4.bc2130.paraphase.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2130.paraphase.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-33/call-run_paraphase/out/m84036_250809_035451_s4.bc2130_paraphase/m84036_250809_035451_s4.bc2130.paraphase.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2130.paraphase.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-33/call-call_f8/_singularity_tmpdir_0u64rekg/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-33/call-call_f8/_singularity_tmpdir_0u64rekg/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:20.235 wdl.w:ptcp.w:call-paraphase-33.t:call-call_f8 NOTICE slurm_singularity run :: pid: 1201522, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-33/call-call_f8/slurm_singularity.log.txt"
2025-09-15 20:24:20.261 wdl.w:ptcp.t:call-pbmm2_align_hifi-88 INFO output :: name: "mapped_bam", value: "m84036_250809_035451_s4.bc2185.mapped.bam"
2025-09-15 20:24:20.264 wdl.w:ptcp.t:call-pbmm2_align_hifi-88 INFO output :: name: "mapped_bam_bai", value: "m84036_250809_035451_s4.bc2185.mapped.bam.bai"
2025-09-15 20:24:20.266 wdl.w:ptcp.t:call-pbmm2_align_hifi-88 INFO output :: name: "mapped_bam_pbi", value: "m84036_250809_035451_s4.bc2185.mapped.bam.pbi"
2025-09-15 20:24:20.268 wdl.w:ptcp.t:call-pbmm2_align_hifi-88 INFO output :: name: "report", value: "mapping_stats.report.json"
2025-09-15 20:24:20.334 wdl.w:ptcp.t:call-pbmm2_align_hifi-88 NOTICE done
2025-09-15 20:24:20.341 wdl.w:ptcp NOTICE finish :: job: "call-pbmm2_align_hifi-88"
2025-09-15 20:24:20.341 wdl.w:ptcp INFO output :: job: "call-pbmm2_align_hifi-88", values: {"report": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-88/out/mapping_stats.report.json", "mapped_bam_pbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-88/out/m84036_250809_035451_s4.bc2185.mapped.bam.pbi", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-88/out/m84036_250809_035451_s4.bc2185.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-88/out/m84036_250809_035451_s4.bc2185.mapped.bam"}
2025-09-15 20:24:20.342 wdl.w:ptcp NOTICE ready :: job: "call-paraphase-88", callee: "paraphase"
2025-09-15 20:24:20.342 wdl.w:ptcp INFO input :: job: "call-paraphase-88", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf", "genome_version": "38", "config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-88/out/m84036_250809_035451_s4.bc2185.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-88/out/m84036_250809_035451_s4.bc2185.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2185"}
2025-09-15 20:24:20.343 wdl.w:ptcp NOTICE ready :: job: "call-sawfish-88", callee: "sawfish"
2025-09-15 20:24:20.343 wdl.w:ptcp INFO input :: job: "call-sawfish-88", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-88/out/m84036_250809_035451_s4.bc2185.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-88/out/m84036_250809_035451_s4.bc2185.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2185"}
2025-09-15 20:24:20.344 wdl.w:ptcp NOTICE ready :: job: "call-trgt-88", callee: "trgt"
2025-09-15 20:24:20.344 wdl.w:ptcp INFO input :: job: "call-trgt-88", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-88/out/m84036_250809_035451_s4.bc2185.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-88/out/m84036_250809_035451_s4.bc2185.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2185"}
2025-09-15 20:24:20.346 wdl.w:ptcp.w:call-paraphase-05.t:call-call_f8 NOTICE task setup :: name: "call_f8", source: "./paraphase.wdl", line: 232, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-05/call-call_f8", thread: 140607146153536
2025-09-15 20:24:20.363 wdl.w:ptcp.w:call-paraphase-05.t:call-call_f8 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:20.363 wdl.w:ptcp.w:call-paraphase-05.t:call-call_f8 INFO input :: name: "genome_version", value: "38"
2025-09-15 20:24:20.363 wdl.w:ptcp.w:call-paraphase-05.t:call-call_f8 INFO input :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2102"
2025-09-15 20:24:20.363 wdl.w:ptcp.w:call-paraphase-05.t:call-call_f8 INFO input :: name: "paraphase_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2102.paraphase.bam.bai"
2025-09-15 20:24:20.363 wdl.w:ptcp.w:call-paraphase-05.t:call-call_f8 INFO input :: name: "paraphase_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2102.paraphase.bam"
2025-09-15 20:24:20.363 wdl.w:ptcp.w:call-paraphase-05.t:call-call_f8 INFO input :: name: "sex", value: "F"
2025-09-15 20:24:20.363 wdl.w:ptcp.w:call-paraphase-05.t:call-call_f8 INFO eval :: name: "threads", value: 1
2025-09-15 20:24:20.363 wdl.w:ptcp.w:call-paraphase-05.t:call-call_f8 INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:20.364 wdl.w:ptcp.w:call-paraphase-05.t:call-call_f8 INFO eval :: name: "disk_size", value: 11
2025-09-15 20:24:20.364 wdl.w:ptcp.w:call-paraphase-05.t:call-call_f8 INFO eval :: name: "sample_sex", value: "F"
2025-09-15 20:24:20.364 wdl.w:ptcp.w:call-paraphase-05.t:call-call_f8 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:20.364 wdl.w:ptcp.w:call-paraphase-05.t:call-call_f8 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:20.364 wdl.w:ptcp.w:call-paraphase-05.t:call-call_f8 INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:20.365 wdl.w:ptcp.w:call-paraphase-05.t:call-call_f8 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:20.396 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:17 [ERROR] - No reads found for TRID=SCA37_DAB1
2025-09-15 20:24:20.396 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:17 [ERROR] - No reads found for TRID=OPDM4_RILPL1
2025-09-15 20:24:20.397 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:17 [ERROR] - No reads found for TRID=OPDM_ABCD3
2025-09-15 20:24:20.397 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:17 [ERROR] - No reads found for TRID=SCA8_ATXN8OS
2025-09-15 20:24:20.397 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:17 [ERROR] - No reads found for TRID=SCA27B_FGF14
2025-09-15 20:24:20.397 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:17 [ERROR] - No reads found for TRID=OPMD_PABPN1
2025-09-15 20:24:20.397 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:17 [ERROR] - No reads found for TRID=SCA2_ATXN2
2025-09-15 20:24:20.397 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:17 [ERROR] - No reads found for TRID=SCA3_ATXN3
2025-09-15 20:24:20.397 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:17 [ERROR] - No reads found for TRID=HDL2_JPH3
2025-09-15 20:24:20.397 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:18 [ERROR] - No reads found for TRID=FECD3_TCF4
2025-09-15 20:24:20.397 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:18 [ERROR] - No reads found for TRID=SCA6_CACNA1A
2025-09-15 20:24:20.397 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:18 [ERROR] - No reads found for TRID=OPDM2_GIPC1
2025-09-15 20:24:20.397 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:18 [ERROR] - No reads found for TRID=SCA4_ZFHX3
2025-09-15 20:24:20.397 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:18 [ERROR] - No reads found for TRID=DRPLA_ATN1
2025-09-15 20:24:20.397 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:18 [ERROR] - No reads found for TRID=SD5_HOXD13
2025-09-15 20:24:20.397 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:18 [ERROR] - No reads found for TRID=CJD_PRNP
2025-09-15 20:24:20.397 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:18 [ERROR] - No reads found for TRID=EPM1_CSTB
2025-09-15 20:24:20.397 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:18 [ERROR] - No reads found for TRID=SCA36_NOP56
2025-09-15 20:24:20.397 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:18 [ERROR] - No reads found for TRID=FRA2A_AFF3
2025-09-15 20:24:20.397 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:18 [ERROR] - No reads found for TRID=SCA31_BEAN1
2025-09-15 20:24:20.397 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:18 [ERROR] - No reads found for TRID=HD_HTT
2025-09-15 20:24:20.397 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:19 [ERROR] - No reads found for TRID=SCA7_ATXN7
2025-09-15 20:24:20.398 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:19 [ERROR] - No reads found for TRID=SCA1_ATXN1
2025-09-15 20:24:20.398 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:19 [ERROR] - No reads found for TRID=OPDM1_LRP12
2025-09-15 20:24:20.398 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:19 [ERROR] - No reads found for TRID=FAME1_SAMD12
2025-09-15 20:24:20.398 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:19 [ERROR] - No reads found for TRID=FTDALS1_C9orf72
2025-09-15 20:24:20.398 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:19 [ERROR] - No reads found for TRID=CCHS_PHOX2B
2025-09-15 20:24:20.398 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:19 [ERROR] - No reads found for TRID=SCA12_PPP2R2B
2025-09-15 20:24:20.400 wdl.w:ptcp.w:call-paraphase-05.t:call-call_f8 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 8, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-05/call-call_f8/_singularity_tmpdir_usxhvsu5"
2025-09-15 20:24:20.401 wdl.w:ptcp.w:call-paraphase-05.t:call-call_f8 INFO Slurm invocation: srun --job-name call-call_f8 --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-05/call-call_f8/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-05/call-call_f8/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-05/call-call_f8/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-05/call-call_f8/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-05/call-run_paraphase/out/m84036_250809_035451_s4.bc2102_paraphase/m84036_250809_035451_s4.bc2102.paraphase.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2102.paraphase.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-05/call-run_paraphase/out/m84036_250809_035451_s4.bc2102_paraphase/m84036_250809_035451_s4.bc2102.paraphase.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2102.paraphase.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-05/call-call_f8/_singularity_tmpdir_usxhvsu5/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-05/call-call_f8/_singularity_tmpdir_usxhvsu5/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:20.412 wdl.w:ptcp.w:call-paraphase-05.t:call-call_f8 NOTICE slurm_singularity run :: pid: 1201524, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-05/call-call_f8/slurm_singularity.log.txt"
2025-09-15 20:24:20.581 wdl.w:ptcp.w:call-paraphase-23.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for f8inv1 for sample m84036_250809_035451_s4.bc2120 at 2025-09-15 20:23:34.319836...
2025-09-15 20:24:20.582 wdl.w:ptcp.w:call-paraphase-23.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for f8inv1 for sample m84036_250809_035451_s4.bc2120 at 2025-09-15 20:23:38.784666...
2025-09-15 20:24:20.583 wdl.w:ptcp.w:call-paraphase-23.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for f8inv1 for sample m84036_250809_035451_s4.bc2120 at 2025-09-15 20:23:39.233811...
2025-09-15 20:24:20.583 wdl.w:ptcp.w:call-paraphase-23.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for cyp21 for sample m84036_250809_035451_s4.bc2120 at 2025-09-15 20:23:44.505375...
2025-09-15 20:24:20.583 wdl.w:ptcp.w:call-paraphase-23.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for cyp21 for sample m84036_250809_035451_s4.bc2120 at 2025-09-15 20:23:45.347519...
2025-09-15 20:24:20.583 wdl.w:ptcp.w:call-paraphase-23.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for hba for sample m84036_250809_035451_s4.bc2120 at 2025-09-15 20:23:47.998957...
2025-09-15 20:24:20.583 wdl.w:ptcp.w:call-paraphase-23.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for hba for sample m84036_250809_035451_s4.bc2120 at 2025-09-15 20:23:48.495850...
2025-09-15 20:24:20.583 wdl.w:ptcp.w:call-paraphase-23.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for gba for sample m84036_250809_035451_s4.bc2120 at 2025-09-15 20:23:53.713177...
2025-09-15 20:24:20.583 wdl.w:ptcp.w:call-paraphase-23.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for gba for sample m84036_250809_035451_s4.bc2120 at 2025-09-15 20:23:54.242903...
2025-09-15 20:24:20.583 wdl.w:ptcp.w:call-paraphase-23.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for hbb for sample m84036_250809_035451_s4.bc2120 at 2025-09-15 20:24:05.483281...
2025-09-15 20:24:20.583 wdl.w:ptcp.w:call-paraphase-23.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for hbb for sample m84036_250809_035451_s4.bc2120 at 2025-09-15 20:24:05.483476...
2025-09-15 20:24:20.583 wdl.w:ptcp.w:call-paraphase-23.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for hbb for sample m84036_250809_035451_s4.bc2120 at 2025-09-15 20:24:06.555462...
2025-09-15 20:24:20.624 wdl.w:ptcp.w:call-trgt-16.t:call-trgt_plot_motifs_allele.slurm_singularity INFO srun: job 51797609 queued and waiting for resources
2025-09-15 20:24:20.625 wdl.w:ptcp.w:call-trgt-16.t:call-trgt_plot_motifs_allele.slurm_singularity INFO srun: job 51797609 has been allocated resources
2025-09-15 20:24:20.625 wdl.w:ptcp.w:call-trgt-16.t:call-trgt_plot_motifs_allele.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:20.647 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:17 [ERROR] - No reads found for TRID=NIID_NOTCH2NLC
2025-09-15 20:24:20.647 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:17 [ERROR] - No reads found for TRID=SCA37_DAB1
2025-09-15 20:24:20.647 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:18 [ERROR] - No reads found for TRID=OPDM4_RILPL1
2025-09-15 20:24:20.647 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:18 [ERROR] - No reads found for TRID=OPDM_ABCD3
2025-09-15 20:24:20.647 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:18 [ERROR] - No reads found for TRID=SCA8_ATXN8OS
2025-09-15 20:24:20.647 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:18 [ERROR] - No reads found for TRID=SCA27B_FGF14
2025-09-15 20:24:20.647 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:18 [ERROR] - No reads found for TRID=OPMD_PABPN1
2025-09-15 20:24:20.648 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:18 [ERROR] - No reads found for TRID=SCA2_ATXN2
2025-09-15 20:24:20.648 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:18 [ERROR] - No reads found for TRID=SCA3_ATXN3
2025-09-15 20:24:20.648 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:18 [ERROR] - No reads found for TRID=HDL2_JPH3
2025-09-15 20:24:20.648 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:19 [ERROR] - No reads found for TRID=FECD3_TCF4
2025-09-15 20:24:20.648 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:19 [ERROR] - No reads found for TRID=SCA6_CACNA1A
2025-09-15 20:24:20.648 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:19 [ERROR] - No reads found for TRID=OPDM2_GIPC1
2025-09-15 20:24:20.648 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:19 [ERROR] - No reads found for TRID=SCA4_ZFHX3
2025-09-15 20:24:20.648 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:19 [ERROR] - No reads found for TRID=DRPLA_ATN1
2025-09-15 20:24:20.648 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:19 [ERROR] - No reads found for TRID=SD5_HOXD13
2025-09-15 20:24:20.648 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:19 [ERROR] - No reads found for TRID=CJD_PRNP
2025-09-15 20:24:20.648 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:19 [ERROR] - No reads found for TRID=EPM1_CSTB
2025-09-15 20:24:20.648 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:19 [ERROR] - No reads found for TRID=SCA36_NOP56
2025-09-15 20:24:20.648 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:20 [ERROR] - No reads found for TRID=FRA2A_AFF3
2025-09-15 20:24:20.648 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:20 [ERROR] - No reads found for TRID=SCA31_BEAN1
2025-09-15 20:24:20.648 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:20 [ERROR] - No reads found for TRID=HD_HTT
2025-09-15 20:24:20.835 wdl.w:ptcp.w:call-sawfish-12.t:call-run_sawfish.stderr VERBOSE [M::mm_idx_gen::27.978*1.42] collected minimizers
2025-09-15 20:24:20.836 wdl.w:ptcp.w:call-sawfish-12.t:call-run_sawfish.stderr VERBOSE [M::mm_idx_gen::34.779*1.71] sorted minimizers
2025-09-15 20:24:20.836 wdl.w:ptcp.w:call-sawfish-12.t:call-run_sawfish.stderr VERBOSE [M::main::34.779*1.71] loaded/built the index for 195 target sequence(s)
2025-09-15 20:24:20.836 wdl.w:ptcp.w:call-sawfish-12.t:call-run_sawfish.stderr VERBOSE [M::mm_mapopt_update::37.587*1.66] mid_occ = 136
2025-09-15 20:24:20.836 wdl.w:ptcp.w:call-sawfish-12.t:call-run_sawfish.stderr VERBOSE [M::mm_idx_stat] kmer size: 19; skip: 19; is_hpc: 0; #seq: 195
2025-09-15 20:24:20.836 wdl.w:ptcp.w:call-sawfish-12.t:call-run_sawfish.stderr VERBOSE [M::mm_idx_stat::39.935*1.62] distinct minimizers: 214664461 (92.23% are singletons); average occurrences: 1.372; average spacing: 10.529; total length: 3099922541
2025-09-15 20:24:20.836 wdl.w:ptcp.w:call-sawfish-12.t:call-run_sawfish.stderr VERBOSE [M::main] Version: 2.26-r1175
2025-09-15 20:24:20.836 wdl.w:ptcp.w:call-sawfish-12.t:call-run_sawfish.stderr VERBOSE [M::main] CMD: /opt/pacbio/smrttools/install/smrtlink-release_25.1.0.257715/bundles/smrttools/install/smrttools-release_25.1.0.257715/private/thirdparty/minimap2/minimap2_2.26-pacbio2/binwrap/../../../../../private/thirdparty/minimap2/minimap2_2.26-pacbio2/bin/minimap2 -a -y -x map-hifi -Y -E 1,0 /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa -
2025-09-15 20:24:20.836 wdl.w:ptcp.w:call-sawfish-12.t:call-run_sawfish.stderr VERBOSE [M::main] Real time: 40.173 sec; CPU: 65.005 sec; Peak RSS: 11.881 GB
2025-09-15 20:24:20.904 wdl.w:ptcp.w:call-paraphase-13.t:call-call_f8 INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2110.f8inversion.vcf"
2025-09-15 20:24:20.907 wdl.w:ptcp.w:call-paraphase-13.t:call-call_f8 INFO output :: name: "json", value: "m84036_250809_035451_s4.bc2110.f8inversion.json"
2025-09-15 20:24:20.930 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:17 [ERROR] - No reads found for TRID=SCA8_ATXN8OS
2025-09-15 20:24:20.930 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:17 [ERROR] - No reads found for TRID=SCA27B_FGF14
2025-09-15 20:24:20.930 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:18 [ERROR] - No reads found for TRID=OPMD_PABPN1
2025-09-15 20:24:20.930 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:18 [ERROR] - No reads found for TRID=SCA2_ATXN2
2025-09-15 20:24:20.930 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:18 [ERROR] - No reads found for TRID=SCA3_ATXN3
2025-09-15 20:24:20.930 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:18 [ERROR] - No reads found for TRID=HDL2_JPH3
2025-09-15 20:24:20.930 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:18 [ERROR] - No reads found for TRID=FECD3_TCF4
2025-09-15 20:24:20.930 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:18 [ERROR] - No reads found for TRID=SCA6_CACNA1A
2025-09-15 20:24:20.931 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:18 [ERROR] - No reads found for TRID=OPDM2_GIPC1
2025-09-15 20:24:20.931 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:18 [ERROR] - No reads found for TRID=SCA4_ZFHX3
2025-09-15 20:24:20.931 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:18 [ERROR] - No reads found for TRID=DRPLA_ATN1
2025-09-15 20:24:20.931 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:18 [ERROR] - No reads found for TRID=SD5_HOXD13
2025-09-15 20:24:20.931 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:18 [ERROR] - No reads found for TRID=CJD_PRNP
2025-09-15 20:24:20.931 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:18 [ERROR] - No reads found for TRID=EPM1_CSTB
2025-09-15 20:24:20.931 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:18 [ERROR] - No reads found for TRID=SCA36_NOP56
2025-09-15 20:24:20.931 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:19 [ERROR] - No reads found for TRID=FRA2A_AFF3
2025-09-15 20:24:20.931 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:19 [ERROR] - No reads found for TRID=SCA31_BEAN1
2025-09-15 20:24:20.931 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:19 [ERROR] - No reads found for TRID=HD_HTT
2025-09-15 20:24:20.931 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:19 [ERROR] - No reads found for TRID=SCA7_ATXN7
2025-09-15 20:24:20.931 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:19 [ERROR] - No reads found for TRID=SCA1_ATXN1
2025-09-15 20:24:20.931 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:19 [ERROR] - No reads found for TRID=OPDM1_LRP12
2025-09-15 20:24:20.931 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:19 [ERROR] - No reads found for TRID=FAME1_SAMD12
2025-09-15 20:24:20.931 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:19 [ERROR] - No reads found for TRID=FTDALS1_C9orf72
2025-09-15 20:24:20.931 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:19 [ERROR] - No reads found for TRID=CCHS_PHOX2B
2025-09-15 20:24:20.931 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:20 [ERROR] - No reads found for TRID=SCA12_PPP2R2B
2025-09-15 20:24:20.972 wdl.w:ptcp.w:call-paraphase-13.t:call-call_f8 NOTICE done
2025-09-15 20:24:20.974 wdl.w:ptcp.w:call-trgt-33.t:call-trgt_plot_meth_waterfall INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2130.meth_waterfall.trgt_plots.zip"
2025-09-15 20:24:20.977 wdl.w:ptcp.w:call-paraphase-13 NOTICE finish :: job: "call-call_f8"
2025-09-15 20:24:20.977 wdl.w:ptcp.w:call-paraphase-13 INFO output :: job: "call-call_f8", values: {"json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-13/call-call_f8/out/m84036_250809_035451_s4.bc2110.f8inversion.json", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-13/call-call_f8/out/m84036_250809_035451_s4.bc2110.f8inversion.vcf"}
2025-09-15 20:24:20.978 wdl.w:ptcp.w:call-paraphase-13 INFO visit :: node: "output-f8_json", values: {"f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-13/call-call_f8/out/m84036_250809_035451_s4.bc2110.f8inversion.json"}
2025-09-15 20:24:20.978 wdl.w:ptcp.w:call-paraphase-13 INFO visit :: node: "output-f8_vcf", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-13/call-call_f8/out/m84036_250809_035451_s4.bc2110.f8inversion.vcf"}
2025-09-15 20:24:20.978 wdl.w:ptcp.w:call-paraphase-13 INFO visit :: node: "outputs", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-13/call-call_f8/out/m84036_250809_035451_s4.bc2110.f8inversion.vcf", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-13/call-run_paraphase/out/m84036_250809_035451_s4.bc2110_paraphase/m84036_250809_035451_s4.bc2110.paraphase.json", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-13/call-run_paraphase/out/m84036_250809_035451_s4.bc2110_paraphase/m84036_250809_035451_s4.bc2110.paraphase.bam", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-13/call-run_paraphase/out/m84036_250809_035451_s4.bc2110_paraphase/m84036_250809_035451_s4.bc2110.paraphase.bam.bai", "paraphase_vcfs": [], "havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-13/call-run_paraphase/out/m84036_250809_035451_s4.bc2110.havanno.json", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-13/call-call_f8/out/m84036_250809_035451_s4.bc2110.f8inversion.json"}
2025-09-15 20:24:20.987 wdl.w:ptcp.w:call-trgt-25.t:call-trgt_plot_meth_allele NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-25/call-trgt_plot_meth_allele", thread: 140607129368128
2025-09-15 20:24:21.011 wdl.w:ptcp.w:call-trgt-25.t:call-trgt_plot_meth_allele INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:21.011 wdl.w:ptcp.w:call-trgt-25.t:call-trgt_plot_meth_allele INFO input :: name: "waterfall", value: false
2025-09-15 20:24:21.012 wdl.w:ptcp.w:call-trgt-25.t:call-trgt_plot_meth_allele INFO input :: name: "methylation", value: true
2025-09-15 20:24:21.012 wdl.w:ptcp.w:call-trgt-25.t:call-trgt_plot_meth_allele INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:21.012 wdl.w:ptcp.w:call-trgt-25.t:call-trgt_plot_meth_allele INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:21.012 wdl.w:ptcp.w:call-trgt-25.t:call-trgt_plot_meth_allele INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:21.012 wdl.w:ptcp.w:call-trgt-25.t:call-trgt_plot_meth_allele INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2122.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:21.012 wdl.w:ptcp.w:call-trgt-25.t:call-trgt_plot_meth_allele INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2122.trgt.sorted.spanning.bam"
2025-09-15 20:24:21.012 wdl.w:ptcp.w:call-trgt-25.t:call-trgt_plot_meth_allele INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2122.trgt.vcf"
2025-09-15 20:24:21.012 wdl.w:ptcp.w:call-trgt-25.t:call-trgt_plot_meth_allele INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2122"
2025-09-15 20:24:21.012 wdl.w:ptcp.w:call-trgt-25.t:call-trgt_plot_meth_allele INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:21.013 wdl.w:ptcp.w:call-trgt-25.t:call-trgt_plot_meth_allele INFO eval :: name: "plot_type", value: "allele"
2025-09-15 20:24:21.013 wdl.w:ptcp.w:call-trgt-25.t:call-trgt_plot_meth_allele INFO eval :: name: "show", value: "meth"
2025-09-15 20:24:21.013 wdl.w:ptcp.w:call-trgt-25.t:call-trgt_plot_meth_allele INFO eval :: name: "threads", value: 1
2025-09-15 20:24:21.013 wdl.w:ptcp.w:call-trgt-25.t:call-trgt_plot_meth_allele INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:21.013 wdl.w:ptcp.w:call-trgt-25.t:call-trgt_plot_meth_allele INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2122.meth_allele"
2025-09-15 20:24:21.014 wdl.w:ptcp.w:call-trgt-25.t:call-trgt_plot_meth_allele INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:21.014 wdl.w:ptcp.w:call-trgt-25.t:call-trgt_plot_meth_allele WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:21.014 wdl.w:ptcp.w:call-trgt-25.t:call-trgt_plot_meth_allele INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:21.014 wdl.w:ptcp.w:call-trgt-25.t:call-trgt_plot_meth_allele INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:21.048 wdl.w:ptcp.w:call-paraphase-13 NOTICE done
2025-09-15 20:24:21.054 wdl.w:ptcp NOTICE finish :: job: "call-paraphase-13"
2025-09-15 20:24:21.055 wdl.w:ptcp INFO output :: job: "call-paraphase-13", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-13/out/m84036_250809_035451_s4.bc2110.f8inversion.vcf", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-13/out/m84036_250809_035451_s4.bc2110_paraphase/m84036_250809_035451_s4.bc2110.paraphase.json", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-13/out/m84036_250809_035451_s4.bc2110_paraphase/m84036_250809_035451_s4.bc2110.paraphase.bam", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-13/out/m84036_250809_035451_s4.bc2110_paraphase/m84036_250809_035451_s4.bc2110.paraphase.bam.bai", "paraphase_vcfs": [], "havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-13/out/m84036_250809_035451_s4.bc2110.havanno.json", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-13/out/m84036_250809_035451_s4.bc2110.f8inversion.json"}
2025-09-15 20:24:21.062 wdl.w:ptcp.w:call-trgt-62 NOTICE workflow start :: name: "trgt", source: "./trgt.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-62"
2025-09-15 20:24:21.081 wdl.w:ptcp.w:call-trgt-62 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:24:21.081 wdl.w:ptcp.w:call-trgt-62 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-62/out/m84036_250809_035451_s4.bc2159.mapped.bam"}
2025-09-15 20:24:21.081 wdl.w:ptcp.w:call-trgt-62 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-62/out/m84036_250809_035451_s4.bc2159.mapped.bam.bai"}
2025-09-15 20:24:21.081 wdl.w:ptcp.w:call-trgt-62 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:24:21.081 wdl.w:ptcp.w:call-trgt-62 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:24:21.081 wdl.w:ptcp.w:call-trgt-62 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2159"}
2025-09-15 20:24:21.082 wdl.w:ptcp.w:call-trgt-62 INFO visit :: node: "decl-sex", values: {"sex": "F"}
2025-09-15 20:24:21.082 wdl.w:ptcp.w:call-trgt-62 INFO visit :: node: "decl-trgt_bed", values: {"trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"}
2025-09-15 20:24:21.082 wdl.w:ptcp.w:call-trgt-62 NOTICE ready :: job: "call-get_reads_overlapping_repeats", callee: "get_reads_overlapping_repeats"
2025-09-15 20:24:21.082 wdl.w:ptcp.w:call-trgt-62 INFO input :: job: "call-get_reads_overlapping_repeats", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-62/out/m84036_250809_035451_s4.bc2159.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-62/out/m84036_250809_035451_s4.bc2159.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2159"}
2025-09-15 20:24:21.083 wdl.w:ptcp.w:call-trgt-62 NOTICE ready :: job: "call-trgt_genotype", callee: "trgt_genotype"
2025-09-15 20:24:21.083 wdl.w:ptcp.w:call-trgt-62 INFO input :: job: "call-trgt_genotype", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-62/out/m84036_250809_035451_s4.bc2159.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-62/out/m84036_250809_035451_s4.bc2159.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2159"}
2025-09-15 20:24:21.109 wdl.w:ptcp.w:call-trgt-25.t:call-trgt_plot_meth_allele INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-25/call-trgt_plot_meth_allele/_singularity_tmpdir_uviscy3m"
2025-09-15 20:24:21.109 wdl.w:ptcp.w:call-trgt-25.t:call-trgt_plot_meth_allele INFO Slurm invocation: srun --job-name call-trgt_plot_meth_allele --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-25/call-trgt_plot_meth_allele/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-25/call-trgt_plot_meth_allele/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-25/call-trgt_plot_meth_allele/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-25/call-trgt_plot_meth_allele/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-25/call-trgt_genotype/out/m84036_250809_035451_s4.bc2122.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2122.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-25/call-trgt_genotype/out/m84036_250809_035451_s4.bc2122.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2122.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-25/call-trgt_genotype/out/m84036_250809_035451_s4.bc2122.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2122.trgt.sorted.spanning.bam:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-25/call-trgt_plot_meth_allele/_singularity_tmpdir_uviscy3m/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-25/call-trgt_plot_meth_allele/_singularity_tmpdir_uviscy3m/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:21.129 wdl.w:ptcp.w:call-trgt-16.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO srun: job 51797610 queued and waiting for resources
2025-09-15 20:24:21.129 wdl.w:ptcp.w:call-trgt-16.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO srun: job 51797610 has been allocated resources
2025-09-15 20:24:21.129 wdl.w:ptcp.w:call-trgt-16.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:21.134 wdl.w:ptcp.w:call-trgt-33.t:call-trgt_plot_meth_waterfall NOTICE done
2025-09-15 20:24:21.139 wdl.w:ptcp.w:call-trgt-33 NOTICE finish :: job: "call-trgt_plot_meth_waterfall"
2025-09-15 20:24:21.139 wdl.w:ptcp.w:call-trgt-33 INFO output :: job: "call-trgt_plot_meth_waterfall", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-33/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2130.meth_waterfall.trgt_plots.zip"}
2025-09-15 20:24:21.139 wdl.w:ptcp.w:call-trgt-33 INFO visit :: node: "output-images_meth_waterfall", values: {"images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-33/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2130.meth_waterfall.trgt_plots.zip"}
2025-09-15 20:24:21.143 wdl.w:ptcp.w:call-trgt-25.t:call-trgt_plot_meth_allele NOTICE slurm_singularity run :: pid: 1201538, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-25/call-trgt_plot_meth_allele/slurm_singularity.log.txt"
2025-09-15 20:24:21.146 wdl.w:ptcp.w:call-trgt-25.t:call-trgt_plot_meth_waterfall NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-25/call-trgt_plot_meth_waterfall", thread: 140608236680768
2025-09-15 20:24:21.162 wdl.w:ptcp.w:call-trgt-25.t:call-trgt_plot_meth_waterfall INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:21.162 wdl.w:ptcp.w:call-trgt-25.t:call-trgt_plot_meth_waterfall INFO input :: name: "waterfall", value: true
2025-09-15 20:24:21.162 wdl.w:ptcp.w:call-trgt-25.t:call-trgt_plot_meth_waterfall INFO input :: name: "methylation", value: true
2025-09-15 20:24:21.162 wdl.w:ptcp.w:call-trgt-25.t:call-trgt_plot_meth_waterfall INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:21.162 wdl.w:ptcp.w:call-trgt-25.t:call-trgt_plot_meth_waterfall INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:21.163 wdl.w:ptcp.w:call-trgt-25.t:call-trgt_plot_meth_waterfall INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:21.163 wdl.w:ptcp.w:call-trgt-25.t:call-trgt_plot_meth_waterfall INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2122.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:21.163 wdl.w:ptcp.w:call-trgt-25.t:call-trgt_plot_meth_waterfall INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2122.trgt.sorted.spanning.bam"
2025-09-15 20:24:21.163 wdl.w:ptcp.w:call-trgt-25.t:call-trgt_plot_meth_waterfall INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2122.trgt.vcf"
2025-09-15 20:24:21.163 wdl.w:ptcp.w:call-trgt-25.t:call-trgt_plot_meth_waterfall INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2122"
2025-09-15 20:24:21.163 wdl.w:ptcp.w:call-trgt-25.t:call-trgt_plot_meth_waterfall INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:21.163 wdl.w:ptcp.w:call-trgt-25.t:call-trgt_plot_meth_waterfall INFO eval :: name: "plot_type", value: "waterfall"
2025-09-15 20:24:21.163 wdl.w:ptcp.w:call-trgt-25.t:call-trgt_plot_meth_waterfall INFO eval :: name: "show", value: "meth"
2025-09-15 20:24:21.163 wdl.w:ptcp.w:call-trgt-25.t:call-trgt_plot_meth_waterfall INFO eval :: name: "threads", value: 1
2025-09-15 20:24:21.164 wdl.w:ptcp.w:call-trgt-25.t:call-trgt_plot_meth_waterfall INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:21.164 wdl.w:ptcp.w:call-trgt-25.t:call-trgt_plot_meth_waterfall INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2122.meth_waterfall"
2025-09-15 20:24:21.164 wdl.w:ptcp.w:call-trgt-25.t:call-trgt_plot_meth_waterfall INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:21.164 wdl.w:ptcp.w:call-trgt-25.t:call-trgt_plot_meth_waterfall WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:21.164 wdl.w:ptcp.w:call-trgt-25.t:call-trgt_plot_meth_waterfall INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:21.165 wdl.w:ptcp.w:call-trgt-25.t:call-trgt_plot_meth_waterfall INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:21.229 wdl.w:ptcp.w:call-trgt-25.t:call-trgt_plot_meth_waterfall INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-25/call-trgt_plot_meth_waterfall/_singularity_tmpdir_rbu6lqf7"
2025-09-15 20:24:21.229 wdl.w:ptcp.w:call-trgt-25.t:call-trgt_plot_meth_waterfall INFO Slurm invocation: srun --job-name call-trgt_plot_meth_waterfall --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-25/call-trgt_plot_meth_waterfall/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-25/call-trgt_plot_meth_waterfall/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-25/call-trgt_plot_meth_waterfall/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-25/call-trgt_plot_meth_waterfall/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-25/call-trgt_genotype/out/m84036_250809_035451_s4.bc2122.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2122.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-25/call-trgt_genotype/out/m84036_250809_035451_s4.bc2122.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2122.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-25/call-trgt_genotype/out/m84036_250809_035451_s4.bc2122.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2122.trgt.sorted.spanning.bam:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-25/call-trgt_plot_meth_waterfall/_singularity_tmpdir_rbu6lqf7/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-25/call-trgt_plot_meth_waterfall/_singularity_tmpdir_rbu6lqf7/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:21.240 wdl.w:ptcp.w:call-trgt-25.t:call-trgt_plot_meth_waterfall NOTICE slurm_singularity run :: pid: 1201541, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-25/call-trgt_plot_meth_waterfall/slurm_singularity.log.txt"
2025-09-15 20:24:21.245 wdl.w:ptcp.w:call-paraphase-33.t:call-call_f8.slurm_singularity INFO srun: job 51797611 queued and waiting for resources
2025-09-15 20:24:21.245 wdl.w:ptcp.w:call-paraphase-33.t:call-call_f8.slurm_singularity INFO srun: job 51797611 has been allocated resources
2025-09-15 20:24:21.245 wdl.w:ptcp.w:call-paraphase-33.t:call-call_f8.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:21.316 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_meth_allele INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2124.meth_allele.trgt_plots.zip"
2025-09-15 20:24:21.332 wdl.w:ptcp.w:call-trgt-24.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:20 [ERROR] - No reads found for TRID=PRTS_ARX
2025-09-15 20:24:21.333 wdl.w:ptcp.w:call-trgt-24.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:20 [ERROR] - No reads found for TRID=EIEE1_ARX
2025-09-15 20:24:21.381 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_meth_allele NOTICE done
2025-09-15 20:24:21.386 wdl.w:ptcp.w:call-trgt-27 NOTICE finish :: job: "call-trgt_plot_meth_allele"
2025-09-15 20:24:21.387 wdl.w:ptcp.w:call-trgt-27 INFO output :: job: "call-trgt_plot_meth_allele", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-27/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2124.meth_allele.trgt_plots.zip"}
2025-09-15 20:24:21.387 wdl.w:ptcp.w:call-trgt-27 INFO visit :: node: "output-images_meth_allele", values: {"images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-27/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2124.meth_allele.trgt_plots.zip"}
2025-09-15 20:24:21.391 wdl.w:ptcp.w:call-trgt-25.t:call-trgt_plot_motifs_allele NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-25/call-trgt_plot_motifs_allele", thread: 140608228288064
2025-09-15 20:24:21.407 wdl.w:ptcp.w:call-trgt-25.t:call-trgt_plot_motifs_allele INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:21.407 wdl.w:ptcp.w:call-trgt-25.t:call-trgt_plot_motifs_allele INFO input :: name: "waterfall", value: false
2025-09-15 20:24:21.408 wdl.w:ptcp.w:call-trgt-25.t:call-trgt_plot_motifs_allele INFO input :: name: "methylation", value: false
2025-09-15 20:24:21.408 wdl.w:ptcp.w:call-trgt-25.t:call-trgt_plot_motifs_allele INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:21.408 wdl.w:ptcp.w:call-trgt-25.t:call-trgt_plot_motifs_allele INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:21.408 wdl.w:ptcp.w:call-trgt-25.t:call-trgt_plot_motifs_allele INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:21.408 wdl.w:ptcp.w:call-trgt-25.t:call-trgt_plot_motifs_allele INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2122.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:21.408 wdl.w:ptcp.w:call-trgt-25.t:call-trgt_plot_motifs_allele INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2122.trgt.sorted.spanning.bam"
2025-09-15 20:24:21.408 wdl.w:ptcp.w:call-trgt-25.t:call-trgt_plot_motifs_allele INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2122.trgt.vcf"
2025-09-15 20:24:21.408 wdl.w:ptcp.w:call-trgt-25.t:call-trgt_plot_motifs_allele INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2122"
2025-09-15 20:24:21.408 wdl.w:ptcp.w:call-trgt-25.t:call-trgt_plot_motifs_allele INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:21.408 wdl.w:ptcp.w:call-trgt-25.t:call-trgt_plot_motifs_allele INFO eval :: name: "plot_type", value: "allele"
2025-09-15 20:24:21.408 wdl.w:ptcp.w:call-trgt-25.t:call-trgt_plot_motifs_allele INFO eval :: name: "show", value: "motifs"
2025-09-15 20:24:21.408 wdl.w:ptcp.w:call-trgt-25.t:call-trgt_plot_motifs_allele INFO eval :: name: "threads", value: 1
2025-09-15 20:24:21.409 wdl.w:ptcp.w:call-trgt-25.t:call-trgt_plot_motifs_allele INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:21.409 wdl.w:ptcp.w:call-trgt-25.t:call-trgt_plot_motifs_allele INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2122.motifs_allele"
2025-09-15 20:24:21.409 wdl.w:ptcp.w:call-trgt-25.t:call-trgt_plot_motifs_allele INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:21.409 wdl.w:ptcp.w:call-trgt-25.t:call-trgt_plot_motifs_allele WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:21.410 wdl.w:ptcp.w:call-trgt-25.t:call-trgt_plot_motifs_allele INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:21.410 wdl.w:ptcp.w:call-trgt-25.t:call-trgt_plot_motifs_allele INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:21.423 wdl.w:ptcp.w:call-paraphase-05.t:call-call_f8.slurm_singularity INFO srun: job 51797612 queued and waiting for resources
2025-09-15 20:24:21.424 wdl.w:ptcp.w:call-paraphase-05.t:call-call_f8.slurm_singularity INFO srun: job 51797612 has been allocated resources
2025-09-15 20:24:21.424 wdl.w:ptcp.w:call-paraphase-05.t:call-call_f8.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:21.470 wdl.w:ptcp.w:call-sawfish-21.t:call-run_sawfish.stderr VERBOSE [M::mm_idx_gen::42.867*1.68] sorted minimizers
2025-09-15 20:24:21.470 wdl.w:ptcp.w:call-sawfish-21.t:call-run_sawfish.stderr VERBOSE [M::main::42.867*1.68] loaded/built the index for 195 target sequence(s)
2025-09-15 20:24:21.470 wdl.w:ptcp.w:call-sawfish-21.t:call-run_sawfish.stderr VERBOSE [M::mm_mapopt_update::46.063*1.64] mid_occ = 136
2025-09-15 20:24:21.470 wdl.w:ptcp.w:call-sawfish-21.t:call-run_sawfish.stderr VERBOSE [M::mm_idx_stat] kmer size: 19; skip: 19; is_hpc: 0; #seq: 195
2025-09-15 20:24:21.470 wdl.w:ptcp.w:call-sawfish-21.t:call-run_sawfish.stderr VERBOSE [M::mm_idx_stat::48.847*1.60] distinct minimizers: 214664461 (92.23% are singletons); average occurrences: 1.372; average spacing: 10.529; total length: 3099922541
2025-09-15 20:24:21.470 wdl.w:ptcp.w:call-sawfish-21.t:call-run_sawfish.stderr VERBOSE [M::main] Version: 2.26-r1175
2025-09-15 20:24:21.470 wdl.w:ptcp.w:call-sawfish-21.t:call-run_sawfish.stderr VERBOSE [M::main] CMD: /opt/pacbio/smrttools/install/smrtlink-release_25.1.0.257715/bundles/smrttools/install/smrttools-release_25.1.0.257715/private/thirdparty/minimap2/minimap2_2.26-pacbio2/binwrap/../../../../../private/thirdparty/minimap2/minimap2_2.26-pacbio2/bin/minimap2 -a -y -x map-hifi -Y -E 1,0 /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa -
2025-09-15 20:24:21.470 wdl.w:ptcp.w:call-sawfish-21.t:call-run_sawfish.stderr VERBOSE [M::main] Real time: 49.174 sec; CPU: 78.448 sec; Peak RSS: 11.884 GB
2025-09-15 20:24:21.476 wdl.w:ptcp.w:call-trgt-25.t:call-trgt_plot_motifs_allele INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-25/call-trgt_plot_motifs_allele/_singularity_tmpdir_jushp9tj"
2025-09-15 20:24:21.476 wdl.w:ptcp.w:call-trgt-25.t:call-trgt_plot_motifs_allele INFO Slurm invocation: srun --job-name call-trgt_plot_motifs_allele --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-25/call-trgt_plot_motifs_allele/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-25/call-trgt_plot_motifs_allele/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-25/call-trgt_plot_motifs_allele/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-25/call-trgt_plot_motifs_allele/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-25/call-trgt_genotype/out/m84036_250809_035451_s4.bc2122.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2122.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-25/call-trgt_genotype/out/m84036_250809_035451_s4.bc2122.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2122.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-25/call-trgt_genotype/out/m84036_250809_035451_s4.bc2122.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2122.trgt.sorted.spanning.bam:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-25/call-trgt_plot_motifs_allele/_singularity_tmpdir_jushp9tj/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-25/call-trgt_plot_motifs_allele/_singularity_tmpdir_jushp9tj/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:21.479 wdl.w:ptcp.w:call-sawfish-22.t:call-run_sawfish.stderr VERBOSE [M::mm_idx_gen::49.249*1.67] collected minimizers
2025-09-15 20:24:21.480 wdl.w:ptcp.w:call-sawfish-22.t:call-run_sawfish.stderr VERBOSE [M::mm_idx_gen::60.714*1.90] sorted minimizers
2025-09-15 20:24:21.480 wdl.w:ptcp.w:call-sawfish-22.t:call-run_sawfish.stderr VERBOSE [M::main::60.715*1.90] loaded/built the index for 195 target sequence(s)
2025-09-15 20:24:21.480 wdl.w:ptcp.w:call-sawfish-22.t:call-run_sawfish.stderr VERBOSE [M::mm_mapopt_update::68.366*1.80] mid_occ = 136
2025-09-15 20:24:21.480 wdl.w:ptcp.w:call-sawfish-22.t:call-run_sawfish.stderr VERBOSE [M::mm_idx_stat] kmer size: 19; skip: 19; is_hpc: 0; #seq: 195
2025-09-15 20:24:21.480 wdl.w:ptcp.w:call-sawfish-22.t:call-run_sawfish.stderr VERBOSE [M::mm_idx_stat::73.477*1.75] distinct minimizers: 214664461 (92.23% are singletons); average occurrences: 1.372; average spacing: 10.529; total length: 3099922541
2025-09-15 20:24:21.480 wdl.w:ptcp.w:call-sawfish-22.t:call-run_sawfish.stderr VERBOSE [M::bam2fq_mainloop] discarded 0 singletons
2025-09-15 20:24:21.480 wdl.w:ptcp.w:call-sawfish-22.t:call-run_sawfish.stderr VERBOSE [M::bam2fq_mainloop] processed 221 reads
2025-09-15 20:24:21.480 wdl.w:ptcp.w:call-sawfish-22.t:call-run_sawfish.stderr VERBOSE [M::worker_pipeline::73.914*1.75] mapped 221 sequences
2025-09-15 20:24:21.480 wdl.w:ptcp.w:call-sawfish-22.t:call-run_sawfish.stderr VERBOSE [M::main] Version: 2.26-r1175
2025-09-15 20:24:21.480 wdl.w:ptcp.w:call-sawfish-22.t:call-run_sawfish.stderr VERBOSE [M::main] CMD: /opt/pacbio/smrttools/install/smrtlink-release_25.1.0.257715/bundles/smrttools/install/smrttools-release_25.1.0.257715/private/thirdparty/minimap2/minimap2_2.26-pacbio2/binwrap/../../../../../private/thirdparty/minimap2/minimap2_2.26-pacbio2/bin/minimap2 -a -y -x map-hifi -Y -E 1,0 /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa -
2025-09-15 20:24:21.480 wdl.w:ptcp.w:call-sawfish-22.t:call-run_sawfish.stderr VERBOSE [M::main] Real time: 74.299 sec; CPU: 129.707 sec; Peak RSS: 11.886 GB
2025-09-15 20:24:21.487 wdl.w:ptcp.w:call-paraphase-14.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for hbb for sample m84036_250809_035451_s4.bc2111 at 2025-09-15 20:24:13.324230...
2025-09-15 20:24:21.492 wdl.w:ptcp.w:call-sawfish-14.t:call-run_sawfish.stderr VERBOSE [M::mm_idx_gen::72.041*1.67] collected minimizers
2025-09-15 20:24:21.493 wdl.w:ptcp.w:call-sawfish-05.t:call-run_sawfish.stderr VERBOSE [M::mm_idx_gen::32.852*1.44] collected minimizers
2025-09-15 20:24:21.495 wdl.w:ptcp.w:call-sawfish-05.t:call-run_sawfish.stderr VERBOSE [M::mm_idx_gen::39.419*1.69] sorted minimizers
2025-09-15 20:24:21.495 wdl.w:ptcp.w:call-sawfish-05.t:call-run_sawfish.stderr VERBOSE [M::main::39.419*1.69] loaded/built the index for 195 target sequence(s)
2025-09-15 20:24:21.495 wdl.w:ptcp.w:call-sawfish-05.t:call-run_sawfish.stderr VERBOSE [M::mm_mapopt_update::42.410*1.64] mid_occ = 136
2025-09-15 20:24:21.495 wdl.w:ptcp.w:call-sawfish-05.t:call-run_sawfish.stderr VERBOSE [M::mm_idx_stat] kmer size: 19; skip: 19; is_hpc: 0; #seq: 195
2025-09-15 20:24:21.495 wdl.w:ptcp.w:call-sawfish-05.t:call-run_sawfish.stderr VERBOSE [M::mm_idx_stat::44.979*1.61] distinct minimizers: 214664461 (92.23% are singletons); average occurrences: 1.372; average spacing: 10.529; total length: 3099922541
2025-09-15 20:24:21.495 wdl.w:ptcp.w:call-sawfish-05.t:call-run_sawfish.stderr VERBOSE [M::main] Version: 2.26-r1175
2025-09-15 20:24:21.495 wdl.w:ptcp.w:call-sawfish-05.t:call-run_sawfish.stderr VERBOSE [M::main] CMD: /opt/pacbio/smrttools/install/smrtlink-release_25.1.0.257715/bundles/smrttools/install/smrttools-release_25.1.0.257715/private/thirdparty/minimap2/minimap2_2.26-pacbio2/binwrap/../../../../../private/thirdparty/minimap2/minimap2_2.26-pacbio2/bin/minimap2 -a -y -x map-hifi -Y -E 1,0 /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa -
2025-09-15 20:24:21.495 wdl.w:ptcp.w:call-sawfish-05.t:call-run_sawfish.stderr VERBOSE [M::main] Real time: 45.276 sec; CPU: 72.497 sec; Peak RSS: 11.886 GB
2025-09-15 20:24:21.516 wdl.w:ptcp.w:call-trgt-25.t:call-trgt_plot_motifs_allele NOTICE slurm_singularity run :: pid: 1201548, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-25/call-trgt_plot_motifs_allele/slurm_singularity.log.txt"
2025-09-15 20:24:21.595 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_motifs_allele INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2124.motifs_allele.trgt_plots.zip"
2025-09-15 20:24:21.632 wdl.w:ptcp.w:call-sawfish-13.t:call-run_sawfish.stderr VERBOSE [M::mm_idx_gen::32.785*1.45] collected minimizers
2025-09-15 20:24:21.635 wdl.w:ptcp.w:call-sawfish-13.t:call-run_sawfish.stderr VERBOSE [M::mm_idx_gen::39.356*1.70] sorted minimizers
2025-09-15 20:24:21.635 wdl.w:ptcp.w:call-sawfish-13.t:call-run_sawfish.stderr VERBOSE [M::main::39.356*1.70] loaded/built the index for 195 target sequence(s)
2025-09-15 20:24:21.635 wdl.w:ptcp.w:call-sawfish-13.t:call-run_sawfish.stderr VERBOSE [M::mm_mapopt_update::42.283*1.65] mid_occ = 136
2025-09-15 20:24:21.635 wdl.w:ptcp.w:call-sawfish-13.t:call-run_sawfish.stderr VERBOSE [M::mm_idx_stat] kmer size: 19; skip: 19; is_hpc: 0; #seq: 195
2025-09-15 20:24:21.635 wdl.w:ptcp.w:call-sawfish-13.t:call-run_sawfish.stderr VERBOSE [M::mm_idx_stat::44.824*1.61] distinct minimizers: 214664461 (92.23% are singletons); average occurrences: 1.372; average spacing: 10.529; total length: 3099922541
2025-09-15 20:24:21.635 wdl.w:ptcp.w:call-sawfish-13.t:call-run_sawfish.stderr VERBOSE [M::main] Version: 2.26-r1175
2025-09-15 20:24:21.635 wdl.w:ptcp.w:call-sawfish-13.t:call-run_sawfish.stderr VERBOSE [M::main] CMD: /opt/pacbio/smrttools/install/smrtlink-release_25.1.0.257715/bundles/smrttools/install/smrttools-release_25.1.0.257715/private/thirdparty/minimap2/minimap2_2.26-pacbio2/binwrap/../../../../../private/thirdparty/minimap2/minimap2_2.26-pacbio2/bin/minimap2 -a -y -x map-hifi -Y -E 1,0 /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa -
2025-09-15 20:24:21.635 wdl.w:ptcp.w:call-sawfish-13.t:call-run_sawfish.stderr VERBOSE [M::main] Real time: 45.135 sec; CPU: 72.517 sec; Peak RSS: 11.886 GB
2025-09-15 20:24:21.664 wdl.w:ptcp.w:call-trgt-12.t:call-trgt_plot_meth_allele INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2109.meth_allele.trgt_plots.zip"
2025-09-15 20:24:21.695 wdl.w:ptcp.w:call-trgt-33.t:call-trgt_plot_meth_allele INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2130.meth_allele.trgt_plots.zip"
2025-09-15 20:24:21.703 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_motifs_allele NOTICE done
2025-09-15 20:24:21.708 wdl.w:ptcp.w:call-trgt-27 NOTICE finish :: job: "call-trgt_plot_motifs_allele"
2025-09-15 20:24:21.708 wdl.w:ptcp.w:call-trgt-27 INFO output :: job: "call-trgt_plot_motifs_allele", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-27/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2124.motifs_allele.trgt_plots.zip"}
2025-09-15 20:24:21.708 wdl.w:ptcp.w:call-trgt-27 INFO visit :: node: "output-images_motifs_allele", values: {"images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-27/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2124.motifs_allele.trgt_plots.zip"}
2025-09-15 20:24:21.709 wdl.w:ptcp.w:call-paraphase-03.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for smn1 for sample m84036_250809_035451_s4.bc2100 at 2025-09-15 20:24:02.975505...
2025-09-15 20:24:21.721 wdl.w:ptcp.w:call-trgt-25.t:call-trgt_plot_motifs_waterfall NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-25/call-trgt_plot_motifs_waterfall", thread: 140610887464512
2025-09-15 20:24:21.743 wdl.w:ptcp.w:call-trgt-25.t:call-trgt_plot_motifs_waterfall INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:21.743 wdl.w:ptcp.w:call-trgt-25.t:call-trgt_plot_motifs_waterfall INFO input :: name: "waterfall", value: true
2025-09-15 20:24:21.743 wdl.w:ptcp.w:call-trgt-25.t:call-trgt_plot_motifs_waterfall INFO input :: name: "methylation", value: false
2025-09-15 20:24:21.743 wdl.w:ptcp.w:call-trgt-25.t:call-trgt_plot_motifs_waterfall INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:21.743 wdl.w:ptcp.w:call-trgt-25.t:call-trgt_plot_motifs_waterfall INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:21.743 wdl.w:ptcp.w:call-trgt-25.t:call-trgt_plot_motifs_waterfall INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:21.743 wdl.w:ptcp.w:call-trgt-25.t:call-trgt_plot_motifs_waterfall INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2122.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:21.743 wdl.w:ptcp.w:call-trgt-25.t:call-trgt_plot_motifs_waterfall INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2122.trgt.sorted.spanning.bam"
2025-09-15 20:24:21.743 wdl.w:ptcp.w:call-trgt-25.t:call-trgt_plot_motifs_waterfall INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2122.trgt.vcf"
2025-09-15 20:24:21.743 wdl.w:ptcp.w:call-trgt-25.t:call-trgt_plot_motifs_waterfall INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2122"
2025-09-15 20:24:21.744 wdl.w:ptcp.w:call-trgt-25.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:21.744 wdl.w:ptcp.w:call-trgt-25.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "plot_type", value: "waterfall"
2025-09-15 20:24:21.744 wdl.w:ptcp.w:call-trgt-25.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "show", value: "motifs"
2025-09-15 20:24:21.744 wdl.w:ptcp.w:call-trgt-25.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "threads", value: 1
2025-09-15 20:24:21.745 wdl.w:ptcp.w:call-trgt-25.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:21.745 wdl.w:ptcp.w:call-trgt-25.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2122.motifs_waterfall"
2025-09-15 20:24:21.745 wdl.w:ptcp.w:call-trgt-25.t:call-trgt_plot_motifs_waterfall INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:21.745 wdl.w:ptcp.w:call-trgt-25.t:call-trgt_plot_motifs_waterfall WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:21.745 wdl.w:ptcp.w:call-trgt-25.t:call-trgt_plot_motifs_waterfall INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:21.746 wdl.w:ptcp.w:call-trgt-25.t:call-trgt_plot_motifs_waterfall INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:21.791 wdl.w:ptcp.w:call-trgt-09.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:21 [ERROR] - No reads found for TRID=PRTS_ARX
2025-09-15 20:24:21.792 wdl.w:ptcp.w:call-trgt-09.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:21 [ERROR] - No reads found for TRID=EIEE1_ARX
2025-09-15 20:24:21.819 wdl.w:ptcp.w:call-trgt-12.t:call-trgt_plot_meth_allele NOTICE done
2025-09-15 20:24:21.824 wdl.w:ptcp.w:call-trgt-12 NOTICE finish :: job: "call-trgt_plot_meth_allele"
2025-09-15 20:24:21.825 wdl.w:ptcp.w:call-trgt-12 INFO output :: job: "call-trgt_plot_meth_allele", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-12/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2109.meth_allele.trgt_plots.zip"}
2025-09-15 20:24:21.825 wdl.w:ptcp.w:call-trgt-12 INFO visit :: node: "output-images_meth_allele", values: {"images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-12/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2109.meth_allele.trgt_plots.zip"}
2025-09-15 20:24:21.829 wdl.w:ptcp.w:call-trgt-25.t:call-trgt_plot_motifs_waterfall INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-25/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_ild0dltb"
2025-09-15 20:24:21.829 wdl.w:ptcp.w:call-trgt-25.t:call-trgt_plot_motifs_waterfall INFO Slurm invocation: srun --job-name call-trgt_plot_motifs_waterfall --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-25/call-trgt_plot_motifs_waterfall/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-25/call-trgt_plot_motifs_waterfall/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-25/call-trgt_plot_motifs_waterfall/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-25/call-trgt_plot_motifs_waterfall/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-25/call-trgt_genotype/out/m84036_250809_035451_s4.bc2122.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2122.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-25/call-trgt_genotype/out/m84036_250809_035451_s4.bc2122.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2122.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-25/call-trgt_genotype/out/m84036_250809_035451_s4.bc2122.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2122.trgt.sorted.spanning.bam:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-25/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_ild0dltb/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-25/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_ild0dltb/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:21.832 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_plot_meth_allele NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-02/call-trgt_plot_meth_allele", thread: 140608194717248
2025-09-15 20:24:21.853 wdl.w:ptcp.w:call-trgt-33.t:call-trgt_plot_meth_allele NOTICE done
2025-09-15 20:24:21.855 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_plot_meth_allele INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:21.855 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_plot_meth_allele INFO input :: name: "waterfall", value: false
2025-09-15 20:24:21.855 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_plot_meth_allele INFO input :: name: "methylation", value: true
2025-09-15 20:24:21.855 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_plot_meth_allele INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:21.855 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_plot_meth_allele INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:21.855 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_plot_meth_allele INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:21.855 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_plot_meth_allele INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2099.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:21.855 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_plot_meth_allele INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2099.trgt.sorted.spanning.bam"
2025-09-15 20:24:21.855 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_plot_meth_allele INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2099.trgt.vcf"
2025-09-15 20:24:21.855 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_plot_meth_allele INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2099"
2025-09-15 20:24:21.856 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_plot_meth_allele INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:21.856 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_plot_meth_allele INFO eval :: name: "plot_type", value: "allele"
2025-09-15 20:24:21.856 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_plot_meth_allele INFO eval :: name: "show", value: "meth"
2025-09-15 20:24:21.856 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_plot_meth_allele INFO eval :: name: "threads", value: 1
2025-09-15 20:24:21.856 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_plot_meth_allele INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:21.857 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_plot_meth_allele INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2099.meth_allele"
2025-09-15 20:24:21.857 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_plot_meth_allele INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:21.857 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_plot_meth_allele WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:21.857 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_plot_meth_allele INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:21.857 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_plot_meth_allele INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:21.859 wdl.w:ptcp.w:call-trgt-33 NOTICE finish :: job: "call-trgt_plot_meth_allele"
2025-09-15 20:24:21.859 wdl.w:ptcp.w:call-trgt-33 INFO output :: job: "call-trgt_plot_meth_allele", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-33/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2130.meth_allele.trgt_plots.zip"}
2025-09-15 20:24:21.859 wdl.w:ptcp.w:call-trgt-33 INFO visit :: node: "output-images_meth_allele", values: {"images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-33/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2130.meth_allele.trgt_plots.zip"}
2025-09-15 20:24:21.867 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_plot_meth_waterfall NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-02/call-trgt_plot_meth_waterfall", thread: 140607683024448
2025-09-15 20:24:21.872 wdl.w:ptcp.w:call-trgt-25.t:call-trgt_plot_motifs_waterfall NOTICE slurm_singularity run :: pid: 1201563, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-25/call-trgt_plot_motifs_waterfall/slurm_singularity.log.txt"
2025-09-15 20:24:21.891 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_plot_meth_waterfall INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:21.891 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_plot_meth_waterfall INFO input :: name: "waterfall", value: true
2025-09-15 20:24:21.891 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_plot_meth_waterfall INFO input :: name: "methylation", value: true
2025-09-15 20:24:21.891 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_plot_meth_waterfall INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:21.891 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_plot_meth_waterfall INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:21.891 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_plot_meth_waterfall INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:21.891 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_plot_meth_waterfall INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2099.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:21.891 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_plot_meth_waterfall INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2099.trgt.sorted.spanning.bam"
2025-09-15 20:24:21.891 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_plot_meth_waterfall INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2099.trgt.vcf"
2025-09-15 20:24:21.891 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_plot_meth_waterfall INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2099"
2025-09-15 20:24:21.891 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_plot_meth_waterfall INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:21.892 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_plot_meth_waterfall INFO eval :: name: "plot_type", value: "waterfall"
2025-09-15 20:24:21.892 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_plot_meth_waterfall INFO eval :: name: "show", value: "meth"
2025-09-15 20:24:21.892 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_plot_meth_waterfall INFO eval :: name: "threads", value: 1
2025-09-15 20:24:21.892 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_plot_meth_waterfall INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:21.892 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_plot_meth_waterfall INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2099.meth_waterfall"
2025-09-15 20:24:21.894 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_plot_meth_waterfall INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:21.894 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_plot_meth_waterfall WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:21.894 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_plot_meth_waterfall INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:21.895 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_plot_meth_waterfall INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:21.894 wdl.w:ptcp.w:call-sawfish-09.t:call-run_sawfish.stderr VERBOSE [M::mm_idx_gen::28.285*1.41] collected minimizers
2025-09-15 20:24:21.896 wdl.w:ptcp.w:call-sawfish-09.t:call-run_sawfish.stderr VERBOSE [M::mm_idx_gen::35.358*1.71] sorted minimizers
2025-09-15 20:24:21.896 wdl.w:ptcp.w:call-sawfish-09.t:call-run_sawfish.stderr VERBOSE [M::main::35.358*1.71] loaded/built the index for 195 target sequence(s)
2025-09-15 20:24:21.896 wdl.w:ptcp.w:call-sawfish-09.t:call-run_sawfish.stderr VERBOSE [M::mm_mapopt_update::38.270*1.66] mid_occ = 136
2025-09-15 20:24:21.896 wdl.w:ptcp.w:call-sawfish-09.t:call-run_sawfish.stderr VERBOSE [M::mm_idx_stat] kmer size: 19; skip: 19; is_hpc: 0; #seq: 195
2025-09-15 20:24:21.896 wdl.w:ptcp.w:call-sawfish-09.t:call-run_sawfish.stderr VERBOSE [M::mm_idx_stat::40.604*1.62] distinct minimizers: 214664461 (92.23% are singletons); average occurrences: 1.372; average spacing: 10.529; total length: 3099922541
2025-09-15 20:24:21.896 wdl.w:ptcp.w:call-sawfish-09.t:call-run_sawfish.stderr VERBOSE [M::main] Version: 2.26-r1175
2025-09-15 20:24:21.896 wdl.w:ptcp.w:call-sawfish-09.t:call-run_sawfish.stderr VERBOSE [M::main] CMD: /opt/pacbio/smrttools/install/smrtlink-release_25.1.0.257715/bundles/smrttools/install/smrttools-release_25.1.0.257715/private/thirdparty/minimap2/minimap2_2.26-pacbio2/binwrap/../../../../../private/thirdparty/minimap2/minimap2_2.26-pacbio2/bin/minimap2 -a -y -x map-hifi -Y -E 1,0 /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa -
2025-09-15 20:24:21.896 wdl.w:ptcp.w:call-sawfish-09.t:call-run_sawfish.stderr VERBOSE [M::main] Real time: 40.894 sec; CPU: 66.107 sec; Peak RSS: 11.882 GB
2025-09-15 20:24:21.942 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_plot_meth_allele INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-02/call-trgt_plot_meth_allele/_singularity_tmpdir_4guo94bp"
2025-09-15 20:24:21.942 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_plot_meth_allele INFO Slurm invocation: srun --job-name call-trgt_plot_meth_allele --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-02/call-trgt_plot_meth_allele/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-02/call-trgt_plot_meth_allele/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-02/call-trgt_plot_meth_allele/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-02/call-trgt_plot_meth_allele/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-02/call-trgt_genotype/out/m84036_250809_035451_s4.bc2099.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2099.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-02/call-trgt_genotype/out/m84036_250809_035451_s4.bc2099.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2099.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-02/call-trgt_genotype/out/m84036_250809_035451_s4.bc2099.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2099.trgt.sorted.spanning.bam:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-02/call-trgt_plot_meth_allele/_singularity_tmpdir_4guo94bp/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-02/call-trgt_plot_meth_allele/_singularity_tmpdir_4guo94bp/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:21.962 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_plot_meth_allele NOTICE slurm_singularity run :: pid: 1201566, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-02/call-trgt_plot_meth_allele/slurm_singularity.log.txt"
2025-09-15 20:24:21.983 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_plot_meth_waterfall INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-02/call-trgt_plot_meth_waterfall/_singularity_tmpdir_by3e46g1"
2025-09-15 20:24:21.983 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_plot_meth_waterfall INFO Slurm invocation: srun --job-name call-trgt_plot_meth_waterfall --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-02/call-trgt_plot_meth_waterfall/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-02/call-trgt_plot_meth_waterfall/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-02/call-trgt_plot_meth_waterfall/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-02/call-trgt_plot_meth_waterfall/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-02/call-trgt_genotype/out/m84036_250809_035451_s4.bc2099.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2099.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-02/call-trgt_genotype/out/m84036_250809_035451_s4.bc2099.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2099.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-02/call-trgt_genotype/out/m84036_250809_035451_s4.bc2099.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2099.trgt.sorted.spanning.bam:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-02/call-trgt_plot_meth_waterfall/_singularity_tmpdir_by3e46g1/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-02/call-trgt_plot_meth_waterfall/_singularity_tmpdir_by3e46g1/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:21.994 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_plot_meth_waterfall NOTICE slurm_singularity run :: pid: 1201573, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-02/call-trgt_plot_meth_waterfall/slurm_singularity.log.txt"
2025-09-15 20:24:22.021 wdl.w:ptcp.w:call-trgt-12.t:call-trgt_plot_motifs_allele INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2109.motifs_allele.trgt_plots.zip"
2025-09-15 20:24:22.070 wdl.w:ptcp.w:call-trgt-05.t:call-trgt_plot_motifs_allele INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2102.motifs_allele.trgt_plots.zip"
2025-09-15 20:24:22.103 wdl.w:ptcp.w:call-trgt-13.t:call-trgt_plot_motifs_allele INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2110.motifs_allele.trgt_plots.zip"
2025-09-15 20:24:22.158 wdl.w:ptcp.w:call-trgt-25.t:call-trgt_plot_meth_allele.slurm_singularity INFO srun: job 51797613 queued and waiting for resources
2025-09-15 20:24:22.158 wdl.w:ptcp.w:call-trgt-25.t:call-trgt_plot_meth_allele.slurm_singularity INFO srun: job 51797613 has been allocated resources
2025-09-15 20:24:22.159 wdl.w:ptcp.w:call-trgt-25.t:call-trgt_plot_meth_allele.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:22.175 wdl.w:ptcp.w:call-sawfish-29.t:call-run_sawfish.stderr VERBOSE [M::mm_idx_gen::29.850*1.44] collected minimizers
2025-09-15 20:24:22.177 wdl.w:ptcp.w:call-sawfish-29.t:call-run_sawfish.stderr VERBOSE [M::mm_idx_gen::35.885*1.69] sorted minimizers
2025-09-15 20:24:22.177 wdl.w:ptcp.w:call-sawfish-29.t:call-run_sawfish.stderr VERBOSE [M::main::35.885*1.69] loaded/built the index for 195 target sequence(s)
2025-09-15 20:24:22.177 wdl.w:ptcp.w:call-sawfish-29.t:call-run_sawfish.stderr VERBOSE [M::mm_mapopt_update::38.678*1.64] mid_occ = 136
2025-09-15 20:24:22.177 wdl.w:ptcp.w:call-sawfish-29.t:call-run_sawfish.stderr VERBOSE [M::mm_idx_stat] kmer size: 19; skip: 19; is_hpc: 0; #seq: 195
2025-09-15 20:24:22.177 wdl.w:ptcp.w:call-sawfish-29.t:call-run_sawfish.stderr VERBOSE [M::mm_idx_stat::40.961*1.61] distinct minimizers: 214664461 (92.23% are singletons); average occurrences: 1.372; average spacing: 10.529; total length: 3099922541
2025-09-15 20:24:22.177 wdl.w:ptcp.w:call-sawfish-29.t:call-run_sawfish.stderr VERBOSE [M::worker_pipeline::40.977*1.61] mapped 1 sequences
2025-09-15 20:24:22.177 wdl.w:ptcp.w:call-sawfish-29.t:call-run_sawfish.stderr VERBOSE [M::main] Version: 2.26-r1175
2025-09-15 20:24:22.177 wdl.w:ptcp.w:call-sawfish-29.t:call-run_sawfish.stderr VERBOSE [M::main] CMD: /opt/pacbio/smrttools/install/smrtlink-release_25.1.0.257715/bundles/smrttools/install/smrttools-release_25.1.0.257715/private/thirdparty/minimap2/minimap2_2.26-pacbio2/binwrap/../../../../../private/thirdparty/minimap2/minimap2_2.26-pacbio2/bin/minimap2 -a -y -x map-hifi -Y -E 1,0 /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa -
2025-09-15 20:24:22.177 wdl.w:ptcp.w:call-sawfish-29.t:call-run_sawfish.stderr VERBOSE [M::main] Real time: 41.041 sec; CPU: 65.915 sec; Peak RSS: 11.877 GB
2025-09-15 20:24:22.181 wdl.w:ptcp.w:call-trgt-12.t:call-trgt_plot_motifs_allele NOTICE done
2025-09-15 20:24:22.243 wdl.w:ptcp.w:call-trgt-12 NOTICE finish :: job: "call-trgt_plot_motifs_allele"
2025-09-15 20:24:22.244 wdl.w:ptcp.w:call-trgt-12 INFO output :: job: "call-trgt_plot_motifs_allele", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-12/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2109.motifs_allele.trgt_plots.zip"}
2025-09-15 20:24:22.244 wdl.w:ptcp.w:call-trgt-12 INFO visit :: node: "output-images_motifs_allele", values: {"images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-12/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2109.motifs_allele.trgt_plots.zip"}
2025-09-15 20:24:22.270 wdl.w:ptcp.w:call-trgt-25.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO srun: job 51797614 queued and waiting for resources
2025-09-15 20:24:22.270 wdl.w:ptcp.w:call-trgt-25.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO srun: job 51797614 has been allocated resources
2025-09-15 20:24:22.270 wdl.w:ptcp.w:call-trgt-25.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:22.274 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_plot_motifs_allele NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-02/call-trgt_plot_motifs_allele", thread: 140609310422592
2025-09-15 20:24:22.283 wdl.w:ptcp.w:call-paraphase-05.t:call-call_f8 INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2102.f8inversion.vcf"
2025-09-15 20:24:22.287 wdl.w:ptcp.w:call-paraphase-05.t:call-call_f8 INFO output :: name: "json", value: "m84036_250809_035451_s4.bc2102.f8inversion.json"
2025-09-15 20:24:22.301 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_plot_motifs_allele INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:22.301 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_plot_motifs_allele INFO input :: name: "waterfall", value: false
2025-09-15 20:24:22.302 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_plot_motifs_allele INFO input :: name: "methylation", value: false
2025-09-15 20:24:22.302 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_plot_motifs_allele INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:22.302 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_plot_motifs_allele INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:22.302 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_plot_motifs_allele INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:22.302 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_plot_motifs_allele INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2099.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:22.302 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_plot_motifs_allele INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2099.trgt.sorted.spanning.bam"
2025-09-15 20:24:22.302 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_plot_motifs_allele INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2099.trgt.vcf"
2025-09-15 20:24:22.302 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_plot_motifs_allele INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2099"
2025-09-15 20:24:22.302 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_plot_motifs_allele INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:22.303 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_plot_motifs_allele INFO eval :: name: "plot_type", value: "allele"
2025-09-15 20:24:22.303 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_plot_motifs_allele INFO eval :: name: "show", value: "motifs"
2025-09-15 20:24:22.303 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_plot_motifs_allele INFO eval :: name: "threads", value: 1
2025-09-15 20:24:22.303 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_plot_motifs_allele INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:22.303 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_plot_motifs_allele INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2099.motifs_allele"
2025-09-15 20:24:22.304 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_plot_motifs_allele INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:22.304 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_plot_motifs_allele WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:22.304 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_plot_motifs_allele INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:22.304 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_plot_motifs_allele INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:22.321 wdl.w:ptcp.w:call-trgt-05.t:call-trgt_plot_motifs_allele NOTICE done
2025-09-15 20:24:22.326 wdl.w:ptcp.w:call-trgt-05 NOTICE finish :: job: "call-trgt_plot_motifs_allele"
2025-09-15 20:24:22.327 wdl.w:ptcp.w:call-trgt-05 INFO output :: job: "call-trgt_plot_motifs_allele", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-05/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2102.motifs_allele.trgt_plots.zip"}
2025-09-15 20:24:22.327 wdl.w:ptcp.w:call-trgt-05 INFO visit :: node: "output-images_motifs_allele", values: {"images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-05/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2102.motifs_allele.trgt_plots.zip"}
2025-09-15 20:24:22.336 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_plot_motifs_waterfall NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-02/call-trgt_plot_motifs_waterfall", thread: 140608219895360
2025-09-15 20:24:22.337 wdl.w:ptcp.w:call-paraphase-33.t:call-call_f8 INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2130.f8inversion.vcf"
2025-09-15 20:24:22.341 wdl.w:ptcp.w:call-paraphase-33.t:call-call_f8 INFO output :: name: "json", value: "m84036_250809_035451_s4.bc2130.f8inversion.json"
2025-09-15 20:24:22.352 wdl.w:ptcp.w:call-trgt-13.t:call-trgt_plot_motifs_allele NOTICE done
2025-09-15 20:24:22.357 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_plot_motifs_waterfall INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:22.357 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_plot_motifs_waterfall INFO input :: name: "waterfall", value: true
2025-09-15 20:24:22.357 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_plot_motifs_waterfall INFO input :: name: "methylation", value: false
2025-09-15 20:24:22.357 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_plot_motifs_waterfall INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:22.357 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_plot_motifs_waterfall INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:22.357 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_plot_motifs_waterfall INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:22.357 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_plot_motifs_waterfall INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2099.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:22.357 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_plot_motifs_waterfall INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2099.trgt.sorted.spanning.bam"
2025-09-15 20:24:22.357 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_plot_motifs_waterfall INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2099.trgt.vcf"
2025-09-15 20:24:22.357 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_plot_motifs_waterfall INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2099"
2025-09-15 20:24:22.357 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:22.358 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "plot_type", value: "waterfall"
2025-09-15 20:24:22.358 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "show", value: "motifs"
2025-09-15 20:24:22.358 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "threads", value: 1
2025-09-15 20:24:22.358 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:22.358 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2099.motifs_waterfall"
2025-09-15 20:24:22.358 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_plot_motifs_waterfall INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:22.359 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_plot_motifs_waterfall WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:22.359 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_plot_motifs_waterfall INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:22.359 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_plot_motifs_waterfall INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:22.361 wdl.w:ptcp.w:call-trgt-13 NOTICE finish :: job: "call-trgt_plot_motifs_allele"
2025-09-15 20:24:22.362 wdl.w:ptcp.w:call-trgt-13 INFO output :: job: "call-trgt_plot_motifs_allele", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-13/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2110.motifs_allele.trgt_plots.zip"}
2025-09-15 20:24:22.362 wdl.w:ptcp.w:call-trgt-13 INFO visit :: node: "output-images_motifs_allele", values: {"images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-13/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2110.motifs_allele.trgt_plots.zip"}
2025-09-15 20:24:22.371 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_plot_meth_allele NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-03/call-trgt_plot_meth_allele", thread: 140607112582720
2025-09-15 20:24:22.381 wdl.w:ptcp.w:call-paraphase-05.t:call-call_f8 NOTICE done
2025-09-15 20:24:22.386 wdl.w:ptcp.w:call-paraphase-05 NOTICE finish :: job: "call-call_f8"
2025-09-15 20:24:22.386 wdl.w:ptcp.w:call-paraphase-05 INFO output :: job: "call-call_f8", values: {"json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-05/call-call_f8/out/m84036_250809_035451_s4.bc2102.f8inversion.json", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-05/call-call_f8/out/m84036_250809_035451_s4.bc2102.f8inversion.vcf"}
2025-09-15 20:24:22.387 wdl.w:ptcp.w:call-paraphase-05 INFO visit :: node: "output-f8_json", values: {"f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-05/call-call_f8/out/m84036_250809_035451_s4.bc2102.f8inversion.json"}
2025-09-15 20:24:22.387 wdl.w:ptcp.w:call-paraphase-05 INFO visit :: node: "output-f8_vcf", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-05/call-call_f8/out/m84036_250809_035451_s4.bc2102.f8inversion.vcf"}
2025-09-15 20:24:22.387 wdl.w:ptcp.w:call-paraphase-05 INFO visit :: node: "outputs", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-05/call-call_f8/out/m84036_250809_035451_s4.bc2102.f8inversion.vcf", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-05/call-run_paraphase/out/m84036_250809_035451_s4.bc2102_paraphase/m84036_250809_035451_s4.bc2102.paraphase.json", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-05/call-run_paraphase/out/m84036_250809_035451_s4.bc2102_paraphase/m84036_250809_035451_s4.bc2102.paraphase.bam", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-05/call-run_paraphase/out/m84036_250809_035451_s4.bc2102_paraphase/m84036_250809_035451_s4.bc2102.paraphase.bam.bai", "paraphase_vcfs": [], "havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-05/call-run_paraphase/out/m84036_250809_035451_s4.bc2102.havanno.json", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-05/call-call_f8/out/m84036_250809_035451_s4.bc2102.f8inversion.json"}
2025-09-15 20:24:22.393 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_plot_meth_waterfall NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-03/call-trgt_plot_meth_waterfall", thread: 140607146153536
2025-09-15 20:24:22.401 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_plot_motifs_allele INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-02/call-trgt_plot_motifs_allele/_singularity_tmpdir_hheb0ie3"
2025-09-15 20:24:22.401 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_plot_motifs_allele INFO Slurm invocation: srun --job-name call-trgt_plot_motifs_allele --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-02/call-trgt_plot_motifs_allele/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-02/call-trgt_plot_motifs_allele/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-02/call-trgt_plot_motifs_allele/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-02/call-trgt_plot_motifs_allele/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-02/call-trgt_genotype/out/m84036_250809_035451_s4.bc2099.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2099.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-02/call-trgt_genotype/out/m84036_250809_035451_s4.bc2099.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2099.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-02/call-trgt_genotype/out/m84036_250809_035451_s4.bc2099.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2099.trgt.sorted.spanning.bam:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-02/call-trgt_plot_motifs_allele/_singularity_tmpdir_hheb0ie3/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-02/call-trgt_plot_motifs_allele/_singularity_tmpdir_hheb0ie3/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:22.401 wdl.w:ptcp.w:call-trgt-29.t:call-trgt_plot_meth_waterfall INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2126.meth_waterfall.trgt_plots.zip"
2025-09-15 20:24:22.403 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_plot_meth_allele INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:22.407 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_plot_meth_allele INFO input :: name: "waterfall", value: false
2025-09-15 20:24:22.410 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_plot_meth_allele INFO input :: name: "methylation", value: true
2025-09-15 20:24:22.410 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_plot_meth_allele INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:22.410 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_plot_meth_allele INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:22.410 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_plot_meth_allele INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:22.410 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_plot_meth_allele INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2100.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:22.410 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_plot_meth_allele INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2100.trgt.sorted.spanning.bam"
2025-09-15 20:24:22.410 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_plot_meth_allele INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2100.trgt.vcf"
2025-09-15 20:24:22.410 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_plot_meth_allele INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2100"
2025-09-15 20:24:22.410 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_plot_meth_allele INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:22.410 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_plot_meth_allele INFO eval :: name: "plot_type", value: "allele"
2025-09-15 20:24:22.411 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_plot_meth_allele INFO eval :: name: "show", value: "meth"
2025-09-15 20:24:22.411 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_plot_meth_allele INFO eval :: name: "threads", value: 1
2025-09-15 20:24:22.411 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_plot_meth_allele INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:22.411 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_plot_meth_allele INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2100.meth_allele"
2025-09-15 20:24:22.411 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_plot_meth_allele INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:22.411 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_plot_meth_allele WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:22.412 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_plot_meth_allele INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:22.412 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_plot_meth_allele INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:22.423 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_plot_meth_waterfall INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:22.424 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_plot_meth_waterfall INFO input :: name: "waterfall", value: true
2025-09-15 20:24:22.424 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_plot_meth_waterfall INFO input :: name: "methylation", value: true
2025-09-15 20:24:22.424 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_plot_meth_waterfall INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:22.424 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_plot_meth_waterfall INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:22.424 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_plot_meth_waterfall INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:22.424 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_plot_meth_waterfall INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2100.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:22.424 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_plot_meth_waterfall INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2100.trgt.sorted.spanning.bam"
2025-09-15 20:24:22.424 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_plot_meth_waterfall INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2100.trgt.vcf"
2025-09-15 20:24:22.424 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_plot_meth_waterfall INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2100"
2025-09-15 20:24:22.424 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_plot_meth_waterfall INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:22.424 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_plot_meth_waterfall INFO eval :: name: "plot_type", value: "waterfall"
2025-09-15 20:24:22.425 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_plot_meth_waterfall INFO eval :: name: "show", value: "meth"
2025-09-15 20:24:22.425 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_plot_meth_waterfall INFO eval :: name: "threads", value: 1
2025-09-15 20:24:22.425 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_plot_meth_waterfall INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:22.425 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_plot_meth_waterfall INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2100.meth_waterfall"
2025-09-15 20:24:22.425 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_plot_meth_waterfall INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:22.425 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_plot_meth_waterfall WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:22.426 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_plot_meth_waterfall INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:22.426 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_plot_meth_waterfall INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:22.449 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_plot_motifs_allele NOTICE slurm_singularity run :: pid: 1201590, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-02/call-trgt_plot_motifs_allele/slurm_singularity.log.txt"
2025-09-15 20:24:22.454 wdl.w:ptcp.w:call-paraphase-33.t:call-call_f8 NOTICE done
2025-09-15 20:24:22.470 wdl.w:ptcp.w:call-paraphase-05 NOTICE done
2025-09-15 20:24:22.471 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_plot_motifs_waterfall INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-02/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_nfqizzn1"
2025-09-15 20:24:22.471 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_plot_motifs_waterfall INFO Slurm invocation: srun --job-name call-trgt_plot_motifs_waterfall --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-02/call-trgt_plot_motifs_waterfall/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-02/call-trgt_plot_motifs_waterfall/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-02/call-trgt_plot_motifs_waterfall/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-02/call-trgt_plot_motifs_waterfall/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-02/call-trgt_genotype/out/m84036_250809_035451_s4.bc2099.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2099.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-02/call-trgt_genotype/out/m84036_250809_035451_s4.bc2099.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2099.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-02/call-trgt_genotype/out/m84036_250809_035451_s4.bc2099.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2099.trgt.sorted.spanning.bam:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-02/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_nfqizzn1/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-02/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_nfqizzn1/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:22.475 wdl.w:ptcp NOTICE finish :: job: "call-paraphase-05"
2025-09-15 20:24:22.475 wdl.w:ptcp INFO output :: job: "call-paraphase-05", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-05/out/m84036_250809_035451_s4.bc2102.f8inversion.vcf", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-05/out/m84036_250809_035451_s4.bc2102_paraphase/m84036_250809_035451_s4.bc2102.paraphase.json", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-05/out/m84036_250809_035451_s4.bc2102_paraphase/m84036_250809_035451_s4.bc2102.paraphase.bam", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-05/out/m84036_250809_035451_s4.bc2102_paraphase/m84036_250809_035451_s4.bc2102.paraphase.bam.bai", "paraphase_vcfs": [], "havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-05/out/m84036_250809_035451_s4.bc2102.havanno.json", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-05/out/m84036_250809_035451_s4.bc2102.f8inversion.json"}
2025-09-15 20:24:22.484 wdl.w:ptcp.w:call-paraphase-48 NOTICE workflow start :: name: "paraphase", source: "./paraphase.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-48"
2025-09-15 20:24:22.488 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_plot_motifs_waterfall NOTICE slurm_singularity run :: pid: 1201592, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-02/call-trgt_plot_motifs_waterfall/slurm_singularity.log.txt"
2025-09-15 20:24:22.503 wdl.w:ptcp.w:call-paraphase-48 INFO visit :: node: "decl-annotation_vcf", values: {"annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf"}
2025-09-15 20:24:22.503 wdl.w:ptcp.w:call-paraphase-48 INFO visit :: node: "decl-config_file", values: {"config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml"}
2025-09-15 20:24:22.503 wdl.w:ptcp.w:call-paraphase-48 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:24:22.503 wdl.w:ptcp.w:call-paraphase-48 INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:24:22.503 wdl.w:ptcp.w:call-paraphase-48 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-48/out/m84036_250809_035451_s4.bc2145.mapped.bam"}
2025-09-15 20:24:22.504 wdl.w:ptcp.w:call-paraphase-48 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-48/out/m84036_250809_035451_s4.bc2145.mapped.bam.bai"}
2025-09-15 20:24:22.504 wdl.w:ptcp.w:call-paraphase-48 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:24:22.504 wdl.w:ptcp.w:call-paraphase-48 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:24:22.504 wdl.w:ptcp.w:call-paraphase-48 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2145"}
2025-09-15 20:24:22.504 wdl.w:ptcp.w:call-paraphase-48 INFO visit :: node: "decl-sex", values: {"sex": "F"}
2025-09-15 20:24:22.504 wdl.w:ptcp.w:call-paraphase-48 NOTICE ready :: job: "call-run_paraphase", callee: "run_paraphase"
2025-09-15 20:24:22.504 wdl.w:ptcp.w:call-paraphase-48 INFO input :: job: "call-run_paraphase", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf", "genome_version": "38", "config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-48/out/m84036_250809_035451_s4.bc2145.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-48/out/m84036_250809_035451_s4.bc2145.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2145"}
2025-09-15 20:24:22.505 wdl.w:ptcp.w:call-paraphase-33 NOTICE finish :: job: "call-call_f8"
2025-09-15 20:24:22.505 wdl.w:ptcp.w:call-paraphase-33 INFO output :: job: "call-call_f8", values: {"json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-33/call-call_f8/out/m84036_250809_035451_s4.bc2130.f8inversion.json", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-33/call-call_f8/out/m84036_250809_035451_s4.bc2130.f8inversion.vcf"}
2025-09-15 20:24:22.506 wdl.w:ptcp.w:call-paraphase-33 INFO visit :: node: "output-f8_json", values: {"f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-33/call-call_f8/out/m84036_250809_035451_s4.bc2130.f8inversion.json"}
2025-09-15 20:24:22.506 wdl.w:ptcp.w:call-paraphase-33 INFO visit :: node: "output-f8_vcf", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-33/call-call_f8/out/m84036_250809_035451_s4.bc2130.f8inversion.vcf"}
2025-09-15 20:24:22.506 wdl.w:ptcp.w:call-paraphase-33 INFO visit :: node: "outputs", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-33/call-call_f8/out/m84036_250809_035451_s4.bc2130.f8inversion.vcf", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-33/call-run_paraphase/out/m84036_250809_035451_s4.bc2130_paraphase/m84036_250809_035451_s4.bc2130.paraphase.json", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-33/call-run_paraphase/out/m84036_250809_035451_s4.bc2130_paraphase/m84036_250809_035451_s4.bc2130.paraphase.bam", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-33/call-run_paraphase/out/m84036_250809_035451_s4.bc2130_paraphase/m84036_250809_035451_s4.bc2130.paraphase.bam.bai", "paraphase_vcfs": [], "havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-33/call-run_paraphase/out/m84036_250809_035451_s4.bc2130.havanno.json", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-33/call-call_f8/out/m84036_250809_035451_s4.bc2130.f8inversion.json"}
2025-09-15 20:24:22.517 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_plot_motifs_allele NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-03/call-trgt_plot_motifs_allele", thread: 140606609282624
2025-09-15 20:24:22.530 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_plot_meth_allele INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-03/call-trgt_plot_meth_allele/_singularity_tmpdir_1itsqsjn"
2025-09-15 20:24:22.530 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_plot_meth_allele INFO Slurm invocation: srun --job-name call-trgt_plot_meth_allele --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-03/call-trgt_plot_meth_allele/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-03/call-trgt_plot_meth_allele/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-03/call-trgt_plot_meth_allele/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-03/call-trgt_plot_meth_allele/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-03/call-trgt_genotype/out/m84036_250809_035451_s4.bc2100.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2100.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-03/call-trgt_genotype/out/m84036_250809_035451_s4.bc2100.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2100.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-03/call-trgt_genotype/out/m84036_250809_035451_s4.bc2100.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2100.trgt.sorted.spanning.bam.bai:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-03/call-trgt_plot_meth_allele/_singularity_tmpdir_1itsqsjn/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-03/call-trgt_plot_meth_allele/_singularity_tmpdir_1itsqsjn/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:22.545 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_plot_motifs_allele INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:22.545 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_plot_motifs_allele INFO input :: name: "waterfall", value: false
2025-09-15 20:24:22.545 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_plot_motifs_allele INFO input :: name: "methylation", value: false
2025-09-15 20:24:22.545 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_plot_motifs_allele INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:22.545 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_plot_motifs_allele INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:22.545 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_plot_motifs_allele INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:22.545 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_plot_motifs_allele INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2100.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:22.545 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_plot_motifs_allele INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2100.trgt.sorted.spanning.bam"
2025-09-15 20:24:22.545 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_plot_motifs_allele INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2100.trgt.vcf"
2025-09-15 20:24:22.545 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_plot_motifs_allele INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2100"
2025-09-15 20:24:22.545 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_plot_motifs_allele INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:22.546 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_plot_motifs_allele INFO eval :: name: "plot_type", value: "allele"
2025-09-15 20:24:22.546 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_plot_motifs_allele INFO eval :: name: "show", value: "motifs"
2025-09-15 20:24:22.546 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_plot_motifs_allele INFO eval :: name: "threads", value: 1
2025-09-15 20:24:22.546 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_plot_motifs_allele INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:22.546 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_plot_motifs_allele INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2100.motifs_allele"
2025-09-15 20:24:22.547 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_plot_motifs_allele INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:22.547 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_plot_motifs_allele WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:22.547 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_plot_motifs_allele INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:22.547 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_plot_motifs_allele INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:22.547 wdl.w:ptcp.w:call-trgt-25.t:call-trgt_plot_motifs_allele.slurm_singularity INFO srun: job 51797615 queued and waiting for resources
2025-09-15 20:24:22.548 wdl.w:ptcp.w:call-trgt-25.t:call-trgt_plot_motifs_allele.slurm_singularity INFO srun: job 51797615 has been allocated resources
2025-09-15 20:24:22.548 wdl.w:ptcp.w:call-trgt-25.t:call-trgt_plot_motifs_allele.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:22.556 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_plot_meth_allele NOTICE slurm_singularity run :: pid: 1201600, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-03/call-trgt_plot_meth_allele/slurm_singularity.log.txt"
2025-09-15 20:24:22.558 wdl.w:ptcp.w:call-trgt-24.t:call-trgt_plot_motifs_allele INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2121.motifs_allele.trgt_plots.zip"
2025-09-15 20:24:22.564 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_plot_meth_waterfall INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-03/call-trgt_plot_meth_waterfall/_singularity_tmpdir_om5pwnsi"
2025-09-15 20:24:22.564 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_plot_meth_waterfall INFO Slurm invocation: srun --job-name call-trgt_plot_meth_waterfall --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-03/call-trgt_plot_meth_waterfall/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-03/call-trgt_plot_meth_waterfall/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-03/call-trgt_plot_meth_waterfall/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-03/call-trgt_plot_meth_waterfall/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-03/call-trgt_genotype/out/m84036_250809_035451_s4.bc2100.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2100.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-03/call-trgt_genotype/out/m84036_250809_035451_s4.bc2100.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2100.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-03/call-trgt_genotype/out/m84036_250809_035451_s4.bc2100.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2100.trgt.sorted.spanning.bam.bai:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-03/call-trgt_plot_meth_waterfall/_singularity_tmpdir_om5pwnsi/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-03/call-trgt_plot_meth_waterfall/_singularity_tmpdir_om5pwnsi/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:22.578 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_plot_meth_waterfall NOTICE slurm_singularity run :: pid: 1201602, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-03/call-trgt_plot_meth_waterfall/slurm_singularity.log.txt"
2025-09-15 20:24:22.603 wdl.w:ptcp.w:call-trgt-29.t:call-trgt_plot_meth_waterfall NOTICE done
2025-09-15 20:24:22.610 wdl.w:ptcp.w:call-trgt-29 NOTICE finish :: job: "call-trgt_plot_meth_waterfall"
2025-09-15 20:24:22.611 wdl.w:ptcp.w:call-trgt-29 INFO output :: job: "call-trgt_plot_meth_waterfall", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-29/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2126.meth_waterfall.trgt_plots.zip"}
2025-09-15 20:24:22.611 wdl.w:ptcp.w:call-trgt-29 INFO visit :: node: "output-images_meth_waterfall", values: {"images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-29/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2126.meth_waterfall.trgt_plots.zip"}
2025-09-15 20:24:22.618 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_plot_motifs_waterfall NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-03/call-trgt_plot_motifs_waterfall", thread: 140607657846336
2025-09-15 20:24:22.625 wdl.w:ptcp.w:call-paraphase-33 NOTICE done
2025-09-15 20:24:22.631 wdl.w:ptcp NOTICE finish :: job: "call-paraphase-33"
2025-09-15 20:24:22.632 wdl.w:ptcp INFO output :: job: "call-paraphase-33", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-33/out/m84036_250809_035451_s4.bc2130.f8inversion.vcf", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-33/out/m84036_250809_035451_s4.bc2130_paraphase/m84036_250809_035451_s4.bc2130.paraphase.json", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-33/out/m84036_250809_035451_s4.bc2130_paraphase/m84036_250809_035451_s4.bc2130.paraphase.bam", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-33/out/m84036_250809_035451_s4.bc2130_paraphase/m84036_250809_035451_s4.bc2130.paraphase.bam.bai", "paraphase_vcfs": [], "havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-33/out/m84036_250809_035451_s4.bc2130.havanno.json", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-33/out/m84036_250809_035451_s4.bc2130.f8inversion.json"}
2025-09-15 20:24:22.639 wdl.w:ptcp.w:call-sawfish-48 NOTICE workflow start :: name: "sawfish", source: "./sawfish.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-48"
2025-09-15 20:24:22.641 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_plot_motifs_allele INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-03/call-trgt_plot_motifs_allele/_singularity_tmpdir_9caliia9"
2025-09-15 20:24:22.642 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_plot_motifs_allele INFO Slurm invocation: srun --job-name call-trgt_plot_motifs_allele --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-03/call-trgt_plot_motifs_allele/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-03/call-trgt_plot_motifs_allele/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-03/call-trgt_plot_motifs_allele/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-03/call-trgt_plot_motifs_allele/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-03/call-trgt_genotype/out/m84036_250809_035451_s4.bc2100.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2100.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-03/call-trgt_genotype/out/m84036_250809_035451_s4.bc2100.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2100.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-03/call-trgt_genotype/out/m84036_250809_035451_s4.bc2100.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2100.trgt.sorted.spanning.bam.bai:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-03/call-trgt_plot_motifs_allele/_singularity_tmpdir_9caliia9/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-03/call-trgt_plot_motifs_allele/_singularity_tmpdir_9caliia9/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:22.642 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_plot_motifs_waterfall INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:22.643 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_plot_motifs_waterfall INFO input :: name: "waterfall", value: true
2025-09-15 20:24:22.655 wdl.w:ptcp.w:call-sawfish-48 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:24:22.655 wdl.w:ptcp.w:call-sawfish-48 INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:24:22.655 wdl.w:ptcp.w:call-sawfish-48 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-48/out/m84036_250809_035451_s4.bc2145.mapped.bam"}
2025-09-15 20:24:22.655 wdl.w:ptcp.w:call-sawfish-48 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-48/out/m84036_250809_035451_s4.bc2145.mapped.bam.bai"}
2025-09-15 20:24:22.656 wdl.w:ptcp.w:call-sawfish-48 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:24:22.656 wdl.w:ptcp.w:call-sawfish-48 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:24:22.656 wdl.w:ptcp.w:call-sawfish-48 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2145"}
2025-09-15 20:24:22.655 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_plot_motifs_waterfall INFO input :: name: "methylation", value: false
2025-09-15 20:24:22.656 wdl.w:ptcp.w:call-sawfish-48 NOTICE ready :: job: "call-run_sawfish", callee: "run_sawfish"
2025-09-15 20:24:22.656 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_plot_motifs_waterfall INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:22.656 wdl.w:ptcp.w:call-sawfish-48 INFO input :: job: "call-run_sawfish", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-48/out/m84036_250809_035451_s4.bc2145.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-48/out/m84036_250809_035451_s4.bc2145.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2145"}
2025-09-15 20:24:22.656 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_plot_motifs_waterfall INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:22.656 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_plot_motifs_waterfall INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:22.656 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_plot_motifs_waterfall INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2100.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:22.657 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_plot_motifs_waterfall INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2100.trgt.sorted.spanning.bam"
2025-09-15 20:24:22.657 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_plot_motifs_waterfall INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2100.trgt.vcf"
2025-09-15 20:24:22.657 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_plot_motifs_waterfall INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2100"
2025-09-15 20:24:22.657 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:22.657 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "plot_type", value: "waterfall"
2025-09-15 20:24:22.657 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "show", value: "motifs"
2025-09-15 20:24:22.657 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "threads", value: 1
2025-09-15 20:24:22.660 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:22.660 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2100.motifs_waterfall"
2025-09-15 20:24:22.661 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_plot_motifs_waterfall INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:22.661 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_plot_motifs_waterfall WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:22.661 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_plot_motifs_waterfall INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:22.661 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_plot_motifs_waterfall INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:22.668 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_plot_motifs_allele NOTICE slurm_singularity run :: pid: 1201604, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-03/call-trgt_plot_motifs_allele/slurm_singularity.log.txt"
2025-09-15 20:24:22.672 wdl.w:ptcp.w:call-trgt-16.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:21 [ERROR] - No reads found for TRID=PRTS_ARX
2025-09-15 20:24:22.672 wdl.w:ptcp.w:call-trgt-16.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:21 [ERROR] - No reads found for TRID=EIEE1_ARX
2025-09-15 20:24:22.717 wdl.w:ptcp.w:call-trgt-33.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:18 [ERROR] - No reads found for TRID=PRTS_ARX
2025-09-15 20:24:22.718 wdl.w:ptcp.w:call-trgt-33.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:19 [ERROR] - No reads found for TRID=EIEE1_ARX
2025-09-15 20:24:22.739 wdl.w:ptcp.w:call-trgt-24.t:call-trgt_plot_motifs_allele NOTICE done
2025-09-15 20:24:22.745 wdl.w:ptcp.w:call-trgt-24 NOTICE finish :: job: "call-trgt_plot_motifs_allele"
2025-09-15 20:24:22.745 wdl.w:ptcp.w:call-trgt-24 INFO output :: job: "call-trgt_plot_motifs_allele", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-24/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2121.motifs_allele.trgt_plots.zip"}
2025-09-15 20:24:22.745 wdl.w:ptcp.w:call-trgt-24 INFO visit :: node: "output-images_motifs_allele", values: {"images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-24/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2121.motifs_allele.trgt_plots.zip"}
2025-09-15 20:24:22.752 wdl.w:ptcp.w:call-paraphase-29.t:call-call_f8 NOTICE task setup :: name: "call_f8", source: "./paraphase.wdl", line: 232, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-29/call-call_f8", thread: 140607691417152
2025-09-15 20:24:22.753 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_plot_motifs_waterfall INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-03/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_7g9wa3at"
2025-09-15 20:24:22.753 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_plot_motifs_waterfall INFO Slurm invocation: srun --job-name call-trgt_plot_motifs_waterfall --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-03/call-trgt_plot_motifs_waterfall/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-03/call-trgt_plot_motifs_waterfall/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-03/call-trgt_plot_motifs_waterfall/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-03/call-trgt_plot_motifs_waterfall/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-03/call-trgt_genotype/out/m84036_250809_035451_s4.bc2100.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2100.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-03/call-trgt_genotype/out/m84036_250809_035451_s4.bc2100.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2100.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-03/call-trgt_genotype/out/m84036_250809_035451_s4.bc2100.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2100.trgt.sorted.spanning.bam.bai:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-03/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_7g9wa3at/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-03/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_7g9wa3at/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:22.771 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_plot_motifs_waterfall NOTICE slurm_singularity run :: pid: 1201606, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-03/call-trgt_plot_motifs_waterfall/slurm_singularity.log.txt"
2025-09-15 20:24:22.773 wdl.w:ptcp.w:call-paraphase-29.t:call-call_f8 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:22.773 wdl.w:ptcp.w:call-paraphase-29.t:call-call_f8 INFO input :: name: "genome_version", value: "38"
2025-09-15 20:24:22.773 wdl.w:ptcp.w:call-paraphase-29.t:call-call_f8 INFO input :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2126"
2025-09-15 20:24:22.773 wdl.w:ptcp.w:call-paraphase-29.t:call-call_f8 INFO input :: name: "paraphase_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2126.paraphase.bam.bai"
2025-09-15 20:24:22.773 wdl.w:ptcp.w:call-paraphase-29.t:call-call_f8 INFO input :: name: "paraphase_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2126.paraphase.bam"
2025-09-15 20:24:22.773 wdl.w:ptcp.w:call-paraphase-29.t:call-call_f8 INFO input :: name: "sex", value: "F"
2025-09-15 20:24:22.774 wdl.w:ptcp.w:call-paraphase-29.t:call-call_f8 INFO eval :: name: "threads", value: 1
2025-09-15 20:24:22.774 wdl.w:ptcp.w:call-paraphase-29.t:call-call_f8 INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:22.774 wdl.w:ptcp.w:call-paraphase-29.t:call-call_f8 INFO eval :: name: "disk_size", value: 11
2025-09-15 20:24:22.774 wdl.w:ptcp.w:call-paraphase-29.t:call-call_f8 INFO eval :: name: "sample_sex", value: "F"
2025-09-15 20:24:22.775 wdl.w:ptcp.w:call-paraphase-29.t:call-call_f8 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:22.775 wdl.w:ptcp.w:call-paraphase-29.t:call-call_f8 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:22.775 wdl.w:ptcp.w:call-paraphase-29.t:call-call_f8 INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:22.775 wdl.w:ptcp.w:call-paraphase-29.t:call-call_f8 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:22.819 wdl.w:ptcp.w:call-paraphase-29.t:call-call_f8 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 8, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-29/call-call_f8/_singularity_tmpdir_9amth_u3"
2025-09-15 20:24:22.819 wdl.w:ptcp.w:call-paraphase-29.t:call-call_f8 INFO Slurm invocation: srun --job-name call-call_f8 --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-29/call-call_f8/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-29/call-call_f8/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-29/call-call_f8/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-29/call-call_f8/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-29/call-run_paraphase/out/m84036_250809_035451_s4.bc2126_paraphase/m84036_250809_035451_s4.bc2126.paraphase.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2126.paraphase.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-29/call-run_paraphase/out/m84036_250809_035451_s4.bc2126_paraphase/m84036_250809_035451_s4.bc2126.paraphase.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2126.paraphase.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-29/call-call_f8/_singularity_tmpdir_9amth_u3/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-29/call-call_f8/_singularity_tmpdir_9amth_u3/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:22.828 wdl.w:ptcp.w:call-paraphase-29.t:call-call_f8 NOTICE slurm_singularity run :: pid: 1201608, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-29/call-call_f8/slurm_singularity.log.txt"
2025-09-15 20:24:22.881 wdl.w:ptcp.w:call-trgt-25.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO srun: job 51797616 queued and waiting for resources
2025-09-15 20:24:22.881 wdl.w:ptcp.w:call-trgt-25.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO srun: job 51797616 has been allocated resources
2025-09-15 20:24:22.881 wdl.w:ptcp.w:call-trgt-25.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:22.964 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:22 [ERROR] - No reads found for TRID=SCA37_DAB1
2025-09-15 20:24:22.964 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:22 [ERROR] - No reads found for TRID=SCA2_ATXN2
2025-09-15 20:24:22.965 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:22 [ERROR] - No reads found for TRID=OPDM4_RILPL1
2025-09-15 20:24:22.965 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:22 [ERROR] - No reads found for TRID=SCA3_ATXN3
2025-09-15 20:24:22.965 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:22 [ERROR] - No reads found for TRID=SCA27B_FGF14
2025-09-15 20:24:22.972 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_plot_meth_allele.slurm_singularity INFO srun: job 51797617 queued and waiting for resources
2025-09-15 20:24:22.972 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_plot_meth_allele.slurm_singularity INFO srun: job 51797617 has been allocated resources
2025-09-15 20:24:22.972 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_plot_meth_allele.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:22.997 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:22 [ERROR] - No reads found for TRID=SCA37_DAB1
2025-09-15 20:24:23.007 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO srun: job 51797618 queued and waiting for resources
2025-09-15 20:24:23.007 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO srun: job 51797618 has been allocated resources
2025-09-15 20:24:23.007 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:23.028 wdl.w:ptcp.w:call-trgt-29.t:call-trgt_plot_motifs_waterfall INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2126.motifs_waterfall.trgt_plots.zip"
2025-09-15 20:24:23.065 wdl.w:ptcp.w:call-trgt-13.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:18 [ERROR] - No reads found for TRID=PRTS_ARX
2025-09-15 20:24:23.065 wdl.w:ptcp.w:call-trgt-13.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:18 [ERROR] - No reads found for TRID=EIEE1_ARX
2025-09-15 20:24:23.113 wdl.w:ptcp.t:call-pbmm2_align_hifi-83 INFO output :: name: "mapped_bam", value: "m84036_250809_035451_s4.bc2180.mapped.bam"
2025-09-15 20:24:23.116 wdl.w:ptcp.t:call-pbmm2_align_hifi-83 INFO output :: name: "mapped_bam_bai", value: "m84036_250809_035451_s4.bc2180.mapped.bam.bai"
2025-09-15 20:24:23.117 wdl.w:ptcp.t:call-pbmm2_align_hifi-83 INFO output :: name: "mapped_bam_pbi", value: "m84036_250809_035451_s4.bc2180.mapped.bam.pbi"
2025-09-15 20:24:23.118 wdl.w:ptcp.t:call-pbmm2_align_hifi-83 INFO output :: name: "report", value: "mapping_stats.report.json"
2025-09-15 20:24:23.173 wdl.w:ptcp.w:call-trgt-29.t:call-trgt_plot_motifs_waterfall NOTICE done
2025-09-15 20:24:23.178 wdl.w:ptcp.w:call-trgt-29 NOTICE finish :: job: "call-trgt_plot_motifs_waterfall"
2025-09-15 20:24:23.178 wdl.w:ptcp.w:call-trgt-29 INFO output :: job: "call-trgt_plot_motifs_waterfall", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-29/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2126.motifs_waterfall.trgt_plots.zip"}
2025-09-15 20:24:23.179 wdl.w:ptcp.w:call-trgt-29 INFO visit :: node: "output-images_motifs_waterfall", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-29/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2126.motifs_waterfall.trgt_plots.zip"}
2025-09-15 20:24:23.179 wdl.w:ptcp.w:call-trgt-29 INFO visit :: node: "outputs", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-29/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2126.motifs_waterfall.trgt_plots.zip", "images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-29/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2126.meth_allele.trgt_plots.zip", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-29/call-trgt_genotype/out/m84036_250809_035451_s4.bc2126.trgt.sorted.spanning.bam.bai", "images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-29/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2126.motifs_allele.trgt_plots.zip", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-29/call-trgt_genotype/out/m84036_250809_035451_s4.bc2126.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-29/call-trgt_genotype/out/m84036_250809_035451_s4.bc2126.trgt.vcf", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-29/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2126.repeats.bam", "images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-29/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2126.meth_waterfall.trgt_plots.zip", "reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-29/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2126.repeats.bam.bai"}
2025-09-15 20:24:23.191 wdl.w:ptcp.w:call-paraphase-21.t:call-call_f8 NOTICE task setup :: name: "call_f8", source: "./paraphase.wdl", line: 232, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-21/call-call_f8", thread: 140608203109952
2025-09-15 20:24:23.211 wdl.w:ptcp.w:call-paraphase-21.t:call-call_f8 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:23.211 wdl.w:ptcp.w:call-paraphase-21.t:call-call_f8 INFO input :: name: "genome_version", value: "38"
2025-09-15 20:24:23.211 wdl.w:ptcp.w:call-paraphase-21.t:call-call_f8 INFO input :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2118"
2025-09-15 20:24:23.211 wdl.w:ptcp.w:call-paraphase-21.t:call-call_f8 INFO input :: name: "paraphase_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2118.paraphase.bam.bai"
2025-09-15 20:24:23.211 wdl.w:ptcp.w:call-paraphase-21.t:call-call_f8 INFO input :: name: "paraphase_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2118.paraphase.bam"
2025-09-15 20:24:23.211 wdl.w:ptcp.w:call-paraphase-21.t:call-call_f8 INFO input :: name: "sex", value: "F"
2025-09-15 20:24:23.211 wdl.w:ptcp.w:call-paraphase-21.t:call-call_f8 INFO eval :: name: "threads", value: 1
2025-09-15 20:24:23.211 wdl.w:ptcp.w:call-paraphase-21.t:call-call_f8 INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:23.211 wdl.w:ptcp.w:call-paraphase-21.t:call-call_f8 INFO eval :: name: "disk_size", value: 11
2025-09-15 20:24:23.212 wdl.w:ptcp.w:call-paraphase-21.t:call-call_f8 INFO eval :: name: "sample_sex", value: "F"
2025-09-15 20:24:23.212 wdl.w:ptcp.w:call-paraphase-21.t:call-call_f8 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:23.212 wdl.w:ptcp.w:call-paraphase-21.t:call-call_f8 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:23.212 wdl.w:ptcp.w:call-paraphase-21.t:call-call_f8 INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:23.212 wdl.w:ptcp.w:call-paraphase-21.t:call-call_f8 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:23.219 wdl.w:ptcp.t:call-pbmm2_align_hifi-83 NOTICE done
2025-09-15 20:24:23.224 wdl.w:ptcp NOTICE finish :: job: "call-pbmm2_align_hifi-83"
2025-09-15 20:24:23.225 wdl.w:ptcp INFO output :: job: "call-pbmm2_align_hifi-83", values: {"report": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-83/out/mapping_stats.report.json", "mapped_bam_pbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-83/out/m84036_250809_035451_s4.bc2180.mapped.bam.pbi", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-83/out/m84036_250809_035451_s4.bc2180.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-83/out/m84036_250809_035451_s4.bc2180.mapped.bam"}
2025-09-15 20:24:23.225 wdl.w:ptcp NOTICE ready :: job: "call-paraphase-83", callee: "paraphase"
2025-09-15 20:24:23.226 wdl.w:ptcp INFO input :: job: "call-paraphase-83", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf", "genome_version": "38", "config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-83/out/m84036_250809_035451_s4.bc2180.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-83/out/m84036_250809_035451_s4.bc2180.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2180"}
2025-09-15 20:24:23.227 wdl.w:ptcp NOTICE ready :: job: "call-sawfish-83", callee: "sawfish"
2025-09-15 20:24:23.227 wdl.w:ptcp INFO input :: job: "call-sawfish-83", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-83/out/m84036_250809_035451_s4.bc2180.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-83/out/m84036_250809_035451_s4.bc2180.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2180"}
2025-09-15 20:24:23.228 wdl.w:ptcp NOTICE ready :: job: "call-trgt-83", callee: "trgt"
2025-09-15 20:24:23.228 wdl.w:ptcp INFO input :: job: "call-trgt-83", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-83/out/m84036_250809_035451_s4.bc2180.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-83/out/m84036_250809_035451_s4.bc2180.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2180"}
2025-09-15 20:24:23.230 wdl.w:ptcp INFO visit :: node: "gather-call-pbmm2_align_hifi", values: "(((large)))"
2025-09-15 20:24:23.230 wdl.w:ptcp INFO visit :: node: "output-mapped_bam", values: "(((large)))"
2025-09-15 20:24:23.231 wdl.w:ptcp INFO visit :: node: "output-mapped_bam_bai", values: "(((large)))"
2025-09-15 20:24:23.234 wdl.w:ptcp.w:call-paraphase-09.t:call-call_f8 NOTICE task setup :: name: "call_f8", source: "./paraphase.wdl", line: 232, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-09/call-call_f8", thread: 140607666239040
2025-09-15 20:24:23.240 wdl.w:ptcp.w:call-trgt-13.t:call-trgt_plot_meth_allele INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2110.meth_allele.trgt_plots.zip"
2025-09-15 20:24:23.250 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_meth_waterfall INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2124.meth_waterfall.trgt_plots.zip"
2025-09-15 20:24:23.274 wdl.w:ptcp.w:call-paraphase-09.t:call-call_f8 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:23.275 wdl.w:ptcp.w:call-paraphase-09.t:call-call_f8 INFO input :: name: "genome_version", value: "38"
2025-09-15 20:24:23.275 wdl.w:ptcp.w:call-paraphase-09.t:call-call_f8 INFO input :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2106"
2025-09-15 20:24:23.275 wdl.w:ptcp.w:call-paraphase-09.t:call-call_f8 INFO input :: name: "paraphase_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2106.paraphase.bam.bai"
2025-09-15 20:24:23.275 wdl.w:ptcp.w:call-paraphase-09.t:call-call_f8 INFO input :: name: "paraphase_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2106.paraphase.bam"
2025-09-15 20:24:23.275 wdl.w:ptcp.w:call-paraphase-09.t:call-call_f8 INFO input :: name: "sex", value: "F"
2025-09-15 20:24:23.275 wdl.w:ptcp.w:call-paraphase-09.t:call-call_f8 INFO eval :: name: "threads", value: 1
2025-09-15 20:24:23.275 wdl.w:ptcp.w:call-paraphase-09.t:call-call_f8 INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:23.275 wdl.w:ptcp.w:call-paraphase-09.t:call-call_f8 INFO eval :: name: "disk_size", value: 11
2025-09-15 20:24:23.276 wdl.w:ptcp.w:call-paraphase-09.t:call-call_f8 INFO eval :: name: "sample_sex", value: "F"
2025-09-15 20:24:23.276 wdl.w:ptcp.w:call-paraphase-09.t:call-call_f8 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:23.276 wdl.w:ptcp.w:call-paraphase-09.t:call-call_f8 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:23.277 wdl.w:ptcp.w:call-paraphase-09.t:call-call_f8 INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:23.277 wdl.w:ptcp.w:call-paraphase-09.t:call-call_f8 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:23.283 wdl.w:ptcp.w:call-paraphase-21.t:call-call_f8 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 8, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-21/call-call_f8/_singularity_tmpdir_gxbkc2ho"
2025-09-15 20:24:23.283 wdl.w:ptcp.w:call-paraphase-21.t:call-call_f8 INFO Slurm invocation: srun --job-name call-call_f8 --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-21/call-call_f8/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-21/call-call_f8/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-21/call-call_f8/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-21/call-call_f8/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-21/call-run_paraphase/out/m84036_250809_035451_s4.bc2118_paraphase/m84036_250809_035451_s4.bc2118.paraphase.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2118.paraphase.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-21/call-run_paraphase/out/m84036_250809_035451_s4.bc2118_paraphase/m84036_250809_035451_s4.bc2118.paraphase.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2118.paraphase.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-21/call-call_f8/_singularity_tmpdir_gxbkc2ho/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-21/call-call_f8/_singularity_tmpdir_gxbkc2ho/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:23.286 wdl.w:ptcp.w:call-trgt-29 NOTICE done
2025-09-15 20:24:23.290 wdl.w:ptcp NOTICE finish :: job: "call-trgt-29"
2025-09-15 20:24:23.290 wdl.w:ptcp INFO output :: job: "call-trgt-29", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-29/out/m84036_250809_035451_s4.bc2126.motifs_waterfall.trgt_plots.zip", "images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-29/out/m84036_250809_035451_s4.bc2126.meth_allele.trgt_plots.zip", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-29/out/m84036_250809_035451_s4.bc2126.trgt.sorted.spanning.bam.bai", "images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-29/out/m84036_250809_035451_s4.bc2126.motifs_allele.trgt_plots.zip", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-29/out/m84036_250809_035451_s4.bc2126.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-29/out/m84036_250809_035451_s4.bc2126.trgt.vcf", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-29/out/m84036_250809_035451_s4.bc2126.repeats.bam", "images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-29/out/m84036_250809_035451_s4.bc2126.meth_waterfall.trgt_plots.zip", "reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-29/out/m84036_250809_035451_s4.bc2126.repeats.bam.bai"}
2025-09-15 20:24:23.296 wdl.w:ptcp.w:call-trgt-13.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:19 [ERROR] - No reads found for TRID=PRTS_ARX
2025-09-15 20:24:23.296 wdl.w:ptcp.w:call-trgt-13.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:19 [ERROR] - No reads found for TRID=EIEE1_ARX
2025-09-15 20:24:23.298 wdl.w:ptcp.w:call-trgt-48 NOTICE workflow start :: name: "trgt", source: "./trgt.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-48"
2025-09-15 20:24:23.323 wdl.w:ptcp.w:call-trgt-48 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:24:23.323 wdl.w:ptcp.w:call-trgt-48 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-48/out/m84036_250809_035451_s4.bc2145.mapped.bam"}
2025-09-15 20:24:23.323 wdl.w:ptcp.w:call-trgt-48 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-48/out/m84036_250809_035451_s4.bc2145.mapped.bam.bai"}
2025-09-15 20:24:23.323 wdl.w:ptcp.w:call-trgt-48 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:24:23.323 wdl.w:ptcp.w:call-trgt-48 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:24:23.323 wdl.w:ptcp.w:call-trgt-48 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2145"}
2025-09-15 20:24:23.323 wdl.w:ptcp.w:call-trgt-48 INFO visit :: node: "decl-sex", values: {"sex": "F"}
2025-09-15 20:24:23.323 wdl.w:ptcp.w:call-trgt-48 INFO visit :: node: "decl-trgt_bed", values: {"trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"}
2025-09-15 20:24:23.324 wdl.w:ptcp.w:call-trgt-48 NOTICE ready :: job: "call-get_reads_overlapping_repeats", callee: "get_reads_overlapping_repeats"
2025-09-15 20:24:23.324 wdl.w:ptcp.w:call-trgt-48 INFO input :: job: "call-get_reads_overlapping_repeats", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-48/out/m84036_250809_035451_s4.bc2145.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-48/out/m84036_250809_035451_s4.bc2145.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2145"}
2025-09-15 20:24:23.324 wdl.w:ptcp.w:call-trgt-48 NOTICE ready :: job: "call-trgt_genotype", callee: "trgt_genotype"
2025-09-15 20:24:23.324 wdl.w:ptcp.w:call-trgt-48 INFO input :: job: "call-trgt_genotype", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-48/out/m84036_250809_035451_s4.bc2145.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-48/out/m84036_250809_035451_s4.bc2145.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2145"}
2025-09-15 20:24:23.341 wdl.w:ptcp.w:call-paraphase-21.t:call-call_f8 NOTICE slurm_singularity run :: pid: 1201644, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-21/call-call_f8/slurm_singularity.log.txt"
2025-09-15 20:24:23.364 wdl.w:ptcp.w:call-paraphase-09.t:call-call_f8 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 8, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-09/call-call_f8/_singularity_tmpdir_7uzlsup3"
2025-09-15 20:24:23.364 wdl.w:ptcp.w:call-paraphase-09.t:call-call_f8 INFO Slurm invocation: srun --job-name call-call_f8 --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-09/call-call_f8/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-09/call-call_f8/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-09/call-call_f8/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-09/call-call_f8/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-09/call-run_paraphase/out/m84036_250809_035451_s4.bc2106_paraphase/m84036_250809_035451_s4.bc2106.paraphase.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2106.paraphase.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-09/call-run_paraphase/out/m84036_250809_035451_s4.bc2106_paraphase/m84036_250809_035451_s4.bc2106.paraphase.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2106.paraphase.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-09/call-call_f8/_singularity_tmpdir_7uzlsup3/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-09/call-call_f8/_singularity_tmpdir_7uzlsup3/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:23.372 wdl.w:ptcp.w:call-trgt-27.t:call-trgt_plot_meth_waterfall NOTICE done
2025-09-15 20:24:23.382 wdl.w:ptcp.w:call-paraphase-09.t:call-call_f8 NOTICE slurm_singularity run :: pid: 1201646, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-09/call-call_f8/slurm_singularity.log.txt"
2025-09-15 20:24:23.401 wdl.w:ptcp.w:call-trgt-13.t:call-trgt_plot_meth_allele NOTICE done
2025-09-15 20:24:23.414 wdl.w:ptcp.w:call-trgt-27 NOTICE finish :: job: "call-trgt_plot_meth_waterfall"
2025-09-15 20:24:23.414 wdl.w:ptcp.w:call-trgt-27 INFO output :: job: "call-trgt_plot_meth_waterfall", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-27/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2124.meth_waterfall.trgt_plots.zip"}
2025-09-15 20:24:23.414 wdl.w:ptcp.w:call-trgt-27 INFO visit :: node: "output-images_meth_waterfall", values: {"images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-27/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2124.meth_waterfall.trgt_plots.zip"}
2025-09-15 20:24:23.414 wdl.w:ptcp.w:call-trgt-27 INFO visit :: node: "outputs", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-27/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2124.motifs_waterfall.trgt_plots.zip", "images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-27/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2124.meth_allele.trgt_plots.zip", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-27/call-trgt_genotype/out/m84036_250809_035451_s4.bc2124.trgt.sorted.spanning.bam.bai", "images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-27/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2124.motifs_allele.trgt_plots.zip", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-27/call-trgt_genotype/out/m84036_250809_035451_s4.bc2124.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-27/call-trgt_genotype/out/m84036_250809_035451_s4.bc2124.trgt.vcf", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-27/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2124.repeats.bam", "images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-27/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2124.meth_waterfall.trgt_plots.zip", "reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-27/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2124.repeats.bam.bai"}
2025-09-15 20:24:23.416 wdl.w:ptcp.w:call-trgt-13 NOTICE finish :: job: "call-trgt_plot_meth_allele"
2025-09-15 20:24:23.416 wdl.w:ptcp.w:call-trgt-13 INFO output :: job: "call-trgt_plot_meth_allele", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-13/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2110.meth_allele.trgt_plots.zip"}
2025-09-15 20:24:23.416 wdl.w:ptcp.w:call-trgt-13 INFO visit :: node: "output-images_meth_allele", values: {"images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-13/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2110.meth_allele.trgt_plots.zip"}
2025-09-15 20:24:23.421 wdl.w:ptcp.w:call-trgt-32.t:call-trgt_plot_meth_allele NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-32/call-trgt_plot_meth_allele", thread: 140608748373568
2025-09-15 20:24:23.423 wdl.w:ptcp.w:call-trgt-32.t:call-trgt_plot_meth_waterfall NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-32/call-trgt_plot_meth_waterfall", thread: 140613823374912
2025-09-15 20:24:23.441 wdl.w:ptcp.w:call-trgt-32.t:call-trgt_plot_meth_allele INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:23.442 wdl.w:ptcp.w:call-trgt-32.t:call-trgt_plot_meth_allele INFO input :: name: "waterfall", value: false
2025-09-15 20:24:23.442 wdl.w:ptcp.w:call-trgt-32.t:call-trgt_plot_meth_allele INFO input :: name: "methylation", value: true
2025-09-15 20:24:23.442 wdl.w:ptcp.w:call-trgt-32.t:call-trgt_plot_meth_waterfall INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:23.442 wdl.w:ptcp.w:call-trgt-32.t:call-trgt_plot_meth_allele INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:23.442 wdl.w:ptcp.w:call-trgt-32.t:call-trgt_plot_meth_waterfall INFO input :: name: "waterfall", value: true
2025-09-15 20:24:23.442 wdl.w:ptcp.w:call-trgt-32.t:call-trgt_plot_meth_allele INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:23.443 wdl.w:ptcp.w:call-trgt-32.t:call-trgt_plot_meth_waterfall INFO input :: name: "methylation", value: true
2025-09-15 20:24:23.443 wdl.w:ptcp.w:call-trgt-32.t:call-trgt_plot_meth_allele INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:23.443 wdl.w:ptcp.w:call-trgt-32.t:call-trgt_plot_meth_waterfall INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:23.443 wdl.w:ptcp.w:call-trgt-32.t:call-trgt_plot_meth_allele INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2129.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:23.443 wdl.w:ptcp.w:call-trgt-32.t:call-trgt_plot_meth_waterfall INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:23.443 wdl.w:ptcp.w:call-trgt-32.t:call-trgt_plot_meth_allele INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2129.trgt.sorted.spanning.bam"
2025-09-15 20:24:23.443 wdl.w:ptcp.w:call-trgt-32.t:call-trgt_plot_meth_waterfall INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:23.443 wdl.w:ptcp.w:call-trgt-32.t:call-trgt_plot_meth_allele INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2129.trgt.vcf"
2025-09-15 20:24:23.443 wdl.w:ptcp.w:call-trgt-32.t:call-trgt_plot_meth_waterfall INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2129.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:23.443 wdl.w:ptcp.w:call-trgt-32.t:call-trgt_plot_meth_allele INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2129"
2025-09-15 20:24:23.443 wdl.w:ptcp.w:call-trgt-32.t:call-trgt_plot_meth_waterfall INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2129.trgt.sorted.spanning.bam"
2025-09-15 20:24:23.444 wdl.w:ptcp.w:call-trgt-32.t:call-trgt_plot_meth_allele INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:23.444 wdl.w:ptcp.w:call-trgt-32.t:call-trgt_plot_meth_waterfall INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2129.trgt.vcf"
2025-09-15 20:24:23.444 wdl.w:ptcp.w:call-trgt-32.t:call-trgt_plot_meth_allele INFO eval :: name: "plot_type", value: "allele"
2025-09-15 20:24:23.444 wdl.w:ptcp.w:call-trgt-32.t:call-trgt_plot_meth_waterfall INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2129"
2025-09-15 20:24:23.444 wdl.w:ptcp.w:call-trgt-32.t:call-trgt_plot_meth_allele INFO eval :: name: "show", value: "meth"
2025-09-15 20:24:23.444 wdl.w:ptcp.w:call-trgt-32.t:call-trgt_plot_meth_waterfall INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:23.444 wdl.w:ptcp.w:call-trgt-32.t:call-trgt_plot_meth_allele INFO eval :: name: "threads", value: 1
2025-09-15 20:24:23.445 wdl.w:ptcp.w:call-trgt-32.t:call-trgt_plot_meth_waterfall INFO eval :: name: "plot_type", value: "waterfall"
2025-09-15 20:24:23.445 wdl.w:ptcp.w:call-trgt-32.t:call-trgt_plot_meth_waterfall INFO eval :: name: "show", value: "meth"
2025-09-15 20:24:23.445 wdl.w:ptcp.w:call-trgt-32.t:call-trgt_plot_meth_allele INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:23.445 wdl.w:ptcp.w:call-trgt-32.t:call-trgt_plot_meth_waterfall INFO eval :: name: "threads", value: 1
2025-09-15 20:24:23.445 wdl.w:ptcp.w:call-trgt-32.t:call-trgt_plot_meth_allele INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2129.meth_allele"
2025-09-15 20:24:23.446 wdl.w:ptcp.w:call-trgt-32.t:call-trgt_plot_meth_waterfall INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:23.446 wdl.w:ptcp.w:call-trgt-32.t:call-trgt_plot_meth_allele INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:23.446 wdl.w:ptcp.w:call-trgt-32.t:call-trgt_plot_meth_waterfall INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2129.meth_waterfall"
2025-09-15 20:24:23.446 wdl.w:ptcp.w:call-trgt-32.t:call-trgt_plot_meth_allele WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:23.446 wdl.w:ptcp.w:call-trgt-32.t:call-trgt_plot_meth_waterfall INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:23.447 wdl.w:ptcp.w:call-trgt-32.t:call-trgt_plot_meth_waterfall WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:23.447 wdl.w:ptcp.w:call-trgt-32.t:call-trgt_plot_meth_allele INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:23.447 wdl.w:ptcp.w:call-trgt-32.t:call-trgt_plot_meth_allele INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:23.447 wdl.w:ptcp.w:call-trgt-32.t:call-trgt_plot_meth_waterfall INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:23.447 wdl.w:ptcp.w:call-trgt-32.t:call-trgt_plot_meth_waterfall INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:23.451 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:23 [ERROR] - No reads found for TRID=SCA37_DAB1
2025-09-15 20:24:23.461 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_plot_motifs_allele.slurm_singularity INFO srun: job 51797619 queued and waiting for resources
2025-09-15 20:24:23.461 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_plot_motifs_allele.slurm_singularity INFO srun: job 51797619 has been allocated resources
2025-09-15 20:24:23.461 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_plot_motifs_allele.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:23.501 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO srun: job 51797620 queued and waiting for resources
2025-09-15 20:24:23.501 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO srun: job 51797620 has been allocated resources
2025-09-15 20:24:23.501 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:23.516 wdl.w:ptcp.w:call-trgt-27 NOTICE done
2025-09-15 20:24:23.523 wdl.w:ptcp NOTICE finish :: job: "call-trgt-27"
2025-09-15 20:24:23.523 wdl.w:ptcp INFO output :: job: "call-trgt-27", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-27/out/m84036_250809_035451_s4.bc2124.motifs_waterfall.trgt_plots.zip", "images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-27/out/m84036_250809_035451_s4.bc2124.meth_allele.trgt_plots.zip", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-27/out/m84036_250809_035451_s4.bc2124.trgt.sorted.spanning.bam.bai", "images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-27/out/m84036_250809_035451_s4.bc2124.motifs_allele.trgt_plots.zip", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-27/out/m84036_250809_035451_s4.bc2124.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-27/out/m84036_250809_035451_s4.bc2124.trgt.vcf", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-27/out/m84036_250809_035451_s4.bc2124.repeats.bam", "images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-27/out/m84036_250809_035451_s4.bc2124.meth_waterfall.trgt_plots.zip", "reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-27/out/m84036_250809_035451_s4.bc2124.repeats.bam.bai"}
2025-09-15 20:24:23.533 wdl.w:ptcp.w:call-trgt-32.t:call-trgt_plot_meth_allele INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-32/call-trgt_plot_meth_allele/_singularity_tmpdir_eo4p_5k7"
2025-09-15 20:24:23.533 wdl.w:ptcp.w:call-trgt-32.t:call-trgt_plot_meth_allele INFO Slurm invocation: srun --job-name call-trgt_plot_meth_allele --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-32/call-trgt_plot_meth_allele/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-32/call-trgt_plot_meth_allele/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-32/call-trgt_plot_meth_allele/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-32/call-trgt_plot_meth_allele/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-32/call-trgt_genotype/out/m84036_250809_035451_s4.bc2129.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2129.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-32/call-trgt_genotype/out/m84036_250809_035451_s4.bc2129.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2129.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-32/call-trgt_genotype/out/m84036_250809_035451_s4.bc2129.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2129.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-32/call-trgt_plot_meth_allele/_singularity_tmpdir_eo4p_5k7/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-32/call-trgt_plot_meth_allele/_singularity_tmpdir_eo4p_5k7/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:23.534 wdl.w:ptcp.w:call-paraphase-57 NOTICE workflow start :: name: "paraphase", source: "./paraphase.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-57"
2025-09-15 20:24:23.544 wdl.w:ptcp.w:call-trgt-12.t:call-trgt_plot_meth_waterfall INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2109.meth_waterfall.trgt_plots.zip"
2025-09-15 20:24:23.546 wdl.w:ptcp.w:call-trgt-32.t:call-trgt_plot_meth_waterfall INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-32/call-trgt_plot_meth_waterfall/_singularity_tmpdir_bliimvp4"
2025-09-15 20:24:23.547 wdl.w:ptcp.w:call-trgt-32.t:call-trgt_plot_meth_waterfall INFO Slurm invocation: srun --job-name call-trgt_plot_meth_waterfall --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-32/call-trgt_plot_meth_waterfall/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-32/call-trgt_plot_meth_waterfall/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-32/call-trgt_plot_meth_waterfall/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-32/call-trgt_plot_meth_waterfall/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-32/call-trgt_genotype/out/m84036_250809_035451_s4.bc2129.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2129.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-32/call-trgt_genotype/out/m84036_250809_035451_s4.bc2129.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2129.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-32/call-trgt_genotype/out/m84036_250809_035451_s4.bc2129.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2129.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-32/call-trgt_plot_meth_waterfall/_singularity_tmpdir_bliimvp4/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-32/call-trgt_plot_meth_waterfall/_singularity_tmpdir_bliimvp4/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:23.546 wdl.w:ptcp.w:call-sawfish-15.t:call-run_sawfish.stderr VERBOSE [M::mm_idx_gen::47.778*1.64] collected minimizers
2025-09-15 20:24:23.551 wdl.w:ptcp.w:call-sawfish-15.t:call-run_sawfish.stderr VERBOSE [M::mm_idx_gen::58.642*1.87] sorted minimizers
2025-09-15 20:24:23.551 wdl.w:ptcp.w:call-sawfish-15.t:call-run_sawfish.stderr VERBOSE [M::main::58.643*1.87] loaded/built the index for 195 target sequence(s)
2025-09-15 20:24:23.551 wdl.w:ptcp.w:call-sawfish-15.t:call-run_sawfish.stderr VERBOSE [M::mm_mapopt_update::64.488*1.79] mid_occ = 136
2025-09-15 20:24:23.551 wdl.w:ptcp.w:call-sawfish-15.t:call-run_sawfish.stderr VERBOSE [M::mm_idx_stat] kmer size: 19; skip: 19; is_hpc: 0; #seq: 195
2025-09-15 20:24:23.551 wdl.w:ptcp.w:call-sawfish-15.t:call-run_sawfish.stderr VERBOSE [M::mm_idx_stat::68.024*1.75] distinct minimizers: 214664461 (92.23% are singletons); average occurrences: 1.372; average spacing: 10.529; total length: 3099922541
2025-09-15 20:24:23.551 wdl.w:ptcp.w:call-sawfish-15.t:call-run_sawfish.stderr VERBOSE [M::bam2fq_mainloop] discarded 0 singletons
2025-09-15 20:24:23.551 wdl.w:ptcp.w:call-sawfish-15.t:call-run_sawfish.stderr VERBOSE [M::bam2fq_mainloop] processed 301 reads
2025-09-15 20:24:23.551 wdl.w:ptcp.w:call-sawfish-15.t:call-run_sawfish.stderr VERBOSE [M::worker_pipeline::68.685*1.76] mapped 301 sequences
2025-09-15 20:24:23.551 wdl.w:ptcp.w:call-sawfish-15.t:call-run_sawfish.stderr VERBOSE [M::main] Version: 2.26-r1175
2025-09-15 20:24:23.551 wdl.w:ptcp.w:call-sawfish-15.t:call-run_sawfish.stderr VERBOSE [M::main] CMD: /opt/pacbio/smrttools/install/smrtlink-release_25.1.0.257715/bundles/smrttools/install/smrttools-release_25.1.0.257715/private/thirdparty/minimap2/minimap2_2.26-pacbio2/binwrap/../../../../../private/thirdparty/minimap2/minimap2_2.26-pacbio2/bin/minimap2 -a -y -x map-hifi -Y -E 1,0 /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa -
2025-09-15 20:24:23.551 wdl.w:ptcp.w:call-sawfish-15.t:call-run_sawfish.stderr VERBOSE [M::main] Real time: 69.058 sec; CPU: 121.192 sec; Peak RSS: 11.885 GB
2025-09-15 20:24:23.551 wdl.w:ptcp.w:call-sawfish-15.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:10][sawfish][INFO] Starting sawfish 2.0.3
2025-09-15 20:24:23.552 wdl.w:ptcp.w:call-sawfish-15.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:10][sawfish][INFO] cmdline: sawfish discover --disable-cnv --threads 16 --ref /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa --bam m84036_250809_035451_s4.bc2112.minimap2.bam --output-dir m84036_250809_035451_s4.bc2112_sawfish_discover
2025-09-15 20:24:23.552 wdl.w:ptcp.w:call-sawfish-15.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:10][sawfish][INFO] Running on 16 threads
2025-09-15 20:24:23.552 wdl.w:ptcp.w:call-sawfish-15.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:10][sawfish][INFO] Writing discover settings to file: 'm84036_250809_035451_s4.bc2112_sawfish_discover/discover.settings.json'
2025-09-15 20:24:23.552 wdl.w:ptcp.w:call-sawfish-15.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:10][sawfish][INFO] Reading reference genome from file '/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa'
2025-09-15 20:24:23.552 wdl.w:ptcp.w:call-sawfish-15.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:17][sawfish][INFO] Processing alignment file '/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2112.minimap2.bam'
2025-09-15 20:24:23.552 wdl.w:ptcp.w:call-sawfish-15.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:17][sawfish][INFO] Finished processing all alignments
2025-09-15 20:24:23.552 wdl.w:ptcp.w:call-sawfish-15.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:17][sawfish][INFO] Writing depth bins to binary file: 'm84036_250809_035451_s4.bc2112_sawfish_discover/depth.mpack'
2025-09-15 20:24:23.552 wdl.w:ptcp.w:call-sawfish-15.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:17][sawfish][INFO] Writing max sv depth genome regions to bed file: 'm84036_250809_035451_s4.bc2112_sawfish_discover/max.depth.bed'
2025-09-15 20:24:23.552 wdl.w:ptcp.w:call-sawfish-15.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:17][sawfish][INFO] Completing breakpoint observation clustering
2025-09-15 20:24:23.552 wdl.w:ptcp.w:call-sawfish-15.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:17][sawfish][INFO] Finished breakpoint observation clustering
2025-09-15 20:24:23.553 wdl.w:ptcp.w:call-sawfish-15.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:17][sawfish][INFO] Consolidating adjacent indel candidates
2025-09-15 20:24:23.553 wdl.w:ptcp.w:call-sawfish-15.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:17][sawfish][INFO] Finding large insertion candidates
2025-09-15 20:24:23.553 wdl.w:ptcp.w:call-sawfish-15.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:17][sawfish][INFO] Writing breakpoint_cluster debug bed file: 'm84036_250809_035451_s4.bc2112_sawfish_discover/debug.breakpoint_clusters.bed'
2025-09-15 20:24:23.553 wdl.w:ptcp.w:call-sawfish-15.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:17][sawfish][INFO] Refining SV Candidates
2025-09-15 20:24:23.553 wdl.w:ptcp.w:call-sawfish-15.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:17][sawfish][INFO] Writing debug assembly region bed file: 'm84036_250809_035451_s4.bc2112_sawfish_discover/assembly.regions.bed'
2025-09-15 20:24:23.553 wdl.w:ptcp.w:call-sawfish-15.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:17][sawfish][INFO] Starting refinement of breakpoint evidence clusters
2025-09-15 20:24:23.553 wdl.w:ptcp.w:call-sawfish-15.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:18][sawfish][INFO] Finished refining all breakpoint evidence clusters
2025-09-15 20:24:23.553 wdl.w:ptcp.w:call-sawfish-15.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:18][sawfish][INFO] Writing all contig alignments to bam file: 'm84036_250809_035451_s4.bc2112_sawfish_discover/contig.alignment.bam'
2025-09-15 20:24:23.553 wdl.w:ptcp.w:call-sawfish-15.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:19][sawfish][INFO] Writing candidate structural variants to file: 'm84036_250809_035451_s4.bc2112_sawfish_discover/candidate.sv.bcf'
2025-09-15 20:24:23.553 wdl.w:ptcp.w:call-sawfish-15.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:19][sawfish][INFO] Writing run statistics to file: 'm84036_250809_035451_s4.bc2112_sawfish_discover/run.stats.json'
2025-09-15 20:24:23.553 wdl.w:ptcp.w:call-sawfish-15.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:19][sawfish][INFO] sawfish completed. Total Runtime: 00:00:08.881
2025-09-15 20:24:23.559 wdl.w:ptcp.w:call-trgt-13.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:19 [ERROR] - No reads found for TRID=PRTS_ARX
2025-09-15 20:24:23.560 wdl.w:ptcp.w:call-trgt-13.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:19 [ERROR] - No reads found for TRID=EIEE1_ARX
2025-09-15 20:24:23.563 wdl.w:ptcp.w:call-trgt-33.t:call-trgt_plot_motifs_waterfall INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2130.motifs_waterfall.trgt_plots.zip"
2025-09-15 20:24:23.568 wdl.w:ptcp.w:call-paraphase-57 INFO visit :: node: "decl-annotation_vcf", values: {"annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf"}
2025-09-15 20:24:23.568 wdl.w:ptcp.w:call-paraphase-57 INFO visit :: node: "decl-config_file", values: {"config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml"}
2025-09-15 20:24:23.568 wdl.w:ptcp.w:call-paraphase-57 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:24:23.568 wdl.w:ptcp.w:call-paraphase-57 INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:24:23.568 wdl.w:ptcp.w:call-paraphase-57 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-57/out/m84036_250809_035451_s4.bc2154.mapped.bam"}
2025-09-15 20:24:23.568 wdl.w:ptcp.w:call-paraphase-57 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-57/out/m84036_250809_035451_s4.bc2154.mapped.bam.bai"}
2025-09-15 20:24:23.569 wdl.w:ptcp.w:call-paraphase-57 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:24:23.569 wdl.w:ptcp.w:call-paraphase-57 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:24:23.569 wdl.w:ptcp.w:call-paraphase-57 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2154"}
2025-09-15 20:24:23.569 wdl.w:ptcp.w:call-paraphase-57 INFO visit :: node: "decl-sex", values: {"sex": "F"}
2025-09-15 20:24:23.569 wdl.w:ptcp.w:call-paraphase-57 NOTICE ready :: job: "call-run_paraphase", callee: "run_paraphase"
2025-09-15 20:24:23.569 wdl.w:ptcp.w:call-paraphase-57 INFO input :: job: "call-run_paraphase", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf", "genome_version": "38", "config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-57/out/m84036_250809_035451_s4.bc2154.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-57/out/m84036_250809_035451_s4.bc2154.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2154"}
2025-09-15 20:24:23.578 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_plot_meth_allele.slurm_singularity INFO srun: job 51797621 queued and waiting for resources
2025-09-15 20:24:23.578 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_plot_meth_allele.slurm_singularity INFO srun: job 51797621 has been allocated resources
2025-09-15 20:24:23.578 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_plot_meth_allele.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:23.582 wdl.w:ptcp.w:call-trgt-32.t:call-trgt_plot_meth_allele NOTICE slurm_singularity run :: pid: 1201660, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-32/call-trgt_plot_meth_allele/slurm_singularity.log.txt"
2025-09-15 20:24:23.582 wdl.w:ptcp.w:call-trgt-32.t:call-trgt_plot_meth_waterfall NOTICE slurm_singularity run :: pid: 1201661, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-32/call-trgt_plot_meth_waterfall/slurm_singularity.log.txt"
2025-09-15 20:24:23.594 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO srun: job 51797622 queued and waiting for resources
2025-09-15 20:24:23.594 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO srun: job 51797622 has been allocated resources
2025-09-15 20:24:23.594 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:23.676 wdl.w:ptcp.w:call-trgt-13.t:call-trgt_plot_motifs_waterfall INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2110.motifs_waterfall.trgt_plots.zip"
2025-09-15 20:24:23.687 wdl.w:ptcp.w:call-trgt-16.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:22 [ERROR] - No reads found for TRID=PRTS_ARX
2025-09-15 20:24:23.687 wdl.w:ptcp.w:call-trgt-16.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:22 [ERROR] - No reads found for TRID=EIEE1_ARX
2025-09-15 20:24:23.688 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_plot_motifs_allele.slurm_singularity INFO srun: job 51797623 queued and waiting for resources
2025-09-15 20:24:23.689 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_plot_motifs_allele.slurm_singularity INFO srun: job 51797623 has been allocated resources
2025-09-15 20:24:23.689 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_plot_motifs_allele.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:23.705 wdl.w:ptcp.w:call-trgt-05.t:call-trgt_plot_meth_allele INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2102.meth_allele.trgt_plots.zip"
2025-09-15 20:24:23.730 wdl.w:ptcp.w:call-trgt-12.t:call-trgt_plot_meth_waterfall NOTICE done
2025-09-15 20:24:23.755 wdl.w:ptcp.w:call-trgt-33.t:call-trgt_plot_motifs_waterfall NOTICE done
2025-09-15 20:24:23.762 wdl.w:ptcp.w:call-trgt-12 NOTICE finish :: job: "call-trgt_plot_meth_waterfall"
2025-09-15 20:24:23.762 wdl.w:ptcp.w:call-trgt-12 INFO output :: job: "call-trgt_plot_meth_waterfall", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-12/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2109.meth_waterfall.trgt_plots.zip"}
2025-09-15 20:24:23.763 wdl.w:ptcp.w:call-trgt-12 INFO visit :: node: "output-images_meth_waterfall", values: {"images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-12/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2109.meth_waterfall.trgt_plots.zip"}
2025-09-15 20:24:23.775 wdl.w:ptcp.w:call-trgt-32.t:call-trgt_plot_motifs_allele NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-32/call-trgt_plot_motifs_allele", thread: 140608765158976
2025-09-15 20:24:23.778 wdl.w:ptcp.w:call-trgt-33 NOTICE finish :: job: "call-trgt_plot_motifs_waterfall"
2025-09-15 20:24:23.778 wdl.w:ptcp.w:call-trgt-33 INFO output :: job: "call-trgt_plot_motifs_waterfall", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-33/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2130.motifs_waterfall.trgt_plots.zip"}
2025-09-15 20:24:23.779 wdl.w:ptcp.w:call-trgt-33 INFO visit :: node: "output-images_motifs_waterfall", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-33/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2130.motifs_waterfall.trgt_plots.zip"}
2025-09-15 20:24:23.779 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO srun: job 51797624 queued and waiting for resources
2025-09-15 20:24:23.779 wdl.w:ptcp.w:call-trgt-33 INFO visit :: node: "outputs", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-33/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2130.motifs_waterfall.trgt_plots.zip", "images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-33/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2130.meth_allele.trgt_plots.zip", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-33/call-trgt_genotype/out/m84036_250809_035451_s4.bc2130.trgt.sorted.spanning.bam.bai", "images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-33/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2130.motifs_allele.trgt_plots.zip", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-33/call-trgt_genotype/out/m84036_250809_035451_s4.bc2130.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-33/call-trgt_genotype/out/m84036_250809_035451_s4.bc2130.trgt.vcf", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-33/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2130.repeats.bam", "images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-33/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2130.meth_waterfall.trgt_plots.zip", "reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-33/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2130.repeats.bam.bai"}
2025-09-15 20:24:23.780 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO srun: job 51797624 has been allocated resources
2025-09-15 20:24:23.780 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:23.786 wdl.w:ptcp.w:call-trgt-32.t:call-trgt_plot_motifs_waterfall NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-32/call-trgt_plot_motifs_waterfall", thread: 140610342200896
2025-09-15 20:24:23.804 wdl.w:ptcp.w:call-trgt-32.t:call-trgt_plot_motifs_allele INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:23.805 wdl.w:ptcp.w:call-trgt-32.t:call-trgt_plot_motifs_allele INFO input :: name: "waterfall", value: false
2025-09-15 20:24:23.805 wdl.w:ptcp.w:call-trgt-32.t:call-trgt_plot_motifs_allele INFO input :: name: "methylation", value: false
2025-09-15 20:24:23.805 wdl.w:ptcp.w:call-trgt-32.t:call-trgt_plot_motifs_allele INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:23.805 wdl.w:ptcp.w:call-trgt-32.t:call-trgt_plot_motifs_allele INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:23.805 wdl.w:ptcp.w:call-trgt-32.t:call-trgt_plot_motifs_allele INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:23.805 wdl.w:ptcp.w:call-trgt-32.t:call-trgt_plot_motifs_allele INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2129.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:23.805 wdl.w:ptcp.w:call-trgt-32.t:call-trgt_plot_motifs_allele INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2129.trgt.sorted.spanning.bam"
2025-09-15 20:24:23.805 wdl.w:ptcp.w:call-trgt-32.t:call-trgt_plot_motifs_allele INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2129.trgt.vcf"
2025-09-15 20:24:23.805 wdl.w:ptcp.w:call-trgt-32.t:call-trgt_plot_motifs_allele INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2129"
2025-09-15 20:24:23.805 wdl.w:ptcp.w:call-trgt-32.t:call-trgt_plot_motifs_allele INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:23.806 wdl.w:ptcp.w:call-trgt-32.t:call-trgt_plot_motifs_allele INFO eval :: name: "plot_type", value: "allele"
2025-09-15 20:24:23.806 wdl.w:ptcp.w:call-trgt-32.t:call-trgt_plot_motifs_allele INFO eval :: name: "show", value: "motifs"
2025-09-15 20:24:23.806 wdl.w:ptcp.w:call-trgt-32.t:call-trgt_plot_motifs_allele INFO eval :: name: "threads", value: 1
2025-09-15 20:24:23.806 wdl.w:ptcp.w:call-trgt-32.t:call-trgt_plot_motifs_allele INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:23.807 wdl.w:ptcp.w:call-trgt-32.t:call-trgt_plot_motifs_allele INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2129.motifs_allele"
2025-09-15 20:24:23.807 wdl.w:ptcp.w:call-trgt-32.t:call-trgt_plot_motifs_allele INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:23.807 wdl.w:ptcp.w:call-trgt-32.t:call-trgt_plot_motifs_allele WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:23.808 wdl.w:ptcp.w:call-trgt-32.t:call-trgt_plot_motifs_allele INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:23.808 wdl.w:ptcp.w:call-trgt-32.t:call-trgt_plot_motifs_allele INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:23.812 wdl.w:ptcp.w:call-trgt-32.t:call-trgt_plot_motifs_waterfall INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:23.812 wdl.w:ptcp.w:call-trgt-32.t:call-trgt_plot_motifs_waterfall INFO input :: name: "waterfall", value: true
2025-09-15 20:24:23.812 wdl.w:ptcp.w:call-trgt-32.t:call-trgt_plot_motifs_waterfall INFO input :: name: "methylation", value: false
2025-09-15 20:24:23.812 wdl.w:ptcp.w:call-trgt-32.t:call-trgt_plot_motifs_waterfall INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:23.812 wdl.w:ptcp.w:call-trgt-32.t:call-trgt_plot_motifs_waterfall INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:23.812 wdl.w:ptcp.w:call-trgt-32.t:call-trgt_plot_motifs_waterfall INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:23.812 wdl.w:ptcp.w:call-trgt-32.t:call-trgt_plot_motifs_waterfall INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2129.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:23.812 wdl.w:ptcp.w:call-trgt-32.t:call-trgt_plot_motifs_waterfall INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2129.trgt.sorted.spanning.bam"
2025-09-15 20:24:23.812 wdl.w:ptcp.w:call-trgt-32.t:call-trgt_plot_motifs_waterfall INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2129.trgt.vcf"
2025-09-15 20:24:23.813 wdl.w:ptcp.w:call-trgt-32.t:call-trgt_plot_motifs_waterfall INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2129"
2025-09-15 20:24:23.813 wdl.w:ptcp.w:call-trgt-32.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:23.813 wdl.w:ptcp.w:call-trgt-32.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "plot_type", value: "waterfall"
2025-09-15 20:24:23.813 wdl.w:ptcp.w:call-trgt-32.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "show", value: "motifs"
2025-09-15 20:24:23.813 wdl.w:ptcp.w:call-trgt-32.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "threads", value: 1
2025-09-15 20:24:23.814 wdl.w:ptcp.w:call-trgt-32.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:23.814 wdl.w:ptcp.w:call-trgt-32.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2129.motifs_waterfall"
2025-09-15 20:24:23.814 wdl.w:ptcp.w:call-trgt-32.t:call-trgt_plot_motifs_waterfall INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:23.814 wdl.w:ptcp.w:call-trgt-32.t:call-trgt_plot_motifs_waterfall WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:23.815 wdl.w:ptcp.w:call-trgt-32.t:call-trgt_plot_motifs_waterfall INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:23.815 wdl.w:ptcp.w:call-trgt-32.t:call-trgt_plot_motifs_waterfall INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:23.847 wdl.w:ptcp.w:call-paraphase-29.t:call-call_f8.slurm_singularity INFO srun: job 51797625 queued and waiting for resources
2025-09-15 20:24:23.847 wdl.w:ptcp.w:call-paraphase-29.t:call-call_f8.slurm_singularity INFO srun: job 51797625 has been allocated resources
2025-09-15 20:24:23.847 wdl.w:ptcp.w:call-paraphase-29.t:call-call_f8.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:23.873 wdl.w:ptcp.w:call-trgt-13.t:call-trgt_plot_motifs_waterfall NOTICE done
2025-09-15 20:24:23.906 wdl.w:ptcp.w:call-trgt-33 NOTICE done
2025-09-15 20:24:23.908 wdl.w:ptcp.w:call-trgt-13 NOTICE finish :: job: "call-trgt_plot_motifs_waterfall"
2025-09-15 20:24:23.908 wdl.w:ptcp.w:call-trgt-05.t:call-trgt_plot_meth_allele NOTICE done
2025-09-15 20:24:23.909 wdl.w:ptcp.w:call-trgt-13 INFO output :: job: "call-trgt_plot_motifs_waterfall", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-13/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2110.motifs_waterfall.trgt_plots.zip"}
2025-09-15 20:24:23.909 wdl.w:ptcp.w:call-trgt-13 INFO visit :: node: "output-images_motifs_waterfall", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-13/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2110.motifs_waterfall.trgt_plots.zip"}
2025-09-15 20:24:23.910 wdl.w:ptcp.w:call-trgt-32.t:call-trgt_plot_motifs_allele INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-32/call-trgt_plot_motifs_allele/_singularity_tmpdir_vsk_ujp1"
2025-09-15 20:24:23.910 wdl.w:ptcp.w:call-trgt-32.t:call-trgt_plot_motifs_allele INFO Slurm invocation: srun --job-name call-trgt_plot_motifs_allele --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-32/call-trgt_plot_motifs_allele/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-32/call-trgt_plot_motifs_allele/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-32/call-trgt_plot_motifs_allele/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-32/call-trgt_plot_motifs_allele/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-32/call-trgt_genotype/out/m84036_250809_035451_s4.bc2129.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2129.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-32/call-trgt_genotype/out/m84036_250809_035451_s4.bc2129.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2129.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-32/call-trgt_genotype/out/m84036_250809_035451_s4.bc2129.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2129.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-32/call-trgt_plot_motifs_allele/_singularity_tmpdir_vsk_ujp1/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-32/call-trgt_plot_motifs_allele/_singularity_tmpdir_vsk_ujp1/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:23.916 wdl.w:ptcp.w:call-paraphase-16.t:call-call_f8 NOTICE task setup :: name: "call_f8", source: "./paraphase.wdl", line: 232, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-16/call-call_f8", thread: 140607120975424
2025-09-15 20:24:23.918 wdl.w:ptcp NOTICE finish :: job: "call-trgt-33"
2025-09-15 20:24:23.918 wdl.w:ptcp INFO output :: job: "call-trgt-33", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-33/out/m84036_250809_035451_s4.bc2130.motifs_waterfall.trgt_plots.zip", "images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-33/out/m84036_250809_035451_s4.bc2130.meth_allele.trgt_plots.zip", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-33/out/m84036_250809_035451_s4.bc2130.trgt.sorted.spanning.bam.bai", "images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-33/out/m84036_250809_035451_s4.bc2130.motifs_allele.trgt_plots.zip", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-33/out/m84036_250809_035451_s4.bc2130.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-33/out/m84036_250809_035451_s4.bc2130.trgt.vcf", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-33/out/m84036_250809_035451_s4.bc2130.repeats.bam", "images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-33/out/m84036_250809_035451_s4.bc2130.meth_waterfall.trgt_plots.zip", "reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-33/out/m84036_250809_035451_s4.bc2130.repeats.bam.bai"}
2025-09-15 20:24:23.926 wdl.w:ptcp.w:call-trgt-32.t:call-trgt_plot_motifs_waterfall INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-32/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_iyo97oan"
2025-09-15 20:24:23.926 wdl.w:ptcp.w:call-trgt-32.t:call-trgt_plot_motifs_waterfall INFO Slurm invocation: srun --job-name call-trgt_plot_motifs_waterfall --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-32/call-trgt_plot_motifs_waterfall/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-32/call-trgt_plot_motifs_waterfall/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-32/call-trgt_plot_motifs_waterfall/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-32/call-trgt_plot_motifs_waterfall/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-32/call-trgt_genotype/out/m84036_250809_035451_s4.bc2129.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2129.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-32/call-trgt_genotype/out/m84036_250809_035451_s4.bc2129.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2129.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-32/call-trgt_genotype/out/m84036_250809_035451_s4.bc2129.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2129.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-32/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_iyo97oan/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-32/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_iyo97oan/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:23.928 wdl.w:ptcp.w:call-sawfish-57 NOTICE workflow start :: name: "sawfish", source: "./sawfish.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-57"
2025-09-15 20:24:23.942 wdl.w:ptcp.w:call-trgt-05 NOTICE finish :: job: "call-trgt_plot_meth_allele"
2025-09-15 20:24:23.942 wdl.w:ptcp.w:call-trgt-05 INFO output :: job: "call-trgt_plot_meth_allele", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-05/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2102.meth_allele.trgt_plots.zip"}
2025-09-15 20:24:23.942 wdl.w:ptcp.w:call-trgt-05 INFO visit :: node: "output-images_meth_allele", values: {"images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-05/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2102.meth_allele.trgt_plots.zip"}
2025-09-15 20:24:23.946 wdl.w:ptcp.w:call-paraphase-16.t:call-call_f8 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:23.946 wdl.w:ptcp.w:call-paraphase-16.t:call-call_f8 INFO input :: name: "genome_version", value: "38"
2025-09-15 20:24:23.946 wdl.w:ptcp.w:call-paraphase-16.t:call-call_f8 INFO input :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2113"
2025-09-15 20:24:23.946 wdl.w:ptcp.w:call-paraphase-16.t:call-call_f8 INFO input :: name: "paraphase_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2113.paraphase.bam.bai"
2025-09-15 20:24:23.946 wdl.w:ptcp.w:call-paraphase-16.t:call-call_f8 INFO input :: name: "paraphase_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2113.paraphase.bam"
2025-09-15 20:24:23.946 wdl.w:ptcp.w:call-paraphase-16.t:call-call_f8 INFO input :: name: "sex", value: "F"
2025-09-15 20:24:23.947 wdl.w:ptcp.w:call-paraphase-16.t:call-call_f8 INFO eval :: name: "threads", value: 1
2025-09-15 20:24:23.947 wdl.w:ptcp.w:call-paraphase-16.t:call-call_f8 INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:23.947 wdl.w:ptcp.w:call-paraphase-16.t:call-call_f8 INFO eval :: name: "disk_size", value: 11
2025-09-15 20:24:23.947 wdl.w:ptcp.w:call-paraphase-16.t:call-call_f8 INFO eval :: name: "sample_sex", value: "F"
2025-09-15 20:24:23.948 wdl.w:ptcp.w:call-paraphase-16.t:call-call_f8 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:23.948 wdl.w:ptcp.w:call-paraphase-16.t:call-call_f8 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:23.948 wdl.w:ptcp.w:call-paraphase-16.t:call-call_f8 INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:23.948 wdl.w:ptcp.w:call-paraphase-16.t:call-call_f8 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:23.949 wdl.w:ptcp.w:call-sawfish-57 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:24:23.949 wdl.w:ptcp.w:call-sawfish-57 INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:24:23.949 wdl.w:ptcp.w:call-sawfish-57 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-57/out/m84036_250809_035451_s4.bc2154.mapped.bam"}
2025-09-15 20:24:23.949 wdl.w:ptcp.w:call-sawfish-57 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-57/out/m84036_250809_035451_s4.bc2154.mapped.bam.bai"}
2025-09-15 20:24:23.949 wdl.w:ptcp.w:call-sawfish-57 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:24:23.949 wdl.w:ptcp.w:call-sawfish-57 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:24:23.949 wdl.w:ptcp.w:call-sawfish-57 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2154"}
2025-09-15 20:24:23.950 wdl.w:ptcp.w:call-sawfish-57 NOTICE ready :: job: "call-run_sawfish", callee: "run_sawfish"
2025-09-15 20:24:23.950 wdl.w:ptcp.w:call-sawfish-57 INFO input :: job: "call-run_sawfish", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-57/out/m84036_250809_035451_s4.bc2154.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-57/out/m84036_250809_035451_s4.bc2154.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2154"}
2025-09-15 20:24:23.950 wdl.w:ptcp.w:call-paraphase-24.t:call-call_f8 NOTICE task setup :: name: "call_f8", source: "./paraphase.wdl", line: 232, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-24/call-call_f8", thread: 140607137760832
2025-09-15 20:24:23.961 wdl.w:ptcp.w:call-trgt-32.t:call-trgt_plot_motifs_waterfall NOTICE slurm_singularity run :: pid: 1201677, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-32/call-trgt_plot_motifs_waterfall/slurm_singularity.log.txt"
2025-09-15 20:24:23.961 wdl.w:ptcp.w:call-trgt-32.t:call-trgt_plot_motifs_allele NOTICE slurm_singularity run :: pid: 1201676, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-32/call-trgt_plot_motifs_allele/slurm_singularity.log.txt"
2025-09-15 20:24:23.973 wdl.w:ptcp.w:call-paraphase-24.t:call-call_f8 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:23.973 wdl.w:ptcp.w:call-paraphase-24.t:call-call_f8 INFO input :: name: "genome_version", value: "38"
2025-09-15 20:24:23.973 wdl.w:ptcp.w:call-paraphase-24.t:call-call_f8 INFO input :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2121"
2025-09-15 20:24:23.973 wdl.w:ptcp.w:call-paraphase-24.t:call-call_f8 INFO input :: name: "paraphase_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2121.paraphase.bam.bai"
2025-09-15 20:24:23.973 wdl.w:ptcp.w:call-paraphase-24.t:call-call_f8 INFO input :: name: "paraphase_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2121.paraphase.bam"
2025-09-15 20:24:23.973 wdl.w:ptcp.w:call-paraphase-24.t:call-call_f8 INFO input :: name: "sex", value: "F"
2025-09-15 20:24:23.974 wdl.w:ptcp.w:call-paraphase-24.t:call-call_f8 INFO eval :: name: "threads", value: 1
2025-09-15 20:24:23.974 wdl.w:ptcp.w:call-paraphase-24.t:call-call_f8 INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:23.974 wdl.w:ptcp.w:call-paraphase-24.t:call-call_f8 INFO eval :: name: "disk_size", value: 11
2025-09-15 20:24:23.974 wdl.w:ptcp.w:call-paraphase-24.t:call-call_f8 INFO eval :: name: "sample_sex", value: "F"
2025-09-15 20:24:23.974 wdl.w:ptcp.w:call-paraphase-24.t:call-call_f8 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:23.975 wdl.w:ptcp.w:call-paraphase-24.t:call-call_f8 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:23.975 wdl.w:ptcp.w:call-paraphase-24.t:call-call_f8 INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:23.975 wdl.w:ptcp.w:call-paraphase-24.t:call-call_f8 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:23.998 wdl.w:ptcp.w:call-paraphase-16.t:call-call_f8 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 8, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-16/call-call_f8/_singularity_tmpdir_xt6euv7f"
2025-09-15 20:24:23.998 wdl.w:ptcp.w:call-paraphase-16.t:call-call_f8 INFO Slurm invocation: srun --job-name call-call_f8 --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-16/call-call_f8/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-16/call-call_f8/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-16/call-call_f8/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-16/call-call_f8/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-16/call-run_paraphase/out/m84036_250809_035451_s4.bc2113_paraphase/m84036_250809_035451_s4.bc2113.paraphase.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2113.paraphase.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-16/call-run_paraphase/out/m84036_250809_035451_s4.bc2113_paraphase/m84036_250809_035451_s4.bc2113.paraphase.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2113.paraphase.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-16/call-call_f8/_singularity_tmpdir_xt6euv7f/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-16/call-call_f8/_singularity_tmpdir_xt6euv7f/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:24.019 wdl.w:ptcp.w:call-paraphase-16.t:call-call_f8 NOTICE slurm_singularity run :: pid: 1201680, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-16/call-call_f8/slurm_singularity.log.txt"
2025-09-15 20:24:24.027 wdl.w:ptcp.w:call-paraphase-24.t:call-call_f8 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 8, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-24/call-call_f8/_singularity_tmpdir_q0iftwzc"
2025-09-15 20:24:24.028 wdl.w:ptcp.w:call-paraphase-24.t:call-call_f8 INFO Slurm invocation: srun --job-name call-call_f8 --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-24/call-call_f8/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-24/call-call_f8/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-24/call-call_f8/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-24/call-call_f8/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-24/call-run_paraphase/out/m84036_250809_035451_s4.bc2121_paraphase/m84036_250809_035451_s4.bc2121.paraphase.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2121.paraphase.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-24/call-run_paraphase/out/m84036_250809_035451_s4.bc2121_paraphase/m84036_250809_035451_s4.bc2121.paraphase.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2121.paraphase.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-24/call-call_f8/_singularity_tmpdir_q0iftwzc/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-24/call-call_f8/_singularity_tmpdir_q0iftwzc/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:24.037 wdl.w:ptcp.w:call-paraphase-24.t:call-call_f8 NOTICE slurm_singularity run :: pid: 1201682, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-24/call-call_f8/slurm_singularity.log.txt"
2025-09-15 20:24:24.260 wdl.w:ptcp.w:call-trgt-09.t:call-trgt_plot_meth_allele INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2106.meth_allele.trgt_plots.zip"
2025-09-15 20:24:24.293 wdl.w:ptcp.w:call-trgt-12.t:call-trgt_plot_motifs_waterfall INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2109.motifs_waterfall.trgt_plots.zip"
2025-09-15 20:24:24.351 wdl.w:ptcp.w:call-paraphase-21.t:call-call_f8.slurm_singularity INFO srun: job 51797626 queued and waiting for resources
2025-09-15 20:24:24.352 wdl.w:ptcp.w:call-paraphase-21.t:call-call_f8.slurm_singularity INFO srun: job 51797626 has been allocated resources
2025-09-15 20:24:24.352 wdl.w:ptcp.w:call-paraphase-21.t:call-call_f8.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:24.392 wdl.w:ptcp.w:call-paraphase-09.t:call-call_f8.slurm_singularity INFO srun: job 51797627 queued and waiting for resources
2025-09-15 20:24:24.392 wdl.w:ptcp.w:call-paraphase-09.t:call-call_f8.slurm_singularity INFO srun: job 51797627 has been allocated resources
2025-09-15 20:24:24.392 wdl.w:ptcp.w:call-paraphase-09.t:call-call_f8.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:24.398 wdl.w:ptcp.w:call-trgt-09.t:call-trgt_plot_meth_allele NOTICE done
2025-09-15 20:24:24.422 wdl.w:ptcp.w:call-trgt-12.t:call-trgt_plot_motifs_waterfall NOTICE done
2025-09-15 20:24:24.426 wdl.w:ptcp.w:call-trgt-09 NOTICE finish :: job: "call-trgt_plot_meth_allele"
2025-09-15 20:24:24.426 wdl.w:ptcp.w:call-trgt-09 INFO output :: job: "call-trgt_plot_meth_allele", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-09/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2106.meth_allele.trgt_plots.zip"}
2025-09-15 20:24:24.427 wdl.w:ptcp.w:call-trgt-09 INFO visit :: node: "output-images_meth_allele", values: {"images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-09/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2106.meth_allele.trgt_plots.zip"}
2025-09-15 20:24:24.432 wdl.w:ptcp.w:call-paraphase-12.t:call-call_f8 NOTICE task setup :: name: "call_f8", source: "./paraphase.wdl", line: 232, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-12/call-call_f8", thread: 140608211502656
2025-09-15 20:24:24.450 wdl.w:ptcp.w:call-paraphase-12.t:call-call_f8 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:24.450 wdl.w:ptcp.w:call-paraphase-12.t:call-call_f8 INFO input :: name: "genome_version", value: "38"
2025-09-15 20:24:24.451 wdl.w:ptcp.w:call-paraphase-12.t:call-call_f8 INFO input :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2109"
2025-09-15 20:24:24.451 wdl.w:ptcp.w:call-paraphase-12.t:call-call_f8 INFO input :: name: "paraphase_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2109.paraphase.bam.bai"
2025-09-15 20:24:24.451 wdl.w:ptcp.w:call-paraphase-12.t:call-call_f8 INFO input :: name: "paraphase_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2109.paraphase.bam"
2025-09-15 20:24:24.451 wdl.w:ptcp.w:call-paraphase-12.t:call-call_f8 INFO input :: name: "sex", value: "F"
2025-09-15 20:24:24.451 wdl.w:ptcp.w:call-paraphase-12.t:call-call_f8 INFO eval :: name: "threads", value: 1
2025-09-15 20:24:24.451 wdl.w:ptcp.w:call-paraphase-12.t:call-call_f8 INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:24.451 wdl.w:ptcp.w:call-paraphase-12.t:call-call_f8 INFO eval :: name: "disk_size", value: 11
2025-09-15 20:24:24.451 wdl.w:ptcp.w:call-paraphase-12.t:call-call_f8 INFO eval :: name: "sample_sex", value: "F"
2025-09-15 20:24:24.452 wdl.w:ptcp.w:call-paraphase-12.t:call-call_f8 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:24.452 wdl.w:ptcp.w:call-paraphase-12.t:call-call_f8 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:24.452 wdl.w:ptcp.w:call-paraphase-12.t:call-call_f8 INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:24.452 wdl.w:ptcp.w:call-paraphase-12.t:call-call_f8 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:24.454 wdl.w:ptcp.w:call-trgt-12 NOTICE finish :: job: "call-trgt_plot_motifs_waterfall"
2025-09-15 20:24:24.454 wdl.w:ptcp.w:call-trgt-12 INFO output :: job: "call-trgt_plot_motifs_waterfall", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-12/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2109.motifs_waterfall.trgt_plots.zip"}
2025-09-15 20:24:24.454 wdl.w:ptcp.w:call-trgt-12 INFO visit :: node: "output-images_motifs_waterfall", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-12/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2109.motifs_waterfall.trgt_plots.zip"}
2025-09-15 20:24:24.455 wdl.w:ptcp.w:call-trgt-12 INFO visit :: node: "outputs", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-12/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2109.motifs_waterfall.trgt_plots.zip", "images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-12/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2109.meth_allele.trgt_plots.zip", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-12/call-trgt_genotype/out/m84036_250809_035451_s4.bc2109.trgt.sorted.spanning.bam.bai", "images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-12/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2109.motifs_allele.trgt_plots.zip", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-12/call-trgt_genotype/out/m84036_250809_035451_s4.bc2109.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-12/call-trgt_genotype/out/m84036_250809_035451_s4.bc2109.trgt.vcf", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-12/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2109.repeats.bam", "images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-12/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2109.meth_waterfall.trgt_plots.zip", "reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-12/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2109.repeats.bam.bai"}
2025-09-15 20:24:24.463 wdl.w:ptcp.w:call-trgt-08.t:call-trgt_plot_meth_allele NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-08/call-trgt_plot_meth_allele", thread: 140606626068032
2025-09-15 20:24:24.495 wdl.w:ptcp.w:call-trgt-08.t:call-trgt_plot_meth_allele INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:24.495 wdl.w:ptcp.w:call-trgt-08.t:call-trgt_plot_meth_allele INFO input :: name: "waterfall", value: false
2025-09-15 20:24:24.496 wdl.w:ptcp.w:call-trgt-08.t:call-trgt_plot_meth_allele INFO input :: name: "methylation", value: true
2025-09-15 20:24:24.496 wdl.w:ptcp.w:call-trgt-08.t:call-trgt_plot_meth_allele INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:24.496 wdl.w:ptcp.w:call-trgt-08.t:call-trgt_plot_meth_allele INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:24.496 wdl.w:ptcp.w:call-trgt-08.t:call-trgt_plot_meth_allele INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:24.496 wdl.w:ptcp.w:call-trgt-08.t:call-trgt_plot_meth_allele INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2105.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:24.496 wdl.w:ptcp.w:call-trgt-08.t:call-trgt_plot_meth_allele INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2105.trgt.sorted.spanning.bam"
2025-09-15 20:24:24.496 wdl.w:ptcp.w:call-trgt-08.t:call-trgt_plot_meth_allele INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2105.trgt.vcf"
2025-09-15 20:24:24.496 wdl.w:ptcp.w:call-trgt-08.t:call-trgt_plot_meth_allele INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2105"
2025-09-15 20:24:24.496 wdl.w:ptcp.w:call-trgt-08.t:call-trgt_plot_meth_allele INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:24.496 wdl.w:ptcp.w:call-trgt-08.t:call-trgt_plot_meth_allele INFO eval :: name: "plot_type", value: "allele"
2025-09-15 20:24:24.496 wdl.w:ptcp.w:call-trgt-08.t:call-trgt_plot_meth_allele INFO eval :: name: "show", value: "meth"
2025-09-15 20:24:24.498 wdl.w:ptcp.w:call-trgt-08.t:call-trgt_plot_meth_allele INFO eval :: name: "threads", value: 1
2025-09-15 20:24:24.498 wdl.w:ptcp.w:call-trgt-08.t:call-trgt_plot_meth_allele INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:24.498 wdl.w:ptcp.w:call-trgt-08.t:call-trgt_plot_meth_allele INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2105.meth_allele"
2025-09-15 20:24:24.499 wdl.w:ptcp.w:call-trgt-08.t:call-trgt_plot_meth_allele INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:24.499 wdl.w:ptcp.w:call-trgt-08.t:call-trgt_plot_meth_allele WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:24.499 wdl.w:ptcp.w:call-trgt-08.t:call-trgt_plot_meth_allele INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:24.499 wdl.w:ptcp.w:call-trgt-08.t:call-trgt_plot_meth_allele INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:24.509 wdl.w:ptcp.w:call-paraphase-12.t:call-call_f8 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 8, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-12/call-call_f8/_singularity_tmpdir_tchdmzc1"
2025-09-15 20:24:24.510 wdl.w:ptcp.w:call-paraphase-12.t:call-call_f8 INFO Slurm invocation: srun --job-name call-call_f8 --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-12/call-call_f8/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-12/call-call_f8/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-12/call-call_f8/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-12/call-call_f8/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-12/call-run_paraphase/out/m84036_250809_035451_s4.bc2109_paraphase/m84036_250809_035451_s4.bc2109.paraphase.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2109.paraphase.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-12/call-run_paraphase/out/m84036_250809_035451_s4.bc2109_paraphase/m84036_250809_035451_s4.bc2109.paraphase.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2109.paraphase.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-12/call-call_f8/_singularity_tmpdir_tchdmzc1/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-12/call-call_f8/_singularity_tmpdir_tchdmzc1/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:24.516 wdl.w:ptcp.w:call-paraphase-29.t:call-call_f8 INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2126.f8inversion.vcf"
2025-09-15 20:24:24.519 wdl.w:ptcp.w:call-paraphase-29.t:call-call_f8 INFO output :: name: "json", value: "m84036_250809_035451_s4.bc2126.f8inversion.json"
2025-09-15 20:24:24.547 wdl.w:ptcp.w:call-paraphase-12.t:call-call_f8 NOTICE slurm_singularity run :: pid: 1201707, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-12/call-call_f8/slurm_singularity.log.txt"
2025-09-15 20:24:24.574 wdl.w:ptcp.w:call-trgt-12 NOTICE done
2025-09-15 20:24:24.582 wdl.w:ptcp NOTICE finish :: job: "call-trgt-12"
2025-09-15 20:24:24.582 wdl.w:ptcp INFO output :: job: "call-trgt-12", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-12/out/m84036_250809_035451_s4.bc2109.motifs_waterfall.trgt_plots.zip", "images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-12/out/m84036_250809_035451_s4.bc2109.meth_allele.trgt_plots.zip", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-12/out/m84036_250809_035451_s4.bc2109.trgt.sorted.spanning.bam.bai", "images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-12/out/m84036_250809_035451_s4.bc2109.motifs_allele.trgt_plots.zip", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-12/out/m84036_250809_035451_s4.bc2109.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-12/out/m84036_250809_035451_s4.bc2109.trgt.vcf", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-12/out/m84036_250809_035451_s4.bc2109.repeats.bam", "images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-12/out/m84036_250809_035451_s4.bc2109.meth_waterfall.trgt_plots.zip", "reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-12/out/m84036_250809_035451_s4.bc2109.repeats.bam.bai"}
2025-09-15 20:24:24.586 wdl.w:ptcp.w:call-trgt-08.t:call-trgt_plot_meth_allele INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-08/call-trgt_plot_meth_allele/_singularity_tmpdir_5rgqfiyg"
2025-09-15 20:24:24.586 wdl.w:ptcp.w:call-paraphase-19.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for f8inv1 for sample m84036_250809_035451_s4.bc2116 at 2025-09-15 20:24:13.249715...
2025-09-15 20:24:24.587 wdl.w:ptcp.w:call-trgt-08.t:call-trgt_plot_meth_allele INFO Slurm invocation: srun --job-name call-trgt_plot_meth_allele --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-08/call-trgt_plot_meth_allele/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-08/call-trgt_plot_meth_allele/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-08/call-trgt_plot_meth_allele/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-08/call-trgt_plot_meth_allele/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-08/call-trgt_genotype/out/m84036_250809_035451_s4.bc2105.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2105.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-08/call-trgt_genotype/out/m84036_250809_035451_s4.bc2105.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2105.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-08/call-trgt_genotype/out/m84036_250809_035451_s4.bc2105.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2105.trgt.sorted.spanning.bam.bai:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-08/call-trgt_plot_meth_allele/_singularity_tmpdir_5rgqfiyg/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-08/call-trgt_plot_meth_allele/_singularity_tmpdir_5rgqfiyg/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:24.587 wdl.w:ptcp.w:call-paraphase-19.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for f8inv1 for sample m84036_250809_035451_s4.bc2116 at 2025-09-15 20:24:13.591352...
2025-09-15 20:24:24.587 wdl.w:ptcp.w:call-paraphase-19.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for hba for sample m84036_250809_035451_s4.bc2116 at 2025-09-15 20:24:16.685839...
2025-09-15 20:24:24.587 wdl.w:ptcp.w:call-paraphase-19.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for hba for sample m84036_250809_035451_s4.bc2116 at 2025-09-15 20:24:17.058351...
2025-09-15 20:24:24.587 wdl.w:ptcp.w:call-paraphase-19.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for cyp21 for sample m84036_250809_035451_s4.bc2116 at 2025-09-15 20:24:23.224461...
2025-09-15 20:24:24.596 wdl.w:ptcp.w:call-trgt-57 NOTICE workflow start :: name: "trgt", source: "./trgt.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-57"
2025-09-15 20:24:24.607 wdl.w:ptcp.w:call-trgt-32.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO srun: job 51797629 queued and waiting for resources
2025-09-15 20:24:24.607 wdl.w:ptcp.w:call-trgt-32.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO srun: job 51797629 has been allocated resources
2025-09-15 20:24:24.607 wdl.w:ptcp.w:call-trgt-32.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:24.612 wdl.w:ptcp.w:call-trgt-32.t:call-trgt_plot_meth_allele.slurm_singularity INFO srun: job 51797628 queued and waiting for resources
2025-09-15 20:24:24.612 wdl.w:ptcp.w:call-trgt-32.t:call-trgt_plot_meth_allele.slurm_singularity INFO srun: job 51797628 has been allocated resources
2025-09-15 20:24:24.612 wdl.w:ptcp.w:call-trgt-32.t:call-trgt_plot_meth_allele.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:24.624 wdl.w:ptcp.w:call-trgt-08.t:call-trgt_plot_meth_allele NOTICE slurm_singularity run :: pid: 1201709, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-08/call-trgt_plot_meth_allele/slurm_singularity.log.txt"
2025-09-15 20:24:24.632 wdl.w:ptcp.w:call-trgt-57 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:24:24.632 wdl.w:ptcp.w:call-trgt-57 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-57/out/m84036_250809_035451_s4.bc2154.mapped.bam"}
2025-09-15 20:24:24.632 wdl.w:ptcp.w:call-trgt-57 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-57/out/m84036_250809_035451_s4.bc2154.mapped.bam.bai"}
2025-09-15 20:24:24.633 wdl.w:ptcp.w:call-trgt-57 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:24:24.633 wdl.w:ptcp.w:call-trgt-57 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:24:24.633 wdl.w:ptcp.w:call-trgt-57 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2154"}
2025-09-15 20:24:24.633 wdl.w:ptcp.w:call-trgt-57 INFO visit :: node: "decl-sex", values: {"sex": "F"}
2025-09-15 20:24:24.633 wdl.w:ptcp.w:call-trgt-57 INFO visit :: node: "decl-trgt_bed", values: {"trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"}
2025-09-15 20:24:24.633 wdl.w:ptcp.w:call-trgt-57 NOTICE ready :: job: "call-get_reads_overlapping_repeats", callee: "get_reads_overlapping_repeats"
2025-09-15 20:24:24.633 wdl.w:ptcp.w:call-trgt-57 INFO input :: job: "call-get_reads_overlapping_repeats", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-57/out/m84036_250809_035451_s4.bc2154.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-57/out/m84036_250809_035451_s4.bc2154.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2154"}
2025-09-15 20:24:24.634 wdl.w:ptcp.w:call-trgt-57 NOTICE ready :: job: "call-trgt_genotype", callee: "trgt_genotype"
2025-09-15 20:24:24.634 wdl.w:ptcp.w:call-trgt-57 INFO input :: job: "call-trgt_genotype", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-57/out/m84036_250809_035451_s4.bc2154.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-57/out/m84036_250809_035451_s4.bc2154.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2154"}
2025-09-15 20:24:24.644 wdl.w:ptcp.w:call-paraphase-29.t:call-call_f8 NOTICE done
2025-09-15 20:24:24.651 wdl.w:ptcp.w:call-paraphase-29 NOTICE finish :: job: "call-call_f8"
2025-09-15 20:24:24.651 wdl.w:ptcp.w:call-paraphase-29 INFO output :: job: "call-call_f8", values: {"json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-29/call-call_f8/out/m84036_250809_035451_s4.bc2126.f8inversion.json", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-29/call-call_f8/out/m84036_250809_035451_s4.bc2126.f8inversion.vcf"}
2025-09-15 20:24:24.652 wdl.w:ptcp.w:call-paraphase-29 INFO visit :: node: "output-f8_json", values: {"f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-29/call-call_f8/out/m84036_250809_035451_s4.bc2126.f8inversion.json"}
2025-09-15 20:24:24.652 wdl.w:ptcp.w:call-paraphase-29 INFO visit :: node: "output-f8_vcf", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-29/call-call_f8/out/m84036_250809_035451_s4.bc2126.f8inversion.vcf"}
2025-09-15 20:24:24.652 wdl.w:ptcp.w:call-paraphase-29 INFO visit :: node: "outputs", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-29/call-call_f8/out/m84036_250809_035451_s4.bc2126.f8inversion.vcf", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-29/call-run_paraphase/out/m84036_250809_035451_s4.bc2126_paraphase/m84036_250809_035451_s4.bc2126.paraphase.json", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-29/call-run_paraphase/out/m84036_250809_035451_s4.bc2126_paraphase/m84036_250809_035451_s4.bc2126.paraphase.bam", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-29/call-run_paraphase/out/m84036_250809_035451_s4.bc2126_paraphase/m84036_250809_035451_s4.bc2126.paraphase.bam.bai", "paraphase_vcfs": [], "havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-29/call-run_paraphase/out/m84036_250809_035451_s4.bc2126.havanno.json", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-29/call-call_f8/out/m84036_250809_035451_s4.bc2126.f8inversion.json"}
2025-09-15 20:24:24.656 wdl.w:ptcp.w:call-trgt-08.t:call-trgt_plot_meth_waterfall NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-08/call-trgt_plot_meth_waterfall", thread: 140607691417152
2025-09-15 20:24:24.681 wdl.w:ptcp.w:call-trgt-08.t:call-trgt_plot_meth_waterfall INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:24.681 wdl.w:ptcp.w:call-trgt-08.t:call-trgt_plot_meth_waterfall INFO input :: name: "waterfall", value: true
2025-09-15 20:24:24.681 wdl.w:ptcp.w:call-trgt-08.t:call-trgt_plot_meth_waterfall INFO input :: name: "methylation", value: true
2025-09-15 20:24:24.681 wdl.w:ptcp.w:call-trgt-08.t:call-trgt_plot_meth_waterfall INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:24.681 wdl.w:ptcp.w:call-trgt-08.t:call-trgt_plot_meth_waterfall INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:24.682 wdl.w:ptcp.w:call-trgt-08.t:call-trgt_plot_meth_waterfall INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:24.682 wdl.w:ptcp.w:call-trgt-08.t:call-trgt_plot_meth_waterfall INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2105.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:24.682 wdl.w:ptcp.w:call-trgt-08.t:call-trgt_plot_meth_waterfall INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2105.trgt.sorted.spanning.bam"
2025-09-15 20:24:24.682 wdl.w:ptcp.w:call-trgt-08.t:call-trgt_plot_meth_waterfall INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2105.trgt.vcf"
2025-09-15 20:24:24.682 wdl.w:ptcp.w:call-trgt-08.t:call-trgt_plot_meth_waterfall INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2105"
2025-09-15 20:24:24.682 wdl.w:ptcp.w:call-trgt-08.t:call-trgt_plot_meth_waterfall INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:24.682 wdl.w:ptcp.w:call-trgt-08.t:call-trgt_plot_meth_waterfall INFO eval :: name: "plot_type", value: "waterfall"
2025-09-15 20:24:24.682 wdl.w:ptcp.w:call-trgt-08.t:call-trgt_plot_meth_waterfall INFO eval :: name: "show", value: "meth"
2025-09-15 20:24:24.682 wdl.w:ptcp.w:call-trgt-08.t:call-trgt_plot_meth_waterfall INFO eval :: name: "threads", value: 1
2025-09-15 20:24:24.683 wdl.w:ptcp.w:call-trgt-08.t:call-trgt_plot_meth_waterfall INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:24.683 wdl.w:ptcp.w:call-trgt-08.t:call-trgt_plot_meth_waterfall INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2105.meth_waterfall"
2025-09-15 20:24:24.683 wdl.w:ptcp.w:call-trgt-08.t:call-trgt_plot_meth_waterfall INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:24.683 wdl.w:ptcp.w:call-trgt-08.t:call-trgt_plot_meth_waterfall WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:24.684 wdl.w:ptcp.w:call-trgt-08.t:call-trgt_plot_meth_waterfall INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:24.684 wdl.w:ptcp.w:call-trgt-08.t:call-trgt_plot_meth_waterfall INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:24.693 wdl.w:ptcp.w:call-trgt-13.t:call-trgt_plot_meth_waterfall INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2110.meth_waterfall.trgt_plots.zip"
2025-09-15 20:24:24.709 wdl.w:ptcp.w:call-trgt-05.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:23 [ERROR] - No reads found for TRID=PRTS_ARX
2025-09-15 20:24:24.709 wdl.w:ptcp.w:call-trgt-05.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:23 [ERROR] - No reads found for TRID=EIEE1_ARX
2025-09-15 20:24:24.759 wdl.w:ptcp.w:call-paraphase-29 NOTICE done
2025-09-15 20:24:24.767 wdl.w:ptcp NOTICE finish :: job: "call-paraphase-29"
2025-09-15 20:24:24.768 wdl.w:ptcp INFO output :: job: "call-paraphase-29", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-29/out/m84036_250809_035451_s4.bc2126.f8inversion.vcf", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-29/out/m84036_250809_035451_s4.bc2126_paraphase/m84036_250809_035451_s4.bc2126.paraphase.json", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-29/out/m84036_250809_035451_s4.bc2126_paraphase/m84036_250809_035451_s4.bc2126.paraphase.bam", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-29/out/m84036_250809_035451_s4.bc2126_paraphase/m84036_250809_035451_s4.bc2126.paraphase.bam.bai", "paraphase_vcfs": [], "havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-29/out/m84036_250809_035451_s4.bc2126.havanno.json", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-29/out/m84036_250809_035451_s4.bc2126.f8inversion.json"}
2025-09-15 20:24:24.776 wdl.w:ptcp.w:call-paraphase-49 NOTICE workflow start :: name: "paraphase", source: "./paraphase.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-49"
2025-09-15 20:24:24.777 wdl.w:ptcp.w:call-trgt-08.t:call-trgt_plot_meth_waterfall INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-08/call-trgt_plot_meth_waterfall/_singularity_tmpdir_lew42x_1"
2025-09-15 20:24:24.777 wdl.w:ptcp.w:call-trgt-08.t:call-trgt_plot_meth_waterfall INFO Slurm invocation: srun --job-name call-trgt_plot_meth_waterfall --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-08/call-trgt_plot_meth_waterfall/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-08/call-trgt_plot_meth_waterfall/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-08/call-trgt_plot_meth_waterfall/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-08/call-trgt_plot_meth_waterfall/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-08/call-trgt_genotype/out/m84036_250809_035451_s4.bc2105.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2105.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-08/call-trgt_genotype/out/m84036_250809_035451_s4.bc2105.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2105.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-08/call-trgt_genotype/out/m84036_250809_035451_s4.bc2105.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2105.trgt.sorted.spanning.bam.bai:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-08/call-trgt_plot_meth_waterfall/_singularity_tmpdir_lew42x_1/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-08/call-trgt_plot_meth_waterfall/_singularity_tmpdir_lew42x_1/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:24.793 wdl.w:ptcp.w:call-trgt-16.t:call-trgt_plot_motifs_allele INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2113.motifs_allele.trgt_plots.zip"
2025-09-15 20:24:24.802 wdl.w:ptcp.w:call-paraphase-49 INFO visit :: node: "decl-annotation_vcf", values: {"annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf"}
2025-09-15 20:24:24.802 wdl.w:ptcp.w:call-trgt-08.t:call-trgt_plot_meth_waterfall NOTICE slurm_singularity run :: pid: 1201723, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-08/call-trgt_plot_meth_waterfall/slurm_singularity.log.txt"
2025-09-15 20:24:24.802 wdl.w:ptcp.w:call-paraphase-49 INFO visit :: node: "decl-config_file", values: {"config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml"}
2025-09-15 20:24:24.803 wdl.w:ptcp.w:call-paraphase-49 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:24:24.803 wdl.w:ptcp.w:call-paraphase-49 INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:24:24.803 wdl.w:ptcp.w:call-paraphase-49 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-49/out/m84036_250809_035451_s4.bc2146.mapped.bam"}
2025-09-15 20:24:24.803 wdl.w:ptcp.w:call-paraphase-49 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-49/out/m84036_250809_035451_s4.bc2146.mapped.bam.bai"}
2025-09-15 20:24:24.803 wdl.w:ptcp.w:call-paraphase-49 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:24:24.803 wdl.w:ptcp.w:call-paraphase-49 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:24:24.803 wdl.w:ptcp.w:call-paraphase-49 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2146"}
2025-09-15 20:24:24.803 wdl.w:ptcp.w:call-paraphase-49 INFO visit :: node: "decl-sex", values: {"sex": "F"}
2025-09-15 20:24:24.803 wdl.w:ptcp.w:call-paraphase-49 NOTICE ready :: job: "call-run_paraphase", callee: "run_paraphase"
2025-09-15 20:24:24.803 wdl.w:ptcp.w:call-paraphase-49 INFO input :: job: "call-run_paraphase", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf", "genome_version": "38", "config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-49/out/m84036_250809_035451_s4.bc2146.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-49/out/m84036_250809_035451_s4.bc2146.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2146"}
2025-09-15 20:24:24.862 wdl.w:ptcp.w:call-trgt-13.t:call-trgt_plot_meth_waterfall NOTICE done
2025-09-15 20:24:24.876 wdl.w:ptcp.w:call-trgt-24.t:call-trgt_plot_meth_allele INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2121.meth_allele.trgt_plots.zip"
2025-09-15 20:24:24.881 wdl.w:ptcp.w:call-trgt-13 NOTICE finish :: job: "call-trgt_plot_meth_waterfall"
2025-09-15 20:24:24.881 wdl.w:ptcp.w:call-trgt-13 INFO output :: job: "call-trgt_plot_meth_waterfall", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-13/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2110.meth_waterfall.trgt_plots.zip"}
2025-09-15 20:24:24.881 wdl.w:ptcp.w:call-trgt-13 INFO visit :: node: "output-images_meth_waterfall", values: {"images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-13/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2110.meth_waterfall.trgt_plots.zip"}
2025-09-15 20:24:24.882 wdl.w:ptcp.w:call-trgt-13 INFO visit :: node: "outputs", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-13/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2110.motifs_waterfall.trgt_plots.zip", "images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-13/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2110.meth_allele.trgt_plots.zip", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-13/call-trgt_genotype/out/m84036_250809_035451_s4.bc2110.trgt.sorted.spanning.bam.bai", "images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-13/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2110.motifs_allele.trgt_plots.zip", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-13/call-trgt_genotype/out/m84036_250809_035451_s4.bc2110.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-13/call-trgt_genotype/out/m84036_250809_035451_s4.bc2110.trgt.vcf", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-13/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2110.repeats.bam", "images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-13/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2110.meth_waterfall.trgt_plots.zip", "reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-13/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2110.repeats.bam.bai"}
2025-09-15 20:24:24.889 wdl.w:ptcp.w:call-trgt-08.t:call-trgt_plot_motifs_allele NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-08/call-trgt_plot_motifs_allele", thread: 140607649453632
2025-09-15 20:24:24.914 wdl.w:ptcp.w:call-trgt-08.t:call-trgt_plot_motifs_allele INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:24.914 wdl.w:ptcp.w:call-trgt-08.t:call-trgt_plot_motifs_allele INFO input :: name: "waterfall", value: false
2025-09-15 20:24:24.915 wdl.w:ptcp.w:call-trgt-08.t:call-trgt_plot_motifs_allele INFO input :: name: "methylation", value: false
2025-09-15 20:24:24.915 wdl.w:ptcp.w:call-trgt-08.t:call-trgt_plot_motifs_allele INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:24.915 wdl.w:ptcp.w:call-trgt-08.t:call-trgt_plot_motifs_allele INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:24.915 wdl.w:ptcp.w:call-trgt-08.t:call-trgt_plot_motifs_allele INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:24.915 wdl.w:ptcp.w:call-trgt-08.t:call-trgt_plot_motifs_allele INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2105.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:24.915 wdl.w:ptcp.w:call-trgt-08.t:call-trgt_plot_motifs_allele INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2105.trgt.sorted.spanning.bam"
2025-09-15 20:24:24.915 wdl.w:ptcp.w:call-trgt-08.t:call-trgt_plot_motifs_allele INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2105.trgt.vcf"
2025-09-15 20:24:24.915 wdl.w:ptcp.w:call-trgt-08.t:call-trgt_plot_motifs_allele INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2105"
2025-09-15 20:24:24.915 wdl.w:ptcp.w:call-trgt-08.t:call-trgt_plot_motifs_allele INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:24.916 wdl.w:ptcp.w:call-trgt-08.t:call-trgt_plot_motifs_allele INFO eval :: name: "plot_type", value: "allele"
2025-09-15 20:24:24.916 wdl.w:ptcp.w:call-trgt-08.t:call-trgt_plot_motifs_allele INFO eval :: name: "show", value: "motifs"
2025-09-15 20:24:24.916 wdl.w:ptcp.w:call-trgt-08.t:call-trgt_plot_motifs_allele INFO eval :: name: "threads", value: 1
2025-09-15 20:24:24.916 wdl.w:ptcp.w:call-trgt-08.t:call-trgt_plot_motifs_allele INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:24.917 wdl.w:ptcp.w:call-trgt-08.t:call-trgt_plot_motifs_allele INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2105.motifs_allele"
2025-09-15 20:24:24.917 wdl.w:ptcp.w:call-trgt-08.t:call-trgt_plot_motifs_allele INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:24.917 wdl.w:ptcp.w:call-trgt-08.t:call-trgt_plot_motifs_allele WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:24.918 wdl.w:ptcp.w:call-trgt-08.t:call-trgt_plot_motifs_allele INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:24.918 wdl.w:ptcp.w:call-trgt-08.t:call-trgt_plot_motifs_allele INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:24.961 wdl.w:ptcp.w:call-paraphase-09.t:call-call_f8 INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2106.f8inversion.vcf"
2025-09-15 20:24:24.967 wdl.w:ptcp.w:call-paraphase-09.t:call-call_f8 INFO output :: name: "json", value: "m84036_250809_035451_s4.bc2106.f8inversion.json"
2025-09-15 20:24:24.972 wdl.w:ptcp.w:call-trgt-16.t:call-trgt_plot_motifs_allele NOTICE done
2025-09-15 20:24:24.977 wdl.w:ptcp.w:call-trgt-32.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO srun: job 51797630 queued and waiting for resources
2025-09-15 20:24:24.977 wdl.w:ptcp.w:call-trgt-32.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO srun: job 51797630 has been allocated resources
2025-09-15 20:24:24.977 wdl.w:ptcp.w:call-trgt-32.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:24.982 wdl.w:ptcp.w:call-trgt-32.t:call-trgt_plot_motifs_allele.slurm_singularity INFO srun: job 51797631 queued and waiting for resources
2025-09-15 20:24:24.982 wdl.w:ptcp.w:call-trgt-32.t:call-trgt_plot_motifs_allele.slurm_singularity INFO srun: job 51797631 has been allocated resources
2025-09-15 20:24:24.983 wdl.w:ptcp.w:call-trgt-32.t:call-trgt_plot_motifs_allele.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:24.995 wdl.w:ptcp.w:call-trgt-13 NOTICE done
2025-09-15 20:24:24.997 wdl.w:ptcp.w:call-trgt-16 NOTICE finish :: job: "call-trgt_plot_motifs_allele"
2025-09-15 20:24:24.997 wdl.w:ptcp.w:call-trgt-16 INFO output :: job: "call-trgt_plot_motifs_allele", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-16/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2113.motifs_allele.trgt_plots.zip"}
2025-09-15 20:24:24.998 wdl.w:ptcp.w:call-trgt-16 INFO visit :: node: "output-images_motifs_allele", values: {"images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-16/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2113.motifs_allele.trgt_plots.zip"}
2025-09-15 20:24:25.004 wdl.w:ptcp.w:call-trgt-08.t:call-trgt_plot_motifs_waterfall NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-08/call-trgt_plot_motifs_waterfall", thread: 140608773551680
2025-09-15 20:24:25.013 wdl.w:ptcp.w:call-trgt-08.t:call-trgt_plot_motifs_allele INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-08/call-trgt_plot_motifs_allele/_singularity_tmpdir_4zujq_3v"
2025-09-15 20:24:25.013 wdl.w:ptcp.w:call-trgt-08.t:call-trgt_plot_motifs_allele INFO Slurm invocation: srun --job-name call-trgt_plot_motifs_allele --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-08/call-trgt_plot_motifs_allele/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-08/call-trgt_plot_motifs_allele/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-08/call-trgt_plot_motifs_allele/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-08/call-trgt_plot_motifs_allele/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-08/call-trgt_genotype/out/m84036_250809_035451_s4.bc2105.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2105.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-08/call-trgt_genotype/out/m84036_250809_035451_s4.bc2105.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2105.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-08/call-trgt_genotype/out/m84036_250809_035451_s4.bc2105.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2105.trgt.sorted.spanning.bam.bai:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-08/call-trgt_plot_motifs_allele/_singularity_tmpdir_4zujq_3v/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-08/call-trgt_plot_motifs_allele/_singularity_tmpdir_4zujq_3v/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:25.030 wdl.w:ptcp.w:call-trgt-08.t:call-trgt_plot_motifs_waterfall INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:25.030 wdl.w:ptcp.w:call-trgt-08.t:call-trgt_plot_motifs_waterfall INFO input :: name: "waterfall", value: true
2025-09-15 20:24:25.030 wdl.w:ptcp.w:call-trgt-08.t:call-trgt_plot_motifs_waterfall INFO input :: name: "methylation", value: false
2025-09-15 20:24:25.031 wdl.w:ptcp.w:call-trgt-08.t:call-trgt_plot_motifs_waterfall INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:25.031 wdl.w:ptcp.w:call-trgt-08.t:call-trgt_plot_motifs_waterfall INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:25.031 wdl.w:ptcp.w:call-trgt-08.t:call-trgt_plot_motifs_waterfall INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:25.031 wdl.w:ptcp.w:call-trgt-08.t:call-trgt_plot_motifs_waterfall INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2105.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:25.031 wdl.w:ptcp.w:call-trgt-08.t:call-trgt_plot_motifs_waterfall INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2105.trgt.sorted.spanning.bam"
2025-09-15 20:24:25.031 wdl.w:ptcp.w:call-trgt-08.t:call-trgt_plot_motifs_waterfall INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2105.trgt.vcf"
2025-09-15 20:24:25.031 wdl.w:ptcp.w:call-trgt-08.t:call-trgt_plot_motifs_waterfall INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2105"
2025-09-15 20:24:25.031 wdl.w:ptcp.w:call-trgt-08.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:25.031 wdl.w:ptcp.w:call-trgt-08.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "plot_type", value: "waterfall"
2025-09-15 20:24:25.032 wdl.w:ptcp.w:call-trgt-08.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "show", value: "motifs"
2025-09-15 20:24:25.032 wdl.w:ptcp.w:call-trgt-08.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "threads", value: 1
2025-09-15 20:24:25.032 wdl.w:ptcp.w:call-trgt-08.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:25.032 wdl.w:ptcp.w:call-trgt-08.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2105.motifs_waterfall"
2025-09-15 20:24:25.032 wdl.w:ptcp.w:call-trgt-08.t:call-trgt_plot_motifs_waterfall INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:25.033 wdl.w:ptcp.w:call-trgt-08.t:call-trgt_plot_motifs_waterfall WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:25.034 wdl.w:ptcp NOTICE finish :: job: "call-trgt-13"
2025-09-15 20:24:25.034 wdl.w:ptcp INFO output :: job: "call-trgt-13", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-13/out/m84036_250809_035451_s4.bc2110.motifs_waterfall.trgt_plots.zip", "images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-13/out/m84036_250809_035451_s4.bc2110.meth_allele.trgt_plots.zip", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-13/out/m84036_250809_035451_s4.bc2110.trgt.sorted.spanning.bam.bai", "images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-13/out/m84036_250809_035451_s4.bc2110.motifs_allele.trgt_plots.zip", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-13/out/m84036_250809_035451_s4.bc2110.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-13/out/m84036_250809_035451_s4.bc2110.trgt.vcf", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-13/out/m84036_250809_035451_s4.bc2110.repeats.bam", "images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-13/out/m84036_250809_035451_s4.bc2110.meth_waterfall.trgt_plots.zip", "reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-13/out/m84036_250809_035451_s4.bc2110.repeats.bam.bai"}
2025-09-15 20:24:25.035 wdl.w:ptcp.w:call-trgt-08.t:call-trgt_plot_motifs_waterfall INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:25.035 wdl.w:ptcp.w:call-paraphase-16.t:call-call_f8.slurm_singularity INFO srun: job 51797632 queued and waiting for resources
2025-09-15 20:24:25.035 wdl.w:ptcp.w:call-trgt-08.t:call-trgt_plot_motifs_waterfall INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:25.035 wdl.w:ptcp.w:call-paraphase-16.t:call-call_f8.slurm_singularity INFO srun: job 51797632 has been allocated resources
2025-09-15 20:24:25.036 wdl.w:ptcp.w:call-paraphase-16.t:call-call_f8.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:25.042 wdl.w:ptcp.w:call-sawfish-49 NOTICE workflow start :: name: "sawfish", source: "./sawfish.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-49"
2025-09-15 20:24:25.043 wdl.w:ptcp.w:call-trgt-08.t:call-trgt_plot_motifs_allele NOTICE slurm_singularity run :: pid: 1201732, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-08/call-trgt_plot_motifs_allele/slurm_singularity.log.txt"
2025-09-15 20:24:25.057 wdl.w:ptcp.w:call-paraphase-24.t:call-call_f8.slurm_singularity INFO srun: job 51797633 queued and waiting for resources
2025-09-15 20:24:25.057 wdl.w:ptcp.w:call-paraphase-24.t:call-call_f8.slurm_singularity INFO srun: job 51797633 has been allocated resources
2025-09-15 20:24:25.057 wdl.w:ptcp.w:call-paraphase-24.t:call-call_f8.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:25.060 wdl.w:ptcp.w:call-paraphase-09.t:call-call_f8 NOTICE done
2025-09-15 20:24:25.063 wdl.w:ptcp.w:call-trgt-24.t:call-trgt_plot_meth_allele NOTICE done
2025-09-15 20:24:25.064 wdl.w:ptcp.w:call-sawfish-49 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:24:25.065 wdl.w:ptcp.w:call-sawfish-49 INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:24:25.065 wdl.w:ptcp.w:call-sawfish-49 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-49/out/m84036_250809_035451_s4.bc2146.mapped.bam"}
2025-09-15 20:24:25.065 wdl.w:ptcp.w:call-sawfish-49 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-49/out/m84036_250809_035451_s4.bc2146.mapped.bam.bai"}
2025-09-15 20:24:25.065 wdl.w:ptcp.w:call-sawfish-49 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:24:25.065 wdl.w:ptcp.w:call-sawfish-49 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:24:25.065 wdl.w:ptcp.w:call-sawfish-49 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2146"}
2025-09-15 20:24:25.065 wdl.w:ptcp.w:call-sawfish-49 NOTICE ready :: job: "call-run_sawfish", callee: "run_sawfish"
2025-09-15 20:24:25.065 wdl.w:ptcp.w:call-sawfish-49 INFO input :: job: "call-run_sawfish", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-49/out/m84036_250809_035451_s4.bc2146.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-49/out/m84036_250809_035451_s4.bc2146.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2146"}
2025-09-15 20:24:25.067 wdl.w:ptcp.w:call-paraphase-09 NOTICE finish :: job: "call-call_f8"
2025-09-15 20:24:25.067 wdl.w:ptcp.w:call-paraphase-09 INFO output :: job: "call-call_f8", values: {"json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-09/call-call_f8/out/m84036_250809_035451_s4.bc2106.f8inversion.json", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-09/call-call_f8/out/m84036_250809_035451_s4.bc2106.f8inversion.vcf"}
2025-09-15 20:24:25.067 wdl.w:ptcp.w:call-paraphase-09 INFO visit :: node: "output-f8_json", values: {"f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-09/call-call_f8/out/m84036_250809_035451_s4.bc2106.f8inversion.json"}
2025-09-15 20:24:25.067 wdl.w:ptcp.w:call-paraphase-09 INFO visit :: node: "output-f8_vcf", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-09/call-call_f8/out/m84036_250809_035451_s4.bc2106.f8inversion.vcf"}
2025-09-15 20:24:25.067 wdl.w:ptcp.w:call-paraphase-09 INFO visit :: node: "outputs", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-09/call-call_f8/out/m84036_250809_035451_s4.bc2106.f8inversion.vcf", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-09/call-run_paraphase/out/m84036_250809_035451_s4.bc2106_paraphase/m84036_250809_035451_s4.bc2106.paraphase.json", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-09/call-run_paraphase/out/m84036_250809_035451_s4.bc2106_paraphase/m84036_250809_035451_s4.bc2106.paraphase.bam", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-09/call-run_paraphase/out/m84036_250809_035451_s4.bc2106_paraphase/m84036_250809_035451_s4.bc2106.paraphase.bam.bai", "paraphase_vcfs": [], "havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-09/call-run_paraphase/out/m84036_250809_035451_s4.bc2106.havanno.json", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-09/call-call_f8/out/m84036_250809_035451_s4.bc2106.f8inversion.json"}
2025-09-15 20:24:25.075 wdl.w:ptcp.w:call-paraphase-25.t:call-call_f8 NOTICE task setup :: name: "call_f8", source: "./paraphase.wdl", line: 232, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-25/call-call_f8", thread: 140607666239040
2025-09-15 20:24:25.080 wdl.w:ptcp.w:call-trgt-24 NOTICE finish :: job: "call-trgt_plot_meth_allele"
2025-09-15 20:24:25.081 wdl.w:ptcp.w:call-trgt-24 INFO output :: job: "call-trgt_plot_meth_allele", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-24/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2121.meth_allele.trgt_plots.zip"}
2025-09-15 20:24:25.081 wdl.w:ptcp.w:call-trgt-24 INFO visit :: node: "output-images_meth_allele", values: {"images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-24/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2121.meth_allele.trgt_plots.zip"}
2025-09-15 20:24:25.091 wdl.w:ptcp.w:call-paraphase-32.t:call-call_f8 NOTICE task setup :: name: "call_f8", source: "./paraphase.wdl", line: 232, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-32/call-call_f8", thread: 140609838900800
2025-09-15 20:24:25.100 wdl.w:ptcp.w:call-trgt-16.t:call-trgt_plot_meth_allele INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2113.meth_allele.trgt_plots.zip"
2025-09-15 20:24:25.103 wdl.w:ptcp.w:call-paraphase-25.t:call-call_f8 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:25.103 wdl.w:ptcp.w:call-paraphase-25.t:call-call_f8 INFO input :: name: "genome_version", value: "38"
2025-09-15 20:24:25.103 wdl.w:ptcp.w:call-paraphase-25.t:call-call_f8 INFO input :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2122"
2025-09-15 20:24:25.103 wdl.w:ptcp.w:call-paraphase-25.t:call-call_f8 INFO input :: name: "paraphase_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2122.paraphase.bam.bai"
2025-09-15 20:24:25.103 wdl.w:ptcp.w:call-paraphase-25.t:call-call_f8 INFO input :: name: "paraphase_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2122.paraphase.bam"
2025-09-15 20:24:25.103 wdl.w:ptcp.w:call-paraphase-25.t:call-call_f8 INFO input :: name: "sex", value: "F"
2025-09-15 20:24:25.104 wdl.w:ptcp.w:call-paraphase-25.t:call-call_f8 INFO eval :: name: "threads", value: 1
2025-09-15 20:24:25.104 wdl.w:ptcp.w:call-paraphase-25.t:call-call_f8 INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:25.104 wdl.w:ptcp.w:call-paraphase-25.t:call-call_f8 INFO eval :: name: "disk_size", value: 11
2025-09-15 20:24:25.104 wdl.w:ptcp.w:call-paraphase-25.t:call-call_f8 INFO eval :: name: "sample_sex", value: "F"
2025-09-15 20:24:25.106 wdl.w:ptcp.w:call-paraphase-25.t:call-call_f8 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:25.107 wdl.w:ptcp.w:call-paraphase-25.t:call-call_f8 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:25.108 wdl.w:ptcp.w:call-paraphase-25.t:call-call_f8 INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:25.108 wdl.w:ptcp.w:call-paraphase-25.t:call-call_f8 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:25.115 wdl.w:ptcp.w:call-paraphase-32.t:call-call_f8 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:25.115 wdl.w:ptcp.w:call-paraphase-32.t:call-call_f8 INFO input :: name: "genome_version", value: "38"
2025-09-15 20:24:25.115 wdl.w:ptcp.w:call-paraphase-32.t:call-call_f8 INFO input :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2129"
2025-09-15 20:24:25.115 wdl.w:ptcp.w:call-paraphase-32.t:call-call_f8 INFO input :: name: "paraphase_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2129.paraphase.bam.bai"
2025-09-15 20:24:25.115 wdl.w:ptcp.w:call-paraphase-32.t:call-call_f8 INFO input :: name: "paraphase_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2129.paraphase.bam"
2025-09-15 20:24:25.115 wdl.w:ptcp.w:call-paraphase-32.t:call-call_f8 INFO input :: name: "sex", value: "F"
2025-09-15 20:24:25.115 wdl.w:ptcp.w:call-paraphase-32.t:call-call_f8 INFO eval :: name: "threads", value: 1
2025-09-15 20:24:25.116 wdl.w:ptcp.w:call-paraphase-32.t:call-call_f8 INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:25.116 wdl.w:ptcp.w:call-paraphase-32.t:call-call_f8 INFO eval :: name: "disk_size", value: 11
2025-09-15 20:24:25.116 wdl.w:ptcp.w:call-paraphase-32.t:call-call_f8 INFO eval :: name: "sample_sex", value: "F"
2025-09-15 20:24:25.116 wdl.w:ptcp.w:call-paraphase-32.t:call-call_f8 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:25.116 wdl.w:ptcp.w:call-paraphase-32.t:call-call_f8 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:25.117 wdl.w:ptcp.w:call-paraphase-32.t:call-call_f8 INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:25.117 wdl.w:ptcp.w:call-paraphase-32.t:call-call_f8 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:25.125 wdl.w:ptcp.w:call-trgt-08.t:call-trgt_plot_motifs_waterfall INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-08/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_2w7gj7yl"
2025-09-15 20:24:25.126 wdl.w:ptcp.w:call-trgt-08.t:call-trgt_plot_motifs_waterfall INFO Slurm invocation: srun --job-name call-trgt_plot_motifs_waterfall --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-08/call-trgt_plot_motifs_waterfall/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-08/call-trgt_plot_motifs_waterfall/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-08/call-trgt_plot_motifs_waterfall/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-08/call-trgt_plot_motifs_waterfall/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-08/call-trgt_genotype/out/m84036_250809_035451_s4.bc2105.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2105.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-08/call-trgt_genotype/out/m84036_250809_035451_s4.bc2105.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2105.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-08/call-trgt_genotype/out/m84036_250809_035451_s4.bc2105.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2105.trgt.sorted.spanning.bam.bai:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-08/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_2w7gj7yl/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-08/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_2w7gj7yl/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:25.142 wdl.w:ptcp.w:call-sawfish-31.t:call-run_sawfish.stderr VERBOSE [M::mm_idx_gen::49.041*1.63] collected minimizers
2025-09-15 20:24:25.143 wdl.w:ptcp.w:call-sawfish-31.t:call-run_sawfish.stderr VERBOSE [M::mm_idx_gen::58.800*1.84] sorted minimizers
2025-09-15 20:24:25.143 wdl.w:ptcp.w:call-sawfish-31.t:call-run_sawfish.stderr VERBOSE [M::main::58.801*1.84] loaded/built the index for 195 target sequence(s)
2025-09-15 20:24:25.143 wdl.w:ptcp.w:call-sawfish-31.t:call-run_sawfish.stderr VERBOSE [M::mm_mapopt_update::63.938*1.77] mid_occ = 136
2025-09-15 20:24:25.143 wdl.w:ptcp.w:call-sawfish-31.t:call-run_sawfish.stderr VERBOSE [M::mm_idx_stat] kmer size: 19; skip: 19; is_hpc: 0; #seq: 195
2025-09-15 20:24:25.143 wdl.w:ptcp.w:call-sawfish-31.t:call-run_sawfish.stderr VERBOSE [M::mm_idx_stat::67.979*1.73] distinct minimizers: 214664461 (92.23% are singletons); average occurrences: 1.372; average spacing: 10.529; total length: 3099922541
2025-09-15 20:24:25.143 wdl.w:ptcp.w:call-sawfish-31.t:call-run_sawfish.stderr VERBOSE [M::bam2fq_mainloop] discarded 0 singletons
2025-09-15 20:24:25.143 wdl.w:ptcp.w:call-sawfish-31.t:call-run_sawfish.stderr VERBOSE [M::bam2fq_mainloop] processed 264 reads
2025-09-15 20:24:25.144 wdl.w:ptcp.w:call-sawfish-31.t:call-run_sawfish.stderr VERBOSE [M::worker_pipeline::68.488*1.73] mapped 264 sequences
2025-09-15 20:24:25.144 wdl.w:ptcp.w:call-sawfish-31.t:call-run_sawfish.stderr VERBOSE [M::main] Version: 2.26-r1175
2025-09-15 20:24:25.144 wdl.w:ptcp.w:call-sawfish-31.t:call-run_sawfish.stderr VERBOSE [M::main] CMD: /opt/pacbio/smrttools/install/smrtlink-release_25.1.0.257715/bundles/smrttools/install/smrttools-release_25.1.0.257715/private/thirdparty/minimap2/minimap2_2.26-pacbio2/binwrap/../../../../../private/thirdparty/minimap2/minimap2_2.26-pacbio2/bin/minimap2 -a -y -x map-hifi -Y -E 1,0 /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa -
2025-09-15 20:24:25.144 wdl.w:ptcp.w:call-sawfish-31.t:call-run_sawfish.stderr VERBOSE [M::main] Real time: 68.838 sec; CPU: 119.053 sec; Peak RSS: 11.886 GB
2025-09-15 20:24:25.144 wdl.w:ptcp.w:call-sawfish-31.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:10][sawfish][INFO] Starting sawfish 2.0.3
2025-09-15 20:24:25.144 wdl.w:ptcp.w:call-sawfish-31.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:10][sawfish][INFO] cmdline: sawfish discover --disable-cnv --threads 16 --ref /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa --bam m84036_250809_035451_s4.bc2128.minimap2.bam --output-dir m84036_250809_035451_s4.bc2128_sawfish_discover
2025-09-15 20:24:25.144 wdl.w:ptcp.w:call-sawfish-31.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:10][sawfish][INFO] Running on 16 threads
2025-09-15 20:24:25.144 wdl.w:ptcp.w:call-sawfish-31.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:10][sawfish][INFO] Writing discover settings to file: 'm84036_250809_035451_s4.bc2128_sawfish_discover/discover.settings.json'
2025-09-15 20:24:25.144 wdl.w:ptcp.w:call-sawfish-31.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:10][sawfish][INFO] Reading reference genome from file '/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa'
2025-09-15 20:24:25.144 wdl.w:ptcp.w:call-sawfish-31.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:16][sawfish][INFO] Processing alignment file '/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2128.minimap2.bam'
2025-09-15 20:24:25.144 wdl.w:ptcp.w:call-sawfish-31.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:16][sawfish][INFO] Finished processing all alignments
2025-09-15 20:24:25.144 wdl.w:ptcp.w:call-sawfish-31.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:16][sawfish][INFO] Writing depth bins to binary file: 'm84036_250809_035451_s4.bc2128_sawfish_discover/depth.mpack'
2025-09-15 20:24:25.144 wdl.w:ptcp.w:call-sawfish-31.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:16][sawfish][INFO] Writing max sv depth genome regions to bed file: 'm84036_250809_035451_s4.bc2128_sawfish_discover/max.depth.bed'
2025-09-15 20:24:25.144 wdl.w:ptcp.w:call-sawfish-31.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:16][sawfish][INFO] Completing breakpoint observation clustering
2025-09-15 20:24:25.144 wdl.w:ptcp.w:call-sawfish-31.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:16][sawfish][INFO] Finished breakpoint observation clustering
2025-09-15 20:24:25.144 wdl.w:ptcp.w:call-sawfish-31.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:16][sawfish][INFO] Consolidating adjacent indel candidates
2025-09-15 20:24:25.144 wdl.w:ptcp.w:call-sawfish-31.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:16][sawfish][INFO] Finding large insertion candidates
2025-09-15 20:24:25.144 wdl.w:ptcp.w:call-sawfish-31.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:16][sawfish][INFO] Writing breakpoint_cluster debug bed file: 'm84036_250809_035451_s4.bc2128_sawfish_discover/debug.breakpoint_clusters.bed'
2025-09-15 20:24:25.144 wdl.w:ptcp.w:call-sawfish-31.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:16][sawfish][INFO] Refining SV Candidates
2025-09-15 20:24:25.145 wdl.w:ptcp.w:call-sawfish-31.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:16][sawfish][INFO] Writing debug assembly region bed file: 'm84036_250809_035451_s4.bc2128_sawfish_discover/assembly.regions.bed'
2025-09-15 20:24:25.145 wdl.w:ptcp.w:call-sawfish-31.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:16][sawfish][INFO] Starting refinement of breakpoint evidence clusters
2025-09-15 20:24:25.145 wdl.w:ptcp.w:call-sawfish-31.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:17][sawfish][INFO] Finished refining all breakpoint evidence clusters
2025-09-15 20:24:25.145 wdl.w:ptcp.w:call-sawfish-31.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:17][sawfish][INFO] Writing all contig alignments to bam file: 'm84036_250809_035451_s4.bc2128_sawfish_discover/contig.alignment.bam'
2025-09-15 20:24:25.145 wdl.w:ptcp.w:call-sawfish-31.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:17][sawfish][INFO] Writing candidate structural variants to file: 'm84036_250809_035451_s4.bc2128_sawfish_discover/candidate.sv.bcf'
2025-09-15 20:24:25.145 wdl.w:ptcp.w:call-sawfish-31.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:17][sawfish][INFO] Writing run statistics to file: 'm84036_250809_035451_s4.bc2128_sawfish_discover/run.stats.json'
2025-09-15 20:24:25.145 wdl.w:ptcp.w:call-sawfish-31.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:18][sawfish][INFO] sawfish completed. Total Runtime: 00:00:07.440
2025-09-15 20:24:25.160 wdl.w:ptcp.w:call-trgt-08.t:call-trgt_plot_motifs_waterfall NOTICE slurm_singularity run :: pid: 1201735, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-08/call-trgt_plot_motifs_waterfall/slurm_singularity.log.txt"
2025-09-15 20:24:25.167 wdl.w:ptcp.w:call-paraphase-25.t:call-call_f8 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 8, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-25/call-call_f8/_singularity_tmpdir_oomejjpo"
2025-09-15 20:24:25.167 wdl.w:ptcp.w:call-paraphase-25.t:call-call_f8 INFO Slurm invocation: srun --job-name call-call_f8 --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-25/call-call_f8/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-25/call-call_f8/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-25/call-call_f8/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-25/call-call_f8/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-25/call-run_paraphase/out/m84036_250809_035451_s4.bc2122_paraphase/m84036_250809_035451_s4.bc2122.paraphase.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2122.paraphase.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-25/call-run_paraphase/out/m84036_250809_035451_s4.bc2122_paraphase/m84036_250809_035451_s4.bc2122.paraphase.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2122.paraphase.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-25/call-call_f8/_singularity_tmpdir_oomejjpo/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-25/call-call_f8/_singularity_tmpdir_oomejjpo/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:25.176 wdl.w:ptcp.w:call-paraphase-32.t:call-call_f8 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 8, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-32/call-call_f8/_singularity_tmpdir_1d5rx59y"
2025-09-15 20:24:25.176 wdl.w:ptcp.w:call-paraphase-32.t:call-call_f8 INFO Slurm invocation: srun --job-name call-call_f8 --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-32/call-call_f8/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-32/call-call_f8/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-32/call-call_f8/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-32/call-call_f8/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-32/call-run_paraphase/out/m84036_250809_035451_s4.bc2129_paraphase/m84036_250809_035451_s4.bc2129.paraphase.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2129.paraphase.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-32/call-run_paraphase/out/m84036_250809_035451_s4.bc2129_paraphase/m84036_250809_035451_s4.bc2129.paraphase.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2129.paraphase.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-32/call-call_f8/_singularity_tmpdir_1d5rx59y/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-32/call-call_f8/_singularity_tmpdir_1d5rx59y/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:25.185 wdl.w:ptcp.w:call-paraphase-32.t:call-call_f8 NOTICE slurm_singularity run :: pid: 1201738, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-32/call-call_f8/slurm_singularity.log.txt"
2025-09-15 20:24:25.185 wdl.w:ptcp.w:call-paraphase-25.t:call-call_f8 NOTICE slurm_singularity run :: pid: 1201736, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-25/call-call_f8/slurm_singularity.log.txt"
2025-09-15 20:24:25.193 wdl.w:ptcp.w:call-trgt-25.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:24 [ERROR] - No reads found for TRID=PRTS_ARX
2025-09-15 20:24:25.193 wdl.w:ptcp.w:call-trgt-25.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:24 [ERROR] - No reads found for TRID=EIEE1_ARX
2025-09-15 20:24:25.197 wdl.w:ptcp.w:call-paraphase-09 NOTICE done
2025-09-15 20:24:25.204 wdl.w:ptcp NOTICE finish :: job: "call-paraphase-09"
2025-09-15 20:24:25.204 wdl.w:ptcp INFO output :: job: "call-paraphase-09", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-09/out/m84036_250809_035451_s4.bc2106.f8inversion.vcf", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-09/out/m84036_250809_035451_s4.bc2106_paraphase/m84036_250809_035451_s4.bc2106.paraphase.json", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-09/out/m84036_250809_035451_s4.bc2106_paraphase/m84036_250809_035451_s4.bc2106.paraphase.bam", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-09/out/m84036_250809_035451_s4.bc2106_paraphase/m84036_250809_035451_s4.bc2106.paraphase.bam.bai", "paraphase_vcfs": [], "havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-09/out/m84036_250809_035451_s4.bc2106.havanno.json", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-09/out/m84036_250809_035451_s4.bc2106.f8inversion.json"}
2025-09-15 20:24:25.211 wdl.w:ptcp.w:call-trgt-49 NOTICE workflow start :: name: "trgt", source: "./trgt.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-49"
2025-09-15 20:24:25.228 wdl.w:ptcp.w:call-trgt-49 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:24:25.228 wdl.w:ptcp.w:call-trgt-49 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-49/out/m84036_250809_035451_s4.bc2146.mapped.bam"}
2025-09-15 20:24:25.228 wdl.w:ptcp.w:call-trgt-49 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-49/out/m84036_250809_035451_s4.bc2146.mapped.bam.bai"}
2025-09-15 20:24:25.229 wdl.w:ptcp.w:call-trgt-49 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:24:25.229 wdl.w:ptcp.w:call-trgt-49 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:24:25.229 wdl.w:ptcp.w:call-trgt-49 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2146"}
2025-09-15 20:24:25.229 wdl.w:ptcp.w:call-trgt-49 INFO visit :: node: "decl-sex", values: {"sex": "F"}
2025-09-15 20:24:25.229 wdl.w:ptcp.w:call-trgt-49 INFO visit :: node: "decl-trgt_bed", values: {"trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"}
2025-09-15 20:24:25.229 wdl.w:ptcp.w:call-trgt-49 NOTICE ready :: job: "call-get_reads_overlapping_repeats", callee: "get_reads_overlapping_repeats"
2025-09-15 20:24:25.229 wdl.w:ptcp.w:call-trgt-49 INFO input :: job: "call-get_reads_overlapping_repeats", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-49/out/m84036_250809_035451_s4.bc2146.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-49/out/m84036_250809_035451_s4.bc2146.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2146"}
2025-09-15 20:24:25.230 wdl.w:ptcp.w:call-trgt-49 NOTICE ready :: job: "call-trgt_genotype", callee: "trgt_genotype"
2025-09-15 20:24:25.230 wdl.w:ptcp.w:call-trgt-49 INFO input :: job: "call-trgt_genotype", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-49/out/m84036_250809_035451_s4.bc2146.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-49/out/m84036_250809_035451_s4.bc2146.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2146"}
2025-09-15 20:24:25.243 wdl.w:ptcp.w:call-trgt-16.t:call-trgt_plot_meth_allele NOTICE done
2025-09-15 20:24:25.248 wdl.w:ptcp.w:call-trgt-16 NOTICE finish :: job: "call-trgt_plot_meth_allele"
2025-09-15 20:24:25.248 wdl.w:ptcp.w:call-trgt-16 INFO output :: job: "call-trgt_plot_meth_allele", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-16/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2113.meth_allele.trgt_plots.zip"}
2025-09-15 20:24:25.248 wdl.w:ptcp.w:call-trgt-16 INFO visit :: node: "output-images_meth_allele", values: {"images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-16/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2113.meth_allele.trgt_plots.zip"}
2025-09-15 20:24:25.252 wdl.w:ptcp.w:call-trgt-00.t:call-trgt_plot_meth_allele NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-00/call-trgt_plot_meth_allele", thread: 140606617675328
2025-09-15 20:24:25.269 wdl.w:ptcp.w:call-trgt-00.t:call-trgt_plot_meth_allele INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:25.270 wdl.w:ptcp.w:call-trgt-00.t:call-trgt_plot_meth_allele INFO input :: name: "waterfall", value: false
2025-09-15 20:24:25.270 wdl.w:ptcp.w:call-trgt-00.t:call-trgt_plot_meth_allele INFO input :: name: "methylation", value: true
2025-09-15 20:24:25.270 wdl.w:ptcp.w:call-trgt-00.t:call-trgt_plot_meth_allele INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:25.270 wdl.w:ptcp.w:call-trgt-00.t:call-trgt_plot_meth_allele INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:25.270 wdl.w:ptcp.w:call-trgt-00.t:call-trgt_plot_meth_allele INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:25.270 wdl.w:ptcp.w:call-trgt-00.t:call-trgt_plot_meth_allele INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2097.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:25.270 wdl.w:ptcp.w:call-trgt-00.t:call-trgt_plot_meth_allele INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2097.trgt.sorted.spanning.bam"
2025-09-15 20:24:25.270 wdl.w:ptcp.w:call-trgt-00.t:call-trgt_plot_meth_allele INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2097.trgt.vcf"
2025-09-15 20:24:25.270 wdl.w:ptcp.w:call-trgt-00.t:call-trgt_plot_meth_allele INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2097"
2025-09-15 20:24:25.270 wdl.w:ptcp.w:call-trgt-00.t:call-trgt_plot_meth_allele INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:25.271 wdl.w:ptcp.w:call-trgt-00.t:call-trgt_plot_meth_allele INFO eval :: name: "plot_type", value: "allele"
2025-09-15 20:24:25.271 wdl.w:ptcp.w:call-trgt-00.t:call-trgt_plot_meth_allele INFO eval :: name: "show", value: "meth"
2025-09-15 20:24:25.271 wdl.w:ptcp.w:call-trgt-00.t:call-trgt_plot_meth_allele INFO eval :: name: "threads", value: 1
2025-09-15 20:24:25.271 wdl.w:ptcp.w:call-trgt-00.t:call-trgt_plot_meth_allele INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:25.271 wdl.w:ptcp.w:call-trgt-00.t:call-trgt_plot_meth_allele INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2097.meth_allele"
2025-09-15 20:24:25.271 wdl.w:ptcp.w:call-trgt-00.t:call-trgt_plot_meth_allele INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:25.272 wdl.w:ptcp.w:call-trgt-00.t:call-trgt_plot_meth_allele WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:25.272 wdl.w:ptcp.w:call-trgt-00.t:call-trgt_plot_meth_allele INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:25.272 wdl.w:ptcp.w:call-trgt-00.t:call-trgt_plot_meth_allele INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:25.293 wdl.w:ptcp.w:call-trgt-05.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:22 [ERROR] - No reads found for TRID=PRTS_ARX
2025-09-15 20:24:25.293 wdl.w:ptcp.w:call-trgt-05.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:22 [ERROR] - No reads found for TRID=EIEE1_ARX
2025-09-15 20:24:25.296 wdl.w:ptcp.w:call-paraphase-31.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for cyp21 for sample m84036_250809_035451_s4.bc2128 at 2025-09-15 20:23:39.623537...
2025-09-15 20:24:25.298 wdl.w:ptcp.w:call-paraphase-31.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for cyp21 for sample m84036_250809_035451_s4.bc2128 at 2025-09-15 20:23:40.274702...
2025-09-15 20:24:25.298 wdl.w:ptcp.w:call-paraphase-31.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for hba for sample m84036_250809_035451_s4.bc2128 at 2025-09-15 20:23:43.900914...
2025-09-15 20:24:25.298 wdl.w:ptcp.w:call-paraphase-31.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for hba for sample m84036_250809_035451_s4.bc2128 at 2025-09-15 20:23:44.251997...
2025-09-15 20:24:25.298 wdl.w:ptcp.w:call-paraphase-31.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for gba for sample m84036_250809_035451_s4.bc2128 at 2025-09-15 20:23:51.161541...
2025-09-15 20:24:25.298 wdl.w:ptcp.w:call-paraphase-31.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for gba for sample m84036_250809_035451_s4.bc2128 at 2025-09-15 20:23:51.504660...
2025-09-15 20:24:25.298 wdl.w:ptcp.w:call-paraphase-31.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for hbb for sample m84036_250809_035451_s4.bc2128 at 2025-09-15 20:24:01.801237...
2025-09-15 20:24:25.298 wdl.w:ptcp.w:call-paraphase-31.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for hbb for sample m84036_250809_035451_s4.bc2128 at 2025-09-15 20:24:01.801483...
2025-09-15 20:24:25.298 wdl.w:ptcp.w:call-paraphase-31.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for hbb for sample m84036_250809_035451_s4.bc2128 at 2025-09-15 20:24:02.656888...
2025-09-15 20:24:25.298 wdl.w:ptcp.w:call-paraphase-31.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for hbb for sample m84036_250809_035451_s4.bc2128 at 2025-09-15 20:24:05.488172...
2025-09-15 20:24:25.298 wdl.w:ptcp.w:call-paraphase-31.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for hbb for sample m84036_250809_035451_s4.bc2128 at 2025-09-15 20:24:05.681468...
2025-09-15 20:24:25.342 wdl.w:ptcp.w:call-trgt-00.t:call-trgt_plot_meth_allele INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-00/call-trgt_plot_meth_allele/_singularity_tmpdir_okmsw32s"
2025-09-15 20:24:25.342 wdl.w:ptcp.w:call-trgt-00.t:call-trgt_plot_meth_allele INFO Slurm invocation: srun --job-name call-trgt_plot_meth_allele --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-00/call-trgt_plot_meth_allele/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-00/call-trgt_plot_meth_allele/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-00/call-trgt_plot_meth_allele/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-00/call-trgt_plot_meth_allele/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-00/call-trgt_genotype/out/m84036_250809_035451_s4.bc2097.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2097.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-00/call-trgt_genotype/out/m84036_250809_035451_s4.bc2097.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2097.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-00/call-trgt_genotype/out/m84036_250809_035451_s4.bc2097.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2097.trgt.sorted.spanning.bam:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-00/call-trgt_plot_meth_allele/_singularity_tmpdir_okmsw32s/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-00/call-trgt_plot_meth_allele/_singularity_tmpdir_okmsw32s/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:25.370 wdl.w:ptcp.w:call-trgt-00.t:call-trgt_plot_meth_allele NOTICE slurm_singularity run :: pid: 1201741, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-00/call-trgt_plot_meth_allele/slurm_singularity.log.txt"
2025-09-15 20:24:25.410 wdl.w:ptcp.w:call-paraphase-24.t:call-call_f8 INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2121.f8inversion.vcf"
2025-09-15 20:24:25.414 wdl.w:ptcp.w:call-paraphase-24.t:call-call_f8 INFO output :: name: "json", value: "m84036_250809_035451_s4.bc2121.f8inversion.json"
2025-09-15 20:24:25.442 wdl.w:ptcp.w:call-paraphase-21.t:call-call_f8 INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2118.f8inversion.vcf"
2025-09-15 20:24:25.447 wdl.w:ptcp.w:call-paraphase-21.t:call-call_f8 INFO output :: name: "json", value: "m84036_250809_035451_s4.bc2118.f8inversion.json"
2025-09-15 20:24:25.475 wdl.w:ptcp.w:call-paraphase-24.t:call-call_f8 NOTICE done
2025-09-15 20:24:25.480 wdl.w:ptcp.w:call-paraphase-24 NOTICE finish :: job: "call-call_f8"
2025-09-15 20:24:25.480 wdl.w:ptcp.w:call-paraphase-24 INFO output :: job: "call-call_f8", values: {"json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-24/call-call_f8/out/m84036_250809_035451_s4.bc2121.f8inversion.json", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-24/call-call_f8/out/m84036_250809_035451_s4.bc2121.f8inversion.vcf"}
2025-09-15 20:24:25.480 wdl.w:ptcp.w:call-paraphase-24 INFO visit :: node: "output-f8_json", values: {"f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-24/call-call_f8/out/m84036_250809_035451_s4.bc2121.f8inversion.json"}
2025-09-15 20:24:25.480 wdl.w:ptcp.w:call-paraphase-24 INFO visit :: node: "output-f8_vcf", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-24/call-call_f8/out/m84036_250809_035451_s4.bc2121.f8inversion.vcf"}
2025-09-15 20:24:25.481 wdl.w:ptcp.w:call-paraphase-24 INFO visit :: node: "outputs", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-24/call-call_f8/out/m84036_250809_035451_s4.bc2121.f8inversion.vcf", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-24/call-run_paraphase/out/m84036_250809_035451_s4.bc2121_paraphase/m84036_250809_035451_s4.bc2121.paraphase.json", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-24/call-run_paraphase/out/m84036_250809_035451_s4.bc2121_paraphase/m84036_250809_035451_s4.bc2121.paraphase.bam", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-24/call-run_paraphase/out/m84036_250809_035451_s4.bc2121_paraphase/m84036_250809_035451_s4.bc2121.paraphase.bam.bai", "paraphase_vcfs": [], "havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-24/call-run_paraphase/out/m84036_250809_035451_s4.bc2121.havanno.json", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-24/call-call_f8/out/m84036_250809_035451_s4.bc2121.f8inversion.json"}
2025-09-15 20:24:25.486 wdl.w:ptcp.w:call-trgt-00.t:call-trgt_plot_meth_waterfall NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-00/call-trgt_plot_meth_waterfall", thread: 140607137760832
2025-09-15 20:24:25.517 wdl.w:ptcp.w:call-paraphase-21.t:call-call_f8 NOTICE done
2025-09-15 20:24:25.522 wdl.w:ptcp.w:call-trgt-00.t:call-trgt_plot_meth_waterfall INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:25.522 wdl.w:ptcp.w:call-paraphase-21 NOTICE finish :: job: "call-call_f8"
2025-09-15 20:24:25.522 wdl.w:ptcp.w:call-trgt-00.t:call-trgt_plot_meth_waterfall INFO input :: name: "waterfall", value: true
2025-09-15 20:24:25.522 wdl.w:ptcp.w:call-paraphase-21 INFO output :: job: "call-call_f8", values: {"json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-21/call-call_f8/out/m84036_250809_035451_s4.bc2118.f8inversion.json", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-21/call-call_f8/out/m84036_250809_035451_s4.bc2118.f8inversion.vcf"}
2025-09-15 20:24:25.522 wdl.w:ptcp.w:call-trgt-00.t:call-trgt_plot_meth_waterfall INFO input :: name: "methylation", value: true
2025-09-15 20:24:25.522 wdl.w:ptcp.w:call-paraphase-21 INFO visit :: node: "output-f8_json", values: {"f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-21/call-call_f8/out/m84036_250809_035451_s4.bc2118.f8inversion.json"}
2025-09-15 20:24:25.523 wdl.w:ptcp.w:call-trgt-00.t:call-trgt_plot_meth_waterfall INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:25.523 wdl.w:ptcp.w:call-paraphase-21 INFO visit :: node: "output-f8_vcf", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-21/call-call_f8/out/m84036_250809_035451_s4.bc2118.f8inversion.vcf"}
2025-09-15 20:24:25.523 wdl.w:ptcp.w:call-trgt-00.t:call-trgt_plot_meth_waterfall INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:25.523 wdl.w:ptcp.w:call-paraphase-21 INFO visit :: node: "outputs", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-21/call-call_f8/out/m84036_250809_035451_s4.bc2118.f8inversion.vcf", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-21/call-run_paraphase/out/m84036_250809_035451_s4.bc2118_paraphase/m84036_250809_035451_s4.bc2118.paraphase.json", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-21/call-run_paraphase/out/m84036_250809_035451_s4.bc2118_paraphase/m84036_250809_035451_s4.bc2118.paraphase.bam", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-21/call-run_paraphase/out/m84036_250809_035451_s4.bc2118_paraphase/m84036_250809_035451_s4.bc2118.paraphase.bam.bai", "paraphase_vcfs": [], "havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-21/call-run_paraphase/out/m84036_250809_035451_s4.bc2118.havanno.json", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-21/call-call_f8/out/m84036_250809_035451_s4.bc2118.f8inversion.json"}
2025-09-15 20:24:25.523 wdl.w:ptcp.w:call-trgt-00.t:call-trgt_plot_meth_waterfall INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:25.523 wdl.w:ptcp.w:call-trgt-00.t:call-trgt_plot_meth_waterfall INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2097.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:25.523 wdl.w:ptcp.w:call-trgt-00.t:call-trgt_plot_meth_waterfall INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2097.trgt.sorted.spanning.bam"
2025-09-15 20:24:25.524 wdl.w:ptcp.w:call-trgt-00.t:call-trgt_plot_meth_waterfall INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2097.trgt.vcf"
2025-09-15 20:24:25.524 wdl.w:ptcp.w:call-trgt-00.t:call-trgt_plot_meth_waterfall INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2097"
2025-09-15 20:24:25.524 wdl.w:ptcp.w:call-trgt-00.t:call-trgt_plot_meth_waterfall INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:25.524 wdl.w:ptcp.w:call-trgt-00.t:call-trgt_plot_meth_waterfall INFO eval :: name: "plot_type", value: "waterfall"
2025-09-15 20:24:25.524 wdl.w:ptcp.w:call-trgt-00.t:call-trgt_plot_meth_waterfall INFO eval :: name: "show", value: "meth"
2025-09-15 20:24:25.524 wdl.w:ptcp.w:call-trgt-00.t:call-trgt_plot_meth_waterfall INFO eval :: name: "threads", value: 1
2025-09-15 20:24:25.524 wdl.w:ptcp.w:call-trgt-00.t:call-trgt_plot_meth_waterfall INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:25.525 wdl.w:ptcp.w:call-trgt-00.t:call-trgt_plot_meth_waterfall INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2097.meth_waterfall"
2025-09-15 20:24:25.525 wdl.w:ptcp.w:call-trgt-00.t:call-trgt_plot_meth_waterfall INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:25.525 wdl.w:ptcp.w:call-trgt-00.t:call-trgt_plot_meth_waterfall WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:25.525 wdl.w:ptcp.w:call-trgt-00.t:call-trgt_plot_meth_waterfall INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:25.526 wdl.w:ptcp.w:call-trgt-00.t:call-trgt_plot_meth_waterfall INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:25.528 wdl.w:ptcp.w:call-trgt-00.t:call-trgt_plot_motifs_allele NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-00/call-trgt_plot_motifs_allele", thread: 140608203109952
2025-09-15 20:24:25.556 wdl.w:ptcp.w:call-trgt-00.t:call-trgt_plot_motifs_allele INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:25.556 wdl.w:ptcp.w:call-trgt-00.t:call-trgt_plot_motifs_allele INFO input :: name: "waterfall", value: false
2025-09-15 20:24:25.556 wdl.w:ptcp.w:call-trgt-00.t:call-trgt_plot_motifs_allele INFO input :: name: "methylation", value: false
2025-09-15 20:24:25.556 wdl.w:ptcp.w:call-trgt-00.t:call-trgt_plot_motifs_allele INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:25.556 wdl.w:ptcp.w:call-trgt-00.t:call-trgt_plot_motifs_allele INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:25.556 wdl.w:ptcp.w:call-trgt-00.t:call-trgt_plot_motifs_allele INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:25.556 wdl.w:ptcp.w:call-trgt-00.t:call-trgt_plot_motifs_allele INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2097.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:25.556 wdl.w:ptcp.w:call-trgt-00.t:call-trgt_plot_motifs_allele INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2097.trgt.sorted.spanning.bam"
2025-09-15 20:24:25.557 wdl.w:ptcp.w:call-trgt-00.t:call-trgt_plot_motifs_allele INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2097.trgt.vcf"
2025-09-15 20:24:25.557 wdl.w:ptcp.w:call-trgt-00.t:call-trgt_plot_motifs_allele INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2097"
2025-09-15 20:24:25.557 wdl.w:ptcp.w:call-trgt-00.t:call-trgt_plot_motifs_allele INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:25.557 wdl.w:ptcp.w:call-trgt-00.t:call-trgt_plot_motifs_allele INFO eval :: name: "plot_type", value: "allele"
2025-09-15 20:24:25.557 wdl.w:ptcp.w:call-trgt-00.t:call-trgt_plot_motifs_allele INFO eval :: name: "show", value: "motifs"
2025-09-15 20:24:25.558 wdl.w:ptcp.w:call-trgt-00.t:call-trgt_plot_motifs_allele INFO eval :: name: "threads", value: 1
2025-09-15 20:24:25.558 wdl.w:ptcp.w:call-trgt-00.t:call-trgt_plot_motifs_allele INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:25.558 wdl.w:ptcp.w:call-trgt-00.t:call-trgt_plot_motifs_allele INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2097.motifs_allele"
2025-09-15 20:24:25.559 wdl.w:ptcp.w:call-trgt-00.t:call-trgt_plot_motifs_allele INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:25.559 wdl.w:ptcp.w:call-trgt-00.t:call-trgt_plot_motifs_allele WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:25.559 wdl.w:ptcp.w:call-trgt-00.t:call-trgt_plot_motifs_allele INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:25.559 wdl.w:ptcp.w:call-trgt-00.t:call-trgt_plot_motifs_allele INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:25.562 wdl.w:ptcp.w:call-paraphase-12.t:call-call_f8.slurm_singularity INFO srun: job 51797634 queued and waiting for resources
2025-09-15 20:24:25.562 wdl.w:ptcp.w:call-paraphase-12.t:call-call_f8.slurm_singularity INFO srun: job 51797634 has been allocated resources
2025-09-15 20:24:25.562 wdl.w:ptcp.w:call-paraphase-12.t:call-call_f8.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:25.564 wdl.w:ptcp.w:call-paraphase-24 NOTICE done
2025-09-15 20:24:25.571 wdl.w:ptcp NOTICE finish :: job: "call-paraphase-24"
2025-09-15 20:24:25.572 wdl.w:ptcp INFO output :: job: "call-paraphase-24", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-24/out/m84036_250809_035451_s4.bc2121.f8inversion.vcf", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-24/out/m84036_250809_035451_s4.bc2121_paraphase/m84036_250809_035451_s4.bc2121.paraphase.json", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-24/out/m84036_250809_035451_s4.bc2121_paraphase/m84036_250809_035451_s4.bc2121.paraphase.bam", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-24/out/m84036_250809_035451_s4.bc2121_paraphase/m84036_250809_035451_s4.bc2121.paraphase.bam.bai", "paraphase_vcfs": [], "havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-24/out/m84036_250809_035451_s4.bc2121.havanno.json", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-24/out/m84036_250809_035451_s4.bc2121.f8inversion.json"}
2025-09-15 20:24:25.577 wdl.w:ptcp.w:call-paraphase-54 NOTICE workflow start :: name: "paraphase", source: "./paraphase.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-54"
2025-09-15 20:24:25.594 wdl.w:ptcp.w:call-paraphase-54 INFO visit :: node: "decl-annotation_vcf", values: {"annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf"}
2025-09-15 20:24:25.594 wdl.w:ptcp.w:call-paraphase-54 INFO visit :: node: "decl-config_file", values: {"config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml"}
2025-09-15 20:24:25.594 wdl.w:ptcp.w:call-paraphase-54 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:24:25.594 wdl.w:ptcp.w:call-paraphase-54 INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:24:25.594 wdl.w:ptcp.w:call-paraphase-54 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-54/out/m84036_250809_035451_s4.bc2151.mapped.bam"}
2025-09-15 20:24:25.594 wdl.w:ptcp.w:call-paraphase-54 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-54/out/m84036_250809_035451_s4.bc2151.mapped.bam.bai"}
2025-09-15 20:24:25.594 wdl.w:ptcp.w:call-paraphase-54 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:24:25.595 wdl.w:ptcp.w:call-paraphase-54 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:24:25.595 wdl.w:ptcp.w:call-paraphase-54 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2151"}
2025-09-15 20:24:25.595 wdl.w:ptcp.w:call-paraphase-54 INFO visit :: node: "decl-sex", values: {"sex": "F"}
2025-09-15 20:24:25.595 wdl.w:ptcp.w:call-paraphase-54 NOTICE ready :: job: "call-run_paraphase", callee: "run_paraphase"
2025-09-15 20:24:25.595 wdl.w:ptcp.w:call-paraphase-54 INFO input :: job: "call-run_paraphase", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf", "genome_version": "38", "config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-54/out/m84036_250809_035451_s4.bc2151.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-54/out/m84036_250809_035451_s4.bc2151.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2151"}
2025-09-15 20:24:25.617 wdl.w:ptcp.w:call-trgt-25.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:25 [ERROR] - No reads found for TRID=PRTS_ARX
2025-09-15 20:24:25.618 wdl.w:ptcp.w:call-trgt-25.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:25 [ERROR] - No reads found for TRID=EIEE1_ARX
2025-09-15 20:24:25.631 wdl.w:ptcp.w:call-trgt-00.t:call-trgt_plot_meth_waterfall INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-00/call-trgt_plot_meth_waterfall/_singularity_tmpdir_ujbr_bbt"
2025-09-15 20:24:25.631 wdl.w:ptcp.w:call-trgt-00.t:call-trgt_plot_meth_waterfall INFO Slurm invocation: srun --job-name call-trgt_plot_meth_waterfall --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-00/call-trgt_plot_meth_waterfall/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-00/call-trgt_plot_meth_waterfall/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-00/call-trgt_plot_meth_waterfall/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-00/call-trgt_plot_meth_waterfall/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-00/call-trgt_genotype/out/m84036_250809_035451_s4.bc2097.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2097.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-00/call-trgt_genotype/out/m84036_250809_035451_s4.bc2097.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2097.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-00/call-trgt_genotype/out/m84036_250809_035451_s4.bc2097.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2097.trgt.sorted.spanning.bam:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-00/call-trgt_plot_meth_waterfall/_singularity_tmpdir_ujbr_bbt/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-00/call-trgt_plot_meth_waterfall/_singularity_tmpdir_ujbr_bbt/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:25.637 wdl.w:ptcp.w:call-paraphase-21 NOTICE done
2025-09-15 20:24:25.651 wdl.w:ptcp NOTICE finish :: job: "call-paraphase-21"
2025-09-15 20:24:25.651 wdl.w:ptcp INFO output :: job: "call-paraphase-21", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-21/out/m84036_250809_035451_s4.bc2118.f8inversion.vcf", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-21/out/m84036_250809_035451_s4.bc2118_paraphase/m84036_250809_035451_s4.bc2118.paraphase.json", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-21/out/m84036_250809_035451_s4.bc2118_paraphase/m84036_250809_035451_s4.bc2118.paraphase.bam", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-21/out/m84036_250809_035451_s4.bc2118_paraphase/m84036_250809_035451_s4.bc2118.paraphase.bam.bai", "paraphase_vcfs": [], "havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-21/out/m84036_250809_035451_s4.bc2118.havanno.json", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-21/out/m84036_250809_035451_s4.bc2118.f8inversion.json"}
2025-09-15 20:24:25.652 wdl.w:ptcp.w:call-trgt-08.t:call-trgt_plot_meth_allele.slurm_singularity INFO srun: job 51797635 queued and waiting for resources
2025-09-15 20:24:25.652 wdl.w:ptcp.w:call-trgt-08.t:call-trgt_plot_meth_allele.slurm_singularity INFO srun: job 51797635 has been allocated resources
2025-09-15 20:24:25.652 wdl.w:ptcp.w:call-trgt-08.t:call-trgt_plot_meth_allele.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:25.662 wdl.w:ptcp.w:call-sawfish-54 NOTICE workflow start :: name: "sawfish", source: "./sawfish.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-54"
2025-09-15 20:24:25.676 wdl.w:ptcp.w:call-trgt-00.t:call-trgt_plot_motifs_allele INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-00/call-trgt_plot_motifs_allele/_singularity_tmpdir_ejc30ilp"
2025-09-15 20:24:25.676 wdl.w:ptcp.w:call-trgt-00.t:call-trgt_plot_meth_waterfall NOTICE slurm_singularity run :: pid: 1201770, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-00/call-trgt_plot_meth_waterfall/slurm_singularity.log.txt"
2025-09-15 20:24:25.677 wdl.w:ptcp.w:call-sawfish-54 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:24:25.677 wdl.w:ptcp.w:call-trgt-00.t:call-trgt_plot_motifs_allele INFO Slurm invocation: srun --job-name call-trgt_plot_motifs_allele --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-00/call-trgt_plot_motifs_allele/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-00/call-trgt_plot_motifs_allele/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-00/call-trgt_plot_motifs_allele/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-00/call-trgt_plot_motifs_allele/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-00/call-trgt_genotype/out/m84036_250809_035451_s4.bc2097.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2097.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-00/call-trgt_genotype/out/m84036_250809_035451_s4.bc2097.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2097.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-00/call-trgt_genotype/out/m84036_250809_035451_s4.bc2097.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2097.trgt.sorted.spanning.bam:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-00/call-trgt_plot_motifs_allele/_singularity_tmpdir_ejc30ilp/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-00/call-trgt_plot_motifs_allele/_singularity_tmpdir_ejc30ilp/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:25.677 wdl.w:ptcp.w:call-sawfish-54 INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:24:25.678 wdl.w:ptcp.w:call-sawfish-54 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-54/out/m84036_250809_035451_s4.bc2151.mapped.bam"}
2025-09-15 20:24:25.678 wdl.w:ptcp.w:call-sawfish-54 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-54/out/m84036_250809_035451_s4.bc2151.mapped.bam.bai"}
2025-09-15 20:24:25.678 wdl.w:ptcp.w:call-sawfish-54 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:24:25.679 wdl.w:ptcp.w:call-sawfish-54 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:24:25.680 wdl.w:ptcp.w:call-sawfish-54 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2151"}
2025-09-15 20:24:25.680 wdl.w:ptcp.w:call-sawfish-54 NOTICE ready :: job: "call-run_sawfish", callee: "run_sawfish"
2025-09-15 20:24:25.681 wdl.w:ptcp.w:call-sawfish-54 INFO input :: job: "call-run_sawfish", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-54/out/m84036_250809_035451_s4.bc2151.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-54/out/m84036_250809_035451_s4.bc2151.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2151"}
2025-09-15 20:24:25.688 wdl.w:ptcp.w:call-paraphase-18.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for f8inv1 for sample m84036_250809_035451_s4.bc2115 at 2025-09-15 20:24:14.643652...
2025-09-15 20:24:25.688 wdl.w:ptcp.w:call-paraphase-18.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for f8inv1 for sample m84036_250809_035451_s4.bc2115 at 2025-09-15 20:24:14.993992...
2025-09-15 20:24:25.688 wdl.w:ptcp.w:call-trgt-00.t:call-trgt_plot_motifs_allele NOTICE slurm_singularity run :: pid: 1201772, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-00/call-trgt_plot_motifs_allele/slurm_singularity.log.txt"
2025-09-15 20:24:25.759 wdl.w:ptcp.w:call-paraphase-16.t:call-call_f8 INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2113.f8inversion.vcf"
2025-09-15 20:24:25.762 wdl.w:ptcp.w:call-paraphase-16.t:call-call_f8 INFO output :: name: "json", value: "m84036_250809_035451_s4.bc2113.f8inversion.json"
2025-09-15 20:24:25.770 wdl.w:ptcp.w:call-sawfish-31.t:call-run_sawfish INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2128_sawfish/m84036_250809_035451_s4.bc2128.sv.vcf.gz"
2025-09-15 20:24:25.773 wdl.w:ptcp.w:call-sawfish-31.t:call-run_sawfish INFO output :: name: "vcf_tbi", value: "m84036_250809_035451_s4.bc2128_sawfish/m84036_250809_035451_s4.bc2128.sv.vcf.gz.tbi"
2025-09-15 20:24:25.774 wdl.w:ptcp.w:call-sawfish-31.t:call-run_sawfish INFO output :: name: "minimap2_bam", value: "m84036_250809_035451_s4.bc2128.minimap2.bam"
2025-09-15 20:24:25.776 wdl.w:ptcp.w:call-sawfish-31.t:call-run_sawfish INFO output :: name: "minimap2_bam_bai", value: "m84036_250809_035451_s4.bc2128.minimap2.bam.bai"
2025-09-15 20:24:25.814 wdl.w:ptcp.w:call-trgt-08.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO srun: job 51797636 queued and waiting for resources
2025-09-15 20:24:25.815 wdl.w:ptcp.w:call-trgt-08.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO srun: job 51797636 has been allocated resources
2025-09-15 20:24:25.815 wdl.w:ptcp.w:call-trgt-08.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:25.837 wdl.w:ptcp.w:call-paraphase-16.t:call-call_f8 NOTICE done
2025-09-15 20:24:25.842 wdl.w:ptcp.w:call-paraphase-16 NOTICE finish :: job: "call-call_f8"
2025-09-15 20:24:25.842 wdl.w:ptcp.w:call-paraphase-16 INFO output :: job: "call-call_f8", values: {"json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-16/call-call_f8/out/m84036_250809_035451_s4.bc2113.f8inversion.json", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-16/call-call_f8/out/m84036_250809_035451_s4.bc2113.f8inversion.vcf"}
2025-09-15 20:24:25.842 wdl.w:ptcp.w:call-paraphase-16 INFO visit :: node: "output-f8_json", values: {"f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-16/call-call_f8/out/m84036_250809_035451_s4.bc2113.f8inversion.json"}
2025-09-15 20:24:25.843 wdl.w:ptcp.w:call-paraphase-16 INFO visit :: node: "output-f8_vcf", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-16/call-call_f8/out/m84036_250809_035451_s4.bc2113.f8inversion.vcf"}
2025-09-15 20:24:25.843 wdl.w:ptcp.w:call-paraphase-16 INFO visit :: node: "outputs", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-16/call-call_f8/out/m84036_250809_035451_s4.bc2113.f8inversion.vcf", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-16/call-run_paraphase/out/m84036_250809_035451_s4.bc2113_paraphase/m84036_250809_035451_s4.bc2113.paraphase.json", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-16/call-run_paraphase/out/m84036_250809_035451_s4.bc2113_paraphase/m84036_250809_035451_s4.bc2113.paraphase.bam", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-16/call-run_paraphase/out/m84036_250809_035451_s4.bc2113_paraphase/m84036_250809_035451_s4.bc2113.paraphase.bam.bai", "paraphase_vcfs": [], "havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-16/call-run_paraphase/out/m84036_250809_035451_s4.bc2113.havanno.json", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-16/call-call_f8/out/m84036_250809_035451_s4.bc2113.f8inversion.json"}
2025-09-15 20:24:25.849 wdl.w:ptcp.w:call-trgt-00.t:call-trgt_plot_motifs_waterfall NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-00/call-trgt_plot_motifs_waterfall", thread: 140607120975424
2025-09-15 20:24:25.869 wdl.w:ptcp.w:call-trgt-00.t:call-trgt_plot_motifs_waterfall INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:25.869 wdl.w:ptcp.w:call-trgt-00.t:call-trgt_plot_motifs_waterfall INFO input :: name: "waterfall", value: true
2025-09-15 20:24:25.869 wdl.w:ptcp.w:call-trgt-00.t:call-trgt_plot_motifs_waterfall INFO input :: name: "methylation", value: false
2025-09-15 20:24:25.869 wdl.w:ptcp.w:call-trgt-00.t:call-trgt_plot_motifs_waterfall INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:25.869 wdl.w:ptcp.w:call-trgt-00.t:call-trgt_plot_motifs_waterfall INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:25.869 wdl.w:ptcp.w:call-trgt-00.t:call-trgt_plot_motifs_waterfall INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:25.869 wdl.w:ptcp.w:call-trgt-00.t:call-trgt_plot_motifs_waterfall INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2097.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:25.869 wdl.w:ptcp.w:call-trgt-00.t:call-trgt_plot_motifs_waterfall INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2097.trgt.sorted.spanning.bam"
2025-09-15 20:24:25.870 wdl.w:ptcp.w:call-trgt-00.t:call-trgt_plot_motifs_waterfall INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2097.trgt.vcf"
2025-09-15 20:24:25.870 wdl.w:ptcp.w:call-trgt-00.t:call-trgt_plot_motifs_waterfall INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2097"
2025-09-15 20:24:25.870 wdl.w:ptcp.w:call-trgt-00.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:25.870 wdl.w:ptcp.w:call-trgt-00.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "plot_type", value: "waterfall"
2025-09-15 20:24:25.870 wdl.w:ptcp.w:call-trgt-00.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "show", value: "motifs"
2025-09-15 20:24:25.870 wdl.w:ptcp.w:call-trgt-00.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "threads", value: 1
2025-09-15 20:24:25.870 wdl.w:ptcp.w:call-trgt-00.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:25.871 wdl.w:ptcp.w:call-trgt-00.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2097.motifs_waterfall"
2025-09-15 20:24:25.871 wdl.w:ptcp.w:call-trgt-00.t:call-trgt_plot_motifs_waterfall INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:25.871 wdl.w:ptcp.w:call-trgt-00.t:call-trgt_plot_motifs_waterfall WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:25.871 wdl.w:ptcp.w:call-trgt-00.t:call-trgt_plot_motifs_waterfall INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:25.871 wdl.w:ptcp.w:call-trgt-00.t:call-trgt_plot_motifs_waterfall INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:25.882 wdl.w:ptcp.w:call-sawfish-34.t:call-run_sawfish.stderr VERBOSE [M::mm_idx_gen::50.889*1.67] collected minimizers
2025-09-15 20:24:25.883 wdl.w:ptcp.w:call-sawfish-34.t:call-run_sawfish.stderr VERBOSE [M::mm_idx_gen::60.899*1.88] sorted minimizers
2025-09-15 20:24:25.883 wdl.w:ptcp.w:call-sawfish-34.t:call-run_sawfish.stderr VERBOSE [M::main::60.899*1.88] loaded/built the index for 195 target sequence(s)
2025-09-15 20:24:25.883 wdl.w:ptcp.w:call-sawfish-34.t:call-run_sawfish.stderr VERBOSE [M::mm_mapopt_update::66.465*1.80] mid_occ = 136
2025-09-15 20:24:25.883 wdl.w:ptcp.w:call-sawfish-34.t:call-run_sawfish.stderr VERBOSE [M::mm_idx_stat] kmer size: 19; skip: 19; is_hpc: 0; #seq: 195
2025-09-15 20:24:25.883 wdl.w:ptcp.w:call-sawfish-34.t:call-run_sawfish.stderr VERBOSE [M::mm_idx_stat::70.912*1.75] distinct minimizers: 214664461 (92.23% are singletons); average occurrences: 1.372; average spacing: 10.529; total length: 3099922541
2025-09-15 20:24:25.883 wdl.w:ptcp.w:call-sawfish-34.t:call-run_sawfish.stderr VERBOSE [M::bam2fq_mainloop] discarded 0 singletons
2025-09-15 20:24:25.884 wdl.w:ptcp.w:call-sawfish-34.t:call-run_sawfish.stderr VERBOSE [M::bam2fq_mainloop] processed 244 reads
2025-09-15 20:24:25.884 wdl.w:ptcp.w:call-sawfish-34.t:call-run_sawfish.stderr VERBOSE [M::worker_pipeline::71.443*1.76] mapped 244 sequences
2025-09-15 20:24:25.884 wdl.w:ptcp.w:call-sawfish-34.t:call-run_sawfish.stderr VERBOSE [M::main] Version: 2.26-r1175
2025-09-15 20:24:25.884 wdl.w:ptcp.w:call-sawfish-34.t:call-run_sawfish.stderr VERBOSE [M::main] CMD: /opt/pacbio/smrttools/install/smrtlink-release_25.1.0.257715/bundles/smrttools/install/smrttools-release_25.1.0.257715/private/thirdparty/minimap2/minimap2_2.26-pacbio2/binwrap/../../../../../private/thirdparty/minimap2/minimap2_2.26-pacbio2/bin/minimap2 -a -y -x map-hifi -Y -E 1,0 /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa -
2025-09-15 20:24:25.884 wdl.w:ptcp.w:call-sawfish-34.t:call-run_sawfish.stderr VERBOSE [M::main] Real time: 71.773 sec; CPU: 125.912 sec; Peak RSS: 11.886 GB
2025-09-15 20:24:25.884 wdl.w:ptcp.w:call-sawfish-34.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:14][sawfish][INFO] Starting sawfish 2.0.3
2025-09-15 20:24:25.884 wdl.w:ptcp.w:call-sawfish-34.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:14][sawfish][INFO] cmdline: sawfish discover --disable-cnv --threads 16 --ref /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa --bam m84036_250809_035451_s4.bc2131.minimap2.bam --output-dir m84036_250809_035451_s4.bc2131_sawfish_discover
2025-09-15 20:24:25.884 wdl.w:ptcp.w:call-sawfish-34.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:14][sawfish][INFO] Running on 16 threads
2025-09-15 20:24:25.884 wdl.w:ptcp.w:call-sawfish-34.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:14][sawfish][INFO] Writing discover settings to file: 'm84036_250809_035451_s4.bc2131_sawfish_discover/discover.settings.json'
2025-09-15 20:24:25.884 wdl.w:ptcp.w:call-sawfish-34.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:14][sawfish][INFO] Reading reference genome from file '/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa'
2025-09-15 20:24:25.884 wdl.w:ptcp.w:call-sawfish-34.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:20][sawfish][INFO] Processing alignment file '/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2131.minimap2.bam'
2025-09-15 20:24:25.884 wdl.w:ptcp.w:call-sawfish-34.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:20][sawfish][INFO] Finished processing all alignments
2025-09-15 20:24:25.884 wdl.w:ptcp.w:call-sawfish-34.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:20][sawfish][INFO] Writing depth bins to binary file: 'm84036_250809_035451_s4.bc2131_sawfish_discover/depth.mpack'
2025-09-15 20:24:25.884 wdl.w:ptcp.w:call-sawfish-34.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:20][sawfish][INFO] Writing max sv depth genome regions to bed file: 'm84036_250809_035451_s4.bc2131_sawfish_discover/max.depth.bed'
2025-09-15 20:24:25.884 wdl.w:ptcp.w:call-sawfish-34.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:20][sawfish][INFO] Completing breakpoint observation clustering
2025-09-15 20:24:25.884 wdl.w:ptcp.w:call-sawfish-34.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:20][sawfish][INFO] Finished breakpoint observation clustering
2025-09-15 20:24:25.884 wdl.w:ptcp.w:call-sawfish-34.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:20][sawfish][INFO] Consolidating adjacent indel candidates
2025-09-15 20:24:25.885 wdl.w:ptcp.w:call-sawfish-34.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:20][sawfish][INFO] Finding large insertion candidates
2025-09-15 20:24:25.885 wdl.w:ptcp.w:call-sawfish-34.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:20][sawfish][INFO] Writing breakpoint_cluster debug bed file: 'm84036_250809_035451_s4.bc2131_sawfish_discover/debug.breakpoint_clusters.bed'
2025-09-15 20:24:25.885 wdl.w:ptcp.w:call-sawfish-34.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:20][sawfish][INFO] Refining SV Candidates
2025-09-15 20:24:25.885 wdl.w:ptcp.w:call-sawfish-34.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:20][sawfish][INFO] Writing debug assembly region bed file: 'm84036_250809_035451_s4.bc2131_sawfish_discover/assembly.regions.bed'
2025-09-15 20:24:25.885 wdl.w:ptcp.w:call-sawfish-34.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:20][sawfish][INFO] Starting refinement of breakpoint evidence clusters
2025-09-15 20:24:25.885 wdl.w:ptcp.w:call-sawfish-34.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:21][sawfish][INFO] Finished refining all breakpoint evidence clusters
2025-09-15 20:24:25.885 wdl.w:ptcp.w:call-sawfish-34.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:21][sawfish][INFO] Writing all contig alignments to bam file: 'm84036_250809_035451_s4.bc2131_sawfish_discover/contig.alignment.bam'
2025-09-15 20:24:25.885 wdl.w:ptcp.w:call-sawfish-34.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:21][sawfish][INFO] Writing candidate structural variants to file: 'm84036_250809_035451_s4.bc2131_sawfish_discover/candidate.sv.bcf'
2025-09-15 20:24:25.885 wdl.w:ptcp.w:call-sawfish-34.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:21][sawfish][INFO] Writing run statistics to file: 'm84036_250809_035451_s4.bc2131_sawfish_discover/run.stats.json'
2025-09-15 20:24:25.885 wdl.w:ptcp.w:call-sawfish-34.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:21][sawfish][INFO] sawfish completed. Total Runtime: 00:00:07.545
2025-09-15 20:24:25.909 wdl.w:ptcp.w:call-paraphase-35.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for hba for sample m84036_250809_035451_s4.bc2132 at 2025-09-15 20:23:57.211663...
2025-09-15 20:24:25.910 wdl.w:ptcp.w:call-paraphase-35.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for hba for sample m84036_250809_035451_s4.bc2132 at 2025-09-15 20:23:57.607699...
2025-09-15 20:24:25.910 wdl.w:ptcp.w:call-paraphase-35.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for cyp21 for sample m84036_250809_035451_s4.bc2132 at 2025-09-15 20:24:05.256442...
2025-09-15 20:24:25.910 wdl.w:ptcp.w:call-paraphase-35.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for cyp21 for sample m84036_250809_035451_s4.bc2132 at 2025-09-15 20:24:06.409289...
2025-09-15 20:24:25.910 wdl.w:ptcp.w:call-paraphase-35.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for gba for sample m84036_250809_035451_s4.bc2132 at 2025-09-15 20:24:20.266165...
2025-09-15 20:24:25.910 wdl.w:ptcp.w:call-paraphase-35.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for gba for sample m84036_250809_035451_s4.bc2132 at 2025-09-15 20:24:20.921039...
2025-09-15 20:24:25.911 wdl.w:ptcp.w:call-paraphase-35.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for hbb for sample m84036_250809_035451_s4.bc2132 at 2025-09-15 20:24:23.418356...
2025-09-15 20:24:25.911 wdl.w:ptcp.w:call-paraphase-35.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for hbb for sample m84036_250809_035451_s4.bc2132 at 2025-09-15 20:24:23.418593...
2025-09-15 20:24:25.918 wdl.w:ptcp.w:call-trgt-25.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:25 [ERROR] - No reads found for TRID=PRTS_ARX
2025-09-15 20:24:25.920 wdl.w:ptcp.w:call-paraphase-16 NOTICE done
2025-09-15 20:24:25.928 wdl.w:ptcp NOTICE finish :: job: "call-paraphase-16"
2025-09-15 20:24:25.928 wdl.w:ptcp INFO output :: job: "call-paraphase-16", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-16/out/m84036_250809_035451_s4.bc2113.f8inversion.vcf", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-16/out/m84036_250809_035451_s4.bc2113_paraphase/m84036_250809_035451_s4.bc2113.paraphase.json", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-16/out/m84036_250809_035451_s4.bc2113_paraphase/m84036_250809_035451_s4.bc2113.paraphase.bam", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-16/out/m84036_250809_035451_s4.bc2113_paraphase/m84036_250809_035451_s4.bc2113.paraphase.bam.bai", "paraphase_vcfs": [], "havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-16/out/m84036_250809_035451_s4.bc2113.havanno.json", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-16/out/m84036_250809_035451_s4.bc2113.f8inversion.json"}
2025-09-15 20:24:25.938 wdl.w:ptcp.w:call-trgt-54 NOTICE workflow start :: name: "trgt", source: "./trgt.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-54"
2025-09-15 20:24:25.938 wdl.w:ptcp.w:call-sawfish-31.t:call-run_sawfish NOTICE done
2025-09-15 20:24:25.953 wdl.w:ptcp.w:call-trgt-54 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:24:25.953 wdl.w:ptcp.w:call-trgt-54 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-54/out/m84036_250809_035451_s4.bc2151.mapped.bam"}
2025-09-15 20:24:25.953 wdl.w:ptcp.w:call-trgt-54 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-54/out/m84036_250809_035451_s4.bc2151.mapped.bam.bai"}
2025-09-15 20:24:25.953 wdl.w:ptcp.w:call-trgt-54 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:24:25.953 wdl.w:ptcp.w:call-trgt-54 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:24:25.953 wdl.w:ptcp.w:call-trgt-54 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2151"}
2025-09-15 20:24:25.953 wdl.w:ptcp.w:call-trgt-54 INFO visit :: node: "decl-sex", values: {"sex": "F"}
2025-09-15 20:24:25.954 wdl.w:ptcp.w:call-trgt-54 INFO visit :: node: "decl-trgt_bed", values: {"trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"}
2025-09-15 20:24:25.954 wdl.w:ptcp.w:call-trgt-54 NOTICE ready :: job: "call-get_reads_overlapping_repeats", callee: "get_reads_overlapping_repeats"
2025-09-15 20:24:25.954 wdl.w:ptcp.w:call-trgt-54 INFO input :: job: "call-get_reads_overlapping_repeats", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-54/out/m84036_250809_035451_s4.bc2151.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-54/out/m84036_250809_035451_s4.bc2151.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2151"}
2025-09-15 20:24:25.955 wdl.w:ptcp.w:call-trgt-54 NOTICE ready :: job: "call-trgt_genotype", callee: "trgt_genotype"
2025-09-15 20:24:25.955 wdl.w:ptcp.w:call-trgt-54 INFO input :: job: "call-trgt_genotype", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-54/out/m84036_250809_035451_s4.bc2151.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-54/out/m84036_250809_035451_s4.bc2151.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2151"}
2025-09-15 20:24:25.958 wdl.w:ptcp.w:call-trgt-09.t:call-trgt_plot_motifs_allele INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2106.motifs_allele.trgt_plots.zip"
2025-09-15 20:24:25.960 wdl.w:ptcp.w:call-sawfish-31 NOTICE finish :: job: "call-run_sawfish"
2025-09-15 20:24:25.960 wdl.w:ptcp.w:call-sawfish-31 INFO output :: job: "call-run_sawfish", values: {"minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-31/call-run_sawfish/out/m84036_250809_035451_s4.bc2128.minimap2.bam.bai", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-31/call-run_sawfish/out/m84036_250809_035451_s4.bc2128.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-31/call-run_sawfish/out/m84036_250809_035451_s4.bc2128_sawfish/m84036_250809_035451_s4.bc2128.sv.vcf.gz.tbi", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-31/call-run_sawfish/out/m84036_250809_035451_s4.bc2128_sawfish/m84036_250809_035451_s4.bc2128.sv.vcf.gz"}
2025-09-15 20:24:25.961 wdl.w:ptcp.w:call-sawfish-31 INFO visit :: node: "output-minimap2_bam", values: {"minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-31/call-run_sawfish/out/m84036_250809_035451_s4.bc2128.minimap2.bam"}
2025-09-15 20:24:25.961 wdl.w:ptcp.w:call-sawfish-31 INFO visit :: node: "output-minimap2_bam_bai", values: {"minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-31/call-run_sawfish/out/m84036_250809_035451_s4.bc2128.minimap2.bam.bai"}
2025-09-15 20:24:25.961 wdl.w:ptcp.w:call-sawfish-31 INFO visit :: node: "output-vcf", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-31/call-run_sawfish/out/m84036_250809_035451_s4.bc2128_sawfish/m84036_250809_035451_s4.bc2128.sv.vcf.gz"}
2025-09-15 20:24:25.961 wdl.w:ptcp.w:call-sawfish-31 INFO visit :: node: "output-vcf_tbi", values: {"vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-31/call-run_sawfish/out/m84036_250809_035451_s4.bc2128_sawfish/m84036_250809_035451_s4.bc2128.sv.vcf.gz.tbi"}
2025-09-15 20:24:25.961 wdl.w:ptcp.w:call-sawfish-31 INFO visit :: node: "outputs", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-31/call-run_sawfish/out/m84036_250809_035451_s4.bc2128_sawfish/m84036_250809_035451_s4.bc2128.sv.vcf.gz", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-31/call-run_sawfish/out/m84036_250809_035451_s4.bc2128.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-31/call-run_sawfish/out/m84036_250809_035451_s4.bc2128_sawfish/m84036_250809_035451_s4.bc2128.sv.vcf.gz.tbi", "minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-31/call-run_sawfish/out/m84036_250809_035451_s4.bc2128.minimap2.bam.bai"}
2025-09-15 20:24:25.965 wdl.w:ptcp.w:call-trgt-00.t:call-trgt_plot_motifs_waterfall INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-00/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_iif9xygb"
2025-09-15 20:24:25.966 wdl.w:ptcp.w:call-trgt-00.t:call-trgt_plot_motifs_waterfall INFO Slurm invocation: srun --job-name call-trgt_plot_motifs_waterfall --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-00/call-trgt_plot_motifs_waterfall/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-00/call-trgt_plot_motifs_waterfall/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-00/call-trgt_plot_motifs_waterfall/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-00/call-trgt_plot_motifs_waterfall/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-00/call-trgt_genotype/out/m84036_250809_035451_s4.bc2097.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2097.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-00/call-trgt_genotype/out/m84036_250809_035451_s4.bc2097.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2097.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-00/call-trgt_genotype/out/m84036_250809_035451_s4.bc2097.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2097.trgt.sorted.spanning.bam:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-00/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_iif9xygb/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-00/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_iif9xygb/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:25.970 wdl.w:ptcp.w:call-trgt-01.t:call-trgt_plot_meth_allele NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-01/call-trgt_plot_meth_allele", thread: 140613580211776
2025-09-15 20:24:25.993 wdl.w:ptcp.w:call-trgt-01.t:call-trgt_plot_meth_allele INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:25.993 wdl.w:ptcp.w:call-trgt-01.t:call-trgt_plot_meth_allele INFO input :: name: "waterfall", value: false
2025-09-15 20:24:25.993 wdl.w:ptcp.w:call-trgt-01.t:call-trgt_plot_meth_allele INFO input :: name: "methylation", value: true
2025-09-15 20:24:25.993 wdl.w:ptcp.w:call-trgt-01.t:call-trgt_plot_meth_allele INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:25.993 wdl.w:ptcp.w:call-trgt-01.t:call-trgt_plot_meth_allele INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:25.993 wdl.w:ptcp.w:call-trgt-01.t:call-trgt_plot_meth_allele INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:25.993 wdl.w:ptcp.w:call-trgt-01.t:call-trgt_plot_meth_allele INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2098.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:25.993 wdl.w:ptcp.w:call-trgt-01.t:call-trgt_plot_meth_allele INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2098.trgt.sorted.spanning.bam"
2025-09-15 20:24:25.993 wdl.w:ptcp.w:call-trgt-01.t:call-trgt_plot_meth_allele INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2098.trgt.vcf"
2025-09-15 20:24:25.993 wdl.w:ptcp.w:call-trgt-01.t:call-trgt_plot_meth_allele INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2098"
2025-09-15 20:24:25.994 wdl.w:ptcp.w:call-trgt-01.t:call-trgt_plot_meth_allele INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:25.994 wdl.w:ptcp.w:call-trgt-01.t:call-trgt_plot_meth_allele INFO eval :: name: "plot_type", value: "allele"
2025-09-15 20:24:25.994 wdl.w:ptcp.w:call-trgt-01.t:call-trgt_plot_meth_allele INFO eval :: name: "show", value: "meth"
2025-09-15 20:24:25.994 wdl.w:ptcp.w:call-trgt-01.t:call-trgt_plot_meth_allele INFO eval :: name: "threads", value: 1
2025-09-15 20:24:25.994 wdl.w:ptcp.w:call-trgt-01.t:call-trgt_plot_meth_allele INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:25.994 wdl.w:ptcp.w:call-trgt-01.t:call-trgt_plot_meth_allele INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2098.meth_allele"
2025-09-15 20:24:25.995 wdl.w:ptcp.w:call-trgt-01.t:call-trgt_plot_meth_allele INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:25.995 wdl.w:ptcp.w:call-trgt-01.t:call-trgt_plot_meth_allele WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:25.995 wdl.w:ptcp.w:call-trgt-01.t:call-trgt_plot_meth_allele INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:25.995 wdl.w:ptcp.w:call-trgt-01.t:call-trgt_plot_meth_allele INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:26.009 wdl.w:ptcp.w:call-trgt-00.t:call-trgt_plot_motifs_waterfall NOTICE slurm_singularity run :: pid: 1201787, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-00/call-trgt_plot_motifs_waterfall/slurm_singularity.log.txt"
2025-09-15 20:24:26.020 wdl.w:ptcp.w:call-sawfish-31 NOTICE done
2025-09-15 20:24:26.027 wdl.w:ptcp NOTICE finish :: job: "call-sawfish-31"
2025-09-15 20:24:26.027 wdl.w:ptcp INFO output :: job: "call-sawfish-31", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-31/out/m84036_250809_035451_s4.bc2128_sawfish/m84036_250809_035451_s4.bc2128.sv.vcf.gz", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-31/out/m84036_250809_035451_s4.bc2128.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-31/out/m84036_250809_035451_s4.bc2128_sawfish/m84036_250809_035451_s4.bc2128.sv.vcf.gz.tbi", "minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-31/out/m84036_250809_035451_s4.bc2128.minimap2.bam.bai"}
2025-09-15 20:24:26.036 wdl.w:ptcp.w:call-paraphase-59 NOTICE workflow start :: name: "paraphase", source: "./paraphase.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-59"
2025-09-15 20:24:26.046 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:23 [ERROR] - No reads found for TRID=SCA2_ATXN2
2025-09-15 20:24:26.046 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:23 [ERROR] - No reads found for TRID=OPDM4_RILPL1
2025-09-15 20:24:26.046 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:23 [ERROR] - No reads found for TRID=SCA3_ATXN3
2025-09-15 20:24:26.046 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:23 [ERROR] - No reads found for TRID=SCA27B_FGF14
2025-09-15 20:24:26.046 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:23 [ERROR] - No reads found for TRID=HDL2_JPH3
2025-09-15 20:24:26.046 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:23 [ERROR] - No reads found for TRID=SCA4_ZFHX3
2025-09-15 20:24:26.046 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:23 [ERROR] - No reads found for TRID=SCA6_CACNA1A
2025-09-15 20:24:26.046 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:23 [ERROR] - No reads found for TRID=OPDM2_GIPC1
2025-09-15 20:24:26.046 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:24 [ERROR] - No reads found for TRID=DM1_DMPK
2025-09-15 20:24:26.047 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:24 [ERROR] - No reads found for TRID=SD5_HOXD13
2025-09-15 20:24:26.047 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:24 [ERROR] - No reads found for TRID=OPMD_PABPN1
2025-09-15 20:24:26.047 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:24 [ERROR] - No reads found for TRID=EPM1_CSTB
2025-09-15 20:24:26.047 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:24 [ERROR] - No reads found for TRID=CJD_PRNP
2025-09-15 20:24:26.047 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:24 [ERROR] - No reads found for TRID=SCA7_ATXN7
2025-09-15 20:24:26.047 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:24 [ERROR] - No reads found for TRID=FRA2A_AFF3
2025-09-15 20:24:26.047 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:24 [ERROR] - No reads found for TRID=SCA36_NOP56
2025-09-15 20:24:26.047 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:25 [ERROR] - No reads found for TRID=CCHS_PHOX2B
2025-09-15 20:24:26.047 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:25 [ERROR] - No reads found for TRID=SCA1_ATXN1
2025-09-15 20:24:26.047 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:25 [ERROR] - No reads found for TRID=SCA12_PPP2R2B
2025-09-15 20:24:26.047 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:25 [ERROR] - No reads found for TRID=FAME1_SAMD12
2025-09-15 20:24:26.047 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:25 [ERROR] - No reads found for TRID=OPDM1_LRP12
2025-09-15 20:24:26.054 wdl.w:ptcp.w:call-paraphase-59 INFO visit :: node: "decl-annotation_vcf", values: {"annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf"}
2025-09-15 20:24:26.054 wdl.w:ptcp.w:call-paraphase-59 INFO visit :: node: "decl-config_file", values: {"config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml"}
2025-09-15 20:24:26.054 wdl.w:ptcp.w:call-paraphase-59 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:24:26.054 wdl.w:ptcp.w:call-paraphase-59 INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:24:26.055 wdl.w:ptcp.w:call-paraphase-59 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-59/out/m84036_250809_035451_s4.bc2156.mapped.bam"}
2025-09-15 20:24:26.055 wdl.w:ptcp.w:call-paraphase-59 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-59/out/m84036_250809_035451_s4.bc2156.mapped.bam.bai"}
2025-09-15 20:24:26.055 wdl.w:ptcp.w:call-paraphase-59 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:24:26.055 wdl.w:ptcp.w:call-paraphase-59 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:24:26.055 wdl.w:ptcp.w:call-paraphase-59 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2156"}
2025-09-15 20:24:26.055 wdl.w:ptcp.w:call-paraphase-59 INFO visit :: node: "decl-sex", values: {"sex": "F"}
2025-09-15 20:24:26.055 wdl.w:ptcp.w:call-paraphase-59 NOTICE ready :: job: "call-run_paraphase", callee: "run_paraphase"
2025-09-15 20:24:26.056 wdl.w:ptcp.w:call-paraphase-59 INFO input :: job: "call-run_paraphase", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf", "genome_version": "38", "config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-59/out/m84036_250809_035451_s4.bc2156.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-59/out/m84036_250809_035451_s4.bc2156.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2156"}
2025-09-15 20:24:26.058 wdl.w:ptcp.w:call-trgt-08.t:call-trgt_plot_motifs_allele.slurm_singularity INFO srun: job 51797637 queued and waiting for resources
2025-09-15 20:24:26.058 wdl.w:ptcp.w:call-trgt-08.t:call-trgt_plot_motifs_allele.slurm_singularity INFO srun: job 51797637 has been allocated resources
2025-09-15 20:24:26.058 wdl.w:ptcp.w:call-trgt-08.t:call-trgt_plot_motifs_allele.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:26.067 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:23 [ERROR] - No reads found for TRID=HDL2_JPH3
2025-09-15 20:24:26.067 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:23 [ERROR] - No reads found for TRID=SCA4_ZFHX3
2025-09-15 20:24:26.067 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:23 [ERROR] - No reads found for TRID=SCA6_CACNA1A
2025-09-15 20:24:26.067 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:23 [ERROR] - No reads found for TRID=OPDM2_GIPC1
2025-09-15 20:24:26.068 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:23 [ERROR] - No reads found for TRID=DM1_DMPK
2025-09-15 20:24:26.068 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:23 [ERROR] - No reads found for TRID=SD5_HOXD13
2025-09-15 20:24:26.068 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:23 [ERROR] - No reads found for TRID=OPMD_PABPN1
2025-09-15 20:24:26.068 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:23 [ERROR] - No reads found for TRID=EPM1_CSTB
2025-09-15 20:24:26.068 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:23 [ERROR] - No reads found for TRID=CJD_PRNP
2025-09-15 20:24:26.068 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:23 [ERROR] - No reads found for TRID=SCA7_ATXN7
2025-09-15 20:24:26.068 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:23 [ERROR] - No reads found for TRID=FRA2A_AFF3
2025-09-15 20:24:26.068 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:23 [ERROR] - No reads found for TRID=SCA36_NOP56
2025-09-15 20:24:26.068 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:23 [ERROR] - No reads found for TRID=CCHS_PHOX2B
2025-09-15 20:24:26.068 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:23 [ERROR] - No reads found for TRID=SCA1_ATXN1
2025-09-15 20:24:26.068 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:23 [ERROR] - No reads found for TRID=SCA12_PPP2R2B
2025-09-15 20:24:26.068 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:23 [ERROR] - No reads found for TRID=FAME1_SAMD12
2025-09-15 20:24:26.068 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:23 [ERROR] - No reads found for TRID=OPDM1_LRP12
2025-09-15 20:24:26.068 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:24 [ERROR] - No reads found for TRID=SBMA_AR
2025-09-15 20:24:26.080 wdl.w:ptcp.w:call-trgt-01.t:call-trgt_plot_meth_allele INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-01/call-trgt_plot_meth_allele/_singularity_tmpdir_11rte8xj"
2025-09-15 20:24:26.081 wdl.w:ptcp.w:call-trgt-01.t:call-trgt_plot_meth_allele INFO Slurm invocation: srun --job-name call-trgt_plot_meth_allele --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-01/call-trgt_plot_meth_allele/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-01/call-trgt_plot_meth_allele/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-01/call-trgt_plot_meth_allele/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-01/call-trgt_plot_meth_allele/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-01/call-trgt_genotype/out/m84036_250809_035451_s4.bc2098.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2098.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-01/call-trgt_genotype/out/m84036_250809_035451_s4.bc2098.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2098.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-01/call-trgt_genotype/out/m84036_250809_035451_s4.bc2098.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2098.trgt.sorted.spanning.bam.bai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-01/call-trgt_plot_meth_allele/_singularity_tmpdir_11rte8xj/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-01/call-trgt_plot_meth_allele/_singularity_tmpdir_11rte8xj/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:26.101 wdl.w:ptcp.w:call-trgt-09.t:call-trgt_plot_motifs_allele NOTICE done
2025-09-15 20:24:26.102 wdl.w:ptcp.w:call-trgt-01.t:call-trgt_plot_meth_allele NOTICE slurm_singularity run :: pid: 1201790, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-01/call-trgt_plot_meth_allele/slurm_singularity.log.txt"
2025-09-15 20:24:26.105 wdl.w:ptcp.w:call-trgt-09 NOTICE finish :: job: "call-trgt_plot_motifs_allele"
2025-09-15 20:24:26.105 wdl.w:ptcp.w:call-trgt-09 INFO output :: job: "call-trgt_plot_motifs_allele", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-09/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2106.motifs_allele.trgt_plots.zip"}
2025-09-15 20:24:26.106 wdl.w:ptcp.w:call-trgt-09 INFO visit :: node: "output-images_motifs_allele", values: {"images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-09/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2106.motifs_allele.trgt_plots.zip"}
2025-09-15 20:24:26.111 wdl.w:ptcp.w:call-trgt-01.t:call-trgt_plot_meth_waterfall NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-01/call-trgt_plot_meth_waterfall", thread: 140608186324544
2025-09-15 20:24:26.126 wdl.w:ptcp.w:call-paraphase-12.t:call-call_f8 INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2109.f8inversion.vcf"
2025-09-15 20:24:26.128 wdl.w:ptcp.w:call-trgt-01.t:call-trgt_plot_meth_waterfall INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:26.128 wdl.w:ptcp.w:call-trgt-01.t:call-trgt_plot_meth_waterfall INFO input :: name: "waterfall", value: true
2025-09-15 20:24:26.128 wdl.w:ptcp.w:call-trgt-01.t:call-trgt_plot_meth_waterfall INFO input :: name: "methylation", value: true
2025-09-15 20:24:26.128 wdl.w:ptcp.w:call-trgt-01.t:call-trgt_plot_meth_waterfall INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:26.128 wdl.w:ptcp.w:call-trgt-01.t:call-trgt_plot_meth_waterfall INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:26.128 wdl.w:ptcp.w:call-trgt-01.t:call-trgt_plot_meth_waterfall INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:26.128 wdl.w:ptcp.w:call-trgt-01.t:call-trgt_plot_meth_waterfall INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2098.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:26.128 wdl.w:ptcp.w:call-trgt-01.t:call-trgt_plot_meth_waterfall INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2098.trgt.sorted.spanning.bam"
2025-09-15 20:24:26.128 wdl.w:ptcp.w:call-trgt-01.t:call-trgt_plot_meth_waterfall INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2098.trgt.vcf"
2025-09-15 20:24:26.128 wdl.w:ptcp.w:call-trgt-01.t:call-trgt_plot_meth_waterfall INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2098"
2025-09-15 20:24:26.129 wdl.w:ptcp.w:call-trgt-01.t:call-trgt_plot_meth_waterfall INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:26.129 wdl.w:ptcp.w:call-trgt-01.t:call-trgt_plot_meth_waterfall INFO eval :: name: "plot_type", value: "waterfall"
2025-09-15 20:24:26.129 wdl.w:ptcp.w:call-trgt-01.t:call-trgt_plot_meth_waterfall INFO eval :: name: "show", value: "meth"
2025-09-15 20:24:26.129 wdl.w:ptcp.w:call-trgt-01.t:call-trgt_plot_meth_waterfall INFO eval :: name: "threads", value: 1
2025-09-15 20:24:26.129 wdl.w:ptcp.w:call-trgt-01.t:call-trgt_plot_meth_waterfall INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:26.129 wdl.w:ptcp.w:call-trgt-01.t:call-trgt_plot_meth_waterfall INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2098.meth_waterfall"
2025-09-15 20:24:26.130 wdl.w:ptcp.w:call-paraphase-12.t:call-call_f8 INFO output :: name: "json", value: "m84036_250809_035451_s4.bc2109.f8inversion.json"
2025-09-15 20:24:26.130 wdl.w:ptcp.w:call-trgt-01.t:call-trgt_plot_meth_waterfall INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:26.130 wdl.w:ptcp.w:call-trgt-01.t:call-trgt_plot_meth_waterfall WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:26.130 wdl.w:ptcp.w:call-trgt-01.t:call-trgt_plot_meth_waterfall INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:26.131 wdl.w:ptcp.w:call-trgt-01.t:call-trgt_plot_meth_waterfall INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:26.173 wdl.w:ptcp.w:call-trgt-08.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO srun: job 51797638 queued and waiting for resources
2025-09-15 20:24:26.173 wdl.w:ptcp.w:call-trgt-08.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO srun: job 51797638 has been allocated resources
2025-09-15 20:24:26.173 wdl.w:ptcp.w:call-trgt-08.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:26.195 wdl.w:ptcp.w:call-paraphase-12.t:call-call_f8 NOTICE done
2025-09-15 20:24:26.198 wdl.w:ptcp.w:call-paraphase-25.t:call-call_f8.slurm_singularity INFO srun: job 51797640 queued and waiting for resources
2025-09-15 20:24:26.198 wdl.w:ptcp.w:call-paraphase-25.t:call-call_f8.slurm_singularity INFO srun: job 51797640 has been allocated resources
2025-09-15 20:24:26.198 wdl.w:ptcp.w:call-paraphase-25.t:call-call_f8.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:26.200 wdl.w:ptcp.w:call-paraphase-32.t:call-call_f8.slurm_singularity INFO srun: job 51797639 queued and waiting for resources
2025-09-15 20:24:26.200 wdl.w:ptcp.w:call-paraphase-32.t:call-call_f8.slurm_singularity INFO srun: job 51797639 has been allocated resources
2025-09-15 20:24:26.200 wdl.w:ptcp.w:call-paraphase-32.t:call-call_f8.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:26.202 wdl.w:ptcp.w:call-paraphase-12 NOTICE finish :: job: "call-call_f8"
2025-09-15 20:24:26.202 wdl.w:ptcp.w:call-paraphase-12 INFO output :: job: "call-call_f8", values: {"json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-12/call-call_f8/out/m84036_250809_035451_s4.bc2109.f8inversion.json", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-12/call-call_f8/out/m84036_250809_035451_s4.bc2109.f8inversion.vcf"}
2025-09-15 20:24:26.203 wdl.w:ptcp.w:call-paraphase-12 INFO visit :: node: "output-f8_json", values: {"f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-12/call-call_f8/out/m84036_250809_035451_s4.bc2109.f8inversion.json"}
2025-09-15 20:24:26.203 wdl.w:ptcp.w:call-paraphase-12 INFO visit :: node: "output-f8_vcf", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-12/call-call_f8/out/m84036_250809_035451_s4.bc2109.f8inversion.vcf"}
2025-09-15 20:24:26.203 wdl.w:ptcp.w:call-paraphase-12 INFO visit :: node: "outputs", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-12/call-call_f8/out/m84036_250809_035451_s4.bc2109.f8inversion.vcf", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-12/call-run_paraphase/out/m84036_250809_035451_s4.bc2109_paraphase/m84036_250809_035451_s4.bc2109.paraphase.json", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-12/call-run_paraphase/out/m84036_250809_035451_s4.bc2109_paraphase/m84036_250809_035451_s4.bc2109.paraphase.bam", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-12/call-run_paraphase/out/m84036_250809_035451_s4.bc2109_paraphase/m84036_250809_035451_s4.bc2109.paraphase.bam.bai", "paraphase_vcfs": [], "havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-12/call-run_paraphase/out/m84036_250809_035451_s4.bc2109.havanno.json", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-12/call-call_f8/out/m84036_250809_035451_s4.bc2109.f8inversion.json"}
2025-09-15 20:24:26.211 wdl.w:ptcp.w:call-trgt-01.t:call-trgt_plot_motifs_allele NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-01/call-trgt_plot_motifs_allele", thread: 140608211502656
2025-09-15 20:24:26.221 wdl.w:ptcp.w:call-trgt-01.t:call-trgt_plot_meth_waterfall INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-01/call-trgt_plot_meth_waterfall/_singularity_tmpdir_ylqsosz3"
2025-09-15 20:24:26.221 wdl.w:ptcp.w:call-trgt-01.t:call-trgt_plot_meth_waterfall INFO Slurm invocation: srun --job-name call-trgt_plot_meth_waterfall --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-01/call-trgt_plot_meth_waterfall/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-01/call-trgt_plot_meth_waterfall/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-01/call-trgt_plot_meth_waterfall/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-01/call-trgt_plot_meth_waterfall/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-01/call-trgt_genotype/out/m84036_250809_035451_s4.bc2098.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2098.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-01/call-trgt_genotype/out/m84036_250809_035451_s4.bc2098.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2098.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-01/call-trgt_genotype/out/m84036_250809_035451_s4.bc2098.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2098.trgt.sorted.spanning.bam.bai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-01/call-trgt_plot_meth_waterfall/_singularity_tmpdir_ylqsosz3/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-01/call-trgt_plot_meth_waterfall/_singularity_tmpdir_ylqsosz3/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:26.225 wdl.w:ptcp.w:call-trgt-24.t:call-trgt_plot_meth_waterfall INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2121.meth_waterfall.trgt_plots.zip"
2025-09-15 20:24:26.229 wdl.w:ptcp.w:call-trgt-01.t:call-trgt_plot_motifs_allele INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:26.229 wdl.w:ptcp.w:call-trgt-01.t:call-trgt_plot_motifs_allele INFO input :: name: "waterfall", value: false
2025-09-15 20:24:26.229 wdl.w:ptcp.w:call-trgt-01.t:call-trgt_plot_motifs_allele INFO input :: name: "methylation", value: false
2025-09-15 20:24:26.229 wdl.w:ptcp.w:call-trgt-01.t:call-trgt_plot_motifs_allele INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:26.230 wdl.w:ptcp.w:call-trgt-01.t:call-trgt_plot_motifs_allele INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:26.230 wdl.w:ptcp.w:call-trgt-01.t:call-trgt_plot_motifs_allele INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:26.230 wdl.w:ptcp.w:call-trgt-01.t:call-trgt_plot_motifs_allele INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2098.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:26.230 wdl.w:ptcp.w:call-trgt-01.t:call-trgt_plot_motifs_allele INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2098.trgt.sorted.spanning.bam"
2025-09-15 20:24:26.230 wdl.w:ptcp.w:call-trgt-01.t:call-trgt_plot_motifs_allele INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2098.trgt.vcf"
2025-09-15 20:24:26.230 wdl.w:ptcp.w:call-trgt-01.t:call-trgt_plot_motifs_allele INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2098"
2025-09-15 20:24:26.230 wdl.w:ptcp.w:call-trgt-01.t:call-trgt_plot_motifs_allele INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:26.230 wdl.w:ptcp.w:call-trgt-01.t:call-trgt_plot_motifs_allele INFO eval :: name: "plot_type", value: "allele"
2025-09-15 20:24:26.231 wdl.w:ptcp.w:call-trgt-01.t:call-trgt_plot_motifs_allele INFO eval :: name: "show", value: "motifs"
2025-09-15 20:24:26.231 wdl.w:ptcp.w:call-trgt-01.t:call-trgt_plot_motifs_allele INFO eval :: name: "threads", value: 1
2025-09-15 20:24:26.231 wdl.w:ptcp.w:call-trgt-01.t:call-trgt_plot_motifs_allele INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:26.231 wdl.w:ptcp.w:call-trgt-01.t:call-trgt_plot_motifs_allele INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2098.motifs_allele"
2025-09-15 20:24:26.232 wdl.w:ptcp.w:call-trgt-01.t:call-trgt_plot_motifs_allele INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:26.232 wdl.w:ptcp.w:call-trgt-01.t:call-trgt_plot_motifs_allele WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:26.232 wdl.w:ptcp.w:call-trgt-01.t:call-trgt_plot_motifs_allele INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:26.232 wdl.w:ptcp.w:call-trgt-01.t:call-trgt_plot_motifs_allele INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:26.256 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_plot_meth_allele INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2099.meth_allele.trgt_plots.zip"
2025-09-15 20:24:26.259 wdl.w:ptcp.w:call-trgt-01.t:call-trgt_plot_meth_waterfall NOTICE slurm_singularity run :: pid: 1201805, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-01/call-trgt_plot_meth_waterfall/slurm_singularity.log.txt"
2025-09-15 20:24:26.277 wdl.w:ptcp.w:call-trgt-05.t:call-trgt_plot_motifs_waterfall INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2102.motifs_waterfall.trgt_plots.zip"
2025-09-15 20:24:26.294 wdl.w:ptcp.w:call-paraphase-12 NOTICE done
2025-09-15 20:24:26.301 wdl.w:ptcp NOTICE finish :: job: "call-paraphase-12"
2025-09-15 20:24:26.301 wdl.w:ptcp INFO output :: job: "call-paraphase-12", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-12/out/m84036_250809_035451_s4.bc2109.f8inversion.vcf", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-12/out/m84036_250809_035451_s4.bc2109_paraphase/m84036_250809_035451_s4.bc2109.paraphase.json", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-12/out/m84036_250809_035451_s4.bc2109_paraphase/m84036_250809_035451_s4.bc2109.paraphase.bam", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-12/out/m84036_250809_035451_s4.bc2109_paraphase/m84036_250809_035451_s4.bc2109.paraphase.bam.bai", "paraphase_vcfs": [], "havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-12/out/m84036_250809_035451_s4.bc2109.havanno.json", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-12/out/m84036_250809_035451_s4.bc2109.f8inversion.json"}
2025-09-15 20:24:26.309 wdl.w:ptcp.w:call-sawfish-59 NOTICE workflow start :: name: "sawfish", source: "./sawfish.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-59"
2025-09-15 20:24:26.321 wdl.w:ptcp.w:call-trgt-01.t:call-trgt_plot_motifs_allele INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-01/call-trgt_plot_motifs_allele/_singularity_tmpdir_b5gg7sac"
2025-09-15 20:24:26.321 wdl.w:ptcp.w:call-trgt-01.t:call-trgt_plot_motifs_allele INFO Slurm invocation: srun --job-name call-trgt_plot_motifs_allele --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-01/call-trgt_plot_motifs_allele/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-01/call-trgt_plot_motifs_allele/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-01/call-trgt_plot_motifs_allele/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-01/call-trgt_plot_motifs_allele/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-01/call-trgt_genotype/out/m84036_250809_035451_s4.bc2098.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2098.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-01/call-trgt_genotype/out/m84036_250809_035451_s4.bc2098.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2098.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-01/call-trgt_genotype/out/m84036_250809_035451_s4.bc2098.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2098.trgt.sorted.spanning.bam.bai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-01/call-trgt_plot_motifs_allele/_singularity_tmpdir_b5gg7sac/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-01/call-trgt_plot_motifs_allele/_singularity_tmpdir_b5gg7sac/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:26.323 wdl.w:ptcp.w:call-sawfish-59 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:24:26.324 wdl.w:ptcp.w:call-sawfish-59 INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:24:26.325 wdl.w:ptcp.w:call-sawfish-59 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-59/out/m84036_250809_035451_s4.bc2156.mapped.bam"}
2025-09-15 20:24:26.325 wdl.w:ptcp.w:call-sawfish-59 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-59/out/m84036_250809_035451_s4.bc2156.mapped.bam.bai"}
2025-09-15 20:24:26.325 wdl.w:ptcp.w:call-sawfish-59 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:24:26.325 wdl.w:ptcp.w:call-sawfish-59 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:24:26.325 wdl.w:ptcp.w:call-sawfish-59 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2156"}
2025-09-15 20:24:26.325 wdl.w:ptcp.w:call-sawfish-59 NOTICE ready :: job: "call-run_sawfish", callee: "run_sawfish"
2025-09-15 20:24:26.325 wdl.w:ptcp.w:call-sawfish-59 INFO input :: job: "call-run_sawfish", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-59/out/m84036_250809_035451_s4.bc2156.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-59/out/m84036_250809_035451_s4.bc2156.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2156"}
2025-09-15 20:24:26.339 wdl.w:ptcp.w:call-trgt-01.t:call-trgt_plot_motifs_allele NOTICE slurm_singularity run :: pid: 1201807, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-01/call-trgt_plot_motifs_allele/slurm_singularity.log.txt"
2025-09-15 20:24:26.374 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_plot_meth_allele NOTICE done
2025-09-15 20:24:26.380 wdl.w:ptcp.w:call-trgt-02 NOTICE finish :: job: "call-trgt_plot_meth_allele"
2025-09-15 20:24:26.380 wdl.w:ptcp.w:call-trgt-02 INFO output :: job: "call-trgt_plot_meth_allele", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-02/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2099.meth_allele.trgt_plots.zip"}
2025-09-15 20:24:26.380 wdl.w:ptcp.w:call-trgt-02 INFO visit :: node: "output-images_meth_allele", values: {"images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-02/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2099.meth_allele.trgt_plots.zip"}
2025-09-15 20:24:26.385 wdl.w:ptcp.w:call-trgt-00.t:call-trgt_plot_meth_allele.slurm_singularity INFO srun: job 51797641 queued and waiting for resources
2025-09-15 20:24:26.385 wdl.w:ptcp.w:call-trgt-00.t:call-trgt_plot_meth_allele.slurm_singularity INFO srun: job 51797641 has been allocated resources
2025-09-15 20:24:26.385 wdl.w:ptcp.w:call-trgt-00.t:call-trgt_plot_meth_allele.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:26.385 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_plot_motifs_waterfall INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2100.motifs_waterfall.trgt_plots.zip"
2025-09-15 20:24:26.387 wdl.w:ptcp.w:call-trgt-01.t:call-trgt_plot_motifs_waterfall NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-01/call-trgt_plot_motifs_waterfall", thread: 140608194717248
2025-09-15 20:24:26.393 wdl.w:ptcp.w:call-trgt-24.t:call-trgt_plot_meth_waterfall NOTICE done
2025-09-15 20:24:26.426 wdl.w:ptcp.w:call-trgt-24 NOTICE finish :: job: "call-trgt_plot_meth_waterfall"
2025-09-15 20:24:26.426 wdl.w:ptcp.w:call-trgt-24 INFO output :: job: "call-trgt_plot_meth_waterfall", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-24/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2121.meth_waterfall.trgt_plots.zip"}
2025-09-15 20:24:26.426 wdl.w:ptcp.w:call-trgt-24 INFO visit :: node: "output-images_meth_waterfall", values: {"images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-24/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2121.meth_waterfall.trgt_plots.zip"}
2025-09-15 20:24:26.427 wdl.w:ptcp.w:call-trgt-01.t:call-trgt_plot_motifs_waterfall INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:26.427 wdl.w:ptcp.w:call-trgt-01.t:call-trgt_plot_motifs_waterfall INFO input :: name: "waterfall", value: true
2025-09-15 20:24:26.427 wdl.w:ptcp.w:call-trgt-01.t:call-trgt_plot_motifs_waterfall INFO input :: name: "methylation", value: false
2025-09-15 20:24:26.427 wdl.w:ptcp.w:call-trgt-01.t:call-trgt_plot_motifs_waterfall INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:26.427 wdl.w:ptcp.w:call-trgt-01.t:call-trgt_plot_motifs_waterfall INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:26.427 wdl.w:ptcp.w:call-trgt-01.t:call-trgt_plot_motifs_waterfall INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:26.427 wdl.w:ptcp.w:call-trgt-01.t:call-trgt_plot_motifs_waterfall INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2098.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:26.427 wdl.w:ptcp.w:call-trgt-01.t:call-trgt_plot_motifs_waterfall INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2098.trgt.sorted.spanning.bam"
2025-09-15 20:24:26.427 wdl.w:ptcp.w:call-trgt-01.t:call-trgt_plot_motifs_waterfall INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2098.trgt.vcf"
2025-09-15 20:24:26.427 wdl.w:ptcp.w:call-trgt-01.t:call-trgt_plot_motifs_waterfall INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2098"
2025-09-15 20:24:26.428 wdl.w:ptcp.w:call-trgt-01.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:26.428 wdl.w:ptcp.w:call-trgt-01.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "plot_type", value: "waterfall"
2025-09-15 20:24:26.428 wdl.w:ptcp.w:call-trgt-01.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "show", value: "motifs"
2025-09-15 20:24:26.428 wdl.w:ptcp.w:call-trgt-01.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "threads", value: 1
2025-09-15 20:24:26.428 wdl.w:ptcp.w:call-trgt-01.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:26.428 wdl.w:ptcp.w:call-trgt-01.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2098.motifs_waterfall"
2025-09-15 20:24:26.429 wdl.w:ptcp.w:call-trgt-01.t:call-trgt_plot_motifs_waterfall INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:26.429 wdl.w:ptcp.w:call-trgt-01.t:call-trgt_plot_motifs_waterfall WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:26.429 wdl.w:ptcp.w:call-trgt-01.t:call-trgt_plot_motifs_waterfall INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:26.430 wdl.w:ptcp.w:call-trgt-01.t:call-trgt_plot_motifs_waterfall INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:26.435 wdl.w:ptcp.w:call-paraphase-08.t:call-call_f8 NOTICE task setup :: name: "call_f8", source: "./paraphase.wdl", line: 232, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-08/call-call_f8", thread: 140610367379008
2025-09-15 20:24:26.442 wdl.w:ptcp.w:call-trgt-05.t:call-trgt_plot_motifs_waterfall NOTICE done
2025-09-15 20:24:26.448 wdl.w:ptcp.w:call-trgt-05 NOTICE finish :: job: "call-trgt_plot_motifs_waterfall"
2025-09-15 20:24:26.449 wdl.w:ptcp.w:call-trgt-05 INFO output :: job: "call-trgt_plot_motifs_waterfall", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-05/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2102.motifs_waterfall.trgt_plots.zip"}
2025-09-15 20:24:26.449 wdl.w:ptcp.w:call-trgt-05 INFO visit :: node: "output-images_motifs_waterfall", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-05/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2102.motifs_waterfall.trgt_plots.zip"}
2025-09-15 20:24:26.454 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_plot_motifs_waterfall INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2099.motifs_waterfall.trgt_plots.zip"
2025-09-15 20:24:26.459 wdl.w:ptcp.w:call-trgt-44.t:call-get_reads_overlapping_repeats NOTICE task setup :: name: "get_reads_overlapping_repeats", source: "./trgt.wdl", line: 182, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-44/call-get_reads_overlapping_repeats", thread: 140607674631744
2025-09-15 20:24:26.466 wdl.w:ptcp.w:call-paraphase-08.t:call-call_f8 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:26.466 wdl.w:ptcp.w:call-paraphase-08.t:call-call_f8 INFO input :: name: "genome_version", value: "38"
2025-09-15 20:24:26.466 wdl.w:ptcp.w:call-paraphase-08.t:call-call_f8 INFO input :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2105"
2025-09-15 20:24:26.466 wdl.w:ptcp.w:call-paraphase-08.t:call-call_f8 INFO input :: name: "paraphase_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2105.paraphase.bam.bai"
2025-09-15 20:24:26.466 wdl.w:ptcp.w:call-paraphase-08.t:call-call_f8 INFO input :: name: "paraphase_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2105.paraphase.bam"
2025-09-15 20:24:26.466 wdl.w:ptcp.w:call-paraphase-08.t:call-call_f8 INFO input :: name: "sex", value: "F"
2025-09-15 20:24:26.467 wdl.w:ptcp.w:call-paraphase-08.t:call-call_f8 INFO eval :: name: "threads", value: 1
2025-09-15 20:24:26.467 wdl.w:ptcp.w:call-paraphase-08.t:call-call_f8 INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:26.467 wdl.w:ptcp.w:call-paraphase-08.t:call-call_f8 INFO eval :: name: "disk_size", value: 11
2025-09-15 20:24:26.467 wdl.w:ptcp.w:call-paraphase-08.t:call-call_f8 INFO eval :: name: "sample_sex", value: "F"
2025-09-15 20:24:26.468 wdl.w:ptcp.w:call-paraphase-08.t:call-call_f8 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:26.468 wdl.w:ptcp.w:call-paraphase-08.t:call-call_f8 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:26.468 wdl.w:ptcp.w:call-paraphase-08.t:call-call_f8 INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:26.468 wdl.w:ptcp.w:call-paraphase-08.t:call-call_f8 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:26.492 wdl.w:ptcp.w:call-trgt-44.t:call-get_reads_overlapping_repeats INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:26.492 wdl.w:ptcp.w:call-trgt-44.t:call-get_reads_overlapping_repeats INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:26.492 wdl.w:ptcp.w:call-trgt-44.t:call-get_reads_overlapping_repeats INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2141.mapped.bam.bai"
2025-09-15 20:24:26.492 wdl.w:ptcp.w:call-trgt-44.t:call-get_reads_overlapping_repeats INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2141.mapped.bam"
2025-09-15 20:24:26.492 wdl.w:ptcp.w:call-trgt-44.t:call-get_reads_overlapping_repeats INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2141"
2025-09-15 20:24:26.493 wdl.w:ptcp.w:call-trgt-44.t:call-get_reads_overlapping_repeats INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:26.493 wdl.w:ptcp.w:call-trgt-44.t:call-get_reads_overlapping_repeats INFO eval :: name: "expand_size", value: 3000
2025-09-15 20:24:26.493 wdl.w:ptcp.w:call-trgt-44.t:call-get_reads_overlapping_repeats INFO eval :: name: "threads", value: 1
2025-09-15 20:24:26.493 wdl.w:ptcp.w:call-trgt-44.t:call-get_reads_overlapping_repeats INFO eval :: name: "expanded_bed_name", value: "m84036_250809_035451_s4.bc2141.expanded.bed"
2025-09-15 20:24:26.493 wdl.w:ptcp.w:call-trgt-44.t:call-get_reads_overlapping_repeats INFO eval :: name: "disk_size", value: 11
2025-09-15 20:24:26.493 wdl.w:ptcp.w:call-trgt-44.t:call-get_reads_overlapping_repeats INFO eval :: name: "output_name", value: "m84036_250809_035451_s4.bc2141.repeats.bam"
2025-09-15 20:24:26.493 wdl.w:ptcp.w:call-trgt-44.t:call-get_reads_overlapping_repeats INFO eval :: name: "index_name", value: "m84036_250809_035451_s4.bc2141.repeats.bam.bai"
2025-09-15 20:24:26.493 wdl.w:ptcp.w:call-trgt-44.t:call-get_reads_overlapping_repeats INFO eval :: name: "output_name_with_index", value: "m84036_250809_035451_s4.bc2141.repeats.bam##idx##m84036_250809_035451_s4.bc2141.repeats.bam.bai"
2025-09-15 20:24:26.494 wdl.w:ptcp.w:call-trgt-44.t:call-get_reads_overlapping_repeats INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:26.494 wdl.w:ptcp.w:call-trgt-44.t:call-get_reads_overlapping_repeats WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:26.494 wdl.w:ptcp.w:call-trgt-44.t:call-get_reads_overlapping_repeats INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:26.494 wdl.w:ptcp.w:call-trgt-44.t:call-get_reads_overlapping_repeats INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:26.498 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_plot_motifs_waterfall NOTICE done
2025-09-15 20:24:26.504 wdl.w:ptcp.w:call-trgt-03 NOTICE finish :: job: "call-trgt_plot_motifs_waterfall"
2025-09-15 20:24:26.505 wdl.w:ptcp.w:call-trgt-03 INFO output :: job: "call-trgt_plot_motifs_waterfall", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-03/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2100.motifs_waterfall.trgt_plots.zip"}
2025-09-15 20:24:26.505 wdl.w:ptcp.w:call-trgt-03 INFO visit :: node: "output-images_motifs_waterfall", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-03/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2100.motifs_waterfall.trgt_plots.zip"}
2025-09-15 20:24:26.509 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:23 [ERROR] - No reads found for TRID=SCA2_ATXN2
2025-09-15 20:24:26.509 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:23 [ERROR] - No reads found for TRID=OPDM4_RILPL1
2025-09-15 20:24:26.509 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:23 [ERROR] - No reads found for TRID=SCA3_ATXN3
2025-09-15 20:24:26.510 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:24 [ERROR] - No reads found for TRID=SCA27B_FGF14
2025-09-15 20:24:26.510 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:24 [ERROR] - No reads found for TRID=HDL2_JPH3
2025-09-15 20:24:26.510 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:24 [ERROR] - No reads found for TRID=SCA4_ZFHX3
2025-09-15 20:24:26.510 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:24 [ERROR] - No reads found for TRID=SCA6_CACNA1A
2025-09-15 20:24:26.510 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:24 [ERROR] - No reads found for TRID=OPDM2_GIPC1
2025-09-15 20:24:26.510 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:24 [ERROR] - No reads found for TRID=DM1_DMPK
2025-09-15 20:24:26.510 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:24 [ERROR] - No reads found for TRID=SD5_HOXD13
2025-09-15 20:24:26.510 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:24 [ERROR] - No reads found for TRID=OPMD_PABPN1
2025-09-15 20:24:26.510 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:25 [ERROR] - No reads found for TRID=EPM1_CSTB
2025-09-15 20:24:26.510 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:25 [ERROR] - No reads found for TRID=CJD_PRNP
2025-09-15 20:24:26.510 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:25 [ERROR] - No reads found for TRID=SCA7_ATXN7
2025-09-15 20:24:26.510 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:25 [ERROR] - No reads found for TRID=FRA2A_AFF3
2025-09-15 20:24:26.510 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:25 [ERROR] - No reads found for TRID=SCA36_NOP56
2025-09-15 20:24:26.510 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:25 [ERROR] - No reads found for TRID=CCHS_PHOX2B
2025-09-15 20:24:26.510 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:25 [ERROR] - No reads found for TRID=SCA1_ATXN1
2025-09-15 20:24:26.510 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:26 [ERROR] - No reads found for TRID=SCA12_PPP2R2B
2025-09-15 20:24:26.511 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:26 [ERROR] - No reads found for TRID=FAME1_SAMD12
2025-09-15 20:24:26.511 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:26 [ERROR] - No reads found for TRID=OPDM1_LRP12
2025-09-15 20:24:26.512 wdl.w:ptcp.w:call-trgt-44.t:call-trgt_genotype NOTICE task setup :: name: "trgt_genotype", source: "./trgt.wdl", line: 272, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-44/call-trgt_genotype", thread: 140607657846336
2025-09-15 20:24:26.514 wdl.w:ptcp.w:call-trgt-01.t:call-trgt_plot_motifs_waterfall INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-01/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_6hbreflo"
2025-09-15 20:24:26.514 wdl.w:ptcp.w:call-trgt-01.t:call-trgt_plot_motifs_waterfall INFO Slurm invocation: srun --job-name call-trgt_plot_motifs_waterfall --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-01/call-trgt_plot_motifs_waterfall/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-01/call-trgt_plot_motifs_waterfall/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-01/call-trgt_plot_motifs_waterfall/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-01/call-trgt_plot_motifs_waterfall/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-01/call-trgt_genotype/out/m84036_250809_035451_s4.bc2098.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2098.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-01/call-trgt_genotype/out/m84036_250809_035451_s4.bc2098.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2098.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-01/call-trgt_genotype/out/m84036_250809_035451_s4.bc2098.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2098.trgt.sorted.spanning.bam.bai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-01/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_6hbreflo/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-01/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_6hbreflo/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:26.543 wdl.w:ptcp.w:call-trgt-44.t:call-trgt_genotype INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:26.543 wdl.w:ptcp.w:call-trgt-44.t:call-trgt_genotype INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:26.543 wdl.w:ptcp.w:call-trgt-44.t:call-trgt_genotype INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:26.543 wdl.w:ptcp.w:call-trgt-44.t:call-trgt_genotype INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:26.543 wdl.w:ptcp.w:call-trgt-44.t:call-trgt_genotype INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2141.mapped.bam.bai"
2025-09-15 20:24:26.543 wdl.w:ptcp.w:call-trgt-44.t:call-trgt_genotype INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2141.mapped.bam"
2025-09-15 20:24:26.543 wdl.w:ptcp.w:call-trgt-44.t:call-trgt_genotype INFO input :: name: "sex", value: "F"
2025-09-15 20:24:26.543 wdl.w:ptcp.w:call-trgt-44.t:call-trgt_genotype INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2141"
2025-09-15 20:24:26.544 wdl.w:ptcp.w:call-trgt-44.t:call-trgt_genotype INFO eval :: name: "mem_gb", value: 16
2025-09-15 20:24:26.544 wdl.w:ptcp.w:call-trgt-44.t:call-trgt_genotype INFO eval :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2141.trgt"
2025-09-15 20:24:26.544 wdl.w:ptcp.w:call-trgt-44.t:call-trgt_genotype INFO eval :: name: "threads", value: 8
2025-09-15 20:24:26.544 wdl.w:ptcp.w:call-trgt-44.t:call-trgt_genotype INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:26.544 wdl.w:ptcp.w:call-trgt-44.t:call-trgt_genotype INFO eval :: name: "karyotype", value: "XX"
2025-09-15 20:24:26.545 wdl.w:ptcp.w:call-trgt-44.t:call-trgt_genotype INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 8, memory_reservation: 16000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:26.545 wdl.w:ptcp.w:call-paraphase-08.t:call-call_f8 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 8, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-08/call-call_f8/_singularity_tmpdir_pmx47jom"
2025-09-15 20:24:26.545 wdl.w:ptcp.w:call-trgt-44.t:call-trgt_genotype WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:26.545 wdl.w:ptcp.w:call-paraphase-08.t:call-call_f8 INFO Slurm invocation: srun --job-name call-call_f8 --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-08/call-call_f8/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-08/call-call_f8/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-08/call-call_f8/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-08/call-call_f8/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-08/call-run_paraphase/out/m84036_250809_035451_s4.bc2105_paraphase/m84036_250809_035451_s4.bc2105.paraphase.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2105.paraphase.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-08/call-run_paraphase/out/m84036_250809_035451_s4.bc2105_paraphase/m84036_250809_035451_s4.bc2105.paraphase.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2105.paraphase.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-08/call-call_f8/_singularity_tmpdir_pmx47jom/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-08/call-call_f8/_singularity_tmpdir_pmx47jom/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:26.546 wdl.w:ptcp.w:call-trgt-44.t:call-trgt_genotype INFO provisioned :: seconds_waited: 0, cpu: 8, mem_bytes: 16000000000
2025-09-15 20:24:26.546 wdl.w:ptcp.w:call-trgt-44.t:call-trgt_genotype INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:26.555 wdl.w:ptcp.w:call-trgt-01.t:call-trgt_plot_motifs_waterfall NOTICE slurm_singularity run :: pid: 1201821, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-01/call-trgt_plot_motifs_waterfall/slurm_singularity.log.txt"
2025-09-15 20:24:26.558 wdl.w:ptcp.w:call-paraphase-08.t:call-call_f8 NOTICE slurm_singularity run :: pid: 1201822, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-08/call-call_f8/slurm_singularity.log.txt"
2025-09-15 20:24:26.571 wdl.w:ptcp.w:call-trgt-44.t:call-get_reads_overlapping_repeats INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 9, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-44/call-get_reads_overlapping_repeats/_singularity_tmpdir_9udvolg_"
2025-09-15 20:24:26.571 wdl.w:ptcp.w:call-trgt-44.t:call-get_reads_overlapping_repeats INFO Slurm invocation: srun --job-name call-get_reads_overlapping_repeats --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-44/call-get_reads_overlapping_repeats/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-44/call-get_reads_overlapping_repeats/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-44/call-get_reads_overlapping_repeats/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-44/call-get_reads_overlapping_repeats/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-44/out/m84036_250809_035451_s4.bc2141.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2141.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-44/out/m84036_250809_035451_s4.bc2141.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2141.mapped.bam:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-44/call-get_reads_overlapping_repeats/_singularity_tmpdir_9udvolg_/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-44/call-get_reads_overlapping_repeats/_singularity_tmpdir_9udvolg_/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:26.581 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_plot_motifs_waterfall NOTICE done
2025-09-15 20:24:26.585 wdl.w:ptcp.w:call-trgt-02 NOTICE finish :: job: "call-trgt_plot_motifs_waterfall"
2025-09-15 20:24:26.585 wdl.w:ptcp.w:call-trgt-02 INFO output :: job: "call-trgt_plot_motifs_waterfall", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-02/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2099.motifs_waterfall.trgt_plots.zip"}
2025-09-15 20:24:26.585 wdl.w:ptcp.w:call-trgt-02 INFO visit :: node: "output-images_motifs_waterfall", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-02/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2099.motifs_waterfall.trgt_plots.zip"}
2025-09-15 20:24:26.591 wdl.w:ptcp.w:call-trgt-44.t:call-get_reads_overlapping_repeats NOTICE slurm_singularity run :: pid: 1201825, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-44/call-get_reads_overlapping_repeats/slurm_singularity.log.txt"
2025-09-15 20:24:26.593 wdl.w:ptcp.w:call-paraphase-01.t:call-call_f8 NOTICE task setup :: name: "call_f8", source: "./paraphase.wdl", line: 232, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-01/call-call_f8", thread: 140608219895360
2025-09-15 20:24:26.612 wdl.w:ptcp.w:call-paraphase-01.t:call-call_f8 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:26.612 wdl.w:ptcp.w:call-paraphase-01.t:call-call_f8 INFO input :: name: "genome_version", value: "38"
2025-09-15 20:24:26.612 wdl.w:ptcp.w:call-paraphase-01.t:call-call_f8 INFO input :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2098"
2025-09-15 20:24:26.613 wdl.w:ptcp.w:call-paraphase-01.t:call-call_f8 INFO input :: name: "paraphase_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2098.paraphase.bam.bai"
2025-09-15 20:24:26.613 wdl.w:ptcp.w:call-paraphase-01.t:call-call_f8 INFO input :: name: "paraphase_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2098.paraphase.bam"
2025-09-15 20:24:26.613 wdl.w:ptcp.w:call-paraphase-01.t:call-call_f8 INFO input :: name: "sex", value: "F"
2025-09-15 20:24:26.613 wdl.w:ptcp.w:call-paraphase-01.t:call-call_f8 INFO eval :: name: "threads", value: 1
2025-09-15 20:24:26.613 wdl.w:ptcp.w:call-paraphase-01.t:call-call_f8 INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:26.613 wdl.w:ptcp.w:call-paraphase-01.t:call-call_f8 INFO eval :: name: "disk_size", value: 11
2025-09-15 20:24:26.614 wdl.w:ptcp.w:call-paraphase-01.t:call-call_f8 INFO eval :: name: "sample_sex", value: "F"
2025-09-15 20:24:26.614 wdl.w:ptcp.w:call-paraphase-01.t:call-call_f8 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:26.614 wdl.w:ptcp.w:call-paraphase-01.t:call-call_f8 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:26.614 wdl.w:ptcp.w:call-paraphase-01.t:call-call_f8 INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:26.614 wdl.w:ptcp.w:call-paraphase-01.t:call-call_f8 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:26.628 wdl.w:ptcp.w:call-trgt-44.t:call-trgt_genotype INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 11, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-44/call-trgt_genotype/_singularity_tmpdir_0jfir5rq"
2025-09-15 20:24:26.629 wdl.w:ptcp.w:call-trgt-44.t:call-trgt_genotype INFO Slurm invocation: srun --job-name call-trgt_genotype --partition compute,compute9 --cpus-per-task 8 --mem 15259M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-44/call-trgt_genotype/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-44/call-trgt_genotype/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-44/call-trgt_genotype/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-44/call-trgt_genotype/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-44/out/m84036_250809_035451_s4.bc2141.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2141.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-44/out/m84036_250809_035451_s4.bc2141.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2141.mapped.bam:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-44/call-trgt_genotype/_singularity_tmpdir_0jfir5rq/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-44/call-trgt_genotype/_singularity_tmpdir_0jfir5rq/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:26.641 wdl.w:ptcp.w:call-trgt-44.t:call-trgt_genotype NOTICE slurm_singularity run :: pid: 1201827, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-44/call-trgt_genotype/slurm_singularity.log.txt"
2025-09-15 20:24:26.649 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:23 [ERROR] - No reads found for TRID=SCA37_DAB1
2025-09-15 20:24:26.649 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:23 [ERROR] - No reads found for TRID=SCA37_DAB1
2025-09-15 20:24:26.649 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:23 [ERROR] - No reads found for TRID=OPDM_ABCD3
2025-09-15 20:24:26.649 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:23 [ERROR] - No reads found for TRID=OPDM_ABCD3
2025-09-15 20:24:26.649 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:23 [ERROR] - No reads found for TRID=NIID_NOTCH2NLC
2025-09-15 20:24:26.649 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:23 [ERROR] - No reads found for TRID=NIID_NOTCH2NLC
2025-09-15 20:24:26.649 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:24 [ERROR] - No reads found for TRID=DRPLA_ATN1
2025-09-15 20:24:26.650 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:24 [ERROR] - No reads found for TRID=DRPLA_ATN1
2025-09-15 20:24:26.650 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:24 [ERROR] - No reads found for TRID=OPDM4_RILPL1
2025-09-15 20:24:26.650 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:24 [ERROR] - No reads found for TRID=OPDM4_RILPL1
2025-09-15 20:24:26.650 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:24 [ERROR] - No reads found for TRID=OPMD_PABPN1
2025-09-15 20:24:26.650 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:24 [ERROR] - No reads found for TRID=OPMD_PABPN1
2025-09-15 20:24:26.650 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:24 [ERROR] - No reads found for TRID=SCA3_ATXN3
2025-09-15 20:24:26.650 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:24 [ERROR] - No reads found for TRID=SCA3_ATXN3
2025-09-15 20:24:26.650 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:24 [ERROR] - No reads found for TRID=SCA27B_FGF14
2025-09-15 20:24:26.650 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:24 [ERROR] - No reads found for TRID=SCA27B_FGF14
2025-09-15 20:24:26.650 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:24 [ERROR] - No reads found for TRID=SCA31_BEAN1
2025-09-15 20:24:26.650 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:24 [ERROR] - No reads found for TRID=SCA31_BEAN1
2025-09-15 20:24:26.650 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:24 [ERROR] - No reads found for TRID=SCA4_ZFHX3
2025-09-15 20:24:26.650 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:24 [ERROR] - No reads found for TRID=SCA4_ZFHX3
2025-09-15 20:24:26.650 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:24 [ERROR] - No reads found for TRID=HDL2_JPH3
2025-09-15 20:24:26.650 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:24 [ERROR] - No reads found for TRID=HDL2_JPH3
2025-09-15 20:24:26.650 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:25 [ERROR] - No reads found for TRID=SCA6_CACNA1A
2025-09-15 20:24:26.650 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:25 [ERROR] - No reads found for TRID=SCA6_CACNA1A
2025-09-15 20:24:26.651 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:25 [ERROR] - No reads found for TRID=FECD3_TCF4
2025-09-15 20:24:26.651 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:25 [ERROR] - No reads found for TRID=FECD3_TCF4
2025-09-15 20:24:26.651 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:25 [ERROR] - No reads found for TRID=OPDM2_GIPC1
2025-09-15 20:24:26.651 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:25 [ERROR] - No reads found for TRID=OPDM2_GIPC1
2025-09-15 20:24:26.651 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:25 [ERROR] - No reads found for TRID=FRA2A_AFF3
2025-09-15 20:24:26.651 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:25 [ERROR] - No reads found for TRID=FRA2A_AFF3
2025-09-15 20:24:26.651 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:25 [ERROR] - No reads found for TRID=SD5_HOXD13
2025-09-15 20:24:26.651 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:25 [ERROR] - No reads found for TRID=SD5_HOXD13
2025-09-15 20:24:26.651 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:25 [ERROR] - No reads found for TRID=SCA36_NOP56
2025-09-15 20:24:26.651 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:25 [ERROR] - No reads found for TRID=SCA36_NOP56
2025-09-15 20:24:26.651 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:25 [ERROR] - No reads found for TRID=CJD_PRNP
2025-09-15 20:24:26.651 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:25 [ERROR] - No reads found for TRID=CJD_PRNP
2025-09-15 20:24:26.651 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:26 [ERROR] - No reads found for TRID=EPM1_CSTB
2025-09-15 20:24:26.651 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:25 [ERROR] - No reads found for TRID=EPM1_CSTB
2025-09-15 20:24:26.652 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:26 [ERROR] - No reads found for TRID=CCHS_PHOX2B
2025-09-15 20:24:26.652 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:26 [ERROR] - No reads found for TRID=CCHS_PHOX2B
2025-09-15 20:24:26.681 wdl.w:ptcp.w:call-paraphase-01.t:call-call_f8 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 8, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-01/call-call_f8/_singularity_tmpdir_d7005hqg"
2025-09-15 20:24:26.681 wdl.w:ptcp.w:call-paraphase-01.t:call-call_f8 INFO Slurm invocation: srun --job-name call-call_f8 --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-01/call-call_f8/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-01/call-call_f8/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-01/call-call_f8/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-01/call-call_f8/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-01/call-run_paraphase/out/m84036_250809_035451_s4.bc2098_paraphase/m84036_250809_035451_s4.bc2098.paraphase.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2098.paraphase.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-01/call-run_paraphase/out/m84036_250809_035451_s4.bc2098_paraphase/m84036_250809_035451_s4.bc2098.paraphase.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2098.paraphase.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-01/call-call_f8/_singularity_tmpdir_d7005hqg/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-01/call-call_f8/_singularity_tmpdir_d7005hqg/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:26.688 wdl.w:ptcp.w:call-trgt-00.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO srun: job 51797642 queued and waiting for resources
2025-09-15 20:24:26.688 wdl.w:ptcp.w:call-trgt-00.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO srun: job 51797642 has been allocated resources
2025-09-15 20:24:26.688 wdl.w:ptcp.w:call-trgt-00.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:26.698 wdl.w:ptcp.w:call-paraphase-01.t:call-call_f8 NOTICE slurm_singularity run :: pid: 1201829, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-01/call-call_f8/slurm_singularity.log.txt"
2025-09-15 20:24:26.699 wdl.w:ptcp.w:call-trgt-00.t:call-trgt_plot_motifs_allele.slurm_singularity INFO srun: job 51797643 queued and waiting for resources
2025-09-15 20:24:26.699 wdl.w:ptcp.w:call-trgt-00.t:call-trgt_plot_motifs_allele.slurm_singularity INFO srun: job 51797643 has been allocated resources
2025-09-15 20:24:26.699 wdl.w:ptcp.w:call-trgt-00.t:call-trgt_plot_motifs_allele.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:26.726 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:23 [ERROR] - No reads found for TRID=SCA37_DAB1
2025-09-15 20:24:26.726 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:23 [ERROR] - No reads found for TRID=OPDM_ABCD3
2025-09-15 20:24:26.726 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:23 [ERROR] - No reads found for TRID=NIID_NOTCH2NLC
2025-09-15 20:24:26.726 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:24 [ERROR] - No reads found for TRID=DRPLA_ATN1
2025-09-15 20:24:26.726 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:24 [ERROR] - No reads found for TRID=OPDM4_RILPL1
2025-09-15 20:24:26.726 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:24 [ERROR] - No reads found for TRID=OPMD_PABPN1
2025-09-15 20:24:26.726 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:24 [ERROR] - No reads found for TRID=SCA3_ATXN3
2025-09-15 20:24:26.726 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:24 [ERROR] - No reads found for TRID=SCA27B_FGF14
2025-09-15 20:24:26.726 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:24 [ERROR] - No reads found for TRID=SCA31_BEAN1
2025-09-15 20:24:26.726 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:24 [ERROR] - No reads found for TRID=SCA4_ZFHX3
2025-09-15 20:24:26.726 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:24 [ERROR] - No reads found for TRID=HDL2_JPH3
2025-09-15 20:24:26.726 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:25 [ERROR] - No reads found for TRID=SCA6_CACNA1A
2025-09-15 20:24:26.726 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:25 [ERROR] - No reads found for TRID=FECD3_TCF4
2025-09-15 20:24:26.726 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:25 [ERROR] - No reads found for TRID=OPDM2_GIPC1
2025-09-15 20:24:26.726 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:25 [ERROR] - No reads found for TRID=FRA2A_AFF3
2025-09-15 20:24:26.726 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:25 [ERROR] - No reads found for TRID=SD5_HOXD13
2025-09-15 20:24:26.727 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:25 [ERROR] - No reads found for TRID=SCA36_NOP56
2025-09-15 20:24:26.727 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:25 [ERROR] - No reads found for TRID=CJD_PRNP
2025-09-15 20:24:26.727 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:25 [ERROR] - No reads found for TRID=EPM1_CSTB
2025-09-15 20:24:26.727 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:26 [ERROR] - No reads found for TRID=CCHS_PHOX2B
2025-09-15 20:24:26.927 wdl.w:ptcp.w:call-paraphase-38.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for hba for sample m84036_250809_035451_s4.bc2135 at 2025-09-15 20:24:04.520126...
2025-09-15 20:24:26.927 wdl.w:ptcp.w:call-paraphase-38.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for smn1 for sample m84036_250809_035451_s4.bc2135 at 2025-09-15 20:24:04.903613...
2025-09-15 20:24:26.927 wdl.w:ptcp.w:call-paraphase-38.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for gba for sample m84036_250809_035451_s4.bc2135 at 2025-09-15 20:24:05.295775...
2025-09-15 20:24:26.928 wdl.w:ptcp.w:call-paraphase-38.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for cyp21 for sample m84036_250809_035451_s4.bc2135 at 2025-09-15 20:24:06.469630...
2025-09-15 20:24:26.928 wdl.w:ptcp.w:call-paraphase-38.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for smn1 for sample m84036_250809_035451_s4.bc2135 at 2025-09-15 20:24:23.492395...
2025-09-15 20:24:26.928 wdl.w:ptcp.w:call-paraphase-38.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning to gene2 region for smn1 for sample m84036_250809_035451_s4.bc2135 at 2025-09-15 20:24:23.946591...
2025-09-15 20:24:27.019 wdl.w:ptcp.w:call-trgt-00.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO srun: job 51797644 queued and waiting for resources
2025-09-15 20:24:27.019 wdl.w:ptcp.w:call-trgt-00.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO srun: job 51797644 has been allocated resources
2025-09-15 20:24:27.019 wdl.w:ptcp.w:call-trgt-00.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:27.112 wdl.w:ptcp.w:call-trgt-01.t:call-trgt_plot_meth_allele.slurm_singularity INFO srun: job 51797645 queued and waiting for resources
2025-09-15 20:24:27.112 wdl.w:ptcp.w:call-trgt-01.t:call-trgt_plot_meth_allele.slurm_singularity INFO srun: job 51797645 has been allocated resources
2025-09-15 20:24:27.112 wdl.w:ptcp.w:call-trgt-01.t:call-trgt_plot_meth_allele.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:27.119 wdl.w:ptcp.w:call-paraphase-25.t:call-call_f8 INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2122.f8inversion.vcf"
2025-09-15 20:24:27.122 wdl.w:ptcp.w:call-paraphase-25.t:call-call_f8 INFO output :: name: "json", value: "m84036_250809_035451_s4.bc2122.f8inversion.json"
2025-09-15 20:24:27.125 wdl.w:ptcp.w:call-paraphase-32.t:call-call_f8 INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2129.f8inversion.vcf"
2025-09-15 20:24:27.130 wdl.w:ptcp.w:call-paraphase-32.t:call-call_f8 INFO output :: name: "json", value: "m84036_250809_035451_s4.bc2129.f8inversion.json"
2025-09-15 20:24:27.140 wdl.w:ptcp.w:call-trgt-25.t:call-trgt_plot_meth_allele INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2122.meth_allele.trgt_plots.zip"
2025-09-15 20:24:27.205 wdl.w:ptcp.w:call-paraphase-32.t:call-call_f8 NOTICE done
2025-09-15 20:24:27.216 wdl.w:ptcp.w:call-paraphase-32 NOTICE finish :: job: "call-call_f8"
2025-09-15 20:24:27.217 wdl.w:ptcp.w:call-paraphase-32 INFO output :: job: "call-call_f8", values: {"json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-32/call-call_f8/out/m84036_250809_035451_s4.bc2129.f8inversion.json", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-32/call-call_f8/out/m84036_250809_035451_s4.bc2129.f8inversion.vcf"}
2025-09-15 20:24:27.217 wdl.w:ptcp.w:call-paraphase-32 INFO visit :: node: "output-f8_json", values: {"f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-32/call-call_f8/out/m84036_250809_035451_s4.bc2129.f8inversion.json"}
2025-09-15 20:24:27.217 wdl.w:ptcp.w:call-paraphase-32 INFO visit :: node: "output-f8_vcf", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-32/call-call_f8/out/m84036_250809_035451_s4.bc2129.f8inversion.vcf"}
2025-09-15 20:24:27.217 wdl.w:ptcp.w:call-paraphase-32 INFO visit :: node: "outputs", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-32/call-call_f8/out/m84036_250809_035451_s4.bc2129.f8inversion.vcf", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-32/call-run_paraphase/out/m84036_250809_035451_s4.bc2129_paraphase/m84036_250809_035451_s4.bc2129.paraphase.json", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-32/call-run_paraphase/out/m84036_250809_035451_s4.bc2129_paraphase/m84036_250809_035451_s4.bc2129.paraphase.bam", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-32/call-run_paraphase/out/m84036_250809_035451_s4.bc2129_paraphase/m84036_250809_035451_s4.bc2129.paraphase.bam.bai", "paraphase_vcfs": [], "havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-32/call-run_paraphase/out/m84036_250809_035451_s4.bc2129.havanno.json", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-32/call-call_f8/out/m84036_250809_035451_s4.bc2129.f8inversion.json"}
2025-09-15 20:24:27.218 wdl.w:ptcp.w:call-paraphase-25.t:call-call_f8 NOTICE done
2025-09-15 20:24:27.224 wdl.w:ptcp.w:call-paraphase-25 NOTICE finish :: job: "call-call_f8"
2025-09-15 20:24:27.224 wdl.w:ptcp.w:call-paraphase-25 INFO output :: job: "call-call_f8", values: {"json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-25/call-call_f8/out/m84036_250809_035451_s4.bc2122.f8inversion.json", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-25/call-call_f8/out/m84036_250809_035451_s4.bc2122.f8inversion.vcf"}
2025-09-15 20:24:27.224 wdl.w:ptcp.w:call-paraphase-25 INFO visit :: node: "output-f8_json", values: {"f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-25/call-call_f8/out/m84036_250809_035451_s4.bc2122.f8inversion.json"}
2025-09-15 20:24:27.225 wdl.w:ptcp.w:call-paraphase-25 INFO visit :: node: "output-f8_vcf", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-25/call-call_f8/out/m84036_250809_035451_s4.bc2122.f8inversion.vcf"}
2025-09-15 20:24:27.225 wdl.w:ptcp.w:call-paraphase-25 INFO visit :: node: "outputs", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-25/call-call_f8/out/m84036_250809_035451_s4.bc2122.f8inversion.vcf", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-25/call-run_paraphase/out/m84036_250809_035451_s4.bc2122_paraphase/m84036_250809_035451_s4.bc2122.paraphase.json", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-25/call-run_paraphase/out/m84036_250809_035451_s4.bc2122_paraphase/m84036_250809_035451_s4.bc2122.paraphase.bam", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-25/call-run_paraphase/out/m84036_250809_035451_s4.bc2122_paraphase/m84036_250809_035451_s4.bc2122.paraphase.bam.bai", "paraphase_vcfs": [], "havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-25/call-run_paraphase/out/m84036_250809_035451_s4.bc2122.havanno.json", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-25/call-call_f8/out/m84036_250809_035451_s4.bc2122.f8inversion.json"}
2025-09-15 20:24:27.226 wdl.w:ptcp.w:call-paraphase-52.t:call-run_paraphase NOTICE task setup :: name: "run_paraphase", source: "./paraphase.wdl", line: 127, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-52/call-run_paraphase", thread: 140609838900800
2025-09-15 20:24:27.235 wdl.w:ptcp.w:call-sawfish-52.t:call-run_sawfish NOTICE task setup :: name: "run_sawfish", source: "./sawfish.wdl", line: 83, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-52/call-run_sawfish", thread: 140607666239040
2025-09-15 20:24:27.256 wdl.w:ptcp.w:call-paraphase-52.t:call-run_paraphase INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:27.256 wdl.w:ptcp.w:call-paraphase-52.t:call-run_paraphase INFO input :: name: "annotation_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf"
2025-09-15 20:24:27.256 wdl.w:ptcp.w:call-paraphase-52.t:call-run_paraphase INFO input :: name: "genome_version", value: "38"
2025-09-15 20:24:27.256 wdl.w:ptcp.w:call-paraphase-52.t:call-run_paraphase INFO input :: name: "config_file", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/paraphase_config.GRCh38.yaml"
2025-09-15 20:24:27.256 wdl.w:ptcp.w:call-paraphase-52.t:call-run_paraphase INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:27.256 wdl.w:ptcp.w:call-paraphase-52.t:call-run_paraphase INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:27.256 wdl.w:ptcp.w:call-paraphase-52.t:call-run_paraphase INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2149.mapped.bam.bai"
2025-09-15 20:24:27.256 wdl.w:ptcp.w:call-sawfish-52.t:call-run_sawfish INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:27.257 wdl.w:ptcp.w:call-paraphase-52.t:call-run_paraphase INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2149.mapped.bam"
2025-09-15 20:24:27.257 wdl.w:ptcp.w:call-sawfish-52.t:call-run_sawfish INFO input :: name: "genome_version", value: "38"
2025-09-15 20:24:27.257 wdl.w:ptcp.w:call-paraphase-52.t:call-run_paraphase INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2149"
2025-09-15 20:24:27.257 wdl.w:ptcp.w:call-sawfish-52.t:call-run_sawfish INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:27.258 wdl.w:ptcp.w:call-paraphase-52.t:call-run_paraphase INFO eval :: name: "threads", value: 4
2025-09-15 20:24:27.258 wdl.w:ptcp.w:call-sawfish-52.t:call-run_sawfish INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:27.258 wdl.w:ptcp.w:call-paraphase-52.t:call-run_paraphase INFO eval :: name: "mem_gb", value: 8
2025-09-15 20:24:27.258 wdl.w:ptcp.w:call-sawfish-52.t:call-run_sawfish INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2149.mapped.bam.bai"
2025-09-15 20:24:27.259 wdl.w:ptcp.w:call-sawfish-52.t:call-run_sawfish INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2149.mapped.bam"
2025-09-15 20:24:27.259 wdl.w:ptcp.w:call-paraphase-52.t:call-run_paraphase INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:27.259 wdl.w:ptcp.w:call-sawfish-52.t:call-run_sawfish INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2149"
2025-09-15 20:24:27.259 wdl.w:ptcp.w:call-paraphase-52.t:call-run_paraphase INFO eval :: name: "out_dir", value: "m84036_250809_035451_s4.bc2149_paraphase"
2025-09-15 20:24:27.259 wdl.w:ptcp.w:call-sawfish-52.t:call-run_sawfish INFO eval :: name: "mem_gb", value: 32
2025-09-15 20:24:27.260 wdl.w:ptcp.w:call-sawfish-52.t:call-run_sawfish INFO eval :: name: "threads", value: 16
2025-09-15 20:24:27.260 wdl.w:ptcp.w:call-paraphase-52.t:call-run_paraphase INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 4, memory_reservation: 8000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:27.260 wdl.w:ptcp.w:call-paraphase-52.t:call-run_paraphase WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:27.260 wdl.w:ptcp.w:call-sawfish-52.t:call-run_sawfish INFO eval :: name: "disk_size", value: 30
2025-09-15 20:24:27.261 wdl.w:ptcp.w:call-sawfish-52.t:call-run_sawfish INFO eval :: name: "discover_dirname", value: "m84036_250809_035451_s4.bc2149_sawfish_discover"
2025-09-15 20:24:27.261 wdl.w:ptcp.w:call-sawfish-52.t:call-run_sawfish INFO eval :: name: "call_dirname", value: "m84036_250809_035451_s4.bc2149_sawfish"
2025-09-15 20:24:27.261 wdl.w:ptcp.w:call-sawfish-52.t:call-run_sawfish INFO eval :: name: "minimap2_bam_filename", value: "m84036_250809_035451_s4.bc2149.minimap2.bam"
2025-09-15 20:24:27.262 wdl.w:ptcp.w:call-paraphase-52.t:call-run_paraphase INFO provisioned :: seconds_waited: 0, cpu: 4, mem_bytes: 8000000000
2025-09-15 20:24:27.262 wdl.w:ptcp.w:call-sawfish-52.t:call-run_sawfish INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 16, memory_reservation: 32000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:27.262 wdl.w:ptcp.w:call-paraphase-52.t:call-run_paraphase INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:27.262 wdl.w:ptcp.w:call-sawfish-52.t:call-run_sawfish WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:27.263 wdl.w:ptcp.w:call-sawfish-52.t:call-run_sawfish INFO provisioned :: seconds_waited: 0, cpu: 16, mem_bytes: 32000000000
2025-09-15 20:24:27.263 wdl.w:ptcp.w:call-sawfish-52.t:call-run_sawfish INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:27.279 wdl.w:ptcp.w:call-trgt-01.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO srun: job 51797646 queued and waiting for resources
2025-09-15 20:24:27.279 wdl.w:ptcp.w:call-trgt-01.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO srun: job 51797646 has been allocated resources
2025-09-15 20:24:27.279 wdl.w:ptcp.w:call-trgt-01.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:27.292 wdl.w:ptcp.w:call-trgt-25.t:call-trgt_plot_meth_allele NOTICE done
2025-09-15 20:24:27.292 wdl.w:ptcp.w:call-trgt-05.t:call-trgt_plot_meth_waterfall INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2102.meth_waterfall.trgt_plots.zip"
2025-09-15 20:24:27.298 wdl.w:ptcp.w:call-trgt-25 NOTICE finish :: job: "call-trgt_plot_meth_allele"
2025-09-15 20:24:27.298 wdl.w:ptcp.w:call-trgt-25 INFO output :: job: "call-trgt_plot_meth_allele", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-25/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2122.meth_allele.trgt_plots.zip"}
2025-09-15 20:24:27.299 wdl.w:ptcp.w:call-trgt-25 INFO visit :: node: "output-images_meth_allele", values: {"images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-25/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2122.meth_allele.trgt_plots.zip"}
2025-09-15 20:24:27.300 wdl.w:ptcp.w:call-trgt-16.t:call-trgt_plot_meth_waterfall INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2113.meth_waterfall.trgt_plots.zip"
2025-09-15 20:24:27.305 wdl.w:ptcp.w:call-trgt-52.t:call-get_reads_overlapping_repeats NOTICE task setup :: name: "get_reads_overlapping_repeats", source: "./trgt.wdl", line: 182, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-52/call-get_reads_overlapping_repeats", thread: 140607129368128
2025-09-15 20:24:27.310 wdl.w:ptcp.w:call-paraphase-32 NOTICE done
2025-09-15 20:24:27.318 wdl.w:ptcp NOTICE finish :: job: "call-paraphase-32"
2025-09-15 20:24:27.318 wdl.w:ptcp INFO output :: job: "call-paraphase-32", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-32/out/m84036_250809_035451_s4.bc2129.f8inversion.vcf", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-32/out/m84036_250809_035451_s4.bc2129_paraphase/m84036_250809_035451_s4.bc2129.paraphase.json", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-32/out/m84036_250809_035451_s4.bc2129_paraphase/m84036_250809_035451_s4.bc2129.paraphase.bam", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-32/out/m84036_250809_035451_s4.bc2129_paraphase/m84036_250809_035451_s4.bc2129.paraphase.bam.bai", "paraphase_vcfs": [], "havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-32/out/m84036_250809_035451_s4.bc2129.havanno.json", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-32/out/m84036_250809_035451_s4.bc2129.f8inversion.json"}
2025-09-15 20:24:27.325 wdl.w:ptcp.w:call-trgt-59 NOTICE workflow start :: name: "trgt", source: "./trgt.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-59"
2025-09-15 20:24:27.326 wdl.w:ptcp.w:call-paraphase-25 NOTICE done
2025-09-15 20:24:27.328 wdl.w:ptcp.w:call-trgt-52.t:call-get_reads_overlapping_repeats INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:27.328 wdl.w:ptcp.w:call-trgt-52.t:call-get_reads_overlapping_repeats INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:27.329 wdl.w:ptcp.w:call-trgt-52.t:call-get_reads_overlapping_repeats INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2149.mapped.bam.bai"
2025-09-15 20:24:27.329 wdl.w:ptcp.w:call-trgt-52.t:call-get_reads_overlapping_repeats INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2149.mapped.bam"
2025-09-15 20:24:27.329 wdl.w:ptcp.w:call-trgt-52.t:call-get_reads_overlapping_repeats INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2149"
2025-09-15 20:24:27.329 wdl.w:ptcp.w:call-trgt-52.t:call-get_reads_overlapping_repeats INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:27.330 wdl.w:ptcp.w:call-trgt-52.t:call-get_reads_overlapping_repeats INFO eval :: name: "expand_size", value: 3000
2025-09-15 20:24:27.330 wdl.w:ptcp.w:call-trgt-52.t:call-get_reads_overlapping_repeats INFO eval :: name: "threads", value: 1
2025-09-15 20:24:27.330 wdl.w:ptcp.w:call-trgt-52.t:call-get_reads_overlapping_repeats INFO eval :: name: "expanded_bed_name", value: "m84036_250809_035451_s4.bc2149.expanded.bed"
2025-09-15 20:24:27.330 wdl.w:ptcp.w:call-trgt-52.t:call-get_reads_overlapping_repeats INFO eval :: name: "disk_size", value: 11
2025-09-15 20:24:27.330 wdl.w:ptcp.w:call-trgt-52.t:call-get_reads_overlapping_repeats INFO eval :: name: "output_name", value: "m84036_250809_035451_s4.bc2149.repeats.bam"
2025-09-15 20:24:27.330 wdl.w:ptcp.w:call-trgt-52.t:call-get_reads_overlapping_repeats INFO eval :: name: "index_name", value: "m84036_250809_035451_s4.bc2149.repeats.bam.bai"
2025-09-15 20:24:27.330 wdl.w:ptcp.w:call-trgt-52.t:call-get_reads_overlapping_repeats INFO eval :: name: "output_name_with_index", value: "m84036_250809_035451_s4.bc2149.repeats.bam##idx##m84036_250809_035451_s4.bc2149.repeats.bam.bai"
2025-09-15 20:24:27.331 wdl.w:ptcp.w:call-trgt-52.t:call-get_reads_overlapping_repeats INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:27.331 wdl.w:ptcp.w:call-trgt-52.t:call-get_reads_overlapping_repeats WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:27.332 wdl.w:ptcp.w:call-trgt-52.t:call-get_reads_overlapping_repeats INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:27.332 wdl.w:ptcp.w:call-trgt-52.t:call-get_reads_overlapping_repeats INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:27.333 wdl.w:ptcp NOTICE finish :: job: "call-paraphase-25"
2025-09-15 20:24:27.333 wdl.w:ptcp INFO output :: job: "call-paraphase-25", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-25/out/m84036_250809_035451_s4.bc2122.f8inversion.vcf", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-25/out/m84036_250809_035451_s4.bc2122_paraphase/m84036_250809_035451_s4.bc2122.paraphase.json", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-25/out/m84036_250809_035451_s4.bc2122_paraphase/m84036_250809_035451_s4.bc2122.paraphase.bam", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-25/out/m84036_250809_035451_s4.bc2122_paraphase/m84036_250809_035451_s4.bc2122.paraphase.bam.bai", "paraphase_vcfs": [], "havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-25/out/m84036_250809_035451_s4.bc2122.havanno.json", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-25/out/m84036_250809_035451_s4.bc2122.f8inversion.json"}
2025-09-15 20:24:27.343 wdl.w:ptcp.w:call-trgt-59 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:24:27.343 wdl.w:ptcp.w:call-trgt-59 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-59/out/m84036_250809_035451_s4.bc2156.mapped.bam"}
2025-09-15 20:24:27.343 wdl.w:ptcp.w:call-trgt-59 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-59/out/m84036_250809_035451_s4.bc2156.mapped.bam.bai"}
2025-09-15 20:24:27.343 wdl.w:ptcp.w:call-trgt-59 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:24:27.344 wdl.w:ptcp.w:call-trgt-59 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:24:27.344 wdl.w:ptcp.w:call-trgt-59 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2156"}
2025-09-15 20:24:27.344 wdl.w:ptcp.w:call-trgt-59 INFO visit :: node: "decl-sex", values: {"sex": "F"}
2025-09-15 20:24:27.344 wdl.w:ptcp.w:call-trgt-59 INFO visit :: node: "decl-trgt_bed", values: {"trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"}
2025-09-15 20:24:27.344 wdl.w:ptcp.w:call-trgt-59 NOTICE ready :: job: "call-get_reads_overlapping_repeats", callee: "get_reads_overlapping_repeats"
2025-09-15 20:24:27.344 wdl.w:ptcp.w:call-paraphase-53 NOTICE workflow start :: name: "paraphase", source: "./paraphase.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-53"
2025-09-15 20:24:27.344 wdl.w:ptcp.w:call-trgt-59 INFO input :: job: "call-get_reads_overlapping_repeats", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-59/out/m84036_250809_035451_s4.bc2156.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-59/out/m84036_250809_035451_s4.bc2156.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2156"}
2025-09-15 20:24:27.346 wdl.w:ptcp.w:call-trgt-59 NOTICE ready :: job: "call-trgt_genotype", callee: "trgt_genotype"
2025-09-15 20:24:27.346 wdl.w:ptcp.w:call-trgt-59 INFO input :: job: "call-trgt_genotype", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-59/out/m84036_250809_035451_s4.bc2156.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-59/out/m84036_250809_035451_s4.bc2156.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2156"}
2025-09-15 20:24:27.346 wdl.w:ptcp.w:call-sawfish-52.t:call-run_sawfish INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 10, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-52/call-run_sawfish/_singularity_tmpdir_67ogmd2r"
2025-09-15 20:24:27.346 wdl.w:ptcp.w:call-sawfish-52.t:call-run_sawfish INFO Slurm invocation: srun --job-name call-run_sawfish --partition compute,compute9 --cpus-per-task 16 --mem 30518M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-52/call-run_sawfish/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-52/call-run_sawfish/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-52/call-run_sawfish/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-52/call-run_sawfish/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-52/out/m84036_250809_035451_s4.bc2149.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2149.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-52/out/m84036_250809_035451_s4.bc2149.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2149.mapped.bam.bai:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-52/call-run_sawfish/_singularity_tmpdir_67ogmd2r/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-52/call-run_sawfish/_singularity_tmpdir_67ogmd2r/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:27.365 wdl.w:ptcp.w:call-trgt-01.t:call-trgt_plot_motifs_allele.slurm_singularity INFO srun: job 51797647 queued and waiting for resources
2025-09-15 20:24:27.366 wdl.w:ptcp.w:call-trgt-01.t:call-trgt_plot_motifs_allele.slurm_singularity INFO srun: job 51797647 has been allocated resources
2025-09-15 20:24:27.366 wdl.w:ptcp.w:call-trgt-01.t:call-trgt_plot_motifs_allele.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:27.375 wdl.w:ptcp.w:call-paraphase-53 INFO visit :: node: "decl-annotation_vcf", values: {"annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf"}
2025-09-15 20:24:27.376 wdl.w:ptcp.w:call-paraphase-53 INFO visit :: node: "decl-config_file", values: {"config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml"}
2025-09-15 20:24:27.376 wdl.w:ptcp.w:call-paraphase-53 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:24:27.376 wdl.w:ptcp.w:call-paraphase-53 INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:24:27.376 wdl.w:ptcp.w:call-paraphase-53 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-53/out/m84036_250809_035451_s4.bc2150.mapped.bam"}
2025-09-15 20:24:27.376 wdl.w:ptcp.w:call-paraphase-53 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-53/out/m84036_250809_035451_s4.bc2150.mapped.bam.bai"}
2025-09-15 20:24:27.376 wdl.w:ptcp.w:call-paraphase-53 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:24:27.376 wdl.w:ptcp.w:call-paraphase-53 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:24:27.376 wdl.w:ptcp.w:call-paraphase-53 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2150"}
2025-09-15 20:24:27.376 wdl.w:ptcp.w:call-paraphase-53 INFO visit :: node: "decl-sex", values: {"sex": "F"}
2025-09-15 20:24:27.377 wdl.w:ptcp.w:call-paraphase-53 NOTICE ready :: job: "call-run_paraphase", callee: "run_paraphase"
2025-09-15 20:24:27.377 wdl.w:ptcp.w:call-paraphase-53 INFO input :: job: "call-run_paraphase", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf", "genome_version": "38", "config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-53/out/m84036_250809_035451_s4.bc2150.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-53/out/m84036_250809_035451_s4.bc2150.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2150"}
2025-09-15 20:24:27.387 wdl.w:ptcp.w:call-paraphase-52.t:call-run_paraphase INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-52/call-run_paraphase/_singularity_tmpdir_szxedk2a"
2025-09-15 20:24:27.388 wdl.w:ptcp.w:call-paraphase-52.t:call-run_paraphase INFO Slurm invocation: srun --job-name call-run_paraphase --partition compute,compute9 --cpus-per-task 4 --mem 7629M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-52/call-run_paraphase/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-52/call-run_paraphase/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-52/call-run_paraphase/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-52/call-run_paraphase/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-52/out/m84036_250809_035451_s4.bc2149.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2149.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-52/out/m84036_250809_035451_s4.bc2149.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2149.mapped.bam.bai:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/variant_list/variant_list.GRCh38.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf:ro --bind /ptcp/meta/paraphase/paraphase_config.GRCh38.yaml:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/paraphase_config.GRCh38.yaml:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-52/call-run_paraphase/_singularity_tmpdir_szxedk2a/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-52/call-run_paraphase/_singularity_tmpdir_szxedk2a/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:27.418 wdl.w:ptcp.w:call-paraphase-52.t:call-run_paraphase NOTICE slurm_singularity run :: pid: 1201862, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-52/call-run_paraphase/slurm_singularity.log.txt"
2025-09-15 20:24:27.418 wdl.w:ptcp.w:call-sawfish-52.t:call-run_sawfish NOTICE slurm_singularity run :: pid: 1201861, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-52/call-run_sawfish/slurm_singularity.log.txt"
2025-09-15 20:24:27.423 wdl.w:ptcp.w:call-trgt-52.t:call-get_reads_overlapping_repeats INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 9, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-52/call-get_reads_overlapping_repeats/_singularity_tmpdir_wi89qwg9"
2025-09-15 20:24:27.423 wdl.w:ptcp.w:call-trgt-52.t:call-get_reads_overlapping_repeats INFO Slurm invocation: srun --job-name call-get_reads_overlapping_repeats --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-52/call-get_reads_overlapping_repeats/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-52/call-get_reads_overlapping_repeats/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-52/call-get_reads_overlapping_repeats/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-52/call-get_reads_overlapping_repeats/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-52/out/m84036_250809_035451_s4.bc2149.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2149.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-52/out/m84036_250809_035451_s4.bc2149.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2149.mapped.bam.bai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-52/call-get_reads_overlapping_repeats/_singularity_tmpdir_wi89qwg9/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-52/call-get_reads_overlapping_repeats/_singularity_tmpdir_wi89qwg9/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:27.439 wdl.w:ptcp.w:call-trgt-52.t:call-get_reads_overlapping_repeats NOTICE slurm_singularity run :: pid: 1201863, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-52/call-get_reads_overlapping_repeats/slurm_singularity.log.txt"
2025-09-15 20:24:27.461 wdl.w:ptcp.w:call-trgt-16.t:call-trgt_plot_meth_waterfall NOTICE done
2025-09-15 20:24:27.466 wdl.w:ptcp.w:call-trgt-16 NOTICE finish :: job: "call-trgt_plot_meth_waterfall"
2025-09-15 20:24:27.466 wdl.w:ptcp.w:call-trgt-16 INFO output :: job: "call-trgt_plot_meth_waterfall", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-16/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2113.meth_waterfall.trgt_plots.zip"}
2025-09-15 20:24:27.466 wdl.w:ptcp.w:call-trgt-16 INFO visit :: node: "output-images_meth_waterfall", values: {"images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-16/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2113.meth_waterfall.trgt_plots.zip"}
2025-09-15 20:24:27.468 wdl.w:ptcp.w:call-trgt-05.t:call-trgt_plot_meth_waterfall NOTICE done
2025-09-15 20:24:27.472 wdl.w:ptcp.w:call-trgt-05 NOTICE finish :: job: "call-trgt_plot_meth_waterfall"
2025-09-15 20:24:27.472 wdl.w:ptcp.w:call-trgt-05 INFO output :: job: "call-trgt_plot_meth_waterfall", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-05/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2102.meth_waterfall.trgt_plots.zip"}
2025-09-15 20:24:27.473 wdl.w:ptcp.w:call-trgt-05 INFO visit :: node: "output-images_meth_waterfall", values: {"images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-05/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2102.meth_waterfall.trgt_plots.zip"}
2025-09-15 20:24:27.473 wdl.w:ptcp.w:call-trgt-05 INFO visit :: node: "outputs", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-05/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2102.motifs_waterfall.trgt_plots.zip", "images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-05/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2102.meth_allele.trgt_plots.zip", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-05/call-trgt_genotype/out/m84036_250809_035451_s4.bc2102.trgt.sorted.spanning.bam.bai", "images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-05/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2102.motifs_allele.trgt_plots.zip", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-05/call-trgt_genotype/out/m84036_250809_035451_s4.bc2102.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-05/call-trgt_genotype/out/m84036_250809_035451_s4.bc2102.trgt.vcf", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-05/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2102.repeats.bam", "images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-05/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2102.meth_waterfall.trgt_plots.zip", "reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-05/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2102.repeats.bam.bai"}
2025-09-15 20:24:27.473 wdl.w:ptcp.w:call-trgt-52.t:call-trgt_genotype NOTICE task setup :: name: "trgt_genotype", source: "./trgt.wdl", line: 272, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-52/call-trgt_genotype", thread: 140607162938944
2025-09-15 20:24:27.479 wdl.w:ptcp.w:call-paraphase-00.t:call-call_f8 NOTICE task setup :: name: "call_f8", source: "./paraphase.wdl", line: 232, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-00/call-call_f8", thread: 140610879071808
2025-09-15 20:24:27.495 wdl.w:ptcp.w:call-trgt-52.t:call-trgt_genotype INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:27.495 wdl.w:ptcp.w:call-trgt-52.t:call-trgt_genotype INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:27.495 wdl.w:ptcp.w:call-trgt-52.t:call-trgt_genotype INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:27.495 wdl.w:ptcp.w:call-trgt-52.t:call-trgt_genotype INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:27.496 wdl.w:ptcp.w:call-trgt-52.t:call-trgt_genotype INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2149.mapped.bam.bai"
2025-09-15 20:24:27.496 wdl.w:ptcp.w:call-trgt-52.t:call-trgt_genotype INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2149.mapped.bam"
2025-09-15 20:24:27.496 wdl.w:ptcp.w:call-trgt-52.t:call-trgt_genotype INFO input :: name: "sex", value: "F"
2025-09-15 20:24:27.496 wdl.w:ptcp.w:call-trgt-52.t:call-trgt_genotype INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2149"
2025-09-15 20:24:27.496 wdl.w:ptcp.w:call-trgt-52.t:call-trgt_genotype INFO eval :: name: "mem_gb", value: 16
2025-09-15 20:24:27.496 wdl.w:ptcp.w:call-trgt-52.t:call-trgt_genotype INFO eval :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2149.trgt"
2025-09-15 20:24:27.496 wdl.w:ptcp.w:call-trgt-52.t:call-trgt_genotype INFO eval :: name: "threads", value: 8
2025-09-15 20:24:27.497 wdl.w:ptcp.w:call-trgt-52.t:call-trgt_genotype INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:27.497 wdl.w:ptcp.w:call-trgt-52.t:call-trgt_genotype INFO eval :: name: "karyotype", value: "XX"
2025-09-15 20:24:27.497 wdl.w:ptcp.w:call-trgt-52.t:call-trgt_genotype INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 8, memory_reservation: 16000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:27.497 wdl.w:ptcp.w:call-trgt-52.t:call-trgt_genotype WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:27.498 wdl.w:ptcp.w:call-trgt-52.t:call-trgt_genotype INFO provisioned :: seconds_waited: 0, cpu: 8, mem_bytes: 16000000000
2025-09-15 20:24:27.498 wdl.w:ptcp.w:call-trgt-52.t:call-trgt_genotype INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:27.500 wdl.w:ptcp.w:call-paraphase-00.t:call-call_f8 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:27.500 wdl.w:ptcp.w:call-paraphase-00.t:call-call_f8 INFO input :: name: "genome_version", value: "38"
2025-09-15 20:24:27.500 wdl.w:ptcp.w:call-paraphase-00.t:call-call_f8 INFO input :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2097"
2025-09-15 20:24:27.501 wdl.w:ptcp.w:call-paraphase-00.t:call-call_f8 INFO input :: name: "paraphase_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2097.paraphase.bam.bai"
2025-09-15 20:24:27.501 wdl.w:ptcp.w:call-paraphase-00.t:call-call_f8 INFO input :: name: "paraphase_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2097.paraphase.bam"
2025-09-15 20:24:27.501 wdl.w:ptcp.w:call-paraphase-00.t:call-call_f8 INFO input :: name: "sex", value: "F"
2025-09-15 20:24:27.501 wdl.w:ptcp.w:call-paraphase-00.t:call-call_f8 INFO eval :: name: "threads", value: 1
2025-09-15 20:24:27.501 wdl.w:ptcp.w:call-paraphase-00.t:call-call_f8 INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:27.501 wdl.w:ptcp.w:call-paraphase-00.t:call-call_f8 INFO eval :: name: "disk_size", value: 11
2025-09-15 20:24:27.501 wdl.w:ptcp.w:call-paraphase-00.t:call-call_f8 INFO eval :: name: "sample_sex", value: "F"
2025-09-15 20:24:27.502 wdl.w:ptcp.w:call-paraphase-00.t:call-call_f8 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:27.502 wdl.w:ptcp.w:call-paraphase-00.t:call-call_f8 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:27.502 wdl.w:ptcp.w:call-paraphase-00.t:call-call_f8 INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:27.502 wdl.w:ptcp.w:call-paraphase-00.t:call-call_f8 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:27.525 wdl.w:ptcp.w:call-paraphase-30.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for gba for sample m84036_250809_035451_s4.bc2127 at 2025-09-15 20:24:14.682773...
2025-09-15 20:24:27.526 wdl.w:ptcp.w:call-paraphase-30.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for gba for sample m84036_250809_035451_s4.bc2127 at 2025-09-15 20:24:15.141964...
2025-09-15 20:24:27.526 wdl.w:ptcp.w:call-paraphase-30.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for hbb for sample m84036_250809_035451_s4.bc2127 at 2025-09-15 20:24:27.485192...
2025-09-15 20:24:27.526 wdl.w:ptcp.w:call-paraphase-30.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for hbb for sample m84036_250809_035451_s4.bc2127 at 2025-09-15 20:24:27.485387...
2025-09-15 20:24:27.556 wdl.w:ptcp.w:call-trgt-16.t:call-trgt_plot_motifs_waterfall INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2113.motifs_waterfall.trgt_plots.zip"
2025-09-15 20:24:27.557 wdl.w:ptcp.w:call-paraphase-00.t:call-call_f8 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 8, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-00/call-call_f8/_singularity_tmpdir_n5x5nuoy"
2025-09-15 20:24:27.557 wdl.w:ptcp.w:call-paraphase-00.t:call-call_f8 INFO Slurm invocation: srun --job-name call-call_f8 --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-00/call-call_f8/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-00/call-call_f8/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-00/call-call_f8/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-00/call-call_f8/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-00/call-run_paraphase/out/m84036_250809_035451_s4.bc2097_paraphase/m84036_250809_035451_s4.bc2097.paraphase.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2097.paraphase.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-00/call-run_paraphase/out/m84036_250809_035451_s4.bc2097_paraphase/m84036_250809_035451_s4.bc2097.paraphase.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2097.paraphase.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-00/call-call_f8/_singularity_tmpdir_n5x5nuoy/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-00/call-call_f8/_singularity_tmpdir_n5x5nuoy/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:27.567 wdl.w:ptcp.w:call-trgt-01.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO srun: job 51797648 queued and waiting for resources
2025-09-15 20:24:27.567 wdl.w:ptcp.w:call-trgt-01.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO srun: job 51797648 has been allocated resources
2025-09-15 20:24:27.567 wdl.w:ptcp.w:call-trgt-01.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:27.569 wdl.w:ptcp.w:call-paraphase-08.t:call-call_f8.slurm_singularity INFO srun: job 51797649 queued and waiting for resources
2025-09-15 20:24:27.569 wdl.w:ptcp.w:call-paraphase-08.t:call-call_f8.slurm_singularity INFO srun: job 51797649 has been allocated resources
2025-09-15 20:24:27.569 wdl.w:ptcp.w:call-paraphase-08.t:call-call_f8.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:27.586 wdl.w:ptcp.w:call-trgt-52.t:call-trgt_genotype INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 11, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-52/call-trgt_genotype/_singularity_tmpdir__8zf978i"
2025-09-15 20:24:27.586 wdl.w:ptcp.w:call-trgt-52.t:call-trgt_genotype INFO Slurm invocation: srun --job-name call-trgt_genotype --partition compute,compute9 --cpus-per-task 8 --mem 15259M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-52/call-trgt_genotype/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-52/call-trgt_genotype/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-52/call-trgt_genotype/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-52/call-trgt_genotype/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-52/out/m84036_250809_035451_s4.bc2149.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2149.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-52/out/m84036_250809_035451_s4.bc2149.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2149.mapped.bam.bai:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-52/call-trgt_genotype/_singularity_tmpdir__8zf978i/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-52/call-trgt_genotype/_singularity_tmpdir__8zf978i/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:27.586 wdl.w:ptcp.w:call-paraphase-00.t:call-call_f8 NOTICE slurm_singularity run :: pid: 1201883, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-00/call-call_f8/slurm_singularity.log.txt"
2025-09-15 20:24:27.588 wdl.w:ptcp.w:call-trgt-05 NOTICE done
2025-09-15 20:24:27.593 wdl.w:ptcp NOTICE finish :: job: "call-trgt-05"
2025-09-15 20:24:27.594 wdl.w:ptcp INFO output :: job: "call-trgt-05", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-05/out/m84036_250809_035451_s4.bc2102.motifs_waterfall.trgt_plots.zip", "images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-05/out/m84036_250809_035451_s4.bc2102.meth_allele.trgt_plots.zip", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-05/out/m84036_250809_035451_s4.bc2102.trgt.sorted.spanning.bam.bai", "images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-05/out/m84036_250809_035451_s4.bc2102.motifs_allele.trgt_plots.zip", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-05/out/m84036_250809_035451_s4.bc2102.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-05/out/m84036_250809_035451_s4.bc2102.trgt.vcf", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-05/out/m84036_250809_035451_s4.bc2102.repeats.bam", "images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-05/out/m84036_250809_035451_s4.bc2102.meth_waterfall.trgt_plots.zip", "reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-05/out/m84036_250809_035451_s4.bc2102.repeats.bam.bai"}
2025-09-15 20:24:27.604 wdl.w:ptcp.w:call-trgt-44.t:call-get_reads_overlapping_repeats.slurm_singularity INFO srun: job 51797650 queued and waiting for resources
2025-09-15 20:24:27.605 wdl.w:ptcp.w:call-trgt-44.t:call-get_reads_overlapping_repeats.slurm_singularity INFO srun: job 51797650 has been allocated resources
2025-09-15 20:24:27.605 wdl.w:ptcp.w:call-trgt-44.t:call-get_reads_overlapping_repeats.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:27.606 wdl.w:ptcp.w:call-sawfish-53 NOTICE workflow start :: name: "sawfish", source: "./sawfish.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-53"
2025-09-15 20:24:27.608 wdl.w:ptcp.w:call-trgt-52.t:call-trgt_genotype NOTICE slurm_singularity run :: pid: 1201884, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-52/call-trgt_genotype/slurm_singularity.log.txt"
2025-09-15 20:24:27.623 wdl.w:ptcp.w:call-sawfish-53 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:24:27.623 wdl.w:ptcp.w:call-sawfish-53 INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:24:27.623 wdl.w:ptcp.w:call-sawfish-53 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-53/out/m84036_250809_035451_s4.bc2150.mapped.bam"}
2025-09-15 20:24:27.623 wdl.w:ptcp.w:call-sawfish-53 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-53/out/m84036_250809_035451_s4.bc2150.mapped.bam.bai"}
2025-09-15 20:24:27.623 wdl.w:ptcp.w:call-sawfish-53 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:24:27.623 wdl.w:ptcp.w:call-sawfish-53 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:24:27.623 wdl.w:ptcp.w:call-sawfish-53 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2150"}
2025-09-15 20:24:27.624 wdl.w:ptcp.w:call-sawfish-53 NOTICE ready :: job: "call-run_sawfish", callee: "run_sawfish"
2025-09-15 20:24:27.624 wdl.w:ptcp.w:call-sawfish-53 INFO input :: job: "call-run_sawfish", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-53/out/m84036_250809_035451_s4.bc2150.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-53/out/m84036_250809_035451_s4.bc2150.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2150"}
2025-09-15 20:24:27.653 wdl.w:ptcp.w:call-trgt-44.t:call-trgt_genotype.slurm_singularity INFO srun: job 51797651 queued and waiting for resources
2025-09-15 20:24:27.653 wdl.w:ptcp.w:call-trgt-44.t:call-trgt_genotype.slurm_singularity INFO srun: job 51797651 has been allocated resources
2025-09-15 20:24:27.653 wdl.w:ptcp.w:call-trgt-44.t:call-trgt_genotype.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:27.697 wdl.w:ptcp.w:call-trgt-16.t:call-trgt_plot_motifs_waterfall NOTICE done
2025-09-15 20:24:27.713 wdl.w:ptcp.w:call-paraphase-01.t:call-call_f8.slurm_singularity INFO srun: job 51797652 queued and waiting for resources
2025-09-15 20:24:27.713 wdl.w:ptcp.w:call-paraphase-01.t:call-call_f8.slurm_singularity INFO srun: job 51797652 has been allocated resources
2025-09-15 20:24:27.713 wdl.w:ptcp.w:call-paraphase-01.t:call-call_f8.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:27.733 wdl.w:ptcp.w:call-trgt-24.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:23 [ERROR] - No reads found for TRID=PRTS_ARX
2025-09-15 20:24:27.734 wdl.w:ptcp.w:call-trgt-24.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:23 [ERROR] - No reads found for TRID=EIEE1_ARX
2025-09-15 20:24:27.749 wdl.w:ptcp.w:call-trgt-16 NOTICE finish :: job: "call-trgt_plot_motifs_waterfall"
2025-09-15 20:24:27.749 wdl.w:ptcp.w:call-trgt-16 INFO output :: job: "call-trgt_plot_motifs_waterfall", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-16/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2113.motifs_waterfall.trgt_plots.zip"}
2025-09-15 20:24:27.750 wdl.w:ptcp.w:call-trgt-16 INFO visit :: node: "output-images_motifs_waterfall", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-16/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2113.motifs_waterfall.trgt_plots.zip"}
2025-09-15 20:24:27.750 wdl.w:ptcp.w:call-trgt-16 INFO visit :: node: "outputs", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-16/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2113.motifs_waterfall.trgt_plots.zip", "images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-16/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2113.meth_allele.trgt_plots.zip", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-16/call-trgt_genotype/out/m84036_250809_035451_s4.bc2113.trgt.sorted.spanning.bam.bai", "images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-16/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2113.motifs_allele.trgt_plots.zip", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-16/call-trgt_genotype/out/m84036_250809_035451_s4.bc2113.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-16/call-trgt_genotype/out/m84036_250809_035451_s4.bc2113.trgt.vcf", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-16/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2113.repeats.bam", "images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-16/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2113.meth_waterfall.trgt_plots.zip", "reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-16/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2113.repeats.bam.bai"}
2025-09-15 20:24:27.757 wdl.w:ptcp.w:call-paraphase-47.t:call-run_paraphase NOTICE task setup :: name: "run_paraphase", source: "./paraphase.wdl", line: 127, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-47/call-run_paraphase", thread: 140607154546240
2025-09-15 20:24:27.780 wdl.w:ptcp.w:call-trgt-24.t:call-trgt_plot_motifs_waterfall INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2121.motifs_waterfall.trgt_plots.zip"
2025-09-15 20:24:27.784 wdl.w:ptcp.w:call-paraphase-47.t:call-run_paraphase INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:27.784 wdl.w:ptcp.w:call-paraphase-47.t:call-run_paraphase INFO input :: name: "annotation_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf"
2025-09-15 20:24:27.785 wdl.w:ptcp.w:call-paraphase-47.t:call-run_paraphase INFO input :: name: "genome_version", value: "38"
2025-09-15 20:24:27.785 wdl.w:ptcp.w:call-paraphase-47.t:call-run_paraphase INFO input :: name: "config_file", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/paraphase_config.GRCh38.yaml"
2025-09-15 20:24:27.785 wdl.w:ptcp.w:call-paraphase-47.t:call-run_paraphase INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:27.785 wdl.w:ptcp.w:call-paraphase-47.t:call-run_paraphase INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:27.785 wdl.w:ptcp.w:call-paraphase-47.t:call-run_paraphase INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2144.mapped.bam.bai"
2025-09-15 20:24:27.785 wdl.w:ptcp.w:call-paraphase-47.t:call-run_paraphase INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2144.mapped.bam"
2025-09-15 20:24:27.785 wdl.w:ptcp.w:call-paraphase-47.t:call-run_paraphase INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2144"
2025-09-15 20:24:27.785 wdl.w:ptcp.w:call-paraphase-47.t:call-run_paraphase INFO eval :: name: "threads", value: 4
2025-09-15 20:24:27.785 wdl.w:ptcp.w:call-paraphase-47.t:call-run_paraphase INFO eval :: name: "mem_gb", value: 8
2025-09-15 20:24:27.786 wdl.w:ptcp.w:call-paraphase-47.t:call-run_paraphase INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:27.786 wdl.w:ptcp.w:call-paraphase-47.t:call-run_paraphase INFO eval :: name: "out_dir", value: "m84036_250809_035451_s4.bc2144_paraphase"
2025-09-15 20:24:27.787 wdl.w:ptcp.w:call-paraphase-47.t:call-run_paraphase INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 4, memory_reservation: 8000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:27.787 wdl.w:ptcp.w:call-paraphase-47.t:call-run_paraphase WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:27.788 wdl.w:ptcp.w:call-paraphase-47.t:call-run_paraphase INFO provisioned :: seconds_waited: 0, cpu: 4, mem_bytes: 8000000000
2025-09-15 20:24:27.788 wdl.w:ptcp.w:call-paraphase-47.t:call-run_paraphase INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:27.846 wdl.w:ptcp.w:call-trgt-16 NOTICE done
2025-09-15 20:24:27.852 wdl.w:ptcp NOTICE finish :: job: "call-trgt-16"
2025-09-15 20:24:27.852 wdl.w:ptcp INFO output :: job: "call-trgt-16", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-16/out/m84036_250809_035451_s4.bc2113.motifs_waterfall.trgt_plots.zip", "images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-16/out/m84036_250809_035451_s4.bc2113.meth_allele.trgt_plots.zip", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-16/out/m84036_250809_035451_s4.bc2113.trgt.sorted.spanning.bam.bai", "images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-16/out/m84036_250809_035451_s4.bc2113.motifs_allele.trgt_plots.zip", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-16/out/m84036_250809_035451_s4.bc2113.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-16/out/m84036_250809_035451_s4.bc2113.trgt.vcf", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-16/out/m84036_250809_035451_s4.bc2113.repeats.bam", "images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-16/out/m84036_250809_035451_s4.bc2113.meth_waterfall.trgt_plots.zip", "reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-16/out/m84036_250809_035451_s4.bc2113.repeats.bam.bai"}
2025-09-15 20:24:27.852 wdl.w:ptcp.w:call-sawfish-03.t:call-run_sawfish.stderr VERBOSE [M::mm_idx_gen::34.366*1.46] collected minimizers
2025-09-15 20:24:27.860 wdl.w:ptcp.w:call-trgt-53 NOTICE workflow start :: name: "trgt", source: "./trgt.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-53"
2025-09-15 20:24:27.875 wdl.w:ptcp.w:call-trgt-53 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:24:27.875 wdl.w:ptcp.w:call-trgt-53 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-53/out/m84036_250809_035451_s4.bc2150.mapped.bam"}
2025-09-15 20:24:27.876 wdl.w:ptcp.w:call-trgt-53 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-53/out/m84036_250809_035451_s4.bc2150.mapped.bam.bai"}
2025-09-15 20:24:27.876 wdl.w:ptcp.w:call-trgt-53 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:24:27.876 wdl.w:ptcp.w:call-trgt-53 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:24:27.876 wdl.w:ptcp.w:call-trgt-53 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2150"}
2025-09-15 20:24:27.876 wdl.w:ptcp.w:call-paraphase-47.t:call-run_paraphase INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-47/call-run_paraphase/_singularity_tmpdir_29m0fiyh"
2025-09-15 20:24:27.876 wdl.w:ptcp.w:call-trgt-53 INFO visit :: node: "decl-sex", values: {"sex": "F"}
2025-09-15 20:24:27.876 wdl.w:ptcp.w:call-paraphase-47.t:call-run_paraphase INFO Slurm invocation: srun --job-name call-run_paraphase --partition compute,compute9 --cpus-per-task 4 --mem 7629M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-47/call-run_paraphase/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-47/call-run_paraphase/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-47/call-run_paraphase/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-47/call-run_paraphase/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-47/out/m84036_250809_035451_s4.bc2144.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2144.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-47/out/m84036_250809_035451_s4.bc2144.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2144.mapped.bam:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/variant_list/variant_list.GRCh38.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf:ro --bind /ptcp/meta/paraphase/paraphase_config.GRCh38.yaml:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/paraphase_config.GRCh38.yaml:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-47/call-run_paraphase/_singularity_tmpdir_29m0fiyh/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-47/call-run_paraphase/_singularity_tmpdir_29m0fiyh/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:27.877 wdl.w:ptcp.w:call-trgt-53 INFO visit :: node: "decl-trgt_bed", values: {"trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"}
2025-09-15 20:24:27.877 wdl.w:ptcp.w:call-trgt-53 NOTICE ready :: job: "call-get_reads_overlapping_repeats", callee: "get_reads_overlapping_repeats"
2025-09-15 20:24:27.879 wdl.w:ptcp.w:call-trgt-53 INFO input :: job: "call-get_reads_overlapping_repeats", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-53/out/m84036_250809_035451_s4.bc2150.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-53/out/m84036_250809_035451_s4.bc2150.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2150"}
2025-09-15 20:24:27.880 wdl.w:ptcp.w:call-trgt-53 NOTICE ready :: job: "call-trgt_genotype", callee: "trgt_genotype"
2025-09-15 20:24:27.880 wdl.w:ptcp.w:call-trgt-53 INFO input :: job: "call-trgt_genotype", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-53/out/m84036_250809_035451_s4.bc2150.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-53/out/m84036_250809_035451_s4.bc2150.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2150"}
2025-09-15 20:24:27.881 wdl.w:ptcp.w:call-trgt-09.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:24 [ERROR] - No reads found for TRID=PRTS_ARX
2025-09-15 20:24:27.881 wdl.w:ptcp.w:call-trgt-09.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:24 [ERROR] - No reads found for TRID=EIEE1_ARX
2025-09-15 20:24:27.913 wdl.w:ptcp.w:call-paraphase-47.t:call-run_paraphase NOTICE slurm_singularity run :: pid: 1201898, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-47/call-run_paraphase/slurm_singularity.log.txt"
2025-09-15 20:24:27.923 wdl.w:ptcp.w:call-trgt-24.t:call-trgt_plot_motifs_waterfall NOTICE done
2025-09-15 20:24:27.931 wdl.w:ptcp.w:call-trgt-24 NOTICE finish :: job: "call-trgt_plot_motifs_waterfall"
2025-09-15 20:24:27.932 wdl.w:ptcp.w:call-trgt-24 INFO output :: job: "call-trgt_plot_motifs_waterfall", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-24/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2121.motifs_waterfall.trgt_plots.zip"}
2025-09-15 20:24:27.932 wdl.w:ptcp.w:call-trgt-24 INFO visit :: node: "output-images_motifs_waterfall", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-24/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2121.motifs_waterfall.trgt_plots.zip"}
2025-09-15 20:24:27.932 wdl.w:ptcp.w:call-trgt-24 INFO visit :: node: "outputs", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-24/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2121.motifs_waterfall.trgt_plots.zip", "images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-24/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2121.meth_allele.trgt_plots.zip", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-24/call-trgt_genotype/out/m84036_250809_035451_s4.bc2121.trgt.sorted.spanning.bam.bai", "images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-24/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2121.motifs_allele.trgt_plots.zip", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-24/call-trgt_genotype/out/m84036_250809_035451_s4.bc2121.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-24/call-trgt_genotype/out/m84036_250809_035451_s4.bc2121.trgt.vcf", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-24/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2121.repeats.bam", "images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-24/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2121.meth_waterfall.trgt_plots.zip", "reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-24/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2121.repeats.bam.bai"}
2025-09-15 20:24:27.940 wdl.w:ptcp.w:call-trgt-09.t:call-trgt_plot_motifs_waterfall INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2106.motifs_waterfall.trgt_plots.zip"
2025-09-15 20:24:27.941 wdl.w:ptcp.w:call-sawfish-47.t:call-run_sawfish NOTICE task setup :: name: "run_sawfish", source: "./sawfish.wdl", line: 83, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-47/call-run_sawfish", thread: 140607699809856
2025-09-15 20:24:27.960 wdl.w:ptcp.w:call-sawfish-47.t:call-run_sawfish INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:27.960 wdl.w:ptcp.w:call-sawfish-47.t:call-run_sawfish INFO input :: name: "genome_version", value: "38"
2025-09-15 20:24:27.960 wdl.w:ptcp.w:call-sawfish-47.t:call-run_sawfish INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:27.960 wdl.w:ptcp.w:call-sawfish-47.t:call-run_sawfish INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:27.960 wdl.w:ptcp.w:call-sawfish-47.t:call-run_sawfish INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2144.mapped.bam.bai"
2025-09-15 20:24:27.960 wdl.w:ptcp.w:call-sawfish-47.t:call-run_sawfish INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2144.mapped.bam"
2025-09-15 20:24:27.960 wdl.w:ptcp.w:call-sawfish-47.t:call-run_sawfish INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2144"
2025-09-15 20:24:27.960 wdl.w:ptcp.w:call-sawfish-47.t:call-run_sawfish INFO eval :: name: "mem_gb", value: 32
2025-09-15 20:24:27.960 wdl.w:ptcp.w:call-sawfish-47.t:call-run_sawfish INFO eval :: name: "threads", value: 16
2025-09-15 20:24:27.961 wdl.w:ptcp.w:call-sawfish-47.t:call-run_sawfish INFO eval :: name: "disk_size", value: 30
2025-09-15 20:24:27.961 wdl.w:ptcp.w:call-sawfish-47.t:call-run_sawfish INFO eval :: name: "discover_dirname", value: "m84036_250809_035451_s4.bc2144_sawfish_discover"
2025-09-15 20:24:27.961 wdl.w:ptcp.w:call-sawfish-47.t:call-run_sawfish INFO eval :: name: "call_dirname", value: "m84036_250809_035451_s4.bc2144_sawfish"
2025-09-15 20:24:27.961 wdl.w:ptcp.w:call-sawfish-47.t:call-run_sawfish INFO eval :: name: "minimap2_bam_filename", value: "m84036_250809_035451_s4.bc2144.minimap2.bam"
2025-09-15 20:24:27.961 wdl.w:ptcp.w:call-sawfish-47.t:call-run_sawfish INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 16, memory_reservation: 32000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:27.962 wdl.w:ptcp.w:call-sawfish-47.t:call-run_sawfish WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:27.962 wdl.w:ptcp.w:call-sawfish-47.t:call-run_sawfish INFO provisioned :: seconds_waited: 0, cpu: 16, mem_bytes: 32000000000
2025-09-15 20:24:27.962 wdl.w:ptcp.w:call-sawfish-47.t:call-run_sawfish INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:28.002 wdl.w:ptcp.w:call-sawfish-08.t:call-run_sawfish.stderr VERBOSE [M::mm_idx_gen::34.339*1.46] collected minimizers
2025-09-15 20:24:28.005 wdl.w:ptcp.w:call-sawfish-23.t:call-run_sawfish.stderr VERBOSE [M::mm_idx_gen::50.950*1.65] collected minimizers
2025-09-15 20:24:28.006 wdl.w:ptcp.w:call-sawfish-23.t:call-run_sawfish.stderr VERBOSE [M::mm_idx_gen::61.219*1.86] sorted minimizers
2025-09-15 20:24:28.007 wdl.w:ptcp.w:call-sawfish-23.t:call-run_sawfish.stderr VERBOSE [M::main::61.221*1.86] loaded/built the index for 195 target sequence(s)
2025-09-15 20:24:28.007 wdl.w:ptcp.w:call-sawfish-23.t:call-run_sawfish.stderr VERBOSE [M::mm_mapopt_update::66.862*1.79] mid_occ = 136
2025-09-15 20:24:28.007 wdl.w:ptcp.w:call-sawfish-23.t:call-run_sawfish.stderr VERBOSE [M::mm_idx_stat] kmer size: 19; skip: 19; is_hpc: 0; #seq: 195
2025-09-15 20:24:28.007 wdl.w:ptcp.w:call-sawfish-23.t:call-run_sawfish.stderr VERBOSE [M::mm_idx_stat::71.162*1.74] distinct minimizers: 214664461 (92.23% are singletons); average occurrences: 1.372; average spacing: 10.529; total length: 3099922541
2025-09-15 20:24:28.007 wdl.w:ptcp.w:call-sawfish-23.t:call-run_sawfish.stderr VERBOSE [M::bam2fq_mainloop] discarded 0 singletons
2025-09-15 20:24:28.007 wdl.w:ptcp.w:call-sawfish-23.t:call-run_sawfish.stderr VERBOSE [M::bam2fq_mainloop] processed 263 reads
2025-09-15 20:24:28.007 wdl.w:ptcp.w:call-sawfish-23.t:call-run_sawfish.stderr VERBOSE [M::worker_pipeline::71.668*1.74] mapped 263 sequences
2025-09-15 20:24:28.007 wdl.w:ptcp.w:call-sawfish-23.t:call-run_sawfish.stderr VERBOSE [M::main] Version: 2.26-r1175
2025-09-15 20:24:28.007 wdl.w:ptcp.w:call-sawfish-23.t:call-run_sawfish.stderr VERBOSE [M::main] CMD: /opt/pacbio/smrttools/install/smrtlink-release_25.1.0.257715/bundles/smrttools/install/smrttools-release_25.1.0.257715/private/thirdparty/minimap2/minimap2_2.26-pacbio2/binwrap/../../../../../private/thirdparty/minimap2/minimap2_2.26-pacbio2/bin/minimap2 -a -y -x map-hifi -Y -E 1,0 /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa -
2025-09-15 20:24:28.007 wdl.w:ptcp.w:call-sawfish-23.t:call-run_sawfish.stderr VERBOSE [M::main] Real time: 71.963 sec; CPU: 125.282 sec; Peak RSS: 11.886 GB
2025-09-15 20:24:28.007 wdl.w:ptcp.w:call-sawfish-23.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:14][sawfish][INFO] Starting sawfish 2.0.3
2025-09-15 20:24:28.007 wdl.w:ptcp.w:call-sawfish-23.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:14][sawfish][INFO] cmdline: sawfish discover --disable-cnv --threads 16 --ref /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa --bam m84036_250809_035451_s4.bc2120.minimap2.bam --output-dir m84036_250809_035451_s4.bc2120_sawfish_discover
2025-09-15 20:24:28.007 wdl.w:ptcp.w:call-sawfish-23.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:14][sawfish][INFO] Running on 16 threads
2025-09-15 20:24:28.007 wdl.w:ptcp.w:call-sawfish-23.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:14][sawfish][INFO] Writing discover settings to file: 'm84036_250809_035451_s4.bc2120_sawfish_discover/discover.settings.json'
2025-09-15 20:24:28.007 wdl.w:ptcp.w:call-sawfish-23.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:14][sawfish][INFO] Reading reference genome from file '/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa'
2025-09-15 20:24:28.007 wdl.w:ptcp.w:call-sawfish-23.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:20][sawfish][INFO] Processing alignment file '/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2120.minimap2.bam'
2025-09-15 20:24:28.007 wdl.w:ptcp.w:call-sawfish-23.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:20][sawfish][INFO] Finished processing all alignments
2025-09-15 20:24:28.007 wdl.w:ptcp.w:call-sawfish-23.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:20][sawfish][INFO] Writing depth bins to binary file: 'm84036_250809_035451_s4.bc2120_sawfish_discover/depth.mpack'
2025-09-15 20:24:28.008 wdl.w:ptcp.w:call-sawfish-23.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:20][sawfish][INFO] Writing max sv depth genome regions to bed file: 'm84036_250809_035451_s4.bc2120_sawfish_discover/max.depth.bed'
2025-09-15 20:24:28.008 wdl.w:ptcp.w:call-sawfish-23.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:20][sawfish][INFO] Completing breakpoint observation clustering
2025-09-15 20:24:28.008 wdl.w:ptcp.w:call-sawfish-23.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:20][sawfish][INFO] Finished breakpoint observation clustering
2025-09-15 20:24:28.008 wdl.w:ptcp.w:call-sawfish-23.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:20][sawfish][INFO] Consolidating adjacent indel candidates
2025-09-15 20:24:28.008 wdl.w:ptcp.w:call-sawfish-23.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:20][sawfish][INFO] Finding large insertion candidates
2025-09-15 20:24:28.008 wdl.w:ptcp.w:call-sawfish-23.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:20][sawfish][INFO] Writing breakpoint_cluster debug bed file: 'm84036_250809_035451_s4.bc2120_sawfish_discover/debug.breakpoint_clusters.bed'
2025-09-15 20:24:28.008 wdl.w:ptcp.w:call-sawfish-23.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:20][sawfish][INFO] Refining SV Candidates
2025-09-15 20:24:28.008 wdl.w:ptcp.w:call-sawfish-23.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:20][sawfish][INFO] Writing debug assembly region bed file: 'm84036_250809_035451_s4.bc2120_sawfish_discover/assembly.regions.bed'
2025-09-15 20:24:28.008 wdl.w:ptcp.w:call-sawfish-23.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:20][sawfish][INFO] Starting refinement of breakpoint evidence clusters
2025-09-15 20:24:28.008 wdl.w:ptcp.w:call-sawfish-23.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:21][sawfish][INFO] Finished refining all breakpoint evidence clusters
2025-09-15 20:24:28.009 wdl.w:ptcp.w:call-sawfish-23.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:21][sawfish][INFO] Writing all contig alignments to bam file: 'm84036_250809_035451_s4.bc2120_sawfish_discover/contig.alignment.bam'
2025-09-15 20:24:28.009 wdl.w:ptcp.w:call-sawfish-23.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:21][sawfish][INFO] Writing candidate structural variants to file: 'm84036_250809_035451_s4.bc2120_sawfish_discover/candidate.sv.bcf'
2025-09-15 20:24:28.009 wdl.w:ptcp.w:call-sawfish-23.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:21][sawfish][INFO] Writing run statistics to file: 'm84036_250809_035451_s4.bc2120_sawfish_discover/run.stats.json'
2025-09-15 20:24:28.009 wdl.w:ptcp.w:call-sawfish-23.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:22][sawfish][INFO] sawfish completed. Total Runtime: 00:00:07.906
2025-09-15 20:24:28.021 wdl.w:ptcp.w:call-trgt-32.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:26 [ERROR] - No reads found for TRID=PRTS_ARX
2025-09-15 20:24:28.021 wdl.w:ptcp.w:call-trgt-32.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:26 [ERROR] - No reads found for TRID=EIEE1_ARX
2025-09-15 20:24:28.064 wdl.w:ptcp.w:call-trgt-24 NOTICE done
2025-09-15 20:24:28.064 wdl.w:ptcp.w:call-sawfish-47.t:call-run_sawfish INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 10, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-47/call-run_sawfish/_singularity_tmpdir_90cu6yec"
2025-09-15 20:24:28.065 wdl.w:ptcp.w:call-sawfish-47.t:call-run_sawfish INFO Slurm invocation: srun --job-name call-run_sawfish --partition compute,compute9 --cpus-per-task 16 --mem 30518M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-47/call-run_sawfish/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-47/call-run_sawfish/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-47/call-run_sawfish/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-47/call-run_sawfish/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-47/out/m84036_250809_035451_s4.bc2144.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2144.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-47/out/m84036_250809_035451_s4.bc2144.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2144.mapped.bam:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-47/call-run_sawfish/_singularity_tmpdir_90cu6yec/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-47/call-run_sawfish/_singularity_tmpdir_90cu6yec/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:28.068 wdl.w:ptcp NOTICE finish :: job: "call-trgt-24"
2025-09-15 20:24:28.068 wdl.w:ptcp INFO output :: job: "call-trgt-24", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-24/out/m84036_250809_035451_s4.bc2121.motifs_waterfall.trgt_plots.zip", "images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-24/out/m84036_250809_035451_s4.bc2121.meth_allele.trgt_plots.zip", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-24/out/m84036_250809_035451_s4.bc2121.trgt.sorted.spanning.bam.bai", "images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-24/out/m84036_250809_035451_s4.bc2121.motifs_allele.trgt_plots.zip", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-24/out/m84036_250809_035451_s4.bc2121.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-24/out/m84036_250809_035451_s4.bc2121.trgt.vcf", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-24/out/m84036_250809_035451_s4.bc2121.repeats.bam", "images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-24/out/m84036_250809_035451_s4.bc2121.meth_waterfall.trgt_plots.zip", "reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-24/out/m84036_250809_035451_s4.bc2121.repeats.bam.bai"}
2025-09-15 20:24:28.077 wdl.w:ptcp.w:call-paraphase-56 NOTICE workflow start :: name: "paraphase", source: "./paraphase.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-56"
2025-09-15 20:24:28.095 wdl.w:ptcp.w:call-sawfish-47.t:call-run_sawfish NOTICE slurm_singularity run :: pid: 1201901, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-47/call-run_sawfish/slurm_singularity.log.txt"
2025-09-15 20:24:28.099 wdl.w:ptcp.w:call-paraphase-56 INFO visit :: node: "decl-annotation_vcf", values: {"annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf"}
2025-09-15 20:24:28.099 wdl.w:ptcp.w:call-paraphase-56 INFO visit :: node: "decl-config_file", values: {"config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml"}
2025-09-15 20:24:28.099 wdl.w:ptcp.w:call-paraphase-56 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:24:28.099 wdl.w:ptcp.w:call-paraphase-56 INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:24:28.100 wdl.w:ptcp.w:call-paraphase-56 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-56/out/m84036_250809_035451_s4.bc2153.mapped.bam"}
2025-09-15 20:24:28.100 wdl.w:ptcp.w:call-paraphase-56 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-56/out/m84036_250809_035451_s4.bc2153.mapped.bam.bai"}
2025-09-15 20:24:28.100 wdl.w:ptcp.w:call-paraphase-56 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:24:28.100 wdl.w:ptcp.w:call-paraphase-56 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:24:28.100 wdl.w:ptcp.w:call-paraphase-56 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2153"}
2025-09-15 20:24:28.100 wdl.w:ptcp.w:call-paraphase-56 INFO visit :: node: "decl-sex", values: {"sex": "F"}
2025-09-15 20:24:28.100 wdl.w:ptcp.w:call-paraphase-56 NOTICE ready :: job: "call-run_paraphase", callee: "run_paraphase"
2025-09-15 20:24:28.100 wdl.w:ptcp.w:call-paraphase-56 INFO input :: job: "call-run_paraphase", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf", "genome_version": "38", "config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-56/out/m84036_250809_035451_s4.bc2153.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-56/out/m84036_250809_035451_s4.bc2153.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2153"}
2025-09-15 20:24:28.127 wdl.w:ptcp.w:call-trgt-09.t:call-trgt_plot_motifs_waterfall NOTICE done
2025-09-15 20:24:28.134 wdl.w:ptcp.w:call-trgt-09 NOTICE finish :: job: "call-trgt_plot_motifs_waterfall"
2025-09-15 20:24:28.134 wdl.w:ptcp.w:call-trgt-09 INFO output :: job: "call-trgt_plot_motifs_waterfall", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-09/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2106.motifs_waterfall.trgt_plots.zip"}
2025-09-15 20:24:28.134 wdl.w:ptcp.w:call-trgt-09 INFO visit :: node: "output-images_motifs_waterfall", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-09/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2106.motifs_waterfall.trgt_plots.zip"}
2025-09-15 20:24:28.142 wdl.w:ptcp.w:call-trgt-47.t:call-get_reads_overlapping_repeats NOTICE task setup :: name: "get_reads_overlapping_repeats", source: "./trgt.wdl", line: 182, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-47/call-get_reads_overlapping_repeats", thread: 140609822115392
2025-09-15 20:24:28.164 wdl.w:ptcp.w:call-trgt-47.t:call-get_reads_overlapping_repeats INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:28.164 wdl.w:ptcp.w:call-trgt-47.t:call-get_reads_overlapping_repeats INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:28.164 wdl.w:ptcp.w:call-trgt-47.t:call-get_reads_overlapping_repeats INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2144.mapped.bam.bai"
2025-09-15 20:24:28.164 wdl.w:ptcp.w:call-trgt-47.t:call-get_reads_overlapping_repeats INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2144.mapped.bam"
2025-09-15 20:24:28.164 wdl.w:ptcp.w:call-trgt-47.t:call-get_reads_overlapping_repeats INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2144"
2025-09-15 20:24:28.164 wdl.w:ptcp.w:call-trgt-47.t:call-get_reads_overlapping_repeats INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:28.165 wdl.w:ptcp.w:call-trgt-47.t:call-get_reads_overlapping_repeats INFO eval :: name: "expand_size", value: 3000
2025-09-15 20:24:28.165 wdl.w:ptcp.w:call-trgt-47.t:call-get_reads_overlapping_repeats INFO eval :: name: "threads", value: 1
2025-09-15 20:24:28.165 wdl.w:ptcp.w:call-trgt-47.t:call-get_reads_overlapping_repeats INFO eval :: name: "expanded_bed_name", value: "m84036_250809_035451_s4.bc2144.expanded.bed"
2025-09-15 20:24:28.165 wdl.w:ptcp.w:call-trgt-47.t:call-get_reads_overlapping_repeats INFO eval :: name: "disk_size", value: 11
2025-09-15 20:24:28.165 wdl.w:ptcp.w:call-trgt-47.t:call-get_reads_overlapping_repeats INFO eval :: name: "output_name", value: "m84036_250809_035451_s4.bc2144.repeats.bam"
2025-09-15 20:24:28.165 wdl.w:ptcp.w:call-trgt-47.t:call-get_reads_overlapping_repeats INFO eval :: name: "index_name", value: "m84036_250809_035451_s4.bc2144.repeats.bam.bai"
2025-09-15 20:24:28.165 wdl.w:ptcp.w:call-trgt-47.t:call-get_reads_overlapping_repeats INFO eval :: name: "output_name_with_index", value: "m84036_250809_035451_s4.bc2144.repeats.bam##idx##m84036_250809_035451_s4.bc2144.repeats.bam.bai"
2025-09-15 20:24:28.165 wdl.w:ptcp.w:call-trgt-47.t:call-get_reads_overlapping_repeats INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:28.166 wdl.w:ptcp.w:call-trgt-47.t:call-get_reads_overlapping_repeats WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:28.166 wdl.w:ptcp.w:call-trgt-47.t:call-get_reads_overlapping_repeats INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:28.166 wdl.w:ptcp.w:call-trgt-47.t:call-get_reads_overlapping_repeats INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:28.235 wdl.w:ptcp.w:call-trgt-47.t:call-get_reads_overlapping_repeats INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 9, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-47/call-get_reads_overlapping_repeats/_singularity_tmpdir_dwf79c87"
2025-09-15 20:24:28.235 wdl.w:ptcp.w:call-trgt-47.t:call-get_reads_overlapping_repeats INFO Slurm invocation: srun --job-name call-get_reads_overlapping_repeats --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-47/call-get_reads_overlapping_repeats/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-47/call-get_reads_overlapping_repeats/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-47/call-get_reads_overlapping_repeats/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-47/call-get_reads_overlapping_repeats/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-47/out/m84036_250809_035451_s4.bc2144.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2144.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-47/out/m84036_250809_035451_s4.bc2144.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2144.mapped.bam:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-47/call-get_reads_overlapping_repeats/_singularity_tmpdir_dwf79c87/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-47/call-get_reads_overlapping_repeats/_singularity_tmpdir_dwf79c87/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:28.252 wdl.w:ptcp.w:call-trgt-47.t:call-get_reads_overlapping_repeats NOTICE slurm_singularity run :: pid: 1201914, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-47/call-get_reads_overlapping_repeats/slurm_singularity.log.txt"
2025-09-15 20:24:28.256 wdl.w:ptcp.w:call-paraphase-08.t:call-call_f8 INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2105.f8inversion.vcf"
2025-09-15 20:24:28.260 wdl.w:ptcp.w:call-paraphase-08.t:call-call_f8 INFO output :: name: "json", value: "m84036_250809_035451_s4.bc2105.f8inversion.json"
2025-09-15 20:24:28.336 wdl.w:ptcp.w:call-paraphase-08.t:call-call_f8 NOTICE done
2025-09-15 20:24:28.343 wdl.w:ptcp.w:call-paraphase-08 NOTICE finish :: job: "call-call_f8"
2025-09-15 20:24:28.343 wdl.w:ptcp.w:call-paraphase-08 INFO output :: job: "call-call_f8", values: {"json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-08/call-call_f8/out/m84036_250809_035451_s4.bc2105.f8inversion.json", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-08/call-call_f8/out/m84036_250809_035451_s4.bc2105.f8inversion.vcf"}
2025-09-15 20:24:28.344 wdl.w:ptcp.w:call-paraphase-08 INFO visit :: node: "output-f8_json", values: {"f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-08/call-call_f8/out/m84036_250809_035451_s4.bc2105.f8inversion.json"}
2025-09-15 20:24:28.344 wdl.w:ptcp.w:call-paraphase-08 INFO visit :: node: "output-f8_vcf", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-08/call-call_f8/out/m84036_250809_035451_s4.bc2105.f8inversion.vcf"}
2025-09-15 20:24:28.344 wdl.w:ptcp.w:call-paraphase-08 INFO visit :: node: "outputs", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-08/call-call_f8/out/m84036_250809_035451_s4.bc2105.f8inversion.vcf", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-08/call-run_paraphase/out/m84036_250809_035451_s4.bc2105_paraphase/m84036_250809_035451_s4.bc2105.paraphase.json", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-08/call-run_paraphase/out/m84036_250809_035451_s4.bc2105_paraphase/m84036_250809_035451_s4.bc2105.paraphase.bam", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-08/call-run_paraphase/out/m84036_250809_035451_s4.bc2105_paraphase/m84036_250809_035451_s4.bc2105.paraphase.bam.bai", "paraphase_vcfs": [], "havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-08/call-run_paraphase/out/m84036_250809_035451_s4.bc2105.havanno.json", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-08/call-call_f8/out/m84036_250809_035451_s4.bc2105.f8inversion.json"}
2025-09-15 20:24:28.351 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_genotype NOTICE task setup :: name: "trgt_genotype", source: "./trgt.wdl", line: 272, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-47/call-trgt_genotype", thread: 140610367379008
2025-09-15 20:24:28.369 wdl.w:ptcp.w:call-trgt-25.t:call-trgt_plot_motifs_allele INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2122.motifs_allele.trgt_plots.zip"
2025-09-15 20:24:28.374 wdl.w:ptcp.w:call-paraphase-10.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for f8inv1 for sample m84036_250809_035451_s4.bc2107 at 2025-09-15 20:24:20.375679...
2025-09-15 20:24:28.377 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_genotype INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:28.377 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_genotype INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:28.377 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_genotype INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:28.377 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_genotype INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:28.377 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_genotype INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2144.mapped.bam.bai"
2025-09-15 20:24:28.377 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_genotype INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2144.mapped.bam"
2025-09-15 20:24:28.377 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_genotype INFO input :: name: "sex", value: "F"
2025-09-15 20:24:28.377 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_genotype INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2144"
2025-09-15 20:24:28.377 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_genotype INFO eval :: name: "mem_gb", value: 16
2025-09-15 20:24:28.377 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_genotype INFO eval :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2144.trgt"
2025-09-15 20:24:28.378 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_genotype INFO eval :: name: "threads", value: 8
2025-09-15 20:24:28.378 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_genotype INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:28.378 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_genotype INFO eval :: name: "karyotype", value: "XX"
2025-09-15 20:24:28.378 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_genotype INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 8, memory_reservation: 16000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:28.378 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_genotype WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:28.379 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_genotype INFO provisioned :: seconds_waited: 0, cpu: 8, mem_bytes: 16000000000
2025-09-15 20:24:28.379 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_genotype INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:28.413 wdl.w:ptcp.w:call-paraphase-01.t:call-call_f8 INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2098.f8inversion.vcf"
2025-09-15 20:24:28.419 wdl.w:ptcp.w:call-paraphase-01.t:call-call_f8 INFO output :: name: "json", value: "m84036_250809_035451_s4.bc2098.f8inversion.json"
2025-09-15 20:24:28.423 wdl.w:ptcp.w:call-sawfish-52.t:call-run_sawfish.stderr VERBOSE [M::bam2fq_mainloop] discarded 0 singletons
2025-09-15 20:24:28.423 wdl.w:ptcp.w:call-sawfish-52.t:call-run_sawfish.stderr VERBOSE [M::bam2fq_mainloop] processed 0 reads
2025-09-15 20:24:28.438 wdl.w:ptcp.w:call-paraphase-52.t:call-run_paraphase.slurm_singularity INFO srun: job 51797653 queued and waiting for resources
2025-09-15 20:24:28.438 wdl.w:ptcp.w:call-paraphase-52.t:call-run_paraphase.slurm_singularity INFO srun: job 51797653 has been allocated resources
2025-09-15 20:24:28.438 wdl.w:ptcp.w:call-paraphase-52.t:call-run_paraphase.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:28.439 wdl.w:ptcp.w:call-sawfish-52.t:call-run_sawfish.slurm_singularity INFO srun: job 51797654 queued and waiting for resources
2025-09-15 20:24:28.439 wdl.w:ptcp.w:call-sawfish-52.t:call-run_sawfish.slurm_singularity INFO srun: job 51797654 has been allocated resources
2025-09-15 20:24:28.439 wdl.w:ptcp.w:call-sawfish-52.t:call-run_sawfish.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:28.457 wdl.w:ptcp.w:call-trgt-52.t:call-get_reads_overlapping_repeats.slurm_singularity INFO srun: job 51797655 queued and waiting for resources
2025-09-15 20:24:28.457 wdl.w:ptcp.w:call-trgt-52.t:call-get_reads_overlapping_repeats.slurm_singularity INFO srun: job 51797655 has been allocated resources
2025-09-15 20:24:28.457 wdl.w:ptcp.w:call-trgt-52.t:call-get_reads_overlapping_repeats.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:28.465 wdl.w:ptcp.w:call-paraphase-08 NOTICE done
2025-09-15 20:24:28.475 wdl.w:ptcp NOTICE finish :: job: "call-paraphase-08"
2025-09-15 20:24:28.475 wdl.w:ptcp INFO output :: job: "call-paraphase-08", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-08/out/m84036_250809_035451_s4.bc2105.f8inversion.vcf", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-08/out/m84036_250809_035451_s4.bc2105_paraphase/m84036_250809_035451_s4.bc2105.paraphase.json", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-08/out/m84036_250809_035451_s4.bc2105_paraphase/m84036_250809_035451_s4.bc2105.paraphase.bam", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-08/out/m84036_250809_035451_s4.bc2105_paraphase/m84036_250809_035451_s4.bc2105.paraphase.bam.bai", "paraphase_vcfs": [], "havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-08/out/m84036_250809_035451_s4.bc2105.havanno.json", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-08/out/m84036_250809_035451_s4.bc2105.f8inversion.json"}
2025-09-15 20:24:28.486 wdl.w:ptcp.w:call-sawfish-56 NOTICE workflow start :: name: "sawfish", source: "./sawfish.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-56"
2025-09-15 20:24:28.503 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_plot_motifs_allele INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2100.motifs_allele.trgt_plots.zip"
2025-09-15 20:24:28.507 wdl.w:ptcp.w:call-sawfish-56 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:24:28.507 wdl.w:ptcp.w:call-sawfish-56 INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:24:28.507 wdl.w:ptcp.w:call-sawfish-56 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-56/out/m84036_250809_035451_s4.bc2153.mapped.bam"}
2025-09-15 20:24:28.507 wdl.w:ptcp.w:call-sawfish-56 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-56/out/m84036_250809_035451_s4.bc2153.mapped.bam.bai"}
2025-09-15 20:24:28.508 wdl.w:ptcp.w:call-sawfish-56 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:24:28.508 wdl.w:ptcp.w:call-sawfish-56 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:24:28.508 wdl.w:ptcp.w:call-sawfish-56 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2153"}
2025-09-15 20:24:28.508 wdl.w:ptcp.w:call-sawfish-56 NOTICE ready :: job: "call-run_sawfish", callee: "run_sawfish"
2025-09-15 20:24:28.508 wdl.w:ptcp.w:call-sawfish-56 INFO input :: job: "call-run_sawfish", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-56/out/m84036_250809_035451_s4.bc2153.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-56/out/m84036_250809_035451_s4.bc2153.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2153"}
2025-09-15 20:24:28.516 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_genotype INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 11, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-47/call-trgt_genotype/_singularity_tmpdir_9nlxkg3r"
2025-09-15 20:24:28.516 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_genotype INFO Slurm invocation: srun --job-name call-trgt_genotype --partition compute,compute9 --cpus-per-task 8 --mem 15259M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-47/call-trgt_genotype/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-47/call-trgt_genotype/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-47/call-trgt_genotype/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-47/call-trgt_genotype/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-47/out/m84036_250809_035451_s4.bc2144.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2144.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-47/out/m84036_250809_035451_s4.bc2144.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2144.mapped.bam:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-47/call-trgt_genotype/_singularity_tmpdir_9nlxkg3r/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-47/call-trgt_genotype/_singularity_tmpdir_9nlxkg3r/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:28.522 wdl.w:ptcp.w:call-trgt-32.t:call-trgt_plot_motifs_allele INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2129.motifs_allele.trgt_plots.zip"
2025-09-15 20:24:28.543 wdl.w:ptcp.w:call-paraphase-01.t:call-call_f8 NOTICE done
2025-09-15 20:24:28.547 wdl.w:ptcp.w:call-paraphase-01 NOTICE finish :: job: "call-call_f8"
2025-09-15 20:24:28.547 wdl.w:ptcp.w:call-paraphase-01 INFO output :: job: "call-call_f8", values: {"json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-01/call-call_f8/out/m84036_250809_035451_s4.bc2098.f8inversion.json", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-01/call-call_f8/out/m84036_250809_035451_s4.bc2098.f8inversion.vcf"}
2025-09-15 20:24:28.547 wdl.w:ptcp.w:call-paraphase-01 INFO visit :: node: "output-f8_json", values: {"f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-01/call-call_f8/out/m84036_250809_035451_s4.bc2098.f8inversion.json"}
2025-09-15 20:24:28.547 wdl.w:ptcp.w:call-paraphase-01 INFO visit :: node: "output-f8_vcf", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-01/call-call_f8/out/m84036_250809_035451_s4.bc2098.f8inversion.vcf"}
2025-09-15 20:24:28.547 wdl.w:ptcp.w:call-paraphase-01 INFO visit :: node: "outputs", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-01/call-call_f8/out/m84036_250809_035451_s4.bc2098.f8inversion.vcf", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-01/call-run_paraphase/out/m84036_250809_035451_s4.bc2098_paraphase/m84036_250809_035451_s4.bc2098.paraphase.json", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-01/call-run_paraphase/out/m84036_250809_035451_s4.bc2098_paraphase/m84036_250809_035451_s4.bc2098.paraphase.bam", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-01/call-run_paraphase/out/m84036_250809_035451_s4.bc2098_paraphase/m84036_250809_035451_s4.bc2098.paraphase.bam.bai", "paraphase_vcfs": [], "havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-01/call-run_paraphase/out/m84036_250809_035451_s4.bc2098.havanno.json", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-01/call-call_f8/out/m84036_250809_035451_s4.bc2098.f8inversion.json"}
2025-09-15 20:24:28.559 wdl.w:ptcp.w:call-paraphase-50.t:call-run_paraphase NOTICE task setup :: name: "run_paraphase", source: "./paraphase.wdl", line: 127, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-50/call-run_paraphase", thread: 140608219895360
2025-09-15 20:24:28.586 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_genotype NOTICE slurm_singularity run :: pid: 1201926, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-47/call-trgt_genotype/slurm_singularity.log.txt"
2025-09-15 20:24:28.590 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_plot_meth_waterfall INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2100.meth_waterfall.trgt_plots.zip"
2025-09-15 20:24:28.591 wdl.w:ptcp.w:call-trgt-25.t:call-trgt_plot_motifs_allele NOTICE done
2025-09-15 20:24:28.596 wdl.w:ptcp.w:call-paraphase-50.t:call-run_paraphase INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:28.596 wdl.w:ptcp.w:call-paraphase-50.t:call-run_paraphase INFO input :: name: "annotation_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf"
2025-09-15 20:24:28.596 wdl.w:ptcp.w:call-paraphase-50.t:call-run_paraphase INFO input :: name: "genome_version", value: "38"
2025-09-15 20:24:28.596 wdl.w:ptcp.w:call-paraphase-50.t:call-run_paraphase INFO input :: name: "config_file", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/paraphase_config.GRCh38.yaml"
2025-09-15 20:24:28.596 wdl.w:ptcp.w:call-paraphase-50.t:call-run_paraphase INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:28.597 wdl.w:ptcp.w:call-paraphase-50.t:call-run_paraphase INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:28.597 wdl.w:ptcp.w:call-paraphase-50.t:call-run_paraphase INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2147.mapped.bam.bai"
2025-09-15 20:24:28.597 wdl.w:ptcp.w:call-paraphase-50.t:call-run_paraphase INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2147.mapped.bam"
2025-09-15 20:24:28.597 wdl.w:ptcp.w:call-paraphase-50.t:call-run_paraphase INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2147"
2025-09-15 20:24:28.597 wdl.w:ptcp.w:call-paraphase-50.t:call-run_paraphase INFO eval :: name: "threads", value: 4
2025-09-15 20:24:28.597 wdl.w:ptcp.w:call-paraphase-50.t:call-run_paraphase INFO eval :: name: "mem_gb", value: 8
2025-09-15 20:24:28.597 wdl.w:ptcp.w:call-paraphase-50.t:call-run_paraphase INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:28.597 wdl.w:ptcp.w:call-paraphase-50.t:call-run_paraphase INFO eval :: name: "out_dir", value: "m84036_250809_035451_s4.bc2147_paraphase"
2025-09-15 20:24:28.598 wdl.w:ptcp.w:call-trgt-25 NOTICE finish :: job: "call-trgt_plot_motifs_allele"
2025-09-15 20:24:28.598 wdl.w:ptcp.w:call-paraphase-50.t:call-run_paraphase INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 4, memory_reservation: 8000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:28.599 wdl.w:ptcp.w:call-trgt-25 INFO output :: job: "call-trgt_plot_motifs_allele", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-25/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2122.motifs_allele.trgt_plots.zip"}
2025-09-15 20:24:28.599 wdl.w:ptcp.w:call-paraphase-50.t:call-run_paraphase WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:28.599 wdl.w:ptcp.w:call-trgt-25 INFO visit :: node: "output-images_motifs_allele", values: {"images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-25/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2122.motifs_allele.trgt_plots.zip"}
2025-09-15 20:24:28.601 wdl.w:ptcp.w:call-paraphase-50.t:call-run_paraphase INFO provisioned :: seconds_waited: 0, cpu: 4, mem_bytes: 8000000000
2025-09-15 20:24:28.601 wdl.w:ptcp.w:call-paraphase-50.t:call-run_paraphase INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:28.605 wdl.w:ptcp.w:call-paraphase-00.t:call-call_f8.slurm_singularity INFO srun: job 51797656 queued and waiting for resources
2025-09-15 20:24:28.605 wdl.w:ptcp.w:call-paraphase-00.t:call-call_f8.slurm_singularity INFO srun: job 51797656 has been allocated resources
2025-09-15 20:24:28.605 wdl.w:ptcp.w:call-paraphase-00.t:call-call_f8.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:28.611 wdl.w:ptcp.w:call-sawfish-50.t:call-run_sawfish NOTICE task setup :: name: "run_sawfish", source: "./sawfish.wdl", line: 83, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-50/call-run_sawfish", thread: 140608228288064
2025-09-15 20:24:28.634 wdl.w:ptcp.w:call-trgt-52.t:call-trgt_genotype.slurm_singularity INFO srun: job 51797657 queued and waiting for resources
2025-09-15 20:24:28.634 wdl.w:ptcp.w:call-trgt-52.t:call-trgt_genotype.slurm_singularity INFO srun: job 51797657 has been allocated resources
2025-09-15 20:24:28.634 wdl.w:ptcp.w:call-trgt-52.t:call-trgt_genotype.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:28.635 wdl.w:ptcp.w:call-trgt-52.t:call-trgt_genotype.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:24:28.637 wdl.w:ptcp.w:call-sawfish-50.t:call-run_sawfish INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:28.637 wdl.w:ptcp.w:call-sawfish-50.t:call-run_sawfish INFO input :: name: "genome_version", value: "38"
2025-09-15 20:24:28.638 wdl.w:ptcp.w:call-sawfish-50.t:call-run_sawfish INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:28.638 wdl.w:ptcp.w:call-sawfish-50.t:call-run_sawfish INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:28.638 wdl.w:ptcp.w:call-sawfish-50.t:call-run_sawfish INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2147.mapped.bam.bai"
2025-09-15 20:24:28.638 wdl.w:ptcp.w:call-sawfish-50.t:call-run_sawfish INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2147.mapped.bam"
2025-09-15 20:24:28.638 wdl.w:ptcp.w:call-sawfish-50.t:call-run_sawfish INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2147"
2025-09-15 20:24:28.638 wdl.w:ptcp.w:call-sawfish-50.t:call-run_sawfish INFO eval :: name: "mem_gb", value: 32
2025-09-15 20:24:28.639 wdl.w:ptcp.w:call-sawfish-50.t:call-run_sawfish INFO eval :: name: "threads", value: 16
2025-09-15 20:24:28.639 wdl.w:ptcp.w:call-sawfish-50.t:call-run_sawfish INFO eval :: name: "disk_size", value: 30
2025-09-15 20:24:28.639 wdl.w:ptcp.w:call-sawfish-50.t:call-run_sawfish INFO eval :: name: "discover_dirname", value: "m84036_250809_035451_s4.bc2147_sawfish_discover"
2025-09-15 20:24:28.640 wdl.w:ptcp.w:call-sawfish-50.t:call-run_sawfish INFO eval :: name: "call_dirname", value: "m84036_250809_035451_s4.bc2147_sawfish"
2025-09-15 20:24:28.640 wdl.w:ptcp.w:call-sawfish-50.t:call-run_sawfish INFO eval :: name: "minimap2_bam_filename", value: "m84036_250809_035451_s4.bc2147.minimap2.bam"
2025-09-15 20:24:28.641 wdl.w:ptcp.w:call-sawfish-50.t:call-run_sawfish INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 16, memory_reservation: 32000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:28.641 wdl.w:ptcp.w:call-sawfish-50.t:call-run_sawfish WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:28.642 wdl.w:ptcp.w:call-sawfish-50.t:call-run_sawfish INFO provisioned :: seconds_waited: 0, cpu: 16, mem_bytes: 32000000000
2025-09-15 20:24:28.642 wdl.w:ptcp.w:call-sawfish-50.t:call-run_sawfish INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:28.644 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_plot_meth_waterfall INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2099.meth_waterfall.trgt_plots.zip"
2025-09-15 20:24:28.651 wdl.w:ptcp.w:call-paraphase-01 NOTICE done
2025-09-15 20:24:28.664 wdl.w:ptcp NOTICE finish :: job: "call-paraphase-01"
2025-09-15 20:24:28.664 wdl.w:ptcp INFO output :: job: "call-paraphase-01", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-01/out/m84036_250809_035451_s4.bc2098.f8inversion.vcf", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-01/out/m84036_250809_035451_s4.bc2098_paraphase/m84036_250809_035451_s4.bc2098.paraphase.json", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-01/out/m84036_250809_035451_s4.bc2098_paraphase/m84036_250809_035451_s4.bc2098.paraphase.bam", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-01/out/m84036_250809_035451_s4.bc2098_paraphase/m84036_250809_035451_s4.bc2098.paraphase.bam.bai", "paraphase_vcfs": [], "havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-01/out/m84036_250809_035451_s4.bc2098.havanno.json", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-01/out/m84036_250809_035451_s4.bc2098.f8inversion.json"}
2025-09-15 20:24:28.667 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_plot_motifs_allele NOTICE done
2025-09-15 20:24:28.674 wdl.w:ptcp.w:call-trgt-03 NOTICE finish :: job: "call-trgt_plot_motifs_allele"
2025-09-15 20:24:28.674 wdl.w:ptcp.w:call-trgt-03 INFO output :: job: "call-trgt_plot_motifs_allele", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-03/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2100.motifs_allele.trgt_plots.zip"}
2025-09-15 20:24:28.674 wdl.w:ptcp.w:call-trgt-03 INFO visit :: node: "output-images_motifs_allele", values: {"images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-03/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2100.motifs_allele.trgt_plots.zip"}
2025-09-15 20:24:28.680 wdl.w:ptcp.w:call-trgt-56 NOTICE workflow start :: name: "trgt", source: "./trgt.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-56"
2025-09-15 20:24:28.686 wdl.w:ptcp.w:call-trgt-50.t:call-get_reads_overlapping_repeats NOTICE task setup :: name: "get_reads_overlapping_repeats", source: "./trgt.wdl", line: 182, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-50/call-get_reads_overlapping_repeats", thread: 140606609282624
2025-09-15 20:24:28.707 wdl.w:ptcp.w:call-trgt-56 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:24:28.707 wdl.w:ptcp.w:call-trgt-56 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-56/out/m84036_250809_035451_s4.bc2153.mapped.bam"}
2025-09-15 20:24:28.707 wdl.w:ptcp.w:call-trgt-56 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-56/out/m84036_250809_035451_s4.bc2153.mapped.bam.bai"}
2025-09-15 20:24:28.707 wdl.w:ptcp.w:call-trgt-56 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:24:28.708 wdl.w:ptcp.w:call-trgt-56 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:24:28.708 wdl.w:ptcp.w:call-trgt-56 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2153"}
2025-09-15 20:24:28.708 wdl.w:ptcp.w:call-trgt-56 INFO visit :: node: "decl-sex", values: {"sex": "F"}
2025-09-15 20:24:28.709 wdl.w:ptcp.w:call-trgt-56 INFO visit :: node: "decl-trgt_bed", values: {"trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"}
2025-09-15 20:24:28.710 wdl.w:ptcp.w:call-trgt-56 NOTICE ready :: job: "call-get_reads_overlapping_repeats", callee: "get_reads_overlapping_repeats"
2025-09-15 20:24:28.710 wdl.w:ptcp.w:call-trgt-56 INFO input :: job: "call-get_reads_overlapping_repeats", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-56/out/m84036_250809_035451_s4.bc2153.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-56/out/m84036_250809_035451_s4.bc2153.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2153"}
2025-09-15 20:24:28.712 wdl.w:ptcp.w:call-trgt-56 NOTICE ready :: job: "call-trgt_genotype", callee: "trgt_genotype"
2025-09-15 20:24:28.712 wdl.w:ptcp.w:call-trgt-56 INFO input :: job: "call-trgt_genotype", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-56/out/m84036_250809_035451_s4.bc2153.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-56/out/m84036_250809_035451_s4.bc2153.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2153"}
2025-09-15 20:24:28.721 wdl.w:ptcp.w:call-trgt-50.t:call-get_reads_overlapping_repeats INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:28.721 wdl.w:ptcp.w:call-trgt-50.t:call-get_reads_overlapping_repeats INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:28.721 wdl.w:ptcp.w:call-trgt-50.t:call-get_reads_overlapping_repeats INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2147.mapped.bam.bai"
2025-09-15 20:24:28.722 wdl.w:ptcp.w:call-trgt-50.t:call-get_reads_overlapping_repeats INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2147.mapped.bam"
2025-09-15 20:24:28.722 wdl.w:ptcp.w:call-trgt-50.t:call-get_reads_overlapping_repeats INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2147"
2025-09-15 20:24:28.722 wdl.w:ptcp.w:call-trgt-50.t:call-get_reads_overlapping_repeats INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:28.722 wdl.w:ptcp.w:call-trgt-50.t:call-get_reads_overlapping_repeats INFO eval :: name: "expand_size", value: 3000
2025-09-15 20:24:28.722 wdl.w:ptcp.w:call-trgt-50.t:call-get_reads_overlapping_repeats INFO eval :: name: "threads", value: 1
2025-09-15 20:24:28.722 wdl.w:ptcp.w:call-trgt-50.t:call-get_reads_overlapping_repeats INFO eval :: name: "expanded_bed_name", value: "m84036_250809_035451_s4.bc2147.expanded.bed"
2025-09-15 20:24:28.722 wdl.w:ptcp.w:call-trgt-50.t:call-get_reads_overlapping_repeats INFO eval :: name: "disk_size", value: 11
2025-09-15 20:24:28.723 wdl.w:ptcp.w:call-trgt-50.t:call-get_reads_overlapping_repeats INFO eval :: name: "output_name", value: "m84036_250809_035451_s4.bc2147.repeats.bam"
2025-09-15 20:24:28.723 wdl.w:ptcp.w:call-trgt-50.t:call-get_reads_overlapping_repeats INFO eval :: name: "index_name", value: "m84036_250809_035451_s4.bc2147.repeats.bam.bai"
2025-09-15 20:24:28.723 wdl.w:ptcp.w:call-trgt-50.t:call-get_reads_overlapping_repeats INFO eval :: name: "output_name_with_index", value: "m84036_250809_035451_s4.bc2147.repeats.bam##idx##m84036_250809_035451_s4.bc2147.repeats.bam.bai"
2025-09-15 20:24:28.723 wdl.w:ptcp.w:call-trgt-50.t:call-get_reads_overlapping_repeats INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:28.723 wdl.w:ptcp.w:call-trgt-50.t:call-get_reads_overlapping_repeats WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:28.724 wdl.w:ptcp.w:call-trgt-50.t:call-get_reads_overlapping_repeats INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:28.724 wdl.w:ptcp.w:call-trgt-50.t:call-get_reads_overlapping_repeats INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:28.760 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_plot_meth_allele INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2100.meth_allele.trgt_plots.zip"
2025-09-15 20:24:28.784 wdl.w:ptcp.w:call-paraphase-50.t:call-run_paraphase INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-50/call-run_paraphase/_singularity_tmpdir_azj6xtox"
2025-09-15 20:24:28.784 wdl.w:ptcp.w:call-paraphase-50.t:call-run_paraphase INFO Slurm invocation: srun --job-name call-run_paraphase --partition compute,compute9 --cpus-per-task 4 --mem 7629M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-50/call-run_paraphase/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-50/call-run_paraphase/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-50/call-run_paraphase/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-50/call-run_paraphase/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-50/out/m84036_250809_035451_s4.bc2147.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2147.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-50/out/m84036_250809_035451_s4.bc2147.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2147.mapped.bam.bai:ro --bind /ptcp/meta/variant_list/variant_list.GRCh38.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf:ro --bind /ptcp/meta/paraphase/paraphase_config.GRCh38.yaml:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/paraphase_config.GRCh38.yaml:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-50/call-run_paraphase/_singularity_tmpdir_azj6xtox/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-50/call-run_paraphase/_singularity_tmpdir_azj6xtox/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:28.788 wdl.w:ptcp.w:call-sawfish-50.t:call-run_sawfish INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 10, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-50/call-run_sawfish/_singularity_tmpdir_quz92st6"
2025-09-15 20:24:28.788 wdl.w:ptcp.w:call-sawfish-50.t:call-run_sawfish INFO Slurm invocation: srun --job-name call-run_sawfish --partition compute,compute9 --cpus-per-task 16 --mem 30518M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-50/call-run_sawfish/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-50/call-run_sawfish/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-50/call-run_sawfish/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-50/call-run_sawfish/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-50/out/m84036_250809_035451_s4.bc2147.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2147.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-50/out/m84036_250809_035451_s4.bc2147.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2147.mapped.bam.bai:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-50/call-run_sawfish/_singularity_tmpdir_quz92st6/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-50/call-run_sawfish/_singularity_tmpdir_quz92st6/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:28.790 wdl.w:ptcp.w:call-trgt-32.t:call-trgt_plot_motifs_allele NOTICE done
2025-09-15 20:24:28.789 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_plot_meth_waterfall NOTICE done
2025-09-15 20:24:28.795 wdl.w:ptcp.w:call-trgt-32 NOTICE finish :: job: "call-trgt_plot_motifs_allele"
2025-09-15 20:24:28.796 wdl.w:ptcp.w:call-trgt-32 INFO output :: job: "call-trgt_plot_motifs_allele", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-32/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2129.motifs_allele.trgt_plots.zip"}
2025-09-15 20:24:28.796 wdl.w:ptcp.w:call-trgt-32 INFO visit :: node: "output-images_motifs_allele", values: {"images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-32/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2129.motifs_allele.trgt_plots.zip"}
2025-09-15 20:24:28.796 wdl.w:ptcp.w:call-trgt-03 NOTICE finish :: job: "call-trgt_plot_meth_waterfall"
2025-09-15 20:24:28.796 wdl.w:ptcp.w:call-trgt-03 INFO output :: job: "call-trgt_plot_meth_waterfall", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-03/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2100.meth_waterfall.trgt_plots.zip"}
2025-09-15 20:24:28.797 wdl.w:ptcp.w:call-trgt-03 INFO visit :: node: "output-images_meth_waterfall", values: {"images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-03/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2100.meth_waterfall.trgt_plots.zip"}
2025-09-15 20:24:28.807 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_genotype NOTICE task setup :: name: "trgt_genotype", source: "./trgt.wdl", line: 272, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-50/call-trgt_genotype", thread: 140608765158976
2025-09-15 20:24:28.809 wdl.w:ptcp.w:call-trgt-36.t:call-trgt_plot_meth_allele NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-36/call-trgt_plot_meth_allele", thread: 140607146153536
2025-09-15 20:24:28.812 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_plot_meth_waterfall NOTICE done
2025-09-15 20:24:28.836 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_genotype INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:28.836 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_genotype INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:28.836 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_genotype INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:28.836 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_genotype INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:28.837 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_genotype INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2147.mapped.bam.bai"
2025-09-15 20:24:28.837 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_genotype INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2147.mapped.bam"
2025-09-15 20:24:28.837 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_genotype INFO input :: name: "sex", value: "F"
2025-09-15 20:24:28.837 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_genotype INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2147"
2025-09-15 20:24:28.837 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_genotype INFO eval :: name: "mem_gb", value: 16
2025-09-15 20:24:28.837 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_genotype INFO eval :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2147.trgt"
2025-09-15 20:24:28.837 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_genotype INFO eval :: name: "threads", value: 8
2025-09-15 20:24:28.838 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_genotype INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:28.838 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_genotype INFO eval :: name: "karyotype", value: "XX"
2025-09-15 20:24:28.838 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_genotype INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 8, memory_reservation: 16000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:28.838 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_genotype WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:28.839 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_genotype INFO provisioned :: seconds_waited: 0, cpu: 8, mem_bytes: 16000000000
2025-09-15 20:24:28.839 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_genotype INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:28.841 wdl.w:ptcp.w:call-sawfish-50.t:call-run_sawfish NOTICE slurm_singularity run :: pid: 1201937, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-50/call-run_sawfish/slurm_singularity.log.txt"
2025-09-15 20:24:28.841 wdl.w:ptcp.w:call-paraphase-50.t:call-run_paraphase NOTICE slurm_singularity run :: pid: 1201936, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-50/call-run_paraphase/slurm_singularity.log.txt"
2025-09-15 20:24:28.846 wdl.w:ptcp.w:call-trgt-50.t:call-get_reads_overlapping_repeats INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 9, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-50/call-get_reads_overlapping_repeats/_singularity_tmpdir_l_w4x01a"
2025-09-15 20:24:28.846 wdl.w:ptcp.w:call-trgt-50.t:call-get_reads_overlapping_repeats INFO Slurm invocation: srun --job-name call-get_reads_overlapping_repeats --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-50/call-get_reads_overlapping_repeats/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-50/call-get_reads_overlapping_repeats/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-50/call-get_reads_overlapping_repeats/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-50/call-get_reads_overlapping_repeats/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-50/out/m84036_250809_035451_s4.bc2147.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2147.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-50/out/m84036_250809_035451_s4.bc2147.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2147.mapped.bam.bai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-50/call-get_reads_overlapping_repeats/_singularity_tmpdir_l_w4x01a/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-50/call-get_reads_overlapping_repeats/_singularity_tmpdir_l_w4x01a/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:28.859 wdl.w:ptcp.w:call-trgt-02 NOTICE finish :: job: "call-trgt_plot_meth_waterfall"
2025-09-15 20:24:28.859 wdl.w:ptcp.w:call-trgt-02 INFO output :: job: "call-trgt_plot_meth_waterfall", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-02/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2099.meth_waterfall.trgt_plots.zip"}
2025-09-15 20:24:28.859 wdl.w:ptcp.w:call-trgt-02 INFO visit :: node: "output-images_meth_waterfall", values: {"images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-02/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2099.meth_waterfall.trgt_plots.zip"}
2025-09-15 20:24:28.867 wdl.w:ptcp.w:call-trgt-36.t:call-trgt_plot_meth_waterfall NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-36/call-trgt_plot_meth_waterfall", thread: 140607683024448
2025-09-15 20:24:28.871 wdl.w:ptcp.w:call-trgt-36.t:call-trgt_plot_meth_allele INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:28.871 wdl.w:ptcp.w:call-trgt-36.t:call-trgt_plot_meth_allele INFO input :: name: "waterfall", value: false
2025-09-15 20:24:28.871 wdl.w:ptcp.w:call-trgt-36.t:call-trgt_plot_meth_allele INFO input :: name: "methylation", value: true
2025-09-15 20:24:28.871 wdl.w:ptcp.w:call-trgt-36.t:call-trgt_plot_meth_allele INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:28.871 wdl.w:ptcp.w:call-trgt-36.t:call-trgt_plot_meth_allele INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:28.871 wdl.w:ptcp.w:call-trgt-36.t:call-trgt_plot_meth_allele INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:28.871 wdl.w:ptcp.w:call-trgt-36.t:call-trgt_plot_meth_allele INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2133.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:28.871 wdl.w:ptcp.w:call-trgt-36.t:call-trgt_plot_meth_allele INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2133.trgt.sorted.spanning.bam"
2025-09-15 20:24:28.871 wdl.w:ptcp.w:call-trgt-36.t:call-trgt_plot_meth_allele INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2133.trgt.vcf"
2025-09-15 20:24:28.872 wdl.w:ptcp.w:call-trgt-36.t:call-trgt_plot_meth_allele INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2133"
2025-09-15 20:24:28.872 wdl.w:ptcp.w:call-trgt-36.t:call-trgt_plot_meth_allele INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:28.872 wdl.w:ptcp.w:call-trgt-36.t:call-trgt_plot_meth_allele INFO eval :: name: "plot_type", value: "allele"
2025-09-15 20:24:28.872 wdl.w:ptcp.w:call-trgt-36.t:call-trgt_plot_meth_allele INFO eval :: name: "show", value: "meth"
2025-09-15 20:24:28.872 wdl.w:ptcp.w:call-trgt-36.t:call-trgt_plot_meth_allele INFO eval :: name: "threads", value: 1
2025-09-15 20:24:28.872 wdl.w:ptcp.w:call-trgt-36.t:call-trgt_plot_meth_allele INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:28.872 wdl.w:ptcp.w:call-trgt-36.t:call-trgt_plot_meth_allele INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2133.meth_allele"
2025-09-15 20:24:28.873 wdl.w:ptcp.w:call-trgt-36.t:call-trgt_plot_meth_allele INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:28.873 wdl.w:ptcp.w:call-trgt-50.t:call-get_reads_overlapping_repeats NOTICE slurm_singularity run :: pid: 1201939, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-50/call-get_reads_overlapping_repeats/slurm_singularity.log.txt"
2025-09-15 20:24:28.873 wdl.w:ptcp.w:call-trgt-36.t:call-trgt_plot_meth_allele WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:28.873 wdl.w:ptcp.w:call-trgt-36.t:call-trgt_plot_meth_allele INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:28.874 wdl.w:ptcp.w:call-trgt-36.t:call-trgt_plot_meth_allele INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:28.881 wdl.w:ptcp.w:call-trgt-25.t:call-trgt_plot_meth_waterfall INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2122.meth_waterfall.trgt_plots.zip"
2025-09-15 20:24:28.884 wdl.w:ptcp.w:call-trgt-09.t:call-trgt_plot_meth_waterfall INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2106.meth_waterfall.trgt_plots.zip"
2025-09-15 20:24:28.891 wdl.w:ptcp.w:call-trgt-36.t:call-trgt_plot_meth_waterfall INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:28.891 wdl.w:ptcp.w:call-trgt-36.t:call-trgt_plot_meth_waterfall INFO input :: name: "waterfall", value: true
2025-09-15 20:24:28.891 wdl.w:ptcp.w:call-trgt-36.t:call-trgt_plot_meth_waterfall INFO input :: name: "methylation", value: true
2025-09-15 20:24:28.891 wdl.w:ptcp.w:call-trgt-36.t:call-trgt_plot_meth_waterfall INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:28.891 wdl.w:ptcp.w:call-trgt-36.t:call-trgt_plot_meth_waterfall INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:28.891 wdl.w:ptcp.w:call-trgt-36.t:call-trgt_plot_meth_waterfall INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:28.891 wdl.w:ptcp.w:call-trgt-36.t:call-trgt_plot_meth_waterfall INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2133.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:28.891 wdl.w:ptcp.w:call-trgt-36.t:call-trgt_plot_meth_waterfall INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2133.trgt.sorted.spanning.bam"
2025-09-15 20:24:28.892 wdl.w:ptcp.w:call-trgt-36.t:call-trgt_plot_meth_waterfall INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2133.trgt.vcf"
2025-09-15 20:24:28.892 wdl.w:ptcp.w:call-trgt-36.t:call-trgt_plot_meth_waterfall INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2133"
2025-09-15 20:24:28.892 wdl.w:ptcp.w:call-trgt-36.t:call-trgt_plot_meth_waterfall INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:28.892 wdl.w:ptcp.w:call-trgt-36.t:call-trgt_plot_meth_waterfall INFO eval :: name: "plot_type", value: "waterfall"
2025-09-15 20:24:28.892 wdl.w:ptcp.w:call-trgt-36.t:call-trgt_plot_meth_waterfall INFO eval :: name: "show", value: "meth"
2025-09-15 20:24:28.893 wdl.w:ptcp.w:call-trgt-36.t:call-trgt_plot_meth_waterfall INFO eval :: name: "threads", value: 1
2025-09-15 20:24:28.893 wdl.w:ptcp.w:call-trgt-36.t:call-trgt_plot_meth_waterfall INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:28.893 wdl.w:ptcp.w:call-trgt-36.t:call-trgt_plot_meth_waterfall INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2133.meth_waterfall"
2025-09-15 20:24:28.893 wdl.w:ptcp.w:call-trgt-36.t:call-trgt_plot_meth_waterfall INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:28.893 wdl.w:ptcp.w:call-trgt-36.t:call-trgt_plot_meth_waterfall WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:28.894 wdl.w:ptcp.w:call-trgt-36.t:call-trgt_plot_meth_waterfall INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:28.894 wdl.w:ptcp.w:call-trgt-36.t:call-trgt_plot_meth_waterfall INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:28.902 wdl.w:ptcp.w:call-trgt-03.t:call-trgt_plot_meth_allele NOTICE done
2025-09-15 20:24:28.912 wdl.w:ptcp.w:call-trgt-03 NOTICE finish :: job: "call-trgt_plot_meth_allele"
2025-09-15 20:24:28.912 wdl.w:ptcp.w:call-trgt-03 INFO output :: job: "call-trgt_plot_meth_allele", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-03/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2100.meth_allele.trgt_plots.zip"}
2025-09-15 20:24:28.912 wdl.w:ptcp.w:call-trgt-03 INFO visit :: node: "output-images_meth_allele", values: {"images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-03/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2100.meth_allele.trgt_plots.zip"}
2025-09-15 20:24:28.913 wdl.w:ptcp.w:call-trgt-03 INFO visit :: node: "outputs", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-03/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2100.motifs_waterfall.trgt_plots.zip", "images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-03/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2100.meth_allele.trgt_plots.zip", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-03/call-trgt_genotype/out/m84036_250809_035451_s4.bc2100.trgt.sorted.spanning.bam.bai", "images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-03/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2100.motifs_allele.trgt_plots.zip", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-03/call-trgt_genotype/out/m84036_250809_035451_s4.bc2100.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-03/call-trgt_genotype/out/m84036_250809_035451_s4.bc2100.trgt.vcf", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-03/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2100.repeats.bam", "images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-03/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2100.meth_waterfall.trgt_plots.zip", "reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-03/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2100.repeats.bam.bai"}
2025-09-15 20:24:28.922 wdl.w:ptcp.w:call-trgt-36.t:call-trgt_plot_motifs_allele NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-36/call-trgt_plot_motifs_allele", thread: 140607112582720
2025-09-15 20:24:28.933 wdl.w:ptcp.w:call-paraphase-47.t:call-run_paraphase.slurm_singularity INFO srun: job 51797658 queued and waiting for resources
2025-09-15 20:24:28.933 wdl.w:ptcp.w:call-paraphase-47.t:call-run_paraphase.slurm_singularity INFO srun: job 51797658 has been allocated resources
2025-09-15 20:24:28.933 wdl.w:ptcp.w:call-paraphase-47.t:call-run_paraphase.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:28.933 wdl.w:ptcp.w:call-paraphase-47.t:call-run_paraphase.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:24:28.941 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_genotype INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 11, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-50/call-trgt_genotype/_singularity_tmpdir_qel3z5yu"
2025-09-15 20:24:28.941 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_genotype INFO Slurm invocation: srun --job-name call-trgt_genotype --partition compute,compute9 --cpus-per-task 8 --mem 15259M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-50/call-trgt_genotype/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-50/call-trgt_genotype/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-50/call-trgt_genotype/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-50/call-trgt_genotype/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-50/out/m84036_250809_035451_s4.bc2147.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2147.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-50/out/m84036_250809_035451_s4.bc2147.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2147.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-50/call-trgt_genotype/_singularity_tmpdir_qel3z5yu/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-50/call-trgt_genotype/_singularity_tmpdir_qel3z5yu/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:28.942 wdl.w:ptcp.w:call-trgt-36.t:call-trgt_plot_motifs_allele INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:28.945 wdl.w:ptcp.w:call-trgt-36.t:call-trgt_plot_motifs_allele INFO input :: name: "waterfall", value: false
2025-09-15 20:24:28.947 wdl.w:ptcp.w:call-trgt-36.t:call-trgt_plot_motifs_allele INFO input :: name: "methylation", value: false
2025-09-15 20:24:28.947 wdl.w:ptcp.w:call-trgt-36.t:call-trgt_plot_motifs_allele INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:28.947 wdl.w:ptcp.w:call-trgt-36.t:call-trgt_plot_motifs_allele INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:28.947 wdl.w:ptcp.w:call-trgt-36.t:call-trgt_plot_motifs_allele INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:28.947 wdl.w:ptcp.w:call-trgt-36.t:call-trgt_plot_motifs_allele INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2133.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:28.947 wdl.w:ptcp.w:call-trgt-36.t:call-trgt_plot_motifs_allele INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2133.trgt.sorted.spanning.bam"
2025-09-15 20:24:28.948 wdl.w:ptcp.w:call-trgt-36.t:call-trgt_plot_motifs_allele INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2133.trgt.vcf"
2025-09-15 20:24:28.948 wdl.w:ptcp.w:call-trgt-36.t:call-trgt_plot_motifs_allele INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2133"
2025-09-15 20:24:28.948 wdl.w:ptcp.w:call-trgt-36.t:call-trgt_plot_motifs_allele INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:28.948 wdl.w:ptcp.w:call-trgt-36.t:call-trgt_plot_motifs_allele INFO eval :: name: "plot_type", value: "allele"
2025-09-15 20:24:28.948 wdl.w:ptcp.w:call-trgt-36.t:call-trgt_plot_motifs_allele INFO eval :: name: "show", value: "motifs"
2025-09-15 20:24:28.948 wdl.w:ptcp.w:call-trgt-36.t:call-trgt_plot_motifs_allele INFO eval :: name: "threads", value: 1
2025-09-15 20:24:28.947 wdl.w:ptcp.w:call-sawfish-01.t:call-run_sawfish.stderr VERBOSE [M::mm_idx_gen::33.446*1.49] collected minimizers
2025-09-15 20:24:28.948 wdl.w:ptcp.w:call-trgt-36.t:call-trgt_plot_motifs_allele INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:28.949 wdl.w:ptcp.w:call-sawfish-01.t:call-run_sawfish.stderr VERBOSE [M::mm_idx_gen::40.281*1.74] sorted minimizers
2025-09-15 20:24:28.949 wdl.w:ptcp.w:call-trgt-36.t:call-trgt_plot_motifs_allele INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2133.motifs_allele"
2025-09-15 20:24:28.949 wdl.w:ptcp.w:call-sawfish-01.t:call-run_sawfish.stderr VERBOSE [M::main::40.281*1.74] loaded/built the index for 195 target sequence(s)
2025-09-15 20:24:28.949 wdl.w:ptcp.w:call-sawfish-01.t:call-run_sawfish.stderr VERBOSE [M::mm_mapopt_update::43.322*1.69] mid_occ = 136
2025-09-15 20:24:28.950 wdl.w:ptcp.w:call-sawfish-01.t:call-run_sawfish.stderr VERBOSE [M::mm_idx_stat] kmer size: 19; skip: 19; is_hpc: 0; #seq: 195
2025-09-15 20:24:28.950 wdl.w:ptcp.w:call-trgt-36.t:call-trgt_plot_motifs_allele INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:28.950 wdl.w:ptcp.w:call-trgt-36.t:call-trgt_plot_motifs_allele WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:28.951 wdl.w:ptcp.w:call-trgt-36.t:call-trgt_plot_motifs_allele INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:28.951 wdl.w:ptcp.w:call-trgt-36.t:call-trgt_plot_motifs_allele INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:28.953 wdl.w:ptcp.w:call-sawfish-15.t:call-run_sawfish INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2112_sawfish/m84036_250809_035451_s4.bc2112.sv.vcf.gz"
2025-09-15 20:24:28.960 wdl.w:ptcp.w:call-sawfish-15.t:call-run_sawfish INFO output :: name: "vcf_tbi", value: "m84036_250809_035451_s4.bc2112_sawfish/m84036_250809_035451_s4.bc2112.sv.vcf.gz.tbi"
2025-09-15 20:24:28.962 wdl.w:ptcp.w:call-sawfish-15.t:call-run_sawfish INFO output :: name: "minimap2_bam", value: "m84036_250809_035451_s4.bc2112.minimap2.bam"
2025-09-15 20:24:28.965 wdl.w:ptcp.w:call-sawfish-15.t:call-run_sawfish INFO output :: name: "minimap2_bam_bai", value: "m84036_250809_035451_s4.bc2112.minimap2.bam.bai"
2025-09-15 20:24:28.969 wdl.w:ptcp.w:call-trgt-25.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:25 [ERROR] - No reads found for TRID=EIEE1_ARX
2025-09-15 20:24:28.992 wdl.w:ptcp.w:call-trgt-36.t:call-trgt_plot_meth_allele INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-36/call-trgt_plot_meth_allele/_singularity_tmpdir_5k8v3r_f"
2025-09-15 20:24:28.993 wdl.w:ptcp.w:call-trgt-36.t:call-trgt_plot_meth_allele INFO Slurm invocation: srun --job-name call-trgt_plot_meth_allele --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-36/call-trgt_plot_meth_allele/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-36/call-trgt_plot_meth_allele/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-36/call-trgt_plot_meth_allele/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-36/call-trgt_plot_meth_allele/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-36/call-trgt_genotype/out/m84036_250809_035451_s4.bc2133.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2133.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-36/call-trgt_genotype/out/m84036_250809_035451_s4.bc2133.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2133.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-36/call-trgt_genotype/out/m84036_250809_035451_s4.bc2133.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2133.trgt.sorted.spanning.bam.bai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-36/call-trgt_plot_meth_allele/_singularity_tmpdir_5k8v3r_f/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-36/call-trgt_plot_meth_allele/_singularity_tmpdir_5k8v3r_f/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:29.004 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_genotype NOTICE slurm_singularity run :: pid: 1201954, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-50/call-trgt_genotype/slurm_singularity.log.txt"
2025-09-15 20:24:29.005 wdl.w:ptcp.w:call-trgt-36.t:call-trgt_plot_meth_allele NOTICE slurm_singularity run :: pid: 1201956, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-36/call-trgt_plot_meth_allele/slurm_singularity.log.txt"
2025-09-15 20:24:29.009 wdl.w:ptcp.w:call-trgt-36.t:call-trgt_plot_meth_waterfall INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-36/call-trgt_plot_meth_waterfall/_singularity_tmpdir__vqx8trk"
2025-09-15 20:24:29.010 wdl.w:ptcp.w:call-trgt-36.t:call-trgt_plot_meth_waterfall INFO Slurm invocation: srun --job-name call-trgt_plot_meth_waterfall --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-36/call-trgt_plot_meth_waterfall/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-36/call-trgt_plot_meth_waterfall/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-36/call-trgt_plot_meth_waterfall/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-36/call-trgt_plot_meth_waterfall/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-36/call-trgt_genotype/out/m84036_250809_035451_s4.bc2133.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2133.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-36/call-trgt_genotype/out/m84036_250809_035451_s4.bc2133.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2133.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-36/call-trgt_genotype/out/m84036_250809_035451_s4.bc2133.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2133.trgt.sorted.spanning.bam.bai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-36/call-trgt_plot_meth_waterfall/_singularity_tmpdir__vqx8trk/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-36/call-trgt_plot_meth_waterfall/_singularity_tmpdir__vqx8trk/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:29.024 wdl.w:ptcp.w:call-trgt-36.t:call-trgt_plot_meth_waterfall NOTICE slurm_singularity run :: pid: 1201957, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-36/call-trgt_plot_meth_waterfall/slurm_singularity.log.txt"
2025-09-15 20:24:29.043 wdl.w:ptcp.w:call-trgt-03 NOTICE done
2025-09-15 20:24:29.049 wdl.w:ptcp NOTICE finish :: job: "call-trgt-03"
2025-09-15 20:24:29.049 wdl.w:ptcp INFO output :: job: "call-trgt-03", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-03/out/m84036_250809_035451_s4.bc2100.motifs_waterfall.trgt_plots.zip", "images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-03/out/m84036_250809_035451_s4.bc2100.meth_allele.trgt_plots.zip", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-03/out/m84036_250809_035451_s4.bc2100.trgt.sorted.spanning.bam.bai", "images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-03/out/m84036_250809_035451_s4.bc2100.motifs_allele.trgt_plots.zip", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-03/out/m84036_250809_035451_s4.bc2100.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-03/out/m84036_250809_035451_s4.bc2100.trgt.vcf", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-03/out/m84036_250809_035451_s4.bc2100.repeats.bam", "images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-03/out/m84036_250809_035451_s4.bc2100.meth_waterfall.trgt_plots.zip", "reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-03/out/m84036_250809_035451_s4.bc2100.repeats.bam.bai"}
2025-09-15 20:24:29.051 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_plot_motifs_allele INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2099.motifs_allele.trgt_plots.zip"
2025-09-15 20:24:29.059 wdl.w:ptcp.w:call-paraphase-43 NOTICE workflow start :: name: "paraphase", source: "./paraphase.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-43"
2025-09-15 20:24:29.066 wdl.w:ptcp.w:call-trgt-36.t:call-trgt_plot_motifs_allele INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-36/call-trgt_plot_motifs_allele/_singularity_tmpdir_hjpac7u1"
2025-09-15 20:24:29.066 wdl.w:ptcp.w:call-trgt-36.t:call-trgt_plot_motifs_allele INFO Slurm invocation: srun --job-name call-trgt_plot_motifs_allele --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-36/call-trgt_plot_motifs_allele/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-36/call-trgt_plot_motifs_allele/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-36/call-trgt_plot_motifs_allele/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-36/call-trgt_plot_motifs_allele/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-36/call-trgt_genotype/out/m84036_250809_035451_s4.bc2133.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2133.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-36/call-trgt_genotype/out/m84036_250809_035451_s4.bc2133.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2133.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-36/call-trgt_genotype/out/m84036_250809_035451_s4.bc2133.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2133.trgt.sorted.spanning.bam.bai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-36/call-trgt_plot_motifs_allele/_singularity_tmpdir_hjpac7u1/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-36/call-trgt_plot_motifs_allele/_singularity_tmpdir_hjpac7u1/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:29.078 wdl.w:ptcp.w:call-paraphase-43 INFO visit :: node: "decl-annotation_vcf", values: {"annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf"}
2025-09-15 20:24:29.079 wdl.w:ptcp.w:call-paraphase-43 INFO visit :: node: "decl-config_file", values: {"config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml"}
2025-09-15 20:24:29.079 wdl.w:ptcp.w:call-paraphase-43 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:24:29.079 wdl.w:ptcp.w:call-paraphase-43 INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:24:29.080 wdl.w:ptcp.w:call-paraphase-43 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-43/out/m84036_250809_035451_s4.bc2140.mapped.bam"}
2025-09-15 20:24:29.080 wdl.w:ptcp.w:call-paraphase-43 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-43/out/m84036_250809_035451_s4.bc2140.mapped.bam.bai"}
2025-09-15 20:24:29.080 wdl.w:ptcp.w:call-paraphase-43 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:24:29.080 wdl.w:ptcp.w:call-paraphase-43 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:24:29.080 wdl.w:ptcp.w:call-paraphase-43 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2140"}
2025-09-15 20:24:29.080 wdl.w:ptcp.w:call-paraphase-43 INFO visit :: node: "decl-sex", values: {"sex": "F"}
2025-09-15 20:24:29.080 wdl.w:ptcp.w:call-paraphase-43 NOTICE ready :: job: "call-run_paraphase", callee: "run_paraphase"
2025-09-15 20:24:29.081 wdl.w:ptcp.w:call-paraphase-43 INFO input :: job: "call-run_paraphase", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf", "genome_version": "38", "config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-43/out/m84036_250809_035451_s4.bc2140.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-43/out/m84036_250809_035451_s4.bc2140.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2140"}
2025-09-15 20:24:29.082 wdl.w:ptcp.w:call-trgt-25.t:call-trgt_plot_meth_waterfall NOTICE done
2025-09-15 20:24:29.083 wdl.w:ptcp.w:call-trgt-09.t:call-trgt_plot_meth_waterfall NOTICE done
2025-09-15 20:24:29.088 wdl.w:ptcp.w:call-trgt-36.t:call-trgt_plot_motifs_allele NOTICE slurm_singularity run :: pid: 1201966, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-36/call-trgt_plot_motifs_allele/slurm_singularity.log.txt"
2025-09-15 20:24:29.089 wdl.w:ptcp.w:call-trgt-25 NOTICE finish :: job: "call-trgt_plot_meth_waterfall"
2025-09-15 20:24:29.090 wdl.w:ptcp.w:call-trgt-09 NOTICE finish :: job: "call-trgt_plot_meth_waterfall"
2025-09-15 20:24:29.090 wdl.w:ptcp.w:call-trgt-25 INFO output :: job: "call-trgt_plot_meth_waterfall", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-25/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2122.meth_waterfall.trgt_plots.zip"}
2025-09-15 20:24:29.090 wdl.w:ptcp.w:call-trgt-09 INFO output :: job: "call-trgt_plot_meth_waterfall", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-09/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2106.meth_waterfall.trgt_plots.zip"}
2025-09-15 20:24:29.090 wdl.w:ptcp.w:call-trgt-25 INFO visit :: node: "output-images_meth_waterfall", values: {"images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-25/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2122.meth_waterfall.trgt_plots.zip"}
2025-09-15 20:24:29.091 wdl.w:ptcp.w:call-trgt-09 INFO visit :: node: "output-images_meth_waterfall", values: {"images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-09/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2106.meth_waterfall.trgt_plots.zip"}
2025-09-15 20:24:29.091 wdl.w:ptcp.w:call-trgt-09 INFO visit :: node: "outputs", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-09/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2106.motifs_waterfall.trgt_plots.zip", "images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-09/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2106.meth_allele.trgt_plots.zip", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-09/call-trgt_genotype/out/m84036_250809_035451_s4.bc2106.trgt.sorted.spanning.bam.bai", "images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-09/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2106.motifs_allele.trgt_plots.zip", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-09/call-trgt_genotype/out/m84036_250809_035451_s4.bc2106.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-09/call-trgt_genotype/out/m84036_250809_035451_s4.bc2106.trgt.vcf", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-09/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2106.repeats.bam", "images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-09/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2106.meth_waterfall.trgt_plots.zip", "reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-09/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2106.repeats.bam.bai"}
2025-09-15 20:24:29.098 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_meth_allele NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-38/call-trgt_plot_meth_allele", thread: 140608731588160
2025-09-15 20:24:29.099 wdl.w:ptcp.w:call-trgt-36.t:call-trgt_plot_motifs_waterfall NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-36/call-trgt_plot_motifs_waterfall", thread: 140608236680768
2025-09-15 20:24:29.111 wdl.w:ptcp.w:call-sawfish-47.t:call-run_sawfish.slurm_singularity INFO srun: job 51797659 queued and waiting for resources
2025-09-15 20:24:29.111 wdl.w:ptcp.w:call-sawfish-47.t:call-run_sawfish.slurm_singularity INFO srun: job 51797659 has been allocated resources
2025-09-15 20:24:29.112 wdl.w:ptcp.w:call-sawfish-47.t:call-run_sawfish.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:29.112 wdl.w:ptcp.w:call-sawfish-47.t:call-run_sawfish.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:24:29.122 wdl.w:ptcp.w:call-trgt-36.t:call-trgt_plot_motifs_waterfall INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:29.122 wdl.w:ptcp.w:call-trgt-36.t:call-trgt_plot_motifs_waterfall INFO input :: name: "waterfall", value: true
2025-09-15 20:24:29.122 wdl.w:ptcp.w:call-trgt-36.t:call-trgt_plot_motifs_waterfall INFO input :: name: "methylation", value: false
2025-09-15 20:24:29.122 wdl.w:ptcp.w:call-trgt-36.t:call-trgt_plot_motifs_waterfall INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:29.122 wdl.w:ptcp.w:call-trgt-36.t:call-trgt_plot_motifs_waterfall INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:29.123 wdl.w:ptcp.w:call-trgt-36.t:call-trgt_plot_motifs_waterfall INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:29.123 wdl.w:ptcp.w:call-trgt-36.t:call-trgt_plot_motifs_waterfall INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2133.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:29.123 wdl.w:ptcp.w:call-trgt-36.t:call-trgt_plot_motifs_waterfall INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2133.trgt.sorted.spanning.bam"
2025-09-15 20:24:29.123 wdl.w:ptcp.w:call-trgt-36.t:call-trgt_plot_motifs_waterfall INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2133.trgt.vcf"
2025-09-15 20:24:29.123 wdl.w:ptcp.w:call-trgt-36.t:call-trgt_plot_motifs_waterfall INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2133"
2025-09-15 20:24:29.123 wdl.w:ptcp.w:call-trgt-36.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:29.123 wdl.w:ptcp.w:call-trgt-36.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "plot_type", value: "waterfall"
2025-09-15 20:24:29.123 wdl.w:ptcp.w:call-trgt-36.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "show", value: "motifs"
2025-09-15 20:24:29.124 wdl.w:ptcp.w:call-trgt-36.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "threads", value: 1
2025-09-15 20:24:29.124 wdl.w:ptcp.w:call-trgt-36.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:29.124 wdl.w:ptcp.w:call-trgt-36.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2133.motifs_waterfall"
2025-09-15 20:24:29.124 wdl.w:ptcp.w:call-trgt-36.t:call-trgt_plot_motifs_waterfall INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:29.125 wdl.w:ptcp.w:call-trgt-36.t:call-trgt_plot_motifs_waterfall WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:29.125 wdl.w:ptcp.w:call-trgt-36.t:call-trgt_plot_motifs_waterfall INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:29.125 wdl.w:ptcp.w:call-trgt-36.t:call-trgt_plot_motifs_waterfall INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:29.130 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_meth_allele INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:29.130 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_meth_allele INFO input :: name: "waterfall", value: false
2025-09-15 20:24:29.130 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_meth_allele INFO input :: name: "methylation", value: true
2025-09-15 20:24:29.131 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_meth_allele INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:29.131 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_meth_allele INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:29.131 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_meth_allele INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:29.131 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_meth_allele INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2135.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:29.131 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_meth_allele INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2135.trgt.sorted.spanning.bam"
2025-09-15 20:24:29.131 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_meth_allele INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2135.trgt.vcf"
2025-09-15 20:24:29.131 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_meth_allele INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2135"
2025-09-15 20:24:29.131 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_meth_allele INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:29.132 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_meth_allele INFO eval :: name: "plot_type", value: "allele"
2025-09-15 20:24:29.132 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_meth_allele INFO eval :: name: "show", value: "meth"
2025-09-15 20:24:29.132 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_meth_allele INFO eval :: name: "threads", value: 1
2025-09-15 20:24:29.132 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_meth_allele INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:29.133 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_meth_allele INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2135.meth_allele"
2025-09-15 20:24:29.133 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_meth_allele INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:29.133 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_meth_allele WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:29.133 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_meth_allele INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:29.134 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_meth_allele INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:29.138 wdl.w:ptcp.w:call-sawfish-35.t:call-run_sawfish.stderr VERBOSE [M::mm_idx_gen::49.664*1.77] collected minimizers
2025-09-15 20:24:29.139 wdl.w:ptcp.w:call-sawfish-35.t:call-run_sawfish.stderr VERBOSE [M::mm_idx_gen::60.677*1.97] sorted minimizers
2025-09-15 20:24:29.140 wdl.w:ptcp.w:call-sawfish-35.t:call-run_sawfish.stderr VERBOSE [M::main::60.679*1.97] loaded/built the index for 195 target sequence(s)
2025-09-15 20:24:29.140 wdl.w:ptcp.w:call-sawfish-35.t:call-run_sawfish.stderr VERBOSE [M::mm_mapopt_update::67.610*1.87] mid_occ = 136
2025-09-15 20:24:29.140 wdl.w:ptcp.w:call-sawfish-35.t:call-run_sawfish.stderr VERBOSE [M::mm_idx_stat] kmer size: 19; skip: 19; is_hpc: 0; #seq: 195
2025-09-15 20:24:29.140 wdl.w:ptcp.w:call-paraphase-00.t:call-call_f8 INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2097.f8inversion.vcf"
2025-09-15 20:24:29.141 wdl.w:ptcp.w:call-sawfish-35.t:call-run_sawfish.stderr VERBOSE [M::mm_idx_stat::72.812*1.81] distinct minimizers: 214664461 (92.23% are singletons); average occurrences: 1.372; average spacing: 10.529; total length: 3099922541
2025-09-15 20:24:29.141 wdl.w:ptcp.w:call-sawfish-35.t:call-run_sawfish.stderr VERBOSE [M::bam2fq_mainloop] discarded 0 singletons
2025-09-15 20:24:29.141 wdl.w:ptcp.w:call-sawfish-35.t:call-run_sawfish.stderr VERBOSE [M::bam2fq_mainloop] processed 258 reads
2025-09-15 20:24:29.141 wdl.w:ptcp.w:call-sawfish-35.t:call-run_sawfish.stderr VERBOSE [M::worker_pipeline::73.351*1.81] mapped 258 sequences
2025-09-15 20:24:29.141 wdl.w:ptcp.w:call-sawfish-35.t:call-run_sawfish.stderr VERBOSE [M::main] Version: 2.26-r1175
2025-09-15 20:24:29.141 wdl.w:ptcp.w:call-sawfish-35.t:call-run_sawfish.stderr VERBOSE [M::main] CMD: /opt/pacbio/smrttools/install/smrtlink-release_25.1.0.257715/bundles/smrttools/install/smrttools-release_25.1.0.257715/private/thirdparty/minimap2/minimap2_2.26-pacbio2/binwrap/../../../../../private/thirdparty/minimap2/minimap2_2.26-pacbio2/bin/minimap2 -a -y -x map-hifi -Y -E 1,0 /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa -
2025-09-15 20:24:29.141 wdl.w:ptcp.w:call-sawfish-35.t:call-run_sawfish.stderr VERBOSE [M::main] Real time: 73.995 sec; CPU: 133.457 sec; Peak RSS: 11.886 GB
2025-09-15 20:24:29.141 wdl.w:ptcp.w:call-sawfish-35.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:16][sawfish][INFO] Starting sawfish 2.0.3
2025-09-15 20:24:29.141 wdl.w:ptcp.w:call-sawfish-35.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:16][sawfish][INFO] cmdline: sawfish discover --disable-cnv --threads 16 --ref /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa --bam m84036_250809_035451_s4.bc2132.minimap2.bam --output-dir m84036_250809_035451_s4.bc2132_sawfish_discover
2025-09-15 20:24:29.141 wdl.w:ptcp.w:call-sawfish-35.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:16][sawfish][INFO] Running on 16 threads
2025-09-15 20:24:29.141 wdl.w:ptcp.w:call-sawfish-35.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:16][sawfish][INFO] Writing discover settings to file: 'm84036_250809_035451_s4.bc2132_sawfish_discover/discover.settings.json'
2025-09-15 20:24:29.141 wdl.w:ptcp.w:call-sawfish-35.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:16][sawfish][INFO] Reading reference genome from file '/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa'
2025-09-15 20:24:29.142 wdl.w:ptcp.w:call-sawfish-35.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:25][sawfish][INFO] Processing alignment file '/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2132.minimap2.bam'
2025-09-15 20:24:29.142 wdl.w:ptcp.w:call-sawfish-35.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:25][sawfish][INFO] Finished processing all alignments
2025-09-15 20:24:29.142 wdl.w:ptcp.w:call-sawfish-35.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:25][sawfish][INFO] Writing depth bins to binary file: 'm84036_250809_035451_s4.bc2132_sawfish_discover/depth.mpack'
2025-09-15 20:24:29.142 wdl.w:ptcp.w:call-sawfish-35.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:26][sawfish][INFO] Writing max sv depth genome regions to bed file: 'm84036_250809_035451_s4.bc2132_sawfish_discover/max.depth.bed'
2025-09-15 20:24:29.142 wdl.w:ptcp.w:call-sawfish-35.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:26][sawfish][INFO] Completing breakpoint observation clustering
2025-09-15 20:24:29.142 wdl.w:ptcp.w:call-sawfish-35.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:26][sawfish][INFO] Finished breakpoint observation clustering
2025-09-15 20:24:29.142 wdl.w:ptcp.w:call-sawfish-35.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:26][sawfish][INFO] Consolidating adjacent indel candidates
2025-09-15 20:24:29.142 wdl.w:ptcp.w:call-sawfish-35.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:26][sawfish][INFO] Finding large insertion candidates
2025-09-15 20:24:29.142 wdl.w:ptcp.w:call-sawfish-35.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:26][sawfish][INFO] Writing breakpoint_cluster debug bed file: 'm84036_250809_035451_s4.bc2132_sawfish_discover/debug.breakpoint_clusters.bed'
2025-09-15 20:24:29.142 wdl.w:ptcp.w:call-sawfish-35.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:26][sawfish][INFO] Refining SV Candidates
2025-09-15 20:24:29.142 wdl.w:ptcp.w:call-sawfish-35.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:26][sawfish][INFO] Writing debug assembly region bed file: 'm84036_250809_035451_s4.bc2132_sawfish_discover/assembly.regions.bed'
2025-09-15 20:24:29.142 wdl.w:ptcp.w:call-sawfish-35.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:26][sawfish][INFO] Starting refinement of breakpoint evidence clusters
2025-09-15 20:24:29.142 wdl.w:ptcp.w:call-sawfish-35.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:26][sawfish][INFO] Finished refining all breakpoint evidence clusters
2025-09-15 20:24:29.143 wdl.w:ptcp.w:call-sawfish-35.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:26][sawfish][INFO] Writing all contig alignments to bam file: 'm84036_250809_035451_s4.bc2132_sawfish_discover/contig.alignment.bam'
2025-09-15 20:24:29.143 wdl.w:ptcp.w:call-sawfish-35.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:27][sawfish][INFO] Writing candidate structural variants to file: 'm84036_250809_035451_s4.bc2132_sawfish_discover/candidate.sv.bcf'
2025-09-15 20:24:29.143 wdl.w:ptcp.w:call-sawfish-35.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:27][sawfish][INFO] Writing run statistics to file: 'm84036_250809_035451_s4.bc2132_sawfish_discover/run.stats.json'
2025-09-15 20:24:29.143 wdl.w:ptcp.w:call-sawfish-35.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:27][sawfish][INFO] sawfish completed. Total Runtime: 00:00:10.832
2025-09-15 20:24:29.146 wdl.w:ptcp.w:call-paraphase-00.t:call-call_f8 INFO output :: name: "json", value: "m84036_250809_035451_s4.bc2097.f8inversion.json"
2025-09-15 20:24:29.188 wdl.w:ptcp.w:call-trgt-02.t:call-trgt_plot_motifs_allele NOTICE done
2025-09-15 20:24:29.195 wdl.w:ptcp.w:call-trgt-02 NOTICE finish :: job: "call-trgt_plot_motifs_allele"
2025-09-15 20:24:29.195 wdl.w:ptcp.w:call-trgt-02 INFO output :: job: "call-trgt_plot_motifs_allele", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-02/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2099.motifs_allele.trgt_plots.zip"}
2025-09-15 20:24:29.195 wdl.w:ptcp.w:call-trgt-02 INFO visit :: node: "output-images_motifs_allele", values: {"images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-02/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2099.motifs_allele.trgt_plots.zip"}
2025-09-15 20:24:29.195 wdl.w:ptcp.w:call-trgt-02 INFO visit :: node: "outputs", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-02/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2099.motifs_waterfall.trgt_plots.zip", "images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-02/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2099.meth_allele.trgt_plots.zip", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-02/call-trgt_genotype/out/m84036_250809_035451_s4.bc2099.trgt.sorted.spanning.bam.bai", "images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-02/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2099.motifs_allele.trgt_plots.zip", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-02/call-trgt_genotype/out/m84036_250809_035451_s4.bc2099.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-02/call-trgt_genotype/out/m84036_250809_035451_s4.bc2099.trgt.vcf", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-02/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2099.repeats.bam", "images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-02/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2099.meth_waterfall.trgt_plots.zip", "reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-02/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2099.repeats.bam.bai"}
2025-09-15 20:24:29.196 wdl.w:ptcp.w:call-sawfish-15.t:call-run_sawfish NOTICE done
2025-09-15 20:24:29.204 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_meth_waterfall NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-38/call-trgt_plot_meth_waterfall", thread: 140609310422592
2025-09-15 20:24:29.205 wdl.w:ptcp.w:call-sawfish-15 NOTICE finish :: job: "call-run_sawfish"
2025-09-15 20:24:29.205 wdl.w:ptcp.w:call-sawfish-15 INFO output :: job: "call-run_sawfish", values: {"minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-15/call-run_sawfish/out/m84036_250809_035451_s4.bc2112.minimap2.bam.bai", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-15/call-run_sawfish/out/m84036_250809_035451_s4.bc2112.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-15/call-run_sawfish/out/m84036_250809_035451_s4.bc2112_sawfish/m84036_250809_035451_s4.bc2112.sv.vcf.gz.tbi", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-15/call-run_sawfish/out/m84036_250809_035451_s4.bc2112_sawfish/m84036_250809_035451_s4.bc2112.sv.vcf.gz"}
2025-09-15 20:24:29.206 wdl.w:ptcp.w:call-sawfish-15 INFO visit :: node: "output-minimap2_bam", values: {"minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-15/call-run_sawfish/out/m84036_250809_035451_s4.bc2112.minimap2.bam"}
2025-09-15 20:24:29.206 wdl.w:ptcp.w:call-sawfish-15 INFO visit :: node: "output-minimap2_bam_bai", values: {"minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-15/call-run_sawfish/out/m84036_250809_035451_s4.bc2112.minimap2.bam.bai"}
2025-09-15 20:24:29.206 wdl.w:ptcp.w:call-sawfish-15 INFO visit :: node: "output-vcf", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-15/call-run_sawfish/out/m84036_250809_035451_s4.bc2112_sawfish/m84036_250809_035451_s4.bc2112.sv.vcf.gz"}
2025-09-15 20:24:29.206 wdl.w:ptcp.w:call-sawfish-15 INFO visit :: node: "output-vcf_tbi", values: {"vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-15/call-run_sawfish/out/m84036_250809_035451_s4.bc2112_sawfish/m84036_250809_035451_s4.bc2112.sv.vcf.gz.tbi"}
2025-09-15 20:24:29.207 wdl.w:ptcp.w:call-sawfish-15 INFO visit :: node: "outputs", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-15/call-run_sawfish/out/m84036_250809_035451_s4.bc2112_sawfish/m84036_250809_035451_s4.bc2112.sv.vcf.gz", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-15/call-run_sawfish/out/m84036_250809_035451_s4.bc2112.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-15/call-run_sawfish/out/m84036_250809_035451_s4.bc2112_sawfish/m84036_250809_035451_s4.bc2112.sv.vcf.gz.tbi", "minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-15/call-run_sawfish/out/m84036_250809_035451_s4.bc2112.minimap2.bam.bai"}
2025-09-15 20:24:29.216 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_motifs_allele NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-38/call-trgt_plot_motifs_allele", thread: 140611449513536
2025-09-15 20:24:29.217 wdl.w:ptcp.w:call-trgt-09 NOTICE done
2025-09-15 20:24:29.225 wdl.w:ptcp NOTICE finish :: job: "call-trgt-09"
2025-09-15 20:24:29.225 wdl.w:ptcp INFO output :: job: "call-trgt-09", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-09/out/m84036_250809_035451_s4.bc2106.motifs_waterfall.trgt_plots.zip", "images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-09/out/m84036_250809_035451_s4.bc2106.meth_allele.trgt_plots.zip", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-09/out/m84036_250809_035451_s4.bc2106.trgt.sorted.spanning.bam.bai", "images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-09/out/m84036_250809_035451_s4.bc2106.motifs_allele.trgt_plots.zip", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-09/out/m84036_250809_035451_s4.bc2106.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-09/out/m84036_250809_035451_s4.bc2106.trgt.vcf", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-09/out/m84036_250809_035451_s4.bc2106.repeats.bam", "images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-09/out/m84036_250809_035451_s4.bc2106.meth_waterfall.trgt_plots.zip", "reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-09/out/m84036_250809_035451_s4.bc2106.repeats.bam.bai"}
2025-09-15 20:24:29.229 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_meth_waterfall INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:29.229 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_meth_waterfall INFO input :: name: "waterfall", value: true
2025-09-15 20:24:29.229 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_meth_waterfall INFO input :: name: "methylation", value: true
2025-09-15 20:24:29.229 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_meth_waterfall INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:29.229 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_meth_waterfall INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:29.229 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_meth_waterfall INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:29.229 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_meth_waterfall INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2135.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:29.229 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_meth_waterfall INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2135.trgt.sorted.spanning.bam"
2025-09-15 20:24:29.229 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_meth_waterfall INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2135.trgt.vcf"
2025-09-15 20:24:29.229 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_meth_waterfall INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2135"
2025-09-15 20:24:29.230 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_meth_waterfall INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:29.230 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_meth_waterfall INFO eval :: name: "plot_type", value: "waterfall"
2025-09-15 20:24:29.230 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_meth_waterfall INFO eval :: name: "show", value: "meth"
2025-09-15 20:24:29.230 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_meth_waterfall INFO eval :: name: "threads", value: 1
2025-09-15 20:24:29.230 wdl.w:ptcp.w:call-paraphase-00.t:call-call_f8 NOTICE done
2025-09-15 20:24:29.230 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_meth_waterfall INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:29.231 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_meth_waterfall INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2135.meth_waterfall"
2025-09-15 20:24:29.231 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_meth_waterfall INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:29.232 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_meth_waterfall WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:29.231 wdl.w:ptcp.w:call-trgt-25.t:call-trgt_plot_motifs_waterfall INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2122.motifs_waterfall.trgt_plots.zip"
2025-09-15 20:24:29.232 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_meth_waterfall INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:29.232 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_meth_waterfall INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:29.235 wdl.w:ptcp.w:call-sawfish-43 NOTICE workflow start :: name: "sawfish", source: "./sawfish.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-43"
2025-09-15 20:24:29.238 wdl.w:ptcp.w:call-paraphase-00 NOTICE finish :: job: "call-call_f8"
2025-09-15 20:24:29.239 wdl.w:ptcp.w:call-paraphase-00 INFO output :: job: "call-call_f8", values: {"json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-00/call-call_f8/out/m84036_250809_035451_s4.bc2097.f8inversion.json", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-00/call-call_f8/out/m84036_250809_035451_s4.bc2097.f8inversion.vcf"}
2025-09-15 20:24:29.239 wdl.w:ptcp.w:call-paraphase-00 INFO visit :: node: "output-f8_json", values: {"f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-00/call-call_f8/out/m84036_250809_035451_s4.bc2097.f8inversion.json"}
2025-09-15 20:24:29.240 wdl.w:ptcp.w:call-paraphase-00 INFO visit :: node: "output-f8_vcf", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-00/call-call_f8/out/m84036_250809_035451_s4.bc2097.f8inversion.vcf"}
2025-09-15 20:24:29.240 wdl.w:ptcp.w:call-paraphase-00 INFO visit :: node: "outputs", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-00/call-call_f8/out/m84036_250809_035451_s4.bc2097.f8inversion.vcf", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-00/call-run_paraphase/out/m84036_250809_035451_s4.bc2097_paraphase/m84036_250809_035451_s4.bc2097.paraphase.json", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-00/call-run_paraphase/out/m84036_250809_035451_s4.bc2097_paraphase/m84036_250809_035451_s4.bc2097.paraphase.bam", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-00/call-run_paraphase/out/m84036_250809_035451_s4.bc2097_paraphase/m84036_250809_035451_s4.bc2097.paraphase.bam.bai", "paraphase_vcfs": [], "havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-00/call-run_paraphase/out/m84036_250809_035451_s4.bc2097.havanno.json", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-00/call-call_f8/out/m84036_250809_035451_s4.bc2097.f8inversion.json"}
2025-09-15 20:24:29.249 wdl.w:ptcp.w:call-trgt-36.t:call-trgt_plot_motifs_waterfall INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-36/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_xs4br7sj"
2025-09-15 20:24:29.249 wdl.w:ptcp.w:call-trgt-36.t:call-trgt_plot_motifs_waterfall INFO Slurm invocation: srun --job-name call-trgt_plot_motifs_waterfall --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-36/call-trgt_plot_motifs_waterfall/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-36/call-trgt_plot_motifs_waterfall/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-36/call-trgt_plot_motifs_waterfall/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-36/call-trgt_plot_motifs_waterfall/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-36/call-trgt_genotype/out/m84036_250809_035451_s4.bc2133.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2133.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-36/call-trgt_genotype/out/m84036_250809_035451_s4.bc2133.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2133.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-36/call-trgt_genotype/out/m84036_250809_035451_s4.bc2133.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2133.trgt.sorted.spanning.bam.bai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-36/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_xs4br7sj/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-36/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_xs4br7sj/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:29.250 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_motifs_waterfall NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-38/call-trgt_plot_motifs_waterfall", thread: 140610879071808
2025-09-15 20:24:29.253 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_meth_allele INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-38/call-trgt_plot_meth_allele/_singularity_tmpdir_5j_aqed1"
2025-09-15 20:24:29.254 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_meth_allele INFO Slurm invocation: srun --job-name call-trgt_plot_meth_allele --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-38/call-trgt_plot_meth_allele/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-38/call-trgt_plot_meth_allele/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-38/call-trgt_plot_meth_allele/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-38/call-trgt_plot_meth_allele/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-38/call-trgt_genotype/out/m84036_250809_035451_s4.bc2135.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2135.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-38/call-trgt_genotype/out/m84036_250809_035451_s4.bc2135.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2135.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-38/call-trgt_genotype/out/m84036_250809_035451_s4.bc2135.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2135.trgt.vcf:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-38/call-trgt_plot_meth_allele/_singularity_tmpdir_5j_aqed1/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-38/call-trgt_plot_meth_allele/_singularity_tmpdir_5j_aqed1/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:29.258 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_motifs_allele INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:29.259 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_motifs_allele INFO input :: name: "waterfall", value: false
2025-09-15 20:24:29.259 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_motifs_allele INFO input :: name: "methylation", value: false
2025-09-15 20:24:29.259 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_motifs_allele INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:29.259 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_motifs_allele INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:29.259 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_motifs_allele INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:29.259 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_motifs_allele INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2135.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:29.259 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_motifs_allele INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2135.trgt.sorted.spanning.bam"
2025-09-15 20:24:29.259 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_motifs_allele INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2135.trgt.vcf"
2025-09-15 20:24:29.260 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_motifs_allele INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2135"
2025-09-15 20:24:29.260 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_motifs_allele INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:29.260 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_motifs_allele INFO eval :: name: "plot_type", value: "allele"
2025-09-15 20:24:29.260 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_motifs_allele INFO eval :: name: "show", value: "motifs"
2025-09-15 20:24:29.260 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_motifs_allele INFO eval :: name: "threads", value: 1
2025-09-15 20:24:29.261 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_motifs_allele INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:29.261 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_motifs_allele INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2135.motifs_allele"
2025-09-15 20:24:29.262 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_motifs_allele INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:29.263 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_motifs_allele WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:29.263 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_motifs_allele INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:29.263 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_motifs_allele INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:29.264 wdl.w:ptcp.w:call-sawfish-43 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:24:29.265 wdl.w:ptcp.w:call-sawfish-43 INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:24:29.265 wdl.w:ptcp.w:call-sawfish-43 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-43/out/m84036_250809_035451_s4.bc2140.mapped.bam"}
2025-09-15 20:24:29.265 wdl.w:ptcp.w:call-sawfish-43 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-43/out/m84036_250809_035451_s4.bc2140.mapped.bam.bai"}
2025-09-15 20:24:29.265 wdl.w:ptcp.w:call-sawfish-43 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:24:29.266 wdl.w:ptcp.w:call-sawfish-43 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:24:29.266 wdl.w:ptcp.w:call-sawfish-43 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2140"}
2025-09-15 20:24:29.266 wdl.w:ptcp.w:call-sawfish-43 NOTICE ready :: job: "call-run_sawfish", callee: "run_sawfish"
2025-09-15 20:24:29.266 wdl.w:ptcp.w:call-sawfish-43 INFO input :: job: "call-run_sawfish", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-43/out/m84036_250809_035451_s4.bc2140.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-43/out/m84036_250809_035451_s4.bc2140.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2140"}
2025-09-15 20:24:29.269 wdl.w:ptcp.w:call-trgt-47.t:call-get_reads_overlapping_repeats.slurm_singularity INFO srun: job 51797660 queued and waiting for resources
2025-09-15 20:24:29.270 wdl.w:ptcp.w:call-trgt-47.t:call-get_reads_overlapping_repeats.slurm_singularity INFO srun: job 51797660 has been allocated resources
2025-09-15 20:24:29.270 wdl.w:ptcp.w:call-trgt-47.t:call-get_reads_overlapping_repeats.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:29.276 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_motifs_waterfall INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:29.276 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_motifs_waterfall INFO input :: name: "waterfall", value: true
2025-09-15 20:24:29.277 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_motifs_waterfall INFO input :: name: "methylation", value: false
2025-09-15 20:24:29.277 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_motifs_waterfall INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:29.277 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_motifs_waterfall INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:29.277 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_motifs_waterfall INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:29.277 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_motifs_waterfall INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2135.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:29.277 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_motifs_waterfall INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2135.trgt.sorted.spanning.bam"
2025-09-15 20:24:29.277 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_motifs_waterfall INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2135.trgt.vcf"
2025-09-15 20:24:29.277 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_motifs_waterfall INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2135"
2025-09-15 20:24:29.277 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:29.278 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "plot_type", value: "waterfall"
2025-09-15 20:24:29.278 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "show", value: "motifs"
2025-09-15 20:24:29.278 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "threads", value: 1
2025-09-15 20:24:29.278 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:29.278 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2135.motifs_waterfall"
2025-09-15 20:24:29.279 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_motifs_waterfall INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:29.279 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_motifs_waterfall WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:29.280 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_motifs_waterfall INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:29.280 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_motifs_waterfall INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:29.285 wdl.w:ptcp.w:call-sawfish-15 NOTICE done
2025-09-15 20:24:29.289 wdl.w:ptcp.w:call-sawfish-34.t:call-run_sawfish INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2131_sawfish/m84036_250809_035451_s4.bc2131.sv.vcf.gz"
2025-09-15 20:24:29.292 wdl.w:ptcp NOTICE finish :: job: "call-sawfish-15"
2025-09-15 20:24:29.292 wdl.w:ptcp INFO output :: job: "call-sawfish-15", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-15/out/m84036_250809_035451_s4.bc2112_sawfish/m84036_250809_035451_s4.bc2112.sv.vcf.gz", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-15/out/m84036_250809_035451_s4.bc2112.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-15/out/m84036_250809_035451_s4.bc2112_sawfish/m84036_250809_035451_s4.bc2112.sv.vcf.gz.tbi", "minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-15/out/m84036_250809_035451_s4.bc2112.minimap2.bam.bai"}
2025-09-15 20:24:29.298 wdl.w:ptcp.w:call-sawfish-34.t:call-run_sawfish INFO output :: name: "vcf_tbi", value: "m84036_250809_035451_s4.bc2131_sawfish/m84036_250809_035451_s4.bc2131.sv.vcf.gz.tbi"
2025-09-15 20:24:29.300 wdl.w:ptcp.w:call-sawfish-34.t:call-run_sawfish INFO output :: name: "minimap2_bam", value: "m84036_250809_035451_s4.bc2131.minimap2.bam"
2025-09-15 20:24:29.301 wdl.w:ptcp.w:call-trgt-36.t:call-trgt_plot_motifs_waterfall NOTICE slurm_singularity run :: pid: 1201991, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-36/call-trgt_plot_motifs_waterfall/slurm_singularity.log.txt"
2025-09-15 20:24:29.302 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_meth_allele NOTICE slurm_singularity run :: pid: 1201992, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-38/call-trgt_plot_meth_allele/slurm_singularity.log.txt"
2025-09-15 20:24:29.302 wdl.w:ptcp.w:call-trgt-43 NOTICE workflow start :: name: "trgt", source: "./trgt.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-43"
2025-09-15 20:24:29.303 wdl.w:ptcp.w:call-sawfish-34.t:call-run_sawfish INFO output :: name: "minimap2_bam_bai", value: "m84036_250809_035451_s4.bc2131.minimap2.bam.bai"
2025-09-15 20:24:29.328 wdl.w:ptcp.w:call-trgt-02 NOTICE done
2025-09-15 20:24:29.331 wdl.w:ptcp.w:call-trgt-43 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:24:29.331 wdl.w:ptcp.w:call-trgt-43 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-43/out/m84036_250809_035451_s4.bc2140.mapped.bam"}
2025-09-15 20:24:29.332 wdl.w:ptcp.w:call-trgt-43 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-43/out/m84036_250809_035451_s4.bc2140.mapped.bam.bai"}
2025-09-15 20:24:29.332 wdl.w:ptcp.w:call-trgt-43 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:24:29.332 wdl.w:ptcp.w:call-trgt-43 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:24:29.332 wdl.w:ptcp.w:call-trgt-43 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2140"}
2025-09-15 20:24:29.332 wdl.w:ptcp.w:call-trgt-43 INFO visit :: node: "decl-sex", values: {"sex": "F"}
2025-09-15 20:24:29.332 wdl.w:ptcp.w:call-trgt-43 INFO visit :: node: "decl-trgt_bed", values: {"trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"}
2025-09-15 20:24:29.332 wdl.w:ptcp.w:call-trgt-43 NOTICE ready :: job: "call-get_reads_overlapping_repeats", callee: "get_reads_overlapping_repeats"
2025-09-15 20:24:29.332 wdl.w:ptcp.w:call-trgt-43 INFO input :: job: "call-get_reads_overlapping_repeats", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-43/out/m84036_250809_035451_s4.bc2140.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-43/out/m84036_250809_035451_s4.bc2140.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2140"}
2025-09-15 20:24:29.334 wdl.w:ptcp.w:call-trgt-43 NOTICE ready :: job: "call-trgt_genotype", callee: "trgt_genotype"
2025-09-15 20:24:29.334 wdl.w:ptcp.w:call-trgt-43 INFO input :: job: "call-trgt_genotype", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-43/out/m84036_250809_035451_s4.bc2140.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-43/out/m84036_250809_035451_s4.bc2140.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2140"}
2025-09-15 20:24:29.335 wdl.w:ptcp NOTICE finish :: job: "call-trgt-02"
2025-09-15 20:24:29.336 wdl.w:ptcp INFO output :: job: "call-trgt-02", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-02/out/m84036_250809_035451_s4.bc2099.motifs_waterfall.trgt_plots.zip", "images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-02/out/m84036_250809_035451_s4.bc2099.meth_allele.trgt_plots.zip", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-02/out/m84036_250809_035451_s4.bc2099.trgt.sorted.spanning.bam.bai", "images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-02/out/m84036_250809_035451_s4.bc2099.motifs_allele.trgt_plots.zip", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-02/out/m84036_250809_035451_s4.bc2099.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-02/out/m84036_250809_035451_s4.bc2099.trgt.vcf", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-02/out/m84036_250809_035451_s4.bc2099.repeats.bam", "images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-02/out/m84036_250809_035451_s4.bc2099.meth_waterfall.trgt_plots.zip", "reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-02/out/m84036_250809_035451_s4.bc2099.repeats.bam.bai"}
2025-09-15 20:24:29.343 wdl.w:ptcp.w:call-paraphase-55 NOTICE workflow start :: name: "paraphase", source: "./paraphase.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-55"
2025-09-15 20:24:29.343 wdl.w:ptcp.w:call-paraphase-00 NOTICE done
2025-09-15 20:24:29.354 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_meth_waterfall INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-38/call-trgt_plot_meth_waterfall/_singularity_tmpdir_o1n60w_n"
2025-09-15 20:24:29.354 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_meth_waterfall INFO Slurm invocation: srun --job-name call-trgt_plot_meth_waterfall --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-38/call-trgt_plot_meth_waterfall/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-38/call-trgt_plot_meth_waterfall/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-38/call-trgt_plot_meth_waterfall/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-38/call-trgt_plot_meth_waterfall/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-38/call-trgt_genotype/out/m84036_250809_035451_s4.bc2135.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2135.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-38/call-trgt_genotype/out/m84036_250809_035451_s4.bc2135.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2135.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-38/call-trgt_genotype/out/m84036_250809_035451_s4.bc2135.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2135.trgt.vcf:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-38/call-trgt_plot_meth_waterfall/_singularity_tmpdir_o1n60w_n/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-38/call-trgt_plot_meth_waterfall/_singularity_tmpdir_o1n60w_n/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:29.368 wdl.w:ptcp.w:call-paraphase-55 INFO visit :: node: "decl-annotation_vcf", values: {"annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf"}
2025-09-15 20:24:29.368 wdl.w:ptcp.w:call-paraphase-55 INFO visit :: node: "decl-config_file", values: {"config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml"}
2025-09-15 20:24:29.369 wdl.w:ptcp.w:call-paraphase-55 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:24:29.369 wdl.w:ptcp.w:call-paraphase-55 INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:24:29.370 wdl.w:ptcp.w:call-paraphase-55 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-55/out/m84036_250809_035451_s4.bc2152.mapped.bam"}
2025-09-15 20:24:29.370 wdl.w:ptcp.w:call-paraphase-55 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-55/out/m84036_250809_035451_s4.bc2152.mapped.bam.bai"}
2025-09-15 20:24:29.370 wdl.w:ptcp.w:call-paraphase-55 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:24:29.370 wdl.w:ptcp.w:call-paraphase-55 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:24:29.370 wdl.w:ptcp.w:call-paraphase-55 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2152"}
2025-09-15 20:24:29.370 wdl.w:ptcp.w:call-paraphase-55 INFO visit :: node: "decl-sex", values: {"sex": "F"}
2025-09-15 20:24:29.370 wdl.w:ptcp.w:call-paraphase-55 NOTICE ready :: job: "call-run_paraphase", callee: "run_paraphase"
2025-09-15 20:24:29.370 wdl.w:ptcp.w:call-paraphase-55 INFO input :: job: "call-run_paraphase", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf", "genome_version": "38", "config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-55/out/m84036_250809_035451_s4.bc2152.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-55/out/m84036_250809_035451_s4.bc2152.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2152"}
2025-09-15 20:24:29.372 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_motifs_allele INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-38/call-trgt_plot_motifs_allele/_singularity_tmpdir_rbmi7x2i"
2025-09-15 20:24:29.373 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_motifs_allele INFO Slurm invocation: srun --job-name call-trgt_plot_motifs_allele --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-38/call-trgt_plot_motifs_allele/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-38/call-trgt_plot_motifs_allele/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-38/call-trgt_plot_motifs_allele/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-38/call-trgt_plot_motifs_allele/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-38/call-trgt_genotype/out/m84036_250809_035451_s4.bc2135.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2135.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-38/call-trgt_genotype/out/m84036_250809_035451_s4.bc2135.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2135.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-38/call-trgt_genotype/out/m84036_250809_035451_s4.bc2135.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2135.trgt.vcf:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-38/call-trgt_plot_motifs_allele/_singularity_tmpdir_rbmi7x2i/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-38/call-trgt_plot_motifs_allele/_singularity_tmpdir_rbmi7x2i/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:29.374 wdl.w:ptcp NOTICE finish :: job: "call-paraphase-00"
2025-09-15 20:24:29.376 wdl.w:ptcp INFO output :: job: "call-paraphase-00", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-00/out/m84036_250809_035451_s4.bc2097.f8inversion.vcf", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-00/out/m84036_250809_035451_s4.bc2097_paraphase/m84036_250809_035451_s4.bc2097.paraphase.json", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-00/out/m84036_250809_035451_s4.bc2097_paraphase/m84036_250809_035451_s4.bc2097.paraphase.bam", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-00/out/m84036_250809_035451_s4.bc2097_paraphase/m84036_250809_035451_s4.bc2097.paraphase.bam.bai", "paraphase_vcfs": [], "havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-00/out/m84036_250809_035451_s4.bc2097.havanno.json", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-00/out/m84036_250809_035451_s4.bc2097.f8inversion.json"}
2025-09-15 20:24:29.378 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_motifs_waterfall INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-38/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_3_19o5ao"
2025-09-15 20:24:29.379 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_motifs_waterfall INFO Slurm invocation: srun --job-name call-trgt_plot_motifs_waterfall --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-38/call-trgt_plot_motifs_waterfall/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-38/call-trgt_plot_motifs_waterfall/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-38/call-trgt_plot_motifs_waterfall/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-38/call-trgt_plot_motifs_waterfall/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-38/call-trgt_genotype/out/m84036_250809_035451_s4.bc2135.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2135.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-38/call-trgt_genotype/out/m84036_250809_035451_s4.bc2135.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2135.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-38/call-trgt_genotype/out/m84036_250809_035451_s4.bc2135.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2135.trgt.vcf:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-38/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_3_19o5ao/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-38/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_3_19o5ao/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:29.383 wdl.w:ptcp.w:call-sawfish-55 NOTICE workflow start :: name: "sawfish", source: "./sawfish.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-55"
2025-09-15 20:24:29.383 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_meth_waterfall NOTICE slurm_singularity run :: pid: 1201995, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-38/call-trgt_plot_meth_waterfall/slurm_singularity.log.txt"
2025-09-15 20:24:29.386 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_motifs_allele NOTICE slurm_singularity run :: pid: 1201996, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-38/call-trgt_plot_motifs_allele/slurm_singularity.log.txt"
2025-09-15 20:24:29.386 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_motifs_waterfall NOTICE slurm_singularity run :: pid: 1201997, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-38/call-trgt_plot_motifs_waterfall/slurm_singularity.log.txt"
2025-09-15 20:24:29.397 wdl.w:ptcp.w:call-paraphase-02.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for f8inv1 for sample m84036_250809_035451_s4.bc2099 at 2025-09-15 20:24:28.452634...
2025-09-15 20:24:29.397 wdl.w:ptcp.w:call-paraphase-02.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for f8inv1 for sample m84036_250809_035451_s4.bc2099 at 2025-09-15 20:24:28.453474...
2025-09-15 20:24:29.399 wdl.w:ptcp.w:call-sawfish-55 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:24:29.399 wdl.w:ptcp.w:call-sawfish-55 INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:24:29.399 wdl.w:ptcp.w:call-sawfish-55 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-55/out/m84036_250809_035451_s4.bc2152.mapped.bam"}
2025-09-15 20:24:29.399 wdl.w:ptcp.w:call-sawfish-55 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-55/out/m84036_250809_035451_s4.bc2152.mapped.bam.bai"}
2025-09-15 20:24:29.399 wdl.w:ptcp.w:call-sawfish-55 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:24:29.400 wdl.w:ptcp.w:call-sawfish-55 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:24:29.400 wdl.w:ptcp.w:call-sawfish-55 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2152"}
2025-09-15 20:24:29.400 wdl.w:ptcp.w:call-sawfish-55 NOTICE ready :: job: "call-run_sawfish", callee: "run_sawfish"
2025-09-15 20:24:29.400 wdl.w:ptcp.w:call-sawfish-55 INFO input :: job: "call-run_sawfish", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-55/out/m84036_250809_035451_s4.bc2152.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-55/out/m84036_250809_035451_s4.bc2152.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2152"}
2025-09-15 20:24:29.411 wdl.w:ptcp.w:call-trgt-25.t:call-trgt_plot_motifs_waterfall NOTICE done
2025-09-15 20:24:29.416 wdl.w:ptcp.w:call-trgt-25 NOTICE finish :: job: "call-trgt_plot_motifs_waterfall"
2025-09-15 20:24:29.417 wdl.w:ptcp.w:call-trgt-25 INFO output :: job: "call-trgt_plot_motifs_waterfall", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-25/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2122.motifs_waterfall.trgt_plots.zip"}
2025-09-15 20:24:29.417 wdl.w:ptcp.w:call-trgt-25 INFO visit :: node: "output-images_motifs_waterfall", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-25/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2122.motifs_waterfall.trgt_plots.zip"}
2025-09-15 20:24:29.417 wdl.w:ptcp.w:call-trgt-25 INFO visit :: node: "outputs", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-25/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2122.motifs_waterfall.trgt_plots.zip", "images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-25/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2122.meth_allele.trgt_plots.zip", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-25/call-trgt_genotype/out/m84036_250809_035451_s4.bc2122.trgt.sorted.spanning.bam.bai", "images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-25/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2122.motifs_allele.trgt_plots.zip", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-25/call-trgt_genotype/out/m84036_250809_035451_s4.bc2122.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-25/call-trgt_genotype/out/m84036_250809_035451_s4.bc2122.trgt.vcf", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-25/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2122.repeats.bam", "images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-25/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2122.meth_waterfall.trgt_plots.zip", "reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-25/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2122.repeats.bam.bai"}
2025-09-15 20:24:29.425 wdl.w:ptcp.w:call-trgt-37.t:call-trgt_plot_meth_allele NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-37/call-trgt_plot_meth_allele", thread: 140610887464512
2025-09-15 20:24:29.452 wdl.w:ptcp.w:call-trgt-37.t:call-trgt_plot_meth_allele INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:29.452 wdl.w:ptcp.w:call-trgt-37.t:call-trgt_plot_meth_allele INFO input :: name: "waterfall", value: false
2025-09-15 20:24:29.452 wdl.w:ptcp.w:call-trgt-37.t:call-trgt_plot_meth_allele INFO input :: name: "methylation", value: true
2025-09-15 20:24:29.452 wdl.w:ptcp.w:call-trgt-37.t:call-trgt_plot_meth_allele INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:29.452 wdl.w:ptcp.w:call-trgt-37.t:call-trgt_plot_meth_allele INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:29.452 wdl.w:ptcp.w:call-trgt-37.t:call-trgt_plot_meth_allele INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:29.452 wdl.w:ptcp.w:call-trgt-37.t:call-trgt_plot_meth_allele INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2134.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:29.452 wdl.w:ptcp.w:call-trgt-37.t:call-trgt_plot_meth_allele INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2134.trgt.sorted.spanning.bam"
2025-09-15 20:24:29.452 wdl.w:ptcp.w:call-trgt-37.t:call-trgt_plot_meth_allele INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2134.trgt.vcf"
2025-09-15 20:24:29.452 wdl.w:ptcp.w:call-trgt-37.t:call-trgt_plot_meth_allele INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2134"
2025-09-15 20:24:29.453 wdl.w:ptcp.w:call-trgt-37.t:call-trgt_plot_meth_allele INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:29.453 wdl.w:ptcp.w:call-trgt-37.t:call-trgt_plot_meth_allele INFO eval :: name: "plot_type", value: "allele"
2025-09-15 20:24:29.453 wdl.w:ptcp.w:call-trgt-37.t:call-trgt_plot_meth_allele INFO eval :: name: "show", value: "meth"
2025-09-15 20:24:29.453 wdl.w:ptcp.w:call-trgt-37.t:call-trgt_plot_meth_allele INFO eval :: name: "threads", value: 1
2025-09-15 20:24:29.453 wdl.w:ptcp.w:call-trgt-37.t:call-trgt_plot_meth_allele INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:29.453 wdl.w:ptcp.w:call-trgt-37.t:call-trgt_plot_meth_allele INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2134.meth_allele"
2025-09-15 20:24:29.454 wdl.w:ptcp.w:call-trgt-37.t:call-trgt_plot_meth_allele INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:29.454 wdl.w:ptcp.w:call-trgt-37.t:call-trgt_plot_meth_allele WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:29.454 wdl.w:ptcp.w:call-trgt-37.t:call-trgt_plot_meth_allele INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:29.454 wdl.w:ptcp.w:call-trgt-37.t:call-trgt_plot_meth_allele INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:29.479 wdl.w:ptcp.w:call-sawfish-34.t:call-run_sawfish NOTICE done
2025-09-15 20:24:29.485 wdl.w:ptcp.w:call-sawfish-34 NOTICE finish :: job: "call-run_sawfish"
2025-09-15 20:24:29.485 wdl.w:ptcp.w:call-sawfish-34 INFO output :: job: "call-run_sawfish", values: {"minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-34/call-run_sawfish/out/m84036_250809_035451_s4.bc2131.minimap2.bam.bai", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-34/call-run_sawfish/out/m84036_250809_035451_s4.bc2131.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-34/call-run_sawfish/out/m84036_250809_035451_s4.bc2131_sawfish/m84036_250809_035451_s4.bc2131.sv.vcf.gz.tbi", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-34/call-run_sawfish/out/m84036_250809_035451_s4.bc2131_sawfish/m84036_250809_035451_s4.bc2131.sv.vcf.gz"}
2025-09-15 20:24:29.485 wdl.w:ptcp.w:call-sawfish-34 INFO visit :: node: "output-minimap2_bam", values: {"minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-34/call-run_sawfish/out/m84036_250809_035451_s4.bc2131.minimap2.bam"}
2025-09-15 20:24:29.486 wdl.w:ptcp.w:call-sawfish-34 INFO visit :: node: "output-minimap2_bam_bai", values: {"minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-34/call-run_sawfish/out/m84036_250809_035451_s4.bc2131.minimap2.bam.bai"}
2025-09-15 20:24:29.486 wdl.w:ptcp.w:call-sawfish-34 INFO visit :: node: "output-vcf", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-34/call-run_sawfish/out/m84036_250809_035451_s4.bc2131_sawfish/m84036_250809_035451_s4.bc2131.sv.vcf.gz"}
2025-09-15 20:24:29.486 wdl.w:ptcp.w:call-sawfish-34 INFO visit :: node: "output-vcf_tbi", values: {"vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-34/call-run_sawfish/out/m84036_250809_035451_s4.bc2131_sawfish/m84036_250809_035451_s4.bc2131.sv.vcf.gz.tbi"}
2025-09-15 20:24:29.486 wdl.w:ptcp.w:call-sawfish-34 INFO visit :: node: "outputs", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-34/call-run_sawfish/out/m84036_250809_035451_s4.bc2131_sawfish/m84036_250809_035451_s4.bc2131.sv.vcf.gz", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-34/call-run_sawfish/out/m84036_250809_035451_s4.bc2131.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-34/call-run_sawfish/out/m84036_250809_035451_s4.bc2131_sawfish/m84036_250809_035451_s4.bc2131.sv.vcf.gz.tbi", "minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-34/call-run_sawfish/out/m84036_250809_035451_s4.bc2131.minimap2.bam.bai"}
2025-09-15 20:24:29.494 wdl.w:ptcp.w:call-trgt-37.t:call-trgt_plot_meth_waterfall NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-37/call-trgt_plot_meth_waterfall", thread: 140613068518976
2025-09-15 20:24:29.505 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:24:29 [INFO] - Running trgt-4.0.0-429afcd [genotype]
2025-09-15 20:24:29.505 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:24:29 [WARN] - PRTS_ARX: Filtered out 2 impure reads
2025-09-15 20:24:29.505 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:24:29 [WARN] - EIEE1_ARX: Filtered out 2 impure reads
2025-09-15 20:24:29.505 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:24:29 [WARN] - FXS_FMR1: Filtered out 1 impure reads
2025-09-15 20:24:29.506 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:24:29 [WARN] - FRAXE_AFF2: Filtered out 7 impure reads
2025-09-15 20:24:29.506 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:24:29 [WARN] - FRDA_FXN: Filtered out 5 impure reads
2025-09-15 20:24:29.506 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:24:29 [INFO] - Total execution time: 179.50ms
2025-09-15 20:24:29.506 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:24:29 [INFO] - trgt end
2025-09-15 20:24:29.514 wdl.w:ptcp.w:call-trgt-37.t:call-trgt_plot_meth_waterfall INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:29.514 wdl.w:ptcp.w:call-trgt-37.t:call-trgt_plot_meth_waterfall INFO input :: name: "waterfall", value: true
2025-09-15 20:24:29.514 wdl.w:ptcp.w:call-trgt-37.t:call-trgt_plot_meth_waterfall INFO input :: name: "methylation", value: true
2025-09-15 20:24:29.514 wdl.w:ptcp.w:call-trgt-37.t:call-trgt_plot_meth_waterfall INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:29.514 wdl.w:ptcp.w:call-trgt-37.t:call-trgt_plot_meth_waterfall INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:29.514 wdl.w:ptcp.w:call-trgt-37.t:call-trgt_plot_meth_waterfall INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:29.514 wdl.w:ptcp.w:call-trgt-37.t:call-trgt_plot_meth_waterfall INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2134.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:29.514 wdl.w:ptcp.w:call-trgt-37.t:call-trgt_plot_meth_waterfall INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2134.trgt.sorted.spanning.bam"
2025-09-15 20:24:29.515 wdl.w:ptcp.w:call-trgt-37.t:call-trgt_plot_meth_waterfall INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2134.trgt.vcf"
2025-09-15 20:24:29.515 wdl.w:ptcp.w:call-trgt-37.t:call-trgt_plot_meth_waterfall INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2134"
2025-09-15 20:24:29.515 wdl.w:ptcp.w:call-trgt-37.t:call-trgt_plot_meth_waterfall INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:29.515 wdl.w:ptcp.w:call-trgt-37.t:call-trgt_plot_meth_waterfall INFO eval :: name: "plot_type", value: "waterfall"
2025-09-15 20:24:29.515 wdl.w:ptcp.w:call-trgt-37.t:call-trgt_plot_meth_waterfall INFO eval :: name: "show", value: "meth"
2025-09-15 20:24:29.515 wdl.w:ptcp.w:call-trgt-37.t:call-trgt_plot_meth_waterfall INFO eval :: name: "threads", value: 1
2025-09-15 20:24:29.515 wdl.w:ptcp.w:call-trgt-37.t:call-trgt_plot_meth_waterfall INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:29.516 wdl.w:ptcp.w:call-trgt-37.t:call-trgt_plot_meth_waterfall INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2134.meth_waterfall"
2025-09-15 20:24:29.516 wdl.w:ptcp.w:call-trgt-37.t:call-trgt_plot_meth_waterfall INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:29.516 wdl.w:ptcp.w:call-trgt-37.t:call-trgt_plot_meth_waterfall WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:29.516 wdl.w:ptcp.w:call-trgt-37.t:call-trgt_plot_meth_waterfall INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:29.517 wdl.w:ptcp.w:call-trgt-37.t:call-trgt_plot_meth_waterfall INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:29.520 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_genotype.slurm_singularity INFO srun: job 51797661 queued and waiting for resources
2025-09-15 20:24:29.520 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_genotype.slurm_singularity INFO srun: job 51797661 has been allocated resources
2025-09-15 20:24:29.520 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_genotype.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:29.525 wdl.w:ptcp.w:call-trgt-25 NOTICE done
2025-09-15 20:24:29.530 wdl.w:ptcp NOTICE finish :: job: "call-trgt-25"
2025-09-15 20:24:29.530 wdl.w:ptcp INFO output :: job: "call-trgt-25", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-25/out/m84036_250809_035451_s4.bc2122.motifs_waterfall.trgt_plots.zip", "images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-25/out/m84036_250809_035451_s4.bc2122.meth_allele.trgt_plots.zip", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-25/out/m84036_250809_035451_s4.bc2122.trgt.sorted.spanning.bam.bai", "images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-25/out/m84036_250809_035451_s4.bc2122.motifs_allele.trgt_plots.zip", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-25/out/m84036_250809_035451_s4.bc2122.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-25/out/m84036_250809_035451_s4.bc2122.trgt.vcf", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-25/out/m84036_250809_035451_s4.bc2122.repeats.bam", "images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-25/out/m84036_250809_035451_s4.bc2122.meth_waterfall.trgt_plots.zip", "reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-25/out/m84036_250809_035451_s4.bc2122.repeats.bam.bai"}
2025-09-15 20:24:29.536 wdl.w:ptcp.w:call-trgt-55 NOTICE workflow start :: name: "trgt", source: "./trgt.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-55"
2025-09-15 20:24:29.544 wdl.w:ptcp.w:call-sawfish-34 NOTICE done
2025-09-15 20:24:29.549 wdl.w:ptcp.w:call-trgt-47.t:call-get_reads_overlapping_repeats INFO output :: name: "reads_overlapping_repeats", value: "m84036_250809_035451_s4.bc2144.repeats.bam"
2025-09-15 20:24:29.552 wdl.w:ptcp NOTICE finish :: job: "call-sawfish-34"
2025-09-15 20:24:29.552 wdl.w:ptcp INFO output :: job: "call-sawfish-34", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-34/out/m84036_250809_035451_s4.bc2131_sawfish/m84036_250809_035451_s4.bc2131.sv.vcf.gz", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-34/out/m84036_250809_035451_s4.bc2131.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-34/out/m84036_250809_035451_s4.bc2131_sawfish/m84036_250809_035451_s4.bc2131.sv.vcf.gz.tbi", "minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-34/out/m84036_250809_035451_s4.bc2131.minimap2.bam.bai"}
2025-09-15 20:24:29.552 wdl.w:ptcp.w:call-trgt-37.t:call-trgt_plot_meth_allele INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-37/call-trgt_plot_meth_allele/_singularity_tmpdir_ud4ky75m"
2025-09-15 20:24:29.553 wdl.w:ptcp.w:call-trgt-37.t:call-trgt_plot_meth_allele INFO Slurm invocation: srun --job-name call-trgt_plot_meth_allele --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-37/call-trgt_plot_meth_allele/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-37/call-trgt_plot_meth_allele/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-37/call-trgt_plot_meth_allele/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-37/call-trgt_plot_meth_allele/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-37/call-trgt_genotype/out/m84036_250809_035451_s4.bc2134.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2134.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-37/call-trgt_genotype/out/m84036_250809_035451_s4.bc2134.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2134.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-37/call-trgt_genotype/out/m84036_250809_035451_s4.bc2134.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2134.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-37/call-trgt_plot_meth_allele/_singularity_tmpdir_ud4ky75m/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-37/call-trgt_plot_meth_allele/_singularity_tmpdir_ud4ky75m/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:29.554 wdl.w:ptcp.w:call-trgt-47.t:call-get_reads_overlapping_repeats INFO output :: name: "reads_overlapping_repeats_bai", value: "m84036_250809_035451_s4.bc2144.repeats.bam.bai"
2025-09-15 20:24:29.557 wdl.w:ptcp.w:call-trgt-55 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:24:29.558 wdl.w:ptcp.w:call-trgt-55 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-55/out/m84036_250809_035451_s4.bc2152.mapped.bam"}
2025-09-15 20:24:29.558 wdl.w:ptcp.w:call-trgt-55 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-55/out/m84036_250809_035451_s4.bc2152.mapped.bam.bai"}
2025-09-15 20:24:29.558 wdl.w:ptcp.w:call-trgt-55 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:24:29.558 wdl.w:ptcp.w:call-trgt-55 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:24:29.558 wdl.w:ptcp.w:call-trgt-55 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2152"}
2025-09-15 20:24:29.558 wdl.w:ptcp.w:call-trgt-55 INFO visit :: node: "decl-sex", values: {"sex": "F"}
2025-09-15 20:24:29.558 wdl.w:ptcp.w:call-trgt-55 INFO visit :: node: "decl-trgt_bed", values: {"trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"}
2025-09-15 20:24:29.560 wdl.w:ptcp.w:call-trgt-55 NOTICE ready :: job: "call-get_reads_overlapping_repeats", callee: "get_reads_overlapping_repeats"
2025-09-15 20:24:29.560 wdl.w:ptcp.w:call-paraphase-42 NOTICE workflow start :: name: "paraphase", source: "./paraphase.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-42"
2025-09-15 20:24:29.560 wdl.w:ptcp.w:call-trgt-55 INFO input :: job: "call-get_reads_overlapping_repeats", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-55/out/m84036_250809_035451_s4.bc2152.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-55/out/m84036_250809_035451_s4.bc2152.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2152"}
2025-09-15 20:24:29.562 wdl.w:ptcp.w:call-trgt-55 NOTICE ready :: job: "call-trgt_genotype", callee: "trgt_genotype"
2025-09-15 20:24:29.562 wdl.w:ptcp.w:call-trgt-55 INFO input :: job: "call-trgt_genotype", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-55/out/m84036_250809_035451_s4.bc2152.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-55/out/m84036_250809_035451_s4.bc2152.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2152"}
2025-09-15 20:24:29.563 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_genotype INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2144.trgt.vcf"
2025-09-15 20:24:29.567 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_genotype INFO output :: name: "spanning_bam", value: "m84036_250809_035451_s4.bc2144.trgt.sorted.spanning.bam"
2025-09-15 20:24:29.569 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_genotype INFO output :: name: "spanning_bam_bai", value: "m84036_250809_035451_s4.bc2144.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:29.634 wdl.w:ptcp.w:call-paraphase-42 INFO visit :: node: "decl-annotation_vcf", values: {"annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf"}
2025-09-15 20:24:29.635 wdl.w:ptcp.w:call-trgt-37.t:call-trgt_plot_meth_allele NOTICE slurm_singularity run :: pid: 1202029, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-37/call-trgt_plot_meth_allele/slurm_singularity.log.txt"
2025-09-15 20:24:29.635 wdl.w:ptcp.w:call-paraphase-42 INFO visit :: node: "decl-config_file", values: {"config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml"}
2025-09-15 20:24:29.635 wdl.w:ptcp.w:call-paraphase-42 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:24:29.636 wdl.w:ptcp.w:call-paraphase-42 INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:24:29.636 wdl.w:ptcp.w:call-paraphase-42 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-42/out/m84036_250809_035451_s4.bc2139.mapped.bam"}
2025-09-15 20:24:29.636 wdl.w:ptcp.w:call-paraphase-42 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-42/out/m84036_250809_035451_s4.bc2139.mapped.bam.bai"}
2025-09-15 20:24:29.636 wdl.w:ptcp.w:call-paraphase-42 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:24:29.636 wdl.w:ptcp.w:call-paraphase-42 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:24:29.636 wdl.w:ptcp.w:call-paraphase-42 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2139"}
2025-09-15 20:24:29.636 wdl.w:ptcp.w:call-paraphase-42 INFO visit :: node: "decl-sex", values: {"sex": "F"}
2025-09-15 20:24:29.636 wdl.w:ptcp.w:call-paraphase-42 NOTICE ready :: job: "call-run_paraphase", callee: "run_paraphase"
2025-09-15 20:24:29.636 wdl.w:ptcp.w:call-paraphase-42 INFO input :: job: "call-run_paraphase", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf", "genome_version": "38", "config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-42/out/m84036_250809_035451_s4.bc2139.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-42/out/m84036_250809_035451_s4.bc2139.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2139"}
2025-09-15 20:24:29.673 wdl.w:ptcp.w:call-trgt-37.t:call-trgt_plot_meth_waterfall INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-37/call-trgt_plot_meth_waterfall/_singularity_tmpdir_lftxwv9c"
2025-09-15 20:24:29.673 wdl.w:ptcp.w:call-trgt-37.t:call-trgt_plot_meth_waterfall INFO Slurm invocation: srun --job-name call-trgt_plot_meth_waterfall --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-37/call-trgt_plot_meth_waterfall/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-37/call-trgt_plot_meth_waterfall/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-37/call-trgt_plot_meth_waterfall/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-37/call-trgt_plot_meth_waterfall/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-37/call-trgt_genotype/out/m84036_250809_035451_s4.bc2134.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2134.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-37/call-trgt_genotype/out/m84036_250809_035451_s4.bc2134.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2134.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-37/call-trgt_genotype/out/m84036_250809_035451_s4.bc2134.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2134.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-37/call-trgt_plot_meth_waterfall/_singularity_tmpdir_lftxwv9c/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-37/call-trgt_plot_meth_waterfall/_singularity_tmpdir_lftxwv9c/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:29.691 wdl.w:ptcp.w:call-trgt-37.t:call-trgt_plot_meth_waterfall NOTICE slurm_singularity run :: pid: 1202095, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-37/call-trgt_plot_meth_waterfall/slurm_singularity.log.txt"
2025-09-15 20:24:29.698 wdl.w:ptcp.w:call-trgt-47.t:call-get_reads_overlapping_repeats NOTICE done
2025-09-15 20:24:29.727 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_genotype NOTICE done
2025-09-15 20:24:29.734 wdl.w:ptcp.w:call-trgt-47 NOTICE finish :: job: "call-trgt_genotype"
2025-09-15 20:24:29.734 wdl.w:ptcp.w:call-trgt-47 INFO output :: job: "call-trgt_genotype", values: {"spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-47/call-trgt_genotype/out/m84036_250809_035451_s4.bc2144.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-47/call-trgt_genotype/out/m84036_250809_035451_s4.bc2144.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-47/call-trgt_genotype/out/m84036_250809_035451_s4.bc2144.trgt.vcf"}
2025-09-15 20:24:29.735 wdl.w:ptcp.w:call-trgt-47 NOTICE ready :: job: "call-trgt_plot_meth_allele", callee: "trgt_plot"
2025-09-15 20:24:29.735 wdl.w:ptcp.w:call-trgt-47 INFO input :: job: "call-trgt_plot_meth_allele", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": false, "methylation": true, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-47/call-trgt_genotype/out/m84036_250809_035451_s4.bc2144.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-47/call-trgt_genotype/out/m84036_250809_035451_s4.bc2144.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-47/call-trgt_genotype/out/m84036_250809_035451_s4.bc2144.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2144"}
2025-09-15 20:24:29.737 wdl.w:ptcp.w:call-trgt-47 NOTICE ready :: job: "call-trgt_plot_meth_waterfall", callee: "trgt_plot"
2025-09-15 20:24:29.737 wdl.w:ptcp.w:call-trgt-47 INFO input :: job: "call-trgt_plot_meth_waterfall", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": true, "methylation": true, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-47/call-trgt_genotype/out/m84036_250809_035451_s4.bc2144.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-47/call-trgt_genotype/out/m84036_250809_035451_s4.bc2144.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-47/call-trgt_genotype/out/m84036_250809_035451_s4.bc2144.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2144"}
2025-09-15 20:24:29.738 wdl.w:ptcp.w:call-trgt-47 NOTICE ready :: job: "call-trgt_plot_motifs_allele", callee: "trgt_plot"
2025-09-15 20:24:29.738 wdl.w:ptcp.w:call-trgt-47 INFO input :: job: "call-trgt_plot_motifs_allele", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": false, "methylation": false, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-47/call-trgt_genotype/out/m84036_250809_035451_s4.bc2144.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-47/call-trgt_genotype/out/m84036_250809_035451_s4.bc2144.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-47/call-trgt_genotype/out/m84036_250809_035451_s4.bc2144.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2144"}
2025-09-15 20:24:29.739 wdl.w:ptcp.w:call-trgt-47 NOTICE ready :: job: "call-trgt_plot_motifs_waterfall", callee: "trgt_plot"
2025-09-15 20:24:29.739 wdl.w:ptcp.w:call-trgt-47 INFO input :: job: "call-trgt_plot_motifs_waterfall", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": true, "methylation": false, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-47/call-trgt_genotype/out/m84036_250809_035451_s4.bc2144.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-47/call-trgt_genotype/out/m84036_250809_035451_s4.bc2144.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-47/call-trgt_genotype/out/m84036_250809_035451_s4.bc2144.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2144"}
2025-09-15 20:24:29.740 wdl.w:ptcp.w:call-trgt-47 INFO visit :: node: "output-spanning_bam", values: {"spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-47/call-trgt_genotype/out/m84036_250809_035451_s4.bc2144.trgt.sorted.spanning.bam"}
2025-09-15 20:24:29.740 wdl.w:ptcp.w:call-trgt-47 INFO visit :: node: "output-spanning_bam_bai", values: {"spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-47/call-trgt_genotype/out/m84036_250809_035451_s4.bc2144.trgt.sorted.spanning.bam.bai"}
2025-09-15 20:24:29.740 wdl.w:ptcp.w:call-trgt-47 INFO visit :: node: "output-vcf", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-47/call-trgt_genotype/out/m84036_250809_035451_s4.bc2144.trgt.vcf"}
2025-09-15 20:24:29.747 wdl.w:ptcp.w:call-trgt-37.t:call-trgt_plot_motifs_allele NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-37/call-trgt_plot_motifs_allele", thread: 140610367379008
2025-09-15 20:24:29.763 wdl.w:ptcp.w:call-trgt-00.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:29 [ERROR] - No reads found for TRID=PRTS_ARX
2025-09-15 20:24:29.763 wdl.w:ptcp.w:call-trgt-00.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:29 [ERROR] - No reads found for TRID=EIEE1_ARX
2025-09-15 20:24:29.779 wdl.w:ptcp.w:call-trgt-37.t:call-trgt_plot_motifs_allele INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:29.779 wdl.w:ptcp.w:call-trgt-37.t:call-trgt_plot_motifs_allele INFO input :: name: "waterfall", value: false
2025-09-15 20:24:29.779 wdl.w:ptcp.w:call-trgt-37.t:call-trgt_plot_motifs_allele INFO input :: name: "methylation", value: false
2025-09-15 20:24:29.779 wdl.w:ptcp.w:call-trgt-37.t:call-trgt_plot_motifs_allele INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:29.779 wdl.w:ptcp.w:call-trgt-37.t:call-trgt_plot_motifs_allele INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:29.779 wdl.w:ptcp.w:call-trgt-37.t:call-trgt_plot_motifs_allele INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:29.779 wdl.w:ptcp.w:call-trgt-37.t:call-trgt_plot_motifs_allele INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2134.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:29.780 wdl.w:ptcp.w:call-trgt-37.t:call-trgt_plot_motifs_allele INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2134.trgt.sorted.spanning.bam"
2025-09-15 20:24:29.780 wdl.w:ptcp.w:call-trgt-37.t:call-trgt_plot_motifs_allele INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2134.trgt.vcf"
2025-09-15 20:24:29.780 wdl.w:ptcp.w:call-trgt-37.t:call-trgt_plot_motifs_allele INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2134"
2025-09-15 20:24:29.780 wdl.w:ptcp.w:call-trgt-37.t:call-trgt_plot_motifs_allele INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:29.780 wdl.w:ptcp.w:call-trgt-37.t:call-trgt_plot_motifs_allele INFO eval :: name: "plot_type", value: "allele"
2025-09-15 20:24:29.780 wdl.w:ptcp.w:call-trgt-37.t:call-trgt_plot_motifs_allele INFO eval :: name: "show", value: "motifs"
2025-09-15 20:24:29.780 wdl.w:ptcp.w:call-trgt-37.t:call-trgt_plot_motifs_allele INFO eval :: name: "threads", value: 1
2025-09-15 20:24:29.781 wdl.w:ptcp.w:call-trgt-37.t:call-trgt_plot_motifs_allele INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:29.781 wdl.w:ptcp.w:call-trgt-37.t:call-trgt_plot_motifs_allele INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2134.motifs_allele"
2025-09-15 20:24:29.781 wdl.w:ptcp.w:call-trgt-37.t:call-trgt_plot_motifs_allele INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:29.781 wdl.w:ptcp.w:call-trgt-37.t:call-trgt_plot_motifs_allele WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:29.781 wdl.w:ptcp.w:call-trgt-37.t:call-trgt_plot_motifs_allele INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:29.782 wdl.w:ptcp.w:call-trgt-37.t:call-trgt_plot_motifs_allele INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:29.844 wdl.w:ptcp.w:call-paraphase-51.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for hba for sample m84036_250809_035451_s4.bc2148 at 2025-09-15 20:24:09.796635...
2025-09-15 20:24:29.845 wdl.w:ptcp.w:call-paraphase-51.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for smn1 for sample m84036_250809_035451_s4.bc2148 at 2025-09-15 20:24:09.989940...
2025-09-15 20:24:29.845 wdl.w:ptcp.w:call-paraphase-51.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for gba for sample m84036_250809_035451_s4.bc2148 at 2025-09-15 20:24:10.781350...
2025-09-15 20:24:29.845 wdl.w:ptcp.w:call-paraphase-51.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for cyp21 for sample m84036_250809_035451_s4.bc2148 at 2025-09-15 20:24:11.759061...
2025-09-15 20:24:29.861 wdl.w:ptcp.w:call-paraphase-50.t:call-run_paraphase.slurm_singularity INFO srun: job 51797663 queued and waiting for resources
2025-09-15 20:24:29.861 wdl.w:ptcp.w:call-paraphase-50.t:call-run_paraphase.slurm_singularity INFO srun: job 51797663 has been allocated resources
2025-09-15 20:24:29.861 wdl.w:ptcp.w:call-paraphase-50.t:call-run_paraphase.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:29.867 wdl.w:ptcp.w:call-sawfish-50.t:call-run_sawfish.slurm_singularity INFO srun: job 51797662 queued and waiting for resources
2025-09-15 20:24:29.867 wdl.w:ptcp.w:call-sawfish-50.t:call-run_sawfish.slurm_singularity INFO srun: job 51797662 has been allocated resources
2025-09-15 20:24:29.867 wdl.w:ptcp.w:call-sawfish-50.t:call-run_sawfish.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:29.887 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:24:29 [INFO] - Running trgt-4.0.0-429afcd [genotype]
2025-09-15 20:24:29.887 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:24:29 [WARN] - EIEE1_ARX: Filtered out 2 impure reads
2025-09-15 20:24:29.887 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:24:29 [WARN] - PRTS_ARX: Filtered out 1 impure reads
2025-09-15 20:24:29.887 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:24:29 [WARN] - FXS_FMR1: Filtered out 4 impure reads
2025-09-15 20:24:29.887 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:24:29 [WARN] - FRAXE_AFF2: Filtered out 12 impure reads
2025-09-15 20:24:29.887 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:24:29 [WARN] - FRDA_FXN: Filtered out 3 impure reads
2025-09-15 20:24:29.887 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:24:29 [INFO] - Total execution time: 130.61ms
2025-09-15 20:24:29.887 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:24:29 [INFO] - trgt end
2025-09-15 20:24:29.891 wdl.w:ptcp.w:call-trgt-50.t:call-get_reads_overlapping_repeats.slurm_singularity INFO srun: job 51797664 queued and waiting for resources
2025-09-15 20:24:29.891 wdl.w:ptcp.w:call-trgt-50.t:call-get_reads_overlapping_repeats.slurm_singularity INFO srun: job 51797664 has been allocated resources
2025-09-15 20:24:29.891 wdl.w:ptcp.w:call-trgt-50.t:call-get_reads_overlapping_repeats.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:29.897 wdl.w:ptcp.w:call-trgt-37.t:call-trgt_plot_motifs_allele INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-37/call-trgt_plot_motifs_allele/_singularity_tmpdir_j0xobpij"
2025-09-15 20:24:29.897 wdl.w:ptcp.w:call-trgt-37.t:call-trgt_plot_motifs_allele INFO Slurm invocation: srun --job-name call-trgt_plot_motifs_allele --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-37/call-trgt_plot_motifs_allele/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-37/call-trgt_plot_motifs_allele/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-37/call-trgt_plot_motifs_allele/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-37/call-trgt_plot_motifs_allele/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-37/call-trgt_genotype/out/m84036_250809_035451_s4.bc2134.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2134.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-37/call-trgt_genotype/out/m84036_250809_035451_s4.bc2134.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2134.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-37/call-trgt_genotype/out/m84036_250809_035451_s4.bc2134.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2134.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-37/call-trgt_plot_motifs_allele/_singularity_tmpdir_j0xobpij/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-37/call-trgt_plot_motifs_allele/_singularity_tmpdir_j0xobpij/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:29.901 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_genotype.slurm_singularity INFO srun: job 51797665 queued and waiting for resources
2025-09-15 20:24:29.902 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_genotype.slurm_singularity INFO srun: job 51797665 has been allocated resources
2025-09-15 20:24:29.904 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_genotype.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:29.904 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_genotype.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:24:29.917 wdl.w:ptcp.w:call-trgt-47 NOTICE finish :: job: "call-get_reads_overlapping_repeats"
2025-09-15 20:24:29.917 wdl.w:ptcp.w:call-trgt-47 INFO output :: job: "call-get_reads_overlapping_repeats", values: {"reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-47/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2144.repeats.bam.bai", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-47/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2144.repeats.bam"}
2025-09-15 20:24:29.918 wdl.w:ptcp.w:call-trgt-47 INFO visit :: node: "output-reads_overlapping_repeats", values: {"reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-47/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2144.repeats.bam"}
2025-09-15 20:24:29.918 wdl.w:ptcp.w:call-trgt-47 INFO visit :: node: "output-reads_overlapping_repeats_bai", values: {"reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-47/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2144.repeats.bam.bai"}
2025-09-15 20:24:29.923 wdl.w:ptcp.w:call-trgt-37.t:call-trgt_plot_motifs_waterfall NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-37/call-trgt_plot_motifs_waterfall", thread: 140609822115392
2025-09-15 20:24:29.936 wdl.w:ptcp.w:call-trgt-37.t:call-trgt_plot_motifs_allele NOTICE slurm_singularity run :: pid: 1202111, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-37/call-trgt_plot_motifs_allele/slurm_singularity.log.txt"
2025-09-15 20:24:29.944 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_genotype INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2147.trgt.vcf"
2025-09-15 20:24:29.948 wdl.w:ptcp.w:call-trgt-37.t:call-trgt_plot_motifs_waterfall INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:29.948 wdl.w:ptcp.w:call-trgt-37.t:call-trgt_plot_motifs_waterfall INFO input :: name: "waterfall", value: true
2025-09-15 20:24:29.948 wdl.w:ptcp.w:call-trgt-37.t:call-trgt_plot_motifs_waterfall INFO input :: name: "methylation", value: false
2025-09-15 20:24:29.948 wdl.w:ptcp.w:call-trgt-37.t:call-trgt_plot_motifs_waterfall INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:29.948 wdl.w:ptcp.w:call-trgt-37.t:call-trgt_plot_motifs_waterfall INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:29.948 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_genotype INFO output :: name: "spanning_bam", value: "m84036_250809_035451_s4.bc2147.trgt.sorted.spanning.bam"
2025-09-15 20:24:29.949 wdl.w:ptcp.w:call-trgt-37.t:call-trgt_plot_motifs_waterfall INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:29.949 wdl.w:ptcp.w:call-trgt-37.t:call-trgt_plot_motifs_waterfall INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2134.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:29.949 wdl.w:ptcp.w:call-trgt-37.t:call-trgt_plot_motifs_waterfall INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2134.trgt.sorted.spanning.bam"
2025-09-15 20:24:29.949 wdl.w:ptcp.w:call-trgt-37.t:call-trgt_plot_motifs_waterfall INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2134.trgt.vcf"
2025-09-15 20:24:29.949 wdl.w:ptcp.w:call-trgt-37.t:call-trgt_plot_motifs_waterfall INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2134"
2025-09-15 20:24:29.949 wdl.w:ptcp.w:call-trgt-37.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:29.949 wdl.w:ptcp.w:call-trgt-37.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "plot_type", value: "waterfall"
2025-09-15 20:24:29.949 wdl.w:ptcp.w:call-trgt-37.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "show", value: "motifs"
2025-09-15 20:24:29.949 wdl.w:ptcp.w:call-trgt-37.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "threads", value: 1
2025-09-15 20:24:29.950 wdl.w:ptcp.w:call-trgt-37.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:29.950 wdl.w:ptcp.w:call-trgt-37.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2134.motifs_waterfall"
2025-09-15 20:24:29.950 wdl.w:ptcp.w:call-trgt-37.t:call-trgt_plot_motifs_waterfall INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:29.951 wdl.w:ptcp.w:call-trgt-37.t:call-trgt_plot_motifs_waterfall WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:29.951 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_genotype INFO output :: name: "spanning_bam_bai", value: "m84036_250809_035451_s4.bc2147.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:29.951 wdl.w:ptcp.w:call-trgt-37.t:call-trgt_plot_motifs_waterfall INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:29.951 wdl.w:ptcp.w:call-trgt-37.t:call-trgt_plot_motifs_waterfall INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:29.983 wdl.w:ptcp.w:call-sawfish-12.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:15][sawfish][INFO] Starting sawfish 2.0.3
2025-09-15 20:24:29.983 wdl.w:ptcp.w:call-sawfish-12.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:15][sawfish][INFO] cmdline: sawfish discover --disable-cnv --threads 16 --ref /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa --bam m84036_250809_035451_s4.bc2109.minimap2.bam --output-dir m84036_250809_035451_s4.bc2109_sawfish_discover
2025-09-15 20:24:29.984 wdl.w:ptcp.w:call-sawfish-12.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:15][sawfish][INFO] Running on 16 threads
2025-09-15 20:24:29.984 wdl.w:ptcp.w:call-sawfish-12.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:15][sawfish][INFO] Writing discover settings to file: 'm84036_250809_035451_s4.bc2109_sawfish_discover/discover.settings.json'
2025-09-15 20:24:29.984 wdl.w:ptcp.w:call-sawfish-12.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:15][sawfish][INFO] Reading reference genome from file '/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa'
2025-09-15 20:24:29.984 wdl.w:ptcp.w:call-sawfish-12.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:28][sawfish][INFO] Processing alignment file '/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2109.minimap2.bam'
2025-09-15 20:24:29.984 wdl.w:ptcp.w:call-sawfish-12.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:28][sawfish][INFO] Finished processing all alignments
2025-09-15 20:24:29.984 wdl.w:ptcp.w:call-sawfish-12.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:28][sawfish][INFO] Writing depth bins to binary file: 'm84036_250809_035451_s4.bc2109_sawfish_discover/depth.mpack'
2025-09-15 20:24:29.984 wdl.w:ptcp.w:call-sawfish-12.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:28][sawfish][INFO] Writing max sv depth genome regions to bed file: 'm84036_250809_035451_s4.bc2109_sawfish_discover/max.depth.bed'
2025-09-15 20:24:29.984 wdl.w:ptcp.w:call-sawfish-12.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:28][sawfish][INFO] Completing breakpoint observation clustering
2025-09-15 20:24:29.984 wdl.w:ptcp.w:call-sawfish-12.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:28][sawfish][INFO] Finished breakpoint observation clustering
2025-09-15 20:24:29.984 wdl.w:ptcp.w:call-sawfish-12.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:28][sawfish][INFO] Consolidating adjacent indel candidates
2025-09-15 20:24:29.984 wdl.w:ptcp.w:call-sawfish-12.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:28][sawfish][INFO] Finding large insertion candidates
2025-09-15 20:24:29.985 wdl.w:ptcp.w:call-sawfish-12.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:28][sawfish][INFO] Writing breakpoint_cluster debug bed file: 'm84036_250809_035451_s4.bc2109_sawfish_discover/debug.breakpoint_clusters.bed'
2025-09-15 20:24:29.985 wdl.w:ptcp.w:call-sawfish-12.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:28][sawfish][INFO] Refining SV Candidates
2025-09-15 20:24:29.985 wdl.w:ptcp.w:call-sawfish-12.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:28][sawfish][INFO] Writing debug assembly region bed file: 'm84036_250809_035451_s4.bc2109_sawfish_discover/assembly.regions.bed'
2025-09-15 20:24:29.985 wdl.w:ptcp.w:call-sawfish-12.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:28][sawfish][INFO] Starting refinement of breakpoint evidence clusters
2025-09-15 20:24:29.985 wdl.w:ptcp.w:call-sawfish-12.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:28][sawfish][INFO] Finished refining all breakpoint evidence clusters
2025-09-15 20:24:29.985 wdl.w:ptcp.w:call-sawfish-12.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:28][sawfish][INFO] Writing all contig alignments to bam file: 'm84036_250809_035451_s4.bc2109_sawfish_discover/contig.alignment.bam'
2025-09-15 20:24:29.985 wdl.w:ptcp.w:call-sawfish-12.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:28][sawfish][INFO] Writing candidate structural variants to file: 'm84036_250809_035451_s4.bc2109_sawfish_discover/candidate.sv.bcf'
2025-09-15 20:24:29.985 wdl.w:ptcp.w:call-sawfish-12.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:28][sawfish][INFO] Writing run statistics to file: 'm84036_250809_035451_s4.bc2109_sawfish_discover/run.stats.json'
2025-09-15 20:24:29.985 wdl.w:ptcp.w:call-sawfish-12.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:28][sawfish][INFO] sawfish completed. Total Runtime: 00:00:12.600
2025-09-15 20:24:30.020 wdl.w:ptcp.w:call-trgt-36.t:call-trgt_plot_meth_allele.slurm_singularity INFO srun: job 51797666 queued and waiting for resources
2025-09-15 20:24:30.020 wdl.w:ptcp.w:call-trgt-36.t:call-trgt_plot_meth_allele.slurm_singularity INFO srun: job 51797666 has been allocated resources
2025-09-15 20:24:30.020 wdl.w:ptcp.w:call-trgt-36.t:call-trgt_plot_meth_allele.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:30.020 wdl.w:ptcp.w:call-trgt-36.t:call-trgt_plot_meth_allele.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:24:30.036 wdl.w:ptcp.w:call-trgt-36.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO srun: job 51797667 queued and waiting for resources
2025-09-15 20:24:30.036 wdl.w:ptcp.w:call-trgt-36.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO srun: job 51797667 has been allocated resources
2025-09-15 20:24:30.036 wdl.w:ptcp.w:call-trgt-36.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:30.036 wdl.w:ptcp.w:call-trgt-36.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:24:30.038 wdl.w:ptcp.w:call-sawfish-23.t:call-run_sawfish INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2120_sawfish/m84036_250809_035451_s4.bc2120.sv.vcf.gz"
2025-09-15 20:24:30.038 wdl.w:ptcp.w:call-trgt-37.t:call-trgt_plot_motifs_waterfall INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-37/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_uk5jy2lg"
2025-09-15 20:24:30.039 wdl.w:ptcp.w:call-trgt-37.t:call-trgt_plot_motifs_waterfall INFO Slurm invocation: srun --job-name call-trgt_plot_motifs_waterfall --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-37/call-trgt_plot_motifs_waterfall/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-37/call-trgt_plot_motifs_waterfall/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-37/call-trgt_plot_motifs_waterfall/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-37/call-trgt_plot_motifs_waterfall/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-37/call-trgt_genotype/out/m84036_250809_035451_s4.bc2134.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2134.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-37/call-trgt_genotype/out/m84036_250809_035451_s4.bc2134.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2134.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-37/call-trgt_genotype/out/m84036_250809_035451_s4.bc2134.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2134.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-37/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_uk5jy2lg/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-37/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_uk5jy2lg/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:30.043 wdl.w:ptcp.w:call-sawfish-23.t:call-run_sawfish INFO output :: name: "vcf_tbi", value: "m84036_250809_035451_s4.bc2120_sawfish/m84036_250809_035451_s4.bc2120.sv.vcf.gz.tbi"
2025-09-15 20:24:30.044 wdl.w:ptcp.w:call-sawfish-23.t:call-run_sawfish INFO output :: name: "minimap2_bam", value: "m84036_250809_035451_s4.bc2120.minimap2.bam"
2025-09-15 20:24:30.046 wdl.w:ptcp.w:call-sawfish-23.t:call-run_sawfish INFO output :: name: "minimap2_bam_bai", value: "m84036_250809_035451_s4.bc2120.minimap2.bam.bai"
2025-09-15 20:24:30.054 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_genotype NOTICE done
2025-09-15 20:24:30.060 wdl.w:ptcp.w:call-trgt-37.t:call-trgt_plot_motifs_waterfall NOTICE slurm_singularity run :: pid: 1202114, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-37/call-trgt_plot_motifs_waterfall/slurm_singularity.log.txt"
2025-09-15 20:24:30.073 wdl.w:ptcp.w:call-trgt-50 NOTICE finish :: job: "call-trgt_genotype"
2025-09-15 20:24:30.074 wdl.w:ptcp.w:call-trgt-50 INFO output :: job: "call-trgt_genotype", values: {"spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-50/call-trgt_genotype/out/m84036_250809_035451_s4.bc2147.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-50/call-trgt_genotype/out/m84036_250809_035451_s4.bc2147.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-50/call-trgt_genotype/out/m84036_250809_035451_s4.bc2147.trgt.vcf"}
2025-09-15 20:24:30.074 wdl.w:ptcp.w:call-trgt-50 NOTICE ready :: job: "call-trgt_plot_meth_allele", callee: "trgt_plot"
2025-09-15 20:24:30.074 wdl.w:ptcp.w:call-trgt-50 INFO input :: job: "call-trgt_plot_meth_allele", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": false, "methylation": true, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-50/call-trgt_genotype/out/m84036_250809_035451_s4.bc2147.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-50/call-trgt_genotype/out/m84036_250809_035451_s4.bc2147.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-50/call-trgt_genotype/out/m84036_250809_035451_s4.bc2147.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2147"}
2025-09-15 20:24:30.077 wdl.w:ptcp.w:call-trgt-50 NOTICE ready :: job: "call-trgt_plot_meth_waterfall", callee: "trgt_plot"
2025-09-15 20:24:30.077 wdl.w:ptcp.w:call-trgt-50 INFO input :: job: "call-trgt_plot_meth_waterfall", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": true, "methylation": true, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-50/call-trgt_genotype/out/m84036_250809_035451_s4.bc2147.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-50/call-trgt_genotype/out/m84036_250809_035451_s4.bc2147.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-50/call-trgt_genotype/out/m84036_250809_035451_s4.bc2147.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2147"}
2025-09-15 20:24:30.078 wdl.w:ptcp.w:call-trgt-50 NOTICE ready :: job: "call-trgt_plot_motifs_allele", callee: "trgt_plot"
2025-09-15 20:24:30.078 wdl.w:ptcp.w:call-trgt-50 INFO input :: job: "call-trgt_plot_motifs_allele", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": false, "methylation": false, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-50/call-trgt_genotype/out/m84036_250809_035451_s4.bc2147.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-50/call-trgt_genotype/out/m84036_250809_035451_s4.bc2147.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-50/call-trgt_genotype/out/m84036_250809_035451_s4.bc2147.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2147"}
2025-09-15 20:24:30.080 wdl.w:ptcp.w:call-trgt-50 NOTICE ready :: job: "call-trgt_plot_motifs_waterfall", callee: "trgt_plot"
2025-09-15 20:24:30.080 wdl.w:ptcp.w:call-trgt-50 INFO input :: job: "call-trgt_plot_motifs_waterfall", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": true, "methylation": false, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-50/call-trgt_genotype/out/m84036_250809_035451_s4.bc2147.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-50/call-trgt_genotype/out/m84036_250809_035451_s4.bc2147.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-50/call-trgt_genotype/out/m84036_250809_035451_s4.bc2147.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2147"}
2025-09-15 20:24:30.079 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_meth_allele NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-51/call-trgt_plot_meth_allele", thread: 140608765158976
2025-09-15 20:24:30.080 wdl.w:ptcp.w:call-trgt-50 INFO visit :: node: "output-spanning_bam", values: {"spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-50/call-trgt_genotype/out/m84036_250809_035451_s4.bc2147.trgt.sorted.spanning.bam"}
2025-09-15 20:24:30.080 wdl.w:ptcp.w:call-trgt-50 INFO visit :: node: "output-spanning_bam_bai", values: {"spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-50/call-trgt_genotype/out/m84036_250809_035451_s4.bc2147.trgt.sorted.spanning.bam.bai"}
2025-09-15 20:24:30.081 wdl.w:ptcp.w:call-trgt-50 INFO visit :: node: "output-vcf", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-50/call-trgt_genotype/out/m84036_250809_035451_s4.bc2147.trgt.vcf"}
2025-09-15 20:24:30.101 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_meth_allele INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:30.101 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_meth_allele INFO input :: name: "waterfall", value: false
2025-09-15 20:24:30.101 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_meth_allele INFO input :: name: "methylation", value: true
2025-09-15 20:24:30.101 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_meth_allele INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:30.101 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_meth_allele INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:30.101 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_meth_allele INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:30.101 wdl.w:ptcp.w:call-trgt-36.t:call-trgt_plot_motifs_allele.slurm_singularity INFO srun: job 51797668 queued and waiting for resources
2025-09-15 20:24:30.102 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_meth_allele INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2148.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:30.102 wdl.w:ptcp.w:call-trgt-36.t:call-trgt_plot_motifs_allele.slurm_singularity INFO srun: job 51797668 has been allocated resources
2025-09-15 20:24:30.102 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_meth_allele INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2148.trgt.sorted.spanning.bam"
2025-09-15 20:24:30.102 wdl.w:ptcp.w:call-trgt-36.t:call-trgt_plot_motifs_allele.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:30.102 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_meth_allele INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2148.trgt.vcf"
2025-09-15 20:24:30.102 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_meth_allele INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2148"
2025-09-15 20:24:30.103 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_meth_allele INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:30.103 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_meth_allele INFO eval :: name: "plot_type", value: "allele"
2025-09-15 20:24:30.103 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_meth_allele INFO eval :: name: "show", value: "meth"
2025-09-15 20:24:30.103 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_meth_allele INFO eval :: name: "threads", value: 1
2025-09-15 20:24:30.103 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_meth_allele INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:30.103 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_meth_allele INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2148.meth_allele"
2025-09-15 20:24:30.104 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_meth_allele INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:30.104 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_meth_allele WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:30.104 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_meth_allele INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:30.104 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_meth_allele INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:30.134 wdl.w:ptcp.w:call-trgt-52.t:call-trgt_genotype INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2149.trgt.vcf"
2025-09-15 20:24:30.139 wdl.w:ptcp.w:call-trgt-52.t:call-trgt_genotype INFO output :: name: "spanning_bam", value: "m84036_250809_035451_s4.bc2149.trgt.sorted.spanning.bam"
2025-09-15 20:24:30.140 wdl.w:ptcp.w:call-trgt-52.t:call-trgt_genotype INFO output :: name: "spanning_bam_bai", value: "m84036_250809_035451_s4.bc2149.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:30.166 wdl.w:ptcp.w:call-trgt-01.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:29 [ERROR] - No reads found for TRID=PRTS_ARX
2025-09-15 20:24:30.167 wdl.w:ptcp.w:call-trgt-01.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:29 [ERROR] - No reads found for TRID=EIEE1_ARX
2025-09-15 20:24:30.167 wdl.w:ptcp.w:call-trgt-50.t:call-get_reads_overlapping_repeats INFO output :: name: "reads_overlapping_repeats", value: "m84036_250809_035451_s4.bc2147.repeats.bam"
2025-09-15 20:24:30.171 wdl.w:ptcp.w:call-trgt-50.t:call-get_reads_overlapping_repeats INFO output :: name: "reads_overlapping_repeats_bai", value: "m84036_250809_035451_s4.bc2147.repeats.bam.bai"
2025-09-15 20:24:30.198 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_meth_allele INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-51/call-trgt_plot_meth_allele/_singularity_tmpdir_rbqk6nap"
2025-09-15 20:24:30.198 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_meth_allele INFO Slurm invocation: srun --job-name call-trgt_plot_meth_allele --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-51/call-trgt_plot_meth_allele/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-51/call-trgt_plot_meth_allele/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-51/call-trgt_plot_meth_allele/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-51/call-trgt_plot_meth_allele/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-51/call-trgt_genotype/out/m84036_250809_035451_s4.bc2148.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2148.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-51/call-trgt_genotype/out/m84036_250809_035451_s4.bc2148.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2148.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-51/call-trgt_genotype/out/m84036_250809_035451_s4.bc2148.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2148.trgt.vcf:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-51/call-trgt_plot_meth_allele/_singularity_tmpdir_rbqk6nap/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-51/call-trgt_plot_meth_allele/_singularity_tmpdir_rbqk6nap/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:30.211 wdl.w:ptcp.w:call-sawfish-23.t:call-run_sawfish NOTICE done
2025-09-15 20:24:30.225 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_meth_allele NOTICE slurm_singularity run :: pid: 1202123, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-51/call-trgt_plot_meth_allele/slurm_singularity.log.txt"
2025-09-15 20:24:30.228 wdl.w:ptcp.w:call-trgt-52.t:call-trgt_genotype NOTICE done
2025-09-15 20:24:30.234 wdl.w:ptcp.w:call-sawfish-23 NOTICE finish :: job: "call-run_sawfish"
2025-09-15 20:24:30.234 wdl.w:ptcp.w:call-sawfish-23 INFO output :: job: "call-run_sawfish", values: {"minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-23/call-run_sawfish/out/m84036_250809_035451_s4.bc2120.minimap2.bam.bai", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-23/call-run_sawfish/out/m84036_250809_035451_s4.bc2120.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-23/call-run_sawfish/out/m84036_250809_035451_s4.bc2120_sawfish/m84036_250809_035451_s4.bc2120.sv.vcf.gz.tbi", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-23/call-run_sawfish/out/m84036_250809_035451_s4.bc2120_sawfish/m84036_250809_035451_s4.bc2120.sv.vcf.gz"}
2025-09-15 20:24:30.234 wdl.w:ptcp.w:call-trgt-52 NOTICE finish :: job: "call-trgt_genotype"
2025-09-15 20:24:30.234 wdl.w:ptcp.w:call-sawfish-23 INFO visit :: node: "output-minimap2_bam", values: {"minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-23/call-run_sawfish/out/m84036_250809_035451_s4.bc2120.minimap2.bam"}
2025-09-15 20:24:30.235 wdl.w:ptcp.w:call-trgt-52 INFO output :: job: "call-trgt_genotype", values: {"spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-52/call-trgt_genotype/out/m84036_250809_035451_s4.bc2149.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-52/call-trgt_genotype/out/m84036_250809_035451_s4.bc2149.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-52/call-trgt_genotype/out/m84036_250809_035451_s4.bc2149.trgt.vcf"}
2025-09-15 20:24:30.235 wdl.w:ptcp.w:call-sawfish-23 INFO visit :: node: "output-minimap2_bam_bai", values: {"minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-23/call-run_sawfish/out/m84036_250809_035451_s4.bc2120.minimap2.bam.bai"}
2025-09-15 20:24:30.235 wdl.w:ptcp.w:call-trgt-52 NOTICE ready :: job: "call-trgt_plot_meth_allele", callee: "trgt_plot"
2025-09-15 20:24:30.235 wdl.w:ptcp.w:call-sawfish-23 INFO visit :: node: "output-vcf", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-23/call-run_sawfish/out/m84036_250809_035451_s4.bc2120_sawfish/m84036_250809_035451_s4.bc2120.sv.vcf.gz"}
2025-09-15 20:24:30.236 wdl.w:ptcp.w:call-trgt-52 INFO input :: job: "call-trgt_plot_meth_allele", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": false, "methylation": true, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-52/call-trgt_genotype/out/m84036_250809_035451_s4.bc2149.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-52/call-trgt_genotype/out/m84036_250809_035451_s4.bc2149.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-52/call-trgt_genotype/out/m84036_250809_035451_s4.bc2149.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2149"}
2025-09-15 20:24:30.236 wdl.w:ptcp.w:call-sawfish-23 INFO visit :: node: "output-vcf_tbi", values: {"vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-23/call-run_sawfish/out/m84036_250809_035451_s4.bc2120_sawfish/m84036_250809_035451_s4.bc2120.sv.vcf.gz.tbi"}
2025-09-15 20:24:30.236 wdl.w:ptcp.w:call-sawfish-23 INFO visit :: node: "outputs", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-23/call-run_sawfish/out/m84036_250809_035451_s4.bc2120_sawfish/m84036_250809_035451_s4.bc2120.sv.vcf.gz", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-23/call-run_sawfish/out/m84036_250809_035451_s4.bc2120.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-23/call-run_sawfish/out/m84036_250809_035451_s4.bc2120_sawfish/m84036_250809_035451_s4.bc2120.sv.vcf.gz.tbi", "minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-23/call-run_sawfish/out/m84036_250809_035451_s4.bc2120.minimap2.bam.bai"}
2025-09-15 20:24:30.237 wdl.w:ptcp.w:call-trgt-52 NOTICE ready :: job: "call-trgt_plot_meth_waterfall", callee: "trgt_plot"
2025-09-15 20:24:30.237 wdl.w:ptcp.w:call-trgt-52 INFO input :: job: "call-trgt_plot_meth_waterfall", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": true, "methylation": true, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-52/call-trgt_genotype/out/m84036_250809_035451_s4.bc2149.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-52/call-trgt_genotype/out/m84036_250809_035451_s4.bc2149.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-52/call-trgt_genotype/out/m84036_250809_035451_s4.bc2149.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2149"}
2025-09-15 20:24:30.237 wdl.w:ptcp.w:call-trgt-52 NOTICE ready :: job: "call-trgt_plot_motifs_allele", callee: "trgt_plot"
2025-09-15 20:24:30.238 wdl.w:ptcp.w:call-trgt-52 INFO input :: job: "call-trgt_plot_motifs_allele", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": false, "methylation": false, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-52/call-trgt_genotype/out/m84036_250809_035451_s4.bc2149.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-52/call-trgt_genotype/out/m84036_250809_035451_s4.bc2149.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-52/call-trgt_genotype/out/m84036_250809_035451_s4.bc2149.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2149"}
2025-09-15 20:24:30.238 wdl.w:ptcp.w:call-trgt-52 NOTICE ready :: job: "call-trgt_plot_motifs_waterfall", callee: "trgt_plot"
2025-09-15 20:24:30.238 wdl.w:ptcp.w:call-trgt-52 INFO input :: job: "call-trgt_plot_motifs_waterfall", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": true, "methylation": false, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-52/call-trgt_genotype/out/m84036_250809_035451_s4.bc2149.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-52/call-trgt_genotype/out/m84036_250809_035451_s4.bc2149.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-52/call-trgt_genotype/out/m84036_250809_035451_s4.bc2149.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2149"}
2025-09-15 20:24:30.239 wdl.w:ptcp.w:call-trgt-52 INFO visit :: node: "output-spanning_bam", values: {"spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-52/call-trgt_genotype/out/m84036_250809_035451_s4.bc2149.trgt.sorted.spanning.bam"}
2025-09-15 20:24:30.239 wdl.w:ptcp.w:call-trgt-52 INFO visit :: node: "output-spanning_bam_bai", values: {"spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-52/call-trgt_genotype/out/m84036_250809_035451_s4.bc2149.trgt.sorted.spanning.bam.bai"}
2025-09-15 20:24:30.239 wdl.w:ptcp.w:call-trgt-52 INFO visit :: node: "output-vcf", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-52/call-trgt_genotype/out/m84036_250809_035451_s4.bc2149.trgt.vcf"}
2025-09-15 20:24:30.241 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_meth_waterfall NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-51/call-trgt_plot_meth_waterfall", thread: 140612531648064
2025-09-15 20:24:30.243 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_motifs_allele NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-51/call-trgt_plot_motifs_allele", thread: 140607162938944
2025-09-15 20:24:30.252 wdl.w:ptcp.w:call-trgt-50.t:call-get_reads_overlapping_repeats NOTICE done
2025-09-15 20:24:30.257 wdl.w:ptcp.w:call-trgt-50 NOTICE finish :: job: "call-get_reads_overlapping_repeats"
2025-09-15 20:24:30.258 wdl.w:ptcp.w:call-trgt-50 INFO output :: job: "call-get_reads_overlapping_repeats", values: {"reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-50/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2147.repeats.bam.bai", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-50/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2147.repeats.bam"}
2025-09-15 20:24:30.258 wdl.w:ptcp.w:call-trgt-50 INFO visit :: node: "output-reads_overlapping_repeats", values: {"reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-50/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2147.repeats.bam"}
2025-09-15 20:24:30.259 wdl.w:ptcp.w:call-trgt-50 INFO visit :: node: "output-reads_overlapping_repeats_bai", values: {"reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-50/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2147.repeats.bam.bai"}
2025-09-15 20:24:30.264 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_motifs_waterfall NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-51/call-trgt_plot_motifs_waterfall", thread: 140606609282624
2025-09-15 20:24:30.266 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_motifs_allele INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:30.266 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_motifs_allele INFO input :: name: "waterfall", value: false
2025-09-15 20:24:30.266 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_motifs_allele INFO input :: name: "methylation", value: false
2025-09-15 20:24:30.266 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_motifs_allele INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:30.266 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_motifs_allele INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:30.266 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_motifs_allele INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:30.266 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_motifs_allele INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2148.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:30.266 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_motifs_allele INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2148.trgt.sorted.spanning.bam"
2025-09-15 20:24:30.266 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_motifs_allele INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2148.trgt.vcf"
2025-09-15 20:24:30.266 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_motifs_allele INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2148"
2025-09-15 20:24:30.267 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_motifs_allele INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:30.267 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_motifs_allele INFO eval :: name: "plot_type", value: "allele"
2025-09-15 20:24:30.267 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_motifs_allele INFO eval :: name: "show", value: "motifs"
2025-09-15 20:24:30.267 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_motifs_allele INFO eval :: name: "threads", value: 1
2025-09-15 20:24:30.267 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_motifs_allele INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:30.267 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_motifs_allele INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2148.motifs_allele"
2025-09-15 20:24:30.268 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_motifs_allele INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:30.268 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_motifs_allele WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:30.268 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_motifs_allele INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:30.268 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_motifs_allele INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:30.269 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_meth_waterfall INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:30.270 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_meth_waterfall INFO input :: name: "waterfall", value: true
2025-09-15 20:24:30.270 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_meth_waterfall INFO input :: name: "methylation", value: true
2025-09-15 20:24:30.270 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_meth_waterfall INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:30.270 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_meth_waterfall INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:30.270 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_meth_waterfall INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:30.270 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_meth_waterfall INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2148.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:30.270 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_meth_waterfall INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2148.trgt.sorted.spanning.bam"
2025-09-15 20:24:30.270 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_meth_waterfall INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2148.trgt.vcf"
2025-09-15 20:24:30.270 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_meth_waterfall INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2148"
2025-09-15 20:24:30.270 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_meth_waterfall INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:30.270 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_meth_waterfall INFO eval :: name: "plot_type", value: "waterfall"
2025-09-15 20:24:30.271 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_meth_waterfall INFO eval :: name: "show", value: "meth"
2025-09-15 20:24:30.271 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_meth_waterfall INFO eval :: name: "threads", value: 1
2025-09-15 20:24:30.271 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_meth_waterfall INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:30.271 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_meth_waterfall INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2148.meth_waterfall"
2025-09-15 20:24:30.271 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_meth_waterfall INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:30.271 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_meth_waterfall WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:30.272 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_meth_waterfall INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:30.272 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_meth_waterfall INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:30.291 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_motifs_waterfall INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:30.291 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_motifs_waterfall INFO input :: name: "waterfall", value: true
2025-09-15 20:24:30.291 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_motifs_waterfall INFO input :: name: "methylation", value: false
2025-09-15 20:24:30.291 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_motifs_waterfall INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:30.291 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_motifs_waterfall INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:30.291 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_motifs_waterfall INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:30.291 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_motifs_waterfall INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2148.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:30.291 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_motifs_waterfall INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2148.trgt.sorted.spanning.bam"
2025-09-15 20:24:30.291 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_motifs_waterfall INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2148.trgt.vcf"
2025-09-15 20:24:30.291 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_motifs_waterfall INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2148"
2025-09-15 20:24:30.292 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:30.292 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "plot_type", value: "waterfall"
2025-09-15 20:24:30.292 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "show", value: "motifs"
2025-09-15 20:24:30.292 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "threads", value: 1
2025-09-15 20:24:30.292 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:30.292 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2148.motifs_waterfall"
2025-09-15 20:24:30.293 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_motifs_waterfall INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:30.293 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_motifs_waterfall WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:30.293 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_motifs_waterfall INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:30.293 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_motifs_waterfall INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:30.304 wdl.w:ptcp.w:call-sawfish-23 NOTICE done
2025-09-15 20:24:30.306 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:30 [ERROR] - No reads found for TRID=SCA2_ATXN2
2025-09-15 20:24:30.306 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:30 [ERROR] - No reads found for TRID=OPDM4_RILPL1
2025-09-15 20:24:30.306 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:30 [ERROR] - No reads found for TRID=SCA27B_FGF14
2025-09-15 20:24:30.306 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:30 [ERROR] - No reads found for TRID=OPDM_ABCD3
2025-09-15 20:24:30.306 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:30 [ERROR] - No reads found for TRID=SCA37_DAB1
2025-09-15 20:24:30.306 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:30 [ERROR] - No reads found for TRID=NIID_NOTCH2NLC
2025-09-15 20:24:30.306 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:30 [ERROR] - No reads found for TRID=OPMD_PABPN1
2025-09-15 20:24:30.311 wdl.w:ptcp NOTICE finish :: job: "call-sawfish-23"
2025-09-15 20:24:30.311 wdl.w:ptcp INFO output :: job: "call-sawfish-23", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-23/out/m84036_250809_035451_s4.bc2120_sawfish/m84036_250809_035451_s4.bc2120.sv.vcf.gz", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-23/out/m84036_250809_035451_s4.bc2120.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-23/out/m84036_250809_035451_s4.bc2120_sawfish/m84036_250809_035451_s4.bc2120.sv.vcf.gz.tbi", "minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-23/out/m84036_250809_035451_s4.bc2120.minimap2.bam.bai"}
2025-09-15 20:24:30.314 wdl.w:ptcp.w:call-trgt-36.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO srun: job 51797669 queued and waiting for resources
2025-09-15 20:24:30.314 wdl.w:ptcp.w:call-trgt-36.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO srun: job 51797669 has been allocated resources
2025-09-15 20:24:30.314 wdl.w:ptcp.w:call-trgt-36.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:30.320 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_meth_allele.slurm_singularity INFO srun: job 51797670 queued and waiting for resources
2025-09-15 20:24:30.321 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_meth_allele.slurm_singularity INFO srun: job 51797670 has been allocated resources
2025-09-15 20:24:30.321 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_meth_allele.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:30.327 wdl.w:ptcp.w:call-sawfish-42 NOTICE workflow start :: name: "sawfish", source: "./sawfish.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-42"
2025-09-15 20:24:30.329 wdl.w:ptcp.w:call-trgt-44.t:call-trgt_genotype INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2141.trgt.vcf"
2025-09-15 20:24:30.335 wdl.w:ptcp.w:call-trgt-44.t:call-trgt_genotype INFO output :: name: "spanning_bam", value: "m84036_250809_035451_s4.bc2141.trgt.sorted.spanning.bam"
2025-09-15 20:24:30.337 wdl.w:ptcp.w:call-trgt-44.t:call-trgt_genotype INFO output :: name: "spanning_bam_bai", value: "m84036_250809_035451_s4.bc2141.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:30.346 wdl.w:ptcp.w:call-sawfish-42 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:24:30.347 wdl.w:ptcp.w:call-sawfish-42 INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:24:30.347 wdl.w:ptcp.w:call-sawfish-42 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-42/out/m84036_250809_035451_s4.bc2139.mapped.bam"}
2025-09-15 20:24:30.347 wdl.w:ptcp.w:call-sawfish-42 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-42/out/m84036_250809_035451_s4.bc2139.mapped.bam.bai"}
2025-09-15 20:24:30.347 wdl.w:ptcp.w:call-sawfish-42 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:24:30.347 wdl.w:ptcp.w:call-sawfish-42 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:24:30.347 wdl.w:ptcp.w:call-sawfish-42 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2139"}
2025-09-15 20:24:30.347 wdl.w:ptcp.w:call-sawfish-42 NOTICE ready :: job: "call-run_sawfish", callee: "run_sawfish"
2025-09-15 20:24:30.347 wdl.w:ptcp.w:call-sawfish-42 INFO input :: job: "call-run_sawfish", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-42/out/m84036_250809_035451_s4.bc2139.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-42/out/m84036_250809_035451_s4.bc2139.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2139"}
2025-09-15 20:24:30.367 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_motifs_allele INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-51/call-trgt_plot_motifs_allele/_singularity_tmpdir_3qga46sq"
2025-09-15 20:24:30.367 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_motifs_allele INFO Slurm invocation: srun --job-name call-trgt_plot_motifs_allele --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-51/call-trgt_plot_motifs_allele/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-51/call-trgt_plot_motifs_allele/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-51/call-trgt_plot_motifs_allele/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-51/call-trgt_plot_motifs_allele/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-51/call-trgt_genotype/out/m84036_250809_035451_s4.bc2148.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2148.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-51/call-trgt_genotype/out/m84036_250809_035451_s4.bc2148.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2148.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-51/call-trgt_genotype/out/m84036_250809_035451_s4.bc2148.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2148.trgt.vcf:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-51/call-trgt_plot_motifs_allele/_singularity_tmpdir_3qga46sq/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-51/call-trgt_plot_motifs_allele/_singularity_tmpdir_3qga46sq/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:30.371 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_meth_waterfall INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-51/call-trgt_plot_meth_waterfall/_singularity_tmpdir_xb7kdq2o"
2025-09-15 20:24:30.372 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_meth_waterfall INFO Slurm invocation: srun --job-name call-trgt_plot_meth_waterfall --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-51/call-trgt_plot_meth_waterfall/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-51/call-trgt_plot_meth_waterfall/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-51/call-trgt_plot_meth_waterfall/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-51/call-trgt_plot_meth_waterfall/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-51/call-trgt_genotype/out/m84036_250809_035451_s4.bc2148.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2148.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-51/call-trgt_genotype/out/m84036_250809_035451_s4.bc2148.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2148.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-51/call-trgt_genotype/out/m84036_250809_035451_s4.bc2148.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2148.trgt.vcf:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-51/call-trgt_plot_meth_waterfall/_singularity_tmpdir_xb7kdq2o/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-51/call-trgt_plot_meth_waterfall/_singularity_tmpdir_xb7kdq2o/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:30.381 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_motifs_waterfall INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-51/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_nsq58mau"
2025-09-15 20:24:30.381 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_motifs_waterfall INFO Slurm invocation: srun --job-name call-trgt_plot_motifs_waterfall --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-51/call-trgt_plot_motifs_waterfall/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-51/call-trgt_plot_motifs_waterfall/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-51/call-trgt_plot_motifs_waterfall/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-51/call-trgt_plot_motifs_waterfall/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-51/call-trgt_genotype/out/m84036_250809_035451_s4.bc2148.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2148.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-51/call-trgt_genotype/out/m84036_250809_035451_s4.bc2148.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2148.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-51/call-trgt_genotype/out/m84036_250809_035451_s4.bc2148.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2148.trgt.vcf:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-51/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_nsq58mau/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-51/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_nsq58mau/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:30.396 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO srun: job 51797671 queued and waiting for resources
2025-09-15 20:24:30.396 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO srun: job 51797671 has been allocated resources
2025-09-15 20:24:30.396 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:30.399 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO srun: job 51797673 queued and waiting for resources
2025-09-15 20:24:30.400 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO srun: job 51797673 has been allocated resources
2025-09-15 20:24:30.400 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:30.400 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_motifs_allele NOTICE slurm_singularity run :: pid: 1202136, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-51/call-trgt_plot_motifs_allele/slurm_singularity.log.txt"
2025-09-15 20:24:30.400 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_motifs_waterfall NOTICE slurm_singularity run :: pid: 1202138, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-51/call-trgt_plot_motifs_waterfall/slurm_singularity.log.txt"
2025-09-15 20:24:30.401 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_meth_waterfall NOTICE slurm_singularity run :: pid: 1202137, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-51/call-trgt_plot_meth_waterfall/slurm_singularity.log.txt"
2025-09-15 20:24:30.402 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_motifs_allele.slurm_singularity INFO srun: job 51797672 queued and waiting for resources
2025-09-15 20:24:30.402 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_motifs_allele.slurm_singularity INFO srun: job 51797672 has been allocated resources
2025-09-15 20:24:30.402 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_motifs_allele.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:30.431 wdl.w:ptcp.w:call-trgt-01.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:29 [ERROR] - No reads found for TRID=PRTS_ARX
2025-09-15 20:24:30.432 wdl.w:ptcp.w:call-trgt-01.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:29 [ERROR] - No reads found for TRID=EIEE1_ARX
2025-09-15 20:24:30.435 wdl.w:ptcp.w:call-trgt-44.t:call-trgt_genotype NOTICE done
2025-09-15 20:24:30.442 wdl.w:ptcp.w:call-trgt-44 NOTICE finish :: job: "call-trgt_genotype"
2025-09-15 20:24:30.442 wdl.w:ptcp.w:call-trgt-44 INFO output :: job: "call-trgt_genotype", values: {"spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-44/call-trgt_genotype/out/m84036_250809_035451_s4.bc2141.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-44/call-trgt_genotype/out/m84036_250809_035451_s4.bc2141.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-44/call-trgt_genotype/out/m84036_250809_035451_s4.bc2141.trgt.vcf"}
2025-09-15 20:24:30.442 wdl.w:ptcp.w:call-trgt-44 NOTICE ready :: job: "call-trgt_plot_meth_allele", callee: "trgt_plot"
2025-09-15 20:24:30.442 wdl.w:ptcp.w:call-trgt-44 INFO input :: job: "call-trgt_plot_meth_allele", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": false, "methylation": true, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-44/call-trgt_genotype/out/m84036_250809_035451_s4.bc2141.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-44/call-trgt_genotype/out/m84036_250809_035451_s4.bc2141.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-44/call-trgt_genotype/out/m84036_250809_035451_s4.bc2141.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2141"}
2025-09-15 20:24:30.445 wdl.w:ptcp.w:call-trgt-44 NOTICE ready :: job: "call-trgt_plot_meth_waterfall", callee: "trgt_plot"
2025-09-15 20:24:30.445 wdl.w:ptcp.w:call-trgt-44 INFO input :: job: "call-trgt_plot_meth_waterfall", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": true, "methylation": true, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-44/call-trgt_genotype/out/m84036_250809_035451_s4.bc2141.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-44/call-trgt_genotype/out/m84036_250809_035451_s4.bc2141.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-44/call-trgt_genotype/out/m84036_250809_035451_s4.bc2141.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2141"}
2025-09-15 20:24:30.446 wdl.w:ptcp.w:call-trgt-44 NOTICE ready :: job: "call-trgt_plot_motifs_allele", callee: "trgt_plot"
2025-09-15 20:24:30.446 wdl.w:ptcp.w:call-trgt-44 INFO input :: job: "call-trgt_plot_motifs_allele", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": false, "methylation": false, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-44/call-trgt_genotype/out/m84036_250809_035451_s4.bc2141.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-44/call-trgt_genotype/out/m84036_250809_035451_s4.bc2141.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-44/call-trgt_genotype/out/m84036_250809_035451_s4.bc2141.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2141"}
2025-09-15 20:24:30.446 wdl.w:ptcp.w:call-trgt-44 NOTICE ready :: job: "call-trgt_plot_motifs_waterfall", callee: "trgt_plot"
2025-09-15 20:24:30.446 wdl.w:ptcp.w:call-trgt-44 INFO input :: job: "call-trgt_plot_motifs_waterfall", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": true, "methylation": false, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-44/call-trgt_genotype/out/m84036_250809_035451_s4.bc2141.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-44/call-trgt_genotype/out/m84036_250809_035451_s4.bc2141.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-44/call-trgt_genotype/out/m84036_250809_035451_s4.bc2141.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2141"}
2025-09-15 20:24:30.447 wdl.w:ptcp.w:call-trgt-44 INFO visit :: node: "output-spanning_bam", values: {"spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-44/call-trgt_genotype/out/m84036_250809_035451_s4.bc2141.trgt.sorted.spanning.bam"}
2025-09-15 20:24:30.447 wdl.w:ptcp.w:call-trgt-44 INFO visit :: node: "output-spanning_bam_bai", values: {"spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-44/call-trgt_genotype/out/m84036_250809_035451_s4.bc2141.trgt.sorted.spanning.bam.bai"}
2025-09-15 20:24:30.447 wdl.w:ptcp.w:call-trgt-44 INFO visit :: node: "output-vcf", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-44/call-trgt_genotype/out/m84036_250809_035451_s4.bc2141.trgt.vcf"}
2025-09-15 20:24:30.448 wdl.w:ptcp.w:call-paraphase-63.t:call-run_paraphase NOTICE task setup :: name: "run_paraphase", source: "./paraphase.wdl", line: 127, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-63/call-run_paraphase", thread: 140607657846336
2025-09-15 20:24:30.469 wdl.w:ptcp.w:call-paraphase-63.t:call-run_paraphase INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:30.469 wdl.w:ptcp.w:call-paraphase-63.t:call-run_paraphase INFO input :: name: "annotation_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf"
2025-09-15 20:24:30.469 wdl.w:ptcp.w:call-paraphase-63.t:call-run_paraphase INFO input :: name: "genome_version", value: "38"
2025-09-15 20:24:30.469 wdl.w:ptcp.w:call-paraphase-63.t:call-run_paraphase INFO input :: name: "config_file", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/paraphase_config.GRCh38.yaml"
2025-09-15 20:24:30.469 wdl.w:ptcp.w:call-paraphase-63.t:call-run_paraphase INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:30.469 wdl.w:ptcp.w:call-paraphase-63.t:call-run_paraphase INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:30.470 wdl.w:ptcp.w:call-paraphase-63.t:call-run_paraphase INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2160.mapped.bam.bai"
2025-09-15 20:24:30.470 wdl.w:ptcp.w:call-paraphase-63.t:call-run_paraphase INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2160.mapped.bam"
2025-09-15 20:24:30.470 wdl.w:ptcp.w:call-paraphase-63.t:call-run_paraphase INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2160"
2025-09-15 20:24:30.470 wdl.w:ptcp.w:call-paraphase-63.t:call-run_paraphase INFO eval :: name: "threads", value: 4
2025-09-15 20:24:30.470 wdl.w:ptcp.w:call-paraphase-63.t:call-run_paraphase INFO eval :: name: "mem_gb", value: 8
2025-09-15 20:24:30.470 wdl.w:ptcp.w:call-paraphase-63.t:call-run_paraphase INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:30.470 wdl.w:ptcp.w:call-paraphase-63.t:call-run_paraphase INFO eval :: name: "out_dir", value: "m84036_250809_035451_s4.bc2160_paraphase"
2025-09-15 20:24:30.471 wdl.w:ptcp.w:call-paraphase-63.t:call-run_paraphase INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 4, memory_reservation: 8000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:30.471 wdl.w:ptcp.w:call-paraphase-63.t:call-run_paraphase WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:30.471 wdl.w:ptcp.w:call-paraphase-63.t:call-run_paraphase INFO provisioned :: seconds_waited: 0, cpu: 4, mem_bytes: 8000000000
2025-09-15 20:24:30.472 wdl.w:ptcp.w:call-paraphase-63.t:call-run_paraphase INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:30.534 wdl.w:ptcp.w:call-paraphase-63.t:call-run_paraphase INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-63/call-run_paraphase/_singularity_tmpdir_g5qqu79o"
2025-09-15 20:24:30.534 wdl.w:ptcp.w:call-paraphase-63.t:call-run_paraphase INFO Slurm invocation: srun --job-name call-run_paraphase --partition compute,compute9 --cpus-per-task 4 --mem 7629M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-63/call-run_paraphase/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-63/call-run_paraphase/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-63/call-run_paraphase/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-63/call-run_paraphase/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-63/out/m84036_250809_035451_s4.bc2160.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2160.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-63/out/m84036_250809_035451_s4.bc2160.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2160.mapped.bam:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/variant_list/variant_list.GRCh38.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf:ro --bind /ptcp/meta/paraphase/paraphase_config.GRCh38.yaml:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/paraphase_config.GRCh38.yaml:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-63/call-run_paraphase/_singularity_tmpdir_g5qqu79o/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-63/call-run_paraphase/_singularity_tmpdir_g5qqu79o/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:30.554 wdl.w:ptcp.w:call-paraphase-63.t:call-run_paraphase NOTICE slurm_singularity run :: pid: 1202142, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-63/call-run_paraphase/slurm_singularity.log.txt"
2025-09-15 20:24:30.643 wdl.w:ptcp.w:call-trgt-37.t:call-trgt_plot_meth_allele.slurm_singularity INFO srun: job 51797674 queued and waiting for resources
2025-09-15 20:24:30.644 wdl.w:ptcp.w:call-trgt-37.t:call-trgt_plot_meth_allele.slurm_singularity INFO srun: job 51797674 has been allocated resources
2025-09-15 20:24:30.644 wdl.w:ptcp.w:call-trgt-37.t:call-trgt_plot_meth_allele.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:30.657 wdl.w:ptcp.w:call-sawfish-22.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:16][sawfish][INFO] Starting sawfish 2.0.3
2025-09-15 20:24:30.657 wdl.w:ptcp.w:call-sawfish-22.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:16][sawfish][INFO] cmdline: sawfish discover --disable-cnv --threads 16 --ref /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa --bam m84036_250809_035451_s4.bc2119.minimap2.bam --output-dir m84036_250809_035451_s4.bc2119_sawfish_discover
2025-09-15 20:24:30.657 wdl.w:ptcp.w:call-sawfish-22.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:16][sawfish][INFO] Running on 16 threads
2025-09-15 20:24:30.657 wdl.w:ptcp.w:call-sawfish-22.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:16][sawfish][INFO] Writing discover settings to file: 'm84036_250809_035451_s4.bc2119_sawfish_discover/discover.settings.json'
2025-09-15 20:24:30.657 wdl.w:ptcp.w:call-sawfish-22.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:16][sawfish][INFO] Reading reference genome from file '/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa'
2025-09-15 20:24:30.657 wdl.w:ptcp.w:call-sawfish-22.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:23][sawfish][INFO] Processing alignment file '/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2119.minimap2.bam'
2025-09-15 20:24:30.658 wdl.w:ptcp.w:call-sawfish-22.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:23][sawfish][INFO] Finished processing all alignments
2025-09-15 20:24:30.658 wdl.w:ptcp.w:call-sawfish-22.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:23][sawfish][INFO] Writing depth bins to binary file: 'm84036_250809_035451_s4.bc2119_sawfish_discover/depth.mpack'
2025-09-15 20:24:30.658 wdl.w:ptcp.w:call-sawfish-22.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:23][sawfish][INFO] Writing max sv depth genome regions to bed file: 'm84036_250809_035451_s4.bc2119_sawfish_discover/max.depth.bed'
2025-09-15 20:24:30.658 wdl.w:ptcp.w:call-sawfish-22.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:23][sawfish][INFO] Completing breakpoint observation clustering
2025-09-15 20:24:30.658 wdl.w:ptcp.w:call-sawfish-22.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:23][sawfish][INFO] Finished breakpoint observation clustering
2025-09-15 20:24:30.658 wdl.w:ptcp.w:call-sawfish-22.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:23][sawfish][INFO] Consolidating adjacent indel candidates
2025-09-15 20:24:30.658 wdl.w:ptcp.w:call-sawfish-22.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:23][sawfish][INFO] Finding large insertion candidates
2025-09-15 20:24:30.658 wdl.w:ptcp.w:call-sawfish-22.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:23][sawfish][INFO] Writing breakpoint_cluster debug bed file: 'm84036_250809_035451_s4.bc2119_sawfish_discover/debug.breakpoint_clusters.bed'
2025-09-15 20:24:30.658 wdl.w:ptcp.w:call-sawfish-22.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:23][sawfish][INFO] Refining SV Candidates
2025-09-15 20:24:30.658 wdl.w:ptcp.w:call-sawfish-22.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:23][sawfish][INFO] Writing debug assembly region bed file: 'm84036_250809_035451_s4.bc2119_sawfish_discover/assembly.regions.bed'
2025-09-15 20:24:30.658 wdl.w:ptcp.w:call-sawfish-22.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:23][sawfish][INFO] Starting refinement of breakpoint evidence clusters
2025-09-15 20:24:30.658 wdl.w:ptcp.w:call-sawfish-22.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:24][sawfish][INFO] Finished refining all breakpoint evidence clusters
2025-09-15 20:24:30.658 wdl.w:ptcp.w:call-sawfish-22.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:24][sawfish][INFO] Writing all contig alignments to bam file: 'm84036_250809_035451_s4.bc2119_sawfish_discover/contig.alignment.bam'
2025-09-15 20:24:30.658 wdl.w:ptcp.w:call-sawfish-22.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:24][sawfish][INFO] Writing candidate structural variants to file: 'm84036_250809_035451_s4.bc2119_sawfish_discover/candidate.sv.bcf'
2025-09-15 20:24:30.658 wdl.w:ptcp.w:call-sawfish-22.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:24][sawfish][INFO] Writing run statistics to file: 'm84036_250809_035451_s4.bc2119_sawfish_discover/run.stats.json'
2025-09-15 20:24:30.658 wdl.w:ptcp.w:call-sawfish-22.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:24][sawfish][INFO] sawfish completed. Total Runtime: 00:00:08.605
2025-09-15 20:24:30.663 wdl.w:ptcp.w:call-sawfish-21.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:20][sawfish][INFO] Starting sawfish 2.0.3
2025-09-15 20:24:30.664 wdl.w:ptcp.w:call-sawfish-21.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:20][sawfish][INFO] cmdline: sawfish discover --disable-cnv --threads 16 --ref /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa --bam m84036_250809_035451_s4.bc2118.minimap2.bam --output-dir m84036_250809_035451_s4.bc2118_sawfish_discover
2025-09-15 20:24:30.664 wdl.w:ptcp.w:call-sawfish-21.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:20][sawfish][INFO] Running on 16 threads
2025-09-15 20:24:30.664 wdl.w:ptcp.w:call-sawfish-21.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:20][sawfish][INFO] Writing discover settings to file: 'm84036_250809_035451_s4.bc2118_sawfish_discover/discover.settings.json'
2025-09-15 20:24:30.664 wdl.w:ptcp.w:call-sawfish-21.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:20][sawfish][INFO] Reading reference genome from file '/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa'
2025-09-15 20:24:30.711 wdl.w:ptcp.w:call-trgt-37.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO srun: job 51797675 queued and waiting for resources
2025-09-15 20:24:30.711 wdl.w:ptcp.w:call-trgt-37.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO srun: job 51797675 has been allocated resources
2025-09-15 20:24:30.711 wdl.w:ptcp.w:call-trgt-37.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:30.711 wdl.w:ptcp.w:call-paraphase-14.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for hbb for sample m84036_250809_035451_s4.bc2111 at 2025-09-15 20:24:19.178010...
2025-09-15 20:24:30.711 wdl.w:ptcp.w:call-paraphase-14.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for hbb for sample m84036_250809_035451_s4.bc2111 at 2025-09-15 20:24:19.469945...
2025-09-15 20:24:30.795 wdl.w:ptcp.w:call-paraphase-46.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for hba for sample m84036_250809_035451_s4.bc2143 at 2025-09-15 20:24:10.178966...
2025-09-15 20:24:30.796 wdl.w:ptcp.w:call-paraphase-46.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for smn1 for sample m84036_250809_035451_s4.bc2143 at 2025-09-15 20:24:10.418645...
2025-09-15 20:24:30.796 wdl.w:ptcp.w:call-paraphase-46.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for gba for sample m84036_250809_035451_s4.bc2143 at 2025-09-15 20:24:10.726150...
2025-09-15 20:24:30.797 wdl.w:ptcp.w:call-paraphase-46.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for cyp21 for sample m84036_250809_035451_s4.bc2143 at 2025-09-15 20:24:11.572061...
2025-09-15 20:24:30.797 wdl.w:ptcp.w:call-paraphase-46.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for smn1 for sample m84036_250809_035451_s4.bc2143 at 2025-09-15 20:24:28.170978...
2025-09-15 20:24:30.797 wdl.w:ptcp.w:call-paraphase-46.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning to gene2 region for smn1 for sample m84036_250809_035451_s4.bc2143 at 2025-09-15 20:24:28.699464...
2025-09-15 20:24:30.820 wdl.w:ptcp.w:call-paraphase-26.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for f8inv1 for sample m84036_250809_035451_s4.bc2123 at 2025-09-15 20:24:05.942785...
2025-09-15 20:24:30.820 wdl.w:ptcp.w:call-paraphase-26.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for f8inv1 for sample m84036_250809_035451_s4.bc2123 at 2025-09-15 20:24:11.667974...
2025-09-15 20:24:30.820 wdl.w:ptcp.w:call-paraphase-26.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for f8inv1 for sample m84036_250809_035451_s4.bc2123 at 2025-09-15 20:24:12.012895...
2025-09-15 20:24:30.820 wdl.w:ptcp.w:call-paraphase-26.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for hba for sample m84036_250809_035451_s4.bc2123 at 2025-09-15 20:24:17.207132...
2025-09-15 20:24:30.820 wdl.w:ptcp.w:call-paraphase-26.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for hba for sample m84036_250809_035451_s4.bc2123 at 2025-09-15 20:24:17.514203...
2025-09-15 20:24:30.820 wdl.w:ptcp.w:call-paraphase-26.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for cyp21 for sample m84036_250809_035451_s4.bc2123 at 2025-09-15 20:24:23.527924...
2025-09-15 20:24:30.820 wdl.w:ptcp.w:call-paraphase-26.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for cyp21 for sample m84036_250809_035451_s4.bc2123 at 2025-09-15 20:24:24.494049...
2025-09-15 20:24:30.885 wdl.w:ptcp.w:call-paraphase-03.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for f8inv1 for sample m84036_250809_035451_s4.bc2100 at 2025-09-15 20:24:27.589472...
2025-09-15 20:24:30.885 wdl.w:ptcp.w:call-paraphase-03.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for f8inv1 for sample m84036_250809_035451_s4.bc2100 at 2025-09-15 20:24:27.589668...
2025-09-15 20:24:30.908 wdl.w:ptcp.w:call-sawfish-03.t:call-run_sawfish.stderr VERBOSE [M::mm_idx_gen::41.225*1.71] sorted minimizers
2025-09-15 20:24:30.908 wdl.w:ptcp.w:call-sawfish-03.t:call-run_sawfish.stderr VERBOSE [M::main::41.225*1.71] loaded/built the index for 195 target sequence(s)
2025-09-15 20:24:30.908 wdl.w:ptcp.w:call-sawfish-03.t:call-run_sawfish.stderr VERBOSE [M::mm_mapopt_update::44.247*1.66] mid_occ = 136
2025-09-15 20:24:30.908 wdl.w:ptcp.w:call-sawfish-03.t:call-run_sawfish.stderr VERBOSE [M::mm_idx_stat] kmer size: 19; skip: 19; is_hpc: 0; #seq: 195
2025-09-15 20:24:30.908 wdl.w:ptcp.w:call-sawfish-03.t:call-run_sawfish.stderr VERBOSE [M::mm_idx_stat::46.851*1.62] distinct minimizers: 214664461 (92.23% are singletons); average occurrences: 1.372; average spacing: 10.529; total length: 3099922541
2025-09-15 20:24:30.908 wdl.w:ptcp.w:call-sawfish-03.t:call-run_sawfish.stderr VERBOSE [M::bam2fq_mainloop] discarded 0 singletons
2025-09-15 20:24:30.908 wdl.w:ptcp.w:call-sawfish-03.t:call-run_sawfish.stderr VERBOSE [M::bam2fq_mainloop] processed 503 reads
2025-09-15 20:24:30.908 wdl.w:ptcp.w:call-sawfish-03.t:call-run_sawfish.stderr VERBOSE [M::worker_pipeline::47.429*1.62] mapped 503 sequences
2025-09-15 20:24:30.908 wdl.w:ptcp.w:call-sawfish-03.t:call-run_sawfish.stderr VERBOSE [M::main] Version: 2.26-r1175
2025-09-15 20:24:30.908 wdl.w:ptcp.w:call-sawfish-03.t:call-run_sawfish.stderr VERBOSE [M::main] CMD: /opt/pacbio/smrttools/install/smrtlink-release_25.1.0.257715/bundles/smrttools/install/smrttools-release_25.1.0.257715/private/thirdparty/minimap2/minimap2_2.26-pacbio2/binwrap/../../../../../private/thirdparty/minimap2/minimap2_2.26-pacbio2/bin/minimap2 -a -y -x map-hifi -Y -E 1,0 /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa -
2025-09-15 20:24:30.908 wdl.w:ptcp.w:call-sawfish-03.t:call-run_sawfish.stderr VERBOSE [M::main] Real time: 47.649 sec; CPU: 77.225 sec; Peak RSS: 11.886 GB
2025-09-15 20:24:30.945 wdl.w:ptcp.w:call-trgt-37.t:call-trgt_plot_motifs_allele.slurm_singularity INFO srun: job 51797676 queued and waiting for resources
2025-09-15 20:24:30.946 wdl.w:ptcp.w:call-trgt-37.t:call-trgt_plot_motifs_allele.slurm_singularity INFO srun: job 51797676 has been allocated resources
2025-09-15 20:24:30.946 wdl.w:ptcp.w:call-trgt-37.t:call-trgt_plot_motifs_allele.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:31.056 wdl.w:ptcp.w:call-sawfish-09.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:17][sawfish][INFO] Starting sawfish 2.0.3
2025-09-15 20:24:31.056 wdl.w:ptcp.w:call-sawfish-09.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:17][sawfish][INFO] cmdline: sawfish discover --disable-cnv --threads 16 --ref /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa --bam m84036_250809_035451_s4.bc2106.minimap2.bam --output-dir m84036_250809_035451_s4.bc2106_sawfish_discover
2025-09-15 20:24:31.056 wdl.w:ptcp.w:call-sawfish-09.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:17][sawfish][INFO] Running on 16 threads
2025-09-15 20:24:31.056 wdl.w:ptcp.w:call-sawfish-09.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:17][sawfish][INFO] Writing discover settings to file: 'm84036_250809_035451_s4.bc2106_sawfish_discover/discover.settings.json'
2025-09-15 20:24:31.056 wdl.w:ptcp.w:call-sawfish-09.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:17][sawfish][INFO] Reading reference genome from file '/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa'
2025-09-15 20:24:31.056 wdl.w:ptcp.w:call-sawfish-09.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:28][sawfish][INFO] Processing alignment file '/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2106.minimap2.bam'
2025-09-15 20:24:31.056 wdl.w:ptcp.w:call-sawfish-09.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:28][sawfish][INFO] Finished processing all alignments
2025-09-15 20:24:31.057 wdl.w:ptcp.w:call-sawfish-09.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:28][sawfish][INFO] Writing depth bins to binary file: 'm84036_250809_035451_s4.bc2106_sawfish_discover/depth.mpack'
2025-09-15 20:24:31.057 wdl.w:ptcp.w:call-sawfish-09.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:28][sawfish][INFO] Writing max sv depth genome regions to bed file: 'm84036_250809_035451_s4.bc2106_sawfish_discover/max.depth.bed'
2025-09-15 20:24:31.057 wdl.w:ptcp.w:call-sawfish-09.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:28][sawfish][INFO] Completing breakpoint observation clustering
2025-09-15 20:24:31.057 wdl.w:ptcp.w:call-sawfish-09.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:28][sawfish][INFO] Finished breakpoint observation clustering
2025-09-15 20:24:31.057 wdl.w:ptcp.w:call-sawfish-09.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:28][sawfish][INFO] Consolidating adjacent indel candidates
2025-09-15 20:24:31.057 wdl.w:ptcp.w:call-sawfish-09.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:28][sawfish][INFO] Finding large insertion candidates
2025-09-15 20:24:31.057 wdl.w:ptcp.w:call-sawfish-09.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:28][sawfish][INFO] Writing breakpoint_cluster debug bed file: 'm84036_250809_035451_s4.bc2106_sawfish_discover/debug.breakpoint_clusters.bed'
2025-09-15 20:24:31.057 wdl.w:ptcp.w:call-sawfish-09.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:28][sawfish][INFO] Refining SV Candidates
2025-09-15 20:24:31.057 wdl.w:ptcp.w:call-sawfish-09.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:28][sawfish][INFO] Writing debug assembly region bed file: 'm84036_250809_035451_s4.bc2106_sawfish_discover/assembly.regions.bed'
2025-09-15 20:24:31.057 wdl.w:ptcp.w:call-sawfish-09.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:28][sawfish][INFO] Starting refinement of breakpoint evidence clusters
2025-09-15 20:24:31.057 wdl.w:ptcp.w:call-sawfish-09.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:28][sawfish][INFO] Finished refining all breakpoint evidence clusters
2025-09-15 20:24:31.057 wdl.w:ptcp.w:call-sawfish-09.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:28][sawfish][INFO] Writing all contig alignments to bam file: 'm84036_250809_035451_s4.bc2106_sawfish_discover/contig.alignment.bam'
2025-09-15 20:24:31.057 wdl.w:ptcp.w:call-sawfish-09.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:28][sawfish][INFO] Writing candidate structural variants to file: 'm84036_250809_035451_s4.bc2106_sawfish_discover/candidate.sv.bcf'
2025-09-15 20:24:31.057 wdl.w:ptcp.w:call-sawfish-09.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:28][sawfish][INFO] Writing run statistics to file: 'm84036_250809_035451_s4.bc2106_sawfish_discover/run.stats.json'
2025-09-15 20:24:31.057 wdl.w:ptcp.w:call-sawfish-09.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:28][sawfish][INFO] sawfish completed. Total Runtime: 00:00:11.146
2025-09-15 20:24:31.068 wdl.w:ptcp.w:call-sawfish-08.t:call-run_sawfish.stderr VERBOSE [M::mm_idx_gen::41.199*1.71] sorted minimizers
2025-09-15 20:24:31.068 wdl.w:ptcp.w:call-sawfish-08.t:call-run_sawfish.stderr VERBOSE [M::main::41.199*1.71] loaded/built the index for 195 target sequence(s)
2025-09-15 20:24:31.068 wdl.w:ptcp.w:call-sawfish-08.t:call-run_sawfish.stderr VERBOSE [M::mm_mapopt_update::44.221*1.66] mid_occ = 136
2025-09-15 20:24:31.068 wdl.w:ptcp.w:call-trgt-37.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO srun: job 51797677 queued and waiting for resources
2025-09-15 20:24:31.068 wdl.w:ptcp.w:call-sawfish-08.t:call-run_sawfish.stderr VERBOSE [M::mm_idx_stat] kmer size: 19; skip: 19; is_hpc: 0; #seq: 195
2025-09-15 20:24:31.069 wdl.w:ptcp.w:call-trgt-37.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO srun: job 51797677 has been allocated resources
2025-09-15 20:24:31.069 wdl.w:ptcp.w:call-sawfish-08.t:call-run_sawfish.stderr VERBOSE [M::mm_idx_stat::46.824*1.62] distinct minimizers: 214664461 (92.23% are singletons); average occurrences: 1.372; average spacing: 10.529; total length: 3099922541
2025-09-15 20:24:31.069 wdl.w:ptcp.w:call-trgt-37.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:31.069 wdl.w:ptcp.w:call-sawfish-08.t:call-run_sawfish.stderr VERBOSE [M::main] Version: 2.26-r1175
2025-09-15 20:24:31.069 wdl.w:ptcp.w:call-sawfish-08.t:call-run_sawfish.stderr VERBOSE [M::main] CMD: /opt/pacbio/smrttools/install/smrtlink-release_25.1.0.257715/bundles/smrttools/install/smrttools-release_25.1.0.257715/private/thirdparty/minimap2/minimap2_2.26-pacbio2/binwrap/../../../../../private/thirdparty/minimap2/minimap2_2.26-pacbio2/bin/minimap2 -a -y -x map-hifi -Y -E 1,0 /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa -
2025-09-15 20:24:31.069 wdl.w:ptcp.w:call-sawfish-08.t:call-run_sawfish.stderr VERBOSE [M::main] Real time: 47.138 sec; CPU: 76.208 sec; Peak RSS: 11.886 GB
2025-09-15 20:24:31.227 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:30 [ERROR] - No reads found for TRID=OPDM_ABCD3
2025-09-15 20:24:31.227 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:30 [ERROR] - No reads found for TRID=NIID_NOTCH2NLC
2025-09-15 20:24:31.227 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:30 [ERROR] - No reads found for TRID=DRPLA_ATN1
2025-09-15 20:24:31.227 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:30 [ERROR] - No reads found for TRID=SCA37_DAB1
2025-09-15 20:24:31.228 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:30 [ERROR] - No reads found for TRID=SCA8_ATXN8OS
2025-09-15 20:24:31.228 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:31 [ERROR] - No reads found for TRID=OPDM4_RILPL1
2025-09-15 20:24:31.228 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:31 [ERROR] - No reads found for TRID=OPMD_PABPN1
2025-09-15 20:24:31.228 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:31 [ERROR] - No reads found for TRID=SCA27B_FGF14
2025-09-15 20:24:31.228 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:31 [ERROR] - No reads found for TRID=SCA31_BEAN1
2025-09-15 20:24:31.228 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:31 [ERROR] - No reads found for TRID=SCA4_ZFHX3
2025-09-15 20:24:31.228 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:31 [ERROR] - No reads found for TRID=HDL2_JPH3
2025-09-15 20:24:31.234 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_meth_allele.slurm_singularity INFO srun: job 51797678 queued and waiting for resources
2025-09-15 20:24:31.234 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_meth_allele.slurm_singularity INFO srun: job 51797678 has been allocated resources
2025-09-15 20:24:31.234 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_meth_allele.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:31.413 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO srun: job 51797679 queued and waiting for resources
2025-09-15 20:24:31.414 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO srun: job 51797681 queued and waiting for resources
2025-09-15 20:24:31.415 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_motifs_allele.slurm_singularity INFO srun: job 51797680 queued and waiting for resources
2025-09-15 20:24:31.443 wdl.w:ptcp.w:call-sawfish-29.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:16][sawfish][INFO] Starting sawfish 2.0.3
2025-09-15 20:24:31.444 wdl.w:ptcp.w:call-sawfish-29.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:16][sawfish][INFO] cmdline: sawfish discover --disable-cnv --threads 16 --ref /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa --bam m84036_250809_035451_s4.bc2126.minimap2.bam --output-dir m84036_250809_035451_s4.bc2126_sawfish_discover
2025-09-15 20:24:31.444 wdl.w:ptcp.w:call-sawfish-29.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:16][sawfish][INFO] Running on 16 threads
2025-09-15 20:24:31.444 wdl.w:ptcp.w:call-sawfish-29.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:16][sawfish][INFO] Writing discover settings to file: 'm84036_250809_035451_s4.bc2126_sawfish_discover/discover.settings.json'
2025-09-15 20:24:31.444 wdl.w:ptcp.w:call-sawfish-29.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:16][sawfish][INFO] Reading reference genome from file '/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa'
2025-09-15 20:24:31.444 wdl.w:ptcp.w:call-sawfish-29.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:28][sawfish][INFO] Processing alignment file '/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2126.minimap2.bam'
2025-09-15 20:24:31.444 wdl.w:ptcp.w:call-sawfish-29.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:28][sawfish][INFO] Finished processing all alignments
2025-09-15 20:24:31.444 wdl.w:ptcp.w:call-sawfish-29.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:28][sawfish][INFO] Writing depth bins to binary file: 'm84036_250809_035451_s4.bc2126_sawfish_discover/depth.mpack'
2025-09-15 20:24:31.444 wdl.w:ptcp.w:call-sawfish-29.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:28][sawfish][INFO] Writing max sv depth genome regions to bed file: 'm84036_250809_035451_s4.bc2126_sawfish_discover/max.depth.bed'
2025-09-15 20:24:31.444 wdl.w:ptcp.w:call-sawfish-29.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:28][sawfish][INFO] Completing breakpoint observation clustering
2025-09-15 20:24:31.444 wdl.w:ptcp.w:call-sawfish-29.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:28][sawfish][INFO] Finished breakpoint observation clustering
2025-09-15 20:24:31.444 wdl.w:ptcp.w:call-sawfish-29.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:28][sawfish][INFO] Consolidating adjacent indel candidates
2025-09-15 20:24:31.444 wdl.w:ptcp.w:call-sawfish-29.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:28][sawfish][INFO] Finding large insertion candidates
2025-09-15 20:24:31.444 wdl.w:ptcp.w:call-sawfish-29.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:28][sawfish][INFO] Writing breakpoint_cluster debug bed file: 'm84036_250809_035451_s4.bc2126_sawfish_discover/debug.breakpoint_clusters.bed'
2025-09-15 20:24:31.445 wdl.w:ptcp.w:call-sawfish-29.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:28][sawfish][INFO] Refining SV Candidates
2025-09-15 20:24:31.445 wdl.w:ptcp.w:call-sawfish-29.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:28][sawfish][INFO] Writing debug assembly region bed file: 'm84036_250809_035451_s4.bc2126_sawfish_discover/assembly.regions.bed'
2025-09-15 20:24:31.445 wdl.w:ptcp.w:call-sawfish-29.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:28][sawfish][INFO] Starting refinement of breakpoint evidence clusters
2025-09-15 20:24:31.445 wdl.w:ptcp.w:call-sawfish-29.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:28][sawfish][INFO] Finished refining all breakpoint evidence clusters
2025-09-15 20:24:31.445 wdl.w:ptcp.w:call-sawfish-29.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:28][sawfish][INFO] Writing all contig alignments to bam file: 'm84036_250809_035451_s4.bc2126_sawfish_discover/contig.alignment.bam'
2025-09-15 20:24:31.445 wdl.w:ptcp.w:call-sawfish-29.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:28][sawfish][INFO] Writing candidate structural variants to file: 'm84036_250809_035451_s4.bc2126_sawfish_discover/candidate.sv.bcf'
2025-09-15 20:24:31.445 wdl.w:ptcp.w:call-sawfish-29.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:28][sawfish][INFO] Writing run statistics to file: 'm84036_250809_035451_s4.bc2126_sawfish_discover/run.stats.json'
2025-09-15 20:24:31.445 wdl.w:ptcp.w:call-sawfish-29.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:28][sawfish][INFO] sawfish completed. Total Runtime: 00:00:11.712
2025-09-15 20:24:31.566 wdl.w:ptcp.w:call-paraphase-63.t:call-run_paraphase.slurm_singularity INFO srun: job 51797682 queued and waiting for resources
2025-09-15 20:24:32.017 wdl.w:ptcp.w:call-sawfish-01.t:call-run_sawfish.stderr VERBOSE [M::mm_idx_stat::45.963*1.65] distinct minimizers: 214664461 (92.23% are singletons); average occurrences: 1.372; average spacing: 10.529; total length: 3099922541
2025-09-15 20:24:32.017 wdl.w:ptcp.w:call-sawfish-01.t:call-run_sawfish.stderr VERBOSE [M::main] Version: 2.26-r1175
2025-09-15 20:24:32.017 wdl.w:ptcp.w:call-sawfish-01.t:call-run_sawfish.stderr VERBOSE [M::main] CMD: /opt/pacbio/smrttools/install/smrtlink-release_25.1.0.257715/bundles/smrttools/install/smrttools-release_25.1.0.257715/private/thirdparty/minimap2/minimap2_2.26-pacbio2/binwrap/../../../../../private/thirdparty/minimap2/minimap2_2.26-pacbio2/bin/minimap2 -a -y -x map-hifi -Y -E 1,0 /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa -
2025-09-15 20:24:32.017 wdl.w:ptcp.w:call-sawfish-01.t:call-run_sawfish.stderr VERBOSE [M::main] Real time: 46.284 sec; CPU: 75.955 sec; Peak RSS: 11.886 GB
2025-09-15 20:24:32.147 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_meth_allele INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2135.meth_allele.trgt_plots.zip"
2025-09-15 20:24:32.221 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_meth_allele NOTICE done
2025-09-15 20:24:32.227 wdl.w:ptcp.w:call-trgt-38 NOTICE finish :: job: "call-trgt_plot_meth_allele"
2025-09-15 20:24:32.227 wdl.w:ptcp.w:call-trgt-38 INFO output :: job: "call-trgt_plot_meth_allele", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-38/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2135.meth_allele.trgt_plots.zip"}
2025-09-15 20:24:32.227 wdl.w:ptcp.w:call-trgt-38 INFO visit :: node: "output-images_meth_allele", values: {"images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-38/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2135.meth_allele.trgt_plots.zip"}
2025-09-15 20:24:32.232 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_plot_meth_allele NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-46/call-trgt_plot_meth_allele", thread: 140608731588160
2025-09-15 20:24:32.234 wdl.w:ptcp.w:call-sawfish-09.t:call-run_sawfish INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2106_sawfish/m84036_250809_035451_s4.bc2106.sv.vcf.gz"
2025-09-15 20:24:32.238 wdl.w:ptcp.w:call-sawfish-09.t:call-run_sawfish INFO output :: name: "vcf_tbi", value: "m84036_250809_035451_s4.bc2106_sawfish/m84036_250809_035451_s4.bc2106.sv.vcf.gz.tbi"
2025-09-15 20:24:32.240 wdl.w:ptcp.w:call-sawfish-09.t:call-run_sawfish INFO output :: name: "minimap2_bam", value: "m84036_250809_035451_s4.bc2106.minimap2.bam"
2025-09-15 20:24:32.241 wdl.w:ptcp.w:call-sawfish-09.t:call-run_sawfish INFO output :: name: "minimap2_bam_bai", value: "m84036_250809_035451_s4.bc2106.minimap2.bam.bai"
2025-09-15 20:24:32.253 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_plot_meth_allele INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:32.253 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_plot_meth_allele INFO input :: name: "waterfall", value: false
2025-09-15 20:24:32.253 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_plot_meth_allele INFO input :: name: "methylation", value: true
2025-09-15 20:24:32.253 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_plot_meth_allele INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:32.253 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_plot_meth_allele INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:32.253 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_plot_meth_allele INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:32.253 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_plot_meth_allele INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2143.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:32.254 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_plot_meth_allele INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2143.trgt.sorted.spanning.bam"
2025-09-15 20:24:32.254 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_plot_meth_allele INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2143.trgt.vcf"
2025-09-15 20:24:32.254 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_plot_meth_allele INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2143"
2025-09-15 20:24:32.254 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_plot_meth_allele INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:32.254 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_plot_meth_allele INFO eval :: name: "plot_type", value: "allele"
2025-09-15 20:24:32.254 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_plot_meth_allele INFO eval :: name: "show", value: "meth"
2025-09-15 20:24:32.254 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_plot_meth_allele INFO eval :: name: "threads", value: 1
2025-09-15 20:24:32.254 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_plot_meth_allele INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:32.254 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_plot_meth_allele INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2143.meth_allele"
2025-09-15 20:24:32.255 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_plot_meth_allele INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:32.255 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_plot_meth_allele WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:32.255 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_plot_meth_allele INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:32.255 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_plot_meth_allele INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:32.338 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_plot_meth_allele INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-46/call-trgt_plot_meth_allele/_singularity_tmpdir_b4utl7p7"
2025-09-15 20:24:32.338 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_plot_meth_allele INFO Slurm invocation: srun --job-name call-trgt_plot_meth_allele --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-46/call-trgt_plot_meth_allele/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-46/call-trgt_plot_meth_allele/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-46/call-trgt_plot_meth_allele/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-46/call-trgt_plot_meth_allele/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-46/call-trgt_genotype/out/m84036_250809_035451_s4.bc2143.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2143.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-46/call-trgt_genotype/out/m84036_250809_035451_s4.bc2143.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2143.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-46/call-trgt_genotype/out/m84036_250809_035451_s4.bc2143.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2143.trgt.sorted.spanning.bam:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-46/call-trgt_plot_meth_allele/_singularity_tmpdir_b4utl7p7/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-46/call-trgt_plot_meth_allele/_singularity_tmpdir_b4utl7p7/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:32.375 wdl.w:ptcp.w:call-sawfish-29.t:call-run_sawfish INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2126_sawfish/m84036_250809_035451_s4.bc2126.sv.vcf.gz"
2025-09-15 20:24:32.380 wdl.w:ptcp.w:call-sawfish-29.t:call-run_sawfish INFO output :: name: "vcf_tbi", value: "m84036_250809_035451_s4.bc2126_sawfish/m84036_250809_035451_s4.bc2126.sv.vcf.gz.tbi"
2025-09-15 20:24:32.381 wdl.w:ptcp.w:call-sawfish-29.t:call-run_sawfish INFO output :: name: "minimap2_bam", value: "m84036_250809_035451_s4.bc2126.minimap2.bam"
2025-09-15 20:24:32.383 wdl.w:ptcp.w:call-sawfish-29.t:call-run_sawfish INFO output :: name: "minimap2_bam_bai", value: "m84036_250809_035451_s4.bc2126.minimap2.bam.bai"
2025-09-15 20:24:32.387 wdl.w:ptcp.w:call-trgt-36.t:call-trgt_plot_meth_allele INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2133.meth_allele.trgt_plots.zip"
2025-09-15 20:24:32.397 wdl.w:ptcp.w:call-trgt-00.t:call-trgt_plot_motifs_allele INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2097.motifs_allele.trgt_plots.zip"
2025-09-15 20:24:32.410 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_plot_meth_allele NOTICE slurm_singularity run :: pid: 1202169, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-46/call-trgt_plot_meth_allele/slurm_singularity.log.txt"
2025-09-15 20:24:32.410 wdl.w:ptcp.w:call-sawfish-09.t:call-run_sawfish NOTICE done
2025-09-15 20:24:32.417 wdl.w:ptcp.w:call-sawfish-09 NOTICE finish :: job: "call-run_sawfish"
2025-09-15 20:24:32.417 wdl.w:ptcp.w:call-sawfish-09 INFO output :: job: "call-run_sawfish", values: {"minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-09/call-run_sawfish/out/m84036_250809_035451_s4.bc2106.minimap2.bam.bai", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-09/call-run_sawfish/out/m84036_250809_035451_s4.bc2106.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-09/call-run_sawfish/out/m84036_250809_035451_s4.bc2106_sawfish/m84036_250809_035451_s4.bc2106.sv.vcf.gz.tbi", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-09/call-run_sawfish/out/m84036_250809_035451_s4.bc2106_sawfish/m84036_250809_035451_s4.bc2106.sv.vcf.gz"}
2025-09-15 20:24:32.417 wdl.w:ptcp.w:call-sawfish-09 INFO visit :: node: "output-minimap2_bam", values: {"minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-09/call-run_sawfish/out/m84036_250809_035451_s4.bc2106.minimap2.bam"}
2025-09-15 20:24:32.417 wdl.w:ptcp.w:call-sawfish-09 INFO visit :: node: "output-minimap2_bam_bai", values: {"minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-09/call-run_sawfish/out/m84036_250809_035451_s4.bc2106.minimap2.bam.bai"}
2025-09-15 20:24:32.418 wdl.w:ptcp.w:call-sawfish-09 INFO visit :: node: "output-vcf", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-09/call-run_sawfish/out/m84036_250809_035451_s4.bc2106_sawfish/m84036_250809_035451_s4.bc2106.sv.vcf.gz"}
2025-09-15 20:24:32.418 wdl.w:ptcp.w:call-sawfish-09 INFO visit :: node: "output-vcf_tbi", values: {"vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-09/call-run_sawfish/out/m84036_250809_035451_s4.bc2106_sawfish/m84036_250809_035451_s4.bc2106.sv.vcf.gz.tbi"}
2025-09-15 20:24:32.418 wdl.w:ptcp.w:call-sawfish-09 INFO visit :: node: "outputs", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-09/call-run_sawfish/out/m84036_250809_035451_s4.bc2106_sawfish/m84036_250809_035451_s4.bc2106.sv.vcf.gz", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-09/call-run_sawfish/out/m84036_250809_035451_s4.bc2106.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-09/call-run_sawfish/out/m84036_250809_035451_s4.bc2106_sawfish/m84036_250809_035451_s4.bc2106.sv.vcf.gz.tbi", "minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-09/call-run_sawfish/out/m84036_250809_035451_s4.bc2106.minimap2.bam.bai"}
2025-09-15 20:24:32.422 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_plot_meth_waterfall NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-46/call-trgt_plot_meth_waterfall", thread: 140609847293504
2025-09-15 20:24:32.431 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO srun: job 51797679 has been allocated resources
2025-09-15 20:24:32.431 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:32.433 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_motifs_allele.slurm_singularity INFO srun: job 51797680 has been allocated resources
2025-09-15 20:24:32.433 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_motifs_allele.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:32.433 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO srun: job 51797681 has been allocated resources
2025-09-15 20:24:32.433 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:32.446 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_plot_meth_waterfall INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:32.446 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_plot_meth_waterfall INFO input :: name: "waterfall", value: true
2025-09-15 20:24:32.446 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_plot_meth_waterfall INFO input :: name: "methylation", value: true
2025-09-15 20:24:32.446 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_plot_meth_waterfall INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:32.446 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_plot_meth_waterfall INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:32.446 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_plot_meth_waterfall INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:32.446 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_plot_meth_waterfall INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2143.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:32.446 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_plot_meth_waterfall INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2143.trgt.sorted.spanning.bam"
2025-09-15 20:24:32.446 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_plot_meth_waterfall INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2143.trgt.vcf"
2025-09-15 20:24:32.447 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_plot_meth_waterfall INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2143"
2025-09-15 20:24:32.447 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_plot_meth_waterfall INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:32.447 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_plot_meth_waterfall INFO eval :: name: "plot_type", value: "waterfall"
2025-09-15 20:24:32.447 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_plot_meth_waterfall INFO eval :: name: "show", value: "meth"
2025-09-15 20:24:32.447 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_plot_meth_waterfall INFO eval :: name: "threads", value: 1
2025-09-15 20:24:32.447 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_plot_meth_waterfall INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:32.448 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_plot_meth_waterfall INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2143.meth_waterfall"
2025-09-15 20:24:32.448 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_plot_meth_waterfall INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:32.448 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_plot_meth_waterfall WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:32.449 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_plot_meth_waterfall INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:32.449 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_plot_meth_waterfall INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:32.501 wdl.w:ptcp.w:call-sawfish-09 NOTICE done
2025-09-15 20:24:32.508 wdl.w:ptcp NOTICE finish :: job: "call-sawfish-09"
2025-09-15 20:24:32.508 wdl.w:ptcp INFO output :: job: "call-sawfish-09", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-09/out/m84036_250809_035451_s4.bc2106_sawfish/m84036_250809_035451_s4.bc2106.sv.vcf.gz", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-09/out/m84036_250809_035451_s4.bc2106.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-09/out/m84036_250809_035451_s4.bc2106_sawfish/m84036_250809_035451_s4.bc2106.sv.vcf.gz.tbi", "minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-09/out/m84036_250809_035451_s4.bc2106.minimap2.bam.bai"}
2025-09-15 20:24:32.509 wdl.w:ptcp NOTICE ready :: job: "call-tar_outputs-09", callee: "tar_outputs"
2025-09-15 20:24:32.509 wdl.w:ptcp INFO input :: job: "call-tar_outputs-09", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "sawfish_vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-09/out/m84036_250809_035451_s4.bc2106_sawfish/m84036_250809_035451_s4.bc2106.sv.vcf.gz.tbi", "sawfish_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-09/out/m84036_250809_035451_s4.bc2106_sawfish/m84036_250809_035451_s4.bc2106.sv.vcf.gz", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-09/out/m84036_250809_035451_s4.bc2106.f8inversion.json", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-09/out/m84036_250809_035451_s4.bc2106_paraphase/m84036_250809_035451_s4.bc2106.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-09/out/m84036_250809_035451_s4.bc2106_paraphase/m84036_250809_035451_s4.bc2106.paraphase.bam", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-09/out/m84036_250809_035451_s4.bc2106_paraphase/m84036_250809_035451_s4.bc2106.paraphase.json", "trgt_spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-09/out/m84036_250809_035451_s4.bc2106.trgt.sorted.spanning.bam.bai", "trgt_spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-09/out/m84036_250809_035451_s4.bc2106.trgt.sorted.spanning.bam", "trgt_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-09/out/m84036_250809_035451_s4.bc2106.trgt.vcf", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-09/out/m84036_250809_035451_s4.bc2106.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-09/out/m84036_250809_035451_s4.bc2106.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2106"}
2025-09-15 20:24:32.519 wdl.w:ptcp.w:call-trgt-42 NOTICE workflow start :: name: "trgt", source: "./trgt.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-42"
2025-09-15 20:24:32.541 wdl.w:ptcp.w:call-trgt-42 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:24:32.541 wdl.w:ptcp.w:call-trgt-42 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-42/out/m84036_250809_035451_s4.bc2139.mapped.bam"}
2025-09-15 20:24:32.541 wdl.w:ptcp.w:call-trgt-42 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-42/out/m84036_250809_035451_s4.bc2139.mapped.bam.bai"}
2025-09-15 20:24:32.541 wdl.w:ptcp.w:call-trgt-42 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:24:32.541 wdl.w:ptcp.w:call-trgt-42 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:24:32.541 wdl.w:ptcp.w:call-trgt-42 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2139"}
2025-09-15 20:24:32.541 wdl.w:ptcp.w:call-trgt-42 INFO visit :: node: "decl-sex", values: {"sex": "F"}
2025-09-15 20:24:32.542 wdl.w:ptcp.w:call-trgt-42 INFO visit :: node: "decl-trgt_bed", values: {"trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"}
2025-09-15 20:24:32.542 wdl.w:ptcp.w:call-trgt-42 NOTICE ready :: job: "call-get_reads_overlapping_repeats", callee: "get_reads_overlapping_repeats"
2025-09-15 20:24:32.542 wdl.w:ptcp.w:call-trgt-42 INFO input :: job: "call-get_reads_overlapping_repeats", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-42/out/m84036_250809_035451_s4.bc2139.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-42/out/m84036_250809_035451_s4.bc2139.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2139"}
2025-09-15 20:24:32.543 wdl.w:ptcp.w:call-trgt-42 NOTICE ready :: job: "call-trgt_genotype", callee: "trgt_genotype"
2025-09-15 20:24:32.543 wdl.w:ptcp.w:call-trgt-01.t:call-trgt_plot_motifs_allele INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2098.motifs_allele.trgt_plots.zip"
2025-09-15 20:24:32.544 wdl.w:ptcp.w:call-trgt-42 INFO input :: job: "call-trgt_genotype", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-42/out/m84036_250809_035451_s4.bc2139.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-42/out/m84036_250809_035451_s4.bc2139.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2139"}
2025-09-15 20:24:32.561 wdl.w:ptcp.w:call-trgt-44.t:call-get_reads_overlapping_repeats INFO output :: name: "reads_overlapping_repeats", value: "m84036_250809_035451_s4.bc2141.repeats.bam"
2025-09-15 20:24:32.562 wdl.w:ptcp.w:call-trgt-00.t:call-trgt_plot_motifs_allele NOTICE done
2025-09-15 20:24:32.564 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_plot_meth_waterfall INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-46/call-trgt_plot_meth_waterfall/_singularity_tmpdir_3gt4i62u"
2025-09-15 20:24:32.564 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_plot_meth_waterfall INFO Slurm invocation: srun --job-name call-trgt_plot_meth_waterfall --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-46/call-trgt_plot_meth_waterfall/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-46/call-trgt_plot_meth_waterfall/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-46/call-trgt_plot_meth_waterfall/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-46/call-trgt_plot_meth_waterfall/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-46/call-trgt_genotype/out/m84036_250809_035451_s4.bc2143.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2143.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-46/call-trgt_genotype/out/m84036_250809_035451_s4.bc2143.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2143.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-46/call-trgt_genotype/out/m84036_250809_035451_s4.bc2143.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2143.trgt.sorted.spanning.bam:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-46/call-trgt_plot_meth_waterfall/_singularity_tmpdir_3gt4i62u/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-46/call-trgt_plot_meth_waterfall/_singularity_tmpdir_3gt4i62u/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:32.568 wdl.w:ptcp.w:call-trgt-00 NOTICE finish :: job: "call-trgt_plot_motifs_allele"
2025-09-15 20:24:32.568 wdl.w:ptcp.w:call-trgt-00 INFO output :: job: "call-trgt_plot_motifs_allele", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-00/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2097.motifs_allele.trgt_plots.zip"}
2025-09-15 20:24:32.569 wdl.w:ptcp.w:call-trgt-00 INFO visit :: node: "output-images_motifs_allele", values: {"images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-00/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2097.motifs_allele.trgt_plots.zip"}
2025-09-15 20:24:32.569 wdl.w:ptcp.w:call-trgt-44.t:call-get_reads_overlapping_repeats INFO output :: name: "reads_overlapping_repeats_bai", value: "m84036_250809_035451_s4.bc2141.repeats.bam.bai"
2025-09-15 20:24:32.578 wdl.w:ptcp.w:call-sawfish-29.t:call-run_sawfish NOTICE done
2025-09-15 20:24:32.578 wdl.w:ptcp.w:call-paraphase-63.t:call-run_paraphase.slurm_singularity INFO srun: job 51797682 has been allocated resources
2025-09-15 20:24:32.578 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_plot_motifs_allele NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-46/call-trgt_plot_motifs_allele", thread: 140608203109952
2025-09-15 20:24:32.579 wdl.w:ptcp.w:call-paraphase-63.t:call-run_paraphase.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:32.587 wdl.w:ptcp.w:call-trgt-36.t:call-trgt_plot_meth_allele NOTICE done
2025-09-15 20:24:32.592 wdl.w:ptcp.w:call-trgt-36 NOTICE finish :: job: "call-trgt_plot_meth_allele"
2025-09-15 20:24:32.592 wdl.w:ptcp.w:call-trgt-36 INFO output :: job: "call-trgt_plot_meth_allele", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-36/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2133.meth_allele.trgt_plots.zip"}
2025-09-15 20:24:32.592 wdl.w:ptcp.w:call-trgt-36 INFO visit :: node: "output-images_meth_allele", values: {"images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-36/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2133.meth_allele.trgt_plots.zip"}
2025-09-15 20:24:32.598 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_plot_motifs_allele INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:32.598 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_plot_motifs_allele INFO input :: name: "waterfall", value: false
2025-09-15 20:24:32.598 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_plot_motifs_allele INFO input :: name: "methylation", value: false
2025-09-15 20:24:32.598 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_plot_motifs_allele INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:32.599 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_plot_motifs_allele INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:32.599 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_plot_motifs_allele INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:32.599 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_plot_motifs_allele INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2143.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:32.599 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_plot_motifs_allele INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2143.trgt.sorted.spanning.bam"
2025-09-15 20:24:32.599 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_plot_motifs_allele INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2143.trgt.vcf"
2025-09-15 20:24:32.599 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_plot_motifs_allele INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2143"
2025-09-15 20:24:32.599 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_plot_motifs_allele INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:32.599 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_plot_motifs_waterfall NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-46/call-trgt_plot_motifs_waterfall", thread: 140607146153536
2025-09-15 20:24:32.600 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_plot_motifs_allele INFO eval :: name: "plot_type", value: "allele"
2025-09-15 20:24:32.600 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_plot_motifs_allele INFO eval :: name: "show", value: "motifs"
2025-09-15 20:24:32.600 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_plot_motifs_allele INFO eval :: name: "threads", value: 1
2025-09-15 20:24:32.600 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_plot_motifs_allele INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:32.601 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_plot_motifs_allele INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2143.motifs_allele"
2025-09-15 20:24:32.601 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_plot_motifs_allele INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:32.601 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_plot_motifs_allele WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:32.602 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_plot_motifs_allele INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:32.602 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_plot_motifs_allele INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:32.600 wdl.w:ptcp.w:call-sawfish-29 NOTICE finish :: job: "call-run_sawfish"
2025-09-15 20:24:32.602 wdl.w:ptcp.w:call-sawfish-29 INFO output :: job: "call-run_sawfish", values: {"minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-29/call-run_sawfish/out/m84036_250809_035451_s4.bc2126.minimap2.bam.bai", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-29/call-run_sawfish/out/m84036_250809_035451_s4.bc2126.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-29/call-run_sawfish/out/m84036_250809_035451_s4.bc2126_sawfish/m84036_250809_035451_s4.bc2126.sv.vcf.gz.tbi", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-29/call-run_sawfish/out/m84036_250809_035451_s4.bc2126_sawfish/m84036_250809_035451_s4.bc2126.sv.vcf.gz"}
2025-09-15 20:24:32.603 wdl.w:ptcp.w:call-sawfish-29 INFO visit :: node: "output-minimap2_bam", values: {"minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-29/call-run_sawfish/out/m84036_250809_035451_s4.bc2126.minimap2.bam"}
2025-09-15 20:24:32.603 wdl.w:ptcp.w:call-sawfish-29 INFO visit :: node: "output-minimap2_bam_bai", values: {"minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-29/call-run_sawfish/out/m84036_250809_035451_s4.bc2126.minimap2.bam.bai"}
2025-09-15 20:24:32.603 wdl.w:ptcp.w:call-sawfish-29 INFO visit :: node: "output-vcf", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-29/call-run_sawfish/out/m84036_250809_035451_s4.bc2126_sawfish/m84036_250809_035451_s4.bc2126.sv.vcf.gz"}
2025-09-15 20:24:32.603 wdl.w:ptcp.w:call-sawfish-29 INFO visit :: node: "output-vcf_tbi", values: {"vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-29/call-run_sawfish/out/m84036_250809_035451_s4.bc2126_sawfish/m84036_250809_035451_s4.bc2126.sv.vcf.gz.tbi"}
2025-09-15 20:24:32.603 wdl.w:ptcp.w:call-sawfish-29 INFO visit :: node: "outputs", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-29/call-run_sawfish/out/m84036_250809_035451_s4.bc2126_sawfish/m84036_250809_035451_s4.bc2126.sv.vcf.gz", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-29/call-run_sawfish/out/m84036_250809_035451_s4.bc2126.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-29/call-run_sawfish/out/m84036_250809_035451_s4.bc2126_sawfish/m84036_250809_035451_s4.bc2126.sv.vcf.gz.tbi", "minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-29/call-run_sawfish/out/m84036_250809_035451_s4.bc2126.minimap2.bam.bai"}
2025-09-15 20:24:32.610 wdl.w:ptcp.w:call-trgt-45.t:call-trgt_plot_meth_allele NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-45/call-trgt_plot_meth_allele", thread: 140609302029888
2025-09-15 20:24:32.621 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_plot_meth_waterfall NOTICE slurm_singularity run :: pid: 1202178, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-46/call-trgt_plot_meth_waterfall/slurm_singularity.log.txt"
2025-09-15 20:24:32.627 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_plot_motifs_waterfall INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:32.627 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_plot_motifs_waterfall INFO input :: name: "waterfall", value: true
2025-09-15 20:24:32.628 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_plot_motifs_waterfall INFO input :: name: "methylation", value: false
2025-09-15 20:24:32.628 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_plot_motifs_waterfall INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:32.628 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_plot_motifs_waterfall INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:32.628 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_plot_motifs_waterfall INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:32.628 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_plot_motifs_waterfall INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2143.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:32.628 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_plot_motifs_waterfall INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2143.trgt.sorted.spanning.bam"
2025-09-15 20:24:32.628 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_plot_motifs_waterfall INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2143.trgt.vcf"
2025-09-15 20:24:32.628 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_plot_motifs_waterfall INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2143"
2025-09-15 20:24:32.629 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:32.629 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "plot_type", value: "waterfall"
2025-09-15 20:24:32.629 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "show", value: "motifs"
2025-09-15 20:24:32.630 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "threads", value: 1
2025-09-15 20:24:32.630 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:32.630 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2143.motifs_waterfall"
2025-09-15 20:24:32.631 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_plot_motifs_waterfall INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:32.631 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_plot_motifs_waterfall WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:32.631 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_plot_motifs_waterfall INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:32.632 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_plot_motifs_waterfall INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:32.639 wdl.w:ptcp.w:call-trgt-45.t:call-trgt_plot_meth_allele INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:32.639 wdl.w:ptcp.w:call-trgt-45.t:call-trgt_plot_meth_allele INFO input :: name: "waterfall", value: false
2025-09-15 20:24:32.639 wdl.w:ptcp.w:call-trgt-45.t:call-trgt_plot_meth_allele INFO input :: name: "methylation", value: true
2025-09-15 20:24:32.640 wdl.w:ptcp.w:call-trgt-45.t:call-trgt_plot_meth_allele INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:32.640 wdl.w:ptcp.w:call-trgt-45.t:call-trgt_plot_meth_allele INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:32.640 wdl.w:ptcp.w:call-trgt-45.t:call-trgt_plot_meth_allele INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:32.640 wdl.w:ptcp.w:call-trgt-45.t:call-trgt_plot_meth_allele INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2142.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:32.640 wdl.w:ptcp.w:call-trgt-45.t:call-trgt_plot_meth_allele INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2142.trgt.sorted.spanning.bam"
2025-09-15 20:24:32.640 wdl.w:ptcp.w:call-trgt-45.t:call-trgt_plot_meth_allele INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2142.trgt.vcf"
2025-09-15 20:24:32.640 wdl.w:ptcp.w:call-trgt-45.t:call-trgt_plot_meth_allele INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2142"
2025-09-15 20:24:32.641 wdl.w:ptcp.w:call-trgt-45.t:call-trgt_plot_meth_allele INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:32.641 wdl.w:ptcp.w:call-trgt-45.t:call-trgt_plot_meth_allele INFO eval :: name: "plot_type", value: "allele"
2025-09-15 20:24:32.641 wdl.w:ptcp.w:call-trgt-45.t:call-trgt_plot_meth_allele INFO eval :: name: "show", value: "meth"
2025-09-15 20:24:32.641 wdl.w:ptcp.w:call-trgt-45.t:call-trgt_plot_meth_allele INFO eval :: name: "threads", value: 1
2025-09-15 20:24:32.641 wdl.w:ptcp.w:call-trgt-45.t:call-trgt_plot_meth_allele INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:32.641 wdl.w:ptcp.w:call-trgt-45.t:call-trgt_plot_meth_allele INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2142.meth_allele"
2025-09-15 20:24:32.642 wdl.w:ptcp.w:call-trgt-45.t:call-trgt_plot_meth_allele INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:32.642 wdl.w:ptcp.w:call-trgt-45.t:call-trgt_plot_meth_allele WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:32.642 wdl.w:ptcp.w:call-trgt-45.t:call-trgt_plot_meth_allele INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:32.642 wdl.w:ptcp.w:call-trgt-45.t:call-trgt_plot_meth_allele INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:32.654 wdl.w:ptcp.w:call-trgt-44.t:call-get_reads_overlapping_repeats NOTICE done
2025-09-15 20:24:32.658 wdl.w:ptcp.w:call-trgt-44 NOTICE finish :: job: "call-get_reads_overlapping_repeats"
2025-09-15 20:24:32.658 wdl.w:ptcp.w:call-trgt-44 INFO output :: job: "call-get_reads_overlapping_repeats", values: {"reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-44/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2141.repeats.bam.bai", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-44/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2141.repeats.bam"}
2025-09-15 20:24:32.659 wdl.w:ptcp.w:call-trgt-44 INFO visit :: node: "output-reads_overlapping_repeats", values: {"reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-44/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2141.repeats.bam"}
2025-09-15 20:24:32.659 wdl.w:ptcp.w:call-trgt-44 INFO visit :: node: "output-reads_overlapping_repeats_bai", values: {"reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-44/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2141.repeats.bam.bai"}
2025-09-15 20:24:32.659 wdl.w:ptcp.w:call-sawfish-29 NOTICE done
2025-09-15 20:24:32.668 wdl.w:ptcp NOTICE finish :: job: "call-sawfish-29"
2025-09-15 20:24:32.668 wdl.w:ptcp INFO output :: job: "call-sawfish-29", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-29/out/m84036_250809_035451_s4.bc2126_sawfish/m84036_250809_035451_s4.bc2126.sv.vcf.gz", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-29/out/m84036_250809_035451_s4.bc2126.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-29/out/m84036_250809_035451_s4.bc2126_sawfish/m84036_250809_035451_s4.bc2126.sv.vcf.gz.tbi", "minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-29/out/m84036_250809_035451_s4.bc2126.minimap2.bam.bai"}
2025-09-15 20:24:32.669 wdl.w:ptcp NOTICE ready :: job: "call-tar_outputs-29", callee: "tar_outputs"
2025-09-15 20:24:32.669 wdl.w:ptcp INFO input :: job: "call-tar_outputs-29", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "sawfish_vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-29/out/m84036_250809_035451_s4.bc2126_sawfish/m84036_250809_035451_s4.bc2126.sv.vcf.gz.tbi", "sawfish_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-29/out/m84036_250809_035451_s4.bc2126_sawfish/m84036_250809_035451_s4.bc2126.sv.vcf.gz", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-29/out/m84036_250809_035451_s4.bc2126.f8inversion.json", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-29/out/m84036_250809_035451_s4.bc2126_paraphase/m84036_250809_035451_s4.bc2126.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-29/out/m84036_250809_035451_s4.bc2126_paraphase/m84036_250809_035451_s4.bc2126.paraphase.bam", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-29/out/m84036_250809_035451_s4.bc2126_paraphase/m84036_250809_035451_s4.bc2126.paraphase.json", "trgt_spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-29/out/m84036_250809_035451_s4.bc2126.trgt.sorted.spanning.bam.bai", "trgt_spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-29/out/m84036_250809_035451_s4.bc2126.trgt.sorted.spanning.bam", "trgt_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-29/out/m84036_250809_035451_s4.bc2126.trgt.vcf", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-29/out/m84036_250809_035451_s4.bc2126.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-29/out/m84036_250809_035451_s4.bc2126.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2126"}
2025-09-15 20:24:32.669 wdl.w:ptcp.w:call-trgt-45.t:call-trgt_plot_meth_waterfall NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-45/call-trgt_plot_meth_waterfall", thread: 140607674631744
2025-09-15 20:24:32.677 wdl.w:ptcp.w:call-paraphase-58 NOTICE workflow start :: name: "paraphase", source: "./paraphase.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-58"
2025-09-15 20:24:32.693 wdl.w:ptcp.w:call-trgt-45.t:call-trgt_plot_meth_waterfall INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:32.693 wdl.w:ptcp.w:call-trgt-45.t:call-trgt_plot_meth_waterfall INFO input :: name: "waterfall", value: true
2025-09-15 20:24:32.694 wdl.w:ptcp.w:call-trgt-45.t:call-trgt_plot_meth_waterfall INFO input :: name: "methylation", value: true
2025-09-15 20:24:32.694 wdl.w:ptcp.w:call-trgt-45.t:call-trgt_plot_meth_waterfall INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:32.693 wdl.w:ptcp.w:call-sawfish-00.t:call-run_sawfish.stderr VERBOSE [M::mm_idx_gen::33.795*1.45] collected minimizers
2025-09-15 20:24:32.694 wdl.w:ptcp.w:call-trgt-45.t:call-trgt_plot_meth_waterfall INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:32.695 wdl.w:ptcp.w:call-sawfish-00.t:call-run_sawfish.stderr VERBOSE [M::mm_idx_gen::40.651*1.70] sorted minimizers
2025-09-15 20:24:32.695 wdl.w:ptcp.w:call-trgt-45.t:call-trgt_plot_meth_waterfall INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:32.695 wdl.w:ptcp.w:call-sawfish-00.t:call-run_sawfish.stderr VERBOSE [M::main::40.651*1.70] loaded/built the index for 195 target sequence(s)
2025-09-15 20:24:32.695 wdl.w:ptcp.w:call-trgt-45.t:call-trgt_plot_meth_waterfall INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2142.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:32.695 wdl.w:ptcp.w:call-sawfish-00.t:call-run_sawfish.stderr VERBOSE [M::mm_mapopt_update::43.681*1.65] mid_occ = 136
2025-09-15 20:24:32.695 wdl.w:ptcp.w:call-trgt-45.t:call-trgt_plot_meth_waterfall INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2142.trgt.sorted.spanning.bam"
2025-09-15 20:24:32.696 wdl.w:ptcp.w:call-sawfish-00.t:call-run_sawfish.stderr VERBOSE [M::mm_idx_stat] kmer size: 19; skip: 19; is_hpc: 0; #seq: 195
2025-09-15 20:24:32.696 wdl.w:ptcp.w:call-trgt-45.t:call-trgt_plot_meth_waterfall INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2142.trgt.vcf"
2025-09-15 20:24:32.696 wdl.w:ptcp.w:call-sawfish-00.t:call-run_sawfish.stderr VERBOSE [M::mm_idx_stat::46.318*1.62] distinct minimizers: 214664461 (92.23% are singletons); average occurrences: 1.372; average spacing: 10.529; total length: 3099922541
2025-09-15 20:24:32.696 wdl.w:ptcp.w:call-trgt-45.t:call-trgt_plot_meth_waterfall INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2142"
2025-09-15 20:24:32.696 wdl.w:ptcp.w:call-sawfish-00.t:call-run_sawfish.stderr VERBOSE [M::worker_pipeline::46.322*1.62] mapped 1 sequences
2025-09-15 20:24:32.697 wdl.w:ptcp.w:call-trgt-45.t:call-trgt_plot_meth_waterfall INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:32.697 wdl.w:ptcp.w:call-sawfish-00.t:call-run_sawfish.stderr VERBOSE [M::main] Version: 2.26-r1175
2025-09-15 20:24:32.697 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_plot_motifs_allele INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-46/call-trgt_plot_motifs_allele/_singularity_tmpdir_267wzwbl"
2025-09-15 20:24:32.698 wdl.w:ptcp.w:call-sawfish-00.t:call-run_sawfish.stderr VERBOSE [M::main] CMD: /opt/pacbio/smrttools/install/smrtlink-release_25.1.0.257715/bundles/smrttools/install/smrttools-release_25.1.0.257715/private/thirdparty/minimap2/minimap2_2.26-pacbio2/binwrap/../../../../../private/thirdparty/minimap2/minimap2_2.26-pacbio2/bin/minimap2 -a -y -x map-hifi -Y -E 1,0 /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa -
2025-09-15 20:24:32.698 wdl.w:ptcp.w:call-trgt-45.t:call-trgt_plot_meth_waterfall INFO eval :: name: "plot_type", value: "waterfall"
2025-09-15 20:24:32.698 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_plot_motifs_allele INFO Slurm invocation: srun --job-name call-trgt_plot_motifs_allele --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-46/call-trgt_plot_motifs_allele/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-46/call-trgt_plot_motifs_allele/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-46/call-trgt_plot_motifs_allele/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-46/call-trgt_plot_motifs_allele/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-46/call-trgt_genotype/out/m84036_250809_035451_s4.bc2143.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2143.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-46/call-trgt_genotype/out/m84036_250809_035451_s4.bc2143.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2143.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-46/call-trgt_genotype/out/m84036_250809_035451_s4.bc2143.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2143.trgt.sorted.spanning.bam:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-46/call-trgt_plot_motifs_allele/_singularity_tmpdir_267wzwbl/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-46/call-trgt_plot_motifs_allele/_singularity_tmpdir_267wzwbl/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:32.698 wdl.w:ptcp.w:call-sawfish-00.t:call-run_sawfish.stderr VERBOSE [M::main] Real time: 46.593 sec; CPU: 75.104 sec; Peak RSS: 11.886 GB
2025-09-15 20:24:32.698 wdl.w:ptcp.w:call-trgt-45.t:call-trgt_plot_meth_waterfall INFO eval :: name: "show", value: "meth"
2025-09-15 20:24:32.699 wdl.w:ptcp.w:call-paraphase-58 INFO visit :: node: "decl-annotation_vcf", values: {"annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf"}
2025-09-15 20:24:32.699 wdl.w:ptcp.w:call-trgt-45.t:call-trgt_plot_meth_waterfall INFO eval :: name: "threads", value: 1
2025-09-15 20:24:32.700 wdl.w:ptcp.w:call-paraphase-58 INFO visit :: node: "decl-config_file", values: {"config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml"}
2025-09-15 20:24:32.702 wdl.w:ptcp.w:call-paraphase-58 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:24:32.701 wdl.w:ptcp.w:call-trgt-45.t:call-trgt_plot_meth_waterfall INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:32.702 wdl.w:ptcp.w:call-paraphase-58 INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:24:32.702 wdl.w:ptcp.w:call-trgt-45.t:call-trgt_plot_meth_waterfall INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2142.meth_waterfall"
2025-09-15 20:24:32.702 wdl.w:ptcp.w:call-paraphase-58 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-58/out/m84036_250809_035451_s4.bc2155.mapped.bam"}
2025-09-15 20:24:32.702 wdl.w:ptcp.w:call-paraphase-58 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-58/out/m84036_250809_035451_s4.bc2155.mapped.bam.bai"}
2025-09-15 20:24:32.702 wdl.w:ptcp.w:call-trgt-45.t:call-trgt_plot_meth_waterfall INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:32.703 wdl.w:ptcp.w:call-paraphase-58 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:24:32.703 wdl.w:ptcp.w:call-trgt-45.t:call-trgt_plot_meth_waterfall WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:32.703 wdl.w:ptcp.w:call-paraphase-58 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:24:32.703 wdl.w:ptcp.w:call-paraphase-58 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2155"}
2025-09-15 20:24:32.704 wdl.w:ptcp.w:call-paraphase-58 INFO visit :: node: "decl-sex", values: {"sex": "F"}
2025-09-15 20:24:32.704 wdl.w:ptcp.w:call-paraphase-58 NOTICE ready :: job: "call-run_paraphase", callee: "run_paraphase"
2025-09-15 20:24:32.704 wdl.w:ptcp.w:call-paraphase-58 INFO input :: job: "call-run_paraphase", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf", "genome_version": "38", "config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-58/out/m84036_250809_035451_s4.bc2155.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-58/out/m84036_250809_035451_s4.bc2155.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2155"}
2025-09-15 20:24:32.704 wdl.w:ptcp.w:call-trgt-45.t:call-trgt_plot_meth_waterfall INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:32.704 wdl.w:ptcp.w:call-trgt-45.t:call-trgt_plot_meth_waterfall INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:32.720 wdl.w:ptcp.w:call-trgt-01.t:call-trgt_plot_motifs_allele NOTICE done
2025-09-15 20:24:32.724 wdl.w:ptcp.w:call-trgt-01 NOTICE finish :: job: "call-trgt_plot_motifs_allele"
2025-09-15 20:24:32.724 wdl.w:ptcp.w:call-trgt-01 INFO output :: job: "call-trgt_plot_motifs_allele", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-01/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2098.motifs_allele.trgt_plots.zip"}
2025-09-15 20:24:32.725 wdl.w:ptcp.w:call-trgt-01 INFO visit :: node: "output-images_motifs_allele", values: {"images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-01/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2098.motifs_allele.trgt_plots.zip"}
2025-09-15 20:24:32.730 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_plot_motifs_allele NOTICE slurm_singularity run :: pid: 1202180, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-46/call-trgt_plot_motifs_allele/slurm_singularity.log.txt"
2025-09-15 20:24:32.733 wdl.w:ptcp.w:call-trgt-45.t:call-trgt_plot_motifs_allele NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-45/call-trgt_plot_motifs_allele", thread: 140608211502656
2025-09-15 20:24:32.747 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_plot_motifs_waterfall INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-46/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_37dtir3t"
2025-09-15 20:24:32.748 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_plot_motifs_waterfall INFO Slurm invocation: srun --job-name call-trgt_plot_motifs_waterfall --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-46/call-trgt_plot_motifs_waterfall/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-46/call-trgt_plot_motifs_waterfall/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-46/call-trgt_plot_motifs_waterfall/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-46/call-trgt_plot_motifs_waterfall/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-46/call-trgt_genotype/out/m84036_250809_035451_s4.bc2143.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2143.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-46/call-trgt_genotype/out/m84036_250809_035451_s4.bc2143.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2143.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-46/call-trgt_genotype/out/m84036_250809_035451_s4.bc2143.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2143.trgt.sorted.spanning.bam:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-46/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_37dtir3t/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-46/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_37dtir3t/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:32.759 wdl.w:ptcp.w:call-trgt-45.t:call-trgt_plot_motifs_allele INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:32.759 wdl.w:ptcp.w:call-trgt-45.t:call-trgt_plot_motifs_allele INFO input :: name: "waterfall", value: false
2025-09-15 20:24:32.759 wdl.w:ptcp.w:call-trgt-45.t:call-trgt_plot_motifs_allele INFO input :: name: "methylation", value: false
2025-09-15 20:24:32.759 wdl.w:ptcp.w:call-trgt-45.t:call-trgt_plot_motifs_allele INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:32.759 wdl.w:ptcp.w:call-trgt-45.t:call-trgt_plot_motifs_allele INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:32.759 wdl.w:ptcp.w:call-trgt-45.t:call-trgt_plot_motifs_allele INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:32.759 wdl.w:ptcp.w:call-trgt-45.t:call-trgt_plot_motifs_allele INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2142.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:32.759 wdl.w:ptcp.w:call-trgt-45.t:call-trgt_plot_motifs_allele INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2142.trgt.sorted.spanning.bam"
2025-09-15 20:24:32.759 wdl.w:ptcp.w:call-trgt-45.t:call-trgt_plot_motifs_allele INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2142.trgt.vcf"
2025-09-15 20:24:32.759 wdl.w:ptcp.w:call-trgt-45.t:call-trgt_plot_motifs_allele INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2142"
2025-09-15 20:24:32.760 wdl.w:ptcp.w:call-trgt-45.t:call-trgt_plot_motifs_allele INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:32.760 wdl.w:ptcp.w:call-trgt-45.t:call-trgt_plot_motifs_allele INFO eval :: name: "plot_type", value: "allele"
2025-09-15 20:24:32.760 wdl.w:ptcp.w:call-trgt-45.t:call-trgt_plot_motifs_allele INFO eval :: name: "show", value: "motifs"
2025-09-15 20:24:32.760 wdl.w:ptcp.w:call-trgt-45.t:call-trgt_plot_motifs_allele INFO eval :: name: "threads", value: 1
2025-09-15 20:24:32.760 wdl.w:ptcp.w:call-trgt-45.t:call-trgt_plot_motifs_allele INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:32.760 wdl.w:ptcp.w:call-trgt-45.t:call-trgt_plot_motifs_allele INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2142.motifs_allele"
2025-09-15 20:24:32.761 wdl.w:ptcp.w:call-trgt-45.t:call-trgt_plot_meth_allele INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-45/call-trgt_plot_meth_allele/_singularity_tmpdir_neaf0p0c"
2025-09-15 20:24:32.761 wdl.w:ptcp.w:call-trgt-45.t:call-trgt_plot_meth_allele INFO Slurm invocation: srun --job-name call-trgt_plot_meth_allele --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-45/call-trgt_plot_meth_allele/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-45/call-trgt_plot_meth_allele/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-45/call-trgt_plot_meth_allele/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-45/call-trgt_plot_meth_allele/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-45/call-trgt_genotype/out/m84036_250809_035451_s4.bc2142.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2142.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-45/call-trgt_genotype/out/m84036_250809_035451_s4.bc2142.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2142.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-45/call-trgt_genotype/out/m84036_250809_035451_s4.bc2142.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2142.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-45/call-trgt_plot_meth_allele/_singularity_tmpdir_neaf0p0c/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-45/call-trgt_plot_meth_allele/_singularity_tmpdir_neaf0p0c/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:32.761 wdl.w:ptcp.w:call-trgt-45.t:call-trgt_plot_motifs_allele INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:32.763 wdl.w:ptcp.w:call-trgt-45.t:call-trgt_plot_motifs_allele WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:32.764 wdl.w:ptcp.w:call-trgt-45.t:call-trgt_plot_motifs_allele INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:32.765 wdl.w:ptcp.w:call-trgt-45.t:call-trgt_plot_motifs_allele INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:32.766 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_plot_motifs_waterfall NOTICE slurm_singularity run :: pid: 1202188, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-46/call-trgt_plot_motifs_waterfall/slurm_singularity.log.txt"
2025-09-15 20:24:32.768 wdl.w:ptcp.w:call-trgt-45.t:call-trgt_plot_meth_allele NOTICE slurm_singularity run :: pid: 1202189, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-45/call-trgt_plot_meth_allele/slurm_singularity.log.txt"
2025-09-15 20:24:32.801 wdl.w:ptcp.w:call-sawfish-12.t:call-run_sawfish INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2109_sawfish/m84036_250809_035451_s4.bc2109.sv.vcf.gz"
2025-09-15 20:24:32.804 wdl.w:ptcp.w:call-trgt-45.t:call-trgt_plot_meth_waterfall INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-45/call-trgt_plot_meth_waterfall/_singularity_tmpdir_h51p6ha2"
2025-09-15 20:24:32.804 wdl.w:ptcp.w:call-trgt-45.t:call-trgt_plot_meth_waterfall INFO Slurm invocation: srun --job-name call-trgt_plot_meth_waterfall --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-45/call-trgt_plot_meth_waterfall/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-45/call-trgt_plot_meth_waterfall/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-45/call-trgt_plot_meth_waterfall/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-45/call-trgt_plot_meth_waterfall/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-45/call-trgt_genotype/out/m84036_250809_035451_s4.bc2142.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2142.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-45/call-trgt_genotype/out/m84036_250809_035451_s4.bc2142.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2142.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-45/call-trgt_genotype/out/m84036_250809_035451_s4.bc2142.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2142.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-45/call-trgt_plot_meth_waterfall/_singularity_tmpdir_h51p6ha2/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-45/call-trgt_plot_meth_waterfall/_singularity_tmpdir_h51p6ha2/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:32.806 wdl.w:ptcp.w:call-sawfish-12.t:call-run_sawfish INFO output :: name: "vcf_tbi", value: "m84036_250809_035451_s4.bc2109_sawfish/m84036_250809_035451_s4.bc2109.sv.vcf.gz.tbi"
2025-09-15 20:24:32.807 wdl.w:ptcp.w:call-sawfish-12.t:call-run_sawfish INFO output :: name: "minimap2_bam", value: "m84036_250809_035451_s4.bc2109.minimap2.bam"
2025-09-15 20:24:32.809 wdl.w:ptcp.w:call-sawfish-12.t:call-run_sawfish INFO output :: name: "minimap2_bam_bai", value: "m84036_250809_035451_s4.bc2109.minimap2.bam.bai"
2025-09-15 20:24:32.827 wdl.w:ptcp.w:call-trgt-45.t:call-trgt_plot_meth_waterfall NOTICE slurm_singularity run :: pid: 1202208, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-45/call-trgt_plot_meth_waterfall/slurm_singularity.log.txt"
2025-09-15 20:24:32.866 wdl.w:ptcp.w:call-trgt-45.t:call-trgt_plot_motifs_allele INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-45/call-trgt_plot_motifs_allele/_singularity_tmpdir_lwb_ar9z"
2025-09-15 20:24:32.866 wdl.w:ptcp.w:call-trgt-45.t:call-trgt_plot_motifs_allele INFO Slurm invocation: srun --job-name call-trgt_plot_motifs_allele --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-45/call-trgt_plot_motifs_allele/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-45/call-trgt_plot_motifs_allele/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-45/call-trgt_plot_motifs_allele/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-45/call-trgt_plot_motifs_allele/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-45/call-trgt_genotype/out/m84036_250809_035451_s4.bc2142.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2142.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-45/call-trgt_genotype/out/m84036_250809_035451_s4.bc2142.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2142.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-45/call-trgt_genotype/out/m84036_250809_035451_s4.bc2142.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2142.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-45/call-trgt_plot_motifs_allele/_singularity_tmpdir_lwb_ar9z/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-45/call-trgt_plot_motifs_allele/_singularity_tmpdir_lwb_ar9z/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:32.880 wdl.w:ptcp.w:call-trgt-45.t:call-trgt_plot_motifs_allele NOTICE slurm_singularity run :: pid: 1202216, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-45/call-trgt_plot_motifs_allele/slurm_singularity.log.txt"
2025-09-15 20:24:32.884 wdl.w:ptcp.w:call-sawfish-04.t:call-run_sawfish INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2101_sawfish/m84036_250809_035451_s4.bc2101.sv.vcf.gz"
2025-09-15 20:24:32.889 wdl.w:ptcp.w:call-sawfish-04.t:call-run_sawfish INFO output :: name: "vcf_tbi", value: "m84036_250809_035451_s4.bc2101_sawfish/m84036_250809_035451_s4.bc2101.sv.vcf.gz.tbi"
2025-09-15 20:24:32.891 wdl.w:ptcp.w:call-sawfish-04.t:call-run_sawfish INFO output :: name: "minimap2_bam", value: "m84036_250809_035451_s4.bc2101.minimap2.bam"
2025-09-15 20:24:32.893 wdl.w:ptcp.w:call-sawfish-04.t:call-run_sawfish INFO output :: name: "minimap2_bam_bai", value: "m84036_250809_035451_s4.bc2101.minimap2.bam.bai"
2025-09-15 20:24:32.931 wdl.w:ptcp.w:call-trgt-01.t:call-trgt_plot_meth_allele INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2098.meth_allele.trgt_plots.zip"
2025-09-15 20:24:32.963 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_meth_allele INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2148.meth_allele.trgt_plots.zip"
2025-09-15 20:24:32.978 wdl.w:ptcp.w:call-sawfish-12.t:call-run_sawfish NOTICE done
2025-09-15 20:24:32.986 wdl.w:ptcp.w:call-sawfish-12 NOTICE finish :: job: "call-run_sawfish"
2025-09-15 20:24:32.986 wdl.w:ptcp.w:call-sawfish-12 INFO output :: job: "call-run_sawfish", values: {"minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-12/call-run_sawfish/out/m84036_250809_035451_s4.bc2109.minimap2.bam.bai", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-12/call-run_sawfish/out/m84036_250809_035451_s4.bc2109.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-12/call-run_sawfish/out/m84036_250809_035451_s4.bc2109_sawfish/m84036_250809_035451_s4.bc2109.sv.vcf.gz.tbi", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-12/call-run_sawfish/out/m84036_250809_035451_s4.bc2109_sawfish/m84036_250809_035451_s4.bc2109.sv.vcf.gz"}
2025-09-15 20:24:32.986 wdl.w:ptcp.w:call-sawfish-12 INFO visit :: node: "output-minimap2_bam", values: {"minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-12/call-run_sawfish/out/m84036_250809_035451_s4.bc2109.minimap2.bam"}
2025-09-15 20:24:32.987 wdl.w:ptcp.w:call-sawfish-12 INFO visit :: node: "output-minimap2_bam_bai", values: {"minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-12/call-run_sawfish/out/m84036_250809_035451_s4.bc2109.minimap2.bam.bai"}
2025-09-15 20:24:32.987 wdl.w:ptcp.w:call-sawfish-12 INFO visit :: node: "output-vcf", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-12/call-run_sawfish/out/m84036_250809_035451_s4.bc2109_sawfish/m84036_250809_035451_s4.bc2109.sv.vcf.gz"}
2025-09-15 20:24:32.987 wdl.w:ptcp.w:call-sawfish-12 INFO visit :: node: "output-vcf_tbi", values: {"vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-12/call-run_sawfish/out/m84036_250809_035451_s4.bc2109_sawfish/m84036_250809_035451_s4.bc2109.sv.vcf.gz.tbi"}
2025-09-15 20:24:32.987 wdl.w:ptcp.w:call-sawfish-12 INFO visit :: node: "outputs", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-12/call-run_sawfish/out/m84036_250809_035451_s4.bc2109_sawfish/m84036_250809_035451_s4.bc2109.sv.vcf.gz", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-12/call-run_sawfish/out/m84036_250809_035451_s4.bc2109.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-12/call-run_sawfish/out/m84036_250809_035451_s4.bc2109_sawfish/m84036_250809_035451_s4.bc2109.sv.vcf.gz.tbi", "minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-12/call-run_sawfish/out/m84036_250809_035451_s4.bc2109.minimap2.bam.bai"}
2025-09-15 20:24:32.993 wdl.w:ptcp.w:call-trgt-45.t:call-trgt_plot_motifs_waterfall NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-45/call-trgt_plot_motifs_waterfall", thread: 140611944420928
2025-09-15 20:24:33.013 wdl.w:ptcp.w:call-trgt-45.t:call-trgt_plot_motifs_waterfall INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:33.013 wdl.w:ptcp.w:call-trgt-45.t:call-trgt_plot_motifs_waterfall INFO input :: name: "waterfall", value: true
2025-09-15 20:24:33.013 wdl.w:ptcp.w:call-trgt-45.t:call-trgt_plot_motifs_waterfall INFO input :: name: "methylation", value: false
2025-09-15 20:24:33.013 wdl.w:ptcp.w:call-trgt-45.t:call-trgt_plot_motifs_waterfall INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:33.013 wdl.w:ptcp.w:call-trgt-45.t:call-trgt_plot_motifs_waterfall INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:33.013 wdl.w:ptcp.w:call-trgt-45.t:call-trgt_plot_motifs_waterfall INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:33.013 wdl.w:ptcp.w:call-trgt-45.t:call-trgt_plot_motifs_waterfall INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2142.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:33.013 wdl.w:ptcp.w:call-trgt-45.t:call-trgt_plot_motifs_waterfall INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2142.trgt.sorted.spanning.bam"
2025-09-15 20:24:33.013 wdl.w:ptcp.w:call-trgt-45.t:call-trgt_plot_motifs_waterfall INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2142.trgt.vcf"
2025-09-15 20:24:33.013 wdl.w:ptcp.w:call-trgt-45.t:call-trgt_plot_motifs_waterfall INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2142"
2025-09-15 20:24:33.014 wdl.w:ptcp.w:call-trgt-45.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:33.014 wdl.w:ptcp.w:call-trgt-45.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "plot_type", value: "waterfall"
2025-09-15 20:24:33.014 wdl.w:ptcp.w:call-trgt-45.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "show", value: "motifs"
2025-09-15 20:24:33.014 wdl.w:ptcp.w:call-trgt-45.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "threads", value: 1
2025-09-15 20:24:33.014 wdl.w:ptcp.w:call-trgt-45.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:33.014 wdl.w:ptcp.w:call-trgt-45.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2142.motifs_waterfall"
2025-09-15 20:24:33.015 wdl.w:ptcp.w:call-trgt-45.t:call-trgt_plot_motifs_waterfall INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:33.015 wdl.w:ptcp.w:call-trgt-45.t:call-trgt_plot_motifs_waterfall WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:33.016 wdl.w:ptcp.w:call-trgt-45.t:call-trgt_plot_motifs_waterfall INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:33.016 wdl.w:ptcp.w:call-trgt-45.t:call-trgt_plot_motifs_waterfall INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:33.066 wdl.w:ptcp.w:call-sawfish-12 NOTICE done
2025-09-15 20:24:33.067 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_meth_allele NOTICE done
2025-09-15 20:24:33.068 wdl.w:ptcp.w:call-trgt-36.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:31 [ERROR] - No reads found for TRID=PRTS_ARX
2025-09-15 20:24:33.068 wdl.w:ptcp.w:call-trgt-36.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:31 [ERROR] - No reads found for TRID=EIEE1_ARX
2025-09-15 20:24:33.069 wdl.w:ptcp.w:call-sawfish-04.t:call-run_sawfish NOTICE done
2025-09-15 20:24:33.074 wdl.w:ptcp NOTICE finish :: job: "call-sawfish-12"
2025-09-15 20:24:33.074 wdl.w:ptcp INFO output :: job: "call-sawfish-12", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-12/out/m84036_250809_035451_s4.bc2109_sawfish/m84036_250809_035451_s4.bc2109.sv.vcf.gz", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-12/out/m84036_250809_035451_s4.bc2109.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-12/out/m84036_250809_035451_s4.bc2109_sawfish/m84036_250809_035451_s4.bc2109.sv.vcf.gz.tbi", "minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-12/out/m84036_250809_035451_s4.bc2109.minimap2.bam.bai"}
2025-09-15 20:24:33.075 wdl.w:ptcp NOTICE ready :: job: "call-tar_outputs-12", callee: "tar_outputs"
2025-09-15 20:24:33.075 wdl.w:ptcp INFO input :: job: "call-tar_outputs-12", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "sawfish_vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-12/out/m84036_250809_035451_s4.bc2109_sawfish/m84036_250809_035451_s4.bc2109.sv.vcf.gz.tbi", "sawfish_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-12/out/m84036_250809_035451_s4.bc2109_sawfish/m84036_250809_035451_s4.bc2109.sv.vcf.gz", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-12/out/m84036_250809_035451_s4.bc2109.f8inversion.json", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-12/out/m84036_250809_035451_s4.bc2109_paraphase/m84036_250809_035451_s4.bc2109.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-12/out/m84036_250809_035451_s4.bc2109_paraphase/m84036_250809_035451_s4.bc2109.paraphase.bam", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-12/out/m84036_250809_035451_s4.bc2109_paraphase/m84036_250809_035451_s4.bc2109.paraphase.json", "trgt_spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-12/out/m84036_250809_035451_s4.bc2109.trgt.sorted.spanning.bam.bai", "trgt_spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-12/out/m84036_250809_035451_s4.bc2109.trgt.sorted.spanning.bam", "trgt_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-12/out/m84036_250809_035451_s4.bc2109.trgt.vcf", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-12/out/m84036_250809_035451_s4.bc2109.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-12/out/m84036_250809_035451_s4.bc2109.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2109"}
2025-09-15 20:24:33.076 wdl.w:ptcp.w:call-sawfish-04 NOTICE finish :: job: "call-run_sawfish"
2025-09-15 20:24:33.076 wdl.w:ptcp.w:call-sawfish-04 INFO output :: job: "call-run_sawfish", values: {"minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-04/call-run_sawfish/out/m84036_250809_035451_s4.bc2101.minimap2.bam.bai", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-04/call-run_sawfish/out/m84036_250809_035451_s4.bc2101.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-04/call-run_sawfish/out/m84036_250809_035451_s4.bc2101_sawfish/m84036_250809_035451_s4.bc2101.sv.vcf.gz.tbi", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-04/call-run_sawfish/out/m84036_250809_035451_s4.bc2101_sawfish/m84036_250809_035451_s4.bc2101.sv.vcf.gz"}
2025-09-15 20:24:33.076 wdl.w:ptcp.w:call-sawfish-04 INFO visit :: node: "output-minimap2_bam", values: {"minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-04/call-run_sawfish/out/m84036_250809_035451_s4.bc2101.minimap2.bam"}
2025-09-15 20:24:33.077 wdl.w:ptcp.w:call-sawfish-04 INFO visit :: node: "output-minimap2_bam_bai", values: {"minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-04/call-run_sawfish/out/m84036_250809_035451_s4.bc2101.minimap2.bam.bai"}
2025-09-15 20:24:33.077 wdl.w:ptcp.w:call-sawfish-04 INFO visit :: node: "output-vcf", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-04/call-run_sawfish/out/m84036_250809_035451_s4.bc2101_sawfish/m84036_250809_035451_s4.bc2101.sv.vcf.gz"}
2025-09-15 20:24:33.077 wdl.w:ptcp.w:call-sawfish-04 INFO visit :: node: "output-vcf_tbi", values: {"vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-04/call-run_sawfish/out/m84036_250809_035451_s4.bc2101_sawfish/m84036_250809_035451_s4.bc2101.sv.vcf.gz.tbi"}
2025-09-15 20:24:33.077 wdl.w:ptcp.w:call-sawfish-04 INFO visit :: node: "outputs", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-04/call-run_sawfish/out/m84036_250809_035451_s4.bc2101_sawfish/m84036_250809_035451_s4.bc2101.sv.vcf.gz", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-04/call-run_sawfish/out/m84036_250809_035451_s4.bc2101.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-04/call-run_sawfish/out/m84036_250809_035451_s4.bc2101_sawfish/m84036_250809_035451_s4.bc2101.sv.vcf.gz.tbi", "minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-04/call-run_sawfish/out/m84036_250809_035451_s4.bc2101.minimap2.bam.bai"}
2025-09-15 20:24:33.083 wdl.w:ptcp.w:call-sawfish-58 NOTICE workflow start :: name: "sawfish", source: "./sawfish.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-58"
2025-09-15 20:24:33.086 wdl.w:ptcp.w:call-sawfish-63.t:call-run_sawfish NOTICE task setup :: name: "run_sawfish", source: "./sawfish.wdl", line: 83, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-63/call-run_sawfish", thread: 140612489684544
2025-09-15 20:24:33.089 wdl.w:ptcp.w:call-trgt-01.t:call-trgt_plot_meth_allele NOTICE done
2025-09-15 20:24:33.100 wdl.w:ptcp.w:call-trgt-51 NOTICE finish :: job: "call-trgt_plot_meth_allele"
2025-09-15 20:24:33.101 wdl.w:ptcp.w:call-trgt-51 INFO output :: job: "call-trgt_plot_meth_allele", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-51/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2148.meth_allele.trgt_plots.zip"}
2025-09-15 20:24:33.101 wdl.w:ptcp.w:call-trgt-51 INFO visit :: node: "output-images_meth_allele", values: {"images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-51/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2148.meth_allele.trgt_plots.zip"}
2025-09-15 20:24:33.102 wdl.w:ptcp.w:call-sawfish-58 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:24:33.102 wdl.w:ptcp.w:call-sawfish-58 INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:24:33.102 wdl.w:ptcp.w:call-sawfish-58 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-58/out/m84036_250809_035451_s4.bc2155.mapped.bam"}
2025-09-15 20:24:33.102 wdl.w:ptcp.w:call-sawfish-58 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-58/out/m84036_250809_035451_s4.bc2155.mapped.bam.bai"}
2025-09-15 20:24:33.102 wdl.w:ptcp.w:call-sawfish-58 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:24:33.102 wdl.w:ptcp.w:call-sawfish-58 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:24:33.102 wdl.w:ptcp.w:call-sawfish-58 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2155"}
2025-09-15 20:24:33.103 wdl.w:ptcp.w:call-sawfish-58 NOTICE ready :: job: "call-run_sawfish", callee: "run_sawfish"
2025-09-15 20:24:33.103 wdl.w:ptcp.w:call-sawfish-58 INFO input :: job: "call-run_sawfish", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-58/out/m84036_250809_035451_s4.bc2155.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-58/out/m84036_250809_035451_s4.bc2155.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2155"}
2025-09-15 20:24:33.104 wdl.w:ptcp.w:call-trgt-01 NOTICE finish :: job: "call-trgt_plot_meth_allele"
2025-09-15 20:24:33.104 wdl.w:ptcp.w:call-trgt-01 INFO output :: job: "call-trgt_plot_meth_allele", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-01/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2098.meth_allele.trgt_plots.zip"}
2025-09-15 20:24:33.104 wdl.w:ptcp.w:call-trgt-01 INFO visit :: node: "output-images_meth_allele", values: {"images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-01/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2098.meth_allele.trgt_plots.zip"}
2025-09-15 20:24:33.110 wdl.w:ptcp.w:call-trgt-63.t:call-get_reads_overlapping_repeats NOTICE task setup :: name: "get_reads_overlapping_repeats", source: "./trgt.wdl", line: 182, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-63/call-get_reads_overlapping_repeats", thread: 140608765158976
2025-09-15 20:24:33.113 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_genotype NOTICE task setup :: name: "trgt_genotype", source: "./trgt.wdl", line: 272, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-63/call-trgt_genotype", thread: 140613580211776
2025-09-15 20:24:33.114 wdl.w:ptcp.w:call-sawfish-63.t:call-run_sawfish INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:33.115 wdl.w:ptcp.w:call-sawfish-63.t:call-run_sawfish INFO input :: name: "genome_version", value: "38"
2025-09-15 20:24:33.115 wdl.w:ptcp.w:call-sawfish-63.t:call-run_sawfish INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:33.115 wdl.w:ptcp.w:call-sawfish-63.t:call-run_sawfish INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:33.115 wdl.w:ptcp.w:call-sawfish-63.t:call-run_sawfish INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2160.mapped.bam.bai"
2025-09-15 20:24:33.115 wdl.w:ptcp.w:call-sawfish-63.t:call-run_sawfish INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2160.mapped.bam"
2025-09-15 20:24:33.115 wdl.w:ptcp.w:call-sawfish-63.t:call-run_sawfish INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2160"
2025-09-15 20:24:33.115 wdl.w:ptcp.w:call-sawfish-63.t:call-run_sawfish INFO eval :: name: "mem_gb", value: 32
2025-09-15 20:24:33.115 wdl.w:ptcp.w:call-sawfish-63.t:call-run_sawfish INFO eval :: name: "threads", value: 16
2025-09-15 20:24:33.115 wdl.w:ptcp.w:call-sawfish-63.t:call-run_sawfish INFO eval :: name: "disk_size", value: 30
2025-09-15 20:24:33.116 wdl.w:ptcp.w:call-sawfish-63.t:call-run_sawfish INFO eval :: name: "discover_dirname", value: "m84036_250809_035451_s4.bc2160_sawfish_discover"
2025-09-15 20:24:33.116 wdl.w:ptcp.w:call-sawfish-63.t:call-run_sawfish INFO eval :: name: "call_dirname", value: "m84036_250809_035451_s4.bc2160_sawfish"
2025-09-15 20:24:33.116 wdl.w:ptcp.w:call-sawfish-63.t:call-run_sawfish INFO eval :: name: "minimap2_bam_filename", value: "m84036_250809_035451_s4.bc2160.minimap2.bam"
2025-09-15 20:24:33.116 wdl.w:ptcp.w:call-sawfish-63.t:call-run_sawfish INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 16, memory_reservation: 32000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:33.116 wdl.w:ptcp.w:call-sawfish-63.t:call-run_sawfish WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:33.117 wdl.w:ptcp.w:call-sawfish-63.t:call-run_sawfish INFO provisioned :: seconds_waited: 0, cpu: 16, mem_bytes: 32000000000
2025-09-15 20:24:33.117 wdl.w:ptcp.w:call-sawfish-63.t:call-run_sawfish INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:33.119 wdl.w:ptcp.w:call-trgt-45.t:call-trgt_plot_motifs_waterfall INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-45/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_x8xhxsku"
2025-09-15 20:24:33.119 wdl.w:ptcp.w:call-trgt-45.t:call-trgt_plot_motifs_waterfall INFO Slurm invocation: srun --job-name call-trgt_plot_motifs_waterfall --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-45/call-trgt_plot_motifs_waterfall/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-45/call-trgt_plot_motifs_waterfall/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-45/call-trgt_plot_motifs_waterfall/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-45/call-trgt_plot_motifs_waterfall/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-45/call-trgt_genotype/out/m84036_250809_035451_s4.bc2142.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2142.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-45/call-trgt_genotype/out/m84036_250809_035451_s4.bc2142.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2142.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-45/call-trgt_genotype/out/m84036_250809_035451_s4.bc2142.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2142.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-45/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_x8xhxsku/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-45/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_x8xhxsku/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:33.131 wdl.w:ptcp.w:call-trgt-36.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:31 [ERROR] - No reads found for TRID=PRTS_ARX
2025-09-15 20:24:33.131 wdl.w:ptcp.w:call-trgt-36.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:31 [ERROR] - No reads found for TRID=EIEE1_ARX
2025-09-15 20:24:33.134 wdl.w:ptcp.w:call-trgt-63.t:call-get_reads_overlapping_repeats INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:33.134 wdl.w:ptcp.w:call-trgt-63.t:call-get_reads_overlapping_repeats INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:33.134 wdl.w:ptcp.w:call-trgt-63.t:call-get_reads_overlapping_repeats INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2160.mapped.bam.bai"
2025-09-15 20:24:33.134 wdl.w:ptcp.w:call-trgt-63.t:call-get_reads_overlapping_repeats INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2160.mapped.bam"
2025-09-15 20:24:33.134 wdl.w:ptcp.w:call-trgt-63.t:call-get_reads_overlapping_repeats INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2160"
2025-09-15 20:24:33.135 wdl.w:ptcp.w:call-trgt-63.t:call-get_reads_overlapping_repeats INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:33.135 wdl.w:ptcp.w:call-trgt-63.t:call-get_reads_overlapping_repeats INFO eval :: name: "expand_size", value: 3000
2025-09-15 20:24:33.135 wdl.w:ptcp.w:call-trgt-63.t:call-get_reads_overlapping_repeats INFO eval :: name: "threads", value: 1
2025-09-15 20:24:33.135 wdl.w:ptcp.w:call-trgt-63.t:call-get_reads_overlapping_repeats INFO eval :: name: "expanded_bed_name", value: "m84036_250809_035451_s4.bc2160.expanded.bed"
2025-09-15 20:24:33.135 wdl.w:ptcp.w:call-trgt-63.t:call-get_reads_overlapping_repeats INFO eval :: name: "disk_size", value: 11
2025-09-15 20:24:33.135 wdl.w:ptcp.w:call-trgt-63.t:call-get_reads_overlapping_repeats INFO eval :: name: "output_name", value: "m84036_250809_035451_s4.bc2160.repeats.bam"
2025-09-15 20:24:33.135 wdl.w:ptcp.w:call-trgt-63.t:call-get_reads_overlapping_repeats INFO eval :: name: "index_name", value: "m84036_250809_035451_s4.bc2160.repeats.bam.bai"
2025-09-15 20:24:33.135 wdl.w:ptcp.w:call-trgt-63.t:call-get_reads_overlapping_repeats INFO eval :: name: "output_name_with_index", value: "m84036_250809_035451_s4.bc2160.repeats.bam##idx##m84036_250809_035451_s4.bc2160.repeats.bam.bai"
2025-09-15 20:24:33.136 wdl.w:ptcp.w:call-trgt-63.t:call-get_reads_overlapping_repeats INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:33.136 wdl.w:ptcp.w:call-trgt-63.t:call-get_reads_overlapping_repeats WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:33.136 wdl.w:ptcp.w:call-trgt-63.t:call-get_reads_overlapping_repeats INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:33.136 wdl.w:ptcp.w:call-trgt-63.t:call-get_reads_overlapping_repeats INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:33.140 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_genotype INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:33.141 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_genotype INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:33.141 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_genotype INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:33.141 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_genotype INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:33.141 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_genotype INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2160.mapped.bam.bai"
2025-09-15 20:24:33.141 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_genotype INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2160.mapped.bam"
2025-09-15 20:24:33.141 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_genotype INFO input :: name: "sex", value: "F"
2025-09-15 20:24:33.141 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_genotype INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2160"
2025-09-15 20:24:33.141 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_genotype INFO eval :: name: "mem_gb", value: 16
2025-09-15 20:24:33.141 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_genotype INFO eval :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2160.trgt"
2025-09-15 20:24:33.141 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_genotype INFO eval :: name: "threads", value: 8
2025-09-15 20:24:33.142 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_genotype INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:33.142 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_genotype INFO eval :: name: "karyotype", value: "XX"
2025-09-15 20:24:33.142 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_genotype INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 8, memory_reservation: 16000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:33.142 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_genotype WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:33.143 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_genotype INFO provisioned :: seconds_waited: 0, cpu: 8, mem_bytes: 16000000000
2025-09-15 20:24:33.143 wdl.w:ptcp.w:call-sawfish-04 NOTICE done
2025-09-15 20:24:33.144 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_genotype INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:33.151 wdl.w:ptcp NOTICE finish :: job: "call-sawfish-04"
2025-09-15 20:24:33.151 wdl.w:ptcp INFO output :: job: "call-sawfish-04", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-04/out/m84036_250809_035451_s4.bc2101_sawfish/m84036_250809_035451_s4.bc2101.sv.vcf.gz", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-04/out/m84036_250809_035451_s4.bc2101.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-04/out/m84036_250809_035451_s4.bc2101_sawfish/m84036_250809_035451_s4.bc2101.sv.vcf.gz.tbi", "minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-04/out/m84036_250809_035451_s4.bc2101.minimap2.bam.bai"}
2025-09-15 20:24:33.152 wdl.w:ptcp NOTICE ready :: job: "call-tar_outputs-04", callee: "tar_outputs"
2025-09-15 20:24:33.152 wdl.w:ptcp INFO input :: job: "call-tar_outputs-04", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "sawfish_vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-04/out/m84036_250809_035451_s4.bc2101_sawfish/m84036_250809_035451_s4.bc2101.sv.vcf.gz.tbi", "sawfish_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-04/out/m84036_250809_035451_s4.bc2101_sawfish/m84036_250809_035451_s4.bc2101.sv.vcf.gz", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-04/out/m84036_250809_035451_s4.bc2101.f8inversion.json", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-04/out/m84036_250809_035451_s4.bc2101_paraphase/m84036_250809_035451_s4.bc2101.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-04/out/m84036_250809_035451_s4.bc2101_paraphase/m84036_250809_035451_s4.bc2101.paraphase.bam", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-04/out/m84036_250809_035451_s4.bc2101_paraphase/m84036_250809_035451_s4.bc2101.paraphase.json", "trgt_spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-04/out/m84036_250809_035451_s4.bc2101.trgt.sorted.spanning.bam.bai", "trgt_spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-04/out/m84036_250809_035451_s4.bc2101.trgt.sorted.spanning.bam", "trgt_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-04/out/m84036_250809_035451_s4.bc2101.trgt.vcf", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-04/out/m84036_250809_035451_s4.bc2101.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-04/out/m84036_250809_035451_s4.bc2101.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2101"}
2025-09-15 20:24:33.156 wdl.w:ptcp.w:call-trgt-45.t:call-trgt_plot_motifs_waterfall NOTICE slurm_singularity run :: pid: 1202224, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-45/call-trgt_plot_motifs_waterfall/slurm_singularity.log.txt"
2025-09-15 20:24:33.163 wdl.w:ptcp.w:call-trgt-58 NOTICE workflow start :: name: "trgt", source: "./trgt.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-58"
2025-09-15 20:24:33.184 wdl.w:ptcp.w:call-trgt-58 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:24:33.184 wdl.w:ptcp.w:call-trgt-58 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-58/out/m84036_250809_035451_s4.bc2155.mapped.bam"}
2025-09-15 20:24:33.184 wdl.w:ptcp.w:call-trgt-58 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-58/out/m84036_250809_035451_s4.bc2155.mapped.bam.bai"}
2025-09-15 20:24:33.184 wdl.w:ptcp.w:call-trgt-58 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:24:33.184 wdl.w:ptcp.w:call-trgt-58 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:24:33.184 wdl.w:ptcp.w:call-trgt-58 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2155"}
2025-09-15 20:24:33.184 wdl.w:ptcp.w:call-trgt-58 INFO visit :: node: "decl-sex", values: {"sex": "F"}
2025-09-15 20:24:33.184 wdl.w:ptcp.w:call-trgt-58 INFO visit :: node: "decl-trgt_bed", values: {"trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"}
2025-09-15 20:24:33.185 wdl.w:ptcp.w:call-trgt-58 NOTICE ready :: job: "call-get_reads_overlapping_repeats", callee: "get_reads_overlapping_repeats"
2025-09-15 20:24:33.185 wdl.w:ptcp.w:call-trgt-58 INFO input :: job: "call-get_reads_overlapping_repeats", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-58/out/m84036_250809_035451_s4.bc2155.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-58/out/m84036_250809_035451_s4.bc2155.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2155"}
2025-09-15 20:24:33.185 wdl.w:ptcp.w:call-trgt-58 NOTICE ready :: job: "call-trgt_genotype", callee: "trgt_genotype"
2025-09-15 20:24:33.186 wdl.w:ptcp.w:call-trgt-58 INFO input :: job: "call-trgt_genotype", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-58/out/m84036_250809_035451_s4.bc2155.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-58/out/m84036_250809_035451_s4.bc2155.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2155"}
2025-09-15 20:24:33.199 wdl.w:ptcp.w:call-sawfish-63.t:call-run_sawfish INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 10, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-63/call-run_sawfish/_singularity_tmpdir_ktoz621v"
2025-09-15 20:24:33.200 wdl.w:ptcp.w:call-sawfish-63.t:call-run_sawfish INFO Slurm invocation: srun --job-name call-run_sawfish --partition compute,compute9 --cpus-per-task 16 --mem 30518M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-63/call-run_sawfish/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-63/call-run_sawfish/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-63/call-run_sawfish/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-63/call-run_sawfish/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-63/out/m84036_250809_035451_s4.bc2160.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2160.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-63/out/m84036_250809_035451_s4.bc2160.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2160.mapped.bam:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-63/call-run_sawfish/_singularity_tmpdir_ktoz621v/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-63/call-run_sawfish/_singularity_tmpdir_ktoz621v/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:33.206 wdl.w:ptcp.w:call-trgt-63.t:call-get_reads_overlapping_repeats INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 9, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-63/call-get_reads_overlapping_repeats/_singularity_tmpdir_46uyewma"
2025-09-15 20:24:33.207 wdl.w:ptcp.w:call-trgt-63.t:call-get_reads_overlapping_repeats INFO Slurm invocation: srun --job-name call-get_reads_overlapping_repeats --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-63/call-get_reads_overlapping_repeats/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-63/call-get_reads_overlapping_repeats/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-63/call-get_reads_overlapping_repeats/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-63/call-get_reads_overlapping_repeats/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-63/out/m84036_250809_035451_s4.bc2160.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2160.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-63/out/m84036_250809_035451_s4.bc2160.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2160.mapped.bam:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-63/call-get_reads_overlapping_repeats/_singularity_tmpdir_46uyewma/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-63/call-get_reads_overlapping_repeats/_singularity_tmpdir_46uyewma/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:33.217 wdl.w:ptcp.w:call-trgt-63.t:call-get_reads_overlapping_repeats NOTICE slurm_singularity run :: pid: 1202227, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-63/call-get_reads_overlapping_repeats/slurm_singularity.log.txt"
2025-09-15 20:24:33.218 wdl.w:ptcp.w:call-sawfish-63.t:call-run_sawfish NOTICE slurm_singularity run :: pid: 1202226, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-63/call-run_sawfish/slurm_singularity.log.txt"
2025-09-15 20:24:33.226 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_genotype INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 11, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-63/call-trgt_genotype/_singularity_tmpdir_g8lvcvhe"
2025-09-15 20:24:33.226 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_genotype INFO Slurm invocation: srun --job-name call-trgt_genotype --partition compute,compute9 --cpus-per-task 8 --mem 15259M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-63/call-trgt_genotype/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-63/call-trgt_genotype/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-63/call-trgt_genotype/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-63/call-trgt_genotype/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-63/out/m84036_250809_035451_s4.bc2160.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2160.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-63/out/m84036_250809_035451_s4.bc2160.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2160.mapped.bam:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-63/call-trgt_genotype/_singularity_tmpdir_g8lvcvhe/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-63/call-trgt_genotype/_singularity_tmpdir_g8lvcvhe/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:33.236 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_genotype NOTICE slurm_singularity run :: pid: 1202230, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-63/call-trgt_genotype/slurm_singularity.log.txt"
2025-09-15 20:24:33.333 wdl.w:ptcp.w:call-trgt-32.t:call-trgt_plot_meth_allele INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2129.meth_allele.trgt_plots.zip"
2025-09-15 20:24:33.351 wdl.w:ptcp.w:call-trgt-36.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:32 [ERROR] - No reads found for TRID=PRTS_ARX
2025-09-15 20:24:33.352 wdl.w:ptcp.w:call-trgt-36.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:32 [ERROR] - No reads found for TRID=EIEE1_ARX
2025-09-15 20:24:33.412 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:33 [ERROR] - No reads found for TRID=OPDM_ABCD3
2025-09-15 20:24:33.413 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:33 [ERROR] - No reads found for TRID=OPDM4_RILPL1
2025-09-15 20:24:33.413 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:33 [ERROR] - No reads found for TRID=NIID_NOTCH2NLC
2025-09-15 20:24:33.413 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:33 [ERROR] - No reads found for TRID=SCA8_ATXN8OS
2025-09-15 20:24:33.422 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_plot_meth_allele.slurm_singularity INFO srun: job 51797683 queued and waiting for resources
2025-09-15 20:24:33.422 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_plot_meth_allele.slurm_singularity INFO srun: job 51797683 has been allocated resources
2025-09-15 20:24:33.422 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_plot_meth_allele.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:33.440 wdl.w:ptcp.w:call-trgt-32.t:call-trgt_plot_meth_allele NOTICE done
2025-09-15 20:24:33.441 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:30 [ERROR] - No reads found for TRID=SCA2_ATXN2
2025-09-15 20:24:33.441 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:30 [ERROR] - No reads found for TRID=OPDM4_RILPL1
2025-09-15 20:24:33.441 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:30 [ERROR] - No reads found for TRID=SCA27B_FGF14
2025-09-15 20:24:33.441 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:30 [ERROR] - No reads found for TRID=OPDM_ABCD3
2025-09-15 20:24:33.441 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:31 [ERROR] - No reads found for TRID=SCA37_DAB1
2025-09-15 20:24:33.441 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:31 [ERROR] - No reads found for TRID=NIID_NOTCH2NLC
2025-09-15 20:24:33.441 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:31 [ERROR] - No reads found for TRID=OPMD_PABPN1
2025-09-15 20:24:33.441 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:31 [ERROR] - No reads found for TRID=SCA3_ATXN3
2025-09-15 20:24:33.441 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:31 [ERROR] - No reads found for TRID=SCA31_BEAN1
2025-09-15 20:24:33.441 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:31 [ERROR] - No reads found for TRID=HDL2_JPH3
2025-09-15 20:24:33.441 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:31 [ERROR] - No reads found for TRID=FECD3_TCF4
2025-09-15 20:24:33.442 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:32 [ERROR] - No reads found for TRID=SCA6_CACNA1A
2025-09-15 20:24:33.442 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:32 [ERROR] - No reads found for TRID=OPDM2_GIPC1
2025-09-15 20:24:33.442 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:32 [ERROR] - No reads found for TRID=DM1_DMPK
2025-09-15 20:24:33.442 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:32 [ERROR] - No reads found for TRID=FRA2A_AFF3
2025-09-15 20:24:33.442 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:32 [ERROR] - No reads found for TRID=SD5_HOXD13
2025-09-15 20:24:33.442 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:32 [ERROR] - No reads found for TRID=SCA36_NOP56
2025-09-15 20:24:33.442 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:32 [ERROR] - No reads found for TRID=CJD_PRNP
2025-09-15 20:24:33.442 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:32 [ERROR] - No reads found for TRID=EPM1_CSTB
2025-09-15 20:24:33.442 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:32 [ERROR] - No reads found for TRID=SCA10_ATXN10
2025-09-15 20:24:33.442 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:33 [ERROR] - No reads found for TRID=SCA7_ATXN7
2025-09-15 20:24:33.442 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:33 [ERROR] - No reads found for TRID=DM2_CNBP
2025-09-15 20:24:33.442 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:33 [ERROR] - No reads found for TRID=SCA4_ZFHX3
2025-09-15 20:24:33.445 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:30 [ERROR] - No reads found for TRID=SCA2_ATXN2
2025-09-15 20:24:33.445 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:30 [ERROR] - No reads found for TRID=OPDM4_RILPL1
2025-09-15 20:24:33.445 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:30 [ERROR] - No reads found for TRID=SCA27B_FGF14
2025-09-15 20:24:33.445 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:30 [ERROR] - No reads found for TRID=OPDM_ABCD3
2025-09-15 20:24:33.445 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:31 [ERROR] - No reads found for TRID=SCA37_DAB1
2025-09-15 20:24:33.445 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:31 [ERROR] - No reads found for TRID=NIID_NOTCH2NLC
2025-09-15 20:24:33.445 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:31 [ERROR] - No reads found for TRID=OPMD_PABPN1
2025-09-15 20:24:33.445 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:31 [ERROR] - No reads found for TRID=SCA3_ATXN3
2025-09-15 20:24:33.446 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:31 [ERROR] - No reads found for TRID=SCA31_BEAN1
2025-09-15 20:24:33.446 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:31 [ERROR] - No reads found for TRID=HDL2_JPH3
2025-09-15 20:24:33.446 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:31 [ERROR] - No reads found for TRID=FECD3_TCF4
2025-09-15 20:24:33.446 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:32 [ERROR] - No reads found for TRID=SCA6_CACNA1A
2025-09-15 20:24:33.446 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:32 [ERROR] - No reads found for TRID=OPDM2_GIPC1
2025-09-15 20:24:33.446 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:32 [ERROR] - No reads found for TRID=DM1_DMPK
2025-09-15 20:24:33.446 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:32 [ERROR] - No reads found for TRID=FRA2A_AFF3
2025-09-15 20:24:33.446 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:32 [ERROR] - No reads found for TRID=SD5_HOXD13
2025-09-15 20:24:33.446 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:32 [ERROR] - No reads found for TRID=SCA36_NOP56
2025-09-15 20:24:33.446 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:32 [ERROR] - No reads found for TRID=CJD_PRNP
2025-09-15 20:24:33.446 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:32 [ERROR] - No reads found for TRID=EPM1_CSTB
2025-09-15 20:24:33.446 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:32 [ERROR] - No reads found for TRID=SCA10_ATXN10
2025-09-15 20:24:33.446 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:33 [ERROR] - No reads found for TRID=SCA7_ATXN7
2025-09-15 20:24:33.446 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:33 [ERROR] - No reads found for TRID=DM2_CNBP
2025-09-15 20:24:33.446 wdl.w:ptcp.w:call-trgt-32 NOTICE finish :: job: "call-trgt_plot_meth_allele"
2025-09-15 20:24:33.447 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:33 [ERROR] - No reads found for TRID=SCA4_ZFHX3
2025-09-15 20:24:33.447 wdl.w:ptcp.w:call-trgt-32 INFO output :: job: "call-trgt_plot_meth_allele", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-32/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2129.meth_allele.trgt_plots.zip"}
2025-09-15 20:24:33.447 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:33 [ERROR] - No reads found for TRID=CCHS_PHOX2B
2025-09-15 20:24:33.447 wdl.w:ptcp.w:call-trgt-32 INFO visit :: node: "output-images_meth_allele", values: {"images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-32/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2129.meth_allele.trgt_plots.zip"}
2025-09-15 20:24:33.450 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:30 [ERROR] - No reads found for TRID=SCA2_ATXN2
2025-09-15 20:24:33.450 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:30 [ERROR] - No reads found for TRID=OPDM4_RILPL1
2025-09-15 20:24:33.450 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:30 [ERROR] - No reads found for TRID=SCA27B_FGF14
2025-09-15 20:24:33.450 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:30 [ERROR] - No reads found for TRID=OPDM_ABCD3
2025-09-15 20:24:33.450 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:31 [ERROR] - No reads found for TRID=SCA37_DAB1
2025-09-15 20:24:33.450 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:31 [ERROR] - No reads found for TRID=NIID_NOTCH2NLC
2025-09-15 20:24:33.450 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:31 [ERROR] - No reads found for TRID=OPMD_PABPN1
2025-09-15 20:24:33.450 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:31 [ERROR] - No reads found for TRID=SCA3_ATXN3
2025-09-15 20:24:33.450 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:31 [ERROR] - No reads found for TRID=SCA31_BEAN1
2025-09-15 20:24:33.450 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:31 [ERROR] - No reads found for TRID=HDL2_JPH3
2025-09-15 20:24:33.450 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:31 [ERROR] - No reads found for TRID=FECD3_TCF4
2025-09-15 20:24:33.451 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:31 [ERROR] - No reads found for TRID=SCA6_CACNA1A
2025-09-15 20:24:33.451 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:32 [ERROR] - No reads found for TRID=OPDM2_GIPC1
2025-09-15 20:24:33.451 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:32 [ERROR] - No reads found for TRID=DM1_DMPK
2025-09-15 20:24:33.451 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:32 [ERROR] - No reads found for TRID=FRA2A_AFF3
2025-09-15 20:24:33.451 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:32 [ERROR] - No reads found for TRID=SD5_HOXD13
2025-09-15 20:24:33.451 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:32 [ERROR] - No reads found for TRID=SCA36_NOP56
2025-09-15 20:24:33.451 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:32 [ERROR] - No reads found for TRID=CJD_PRNP
2025-09-15 20:24:33.451 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:32 [ERROR] - No reads found for TRID=EPM1_CSTB
2025-09-15 20:24:33.451 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:32 [ERROR] - No reads found for TRID=SCA10_ATXN10
2025-09-15 20:24:33.451 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:32 [ERROR] - No reads found for TRID=SCA7_ATXN7
2025-09-15 20:24:33.451 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:33 [ERROR] - No reads found for TRID=DM2_CNBP
2025-09-15 20:24:33.451 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:33 [ERROR] - No reads found for TRID=SCA4_ZFHX3
2025-09-15 20:24:33.451 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:33 [ERROR] - No reads found for TRID=CCHS_PHOX2B
2025-09-15 20:24:33.459 wdl.w:ptcp.w:call-trgt-36.t:call-trgt_plot_meth_waterfall INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2133.meth_waterfall.trgt_plots.zip"
2025-09-15 20:24:33.461 wdl.w:ptcp.w:call-paraphase-36.t:call-call_f8 NOTICE task setup :: name: "call_f8", source: "./paraphase.wdl", line: 232, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-36/call-call_f8", thread: 140608748373568
2025-09-15 20:24:33.489 wdl.w:ptcp.w:call-paraphase-36.t:call-call_f8 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:33.489 wdl.w:ptcp.w:call-paraphase-36.t:call-call_f8 INFO input :: name: "genome_version", value: "38"
2025-09-15 20:24:33.490 wdl.w:ptcp.w:call-paraphase-36.t:call-call_f8 INFO input :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2133"
2025-09-15 20:24:33.490 wdl.w:ptcp.w:call-paraphase-36.t:call-call_f8 INFO input :: name: "paraphase_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2133.paraphase.bam.bai"
2025-09-15 20:24:33.490 wdl.w:ptcp.w:call-paraphase-36.t:call-call_f8 INFO input :: name: "paraphase_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2133.paraphase.bam"
2025-09-15 20:24:33.490 wdl.w:ptcp.w:call-paraphase-36.t:call-call_f8 INFO input :: name: "sex", value: "F"
2025-09-15 20:24:33.490 wdl.w:ptcp.w:call-paraphase-36.t:call-call_f8 INFO eval :: name: "threads", value: 1
2025-09-15 20:24:33.491 wdl.w:ptcp.w:call-paraphase-36.t:call-call_f8 INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:33.491 wdl.w:ptcp.w:call-paraphase-36.t:call-call_f8 INFO eval :: name: "disk_size", value: 11
2025-09-15 20:24:33.491 wdl.w:ptcp.w:call-paraphase-36.t:call-call_f8 INFO eval :: name: "sample_sex", value: "F"
2025-09-15 20:24:33.491 wdl.w:ptcp.w:call-paraphase-36.t:call-call_f8 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:33.492 wdl.w:ptcp.w:call-paraphase-36.t:call-call_f8 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:33.492 wdl.w:ptcp.w:call-paraphase-36.t:call-call_f8 INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:33.492 wdl.w:ptcp.w:call-paraphase-36.t:call-call_f8 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:33.500 wdl.w:ptcp.w:call-trgt-08.t:call-trgt_plot_meth_allele INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2105.meth_allele.trgt_plots.zip"
2025-09-15 20:24:33.549 wdl.w:ptcp.w:call-paraphase-36.t:call-call_f8 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 8, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-36/call-call_f8/_singularity_tmpdir_46hoyo6j"
2025-09-15 20:24:33.549 wdl.w:ptcp.w:call-paraphase-36.t:call-call_f8 INFO Slurm invocation: srun --job-name call-call_f8 --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-36/call-call_f8/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-36/call-call_f8/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-36/call-call_f8/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-36/call-call_f8/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-36/call-run_paraphase/out/m84036_250809_035451_s4.bc2133_paraphase/m84036_250809_035451_s4.bc2133.paraphase.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2133.paraphase.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-36/call-run_paraphase/out/m84036_250809_035451_s4.bc2133_paraphase/m84036_250809_035451_s4.bc2133.paraphase.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2133.paraphase.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-36/call-call_f8/_singularity_tmpdir_46hoyo6j/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-36/call-call_f8/_singularity_tmpdir_46hoyo6j/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:33.578 wdl.w:ptcp.w:call-paraphase-36.t:call-call_f8 NOTICE slurm_singularity run :: pid: 1202255, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-36/call-call_f8/slurm_singularity.log.txt"
2025-09-15 20:24:33.599 wdl.w:ptcp.w:call-trgt-36.t:call-trgt_plot_meth_waterfall NOTICE done
2025-09-15 20:24:33.606 wdl.w:ptcp.w:call-trgt-36 NOTICE finish :: job: "call-trgt_plot_meth_waterfall"
2025-09-15 20:24:33.606 wdl.w:ptcp.w:call-trgt-36 INFO output :: job: "call-trgt_plot_meth_waterfall", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-36/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2133.meth_waterfall.trgt_plots.zip"}
2025-09-15 20:24:33.606 wdl.w:ptcp.w:call-trgt-36 INFO visit :: node: "output-images_meth_waterfall", values: {"images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-36/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2133.meth_waterfall.trgt_plots.zip"}
2025-09-15 20:24:33.611 wdl.w:ptcp.w:call-paraphase-45.t:call-call_f8 NOTICE task setup :: name: "call_f8", source: "./paraphase.wdl", line: 232, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-45/call-call_f8", thread: 140607683024448
2025-09-15 20:24:33.623 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:33 [ERROR] - No reads found for TRID=OPDM_ABCD3
2025-09-15 20:24:33.623 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:33 [ERROR] - No reads found for TRID=OPDM4_RILPL1
2025-09-15 20:24:33.623 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:33 [ERROR] - No reads found for TRID=NIID_NOTCH2NLC
2025-09-15 20:24:33.631 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO srun: job 51797684 queued and waiting for resources
2025-09-15 20:24:33.631 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO srun: job 51797684 has been allocated resources
2025-09-15 20:24:33.631 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:33.633 wdl.w:ptcp.w:call-paraphase-45.t:call-call_f8 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:33.634 wdl.w:ptcp.w:call-paraphase-45.t:call-call_f8 INFO input :: name: "genome_version", value: "38"
2025-09-15 20:24:33.634 wdl.w:ptcp.w:call-paraphase-45.t:call-call_f8 INFO input :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2142"
2025-09-15 20:24:33.634 wdl.w:ptcp.w:call-paraphase-45.t:call-call_f8 INFO input :: name: "paraphase_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2142.paraphase.bam.bai"
2025-09-15 20:24:33.634 wdl.w:ptcp.w:call-paraphase-45.t:call-call_f8 INFO input :: name: "paraphase_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2142.paraphase.bam"
2025-09-15 20:24:33.634 wdl.w:ptcp.w:call-paraphase-45.t:call-call_f8 INFO input :: name: "sex", value: "F"
2025-09-15 20:24:33.634 wdl.w:ptcp.w:call-paraphase-45.t:call-call_f8 INFO eval :: name: "threads", value: 1
2025-09-15 20:24:33.634 wdl.w:ptcp.w:call-paraphase-45.t:call-call_f8 INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:33.634 wdl.w:ptcp.w:call-paraphase-45.t:call-call_f8 INFO eval :: name: "disk_size", value: 11
2025-09-15 20:24:33.634 wdl.w:ptcp.w:call-paraphase-45.t:call-call_f8 INFO eval :: name: "sample_sex", value: "F"
2025-09-15 20:24:33.635 wdl.w:ptcp.w:call-paraphase-45.t:call-call_f8 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:33.635 wdl.w:ptcp.w:call-paraphase-45.t:call-call_f8 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:33.635 wdl.w:ptcp.w:call-paraphase-45.t:call-call_f8 INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:33.635 wdl.w:ptcp.w:call-paraphase-45.t:call-call_f8 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:33.642 wdl.w:ptcp.w:call-trgt-08.t:call-trgt_plot_meth_allele NOTICE done
2025-09-15 20:24:33.647 wdl.w:ptcp.w:call-trgt-08 NOTICE finish :: job: "call-trgt_plot_meth_allele"
2025-09-15 20:24:33.647 wdl.w:ptcp.w:call-trgt-08 INFO output :: job: "call-trgt_plot_meth_allele", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-08/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2105.meth_allele.trgt_plots.zip"}
2025-09-15 20:24:33.647 wdl.w:ptcp.w:call-trgt-08 INFO visit :: node: "output-images_meth_allele", values: {"images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-08/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2105.meth_allele.trgt_plots.zip"}
2025-09-15 20:24:33.655 wdl.w:ptcp.w:call-paraphase-37.t:call-call_f8 NOTICE task setup :: name: "call_f8", source: "./paraphase.wdl", line: 232, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-37/call-call_f8", thread: 140606626068032
2025-09-15 20:24:33.671 wdl.w:ptcp.w:call-paraphase-37.t:call-call_f8 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:33.671 wdl.w:ptcp.w:call-paraphase-37.t:call-call_f8 INFO input :: name: "genome_version", value: "38"
2025-09-15 20:24:33.671 wdl.w:ptcp.w:call-paraphase-37.t:call-call_f8 INFO input :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2134"
2025-09-15 20:24:33.672 wdl.w:ptcp.w:call-paraphase-37.t:call-call_f8 INFO input :: name: "paraphase_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2134.paraphase.bam.bai"
2025-09-15 20:24:33.672 wdl.w:ptcp.w:call-paraphase-37.t:call-call_f8 INFO input :: name: "paraphase_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2134.paraphase.bam"
2025-09-15 20:24:33.672 wdl.w:ptcp.w:call-paraphase-37.t:call-call_f8 INFO input :: name: "sex", value: "F"
2025-09-15 20:24:33.672 wdl.w:ptcp.w:call-paraphase-37.t:call-call_f8 INFO eval :: name: "threads", value: 1
2025-09-15 20:24:33.672 wdl.w:ptcp.w:call-paraphase-37.t:call-call_f8 INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:33.672 wdl.w:ptcp.w:call-paraphase-37.t:call-call_f8 INFO eval :: name: "disk_size", value: 11
2025-09-15 20:24:33.672 wdl.w:ptcp.w:call-paraphase-37.t:call-call_f8 INFO eval :: name: "sample_sex", value: "F"
2025-09-15 20:24:33.673 wdl.w:ptcp.w:call-paraphase-37.t:call-call_f8 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:33.673 wdl.w:ptcp.w:call-paraphase-37.t:call-call_f8 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:33.673 wdl.w:ptcp.w:call-paraphase-37.t:call-call_f8 INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:33.673 wdl.w:ptcp.w:call-paraphase-37.t:call-call_f8 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:33.680 wdl.w:ptcp.w:call-trgt-37.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:32 [ERROR] - No reads found for TRID=PRTS_ARX
2025-09-15 20:24:33.680 wdl.w:ptcp.w:call-trgt-37.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:32 [ERROR] - No reads found for TRID=EIEE1_ARX
2025-09-15 20:24:33.682 wdl.w:ptcp.w:call-paraphase-45.t:call-call_f8 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 8, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-45/call-call_f8/_singularity_tmpdir_hl5u9s2n"
2025-09-15 20:24:33.682 wdl.w:ptcp.w:call-paraphase-45.t:call-call_f8 INFO Slurm invocation: srun --job-name call-call_f8 --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-45/call-call_f8/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-45/call-call_f8/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-45/call-call_f8/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-45/call-call_f8/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-45/call-run_paraphase/out/m84036_250809_035451_s4.bc2142_paraphase/m84036_250809_035451_s4.bc2142.paraphase.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2142.paraphase.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-45/call-run_paraphase/out/m84036_250809_035451_s4.bc2142_paraphase/m84036_250809_035451_s4.bc2142.paraphase.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2142.paraphase.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-45/call-call_f8/_singularity_tmpdir_hl5u9s2n/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-45/call-call_f8/_singularity_tmpdir_hl5u9s2n/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:33.705 wdl.w:ptcp.w:call-paraphase-45.t:call-call_f8 NOTICE slurm_singularity run :: pid: 1202257, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-45/call-call_f8/slurm_singularity.log.txt"
2025-09-15 20:24:33.710 wdl.w:ptcp.w:call-paraphase-06.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for f8inv1 for sample m84036_250809_035451_s4.bc2103 at 2025-09-15 20:24:14.658390...
2025-09-15 20:24:33.710 wdl.w:ptcp.w:call-paraphase-06.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for f8inv1 for sample m84036_250809_035451_s4.bc2103 at 2025-09-15 20:24:15.068377...
2025-09-15 20:24:33.710 wdl.w:ptcp.w:call-paraphase-06.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for hba for sample m84036_250809_035451_s4.bc2103 at 2025-09-15 20:24:19.836533...
2025-09-15 20:24:33.710 wdl.w:ptcp.w:call-paraphase-06.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for hba for sample m84036_250809_035451_s4.bc2103 at 2025-09-15 20:24:20.302355...
2025-09-15 20:24:33.716 wdl.w:ptcp.w:call-sawfish-22.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:24][sawfish][INFO] Starting sawfish 2.0.3
2025-09-15 20:24:33.716 wdl.w:ptcp.w:call-sawfish-22.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:24][sawfish][INFO] cmdline: sawfish joint-call --threads 16 --sample m84036_250809_035451_s4.bc2119_sawfish_discover --output-dir m84036_250809_035451_s4.bc2119_sawfish
2025-09-15 20:24:33.716 wdl.w:ptcp.w:call-sawfish-22.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:24][sawfish][INFO] Running on 16 threads
2025-09-15 20:24:33.716 wdl.w:ptcp.w:call-sawfish-22.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:24][sawfish][INFO] Reading reference genome from file '/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa'
2025-09-15 20:24:33.716 wdl.w:ptcp.w:call-sawfish-22.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:31][sawfish][INFO] Reading sawfish-discover results from 1 samples
2025-09-15 20:24:33.716 wdl.w:ptcp.w:call-sawfish-22.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:32][sawfish][INFO] Writing depth track to bigwig file: 'm84036_250809_035451_s4.bc2119_sawfish/samples/sample0001_UnknownSampleName/depth.bw'
2025-09-15 20:24:33.716 wdl.w:ptcp.w:call-sawfish-22.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:32][sawfish][INFO] Merging SV haplotypes
2025-09-15 20:24:33.716 wdl.w:ptcp.w:call-sawfish-22.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:32][sawfish][INFO] Finished merging SV haplotypes across samples
2025-09-15 20:24:33.716 wdl.w:ptcp.w:call-sawfish-22.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:32][sawfish][INFO] Writing merged contig alignments to bam file: 'm84036_250809_035451_s4.bc2119_sawfish/contig.alignment.bam'
2025-09-15 20:24:33.716 wdl.w:ptcp.w:call-sawfish-22.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:32][sawfish][INFO] Starting SV candidate cluster genotyping
2025-09-15 20:24:33.717 wdl.w:ptcp.w:call-sawfish-22.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:33][sawfish][INFO] Finished genotyping all SV candidate clusters
2025-09-15 20:24:33.717 wdl.w:ptcp.w:call-sawfish-22.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:33][sawfish][INFO] Starting joint CNV/SV refinement
2025-09-15 20:24:33.717 wdl.w:ptcp.w:call-sawfish-22.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:33][sawfish][INFO] Merged 0 CNVs into corresponding breakpoint-based SVs
2025-09-15 20:24:33.717 wdl.w:ptcp.w:call-sawfish-22.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:33][sawfish][INFO] Writing genotyped structural variants to file: 'm84036_250809_035451_s4.bc2119_sawfish/genotyped.sv.vcf.gz'
2025-09-15 20:24:33.717 wdl.w:ptcp.w:call-sawfish-22.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:33][sawfish][INFO] Writing run statistics to file: 'm84036_250809_035451_s4.bc2119_sawfish/run.stats.json'
2025-09-15 20:24:33.717 wdl.w:ptcp.w:call-sawfish-22.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:33][sawfish][INFO] sawfish completed. Total Runtime: 00:00:08.811
2025-09-15 20:24:33.728 wdl.w:ptcp.w:call-paraphase-37.t:call-call_f8 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 8, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-37/call-call_f8/_singularity_tmpdir_bymndd_g"
2025-09-15 20:24:33.729 wdl.w:ptcp.w:call-paraphase-37.t:call-call_f8 INFO Slurm invocation: srun --job-name call-call_f8 --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-37/call-call_f8/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-37/call-call_f8/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-37/call-call_f8/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-37/call-call_f8/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-37/call-run_paraphase/out/m84036_250809_035451_s4.bc2134_paraphase/m84036_250809_035451_s4.bc2134.paraphase.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2134.paraphase.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-37/call-run_paraphase/out/m84036_250809_035451_s4.bc2134_paraphase/m84036_250809_035451_s4.bc2134.paraphase.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2134.paraphase.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-37/call-call_f8/_singularity_tmpdir_bymndd_g/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-37/call-call_f8/_singularity_tmpdir_bymndd_g/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:33.733 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:33 [ERROR] - No reads found for TRID=OPDM_ABCD3
2025-09-15 20:24:33.733 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:33 [ERROR] - No reads found for TRID=OPDM4_RILPL1
2025-09-15 20:24:33.733 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:33 [ERROR] - No reads found for TRID=NIID_NOTCH2NLC
2025-09-15 20:24:33.733 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:33 [ERROR] - No reads found for TRID=SCA8_ATXN8OS
2025-09-15 20:24:33.734 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:33 [ERROR] - No reads found for TRID=SCA27B_FGF14
2025-09-15 20:24:33.734 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:33 [ERROR] - No reads found for TRID=OPMD_PABPN1
2025-09-15 20:24:33.749 wdl.w:ptcp.w:call-paraphase-37.t:call-call_f8 NOTICE slurm_singularity run :: pid: 1202265, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-37/call-call_f8/slurm_singularity.log.txt"
2025-09-15 20:24:33.749 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_plot_motifs_allele.slurm_singularity INFO srun: job 51797685 queued and waiting for resources
2025-09-15 20:24:33.749 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_plot_motifs_allele.slurm_singularity INFO srun: job 51797685 has been allocated resources
2025-09-15 20:24:33.749 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_plot_motifs_allele.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:33.762 wdl.w:ptcp.w:call-sawfish-22.t:call-run_sawfish INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2119_sawfish/m84036_250809_035451_s4.bc2119.sv.vcf.gz"
2025-09-15 20:24:33.767 wdl.w:ptcp.w:call-trgt-32.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:30 [ERROR] - No reads found for TRID=PRTS_ARX
2025-09-15 20:24:33.767 wdl.w:ptcp.w:call-trgt-32.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:30 [ERROR] - No reads found for TRID=EIEE1_ARX
2025-09-15 20:24:33.768 wdl.w:ptcp.w:call-sawfish-22.t:call-run_sawfish INFO output :: name: "vcf_tbi", value: "m84036_250809_035451_s4.bc2119_sawfish/m84036_250809_035451_s4.bc2119.sv.vcf.gz.tbi"
2025-09-15 20:24:33.769 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:33 [ERROR] - No reads found for TRID=OPDM_ABCD3
2025-09-15 20:24:33.769 wdl.w:ptcp.w:call-sawfish-22.t:call-run_sawfish INFO output :: name: "minimap2_bam", value: "m84036_250809_035451_s4.bc2119.minimap2.bam"
2025-09-15 20:24:33.769 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:33 [ERROR] - No reads found for TRID=OPDM4_RILPL1
2025-09-15 20:24:33.770 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:33 [ERROR] - No reads found for TRID=NIID_NOTCH2NLC
2025-09-15 20:24:33.770 wdl.w:ptcp.w:call-sawfish-22.t:call-run_sawfish INFO output :: name: "minimap2_bam_bai", value: "m84036_250809_035451_s4.bc2119.minimap2.bam.bai"
2025-09-15 20:24:33.779 wdl.w:ptcp.w:call-trgt-45.t:call-trgt_plot_meth_allele.slurm_singularity INFO srun: job 51797687 queued and waiting for resources
2025-09-15 20:24:33.779 wdl.w:ptcp.w:call-trgt-45.t:call-trgt_plot_meth_allele.slurm_singularity INFO srun: job 51797687 has been allocated resources
2025-09-15 20:24:33.779 wdl.w:ptcp.w:call-trgt-45.t:call-trgt_plot_meth_allele.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:33.781 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO srun: job 51797686 queued and waiting for resources
2025-09-15 20:24:33.781 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO srun: job 51797686 has been allocated resources
2025-09-15 20:24:33.781 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:33.840 wdl.w:ptcp.w:call-trgt-45.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO srun: job 51797688 queued and waiting for resources
2025-09-15 20:24:33.840 wdl.w:ptcp.w:call-trgt-45.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO srun: job 51797688 has been allocated resources
2025-09-15 20:24:33.840 wdl.w:ptcp.w:call-trgt-45.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:33.850 wdl.w:ptcp.w:call-trgt-52.t:call-get_reads_overlapping_repeats INFO output :: name: "reads_overlapping_repeats", value: "m84036_250809_035451_s4.bc2149.repeats.bam"
2025-09-15 20:24:33.856 wdl.w:ptcp.w:call-trgt-52.t:call-get_reads_overlapping_repeats INFO output :: name: "reads_overlapping_repeats_bai", value: "m84036_250809_035451_s4.bc2149.repeats.bam.bai"
2025-09-15 20:24:33.893 wdl.w:ptcp.w:call-trgt-45.t:call-trgt_plot_motifs_allele.slurm_singularity INFO srun: job 51797689 queued and waiting for resources
2025-09-15 20:24:33.893 wdl.w:ptcp.w:call-trgt-45.t:call-trgt_plot_motifs_allele.slurm_singularity INFO srun: job 51797689 has been allocated resources
2025-09-15 20:24:33.893 wdl.w:ptcp.w:call-trgt-45.t:call-trgt_plot_motifs_allele.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:33.919 wdl.w:ptcp.w:call-sawfish-22.t:call-run_sawfish NOTICE done
2025-09-15 20:24:33.925 wdl.w:ptcp.w:call-sawfish-22 NOTICE finish :: job: "call-run_sawfish"
2025-09-15 20:24:33.925 wdl.w:ptcp.w:call-sawfish-22 INFO output :: job: "call-run_sawfish", values: {"minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-22/call-run_sawfish/out/m84036_250809_035451_s4.bc2119.minimap2.bam.bai", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-22/call-run_sawfish/out/m84036_250809_035451_s4.bc2119.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-22/call-run_sawfish/out/m84036_250809_035451_s4.bc2119_sawfish/m84036_250809_035451_s4.bc2119.sv.vcf.gz.tbi", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-22/call-run_sawfish/out/m84036_250809_035451_s4.bc2119_sawfish/m84036_250809_035451_s4.bc2119.sv.vcf.gz"}
2025-09-15 20:24:33.925 wdl.w:ptcp.w:call-sawfish-22 INFO visit :: node: "output-minimap2_bam", values: {"minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-22/call-run_sawfish/out/m84036_250809_035451_s4.bc2119.minimap2.bam"}
2025-09-15 20:24:33.926 wdl.w:ptcp.w:call-sawfish-22 INFO visit :: node: "output-minimap2_bam_bai", values: {"minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-22/call-run_sawfish/out/m84036_250809_035451_s4.bc2119.minimap2.bam.bai"}
2025-09-15 20:24:33.926 wdl.w:ptcp.w:call-sawfish-22 INFO visit :: node: "output-vcf", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-22/call-run_sawfish/out/m84036_250809_035451_s4.bc2119_sawfish/m84036_250809_035451_s4.bc2119.sv.vcf.gz"}
2025-09-15 20:24:33.926 wdl.w:ptcp.w:call-sawfish-22 INFO visit :: node: "output-vcf_tbi", values: {"vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-22/call-run_sawfish/out/m84036_250809_035451_s4.bc2119_sawfish/m84036_250809_035451_s4.bc2119.sv.vcf.gz.tbi"}
2025-09-15 20:24:33.926 wdl.w:ptcp.w:call-sawfish-22 INFO visit :: node: "outputs", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-22/call-run_sawfish/out/m84036_250809_035451_s4.bc2119_sawfish/m84036_250809_035451_s4.bc2119.sv.vcf.gz", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-22/call-run_sawfish/out/m84036_250809_035451_s4.bc2119.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-22/call-run_sawfish/out/m84036_250809_035451_s4.bc2119_sawfish/m84036_250809_035451_s4.bc2119.sv.vcf.gz.tbi", "minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-22/call-run_sawfish/out/m84036_250809_035451_s4.bc2119.minimap2.bam.bai"}
2025-09-15 20:24:33.934 wdl.w:ptcp.w:call-paraphase-39.t:call-run_paraphase NOTICE task setup :: name: "run_paraphase", source: "./paraphase.wdl", line: 127, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-39/call-run_paraphase", thread: 140606047233600
2025-09-15 20:24:33.935 wdl.w:ptcp.w:call-trgt-52.t:call-get_reads_overlapping_repeats NOTICE done
2025-09-15 20:24:33.941 wdl.w:ptcp.w:call-trgt-52 NOTICE finish :: job: "call-get_reads_overlapping_repeats"
2025-09-15 20:24:33.941 wdl.w:ptcp.w:call-trgt-52 INFO output :: job: "call-get_reads_overlapping_repeats", values: {"reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-52/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2149.repeats.bam.bai", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-52/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2149.repeats.bam"}
2025-09-15 20:24:33.941 wdl.w:ptcp.w:call-trgt-52 INFO visit :: node: "output-reads_overlapping_repeats", values: {"reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-52/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2149.repeats.bam"}
2025-09-15 20:24:33.941 wdl.w:ptcp.w:call-trgt-52 INFO visit :: node: "output-reads_overlapping_repeats_bai", values: {"reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-52/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2149.repeats.bam.bai"}
2025-09-15 20:24:33.948 wdl.w:ptcp.w:call-sawfish-39.t:call-run_sawfish NOTICE task setup :: name: "run_sawfish", source: "./sawfish.wdl", line: 83, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-39/call-run_sawfish", thread: 140607129368128
2025-09-15 20:24:33.962 wdl.w:ptcp.w:call-paraphase-39.t:call-run_paraphase INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:33.962 wdl.w:ptcp.w:call-paraphase-39.t:call-run_paraphase INFO input :: name: "annotation_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf"
2025-09-15 20:24:33.962 wdl.w:ptcp.w:call-paraphase-39.t:call-run_paraphase INFO input :: name: "genome_version", value: "38"
2025-09-15 20:24:33.963 wdl.w:ptcp.w:call-paraphase-39.t:call-run_paraphase INFO input :: name: "config_file", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/paraphase_config.GRCh38.yaml"
2025-09-15 20:24:33.963 wdl.w:ptcp.w:call-paraphase-39.t:call-run_paraphase INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:33.963 wdl.w:ptcp.w:call-paraphase-39.t:call-run_paraphase INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:33.963 wdl.w:ptcp.w:call-paraphase-39.t:call-run_paraphase INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2136.mapped.bam.bai"
2025-09-15 20:24:33.963 wdl.w:ptcp.w:call-paraphase-39.t:call-run_paraphase INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2136.mapped.bam"
2025-09-15 20:24:33.963 wdl.w:ptcp.w:call-paraphase-39.t:call-run_paraphase INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2136"
2025-09-15 20:24:33.964 wdl.w:ptcp.w:call-paraphase-39.t:call-run_paraphase INFO eval :: name: "threads", value: 4
2025-09-15 20:24:33.964 wdl.w:ptcp.w:call-paraphase-39.t:call-run_paraphase INFO eval :: name: "mem_gb", value: 8
2025-09-15 20:24:33.965 wdl.w:ptcp.w:call-paraphase-39.t:call-run_paraphase INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:33.965 wdl.w:ptcp.w:call-paraphase-39.t:call-run_paraphase INFO eval :: name: "out_dir", value: "m84036_250809_035451_s4.bc2136_paraphase"
2025-09-15 20:24:33.965 wdl.w:ptcp.w:call-paraphase-39.t:call-run_paraphase INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 4, memory_reservation: 8000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:33.965 wdl.w:ptcp.w:call-paraphase-39.t:call-run_paraphase WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:33.966 wdl.w:ptcp.w:call-paraphase-39.t:call-run_paraphase INFO provisioned :: seconds_waited: 0, cpu: 4, mem_bytes: 8000000000
2025-09-15 20:24:33.966 wdl.w:ptcp.w:call-paraphase-39.t:call-run_paraphase INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:33.968 wdl.w:ptcp.w:call-sawfish-39.t:call-run_sawfish INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:33.968 wdl.w:ptcp.w:call-sawfish-39.t:call-run_sawfish INFO input :: name: "genome_version", value: "38"
2025-09-15 20:24:33.968 wdl.w:ptcp.w:call-sawfish-39.t:call-run_sawfish INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:33.968 wdl.w:ptcp.w:call-sawfish-39.t:call-run_sawfish INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:33.968 wdl.w:ptcp.w:call-sawfish-39.t:call-run_sawfish INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2136.mapped.bam.bai"
2025-09-15 20:24:33.968 wdl.w:ptcp.w:call-sawfish-39.t:call-run_sawfish INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2136.mapped.bam"
2025-09-15 20:24:33.968 wdl.w:ptcp.w:call-sawfish-39.t:call-run_sawfish INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2136"
2025-09-15 20:24:33.968 wdl.w:ptcp.w:call-sawfish-39.t:call-run_sawfish INFO eval :: name: "mem_gb", value: 32
2025-09-15 20:24:33.968 wdl.w:ptcp.w:call-sawfish-39.t:call-run_sawfish INFO eval :: name: "threads", value: 16
2025-09-15 20:24:33.969 wdl.w:ptcp.w:call-sawfish-39.t:call-run_sawfish INFO eval :: name: "disk_size", value: 30
2025-09-15 20:24:33.969 wdl.w:ptcp.w:call-sawfish-39.t:call-run_sawfish INFO eval :: name: "discover_dirname", value: "m84036_250809_035451_s4.bc2136_sawfish_discover"
2025-09-15 20:24:33.969 wdl.w:ptcp.w:call-sawfish-39.t:call-run_sawfish INFO eval :: name: "call_dirname", value: "m84036_250809_035451_s4.bc2136_sawfish"
2025-09-15 20:24:33.969 wdl.w:ptcp.w:call-sawfish-39.t:call-run_sawfish INFO eval :: name: "minimap2_bam_filename", value: "m84036_250809_035451_s4.bc2136.minimap2.bam"
2025-09-15 20:24:33.969 wdl.w:ptcp.w:call-sawfish-39.t:call-run_sawfish INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 16, memory_reservation: 32000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:33.969 wdl.w:ptcp.w:call-sawfish-39.t:call-run_sawfish WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:33.970 wdl.w:ptcp.w:call-sawfish-39.t:call-run_sawfish INFO provisioned :: seconds_waited: 0, cpu: 16, mem_bytes: 32000000000
2025-09-15 20:24:33.970 wdl.w:ptcp.w:call-sawfish-39.t:call-run_sawfish INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:33.975 wdl.w:ptcp.w:call-trgt-37.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:32 [ERROR] - No reads found for TRID=PRTS_ARX
2025-09-15 20:24:33.975 wdl.w:ptcp.w:call-trgt-37.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:32 [ERROR] - No reads found for TRID=EIEE1_ARX
2025-09-15 20:24:33.993 wdl.w:ptcp.w:call-sawfish-22 NOTICE done
2025-09-15 20:24:34.009 wdl.w:ptcp NOTICE finish :: job: "call-sawfish-22"
2025-09-15 20:24:34.009 wdl.w:ptcp INFO output :: job: "call-sawfish-22", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-22/out/m84036_250809_035451_s4.bc2119_sawfish/m84036_250809_035451_s4.bc2119.sv.vcf.gz", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-22/out/m84036_250809_035451_s4.bc2119.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-22/out/m84036_250809_035451_s4.bc2119_sawfish/m84036_250809_035451_s4.bc2119.sv.vcf.gz.tbi", "minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-22/out/m84036_250809_035451_s4.bc2119.minimap2.bam.bai"}
2025-09-15 20:24:34.017 wdl.w:ptcp.w:call-paraphase-61 NOTICE workflow start :: name: "paraphase", source: "./paraphase.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-61"
2025-09-15 20:24:34.037 wdl.w:ptcp.w:call-paraphase-61 INFO visit :: node: "decl-annotation_vcf", values: {"annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf"}
2025-09-15 20:24:34.037 wdl.w:ptcp.w:call-paraphase-61 INFO visit :: node: "decl-config_file", values: {"config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml"}
2025-09-15 20:24:34.037 wdl.w:ptcp.w:call-paraphase-61 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:24:34.037 wdl.w:ptcp.w:call-paraphase-61 INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:24:34.037 wdl.w:ptcp.w:call-paraphase-61 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-61/out/m84036_250809_035451_s4.bc2158.mapped.bam"}
2025-09-15 20:24:34.037 wdl.w:ptcp.w:call-paraphase-61 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-61/out/m84036_250809_035451_s4.bc2158.mapped.bam.bai"}
2025-09-15 20:24:34.037 wdl.w:ptcp.w:call-paraphase-61 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:24:34.037 wdl.w:ptcp.w:call-paraphase-61 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:24:34.037 wdl.w:ptcp.w:call-paraphase-61 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2158"}
2025-09-15 20:24:34.038 wdl.w:ptcp.w:call-paraphase-61 INFO visit :: node: "decl-sex", values: {"sex": "F"}
2025-09-15 20:24:34.038 wdl.w:ptcp.w:call-paraphase-61 NOTICE ready :: job: "call-run_paraphase", callee: "run_paraphase"
2025-09-15 20:24:34.038 wdl.w:ptcp.w:call-paraphase-61 INFO input :: job: "call-run_paraphase", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf", "genome_version": "38", "config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-61/out/m84036_250809_035451_s4.bc2158.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-61/out/m84036_250809_035451_s4.bc2158.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2158"}
2025-09-15 20:24:34.039 wdl.w:ptcp.w:call-trgt-36.t:call-trgt_plot_motifs_allele INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2133.motifs_allele.trgt_plots.zip"
2025-09-15 20:24:34.041 wdl.w:ptcp.w:call-sawfish-39.t:call-run_sawfish INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 10, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-39/call-run_sawfish/_singularity_tmpdir_u_ftmq3_"
2025-09-15 20:24:34.042 wdl.w:ptcp.w:call-sawfish-39.t:call-run_sawfish INFO Slurm invocation: srun --job-name call-run_sawfish --partition compute,compute9 --cpus-per-task 16 --mem 30518M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-39/call-run_sawfish/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-39/call-run_sawfish/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-39/call-run_sawfish/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-39/call-run_sawfish/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-39/out/m84036_250809_035451_s4.bc2136.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2136.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-39/out/m84036_250809_035451_s4.bc2136.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2136.mapped.bam.bai:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-39/call-run_sawfish/_singularity_tmpdir_u_ftmq3_/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-39/call-run_sawfish/_singularity_tmpdir_u_ftmq3_/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:34.051 wdl.w:ptcp.w:call-paraphase-39.t:call-run_paraphase INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-39/call-run_paraphase/_singularity_tmpdir_ykbkj3_u"
2025-09-15 20:24:34.051 wdl.w:ptcp.w:call-paraphase-39.t:call-run_paraphase INFO Slurm invocation: srun --job-name call-run_paraphase --partition compute,compute9 --cpus-per-task 4 --mem 7629M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-39/call-run_paraphase/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-39/call-run_paraphase/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-39/call-run_paraphase/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-39/call-run_paraphase/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-39/out/m84036_250809_035451_s4.bc2136.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2136.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-39/out/m84036_250809_035451_s4.bc2136.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2136.mapped.bam.bai:ro --bind /ptcp/meta/variant_list/variant_list.GRCh38.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf:ro --bind /ptcp/meta/paraphase/paraphase_config.GRCh38.yaml:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/paraphase_config.GRCh38.yaml:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-39/call-run_paraphase/_singularity_tmpdir_ykbkj3_u/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-39/call-run_paraphase/_singularity_tmpdir_ykbkj3_u/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:34.075 wdl.w:ptcp.w:call-sawfish-39.t:call-run_sawfish NOTICE slurm_singularity run :: pid: 1202279, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-39/call-run_sawfish/slurm_singularity.log.txt"
2025-09-15 20:24:34.075 wdl.w:ptcp.w:call-paraphase-39.t:call-run_paraphase NOTICE slurm_singularity run :: pid: 1202280, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-39/call-run_paraphase/slurm_singularity.log.txt"
2025-09-15 20:24:34.109 wdl.w:ptcp.w:call-trgt-37.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:34 [ERROR] - No reads found for TRID=PRTS_ARX
2025-09-15 20:24:34.111 wdl.w:ptcp.w:call-sawfish-08.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:29][sawfish][INFO] Starting sawfish 2.0.3
2025-09-15 20:24:34.111 wdl.w:ptcp.w:call-sawfish-08.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:29][sawfish][INFO] cmdline: sawfish discover --disable-cnv --threads 16 --ref /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa --bam m84036_250809_035451_s4.bc2105.minimap2.bam --output-dir m84036_250809_035451_s4.bc2105_sawfish_discover
2025-09-15 20:24:34.111 wdl.w:ptcp.w:call-sawfish-08.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:29][sawfish][INFO] Running on 16 threads
2025-09-15 20:24:34.111 wdl.w:ptcp.w:call-sawfish-08.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:29][sawfish][INFO] Writing discover settings to file: 'm84036_250809_035451_s4.bc2105_sawfish_discover/discover.settings.json'
2025-09-15 20:24:34.111 wdl.w:ptcp.w:call-sawfish-08.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:29][sawfish][INFO] Reading reference genome from file '/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa'
2025-09-15 20:24:34.111 wdl.w:ptcp.w:call-sawfish-08.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:33][sawfish][INFO] Processing alignment file '/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2105.minimap2.bam'
2025-09-15 20:24:34.111 wdl.w:ptcp.w:call-sawfish-08.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:33][sawfish][INFO] Finished processing all alignments
2025-09-15 20:24:34.111 wdl.w:ptcp.w:call-sawfish-08.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:33][sawfish][INFO] Writing depth bins to binary file: 'm84036_250809_035451_s4.bc2105_sawfish_discover/depth.mpack'
2025-09-15 20:24:34.111 wdl.w:ptcp.w:call-sawfish-08.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:33][sawfish][INFO] Writing max sv depth genome regions to bed file: 'm84036_250809_035451_s4.bc2105_sawfish_discover/max.depth.bed'
2025-09-15 20:24:34.111 wdl.w:ptcp.w:call-sawfish-08.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:33][sawfish][INFO] Completing breakpoint observation clustering
2025-09-15 20:24:34.112 wdl.w:ptcp.w:call-sawfish-08.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:33][sawfish][INFO] Finished breakpoint observation clustering
2025-09-15 20:24:34.112 wdl.w:ptcp.w:call-sawfish-08.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:33][sawfish][INFO] Consolidating adjacent indel candidates
2025-09-15 20:24:34.112 wdl.w:ptcp.w:call-sawfish-08.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:33][sawfish][INFO] Finding large insertion candidates
2025-09-15 20:24:34.112 wdl.w:ptcp.w:call-sawfish-08.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:33][sawfish][INFO] Writing breakpoint_cluster debug bed file: 'm84036_250809_035451_s4.bc2105_sawfish_discover/debug.breakpoint_clusters.bed'
2025-09-15 20:24:34.112 wdl.w:ptcp.w:call-sawfish-08.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:33][sawfish][INFO] Refining SV Candidates
2025-09-15 20:24:34.112 wdl.w:ptcp.w:call-sawfish-08.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:33][sawfish][INFO] Writing debug assembly region bed file: 'm84036_250809_035451_s4.bc2105_sawfish_discover/assembly.regions.bed'
2025-09-15 20:24:34.112 wdl.w:ptcp.w:call-sawfish-08.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:33][sawfish][INFO] Starting refinement of breakpoint evidence clusters
2025-09-15 20:24:34.112 wdl.w:ptcp.w:call-sawfish-08.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:33][sawfish][INFO] Finished refining all breakpoint evidence clusters
2025-09-15 20:24:34.112 wdl.w:ptcp.w:call-sawfish-08.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:33][sawfish][INFO] Writing all contig alignments to bam file: 'm84036_250809_035451_s4.bc2105_sawfish_discover/contig.alignment.bam'
2025-09-15 20:24:34.112 wdl.w:ptcp.w:call-sawfish-08.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:33][sawfish][INFO] Writing candidate structural variants to file: 'm84036_250809_035451_s4.bc2105_sawfish_discover/candidate.sv.bcf'
2025-09-15 20:24:34.112 wdl.w:ptcp.w:call-sawfish-08.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:33][sawfish][INFO] Writing run statistics to file: 'm84036_250809_035451_s4.bc2105_sawfish_discover/run.stats.json'
2025-09-15 20:24:34.112 wdl.w:ptcp.w:call-sawfish-08.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:33][sawfish][INFO] sawfish completed. Total Runtime: 00:00:03.605
2025-09-15 20:24:34.125 wdl.w:ptcp.w:call-trgt-32.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:30 [ERROR] - No reads found for TRID=PRTS_ARX
2025-09-15 20:24:34.126 wdl.w:ptcp.w:call-trgt-32.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:30 [ERROR] - No reads found for TRID=EIEE1_ARX
2025-09-15 20:24:34.158 wdl.w:ptcp.w:call-trgt-36.t:call-trgt_plot_motifs_allele NOTICE done
2025-09-15 20:24:34.163 wdl.w:ptcp.w:call-trgt-36 NOTICE finish :: job: "call-trgt_plot_motifs_allele"
2025-09-15 20:24:34.163 wdl.w:ptcp.w:call-trgt-36 INFO output :: job: "call-trgt_plot_motifs_allele", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-36/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2133.motifs_allele.trgt_plots.zip"}
2025-09-15 20:24:34.164 wdl.w:ptcp.w:call-trgt-36 INFO visit :: node: "output-images_motifs_allele", values: {"images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-36/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2133.motifs_allele.trgt_plots.zip"}
2025-09-15 20:24:34.165 wdl.w:ptcp.w:call-trgt-45.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO srun: job 51797690 queued and waiting for resources
2025-09-15 20:24:34.165 wdl.w:ptcp.w:call-trgt-45.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO srun: job 51797690 has been allocated resources
2025-09-15 20:24:34.165 wdl.w:ptcp.w:call-trgt-45.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:34.171 wdl.w:ptcp.w:call-paraphase-44.t:call-call_f8 NOTICE task setup :: name: "call_f8", source: "./paraphase.wdl", line: 232, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-44/call-call_f8", thread: 140607112582720
2025-09-15 20:24:34.184 wdl.w:ptcp.w:call-trgt-00.t:call-trgt_plot_meth_allele INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2097.meth_allele.trgt_plots.zip"
2025-09-15 20:24:34.199 wdl.w:ptcp.w:call-paraphase-44.t:call-call_f8 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:34.199 wdl.w:ptcp.w:call-paraphase-44.t:call-call_f8 INFO input :: name: "genome_version", value: "38"
2025-09-15 20:24:34.199 wdl.w:ptcp.w:call-paraphase-44.t:call-call_f8 INFO input :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2141"
2025-09-15 20:24:34.199 wdl.w:ptcp.w:call-paraphase-44.t:call-call_f8 INFO input :: name: "paraphase_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2141.paraphase.bam.bai"
2025-09-15 20:24:34.199 wdl.w:ptcp.w:call-paraphase-44.t:call-call_f8 INFO input :: name: "paraphase_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2141.paraphase.bam"
2025-09-15 20:24:34.199 wdl.w:ptcp.w:call-paraphase-44.t:call-call_f8 INFO input :: name: "sex", value: "F"
2025-09-15 20:24:34.199 wdl.w:ptcp.w:call-paraphase-44.t:call-call_f8 INFO eval :: name: "threads", value: 1
2025-09-15 20:24:34.199 wdl.w:ptcp.w:call-paraphase-44.t:call-call_f8 INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:34.199 wdl.w:ptcp.w:call-paraphase-44.t:call-call_f8 INFO eval :: name: "disk_size", value: 11
2025-09-15 20:24:34.200 wdl.w:ptcp.w:call-paraphase-44.t:call-call_f8 INFO eval :: name: "sample_sex", value: "F"
2025-09-15 20:24:34.200 wdl.w:ptcp.w:call-paraphase-44.t:call-call_f8 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:34.200 wdl.w:ptcp.w:call-paraphase-44.t:call-call_f8 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:34.200 wdl.w:ptcp.w:call-paraphase-44.t:call-call_f8 INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:34.200 wdl.w:ptcp.w:call-paraphase-44.t:call-call_f8 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:34.229 wdl.w:ptcp.w:call-trgt-63.t:call-get_reads_overlapping_repeats.slurm_singularity INFO srun: job 51797692 queued and waiting for resources
2025-09-15 20:24:34.229 wdl.w:ptcp.w:call-trgt-63.t:call-get_reads_overlapping_repeats.slurm_singularity INFO srun: job 51797692 has been allocated resources
2025-09-15 20:24:34.229 wdl.w:ptcp.w:call-trgt-63.t:call-get_reads_overlapping_repeats.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:34.232 wdl.w:ptcp.w:call-sawfish-63.t:call-run_sawfish.slurm_singularity INFO srun: job 51797691 queued and waiting for resources
2025-09-15 20:24:34.232 wdl.w:ptcp.w:call-sawfish-63.t:call-run_sawfish.slurm_singularity INFO srun: job 51797691 has been allocated resources
2025-09-15 20:24:34.232 wdl.w:ptcp.w:call-sawfish-63.t:call-run_sawfish.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:34.240 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:24:33 [INFO] - Running trgt-4.0.0-429afcd [genotype]
2025-09-15 20:24:34.240 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:24:34 [WARN] - PRTS_ARX: Filtered out 8 impure reads
2025-09-15 20:24:34.240 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:24:34 [WARN] - EIEE1_ARX: Filtered out 7 impure reads
2025-09-15 20:24:34.240 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:24:34 [WARN] - FXS_FMR1: Filtered out 5 impure reads
2025-09-15 20:24:34.240 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:24:34 [WARN] - FRDA_FXN: Filtered out 2 impure reads
2025-09-15 20:24:34.240 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:24:34 [WARN] - FRAXE_AFF2: Filtered out 16 impure reads
2025-09-15 20:24:34.240 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:24:34 [INFO] - Total execution time: 227.09ms
2025-09-15 20:24:34.241 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:24:34 [INFO] - trgt end
2025-09-15 20:24:34.250 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_genotype.slurm_singularity INFO srun: job 51797693 queued and waiting for resources
2025-09-15 20:24:34.251 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_genotype.slurm_singularity INFO srun: job 51797693 has been allocated resources
2025-09-15 20:24:34.251 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_genotype.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:34.259 wdl.w:ptcp.w:call-paraphase-44.t:call-call_f8 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 8, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-44/call-call_f8/_singularity_tmpdir_a3wug96t"
2025-09-15 20:24:34.259 wdl.w:ptcp.w:call-paraphase-44.t:call-call_f8 INFO Slurm invocation: srun --job-name call-call_f8 --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-44/call-call_f8/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-44/call-call_f8/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-44/call-call_f8/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-44/call-call_f8/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-44/call-run_paraphase/out/m84036_250809_035451_s4.bc2141_paraphase/m84036_250809_035451_s4.bc2141.paraphase.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2141.paraphase.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-44/call-run_paraphase/out/m84036_250809_035451_s4.bc2141_paraphase/m84036_250809_035451_s4.bc2141.paraphase.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2141.paraphase.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-44/call-call_f8/_singularity_tmpdir_a3wug96t/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-44/call-call_f8/_singularity_tmpdir_a3wug96t/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:34.296 wdl.w:ptcp.w:call-paraphase-44.t:call-call_f8 NOTICE slurm_singularity run :: pid: 1202294, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-44/call-call_f8/slurm_singularity.log.txt"
2025-09-15 20:24:34.303 wdl.w:ptcp.w:call-trgt-00.t:call-trgt_plot_meth_allele NOTICE done
2025-09-15 20:24:34.310 wdl.w:ptcp.w:call-trgt-00 NOTICE finish :: job: "call-trgt_plot_meth_allele"
2025-09-15 20:24:34.310 wdl.w:ptcp.w:call-trgt-00 INFO output :: job: "call-trgt_plot_meth_allele", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-00/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2097.meth_allele.trgt_plots.zip"}
2025-09-15 20:24:34.311 wdl.w:ptcp.w:call-trgt-00 INFO visit :: node: "output-images_meth_allele", values: {"images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-00/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2097.meth_allele.trgt_plots.zip"}
2025-09-15 20:24:34.315 wdl.w:ptcp.w:call-trgt-39.t:call-get_reads_overlapping_repeats NOTICE task setup :: name: "get_reads_overlapping_repeats", source: "./trgt.wdl", line: 182, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-39/call-get_reads_overlapping_repeats", thread: 140606617675328
2025-09-15 20:24:34.333 wdl.w:ptcp.w:call-trgt-39.t:call-get_reads_overlapping_repeats INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:34.333 wdl.w:ptcp.w:call-trgt-39.t:call-get_reads_overlapping_repeats INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:34.333 wdl.w:ptcp.w:call-trgt-39.t:call-get_reads_overlapping_repeats INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2136.mapped.bam.bai"
2025-09-15 20:24:34.333 wdl.w:ptcp.w:call-trgt-39.t:call-get_reads_overlapping_repeats INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2136.mapped.bam"
2025-09-15 20:24:34.333 wdl.w:ptcp.w:call-trgt-39.t:call-get_reads_overlapping_repeats INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2136"
2025-09-15 20:24:34.333 wdl.w:ptcp.w:call-trgt-39.t:call-get_reads_overlapping_repeats INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:34.333 wdl.w:ptcp.w:call-trgt-39.t:call-get_reads_overlapping_repeats INFO eval :: name: "expand_size", value: 3000
2025-09-15 20:24:34.333 wdl.w:ptcp.w:call-trgt-39.t:call-get_reads_overlapping_repeats INFO eval :: name: "threads", value: 1
2025-09-15 20:24:34.333 wdl.w:ptcp.w:call-trgt-39.t:call-get_reads_overlapping_repeats INFO eval :: name: "expanded_bed_name", value: "m84036_250809_035451_s4.bc2136.expanded.bed"
2025-09-15 20:24:34.334 wdl.w:ptcp.w:call-trgt-39.t:call-get_reads_overlapping_repeats INFO eval :: name: "disk_size", value: 11
2025-09-15 20:24:34.334 wdl.w:ptcp.w:call-trgt-39.t:call-get_reads_overlapping_repeats INFO eval :: name: "output_name", value: "m84036_250809_035451_s4.bc2136.repeats.bam"
2025-09-15 20:24:34.334 wdl.w:ptcp.w:call-trgt-39.t:call-get_reads_overlapping_repeats INFO eval :: name: "index_name", value: "m84036_250809_035451_s4.bc2136.repeats.bam.bai"
2025-09-15 20:24:34.334 wdl.w:ptcp.w:call-trgt-39.t:call-get_reads_overlapping_repeats INFO eval :: name: "output_name_with_index", value: "m84036_250809_035451_s4.bc2136.repeats.bam##idx##m84036_250809_035451_s4.bc2136.repeats.bam.bai"
2025-09-15 20:24:34.334 wdl.w:ptcp.w:call-trgt-39.t:call-get_reads_overlapping_repeats INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:34.334 wdl.w:ptcp.w:call-trgt-39.t:call-get_reads_overlapping_repeats WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:34.335 wdl.w:ptcp.w:call-trgt-39.t:call-get_reads_overlapping_repeats INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:34.335 wdl.w:ptcp.w:call-trgt-39.t:call-get_reads_overlapping_repeats INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:34.379 wdl.w:ptcp.w:call-trgt-39.t:call-get_reads_overlapping_repeats INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 9, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-39/call-get_reads_overlapping_repeats/_singularity_tmpdir_x3o2whbj"
2025-09-15 20:24:34.380 wdl.w:ptcp.w:call-trgt-39.t:call-get_reads_overlapping_repeats INFO Slurm invocation: srun --job-name call-get_reads_overlapping_repeats --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-39/call-get_reads_overlapping_repeats/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-39/call-get_reads_overlapping_repeats/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-39/call-get_reads_overlapping_repeats/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-39/call-get_reads_overlapping_repeats/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-39/out/m84036_250809_035451_s4.bc2136.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2136.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-39/out/m84036_250809_035451_s4.bc2136.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2136.mapped.bam.bai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-39/call-get_reads_overlapping_repeats/_singularity_tmpdir_x3o2whbj/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-39/call-get_reads_overlapping_repeats/_singularity_tmpdir_x3o2whbj/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:34.392 wdl.w:ptcp.w:call-trgt-39.t:call-get_reads_overlapping_repeats NOTICE slurm_singularity run :: pid: 1202296, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-39/call-get_reads_overlapping_repeats/slurm_singularity.log.txt"
2025-09-15 20:24:34.452 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_genotype INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2160.trgt.vcf"
2025-09-15 20:24:34.455 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_genotype INFO output :: name: "spanning_bam", value: "m84036_250809_035451_s4.bc2160.trgt.sorted.spanning.bam"
2025-09-15 20:24:34.456 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_genotype INFO output :: name: "spanning_bam_bai", value: "m84036_250809_035451_s4.bc2160.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:34.464 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:32 [ERROR] - No reads found for TRID=OPDM_ABCD3
2025-09-15 20:24:34.464 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:32 [ERROR] - No reads found for TRID=OPDM_ABCD3
2025-09-15 20:24:34.464 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:32 [ERROR] - No reads found for TRID=NIID_NOTCH2NLC
2025-09-15 20:24:34.464 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:32 [ERROR] - No reads found for TRID=NIID_NOTCH2NLC
2025-09-15 20:24:34.465 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:32 [ERROR] - No reads found for TRID=DRPLA_ATN1
2025-09-15 20:24:34.465 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:32 [ERROR] - No reads found for TRID=DRPLA_ATN1
2025-09-15 20:24:34.465 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:32 [ERROR] - No reads found for TRID=SCA37_DAB1
2025-09-15 20:24:34.465 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:32 [ERROR] - No reads found for TRID=SCA37_DAB1
2025-09-15 20:24:34.465 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:32 [ERROR] - No reads found for TRID=SCA8_ATXN8OS
2025-09-15 20:24:34.465 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:32 [ERROR] - No reads found for TRID=OPDM_ABCD3
2025-09-15 20:24:34.465 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:32 [ERROR] - No reads found for TRID=SCA8_ATXN8OS
2025-09-15 20:24:34.465 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:33 [ERROR] - No reads found for TRID=OPDM4_RILPL1
2025-09-15 20:24:34.466 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:32 [ERROR] - No reads found for TRID=NIID_NOTCH2NLC
2025-09-15 20:24:34.466 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:32 [ERROR] - No reads found for TRID=OPDM4_RILPL1
2025-09-15 20:24:34.466 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:33 [ERROR] - No reads found for TRID=OPMD_PABPN1
2025-09-15 20:24:34.466 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:32 [ERROR] - No reads found for TRID=DRPLA_ATN1
2025-09-15 20:24:34.466 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:33 [ERROR] - No reads found for TRID=OPMD_PABPN1
2025-09-15 20:24:34.466 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:33 [ERROR] - No reads found for TRID=SCA27B_FGF14
2025-09-15 20:24:34.466 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:32 [ERROR] - No reads found for TRID=SCA37_DAB1
2025-09-15 20:24:34.466 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:33 [ERROR] - No reads found for TRID=SCA27B_FGF14
2025-09-15 20:24:34.466 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:33 [ERROR] - No reads found for TRID=SCA31_BEAN1
2025-09-15 20:24:34.467 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:32 [ERROR] - No reads found for TRID=SCA8_ATXN8OS
2025-09-15 20:24:34.467 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:33 [ERROR] - No reads found for TRID=SCA31_BEAN1
2025-09-15 20:24:34.467 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:33 [ERROR] - No reads found for TRID=SCA4_ZFHX3
2025-09-15 20:24:34.467 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:32 [ERROR] - No reads found for TRID=OPDM4_RILPL1
2025-09-15 20:24:34.467 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:33 [ERROR] - No reads found for TRID=SCA4_ZFHX3
2025-09-15 20:24:34.467 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:33 [ERROR] - No reads found for TRID=HDL2_JPH3
2025-09-15 20:24:34.467 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:32 [ERROR] - No reads found for TRID=OPMD_PABPN1
2025-09-15 20:24:34.467 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:33 [ERROR] - No reads found for TRID=HDL2_JPH3
2025-09-15 20:24:34.467 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:33 [ERROR] - No reads found for TRID=OPDM2_GIPC1
2025-09-15 20:24:34.468 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:32 [ERROR] - No reads found for TRID=SCA27B_FGF14
2025-09-15 20:24:34.468 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:33 [ERROR] - No reads found for TRID=OPDM2_GIPC1
2025-09-15 20:24:34.468 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:33 [ERROR] - No reads found for TRID=FRA2A_AFF3
2025-09-15 20:24:34.468 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:32 [ERROR] - No reads found for TRID=SCA31_BEAN1
2025-09-15 20:24:34.468 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:33 [ERROR] - No reads found for TRID=FRA2A_AFF3
2025-09-15 20:24:34.468 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:33 [ERROR] - No reads found for TRID=SD5_HOXD13
2025-09-15 20:24:34.468 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:32 [ERROR] - No reads found for TRID=SCA4_ZFHX3
2025-09-15 20:24:34.468 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:33 [ERROR] - No reads found for TRID=SD5_HOXD13
2025-09-15 20:24:34.468 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:33 [ERROR] - No reads found for TRID=SCA36_NOP56
2025-09-15 20:24:34.469 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:32 [ERROR] - No reads found for TRID=HDL2_JPH3
2025-09-15 20:24:34.469 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:33 [ERROR] - No reads found for TRID=SCA36_NOP56
2025-09-15 20:24:34.469 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:33 [ERROR] - No reads found for TRID=DM1_DMPK
2025-09-15 20:24:34.469 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:33 [ERROR] - No reads found for TRID=OPDM2_GIPC1
2025-09-15 20:24:34.469 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:33 [ERROR] - No reads found for TRID=DM1_DMPK
2025-09-15 20:24:34.469 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:33 [ERROR] - No reads found for TRID=SCA3_ATXN3
2025-09-15 20:24:34.469 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:33 [ERROR] - No reads found for TRID=FRA2A_AFF3
2025-09-15 20:24:34.469 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:33 [ERROR] - No reads found for TRID=SCA3_ATXN3
2025-09-15 20:24:34.469 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:33 [ERROR] - No reads found for TRID=CJD_PRNP
2025-09-15 20:24:34.470 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:33 [ERROR] - No reads found for TRID=SD5_HOXD13
2025-09-15 20:24:34.470 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:33 [ERROR] - No reads found for TRID=CJD_PRNP
2025-09-15 20:24:34.470 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:33 [ERROR] - No reads found for TRID=SCA10_ATXN10
2025-09-15 20:24:34.470 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:33 [ERROR] - No reads found for TRID=SCA36_NOP56
2025-09-15 20:24:34.470 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:33 [ERROR] - No reads found for TRID=SCA10_ATXN10
2025-09-15 20:24:34.470 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:33 [ERROR] - No reads found for TRID=SCA6_CACNA1A
2025-09-15 20:24:34.470 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:33 [ERROR] - No reads found for TRID=DM1_DMPK
2025-09-15 20:24:34.470 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:33 [ERROR] - No reads found for TRID=SCA6_CACNA1A
2025-09-15 20:24:34.470 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:33 [ERROR] - No reads found for TRID=DM2_CNBP
2025-09-15 20:24:34.470 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:33 [ERROR] - No reads found for TRID=SCA3_ATXN3
2025-09-15 20:24:34.470 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:33 [ERROR] - No reads found for TRID=DM2_CNBP
2025-09-15 20:24:34.471 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:33 [ERROR] - No reads found for TRID=SCA7_ATXN7
2025-09-15 20:24:34.471 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:33 [ERROR] - No reads found for TRID=CJD_PRNP
2025-09-15 20:24:34.471 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:33 [ERROR] - No reads found for TRID=SCA7_ATXN7
2025-09-15 20:24:34.471 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:33 [ERROR] - No reads found for TRID=CANVAS_RFC1
2025-09-15 20:24:34.471 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:33 [ERROR] - No reads found for TRID=SCA10_ATXN10
2025-09-15 20:24:34.471 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:33 [ERROR] - No reads found for TRID=CANVAS_RFC1
2025-09-15 20:24:34.471 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:33 [ERROR] - No reads found for TRID=SCA12_PPP2R2B
2025-09-15 20:24:34.471 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:33 [ERROR] - No reads found for TRID=SCA6_CACNA1A
2025-09-15 20:24:34.471 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:33 [ERROR] - No reads found for TRID=SCA12_PPP2R2B
2025-09-15 20:24:34.471 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:33 [ERROR] - No reads found for TRID=SCA1_ATXN1
2025-09-15 20:24:34.472 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:33 [ERROR] - No reads found for TRID=DM2_CNBP
2025-09-15 20:24:34.472 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:33 [ERROR] - No reads found for TRID=SCA1_ATXN1
2025-09-15 20:24:34.472 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:33 [ERROR] - No reads found for TRID=EPM1_CSTB
2025-09-15 20:24:34.472 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:33 [ERROR] - No reads found for TRID=SCA7_ATXN7
2025-09-15 20:24:34.472 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:33 [ERROR] - No reads found for TRID=EPM1_CSTB
2025-09-15 20:24:34.472 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:34 [ERROR] - No reads found for TRID=OPDM1_LRP12
2025-09-15 20:24:34.472 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:33 [ERROR] - No reads found for TRID=CANVAS_RFC1
2025-09-15 20:24:34.472 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:34 [ERROR] - No reads found for TRID=OPDM1_LRP12
2025-09-15 20:24:34.472 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:34 [ERROR] - No reads found for TRID=CCHS_PHOX2B
2025-09-15 20:24:34.473 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:33 [ERROR] - No reads found for TRID=SCA12_PPP2R2B
2025-09-15 20:24:34.473 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:34 [ERROR] - No reads found for TRID=CCHS_PHOX2B
2025-09-15 20:24:34.473 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:34 [ERROR] - No reads found for TRID=FAME1_SAMD12
2025-09-15 20:24:34.473 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:33 [ERROR] - No reads found for TRID=SCA1_ATXN1
2025-09-15 20:24:34.473 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:34 [ERROR] - No reads found for TRID=FAME1_SAMD12
2025-09-15 20:24:34.473 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:34 [ERROR] - No reads found for TRID=FTDALS1_C9orf72
2025-09-15 20:24:34.473 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:33 [ERROR] - No reads found for TRID=EPM1_CSTB
2025-09-15 20:24:34.474 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:34 [ERROR] - No reads found for TRID=FTDALS1_C9orf72
2025-09-15 20:24:34.474 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:34 [ERROR] - No reads found for TRID=SBMA_AR
2025-09-15 20:24:34.474 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:33 [ERROR] - No reads found for TRID=OPDM1_LRP12
2025-09-15 20:24:34.474 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:34 [ERROR] - No reads found for TRID=SBMA_AR
2025-09-15 20:24:34.474 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:33 [ERROR] - No reads found for TRID=CCHS_PHOX2B
2025-09-15 20:24:34.474 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:33 [ERROR] - No reads found for TRID=FAME1_SAMD12
2025-09-15 20:24:34.474 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:33 [ERROR] - No reads found for TRID=FTDALS1_C9orf72
2025-09-15 20:24:34.474 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:33 [ERROR] - No reads found for TRID=SBMA_AR
2025-09-15 20:24:34.544 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_genotype NOTICE done
2025-09-15 20:24:34.549 wdl.w:ptcp.w:call-trgt-63 NOTICE finish :: job: "call-trgt_genotype"
2025-09-15 20:24:34.550 wdl.w:ptcp.w:call-trgt-63 INFO output :: job: "call-trgt_genotype", values: {"spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-63/call-trgt_genotype/out/m84036_250809_035451_s4.bc2160.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-63/call-trgt_genotype/out/m84036_250809_035451_s4.bc2160.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-63/call-trgt_genotype/out/m84036_250809_035451_s4.bc2160.trgt.vcf"}
2025-09-15 20:24:34.550 wdl.w:ptcp.w:call-trgt-63 NOTICE ready :: job: "call-trgt_plot_meth_allele", callee: "trgt_plot"
2025-09-15 20:24:34.550 wdl.w:ptcp.w:call-trgt-63 INFO input :: job: "call-trgt_plot_meth_allele", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": false, "methylation": true, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-63/call-trgt_genotype/out/m84036_250809_035451_s4.bc2160.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-63/call-trgt_genotype/out/m84036_250809_035451_s4.bc2160.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-63/call-trgt_genotype/out/m84036_250809_035451_s4.bc2160.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2160"}
2025-09-15 20:24:34.551 wdl.w:ptcp.w:call-trgt-63 NOTICE ready :: job: "call-trgt_plot_meth_waterfall", callee: "trgt_plot"
2025-09-15 20:24:34.552 wdl.w:ptcp.w:call-trgt-63 INFO input :: job: "call-trgt_plot_meth_waterfall", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": true, "methylation": true, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-63/call-trgt_genotype/out/m84036_250809_035451_s4.bc2160.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-63/call-trgt_genotype/out/m84036_250809_035451_s4.bc2160.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-63/call-trgt_genotype/out/m84036_250809_035451_s4.bc2160.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2160"}
2025-09-15 20:24:34.553 wdl.w:ptcp.w:call-trgt-63 NOTICE ready :: job: "call-trgt_plot_motifs_allele", callee: "trgt_plot"
2025-09-15 20:24:34.553 wdl.w:ptcp.w:call-trgt-63 INFO input :: job: "call-trgt_plot_motifs_allele", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": false, "methylation": false, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-63/call-trgt_genotype/out/m84036_250809_035451_s4.bc2160.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-63/call-trgt_genotype/out/m84036_250809_035451_s4.bc2160.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-63/call-trgt_genotype/out/m84036_250809_035451_s4.bc2160.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2160"}
2025-09-15 20:24:34.554 wdl.w:ptcp.w:call-trgt-63 NOTICE ready :: job: "call-trgt_plot_motifs_waterfall", callee: "trgt_plot"
2025-09-15 20:24:34.554 wdl.w:ptcp.w:call-trgt-63 INFO input :: job: "call-trgt_plot_motifs_waterfall", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": true, "methylation": false, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-63/call-trgt_genotype/out/m84036_250809_035451_s4.bc2160.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-63/call-trgt_genotype/out/m84036_250809_035451_s4.bc2160.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-63/call-trgt_genotype/out/m84036_250809_035451_s4.bc2160.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2160"}
2025-09-15 20:24:34.555 wdl.w:ptcp.w:call-trgt-63 INFO visit :: node: "output-spanning_bam", values: {"spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-63/call-trgt_genotype/out/m84036_250809_035451_s4.bc2160.trgt.sorted.spanning.bam"}
2025-09-15 20:24:34.555 wdl.w:ptcp.w:call-trgt-63 INFO visit :: node: "output-spanning_bam_bai", values: {"spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-63/call-trgt_genotype/out/m84036_250809_035451_s4.bc2160.trgt.sorted.spanning.bam.bai"}
2025-09-15 20:24:34.555 wdl.w:ptcp.w:call-trgt-63 INFO visit :: node: "output-vcf", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-63/call-trgt_genotype/out/m84036_250809_035451_s4.bc2160.trgt.vcf"}
2025-09-15 20:24:34.555 wdl.w:ptcp.w:call-trgt-39.t:call-trgt_genotype NOTICE task setup :: name: "trgt_genotype", source: "./trgt.wdl", line: 272, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-39/call-trgt_genotype", thread: 140613580211776
2025-09-15 20:24:34.573 wdl.w:ptcp.w:call-trgt-39.t:call-trgt_genotype INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:34.573 wdl.w:ptcp.w:call-trgt-39.t:call-trgt_genotype INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:34.573 wdl.w:ptcp.w:call-trgt-39.t:call-trgt_genotype INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:34.573 wdl.w:ptcp.w:call-trgt-39.t:call-trgt_genotype INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:34.573 wdl.w:ptcp.w:call-trgt-39.t:call-trgt_genotype INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2136.mapped.bam.bai"
2025-09-15 20:24:34.573 wdl.w:ptcp.w:call-trgt-39.t:call-trgt_genotype INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2136.mapped.bam"
2025-09-15 20:24:34.573 wdl.w:ptcp.w:call-trgt-39.t:call-trgt_genotype INFO input :: name: "sex", value: "F"
2025-09-15 20:24:34.573 wdl.w:ptcp.w:call-trgt-39.t:call-trgt_genotype INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2136"
2025-09-15 20:24:34.574 wdl.w:ptcp.w:call-trgt-39.t:call-trgt_genotype INFO eval :: name: "mem_gb", value: 16
2025-09-15 20:24:34.574 wdl.w:ptcp.w:call-trgt-39.t:call-trgt_genotype INFO eval :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2136.trgt"
2025-09-15 20:24:34.574 wdl.w:ptcp.w:call-trgt-39.t:call-trgt_genotype INFO eval :: name: "threads", value: 8
2025-09-15 20:24:34.574 wdl.w:ptcp.w:call-trgt-39.t:call-trgt_genotype INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:34.574 wdl.w:ptcp.w:call-trgt-39.t:call-trgt_genotype INFO eval :: name: "karyotype", value: "XX"
2025-09-15 20:24:34.575 wdl.w:ptcp.w:call-trgt-39.t:call-trgt_genotype INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 8, memory_reservation: 16000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:34.575 wdl.w:ptcp.w:call-trgt-39.t:call-trgt_genotype WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:34.575 wdl.w:ptcp.w:call-trgt-39.t:call-trgt_genotype INFO provisioned :: seconds_waited: 0, cpu: 8, mem_bytes: 16000000000
2025-09-15 20:24:34.575 wdl.w:ptcp.w:call-trgt-39.t:call-trgt_genotype INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:34.590 wdl.w:ptcp.w:call-paraphase-36.t:call-call_f8.slurm_singularity INFO srun: job 51797694 queued and waiting for resources
2025-09-15 20:24:34.590 wdl.w:ptcp.w:call-paraphase-36.t:call-call_f8.slurm_singularity INFO srun: job 51797694 has been allocated resources
2025-09-15 20:24:34.590 wdl.w:ptcp.w:call-paraphase-36.t:call-call_f8.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:34.597 wdl.w:ptcp.w:call-trgt-32.t:call-trgt_plot_motifs_waterfall INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2129.motifs_waterfall.trgt_plots.zip"
2025-09-15 20:24:34.653 wdl.w:ptcp.w:call-trgt-37.t:call-trgt_plot_motifs_allele INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2134.motifs_allele.trgt_plots.zip"
2025-09-15 20:24:34.662 wdl.w:ptcp.w:call-trgt-63.t:call-get_reads_overlapping_repeats INFO output :: name: "reads_overlapping_repeats", value: "m84036_250809_035451_s4.bc2160.repeats.bam"
2025-09-15 20:24:34.663 wdl.w:ptcp.w:call-trgt-39.t:call-trgt_genotype INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 11, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-39/call-trgt_genotype/_singularity_tmpdir_9456povr"
2025-09-15 20:24:34.663 wdl.w:ptcp.w:call-trgt-39.t:call-trgt_genotype INFO Slurm invocation: srun --job-name call-trgt_genotype --partition compute,compute9 --cpus-per-task 8 --mem 15259M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-39/call-trgt_genotype/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-39/call-trgt_genotype/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-39/call-trgt_genotype/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-39/call-trgt_genotype/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-39/out/m84036_250809_035451_s4.bc2136.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2136.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-39/out/m84036_250809_035451_s4.bc2136.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2136.mapped.bam.bai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-39/call-trgt_genotype/_singularity_tmpdir_9456povr/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-39/call-trgt_genotype/_singularity_tmpdir_9456povr/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:34.665 wdl.w:ptcp.w:call-trgt-63.t:call-get_reads_overlapping_repeats INFO output :: name: "reads_overlapping_repeats_bai", value: "m84036_250809_035451_s4.bc2160.repeats.bam.bai"
2025-09-15 20:24:34.687 wdl.w:ptcp.w:call-trgt-39.t:call-trgt_genotype NOTICE slurm_singularity run :: pid: 1202314, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-39/call-trgt_genotype/slurm_singularity.log.txt"
2025-09-15 20:24:34.701 wdl.w:ptcp.w:call-trgt-36.t:call-trgt_plot_motifs_waterfall INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2133.motifs_waterfall.trgt_plots.zip"
2025-09-15 20:24:34.724 wdl.w:ptcp.w:call-paraphase-45.t:call-call_f8.slurm_singularity INFO srun: job 51797695 queued and waiting for resources
2025-09-15 20:24:34.724 wdl.w:ptcp.w:call-paraphase-45.t:call-call_f8.slurm_singularity INFO srun: job 51797695 has been allocated resources
2025-09-15 20:24:34.724 wdl.w:ptcp.w:call-paraphase-45.t:call-call_f8.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:34.745 wdl.w:ptcp.w:call-trgt-32.t:call-trgt_plot_motifs_waterfall NOTICE done
2025-09-15 20:24:34.751 wdl.w:ptcp.w:call-trgt-32 NOTICE finish :: job: "call-trgt_plot_motifs_waterfall"
2025-09-15 20:24:34.751 wdl.w:ptcp.w:call-trgt-32 INFO output :: job: "call-trgt_plot_motifs_waterfall", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-32/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2129.motifs_waterfall.trgt_plots.zip"}
2025-09-15 20:24:34.751 wdl.w:ptcp.w:call-trgt-32 INFO visit :: node: "output-images_motifs_waterfall", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-32/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2129.motifs_waterfall.trgt_plots.zip"}
2025-09-15 20:24:34.762 wdl.w:ptcp.w:call-paraphase-41.t:call-run_paraphase NOTICE task setup :: name: "run_paraphase", source: "./paraphase.wdl", line: 127, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-41/call-run_paraphase", thread: 140610342200896
2025-09-15 20:24:34.764 wdl.w:ptcp.w:call-trgt-63.t:call-get_reads_overlapping_repeats NOTICE done
2025-09-15 20:24:34.765 wdl.w:ptcp.w:call-paraphase-37.t:call-call_f8.slurm_singularity INFO srun: job 51797696 queued and waiting for resources
2025-09-15 20:24:34.765 wdl.w:ptcp.w:call-paraphase-37.t:call-call_f8.slurm_singularity INFO srun: job 51797696 has been allocated resources
2025-09-15 20:24:34.765 wdl.w:ptcp.w:call-paraphase-37.t:call-call_f8.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:34.767 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_meth_waterfall INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2148.meth_waterfall.trgt_plots.zip"
2025-09-15 20:24:34.770 wdl.w:ptcp.w:call-trgt-63 NOTICE finish :: job: "call-get_reads_overlapping_repeats"
2025-09-15 20:24:34.770 wdl.w:ptcp.w:call-trgt-63 INFO output :: job: "call-get_reads_overlapping_repeats", values: {"reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-63/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2160.repeats.bam.bai", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-63/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2160.repeats.bam"}
2025-09-15 20:24:34.771 wdl.w:ptcp.w:call-trgt-63 INFO visit :: node: "output-reads_overlapping_repeats", values: {"reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-63/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2160.repeats.bam"}
2025-09-15 20:24:34.771 wdl.w:ptcp.w:call-trgt-63 INFO visit :: node: "output-reads_overlapping_repeats_bai", values: {"reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-63/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2160.repeats.bam.bai"}
2025-09-15 20:24:34.781 wdl.w:ptcp.w:call-sawfish-41.t:call-run_sawfish NOTICE task setup :: name: "run_sawfish", source: "./sawfish.wdl", line: 83, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-41/call-run_sawfish", thread: 140608765158976
2025-09-15 20:24:34.798 wdl.w:ptcp.w:call-paraphase-41.t:call-run_paraphase INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:34.798 wdl.w:ptcp.w:call-paraphase-41.t:call-run_paraphase INFO input :: name: "annotation_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf"
2025-09-15 20:24:34.798 wdl.w:ptcp.w:call-paraphase-41.t:call-run_paraphase INFO input :: name: "genome_version", value: "38"
2025-09-15 20:24:34.798 wdl.w:ptcp.w:call-paraphase-41.t:call-run_paraphase INFO input :: name: "config_file", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/paraphase_config.GRCh38.yaml"
2025-09-15 20:24:34.798 wdl.w:ptcp.w:call-paraphase-41.t:call-run_paraphase INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:34.798 wdl.w:ptcp.w:call-paraphase-41.t:call-run_paraphase INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:34.799 wdl.w:ptcp.w:call-paraphase-41.t:call-run_paraphase INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2138.mapped.bam.bai"
2025-09-15 20:24:34.799 wdl.w:ptcp.w:call-paraphase-41.t:call-run_paraphase INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2138.mapped.bam"
2025-09-15 20:24:34.799 wdl.w:ptcp.w:call-paraphase-41.t:call-run_paraphase INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2138"
2025-09-15 20:24:34.799 wdl.w:ptcp.w:call-paraphase-41.t:call-run_paraphase INFO eval :: name: "threads", value: 4
2025-09-15 20:24:34.799 wdl.w:ptcp.w:call-paraphase-41.t:call-run_paraphase INFO eval :: name: "mem_gb", value: 8
2025-09-15 20:24:34.800 wdl.w:ptcp.w:call-paraphase-41.t:call-run_paraphase INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:34.800 wdl.w:ptcp.w:call-paraphase-41.t:call-run_paraphase INFO eval :: name: "out_dir", value: "m84036_250809_035451_s4.bc2138_paraphase"
2025-09-15 20:24:34.801 wdl.w:ptcp.w:call-paraphase-41.t:call-run_paraphase INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 4, memory_reservation: 8000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:34.801 wdl.w:ptcp.w:call-paraphase-41.t:call-run_paraphase WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:34.802 wdl.w:ptcp.w:call-paraphase-41.t:call-run_paraphase INFO provisioned :: seconds_waited: 0, cpu: 4, mem_bytes: 8000000000
2025-09-15 20:24:34.802 wdl.w:ptcp.w:call-paraphase-41.t:call-run_paraphase INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:34.809 wdl.w:ptcp.w:call-sawfish-41.t:call-run_sawfish INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:34.809 wdl.w:ptcp.w:call-sawfish-41.t:call-run_sawfish INFO input :: name: "genome_version", value: "38"
2025-09-15 20:24:34.809 wdl.w:ptcp.w:call-sawfish-41.t:call-run_sawfish INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:34.809 wdl.w:ptcp.w:call-sawfish-41.t:call-run_sawfish INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:34.810 wdl.w:ptcp.w:call-sawfish-41.t:call-run_sawfish INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2138.mapped.bam.bai"
2025-09-15 20:24:34.810 wdl.w:ptcp.w:call-sawfish-41.t:call-run_sawfish INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2138.mapped.bam"
2025-09-15 20:24:34.810 wdl.w:ptcp.w:call-sawfish-41.t:call-run_sawfish INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2138"
2025-09-15 20:24:34.810 wdl.w:ptcp.w:call-sawfish-41.t:call-run_sawfish INFO eval :: name: "mem_gb", value: 32
2025-09-15 20:24:34.810 wdl.w:ptcp.w:call-sawfish-41.t:call-run_sawfish INFO eval :: name: "threads", value: 16
2025-09-15 20:24:34.811 wdl.w:ptcp.w:call-sawfish-41.t:call-run_sawfish INFO eval :: name: "disk_size", value: 30
2025-09-15 20:24:34.811 wdl.w:ptcp.w:call-sawfish-41.t:call-run_sawfish INFO eval :: name: "discover_dirname", value: "m84036_250809_035451_s4.bc2138_sawfish_discover"
2025-09-15 20:24:34.811 wdl.w:ptcp.w:call-sawfish-41.t:call-run_sawfish INFO eval :: name: "call_dirname", value: "m84036_250809_035451_s4.bc2138_sawfish"
2025-09-15 20:24:34.811 wdl.w:ptcp.w:call-sawfish-41.t:call-run_sawfish INFO eval :: name: "minimap2_bam_filename", value: "m84036_250809_035451_s4.bc2138.minimap2.bam"
2025-09-15 20:24:34.811 wdl.w:ptcp.w:call-sawfish-41.t:call-run_sawfish INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 16, memory_reservation: 32000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:34.811 wdl.w:ptcp.w:call-sawfish-41.t:call-run_sawfish WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:34.812 wdl.w:ptcp.w:call-sawfish-41.t:call-run_sawfish INFO provisioned :: seconds_waited: 0, cpu: 16, mem_bytes: 32000000000
2025-09-15 20:24:34.812 wdl.w:ptcp.w:call-sawfish-41.t:call-run_sawfish INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:34.848 wdl.w:ptcp.w:call-trgt-37.t:call-trgt_plot_motifs_allele NOTICE done
2025-09-15 20:24:34.855 wdl.w:ptcp.w:call-trgt-37 NOTICE finish :: job: "call-trgt_plot_motifs_allele"
2025-09-15 20:24:34.855 wdl.w:ptcp.w:call-trgt-37 INFO output :: job: "call-trgt_plot_motifs_allele", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-37/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2134.motifs_allele.trgt_plots.zip"}
2025-09-15 20:24:34.856 wdl.w:ptcp.w:call-trgt-37 INFO visit :: node: "output-images_motifs_allele", values: {"images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-37/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2134.motifs_allele.trgt_plots.zip"}
2025-09-15 20:24:34.864 wdl.w:ptcp.w:call-trgt-41.t:call-get_reads_overlapping_repeats NOTICE task setup :: name: "get_reads_overlapping_repeats", source: "./trgt.wdl", line: 182, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-41/call-get_reads_overlapping_repeats", thread: 140610367379008
2025-09-15 20:24:34.890 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_meth_waterfall NOTICE done
2025-09-15 20:24:34.896 wdl.w:ptcp.w:call-trgt-41.t:call-get_reads_overlapping_repeats INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:34.896 wdl.w:ptcp.w:call-trgt-41.t:call-get_reads_overlapping_repeats INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:34.896 wdl.w:ptcp.w:call-trgt-41.t:call-get_reads_overlapping_repeats INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2138.mapped.bam.bai"
2025-09-15 20:24:34.896 wdl.w:ptcp.w:call-trgt-41.t:call-get_reads_overlapping_repeats INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2138.mapped.bam"
2025-09-15 20:24:34.896 wdl.w:ptcp.w:call-trgt-41.t:call-get_reads_overlapping_repeats INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2138"
2025-09-15 20:24:34.897 wdl.w:ptcp.w:call-trgt-41.t:call-get_reads_overlapping_repeats INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:34.897 wdl.w:ptcp.w:call-trgt-41.t:call-get_reads_overlapping_repeats INFO eval :: name: "expand_size", value: 3000
2025-09-15 20:24:34.897 wdl.w:ptcp.w:call-trgt-41.t:call-get_reads_overlapping_repeats INFO eval :: name: "threads", value: 1
2025-09-15 20:24:34.897 wdl.w:ptcp.w:call-trgt-41.t:call-get_reads_overlapping_repeats INFO eval :: name: "expanded_bed_name", value: "m84036_250809_035451_s4.bc2138.expanded.bed"
2025-09-15 20:24:34.897 wdl.w:ptcp.w:call-trgt-41.t:call-get_reads_overlapping_repeats INFO eval :: name: "disk_size", value: 11
2025-09-15 20:24:34.897 wdl.w:ptcp.w:call-trgt-41.t:call-get_reads_overlapping_repeats INFO eval :: name: "output_name", value: "m84036_250809_035451_s4.bc2138.repeats.bam"
2025-09-15 20:24:34.897 wdl.w:ptcp.w:call-trgt-41.t:call-get_reads_overlapping_repeats INFO eval :: name: "index_name", value: "m84036_250809_035451_s4.bc2138.repeats.bam.bai"
2025-09-15 20:24:34.897 wdl.w:ptcp.w:call-trgt-41.t:call-get_reads_overlapping_repeats INFO eval :: name: "output_name_with_index", value: "m84036_250809_035451_s4.bc2138.repeats.bam##idx##m84036_250809_035451_s4.bc2138.repeats.bam.bai"
2025-09-15 20:24:34.898 wdl.w:ptcp.w:call-trgt-41.t:call-get_reads_overlapping_repeats INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:34.898 wdl.w:ptcp.w:call-trgt-41.t:call-get_reads_overlapping_repeats WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:34.898 wdl.w:ptcp.w:call-trgt-41.t:call-get_reads_overlapping_repeats INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:34.898 wdl.w:ptcp.w:call-trgt-41.t:call-get_reads_overlapping_repeats INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:34.905 wdl.w:ptcp.w:call-trgt-51 NOTICE finish :: job: "call-trgt_plot_meth_waterfall"
2025-09-15 20:24:34.905 wdl.w:ptcp.w:call-trgt-51 INFO output :: job: "call-trgt_plot_meth_waterfall", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-51/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2148.meth_waterfall.trgt_plots.zip"}
2025-09-15 20:24:34.905 wdl.w:ptcp.w:call-trgt-51 INFO visit :: node: "output-images_meth_waterfall", values: {"images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-51/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2148.meth_waterfall.trgt_plots.zip"}
2025-09-15 20:24:34.917 wdl.w:ptcp.w:call-trgt-41.t:call-trgt_genotype NOTICE task setup :: name: "trgt_genotype", source: "./trgt.wdl", line: 272, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-41/call-trgt_genotype", thread: 140612531648064
2025-09-15 20:24:34.921 wdl.w:ptcp.w:call-trgt-36.t:call-trgt_plot_motifs_waterfall NOTICE done
2025-09-15 20:24:34.926 wdl.w:ptcp.w:call-trgt-36 NOTICE finish :: job: "call-trgt_plot_motifs_waterfall"
2025-09-15 20:24:34.926 wdl.w:ptcp.w:call-trgt-36 INFO output :: job: "call-trgt_plot_motifs_waterfall", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-36/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2133.motifs_waterfall.trgt_plots.zip"}
2025-09-15 20:24:34.927 wdl.w:ptcp.w:call-trgt-36 INFO visit :: node: "output-images_motifs_waterfall", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-36/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2133.motifs_waterfall.trgt_plots.zip"}
2025-09-15 20:24:34.927 wdl.w:ptcp.w:call-trgt-36 INFO visit :: node: "outputs", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-36/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2133.motifs_waterfall.trgt_plots.zip", "images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-36/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2133.meth_allele.trgt_plots.zip", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-36/call-trgt_genotype/out/m84036_250809_035451_s4.bc2133.trgt.sorted.spanning.bam.bai", "images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-36/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2133.motifs_allele.trgt_plots.zip", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-36/call-trgt_genotype/out/m84036_250809_035451_s4.bc2133.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-36/call-trgt_genotype/out/m84036_250809_035451_s4.bc2133.trgt.vcf", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-36/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2133.repeats.bam", "images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-36/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2133.meth_waterfall.trgt_plots.zip", "reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-36/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2133.repeats.bam.bai"}
2025-09-15 20:24:34.932 wdl.w:ptcp.w:call-sawfish-41.t:call-run_sawfish INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 10, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-41/call-run_sawfish/_singularity_tmpdir_knll2djc"
2025-09-15 20:24:34.933 wdl.w:ptcp.w:call-sawfish-41.t:call-run_sawfish INFO Slurm invocation: srun --job-name call-run_sawfish --partition compute,compute9 --cpus-per-task 16 --mem 30518M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-41/call-run_sawfish/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-41/call-run_sawfish/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-41/call-run_sawfish/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-41/call-run_sawfish/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-41/out/m84036_250809_035451_s4.bc2138.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2138.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-41/out/m84036_250809_035451_s4.bc2138.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2138.mapped.bam.bai:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-41/call-run_sawfish/_singularity_tmpdir_knll2djc/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-41/call-run_sawfish/_singularity_tmpdir_knll2djc/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:34.934 wdl.w:ptcp.w:call-paraphase-36.t:call-call_f8 INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2133.f8inversion.vcf"
2025-09-15 20:24:34.936 wdl.w:ptcp.w:call-paraphase-40.t:call-run_paraphase NOTICE task setup :: name: "run_paraphase", source: "./paraphase.wdl", line: 127, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-40/call-run_paraphase", thread: 140608236680768
2025-09-15 20:24:34.939 wdl.w:ptcp.w:call-paraphase-41.t:call-run_paraphase INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-41/call-run_paraphase/_singularity_tmpdir_59vbnt9i"
2025-09-15 20:24:34.939 wdl.w:ptcp.w:call-paraphase-41.t:call-run_paraphase INFO Slurm invocation: srun --job-name call-run_paraphase --partition compute,compute9 --cpus-per-task 4 --mem 7629M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-41/call-run_paraphase/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-41/call-run_paraphase/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-41/call-run_paraphase/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-41/call-run_paraphase/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-41/out/m84036_250809_035451_s4.bc2138.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2138.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-41/out/m84036_250809_035451_s4.bc2138.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2138.mapped.bam.bai:ro --bind /ptcp/meta/variant_list/variant_list.GRCh38.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf:ro --bind /ptcp/meta/paraphase/paraphase_config.GRCh38.yaml:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/paraphase_config.GRCh38.yaml:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-41/call-run_paraphase/_singularity_tmpdir_59vbnt9i/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-41/call-run_paraphase/_singularity_tmpdir_59vbnt9i/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:34.940 wdl.w:ptcp.w:call-trgt-41.t:call-trgt_genotype INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:34.941 wdl.w:ptcp.w:call-paraphase-36.t:call-call_f8 INFO output :: name: "json", value: "m84036_250809_035451_s4.bc2133.f8inversion.json"
2025-09-15 20:24:34.941 wdl.w:ptcp.w:call-trgt-41.t:call-trgt_genotype INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:34.941 wdl.w:ptcp.w:call-trgt-41.t:call-trgt_genotype INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:34.941 wdl.w:ptcp.w:call-trgt-41.t:call-trgt_genotype INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:34.941 wdl.w:ptcp.w:call-trgt-41.t:call-trgt_genotype INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2138.mapped.bam.bai"
2025-09-15 20:24:34.942 wdl.w:ptcp.w:call-trgt-41.t:call-trgt_genotype INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2138.mapped.bam"
2025-09-15 20:24:34.942 wdl.w:ptcp.w:call-trgt-41.t:call-trgt_genotype INFO input :: name: "sex", value: "F"
2025-09-15 20:24:34.942 wdl.w:ptcp.w:call-trgt-41.t:call-trgt_genotype INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2138"
2025-09-15 20:24:34.942 wdl.w:ptcp.w:call-trgt-41.t:call-trgt_genotype INFO eval :: name: "mem_gb", value: 16
2025-09-15 20:24:34.942 wdl.w:ptcp.w:call-trgt-41.t:call-trgt_genotype INFO eval :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2138.trgt"
2025-09-15 20:24:34.942 wdl.w:ptcp.w:call-trgt-41.t:call-trgt_genotype INFO eval :: name: "threads", value: 8
2025-09-15 20:24:34.942 wdl.w:ptcp.w:call-trgt-41.t:call-trgt_genotype INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:34.942 wdl.w:ptcp.w:call-trgt-41.t:call-trgt_genotype INFO eval :: name: "karyotype", value: "XX"
2025-09-15 20:24:34.943 wdl.w:ptcp.w:call-trgt-41.t:call-trgt_genotype INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 8, memory_reservation: 16000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:34.943 wdl.w:ptcp.w:call-trgt-41.t:call-trgt_genotype WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:34.944 wdl.w:ptcp.w:call-trgt-41.t:call-trgt_genotype INFO provisioned :: seconds_waited: 0, cpu: 8, mem_bytes: 16000000000
2025-09-15 20:24:34.944 wdl.w:ptcp.w:call-trgt-41.t:call-trgt_genotype INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:34.953 wdl.w:ptcp.w:call-trgt-08.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:31 [ERROR] - No reads found for TRID=PRTS_ARX
2025-09-15 20:24:34.953 wdl.w:ptcp.w:call-trgt-08.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:31 [ERROR] - No reads found for TRID=EIEE1_ARX
2025-09-15 20:24:34.967 wdl.w:ptcp.w:call-paraphase-40.t:call-run_paraphase INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:34.967 wdl.w:ptcp.w:call-paraphase-40.t:call-run_paraphase INFO input :: name: "annotation_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf"
2025-09-15 20:24:34.967 wdl.w:ptcp.w:call-paraphase-40.t:call-run_paraphase INFO input :: name: "genome_version", value: "38"
2025-09-15 20:24:34.967 wdl.w:ptcp.w:call-paraphase-40.t:call-run_paraphase INFO input :: name: "config_file", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/paraphase_config.GRCh38.yaml"
2025-09-15 20:24:34.967 wdl.w:ptcp.w:call-paraphase-40.t:call-run_paraphase INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:34.967 wdl.w:ptcp.w:call-paraphase-40.t:call-run_paraphase INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:34.967 wdl.w:ptcp.w:call-paraphase-40.t:call-run_paraphase INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2137.mapped.bam.bai"
2025-09-15 20:24:34.967 wdl.w:ptcp.w:call-paraphase-40.t:call-run_paraphase INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2137.mapped.bam"
2025-09-15 20:24:34.967 wdl.w:ptcp.w:call-paraphase-40.t:call-run_paraphase INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2137"
2025-09-15 20:24:34.968 wdl.w:ptcp.w:call-paraphase-40.t:call-run_paraphase INFO eval :: name: "threads", value: 4
2025-09-15 20:24:34.968 wdl.w:ptcp.w:call-paraphase-40.t:call-run_paraphase INFO eval :: name: "mem_gb", value: 8
2025-09-15 20:24:34.968 wdl.w:ptcp.w:call-paraphase-40.t:call-run_paraphase INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:34.968 wdl.w:ptcp.w:call-paraphase-40.t:call-run_paraphase INFO eval :: name: "out_dir", value: "m84036_250809_035451_s4.bc2137_paraphase"
2025-09-15 20:24:34.968 wdl.w:ptcp.w:call-paraphase-40.t:call-run_paraphase INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 4, memory_reservation: 8000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:34.969 wdl.w:ptcp.w:call-paraphase-40.t:call-run_paraphase WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:34.969 wdl.w:ptcp.w:call-paraphase-40.t:call-run_paraphase INFO provisioned :: seconds_waited: 0, cpu: 4, mem_bytes: 8000000000
2025-09-15 20:24:34.969 wdl.w:ptcp.w:call-paraphase-40.t:call-run_paraphase INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:34.979 wdl.w:ptcp.w:call-sawfish-41.t:call-run_sawfish NOTICE slurm_singularity run :: pid: 1202322, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-41/call-run_sawfish/slurm_singularity.log.txt"
2025-09-15 20:24:34.979 wdl.w:ptcp.w:call-paraphase-41.t:call-run_paraphase NOTICE slurm_singularity run :: pid: 1202323, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-41/call-run_paraphase/slurm_singularity.log.txt"
2025-09-15 20:24:34.995 wdl.w:ptcp.w:call-trgt-41.t:call-get_reads_overlapping_repeats INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 9, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-41/call-get_reads_overlapping_repeats/_singularity_tmpdir_4lzhu811"
2025-09-15 20:24:34.996 wdl.w:ptcp.w:call-trgt-41.t:call-get_reads_overlapping_repeats INFO Slurm invocation: srun --job-name call-get_reads_overlapping_repeats --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-41/call-get_reads_overlapping_repeats/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-41/call-get_reads_overlapping_repeats/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-41/call-get_reads_overlapping_repeats/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-41/call-get_reads_overlapping_repeats/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-41/out/m84036_250809_035451_s4.bc2138.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2138.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-41/out/m84036_250809_035451_s4.bc2138.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2138.mapped.bam.bai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-41/call-get_reads_overlapping_repeats/_singularity_tmpdir_4lzhu811/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-41/call-get_reads_overlapping_repeats/_singularity_tmpdir_4lzhu811/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:35.018 wdl.w:ptcp.w:call-trgt-41.t:call-get_reads_overlapping_repeats NOTICE slurm_singularity run :: pid: 1202327, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-41/call-get_reads_overlapping_repeats/slurm_singularity.log.txt"
2025-09-15 20:24:35.028 wdl.w:ptcp.w:call-trgt-08.t:call-trgt_plot_motifs_allele INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2105.motifs_allele.trgt_plots.zip"
2025-09-15 20:24:35.037 wdl.w:ptcp.w:call-paraphase-36.t:call-call_f8 NOTICE done
2025-09-15 20:24:35.046 wdl.w:ptcp.w:call-trgt-41.t:call-trgt_genotype INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 11, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-41/call-trgt_genotype/_singularity_tmpdir_uzag4j80"
2025-09-15 20:24:35.046 wdl.w:ptcp.w:call-trgt-41.t:call-trgt_genotype INFO Slurm invocation: srun --job-name call-trgt_genotype --partition compute,compute9 --cpus-per-task 8 --mem 15259M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-41/call-trgt_genotype/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-41/call-trgt_genotype/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-41/call-trgt_genotype/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-41/call-trgt_genotype/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-41/out/m84036_250809_035451_s4.bc2138.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2138.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-41/out/m84036_250809_035451_s4.bc2138.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2138.mapped.bam.bai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-41/call-trgt_genotype/_singularity_tmpdir_uzag4j80/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-41/call-trgt_genotype/_singularity_tmpdir_uzag4j80/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:35.049 wdl.w:ptcp.w:call-paraphase-36 NOTICE finish :: job: "call-call_f8"
2025-09-15 20:24:35.050 wdl.w:ptcp.w:call-paraphase-36 INFO output :: job: "call-call_f8", values: {"json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-36/call-call_f8/out/m84036_250809_035451_s4.bc2133.f8inversion.json", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-36/call-call_f8/out/m84036_250809_035451_s4.bc2133.f8inversion.vcf"}
2025-09-15 20:24:35.050 wdl.w:ptcp.w:call-paraphase-36 INFO visit :: node: "output-f8_json", values: {"f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-36/call-call_f8/out/m84036_250809_035451_s4.bc2133.f8inversion.json"}
2025-09-15 20:24:35.050 wdl.w:ptcp.w:call-paraphase-36 INFO visit :: node: "output-f8_vcf", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-36/call-call_f8/out/m84036_250809_035451_s4.bc2133.f8inversion.vcf"}
2025-09-15 20:24:35.050 wdl.w:ptcp.w:call-paraphase-36 INFO visit :: node: "outputs", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-36/call-call_f8/out/m84036_250809_035451_s4.bc2133.f8inversion.vcf", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-36/call-run_paraphase/out/m84036_250809_035451_s4.bc2133_paraphase/m84036_250809_035451_s4.bc2133.paraphase.json", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-36/call-run_paraphase/out/m84036_250809_035451_s4.bc2133_paraphase/m84036_250809_035451_s4.bc2133.paraphase.bam", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-36/call-run_paraphase/out/m84036_250809_035451_s4.bc2133_paraphase/m84036_250809_035451_s4.bc2133.paraphase.bam.bai", "paraphase_vcfs": [], "havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-36/call-run_paraphase/out/m84036_250809_035451_s4.bc2133.havanno.json", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-36/call-call_f8/out/m84036_250809_035451_s4.bc2133.f8inversion.json"}
2025-09-15 20:24:35.053 wdl.w:ptcp.w:call-trgt-36 NOTICE done
2025-09-15 20:24:35.058 wdl.w:ptcp NOTICE finish :: job: "call-trgt-36"
2025-09-15 20:24:35.058 wdl.w:ptcp INFO output :: job: "call-trgt-36", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-36/out/m84036_250809_035451_s4.bc2133.motifs_waterfall.trgt_plots.zip", "images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-36/out/m84036_250809_035451_s4.bc2133.meth_allele.trgt_plots.zip", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-36/out/m84036_250809_035451_s4.bc2133.trgt.sorted.spanning.bam.bai", "images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-36/out/m84036_250809_035451_s4.bc2133.motifs_allele.trgt_plots.zip", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-36/out/m84036_250809_035451_s4.bc2133.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-36/out/m84036_250809_035451_s4.bc2133.trgt.vcf", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-36/out/m84036_250809_035451_s4.bc2133.repeats.bam", "images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-36/out/m84036_250809_035451_s4.bc2133.meth_waterfall.trgt_plots.zip", "reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-36/out/m84036_250809_035451_s4.bc2133.repeats.bam.bai"}
2025-09-15 20:24:35.060 wdl.w:ptcp.w:call-sawfish-40.t:call-run_sawfish NOTICE task setup :: name: "run_sawfish", source: "./sawfish.wdl", line: 83, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-40/call-run_sawfish", thread: 140608748373568
2025-09-15 20:24:35.062 wdl.w:ptcp.w:call-sawfish-01.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:29][sawfish][INFO] Starting sawfish 2.0.3
2025-09-15 20:24:35.062 wdl.w:ptcp.w:call-sawfish-01.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:29][sawfish][INFO] cmdline: sawfish discover --disable-cnv --threads 16 --ref /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa --bam m84036_250809_035451_s4.bc2098.minimap2.bam --output-dir m84036_250809_035451_s4.bc2098_sawfish_discover
2025-09-15 20:24:35.062 wdl.w:ptcp.w:call-sawfish-01.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:29][sawfish][INFO] Running on 16 threads
2025-09-15 20:24:35.062 wdl.w:ptcp.w:call-sawfish-01.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:29][sawfish][INFO] Writing discover settings to file: 'm84036_250809_035451_s4.bc2098_sawfish_discover/discover.settings.json'
2025-09-15 20:24:35.062 wdl.w:ptcp.w:call-sawfish-01.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:29][sawfish][INFO] Reading reference genome from file '/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa'
2025-09-15 20:24:35.062 wdl.w:ptcp.w:call-sawfish-01.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:33][sawfish][INFO] Processing alignment file '/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2098.minimap2.bam'
2025-09-15 20:24:35.062 wdl.w:ptcp.w:call-sawfish-01.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:33][sawfish][INFO] Finished processing all alignments
2025-09-15 20:24:35.062 wdl.w:ptcp.w:call-sawfish-01.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:33][sawfish][INFO] Writing depth bins to binary file: 'm84036_250809_035451_s4.bc2098_sawfish_discover/depth.mpack'
2025-09-15 20:24:35.062 wdl.w:ptcp.w:call-sawfish-01.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:33][sawfish][INFO] Writing max sv depth genome regions to bed file: 'm84036_250809_035451_s4.bc2098_sawfish_discover/max.depth.bed'
2025-09-15 20:24:35.062 wdl.w:ptcp.w:call-sawfish-01.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:33][sawfish][INFO] Completing breakpoint observation clustering
2025-09-15 20:24:35.062 wdl.w:ptcp.w:call-sawfish-01.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:33][sawfish][INFO] Finished breakpoint observation clustering
2025-09-15 20:24:35.062 wdl.w:ptcp.w:call-sawfish-01.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:33][sawfish][INFO] Consolidating adjacent indel candidates
2025-09-15 20:24:35.063 wdl.w:ptcp.w:call-sawfish-01.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:33][sawfish][INFO] Finding large insertion candidates
2025-09-15 20:24:35.063 wdl.w:ptcp.w:call-sawfish-01.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:33][sawfish][INFO] Writing breakpoint_cluster debug bed file: 'm84036_250809_035451_s4.bc2098_sawfish_discover/debug.breakpoint_clusters.bed'
2025-09-15 20:24:35.063 wdl.w:ptcp.w:call-sawfish-01.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:33][sawfish][INFO] Refining SV Candidates
2025-09-15 20:24:35.063 wdl.w:ptcp.w:call-sawfish-01.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:33][sawfish][INFO] Writing debug assembly region bed file: 'm84036_250809_035451_s4.bc2098_sawfish_discover/assembly.regions.bed'
2025-09-15 20:24:35.063 wdl.w:ptcp.w:call-sawfish-01.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:33][sawfish][INFO] Starting refinement of breakpoint evidence clusters
2025-09-15 20:24:35.063 wdl.w:ptcp.w:call-sawfish-01.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:33][sawfish][INFO] Finished refining all breakpoint evidence clusters
2025-09-15 20:24:35.063 wdl.w:ptcp.w:call-sawfish-01.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:33][sawfish][INFO] Writing all contig alignments to bam file: 'm84036_250809_035451_s4.bc2098_sawfish_discover/contig.alignment.bam'
2025-09-15 20:24:35.063 wdl.w:ptcp.w:call-sawfish-01.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:33][sawfish][INFO] Writing candidate structural variants to file: 'm84036_250809_035451_s4.bc2098_sawfish_discover/candidate.sv.bcf'
2025-09-15 20:24:35.063 wdl.w:ptcp.w:call-sawfish-01.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:33][sawfish][INFO] Writing run statistics to file: 'm84036_250809_035451_s4.bc2098_sawfish_discover/run.stats.json'
2025-09-15 20:24:35.063 wdl.w:ptcp.w:call-sawfish-01.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:33][sawfish][INFO] sawfish completed. Total Runtime: 00:00:03.742
2025-09-15 20:24:35.066 wdl.w:ptcp.w:call-trgt-41.t:call-trgt_genotype NOTICE slurm_singularity run :: pid: 1202329, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-41/call-trgt_genotype/slurm_singularity.log.txt"
2025-09-15 20:24:35.068 wdl.w:ptcp.w:call-paraphase-35.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for hbb for sample m84036_250809_035451_s4.bc2132 at 2025-09-15 20:24:25.031502...
2025-09-15 20:24:35.068 wdl.w:ptcp.w:call-sawfish-61 NOTICE workflow start :: name: "sawfish", source: "./sawfish.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-61"
2025-09-15 20:24:35.073 wdl.w:ptcp.w:call-paraphase-40.t:call-run_paraphase INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-40/call-run_paraphase/_singularity_tmpdir_tc0r7q6z"
2025-09-15 20:24:35.073 wdl.w:ptcp.w:call-paraphase-40.t:call-run_paraphase INFO Slurm invocation: srun --job-name call-run_paraphase --partition compute,compute9 --cpus-per-task 4 --mem 7629M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-40/call-run_paraphase/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-40/call-run_paraphase/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-40/call-run_paraphase/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-40/call-run_paraphase/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-40/out/m84036_250809_035451_s4.bc2137.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2137.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-40/out/m84036_250809_035451_s4.bc2137.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2137.mapped.bam.bai:ro --bind /ptcp/meta/variant_list/variant_list.GRCh38.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf:ro --bind /ptcp/meta/paraphase/paraphase_config.GRCh38.yaml:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/paraphase_config.GRCh38.yaml:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-40/call-run_paraphase/_singularity_tmpdir_tc0r7q6z/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-40/call-run_paraphase/_singularity_tmpdir_tc0r7q6z/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:35.081 wdl.w:ptcp.w:call-sawfish-40.t:call-run_sawfish INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:35.082 wdl.w:ptcp.w:call-sawfish-40.t:call-run_sawfish INFO input :: name: "genome_version", value: "38"
2025-09-15 20:24:35.083 wdl.w:ptcp.w:call-sawfish-40.t:call-run_sawfish INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:35.083 wdl.w:ptcp.w:call-sawfish-40.t:call-run_sawfish INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:35.083 wdl.w:ptcp.w:call-sawfish-40.t:call-run_sawfish INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2137.mapped.bam.bai"
2025-09-15 20:24:35.083 wdl.w:ptcp.w:call-sawfish-40.t:call-run_sawfish INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2137.mapped.bam"
2025-09-15 20:24:35.083 wdl.w:ptcp.w:call-sawfish-40.t:call-run_sawfish INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2137"
2025-09-15 20:24:35.084 wdl.w:ptcp.w:call-sawfish-40.t:call-run_sawfish INFO eval :: name: "mem_gb", value: 32
2025-09-15 20:24:35.084 wdl.w:ptcp.w:call-sawfish-40.t:call-run_sawfish INFO eval :: name: "threads", value: 16
2025-09-15 20:24:35.084 wdl.w:ptcp.w:call-sawfish-40.t:call-run_sawfish INFO eval :: name: "disk_size", value: 30
2025-09-15 20:24:35.085 wdl.w:ptcp.w:call-sawfish-40.t:call-run_sawfish INFO eval :: name: "discover_dirname", value: "m84036_250809_035451_s4.bc2137_sawfish_discover"
2025-09-15 20:24:35.085 wdl.w:ptcp.w:call-sawfish-40.t:call-run_sawfish INFO eval :: name: "call_dirname", value: "m84036_250809_035451_s4.bc2137_sawfish"
2025-09-15 20:24:35.085 wdl.w:ptcp.w:call-sawfish-40.t:call-run_sawfish INFO eval :: name: "minimap2_bam_filename", value: "m84036_250809_035451_s4.bc2137.minimap2.bam"
2025-09-15 20:24:35.086 wdl.w:ptcp.w:call-sawfish-40.t:call-run_sawfish INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 16, memory_reservation: 32000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:35.087 wdl.w:ptcp.w:call-sawfish-40.t:call-run_sawfish WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:35.087 wdl.w:ptcp.w:call-paraphase-39.t:call-run_paraphase.slurm_singularity INFO srun: job 51797697 queued and waiting for resources
2025-09-15 20:24:35.087 wdl.w:ptcp.w:call-sawfish-40.t:call-run_sawfish INFO provisioned :: seconds_waited: 0, cpu: 16, mem_bytes: 32000000000
2025-09-15 20:24:35.088 wdl.w:ptcp.w:call-paraphase-39.t:call-run_paraphase.slurm_singularity INFO srun: job 51797697 has been allocated resources
2025-09-15 20:24:35.088 wdl.w:ptcp.w:call-sawfish-40.t:call-run_sawfish INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:35.088 wdl.w:ptcp.w:call-sawfish-61 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:24:35.088 wdl.w:ptcp.w:call-paraphase-39.t:call-run_paraphase.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:35.089 wdl.w:ptcp.w:call-sawfish-61 INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:24:35.089 wdl.w:ptcp.w:call-sawfish-61 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-61/out/m84036_250809_035451_s4.bc2158.mapped.bam"}
2025-09-15 20:24:35.089 wdl.w:ptcp.w:call-sawfish-61 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-61/out/m84036_250809_035451_s4.bc2158.mapped.bam.bai"}
2025-09-15 20:24:35.089 wdl.w:ptcp.w:call-sawfish-61 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:24:35.089 wdl.w:ptcp.w:call-sawfish-61 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:24:35.089 wdl.w:ptcp.w:call-sawfish-61 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2158"}
2025-09-15 20:24:35.089 wdl.w:ptcp.w:call-sawfish-61 NOTICE ready :: job: "call-run_sawfish", callee: "run_sawfish"
2025-09-15 20:24:35.089 wdl.w:ptcp.w:call-sawfish-61 INFO input :: job: "call-run_sawfish", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-61/out/m84036_250809_035451_s4.bc2158.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-61/out/m84036_250809_035451_s4.bc2158.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2158"}
2025-09-15 20:24:35.091 wdl.w:ptcp.w:call-sawfish-39.t:call-run_sawfish.slurm_singularity INFO srun: job 51797698 queued and waiting for resources
2025-09-15 20:24:35.091 wdl.w:ptcp.w:call-sawfish-39.t:call-run_sawfish.slurm_singularity INFO srun: job 51797698 has been allocated resources
2025-09-15 20:24:35.091 wdl.w:ptcp.w:call-sawfish-39.t:call-run_sawfish.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:35.100 wdl.w:ptcp.w:call-paraphase-40.t:call-run_paraphase NOTICE slurm_singularity run :: pid: 1202331, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-40/call-run_paraphase/slurm_singularity.log.txt"
2025-09-15 20:24:35.148 wdl.w:ptcp.w:call-paraphase-36 NOTICE done
2025-09-15 20:24:35.154 wdl.w:ptcp NOTICE finish :: job: "call-paraphase-36"
2025-09-15 20:24:35.155 wdl.w:ptcp INFO output :: job: "call-paraphase-36", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-36/out/m84036_250809_035451_s4.bc2133.f8inversion.vcf", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-36/out/m84036_250809_035451_s4.bc2133_paraphase/m84036_250809_035451_s4.bc2133.paraphase.json", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-36/out/m84036_250809_035451_s4.bc2133_paraphase/m84036_250809_035451_s4.bc2133.paraphase.bam", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-36/out/m84036_250809_035451_s4.bc2133_paraphase/m84036_250809_035451_s4.bc2133.paraphase.bam.bai", "paraphase_vcfs": [], "havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-36/out/m84036_250809_035451_s4.bc2133.havanno.json", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-36/out/m84036_250809_035451_s4.bc2133.f8inversion.json"}
2025-09-15 20:24:35.157 wdl.w:ptcp.w:call-sawfish-40.t:call-run_sawfish INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 10, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-40/call-run_sawfish/_singularity_tmpdir_fw5bdqp7"
2025-09-15 20:24:35.157 wdl.w:ptcp.w:call-sawfish-40.t:call-run_sawfish INFO Slurm invocation: srun --job-name call-run_sawfish --partition compute,compute9 --cpus-per-task 16 --mem 30518M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-40/call-run_sawfish/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-40/call-run_sawfish/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-40/call-run_sawfish/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-40/call-run_sawfish/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-40/out/m84036_250809_035451_s4.bc2137.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2137.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-40/out/m84036_250809_035451_s4.bc2137.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2137.mapped.bam.bai:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-40/call-run_sawfish/_singularity_tmpdir_fw5bdqp7/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-40/call-run_sawfish/_singularity_tmpdir_fw5bdqp7/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:35.160 wdl.w:ptcp.w:call-trgt-61 NOTICE workflow start :: name: "trgt", source: "./trgt.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-61"
2025-09-15 20:24:35.176 wdl.w:ptcp.w:call-trgt-61 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:24:35.176 wdl.w:ptcp.w:call-trgt-61 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-61/out/m84036_250809_035451_s4.bc2158.mapped.bam"}
2025-09-15 20:24:35.176 wdl.w:ptcp.w:call-sawfish-40.t:call-run_sawfish NOTICE slurm_singularity run :: pid: 1202333, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-40/call-run_sawfish/slurm_singularity.log.txt"
2025-09-15 20:24:35.176 wdl.w:ptcp.w:call-trgt-61 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-61/out/m84036_250809_035451_s4.bc2158.mapped.bam.bai"}
2025-09-15 20:24:35.177 wdl.w:ptcp.w:call-trgt-61 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:24:35.177 wdl.w:ptcp.w:call-trgt-61 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:24:35.177 wdl.w:ptcp.w:call-trgt-61 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2158"}
2025-09-15 20:24:35.177 wdl.w:ptcp.w:call-trgt-61 INFO visit :: node: "decl-sex", values: {"sex": "F"}
2025-09-15 20:24:35.177 wdl.w:ptcp.w:call-trgt-61 INFO visit :: node: "decl-trgt_bed", values: {"trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"}
2025-09-15 20:24:35.177 wdl.w:ptcp.w:call-trgt-61 NOTICE ready :: job: "call-get_reads_overlapping_repeats", callee: "get_reads_overlapping_repeats"
2025-09-15 20:24:35.177 wdl.w:ptcp.w:call-trgt-61 INFO input :: job: "call-get_reads_overlapping_repeats", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-61/out/m84036_250809_035451_s4.bc2158.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-61/out/m84036_250809_035451_s4.bc2158.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2158"}
2025-09-15 20:24:35.178 wdl.w:ptcp.w:call-trgt-61 NOTICE ready :: job: "call-trgt_genotype", callee: "trgt_genotype"
2025-09-15 20:24:35.178 wdl.w:ptcp.w:call-trgt-61 INFO input :: job: "call-trgt_genotype", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-61/out/m84036_250809_035451_s4.bc2158.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-61/out/m84036_250809_035451_s4.bc2158.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2158"}
2025-09-15 20:24:35.181 wdl.w:ptcp.w:call-trgt-08.t:call-trgt_plot_motifs_allele NOTICE done
2025-09-15 20:24:35.186 wdl.w:ptcp.w:call-trgt-08 NOTICE finish :: job: "call-trgt_plot_motifs_allele"
2025-09-15 20:24:35.186 wdl.w:ptcp.w:call-trgt-08 INFO output :: job: "call-trgt_plot_motifs_allele", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-08/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2105.motifs_allele.trgt_plots.zip"}
2025-09-15 20:24:35.186 wdl.w:ptcp.w:call-trgt-08 INFO visit :: node: "output-images_motifs_allele", values: {"images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-08/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2105.motifs_allele.trgt_plots.zip"}
2025-09-15 20:24:35.191 wdl.w:ptcp.w:call-trgt-40.t:call-get_reads_overlapping_repeats NOTICE task setup :: name: "get_reads_overlapping_repeats", source: "./trgt.wdl", line: 182, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-40/call-get_reads_overlapping_repeats", thread: 140607649453632
2025-09-15 20:24:35.209 wdl.w:ptcp.w:call-trgt-40.t:call-get_reads_overlapping_repeats INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:35.209 wdl.w:ptcp.w:call-trgt-40.t:call-get_reads_overlapping_repeats INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:35.209 wdl.w:ptcp.w:call-trgt-40.t:call-get_reads_overlapping_repeats INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2137.mapped.bam.bai"
2025-09-15 20:24:35.209 wdl.w:ptcp.w:call-trgt-40.t:call-get_reads_overlapping_repeats INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2137.mapped.bam"
2025-09-15 20:24:35.209 wdl.w:ptcp.w:call-trgt-40.t:call-get_reads_overlapping_repeats INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2137"
2025-09-15 20:24:35.210 wdl.w:ptcp.w:call-trgt-40.t:call-get_reads_overlapping_repeats INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:35.210 wdl.w:ptcp.w:call-trgt-40.t:call-get_reads_overlapping_repeats INFO eval :: name: "expand_size", value: 3000
2025-09-15 20:24:35.210 wdl.w:ptcp.w:call-trgt-40.t:call-get_reads_overlapping_repeats INFO eval :: name: "threads", value: 1
2025-09-15 20:24:35.210 wdl.w:ptcp.w:call-trgt-40.t:call-get_reads_overlapping_repeats INFO eval :: name: "expanded_bed_name", value: "m84036_250809_035451_s4.bc2137.expanded.bed"
2025-09-15 20:24:35.210 wdl.w:ptcp.w:call-trgt-40.t:call-get_reads_overlapping_repeats INFO eval :: name: "disk_size", value: 11
2025-09-15 20:24:35.210 wdl.w:ptcp.w:call-trgt-40.t:call-get_reads_overlapping_repeats INFO eval :: name: "output_name", value: "m84036_250809_035451_s4.bc2137.repeats.bam"
2025-09-15 20:24:35.211 wdl.w:ptcp.w:call-trgt-40.t:call-get_reads_overlapping_repeats INFO eval :: name: "index_name", value: "m84036_250809_035451_s4.bc2137.repeats.bam.bai"
2025-09-15 20:24:35.211 wdl.w:ptcp.w:call-trgt-40.t:call-get_reads_overlapping_repeats INFO eval :: name: "output_name_with_index", value: "m84036_250809_035451_s4.bc2137.repeats.bam##idx##m84036_250809_035451_s4.bc2137.repeats.bam.bai"
2025-09-15 20:24:35.211 wdl.w:ptcp.w:call-trgt-40.t:call-get_reads_overlapping_repeats INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:35.211 wdl.w:ptcp.w:call-trgt-40.t:call-get_reads_overlapping_repeats WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:35.211 wdl.w:ptcp.w:call-trgt-40.t:call-get_reads_overlapping_repeats INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:35.212 wdl.w:ptcp.w:call-trgt-40.t:call-get_reads_overlapping_repeats INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:35.255 wdl.w:ptcp.w:call-paraphase-45.t:call-call_f8 INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2142.f8inversion.vcf"
2025-09-15 20:24:35.259 wdl.w:ptcp.w:call-paraphase-45.t:call-call_f8 INFO output :: name: "json", value: "m84036_250809_035451_s4.bc2142.f8inversion.json"
2025-09-15 20:24:35.266 wdl.w:ptcp.w:call-trgt-40.t:call-get_reads_overlapping_repeats INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 9, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-40/call-get_reads_overlapping_repeats/_singularity_tmpdir_3qdxmwy1"
2025-09-15 20:24:35.266 wdl.w:ptcp.w:call-trgt-40.t:call-get_reads_overlapping_repeats INFO Slurm invocation: srun --job-name call-get_reads_overlapping_repeats --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-40/call-get_reads_overlapping_repeats/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-40/call-get_reads_overlapping_repeats/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-40/call-get_reads_overlapping_repeats/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-40/call-get_reads_overlapping_repeats/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-40/out/m84036_250809_035451_s4.bc2137.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2137.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-40/out/m84036_250809_035451_s4.bc2137.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2137.mapped.bam.bai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-40/call-get_reads_overlapping_repeats/_singularity_tmpdir_3qdxmwy1/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-40/call-get_reads_overlapping_repeats/_singularity_tmpdir_3qdxmwy1/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:35.285 wdl.w:ptcp.w:call-trgt-40.t:call-get_reads_overlapping_repeats NOTICE slurm_singularity run :: pid: 1202366, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-40/call-get_reads_overlapping_repeats/slurm_singularity.log.txt"
2025-09-15 20:24:35.305 wdl.w:ptcp.w:call-paraphase-44.t:call-call_f8.slurm_singularity INFO srun: job 51797699 queued and waiting for resources
2025-09-15 20:24:35.305 wdl.w:ptcp.w:call-paraphase-44.t:call-call_f8.slurm_singularity INFO srun: job 51797699 has been allocated resources
2025-09-15 20:24:35.305 wdl.w:ptcp.w:call-paraphase-44.t:call-call_f8.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:35.308 wdl.w:ptcp.w:call-trgt-08.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:33 [ERROR] - No reads found for TRID=PRTS_ARX
2025-09-15 20:24:35.308 wdl.w:ptcp.w:call-trgt-08.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:33 [ERROR] - No reads found for TRID=EIEE1_ARX
2025-09-15 20:24:35.323 wdl.w:ptcp.w:call-paraphase-45.t:call-call_f8 NOTICE done
2025-09-15 20:24:35.338 wdl.w:ptcp.w:call-paraphase-45 NOTICE finish :: job: "call-call_f8"
2025-09-15 20:24:35.339 wdl.w:ptcp.w:call-paraphase-45 INFO output :: job: "call-call_f8", values: {"json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-45/call-call_f8/out/m84036_250809_035451_s4.bc2142.f8inversion.json", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-45/call-call_f8/out/m84036_250809_035451_s4.bc2142.f8inversion.vcf"}
2025-09-15 20:24:35.340 wdl.w:ptcp.w:call-paraphase-45 INFO visit :: node: "output-f8_json", values: {"f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-45/call-call_f8/out/m84036_250809_035451_s4.bc2142.f8inversion.json"}
2025-09-15 20:24:35.341 wdl.w:ptcp.w:call-paraphase-45 INFO visit :: node: "output-f8_vcf", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-45/call-call_f8/out/m84036_250809_035451_s4.bc2142.f8inversion.vcf"}
2025-09-15 20:24:35.341 wdl.w:ptcp.w:call-paraphase-45 INFO visit :: node: "outputs", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-45/call-call_f8/out/m84036_250809_035451_s4.bc2142.f8inversion.vcf", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-45/call-run_paraphase/out/m84036_250809_035451_s4.bc2142_paraphase/m84036_250809_035451_s4.bc2142.paraphase.json", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-45/call-run_paraphase/out/m84036_250809_035451_s4.bc2142_paraphase/m84036_250809_035451_s4.bc2142.paraphase.bam", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-45/call-run_paraphase/out/m84036_250809_035451_s4.bc2142_paraphase/m84036_250809_035451_s4.bc2142.paraphase.bam.bai", "paraphase_vcfs": [], "havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-45/call-run_paraphase/out/m84036_250809_035451_s4.bc2142.havanno.json", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-45/call-call_f8/out/m84036_250809_035451_s4.bc2142.f8inversion.json"}
2025-09-15 20:24:35.351 wdl.w:ptcp.w:call-trgt-40.t:call-trgt_genotype NOTICE task setup :: name: "trgt_genotype", source: "./trgt.wdl", line: 272, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-40/call-trgt_genotype", thread: 140607683024448
2025-09-15 20:24:35.365 wdl.w:ptcp.w:call-trgt-39.t:call-get_reads_overlapping_repeats.slurm_singularity INFO srun: job 51797700 queued and waiting for resources
2025-09-15 20:24:35.365 wdl.w:ptcp.w:call-trgt-39.t:call-get_reads_overlapping_repeats.slurm_singularity INFO srun: job 51797700 has been allocated resources
2025-09-15 20:24:35.365 wdl.w:ptcp.w:call-trgt-39.t:call-get_reads_overlapping_repeats.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:35.376 wdl.w:ptcp.w:call-trgt-40.t:call-trgt_genotype INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:35.376 wdl.w:ptcp.w:call-trgt-40.t:call-trgt_genotype INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:35.376 wdl.w:ptcp.w:call-trgt-40.t:call-trgt_genotype INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:35.376 wdl.w:ptcp.w:call-trgt-40.t:call-trgt_genotype INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:35.376 wdl.w:ptcp.w:call-trgt-40.t:call-trgt_genotype INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2137.mapped.bam.bai"
2025-09-15 20:24:35.376 wdl.w:ptcp.w:call-trgt-40.t:call-trgt_genotype INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2137.mapped.bam"
2025-09-15 20:24:35.376 wdl.w:ptcp.w:call-trgt-40.t:call-trgt_genotype INFO input :: name: "sex", value: "F"
2025-09-15 20:24:35.376 wdl.w:ptcp.w:call-trgt-40.t:call-trgt_genotype INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2137"
2025-09-15 20:24:35.377 wdl.w:ptcp.w:call-trgt-40.t:call-trgt_genotype INFO eval :: name: "mem_gb", value: 16
2025-09-15 20:24:35.377 wdl.w:ptcp.w:call-trgt-40.t:call-trgt_genotype INFO eval :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2137.trgt"
2025-09-15 20:24:35.377 wdl.w:ptcp.w:call-trgt-40.t:call-trgt_genotype INFO eval :: name: "threads", value: 8
2025-09-15 20:24:35.377 wdl.w:ptcp.w:call-trgt-40.t:call-trgt_genotype INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:35.377 wdl.w:ptcp.w:call-trgt-40.t:call-trgt_genotype INFO eval :: name: "karyotype", value: "XX"
2025-09-15 20:24:35.378 wdl.w:ptcp.w:call-trgt-40.t:call-trgt_genotype INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 8, memory_reservation: 16000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:35.378 wdl.w:ptcp.w:call-trgt-40.t:call-trgt_genotype WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:35.378 wdl.w:ptcp.w:call-trgt-40.t:call-trgt_genotype INFO provisioned :: seconds_waited: 0, cpu: 8, mem_bytes: 16000000000
2025-09-15 20:24:35.378 wdl.w:ptcp.w:call-trgt-40.t:call-trgt_genotype INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:35.402 wdl.w:ptcp.w:call-trgt-39.t:call-get_reads_overlapping_repeats INFO output :: name: "reads_overlapping_repeats", value: "m84036_250809_035451_s4.bc2136.repeats.bam"
2025-09-15 20:24:35.406 wdl.w:ptcp.w:call-trgt-39.t:call-get_reads_overlapping_repeats INFO output :: name: "reads_overlapping_repeats_bai", value: "m84036_250809_035451_s4.bc2136.repeats.bam.bai"
2025-09-15 20:24:35.413 wdl.w:ptcp.w:call-paraphase-45 NOTICE done
2025-09-15 20:24:35.419 wdl.w:ptcp NOTICE finish :: job: "call-paraphase-45"
2025-09-15 20:24:35.419 wdl.w:ptcp INFO output :: job: "call-paraphase-45", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-45/out/m84036_250809_035451_s4.bc2142.f8inversion.vcf", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-45/out/m84036_250809_035451_s4.bc2142_paraphase/m84036_250809_035451_s4.bc2142.paraphase.json", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-45/out/m84036_250809_035451_s4.bc2142_paraphase/m84036_250809_035451_s4.bc2142.paraphase.bam", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-45/out/m84036_250809_035451_s4.bc2142_paraphase/m84036_250809_035451_s4.bc2142.paraphase.bam.bai", "paraphase_vcfs": [], "havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-45/out/m84036_250809_035451_s4.bc2142.havanno.json", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-45/out/m84036_250809_035451_s4.bc2142.f8inversion.json"}
2025-09-15 20:24:35.427 wdl.w:ptcp.w:call-paraphase-67 NOTICE workflow start :: name: "paraphase", source: "./paraphase.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-67"
2025-09-15 20:24:35.430 wdl.w:ptcp.w:call-paraphase-37.t:call-call_f8 INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2134.f8inversion.vcf"
2025-09-15 20:24:35.434 wdl.w:ptcp.w:call-paraphase-37.t:call-call_f8 INFO output :: name: "json", value: "m84036_250809_035451_s4.bc2134.f8inversion.json"
2025-09-15 20:24:35.442 wdl.w:ptcp.w:call-paraphase-67 INFO visit :: node: "decl-annotation_vcf", values: {"annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf"}
2025-09-15 20:24:35.442 wdl.w:ptcp.w:call-paraphase-67 INFO visit :: node: "decl-config_file", values: {"config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml"}
2025-09-15 20:24:35.442 wdl.w:ptcp.w:call-paraphase-67 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:24:35.442 wdl.w:ptcp.w:call-paraphase-67 INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:24:35.443 wdl.w:ptcp.w:call-paraphase-67 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-67/out/m84036_250809_035451_s4.bc2164.mapped.bam"}
2025-09-15 20:24:35.443 wdl.w:ptcp.w:call-paraphase-67 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-67/out/m84036_250809_035451_s4.bc2164.mapped.bam.bai"}
2025-09-15 20:24:35.443 wdl.w:ptcp.w:call-paraphase-67 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:24:35.443 wdl.w:ptcp.w:call-paraphase-67 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:24:35.443 wdl.w:ptcp.w:call-paraphase-67 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2164"}
2025-09-15 20:24:35.443 wdl.w:ptcp.w:call-paraphase-67 INFO visit :: node: "decl-sex", values: {"sex": "F"}
2025-09-15 20:24:35.443 wdl.w:ptcp.w:call-paraphase-67 NOTICE ready :: job: "call-run_paraphase", callee: "run_paraphase"
2025-09-15 20:24:35.443 wdl.w:ptcp.w:call-paraphase-67 INFO input :: job: "call-run_paraphase", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf", "genome_version": "38", "config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-67/out/m84036_250809_035451_s4.bc2164.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-67/out/m84036_250809_035451_s4.bc2164.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2164"}
2025-09-15 20:24:35.453 wdl.w:ptcp.w:call-trgt-40.t:call-trgt_genotype INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 11, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-40/call-trgt_genotype/_singularity_tmpdir_obxw3d5a"
2025-09-15 20:24:35.454 wdl.w:ptcp.w:call-trgt-40.t:call-trgt_genotype INFO Slurm invocation: srun --job-name call-trgt_genotype --partition compute,compute9 --cpus-per-task 8 --mem 15259M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-40/call-trgt_genotype/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-40/call-trgt_genotype/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-40/call-trgt_genotype/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-40/call-trgt_genotype/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-40/out/m84036_250809_035451_s4.bc2137.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2137.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-40/out/m84036_250809_035451_s4.bc2137.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2137.mapped.bam.bai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-40/call-trgt_genotype/_singularity_tmpdir_obxw3d5a/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-40/call-trgt_genotype/_singularity_tmpdir_obxw3d5a/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:35.487 wdl.w:ptcp.w:call-trgt-39.t:call-get_reads_overlapping_repeats NOTICE done
2025-09-15 20:24:35.492 wdl.w:ptcp.w:call-trgt-39 NOTICE finish :: job: "call-get_reads_overlapping_repeats"
2025-09-15 20:24:35.492 wdl.w:ptcp.w:call-trgt-39 INFO output :: job: "call-get_reads_overlapping_repeats", values: {"reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-39/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2136.repeats.bam.bai", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-39/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2136.repeats.bam"}
2025-09-15 20:24:35.492 wdl.w:ptcp.w:call-trgt-40.t:call-trgt_genotype NOTICE slurm_singularity run :: pid: 1202377, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-40/call-trgt_genotype/slurm_singularity.log.txt"
2025-09-15 20:24:35.493 wdl.w:ptcp.w:call-trgt-39 INFO visit :: node: "output-reads_overlapping_repeats", values: {"reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-39/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2136.repeats.bam"}
2025-09-15 20:24:35.493 wdl.w:ptcp.w:call-trgt-39 INFO visit :: node: "output-reads_overlapping_repeats_bai", values: {"reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-39/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2136.repeats.bam.bai"}
2025-09-15 20:24:35.502 wdl.w:ptcp.w:call-paraphase-62.t:call-run_paraphase NOTICE task setup :: name: "run_paraphase", source: "./paraphase.wdl", line: 127, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-62/call-run_paraphase", thread: 140606617675328
2025-09-15 20:24:35.505 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_motifs_allele INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2148.motifs_allele.trgt_plots.zip"
2025-09-15 20:24:35.511 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_motifs_waterfall INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2148.motifs_waterfall.trgt_plots.zip"
2025-09-15 20:24:35.517 wdl.w:ptcp.w:call-paraphase-37.t:call-call_f8 NOTICE done
2025-09-15 20:24:35.535 wdl.w:ptcp.w:call-paraphase-62.t:call-run_paraphase INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:35.535 wdl.w:ptcp.w:call-paraphase-62.t:call-run_paraphase INFO input :: name: "annotation_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf"
2025-09-15 20:24:35.535 wdl.w:ptcp.w:call-paraphase-62.t:call-run_paraphase INFO input :: name: "genome_version", value: "38"
2025-09-15 20:24:35.536 wdl.w:ptcp.w:call-paraphase-62.t:call-run_paraphase INFO input :: name: "config_file", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/paraphase_config.GRCh38.yaml"
2025-09-15 20:24:35.536 wdl.w:ptcp.w:call-paraphase-62.t:call-run_paraphase INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:35.536 wdl.w:ptcp.w:call-paraphase-62.t:call-run_paraphase INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:35.536 wdl.w:ptcp.w:call-paraphase-62.t:call-run_paraphase INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2159.mapped.bam.bai"
2025-09-15 20:24:35.536 wdl.w:ptcp.w:call-paraphase-62.t:call-run_paraphase INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2159.mapped.bam"
2025-09-15 20:24:35.536 wdl.w:ptcp.w:call-paraphase-62.t:call-run_paraphase INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2159"
2025-09-15 20:24:35.536 wdl.w:ptcp.w:call-paraphase-62.t:call-run_paraphase INFO eval :: name: "threads", value: 4
2025-09-15 20:24:35.536 wdl.w:ptcp.w:call-paraphase-62.t:call-run_paraphase INFO eval :: name: "mem_gb", value: 8
2025-09-15 20:24:35.537 wdl.w:ptcp.w:call-paraphase-62.t:call-run_paraphase INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:35.537 wdl.w:ptcp.w:call-paraphase-62.t:call-run_paraphase INFO eval :: name: "out_dir", value: "m84036_250809_035451_s4.bc2159_paraphase"
2025-09-15 20:24:35.537 wdl.w:ptcp.w:call-paraphase-62.t:call-run_paraphase INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 4, memory_reservation: 8000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:35.537 wdl.w:ptcp.w:call-paraphase-62.t:call-run_paraphase WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:35.538 wdl.w:ptcp.w:call-paraphase-62.t:call-run_paraphase INFO provisioned :: seconds_waited: 0, cpu: 4, mem_bytes: 8000000000
2025-09-15 20:24:35.538 wdl.w:ptcp.w:call-paraphase-62.t:call-run_paraphase INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:35.539 wdl.w:ptcp.w:call-paraphase-37 NOTICE finish :: job: "call-call_f8"
2025-09-15 20:24:35.539 wdl.w:ptcp.w:call-paraphase-37 INFO output :: job: "call-call_f8", values: {"json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-37/call-call_f8/out/m84036_250809_035451_s4.bc2134.f8inversion.json", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-37/call-call_f8/out/m84036_250809_035451_s4.bc2134.f8inversion.vcf"}
2025-09-15 20:24:35.539 wdl.w:ptcp.w:call-paraphase-37 INFO visit :: node: "output-f8_json", values: {"f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-37/call-call_f8/out/m84036_250809_035451_s4.bc2134.f8inversion.json"}
2025-09-15 20:24:35.540 wdl.w:ptcp.w:call-paraphase-37 INFO visit :: node: "output-f8_vcf", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-37/call-call_f8/out/m84036_250809_035451_s4.bc2134.f8inversion.vcf"}
2025-09-15 20:24:35.540 wdl.w:ptcp.w:call-paraphase-37 INFO visit :: node: "outputs", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-37/call-call_f8/out/m84036_250809_035451_s4.bc2134.f8inversion.vcf", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-37/call-run_paraphase/out/m84036_250809_035451_s4.bc2134_paraphase/m84036_250809_035451_s4.bc2134.paraphase.json", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-37/call-run_paraphase/out/m84036_250809_035451_s4.bc2134_paraphase/m84036_250809_035451_s4.bc2134.paraphase.bam", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-37/call-run_paraphase/out/m84036_250809_035451_s4.bc2134_paraphase/m84036_250809_035451_s4.bc2134.paraphase.bam.bai", "paraphase_vcfs": [], "havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-37/call-run_paraphase/out/m84036_250809_035451_s4.bc2134.havanno.json", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-37/call-call_f8/out/m84036_250809_035451_s4.bc2134.f8inversion.json"}
2025-09-15 20:24:35.550 wdl.w:ptcp.w:call-sawfish-62.t:call-run_sawfish NOTICE task setup :: name: "run_sawfish", source: "./sawfish.wdl", line: 83, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-62/call-run_sawfish", thread: 140606626068032
2025-09-15 20:24:35.551 wdl.w:ptcp.w:call-trgt-08.t:call-trgt_plot_meth_waterfall INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2105.meth_waterfall.trgt_plots.zip"
2025-09-15 20:24:35.568 wdl.w:ptcp.w:call-sawfish-62.t:call-run_sawfish INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:35.568 wdl.w:ptcp.w:call-sawfish-62.t:call-run_sawfish INFO input :: name: "genome_version", value: "38"
2025-09-15 20:24:35.569 wdl.w:ptcp.w:call-sawfish-62.t:call-run_sawfish INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:35.569 wdl.w:ptcp.w:call-sawfish-62.t:call-run_sawfish INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:35.569 wdl.w:ptcp.w:call-sawfish-62.t:call-run_sawfish INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2159.mapped.bam.bai"
2025-09-15 20:24:35.569 wdl.w:ptcp.w:call-sawfish-62.t:call-run_sawfish INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2159.mapped.bam"
2025-09-15 20:24:35.569 wdl.w:ptcp.w:call-sawfish-62.t:call-run_sawfish INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2159"
2025-09-15 20:24:35.569 wdl.w:ptcp.w:call-sawfish-62.t:call-run_sawfish INFO eval :: name: "mem_gb", value: 32
2025-09-15 20:24:35.569 wdl.w:ptcp.w:call-sawfish-62.t:call-run_sawfish INFO eval :: name: "threads", value: 16
2025-09-15 20:24:35.570 wdl.w:ptcp.w:call-sawfish-62.t:call-run_sawfish INFO eval :: name: "disk_size", value: 30
2025-09-15 20:24:35.570 wdl.w:ptcp.w:call-sawfish-62.t:call-run_sawfish INFO eval :: name: "discover_dirname", value: "m84036_250809_035451_s4.bc2159_sawfish_discover"
2025-09-15 20:24:35.571 wdl.w:ptcp.w:call-sawfish-62.t:call-run_sawfish INFO eval :: name: "call_dirname", value: "m84036_250809_035451_s4.bc2159_sawfish"
2025-09-15 20:24:35.571 wdl.w:ptcp.w:call-sawfish-62.t:call-run_sawfish INFO eval :: name: "minimap2_bam_filename", value: "m84036_250809_035451_s4.bc2159.minimap2.bam"
2025-09-15 20:24:35.571 wdl.w:ptcp.w:call-sawfish-62.t:call-run_sawfish INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 16, memory_reservation: 32000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:35.571 wdl.w:ptcp.w:call-sawfish-62.t:call-run_sawfish WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:35.572 wdl.w:ptcp.w:call-sawfish-62.t:call-run_sawfish INFO provisioned :: seconds_waited: 0, cpu: 16, mem_bytes: 32000000000
2025-09-15 20:24:35.572 wdl.w:ptcp.w:call-sawfish-62.t:call-run_sawfish INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:35.607 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_motifs_allele NOTICE done
2025-09-15 20:24:35.611 wdl.w:ptcp.w:call-trgt-51 NOTICE finish :: job: "call-trgt_plot_motifs_allele"
2025-09-15 20:24:35.612 wdl.w:ptcp.w:call-trgt-51 INFO output :: job: "call-trgt_plot_motifs_allele", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-51/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2148.motifs_allele.trgt_plots.zip"}
2025-09-15 20:24:35.612 wdl.w:ptcp.w:call-trgt-51 INFO visit :: node: "output-images_motifs_allele", values: {"images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-51/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2148.motifs_allele.trgt_plots.zip"}
2025-09-15 20:24:35.613 wdl.w:ptcp.w:call-trgt-51.t:call-trgt_plot_motifs_waterfall NOTICE done
2025-09-15 20:24:35.619 wdl.w:ptcp.w:call-trgt-51 NOTICE finish :: job: "call-trgt_plot_motifs_waterfall"
2025-09-15 20:24:35.619 wdl.w:ptcp.w:call-trgt-51 INFO output :: job: "call-trgt_plot_motifs_waterfall", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-51/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2148.motifs_waterfall.trgt_plots.zip"}
2025-09-15 20:24:35.620 wdl.w:ptcp.w:call-trgt-51 INFO visit :: node: "output-images_motifs_waterfall", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-51/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2148.motifs_waterfall.trgt_plots.zip"}
2025-09-15 20:24:35.620 wdl.w:ptcp.w:call-trgt-51 INFO visit :: node: "outputs", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-51/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2148.motifs_waterfall.trgt_plots.zip", "images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-51/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2148.meth_allele.trgt_plots.zip", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-51/call-trgt_genotype/out/m84036_250809_035451_s4.bc2148.trgt.sorted.spanning.bam.bai", "images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-51/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2148.motifs_allele.trgt_plots.zip", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-51/call-trgt_genotype/out/m84036_250809_035451_s4.bc2148.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-51/call-trgt_genotype/out/m84036_250809_035451_s4.bc2148.trgt.vcf", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-51/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2148.repeats.bam", "images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-51/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2148.meth_waterfall.trgt_plots.zip", "reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-51/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2148.repeats.bam.bai"}
2025-09-15 20:24:35.621 wdl.w:ptcp.w:call-trgt-62.t:call-get_reads_overlapping_repeats NOTICE task setup :: name: "get_reads_overlapping_repeats", source: "./trgt.wdl", line: 182, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-62/call-get_reads_overlapping_repeats", thread: 140607162938944
2025-09-15 20:24:35.632 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_genotype NOTICE task setup :: name: "trgt_genotype", source: "./trgt.wdl", line: 272, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-62/call-trgt_genotype", thread: 140606609282624
2025-09-15 20:24:35.633 wdl.w:ptcp.w:call-paraphase-37 NOTICE done
2025-09-15 20:24:35.639 wdl.w:ptcp NOTICE finish :: job: "call-paraphase-37"
2025-09-15 20:24:35.640 wdl.w:ptcp INFO output :: job: "call-paraphase-37", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-37/out/m84036_250809_035451_s4.bc2134.f8inversion.vcf", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-37/out/m84036_250809_035451_s4.bc2134_paraphase/m84036_250809_035451_s4.bc2134.paraphase.json", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-37/out/m84036_250809_035451_s4.bc2134_paraphase/m84036_250809_035451_s4.bc2134.paraphase.bam", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-37/out/m84036_250809_035451_s4.bc2134_paraphase/m84036_250809_035451_s4.bc2134.paraphase.bam.bai", "paraphase_vcfs": [], "havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-37/out/m84036_250809_035451_s4.bc2134.havanno.json", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-37/out/m84036_250809_035451_s4.bc2134.f8inversion.json"}
2025-09-15 20:24:35.647 wdl.w:ptcp.w:call-sawfish-67 NOTICE workflow start :: name: "sawfish", source: "./sawfish.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-67"
2025-09-15 20:24:35.647 wdl.w:ptcp.w:call-paraphase-62.t:call-run_paraphase INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-62/call-run_paraphase/_singularity_tmpdir_5z6on2__"
2025-09-15 20:24:35.648 wdl.w:ptcp.w:call-paraphase-62.t:call-run_paraphase INFO Slurm invocation: srun --job-name call-run_paraphase --partition compute,compute9 --cpus-per-task 4 --mem 7629M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-62/call-run_paraphase/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-62/call-run_paraphase/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-62/call-run_paraphase/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-62/call-run_paraphase/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-62/out/m84036_250809_035451_s4.bc2159.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2159.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-62/out/m84036_250809_035451_s4.bc2159.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2159.mapped.bam.bai:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/variant_list/variant_list.GRCh38.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf:ro --bind /ptcp/meta/paraphase/paraphase_config.GRCh38.yaml:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/paraphase_config.GRCh38.yaml:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-62/call-run_paraphase/_singularity_tmpdir_5z6on2__/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-62/call-run_paraphase/_singularity_tmpdir_5z6on2__/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:35.649 wdl.w:ptcp.w:call-trgt-62.t:call-get_reads_overlapping_repeats INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:35.650 wdl.w:ptcp.w:call-trgt-62.t:call-get_reads_overlapping_repeats INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:35.650 wdl.w:ptcp.w:call-trgt-62.t:call-get_reads_overlapping_repeats INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2159.mapped.bam.bai"
2025-09-15 20:24:35.650 wdl.w:ptcp.w:call-trgt-62.t:call-get_reads_overlapping_repeats INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2159.mapped.bam"
2025-09-15 20:24:35.650 wdl.w:ptcp.w:call-trgt-62.t:call-get_reads_overlapping_repeats INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2159"
2025-09-15 20:24:35.650 wdl.w:ptcp.w:call-trgt-62.t:call-get_reads_overlapping_repeats INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:35.650 wdl.w:ptcp.w:call-trgt-62.t:call-get_reads_overlapping_repeats INFO eval :: name: "expand_size", value: 3000
2025-09-15 20:24:35.651 wdl.w:ptcp.w:call-trgt-62.t:call-get_reads_overlapping_repeats INFO eval :: name: "threads", value: 1
2025-09-15 20:24:35.651 wdl.w:ptcp.w:call-trgt-62.t:call-get_reads_overlapping_repeats INFO eval :: name: "expanded_bed_name", value: "m84036_250809_035451_s4.bc2159.expanded.bed"
2025-09-15 20:24:35.651 wdl.w:ptcp.w:call-trgt-62.t:call-get_reads_overlapping_repeats INFO eval :: name: "disk_size", value: 11
2025-09-15 20:24:35.651 wdl.w:ptcp.w:call-trgt-62.t:call-get_reads_overlapping_repeats INFO eval :: name: "output_name", value: "m84036_250809_035451_s4.bc2159.repeats.bam"
2025-09-15 20:24:35.651 wdl.w:ptcp.w:call-trgt-62.t:call-get_reads_overlapping_repeats INFO eval :: name: "index_name", value: "m84036_250809_035451_s4.bc2159.repeats.bam.bai"
2025-09-15 20:24:35.651 wdl.w:ptcp.w:call-trgt-62.t:call-get_reads_overlapping_repeats INFO eval :: name: "output_name_with_index", value: "m84036_250809_035451_s4.bc2159.repeats.bam##idx##m84036_250809_035451_s4.bc2159.repeats.bam.bai"
2025-09-15 20:24:35.652 wdl.w:ptcp.w:call-trgt-62.t:call-get_reads_overlapping_repeats INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:35.652 wdl.w:ptcp.w:call-trgt-62.t:call-get_reads_overlapping_repeats WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:35.652 wdl.w:ptcp.w:call-trgt-62.t:call-get_reads_overlapping_repeats INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:35.653 wdl.w:ptcp.w:call-trgt-62.t:call-get_reads_overlapping_repeats INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:35.654 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_genotype INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:35.654 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_genotype INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:35.654 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_genotype INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:35.654 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_genotype INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:35.654 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_genotype INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2159.mapped.bam.bai"
2025-09-15 20:24:35.654 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_genotype INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2159.mapped.bam"
2025-09-15 20:24:35.654 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_genotype INFO input :: name: "sex", value: "F"
2025-09-15 20:24:35.654 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_genotype INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2159"
2025-09-15 20:24:35.655 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_genotype INFO eval :: name: "mem_gb", value: 16
2025-09-15 20:24:35.655 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_genotype INFO eval :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2159.trgt"
2025-09-15 20:24:35.655 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_genotype INFO eval :: name: "threads", value: 8
2025-09-15 20:24:35.655 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_genotype INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:35.656 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_genotype INFO eval :: name: "karyotype", value: "XX"
2025-09-15 20:24:35.656 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_genotype INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 8, memory_reservation: 16000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:35.657 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_genotype WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:35.657 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_genotype INFO provisioned :: seconds_waited: 0, cpu: 8, mem_bytes: 16000000000
2025-09-15 20:24:35.657 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_genotype INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:35.660 wdl.w:ptcp.w:call-sawfish-62.t:call-run_sawfish INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 10, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-62/call-run_sawfish/_singularity_tmpdir_u94d7fat"
2025-09-15 20:24:35.660 wdl.w:ptcp.w:call-sawfish-62.t:call-run_sawfish INFO Slurm invocation: srun --job-name call-run_sawfish --partition compute,compute9 --cpus-per-task 16 --mem 30518M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-62/call-run_sawfish/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-62/call-run_sawfish/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-62/call-run_sawfish/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-62/call-run_sawfish/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-62/out/m84036_250809_035451_s4.bc2159.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2159.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-62/out/m84036_250809_035451_s4.bc2159.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2159.mapped.bam:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-62/call-run_sawfish/_singularity_tmpdir_u94d7fat/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-62/call-run_sawfish/_singularity_tmpdir_u94d7fat/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:35.666 wdl.w:ptcp.w:call-sawfish-67 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:24:35.666 wdl.w:ptcp.w:call-sawfish-67 INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:24:35.666 wdl.w:ptcp.w:call-sawfish-67 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-67/out/m84036_250809_035451_s4.bc2164.mapped.bam"}
2025-09-15 20:24:35.666 wdl.w:ptcp.w:call-sawfish-67 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-67/out/m84036_250809_035451_s4.bc2164.mapped.bam.bai"}
2025-09-15 20:24:35.666 wdl.w:ptcp.w:call-sawfish-67 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:24:35.666 wdl.w:ptcp.w:call-sawfish-67 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:24:35.666 wdl.w:ptcp.w:call-sawfish-67 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2164"}
2025-09-15 20:24:35.667 wdl.w:ptcp.w:call-sawfish-67 NOTICE ready :: job: "call-run_sawfish", callee: "run_sawfish"
2025-09-15 20:24:35.667 wdl.w:ptcp.w:call-sawfish-67 INFO input :: job: "call-run_sawfish", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-67/out/m84036_250809_035451_s4.bc2164.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-67/out/m84036_250809_035451_s4.bc2164.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2164"}
2025-09-15 20:24:35.675 wdl.w:ptcp.w:call-sawfish-62.t:call-run_sawfish NOTICE slurm_singularity run :: pid: 1202381, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-62/call-run_sawfish/slurm_singularity.log.txt"
2025-09-15 20:24:35.675 wdl.w:ptcp.w:call-paraphase-62.t:call-run_paraphase NOTICE slurm_singularity run :: pid: 1202380, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-62/call-run_paraphase/slurm_singularity.log.txt"
2025-09-15 20:24:35.690 wdl.w:ptcp.w:call-trgt-39.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:24:35 [INFO] - Running trgt-4.0.0-429afcd [genotype]
2025-09-15 20:24:35.690 wdl.w:ptcp.w:call-trgt-39.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:24:35 [WARN] - DM1_DMPK: Filtered out 1 impure reads
2025-09-15 20:24:35.690 wdl.w:ptcp.w:call-trgt-39.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:24:35 [WARN] - PRTS_ARX: Filtered out 3 impure reads
2025-09-15 20:24:35.690 wdl.w:ptcp.w:call-trgt-39.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:24:35 [WARN] - EIEE1_ARX: Filtered out 1 impure reads
2025-09-15 20:24:35.690 wdl.w:ptcp.w:call-trgt-39.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:24:35 [WARN] - FRAXE_AFF2: Filtered out 12 impure reads
2025-09-15 20:24:35.691 wdl.w:ptcp.w:call-trgt-39.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:24:35 [WARN] - FXS_FMR1: Filtered out 10 impure reads
2025-09-15 20:24:35.691 wdl.w:ptcp.w:call-trgt-39.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:24:35 [WARN] - FRDA_FXN: Filtered out 3 impure reads
2025-09-15 20:24:35.691 wdl.w:ptcp.w:call-trgt-39.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:24:35 [INFO] - Total execution time: 122.72ms
2025-09-15 20:24:35.691 wdl.w:ptcp.w:call-trgt-39.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:24:35 [INFO] - trgt end
2025-09-15 20:24:35.702 wdl.w:ptcp.w:call-trgt-08.t:call-trgt_plot_meth_waterfall NOTICE done
2025-09-15 20:24:35.703 wdl.w:ptcp.w:call-trgt-39.t:call-trgt_genotype.slurm_singularity INFO srun: job 51797701 queued and waiting for resources
2025-09-15 20:24:35.703 wdl.w:ptcp.w:call-trgt-39.t:call-trgt_genotype.slurm_singularity INFO srun: job 51797701 has been allocated resources
2025-09-15 20:24:35.703 wdl.w:ptcp.w:call-trgt-39.t:call-trgt_genotype.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:35.721 wdl.w:ptcp.w:call-trgt-08 NOTICE finish :: job: "call-trgt_plot_meth_waterfall"
2025-09-15 20:24:35.721 wdl.w:ptcp.w:call-trgt-08 INFO output :: job: "call-trgt_plot_meth_waterfall", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-08/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2105.meth_waterfall.trgt_plots.zip"}
2025-09-15 20:24:35.721 wdl.w:ptcp.w:call-trgt-08 INFO visit :: node: "output-images_meth_waterfall", values: {"images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-08/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2105.meth_waterfall.trgt_plots.zip"}
2025-09-15 20:24:35.728 wdl.w:ptcp.w:call-paraphase-48.t:call-run_paraphase NOTICE task setup :: name: "run_paraphase", source: "./paraphase.wdl", line: 127, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-48/call-run_paraphase", thread: 140607691417152
2025-09-15 20:24:35.731 wdl.w:ptcp.w:call-trgt-62.t:call-get_reads_overlapping_repeats INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 9, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-62/call-get_reads_overlapping_repeats/_singularity_tmpdir_8zzzmaof"
2025-09-15 20:24:35.731 wdl.w:ptcp.w:call-trgt-62.t:call-get_reads_overlapping_repeats INFO Slurm invocation: srun --job-name call-get_reads_overlapping_repeats --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-62/call-get_reads_overlapping_repeats/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-62/call-get_reads_overlapping_repeats/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-62/call-get_reads_overlapping_repeats/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-62/call-get_reads_overlapping_repeats/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-62/out/m84036_250809_035451_s4.bc2159.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2159.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-62/out/m84036_250809_035451_s4.bc2159.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2159.mapped.bam:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-62/call-get_reads_overlapping_repeats/_singularity_tmpdir_8zzzmaof/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-62/call-get_reads_overlapping_repeats/_singularity_tmpdir_8zzzmaof/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:35.736 wdl.w:ptcp.w:call-trgt-51 NOTICE done
2025-09-15 20:24:35.737 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_genotype INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 11, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-62/call-trgt_genotype/_singularity_tmpdir_lvubznij"
2025-09-15 20:24:35.737 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_genotype INFO Slurm invocation: srun --job-name call-trgt_genotype --partition compute,compute9 --cpus-per-task 8 --mem 15259M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-62/call-trgt_genotype/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-62/call-trgt_genotype/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-62/call-trgt_genotype/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-62/call-trgt_genotype/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-62/out/m84036_250809_035451_s4.bc2159.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2159.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-62/out/m84036_250809_035451_s4.bc2159.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2159.mapped.bam.bai:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-62/call-trgt_genotype/_singularity_tmpdir_lvubznij/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-62/call-trgt_genotype/_singularity_tmpdir_lvubznij/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:35.740 wdl.w:ptcp NOTICE finish :: job: "call-trgt-51"
2025-09-15 20:24:35.740 wdl.w:ptcp INFO output :: job: "call-trgt-51", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-51/out/m84036_250809_035451_s4.bc2148.motifs_waterfall.trgt_plots.zip", "images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-51/out/m84036_250809_035451_s4.bc2148.meth_allele.trgt_plots.zip", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-51/out/m84036_250809_035451_s4.bc2148.trgt.sorted.spanning.bam.bai", "images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-51/out/m84036_250809_035451_s4.bc2148.motifs_allele.trgt_plots.zip", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-51/out/m84036_250809_035451_s4.bc2148.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-51/out/m84036_250809_035451_s4.bc2148.trgt.vcf", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-51/out/m84036_250809_035451_s4.bc2148.repeats.bam", "images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-51/out/m84036_250809_035451_s4.bc2148.meth_waterfall.trgt_plots.zip", "reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-51/out/m84036_250809_035451_s4.bc2148.repeats.bam.bai"}
2025-09-15 20:24:35.747 wdl.w:ptcp.w:call-trgt-67 NOTICE workflow start :: name: "trgt", source: "./trgt.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-67"
2025-09-15 20:24:35.752 wdl.w:ptcp.w:call-paraphase-48.t:call-run_paraphase INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:35.752 wdl.w:ptcp.w:call-paraphase-48.t:call-run_paraphase INFO input :: name: "annotation_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf"
2025-09-15 20:24:35.752 wdl.w:ptcp.w:call-paraphase-48.t:call-run_paraphase INFO input :: name: "genome_version", value: "38"
2025-09-15 20:24:35.753 wdl.w:ptcp.w:call-paraphase-48.t:call-run_paraphase INFO input :: name: "config_file", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/paraphase_config.GRCh38.yaml"
2025-09-15 20:24:35.753 wdl.w:ptcp.w:call-paraphase-48.t:call-run_paraphase INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:35.753 wdl.w:ptcp.w:call-paraphase-48.t:call-run_paraphase INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:35.753 wdl.w:ptcp.w:call-paraphase-48.t:call-run_paraphase INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2145.mapped.bam.bai"
2025-09-15 20:24:35.753 wdl.w:ptcp.w:call-paraphase-48.t:call-run_paraphase INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2145.mapped.bam"
2025-09-15 20:24:35.753 wdl.w:ptcp.w:call-paraphase-48.t:call-run_paraphase INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2145"
2025-09-15 20:24:35.754 wdl.w:ptcp.w:call-paraphase-48.t:call-run_paraphase INFO eval :: name: "threads", value: 4
2025-09-15 20:24:35.755 wdl.w:ptcp.w:call-paraphase-48.t:call-run_paraphase INFO eval :: name: "mem_gb", value: 8
2025-09-15 20:24:35.755 wdl.w:ptcp.w:call-paraphase-48.t:call-run_paraphase INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:35.755 wdl.w:ptcp.w:call-paraphase-48.t:call-run_paraphase INFO eval :: name: "out_dir", value: "m84036_250809_035451_s4.bc2145_paraphase"
2025-09-15 20:24:35.755 wdl.w:ptcp.w:call-paraphase-48.t:call-run_paraphase INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 4, memory_reservation: 8000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:35.756 wdl.w:ptcp.w:call-paraphase-48.t:call-run_paraphase WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:35.756 wdl.w:ptcp.w:call-paraphase-48.t:call-run_paraphase INFO provisioned :: seconds_waited: 0, cpu: 4, mem_bytes: 8000000000
2025-09-15 20:24:35.756 wdl.w:ptcp.w:call-paraphase-48.t:call-run_paraphase INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:35.760 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_genotype NOTICE slurm_singularity run :: pid: 1202403, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-62/call-trgt_genotype/slurm_singularity.log.txt"
2025-09-15 20:24:35.760 wdl.w:ptcp.w:call-trgt-62.t:call-get_reads_overlapping_repeats NOTICE slurm_singularity run :: pid: 1202401, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-62/call-get_reads_overlapping_repeats/slurm_singularity.log.txt"
2025-09-15 20:24:35.766 wdl.w:ptcp.w:call-trgt-67 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:24:35.766 wdl.w:ptcp.w:call-trgt-67 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-67/out/m84036_250809_035451_s4.bc2164.mapped.bam"}
2025-09-15 20:24:35.766 wdl.w:ptcp.w:call-trgt-67 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-67/out/m84036_250809_035451_s4.bc2164.mapped.bam.bai"}
2025-09-15 20:24:35.766 wdl.w:ptcp.w:call-trgt-67 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:24:35.766 wdl.w:ptcp.w:call-trgt-67 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:24:35.766 wdl.w:ptcp.w:call-trgt-67 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2164"}
2025-09-15 20:24:35.767 wdl.w:ptcp.w:call-trgt-67 INFO visit :: node: "decl-sex", values: {"sex": "F"}
2025-09-15 20:24:35.767 wdl.w:ptcp.w:call-trgt-39.t:call-trgt_genotype INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2136.trgt.vcf"
2025-09-15 20:24:35.767 wdl.w:ptcp.w:call-trgt-67 INFO visit :: node: "decl-trgt_bed", values: {"trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"}
2025-09-15 20:24:35.767 wdl.w:ptcp.w:call-trgt-67 NOTICE ready :: job: "call-get_reads_overlapping_repeats", callee: "get_reads_overlapping_repeats"
2025-09-15 20:24:35.767 wdl.w:ptcp.w:call-trgt-67 INFO input :: job: "call-get_reads_overlapping_repeats", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-67/out/m84036_250809_035451_s4.bc2164.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-67/out/m84036_250809_035451_s4.bc2164.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2164"}
2025-09-15 20:24:35.769 wdl.w:ptcp.w:call-trgt-67 NOTICE ready :: job: "call-trgt_genotype", callee: "trgt_genotype"
2025-09-15 20:24:35.769 wdl.w:ptcp.w:call-trgt-67 INFO input :: job: "call-trgt_genotype", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-67/out/m84036_250809_035451_s4.bc2164.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-67/out/m84036_250809_035451_s4.bc2164.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2164"}
2025-09-15 20:24:35.772 wdl.w:ptcp.w:call-trgt-39.t:call-trgt_genotype INFO output :: name: "spanning_bam", value: "m84036_250809_035451_s4.bc2136.trgt.sorted.spanning.bam"
2025-09-15 20:24:35.773 wdl.w:ptcp.w:call-trgt-39.t:call-trgt_genotype INFO output :: name: "spanning_bam_bai", value: "m84036_250809_035451_s4.bc2136.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:35.833 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_motifs_waterfall INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2135.motifs_waterfall.trgt_plots.zip"
2025-09-15 20:24:35.839 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_plot_meth_allele INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2143.meth_allele.trgt_plots.zip"
2025-09-15 20:24:35.840 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_motifs_allele INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2135.motifs_allele.trgt_plots.zip"
2025-09-15 20:24:35.844 wdl.w:ptcp.w:call-paraphase-44.t:call-call_f8 INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2141.f8inversion.vcf"
2025-09-15 20:24:35.850 wdl.w:ptcp.w:call-paraphase-44.t:call-call_f8 INFO output :: name: "json", value: "m84036_250809_035451_s4.bc2141.f8inversion.json"
2025-09-15 20:24:35.882 wdl.w:ptcp.w:call-paraphase-48.t:call-run_paraphase INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-48/call-run_paraphase/_singularity_tmpdir_lyq6bgst"
2025-09-15 20:24:35.882 wdl.w:ptcp.w:call-paraphase-48.t:call-run_paraphase INFO Slurm invocation: srun --job-name call-run_paraphase --partition compute,compute9 --cpus-per-task 4 --mem 7629M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-48/call-run_paraphase/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-48/call-run_paraphase/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-48/call-run_paraphase/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-48/call-run_paraphase/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-48/out/m84036_250809_035451_s4.bc2145.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2145.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-48/out/m84036_250809_035451_s4.bc2145.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2145.mapped.bam.bai:ro --bind /ptcp/meta/variant_list/variant_list.GRCh38.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf:ro --bind /ptcp/meta/paraphase/paraphase_config.GRCh38.yaml:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/paraphase_config.GRCh38.yaml:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-48/call-run_paraphase/_singularity_tmpdir_lyq6bgst/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-48/call-run_paraphase/_singularity_tmpdir_lyq6bgst/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:35.882 wdl.w:ptcp.w:call-paraphase-52.t:call-run_paraphase INFO output :: name: "paraphase_bam", value: "m84036_250809_035451_s4.bc2149_paraphase/m84036_250809_035451_s4.bc2149.paraphase.bam"
2025-09-15 20:24:35.893 wdl.w:ptcp.w:call-paraphase-52.t:call-run_paraphase INFO output :: name: "paraphase_bam_bai", value: "m84036_250809_035451_s4.bc2149_paraphase/m84036_250809_035451_s4.bc2149.paraphase.bam.bai"
2025-09-15 20:24:35.894 wdl.w:ptcp.w:call-paraphase-52.t:call-run_paraphase INFO output :: name: "paraphase_json", value: "m84036_250809_035451_s4.bc2149_paraphase/m84036_250809_035451_s4.bc2149.paraphase.json"
2025-09-15 20:24:35.896 wdl.w:ptcp.w:call-trgt-39.t:call-trgt_genotype NOTICE done
2025-09-15 20:24:35.897 wdl.w:ptcp.w:call-paraphase-52.t:call-run_paraphase INFO output :: name: "paraphase_vcfs", value: []
2025-09-15 20:24:35.898 wdl.w:ptcp.w:call-paraphase-52.t:call-run_paraphase INFO output :: name: "havanno_json", value: "m84036_250809_035451_s4.bc2149.havanno.json"
2025-09-15 20:24:35.904 wdl.w:ptcp.w:call-trgt-39 NOTICE finish :: job: "call-trgt_genotype"
2025-09-15 20:24:35.904 wdl.w:ptcp.w:call-trgt-39 INFO output :: job: "call-trgt_genotype", values: {"spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-39/call-trgt_genotype/out/m84036_250809_035451_s4.bc2136.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-39/call-trgt_genotype/out/m84036_250809_035451_s4.bc2136.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-39/call-trgt_genotype/out/m84036_250809_035451_s4.bc2136.trgt.vcf"}
2025-09-15 20:24:35.905 wdl.w:ptcp.w:call-trgt-39 NOTICE ready :: job: "call-trgt_plot_meth_allele", callee: "trgt_plot"
2025-09-15 20:24:35.905 wdl.w:ptcp.w:call-trgt-39 INFO input :: job: "call-trgt_plot_meth_allele", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": false, "methylation": true, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-39/call-trgt_genotype/out/m84036_250809_035451_s4.bc2136.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-39/call-trgt_genotype/out/m84036_250809_035451_s4.bc2136.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-39/call-trgt_genotype/out/m84036_250809_035451_s4.bc2136.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2136"}
2025-09-15 20:24:35.906 wdl.w:ptcp.w:call-trgt-39 NOTICE ready :: job: "call-trgt_plot_meth_waterfall", callee: "trgt_plot"
2025-09-15 20:24:35.907 wdl.w:ptcp.w:call-trgt-39 INFO input :: job: "call-trgt_plot_meth_waterfall", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": true, "methylation": true, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-39/call-trgt_genotype/out/m84036_250809_035451_s4.bc2136.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-39/call-trgt_genotype/out/m84036_250809_035451_s4.bc2136.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-39/call-trgt_genotype/out/m84036_250809_035451_s4.bc2136.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2136"}
2025-09-15 20:24:35.909 wdl.w:ptcp.w:call-trgt-39 NOTICE ready :: job: "call-trgt_plot_motifs_allele", callee: "trgt_plot"
2025-09-15 20:24:35.909 wdl.w:ptcp.w:call-trgt-39 INFO input :: job: "call-trgt_plot_motifs_allele", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": false, "methylation": false, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-39/call-trgt_genotype/out/m84036_250809_035451_s4.bc2136.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-39/call-trgt_genotype/out/m84036_250809_035451_s4.bc2136.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-39/call-trgt_genotype/out/m84036_250809_035451_s4.bc2136.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2136"}
2025-09-15 20:24:35.910 wdl.w:ptcp.w:call-trgt-39 NOTICE ready :: job: "call-trgt_plot_motifs_waterfall", callee: "trgt_plot"
2025-09-15 20:24:35.910 wdl.w:ptcp.w:call-trgt-39 INFO input :: job: "call-trgt_plot_motifs_waterfall", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": true, "methylation": false, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-39/call-trgt_genotype/out/m84036_250809_035451_s4.bc2136.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-39/call-trgt_genotype/out/m84036_250809_035451_s4.bc2136.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-39/call-trgt_genotype/out/m84036_250809_035451_s4.bc2136.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2136"}
2025-09-15 20:24:35.912 wdl.w:ptcp.w:call-trgt-39 INFO visit :: node: "output-spanning_bam", values: {"spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-39/call-trgt_genotype/out/m84036_250809_035451_s4.bc2136.trgt.sorted.spanning.bam"}
2025-09-15 20:24:35.912 wdl.w:ptcp.w:call-trgt-39 INFO visit :: node: "output-spanning_bam_bai", values: {"spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-39/call-trgt_genotype/out/m84036_250809_035451_s4.bc2136.trgt.sorted.spanning.bam.bai"}
2025-09-15 20:24:35.912 wdl.w:ptcp.w:call-trgt-39 INFO visit :: node: "output-vcf", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-39/call-trgt_genotype/out/m84036_250809_035451_s4.bc2136.trgt.vcf"}
2025-09-15 20:24:35.914 wdl.w:ptcp.w:call-trgt-00.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:32 [ERROR] - No reads found for TRID=PRTS_ARX
2025-09-15 20:24:35.916 wdl.w:ptcp.w:call-trgt-00.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:32 [ERROR] - No reads found for TRID=EIEE1_ARX
2025-09-15 20:24:35.919 wdl.w:ptcp.w:call-paraphase-48.t:call-run_paraphase NOTICE slurm_singularity run :: pid: 1202420, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-48/call-run_paraphase/slurm_singularity.log.txt"
2025-09-15 20:24:35.919 wdl.w:ptcp.w:call-sawfish-48.t:call-run_sawfish NOTICE task setup :: name: "run_sawfish", source: "./sawfish.wdl", line: 83, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-48/call-run_sawfish", thread: 140613580211776
2025-09-15 20:24:35.952 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_meth_waterfall INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2135.meth_waterfall.trgt_plots.zip"
2025-09-15 20:24:35.958 wdl.w:ptcp.w:call-sawfish-48.t:call-run_sawfish INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:35.958 wdl.w:ptcp.w:call-sawfish-48.t:call-run_sawfish INFO input :: name: "genome_version", value: "38"
2025-09-15 20:24:35.958 wdl.w:ptcp.w:call-sawfish-48.t:call-run_sawfish INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:35.958 wdl.w:ptcp.w:call-sawfish-48.t:call-run_sawfish INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:35.958 wdl.w:ptcp.w:call-sawfish-48.t:call-run_sawfish INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2145.mapped.bam.bai"
2025-09-15 20:24:35.958 wdl.w:ptcp.w:call-sawfish-48.t:call-run_sawfish INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2145.mapped.bam"
2025-09-15 20:24:35.958 wdl.w:ptcp.w:call-sawfish-48.t:call-run_sawfish INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2145"
2025-09-15 20:24:35.959 wdl.w:ptcp.w:call-sawfish-48.t:call-run_sawfish INFO eval :: name: "mem_gb", value: 32
2025-09-15 20:24:35.959 wdl.w:ptcp.w:call-sawfish-48.t:call-run_sawfish INFO eval :: name: "threads", value: 16
2025-09-15 20:24:35.959 wdl.w:ptcp.w:call-sawfish-48.t:call-run_sawfish INFO eval :: name: "disk_size", value: 30
2025-09-15 20:24:35.959 wdl.w:ptcp.w:call-sawfish-48.t:call-run_sawfish INFO eval :: name: "discover_dirname", value: "m84036_250809_035451_s4.bc2145_sawfish_discover"
2025-09-15 20:24:35.960 wdl.w:ptcp.w:call-sawfish-48.t:call-run_sawfish INFO eval :: name: "call_dirname", value: "m84036_250809_035451_s4.bc2145_sawfish"
2025-09-15 20:24:35.960 wdl.w:ptcp.w:call-sawfish-48.t:call-run_sawfish INFO eval :: name: "minimap2_bam_filename", value: "m84036_250809_035451_s4.bc2145.minimap2.bam"
2025-09-15 20:24:35.961 wdl.w:ptcp.w:call-sawfish-48.t:call-run_sawfish INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 16, memory_reservation: 32000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:35.961 wdl.w:ptcp.w:call-sawfish-48.t:call-run_sawfish WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:35.962 wdl.w:ptcp.w:call-sawfish-48.t:call-run_sawfish INFO provisioned :: seconds_waited: 0, cpu: 16, mem_bytes: 32000000000
2025-09-15 20:24:35.962 wdl.w:ptcp.w:call-sawfish-48.t:call-run_sawfish INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:35.964 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_motifs_waterfall NOTICE done
2025-09-15 20:24:35.968 wdl.w:ptcp.w:call-paraphase-44.t:call-call_f8 NOTICE done
2025-09-15 20:24:35.970 wdl.w:ptcp.w:call-trgt-38 NOTICE finish :: job: "call-trgt_plot_motifs_waterfall"
2025-09-15 20:24:35.971 wdl.w:ptcp.w:call-trgt-38 INFO output :: job: "call-trgt_plot_motifs_waterfall", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-38/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2135.motifs_waterfall.trgt_plots.zip"}
2025-09-15 20:24:35.971 wdl.w:ptcp.w:call-trgt-38 INFO visit :: node: "output-images_motifs_waterfall", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-38/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2135.motifs_waterfall.trgt_plots.zip"}
2025-09-15 20:24:35.973 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_motifs_allele NOTICE done
2025-09-15 20:24:35.974 wdl.w:ptcp.w:call-paraphase-44 NOTICE finish :: job: "call-call_f8"
2025-09-15 20:24:35.975 wdl.w:ptcp.w:call-paraphase-44 INFO output :: job: "call-call_f8", values: {"json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-44/call-call_f8/out/m84036_250809_035451_s4.bc2141.f8inversion.json", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-44/call-call_f8/out/m84036_250809_035451_s4.bc2141.f8inversion.vcf"}
2025-09-15 20:24:35.975 wdl.w:ptcp.w:call-paraphase-44 INFO visit :: node: "output-f8_json", values: {"f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-44/call-call_f8/out/m84036_250809_035451_s4.bc2141.f8inversion.json"}
2025-09-15 20:24:35.975 wdl.w:ptcp.w:call-paraphase-44 INFO visit :: node: "output-f8_vcf", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-44/call-call_f8/out/m84036_250809_035451_s4.bc2141.f8inversion.vcf"}
2025-09-15 20:24:35.975 wdl.w:ptcp.w:call-paraphase-44 INFO visit :: node: "outputs", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-44/call-call_f8/out/m84036_250809_035451_s4.bc2141.f8inversion.vcf", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-44/call-run_paraphase/out/m84036_250809_035451_s4.bc2141_paraphase/m84036_250809_035451_s4.bc2141.paraphase.json", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-44/call-run_paraphase/out/m84036_250809_035451_s4.bc2141_paraphase/m84036_250809_035451_s4.bc2141.paraphase.bam", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-44/call-run_paraphase/out/m84036_250809_035451_s4.bc2141_paraphase/m84036_250809_035451_s4.bc2141.paraphase.bam.bai", "paraphase_vcfs": [], "havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-44/call-run_paraphase/out/m84036_250809_035451_s4.bc2141.havanno.json", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-44/call-call_f8/out/m84036_250809_035451_s4.bc2141.f8inversion.json"}
2025-09-15 20:24:35.977 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_plot_meth_allele NOTICE done
2025-09-15 20:24:35.979 wdl.w:ptcp.w:call-trgt-38 NOTICE finish :: job: "call-trgt_plot_motifs_allele"
2025-09-15 20:24:35.979 wdl.w:ptcp.w:call-trgt-38 INFO output :: job: "call-trgt_plot_motifs_allele", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-38/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2135.motifs_allele.trgt_plots.zip"}
2025-09-15 20:24:35.979 wdl.w:ptcp.w:call-trgt-38 INFO visit :: node: "output-images_motifs_allele", values: {"images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-38/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2135.motifs_allele.trgt_plots.zip"}
2025-09-15 20:24:35.981 wdl.w:ptcp.w:call-trgt-48.t:call-get_reads_overlapping_repeats NOTICE task setup :: name: "get_reads_overlapping_repeats", source: "./trgt.wdl", line: 182, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-48/call-get_reads_overlapping_repeats", thread: 140610879071808
2025-09-15 20:24:35.987 wdl.w:ptcp.w:call-trgt-46 NOTICE finish :: job: "call-trgt_plot_meth_allele"
2025-09-15 20:24:35.987 wdl.w:ptcp.w:call-trgt-46 INFO output :: job: "call-trgt_plot_meth_allele", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-46/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2143.meth_allele.trgt_plots.zip"}
2025-09-15 20:24:35.987 wdl.w:ptcp.w:call-trgt-46 INFO visit :: node: "output-images_meth_allele", values: {"images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-46/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2143.meth_allele.trgt_plots.zip"}
2025-09-15 20:24:35.992 wdl.w:ptcp.w:call-sawfish-41.t:call-run_sawfish.stderr VERBOSE [M::bam2fq_mainloop] discarded 0 singletons
2025-09-15 20:24:35.992 wdl.w:ptcp.w:call-sawfish-41.t:call-run_sawfish.stderr VERBOSE [M::bam2fq_mainloop] processed 1 reads
2025-09-15 20:24:35.993 wdl.w:ptcp.w:call-paraphase-57.t:call-run_paraphase NOTICE task setup :: name: "run_paraphase", source: "./paraphase.wdl", line: 127, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-57/call-run_paraphase", thread: 140611449513536
2025-09-15 20:24:35.994 wdl.w:ptcp.w:call-trgt-48.t:call-trgt_genotype NOTICE task setup :: name: "trgt_genotype", source: "./trgt.wdl", line: 272, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-48/call-trgt_genotype", thread: 140607112582720
2025-09-15 20:24:36.000 wdl.w:ptcp.w:call-sawfish-57.t:call-run_sawfish NOTICE task setup :: name: "run_sawfish", source: "./sawfish.wdl", line: 83, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-57/call-run_sawfish", thread: 140608731588160
2025-09-15 20:24:36.002 wdl.w:ptcp.w:call-paraphase-41.t:call-run_paraphase.slurm_singularity INFO srun: job 51797703 queued and waiting for resources
2025-09-15 20:24:36.002 wdl.w:ptcp.w:call-paraphase-41.t:call-run_paraphase.slurm_singularity INFO srun: job 51797703 has been allocated resources
2025-09-15 20:24:36.002 wdl.w:ptcp.w:call-paraphase-41.t:call-run_paraphase.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:36.002 wdl.w:ptcp.w:call-paraphase-41.t:call-run_paraphase.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:24:36.007 wdl.w:ptcp.w:call-trgt-48.t:call-get_reads_overlapping_repeats INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:36.008 wdl.w:ptcp.w:call-trgt-48.t:call-get_reads_overlapping_repeats INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:36.008 wdl.w:ptcp.w:call-trgt-48.t:call-get_reads_overlapping_repeats INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2145.mapped.bam.bai"
2025-09-15 20:24:36.008 wdl.w:ptcp.w:call-trgt-48.t:call-get_reads_overlapping_repeats INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2145.mapped.bam"
2025-09-15 20:24:36.008 wdl.w:ptcp.w:call-trgt-48.t:call-get_reads_overlapping_repeats INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2145"
2025-09-15 20:24:36.008 wdl.w:ptcp.w:call-trgt-48.t:call-get_reads_overlapping_repeats INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:36.008 wdl.w:ptcp.w:call-trgt-48.t:call-get_reads_overlapping_repeats INFO eval :: name: "expand_size", value: 3000
2025-09-15 20:24:36.008 wdl.w:ptcp.w:call-trgt-48.t:call-get_reads_overlapping_repeats INFO eval :: name: "threads", value: 1
2025-09-15 20:24:36.008 wdl.w:ptcp.w:call-trgt-48.t:call-get_reads_overlapping_repeats INFO eval :: name: "expanded_bed_name", value: "m84036_250809_035451_s4.bc2145.expanded.bed"
2025-09-15 20:24:36.009 wdl.w:ptcp.w:call-trgt-48.t:call-get_reads_overlapping_repeats INFO eval :: name: "disk_size", value: 11
2025-09-15 20:24:36.009 wdl.w:ptcp.w:call-trgt-48.t:call-get_reads_overlapping_repeats INFO eval :: name: "output_name", value: "m84036_250809_035451_s4.bc2145.repeats.bam"
2025-09-15 20:24:36.009 wdl.w:ptcp.w:call-trgt-48.t:call-get_reads_overlapping_repeats INFO eval :: name: "index_name", value: "m84036_250809_035451_s4.bc2145.repeats.bam.bai"
2025-09-15 20:24:36.009 wdl.w:ptcp.w:call-trgt-48.t:call-get_reads_overlapping_repeats INFO eval :: name: "output_name_with_index", value: "m84036_250809_035451_s4.bc2145.repeats.bam##idx##m84036_250809_035451_s4.bc2145.repeats.bam.bai"
2025-09-15 20:24:36.010 wdl.w:ptcp.w:call-trgt-48.t:call-get_reads_overlapping_repeats INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:36.010 wdl.w:ptcp.w:call-trgt-48.t:call-get_reads_overlapping_repeats WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:36.010 wdl.w:ptcp.w:call-sawfish-41.t:call-run_sawfish.slurm_singularity INFO srun: job 51797702 queued and waiting for resources
2025-09-15 20:24:36.010 wdl.w:ptcp.w:call-sawfish-41.t:call-run_sawfish.slurm_singularity INFO srun: job 51797702 has been allocated resources
2025-09-15 20:24:36.011 wdl.w:ptcp.w:call-sawfish-41.t:call-run_sawfish.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:36.011 wdl.w:ptcp.w:call-trgt-48.t:call-get_reads_overlapping_repeats INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:36.011 wdl.w:ptcp.w:call-trgt-48.t:call-get_reads_overlapping_repeats INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:36.025 wdl.w:ptcp.w:call-trgt-48.t:call-trgt_genotype INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:36.025 wdl.w:ptcp.w:call-trgt-48.t:call-trgt_genotype INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:36.025 wdl.w:ptcp.w:call-trgt-48.t:call-trgt_genotype INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:36.025 wdl.w:ptcp.w:call-trgt-48.t:call-trgt_genotype INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:36.025 wdl.w:ptcp.w:call-trgt-48.t:call-trgt_genotype INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2145.mapped.bam.bai"
2025-09-15 20:24:36.025 wdl.w:ptcp.w:call-trgt-48.t:call-trgt_genotype INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2145.mapped.bam"
2025-09-15 20:24:36.026 wdl.w:ptcp.w:call-trgt-48.t:call-trgt_genotype INFO input :: name: "sex", value: "F"
2025-09-15 20:24:36.026 wdl.w:ptcp.w:call-trgt-48.t:call-trgt_genotype INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2145"
2025-09-15 20:24:36.026 wdl.w:ptcp.w:call-trgt-48.t:call-trgt_genotype INFO eval :: name: "mem_gb", value: 16
2025-09-15 20:24:36.026 wdl.w:ptcp.w:call-trgt-48.t:call-trgt_genotype INFO eval :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2145.trgt"
2025-09-15 20:24:36.027 wdl.w:ptcp.w:call-trgt-48.t:call-trgt_genotype INFO eval :: name: "threads", value: 8
2025-09-15 20:24:36.027 wdl.w:ptcp.w:call-trgt-48.t:call-trgt_genotype INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:36.028 wdl.w:ptcp.w:call-trgt-48.t:call-trgt_genotype INFO eval :: name: "karyotype", value: "XX"
2025-09-15 20:24:36.028 wdl.w:ptcp.w:call-trgt-48.t:call-trgt_genotype INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 8, memory_reservation: 16000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:36.028 wdl.w:ptcp.w:call-trgt-48.t:call-trgt_genotype WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:36.029 wdl.w:ptcp.w:call-trgt-48.t:call-trgt_genotype INFO provisioned :: seconds_waited: 0, cpu: 8, mem_bytes: 16000000000
2025-09-15 20:24:36.029 wdl.w:ptcp.w:call-trgt-48.t:call-trgt_genotype INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:36.034 wdl.w:ptcp.w:call-paraphase-57.t:call-run_paraphase INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:36.034 wdl.w:ptcp.w:call-sawfish-57.t:call-run_sawfish INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:36.034 wdl.w:ptcp.w:call-paraphase-57.t:call-run_paraphase INFO input :: name: "annotation_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf"
2025-09-15 20:24:36.034 wdl.w:ptcp.w:call-sawfish-57.t:call-run_sawfish INFO input :: name: "genome_version", value: "38"
2025-09-15 20:24:36.035 wdl.w:ptcp.w:call-paraphase-57.t:call-run_paraphase INFO input :: name: "genome_version", value: "38"
2025-09-15 20:24:36.035 wdl.w:ptcp.w:call-sawfish-57.t:call-run_sawfish INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:36.035 wdl.w:ptcp.w:call-paraphase-57.t:call-run_paraphase INFO input :: name: "config_file", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/paraphase_config.GRCh38.yaml"
2025-09-15 20:24:36.035 wdl.w:ptcp.w:call-sawfish-57.t:call-run_sawfish INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:36.036 wdl.w:ptcp.w:call-paraphase-57.t:call-run_paraphase INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:36.036 wdl.w:ptcp.w:call-sawfish-57.t:call-run_sawfish INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2154.mapped.bam.bai"
2025-09-15 20:24:36.036 wdl.w:ptcp.w:call-paraphase-57.t:call-run_paraphase INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:36.036 wdl.w:ptcp.w:call-sawfish-57.t:call-run_sawfish INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2154.mapped.bam"
2025-09-15 20:24:36.037 wdl.w:ptcp.w:call-paraphase-57.t:call-run_paraphase INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2154.mapped.bam.bai"
2025-09-15 20:24:36.037 wdl.w:ptcp.w:call-sawfish-57.t:call-run_sawfish INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2154"
2025-09-15 20:24:36.037 wdl.w:ptcp.w:call-paraphase-57.t:call-run_paraphase INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2154.mapped.bam"
2025-09-15 20:24:36.037 wdl.w:ptcp.w:call-sawfish-57.t:call-run_sawfish INFO eval :: name: "mem_gb", value: 32
2025-09-15 20:24:36.037 wdl.w:ptcp.w:call-paraphase-57.t:call-run_paraphase INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2154"
2025-09-15 20:24:36.037 wdl.w:ptcp.w:call-sawfish-57.t:call-run_sawfish INFO eval :: name: "threads", value: 16
2025-09-15 20:24:36.038 wdl.w:ptcp.w:call-paraphase-57.t:call-run_paraphase INFO eval :: name: "threads", value: 4
2025-09-15 20:24:36.038 wdl.w:ptcp.w:call-paraphase-57.t:call-run_paraphase INFO eval :: name: "mem_gb", value: 8
2025-09-15 20:24:36.038 wdl.w:ptcp.w:call-sawfish-57.t:call-run_sawfish INFO eval :: name: "disk_size", value: 30
2025-09-15 20:24:36.039 wdl.w:ptcp.w:call-sawfish-57.t:call-run_sawfish INFO eval :: name: "discover_dirname", value: "m84036_250809_035451_s4.bc2154_sawfish_discover"
2025-09-15 20:24:36.039 wdl.w:ptcp.w:call-paraphase-57.t:call-run_paraphase INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:36.039 wdl.w:ptcp.w:call-trgt-41.t:call-get_reads_overlapping_repeats.slurm_singularity INFO srun: job 51797704 queued and waiting for resources
2025-09-15 20:24:36.039 wdl.w:ptcp.w:call-sawfish-57.t:call-run_sawfish INFO eval :: name: "call_dirname", value: "m84036_250809_035451_s4.bc2154_sawfish"
2025-09-15 20:24:36.039 wdl.w:ptcp.w:call-paraphase-57.t:call-run_paraphase INFO eval :: name: "out_dir", value: "m84036_250809_035451_s4.bc2154_paraphase"
2025-09-15 20:24:36.040 wdl.w:ptcp.w:call-trgt-41.t:call-get_reads_overlapping_repeats.slurm_singularity INFO srun: job 51797704 has been allocated resources
2025-09-15 20:24:36.040 wdl.w:ptcp.w:call-sawfish-57.t:call-run_sawfish INFO eval :: name: "minimap2_bam_filename", value: "m84036_250809_035451_s4.bc2154.minimap2.bam"
2025-09-15 20:24:36.040 wdl.w:ptcp.w:call-trgt-41.t:call-get_reads_overlapping_repeats.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:36.041 wdl.w:ptcp.w:call-paraphase-57.t:call-run_paraphase INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 4, memory_reservation: 8000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:36.041 wdl.w:ptcp.w:call-trgt-41.t:call-get_reads_overlapping_repeats.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:24:36.041 wdl.w:ptcp.w:call-paraphase-57.t:call-run_paraphase WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:36.041 wdl.w:ptcp.w:call-sawfish-57.t:call-run_sawfish INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 16, memory_reservation: 32000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:36.042 wdl.w:ptcp.w:call-sawfish-57.t:call-run_sawfish WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:36.043 wdl.w:ptcp.w:call-paraphase-57.t:call-run_paraphase INFO provisioned :: seconds_waited: 0, cpu: 4, mem_bytes: 8000000000
2025-09-15 20:24:36.043 wdl.w:ptcp.w:call-paraphase-57.t:call-run_paraphase INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:36.044 wdl.w:ptcp.w:call-sawfish-57.t:call-run_sawfish INFO provisioned :: seconds_waited: 0, cpu: 16, mem_bytes: 32000000000
2025-09-15 20:24:36.044 wdl.w:ptcp.w:call-sawfish-57.t:call-run_sawfish INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:36.059 wdl.w:ptcp.w:call-sawfish-48.t:call-run_sawfish INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 10, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-48/call-run_sawfish/_singularity_tmpdir_4v0_u39p"
2025-09-15 20:24:36.059 wdl.w:ptcp.w:call-sawfish-48.t:call-run_sawfish INFO Slurm invocation: srun --job-name call-run_sawfish --partition compute,compute9 --cpus-per-task 16 --mem 30518M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-48/call-run_sawfish/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-48/call-run_sawfish/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-48/call-run_sawfish/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-48/call-run_sawfish/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-48/out/m84036_250809_035451_s4.bc2145.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2145.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-48/out/m84036_250809_035451_s4.bc2145.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2145.mapped.bam.bai:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-48/call-run_sawfish/_singularity_tmpdir_4v0_u39p/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-48/call-run_sawfish/_singularity_tmpdir_4v0_u39p/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:36.077 wdl.w:ptcp.w:call-paraphase-38.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for smn1 for sample m84036_250809_035451_s4.bc2135 at 2025-09-15 20:24:26.489155...
2025-09-15 20:24:36.079 wdl.w:ptcp.w:call-paraphase-44 NOTICE done
2025-09-15 20:24:36.082 wdl.w:ptcp.w:call-paraphase-52.t:call-run_paraphase NOTICE done
2025-09-15 20:24:36.086 wdl.w:ptcp.w:call-trgt-41.t:call-trgt_genotype.slurm_singularity INFO srun: job 51797705 queued and waiting for resources
2025-09-15 20:24:36.086 wdl.w:ptcp.w:call-trgt-41.t:call-trgt_genotype.slurm_singularity INFO srun: job 51797705 has been allocated resources
2025-09-15 20:24:36.086 wdl.w:ptcp.w:call-trgt-41.t:call-trgt_genotype.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:36.089 wdl.w:ptcp NOTICE finish :: job: "call-paraphase-44"
2025-09-15 20:24:36.089 wdl.w:ptcp INFO output :: job: "call-paraphase-44", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-44/out/m84036_250809_035451_s4.bc2141.f8inversion.vcf", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-44/out/m84036_250809_035451_s4.bc2141_paraphase/m84036_250809_035451_s4.bc2141.paraphase.json", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-44/out/m84036_250809_035451_s4.bc2141_paraphase/m84036_250809_035451_s4.bc2141.paraphase.bam", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-44/out/m84036_250809_035451_s4.bc2141_paraphase/m84036_250809_035451_s4.bc2141.paraphase.bam.bai", "paraphase_vcfs": [], "havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-44/out/m84036_250809_035451_s4.bc2141.havanno.json", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-44/out/m84036_250809_035451_s4.bc2141.f8inversion.json"}
2025-09-15 20:24:36.090 wdl.w:ptcp.w:call-paraphase-52 NOTICE finish :: job: "call-run_paraphase"
2025-09-15 20:24:36.090 wdl.w:ptcp.w:call-paraphase-52 INFO output :: job: "call-run_paraphase", values: {"havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-52/call-run_paraphase/out/m84036_250809_035451_s4.bc2149.havanno.json", "paraphase_vcfs": [], "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-52/call-run_paraphase/out/m84036_250809_035451_s4.bc2149_paraphase/m84036_250809_035451_s4.bc2149.paraphase.json", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-52/call-run_paraphase/out/m84036_250809_035451_s4.bc2149_paraphase/m84036_250809_035451_s4.bc2149.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-52/call-run_paraphase/out/m84036_250809_035451_s4.bc2149_paraphase/m84036_250809_035451_s4.bc2149.paraphase.bam"}
2025-09-15 20:24:36.090 wdl.w:ptcp.w:call-paraphase-52 NOTICE ready :: job: "call-call_f8", callee: "call_f8"
2025-09-15 20:24:36.091 wdl.w:ptcp.w:call-paraphase-52 INFO input :: job: "call-call_f8", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "out_prefix": "m84036_250809_035451_s4.bc2149", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-52/call-run_paraphase/out/m84036_250809_035451_s4.bc2149_paraphase/m84036_250809_035451_s4.bc2149.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-52/call-run_paraphase/out/m84036_250809_035451_s4.bc2149_paraphase/m84036_250809_035451_s4.bc2149.paraphase.bam", "sex": "F"}
2025-09-15 20:24:36.093 wdl.w:ptcp.w:call-paraphase-52 INFO visit :: node: "output-havanno_json", values: {"havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-52/call-run_paraphase/out/m84036_250809_035451_s4.bc2149.havanno.json"}
2025-09-15 20:24:36.093 wdl.w:ptcp.w:call-paraphase-52 INFO visit :: node: "output-paraphase_bam", values: {"paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-52/call-run_paraphase/out/m84036_250809_035451_s4.bc2149_paraphase/m84036_250809_035451_s4.bc2149.paraphase.bam"}
2025-09-15 20:24:36.093 wdl.w:ptcp.w:call-paraphase-52 INFO visit :: node: "output-paraphase_bam_bai", values: {"paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-52/call-run_paraphase/out/m84036_250809_035451_s4.bc2149_paraphase/m84036_250809_035451_s4.bc2149.paraphase.bam.bai"}
2025-09-15 20:24:36.093 wdl.w:ptcp.w:call-paraphase-52 INFO visit :: node: "output-paraphase_json", values: {"paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-52/call-run_paraphase/out/m84036_250809_035451_s4.bc2149_paraphase/m84036_250809_035451_s4.bc2149.paraphase.json"}
2025-09-15 20:24:36.093 wdl.w:ptcp.w:call-paraphase-52 INFO visit :: node: "output-paraphase_vcfs", values: {"paraphase_vcfs": []}
2025-09-15 20:24:36.094 wdl.w:ptcp.w:call-trgt-38.t:call-trgt_plot_meth_waterfall NOTICE done
2025-09-15 20:24:36.102 wdl.w:ptcp.w:call-trgt-38 NOTICE finish :: job: "call-trgt_plot_meth_waterfall"
2025-09-15 20:24:36.102 wdl.w:ptcp.w:call-trgt-38 INFO output :: job: "call-trgt_plot_meth_waterfall", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-38/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2135.meth_waterfall.trgt_plots.zip"}
2025-09-15 20:24:36.102 wdl.w:ptcp.w:call-trgt-38 INFO visit :: node: "output-images_meth_waterfall", values: {"images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-38/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2135.meth_waterfall.trgt_plots.zip"}
2025-09-15 20:24:36.103 wdl.w:ptcp.w:call-trgt-38 INFO visit :: node: "outputs", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-38/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2135.motifs_waterfall.trgt_plots.zip", "images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-38/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2135.meth_allele.trgt_plots.zip", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-38/call-trgt_genotype/out/m84036_250809_035451_s4.bc2135.trgt.sorted.spanning.bam.bai", "images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-38/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2135.motifs_allele.trgt_plots.zip", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-38/call-trgt_genotype/out/m84036_250809_035451_s4.bc2135.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-38/call-trgt_genotype/out/m84036_250809_035451_s4.bc2135.trgt.vcf", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-38/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2135.repeats.bam", "images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-38/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2135.meth_waterfall.trgt_plots.zip", "reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-38/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2135.repeats.bam.bai"}
2025-09-15 20:24:36.104 wdl.w:ptcp.w:call-trgt-57.t:call-get_reads_overlapping_repeats NOTICE task setup :: name: "get_reads_overlapping_repeats", source: "./trgt.wdl", line: 182, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-57/call-get_reads_overlapping_repeats", thread: 140609838900800
2025-09-15 20:24:36.105 wdl.w:ptcp.w:call-trgt-48.t:call-get_reads_overlapping_repeats INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 9, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-48/call-get_reads_overlapping_repeats/_singularity_tmpdir_n_79_h9r"
2025-09-15 20:24:36.105 wdl.w:ptcp.w:call-trgt-48.t:call-get_reads_overlapping_repeats INFO Slurm invocation: srun --job-name call-get_reads_overlapping_repeats --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-48/call-get_reads_overlapping_repeats/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-48/call-get_reads_overlapping_repeats/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-48/call-get_reads_overlapping_repeats/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-48/call-get_reads_overlapping_repeats/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-48/out/m84036_250809_035451_s4.bc2145.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2145.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-48/out/m84036_250809_035451_s4.bc2145.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2145.mapped.bam.bai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-48/call-get_reads_overlapping_repeats/_singularity_tmpdir_n_79_h9r/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-48/call-get_reads_overlapping_repeats/_singularity_tmpdir_n_79_h9r/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:36.106 wdl.w:ptcp.w:call-paraphase-64 NOTICE workflow start :: name: "paraphase", source: "./paraphase.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-64"
2025-09-15 20:24:36.109 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_plot_meth_waterfall INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2143.meth_waterfall.trgt_plots.zip"
2025-09-15 20:24:36.115 wdl.w:ptcp.w:call-trgt-57.t:call-trgt_genotype NOTICE task setup :: name: "trgt_genotype", source: "./trgt.wdl", line: 272, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-57/call-trgt_genotype", thread: 140609310422592
2025-09-15 20:24:36.132 wdl.w:ptcp.w:call-sawfish-48.t:call-run_sawfish NOTICE slurm_singularity run :: pid: 1202428, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-48/call-run_sawfish/slurm_singularity.log.txt"
2025-09-15 20:24:36.134 wdl.w:ptcp.w:call-trgt-48.t:call-get_reads_overlapping_repeats NOTICE slurm_singularity run :: pid: 1202430, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-48/call-get_reads_overlapping_repeats/slurm_singularity.log.txt"
2025-09-15 20:24:36.134 wdl.w:ptcp.w:call-trgt-57.t:call-get_reads_overlapping_repeats INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:36.135 wdl.w:ptcp.w:call-trgt-57.t:call-get_reads_overlapping_repeats INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:36.135 wdl.w:ptcp.w:call-trgt-57.t:call-get_reads_overlapping_repeats INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2154.mapped.bam.bai"
2025-09-15 20:24:36.135 wdl.w:ptcp.w:call-trgt-57.t:call-get_reads_overlapping_repeats INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2154.mapped.bam"
2025-09-15 20:24:36.135 wdl.w:ptcp.w:call-trgt-57.t:call-get_reads_overlapping_repeats INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2154"
2025-09-15 20:24:36.135 wdl.w:ptcp.w:call-trgt-57.t:call-get_reads_overlapping_repeats INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:36.136 wdl.w:ptcp.w:call-trgt-57.t:call-get_reads_overlapping_repeats INFO eval :: name: "expand_size", value: 3000
2025-09-15 20:24:36.135 wdl.w:ptcp.w:call-paraphase-40.t:call-run_paraphase.slurm_singularity INFO srun: job 51797706 queued and waiting for resources
2025-09-15 20:24:36.136 wdl.w:ptcp.w:call-paraphase-40.t:call-run_paraphase.slurm_singularity INFO srun: job 51797706 has been allocated resources
2025-09-15 20:24:36.136 wdl.w:ptcp.w:call-trgt-57.t:call-get_reads_overlapping_repeats INFO eval :: name: "threads", value: 1
2025-09-15 20:24:36.137 wdl.w:ptcp.w:call-paraphase-64 INFO visit :: node: "decl-annotation_vcf", values: {"annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf"}
2025-09-15 20:24:36.137 wdl.w:ptcp.w:call-paraphase-40.t:call-run_paraphase.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:36.138 wdl.w:ptcp.w:call-trgt-57.t:call-get_reads_overlapping_repeats INFO eval :: name: "expanded_bed_name", value: "m84036_250809_035451_s4.bc2154.expanded.bed"
2025-09-15 20:24:36.138 wdl.w:ptcp.w:call-paraphase-64 INFO visit :: node: "decl-config_file", values: {"config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml"}
2025-09-15 20:24:36.138 wdl.w:ptcp.w:call-paraphase-40.t:call-run_paraphase.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:24:36.138 wdl.w:ptcp.w:call-paraphase-64 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:24:36.138 wdl.w:ptcp.w:call-trgt-57.t:call-get_reads_overlapping_repeats INFO eval :: name: "disk_size", value: 11
2025-09-15 20:24:36.139 wdl.w:ptcp.w:call-paraphase-64 INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:24:36.139 wdl.w:ptcp.w:call-trgt-57.t:call-get_reads_overlapping_repeats INFO eval :: name: "output_name", value: "m84036_250809_035451_s4.bc2154.repeats.bam"
2025-09-15 20:24:36.139 wdl.w:ptcp.w:call-paraphase-64 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-64/out/m84036_250809_035451_s4.bc2161.mapped.bam"}
2025-09-15 20:24:36.140 wdl.w:ptcp.w:call-trgt-57.t:call-get_reads_overlapping_repeats INFO eval :: name: "index_name", value: "m84036_250809_035451_s4.bc2154.repeats.bam.bai"
2025-09-15 20:24:36.140 wdl.w:ptcp.w:call-paraphase-64 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-64/out/m84036_250809_035451_s4.bc2161.mapped.bam.bai"}
2025-09-15 20:24:36.140 wdl.w:ptcp.w:call-trgt-57.t:call-get_reads_overlapping_repeats INFO eval :: name: "output_name_with_index", value: "m84036_250809_035451_s4.bc2154.repeats.bam##idx##m84036_250809_035451_s4.bc2154.repeats.bam.bai"
2025-09-15 20:24:36.140 wdl.w:ptcp.w:call-paraphase-64 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:24:36.141 wdl.w:ptcp.w:call-paraphase-64 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:24:36.141 wdl.w:ptcp.w:call-paraphase-64 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2161"}
2025-09-15 20:24:36.142 wdl.w:ptcp.w:call-paraphase-64 INFO visit :: node: "decl-sex", values: {"sex": "F"}
2025-09-15 20:24:36.142 wdl.w:ptcp.w:call-trgt-57.t:call-get_reads_overlapping_repeats INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:36.142 wdl.w:ptcp.w:call-paraphase-64 NOTICE ready :: job: "call-run_paraphase", callee: "run_paraphase"
2025-09-15 20:24:36.143 wdl.w:ptcp.w:call-trgt-57.t:call-get_reads_overlapping_repeats WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:36.143 wdl.w:ptcp.w:call-paraphase-64 INFO input :: job: "call-run_paraphase", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf", "genome_version": "38", "config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-64/out/m84036_250809_035451_s4.bc2161.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-64/out/m84036_250809_035451_s4.bc2161.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2161"}
2025-09-15 20:24:36.143 wdl.w:ptcp.w:call-trgt-00.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:34 [ERROR] - No reads found for TRID=PRTS_ARX
2025-09-15 20:24:36.144 wdl.w:ptcp.w:call-trgt-00.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:34 [ERROR] - No reads found for TRID=EIEE1_ARX
2025-09-15 20:24:36.145 wdl.w:ptcp.w:call-trgt-57.t:call-get_reads_overlapping_repeats INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:36.146 wdl.w:ptcp.w:call-trgt-57.t:call-get_reads_overlapping_repeats INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:36.152 wdl.w:ptcp.w:call-trgt-57.t:call-trgt_genotype INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:36.152 wdl.w:ptcp.w:call-trgt-57.t:call-trgt_genotype INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:36.152 wdl.w:ptcp.w:call-trgt-57.t:call-trgt_genotype INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:36.152 wdl.w:ptcp.w:call-trgt-57.t:call-trgt_genotype INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:36.152 wdl.w:ptcp.w:call-trgt-57.t:call-trgt_genotype INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2154.mapped.bam.bai"
2025-09-15 20:24:36.152 wdl.w:ptcp.w:call-trgt-57.t:call-trgt_genotype INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2154.mapped.bam"
2025-09-15 20:24:36.153 wdl.w:ptcp.w:call-trgt-57.t:call-trgt_genotype INFO input :: name: "sex", value: "F"
2025-09-15 20:24:36.153 wdl.w:ptcp.w:call-trgt-57.t:call-trgt_genotype INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2154"
2025-09-15 20:24:36.153 wdl.w:ptcp.w:call-trgt-57.t:call-trgt_genotype INFO eval :: name: "mem_gb", value: 16
2025-09-15 20:24:36.153 wdl.w:ptcp.w:call-trgt-57.t:call-trgt_genotype INFO eval :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2154.trgt"
2025-09-15 20:24:36.153 wdl.w:ptcp.w:call-trgt-57.t:call-trgt_genotype INFO eval :: name: "threads", value: 8
2025-09-15 20:24:36.153 wdl.w:ptcp.w:call-trgt-57.t:call-trgt_genotype INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:36.154 wdl.w:ptcp.w:call-trgt-57.t:call-trgt_genotype INFO eval :: name: "karyotype", value: "XX"
2025-09-15 20:24:36.154 wdl.w:ptcp.w:call-trgt-57.t:call-trgt_genotype INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 8, memory_reservation: 16000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:36.154 wdl.w:ptcp.w:call-trgt-57.t:call-trgt_genotype WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:36.154 wdl.w:ptcp.w:call-trgt-57.t:call-trgt_genotype INFO provisioned :: seconds_waited: 0, cpu: 8, mem_bytes: 16000000000
2025-09-15 20:24:36.155 wdl.w:ptcp.w:call-trgt-57.t:call-trgt_genotype INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:36.157 wdl.w:ptcp.w:call-trgt-48.t:call-trgt_genotype INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 11, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-48/call-trgt_genotype/_singularity_tmpdir_2jjajmsp"
2025-09-15 20:24:36.157 wdl.w:ptcp.w:call-trgt-48.t:call-trgt_genotype INFO Slurm invocation: srun --job-name call-trgt_genotype --partition compute,compute9 --cpus-per-task 8 --mem 15259M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-48/call-trgt_genotype/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-48/call-trgt_genotype/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-48/call-trgt_genotype/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-48/call-trgt_genotype/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-48/out/m84036_250809_035451_s4.bc2145.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2145.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-48/out/m84036_250809_035451_s4.bc2145.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2145.mapped.bam.bai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-48/call-trgt_genotype/_singularity_tmpdir_2jjajmsp/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-48/call-trgt_genotype/_singularity_tmpdir_2jjajmsp/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:36.163 wdl.w:ptcp.w:call-sawfish-57.t:call-run_sawfish INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 10, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-57/call-run_sawfish/_singularity_tmpdir_byvy387a"
2025-09-15 20:24:36.163 wdl.w:ptcp.w:call-sawfish-57.t:call-run_sawfish INFO Slurm invocation: srun --job-name call-run_sawfish --partition compute,compute9 --cpus-per-task 16 --mem 30518M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-57/call-run_sawfish/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-57/call-run_sawfish/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-57/call-run_sawfish/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-57/call-run_sawfish/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-57/out/m84036_250809_035451_s4.bc2154.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2154.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-57/out/m84036_250809_035451_s4.bc2154.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2154.mapped.bam.bai:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-57/call-run_sawfish/_singularity_tmpdir_byvy387a/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-57/call-run_sawfish/_singularity_tmpdir_byvy387a/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:36.166 wdl.w:ptcp.w:call-trgt-37.t:call-trgt_plot_meth_allele INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2134.meth_allele.trgt_plots.zip"
2025-09-15 20:24:36.181 wdl.w:ptcp.w:call-sawfish-40.t:call-run_sawfish.stderr VERBOSE [M::bam2fq_mainloop] discarded 0 singletons
2025-09-15 20:24:36.181 wdl.w:ptcp.w:call-sawfish-40.t:call-run_sawfish.stderr VERBOSE [M::bam2fq_mainloop] processed 0 reads
2025-09-15 20:24:36.192 wdl.w:ptcp.w:call-paraphase-57.t:call-run_paraphase INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-57/call-run_paraphase/_singularity_tmpdir_ga6lugk7"
2025-09-15 20:24:36.192 wdl.w:ptcp.w:call-paraphase-57.t:call-run_paraphase INFO Slurm invocation: srun --job-name call-run_paraphase --partition compute,compute9 --cpus-per-task 4 --mem 7629M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-57/call-run_paraphase/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-57/call-run_paraphase/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-57/call-run_paraphase/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-57/call-run_paraphase/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-57/out/m84036_250809_035451_s4.bc2154.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2154.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-57/out/m84036_250809_035451_s4.bc2154.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2154.mapped.bam.bai:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/variant_list/variant_list.GRCh38.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf:ro --bind /ptcp/meta/paraphase/paraphase_config.GRCh38.yaml:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/paraphase_config.GRCh38.yaml:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-57/call-run_paraphase/_singularity_tmpdir_ga6lugk7/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-57/call-run_paraphase/_singularity_tmpdir_ga6lugk7/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:36.197 wdl.w:ptcp.w:call-sawfish-40.t:call-run_sawfish.slurm_singularity INFO srun: job 51797707 queued and waiting for resources
2025-09-15 20:24:36.197 wdl.w:ptcp.w:call-sawfish-40.t:call-run_sawfish.slurm_singularity INFO srun: job 51797707 has been allocated resources
2025-09-15 20:24:36.197 wdl.w:ptcp.w:call-sawfish-40.t:call-run_sawfish.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:36.197 wdl.w:ptcp.w:call-sawfish-40.t:call-run_sawfish.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:24:36.203 wdl.w:ptcp.w:call-sawfish-57.t:call-run_sawfish NOTICE slurm_singularity run :: pid: 1202435, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-57/call-run_sawfish/slurm_singularity.log.txt"
2025-09-15 20:24:36.206 wdl.w:ptcp.w:call-trgt-48.t:call-trgt_genotype NOTICE slurm_singularity run :: pid: 1202434, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-48/call-trgt_genotype/slurm_singularity.log.txt"
2025-09-15 20:24:36.209 wdl.w:ptcp.w:call-paraphase-57.t:call-run_paraphase NOTICE slurm_singularity run :: pid: 1202446, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-57/call-run_paraphase/slurm_singularity.log.txt"
2025-09-15 20:24:36.230 wdl.w:ptcp.w:call-trgt-00.t:call-trgt_plot_meth_waterfall INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2097.meth_waterfall.trgt_plots.zip"
2025-09-15 20:24:36.232 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_plot_meth_waterfall NOTICE done
2025-09-15 20:24:36.238 wdl.w:ptcp.w:call-trgt-57.t:call-get_reads_overlapping_repeats INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 9, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-57/call-get_reads_overlapping_repeats/_singularity_tmpdir_8gp7qkjo"
2025-09-15 20:24:36.238 wdl.w:ptcp.w:call-trgt-57.t:call-get_reads_overlapping_repeats INFO Slurm invocation: srun --job-name call-get_reads_overlapping_repeats --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-57/call-get_reads_overlapping_repeats/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-57/call-get_reads_overlapping_repeats/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-57/call-get_reads_overlapping_repeats/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-57/call-get_reads_overlapping_repeats/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-57/out/m84036_250809_035451_s4.bc2154.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2154.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-57/out/m84036_250809_035451_s4.bc2154.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2154.mapped.bam.bai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-57/call-get_reads_overlapping_repeats/_singularity_tmpdir_8gp7qkjo/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-57/call-get_reads_overlapping_repeats/_singularity_tmpdir_8gp7qkjo/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:36.238 wdl.w:ptcp.w:call-trgt-46 NOTICE finish :: job: "call-trgt_plot_meth_waterfall"
2025-09-15 20:24:36.240 wdl.w:ptcp.w:call-trgt-46 INFO output :: job: "call-trgt_plot_meth_waterfall", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-46/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2143.meth_waterfall.trgt_plots.zip"}
2025-09-15 20:24:36.242 wdl.w:ptcp.w:call-trgt-46 INFO visit :: node: "output-images_meth_waterfall", values: {"images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-46/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2143.meth_waterfall.trgt_plots.zip"}
2025-09-15 20:24:36.253 wdl.w:ptcp.w:call-paraphase-49.t:call-run_paraphase NOTICE task setup :: name: "run_paraphase", source: "./paraphase.wdl", line: 127, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-49/call-run_paraphase", thread: 140609847293504
2025-09-15 20:24:36.254 wdl.w:ptcp.w:call-trgt-38 NOTICE done
2025-09-15 20:24:36.259 wdl.w:ptcp NOTICE finish :: job: "call-trgt-38"
2025-09-15 20:24:36.259 wdl.w:ptcp INFO output :: job: "call-trgt-38", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-38/out/m84036_250809_035451_s4.bc2135.motifs_waterfall.trgt_plots.zip", "images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-38/out/m84036_250809_035451_s4.bc2135.meth_allele.trgt_plots.zip", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-38/out/m84036_250809_035451_s4.bc2135.trgt.sorted.spanning.bam.bai", "images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-38/out/m84036_250809_035451_s4.bc2135.motifs_allele.trgt_plots.zip", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-38/out/m84036_250809_035451_s4.bc2135.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-38/out/m84036_250809_035451_s4.bc2135.trgt.vcf", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-38/out/m84036_250809_035451_s4.bc2135.repeats.bam", "images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-38/out/m84036_250809_035451_s4.bc2135.meth_waterfall.trgt_plots.zip", "reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-38/out/m84036_250809_035451_s4.bc2135.repeats.bam.bai"}
2025-09-15 20:24:36.260 wdl.w:ptcp.w:call-trgt-57.t:call-trgt_genotype INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 11, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-57/call-trgt_genotype/_singularity_tmpdir_uz2w27gl"
2025-09-15 20:24:36.260 wdl.w:ptcp.w:call-trgt-57.t:call-trgt_genotype INFO Slurm invocation: srun --job-name call-trgt_genotype --partition compute,compute9 --cpus-per-task 8 --mem 15259M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-57/call-trgt_genotype/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-57/call-trgt_genotype/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-57/call-trgt_genotype/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-57/call-trgt_genotype/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-57/out/m84036_250809_035451_s4.bc2154.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2154.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-57/out/m84036_250809_035451_s4.bc2154.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2154.mapped.bam.bai:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-57/call-trgt_genotype/_singularity_tmpdir_uz2w27gl/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-57/call-trgt_genotype/_singularity_tmpdir_uz2w27gl/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:36.269 wdl.w:ptcp.w:call-sawfish-64 NOTICE workflow start :: name: "sawfish", source: "./sawfish.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-64"
2025-09-15 20:24:36.274 wdl.w:ptcp.w:call-trgt-57.t:call-get_reads_overlapping_repeats NOTICE slurm_singularity run :: pid: 1202450, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-57/call-get_reads_overlapping_repeats/slurm_singularity.log.txt"
2025-09-15 20:24:36.277 wdl.w:ptcp.w:call-paraphase-49.t:call-run_paraphase INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:36.278 wdl.w:ptcp.w:call-paraphase-49.t:call-run_paraphase INFO input :: name: "annotation_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf"
2025-09-15 20:24:36.278 wdl.w:ptcp.w:call-paraphase-49.t:call-run_paraphase INFO input :: name: "genome_version", value: "38"
2025-09-15 20:24:36.278 wdl.w:ptcp.w:call-paraphase-49.t:call-run_paraphase INFO input :: name: "config_file", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/paraphase_config.GRCh38.yaml"
2025-09-15 20:24:36.278 wdl.w:ptcp.w:call-paraphase-49.t:call-run_paraphase INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:36.278 wdl.w:ptcp.w:call-paraphase-49.t:call-run_paraphase INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:36.278 wdl.w:ptcp.w:call-paraphase-49.t:call-run_paraphase INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2146.mapped.bam.bai"
2025-09-15 20:24:36.278 wdl.w:ptcp.w:call-paraphase-49.t:call-run_paraphase INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2146.mapped.bam"
2025-09-15 20:24:36.278 wdl.w:ptcp.w:call-paraphase-49.t:call-run_paraphase INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2146"
2025-09-15 20:24:36.278 wdl.w:ptcp.w:call-paraphase-49.t:call-run_paraphase INFO eval :: name: "threads", value: 4
2025-09-15 20:24:36.278 wdl.w:ptcp.w:call-paraphase-49.t:call-run_paraphase INFO eval :: name: "mem_gb", value: 8
2025-09-15 20:24:36.279 wdl.w:ptcp.w:call-trgt-57.t:call-trgt_genotype NOTICE slurm_singularity run :: pid: 1202451, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-57/call-trgt_genotype/slurm_singularity.log.txt"
2025-09-15 20:24:36.279 wdl.w:ptcp.w:call-paraphase-49.t:call-run_paraphase INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:36.279 wdl.w:ptcp.w:call-paraphase-49.t:call-run_paraphase INFO eval :: name: "out_dir", value: "m84036_250809_035451_s4.bc2146_paraphase"
2025-09-15 20:24:36.280 wdl.w:ptcp.w:call-paraphase-49.t:call-run_paraphase INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 4, memory_reservation: 8000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:36.280 wdl.w:ptcp.w:call-paraphase-49.t:call-run_paraphase WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:36.282 wdl.w:ptcp.w:call-paraphase-49.t:call-run_paraphase INFO provisioned :: seconds_waited: 0, cpu: 4, mem_bytes: 8000000000
2025-09-15 20:24:36.282 wdl.w:ptcp.w:call-paraphase-49.t:call-run_paraphase INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:36.286 wdl.w:ptcp.w:call-sawfish-64 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:24:36.286 wdl.w:ptcp.w:call-sawfish-64 INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:24:36.287 wdl.w:ptcp.w:call-sawfish-64 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-64/out/m84036_250809_035451_s4.bc2161.mapped.bam"}
2025-09-15 20:24:36.287 wdl.w:ptcp.w:call-sawfish-64 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-64/out/m84036_250809_035451_s4.bc2161.mapped.bam.bai"}
2025-09-15 20:24:36.287 wdl.w:ptcp.w:call-sawfish-64 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:24:36.287 wdl.w:ptcp.w:call-sawfish-64 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:24:36.287 wdl.w:ptcp.w:call-sawfish-64 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2161"}
2025-09-15 20:24:36.287 wdl.w:ptcp.w:call-sawfish-64 NOTICE ready :: job: "call-run_sawfish", callee: "run_sawfish"
2025-09-15 20:24:36.288 wdl.w:ptcp.w:call-sawfish-64 INFO input :: job: "call-run_sawfish", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-64/out/m84036_250809_035451_s4.bc2161.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-64/out/m84036_250809_035451_s4.bc2161.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2161"}
2025-09-15 20:24:36.298 wdl.w:ptcp.w:call-trgt-40.t:call-get_reads_overlapping_repeats.slurm_singularity INFO srun: job 51797708 queued and waiting for resources
2025-09-15 20:24:36.298 wdl.w:ptcp.w:call-trgt-40.t:call-get_reads_overlapping_repeats.slurm_singularity INFO srun: job 51797708 has been allocated resources
2025-09-15 20:24:36.299 wdl.w:ptcp.w:call-trgt-40.t:call-get_reads_overlapping_repeats.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:36.339 wdl.w:ptcp.w:call-trgt-37.t:call-trgt_plot_meth_allele NOTICE done
2025-09-15 20:24:36.343 wdl.w:ptcp.w:call-trgt-37 NOTICE finish :: job: "call-trgt_plot_meth_allele"
2025-09-15 20:24:36.344 wdl.w:ptcp.w:call-trgt-37 INFO output :: job: "call-trgt_plot_meth_allele", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-37/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2134.meth_allele.trgt_plots.zip"}
2025-09-15 20:24:36.344 wdl.w:ptcp.w:call-trgt-37 INFO visit :: node: "output-images_meth_allele", values: {"images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-37/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2134.meth_allele.trgt_plots.zip"}
2025-09-15 20:24:36.354 wdl.w:ptcp.w:call-sawfish-49.t:call-run_sawfish NOTICE task setup :: name: "run_sawfish", source: "./sawfish.wdl", line: 83, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-49/call-run_sawfish", thread: 140610887464512
2025-09-15 20:24:36.357 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_plot_motifs_allele INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2143.motifs_allele.trgt_plots.zip"
2025-09-15 20:24:36.372 wdl.w:ptcp.w:call-paraphase-49.t:call-run_paraphase INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-49/call-run_paraphase/_singularity_tmpdir_uwo6nf4d"
2025-09-15 20:24:36.372 wdl.w:ptcp.w:call-paraphase-49.t:call-run_paraphase INFO Slurm invocation: srun --job-name call-run_paraphase --partition compute,compute9 --cpus-per-task 4 --mem 7629M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-49/call-run_paraphase/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-49/call-run_paraphase/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-49/call-run_paraphase/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-49/call-run_paraphase/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-49/out/m84036_250809_035451_s4.bc2146.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2146.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-49/out/m84036_250809_035451_s4.bc2146.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2146.mapped.bam:ro --bind /ptcp/meta/variant_list/variant_list.GRCh38.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf:ro --bind /ptcp/meta/paraphase/paraphase_config.GRCh38.yaml:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/paraphase_config.GRCh38.yaml:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-49/call-run_paraphase/_singularity_tmpdir_uwo6nf4d/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-49/call-run_paraphase/_singularity_tmpdir_uwo6nf4d/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:36.377 wdl.w:ptcp.w:call-trgt-01.t:call-trgt_plot_motifs_waterfall INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2098.motifs_waterfall.trgt_plots.zip"
2025-09-15 20:24:36.386 wdl.w:ptcp.w:call-sawfish-49.t:call-run_sawfish INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:36.386 wdl.w:ptcp.w:call-sawfish-49.t:call-run_sawfish INFO input :: name: "genome_version", value: "38"
2025-09-15 20:24:36.386 wdl.w:ptcp.w:call-sawfish-49.t:call-run_sawfish INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:36.386 wdl.w:ptcp.w:call-sawfish-49.t:call-run_sawfish INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:36.386 wdl.w:ptcp.w:call-sawfish-49.t:call-run_sawfish INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2146.mapped.bam.bai"
2025-09-15 20:24:36.386 wdl.w:ptcp.w:call-sawfish-49.t:call-run_sawfish INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2146.mapped.bam"
2025-09-15 20:24:36.386 wdl.w:ptcp.w:call-sawfish-49.t:call-run_sawfish INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2146"
2025-09-15 20:24:36.386 wdl.w:ptcp.w:call-sawfish-49.t:call-run_sawfish INFO eval :: name: "mem_gb", value: 32
2025-09-15 20:24:36.386 wdl.w:ptcp.w:call-sawfish-49.t:call-run_sawfish INFO eval :: name: "threads", value: 16
2025-09-15 20:24:36.387 wdl.w:ptcp.w:call-sawfish-49.t:call-run_sawfish INFO eval :: name: "disk_size", value: 30
2025-09-15 20:24:36.387 wdl.w:ptcp.w:call-sawfish-49.t:call-run_sawfish INFO eval :: name: "discover_dirname", value: "m84036_250809_035451_s4.bc2146_sawfish_discover"
2025-09-15 20:24:36.387 wdl.w:ptcp.w:call-sawfish-49.t:call-run_sawfish INFO eval :: name: "call_dirname", value: "m84036_250809_035451_s4.bc2146_sawfish"
2025-09-15 20:24:36.387 wdl.w:ptcp.w:call-sawfish-49.t:call-run_sawfish INFO eval :: name: "minimap2_bam_filename", value: "m84036_250809_035451_s4.bc2146.minimap2.bam"
2025-09-15 20:24:36.387 wdl.w:ptcp.w:call-sawfish-49.t:call-run_sawfish INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 16, memory_reservation: 32000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:36.387 wdl.w:ptcp.w:call-sawfish-49.t:call-run_sawfish WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:36.388 wdl.w:ptcp.w:call-sawfish-49.t:call-run_sawfish INFO provisioned :: seconds_waited: 0, cpu: 16, mem_bytes: 32000000000
2025-09-15 20:24:36.388 wdl.w:ptcp.w:call-sawfish-49.t:call-run_sawfish INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:36.389 wdl.w:ptcp.w:call-trgt-00.t:call-trgt_plot_meth_waterfall NOTICE done
2025-09-15 20:24:36.395 wdl.w:ptcp.w:call-trgt-00 NOTICE finish :: job: "call-trgt_plot_meth_waterfall"
2025-09-15 20:24:36.395 wdl.w:ptcp.w:call-trgt-00 INFO output :: job: "call-trgt_plot_meth_waterfall", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-00/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2097.meth_waterfall.trgt_plots.zip"}
2025-09-15 20:24:36.395 wdl.w:ptcp.w:call-trgt-00 INFO visit :: node: "output-images_meth_waterfall", values: {"images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-00/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2097.meth_waterfall.trgt_plots.zip"}
2025-09-15 20:24:36.401 wdl.w:ptcp.w:call-trgt-49.t:call-get_reads_overlapping_repeats NOTICE task setup :: name: "get_reads_overlapping_repeats", source: "./trgt.wdl", line: 182, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-49/call-get_reads_overlapping_repeats", thread: 140607137760832
2025-09-15 20:24:36.417 wdl.w:ptcp.w:call-trgt-01.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:33 [ERROR] - No reads found for TRID=PRTS_ARX
2025-09-15 20:24:36.417 wdl.w:ptcp.w:call-trgt-01.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:33 [ERROR] - No reads found for TRID=EIEE1_ARX
2025-09-15 20:24:36.420 wdl.w:ptcp.w:call-trgt-49.t:call-get_reads_overlapping_repeats INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:36.420 wdl.w:ptcp.w:call-trgt-49.t:call-get_reads_overlapping_repeats INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:36.420 wdl.w:ptcp.w:call-trgt-49.t:call-get_reads_overlapping_repeats INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2146.mapped.bam.bai"
2025-09-15 20:24:36.420 wdl.w:ptcp.w:call-trgt-49.t:call-get_reads_overlapping_repeats INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2146.mapped.bam"
2025-09-15 20:24:36.421 wdl.w:ptcp.w:call-trgt-49.t:call-get_reads_overlapping_repeats INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2146"
2025-09-15 20:24:36.421 wdl.w:ptcp.w:call-trgt-49.t:call-get_reads_overlapping_repeats INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:36.421 wdl.w:ptcp.w:call-trgt-49.t:call-get_reads_overlapping_repeats INFO eval :: name: "expand_size", value: 3000
2025-09-15 20:24:36.421 wdl.w:ptcp.w:call-trgt-49.t:call-get_reads_overlapping_repeats INFO eval :: name: "threads", value: 1
2025-09-15 20:24:36.421 wdl.w:ptcp.w:call-trgt-49.t:call-get_reads_overlapping_repeats INFO eval :: name: "expanded_bed_name", value: "m84036_250809_035451_s4.bc2146.expanded.bed"
2025-09-15 20:24:36.421 wdl.w:ptcp.w:call-trgt-49.t:call-get_reads_overlapping_repeats INFO eval :: name: "disk_size", value: 11
2025-09-15 20:24:36.421 wdl.w:ptcp.w:call-trgt-49.t:call-get_reads_overlapping_repeats INFO eval :: name: "output_name", value: "m84036_250809_035451_s4.bc2146.repeats.bam"
2025-09-15 20:24:36.421 wdl.w:ptcp.w:call-trgt-49.t:call-get_reads_overlapping_repeats INFO eval :: name: "index_name", value: "m84036_250809_035451_s4.bc2146.repeats.bam.bai"
2025-09-15 20:24:36.422 wdl.w:ptcp.w:call-trgt-49.t:call-get_reads_overlapping_repeats INFO eval :: name: "output_name_with_index", value: "m84036_250809_035451_s4.bc2146.repeats.bam##idx##m84036_250809_035451_s4.bc2146.repeats.bam.bai"
2025-09-15 20:24:36.422 wdl.w:ptcp.w:call-trgt-49.t:call-get_reads_overlapping_repeats INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:36.422 wdl.w:ptcp.w:call-trgt-49.t:call-get_reads_overlapping_repeats WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:36.422 wdl.w:ptcp.w:call-trgt-49.t:call-get_reads_overlapping_repeats INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:36.423 wdl.w:ptcp.w:call-trgt-49.t:call-get_reads_overlapping_repeats INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:36.425 wdl.w:ptcp.w:call-trgt-32.t:call-trgt_plot_meth_waterfall INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2129.meth_waterfall.trgt_plots.zip"
2025-09-15 20:24:36.426 wdl.w:ptcp.w:call-paraphase-49.t:call-run_paraphase NOTICE slurm_singularity run :: pid: 1202482, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-49/call-run_paraphase/slurm_singularity.log.txt"
2025-09-15 20:24:36.465 wdl.w:ptcp.w:call-sawfish-49.t:call-run_sawfish INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 10, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-49/call-run_sawfish/_singularity_tmpdir_j5a1opo8"
2025-09-15 20:24:36.466 wdl.w:ptcp.w:call-sawfish-49.t:call-run_sawfish INFO Slurm invocation: srun --job-name call-run_sawfish --partition compute,compute9 --cpus-per-task 16 --mem 30518M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-49/call-run_sawfish/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-49/call-run_sawfish/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-49/call-run_sawfish/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-49/call-run_sawfish/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-49/out/m84036_250809_035451_s4.bc2146.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2146.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-49/out/m84036_250809_035451_s4.bc2146.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2146.mapped.bam:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-49/call-run_sawfish/_singularity_tmpdir_j5a1opo8/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-49/call-run_sawfish/_singularity_tmpdir_j5a1opo8/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:36.473 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_plot_motifs_allele NOTICE done
2025-09-15 20:24:36.476 wdl.w:ptcp.w:call-trgt-46 NOTICE finish :: job: "call-trgt_plot_motifs_allele"
2025-09-15 20:24:36.476 wdl.w:ptcp.w:call-trgt-46 INFO output :: job: "call-trgt_plot_motifs_allele", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-46/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2143.motifs_allele.trgt_plots.zip"}
2025-09-15 20:24:36.476 wdl.w:ptcp.w:call-trgt-46 INFO visit :: node: "output-images_motifs_allele", values: {"images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-46/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2143.motifs_allele.trgt_plots.zip"}
2025-09-15 20:24:36.483 wdl.w:ptcp.w:call-trgt-49.t:call-trgt_genotype NOTICE task setup :: name: "trgt_genotype", source: "./trgt.wdl", line: 272, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-49/call-trgt_genotype", thread: 140608203109952
2025-09-15 20:24:36.488 wdl.w:ptcp.w:call-sawfish-49.t:call-run_sawfish NOTICE slurm_singularity run :: pid: 1202484, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-49/call-run_sawfish/slurm_singularity.log.txt"
2025-09-15 20:24:36.503 wdl.w:ptcp.w:call-trgt-49.t:call-get_reads_overlapping_repeats INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 9, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-49/call-get_reads_overlapping_repeats/_singularity_tmpdir_ne49pcfr"
2025-09-15 20:24:36.503 wdl.w:ptcp.w:call-trgt-49.t:call-get_reads_overlapping_repeats INFO Slurm invocation: srun --job-name call-get_reads_overlapping_repeats --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-49/call-get_reads_overlapping_repeats/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-49/call-get_reads_overlapping_repeats/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-49/call-get_reads_overlapping_repeats/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-49/call-get_reads_overlapping_repeats/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-49/out/m84036_250809_035451_s4.bc2146.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2146.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-49/out/m84036_250809_035451_s4.bc2146.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2146.mapped.bam:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-49/call-get_reads_overlapping_repeats/_singularity_tmpdir_ne49pcfr/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-49/call-get_reads_overlapping_repeats/_singularity_tmpdir_ne49pcfr/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:36.503 wdl.w:ptcp.w:call-trgt-40.t:call-trgt_genotype.slurm_singularity INFO srun: job 51797709 queued and waiting for resources
2025-09-15 20:24:36.504 wdl.w:ptcp.w:call-trgt-40.t:call-trgt_genotype.slurm_singularity INFO srun: job 51797709 has been allocated resources
2025-09-15 20:24:36.504 wdl.w:ptcp.w:call-trgt-40.t:call-trgt_genotype.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:36.505 wdl.w:ptcp.w:call-trgt-49.t:call-trgt_genotype INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:36.507 wdl.w:ptcp.w:call-trgt-49.t:call-trgt_genotype INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:36.507 wdl.w:ptcp.w:call-trgt-49.t:call-trgt_genotype INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:36.509 wdl.w:ptcp.w:call-trgt-49.t:call-trgt_genotype INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:36.509 wdl.w:ptcp.w:call-trgt-49.t:call-trgt_genotype INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2146.mapped.bam.bai"
2025-09-15 20:24:36.509 wdl.w:ptcp.w:call-trgt-49.t:call-trgt_genotype INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2146.mapped.bam"
2025-09-15 20:24:36.509 wdl.w:ptcp.w:call-trgt-49.t:call-trgt_genotype INFO input :: name: "sex", value: "F"
2025-09-15 20:24:36.509 wdl.w:ptcp.w:call-trgt-49.t:call-trgt_genotype INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2146"
2025-09-15 20:24:36.510 wdl.w:ptcp.w:call-trgt-49.t:call-trgt_genotype INFO eval :: name: "mem_gb", value: 16
2025-09-15 20:24:36.510 wdl.w:ptcp.w:call-trgt-49.t:call-trgt_genotype INFO eval :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2146.trgt"
2025-09-15 20:24:36.510 wdl.w:ptcp.w:call-trgt-49.t:call-trgt_genotype INFO eval :: name: "threads", value: 8
2025-09-15 20:24:36.510 wdl.w:ptcp.w:call-trgt-49.t:call-trgt_genotype INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:36.511 wdl.w:ptcp.w:call-trgt-49.t:call-trgt_genotype INFO eval :: name: "karyotype", value: "XX"
2025-09-15 20:24:36.511 wdl.w:ptcp.w:call-trgt-49.t:call-trgt_genotype INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 8, memory_reservation: 16000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:36.511 wdl.w:ptcp.w:call-trgt-49.t:call-trgt_genotype WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:36.512 wdl.w:ptcp.w:call-trgt-49.t:call-trgt_genotype INFO provisioned :: seconds_waited: 0, cpu: 8, mem_bytes: 16000000000
2025-09-15 20:24:36.512 wdl.w:ptcp.w:call-trgt-49.t:call-trgt_genotype INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:36.519 wdl.w:ptcp.w:call-trgt-49.t:call-get_reads_overlapping_repeats NOTICE slurm_singularity run :: pid: 1202486, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-49/call-get_reads_overlapping_repeats/slurm_singularity.log.txt"
2025-09-15 20:24:36.547 wdl.w:ptcp.w:call-trgt-01.t:call-trgt_plot_motifs_waterfall NOTICE done
2025-09-15 20:24:36.554 wdl.w:ptcp.w:call-trgt-01 NOTICE finish :: job: "call-trgt_plot_motifs_waterfall"
2025-09-15 20:24:36.555 wdl.w:ptcp.w:call-trgt-01 INFO output :: job: "call-trgt_plot_motifs_waterfall", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-01/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2098.motifs_waterfall.trgt_plots.zip"}
2025-09-15 20:24:36.555 wdl.w:ptcp.w:call-trgt-01 INFO visit :: node: "output-images_motifs_waterfall", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-01/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2098.motifs_waterfall.trgt_plots.zip"}
2025-09-15 20:24:36.562 wdl.w:ptcp.w:call-paraphase-54.t:call-run_paraphase NOTICE task setup :: name: "run_paraphase", source: "./paraphase.wdl", line: 127, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-54/call-run_paraphase", thread: 140608194717248
2025-09-15 20:24:36.584 wdl.w:ptcp.w:call-paraphase-54.t:call-run_paraphase INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:36.584 wdl.w:ptcp.w:call-paraphase-54.t:call-run_paraphase INFO input :: name: "annotation_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf"
2025-09-15 20:24:36.584 wdl.w:ptcp.w:call-paraphase-54.t:call-run_paraphase INFO input :: name: "genome_version", value: "38"
2025-09-15 20:24:36.584 wdl.w:ptcp.w:call-paraphase-54.t:call-run_paraphase INFO input :: name: "config_file", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/paraphase_config.GRCh38.yaml"
2025-09-15 20:24:36.584 wdl.w:ptcp.w:call-paraphase-54.t:call-run_paraphase INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:36.584 wdl.w:ptcp.w:call-paraphase-54.t:call-run_paraphase INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:36.584 wdl.w:ptcp.w:call-paraphase-54.t:call-run_paraphase INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2151.mapped.bam.bai"
2025-09-15 20:24:36.585 wdl.w:ptcp.w:call-paraphase-54.t:call-run_paraphase INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2151.mapped.bam"
2025-09-15 20:24:36.585 wdl.w:ptcp.w:call-paraphase-54.t:call-run_paraphase INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2151"
2025-09-15 20:24:36.585 wdl.w:ptcp.w:call-paraphase-54.t:call-run_paraphase INFO eval :: name: "threads", value: 4
2025-09-15 20:24:36.585 wdl.w:ptcp.w:call-paraphase-54.t:call-run_paraphase INFO eval :: name: "mem_gb", value: 8
2025-09-15 20:24:36.585 wdl.w:ptcp.w:call-paraphase-54.t:call-run_paraphase INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:36.585 wdl.w:ptcp.w:call-trgt-32.t:call-trgt_plot_meth_waterfall NOTICE done
2025-09-15 20:24:36.585 wdl.w:ptcp.w:call-paraphase-54.t:call-run_paraphase INFO eval :: name: "out_dir", value: "m84036_250809_035451_s4.bc2151_paraphase"
2025-09-15 20:24:36.586 wdl.w:ptcp.w:call-paraphase-54.t:call-run_paraphase INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 4, memory_reservation: 8000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:36.586 wdl.w:ptcp.w:call-paraphase-54.t:call-run_paraphase WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:36.587 wdl.w:ptcp.w:call-paraphase-54.t:call-run_paraphase INFO provisioned :: seconds_waited: 0, cpu: 4, mem_bytes: 8000000000
2025-09-15 20:24:36.587 wdl.w:ptcp.w:call-paraphase-54.t:call-run_paraphase INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:36.590 wdl.w:ptcp.w:call-trgt-32 NOTICE finish :: job: "call-trgt_plot_meth_waterfall"
2025-09-15 20:24:36.591 wdl.w:ptcp.w:call-trgt-32 INFO output :: job: "call-trgt_plot_meth_waterfall", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-32/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2129.meth_waterfall.trgt_plots.zip"}
2025-09-15 20:24:36.591 wdl.w:ptcp.w:call-trgt-32 INFO visit :: node: "output-images_meth_waterfall", values: {"images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-32/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2129.meth_waterfall.trgt_plots.zip"}
2025-09-15 20:24:36.593 wdl.w:ptcp.w:call-trgt-32 INFO visit :: node: "outputs", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-32/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2129.motifs_waterfall.trgt_plots.zip", "images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-32/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2129.meth_allele.trgt_plots.zip", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-32/call-trgt_genotype/out/m84036_250809_035451_s4.bc2129.trgt.sorted.spanning.bam.bai", "images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-32/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2129.motifs_allele.trgt_plots.zip", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-32/call-trgt_genotype/out/m84036_250809_035451_s4.bc2129.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-32/call-trgt_genotype/out/m84036_250809_035451_s4.bc2129.trgt.vcf", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-32/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2129.repeats.bam", "images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-32/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2129.meth_waterfall.trgt_plots.zip", "reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-32/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2129.repeats.bam.bai"}
2025-09-15 20:24:36.595 wdl.w:ptcp.w:call-trgt-49.t:call-trgt_genotype INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 11, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-49/call-trgt_genotype/_singularity_tmpdir_ypmwe4r1"
2025-09-15 20:24:36.595 wdl.w:ptcp.w:call-trgt-49.t:call-trgt_genotype INFO Slurm invocation: srun --job-name call-trgt_genotype --partition compute,compute9 --cpus-per-task 8 --mem 15259M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-49/call-trgt_genotype/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-49/call-trgt_genotype/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-49/call-trgt_genotype/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-49/call-trgt_genotype/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-49/out/m84036_250809_035451_s4.bc2146.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2146.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-49/out/m84036_250809_035451_s4.bc2146.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2146.mapped.bam:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-49/call-trgt_genotype/_singularity_tmpdir_ypmwe4r1/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-49/call-trgt_genotype/_singularity_tmpdir_ypmwe4r1/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:36.598 wdl.w:ptcp.w:call-sawfish-54.t:call-run_sawfish NOTICE task setup :: name: "run_sawfish", source: "./sawfish.wdl", line: 83, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-54/call-run_sawfish", thread: 140613823374912
2025-09-15 20:24:36.616 wdl.w:ptcp.w:call-trgt-49.t:call-trgt_genotype NOTICE slurm_singularity run :: pid: 1202489, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-49/call-trgt_genotype/slurm_singularity.log.txt"
2025-09-15 20:24:36.617 wdl.w:ptcp.w:call-sawfish-54.t:call-run_sawfish INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:36.617 wdl.w:ptcp.w:call-sawfish-54.t:call-run_sawfish INFO input :: name: "genome_version", value: "38"
2025-09-15 20:24:36.617 wdl.w:ptcp.w:call-sawfish-54.t:call-run_sawfish INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:36.617 wdl.w:ptcp.w:call-sawfish-54.t:call-run_sawfish INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:36.617 wdl.w:ptcp.w:call-sawfish-54.t:call-run_sawfish INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2151.mapped.bam.bai"
2025-09-15 20:24:36.617 wdl.w:ptcp.w:call-sawfish-54.t:call-run_sawfish INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2151.mapped.bam"
2025-09-15 20:24:36.617 wdl.w:ptcp.w:call-sawfish-54.t:call-run_sawfish INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2151"
2025-09-15 20:24:36.618 wdl.w:ptcp.w:call-sawfish-54.t:call-run_sawfish INFO eval :: name: "mem_gb", value: 32
2025-09-15 20:24:36.618 wdl.w:ptcp.w:call-sawfish-54.t:call-run_sawfish INFO eval :: name: "threads", value: 16
2025-09-15 20:24:36.618 wdl.w:ptcp.w:call-sawfish-54.t:call-run_sawfish INFO eval :: name: "disk_size", value: 30
2025-09-15 20:24:36.618 wdl.w:ptcp.w:call-sawfish-54.t:call-run_sawfish INFO eval :: name: "discover_dirname", value: "m84036_250809_035451_s4.bc2151_sawfish_discover"
2025-09-15 20:24:36.618 wdl.w:ptcp.w:call-sawfish-54.t:call-run_sawfish INFO eval :: name: "call_dirname", value: "m84036_250809_035451_s4.bc2151_sawfish"
2025-09-15 20:24:36.618 wdl.w:ptcp.w:call-sawfish-54.t:call-run_sawfish INFO eval :: name: "minimap2_bam_filename", value: "m84036_250809_035451_s4.bc2151.minimap2.bam"
2025-09-15 20:24:36.619 wdl.w:ptcp.w:call-sawfish-54.t:call-run_sawfish INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 16, memory_reservation: 32000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:36.619 wdl.w:ptcp.w:call-sawfish-54.t:call-run_sawfish WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:36.620 wdl.w:ptcp.w:call-sawfish-54.t:call-run_sawfish INFO provisioned :: seconds_waited: 0, cpu: 16, mem_bytes: 32000000000
2025-09-15 20:24:36.620 wdl.w:ptcp.w:call-sawfish-54.t:call-run_sawfish INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:36.629 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:24:36 [INFO] - Running trgt-4.0.0-429afcd [genotype]
2025-09-15 20:24:36.629 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:24:36 [WARN] - PRTS_ARX: Filtered out 4 impure reads
2025-09-15 20:24:36.629 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:24:36 [WARN] - EIEE1_ARX: Filtered out 6 impure reads
2025-09-15 20:24:36.629 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:24:36 [WARN] - FXS_FMR1: Filtered out 5 impure reads
2025-09-15 20:24:36.629 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:24:36 [WARN] - FRAXE_AFF2: Filtered out 23 impure reads
2025-09-15 20:24:36.629 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:24:36 [WARN] - FRDA_FXN: Filtered out 1 impure reads
2025-09-15 20:24:36.630 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:24:36 [INFO] - Total execution time: 228.95ms
2025-09-15 20:24:36.630 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:24:36 [INFO] - trgt end
2025-09-15 20:24:36.640 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_genotype.slurm_singularity INFO srun: job 51797713 queued and waiting for resources
2025-09-15 20:24:36.640 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_genotype.slurm_singularity INFO srun: job 51797713 has been allocated resources
2025-09-15 20:24:36.640 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_genotype.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:36.640 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_genotype.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:24:36.670 wdl.w:ptcp.w:call-paraphase-54.t:call-run_paraphase INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-54/call-run_paraphase/_singularity_tmpdir_9otl4_qu"
2025-09-15 20:24:36.671 wdl.w:ptcp.w:call-paraphase-54.t:call-run_paraphase INFO Slurm invocation: srun --job-name call-run_paraphase --partition compute,compute9 --cpus-per-task 4 --mem 7629M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-54/call-run_paraphase/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-54/call-run_paraphase/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-54/call-run_paraphase/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-54/call-run_paraphase/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-54/out/m84036_250809_035451_s4.bc2151.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2151.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-54/out/m84036_250809_035451_s4.bc2151.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2151.mapped.bam:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/variant_list/variant_list.GRCh38.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf:ro --bind /ptcp/meta/paraphase/paraphase_config.GRCh38.yaml:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/paraphase_config.GRCh38.yaml:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-54/call-run_paraphase/_singularity_tmpdir_9otl4_qu/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-54/call-run_paraphase/_singularity_tmpdir_9otl4_qu/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:36.682 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_genotype INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2159.trgt.vcf"
2025-09-15 20:24:36.686 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_genotype INFO output :: name: "spanning_bam", value: "m84036_250809_035451_s4.bc2159.trgt.sorted.spanning.bam"
2025-09-15 20:24:36.688 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_genotype INFO output :: name: "spanning_bam_bai", value: "m84036_250809_035451_s4.bc2159.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:36.690 wdl.w:ptcp.w:call-paraphase-62.t:call-run_paraphase.slurm_singularity INFO srun: job 51797711 queued and waiting for resources
2025-09-15 20:24:36.690 wdl.w:ptcp.w:call-paraphase-62.t:call-run_paraphase.slurm_singularity INFO srun: job 51797711 has been allocated resources
2025-09-15 20:24:36.690 wdl.w:ptcp.w:call-paraphase-62.t:call-run_paraphase.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:36.690 wdl.w:ptcp.w:call-paraphase-62.t:call-run_paraphase.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:24:36.691 wdl.w:ptcp.w:call-sawfish-62.t:call-run_sawfish.slurm_singularity INFO srun: job 51797710 queued and waiting for resources
2025-09-15 20:24:36.691 wdl.w:ptcp.w:call-sawfish-62.t:call-run_sawfish.slurm_singularity INFO srun: job 51797710 has been allocated resources
2025-09-15 20:24:36.691 wdl.w:ptcp.w:call-sawfish-62.t:call-run_sawfish.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:36.691 wdl.w:ptcp.w:call-sawfish-62.t:call-run_sawfish.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:24:36.695 wdl.w:ptcp.w:call-trgt-32 NOTICE done
2025-09-15 20:24:36.699 wdl.w:ptcp.w:call-sawfish-54.t:call-run_sawfish INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 10, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-54/call-run_sawfish/_singularity_tmpdir_rs8r0_ch"
2025-09-15 20:24:36.699 wdl.w:ptcp.w:call-sawfish-54.t:call-run_sawfish INFO Slurm invocation: srun --job-name call-run_sawfish --partition compute,compute9 --cpus-per-task 16 --mem 30518M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-54/call-run_sawfish/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-54/call-run_sawfish/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-54/call-run_sawfish/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-54/call-run_sawfish/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-54/out/m84036_250809_035451_s4.bc2151.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2151.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-54/out/m84036_250809_035451_s4.bc2151.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2151.mapped.bam:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-54/call-run_sawfish/_singularity_tmpdir_rs8r0_ch/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-54/call-run_sawfish/_singularity_tmpdir_rs8r0_ch/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:36.700 wdl.w:ptcp NOTICE finish :: job: "call-trgt-32"
2025-09-15 20:24:36.700 wdl.w:ptcp INFO output :: job: "call-trgt-32", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-32/out/m84036_250809_035451_s4.bc2129.motifs_waterfall.trgt_plots.zip", "images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-32/out/m84036_250809_035451_s4.bc2129.meth_allele.trgt_plots.zip", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-32/out/m84036_250809_035451_s4.bc2129.trgt.sorted.spanning.bam.bai", "images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-32/out/m84036_250809_035451_s4.bc2129.motifs_allele.trgt_plots.zip", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-32/out/m84036_250809_035451_s4.bc2129.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-32/out/m84036_250809_035451_s4.bc2129.trgt.vcf", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-32/out/m84036_250809_035451_s4.bc2129.repeats.bam", "images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-32/out/m84036_250809_035451_s4.bc2129.meth_waterfall.trgt_plots.zip", "reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-32/out/m84036_250809_035451_s4.bc2129.repeats.bam.bai"}
2025-09-15 20:24:36.706 wdl.w:ptcp.w:call-trgt-64 NOTICE workflow start :: name: "trgt", source: "./trgt.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-64"
2025-09-15 20:24:36.708 wdl.w:ptcp.w:call-paraphase-54.t:call-run_paraphase NOTICE slurm_singularity run :: pid: 1202506, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-54/call-run_paraphase/slurm_singularity.log.txt"
2025-09-15 20:24:36.710 wdl.w:ptcp.w:call-sawfish-54.t:call-run_sawfish NOTICE slurm_singularity run :: pid: 1202507, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-54/call-run_sawfish/slurm_singularity.log.txt"
2025-09-15 20:24:36.722 wdl.w:ptcp.w:call-trgt-64 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:24:36.722 wdl.w:ptcp.w:call-trgt-64 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-64/out/m84036_250809_035451_s4.bc2161.mapped.bam"}
2025-09-15 20:24:36.723 wdl.w:ptcp.w:call-trgt-64 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-64/out/m84036_250809_035451_s4.bc2161.mapped.bam.bai"}
2025-09-15 20:24:36.723 wdl.w:ptcp.w:call-trgt-64 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:24:36.723 wdl.w:ptcp.w:call-trgt-64 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:24:36.723 wdl.w:ptcp.w:call-trgt-64 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2161"}
2025-09-15 20:24:36.723 wdl.w:ptcp.w:call-trgt-64 INFO visit :: node: "decl-sex", values: {"sex": "F"}
2025-09-15 20:24:36.723 wdl.w:ptcp.w:call-trgt-64 INFO visit :: node: "decl-trgt_bed", values: {"trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"}
2025-09-15 20:24:36.723 wdl.w:ptcp.w:call-trgt-64 NOTICE ready :: job: "call-get_reads_overlapping_repeats", callee: "get_reads_overlapping_repeats"
2025-09-15 20:24:36.723 wdl.w:ptcp.w:call-trgt-64 INFO input :: job: "call-get_reads_overlapping_repeats", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-64/out/m84036_250809_035451_s4.bc2161.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-64/out/m84036_250809_035451_s4.bc2161.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2161"}
2025-09-15 20:24:36.727 wdl.w:ptcp.w:call-trgt-64 NOTICE ready :: job: "call-trgt_genotype", callee: "trgt_genotype"
2025-09-15 20:24:36.728 wdl.w:ptcp.w:call-trgt-64 INFO input :: job: "call-trgt_genotype", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-64/out/m84036_250809_035451_s4.bc2161.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-64/out/m84036_250809_035451_s4.bc2161.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2161"}
2025-09-15 20:24:36.759 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_genotype NOTICE done
2025-09-15 20:24:36.771 wdl.w:ptcp.w:call-trgt-62.t:call-get_reads_overlapping_repeats.slurm_singularity INFO srun: job 51797712 queued and waiting for resources
2025-09-15 20:24:36.771 wdl.w:ptcp.w:call-trgt-62.t:call-get_reads_overlapping_repeats.slurm_singularity INFO srun: job 51797712 has been allocated resources
2025-09-15 20:24:36.771 wdl.w:ptcp.w:call-trgt-62.t:call-get_reads_overlapping_repeats.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:36.799 wdl.w:ptcp.w:call-trgt-62 NOTICE finish :: job: "call-trgt_genotype"
2025-09-15 20:24:36.800 wdl.w:ptcp.w:call-trgt-62 INFO output :: job: "call-trgt_genotype", values: {"spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-62/call-trgt_genotype/out/m84036_250809_035451_s4.bc2159.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-62/call-trgt_genotype/out/m84036_250809_035451_s4.bc2159.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-62/call-trgt_genotype/out/m84036_250809_035451_s4.bc2159.trgt.vcf"}
2025-09-15 20:24:36.800 wdl.w:ptcp.w:call-trgt-62 NOTICE ready :: job: "call-trgt_plot_meth_allele", callee: "trgt_plot"
2025-09-15 20:24:36.800 wdl.w:ptcp.w:call-trgt-62 INFO input :: job: "call-trgt_plot_meth_allele", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": false, "methylation": true, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-62/call-trgt_genotype/out/m84036_250809_035451_s4.bc2159.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-62/call-trgt_genotype/out/m84036_250809_035451_s4.bc2159.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-62/call-trgt_genotype/out/m84036_250809_035451_s4.bc2159.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2159"}
2025-09-15 20:24:36.803 wdl.w:ptcp.w:call-trgt-62 NOTICE ready :: job: "call-trgt_plot_meth_waterfall", callee: "trgt_plot"
2025-09-15 20:24:36.803 wdl.w:ptcp.w:call-trgt-62 INFO input :: job: "call-trgt_plot_meth_waterfall", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": true, "methylation": true, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-62/call-trgt_genotype/out/m84036_250809_035451_s4.bc2159.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-62/call-trgt_genotype/out/m84036_250809_035451_s4.bc2159.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-62/call-trgt_genotype/out/m84036_250809_035451_s4.bc2159.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2159"}
2025-09-15 20:24:36.804 wdl.w:ptcp.w:call-trgt-62 NOTICE ready :: job: "call-trgt_plot_motifs_allele", callee: "trgt_plot"
2025-09-15 20:24:36.804 wdl.w:ptcp.w:call-trgt-62 INFO input :: job: "call-trgt_plot_motifs_allele", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": false, "methylation": false, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-62/call-trgt_genotype/out/m84036_250809_035451_s4.bc2159.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-62/call-trgt_genotype/out/m84036_250809_035451_s4.bc2159.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-62/call-trgt_genotype/out/m84036_250809_035451_s4.bc2159.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2159"}
2025-09-15 20:24:36.804 wdl.w:ptcp.w:call-trgt-62 NOTICE ready :: job: "call-trgt_plot_motifs_waterfall", callee: "trgt_plot"
2025-09-15 20:24:36.805 wdl.w:ptcp.w:call-trgt-62 INFO input :: job: "call-trgt_plot_motifs_waterfall", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": true, "methylation": false, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-62/call-trgt_genotype/out/m84036_250809_035451_s4.bc2159.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-62/call-trgt_genotype/out/m84036_250809_035451_s4.bc2159.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-62/call-trgt_genotype/out/m84036_250809_035451_s4.bc2159.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2159"}
2025-09-15 20:24:36.805 wdl.w:ptcp.w:call-trgt-62 INFO visit :: node: "output-spanning_bam", values: {"spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-62/call-trgt_genotype/out/m84036_250809_035451_s4.bc2159.trgt.sorted.spanning.bam"}
2025-09-15 20:24:36.805 wdl.w:ptcp.w:call-trgt-62 INFO visit :: node: "output-spanning_bam_bai", values: {"spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-62/call-trgt_genotype/out/m84036_250809_035451_s4.bc2159.trgt.sorted.spanning.bam.bai"}
2025-09-15 20:24:36.805 wdl.w:ptcp.w:call-trgt-62 INFO visit :: node: "output-vcf", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-62/call-trgt_genotype/out/m84036_250809_035451_s4.bc2159.trgt.vcf"}
2025-09-15 20:24:36.805 wdl.w:ptcp.w:call-trgt-54.t:call-get_reads_overlapping_repeats NOTICE task setup :: name: "get_reads_overlapping_repeats", source: "./trgt.wdl", line: 182, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-54/call-get_reads_overlapping_repeats", thread: 140606609282624
2025-09-15 20:24:36.827 wdl.w:ptcp.w:call-trgt-54.t:call-get_reads_overlapping_repeats INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:36.827 wdl.w:ptcp.w:call-trgt-54.t:call-get_reads_overlapping_repeats INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:36.827 wdl.w:ptcp.w:call-trgt-54.t:call-get_reads_overlapping_repeats INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2151.mapped.bam.bai"
2025-09-15 20:24:36.828 wdl.w:ptcp.w:call-trgt-54.t:call-get_reads_overlapping_repeats INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2151.mapped.bam"
2025-09-15 20:24:36.828 wdl.w:ptcp.w:call-trgt-54.t:call-get_reads_overlapping_repeats INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2151"
2025-09-15 20:24:36.828 wdl.w:ptcp.w:call-trgt-54.t:call-get_reads_overlapping_repeats INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:36.828 wdl.w:ptcp.w:call-trgt-54.t:call-get_reads_overlapping_repeats INFO eval :: name: "expand_size", value: 3000
2025-09-15 20:24:36.828 wdl.w:ptcp.w:call-trgt-54.t:call-get_reads_overlapping_repeats INFO eval :: name: "threads", value: 1
2025-09-15 20:24:36.828 wdl.w:ptcp.w:call-trgt-54.t:call-get_reads_overlapping_repeats INFO eval :: name: "expanded_bed_name", value: "m84036_250809_035451_s4.bc2151.expanded.bed"
2025-09-15 20:24:36.828 wdl.w:ptcp.w:call-trgt-54.t:call-get_reads_overlapping_repeats INFO eval :: name: "disk_size", value: 11
2025-09-15 20:24:36.829 wdl.w:ptcp.w:call-trgt-54.t:call-get_reads_overlapping_repeats INFO eval :: name: "output_name", value: "m84036_250809_035451_s4.bc2151.repeats.bam"
2025-09-15 20:24:36.829 wdl.w:ptcp.w:call-trgt-54.t:call-get_reads_overlapping_repeats INFO eval :: name: "index_name", value: "m84036_250809_035451_s4.bc2151.repeats.bam.bai"
2025-09-15 20:24:36.829 wdl.w:ptcp.w:call-trgt-54.t:call-get_reads_overlapping_repeats INFO eval :: name: "output_name_with_index", value: "m84036_250809_035451_s4.bc2151.repeats.bam##idx##m84036_250809_035451_s4.bc2151.repeats.bam.bai"
2025-09-15 20:24:36.829 wdl.w:ptcp.w:call-trgt-54.t:call-get_reads_overlapping_repeats INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:36.829 wdl.w:ptcp.w:call-trgt-54.t:call-get_reads_overlapping_repeats WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:36.829 wdl.w:ptcp.w:call-trgt-54.t:call-get_reads_overlapping_repeats INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:36.830 wdl.w:ptcp.w:call-trgt-54.t:call-get_reads_overlapping_repeats INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:36.838 wdl.w:ptcp.w:call-trgt-45.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:36 [ERROR] - No reads found for TRID=PRTS_ARX
2025-09-15 20:24:36.838 wdl.w:ptcp.w:call-trgt-45.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:36 [ERROR] - No reads found for TRID=EIEE1_ARX
2025-09-15 20:24:36.839 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:33 [ERROR] - No reads found for TRID=SCA8_ATXN8OS
2025-09-15 20:24:36.839 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:33 [ERROR] - No reads found for TRID=SCA27B_FGF14
2025-09-15 20:24:36.839 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:33 [ERROR] - No reads found for TRID=OPMD_PABPN1
2025-09-15 20:24:36.839 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:34 [ERROR] - No reads found for TRID=SCA2_ATXN2
2025-09-15 20:24:36.839 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:34 [ERROR] - No reads found for TRID=SCA3_ATXN3
2025-09-15 20:24:36.839 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:34 [ERROR] - No reads found for TRID=SCA37_DAB1
2025-09-15 20:24:36.840 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:34 [ERROR] - No reads found for TRID=HDL2_JPH3
2025-09-15 20:24:36.840 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:34 [ERROR] - No reads found for TRID=SCA31_BEAN1
2025-09-15 20:24:36.840 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:34 [ERROR] - No reads found for TRID=SCA6_CACNA1A
2025-09-15 20:24:36.840 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:34 [ERROR] - No reads found for TRID=OPDM2_GIPC1
2025-09-15 20:24:36.840 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:34 [ERROR] - No reads found for TRID=DM1_DMPK
2025-09-15 20:24:36.840 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:34 [ERROR] - No reads found for TRID=FRA2A_AFF3
2025-09-15 20:24:36.840 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:34 [ERROR] - No reads found for TRID=SD5_HOXD13
2025-09-15 20:24:36.840 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:34 [ERROR] - No reads found for TRID=SCA36_NOP56
2025-09-15 20:24:36.840 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:34 [ERROR] - No reads found for TRID=CJD_PRNP
2025-09-15 20:24:36.840 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:34 [ERROR] - No reads found for TRID=EPM1_CSTB
2025-09-15 20:24:36.840 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:34 [ERROR] - No reads found for TRID=SCA10_ATXN10
2025-09-15 20:24:36.840 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:34 [ERROR] - No reads found for TRID=SCA7_ATXN7
2025-09-15 20:24:36.840 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:34 [ERROR] - No reads found for TRID=SCA4_ZFHX3
2025-09-15 20:24:36.840 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:35 [ERROR] - No reads found for TRID=HD_HTT
2025-09-15 20:24:36.840 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:35 [ERROR] - No reads found for TRID=SCA12_PPP2R2B
2025-09-15 20:24:36.840 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:35 [ERROR] - No reads found for TRID=CCHS_PHOX2B
2025-09-15 20:24:36.840 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:35 [ERROR] - No reads found for TRID=OPDM1_LRP12
2025-09-15 20:24:36.841 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:35 [ERROR] - No reads found for TRID=FAME1_SAMD12
2025-09-15 20:24:36.841 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:35 [ERROR] - No reads found for TRID=FTDALS1_C9orf72
2025-09-15 20:24:36.841 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:35 [ERROR] - No reads found for TRID=SCA17_TBP
2025-09-15 20:24:36.841 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:35 [ERROR] - No reads found for TRID=FECD3_TCF4
2025-09-15 20:24:36.841 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:35 [ERROR] - No reads found for TRID=SCA1_ATXN1
2025-09-15 20:24:36.857 wdl.w:ptcp.w:call-paraphase-22.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for rpgr for sample m84036_250809_035451_s4.bc2119 at 2025-09-15 20:24:14.309760...
2025-09-15 20:24:36.857 wdl.w:ptcp.w:call-paraphase-22.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for rpgr for sample m84036_250809_035451_s4.bc2119 at 2025-09-15 20:24:15.073381...
2025-09-15 20:24:36.857 wdl.w:ptcp.w:call-paraphase-22.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for rpgr for sample m84036_250809_035451_s4.bc2119 at 2025-09-15 20:24:15.197036...
2025-09-15 20:24:36.857 wdl.w:ptcp.w:call-paraphase-22.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for f8inv22 for sample m84036_250809_035451_s4.bc2119 at 2025-09-15 20:24:36.748854...
2025-09-15 20:24:36.857 wdl.w:ptcp.w:call-paraphase-22.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for f8inv22 for sample m84036_250809_035451_s4.bc2119 at 2025-09-15 20:24:36.749543...
2025-09-15 20:24:36.887 wdl.w:ptcp.w:call-trgt-45.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:36 [ERROR] - No reads found for TRID=PRTS_ARX
2025-09-15 20:24:36.887 wdl.w:ptcp.w:call-trgt-45.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:36 [ERROR] - No reads found for TRID=EIEE1_ARX
2025-09-15 20:24:36.895 wdl.w:ptcp.w:call-trgt-54.t:call-get_reads_overlapping_repeats INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 9, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-54/call-get_reads_overlapping_repeats/_singularity_tmpdir_tbyvpphf"
2025-09-15 20:24:36.896 wdl.w:ptcp.w:call-trgt-54.t:call-get_reads_overlapping_repeats INFO Slurm invocation: srun --job-name call-get_reads_overlapping_repeats --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-54/call-get_reads_overlapping_repeats/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-54/call-get_reads_overlapping_repeats/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-54/call-get_reads_overlapping_repeats/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-54/call-get_reads_overlapping_repeats/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-54/out/m84036_250809_035451_s4.bc2151.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2151.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-54/out/m84036_250809_035451_s4.bc2151.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2151.mapped.bam:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-54/call-get_reads_overlapping_repeats/_singularity_tmpdir_tbyvpphf/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-54/call-get_reads_overlapping_repeats/_singularity_tmpdir_tbyvpphf/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:36.928 wdl.w:ptcp.w:call-trgt-54.t:call-get_reads_overlapping_repeats NOTICE slurm_singularity run :: pid: 1202526, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-54/call-get_reads_overlapping_repeats/slurm_singularity.log.txt"
2025-09-15 20:24:36.932 wdl.w:ptcp.w:call-paraphase-48.t:call-run_paraphase.slurm_singularity INFO srun: job 51797714 queued and waiting for resources
2025-09-15 20:24:36.932 wdl.w:ptcp.w:call-paraphase-48.t:call-run_paraphase.slurm_singularity INFO srun: job 51797714 has been allocated resources
2025-09-15 20:24:36.932 wdl.w:ptcp.w:call-paraphase-48.t:call-run_paraphase.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:36.933 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_plot_motifs_waterfall INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2143.motifs_waterfall.trgt_plots.zip"
2025-09-15 20:24:36.954 wdl.w:ptcp.w:call-trgt-45.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:35 [ERROR] - No reads found for TRID=PRTS_ARX
2025-09-15 20:24:36.954 wdl.w:ptcp.w:call-trgt-45.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:35 [ERROR] - No reads found for TRID=EIEE1_ARX
2025-09-15 20:24:36.994 wdl.w:ptcp.w:call-trgt-62.t:call-get_reads_overlapping_repeats INFO output :: name: "reads_overlapping_repeats", value: "m84036_250809_035451_s4.bc2159.repeats.bam"
2025-09-15 20:24:36.997 wdl.w:ptcp.w:call-trgt-62.t:call-get_reads_overlapping_repeats INFO output :: name: "reads_overlapping_repeats_bai", value: "m84036_250809_035451_s4.bc2159.repeats.bam.bai"
2025-09-15 20:24:37.042 wdl.w:ptcp.w:call-trgt-46.t:call-trgt_plot_motifs_waterfall NOTICE done
2025-09-15 20:24:37.047 wdl.w:ptcp.w:call-trgt-46 NOTICE finish :: job: "call-trgt_plot_motifs_waterfall"
2025-09-15 20:24:37.047 wdl.w:ptcp.w:call-trgt-46 INFO output :: job: "call-trgt_plot_motifs_waterfall", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-46/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2143.motifs_waterfall.trgt_plots.zip"}
2025-09-15 20:24:37.048 wdl.w:ptcp.w:call-trgt-46 INFO visit :: node: "output-images_motifs_waterfall", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-46/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2143.motifs_waterfall.trgt_plots.zip"}
2025-09-15 20:24:37.048 wdl.w:ptcp.w:call-trgt-46 INFO visit :: node: "outputs", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-46/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2143.motifs_waterfall.trgt_plots.zip", "images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-46/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2143.meth_allele.trgt_plots.zip", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-46/call-trgt_genotype/out/m84036_250809_035451_s4.bc2143.trgt.sorted.spanning.bam.bai", "images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-46/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2143.motifs_allele.trgt_plots.zip", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-46/call-trgt_genotype/out/m84036_250809_035451_s4.bc2143.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-46/call-trgt_genotype/out/m84036_250809_035451_s4.bc2143.trgt.vcf", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-46/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2143.repeats.bam", "images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-46/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2143.meth_waterfall.trgt_plots.zip", "reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-46/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2143.repeats.bam.bai"}
2025-09-15 20:24:37.065 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_genotype NOTICE task setup :: name: "trgt_genotype", source: "./trgt.wdl", line: 272, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-54/call-trgt_genotype", thread: 140607146153536
2025-09-15 20:24:37.076 wdl.w:ptcp.w:call-trgt-37.t:call-trgt_plot_motifs_waterfall INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2134.motifs_waterfall.trgt_plots.zip"
2025-09-15 20:24:37.083 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_genotype INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:37.083 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_genotype INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:37.083 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_genotype INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:37.083 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_genotype INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:37.083 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_genotype INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2151.mapped.bam.bai"
2025-09-15 20:24:37.083 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_genotype INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2151.mapped.bam"
2025-09-15 20:24:37.083 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_genotype INFO input :: name: "sex", value: "F"
2025-09-15 20:24:37.083 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_genotype INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2151"
2025-09-15 20:24:37.083 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_genotype INFO eval :: name: "mem_gb", value: 16
2025-09-15 20:24:37.083 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_genotype INFO eval :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2151.trgt"
2025-09-15 20:24:37.083 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_genotype INFO eval :: name: "threads", value: 8
2025-09-15 20:24:37.084 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_genotype INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:37.084 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_genotype INFO eval :: name: "karyotype", value: "XX"
2025-09-15 20:24:37.084 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_genotype INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 8, memory_reservation: 16000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:37.084 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_genotype WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:37.085 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_genotype INFO provisioned :: seconds_waited: 0, cpu: 8, mem_bytes: 16000000000
2025-09-15 20:24:37.085 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_genotype INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:37.092 wdl.w:ptcp.w:call-trgt-62.t:call-get_reads_overlapping_repeats NOTICE done
2025-09-15 20:24:37.098 wdl.w:ptcp.w:call-trgt-62 NOTICE finish :: job: "call-get_reads_overlapping_repeats"
2025-09-15 20:24:37.099 wdl.w:ptcp.w:call-trgt-62 INFO output :: job: "call-get_reads_overlapping_repeats", values: {"reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-62/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2159.repeats.bam.bai", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-62/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2159.repeats.bam"}
2025-09-15 20:24:37.099 wdl.w:ptcp.w:call-trgt-62 INFO visit :: node: "output-reads_overlapping_repeats", values: {"reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-62/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2159.repeats.bam"}
2025-09-15 20:24:37.099 wdl.w:ptcp.w:call-trgt-62 INFO visit :: node: "output-reads_overlapping_repeats_bai", values: {"reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-62/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2159.repeats.bam.bai"}
2025-09-15 20:24:37.110 wdl.w:ptcp.w:call-paraphase-59.t:call-run_paraphase NOTICE task setup :: name: "run_paraphase", source: "./paraphase.wdl", line: 127, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-59/call-run_paraphase", thread: 140607162938944
2025-09-15 20:24:37.130 wdl.w:ptcp.w:call-paraphase-59.t:call-run_paraphase INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:37.130 wdl.w:ptcp.w:call-paraphase-59.t:call-run_paraphase INFO input :: name: "annotation_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf"
2025-09-15 20:24:37.130 wdl.w:ptcp.w:call-paraphase-59.t:call-run_paraphase INFO input :: name: "genome_version", value: "38"
2025-09-15 20:24:37.131 wdl.w:ptcp.w:call-paraphase-59.t:call-run_paraphase INFO input :: name: "config_file", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/paraphase_config.GRCh38.yaml"
2025-09-15 20:24:37.131 wdl.w:ptcp.w:call-paraphase-59.t:call-run_paraphase INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:37.131 wdl.w:ptcp.w:call-paraphase-59.t:call-run_paraphase INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:37.131 wdl.w:ptcp.w:call-paraphase-59.t:call-run_paraphase INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2156.mapped.bam.bai"
2025-09-15 20:24:37.131 wdl.w:ptcp.w:call-paraphase-59.t:call-run_paraphase INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2156.mapped.bam"
2025-09-15 20:24:37.131 wdl.w:ptcp.w:call-paraphase-59.t:call-run_paraphase INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2156"
2025-09-15 20:24:37.131 wdl.w:ptcp.w:call-paraphase-59.t:call-run_paraphase INFO eval :: name: "threads", value: 4
2025-09-15 20:24:37.131 wdl.w:ptcp.w:call-paraphase-59.t:call-run_paraphase INFO eval :: name: "mem_gb", value: 8
2025-09-15 20:24:37.131 wdl.w:ptcp.w:call-paraphase-59.t:call-run_paraphase INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:37.132 wdl.w:ptcp.w:call-paraphase-59.t:call-run_paraphase INFO eval :: name: "out_dir", value: "m84036_250809_035451_s4.bc2156_paraphase"
2025-09-15 20:24:37.132 wdl.w:ptcp.w:call-paraphase-59.t:call-run_paraphase INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 4, memory_reservation: 8000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:37.132 wdl.w:ptcp.w:call-paraphase-59.t:call-run_paraphase WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:37.133 wdl.w:ptcp.w:call-paraphase-59.t:call-run_paraphase INFO provisioned :: seconds_waited: 0, cpu: 4, mem_bytes: 8000000000
2025-09-15 20:24:37.133 wdl.w:ptcp.w:call-paraphase-59.t:call-run_paraphase INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:37.149 wdl.w:ptcp.w:call-sawfish-48.t:call-run_sawfish.slurm_singularity INFO srun: job 51797715 queued and waiting for resources
2025-09-15 20:24:37.150 wdl.w:ptcp.w:call-sawfish-48.t:call-run_sawfish.slurm_singularity INFO srun: job 51797715 has been allocated resources
2025-09-15 20:24:37.150 wdl.w:ptcp.w:call-sawfish-48.t:call-run_sawfish.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:37.150 wdl.w:ptcp.w:call-sawfish-48.t:call-run_sawfish.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:24:37.160 wdl.w:ptcp.w:call-trgt-48.t:call-get_reads_overlapping_repeats.slurm_singularity INFO srun: job 51797716 queued and waiting for resources
2025-09-15 20:24:37.160 wdl.w:ptcp.w:call-trgt-48.t:call-get_reads_overlapping_repeats.slurm_singularity INFO srun: job 51797716 has been allocated resources
2025-09-15 20:24:37.160 wdl.w:ptcp.w:call-trgt-48.t:call-get_reads_overlapping_repeats.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:37.160 wdl.w:ptcp.w:call-trgt-48.t:call-get_reads_overlapping_repeats.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:24:37.192 wdl.w:ptcp.w:call-trgt-46 NOTICE done
2025-09-15 20:24:37.194 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_genotype INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 11, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-54/call-trgt_genotype/_singularity_tmpdir_swr6ehj_"
2025-09-15 20:24:37.194 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_genotype INFO Slurm invocation: srun --job-name call-trgt_genotype --partition compute,compute9 --cpus-per-task 8 --mem 15259M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-54/call-trgt_genotype/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-54/call-trgt_genotype/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-54/call-trgt_genotype/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-54/call-trgt_genotype/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-54/out/m84036_250809_035451_s4.bc2151.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2151.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-54/out/m84036_250809_035451_s4.bc2151.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2151.mapped.bam:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-54/call-trgt_genotype/_singularity_tmpdir_swr6ehj_/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-54/call-trgt_genotype/_singularity_tmpdir_swr6ehj_/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:37.202 wdl.w:ptcp NOTICE finish :: job: "call-trgt-46"
2025-09-15 20:24:37.202 wdl.w:ptcp INFO output :: job: "call-trgt-46", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-46/out/m84036_250809_035451_s4.bc2143.motifs_waterfall.trgt_plots.zip", "images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-46/out/m84036_250809_035451_s4.bc2143.meth_allele.trgt_plots.zip", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-46/out/m84036_250809_035451_s4.bc2143.trgt.sorted.spanning.bam.bai", "images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-46/out/m84036_250809_035451_s4.bc2143.motifs_allele.trgt_plots.zip", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-46/out/m84036_250809_035451_s4.bc2143.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-46/out/m84036_250809_035451_s4.bc2143.trgt.vcf", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-46/out/m84036_250809_035451_s4.bc2143.repeats.bam", "images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-46/out/m84036_250809_035451_s4.bc2143.meth_waterfall.trgt_plots.zip", "reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-46/out/m84036_250809_035451_s4.bc2143.repeats.bam.bai"}
2025-09-15 20:24:37.213 wdl.w:ptcp.w:call-paraphase-69 NOTICE workflow start :: name: "paraphase", source: "./paraphase.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-69"
2025-09-15 20:24:37.216 wdl.w:ptcp.w:call-sawfish-57.t:call-run_sawfish.slurm_singularity INFO srun: job 51797717 queued and waiting for resources
2025-09-15 20:24:37.216 wdl.w:ptcp.w:call-sawfish-57.t:call-run_sawfish.slurm_singularity INFO srun: job 51797717 has been allocated resources
2025-09-15 20:24:37.216 wdl.w:ptcp.w:call-sawfish-57.t:call-run_sawfish.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:37.216 wdl.w:ptcp.w:call-sawfish-57.t:call-run_sawfish.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:24:37.223 wdl.w:ptcp.w:call-trgt-48.t:call-trgt_genotype.slurm_singularity INFO srun: job 51797718 queued and waiting for resources
2025-09-15 20:24:37.224 wdl.w:ptcp.w:call-trgt-48.t:call-trgt_genotype.slurm_singularity INFO srun: job 51797718 has been allocated resources
2025-09-15 20:24:37.224 wdl.w:ptcp.w:call-trgt-48.t:call-trgt_genotype.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:37.224 wdl.w:ptcp.w:call-trgt-48.t:call-trgt_genotype.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:24:37.229 wdl.w:ptcp.w:call-paraphase-57.t:call-run_paraphase.slurm_singularity INFO srun: job 51797719 queued and waiting for resources
2025-09-15 20:24:37.229 wdl.w:ptcp.w:call-paraphase-57.t:call-run_paraphase.slurm_singularity INFO srun: job 51797719 has been allocated resources
2025-09-15 20:24:37.230 wdl.w:ptcp.w:call-paraphase-57.t:call-run_paraphase.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:37.230 wdl.w:ptcp.w:call-paraphase-57.t:call-run_paraphase.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:24:37.234 wdl.w:ptcp.w:call-paraphase-69 INFO visit :: node: "decl-annotation_vcf", values: {"annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf"}
2025-09-15 20:24:37.234 wdl.w:ptcp.w:call-paraphase-69 INFO visit :: node: "decl-config_file", values: {"config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml"}
2025-09-15 20:24:37.235 wdl.w:ptcp.w:call-paraphase-69 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:24:37.235 wdl.w:ptcp.w:call-paraphase-69 INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:24:37.235 wdl.w:ptcp.w:call-paraphase-69 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-69/out/m84036_250809_035451_s4.bc2166.mapped.bam"}
2025-09-15 20:24:37.235 wdl.w:ptcp.w:call-paraphase-69 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-69/out/m84036_250809_035451_s4.bc2166.mapped.bam.bai"}
2025-09-15 20:24:37.235 wdl.w:ptcp.w:call-paraphase-69 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:24:37.235 wdl.w:ptcp.w:call-paraphase-69 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:24:37.235 wdl.w:ptcp.w:call-paraphase-69 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2166"}
2025-09-15 20:24:37.235 wdl.w:ptcp.w:call-paraphase-69 INFO visit :: node: "decl-sex", values: {"sex": "F"}
2025-09-15 20:24:37.235 wdl.w:ptcp.w:call-paraphase-69 NOTICE ready :: job: "call-run_paraphase", callee: "run_paraphase"
2025-09-15 20:24:37.236 wdl.w:ptcp.w:call-paraphase-69 INFO input :: job: "call-run_paraphase", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf", "genome_version": "38", "config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-69/out/m84036_250809_035451_s4.bc2166.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-69/out/m84036_250809_035451_s4.bc2166.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2166"}
2025-09-15 20:24:37.243 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_genotype NOTICE slurm_singularity run :: pid: 1202535, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-54/call-trgt_genotype/slurm_singularity.log.txt"
2025-09-15 20:24:37.244 wdl.w:ptcp.w:call-paraphase-59.t:call-run_paraphase INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-59/call-run_paraphase/_singularity_tmpdir_ojnerrns"
2025-09-15 20:24:37.244 wdl.w:ptcp.w:call-paraphase-59.t:call-run_paraphase INFO Slurm invocation: srun --job-name call-run_paraphase --partition compute,compute9 --cpus-per-task 4 --mem 7629M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-59/call-run_paraphase/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-59/call-run_paraphase/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-59/call-run_paraphase/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-59/call-run_paraphase/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-59/out/m84036_250809_035451_s4.bc2156.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2156.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-59/out/m84036_250809_035451_s4.bc2156.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2156.mapped.bam:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/variant_list/variant_list.GRCh38.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf:ro --bind /ptcp/meta/paraphase/paraphase_config.GRCh38.yaml:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/paraphase_config.GRCh38.yaml:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-59/call-run_paraphase/_singularity_tmpdir_ojnerrns/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-59/call-run_paraphase/_singularity_tmpdir_ojnerrns/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:37.255 wdl.w:ptcp.w:call-trgt-08.t:call-trgt_plot_motifs_waterfall INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2105.motifs_waterfall.trgt_plots.zip"
2025-09-15 20:24:37.275 wdl.w:ptcp.w:call-paraphase-59.t:call-run_paraphase NOTICE slurm_singularity run :: pid: 1202538, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-59/call-run_paraphase/slurm_singularity.log.txt"
2025-09-15 20:24:37.290 wdl.w:ptcp.w:call-trgt-57.t:call-get_reads_overlapping_repeats.slurm_singularity INFO srun: job 51797720 queued and waiting for resources
2025-09-15 20:24:37.290 wdl.w:ptcp.w:call-trgt-57.t:call-get_reads_overlapping_repeats.slurm_singularity INFO srun: job 51797720 has been allocated resources
2025-09-15 20:24:37.290 wdl.w:ptcp.w:call-trgt-57.t:call-get_reads_overlapping_repeats.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:37.296 wdl.w:ptcp.w:call-trgt-57.t:call-trgt_genotype.slurm_singularity INFO srun: job 51797721 queued and waiting for resources
2025-09-15 20:24:37.296 wdl.w:ptcp.w:call-trgt-57.t:call-trgt_genotype.slurm_singularity INFO srun: job 51797721 has been allocated resources
2025-09-15 20:24:37.296 wdl.w:ptcp.w:call-trgt-57.t:call-trgt_genotype.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:37.296 wdl.w:ptcp.w:call-trgt-57.t:call-trgt_genotype.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:24:37.309 wdl.w:ptcp.w:call-trgt-37.t:call-trgt_plot_motifs_waterfall NOTICE done
2025-09-15 20:24:37.314 wdl.w:ptcp.w:call-trgt-37 NOTICE finish :: job: "call-trgt_plot_motifs_waterfall"
2025-09-15 20:24:37.314 wdl.w:ptcp.w:call-trgt-37 INFO output :: job: "call-trgt_plot_motifs_waterfall", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-37/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2134.motifs_waterfall.trgt_plots.zip"}
2025-09-15 20:24:37.314 wdl.w:ptcp.w:call-trgt-37 INFO visit :: node: "output-images_motifs_waterfall", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-37/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2134.motifs_waterfall.trgt_plots.zip"}
2025-09-15 20:24:37.324 wdl.w:ptcp.w:call-sawfish-59.t:call-run_sawfish NOTICE task setup :: name: "run_sawfish", source: "./sawfish.wdl", line: 83, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-59/call-run_sawfish", thread: 140609822115392
2025-09-15 20:24:37.342 wdl.w:ptcp.w:call-sawfish-59.t:call-run_sawfish INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:37.342 wdl.w:ptcp.w:call-sawfish-59.t:call-run_sawfish INFO input :: name: "genome_version", value: "38"
2025-09-15 20:24:37.342 wdl.w:ptcp.w:call-sawfish-59.t:call-run_sawfish INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:37.342 wdl.w:ptcp.w:call-sawfish-59.t:call-run_sawfish INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:37.342 wdl.w:ptcp.w:call-sawfish-59.t:call-run_sawfish INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2156.mapped.bam.bai"
2025-09-15 20:24:37.342 wdl.w:ptcp.w:call-trgt-41.t:call-trgt_genotype INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2138.trgt.vcf"
2025-09-15 20:24:37.342 wdl.w:ptcp.w:call-sawfish-59.t:call-run_sawfish INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2156.mapped.bam"
2025-09-15 20:24:37.343 wdl.w:ptcp.w:call-sawfish-59.t:call-run_sawfish INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2156"
2025-09-15 20:24:37.343 wdl.w:ptcp.w:call-sawfish-59.t:call-run_sawfish INFO eval :: name: "mem_gb", value: 32
2025-09-15 20:24:37.343 wdl.w:ptcp.w:call-sawfish-59.t:call-run_sawfish INFO eval :: name: "threads", value: 16
2025-09-15 20:24:37.343 wdl.w:ptcp.w:call-sawfish-59.t:call-run_sawfish INFO eval :: name: "disk_size", value: 30
2025-09-15 20:24:37.343 wdl.w:ptcp.w:call-sawfish-59.t:call-run_sawfish INFO eval :: name: "discover_dirname", value: "m84036_250809_035451_s4.bc2156_sawfish_discover"
2025-09-15 20:24:37.343 wdl.w:ptcp.w:call-sawfish-59.t:call-run_sawfish INFO eval :: name: "call_dirname", value: "m84036_250809_035451_s4.bc2156_sawfish"
2025-09-15 20:24:37.344 wdl.w:ptcp.w:call-sawfish-59.t:call-run_sawfish INFO eval :: name: "minimap2_bam_filename", value: "m84036_250809_035451_s4.bc2156.minimap2.bam"
2025-09-15 20:24:37.344 wdl.w:ptcp.w:call-sawfish-59.t:call-run_sawfish INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 16, memory_reservation: 32000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:37.344 wdl.w:ptcp.w:call-sawfish-59.t:call-run_sawfish WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:37.344 wdl.w:ptcp.w:call-sawfish-59.t:call-run_sawfish INFO provisioned :: seconds_waited: 0, cpu: 16, mem_bytes: 32000000000
2025-09-15 20:24:37.345 wdl.w:ptcp.w:call-sawfish-59.t:call-run_sawfish INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:37.347 wdl.w:ptcp.w:call-trgt-41.t:call-trgt_genotype INFO output :: name: "spanning_bam", value: "m84036_250809_035451_s4.bc2138.trgt.sorted.spanning.bam"
2025-09-15 20:24:37.349 wdl.w:ptcp.w:call-trgt-41.t:call-trgt_genotype INFO output :: name: "spanning_bam_bai", value: "m84036_250809_035451_s4.bc2138.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:37.411 wdl.w:ptcp.w:call-trgt-45.t:call-trgt_plot_motifs_allele INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2142.motifs_allele.trgt_plots.zip"
2025-09-15 20:24:37.445 wdl.w:ptcp.w:call-paraphase-49.t:call-run_paraphase.slurm_singularity INFO srun: job 51797722 queued and waiting for resources
2025-09-15 20:24:37.445 wdl.w:ptcp.w:call-paraphase-49.t:call-run_paraphase.slurm_singularity INFO srun: job 51797722 has been allocated resources
2025-09-15 20:24:37.445 wdl.w:ptcp.w:call-paraphase-49.t:call-run_paraphase.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:37.445 wdl.w:ptcp.w:call-sawfish-59.t:call-run_sawfish INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 10, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-59/call-run_sawfish/_singularity_tmpdir_j1xrki3d"
2025-09-15 20:24:37.446 wdl.w:ptcp.w:call-sawfish-59.t:call-run_sawfish INFO Slurm invocation: srun --job-name call-run_sawfish --partition compute,compute9 --cpus-per-task 16 --mem 30518M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-59/call-run_sawfish/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-59/call-run_sawfish/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-59/call-run_sawfish/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-59/call-run_sawfish/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-59/out/m84036_250809_035451_s4.bc2156.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2156.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-59/out/m84036_250809_035451_s4.bc2156.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2156.mapped.bam:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-59/call-run_sawfish/_singularity_tmpdir_j1xrki3d/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-59/call-run_sawfish/_singularity_tmpdir_j1xrki3d/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:37.470 wdl.w:ptcp.w:call-trgt-08.t:call-trgt_plot_motifs_waterfall NOTICE done
2025-09-15 20:24:37.477 wdl.w:ptcp.w:call-trgt-08 NOTICE finish :: job: "call-trgt_plot_motifs_waterfall"
2025-09-15 20:24:37.478 wdl.w:ptcp.w:call-trgt-08 INFO output :: job: "call-trgt_plot_motifs_waterfall", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-08/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2105.motifs_waterfall.trgt_plots.zip"}
2025-09-15 20:24:37.479 wdl.w:ptcp.w:call-trgt-08 INFO visit :: node: "output-images_motifs_waterfall", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-08/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2105.motifs_waterfall.trgt_plots.zip"}
2025-09-15 20:24:37.479 wdl.w:ptcp.w:call-trgt-08 INFO visit :: node: "outputs", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-08/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2105.motifs_waterfall.trgt_plots.zip", "images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-08/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2105.meth_allele.trgt_plots.zip", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-08/call-trgt_genotype/out/m84036_250809_035451_s4.bc2105.trgt.sorted.spanning.bam.bai", "images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-08/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2105.motifs_allele.trgt_plots.zip", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-08/call-trgt_genotype/out/m84036_250809_035451_s4.bc2105.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-08/call-trgt_genotype/out/m84036_250809_035451_s4.bc2105.trgt.vcf", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-08/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2105.repeats.bam", "images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-08/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2105.meth_waterfall.trgt_plots.zip", "reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-08/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2105.repeats.bam.bai"}
2025-09-15 20:24:37.484 wdl.w:ptcp.w:call-sawfish-59.t:call-run_sawfish NOTICE slurm_singularity run :: pid: 1202552, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-59/call-run_sawfish/slurm_singularity.log.txt"
2025-09-15 20:24:37.488 wdl.w:ptcp.w:call-trgt-59.t:call-get_reads_overlapping_repeats NOTICE task setup :: name: "get_reads_overlapping_repeats", source: "./trgt.wdl", line: 182, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-59/call-get_reads_overlapping_repeats", thread: 140608773551680
2025-09-15 20:24:37.490 wdl.w:ptcp.w:call-trgt-41.t:call-trgt_genotype NOTICE done
2025-09-15 20:24:37.492 wdl.w:ptcp.w:call-sawfish-49.t:call-run_sawfish.stderr VERBOSE [M::bam2fq_mainloop] discarded 0 singletons
2025-09-15 20:24:37.492 wdl.w:ptcp.w:call-sawfish-49.t:call-run_sawfish.stderr VERBOSE [M::bam2fq_mainloop] processed 0 reads
2025-09-15 20:24:37.503 wdl.w:ptcp.w:call-sawfish-49.t:call-run_sawfish.slurm_singularity INFO srun: job 51797723 queued and waiting for resources
2025-09-15 20:24:37.503 wdl.w:ptcp.w:call-sawfish-49.t:call-run_sawfish.slurm_singularity INFO srun: job 51797723 has been allocated resources
2025-09-15 20:24:37.503 wdl.w:ptcp.w:call-sawfish-49.t:call-run_sawfish.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:37.503 wdl.w:ptcp.w:call-sawfish-49.t:call-run_sawfish.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:24:37.510 wdl.w:ptcp.w:call-trgt-59.t:call-get_reads_overlapping_repeats INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:37.510 wdl.w:ptcp.w:call-trgt-59.t:call-get_reads_overlapping_repeats INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:37.510 wdl.w:ptcp.w:call-trgt-59.t:call-get_reads_overlapping_repeats INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2156.mapped.bam.bai"
2025-09-15 20:24:37.510 wdl.w:ptcp.w:call-trgt-59.t:call-get_reads_overlapping_repeats INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2156.mapped.bam"
2025-09-15 20:24:37.510 wdl.w:ptcp.w:call-trgt-59.t:call-get_reads_overlapping_repeats INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2156"
2025-09-15 20:24:37.510 wdl.w:ptcp.w:call-trgt-59.t:call-get_reads_overlapping_repeats INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:37.510 wdl.w:ptcp.w:call-trgt-59.t:call-get_reads_overlapping_repeats INFO eval :: name: "expand_size", value: 3000
2025-09-15 20:24:37.510 wdl.w:ptcp.w:call-trgt-59.t:call-get_reads_overlapping_repeats INFO eval :: name: "threads", value: 1
2025-09-15 20:24:37.511 wdl.w:ptcp.w:call-trgt-59.t:call-get_reads_overlapping_repeats INFO eval :: name: "expanded_bed_name", value: "m84036_250809_035451_s4.bc2156.expanded.bed"
2025-09-15 20:24:37.511 wdl.w:ptcp.w:call-trgt-59.t:call-get_reads_overlapping_repeats INFO eval :: name: "disk_size", value: 11
2025-09-15 20:24:37.511 wdl.w:ptcp.w:call-trgt-59.t:call-get_reads_overlapping_repeats INFO eval :: name: "output_name", value: "m84036_250809_035451_s4.bc2156.repeats.bam"
2025-09-15 20:24:37.511 wdl.w:ptcp.w:call-trgt-59.t:call-get_reads_overlapping_repeats INFO eval :: name: "index_name", value: "m84036_250809_035451_s4.bc2156.repeats.bam.bai"
2025-09-15 20:24:37.511 wdl.w:ptcp.w:call-trgt-59.t:call-get_reads_overlapping_repeats INFO eval :: name: "output_name_with_index", value: "m84036_250809_035451_s4.bc2156.repeats.bam##idx##m84036_250809_035451_s4.bc2156.repeats.bam.bai"
2025-09-15 20:24:37.512 wdl.w:ptcp.w:call-trgt-59.t:call-get_reads_overlapping_repeats INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:37.512 wdl.w:ptcp.w:call-trgt-59.t:call-get_reads_overlapping_repeats WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:37.512 wdl.w:ptcp.w:call-trgt-59.t:call-get_reads_overlapping_repeats INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:37.512 wdl.w:ptcp.w:call-trgt-59.t:call-get_reads_overlapping_repeats INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:37.533 wdl.w:ptcp.w:call-trgt-41 NOTICE finish :: job: "call-trgt_genotype"
2025-09-15 20:24:37.534 wdl.w:ptcp.w:call-trgt-41 INFO output :: job: "call-trgt_genotype", values: {"spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-41/call-trgt_genotype/out/m84036_250809_035451_s4.bc2138.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-41/call-trgt_genotype/out/m84036_250809_035451_s4.bc2138.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-41/call-trgt_genotype/out/m84036_250809_035451_s4.bc2138.trgt.vcf"}
2025-09-15 20:24:37.534 wdl.w:ptcp.w:call-trgt-41 NOTICE ready :: job: "call-trgt_plot_meth_allele", callee: "trgt_plot"
2025-09-15 20:24:37.534 wdl.w:ptcp.w:call-trgt-41 INFO input :: job: "call-trgt_plot_meth_allele", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": false, "methylation": true, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-41/call-trgt_genotype/out/m84036_250809_035451_s4.bc2138.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-41/call-trgt_genotype/out/m84036_250809_035451_s4.bc2138.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-41/call-trgt_genotype/out/m84036_250809_035451_s4.bc2138.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2138"}
2025-09-15 20:24:37.536 wdl.w:ptcp.w:call-trgt-41 NOTICE ready :: job: "call-trgt_plot_meth_waterfall", callee: "trgt_plot"
2025-09-15 20:24:37.536 wdl.w:ptcp.w:call-trgt-41 INFO input :: job: "call-trgt_plot_meth_waterfall", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": true, "methylation": true, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-41/call-trgt_genotype/out/m84036_250809_035451_s4.bc2138.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-41/call-trgt_genotype/out/m84036_250809_035451_s4.bc2138.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-41/call-trgt_genotype/out/m84036_250809_035451_s4.bc2138.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2138"}
2025-09-15 20:24:37.537 wdl.w:ptcp.w:call-trgt-49.t:call-get_reads_overlapping_repeats.slurm_singularity INFO srun: job 51797724 queued and waiting for resources
2025-09-15 20:24:37.537 wdl.w:ptcp.w:call-trgt-49.t:call-get_reads_overlapping_repeats.slurm_singularity INFO srun: job 51797724 has been allocated resources
2025-09-15 20:24:37.537 wdl.w:ptcp.w:call-trgt-49.t:call-get_reads_overlapping_repeats.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:37.537 wdl.w:ptcp.w:call-trgt-49.t:call-get_reads_overlapping_repeats.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:24:37.537 wdl.w:ptcp.w:call-trgt-41 NOTICE ready :: job: "call-trgt_plot_motifs_allele", callee: "trgt_plot"
2025-09-15 20:24:37.538 wdl.w:ptcp.w:call-trgt-41 INFO input :: job: "call-trgt_plot_motifs_allele", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": false, "methylation": false, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-41/call-trgt_genotype/out/m84036_250809_035451_s4.bc2138.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-41/call-trgt_genotype/out/m84036_250809_035451_s4.bc2138.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-41/call-trgt_genotype/out/m84036_250809_035451_s4.bc2138.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2138"}
2025-09-15 20:24:37.538 wdl.w:ptcp.w:call-trgt-41 NOTICE ready :: job: "call-trgt_plot_motifs_waterfall", callee: "trgt_plot"
2025-09-15 20:24:37.539 wdl.w:ptcp.w:call-trgt-41 INFO input :: job: "call-trgt_plot_motifs_waterfall", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": true, "methylation": false, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-41/call-trgt_genotype/out/m84036_250809_035451_s4.bc2138.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-41/call-trgt_genotype/out/m84036_250809_035451_s4.bc2138.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-41/call-trgt_genotype/out/m84036_250809_035451_s4.bc2138.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2138"}
2025-09-15 20:24:37.539 wdl.w:ptcp.w:call-trgt-41 INFO visit :: node: "output-spanning_bam", values: {"spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-41/call-trgt_genotype/out/m84036_250809_035451_s4.bc2138.trgt.sorted.spanning.bam"}
2025-09-15 20:24:37.539 wdl.w:ptcp.w:call-trgt-41 INFO visit :: node: "output-spanning_bam_bai", values: {"spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-41/call-trgt_genotype/out/m84036_250809_035451_s4.bc2138.trgt.sorted.spanning.bam.bai"}
2025-09-15 20:24:37.539 wdl.w:ptcp.w:call-trgt-41 INFO visit :: node: "output-vcf", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-41/call-trgt_genotype/out/m84036_250809_035451_s4.bc2138.trgt.vcf"}
2025-09-15 20:24:37.545 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_genotype NOTICE task setup :: name: "trgt_genotype", source: "./trgt.wdl", line: 272, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-59/call-trgt_genotype", thread: 140612531648064
2025-09-15 20:24:37.557 wdl.w:ptcp.w:call-paraphase-10.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for f8inv1 for sample m84036_250809_035451_s4.bc2107 at 2025-09-15 20:24:27.136326...
2025-09-15 20:24:37.557 wdl.w:ptcp.w:call-paraphase-10.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for f8inv1 for sample m84036_250809_035451_s4.bc2107 at 2025-09-15 20:24:27.606188...
2025-09-15 20:24:37.564 wdl.w:ptcp.w:call-sawfish-18.t:call-run_sawfish.stderr VERBOSE [M::mm_idx_gen::61.781*1.57] collected minimizers
2025-09-15 20:24:37.589 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_genotype INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:37.589 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_genotype INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:37.589 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_genotype INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:37.589 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_genotype INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:37.589 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_genotype INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2156.mapped.bam.bai"
2025-09-15 20:24:37.589 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_genotype INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2156.mapped.bam"
2025-09-15 20:24:37.589 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_genotype INFO input :: name: "sex", value: "F"
2025-09-15 20:24:37.589 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_genotype INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2156"
2025-09-15 20:24:37.590 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_genotype INFO eval :: name: "mem_gb", value: 16
2025-09-15 20:24:37.590 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_genotype INFO eval :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2156.trgt"
2025-09-15 20:24:37.590 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_genotype INFO eval :: name: "threads", value: 8
2025-09-15 20:24:37.590 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_genotype INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:37.590 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_genotype INFO eval :: name: "karyotype", value: "XX"
2025-09-15 20:24:37.591 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_genotype INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 8, memory_reservation: 16000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:37.591 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_genotype WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:37.591 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_genotype INFO provisioned :: seconds_waited: 0, cpu: 8, mem_bytes: 16000000000
2025-09-15 20:24:37.591 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_genotype INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:37.593 wdl.w:ptcp.w:call-trgt-59.t:call-get_reads_overlapping_repeats INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 9, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-59/call-get_reads_overlapping_repeats/_singularity_tmpdir__k1km3ld"
2025-09-15 20:24:37.593 wdl.w:ptcp.w:call-trgt-59.t:call-get_reads_overlapping_repeats INFO Slurm invocation: srun --job-name call-get_reads_overlapping_repeats --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-59/call-get_reads_overlapping_repeats/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-59/call-get_reads_overlapping_repeats/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-59/call-get_reads_overlapping_repeats/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-59/call-get_reads_overlapping_repeats/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-59/out/m84036_250809_035451_s4.bc2156.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2156.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-59/out/m84036_250809_035451_s4.bc2156.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2156.mapped.bam:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-59/call-get_reads_overlapping_repeats/_singularity_tmpdir__k1km3ld/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-59/call-get_reads_overlapping_repeats/_singularity_tmpdir__k1km3ld/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:37.613 wdl.w:ptcp.w:call-trgt-08 NOTICE done
2025-09-15 20:24:37.617 wdl.w:ptcp.w:call-trgt-45.t:call-trgt_plot_motifs_allele NOTICE done
2025-09-15 20:24:37.617 wdl.w:ptcp NOTICE finish :: job: "call-trgt-08"
2025-09-15 20:24:37.618 wdl.w:ptcp INFO output :: job: "call-trgt-08", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-08/out/m84036_250809_035451_s4.bc2105.motifs_waterfall.trgt_plots.zip", "images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-08/out/m84036_250809_035451_s4.bc2105.meth_allele.trgt_plots.zip", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-08/out/m84036_250809_035451_s4.bc2105.trgt.sorted.spanning.bam.bai", "images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-08/out/m84036_250809_035451_s4.bc2105.motifs_allele.trgt_plots.zip", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-08/out/m84036_250809_035451_s4.bc2105.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-08/out/m84036_250809_035451_s4.bc2105.trgt.vcf", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-08/out/m84036_250809_035451_s4.bc2105.repeats.bam", "images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-08/out/m84036_250809_035451_s4.bc2105.meth_waterfall.trgt_plots.zip", "reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-08/out/m84036_250809_035451_s4.bc2105.repeats.bam.bai"}
2025-09-15 20:24:37.623 wdl.w:ptcp.w:call-sawfish-69 NOTICE workflow start :: name: "sawfish", source: "./sawfish.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-69"
2025-09-15 20:24:37.626 wdl.w:ptcp.w:call-trgt-49.t:call-trgt_genotype.slurm_singularity INFO srun: job 51797725 queued and waiting for resources
2025-09-15 20:24:37.627 wdl.w:ptcp.w:call-trgt-49.t:call-trgt_genotype.slurm_singularity INFO srun: job 51797725 has been allocated resources
2025-09-15 20:24:37.627 wdl.w:ptcp.w:call-trgt-49.t:call-trgt_genotype.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:37.627 wdl.w:ptcp.w:call-trgt-49.t:call-trgt_genotype.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:24:37.638 wdl.w:ptcp.w:call-sawfish-69 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:24:37.638 wdl.w:ptcp.w:call-sawfish-69 INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:24:37.638 wdl.w:ptcp.w:call-sawfish-69 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-69/out/m84036_250809_035451_s4.bc2166.mapped.bam"}
2025-09-15 20:24:37.639 wdl.w:ptcp.w:call-sawfish-69 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-69/out/m84036_250809_035451_s4.bc2166.mapped.bam.bai"}
2025-09-15 20:24:37.639 wdl.w:ptcp.w:call-sawfish-69 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:24:37.639 wdl.w:ptcp.w:call-sawfish-69 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:24:37.639 wdl.w:ptcp.w:call-sawfish-69 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2166"}
2025-09-15 20:24:37.639 wdl.w:ptcp.w:call-sawfish-69 NOTICE ready :: job: "call-run_sawfish", callee: "run_sawfish"
2025-09-15 20:24:37.639 wdl.w:ptcp.w:call-sawfish-69 INFO input :: job: "call-run_sawfish", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-69/out/m84036_250809_035451_s4.bc2166.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-69/out/m84036_250809_035451_s4.bc2166.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2166"}
2025-09-15 20:24:37.639 wdl.w:ptcp.w:call-trgt-59.t:call-get_reads_overlapping_repeats NOTICE slurm_singularity run :: pid: 1202554, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-59/call-get_reads_overlapping_repeats/slurm_singularity.log.txt"
2025-09-15 20:24:37.649 wdl.w:ptcp.w:call-sawfish-10.t:call-run_sawfish.stderr VERBOSE [M::mm_idx_gen::62.099*1.62] collected minimizers
2025-09-15 20:24:37.667 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_genotype INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 11, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-59/call-trgt_genotype/_singularity_tmpdir_dj4gtnp0"
2025-09-15 20:24:37.667 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_genotype INFO Slurm invocation: srun --job-name call-trgt_genotype --partition compute,compute9 --cpus-per-task 8 --mem 15259M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-59/call-trgt_genotype/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-59/call-trgt_genotype/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-59/call-trgt_genotype/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-59/call-trgt_genotype/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-59/out/m84036_250809_035451_s4.bc2156.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2156.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-59/out/m84036_250809_035451_s4.bc2156.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2156.mapped.bam:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-59/call-trgt_genotype/_singularity_tmpdir_dj4gtnp0/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-59/call-trgt_genotype/_singularity_tmpdir_dj4gtnp0/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:37.670 wdl.w:ptcp.w:call-trgt-45 NOTICE finish :: job: "call-trgt_plot_motifs_allele"
2025-09-15 20:24:37.670 wdl.w:ptcp.w:call-trgt-45 INFO output :: job: "call-trgt_plot_motifs_allele", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-45/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2142.motifs_allele.trgt_plots.zip"}
2025-09-15 20:24:37.670 wdl.w:ptcp.w:call-trgt-45 INFO visit :: node: "output-images_motifs_allele", values: {"images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-45/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2142.motifs_allele.trgt_plots.zip"}
2025-09-15 20:24:37.678 wdl.w:ptcp.w:call-paraphase-53.t:call-run_paraphase NOTICE task setup :: name: "run_paraphase", source: "./paraphase.wdl", line: 127, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-53/call-run_paraphase", thread: 140608211502656
2025-09-15 20:24:37.689 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_genotype NOTICE slurm_singularity run :: pid: 1202556, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-59/call-trgt_genotype/slurm_singularity.log.txt"
2025-09-15 20:24:37.696 wdl.w:ptcp.w:call-paraphase-53.t:call-run_paraphase INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:37.696 wdl.w:ptcp.w:call-paraphase-53.t:call-run_paraphase INFO input :: name: "annotation_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf"
2025-09-15 20:24:37.696 wdl.w:ptcp.w:call-paraphase-53.t:call-run_paraphase INFO input :: name: "genome_version", value: "38"
2025-09-15 20:24:37.696 wdl.w:ptcp.w:call-paraphase-53.t:call-run_paraphase INFO input :: name: "config_file", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/paraphase_config.GRCh38.yaml"
2025-09-15 20:24:37.696 wdl.w:ptcp.w:call-paraphase-53.t:call-run_paraphase INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:37.696 wdl.w:ptcp.w:call-paraphase-53.t:call-run_paraphase INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:37.696 wdl.w:ptcp.w:call-paraphase-53.t:call-run_paraphase INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2150.mapped.bam.bai"
2025-09-15 20:24:37.696 wdl.w:ptcp.w:call-paraphase-53.t:call-run_paraphase INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2150.mapped.bam"
2025-09-15 20:24:37.697 wdl.w:ptcp.w:call-paraphase-53.t:call-run_paraphase INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2150"
2025-09-15 20:24:37.697 wdl.w:ptcp.w:call-paraphase-53.t:call-run_paraphase INFO eval :: name: "threads", value: 4
2025-09-15 20:24:37.697 wdl.w:ptcp.w:call-paraphase-53.t:call-run_paraphase INFO eval :: name: "mem_gb", value: 8
2025-09-15 20:24:37.697 wdl.w:ptcp.w:call-paraphase-53.t:call-run_paraphase INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:37.697 wdl.w:ptcp.w:call-paraphase-53.t:call-run_paraphase INFO eval :: name: "out_dir", value: "m84036_250809_035451_s4.bc2150_paraphase"
2025-09-15 20:24:37.698 wdl.w:ptcp.w:call-paraphase-53.t:call-run_paraphase INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 4, memory_reservation: 8000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:37.698 wdl.w:ptcp.w:call-paraphase-53.t:call-run_paraphase WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:37.698 wdl.w:ptcp.w:call-paraphase-53.t:call-run_paraphase INFO provisioned :: seconds_waited: 0, cpu: 4, mem_bytes: 8000000000
2025-09-15 20:24:37.698 wdl.w:ptcp.w:call-paraphase-53.t:call-run_paraphase INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:37.719 wdl.w:ptcp.w:call-paraphase-54.t:call-run_paraphase.slurm_singularity INFO srun: job 51797726 queued and waiting for resources
2025-09-15 20:24:37.719 wdl.w:ptcp.w:call-paraphase-54.t:call-run_paraphase.slurm_singularity INFO srun: job 51797726 has been allocated resources
2025-09-15 20:24:37.719 wdl.w:ptcp.w:call-paraphase-54.t:call-run_paraphase.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:37.719 wdl.w:ptcp.w:call-paraphase-54.t:call-run_paraphase.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:24:37.721 wdl.w:ptcp.w:call-sawfish-54.t:call-run_sawfish.slurm_singularity INFO srun: job 51797727 queued and waiting for resources
2025-09-15 20:24:37.721 wdl.w:ptcp.w:call-sawfish-54.t:call-run_sawfish.slurm_singularity INFO srun: job 51797727 has been allocated resources
2025-09-15 20:24:37.721 wdl.w:ptcp.w:call-sawfish-54.t:call-run_sawfish.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:37.721 wdl.w:ptcp.w:call-sawfish-54.t:call-run_sawfish.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:24:37.764 wdl.w:ptcp.w:call-paraphase-53.t:call-run_paraphase INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-53/call-run_paraphase/_singularity_tmpdir_3vtuur51"
2025-09-15 20:24:37.764 wdl.w:ptcp.w:call-paraphase-53.t:call-run_paraphase INFO Slurm invocation: srun --job-name call-run_paraphase --partition compute,compute9 --cpus-per-task 4 --mem 7629M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-53/call-run_paraphase/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-53/call-run_paraphase/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-53/call-run_paraphase/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-53/call-run_paraphase/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-53/out/m84036_250809_035451_s4.bc2150.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2150.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-53/out/m84036_250809_035451_s4.bc2150.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2150.mapped.bam.bai:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/variant_list/variant_list.GRCh38.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf:ro --bind /ptcp/meta/paraphase/paraphase_config.GRCh38.yaml:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/paraphase_config.GRCh38.yaml:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-53/call-run_paraphase/_singularity_tmpdir_3vtuur51/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-53/call-run_paraphase/_singularity_tmpdir_3vtuur51/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:37.777 wdl.w:ptcp.w:call-paraphase-53.t:call-run_paraphase NOTICE slurm_singularity run :: pid: 1202558, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-53/call-run_paraphase/slurm_singularity.log.txt"
2025-09-15 20:24:37.803 wdl.w:ptcp.w:call-trgt-54.t:call-get_reads_overlapping_repeats.slurm_singularity INFO srun: job 51797728 queued and waiting for resources
2025-09-15 20:24:37.803 wdl.w:ptcp.w:call-trgt-54.t:call-get_reads_overlapping_repeats.slurm_singularity INFO srun: job 51797728 has been allocated resources
2025-09-15 20:24:37.803 wdl.w:ptcp.w:call-trgt-54.t:call-get_reads_overlapping_repeats.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:37.835 wdl.w:ptcp.w:call-trgt-54.t:call-get_reads_overlapping_repeats INFO output :: name: "reads_overlapping_repeats", value: "m84036_250809_035451_s4.bc2151.repeats.bam"
2025-09-15 20:24:37.839 wdl.w:ptcp.w:call-trgt-54.t:call-get_reads_overlapping_repeats INFO output :: name: "reads_overlapping_repeats_bai", value: "m84036_250809_035451_s4.bc2151.repeats.bam.bai"
2025-09-15 20:24:37.923 wdl.w:ptcp.w:call-trgt-54.t:call-get_reads_overlapping_repeats NOTICE done
2025-09-15 20:24:37.928 wdl.w:ptcp.w:call-trgt-54 NOTICE finish :: job: "call-get_reads_overlapping_repeats"
2025-09-15 20:24:37.928 wdl.w:ptcp.w:call-trgt-54 INFO output :: job: "call-get_reads_overlapping_repeats", values: {"reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-54/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2151.repeats.bam.bai", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-54/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2151.repeats.bam"}
2025-09-15 20:24:37.928 wdl.w:ptcp.w:call-trgt-54 INFO visit :: node: "output-reads_overlapping_repeats", values: {"reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-54/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2151.repeats.bam"}
2025-09-15 20:24:37.929 wdl.w:ptcp.w:call-trgt-54 INFO visit :: node: "output-reads_overlapping_repeats_bai", values: {"reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-54/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2151.repeats.bam.bai"}
2025-09-15 20:24:37.982 wdl.w:ptcp.w:call-sawfish-53.t:call-run_sawfish NOTICE task setup :: name: "run_sawfish", source: "./sawfish.wdl", line: 83, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-53/call-run_sawfish", thread: 140606609282624
2025-09-15 20:24:38.028 wdl.w:ptcp.w:call-sawfish-53.t:call-run_sawfish INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:38.028 wdl.w:ptcp.w:call-sawfish-53.t:call-run_sawfish INFO input :: name: "genome_version", value: "38"
2025-09-15 20:24:38.028 wdl.w:ptcp.w:call-sawfish-53.t:call-run_sawfish INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:38.028 wdl.w:ptcp.w:call-sawfish-53.t:call-run_sawfish INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:38.028 wdl.w:ptcp.w:call-sawfish-53.t:call-run_sawfish INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2150.mapped.bam.bai"
2025-09-15 20:24:38.028 wdl.w:ptcp.w:call-sawfish-53.t:call-run_sawfish INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2150.mapped.bam"
2025-09-15 20:24:38.029 wdl.w:ptcp.w:call-sawfish-53.t:call-run_sawfish INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2150"
2025-09-15 20:24:38.029 wdl.w:ptcp.w:call-sawfish-53.t:call-run_sawfish INFO eval :: name: "mem_gb", value: 32
2025-09-15 20:24:38.029 wdl.w:ptcp.w:call-sawfish-53.t:call-run_sawfish INFO eval :: name: "threads", value: 16
2025-09-15 20:24:38.029 wdl.w:ptcp.w:call-sawfish-53.t:call-run_sawfish INFO eval :: name: "disk_size", value: 30
2025-09-15 20:24:38.029 wdl.w:ptcp.w:call-sawfish-53.t:call-run_sawfish INFO eval :: name: "discover_dirname", value: "m84036_250809_035451_s4.bc2150_sawfish_discover"
2025-09-15 20:24:38.029 wdl.w:ptcp.w:call-sawfish-53.t:call-run_sawfish INFO eval :: name: "call_dirname", value: "m84036_250809_035451_s4.bc2150_sawfish"
2025-09-15 20:24:38.030 wdl.w:ptcp.w:call-sawfish-53.t:call-run_sawfish INFO eval :: name: "minimap2_bam_filename", value: "m84036_250809_035451_s4.bc2150.minimap2.bam"
2025-09-15 20:24:38.030 wdl.w:ptcp.w:call-sawfish-53.t:call-run_sawfish INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 16, memory_reservation: 32000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:38.030 wdl.w:ptcp.w:call-sawfish-53.t:call-run_sawfish WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:38.030 wdl.w:ptcp.w:call-sawfish-53.t:call-run_sawfish INFO provisioned :: seconds_waited: 0, cpu: 16, mem_bytes: 32000000000
2025-09-15 20:24:38.031 wdl.w:ptcp.w:call-sawfish-53.t:call-run_sawfish INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:38.060 wdl.w:ptcp.w:call-paraphase-47.t:call-run_paraphase.stderr VERBOSE INFO:root:Processing sample m84036_250809_035451_s4.bc2144 at 2025-09-15 20:24:33.697449...
2025-09-15 20:24:38.061 wdl.w:ptcp.w:call-paraphase-47.t:call-run_paraphase.stderr VERBOSE INFO:root:Checking sample sex at 2025-09-15 20:24:33.699434...
2025-09-15 20:24:38.061 wdl.w:ptcp.w:call-paraphase-47.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for cyp21 for sample m84036_250809_035451_s4.bc2144 at 2025-09-15 20:24:33.760741...
2025-09-15 20:24:38.061 wdl.w:ptcp.w:call-paraphase-47.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for cyp21 for sample m84036_250809_035451_s4.bc2144 at 2025-09-15 20:24:33.761247...
2025-09-15 20:24:38.061 wdl.w:ptcp.w:call-paraphase-47.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for smn1 for sample m84036_250809_035451_s4.bc2144 at 2025-09-15 20:24:33.760872...
2025-09-15 20:24:38.061 wdl.w:ptcp.w:call-paraphase-47.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for gba for sample m84036_250809_035451_s4.bc2144 at 2025-09-15 20:24:33.760905...
2025-09-15 20:24:38.062 wdl.w:ptcp.w:call-paraphase-47.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for hba for sample m84036_250809_035451_s4.bc2144 at 2025-09-15 20:24:33.760926...
2025-09-15 20:24:38.062 wdl.w:ptcp.w:call-paraphase-47.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for smn1 for sample m84036_250809_035451_s4.bc2144 at 2025-09-15 20:24:33.761303...
2025-09-15 20:24:38.062 wdl.w:ptcp.w:call-paraphase-47.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for gba for sample m84036_250809_035451_s4.bc2144 at 2025-09-15 20:24:33.761322...
2025-09-15 20:24:38.062 wdl.w:ptcp.w:call-paraphase-47.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for hba for sample m84036_250809_035451_s4.bc2144 at 2025-09-15 20:24:33.761326...
2025-09-15 20:24:38.108 wdl.w:ptcp.w:call-sawfish-53.t:call-run_sawfish INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 10, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-53/call-run_sawfish/_singularity_tmpdir_a9ff15nk"
2025-09-15 20:24:38.108 wdl.w:ptcp.w:call-sawfish-53.t:call-run_sawfish INFO Slurm invocation: srun --job-name call-run_sawfish --partition compute,compute9 --cpus-per-task 16 --mem 30518M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-53/call-run_sawfish/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-53/call-run_sawfish/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-53/call-run_sawfish/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-53/call-run_sawfish/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-53/out/m84036_250809_035451_s4.bc2150.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2150.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-53/out/m84036_250809_035451_s4.bc2150.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2150.mapped.bam.bai:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-53/call-run_sawfish/_singularity_tmpdir_a9ff15nk/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-53/call-run_sawfish/_singularity_tmpdir_a9ff15nk/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:38.128 wdl.w:ptcp.w:call-sawfish-01.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:33][sawfish][INFO] Starting sawfish 2.0.3
2025-09-15 20:24:38.128 wdl.w:ptcp.w:call-sawfish-01.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:33][sawfish][INFO] cmdline: sawfish joint-call --threads 16 --sample m84036_250809_035451_s4.bc2098_sawfish_discover --output-dir m84036_250809_035451_s4.bc2098_sawfish
2025-09-15 20:24:38.128 wdl.w:ptcp.w:call-sawfish-01.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:33][sawfish][INFO] Running on 16 threads
2025-09-15 20:24:38.129 wdl.w:ptcp.w:call-sawfish-01.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:33][sawfish][INFO] Reading reference genome from file '/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa'
2025-09-15 20:24:38.129 wdl.w:ptcp.w:call-sawfish-01.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:36][sawfish][INFO] Reading sawfish-discover results from 1 samples
2025-09-15 20:24:38.129 wdl.w:ptcp.w:call-sawfish-01.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:37][sawfish][INFO] Writing depth track to bigwig file: 'm84036_250809_035451_s4.bc2098_sawfish/samples/sample0001_UnknownSampleName/depth.bw'
2025-09-15 20:24:38.129 wdl.w:ptcp.w:call-sawfish-01.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:37][sawfish][INFO] Merging SV haplotypes
2025-09-15 20:24:38.129 wdl.w:ptcp.w:call-sawfish-01.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:37][sawfish][INFO] Finished merging SV haplotypes across samples
2025-09-15 20:24:38.129 wdl.w:ptcp.w:call-sawfish-01.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:37][sawfish][INFO] Writing merged contig alignments to bam file: 'm84036_250809_035451_s4.bc2098_sawfish/contig.alignment.bam'
2025-09-15 20:24:38.129 wdl.w:ptcp.w:call-sawfish-01.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:37][sawfish][INFO] Starting SV candidate cluster genotyping
2025-09-15 20:24:38.129 wdl.w:ptcp.w:call-sawfish-01.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:37][sawfish][INFO] Finished genotyping all SV candidate clusters
2025-09-15 20:24:38.129 wdl.w:ptcp.w:call-sawfish-01.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:37][sawfish][INFO] Starting joint CNV/SV refinement
2025-09-15 20:24:38.129 wdl.w:ptcp.w:call-sawfish-01.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:37][sawfish][INFO] Merged 0 CNVs into corresponding breakpoint-based SVs
2025-09-15 20:24:38.129 wdl.w:ptcp.w:call-sawfish-01.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:37][sawfish][INFO] Writing genotyped structural variants to file: 'm84036_250809_035451_s4.bc2098_sawfish/genotyped.sv.vcf.gz'
2025-09-15 20:24:38.129 wdl.w:ptcp.w:call-sawfish-01.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:37][sawfish][INFO] Writing run statistics to file: 'm84036_250809_035451_s4.bc2098_sawfish/run.stats.json'
2025-09-15 20:24:38.129 wdl.w:ptcp.w:call-sawfish-01.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:37][sawfish][INFO] sawfish completed. Total Runtime: 00:00:04.225
2025-09-15 20:24:38.130 wdl.w:ptcp.w:call-sawfish-53.t:call-run_sawfish NOTICE slurm_singularity run :: pid: 1202582, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-53/call-run_sawfish/slurm_singularity.log.txt"
2025-09-15 20:24:38.143 wdl.w:ptcp.w:call-paraphase-35.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for hbb for sample m84036_250809_035451_s4.bc2132 at 2025-09-15 20:24:30.605790...
2025-09-15 20:24:38.143 wdl.w:ptcp.w:call-paraphase-35.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for hbb for sample m84036_250809_035451_s4.bc2132 at 2025-09-15 20:24:30.924420...
2025-09-15 20:24:38.143 wdl.w:ptcp.w:call-paraphase-35.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for f8inv1 for sample m84036_250809_035451_s4.bc2132 at 2025-09-15 20:24:37.365431...
2025-09-15 20:24:38.144 wdl.w:ptcp.w:call-paraphase-35.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for f8inv1 for sample m84036_250809_035451_s4.bc2132 at 2025-09-15 20:24:37.366462...
2025-09-15 20:24:38.146 wdl.w:ptcp.w:call-trgt-48.t:call-trgt_genotype INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2145.trgt.vcf"
2025-09-15 20:24:38.150 wdl.w:ptcp.w:call-trgt-48.t:call-trgt_genotype INFO output :: name: "spanning_bam", value: "m84036_250809_035451_s4.bc2145.trgt.sorted.spanning.bam"
2025-09-15 20:24:38.151 wdl.w:ptcp.w:call-trgt-48.t:call-trgt_genotype INFO output :: name: "spanning_bam_bai", value: "m84036_250809_035451_s4.bc2145.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:38.261 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_genotype.slurm_singularity INFO srun: job 51797729 queued and waiting for resources
2025-09-15 20:24:38.261 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_genotype.slurm_singularity INFO srun: job 51797729 has been allocated resources
2025-09-15 20:24:38.261 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_genotype.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:38.261 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_genotype.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:24:38.264 wdl.w:ptcp.w:call-trgt-48.t:call-trgt_genotype NOTICE done
2025-09-15 20:24:38.270 wdl.w:ptcp.w:call-trgt-48 NOTICE finish :: job: "call-trgt_genotype"
2025-09-15 20:24:38.270 wdl.w:ptcp.w:call-trgt-48 INFO output :: job: "call-trgt_genotype", values: {"spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-48/call-trgt_genotype/out/m84036_250809_035451_s4.bc2145.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-48/call-trgt_genotype/out/m84036_250809_035451_s4.bc2145.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-48/call-trgt_genotype/out/m84036_250809_035451_s4.bc2145.trgt.vcf"}
2025-09-15 20:24:38.271 wdl.w:ptcp.w:call-trgt-48 NOTICE ready :: job: "call-trgt_plot_meth_allele", callee: "trgt_plot"
2025-09-15 20:24:38.271 wdl.w:ptcp.w:call-trgt-48 INFO input :: job: "call-trgt_plot_meth_allele", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": false, "methylation": true, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-48/call-trgt_genotype/out/m84036_250809_035451_s4.bc2145.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-48/call-trgt_genotype/out/m84036_250809_035451_s4.bc2145.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-48/call-trgt_genotype/out/m84036_250809_035451_s4.bc2145.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2145"}
2025-09-15 20:24:38.272 wdl.w:ptcp.w:call-trgt-48 NOTICE ready :: job: "call-trgt_plot_meth_waterfall", callee: "trgt_plot"
2025-09-15 20:24:38.273 wdl.w:ptcp.w:call-trgt-48 INFO input :: job: "call-trgt_plot_meth_waterfall", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": true, "methylation": true, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-48/call-trgt_genotype/out/m84036_250809_035451_s4.bc2145.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-48/call-trgt_genotype/out/m84036_250809_035451_s4.bc2145.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-48/call-trgt_genotype/out/m84036_250809_035451_s4.bc2145.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2145"}
2025-09-15 20:24:38.273 wdl.w:ptcp.w:call-trgt-48 NOTICE ready :: job: "call-trgt_plot_motifs_allele", callee: "trgt_plot"
2025-09-15 20:24:38.274 wdl.w:ptcp.w:call-trgt-48 INFO input :: job: "call-trgt_plot_motifs_allele", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": false, "methylation": false, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-48/call-trgt_genotype/out/m84036_250809_035451_s4.bc2145.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-48/call-trgt_genotype/out/m84036_250809_035451_s4.bc2145.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-48/call-trgt_genotype/out/m84036_250809_035451_s4.bc2145.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2145"}
2025-09-15 20:24:38.274 wdl.w:ptcp.w:call-trgt-48 NOTICE ready :: job: "call-trgt_plot_motifs_waterfall", callee: "trgt_plot"
2025-09-15 20:24:38.274 wdl.w:ptcp.w:call-trgt-48 INFO input :: job: "call-trgt_plot_motifs_waterfall", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": true, "methylation": false, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-48/call-trgt_genotype/out/m84036_250809_035451_s4.bc2145.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-48/call-trgt_genotype/out/m84036_250809_035451_s4.bc2145.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-48/call-trgt_genotype/out/m84036_250809_035451_s4.bc2145.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2145"}
2025-09-15 20:24:38.275 wdl.w:ptcp.w:call-trgt-48 INFO visit :: node: "output-spanning_bam", values: {"spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-48/call-trgt_genotype/out/m84036_250809_035451_s4.bc2145.trgt.sorted.spanning.bam"}
2025-09-15 20:24:38.275 wdl.w:ptcp.w:call-trgt-48 INFO visit :: node: "output-spanning_bam_bai", values: {"spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-48/call-trgt_genotype/out/m84036_250809_035451_s4.bc2145.trgt.sorted.spanning.bam.bai"}
2025-09-15 20:24:38.275 wdl.w:ptcp.w:call-trgt-48 INFO visit :: node: "output-vcf", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-48/call-trgt_genotype/out/m84036_250809_035451_s4.bc2145.trgt.vcf"}
2025-09-15 20:24:38.281 wdl.w:ptcp.w:call-trgt-53.t:call-get_reads_overlapping_repeats NOTICE task setup :: name: "get_reads_overlapping_repeats", source: "./trgt.wdl", line: 182, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-53/call-get_reads_overlapping_repeats", thread: 140607112582720
2025-09-15 20:24:38.290 wdl.w:ptcp.w:call-paraphase-59.t:call-run_paraphase.slurm_singularity INFO srun: job 51797730 queued and waiting for resources
2025-09-15 20:24:38.290 wdl.w:ptcp.w:call-paraphase-59.t:call-run_paraphase.slurm_singularity INFO srun: job 51797730 has been allocated resources
2025-09-15 20:24:38.290 wdl.w:ptcp.w:call-paraphase-59.t:call-run_paraphase.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:38.290 wdl.w:ptcp.w:call-paraphase-59.t:call-run_paraphase.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:24:38.297 wdl.w:ptcp.w:call-sawfish-35.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:27][sawfish][INFO] Starting sawfish 2.0.3
2025-09-15 20:24:38.297 wdl.w:ptcp.w:call-sawfish-35.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:27][sawfish][INFO] cmdline: sawfish joint-call --threads 16 --sample m84036_250809_035451_s4.bc2132_sawfish_discover --output-dir m84036_250809_035451_s4.bc2132_sawfish
2025-09-15 20:24:38.297 wdl.w:ptcp.w:call-sawfish-35.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:27][sawfish][INFO] Running on 16 threads
2025-09-15 20:24:38.297 wdl.w:ptcp.w:call-sawfish-35.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:27][sawfish][INFO] Reading reference genome from file '/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa'
2025-09-15 20:24:38.303 wdl.w:ptcp.w:call-trgt-53.t:call-get_reads_overlapping_repeats INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:38.303 wdl.w:ptcp.w:call-trgt-53.t:call-get_reads_overlapping_repeats INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:38.303 wdl.w:ptcp.w:call-trgt-53.t:call-get_reads_overlapping_repeats INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2150.mapped.bam.bai"
2025-09-15 20:24:38.303 wdl.w:ptcp.w:call-trgt-53.t:call-get_reads_overlapping_repeats INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2150.mapped.bam"
2025-09-15 20:24:38.303 wdl.w:ptcp.w:call-trgt-53.t:call-get_reads_overlapping_repeats INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2150"
2025-09-15 20:24:38.303 wdl.w:ptcp.w:call-trgt-53.t:call-get_reads_overlapping_repeats INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:38.303 wdl.w:ptcp.w:call-trgt-53.t:call-get_reads_overlapping_repeats INFO eval :: name: "expand_size", value: 3000
2025-09-15 20:24:38.304 wdl.w:ptcp.w:call-trgt-53.t:call-get_reads_overlapping_repeats INFO eval :: name: "threads", value: 1
2025-09-15 20:24:38.304 wdl.w:ptcp.w:call-trgt-53.t:call-get_reads_overlapping_repeats INFO eval :: name: "expanded_bed_name", value: "m84036_250809_035451_s4.bc2150.expanded.bed"
2025-09-15 20:24:38.304 wdl.w:ptcp.w:call-trgt-53.t:call-get_reads_overlapping_repeats INFO eval :: name: "disk_size", value: 11
2025-09-15 20:24:38.304 wdl.w:ptcp.w:call-trgt-53.t:call-get_reads_overlapping_repeats INFO eval :: name: "output_name", value: "m84036_250809_035451_s4.bc2150.repeats.bam"
2025-09-15 20:24:38.304 wdl.w:ptcp.w:call-trgt-53.t:call-get_reads_overlapping_repeats INFO eval :: name: "index_name", value: "m84036_250809_035451_s4.bc2150.repeats.bam.bai"
2025-09-15 20:24:38.304 wdl.w:ptcp.w:call-trgt-53.t:call-get_reads_overlapping_repeats INFO eval :: name: "output_name_with_index", value: "m84036_250809_035451_s4.bc2150.repeats.bam##idx##m84036_250809_035451_s4.bc2150.repeats.bam.bai"
2025-09-15 20:24:38.305 wdl.w:ptcp.w:call-trgt-53.t:call-get_reads_overlapping_repeats INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:38.305 wdl.w:ptcp.w:call-trgt-53.t:call-get_reads_overlapping_repeats WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:38.305 wdl.w:ptcp.w:call-trgt-53.t:call-get_reads_overlapping_repeats INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:38.305 wdl.w:ptcp.w:call-trgt-53.t:call-get_reads_overlapping_repeats INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:38.374 wdl.w:ptcp.w:call-trgt-53.t:call-get_reads_overlapping_repeats INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 9, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-53/call-get_reads_overlapping_repeats/_singularity_tmpdir_93yt_0h_"
2025-09-15 20:24:38.374 wdl.w:ptcp.w:call-trgt-53.t:call-get_reads_overlapping_repeats INFO Slurm invocation: srun --job-name call-get_reads_overlapping_repeats --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-53/call-get_reads_overlapping_repeats/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-53/call-get_reads_overlapping_repeats/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-53/call-get_reads_overlapping_repeats/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-53/call-get_reads_overlapping_repeats/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-53/out/m84036_250809_035451_s4.bc2150.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2150.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-53/out/m84036_250809_035451_s4.bc2150.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2150.mapped.bam.bai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-53/call-get_reads_overlapping_repeats/_singularity_tmpdir_93yt_0h_/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-53/call-get_reads_overlapping_repeats/_singularity_tmpdir_93yt_0h_/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:38.375 wdl.w:ptcp.w:call-trgt-57.t:call-trgt_genotype INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2154.trgt.vcf"
2025-09-15 20:24:38.380 wdl.w:ptcp.w:call-trgt-57.t:call-trgt_genotype INFO output :: name: "spanning_bam", value: "m84036_250809_035451_s4.bc2154.trgt.sorted.spanning.bam"
2025-09-15 20:24:38.382 wdl.w:ptcp.w:call-trgt-57.t:call-trgt_genotype INFO output :: name: "spanning_bam_bai", value: "m84036_250809_035451_s4.bc2154.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:38.409 wdl.w:ptcp.w:call-trgt-53.t:call-get_reads_overlapping_repeats NOTICE slurm_singularity run :: pid: 1202590, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-53/call-get_reads_overlapping_repeats/slurm_singularity.log.txt"
2025-09-15 20:24:38.484 wdl.w:ptcp.w:call-sawfish-08.t:call-run_sawfish INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2105_sawfish/m84036_250809_035451_s4.bc2105.sv.vcf.gz"
2025-09-15 20:24:38.485 wdl.w:ptcp.w:call-trgt-57.t:call-trgt_genotype NOTICE done
2025-09-15 20:24:38.490 wdl.w:ptcp.w:call-sawfish-08.t:call-run_sawfish INFO output :: name: "vcf_tbi", value: "m84036_250809_035451_s4.bc2105_sawfish/m84036_250809_035451_s4.bc2105.sv.vcf.gz.tbi"
2025-09-15 20:24:38.492 wdl.w:ptcp.w:call-sawfish-08.t:call-run_sawfish INFO output :: name: "minimap2_bam", value: "m84036_250809_035451_s4.bc2105.minimap2.bam"
2025-09-15 20:24:38.493 wdl.w:ptcp.w:call-trgt-57 NOTICE finish :: job: "call-trgt_genotype"
2025-09-15 20:24:38.494 wdl.w:ptcp.w:call-trgt-57 INFO output :: job: "call-trgt_genotype", values: {"spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-57/call-trgt_genotype/out/m84036_250809_035451_s4.bc2154.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-57/call-trgt_genotype/out/m84036_250809_035451_s4.bc2154.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-57/call-trgt_genotype/out/m84036_250809_035451_s4.bc2154.trgt.vcf"}
2025-09-15 20:24:38.494 wdl.w:ptcp.w:call-trgt-57 NOTICE ready :: job: "call-trgt_plot_meth_allele", callee: "trgt_plot"
2025-09-15 20:24:38.495 wdl.w:ptcp.w:call-trgt-57 INFO input :: job: "call-trgt_plot_meth_allele", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": false, "methylation": true, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-57/call-trgt_genotype/out/m84036_250809_035451_s4.bc2154.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-57/call-trgt_genotype/out/m84036_250809_035451_s4.bc2154.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-57/call-trgt_genotype/out/m84036_250809_035451_s4.bc2154.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2154"}
2025-09-15 20:24:38.495 wdl.w:ptcp.w:call-sawfish-08.t:call-run_sawfish INFO output :: name: "minimap2_bam_bai", value: "m84036_250809_035451_s4.bc2105.minimap2.bam.bai"
2025-09-15 20:24:38.498 wdl.w:ptcp.w:call-trgt-57 NOTICE ready :: job: "call-trgt_plot_meth_waterfall", callee: "trgt_plot"
2025-09-15 20:24:38.498 wdl.w:ptcp.w:call-trgt-57 INFO input :: job: "call-trgt_plot_meth_waterfall", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": true, "methylation": true, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-57/call-trgt_genotype/out/m84036_250809_035451_s4.bc2154.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-57/call-trgt_genotype/out/m84036_250809_035451_s4.bc2154.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-57/call-trgt_genotype/out/m84036_250809_035451_s4.bc2154.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2154"}
2025-09-15 20:24:38.499 wdl.w:ptcp.w:call-trgt-57 NOTICE ready :: job: "call-trgt_plot_motifs_allele", callee: "trgt_plot"
2025-09-15 20:24:38.499 wdl.w:ptcp.w:call-sawfish-59.t:call-run_sawfish.slurm_singularity INFO srun: job 51797731 queued and waiting for resources
2025-09-15 20:24:38.499 wdl.w:ptcp.w:call-trgt-57 INFO input :: job: "call-trgt_plot_motifs_allele", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": false, "methylation": false, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-57/call-trgt_genotype/out/m84036_250809_035451_s4.bc2154.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-57/call-trgt_genotype/out/m84036_250809_035451_s4.bc2154.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-57/call-trgt_genotype/out/m84036_250809_035451_s4.bc2154.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2154"}
2025-09-15 20:24:38.499 wdl.w:ptcp.w:call-sawfish-59.t:call-run_sawfish.slurm_singularity INFO srun: job 51797731 has been allocated resources
2025-09-15 20:24:38.499 wdl.w:ptcp.w:call-sawfish-59.t:call-run_sawfish.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:38.499 wdl.w:ptcp.w:call-sawfish-59.t:call-run_sawfish.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:24:38.500 wdl.w:ptcp.w:call-trgt-57 NOTICE ready :: job: "call-trgt_plot_motifs_waterfall", callee: "trgt_plot"
2025-09-15 20:24:38.501 wdl.w:ptcp.w:call-trgt-57 INFO input :: job: "call-trgt_plot_motifs_waterfall", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": true, "methylation": false, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-57/call-trgt_genotype/out/m84036_250809_035451_s4.bc2154.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-57/call-trgt_genotype/out/m84036_250809_035451_s4.bc2154.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-57/call-trgt_genotype/out/m84036_250809_035451_s4.bc2154.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2154"}
2025-09-15 20:24:38.501 wdl.w:ptcp.w:call-trgt-57 INFO visit :: node: "output-spanning_bam", values: {"spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-57/call-trgt_genotype/out/m84036_250809_035451_s4.bc2154.trgt.sorted.spanning.bam"}
2025-09-15 20:24:38.501 wdl.w:ptcp.w:call-trgt-57 INFO visit :: node: "output-spanning_bam_bai", values: {"spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-57/call-trgt_genotype/out/m84036_250809_035451_s4.bc2154.trgt.sorted.spanning.bam.bai"}
2025-09-15 20:24:38.501 wdl.w:ptcp.w:call-trgt-57 INFO visit :: node: "output-vcf", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-57/call-trgt_genotype/out/m84036_250809_035451_s4.bc2154.trgt.vcf"}
2025-09-15 20:24:38.506 wdl.w:ptcp.w:call-trgt-53.t:call-trgt_genotype NOTICE task setup :: name: "trgt_genotype", source: "./trgt.wdl", line: 272, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-53/call-trgt_genotype", thread: 140609310422592
2025-09-15 20:24:38.517 wdl.w:ptcp.w:call-sawfish-01.t:call-run_sawfish INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2098_sawfish/m84036_250809_035451_s4.bc2098.sv.vcf.gz"
2025-09-15 20:24:38.525 wdl.w:ptcp.w:call-sawfish-01.t:call-run_sawfish INFO output :: name: "vcf_tbi", value: "m84036_250809_035451_s4.bc2098_sawfish/m84036_250809_035451_s4.bc2098.sv.vcf.gz.tbi"
2025-09-15 20:24:38.526 wdl.w:ptcp.w:call-sawfish-01.t:call-run_sawfish INFO output :: name: "minimap2_bam", value: "m84036_250809_035451_s4.bc2098.minimap2.bam"
2025-09-15 20:24:38.529 wdl.w:ptcp.w:call-sawfish-01.t:call-run_sawfish INFO output :: name: "minimap2_bam_bai", value: "m84036_250809_035451_s4.bc2098.minimap2.bam.bai"
2025-09-15 20:24:38.543 wdl.w:ptcp.w:call-trgt-53.t:call-trgt_genotype INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:38.543 wdl.w:ptcp.w:call-trgt-53.t:call-trgt_genotype INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:38.543 wdl.w:ptcp.w:call-trgt-53.t:call-trgt_genotype INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:38.543 wdl.w:ptcp.w:call-trgt-53.t:call-trgt_genotype INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:38.543 wdl.w:ptcp.w:call-trgt-53.t:call-trgt_genotype INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2150.mapped.bam.bai"
2025-09-15 20:24:38.543 wdl.w:ptcp.w:call-trgt-53.t:call-trgt_genotype INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2150.mapped.bam"
2025-09-15 20:24:38.543 wdl.w:ptcp.w:call-trgt-53.t:call-trgt_genotype INFO input :: name: "sex", value: "F"
2025-09-15 20:24:38.544 wdl.w:ptcp.w:call-trgt-53.t:call-trgt_genotype INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2150"
2025-09-15 20:24:38.544 wdl.w:ptcp.w:call-trgt-53.t:call-trgt_genotype INFO eval :: name: "mem_gb", value: 16
2025-09-15 20:24:38.544 wdl.w:ptcp.w:call-trgt-53.t:call-trgt_genotype INFO eval :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2150.trgt"
2025-09-15 20:24:38.544 wdl.w:ptcp.w:call-trgt-53.t:call-trgt_genotype INFO eval :: name: "threads", value: 8
2025-09-15 20:24:38.544 wdl.w:ptcp.w:call-trgt-53.t:call-trgt_genotype INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:38.544 wdl.w:ptcp.w:call-trgt-53.t:call-trgt_genotype INFO eval :: name: "karyotype", value: "XX"
2025-09-15 20:24:38.545 wdl.w:ptcp.w:call-trgt-53.t:call-trgt_genotype INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 8, memory_reservation: 16000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:38.545 wdl.w:ptcp.w:call-trgt-53.t:call-trgt_genotype WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:38.545 wdl.w:ptcp.w:call-trgt-53.t:call-trgt_genotype INFO provisioned :: seconds_waited: 0, cpu: 8, mem_bytes: 16000000000
2025-09-15 20:24:38.545 wdl.w:ptcp.w:call-trgt-53.t:call-trgt_genotype INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:38.619 wdl.w:ptcp.w:call-trgt-40.t:call-trgt_genotype INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2137.trgt.vcf"
2025-09-15 20:24:38.622 wdl.w:ptcp.w:call-paraphase-02.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for f8inv1 for sample m84036_250809_035451_s4.bc2099 at 2025-09-15 20:24:30.803984...
2025-09-15 20:24:38.626 wdl.w:ptcp.w:call-trgt-40.t:call-trgt_genotype INFO output :: name: "spanning_bam", value: "m84036_250809_035451_s4.bc2137.trgt.sorted.spanning.bam"
2025-09-15 20:24:38.627 wdl.w:ptcp.w:call-trgt-40.t:call-trgt_genotype INFO output :: name: "spanning_bam_bai", value: "m84036_250809_035451_s4.bc2137.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:38.658 wdl.w:ptcp.w:call-trgt-59.t:call-get_reads_overlapping_repeats.slurm_singularity INFO srun: job 51797732 queued and waiting for resources
2025-09-15 20:24:38.658 wdl.w:ptcp.w:call-trgt-59.t:call-get_reads_overlapping_repeats.slurm_singularity INFO srun: job 51797732 has been allocated resources
2025-09-15 20:24:38.658 wdl.w:ptcp.w:call-trgt-59.t:call-get_reads_overlapping_repeats.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:38.659 wdl.w:ptcp.w:call-trgt-59.t:call-get_reads_overlapping_repeats.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:24:38.673 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:24:38 [INFO] - Running trgt-4.0.0-429afcd [genotype]
2025-09-15 20:24:38.673 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:24:38 [WARN] - PRTS_ARX: Filtered out 5 impure reads
2025-09-15 20:24:38.673 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:24:38 [WARN] - EIEE1_ARX: Filtered out 1 impure reads
2025-09-15 20:24:38.674 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:24:38 [WARN] - FXS_FMR1: Filtered out 4 impure reads
2025-09-15 20:24:38.674 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:24:38 [WARN] - FRAXE_AFF2: Filtered out 19 impure reads
2025-09-15 20:24:38.674 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:24:38 [WARN] - FRDA_FXN: Filtered out 3 impure reads
2025-09-15 20:24:38.674 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:24:38 [INFO] - Total execution time: 211.88ms
2025-09-15 20:24:38.674 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:24:38 [INFO] - trgt end
2025-09-15 20:24:38.685 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_genotype.slurm_singularity INFO srun: job 51797733 queued and waiting for resources
2025-09-15 20:24:38.685 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_genotype.slurm_singularity INFO srun: job 51797733 has been allocated resources
2025-09-15 20:24:38.685 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_genotype.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:38.688 wdl.w:ptcp.w:call-trgt-53.t:call-trgt_genotype INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 11, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-53/call-trgt_genotype/_singularity_tmpdir_7xop8doz"
2025-09-15 20:24:38.688 wdl.w:ptcp.w:call-trgt-53.t:call-trgt_genotype INFO Slurm invocation: srun --job-name call-trgt_genotype --partition compute,compute9 --cpus-per-task 8 --mem 15259M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-53/call-trgt_genotype/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-53/call-trgt_genotype/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-53/call-trgt_genotype/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-53/call-trgt_genotype/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-53/out/m84036_250809_035451_s4.bc2150.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2150.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-53/out/m84036_250809_035451_s4.bc2150.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2150.mapped.bam.bai:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-53/call-trgt_genotype/_singularity_tmpdir_7xop8doz/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-53/call-trgt_genotype/_singularity_tmpdir_7xop8doz/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:38.722 wdl.w:ptcp.w:call-trgt-53.t:call-trgt_genotype NOTICE slurm_singularity run :: pid: 1202602, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-53/call-trgt_genotype/slurm_singularity.log.txt"
2025-09-15 20:24:38.724 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_genotype INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2151.trgt.vcf"
2025-09-15 20:24:38.731 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_genotype INFO output :: name: "spanning_bam", value: "m84036_250809_035451_s4.bc2151.trgt.sorted.spanning.bam"
2025-09-15 20:24:38.731 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_genotype INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2156.trgt.vcf"
2025-09-15 20:24:38.732 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_genotype INFO output :: name: "spanning_bam_bai", value: "m84036_250809_035451_s4.bc2151.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:38.736 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_genotype INFO output :: name: "spanning_bam", value: "m84036_250809_035451_s4.bc2156.trgt.sorted.spanning.bam"
2025-09-15 20:24:38.737 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_genotype INFO output :: name: "spanning_bam_bai", value: "m84036_250809_035451_s4.bc2156.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:38.741 wdl.w:ptcp.w:call-trgt-40.t:call-trgt_genotype NOTICE done
2025-09-15 20:24:38.748 wdl.w:ptcp.w:call-trgt-40 NOTICE finish :: job: "call-trgt_genotype"
2025-09-15 20:24:38.748 wdl.w:ptcp.w:call-trgt-40 INFO output :: job: "call-trgt_genotype", values: {"spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-40/call-trgt_genotype/out/m84036_250809_035451_s4.bc2137.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-40/call-trgt_genotype/out/m84036_250809_035451_s4.bc2137.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-40/call-trgt_genotype/out/m84036_250809_035451_s4.bc2137.trgt.vcf"}
2025-09-15 20:24:38.749 wdl.w:ptcp.w:call-trgt-40 NOTICE ready :: job: "call-trgt_plot_meth_allele", callee: "trgt_plot"
2025-09-15 20:24:38.749 wdl.w:ptcp.w:call-trgt-40 INFO input :: job: "call-trgt_plot_meth_allele", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": false, "methylation": true, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-40/call-trgt_genotype/out/m84036_250809_035451_s4.bc2137.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-40/call-trgt_genotype/out/m84036_250809_035451_s4.bc2137.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-40/call-trgt_genotype/out/m84036_250809_035451_s4.bc2137.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2137"}
2025-09-15 20:24:38.749 wdl.w:ptcp.w:call-sawfish-08.t:call-run_sawfish NOTICE done
2025-09-15 20:24:38.750 wdl.w:ptcp.w:call-trgt-40 NOTICE ready :: job: "call-trgt_plot_meth_waterfall", callee: "trgt_plot"
2025-09-15 20:24:38.750 wdl.w:ptcp.w:call-trgt-40 INFO input :: job: "call-trgt_plot_meth_waterfall", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": true, "methylation": true, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-40/call-trgt_genotype/out/m84036_250809_035451_s4.bc2137.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-40/call-trgt_genotype/out/m84036_250809_035451_s4.bc2137.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-40/call-trgt_genotype/out/m84036_250809_035451_s4.bc2137.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2137"}
2025-09-15 20:24:38.751 wdl.w:ptcp.w:call-trgt-40 NOTICE ready :: job: "call-trgt_plot_motifs_allele", callee: "trgt_plot"
2025-09-15 20:24:38.751 wdl.w:ptcp.w:call-trgt-40 INFO input :: job: "call-trgt_plot_motifs_allele", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": false, "methylation": false, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-40/call-trgt_genotype/out/m84036_250809_035451_s4.bc2137.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-40/call-trgt_genotype/out/m84036_250809_035451_s4.bc2137.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-40/call-trgt_genotype/out/m84036_250809_035451_s4.bc2137.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2137"}
2025-09-15 20:24:38.752 wdl.w:ptcp.w:call-trgt-40 NOTICE ready :: job: "call-trgt_plot_motifs_waterfall", callee: "trgt_plot"
2025-09-15 20:24:38.753 wdl.w:ptcp.w:call-trgt-40 INFO input :: job: "call-trgt_plot_motifs_waterfall", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": true, "methylation": false, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-40/call-trgt_genotype/out/m84036_250809_035451_s4.bc2137.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-40/call-trgt_genotype/out/m84036_250809_035451_s4.bc2137.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-40/call-trgt_genotype/out/m84036_250809_035451_s4.bc2137.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2137"}
2025-09-15 20:24:38.753 wdl.w:ptcp.w:call-trgt-40 INFO visit :: node: "output-spanning_bam", values: {"spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-40/call-trgt_genotype/out/m84036_250809_035451_s4.bc2137.trgt.sorted.spanning.bam"}
2025-09-15 20:24:38.753 wdl.w:ptcp.w:call-trgt-40 INFO visit :: node: "output-spanning_bam_bai", values: {"spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-40/call-trgt_genotype/out/m84036_250809_035451_s4.bc2137.trgt.sorted.spanning.bam.bai"}
2025-09-15 20:24:38.754 wdl.w:ptcp.w:call-trgt-40 INFO visit :: node: "output-vcf", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-40/call-trgt_genotype/out/m84036_250809_035451_s4.bc2137.trgt.vcf"}
2025-09-15 20:24:38.755 wdl.w:ptcp.w:call-sawfish-08 NOTICE finish :: job: "call-run_sawfish"
2025-09-15 20:24:38.755 wdl.w:ptcp.w:call-sawfish-08 INFO output :: job: "call-run_sawfish", values: {"minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-08/call-run_sawfish/out/m84036_250809_035451_s4.bc2105.minimap2.bam.bai", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-08/call-run_sawfish/out/m84036_250809_035451_s4.bc2105.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-08/call-run_sawfish/out/m84036_250809_035451_s4.bc2105_sawfish/m84036_250809_035451_s4.bc2105.sv.vcf.gz.tbi", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-08/call-run_sawfish/out/m84036_250809_035451_s4.bc2105_sawfish/m84036_250809_035451_s4.bc2105.sv.vcf.gz"}
2025-09-15 20:24:38.756 wdl.w:ptcp.w:call-sawfish-08 INFO visit :: node: "output-minimap2_bam", values: {"minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-08/call-run_sawfish/out/m84036_250809_035451_s4.bc2105.minimap2.bam"}
2025-09-15 20:24:38.756 wdl.w:ptcp.w:call-sawfish-08 INFO visit :: node: "output-minimap2_bam_bai", values: {"minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-08/call-run_sawfish/out/m84036_250809_035451_s4.bc2105.minimap2.bam.bai"}
2025-09-15 20:24:38.756 wdl.w:ptcp.w:call-sawfish-08 INFO visit :: node: "output-vcf", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-08/call-run_sawfish/out/m84036_250809_035451_s4.bc2105_sawfish/m84036_250809_035451_s4.bc2105.sv.vcf.gz"}
2025-09-15 20:24:38.756 wdl.w:ptcp.w:call-sawfish-08 INFO visit :: node: "output-vcf_tbi", values: {"vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-08/call-run_sawfish/out/m84036_250809_035451_s4.bc2105_sawfish/m84036_250809_035451_s4.bc2105.sv.vcf.gz.tbi"}
2025-09-15 20:24:38.756 wdl.w:ptcp.w:call-sawfish-08 INFO visit :: node: "outputs", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-08/call-run_sawfish/out/m84036_250809_035451_s4.bc2105_sawfish/m84036_250809_035451_s4.bc2105.sv.vcf.gz", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-08/call-run_sawfish/out/m84036_250809_035451_s4.bc2105.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-08/call-run_sawfish/out/m84036_250809_035451_s4.bc2105_sawfish/m84036_250809_035451_s4.bc2105.sv.vcf.gz.tbi", "minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-08/call-run_sawfish/out/m84036_250809_035451_s4.bc2105.minimap2.bam.bai"}
2025-09-15 20:24:38.756 wdl.w:ptcp.w:call-paraphase-56.t:call-run_paraphase NOTICE task setup :: name: "run_paraphase", source: "./paraphase.wdl", line: 127, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-56/call-run_paraphase", thread: 140607683024448
2025-09-15 20:24:38.765 wdl.w:ptcp.w:call-sawfish-56.t:call-run_sawfish NOTICE task setup :: name: "run_sawfish", source: "./sawfish.wdl", line: 83, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-56/call-run_sawfish", thread: 140608723195456
2025-09-15 20:24:38.773 wdl.w:ptcp.w:call-trgt-00.t:call-trgt_plot_motifs_waterfall INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2097.motifs_waterfall.trgt_plots.zip"
2025-09-15 20:24:38.779 wdl.w:ptcp.w:call-sawfish-01.t:call-run_sawfish NOTICE done
2025-09-15 20:24:38.783 wdl.w:ptcp.w:call-paraphase-56.t:call-run_paraphase INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:38.783 wdl.w:ptcp.w:call-paraphase-56.t:call-run_paraphase INFO input :: name: "annotation_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf"
2025-09-15 20:24:38.783 wdl.w:ptcp.w:call-paraphase-56.t:call-run_paraphase INFO input :: name: "genome_version", value: "38"
2025-09-15 20:24:38.784 wdl.w:ptcp.w:call-paraphase-56.t:call-run_paraphase INFO input :: name: "config_file", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/paraphase_config.GRCh38.yaml"
2025-09-15 20:24:38.784 wdl.w:ptcp.w:call-paraphase-56.t:call-run_paraphase INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:38.784 wdl.w:ptcp.w:call-paraphase-56.t:call-run_paraphase INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:38.784 wdl.w:ptcp.w:call-paraphase-56.t:call-run_paraphase INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2153.mapped.bam.bai"
2025-09-15 20:24:38.784 wdl.w:ptcp.w:call-paraphase-56.t:call-run_paraphase INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2153.mapped.bam"
2025-09-15 20:24:38.784 wdl.w:ptcp.w:call-paraphase-56.t:call-run_paraphase INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2153"
2025-09-15 20:24:38.784 wdl.w:ptcp.w:call-paraphase-56.t:call-run_paraphase INFO eval :: name: "threads", value: 4
2025-09-15 20:24:38.785 wdl.w:ptcp.w:call-paraphase-56.t:call-run_paraphase INFO eval :: name: "mem_gb", value: 8
2025-09-15 20:24:38.785 wdl.w:ptcp.w:call-paraphase-56.t:call-run_paraphase INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:38.785 wdl.w:ptcp.w:call-paraphase-56.t:call-run_paraphase INFO eval :: name: "out_dir", value: "m84036_250809_035451_s4.bc2153_paraphase"
2025-09-15 20:24:38.786 wdl.w:ptcp.w:call-paraphase-56.t:call-run_paraphase INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 4, memory_reservation: 8000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:38.786 wdl.w:ptcp.w:call-sawfish-56.t:call-run_sawfish INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:38.786 wdl.w:ptcp.w:call-paraphase-56.t:call-run_paraphase WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:38.787 wdl.w:ptcp.w:call-sawfish-56.t:call-run_sawfish INFO input :: name: "genome_version", value: "38"
2025-09-15 20:24:38.787 wdl.w:ptcp.w:call-sawfish-01 NOTICE finish :: job: "call-run_sawfish"
2025-09-15 20:24:38.787 wdl.w:ptcp.w:call-sawfish-56.t:call-run_sawfish INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:38.787 wdl.w:ptcp.w:call-sawfish-01 INFO output :: job: "call-run_sawfish", values: {"minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-01/call-run_sawfish/out/m84036_250809_035451_s4.bc2098.minimap2.bam.bai", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-01/call-run_sawfish/out/m84036_250809_035451_s4.bc2098.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-01/call-run_sawfish/out/m84036_250809_035451_s4.bc2098_sawfish/m84036_250809_035451_s4.bc2098.sv.vcf.gz.tbi", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-01/call-run_sawfish/out/m84036_250809_035451_s4.bc2098_sawfish/m84036_250809_035451_s4.bc2098.sv.vcf.gz"}
2025-09-15 20:24:38.787 wdl.w:ptcp.w:call-sawfish-56.t:call-run_sawfish INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:38.788 wdl.w:ptcp.w:call-sawfish-01 INFO visit :: node: "output-minimap2_bam", values: {"minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-01/call-run_sawfish/out/m84036_250809_035451_s4.bc2098.minimap2.bam"}
2025-09-15 20:24:38.788 wdl.w:ptcp.w:call-sawfish-56.t:call-run_sawfish INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2153.mapped.bam.bai"
2025-09-15 20:24:38.788 wdl.w:ptcp.w:call-sawfish-01 INFO visit :: node: "output-minimap2_bam_bai", values: {"minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-01/call-run_sawfish/out/m84036_250809_035451_s4.bc2098.minimap2.bam.bai"}
2025-09-15 20:24:38.789 wdl.w:ptcp.w:call-paraphase-56.t:call-run_paraphase INFO provisioned :: seconds_waited: 0, cpu: 4, mem_bytes: 8000000000
2025-09-15 20:24:38.789 wdl.w:ptcp.w:call-sawfish-56.t:call-run_sawfish INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2153.mapped.bam"
2025-09-15 20:24:38.789 wdl.w:ptcp.w:call-sawfish-01 INFO visit :: node: "output-vcf", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-01/call-run_sawfish/out/m84036_250809_035451_s4.bc2098_sawfish/m84036_250809_035451_s4.bc2098.sv.vcf.gz"}
2025-09-15 20:24:38.789 wdl.w:ptcp.w:call-paraphase-56.t:call-run_paraphase INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:38.789 wdl.w:ptcp.w:call-sawfish-56.t:call-run_sawfish INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2153"
2025-09-15 20:24:38.789 wdl.w:ptcp.w:call-sawfish-01 INFO visit :: node: "output-vcf_tbi", values: {"vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-01/call-run_sawfish/out/m84036_250809_035451_s4.bc2098_sawfish/m84036_250809_035451_s4.bc2098.sv.vcf.gz.tbi"}
2025-09-15 20:24:38.790 wdl.w:ptcp.w:call-sawfish-01 INFO visit :: node: "outputs", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-01/call-run_sawfish/out/m84036_250809_035451_s4.bc2098_sawfish/m84036_250809_035451_s4.bc2098.sv.vcf.gz", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-01/call-run_sawfish/out/m84036_250809_035451_s4.bc2098.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-01/call-run_sawfish/out/m84036_250809_035451_s4.bc2098_sawfish/m84036_250809_035451_s4.bc2098.sv.vcf.gz.tbi", "minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-01/call-run_sawfish/out/m84036_250809_035451_s4.bc2098.minimap2.bam.bai"}
2025-09-15 20:24:38.790 wdl.w:ptcp.w:call-paraphase-53.t:call-run_paraphase.slurm_singularity INFO srun: job 51797734 queued and waiting for resources
2025-09-15 20:24:38.790 wdl.w:ptcp.w:call-sawfish-56.t:call-run_sawfish INFO eval :: name: "mem_gb", value: 32
2025-09-15 20:24:38.791 wdl.w:ptcp.w:call-paraphase-53.t:call-run_paraphase.slurm_singularity INFO srun: job 51797734 has been allocated resources
2025-09-15 20:24:38.791 wdl.w:ptcp.w:call-sawfish-56.t:call-run_sawfish INFO eval :: name: "threads", value: 16
2025-09-15 20:24:38.791 wdl.w:ptcp.w:call-paraphase-53.t:call-run_paraphase.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:38.791 wdl.w:ptcp.w:call-paraphase-53.t:call-run_paraphase.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:24:38.791 wdl.w:ptcp.w:call-sawfish-56.t:call-run_sawfish INFO eval :: name: "disk_size", value: 30
2025-09-15 20:24:38.792 wdl.w:ptcp.w:call-sawfish-56.t:call-run_sawfish INFO eval :: name: "discover_dirname", value: "m84036_250809_035451_s4.bc2153_sawfish_discover"
2025-09-15 20:24:38.792 wdl.w:ptcp.w:call-sawfish-56.t:call-run_sawfish INFO eval :: name: "call_dirname", value: "m84036_250809_035451_s4.bc2153_sawfish"
2025-09-15 20:24:38.792 wdl.w:ptcp.w:call-sawfish-56.t:call-run_sawfish INFO eval :: name: "minimap2_bam_filename", value: "m84036_250809_035451_s4.bc2153.minimap2.bam"
2025-09-15 20:24:38.792 wdl.w:ptcp.w:call-sawfish-56.t:call-run_sawfish INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 16, memory_reservation: 32000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:38.792 wdl.w:ptcp.w:call-sawfish-56.t:call-run_sawfish WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:38.793 wdl.w:ptcp.w:call-sawfish-56.t:call-run_sawfish INFO provisioned :: seconds_waited: 0, cpu: 16, mem_bytes: 32000000000
2025-09-15 20:24:38.793 wdl.w:ptcp.w:call-sawfish-56.t:call-run_sawfish INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:38.796 wdl.w:ptcp.w:call-trgt-56.t:call-get_reads_overlapping_repeats NOTICE task setup :: name: "get_reads_overlapping_repeats", source: "./trgt.wdl", line: 182, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-56/call-get_reads_overlapping_repeats", thread: 140610912642624
2025-09-15 20:24:38.822 wdl.w:ptcp.w:call-trgt-56.t:call-get_reads_overlapping_repeats INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:38.823 wdl.w:ptcp.w:call-trgt-56.t:call-get_reads_overlapping_repeats INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:38.823 wdl.w:ptcp.w:call-trgt-56.t:call-get_reads_overlapping_repeats INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2153.mapped.bam.bai"
2025-09-15 20:24:38.823 wdl.w:ptcp.w:call-trgt-56.t:call-get_reads_overlapping_repeats INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2153.mapped.bam"
2025-09-15 20:24:38.823 wdl.w:ptcp.w:call-trgt-56.t:call-get_reads_overlapping_repeats INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2153"
2025-09-15 20:24:38.823 wdl.w:ptcp.w:call-trgt-56.t:call-get_reads_overlapping_repeats INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:38.823 wdl.w:ptcp.w:call-trgt-56.t:call-get_reads_overlapping_repeats INFO eval :: name: "expand_size", value: 3000
2025-09-15 20:24:38.823 wdl.w:ptcp.w:call-trgt-56.t:call-get_reads_overlapping_repeats INFO eval :: name: "threads", value: 1
2025-09-15 20:24:38.823 wdl.w:ptcp.w:call-trgt-56.t:call-get_reads_overlapping_repeats INFO eval :: name: "expanded_bed_name", value: "m84036_250809_035451_s4.bc2153.expanded.bed"
2025-09-15 20:24:38.823 wdl.w:ptcp.w:call-trgt-56.t:call-get_reads_overlapping_repeats INFO eval :: name: "disk_size", value: 11
2025-09-15 20:24:38.824 wdl.w:ptcp.w:call-trgt-56.t:call-get_reads_overlapping_repeats INFO eval :: name: "output_name", value: "m84036_250809_035451_s4.bc2153.repeats.bam"
2025-09-15 20:24:38.824 wdl.w:ptcp.w:call-trgt-56.t:call-get_reads_overlapping_repeats INFO eval :: name: "index_name", value: "m84036_250809_035451_s4.bc2153.repeats.bam.bai"
2025-09-15 20:24:38.824 wdl.w:ptcp.w:call-trgt-56.t:call-get_reads_overlapping_repeats INFO eval :: name: "output_name_with_index", value: "m84036_250809_035451_s4.bc2153.repeats.bam##idx##m84036_250809_035451_s4.bc2153.repeats.bam.bai"
2025-09-15 20:24:38.824 wdl.w:ptcp.w:call-trgt-56.t:call-get_reads_overlapping_repeats INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:38.824 wdl.w:ptcp.w:call-trgt-56.t:call-get_reads_overlapping_repeats WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:38.825 wdl.w:ptcp.w:call-trgt-56.t:call-get_reads_overlapping_repeats INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:38.825 wdl.w:ptcp.w:call-trgt-56.t:call-get_reads_overlapping_repeats INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:38.825 wdl.w:ptcp.w:call-sawfish-08 NOTICE done
2025-09-15 20:24:38.829 wdl.w:ptcp.w:call-sawfish-35.t:call-run_sawfish INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2132_sawfish/m84036_250809_035451_s4.bc2132.sv.vcf.gz"
2025-09-15 20:24:38.838 wdl.w:ptcp.w:call-sawfish-35.t:call-run_sawfish INFO output :: name: "vcf_tbi", value: "m84036_250809_035451_s4.bc2132_sawfish/m84036_250809_035451_s4.bc2132.sv.vcf.gz.tbi"
2025-09-15 20:24:38.838 wdl.w:ptcp NOTICE finish :: job: "call-sawfish-08"
2025-09-15 20:24:38.839 wdl.w:ptcp INFO output :: job: "call-sawfish-08", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-08/out/m84036_250809_035451_s4.bc2105_sawfish/m84036_250809_035451_s4.bc2105.sv.vcf.gz", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-08/out/m84036_250809_035451_s4.bc2105.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-08/out/m84036_250809_035451_s4.bc2105_sawfish/m84036_250809_035451_s4.bc2105.sv.vcf.gz.tbi", "minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-08/out/m84036_250809_035451_s4.bc2105.minimap2.bam.bai"}
2025-09-15 20:24:38.839 wdl.w:ptcp NOTICE ready :: job: "call-tar_outputs-08", callee: "tar_outputs"
2025-09-15 20:24:38.839 wdl.w:ptcp INFO input :: job: "call-tar_outputs-08", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "sawfish_vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-08/out/m84036_250809_035451_s4.bc2105_sawfish/m84036_250809_035451_s4.bc2105.sv.vcf.gz.tbi", "sawfish_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-08/out/m84036_250809_035451_s4.bc2105_sawfish/m84036_250809_035451_s4.bc2105.sv.vcf.gz", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-08/out/m84036_250809_035451_s4.bc2105.f8inversion.json", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-08/out/m84036_250809_035451_s4.bc2105_paraphase/m84036_250809_035451_s4.bc2105.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-08/out/m84036_250809_035451_s4.bc2105_paraphase/m84036_250809_035451_s4.bc2105.paraphase.bam", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-08/out/m84036_250809_035451_s4.bc2105_paraphase/m84036_250809_035451_s4.bc2105.paraphase.json", "trgt_spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-08/out/m84036_250809_035451_s4.bc2105.trgt.sorted.spanning.bam.bai", "trgt_spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-08/out/m84036_250809_035451_s4.bc2105.trgt.sorted.spanning.bam", "trgt_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-08/out/m84036_250809_035451_s4.bc2105.trgt.vcf", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-08/out/m84036_250809_035451_s4.bc2105.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-08/out/m84036_250809_035451_s4.bc2105.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2105"}
2025-09-15 20:24:38.840 wdl.w:ptcp.w:call-sawfish-35.t:call-run_sawfish INFO output :: name: "minimap2_bam", value: "m84036_250809_035451_s4.bc2132.minimap2.bam"
2025-09-15 20:24:38.843 wdl.w:ptcp.w:call-sawfish-35.t:call-run_sawfish INFO output :: name: "minimap2_bam_bai", value: "m84036_250809_035451_s4.bc2132.minimap2.bam.bai"
2025-09-15 20:24:38.849 wdl.w:ptcp.w:call-trgt-69 NOTICE workflow start :: name: "trgt", source: "./trgt.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-69"
2025-09-15 20:24:38.861 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_genotype NOTICE done
2025-09-15 20:24:38.869 wdl.w:ptcp.w:call-trgt-54 NOTICE finish :: job: "call-trgt_genotype"
2025-09-15 20:24:38.870 wdl.w:ptcp.w:call-trgt-54 INFO output :: job: "call-trgt_genotype", values: {"spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-54/call-trgt_genotype/out/m84036_250809_035451_s4.bc2151.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-54/call-trgt_genotype/out/m84036_250809_035451_s4.bc2151.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-54/call-trgt_genotype/out/m84036_250809_035451_s4.bc2151.trgt.vcf"}
2025-09-15 20:24:38.870 wdl.w:ptcp.w:call-sawfish-01 NOTICE done
2025-09-15 20:24:38.871 wdl.w:ptcp.w:call-trgt-54 NOTICE ready :: job: "call-trgt_plot_meth_allele", callee: "trgt_plot"
2025-09-15 20:24:38.872 wdl.w:ptcp.w:call-trgt-54 INFO input :: job: "call-trgt_plot_meth_allele", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": false, "methylation": true, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-54/call-trgt_genotype/out/m84036_250809_035451_s4.bc2151.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-54/call-trgt_genotype/out/m84036_250809_035451_s4.bc2151.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-54/call-trgt_genotype/out/m84036_250809_035451_s4.bc2151.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2151"}
2025-09-15 20:24:38.874 wdl.w:ptcp.w:call-trgt-54 NOTICE ready :: job: "call-trgt_plot_meth_waterfall", callee: "trgt_plot"
2025-09-15 20:24:38.873 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_genotype NOTICE done
2025-09-15 20:24:38.874 wdl.w:ptcp.w:call-trgt-54 INFO input :: job: "call-trgt_plot_meth_waterfall", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": true, "methylation": true, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-54/call-trgt_genotype/out/m84036_250809_035451_s4.bc2151.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-54/call-trgt_genotype/out/m84036_250809_035451_s4.bc2151.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-54/call-trgt_genotype/out/m84036_250809_035451_s4.bc2151.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2151"}
2025-09-15 20:24:38.876 wdl.w:ptcp.w:call-trgt-54 NOTICE ready :: job: "call-trgt_plot_motifs_allele", callee: "trgt_plot"
2025-09-15 20:24:38.876 wdl.w:ptcp.w:call-trgt-54 INFO input :: job: "call-trgt_plot_motifs_allele", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": false, "methylation": false, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-54/call-trgt_genotype/out/m84036_250809_035451_s4.bc2151.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-54/call-trgt_genotype/out/m84036_250809_035451_s4.bc2151.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-54/call-trgt_genotype/out/m84036_250809_035451_s4.bc2151.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2151"}
2025-09-15 20:24:38.878 wdl.w:ptcp.w:call-trgt-54 NOTICE ready :: job: "call-trgt_plot_motifs_waterfall", callee: "trgt_plot"
2025-09-15 20:24:38.878 wdl.w:ptcp.w:call-trgt-54 INFO input :: job: "call-trgt_plot_motifs_waterfall", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": true, "methylation": false, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-54/call-trgt_genotype/out/m84036_250809_035451_s4.bc2151.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-54/call-trgt_genotype/out/m84036_250809_035451_s4.bc2151.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-54/call-trgt_genotype/out/m84036_250809_035451_s4.bc2151.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2151"}
2025-09-15 20:24:38.878 wdl.w:ptcp.w:call-trgt-54 INFO visit :: node: "output-spanning_bam", values: {"spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-54/call-trgt_genotype/out/m84036_250809_035451_s4.bc2151.trgt.sorted.spanning.bam"}
2025-09-15 20:24:38.879 wdl.w:ptcp.w:call-trgt-54 INFO visit :: node: "output-spanning_bam_bai", values: {"spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-54/call-trgt_genotype/out/m84036_250809_035451_s4.bc2151.trgt.sorted.spanning.bam.bai"}
2025-09-15 20:24:38.879 wdl.w:ptcp.w:call-trgt-54 INFO visit :: node: "output-vcf", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-54/call-trgt_genotype/out/m84036_250809_035451_s4.bc2151.trgt.vcf"}
2025-09-15 20:24:38.879 wdl.w:ptcp NOTICE finish :: job: "call-sawfish-01"
2025-09-15 20:24:38.879 wdl.w:ptcp.w:call-trgt-56.t:call-trgt_genotype NOTICE task setup :: name: "trgt_genotype", source: "./trgt.wdl", line: 272, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-56/call-trgt_genotype", thread: 140607146153536
2025-09-15 20:24:38.880 wdl.w:ptcp INFO output :: job: "call-sawfish-01", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-01/out/m84036_250809_035451_s4.bc2098_sawfish/m84036_250809_035451_s4.bc2098.sv.vcf.gz", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-01/out/m84036_250809_035451_s4.bc2098.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-01/out/m84036_250809_035451_s4.bc2098_sawfish/m84036_250809_035451_s4.bc2098.sv.vcf.gz.tbi", "minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-01/out/m84036_250809_035451_s4.bc2098.minimap2.bam.bai"}
2025-09-15 20:24:38.881 wdl.w:ptcp.w:call-trgt-69 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:24:38.882 wdl.w:ptcp.w:call-trgt-59 NOTICE finish :: job: "call-trgt_genotype"
2025-09-15 20:24:38.882 wdl.w:ptcp.w:call-trgt-69 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-69/out/m84036_250809_035451_s4.bc2166.mapped.bam"}
2025-09-15 20:24:38.882 wdl.w:ptcp.w:call-trgt-59 INFO output :: job: "call-trgt_genotype", values: {"spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-59/call-trgt_genotype/out/m84036_250809_035451_s4.bc2156.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-59/call-trgt_genotype/out/m84036_250809_035451_s4.bc2156.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-59/call-trgt_genotype/out/m84036_250809_035451_s4.bc2156.trgt.vcf"}
2025-09-15 20:24:38.882 wdl.w:ptcp.w:call-trgt-69 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-69/out/m84036_250809_035451_s4.bc2166.mapped.bam.bai"}
2025-09-15 20:24:38.883 wdl.w:ptcp.w:call-trgt-59 NOTICE ready :: job: "call-trgt_plot_meth_allele", callee: "trgt_plot"
2025-09-15 20:24:38.883 wdl.w:ptcp.w:call-trgt-69 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:24:38.883 wdl.w:ptcp.w:call-trgt-59 INFO input :: job: "call-trgt_plot_meth_allele", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": false, "methylation": true, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-59/call-trgt_genotype/out/m84036_250809_035451_s4.bc2156.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-59/call-trgt_genotype/out/m84036_250809_035451_s4.bc2156.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-59/call-trgt_genotype/out/m84036_250809_035451_s4.bc2156.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2156"}
2025-09-15 20:24:38.883 wdl.w:ptcp.w:call-trgt-69 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:24:38.883 wdl.w:ptcp.w:call-trgt-69 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2166"}
2025-09-15 20:24:38.883 wdl.w:ptcp.w:call-trgt-69 INFO visit :: node: "decl-sex", values: {"sex": "F"}
2025-09-15 20:24:38.883 wdl.w:ptcp.w:call-trgt-69 INFO visit :: node: "decl-trgt_bed", values: {"trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"}
2025-09-15 20:24:38.883 wdl.w:ptcp.w:call-trgt-69 NOTICE ready :: job: "call-get_reads_overlapping_repeats", callee: "get_reads_overlapping_repeats"
2025-09-15 20:24:38.884 wdl.w:ptcp.w:call-trgt-69 INFO input :: job: "call-get_reads_overlapping_repeats", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-69/out/m84036_250809_035451_s4.bc2166.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-69/out/m84036_250809_035451_s4.bc2166.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2166"}
2025-09-15 20:24:38.885 wdl.w:ptcp.w:call-trgt-69 NOTICE ready :: job: "call-trgt_genotype", callee: "trgt_genotype"
2025-09-15 20:24:38.885 wdl.w:ptcp.w:call-trgt-59 NOTICE ready :: job: "call-trgt_plot_meth_waterfall", callee: "trgt_plot"
2025-09-15 20:24:38.885 wdl.w:ptcp.w:call-trgt-69 INFO input :: job: "call-trgt_genotype", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-69/out/m84036_250809_035451_s4.bc2166.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-69/out/m84036_250809_035451_s4.bc2166.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2166"}
2025-09-15 20:24:38.885 wdl.w:ptcp.w:call-trgt-59 INFO input :: job: "call-trgt_plot_meth_waterfall", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": true, "methylation": true, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-59/call-trgt_genotype/out/m84036_250809_035451_s4.bc2156.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-59/call-trgt_genotype/out/m84036_250809_035451_s4.bc2156.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-59/call-trgt_genotype/out/m84036_250809_035451_s4.bc2156.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2156"}
2025-09-15 20:24:38.887 wdl.w:ptcp.w:call-trgt-59 NOTICE ready :: job: "call-trgt_plot_motifs_allele", callee: "trgt_plot"
2025-09-15 20:24:38.887 wdl.w:ptcp.w:call-trgt-59 INFO input :: job: "call-trgt_plot_motifs_allele", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": false, "methylation": false, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-59/call-trgt_genotype/out/m84036_250809_035451_s4.bc2156.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-59/call-trgt_genotype/out/m84036_250809_035451_s4.bc2156.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-59/call-trgt_genotype/out/m84036_250809_035451_s4.bc2156.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2156"}
2025-09-15 20:24:38.889 wdl.w:ptcp.w:call-trgt-59 NOTICE ready :: job: "call-trgt_plot_motifs_waterfall", callee: "trgt_plot"
2025-09-15 20:24:38.889 wdl.w:ptcp.w:call-trgt-59 INFO input :: job: "call-trgt_plot_motifs_waterfall", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": true, "methylation": false, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-59/call-trgt_genotype/out/m84036_250809_035451_s4.bc2156.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-59/call-trgt_genotype/out/m84036_250809_035451_s4.bc2156.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-59/call-trgt_genotype/out/m84036_250809_035451_s4.bc2156.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2156"}
2025-09-15 20:24:38.890 wdl.w:ptcp.w:call-trgt-59 INFO visit :: node: "output-spanning_bam", values: {"spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-59/call-trgt_genotype/out/m84036_250809_035451_s4.bc2156.trgt.sorted.spanning.bam"}
2025-09-15 20:24:38.890 wdl.w:ptcp.w:call-trgt-59 INFO visit :: node: "output-spanning_bam_bai", values: {"spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-59/call-trgt_genotype/out/m84036_250809_035451_s4.bc2156.trgt.sorted.spanning.bam.bai"}
2025-09-15 20:24:38.890 wdl.w:ptcp.w:call-trgt-59 INFO visit :: node: "output-vcf", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-59/call-trgt_genotype/out/m84036_250809_035451_s4.bc2156.trgt.vcf"}
2025-09-15 20:24:38.893 wdl.w:ptcp.w:call-paraphase-60 NOTICE workflow start :: name: "paraphase", source: "./paraphase.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-60"
2025-09-15 20:24:38.894 wdl.w:ptcp.w:call-paraphase-43.t:call-run_paraphase NOTICE task setup :: name: "run_paraphase", source: "./paraphase.wdl", line: 127, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-43/call-run_paraphase", thread: 140612531648064
2025-09-15 20:24:38.897 wdl.w:ptcp.w:call-trgt-49.t:call-trgt_genotype INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2146.trgt.vcf"
2025-09-15 20:24:38.899 wdl.w:ptcp.w:call-trgt-01.t:call-trgt_plot_meth_waterfall INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2098.meth_waterfall.trgt_plots.zip"
2025-09-15 20:24:38.903 wdl.w:ptcp.w:call-trgt-49.t:call-trgt_genotype INFO output :: name: "spanning_bam", value: "m84036_250809_035451_s4.bc2146.trgt.sorted.spanning.bam"
2025-09-15 20:24:38.906 wdl.w:ptcp.w:call-trgt-49.t:call-trgt_genotype INFO output :: name: "spanning_bam_bai", value: "m84036_250809_035451_s4.bc2146.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:38.911 wdl.w:ptcp.w:call-trgt-56.t:call-trgt_genotype INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:38.911 wdl.w:ptcp.w:call-trgt-56.t:call-trgt_genotype INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:38.912 wdl.w:ptcp.w:call-trgt-56.t:call-trgt_genotype INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:38.912 wdl.w:ptcp.w:call-trgt-56.t:call-trgt_genotype INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:38.912 wdl.w:ptcp.w:call-trgt-56.t:call-trgt_genotype INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2153.mapped.bam.bai"
2025-09-15 20:24:38.912 wdl.w:ptcp.w:call-trgt-56.t:call-trgt_genotype INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2153.mapped.bam"
2025-09-15 20:24:38.912 wdl.w:ptcp.w:call-trgt-56.t:call-trgt_genotype INFO input :: name: "sex", value: "F"
2025-09-15 20:24:38.912 wdl.w:ptcp.w:call-trgt-56.t:call-trgt_genotype INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2153"
2025-09-15 20:24:38.912 wdl.w:ptcp.w:call-trgt-56.t:call-trgt_genotype INFO eval :: name: "mem_gb", value: 16
2025-09-15 20:24:38.913 wdl.w:ptcp.w:call-trgt-56.t:call-trgt_genotype INFO eval :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2153.trgt"
2025-09-15 20:24:38.913 wdl.w:ptcp.w:call-trgt-56.t:call-trgt_genotype INFO eval :: name: "threads", value: 8
2025-09-15 20:24:38.913 wdl.w:ptcp.w:call-trgt-56.t:call-trgt_genotype INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:38.914 wdl.w:ptcp.w:call-trgt-56.t:call-trgt_genotype INFO eval :: name: "karyotype", value: "XX"
2025-09-15 20:24:38.915 wdl.w:ptcp.w:call-trgt-56.t:call-trgt_genotype INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 8, memory_reservation: 16000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:38.916 wdl.w:ptcp.w:call-trgt-56.t:call-trgt_genotype WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:38.917 wdl.w:ptcp.w:call-trgt-56.t:call-trgt_genotype INFO provisioned :: seconds_waited: 0, cpu: 8, mem_bytes: 16000000000
2025-09-15 20:24:38.917 wdl.w:ptcp.w:call-trgt-56.t:call-trgt_genotype INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:38.918 wdl.w:ptcp.w:call-sawfish-56.t:call-run_sawfish INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 10, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-56/call-run_sawfish/_singularity_tmpdir_ev_cm5ro"
2025-09-15 20:24:38.918 wdl.w:ptcp.w:call-sawfish-56.t:call-run_sawfish INFO Slurm invocation: srun --job-name call-run_sawfish --partition compute,compute9 --cpus-per-task 16 --mem 30518M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-56/call-run_sawfish/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-56/call-run_sawfish/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-56/call-run_sawfish/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-56/call-run_sawfish/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-56/out/m84036_250809_035451_s4.bc2153.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2153.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-56/out/m84036_250809_035451_s4.bc2153.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2153.mapped.bam.bai:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-56/call-run_sawfish/_singularity_tmpdir_ev_cm5ro/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-56/call-run_sawfish/_singularity_tmpdir_ev_cm5ro/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:38.926 wdl.w:ptcp.w:call-paraphase-43.t:call-run_paraphase INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:38.926 wdl.w:ptcp.w:call-paraphase-43.t:call-run_paraphase INFO input :: name: "annotation_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf"
2025-09-15 20:24:38.927 wdl.w:ptcp.w:call-paraphase-43.t:call-run_paraphase INFO input :: name: "genome_version", value: "38"
2025-09-15 20:24:38.927 wdl.w:ptcp.w:call-paraphase-43.t:call-run_paraphase INFO input :: name: "config_file", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/paraphase_config.GRCh38.yaml"
2025-09-15 20:24:38.927 wdl.w:ptcp.w:call-paraphase-43.t:call-run_paraphase INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:38.927 wdl.w:ptcp.w:call-paraphase-43.t:call-run_paraphase INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:38.927 wdl.w:ptcp.w:call-paraphase-43.t:call-run_paraphase INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2140.mapped.bam.bai"
2025-09-15 20:24:38.928 wdl.w:ptcp.w:call-paraphase-43.t:call-run_paraphase INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2140.mapped.bam"
2025-09-15 20:24:38.928 wdl.w:ptcp.w:call-paraphase-43.t:call-run_paraphase INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2140"
2025-09-15 20:24:38.928 wdl.w:ptcp.w:call-paraphase-43.t:call-run_paraphase INFO eval :: name: "threads", value: 4
2025-09-15 20:24:38.929 wdl.w:ptcp.w:call-paraphase-43.t:call-run_paraphase INFO eval :: name: "mem_gb", value: 8
2025-09-15 20:24:38.929 wdl.w:ptcp.w:call-paraphase-43.t:call-run_paraphase INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:38.929 wdl.w:ptcp.w:call-paraphase-43.t:call-run_paraphase INFO eval :: name: "out_dir", value: "m84036_250809_035451_s4.bc2140_paraphase"
2025-09-15 20:24:38.930 wdl.w:ptcp.w:call-paraphase-43.t:call-run_paraphase INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 4, memory_reservation: 8000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:38.930 wdl.w:ptcp.w:call-paraphase-43.t:call-run_paraphase WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:38.930 wdl.w:ptcp.w:call-paraphase-43.t:call-run_paraphase INFO provisioned :: seconds_waited: 0, cpu: 4, mem_bytes: 8000000000
2025-09-15 20:24:38.931 wdl.w:ptcp.w:call-paraphase-43.t:call-run_paraphase INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:38.933 wdl.w:ptcp.w:call-paraphase-60 INFO visit :: node: "decl-annotation_vcf", values: {"annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf"}
2025-09-15 20:24:38.933 wdl.w:ptcp.w:call-paraphase-60 INFO visit :: node: "decl-config_file", values: {"config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml"}
2025-09-15 20:24:38.933 wdl.w:ptcp.w:call-paraphase-60 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:24:38.933 wdl.w:ptcp.w:call-paraphase-60 INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:24:38.934 wdl.w:ptcp.w:call-paraphase-60 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-60/out/m84036_250809_035451_s4.bc2157.mapped.bam"}
2025-09-15 20:24:38.934 wdl.w:ptcp.w:call-paraphase-60 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-60/out/m84036_250809_035451_s4.bc2157.mapped.bam.bai"}
2025-09-15 20:24:38.934 wdl.w:ptcp.w:call-paraphase-60 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:24:38.934 wdl.w:ptcp.w:call-paraphase-60 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:24:38.934 wdl.w:ptcp.w:call-paraphase-60 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2157"}
2025-09-15 20:24:38.934 wdl.w:ptcp.w:call-paraphase-60 INFO visit :: node: "decl-sex", values: {"sex": "F"}
2025-09-15 20:24:38.935 wdl.w:ptcp.w:call-paraphase-60 NOTICE ready :: job: "call-run_paraphase", callee: "run_paraphase"
2025-09-15 20:24:38.935 wdl.w:ptcp.w:call-paraphase-60 INFO input :: job: "call-run_paraphase", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf", "genome_version": "38", "config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-60/out/m84036_250809_035451_s4.bc2157.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-60/out/m84036_250809_035451_s4.bc2157.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2157"}
2025-09-15 20:24:38.936 wdl.w:ptcp.w:call-paraphase-56.t:call-run_paraphase INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-56/call-run_paraphase/_singularity_tmpdir_8d_8d3ls"
2025-09-15 20:24:38.936 wdl.w:ptcp.w:call-paraphase-56.t:call-run_paraphase INFO Slurm invocation: srun --job-name call-run_paraphase --partition compute,compute9 --cpus-per-task 4 --mem 7629M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-56/call-run_paraphase/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-56/call-run_paraphase/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-56/call-run_paraphase/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-56/call-run_paraphase/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/variant_list/variant_list.GRCh38.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-56/out/m84036_250809_035451_s4.bc2153.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2153.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-56/out/m84036_250809_035451_s4.bc2153.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2153.mapped.bam.bai:ro --bind /ptcp/meta/paraphase/paraphase_config.GRCh38.yaml:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/paraphase_config.GRCh38.yaml:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-56/call-run_paraphase/_singularity_tmpdir_8d_8d3ls/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-56/call-run_paraphase/_singularity_tmpdir_8d_8d3ls/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:38.940 wdl.w:ptcp.w:call-trgt-56.t:call-get_reads_overlapping_repeats INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 9, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-56/call-get_reads_overlapping_repeats/_singularity_tmpdir_cz5oftuo"
2025-09-15 20:24:38.940 wdl.w:ptcp.w:call-trgt-56.t:call-get_reads_overlapping_repeats INFO Slurm invocation: srun --job-name call-get_reads_overlapping_repeats --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-56/call-get_reads_overlapping_repeats/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-56/call-get_reads_overlapping_repeats/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-56/call-get_reads_overlapping_repeats/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-56/call-get_reads_overlapping_repeats/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-56/out/m84036_250809_035451_s4.bc2153.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2153.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-56/out/m84036_250809_035451_s4.bc2153.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2153.mapped.bam.bai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-56/call-get_reads_overlapping_repeats/_singularity_tmpdir_cz5oftuo/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-56/call-get_reads_overlapping_repeats/_singularity_tmpdir_cz5oftuo/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:38.987 wdl.w:ptcp.w:call-sawfish-56.t:call-run_sawfish NOTICE slurm_singularity run :: pid: 1202613, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-56/call-run_sawfish/slurm_singularity.log.txt"
2025-09-15 20:24:38.987 wdl.w:ptcp.w:call-paraphase-56.t:call-run_paraphase NOTICE slurm_singularity run :: pid: 1202615, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-56/call-run_paraphase/slurm_singularity.log.txt"
2025-09-15 20:24:38.987 wdl.w:ptcp.w:call-trgt-56.t:call-get_reads_overlapping_repeats NOTICE slurm_singularity run :: pid: 1202616, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-56/call-get_reads_overlapping_repeats/slurm_singularity.log.txt"
2025-09-15 20:24:38.995 wdl.w:ptcp.w:call-trgt-59.t:call-get_reads_overlapping_repeats INFO output :: name: "reads_overlapping_repeats", value: "m84036_250809_035451_s4.bc2156.repeats.bam"
2025-09-15 20:24:38.999 wdl.w:ptcp.w:call-trgt-59.t:call-get_reads_overlapping_repeats INFO output :: name: "reads_overlapping_repeats_bai", value: "m84036_250809_035451_s4.bc2156.repeats.bam.bai"
2025-09-15 20:24:39.016 wdl.w:ptcp.w:call-paraphase-51.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for smn1 for sample m84036_250809_035451_s4.bc2148 at 2025-09-15 20:24:33.369300...
2025-09-15 20:24:39.016 wdl.w:ptcp.w:call-paraphase-51.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning to gene2 region for smn1 for sample m84036_250809_035451_s4.bc2148 at 2025-09-15 20:24:34.014252...
2025-09-15 20:24:39.019 wdl.w:ptcp.w:call-trgt-00.t:call-trgt_plot_motifs_waterfall NOTICE done
2025-09-15 20:24:39.024 wdl.w:ptcp.w:call-trgt-49.t:call-trgt_genotype NOTICE done
2025-09-15 20:24:39.024 wdl.w:ptcp.w:call-trgt-56.t:call-trgt_genotype INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 11, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-56/call-trgt_genotype/_singularity_tmpdir_oxxvj3_1"
2025-09-15 20:24:39.024 wdl.w:ptcp.w:call-trgt-56.t:call-trgt_genotype INFO Slurm invocation: srun --job-name call-trgt_genotype --partition compute,compute9 --cpus-per-task 8 --mem 15259M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-56/call-trgt_genotype/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-56/call-trgt_genotype/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-56/call-trgt_genotype/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-56/call-trgt_genotype/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-56/out/m84036_250809_035451_s4.bc2153.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2153.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-56/out/m84036_250809_035451_s4.bc2153.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2153.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-56/call-trgt_genotype/_singularity_tmpdir_oxxvj3_1/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-56/call-trgt_genotype/_singularity_tmpdir_oxxvj3_1/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:39.037 wdl.w:ptcp.w:call-trgt-00 NOTICE finish :: job: "call-trgt_plot_motifs_waterfall"
2025-09-15 20:24:39.037 wdl.w:ptcp.w:call-trgt-00 INFO output :: job: "call-trgt_plot_motifs_waterfall", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-00/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2097.motifs_waterfall.trgt_plots.zip"}
2025-09-15 20:24:39.037 wdl.w:ptcp.w:call-trgt-00 INFO visit :: node: "output-images_motifs_waterfall", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-00/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2097.motifs_waterfall.trgt_plots.zip"}
2025-09-15 20:24:39.037 wdl.w:ptcp.w:call-trgt-00 INFO visit :: node: "outputs", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-00/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2097.motifs_waterfall.trgt_plots.zip", "images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-00/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2097.meth_allele.trgt_plots.zip", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-00/call-trgt_genotype/out/m84036_250809_035451_s4.bc2097.trgt.sorted.spanning.bam.bai", "images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-00/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2097.motifs_allele.trgt_plots.zip", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-00/call-trgt_genotype/out/m84036_250809_035451_s4.bc2097.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-00/call-trgt_genotype/out/m84036_250809_035451_s4.bc2097.trgt.vcf", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-00/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2097.repeats.bam", "images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-00/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2097.meth_waterfall.trgt_plots.zip", "reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-00/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2097.repeats.bam.bai"}
2025-09-15 20:24:39.044 wdl.w:ptcp.w:call-trgt-49 NOTICE finish :: job: "call-trgt_genotype"
2025-09-15 20:24:39.044 wdl.w:ptcp.w:call-trgt-49 INFO output :: job: "call-trgt_genotype", values: {"spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-49/call-trgt_genotype/out/m84036_250809_035451_s4.bc2146.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-49/call-trgt_genotype/out/m84036_250809_035451_s4.bc2146.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-49/call-trgt_genotype/out/m84036_250809_035451_s4.bc2146.trgt.vcf"}
2025-09-15 20:24:39.045 wdl.w:ptcp.w:call-trgt-49 NOTICE ready :: job: "call-trgt_plot_meth_allele", callee: "trgt_plot"
2025-09-15 20:24:39.045 wdl.w:ptcp.w:call-trgt-49 INFO input :: job: "call-trgt_plot_meth_allele", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": false, "methylation": true, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-49/call-trgt_genotype/out/m84036_250809_035451_s4.bc2146.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-49/call-trgt_genotype/out/m84036_250809_035451_s4.bc2146.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-49/call-trgt_genotype/out/m84036_250809_035451_s4.bc2146.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2146"}
2025-09-15 20:24:39.047 wdl.w:ptcp.w:call-paraphase-50.t:call-run_paraphase.stderr VERBOSE INFO:root:Processing sample m84036_250809_035451_s4.bc2147 at 2025-09-15 20:24:34.660980...
2025-09-15 20:24:39.050 wdl.w:ptcp.w:call-paraphase-50.t:call-run_paraphase.stderr VERBOSE INFO:root:Checking sample sex at 2025-09-15 20:24:34.662769...
2025-09-15 20:24:39.050 wdl.w:ptcp.w:call-paraphase-50.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for cyp21 for sample m84036_250809_035451_s4.bc2147 at 2025-09-15 20:24:34.703967...
2025-09-15 20:24:39.051 wdl.w:ptcp.w:call-trgt-49 NOTICE ready :: job: "call-trgt_plot_meth_waterfall", callee: "trgt_plot"
2025-09-15 20:24:39.051 wdl.w:ptcp.w:call-paraphase-50.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for cyp21 for sample m84036_250809_035451_s4.bc2147 at 2025-09-15 20:24:34.704358...
2025-09-15 20:24:39.051 wdl.w:ptcp.w:call-trgt-49 INFO input :: job: "call-trgt_plot_meth_waterfall", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": true, "methylation": true, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-49/call-trgt_genotype/out/m84036_250809_035451_s4.bc2146.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-49/call-trgt_genotype/out/m84036_250809_035451_s4.bc2146.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-49/call-trgt_genotype/out/m84036_250809_035451_s4.bc2146.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2146"}
2025-09-15 20:24:39.051 wdl.w:ptcp.w:call-paraphase-50.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for smn1 for sample m84036_250809_035451_s4.bc2147 at 2025-09-15 20:24:34.704118...
2025-09-15 20:24:39.052 wdl.w:ptcp.w:call-paraphase-50.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for smn1 for sample m84036_250809_035451_s4.bc2147 at 2025-09-15 20:24:34.704490...
2025-09-15 20:24:39.052 wdl.w:ptcp.w:call-paraphase-50.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for hba for sample m84036_250809_035451_s4.bc2147 at 2025-09-15 20:24:34.704233...
2025-09-15 20:24:39.052 wdl.w:ptcp.w:call-paraphase-50.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for gba for sample m84036_250809_035451_s4.bc2147 at 2025-09-15 20:24:34.704228...
2025-09-15 20:24:39.052 wdl.w:ptcp.w:call-paraphase-50.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for hba for sample m84036_250809_035451_s4.bc2147 at 2025-09-15 20:24:34.704588...
2025-09-15 20:24:39.052 wdl.w:ptcp.w:call-paraphase-50.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for gba for sample m84036_250809_035451_s4.bc2147 at 2025-09-15 20:24:34.704600...
2025-09-15 20:24:39.053 wdl.w:ptcp.w:call-trgt-49 NOTICE ready :: job: "call-trgt_plot_motifs_allele", callee: "trgt_plot"
2025-09-15 20:24:39.053 wdl.w:ptcp.w:call-trgt-49 INFO input :: job: "call-trgt_plot_motifs_allele", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": false, "methylation": false, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-49/call-trgt_genotype/out/m84036_250809_035451_s4.bc2146.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-49/call-trgt_genotype/out/m84036_250809_035451_s4.bc2146.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-49/call-trgt_genotype/out/m84036_250809_035451_s4.bc2146.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2146"}
2025-09-15 20:24:39.053 wdl.w:ptcp.w:call-sawfish-43.t:call-run_sawfish NOTICE task setup :: name: "run_sawfish", source: "./sawfish.wdl", line: 83, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-43/call-run_sawfish", thread: 140607120975424
2025-09-15 20:24:39.055 wdl.w:ptcp.w:call-trgt-49 NOTICE ready :: job: "call-trgt_plot_motifs_waterfall", callee: "trgt_plot"
2025-09-15 20:24:39.055 wdl.w:ptcp.w:call-trgt-49 INFO input :: job: "call-trgt_plot_motifs_waterfall", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": true, "methylation": false, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-49/call-trgt_genotype/out/m84036_250809_035451_s4.bc2146.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-49/call-trgt_genotype/out/m84036_250809_035451_s4.bc2146.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-49/call-trgt_genotype/out/m84036_250809_035451_s4.bc2146.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2146"}
2025-09-15 20:24:39.056 wdl.w:ptcp.w:call-trgt-49 INFO visit :: node: "output-spanning_bam", values: {"spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-49/call-trgt_genotype/out/m84036_250809_035451_s4.bc2146.trgt.sorted.spanning.bam"}
2025-09-15 20:24:39.056 wdl.w:ptcp.w:call-trgt-49 INFO visit :: node: "output-spanning_bam_bai", values: {"spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-49/call-trgt_genotype/out/m84036_250809_035451_s4.bc2146.trgt.sorted.spanning.bam.bai"}
2025-09-15 20:24:39.056 wdl.w:ptcp.w:call-trgt-49 INFO visit :: node: "output-vcf", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-49/call-trgt_genotype/out/m84036_250809_035451_s4.bc2146.trgt.vcf"}
2025-09-15 20:24:39.060 wdl.w:ptcp.w:call-trgt-43.t:call-get_reads_overlapping_repeats NOTICE task setup :: name: "get_reads_overlapping_repeats", source: "./trgt.wdl", line: 182, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-43/call-get_reads_overlapping_repeats", thread: 140608203109952
2025-09-15 20:24:39.070 wdl.w:ptcp.w:call-trgt-56.t:call-trgt_genotype NOTICE slurm_singularity run :: pid: 1202620, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-56/call-trgt_genotype/slurm_singularity.log.txt"
2025-09-15 20:24:39.081 wdl.w:ptcp.w:call-sawfish-43.t:call-run_sawfish INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:39.081 wdl.w:ptcp.w:call-sawfish-43.t:call-run_sawfish INFO input :: name: "genome_version", value: "38"
2025-09-15 20:24:39.082 wdl.w:ptcp.w:call-sawfish-43.t:call-run_sawfish INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:39.082 wdl.w:ptcp.w:call-sawfish-43.t:call-run_sawfish INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:39.082 wdl.w:ptcp.w:call-sawfish-43.t:call-run_sawfish INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2140.mapped.bam.bai"
2025-09-15 20:24:39.082 wdl.w:ptcp.w:call-sawfish-43.t:call-run_sawfish INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2140.mapped.bam"
2025-09-15 20:24:39.082 wdl.w:ptcp.w:call-sawfish-43.t:call-run_sawfish INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2140"
2025-09-15 20:24:39.082 wdl.w:ptcp.w:call-sawfish-43.t:call-run_sawfish INFO eval :: name: "mem_gb", value: 32
2025-09-15 20:24:39.083 wdl.w:ptcp.w:call-sawfish-43.t:call-run_sawfish INFO eval :: name: "threads", value: 16
2025-09-15 20:24:39.084 wdl.w:ptcp.w:call-sawfish-43.t:call-run_sawfish INFO eval :: name: "disk_size", value: 30
2025-09-15 20:24:39.084 wdl.w:ptcp.w:call-sawfish-43.t:call-run_sawfish INFO eval :: name: "discover_dirname", value: "m84036_250809_035451_s4.bc2140_sawfish_discover"
2025-09-15 20:24:39.085 wdl.w:ptcp.w:call-sawfish-43.t:call-run_sawfish INFO eval :: name: "call_dirname", value: "m84036_250809_035451_s4.bc2140_sawfish"
2025-09-15 20:24:39.086 wdl.w:ptcp.w:call-sawfish-43.t:call-run_sawfish INFO eval :: name: "minimap2_bam_filename", value: "m84036_250809_035451_s4.bc2140.minimap2.bam"
2025-09-15 20:24:39.086 wdl.w:ptcp.w:call-sawfish-43.t:call-run_sawfish INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 16, memory_reservation: 32000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:39.086 wdl.w:ptcp.w:call-sawfish-43.t:call-run_sawfish WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:39.088 wdl.w:ptcp.w:call-sawfish-43.t:call-run_sawfish INFO provisioned :: seconds_waited: 0, cpu: 16, mem_bytes: 32000000000
2025-09-15 20:24:39.088 wdl.w:ptcp.w:call-sawfish-43.t:call-run_sawfish INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:39.088 wdl.w:ptcp.w:call-paraphase-43.t:call-run_paraphase INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-43/call-run_paraphase/_singularity_tmpdir_8j67brhc"
2025-09-15 20:24:39.089 wdl.w:ptcp.w:call-paraphase-43.t:call-run_paraphase INFO Slurm invocation: srun --job-name call-run_paraphase --partition compute,compute9 --cpus-per-task 4 --mem 7629M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-43/call-run_paraphase/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-43/call-run_paraphase/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-43/call-run_paraphase/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-43/call-run_paraphase/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-43/out/m84036_250809_035451_s4.bc2140.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2140.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-43/out/m84036_250809_035451_s4.bc2140.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2140.mapped.bam.bai:ro --bind /ptcp/meta/variant_list/variant_list.GRCh38.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf:ro --bind /ptcp/meta/paraphase/paraphase_config.GRCh38.yaml:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/paraphase_config.GRCh38.yaml:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-43/call-run_paraphase/_singularity_tmpdir_8j67brhc/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-43/call-run_paraphase/_singularity_tmpdir_8j67brhc/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:39.094 wdl.w:ptcp.w:call-trgt-43.t:call-get_reads_overlapping_repeats INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:39.094 wdl.w:ptcp.w:call-trgt-43.t:call-get_reads_overlapping_repeats INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:39.094 wdl.w:ptcp.w:call-trgt-43.t:call-get_reads_overlapping_repeats INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2140.mapped.bam.bai"
2025-09-15 20:24:39.094 wdl.w:ptcp.w:call-trgt-43.t:call-get_reads_overlapping_repeats INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2140.mapped.bam"
2025-09-15 20:24:39.094 wdl.w:ptcp.w:call-trgt-43.t:call-get_reads_overlapping_repeats INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2140"
2025-09-15 20:24:39.094 wdl.w:ptcp.w:call-trgt-43.t:call-get_reads_overlapping_repeats INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:39.094 wdl.w:ptcp.w:call-trgt-43.t:call-get_reads_overlapping_repeats INFO eval :: name: "expand_size", value: 3000
2025-09-15 20:24:39.095 wdl.w:ptcp.w:call-trgt-43.t:call-get_reads_overlapping_repeats INFO eval :: name: "threads", value: 1
2025-09-15 20:24:39.095 wdl.w:ptcp.w:call-trgt-43.t:call-get_reads_overlapping_repeats INFO eval :: name: "expanded_bed_name", value: "m84036_250809_035451_s4.bc2140.expanded.bed"
2025-09-15 20:24:39.095 wdl.w:ptcp.w:call-trgt-43.t:call-get_reads_overlapping_repeats INFO eval :: name: "disk_size", value: 11
2025-09-15 20:24:39.095 wdl.w:ptcp.w:call-trgt-43.t:call-get_reads_overlapping_repeats INFO eval :: name: "output_name", value: "m84036_250809_035451_s4.bc2140.repeats.bam"
2025-09-15 20:24:39.095 wdl.w:ptcp.w:call-trgt-43.t:call-get_reads_overlapping_repeats INFO eval :: name: "index_name", value: "m84036_250809_035451_s4.bc2140.repeats.bam.bai"
2025-09-15 20:24:39.095 wdl.w:ptcp.w:call-trgt-43.t:call-get_reads_overlapping_repeats INFO eval :: name: "output_name_with_index", value: "m84036_250809_035451_s4.bc2140.repeats.bam##idx##m84036_250809_035451_s4.bc2140.repeats.bam.bai"
2025-09-15 20:24:39.096 wdl.w:ptcp.w:call-trgt-43.t:call-get_reads_overlapping_repeats INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:39.096 wdl.w:ptcp.w:call-trgt-43.t:call-get_reads_overlapping_repeats WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:39.096 wdl.w:ptcp.w:call-trgt-43.t:call-get_reads_overlapping_repeats INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:39.096 wdl.w:ptcp.w:call-trgt-43.t:call-get_reads_overlapping_repeats INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:39.103 wdl.w:ptcp.w:call-sawfish-35.t:call-run_sawfish NOTICE done
2025-09-15 20:24:39.113 wdl.w:ptcp.w:call-paraphase-43.t:call-run_paraphase NOTICE slurm_singularity run :: pid: 1202627, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-43/call-run_paraphase/slurm_singularity.log.txt"
2025-09-15 20:24:39.116 wdl.w:ptcp.w:call-trgt-59.t:call-get_reads_overlapping_repeats NOTICE done
2025-09-15 20:24:39.121 wdl.w:ptcp.w:call-trgt-59 NOTICE finish :: job: "call-get_reads_overlapping_repeats"
2025-09-15 20:24:39.121 wdl.w:ptcp.w:call-trgt-59 INFO output :: job: "call-get_reads_overlapping_repeats", values: {"reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-59/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2156.repeats.bam.bai", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-59/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2156.repeats.bam"}
2025-09-15 20:24:39.121 wdl.w:ptcp.w:call-trgt-59 INFO visit :: node: "output-reads_overlapping_repeats", values: {"reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-59/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2156.repeats.bam"}
2025-09-15 20:24:39.121 wdl.w:ptcp.w:call-trgt-59 INFO visit :: node: "output-reads_overlapping_repeats_bai", values: {"reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-59/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2156.repeats.bam.bai"}
2025-09-15 20:24:39.122 wdl.w:ptcp.w:call-sawfish-35 NOTICE finish :: job: "call-run_sawfish"
2025-09-15 20:24:39.122 wdl.w:ptcp.w:call-sawfish-35 INFO output :: job: "call-run_sawfish", values: {"minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-35/call-run_sawfish/out/m84036_250809_035451_s4.bc2132.minimap2.bam.bai", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-35/call-run_sawfish/out/m84036_250809_035451_s4.bc2132.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-35/call-run_sawfish/out/m84036_250809_035451_s4.bc2132_sawfish/m84036_250809_035451_s4.bc2132.sv.vcf.gz.tbi", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-35/call-run_sawfish/out/m84036_250809_035451_s4.bc2132_sawfish/m84036_250809_035451_s4.bc2132.sv.vcf.gz"}
2025-09-15 20:24:39.123 wdl.w:ptcp.w:call-sawfish-35 INFO visit :: node: "output-minimap2_bam", values: {"minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-35/call-run_sawfish/out/m84036_250809_035451_s4.bc2132.minimap2.bam"}
2025-09-15 20:24:39.123 wdl.w:ptcp.w:call-sawfish-35 INFO visit :: node: "output-minimap2_bam_bai", values: {"minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-35/call-run_sawfish/out/m84036_250809_035451_s4.bc2132.minimap2.bam.bai"}
2025-09-15 20:24:39.123 wdl.w:ptcp.w:call-sawfish-35 INFO visit :: node: "output-vcf", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-35/call-run_sawfish/out/m84036_250809_035451_s4.bc2132_sawfish/m84036_250809_035451_s4.bc2132.sv.vcf.gz"}
2025-09-15 20:24:39.123 wdl.w:ptcp.w:call-sawfish-35 INFO visit :: node: "output-vcf_tbi", values: {"vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-35/call-run_sawfish/out/m84036_250809_035451_s4.bc2132_sawfish/m84036_250809_035451_s4.bc2132.sv.vcf.gz.tbi"}
2025-09-15 20:24:39.123 wdl.w:ptcp.w:call-sawfish-35 INFO visit :: node: "outputs", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-35/call-run_sawfish/out/m84036_250809_035451_s4.bc2132_sawfish/m84036_250809_035451_s4.bc2132.sv.vcf.gz", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-35/call-run_sawfish/out/m84036_250809_035451_s4.bc2132.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-35/call-run_sawfish/out/m84036_250809_035451_s4.bc2132_sawfish/m84036_250809_035451_s4.bc2132.sv.vcf.gz.tbi", "minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-35/call-run_sawfish/out/m84036_250809_035451_s4.bc2132.minimap2.bam.bai"}
2025-09-15 20:24:39.131 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_genotype NOTICE task setup :: name: "trgt_genotype", source: "./trgt.wdl", line: 272, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-43/call-trgt_genotype", thread: 140608773551680
2025-09-15 20:24:39.132 wdl.w:ptcp.w:call-paraphase-55.t:call-run_paraphase NOTICE task setup :: name: "run_paraphase", source: "./paraphase.wdl", line: 127, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-55/call-run_paraphase", thread: 140613555033664
2025-09-15 20:24:39.134 wdl.w:ptcp.w:call-sawfish-53.t:call-run_sawfish.stderr VERBOSE [M::bam2fq_mainloop] discarded 0 singletons
2025-09-15 20:24:39.134 wdl.w:ptcp.w:call-sawfish-53.t:call-run_sawfish.stderr VERBOSE [M::bam2fq_mainloop] processed 0 reads
2025-09-15 20:24:39.146 wdl.w:ptcp.w:call-sawfish-53.t:call-run_sawfish.slurm_singularity INFO srun: job 51797735 queued and waiting for resources
2025-09-15 20:24:39.146 wdl.w:ptcp.w:call-sawfish-53.t:call-run_sawfish.slurm_singularity INFO srun: job 51797735 has been allocated resources
2025-09-15 20:24:39.146 wdl.w:ptcp.w:call-sawfish-53.t:call-run_sawfish.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:39.146 wdl.w:ptcp.w:call-sawfish-53.t:call-run_sawfish.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:24:39.148 wdl.w:ptcp.w:call-trgt-01.t:call-trgt_plot_meth_waterfall NOTICE done
2025-09-15 20:24:39.152 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_genotype INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:39.152 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_genotype INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:39.152 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_genotype INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:39.153 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_genotype INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:39.153 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_genotype INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2140.mapped.bam.bai"
2025-09-15 20:24:39.153 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_genotype INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2140.mapped.bam"
2025-09-15 20:24:39.153 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_genotype INFO input :: name: "sex", value: "F"
2025-09-15 20:24:39.153 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_genotype INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2140"
2025-09-15 20:24:39.153 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_genotype INFO eval :: name: "mem_gb", value: 16
2025-09-15 20:24:39.154 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_genotype INFO eval :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2140.trgt"
2025-09-15 20:24:39.154 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_genotype INFO eval :: name: "threads", value: 8
2025-09-15 20:24:39.154 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_genotype INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:39.154 wdl.w:ptcp.w:call-trgt-01 NOTICE finish :: job: "call-trgt_plot_meth_waterfall"
2025-09-15 20:24:39.155 wdl.w:ptcp.w:call-trgt-01 INFO output :: job: "call-trgt_plot_meth_waterfall", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-01/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2098.meth_waterfall.trgt_plots.zip"}
2025-09-15 20:24:39.155 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_genotype INFO eval :: name: "karyotype", value: "XX"
2025-09-15 20:24:39.155 wdl.w:ptcp.w:call-trgt-01 INFO visit :: node: "output-images_meth_waterfall", values: {"images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-01/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2098.meth_waterfall.trgt_plots.zip"}
2025-09-15 20:24:39.156 wdl.w:ptcp.w:call-trgt-01 INFO visit :: node: "outputs", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-01/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2098.motifs_waterfall.trgt_plots.zip", "images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-01/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2098.meth_allele.trgt_plots.zip", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-01/call-trgt_genotype/out/m84036_250809_035451_s4.bc2098.trgt.sorted.spanning.bam.bai", "images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-01/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2098.motifs_allele.trgt_plots.zip", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-01/call-trgt_genotype/out/m84036_250809_035451_s4.bc2098.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-01/call-trgt_genotype/out/m84036_250809_035451_s4.bc2098.trgt.vcf", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-01/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2098.repeats.bam", "images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-01/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2098.meth_waterfall.trgt_plots.zip", "reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-01/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2098.repeats.bam.bai"}
2025-09-15 20:24:39.156 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_genotype INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 8, memory_reservation: 16000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:39.157 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_genotype WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:39.157 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_genotype INFO provisioned :: seconds_waited: 0, cpu: 8, mem_bytes: 16000000000
2025-09-15 20:24:39.157 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_genotype INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:39.165 wdl.w:ptcp.w:call-paraphase-55.t:call-run_paraphase INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:39.165 wdl.w:ptcp.w:call-paraphase-55.t:call-run_paraphase INFO input :: name: "annotation_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf"
2025-09-15 20:24:39.165 wdl.w:ptcp.w:call-paraphase-55.t:call-run_paraphase INFO input :: name: "genome_version", value: "38"
2025-09-15 20:24:39.165 wdl.w:ptcp.w:call-sawfish-55.t:call-run_sawfish NOTICE task setup :: name: "run_sawfish", source: "./sawfish.wdl", line: 83, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-55/call-run_sawfish", thread: 140608186324544
2025-09-15 20:24:39.165 wdl.w:ptcp.w:call-paraphase-55.t:call-run_paraphase INFO input :: name: "config_file", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/paraphase_config.GRCh38.yaml"
2025-09-15 20:24:39.166 wdl.w:ptcp.w:call-paraphase-55.t:call-run_paraphase INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:39.166 wdl.w:ptcp.w:call-paraphase-55.t:call-run_paraphase INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:39.166 wdl.w:ptcp.w:call-paraphase-55.t:call-run_paraphase INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2152.mapped.bam.bai"
2025-09-15 20:24:39.166 wdl.w:ptcp.w:call-paraphase-55.t:call-run_paraphase INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2152.mapped.bam"
2025-09-15 20:24:39.166 wdl.w:ptcp.w:call-paraphase-55.t:call-run_paraphase INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2152"
2025-09-15 20:24:39.166 wdl.w:ptcp.w:call-paraphase-55.t:call-run_paraphase INFO eval :: name: "threads", value: 4
2025-09-15 20:24:39.166 wdl.w:ptcp.w:call-trgt-43.t:call-get_reads_overlapping_repeats INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 9, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-43/call-get_reads_overlapping_repeats/_singularity_tmpdir_9hopctp7"
2025-09-15 20:24:39.167 wdl.w:ptcp.w:call-paraphase-55.t:call-run_paraphase INFO eval :: name: "mem_gb", value: 8
2025-09-15 20:24:39.167 wdl.w:ptcp.w:call-trgt-43.t:call-get_reads_overlapping_repeats INFO Slurm invocation: srun --job-name call-get_reads_overlapping_repeats --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-43/call-get_reads_overlapping_repeats/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-43/call-get_reads_overlapping_repeats/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-43/call-get_reads_overlapping_repeats/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-43/call-get_reads_overlapping_repeats/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-43/out/m84036_250809_035451_s4.bc2140.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2140.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-43/out/m84036_250809_035451_s4.bc2140.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2140.mapped.bam.bai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-43/call-get_reads_overlapping_repeats/_singularity_tmpdir_9hopctp7/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-43/call-get_reads_overlapping_repeats/_singularity_tmpdir_9hopctp7/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:39.167 wdl.w:ptcp.w:call-paraphase-55.t:call-run_paraphase INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:39.167 wdl.w:ptcp.w:call-paraphase-55.t:call-run_paraphase INFO eval :: name: "out_dir", value: "m84036_250809_035451_s4.bc2152_paraphase"
2025-09-15 20:24:39.170 wdl.w:ptcp.w:call-paraphase-55.t:call-run_paraphase INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 4, memory_reservation: 8000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:39.171 wdl.w:ptcp.w:call-paraphase-55.t:call-run_paraphase WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:39.172 wdl.w:ptcp.w:call-paraphase-55.t:call-run_paraphase INFO provisioned :: seconds_waited: 0, cpu: 4, mem_bytes: 8000000000
2025-09-15 20:24:39.172 wdl.w:ptcp.w:call-paraphase-55.t:call-run_paraphase INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:39.188 wdl.w:ptcp.w:call-sawfish-35 NOTICE done
2025-09-15 20:24:39.189 wdl.w:ptcp.w:call-trgt-00 NOTICE done
2025-09-15 20:24:39.189 wdl.w:ptcp.w:call-sawfish-55.t:call-run_sawfish INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:39.190 wdl.w:ptcp.w:call-sawfish-55.t:call-run_sawfish INFO input :: name: "genome_version", value: "38"
2025-09-15 20:24:39.190 wdl.w:ptcp.w:call-sawfish-55.t:call-run_sawfish INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:39.190 wdl.w:ptcp.w:call-sawfish-55.t:call-run_sawfish INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:39.190 wdl.w:ptcp.w:call-sawfish-55.t:call-run_sawfish INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2152.mapped.bam.bai"
2025-09-15 20:24:39.190 wdl.w:ptcp.w:call-sawfish-55.t:call-run_sawfish INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2152.mapped.bam"
2025-09-15 20:24:39.190 wdl.w:ptcp.w:call-sawfish-55.t:call-run_sawfish INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2152"
2025-09-15 20:24:39.190 wdl.w:ptcp.w:call-sawfish-55.t:call-run_sawfish INFO eval :: name: "mem_gb", value: 32
2025-09-15 20:24:39.191 wdl.w:ptcp.w:call-sawfish-55.t:call-run_sawfish INFO eval :: name: "threads", value: 16
2025-09-15 20:24:39.191 wdl.w:ptcp.w:call-sawfish-55.t:call-run_sawfish INFO eval :: name: "disk_size", value: 30
2025-09-15 20:24:39.191 wdl.w:ptcp.w:call-sawfish-55.t:call-run_sawfish INFO eval :: name: "discover_dirname", value: "m84036_250809_035451_s4.bc2152_sawfish_discover"
2025-09-15 20:24:39.191 wdl.w:ptcp.w:call-sawfish-55.t:call-run_sawfish INFO eval :: name: "call_dirname", value: "m84036_250809_035451_s4.bc2152_sawfish"
2025-09-15 20:24:39.191 wdl.w:ptcp.w:call-sawfish-55.t:call-run_sawfish INFO eval :: name: "minimap2_bam_filename", value: "m84036_250809_035451_s4.bc2152.minimap2.bam"
2025-09-15 20:24:39.192 wdl.w:ptcp.w:call-sawfish-55.t:call-run_sawfish INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 16, memory_reservation: 32000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:39.192 wdl.w:ptcp.w:call-sawfish-55.t:call-run_sawfish WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:39.192 wdl.w:ptcp.w:call-sawfish-55.t:call-run_sawfish INFO provisioned :: seconds_waited: 0, cpu: 16, mem_bytes: 32000000000
2025-09-15 20:24:39.192 wdl.w:ptcp.w:call-sawfish-55.t:call-run_sawfish INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:39.192 wdl.w:ptcp.w:call-sawfish-43.t:call-run_sawfish INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 10, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-43/call-run_sawfish/_singularity_tmpdir_k5w0g2kx"
2025-09-15 20:24:39.192 wdl.w:ptcp.w:call-sawfish-43.t:call-run_sawfish INFO Slurm invocation: srun --job-name call-run_sawfish --partition compute,compute9 --cpus-per-task 16 --mem 30518M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-43/call-run_sawfish/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-43/call-run_sawfish/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-43/call-run_sawfish/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-43/call-run_sawfish/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-43/out/m84036_250809_035451_s4.bc2140.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2140.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-43/out/m84036_250809_035451_s4.bc2140.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2140.mapped.bam.bai:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-43/call-run_sawfish/_singularity_tmpdir_k5w0g2kx/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-43/call-run_sawfish/_singularity_tmpdir_k5w0g2kx/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:39.196 wdl.w:ptcp NOTICE finish :: job: "call-sawfish-35"
2025-09-15 20:24:39.196 wdl.w:ptcp INFO output :: job: "call-sawfish-35", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-35/out/m84036_250809_035451_s4.bc2132_sawfish/m84036_250809_035451_s4.bc2132.sv.vcf.gz", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-35/out/m84036_250809_035451_s4.bc2132.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-35/out/m84036_250809_035451_s4.bc2132_sawfish/m84036_250809_035451_s4.bc2132.sv.vcf.gz.tbi", "minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-35/out/m84036_250809_035451_s4.bc2132.minimap2.bam.bai"}
2025-09-15 20:24:39.206 wdl.w:ptcp.w:call-sawfish-60 NOTICE workflow start :: name: "sawfish", source: "./sawfish.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-60"
2025-09-15 20:24:39.211 wdl.w:ptcp.w:call-trgt-43.t:call-get_reads_overlapping_repeats NOTICE slurm_singularity run :: pid: 1202635, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-43/call-get_reads_overlapping_repeats/slurm_singularity.log.txt"
2025-09-15 20:24:39.211 wdl.w:ptcp.w:call-sawfish-43.t:call-run_sawfish NOTICE slurm_singularity run :: pid: 1202652, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-43/call-run_sawfish/slurm_singularity.log.txt"
2025-09-15 20:24:39.213 wdl.w:ptcp NOTICE finish :: job: "call-trgt-00"
2025-09-15 20:24:39.213 wdl.w:ptcp INFO output :: job: "call-trgt-00", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-00/out/m84036_250809_035451_s4.bc2097.motifs_waterfall.trgt_plots.zip", "images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-00/out/m84036_250809_035451_s4.bc2097.meth_allele.trgt_plots.zip", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-00/out/m84036_250809_035451_s4.bc2097.trgt.sorted.spanning.bam.bai", "images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-00/out/m84036_250809_035451_s4.bc2097.motifs_allele.trgt_plots.zip", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-00/out/m84036_250809_035451_s4.bc2097.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-00/out/m84036_250809_035451_s4.bc2097.trgt.vcf", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-00/out/m84036_250809_035451_s4.bc2097.repeats.bam", "images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-00/out/m84036_250809_035451_s4.bc2097.meth_waterfall.trgt_plots.zip", "reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-00/out/m84036_250809_035451_s4.bc2097.repeats.bam.bai"}
2025-09-15 20:24:39.221 wdl.w:ptcp.w:call-trgt-60 NOTICE workflow start :: name: "trgt", source: "./trgt.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-60"
2025-09-15 20:24:39.227 wdl.w:ptcp.w:call-sawfish-60 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:24:39.227 wdl.w:ptcp.w:call-sawfish-60 INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:24:39.227 wdl.w:ptcp.w:call-sawfish-60 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-60/out/m84036_250809_035451_s4.bc2157.mapped.bam"}
2025-09-15 20:24:39.227 wdl.w:ptcp.w:call-sawfish-60 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-60/out/m84036_250809_035451_s4.bc2157.mapped.bam.bai"}
2025-09-15 20:24:39.227 wdl.w:ptcp.w:call-sawfish-60 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:24:39.227 wdl.w:ptcp.w:call-sawfish-60 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:24:39.227 wdl.w:ptcp.w:call-sawfish-60 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2157"}
2025-09-15 20:24:39.227 wdl.w:ptcp.w:call-sawfish-60 NOTICE ready :: job: "call-run_sawfish", callee: "run_sawfish"
2025-09-15 20:24:39.227 wdl.w:ptcp.w:call-sawfish-60 INFO input :: job: "call-run_sawfish", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-60/out/m84036_250809_035451_s4.bc2157.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-60/out/m84036_250809_035451_s4.bc2157.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2157"}
2025-09-15 20:24:39.234 wdl.w:ptcp.w:call-trgt-60 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:24:39.234 wdl.w:ptcp.w:call-trgt-60 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-60/out/m84036_250809_035451_s4.bc2157.mapped.bam"}
2025-09-15 20:24:39.235 wdl.w:ptcp.w:call-trgt-60 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-60/out/m84036_250809_035451_s4.bc2157.mapped.bam.bai"}
2025-09-15 20:24:39.235 wdl.w:ptcp.w:call-trgt-60 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:24:39.235 wdl.w:ptcp.w:call-trgt-60 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:24:39.235 wdl.w:ptcp.w:call-trgt-60 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2157"}
2025-09-15 20:24:39.235 wdl.w:ptcp.w:call-trgt-60 INFO visit :: node: "decl-sex", values: {"sex": "F"}
2025-09-15 20:24:39.235 wdl.w:ptcp.w:call-trgt-60 INFO visit :: node: "decl-trgt_bed", values: {"trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"}
2025-09-15 20:24:39.235 wdl.w:ptcp.w:call-trgt-60 NOTICE ready :: job: "call-get_reads_overlapping_repeats", callee: "get_reads_overlapping_repeats"
2025-09-15 20:24:39.235 wdl.w:ptcp.w:call-trgt-60 INFO input :: job: "call-get_reads_overlapping_repeats", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-60/out/m84036_250809_035451_s4.bc2157.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-60/out/m84036_250809_035451_s4.bc2157.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2157"}
2025-09-15 20:24:39.236 wdl.w:ptcp.w:call-trgt-60 NOTICE ready :: job: "call-trgt_genotype", callee: "trgt_genotype"
2025-09-15 20:24:39.236 wdl.w:ptcp.w:call-trgt-60 INFO input :: job: "call-trgt_genotype", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-60/out/m84036_250809_035451_s4.bc2157.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-60/out/m84036_250809_035451_s4.bc2157.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2157"}
2025-09-15 20:24:39.258 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_genotype INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 11, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-43/call-trgt_genotype/_singularity_tmpdir_xipc0dwk"
2025-09-15 20:24:39.258 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_genotype INFO Slurm invocation: srun --job-name call-trgt_genotype --partition compute,compute9 --cpus-per-task 8 --mem 15259M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-43/call-trgt_genotype/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-43/call-trgt_genotype/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-43/call-trgt_genotype/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-43/call-trgt_genotype/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-43/out/m84036_250809_035451_s4.bc2140.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2140.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-43/out/m84036_250809_035451_s4.bc2140.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2140.mapped.bam.bai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-43/call-trgt_genotype/_singularity_tmpdir_xipc0dwk/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-43/call-trgt_genotype/_singularity_tmpdir_xipc0dwk/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:39.280 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_genotype NOTICE slurm_singularity run :: pid: 1202700, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-43/call-trgt_genotype/slurm_singularity.log.txt"
2025-09-15 20:24:39.285 wdl.w:ptcp.w:call-paraphase-55.t:call-run_paraphase INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-55/call-run_paraphase/_singularity_tmpdir_5k0g2w4p"
2025-09-15 20:24:39.285 wdl.w:ptcp.w:call-trgt-01 NOTICE done
2025-09-15 20:24:39.285 wdl.w:ptcp.w:call-paraphase-55.t:call-run_paraphase INFO Slurm invocation: srun --job-name call-run_paraphase --partition compute,compute9 --cpus-per-task 4 --mem 7629M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-55/call-run_paraphase/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-55/call-run_paraphase/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-55/call-run_paraphase/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-55/call-run_paraphase/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-55/out/m84036_250809_035451_s4.bc2152.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2152.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-55/out/m84036_250809_035451_s4.bc2152.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2152.mapped.bam:ro --bind /ptcp/meta/variant_list/variant_list.GRCh38.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf:ro --bind /ptcp/meta/paraphase/paraphase_config.GRCh38.yaml:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/paraphase_config.GRCh38.yaml:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-55/call-run_paraphase/_singularity_tmpdir_5k0g2w4p/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-55/call-run_paraphase/_singularity_tmpdir_5k0g2w4p/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:39.290 wdl.w:ptcp NOTICE finish :: job: "call-trgt-01"
2025-09-15 20:24:39.290 wdl.w:ptcp INFO output :: job: "call-trgt-01", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-01/out/m84036_250809_035451_s4.bc2098.motifs_waterfall.trgt_plots.zip", "images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-01/out/m84036_250809_035451_s4.bc2098.meth_allele.trgt_plots.zip", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-01/out/m84036_250809_035451_s4.bc2098.trgt.sorted.spanning.bam.bai", "images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-01/out/m84036_250809_035451_s4.bc2098.motifs_allele.trgt_plots.zip", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-01/out/m84036_250809_035451_s4.bc2098.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-01/out/m84036_250809_035451_s4.bc2098.trgt.vcf", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-01/out/m84036_250809_035451_s4.bc2098.repeats.bam", "images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-01/out/m84036_250809_035451_s4.bc2098.meth_waterfall.trgt_plots.zip", "reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-01/out/m84036_250809_035451_s4.bc2098.repeats.bam.bai"}
2025-09-15 20:24:39.291 wdl.w:ptcp NOTICE ready :: job: "call-tar_outputs-01", callee: "tar_outputs"
2025-09-15 20:24:39.291 wdl.w:ptcp INFO input :: job: "call-tar_outputs-01", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "sawfish_vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-01/out/m84036_250809_035451_s4.bc2098_sawfish/m84036_250809_035451_s4.bc2098.sv.vcf.gz.tbi", "sawfish_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-01/out/m84036_250809_035451_s4.bc2098_sawfish/m84036_250809_035451_s4.bc2098.sv.vcf.gz", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-01/out/m84036_250809_035451_s4.bc2098.f8inversion.json", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-01/out/m84036_250809_035451_s4.bc2098_paraphase/m84036_250809_035451_s4.bc2098.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-01/out/m84036_250809_035451_s4.bc2098_paraphase/m84036_250809_035451_s4.bc2098.paraphase.bam", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-01/out/m84036_250809_035451_s4.bc2098_paraphase/m84036_250809_035451_s4.bc2098.paraphase.json", "trgt_spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-01/out/m84036_250809_035451_s4.bc2098.trgt.sorted.spanning.bam.bai", "trgt_spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-01/out/m84036_250809_035451_s4.bc2098.trgt.sorted.spanning.bam", "trgt_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-01/out/m84036_250809_035451_s4.bc2098.trgt.vcf", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-01/out/m84036_250809_035451_s4.bc2098.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-01/out/m84036_250809_035451_s4.bc2098.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2098"}
2025-09-15 20:24:39.298 wdl.w:ptcp.w:call-paraphase-65 NOTICE workflow start :: name: "paraphase", source: "./paraphase.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-65"
2025-09-15 20:24:39.305 wdl.w:ptcp.w:call-sawfish-55.t:call-run_sawfish INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 10, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-55/call-run_sawfish/_singularity_tmpdir_n2i7q87s"
2025-09-15 20:24:39.306 wdl.w:ptcp.w:call-sawfish-55.t:call-run_sawfish INFO Slurm invocation: srun --job-name call-run_sawfish --partition compute,compute9 --cpus-per-task 16 --mem 30518M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-55/call-run_sawfish/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-55/call-run_sawfish/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-55/call-run_sawfish/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-55/call-run_sawfish/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-55/out/m84036_250809_035451_s4.bc2152.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2152.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-55/out/m84036_250809_035451_s4.bc2152.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2152.mapped.bam:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-55/call-run_sawfish/_singularity_tmpdir_n2i7q87s/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-55/call-run_sawfish/_singularity_tmpdir_n2i7q87s/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:39.316 wdl.w:ptcp.w:call-paraphase-65 INFO visit :: node: "decl-annotation_vcf", values: {"annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf"}
2025-09-15 20:24:39.316 wdl.w:ptcp.w:call-paraphase-65 INFO visit :: node: "decl-config_file", values: {"config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml"}
2025-09-15 20:24:39.317 wdl.w:ptcp.w:call-paraphase-65 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:24:39.317 wdl.w:ptcp.w:call-paraphase-65 INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:24:39.317 wdl.w:ptcp.w:call-paraphase-65 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-65/out/m84036_250809_035451_s4.bc2162.mapped.bam"}
2025-09-15 20:24:39.317 wdl.w:ptcp.w:call-paraphase-65 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-65/out/m84036_250809_035451_s4.bc2162.mapped.bam.bai"}
2025-09-15 20:24:39.317 wdl.w:ptcp.w:call-paraphase-65 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:24:39.317 wdl.w:ptcp.w:call-paraphase-65 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:24:39.317 wdl.w:ptcp.w:call-paraphase-65 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2162"}
2025-09-15 20:24:39.317 wdl.w:ptcp.w:call-paraphase-65 INFO visit :: node: "decl-sex", values: {"sex": "F"}
2025-09-15 20:24:39.317 wdl.w:ptcp.w:call-paraphase-65 NOTICE ready :: job: "call-run_paraphase", callee: "run_paraphase"
2025-09-15 20:24:39.317 wdl.w:ptcp.w:call-paraphase-65 INFO input :: job: "call-run_paraphase", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf", "genome_version": "38", "config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-65/out/m84036_250809_035451_s4.bc2162.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-65/out/m84036_250809_035451_s4.bc2162.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2162"}
2025-09-15 20:24:39.321 wdl.w:ptcp.w:call-sawfish-55.t:call-run_sawfish NOTICE slurm_singularity run :: pid: 1202747, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-55/call-run_sawfish/slurm_singularity.log.txt"
2025-09-15 20:24:39.321 wdl.w:ptcp.w:call-trgt-41.t:call-get_reads_overlapping_repeats INFO output :: name: "reads_overlapping_repeats", value: "m84036_250809_035451_s4.bc2138.repeats.bam"
2025-09-15 20:24:39.323 wdl.w:ptcp.w:call-paraphase-55.t:call-run_paraphase NOTICE slurm_singularity run :: pid: 1202745, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-55/call-run_paraphase/slurm_singularity.log.txt"
2025-09-15 20:24:39.325 wdl.w:ptcp.w:call-trgt-41.t:call-get_reads_overlapping_repeats INFO output :: name: "reads_overlapping_repeats_bai", value: "m84036_250809_035451_s4.bc2138.repeats.bam.bai"
2025-09-15 20:24:39.382 wdl.w:ptcp.w:call-trgt-41.t:call-get_reads_overlapping_repeats NOTICE done
2025-09-15 20:24:39.387 wdl.w:ptcp.w:call-trgt-41 NOTICE finish :: job: "call-get_reads_overlapping_repeats"
2025-09-15 20:24:39.387 wdl.w:ptcp.w:call-trgt-41 INFO output :: job: "call-get_reads_overlapping_repeats", values: {"reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-41/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2138.repeats.bam.bai", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-41/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2138.repeats.bam"}
2025-09-15 20:24:39.387 wdl.w:ptcp.w:call-trgt-41 INFO visit :: node: "output-reads_overlapping_repeats", values: {"reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-41/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2138.repeats.bam"}
2025-09-15 20:24:39.387 wdl.w:ptcp.w:call-trgt-41 INFO visit :: node: "output-reads_overlapping_repeats_bai", values: {"reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-41/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2138.repeats.bam.bai"}
2025-09-15 20:24:39.393 wdl.w:ptcp.w:call-trgt-55.t:call-get_reads_overlapping_repeats NOTICE task setup :: name: "get_reads_overlapping_repeats", source: "./trgt.wdl", line: 182, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-55/call-get_reads_overlapping_repeats", thread: 140610367379008
2025-09-15 20:24:39.412 wdl.w:ptcp.w:call-trgt-55.t:call-get_reads_overlapping_repeats INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:39.412 wdl.w:ptcp.w:call-trgt-55.t:call-get_reads_overlapping_repeats INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:39.412 wdl.w:ptcp.w:call-trgt-55.t:call-get_reads_overlapping_repeats INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2152.mapped.bam.bai"
2025-09-15 20:24:39.412 wdl.w:ptcp.w:call-trgt-55.t:call-get_reads_overlapping_repeats INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2152.mapped.bam"
2025-09-15 20:24:39.412 wdl.w:ptcp.w:call-trgt-55.t:call-get_reads_overlapping_repeats INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2152"
2025-09-15 20:24:39.412 wdl.w:ptcp.w:call-trgt-55.t:call-get_reads_overlapping_repeats INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:39.412 wdl.w:ptcp.w:call-trgt-55.t:call-get_reads_overlapping_repeats INFO eval :: name: "expand_size", value: 3000
2025-09-15 20:24:39.413 wdl.w:ptcp.w:call-trgt-55.t:call-get_reads_overlapping_repeats INFO eval :: name: "threads", value: 1
2025-09-15 20:24:39.413 wdl.w:ptcp.w:call-trgt-55.t:call-get_reads_overlapping_repeats INFO eval :: name: "expanded_bed_name", value: "m84036_250809_035451_s4.bc2152.expanded.bed"
2025-09-15 20:24:39.413 wdl.w:ptcp.w:call-trgt-55.t:call-get_reads_overlapping_repeats INFO eval :: name: "disk_size", value: 11
2025-09-15 20:24:39.413 wdl.w:ptcp.w:call-trgt-55.t:call-get_reads_overlapping_repeats INFO eval :: name: "output_name", value: "m84036_250809_035451_s4.bc2152.repeats.bam"
2025-09-15 20:24:39.413 wdl.w:ptcp.w:call-trgt-55.t:call-get_reads_overlapping_repeats INFO eval :: name: "index_name", value: "m84036_250809_035451_s4.bc2152.repeats.bam.bai"
2025-09-15 20:24:39.413 wdl.w:ptcp.w:call-trgt-55.t:call-get_reads_overlapping_repeats INFO eval :: name: "output_name_with_index", value: "m84036_250809_035451_s4.bc2152.repeats.bam##idx##m84036_250809_035451_s4.bc2152.repeats.bam.bai"
2025-09-15 20:24:39.413 wdl.w:ptcp.w:call-trgt-55.t:call-get_reads_overlapping_repeats INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:39.414 wdl.w:ptcp.w:call-trgt-55.t:call-get_reads_overlapping_repeats WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:39.414 wdl.w:ptcp.w:call-trgt-55.t:call-get_reads_overlapping_repeats INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:39.414 wdl.w:ptcp.w:call-trgt-55.t:call-get_reads_overlapping_repeats INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:39.419 wdl.w:ptcp.w:call-trgt-53.t:call-get_reads_overlapping_repeats.slurm_singularity INFO srun: job 51797736 queued and waiting for resources
2025-09-15 20:24:39.419 wdl.w:ptcp.w:call-trgt-53.t:call-get_reads_overlapping_repeats.slurm_singularity INFO srun: job 51797736 has been allocated resources
2025-09-15 20:24:39.419 wdl.w:ptcp.w:call-trgt-53.t:call-get_reads_overlapping_repeats.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:39.457 wdl.w:ptcp.w:call-trgt-45.t:call-trgt_plot_meth_allele INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2142.meth_allele.trgt_plots.zip"
2025-09-15 20:24:39.471 wdl.w:ptcp.w:call-trgt-55.t:call-get_reads_overlapping_repeats INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 9, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-55/call-get_reads_overlapping_repeats/_singularity_tmpdir_czbgolg5"
2025-09-15 20:24:39.471 wdl.w:ptcp.w:call-trgt-55.t:call-get_reads_overlapping_repeats INFO Slurm invocation: srun --job-name call-get_reads_overlapping_repeats --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-55/call-get_reads_overlapping_repeats/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-55/call-get_reads_overlapping_repeats/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-55/call-get_reads_overlapping_repeats/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-55/call-get_reads_overlapping_repeats/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-55/out/m84036_250809_035451_s4.bc2152.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2152.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-55/out/m84036_250809_035451_s4.bc2152.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2152.mapped.bam:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-55/call-get_reads_overlapping_repeats/_singularity_tmpdir_czbgolg5/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-55/call-get_reads_overlapping_repeats/_singularity_tmpdir_czbgolg5/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:39.500 wdl.w:ptcp.w:call-trgt-55.t:call-get_reads_overlapping_repeats NOTICE slurm_singularity run :: pid: 1202769, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-55/call-get_reads_overlapping_repeats/slurm_singularity.log.txt"
2025-09-15 20:24:39.560 wdl.w:ptcp.w:call-trgt-45.t:call-trgt_plot_meth_allele NOTICE done
2025-09-15 20:24:39.565 wdl.w:ptcp.w:call-trgt-45 NOTICE finish :: job: "call-trgt_plot_meth_allele"
2025-09-15 20:24:39.566 wdl.w:ptcp.w:call-trgt-45 INFO output :: job: "call-trgt_plot_meth_allele", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-45/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2142.meth_allele.trgt_plots.zip"}
2025-09-15 20:24:39.566 wdl.w:ptcp.w:call-trgt-45 INFO visit :: node: "output-images_meth_allele", values: {"images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-45/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2142.meth_allele.trgt_plots.zip"}
2025-09-15 20:24:39.571 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_genotype NOTICE task setup :: name: "trgt_genotype", source: "./trgt.wdl", line: 272, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-55/call-trgt_genotype", thread: 140609302029888
2025-09-15 20:24:39.587 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_genotype INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:39.587 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_genotype INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:39.587 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_genotype INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:39.587 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_genotype INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:39.587 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_genotype INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2152.mapped.bam.bai"
2025-09-15 20:24:39.587 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_genotype INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2152.mapped.bam"
2025-09-15 20:24:39.587 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_genotype INFO input :: name: "sex", value: "F"
2025-09-15 20:24:39.587 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_genotype INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2152"
2025-09-15 20:24:39.587 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_genotype INFO eval :: name: "mem_gb", value: 16
2025-09-15 20:24:39.588 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_genotype INFO eval :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2152.trgt"
2025-09-15 20:24:39.588 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_genotype INFO eval :: name: "threads", value: 8
2025-09-15 20:24:39.588 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_genotype INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:39.588 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_genotype INFO eval :: name: "karyotype", value: "XX"
2025-09-15 20:24:39.588 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_genotype INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 8, memory_reservation: 16000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:39.588 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_genotype WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:39.589 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_genotype INFO provisioned :: seconds_waited: 0, cpu: 8, mem_bytes: 16000000000
2025-09-15 20:24:39.589 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_genotype INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:39.644 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_genotype INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 11, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-55/call-trgt_genotype/_singularity_tmpdir_1ocw08o4"
2025-09-15 20:24:39.644 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_genotype INFO Slurm invocation: srun --job-name call-trgt_genotype --partition compute,compute9 --cpus-per-task 8 --mem 15259M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-55/call-trgt_genotype/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-55/call-trgt_genotype/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-55/call-trgt_genotype/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-55/call-trgt_genotype/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-55/out/m84036_250809_035451_s4.bc2152.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2152.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-55/out/m84036_250809_035451_s4.bc2152.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2152.mapped.bam:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-55/call-trgt_genotype/_singularity_tmpdir_1ocw08o4/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-55/call-trgt_genotype/_singularity_tmpdir_1ocw08o4/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:39.647 wdl.w:ptcp.w:call-sawfish-32.t:call-run_sawfish INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2129_sawfish/m84036_250809_035451_s4.bc2129.sv.vcf.gz"
2025-09-15 20:24:39.656 wdl.w:ptcp.w:call-sawfish-32.t:call-run_sawfish INFO output :: name: "vcf_tbi", value: "m84036_250809_035451_s4.bc2129_sawfish/m84036_250809_035451_s4.bc2129.sv.vcf.gz.tbi"
2025-09-15 20:24:39.657 wdl.w:ptcp.w:call-sawfish-32.t:call-run_sawfish INFO output :: name: "minimap2_bam", value: "m84036_250809_035451_s4.bc2129.minimap2.bam"
2025-09-15 20:24:39.659 wdl.w:ptcp.w:call-sawfish-32.t:call-run_sawfish INFO output :: name: "minimap2_bam_bai", value: "m84036_250809_035451_s4.bc2129.minimap2.bam.bai"
2025-09-15 20:24:39.672 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_genotype NOTICE slurm_singularity run :: pid: 1202777, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-55/call-trgt_genotype/slurm_singularity.log.txt"
2025-09-15 20:24:39.733 wdl.w:ptcp.w:call-trgt-53.t:call-trgt_genotype.slurm_singularity INFO srun: job 51797737 queued and waiting for resources
2025-09-15 20:24:39.733 wdl.w:ptcp.w:call-trgt-53.t:call-trgt_genotype.slurm_singularity INFO srun: job 51797737 has been allocated resources
2025-09-15 20:24:39.733 wdl.w:ptcp.w:call-trgt-53.t:call-trgt_genotype.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:39.747 wdl.w:ptcp.w:call-trgt-45.t:call-trgt_plot_meth_waterfall INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2142.meth_waterfall.trgt_plots.zip"
2025-09-15 20:24:39.801 wdl.w:ptcp.w:call-sawfish-32.t:call-run_sawfish NOTICE done
2025-09-15 20:24:39.807 wdl.w:ptcp.w:call-sawfish-32 NOTICE finish :: job: "call-run_sawfish"
2025-09-15 20:24:39.808 wdl.w:ptcp.w:call-sawfish-32 INFO output :: job: "call-run_sawfish", values: {"minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-32/call-run_sawfish/out/m84036_250809_035451_s4.bc2129.minimap2.bam.bai", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-32/call-run_sawfish/out/m84036_250809_035451_s4.bc2129.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-32/call-run_sawfish/out/m84036_250809_035451_s4.bc2129_sawfish/m84036_250809_035451_s4.bc2129.sv.vcf.gz.tbi", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-32/call-run_sawfish/out/m84036_250809_035451_s4.bc2129_sawfish/m84036_250809_035451_s4.bc2129.sv.vcf.gz"}
2025-09-15 20:24:39.808 wdl.w:ptcp.w:call-sawfish-32 INFO visit :: node: "output-minimap2_bam", values: {"minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-32/call-run_sawfish/out/m84036_250809_035451_s4.bc2129.minimap2.bam"}
2025-09-15 20:24:39.808 wdl.w:ptcp.w:call-sawfish-32 INFO visit :: node: "output-minimap2_bam_bai", values: {"minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-32/call-run_sawfish/out/m84036_250809_035451_s4.bc2129.minimap2.bam.bai"}
2025-09-15 20:24:39.808 wdl.w:ptcp.w:call-sawfish-32 INFO visit :: node: "output-vcf", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-32/call-run_sawfish/out/m84036_250809_035451_s4.bc2129_sawfish/m84036_250809_035451_s4.bc2129.sv.vcf.gz"}
2025-09-15 20:24:39.808 wdl.w:ptcp.w:call-sawfish-32 INFO visit :: node: "output-vcf_tbi", values: {"vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-32/call-run_sawfish/out/m84036_250809_035451_s4.bc2129_sawfish/m84036_250809_035451_s4.bc2129.sv.vcf.gz.tbi"}
2025-09-15 20:24:39.809 wdl.w:ptcp.w:call-sawfish-32 INFO visit :: node: "outputs", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-32/call-run_sawfish/out/m84036_250809_035451_s4.bc2129_sawfish/m84036_250809_035451_s4.bc2129.sv.vcf.gz", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-32/call-run_sawfish/out/m84036_250809_035451_s4.bc2129.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-32/call-run_sawfish/out/m84036_250809_035451_s4.bc2129_sawfish/m84036_250809_035451_s4.bc2129.sv.vcf.gz.tbi", "minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-32/call-run_sawfish/out/m84036_250809_035451_s4.bc2129.minimap2.bam.bai"}
2025-09-15 20:24:39.815 wdl.w:ptcp.w:call-paraphase-42.t:call-run_paraphase NOTICE task setup :: name: "run_paraphase", source: "./paraphase.wdl", line: 127, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-42/call-run_paraphase", thread: 140610921035328
2025-09-15 20:24:39.839 wdl.w:ptcp.w:call-paraphase-42.t:call-run_paraphase INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:39.839 wdl.w:ptcp.w:call-paraphase-42.t:call-run_paraphase INFO input :: name: "annotation_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf"
2025-09-15 20:24:39.839 wdl.w:ptcp.w:call-paraphase-42.t:call-run_paraphase INFO input :: name: "genome_version", value: "38"
2025-09-15 20:24:39.839 wdl.w:ptcp.w:call-paraphase-42.t:call-run_paraphase INFO input :: name: "config_file", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/paraphase_config.GRCh38.yaml"
2025-09-15 20:24:39.839 wdl.w:ptcp.w:call-paraphase-42.t:call-run_paraphase INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:39.839 wdl.w:ptcp.w:call-paraphase-42.t:call-run_paraphase INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:39.839 wdl.w:ptcp.w:call-paraphase-42.t:call-run_paraphase INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2139.mapped.bam.bai"
2025-09-15 20:24:39.839 wdl.w:ptcp.w:call-paraphase-42.t:call-run_paraphase INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2139.mapped.bam"
2025-09-15 20:24:39.839 wdl.w:ptcp.w:call-paraphase-42.t:call-run_paraphase INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2139"
2025-09-15 20:24:39.840 wdl.w:ptcp.w:call-paraphase-42.t:call-run_paraphase INFO eval :: name: "threads", value: 4
2025-09-15 20:24:39.840 wdl.w:ptcp.w:call-paraphase-42.t:call-run_paraphase INFO eval :: name: "mem_gb", value: 8
2025-09-15 20:24:39.840 wdl.w:ptcp.w:call-paraphase-42.t:call-run_paraphase INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:39.840 wdl.w:ptcp.w:call-paraphase-42.t:call-run_paraphase INFO eval :: name: "out_dir", value: "m84036_250809_035451_s4.bc2139_paraphase"
2025-09-15 20:24:39.841 wdl.w:ptcp.w:call-paraphase-42.t:call-run_paraphase INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 4, memory_reservation: 8000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:39.841 wdl.w:ptcp.w:call-paraphase-42.t:call-run_paraphase WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:39.841 wdl.w:ptcp.w:call-paraphase-42.t:call-run_paraphase INFO provisioned :: seconds_waited: 0, cpu: 4, mem_bytes: 8000000000
2025-09-15 20:24:39.841 wdl.w:ptcp.w:call-paraphase-42.t:call-run_paraphase INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:39.848 wdl.w:ptcp.w:call-sawfish-21.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:37][sawfish][INFO] Processing alignment file '/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2118.minimap2.bam'
2025-09-15 20:24:39.848 wdl.w:ptcp.w:call-sawfish-21.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:37][sawfish][INFO] Finished processing all alignments
2025-09-15 20:24:39.848 wdl.w:ptcp.w:call-sawfish-21.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:37][sawfish][INFO] Writing depth bins to binary file: 'm84036_250809_035451_s4.bc2118_sawfish_discover/depth.mpack'
2025-09-15 20:24:39.848 wdl.w:ptcp.w:call-sawfish-21.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:38][sawfish][INFO] Writing max sv depth genome regions to bed file: 'm84036_250809_035451_s4.bc2118_sawfish_discover/max.depth.bed'
2025-09-15 20:24:39.849 wdl.w:ptcp.w:call-sawfish-21.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:38][sawfish][INFO] Completing breakpoint observation clustering
2025-09-15 20:24:39.849 wdl.w:ptcp.w:call-sawfish-21.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:38][sawfish][INFO] Finished breakpoint observation clustering
2025-09-15 20:24:39.849 wdl.w:ptcp.w:call-sawfish-21.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:38][sawfish][INFO] Consolidating adjacent indel candidates
2025-09-15 20:24:39.849 wdl.w:ptcp.w:call-sawfish-21.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:38][sawfish][INFO] Finding large insertion candidates
2025-09-15 20:24:39.849 wdl.w:ptcp.w:call-sawfish-21.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:38][sawfish][INFO] Writing breakpoint_cluster debug bed file: 'm84036_250809_035451_s4.bc2118_sawfish_discover/debug.breakpoint_clusters.bed'
2025-09-15 20:24:39.849 wdl.w:ptcp.w:call-sawfish-21.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:38][sawfish][INFO] Refining SV Candidates
2025-09-15 20:24:39.849 wdl.w:ptcp.w:call-sawfish-21.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:38][sawfish][INFO] Writing debug assembly region bed file: 'm84036_250809_035451_s4.bc2118_sawfish_discover/assembly.regions.bed'
2025-09-15 20:24:39.849 wdl.w:ptcp.w:call-sawfish-21.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:38][sawfish][INFO] Starting refinement of breakpoint evidence clusters
2025-09-15 20:24:39.849 wdl.w:ptcp.w:call-sawfish-21.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:38][sawfish][INFO] Finished refining all breakpoint evidence clusters
2025-09-15 20:24:39.849 wdl.w:ptcp.w:call-sawfish-21.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:38][sawfish][INFO] Writing all contig alignments to bam file: 'm84036_250809_035451_s4.bc2118_sawfish_discover/contig.alignment.bam'
2025-09-15 20:24:39.849 wdl.w:ptcp.w:call-sawfish-21.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:38][sawfish][INFO] Writing candidate structural variants to file: 'm84036_250809_035451_s4.bc2118_sawfish_discover/candidate.sv.bcf'
2025-09-15 20:24:39.849 wdl.w:ptcp.w:call-sawfish-21.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:38][sawfish][INFO] Writing run statistics to file: 'm84036_250809_035451_s4.bc2118_sawfish_discover/run.stats.json'
2025-09-15 20:24:39.849 wdl.w:ptcp.w:call-sawfish-21.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:38][sawfish][INFO] sawfish completed. Total Runtime: 00:00:17.564
2025-09-15 20:24:39.866 wdl.w:ptcp.w:call-sawfish-32 NOTICE done
2025-09-15 20:24:39.880 wdl.w:ptcp NOTICE finish :: job: "call-sawfish-32"
2025-09-15 20:24:39.880 wdl.w:ptcp INFO output :: job: "call-sawfish-32", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-32/out/m84036_250809_035451_s4.bc2129_sawfish/m84036_250809_035451_s4.bc2129.sv.vcf.gz", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-32/out/m84036_250809_035451_s4.bc2129.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-32/out/m84036_250809_035451_s4.bc2129_sawfish/m84036_250809_035451_s4.bc2129.sv.vcf.gz.tbi", "minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-32/out/m84036_250809_035451_s4.bc2129.minimap2.bam.bai"}
2025-09-15 20:24:39.881 wdl.w:ptcp NOTICE ready :: job: "call-tar_outputs-32", callee: "tar_outputs"
2025-09-15 20:24:39.881 wdl.w:ptcp INFO input :: job: "call-tar_outputs-32", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "sawfish_vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-32/out/m84036_250809_035451_s4.bc2129_sawfish/m84036_250809_035451_s4.bc2129.sv.vcf.gz.tbi", "sawfish_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-32/out/m84036_250809_035451_s4.bc2129_sawfish/m84036_250809_035451_s4.bc2129.sv.vcf.gz", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-32/out/m84036_250809_035451_s4.bc2129.f8inversion.json", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-32/out/m84036_250809_035451_s4.bc2129_paraphase/m84036_250809_035451_s4.bc2129.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-32/out/m84036_250809_035451_s4.bc2129_paraphase/m84036_250809_035451_s4.bc2129.paraphase.bam", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-32/out/m84036_250809_035451_s4.bc2129_paraphase/m84036_250809_035451_s4.bc2129.paraphase.json", "trgt_spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-32/out/m84036_250809_035451_s4.bc2129.trgt.sorted.spanning.bam.bai", "trgt_spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-32/out/m84036_250809_035451_s4.bc2129.trgt.sorted.spanning.bam", "trgt_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-32/out/m84036_250809_035451_s4.bc2129.trgt.vcf", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-32/out/m84036_250809_035451_s4.bc2129.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-32/out/m84036_250809_035451_s4.bc2129.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2129"}
2025-09-15 20:24:39.881 wdl.w:ptcp.w:call-trgt-37.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:34 [ERROR] - No reads found for TRID=PRTS_ARX
2025-09-15 20:24:39.882 wdl.w:ptcp.w:call-trgt-37.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:34 [ERROR] - No reads found for TRID=EIEE1_ARX
2025-09-15 20:24:39.890 wdl.w:ptcp.w:call-sawfish-65 NOTICE workflow start :: name: "sawfish", source: "./sawfish.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-65"
2025-09-15 20:24:39.895 wdl.w:ptcp.w:call-trgt-45.t:call-trgt_plot_meth_waterfall NOTICE done
2025-09-15 20:24:39.897 wdl.w:ptcp.w:call-sawfish-11.t:call-run_sawfish.stderr VERBOSE [M::mm_idx_gen::60.197*1.57] collected minimizers
2025-09-15 20:24:39.908 wdl.w:ptcp.w:call-sawfish-65 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:24:39.908 wdl.w:ptcp.w:call-sawfish-65 INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:24:39.909 wdl.w:ptcp.w:call-sawfish-65 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-65/out/m84036_250809_035451_s4.bc2162.mapped.bam"}
2025-09-15 20:24:39.909 wdl.w:ptcp.w:call-sawfish-65 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-65/out/m84036_250809_035451_s4.bc2162.mapped.bam.bai"}
2025-09-15 20:24:39.909 wdl.w:ptcp.w:call-sawfish-65 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:24:39.909 wdl.w:ptcp.w:call-sawfish-65 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:24:39.909 wdl.w:ptcp.w:call-sawfish-65 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2162"}
2025-09-15 20:24:39.909 wdl.w:ptcp.w:call-sawfish-65 NOTICE ready :: job: "call-run_sawfish", callee: "run_sawfish"
2025-09-15 20:24:39.909 wdl.w:ptcp.w:call-sawfish-65 INFO input :: job: "call-run_sawfish", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-65/out/m84036_250809_035451_s4.bc2162.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-65/out/m84036_250809_035451_s4.bc2162.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2162"}
2025-09-15 20:24:39.924 wdl.w:ptcp.w:call-paraphase-42.t:call-run_paraphase INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-42/call-run_paraphase/_singularity_tmpdir_emf6jejo"
2025-09-15 20:24:39.924 wdl.w:ptcp.w:call-paraphase-42.t:call-run_paraphase INFO Slurm invocation: srun --job-name call-run_paraphase --partition compute,compute9 --cpus-per-task 4 --mem 7629M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-42/call-run_paraphase/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-42/call-run_paraphase/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-42/call-run_paraphase/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-42/call-run_paraphase/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/variant_list/variant_list.GRCh38.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-42/out/m84036_250809_035451_s4.bc2139.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2139.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-42/out/m84036_250809_035451_s4.bc2139.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2139.mapped.bam:ro --bind /ptcp/meta/paraphase/paraphase_config.GRCh38.yaml:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/paraphase_config.GRCh38.yaml:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-42/call-run_paraphase/_singularity_tmpdir_emf6jejo/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-42/call-run_paraphase/_singularity_tmpdir_emf6jejo/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:39.925 wdl.w:ptcp.w:call-paraphase-07.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for f8inv1 for sample m84036_250809_035451_s4.bc2104 at 2025-09-15 20:24:05.027966...
2025-09-15 20:24:39.928 wdl.w:ptcp.w:call-paraphase-07.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for f8inv1 for sample m84036_250809_035451_s4.bc2104 at 2025-09-15 20:24:14.278938...
2025-09-15 20:24:39.929 wdl.w:ptcp.w:call-paraphase-07.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for f8inv1 for sample m84036_250809_035451_s4.bc2104 at 2025-09-15 20:24:14.842720...
2025-09-15 20:24:39.929 wdl.w:ptcp.w:call-paraphase-07.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for hba for sample m84036_250809_035451_s4.bc2104 at 2025-09-15 20:24:19.732865...
2025-09-15 20:24:39.929 wdl.w:ptcp.w:call-paraphase-07.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for hba for sample m84036_250809_035451_s4.bc2104 at 2025-09-15 20:24:20.406784...
2025-09-15 20:24:39.935 wdl.w:ptcp.w:call-trgt-45 NOTICE finish :: job: "call-trgt_plot_meth_waterfall"
2025-09-15 20:24:39.935 wdl.w:ptcp.w:call-trgt-45 INFO output :: job: "call-trgt_plot_meth_waterfall", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-45/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2142.meth_waterfall.trgt_plots.zip"}
2025-09-15 20:24:39.936 wdl.w:ptcp.w:call-trgt-45 INFO visit :: node: "output-images_meth_waterfall", values: {"images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-45/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2142.meth_waterfall.trgt_plots.zip"}
2025-09-15 20:24:39.948 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_meth_allele NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-47/call-trgt_plot_meth_allele", thread: 140607674631744
2025-09-15 20:24:39.964 wdl.w:ptcp.w:call-paraphase-42.t:call-run_paraphase NOTICE slurm_singularity run :: pid: 1202785, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-42/call-run_paraphase/slurm_singularity.log.txt"
2025-09-15 20:24:39.970 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_meth_allele INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:39.970 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_meth_allele INFO input :: name: "waterfall", value: false
2025-09-15 20:24:39.970 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_meth_allele INFO input :: name: "methylation", value: true
2025-09-15 20:24:39.970 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_meth_allele INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:39.970 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_meth_allele INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:39.970 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_meth_allele INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:39.970 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_meth_allele INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2144.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:39.971 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_meth_allele INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2144.trgt.sorted.spanning.bam"
2025-09-15 20:24:39.971 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_meth_allele INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2144.trgt.vcf"
2025-09-15 20:24:39.971 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_meth_allele INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2144"
2025-09-15 20:24:39.971 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_meth_allele INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:39.971 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_meth_allele INFO eval :: name: "plot_type", value: "allele"
2025-09-15 20:24:39.971 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_meth_allele INFO eval :: name: "show", value: "meth"
2025-09-15 20:24:39.971 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_meth_allele INFO eval :: name: "threads", value: 1
2025-09-15 20:24:39.971 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_meth_allele INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:39.971 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_meth_allele INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2144.meth_allele"
2025-09-15 20:24:39.972 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_meth_allele INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:39.972 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_meth_allele WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:39.972 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_meth_allele INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:39.972 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_meth_allele INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:39.990 wdl.w:ptcp.w:call-sawfish-56.t:call-run_sawfish.stderr VERBOSE [M::bam2fq_mainloop] discarded 0 singletons
2025-09-15 20:24:39.990 wdl.w:ptcp.w:call-sawfish-56.t:call-run_sawfish.stderr VERBOSE [M::bam2fq_mainloop] processed 1 reads
2025-09-15 20:24:39.998 wdl.w:ptcp.w:call-trgt-56.t:call-get_reads_overlapping_repeats.slurm_singularity INFO srun: job 51797738 queued and waiting for resources
2025-09-15 20:24:39.998 wdl.w:ptcp.w:call-trgt-56.t:call-get_reads_overlapping_repeats.slurm_singularity INFO srun: job 51797738 has been allocated resources
2025-09-15 20:24:39.998 wdl.w:ptcp.w:call-trgt-56.t:call-get_reads_overlapping_repeats.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:39.999 wdl.w:ptcp.w:call-sawfish-56.t:call-run_sawfish.slurm_singularity INFO srun: job 51797740 queued and waiting for resources
2025-09-15 20:24:40.000 wdl.w:ptcp.w:call-sawfish-56.t:call-run_sawfish.slurm_singularity INFO srun: job 51797740 has been allocated resources
2025-09-15 20:24:40.000 wdl.w:ptcp.w:call-sawfish-56.t:call-run_sawfish.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:40.017 wdl.w:ptcp.w:call-paraphase-56.t:call-run_paraphase.slurm_singularity INFO srun: job 51797739 queued and waiting for resources
2025-09-15 20:24:40.017 wdl.w:ptcp.w:call-paraphase-56.t:call-run_paraphase.slurm_singularity INFO srun: job 51797739 has been allocated resources
2025-09-15 20:24:40.017 wdl.w:ptcp.w:call-paraphase-56.t:call-run_paraphase.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:40.035 wdl.w:ptcp.w:call-trgt-43.t:call-get_reads_overlapping_repeats.slurm_singularity INFO srun: job 51797743 queued and waiting for resources
2025-09-15 20:24:40.035 wdl.w:ptcp.w:call-trgt-43.t:call-get_reads_overlapping_repeats.slurm_singularity INFO srun: job 51797743 has been allocated resources
2025-09-15 20:24:40.036 wdl.w:ptcp.w:call-trgt-43.t:call-get_reads_overlapping_repeats.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:40.036 wdl.w:ptcp.w:call-trgt-43.t:call-get_reads_overlapping_repeats.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:24:40.048 wdl.w:ptcp.w:call-paraphase-26.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for gba for sample m84036_250809_035451_s4.bc2123 at 2025-09-15 20:24:30.641347...
2025-09-15 20:24:40.048 wdl.w:ptcp.w:call-paraphase-26.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for gba for sample m84036_250809_035451_s4.bc2123 at 2025-09-15 20:24:31.139287...
2025-09-15 20:24:40.073 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_meth_allele INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-47/call-trgt_plot_meth_allele/_singularity_tmpdir_3heg7457"
2025-09-15 20:24:40.073 wdl.w:ptcp.w:call-trgt-37.t:call-trgt_plot_meth_waterfall INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2134.meth_waterfall.trgt_plots.zip"
2025-09-15 20:24:40.074 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_meth_allele INFO Slurm invocation: srun --job-name call-trgt_plot_meth_allele --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-47/call-trgt_plot_meth_allele/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-47/call-trgt_plot_meth_allele/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-47/call-trgt_plot_meth_allele/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-47/call-trgt_plot_meth_allele/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-47/call-trgt_genotype/out/m84036_250809_035451_s4.bc2144.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2144.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-47/call-trgt_genotype/out/m84036_250809_035451_s4.bc2144.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2144.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-47/call-trgt_genotype/out/m84036_250809_035451_s4.bc2144.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2144.trgt.sorted.spanning.bam.bai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-47/call-trgt_plot_meth_allele/_singularity_tmpdir_3heg7457/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-47/call-trgt_plot_meth_allele/_singularity_tmpdir_3heg7457/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:40.080 wdl.w:ptcp.w:call-sawfish-03.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:30][sawfish][INFO] Starting sawfish 2.0.3
2025-09-15 20:24:40.080 wdl.w:ptcp.w:call-sawfish-03.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:30][sawfish][INFO] cmdline: sawfish discover --disable-cnv --threads 16 --ref /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa --bam m84036_250809_035451_s4.bc2100.minimap2.bam --output-dir m84036_250809_035451_s4.bc2100_sawfish_discover
2025-09-15 20:24:40.081 wdl.w:ptcp.w:call-sawfish-03.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:30][sawfish][INFO] Running on 16 threads
2025-09-15 20:24:40.081 wdl.w:ptcp.w:call-sawfish-03.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:30][sawfish][INFO] Writing discover settings to file: 'm84036_250809_035451_s4.bc2100_sawfish_discover/discover.settings.json'
2025-09-15 20:24:40.081 wdl.w:ptcp.w:call-sawfish-03.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:30][sawfish][INFO] Reading reference genome from file '/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa'
2025-09-15 20:24:40.081 wdl.w:ptcp.w:call-sawfish-03.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:34][sawfish][INFO] Processing alignment file '/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2100.minimap2.bam'
2025-09-15 20:24:40.081 wdl.w:ptcp.w:call-sawfish-03.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:34][sawfish][INFO] Finished processing all alignments
2025-09-15 20:24:40.081 wdl.w:ptcp.w:call-sawfish-03.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:34][sawfish][INFO] Writing depth bins to binary file: 'm84036_250809_035451_s4.bc2100_sawfish_discover/depth.mpack'
2025-09-15 20:24:40.082 wdl.w:ptcp.w:call-sawfish-03.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:34][sawfish][INFO] Writing max sv depth genome regions to bed file: 'm84036_250809_035451_s4.bc2100_sawfish_discover/max.depth.bed'
2025-09-15 20:24:40.082 wdl.w:ptcp.w:call-sawfish-03.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:34][sawfish][INFO] Completing breakpoint observation clustering
2025-09-15 20:24:40.082 wdl.w:ptcp.w:call-sawfish-03.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:34][sawfish][INFO] Finished breakpoint observation clustering
2025-09-15 20:24:40.082 wdl.w:ptcp.w:call-sawfish-03.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:34][sawfish][INFO] Consolidating adjacent indel candidates
2025-09-15 20:24:40.082 wdl.w:ptcp.w:call-sawfish-03.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:34][sawfish][INFO] Finding large insertion candidates
2025-09-15 20:24:40.082 wdl.w:ptcp.w:call-sawfish-03.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:34][sawfish][INFO] Writing breakpoint_cluster debug bed file: 'm84036_250809_035451_s4.bc2100_sawfish_discover/debug.breakpoint_clusters.bed'
2025-09-15 20:24:40.082 wdl.w:ptcp.w:call-sawfish-03.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:34][sawfish][INFO] Refining SV Candidates
2025-09-15 20:24:40.082 wdl.w:ptcp.w:call-sawfish-03.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:34][sawfish][INFO] Writing debug assembly region bed file: 'm84036_250809_035451_s4.bc2100_sawfish_discover/assembly.regions.bed'
2025-09-15 20:24:40.082 wdl.w:ptcp.w:call-sawfish-03.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:34][sawfish][INFO] Starting refinement of breakpoint evidence clusters
2025-09-15 20:24:40.082 wdl.w:ptcp.w:call-sawfish-03.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:34][sawfish][INFO] Finished refining all breakpoint evidence clusters
2025-09-15 20:24:40.082 wdl.w:ptcp.w:call-sawfish-03.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:34][sawfish][INFO] Writing all contig alignments to bam file: 'm84036_250809_035451_s4.bc2100_sawfish_discover/contig.alignment.bam'
2025-09-15 20:24:40.084 wdl.w:ptcp.w:call-sawfish-03.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:34][sawfish][INFO] Writing candidate structural variants to file: 'm84036_250809_035451_s4.bc2100_sawfish_discover/candidate.sv.bcf'
2025-09-15 20:24:40.084 wdl.w:ptcp.w:call-sawfish-03.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:34][sawfish][INFO] Writing run statistics to file: 'm84036_250809_035451_s4.bc2100_sawfish_discover/run.stats.json'
2025-09-15 20:24:40.085 wdl.w:ptcp.w:call-sawfish-03.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:34][sawfish][INFO] sawfish completed. Total Runtime: 00:00:04.206
2025-09-15 20:24:40.090 wdl.w:ptcp.w:call-trgt-43.t:call-get_reads_overlapping_repeats INFO output :: name: "reads_overlapping_repeats", value: "m84036_250809_035451_s4.bc2140.repeats.bam"
2025-09-15 20:24:40.096 wdl.w:ptcp.w:call-trgt-43.t:call-get_reads_overlapping_repeats INFO output :: name: "reads_overlapping_repeats_bai", value: "m84036_250809_035451_s4.bc2140.repeats.bam.bai"
2025-09-15 20:24:40.098 wdl.w:ptcp.w:call-trgt-56.t:call-trgt_genotype.slurm_singularity INFO srun: job 51797741 queued and waiting for resources
2025-09-15 20:24:40.098 wdl.w:ptcp.w:call-trgt-56.t:call-trgt_genotype.slurm_singularity INFO srun: job 51797741 has been allocated resources
2025-09-15 20:24:40.098 wdl.w:ptcp.w:call-trgt-56.t:call-trgt_genotype.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:40.098 wdl.w:ptcp.w:call-trgt-56.t:call-trgt_genotype.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:24:40.125 wdl.w:ptcp.w:call-paraphase-43.t:call-run_paraphase.slurm_singularity INFO srun: job 51797742 queued and waiting for resources
2025-09-15 20:24:40.125 wdl.w:ptcp.w:call-paraphase-43.t:call-run_paraphase.slurm_singularity INFO srun: job 51797742 has been allocated resources
2025-09-15 20:24:40.125 wdl.w:ptcp.w:call-paraphase-43.t:call-run_paraphase.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:40.128 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_meth_allele NOTICE slurm_singularity run :: pid: 1202795, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-47/call-trgt_plot_meth_allele/slurm_singularity.log.txt"
2025-09-15 20:24:40.142 wdl.w:ptcp.w:call-trgt-48.t:call-get_reads_overlapping_repeats INFO output :: name: "reads_overlapping_repeats", value: "m84036_250809_035451_s4.bc2145.repeats.bam"
2025-09-15 20:24:40.145 wdl.w:ptcp.w:call-trgt-40.t:call-get_reads_overlapping_repeats INFO output :: name: "reads_overlapping_repeats", value: "m84036_250809_035451_s4.bc2137.repeats.bam"
2025-09-15 20:24:40.146 wdl.w:ptcp.w:call-trgt-48.t:call-get_reads_overlapping_repeats INFO output :: name: "reads_overlapping_repeats_bai", value: "m84036_250809_035451_s4.bc2145.repeats.bam.bai"
2025-09-15 20:24:40.150 wdl.w:ptcp.w:call-trgt-40.t:call-get_reads_overlapping_repeats INFO output :: name: "reads_overlapping_repeats_bai", value: "m84036_250809_035451_s4.bc2137.repeats.bam.bai"
2025-09-15 20:24:40.189 wdl.w:ptcp.w:call-trgt-43.t:call-get_reads_overlapping_repeats NOTICE done
2025-09-15 20:24:40.195 wdl.w:ptcp.w:call-trgt-43 NOTICE finish :: job: "call-get_reads_overlapping_repeats"
2025-09-15 20:24:40.195 wdl.w:ptcp.w:call-trgt-43 INFO output :: job: "call-get_reads_overlapping_repeats", values: {"reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-43/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2140.repeats.bam.bai", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-43/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2140.repeats.bam"}
2025-09-15 20:24:40.196 wdl.w:ptcp.w:call-trgt-43 INFO visit :: node: "output-reads_overlapping_repeats", values: {"reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-43/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2140.repeats.bam"}
2025-09-15 20:24:40.196 wdl.w:ptcp.w:call-trgt-43 INFO visit :: node: "output-reads_overlapping_repeats_bai", values: {"reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-43/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2140.repeats.bam.bai"}
2025-09-15 20:24:40.204 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_meth_waterfall NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-47/call-trgt_plot_meth_waterfall", thread: 140608203109952
2025-09-15 20:24:40.214 wdl.w:ptcp.w:call-sawfish-48.t:call-run_sawfish.stderr VERBOSE [M::bam2fq_mainloop] discarded 0 singletons
2025-09-15 20:24:40.215 wdl.w:ptcp.w:call-sawfish-48.t:call-run_sawfish.stderr VERBOSE [M::bam2fq_mainloop] processed 0 reads
2025-09-15 20:24:40.223 wdl.w:ptcp.w:call-trgt-37.t:call-trgt_plot_meth_waterfall NOTICE done
2025-09-15 20:24:40.228 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_meth_waterfall INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:40.228 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_meth_waterfall INFO input :: name: "waterfall", value: true
2025-09-15 20:24:40.229 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_meth_waterfall INFO input :: name: "methylation", value: true
2025-09-15 20:24:40.229 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_meth_waterfall INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:40.229 wdl.w:ptcp.w:call-sawfish-43.t:call-run_sawfish.slurm_singularity INFO srun: job 51797744 queued and waiting for resources
2025-09-15 20:24:40.229 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_meth_waterfall INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:40.229 wdl.w:ptcp.w:call-sawfish-43.t:call-run_sawfish.slurm_singularity INFO srun: job 51797744 has been allocated resources
2025-09-15 20:24:40.229 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_meth_waterfall INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:40.229 wdl.w:ptcp.w:call-sawfish-43.t:call-run_sawfish.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:40.229 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_meth_waterfall INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2144.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:40.229 wdl.w:ptcp.w:call-sawfish-43.t:call-run_sawfish.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:24:40.229 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_meth_waterfall INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2144.trgt.sorted.spanning.bam"
2025-09-15 20:24:40.230 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_meth_waterfall INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2144.trgt.vcf"
2025-09-15 20:24:40.230 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_meth_waterfall INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2144"
2025-09-15 20:24:40.230 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_meth_waterfall INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:40.230 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_meth_waterfall INFO eval :: name: "plot_type", value: "waterfall"
2025-09-15 20:24:40.230 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_meth_waterfall INFO eval :: name: "show", value: "meth"
2025-09-15 20:24:40.230 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_meth_waterfall INFO eval :: name: "threads", value: 1
2025-09-15 20:24:40.230 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_meth_waterfall INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:40.231 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_meth_waterfall INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2144.meth_waterfall"
2025-09-15 20:24:40.231 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_meth_waterfall INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:40.231 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_meth_waterfall WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:40.231 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_meth_waterfall INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:40.232 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_meth_waterfall INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:40.233 wdl.w:ptcp.w:call-trgt-37 NOTICE finish :: job: "call-trgt_plot_meth_waterfall"
2025-09-15 20:24:40.233 wdl.w:ptcp.w:call-trgt-37 INFO output :: job: "call-trgt_plot_meth_waterfall", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-37/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2134.meth_waterfall.trgt_plots.zip"}
2025-09-15 20:24:40.233 wdl.w:ptcp.w:call-trgt-37 INFO visit :: node: "output-images_meth_waterfall", values: {"images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-37/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2134.meth_waterfall.trgt_plots.zip"}
2025-09-15 20:24:40.234 wdl.w:ptcp.w:call-trgt-37 INFO visit :: node: "outputs", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-37/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2134.motifs_waterfall.trgt_plots.zip", "images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-37/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2134.meth_allele.trgt_plots.zip", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-37/call-trgt_genotype/out/m84036_250809_035451_s4.bc2134.trgt.sorted.spanning.bam.bai", "images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-37/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2134.motifs_allele.trgt_plots.zip", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-37/call-trgt_genotype/out/m84036_250809_035451_s4.bc2134.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-37/call-trgt_genotype/out/m84036_250809_035451_s4.bc2134.trgt.vcf", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-37/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2134.repeats.bam", "images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-37/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2134.meth_waterfall.trgt_plots.zip", "reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-37/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2134.repeats.bam.bai"}
2025-09-15 20:24:40.241 wdl.w:ptcp.w:call-trgt-48.t:call-get_reads_overlapping_repeats NOTICE done
2025-09-15 20:24:40.243 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_motifs_allele NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-47/call-trgt_plot_motifs_allele", thread: 140613068518976
2025-09-15 20:24:40.246 wdl.w:ptcp.w:call-trgt-48 NOTICE finish :: job: "call-get_reads_overlapping_repeats"
2025-09-15 20:24:40.246 wdl.w:ptcp.w:call-trgt-48 INFO output :: job: "call-get_reads_overlapping_repeats", values: {"reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-48/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2145.repeats.bam.bai", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-48/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2145.repeats.bam"}
2025-09-15 20:24:40.246 wdl.w:ptcp.w:call-trgt-48 INFO visit :: node: "output-reads_overlapping_repeats", values: {"reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-48/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2145.repeats.bam"}
2025-09-15 20:24:40.246 wdl.w:ptcp.w:call-trgt-48 INFO visit :: node: "output-reads_overlapping_repeats_bai", values: {"reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-48/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2145.repeats.bam.bai"}
2025-09-15 20:24:40.255 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_motifs_waterfall NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-47/call-trgt_plot_motifs_waterfall", thread: 140610879071808
2025-09-15 20:24:40.258 wdl.w:ptcp.w:call-trgt-40.t:call-get_reads_overlapping_repeats NOTICE done
2025-09-15 20:24:40.263 wdl.w:ptcp.w:call-trgt-40 NOTICE finish :: job: "call-get_reads_overlapping_repeats"
2025-09-15 20:24:40.264 wdl.w:ptcp.w:call-trgt-40 INFO output :: job: "call-get_reads_overlapping_repeats", values: {"reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-40/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2137.repeats.bam.bai", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-40/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2137.repeats.bam"}
2025-09-15 20:24:40.264 wdl.w:ptcp.w:call-trgt-40 INFO visit :: node: "output-reads_overlapping_repeats", values: {"reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-40/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2137.repeats.bam"}
2025-09-15 20:24:40.264 wdl.w:ptcp.w:call-trgt-40 INFO visit :: node: "output-reads_overlapping_repeats_bai", values: {"reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-40/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2137.repeats.bam.bai"}
2025-09-15 20:24:40.264 wdl.w:ptcp.w:call-sawfish-57.t:call-run_sawfish.stderr VERBOSE [M::bam2fq_mainloop] discarded 0 singletons
2025-09-15 20:24:40.265 wdl.w:ptcp.w:call-sawfish-57.t:call-run_sawfish.stderr VERBOSE [M::bam2fq_mainloop] processed 1 reads
2025-09-15 20:24:40.266 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_motifs_allele INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:40.266 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_motifs_allele INFO input :: name: "waterfall", value: false
2025-09-15 20:24:40.266 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_motifs_allele INFO input :: name: "methylation", value: false
2025-09-15 20:24:40.266 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_motifs_allele INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:40.266 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_motifs_allele INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:40.266 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_motifs_allele INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:40.267 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_motifs_allele INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2144.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:40.267 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_motifs_allele INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2144.trgt.sorted.spanning.bam"
2025-09-15 20:24:40.267 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_motifs_allele INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2144.trgt.vcf"
2025-09-15 20:24:40.267 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_motifs_allele INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2144"
2025-09-15 20:24:40.267 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_motifs_allele INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:40.267 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_motifs_allele INFO eval :: name: "plot_type", value: "allele"
2025-09-15 20:24:40.267 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_motifs_allele INFO eval :: name: "show", value: "motifs"
2025-09-15 20:24:40.267 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_motifs_allele INFO eval :: name: "threads", value: 1
2025-09-15 20:24:40.268 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_motifs_allele INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:40.268 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_motifs_allele INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2144.motifs_allele"
2025-09-15 20:24:40.268 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_motifs_allele INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:40.268 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_motifs_allele WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:40.268 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_motifs_allele INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:40.269 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_motifs_allele INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:40.278 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_meth_allele NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-50/call-trgt_plot_meth_allele", thread: 140607649453632
2025-09-15 20:24:40.283 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:24:40 [INFO] - Running trgt-4.0.0-429afcd [genotype]
2025-09-15 20:24:40.283 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:24:40 [WARN] - CANVAS_RFC1: Filtered out 1 impure reads
2025-09-15 20:24:40.283 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:24:40 [WARN] - PRTS_ARX: Filtered out 2 impure reads
2025-09-15 20:24:40.284 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:24:40 [WARN] - EIEE1_ARX: Filtered out 1 impure reads
2025-09-15 20:24:40.284 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:24:40 [WARN] - FXS_FMR1: Filtered out 6 impure reads
2025-09-15 20:24:40.284 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:24:40 [WARN] - FRAXE_AFF2: Filtered out 19 impure reads
2025-09-15 20:24:40.284 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:24:40 [WARN] - FRDA_FXN: Filtered out 6 impure reads
2025-09-15 20:24:40.284 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:24:40 [INFO] - Total execution time: 212.10ms
2025-09-15 20:24:40.284 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:24:40 [INFO] - trgt end
2025-09-15 20:24:40.297 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_genotype.slurm_singularity INFO srun: job 51797745 queued and waiting for resources
2025-09-15 20:24:40.297 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_genotype.slurm_singularity INFO srun: job 51797745 has been allocated resources
2025-09-15 20:24:40.297 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_genotype.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:40.297 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_genotype.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:24:40.301 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_motifs_waterfall INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:40.301 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_motifs_waterfall INFO input :: name: "waterfall", value: true
2025-09-15 20:24:40.301 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_motifs_waterfall INFO input :: name: "methylation", value: false
2025-09-15 20:24:40.301 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_motifs_waterfall INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:40.301 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_motifs_waterfall INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:40.301 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_motifs_waterfall INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:40.301 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_motifs_waterfall INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2144.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:40.302 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_motifs_waterfall INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2144.trgt.sorted.spanning.bam"
2025-09-15 20:24:40.302 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_motifs_waterfall INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2144.trgt.vcf"
2025-09-15 20:24:40.302 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_motifs_waterfall INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2144"
2025-09-15 20:24:40.302 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:40.302 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "plot_type", value: "waterfall"
2025-09-15 20:24:40.302 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "show", value: "motifs"
2025-09-15 20:24:40.302 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "threads", value: 1
2025-09-15 20:24:40.302 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:40.303 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2144.motifs_waterfall"
2025-09-15 20:24:40.303 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_motifs_waterfall INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:40.303 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_motifs_waterfall WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:40.303 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_motifs_waterfall INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:40.303 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_motifs_waterfall INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:40.310 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_meth_allele INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:40.310 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_meth_allele INFO input :: name: "waterfall", value: false
2025-09-15 20:24:40.310 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_meth_allele INFO input :: name: "methylation", value: true
2025-09-15 20:24:40.310 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_meth_allele INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:40.310 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_meth_allele INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:40.310 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_meth_allele INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:40.310 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_meth_allele INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2147.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:40.310 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_meth_allele INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2147.trgt.sorted.spanning.bam"
2025-09-15 20:24:40.310 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_meth_allele INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2147.trgt.vcf"
2025-09-15 20:24:40.310 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_meth_allele INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2147"
2025-09-15 20:24:40.311 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_meth_allele INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:40.311 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_meth_allele INFO eval :: name: "plot_type", value: "allele"
2025-09-15 20:24:40.311 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_meth_allele INFO eval :: name: "show", value: "meth"
2025-09-15 20:24:40.311 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_meth_allele INFO eval :: name: "threads", value: 1
2025-09-15 20:24:40.311 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_meth_allele INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:40.311 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_meth_allele INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2147.meth_allele"
2025-09-15 20:24:40.312 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_meth_allele INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:40.312 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_meth_allele WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:40.312 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_meth_allele INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:40.312 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_meth_allele INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:40.335 wdl.w:ptcp.w:call-sawfish-55.t:call-run_sawfish.slurm_singularity INFO srun: job 51797746 queued and waiting for resources
2025-09-15 20:24:40.336 wdl.w:ptcp.w:call-sawfish-55.t:call-run_sawfish.slurm_singularity INFO srun: job 51797746 has been allocated resources
2025-09-15 20:24:40.336 wdl.w:ptcp.w:call-sawfish-55.t:call-run_sawfish.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:40.336 wdl.w:ptcp.w:call-sawfish-55.t:call-run_sawfish.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:24:40.339 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_meth_waterfall INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-47/call-trgt_plot_meth_waterfall/_singularity_tmpdir_yaiwniw5"
2025-09-15 20:24:40.339 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_meth_waterfall INFO Slurm invocation: srun --job-name call-trgt_plot_meth_waterfall --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-47/call-trgt_plot_meth_waterfall/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-47/call-trgt_plot_meth_waterfall/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-47/call-trgt_plot_meth_waterfall/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-47/call-trgt_plot_meth_waterfall/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-47/call-trgt_genotype/out/m84036_250809_035451_s4.bc2144.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2144.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-47/call-trgt_genotype/out/m84036_250809_035451_s4.bc2144.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2144.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-47/call-trgt_genotype/out/m84036_250809_035451_s4.bc2144.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2144.trgt.sorted.spanning.bam.bai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-47/call-trgt_plot_meth_waterfall/_singularity_tmpdir_yaiwniw5/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-47/call-trgt_plot_meth_waterfall/_singularity_tmpdir_yaiwniw5/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:40.340 wdl.w:ptcp.w:call-paraphase-55.t:call-run_paraphase.slurm_singularity INFO srun: job 51797747 queued and waiting for resources
2025-09-15 20:24:40.342 wdl.w:ptcp.w:call-paraphase-55.t:call-run_paraphase.slurm_singularity INFO srun: job 51797747 has been allocated resources
2025-09-15 20:24:40.343 wdl.w:ptcp.w:call-paraphase-55.t:call-run_paraphase.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:40.357 wdl.w:ptcp.w:call-trgt-37 NOTICE done
2025-09-15 20:24:40.361 wdl.w:ptcp NOTICE finish :: job: "call-trgt-37"
2025-09-15 20:24:40.361 wdl.w:ptcp INFO output :: job: "call-trgt-37", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-37/out/m84036_250809_035451_s4.bc2134.motifs_waterfall.trgt_plots.zip", "images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-37/out/m84036_250809_035451_s4.bc2134.meth_allele.trgt_plots.zip", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-37/out/m84036_250809_035451_s4.bc2134.trgt.sorted.spanning.bam.bai", "images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-37/out/m84036_250809_035451_s4.bc2134.motifs_allele.trgt_plots.zip", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-37/out/m84036_250809_035451_s4.bc2134.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-37/out/m84036_250809_035451_s4.bc2134.trgt.vcf", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-37/out/m84036_250809_035451_s4.bc2134.repeats.bam", "images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-37/out/m84036_250809_035451_s4.bc2134.meth_waterfall.trgt_plots.zip", "reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-37/out/m84036_250809_035451_s4.bc2134.repeats.bam.bai"}
2025-09-15 20:24:40.366 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_motifs_allele INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-47/call-trgt_plot_motifs_allele/_singularity_tmpdir_rsgiwio5"
2025-09-15 20:24:40.366 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_motifs_allele INFO Slurm invocation: srun --job-name call-trgt_plot_motifs_allele --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-47/call-trgt_plot_motifs_allele/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-47/call-trgt_plot_motifs_allele/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-47/call-trgt_plot_motifs_allele/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-47/call-trgt_plot_motifs_allele/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-47/call-trgt_genotype/out/m84036_250809_035451_s4.bc2144.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2144.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-47/call-trgt_genotype/out/m84036_250809_035451_s4.bc2144.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2144.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-47/call-trgt_genotype/out/m84036_250809_035451_s4.bc2144.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2144.trgt.sorted.spanning.bam.bai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-47/call-trgt_plot_motifs_allele/_singularity_tmpdir_rsgiwio5/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-47/call-trgt_plot_motifs_allele/_singularity_tmpdir_rsgiwio5/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:40.387 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_motifs_allele NOTICE slurm_singularity run :: pid: 1202799, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-47/call-trgt_plot_motifs_allele/slurm_singularity.log.txt"
2025-09-15 20:24:40.388 wdl.w:ptcp.w:call-trgt-65 NOTICE workflow start :: name: "trgt", source: "./trgt.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-65"
2025-09-15 20:24:40.389 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:24:40 [INFO] - Running trgt-4.0.0-429afcd [genotype]
2025-09-15 20:24:40.389 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_meth_waterfall NOTICE slurm_singularity run :: pid: 1202798, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-47/call-trgt_plot_meth_waterfall/slurm_singularity.log.txt"
2025-09-15 20:24:40.389 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:24:40 [WARN] - EIEE1_ARX: Filtered out 2 impure reads
2025-09-15 20:24:40.390 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:24:40 [WARN] - FXS_FMR1: Filtered out 4 impure reads
2025-09-15 20:24:40.390 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:24:40 [WARN] - FRAXE_AFF2: Filtered out 15 impure reads
2025-09-15 20:24:40.390 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:24:40 [WARN] - FRDA_FXN: Filtered out 2 impure reads
2025-09-15 20:24:40.390 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:24:40 [INFO] - Total execution time: 169.51ms
2025-09-15 20:24:40.390 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:24:40 [INFO] - trgt end
2025-09-15 20:24:40.399 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_genotype.slurm_singularity INFO srun: job 51797749 queued and waiting for resources
2025-09-15 20:24:40.399 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_genotype.slurm_singularity INFO srun: job 51797749 has been allocated resources
2025-09-15 20:24:40.399 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_genotype.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:40.399 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_genotype.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:24:40.401 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_motifs_waterfall INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-47/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_t0lv0w1h"
2025-09-15 20:24:40.402 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_motifs_waterfall INFO Slurm invocation: srun --job-name call-trgt_plot_motifs_waterfall --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-47/call-trgt_plot_motifs_waterfall/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-47/call-trgt_plot_motifs_waterfall/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-47/call-trgt_plot_motifs_waterfall/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-47/call-trgt_plot_motifs_waterfall/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-47/call-trgt_genotype/out/m84036_250809_035451_s4.bc2144.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2144.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-47/call-trgt_genotype/out/m84036_250809_035451_s4.bc2144.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2144.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-47/call-trgt_genotype/out/m84036_250809_035451_s4.bc2144.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2144.trgt.sorted.spanning.bam.bai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-47/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_t0lv0w1h/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-47/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_t0lv0w1h/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:40.404 wdl.w:ptcp.w:call-trgt-65 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:24:40.404 wdl.w:ptcp.w:call-trgt-65 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-65/out/m84036_250809_035451_s4.bc2162.mapped.bam"}
2025-09-15 20:24:40.404 wdl.w:ptcp.w:call-trgt-65 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-65/out/m84036_250809_035451_s4.bc2162.mapped.bam.bai"}
2025-09-15 20:24:40.404 wdl.w:ptcp.w:call-trgt-65 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:24:40.404 wdl.w:ptcp.w:call-trgt-65 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:24:40.404 wdl.w:ptcp.w:call-trgt-65 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2162"}
2025-09-15 20:24:40.404 wdl.w:ptcp.w:call-trgt-65 INFO visit :: node: "decl-sex", values: {"sex": "F"}
2025-09-15 20:24:40.404 wdl.w:ptcp.w:call-trgt-65 INFO visit :: node: "decl-trgt_bed", values: {"trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"}
2025-09-15 20:24:40.405 wdl.w:ptcp.w:call-trgt-65 NOTICE ready :: job: "call-get_reads_overlapping_repeats", callee: "get_reads_overlapping_repeats"
2025-09-15 20:24:40.405 wdl.w:ptcp.w:call-trgt-65 INFO input :: job: "call-get_reads_overlapping_repeats", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-65/out/m84036_250809_035451_s4.bc2162.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-65/out/m84036_250809_035451_s4.bc2162.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2162"}
2025-09-15 20:24:40.405 wdl.w:ptcp.w:call-trgt-65 NOTICE ready :: job: "call-trgt_genotype", callee: "trgt_genotype"
2025-09-15 20:24:40.405 wdl.w:ptcp.w:call-trgt-65 INFO input :: job: "call-trgt_genotype", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-65/out/m84036_250809_035451_s4.bc2162.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-65/out/m84036_250809_035451_s4.bc2162.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2162"}
2025-09-15 20:24:40.410 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_meth_allele INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-50/call-trgt_plot_meth_allele/_singularity_tmpdir_ppqjzmsh"
2025-09-15 20:24:40.410 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_meth_allele INFO Slurm invocation: srun --job-name call-trgt_plot_meth_allele --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-50/call-trgt_plot_meth_allele/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-50/call-trgt_plot_meth_allele/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-50/call-trgt_plot_meth_allele/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-50/call-trgt_plot_meth_allele/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-50/call-trgt_genotype/out/m84036_250809_035451_s4.bc2147.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2147.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-50/call-trgt_genotype/out/m84036_250809_035451_s4.bc2147.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2147.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-50/call-trgt_genotype/out/m84036_250809_035451_s4.bc2147.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2147.trgt.sorted.spanning.bam.bai:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-50/call-trgt_plot_meth_allele/_singularity_tmpdir_ppqjzmsh/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-50/call-trgt_plot_meth_allele/_singularity_tmpdir_ppqjzmsh/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:40.419 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_meth_allele NOTICE slurm_singularity run :: pid: 1202810, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-50/call-trgt_plot_meth_allele/slurm_singularity.log.txt"
2025-09-15 20:24:40.419 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_motifs_waterfall NOTICE slurm_singularity run :: pid: 1202809, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-47/call-trgt_plot_motifs_waterfall/slurm_singularity.log.txt"
2025-09-15 20:24:40.436 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_genotype INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2152.trgt.vcf"
2025-09-15 20:24:40.440 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_genotype INFO output :: name: "spanning_bam", value: "m84036_250809_035451_s4.bc2152.trgt.sorted.spanning.bam"
2025-09-15 20:24:40.441 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_genotype INFO output :: name: "spanning_bam_bai", value: "m84036_250809_035451_s4.bc2152.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:40.458 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_genotype INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2140.trgt.vcf"
2025-09-15 20:24:40.460 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_genotype INFO output :: name: "spanning_bam", value: "m84036_250809_035451_s4.bc2140.trgt.sorted.spanning.bam"
2025-09-15 20:24:40.462 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_genotype INFO output :: name: "spanning_bam_bai", value: "m84036_250809_035451_s4.bc2140.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:40.510 wdl.w:ptcp.w:call-trgt-55.t:call-get_reads_overlapping_repeats.slurm_singularity INFO srun: job 51797748 queued and waiting for resources
2025-09-15 20:24:40.510 wdl.w:ptcp.w:call-trgt-55.t:call-get_reads_overlapping_repeats.slurm_singularity INFO srun: job 51797748 has been allocated resources
2025-09-15 20:24:40.510 wdl.w:ptcp.w:call-trgt-55.t:call-get_reads_overlapping_repeats.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:40.518 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_genotype NOTICE done
2025-09-15 20:24:40.525 wdl.w:ptcp.w:call-trgt-55 NOTICE finish :: job: "call-trgt_genotype"
2025-09-15 20:24:40.525 wdl.w:ptcp.w:call-trgt-55 INFO output :: job: "call-trgt_genotype", values: {"spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-55/call-trgt_genotype/out/m84036_250809_035451_s4.bc2152.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-55/call-trgt_genotype/out/m84036_250809_035451_s4.bc2152.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-55/call-trgt_genotype/out/m84036_250809_035451_s4.bc2152.trgt.vcf"}
2025-09-15 20:24:40.526 wdl.w:ptcp.w:call-trgt-55 NOTICE ready :: job: "call-trgt_plot_meth_allele", callee: "trgt_plot"
2025-09-15 20:24:40.526 wdl.w:ptcp.w:call-trgt-55 INFO input :: job: "call-trgt_plot_meth_allele", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": false, "methylation": true, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-55/call-trgt_genotype/out/m84036_250809_035451_s4.bc2152.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-55/call-trgt_genotype/out/m84036_250809_035451_s4.bc2152.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-55/call-trgt_genotype/out/m84036_250809_035451_s4.bc2152.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2152"}
2025-09-15 20:24:40.527 wdl.w:ptcp.w:call-trgt-55 NOTICE ready :: job: "call-trgt_plot_meth_waterfall", callee: "trgt_plot"
2025-09-15 20:24:40.527 wdl.w:ptcp.w:call-trgt-55 INFO input :: job: "call-trgt_plot_meth_waterfall", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": true, "methylation": true, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-55/call-trgt_genotype/out/m84036_250809_035451_s4.bc2152.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-55/call-trgt_genotype/out/m84036_250809_035451_s4.bc2152.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-55/call-trgt_genotype/out/m84036_250809_035451_s4.bc2152.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2152"}
2025-09-15 20:24:40.528 wdl.w:ptcp.w:call-trgt-55 NOTICE ready :: job: "call-trgt_plot_motifs_allele", callee: "trgt_plot"
2025-09-15 20:24:40.528 wdl.w:ptcp.w:call-trgt-55 INFO input :: job: "call-trgt_plot_motifs_allele", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": false, "methylation": false, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-55/call-trgt_genotype/out/m84036_250809_035451_s4.bc2152.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-55/call-trgt_genotype/out/m84036_250809_035451_s4.bc2152.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-55/call-trgt_genotype/out/m84036_250809_035451_s4.bc2152.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2152"}
2025-09-15 20:24:40.529 wdl.w:ptcp.w:call-trgt-55 NOTICE ready :: job: "call-trgt_plot_motifs_waterfall", callee: "trgt_plot"
2025-09-15 20:24:40.529 wdl.w:ptcp.w:call-trgt-55 INFO input :: job: "call-trgt_plot_motifs_waterfall", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": true, "methylation": false, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-55/call-trgt_genotype/out/m84036_250809_035451_s4.bc2152.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-55/call-trgt_genotype/out/m84036_250809_035451_s4.bc2152.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-55/call-trgt_genotype/out/m84036_250809_035451_s4.bc2152.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2152"}
2025-09-15 20:24:40.530 wdl.w:ptcp.w:call-trgt-55 INFO visit :: node: "output-spanning_bam", values: {"spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-55/call-trgt_genotype/out/m84036_250809_035451_s4.bc2152.trgt.sorted.spanning.bam"}
2025-09-15 20:24:40.530 wdl.w:ptcp.w:call-trgt-55 INFO visit :: node: "output-spanning_bam_bai", values: {"spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-55/call-trgt_genotype/out/m84036_250809_035451_s4.bc2152.trgt.sorted.spanning.bam.bai"}
2025-09-15 20:24:40.530 wdl.w:ptcp.w:call-trgt-55 INFO visit :: node: "output-vcf", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-55/call-trgt_genotype/out/m84036_250809_035451_s4.bc2152.trgt.vcf"}
2025-09-15 20:24:40.534 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_meth_waterfall NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-50/call-trgt_plot_meth_waterfall", thread: 140609302029888
2025-09-15 20:24:40.540 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_genotype NOTICE done
2025-09-15 20:24:40.555 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_meth_waterfall INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:40.555 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_meth_waterfall INFO input :: name: "waterfall", value: true
2025-09-15 20:24:40.555 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_meth_waterfall INFO input :: name: "methylation", value: true
2025-09-15 20:24:40.556 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_meth_waterfall INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:40.556 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_meth_waterfall INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:40.556 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_meth_waterfall INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:40.556 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_meth_waterfall INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2147.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:40.556 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_meth_waterfall INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2147.trgt.sorted.spanning.bam"
2025-09-15 20:24:40.556 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_meth_waterfall INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2147.trgt.vcf"
2025-09-15 20:24:40.556 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_meth_waterfall INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2147"
2025-09-15 20:24:40.556 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_meth_waterfall INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:40.556 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_meth_waterfall INFO eval :: name: "plot_type", value: "waterfall"
2025-09-15 20:24:40.556 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_meth_waterfall INFO eval :: name: "show", value: "meth"
2025-09-15 20:24:40.556 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_meth_waterfall INFO eval :: name: "threads", value: 1
2025-09-15 20:24:40.557 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_meth_waterfall INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:40.557 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_meth_waterfall INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2147.meth_waterfall"
2025-09-15 20:24:40.557 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_meth_waterfall INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:40.557 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_meth_waterfall WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:40.557 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_meth_waterfall INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:40.558 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_meth_waterfall INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:40.568 wdl.w:ptcp.w:call-trgt-55.t:call-get_reads_overlapping_repeats INFO output :: name: "reads_overlapping_repeats", value: "m84036_250809_035451_s4.bc2152.repeats.bam"
2025-09-15 20:24:40.571 wdl.w:ptcp.w:call-trgt-55.t:call-get_reads_overlapping_repeats INFO output :: name: "reads_overlapping_repeats_bai", value: "m84036_250809_035451_s4.bc2152.repeats.bam.bai"
2025-09-15 20:24:40.572 wdl.w:ptcp.w:call-trgt-43 NOTICE finish :: job: "call-trgt_genotype"
2025-09-15 20:24:40.572 wdl.w:ptcp.w:call-trgt-43 INFO output :: job: "call-trgt_genotype", values: {"spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-43/call-trgt_genotype/out/m84036_250809_035451_s4.bc2140.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-43/call-trgt_genotype/out/m84036_250809_035451_s4.bc2140.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-43/call-trgt_genotype/out/m84036_250809_035451_s4.bc2140.trgt.vcf"}
2025-09-15 20:24:40.573 wdl.w:ptcp.w:call-trgt-43 NOTICE ready :: job: "call-trgt_plot_meth_allele", callee: "trgt_plot"
2025-09-15 20:24:40.573 wdl.w:ptcp.w:call-trgt-43 INFO input :: job: "call-trgt_plot_meth_allele", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": false, "methylation": true, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-43/call-trgt_genotype/out/m84036_250809_035451_s4.bc2140.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-43/call-trgt_genotype/out/m84036_250809_035451_s4.bc2140.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-43/call-trgt_genotype/out/m84036_250809_035451_s4.bc2140.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2140"}
2025-09-15 20:24:40.575 wdl.w:ptcp.w:call-trgt-43 NOTICE ready :: job: "call-trgt_plot_meth_waterfall", callee: "trgt_plot"
2025-09-15 20:24:40.576 wdl.w:ptcp.w:call-trgt-43 INFO input :: job: "call-trgt_plot_meth_waterfall", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": true, "methylation": true, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-43/call-trgt_genotype/out/m84036_250809_035451_s4.bc2140.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-43/call-trgt_genotype/out/m84036_250809_035451_s4.bc2140.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-43/call-trgt_genotype/out/m84036_250809_035451_s4.bc2140.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2140"}
2025-09-15 20:24:40.577 wdl.w:ptcp.w:call-trgt-43 NOTICE ready :: job: "call-trgt_plot_motifs_allele", callee: "trgt_plot"
2025-09-15 20:24:40.577 wdl.w:ptcp.w:call-trgt-43 INFO input :: job: "call-trgt_plot_motifs_allele", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": false, "methylation": false, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-43/call-trgt_genotype/out/m84036_250809_035451_s4.bc2140.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-43/call-trgt_genotype/out/m84036_250809_035451_s4.bc2140.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-43/call-trgt_genotype/out/m84036_250809_035451_s4.bc2140.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2140"}
2025-09-15 20:24:40.578 wdl.w:ptcp.w:call-trgt-43 NOTICE ready :: job: "call-trgt_plot_motifs_waterfall", callee: "trgt_plot"
2025-09-15 20:24:40.578 wdl.w:ptcp.w:call-trgt-43 INFO input :: job: "call-trgt_plot_motifs_waterfall", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": true, "methylation": false, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-43/call-trgt_genotype/out/m84036_250809_035451_s4.bc2140.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-43/call-trgt_genotype/out/m84036_250809_035451_s4.bc2140.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-43/call-trgt_genotype/out/m84036_250809_035451_s4.bc2140.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2140"}
2025-09-15 20:24:40.579 wdl.w:ptcp.w:call-trgt-43 INFO visit :: node: "output-spanning_bam", values: {"spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-43/call-trgt_genotype/out/m84036_250809_035451_s4.bc2140.trgt.sorted.spanning.bam"}
2025-09-15 20:24:40.579 wdl.w:ptcp.w:call-trgt-43 INFO visit :: node: "output-spanning_bam_bai", values: {"spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-43/call-trgt_genotype/out/m84036_250809_035451_s4.bc2140.trgt.sorted.spanning.bam.bai"}
2025-09-15 20:24:40.579 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_motifs_allele NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-50/call-trgt_plot_motifs_allele", thread: 140608773551680
2025-09-15 20:24:40.579 wdl.w:ptcp.w:call-trgt-43 INFO visit :: node: "output-vcf", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-43/call-trgt_genotype/out/m84036_250809_035451_s4.bc2140.trgt.vcf"}
2025-09-15 20:24:40.583 wdl.w:ptcp.w:call-trgt-57.t:call-get_reads_overlapping_repeats INFO output :: name: "reads_overlapping_repeats", value: "m84036_250809_035451_s4.bc2154.repeats.bam"
2025-09-15 20:24:40.588 wdl.w:ptcp.w:call-trgt-57.t:call-get_reads_overlapping_repeats INFO output :: name: "reads_overlapping_repeats_bai", value: "m84036_250809_035451_s4.bc2154.repeats.bam.bai"
2025-09-15 20:24:40.599 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_motifs_allele INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:40.599 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_motifs_allele INFO input :: name: "waterfall", value: false
2025-09-15 20:24:40.599 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_motifs_allele INFO input :: name: "methylation", value: false
2025-09-15 20:24:40.599 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_motifs_allele INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:40.599 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_motifs_allele INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:40.599 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_motifs_allele INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:40.600 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_motifs_allele INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2147.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:40.600 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_motifs_allele INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2147.trgt.sorted.spanning.bam"
2025-09-15 20:24:40.600 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_motifs_allele INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2147.trgt.vcf"
2025-09-15 20:24:40.600 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_motifs_allele INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2147"
2025-09-15 20:24:40.600 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_motifs_allele INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:40.600 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_motifs_allele INFO eval :: name: "plot_type", value: "allele"
2025-09-15 20:24:40.600 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_motifs_allele INFO eval :: name: "show", value: "motifs"
2025-09-15 20:24:40.600 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_motifs_allele INFO eval :: name: "threads", value: 1
2025-09-15 20:24:40.601 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_motifs_allele INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:40.601 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_motifs_allele INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2147.motifs_allele"
2025-09-15 20:24:40.602 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_motifs_allele INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:40.602 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_motifs_allele WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:40.602 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_motifs_allele INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:40.602 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_motifs_allele INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:40.636 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_meth_waterfall INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-50/call-trgt_plot_meth_waterfall/_singularity_tmpdir_pge1zi6f"
2025-09-15 20:24:40.637 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_meth_waterfall INFO Slurm invocation: srun --job-name call-trgt_plot_meth_waterfall --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-50/call-trgt_plot_meth_waterfall/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-50/call-trgt_plot_meth_waterfall/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-50/call-trgt_plot_meth_waterfall/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-50/call-trgt_plot_meth_waterfall/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-50/call-trgt_genotype/out/m84036_250809_035451_s4.bc2147.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2147.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-50/call-trgt_genotype/out/m84036_250809_035451_s4.bc2147.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2147.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-50/call-trgt_genotype/out/m84036_250809_035451_s4.bc2147.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2147.trgt.sorted.spanning.bam.bai:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-50/call-trgt_plot_meth_waterfall/_singularity_tmpdir_pge1zi6f/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-50/call-trgt_plot_meth_waterfall/_singularity_tmpdir_pge1zi6f/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:40.643 wdl.w:ptcp.w:call-trgt-55.t:call-get_reads_overlapping_repeats NOTICE done
2025-09-15 20:24:40.647 wdl.w:ptcp.w:call-trgt-55 NOTICE finish :: job: "call-get_reads_overlapping_repeats"
2025-09-15 20:24:40.647 wdl.w:ptcp.w:call-trgt-55 INFO output :: job: "call-get_reads_overlapping_repeats", values: {"reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-55/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2152.repeats.bam.bai", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-55/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2152.repeats.bam"}
2025-09-15 20:24:40.648 wdl.w:ptcp.w:call-trgt-55 INFO visit :: node: "output-reads_overlapping_repeats", values: {"reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-55/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2152.repeats.bam"}
2025-09-15 20:24:40.648 wdl.w:ptcp.w:call-trgt-55 INFO visit :: node: "output-reads_overlapping_repeats_bai", values: {"reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-55/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2152.repeats.bam.bai"}
2025-09-15 20:24:40.653 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_motifs_waterfall NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-50/call-trgt_plot_motifs_waterfall", thread: 140610367379008
2025-09-15 20:24:40.662 wdl.w:ptcp.w:call-trgt-57.t:call-get_reads_overlapping_repeats NOTICE done
2025-09-15 20:24:40.676 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_meth_waterfall NOTICE slurm_singularity run :: pid: 1202835, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-50/call-trgt_plot_meth_waterfall/slurm_singularity.log.txt"
2025-09-15 20:24:40.681 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_motifs_allele INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-50/call-trgt_plot_motifs_allele/_singularity_tmpdir_3emec5ba"
2025-09-15 20:24:40.681 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_motifs_allele INFO Slurm invocation: srun --job-name call-trgt_plot_motifs_allele --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-50/call-trgt_plot_motifs_allele/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-50/call-trgt_plot_motifs_allele/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-50/call-trgt_plot_motifs_allele/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-50/call-trgt_plot_motifs_allele/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-50/call-trgt_genotype/out/m84036_250809_035451_s4.bc2147.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2147.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-50/call-trgt_genotype/out/m84036_250809_035451_s4.bc2147.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2147.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-50/call-trgt_genotype/out/m84036_250809_035451_s4.bc2147.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2147.trgt.sorted.spanning.bam.bai:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-50/call-trgt_plot_motifs_allele/_singularity_tmpdir_3emec5ba/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-50/call-trgt_plot_motifs_allele/_singularity_tmpdir_3emec5ba/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:40.691 wdl.w:ptcp.w:call-trgt-57 NOTICE finish :: job: "call-get_reads_overlapping_repeats"
2025-09-15 20:24:40.692 wdl.w:ptcp.w:call-trgt-57 INFO output :: job: "call-get_reads_overlapping_repeats", values: {"reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-57/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2154.repeats.bam.bai", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-57/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2154.repeats.bam"}
2025-09-15 20:24:40.694 wdl.w:ptcp.w:call-trgt-57 INFO visit :: node: "output-reads_overlapping_repeats", values: {"reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-57/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2154.repeats.bam"}
2025-09-15 20:24:40.694 wdl.w:ptcp.w:call-trgt-57 INFO visit :: node: "output-reads_overlapping_repeats_bai", values: {"reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-57/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2154.repeats.bam.bai"}
2025-09-15 20:24:40.695 wdl.w:ptcp.w:call-paraphase-63.t:call-run_paraphase.stderr VERBOSE INFO:root:Processing sample m84036_250809_035451_s4.bc2160 at 2025-09-15 20:24:37.812106...
2025-09-15 20:24:40.696 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_motifs_allele NOTICE slurm_singularity run :: pid: 1202836, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-50/call-trgt_plot_motifs_allele/slurm_singularity.log.txt"
2025-09-15 20:24:40.696 wdl.w:ptcp.w:call-paraphase-63.t:call-run_paraphase.stderr VERBOSE INFO:root:Checking sample sex at 2025-09-15 20:24:37.813148...
2025-09-15 20:24:40.696 wdl.w:ptcp.w:call-paraphase-63.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for smn1 for sample m84036_250809_035451_s4.bc2160 at 2025-09-15 20:24:37.849406...
2025-09-15 20:24:40.696 wdl.w:ptcp.w:call-paraphase-63.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for smn1 for sample m84036_250809_035451_s4.bc2160 at 2025-09-15 20:24:37.849825...
2025-09-15 20:24:40.696 wdl.w:ptcp.w:call-paraphase-63.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for cyp21 for sample m84036_250809_035451_s4.bc2160 at 2025-09-15 20:24:37.849419...
2025-09-15 20:24:40.697 wdl.w:ptcp.w:call-paraphase-63.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for cyp21 for sample m84036_250809_035451_s4.bc2160 at 2025-09-15 20:24:37.849915...
2025-09-15 20:24:40.697 wdl.w:ptcp.w:call-paraphase-63.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for gba for sample m84036_250809_035451_s4.bc2160 at 2025-09-15 20:24:37.849789...
2025-09-15 20:24:40.697 wdl.w:ptcp.w:call-paraphase-63.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for gba for sample m84036_250809_035451_s4.bc2160 at 2025-09-15 20:24:37.850245...
2025-09-15 20:24:40.697 wdl.w:ptcp.w:call-paraphase-63.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for hba for sample m84036_250809_035451_s4.bc2160 at 2025-09-15 20:24:37.850895...
2025-09-15 20:24:40.697 wdl.w:ptcp.w:call-paraphase-63.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for hba for sample m84036_250809_035451_s4.bc2160 at 2025-09-15 20:24:37.851243...
2025-09-15 20:24:40.700 wdl.w:ptcp.w:call-trgt-52.t:call-trgt_plot_meth_allele NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-52/call-trgt_plot_meth_allele", thread: 140609838900800
2025-09-15 20:24:40.702 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_motifs_waterfall INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:40.702 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_motifs_waterfall INFO input :: name: "waterfall", value: true
2025-09-15 20:24:40.702 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_motifs_waterfall INFO input :: name: "methylation", value: false
2025-09-15 20:24:40.702 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_motifs_waterfall INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:40.702 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_motifs_waterfall INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:40.702 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_motifs_waterfall INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:40.702 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_motifs_waterfall INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2147.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:40.702 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_motifs_waterfall INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2147.trgt.sorted.spanning.bam"
2025-09-15 20:24:40.702 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_motifs_waterfall INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2147.trgt.vcf"
2025-09-15 20:24:40.703 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_motifs_waterfall INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2147"
2025-09-15 20:24:40.703 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:40.703 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "plot_type", value: "waterfall"
2025-09-15 20:24:40.703 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "show", value: "motifs"
2025-09-15 20:24:40.703 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "threads", value: 1
2025-09-15 20:24:40.703 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:40.703 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2147.motifs_waterfall"
2025-09-15 20:24:40.704 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_motifs_waterfall INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:40.704 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_motifs_waterfall WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:40.704 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_motifs_waterfall INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:40.704 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_motifs_waterfall INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:40.722 wdl.w:ptcp.w:call-trgt-52.t:call-trgt_plot_meth_allele INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:40.722 wdl.w:ptcp.w:call-trgt-52.t:call-trgt_plot_meth_allele INFO input :: name: "waterfall", value: false
2025-09-15 20:24:40.723 wdl.w:ptcp.w:call-trgt-52.t:call-trgt_plot_meth_allele INFO input :: name: "methylation", value: true
2025-09-15 20:24:40.723 wdl.w:ptcp.w:call-trgt-52.t:call-trgt_plot_meth_allele INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:40.723 wdl.w:ptcp.w:call-trgt-52.t:call-trgt_plot_meth_allele INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:40.723 wdl.w:ptcp.w:call-trgt-52.t:call-trgt_plot_meth_allele INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:40.723 wdl.w:ptcp.w:call-trgt-52.t:call-trgt_plot_meth_allele INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2149.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:40.723 wdl.w:ptcp.w:call-trgt-52.t:call-trgt_plot_meth_allele INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2149.trgt.sorted.spanning.bam"
2025-09-15 20:24:40.723 wdl.w:ptcp.w:call-trgt-52.t:call-trgt_plot_meth_allele INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2149.trgt.vcf"
2025-09-15 20:24:40.723 wdl.w:ptcp.w:call-trgt-52.t:call-trgt_plot_meth_allele INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2149"
2025-09-15 20:24:40.723 wdl.w:ptcp.w:call-trgt-52.t:call-trgt_plot_meth_allele INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:40.723 wdl.w:ptcp.w:call-trgt-52.t:call-trgt_plot_meth_allele INFO eval :: name: "plot_type", value: "allele"
2025-09-15 20:24:40.723 wdl.w:ptcp.w:call-trgt-52.t:call-trgt_plot_meth_allele INFO eval :: name: "show", value: "meth"
2025-09-15 20:24:40.724 wdl.w:ptcp.w:call-trgt-52.t:call-trgt_plot_meth_allele INFO eval :: name: "threads", value: 1
2025-09-15 20:24:40.724 wdl.w:ptcp.w:call-trgt-52.t:call-trgt_plot_meth_allele INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:40.724 wdl.w:ptcp.w:call-trgt-52.t:call-trgt_plot_meth_allele INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2149.meth_allele"
2025-09-15 20:24:40.724 wdl.w:ptcp.w:call-trgt-52.t:call-trgt_plot_meth_allele INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:40.724 wdl.w:ptcp.w:call-trgt-52.t:call-trgt_plot_meth_allele WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:40.725 wdl.w:ptcp.w:call-trgt-52.t:call-trgt_plot_meth_allele INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:40.725 wdl.w:ptcp.w:call-trgt-52.t:call-trgt_plot_meth_allele INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:40.786 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_motifs_waterfall INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-50/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_ia3trtdu"
2025-09-15 20:24:40.786 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_motifs_waterfall INFO Slurm invocation: srun --job-name call-trgt_plot_motifs_waterfall --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-50/call-trgt_plot_motifs_waterfall/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-50/call-trgt_plot_motifs_waterfall/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-50/call-trgt_plot_motifs_waterfall/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-50/call-trgt_plot_motifs_waterfall/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-50/call-trgt_genotype/out/m84036_250809_035451_s4.bc2147.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2147.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-50/call-trgt_genotype/out/m84036_250809_035451_s4.bc2147.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2147.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-50/call-trgt_genotype/out/m84036_250809_035451_s4.bc2147.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2147.trgt.sorted.spanning.bam.bai:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-50/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_ia3trtdu/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-50/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_ia3trtdu/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:40.803 wdl.w:ptcp.w:call-trgt-45.t:call-trgt_plot_motifs_waterfall INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2142.motifs_waterfall.trgt_plots.zip"
2025-09-15 20:24:40.805 wdl.w:ptcp.w:call-trgt-52.t:call-trgt_plot_meth_allele INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-52/call-trgt_plot_meth_allele/_singularity_tmpdir_9pkjfjd7"
2025-09-15 20:24:40.805 wdl.w:ptcp.w:call-trgt-52.t:call-trgt_plot_meth_allele INFO Slurm invocation: srun --job-name call-trgt_plot_meth_allele --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-52/call-trgt_plot_meth_allele/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-52/call-trgt_plot_meth_allele/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-52/call-trgt_plot_meth_allele/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-52/call-trgt_plot_meth_allele/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-52/call-trgt_genotype/out/m84036_250809_035451_s4.bc2149.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2149.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-52/call-trgt_genotype/out/m84036_250809_035451_s4.bc2149.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2149.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-52/call-trgt_genotype/out/m84036_250809_035451_s4.bc2149.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2149.trgt.sorted.spanning.bam:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-52/call-trgt_plot_meth_allele/_singularity_tmpdir_9pkjfjd7/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-52/call-trgt_plot_meth_allele/_singularity_tmpdir_9pkjfjd7/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:40.811 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_motifs_waterfall NOTICE slurm_singularity run :: pid: 1202850, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-50/call-trgt_plot_motifs_waterfall/slurm_singularity.log.txt"
2025-09-15 20:24:40.812 wdl.w:ptcp.w:call-trgt-52.t:call-trgt_plot_meth_allele NOTICE slurm_singularity run :: pid: 1202851, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-52/call-trgt_plot_meth_allele/slurm_singularity.log.txt"
2025-09-15 20:24:40.911 wdl.w:ptcp.w:call-trgt-45.t:call-trgt_plot_motifs_waterfall NOTICE done
2025-09-15 20:24:40.918 wdl.w:ptcp.w:call-trgt-45 NOTICE finish :: job: "call-trgt_plot_motifs_waterfall"
2025-09-15 20:24:40.919 wdl.w:ptcp.w:call-trgt-45 INFO output :: job: "call-trgt_plot_motifs_waterfall", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-45/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2142.motifs_waterfall.trgt_plots.zip"}
2025-09-15 20:24:40.919 wdl.w:ptcp.w:call-trgt-45 INFO visit :: node: "output-images_motifs_waterfall", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-45/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2142.motifs_waterfall.trgt_plots.zip"}
2025-09-15 20:24:40.919 wdl.w:ptcp.w:call-trgt-45 INFO visit :: node: "outputs", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-45/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2142.motifs_waterfall.trgt_plots.zip", "images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-45/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2142.meth_allele.trgt_plots.zip", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-45/call-trgt_genotype/out/m84036_250809_035451_s4.bc2142.trgt.sorted.spanning.bam.bai", "images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-45/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2142.motifs_allele.trgt_plots.zip", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-45/call-trgt_genotype/out/m84036_250809_035451_s4.bc2142.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-45/call-trgt_genotype/out/m84036_250809_035451_s4.bc2142.trgt.vcf", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-45/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2142.repeats.bam", "images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-45/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2142.meth_waterfall.trgt_plots.zip", "reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-45/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2142.repeats.bam.bai"}
2025-09-15 20:24:40.923 wdl.w:ptcp.w:call-trgt-52.t:call-trgt_plot_meth_waterfall NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-52/call-trgt_plot_meth_waterfall", thread: 140611944420928
2025-09-15 20:24:40.943 wdl.w:ptcp.w:call-trgt-52.t:call-trgt_plot_meth_waterfall INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:40.943 wdl.w:ptcp.w:call-trgt-52.t:call-trgt_plot_meth_waterfall INFO input :: name: "waterfall", value: true
2025-09-15 20:24:40.943 wdl.w:ptcp.w:call-trgt-52.t:call-trgt_plot_meth_waterfall INFO input :: name: "methylation", value: true
2025-09-15 20:24:40.943 wdl.w:ptcp.w:call-trgt-52.t:call-trgt_plot_meth_waterfall INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:40.944 wdl.w:ptcp.w:call-trgt-52.t:call-trgt_plot_meth_waterfall INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:40.944 wdl.w:ptcp.w:call-trgt-52.t:call-trgt_plot_meth_waterfall INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:40.944 wdl.w:ptcp.w:call-trgt-52.t:call-trgt_plot_meth_waterfall INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2149.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:40.944 wdl.w:ptcp.w:call-trgt-52.t:call-trgt_plot_meth_waterfall INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2149.trgt.sorted.spanning.bam"
2025-09-15 20:24:40.944 wdl.w:ptcp.w:call-trgt-52.t:call-trgt_plot_meth_waterfall INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2149.trgt.vcf"
2025-09-15 20:24:40.944 wdl.w:ptcp.w:call-trgt-52.t:call-trgt_plot_meth_waterfall INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2149"
2025-09-15 20:24:40.944 wdl.w:ptcp.w:call-trgt-52.t:call-trgt_plot_meth_waterfall INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:40.944 wdl.w:ptcp.w:call-trgt-52.t:call-trgt_plot_meth_waterfall INFO eval :: name: "plot_type", value: "waterfall"
2025-09-15 20:24:40.944 wdl.w:ptcp.w:call-trgt-52.t:call-trgt_plot_meth_waterfall INFO eval :: name: "show", value: "meth"
2025-09-15 20:24:40.944 wdl.w:ptcp.w:call-trgt-52.t:call-trgt_plot_meth_waterfall INFO eval :: name: "threads", value: 1
2025-09-15 20:24:40.945 wdl.w:ptcp.w:call-trgt-52.t:call-trgt_plot_meth_waterfall INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:40.945 wdl.w:ptcp.w:call-trgt-52.t:call-trgt_plot_meth_waterfall INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2149.meth_waterfall"
2025-09-15 20:24:40.945 wdl.w:ptcp.w:call-trgt-52.t:call-trgt_plot_meth_waterfall INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:40.945 wdl.w:ptcp.w:call-trgt-52.t:call-trgt_plot_meth_waterfall WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:40.946 wdl.w:ptcp.w:call-trgt-52.t:call-trgt_plot_meth_waterfall INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:40.946 wdl.w:ptcp.w:call-trgt-52.t:call-trgt_plot_meth_waterfall INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:40.977 wdl.w:ptcp.w:call-paraphase-42.t:call-run_paraphase.slurm_singularity INFO srun: job 51797750 queued and waiting for resources
2025-09-15 20:24:40.978 wdl.w:ptcp.w:call-paraphase-42.t:call-run_paraphase.slurm_singularity INFO srun: job 51797750 has been allocated resources
2025-09-15 20:24:40.978 wdl.w:ptcp.w:call-paraphase-42.t:call-run_paraphase.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:41.015 wdl.w:ptcp.w:call-trgt-52.t:call-trgt_plot_meth_waterfall INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-52/call-trgt_plot_meth_waterfall/_singularity_tmpdir_r_9zayln"
2025-09-15 20:24:41.015 wdl.w:ptcp.w:call-trgt-52.t:call-trgt_plot_meth_waterfall INFO Slurm invocation: srun --job-name call-trgt_plot_meth_waterfall --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-52/call-trgt_plot_meth_waterfall/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-52/call-trgt_plot_meth_waterfall/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-52/call-trgt_plot_meth_waterfall/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-52/call-trgt_plot_meth_waterfall/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-52/call-trgt_genotype/out/m84036_250809_035451_s4.bc2149.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2149.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-52/call-trgt_genotype/out/m84036_250809_035451_s4.bc2149.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2149.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-52/call-trgt_genotype/out/m84036_250809_035451_s4.bc2149.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2149.trgt.sorted.spanning.bam:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-52/call-trgt_plot_meth_waterfall/_singularity_tmpdir_r_9zayln/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-52/call-trgt_plot_meth_waterfall/_singularity_tmpdir_r_9zayln/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:41.017 wdl.w:ptcp.w:call-trgt-45 NOTICE done
2025-09-15 20:24:41.020 wdl.w:ptcp NOTICE finish :: job: "call-trgt-45"
2025-09-15 20:24:41.021 wdl.w:ptcp INFO output :: job: "call-trgt-45", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-45/out/m84036_250809_035451_s4.bc2142.motifs_waterfall.trgt_plots.zip", "images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-45/out/m84036_250809_035451_s4.bc2142.meth_allele.trgt_plots.zip", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-45/out/m84036_250809_035451_s4.bc2142.trgt.sorted.spanning.bam.bai", "images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-45/out/m84036_250809_035451_s4.bc2142.motifs_allele.trgt_plots.zip", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-45/out/m84036_250809_035451_s4.bc2142.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-45/out/m84036_250809_035451_s4.bc2142.trgt.vcf", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-45/out/m84036_250809_035451_s4.bc2142.repeats.bam", "images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-45/out/m84036_250809_035451_s4.bc2142.meth_waterfall.trgt_plots.zip", "reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-45/out/m84036_250809_035451_s4.bc2142.repeats.bam.bai"}
2025-09-15 20:24:41.026 wdl.w:ptcp.w:call-paraphase-71 NOTICE workflow start :: name: "paraphase", source: "./paraphase.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-71"
2025-09-15 20:24:41.031 wdl.w:ptcp.w:call-trgt-52.t:call-trgt_plot_meth_waterfall NOTICE slurm_singularity run :: pid: 1202864, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-52/call-trgt_plot_meth_waterfall/slurm_singularity.log.txt"
2025-09-15 20:24:41.040 wdl.w:ptcp.w:call-paraphase-71 INFO visit :: node: "decl-annotation_vcf", values: {"annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf"}
2025-09-15 20:24:41.040 wdl.w:ptcp.w:call-paraphase-71 INFO visit :: node: "decl-config_file", values: {"config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml"}
2025-09-15 20:24:41.040 wdl.w:ptcp.w:call-paraphase-71 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:24:41.040 wdl.w:ptcp.w:call-paraphase-71 INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:24:41.040 wdl.w:ptcp.w:call-paraphase-71 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-71/out/m84036_250809_035451_s4.bc2168.mapped.bam"}
2025-09-15 20:24:41.040 wdl.w:ptcp.w:call-paraphase-71 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-71/out/m84036_250809_035451_s4.bc2168.mapped.bam.bai"}
2025-09-15 20:24:41.041 wdl.w:ptcp.w:call-paraphase-71 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:24:41.041 wdl.w:ptcp.w:call-paraphase-71 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:24:41.041 wdl.w:ptcp.w:call-paraphase-71 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2168"}
2025-09-15 20:24:41.041 wdl.w:ptcp.w:call-paraphase-71 INFO visit :: node: "decl-sex", values: {"sex": "F"}
2025-09-15 20:24:41.041 wdl.w:ptcp.w:call-paraphase-71 NOTICE ready :: job: "call-run_paraphase", callee: "run_paraphase"
2025-09-15 20:24:41.041 wdl.w:ptcp.w:call-paraphase-71 INFO input :: job: "call-run_paraphase", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf", "genome_version": "38", "config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-71/out/m84036_250809_035451_s4.bc2168.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-71/out/m84036_250809_035451_s4.bc2168.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2168"}
2025-09-15 20:24:41.130 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:41 [ERROR] - No reads found for TRID=SCA37_DAB1
2025-09-15 20:24:41.139 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_meth_allele.slurm_singularity INFO srun: job 51797751 queued and waiting for resources
2025-09-15 20:24:41.139 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_meth_allele.slurm_singularity INFO srun: job 51797751 has been allocated resources
2025-09-15 20:24:41.139 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_meth_allele.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:41.312 wdl.w:ptcp.w:call-paraphase-27.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for cyp21 for sample m84036_250809_035451_s4.bc2124 at 2025-09-15 20:24:28.904950...
2025-09-15 20:24:41.312 wdl.w:ptcp.w:call-paraphase-27.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for cyp21 for sample m84036_250809_035451_s4.bc2124 at 2025-09-15 20:24:29.772655...
2025-09-15 20:24:41.312 wdl.w:ptcp.w:call-paraphase-27.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for hbb for sample m84036_250809_035451_s4.bc2124 at 2025-09-15 20:24:38.536818...
2025-09-15 20:24:41.313 wdl.w:ptcp.w:call-paraphase-27.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for hbb for sample m84036_250809_035451_s4.bc2124 at 2025-09-15 20:24:38.537441...
2025-09-15 20:24:41.360 wdl.w:ptcp.w:call-trgt-53.t:call-trgt_genotype INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2150.trgt.vcf"
2025-09-15 20:24:41.364 wdl.w:ptcp.w:call-trgt-53.t:call-trgt_genotype INFO output :: name: "spanning_bam", value: "m84036_250809_035451_s4.bc2150.trgt.sorted.spanning.bam"
2025-09-15 20:24:41.365 wdl.w:ptcp.w:call-trgt-53.t:call-trgt_genotype INFO output :: name: "spanning_bam_bai", value: "m84036_250809_035451_s4.bc2150.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:41.398 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_motifs_allele.slurm_singularity INFO srun: job 51797752 queued and waiting for resources
2025-09-15 20:24:41.399 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_motifs_allele.slurm_singularity INFO srun: job 51797752 has been allocated resources
2025-09-15 20:24:41.398 wdl.w:ptcp.w:call-trgt-49.t:call-get_reads_overlapping_repeats INFO output :: name: "reads_overlapping_repeats", value: "m84036_250809_035451_s4.bc2146.repeats.bam"
2025-09-15 20:24:41.399 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_motifs_allele.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:41.404 wdl.w:ptcp.w:call-trgt-49.t:call-get_reads_overlapping_repeats INFO output :: name: "reads_overlapping_repeats_bai", value: "m84036_250809_035451_s4.bc2146.repeats.bam.bai"
2025-09-15 20:24:41.405 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO srun: job 51797753 queued and waiting for resources
2025-09-15 20:24:41.405 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO srun: job 51797753 has been allocated resources
2025-09-15 20:24:41.405 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:41.422 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:41 [ERROR] - No reads found for TRID=SCA37_DAB1
2025-09-15 20:24:41.422 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:41 [ERROR] - No reads found for TRID=OPDM_ABCD3
2025-09-15 20:24:41.422 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:41 [ERROR] - No reads found for TRID=NIID_NOTCH2NLC
2025-09-15 20:24:41.422 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:41 [ERROR] - No reads found for TRID=DRPLA_ATN1
2025-09-15 20:24:41.422 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:41 [ERROR] - No reads found for TRID=OPDM4_RILPL1
2025-09-15 20:24:41.422 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:41 [ERROR] - No reads found for TRID=SCA3_ATXN3
2025-09-15 20:24:41.422 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:41 [ERROR] - No reads found for TRID=SCA31_BEAN1
2025-09-15 20:24:41.422 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:41 [ERROR] - No reads found for TRID=OPMD_PABPN1
2025-09-15 20:24:41.422 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:41 [ERROR] - No reads found for TRID=SCA4_ZFHX3
2025-09-15 20:24:41.423 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:41 [ERROR] - No reads found for TRID=SCA6_CACNA1A
2025-09-15 20:24:41.423 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:41 [ERROR] - No reads found for TRID=OPDM2_GIPC1
2025-09-15 20:24:41.423 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:41 [ERROR] - No reads found for TRID=HDL2_JPH3
2025-09-15 20:24:41.423 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:41 [ERROR] - No reads found for TRID=SD5_HOXD13
2025-09-15 20:24:41.432 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_meth_allele.slurm_singularity INFO srun: job 51797754 queued and waiting for resources
2025-09-15 20:24:41.432 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_meth_allele.slurm_singularity INFO srun: job 51797754 has been allocated resources
2025-09-15 20:24:41.432 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO srun: job 51797755 queued and waiting for resources
2025-09-15 20:24:41.432 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_meth_allele.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:41.433 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO srun: job 51797755 has been allocated resources
2025-09-15 20:24:41.433 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:41.449 wdl.w:ptcp.w:call-trgt-53.t:call-trgt_genotype NOTICE done
2025-09-15 20:24:41.467 wdl.w:ptcp.w:call-trgt-53 NOTICE finish :: job: "call-trgt_genotype"
2025-09-15 20:24:41.467 wdl.w:ptcp.w:call-trgt-53 INFO output :: job: "call-trgt_genotype", values: {"spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-53/call-trgt_genotype/out/m84036_250809_035451_s4.bc2150.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-53/call-trgt_genotype/out/m84036_250809_035451_s4.bc2150.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-53/call-trgt_genotype/out/m84036_250809_035451_s4.bc2150.trgt.vcf"}
2025-09-15 20:24:41.468 wdl.w:ptcp.w:call-trgt-53 NOTICE ready :: job: "call-trgt_plot_meth_allele", callee: "trgt_plot"
2025-09-15 20:24:41.468 wdl.w:ptcp.w:call-trgt-53 INFO input :: job: "call-trgt_plot_meth_allele", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": false, "methylation": true, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-53/call-trgt_genotype/out/m84036_250809_035451_s4.bc2150.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-53/call-trgt_genotype/out/m84036_250809_035451_s4.bc2150.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-53/call-trgt_genotype/out/m84036_250809_035451_s4.bc2150.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2150"}
2025-09-15 20:24:41.469 wdl.w:ptcp.w:call-trgt-53 NOTICE ready :: job: "call-trgt_plot_meth_waterfall", callee: "trgt_plot"
2025-09-15 20:24:41.469 wdl.w:ptcp.w:call-trgt-53 INFO input :: job: "call-trgt_plot_meth_waterfall", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": true, "methylation": true, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-53/call-trgt_genotype/out/m84036_250809_035451_s4.bc2150.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-53/call-trgt_genotype/out/m84036_250809_035451_s4.bc2150.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-53/call-trgt_genotype/out/m84036_250809_035451_s4.bc2150.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2150"}
2025-09-15 20:24:41.470 wdl.w:ptcp.w:call-trgt-53 NOTICE ready :: job: "call-trgt_plot_motifs_allele", callee: "trgt_plot"
2025-09-15 20:24:41.470 wdl.w:ptcp.w:call-trgt-53 INFO input :: job: "call-trgt_plot_motifs_allele", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": false, "methylation": false, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-53/call-trgt_genotype/out/m84036_250809_035451_s4.bc2150.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-53/call-trgt_genotype/out/m84036_250809_035451_s4.bc2150.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-53/call-trgt_genotype/out/m84036_250809_035451_s4.bc2150.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2150"}
2025-09-15 20:24:41.471 wdl.w:ptcp.w:call-trgt-53 NOTICE ready :: job: "call-trgt_plot_motifs_waterfall", callee: "trgt_plot"
2025-09-15 20:24:41.471 wdl.w:ptcp.w:call-trgt-53 INFO input :: job: "call-trgt_plot_motifs_waterfall", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": true, "methylation": false, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-53/call-trgt_genotype/out/m84036_250809_035451_s4.bc2150.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-53/call-trgt_genotype/out/m84036_250809_035451_s4.bc2150.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-53/call-trgt_genotype/out/m84036_250809_035451_s4.bc2150.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2150"}
2025-09-15 20:24:41.471 wdl.w:ptcp.w:call-trgt-53 INFO visit :: node: "output-spanning_bam", values: {"spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-53/call-trgt_genotype/out/m84036_250809_035451_s4.bc2150.trgt.sorted.spanning.bam"}
2025-09-15 20:24:41.471 wdl.w:ptcp.w:call-trgt-53 INFO visit :: node: "output-spanning_bam_bai", values: {"spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-53/call-trgt_genotype/out/m84036_250809_035451_s4.bc2150.trgt.sorted.spanning.bam.bai"}
2025-09-15 20:24:41.471 wdl.w:ptcp.w:call-trgt-53 INFO visit :: node: "output-vcf", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-53/call-trgt_genotype/out/m84036_250809_035451_s4.bc2150.trgt.vcf"}
2025-09-15 20:24:41.473 wdl.w:ptcp.w:call-trgt-52.t:call-trgt_plot_motifs_allele NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-52/call-trgt_plot_motifs_allele", thread: 140609310422592
2025-09-15 20:24:41.474 wdl.w:ptcp.w:call-trgt-49.t:call-get_reads_overlapping_repeats NOTICE done
2025-09-15 20:24:41.481 wdl.w:ptcp.w:call-trgt-49 NOTICE finish :: job: "call-get_reads_overlapping_repeats"
2025-09-15 20:24:41.481 wdl.w:ptcp.w:call-trgt-49 INFO output :: job: "call-get_reads_overlapping_repeats", values: {"reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-49/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2146.repeats.bam.bai", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-49/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2146.repeats.bam"}
2025-09-15 20:24:41.481 wdl.w:ptcp.w:call-trgt-49 INFO visit :: node: "output-reads_overlapping_repeats", values: {"reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-49/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2146.repeats.bam"}
2025-09-15 20:24:41.482 wdl.w:ptcp.w:call-trgt-49 INFO visit :: node: "output-reads_overlapping_repeats_bai", values: {"reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-49/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2146.repeats.bam.bai"}
2025-09-15 20:24:41.489 wdl.w:ptcp.w:call-trgt-52.t:call-trgt_plot_motifs_waterfall NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-52/call-trgt_plot_motifs_waterfall", thread: 140607137760832
2025-09-15 20:24:41.491 wdl.w:ptcp.w:call-trgt-52.t:call-trgt_plot_motifs_allele INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:41.492 wdl.w:ptcp.w:call-trgt-52.t:call-trgt_plot_motifs_allele INFO input :: name: "waterfall", value: false
2025-09-15 20:24:41.492 wdl.w:ptcp.w:call-trgt-52.t:call-trgt_plot_motifs_allele INFO input :: name: "methylation", value: false
2025-09-15 20:24:41.492 wdl.w:ptcp.w:call-trgt-52.t:call-trgt_plot_motifs_allele INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:41.492 wdl.w:ptcp.w:call-trgt-52.t:call-trgt_plot_motifs_allele INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:41.492 wdl.w:ptcp.w:call-trgt-52.t:call-trgt_plot_motifs_allele INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:41.492 wdl.w:ptcp.w:call-trgt-52.t:call-trgt_plot_motifs_allele INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2149.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:41.492 wdl.w:ptcp.w:call-trgt-52.t:call-trgt_plot_motifs_allele INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2149.trgt.sorted.spanning.bam"
2025-09-15 20:24:41.492 wdl.w:ptcp.w:call-trgt-52.t:call-trgt_plot_motifs_allele INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2149.trgt.vcf"
2025-09-15 20:24:41.492 wdl.w:ptcp.w:call-trgt-52.t:call-trgt_plot_motifs_allele INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2149"
2025-09-15 20:24:41.492 wdl.w:ptcp.w:call-trgt-52.t:call-trgt_plot_motifs_allele INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:41.492 wdl.w:ptcp.w:call-trgt-52.t:call-trgt_plot_motifs_allele INFO eval :: name: "plot_type", value: "allele"
2025-09-15 20:24:41.492 wdl.w:ptcp.w:call-trgt-52.t:call-trgt_plot_motifs_allele INFO eval :: name: "show", value: "motifs"
2025-09-15 20:24:41.493 wdl.w:ptcp.w:call-trgt-52.t:call-trgt_plot_motifs_allele INFO eval :: name: "threads", value: 1
2025-09-15 20:24:41.493 wdl.w:ptcp.w:call-trgt-52.t:call-trgt_plot_motifs_allele INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:41.493 wdl.w:ptcp.w:call-trgt-52.t:call-trgt_plot_motifs_allele INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2149.motifs_allele"
2025-09-15 20:24:41.493 wdl.w:ptcp.w:call-trgt-52.t:call-trgt_plot_motifs_allele INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:41.493 wdl.w:ptcp.w:call-trgt-52.t:call-trgt_plot_motifs_allele WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:41.494 wdl.w:ptcp.w:call-trgt-52.t:call-trgt_plot_motifs_allele INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:41.494 wdl.w:ptcp.w:call-trgt-52.t:call-trgt_plot_motifs_allele INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:41.503 wdl.w:ptcp.w:call-trgt-52.t:call-trgt_plot_motifs_waterfall INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:41.504 wdl.w:ptcp.w:call-trgt-52.t:call-trgt_plot_motifs_waterfall INFO input :: name: "waterfall", value: true
2025-09-15 20:24:41.504 wdl.w:ptcp.w:call-trgt-52.t:call-trgt_plot_motifs_waterfall INFO input :: name: "methylation", value: false
2025-09-15 20:24:41.504 wdl.w:ptcp.w:call-trgt-52.t:call-trgt_plot_motifs_waterfall INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:41.504 wdl.w:ptcp.w:call-trgt-52.t:call-trgt_plot_motifs_waterfall INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:41.504 wdl.w:ptcp.w:call-trgt-52.t:call-trgt_plot_motifs_waterfall INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:41.504 wdl.w:ptcp.w:call-trgt-52.t:call-trgt_plot_motifs_waterfall INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2149.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:41.504 wdl.w:ptcp.w:call-trgt-52.t:call-trgt_plot_motifs_waterfall INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2149.trgt.sorted.spanning.bam"
2025-09-15 20:24:41.504 wdl.w:ptcp.w:call-trgt-52.t:call-trgt_plot_motifs_waterfall INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2149.trgt.vcf"
2025-09-15 20:24:41.504 wdl.w:ptcp.w:call-trgt-52.t:call-trgt_plot_motifs_waterfall INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2149"
2025-09-15 20:24:41.504 wdl.w:ptcp.w:call-trgt-52.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:41.504 wdl.w:ptcp.w:call-trgt-52.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "plot_type", value: "waterfall"
2025-09-15 20:24:41.504 wdl.w:ptcp.w:call-trgt-52.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "show", value: "motifs"
2025-09-15 20:24:41.505 wdl.w:ptcp.w:call-trgt-52.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "threads", value: 1
2025-09-15 20:24:41.505 wdl.w:ptcp.w:call-trgt-52.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:41.505 wdl.w:ptcp.w:call-trgt-52.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2149.motifs_waterfall"
2025-09-15 20:24:41.506 wdl.w:ptcp.w:call-trgt-52.t:call-trgt_plot_motifs_waterfall INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:41.507 wdl.w:ptcp.w:call-trgt-52.t:call-trgt_plot_motifs_waterfall WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:41.507 wdl.w:ptcp.w:call-trgt-52.t:call-trgt_plot_motifs_waterfall INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:41.507 wdl.w:ptcp.w:call-trgt-52.t:call-trgt_plot_motifs_waterfall INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:41.567 wdl.w:ptcp.w:call-trgt-52.t:call-trgt_plot_motifs_allele INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-52/call-trgt_plot_motifs_allele/_singularity_tmpdir_gixjggxb"
2025-09-15 20:24:41.567 wdl.w:ptcp.w:call-trgt-52.t:call-trgt_plot_motifs_allele INFO Slurm invocation: srun --job-name call-trgt_plot_motifs_allele --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-52/call-trgt_plot_motifs_allele/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-52/call-trgt_plot_motifs_allele/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-52/call-trgt_plot_motifs_allele/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-52/call-trgt_plot_motifs_allele/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-52/call-trgt_genotype/out/m84036_250809_035451_s4.bc2149.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2149.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-52/call-trgt_genotype/out/m84036_250809_035451_s4.bc2149.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2149.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-52/call-trgt_genotype/out/m84036_250809_035451_s4.bc2149.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2149.trgt.sorted.spanning.bam:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-52/call-trgt_plot_motifs_allele/_singularity_tmpdir_gixjggxb/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-52/call-trgt_plot_motifs_allele/_singularity_tmpdir_gixjggxb/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:41.580 wdl.w:ptcp.w:call-trgt-52.t:call-trgt_plot_motifs_waterfall INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-52/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_18wpce05"
2025-09-15 20:24:41.580 wdl.w:ptcp.w:call-trgt-52.t:call-trgt_plot_motifs_waterfall INFO Slurm invocation: srun --job-name call-trgt_plot_motifs_waterfall --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-52/call-trgt_plot_motifs_waterfall/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-52/call-trgt_plot_motifs_waterfall/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-52/call-trgt_plot_motifs_waterfall/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-52/call-trgt_plot_motifs_waterfall/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-52/call-trgt_genotype/out/m84036_250809_035451_s4.bc2149.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2149.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-52/call-trgt_genotype/out/m84036_250809_035451_s4.bc2149.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2149.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-52/call-trgt_genotype/out/m84036_250809_035451_s4.bc2149.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2149.trgt.sorted.spanning.bam:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-52/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_18wpce05/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-52/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_18wpce05/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:41.593 wdl.w:ptcp.w:call-trgt-52.t:call-trgt_plot_motifs_waterfall NOTICE slurm_singularity run :: pid: 1202876, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-52/call-trgt_plot_motifs_waterfall/slurm_singularity.log.txt"
2025-09-15 20:24:41.593 wdl.w:ptcp.w:call-trgt-52.t:call-trgt_plot_motifs_allele NOTICE slurm_singularity run :: pid: 1202875, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-52/call-trgt_plot_motifs_allele/slurm_singularity.log.txt"
2025-09-15 20:24:41.601 wdl.w:ptcp.w:call-trgt-56.t:call-trgt_genotype INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2153.trgt.vcf"
2025-09-15 20:24:41.603 wdl.w:ptcp.w:call-trgt-56.t:call-trgt_genotype INFO output :: name: "spanning_bam", value: "m84036_250809_035451_s4.bc2153.trgt.sorted.spanning.bam"
2025-09-15 20:24:41.604 wdl.w:ptcp.w:call-trgt-56.t:call-trgt_genotype INFO output :: name: "spanning_bam_bai", value: "m84036_250809_035451_s4.bc2153.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:41.665 wdl.w:ptcp.w:call-trgt-56.t:call-trgt_genotype NOTICE done
2025-09-15 20:24:41.670 wdl.w:ptcp.w:call-trgt-56 NOTICE finish :: job: "call-trgt_genotype"
2025-09-15 20:24:41.670 wdl.w:ptcp.w:call-trgt-56 INFO output :: job: "call-trgt_genotype", values: {"spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-56/call-trgt_genotype/out/m84036_250809_035451_s4.bc2153.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-56/call-trgt_genotype/out/m84036_250809_035451_s4.bc2153.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-56/call-trgt_genotype/out/m84036_250809_035451_s4.bc2153.trgt.vcf"}
2025-09-15 20:24:41.670 wdl.w:ptcp.w:call-trgt-56 NOTICE ready :: job: "call-trgt_plot_meth_allele", callee: "trgt_plot"
2025-09-15 20:24:41.670 wdl.w:ptcp.w:call-trgt-56 INFO input :: job: "call-trgt_plot_meth_allele", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": false, "methylation": true, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-56/call-trgt_genotype/out/m84036_250809_035451_s4.bc2153.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-56/call-trgt_genotype/out/m84036_250809_035451_s4.bc2153.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-56/call-trgt_genotype/out/m84036_250809_035451_s4.bc2153.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2153"}
2025-09-15 20:24:41.672 wdl.w:ptcp.w:call-trgt-56 NOTICE ready :: job: "call-trgt_plot_meth_waterfall", callee: "trgt_plot"
2025-09-15 20:24:41.672 wdl.w:ptcp.w:call-trgt-56 INFO input :: job: "call-trgt_plot_meth_waterfall", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": true, "methylation": true, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-56/call-trgt_genotype/out/m84036_250809_035451_s4.bc2153.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-56/call-trgt_genotype/out/m84036_250809_035451_s4.bc2153.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-56/call-trgt_genotype/out/m84036_250809_035451_s4.bc2153.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2153"}
2025-09-15 20:24:41.673 wdl.w:ptcp.w:call-trgt-56 NOTICE ready :: job: "call-trgt_plot_motifs_allele", callee: "trgt_plot"
2025-09-15 20:24:41.673 wdl.w:ptcp.w:call-trgt-56 INFO input :: job: "call-trgt_plot_motifs_allele", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": false, "methylation": false, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-56/call-trgt_genotype/out/m84036_250809_035451_s4.bc2153.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-56/call-trgt_genotype/out/m84036_250809_035451_s4.bc2153.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-56/call-trgt_genotype/out/m84036_250809_035451_s4.bc2153.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2153"}
2025-09-15 20:24:41.674 wdl.w:ptcp.w:call-trgt-56 NOTICE ready :: job: "call-trgt_plot_motifs_waterfall", callee: "trgt_plot"
2025-09-15 20:24:41.674 wdl.w:ptcp.w:call-trgt-56 INFO input :: job: "call-trgt_plot_motifs_waterfall", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": true, "methylation": false, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-56/call-trgt_genotype/out/m84036_250809_035451_s4.bc2153.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-56/call-trgt_genotype/out/m84036_250809_035451_s4.bc2153.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-56/call-trgt_genotype/out/m84036_250809_035451_s4.bc2153.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2153"}
2025-09-15 20:24:41.674 wdl.w:ptcp.w:call-trgt-56 INFO visit :: node: "output-spanning_bam", values: {"spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-56/call-trgt_genotype/out/m84036_250809_035451_s4.bc2153.trgt.sorted.spanning.bam"}
2025-09-15 20:24:41.674 wdl.w:ptcp.w:call-trgt-56 INFO visit :: node: "output-spanning_bam_bai", values: {"spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-56/call-trgt_genotype/out/m84036_250809_035451_s4.bc2153.trgt.sorted.spanning.bam.bai"}
2025-09-15 20:24:41.675 wdl.w:ptcp.w:call-trgt-56 INFO visit :: node: "output-vcf", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-56/call-trgt_genotype/out/m84036_250809_035451_s4.bc2153.trgt.vcf"}
2025-09-15 20:24:41.678 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:41 [ERROR] - No reads found for TRID=OPDM_ABCD3
2025-09-15 20:24:41.678 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:41 [ERROR] - No reads found for TRID=SCA37_DAB1
2025-09-15 20:24:41.678 wdl.w:ptcp.w:call-sawfish-42.t:call-run_sawfish NOTICE task setup :: name: "run_sawfish", source: "./sawfish.wdl", line: 83, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-42/call-run_sawfish", thread: 140607146153536
2025-09-15 20:24:41.691 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO srun: job 51797756 queued and waiting for resources
2025-09-15 20:24:41.691 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO srun: job 51797756 has been allocated resources
2025-09-15 20:24:41.692 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:41.696 wdl.w:ptcp.w:call-sawfish-42.t:call-run_sawfish INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:41.696 wdl.w:ptcp.w:call-sawfish-42.t:call-run_sawfish INFO input :: name: "genome_version", value: "38"
2025-09-15 20:24:41.697 wdl.w:ptcp.w:call-sawfish-42.t:call-run_sawfish INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:41.697 wdl.w:ptcp.w:call-sawfish-42.t:call-run_sawfish INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:41.697 wdl.w:ptcp.w:call-sawfish-42.t:call-run_sawfish INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2139.mapped.bam.bai"
2025-09-15 20:24:41.697 wdl.w:ptcp.w:call-sawfish-42.t:call-run_sawfish INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2139.mapped.bam"
2025-09-15 20:24:41.697 wdl.w:ptcp.w:call-sawfish-42.t:call-run_sawfish INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2139"
2025-09-15 20:24:41.697 wdl.w:ptcp.w:call-sawfish-42.t:call-run_sawfish INFO eval :: name: "mem_gb", value: 32
2025-09-15 20:24:41.697 wdl.w:ptcp.w:call-sawfish-42.t:call-run_sawfish INFO eval :: name: "threads", value: 16
2025-09-15 20:24:41.698 wdl.w:ptcp.w:call-sawfish-42.t:call-run_sawfish INFO eval :: name: "disk_size", value: 30
2025-09-15 20:24:41.698 wdl.w:ptcp.w:call-sawfish-42.t:call-run_sawfish INFO eval :: name: "discover_dirname", value: "m84036_250809_035451_s4.bc2139_sawfish_discover"
2025-09-15 20:24:41.698 wdl.w:ptcp.w:call-sawfish-42.t:call-run_sawfish INFO eval :: name: "call_dirname", value: "m84036_250809_035451_s4.bc2139_sawfish"
2025-09-15 20:24:41.698 wdl.w:ptcp.w:call-sawfish-42.t:call-run_sawfish INFO eval :: name: "minimap2_bam_filename", value: "m84036_250809_035451_s4.bc2139.minimap2.bam"
2025-09-15 20:24:41.698 wdl.w:ptcp.w:call-sawfish-42.t:call-run_sawfish INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 16, memory_reservation: 32000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:41.698 wdl.w:ptcp.w:call-sawfish-42.t:call-run_sawfish WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:41.699 wdl.w:ptcp.w:call-sawfish-42.t:call-run_sawfish INFO provisioned :: seconds_waited: 0, cpu: 16, mem_bytes: 32000000000
2025-09-15 20:24:41.699 wdl.w:ptcp.w:call-sawfish-42.t:call-run_sawfish INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:41.704 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:41 [ERROR] - No reads found for TRID=OPDM_ABCD3
2025-09-15 20:24:41.704 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:41 [ERROR] - No reads found for TRID=SCA37_DAB1
2025-09-15 20:24:41.705 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:41 [ERROR] - No reads found for TRID=DRPLA_ATN1
2025-09-15 20:24:41.705 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:41 [ERROR] - No reads found for TRID=SCA2_ATXN2
2025-09-15 20:24:41.705 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:41 [ERROR] - No reads found for TRID=NIID_NOTCH2NLC
2025-09-15 20:24:41.705 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:41 [ERROR] - No reads found for TRID=OPDM4_RILPL1
2025-09-15 20:24:41.713 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_motifs_allele.slurm_singularity INFO srun: job 51797757 queued and waiting for resources
2025-09-15 20:24:41.713 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_motifs_allele.slurm_singularity INFO srun: job 51797757 has been allocated resources
2025-09-15 20:24:41.713 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_motifs_allele.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:41.751 wdl.w:ptcp.w:call-sawfish-42.t:call-run_sawfish INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 10, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-42/call-run_sawfish/_singularity_tmpdir_7o1zxs_n"
2025-09-15 20:24:41.751 wdl.w:ptcp.w:call-sawfish-42.t:call-run_sawfish INFO Slurm invocation: srun --job-name call-run_sawfish --partition compute,compute9 --cpus-per-task 16 --mem 30518M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-42/call-run_sawfish/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-42/call-run_sawfish/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-42/call-run_sawfish/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-42/call-run_sawfish/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-42/out/m84036_250809_035451_s4.bc2139.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2139.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-42/out/m84036_250809_035451_s4.bc2139.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2139.mapped.bam:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-42/call-run_sawfish/_singularity_tmpdir_7o1zxs_n/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-42/call-run_sawfish/_singularity_tmpdir_7o1zxs_n/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:41.766 wdl.w:ptcp.w:call-sawfish-42.t:call-run_sawfish NOTICE slurm_singularity run :: pid: 1202879, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-42/call-run_sawfish/slurm_singularity.log.txt"
2025-09-15 20:24:41.814 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:41 [ERROR] - No reads found for TRID=OPDM_ABCD3
2025-09-15 20:24:41.815 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:41 [ERROR] - No reads found for TRID=SCA37_DAB1
2025-09-15 20:24:41.815 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:41 [ERROR] - No reads found for TRID=DRPLA_ATN1
2025-09-15 20:24:41.815 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:41 [ERROR] - No reads found for TRID=SCA2_ATXN2
2025-09-15 20:24:41.822 wdl.w:ptcp.w:call-trgt-52.t:call-trgt_plot_meth_allele.slurm_singularity INFO srun: job 51797759 queued and waiting for resources
2025-09-15 20:24:41.822 wdl.w:ptcp.w:call-trgt-52.t:call-trgt_plot_meth_allele.slurm_singularity INFO srun: job 51797759 has been allocated resources
2025-09-15 20:24:41.822 wdl.w:ptcp.w:call-trgt-52.t:call-trgt_plot_meth_allele.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:41.824 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO srun: job 51797758 queued and waiting for resources
2025-09-15 20:24:41.824 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO srun: job 51797758 has been allocated resources
2025-09-15 20:24:41.824 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:41.862 wdl.w:ptcp.w:call-sawfish-00.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:31][sawfish][INFO] Starting sawfish 2.0.3
2025-09-15 20:24:41.862 wdl.w:ptcp.w:call-sawfish-00.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:31][sawfish][INFO] cmdline: sawfish discover --disable-cnv --threads 16 --ref /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa --bam m84036_250809_035451_s4.bc2097.minimap2.bam --output-dir m84036_250809_035451_s4.bc2097_sawfish_discover
2025-09-15 20:24:41.862 wdl.w:ptcp.w:call-sawfish-00.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:31][sawfish][INFO] Running on 16 threads
2025-09-15 20:24:41.862 wdl.w:ptcp.w:call-sawfish-00.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:31][sawfish][INFO] Writing discover settings to file: 'm84036_250809_035451_s4.bc2097_sawfish_discover/discover.settings.json'
2025-09-15 20:24:41.862 wdl.w:ptcp.w:call-sawfish-00.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:31][sawfish][INFO] Reading reference genome from file '/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa'
2025-09-15 20:24:41.862 wdl.w:ptcp.w:call-sawfish-00.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:35][sawfish][INFO] Processing alignment file '/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2097.minimap2.bam'
2025-09-15 20:24:41.862 wdl.w:ptcp.w:call-sawfish-00.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:35][sawfish][INFO] Finished processing all alignments
2025-09-15 20:24:41.862 wdl.w:ptcp.w:call-sawfish-00.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:35][sawfish][INFO] Writing depth bins to binary file: 'm84036_250809_035451_s4.bc2097_sawfish_discover/depth.mpack'
2025-09-15 20:24:41.862 wdl.w:ptcp.w:call-sawfish-00.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:35][sawfish][INFO] Writing max sv depth genome regions to bed file: 'm84036_250809_035451_s4.bc2097_sawfish_discover/max.depth.bed'
2025-09-15 20:24:41.863 wdl.w:ptcp.w:call-sawfish-00.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:35][sawfish][INFO] Completing breakpoint observation clustering
2025-09-15 20:24:41.863 wdl.w:ptcp.w:call-sawfish-00.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:35][sawfish][INFO] Finished breakpoint observation clustering
2025-09-15 20:24:41.863 wdl.w:ptcp.w:call-sawfish-00.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:35][sawfish][INFO] Consolidating adjacent indel candidates
2025-09-15 20:24:41.863 wdl.w:ptcp.w:call-sawfish-00.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:35][sawfish][INFO] Finding large insertion candidates
2025-09-15 20:24:41.863 wdl.w:ptcp.w:call-sawfish-00.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:35][sawfish][INFO] Writing breakpoint_cluster debug bed file: 'm84036_250809_035451_s4.bc2097_sawfish_discover/debug.breakpoint_clusters.bed'
2025-09-15 20:24:41.863 wdl.w:ptcp.w:call-sawfish-00.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:35][sawfish][INFO] Refining SV Candidates
2025-09-15 20:24:41.863 wdl.w:ptcp.w:call-sawfish-00.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:35][sawfish][INFO] Writing debug assembly region bed file: 'm84036_250809_035451_s4.bc2097_sawfish_discover/assembly.regions.bed'
2025-09-15 20:24:41.863 wdl.w:ptcp.w:call-sawfish-00.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:35][sawfish][INFO] Starting refinement of breakpoint evidence clusters
2025-09-15 20:24:41.863 wdl.w:ptcp.w:call-sawfish-00.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:35][sawfish][INFO] Finished refining all breakpoint evidence clusters
2025-09-15 20:24:41.863 wdl.w:ptcp.w:call-sawfish-00.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:35][sawfish][INFO] Writing all contig alignments to bam file: 'm84036_250809_035451_s4.bc2097_sawfish_discover/contig.alignment.bam'
2025-09-15 20:24:41.863 wdl.w:ptcp.w:call-sawfish-00.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:35][sawfish][INFO] Writing candidate structural variants to file: 'm84036_250809_035451_s4.bc2097_sawfish_discover/candidate.sv.bcf'
2025-09-15 20:24:41.863 wdl.w:ptcp.w:call-sawfish-00.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:35][sawfish][INFO] Writing run statistics to file: 'm84036_250809_035451_s4.bc2097_sawfish_discover/run.stats.json'
2025-09-15 20:24:41.863 wdl.w:ptcp.w:call-sawfish-00.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:35][sawfish][INFO] sawfish completed. Total Runtime: 00:00:04.450
2025-09-15 20:24:41.898 wdl.w:ptcp.w:call-sawfish-03.t:call-run_sawfish INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2100_sawfish/m84036_250809_035451_s4.bc2100.sv.vcf.gz"
2025-09-15 20:24:41.898 wdl.w:ptcp.w:call-sawfish-33.t:call-run_sawfish INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2130_sawfish/m84036_250809_035451_s4.bc2130.sv.vcf.gz"
2025-09-15 20:24:41.903 wdl.w:ptcp.w:call-sawfish-03.t:call-run_sawfish INFO output :: name: "vcf_tbi", value: "m84036_250809_035451_s4.bc2100_sawfish/m84036_250809_035451_s4.bc2100.sv.vcf.gz.tbi"
2025-09-15 20:24:41.904 wdl.w:ptcp.w:call-sawfish-33.t:call-run_sawfish INFO output :: name: "vcf_tbi", value: "m84036_250809_035451_s4.bc2130_sawfish/m84036_250809_035451_s4.bc2130.sv.vcf.gz.tbi"
2025-09-15 20:24:41.904 wdl.w:ptcp.w:call-sawfish-03.t:call-run_sawfish INFO output :: name: "minimap2_bam", value: "m84036_250809_035451_s4.bc2100.minimap2.bam"
2025-09-15 20:24:41.905 wdl.w:ptcp.w:call-sawfish-33.t:call-run_sawfish INFO output :: name: "minimap2_bam", value: "m84036_250809_035451_s4.bc2130.minimap2.bam"
2025-09-15 20:24:41.905 wdl.w:ptcp.w:call-sawfish-03.t:call-run_sawfish INFO output :: name: "minimap2_bam_bai", value: "m84036_250809_035451_s4.bc2100.minimap2.bam.bai"
2025-09-15 20:24:41.906 wdl.w:ptcp.w:call-sawfish-33.t:call-run_sawfish INFO output :: name: "minimap2_bam_bai", value: "m84036_250809_035451_s4.bc2130.minimap2.bam.bai"
2025-09-15 20:24:41.983 wdl.w:ptcp.w:call-paraphase-23.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for hbb for sample m84036_250809_035451_s4.bc2120 at 2025-09-15 20:24:10.975074...
2025-09-15 20:24:41.983 wdl.w:ptcp.w:call-paraphase-23.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for hbb for sample m84036_250809_035451_s4.bc2120 at 2025-09-15 20:24:11.312825...
2025-09-15 20:24:42.044 wdl.w:ptcp.w:call-trgt-52.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO srun: job 51797760 queued and waiting for resources
2025-09-15 20:24:42.045 wdl.w:ptcp.w:call-trgt-52.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO srun: job 51797760 has been allocated resources
2025-09-15 20:24:42.045 wdl.w:ptcp.w:call-trgt-52.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:42.082 wdl.w:ptcp.w:call-sawfish-33.t:call-run_sawfish NOTICE done
2025-09-15 20:24:42.089 wdl.w:ptcp.w:call-sawfish-33 NOTICE finish :: job: "call-run_sawfish"
2025-09-15 20:24:42.089 wdl.w:ptcp.w:call-sawfish-33 INFO output :: job: "call-run_sawfish", values: {"minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-33/call-run_sawfish/out/m84036_250809_035451_s4.bc2130.minimap2.bam.bai", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-33/call-run_sawfish/out/m84036_250809_035451_s4.bc2130.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-33/call-run_sawfish/out/m84036_250809_035451_s4.bc2130_sawfish/m84036_250809_035451_s4.bc2130.sv.vcf.gz.tbi", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-33/call-run_sawfish/out/m84036_250809_035451_s4.bc2130_sawfish/m84036_250809_035451_s4.bc2130.sv.vcf.gz"}
2025-09-15 20:24:42.089 wdl.w:ptcp.w:call-sawfish-33 INFO visit :: node: "output-minimap2_bam", values: {"minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-33/call-run_sawfish/out/m84036_250809_035451_s4.bc2130.minimap2.bam"}
2025-09-15 20:24:42.090 wdl.w:ptcp.w:call-sawfish-33 INFO visit :: node: "output-minimap2_bam_bai", values: {"minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-33/call-run_sawfish/out/m84036_250809_035451_s4.bc2130.minimap2.bam.bai"}
2025-09-15 20:24:42.090 wdl.w:ptcp.w:call-sawfish-33 INFO visit :: node: "output-vcf", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-33/call-run_sawfish/out/m84036_250809_035451_s4.bc2130_sawfish/m84036_250809_035451_s4.bc2130.sv.vcf.gz"}
2025-09-15 20:24:42.090 wdl.w:ptcp.w:call-sawfish-33 INFO visit :: node: "output-vcf_tbi", values: {"vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-33/call-run_sawfish/out/m84036_250809_035451_s4.bc2130_sawfish/m84036_250809_035451_s4.bc2130.sv.vcf.gz.tbi"}
2025-09-15 20:24:42.090 wdl.w:ptcp.w:call-sawfish-33 INFO visit :: node: "outputs", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-33/call-run_sawfish/out/m84036_250809_035451_s4.bc2130_sawfish/m84036_250809_035451_s4.bc2130.sv.vcf.gz", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-33/call-run_sawfish/out/m84036_250809_035451_s4.bc2130.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-33/call-run_sawfish/out/m84036_250809_035451_s4.bc2130_sawfish/m84036_250809_035451_s4.bc2130.sv.vcf.gz.tbi", "minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-33/call-run_sawfish/out/m84036_250809_035451_s4.bc2130.minimap2.bam.bai"}
2025-09-15 20:24:42.093 wdl.w:ptcp.w:call-sawfish-03.t:call-run_sawfish NOTICE done
2025-09-15 20:24:42.098 wdl.w:ptcp.w:call-trgt-44.t:call-trgt_plot_meth_allele NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-44/call-trgt_plot_meth_allele", thread: 140610895857216
2025-09-15 20:24:42.122 wdl.w:ptcp.w:call-trgt-44.t:call-trgt_plot_meth_allele INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:42.122 wdl.w:ptcp.w:call-trgt-44.t:call-trgt_plot_meth_allele INFO input :: name: "waterfall", value: false
2025-09-15 20:24:42.122 wdl.w:ptcp.w:call-trgt-44.t:call-trgt_plot_meth_allele INFO input :: name: "methylation", value: true
2025-09-15 20:24:42.122 wdl.w:ptcp.w:call-trgt-44.t:call-trgt_plot_meth_allele INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:42.123 wdl.w:ptcp.w:call-trgt-44.t:call-trgt_plot_meth_allele INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:42.123 wdl.w:ptcp.w:call-trgt-44.t:call-trgt_plot_meth_allele INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:42.123 wdl.w:ptcp.w:call-trgt-44.t:call-trgt_plot_meth_allele INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2141.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:42.123 wdl.w:ptcp.w:call-trgt-44.t:call-trgt_plot_meth_allele INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2141.trgt.sorted.spanning.bam"
2025-09-15 20:24:42.123 wdl.w:ptcp.w:call-trgt-44.t:call-trgt_plot_meth_allele INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2141.trgt.vcf"
2025-09-15 20:24:42.123 wdl.w:ptcp.w:call-trgt-44.t:call-trgt_plot_meth_allele INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2141"
2025-09-15 20:24:42.123 wdl.w:ptcp.w:call-trgt-44.t:call-trgt_plot_meth_allele INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:42.123 wdl.w:ptcp.w:call-trgt-44.t:call-trgt_plot_meth_allele INFO eval :: name: "plot_type", value: "allele"
2025-09-15 20:24:42.123 wdl.w:ptcp.w:call-trgt-44.t:call-trgt_plot_meth_allele INFO eval :: name: "show", value: "meth"
2025-09-15 20:24:42.123 wdl.w:ptcp.w:call-trgt-44.t:call-trgt_plot_meth_allele INFO eval :: name: "threads", value: 1
2025-09-15 20:24:42.124 wdl.w:ptcp.w:call-trgt-44.t:call-trgt_plot_meth_allele INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:42.124 wdl.w:ptcp.w:call-trgt-44.t:call-trgt_plot_meth_allele INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2141.meth_allele"
2025-09-15 20:24:42.124 wdl.w:ptcp.w:call-trgt-44.t:call-trgt_plot_meth_allele INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:42.124 wdl.w:ptcp.w:call-trgt-44.t:call-trgt_plot_meth_allele WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:42.125 wdl.w:ptcp.w:call-trgt-44.t:call-trgt_plot_meth_allele INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:42.125 wdl.w:ptcp.w:call-trgt-44.t:call-trgt_plot_meth_allele INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:42.148 wdl.w:ptcp.w:call-sawfish-03 NOTICE finish :: job: "call-run_sawfish"
2025-09-15 20:24:42.148 wdl.w:ptcp.w:call-sawfish-03 INFO output :: job: "call-run_sawfish", values: {"minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-03/call-run_sawfish/out/m84036_250809_035451_s4.bc2100.minimap2.bam.bai", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-03/call-run_sawfish/out/m84036_250809_035451_s4.bc2100.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-03/call-run_sawfish/out/m84036_250809_035451_s4.bc2100_sawfish/m84036_250809_035451_s4.bc2100.sv.vcf.gz.tbi", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-03/call-run_sawfish/out/m84036_250809_035451_s4.bc2100_sawfish/m84036_250809_035451_s4.bc2100.sv.vcf.gz"}
2025-09-15 20:24:42.148 wdl.w:ptcp.w:call-sawfish-03 INFO visit :: node: "output-minimap2_bam", values: {"minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-03/call-run_sawfish/out/m84036_250809_035451_s4.bc2100.minimap2.bam"}
2025-09-15 20:24:42.148 wdl.w:ptcp.w:call-sawfish-03 INFO visit :: node: "output-minimap2_bam_bai", values: {"minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-03/call-run_sawfish/out/m84036_250809_035451_s4.bc2100.minimap2.bam.bai"}
2025-09-15 20:24:42.148 wdl.w:ptcp.w:call-sawfish-03 INFO visit :: node: "output-vcf", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-03/call-run_sawfish/out/m84036_250809_035451_s4.bc2100_sawfish/m84036_250809_035451_s4.bc2100.sv.vcf.gz"}
2025-09-15 20:24:42.148 wdl.w:ptcp.w:call-sawfish-03 INFO visit :: node: "output-vcf_tbi", values: {"vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-03/call-run_sawfish/out/m84036_250809_035451_s4.bc2100_sawfish/m84036_250809_035451_s4.bc2100.sv.vcf.gz.tbi"}
2025-09-15 20:24:42.149 wdl.w:ptcp.w:call-sawfish-03 INFO visit :: node: "outputs", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-03/call-run_sawfish/out/m84036_250809_035451_s4.bc2100_sawfish/m84036_250809_035451_s4.bc2100.sv.vcf.gz", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-03/call-run_sawfish/out/m84036_250809_035451_s4.bc2100.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-03/call-run_sawfish/out/m84036_250809_035451_s4.bc2100_sawfish/m84036_250809_035451_s4.bc2100.sv.vcf.gz.tbi", "minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-03/call-run_sawfish/out/m84036_250809_035451_s4.bc2100.minimap2.bam.bai"}
2025-09-15 20:24:42.151 wdl.w:ptcp.w:call-sawfish-33 NOTICE done
2025-09-15 20:24:42.159 wdl.w:ptcp NOTICE finish :: job: "call-sawfish-33"
2025-09-15 20:24:42.159 wdl.w:ptcp INFO output :: job: "call-sawfish-33", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-33/out/m84036_250809_035451_s4.bc2130_sawfish/m84036_250809_035451_s4.bc2130.sv.vcf.gz", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-33/out/m84036_250809_035451_s4.bc2130.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-33/out/m84036_250809_035451_s4.bc2130_sawfish/m84036_250809_035451_s4.bc2130.sv.vcf.gz.tbi", "minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-33/out/m84036_250809_035451_s4.bc2130.minimap2.bam.bai"}
2025-09-15 20:24:42.159 wdl.w:ptcp NOTICE ready :: job: "call-tar_outputs-33", callee: "tar_outputs"
2025-09-15 20:24:42.160 wdl.w:ptcp.w:call-trgt-44.t:call-trgt_plot_meth_waterfall NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-44/call-trgt_plot_meth_waterfall", thread: 140609285244480
2025-09-15 20:24:42.160 wdl.w:ptcp INFO input :: job: "call-tar_outputs-33", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "sawfish_vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-33/out/m84036_250809_035451_s4.bc2130_sawfish/m84036_250809_035451_s4.bc2130.sv.vcf.gz.tbi", "sawfish_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-33/out/m84036_250809_035451_s4.bc2130_sawfish/m84036_250809_035451_s4.bc2130.sv.vcf.gz", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-33/out/m84036_250809_035451_s4.bc2130.f8inversion.json", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-33/out/m84036_250809_035451_s4.bc2130_paraphase/m84036_250809_035451_s4.bc2130.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-33/out/m84036_250809_035451_s4.bc2130_paraphase/m84036_250809_035451_s4.bc2130.paraphase.bam", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-33/out/m84036_250809_035451_s4.bc2130_paraphase/m84036_250809_035451_s4.bc2130.paraphase.json", "trgt_spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-33/out/m84036_250809_035451_s4.bc2130.trgt.sorted.spanning.bam.bai", "trgt_spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-33/out/m84036_250809_035451_s4.bc2130.trgt.sorted.spanning.bam", "trgt_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-33/out/m84036_250809_035451_s4.bc2130.trgt.vcf", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-33/out/m84036_250809_035451_s4.bc2130.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-33/out/m84036_250809_035451_s4.bc2130.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2130"}
2025-09-15 20:24:42.166 wdl.w:ptcp.w:call-sawfish-71 NOTICE workflow start :: name: "sawfish", source: "./sawfish.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-71"
2025-09-15 20:24:42.182 wdl.w:ptcp.w:call-trgt-44.t:call-trgt_plot_meth_waterfall INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:42.182 wdl.w:ptcp.w:call-trgt-44.t:call-trgt_plot_meth_waterfall INFO input :: name: "waterfall", value: true
2025-09-15 20:24:42.182 wdl.w:ptcp.w:call-trgt-44.t:call-trgt_plot_meth_waterfall INFO input :: name: "methylation", value: true
2025-09-15 20:24:42.182 wdl.w:ptcp.w:call-trgt-44.t:call-trgt_plot_meth_waterfall INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:42.182 wdl.w:ptcp.w:call-trgt-44.t:call-trgt_plot_meth_waterfall INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:42.182 wdl.w:ptcp.w:call-trgt-44.t:call-trgt_plot_meth_waterfall INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:42.182 wdl.w:ptcp.w:call-trgt-44.t:call-trgt_plot_meth_waterfall INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2141.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:42.183 wdl.w:ptcp.w:call-trgt-44.t:call-trgt_plot_meth_waterfall INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2141.trgt.sorted.spanning.bam"
2025-09-15 20:24:42.183 wdl.w:ptcp.w:call-trgt-44.t:call-trgt_plot_meth_waterfall INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2141.trgt.vcf"
2025-09-15 20:24:42.183 wdl.w:ptcp.w:call-trgt-44.t:call-trgt_plot_meth_waterfall INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2141"
2025-09-15 20:24:42.183 wdl.w:ptcp.w:call-trgt-44.t:call-trgt_plot_meth_waterfall INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:42.183 wdl.w:ptcp.w:call-trgt-44.t:call-trgt_plot_meth_waterfall INFO eval :: name: "plot_type", value: "waterfall"
2025-09-15 20:24:42.183 wdl.w:ptcp.w:call-trgt-44.t:call-trgt_plot_meth_waterfall INFO eval :: name: "show", value: "meth"
2025-09-15 20:24:42.183 wdl.w:ptcp.w:call-trgt-44.t:call-trgt_plot_meth_waterfall INFO eval :: name: "threads", value: 1
2025-09-15 20:24:42.184 wdl.w:ptcp.w:call-trgt-44.t:call-trgt_plot_meth_waterfall INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:42.184 wdl.w:ptcp.w:call-trgt-44.t:call-trgt_plot_meth_waterfall INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2141.meth_waterfall"
2025-09-15 20:24:42.184 wdl.w:ptcp.w:call-trgt-44.t:call-trgt_plot_meth_waterfall INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:42.184 wdl.w:ptcp.w:call-trgt-44.t:call-trgt_plot_meth_waterfall WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:42.184 wdl.w:ptcp.w:call-trgt-44.t:call-trgt_plot_meth_waterfall INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:42.185 wdl.w:ptcp.w:call-trgt-44.t:call-trgt_plot_meth_waterfall INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:42.200 wdl.w:ptcp.w:call-sawfish-71 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:24:42.200 wdl.w:ptcp.w:call-sawfish-71 INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:24:42.200 wdl.w:ptcp.w:call-sawfish-71 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-71/out/m84036_250809_035451_s4.bc2168.mapped.bam"}
2025-09-15 20:24:42.200 wdl.w:ptcp.w:call-sawfish-71 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-71/out/m84036_250809_035451_s4.bc2168.mapped.bam.bai"}
2025-09-15 20:24:42.200 wdl.w:ptcp.w:call-sawfish-71 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:24:42.200 wdl.w:ptcp.w:call-sawfish-71 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:24:42.200 wdl.w:ptcp.w:call-sawfish-71 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2168"}
2025-09-15 20:24:42.200 wdl.w:ptcp.w:call-sawfish-71 NOTICE ready :: job: "call-run_sawfish", callee: "run_sawfish"
2025-09-15 20:24:42.200 wdl.w:ptcp.w:call-sawfish-71 INFO input :: job: "call-run_sawfish", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-71/out/m84036_250809_035451_s4.bc2168.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-71/out/m84036_250809_035451_s4.bc2168.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2168"}
2025-09-15 20:24:42.211 wdl.w:ptcp.w:call-trgt-44.t:call-trgt_plot_meth_allele INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-44/call-trgt_plot_meth_allele/_singularity_tmpdir_ds03u7fx"
2025-09-15 20:24:42.212 wdl.w:ptcp.w:call-trgt-44.t:call-trgt_plot_meth_allele INFO Slurm invocation: srun --job-name call-trgt_plot_meth_allele --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-44/call-trgt_plot_meth_allele/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-44/call-trgt_plot_meth_allele/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-44/call-trgt_plot_meth_allele/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-44/call-trgt_plot_meth_allele/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-44/call-trgt_genotype/out/m84036_250809_035451_s4.bc2141.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2141.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-44/call-trgt_genotype/out/m84036_250809_035451_s4.bc2141.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2141.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-44/call-trgt_genotype/out/m84036_250809_035451_s4.bc2141.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2141.trgt.vcf:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-44/call-trgt_plot_meth_allele/_singularity_tmpdir_ds03u7fx/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-44/call-trgt_plot_meth_allele/_singularity_tmpdir_ds03u7fx/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:42.256 wdl.w:ptcp.w:call-sawfish-03 NOTICE done
2025-09-15 20:24:42.262 wdl.w:ptcp NOTICE finish :: job: "call-sawfish-03"
2025-09-15 20:24:42.262 wdl.w:ptcp INFO output :: job: "call-sawfish-03", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-03/out/m84036_250809_035451_s4.bc2100_sawfish/m84036_250809_035451_s4.bc2100.sv.vcf.gz", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-03/out/m84036_250809_035451_s4.bc2100.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-03/out/m84036_250809_035451_s4.bc2100_sawfish/m84036_250809_035451_s4.bc2100.sv.vcf.gz.tbi", "minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-03/out/m84036_250809_035451_s4.bc2100.minimap2.bam.bai"}
2025-09-15 20:24:42.268 wdl.w:ptcp.w:call-trgt-44.t:call-trgt_plot_meth_waterfall INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-44/call-trgt_plot_meth_waterfall/_singularity_tmpdir_t5wih3it"
2025-09-15 20:24:42.268 wdl.w:ptcp.w:call-trgt-44.t:call-trgt_plot_meth_waterfall INFO Slurm invocation: srun --job-name call-trgt_plot_meth_waterfall --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-44/call-trgt_plot_meth_waterfall/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-44/call-trgt_plot_meth_waterfall/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-44/call-trgt_plot_meth_waterfall/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-44/call-trgt_plot_meth_waterfall/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-44/call-trgt_genotype/out/m84036_250809_035451_s4.bc2141.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2141.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-44/call-trgt_genotype/out/m84036_250809_035451_s4.bc2141.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2141.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-44/call-trgt_genotype/out/m84036_250809_035451_s4.bc2141.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2141.trgt.vcf:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-44/call-trgt_plot_meth_waterfall/_singularity_tmpdir_t5wih3it/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-44/call-trgt_plot_meth_waterfall/_singularity_tmpdir_t5wih3it/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:42.272 wdl.w:ptcp.w:call-trgt-44.t:call-trgt_plot_meth_allele NOTICE slurm_singularity run :: pid: 1202898, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-44/call-trgt_plot_meth_allele/slurm_singularity.log.txt"
2025-09-15 20:24:42.273 wdl.w:ptcp.w:call-trgt-71 NOTICE workflow start :: name: "trgt", source: "./trgt.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-71"
2025-09-15 20:24:42.276 wdl.w:ptcp.w:call-trgt-44.t:call-trgt_plot_meth_waterfall NOTICE slurm_singularity run :: pid: 1202899, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-44/call-trgt_plot_meth_waterfall/slurm_singularity.log.txt"
2025-09-15 20:24:42.289 wdl.w:ptcp.w:call-trgt-71 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:24:42.290 wdl.w:ptcp.w:call-trgt-71 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-71/out/m84036_250809_035451_s4.bc2168.mapped.bam"}
2025-09-15 20:24:42.290 wdl.w:ptcp.w:call-trgt-71 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-71/out/m84036_250809_035451_s4.bc2168.mapped.bam.bai"}
2025-09-15 20:24:42.290 wdl.w:ptcp.w:call-trgt-71 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:24:42.290 wdl.w:ptcp.w:call-trgt-71 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:24:42.290 wdl.w:ptcp.w:call-trgt-71 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2168"}
2025-09-15 20:24:42.290 wdl.w:ptcp.w:call-trgt-71 INFO visit :: node: "decl-sex", values: {"sex": "F"}
2025-09-15 20:24:42.290 wdl.w:ptcp.w:call-trgt-71 INFO visit :: node: "decl-trgt_bed", values: {"trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"}
2025-09-15 20:24:42.290 wdl.w:ptcp.w:call-trgt-71 NOTICE ready :: job: "call-get_reads_overlapping_repeats", callee: "get_reads_overlapping_repeats"
2025-09-15 20:24:42.290 wdl.w:ptcp.w:call-trgt-71 INFO input :: job: "call-get_reads_overlapping_repeats", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-71/out/m84036_250809_035451_s4.bc2168.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-71/out/m84036_250809_035451_s4.bc2168.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2168"}
2025-09-15 20:24:42.291 wdl.w:ptcp.w:call-trgt-71 NOTICE ready :: job: "call-trgt_genotype", callee: "trgt_genotype"
2025-09-15 20:24:42.291 wdl.w:ptcp.w:call-trgt-71 INFO input :: job: "call-trgt_genotype", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-71/out/m84036_250809_035451_s4.bc2168.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-71/out/m84036_250809_035451_s4.bc2168.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2168"}
2025-09-15 20:24:42.494 wdl.w:ptcp.w:call-sawfish-20.t:call-run_sawfish INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2117_sawfish/m84036_250809_035451_s4.bc2117.sv.vcf.gz"
2025-09-15 20:24:42.497 wdl.w:ptcp.w:call-trgt-53.t:call-get_reads_overlapping_repeats INFO output :: name: "reads_overlapping_repeats", value: "m84036_250809_035451_s4.bc2150.repeats.bam"
2025-09-15 20:24:42.499 wdl.w:ptcp.w:call-sawfish-20.t:call-run_sawfish INFO output :: name: "vcf_tbi", value: "m84036_250809_035451_s4.bc2117_sawfish/m84036_250809_035451_s4.bc2117.sv.vcf.gz.tbi"
2025-09-15 20:24:42.501 wdl.w:ptcp.w:call-sawfish-20.t:call-run_sawfish INFO output :: name: "minimap2_bam", value: "m84036_250809_035451_s4.bc2117.minimap2.bam"
2025-09-15 20:24:42.501 wdl.w:ptcp.w:call-trgt-53.t:call-get_reads_overlapping_repeats INFO output :: name: "reads_overlapping_repeats_bai", value: "m84036_250809_035451_s4.bc2150.repeats.bam.bai"
2025-09-15 20:24:42.503 wdl.w:ptcp.w:call-sawfish-20.t:call-run_sawfish INFO output :: name: "minimap2_bam_bai", value: "m84036_250809_035451_s4.bc2117.minimap2.bam.bai"
2025-09-15 20:24:42.571 wdl.w:ptcp.w:call-trgt-53.t:call-get_reads_overlapping_repeats NOTICE done
2025-09-15 20:24:42.576 wdl.w:ptcp.w:call-trgt-53 NOTICE finish :: job: "call-get_reads_overlapping_repeats"
2025-09-15 20:24:42.576 wdl.w:ptcp.w:call-trgt-53 INFO output :: job: "call-get_reads_overlapping_repeats", values: {"reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-53/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2150.repeats.bam.bai", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-53/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2150.repeats.bam"}
2025-09-15 20:24:42.577 wdl.w:ptcp.w:call-trgt-53 INFO visit :: node: "output-reads_overlapping_repeats", values: {"reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-53/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2150.repeats.bam"}
2025-09-15 20:24:42.577 wdl.w:ptcp.w:call-trgt-53 INFO visit :: node: "output-reads_overlapping_repeats_bai", values: {"reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-53/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2150.repeats.bam.bai"}
2025-09-15 20:24:42.583 wdl.w:ptcp.w:call-trgt-44.t:call-trgt_plot_motifs_allele NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-44/call-trgt_plot_motifs_allele", thread: 140607112582720
2025-09-15 20:24:42.603 wdl.w:ptcp.w:call-trgt-44.t:call-trgt_plot_motifs_allele INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:42.603 wdl.w:ptcp.w:call-trgt-52.t:call-trgt_plot_motifs_allele.slurm_singularity INFO srun: job 51797761 queued and waiting for resources
2025-09-15 20:24:42.603 wdl.w:ptcp.w:call-trgt-44.t:call-trgt_plot_motifs_allele INFO input :: name: "waterfall", value: false
2025-09-15 20:24:42.603 wdl.w:ptcp.w:call-trgt-52.t:call-trgt_plot_motifs_allele.slurm_singularity INFO srun: job 51797761 has been allocated resources
2025-09-15 20:24:42.604 wdl.w:ptcp.w:call-trgt-44.t:call-trgt_plot_motifs_allele INFO input :: name: "methylation", value: false
2025-09-15 20:24:42.604 wdl.w:ptcp.w:call-trgt-52.t:call-trgt_plot_motifs_allele.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:42.604 wdl.w:ptcp.w:call-trgt-44.t:call-trgt_plot_motifs_allele INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:42.604 wdl.w:ptcp.w:call-trgt-44.t:call-trgt_plot_motifs_allele INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:42.604 wdl.w:ptcp.w:call-trgt-44.t:call-trgt_plot_motifs_allele INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:42.604 wdl.w:ptcp.w:call-trgt-44.t:call-trgt_plot_motifs_allele INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2141.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:42.604 wdl.w:ptcp.w:call-trgt-44.t:call-trgt_plot_motifs_allele INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2141.trgt.sorted.spanning.bam"
2025-09-15 20:24:42.604 wdl.w:ptcp.w:call-trgt-44.t:call-trgt_plot_motifs_allele INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2141.trgt.vcf"
2025-09-15 20:24:42.604 wdl.w:ptcp.w:call-trgt-44.t:call-trgt_plot_motifs_allele INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2141"
2025-09-15 20:24:42.604 wdl.w:ptcp.w:call-trgt-44.t:call-trgt_plot_motifs_allele INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:42.604 wdl.w:ptcp.w:call-trgt-44.t:call-trgt_plot_motifs_allele INFO eval :: name: "plot_type", value: "allele"
2025-09-15 20:24:42.605 wdl.w:ptcp.w:call-trgt-44.t:call-trgt_plot_motifs_allele INFO eval :: name: "show", value: "motifs"
2025-09-15 20:24:42.605 wdl.w:ptcp.w:call-trgt-44.t:call-trgt_plot_motifs_allele INFO eval :: name: "threads", value: 1
2025-09-15 20:24:42.605 wdl.w:ptcp.w:call-trgt-44.t:call-trgt_plot_motifs_allele INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:42.605 wdl.w:ptcp.w:call-trgt-44.t:call-trgt_plot_motifs_allele INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2141.motifs_allele"
2025-09-15 20:24:42.605 wdl.w:ptcp.w:call-trgt-44.t:call-trgt_plot_motifs_allele INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:42.605 wdl.w:ptcp.w:call-trgt-44.t:call-trgt_plot_motifs_allele WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:42.606 wdl.w:ptcp.w:call-trgt-44.t:call-trgt_plot_motifs_allele INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:42.606 wdl.w:ptcp.w:call-trgt-44.t:call-trgt_plot_motifs_allele INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:42.608 wdl.w:ptcp.w:call-trgt-52.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO srun: job 51797762 queued and waiting for resources
2025-09-15 20:24:42.608 wdl.w:ptcp.w:call-trgt-52.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO srun: job 51797762 has been allocated resources
2025-09-15 20:24:42.608 wdl.w:ptcp.w:call-trgt-52.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:42.637 wdl.w:ptcp.w:call-sawfish-13.t:call-run_sawfish INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2110_sawfish/m84036_250809_035451_s4.bc2110.sv.vcf.gz"
2025-09-15 20:24:42.642 wdl.w:ptcp.w:call-sawfish-13.t:call-run_sawfish INFO output :: name: "vcf_tbi", value: "m84036_250809_035451_s4.bc2110_sawfish/m84036_250809_035451_s4.bc2110.sv.vcf.gz.tbi"
2025-09-15 20:24:42.643 wdl.w:ptcp.w:call-sawfish-13.t:call-run_sawfish INFO output :: name: "minimap2_bam", value: "m84036_250809_035451_s4.bc2110.minimap2.bam"
2025-09-15 20:24:42.644 wdl.w:ptcp.w:call-sawfish-13.t:call-run_sawfish INFO output :: name: "minimap2_bam_bai", value: "m84036_250809_035451_s4.bc2110.minimap2.bam.bai"
2025-09-15 20:24:42.687 wdl.w:ptcp.w:call-sawfish-20.t:call-run_sawfish NOTICE done
2025-09-15 20:24:42.692 wdl.w:ptcp.w:call-sawfish-20 NOTICE finish :: job: "call-run_sawfish"
2025-09-15 20:24:42.692 wdl.w:ptcp.w:call-sawfish-20 INFO output :: job: "call-run_sawfish", values: {"minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-20/call-run_sawfish/out/m84036_250809_035451_s4.bc2117.minimap2.bam.bai", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-20/call-run_sawfish/out/m84036_250809_035451_s4.bc2117.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-20/call-run_sawfish/out/m84036_250809_035451_s4.bc2117_sawfish/m84036_250809_035451_s4.bc2117.sv.vcf.gz.tbi", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-20/call-run_sawfish/out/m84036_250809_035451_s4.bc2117_sawfish/m84036_250809_035451_s4.bc2117.sv.vcf.gz"}
2025-09-15 20:24:42.693 wdl.w:ptcp.w:call-sawfish-20 INFO visit :: node: "output-minimap2_bam", values: {"minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-20/call-run_sawfish/out/m84036_250809_035451_s4.bc2117.minimap2.bam"}
2025-09-15 20:24:42.693 wdl.w:ptcp.w:call-sawfish-20 INFO visit :: node: "output-minimap2_bam_bai", values: {"minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-20/call-run_sawfish/out/m84036_250809_035451_s4.bc2117.minimap2.bam.bai"}
2025-09-15 20:24:42.693 wdl.w:ptcp.w:call-sawfish-20 INFO visit :: node: "output-vcf", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-20/call-run_sawfish/out/m84036_250809_035451_s4.bc2117_sawfish/m84036_250809_035451_s4.bc2117.sv.vcf.gz"}
2025-09-15 20:24:42.693 wdl.w:ptcp.w:call-sawfish-20 INFO visit :: node: "output-vcf_tbi", values: {"vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-20/call-run_sawfish/out/m84036_250809_035451_s4.bc2117_sawfish/m84036_250809_035451_s4.bc2117.sv.vcf.gz.tbi"}
2025-09-15 20:24:42.693 wdl.w:ptcp.w:call-sawfish-20 INFO visit :: node: "outputs", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-20/call-run_sawfish/out/m84036_250809_035451_s4.bc2117_sawfish/m84036_250809_035451_s4.bc2117.sv.vcf.gz", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-20/call-run_sawfish/out/m84036_250809_035451_s4.bc2117.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-20/call-run_sawfish/out/m84036_250809_035451_s4.bc2117_sawfish/m84036_250809_035451_s4.bc2117.sv.vcf.gz.tbi", "minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-20/call-run_sawfish/out/m84036_250809_035451_s4.bc2117.minimap2.bam.bai"}
2025-09-15 20:24:42.695 wdl.w:ptcp.w:call-trgt-44.t:call-trgt_plot_motifs_allele INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-44/call-trgt_plot_motifs_allele/_singularity_tmpdir_xqb2wz81"
2025-09-15 20:24:42.696 wdl.w:ptcp.w:call-trgt-44.t:call-trgt_plot_motifs_allele INFO Slurm invocation: srun --job-name call-trgt_plot_motifs_allele --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-44/call-trgt_plot_motifs_allele/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-44/call-trgt_plot_motifs_allele/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-44/call-trgt_plot_motifs_allele/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-44/call-trgt_plot_motifs_allele/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-44/call-trgt_genotype/out/m84036_250809_035451_s4.bc2141.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2141.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-44/call-trgt_genotype/out/m84036_250809_035451_s4.bc2141.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2141.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-44/call-trgt_genotype/out/m84036_250809_035451_s4.bc2141.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2141.trgt.vcf:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-44/call-trgt_plot_motifs_allele/_singularity_tmpdir_xqb2wz81/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-44/call-trgt_plot_motifs_allele/_singularity_tmpdir_xqb2wz81/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:42.700 wdl.w:ptcp.w:call-trgt-44.t:call-trgt_plot_motifs_waterfall NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-44/call-trgt_plot_motifs_waterfall", thread: 140611415942720
2025-09-15 20:24:42.719 wdl.w:ptcp.w:call-trgt-44.t:call-trgt_plot_motifs_allele NOTICE slurm_singularity run :: pid: 1202916, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-44/call-trgt_plot_motifs_allele/slurm_singularity.log.txt"
2025-09-15 20:24:42.725 wdl.w:ptcp.w:call-trgt-44.t:call-trgt_plot_motifs_waterfall INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:42.725 wdl.w:ptcp.w:call-trgt-44.t:call-trgt_plot_motifs_waterfall INFO input :: name: "waterfall", value: true
2025-09-15 20:24:42.726 wdl.w:ptcp.w:call-trgt-44.t:call-trgt_plot_motifs_waterfall INFO input :: name: "methylation", value: false
2025-09-15 20:24:42.726 wdl.w:ptcp.w:call-trgt-44.t:call-trgt_plot_motifs_waterfall INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:42.726 wdl.w:ptcp.w:call-trgt-44.t:call-trgt_plot_motifs_waterfall INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:42.726 wdl.w:ptcp.w:call-trgt-44.t:call-trgt_plot_motifs_waterfall INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:42.726 wdl.w:ptcp.w:call-trgt-44.t:call-trgt_plot_motifs_waterfall INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2141.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:42.726 wdl.w:ptcp.w:call-trgt-44.t:call-trgt_plot_motifs_waterfall INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2141.trgt.sorted.spanning.bam"
2025-09-15 20:24:42.726 wdl.w:ptcp.w:call-trgt-44.t:call-trgt_plot_motifs_waterfall INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2141.trgt.vcf"
2025-09-15 20:24:42.726 wdl.w:ptcp.w:call-trgt-44.t:call-trgt_plot_motifs_waterfall INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2141"
2025-09-15 20:24:42.726 wdl.w:ptcp.w:call-trgt-44.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:42.726 wdl.w:ptcp.w:call-trgt-44.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "plot_type", value: "waterfall"
2025-09-15 20:24:42.727 wdl.w:ptcp.w:call-trgt-44.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "show", value: "motifs"
2025-09-15 20:24:42.727 wdl.w:ptcp.w:call-trgt-44.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "threads", value: 1
2025-09-15 20:24:42.727 wdl.w:ptcp.w:call-trgt-44.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:42.727 wdl.w:ptcp.w:call-trgt-44.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2141.motifs_waterfall"
2025-09-15 20:24:42.727 wdl.w:ptcp.w:call-trgt-44.t:call-trgt_plot_motifs_waterfall INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:42.728 wdl.w:ptcp.w:call-trgt-44.t:call-trgt_plot_motifs_waterfall WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:42.728 wdl.w:ptcp.w:call-trgt-44.t:call-trgt_plot_motifs_waterfall INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:42.728 wdl.w:ptcp.w:call-trgt-44.t:call-trgt_plot_motifs_waterfall INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:42.751 wdl.w:ptcp.w:call-sawfish-20 NOTICE done
2025-09-15 20:24:42.765 wdl.w:ptcp NOTICE finish :: job: "call-sawfish-20"
2025-09-15 20:24:42.765 wdl.w:ptcp INFO output :: job: "call-sawfish-20", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-20/out/m84036_250809_035451_s4.bc2117_sawfish/m84036_250809_035451_s4.bc2117.sv.vcf.gz", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-20/out/m84036_250809_035451_s4.bc2117.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-20/out/m84036_250809_035451_s4.bc2117_sawfish/m84036_250809_035451_s4.bc2117.sv.vcf.gz.tbi", "minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-20/out/m84036_250809_035451_s4.bc2117.minimap2.bam.bai"}
2025-09-15 20:24:42.766 wdl.w:ptcp NOTICE ready :: job: "call-tar_outputs-20", callee: "tar_outputs"
2025-09-15 20:24:42.766 wdl.w:ptcp INFO input :: job: "call-tar_outputs-20", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "sawfish_vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-20/out/m84036_250809_035451_s4.bc2117_sawfish/m84036_250809_035451_s4.bc2117.sv.vcf.gz.tbi", "sawfish_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-20/out/m84036_250809_035451_s4.bc2117_sawfish/m84036_250809_035451_s4.bc2117.sv.vcf.gz", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-20/out/m84036_250809_035451_s4.bc2117.f8inversion.json", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-20/out/m84036_250809_035451_s4.bc2117_paraphase/m84036_250809_035451_s4.bc2117.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-20/out/m84036_250809_035451_s4.bc2117_paraphase/m84036_250809_035451_s4.bc2117.paraphase.bam", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-20/out/m84036_250809_035451_s4.bc2117_paraphase/m84036_250809_035451_s4.bc2117.paraphase.json", "trgt_spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-20/out/m84036_250809_035451_s4.bc2117.trgt.sorted.spanning.bam.bai", "trgt_spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-20/out/m84036_250809_035451_s4.bc2117.trgt.sorted.spanning.bam", "trgt_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-20/out/m84036_250809_035451_s4.bc2117.trgt.vcf", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-20/out/m84036_250809_035451_s4.bc2117.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-20/out/m84036_250809_035451_s4.bc2117.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2117"}
2025-09-15 20:24:42.776 wdl.w:ptcp.w:call-sawfish-42.t:call-run_sawfish.slurm_singularity INFO srun: job 51797763 queued and waiting for resources
2025-09-15 20:24:42.776 wdl.w:ptcp.w:call-sawfish-42.t:call-run_sawfish.slurm_singularity INFO srun: job 51797763 has been allocated resources
2025-09-15 20:24:42.776 wdl.w:ptcp.w:call-sawfish-42.t:call-run_sawfish.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:42.776 wdl.w:ptcp.w:call-sawfish-42.t:call-run_sawfish.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:24:42.787 wdl.w:ptcp.w:call-paraphase-68 NOTICE workflow start :: name: "paraphase", source: "./paraphase.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-68"
2025-09-15 20:24:42.793 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_motifs_waterfall INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2144.motifs_waterfall.trgt_plots.zip"
2025-09-15 20:24:42.807 wdl.w:ptcp.w:call-paraphase-68 INFO visit :: node: "decl-annotation_vcf", values: {"annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf"}
2025-09-15 20:24:42.807 wdl.w:ptcp.w:call-paraphase-68 INFO visit :: node: "decl-config_file", values: {"config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml"}
2025-09-15 20:24:42.807 wdl.w:ptcp.w:call-paraphase-68 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:24:42.807 wdl.w:ptcp.w:call-paraphase-68 INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:24:42.808 wdl.w:ptcp.w:call-paraphase-68 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-68/out/m84036_250809_035451_s4.bc2165.mapped.bam"}
2025-09-15 20:24:42.808 wdl.w:ptcp.w:call-paraphase-68 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-68/out/m84036_250809_035451_s4.bc2165.mapped.bam.bai"}
2025-09-15 20:24:42.808 wdl.w:ptcp.w:call-paraphase-68 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:24:42.808 wdl.w:ptcp.w:call-paraphase-68 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:24:42.808 wdl.w:ptcp.w:call-paraphase-68 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2165"}
2025-09-15 20:24:42.808 wdl.w:ptcp.w:call-paraphase-68 INFO visit :: node: "decl-sex", values: {"sex": "F"}
2025-09-15 20:24:42.808 wdl.w:ptcp.w:call-paraphase-68 NOTICE ready :: job: "call-run_paraphase", callee: "run_paraphase"
2025-09-15 20:24:42.808 wdl.w:ptcp.w:call-paraphase-68 INFO input :: job: "call-run_paraphase", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf", "genome_version": "38", "config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-68/out/m84036_250809_035451_s4.bc2165.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-68/out/m84036_250809_035451_s4.bc2165.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2165"}
2025-09-15 20:24:42.833 wdl.w:ptcp.w:call-trgt-44.t:call-trgt_plot_motifs_waterfall INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-44/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_7me4w4zu"
2025-09-15 20:24:42.833 wdl.w:ptcp.w:call-trgt-44.t:call-trgt_plot_motifs_waterfall INFO Slurm invocation: srun --job-name call-trgt_plot_motifs_waterfall --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-44/call-trgt_plot_motifs_waterfall/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-44/call-trgt_plot_motifs_waterfall/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-44/call-trgt_plot_motifs_waterfall/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-44/call-trgt_plot_motifs_waterfall/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-44/call-trgt_genotype/out/m84036_250809_035451_s4.bc2141.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2141.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-44/call-trgt_genotype/out/m84036_250809_035451_s4.bc2141.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2141.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-44/call-trgt_genotype/out/m84036_250809_035451_s4.bc2141.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2141.trgt.vcf:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-44/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_7me4w4zu/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-44/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_7me4w4zu/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:42.842 wdl.w:ptcp.w:call-sawfish-13.t:call-run_sawfish NOTICE done
2025-09-15 20:24:42.849 wdl.w:ptcp.w:call-sawfish-13 NOTICE finish :: job: "call-run_sawfish"
2025-09-15 20:24:42.849 wdl.w:ptcp.w:call-sawfish-13 INFO output :: job: "call-run_sawfish", values: {"minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-13/call-run_sawfish/out/m84036_250809_035451_s4.bc2110.minimap2.bam.bai", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-13/call-run_sawfish/out/m84036_250809_035451_s4.bc2110.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-13/call-run_sawfish/out/m84036_250809_035451_s4.bc2110_sawfish/m84036_250809_035451_s4.bc2110.sv.vcf.gz.tbi", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-13/call-run_sawfish/out/m84036_250809_035451_s4.bc2110_sawfish/m84036_250809_035451_s4.bc2110.sv.vcf.gz"}
2025-09-15 20:24:42.850 wdl.w:ptcp.w:call-sawfish-13 INFO visit :: node: "output-minimap2_bam", values: {"minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-13/call-run_sawfish/out/m84036_250809_035451_s4.bc2110.minimap2.bam"}
2025-09-15 20:24:42.850 wdl.w:ptcp.w:call-sawfish-13 INFO visit :: node: "output-minimap2_bam_bai", values: {"minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-13/call-run_sawfish/out/m84036_250809_035451_s4.bc2110.minimap2.bam.bai"}
2025-09-15 20:24:42.850 wdl.w:ptcp.w:call-sawfish-13 INFO visit :: node: "output-vcf", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-13/call-run_sawfish/out/m84036_250809_035451_s4.bc2110_sawfish/m84036_250809_035451_s4.bc2110.sv.vcf.gz"}
2025-09-15 20:24:42.850 wdl.w:ptcp.w:call-sawfish-13 INFO visit :: node: "output-vcf_tbi", values: {"vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-13/call-run_sawfish/out/m84036_250809_035451_s4.bc2110_sawfish/m84036_250809_035451_s4.bc2110.sv.vcf.gz.tbi"}
2025-09-15 20:24:42.850 wdl.w:ptcp.w:call-sawfish-13 INFO visit :: node: "outputs", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-13/call-run_sawfish/out/m84036_250809_035451_s4.bc2110_sawfish/m84036_250809_035451_s4.bc2110.sv.vcf.gz", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-13/call-run_sawfish/out/m84036_250809_035451_s4.bc2110.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-13/call-run_sawfish/out/m84036_250809_035451_s4.bc2110_sawfish/m84036_250809_035451_s4.bc2110.sv.vcf.gz.tbi", "minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-13/call-run_sawfish/out/m84036_250809_035451_s4.bc2110.minimap2.bam.bai"}
2025-09-15 20:24:42.857 wdl.w:ptcp.t:call-tar_outputs-09 NOTICE task setup :: name: "tar_outputs", source: "./common.wdl", line: 279, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-09", thread: 140606080804416
2025-09-15 20:24:42.859 wdl.w:ptcp.w:call-trgt-44.t:call-trgt_plot_motifs_waterfall NOTICE slurm_singularity run :: pid: 1202918, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-44/call-trgt_plot_motifs_waterfall/slurm_singularity.log.txt"
2025-09-15 20:24:42.883 wdl.w:ptcp.t:call-tar_outputs-09 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:42.883 wdl.w:ptcp.t:call-tar_outputs-09 INFO input :: name: "sawfish_vcf_tbi", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2106.sv.vcf.gz.tbi"
2025-09-15 20:24:42.883 wdl.w:ptcp.t:call-tar_outputs-09 INFO input :: name: "sawfish_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2106.sv.vcf.gz"
2025-09-15 20:24:42.883 wdl.w:ptcp.t:call-tar_outputs-09 INFO input :: name: "f8_json", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2106.f8inversion.json"
2025-09-15 20:24:42.884 wdl.w:ptcp.t:call-tar_outputs-09 INFO input :: name: "paraphase_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2106.paraphase.bam.bai"
2025-09-15 20:24:42.884 wdl.w:ptcp.t:call-tar_outputs-09 INFO input :: name: "paraphase_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2106.paraphase.bam"
2025-09-15 20:24:42.884 wdl.w:ptcp.t:call-tar_outputs-09 INFO input :: name: "paraphase_json", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2106.paraphase.json"
2025-09-15 20:24:42.884 wdl.w:ptcp.t:call-tar_outputs-09 INFO input :: name: "trgt_spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2106.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:42.884 wdl.w:ptcp.t:call-tar_outputs-09 INFO input :: name: "trgt_spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2106.trgt.sorted.spanning.bam"
2025-09-15 20:24:42.884 wdl.w:ptcp.t:call-tar_outputs-09 INFO input :: name: "trgt_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2106.trgt.vcf"
2025-09-15 20:24:42.884 wdl.w:ptcp.t:call-tar_outputs-09 INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2106.mapped.bam.bai"
2025-09-15 20:24:42.884 wdl.w:ptcp.t:call-tar_outputs-09 INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2106.mapped.bam"
2025-09-15 20:24:42.884 wdl.w:ptcp.t:call-tar_outputs-09 INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2106"
2025-09-15 20:24:42.884 wdl.w:ptcp.t:call-tar_outputs-09 INFO eval :: name: "threads", value: 1
2025-09-15 20:24:42.885 wdl.w:ptcp.t:call-tar_outputs-09 INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:42.885 wdl.w:ptcp.t:call-tar_outputs-09 INFO eval :: name: "disk_size", value: 6
2025-09-15 20:24:42.885 wdl.w:ptcp.t:call-tar_outputs-09 INFO eval :: name: "output_tarball", value: "m84036_250809_035451_s4.bc2106.tar"
2025-09-15 20:24:42.886 wdl.w:ptcp.t:call-tar_outputs-09 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:42.886 wdl.w:ptcp.t:call-tar_outputs-09 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:42.886 wdl.w:ptcp.t:call-tar_outputs-09 INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:42.887 wdl.w:ptcp.t:call-tar_outputs-09 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:42.894 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_motifs_waterfall NOTICE done
2025-09-15 20:24:42.897 wdl.w:ptcp.w:call-sawfish-21.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:38][sawfish][INFO] Starting sawfish 2.0.3
2025-09-15 20:24:42.897 wdl.w:ptcp.w:call-sawfish-21.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:38][sawfish][INFO] cmdline: sawfish joint-call --threads 16 --sample m84036_250809_035451_s4.bc2118_sawfish_discover --output-dir m84036_250809_035451_s4.bc2118_sawfish
2025-09-15 20:24:42.897 wdl.w:ptcp.w:call-sawfish-21.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:38][sawfish][INFO] Running on 16 threads
2025-09-15 20:24:42.897 wdl.w:ptcp.w:call-sawfish-21.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:38][sawfish][INFO] Reading reference genome from file '/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa'
2025-09-15 20:24:42.897 wdl.w:ptcp.w:call-sawfish-21.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:41][sawfish][INFO] Reading sawfish-discover results from 1 samples
2025-09-15 20:24:42.897 wdl.w:ptcp.w:call-sawfish-21.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:41][sawfish][INFO] Writing depth track to bigwig file: 'm84036_250809_035451_s4.bc2118_sawfish/samples/sample0001_UnknownSampleName/depth.bw'
2025-09-15 20:24:42.898 wdl.w:ptcp.w:call-sawfish-21.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:42][sawfish][INFO] Merging SV haplotypes
2025-09-15 20:24:42.898 wdl.w:ptcp.w:call-sawfish-21.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:42][sawfish][INFO] Finished merging SV haplotypes across samples
2025-09-15 20:24:42.898 wdl.w:ptcp.w:call-sawfish-21.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:42][sawfish][INFO] Writing merged contig alignments to bam file: 'm84036_250809_035451_s4.bc2118_sawfish/contig.alignment.bam'
2025-09-15 20:24:42.898 wdl.w:ptcp.w:call-sawfish-21.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:42][sawfish][INFO] Starting SV candidate cluster genotyping
2025-09-15 20:24:42.898 wdl.w:ptcp.w:call-sawfish-21.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:42][sawfish][INFO] Finished genotyping all SV candidate clusters
2025-09-15 20:24:42.898 wdl.w:ptcp.w:call-sawfish-21.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:42][sawfish][INFO] Starting joint CNV/SV refinement
2025-09-15 20:24:42.898 wdl.w:ptcp.w:call-sawfish-21.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:42][sawfish][INFO] Merged 0 CNVs into corresponding breakpoint-based SVs
2025-09-15 20:24:42.898 wdl.w:ptcp.w:call-sawfish-21.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:42][sawfish][INFO] Writing genotyped structural variants to file: 'm84036_250809_035451_s4.bc2118_sawfish/genotyped.sv.vcf.gz'
2025-09-15 20:24:42.898 wdl.w:ptcp.w:call-sawfish-21.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:42][sawfish][INFO] Writing run statistics to file: 'm84036_250809_035451_s4.bc2118_sawfish/run.stats.json'
2025-09-15 20:24:42.898 wdl.w:ptcp.w:call-sawfish-21.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:42][sawfish][INFO] sawfish completed. Total Runtime: 00:00:04.186
2025-09-15 20:24:42.905 wdl.w:ptcp.w:call-trgt-47 NOTICE finish :: job: "call-trgt_plot_motifs_waterfall"
2025-09-15 20:24:42.905 wdl.w:ptcp.w:call-trgt-47 INFO output :: job: "call-trgt_plot_motifs_waterfall", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-47/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2144.motifs_waterfall.trgt_plots.zip"}
2025-09-15 20:24:42.906 wdl.w:ptcp.w:call-trgt-47 INFO visit :: node: "output-images_motifs_waterfall", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-47/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2144.motifs_waterfall.trgt_plots.zip"}
2025-09-15 20:24:42.907 wdl.w:ptcp.w:call-sawfish-13 NOTICE done
2025-09-15 20:24:42.912 wdl.w:ptcp.w:call-trgt-42.t:call-get_reads_overlapping_repeats NOTICE task setup :: name: "get_reads_overlapping_repeats", source: "./trgt.wdl", line: 182, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-42/call-get_reads_overlapping_repeats", thread: 140610879071808
2025-09-15 20:24:42.913 wdl.w:ptcp NOTICE finish :: job: "call-sawfish-13"
2025-09-15 20:24:42.913 wdl.w:ptcp INFO output :: job: "call-sawfish-13", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-13/out/m84036_250809_035451_s4.bc2110_sawfish/m84036_250809_035451_s4.bc2110.sv.vcf.gz", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-13/out/m84036_250809_035451_s4.bc2110.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-13/out/m84036_250809_035451_s4.bc2110_sawfish/m84036_250809_035451_s4.bc2110.sv.vcf.gz.tbi", "minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-13/out/m84036_250809_035451_s4.bc2110.minimap2.bam.bai"}
2025-09-15 20:24:42.914 wdl.w:ptcp NOTICE ready :: job: "call-tar_outputs-13", callee: "tar_outputs"
2025-09-15 20:24:42.914 wdl.w:ptcp INFO input :: job: "call-tar_outputs-13", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "sawfish_vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-13/out/m84036_250809_035451_s4.bc2110_sawfish/m84036_250809_035451_s4.bc2110.sv.vcf.gz.tbi", "sawfish_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-13/out/m84036_250809_035451_s4.bc2110_sawfish/m84036_250809_035451_s4.bc2110.sv.vcf.gz", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-13/out/m84036_250809_035451_s4.bc2110.f8inversion.json", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-13/out/m84036_250809_035451_s4.bc2110_paraphase/m84036_250809_035451_s4.bc2110.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-13/out/m84036_250809_035451_s4.bc2110_paraphase/m84036_250809_035451_s4.bc2110.paraphase.bam", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-13/out/m84036_250809_035451_s4.bc2110_paraphase/m84036_250809_035451_s4.bc2110.paraphase.json", "trgt_spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-13/out/m84036_250809_035451_s4.bc2110.trgt.sorted.spanning.bam.bai", "trgt_spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-13/out/m84036_250809_035451_s4.bc2110.trgt.sorted.spanning.bam", "trgt_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-13/out/m84036_250809_035451_s4.bc2110.trgt.vcf", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-13/out/m84036_250809_035451_s4.bc2110.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-13/out/m84036_250809_035451_s4.bc2110.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2110"}
2025-09-15 20:24:42.921 wdl.w:ptcp.w:call-sawfish-68 NOTICE workflow start :: name: "sawfish", source: "./sawfish.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-68"
2025-09-15 20:24:42.932 wdl.w:ptcp.w:call-trgt-42.t:call-get_reads_overlapping_repeats INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:42.932 wdl.w:ptcp.w:call-trgt-42.t:call-get_reads_overlapping_repeats INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:42.933 wdl.w:ptcp.w:call-trgt-42.t:call-get_reads_overlapping_repeats INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2139.mapped.bam.bai"
2025-09-15 20:24:42.933 wdl.w:ptcp.w:call-trgt-42.t:call-get_reads_overlapping_repeats INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2139.mapped.bam"
2025-09-15 20:24:42.933 wdl.w:ptcp.w:call-trgt-42.t:call-get_reads_overlapping_repeats INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2139"
2025-09-15 20:24:42.933 wdl.w:ptcp.w:call-trgt-42.t:call-get_reads_overlapping_repeats INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:42.933 wdl.w:ptcp.w:call-trgt-42.t:call-get_reads_overlapping_repeats INFO eval :: name: "expand_size", value: 3000
2025-09-15 20:24:42.933 wdl.w:ptcp.w:call-trgt-42.t:call-get_reads_overlapping_repeats INFO eval :: name: "threads", value: 1
2025-09-15 20:24:42.934 wdl.w:ptcp.w:call-trgt-42.t:call-get_reads_overlapping_repeats INFO eval :: name: "expanded_bed_name", value: "m84036_250809_035451_s4.bc2139.expanded.bed"
2025-09-15 20:24:42.934 wdl.w:ptcp.w:call-trgt-42.t:call-get_reads_overlapping_repeats INFO eval :: name: "disk_size", value: 11
2025-09-15 20:24:42.934 wdl.w:ptcp.w:call-trgt-42.t:call-get_reads_overlapping_repeats INFO eval :: name: "output_name", value: "m84036_250809_035451_s4.bc2139.repeats.bam"
2025-09-15 20:24:42.934 wdl.w:ptcp.w:call-trgt-42.t:call-get_reads_overlapping_repeats INFO eval :: name: "index_name", value: "m84036_250809_035451_s4.bc2139.repeats.bam.bai"
2025-09-15 20:24:42.934 wdl.w:ptcp.w:call-trgt-42.t:call-get_reads_overlapping_repeats INFO eval :: name: "output_name_with_index", value: "m84036_250809_035451_s4.bc2139.repeats.bam##idx##m84036_250809_035451_s4.bc2139.repeats.bam.bai"
2025-09-15 20:24:42.935 wdl.w:ptcp.w:call-trgt-42.t:call-get_reads_overlapping_repeats INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:42.935 wdl.w:ptcp.w:call-trgt-42.t:call-get_reads_overlapping_repeats WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:42.936 wdl.w:ptcp.w:call-trgt-42.t:call-get_reads_overlapping_repeats INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:42.936 wdl.w:ptcp.w:call-trgt-42.t:call-get_reads_overlapping_repeats INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:42.938 wdl.w:ptcp.w:call-sawfish-68 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:24:42.938 wdl.w:ptcp.w:call-sawfish-68 INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:24:42.938 wdl.w:ptcp.w:call-sawfish-68 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-68/out/m84036_250809_035451_s4.bc2165.mapped.bam"}
2025-09-15 20:24:42.938 wdl.w:ptcp.w:call-sawfish-68 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-68/out/m84036_250809_035451_s4.bc2165.mapped.bam.bai"}
2025-09-15 20:24:42.938 wdl.w:ptcp.w:call-sawfish-68 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:24:42.938 wdl.w:ptcp.w:call-sawfish-68 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:24:42.939 wdl.w:ptcp.w:call-sawfish-68 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2165"}
2025-09-15 20:24:42.939 wdl.w:ptcp.w:call-sawfish-68 NOTICE ready :: job: "call-run_sawfish", callee: "run_sawfish"
2025-09-15 20:24:42.939 wdl.w:ptcp.w:call-sawfish-68 INFO input :: job: "call-run_sawfish", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-68/out/m84036_250809_035451_s4.bc2165.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-68/out/m84036_250809_035451_s4.bc2165.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2165"}
2025-09-15 20:24:42.962 wdl.w:ptcp.w:call-sawfish-05.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:21][sawfish][INFO] Starting sawfish 2.0.3
2025-09-15 20:24:42.963 wdl.w:ptcp.w:call-sawfish-05.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:21][sawfish][INFO] cmdline: sawfish discover --disable-cnv --threads 16 --ref /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa --bam m84036_250809_035451_s4.bc2102.minimap2.bam --output-dir m84036_250809_035451_s4.bc2102_sawfish_discover
2025-09-15 20:24:42.963 wdl.w:ptcp.w:call-sawfish-05.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:21][sawfish][INFO] Running on 16 threads
2025-09-15 20:24:42.963 wdl.w:ptcp.w:call-sawfish-05.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:21][sawfish][INFO] Writing discover settings to file: 'm84036_250809_035451_s4.bc2102_sawfish_discover/discover.settings.json'
2025-09-15 20:24:42.964 wdl.w:ptcp.w:call-sawfish-05.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:21][sawfish][INFO] Reading reference genome from file '/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa'
2025-09-15 20:24:42.964 wdl.w:ptcp.w:call-sawfish-05.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:37][sawfish][INFO] Processing alignment file '/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2102.minimap2.bam'
2025-09-15 20:24:42.964 wdl.w:ptcp.w:call-sawfish-05.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:37][sawfish][INFO] Finished processing all alignments
2025-09-15 20:24:42.964 wdl.w:ptcp.w:call-sawfish-05.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:37][sawfish][INFO] Writing depth bins to binary file: 'm84036_250809_035451_s4.bc2102_sawfish_discover/depth.mpack'
2025-09-15 20:24:42.964 wdl.w:ptcp.w:call-sawfish-05.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:38][sawfish][INFO] Writing max sv depth genome regions to bed file: 'm84036_250809_035451_s4.bc2102_sawfish_discover/max.depth.bed'
2025-09-15 20:24:42.964 wdl.w:ptcp.w:call-sawfish-05.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:38][sawfish][INFO] Completing breakpoint observation clustering
2025-09-15 20:24:42.964 wdl.w:ptcp.w:call-sawfish-05.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:38][sawfish][INFO] Finished breakpoint observation clustering
2025-09-15 20:24:42.964 wdl.w:ptcp.w:call-sawfish-05.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:38][sawfish][INFO] Consolidating adjacent indel candidates
2025-09-15 20:24:42.964 wdl.w:ptcp.w:call-sawfish-05.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:38][sawfish][INFO] Finding large insertion candidates
2025-09-15 20:24:42.964 wdl.w:ptcp.w:call-sawfish-05.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:38][sawfish][INFO] Writing breakpoint_cluster debug bed file: 'm84036_250809_035451_s4.bc2102_sawfish_discover/debug.breakpoint_clusters.bed'
2025-09-15 20:24:42.964 wdl.w:ptcp.w:call-sawfish-05.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:38][sawfish][INFO] Refining SV Candidates
2025-09-15 20:24:42.964 wdl.w:ptcp.w:call-sawfish-05.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:38][sawfish][INFO] Writing debug assembly region bed file: 'm84036_250809_035451_s4.bc2102_sawfish_discover/assembly.regions.bed'
2025-09-15 20:24:42.964 wdl.w:ptcp.w:call-sawfish-05.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:38][sawfish][INFO] Starting refinement of breakpoint evidence clusters
2025-09-15 20:24:42.964 wdl.w:ptcp.w:call-sawfish-05.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:38][sawfish][INFO] Finished refining all breakpoint evidence clusters
2025-09-15 20:24:42.964 wdl.w:ptcp.w:call-sawfish-05.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:38][sawfish][INFO] Writing all contig alignments to bam file: 'm84036_250809_035451_s4.bc2102_sawfish_discover/contig.alignment.bam'
2025-09-15 20:24:42.964 wdl.w:ptcp.w:call-sawfish-05.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:38][sawfish][INFO] Writing candidate structural variants to file: 'm84036_250809_035451_s4.bc2102_sawfish_discover/candidate.sv.bcf'
2025-09-15 20:24:42.965 wdl.w:ptcp.w:call-sawfish-05.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:38][sawfish][INFO] Writing run statistics to file: 'm84036_250809_035451_s4.bc2102_sawfish_discover/run.stats.json'
2025-09-15 20:24:42.965 wdl.w:ptcp.w:call-sawfish-05.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:38][sawfish][INFO] sawfish completed. Total Runtime: 00:00:17.062
2025-09-15 20:24:42.965 wdl.w:ptcp.w:call-sawfish-05.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:38][sawfish][INFO] Starting sawfish 2.0.3
2025-09-15 20:24:42.965 wdl.w:ptcp.w:call-sawfish-05.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:38][sawfish][INFO] cmdline: sawfish joint-call --threads 16 --sample m84036_250809_035451_s4.bc2102_sawfish_discover --output-dir m84036_250809_035451_s4.bc2102_sawfish
2025-09-15 20:24:42.965 wdl.w:ptcp.w:call-sawfish-05.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:38][sawfish][INFO] Running on 16 threads
2025-09-15 20:24:42.965 wdl.w:ptcp.w:call-sawfish-05.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:38][sawfish][INFO] Reading reference genome from file '/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa'
2025-09-15 20:24:42.965 wdl.w:ptcp.w:call-sawfish-05.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:41][sawfish][INFO] Reading sawfish-discover results from 1 samples
2025-09-15 20:24:42.965 wdl.w:ptcp.w:call-sawfish-05.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:41][sawfish][INFO] Writing depth track to bigwig file: 'm84036_250809_035451_s4.bc2102_sawfish/samples/sample0001_UnknownSampleName/depth.bw'
2025-09-15 20:24:42.965 wdl.w:ptcp.w:call-sawfish-05.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:42][sawfish][INFO] Merging SV haplotypes
2025-09-15 20:24:42.965 wdl.w:ptcp.w:call-sawfish-05.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:42][sawfish][INFO] Finished merging SV haplotypes across samples
2025-09-15 20:24:42.965 wdl.w:ptcp.w:call-sawfish-05.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:42][sawfish][INFO] Writing merged contig alignments to bam file: 'm84036_250809_035451_s4.bc2102_sawfish/contig.alignment.bam'
2025-09-15 20:24:42.965 wdl.w:ptcp.w:call-sawfish-05.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:42][sawfish][INFO] Starting SV candidate cluster genotyping
2025-09-15 20:24:42.965 wdl.w:ptcp.w:call-sawfish-05.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:42][sawfish][INFO] Finished genotyping all SV candidate clusters
2025-09-15 20:24:42.965 wdl.w:ptcp.w:call-sawfish-05.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:42][sawfish][INFO] Starting joint CNV/SV refinement
2025-09-15 20:24:42.965 wdl.w:ptcp.w:call-sawfish-05.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:42][sawfish][INFO] Merged 0 CNVs into corresponding breakpoint-based SVs
2025-09-15 20:24:42.966 wdl.w:ptcp.w:call-sawfish-05.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:42][sawfish][INFO] Writing genotyped structural variants to file: 'm84036_250809_035451_s4.bc2102_sawfish/genotyped.sv.vcf.gz'
2025-09-15 20:24:42.966 wdl.w:ptcp.w:call-sawfish-05.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:42][sawfish][INFO] Writing run statistics to file: 'm84036_250809_035451_s4.bc2102_sawfish/run.stats.json'
2025-09-15 20:24:42.966 wdl.w:ptcp.w:call-sawfish-05.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:42][sawfish][INFO] sawfish completed. Total Runtime: 00:00:04.150
2025-09-15 20:24:42.995 wdl.w:ptcp.t:call-tar_outputs-09 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 17, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-09/_singularity_tmpdir_fioezta1"
2025-09-15 20:24:42.996 wdl.w:ptcp.t:call-tar_outputs-09 INFO Slurm invocation: srun --job-name call-tar_outputs-09 --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-09/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-09/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-09/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-09/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-09/out/m84036_250809_035451_s4.bc2106_sawfish/m84036_250809_035451_s4.bc2106.sv.vcf.gz.tbi:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2106.sv.vcf.gz.tbi:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-09/out/m84036_250809_035451_s4.bc2106_sawfish/m84036_250809_035451_s4.bc2106.sv.vcf.gz:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2106.sv.vcf.gz:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-09/out/m84036_250809_035451_s4.bc2106_paraphase/m84036_250809_035451_s4.bc2106.paraphase.json:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2106.paraphase.json:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-09/out/m84036_250809_035451_s4.bc2106_paraphase/m84036_250809_035451_s4.bc2106.paraphase.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2106.paraphase.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-09/out/m84036_250809_035451_s4.bc2106_paraphase/m84036_250809_035451_s4.bc2106.paraphase.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2106.paraphase.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-09/out/m84036_250809_035451_s4.bc2106.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2106.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-09/out/m84036_250809_035451_s4.bc2106.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2106.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-09/out/m84036_250809_035451_s4.bc2106.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2106.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-09/out/m84036_250809_035451_s4.bc2106.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2106.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-09/out/m84036_250809_035451_s4.bc2106.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2106.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-09/out/m84036_250809_035451_s4.bc2106.f8inversion.json:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2106.f8inversion.json:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-09/_singularity_tmpdir_fioezta1/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-09/_singularity_tmpdir_fioezta1/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:42.997 wdl.w:ptcp.w:call-trgt-42.t:call-get_reads_overlapping_repeats INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 9, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-42/call-get_reads_overlapping_repeats/_singularity_tmpdir_0zfmy300"
2025-09-15 20:24:42.998 wdl.w:ptcp.w:call-trgt-42.t:call-get_reads_overlapping_repeats INFO Slurm invocation: srun --job-name call-get_reads_overlapping_repeats --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-42/call-get_reads_overlapping_repeats/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-42/call-get_reads_overlapping_repeats/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-42/call-get_reads_overlapping_repeats/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-42/call-get_reads_overlapping_repeats/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-42/out/m84036_250809_035451_s4.bc2139.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2139.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-42/out/m84036_250809_035451_s4.bc2139.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2139.mapped.bam:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-42/call-get_reads_overlapping_repeats/_singularity_tmpdir_0zfmy300/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-42/call-get_reads_overlapping_repeats/_singularity_tmpdir_0zfmy300/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:43.006 wdl.w:ptcp.w:call-sawfish-05.t:call-run_sawfish INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2102_sawfish/m84036_250809_035451_s4.bc2102.sv.vcf.gz"
2025-09-15 20:24:43.012 wdl.w:ptcp.w:call-sawfish-05.t:call-run_sawfish INFO output :: name: "vcf_tbi", value: "m84036_250809_035451_s4.bc2102_sawfish/m84036_250809_035451_s4.bc2102.sv.vcf.gz.tbi"
2025-09-15 20:24:43.013 wdl.w:ptcp.w:call-sawfish-05.t:call-run_sawfish INFO output :: name: "minimap2_bam", value: "m84036_250809_035451_s4.bc2102.minimap2.bam"
2025-09-15 20:24:43.014 wdl.w:ptcp.w:call-sawfish-05.t:call-run_sawfish INFO output :: name: "minimap2_bam_bai", value: "m84036_250809_035451_s4.bc2102.minimap2.bam.bai"
2025-09-15 20:24:43.020 wdl.w:ptcp.t:call-tar_outputs-09 NOTICE slurm_singularity run :: pid: 1202931, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-09/slurm_singularity.log.txt"
2025-09-15 20:24:43.020 wdl.w:ptcp.w:call-trgt-42.t:call-get_reads_overlapping_repeats NOTICE slurm_singularity run :: pid: 1202932, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-42/call-get_reads_overlapping_repeats/slurm_singularity.log.txt"
2025-09-15 20:24:43.097 wdl.w:ptcp.w:call-sawfish-30.t:call-run_sawfish INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2127_sawfish/m84036_250809_035451_s4.bc2127.sv.vcf.gz"
2025-09-15 20:24:43.104 wdl.w:ptcp.w:call-sawfish-30.t:call-run_sawfish INFO output :: name: "vcf_tbi", value: "m84036_250809_035451_s4.bc2127_sawfish/m84036_250809_035451_s4.bc2127.sv.vcf.gz.tbi"
2025-09-15 20:24:43.105 wdl.w:ptcp.w:call-sawfish-30.t:call-run_sawfish INFO output :: name: "minimap2_bam", value: "m84036_250809_035451_s4.bc2127.minimap2.bam"
2025-09-15 20:24:43.107 wdl.w:ptcp.w:call-sawfish-30.t:call-run_sawfish INFO output :: name: "minimap2_bam_bai", value: "m84036_250809_035451_s4.bc2127.minimap2.bam.bai"
2025-09-15 20:24:43.179 wdl.w:ptcp.w:call-sawfish-05.t:call-run_sawfish NOTICE done
2025-09-15 20:24:43.185 wdl.w:ptcp.w:call-sawfish-05 NOTICE finish :: job: "call-run_sawfish"
2025-09-15 20:24:43.186 wdl.w:ptcp.w:call-sawfish-05 INFO output :: job: "call-run_sawfish", values: {"minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-05/call-run_sawfish/out/m84036_250809_035451_s4.bc2102.minimap2.bam.bai", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-05/call-run_sawfish/out/m84036_250809_035451_s4.bc2102.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-05/call-run_sawfish/out/m84036_250809_035451_s4.bc2102_sawfish/m84036_250809_035451_s4.bc2102.sv.vcf.gz.tbi", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-05/call-run_sawfish/out/m84036_250809_035451_s4.bc2102_sawfish/m84036_250809_035451_s4.bc2102.sv.vcf.gz"}
2025-09-15 20:24:43.186 wdl.w:ptcp.w:call-sawfish-05 INFO visit :: node: "output-minimap2_bam", values: {"minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-05/call-run_sawfish/out/m84036_250809_035451_s4.bc2102.minimap2.bam"}
2025-09-15 20:24:43.186 wdl.w:ptcp.w:call-sawfish-05 INFO visit :: node: "output-minimap2_bam_bai", values: {"minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-05/call-run_sawfish/out/m84036_250809_035451_s4.bc2102.minimap2.bam.bai"}
2025-09-15 20:24:43.186 wdl.w:ptcp.w:call-sawfish-05 INFO visit :: node: "output-vcf", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-05/call-run_sawfish/out/m84036_250809_035451_s4.bc2102_sawfish/m84036_250809_035451_s4.bc2102.sv.vcf.gz"}
2025-09-15 20:24:43.186 wdl.w:ptcp.w:call-sawfish-05 INFO visit :: node: "output-vcf_tbi", values: {"vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-05/call-run_sawfish/out/m84036_250809_035451_s4.bc2102_sawfish/m84036_250809_035451_s4.bc2102.sv.vcf.gz.tbi"}
2025-09-15 20:24:43.186 wdl.w:ptcp.w:call-sawfish-05 INFO visit :: node: "outputs", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-05/call-run_sawfish/out/m84036_250809_035451_s4.bc2102_sawfish/m84036_250809_035451_s4.bc2102.sv.vcf.gz", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-05/call-run_sawfish/out/m84036_250809_035451_s4.bc2102.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-05/call-run_sawfish/out/m84036_250809_035451_s4.bc2102_sawfish/m84036_250809_035451_s4.bc2102.sv.vcf.gz.tbi", "minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-05/call-run_sawfish/out/m84036_250809_035451_s4.bc2102.minimap2.bam.bai"}
2025-09-15 20:24:43.194 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_genotype NOTICE task setup :: name: "trgt_genotype", source: "./trgt.wdl", line: 272, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-42/call-trgt_genotype", thread: 140613571819072
2025-09-15 20:24:43.216 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_genotype INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:43.216 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_genotype INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:43.216 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_genotype INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:43.216 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_genotype INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:43.216 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_genotype INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2139.mapped.bam.bai"
2025-09-15 20:24:43.216 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_genotype INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2139.mapped.bam"
2025-09-15 20:24:43.216 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_genotype INFO input :: name: "sex", value: "F"
2025-09-15 20:24:43.216 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_genotype INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2139"
2025-09-15 20:24:43.216 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_genotype INFO eval :: name: "mem_gb", value: 16
2025-09-15 20:24:43.217 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_genotype INFO eval :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2139.trgt"
2025-09-15 20:24:43.217 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_genotype INFO eval :: name: "threads", value: 8
2025-09-15 20:24:43.217 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_genotype INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:43.217 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_genotype INFO eval :: name: "karyotype", value: "XX"
2025-09-15 20:24:43.217 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_genotype INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 8, memory_reservation: 16000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:43.218 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_genotype WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:43.218 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_genotype INFO provisioned :: seconds_waited: 0, cpu: 8, mem_bytes: 16000000000
2025-09-15 20:24:43.218 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_genotype INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:43.223 wdl.w:ptcp.w:call-sawfish-21.t:call-run_sawfish INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2118_sawfish/m84036_250809_035451_s4.bc2118.sv.vcf.gz"
2025-09-15 20:24:43.229 wdl.w:ptcp.w:call-sawfish-21.t:call-run_sawfish INFO output :: name: "vcf_tbi", value: "m84036_250809_035451_s4.bc2118_sawfish/m84036_250809_035451_s4.bc2118.sv.vcf.gz.tbi"
2025-09-15 20:24:43.230 wdl.w:ptcp.w:call-sawfish-21.t:call-run_sawfish INFO output :: name: "minimap2_bam", value: "m84036_250809_035451_s4.bc2118.minimap2.bam"
2025-09-15 20:24:43.232 wdl.w:ptcp.w:call-sawfish-21.t:call-run_sawfish INFO output :: name: "minimap2_bam_bai", value: "m84036_250809_035451_s4.bc2118.minimap2.bam.bai"
2025-09-15 20:24:43.249 wdl.w:ptcp.w:call-sawfish-05 NOTICE done
2025-09-15 20:24:43.254 wdl.w:ptcp NOTICE finish :: job: "call-sawfish-05"
2025-09-15 20:24:43.255 wdl.w:ptcp INFO output :: job: "call-sawfish-05", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-05/out/m84036_250809_035451_s4.bc2102_sawfish/m84036_250809_035451_s4.bc2102.sv.vcf.gz", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-05/out/m84036_250809_035451_s4.bc2102.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-05/out/m84036_250809_035451_s4.bc2102_sawfish/m84036_250809_035451_s4.bc2102.sv.vcf.gz.tbi", "minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-05/out/m84036_250809_035451_s4.bc2102.minimap2.bam.bai"}
2025-09-15 20:24:43.255 wdl.w:ptcp NOTICE ready :: job: "call-tar_outputs-05", callee: "tar_outputs"
2025-09-15 20:24:43.256 wdl.w:ptcp INFO input :: job: "call-tar_outputs-05", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "sawfish_vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-05/out/m84036_250809_035451_s4.bc2102_sawfish/m84036_250809_035451_s4.bc2102.sv.vcf.gz.tbi", "sawfish_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-05/out/m84036_250809_035451_s4.bc2102_sawfish/m84036_250809_035451_s4.bc2102.sv.vcf.gz", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-05/out/m84036_250809_035451_s4.bc2102.f8inversion.json", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-05/out/m84036_250809_035451_s4.bc2102_paraphase/m84036_250809_035451_s4.bc2102.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-05/out/m84036_250809_035451_s4.bc2102_paraphase/m84036_250809_035451_s4.bc2102.paraphase.bam", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-05/out/m84036_250809_035451_s4.bc2102_paraphase/m84036_250809_035451_s4.bc2102.paraphase.json", "trgt_spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-05/out/m84036_250809_035451_s4.bc2102.trgt.sorted.spanning.bam.bai", "trgt_spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-05/out/m84036_250809_035451_s4.bc2102.trgt.sorted.spanning.bam", "trgt_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-05/out/m84036_250809_035451_s4.bc2102.trgt.vcf", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-05/out/m84036_250809_035451_s4.bc2102.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-05/out/m84036_250809_035451_s4.bc2102.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2102"}
2025-09-15 20:24:43.264 wdl.w:ptcp.w:call-trgt-68 NOTICE workflow start :: name: "trgt", source: "./trgt.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-68"
2025-09-15 20:24:43.283 wdl.w:ptcp.w:call-trgt-68 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:24:43.284 wdl.w:ptcp.w:call-trgt-68 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-68/out/m84036_250809_035451_s4.bc2165.mapped.bam"}
2025-09-15 20:24:43.284 wdl.w:ptcp.w:call-trgt-68 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-68/out/m84036_250809_035451_s4.bc2165.mapped.bam.bai"}
2025-09-15 20:24:43.284 wdl.w:ptcp.w:call-trgt-68 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:24:43.284 wdl.w:ptcp.w:call-trgt-68 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:24:43.284 wdl.w:ptcp.w:call-trgt-68 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2165"}
2025-09-15 20:24:43.284 wdl.w:ptcp.w:call-trgt-68 INFO visit :: node: "decl-sex", values: {"sex": "F"}
2025-09-15 20:24:43.284 wdl.w:ptcp.w:call-trgt-68 INFO visit :: node: "decl-trgt_bed", values: {"trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"}
2025-09-15 20:24:43.284 wdl.w:ptcp.w:call-trgt-68 NOTICE ready :: job: "call-get_reads_overlapping_repeats", callee: "get_reads_overlapping_repeats"
2025-09-15 20:24:43.284 wdl.w:ptcp.w:call-trgt-68 INFO input :: job: "call-get_reads_overlapping_repeats", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-68/out/m84036_250809_035451_s4.bc2165.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-68/out/m84036_250809_035451_s4.bc2165.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2165"}
2025-09-15 20:24:43.285 wdl.w:ptcp.w:call-trgt-68 NOTICE ready :: job: "call-trgt_genotype", callee: "trgt_genotype"
2025-09-15 20:24:43.285 wdl.w:ptcp.w:call-trgt-68 INFO input :: job: "call-trgt_genotype", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-68/out/m84036_250809_035451_s4.bc2165.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-68/out/m84036_250809_035451_s4.bc2165.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2165"}
2025-09-15 20:24:43.287 wdl.w:ptcp.w:call-trgt-44.t:call-trgt_plot_meth_allele.slurm_singularity INFO srun: job 51797764 queued and waiting for resources
2025-09-15 20:24:43.287 wdl.w:ptcp.w:call-trgt-44.t:call-trgt_plot_meth_allele.slurm_singularity INFO srun: job 51797764 has been allocated resources
2025-09-15 20:24:43.287 wdl.w:ptcp.w:call-trgt-44.t:call-trgt_plot_meth_allele.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:43.288 wdl.w:ptcp.w:call-sawfish-30.t:call-run_sawfish NOTICE done
2025-09-15 20:24:43.293 wdl.w:ptcp.w:call-trgt-44.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO srun: job 51797765 queued and waiting for resources
2025-09-15 20:24:43.293 wdl.w:ptcp.w:call-trgt-44.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO srun: job 51797765 has been allocated resources
2025-09-15 20:24:43.293 wdl.w:ptcp.w:call-trgt-44.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:43.310 wdl.w:ptcp.w:call-sawfish-30 NOTICE finish :: job: "call-run_sawfish"
2025-09-15 20:24:43.310 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_genotype INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 11, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-42/call-trgt_genotype/_singularity_tmpdir_l8ah4lko"
2025-09-15 20:24:43.310 wdl.w:ptcp.w:call-sawfish-30 INFO output :: job: "call-run_sawfish", values: {"minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-30/call-run_sawfish/out/m84036_250809_035451_s4.bc2127.minimap2.bam.bai", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-30/call-run_sawfish/out/m84036_250809_035451_s4.bc2127.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-30/call-run_sawfish/out/m84036_250809_035451_s4.bc2127_sawfish/m84036_250809_035451_s4.bc2127.sv.vcf.gz.tbi", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-30/call-run_sawfish/out/m84036_250809_035451_s4.bc2127_sawfish/m84036_250809_035451_s4.bc2127.sv.vcf.gz"}
2025-09-15 20:24:43.310 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_genotype INFO Slurm invocation: srun --job-name call-trgt_genotype --partition compute,compute9 --cpus-per-task 8 --mem 15259M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-42/call-trgt_genotype/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-42/call-trgt_genotype/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-42/call-trgt_genotype/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-42/call-trgt_genotype/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-42/out/m84036_250809_035451_s4.bc2139.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2139.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-42/out/m84036_250809_035451_s4.bc2139.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2139.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-42/call-trgt_genotype/_singularity_tmpdir_l8ah4lko/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-42/call-trgt_genotype/_singularity_tmpdir_l8ah4lko/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:43.311 wdl.w:ptcp.w:call-sawfish-30 INFO visit :: node: "output-minimap2_bam", values: {"minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-30/call-run_sawfish/out/m84036_250809_035451_s4.bc2127.minimap2.bam"}
2025-09-15 20:24:43.312 wdl.w:ptcp.w:call-sawfish-30 INFO visit :: node: "output-minimap2_bam_bai", values: {"minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-30/call-run_sawfish/out/m84036_250809_035451_s4.bc2127.minimap2.bam.bai"}
2025-09-15 20:24:43.312 wdl.w:ptcp.w:call-sawfish-30 INFO visit :: node: "output-vcf", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-30/call-run_sawfish/out/m84036_250809_035451_s4.bc2127_sawfish/m84036_250809_035451_s4.bc2127.sv.vcf.gz"}
2025-09-15 20:24:43.314 wdl.w:ptcp.w:call-sawfish-30 INFO visit :: node: "output-vcf_tbi", values: {"vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-30/call-run_sawfish/out/m84036_250809_035451_s4.bc2127_sawfish/m84036_250809_035451_s4.bc2127.sv.vcf.gz.tbi"}
2025-09-15 20:24:43.314 wdl.w:ptcp.w:call-sawfish-30 INFO visit :: node: "outputs", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-30/call-run_sawfish/out/m84036_250809_035451_s4.bc2127_sawfish/m84036_250809_035451_s4.bc2127.sv.vcf.gz", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-30/call-run_sawfish/out/m84036_250809_035451_s4.bc2127.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-30/call-run_sawfish/out/m84036_250809_035451_s4.bc2127_sawfish/m84036_250809_035451_s4.bc2127.sv.vcf.gz.tbi", "minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-30/call-run_sawfish/out/m84036_250809_035451_s4.bc2127.minimap2.bam.bai"}
2025-09-15 20:24:43.321 wdl.w:ptcp.t:call-tar_outputs-29 NOTICE task setup :: name: "tar_outputs", source: "./common.wdl", line: 279, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-29", thread: 140610904249920
2025-09-15 20:24:43.342 wdl.w:ptcp.w:call-sawfish-02.t:call-run_sawfish INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2099_sawfish/m84036_250809_035451_s4.bc2099.sv.vcf.gz"
2025-09-15 20:24:43.350 wdl.w:ptcp.w:call-sawfish-02.t:call-run_sawfish INFO output :: name: "vcf_tbi", value: "m84036_250809_035451_s4.bc2099_sawfish/m84036_250809_035451_s4.bc2099.sv.vcf.gz.tbi"
2025-09-15 20:24:43.351 wdl.w:ptcp.w:call-sawfish-02.t:call-run_sawfish INFO output :: name: "minimap2_bam", value: "m84036_250809_035451_s4.bc2099.minimap2.bam"
2025-09-15 20:24:43.353 wdl.w:ptcp.w:call-sawfish-02.t:call-run_sawfish INFO output :: name: "minimap2_bam_bai", value: "m84036_250809_035451_s4.bc2099.minimap2.bam.bai"
2025-09-15 20:24:43.355 wdl.w:ptcp.t:call-tar_outputs-29 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:43.355 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_genotype NOTICE slurm_singularity run :: pid: 1202948, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-42/call-trgt_genotype/slurm_singularity.log.txt"
2025-09-15 20:24:43.356 wdl.w:ptcp.t:call-tar_outputs-29 INFO input :: name: "sawfish_vcf_tbi", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2126.sv.vcf.gz.tbi"
2025-09-15 20:24:43.356 wdl.w:ptcp.t:call-tar_outputs-29 INFO input :: name: "sawfish_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2126.sv.vcf.gz"
2025-09-15 20:24:43.356 wdl.w:ptcp.t:call-tar_outputs-29 INFO input :: name: "f8_json", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2126.f8inversion.json"
2025-09-15 20:24:43.356 wdl.w:ptcp.t:call-tar_outputs-29 INFO input :: name: "paraphase_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2126.paraphase.bam.bai"
2025-09-15 20:24:43.356 wdl.w:ptcp.t:call-tar_outputs-29 INFO input :: name: "paraphase_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2126.paraphase.bam"
2025-09-15 20:24:43.356 wdl.w:ptcp.t:call-tar_outputs-29 INFO input :: name: "paraphase_json", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2126.paraphase.json"
2025-09-15 20:24:43.356 wdl.w:ptcp.t:call-tar_outputs-29 INFO input :: name: "trgt_spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2126.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:43.356 wdl.w:ptcp.t:call-tar_outputs-29 INFO input :: name: "trgt_spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2126.trgt.sorted.spanning.bam"
2025-09-15 20:24:43.356 wdl.w:ptcp.t:call-tar_outputs-29 INFO input :: name: "trgt_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2126.trgt.vcf"
2025-09-15 20:24:43.357 wdl.w:ptcp.t:call-tar_outputs-29 INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2126.mapped.bam.bai"
2025-09-15 20:24:43.357 wdl.w:ptcp.t:call-tar_outputs-29 INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2126.mapped.bam"
2025-09-15 20:24:43.357 wdl.w:ptcp.t:call-tar_outputs-29 INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2126"
2025-09-15 20:24:43.358 wdl.w:ptcp.t:call-tar_outputs-29 INFO eval :: name: "threads", value: 1
2025-09-15 20:24:43.359 wdl.w:ptcp.t:call-tar_outputs-29 INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:43.359 wdl.w:ptcp.t:call-tar_outputs-29 INFO eval :: name: "disk_size", value: 6
2025-09-15 20:24:43.359 wdl.w:ptcp.t:call-tar_outputs-29 INFO eval :: name: "output_tarball", value: "m84036_250809_035451_s4.bc2126.tar"
2025-09-15 20:24:43.360 wdl.w:ptcp.t:call-tar_outputs-29 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:43.360 wdl.w:ptcp.t:call-tar_outputs-29 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:43.361 wdl.w:ptcp.t:call-tar_outputs-29 INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:43.361 wdl.w:ptcp.t:call-tar_outputs-29 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:43.388 wdl.w:ptcp.w:call-sawfish-30 NOTICE done
2025-09-15 20:24:43.395 wdl.w:ptcp NOTICE finish :: job: "call-sawfish-30"
2025-09-15 20:24:43.396 wdl.w:ptcp INFO output :: job: "call-sawfish-30", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-30/out/m84036_250809_035451_s4.bc2127_sawfish/m84036_250809_035451_s4.bc2127.sv.vcf.gz", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-30/out/m84036_250809_035451_s4.bc2127.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-30/out/m84036_250809_035451_s4.bc2127_sawfish/m84036_250809_035451_s4.bc2127.sv.vcf.gz.tbi", "minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-30/out/m84036_250809_035451_s4.bc2127.minimap2.bam.bai"}
2025-09-15 20:24:43.406 wdl.w:ptcp.w:call-paraphase-66 NOTICE workflow start :: name: "paraphase", source: "./paraphase.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-66"
2025-09-15 20:24:43.422 wdl.w:ptcp.w:call-paraphase-66 INFO visit :: node: "decl-annotation_vcf", values: {"annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf"}
2025-09-15 20:24:43.423 wdl.w:ptcp.w:call-paraphase-66 INFO visit :: node: "decl-config_file", values: {"config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml"}
2025-09-15 20:24:43.423 wdl.w:ptcp.w:call-paraphase-66 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:24:43.423 wdl.w:ptcp.w:call-paraphase-66 INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:24:43.423 wdl.w:ptcp.w:call-paraphase-66 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-66/out/m84036_250809_035451_s4.bc2163.mapped.bam"}
2025-09-15 20:24:43.423 wdl.w:ptcp.w:call-paraphase-66 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-66/out/m84036_250809_035451_s4.bc2163.mapped.bam.bai"}
2025-09-15 20:24:43.423 wdl.w:ptcp.w:call-paraphase-66 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:24:43.423 wdl.w:ptcp.w:call-paraphase-66 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:24:43.423 wdl.w:ptcp.w:call-paraphase-66 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2163"}
2025-09-15 20:24:43.423 wdl.w:ptcp.w:call-paraphase-66 INFO visit :: node: "decl-sex", values: {"sex": "F"}
2025-09-15 20:24:43.424 wdl.w:ptcp.w:call-paraphase-66 NOTICE ready :: job: "call-run_paraphase", callee: "run_paraphase"
2025-09-15 20:24:43.424 wdl.w:ptcp.w:call-paraphase-66 INFO input :: job: "call-run_paraphase", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf", "genome_version": "38", "config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-66/out/m84036_250809_035451_s4.bc2163.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-66/out/m84036_250809_035451_s4.bc2163.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2163"}
2025-09-15 20:24:43.460 wdl.w:ptcp.w:call-sawfish-21.t:call-run_sawfish NOTICE done
2025-09-15 20:24:43.487 wdl.w:ptcp.t:call-tar_outputs-29 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 17, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-29/_singularity_tmpdir_h08i59v0"
2025-09-15 20:24:43.488 wdl.w:ptcp.t:call-tar_outputs-29 INFO Slurm invocation: srun --job-name call-tar_outputs-29 --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-29/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-29/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-29/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-29/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-29/out/m84036_250809_035451_s4.bc2126_paraphase/m84036_250809_035451_s4.bc2126.paraphase.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2126.paraphase.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-29/out/m84036_250809_035451_s4.bc2126_paraphase/m84036_250809_035451_s4.bc2126.paraphase.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2126.paraphase.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-29/out/m84036_250809_035451_s4.bc2126_paraphase/m84036_250809_035451_s4.bc2126.paraphase.json:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2126.paraphase.json:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-29/out/m84036_250809_035451_s4.bc2126.f8inversion.json:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2126.f8inversion.json:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-29/out/m84036_250809_035451_s4.bc2126_sawfish/m84036_250809_035451_s4.bc2126.sv.vcf.gz:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2126.sv.vcf.gz:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-29/out/m84036_250809_035451_s4.bc2126_sawfish/m84036_250809_035451_s4.bc2126.sv.vcf.gz.tbi:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2126.sv.vcf.gz.tbi:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-29/out/m84036_250809_035451_s4.bc2126.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2126.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-29/out/m84036_250809_035451_s4.bc2126.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2126.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-29/out/m84036_250809_035451_s4.bc2126.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2126.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-29/out/m84036_250809_035451_s4.bc2126.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2126.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-29/out/m84036_250809_035451_s4.bc2126.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2126.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-29/_singularity_tmpdir_h08i59v0/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-29/_singularity_tmpdir_h08i59v0/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:43.500 wdl.w:ptcp.t:call-tar_outputs-29 NOTICE slurm_singularity run :: pid: 1202950, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-29/slurm_singularity.log.txt"
2025-09-15 20:24:43.518 wdl.w:ptcp.w:call-sawfish-21 NOTICE finish :: job: "call-run_sawfish"
2025-09-15 20:24:43.518 wdl.w:ptcp.w:call-sawfish-21 INFO output :: job: "call-run_sawfish", values: {"minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-21/call-run_sawfish/out/m84036_250809_035451_s4.bc2118.minimap2.bam.bai", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-21/call-run_sawfish/out/m84036_250809_035451_s4.bc2118.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-21/call-run_sawfish/out/m84036_250809_035451_s4.bc2118_sawfish/m84036_250809_035451_s4.bc2118.sv.vcf.gz.tbi", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-21/call-run_sawfish/out/m84036_250809_035451_s4.bc2118_sawfish/m84036_250809_035451_s4.bc2118.sv.vcf.gz"}
2025-09-15 20:24:43.518 wdl.w:ptcp.w:call-sawfish-21 INFO visit :: node: "output-minimap2_bam", values: {"minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-21/call-run_sawfish/out/m84036_250809_035451_s4.bc2118.minimap2.bam"}
2025-09-15 20:24:43.519 wdl.w:ptcp.w:call-sawfish-21 INFO visit :: node: "output-minimap2_bam_bai", values: {"minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-21/call-run_sawfish/out/m84036_250809_035451_s4.bc2118.minimap2.bam.bai"}
2025-09-15 20:24:43.519 wdl.w:ptcp.w:call-sawfish-21 INFO visit :: node: "output-vcf", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-21/call-run_sawfish/out/m84036_250809_035451_s4.bc2118_sawfish/m84036_250809_035451_s4.bc2118.sv.vcf.gz"}
2025-09-15 20:24:43.519 wdl.w:ptcp.w:call-sawfish-21 INFO visit :: node: "output-vcf_tbi", values: {"vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-21/call-run_sawfish/out/m84036_250809_035451_s4.bc2118_sawfish/m84036_250809_035451_s4.bc2118.sv.vcf.gz.tbi"}
2025-09-15 20:24:43.519 wdl.w:ptcp.w:call-sawfish-21 INFO visit :: node: "outputs", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-21/call-run_sawfish/out/m84036_250809_035451_s4.bc2118_sawfish/m84036_250809_035451_s4.bc2118.sv.vcf.gz", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-21/call-run_sawfish/out/m84036_250809_035451_s4.bc2118.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-21/call-run_sawfish/out/m84036_250809_035451_s4.bc2118_sawfish/m84036_250809_035451_s4.bc2118.sv.vcf.gz.tbi", "minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-21/call-run_sawfish/out/m84036_250809_035451_s4.bc2118.minimap2.bam.bai"}
2025-09-15 20:24:43.521 wdl.w:ptcp.w:call-sawfish-02.t:call-run_sawfish NOTICE done
2025-09-15 20:24:43.525 wdl.w:ptcp.w:call-paraphase-58.t:call-run_paraphase NOTICE task setup :: name: "run_paraphase", source: "./paraphase.wdl", line: 127, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-58/call-run_paraphase", thread: 140610384164416
2025-09-15 20:24:43.527 wdl.w:ptcp.w:call-sawfish-02 NOTICE finish :: job: "call-run_sawfish"
2025-09-15 20:24:43.527 wdl.w:ptcp.w:call-sawfish-02 INFO output :: job: "call-run_sawfish", values: {"minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-02/call-run_sawfish/out/m84036_250809_035451_s4.bc2099.minimap2.bam.bai", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-02/call-run_sawfish/out/m84036_250809_035451_s4.bc2099.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-02/call-run_sawfish/out/m84036_250809_035451_s4.bc2099_sawfish/m84036_250809_035451_s4.bc2099.sv.vcf.gz.tbi", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-02/call-run_sawfish/out/m84036_250809_035451_s4.bc2099_sawfish/m84036_250809_035451_s4.bc2099.sv.vcf.gz"}
2025-09-15 20:24:43.528 wdl.w:ptcp.w:call-sawfish-02 INFO visit :: node: "output-minimap2_bam", values: {"minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-02/call-run_sawfish/out/m84036_250809_035451_s4.bc2099.minimap2.bam"}
2025-09-15 20:24:43.528 wdl.w:ptcp.w:call-sawfish-02 INFO visit :: node: "output-minimap2_bam_bai", values: {"minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-02/call-run_sawfish/out/m84036_250809_035451_s4.bc2099.minimap2.bam.bai"}
2025-09-15 20:24:43.528 wdl.w:ptcp.w:call-sawfish-02 INFO visit :: node: "output-vcf", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-02/call-run_sawfish/out/m84036_250809_035451_s4.bc2099_sawfish/m84036_250809_035451_s4.bc2099.sv.vcf.gz"}
2025-09-15 20:24:43.528 wdl.w:ptcp.w:call-sawfish-02 INFO visit :: node: "output-vcf_tbi", values: {"vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-02/call-run_sawfish/out/m84036_250809_035451_s4.bc2099_sawfish/m84036_250809_035451_s4.bc2099.sv.vcf.gz.tbi"}
2025-09-15 20:24:43.528 wdl.w:ptcp.w:call-sawfish-02 INFO visit :: node: "outputs", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-02/call-run_sawfish/out/m84036_250809_035451_s4.bc2099_sawfish/m84036_250809_035451_s4.bc2099.sv.vcf.gz", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-02/call-run_sawfish/out/m84036_250809_035451_s4.bc2099.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-02/call-run_sawfish/out/m84036_250809_035451_s4.bc2099_sawfish/m84036_250809_035451_s4.bc2099.sv.vcf.gz.tbi", "minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-02/call-run_sawfish/out/m84036_250809_035451_s4.bc2099.minimap2.bam.bai"}
2025-09-15 20:24:43.534 wdl.w:ptcp.t:call-tar_outputs-12 NOTICE task setup :: name: "tar_outputs", source: "./common.wdl", line: 279, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-12", thread: 140611961206336
2025-09-15 20:24:43.549 wdl.w:ptcp.w:call-paraphase-58.t:call-run_paraphase INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:43.549 wdl.w:ptcp.w:call-paraphase-58.t:call-run_paraphase INFO input :: name: "annotation_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf"
2025-09-15 20:24:43.549 wdl.w:ptcp.w:call-paraphase-58.t:call-run_paraphase INFO input :: name: "genome_version", value: "38"
2025-09-15 20:24:43.549 wdl.w:ptcp.w:call-paraphase-58.t:call-run_paraphase INFO input :: name: "config_file", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/paraphase_config.GRCh38.yaml"
2025-09-15 20:24:43.549 wdl.w:ptcp.w:call-paraphase-58.t:call-run_paraphase INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:43.549 wdl.w:ptcp.w:call-paraphase-58.t:call-run_paraphase INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:43.549 wdl.w:ptcp.w:call-paraphase-58.t:call-run_paraphase INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2155.mapped.bam.bai"
2025-09-15 20:24:43.549 wdl.w:ptcp.w:call-paraphase-58.t:call-run_paraphase INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2155.mapped.bam"
2025-09-15 20:24:43.550 wdl.w:ptcp.w:call-paraphase-58.t:call-run_paraphase INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2155"
2025-09-15 20:24:43.550 wdl.w:ptcp.w:call-paraphase-58.t:call-run_paraphase INFO eval :: name: "threads", value: 4
2025-09-15 20:24:43.550 wdl.w:ptcp.w:call-paraphase-58.t:call-run_paraphase INFO eval :: name: "mem_gb", value: 8
2025-09-15 20:24:43.551 wdl.w:ptcp.w:call-paraphase-58.t:call-run_paraphase INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:43.551 wdl.w:ptcp.w:call-paraphase-58.t:call-run_paraphase INFO eval :: name: "out_dir", value: "m84036_250809_035451_s4.bc2155_paraphase"
2025-09-15 20:24:43.552 wdl.w:ptcp.w:call-paraphase-58.t:call-run_paraphase INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 4, memory_reservation: 8000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:43.552 wdl.w:ptcp.w:call-paraphase-58.t:call-run_paraphase WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:43.553 wdl.w:ptcp.w:call-paraphase-58.t:call-run_paraphase INFO provisioned :: seconds_waited: 0, cpu: 4, mem_bytes: 8000000000
2025-09-15 20:24:43.553 wdl.w:ptcp.w:call-paraphase-58.t:call-run_paraphase INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:43.561 wdl.w:ptcp.t:call-tar_outputs-12 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:43.561 wdl.w:ptcp.t:call-tar_outputs-12 INFO input :: name: "sawfish_vcf_tbi", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2109.sv.vcf.gz.tbi"
2025-09-15 20:24:43.561 wdl.w:ptcp.t:call-tar_outputs-12 INFO input :: name: "sawfish_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2109.sv.vcf.gz"
2025-09-15 20:24:43.561 wdl.w:ptcp.t:call-tar_outputs-12 INFO input :: name: "f8_json", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2109.f8inversion.json"
2025-09-15 20:24:43.561 wdl.w:ptcp.t:call-tar_outputs-12 INFO input :: name: "paraphase_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2109.paraphase.bam.bai"
2025-09-15 20:24:43.561 wdl.w:ptcp.t:call-tar_outputs-12 INFO input :: name: "paraphase_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2109.paraphase.bam"
2025-09-15 20:24:43.561 wdl.w:ptcp.t:call-tar_outputs-12 INFO input :: name: "paraphase_json", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2109.paraphase.json"
2025-09-15 20:24:43.561 wdl.w:ptcp.t:call-tar_outputs-12 INFO input :: name: "trgt_spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2109.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:43.561 wdl.w:ptcp.t:call-tar_outputs-12 INFO input :: name: "trgt_spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2109.trgt.sorted.spanning.bam"
2025-09-15 20:24:43.561 wdl.w:ptcp.t:call-tar_outputs-12 INFO input :: name: "trgt_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2109.trgt.vcf"
2025-09-15 20:24:43.561 wdl.w:ptcp.t:call-tar_outputs-12 INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2109.mapped.bam.bai"
2025-09-15 20:24:43.561 wdl.w:ptcp.t:call-tar_outputs-12 INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2109.mapped.bam"
2025-09-15 20:24:43.561 wdl.w:ptcp.t:call-tar_outputs-12 INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2109"
2025-09-15 20:24:43.561 wdl.w:ptcp.t:call-tar_outputs-12 INFO eval :: name: "threads", value: 1
2025-09-15 20:24:43.561 wdl.w:ptcp.t:call-tar_outputs-12 INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:43.562 wdl.w:ptcp.t:call-tar_outputs-12 INFO eval :: name: "disk_size", value: 6
2025-09-15 20:24:43.562 wdl.w:ptcp.t:call-tar_outputs-12 INFO eval :: name: "output_tarball", value: "m84036_250809_035451_s4.bc2109.tar"
2025-09-15 20:24:43.562 wdl.w:ptcp.t:call-tar_outputs-12 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:43.562 wdl.w:ptcp.t:call-tar_outputs-12 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:43.563 wdl.w:ptcp.t:call-tar_outputs-12 INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:43.563 wdl.w:ptcp.t:call-tar_outputs-12 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:43.577 wdl.w:ptcp.w:call-sawfish-21 NOTICE done
2025-09-15 20:24:43.583 wdl.w:ptcp NOTICE finish :: job: "call-sawfish-21"
2025-09-15 20:24:43.584 wdl.w:ptcp INFO output :: job: "call-sawfish-21", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-21/out/m84036_250809_035451_s4.bc2118_sawfish/m84036_250809_035451_s4.bc2118.sv.vcf.gz", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-21/out/m84036_250809_035451_s4.bc2118.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-21/out/m84036_250809_035451_s4.bc2118_sawfish/m84036_250809_035451_s4.bc2118.sv.vcf.gz.tbi", "minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-21/out/m84036_250809_035451_s4.bc2118.minimap2.bam.bai"}
2025-09-15 20:24:43.585 wdl.w:ptcp NOTICE ready :: job: "call-tar_outputs-21", callee: "tar_outputs"
2025-09-15 20:24:43.585 wdl.w:ptcp INFO input :: job: "call-tar_outputs-21", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "sawfish_vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-21/out/m84036_250809_035451_s4.bc2118_sawfish/m84036_250809_035451_s4.bc2118.sv.vcf.gz.tbi", "sawfish_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-21/out/m84036_250809_035451_s4.bc2118_sawfish/m84036_250809_035451_s4.bc2118.sv.vcf.gz", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-21/out/m84036_250809_035451_s4.bc2118.f8inversion.json", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-21/out/m84036_250809_035451_s4.bc2118_paraphase/m84036_250809_035451_s4.bc2118.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-21/out/m84036_250809_035451_s4.bc2118_paraphase/m84036_250809_035451_s4.bc2118.paraphase.bam", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-21/out/m84036_250809_035451_s4.bc2118_paraphase/m84036_250809_035451_s4.bc2118.paraphase.json", "trgt_spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-21/out/m84036_250809_035451_s4.bc2118.trgt.sorted.spanning.bam.bai", "trgt_spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-21/out/m84036_250809_035451_s4.bc2118.trgt.sorted.spanning.bam", "trgt_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-21/out/m84036_250809_035451_s4.bc2118.trgt.vcf", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-21/out/m84036_250809_035451_s4.bc2118.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-21/out/m84036_250809_035451_s4.bc2118.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2118"}
2025-09-15 20:24:43.591 wdl.w:ptcp.w:call-sawfish-66 NOTICE workflow start :: name: "sawfish", source: "./sawfish.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-66"
2025-09-15 20:24:43.601 wdl.w:ptcp.w:call-sawfish-02 NOTICE done
2025-09-15 20:24:43.606 wdl.w:ptcp NOTICE finish :: job: "call-sawfish-02"
2025-09-15 20:24:43.607 wdl.w:ptcp INFO output :: job: "call-sawfish-02", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-02/out/m84036_250809_035451_s4.bc2099_sawfish/m84036_250809_035451_s4.bc2099.sv.vcf.gz", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-02/out/m84036_250809_035451_s4.bc2099.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-02/out/m84036_250809_035451_s4.bc2099_sawfish/m84036_250809_035451_s4.bc2099.sv.vcf.gz.tbi", "minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-02/out/m84036_250809_035451_s4.bc2099.minimap2.bam.bai"}
2025-09-15 20:24:43.613 wdl.w:ptcp.w:call-sawfish-66 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:24:43.613 wdl.w:ptcp.w:call-sawfish-66 INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:24:43.613 wdl.w:ptcp.w:call-sawfish-66 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-66/out/m84036_250809_035451_s4.bc2163.mapped.bam"}
2025-09-15 20:24:43.613 wdl.w:ptcp.w:call-sawfish-66 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-66/out/m84036_250809_035451_s4.bc2163.mapped.bam.bai"}
2025-09-15 20:24:43.614 wdl.w:ptcp.w:call-sawfish-66 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:24:43.614 wdl.w:ptcp.w:call-sawfish-66 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:24:43.614 wdl.w:ptcp.w:call-sawfish-66 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2163"}
2025-09-15 20:24:43.614 wdl.w:ptcp.w:call-sawfish-66 NOTICE ready :: job: "call-run_sawfish", callee: "run_sawfish"
2025-09-15 20:24:43.614 wdl.w:ptcp.w:call-sawfish-66 INFO input :: job: "call-run_sawfish", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-66/out/m84036_250809_035451_s4.bc2163.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-66/out/m84036_250809_035451_s4.bc2163.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2163"}
2025-09-15 20:24:43.614 wdl.w:ptcp.w:call-trgt-66 NOTICE workflow start :: name: "trgt", source: "./trgt.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-66"
2025-09-15 20:24:43.634 wdl.w:ptcp.w:call-trgt-66 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:24:43.634 wdl.w:ptcp.w:call-trgt-66 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-66/out/m84036_250809_035451_s4.bc2163.mapped.bam"}
2025-09-15 20:24:43.635 wdl.w:ptcp.w:call-trgt-66 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-66/out/m84036_250809_035451_s4.bc2163.mapped.bam.bai"}
2025-09-15 20:24:43.635 wdl.w:ptcp.w:call-trgt-66 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:24:43.635 wdl.w:ptcp.w:call-trgt-66 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:24:43.635 wdl.w:ptcp.w:call-trgt-66 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2163"}
2025-09-15 20:24:43.635 wdl.w:ptcp.w:call-trgt-66 INFO visit :: node: "decl-sex", values: {"sex": "F"}
2025-09-15 20:24:43.635 wdl.w:ptcp.w:call-trgt-66 INFO visit :: node: "decl-trgt_bed", values: {"trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"}
2025-09-15 20:24:43.635 wdl.w:ptcp.w:call-trgt-66 NOTICE ready :: job: "call-get_reads_overlapping_repeats", callee: "get_reads_overlapping_repeats"
2025-09-15 20:24:43.635 wdl.w:ptcp.w:call-trgt-66 INFO input :: job: "call-get_reads_overlapping_repeats", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-66/out/m84036_250809_035451_s4.bc2163.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-66/out/m84036_250809_035451_s4.bc2163.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2163"}
2025-09-15 20:24:43.636 wdl.w:ptcp.w:call-trgt-66 NOTICE ready :: job: "call-trgt_genotype", callee: "trgt_genotype"
2025-09-15 20:24:43.636 wdl.w:ptcp.w:call-trgt-66 INFO input :: job: "call-trgt_genotype", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-66/out/m84036_250809_035451_s4.bc2163.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-66/out/m84036_250809_035451_s4.bc2163.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2163"}
2025-09-15 20:24:43.641 wdl.w:ptcp.w:call-paraphase-58.t:call-run_paraphase INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-58/call-run_paraphase/_singularity_tmpdir_ad3z3olt"
2025-09-15 20:24:43.641 wdl.w:ptcp.w:call-paraphase-58.t:call-run_paraphase INFO Slurm invocation: srun --job-name call-run_paraphase --partition compute,compute9 --cpus-per-task 4 --mem 7629M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-58/call-run_paraphase/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-58/call-run_paraphase/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-58/call-run_paraphase/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-58/call-run_paraphase/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-58/out/m84036_250809_035451_s4.bc2155.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2155.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-58/out/m84036_250809_035451_s4.bc2155.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2155.mapped.bam.bai:ro --bind /ptcp/meta/variant_list/variant_list.GRCh38.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf:ro --bind /ptcp/meta/paraphase/paraphase_config.GRCh38.yaml:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/paraphase_config.GRCh38.yaml:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-58/call-run_paraphase/_singularity_tmpdir_ad3z3olt/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-58/call-run_paraphase/_singularity_tmpdir_ad3z3olt/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:43.656 wdl.w:ptcp.w:call-paraphase-58.t:call-run_paraphase NOTICE slurm_singularity run :: pid: 1202952, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-58/call-run_paraphase/slurm_singularity.log.txt"
2025-09-15 20:24:43.675 wdl.w:ptcp.t:call-tar_outputs-12 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 17, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-12/_singularity_tmpdir_k5gigy8w"
2025-09-15 20:24:43.675 wdl.w:ptcp.t:call-tar_outputs-12 INFO Slurm invocation: srun --job-name call-tar_outputs-12 --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-12/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-12/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-12/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-12/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-12/out/m84036_250809_035451_s4.bc2109_sawfish/m84036_250809_035451_s4.bc2109.sv.vcf.gz.tbi:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2109.sv.vcf.gz.tbi:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-12/out/m84036_250809_035451_s4.bc2109_sawfish/m84036_250809_035451_s4.bc2109.sv.vcf.gz:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2109.sv.vcf.gz:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-12/out/m84036_250809_035451_s4.bc2109_paraphase/m84036_250809_035451_s4.bc2109.paraphase.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2109.paraphase.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-12/out/m84036_250809_035451_s4.bc2109_paraphase/m84036_250809_035451_s4.bc2109.paraphase.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2109.paraphase.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-12/out/m84036_250809_035451_s4.bc2109_paraphase/m84036_250809_035451_s4.bc2109.paraphase.json:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2109.paraphase.json:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-12/out/m84036_250809_035451_s4.bc2109.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2109.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-12/out/m84036_250809_035451_s4.bc2109.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2109.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-12/out/m84036_250809_035451_s4.bc2109.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2109.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-12/out/m84036_250809_035451_s4.bc2109.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2109.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-12/out/m84036_250809_035451_s4.bc2109.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2109.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-12/out/m84036_250809_035451_s4.bc2109.f8inversion.json:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2109.f8inversion.json:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-12/_singularity_tmpdir_k5gigy8w/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-12/_singularity_tmpdir_k5gigy8w/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:43.683 wdl.w:ptcp.t:call-tar_outputs-12 NOTICE slurm_singularity run :: pid: 1202954, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-12/slurm_singularity.log.txt"
2025-09-15 20:24:43.737 wdl.w:ptcp.w:call-trgt-44.t:call-trgt_plot_motifs_allele.slurm_singularity INFO srun: job 51797766 queued and waiting for resources
2025-09-15 20:24:43.737 wdl.w:ptcp.w:call-trgt-44.t:call-trgt_plot_motifs_allele.slurm_singularity INFO srun: job 51797766 has been allocated resources
2025-09-15 20:24:43.737 wdl.w:ptcp.w:call-trgt-44.t:call-trgt_plot_motifs_allele.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:43.875 wdl.w:ptcp.w:call-trgt-44.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO srun: job 51797767 queued and waiting for resources
2025-09-15 20:24:43.875 wdl.w:ptcp.w:call-trgt-44.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO srun: job 51797767 has been allocated resources
2025-09-15 20:24:43.875 wdl.w:ptcp.w:call-trgt-44.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:43.985 wdl.w:ptcp.w:call-paraphase-57.t:call-run_paraphase INFO output :: name: "paraphase_bam", value: "m84036_250809_035451_s4.bc2154_paraphase/m84036_250809_035451_s4.bc2154.paraphase.bam"
2025-09-15 20:24:43.991 wdl.w:ptcp.w:call-paraphase-57.t:call-run_paraphase INFO output :: name: "paraphase_bam_bai", value: "m84036_250809_035451_s4.bc2154_paraphase/m84036_250809_035451_s4.bc2154.paraphase.bam.bai"
2025-09-15 20:24:43.993 wdl.w:ptcp.w:call-paraphase-57.t:call-run_paraphase INFO output :: name: "paraphase_json", value: "m84036_250809_035451_s4.bc2154_paraphase/m84036_250809_035451_s4.bc2154.paraphase.json"
2025-09-15 20:24:43.995 wdl.w:ptcp.w:call-paraphase-57.t:call-run_paraphase INFO output :: name: "paraphase_vcfs", value: []
2025-09-15 20:24:43.995 wdl.w:ptcp.w:call-paraphase-57.t:call-run_paraphase INFO output :: name: "havanno_json", value: "m84036_250809_035451_s4.bc2154.havanno.json"
2025-09-15 20:24:44.007 wdl.w:ptcp.w:call-sawfish-19.t:call-run_sawfish.stderr VERBOSE [M::mm_idx_gen::60.904*1.60] collected minimizers
2025-09-15 20:24:44.024 wdl.w:ptcp.t:call-tar_outputs-09.stderr VERBOSE tar: Removing leading `/' from member names
2025-09-15 20:24:44.025 wdl.w:ptcp.t:call-tar_outputs-09.stderr VERBOSE tar: Removing leading `/' from hard link targets
2025-09-15 20:24:44.035 wdl.w:ptcp.w:call-trgt-42.t:call-get_reads_overlapping_repeats.slurm_singularity INFO srun: job 51797768 queued and waiting for resources
2025-09-15 20:24:44.035 wdl.w:ptcp.w:call-trgt-42.t:call-get_reads_overlapping_repeats.slurm_singularity INFO srun: job 51797768 has been allocated resources
2025-09-15 20:24:44.035 wdl.w:ptcp.w:call-trgt-42.t:call-get_reads_overlapping_repeats.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:44.035 wdl.w:ptcp.t:call-tar_outputs-09.slurm_singularity INFO srun: job 51797769 queued and waiting for resources
2025-09-15 20:24:44.035 wdl.w:ptcp.t:call-tar_outputs-09.slurm_singularity INFO srun: job 51797769 has been allocated resources
2025-09-15 20:24:44.035 wdl.w:ptcp.t:call-tar_outputs-09.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:44.070 wdl.w:ptcp.t:call-tar_outputs-09 INFO output :: name: "sample_tarball", value: "m84036_250809_035451_s4.bc2106.tar"
2025-09-15 20:24:44.101 wdl.w:ptcp.w:call-paraphase-57.t:call-run_paraphase NOTICE done
2025-09-15 20:24:44.106 wdl.w:ptcp.w:call-paraphase-57 NOTICE finish :: job: "call-run_paraphase"
2025-09-15 20:24:44.107 wdl.w:ptcp.w:call-paraphase-57 INFO output :: job: "call-run_paraphase", values: {"havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-57/call-run_paraphase/out/m84036_250809_035451_s4.bc2154.havanno.json", "paraphase_vcfs": [], "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-57/call-run_paraphase/out/m84036_250809_035451_s4.bc2154_paraphase/m84036_250809_035451_s4.bc2154.paraphase.json", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-57/call-run_paraphase/out/m84036_250809_035451_s4.bc2154_paraphase/m84036_250809_035451_s4.bc2154.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-57/call-run_paraphase/out/m84036_250809_035451_s4.bc2154_paraphase/m84036_250809_035451_s4.bc2154.paraphase.bam"}
2025-09-15 20:24:44.107 wdl.w:ptcp.w:call-paraphase-57 NOTICE ready :: job: "call-call_f8", callee: "call_f8"
2025-09-15 20:24:44.108 wdl.w:ptcp.w:call-paraphase-57 INFO input :: job: "call-call_f8", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "out_prefix": "m84036_250809_035451_s4.bc2154", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-57/call-run_paraphase/out/m84036_250809_035451_s4.bc2154_paraphase/m84036_250809_035451_s4.bc2154.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-57/call-run_paraphase/out/m84036_250809_035451_s4.bc2154_paraphase/m84036_250809_035451_s4.bc2154.paraphase.bam", "sex": "F"}
2025-09-15 20:24:44.109 wdl.w:ptcp.w:call-paraphase-57 INFO visit :: node: "output-havanno_json", values: {"havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-57/call-run_paraphase/out/m84036_250809_035451_s4.bc2154.havanno.json"}
2025-09-15 20:24:44.109 wdl.w:ptcp.w:call-paraphase-57 INFO visit :: node: "output-paraphase_bam", values: {"paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-57/call-run_paraphase/out/m84036_250809_035451_s4.bc2154_paraphase/m84036_250809_035451_s4.bc2154.paraphase.bam"}
2025-09-15 20:24:44.109 wdl.w:ptcp.w:call-paraphase-57 INFO visit :: node: "output-paraphase_bam_bai", values: {"paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-57/call-run_paraphase/out/m84036_250809_035451_s4.bc2154_paraphase/m84036_250809_035451_s4.bc2154.paraphase.bam.bai"}
2025-09-15 20:24:44.109 wdl.w:ptcp.w:call-paraphase-57 INFO visit :: node: "output-paraphase_json", values: {"paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-57/call-run_paraphase/out/m84036_250809_035451_s4.bc2154_paraphase/m84036_250809_035451_s4.bc2154.paraphase.json"}
2025-09-15 20:24:44.109 wdl.w:ptcp.w:call-paraphase-57 INFO visit :: node: "output-paraphase_vcfs", values: {"paraphase_vcfs": []}
2025-09-15 20:24:44.115 wdl.w:ptcp.w:call-sawfish-58.t:call-run_sawfish NOTICE task setup :: name: "run_sawfish", source: "./sawfish.wdl", line: 83, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-58/call-run_sawfish", thread: 140611449513536
2025-09-15 20:24:44.138 wdl.w:ptcp.w:call-sawfish-58.t:call-run_sawfish INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:44.139 wdl.w:ptcp.w:call-sawfish-58.t:call-run_sawfish INFO input :: name: "genome_version", value: "38"
2025-09-15 20:24:44.139 wdl.w:ptcp.w:call-sawfish-58.t:call-run_sawfish INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:44.139 wdl.w:ptcp.w:call-sawfish-58.t:call-run_sawfish INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:44.139 wdl.w:ptcp.w:call-sawfish-58.t:call-run_sawfish INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2155.mapped.bam.bai"
2025-09-15 20:24:44.139 wdl.w:ptcp.w:call-sawfish-58.t:call-run_sawfish INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2155.mapped.bam"
2025-09-15 20:24:44.139 wdl.w:ptcp.w:call-sawfish-58.t:call-run_sawfish INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2155"
2025-09-15 20:24:44.139 wdl.w:ptcp.w:call-sawfish-58.t:call-run_sawfish INFO eval :: name: "mem_gb", value: 32
2025-09-15 20:24:44.139 wdl.w:ptcp.w:call-sawfish-58.t:call-run_sawfish INFO eval :: name: "threads", value: 16
2025-09-15 20:24:44.140 wdl.w:ptcp.w:call-sawfish-58.t:call-run_sawfish INFO eval :: name: "disk_size", value: 30
2025-09-15 20:24:44.140 wdl.w:ptcp.w:call-sawfish-58.t:call-run_sawfish INFO eval :: name: "discover_dirname", value: "m84036_250809_035451_s4.bc2155_sawfish_discover"
2025-09-15 20:24:44.140 wdl.w:ptcp.w:call-sawfish-58.t:call-run_sawfish INFO eval :: name: "call_dirname", value: "m84036_250809_035451_s4.bc2155_sawfish"
2025-09-15 20:24:44.140 wdl.w:ptcp.w:call-sawfish-58.t:call-run_sawfish INFO eval :: name: "minimap2_bam_filename", value: "m84036_250809_035451_s4.bc2155.minimap2.bam"
2025-09-15 20:24:44.141 wdl.w:ptcp.w:call-sawfish-58.t:call-run_sawfish INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 16, memory_reservation: 32000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:44.141 wdl.w:ptcp.w:call-sawfish-58.t:call-run_sawfish WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:44.141 wdl.w:ptcp.w:call-sawfish-58.t:call-run_sawfish INFO provisioned :: seconds_waited: 0, cpu: 16, mem_bytes: 32000000000
2025-09-15 20:24:44.141 wdl.w:ptcp.w:call-sawfish-58.t:call-run_sawfish INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:44.159 wdl.w:ptcp.t:call-tar_outputs-09 NOTICE done
2025-09-15 20:24:44.164 wdl.w:ptcp NOTICE finish :: job: "call-tar_outputs-09"
2025-09-15 20:24:44.164 wdl.w:ptcp INFO output :: job: "call-tar_outputs-09", values: {"sample_tarball": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-09/out/m84036_250809_035451_s4.bc2106.tar"}
2025-09-15 20:24:44.172 wdl.w:ptcp.t:call-tar_outputs-04 NOTICE task setup :: name: "tar_outputs", source: "./common.wdl", line: 279, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-04", thread: 140606080804416
2025-09-15 20:24:44.174 wdl.w:ptcp.w:call-paraphase-49.t:call-run_paraphase INFO output :: name: "paraphase_bam", value: "m84036_250809_035451_s4.bc2146_paraphase/m84036_250809_035451_s4.bc2146.paraphase.bam"
2025-09-15 20:24:44.178 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:41 [ERROR] - No reads found for TRID=OPDM_ABCD3
2025-09-15 20:24:44.178 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:41 [ERROR] - No reads found for TRID=NIID_NOTCH2NLC
2025-09-15 20:24:44.178 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:41 [ERROR] - No reads found for TRID=DRPLA_ATN1
2025-09-15 20:24:44.178 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:41 [ERROR] - No reads found for TRID=OPDM4_RILPL1
2025-09-15 20:24:44.178 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:41 [ERROR] - No reads found for TRID=SCA3_ATXN3
2025-09-15 20:24:44.178 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:41 [ERROR] - No reads found for TRID=SCA31_BEAN1
2025-09-15 20:24:44.178 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:41 [ERROR] - No reads found for TRID=OPMD_PABPN1
2025-09-15 20:24:44.178 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:41 [ERROR] - No reads found for TRID=SCA4_ZFHX3
2025-09-15 20:24:44.178 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:41 [ERROR] - No reads found for TRID=SCA6_CACNA1A
2025-09-15 20:24:44.178 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:41 [ERROR] - No reads found for TRID=OPDM2_GIPC1
2025-09-15 20:24:44.179 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:42 [ERROR] - No reads found for TRID=HDL2_JPH3
2025-09-15 20:24:44.179 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:42 [ERROR] - No reads found for TRID=SD5_HOXD13
2025-09-15 20:24:44.179 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:42 [ERROR] - No reads found for TRID=SCA36_NOP56
2025-09-15 20:24:44.179 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:42 [ERROR] - No reads found for TRID=CJD_PRNP
2025-09-15 20:24:44.179 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:42 [ERROR] - No reads found for TRID=EPM1_CSTB
2025-09-15 20:24:44.179 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:42 [ERROR] - No reads found for TRID=SCA10_ATXN10
2025-09-15 20:24:44.179 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:42 [ERROR] - No reads found for TRID=DM1_DMPK
2025-09-15 20:24:44.179 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:42 [ERROR] - No reads found for TRID=FRA2A_AFF3
2025-09-15 20:24:44.179 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:42 [ERROR] - No reads found for TRID=HD_HTT
2025-09-15 20:24:44.179 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:43 [ERROR] - No reads found for TRID=CCHS_PHOX2B
2025-09-15 20:24:44.179 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:43 [ERROR] - No reads found for TRID=SCA12_PPP2R2B
2025-09-15 20:24:44.179 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:43 [ERROR] - No reads found for TRID=SCA1_ATXN1
2025-09-15 20:24:44.179 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:43 [ERROR] - No reads found for TRID=FAME1_SAMD12
2025-09-15 20:24:44.179 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:43 [ERROR] - No reads found for TRID=OPDM1_LRP12
2025-09-15 20:24:44.182 wdl.w:ptcp.w:call-paraphase-49.t:call-run_paraphase INFO output :: name: "paraphase_bam_bai", value: "m84036_250809_035451_s4.bc2146_paraphase/m84036_250809_035451_s4.bc2146.paraphase.bam.bai"
2025-09-15 20:24:44.185 wdl.w:ptcp.w:call-paraphase-49.t:call-run_paraphase INFO output :: name: "paraphase_json", value: "m84036_250809_035451_s4.bc2146_paraphase/m84036_250809_035451_s4.bc2146.paraphase.json"
2025-09-15 20:24:44.187 wdl.w:ptcp.w:call-paraphase-49.t:call-run_paraphase INFO output :: name: "paraphase_vcfs", value: []
2025-09-15 20:24:44.188 wdl.w:ptcp.w:call-paraphase-49.t:call-run_paraphase INFO output :: name: "havanno_json", value: "m84036_250809_035451_s4.bc2146.havanno.json"
2025-09-15 20:24:44.199 wdl.w:ptcp.t:call-tar_outputs-04 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:44.200 wdl.w:ptcp.t:call-tar_outputs-04 INFO input :: name: "sawfish_vcf_tbi", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2101.sv.vcf.gz.tbi"
2025-09-15 20:24:44.200 wdl.w:ptcp.t:call-tar_outputs-04 INFO input :: name: "sawfish_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2101.sv.vcf.gz"
2025-09-15 20:24:44.200 wdl.w:ptcp.t:call-tar_outputs-04 INFO input :: name: "f8_json", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2101.f8inversion.json"
2025-09-15 20:24:44.200 wdl.w:ptcp.t:call-tar_outputs-04 INFO input :: name: "paraphase_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2101.paraphase.bam.bai"
2025-09-15 20:24:44.200 wdl.w:ptcp.t:call-tar_outputs-04 INFO input :: name: "paraphase_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2101.paraphase.bam"
2025-09-15 20:24:44.200 wdl.w:ptcp.t:call-tar_outputs-04 INFO input :: name: "paraphase_json", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2101.paraphase.json"
2025-09-15 20:24:44.200 wdl.w:ptcp.t:call-tar_outputs-04 INFO input :: name: "trgt_spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2101.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:44.200 wdl.w:ptcp.t:call-tar_outputs-04 INFO input :: name: "trgt_spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2101.trgt.sorted.spanning.bam"
2025-09-15 20:24:44.200 wdl.w:ptcp.t:call-tar_outputs-04 INFO input :: name: "trgt_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2101.trgt.vcf"
2025-09-15 20:24:44.200 wdl.w:ptcp.t:call-tar_outputs-04 INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2101.mapped.bam.bai"
2025-09-15 20:24:44.200 wdl.w:ptcp.t:call-tar_outputs-04 INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2101.mapped.bam"
2025-09-15 20:24:44.200 wdl.w:ptcp.t:call-tar_outputs-04 INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2101"
2025-09-15 20:24:44.200 wdl.w:ptcp.t:call-tar_outputs-04 INFO eval :: name: "threads", value: 1
2025-09-15 20:24:44.200 wdl.w:ptcp.t:call-tar_outputs-04 INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:44.201 wdl.w:ptcp.t:call-tar_outputs-04 INFO eval :: name: "disk_size", value: 6
2025-09-15 20:24:44.201 wdl.w:ptcp.t:call-tar_outputs-04 INFO eval :: name: "output_tarball", value: "m84036_250809_035451_s4.bc2101.tar"
2025-09-15 20:24:44.201 wdl.w:ptcp.t:call-tar_outputs-04 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:44.201 wdl.w:ptcp.t:call-tar_outputs-04 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:44.202 wdl.w:ptcp.t:call-tar_outputs-04 INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:44.202 wdl.w:ptcp.t:call-tar_outputs-04 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:44.237 wdl.w:ptcp.w:call-sawfish-58.t:call-run_sawfish INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 10, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-58/call-run_sawfish/_singularity_tmpdir_dsdka9b8"
2025-09-15 20:24:44.237 wdl.w:ptcp.w:call-sawfish-58.t:call-run_sawfish INFO Slurm invocation: srun --job-name call-run_sawfish --partition compute,compute9 --cpus-per-task 16 --mem 30518M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-58/call-run_sawfish/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-58/call-run_sawfish/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-58/call-run_sawfish/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-58/call-run_sawfish/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-58/out/m84036_250809_035451_s4.bc2155.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2155.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-58/out/m84036_250809_035451_s4.bc2155.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2155.mapped.bam.bai:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-58/call-run_sawfish/_singularity_tmpdir_dsdka9b8/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-58/call-run_sawfish/_singularity_tmpdir_dsdka9b8/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:44.243 wdl.w:ptcp.w:call-paraphase-39.t:call-run_paraphase.stderr VERBOSE INFO:root:Processing sample m84036_250809_035451_s4.bc2136 at 2025-09-15 20:24:38.756906...
2025-09-15 20:24:44.244 wdl.w:ptcp.w:call-paraphase-39.t:call-run_paraphase.stderr VERBOSE INFO:root:Checking sample sex at 2025-09-15 20:24:38.757616...
2025-09-15 20:24:44.244 wdl.w:ptcp.w:call-paraphase-39.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for cyp21 for sample m84036_250809_035451_s4.bc2136 at 2025-09-15 20:24:38.784889...
2025-09-15 20:24:44.244 wdl.w:ptcp.w:call-paraphase-39.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for cyp21 for sample m84036_250809_035451_s4.bc2136 at 2025-09-15 20:24:38.785392...
2025-09-15 20:24:44.244 wdl.w:ptcp.w:call-paraphase-39.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for smn1 for sample m84036_250809_035451_s4.bc2136 at 2025-09-15 20:24:38.785173...
2025-09-15 20:24:44.244 wdl.w:ptcp.w:call-paraphase-39.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for smn1 for sample m84036_250809_035451_s4.bc2136 at 2025-09-15 20:24:38.785602...
2025-09-15 20:24:44.245 wdl.w:ptcp.w:call-paraphase-39.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for hba for sample m84036_250809_035451_s4.bc2136 at 2025-09-15 20:24:38.786470...
2025-09-15 20:24:44.245 wdl.w:ptcp.w:call-paraphase-39.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for gba for sample m84036_250809_035451_s4.bc2136 at 2025-09-15 20:24:38.786463...
2025-09-15 20:24:44.245 wdl.w:ptcp.w:call-paraphase-39.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for hba for sample m84036_250809_035451_s4.bc2136 at 2025-09-15 20:24:38.786884...
2025-09-15 20:24:44.245 wdl.w:ptcp.w:call-paraphase-39.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for gba for sample m84036_250809_035451_s4.bc2136 at 2025-09-15 20:24:38.786889...
2025-09-15 20:24:44.255 wdl.w:ptcp.w:call-trgt-42.t:call-get_reads_overlapping_repeats INFO output :: name: "reads_overlapping_repeats", value: "m84036_250809_035451_s4.bc2139.repeats.bam"
2025-09-15 20:24:44.260 wdl.w:ptcp.w:call-trgt-42.t:call-get_reads_overlapping_repeats INFO output :: name: "reads_overlapping_repeats_bai", value: "m84036_250809_035451_s4.bc2139.repeats.bam.bai"
2025-09-15 20:24:44.288 wdl.w:ptcp.w:call-sawfish-58.t:call-run_sawfish NOTICE slurm_singularity run :: pid: 1202980, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-58/call-run_sawfish/slurm_singularity.log.txt"
2025-09-15 20:24:44.310 wdl.w:ptcp.w:call-paraphase-49.t:call-run_paraphase NOTICE done
2025-09-15 20:24:44.320 wdl.w:ptcp.w:call-paraphase-49 NOTICE finish :: job: "call-run_paraphase"
2025-09-15 20:24:44.320 wdl.w:ptcp.w:call-paraphase-49 INFO output :: job: "call-run_paraphase", values: {"havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-49/call-run_paraphase/out/m84036_250809_035451_s4.bc2146.havanno.json", "paraphase_vcfs": [], "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-49/call-run_paraphase/out/m84036_250809_035451_s4.bc2146_paraphase/m84036_250809_035451_s4.bc2146.paraphase.json", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-49/call-run_paraphase/out/m84036_250809_035451_s4.bc2146_paraphase/m84036_250809_035451_s4.bc2146.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-49/call-run_paraphase/out/m84036_250809_035451_s4.bc2146_paraphase/m84036_250809_035451_s4.bc2146.paraphase.bam"}
2025-09-15 20:24:44.320 wdl.w:ptcp.w:call-paraphase-49 NOTICE ready :: job: "call-call_f8", callee: "call_f8"
2025-09-15 20:24:44.321 wdl.w:ptcp.w:call-paraphase-49 INFO input :: job: "call-call_f8", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "out_prefix": "m84036_250809_035451_s4.bc2146", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-49/call-run_paraphase/out/m84036_250809_035451_s4.bc2146_paraphase/m84036_250809_035451_s4.bc2146.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-49/call-run_paraphase/out/m84036_250809_035451_s4.bc2146_paraphase/m84036_250809_035451_s4.bc2146.paraphase.bam", "sex": "F"}
2025-09-15 20:24:44.322 wdl.w:ptcp.w:call-paraphase-49 INFO visit :: node: "output-havanno_json", values: {"havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-49/call-run_paraphase/out/m84036_250809_035451_s4.bc2146.havanno.json"}
2025-09-15 20:24:44.322 wdl.w:ptcp.w:call-paraphase-49 INFO visit :: node: "output-paraphase_bam", values: {"paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-49/call-run_paraphase/out/m84036_250809_035451_s4.bc2146_paraphase/m84036_250809_035451_s4.bc2146.paraphase.bam"}
2025-09-15 20:24:44.322 wdl.w:ptcp.w:call-paraphase-49 INFO visit :: node: "output-paraphase_bam_bai", values: {"paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-49/call-run_paraphase/out/m84036_250809_035451_s4.bc2146_paraphase/m84036_250809_035451_s4.bc2146.paraphase.bam.bai"}
2025-09-15 20:24:44.322 wdl.w:ptcp.w:call-paraphase-49 INFO visit :: node: "output-paraphase_json", values: {"paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-49/call-run_paraphase/out/m84036_250809_035451_s4.bc2146_paraphase/m84036_250809_035451_s4.bc2146.paraphase.json"}
2025-09-15 20:24:44.322 wdl.w:ptcp.w:call-paraphase-49 INFO visit :: node: "output-paraphase_vcfs", values: {"paraphase_vcfs": []}
2025-09-15 20:24:44.330 wdl.w:ptcp.w:call-trgt-58.t:call-get_reads_overlapping_repeats NOTICE task setup :: name: "get_reads_overlapping_repeats", source: "./trgt.wdl", line: 182, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-58/call-get_reads_overlapping_repeats", thread: 140609847293504
2025-09-15 20:24:44.335 wdl.w:ptcp.t:call-tar_outputs-04 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 17, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-04/_singularity_tmpdir_y6olhq53"
2025-09-15 20:24:44.335 wdl.w:ptcp.t:call-tar_outputs-04 INFO Slurm invocation: srun --job-name call-tar_outputs-04 --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-04/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-04/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-04/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-04/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-04/out/m84036_250809_035451_s4.bc2101_paraphase/m84036_250809_035451_s4.bc2101.paraphase.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2101.paraphase.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-04/out/m84036_250809_035451_s4.bc2101_paraphase/m84036_250809_035451_s4.bc2101.paraphase.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2101.paraphase.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-04/out/m84036_250809_035451_s4.bc2101_paraphase/m84036_250809_035451_s4.bc2101.paraphase.json:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2101.paraphase.json:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-04/out/m84036_250809_035451_s4.bc2101.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2101.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-04/out/m84036_250809_035451_s4.bc2101.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2101.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-04/out/m84036_250809_035451_s4.bc2101.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2101.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-04/out/m84036_250809_035451_s4.bc2101.f8inversion.json:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2101.f8inversion.json:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-04/out/m84036_250809_035451_s4.bc2101.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2101.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-04/out/m84036_250809_035451_s4.bc2101.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2101.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-04/out/m84036_250809_035451_s4.bc2101_sawfish/m84036_250809_035451_s4.bc2101.sv.vcf.gz.tbi:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2101.sv.vcf.gz.tbi:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-04/out/m84036_250809_035451_s4.bc2101_sawfish/m84036_250809_035451_s4.bc2101.sv.vcf.gz:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2101.sv.vcf.gz:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-04/_singularity_tmpdir_y6olhq53/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-04/_singularity_tmpdir_y6olhq53/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:44.348 wdl.w:ptcp.t:call-tar_outputs-04 NOTICE slurm_singularity run :: pid: 1202982, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-04/slurm_singularity.log.txt"
2025-09-15 20:24:44.351 wdl.w:ptcp.w:call-trgt-42.t:call-get_reads_overlapping_repeats NOTICE done
2025-09-15 20:24:44.352 wdl.w:ptcp.w:call-trgt-58.t:call-get_reads_overlapping_repeats INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:44.353 wdl.w:ptcp.w:call-trgt-58.t:call-get_reads_overlapping_repeats INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:44.353 wdl.w:ptcp.w:call-trgt-58.t:call-get_reads_overlapping_repeats INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2155.mapped.bam.bai"
2025-09-15 20:24:44.353 wdl.w:ptcp.w:call-trgt-58.t:call-get_reads_overlapping_repeats INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2155.mapped.bam"
2025-09-15 20:24:44.354 wdl.w:ptcp.w:call-trgt-58.t:call-get_reads_overlapping_repeats INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2155"
2025-09-15 20:24:44.354 wdl.w:ptcp.w:call-trgt-58.t:call-get_reads_overlapping_repeats INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:44.354 wdl.w:ptcp.w:call-trgt-58.t:call-get_reads_overlapping_repeats INFO eval :: name: "expand_size", value: 3000
2025-09-15 20:24:44.354 wdl.w:ptcp.w:call-trgt-58.t:call-get_reads_overlapping_repeats INFO eval :: name: "threads", value: 1
2025-09-15 20:24:44.354 wdl.w:ptcp.w:call-trgt-58.t:call-get_reads_overlapping_repeats INFO eval :: name: "expanded_bed_name", value: "m84036_250809_035451_s4.bc2155.expanded.bed"
2025-09-15 20:24:44.354 wdl.w:ptcp.w:call-trgt-58.t:call-get_reads_overlapping_repeats INFO eval :: name: "disk_size", value: 11
2025-09-15 20:24:44.355 wdl.w:ptcp.w:call-trgt-58.t:call-get_reads_overlapping_repeats INFO eval :: name: "output_name", value: "m84036_250809_035451_s4.bc2155.repeats.bam"
2025-09-15 20:24:44.355 wdl.w:ptcp.w:call-trgt-58.t:call-get_reads_overlapping_repeats INFO eval :: name: "index_name", value: "m84036_250809_035451_s4.bc2155.repeats.bam.bai"
2025-09-15 20:24:44.355 wdl.w:ptcp.w:call-trgt-58.t:call-get_reads_overlapping_repeats INFO eval :: name: "output_name_with_index", value: "m84036_250809_035451_s4.bc2155.repeats.bam##idx##m84036_250809_035451_s4.bc2155.repeats.bam.bai"
2025-09-15 20:24:44.355 wdl.w:ptcp.w:call-trgt-58.t:call-get_reads_overlapping_repeats INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:44.355 wdl.w:ptcp.w:call-trgt-58.t:call-get_reads_overlapping_repeats WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:44.356 wdl.w:ptcp.w:call-trgt-58.t:call-get_reads_overlapping_repeats INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:44.356 wdl.w:ptcp.w:call-trgt-58.t:call-get_reads_overlapping_repeats INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:44.358 wdl.w:ptcp.w:call-trgt-42 NOTICE finish :: job: "call-get_reads_overlapping_repeats"
2025-09-15 20:24:44.359 wdl.w:ptcp.w:call-trgt-42 INFO output :: job: "call-get_reads_overlapping_repeats", values: {"reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-42/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2139.repeats.bam.bai", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-42/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2139.repeats.bam"}
2025-09-15 20:24:44.359 wdl.w:ptcp.w:call-trgt-42 INFO visit :: node: "output-reads_overlapping_repeats", values: {"reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-42/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2139.repeats.bam"}
2025-09-15 20:24:44.359 wdl.w:ptcp.w:call-trgt-42 INFO visit :: node: "output-reads_overlapping_repeats_bai", values: {"reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-42/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2139.repeats.bam.bai"}
2025-09-15 20:24:44.367 wdl.w:ptcp.w:call-trgt-58.t:call-trgt_genotype NOTICE task setup :: name: "trgt_genotype", source: "./trgt.wdl", line: 272, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-58/call-trgt_genotype", thread: 140610879071808
2025-09-15 20:24:44.369 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_genotype.slurm_singularity INFO srun: job 51797770 queued and waiting for resources
2025-09-15 20:24:44.369 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_genotype.slurm_singularity INFO srun: job 51797770 has been allocated resources
2025-09-15 20:24:44.369 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_genotype.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:44.386 wdl.w:ptcp.w:call-trgt-58.t:call-trgt_genotype INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:44.386 wdl.w:ptcp.w:call-trgt-58.t:call-trgt_genotype INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:44.386 wdl.w:ptcp.w:call-trgt-58.t:call-trgt_genotype INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:44.386 wdl.w:ptcp.w:call-trgt-58.t:call-trgt_genotype INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:44.386 wdl.w:ptcp.w:call-trgt-58.t:call-trgt_genotype INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2155.mapped.bam.bai"
2025-09-15 20:24:44.387 wdl.w:ptcp.w:call-trgt-58.t:call-trgt_genotype INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2155.mapped.bam"
2025-09-15 20:24:44.387 wdl.w:ptcp.w:call-trgt-58.t:call-trgt_genotype INFO input :: name: "sex", value: "F"
2025-09-15 20:24:44.387 wdl.w:ptcp.w:call-trgt-58.t:call-trgt_genotype INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2155"
2025-09-15 20:24:44.387 wdl.w:ptcp.w:call-trgt-58.t:call-trgt_genotype INFO eval :: name: "mem_gb", value: 16
2025-09-15 20:24:44.387 wdl.w:ptcp.w:call-trgt-58.t:call-trgt_genotype INFO eval :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2155.trgt"
2025-09-15 20:24:44.387 wdl.w:ptcp.w:call-trgt-58.t:call-trgt_genotype INFO eval :: name: "threads", value: 8
2025-09-15 20:24:44.387 wdl.w:ptcp.w:call-trgt-58.t:call-trgt_genotype INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:44.388 wdl.w:ptcp.w:call-trgt-58.t:call-trgt_genotype INFO eval :: name: "karyotype", value: "XX"
2025-09-15 20:24:44.388 wdl.w:ptcp.w:call-trgt-58.t:call-trgt_genotype INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 8, memory_reservation: 16000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:44.388 wdl.w:ptcp.w:call-trgt-58.t:call-trgt_genotype WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:44.388 wdl.w:ptcp.w:call-trgt-58.t:call-trgt_genotype INFO provisioned :: seconds_waited: 0, cpu: 8, mem_bytes: 16000000000
2025-09-15 20:24:44.389 wdl.w:ptcp.w:call-trgt-58.t:call-trgt_genotype INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:44.420 wdl.w:ptcp.w:call-trgt-58.t:call-get_reads_overlapping_repeats INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 9, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-58/call-get_reads_overlapping_repeats/_singularity_tmpdir_9r3c7odo"
2025-09-15 20:24:44.420 wdl.w:ptcp.w:call-trgt-58.t:call-get_reads_overlapping_repeats INFO Slurm invocation: srun --job-name call-get_reads_overlapping_repeats --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-58/call-get_reads_overlapping_repeats/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-58/call-get_reads_overlapping_repeats/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-58/call-get_reads_overlapping_repeats/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-58/call-get_reads_overlapping_repeats/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-58/out/m84036_250809_035451_s4.bc2155.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2155.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-58/out/m84036_250809_035451_s4.bc2155.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2155.mapped.bam.bai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-58/call-get_reads_overlapping_repeats/_singularity_tmpdir_9r3c7odo/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-58/call-get_reads_overlapping_repeats/_singularity_tmpdir_9r3c7odo/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:44.434 wdl.w:ptcp.w:call-trgt-58.t:call-get_reads_overlapping_repeats NOTICE slurm_singularity run :: pid: 1202984, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-58/call-get_reads_overlapping_repeats/slurm_singularity.log.txt"
2025-09-15 20:24:44.435 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:41 [ERROR] - No reads found for TRID=SCA37_DAB1
2025-09-15 20:24:44.435 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:41 [ERROR] - No reads found for TRID=OPDM_ABCD3
2025-09-15 20:24:44.436 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:41 [ERROR] - No reads found for TRID=NIID_NOTCH2NLC
2025-09-15 20:24:44.436 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:41 [ERROR] - No reads found for TRID=DRPLA_ATN1
2025-09-15 20:24:44.436 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:41 [ERROR] - No reads found for TRID=OPDM4_RILPL1
2025-09-15 20:24:44.436 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:42 [ERROR] - No reads found for TRID=SCA3_ATXN3
2025-09-15 20:24:44.436 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:42 [ERROR] - No reads found for TRID=SCA31_BEAN1
2025-09-15 20:24:44.436 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:42 [ERROR] - No reads found for TRID=OPMD_PABPN1
2025-09-15 20:24:44.436 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:42 [ERROR] - No reads found for TRID=SCA4_ZFHX3
2025-09-15 20:24:44.436 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:42 [ERROR] - No reads found for TRID=SCA6_CACNA1A
2025-09-15 20:24:44.436 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:42 [ERROR] - No reads found for TRID=OPDM2_GIPC1
2025-09-15 20:24:44.436 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:42 [ERROR] - No reads found for TRID=HDL2_JPH3
2025-09-15 20:24:44.436 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:43 [ERROR] - No reads found for TRID=SD5_HOXD13
2025-09-15 20:24:44.436 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:43 [ERROR] - No reads found for TRID=SCA36_NOP56
2025-09-15 20:24:44.436 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:43 [ERROR] - No reads found for TRID=CJD_PRNP
2025-09-15 20:24:44.436 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:43 [ERROR] - No reads found for TRID=EPM1_CSTB
2025-09-15 20:24:44.436 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:43 [ERROR] - No reads found for TRID=SCA10_ATXN10
2025-09-15 20:24:44.436 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:43 [ERROR] - No reads found for TRID=DM1_DMPK
2025-09-15 20:24:44.436 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:44 [ERROR] - No reads found for TRID=FRA2A_AFF3
2025-09-15 20:24:44.437 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:44 [ERROR] - No reads found for TRID=HD_HTT
2025-09-15 20:24:44.437 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:41 [ERROR] - No reads found for TRID=SCA37_DAB1
2025-09-15 20:24:44.437 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:41 [ERROR] - No reads found for TRID=OPDM_ABCD3
2025-09-15 20:24:44.437 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:41 [ERROR] - No reads found for TRID=NIID_NOTCH2NLC
2025-09-15 20:24:44.437 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:41 [ERROR] - No reads found for TRID=DRPLA_ATN1
2025-09-15 20:24:44.437 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:41 [ERROR] - No reads found for TRID=OPDM4_RILPL1
2025-09-15 20:24:44.437 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:41 [ERROR] - No reads found for TRID=SCA3_ATXN3
2025-09-15 20:24:44.437 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:42 [ERROR] - No reads found for TRID=SCA31_BEAN1
2025-09-15 20:24:44.437 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:42 [ERROR] - No reads found for TRID=OPMD_PABPN1
2025-09-15 20:24:44.437 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:42 [ERROR] - No reads found for TRID=SCA4_ZFHX3
2025-09-15 20:24:44.437 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:42 [ERROR] - No reads found for TRID=SCA6_CACNA1A
2025-09-15 20:24:44.437 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:42 [ERROR] - No reads found for TRID=OPDM2_GIPC1
2025-09-15 20:24:44.437 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:42 [ERROR] - No reads found for TRID=HDL2_JPH3
2025-09-15 20:24:44.438 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:43 [ERROR] - No reads found for TRID=SD5_HOXD13
2025-09-15 20:24:44.438 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:43 [ERROR] - No reads found for TRID=SCA36_NOP56
2025-09-15 20:24:44.438 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:43 [ERROR] - No reads found for TRID=CJD_PRNP
2025-09-15 20:24:44.438 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:43 [ERROR] - No reads found for TRID=EPM1_CSTB
2025-09-15 20:24:44.438 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:43 [ERROR] - No reads found for TRID=SCA10_ATXN10
2025-09-15 20:24:44.438 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:43 [ERROR] - No reads found for TRID=DM1_DMPK
2025-09-15 20:24:44.438 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:44 [ERROR] - No reads found for TRID=FRA2A_AFF3
2025-09-15 20:24:44.438 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:44 [ERROR] - No reads found for TRID=HD_HTT
2025-09-15 20:24:44.438 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:44 [ERROR] - No reads found for TRID=CCHS_PHOX2B
2025-09-15 20:24:44.458 wdl.w:ptcp.w:call-trgt-58.t:call-trgt_genotype INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 11, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-58/call-trgt_genotype/_singularity_tmpdir_2_4ca5jc"
2025-09-15 20:24:44.458 wdl.w:ptcp.w:call-trgt-58.t:call-trgt_genotype INFO Slurm invocation: srun --job-name call-trgt_genotype --partition compute,compute9 --cpus-per-task 8 --mem 15259M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-58/call-trgt_genotype/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-58/call-trgt_genotype/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-58/call-trgt_genotype/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-58/call-trgt_genotype/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-58/out/m84036_250809_035451_s4.bc2155.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2155.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-58/out/m84036_250809_035451_s4.bc2155.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2155.mapped.bam.bai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-58/call-trgt_genotype/_singularity_tmpdir_2_4ca5jc/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-58/call-trgt_genotype/_singularity_tmpdir_2_4ca5jc/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:44.468 wdl.w:ptcp.w:call-trgt-58.t:call-trgt_genotype NOTICE slurm_singularity run :: pid: 1202986, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-58/call-trgt_genotype/slurm_singularity.log.txt"
2025-09-15 20:24:44.475 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:41 [ERROR] - No reads found for TRID=OPDM_ABCD3
2025-09-15 20:24:44.475 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:41 [ERROR] - No reads found for TRID=SCA37_DAB1
2025-09-15 20:24:44.475 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:41 [ERROR] - No reads found for TRID=DRPLA_ATN1
2025-09-15 20:24:44.475 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:41 [ERROR] - No reads found for TRID=SCA2_ATXN2
2025-09-15 20:24:44.475 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:41 [ERROR] - No reads found for TRID=NIID_NOTCH2NLC
2025-09-15 20:24:44.475 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:41 [ERROR] - No reads found for TRID=OPDM4_RILPL1
2025-09-15 20:24:44.475 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:42 [ERROR] - No reads found for TRID=SCA8_ATXN8OS
2025-09-15 20:24:44.475 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:42 [ERROR] - No reads found for TRID=SCA27B_FGF14
2025-09-15 20:24:44.475 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:42 [ERROR] - No reads found for TRID=SCA3_ATXN3
2025-09-15 20:24:44.475 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:42 [ERROR] - No reads found for TRID=SCA4_ZFHX3
2025-09-15 20:24:44.475 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:42 [ERROR] - No reads found for TRID=SCA31_BEAN1
2025-09-15 20:24:44.475 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:42 [ERROR] - No reads found for TRID=SCA6_CACNA1A
2025-09-15 20:24:44.475 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:42 [ERROR] - No reads found for TRID=HDL2_JPH3
2025-09-15 20:24:44.475 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:42 [ERROR] - No reads found for TRID=DM1_DMPK
2025-09-15 20:24:44.476 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:42 [ERROR] - No reads found for TRID=FRA2A_AFF3
2025-09-15 20:24:44.476 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:43 [ERROR] - No reads found for TRID=SD5_HOXD13
2025-09-15 20:24:44.476 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:43 [ERROR] - No reads found for TRID=SCA36_NOP56
2025-09-15 20:24:44.476 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:43 [ERROR] - No reads found for TRID=CJD_PRNP
2025-09-15 20:24:44.476 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:43 [ERROR] - No reads found for TRID=EPM1_CSTB
2025-09-15 20:24:44.476 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:43 [ERROR] - No reads found for TRID=SCA10_ATXN10
2025-09-15 20:24:44.476 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:43 [ERROR] - No reads found for TRID=SCA7_ATXN7
2025-09-15 20:24:44.476 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:43 [ERROR] - No reads found for TRID=HD_HTT
2025-09-15 20:24:44.476 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:43 [ERROR] - No reads found for TRID=FECD3_TCF4
2025-09-15 20:24:44.476 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:43 [ERROR] - No reads found for TRID=CCHS_PHOX2B
2025-09-15 20:24:44.476 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:44 [ERROR] - No reads found for TRID=SCA12_PPP2R2B
2025-09-15 20:24:44.476 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:44 [ERROR] - No reads found for TRID=SCA1_ATXN1
2025-09-15 20:24:44.476 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:44 [ERROR] - No reads found for TRID=OPDM2_GIPC1
2025-09-15 20:24:44.476 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:44 [ERROR] - No reads found for TRID=DM2_CNBP
2025-09-15 20:24:44.476 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:44 [ERROR] - No reads found for TRID=FAME1_SAMD12
2025-09-15 20:24:44.510 wdl.w:ptcp.t:call-tar_outputs-29.slurm_singularity INFO srun: job 51797771 queued and waiting for resources
2025-09-15 20:24:44.510 wdl.w:ptcp.t:call-tar_outputs-29.slurm_singularity INFO srun: job 51797771 has been allocated resources
2025-09-15 20:24:44.510 wdl.w:ptcp.t:call-tar_outputs-29.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:44.667 wdl.w:ptcp.w:call-paraphase-58.t:call-run_paraphase.slurm_singularity INFO srun: job 51797772 queued and waiting for resources
2025-09-15 20:24:44.667 wdl.w:ptcp.w:call-paraphase-58.t:call-run_paraphase.slurm_singularity INFO srun: job 51797772 has been allocated resources
2025-09-15 20:24:44.667 wdl.w:ptcp.w:call-paraphase-58.t:call-run_paraphase.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:44.669 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_motifs_allele INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2147.motifs_allele.trgt_plots.zip"
2025-09-15 20:24:44.695 wdl.w:ptcp.t:call-tar_outputs-12.slurm_singularity INFO srun: job 51797773 queued and waiting for resources
2025-09-15 20:24:44.695 wdl.w:ptcp.t:call-tar_outputs-12.slurm_singularity INFO srun: job 51797773 has been allocated resources
2025-09-15 20:24:44.696 wdl.w:ptcp.t:call-tar_outputs-12.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:44.762 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:41 [ERROR] - No reads found for TRID=DRPLA_ATN1
2025-09-15 20:24:44.763 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:41 [ERROR] - No reads found for TRID=SCA2_ATXN2
2025-09-15 20:24:44.763 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:41 [ERROR] - No reads found for TRID=NIID_NOTCH2NLC
2025-09-15 20:24:44.763 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:42 [ERROR] - No reads found for TRID=OPDM4_RILPL1
2025-09-15 20:24:44.763 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:42 [ERROR] - No reads found for TRID=SCA8_ATXN8OS
2025-09-15 20:24:44.764 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:42 [ERROR] - No reads found for TRID=SCA27B_FGF14
2025-09-15 20:24:44.764 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:42 [ERROR] - No reads found for TRID=SCA3_ATXN3
2025-09-15 20:24:44.764 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:42 [ERROR] - No reads found for TRID=SCA4_ZFHX3
2025-09-15 20:24:44.764 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:42 [ERROR] - No reads found for TRID=SCA31_BEAN1
2025-09-15 20:24:44.764 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:42 [ERROR] - No reads found for TRID=SCA6_CACNA1A
2025-09-15 20:24:44.764 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:42 [ERROR] - No reads found for TRID=HDL2_JPH3
2025-09-15 20:24:44.764 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:42 [ERROR] - No reads found for TRID=DM1_DMPK
2025-09-15 20:24:44.764 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:43 [ERROR] - No reads found for TRID=FRA2A_AFF3
2025-09-15 20:24:44.764 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:43 [ERROR] - No reads found for TRID=SD5_HOXD13
2025-09-15 20:24:44.764 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:43 [ERROR] - No reads found for TRID=SCA36_NOP56
2025-09-15 20:24:44.764 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:43 [ERROR] - No reads found for TRID=CJD_PRNP
2025-09-15 20:24:44.764 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:43 [ERROR] - No reads found for TRID=EPM1_CSTB
2025-09-15 20:24:44.764 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:43 [ERROR] - No reads found for TRID=SCA10_ATXN10
2025-09-15 20:24:44.764 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:43 [ERROR] - No reads found for TRID=SCA7_ATXN7
2025-09-15 20:24:44.764 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:43 [ERROR] - No reads found for TRID=HD_HTT
2025-09-15 20:24:44.764 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:43 [ERROR] - No reads found for TRID=FECD3_TCF4
2025-09-15 20:24:44.764 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:44 [ERROR] - No reads found for TRID=CCHS_PHOX2B
2025-09-15 20:24:44.764 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:44 [ERROR] - No reads found for TRID=SCA12_PPP2R2B
2025-09-15 20:24:44.765 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:44 [ERROR] - No reads found for TRID=SCA1_ATXN1
2025-09-15 20:24:44.765 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:44 [ERROR] - No reads found for TRID=OPDM2_GIPC1
2025-09-15 20:24:44.765 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:44 [ERROR] - No reads found for TRID=DM2_CNBP
2025-09-15 20:24:44.765 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:44 [ERROR] - No reads found for TRID=FAME1_SAMD12
2025-09-15 20:24:44.765 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:44 [ERROR] - No reads found for TRID=SBMA_AR
2025-09-15 20:24:44.778 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_motifs_allele NOTICE done
2025-09-15 20:24:44.783 wdl.w:ptcp.w:call-trgt-50 NOTICE finish :: job: "call-trgt_plot_motifs_allele"
2025-09-15 20:24:44.783 wdl.w:ptcp.w:call-trgt-50 INFO output :: job: "call-trgt_plot_motifs_allele", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-50/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2147.motifs_allele.trgt_plots.zip"}
2025-09-15 20:24:44.784 wdl.w:ptcp.w:call-trgt-50 INFO visit :: node: "output-images_motifs_allele", values: {"images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-50/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2147.motifs_allele.trgt_plots.zip"}
2025-09-15 20:24:44.789 wdl.w:ptcp.w:call-paraphase-61.t:call-run_paraphase NOTICE task setup :: name: "run_paraphase", source: "./paraphase.wdl", line: 127, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-61/call-run_paraphase", thread: 140608773551680
2025-09-15 20:24:44.813 wdl.w:ptcp.w:call-paraphase-61.t:call-run_paraphase INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:44.813 wdl.w:ptcp.w:call-paraphase-61.t:call-run_paraphase INFO input :: name: "annotation_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf"
2025-09-15 20:24:44.813 wdl.w:ptcp.w:call-paraphase-61.t:call-run_paraphase INFO input :: name: "genome_version", value: "38"
2025-09-15 20:24:44.813 wdl.w:ptcp.w:call-paraphase-61.t:call-run_paraphase INFO input :: name: "config_file", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/paraphase_config.GRCh38.yaml"
2025-09-15 20:24:44.813 wdl.w:ptcp.w:call-paraphase-61.t:call-run_paraphase INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:44.814 wdl.w:ptcp.w:call-paraphase-61.t:call-run_paraphase INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:44.814 wdl.w:ptcp.w:call-paraphase-61.t:call-run_paraphase INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2158.mapped.bam.bai"
2025-09-15 20:24:44.814 wdl.w:ptcp.w:call-paraphase-61.t:call-run_paraphase INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2158.mapped.bam"
2025-09-15 20:24:44.814 wdl.w:ptcp.w:call-paraphase-61.t:call-run_paraphase INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2158"
2025-09-15 20:24:44.814 wdl.w:ptcp.w:call-paraphase-61.t:call-run_paraphase INFO eval :: name: "threads", value: 4
2025-09-15 20:24:44.814 wdl.w:ptcp.w:call-paraphase-61.t:call-run_paraphase INFO eval :: name: "mem_gb", value: 8
2025-09-15 20:24:44.815 wdl.w:ptcp.w:call-paraphase-61.t:call-run_paraphase INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:44.815 wdl.w:ptcp.w:call-paraphase-61.t:call-run_paraphase INFO eval :: name: "out_dir", value: "m84036_250809_035451_s4.bc2158_paraphase"
2025-09-15 20:24:44.815 wdl.w:ptcp.w:call-paraphase-61.t:call-run_paraphase INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 4, memory_reservation: 8000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:44.815 wdl.w:ptcp.w:call-paraphase-61.t:call-run_paraphase WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:44.816 wdl.w:ptcp.w:call-paraphase-61.t:call-run_paraphase INFO provisioned :: seconds_waited: 0, cpu: 4, mem_bytes: 8000000000
2025-09-15 20:24:44.816 wdl.w:ptcp.w:call-paraphase-61.t:call-run_paraphase INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:44.826 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:41 [ERROR] - No reads found for TRID=NIID_NOTCH2NLC
2025-09-15 20:24:44.827 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:41 [ERROR] - No reads found for TRID=OPDM4_RILPL1
2025-09-15 20:24:44.827 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:41 [ERROR] - No reads found for TRID=SCA8_ATXN8OS
2025-09-15 20:24:44.827 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:41 [ERROR] - No reads found for TRID=SCA27B_FGF14
2025-09-15 20:24:44.827 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:42 [ERROR] - No reads found for TRID=SCA3_ATXN3
2025-09-15 20:24:44.827 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:42 [ERROR] - No reads found for TRID=SCA4_ZFHX3
2025-09-15 20:24:44.827 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:42 [ERROR] - No reads found for TRID=SCA31_BEAN1
2025-09-15 20:24:44.827 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:42 [ERROR] - No reads found for TRID=SCA6_CACNA1A
2025-09-15 20:24:44.827 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:42 [ERROR] - No reads found for TRID=HDL2_JPH3
2025-09-15 20:24:44.827 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:42 [ERROR] - No reads found for TRID=DM1_DMPK
2025-09-15 20:24:44.827 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:42 [ERROR] - No reads found for TRID=FRA2A_AFF3
2025-09-15 20:24:44.827 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:42 [ERROR] - No reads found for TRID=SD5_HOXD13
2025-09-15 20:24:44.827 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:42 [ERROR] - No reads found for TRID=SCA36_NOP56
2025-09-15 20:24:44.827 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:42 [ERROR] - No reads found for TRID=CJD_PRNP
2025-09-15 20:24:44.827 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:42 [ERROR] - No reads found for TRID=EPM1_CSTB
2025-09-15 20:24:44.827 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:42 [ERROR] - No reads found for TRID=SCA10_ATXN10
2025-09-15 20:24:44.827 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:42 [ERROR] - No reads found for TRID=SCA7_ATXN7
2025-09-15 20:24:44.828 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:42 [ERROR] - No reads found for TRID=HD_HTT
2025-09-15 20:24:44.828 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:42 [ERROR] - No reads found for TRID=FECD3_TCF4
2025-09-15 20:24:44.828 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:43 [ERROR] - No reads found for TRID=CCHS_PHOX2B
2025-09-15 20:24:44.828 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:43 [ERROR] - No reads found for TRID=SCA12_PPP2R2B
2025-09-15 20:24:44.828 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:43 [ERROR] - No reads found for TRID=SCA1_ATXN1
2025-09-15 20:24:44.828 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:43 [ERROR] - No reads found for TRID=OPDM2_GIPC1
2025-09-15 20:24:44.828 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:43 [ERROR] - No reads found for TRID=DM2_CNBP
2025-09-15 20:24:44.828 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:43 [ERROR] - No reads found for TRID=FAME1_SAMD12
2025-09-15 20:24:44.828 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:43 [ERROR] - No reads found for TRID=SBMA_AR
2025-09-15 20:24:44.837 wdl.w:ptcp.w:call-trgt-56.t:call-get_reads_overlapping_repeats INFO output :: name: "reads_overlapping_repeats", value: "m84036_250809_035451_s4.bc2153.repeats.bam"
2025-09-15 20:24:44.841 wdl.w:ptcp.w:call-trgt-56.t:call-get_reads_overlapping_repeats INFO output :: name: "reads_overlapping_repeats_bai", value: "m84036_250809_035451_s4.bc2153.repeats.bam.bai"
2025-09-15 20:24:44.860 wdl.w:ptcp.w:call-trgt-52.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:44 [ERROR] - No reads found for TRID=PRTS_ARX
2025-09-15 20:24:44.860 wdl.w:ptcp.w:call-trgt-52.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:44 [ERROR] - No reads found for TRID=EIEE1_ARX
2025-09-15 20:24:44.895 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_motifs_waterfall INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2147.motifs_waterfall.trgt_plots.zip"
2025-09-15 20:24:44.924 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_meth_allele INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2144.meth_allele.trgt_plots.zip"
2025-09-15 20:24:44.929 wdl.w:ptcp.w:call-paraphase-61.t:call-run_paraphase INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-61/call-run_paraphase/_singularity_tmpdir__zyf0j3e"
2025-09-15 20:24:44.929 wdl.w:ptcp.w:call-paraphase-61.t:call-run_paraphase INFO Slurm invocation: srun --job-name call-run_paraphase --partition compute,compute9 --cpus-per-task 4 --mem 7629M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-61/call-run_paraphase/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-61/call-run_paraphase/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-61/call-run_paraphase/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-61/call-run_paraphase/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/variant_list/variant_list.GRCh38.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-61/out/m84036_250809_035451_s4.bc2158.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2158.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-61/out/m84036_250809_035451_s4.bc2158.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2158.mapped.bam.bai:ro --bind /ptcp/meta/paraphase/paraphase_config.GRCh38.yaml:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/paraphase_config.GRCh38.yaml:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-61/call-run_paraphase/_singularity_tmpdir__zyf0j3e/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-61/call-run_paraphase/_singularity_tmpdir__zyf0j3e/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:44.947 wdl.w:ptcp.w:call-trgt-56.t:call-get_reads_overlapping_repeats NOTICE done
2025-09-15 20:24:44.952 wdl.w:ptcp.w:call-trgt-56 NOTICE finish :: job: "call-get_reads_overlapping_repeats"
2025-09-15 20:24:44.952 wdl.w:ptcp.w:call-trgt-56 INFO output :: job: "call-get_reads_overlapping_repeats", values: {"reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-56/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2153.repeats.bam.bai", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-56/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2153.repeats.bam"}
2025-09-15 20:24:44.952 wdl.w:ptcp.w:call-trgt-56 INFO visit :: node: "output-reads_overlapping_repeats", values: {"reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-56/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2153.repeats.bam"}
2025-09-15 20:24:44.952 wdl.w:ptcp.w:call-trgt-56 INFO visit :: node: "output-reads_overlapping_repeats_bai", values: {"reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-56/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2153.repeats.bam.bai"}
2025-09-15 20:24:44.961 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_plot_meth_allele NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-63/call-trgt_plot_meth_allele", thread: 140610912642624
2025-09-15 20:24:44.990 wdl.w:ptcp.w:call-paraphase-61.t:call-run_paraphase NOTICE slurm_singularity run :: pid: 1203012, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-61/call-run_paraphase/slurm_singularity.log.txt"
2025-09-15 20:24:44.996 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_plot_meth_allele INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:44.996 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_plot_meth_allele INFO input :: name: "waterfall", value: false
2025-09-15 20:24:44.996 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_plot_meth_allele INFO input :: name: "methylation", value: true
2025-09-15 20:24:44.997 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_plot_meth_allele INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:44.997 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_plot_meth_allele INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:44.997 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_plot_meth_allele INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:44.997 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_plot_meth_allele INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2160.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:44.997 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_plot_meth_allele INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2160.trgt.sorted.spanning.bam"
2025-09-15 20:24:44.997 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_plot_meth_allele INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2160.trgt.vcf"
2025-09-15 20:24:44.997 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_plot_meth_allele INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2160"
2025-09-15 20:24:44.998 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_plot_meth_allele INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:44.998 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_plot_meth_allele INFO eval :: name: "plot_type", value: "allele"
2025-09-15 20:24:44.998 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_plot_meth_allele INFO eval :: name: "show", value: "meth"
2025-09-15 20:24:44.998 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_plot_meth_allele INFO eval :: name: "threads", value: 1
2025-09-15 20:24:44.998 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_plot_meth_allele INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:44.998 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_plot_meth_allele INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2160.meth_allele"
2025-09-15 20:24:44.999 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_plot_meth_allele INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:44.999 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_plot_meth_allele WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:44.999 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_plot_meth_allele INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:45.000 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_plot_meth_allele INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:45.023 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_motifs_waterfall NOTICE done
2025-09-15 20:24:45.030 wdl.w:ptcp.w:call-trgt-50 NOTICE finish :: job: "call-trgt_plot_motifs_waterfall"
2025-09-15 20:24:45.030 wdl.w:ptcp.w:call-trgt-50 INFO output :: job: "call-trgt_plot_motifs_waterfall", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-50/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2147.motifs_waterfall.trgt_plots.zip"}
2025-09-15 20:24:45.030 wdl.w:ptcp.w:call-trgt-50 INFO visit :: node: "output-images_motifs_waterfall", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-50/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2147.motifs_waterfall.trgt_plots.zip"}
2025-09-15 20:24:45.050 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_plot_meth_waterfall NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-63/call-trgt_plot_meth_waterfall", thread: 140610367379008
2025-09-15 20:24:45.060 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_genotype INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2139.trgt.vcf"
2025-09-15 20:24:45.067 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_genotype INFO output :: name: "spanning_bam", value: "m84036_250809_035451_s4.bc2139.trgt.sorted.spanning.bam"
2025-09-15 20:24:45.068 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_genotype INFO output :: name: "spanning_bam_bai", value: "m84036_250809_035451_s4.bc2139.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:45.075 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_meth_allele NOTICE done
2025-09-15 20:24:45.082 wdl.w:ptcp.w:call-trgt-47 NOTICE finish :: job: "call-trgt_plot_meth_allele"
2025-09-15 20:24:45.083 wdl.w:ptcp.w:call-trgt-47 INFO output :: job: "call-trgt_plot_meth_allele", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-47/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2144.meth_allele.trgt_plots.zip"}
2025-09-15 20:24:45.083 wdl.w:ptcp.w:call-trgt-47 INFO visit :: node: "output-images_meth_allele", values: {"images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-47/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2144.meth_allele.trgt_plots.zip"}
2025-09-15 20:24:45.095 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_plot_meth_waterfall INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:45.095 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_plot_meth_waterfall INFO input :: name: "waterfall", value: true
2025-09-15 20:24:45.095 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_plot_meth_waterfall INFO input :: name: "methylation", value: true
2025-09-15 20:24:45.095 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_plot_meth_waterfall INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:45.096 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_plot_meth_waterfall INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:45.096 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_plot_meth_waterfall INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:45.096 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_plot_meth_waterfall INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2160.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:45.096 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_plot_meth_waterfall INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2160.trgt.sorted.spanning.bam"
2025-09-15 20:24:45.096 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_plot_meth_waterfall INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2160.trgt.vcf"
2025-09-15 20:24:45.096 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_plot_meth_waterfall INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2160"
2025-09-15 20:24:45.096 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_plot_meth_waterfall INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:45.096 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_plot_meth_waterfall INFO eval :: name: "plot_type", value: "waterfall"
2025-09-15 20:24:45.096 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_plot_meth_waterfall INFO eval :: name: "show", value: "meth"
2025-09-15 20:24:45.097 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_plot_meth_waterfall INFO eval :: name: "threads", value: 1
2025-09-15 20:24:45.096 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_plot_motifs_allele NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-63/call-trgt_plot_motifs_allele", thread: 140607674631744
2025-09-15 20:24:45.097 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_plot_meth_waterfall INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:45.097 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_plot_meth_waterfall INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2160.meth_waterfall"
2025-09-15 20:24:45.098 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_plot_meth_waterfall INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:45.098 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_plot_meth_waterfall WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:45.098 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_plot_meth_waterfall INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:45.098 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_plot_meth_waterfall INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:45.113 wdl.w:ptcp.t:call-tar_outputs-29 INFO output :: name: "sample_tarball", value: "m84036_250809_035451_s4.bc2126.tar"
2025-09-15 20:24:45.120 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_plot_motifs_allele INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:45.120 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_plot_motifs_allele INFO input :: name: "waterfall", value: false
2025-09-15 20:24:45.120 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_plot_motifs_allele INFO input :: name: "methylation", value: false
2025-09-15 20:24:45.121 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_plot_motifs_allele INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:45.121 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_plot_motifs_allele INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:45.121 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_plot_motifs_allele INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:45.121 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_plot_motifs_allele INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2160.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:45.121 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_plot_motifs_allele INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2160.trgt.sorted.spanning.bam"
2025-09-15 20:24:45.121 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_plot_motifs_allele INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2160.trgt.vcf"
2025-09-15 20:24:45.121 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_plot_motifs_allele INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2160"
2025-09-15 20:24:45.122 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_plot_motifs_allele INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:45.122 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_plot_motifs_allele INFO eval :: name: "plot_type", value: "allele"
2025-09-15 20:24:45.122 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_plot_motifs_allele INFO eval :: name: "show", value: "motifs"
2025-09-15 20:24:45.122 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_plot_motifs_allele INFO eval :: name: "threads", value: 1
2025-09-15 20:24:45.123 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_plot_motifs_allele INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:45.123 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_plot_motifs_allele INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2160.motifs_allele"
2025-09-15 20:24:45.123 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_plot_meth_allele INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-63/call-trgt_plot_meth_allele/_singularity_tmpdir_y_w774w_"
2025-09-15 20:24:45.124 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_plot_meth_allele INFO Slurm invocation: srun --job-name call-trgt_plot_meth_allele --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-63/call-trgt_plot_meth_allele/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-63/call-trgt_plot_meth_allele/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-63/call-trgt_plot_meth_allele/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-63/call-trgt_plot_meth_allele/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-63/call-trgt_genotype/out/m84036_250809_035451_s4.bc2160.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2160.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-63/call-trgt_genotype/out/m84036_250809_035451_s4.bc2160.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2160.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-63/call-trgt_genotype/out/m84036_250809_035451_s4.bc2160.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2160.trgt.sorted.spanning.bam.bai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-63/call-trgt_plot_meth_allele/_singularity_tmpdir_y_w774w_/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-63/call-trgt_plot_meth_allele/_singularity_tmpdir_y_w774w_/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:45.124 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_plot_motifs_allele INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:45.124 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_plot_motifs_allele WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:45.124 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_plot_motifs_allele INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:45.126 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_plot_motifs_allele INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:45.151 wdl.w:ptcp.t:call-tar_outputs-12 INFO output :: name: "sample_tarball", value: "m84036_250809_035451_s4.bc2109.tar"
2025-09-15 20:24:45.163 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_plot_meth_allele NOTICE slurm_singularity run :: pid: 1203022, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-63/call-trgt_plot_meth_allele/slurm_singularity.log.txt"
2025-09-15 20:24:45.177 wdl.w:ptcp.w:call-paraphase-41.t:call-run_paraphase.stderr VERBOSE INFO:root:Processing sample m84036_250809_035451_s4.bc2138 at 2025-09-15 20:24:44.182469...
2025-09-15 20:24:45.178 wdl.w:ptcp.w:call-paraphase-41.t:call-run_paraphase.stderr VERBOSE INFO:root:Checking sample sex at 2025-09-15 20:24:44.185457...
2025-09-15 20:24:45.178 wdl.w:ptcp.w:call-paraphase-41.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for cyp21 for sample m84036_250809_035451_s4.bc2138 at 2025-09-15 20:24:44.230880...
2025-09-15 20:24:45.178 wdl.w:ptcp.w:call-paraphase-41.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for cyp21 for sample m84036_250809_035451_s4.bc2138 at 2025-09-15 20:24:44.231301...
2025-09-15 20:24:45.178 wdl.w:ptcp.w:call-paraphase-41.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for smn1 for sample m84036_250809_035451_s4.bc2138 at 2025-09-15 20:24:44.231032...
2025-09-15 20:24:45.179 wdl.w:ptcp.w:call-paraphase-41.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for gba for sample m84036_250809_035451_s4.bc2138 at 2025-09-15 20:24:44.231068...
2025-09-15 20:24:45.179 wdl.w:ptcp.w:call-paraphase-41.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for smn1 for sample m84036_250809_035451_s4.bc2138 at 2025-09-15 20:24:44.231420...
2025-09-15 20:24:45.179 wdl.w:ptcp.w:call-paraphase-41.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for hba for sample m84036_250809_035451_s4.bc2138 at 2025-09-15 20:24:44.231111...
2025-09-15 20:24:45.179 wdl.w:ptcp.w:call-paraphase-41.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for gba for sample m84036_250809_035451_s4.bc2138 at 2025-09-15 20:24:44.231426...
2025-09-15 20:24:45.179 wdl.w:ptcp.w:call-paraphase-41.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for hba for sample m84036_250809_035451_s4.bc2138 at 2025-09-15 20:24:44.231469...
2025-09-15 20:24:45.196 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_genotype NOTICE done
2025-09-15 20:24:45.202 wdl.w:ptcp.w:call-trgt-42 NOTICE finish :: job: "call-trgt_genotype"
2025-09-15 20:24:45.203 wdl.w:ptcp.w:call-trgt-42 INFO output :: job: "call-trgt_genotype", values: {"spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-42/call-trgt_genotype/out/m84036_250809_035451_s4.bc2139.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-42/call-trgt_genotype/out/m84036_250809_035451_s4.bc2139.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-42/call-trgt_genotype/out/m84036_250809_035451_s4.bc2139.trgt.vcf"}
2025-09-15 20:24:45.203 wdl.w:ptcp.w:call-trgt-42 NOTICE ready :: job: "call-trgt_plot_meth_allele", callee: "trgt_plot"
2025-09-15 20:24:45.204 wdl.w:ptcp.w:call-trgt-42 INFO input :: job: "call-trgt_plot_meth_allele", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": false, "methylation": true, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-42/call-trgt_genotype/out/m84036_250809_035451_s4.bc2139.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-42/call-trgt_genotype/out/m84036_250809_035451_s4.bc2139.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-42/call-trgt_genotype/out/m84036_250809_035451_s4.bc2139.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2139"}
2025-09-15 20:24:45.205 wdl.w:ptcp.w:call-trgt-42 NOTICE ready :: job: "call-trgt_plot_meth_waterfall", callee: "trgt_plot"
2025-09-15 20:24:45.205 wdl.w:ptcp.w:call-trgt-42 INFO input :: job: "call-trgt_plot_meth_waterfall", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": true, "methylation": true, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-42/call-trgt_genotype/out/m84036_250809_035451_s4.bc2139.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-42/call-trgt_genotype/out/m84036_250809_035451_s4.bc2139.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-42/call-trgt_genotype/out/m84036_250809_035451_s4.bc2139.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2139"}
2025-09-15 20:24:45.207 wdl.w:ptcp.w:call-trgt-42 NOTICE ready :: job: "call-trgt_plot_motifs_allele", callee: "trgt_plot"
2025-09-15 20:24:45.207 wdl.w:ptcp.w:call-trgt-42 INFO input :: job: "call-trgt_plot_motifs_allele", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": false, "methylation": false, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-42/call-trgt_genotype/out/m84036_250809_035451_s4.bc2139.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-42/call-trgt_genotype/out/m84036_250809_035451_s4.bc2139.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-42/call-trgt_genotype/out/m84036_250809_035451_s4.bc2139.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2139"}
2025-09-15 20:24:45.208 wdl.w:ptcp.w:call-trgt-42 NOTICE ready :: job: "call-trgt_plot_motifs_waterfall", callee: "trgt_plot"
2025-09-15 20:24:45.208 wdl.w:ptcp.w:call-trgt-42 INFO input :: job: "call-trgt_plot_motifs_waterfall", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": true, "methylation": false, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-42/call-trgt_genotype/out/m84036_250809_035451_s4.bc2139.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-42/call-trgt_genotype/out/m84036_250809_035451_s4.bc2139.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-42/call-trgt_genotype/out/m84036_250809_035451_s4.bc2139.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2139"}
2025-09-15 20:24:45.209 wdl.w:ptcp.w:call-trgt-42 INFO visit :: node: "output-spanning_bam", values: {"spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-42/call-trgt_genotype/out/m84036_250809_035451_s4.bc2139.trgt.sorted.spanning.bam"}
2025-09-15 20:24:45.209 wdl.w:ptcp.w:call-trgt-42 INFO visit :: node: "output-spanning_bam_bai", values: {"spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-42/call-trgt_genotype/out/m84036_250809_035451_s4.bc2139.trgt.sorted.spanning.bam.bai"}
2025-09-15 20:24:45.209 wdl.w:ptcp.w:call-trgt-42 INFO visit :: node: "output-vcf", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-42/call-trgt_genotype/out/m84036_250809_035451_s4.bc2139.trgt.vcf"}
2025-09-15 20:24:45.216 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_plot_motifs_waterfall NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-63/call-trgt_plot_motifs_waterfall", thread: 140613571819072
2025-09-15 20:24:45.219 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_plot_meth_waterfall INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-63/call-trgt_plot_meth_waterfall/_singularity_tmpdir_64nzju2n"
2025-09-15 20:24:45.219 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_plot_meth_waterfall INFO Slurm invocation: srun --job-name call-trgt_plot_meth_waterfall --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-63/call-trgt_plot_meth_waterfall/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-63/call-trgt_plot_meth_waterfall/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-63/call-trgt_plot_meth_waterfall/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-63/call-trgt_plot_meth_waterfall/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-63/call-trgt_genotype/out/m84036_250809_035451_s4.bc2160.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2160.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-63/call-trgt_genotype/out/m84036_250809_035451_s4.bc2160.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2160.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-63/call-trgt_genotype/out/m84036_250809_035451_s4.bc2160.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2160.trgt.sorted.spanning.bam.bai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-63/call-trgt_plot_meth_waterfall/_singularity_tmpdir_64nzju2n/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-63/call-trgt_plot_meth_waterfall/_singularity_tmpdir_64nzju2n/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:45.235 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_plot_meth_waterfall NOTICE slurm_singularity run :: pid: 1203024, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-63/call-trgt_plot_meth_waterfall/slurm_singularity.log.txt"
2025-09-15 20:24:45.236 wdl.w:ptcp.t:call-tar_outputs-29 NOTICE done
2025-09-15 20:24:45.237 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_plot_motifs_waterfall INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:45.237 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_plot_motifs_waterfall INFO input :: name: "waterfall", value: true
2025-09-15 20:24:45.237 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_plot_motifs_waterfall INFO input :: name: "methylation", value: false
2025-09-15 20:24:45.237 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_plot_motifs_waterfall INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:45.237 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_plot_motifs_waterfall INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:45.237 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_plot_motifs_waterfall INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:45.237 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_plot_motifs_waterfall INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2160.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:45.238 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_plot_motifs_waterfall INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2160.trgt.sorted.spanning.bam"
2025-09-15 20:24:45.238 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_plot_motifs_waterfall INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2160.trgt.vcf"
2025-09-15 20:24:45.238 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_plot_motifs_waterfall INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2160"
2025-09-15 20:24:45.238 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:45.238 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "plot_type", value: "waterfall"
2025-09-15 20:24:45.238 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "show", value: "motifs"
2025-09-15 20:24:45.238 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "threads", value: 1
2025-09-15 20:24:45.238 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:45.239 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2160.motifs_waterfall"
2025-09-15 20:24:45.239 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_plot_motifs_waterfall INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:45.239 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_plot_motifs_waterfall WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:45.239 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_plot_motifs_waterfall INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:45.240 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_plot_motifs_waterfall INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:45.240 wdl.w:ptcp.t:call-tar_outputs-12 NOTICE done
2025-09-15 20:24:45.241 wdl.w:ptcp NOTICE finish :: job: "call-tar_outputs-29"
2025-09-15 20:24:45.241 wdl.w:ptcp INFO output :: job: "call-tar_outputs-29", values: {"sample_tarball": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-29/out/m84036_250809_035451_s4.bc2126.tar"}
2025-09-15 20:24:45.243 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_plot_motifs_allele INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-63/call-trgt_plot_motifs_allele/_singularity_tmpdir_2f4g6jm7"
2025-09-15 20:24:45.244 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_plot_motifs_allele INFO Slurm invocation: srun --job-name call-trgt_plot_motifs_allele --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-63/call-trgt_plot_motifs_allele/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-63/call-trgt_plot_motifs_allele/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-63/call-trgt_plot_motifs_allele/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-63/call-trgt_plot_motifs_allele/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-63/call-trgt_genotype/out/m84036_250809_035451_s4.bc2160.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2160.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-63/call-trgt_genotype/out/m84036_250809_035451_s4.bc2160.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2160.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-63/call-trgt_genotype/out/m84036_250809_035451_s4.bc2160.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2160.trgt.sorted.spanning.bam.bai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-63/call-trgt_plot_motifs_allele/_singularity_tmpdir_2f4g6jm7/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-63/call-trgt_plot_motifs_allele/_singularity_tmpdir_2f4g6jm7/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:45.245 wdl.w:ptcp NOTICE finish :: job: "call-tar_outputs-12"
2025-09-15 20:24:45.246 wdl.w:ptcp INFO output :: job: "call-tar_outputs-12", values: {"sample_tarball": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-12/out/m84036_250809_035451_s4.bc2109.tar"}
2025-09-15 20:24:45.249 wdl.w:ptcp.w:call-sawfish-61.t:call-run_sawfish NOTICE task setup :: name: "run_sawfish", source: "./sawfish.wdl", line: 83, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-61/call-run_sawfish", thread: 140610904249920
2025-09-15 20:24:45.252 wdl.w:ptcp.w:call-trgt-61.t:call-get_reads_overlapping_repeats NOTICE task setup :: name: "get_reads_overlapping_repeats", source: "./trgt.wdl", line: 182, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-61/call-get_reads_overlapping_repeats", thread: 140611961206336
2025-09-15 20:24:45.257 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_plot_motifs_allele NOTICE slurm_singularity run :: pid: 1203026, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-63/call-trgt_plot_motifs_allele/slurm_singularity.log.txt"
2025-09-15 20:24:45.274 wdl.w:ptcp.w:call-trgt-61.t:call-get_reads_overlapping_repeats INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:45.274 wdl.w:ptcp.w:call-trgt-61.t:call-get_reads_overlapping_repeats INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:45.274 wdl.w:ptcp.w:call-trgt-61.t:call-get_reads_overlapping_repeats INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2158.mapped.bam.bai"
2025-09-15 20:24:45.274 wdl.w:ptcp.w:call-trgt-61.t:call-get_reads_overlapping_repeats INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2158.mapped.bam"
2025-09-15 20:24:45.274 wdl.w:ptcp.w:call-trgt-61.t:call-get_reads_overlapping_repeats INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2158"
2025-09-15 20:24:45.274 wdl.w:ptcp.w:call-trgt-61.t:call-get_reads_overlapping_repeats INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:45.274 wdl.w:ptcp.w:call-trgt-61.t:call-get_reads_overlapping_repeats INFO eval :: name: "expand_size", value: 3000
2025-09-15 20:24:45.275 wdl.w:ptcp.w:call-trgt-61.t:call-get_reads_overlapping_repeats INFO eval :: name: "threads", value: 1
2025-09-15 20:24:45.275 wdl.w:ptcp.w:call-trgt-61.t:call-get_reads_overlapping_repeats INFO eval :: name: "expanded_bed_name", value: "m84036_250809_035451_s4.bc2158.expanded.bed"
2025-09-15 20:24:45.275 wdl.w:ptcp.w:call-trgt-61.t:call-get_reads_overlapping_repeats INFO eval :: name: "disk_size", value: 11
2025-09-15 20:24:45.275 wdl.w:ptcp.w:call-trgt-61.t:call-get_reads_overlapping_repeats INFO eval :: name: "output_name", value: "m84036_250809_035451_s4.bc2158.repeats.bam"
2025-09-15 20:24:45.275 wdl.w:ptcp.w:call-trgt-61.t:call-get_reads_overlapping_repeats INFO eval :: name: "index_name", value: "m84036_250809_035451_s4.bc2158.repeats.bam.bai"
2025-09-15 20:24:45.275 wdl.w:ptcp.w:call-trgt-61.t:call-get_reads_overlapping_repeats INFO eval :: name: "output_name_with_index", value: "m84036_250809_035451_s4.bc2158.repeats.bam##idx##m84036_250809_035451_s4.bc2158.repeats.bam.bai"
2025-09-15 20:24:45.275 wdl.w:ptcp.w:call-trgt-61.t:call-get_reads_overlapping_repeats INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:45.276 wdl.w:ptcp.w:call-trgt-61.t:call-get_reads_overlapping_repeats WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:45.276 wdl.w:ptcp.w:call-trgt-61.t:call-get_reads_overlapping_repeats INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:45.276 wdl.w:ptcp.w:call-trgt-61.t:call-get_reads_overlapping_repeats INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:45.278 wdl.w:ptcp.w:call-sawfish-61.t:call-run_sawfish INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:45.278 wdl.w:ptcp.w:call-sawfish-61.t:call-run_sawfish INFO input :: name: "genome_version", value: "38"
2025-09-15 20:24:45.278 wdl.w:ptcp.w:call-sawfish-61.t:call-run_sawfish INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:45.278 wdl.w:ptcp.w:call-sawfish-61.t:call-run_sawfish INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:45.278 wdl.w:ptcp.w:call-sawfish-61.t:call-run_sawfish INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2158.mapped.bam.bai"
2025-09-15 20:24:45.278 wdl.w:ptcp.w:call-sawfish-61.t:call-run_sawfish INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2158.mapped.bam"
2025-09-15 20:24:45.278 wdl.w:ptcp.w:call-sawfish-61.t:call-run_sawfish INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2158"
2025-09-15 20:24:45.279 wdl.w:ptcp.w:call-sawfish-61.t:call-run_sawfish INFO eval :: name: "mem_gb", value: 32
2025-09-15 20:24:45.279 wdl.w:ptcp.w:call-sawfish-61.t:call-run_sawfish INFO eval :: name: "threads", value: 16
2025-09-15 20:24:45.279 wdl.w:ptcp.w:call-sawfish-61.t:call-run_sawfish INFO eval :: name: "disk_size", value: 30
2025-09-15 20:24:45.279 wdl.w:ptcp.w:call-sawfish-61.t:call-run_sawfish INFO eval :: name: "discover_dirname", value: "m84036_250809_035451_s4.bc2158_sawfish_discover"
2025-09-15 20:24:45.279 wdl.w:ptcp.w:call-sawfish-61.t:call-run_sawfish INFO eval :: name: "call_dirname", value: "m84036_250809_035451_s4.bc2158_sawfish"
2025-09-15 20:24:45.279 wdl.w:ptcp.w:call-sawfish-61.t:call-run_sawfish INFO eval :: name: "minimap2_bam_filename", value: "m84036_250809_035451_s4.bc2158.minimap2.bam"
2025-09-15 20:24:45.280 wdl.w:ptcp.w:call-sawfish-61.t:call-run_sawfish INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 16, memory_reservation: 32000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:45.280 wdl.w:ptcp.w:call-sawfish-61.t:call-run_sawfish WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:45.280 wdl.w:ptcp.w:call-sawfish-61.t:call-run_sawfish INFO provisioned :: seconds_waited: 0, cpu: 16, mem_bytes: 32000000000
2025-09-15 20:24:45.280 wdl.w:ptcp.w:call-sawfish-61.t:call-run_sawfish INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:45.299 wdl.w:ptcp.w:call-sawfish-58.t:call-run_sawfish.slurm_singularity INFO srun: job 51797774 queued and waiting for resources
2025-09-15 20:24:45.299 wdl.w:ptcp.w:call-sawfish-58.t:call-run_sawfish.slurm_singularity INFO srun: job 51797774 has been allocated resources
2025-09-15 20:24:45.299 wdl.w:ptcp.w:call-sawfish-58.t:call-run_sawfish.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:45.309 wdl.w:ptcp.w:call-paraphase-40.t:call-run_paraphase.stderr VERBOSE INFO:root:Processing sample m84036_250809_035451_s4.bc2137 at 2025-09-15 20:24:44.175602...
2025-09-15 20:24:45.311 wdl.w:ptcp.w:call-paraphase-40.t:call-run_paraphase.stderr VERBOSE INFO:root:Checking sample sex at 2025-09-15 20:24:44.176723...
2025-09-15 20:24:45.311 wdl.w:ptcp.w:call-paraphase-40.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for cyp21 for sample m84036_250809_035451_s4.bc2137 at 2025-09-15 20:24:44.226794...
2025-09-15 20:24:45.311 wdl.w:ptcp.w:call-paraphase-40.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for cyp21 for sample m84036_250809_035451_s4.bc2137 at 2025-09-15 20:24:44.227227...
2025-09-15 20:24:45.311 wdl.w:ptcp.w:call-paraphase-40.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for smn1 for sample m84036_250809_035451_s4.bc2137 at 2025-09-15 20:24:44.226942...
2025-09-15 20:24:45.311 wdl.w:ptcp.w:call-paraphase-40.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for smn1 for sample m84036_250809_035451_s4.bc2137 at 2025-09-15 20:24:44.227341...
2025-09-15 20:24:45.311 wdl.w:ptcp.w:call-paraphase-40.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for gba for sample m84036_250809_035451_s4.bc2137 at 2025-09-15 20:24:44.227006...
2025-09-15 20:24:45.311 wdl.w:ptcp.w:call-paraphase-40.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for hba for sample m84036_250809_035451_s4.bc2137 at 2025-09-15 20:24:44.227031...
2025-09-15 20:24:45.311 wdl.w:ptcp.w:call-paraphase-40.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for gba for sample m84036_250809_035451_s4.bc2137 at 2025-09-15 20:24:44.227392...
2025-09-15 20:24:45.311 wdl.w:ptcp.w:call-paraphase-40.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for hba for sample m84036_250809_035451_s4.bc2137 at 2025-09-15 20:24:44.227403...
2025-09-15 20:24:45.341 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_plot_motifs_waterfall INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-63/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_jqlpt0my"
2025-09-15 20:24:45.342 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_plot_motifs_waterfall INFO Slurm invocation: srun --job-name call-trgt_plot_motifs_waterfall --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-63/call-trgt_plot_motifs_waterfall/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-63/call-trgt_plot_motifs_waterfall/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-63/call-trgt_plot_motifs_waterfall/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-63/call-trgt_plot_motifs_waterfall/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-63/call-trgt_genotype/out/m84036_250809_035451_s4.bc2160.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2160.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-63/call-trgt_genotype/out/m84036_250809_035451_s4.bc2160.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2160.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-63/call-trgt_genotype/out/m84036_250809_035451_s4.bc2160.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2160.trgt.sorted.spanning.bam.bai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-63/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_jqlpt0my/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-63/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_jqlpt0my/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:45.354 wdl.w:ptcp.w:call-trgt-61.t:call-get_reads_overlapping_repeats INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 9, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-61/call-get_reads_overlapping_repeats/_singularity_tmpdir_e9th1i7j"
2025-09-15 20:24:45.355 wdl.w:ptcp.w:call-trgt-61.t:call-get_reads_overlapping_repeats INFO Slurm invocation: srun --job-name call-get_reads_overlapping_repeats --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-61/call-get_reads_overlapping_repeats/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-61/call-get_reads_overlapping_repeats/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-61/call-get_reads_overlapping_repeats/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-61/call-get_reads_overlapping_repeats/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-61/out/m84036_250809_035451_s4.bc2158.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2158.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-61/out/m84036_250809_035451_s4.bc2158.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2158.mapped.bam.bai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-61/call-get_reads_overlapping_repeats/_singularity_tmpdir_e9th1i7j/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-61/call-get_reads_overlapping_repeats/_singularity_tmpdir_e9th1i7j/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:45.361 wdl.w:ptcp.t:call-tar_outputs-04.slurm_singularity INFO srun: job 51797775 queued and waiting for resources
2025-09-15 20:24:45.361 wdl.w:ptcp.t:call-tar_outputs-04.slurm_singularity INFO srun: job 51797775 has been allocated resources
2025-09-15 20:24:45.361 wdl.w:ptcp.t:call-tar_outputs-04.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:45.361 wdl.w:ptcp.t:call-tar_outputs-04.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:24:45.361 wdl.w:ptcp.w:call-sawfish-61.t:call-run_sawfish INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 10, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-61/call-run_sawfish/_singularity_tmpdir_3c5o6pdx"
2025-09-15 20:24:45.363 wdl.w:ptcp.w:call-sawfish-61.t:call-run_sawfish INFO Slurm invocation: srun --job-name call-run_sawfish --partition compute,compute9 --cpus-per-task 16 --mem 30518M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-61/call-run_sawfish/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-61/call-run_sawfish/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-61/call-run_sawfish/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-61/call-run_sawfish/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-61/out/m84036_250809_035451_s4.bc2158.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2158.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-61/out/m84036_250809_035451_s4.bc2158.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2158.mapped.bam.bai:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-61/call-run_sawfish/_singularity_tmpdir_3c5o6pdx/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-61/call-run_sawfish/_singularity_tmpdir_3c5o6pdx/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:45.369 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_plot_motifs_waterfall NOTICE slurm_singularity run :: pid: 1203028, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-63/call-trgt_plot_motifs_waterfall/slurm_singularity.log.txt"
2025-09-15 20:24:45.369 wdl.w:ptcp.w:call-trgt-61.t:call-get_reads_overlapping_repeats NOTICE slurm_singularity run :: pid: 1203029, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-61/call-get_reads_overlapping_repeats/slurm_singularity.log.txt"
2025-09-15 20:24:45.369 wdl.w:ptcp.w:call-sawfish-61.t:call-run_sawfish NOTICE slurm_singularity run :: pid: 1203030, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-61/call-run_sawfish/slurm_singularity.log.txt"
2025-09-15 20:24:45.444 wdl.w:ptcp.w:call-trgt-58.t:call-get_reads_overlapping_repeats.slurm_singularity INFO srun: job 51797776 queued and waiting for resources
2025-09-15 20:24:45.444 wdl.w:ptcp.w:call-trgt-58.t:call-get_reads_overlapping_repeats.slurm_singularity INFO srun: job 51797776 has been allocated resources
2025-09-15 20:24:45.444 wdl.w:ptcp.w:call-trgt-58.t:call-get_reads_overlapping_repeats.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:45.444 wdl.w:ptcp.w:call-trgt-58.t:call-get_reads_overlapping_repeats.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:24:45.470 wdl.w:ptcp.w:call-trgt-58.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:24:45 [INFO] - Running trgt-4.0.0-429afcd [genotype]
2025-09-15 20:24:45.470 wdl.w:ptcp.w:call-trgt-58.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:24:45 [WARN] - SCA17_TBP: Filtered out 1 impure reads
2025-09-15 20:24:45.470 wdl.w:ptcp.w:call-trgt-58.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:24:45 [WARN] - EIEE1_ARX: Filtered out 2 impure reads
2025-09-15 20:24:45.470 wdl.w:ptcp.w:call-trgt-58.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:24:45 [WARN] - PRTS_ARX: Filtered out 3 impure reads
2025-09-15 20:24:45.470 wdl.w:ptcp.w:call-trgt-58.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:24:45 [WARN] - FXS_FMR1: Filtered out 6 impure reads
2025-09-15 20:24:45.470 wdl.w:ptcp.w:call-trgt-58.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:24:45 [WARN] - FRAXE_AFF2: Filtered out 26 impure reads
2025-09-15 20:24:45.471 wdl.w:ptcp.w:call-trgt-58.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:24:45 [WARN] - FRDA_FXN: Filtered out 5 impure reads
2025-09-15 20:24:45.471 wdl.w:ptcp.w:call-trgt-58.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:24:45 [INFO] - Total execution time: 386.89ms
2025-09-15 20:24:45.471 wdl.w:ptcp.w:call-trgt-58.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:24:45 [INFO] - trgt end
2025-09-15 20:24:45.479 wdl.w:ptcp.w:call-trgt-58.t:call-trgt_genotype.slurm_singularity INFO srun: job 51797777 queued and waiting for resources
2025-09-15 20:24:45.479 wdl.w:ptcp.w:call-trgt-58.t:call-trgt_genotype.slurm_singularity INFO srun: job 51797777 has been allocated resources
2025-09-15 20:24:45.479 wdl.w:ptcp.w:call-trgt-58.t:call-trgt_genotype.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:45.479 wdl.w:ptcp.w:call-trgt-58.t:call-trgt_genotype.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:24:45.549 wdl.w:ptcp.w:call-trgt-58.t:call-get_reads_overlapping_repeats INFO output :: name: "reads_overlapping_repeats", value: "m84036_250809_035451_s4.bc2155.repeats.bam"
2025-09-15 20:24:45.552 wdl.w:ptcp.w:call-trgt-58.t:call-get_reads_overlapping_repeats INFO output :: name: "reads_overlapping_repeats_bai", value: "m84036_250809_035451_s4.bc2155.repeats.bam.bai"
2025-09-15 20:24:45.566 wdl.w:ptcp.t:call-tar_outputs-04 INFO output :: name: "sample_tarball", value: "m84036_250809_035451_s4.bc2101.tar"
2025-09-15 20:24:45.620 wdl.w:ptcp.w:call-trgt-58.t:call-get_reads_overlapping_repeats NOTICE done
2025-09-15 20:24:45.625 wdl.w:ptcp.w:call-trgt-58 NOTICE finish :: job: "call-get_reads_overlapping_repeats"
2025-09-15 20:24:45.625 wdl.w:ptcp.w:call-trgt-58 INFO output :: job: "call-get_reads_overlapping_repeats", values: {"reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-58/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2155.repeats.bam.bai", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-58/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2155.repeats.bam"}
2025-09-15 20:24:45.625 wdl.w:ptcp.w:call-trgt-58 INFO visit :: node: "output-reads_overlapping_repeats", values: {"reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-58/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2155.repeats.bam"}
2025-09-15 20:24:45.626 wdl.w:ptcp.w:call-trgt-58 INFO visit :: node: "output-reads_overlapping_repeats_bai", values: {"reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-58/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2155.repeats.bam.bai"}
2025-09-15 20:24:45.632 wdl.w:ptcp.w:call-trgt-61.t:call-trgt_genotype NOTICE task setup :: name: "trgt_genotype", source: "./trgt.wdl", line: 272, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-61/call-trgt_genotype", thread: 140609847293504
2025-09-15 20:24:45.639 wdl.w:ptcp.t:call-tar_outputs-04 NOTICE done
2025-09-15 20:24:45.643 wdl.w:ptcp NOTICE finish :: job: "call-tar_outputs-04"
2025-09-15 20:24:45.643 wdl.w:ptcp INFO output :: job: "call-tar_outputs-04", values: {"sample_tarball": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-04/out/m84036_250809_035451_s4.bc2101.tar"}
2025-09-15 20:24:45.645 wdl.w:ptcp.w:call-trgt-52.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:44 [ERROR] - No reads found for TRID=PRTS_ARX
2025-09-15 20:24:45.645 wdl.w:ptcp.w:call-trgt-52.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:44 [ERROR] - No reads found for TRID=EIEE1_ARX
2025-09-15 20:24:45.649 wdl.w:ptcp.w:call-paraphase-67.t:call-run_paraphase NOTICE task setup :: name: "run_paraphase", source: "./paraphase.wdl", line: 127, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-67/call-run_paraphase", thread: 140606080804416
2025-09-15 20:24:45.651 wdl.w:ptcp.w:call-trgt-61.t:call-trgt_genotype INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:45.651 wdl.w:ptcp.w:call-trgt-61.t:call-trgt_genotype INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:45.651 wdl.w:ptcp.w:call-trgt-61.t:call-trgt_genotype INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:45.651 wdl.w:ptcp.w:call-trgt-61.t:call-trgt_genotype INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:45.651 wdl.w:ptcp.w:call-trgt-61.t:call-trgt_genotype INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2158.mapped.bam.bai"
2025-09-15 20:24:45.651 wdl.w:ptcp.w:call-trgt-61.t:call-trgt_genotype INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2158.mapped.bam"
2025-09-15 20:24:45.652 wdl.w:ptcp.w:call-trgt-61.t:call-trgt_genotype INFO input :: name: "sex", value: "F"
2025-09-15 20:24:45.652 wdl.w:ptcp.w:call-trgt-61.t:call-trgt_genotype INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2158"
2025-09-15 20:24:45.652 wdl.w:ptcp.w:call-trgt-61.t:call-trgt_genotype INFO eval :: name: "mem_gb", value: 16
2025-09-15 20:24:45.652 wdl.w:ptcp.w:call-trgt-61.t:call-trgt_genotype INFO eval :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2158.trgt"
2025-09-15 20:24:45.652 wdl.w:ptcp.w:call-trgt-61.t:call-trgt_genotype INFO eval :: name: "threads", value: 8
2025-09-15 20:24:45.652 wdl.w:ptcp.w:call-trgt-61.t:call-trgt_genotype INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:45.652 wdl.w:ptcp.w:call-trgt-61.t:call-trgt_genotype INFO eval :: name: "karyotype", value: "XX"
2025-09-15 20:24:45.653 wdl.w:ptcp.w:call-trgt-61.t:call-trgt_genotype INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 8, memory_reservation: 16000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:45.653 wdl.w:ptcp.w:call-trgt-61.t:call-trgt_genotype WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:45.653 wdl.w:ptcp.w:call-trgt-61.t:call-trgt_genotype INFO provisioned :: seconds_waited: 0, cpu: 8, mem_bytes: 16000000000
2025-09-15 20:24:45.653 wdl.w:ptcp.w:call-trgt-61.t:call-trgt_genotype INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:45.672 wdl.w:ptcp.w:call-paraphase-67.t:call-run_paraphase INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:45.673 wdl.w:ptcp.w:call-paraphase-67.t:call-run_paraphase INFO input :: name: "annotation_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf"
2025-09-15 20:24:45.673 wdl.w:ptcp.w:call-paraphase-67.t:call-run_paraphase INFO input :: name: "genome_version", value: "38"
2025-09-15 20:24:45.673 wdl.w:ptcp.w:call-paraphase-67.t:call-run_paraphase INFO input :: name: "config_file", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/paraphase_config.GRCh38.yaml"
2025-09-15 20:24:45.673 wdl.w:ptcp.w:call-paraphase-67.t:call-run_paraphase INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:45.673 wdl.w:ptcp.w:call-paraphase-67.t:call-run_paraphase INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:45.673 wdl.w:ptcp.w:call-paraphase-67.t:call-run_paraphase INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2164.mapped.bam.bai"
2025-09-15 20:24:45.673 wdl.w:ptcp.w:call-paraphase-67.t:call-run_paraphase INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2164.mapped.bam"
2025-09-15 20:24:45.673 wdl.w:ptcp.w:call-paraphase-67.t:call-run_paraphase INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2164"
2025-09-15 20:24:45.673 wdl.w:ptcp.w:call-paraphase-67.t:call-run_paraphase INFO eval :: name: "threads", value: 4
2025-09-15 20:24:45.673 wdl.w:ptcp.w:call-paraphase-67.t:call-run_paraphase INFO eval :: name: "mem_gb", value: 8
2025-09-15 20:24:45.674 wdl.w:ptcp.w:call-paraphase-67.t:call-run_paraphase INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:45.674 wdl.w:ptcp.w:call-paraphase-67.t:call-run_paraphase INFO eval :: name: "out_dir", value: "m84036_250809_035451_s4.bc2164_paraphase"
2025-09-15 20:24:45.674 wdl.w:ptcp.w:call-paraphase-67.t:call-run_paraphase INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 4, memory_reservation: 8000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:45.674 wdl.w:ptcp.w:call-paraphase-67.t:call-run_paraphase WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:45.675 wdl.w:ptcp.w:call-paraphase-67.t:call-run_paraphase INFO provisioned :: seconds_waited: 0, cpu: 4, mem_bytes: 8000000000
2025-09-15 20:24:45.675 wdl.w:ptcp.w:call-paraphase-67.t:call-run_paraphase INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:45.721 wdl.w:ptcp.w:call-trgt-61.t:call-trgt_genotype INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 11, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-61/call-trgt_genotype/_singularity_tmpdir_0m2vah2k"
2025-09-15 20:24:45.721 wdl.w:ptcp.w:call-trgt-61.t:call-trgt_genotype INFO Slurm invocation: srun --job-name call-trgt_genotype --partition compute,compute9 --cpus-per-task 8 --mem 15259M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-61/call-trgt_genotype/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-61/call-trgt_genotype/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-61/call-trgt_genotype/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-61/call-trgt_genotype/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-61/out/m84036_250809_035451_s4.bc2158.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2158.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-61/out/m84036_250809_035451_s4.bc2158.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2158.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-61/call-trgt_genotype/_singularity_tmpdir_0m2vah2k/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-61/call-trgt_genotype/_singularity_tmpdir_0m2vah2k/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:45.746 wdl.w:ptcp.w:call-paraphase-67.t:call-run_paraphase INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-67/call-run_paraphase/_singularity_tmpdir_7n0rfq0w"
2025-09-15 20:24:45.746 wdl.w:ptcp.w:call-paraphase-67.t:call-run_paraphase INFO Slurm invocation: srun --job-name call-run_paraphase --partition compute,compute9 --cpus-per-task 4 --mem 7629M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-67/call-run_paraphase/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-67/call-run_paraphase/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-67/call-run_paraphase/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-67/call-run_paraphase/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-67/out/m84036_250809_035451_s4.bc2164.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2164.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-67/out/m84036_250809_035451_s4.bc2164.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2164.mapped.bam:ro --bind /ptcp/meta/variant_list/variant_list.GRCh38.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf:ro --bind /ptcp/meta/paraphase/paraphase_config.GRCh38.yaml:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/paraphase_config.GRCh38.yaml:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-67/call-run_paraphase/_singularity_tmpdir_7n0rfq0w/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-67/call-run_paraphase/_singularity_tmpdir_7n0rfq0w/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:45.753 wdl.w:ptcp.w:call-trgt-61.t:call-trgt_genotype NOTICE slurm_singularity run :: pid: 1203067, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-61/call-trgt_genotype/slurm_singularity.log.txt"
2025-09-15 20:24:45.753 wdl.w:ptcp.w:call-paraphase-67.t:call-run_paraphase NOTICE slurm_singularity run :: pid: 1203068, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-67/call-run_paraphase/slurm_singularity.log.txt"
2025-09-15 20:24:45.800 wdl.w:ptcp.w:call-trgt-58.t:call-trgt_genotype INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2155.trgt.vcf"
2025-09-15 20:24:45.803 wdl.w:ptcp.w:call-trgt-58.t:call-trgt_genotype INFO output :: name: "spanning_bam", value: "m84036_250809_035451_s4.bc2155.trgt.sorted.spanning.bam"
2025-09-15 20:24:45.804 wdl.w:ptcp.w:call-trgt-58.t:call-trgt_genotype INFO output :: name: "spanning_bam_bai", value: "m84036_250809_035451_s4.bc2155.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:45.874 wdl.w:ptcp.w:call-trgt-58.t:call-trgt_genotype NOTICE done
2025-09-15 20:24:45.885 wdl.w:ptcp.w:call-trgt-58 NOTICE finish :: job: "call-trgt_genotype"
2025-09-15 20:24:45.886 wdl.w:ptcp.w:call-trgt-58 INFO output :: job: "call-trgt_genotype", values: {"spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-58/call-trgt_genotype/out/m84036_250809_035451_s4.bc2155.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-58/call-trgt_genotype/out/m84036_250809_035451_s4.bc2155.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-58/call-trgt_genotype/out/m84036_250809_035451_s4.bc2155.trgt.vcf"}
2025-09-15 20:24:45.886 wdl.w:ptcp.w:call-trgt-58 NOTICE ready :: job: "call-trgt_plot_meth_allele", callee: "trgt_plot"
2025-09-15 20:24:45.886 wdl.w:ptcp.w:call-trgt-58 INFO input :: job: "call-trgt_plot_meth_allele", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": false, "methylation": true, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-58/call-trgt_genotype/out/m84036_250809_035451_s4.bc2155.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-58/call-trgt_genotype/out/m84036_250809_035451_s4.bc2155.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-58/call-trgt_genotype/out/m84036_250809_035451_s4.bc2155.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2155"}
2025-09-15 20:24:45.891 wdl.w:ptcp.w:call-trgt-58 NOTICE ready :: job: "call-trgt_plot_meth_waterfall", callee: "trgt_plot"
2025-09-15 20:24:45.891 wdl.w:ptcp.w:call-trgt-58 INFO input :: job: "call-trgt_plot_meth_waterfall", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": true, "methylation": true, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-58/call-trgt_genotype/out/m84036_250809_035451_s4.bc2155.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-58/call-trgt_genotype/out/m84036_250809_035451_s4.bc2155.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-58/call-trgt_genotype/out/m84036_250809_035451_s4.bc2155.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2155"}
2025-09-15 20:24:45.892 wdl.w:ptcp.w:call-trgt-58 NOTICE ready :: job: "call-trgt_plot_motifs_allele", callee: "trgt_plot"
2025-09-15 20:24:45.892 wdl.w:ptcp.w:call-trgt-58 INFO input :: job: "call-trgt_plot_motifs_allele", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": false, "methylation": false, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-58/call-trgt_genotype/out/m84036_250809_035451_s4.bc2155.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-58/call-trgt_genotype/out/m84036_250809_035451_s4.bc2155.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-58/call-trgt_genotype/out/m84036_250809_035451_s4.bc2155.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2155"}
2025-09-15 20:24:45.892 wdl.w:ptcp.w:call-sawfish-67.t:call-run_sawfish NOTICE task setup :: name: "run_sawfish", source: "./sawfish.wdl", line: 83, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-67/call-run_sawfish", thread: 140610879071808
2025-09-15 20:24:45.894 wdl.w:ptcp.w:call-trgt-58 NOTICE ready :: job: "call-trgt_plot_motifs_waterfall", callee: "trgt_plot"
2025-09-15 20:24:45.894 wdl.w:ptcp.w:call-trgt-58 INFO input :: job: "call-trgt_plot_motifs_waterfall", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": true, "methylation": false, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-58/call-trgt_genotype/out/m84036_250809_035451_s4.bc2155.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-58/call-trgt_genotype/out/m84036_250809_035451_s4.bc2155.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-58/call-trgt_genotype/out/m84036_250809_035451_s4.bc2155.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2155"}
2025-09-15 20:24:45.894 wdl.w:ptcp.w:call-trgt-58 INFO visit :: node: "output-spanning_bam", values: {"spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-58/call-trgt_genotype/out/m84036_250809_035451_s4.bc2155.trgt.sorted.spanning.bam"}
2025-09-15 20:24:45.895 wdl.w:ptcp.w:call-trgt-58 INFO visit :: node: "output-spanning_bam_bai", values: {"spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-58/call-trgt_genotype/out/m84036_250809_035451_s4.bc2155.trgt.sorted.spanning.bam.bai"}
2025-09-15 20:24:45.895 wdl.w:ptcp.w:call-trgt-58 INFO visit :: node: "output-vcf", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-58/call-trgt_genotype/out/m84036_250809_035451_s4.bc2155.trgt.vcf"}
2025-09-15 20:24:45.910 wdl.w:ptcp.w:call-sawfish-67.t:call-run_sawfish INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:45.910 wdl.w:ptcp.w:call-sawfish-67.t:call-run_sawfish INFO input :: name: "genome_version", value: "38"
2025-09-15 20:24:45.910 wdl.w:ptcp.w:call-sawfish-67.t:call-run_sawfish INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:45.910 wdl.w:ptcp.w:call-sawfish-67.t:call-run_sawfish INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:45.910 wdl.w:ptcp.w:call-sawfish-67.t:call-run_sawfish INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2164.mapped.bam.bai"
2025-09-15 20:24:45.910 wdl.w:ptcp.w:call-sawfish-67.t:call-run_sawfish INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2164.mapped.bam"
2025-09-15 20:24:45.910 wdl.w:ptcp.w:call-sawfish-67.t:call-run_sawfish INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2164"
2025-09-15 20:24:45.910 wdl.w:ptcp.w:call-sawfish-67.t:call-run_sawfish INFO eval :: name: "mem_gb", value: 32
2025-09-15 20:24:45.911 wdl.w:ptcp.w:call-sawfish-67.t:call-run_sawfish INFO eval :: name: "threads", value: 16
2025-09-15 20:24:45.911 wdl.w:ptcp.w:call-sawfish-67.t:call-run_sawfish INFO eval :: name: "disk_size", value: 30
2025-09-15 20:24:45.911 wdl.w:ptcp.w:call-sawfish-67.t:call-run_sawfish INFO eval :: name: "discover_dirname", value: "m84036_250809_035451_s4.bc2164_sawfish_discover"
2025-09-15 20:24:45.911 wdl.w:ptcp.w:call-sawfish-67.t:call-run_sawfish INFO eval :: name: "call_dirname", value: "m84036_250809_035451_s4.bc2164_sawfish"
2025-09-15 20:24:45.911 wdl.w:ptcp.w:call-sawfish-67.t:call-run_sawfish INFO eval :: name: "minimap2_bam_filename", value: "m84036_250809_035451_s4.bc2164.minimap2.bam"
2025-09-15 20:24:45.912 wdl.w:ptcp.w:call-sawfish-67.t:call-run_sawfish INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 16, memory_reservation: 32000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:45.912 wdl.w:ptcp.w:call-sawfish-67.t:call-run_sawfish WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:45.912 wdl.w:ptcp.w:call-sawfish-67.t:call-run_sawfish INFO provisioned :: seconds_waited: 0, cpu: 16, mem_bytes: 32000000000
2025-09-15 20:24:45.912 wdl.w:ptcp.w:call-sawfish-67.t:call-run_sawfish INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:45.974 wdl.w:ptcp.w:call-sawfish-67.t:call-run_sawfish INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 10, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-67/call-run_sawfish/_singularity_tmpdir_eb5z9edo"
2025-09-15 20:24:45.974 wdl.w:ptcp.w:call-sawfish-67.t:call-run_sawfish INFO Slurm invocation: srun --job-name call-run_sawfish --partition compute,compute9 --cpus-per-task 16 --mem 30518M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-67/call-run_sawfish/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-67/call-run_sawfish/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-67/call-run_sawfish/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-67/call-run_sawfish/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-67/out/m84036_250809_035451_s4.bc2164.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2164.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-67/out/m84036_250809_035451_s4.bc2164.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2164.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-67/call-run_sawfish/_singularity_tmpdir_eb5z9edo/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-67/call-run_sawfish/_singularity_tmpdir_eb5z9edo/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:45.990 wdl.w:ptcp.w:call-sawfish-67.t:call-run_sawfish NOTICE slurm_singularity run :: pid: 1203071, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-67/call-run_sawfish/slurm_singularity.log.txt"
2025-09-15 20:24:45.999 wdl.w:ptcp.w:call-paraphase-61.t:call-run_paraphase.slurm_singularity INFO srun: job 51797778 queued and waiting for resources
2025-09-15 20:24:45.999 wdl.w:ptcp.w:call-paraphase-61.t:call-run_paraphase.slurm_singularity INFO srun: job 51797778 has been allocated resources
2025-09-15 20:24:46.000 wdl.w:ptcp.w:call-paraphase-61.t:call-run_paraphase.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:46.069 wdl.w:ptcp.w:call-paraphase-19.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for cyp21 for sample m84036_250809_035451_s4.bc2116 at 2025-09-15 20:24:24.047009...
2025-09-15 20:24:46.069 wdl.w:ptcp.w:call-paraphase-19.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for gba for sample m84036_250809_035451_s4.bc2116 at 2025-09-15 20:24:37.561798...
2025-09-15 20:24:46.069 wdl.w:ptcp.w:call-paraphase-19.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for gba for sample m84036_250809_035451_s4.bc2116 at 2025-09-15 20:24:38.107764...
2025-09-15 20:24:46.069 wdl.w:ptcp.w:call-paraphase-19.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for hbb for sample m84036_250809_035451_s4.bc2116 at 2025-09-15 20:24:39.619921...
2025-09-15 20:24:46.069 wdl.w:ptcp.w:call-paraphase-19.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for hbb for sample m84036_250809_035451_s4.bc2116 at 2025-09-15 20:24:39.620102...
2025-09-15 20:24:46.111 wdl.w:ptcp.w:call-paraphase-48.t:call-run_paraphase.stderr VERBOSE INFO:root:Processing sample m84036_250809_035451_s4.bc2145 at 2025-09-15 20:24:41.761242...
2025-09-15 20:24:46.111 wdl.w:ptcp.w:call-paraphase-48.t:call-run_paraphase.stderr VERBOSE INFO:root:Checking sample sex at 2025-09-15 20:24:41.762941...
2025-09-15 20:24:46.111 wdl.w:ptcp.w:call-paraphase-48.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for cyp21 for sample m84036_250809_035451_s4.bc2145 at 2025-09-15 20:24:41.820235...
2025-09-15 20:24:46.111 wdl.w:ptcp.w:call-paraphase-48.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for cyp21 for sample m84036_250809_035451_s4.bc2145 at 2025-09-15 20:24:41.820760...
2025-09-15 20:24:46.112 wdl.w:ptcp.w:call-paraphase-48.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for smn1 for sample m84036_250809_035451_s4.bc2145 at 2025-09-15 20:24:41.820387...
2025-09-15 20:24:46.112 wdl.w:ptcp.w:call-paraphase-48.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for gba for sample m84036_250809_035451_s4.bc2145 at 2025-09-15 20:24:41.820436...
2025-09-15 20:24:46.112 wdl.w:ptcp.w:call-paraphase-48.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for smn1 for sample m84036_250809_035451_s4.bc2145 at 2025-09-15 20:24:41.820829...
2025-09-15 20:24:46.112 wdl.w:ptcp.w:call-paraphase-48.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for gba for sample m84036_250809_035451_s4.bc2145 at 2025-09-15 20:24:41.820862...
2025-09-15 20:24:46.112 wdl.w:ptcp.w:call-paraphase-48.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for hba for sample m84036_250809_035451_s4.bc2145 at 2025-09-15 20:24:41.821689...
2025-09-15 20:24:46.112 wdl.w:ptcp.w:call-paraphase-48.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for hba for sample m84036_250809_035451_s4.bc2145 at 2025-09-15 20:24:41.822071...
2025-09-15 20:24:46.112 wdl.w:ptcp.w:call-paraphase-48.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for gba for sample m84036_250809_035451_s4.bc2145 at 2025-09-15 20:24:42.436450...
2025-09-15 20:24:46.112 wdl.w:ptcp.w:call-paraphase-48.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for cyp21 for sample m84036_250809_035451_s4.bc2145 at 2025-09-15 20:24:42.440524...
2025-09-15 20:24:46.112 wdl.w:ptcp.w:call-paraphase-48.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for smn1 for sample m84036_250809_035451_s4.bc2145 at 2025-09-15 20:24:42.462933...
2025-09-15 20:24:46.112 wdl.w:ptcp.w:call-paraphase-48.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for hba for sample m84036_250809_035451_s4.bc2145 at 2025-09-15 20:24:42.495553...
2025-09-15 20:24:46.112 wdl.w:ptcp.w:call-paraphase-48.t:call-run_paraphase.stderr VERBOSE WARNING:root:This region does not appear to have coverage. Will not attempt to phase haplotypes.
2025-09-15 20:24:46.112 wdl.w:ptcp.w:call-paraphase-48.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for cyp21 for sample m84036_250809_035451_s4.bc2145 at 2025-09-15 20:24:42.510112...
2025-09-15 20:24:46.112 wdl.w:ptcp.w:call-paraphase-48.t:call-run_paraphase.stderr VERBOSE WARNING:root:This region does not appear to have coverage. Will not attempt to phase haplotypes.
2025-09-15 20:24:46.112 wdl.w:ptcp.w:call-paraphase-48.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for gba for sample m84036_250809_035451_s4.bc2145 at 2025-09-15 20:24:42.523194...
2025-09-15 20:24:46.112 wdl.w:ptcp.w:call-paraphase-48.t:call-run_paraphase.stderr VERBOSE WARNING:root:This region does not appear to have coverage. Will not attempt to phase haplotypes.
2025-09-15 20:24:46.112 wdl.w:ptcp.w:call-paraphase-48.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for hba for sample m84036_250809_035451_s4.bc2145 at 2025-09-15 20:24:42.576262...
2025-09-15 20:24:46.112 wdl.w:ptcp.w:call-paraphase-48.t:call-run_paraphase.stderr VERBOSE WARNING:root:This region does not appear to have coverage. Will not attempt to phase haplotypes.
2025-09-15 20:24:46.112 wdl.w:ptcp.w:call-paraphase-48.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for smn1 for sample m84036_250809_035451_s4.bc2145 at 2025-09-15 20:24:42.609944...
2025-09-15 20:24:46.113 wdl.w:ptcp.w:call-paraphase-48.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for cyp21 for sample m84036_250809_035451_s4.bc2145 at 2025-09-15 20:24:42.910943...
2025-09-15 20:24:46.113 wdl.w:ptcp.w:call-paraphase-48.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for f8inv22 for sample m84036_250809_035451_s4.bc2145 at 2025-09-15 20:24:42.917448...
2025-09-15 20:24:46.113 wdl.w:ptcp.w:call-paraphase-48.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for f8inv22 for sample m84036_250809_035451_s4.bc2145 at 2025-09-15 20:24:42.917516...
2025-09-15 20:24:46.113 wdl.w:ptcp.w:call-paraphase-48.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for gba for sample m84036_250809_035451_s4.bc2145 at 2025-09-15 20:24:42.936101...
2025-09-15 20:24:46.113 wdl.w:ptcp.w:call-paraphase-48.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for rpgr for sample m84036_250809_035451_s4.bc2145 at 2025-09-15 20:24:42.950559...
2025-09-15 20:24:46.113 wdl.w:ptcp.w:call-paraphase-48.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for rpgr for sample m84036_250809_035451_s4.bc2145 at 2025-09-15 20:24:42.954336...
2025-09-15 20:24:46.113 wdl.w:ptcp.w:call-paraphase-48.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for hba for sample m84036_250809_035451_s4.bc2145 at 2025-09-15 20:24:43.052681...
2025-09-15 20:24:46.113 wdl.w:ptcp.w:call-paraphase-48.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for hbb for sample m84036_250809_035451_s4.bc2145 at 2025-09-15 20:24:43.061480...
2025-09-15 20:24:46.113 wdl.w:ptcp.w:call-paraphase-48.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for hbb for sample m84036_250809_035451_s4.bc2145 at 2025-09-15 20:24:43.061550...
2025-09-15 20:24:46.113 wdl.w:ptcp.w:call-paraphase-48.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning to gene2 region for smn1 for sample m84036_250809_035451_s4.bc2145 at 2025-09-15 20:24:43.094790...
2025-09-15 20:24:46.113 wdl.w:ptcp.w:call-paraphase-48.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for f8inv22 for sample m84036_250809_035451_s4.bc2145 at 2025-09-15 20:24:43.436059...
2025-09-15 20:24:46.113 wdl.w:ptcp.w:call-paraphase-48.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for rpgr for sample m84036_250809_035451_s4.bc2145 at 2025-09-15 20:24:43.512219...
2025-09-15 20:24:46.113 wdl.w:ptcp.w:call-paraphase-48.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for hbb for sample m84036_250809_035451_s4.bc2145 at 2025-09-15 20:24:43.562602...
2025-09-15 20:24:46.113 wdl.w:ptcp.w:call-paraphase-48.t:call-run_paraphase.stderr VERBOSE WARNING:root:This region does not appear to have coverage. Will not attempt to phase haplotypes.
2025-09-15 20:24:46.113 wdl.w:ptcp.w:call-paraphase-48.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for f8inv22 for sample m84036_250809_035451_s4.bc2145 at 2025-09-15 20:24:43.569731...
2025-09-15 20:24:46.113 wdl.w:ptcp.w:call-paraphase-48.t:call-run_paraphase.stderr VERBOSE WARNING:root:This region does not appear to have coverage. Will not attempt to phase haplotypes.
2025-09-15 20:24:46.113 wdl.w:ptcp.w:call-paraphase-48.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for rpgr for sample m84036_250809_035451_s4.bc2145 at 2025-09-15 20:24:43.593354...
2025-09-15 20:24:46.114 wdl.w:ptcp.w:call-paraphase-48.t:call-run_paraphase.stderr VERBOSE WARNING:root:This region does not appear to have coverage. Will not attempt to phase haplotypes.
2025-09-15 20:24:46.114 wdl.w:ptcp.w:call-paraphase-48.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for hbb for sample m84036_250809_035451_s4.bc2145 at 2025-09-15 20:24:43.650969...
2025-09-15 20:24:46.114 wdl.w:ptcp.w:call-paraphase-48.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for f8inv22 for sample m84036_250809_035451_s4.bc2145 at 2025-09-15 20:24:43.962832...
2025-09-15 20:24:46.114 wdl.w:ptcp.w:call-paraphase-48.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for rpgr for sample m84036_250809_035451_s4.bc2145 at 2025-09-15 20:24:44.039619...
2025-09-15 20:24:46.114 wdl.w:ptcp.w:call-paraphase-48.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for smn1 for sample m84036_250809_035451_s4.bc2145 at 2025-09-15 20:24:44.054534...
2025-09-15 20:24:46.114 wdl.w:ptcp.w:call-paraphase-48.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for hbb for sample m84036_250809_035451_s4.bc2145 at 2025-09-15 20:24:44.092704...
2025-09-15 20:24:46.114 wdl.w:ptcp.w:call-paraphase-48.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for f8inv1 for sample m84036_250809_035451_s4.bc2145 at 2025-09-15 20:24:44.128802...
2025-09-15 20:24:46.114 wdl.w:ptcp.w:call-paraphase-48.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for f8inv1 for sample m84036_250809_035451_s4.bc2145 at 2025-09-15 20:24:44.128908...
2025-09-15 20:24:46.114 wdl.w:ptcp.w:call-paraphase-48.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for f8inv1 for sample m84036_250809_035451_s4.bc2145 at 2025-09-15 20:24:44.513106...
2025-09-15 20:24:46.114 wdl.w:ptcp.w:call-paraphase-48.t:call-run_paraphase.stderr VERBOSE WARNING:root:This region does not appear to have coverage. Will not attempt to phase haplotypes.
2025-09-15 20:24:46.114 wdl.w:ptcp.w:call-paraphase-48.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for f8inv1 for sample m84036_250809_035451_s4.bc2145 at 2025-09-15 20:24:44.560433...
2025-09-15 20:24:46.114 wdl.w:ptcp.w:call-paraphase-48.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for f8inv1 for sample m84036_250809_035451_s4.bc2145 at 2025-09-15 20:24:44.820768...
2025-09-15 20:24:46.114 wdl.w:ptcp.w:call-paraphase-48.t:call-run_paraphase.stderr VERBOSE INFO:root:Merging all bams for sample m84036_250809_035451_s4.bc2145 at 2025-09-15 20:24:44.839313...
2025-09-15 20:24:46.114 wdl.w:ptcp.w:call-paraphase-48.t:call-run_paraphase.stderr VERBOSE INFO:root:Writing to json for sample m84036_250809_035451_s4.bc2145 at 2025-09-15 20:24:45.324907...
2025-09-15 20:24:46.114 wdl.w:ptcp.w:call-paraphase-48.t:call-run_paraphase.stderr VERBOSE INFO:root:Completed Paraphase analysis at 2025-09-15 20:24:45.700443...
2025-09-15 20:24:46.166 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:46 [ERROR] - No reads found for TRID=OPDM_ABCD3
2025-09-15 20:24:46.166 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:46 [ERROR] - No reads found for TRID=NIID_NOTCH2NLC
2025-09-15 20:24:46.166 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:46 [ERROR] - No reads found for TRID=SCA37_DAB1
2025-09-15 20:24:46.177 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_plot_meth_allele.slurm_singularity INFO srun: job 51797779 queued and waiting for resources
2025-09-15 20:24:46.177 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_plot_meth_allele.slurm_singularity INFO srun: job 51797779 has been allocated resources
2025-09-15 20:24:46.177 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_plot_meth_allele.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:46.242 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO srun: job 51797780 queued and waiting for resources
2025-09-15 20:24:46.242 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO srun: job 51797780 has been allocated resources
2025-09-15 20:24:46.242 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:46.259 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:46 [ERROR] - No reads found for TRID=OPDM_ABCD3
2025-09-15 20:24:46.259 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:46 [ERROR] - No reads found for TRID=NIID_NOTCH2NLC
2025-09-15 20:24:46.259 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:46 [ERROR] - No reads found for TRID=SCA37_DAB1
2025-09-15 20:24:46.267 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_plot_motifs_allele.slurm_singularity INFO srun: job 51797781 queued and waiting for resources
2025-09-15 20:24:46.267 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_plot_motifs_allele.slurm_singularity INFO srun: job 51797781 has been allocated resources
2025-09-15 20:24:46.267 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_plot_motifs_allele.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:46.348 wdl.w:ptcp.w:call-trgt-44.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:45 [ERROR] - No reads found for TRID=PRTS_ARX
2025-09-15 20:24:46.349 wdl.w:ptcp.w:call-trgt-44.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:45 [ERROR] - No reads found for TRID=EIEE1_ARX
2025-09-15 20:24:46.372 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:46 [ERROR] - No reads found for TRID=OPDM_ABCD3
2025-09-15 20:24:46.373 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:46 [ERROR] - No reads found for TRID=NIID_NOTCH2NLC
2025-09-15 20:24:46.373 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:46 [ERROR] - No reads found for TRID=SCA37_DAB1
2025-09-15 20:24:46.373 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:46 [ERROR] - No reads found for TRID=SCA27B_FGF14
2025-09-15 20:24:46.373 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:46 [ERROR] - No reads found for TRID=SCA3_ATXN3
2025-09-15 20:24:46.373 wdl.w:ptcp.w:call-sawfish-61.t:call-run_sawfish.stderr VERBOSE [M::bam2fq_mainloop] discarded 0 singletons
2025-09-15 20:24:46.373 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:46 [ERROR] - No reads found for TRID=SCA4_ZFHX3
2025-09-15 20:24:46.373 wdl.w:ptcp.w:call-sawfish-61.t:call-run_sawfish.stderr VERBOSE [M::bam2fq_mainloop] processed 0 reads
2025-09-15 20:24:46.382 wdl.w:ptcp.w:call-sawfish-61.t:call-run_sawfish.slurm_singularity INFO srun: job 51797784 queued and waiting for resources
2025-09-15 20:24:46.382 wdl.w:ptcp.w:call-sawfish-61.t:call-run_sawfish.slurm_singularity INFO srun: job 51797784 has been allocated resources
2025-09-15 20:24:46.382 wdl.w:ptcp.w:call-sawfish-61.t:call-run_sawfish.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:46.382 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO srun: job 51797783 queued and waiting for resources
2025-09-15 20:24:46.382 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO srun: job 51797783 has been allocated resources
2025-09-15 20:24:46.382 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:46.383 wdl.w:ptcp.w:call-trgt-61.t:call-get_reads_overlapping_repeats.slurm_singularity INFO srun: job 51797782 queued and waiting for resources
2025-09-15 20:24:46.383 wdl.w:ptcp.w:call-trgt-61.t:call-get_reads_overlapping_repeats.slurm_singularity INFO srun: job 51797782 has been allocated resources
2025-09-15 20:24:46.383 wdl.w:ptcp.w:call-trgt-61.t:call-get_reads_overlapping_repeats.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:46.477 wdl.w:ptcp.w:call-sawfish-46.t:call-run_sawfish.stderr VERBOSE [M::mm_idx_gen::35.837*1.36] collected minimizers
2025-09-15 20:24:46.503 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_meth_allele INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2147.meth_allele.trgt_plots.zip"
2025-09-15 20:24:46.531 wdl.w:ptcp.w:call-paraphase-48.t:call-run_paraphase INFO output :: name: "paraphase_bam", value: "m84036_250809_035451_s4.bc2145_paraphase/m84036_250809_035451_s4.bc2145.paraphase.bam"
2025-09-15 20:24:46.546 wdl.w:ptcp.w:call-paraphase-48.t:call-run_paraphase INFO output :: name: "paraphase_bam_bai", value: "m84036_250809_035451_s4.bc2145_paraphase/m84036_250809_035451_s4.bc2145.paraphase.bam.bai"
2025-09-15 20:24:46.548 wdl.w:ptcp.w:call-paraphase-48.t:call-run_paraphase INFO output :: name: "paraphase_json", value: "m84036_250809_035451_s4.bc2145_paraphase/m84036_250809_035451_s4.bc2145.paraphase.json"
2025-09-15 20:24:46.549 wdl.w:ptcp.w:call-paraphase-48.t:call-run_paraphase INFO output :: name: "paraphase_vcfs", value: []
2025-09-15 20:24:46.549 wdl.w:ptcp.w:call-paraphase-48.t:call-run_paraphase INFO output :: name: "havanno_json", value: "m84036_250809_035451_s4.bc2145.havanno.json"
2025-09-15 20:24:46.556 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_meth_waterfall INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2147.meth_waterfall.trgt_plots.zip"
2025-09-15 20:24:46.590 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_meth_allele NOTICE done
2025-09-15 20:24:46.594 wdl.w:ptcp.w:call-trgt-50 NOTICE finish :: job: "call-trgt_plot_meth_allele"
2025-09-15 20:24:46.595 wdl.w:ptcp.w:call-trgt-50 INFO output :: job: "call-trgt_plot_meth_allele", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-50/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2147.meth_allele.trgt_plots.zip"}
2025-09-15 20:24:46.595 wdl.w:ptcp.w:call-trgt-50 INFO visit :: node: "output-images_meth_allele", values: {"images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-50/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2147.meth_allele.trgt_plots.zip"}
2025-09-15 20:24:46.603 wdl.w:ptcp.w:call-trgt-67.t:call-get_reads_overlapping_repeats NOTICE task setup :: name: "get_reads_overlapping_repeats", source: "./trgt.wdl", line: 182, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-67/call-get_reads_overlapping_repeats", thread: 140607649453632
2025-09-15 20:24:46.629 wdl.w:ptcp.w:call-trgt-67.t:call-get_reads_overlapping_repeats INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:46.630 wdl.w:ptcp.w:call-trgt-67.t:call-get_reads_overlapping_repeats INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:46.630 wdl.w:ptcp.w:call-trgt-67.t:call-get_reads_overlapping_repeats INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2164.mapped.bam.bai"
2025-09-15 20:24:46.630 wdl.w:ptcp.w:call-trgt-67.t:call-get_reads_overlapping_repeats INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2164.mapped.bam"
2025-09-15 20:24:46.630 wdl.w:ptcp.w:call-trgt-67.t:call-get_reads_overlapping_repeats INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2164"
2025-09-15 20:24:46.630 wdl.w:ptcp.w:call-trgt-67.t:call-get_reads_overlapping_repeats INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:46.631 wdl.w:ptcp.w:call-trgt-67.t:call-get_reads_overlapping_repeats INFO eval :: name: "expand_size", value: 3000
2025-09-15 20:24:46.631 wdl.w:ptcp.w:call-trgt-67.t:call-get_reads_overlapping_repeats INFO eval :: name: "threads", value: 1
2025-09-15 20:24:46.631 wdl.w:ptcp.w:call-trgt-67.t:call-get_reads_overlapping_repeats INFO eval :: name: "expanded_bed_name", value: "m84036_250809_035451_s4.bc2164.expanded.bed"
2025-09-15 20:24:46.631 wdl.w:ptcp.w:call-trgt-67.t:call-get_reads_overlapping_repeats INFO eval :: name: "disk_size", value: 11
2025-09-15 20:24:46.631 wdl.w:ptcp.w:call-trgt-67.t:call-get_reads_overlapping_repeats INFO eval :: name: "output_name", value: "m84036_250809_035451_s4.bc2164.repeats.bam"
2025-09-15 20:24:46.631 wdl.w:ptcp.w:call-trgt-67.t:call-get_reads_overlapping_repeats INFO eval :: name: "index_name", value: "m84036_250809_035451_s4.bc2164.repeats.bam.bai"
2025-09-15 20:24:46.631 wdl.w:ptcp.w:call-trgt-67.t:call-get_reads_overlapping_repeats INFO eval :: name: "output_name_with_index", value: "m84036_250809_035451_s4.bc2164.repeats.bam##idx##m84036_250809_035451_s4.bc2164.repeats.bam.bai"
2025-09-15 20:24:46.632 wdl.w:ptcp.w:call-trgt-67.t:call-get_reads_overlapping_repeats INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:46.632 wdl.w:ptcp.w:call-trgt-67.t:call-get_reads_overlapping_repeats WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:46.633 wdl.w:ptcp.w:call-trgt-67.t:call-get_reads_overlapping_repeats INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:46.633 wdl.w:ptcp.w:call-trgt-67.t:call-get_reads_overlapping_repeats INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:46.639 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_motifs_allele INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2144.motifs_allele.trgt_plots.zip"
2025-09-15 20:24:46.649 wdl.w:ptcp.w:call-trgt-50.t:call-trgt_plot_meth_waterfall NOTICE done
2025-09-15 20:24:46.655 wdl.w:ptcp.w:call-trgt-50 NOTICE finish :: job: "call-trgt_plot_meth_waterfall"
2025-09-15 20:24:46.655 wdl.w:ptcp.w:call-trgt-50 INFO output :: job: "call-trgt_plot_meth_waterfall", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-50/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2147.meth_waterfall.trgt_plots.zip"}
2025-09-15 20:24:46.655 wdl.w:ptcp.w:call-trgt-50 INFO visit :: node: "output-images_meth_waterfall", values: {"images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-50/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2147.meth_waterfall.trgt_plots.zip"}
2025-09-15 20:24:46.655 wdl.w:ptcp.w:call-trgt-50 INFO visit :: node: "outputs", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-50/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2147.motifs_waterfall.trgt_plots.zip", "images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-50/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2147.meth_allele.trgt_plots.zip", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-50/call-trgt_genotype/out/m84036_250809_035451_s4.bc2147.trgt.sorted.spanning.bam.bai", "images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-50/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2147.motifs_allele.trgt_plots.zip", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-50/call-trgt_genotype/out/m84036_250809_035451_s4.bc2147.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-50/call-trgt_genotype/out/m84036_250809_035451_s4.bc2147.trgt.vcf", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-50/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2147.repeats.bam", "images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-50/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2147.meth_waterfall.trgt_plots.zip", "reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-50/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2147.repeats.bam.bai"}
2025-09-15 20:24:46.663 wdl.w:ptcp.w:call-trgt-67.t:call-trgt_genotype NOTICE task setup :: name: "trgt_genotype", source: "./trgt.wdl", line: 272, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-67/call-trgt_genotype", thread: 140609302029888
2025-09-15 20:24:46.682 wdl.w:ptcp.w:call-paraphase-48.t:call-run_paraphase NOTICE done
2025-09-15 20:24:46.689 wdl.w:ptcp.w:call-trgt-67.t:call-trgt_genotype INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:46.689 wdl.w:ptcp.w:call-trgt-67.t:call-trgt_genotype INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:46.689 wdl.w:ptcp.w:call-trgt-67.t:call-trgt_genotype INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:46.689 wdl.w:ptcp.w:call-trgt-67.t:call-trgt_genotype INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:46.689 wdl.w:ptcp.w:call-trgt-67.t:call-trgt_genotype INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2164.mapped.bam.bai"
2025-09-15 20:24:46.689 wdl.w:ptcp.w:call-trgt-67.t:call-trgt_genotype INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2164.mapped.bam"
2025-09-15 20:24:46.689 wdl.w:ptcp.w:call-trgt-67.t:call-trgt_genotype INFO input :: name: "sex", value: "F"
2025-09-15 20:24:46.689 wdl.w:ptcp.w:call-trgt-67.t:call-trgt_genotype INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2164"
2025-09-15 20:24:46.689 wdl.w:ptcp.w:call-trgt-67.t:call-trgt_genotype INFO eval :: name: "mem_gb", value: 16
2025-09-15 20:24:46.690 wdl.w:ptcp.w:call-trgt-67.t:call-trgt_genotype INFO eval :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2164.trgt"
2025-09-15 20:24:46.690 wdl.w:ptcp.w:call-trgt-67.t:call-trgt_genotype INFO eval :: name: "threads", value: 8
2025-09-15 20:24:46.690 wdl.w:ptcp.w:call-trgt-67.t:call-trgt_genotype INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:46.690 wdl.w:ptcp.w:call-paraphase-48 NOTICE finish :: job: "call-run_paraphase"
2025-09-15 20:24:46.691 wdl.w:ptcp.w:call-paraphase-48 INFO output :: job: "call-run_paraphase", values: {"havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-48/call-run_paraphase/out/m84036_250809_035451_s4.bc2145.havanno.json", "paraphase_vcfs": [], "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-48/call-run_paraphase/out/m84036_250809_035451_s4.bc2145_paraphase/m84036_250809_035451_s4.bc2145.paraphase.json", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-48/call-run_paraphase/out/m84036_250809_035451_s4.bc2145_paraphase/m84036_250809_035451_s4.bc2145.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-48/call-run_paraphase/out/m84036_250809_035451_s4.bc2145_paraphase/m84036_250809_035451_s4.bc2145.paraphase.bam"}
2025-09-15 20:24:46.691 wdl.w:ptcp.w:call-trgt-67.t:call-trgt_genotype INFO eval :: name: "karyotype", value: "XX"
2025-09-15 20:24:46.692 wdl.w:ptcp.w:call-paraphase-48 NOTICE ready :: job: "call-call_f8", callee: "call_f8"
2025-09-15 20:24:46.692 wdl.w:ptcp.w:call-paraphase-48 INFO input :: job: "call-call_f8", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "out_prefix": "m84036_250809_035451_s4.bc2145", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-48/call-run_paraphase/out/m84036_250809_035451_s4.bc2145_paraphase/m84036_250809_035451_s4.bc2145.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-48/call-run_paraphase/out/m84036_250809_035451_s4.bc2145_paraphase/m84036_250809_035451_s4.bc2145.paraphase.bam", "sex": "F"}
2025-09-15 20:24:46.692 wdl.w:ptcp.w:call-trgt-67.t:call-trgt_genotype INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 8, memory_reservation: 16000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:46.693 wdl.w:ptcp.w:call-trgt-67.t:call-trgt_genotype WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:46.693 wdl.w:ptcp.w:call-trgt-67.t:call-trgt_genotype INFO provisioned :: seconds_waited: 0, cpu: 8, mem_bytes: 16000000000
2025-09-15 20:24:46.693 wdl.w:ptcp.w:call-trgt-67.t:call-trgt_genotype INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:46.694 wdl.w:ptcp.w:call-paraphase-48 INFO visit :: node: "output-havanno_json", values: {"havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-48/call-run_paraphase/out/m84036_250809_035451_s4.bc2145.havanno.json"}
2025-09-15 20:24:46.694 wdl.w:ptcp.w:call-paraphase-48 INFO visit :: node: "output-paraphase_bam", values: {"paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-48/call-run_paraphase/out/m84036_250809_035451_s4.bc2145_paraphase/m84036_250809_035451_s4.bc2145.paraphase.bam"}
2025-09-15 20:24:46.694 wdl.w:ptcp.w:call-paraphase-48 INFO visit :: node: "output-paraphase_bam_bai", values: {"paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-48/call-run_paraphase/out/m84036_250809_035451_s4.bc2145_paraphase/m84036_250809_035451_s4.bc2145.paraphase.bam.bai"}
2025-09-15 20:24:46.694 wdl.w:ptcp.w:call-paraphase-48 INFO visit :: node: "output-paraphase_json", values: {"paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-48/call-run_paraphase/out/m84036_250809_035451_s4.bc2145_paraphase/m84036_250809_035451_s4.bc2145.paraphase.json"}
2025-09-15 20:24:46.694 wdl.w:ptcp.w:call-paraphase-48 INFO visit :: node: "output-paraphase_vcfs", values: {"paraphase_vcfs": []}
2025-09-15 20:24:46.701 wdl.w:ptcp.w:call-trgt-39.t:call-trgt_plot_meth_allele NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-39/call-trgt_plot_meth_allele", thread: 140607691417152
2025-09-15 20:24:46.704 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_meth_waterfall INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2144.meth_waterfall.trgt_plots.zip"
2025-09-15 20:24:46.709 wdl.w:ptcp.w:call-trgt-67.t:call-get_reads_overlapping_repeats INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 9, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-67/call-get_reads_overlapping_repeats/_singularity_tmpdir_y1fzopm2"
2025-09-15 20:24:46.709 wdl.w:ptcp.w:call-trgt-67.t:call-get_reads_overlapping_repeats INFO Slurm invocation: srun --job-name call-get_reads_overlapping_repeats --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-67/call-get_reads_overlapping_repeats/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-67/call-get_reads_overlapping_repeats/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-67/call-get_reads_overlapping_repeats/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-67/call-get_reads_overlapping_repeats/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-67/out/m84036_250809_035451_s4.bc2164.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2164.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-67/out/m84036_250809_035451_s4.bc2164.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2164.mapped.bam:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-67/call-get_reads_overlapping_repeats/_singularity_tmpdir_y1fzopm2/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-67/call-get_reads_overlapping_repeats/_singularity_tmpdir_y1fzopm2/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:46.725 wdl.w:ptcp.w:call-trgt-39.t:call-trgt_plot_meth_allele INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:46.727 wdl.w:ptcp.w:call-trgt-39.t:call-trgt_plot_meth_allele INFO input :: name: "waterfall", value: false
2025-09-15 20:24:46.727 wdl.w:ptcp.w:call-trgt-39.t:call-trgt_plot_meth_allele INFO input :: name: "methylation", value: true
2025-09-15 20:24:46.727 wdl.w:ptcp.w:call-trgt-39.t:call-trgt_plot_meth_allele INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:46.727 wdl.w:ptcp.w:call-trgt-39.t:call-trgt_plot_meth_allele INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:46.727 wdl.w:ptcp.w:call-trgt-39.t:call-trgt_plot_meth_allele INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:46.727 wdl.w:ptcp.w:call-trgt-39.t:call-trgt_plot_meth_allele INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2136.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:46.728 wdl.w:ptcp.w:call-trgt-39.t:call-trgt_plot_meth_allele INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2136.trgt.sorted.spanning.bam"
2025-09-15 20:24:46.728 wdl.w:ptcp.w:call-trgt-39.t:call-trgt_plot_meth_allele INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2136.trgt.vcf"
2025-09-15 20:24:46.728 wdl.w:ptcp.w:call-trgt-39.t:call-trgt_plot_meth_allele INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2136"
2025-09-15 20:24:46.728 wdl.w:ptcp.w:call-trgt-39.t:call-trgt_plot_meth_allele INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:46.729 wdl.w:ptcp.w:call-trgt-39.t:call-trgt_plot_meth_allele INFO eval :: name: "plot_type", value: "allele"
2025-09-15 20:24:46.729 wdl.w:ptcp.w:call-trgt-39.t:call-trgt_plot_meth_allele INFO eval :: name: "show", value: "meth"
2025-09-15 20:24:46.729 wdl.w:ptcp.w:call-trgt-39.t:call-trgt_plot_meth_allele INFO eval :: name: "threads", value: 1
2025-09-15 20:24:46.729 wdl.w:ptcp.w:call-trgt-39.t:call-trgt_plot_meth_allele INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:46.729 wdl.w:ptcp.w:call-trgt-39.t:call-trgt_plot_meth_allele INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2136.meth_allele"
2025-09-15 20:24:46.730 wdl.w:ptcp.w:call-trgt-39.t:call-trgt_plot_meth_allele INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:46.730 wdl.w:ptcp.w:call-trgt-39.t:call-trgt_plot_meth_allele WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:46.730 wdl.w:ptcp.w:call-trgt-39.t:call-trgt_plot_meth_allele INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:46.730 wdl.w:ptcp.w:call-trgt-39.t:call-trgt_plot_meth_allele INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:46.756 wdl.w:ptcp.w:call-trgt-44.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:45 [ERROR] - No reads found for TRID=PRTS_ARX
2025-09-15 20:24:46.757 wdl.w:ptcp.w:call-trgt-44.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:45 [ERROR] - No reads found for TRID=EIEE1_ARX
2025-09-15 20:24:46.762 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_motifs_allele NOTICE done
2025-09-15 20:24:46.770 wdl.w:ptcp.w:call-trgt-47 NOTICE finish :: job: "call-trgt_plot_motifs_allele"
2025-09-15 20:24:46.770 wdl.w:ptcp.w:call-trgt-47 INFO output :: job: "call-trgt_plot_motifs_allele", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-47/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2144.motifs_allele.trgt_plots.zip"}
2025-09-15 20:24:46.770 wdl.w:ptcp.w:call-trgt-47 INFO visit :: node: "output-images_motifs_allele", values: {"images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-47/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2144.motifs_allele.trgt_plots.zip"}
2025-09-15 20:24:46.771 wdl.w:ptcp.w:call-trgt-67.t:call-get_reads_overlapping_repeats NOTICE slurm_singularity run :: pid: 1203095, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-67/call-get_reads_overlapping_repeats/slurm_singularity.log.txt"
2025-09-15 20:24:46.774 wdl.w:ptcp.w:call-sawfish-00.t:call-run_sawfish INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2097_sawfish/m84036_250809_035451_s4.bc2097.sv.vcf.gz"
2025-09-15 20:24:46.774 wdl.w:ptcp.w:call-trgt-61.t:call-trgt_genotype.slurm_singularity INFO srun: job 51797785 queued and waiting for resources
2025-09-15 20:24:46.775 wdl.w:ptcp.w:call-trgt-61.t:call-trgt_genotype.slurm_singularity INFO srun: job 51797785 has been allocated resources
2025-09-15 20:24:46.775 wdl.w:ptcp.w:call-trgt-61.t:call-trgt_genotype.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:46.775 wdl.w:ptcp.w:call-paraphase-67.t:call-run_paraphase.slurm_singularity INFO srun: job 51797786 queued and waiting for resources
2025-09-15 20:24:46.775 wdl.w:ptcp.w:call-paraphase-67.t:call-run_paraphase.slurm_singularity INFO srun: job 51797786 has been allocated resources
2025-09-15 20:24:46.776 wdl.w:ptcp.w:call-paraphase-67.t:call-run_paraphase.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:46.783 wdl.w:ptcp.w:call-paraphase-31.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for rpgr for sample m84036_250809_035451_s4.bc2128 at 2025-09-15 20:24:42.281610...
2025-09-15 20:24:46.783 wdl.w:ptcp.w:call-paraphase-31.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for rpgr for sample m84036_250809_035451_s4.bc2128 at 2025-09-15 20:24:42.282413...
2025-09-15 20:24:46.784 wdl.w:ptcp.w:call-sawfish-00.t:call-run_sawfish INFO output :: name: "vcf_tbi", value: "m84036_250809_035451_s4.bc2097_sawfish/m84036_250809_035451_s4.bc2097.sv.vcf.gz.tbi"
2025-09-15 20:24:46.785 wdl.w:ptcp.w:call-trgt-39.t:call-trgt_plot_meth_waterfall NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-39/call-trgt_plot_meth_waterfall", thread: 140613068518976
2025-09-15 20:24:46.786 wdl.w:ptcp.w:call-sawfish-00.t:call-run_sawfish INFO output :: name: "minimap2_bam", value: "m84036_250809_035451_s4.bc2097.minimap2.bam"
2025-09-15 20:24:46.789 wdl.w:ptcp.w:call-sawfish-00.t:call-run_sawfish INFO output :: name: "minimap2_bam_bai", value: "m84036_250809_035451_s4.bc2097.minimap2.bam.bai"
2025-09-15 20:24:46.790 wdl.w:ptcp.w:call-trgt-50 NOTICE done
2025-09-15 20:24:46.796 wdl.w:ptcp.w:call-trgt-67.t:call-trgt_genotype INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 11, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-67/call-trgt_genotype/_singularity_tmpdir_yit8xnun"
2025-09-15 20:24:46.797 wdl.w:ptcp.w:call-trgt-67.t:call-trgt_genotype INFO Slurm invocation: srun --job-name call-trgt_genotype --partition compute,compute9 --cpus-per-task 8 --mem 15259M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-67/call-trgt_genotype/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-67/call-trgt_genotype/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-67/call-trgt_genotype/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-67/call-trgt_genotype/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-67/out/m84036_250809_035451_s4.bc2164.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2164.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-67/out/m84036_250809_035451_s4.bc2164.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2164.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-67/call-trgt_genotype/_singularity_tmpdir_yit8xnun/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-67/call-trgt_genotype/_singularity_tmpdir_yit8xnun/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:46.799 wdl.w:ptcp NOTICE finish :: job: "call-trgt-50"
2025-09-15 20:24:46.800 wdl.w:ptcp INFO output :: job: "call-trgt-50", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-50/out/m84036_250809_035451_s4.bc2147.motifs_waterfall.trgt_plots.zip", "images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-50/out/m84036_250809_035451_s4.bc2147.meth_allele.trgt_plots.zip", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-50/out/m84036_250809_035451_s4.bc2147.trgt.sorted.spanning.bam.bai", "images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-50/out/m84036_250809_035451_s4.bc2147.motifs_allele.trgt_plots.zip", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-50/out/m84036_250809_035451_s4.bc2147.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-50/out/m84036_250809_035451_s4.bc2147.trgt.vcf", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-50/out/m84036_250809_035451_s4.bc2147.repeats.bam", "images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-50/out/m84036_250809_035451_s4.bc2147.meth_waterfall.trgt_plots.zip", "reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-50/out/m84036_250809_035451_s4.bc2147.repeats.bam.bai"}
2025-09-15 20:24:46.812 wdl.w:ptcp.w:call-paraphase-70 NOTICE workflow start :: name: "paraphase", source: "./paraphase.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-70"
2025-09-15 20:24:46.814 wdl.w:ptcp.w:call-trgt-52.t:call-trgt_plot_motifs_allele INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2149.motifs_allele.trgt_plots.zip"
2025-09-15 20:24:46.816 wdl.w:ptcp.w:call-trgt-39.t:call-trgt_plot_meth_waterfall INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:46.816 wdl.w:ptcp.w:call-trgt-39.t:call-trgt_plot_meth_waterfall INFO input :: name: "waterfall", value: true
2025-09-15 20:24:46.816 wdl.w:ptcp.w:call-trgt-39.t:call-trgt_plot_meth_waterfall INFO input :: name: "methylation", value: true
2025-09-15 20:24:46.816 wdl.w:ptcp.w:call-trgt-39.t:call-trgt_plot_meth_waterfall INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:46.816 wdl.w:ptcp.w:call-trgt-39.t:call-trgt_plot_meth_waterfall INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:46.816 wdl.w:ptcp.w:call-trgt-39.t:call-trgt_plot_meth_waterfall INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:46.816 wdl.w:ptcp.w:call-trgt-39.t:call-trgt_plot_meth_waterfall INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2136.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:46.816 wdl.w:ptcp.w:call-trgt-39.t:call-trgt_plot_meth_waterfall INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2136.trgt.sorted.spanning.bam"
2025-09-15 20:24:46.817 wdl.w:ptcp.w:call-trgt-39.t:call-trgt_plot_meth_waterfall INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2136.trgt.vcf"
2025-09-15 20:24:46.817 wdl.w:ptcp.w:call-trgt-39.t:call-trgt_plot_meth_waterfall INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2136"
2025-09-15 20:24:46.817 wdl.w:ptcp.w:call-trgt-39.t:call-trgt_plot_meth_waterfall INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:46.817 wdl.w:ptcp.w:call-trgt-39.t:call-trgt_plot_meth_waterfall INFO eval :: name: "plot_type", value: "waterfall"
2025-09-15 20:24:46.820 wdl.w:ptcp.w:call-trgt-39.t:call-trgt_plot_meth_waterfall INFO eval :: name: "show", value: "meth"
2025-09-15 20:24:46.820 wdl.w:ptcp.w:call-trgt-39.t:call-trgt_plot_meth_waterfall INFO eval :: name: "threads", value: 1
2025-09-15 20:24:46.820 wdl.w:ptcp.w:call-trgt-39.t:call-trgt_plot_meth_waterfall INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:46.820 wdl.w:ptcp.w:call-trgt-39.t:call-trgt_plot_meth_waterfall INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2136.meth_waterfall"
2025-09-15 20:24:46.821 wdl.w:ptcp.w:call-trgt-39.t:call-trgt_plot_meth_waterfall INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:46.821 wdl.w:ptcp.w:call-trgt-39.t:call-trgt_plot_meth_waterfall WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:46.822 wdl.w:ptcp.w:call-trgt-39.t:call-trgt_plot_meth_waterfall INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:46.822 wdl.w:ptcp.w:call-trgt-39.t:call-trgt_plot_meth_waterfall INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:46.827 wdl.w:ptcp.w:call-trgt-44.t:call-trgt_plot_motifs_allele INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2141.motifs_allele.trgt_plots.zip"
2025-09-15 20:24:46.833 wdl.w:ptcp.w:call-paraphase-70 INFO visit :: node: "decl-annotation_vcf", values: {"annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf"}
2025-09-15 20:24:46.833 wdl.w:ptcp.w:call-paraphase-70 INFO visit :: node: "decl-config_file", values: {"config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml"}
2025-09-15 20:24:46.834 wdl.w:ptcp.w:call-paraphase-70 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:24:46.834 wdl.w:ptcp.w:call-paraphase-70 INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:24:46.834 wdl.w:ptcp.w:call-paraphase-70 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-70/out/m84036_250809_035451_s4.bc2167.mapped.bam"}
2025-09-15 20:24:46.834 wdl.w:ptcp.w:call-paraphase-70 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-70/out/m84036_250809_035451_s4.bc2167.mapped.bam.bai"}
2025-09-15 20:24:46.834 wdl.w:ptcp.w:call-paraphase-70 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:24:46.834 wdl.w:ptcp.w:call-paraphase-70 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:24:46.834 wdl.w:ptcp.w:call-paraphase-70 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2167"}
2025-09-15 20:24:46.834 wdl.w:ptcp.w:call-paraphase-70 INFO visit :: node: "decl-sex", values: {"sex": "F"}
2025-09-15 20:24:46.834 wdl.w:ptcp.w:call-paraphase-70 NOTICE ready :: job: "call-run_paraphase", callee: "run_paraphase"
2025-09-15 20:24:46.834 wdl.w:ptcp.w:call-paraphase-70 INFO input :: job: "call-run_paraphase", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf", "genome_version": "38", "config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-70/out/m84036_250809_035451_s4.bc2167.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-70/out/m84036_250809_035451_s4.bc2167.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2167"}
2025-09-15 20:24:46.836 wdl.w:ptcp.w:call-trgt-47.t:call-trgt_plot_meth_waterfall NOTICE done
2025-09-15 20:24:46.850 wdl.w:ptcp.w:call-paraphase-54.t:call-run_paraphase.stderr VERBOSE INFO:root:Processing sample m84036_250809_035451_s4.bc2151 at 2025-09-15 20:24:42.782124...
2025-09-15 20:24:46.852 wdl.w:ptcp.w:call-paraphase-54.t:call-run_paraphase.stderr VERBOSE INFO:root:Checking sample sex at 2025-09-15 20:24:42.783252...
2025-09-15 20:24:46.852 wdl.w:ptcp.w:call-paraphase-54.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for cyp21 for sample m84036_250809_035451_s4.bc2151 at 2025-09-15 20:24:42.829199...
2025-09-15 20:24:46.852 wdl.w:ptcp.w:call-paraphase-54.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for cyp21 for sample m84036_250809_035451_s4.bc2151 at 2025-09-15 20:24:42.829603...
2025-09-15 20:24:46.852 wdl.w:ptcp.w:call-paraphase-54.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for smn1 for sample m84036_250809_035451_s4.bc2151 at 2025-09-15 20:24:42.829375...
2025-09-15 20:24:46.852 wdl.w:ptcp.w:call-paraphase-54.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for gba for sample m84036_250809_035451_s4.bc2151 at 2025-09-15 20:24:42.829415...
2025-09-15 20:24:46.852 wdl.w:ptcp.w:call-paraphase-54.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for smn1 for sample m84036_250809_035451_s4.bc2151 at 2025-09-15 20:24:42.829713...
2025-09-15 20:24:46.852 wdl.w:ptcp.w:call-paraphase-54.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for gba for sample m84036_250809_035451_s4.bc2151 at 2025-09-15 20:24:42.829724...
2025-09-15 20:24:46.852 wdl.w:ptcp.w:call-paraphase-54.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for hba for sample m84036_250809_035451_s4.bc2151 at 2025-09-15 20:24:42.830488...
2025-09-15 20:24:46.852 wdl.w:ptcp.w:call-paraphase-54.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for hba for sample m84036_250809_035451_s4.bc2151 at 2025-09-15 20:24:42.830759...
2025-09-15 20:24:46.856 wdl.w:ptcp.w:call-trgt-39.t:call-trgt_plot_meth_allele INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-39/call-trgt_plot_meth_allele/_singularity_tmpdir_2plr_iqh"
2025-09-15 20:24:46.856 wdl.w:ptcp.w:call-trgt-39.t:call-trgt_plot_meth_allele INFO Slurm invocation: srun --job-name call-trgt_plot_meth_allele --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-39/call-trgt_plot_meth_allele/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-39/call-trgt_plot_meth_allele/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-39/call-trgt_plot_meth_allele/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-39/call-trgt_plot_meth_allele/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-39/call-trgt_genotype/out/m84036_250809_035451_s4.bc2136.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2136.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-39/call-trgt_genotype/out/m84036_250809_035451_s4.bc2136.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2136.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-39/call-trgt_genotype/out/m84036_250809_035451_s4.bc2136.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2136.trgt.vcf:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-39/call-trgt_plot_meth_allele/_singularity_tmpdir_2plr_iqh/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-39/call-trgt_plot_meth_allele/_singularity_tmpdir_2plr_iqh/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:46.858 wdl.w:ptcp.w:call-trgt-47 NOTICE finish :: job: "call-trgt_plot_meth_waterfall"
2025-09-15 20:24:46.859 wdl.w:ptcp.w:call-trgt-47 INFO output :: job: "call-trgt_plot_meth_waterfall", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-47/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2144.meth_waterfall.trgt_plots.zip"}
2025-09-15 20:24:46.859 wdl.w:ptcp.w:call-trgt-47 INFO visit :: node: "output-images_meth_waterfall", values: {"images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-47/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2144.meth_waterfall.trgt_plots.zip"}
2025-09-15 20:24:46.859 wdl.w:ptcp.w:call-trgt-47 INFO visit :: node: "outputs", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-47/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2144.motifs_waterfall.trgt_plots.zip", "images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-47/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2144.meth_allele.trgt_plots.zip", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-47/call-trgt_genotype/out/m84036_250809_035451_s4.bc2144.trgt.sorted.spanning.bam.bai", "images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-47/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2144.motifs_allele.trgt_plots.zip", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-47/call-trgt_genotype/out/m84036_250809_035451_s4.bc2144.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-47/call-trgt_genotype/out/m84036_250809_035451_s4.bc2144.trgt.vcf", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-47/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2144.repeats.bam", "images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-47/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2144.meth_waterfall.trgt_plots.zip", "reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-47/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2144.repeats.bam.bai"}
2025-09-15 20:24:46.873 wdl.w:ptcp.w:call-trgt-39.t:call-trgt_plot_motifs_allele NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-39/call-trgt_plot_motifs_allele", thread: 140608203109952
2025-09-15 20:24:46.881 wdl.w:ptcp.w:call-trgt-67.t:call-trgt_genotype NOTICE slurm_singularity run :: pid: 1203098, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-67/call-trgt_genotype/slurm_singularity.log.txt"
2025-09-15 20:24:46.883 wdl.w:ptcp.w:call-trgt-39.t:call-trgt_plot_meth_allele NOTICE slurm_singularity run :: pid: 1203099, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-39/call-trgt_plot_meth_allele/slurm_singularity.log.txt"
2025-09-15 20:24:46.896 wdl.w:ptcp.w:call-trgt-39.t:call-trgt_plot_motifs_allele INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:46.896 wdl.w:ptcp.w:call-trgt-39.t:call-trgt_plot_motifs_allele INFO input :: name: "waterfall", value: false
2025-09-15 20:24:46.896 wdl.w:ptcp.w:call-trgt-39.t:call-trgt_plot_motifs_allele INFO input :: name: "methylation", value: false
2025-09-15 20:24:46.896 wdl.w:ptcp.w:call-trgt-39.t:call-trgt_plot_motifs_allele INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:46.896 wdl.w:ptcp.w:call-trgt-39.t:call-trgt_plot_motifs_allele INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:46.896 wdl.w:ptcp.w:call-trgt-39.t:call-trgt_plot_motifs_allele INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:46.897 wdl.w:ptcp.w:call-trgt-39.t:call-trgt_plot_motifs_allele INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2136.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:46.897 wdl.w:ptcp.w:call-trgt-39.t:call-trgt_plot_motifs_allele INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2136.trgt.sorted.spanning.bam"
2025-09-15 20:24:46.897 wdl.w:ptcp.w:call-trgt-39.t:call-trgt_plot_motifs_allele INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2136.trgt.vcf"
2025-09-15 20:24:46.897 wdl.w:ptcp.w:call-trgt-39.t:call-trgt_plot_motifs_allele INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2136"
2025-09-15 20:24:46.897 wdl.w:ptcp.w:call-trgt-39.t:call-trgt_plot_motifs_allele INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:46.897 wdl.w:ptcp.w:call-trgt-39.t:call-trgt_plot_motifs_allele INFO eval :: name: "plot_type", value: "allele"
2025-09-15 20:24:46.897 wdl.w:ptcp.w:call-trgt-39.t:call-trgt_plot_motifs_allele INFO eval :: name: "show", value: "motifs"
2025-09-15 20:24:46.897 wdl.w:ptcp.w:call-trgt-39.t:call-trgt_plot_motifs_allele INFO eval :: name: "threads", value: 1
2025-09-15 20:24:46.898 wdl.w:ptcp.w:call-trgt-39.t:call-trgt_plot_motifs_allele INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:46.898 wdl.w:ptcp.w:call-trgt-39.t:call-trgt_plot_motifs_allele INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2136.motifs_allele"
2025-09-15 20:24:46.898 wdl.w:ptcp.w:call-trgt-39.t:call-trgt_plot_motifs_allele INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:46.898 wdl.w:ptcp.w:call-trgt-39.t:call-trgt_plot_motifs_allele WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:46.899 wdl.w:ptcp.w:call-trgt-39.t:call-trgt_plot_motifs_allele INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:46.899 wdl.w:ptcp.w:call-trgt-39.t:call-trgt_plot_motifs_allele INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:46.941 wdl.w:ptcp.w:call-trgt-39.t:call-trgt_plot_meth_waterfall INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-39/call-trgt_plot_meth_waterfall/_singularity_tmpdir_tgxdelfy"
2025-09-15 20:24:46.941 wdl.w:ptcp.w:call-trgt-39.t:call-trgt_plot_meth_waterfall INFO Slurm invocation: srun --job-name call-trgt_plot_meth_waterfall --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-39/call-trgt_plot_meth_waterfall/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-39/call-trgt_plot_meth_waterfall/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-39/call-trgt_plot_meth_waterfall/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-39/call-trgt_plot_meth_waterfall/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-39/call-trgt_genotype/out/m84036_250809_035451_s4.bc2136.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2136.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-39/call-trgt_genotype/out/m84036_250809_035451_s4.bc2136.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2136.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-39/call-trgt_genotype/out/m84036_250809_035451_s4.bc2136.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2136.trgt.vcf:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-39/call-trgt_plot_meth_waterfall/_singularity_tmpdir_tgxdelfy/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-39/call-trgt_plot_meth_waterfall/_singularity_tmpdir_tgxdelfy/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:46.958 wdl.w:ptcp.w:call-trgt-39.t:call-trgt_plot_meth_waterfall NOTICE slurm_singularity run :: pid: 1203102, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-39/call-trgt_plot_meth_waterfall/slurm_singularity.log.txt"
2025-09-15 20:24:46.977 wdl.w:ptcp.w:call-trgt-47 NOTICE done
2025-09-15 20:24:46.982 wdl.w:ptcp NOTICE finish :: job: "call-trgt-47"
2025-09-15 20:24:46.982 wdl.w:ptcp INFO output :: job: "call-trgt-47", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-47/out/m84036_250809_035451_s4.bc2144.motifs_waterfall.trgt_plots.zip", "images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-47/out/m84036_250809_035451_s4.bc2144.meth_allele.trgt_plots.zip", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-47/out/m84036_250809_035451_s4.bc2144.trgt.sorted.spanning.bam.bai", "images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-47/out/m84036_250809_035451_s4.bc2144.motifs_allele.trgt_plots.zip", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-47/out/m84036_250809_035451_s4.bc2144.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-47/out/m84036_250809_035451_s4.bc2144.trgt.vcf", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-47/out/m84036_250809_035451_s4.bc2144.repeats.bam", "images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-47/out/m84036_250809_035451_s4.bc2144.meth_waterfall.trgt_plots.zip", "reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-47/out/m84036_250809_035451_s4.bc2144.repeats.bam.bai"}
2025-09-15 20:24:46.987 wdl.w:ptcp.w:call-trgt-52.t:call-trgt_plot_motifs_allele NOTICE done
2025-09-15 20:24:46.994 wdl.w:ptcp.w:call-trgt-39.t:call-trgt_plot_motifs_allele INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-39/call-trgt_plot_motifs_allele/_singularity_tmpdir_6hm_dy88"
2025-09-15 20:24:46.995 wdl.w:ptcp.w:call-trgt-39.t:call-trgt_plot_motifs_allele INFO Slurm invocation: srun --job-name call-trgt_plot_motifs_allele --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-39/call-trgt_plot_motifs_allele/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-39/call-trgt_plot_motifs_allele/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-39/call-trgt_plot_motifs_allele/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-39/call-trgt_plot_motifs_allele/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-39/call-trgt_genotype/out/m84036_250809_035451_s4.bc2136.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2136.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-39/call-trgt_genotype/out/m84036_250809_035451_s4.bc2136.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2136.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-39/call-trgt_genotype/out/m84036_250809_035451_s4.bc2136.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2136.trgt.vcf:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-39/call-trgt_plot_motifs_allele/_singularity_tmpdir_6hm_dy88/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-39/call-trgt_plot_motifs_allele/_singularity_tmpdir_6hm_dy88/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:46.995 wdl.w:ptcp.w:call-sawfish-70 NOTICE workflow start :: name: "sawfish", source: "./sawfish.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-70"
2025-09-15 20:24:47.000 wdl.w:ptcp.w:call-trgt-44.t:call-trgt_plot_motifs_allele NOTICE done
2025-09-15 20:24:47.006 wdl.w:ptcp.w:call-sawfish-67.t:call-run_sawfish.slurm_singularity INFO srun: job 51797787 queued and waiting for resources
2025-09-15 20:24:47.006 wdl.w:ptcp.w:call-sawfish-67.t:call-run_sawfish.slurm_singularity INFO srun: job 51797787 has been allocated resources
2025-09-15 20:24:47.006 wdl.w:ptcp.w:call-sawfish-67.t:call-run_sawfish.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:47.007 wdl.w:ptcp.w:call-sawfish-67.t:call-run_sawfish.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:24:47.010 wdl.w:ptcp.w:call-sawfish-00.t:call-run_sawfish NOTICE done
2025-09-15 20:24:47.014 wdl.w:ptcp.w:call-trgt-39.t:call-trgt_plot_motifs_allele NOTICE slurm_singularity run :: pid: 1203104, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-39/call-trgt_plot_motifs_allele/slurm_singularity.log.txt"
2025-09-15 20:24:47.019 wdl.w:ptcp.w:call-sawfish-70 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:24:47.019 wdl.w:ptcp.w:call-sawfish-70 INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:24:47.019 wdl.w:ptcp.w:call-sawfish-70 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-70/out/m84036_250809_035451_s4.bc2167.mapped.bam"}
2025-09-15 20:24:47.019 wdl.w:ptcp.w:call-sawfish-70 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-70/out/m84036_250809_035451_s4.bc2167.mapped.bam.bai"}
2025-09-15 20:24:47.019 wdl.w:ptcp.w:call-sawfish-70 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:24:47.019 wdl.w:ptcp.w:call-sawfish-70 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:24:47.019 wdl.w:ptcp.w:call-sawfish-70 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2167"}
2025-09-15 20:24:47.020 wdl.w:ptcp.w:call-sawfish-70 NOTICE ready :: job: "call-run_sawfish", callee: "run_sawfish"
2025-09-15 20:24:47.020 wdl.w:ptcp.w:call-sawfish-70 INFO input :: job: "call-run_sawfish", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-70/out/m84036_250809_035451_s4.bc2167.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-70/out/m84036_250809_035451_s4.bc2167.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2167"}
2025-09-15 20:24:47.024 wdl.w:ptcp.w:call-sawfish-00 NOTICE finish :: job: "call-run_sawfish"
2025-09-15 20:24:47.024 wdl.w:ptcp.w:call-sawfish-00 INFO output :: job: "call-run_sawfish", values: {"minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-00/call-run_sawfish/out/m84036_250809_035451_s4.bc2097.minimap2.bam.bai", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-00/call-run_sawfish/out/m84036_250809_035451_s4.bc2097.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-00/call-run_sawfish/out/m84036_250809_035451_s4.bc2097_sawfish/m84036_250809_035451_s4.bc2097.sv.vcf.gz.tbi", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-00/call-run_sawfish/out/m84036_250809_035451_s4.bc2097_sawfish/m84036_250809_035451_s4.bc2097.sv.vcf.gz"}
2025-09-15 20:24:47.024 wdl.w:ptcp.w:call-sawfish-00 INFO visit :: node: "output-minimap2_bam", values: {"minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-00/call-run_sawfish/out/m84036_250809_035451_s4.bc2097.minimap2.bam"}
2025-09-15 20:24:47.024 wdl.w:ptcp.w:call-sawfish-00 INFO visit :: node: "output-minimap2_bam_bai", values: {"minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-00/call-run_sawfish/out/m84036_250809_035451_s4.bc2097.minimap2.bam.bai"}
2025-09-15 20:24:47.024 wdl.w:ptcp.w:call-sawfish-00 INFO visit :: node: "output-vcf", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-00/call-run_sawfish/out/m84036_250809_035451_s4.bc2097_sawfish/m84036_250809_035451_s4.bc2097.sv.vcf.gz"}
2025-09-15 20:24:47.024 wdl.w:ptcp.w:call-sawfish-00 INFO visit :: node: "output-vcf_tbi", values: {"vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-00/call-run_sawfish/out/m84036_250809_035451_s4.bc2097_sawfish/m84036_250809_035451_s4.bc2097.sv.vcf.gz.tbi"}
2025-09-15 20:24:47.025 wdl.w:ptcp.w:call-sawfish-00 INFO visit :: node: "outputs", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-00/call-run_sawfish/out/m84036_250809_035451_s4.bc2097_sawfish/m84036_250809_035451_s4.bc2097.sv.vcf.gz", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-00/call-run_sawfish/out/m84036_250809_035451_s4.bc2097.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-00/call-run_sawfish/out/m84036_250809_035451_s4.bc2097_sawfish/m84036_250809_035451_s4.bc2097.sv.vcf.gz.tbi", "minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-00/call-run_sawfish/out/m84036_250809_035451_s4.bc2097.minimap2.bam.bai"}
2025-09-15 20:24:47.033 wdl.w:ptcp.w:call-trgt-39.t:call-trgt_plot_motifs_waterfall NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-39/call-trgt_plot_motifs_waterfall", thread: 140610870679104
2025-09-15 20:24:47.037 wdl.w:ptcp.w:call-trgt-52 NOTICE finish :: job: "call-trgt_plot_motifs_allele"
2025-09-15 20:24:47.037 wdl.w:ptcp.w:call-trgt-52 INFO output :: job: "call-trgt_plot_motifs_allele", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-52/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2149.motifs_allele.trgt_plots.zip"}
2025-09-15 20:24:47.038 wdl.w:ptcp.w:call-trgt-52 INFO visit :: node: "output-images_motifs_allele", values: {"images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-52/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2149.motifs_allele.trgt_plots.zip"}
2025-09-15 20:24:47.039 wdl.w:ptcp.w:call-trgt-44 NOTICE finish :: job: "call-trgt_plot_motifs_allele"
2025-09-15 20:24:47.039 wdl.w:ptcp.w:call-trgt-44 INFO output :: job: "call-trgt_plot_motifs_allele", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-44/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2141.motifs_allele.trgt_plots.zip"}
2025-09-15 20:24:47.039 wdl.w:ptcp.w:call-trgt-44 INFO visit :: node: "output-images_motifs_allele", values: {"images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-44/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2141.motifs_allele.trgt_plots.zip"}
2025-09-15 20:24:47.047 wdl.w:ptcp.w:call-paraphase-52.t:call-call_f8 NOTICE task setup :: name: "call_f8", source: "./paraphase.wdl", line: 232, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-52/call-call_f8", thread: 140609310422592
2025-09-15 20:24:47.049 wdl.w:ptcp.w:call-paraphase-64.t:call-run_paraphase NOTICE task setup :: name: "run_paraphase", source: "./paraphase.wdl", line: 127, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-64/call-run_paraphase", thread: 140607112582720
2025-09-15 20:24:47.052 wdl.w:ptcp.w:call-trgt-39.t:call-trgt_plot_motifs_waterfall INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:47.052 wdl.w:ptcp.w:call-trgt-39.t:call-trgt_plot_motifs_waterfall INFO input :: name: "waterfall", value: true
2025-09-15 20:24:47.052 wdl.w:ptcp.w:call-trgt-39.t:call-trgt_plot_motifs_waterfall INFO input :: name: "methylation", value: false
2025-09-15 20:24:47.052 wdl.w:ptcp.w:call-trgt-39.t:call-trgt_plot_motifs_waterfall INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:47.053 wdl.w:ptcp.w:call-trgt-39.t:call-trgt_plot_motifs_waterfall INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:47.053 wdl.w:ptcp.w:call-trgt-39.t:call-trgt_plot_motifs_waterfall INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:47.053 wdl.w:ptcp.w:call-trgt-39.t:call-trgt_plot_motifs_waterfall INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2136.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:47.053 wdl.w:ptcp.w:call-trgt-39.t:call-trgt_plot_motifs_waterfall INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2136.trgt.sorted.spanning.bam"
2025-09-15 20:24:47.053 wdl.w:ptcp.w:call-trgt-39.t:call-trgt_plot_motifs_waterfall INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2136.trgt.vcf"
2025-09-15 20:24:47.053 wdl.w:ptcp.w:call-trgt-39.t:call-trgt_plot_motifs_waterfall INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2136"
2025-09-15 20:24:47.053 wdl.w:ptcp.w:call-trgt-39.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:47.053 wdl.w:ptcp.w:call-trgt-39.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "plot_type", value: "waterfall"
2025-09-15 20:24:47.053 wdl.w:ptcp.w:call-trgt-39.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "show", value: "motifs"
2025-09-15 20:24:47.053 wdl.w:ptcp.w:call-trgt-39.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "threads", value: 1
2025-09-15 20:24:47.054 wdl.w:ptcp.w:call-trgt-39.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:47.054 wdl.w:ptcp.w:call-trgt-39.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2136.motifs_waterfall"
2025-09-15 20:24:47.054 wdl.w:ptcp.w:call-trgt-39.t:call-trgt_plot_motifs_waterfall INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:47.054 wdl.w:ptcp.w:call-trgt-39.t:call-trgt_plot_motifs_waterfall WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:47.054 wdl.w:ptcp.w:call-trgt-39.t:call-trgt_plot_motifs_waterfall INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:47.055 wdl.w:ptcp.w:call-trgt-39.t:call-trgt_plot_motifs_waterfall INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:47.066 wdl.w:ptcp.w:call-paraphase-52.t:call-call_f8 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:47.066 wdl.w:ptcp.w:call-paraphase-52.t:call-call_f8 INFO input :: name: "genome_version", value: "38"
2025-09-15 20:24:47.066 wdl.w:ptcp.w:call-paraphase-52.t:call-call_f8 INFO input :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2149"
2025-09-15 20:24:47.067 wdl.w:ptcp.w:call-paraphase-52.t:call-call_f8 INFO input :: name: "paraphase_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2149.paraphase.bam.bai"
2025-09-15 20:24:47.067 wdl.w:ptcp.w:call-paraphase-52.t:call-call_f8 INFO input :: name: "paraphase_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2149.paraphase.bam"
2025-09-15 20:24:47.067 wdl.w:ptcp.w:call-paraphase-52.t:call-call_f8 INFO input :: name: "sex", value: "F"
2025-09-15 20:24:47.067 wdl.w:ptcp.w:call-paraphase-52.t:call-call_f8 INFO eval :: name: "threads", value: 1
2025-09-15 20:24:47.067 wdl.w:ptcp.w:call-paraphase-52.t:call-call_f8 INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:47.067 wdl.w:ptcp.w:call-paraphase-52.t:call-call_f8 INFO eval :: name: "disk_size", value: 11
2025-09-15 20:24:47.068 wdl.w:ptcp.w:call-paraphase-52.t:call-call_f8 INFO eval :: name: "sample_sex", value: "F"
2025-09-15 20:24:47.068 wdl.w:ptcp.w:call-paraphase-52.t:call-call_f8 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:47.068 wdl.w:ptcp.w:call-paraphase-52.t:call-call_f8 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:47.069 wdl.w:ptcp.w:call-paraphase-52.t:call-call_f8 INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:47.069 wdl.w:ptcp.w:call-paraphase-52.t:call-call_f8 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:47.075 wdl.w:ptcp.w:call-paraphase-64.t:call-run_paraphase INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:47.075 wdl.w:ptcp.w:call-paraphase-64.t:call-run_paraphase INFO input :: name: "annotation_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf"
2025-09-15 20:24:47.075 wdl.w:ptcp.w:call-paraphase-64.t:call-run_paraphase INFO input :: name: "genome_version", value: "38"
2025-09-15 20:24:47.075 wdl.w:ptcp.w:call-paraphase-64.t:call-run_paraphase INFO input :: name: "config_file", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/paraphase_config.GRCh38.yaml"
2025-09-15 20:24:47.076 wdl.w:ptcp.w:call-paraphase-64.t:call-run_paraphase INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:47.076 wdl.w:ptcp.w:call-paraphase-64.t:call-run_paraphase INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:47.076 wdl.w:ptcp.w:call-paraphase-64.t:call-run_paraphase INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2161.mapped.bam.bai"
2025-09-15 20:24:47.076 wdl.w:ptcp.w:call-paraphase-64.t:call-run_paraphase INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2161.mapped.bam"
2025-09-15 20:24:47.076 wdl.w:ptcp.w:call-paraphase-64.t:call-run_paraphase INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2161"
2025-09-15 20:24:47.076 wdl.w:ptcp.w:call-paraphase-64.t:call-run_paraphase INFO eval :: name: "threads", value: 4
2025-09-15 20:24:47.076 wdl.w:ptcp.w:call-paraphase-64.t:call-run_paraphase INFO eval :: name: "mem_gb", value: 8
2025-09-15 20:24:47.076 wdl.w:ptcp.w:call-paraphase-64.t:call-run_paraphase INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:47.076 wdl.w:ptcp.w:call-paraphase-64.t:call-run_paraphase INFO eval :: name: "out_dir", value: "m84036_250809_035451_s4.bc2161_paraphase"
2025-09-15 20:24:47.077 wdl.w:ptcp.w:call-paraphase-64.t:call-run_paraphase INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 4, memory_reservation: 8000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:47.077 wdl.w:ptcp.w:call-paraphase-64.t:call-run_paraphase WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:47.077 wdl.w:ptcp.w:call-paraphase-64.t:call-run_paraphase INFO provisioned :: seconds_waited: 0, cpu: 4, mem_bytes: 8000000000
2025-09-15 20:24:47.078 wdl.w:ptcp.w:call-paraphase-64.t:call-run_paraphase INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:47.094 wdl.w:ptcp.w:call-sawfish-00 NOTICE done
2025-09-15 20:24:47.102 wdl.w:ptcp NOTICE finish :: job: "call-sawfish-00"
2025-09-15 20:24:47.102 wdl.w:ptcp INFO output :: job: "call-sawfish-00", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-00/out/m84036_250809_035451_s4.bc2097_sawfish/m84036_250809_035451_s4.bc2097.sv.vcf.gz", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-00/out/m84036_250809_035451_s4.bc2097.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-00/out/m84036_250809_035451_s4.bc2097_sawfish/m84036_250809_035451_s4.bc2097.sv.vcf.gz.tbi", "minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-00/out/m84036_250809_035451_s4.bc2097.minimap2.bam.bai"}
2025-09-15 20:24:47.103 wdl.w:ptcp NOTICE ready :: job: "call-tar_outputs-00", callee: "tar_outputs"
2025-09-15 20:24:47.103 wdl.w:ptcp INFO input :: job: "call-tar_outputs-00", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "sawfish_vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-00/out/m84036_250809_035451_s4.bc2097_sawfish/m84036_250809_035451_s4.bc2097.sv.vcf.gz.tbi", "sawfish_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-00/out/m84036_250809_035451_s4.bc2097_sawfish/m84036_250809_035451_s4.bc2097.sv.vcf.gz", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-00/out/m84036_250809_035451_s4.bc2097.f8inversion.json", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-00/out/m84036_250809_035451_s4.bc2097_paraphase/m84036_250809_035451_s4.bc2097.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-00/out/m84036_250809_035451_s4.bc2097_paraphase/m84036_250809_035451_s4.bc2097.paraphase.bam", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-00/out/m84036_250809_035451_s4.bc2097_paraphase/m84036_250809_035451_s4.bc2097.paraphase.json", "trgt_spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-00/out/m84036_250809_035451_s4.bc2097.trgt.sorted.spanning.bam.bai", "trgt_spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-00/out/m84036_250809_035451_s4.bc2097.trgt.sorted.spanning.bam", "trgt_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-00/out/m84036_250809_035451_s4.bc2097.trgt.vcf", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-00/out/m84036_250809_035451_s4.bc2097.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-00/out/m84036_250809_035451_s4.bc2097.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2097"}
2025-09-15 20:24:47.109 wdl.w:ptcp.w:call-trgt-70 NOTICE workflow start :: name: "trgt", source: "./trgt.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-70"
2025-09-15 20:24:47.131 wdl.w:ptcp.w:call-trgt-70 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:24:47.131 wdl.w:ptcp.w:call-trgt-70 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-70/out/m84036_250809_035451_s4.bc2167.mapped.bam"}
2025-09-15 20:24:47.132 wdl.w:ptcp.w:call-trgt-70 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-70/out/m84036_250809_035451_s4.bc2167.mapped.bam.bai"}
2025-09-15 20:24:47.132 wdl.w:ptcp.w:call-trgt-70 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:24:47.132 wdl.w:ptcp.w:call-trgt-70 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:24:47.132 wdl.w:ptcp.w:call-trgt-70 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2167"}
2025-09-15 20:24:47.132 wdl.w:ptcp.w:call-trgt-70 INFO visit :: node: "decl-sex", values: {"sex": "F"}
2025-09-15 20:24:47.132 wdl.w:ptcp.w:call-trgt-70 INFO visit :: node: "decl-trgt_bed", values: {"trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"}
2025-09-15 20:24:47.132 wdl.w:ptcp.w:call-trgt-70 NOTICE ready :: job: "call-get_reads_overlapping_repeats", callee: "get_reads_overlapping_repeats"
2025-09-15 20:24:47.132 wdl.w:ptcp.w:call-trgt-70 INFO input :: job: "call-get_reads_overlapping_repeats", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-70/out/m84036_250809_035451_s4.bc2167.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-70/out/m84036_250809_035451_s4.bc2167.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2167"}
2025-09-15 20:24:47.133 wdl.w:ptcp.w:call-trgt-70 NOTICE ready :: job: "call-trgt_genotype", callee: "trgt_genotype"
2025-09-15 20:24:47.133 wdl.w:ptcp.w:call-trgt-70 INFO input :: job: "call-trgt_genotype", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-70/out/m84036_250809_035451_s4.bc2167.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-70/out/m84036_250809_035451_s4.bc2167.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2167"}
2025-09-15 20:24:47.138 wdl.w:ptcp.w:call-paraphase-52.t:call-call_f8 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 8, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-52/call-call_f8/_singularity_tmpdir_akzz3nfr"
2025-09-15 20:24:47.138 wdl.w:ptcp.w:call-paraphase-52.t:call-call_f8 INFO Slurm invocation: srun --job-name call-call_f8 --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-52/call-call_f8/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-52/call-call_f8/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-52/call-call_f8/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-52/call-call_f8/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-52/call-run_paraphase/out/m84036_250809_035451_s4.bc2149_paraphase/m84036_250809_035451_s4.bc2149.paraphase.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2149.paraphase.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-52/call-run_paraphase/out/m84036_250809_035451_s4.bc2149_paraphase/m84036_250809_035451_s4.bc2149.paraphase.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2149.paraphase.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-52/call-call_f8/_singularity_tmpdir_akzz3nfr/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-52/call-call_f8/_singularity_tmpdir_akzz3nfr/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:47.150 wdl.w:ptcp.w:call-trgt-39.t:call-trgt_plot_motifs_waterfall INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-39/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_wj0y8nd7"
2025-09-15 20:24:47.150 wdl.w:ptcp.w:call-trgt-39.t:call-trgt_plot_motifs_waterfall INFO Slurm invocation: srun --job-name call-trgt_plot_motifs_waterfall --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-39/call-trgt_plot_motifs_waterfall/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-39/call-trgt_plot_motifs_waterfall/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-39/call-trgt_plot_motifs_waterfall/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-39/call-trgt_plot_motifs_waterfall/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-39/call-trgt_genotype/out/m84036_250809_035451_s4.bc2136.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2136.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-39/call-trgt_genotype/out/m84036_250809_035451_s4.bc2136.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2136.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-39/call-trgt_genotype/out/m84036_250809_035451_s4.bc2136.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2136.trgt.vcf:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-39/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_wj0y8nd7/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-39/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_wj0y8nd7/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:47.169 wdl.w:ptcp.w:call-paraphase-64.t:call-run_paraphase INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-64/call-run_paraphase/_singularity_tmpdir_jjzatd6c"
2025-09-15 20:24:47.170 wdl.w:ptcp.w:call-paraphase-64.t:call-run_paraphase INFO Slurm invocation: srun --job-name call-run_paraphase --partition compute,compute9 --cpus-per-task 4 --mem 7629M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-64/call-run_paraphase/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-64/call-run_paraphase/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-64/call-run_paraphase/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-64/call-run_paraphase/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-64/out/m84036_250809_035451_s4.bc2161.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2161.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-64/out/m84036_250809_035451_s4.bc2161.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2161.mapped.bam.bai:ro --bind /ptcp/meta/variant_list/variant_list.GRCh38.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf:ro --bind /ptcp/meta/paraphase/paraphase_config.GRCh38.yaml:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/paraphase_config.GRCh38.yaml:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-64/call-run_paraphase/_singularity_tmpdir_jjzatd6c/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-64/call-run_paraphase/_singularity_tmpdir_jjzatd6c/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:47.177 wdl.w:ptcp.w:call-trgt-39.t:call-trgt_plot_motifs_waterfall NOTICE slurm_singularity run :: pid: 1203133, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-39/call-trgt_plot_motifs_waterfall/slurm_singularity.log.txt"
2025-09-15 20:24:47.177 wdl.w:ptcp.w:call-paraphase-52.t:call-call_f8 NOTICE slurm_singularity run :: pid: 1203132, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-52/call-call_f8/slurm_singularity.log.txt"
2025-09-15 20:24:47.178 wdl.w:ptcp.w:call-paraphase-64.t:call-run_paraphase NOTICE slurm_singularity run :: pid: 1203134, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-64/call-run_paraphase/slurm_singularity.log.txt"
2025-09-15 20:24:47.183 wdl.w:ptcp.w:call-sawfish-06.t:call-run_sawfish INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2103_sawfish/m84036_250809_035451_s4.bc2103.sv.vcf.gz"
2025-09-15 20:24:47.190 wdl.w:ptcp.w:call-sawfish-06.t:call-run_sawfish INFO output :: name: "vcf_tbi", value: "m84036_250809_035451_s4.bc2103_sawfish/m84036_250809_035451_s4.bc2103.sv.vcf.gz.tbi"
2025-09-15 20:24:47.191 wdl.w:ptcp.w:call-sawfish-06.t:call-run_sawfish INFO output :: name: "minimap2_bam", value: "m84036_250809_035451_s4.bc2103.minimap2.bam"
2025-09-15 20:24:47.247 wdl.w:ptcp.w:call-sawfish-06.t:call-run_sawfish INFO output :: name: "minimap2_bam_bai", value: "m84036_250809_035451_s4.bc2103.minimap2.bam.bai"
2025-09-15 20:24:47.248 wdl.w:ptcp.w:call-paraphase-47.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for hba for sample m84036_250809_035451_s4.bc2144 at 2025-09-15 20:24:35.173799...
2025-09-15 20:24:47.249 wdl.w:ptcp.w:call-paraphase-47.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for smn1 for sample m84036_250809_035451_s4.bc2144 at 2025-09-15 20:24:35.297995...
2025-09-15 20:24:47.249 wdl.w:ptcp.w:call-paraphase-47.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for gba for sample m84036_250809_035451_s4.bc2144 at 2025-09-15 20:24:35.663714...
2025-09-15 20:24:47.249 wdl.w:ptcp.w:call-paraphase-47.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for cyp21 for sample m84036_250809_035451_s4.bc2144 at 2025-09-15 20:24:36.210955...
2025-09-15 20:24:47.249 wdl.w:ptcp.w:call-paraphase-47.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for smn1 for sample m84036_250809_035451_s4.bc2144 at 2025-09-15 20:24:45.099667...
2025-09-15 20:24:47.249 wdl.w:ptcp.w:call-paraphase-47.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning to gene2 region for smn1 for sample m84036_250809_035451_s4.bc2144 at 2025-09-15 20:24:45.446293...
2025-09-15 20:24:47.274 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:46 [ERROR] - No reads found for TRID=SCA27B_FGF14
2025-09-15 20:24:47.341 wdl.w:ptcp.w:call-trgt-52.t:call-trgt_plot_meth_allele INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2149.meth_allele.trgt_plots.zip"
2025-09-15 20:24:47.408 wdl.w:ptcp.w:call-paraphase-59.t:call-run_paraphase.stderr VERBOSE INFO:root:Processing sample m84036_250809_035451_s4.bc2156 at 2025-09-15 20:24:41.737479...
2025-09-15 20:24:47.409 wdl.w:ptcp.w:call-paraphase-59.t:call-run_paraphase.stderr VERBOSE INFO:root:Checking sample sex at 2025-09-15 20:24:41.738485...
2025-09-15 20:24:47.409 wdl.w:ptcp.w:call-paraphase-59.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for cyp21 for sample m84036_250809_035451_s4.bc2156 at 2025-09-15 20:24:41.771575...
2025-09-15 20:24:47.409 wdl.w:ptcp.w:call-paraphase-59.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for cyp21 for sample m84036_250809_035451_s4.bc2156 at 2025-09-15 20:24:41.771891...
2025-09-15 20:24:47.410 wdl.w:ptcp.w:call-paraphase-59.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for smn1 for sample m84036_250809_035451_s4.bc2156 at 2025-09-15 20:24:41.771693...
2025-09-15 20:24:47.410 wdl.w:ptcp.w:call-paraphase-59.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for gba for sample m84036_250809_035451_s4.bc2156 at 2025-09-15 20:24:41.771718...
2025-09-15 20:24:47.410 wdl.w:ptcp.w:call-paraphase-59.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for hba for sample m84036_250809_035451_s4.bc2156 at 2025-09-15 20:24:41.771749...
2025-09-15 20:24:47.410 wdl.w:ptcp.w:call-paraphase-59.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for smn1 for sample m84036_250809_035451_s4.bc2156 at 2025-09-15 20:24:41.771989...
2025-09-15 20:24:47.410 wdl.w:ptcp.w:call-paraphase-59.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for gba for sample m84036_250809_035451_s4.bc2156 at 2025-09-15 20:24:41.771997...
2025-09-15 20:24:47.410 wdl.w:ptcp.w:call-paraphase-59.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for hba for sample m84036_250809_035451_s4.bc2156 at 2025-09-15 20:24:41.772015...
2025-09-15 20:24:47.430 wdl.w:ptcp.w:call-sawfish-06.t:call-run_sawfish NOTICE done
2025-09-15 20:24:47.448 wdl.w:ptcp.w:call-sawfish-06 NOTICE finish :: job: "call-run_sawfish"
2025-09-15 20:24:47.448 wdl.w:ptcp.w:call-sawfish-06 INFO output :: job: "call-run_sawfish", values: {"minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-06/call-run_sawfish/out/m84036_250809_035451_s4.bc2103.minimap2.bam.bai", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-06/call-run_sawfish/out/m84036_250809_035451_s4.bc2103.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-06/call-run_sawfish/out/m84036_250809_035451_s4.bc2103_sawfish/m84036_250809_035451_s4.bc2103.sv.vcf.gz.tbi", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-06/call-run_sawfish/out/m84036_250809_035451_s4.bc2103_sawfish/m84036_250809_035451_s4.bc2103.sv.vcf.gz"}
2025-09-15 20:24:47.448 wdl.w:ptcp.w:call-sawfish-06 INFO visit :: node: "output-minimap2_bam", values: {"minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-06/call-run_sawfish/out/m84036_250809_035451_s4.bc2103.minimap2.bam"}
2025-09-15 20:24:47.448 wdl.w:ptcp.w:call-sawfish-06 INFO visit :: node: "output-minimap2_bam_bai", values: {"minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-06/call-run_sawfish/out/m84036_250809_035451_s4.bc2103.minimap2.bam.bai"}
2025-09-15 20:24:47.448 wdl.w:ptcp.w:call-sawfish-06 INFO visit :: node: "output-vcf", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-06/call-run_sawfish/out/m84036_250809_035451_s4.bc2103_sawfish/m84036_250809_035451_s4.bc2103.sv.vcf.gz"}
2025-09-15 20:24:47.449 wdl.w:ptcp.w:call-sawfish-06 INFO visit :: node: "output-vcf_tbi", values: {"vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-06/call-run_sawfish/out/m84036_250809_035451_s4.bc2103_sawfish/m84036_250809_035451_s4.bc2103.sv.vcf.gz.tbi"}
2025-09-15 20:24:47.449 wdl.w:ptcp.w:call-sawfish-06 INFO visit :: node: "outputs", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-06/call-run_sawfish/out/m84036_250809_035451_s4.bc2103_sawfish/m84036_250809_035451_s4.bc2103.sv.vcf.gz", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-06/call-run_sawfish/out/m84036_250809_035451_s4.bc2103.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-06/call-run_sawfish/out/m84036_250809_035451_s4.bc2103_sawfish/m84036_250809_035451_s4.bc2103.sv.vcf.gz.tbi", "minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-06/call-run_sawfish/out/m84036_250809_035451_s4.bc2103.minimap2.bam.bai"}
2025-09-15 20:24:47.456 wdl.w:ptcp.w:call-sawfish-64.t:call-run_sawfish NOTICE task setup :: name: "run_sawfish", source: "./sawfish.wdl", line: 83, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-64/call-run_sawfish", thread: 140609268459072
2025-09-15 20:24:47.482 wdl.w:ptcp.w:call-sawfish-64.t:call-run_sawfish INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:47.483 wdl.w:ptcp.w:call-sawfish-64.t:call-run_sawfish INFO input :: name: "genome_version", value: "38"
2025-09-15 20:24:47.483 wdl.w:ptcp.w:call-sawfish-64.t:call-run_sawfish INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:47.483 wdl.w:ptcp.w:call-sawfish-64.t:call-run_sawfish INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:47.483 wdl.w:ptcp.w:call-sawfish-64.t:call-run_sawfish INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2161.mapped.bam.bai"
2025-09-15 20:24:47.483 wdl.w:ptcp.w:call-sawfish-64.t:call-run_sawfish INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2161.mapped.bam"
2025-09-15 20:24:47.483 wdl.w:ptcp.w:call-sawfish-64.t:call-run_sawfish INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2161"
2025-09-15 20:24:47.483 wdl.w:ptcp.w:call-sawfish-64.t:call-run_sawfish INFO eval :: name: "mem_gb", value: 32
2025-09-15 20:24:47.483 wdl.w:ptcp.w:call-sawfish-64.t:call-run_sawfish INFO eval :: name: "threads", value: 16
2025-09-15 20:24:47.483 wdl.w:ptcp.w:call-sawfish-64.t:call-run_sawfish INFO eval :: name: "disk_size", value: 30
2025-09-15 20:24:47.484 wdl.w:ptcp.w:call-sawfish-64.t:call-run_sawfish INFO eval :: name: "discover_dirname", value: "m84036_250809_035451_s4.bc2161_sawfish_discover"
2025-09-15 20:24:47.484 wdl.w:ptcp.w:call-sawfish-64.t:call-run_sawfish INFO eval :: name: "call_dirname", value: "m84036_250809_035451_s4.bc2161_sawfish"
2025-09-15 20:24:47.484 wdl.w:ptcp.w:call-sawfish-64.t:call-run_sawfish INFO eval :: name: "minimap2_bam_filename", value: "m84036_250809_035451_s4.bc2161.minimap2.bam"
2025-09-15 20:24:47.484 wdl.w:ptcp.w:call-sawfish-64.t:call-run_sawfish INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 16, memory_reservation: 32000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:47.484 wdl.w:ptcp.w:call-sawfish-64.t:call-run_sawfish WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:47.485 wdl.w:ptcp.w:call-sawfish-64.t:call-run_sawfish INFO provisioned :: seconds_waited: 0, cpu: 16, mem_bytes: 32000000000
2025-09-15 20:24:47.485 wdl.w:ptcp.w:call-sawfish-64.t:call-run_sawfish INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:47.488 wdl.w:ptcp.w:call-trgt-52.t:call-trgt_plot_meth_allele NOTICE done
2025-09-15 20:24:47.494 wdl.w:ptcp.w:call-trgt-52 NOTICE finish :: job: "call-trgt_plot_meth_allele"
2025-09-15 20:24:47.494 wdl.w:ptcp.w:call-trgt-52 INFO output :: job: "call-trgt_plot_meth_allele", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-52/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2149.meth_allele.trgt_plots.zip"}
2025-09-15 20:24:47.494 wdl.w:ptcp.w:call-trgt-52 INFO visit :: node: "output-images_meth_allele", values: {"images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-52/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2149.meth_allele.trgt_plots.zip"}
2025-09-15 20:24:47.500 wdl.w:ptcp.w:call-trgt-64.t:call-get_reads_overlapping_repeats NOTICE task setup :: name: "get_reads_overlapping_repeats", source: "./trgt.wdl", line: 182, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-64/call-get_reads_overlapping_repeats", thread: 140609838900800
2025-09-15 20:24:47.508 wdl.w:ptcp.w:call-sawfish-06 NOTICE done
2025-09-15 20:24:47.518 wdl.w:ptcp.w:call-trgt-64.t:call-get_reads_overlapping_repeats INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:47.518 wdl.w:ptcp.w:call-trgt-64.t:call-get_reads_overlapping_repeats INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:47.518 wdl.w:ptcp.w:call-trgt-64.t:call-get_reads_overlapping_repeats INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2161.mapped.bam.bai"
2025-09-15 20:24:47.518 wdl.w:ptcp.w:call-trgt-64.t:call-get_reads_overlapping_repeats INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2161.mapped.bam"
2025-09-15 20:24:47.518 wdl.w:ptcp.w:call-trgt-64.t:call-get_reads_overlapping_repeats INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2161"
2025-09-15 20:24:47.518 wdl.w:ptcp.w:call-trgt-64.t:call-get_reads_overlapping_repeats INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:47.518 wdl.w:ptcp.w:call-trgt-64.t:call-get_reads_overlapping_repeats INFO eval :: name: "expand_size", value: 3000
2025-09-15 20:24:47.519 wdl.w:ptcp.w:call-trgt-64.t:call-get_reads_overlapping_repeats INFO eval :: name: "threads", value: 1
2025-09-15 20:24:47.519 wdl.w:ptcp.w:call-trgt-64.t:call-get_reads_overlapping_repeats INFO eval :: name: "expanded_bed_name", value: "m84036_250809_035451_s4.bc2161.expanded.bed"
2025-09-15 20:24:47.519 wdl.w:ptcp.w:call-trgt-64.t:call-get_reads_overlapping_repeats INFO eval :: name: "disk_size", value: 11
2025-09-15 20:24:47.519 wdl.w:ptcp.w:call-trgt-64.t:call-get_reads_overlapping_repeats INFO eval :: name: "output_name", value: "m84036_250809_035451_s4.bc2161.repeats.bam"
2025-09-15 20:24:47.519 wdl.w:ptcp.w:call-trgt-64.t:call-get_reads_overlapping_repeats INFO eval :: name: "index_name", value: "m84036_250809_035451_s4.bc2161.repeats.bam.bai"
2025-09-15 20:24:47.519 wdl.w:ptcp.w:call-trgt-64.t:call-get_reads_overlapping_repeats INFO eval :: name: "output_name_with_index", value: "m84036_250809_035451_s4.bc2161.repeats.bam##idx##m84036_250809_035451_s4.bc2161.repeats.bam.bai"
2025-09-15 20:24:47.519 wdl.w:ptcp.w:call-trgt-64.t:call-get_reads_overlapping_repeats INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:47.520 wdl.w:ptcp.w:call-trgt-64.t:call-get_reads_overlapping_repeats WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:47.520 wdl.w:ptcp.w:call-trgt-64.t:call-get_reads_overlapping_repeats INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:47.520 wdl.w:ptcp.w:call-trgt-64.t:call-get_reads_overlapping_repeats INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:47.544 wdl.w:ptcp.w:call-sawfish-64.t:call-run_sawfish INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 10, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-64/call-run_sawfish/_singularity_tmpdir_7ym3l7q6"
2025-09-15 20:24:47.544 wdl.w:ptcp.w:call-sawfish-64.t:call-run_sawfish INFO Slurm invocation: srun --job-name call-run_sawfish --partition compute,compute9 --cpus-per-task 16 --mem 30518M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-64/call-run_sawfish/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-64/call-run_sawfish/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-64/call-run_sawfish/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-64/call-run_sawfish/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-64/out/m84036_250809_035451_s4.bc2161.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2161.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-64/out/m84036_250809_035451_s4.bc2161.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2161.mapped.bam.bai:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-64/call-run_sawfish/_singularity_tmpdir_7ym3l7q6/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-64/call-run_sawfish/_singularity_tmpdir_7ym3l7q6/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:47.553 wdl.w:ptcp NOTICE finish :: job: "call-sawfish-06"
2025-09-15 20:24:47.553 wdl.w:ptcp INFO output :: job: "call-sawfish-06", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-06/out/m84036_250809_035451_s4.bc2103_sawfish/m84036_250809_035451_s4.bc2103.sv.vcf.gz", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-06/out/m84036_250809_035451_s4.bc2103.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-06/out/m84036_250809_035451_s4.bc2103_sawfish/m84036_250809_035451_s4.bc2103.sv.vcf.gz.tbi", "minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-06/out/m84036_250809_035451_s4.bc2103.minimap2.bam.bai"}
2025-09-15 20:24:47.558 wdl.w:ptcp.w:call-paraphase-79 NOTICE workflow start :: name: "paraphase", source: "./paraphase.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-79"
2025-09-15 20:24:47.572 wdl.w:ptcp.w:call-paraphase-79 INFO visit :: node: "decl-annotation_vcf", values: {"annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf"}
2025-09-15 20:24:47.573 wdl.w:ptcp.w:call-paraphase-79 INFO visit :: node: "decl-config_file", values: {"config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml"}
2025-09-15 20:24:47.573 wdl.w:ptcp.w:call-paraphase-79 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:24:47.573 wdl.w:ptcp.w:call-paraphase-79 INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:24:47.573 wdl.w:ptcp.w:call-paraphase-79 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-79/out/m84036_250809_035451_s4.bc2176.mapped.bam"}
2025-09-15 20:24:47.573 wdl.w:ptcp.w:call-paraphase-79 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-79/out/m84036_250809_035451_s4.bc2176.mapped.bam.bai"}
2025-09-15 20:24:47.573 wdl.w:ptcp.w:call-paraphase-79 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:24:47.573 wdl.w:ptcp.w:call-paraphase-79 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:24:47.573 wdl.w:ptcp.w:call-paraphase-79 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2176"}
2025-09-15 20:24:47.573 wdl.w:ptcp.w:call-paraphase-79 INFO visit :: node: "decl-sex", values: {"sex": "F"}
2025-09-15 20:24:47.573 wdl.w:ptcp.w:call-paraphase-79 NOTICE ready :: job: "call-run_paraphase", callee: "run_paraphase"
2025-09-15 20:24:47.573 wdl.w:ptcp.w:call-paraphase-79 INFO input :: job: "call-run_paraphase", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf", "genome_version": "38", "config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-79/out/m84036_250809_035451_s4.bc2176.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-79/out/m84036_250809_035451_s4.bc2176.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2176"}
2025-09-15 20:24:47.575 wdl.w:ptcp.w:call-trgt-64.t:call-get_reads_overlapping_repeats INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 9, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-64/call-get_reads_overlapping_repeats/_singularity_tmpdir_pel0bgum"
2025-09-15 20:24:47.575 wdl.w:ptcp.w:call-trgt-64.t:call-get_reads_overlapping_repeats INFO Slurm invocation: srun --job-name call-get_reads_overlapping_repeats --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-64/call-get_reads_overlapping_repeats/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-64/call-get_reads_overlapping_repeats/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-64/call-get_reads_overlapping_repeats/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-64/call-get_reads_overlapping_repeats/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-64/out/m84036_250809_035451_s4.bc2161.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2161.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-64/out/m84036_250809_035451_s4.bc2161.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2161.mapped.bam.bai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-64/call-get_reads_overlapping_repeats/_singularity_tmpdir_pel0bgum/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-64/call-get_reads_overlapping_repeats/_singularity_tmpdir_pel0bgum/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:47.587 wdl.w:ptcp.w:call-trgt-64.t:call-get_reads_overlapping_repeats NOTICE slurm_singularity run :: pid: 1203155, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-64/call-get_reads_overlapping_repeats/slurm_singularity.log.txt"
2025-09-15 20:24:47.587 wdl.w:ptcp.w:call-sawfish-64.t:call-run_sawfish NOTICE slurm_singularity run :: pid: 1203154, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-64/call-run_sawfish/slurm_singularity.log.txt"
2025-09-15 20:24:47.681 wdl.w:ptcp.w:call-paraphase-56.t:call-run_paraphase INFO output :: name: "paraphase_bam", value: "m84036_250809_035451_s4.bc2153_paraphase/m84036_250809_035451_s4.bc2153.paraphase.bam"
2025-09-15 20:24:47.687 wdl.w:ptcp.w:call-paraphase-56.t:call-run_paraphase INFO output :: name: "paraphase_bam_bai", value: "m84036_250809_035451_s4.bc2153_paraphase/m84036_250809_035451_s4.bc2153.paraphase.bam.bai"
2025-09-15 20:24:47.688 wdl.w:ptcp.w:call-paraphase-56.t:call-run_paraphase INFO output :: name: "paraphase_json", value: "m84036_250809_035451_s4.bc2153_paraphase/m84036_250809_035451_s4.bc2153.paraphase.json"
2025-09-15 20:24:47.689 wdl.w:ptcp.w:call-paraphase-56.t:call-run_paraphase INFO output :: name: "paraphase_vcfs", value: []
2025-09-15 20:24:47.690 wdl.w:ptcp.w:call-paraphase-56.t:call-run_paraphase INFO output :: name: "havanno_json", value: "m84036_250809_035451_s4.bc2153.havanno.json"
2025-09-15 20:24:47.766 wdl.w:ptcp.w:call-paraphase-56.t:call-run_paraphase NOTICE done
2025-09-15 20:24:47.771 wdl.w:ptcp.w:call-paraphase-56 NOTICE finish :: job: "call-run_paraphase"
2025-09-15 20:24:47.771 wdl.w:ptcp.w:call-paraphase-56 INFO output :: job: "call-run_paraphase", values: {"havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-56/call-run_paraphase/out/m84036_250809_035451_s4.bc2153.havanno.json", "paraphase_vcfs": [], "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-56/call-run_paraphase/out/m84036_250809_035451_s4.bc2153_paraphase/m84036_250809_035451_s4.bc2153.paraphase.json", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-56/call-run_paraphase/out/m84036_250809_035451_s4.bc2153_paraphase/m84036_250809_035451_s4.bc2153.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-56/call-run_paraphase/out/m84036_250809_035451_s4.bc2153_paraphase/m84036_250809_035451_s4.bc2153.paraphase.bam"}
2025-09-15 20:24:47.772 wdl.w:ptcp.w:call-paraphase-56 NOTICE ready :: job: "call-call_f8", callee: "call_f8"
2025-09-15 20:24:47.772 wdl.w:ptcp.w:call-paraphase-56 INFO input :: job: "call-call_f8", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "out_prefix": "m84036_250809_035451_s4.bc2153", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-56/call-run_paraphase/out/m84036_250809_035451_s4.bc2153_paraphase/m84036_250809_035451_s4.bc2153.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-56/call-run_paraphase/out/m84036_250809_035451_s4.bc2153_paraphase/m84036_250809_035451_s4.bc2153.paraphase.bam", "sex": "F"}
2025-09-15 20:24:47.773 wdl.w:ptcp.w:call-paraphase-56 INFO visit :: node: "output-havanno_json", values: {"havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-56/call-run_paraphase/out/m84036_250809_035451_s4.bc2153.havanno.json"}
2025-09-15 20:24:47.773 wdl.w:ptcp.w:call-paraphase-56 INFO visit :: node: "output-paraphase_bam", values: {"paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-56/call-run_paraphase/out/m84036_250809_035451_s4.bc2153_paraphase/m84036_250809_035451_s4.bc2153.paraphase.bam"}
2025-09-15 20:24:47.773 wdl.w:ptcp.w:call-paraphase-56 INFO visit :: node: "output-paraphase_bam_bai", values: {"paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-56/call-run_paraphase/out/m84036_250809_035451_s4.bc2153_paraphase/m84036_250809_035451_s4.bc2153.paraphase.bam.bai"}
2025-09-15 20:24:47.773 wdl.w:ptcp.w:call-paraphase-56 INFO visit :: node: "output-paraphase_json", values: {"paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-56/call-run_paraphase/out/m84036_250809_035451_s4.bc2153_paraphase/m84036_250809_035451_s4.bc2153.paraphase.json"}
2025-09-15 20:24:47.773 wdl.w:ptcp.w:call-paraphase-56 INFO visit :: node: "output-paraphase_vcfs", values: {"paraphase_vcfs": []}
2025-09-15 20:24:47.777 wdl.w:ptcp.w:call-trgt-64.t:call-trgt_genotype NOTICE task setup :: name: "trgt_genotype", source: "./trgt.wdl", line: 272, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-64/call-trgt_genotype", thread: 140607683024448
2025-09-15 20:24:47.779 wdl.w:ptcp.w:call-trgt-67.t:call-get_reads_overlapping_repeats.slurm_singularity INFO srun: job 51797788 queued and waiting for resources
2025-09-15 20:24:47.780 wdl.w:ptcp.w:call-trgt-67.t:call-get_reads_overlapping_repeats.slurm_singularity INFO srun: job 51797788 has been allocated resources
2025-09-15 20:24:47.780 wdl.w:ptcp.w:call-trgt-67.t:call-get_reads_overlapping_repeats.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:47.793 wdl.w:ptcp.w:call-trgt-64.t:call-trgt_genotype INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:47.793 wdl.w:ptcp.w:call-trgt-64.t:call-trgt_genotype INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:47.793 wdl.w:ptcp.w:call-trgt-64.t:call-trgt_genotype INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:47.793 wdl.w:ptcp.w:call-trgt-64.t:call-trgt_genotype INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:47.793 wdl.w:ptcp.w:call-trgt-64.t:call-trgt_genotype INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2161.mapped.bam.bai"
2025-09-15 20:24:47.793 wdl.w:ptcp.w:call-trgt-64.t:call-trgt_genotype INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2161.mapped.bam"
2025-09-15 20:24:47.793 wdl.w:ptcp.w:call-trgt-64.t:call-trgt_genotype INFO input :: name: "sex", value: "F"
2025-09-15 20:24:47.793 wdl.w:ptcp.w:call-trgt-64.t:call-trgt_genotype INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2161"
2025-09-15 20:24:47.793 wdl.w:ptcp.w:call-trgt-64.t:call-trgt_genotype INFO eval :: name: "mem_gb", value: 16
2025-09-15 20:24:47.794 wdl.w:ptcp.w:call-trgt-64.t:call-trgt_genotype INFO eval :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2161.trgt"
2025-09-15 20:24:47.794 wdl.w:ptcp.w:call-trgt-64.t:call-trgt_genotype INFO eval :: name: "threads", value: 8
2025-09-15 20:24:47.794 wdl.w:ptcp.w:call-trgt-64.t:call-trgt_genotype INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:47.794 wdl.w:ptcp.w:call-trgt-64.t:call-trgt_genotype INFO eval :: name: "karyotype", value: "XX"
2025-09-15 20:24:47.794 wdl.w:ptcp.w:call-trgt-64.t:call-trgt_genotype INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 8, memory_reservation: 16000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:47.794 wdl.w:ptcp.w:call-trgt-64.t:call-trgt_genotype WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:47.795 wdl.w:ptcp.w:call-trgt-64.t:call-trgt_genotype INFO provisioned :: seconds_waited: 0, cpu: 8, mem_bytes: 16000000000
2025-09-15 20:24:47.795 wdl.w:ptcp.w:call-trgt-64.t:call-trgt_genotype INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:47.822 wdl.w:ptcp.w:call-paraphase-02.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for f8inv1 for sample m84036_250809_035451_s4.bc2099 at 2025-09-15 20:24:37.666262...
2025-09-15 20:24:47.822 wdl.w:ptcp.w:call-paraphase-02.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for f8inv1 for sample m84036_250809_035451_s4.bc2099 at 2025-09-15 20:24:38.308900...
2025-09-15 20:24:47.859 wdl.w:ptcp.w:call-trgt-64.t:call-trgt_genotype INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 11, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-64/call-trgt_genotype/_singularity_tmpdir_zeplilmp"
2025-09-15 20:24:47.859 wdl.w:ptcp.w:call-trgt-64.t:call-trgt_genotype INFO Slurm invocation: srun --job-name call-trgt_genotype --partition compute,compute9 --cpus-per-task 8 --mem 15259M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-64/call-trgt_genotype/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-64/call-trgt_genotype/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-64/call-trgt_genotype/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-64/call-trgt_genotype/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-64/out/m84036_250809_035451_s4.bc2161.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2161.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-64/out/m84036_250809_035451_s4.bc2161.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2161.mapped.bam.bai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-64/call-trgt_genotype/_singularity_tmpdir_zeplilmp/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-64/call-trgt_genotype/_singularity_tmpdir_zeplilmp/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:47.879 wdl.w:ptcp.w:call-trgt-64.t:call-trgt_genotype NOTICE slurm_singularity run :: pid: 1203169, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-64/call-trgt_genotype/slurm_singularity.log.txt"
2025-09-15 20:24:47.886 wdl.w:ptcp.w:call-trgt-39.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:47 [ERROR] - No reads found for TRID=SCA37_DAB1
2025-09-15 20:24:47.886 wdl.w:ptcp.w:call-trgt-39.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:47 [ERROR] - No reads found for TRID=OPDM_ABCD3
2025-09-15 20:24:47.892 wdl.w:ptcp.w:call-trgt-67.t:call-trgt_genotype.slurm_singularity INFO srun: job 51797789 queued and waiting for resources
2025-09-15 20:24:47.892 wdl.w:ptcp.w:call-trgt-67.t:call-trgt_genotype.slurm_singularity INFO srun: job 51797789 has been allocated resources
2025-09-15 20:24:47.892 wdl.w:ptcp.w:call-trgt-67.t:call-trgt_genotype.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:47.895 wdl.w:ptcp.w:call-trgt-39.t:call-trgt_plot_meth_allele.slurm_singularity INFO srun: job 51797790 queued and waiting for resources
2025-09-15 20:24:47.895 wdl.w:ptcp.w:call-trgt-39.t:call-trgt_plot_meth_allele.slurm_singularity INFO srun: job 51797790 has been allocated resources
2025-09-15 20:24:47.895 wdl.w:ptcp.w:call-trgt-39.t:call-trgt_plot_meth_allele.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:47.922 wdl.w:ptcp.w:call-paraphase-53.t:call-run_paraphase.stderr VERBOSE INFO:root:Processing sample m84036_250809_035451_s4.bc2150 at 2025-09-15 20:24:44.018615...
2025-09-15 20:24:47.922 wdl.w:ptcp.w:call-paraphase-53.t:call-run_paraphase.stderr VERBOSE INFO:root:Checking sample sex at 2025-09-15 20:24:44.021335...
2025-09-15 20:24:47.922 wdl.w:ptcp.w:call-paraphase-53.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for cyp21 for sample m84036_250809_035451_s4.bc2150 at 2025-09-15 20:24:44.090860...
2025-09-15 20:24:47.922 wdl.w:ptcp.w:call-paraphase-53.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for smn1 for sample m84036_250809_035451_s4.bc2150 at 2025-09-15 20:24:44.090965...
2025-09-15 20:24:47.922 wdl.w:ptcp.w:call-paraphase-53.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for cyp21 for sample m84036_250809_035451_s4.bc2150 at 2025-09-15 20:24:44.091295...
2025-09-15 20:24:47.922 wdl.w:ptcp.w:call-paraphase-53.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for gba for sample m84036_250809_035451_s4.bc2150 at 2025-09-15 20:24:44.090999...
2025-09-15 20:24:47.923 wdl.w:ptcp.w:call-paraphase-53.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for hba for sample m84036_250809_035451_s4.bc2150 at 2025-09-15 20:24:44.091036...
2025-09-15 20:24:47.923 wdl.w:ptcp.w:call-paraphase-53.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for smn1 for sample m84036_250809_035451_s4.bc2150 at 2025-09-15 20:24:44.091341...
2025-09-15 20:24:47.923 wdl.w:ptcp.w:call-paraphase-53.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for gba for sample m84036_250809_035451_s4.bc2150 at 2025-09-15 20:24:44.091349...
2025-09-15 20:24:47.923 wdl.w:ptcp.w:call-paraphase-53.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for hba for sample m84036_250809_035451_s4.bc2150 at 2025-09-15 20:24:44.091373...
2025-09-15 20:24:47.923 wdl.w:ptcp.w:call-paraphase-53.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for gba for sample m84036_250809_035451_s4.bc2150 at 2025-09-15 20:24:44.977699...
2025-09-15 20:24:47.923 wdl.w:ptcp.w:call-paraphase-53.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for hba for sample m84036_250809_035451_s4.bc2150 at 2025-09-15 20:24:45.013965...
2025-09-15 20:24:47.923 wdl.w:ptcp.w:call-paraphase-53.t:call-run_paraphase.stderr VERBOSE WARNING:root:This region does not appear to have coverage. Will not attempt to phase haplotypes.
2025-09-15 20:24:47.923 wdl.w:ptcp.w:call-paraphase-53.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for gba for sample m84036_250809_035451_s4.bc2150 at 2025-09-15 20:24:45.122914...
2025-09-15 20:24:47.923 wdl.w:ptcp.w:call-paraphase-53.t:call-run_paraphase.stderr VERBOSE WARNING:root:This region does not appear to have coverage. Will not attempt to phase haplotypes.
2025-09-15 20:24:47.923 wdl.w:ptcp.w:call-paraphase-53.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for hba for sample m84036_250809_035451_s4.bc2150 at 2025-09-15 20:24:45.128139...
2025-09-15 20:24:47.923 wdl.w:ptcp.w:call-paraphase-53.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for smn1 for sample m84036_250809_035451_s4.bc2150 at 2025-09-15 20:24:45.138449...
2025-09-15 20:24:47.923 wdl.w:ptcp.w:call-paraphase-53.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for cyp21 for sample m84036_250809_035451_s4.bc2150 at 2025-09-15 20:24:45.174906...
2025-09-15 20:24:47.923 wdl.w:ptcp.w:call-paraphase-53.t:call-run_paraphase.stderr VERBOSE WARNING:root:This region does not appear to have coverage. Will not attempt to phase haplotypes.
2025-09-15 20:24:47.923 wdl.w:ptcp.w:call-paraphase-53.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for cyp21 for sample m84036_250809_035451_s4.bc2150 at 2025-09-15 20:24:45.351328...
2025-09-15 20:24:47.923 wdl.w:ptcp.w:call-paraphase-53.t:call-run_paraphase.stderr VERBOSE WARNING:root:This region does not appear to have coverage. Will not attempt to phase haplotypes.
2025-09-15 20:24:47.923 wdl.w:ptcp.w:call-paraphase-53.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for smn1 for sample m84036_250809_035451_s4.bc2150 at 2025-09-15 20:24:45.424768...
2025-09-15 20:24:47.923 wdl.w:ptcp.w:call-paraphase-53.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for hba for sample m84036_250809_035451_s4.bc2150 at 2025-09-15 20:24:45.694443...
2025-09-15 20:24:47.923 wdl.w:ptcp.w:call-paraphase-53.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for hbb for sample m84036_250809_035451_s4.bc2150 at 2025-09-15 20:24:45.706465...
2025-09-15 20:24:47.923 wdl.w:ptcp.w:call-paraphase-53.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for hbb for sample m84036_250809_035451_s4.bc2150 at 2025-09-15 20:24:45.706610...
2025-09-15 20:24:47.923 wdl.w:ptcp.w:call-paraphase-53.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for gba for sample m84036_250809_035451_s4.bc2150 at 2025-09-15 20:24:45.762695...
2025-09-15 20:24:47.924 wdl.w:ptcp.w:call-paraphase-53.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for rpgr for sample m84036_250809_035451_s4.bc2150 at 2025-09-15 20:24:45.769391...
2025-09-15 20:24:47.924 wdl.w:ptcp.w:call-paraphase-53.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for rpgr for sample m84036_250809_035451_s4.bc2150 at 2025-09-15 20:24:45.769464...
2025-09-15 20:24:47.924 wdl.w:ptcp.w:call-paraphase-53.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for cyp21 for sample m84036_250809_035451_s4.bc2150 at 2025-09-15 20:24:45.808245...
2025-09-15 20:24:47.924 wdl.w:ptcp.w:call-paraphase-53.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for f8inv22 for sample m84036_250809_035451_s4.bc2150 at 2025-09-15 20:24:45.815682...
2025-09-15 20:24:47.924 wdl.w:ptcp.w:call-paraphase-53.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for f8inv22 for sample m84036_250809_035451_s4.bc2150 at 2025-09-15 20:24:45.815768...
2025-09-15 20:24:47.924 wdl.w:ptcp.w:call-paraphase-53.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning to gene2 region for smn1 for sample m84036_250809_035451_s4.bc2150 at 2025-09-15 20:24:45.937350...
2025-09-15 20:24:47.924 wdl.w:ptcp.w:call-paraphase-53.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for hbb for sample m84036_250809_035451_s4.bc2150 at 2025-09-15 20:24:46.218001...
2025-09-15 20:24:47.924 wdl.w:ptcp.w:call-paraphase-53.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for rpgr for sample m84036_250809_035451_s4.bc2150 at 2025-09-15 20:24:46.227653...
2025-09-15 20:24:47.924 wdl.w:ptcp.w:call-paraphase-53.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for f8inv22 for sample m84036_250809_035451_s4.bc2150 at 2025-09-15 20:24:46.275137...
2025-09-15 20:24:47.924 wdl.w:ptcp.w:call-paraphase-53.t:call-run_paraphase.stderr VERBOSE WARNING:root:This region does not appear to have coverage. Will not attempt to phase haplotypes.
2025-09-15 20:24:47.924 wdl.w:ptcp.w:call-paraphase-53.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for rpgr for sample m84036_250809_035451_s4.bc2150 at 2025-09-15 20:24:46.283791...
2025-09-15 20:24:47.924 wdl.w:ptcp.w:call-paraphase-53.t:call-run_paraphase.stderr VERBOSE WARNING:root:This region does not appear to have coverage. Will not attempt to phase haplotypes.
2025-09-15 20:24:47.924 wdl.w:ptcp.w:call-paraphase-53.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for hbb for sample m84036_250809_035451_s4.bc2150 at 2025-09-15 20:24:46.299366...
2025-09-15 20:24:47.924 wdl.w:ptcp.w:call-paraphase-53.t:call-run_paraphase.stderr VERBOSE WARNING:root:This region does not appear to have coverage. Will not attempt to phase haplotypes.
2025-09-15 20:24:47.924 wdl.w:ptcp.w:call-paraphase-53.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for f8inv22 for sample m84036_250809_035451_s4.bc2150 at 2025-09-15 20:24:46.333299...
2025-09-15 20:24:47.924 wdl.w:ptcp.w:call-paraphase-53.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for rpgr for sample m84036_250809_035451_s4.bc2150 at 2025-09-15 20:24:46.850319...
2025-09-15 20:24:47.924 wdl.w:ptcp.w:call-paraphase-53.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for f8inv22 for sample m84036_250809_035451_s4.bc2150 at 2025-09-15 20:24:46.859595...
2025-09-15 20:24:47.924 wdl.w:ptcp.w:call-paraphase-53.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for hbb for sample m84036_250809_035451_s4.bc2150 at 2025-09-15 20:24:46.864007...
2025-09-15 20:24:47.924 wdl.w:ptcp.w:call-paraphase-53.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for smn1 for sample m84036_250809_035451_s4.bc2150 at 2025-09-15 20:24:46.879710...
2025-09-15 20:24:47.924 wdl.w:ptcp.w:call-paraphase-53.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for f8inv1 for sample m84036_250809_035451_s4.bc2150 at 2025-09-15 20:24:46.930903...
2025-09-15 20:24:47.924 wdl.w:ptcp.w:call-paraphase-53.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for f8inv1 for sample m84036_250809_035451_s4.bc2150 at 2025-09-15 20:24:46.930992...
2025-09-15 20:24:47.925 wdl.w:ptcp.w:call-paraphase-53.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for f8inv1 for sample m84036_250809_035451_s4.bc2150 at 2025-09-15 20:24:47.273705...
2025-09-15 20:24:47.925 wdl.w:ptcp.w:call-paraphase-53.t:call-run_paraphase.stderr VERBOSE WARNING:root:This region does not appear to have coverage. Will not attempt to phase haplotypes.
2025-09-15 20:24:47.925 wdl.w:ptcp.w:call-paraphase-53.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for f8inv1 for sample m84036_250809_035451_s4.bc2150 at 2025-09-15 20:24:47.309190...
2025-09-15 20:24:47.925 wdl.w:ptcp.w:call-paraphase-53.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for f8inv1 for sample m84036_250809_035451_s4.bc2150 at 2025-09-15 20:24:47.470664...
2025-09-15 20:24:47.960 wdl.w:ptcp.w:call-trgt-39.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:47 [ERROR] - No reads found for TRID=SCA37_DAB1
2025-09-15 20:24:47.960 wdl.w:ptcp.w:call-trgt-39.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:47 [ERROR] - No reads found for TRID=OPDM_ABCD3
2025-09-15 20:24:47.960 wdl.w:ptcp.w:call-trgt-39.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:47 [ERROR] - No reads found for TRID=NIID_NOTCH2NLC
2025-09-15 20:24:47.961 wdl.w:ptcp.w:call-trgt-39.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:47 [ERROR] - No reads found for TRID=DRPLA_ATN1
2025-09-15 20:24:47.968 wdl.w:ptcp.w:call-trgt-39.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO srun: job 51797791 queued and waiting for resources
2025-09-15 20:24:47.968 wdl.w:ptcp.w:call-trgt-39.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO srun: job 51797791 has been allocated resources
2025-09-15 20:24:47.968 wdl.w:ptcp.w:call-trgt-39.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:48.017 wdl.w:ptcp.w:call-trgt-39.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:47 [ERROR] - No reads found for TRID=SCA37_DAB1
2025-09-15 20:24:48.018 wdl.w:ptcp.w:call-trgt-39.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:47 [ERROR] - No reads found for TRID=OPDM_ABCD3
2025-09-15 20:24:48.018 wdl.w:ptcp.w:call-trgt-39.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:47 [ERROR] - No reads found for TRID=NIID_NOTCH2NLC
2025-09-15 20:24:48.018 wdl.w:ptcp.w:call-trgt-39.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:48 [ERROR] - No reads found for TRID=DRPLA_ATN1
2025-09-15 20:24:48.030 wdl.w:ptcp.w:call-trgt-39.t:call-trgt_plot_motifs_allele.slurm_singularity INFO srun: job 51797792 queued and waiting for resources
2025-09-15 20:24:48.030 wdl.w:ptcp.w:call-trgt-39.t:call-trgt_plot_motifs_allele.slurm_singularity INFO srun: job 51797792 has been allocated resources
2025-09-15 20:24:48.030 wdl.w:ptcp.w:call-trgt-39.t:call-trgt_plot_motifs_allele.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:48.178 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_plot_meth_allele INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2160.meth_allele.trgt_plots.zip"
2025-09-15 20:24:48.181 wdl.w:ptcp.w:call-trgt-39.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:48 [ERROR] - No reads found for TRID=SCA37_DAB1
2025-09-15 20:24:48.181 wdl.w:ptcp.w:call-trgt-39.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:48 [ERROR] - No reads found for TRID=OPDM_ABCD3
2025-09-15 20:24:48.197 wdl.w:ptcp.w:call-paraphase-64.t:call-run_paraphase.slurm_singularity INFO srun: job 51797795 queued and waiting for resources
2025-09-15 20:24:48.197 wdl.w:ptcp.w:call-paraphase-64.t:call-run_paraphase.slurm_singularity INFO srun: job 51797795 has been allocated resources
2025-09-15 20:24:48.197 wdl.w:ptcp.w:call-paraphase-64.t:call-run_paraphase.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:48.197 wdl.w:ptcp.w:call-paraphase-52.t:call-call_f8.slurm_singularity INFO srun: job 51797794 queued and waiting for resources
2025-09-15 20:24:48.197 wdl.w:ptcp.w:call-paraphase-52.t:call-call_f8.slurm_singularity INFO srun: job 51797794 has been allocated resources
2025-09-15 20:24:48.197 wdl.w:ptcp.w:call-paraphase-52.t:call-call_f8.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:48.198 wdl.w:ptcp.w:call-trgt-39.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO srun: job 51797793 queued and waiting for resources
2025-09-15 20:24:48.198 wdl.w:ptcp.w:call-trgt-39.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO srun: job 51797793 has been allocated resources
2025-09-15 20:24:48.198 wdl.w:ptcp.w:call-trgt-39.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:48.264 wdl.w:ptcp.w:call-paraphase-51.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for smn1 for sample m84036_250809_035451_s4.bc2148 at 2025-09-15 20:24:36.997555...
2025-09-15 20:24:48.282 wdl.w:ptcp.w:call-paraphase-41.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for gba for sample m84036_250809_035451_s4.bc2138 at 2025-09-15 20:24:44.715824...
2025-09-15 20:24:48.282 wdl.w:ptcp.w:call-paraphase-41.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for cyp21 for sample m84036_250809_035451_s4.bc2138 at 2025-09-15 20:24:44.718605...
2025-09-15 20:24:48.283 wdl.w:ptcp.w:call-paraphase-41.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for hba for sample m84036_250809_035451_s4.bc2138 at 2025-09-15 20:24:44.752773...
2025-09-15 20:24:48.283 wdl.w:ptcp.w:call-paraphase-41.t:call-run_paraphase.stderr VERBOSE WARNING:root:This region does not appear to have coverage. Will not attempt to phase haplotypes.
2025-09-15 20:24:48.283 wdl.w:ptcp.w:call-paraphase-41.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for cyp21 for sample m84036_250809_035451_s4.bc2138 at 2025-09-15 20:24:44.764252...
2025-09-15 20:24:48.283 wdl.w:ptcp.w:call-paraphase-41.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for smn1 for sample m84036_250809_035451_s4.bc2138 at 2025-09-15 20:24:44.779850...
2025-09-15 20:24:48.283 wdl.w:ptcp.w:call-paraphase-41.t:call-run_paraphase.stderr VERBOSE WARNING:root:This region does not appear to have coverage. Will not attempt to phase haplotypes.
2025-09-15 20:24:48.283 wdl.w:ptcp.w:call-paraphase-41.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for gba for sample m84036_250809_035451_s4.bc2138 at 2025-09-15 20:24:44.798776...
2025-09-15 20:24:48.283 wdl.w:ptcp.w:call-paraphase-41.t:call-run_paraphase.stderr VERBOSE WARNING:root:This region does not appear to have coverage. Will not attempt to phase haplotypes.
2025-09-15 20:24:48.283 wdl.w:ptcp.w:call-paraphase-41.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for hba for sample m84036_250809_035451_s4.bc2138 at 2025-09-15 20:24:44.804755...
2025-09-15 20:24:48.283 wdl.w:ptcp.w:call-paraphase-41.t:call-run_paraphase.stderr VERBOSE WARNING:root:This region does not appear to have coverage. Will not attempt to phase haplotypes.
2025-09-15 20:24:48.283 wdl.w:ptcp.w:call-paraphase-41.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for smn1 for sample m84036_250809_035451_s4.bc2138 at 2025-09-15 20:24:44.900635...
2025-09-15 20:24:48.283 wdl.w:ptcp.w:call-paraphase-41.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for cyp21 for sample m84036_250809_035451_s4.bc2138 at 2025-09-15 20:24:45.266979...
2025-09-15 20:24:48.283 wdl.w:ptcp.w:call-paraphase-41.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for f8inv22 for sample m84036_250809_035451_s4.bc2138 at 2025-09-15 20:24:45.288056...
2025-09-15 20:24:48.283 wdl.w:ptcp.w:call-paraphase-41.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for f8inv22 for sample m84036_250809_035451_s4.bc2138 at 2025-09-15 20:24:45.288135...
2025-09-15 20:24:48.283 wdl.w:ptcp.w:call-paraphase-41.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for gba for sample m84036_250809_035451_s4.bc2138 at 2025-09-15 20:24:45.351508...
2025-09-15 20:24:48.283 wdl.w:ptcp.w:call-paraphase-41.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for rpgr for sample m84036_250809_035451_s4.bc2138 at 2025-09-15 20:24:45.373293...
2025-09-15 20:24:48.283 wdl.w:ptcp.w:call-paraphase-41.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for rpgr for sample m84036_250809_035451_s4.bc2138 at 2025-09-15 20:24:45.378918...
2025-09-15 20:24:48.283 wdl.w:ptcp.w:call-paraphase-41.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for hba for sample m84036_250809_035451_s4.bc2138 at 2025-09-15 20:24:45.564306...
2025-09-15 20:24:48.283 wdl.w:ptcp.w:call-paraphase-41.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for hbb for sample m84036_250809_035451_s4.bc2138 at 2025-09-15 20:24:45.583489...
2025-09-15 20:24:48.284 wdl.w:ptcp.w:call-paraphase-41.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for hbb for sample m84036_250809_035451_s4.bc2138 at 2025-09-15 20:24:45.583618...
2025-09-15 20:24:48.284 wdl.w:ptcp.w:call-paraphase-41.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning to gene2 region for smn1 for sample m84036_250809_035451_s4.bc2138 at 2025-09-15 20:24:45.693537...
2025-09-15 20:24:48.284 wdl.w:ptcp.w:call-paraphase-41.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for f8inv22 for sample m84036_250809_035451_s4.bc2138 at 2025-09-15 20:24:46.423414...
2025-09-15 20:24:48.284 wdl.w:ptcp.w:call-paraphase-41.t:call-run_paraphase.stderr VERBOSE WARNING:root:This region does not appear to have coverage. Will not attempt to phase haplotypes.
2025-09-15 20:24:48.284 wdl.w:ptcp.w:call-paraphase-41.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for f8inv22 for sample m84036_250809_035451_s4.bc2138 at 2025-09-15 20:24:46.664446...
2025-09-15 20:24:48.284 wdl.w:ptcp.w:call-paraphase-41.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for rpgr for sample m84036_250809_035451_s4.bc2138 at 2025-09-15 20:24:46.689265...
2025-09-15 20:24:48.284 wdl.w:ptcp.w:call-paraphase-41.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for hbb for sample m84036_250809_035451_s4.bc2138 at 2025-09-15 20:24:46.817927...
2025-09-15 20:24:48.284 wdl.w:ptcp.w:call-paraphase-41.t:call-run_paraphase.stderr VERBOSE WARNING:root:This region does not appear to have coverage. Will not attempt to phase haplotypes.
2025-09-15 20:24:48.284 wdl.w:ptcp.w:call-paraphase-41.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for rpgr for sample m84036_250809_035451_s4.bc2138 at 2025-09-15 20:24:46.863845...
2025-09-15 20:24:48.284 wdl.w:ptcp.w:call-paraphase-41.t:call-run_paraphase.stderr VERBOSE WARNING:root:This region does not appear to have coverage. Will not attempt to phase haplotypes.
2025-09-15 20:24:48.285 wdl.w:ptcp.w:call-paraphase-41.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for hbb for sample m84036_250809_035451_s4.bc2138 at 2025-09-15 20:24:46.983062...
2025-09-15 20:24:48.285 wdl.w:ptcp.w:call-paraphase-41.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for f8inv22 for sample m84036_250809_035451_s4.bc2138 at 2025-09-15 20:24:47.166887...
2025-09-15 20:24:48.285 wdl.w:ptcp.w:call-paraphase-41.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for rpgr for sample m84036_250809_035451_s4.bc2138 at 2025-09-15 20:24:47.287029...
2025-09-15 20:24:48.285 wdl.w:ptcp.w:call-paraphase-41.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for hbb for sample m84036_250809_035451_s4.bc2138 at 2025-09-15 20:24:47.296495...
2025-09-15 20:24:48.285 wdl.w:ptcp.w:call-paraphase-41.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for smn1 for sample m84036_250809_035451_s4.bc2138 at 2025-09-15 20:24:47.326818...
2025-09-15 20:24:48.285 wdl.w:ptcp.w:call-paraphase-41.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for f8inv1 for sample m84036_250809_035451_s4.bc2138 at 2025-09-15 20:24:47.377368...
2025-09-15 20:24:48.285 wdl.w:ptcp.w:call-paraphase-41.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for f8inv1 for sample m84036_250809_035451_s4.bc2138 at 2025-09-15 20:24:47.377536...
2025-09-15 20:24:48.285 wdl.w:ptcp.w:call-paraphase-41.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for f8inv1 for sample m84036_250809_035451_s4.bc2138 at 2025-09-15 20:24:47.626655...
2025-09-15 20:24:48.285 wdl.w:ptcp.w:call-paraphase-41.t:call-run_paraphase.stderr VERBOSE WARNING:root:This region does not appear to have coverage. Will not attempt to phase haplotypes.
2025-09-15 20:24:48.285 wdl.w:ptcp.w:call-paraphase-41.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for f8inv1 for sample m84036_250809_035451_s4.bc2138 at 2025-09-15 20:24:47.688380...
2025-09-15 20:24:48.285 wdl.w:ptcp.w:call-paraphase-41.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for f8inv1 for sample m84036_250809_035451_s4.bc2138 at 2025-09-15 20:24:47.832276...
2025-09-15 20:24:48.291 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:46 [ERROR] - No reads found for TRID=SCA3_ATXN3
2025-09-15 20:24:48.292 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:46 [ERROR] - No reads found for TRID=SCA4_ZFHX3
2025-09-15 20:24:48.292 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:46 [ERROR] - No reads found for TRID=HDL2_JPH3
2025-09-15 20:24:48.292 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:46 [ERROR] - No reads found for TRID=OPDM4_RILPL1
2025-09-15 20:24:48.292 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:46 [ERROR] - No reads found for TRID=SCA31_BEAN1
2025-09-15 20:24:48.292 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:46 [ERROR] - No reads found for TRID=DM1_DMPK
2025-09-15 20:24:48.292 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:46 [ERROR] - No reads found for TRID=SCA6_CACNA1A
2025-09-15 20:24:48.292 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:46 [ERROR] - No reads found for TRID=SCA36_NOP56
2025-09-15 20:24:48.292 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:46 [ERROR] - No reads found for TRID=OPDM2_GIPC1
2025-09-15 20:24:48.292 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:47 [ERROR] - No reads found for TRID=EPM1_CSTB
2025-09-15 20:24:48.292 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:47 [ERROR] - No reads found for TRID=CJD_PRNP
2025-09-15 20:24:48.292 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:47 [ERROR] - No reads found for TRID=FRA2A_AFF3
2025-09-15 20:24:48.292 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:47 [ERROR] - No reads found for TRID=SD5_HOXD13
2025-09-15 20:24:48.320 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_plot_meth_allele NOTICE done
2025-09-15 20:24:48.326 wdl.w:ptcp.w:call-trgt-63 NOTICE finish :: job: "call-trgt_plot_meth_allele"
2025-09-15 20:24:48.326 wdl.w:ptcp.w:call-trgt-63 INFO output :: job: "call-trgt_plot_meth_allele", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-63/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2160.meth_allele.trgt_plots.zip"}
2025-09-15 20:24:48.327 wdl.w:ptcp.w:call-trgt-63 INFO visit :: node: "output-images_meth_allele", values: {"images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-63/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2160.meth_allele.trgt_plots.zip"}
2025-09-15 20:24:48.337 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_plot_meth_allele NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-62/call-trgt_plot_meth_allele", thread: 140610912642624
2025-09-15 20:24:48.339 wdl.w:ptcp.w:call-paraphase-22.t:call-run_paraphase INFO output :: name: "paraphase_bam", value: "m84036_250809_035451_s4.bc2119_paraphase/m84036_250809_035451_s4.bc2119.paraphase.bam"
2025-09-15 20:24:48.344 wdl.w:ptcp.w:call-paraphase-22.t:call-run_paraphase INFO output :: name: "paraphase_bam_bai", value: "m84036_250809_035451_s4.bc2119_paraphase/m84036_250809_035451_s4.bc2119.paraphase.bam.bai"
2025-09-15 20:24:48.346 wdl.w:ptcp.w:call-paraphase-22.t:call-run_paraphase INFO output :: name: "paraphase_json", value: "m84036_250809_035451_s4.bc2119_paraphase/m84036_250809_035451_s4.bc2119.paraphase.json"
2025-09-15 20:24:48.352 wdl.w:ptcp.w:call-paraphase-22.t:call-run_paraphase INFO output :: name: "paraphase_vcfs", value: ["/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2119_paraphase/m84036_250809_035451_s4.bc2119_paraphase_vcfs/m84036_250809_035451_s4.bc2119_cyp21.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2119_paraphase/m84036_250809_035451_s4.bc2119_paraphase_vcfs/m84036_250809_035451_s4.bc2119_f8inv1.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2119_paraphase/m84036_250809_035451_s4.bc2119_paraphase_vcfs/m84036_250809_035451_s4.bc2119_f8inv22.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2119_paraphase/m84036_250809_035451_s4.bc2119_paraphase_vcfs/m84036_250809_035451_s4.bc2119_gba.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2119_paraphase/m84036_250809_035451_s4.bc2119_paraphase_vcfs/m84036_250809_035451_s4.bc2119_hba.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2119_paraphase/m84036_250809_035451_s4.bc2119_paraphase_vcfs/m84036_250809_035451_s4.bc2119_hbb.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2119_paraphase/m84036_250809_035451_s4.bc2119_paraphase_vcfs/m84036_250809_035451_s4.bc2119_rpgr.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2119_paraphase/m84036_250809_035451_s4.bc2119_paraphase_vcfs/m84036_250809_035451_s4.bc2119_smn1.vcf"]
2025-09-15 20:24:48.357 wdl.w:ptcp.w:call-paraphase-40.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for gba for sample m84036_250809_035451_s4.bc2137 at 2025-09-15 20:24:44.685609...
2025-09-15 20:24:48.357 wdl.w:ptcp.w:call-paraphase-40.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for cyp21 for sample m84036_250809_035451_s4.bc2137 at 2025-09-15 20:24:44.689120...
2025-09-15 20:24:48.357 wdl.w:ptcp.w:call-paraphase-40.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for hba for sample m84036_250809_035451_s4.bc2137 at 2025-09-15 20:24:44.699100...
2025-09-15 20:24:48.357 wdl.w:ptcp.w:call-paraphase-40.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for smn1 for sample m84036_250809_035451_s4.bc2137 at 2025-09-15 20:24:44.716993...
2025-09-15 20:24:48.358 wdl.w:ptcp.w:call-paraphase-40.t:call-run_paraphase.stderr VERBOSE WARNING:root:This region does not appear to have coverage. Will not attempt to phase haplotypes.
2025-09-15 20:24:48.358 wdl.w:ptcp.w:call-paraphase-40.t:call-run_paraphase.stderr VERBOSE WARNING:root:This region does not appear to have coverage. Will not attempt to phase haplotypes.
2025-09-15 20:24:48.358 wdl.w:ptcp.w:call-paraphase-40.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for gba for sample m84036_250809_035451_s4.bc2137 at 2025-09-15 20:24:44.757792...
2025-09-15 20:24:48.358 wdl.w:ptcp.w:call-paraphase-40.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for cyp21 for sample m84036_250809_035451_s4.bc2137 at 2025-09-15 20:24:44.757809...
2025-09-15 20:24:48.358 wdl.w:ptcp.w:call-paraphase-40.t:call-run_paraphase.stderr VERBOSE WARNING:root:This region does not appear to have coverage. Will not attempt to phase haplotypes.
2025-09-15 20:24:48.358 wdl.w:ptcp.w:call-paraphase-40.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for hba for sample m84036_250809_035451_s4.bc2137 at 2025-09-15 20:24:44.758385...
2025-09-15 20:24:48.358 wdl.w:ptcp.w:call-paraphase-40.t:call-run_paraphase.stderr VERBOSE WARNING:root:This region does not appear to have coverage. Will not attempt to phase haplotypes.
2025-09-15 20:24:48.359 wdl.w:ptcp.w:call-paraphase-40.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for smn1 for sample m84036_250809_035451_s4.bc2137 at 2025-09-15 20:24:44.832078...
2025-09-15 20:24:48.359 wdl.w:ptcp.w:call-paraphase-40.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for gba for sample m84036_250809_035451_s4.bc2137 at 2025-09-15 20:24:45.235731...
2025-09-15 20:24:48.359 wdl.w:ptcp.w:call-paraphase-40.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for rpgr for sample m84036_250809_035451_s4.bc2137 at 2025-09-15 20:24:45.258091...
2025-09-15 20:24:48.359 wdl.w:ptcp.w:call-paraphase-40.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for rpgr for sample m84036_250809_035451_s4.bc2137 at 2025-09-15 20:24:45.258212...
2025-09-15 20:24:48.359 wdl.w:ptcp.w:call-paraphase-40.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for hba for sample m84036_250809_035451_s4.bc2137 at 2025-09-15 20:24:45.260898...
2025-09-15 20:24:48.359 wdl.w:ptcp.w:call-paraphase-40.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for hbb for sample m84036_250809_035451_s4.bc2137 at 2025-09-15 20:24:45.280766...
2025-09-15 20:24:48.359 wdl.w:ptcp.w:call-paraphase-40.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for hbb for sample m84036_250809_035451_s4.bc2137 at 2025-09-15 20:24:45.280849...
2025-09-15 20:24:48.359 wdl.w:ptcp.w:call-paraphase-40.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for cyp21 for sample m84036_250809_035451_s4.bc2137 at 2025-09-15 20:24:45.356034...
2025-09-15 20:24:48.359 wdl.w:ptcp.w:call-paraphase-40.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for f8inv22 for sample m84036_250809_035451_s4.bc2137 at 2025-09-15 20:24:45.387028...
2025-09-15 20:24:48.359 wdl.w:ptcp.w:call-paraphase-40.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for f8inv22 for sample m84036_250809_035451_s4.bc2137 at 2025-09-15 20:24:45.387208...
2025-09-15 20:24:48.359 wdl.w:ptcp.w:call-paraphase-40.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning to gene2 region for smn1 for sample m84036_250809_035451_s4.bc2137 at 2025-09-15 20:24:45.450988...
2025-09-15 20:24:48.360 wdl.w:ptcp.w:call-paraphase-40.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for rpgr for sample m84036_250809_035451_s4.bc2137 at 2025-09-15 20:24:46.479549...
2025-09-15 20:24:48.360 wdl.w:ptcp.w:call-paraphase-22.t:call-run_paraphase INFO output :: name: "havanno_json", value: "m84036_250809_035451_s4.bc2119.havanno.json"
2025-09-15 20:24:48.360 wdl.w:ptcp.w:call-paraphase-40.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for hbb for sample m84036_250809_035451_s4.bc2137 at 2025-09-15 20:24:46.592396...
2025-09-15 20:24:48.360 wdl.w:ptcp.w:call-paraphase-40.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for f8inv22 for sample m84036_250809_035451_s4.bc2137 at 2025-09-15 20:24:46.643301...
2025-09-15 20:24:48.360 wdl.w:ptcp.w:call-paraphase-40.t:call-run_paraphase.stderr VERBOSE WARNING:root:This region does not appear to have coverage. Will not attempt to phase haplotypes.
2025-09-15 20:24:48.360 wdl.w:ptcp.w:call-paraphase-40.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for rpgr for sample m84036_250809_035451_s4.bc2137 at 2025-09-15 20:24:46.726643...
2025-09-15 20:24:48.360 wdl.w:ptcp.w:call-paraphase-40.t:call-run_paraphase.stderr VERBOSE WARNING:root:This region does not appear to have coverage. Will not attempt to phase haplotypes.
2025-09-15 20:24:48.360 wdl.w:ptcp.w:call-paraphase-40.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for hbb for sample m84036_250809_035451_s4.bc2137 at 2025-09-15 20:24:46.797450...
2025-09-15 20:24:48.360 wdl.w:ptcp.w:call-paraphase-40.t:call-run_paraphase.stderr VERBOSE WARNING:root:This region does not appear to have coverage. Will not attempt to phase haplotypes.
2025-09-15 20:24:48.360 wdl.w:ptcp.w:call-paraphase-40.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for f8inv22 for sample m84036_250809_035451_s4.bc2137 at 2025-09-15 20:24:46.815320...
2025-09-15 20:24:48.360 wdl.w:ptcp.w:call-paraphase-40.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for rpgr for sample m84036_250809_035451_s4.bc2137 at 2025-09-15 20:24:47.247670...
2025-09-15 20:24:48.360 wdl.w:ptcp.w:call-paraphase-40.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for f8inv22 for sample m84036_250809_035451_s4.bc2137 at 2025-09-15 20:24:47.276504...
2025-09-15 20:24:48.360 wdl.w:ptcp.w:call-paraphase-40.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for hbb for sample m84036_250809_035451_s4.bc2137 at 2025-09-15 20:24:47.287440...
2025-09-15 20:24:48.360 wdl.w:ptcp.w:call-paraphase-40.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for smn1 for sample m84036_250809_035451_s4.bc2137 at 2025-09-15 20:24:47.308467...
2025-09-15 20:24:48.360 wdl.w:ptcp.w:call-paraphase-40.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for f8inv1 for sample m84036_250809_035451_s4.bc2137 at 2025-09-15 20:24:47.357378...
2025-09-15 20:24:48.361 wdl.w:ptcp.w:call-paraphase-40.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for f8inv1 for sample m84036_250809_035451_s4.bc2137 at 2025-09-15 20:24:47.357536...
2025-09-15 20:24:48.361 wdl.w:ptcp.w:call-paraphase-40.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for f8inv1 for sample m84036_250809_035451_s4.bc2137 at 2025-09-15 20:24:47.560848...
2025-09-15 20:24:48.361 wdl.w:ptcp.w:call-paraphase-40.t:call-run_paraphase.stderr VERBOSE WARNING:root:This region does not appear to have coverage. Will not attempt to phase haplotypes.
2025-09-15 20:24:48.361 wdl.w:ptcp.w:call-paraphase-40.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for f8inv1 for sample m84036_250809_035451_s4.bc2137 at 2025-09-15 20:24:47.585566...
2025-09-15 20:24:48.361 wdl.w:ptcp.w:call-paraphase-40.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for f8inv1 for sample m84036_250809_035451_s4.bc2137 at 2025-09-15 20:24:47.762790...
2025-09-15 20:24:48.364 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_plot_meth_allele INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:48.364 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_plot_meth_allele INFO input :: name: "waterfall", value: false
2025-09-15 20:24:48.364 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_plot_meth_allele INFO input :: name: "methylation", value: true
2025-09-15 20:24:48.364 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_plot_meth_allele INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:48.364 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_plot_meth_allele INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:48.364 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_plot_meth_allele INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:48.364 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_plot_meth_allele INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2159.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:48.364 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_plot_meth_allele INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2159.trgt.sorted.spanning.bam"
2025-09-15 20:24:48.364 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_plot_meth_allele INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2159.trgt.vcf"
2025-09-15 20:24:48.364 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_plot_meth_allele INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2159"
2025-09-15 20:24:48.364 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_plot_meth_allele INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:48.365 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_plot_meth_allele INFO eval :: name: "plot_type", value: "allele"
2025-09-15 20:24:48.365 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_plot_meth_allele INFO eval :: name: "show", value: "meth"
2025-09-15 20:24:48.365 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_plot_meth_allele INFO eval :: name: "threads", value: 1
2025-09-15 20:24:48.365 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_plot_meth_allele INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:48.365 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_plot_meth_allele INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2159.meth_allele"
2025-09-15 20:24:48.366 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_plot_meth_allele INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:48.366 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_plot_meth_allele WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:48.366 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_plot_meth_allele INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:48.366 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_plot_meth_allele INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:48.390 wdl.w:ptcp.w:call-trgt-67.t:call-trgt_genotype INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2164.trgt.vcf"
2025-09-15 20:24:48.396 wdl.w:ptcp.w:call-trgt-67.t:call-trgt_genotype INFO output :: name: "spanning_bam", value: "m84036_250809_035451_s4.bc2164.trgt.sorted.spanning.bam"
2025-09-15 20:24:48.398 wdl.w:ptcp.w:call-trgt-67.t:call-trgt_genotype INFO output :: name: "spanning_bam_bai", value: "m84036_250809_035451_s4.bc2164.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:48.431 wdl.w:ptcp.w:call-trgt-67.t:call-get_reads_overlapping_repeats INFO output :: name: "reads_overlapping_repeats", value: "m84036_250809_035451_s4.bc2164.repeats.bam"
2025-09-15 20:24:48.436 wdl.w:ptcp.w:call-trgt-67.t:call-get_reads_overlapping_repeats INFO output :: name: "reads_overlapping_repeats_bai", value: "m84036_250809_035451_s4.bc2164.repeats.bam.bai"
2025-09-15 20:24:48.507 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_plot_meth_allele INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-62/call-trgt_plot_meth_allele/_singularity_tmpdir_1da6myog"
2025-09-15 20:24:48.508 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_plot_meth_allele INFO Slurm invocation: srun --job-name call-trgt_plot_meth_allele --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-62/call-trgt_plot_meth_allele/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-62/call-trgt_plot_meth_allele/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-62/call-trgt_plot_meth_allele/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-62/call-trgt_plot_meth_allele/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-62/call-trgt_genotype/out/m84036_250809_035451_s4.bc2159.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2159.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-62/call-trgt_genotype/out/m84036_250809_035451_s4.bc2159.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2159.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-62/call-trgt_genotype/out/m84036_250809_035451_s4.bc2159.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2159.trgt.vcf:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-62/call-trgt_plot_meth_allele/_singularity_tmpdir_1da6myog/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-62/call-trgt_plot_meth_allele/_singularity_tmpdir_1da6myog/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:48.517 wdl.w:ptcp.w:call-trgt-67.t:call-trgt_genotype NOTICE done
2025-09-15 20:24:48.524 wdl.w:ptcp.w:call-trgt-67 NOTICE finish :: job: "call-trgt_genotype"
2025-09-15 20:24:48.524 wdl.w:ptcp.w:call-trgt-67 INFO output :: job: "call-trgt_genotype", values: {"spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-67/call-trgt_genotype/out/m84036_250809_035451_s4.bc2164.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-67/call-trgt_genotype/out/m84036_250809_035451_s4.bc2164.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-67/call-trgt_genotype/out/m84036_250809_035451_s4.bc2164.trgt.vcf"}
2025-09-15 20:24:48.525 wdl.w:ptcp.w:call-trgt-67 NOTICE ready :: job: "call-trgt_plot_meth_allele", callee: "trgt_plot"
2025-09-15 20:24:48.525 wdl.w:ptcp.w:call-trgt-67 INFO input :: job: "call-trgt_plot_meth_allele", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": false, "methylation": true, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-67/call-trgt_genotype/out/m84036_250809_035451_s4.bc2164.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-67/call-trgt_genotype/out/m84036_250809_035451_s4.bc2164.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-67/call-trgt_genotype/out/m84036_250809_035451_s4.bc2164.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2164"}
2025-09-15 20:24:48.527 wdl.w:ptcp.w:call-trgt-67 NOTICE ready :: job: "call-trgt_plot_meth_waterfall", callee: "trgt_plot"
2025-09-15 20:24:48.527 wdl.w:ptcp.w:call-trgt-67 INFO input :: job: "call-trgt_plot_meth_waterfall", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": true, "methylation": true, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-67/call-trgt_genotype/out/m84036_250809_035451_s4.bc2164.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-67/call-trgt_genotype/out/m84036_250809_035451_s4.bc2164.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-67/call-trgt_genotype/out/m84036_250809_035451_s4.bc2164.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2164"}
2025-09-15 20:24:48.528 wdl.w:ptcp.w:call-trgt-67 NOTICE ready :: job: "call-trgt_plot_motifs_allele", callee: "trgt_plot"
2025-09-15 20:24:48.528 wdl.w:ptcp.w:call-trgt-67 INFO input :: job: "call-trgt_plot_motifs_allele", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": false, "methylation": false, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-67/call-trgt_genotype/out/m84036_250809_035451_s4.bc2164.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-67/call-trgt_genotype/out/m84036_250809_035451_s4.bc2164.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-67/call-trgt_genotype/out/m84036_250809_035451_s4.bc2164.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2164"}
2025-09-15 20:24:48.529 wdl.w:ptcp.w:call-trgt-67 NOTICE ready :: job: "call-trgt_plot_motifs_waterfall", callee: "trgt_plot"
2025-09-15 20:24:48.529 wdl.w:ptcp.w:call-trgt-67 INFO input :: job: "call-trgt_plot_motifs_waterfall", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": true, "methylation": false, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-67/call-trgt_genotype/out/m84036_250809_035451_s4.bc2164.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-67/call-trgt_genotype/out/m84036_250809_035451_s4.bc2164.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-67/call-trgt_genotype/out/m84036_250809_035451_s4.bc2164.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2164"}
2025-09-15 20:24:48.530 wdl.w:ptcp.w:call-trgt-67 INFO visit :: node: "output-spanning_bam", values: {"spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-67/call-trgt_genotype/out/m84036_250809_035451_s4.bc2164.trgt.sorted.spanning.bam"}
2025-09-15 20:24:48.530 wdl.w:ptcp.w:call-trgt-67 INFO visit :: node: "output-spanning_bam_bai", values: {"spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-67/call-trgt_genotype/out/m84036_250809_035451_s4.bc2164.trgt.sorted.spanning.bam.bai"}
2025-09-15 20:24:48.530 wdl.w:ptcp.w:call-trgt-67 INFO visit :: node: "output-vcf", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-67/call-trgt_genotype/out/m84036_250809_035451_s4.bc2164.trgt.vcf"}
2025-09-15 20:24:48.537 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_plot_meth_waterfall NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-62/call-trgt_plot_meth_waterfall", thread: 140609302029888
2025-09-15 20:24:48.544 wdl.w:ptcp.w:call-trgt-67.t:call-get_reads_overlapping_repeats NOTICE done
2025-09-15 20:24:48.551 wdl.w:ptcp.w:call-trgt-67 NOTICE finish :: job: "call-get_reads_overlapping_repeats"
2025-09-15 20:24:48.551 wdl.w:ptcp.w:call-trgt-67 INFO output :: job: "call-get_reads_overlapping_repeats", values: {"reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-67/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2164.repeats.bam.bai", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-67/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2164.repeats.bam"}
2025-09-15 20:24:48.552 wdl.w:ptcp.w:call-trgt-67 INFO visit :: node: "output-reads_overlapping_repeats", values: {"reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-67/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2164.repeats.bam"}
2025-09-15 20:24:48.552 wdl.w:ptcp.w:call-trgt-67 INFO visit :: node: "output-reads_overlapping_repeats_bai", values: {"reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-67/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2164.repeats.bam.bai"}
2025-09-15 20:24:48.560 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_plot_motifs_waterfall INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2160.motifs_waterfall.trgt_plots.zip"
2025-09-15 20:24:48.561 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_plot_motifs_allele NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-62/call-trgt_plot_motifs_allele", thread: 140607649453632
2025-09-15 20:24:48.563 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_plot_meth_waterfall INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:48.563 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_plot_meth_waterfall INFO input :: name: "waterfall", value: true
2025-09-15 20:24:48.563 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_plot_meth_waterfall INFO input :: name: "methylation", value: true
2025-09-15 20:24:48.563 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_plot_meth_waterfall INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:48.563 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_plot_meth_waterfall INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:48.563 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_plot_meth_waterfall INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:48.563 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_plot_meth_waterfall INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2159.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:48.564 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_plot_meth_waterfall INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2159.trgt.sorted.spanning.bam"
2025-09-15 20:24:48.564 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_plot_meth_waterfall INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2159.trgt.vcf"
2025-09-15 20:24:48.564 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_plot_meth_waterfall INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2159"
2025-09-15 20:24:48.565 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_plot_meth_waterfall INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:48.566 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_plot_meth_waterfall INFO eval :: name: "plot_type", value: "waterfall"
2025-09-15 20:24:48.566 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_plot_meth_waterfall INFO eval :: name: "show", value: "meth"
2025-09-15 20:24:48.566 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_plot_meth_waterfall INFO eval :: name: "threads", value: 1
2025-09-15 20:24:48.567 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_plot_meth_waterfall INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:48.567 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_plot_meth_waterfall INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2159.meth_waterfall"
2025-09-15 20:24:48.567 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_plot_meth_waterfall INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:48.567 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_plot_meth_waterfall WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:48.568 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_plot_meth_waterfall INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:48.568 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_plot_meth_waterfall INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:48.572 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_plot_meth_allele NOTICE slurm_singularity run :: pid: 1203181, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-62/call-trgt_plot_meth_allele/slurm_singularity.log.txt"
2025-09-15 20:24:48.584 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_plot_motifs_allele INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:48.584 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_plot_motifs_allele INFO input :: name: "waterfall", value: false
2025-09-15 20:24:48.584 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_plot_motifs_allele INFO input :: name: "methylation", value: false
2025-09-15 20:24:48.585 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_plot_motifs_allele INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:48.585 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_plot_motifs_allele INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:48.585 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_plot_motifs_allele INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:48.585 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_plot_motifs_allele INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2159.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:48.585 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_plot_motifs_allele INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2159.trgt.sorted.spanning.bam"
2025-09-15 20:24:48.585 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_plot_motifs_allele INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2159.trgt.vcf"
2025-09-15 20:24:48.585 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_plot_motifs_allele INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2159"
2025-09-15 20:24:48.585 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_plot_motifs_allele INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:48.586 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_plot_motifs_allele INFO eval :: name: "plot_type", value: "allele"
2025-09-15 20:24:48.586 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_plot_motifs_allele INFO eval :: name: "show", value: "motifs"
2025-09-15 20:24:48.586 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_plot_motifs_allele INFO eval :: name: "threads", value: 1
2025-09-15 20:24:48.586 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_plot_motifs_allele INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:48.586 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_plot_motifs_allele INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2159.motifs_allele"
2025-09-15 20:24:48.586 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_plot_motifs_allele INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:48.587 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_plot_motifs_allele WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:48.587 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_plot_motifs_allele INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:48.587 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_plot_motifs_allele INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:48.594 wdl.w:ptcp.w:call-sawfish-64.t:call-run_sawfish.stderr VERBOSE [M::bam2fq_mainloop] discarded 0 singletons
2025-09-15 20:24:48.594 wdl.w:ptcp.w:call-sawfish-64.t:call-run_sawfish.stderr VERBOSE [M::bam2fq_mainloop] processed 1 reads
2025-09-15 20:24:48.607 wdl.w:ptcp.w:call-trgt-64.t:call-get_reads_overlapping_repeats.slurm_singularity INFO srun: job 51797796 queued and waiting for resources
2025-09-15 20:24:48.607 wdl.w:ptcp.w:call-trgt-64.t:call-get_reads_overlapping_repeats.slurm_singularity INFO srun: job 51797796 has been allocated resources
2025-09-15 20:24:48.607 wdl.w:ptcp.w:call-trgt-64.t:call-get_reads_overlapping_repeats.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:48.610 wdl.w:ptcp.w:call-sawfish-64.t:call-run_sawfish.slurm_singularity INFO srun: job 51797797 queued and waiting for resources
2025-09-15 20:24:48.610 wdl.w:ptcp.w:call-sawfish-64.t:call-run_sawfish.slurm_singularity INFO srun: job 51797797 has been allocated resources
2025-09-15 20:24:48.610 wdl.w:ptcp.w:call-sawfish-64.t:call-run_sawfish.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:48.670 wdl.w:ptcp.w:call-paraphase-22.t:call-run_paraphase NOTICE done
2025-09-15 20:24:48.677 wdl.w:ptcp.w:call-paraphase-22 NOTICE finish :: job: "call-run_paraphase"
2025-09-15 20:24:48.677 wdl.w:ptcp.w:call-paraphase-22 INFO output :: job: "call-run_paraphase", values: {"havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-22/call-run_paraphase/out/m84036_250809_035451_s4.bc2119.havanno.json", "paraphase_vcfs": ["/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-22/call-run_paraphase/out/m84036_250809_035451_s4.bc2119_paraphase/m84036_250809_035451_s4.bc2119_paraphase_vcfs/m84036_250809_035451_s4.bc2119_cyp21.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-22/call-run_paraphase/out/m84036_250809_035451_s4.bc2119_paraphase/m84036_250809_035451_s4.bc2119_paraphase_vcfs/m84036_250809_035451_s4.bc2119_f8inv1.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-22/call-run_paraphase/out/m84036_250809_035451_s4.bc2119_paraphase/m84036_250809_035451_s4.bc2119_paraphase_vcfs/m84036_250809_035451_s4.bc2119_f8inv22.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-22/call-run_paraphase/out/m84036_250809_035451_s4.bc2119_paraphase/m84036_250809_035451_s4.bc2119_paraphase_vcfs/m84036_250809_035451_s4.bc2119_gba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-22/call-run_paraphase/out/m84036_250809_035451_s4.bc2119_paraphase/m84036_250809_035451_s4.bc2119_paraphase_vcfs/m84036_250809_035451_s4.bc2119_hba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-22/call-run_paraphase/out/m84036_250809_035451_s4.bc2119_paraphase/m84036_250809_035451_s4.bc2119_paraphase_vcfs/m84036_250809_035451_s4.bc2119_hbb.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-22/call-run_paraphase/out/m84036_250809_035451_s4.bc2119_paraphase/m84036_250809_035451_s4.bc2119_paraphase_vcfs/m84036_250809_035451_s4.bc2119_rpgr.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-22/call-run_paraphase/out/m84036_250809_035451_s4.bc2119_paraphase/m84036_250809_035451_s4.bc2119_paraphase_vcfs/m84036_250809_035451_s4.bc2119_smn1.vcf"], "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-22/call-run_paraphase/out/m84036_250809_035451_s4.bc2119_paraphase/m84036_250809_035451_s4.bc2119.paraphase.json", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-22/call-run_paraphase/out/m84036_250809_035451_s4.bc2119_paraphase/m84036_250809_035451_s4.bc2119.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-22/call-run_paraphase/out/m84036_250809_035451_s4.bc2119_paraphase/m84036_250809_035451_s4.bc2119.paraphase.bam"}
2025-09-15 20:24:48.678 wdl.w:ptcp.w:call-paraphase-22 NOTICE ready :: job: "call-call_f8", callee: "call_f8"
2025-09-15 20:24:48.678 wdl.w:ptcp.w:call-paraphase-22 INFO input :: job: "call-call_f8", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "out_prefix": "m84036_250809_035451_s4.bc2119", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-22/call-run_paraphase/out/m84036_250809_035451_s4.bc2119_paraphase/m84036_250809_035451_s4.bc2119.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-22/call-run_paraphase/out/m84036_250809_035451_s4.bc2119_paraphase/m84036_250809_035451_s4.bc2119.paraphase.bam", "sex": "F"}
2025-09-15 20:24:48.679 wdl.w:ptcp.w:call-paraphase-22 INFO visit :: node: "output-havanno_json", values: {"havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-22/call-run_paraphase/out/m84036_250809_035451_s4.bc2119.havanno.json"}
2025-09-15 20:24:48.679 wdl.w:ptcp.w:call-paraphase-22 INFO visit :: node: "output-paraphase_bam", values: {"paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-22/call-run_paraphase/out/m84036_250809_035451_s4.bc2119_paraphase/m84036_250809_035451_s4.bc2119.paraphase.bam"}
2025-09-15 20:24:48.679 wdl.w:ptcp.w:call-paraphase-22 INFO visit :: node: "output-paraphase_bam_bai", values: {"paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-22/call-run_paraphase/out/m84036_250809_035451_s4.bc2119_paraphase/m84036_250809_035451_s4.bc2119.paraphase.bam.bai"}
2025-09-15 20:24:48.680 wdl.w:ptcp.w:call-paraphase-22 INFO visit :: node: "output-paraphase_json", values: {"paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-22/call-run_paraphase/out/m84036_250809_035451_s4.bc2119_paraphase/m84036_250809_035451_s4.bc2119.paraphase.json"}
2025-09-15 20:24:48.680 wdl.w:ptcp.w:call-paraphase-22 INFO visit :: node: "output-paraphase_vcfs", values: {"paraphase_vcfs": ["/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-22/call-run_paraphase/out/m84036_250809_035451_s4.bc2119_paraphase/m84036_250809_035451_s4.bc2119_paraphase_vcfs/m84036_250809_035451_s4.bc2119_cyp21.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-22/call-run_paraphase/out/m84036_250809_035451_s4.bc2119_paraphase/m84036_250809_035451_s4.bc2119_paraphase_vcfs/m84036_250809_035451_s4.bc2119_f8inv1.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-22/call-run_paraphase/out/m84036_250809_035451_s4.bc2119_paraphase/m84036_250809_035451_s4.bc2119_paraphase_vcfs/m84036_250809_035451_s4.bc2119_f8inv22.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-22/call-run_paraphase/out/m84036_250809_035451_s4.bc2119_paraphase/m84036_250809_035451_s4.bc2119_paraphase_vcfs/m84036_250809_035451_s4.bc2119_gba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-22/call-run_paraphase/out/m84036_250809_035451_s4.bc2119_paraphase/m84036_250809_035451_s4.bc2119_paraphase_vcfs/m84036_250809_035451_s4.bc2119_hba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-22/call-run_paraphase/out/m84036_250809_035451_s4.bc2119_paraphase/m84036_250809_035451_s4.bc2119_paraphase_vcfs/m84036_250809_035451_s4.bc2119_hbb.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-22/call-run_paraphase/out/m84036_250809_035451_s4.bc2119_paraphase/m84036_250809_035451_s4.bc2119_paraphase_vcfs/m84036_250809_035451_s4.bc2119_rpgr.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-22/call-run_paraphase/out/m84036_250809_035451_s4.bc2119_paraphase/m84036_250809_035451_s4.bc2119_paraphase_vcfs/m84036_250809_035451_s4.bc2119_smn1.vcf"]}
2025-09-15 20:24:48.685 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_plot_motifs_waterfall NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-62/call-trgt_plot_motifs_waterfall", thread: 140612481291840
2025-09-15 20:24:48.694 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_plot_meth_waterfall INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-62/call-trgt_plot_meth_waterfall/_singularity_tmpdir_ph50tquj"
2025-09-15 20:24:48.695 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_plot_meth_waterfall INFO Slurm invocation: srun --job-name call-trgt_plot_meth_waterfall --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-62/call-trgt_plot_meth_waterfall/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-62/call-trgt_plot_meth_waterfall/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-62/call-trgt_plot_meth_waterfall/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-62/call-trgt_plot_meth_waterfall/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-62/call-trgt_genotype/out/m84036_250809_035451_s4.bc2159.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2159.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-62/call-trgt_genotype/out/m84036_250809_035451_s4.bc2159.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2159.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-62/call-trgt_genotype/out/m84036_250809_035451_s4.bc2159.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2159.trgt.vcf:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-62/call-trgt_plot_meth_waterfall/_singularity_tmpdir_ph50tquj/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-62/call-trgt_plot_meth_waterfall/_singularity_tmpdir_ph50tquj/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:48.696 wdl.w:ptcp.w:call-paraphase-52.t:call-call_f8 INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2149.f8inversion.vcf"
2025-09-15 20:24:48.704 wdl.w:ptcp.w:call-paraphase-52.t:call-call_f8 INFO output :: name: "json", value: "m84036_250809_035451_s4.bc2149.f8inversion.json"
2025-09-15 20:24:48.708 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_plot_motifs_waterfall INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:48.708 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_plot_motifs_waterfall INFO input :: name: "waterfall", value: true
2025-09-15 20:24:48.709 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_plot_motifs_waterfall INFO input :: name: "methylation", value: false
2025-09-15 20:24:48.709 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_plot_motifs_waterfall INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:48.709 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_plot_motifs_waterfall INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:48.709 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_plot_motifs_waterfall INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:48.709 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_plot_motifs_waterfall INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2159.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:48.709 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_plot_motifs_waterfall INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2159.trgt.sorted.spanning.bam"
2025-09-15 20:24:48.709 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_plot_motifs_waterfall INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2159.trgt.vcf"
2025-09-15 20:24:48.709 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_plot_motifs_waterfall INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2159"
2025-09-15 20:24:48.709 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:48.709 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "plot_type", value: "waterfall"
2025-09-15 20:24:48.709 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_plot_motifs_waterfall NOTICE done
2025-09-15 20:24:48.710 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "show", value: "motifs"
2025-09-15 20:24:48.710 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "threads", value: 1
2025-09-15 20:24:48.710 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:48.710 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2159.motifs_waterfall"
2025-09-15 20:24:48.711 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_plot_motifs_waterfall INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:48.711 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_plot_motifs_waterfall WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:48.711 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_plot_motifs_waterfall INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:48.711 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_plot_motifs_waterfall INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:48.715 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_plot_motifs_allele INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-62/call-trgt_plot_motifs_allele/_singularity_tmpdir_oexn_4bp"
2025-09-15 20:24:48.715 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_plot_motifs_allele INFO Slurm invocation: srun --job-name call-trgt_plot_motifs_allele --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-62/call-trgt_plot_motifs_allele/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-62/call-trgt_plot_motifs_allele/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-62/call-trgt_plot_motifs_allele/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-62/call-trgt_plot_motifs_allele/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-62/call-trgt_genotype/out/m84036_250809_035451_s4.bc2159.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2159.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-62/call-trgt_genotype/out/m84036_250809_035451_s4.bc2159.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2159.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-62/call-trgt_genotype/out/m84036_250809_035451_s4.bc2159.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2159.trgt.vcf:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-62/call-trgt_plot_motifs_allele/_singularity_tmpdir_oexn_4bp/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-62/call-trgt_plot_motifs_allele/_singularity_tmpdir_oexn_4bp/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:48.717 wdl.w:ptcp.w:call-trgt-63 NOTICE finish :: job: "call-trgt_plot_motifs_waterfall"
2025-09-15 20:24:48.718 wdl.w:ptcp.w:call-trgt-63 INFO output :: job: "call-trgt_plot_motifs_waterfall", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-63/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2160.motifs_waterfall.trgt_plots.zip"}
2025-09-15 20:24:48.718 wdl.w:ptcp.w:call-trgt-63 INFO visit :: node: "output-images_motifs_waterfall", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-63/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2160.motifs_waterfall.trgt_plots.zip"}
2025-09-15 20:24:48.727 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_plot_motifs_allele NOTICE slurm_singularity run :: pid: 1203191, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-62/call-trgt_plot_motifs_allele/slurm_singularity.log.txt"
2025-09-15 20:24:48.727 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_plot_meth_waterfall NOTICE slurm_singularity run :: pid: 1203190, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-62/call-trgt_plot_meth_waterfall/slurm_singularity.log.txt"
2025-09-15 20:24:48.733 wdl.w:ptcp.w:call-paraphase-69.t:call-run_paraphase NOTICE task setup :: name: "run_paraphase", source: "./paraphase.wdl", line: 127, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-69/call-run_paraphase", thread: 140613571819072
2025-09-15 20:24:48.766 wdl.w:ptcp.w:call-paraphase-69.t:call-run_paraphase INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:48.766 wdl.w:ptcp.w:call-paraphase-69.t:call-run_paraphase INFO input :: name: "annotation_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf"
2025-09-15 20:24:48.766 wdl.w:ptcp.w:call-paraphase-69.t:call-run_paraphase INFO input :: name: "genome_version", value: "38"
2025-09-15 20:24:48.766 wdl.w:ptcp.w:call-paraphase-69.t:call-run_paraphase INFO input :: name: "config_file", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/paraphase_config.GRCh38.yaml"
2025-09-15 20:24:48.766 wdl.w:ptcp.w:call-paraphase-69.t:call-run_paraphase INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:48.766 wdl.w:ptcp.w:call-paraphase-69.t:call-run_paraphase INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:48.766 wdl.w:ptcp.w:call-paraphase-69.t:call-run_paraphase INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2166.mapped.bam.bai"
2025-09-15 20:24:48.766 wdl.w:ptcp.w:call-paraphase-69.t:call-run_paraphase INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2166.mapped.bam"
2025-09-15 20:24:48.766 wdl.w:ptcp.w:call-paraphase-69.t:call-run_paraphase INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2166"
2025-09-15 20:24:48.767 wdl.w:ptcp.w:call-paraphase-69.t:call-run_paraphase INFO eval :: name: "threads", value: 4
2025-09-15 20:24:48.767 wdl.w:ptcp.w:call-paraphase-69.t:call-run_paraphase INFO eval :: name: "mem_gb", value: 8
2025-09-15 20:24:48.767 wdl.w:ptcp.w:call-paraphase-69.t:call-run_paraphase INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:48.767 wdl.w:ptcp.w:call-paraphase-69.t:call-run_paraphase INFO eval :: name: "out_dir", value: "m84036_250809_035451_s4.bc2166_paraphase"
2025-09-15 20:24:48.767 wdl.w:ptcp.w:call-paraphase-69.t:call-run_paraphase INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 4, memory_reservation: 8000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:48.768 wdl.w:ptcp.w:call-paraphase-69.t:call-run_paraphase WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:48.768 wdl.w:ptcp.w:call-paraphase-69.t:call-run_paraphase INFO provisioned :: seconds_waited: 0, cpu: 4, mem_bytes: 8000000000
2025-09-15 20:24:48.768 wdl.w:ptcp.w:call-paraphase-69.t:call-run_paraphase INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:48.784 wdl.w:ptcp.w:call-trgt-52.t:call-trgt_plot_meth_waterfall INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2149.meth_waterfall.trgt_plots.zip"
2025-09-15 20:24:48.799 wdl.w:ptcp.w:call-paraphase-52.t:call-call_f8 NOTICE done
2025-09-15 20:24:48.817 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_plot_motifs_waterfall INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-62/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_fs_qdy9w"
2025-09-15 20:24:48.817 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_plot_motifs_waterfall INFO Slurm invocation: srun --job-name call-trgt_plot_motifs_waterfall --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-62/call-trgt_plot_motifs_waterfall/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-62/call-trgt_plot_motifs_waterfall/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-62/call-trgt_plot_motifs_waterfall/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-62/call-trgt_plot_motifs_waterfall/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-62/call-trgt_genotype/out/m84036_250809_035451_s4.bc2159.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2159.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-62/call-trgt_genotype/out/m84036_250809_035451_s4.bc2159.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2159.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-62/call-trgt_genotype/out/m84036_250809_035451_s4.bc2159.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2159.trgt.vcf:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-62/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_fs_qdy9w/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-62/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_fs_qdy9w/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:48.849 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_plot_motifs_waterfall NOTICE slurm_singularity run :: pid: 1203207, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-62/call-trgt_plot_motifs_waterfall/slurm_singularity.log.txt"
2025-09-15 20:24:48.855 wdl.w:ptcp.w:call-paraphase-52 NOTICE finish :: job: "call-call_f8"
2025-09-15 20:24:48.855 wdl.w:ptcp.w:call-paraphase-52 INFO output :: job: "call-call_f8", values: {"json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-52/call-call_f8/out/m84036_250809_035451_s4.bc2149.f8inversion.json", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-52/call-call_f8/out/m84036_250809_035451_s4.bc2149.f8inversion.vcf"}
2025-09-15 20:24:48.856 wdl.w:ptcp.w:call-paraphase-52 INFO visit :: node: "output-f8_json", values: {"f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-52/call-call_f8/out/m84036_250809_035451_s4.bc2149.f8inversion.json"}
2025-09-15 20:24:48.856 wdl.w:ptcp.w:call-paraphase-52 INFO visit :: node: "output-f8_vcf", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-52/call-call_f8/out/m84036_250809_035451_s4.bc2149.f8inversion.vcf"}
2025-09-15 20:24:48.856 wdl.w:ptcp.w:call-paraphase-52 INFO visit :: node: "outputs", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-52/call-call_f8/out/m84036_250809_035451_s4.bc2149.f8inversion.vcf", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-52/call-run_paraphase/out/m84036_250809_035451_s4.bc2149_paraphase/m84036_250809_035451_s4.bc2149.paraphase.json", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-52/call-run_paraphase/out/m84036_250809_035451_s4.bc2149_paraphase/m84036_250809_035451_s4.bc2149.paraphase.bam", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-52/call-run_paraphase/out/m84036_250809_035451_s4.bc2149_paraphase/m84036_250809_035451_s4.bc2149.paraphase.bam.bai", "paraphase_vcfs": [], "havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-52/call-run_paraphase/out/m84036_250809_035451_s4.bc2149.havanno.json", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-52/call-call_f8/out/m84036_250809_035451_s4.bc2149.f8inversion.json"}
2025-09-15 20:24:48.867 wdl.w:ptcp.w:call-trgt-41.t:call-trgt_plot_meth_allele NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-41/call-trgt_plot_meth_allele", thread: 140609310422592
2025-09-15 20:24:48.871 wdl.w:ptcp.w:call-paraphase-53.t:call-run_paraphase INFO output :: name: "paraphase_bam", value: "m84036_250809_035451_s4.bc2150_paraphase/m84036_250809_035451_s4.bc2150.paraphase.bam"
2025-09-15 20:24:48.872 wdl.w:ptcp.w:call-paraphase-40.t:call-run_paraphase INFO output :: name: "paraphase_bam", value: "m84036_250809_035451_s4.bc2137_paraphase/m84036_250809_035451_s4.bc2137.paraphase.bam"
2025-09-15 20:24:48.880 wdl.w:ptcp.w:call-paraphase-53.t:call-run_paraphase INFO output :: name: "paraphase_bam_bai", value: "m84036_250809_035451_s4.bc2150_paraphase/m84036_250809_035451_s4.bc2150.paraphase.bam.bai"
2025-09-15 20:24:48.880 wdl.w:ptcp.w:call-paraphase-40.t:call-run_paraphase INFO output :: name: "paraphase_bam_bai", value: "m84036_250809_035451_s4.bc2137_paraphase/m84036_250809_035451_s4.bc2137.paraphase.bam.bai"
2025-09-15 20:24:48.884 wdl.w:ptcp.w:call-paraphase-53.t:call-run_paraphase INFO output :: name: "paraphase_json", value: "m84036_250809_035451_s4.bc2150_paraphase/m84036_250809_035451_s4.bc2150.paraphase.json"
2025-09-15 20:24:48.884 wdl.w:ptcp.w:call-paraphase-40.t:call-run_paraphase INFO output :: name: "paraphase_json", value: "m84036_250809_035451_s4.bc2137_paraphase/m84036_250809_035451_s4.bc2137.paraphase.json"
2025-09-15 20:24:48.888 wdl.w:ptcp.w:call-paraphase-53.t:call-run_paraphase INFO output :: name: "paraphase_vcfs", value: []
2025-09-15 20:24:48.888 wdl.w:ptcp.w:call-paraphase-40.t:call-run_paraphase INFO output :: name: "paraphase_vcfs", value: []
2025-09-15 20:24:48.889 wdl.w:ptcp.w:call-paraphase-53.t:call-run_paraphase INFO output :: name: "havanno_json", value: "m84036_250809_035451_s4.bc2150.havanno.json"
2025-09-15 20:24:48.889 wdl.w:ptcp.w:call-paraphase-40.t:call-run_paraphase INFO output :: name: "havanno_json", value: "m84036_250809_035451_s4.bc2137.havanno.json"
2025-09-15 20:24:48.897 wdl.w:ptcp.w:call-paraphase-69.t:call-run_paraphase INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-69/call-run_paraphase/_singularity_tmpdir_ma_la4vo"
2025-09-15 20:24:48.897 wdl.w:ptcp.w:call-paraphase-69.t:call-run_paraphase INFO Slurm invocation: srun --job-name call-run_paraphase --partition compute,compute9 --cpus-per-task 4 --mem 7629M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-69/call-run_paraphase/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-69/call-run_paraphase/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-69/call-run_paraphase/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-69/call-run_paraphase/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-69/out/m84036_250809_035451_s4.bc2166.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2166.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-69/out/m84036_250809_035451_s4.bc2166.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2166.mapped.bam:ro --bind /ptcp/meta/variant_list/variant_list.GRCh38.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf:ro --bind /ptcp/meta/paraphase/paraphase_config.GRCh38.yaml:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/paraphase_config.GRCh38.yaml:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-69/call-run_paraphase/_singularity_tmpdir_ma_la4vo/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-69/call-run_paraphase/_singularity_tmpdir_ma_la4vo/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:48.898 wdl.w:ptcp.w:call-trgt-64.t:call-trgt_genotype.slurm_singularity INFO srun: job 51797798 queued and waiting for resources
2025-09-15 20:24:48.898 wdl.w:ptcp.w:call-trgt-41.t:call-trgt_plot_meth_allele INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:48.899 wdl.w:ptcp.w:call-trgt-64.t:call-trgt_genotype.slurm_singularity INFO srun: job 51797798 has been allocated resources
2025-09-15 20:24:48.899 wdl.w:ptcp.w:call-trgt-41.t:call-trgt_plot_meth_allele INFO input :: name: "waterfall", value: false
2025-09-15 20:24:48.899 wdl.w:ptcp.w:call-trgt-64.t:call-trgt_genotype.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:48.899 wdl.w:ptcp.w:call-trgt-41.t:call-trgt_plot_meth_allele INFO input :: name: "methylation", value: true
2025-09-15 20:24:48.899 wdl.w:ptcp.w:call-trgt-41.t:call-trgt_plot_meth_allele INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:48.900 wdl.w:ptcp.w:call-trgt-41.t:call-trgt_plot_meth_allele INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:48.900 wdl.w:ptcp.w:call-trgt-41.t:call-trgt_plot_meth_allele INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:48.900 wdl.w:ptcp.w:call-trgt-41.t:call-trgt_plot_meth_allele INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2138.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:48.900 wdl.w:ptcp.w:call-trgt-41.t:call-trgt_plot_meth_allele INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2138.trgt.sorted.spanning.bam"
2025-09-15 20:24:48.900 wdl.w:ptcp.w:call-trgt-41.t:call-trgt_plot_meth_allele INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2138.trgt.vcf"
2025-09-15 20:24:48.900 wdl.w:ptcp.w:call-trgt-41.t:call-trgt_plot_meth_allele INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2138"
2025-09-15 20:24:48.901 wdl.w:ptcp.w:call-trgt-41.t:call-trgt_plot_meth_allele INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:48.901 wdl.w:ptcp.w:call-trgt-41.t:call-trgt_plot_meth_allele INFO eval :: name: "plot_type", value: "allele"
2025-09-15 20:24:48.901 wdl.w:ptcp.w:call-trgt-41.t:call-trgt_plot_meth_allele INFO eval :: name: "show", value: "meth"
2025-09-15 20:24:48.901 wdl.w:ptcp.w:call-trgt-41.t:call-trgt_plot_meth_allele INFO eval :: name: "threads", value: 1
2025-09-15 20:24:48.902 wdl.w:ptcp.w:call-trgt-41.t:call-trgt_plot_meth_allele INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:48.902 wdl.w:ptcp.w:call-trgt-41.t:call-trgt_plot_meth_allele INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2138.meth_allele"
2025-09-15 20:24:48.902 wdl.w:ptcp.w:call-trgt-41.t:call-trgt_plot_meth_allele INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:48.902 wdl.w:ptcp.w:call-trgt-41.t:call-trgt_plot_meth_allele WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:48.902 wdl.w:ptcp.w:call-trgt-41.t:call-trgt_plot_meth_allele INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:48.903 wdl.w:ptcp.w:call-trgt-41.t:call-trgt_plot_meth_allele INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:48.905 wdl.w:ptcp.w:call-paraphase-41.t:call-run_paraphase INFO output :: name: "paraphase_bam", value: "m84036_250809_035451_s4.bc2138_paraphase/m84036_250809_035451_s4.bc2138.paraphase.bam"
2025-09-15 20:24:48.912 wdl.w:ptcp.w:call-paraphase-41.t:call-run_paraphase INFO output :: name: "paraphase_bam_bai", value: "m84036_250809_035451_s4.bc2138_paraphase/m84036_250809_035451_s4.bc2138.paraphase.bam.bai"
2025-09-15 20:24:48.914 wdl.w:ptcp.w:call-paraphase-41.t:call-run_paraphase INFO output :: name: "paraphase_json", value: "m84036_250809_035451_s4.bc2138_paraphase/m84036_250809_035451_s4.bc2138.paraphase.json"
2025-09-15 20:24:48.917 wdl.w:ptcp.w:call-paraphase-41.t:call-run_paraphase INFO output :: name: "paraphase_vcfs", value: []
2025-09-15 20:24:48.918 wdl.w:ptcp.w:call-paraphase-41.t:call-run_paraphase INFO output :: name: "havanno_json", value: "m84036_250809_035451_s4.bc2138.havanno.json"
2025-09-15 20:24:48.937 wdl.w:ptcp.w:call-paraphase-69.t:call-run_paraphase NOTICE slurm_singularity run :: pid: 1203215, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-69/call-run_paraphase/slurm_singularity.log.txt"
2025-09-15 20:24:48.937 wdl.w:ptcp.w:call-paraphase-30.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for hbb for sample m84036_250809_035451_s4.bc2127 at 2025-09-15 20:24:28.407435...
2025-09-15 20:24:48.938 wdl.w:ptcp.w:call-paraphase-30.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for hbb for sample m84036_250809_035451_s4.bc2127 at 2025-09-15 20:24:31.546977...
2025-09-15 20:24:48.938 wdl.w:ptcp.w:call-paraphase-30.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for hbb for sample m84036_250809_035451_s4.bc2127 at 2025-09-15 20:24:31.874552...
2025-09-15 20:24:48.975 wdl.w:ptcp.w:call-trgt-39.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:47 [ERROR] - No reads found for TRID=SCA2_ATXN2
2025-09-15 20:24:48.981 wdl.w:ptcp.w:call-paraphase-52 NOTICE done
2025-09-15 20:24:48.990 wdl.w:ptcp NOTICE finish :: job: "call-paraphase-52"
2025-09-15 20:24:48.990 wdl.w:ptcp INFO output :: job: "call-paraphase-52", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-52/out/m84036_250809_035451_s4.bc2149.f8inversion.vcf", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-52/out/m84036_250809_035451_s4.bc2149_paraphase/m84036_250809_035451_s4.bc2149.paraphase.json", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-52/out/m84036_250809_035451_s4.bc2149_paraphase/m84036_250809_035451_s4.bc2149.paraphase.bam", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-52/out/m84036_250809_035451_s4.bc2149_paraphase/m84036_250809_035451_s4.bc2149.paraphase.bam.bai", "paraphase_vcfs": [], "havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-52/out/m84036_250809_035451_s4.bc2149.havanno.json", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-52/out/m84036_250809_035451_s4.bc2149.f8inversion.json"}
2025-09-15 20:24:48.993 wdl.w:ptcp.w:call-trgt-44.t:call-trgt_plot_meth_allele INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2141.meth_allele.trgt_plots.zip"
2025-09-15 20:24:49.000 wdl.w:ptcp.w:call-sawfish-79 NOTICE workflow start :: name: "sawfish", source: "./sawfish.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-79"
2025-09-15 20:24:49.006 wdl.w:ptcp.w:call-trgt-52.t:call-trgt_plot_meth_waterfall NOTICE done
2025-09-15 20:24:49.014 wdl.w:ptcp.w:call-trgt-52 NOTICE finish :: job: "call-trgt_plot_meth_waterfall"
2025-09-15 20:24:49.014 wdl.w:ptcp.w:call-trgt-52 INFO output :: job: "call-trgt_plot_meth_waterfall", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-52/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2149.meth_waterfall.trgt_plots.zip"}
2025-09-15 20:24:49.015 wdl.w:ptcp.w:call-trgt-52 INFO visit :: node: "output-images_meth_waterfall", values: {"images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-52/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2149.meth_waterfall.trgt_plots.zip"}
2025-09-15 20:24:49.018 wdl.w:ptcp.w:call-sawfish-79 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:24:49.018 wdl.w:ptcp.w:call-sawfish-79 INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:24:49.019 wdl.w:ptcp.w:call-sawfish-79 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-79/out/m84036_250809_035451_s4.bc2176.mapped.bam"}
2025-09-15 20:24:49.019 wdl.w:ptcp.w:call-sawfish-79 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-79/out/m84036_250809_035451_s4.bc2176.mapped.bam.bai"}
2025-09-15 20:24:49.019 wdl.w:ptcp.w:call-sawfish-79 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:24:49.019 wdl.w:ptcp.w:call-sawfish-79 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:24:49.019 wdl.w:ptcp.w:call-sawfish-79 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2176"}
2025-09-15 20:24:49.019 wdl.w:ptcp.w:call-sawfish-79 NOTICE ready :: job: "call-run_sawfish", callee: "run_sawfish"
2025-09-15 20:24:49.019 wdl.w:ptcp.w:call-sawfish-79 INFO input :: job: "call-run_sawfish", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-79/out/m84036_250809_035451_s4.bc2176.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-79/out/m84036_250809_035451_s4.bc2176.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2176"}
2025-09-15 20:24:49.023 wdl.w:ptcp.w:call-trgt-41.t:call-trgt_plot_meth_waterfall NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-41/call-trgt_plot_meth_waterfall", thread: 140611944420928
2025-09-15 20:24:49.032 wdl.w:ptcp.w:call-sawfish-11.t:call-run_sawfish.stderr VERBOSE [M::mm_idx_gen::71.562*1.79] sorted minimizers
2025-09-15 20:24:49.033 wdl.w:ptcp.w:call-sawfish-11.t:call-run_sawfish.stderr VERBOSE [M::main::71.563*1.79] loaded/built the index for 195 target sequence(s)
2025-09-15 20:24:49.036 wdl.w:ptcp.w:call-trgt-41.t:call-trgt_plot_meth_allele INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-41/call-trgt_plot_meth_allele/_singularity_tmpdir_5nmxtbox"
2025-09-15 20:24:49.036 wdl.w:ptcp.w:call-trgt-41.t:call-trgt_plot_meth_allele INFO Slurm invocation: srun --job-name call-trgt_plot_meth_allele --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-41/call-trgt_plot_meth_allele/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-41/call-trgt_plot_meth_allele/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-41/call-trgt_plot_meth_allele/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-41/call-trgt_plot_meth_allele/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-41/call-trgt_genotype/out/m84036_250809_035451_s4.bc2138.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2138.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-41/call-trgt_genotype/out/m84036_250809_035451_s4.bc2138.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2138.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-41/call-trgt_genotype/out/m84036_250809_035451_s4.bc2138.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2138.trgt.sorted.spanning.bam:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-41/call-trgt_plot_meth_allele/_singularity_tmpdir_5nmxtbox/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-41/call-trgt_plot_meth_allele/_singularity_tmpdir_5nmxtbox/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:49.042 wdl.w:ptcp.w:call-paraphase-53.t:call-run_paraphase NOTICE done
2025-09-15 20:24:49.045 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:47 [ERROR] - No reads found for TRID=SCA7_ATXN7
2025-09-15 20:24:49.046 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:47 [ERROR] - No reads found for TRID=CCHS_PHOX2B
2025-09-15 20:24:49.046 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:47 [ERROR] - No reads found for TRID=SCA1_ATXN1
2025-09-15 20:24:49.046 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:47 [ERROR] - No reads found for TRID=SCA12_PPP2R2B
2025-09-15 20:24:49.046 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:47 [ERROR] - No reads found for TRID=FAME1_SAMD12
2025-09-15 20:24:49.047 wdl.w:ptcp.w:call-trgt-41.t:call-trgt_plot_meth_waterfall INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:49.047 wdl.w:ptcp.w:call-trgt-41.t:call-trgt_plot_meth_waterfall INFO input :: name: "waterfall", value: true
2025-09-15 20:24:49.047 wdl.w:ptcp.w:call-trgt-41.t:call-trgt_plot_meth_waterfall INFO input :: name: "methylation", value: true
2025-09-15 20:24:49.047 wdl.w:ptcp.w:call-trgt-41.t:call-trgt_plot_meth_waterfall INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:49.047 wdl.w:ptcp.w:call-trgt-41.t:call-trgt_plot_meth_waterfall INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:49.047 wdl.w:ptcp.w:call-trgt-41.t:call-trgt_plot_meth_waterfall INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:49.047 wdl.w:ptcp.w:call-trgt-41.t:call-trgt_plot_meth_waterfall INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2138.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:49.048 wdl.w:ptcp.w:call-trgt-41.t:call-trgt_plot_meth_waterfall INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2138.trgt.sorted.spanning.bam"
2025-09-15 20:24:49.048 wdl.w:ptcp.w:call-trgt-41.t:call-trgt_plot_meth_waterfall INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2138.trgt.vcf"
2025-09-15 20:24:49.048 wdl.w:ptcp.w:call-trgt-41.t:call-trgt_plot_meth_waterfall INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2138"
2025-09-15 20:24:49.048 wdl.w:ptcp.w:call-trgt-41.t:call-trgt_plot_meth_waterfall INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:49.048 wdl.w:ptcp.w:call-trgt-41.t:call-trgt_plot_meth_waterfall INFO eval :: name: "plot_type", value: "waterfall"
2025-09-15 20:24:49.048 wdl.w:ptcp.w:call-trgt-41.t:call-trgt_plot_meth_waterfall INFO eval :: name: "show", value: "meth"
2025-09-15 20:24:49.048 wdl.w:ptcp.w:call-trgt-41.t:call-trgt_plot_meth_waterfall INFO eval :: name: "threads", value: 1
2025-09-15 20:24:49.049 wdl.w:ptcp.w:call-trgt-41.t:call-trgt_plot_meth_waterfall INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:49.049 wdl.w:ptcp.w:call-trgt-41.t:call-trgt_plot_meth_waterfall INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2138.meth_waterfall"
2025-09-15 20:24:49.049 wdl.w:ptcp.w:call-trgt-41.t:call-trgt_plot_meth_waterfall INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:49.049 wdl.w:ptcp.w:call-trgt-41.t:call-trgt_plot_meth_waterfall WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:49.050 wdl.w:ptcp.w:call-trgt-41.t:call-trgt_plot_meth_waterfall INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:49.052 wdl.w:ptcp.w:call-trgt-41.t:call-trgt_plot_meth_waterfall INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:49.057 wdl.w:ptcp.w:call-paraphase-40.t:call-run_paraphase NOTICE done
2025-09-15 20:24:49.084 wdl.w:ptcp.w:call-paraphase-53 NOTICE finish :: job: "call-run_paraphase"
2025-09-15 20:24:49.084 wdl.w:ptcp.w:call-paraphase-40 NOTICE finish :: job: "call-run_paraphase"
2025-09-15 20:24:49.084 wdl.w:ptcp.w:call-paraphase-53 INFO output :: job: "call-run_paraphase", values: {"havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-53/call-run_paraphase/out/m84036_250809_035451_s4.bc2150.havanno.json", "paraphase_vcfs": [], "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-53/call-run_paraphase/out/m84036_250809_035451_s4.bc2150_paraphase/m84036_250809_035451_s4.bc2150.paraphase.json", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-53/call-run_paraphase/out/m84036_250809_035451_s4.bc2150_paraphase/m84036_250809_035451_s4.bc2150.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-53/call-run_paraphase/out/m84036_250809_035451_s4.bc2150_paraphase/m84036_250809_035451_s4.bc2150.paraphase.bam"}
2025-09-15 20:24:49.085 wdl.w:ptcp.w:call-paraphase-40 INFO output :: job: "call-run_paraphase", values: {"havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-40/call-run_paraphase/out/m84036_250809_035451_s4.bc2137.havanno.json", "paraphase_vcfs": [], "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-40/call-run_paraphase/out/m84036_250809_035451_s4.bc2137_paraphase/m84036_250809_035451_s4.bc2137.paraphase.json", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-40/call-run_paraphase/out/m84036_250809_035451_s4.bc2137_paraphase/m84036_250809_035451_s4.bc2137.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-40/call-run_paraphase/out/m84036_250809_035451_s4.bc2137_paraphase/m84036_250809_035451_s4.bc2137.paraphase.bam"}
2025-09-15 20:24:49.085 wdl.w:ptcp.w:call-paraphase-53 NOTICE ready :: job: "call-call_f8", callee: "call_f8"
2025-09-15 20:24:49.087 wdl.w:ptcp.w:call-paraphase-53 INFO input :: job: "call-call_f8", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "out_prefix": "m84036_250809_035451_s4.bc2150", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-53/call-run_paraphase/out/m84036_250809_035451_s4.bc2150_paraphase/m84036_250809_035451_s4.bc2150.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-53/call-run_paraphase/out/m84036_250809_035451_s4.bc2150_paraphase/m84036_250809_035451_s4.bc2150.paraphase.bam", "sex": "F"}
2025-09-15 20:24:49.087 wdl.w:ptcp.w:call-paraphase-40 NOTICE ready :: job: "call-call_f8", callee: "call_f8"
2025-09-15 20:24:49.088 wdl.w:ptcp.w:call-paraphase-40 INFO input :: job: "call-call_f8", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "out_prefix": "m84036_250809_035451_s4.bc2137", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-40/call-run_paraphase/out/m84036_250809_035451_s4.bc2137_paraphase/m84036_250809_035451_s4.bc2137.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-40/call-run_paraphase/out/m84036_250809_035451_s4.bc2137_paraphase/m84036_250809_035451_s4.bc2137.paraphase.bam", "sex": "F"}
2025-09-15 20:24:49.089 wdl.w:ptcp.w:call-paraphase-40 INFO visit :: node: "output-havanno_json", values: {"havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-40/call-run_paraphase/out/m84036_250809_035451_s4.bc2137.havanno.json"}
2025-09-15 20:24:49.089 wdl.w:ptcp.w:call-paraphase-40 INFO visit :: node: "output-paraphase_bam", values: {"paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-40/call-run_paraphase/out/m84036_250809_035451_s4.bc2137_paraphase/m84036_250809_035451_s4.bc2137.paraphase.bam"}
2025-09-15 20:24:49.089 wdl.w:ptcp.w:call-paraphase-40 INFO visit :: node: "output-paraphase_bam_bai", values: {"paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-40/call-run_paraphase/out/m84036_250809_035451_s4.bc2137_paraphase/m84036_250809_035451_s4.bc2137.paraphase.bam.bai"}
2025-09-15 20:24:49.089 wdl.w:ptcp.w:call-paraphase-40 INFO visit :: node: "output-paraphase_json", values: {"paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-40/call-run_paraphase/out/m84036_250809_035451_s4.bc2137_paraphase/m84036_250809_035451_s4.bc2137.paraphase.json"}
2025-09-15 20:24:49.089 wdl.w:ptcp.w:call-paraphase-40 INFO visit :: node: "output-paraphase_vcfs", values: {"paraphase_vcfs": []}
2025-09-15 20:24:49.092 wdl.w:ptcp.w:call-paraphase-53 INFO visit :: node: "output-havanno_json", values: {"havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-53/call-run_paraphase/out/m84036_250809_035451_s4.bc2150.havanno.json"}
2025-09-15 20:24:49.091 wdl.w:ptcp.w:call-paraphase-41.t:call-run_paraphase NOTICE done
2025-09-15 20:24:49.092 wdl.w:ptcp.w:call-paraphase-53 INFO visit :: node: "output-paraphase_bam", values: {"paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-53/call-run_paraphase/out/m84036_250809_035451_s4.bc2150_paraphase/m84036_250809_035451_s4.bc2150.paraphase.bam"}
2025-09-15 20:24:49.092 wdl.w:ptcp.w:call-paraphase-53 INFO visit :: node: "output-paraphase_bam_bai", values: {"paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-53/call-run_paraphase/out/m84036_250809_035451_s4.bc2150_paraphase/m84036_250809_035451_s4.bc2150.paraphase.bam.bai"}
2025-09-15 20:24:49.092 wdl.w:ptcp.w:call-paraphase-53 INFO visit :: node: "output-paraphase_json", values: {"paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-53/call-run_paraphase/out/m84036_250809_035451_s4.bc2150_paraphase/m84036_250809_035451_s4.bc2150.paraphase.json"}
2025-09-15 20:24:49.092 wdl.w:ptcp.w:call-paraphase-53 INFO visit :: node: "output-paraphase_vcfs", values: {"paraphase_vcfs": []}
2025-09-15 20:24:49.095 wdl.w:ptcp.w:call-trgt-41.t:call-trgt_plot_motifs_allele NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-41/call-trgt_plot_motifs_allele", thread: 140608211502656
2025-09-15 20:24:49.100 wdl.w:ptcp.w:call-paraphase-41 NOTICE finish :: job: "call-run_paraphase"
2025-09-15 20:24:49.100 wdl.w:ptcp.w:call-paraphase-41 INFO output :: job: "call-run_paraphase", values: {"havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-41/call-run_paraphase/out/m84036_250809_035451_s4.bc2138.havanno.json", "paraphase_vcfs": [], "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-41/call-run_paraphase/out/m84036_250809_035451_s4.bc2138_paraphase/m84036_250809_035451_s4.bc2138.paraphase.json", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-41/call-run_paraphase/out/m84036_250809_035451_s4.bc2138_paraphase/m84036_250809_035451_s4.bc2138.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-41/call-run_paraphase/out/m84036_250809_035451_s4.bc2138_paraphase/m84036_250809_035451_s4.bc2138.paraphase.bam"}
2025-09-15 20:24:49.100 wdl.w:ptcp.w:call-paraphase-41 NOTICE ready :: job: "call-call_f8", callee: "call_f8"
2025-09-15 20:24:49.100 wdl.w:ptcp.w:call-paraphase-41 INFO input :: job: "call-call_f8", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "out_prefix": "m84036_250809_035451_s4.bc2138", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-41/call-run_paraphase/out/m84036_250809_035451_s4.bc2138_paraphase/m84036_250809_035451_s4.bc2138.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-41/call-run_paraphase/out/m84036_250809_035451_s4.bc2138_paraphase/m84036_250809_035451_s4.bc2138.paraphase.bam", "sex": "F"}
2025-09-15 20:24:49.101 wdl.w:ptcp.w:call-paraphase-41 INFO visit :: node: "output-havanno_json", values: {"havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-41/call-run_paraphase/out/m84036_250809_035451_s4.bc2138.havanno.json"}
2025-09-15 20:24:49.101 wdl.w:ptcp.w:call-paraphase-41 INFO visit :: node: "output-paraphase_bam", values: {"paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-41/call-run_paraphase/out/m84036_250809_035451_s4.bc2138_paraphase/m84036_250809_035451_s4.bc2138.paraphase.bam"}
2025-09-15 20:24:49.102 wdl.w:ptcp.w:call-paraphase-41 INFO visit :: node: "output-paraphase_bam_bai", values: {"paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-41/call-run_paraphase/out/m84036_250809_035451_s4.bc2138_paraphase/m84036_250809_035451_s4.bc2138.paraphase.bam.bai"}
2025-09-15 20:24:49.102 wdl.w:ptcp.w:call-paraphase-41 INFO visit :: node: "output-paraphase_json", values: {"paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-41/call-run_paraphase/out/m84036_250809_035451_s4.bc2138_paraphase/m84036_250809_035451_s4.bc2138.paraphase.json"}
2025-09-15 20:24:49.102 wdl.w:ptcp.w:call-paraphase-41 INFO visit :: node: "output-paraphase_vcfs", values: {"paraphase_vcfs": []}
2025-09-15 20:24:49.106 wdl.w:ptcp.w:call-trgt-41.t:call-trgt_plot_meth_allele NOTICE slurm_singularity run :: pid: 1203225, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-41/call-trgt_plot_meth_allele/slurm_singularity.log.txt"
2025-09-15 20:24:49.108 wdl.w:ptcp.w:call-sawfish-69.t:call-run_sawfish NOTICE task setup :: name: "run_sawfish", source: "./sawfish.wdl", line: 83, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-69/call-run_sawfish", thread: 140610342200896
2025-09-15 20:24:49.109 wdl.w:ptcp.w:call-trgt-52.t:call-trgt_plot_motifs_waterfall INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2149.motifs_waterfall.trgt_plots.zip"
2025-09-15 20:24:49.116 wdl.w:ptcp.w:call-trgt-41.t:call-trgt_plot_motifs_allele INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:49.116 wdl.w:ptcp.w:call-trgt-41.t:call-trgt_plot_motifs_allele INFO input :: name: "waterfall", value: false
2025-09-15 20:24:49.116 wdl.w:ptcp.w:call-trgt-41.t:call-trgt_plot_motifs_allele INFO input :: name: "methylation", value: false
2025-09-15 20:24:49.116 wdl.w:ptcp.w:call-trgt-41.t:call-trgt_plot_motifs_allele INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:49.116 wdl.w:ptcp.w:call-trgt-41.t:call-trgt_plot_motifs_allele INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:49.116 wdl.w:ptcp.w:call-trgt-41.t:call-trgt_plot_motifs_allele INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:49.116 wdl.w:ptcp.w:call-trgt-41.t:call-trgt_plot_motifs_allele INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2138.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:49.116 wdl.w:ptcp.w:call-trgt-41.t:call-trgt_plot_motifs_allele INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2138.trgt.sorted.spanning.bam"
2025-09-15 20:24:49.116 wdl.w:ptcp.w:call-trgt-41.t:call-trgt_plot_motifs_allele INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2138.trgt.vcf"
2025-09-15 20:24:49.116 wdl.w:ptcp.w:call-trgt-41.t:call-trgt_plot_motifs_allele INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2138"
2025-09-15 20:24:49.117 wdl.w:ptcp.w:call-trgt-41.t:call-trgt_plot_motifs_waterfall NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-41/call-trgt_plot_motifs_waterfall", thread: 140608236680768
2025-09-15 20:24:49.117 wdl.w:ptcp.w:call-trgt-41.t:call-trgt_plot_motifs_allele INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:49.117 wdl.w:ptcp.w:call-trgt-41.t:call-trgt_plot_motifs_allele INFO eval :: name: "plot_type", value: "allele"
2025-09-15 20:24:49.117 wdl.w:ptcp.w:call-trgt-41.t:call-trgt_plot_motifs_allele INFO eval :: name: "show", value: "motifs"
2025-09-15 20:24:49.118 wdl.w:ptcp.w:call-trgt-41.t:call-trgt_plot_motifs_allele INFO eval :: name: "threads", value: 1
2025-09-15 20:24:49.118 wdl.w:ptcp.w:call-trgt-41.t:call-trgt_plot_motifs_allele INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:49.118 wdl.w:ptcp.w:call-trgt-41.t:call-trgt_plot_motifs_allele INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2138.motifs_allele"
2025-09-15 20:24:49.119 wdl.w:ptcp.w:call-trgt-41.t:call-trgt_plot_motifs_allele INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:49.119 wdl.w:ptcp.w:call-trgt-41.t:call-trgt_plot_motifs_allele WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:49.119 wdl.w:ptcp.w:call-trgt-41.t:call-trgt_plot_motifs_allele INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:49.119 wdl.w:ptcp.w:call-trgt-41.t:call-trgt_plot_motifs_allele INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:49.135 wdl.w:ptcp.w:call-sawfish-69.t:call-run_sawfish INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:49.135 wdl.w:ptcp.w:call-sawfish-69.t:call-run_sawfish INFO input :: name: "genome_version", value: "38"
2025-09-15 20:24:49.135 wdl.w:ptcp.w:call-sawfish-69.t:call-run_sawfish INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:49.136 wdl.w:ptcp.w:call-sawfish-69.t:call-run_sawfish INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:49.136 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_plot_motifs_allele INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2160.motifs_allele.trgt_plots.zip"
2025-09-15 20:24:49.136 wdl.w:ptcp.w:call-sawfish-69.t:call-run_sawfish INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2166.mapped.bam.bai"
2025-09-15 20:24:49.137 wdl.w:ptcp.w:call-sawfish-69.t:call-run_sawfish INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2166.mapped.bam"
2025-09-15 20:24:49.137 wdl.w:ptcp.w:call-sawfish-69.t:call-run_sawfish INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2166"
2025-09-15 20:24:49.137 wdl.w:ptcp.w:call-sawfish-69.t:call-run_sawfish INFO eval :: name: "mem_gb", value: 32
2025-09-15 20:24:49.137 wdl.w:ptcp.w:call-sawfish-69.t:call-run_sawfish INFO eval :: name: "threads", value: 16
2025-09-15 20:24:49.137 wdl.w:ptcp.w:call-sawfish-69.t:call-run_sawfish INFO eval :: name: "disk_size", value: 30
2025-09-15 20:24:49.138 wdl.w:ptcp.w:call-sawfish-69.t:call-run_sawfish INFO eval :: name: "discover_dirname", value: "m84036_250809_035451_s4.bc2166_sawfish_discover"
2025-09-15 20:24:49.138 wdl.w:ptcp.w:call-sawfish-69.t:call-run_sawfish INFO eval :: name: "call_dirname", value: "m84036_250809_035451_s4.bc2166_sawfish"
2025-09-15 20:24:49.138 wdl.w:ptcp.w:call-sawfish-69.t:call-run_sawfish INFO eval :: name: "minimap2_bam_filename", value: "m84036_250809_035451_s4.bc2166.minimap2.bam"
2025-09-15 20:24:49.138 wdl.w:ptcp.w:call-sawfish-69.t:call-run_sawfish INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 16, memory_reservation: 32000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:49.139 wdl.w:ptcp.w:call-sawfish-69.t:call-run_sawfish WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:49.139 wdl.w:ptcp.w:call-sawfish-69.t:call-run_sawfish INFO provisioned :: seconds_waited: 0, cpu: 16, mem_bytes: 32000000000
2025-09-15 20:24:49.140 wdl.w:ptcp.w:call-sawfish-69.t:call-run_sawfish INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:49.143 wdl.w:ptcp.w:call-trgt-41.t:call-trgt_plot_motifs_waterfall INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:49.143 wdl.w:ptcp.w:call-trgt-41.t:call-trgt_plot_motifs_waterfall INFO input :: name: "waterfall", value: true
2025-09-15 20:24:49.144 wdl.w:ptcp.w:call-trgt-41.t:call-trgt_plot_motifs_waterfall INFO input :: name: "methylation", value: false
2025-09-15 20:24:49.144 wdl.w:ptcp.w:call-trgt-41.t:call-trgt_plot_motifs_waterfall INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:49.144 wdl.w:ptcp.w:call-trgt-41.t:call-trgt_plot_motifs_waterfall INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:49.144 wdl.w:ptcp.w:call-trgt-41.t:call-trgt_plot_motifs_waterfall INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:49.144 wdl.w:ptcp.w:call-trgt-41.t:call-trgt_plot_motifs_waterfall INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2138.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:49.144 wdl.w:ptcp.w:call-trgt-41.t:call-trgt_plot_motifs_waterfall INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2138.trgt.sorted.spanning.bam"
2025-09-15 20:24:49.144 wdl.w:ptcp.w:call-trgt-41.t:call-trgt_plot_motifs_waterfall INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2138.trgt.vcf"
2025-09-15 20:24:49.144 wdl.w:ptcp.w:call-trgt-41.t:call-trgt_plot_motifs_waterfall INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2138"
2025-09-15 20:24:49.144 wdl.w:ptcp.w:call-trgt-41.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:49.145 wdl.w:ptcp.w:call-trgt-41.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "plot_type", value: "waterfall"
2025-09-15 20:24:49.145 wdl.w:ptcp.w:call-trgt-41.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "show", value: "motifs"
2025-09-15 20:24:49.145 wdl.w:ptcp.w:call-trgt-41.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "threads", value: 1
2025-09-15 20:24:49.145 wdl.w:ptcp.w:call-trgt-41.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:49.145 wdl.w:ptcp.w:call-trgt-41.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2138.motifs_waterfall"
2025-09-15 20:24:49.146 wdl.w:ptcp.w:call-trgt-41.t:call-trgt_plot_motifs_waterfall INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:49.146 wdl.w:ptcp.w:call-trgt-41.t:call-trgt_plot_motifs_waterfall WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:49.147 wdl.w:ptcp.w:call-trgt-41.t:call-trgt_plot_motifs_waterfall INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:49.147 wdl.w:ptcp.w:call-trgt-41.t:call-trgt_plot_motifs_waterfall INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:49.184 wdl.w:ptcp.w:call-trgt-44.t:call-trgt_plot_meth_allele NOTICE done
2025-09-15 20:24:49.191 wdl.w:ptcp.w:call-trgt-41.t:call-trgt_plot_meth_waterfall INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-41/call-trgt_plot_meth_waterfall/_singularity_tmpdir_gfks_hjl"
2025-09-15 20:24:49.191 wdl.w:ptcp.w:call-trgt-41.t:call-trgt_plot_meth_waterfall INFO Slurm invocation: srun --job-name call-trgt_plot_meth_waterfall --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-41/call-trgt_plot_meth_waterfall/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-41/call-trgt_plot_meth_waterfall/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-41/call-trgt_plot_meth_waterfall/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-41/call-trgt_plot_meth_waterfall/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-41/call-trgt_genotype/out/m84036_250809_035451_s4.bc2138.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2138.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-41/call-trgt_genotype/out/m84036_250809_035451_s4.bc2138.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2138.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-41/call-trgt_genotype/out/m84036_250809_035451_s4.bc2138.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2138.trgt.sorted.spanning.bam:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-41/call-trgt_plot_meth_waterfall/_singularity_tmpdir_gfks_hjl/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-41/call-trgt_plot_meth_waterfall/_singularity_tmpdir_gfks_hjl/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:49.191 wdl.w:ptcp.w:call-trgt-44 NOTICE finish :: job: "call-trgt_plot_meth_allele"
2025-09-15 20:24:49.192 wdl.w:ptcp.w:call-trgt-44 INFO output :: job: "call-trgt_plot_meth_allele", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-44/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2141.meth_allele.trgt_plots.zip"}
2025-09-15 20:24:49.194 wdl.w:ptcp.w:call-trgt-44 INFO visit :: node: "output-images_meth_allele", values: {"images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-44/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2141.meth_allele.trgt_plots.zip"}
2025-09-15 20:24:49.199 wdl.w:ptcp.w:call-trgt-48.t:call-trgt_plot_meth_allele NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-48/call-trgt_plot_meth_allele", thread: 140610895857216
2025-09-15 20:24:49.230 wdl.w:ptcp.w:call-trgt-48.t:call-trgt_plot_meth_allele INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:49.230 wdl.w:ptcp.w:call-trgt-48.t:call-trgt_plot_meth_allele INFO input :: name: "waterfall", value: false
2025-09-15 20:24:49.230 wdl.w:ptcp.w:call-trgt-48.t:call-trgt_plot_meth_allele INFO input :: name: "methylation", value: true
2025-09-15 20:24:49.230 wdl.w:ptcp.w:call-trgt-48.t:call-trgt_plot_meth_allele INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:49.230 wdl.w:ptcp.w:call-trgt-48.t:call-trgt_plot_meth_allele INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:49.231 wdl.w:ptcp.w:call-trgt-48.t:call-trgt_plot_meth_allele INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:49.231 wdl.w:ptcp.w:call-trgt-48.t:call-trgt_plot_meth_allele INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2145.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:49.231 wdl.w:ptcp.w:call-trgt-48.t:call-trgt_plot_meth_allele INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2145.trgt.sorted.spanning.bam"
2025-09-15 20:24:49.231 wdl.w:ptcp.w:call-trgt-48.t:call-trgt_plot_meth_allele INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2145.trgt.vcf"
2025-09-15 20:24:49.231 wdl.w:ptcp.w:call-trgt-48.t:call-trgt_plot_meth_allele INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2145"
2025-09-15 20:24:49.231 wdl.w:ptcp.w:call-trgt-48.t:call-trgt_plot_meth_allele INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:49.231 wdl.w:ptcp.w:call-trgt-48.t:call-trgt_plot_meth_allele INFO eval :: name: "plot_type", value: "allele"
2025-09-15 20:24:49.231 wdl.w:ptcp.w:call-trgt-48.t:call-trgt_plot_meth_allele INFO eval :: name: "show", value: "meth"
2025-09-15 20:24:49.232 wdl.w:ptcp.w:call-trgt-48.t:call-trgt_plot_meth_allele INFO eval :: name: "threads", value: 1
2025-09-15 20:24:49.232 wdl.w:ptcp.w:call-trgt-48.t:call-trgt_plot_meth_allele INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:49.232 wdl.w:ptcp.w:call-trgt-48.t:call-trgt_plot_meth_allele INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2145.meth_allele"
2025-09-15 20:24:49.232 wdl.w:ptcp.w:call-trgt-48.t:call-trgt_plot_meth_allele INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:49.233 wdl.w:ptcp.w:call-trgt-48.t:call-trgt_plot_meth_allele WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:49.233 wdl.w:ptcp.w:call-trgt-41.t:call-trgt_plot_motifs_allele INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-41/call-trgt_plot_motifs_allele/_singularity_tmpdir_v_bayfju"
2025-09-15 20:24:49.233 wdl.w:ptcp.w:call-trgt-41.t:call-trgt_plot_motifs_allele INFO Slurm invocation: srun --job-name call-trgt_plot_motifs_allele --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-41/call-trgt_plot_motifs_allele/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-41/call-trgt_plot_motifs_allele/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-41/call-trgt_plot_motifs_allele/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-41/call-trgt_plot_motifs_allele/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-41/call-trgt_genotype/out/m84036_250809_035451_s4.bc2138.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2138.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-41/call-trgt_genotype/out/m84036_250809_035451_s4.bc2138.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2138.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-41/call-trgt_genotype/out/m84036_250809_035451_s4.bc2138.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2138.trgt.sorted.spanning.bam:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-41/call-trgt_plot_motifs_allele/_singularity_tmpdir_v_bayfju/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-41/call-trgt_plot_motifs_allele/_singularity_tmpdir_v_bayfju/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:49.233 wdl.w:ptcp.w:call-trgt-48.t:call-trgt_plot_meth_allele INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:49.236 wdl.w:ptcp.w:call-trgt-48.t:call-trgt_plot_meth_allele INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:49.240 wdl.w:ptcp.w:call-trgt-41.t:call-trgt_plot_meth_waterfall NOTICE slurm_singularity run :: pid: 1203227, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-41/call-trgt_plot_meth_waterfall/slurm_singularity.log.txt"
2025-09-15 20:24:49.245 wdl.w:ptcp.w:call-sawfish-69.t:call-run_sawfish INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 10, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-69/call-run_sawfish/_singularity_tmpdir_9vaja_v3"
2025-09-15 20:24:49.245 wdl.w:ptcp.w:call-trgt-41.t:call-trgt_plot_motifs_allele NOTICE slurm_singularity run :: pid: 1203228, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-41/call-trgt_plot_motifs_allele/slurm_singularity.log.txt"
2025-09-15 20:24:49.246 wdl.w:ptcp.w:call-sawfish-69.t:call-run_sawfish INFO Slurm invocation: srun --job-name call-run_sawfish --partition compute,compute9 --cpus-per-task 16 --mem 30518M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-69/call-run_sawfish/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-69/call-run_sawfish/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-69/call-run_sawfish/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-69/call-run_sawfish/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-69/out/m84036_250809_035451_s4.bc2166.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2166.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-69/out/m84036_250809_035451_s4.bc2166.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2166.mapped.bam:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-69/call-run_sawfish/_singularity_tmpdir_9vaja_v3/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-69/call-run_sawfish/_singularity_tmpdir_9vaja_v3/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:49.262 wdl.w:ptcp.w:call-trgt-41.t:call-trgt_plot_motifs_waterfall INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-41/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_3imsbmxa"
2025-09-15 20:24:49.262 wdl.w:ptcp.w:call-trgt-41.t:call-trgt_plot_motifs_waterfall INFO Slurm invocation: srun --job-name call-trgt_plot_motifs_waterfall --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-41/call-trgt_plot_motifs_waterfall/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-41/call-trgt_plot_motifs_waterfall/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-41/call-trgt_plot_motifs_waterfall/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-41/call-trgt_plot_motifs_waterfall/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-41/call-trgt_genotype/out/m84036_250809_035451_s4.bc2138.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2138.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-41/call-trgt_genotype/out/m84036_250809_035451_s4.bc2138.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2138.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-41/call-trgt_genotype/out/m84036_250809_035451_s4.bc2138.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2138.trgt.sorted.spanning.bam:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-41/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_3imsbmxa/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-41/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_3imsbmxa/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:49.269 wdl.w:ptcp.w:call-trgt-41.t:call-trgt_plot_motifs_waterfall NOTICE slurm_singularity run :: pid: 1203232, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-41/call-trgt_plot_motifs_waterfall/slurm_singularity.log.txt"
2025-09-15 20:24:49.269 wdl.w:ptcp.w:call-sawfish-69.t:call-run_sawfish NOTICE slurm_singularity run :: pid: 1203230, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-69/call-run_sawfish/slurm_singularity.log.txt"
2025-09-15 20:24:49.279 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_plot_motifs_allele NOTICE done
2025-09-15 20:24:49.285 wdl.w:ptcp.w:call-trgt-63 NOTICE finish :: job: "call-trgt_plot_motifs_allele"
2025-09-15 20:24:49.286 wdl.w:ptcp.w:call-trgt-63 INFO output :: job: "call-trgt_plot_motifs_allele", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-63/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2160.motifs_allele.trgt_plots.zip"}
2025-09-15 20:24:49.286 wdl.w:ptcp.w:call-trgt-63 INFO visit :: node: "output-images_motifs_allele", values: {"images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-63/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2160.motifs_allele.trgt_plots.zip"}
2025-09-15 20:24:49.296 wdl.w:ptcp.w:call-trgt-48.t:call-trgt_plot_meth_waterfall NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-48/call-trgt_plot_meth_waterfall", thread: 140607674631744
2025-09-15 20:24:49.301 wdl.w:ptcp.w:call-trgt-52.t:call-trgt_plot_motifs_waterfall NOTICE done
2025-09-15 20:24:49.307 wdl.w:ptcp.w:call-trgt-52 NOTICE finish :: job: "call-trgt_plot_motifs_waterfall"
2025-09-15 20:24:49.308 wdl.w:ptcp.w:call-trgt-52 INFO output :: job: "call-trgt_plot_motifs_waterfall", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-52/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2149.motifs_waterfall.trgt_plots.zip"}
2025-09-15 20:24:49.308 wdl.w:ptcp.w:call-trgt-52 INFO visit :: node: "output-images_motifs_waterfall", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-52/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2149.motifs_waterfall.trgt_plots.zip"}
2025-09-15 20:24:49.308 wdl.w:ptcp.w:call-trgt-52 INFO visit :: node: "outputs", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-52/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2149.motifs_waterfall.trgt_plots.zip", "images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-52/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2149.meth_allele.trgt_plots.zip", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-52/call-trgt_genotype/out/m84036_250809_035451_s4.bc2149.trgt.sorted.spanning.bam.bai", "images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-52/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2149.motifs_allele.trgt_plots.zip", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-52/call-trgt_genotype/out/m84036_250809_035451_s4.bc2149.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-52/call-trgt_genotype/out/m84036_250809_035451_s4.bc2149.trgt.vcf", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-52/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2149.repeats.bam", "images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-52/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2149.meth_waterfall.trgt_plots.zip", "reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-52/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2149.repeats.bam.bai"}
2025-09-15 20:24:49.313 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:46 [ERROR] - No reads found for TRID=OPDM_ABCD3
2025-09-15 20:24:49.313 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:46 [ERROR] - No reads found for TRID=NIID_NOTCH2NLC
2025-09-15 20:24:49.313 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:46 [ERROR] - No reads found for TRID=SCA37_DAB1
2025-09-15 20:24:49.313 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:46 [ERROR] - No reads found for TRID=SCA27B_FGF14
2025-09-15 20:24:49.313 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:46 [ERROR] - No reads found for TRID=SCA3_ATXN3
2025-09-15 20:24:49.314 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:46 [ERROR] - No reads found for TRID=SCA4_ZFHX3
2025-09-15 20:24:49.314 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:46 [ERROR] - No reads found for TRID=HDL2_JPH3
2025-09-15 20:24:49.314 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:46 [ERROR] - No reads found for TRID=OPDM4_RILPL1
2025-09-15 20:24:49.312 wdl.w:ptcp.w:call-paraphase-43.t:call-run_paraphase.stderr VERBOSE INFO:root:Processing sample m84036_250809_035451_s4.bc2140 at 2025-09-15 20:24:45.321584...
2025-09-15 20:24:49.314 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:46 [ERROR] - No reads found for TRID=SCA31_BEAN1
2025-09-15 20:24:49.314 wdl.w:ptcp.w:call-paraphase-43.t:call-run_paraphase.stderr VERBOSE INFO:root:Checking sample sex at 2025-09-15 20:24:45.323183...
2025-09-15 20:24:49.314 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:47 [ERROR] - No reads found for TRID=DM1_DMPK
2025-09-15 20:24:49.315 wdl.w:ptcp.w:call-paraphase-43.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for cyp21 for sample m84036_250809_035451_s4.bc2140 at 2025-09-15 20:24:45.375067...
2025-09-15 20:24:49.315 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:47 [ERROR] - No reads found for TRID=SCA6_CACNA1A
2025-09-15 20:24:49.315 wdl.w:ptcp.w:call-paraphase-43.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for cyp21 for sample m84036_250809_035451_s4.bc2140 at 2025-09-15 20:24:45.375518...
2025-09-15 20:24:49.315 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:47 [ERROR] - No reads found for TRID=SCA36_NOP56
2025-09-15 20:24:49.315 wdl.w:ptcp.w:call-paraphase-43.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for smn1 for sample m84036_250809_035451_s4.bc2140 at 2025-09-15 20:24:45.375407...
2025-09-15 20:24:49.315 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:47 [ERROR] - No reads found for TRID=OPDM2_GIPC1
2025-09-15 20:24:49.315 wdl.w:ptcp.w:call-paraphase-43.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for smn1 for sample m84036_250809_035451_s4.bc2140 at 2025-09-15 20:24:45.375630...
2025-09-15 20:24:49.315 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:47 [ERROR] - No reads found for TRID=EPM1_CSTB
2025-09-15 20:24:49.316 wdl.w:ptcp.w:call-paraphase-43.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for gba for sample m84036_250809_035451_s4.bc2140 at 2025-09-15 20:24:45.376149...
2025-09-15 20:24:49.316 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:47 [ERROR] - No reads found for TRID=CJD_PRNP
2025-09-15 20:24:49.316 wdl.w:ptcp.w:call-paraphase-43.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for hba for sample m84036_250809_035451_s4.bc2140 at 2025-09-15 20:24:45.376153...
2025-09-15 20:24:49.316 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:47 [ERROR] - No reads found for TRID=FRA2A_AFF3
2025-09-15 20:24:49.316 wdl.w:ptcp.w:call-paraphase-43.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for gba for sample m84036_250809_035451_s4.bc2140 at 2025-09-15 20:24:45.376355...
2025-09-15 20:24:49.316 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:47 [ERROR] - No reads found for TRID=SD5_HOXD13
2025-09-15 20:24:49.317 wdl.w:ptcp.w:call-paraphase-43.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for hba for sample m84036_250809_035451_s4.bc2140 at 2025-09-15 20:24:45.376357...
2025-09-15 20:24:49.317 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:47 [ERROR] - No reads found for TRID=SCA7_ATXN7
2025-09-15 20:24:49.317 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:47 [ERROR] - No reads found for TRID=CCHS_PHOX2B
2025-09-15 20:24:49.317 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:47 [ERROR] - No reads found for TRID=SCA1_ATXN1
2025-09-15 20:24:49.317 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:47 [ERROR] - No reads found for TRID=SCA12_PPP2R2B
2025-09-15 20:24:49.317 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:47 [ERROR] - No reads found for TRID=FAME1_SAMD12
2025-09-15 20:24:49.321 wdl.w:ptcp.w:call-trgt-48.t:call-trgt_plot_meth_waterfall INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:49.321 wdl.w:ptcp.w:call-trgt-48.t:call-trgt_plot_meth_waterfall INFO input :: name: "waterfall", value: true
2025-09-15 20:24:49.321 wdl.w:ptcp.w:call-trgt-48.t:call-trgt_plot_meth_waterfall INFO input :: name: "methylation", value: true
2025-09-15 20:24:49.321 wdl.w:ptcp.w:call-trgt-48.t:call-trgt_plot_meth_waterfall INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:49.322 wdl.w:ptcp.w:call-trgt-48.t:call-trgt_plot_meth_waterfall INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:49.322 wdl.w:ptcp.w:call-trgt-48.t:call-trgt_plot_meth_waterfall INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:49.322 wdl.w:ptcp.w:call-trgt-48.t:call-trgt_plot_meth_waterfall INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2145.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:49.322 wdl.w:ptcp.w:call-trgt-48.t:call-trgt_plot_meth_waterfall INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2145.trgt.sorted.spanning.bam"
2025-09-15 20:24:49.322 wdl.w:ptcp.w:call-trgt-48.t:call-trgt_plot_motifs_allele NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-48/call-trgt_plot_motifs_allele", thread: 140607137760832
2025-09-15 20:24:49.322 wdl.w:ptcp.w:call-trgt-48.t:call-trgt_plot_meth_waterfall INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2145.trgt.vcf"
2025-09-15 20:24:49.322 wdl.w:ptcp.w:call-trgt-48.t:call-trgt_plot_meth_waterfall INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2145"
2025-09-15 20:24:49.323 wdl.w:ptcp.w:call-trgt-48.t:call-trgt_plot_meth_waterfall INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:49.323 wdl.w:ptcp.w:call-trgt-48.t:call-trgt_plot_meth_waterfall INFO eval :: name: "plot_type", value: "waterfall"
2025-09-15 20:24:49.323 wdl.w:ptcp.w:call-trgt-48.t:call-trgt_plot_meth_waterfall INFO eval :: name: "show", value: "meth"
2025-09-15 20:24:49.323 wdl.w:ptcp.w:call-trgt-48.t:call-trgt_plot_meth_waterfall INFO eval :: name: "threads", value: 1
2025-09-15 20:24:49.323 wdl.w:ptcp.w:call-trgt-48.t:call-trgt_plot_meth_waterfall INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:49.323 wdl.w:ptcp.w:call-trgt-48.t:call-trgt_plot_meth_waterfall INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2145.meth_waterfall"
2025-09-15 20:24:49.324 wdl.w:ptcp.w:call-trgt-48.t:call-trgt_plot_meth_waterfall INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:49.324 wdl.w:ptcp.w:call-trgt-48.t:call-trgt_plot_meth_waterfall WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:49.324 wdl.w:ptcp.w:call-trgt-48.t:call-trgt_plot_meth_waterfall INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:49.324 wdl.w:ptcp.w:call-trgt-48.t:call-trgt_plot_meth_waterfall INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:49.352 wdl.w:ptcp.w:call-trgt-48.t:call-trgt_plot_meth_allele INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-48/call-trgt_plot_meth_allele/_singularity_tmpdir_7x7_tpui"
2025-09-15 20:24:49.352 wdl.w:ptcp.w:call-trgt-48.t:call-trgt_plot_meth_allele INFO Slurm invocation: srun --job-name call-trgt_plot_meth_allele --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-48/call-trgt_plot_meth_allele/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-48/call-trgt_plot_meth_allele/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-48/call-trgt_plot_meth_allele/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-48/call-trgt_plot_meth_allele/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-48/call-trgt_genotype/out/m84036_250809_035451_s4.bc2145.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2145.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-48/call-trgt_genotype/out/m84036_250809_035451_s4.bc2145.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2145.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-48/call-trgt_genotype/out/m84036_250809_035451_s4.bc2145.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2145.trgt.sorted.spanning.bam.bai:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-48/call-trgt_plot_meth_allele/_singularity_tmpdir_7x7_tpui/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-48/call-trgt_plot_meth_allele/_singularity_tmpdir_7x7_tpui/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:49.364 wdl.w:ptcp.w:call-trgt-48.t:call-trgt_plot_motifs_allele INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:49.364 wdl.w:ptcp.w:call-trgt-48.t:call-trgt_plot_motifs_allele INFO input :: name: "waterfall", value: false
2025-09-15 20:24:49.364 wdl.w:ptcp.w:call-trgt-48.t:call-trgt_plot_motifs_allele INFO input :: name: "methylation", value: false
2025-09-15 20:24:49.364 wdl.w:ptcp.w:call-trgt-48.t:call-trgt_plot_motifs_allele INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:49.364 wdl.w:ptcp.w:call-trgt-48.t:call-trgt_plot_motifs_allele INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:49.364 wdl.w:ptcp.w:call-trgt-48.t:call-trgt_plot_motifs_allele INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:49.364 wdl.w:ptcp.w:call-trgt-48.t:call-trgt_plot_motifs_allele INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2145.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:49.364 wdl.w:ptcp.w:call-trgt-48.t:call-trgt_plot_motifs_allele INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2145.trgt.sorted.spanning.bam"
2025-09-15 20:24:49.364 wdl.w:ptcp.w:call-trgt-48.t:call-trgt_plot_motifs_allele INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2145.trgt.vcf"
2025-09-15 20:24:49.364 wdl.w:ptcp.w:call-trgt-48.t:call-trgt_plot_motifs_allele INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2145"
2025-09-15 20:24:49.365 wdl.w:ptcp.w:call-trgt-48.t:call-trgt_plot_motifs_allele INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:49.365 wdl.w:ptcp.w:call-trgt-48.t:call-trgt_plot_motifs_allele INFO eval :: name: "plot_type", value: "allele"
2025-09-15 20:24:49.365 wdl.w:ptcp.w:call-trgt-48.t:call-trgt_plot_motifs_allele INFO eval :: name: "show", value: "motifs"
2025-09-15 20:24:49.365 wdl.w:ptcp.w:call-trgt-48.t:call-trgt_plot_motifs_allele INFO eval :: name: "threads", value: 1
2025-09-15 20:24:49.365 wdl.w:ptcp.w:call-trgt-48.t:call-trgt_plot_motifs_allele INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:49.365 wdl.w:ptcp.w:call-trgt-48.t:call-trgt_plot_motifs_allele INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2145.motifs_allele"
2025-09-15 20:24:49.366 wdl.w:ptcp.w:call-trgt-48.t:call-trgt_plot_motifs_allele INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:49.366 wdl.w:ptcp.w:call-trgt-48.t:call-trgt_plot_motifs_allele WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:49.366 wdl.w:ptcp.w:call-trgt-48.t:call-trgt_plot_motifs_allele INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:49.366 wdl.w:ptcp.w:call-trgt-48.t:call-trgt_plot_motifs_allele INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:49.374 wdl.w:ptcp.w:call-trgt-48.t:call-trgt_plot_meth_allele NOTICE slurm_singularity run :: pid: 1203235, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-48/call-trgt_plot_meth_allele/slurm_singularity.log.txt"
2025-09-15 20:24:49.433 wdl.w:ptcp.w:call-trgt-48.t:call-trgt_plot_meth_waterfall INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-48/call-trgt_plot_meth_waterfall/_singularity_tmpdir_s3dcoxu2"
2025-09-15 20:24:49.433 wdl.w:ptcp.w:call-trgt-48.t:call-trgt_plot_meth_waterfall INFO Slurm invocation: srun --job-name call-trgt_plot_meth_waterfall --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-48/call-trgt_plot_meth_waterfall/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-48/call-trgt_plot_meth_waterfall/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-48/call-trgt_plot_meth_waterfall/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-48/call-trgt_plot_meth_waterfall/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-48/call-trgt_genotype/out/m84036_250809_035451_s4.bc2145.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2145.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-48/call-trgt_genotype/out/m84036_250809_035451_s4.bc2145.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2145.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-48/call-trgt_genotype/out/m84036_250809_035451_s4.bc2145.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2145.trgt.sorted.spanning.bam.bai:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-48/call-trgt_plot_meth_waterfall/_singularity_tmpdir_s3dcoxu2/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-48/call-trgt_plot_meth_waterfall/_singularity_tmpdir_s3dcoxu2/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:49.438 wdl.w:ptcp.w:call-trgt-52 NOTICE done
2025-09-15 20:24:49.442 wdl.w:ptcp NOTICE finish :: job: "call-trgt-52"
2025-09-15 20:24:49.443 wdl.w:ptcp INFO output :: job: "call-trgt-52", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-52/out/m84036_250809_035451_s4.bc2149.motifs_waterfall.trgt_plots.zip", "images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-52/out/m84036_250809_035451_s4.bc2149.meth_allele.trgt_plots.zip", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-52/out/m84036_250809_035451_s4.bc2149.trgt.sorted.spanning.bam.bai", "images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-52/out/m84036_250809_035451_s4.bc2149.motifs_allele.trgt_plots.zip", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-52/out/m84036_250809_035451_s4.bc2149.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-52/out/m84036_250809_035451_s4.bc2149.trgt.vcf", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-52/out/m84036_250809_035451_s4.bc2149.repeats.bam", "images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-52/out/m84036_250809_035451_s4.bc2149.meth_waterfall.trgt_plots.zip", "reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-52/out/m84036_250809_035451_s4.bc2149.repeats.bam.bai"}
2025-09-15 20:24:49.451 wdl.w:ptcp.w:call-trgt-79 NOTICE workflow start :: name: "trgt", source: "./trgt.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-79"
2025-09-15 20:24:49.453 wdl.w:ptcp.w:call-trgt-48.t:call-trgt_plot_meth_waterfall NOTICE slurm_singularity run :: pid: 1203237, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-48/call-trgt_plot_meth_waterfall/slurm_singularity.log.txt"
2025-09-15 20:24:49.465 wdl.w:ptcp.w:call-trgt-48.t:call-trgt_plot_motifs_allele INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-48/call-trgt_plot_motifs_allele/_singularity_tmpdir_zb6uls8m"
2025-09-15 20:24:49.466 wdl.w:ptcp.w:call-trgt-48.t:call-trgt_plot_motifs_allele INFO Slurm invocation: srun --job-name call-trgt_plot_motifs_allele --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-48/call-trgt_plot_motifs_allele/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-48/call-trgt_plot_motifs_allele/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-48/call-trgt_plot_motifs_allele/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-48/call-trgt_plot_motifs_allele/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-48/call-trgt_genotype/out/m84036_250809_035451_s4.bc2145.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2145.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-48/call-trgt_genotype/out/m84036_250809_035451_s4.bc2145.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2145.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-48/call-trgt_genotype/out/m84036_250809_035451_s4.bc2145.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2145.trgt.sorted.spanning.bam.bai:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-48/call-trgt_plot_motifs_allele/_singularity_tmpdir_zb6uls8m/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-48/call-trgt_plot_motifs_allele/_singularity_tmpdir_zb6uls8m/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:49.470 wdl.w:ptcp.w:call-trgt-79 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:24:49.470 wdl.w:ptcp.w:call-trgt-79 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-79/out/m84036_250809_035451_s4.bc2176.mapped.bam"}
2025-09-15 20:24:49.470 wdl.w:ptcp.w:call-trgt-79 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-79/out/m84036_250809_035451_s4.bc2176.mapped.bam.bai"}
2025-09-15 20:24:49.470 wdl.w:ptcp.w:call-trgt-79 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:24:49.470 wdl.w:ptcp.w:call-trgt-79 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:24:49.470 wdl.w:ptcp.w:call-trgt-79 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2176"}
2025-09-15 20:24:49.470 wdl.w:ptcp.w:call-trgt-79 INFO visit :: node: "decl-sex", values: {"sex": "F"}
2025-09-15 20:24:49.470 wdl.w:ptcp.w:call-trgt-79 INFO visit :: node: "decl-trgt_bed", values: {"trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"}
2025-09-15 20:24:49.470 wdl.w:ptcp.w:call-trgt-79 NOTICE ready :: job: "call-get_reads_overlapping_repeats", callee: "get_reads_overlapping_repeats"
2025-09-15 20:24:49.471 wdl.w:ptcp.w:call-trgt-79 INFO input :: job: "call-get_reads_overlapping_repeats", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-79/out/m84036_250809_035451_s4.bc2176.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-79/out/m84036_250809_035451_s4.bc2176.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2176"}
2025-09-15 20:24:49.471 wdl.w:ptcp.w:call-trgt-79 NOTICE ready :: job: "call-trgt_genotype", callee: "trgt_genotype"
2025-09-15 20:24:49.471 wdl.w:ptcp.w:call-trgt-79 INFO input :: job: "call-trgt_genotype", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-79/out/m84036_250809_035451_s4.bc2176.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-79/out/m84036_250809_035451_s4.bc2176.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2176"}
2025-09-15 20:24:49.474 wdl.w:ptcp.w:call-trgt-48.t:call-trgt_plot_motifs_allele NOTICE slurm_singularity run :: pid: 1203239, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-48/call-trgt_plot_motifs_allele/slurm_singularity.log.txt"
2025-09-15 20:24:49.486 wdl.w:ptcp.w:call-paraphase-55.t:call-run_paraphase.stderr VERBOSE INFO:root:Processing sample m84036_250809_035451_s4.bc2152 at 2025-09-15 20:24:45.339240...
2025-09-15 20:24:49.487 wdl.w:ptcp.w:call-paraphase-55.t:call-run_paraphase.stderr VERBOSE INFO:root:Checking sample sex at 2025-09-15 20:24:45.340826...
2025-09-15 20:24:49.487 wdl.w:ptcp.w:call-paraphase-55.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for cyp21 for sample m84036_250809_035451_s4.bc2152 at 2025-09-15 20:24:45.380451...
2025-09-15 20:24:49.487 wdl.w:ptcp.w:call-paraphase-55.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for cyp21 for sample m84036_250809_035451_s4.bc2152 at 2025-09-15 20:24:45.380721...
2025-09-15 20:24:49.488 wdl.w:ptcp.w:call-paraphase-55.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for smn1 for sample m84036_250809_035451_s4.bc2152 at 2025-09-15 20:24:45.380583...
2025-09-15 20:24:49.488 wdl.w:ptcp.w:call-paraphase-55.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for smn1 for sample m84036_250809_035451_s4.bc2152 at 2025-09-15 20:24:45.380843...
2025-09-15 20:24:49.488 wdl.w:ptcp.w:call-paraphase-55.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for gba for sample m84036_250809_035451_s4.bc2152 at 2025-09-15 20:24:45.381463...
2025-09-15 20:24:49.488 wdl.w:ptcp.w:call-paraphase-55.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for gba for sample m84036_250809_035451_s4.bc2152 at 2025-09-15 20:24:45.381663...
2025-09-15 20:24:49.488 wdl.w:ptcp.w:call-paraphase-55.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for hba for sample m84036_250809_035451_s4.bc2152 at 2025-09-15 20:24:45.382146...
2025-09-15 20:24:49.488 wdl.w:ptcp.w:call-paraphase-55.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for hba for sample m84036_250809_035451_s4.bc2152 at 2025-09-15 20:24:45.382331...
2025-09-15 20:24:49.524 wdl.w:ptcp.w:call-sawfish-46.t:call-run_sawfish.stderr VERBOSE [M::mm_idx_gen::42.682*1.61] sorted minimizers
2025-09-15 20:24:49.524 wdl.w:ptcp.w:call-sawfish-46.t:call-run_sawfish.stderr VERBOSE [M::main::42.682*1.61] loaded/built the index for 195 target sequence(s)
2025-09-15 20:24:49.524 wdl.w:ptcp.w:call-sawfish-46.t:call-run_sawfish.stderr VERBOSE [M::mm_mapopt_update::45.737*1.57] mid_occ = 136
2025-09-15 20:24:49.524 wdl.w:ptcp.w:call-sawfish-46.t:call-run_sawfish.stderr VERBOSE [M::mm_idx_stat] kmer size: 19; skip: 19; is_hpc: 0; #seq: 195
2025-09-15 20:24:49.525 wdl.w:ptcp.w:call-sawfish-46.t:call-run_sawfish.stderr VERBOSE [M::mm_idx_stat::48.401*1.54] distinct minimizers: 214664461 (92.23% are singletons); average occurrences: 1.372; average spacing: 10.529; total length: 3099922541
2025-09-15 20:24:49.525 wdl.w:ptcp.w:call-sawfish-46.t:call-run_sawfish.stderr VERBOSE [M::bam2fq_mainloop] discarded 0 singletons
2025-09-15 20:24:49.525 wdl.w:ptcp.w:call-sawfish-46.t:call-run_sawfish.stderr VERBOSE [M::bam2fq_mainloop] processed 174 reads
2025-09-15 20:24:49.574 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:49 [ERROR] - No reads found for TRID=OPDM_ABCD3
2025-09-15 20:24:49.574 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:49 [ERROR] - No reads found for TRID=OPDM4_RILPL1
2025-09-15 20:24:49.574 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:49 [ERROR] - No reads found for TRID=SCA8_ATXN8OS
2025-09-15 20:24:49.574 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:49 [ERROR] - No reads found for TRID=SCA27B_FGF14
2025-09-15 20:24:49.574 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:49 [ERROR] - No reads found for TRID=DRPLA_ATN1
2025-09-15 20:24:49.581 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_plot_meth_allele.slurm_singularity INFO srun: job 51797799 queued and waiting for resources
2025-09-15 20:24:49.581 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_plot_meth_allele.slurm_singularity INFO srun: job 51797799 has been allocated resources
2025-09-15 20:24:49.581 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_plot_meth_allele.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:49.730 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:49 [ERROR] - No reads found for TRID=OPDM_ABCD3
2025-09-15 20:24:49.730 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:49 [ERROR] - No reads found for TRID=OPDM4_RILPL1
2025-09-15 20:24:49.730 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:49 [ERROR] - No reads found for TRID=OPDM_ABCD3
2025-09-15 20:24:49.730 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:49 [ERROR] - No reads found for TRID=SCA8_ATXN8OS
2025-09-15 20:24:49.730 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:49 [ERROR] - No reads found for TRID=OPDM4_RILPL1
2025-09-15 20:24:49.730 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:49 [ERROR] - No reads found for TRID=SCA27B_FGF14
2025-09-15 20:24:49.731 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:49 [ERROR] - No reads found for TRID=SCA8_ATXN8OS
2025-09-15 20:24:49.731 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:49 [ERROR] - No reads found for TRID=SCA27B_FGF14
2025-09-15 20:24:49.738 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_plot_motifs_allele.slurm_singularity INFO srun: job 51797800 queued and waiting for resources
2025-09-15 20:24:49.738 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_plot_motifs_allele.slurm_singularity INFO srun: job 51797800 has been allocated resources
2025-09-15 20:24:49.738 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_plot_motifs_allele.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:49.741 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO srun: job 51797801 queued and waiting for resources
2025-09-15 20:24:49.741 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO srun: job 51797801 has been allocated resources
2025-09-15 20:24:49.741 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:49.803 wdl.w:ptcp.w:call-trgt-39.t:call-trgt_plot_motifs_allele INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2136.motifs_allele.trgt_plots.zip"
2025-09-15 20:24:49.852 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:49 [ERROR] - No reads found for TRID=OPDM_ABCD3
2025-09-15 20:24:49.852 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:49 [ERROR] - No reads found for TRID=OPDM4_RILPL1
2025-09-15 20:24:49.852 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:49 [ERROR] - No reads found for TRID=SCA8_ATXN8OS
2025-09-15 20:24:49.852 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:49 [ERROR] - No reads found for TRID=SCA27B_FGF14
2025-09-15 20:24:49.852 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:49 [ERROR] - No reads found for TRID=DRPLA_ATN1
2025-09-15 20:24:49.861 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO srun: job 51797802 queued and waiting for resources
2025-09-15 20:24:49.861 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO srun: job 51797802 has been allocated resources
2025-09-15 20:24:49.861 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:49.883 wdl.w:ptcp.w:call-trgt-39.t:call-trgt_plot_motifs_allele NOTICE done
2025-09-15 20:24:49.888 wdl.w:ptcp.w:call-trgt-39 NOTICE finish :: job: "call-trgt_plot_motifs_allele"
2025-09-15 20:24:49.888 wdl.w:ptcp.w:call-trgt-39 INFO output :: job: "call-trgt_plot_motifs_allele", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-39/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2136.motifs_allele.trgt_plots.zip"}
2025-09-15 20:24:49.888 wdl.w:ptcp.w:call-trgt-39 INFO visit :: node: "output-images_motifs_allele", values: {"images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-39/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2136.motifs_allele.trgt_plots.zip"}
2025-09-15 20:24:49.896 wdl.w:ptcp.w:call-trgt-48.t:call-trgt_plot_motifs_waterfall NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-48/call-trgt_plot_motifs_waterfall", thread: 140608203109952
2025-09-15 20:24:49.911 wdl.w:ptcp.w:call-trgt-48.t:call-trgt_plot_motifs_waterfall INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:49.911 wdl.w:ptcp.w:call-trgt-48.t:call-trgt_plot_motifs_waterfall INFO input :: name: "waterfall", value: true
2025-09-15 20:24:49.911 wdl.w:ptcp.w:call-trgt-48.t:call-trgt_plot_motifs_waterfall INFO input :: name: "methylation", value: false
2025-09-15 20:24:49.911 wdl.w:ptcp.w:call-trgt-48.t:call-trgt_plot_motifs_waterfall INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:49.911 wdl.w:ptcp.w:call-trgt-48.t:call-trgt_plot_motifs_waterfall INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:49.912 wdl.w:ptcp.w:call-trgt-48.t:call-trgt_plot_motifs_waterfall INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:49.912 wdl.w:ptcp.w:call-trgt-48.t:call-trgt_plot_motifs_waterfall INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2145.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:49.912 wdl.w:ptcp.w:call-trgt-48.t:call-trgt_plot_motifs_waterfall INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2145.trgt.sorted.spanning.bam"
2025-09-15 20:24:49.912 wdl.w:ptcp.w:call-trgt-48.t:call-trgt_plot_motifs_waterfall INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2145.trgt.vcf"
2025-09-15 20:24:49.912 wdl.w:ptcp.w:call-trgt-48.t:call-trgt_plot_motifs_waterfall INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2145"
2025-09-15 20:24:49.913 wdl.w:ptcp.w:call-trgt-48.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:49.913 wdl.w:ptcp.w:call-trgt-48.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "plot_type", value: "waterfall"
2025-09-15 20:24:49.914 wdl.w:ptcp.w:call-trgt-48.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "show", value: "motifs"
2025-09-15 20:24:49.914 wdl.w:ptcp.w:call-trgt-48.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "threads", value: 1
2025-09-15 20:24:49.914 wdl.w:ptcp.w:call-trgt-48.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:49.914 wdl.w:ptcp.w:call-trgt-48.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2145.motifs_waterfall"
2025-09-15 20:24:49.914 wdl.w:ptcp.w:call-trgt-48.t:call-trgt_plot_motifs_waterfall INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:49.914 wdl.w:ptcp.w:call-trgt-48.t:call-trgt_plot_motifs_waterfall WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:49.915 wdl.w:ptcp.w:call-trgt-48.t:call-trgt_plot_motifs_waterfall INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:49.915 wdl.w:ptcp.w:call-trgt-48.t:call-trgt_plot_motifs_waterfall INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:49.947 wdl.w:ptcp.w:call-paraphase-69.t:call-run_paraphase.slurm_singularity INFO srun: job 51797803 queued and waiting for resources
2025-09-15 20:24:49.947 wdl.w:ptcp.w:call-paraphase-69.t:call-run_paraphase.slurm_singularity INFO srun: job 51797803 has been allocated resources
2025-09-15 20:24:49.947 wdl.w:ptcp.w:call-paraphase-69.t:call-run_paraphase.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:49.998 wdl.w:ptcp.w:call-trgt-48.t:call-trgt_plot_motifs_waterfall INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-48/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_cbu4zrm7"
2025-09-15 20:24:49.998 wdl.w:ptcp.w:call-trgt-39.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:47 [ERROR] - No reads found for TRID=OPDM4_RILPL1
2025-09-15 20:24:49.998 wdl.w:ptcp.w:call-trgt-48.t:call-trgt_plot_motifs_waterfall INFO Slurm invocation: srun --job-name call-trgt_plot_motifs_waterfall --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-48/call-trgt_plot_motifs_waterfall/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-48/call-trgt_plot_motifs_waterfall/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-48/call-trgt_plot_motifs_waterfall/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-48/call-trgt_plot_motifs_waterfall/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-48/call-trgt_genotype/out/m84036_250809_035451_s4.bc2145.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2145.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-48/call-trgt_genotype/out/m84036_250809_035451_s4.bc2145.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2145.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-48/call-trgt_genotype/out/m84036_250809_035451_s4.bc2145.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2145.trgt.sorted.spanning.bam.bai:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-48/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_cbu4zrm7/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-48/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_cbu4zrm7/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:49.999 wdl.w:ptcp.w:call-trgt-39.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:48 [ERROR] - No reads found for TRID=SCA27B_FGF14
2025-09-15 20:24:49.999 wdl.w:ptcp.w:call-trgt-39.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:48 [ERROR] - No reads found for TRID=SCA31_BEAN1
2025-09-15 20:24:49.999 wdl.w:ptcp.w:call-trgt-39.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:48 [ERROR] - No reads found for TRID=SCA3_ATXN3
2025-09-15 20:24:49.999 wdl.w:ptcp.w:call-trgt-39.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:48 [ERROR] - No reads found for TRID=HDL2_JPH3
2025-09-15 20:24:49.999 wdl.w:ptcp.w:call-trgt-39.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:48 [ERROR] - No reads found for TRID=FECD3_TCF4
2025-09-15 20:24:50.001 wdl.w:ptcp.w:call-trgt-39.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:48 [ERROR] - No reads found for TRID=SCA6_CACNA1A
2025-09-15 20:24:50.001 wdl.w:ptcp.w:call-trgt-39.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:48 [ERROR] - No reads found for TRID=OPDM2_GIPC1
2025-09-15 20:24:50.001 wdl.w:ptcp.w:call-trgt-39.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:48 [ERROR] - No reads found for TRID=SCA4_ZFHX3
2025-09-15 20:24:50.001 wdl.w:ptcp.w:call-trgt-39.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:48 [ERROR] - No reads found for TRID=SD5_HOXD13
2025-09-15 20:24:50.001 wdl.w:ptcp.w:call-trgt-39.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:48 [ERROR] - No reads found for TRID=CJD_PRNP
2025-09-15 20:24:50.001 wdl.w:ptcp.w:call-trgt-39.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:48 [ERROR] - No reads found for TRID=EPM1_CSTB
2025-09-15 20:24:50.001 wdl.w:ptcp.w:call-trgt-39.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:48 [ERROR] - No reads found for TRID=SCA36_NOP56
2025-09-15 20:24:50.001 wdl.w:ptcp.w:call-trgt-39.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:48 [ERROR] - No reads found for TRID=SCA7_ATXN7
2025-09-15 20:24:50.001 wdl.w:ptcp.w:call-trgt-39.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:48 [ERROR] - No reads found for TRID=DM1_DMPK
2025-09-15 20:24:50.001 wdl.w:ptcp.w:call-trgt-39.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:48 [ERROR] - No reads found for TRID=HD_HTT
2025-09-15 20:24:50.001 wdl.w:ptcp.w:call-trgt-39.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:48 [ERROR] - No reads found for TRID=CCHS_PHOX2B
2025-09-15 20:24:50.008 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_plot_meth_waterfall INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2160.meth_waterfall.trgt_plots.zip"
2025-09-15 20:24:50.044 wdl.w:ptcp.w:call-trgt-48.t:call-trgt_plot_motifs_waterfall NOTICE slurm_singularity run :: pid: 1203350, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-48/call-trgt_plot_motifs_waterfall/slurm_singularity.log.txt"
2025-09-15 20:24:50.090 wdl.w:ptcp.w:call-trgt-63.t:call-trgt_plot_meth_waterfall NOTICE done
2025-09-15 20:24:50.095 wdl.w:ptcp.w:call-trgt-63 NOTICE finish :: job: "call-trgt_plot_meth_waterfall"
2025-09-15 20:24:50.095 wdl.w:ptcp.w:call-trgt-63 INFO output :: job: "call-trgt_plot_meth_waterfall", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-63/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2160.meth_waterfall.trgt_plots.zip"}
2025-09-15 20:24:50.095 wdl.w:ptcp.w:call-trgt-63 INFO visit :: node: "output-images_meth_waterfall", values: {"images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-63/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2160.meth_waterfall.trgt_plots.zip"}
2025-09-15 20:24:50.096 wdl.w:ptcp.w:call-trgt-63 INFO visit :: node: "outputs", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-63/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2160.motifs_waterfall.trgt_plots.zip", "images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-63/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2160.meth_allele.trgt_plots.zip", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-63/call-trgt_genotype/out/m84036_250809_035451_s4.bc2160.trgt.sorted.spanning.bam.bai", "images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-63/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2160.motifs_allele.trgt_plots.zip", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-63/call-trgt_genotype/out/m84036_250809_035451_s4.bc2160.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-63/call-trgt_genotype/out/m84036_250809_035451_s4.bc2160.trgt.vcf", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-63/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2160.repeats.bam", "images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-63/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2160.meth_waterfall.trgt_plots.zip", "reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-63/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2160.repeats.bam.bai"}
2025-09-15 20:24:50.101 wdl.w:ptcp.w:call-trgt-57.t:call-trgt_plot_meth_allele NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-57/call-trgt_plot_meth_allele", thread: 140610367379008
2025-09-15 20:24:50.114 wdl.w:ptcp.w:call-trgt-41.t:call-trgt_plot_meth_allele.slurm_singularity INFO srun: job 51797804 queued and waiting for resources
2025-09-15 20:24:50.114 wdl.w:ptcp.w:call-trgt-41.t:call-trgt_plot_meth_allele.slurm_singularity INFO srun: job 51797804 has been allocated resources
2025-09-15 20:24:50.115 wdl.w:ptcp.w:call-trgt-41.t:call-trgt_plot_meth_allele.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:50.118 wdl.w:ptcp.w:call-trgt-57.t:call-trgt_plot_meth_allele INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:50.118 wdl.w:ptcp.w:call-trgt-57.t:call-trgt_plot_meth_allele INFO input :: name: "waterfall", value: false
2025-09-15 20:24:50.118 wdl.w:ptcp.w:call-trgt-57.t:call-trgt_plot_meth_allele INFO input :: name: "methylation", value: true
2025-09-15 20:24:50.118 wdl.w:ptcp.w:call-trgt-57.t:call-trgt_plot_meth_allele INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:50.118 wdl.w:ptcp.w:call-trgt-57.t:call-trgt_plot_meth_allele INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:50.118 wdl.w:ptcp.w:call-trgt-57.t:call-trgt_plot_meth_allele INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:50.119 wdl.w:ptcp.w:call-trgt-57.t:call-trgt_plot_meth_allele INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2154.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:50.119 wdl.w:ptcp.w:call-trgt-57.t:call-trgt_plot_meth_allele INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2154.trgt.sorted.spanning.bam"
2025-09-15 20:24:50.119 wdl.w:ptcp.w:call-trgt-57.t:call-trgt_plot_meth_allele INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2154.trgt.vcf"
2025-09-15 20:24:50.119 wdl.w:ptcp.w:call-trgt-57.t:call-trgt_plot_meth_allele INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2154"
2025-09-15 20:24:50.119 wdl.w:ptcp.w:call-trgt-57.t:call-trgt_plot_meth_allele INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:50.119 wdl.w:ptcp.w:call-trgt-57.t:call-trgt_plot_meth_allele INFO eval :: name: "plot_type", value: "allele"
2025-09-15 20:24:50.119 wdl.w:ptcp.w:call-trgt-57.t:call-trgt_plot_meth_allele INFO eval :: name: "show", value: "meth"
2025-09-15 20:24:50.119 wdl.w:ptcp.w:call-trgt-57.t:call-trgt_plot_meth_allele INFO eval :: name: "threads", value: 1
2025-09-15 20:24:50.120 wdl.w:ptcp.w:call-trgt-57.t:call-trgt_plot_meth_allele INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:50.120 wdl.w:ptcp.w:call-trgt-57.t:call-trgt_plot_meth_allele INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2154.meth_allele"
2025-09-15 20:24:50.120 wdl.w:ptcp.w:call-trgt-57.t:call-trgt_plot_meth_allele INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:50.120 wdl.w:ptcp.w:call-trgt-57.t:call-trgt_plot_meth_allele WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:50.121 wdl.w:ptcp.w:call-trgt-57.t:call-trgt_plot_meth_allele INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:50.121 wdl.w:ptcp.w:call-trgt-57.t:call-trgt_plot_meth_allele INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:50.133 wdl.w:ptcp.w:call-paraphase-34.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for rpgr for sample m84036_250809_035451_s4.bc2131 at 2025-09-15 20:24:35.378840...
2025-09-15 20:24:50.134 wdl.w:ptcp.w:call-paraphase-34.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for rpgr for sample m84036_250809_035451_s4.bc2131 at 2025-09-15 20:24:35.380039...
2025-09-15 20:24:50.134 wdl.w:ptcp.w:call-paraphase-34.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for rpgr for sample m84036_250809_035451_s4.bc2131 at 2025-09-15 20:24:36.670139...
2025-09-15 20:24:50.134 wdl.w:ptcp.w:call-paraphase-34.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for rpgr for sample m84036_250809_035451_s4.bc2131 at 2025-09-15 20:24:37.614172...
2025-09-15 20:24:50.135 wdl.w:ptcp.w:call-paraphase-34.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for rpgr for sample m84036_250809_035451_s4.bc2131 at 2025-09-15 20:24:37.857058...
2025-09-15 20:24:50.139 wdl.w:ptcp.w:call-paraphase-42.t:call-run_paraphase.stderr VERBOSE INFO:root:Processing sample m84036_250809_035451_s4.bc2139 at 2025-09-15 20:24:45.621133...
2025-09-15 20:24:50.141 wdl.w:ptcp.w:call-paraphase-42.t:call-run_paraphase.stderr VERBOSE INFO:root:Checking sample sex at 2025-09-15 20:24:45.622035...
2025-09-15 20:24:50.141 wdl.w:ptcp.w:call-paraphase-42.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for cyp21 for sample m84036_250809_035451_s4.bc2139 at 2025-09-15 20:24:45.661934...
2025-09-15 20:24:50.141 wdl.w:ptcp.w:call-paraphase-42.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for cyp21 for sample m84036_250809_035451_s4.bc2139 at 2025-09-15 20:24:45.662718...
2025-09-15 20:24:50.141 wdl.w:ptcp.w:call-paraphase-42.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for smn1 for sample m84036_250809_035451_s4.bc2139 at 2025-09-15 20:24:45.662140...
2025-09-15 20:24:50.141 wdl.w:ptcp.w:call-paraphase-42.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for gba for sample m84036_250809_035451_s4.bc2139 at 2025-09-15 20:24:45.662272...
2025-09-15 20:24:50.142 wdl.w:ptcp.w:call-paraphase-42.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for hba for sample m84036_250809_035451_s4.bc2139 at 2025-09-15 20:24:45.662299...
2025-09-15 20:24:50.142 wdl.w:ptcp.w:call-paraphase-42.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for smn1 for sample m84036_250809_035451_s4.bc2139 at 2025-09-15 20:24:45.662857...
2025-09-15 20:24:50.142 wdl.w:ptcp.w:call-paraphase-42.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for gba for sample m84036_250809_035451_s4.bc2139 at 2025-09-15 20:24:45.662920...
2025-09-15 20:24:50.142 wdl.w:ptcp.w:call-paraphase-42.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for hba for sample m84036_250809_035451_s4.bc2139 at 2025-09-15 20:24:45.662929...
2025-09-15 20:24:50.203 wdl.w:ptcp.w:call-trgt-57.t:call-trgt_plot_meth_allele INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-57/call-trgt_plot_meth_allele/_singularity_tmpdir_vcx4a2oz"
2025-09-15 20:24:50.204 wdl.w:ptcp.w:call-trgt-57.t:call-trgt_plot_meth_allele INFO Slurm invocation: srun --job-name call-trgt_plot_meth_allele --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-57/call-trgt_plot_meth_allele/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-57/call-trgt_plot_meth_allele/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-57/call-trgt_plot_meth_allele/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-57/call-trgt_plot_meth_allele/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-57/call-trgt_genotype/out/m84036_250809_035451_s4.bc2154.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2154.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-57/call-trgt_genotype/out/m84036_250809_035451_s4.bc2154.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2154.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-57/call-trgt_genotype/out/m84036_250809_035451_s4.bc2154.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2154.trgt.vcf:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-57/call-trgt_plot_meth_allele/_singularity_tmpdir_vcx4a2oz/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-57/call-trgt_plot_meth_allele/_singularity_tmpdir_vcx4a2oz/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:50.204 wdl.w:ptcp.w:call-trgt-63 NOTICE done
2025-09-15 20:24:50.208 wdl.w:ptcp NOTICE finish :: job: "call-trgt-63"
2025-09-15 20:24:50.208 wdl.w:ptcp INFO output :: job: "call-trgt-63", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-63/out/m84036_250809_035451_s4.bc2160.motifs_waterfall.trgt_plots.zip", "images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-63/out/m84036_250809_035451_s4.bc2160.meth_allele.trgt_plots.zip", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-63/out/m84036_250809_035451_s4.bc2160.trgt.sorted.spanning.bam.bai", "images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-63/out/m84036_250809_035451_s4.bc2160.motifs_allele.trgt_plots.zip", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-63/out/m84036_250809_035451_s4.bc2160.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-63/out/m84036_250809_035451_s4.bc2160.trgt.vcf", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-63/out/m84036_250809_035451_s4.bc2160.repeats.bam", "images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-63/out/m84036_250809_035451_s4.bc2160.meth_waterfall.trgt_plots.zip", "reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-63/out/m84036_250809_035451_s4.bc2160.repeats.bam.bai"}
2025-09-15 20:24:50.212 wdl.w:ptcp.w:call-paraphase-73 NOTICE workflow start :: name: "paraphase", source: "./paraphase.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-73"
2025-09-15 20:24:50.224 wdl.w:ptcp.w:call-trgt-57.t:call-trgt_plot_meth_allele NOTICE slurm_singularity run :: pid: 1203352, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-57/call-trgt_plot_meth_allele/slurm_singularity.log.txt"
2025-09-15 20:24:50.226 wdl.w:ptcp.w:call-paraphase-73 INFO visit :: node: "decl-annotation_vcf", values: {"annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf"}
2025-09-15 20:24:50.226 wdl.w:ptcp.w:call-paraphase-73 INFO visit :: node: "decl-config_file", values: {"config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml"}
2025-09-15 20:24:50.226 wdl.w:ptcp.w:call-paraphase-73 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:24:50.226 wdl.w:ptcp.w:call-paraphase-73 INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:24:50.226 wdl.w:ptcp.w:call-paraphase-73 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-73/out/m84036_250809_035451_s4.bc2170.mapped.bam"}
2025-09-15 20:24:50.226 wdl.w:ptcp.w:call-paraphase-73 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-73/out/m84036_250809_035451_s4.bc2170.mapped.bam.bai"}
2025-09-15 20:24:50.226 wdl.w:ptcp.w:call-paraphase-73 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:24:50.226 wdl.w:ptcp.w:call-paraphase-73 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:24:50.226 wdl.w:ptcp.w:call-paraphase-73 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2170"}
2025-09-15 20:24:50.226 wdl.w:ptcp.w:call-paraphase-73 INFO visit :: node: "decl-sex", values: {"sex": "F"}
2025-09-15 20:24:50.227 wdl.w:ptcp.w:call-paraphase-73 NOTICE ready :: job: "call-run_paraphase", callee: "run_paraphase"
2025-09-15 20:24:50.227 wdl.w:ptcp.w:call-paraphase-73 INFO input :: job: "call-run_paraphase", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf", "genome_version": "38", "config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-73/out/m84036_250809_035451_s4.bc2170.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-73/out/m84036_250809_035451_s4.bc2170.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2170"}
2025-09-15 20:24:50.250 wdl.w:ptcp.w:call-trgt-41.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO srun: job 51797805 queued and waiting for resources
2025-09-15 20:24:50.250 wdl.w:ptcp.w:call-trgt-41.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO srun: job 51797805 has been allocated resources
2025-09-15 20:24:50.250 wdl.w:ptcp.w:call-trgt-41.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:50.254 wdl.w:ptcp.w:call-trgt-41.t:call-trgt_plot_motifs_allele.slurm_singularity INFO srun: job 51797806 queued and waiting for resources
2025-09-15 20:24:50.254 wdl.w:ptcp.w:call-trgt-41.t:call-trgt_plot_motifs_allele.slurm_singularity INFO srun: job 51797806 has been allocated resources
2025-09-15 20:24:50.254 wdl.w:ptcp.w:call-trgt-41.t:call-trgt_plot_motifs_allele.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:50.281 wdl.w:ptcp.w:call-sawfish-69.t:call-run_sawfish.slurm_singularity INFO srun: job 51797808 queued and waiting for resources
2025-09-15 20:24:50.281 wdl.w:ptcp.w:call-sawfish-69.t:call-run_sawfish.slurm_singularity INFO srun: job 51797808 has been allocated resources
2025-09-15 20:24:50.281 wdl.w:ptcp.w:call-sawfish-69.t:call-run_sawfish.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:50.281 wdl.w:ptcp.w:call-sawfish-69.t:call-run_sawfish.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:24:50.282 wdl.w:ptcp.w:call-trgt-41.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO srun: job 51797807 queued and waiting for resources
2025-09-15 20:24:50.282 wdl.w:ptcp.w:call-trgt-41.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO srun: job 51797807 has been allocated resources
2025-09-15 20:24:50.282 wdl.w:ptcp.w:call-trgt-41.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:50.329 wdl.w:ptcp.w:call-sawfish-44.t:call-run_sawfish.stderr VERBOSE [M::mm_idx_gen::34.808*1.39] collected minimizers
2025-09-15 20:24:50.329 wdl.w:ptcp.w:call-sawfish-44.t:call-run_sawfish.stderr VERBOSE [M::mm_idx_gen::41.535*1.64] sorted minimizers
2025-09-15 20:24:50.329 wdl.w:ptcp.w:call-sawfish-44.t:call-run_sawfish.stderr VERBOSE [M::main::41.535*1.64] loaded/built the index for 195 target sequence(s)
2025-09-15 20:24:50.329 wdl.w:ptcp.w:call-sawfish-44.t:call-run_sawfish.stderr VERBOSE [M::mm_mapopt_update::44.554*1.60] mid_occ = 136
2025-09-15 20:24:50.329 wdl.w:ptcp.w:call-sawfish-44.t:call-run_sawfish.stderr VERBOSE [M::mm_idx_stat] kmer size: 19; skip: 19; is_hpc: 0; #seq: 195
2025-09-15 20:24:50.330 wdl.w:ptcp.w:call-sawfish-44.t:call-run_sawfish.stderr VERBOSE [M::mm_idx_stat::47.247*1.57] distinct minimizers: 214664461 (92.23% are singletons); average occurrences: 1.372; average spacing: 10.529; total length: 3099922541
2025-09-15 20:24:50.330 wdl.w:ptcp.w:call-sawfish-44.t:call-run_sawfish.stderr VERBOSE [M::main] Version: 2.26-r1175
2025-09-15 20:24:50.330 wdl.w:ptcp.w:call-sawfish-44.t:call-run_sawfish.stderr VERBOSE [M::main] CMD: /opt/pacbio/smrttools/install/smrtlink-release_25.1.0.257715/bundles/smrttools/install/smrttools-release_25.1.0.257715/private/thirdparty/minimap2/minimap2_2.26-pacbio2/binwrap/../../../../../private/thirdparty/minimap2/minimap2_2.26-pacbio2/bin/minimap2 -a -y -x map-hifi -Y -E 1,0 /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa -
2025-09-15 20:24:50.330 wdl.w:ptcp.w:call-sawfish-44.t:call-run_sawfish.stderr VERBOSE [M::main] Real time: 47.553 sec; CPU: 74.253 sec; Peak RSS: 11.887 GB
2025-09-15 20:24:50.385 wdl.w:ptcp.w:call-trgt-48.t:call-trgt_plot_meth_allele.slurm_singularity INFO srun: job 51797809 queued and waiting for resources
2025-09-15 20:24:50.386 wdl.w:ptcp.w:call-trgt-48.t:call-trgt_plot_meth_allele.slurm_singularity INFO srun: job 51797809 has been allocated resources
2025-09-15 20:24:50.386 wdl.w:ptcp.w:call-trgt-48.t:call-trgt_plot_meth_allele.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:50.386 wdl.w:ptcp.w:call-trgt-48.t:call-trgt_plot_meth_allele.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:24:50.463 wdl.w:ptcp.w:call-paraphase-27.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for hbb for sample m84036_250809_035451_s4.bc2124 at 2025-09-15 20:24:39.441905...
2025-09-15 20:24:50.464 wdl.w:ptcp.w:call-paraphase-27.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for gba for sample m84036_250809_035451_s4.bc2124 at 2025-09-15 20:24:41.424201...
2025-09-15 20:24:50.464 wdl.w:ptcp.w:call-paraphase-27.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for gba for sample m84036_250809_035451_s4.bc2124 at 2025-09-15 20:24:41.968032...
2025-09-15 20:24:50.464 wdl.w:ptcp.w:call-paraphase-27.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for hbb for sample m84036_250809_035451_s4.bc2124 at 2025-09-15 20:24:42.710880...
2025-09-15 20:24:50.464 wdl.w:ptcp.w:call-paraphase-27.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for hbb for sample m84036_250809_035451_s4.bc2124 at 2025-09-15 20:24:42.927302...
2025-09-15 20:24:50.464 wdl.w:ptcp.w:call-trgt-48.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO srun: job 51797810 queued and waiting for resources
2025-09-15 20:24:50.465 wdl.w:ptcp.w:call-trgt-48.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO srun: job 51797810 has been allocated resources
2025-09-15 20:24:50.465 wdl.w:ptcp.w:call-trgt-48.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:50.465 wdl.w:ptcp.w:call-trgt-48.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:24:50.484 wdl.w:ptcp.w:call-trgt-48.t:call-trgt_plot_motifs_allele.slurm_singularity INFO srun: job 51797811 queued and waiting for resources
2025-09-15 20:24:50.484 wdl.w:ptcp.w:call-trgt-48.t:call-trgt_plot_motifs_allele.slurm_singularity INFO srun: job 51797811 has been allocated resources
2025-09-15 20:24:50.485 wdl.w:ptcp.w:call-trgt-48.t:call-trgt_plot_motifs_allele.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:50.485 wdl.w:ptcp.w:call-trgt-48.t:call-trgt_plot_motifs_allele.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:24:50.630 wdl.w:ptcp.w:call-trgt-39.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:48 [ERROR] - No reads found for TRID=SCA12_PPP2R2B
2025-09-15 20:24:50.630 wdl.w:ptcp.w:call-trgt-39.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:49 [ERROR] - No reads found for TRID=SCA1_ATXN1
2025-09-15 20:24:50.631 wdl.w:ptcp.w:call-trgt-39.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:49 [ERROR] - No reads found for TRID=SCA17_TBP
2025-09-15 20:24:50.631 wdl.w:ptcp.w:call-trgt-39.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:49 [ERROR] - No reads found for TRID=OPDM1_LRP12
2025-09-15 20:24:50.631 wdl.w:ptcp.w:call-trgt-39.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:49 [ERROR] - No reads found for TRID=FAME1_SAMD12
2025-09-15 20:24:50.631 wdl.w:ptcp.w:call-trgt-39.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:49 [ERROR] - No reads found for TRID=FRA2A_AFF3
2025-09-15 20:24:50.631 wdl.w:ptcp.w:call-trgt-39.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:49 [ERROR] - No reads found for TRID=SBMA_AR
2025-09-15 20:24:50.631 wdl.w:ptcp.w:call-trgt-39.t:call-trgt_plot_meth_allele INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2136.meth_allele.trgt_plots.zip"
2025-09-15 20:24:50.673 wdl.w:ptcp.w:call-trgt-39.t:call-trgt_plot_meth_waterfall INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2136.meth_waterfall.trgt_plots.zip"
2025-09-15 20:24:50.710 wdl.w:ptcp.w:call-trgt-39.t:call-trgt_plot_meth_allele NOTICE done
2025-09-15 20:24:50.715 wdl.w:ptcp.w:call-trgt-39 NOTICE finish :: job: "call-trgt_plot_meth_allele"
2025-09-15 20:24:50.716 wdl.w:ptcp.w:call-trgt-39 INFO output :: job: "call-trgt_plot_meth_allele", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-39/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2136.meth_allele.trgt_plots.zip"}
2025-09-15 20:24:50.716 wdl.w:ptcp.w:call-trgt-39 INFO visit :: node: "output-images_meth_allele", values: {"images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-39/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2136.meth_allele.trgt_plots.zip"}
2025-09-15 20:24:50.723 wdl.w:ptcp.w:call-trgt-57.t:call-trgt_plot_meth_waterfall NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-57/call-trgt_plot_meth_waterfall", thread: 140607691417152
2025-09-15 20:24:50.740 wdl.w:ptcp.w:call-trgt-57.t:call-trgt_plot_meth_waterfall INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:50.740 wdl.w:ptcp.w:call-trgt-57.t:call-trgt_plot_meth_waterfall INFO input :: name: "waterfall", value: true
2025-09-15 20:24:50.740 wdl.w:ptcp.w:call-trgt-57.t:call-trgt_plot_meth_waterfall INFO input :: name: "methylation", value: true
2025-09-15 20:24:50.740 wdl.w:ptcp.w:call-trgt-57.t:call-trgt_plot_meth_waterfall INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:50.740 wdl.w:ptcp.w:call-trgt-57.t:call-trgt_plot_meth_waterfall INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:50.740 wdl.w:ptcp.w:call-trgt-57.t:call-trgt_plot_meth_waterfall INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:50.740 wdl.w:ptcp.w:call-trgt-57.t:call-trgt_plot_meth_waterfall INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2154.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:50.740 wdl.w:ptcp.w:call-trgt-57.t:call-trgt_plot_meth_waterfall INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2154.trgt.sorted.spanning.bam"
2025-09-15 20:24:50.741 wdl.w:ptcp.w:call-trgt-57.t:call-trgt_plot_meth_waterfall INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2154.trgt.vcf"
2025-09-15 20:24:50.741 wdl.w:ptcp.w:call-trgt-57.t:call-trgt_plot_meth_waterfall INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2154"
2025-09-15 20:24:50.741 wdl.w:ptcp.w:call-trgt-57.t:call-trgt_plot_meth_waterfall INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:50.741 wdl.w:ptcp.w:call-trgt-57.t:call-trgt_plot_meth_waterfall INFO eval :: name: "plot_type", value: "waterfall"
2025-09-15 20:24:50.741 wdl.w:ptcp.w:call-trgt-57.t:call-trgt_plot_meth_waterfall INFO eval :: name: "show", value: "meth"
2025-09-15 20:24:50.741 wdl.w:ptcp.w:call-trgt-57.t:call-trgt_plot_meth_waterfall INFO eval :: name: "threads", value: 1
2025-09-15 20:24:50.742 wdl.w:ptcp.w:call-trgt-57.t:call-trgt_plot_meth_waterfall INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:50.742 wdl.w:ptcp.w:call-trgt-57.t:call-trgt_plot_meth_waterfall INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2154.meth_waterfall"
2025-09-15 20:24:50.742 wdl.w:ptcp.w:call-trgt-57.t:call-trgt_plot_meth_waterfall INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:50.742 wdl.w:ptcp.w:call-trgt-57.t:call-trgt_plot_meth_waterfall WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:50.743 wdl.w:ptcp.w:call-trgt-57.t:call-trgt_plot_meth_waterfall INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:50.743 wdl.w:ptcp.w:call-trgt-57.t:call-trgt_plot_meth_waterfall INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:50.753 wdl.w:ptcp.w:call-trgt-39.t:call-trgt_plot_meth_waterfall NOTICE done
2025-09-15 20:24:50.759 wdl.w:ptcp.w:call-trgt-39 NOTICE finish :: job: "call-trgt_plot_meth_waterfall"
2025-09-15 20:24:50.759 wdl.w:ptcp.w:call-trgt-39 INFO output :: job: "call-trgt_plot_meth_waterfall", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-39/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2136.meth_waterfall.trgt_plots.zip"}
2025-09-15 20:24:50.759 wdl.w:ptcp.w:call-trgt-39 INFO visit :: node: "output-images_meth_waterfall", values: {"images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-39/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2136.meth_waterfall.trgt_plots.zip"}
2025-09-15 20:24:50.766 wdl.w:ptcp.w:call-trgt-57.t:call-trgt_plot_motifs_allele NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-57/call-trgt_plot_motifs_allele", thread: 140613068518976
2025-09-15 20:24:50.783 wdl.w:ptcp.w:call-trgt-57.t:call-trgt_plot_motifs_allele INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:50.783 wdl.w:ptcp.w:call-trgt-57.t:call-trgt_plot_motifs_allele INFO input :: name: "waterfall", value: false
2025-09-15 20:24:50.783 wdl.w:ptcp.w:call-trgt-57.t:call-trgt_plot_motifs_allele INFO input :: name: "methylation", value: false
2025-09-15 20:24:50.783 wdl.w:ptcp.w:call-trgt-57.t:call-trgt_plot_motifs_allele INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:50.784 wdl.w:ptcp.w:call-trgt-57.t:call-trgt_plot_motifs_allele INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:50.784 wdl.w:ptcp.w:call-trgt-57.t:call-trgt_plot_motifs_allele INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:50.784 wdl.w:ptcp.w:call-trgt-57.t:call-trgt_plot_motifs_allele INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2154.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:50.784 wdl.w:ptcp.w:call-trgt-57.t:call-trgt_plot_motifs_allele INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2154.trgt.sorted.spanning.bam"
2025-09-15 20:24:50.784 wdl.w:ptcp.w:call-trgt-57.t:call-trgt_plot_motifs_allele INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2154.trgt.vcf"
2025-09-15 20:24:50.784 wdl.w:ptcp.w:call-trgt-57.t:call-trgt_plot_motifs_allele INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2154"
2025-09-15 20:24:50.784 wdl.w:ptcp.w:call-trgt-57.t:call-trgt_plot_motifs_allele INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:50.784 wdl.w:ptcp.w:call-trgt-57.t:call-trgt_plot_motifs_allele INFO eval :: name: "plot_type", value: "allele"
2025-09-15 20:24:50.784 wdl.w:ptcp.w:call-trgt-57.t:call-trgt_plot_motifs_allele INFO eval :: name: "show", value: "motifs"
2025-09-15 20:24:50.784 wdl.w:ptcp.w:call-trgt-57.t:call-trgt_plot_motifs_allele INFO eval :: name: "threads", value: 1
2025-09-15 20:24:50.785 wdl.w:ptcp.w:call-trgt-57.t:call-trgt_plot_motifs_allele INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:50.785 wdl.w:ptcp.w:call-trgt-57.t:call-trgt_plot_motifs_allele INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2154.motifs_allele"
2025-09-15 20:24:50.785 wdl.w:ptcp.w:call-trgt-57.t:call-trgt_plot_motifs_allele INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:50.785 wdl.w:ptcp.w:call-trgt-57.t:call-trgt_plot_motifs_allele WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:50.785 wdl.w:ptcp.w:call-trgt-57.t:call-trgt_plot_motifs_allele INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:50.786 wdl.w:ptcp.w:call-trgt-57.t:call-trgt_plot_motifs_allele INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:50.813 wdl.w:ptcp.w:call-trgt-57.t:call-trgt_plot_meth_waterfall INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-57/call-trgt_plot_meth_waterfall/_singularity_tmpdir_yuee3kug"
2025-09-15 20:24:50.813 wdl.w:ptcp.w:call-trgt-57.t:call-trgt_plot_meth_waterfall INFO Slurm invocation: srun --job-name call-trgt_plot_meth_waterfall --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-57/call-trgt_plot_meth_waterfall/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-57/call-trgt_plot_meth_waterfall/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-57/call-trgt_plot_meth_waterfall/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-57/call-trgt_plot_meth_waterfall/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-57/call-trgt_genotype/out/m84036_250809_035451_s4.bc2154.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2154.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-57/call-trgt_genotype/out/m84036_250809_035451_s4.bc2154.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2154.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-57/call-trgt_genotype/out/m84036_250809_035451_s4.bc2154.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2154.trgt.vcf:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-57/call-trgt_plot_meth_waterfall/_singularity_tmpdir_yuee3kug/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-57/call-trgt_plot_meth_waterfall/_singularity_tmpdir_yuee3kug/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:50.852 wdl.w:ptcp.w:call-trgt-57.t:call-trgt_plot_meth_waterfall NOTICE slurm_singularity run :: pid: 1203367, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-57/call-trgt_plot_meth_waterfall/slurm_singularity.log.txt"
2025-09-15 20:24:50.860 wdl.w:ptcp.w:call-trgt-39.t:call-trgt_plot_motifs_waterfall INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2136.motifs_waterfall.trgt_plots.zip"
2025-09-15 20:24:50.861 wdl.w:ptcp.w:call-trgt-57.t:call-trgt_plot_motifs_allele INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-57/call-trgt_plot_motifs_allele/_singularity_tmpdir_u3e5ndbk"
2025-09-15 20:24:50.861 wdl.w:ptcp.w:call-trgt-57.t:call-trgt_plot_motifs_allele INFO Slurm invocation: srun --job-name call-trgt_plot_motifs_allele --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-57/call-trgt_plot_motifs_allele/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-57/call-trgt_plot_motifs_allele/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-57/call-trgt_plot_motifs_allele/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-57/call-trgt_plot_motifs_allele/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-57/call-trgt_genotype/out/m84036_250809_035451_s4.bc2154.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2154.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-57/call-trgt_genotype/out/m84036_250809_035451_s4.bc2154.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2154.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-57/call-trgt_genotype/out/m84036_250809_035451_s4.bc2154.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2154.trgt.vcf:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-57/call-trgt_plot_motifs_allele/_singularity_tmpdir_u3e5ndbk/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-57/call-trgt_plot_motifs_allele/_singularity_tmpdir_u3e5ndbk/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:50.872 wdl.w:ptcp.w:call-trgt-57.t:call-trgt_plot_motifs_allele NOTICE slurm_singularity run :: pid: 1203369, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-57/call-trgt_plot_motifs_allele/slurm_singularity.log.txt"
2025-09-15 20:24:50.941 wdl.w:ptcp.w:call-trgt-39.t:call-trgt_plot_motifs_waterfall NOTICE done
2025-09-15 20:24:50.951 wdl.w:ptcp.w:call-trgt-39 NOTICE finish :: job: "call-trgt_plot_motifs_waterfall"
2025-09-15 20:24:50.951 wdl.w:ptcp.w:call-trgt-39 INFO output :: job: "call-trgt_plot_motifs_waterfall", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-39/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2136.motifs_waterfall.trgt_plots.zip"}
2025-09-15 20:24:50.952 wdl.w:ptcp.w:call-trgt-39 INFO visit :: node: "output-images_motifs_waterfall", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-39/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2136.motifs_waterfall.trgt_plots.zip"}
2025-09-15 20:24:50.952 wdl.w:ptcp.w:call-trgt-39 INFO visit :: node: "outputs", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-39/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2136.motifs_waterfall.trgt_plots.zip", "images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-39/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2136.meth_allele.trgt_plots.zip", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-39/call-trgt_genotype/out/m84036_250809_035451_s4.bc2136.trgt.sorted.spanning.bam.bai", "images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-39/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2136.motifs_allele.trgt_plots.zip", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-39/call-trgt_genotype/out/m84036_250809_035451_s4.bc2136.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-39/call-trgt_genotype/out/m84036_250809_035451_s4.bc2136.trgt.vcf", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-39/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2136.repeats.bam", "images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-39/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2136.meth_waterfall.trgt_plots.zip", "reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-39/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2136.repeats.bam.bai"}
2025-09-15 20:24:50.958 wdl.w:ptcp.w:call-trgt-57.t:call-trgt_plot_motifs_waterfall NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-57/call-trgt_plot_motifs_waterfall", thread: 140610870679104
2025-09-15 20:24:50.982 wdl.w:ptcp.w:call-trgt-57.t:call-trgt_plot_motifs_waterfall INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:50.982 wdl.w:ptcp.w:call-trgt-57.t:call-trgt_plot_motifs_waterfall INFO input :: name: "waterfall", value: true
2025-09-15 20:24:50.982 wdl.w:ptcp.w:call-trgt-57.t:call-trgt_plot_motifs_waterfall INFO input :: name: "methylation", value: false
2025-09-15 20:24:50.983 wdl.w:ptcp.w:call-trgt-57.t:call-trgt_plot_motifs_waterfall INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:50.983 wdl.w:ptcp.w:call-trgt-57.t:call-trgt_plot_motifs_waterfall INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:50.983 wdl.w:ptcp.w:call-trgt-57.t:call-trgt_plot_motifs_waterfall INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:50.983 wdl.w:ptcp.w:call-trgt-57.t:call-trgt_plot_motifs_waterfall INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2154.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:50.983 wdl.w:ptcp.w:call-trgt-57.t:call-trgt_plot_motifs_waterfall INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2154.trgt.sorted.spanning.bam"
2025-09-15 20:24:50.983 wdl.w:ptcp.w:call-trgt-57.t:call-trgt_plot_motifs_waterfall INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2154.trgt.vcf"
2025-09-15 20:24:50.983 wdl.w:ptcp.w:call-trgt-57.t:call-trgt_plot_motifs_waterfall INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2154"
2025-09-15 20:24:50.983 wdl.w:ptcp.w:call-trgt-57.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:50.983 wdl.w:ptcp.w:call-trgt-57.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "plot_type", value: "waterfall"
2025-09-15 20:24:50.983 wdl.w:ptcp.w:call-trgt-57.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "show", value: "motifs"
2025-09-15 20:24:50.983 wdl.w:ptcp.w:call-trgt-57.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "threads", value: 1
2025-09-15 20:24:50.984 wdl.w:ptcp.w:call-trgt-57.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:50.984 wdl.w:ptcp.w:call-trgt-57.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2154.motifs_waterfall"
2025-09-15 20:24:50.984 wdl.w:ptcp.w:call-trgt-57.t:call-trgt_plot_motifs_waterfall INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:50.984 wdl.w:ptcp.w:call-trgt-57.t:call-trgt_plot_motifs_waterfall WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:50.985 wdl.w:ptcp.w:call-trgt-57.t:call-trgt_plot_motifs_waterfall INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:50.985 wdl.w:ptcp.w:call-trgt-57.t:call-trgt_plot_motifs_waterfall INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:51.054 wdl.w:ptcp.w:call-trgt-48.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO srun: job 51797812 queued and waiting for resources
2025-09-15 20:24:51.054 wdl.w:ptcp.w:call-trgt-48.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO srun: job 51797812 has been allocated resources
2025-09-15 20:24:51.054 wdl.w:ptcp.w:call-trgt-48.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:51.057 wdl.w:ptcp.w:call-trgt-39 NOTICE done
2025-09-15 20:24:51.062 wdl.w:ptcp NOTICE finish :: job: "call-trgt-39"
2025-09-15 20:24:51.062 wdl.w:ptcp INFO output :: job: "call-trgt-39", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-39/out/m84036_250809_035451_s4.bc2136.motifs_waterfall.trgt_plots.zip", "images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-39/out/m84036_250809_035451_s4.bc2136.meth_allele.trgt_plots.zip", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-39/out/m84036_250809_035451_s4.bc2136.trgt.sorted.spanning.bam.bai", "images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-39/out/m84036_250809_035451_s4.bc2136.motifs_allele.trgt_plots.zip", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-39/out/m84036_250809_035451_s4.bc2136.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-39/out/m84036_250809_035451_s4.bc2136.trgt.vcf", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-39/out/m84036_250809_035451_s4.bc2136.repeats.bam", "images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-39/out/m84036_250809_035451_s4.bc2136.meth_waterfall.trgt_plots.zip", "reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-39/out/m84036_250809_035451_s4.bc2136.repeats.bam.bai"}
2025-09-15 20:24:51.071 wdl.w:ptcp.w:call-sawfish-73 NOTICE workflow start :: name: "sawfish", source: "./sawfish.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-73"
2025-09-15 20:24:51.072 wdl.w:ptcp.w:call-trgt-57.t:call-trgt_plot_motifs_waterfall INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-57/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_9ted8clv"
2025-09-15 20:24:51.072 wdl.w:ptcp.w:call-trgt-57.t:call-trgt_plot_motifs_waterfall INFO Slurm invocation: srun --job-name call-trgt_plot_motifs_waterfall --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-57/call-trgt_plot_motifs_waterfall/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-57/call-trgt_plot_motifs_waterfall/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-57/call-trgt_plot_motifs_waterfall/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-57/call-trgt_plot_motifs_waterfall/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-57/call-trgt_genotype/out/m84036_250809_035451_s4.bc2154.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2154.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-57/call-trgt_genotype/out/m84036_250809_035451_s4.bc2154.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2154.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-57/call-trgt_genotype/out/m84036_250809_035451_s4.bc2154.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2154.trgt.vcf:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-57/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_9ted8clv/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-57/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_9ted8clv/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:51.088 wdl.w:ptcp.w:call-trgt-57.t:call-trgt_plot_motifs_waterfall NOTICE slurm_singularity run :: pid: 1203371, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-57/call-trgt_plot_motifs_waterfall/slurm_singularity.log.txt"
2025-09-15 20:24:51.090 wdl.w:ptcp.w:call-sawfish-73 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:24:51.090 wdl.w:ptcp.w:call-sawfish-73 INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:24:51.090 wdl.w:ptcp.w:call-sawfish-73 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-73/out/m84036_250809_035451_s4.bc2170.mapped.bam"}
2025-09-15 20:24:51.090 wdl.w:ptcp.w:call-sawfish-73 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-73/out/m84036_250809_035451_s4.bc2170.mapped.bam.bai"}
2025-09-15 20:24:51.090 wdl.w:ptcp.w:call-sawfish-73 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:24:51.090 wdl.w:ptcp.w:call-sawfish-73 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:24:51.091 wdl.w:ptcp.w:call-sawfish-73 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2170"}
2025-09-15 20:24:51.091 wdl.w:ptcp.w:call-sawfish-73 NOTICE ready :: job: "call-run_sawfish", callee: "run_sawfish"
2025-09-15 20:24:51.091 wdl.w:ptcp.w:call-sawfish-73 INFO input :: job: "call-run_sawfish", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-73/out/m84036_250809_035451_s4.bc2170.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-73/out/m84036_250809_035451_s4.bc2170.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2170"}
2025-09-15 20:24:51.160 wdl.w:ptcp.w:call-paraphase-23.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for rpgr for sample m84036_250809_035451_s4.bc2120 at 2025-09-15 20:24:45.929877...
2025-09-15 20:24:51.161 wdl.w:ptcp.w:call-paraphase-23.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for rpgr for sample m84036_250809_035451_s4.bc2120 at 2025-09-15 20:24:45.931238...
2025-09-15 20:24:51.161 wdl.w:ptcp.w:call-paraphase-23.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for rpgr for sample m84036_250809_035451_s4.bc2120 at 2025-09-15 20:24:47.909797...
2025-09-15 20:24:51.233 wdl.w:ptcp.w:call-trgt-57.t:call-trgt_plot_meth_allele.slurm_singularity INFO srun: job 51797813 queued and waiting for resources
2025-09-15 20:24:51.233 wdl.w:ptcp.w:call-trgt-57.t:call-trgt_plot_meth_allele.slurm_singularity INFO srun: job 51797813 has been allocated resources
2025-09-15 20:24:51.233 wdl.w:ptcp.w:call-trgt-57.t:call-trgt_plot_meth_allele.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:51.506 wdl.w:ptcp.w:call-trgt-44.t:call-trgt_plot_motifs_waterfall INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2141.motifs_waterfall.trgt_plots.zip"
2025-09-15 20:24:51.614 wdl.w:ptcp.w:call-trgt-44.t:call-trgt_plot_motifs_waterfall NOTICE done
2025-09-15 20:24:51.651 wdl.w:ptcp.w:call-trgt-44 NOTICE finish :: job: "call-trgt_plot_motifs_waterfall"
2025-09-15 20:24:51.651 wdl.w:ptcp.w:call-trgt-44 INFO output :: job: "call-trgt_plot_motifs_waterfall", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-44/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2141.motifs_waterfall.trgt_plots.zip"}
2025-09-15 20:24:51.651 wdl.w:ptcp.w:call-trgt-44 INFO visit :: node: "output-images_motifs_waterfall", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-44/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2141.motifs_waterfall.trgt_plots.zip"}
2025-09-15 20:24:51.660 wdl.w:ptcp.w:call-trgt-40.t:call-trgt_plot_meth_allele NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-40/call-trgt_plot_meth_allele", thread: 140611415942720
2025-09-15 20:24:51.680 wdl.w:ptcp.w:call-trgt-40.t:call-trgt_plot_meth_allele INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:51.680 wdl.w:ptcp.w:call-trgt-40.t:call-trgt_plot_meth_allele INFO input :: name: "waterfall", value: false
2025-09-15 20:24:51.680 wdl.w:ptcp.w:call-trgt-40.t:call-trgt_plot_meth_allele INFO input :: name: "methylation", value: true
2025-09-15 20:24:51.680 wdl.w:ptcp.w:call-trgt-40.t:call-trgt_plot_meth_allele INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:51.680 wdl.w:ptcp.w:call-trgt-40.t:call-trgt_plot_meth_allele INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:51.680 wdl.w:ptcp.w:call-trgt-40.t:call-trgt_plot_meth_allele INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:51.680 wdl.w:ptcp.w:call-trgt-40.t:call-trgt_plot_meth_allele INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2137.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:51.680 wdl.w:ptcp.w:call-trgt-40.t:call-trgt_plot_meth_allele INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2137.trgt.sorted.spanning.bam"
2025-09-15 20:24:51.680 wdl.w:ptcp.w:call-trgt-40.t:call-trgt_plot_meth_allele INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2137.trgt.vcf"
2025-09-15 20:24:51.680 wdl.w:ptcp.w:call-trgt-40.t:call-trgt_plot_meth_allele INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2137"
2025-09-15 20:24:51.681 wdl.w:ptcp.w:call-trgt-40.t:call-trgt_plot_meth_allele INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:51.681 wdl.w:ptcp.w:call-trgt-40.t:call-trgt_plot_meth_allele INFO eval :: name: "plot_type", value: "allele"
2025-09-15 20:24:51.681 wdl.w:ptcp.w:call-trgt-40.t:call-trgt_plot_meth_allele INFO eval :: name: "show", value: "meth"
2025-09-15 20:24:51.681 wdl.w:ptcp.w:call-trgt-40.t:call-trgt_plot_meth_allele INFO eval :: name: "threads", value: 1
2025-09-15 20:24:51.681 wdl.w:ptcp.w:call-trgt-40.t:call-trgt_plot_meth_allele INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:51.681 wdl.w:ptcp.w:call-trgt-40.t:call-trgt_plot_meth_allele INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2137.meth_allele"
2025-09-15 20:24:51.682 wdl.w:ptcp.w:call-trgt-40.t:call-trgt_plot_meth_allele INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:51.682 wdl.w:ptcp.w:call-trgt-40.t:call-trgt_plot_meth_allele WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:51.682 wdl.w:ptcp.w:call-trgt-40.t:call-trgt_plot_meth_allele INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:51.682 wdl.w:ptcp.w:call-trgt-40.t:call-trgt_plot_meth_allele INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:51.695 wdl.w:ptcp.w:call-trgt-44.t:call-trgt_plot_meth_waterfall INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2141.meth_waterfall.trgt_plots.zip"
2025-09-15 20:24:51.704 wdl.w:ptcp.w:call-trgt-61.t:call-get_reads_overlapping_repeats INFO output :: name: "reads_overlapping_repeats", value: "m84036_250809_035451_s4.bc2158.repeats.bam"
2025-09-15 20:24:51.708 wdl.w:ptcp.w:call-trgt-61.t:call-get_reads_overlapping_repeats INFO output :: name: "reads_overlapping_repeats_bai", value: "m84036_250809_035451_s4.bc2158.repeats.bam.bai"
2025-09-15 20:24:51.766 wdl.w:ptcp.w:call-trgt-40.t:call-trgt_plot_meth_allele INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-40/call-trgt_plot_meth_allele/_singularity_tmpdir_7ik9_9vd"
2025-09-15 20:24:51.766 wdl.w:ptcp.w:call-trgt-40.t:call-trgt_plot_meth_allele INFO Slurm invocation: srun --job-name call-trgt_plot_meth_allele --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-40/call-trgt_plot_meth_allele/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-40/call-trgt_plot_meth_allele/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-40/call-trgt_plot_meth_allele/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-40/call-trgt_plot_meth_allele/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-40/call-trgt_genotype/out/m84036_250809_035451_s4.bc2137.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2137.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-40/call-trgt_genotype/out/m84036_250809_035451_s4.bc2137.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2137.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-40/call-trgt_genotype/out/m84036_250809_035451_s4.bc2137.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2137.trgt.vcf:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-40/call-trgt_plot_meth_allele/_singularity_tmpdir_7ik9_9vd/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-40/call-trgt_plot_meth_allele/_singularity_tmpdir_7ik9_9vd/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:51.783 wdl.w:ptcp.w:call-trgt-61.t:call-get_reads_overlapping_repeats NOTICE done
2025-09-15 20:24:51.787 wdl.w:ptcp.w:call-trgt-61 NOTICE finish :: job: "call-get_reads_overlapping_repeats"
2025-09-15 20:24:51.787 wdl.w:ptcp.w:call-trgt-40.t:call-trgt_plot_meth_allele NOTICE slurm_singularity run :: pid: 1203391, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-40/call-trgt_plot_meth_allele/slurm_singularity.log.txt"
2025-09-15 20:24:51.787 wdl.w:ptcp.w:call-trgt-61 INFO output :: job: "call-get_reads_overlapping_repeats", values: {"reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-61/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2158.repeats.bam.bai", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-61/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2158.repeats.bam"}
2025-09-15 20:24:51.788 wdl.w:ptcp.w:call-trgt-61 INFO visit :: node: "output-reads_overlapping_repeats", values: {"reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-61/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2158.repeats.bam"}
2025-09-15 20:24:51.788 wdl.w:ptcp.w:call-trgt-61 INFO visit :: node: "output-reads_overlapping_repeats_bai", values: {"reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-61/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2158.repeats.bam.bai"}
2025-09-15 20:24:51.792 wdl.w:ptcp.w:call-trgt-40.t:call-trgt_plot_meth_waterfall NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-40/call-trgt_plot_meth_waterfall", thread: 140611961206336
2025-09-15 20:24:51.810 wdl.w:ptcp.w:call-trgt-40.t:call-trgt_plot_meth_waterfall INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:51.810 wdl.w:ptcp.w:call-trgt-40.t:call-trgt_plot_meth_waterfall INFO input :: name: "waterfall", value: true
2025-09-15 20:24:51.810 wdl.w:ptcp.w:call-trgt-40.t:call-trgt_plot_meth_waterfall INFO input :: name: "methylation", value: true
2025-09-15 20:24:51.810 wdl.w:ptcp.w:call-trgt-40.t:call-trgt_plot_meth_waterfall INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:51.810 wdl.w:ptcp.w:call-trgt-40.t:call-trgt_plot_meth_waterfall INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:51.810 wdl.w:ptcp.w:call-trgt-40.t:call-trgt_plot_meth_waterfall INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:51.810 wdl.w:ptcp.w:call-trgt-40.t:call-trgt_plot_meth_waterfall INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2137.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:51.811 wdl.w:ptcp.w:call-trgt-40.t:call-trgt_plot_meth_waterfall INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2137.trgt.sorted.spanning.bam"
2025-09-15 20:24:51.811 wdl.w:ptcp.w:call-trgt-40.t:call-trgt_plot_meth_waterfall INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2137.trgt.vcf"
2025-09-15 20:24:51.811 wdl.w:ptcp.w:call-trgt-40.t:call-trgt_plot_meth_waterfall INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2137"
2025-09-15 20:24:51.811 wdl.w:ptcp.w:call-trgt-40.t:call-trgt_plot_meth_waterfall INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:51.811 wdl.w:ptcp.w:call-trgt-40.t:call-trgt_plot_meth_waterfall INFO eval :: name: "plot_type", value: "waterfall"
2025-09-15 20:24:51.811 wdl.w:ptcp.w:call-trgt-40.t:call-trgt_plot_meth_waterfall INFO eval :: name: "show", value: "meth"
2025-09-15 20:24:51.811 wdl.w:ptcp.w:call-trgt-40.t:call-trgt_plot_meth_waterfall INFO eval :: name: "threads", value: 1
2025-09-15 20:24:51.812 wdl.w:ptcp.w:call-trgt-40.t:call-trgt_plot_meth_waterfall INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:51.812 wdl.w:ptcp.w:call-trgt-40.t:call-trgt_plot_meth_waterfall INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2137.meth_waterfall"
2025-09-15 20:24:51.812 wdl.w:ptcp.w:call-trgt-40.t:call-trgt_plot_meth_waterfall INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:51.812 wdl.w:ptcp.w:call-trgt-40.t:call-trgt_plot_meth_waterfall WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:51.813 wdl.w:ptcp.w:call-trgt-40.t:call-trgt_plot_meth_waterfall INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:51.813 wdl.w:ptcp.w:call-trgt-40.t:call-trgt_plot_meth_waterfall INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:51.828 wdl.w:ptcp.w:call-trgt-44.t:call-trgt_plot_meth_waterfall NOTICE done
2025-09-15 20:24:51.833 wdl.w:ptcp.w:call-trgt-44 NOTICE finish :: job: "call-trgt_plot_meth_waterfall"
2025-09-15 20:24:51.833 wdl.w:ptcp.w:call-trgt-44 INFO output :: job: "call-trgt_plot_meth_waterfall", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-44/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2141.meth_waterfall.trgt_plots.zip"}
2025-09-15 20:24:51.834 wdl.w:ptcp.w:call-trgt-44 INFO visit :: node: "output-images_meth_waterfall", values: {"images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-44/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2141.meth_waterfall.trgt_plots.zip"}
2025-09-15 20:24:51.834 wdl.w:ptcp.w:call-trgt-44 INFO visit :: node: "outputs", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-44/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2141.motifs_waterfall.trgt_plots.zip", "images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-44/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2141.meth_allele.trgt_plots.zip", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-44/call-trgt_genotype/out/m84036_250809_035451_s4.bc2141.trgt.sorted.spanning.bam.bai", "images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-44/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2141.motifs_allele.trgt_plots.zip", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-44/call-trgt_genotype/out/m84036_250809_035451_s4.bc2141.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-44/call-trgt_genotype/out/m84036_250809_035451_s4.bc2141.trgt.vcf", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-44/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2141.repeats.bam", "images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-44/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2141.meth_waterfall.trgt_plots.zip", "reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-44/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2141.repeats.bam.bai"}
2025-09-15 20:24:51.840 wdl.w:ptcp.w:call-trgt-40.t:call-trgt_plot_motifs_allele NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-40/call-trgt_plot_motifs_allele", thread: 140609285244480
2025-09-15 20:24:51.867 wdl.w:ptcp.w:call-trgt-40.t:call-trgt_plot_motifs_allele INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:51.867 wdl.w:ptcp.w:call-trgt-40.t:call-trgt_plot_motifs_allele INFO input :: name: "waterfall", value: false
2025-09-15 20:24:51.867 wdl.w:ptcp.w:call-trgt-40.t:call-trgt_plot_motifs_allele INFO input :: name: "methylation", value: false
2025-09-15 20:24:51.867 wdl.w:ptcp.w:call-trgt-40.t:call-trgt_plot_motifs_allele INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:51.867 wdl.w:ptcp.w:call-trgt-40.t:call-trgt_plot_motifs_allele INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:51.867 wdl.w:ptcp.w:call-trgt-40.t:call-trgt_plot_motifs_allele INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:51.867 wdl.w:ptcp.w:call-trgt-40.t:call-trgt_plot_motifs_allele INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2137.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:51.867 wdl.w:ptcp.w:call-trgt-40.t:call-trgt_plot_motifs_allele INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2137.trgt.sorted.spanning.bam"
2025-09-15 20:24:51.867 wdl.w:ptcp.w:call-trgt-40.t:call-trgt_plot_motifs_allele INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2137.trgt.vcf"
2025-09-15 20:24:51.867 wdl.w:ptcp.w:call-trgt-40.t:call-trgt_plot_motifs_allele INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2137"
2025-09-15 20:24:51.868 wdl.w:ptcp.w:call-trgt-40.t:call-trgt_plot_motifs_allele INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:51.868 wdl.w:ptcp.w:call-trgt-57.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO srun: job 51797814 queued and waiting for resources
2025-09-15 20:24:51.868 wdl.w:ptcp.w:call-trgt-40.t:call-trgt_plot_motifs_allele INFO eval :: name: "plot_type", value: "allele"
2025-09-15 20:24:51.868 wdl.w:ptcp.w:call-trgt-57.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO srun: job 51797814 has been allocated resources
2025-09-15 20:24:51.868 wdl.w:ptcp.w:call-trgt-40.t:call-trgt_plot_motifs_allele INFO eval :: name: "show", value: "motifs"
2025-09-15 20:24:51.868 wdl.w:ptcp.w:call-trgt-57.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:51.868 wdl.w:ptcp.w:call-trgt-40.t:call-trgt_plot_motifs_allele INFO eval :: name: "threads", value: 1
2025-09-15 20:24:51.869 wdl.w:ptcp.w:call-trgt-40.t:call-trgt_plot_motifs_allele INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:51.869 wdl.w:ptcp.w:call-trgt-40.t:call-trgt_plot_motifs_allele INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2137.motifs_allele"
2025-09-15 20:24:51.869 wdl.w:ptcp.w:call-trgt-40.t:call-trgt_plot_motifs_allele INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:51.869 wdl.w:ptcp.w:call-trgt-40.t:call-trgt_plot_motifs_allele WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:51.869 wdl.w:ptcp.w:call-trgt-40.t:call-trgt_plot_motifs_allele INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:51.870 wdl.w:ptcp.w:call-trgt-40.t:call-trgt_plot_motifs_allele INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:51.888 wdl.w:ptcp.w:call-trgt-57.t:call-trgt_plot_motifs_allele.slurm_singularity INFO srun: job 51797815 queued and waiting for resources
2025-09-15 20:24:51.888 wdl.w:ptcp.w:call-trgt-57.t:call-trgt_plot_motifs_allele.slurm_singularity INFO srun: job 51797815 has been allocated resources
2025-09-15 20:24:51.888 wdl.w:ptcp.w:call-trgt-57.t:call-trgt_plot_motifs_allele.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:51.888 wdl.w:ptcp.w:call-trgt-40.t:call-trgt_plot_meth_waterfall INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-40/call-trgt_plot_meth_waterfall/_singularity_tmpdir_q51nb4q_"
2025-09-15 20:24:51.889 wdl.w:ptcp.w:call-trgt-40.t:call-trgt_plot_meth_waterfall INFO Slurm invocation: srun --job-name call-trgt_plot_meth_waterfall --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-40/call-trgt_plot_meth_waterfall/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-40/call-trgt_plot_meth_waterfall/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-40/call-trgt_plot_meth_waterfall/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-40/call-trgt_plot_meth_waterfall/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-40/call-trgt_genotype/out/m84036_250809_035451_s4.bc2137.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2137.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-40/call-trgt_genotype/out/m84036_250809_035451_s4.bc2137.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2137.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-40/call-trgt_genotype/out/m84036_250809_035451_s4.bc2137.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2137.trgt.vcf:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-40/call-trgt_plot_meth_waterfall/_singularity_tmpdir_q51nb4q_/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-40/call-trgt_plot_meth_waterfall/_singularity_tmpdir_q51nb4q_/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:51.913 wdl.w:ptcp.w:call-trgt-40.t:call-trgt_plot_meth_waterfall NOTICE slurm_singularity run :: pid: 1203399, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-40/call-trgt_plot_meth_waterfall/slurm_singularity.log.txt"
2025-09-15 20:24:51.927 wdl.w:ptcp.w:call-trgt-61.t:call-trgt_genotype INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2158.trgt.vcf"
2025-09-15 20:24:51.934 wdl.w:ptcp.w:call-trgt-61.t:call-trgt_genotype INFO output :: name: "spanning_bam", value: "m84036_250809_035451_s4.bc2158.trgt.sorted.spanning.bam"
2025-09-15 20:24:51.935 wdl.w:ptcp.w:call-trgt-61.t:call-trgt_genotype INFO output :: name: "spanning_bam_bai", value: "m84036_250809_035451_s4.bc2158.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:51.951 wdl.w:ptcp.w:call-trgt-44 NOTICE done
2025-09-15 20:24:51.955 wdl.w:ptcp NOTICE finish :: job: "call-trgt-44"
2025-09-15 20:24:51.956 wdl.w:ptcp INFO output :: job: "call-trgt-44", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-44/out/m84036_250809_035451_s4.bc2141.motifs_waterfall.trgt_plots.zip", "images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-44/out/m84036_250809_035451_s4.bc2141.meth_allele.trgt_plots.zip", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-44/out/m84036_250809_035451_s4.bc2141.trgt.sorted.spanning.bam.bai", "images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-44/out/m84036_250809_035451_s4.bc2141.motifs_allele.trgt_plots.zip", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-44/out/m84036_250809_035451_s4.bc2141.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-44/out/m84036_250809_035451_s4.bc2141.trgt.vcf", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-44/out/m84036_250809_035451_s4.bc2141.repeats.bam", "images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-44/out/m84036_250809_035451_s4.bc2141.meth_waterfall.trgt_plots.zip", "reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-44/out/m84036_250809_035451_s4.bc2141.repeats.bam.bai"}
2025-09-15 20:24:51.966 wdl.w:ptcp.w:call-trgt-73 NOTICE workflow start :: name: "trgt", source: "./trgt.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-73"
2025-09-15 20:24:51.971 wdl.w:ptcp.w:call-trgt-40.t:call-trgt_plot_motifs_allele INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-40/call-trgt_plot_motifs_allele/_singularity_tmpdir_qcttfrdg"
2025-09-15 20:24:51.971 wdl.w:ptcp.w:call-trgt-40.t:call-trgt_plot_motifs_allele INFO Slurm invocation: srun --job-name call-trgt_plot_motifs_allele --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-40/call-trgt_plot_motifs_allele/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-40/call-trgt_plot_motifs_allele/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-40/call-trgt_plot_motifs_allele/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-40/call-trgt_plot_motifs_allele/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-40/call-trgt_genotype/out/m84036_250809_035451_s4.bc2137.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2137.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-40/call-trgt_genotype/out/m84036_250809_035451_s4.bc2137.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2137.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-40/call-trgt_genotype/out/m84036_250809_035451_s4.bc2137.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2137.trgt.vcf:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-40/call-trgt_plot_motifs_allele/_singularity_tmpdir_qcttfrdg/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-40/call-trgt_plot_motifs_allele/_singularity_tmpdir_qcttfrdg/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:51.982 wdl.w:ptcp.w:call-trgt-73 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:24:51.984 wdl.w:ptcp.w:call-trgt-73 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-73/out/m84036_250809_035451_s4.bc2170.mapped.bam"}
2025-09-15 20:24:51.984 wdl.w:ptcp.w:call-trgt-73 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-73/out/m84036_250809_035451_s4.bc2170.mapped.bam.bai"}
2025-09-15 20:24:51.984 wdl.w:ptcp.w:call-trgt-73 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:24:51.984 wdl.w:ptcp.w:call-trgt-73 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:24:51.984 wdl.w:ptcp.w:call-trgt-73 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2170"}
2025-09-15 20:24:51.984 wdl.w:ptcp.w:call-trgt-73 INFO visit :: node: "decl-sex", values: {"sex": "F"}
2025-09-15 20:24:51.984 wdl.w:ptcp.w:call-trgt-73 INFO visit :: node: "decl-trgt_bed", values: {"trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"}
2025-09-15 20:24:51.984 wdl.w:ptcp.w:call-trgt-73 NOTICE ready :: job: "call-get_reads_overlapping_repeats", callee: "get_reads_overlapping_repeats"
2025-09-15 20:24:51.985 wdl.w:ptcp.w:call-trgt-73 INFO input :: job: "call-get_reads_overlapping_repeats", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-73/out/m84036_250809_035451_s4.bc2170.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-73/out/m84036_250809_035451_s4.bc2170.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2170"}
2025-09-15 20:24:51.986 wdl.w:ptcp.w:call-trgt-73 NOTICE ready :: job: "call-trgt_genotype", callee: "trgt_genotype"
2025-09-15 20:24:51.986 wdl.w:ptcp.w:call-trgt-73 INFO input :: job: "call-trgt_genotype", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-73/out/m84036_250809_035451_s4.bc2170.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-73/out/m84036_250809_035451_s4.bc2170.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2170"}
2025-09-15 20:24:51.986 wdl.w:ptcp.w:call-trgt-40.t:call-trgt_plot_motifs_allele NOTICE slurm_singularity run :: pid: 1203401, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-40/call-trgt_plot_motifs_allele/slurm_singularity.log.txt"
2025-09-15 20:24:52.015 wdl.w:ptcp.w:call-trgt-61.t:call-trgt_genotype NOTICE done
2025-09-15 20:24:52.019 wdl.w:ptcp.w:call-trgt-61 NOTICE finish :: job: "call-trgt_genotype"
2025-09-15 20:24:52.020 wdl.w:ptcp.w:call-trgt-61 INFO output :: job: "call-trgt_genotype", values: {"spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-61/call-trgt_genotype/out/m84036_250809_035451_s4.bc2158.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-61/call-trgt_genotype/out/m84036_250809_035451_s4.bc2158.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-61/call-trgt_genotype/out/m84036_250809_035451_s4.bc2158.trgt.vcf"}
2025-09-15 20:24:52.020 wdl.w:ptcp.w:call-trgt-61 NOTICE ready :: job: "call-trgt_plot_meth_allele", callee: "trgt_plot"
2025-09-15 20:24:52.021 wdl.w:ptcp.w:call-trgt-61 INFO input :: job: "call-trgt_plot_meth_allele", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": false, "methylation": true, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-61/call-trgt_genotype/out/m84036_250809_035451_s4.bc2158.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-61/call-trgt_genotype/out/m84036_250809_035451_s4.bc2158.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-61/call-trgt_genotype/out/m84036_250809_035451_s4.bc2158.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2158"}
2025-09-15 20:24:52.022 wdl.w:ptcp.w:call-trgt-61 NOTICE ready :: job: "call-trgt_plot_meth_waterfall", callee: "trgt_plot"
2025-09-15 20:24:52.022 wdl.w:ptcp.w:call-trgt-61 INFO input :: job: "call-trgt_plot_meth_waterfall", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": true, "methylation": true, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-61/call-trgt_genotype/out/m84036_250809_035451_s4.bc2158.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-61/call-trgt_genotype/out/m84036_250809_035451_s4.bc2158.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-61/call-trgt_genotype/out/m84036_250809_035451_s4.bc2158.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2158"}
2025-09-15 20:24:52.022 wdl.w:ptcp.w:call-trgt-61 NOTICE ready :: job: "call-trgt_plot_motifs_allele", callee: "trgt_plot"
2025-09-15 20:24:52.023 wdl.w:ptcp.w:call-trgt-61 INFO input :: job: "call-trgt_plot_motifs_allele", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": false, "methylation": false, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-61/call-trgt_genotype/out/m84036_250809_035451_s4.bc2158.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-61/call-trgt_genotype/out/m84036_250809_035451_s4.bc2158.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-61/call-trgt_genotype/out/m84036_250809_035451_s4.bc2158.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2158"}
2025-09-15 20:24:52.023 wdl.w:ptcp.w:call-trgt-61 NOTICE ready :: job: "call-trgt_plot_motifs_waterfall", callee: "trgt_plot"
2025-09-15 20:24:52.023 wdl.w:ptcp.w:call-trgt-61 INFO input :: job: "call-trgt_plot_motifs_waterfall", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": true, "methylation": false, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-61/call-trgt_genotype/out/m84036_250809_035451_s4.bc2158.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-61/call-trgt_genotype/out/m84036_250809_035451_s4.bc2158.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-61/call-trgt_genotype/out/m84036_250809_035451_s4.bc2158.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2158"}
2025-09-15 20:24:52.024 wdl.w:ptcp.w:call-trgt-61 INFO visit :: node: "output-spanning_bam", values: {"spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-61/call-trgt_genotype/out/m84036_250809_035451_s4.bc2158.trgt.sorted.spanning.bam"}
2025-09-15 20:24:52.024 wdl.w:ptcp.w:call-trgt-61 INFO visit :: node: "output-spanning_bam_bai", values: {"spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-61/call-trgt_genotype/out/m84036_250809_035451_s4.bc2158.trgt.sorted.spanning.bam.bai"}
2025-09-15 20:24:52.024 wdl.w:ptcp.w:call-trgt-61 INFO visit :: node: "output-vcf", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-61/call-trgt_genotype/out/m84036_250809_035451_s4.bc2158.trgt.vcf"}
2025-09-15 20:24:52.024 wdl.w:ptcp.w:call-trgt-40.t:call-trgt_plot_motifs_waterfall NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-40/call-trgt_plot_motifs_waterfall", thread: 140609847293504
2025-09-15 20:24:52.043 wdl.w:ptcp.w:call-trgt-40.t:call-trgt_plot_motifs_waterfall INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:52.043 wdl.w:ptcp.w:call-trgt-40.t:call-trgt_plot_motifs_waterfall INFO input :: name: "waterfall", value: true
2025-09-15 20:24:52.043 wdl.w:ptcp.w:call-trgt-40.t:call-trgt_plot_motifs_waterfall INFO input :: name: "methylation", value: false
2025-09-15 20:24:52.043 wdl.w:ptcp.w:call-trgt-40.t:call-trgt_plot_motifs_waterfall INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:52.043 wdl.w:ptcp.w:call-trgt-40.t:call-trgt_plot_motifs_waterfall INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:52.043 wdl.w:ptcp.w:call-trgt-40.t:call-trgt_plot_motifs_waterfall INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:52.043 wdl.w:ptcp.w:call-trgt-40.t:call-trgt_plot_motifs_waterfall INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2137.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:52.043 wdl.w:ptcp.w:call-trgt-40.t:call-trgt_plot_motifs_waterfall INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2137.trgt.sorted.spanning.bam"
2025-09-15 20:24:52.043 wdl.w:ptcp.w:call-trgt-40.t:call-trgt_plot_motifs_waterfall INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2137.trgt.vcf"
2025-09-15 20:24:52.043 wdl.w:ptcp.w:call-trgt-40.t:call-trgt_plot_motifs_waterfall INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2137"
2025-09-15 20:24:52.043 wdl.w:ptcp.w:call-trgt-40.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:52.044 wdl.w:ptcp.w:call-trgt-40.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "plot_type", value: "waterfall"
2025-09-15 20:24:52.044 wdl.w:ptcp.w:call-trgt-40.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "show", value: "motifs"
2025-09-15 20:24:52.044 wdl.w:ptcp.w:call-trgt-40.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "threads", value: 1
2025-09-15 20:24:52.044 wdl.w:ptcp.w:call-trgt-40.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:52.044 wdl.w:ptcp.w:call-trgt-40.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2137.motifs_waterfall"
2025-09-15 20:24:52.044 wdl.w:ptcp.w:call-trgt-40.t:call-trgt_plot_motifs_waterfall INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:52.045 wdl.w:ptcp.w:call-trgt-40.t:call-trgt_plot_motifs_waterfall WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:52.045 wdl.w:ptcp.w:call-trgt-40.t:call-trgt_plot_motifs_waterfall INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:52.045 wdl.w:ptcp.w:call-trgt-40.t:call-trgt_plot_motifs_waterfall INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:52.104 wdl.w:ptcp.w:call-trgt-57.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO srun: job 51797816 queued and waiting for resources
2025-09-15 20:24:52.104 wdl.w:ptcp.w:call-trgt-57.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO srun: job 51797816 has been allocated resources
2025-09-15 20:24:52.104 wdl.w:ptcp.w:call-trgt-57.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:52.115 wdl.w:ptcp.w:call-trgt-40.t:call-trgt_plot_motifs_waterfall INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-40/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_dd9sce_o"
2025-09-15 20:24:52.115 wdl.w:ptcp.w:call-trgt-40.t:call-trgt_plot_motifs_waterfall INFO Slurm invocation: srun --job-name call-trgt_plot_motifs_waterfall --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-40/call-trgt_plot_motifs_waterfall/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-40/call-trgt_plot_motifs_waterfall/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-40/call-trgt_plot_motifs_waterfall/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-40/call-trgt_plot_motifs_waterfall/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-40/call-trgt_genotype/out/m84036_250809_035451_s4.bc2137.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2137.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-40/call-trgt_genotype/out/m84036_250809_035451_s4.bc2137.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2137.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-40/call-trgt_genotype/out/m84036_250809_035451_s4.bc2137.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2137.trgt.vcf:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-40/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_dd9sce_o/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-40/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_dd9sce_o/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:52.130 wdl.w:ptcp.w:call-trgt-40.t:call-trgt_plot_motifs_waterfall NOTICE slurm_singularity run :: pid: 1203403, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-40/call-trgt_plot_motifs_waterfall/slurm_singularity.log.txt"
2025-09-15 20:24:52.198 wdl.w:ptcp.w:call-paraphase-46.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for smn1 for sample m84036_250809_035451_s4.bc2143 at 2025-09-15 20:24:30.781266...
2025-09-15 20:24:52.357 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_plot_meth_allele INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2159.meth_allele.trgt_plots.zip"
2025-09-15 20:24:52.442 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_plot_motifs_allele INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2159.motifs_allele.trgt_plots.zip"
2025-09-15 20:24:52.468 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_plot_meth_allele NOTICE done
2025-09-15 20:24:52.473 wdl.w:ptcp.w:call-trgt-62 NOTICE finish :: job: "call-trgt_plot_meth_allele"
2025-09-15 20:24:52.474 wdl.w:ptcp.w:call-trgt-62 INFO output :: job: "call-trgt_plot_meth_allele", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-62/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2159.meth_allele.trgt_plots.zip"}
2025-09-15 20:24:52.474 wdl.w:ptcp.w:call-trgt-62 INFO visit :: node: "output-images_meth_allele", values: {"images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-62/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2159.meth_allele.trgt_plots.zip"}
2025-09-15 20:24:52.482 wdl.w:ptcp.t:call-tar_outputs-08 NOTICE task setup :: name: "tar_outputs", source: "./common.wdl", line: 279, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-08", thread: 140610912642624
2025-09-15 20:24:52.516 wdl.w:ptcp.t:call-tar_outputs-08 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:52.516 wdl.w:ptcp.t:call-tar_outputs-08 INFO input :: name: "sawfish_vcf_tbi", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2105.sv.vcf.gz.tbi"
2025-09-15 20:24:52.516 wdl.w:ptcp.t:call-tar_outputs-08 INFO input :: name: "sawfish_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2105.sv.vcf.gz"
2025-09-15 20:24:52.516 wdl.w:ptcp.t:call-tar_outputs-08 INFO input :: name: "f8_json", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2105.f8inversion.json"
2025-09-15 20:24:52.516 wdl.w:ptcp.t:call-tar_outputs-08 INFO input :: name: "paraphase_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2105.paraphase.bam.bai"
2025-09-15 20:24:52.517 wdl.w:ptcp.t:call-tar_outputs-08 INFO input :: name: "paraphase_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2105.paraphase.bam"
2025-09-15 20:24:52.517 wdl.w:ptcp.t:call-tar_outputs-08 INFO input :: name: "paraphase_json", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2105.paraphase.json"
2025-09-15 20:24:52.517 wdl.w:ptcp.t:call-tar_outputs-08 INFO input :: name: "trgt_spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2105.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:52.517 wdl.w:ptcp.t:call-tar_outputs-08 INFO input :: name: "trgt_spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2105.trgt.sorted.spanning.bam"
2025-09-15 20:24:52.517 wdl.w:ptcp.t:call-tar_outputs-08 INFO input :: name: "trgt_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2105.trgt.vcf"
2025-09-15 20:24:52.517 wdl.w:ptcp.t:call-tar_outputs-08 INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2105.mapped.bam.bai"
2025-09-15 20:24:52.517 wdl.w:ptcp.t:call-tar_outputs-08 INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2105.mapped.bam"
2025-09-15 20:24:52.517 wdl.w:ptcp.t:call-tar_outputs-08 INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2105"
2025-09-15 20:24:52.517 wdl.w:ptcp.t:call-tar_outputs-08 INFO eval :: name: "threads", value: 1
2025-09-15 20:24:52.517 wdl.w:ptcp.t:call-tar_outputs-08 INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:52.518 wdl.w:ptcp.t:call-tar_outputs-08 INFO eval :: name: "disk_size", value: 6
2025-09-15 20:24:52.518 wdl.w:ptcp.t:call-tar_outputs-08 INFO eval :: name: "output_tarball", value: "m84036_250809_035451_s4.bc2105.tar"
2025-09-15 20:24:52.518 wdl.w:ptcp.t:call-tar_outputs-08 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:52.518 wdl.w:ptcp.t:call-tar_outputs-08 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:52.518 wdl.w:ptcp.t:call-tar_outputs-08 INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:52.519 wdl.w:ptcp.t:call-tar_outputs-08 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:52.567 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_plot_motifs_allele NOTICE done
2025-09-15 20:24:52.568 wdl.w:ptcp.w:call-sawfish-46.t:call-run_sawfish.stderr VERBOSE [M::worker_pipeline::48.637*1.54] mapped 174 sequences
2025-09-15 20:24:52.568 wdl.w:ptcp.w:call-sawfish-46.t:call-run_sawfish.stderr VERBOSE [M::main] Version: 2.26-r1175
2025-09-15 20:24:52.569 wdl.w:ptcp.w:call-sawfish-46.t:call-run_sawfish.stderr VERBOSE [M::main] CMD: /opt/pacbio/smrttools/install/smrtlink-release_25.1.0.257715/bundles/smrttools/install/smrttools-release_25.1.0.257715/private/thirdparty/minimap2/minimap2_2.26-pacbio2/binwrap/../../../../../private/thirdparty/minimap2/minimap2_2.26-pacbio2/bin/minimap2 -a -y -x map-hifi -Y -E 1,0 /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa -
2025-09-15 20:24:52.569 wdl.w:ptcp.w:call-sawfish-46.t:call-run_sawfish.stderr VERBOSE [M::main] Real time: 48.822 sec; CPU: 75.186 sec; Peak RSS: 11.886 GB
2025-09-15 20:24:52.575 wdl.w:ptcp.w:call-trgt-62 NOTICE finish :: job: "call-trgt_plot_motifs_allele"
2025-09-15 20:24:52.576 wdl.w:ptcp.w:call-trgt-62 INFO output :: job: "call-trgt_plot_motifs_allele", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-62/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2159.motifs_allele.trgt_plots.zip"}
2025-09-15 20:24:52.576 wdl.w:ptcp.w:call-trgt-62 INFO visit :: node: "output-images_motifs_allele", values: {"images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-62/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2159.motifs_allele.trgt_plots.zip"}
2025-09-15 20:24:52.588 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_meth_allele NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-54/call-trgt_plot_meth_allele", thread: 140607649453632
2025-09-15 20:24:52.613 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_meth_allele INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:52.613 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_meth_allele INFO input :: name: "waterfall", value: false
2025-09-15 20:24:52.613 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_meth_allele INFO input :: name: "methylation", value: true
2025-09-15 20:24:52.613 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_meth_allele INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:52.613 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_meth_allele INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:52.613 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_meth_allele INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:52.613 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_meth_allele INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2151.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:52.613 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_meth_allele INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2151.trgt.sorted.spanning.bam"
2025-09-15 20:24:52.613 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_meth_allele INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2151.trgt.vcf"
2025-09-15 20:24:52.613 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_meth_allele INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2151"
2025-09-15 20:24:52.614 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_meth_allele INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:52.614 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_meth_allele INFO eval :: name: "plot_type", value: "allele"
2025-09-15 20:24:52.614 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_meth_allele INFO eval :: name: "show", value: "meth"
2025-09-15 20:24:52.614 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_meth_allele INFO eval :: name: "threads", value: 1
2025-09-15 20:24:52.614 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_meth_allele INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:52.614 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_meth_allele INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2151.meth_allele"
2025-09-15 20:24:52.615 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_meth_allele INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:52.615 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_meth_allele WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:52.615 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_meth_allele INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:52.615 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_meth_allele INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:52.667 wdl.w:ptcp.t:call-tar_outputs-08 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 17, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-08/_singularity_tmpdir_2rxf959l"
2025-09-15 20:24:52.667 wdl.w:ptcp.t:call-tar_outputs-08 INFO Slurm invocation: srun --job-name call-tar_outputs-08 --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-08/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-08/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-08/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-08/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-08/out/m84036_250809_035451_s4.bc2105_sawfish/m84036_250809_035451_s4.bc2105.sv.vcf.gz.tbi:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2105.sv.vcf.gz.tbi:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-08/out/m84036_250809_035451_s4.bc2105_sawfish/m84036_250809_035451_s4.bc2105.sv.vcf.gz:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2105.sv.vcf.gz:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-08/out/m84036_250809_035451_s4.bc2105.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2105.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-08/out/m84036_250809_035451_s4.bc2105.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2105.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-08/out/m84036_250809_035451_s4.bc2105.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2105.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-08/out/m84036_250809_035451_s4.bc2105.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2105.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-08/out/m84036_250809_035451_s4.bc2105.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2105.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-08/out/m84036_250809_035451_s4.bc2105_paraphase/m84036_250809_035451_s4.bc2105.paraphase.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2105.paraphase.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-08/out/m84036_250809_035451_s4.bc2105_paraphase/m84036_250809_035451_s4.bc2105.paraphase.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2105.paraphase.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-08/out/m84036_250809_035451_s4.bc2105_paraphase/m84036_250809_035451_s4.bc2105.paraphase.json:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2105.paraphase.json:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-08/out/m84036_250809_035451_s4.bc2105.f8inversion.json:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2105.f8inversion.json:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-08/_singularity_tmpdir_2rxf959l/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-08/_singularity_tmpdir_2rxf959l/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:52.670 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_plot_motifs_waterfall INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2159.motifs_waterfall.trgt_plots.zip"
2025-09-15 20:24:52.701 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_meth_allele INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-54/call-trgt_plot_meth_allele/_singularity_tmpdir_4qjonr90"
2025-09-15 20:24:52.702 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_meth_allele INFO Slurm invocation: srun --job-name call-trgt_plot_meth_allele --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-54/call-trgt_plot_meth_allele/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-54/call-trgt_plot_meth_allele/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-54/call-trgt_plot_meth_allele/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-54/call-trgt_plot_meth_allele/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-54/call-trgt_genotype/out/m84036_250809_035451_s4.bc2151.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2151.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-54/call-trgt_genotype/out/m84036_250809_035451_s4.bc2151.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2151.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-54/call-trgt_genotype/out/m84036_250809_035451_s4.bc2151.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2151.trgt.sorted.spanning.bam:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-54/call-trgt_plot_meth_allele/_singularity_tmpdir_4qjonr90/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-54/call-trgt_plot_meth_allele/_singularity_tmpdir_4qjonr90/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:52.708 wdl.w:ptcp.t:call-tar_outputs-08 NOTICE slurm_singularity run :: pid: 1203423, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-08/slurm_singularity.log.txt"
2025-09-15 20:24:52.709 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_meth_allele NOTICE slurm_singularity run :: pid: 1203424, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-54/call-trgt_plot_meth_allele/slurm_singularity.log.txt"
2025-09-15 20:24:52.758 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_plot_motifs_waterfall NOTICE done
2025-09-15 20:24:52.762 wdl.w:ptcp.w:call-trgt-62 NOTICE finish :: job: "call-trgt_plot_motifs_waterfall"
2025-09-15 20:24:52.762 wdl.w:ptcp.w:call-trgt-62 INFO output :: job: "call-trgt_plot_motifs_waterfall", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-62/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2159.motifs_waterfall.trgt_plots.zip"}
2025-09-15 20:24:52.763 wdl.w:ptcp.w:call-trgt-62 INFO visit :: node: "output-images_motifs_waterfall", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-62/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2159.motifs_waterfall.trgt_plots.zip"}
2025-09-15 20:24:52.768 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_meth_waterfall NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-54/call-trgt_plot_meth_waterfall", thread: 140612481291840
2025-09-15 20:24:52.781 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:49 [ERROR] - No reads found for TRID=DRPLA_ATN1
2025-09-15 20:24:52.781 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:49 [ERROR] - No reads found for TRID=SCA3_ATXN3
2025-09-15 20:24:52.781 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:49 [ERROR] - No reads found for TRID=SCA31_BEAN1
2025-09-15 20:24:52.782 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:49 [ERROR] - No reads found for TRID=SCA4_ZFHX3
2025-09-15 20:24:52.782 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:49 [ERROR] - No reads found for TRID=HDL2_JPH3
2025-09-15 20:24:52.782 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:49 [ERROR] - No reads found for TRID=SCA6_CACNA1A
2025-09-15 20:24:52.782 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:50 [ERROR] - No reads found for TRID=SCA37_DAB1
2025-09-15 20:24:52.782 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:50 [ERROR] - No reads found for TRID=DM1_DMPK
2025-09-15 20:24:52.782 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:50 [ERROR] - No reads found for TRID=OPDM2_GIPC1
2025-09-15 20:24:52.782 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:50 [ERROR] - No reads found for TRID=SCA36_NOP56
2025-09-15 20:24:52.782 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:50 [ERROR] - No reads found for TRID=FRA2A_AFF3
2025-09-15 20:24:52.782 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:50 [ERROR] - No reads found for TRID=EPM1_CSTB
2025-09-15 20:24:52.782 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_meth_waterfall INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:52.782 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:50 [ERROR] - No reads found for TRID=CJD_PRNP
2025-09-15 20:24:52.783 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_meth_waterfall INFO input :: name: "waterfall", value: true
2025-09-15 20:24:52.783 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:50 [ERROR] - No reads found for TRID=NIID_NOTCH2NLC
2025-09-15 20:24:52.783 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_meth_waterfall INFO input :: name: "methylation", value: true
2025-09-15 20:24:52.783 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:50 [ERROR] - No reads found for TRID=SCA7_ATXN7
2025-09-15 20:24:52.783 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_meth_waterfall INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:52.783 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:50 [ERROR] - No reads found for TRID=CCHS_PHOX2B
2025-09-15 20:24:52.783 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_meth_waterfall INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:52.783 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:50 [ERROR] - No reads found for TRID=SCA12_PPP2R2B
2025-09-15 20:24:52.783 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_meth_waterfall INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:52.783 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:50 [ERROR] - No reads found for TRID=SCA1_ATXN1
2025-09-15 20:24:52.783 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_meth_waterfall INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2151.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:52.783 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:50 [ERROR] - No reads found for TRID=SCA17_TBP
2025-09-15 20:24:52.783 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_meth_waterfall INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2151.trgt.sorted.spanning.bam"
2025-09-15 20:24:52.783 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:50 [ERROR] - No reads found for TRID=OPDM1_LRP12
2025-09-15 20:24:52.783 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_meth_waterfall INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2151.trgt.vcf"
2025-09-15 20:24:52.784 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:50 [ERROR] - No reads found for TRID=FAME1_SAMD12
2025-09-15 20:24:52.784 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_meth_waterfall INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2151"
2025-09-15 20:24:52.784 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:50 [ERROR] - No reads found for TRID=HD_HTT
2025-09-15 20:24:52.784 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_meth_waterfall INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:52.784 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_meth_waterfall INFO eval :: name: "plot_type", value: "waterfall"
2025-09-15 20:24:52.784 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_meth_waterfall INFO eval :: name: "show", value: "meth"
2025-09-15 20:24:52.784 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_meth_waterfall INFO eval :: name: "threads", value: 1
2025-09-15 20:24:52.784 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_meth_waterfall INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:52.785 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_meth_waterfall INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2151.meth_waterfall"
2025-09-15 20:24:52.785 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_meth_waterfall INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:52.785 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_meth_waterfall WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:52.785 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_meth_waterfall INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:52.785 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_meth_waterfall INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:52.798 wdl.w:ptcp.w:call-trgt-40.t:call-trgt_plot_meth_allele.slurm_singularity INFO srun: job 51797817 queued and waiting for resources
2025-09-15 20:24:52.799 wdl.w:ptcp.w:call-trgt-40.t:call-trgt_plot_meth_allele.slurm_singularity INFO srun: job 51797817 has been allocated resources
2025-09-15 20:24:52.799 wdl.w:ptcp.w:call-trgt-40.t:call-trgt_plot_meth_allele.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:52.829 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_plot_meth_waterfall INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2159.meth_waterfall.trgt_plots.zip"
2025-09-15 20:24:52.859 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_meth_waterfall INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-54/call-trgt_plot_meth_waterfall/_singularity_tmpdir_sh6rse3f"
2025-09-15 20:24:52.859 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_meth_waterfall INFO Slurm invocation: srun --job-name call-trgt_plot_meth_waterfall --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-54/call-trgt_plot_meth_waterfall/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-54/call-trgt_plot_meth_waterfall/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-54/call-trgt_plot_meth_waterfall/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-54/call-trgt_plot_meth_waterfall/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-54/call-trgt_genotype/out/m84036_250809_035451_s4.bc2151.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2151.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-54/call-trgt_genotype/out/m84036_250809_035451_s4.bc2151.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2151.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-54/call-trgt_genotype/out/m84036_250809_035451_s4.bc2151.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2151.trgt.sorted.spanning.bam:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-54/call-trgt_plot_meth_waterfall/_singularity_tmpdir_sh6rse3f/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-54/call-trgt_plot_meth_waterfall/_singularity_tmpdir_sh6rse3f/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:52.875 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_meth_waterfall NOTICE slurm_singularity run :: pid: 1203438, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-54/call-trgt_plot_meth_waterfall/slurm_singularity.log.txt"
2025-09-15 20:24:52.907 wdl.w:ptcp.w:call-trgt-62.t:call-trgt_plot_meth_waterfall NOTICE done
2025-09-15 20:24:52.917 wdl.w:ptcp.w:call-trgt-62 NOTICE finish :: job: "call-trgt_plot_meth_waterfall"
2025-09-15 20:24:52.917 wdl.w:ptcp.w:call-trgt-62 INFO output :: job: "call-trgt_plot_meth_waterfall", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-62/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2159.meth_waterfall.trgt_plots.zip"}
2025-09-15 20:24:52.918 wdl.w:ptcp.w:call-trgt-62 INFO visit :: node: "output-images_meth_waterfall", values: {"images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-62/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2159.meth_waterfall.trgt_plots.zip"}
2025-09-15 20:24:52.918 wdl.w:ptcp.w:call-trgt-62 INFO visit :: node: "outputs", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-62/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2159.motifs_waterfall.trgt_plots.zip", "images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-62/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2159.meth_allele.trgt_plots.zip", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-62/call-trgt_genotype/out/m84036_250809_035451_s4.bc2159.trgt.sorted.spanning.bam.bai", "images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-62/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2159.motifs_allele.trgt_plots.zip", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-62/call-trgt_genotype/out/m84036_250809_035451_s4.bc2159.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-62/call-trgt_genotype/out/m84036_250809_035451_s4.bc2159.trgt.vcf", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-62/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2159.repeats.bam", "images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-62/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2159.meth_waterfall.trgt_plots.zip", "reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-62/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2159.repeats.bam.bai"}
2025-09-15 20:24:52.921 wdl.w:ptcp.w:call-trgt-40.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO srun: job 51797818 queued and waiting for resources
2025-09-15 20:24:52.921 wdl.w:ptcp.w:call-trgt-40.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO srun: job 51797818 has been allocated resources
2025-09-15 20:24:52.921 wdl.w:ptcp.w:call-trgt-40.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:52.922 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_motifs_allele NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-54/call-trgt_plot_motifs_allele", thread: 140609302029888
2025-09-15 20:24:52.945 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_motifs_allele INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:52.945 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_motifs_allele INFO input :: name: "waterfall", value: false
2025-09-15 20:24:52.945 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_motifs_allele INFO input :: name: "methylation", value: false
2025-09-15 20:24:52.945 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_motifs_allele INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:52.945 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_motifs_allele INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:52.945 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_motifs_allele INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:52.945 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_motifs_allele INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2151.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:52.945 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_motifs_allele INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2151.trgt.sorted.spanning.bam"
2025-09-15 20:24:52.945 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_motifs_allele INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2151.trgt.vcf"
2025-09-15 20:24:52.945 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_motifs_allele INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2151"
2025-09-15 20:24:52.946 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_motifs_allele INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:52.946 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_motifs_allele INFO eval :: name: "plot_type", value: "allele"
2025-09-15 20:24:52.946 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_motifs_allele INFO eval :: name: "show", value: "motifs"
2025-09-15 20:24:52.946 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_motifs_allele INFO eval :: name: "threads", value: 1
2025-09-15 20:24:52.946 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_motifs_allele INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:52.946 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_motifs_allele INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2151.motifs_allele"
2025-09-15 20:24:52.947 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_motifs_allele INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:52.947 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_motifs_allele WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:52.947 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_motifs_allele INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:52.947 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_motifs_allele INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:52.999 wdl.w:ptcp.w:call-trgt-40.t:call-trgt_plot_motifs_allele.slurm_singularity INFO srun: job 51797819 queued and waiting for resources
2025-09-15 20:24:52.999 wdl.w:ptcp.w:call-trgt-40.t:call-trgt_plot_motifs_allele.slurm_singularity INFO srun: job 51797819 has been allocated resources
2025-09-15 20:24:52.999 wdl.w:ptcp.w:call-trgt-40.t:call-trgt_plot_motifs_allele.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:53.020 wdl.w:ptcp.w:call-trgt-62 NOTICE done
2025-09-15 20:24:53.026 wdl.w:ptcp NOTICE finish :: job: "call-trgt-62"
2025-09-15 20:24:53.026 wdl.w:ptcp INFO output :: job: "call-trgt-62", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-62/out/m84036_250809_035451_s4.bc2159.motifs_waterfall.trgt_plots.zip", "images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-62/out/m84036_250809_035451_s4.bc2159.meth_allele.trgt_plots.zip", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-62/out/m84036_250809_035451_s4.bc2159.trgt.sorted.spanning.bam.bai", "images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-62/out/m84036_250809_035451_s4.bc2159.motifs_allele.trgt_plots.zip", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-62/out/m84036_250809_035451_s4.bc2159.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-62/out/m84036_250809_035451_s4.bc2159.trgt.vcf", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-62/out/m84036_250809_035451_s4.bc2159.repeats.bam", "images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-62/out/m84036_250809_035451_s4.bc2159.meth_waterfall.trgt_plots.zip", "reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-62/out/m84036_250809_035451_s4.bc2159.repeats.bam.bai"}
2025-09-15 20:24:53.029 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_motifs_allele INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-54/call-trgt_plot_motifs_allele/_singularity_tmpdir_29erspk2"
2025-09-15 20:24:53.030 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_motifs_allele INFO Slurm invocation: srun --job-name call-trgt_plot_motifs_allele --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-54/call-trgt_plot_motifs_allele/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-54/call-trgt_plot_motifs_allele/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-54/call-trgt_plot_motifs_allele/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-54/call-trgt_plot_motifs_allele/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-54/call-trgt_genotype/out/m84036_250809_035451_s4.bc2151.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2151.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-54/call-trgt_genotype/out/m84036_250809_035451_s4.bc2151.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2151.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-54/call-trgt_genotype/out/m84036_250809_035451_s4.bc2151.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2151.trgt.sorted.spanning.bam:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-54/call-trgt_plot_motifs_allele/_singularity_tmpdir_29erspk2/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-54/call-trgt_plot_motifs_allele/_singularity_tmpdir_29erspk2/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:53.031 wdl.w:ptcp.w:call-trgt-64.t:call-trgt_genotype INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2161.trgt.vcf"
2025-09-15 20:24:53.034 wdl.w:ptcp.w:call-paraphase-74 NOTICE workflow start :: name: "paraphase", source: "./paraphase.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-74"
2025-09-15 20:24:53.035 wdl.w:ptcp.w:call-trgt-64.t:call-trgt_genotype INFO output :: name: "spanning_bam", value: "m84036_250809_035451_s4.bc2161.trgt.sorted.spanning.bam"
2025-09-15 20:24:53.037 wdl.w:ptcp.w:call-trgt-64.t:call-trgt_genotype INFO output :: name: "spanning_bam_bai", value: "m84036_250809_035451_s4.bc2161.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:53.050 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_motifs_allele NOTICE slurm_singularity run :: pid: 1203446, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-54/call-trgt_plot_motifs_allele/slurm_singularity.log.txt"
2025-09-15 20:24:53.052 wdl.w:ptcp.w:call-paraphase-74 INFO visit :: node: "decl-annotation_vcf", values: {"annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf"}
2025-09-15 20:24:53.052 wdl.w:ptcp.w:call-paraphase-74 INFO visit :: node: "decl-config_file", values: {"config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml"}
2025-09-15 20:24:53.052 wdl.w:ptcp.w:call-paraphase-74 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:24:53.052 wdl.w:ptcp.w:call-paraphase-74 INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:24:53.052 wdl.w:ptcp.w:call-paraphase-74 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-74/out/m84036_250809_035451_s4.bc2171.mapped.bam"}
2025-09-15 20:24:53.052 wdl.w:ptcp.w:call-paraphase-74 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-74/out/m84036_250809_035451_s4.bc2171.mapped.bam.bai"}
2025-09-15 20:24:53.052 wdl.w:ptcp.w:call-paraphase-74 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:24:53.053 wdl.w:ptcp.w:call-paraphase-74 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:24:53.053 wdl.w:ptcp.w:call-paraphase-74 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2171"}
2025-09-15 20:24:53.053 wdl.w:ptcp.w:call-paraphase-74 INFO visit :: node: "decl-sex", values: {"sex": "F"}
2025-09-15 20:24:53.053 wdl.w:ptcp.w:call-paraphase-74 NOTICE ready :: job: "call-run_paraphase", callee: "run_paraphase"
2025-09-15 20:24:53.053 wdl.w:ptcp.w:call-paraphase-74 INFO input :: job: "call-run_paraphase", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf", "genome_version": "38", "config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-74/out/m84036_250809_035451_s4.bc2171.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-74/out/m84036_250809_035451_s4.bc2171.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2171"}
2025-09-15 20:24:53.109 wdl.w:ptcp.w:call-trgt-64.t:call-trgt_genotype NOTICE done
2025-09-15 20:24:53.116 wdl.w:ptcp.w:call-trgt-64 NOTICE finish :: job: "call-trgt_genotype"
2025-09-15 20:24:53.116 wdl.w:ptcp.w:call-trgt-64 INFO output :: job: "call-trgt_genotype", values: {"spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-64/call-trgt_genotype/out/m84036_250809_035451_s4.bc2161.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-64/call-trgt_genotype/out/m84036_250809_035451_s4.bc2161.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-64/call-trgt_genotype/out/m84036_250809_035451_s4.bc2161.trgt.vcf"}
2025-09-15 20:24:53.117 wdl.w:ptcp.w:call-trgt-64 NOTICE ready :: job: "call-trgt_plot_meth_allele", callee: "trgt_plot"
2025-09-15 20:24:53.117 wdl.w:ptcp.w:call-trgt-64 INFO input :: job: "call-trgt_plot_meth_allele", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": false, "methylation": true, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-64/call-trgt_genotype/out/m84036_250809_035451_s4.bc2161.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-64/call-trgt_genotype/out/m84036_250809_035451_s4.bc2161.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-64/call-trgt_genotype/out/m84036_250809_035451_s4.bc2161.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2161"}
2025-09-15 20:24:53.118 wdl.w:ptcp.w:call-trgt-64 NOTICE ready :: job: "call-trgt_plot_meth_waterfall", callee: "trgt_plot"
2025-09-15 20:24:53.119 wdl.w:ptcp.w:call-trgt-64 INFO input :: job: "call-trgt_plot_meth_waterfall", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": true, "methylation": true, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-64/call-trgt_genotype/out/m84036_250809_035451_s4.bc2161.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-64/call-trgt_genotype/out/m84036_250809_035451_s4.bc2161.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-64/call-trgt_genotype/out/m84036_250809_035451_s4.bc2161.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2161"}
2025-09-15 20:24:53.119 wdl.w:ptcp.w:call-trgt-64 NOTICE ready :: job: "call-trgt_plot_motifs_allele", callee: "trgt_plot"
2025-09-15 20:24:53.120 wdl.w:ptcp.w:call-trgt-64 INFO input :: job: "call-trgt_plot_motifs_allele", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": false, "methylation": false, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-64/call-trgt_genotype/out/m84036_250809_035451_s4.bc2161.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-64/call-trgt_genotype/out/m84036_250809_035451_s4.bc2161.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-64/call-trgt_genotype/out/m84036_250809_035451_s4.bc2161.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2161"}
2025-09-15 20:24:53.121 wdl.w:ptcp.w:call-trgt-64 NOTICE ready :: job: "call-trgt_plot_motifs_waterfall", callee: "trgt_plot"
2025-09-15 20:24:53.121 wdl.w:ptcp.w:call-trgt-64 INFO input :: job: "call-trgt_plot_motifs_waterfall", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": true, "methylation": false, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-64/call-trgt_genotype/out/m84036_250809_035451_s4.bc2161.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-64/call-trgt_genotype/out/m84036_250809_035451_s4.bc2161.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-64/call-trgt_genotype/out/m84036_250809_035451_s4.bc2161.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2161"}
2025-09-15 20:24:53.121 wdl.w:ptcp.w:call-trgt-64 INFO visit :: node: "output-spanning_bam", values: {"spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-64/call-trgt_genotype/out/m84036_250809_035451_s4.bc2161.trgt.sorted.spanning.bam"}
2025-09-15 20:24:53.122 wdl.w:ptcp.w:call-trgt-64 INFO visit :: node: "output-spanning_bam_bai", values: {"spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-64/call-trgt_genotype/out/m84036_250809_035451_s4.bc2161.trgt.sorted.spanning.bam.bai"}
2025-09-15 20:24:53.122 wdl.w:ptcp.w:call-trgt-64 INFO visit :: node: "output-vcf", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-64/call-trgt_genotype/out/m84036_250809_035451_s4.bc2161.trgt.vcf"}
2025-09-15 20:24:53.125 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_motifs_waterfall NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-54/call-trgt_plot_motifs_waterfall", thread: 140607683024448
2025-09-15 20:24:53.138 wdl.w:ptcp.w:call-trgt-40.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO srun: job 51797820 queued and waiting for resources
2025-09-15 20:24:53.138 wdl.w:ptcp.w:call-trgt-40.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO srun: job 51797820 has been allocated resources
2025-09-15 20:24:53.138 wdl.w:ptcp.w:call-trgt-40.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:53.145 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_motifs_waterfall INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:53.145 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_motifs_waterfall INFO input :: name: "waterfall", value: true
2025-09-15 20:24:53.145 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_motifs_waterfall INFO input :: name: "methylation", value: false
2025-09-15 20:24:53.145 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_motifs_waterfall INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:53.145 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_motifs_waterfall INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:53.145 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_motifs_waterfall INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:53.145 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_motifs_waterfall INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2151.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:53.145 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_motifs_waterfall INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2151.trgt.sorted.spanning.bam"
2025-09-15 20:24:53.145 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_motifs_waterfall INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2151.trgt.vcf"
2025-09-15 20:24:53.145 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_motifs_waterfall INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2151"
2025-09-15 20:24:53.145 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:53.146 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "plot_type", value: "waterfall"
2025-09-15 20:24:53.146 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "show", value: "motifs"
2025-09-15 20:24:53.146 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "threads", value: 1
2025-09-15 20:24:53.146 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:53.146 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2151.motifs_waterfall"
2025-09-15 20:24:53.146 wdl.w:ptcp.w:call-trgt-41.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:53 [ERROR] - No reads found for TRID=PRTS_ARX
2025-09-15 20:24:53.147 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_motifs_waterfall INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:53.147 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_motifs_waterfall WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:53.147 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_motifs_waterfall INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:53.147 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_motifs_waterfall INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:53.153 wdl.w:ptcp.w:call-sawfish-19.t:call-run_sawfish.stderr VERBOSE [M::mm_idx_gen::73.716*1.83] sorted minimizers
2025-09-15 20:24:53.154 wdl.w:ptcp.w:call-sawfish-19.t:call-run_sawfish.stderr VERBOSE [M::main::73.717*1.83] loaded/built the index for 195 target sequence(s)
2025-09-15 20:24:53.228 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_motifs_waterfall INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-54/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_log7cvhy"
2025-09-15 20:24:53.228 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_motifs_waterfall INFO Slurm invocation: srun --job-name call-trgt_plot_motifs_waterfall --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-54/call-trgt_plot_motifs_waterfall/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-54/call-trgt_plot_motifs_waterfall/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-54/call-trgt_plot_motifs_waterfall/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-54/call-trgt_plot_motifs_waterfall/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-54/call-trgt_genotype/out/m84036_250809_035451_s4.bc2151.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2151.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-54/call-trgt_genotype/out/m84036_250809_035451_s4.bc2151.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2151.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-54/call-trgt_genotype/out/m84036_250809_035451_s4.bc2151.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2151.trgt.sorted.spanning.bam:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-54/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_log7cvhy/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-54/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_log7cvhy/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:53.252 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_motifs_waterfall NOTICE slurm_singularity run :: pid: 1203449, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-54/call-trgt_plot_motifs_waterfall/slurm_singularity.log.txt"
2025-09-15 20:24:53.282 wdl.w:ptcp.w:call-paraphase-61.t:call-run_paraphase INFO output :: name: "paraphase_bam", value: "m84036_250809_035451_s4.bc2158_paraphase/m84036_250809_035451_s4.bc2158.paraphase.bam"
2025-09-15 20:24:53.288 wdl.w:ptcp.w:call-paraphase-61.t:call-run_paraphase INFO output :: name: "paraphase_bam_bai", value: "m84036_250809_035451_s4.bc2158_paraphase/m84036_250809_035451_s4.bc2158.paraphase.bam.bai"
2025-09-15 20:24:53.289 wdl.w:ptcp.w:call-paraphase-61.t:call-run_paraphase INFO output :: name: "paraphase_json", value: "m84036_250809_035451_s4.bc2158_paraphase/m84036_250809_035451_s4.bc2158.paraphase.json"
2025-09-15 20:24:53.291 wdl.w:ptcp.w:call-paraphase-61.t:call-run_paraphase INFO output :: name: "paraphase_vcfs", value: []
2025-09-15 20:24:53.291 wdl.w:ptcp.w:call-paraphase-61.t:call-run_paraphase INFO output :: name: "havanno_json", value: "m84036_250809_035451_s4.bc2158.havanno.json"
2025-09-15 20:24:53.293 wdl.w:ptcp.w:call-trgt-41.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:52 [ERROR] - No reads found for TRID=PRTS_ARX
2025-09-15 20:24:53.294 wdl.w:ptcp.w:call-trgt-41.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:52 [ERROR] - No reads found for TRID=EIEE1_ARX
2025-09-15 20:24:53.321 wdl.w:ptcp.w:call-sawfish-69.t:call-run_sawfish.stderr VERBOSE [M::bam2fq_mainloop] discarded 0 singletons
2025-09-15 20:24:53.321 wdl.w:ptcp.w:call-sawfish-69.t:call-run_sawfish.stderr VERBOSE [M::bam2fq_mainloop] processed 0 reads
2025-09-15 20:24:53.373 wdl.w:ptcp.w:call-sawfish-44.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:49][sawfish][INFO] Starting sawfish 2.0.3
2025-09-15 20:24:53.373 wdl.w:ptcp.w:call-sawfish-44.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:49][sawfish][INFO] cmdline: sawfish discover --disable-cnv --threads 16 --ref /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa --bam m84036_250809_035451_s4.bc2141.minimap2.bam --output-dir m84036_250809_035451_s4.bc2141_sawfish_discover
2025-09-15 20:24:53.373 wdl.w:ptcp.w:call-sawfish-44.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:49][sawfish][INFO] Running on 16 threads
2025-09-15 20:24:53.374 wdl.w:ptcp.w:call-sawfish-44.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:49][sawfish][INFO] Writing discover settings to file: 'm84036_250809_035451_s4.bc2141_sawfish_discover/discover.settings.json'
2025-09-15 20:24:53.374 wdl.w:ptcp.w:call-sawfish-44.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:49][sawfish][INFO] Reading reference genome from file '/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa'
2025-09-15 20:24:53.374 wdl.w:ptcp.w:call-sawfish-44.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:52][sawfish][INFO] Processing alignment file '/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2141.minimap2.bam'
2025-09-15 20:24:53.374 wdl.w:ptcp.w:call-sawfish-44.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:52][sawfish][INFO] Finished processing all alignments
2025-09-15 20:24:53.374 wdl.w:ptcp.w:call-sawfish-44.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:52][sawfish][INFO] Writing depth bins to binary file: 'm84036_250809_035451_s4.bc2141_sawfish_discover/depth.mpack'
2025-09-15 20:24:53.374 wdl.w:ptcp.w:call-sawfish-44.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:53][sawfish][INFO] Writing max sv depth genome regions to bed file: 'm84036_250809_035451_s4.bc2141_sawfish_discover/max.depth.bed'
2025-09-15 20:24:53.374 wdl.w:ptcp.w:call-sawfish-44.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:53][sawfish][INFO] Completing breakpoint observation clustering
2025-09-15 20:24:53.374 wdl.w:ptcp.w:call-sawfish-44.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:53][sawfish][INFO] Finished breakpoint observation clustering
2025-09-15 20:24:53.374 wdl.w:ptcp.w:call-sawfish-44.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:53][sawfish][INFO] Consolidating adjacent indel candidates
2025-09-15 20:24:53.374 wdl.w:ptcp.w:call-sawfish-44.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:53][sawfish][INFO] Finding large insertion candidates
2025-09-15 20:24:53.374 wdl.w:ptcp.w:call-sawfish-44.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:53][sawfish][INFO] Writing breakpoint_cluster debug bed file: 'm84036_250809_035451_s4.bc2141_sawfish_discover/debug.breakpoint_clusters.bed'
2025-09-15 20:24:53.374 wdl.w:ptcp.w:call-sawfish-44.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:53][sawfish][INFO] Refining SV Candidates
2025-09-15 20:24:53.374 wdl.w:ptcp.w:call-sawfish-44.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:53][sawfish][INFO] Writing debug assembly region bed file: 'm84036_250809_035451_s4.bc2141_sawfish_discover/assembly.regions.bed'
2025-09-15 20:24:53.374 wdl.w:ptcp.w:call-sawfish-44.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:53][sawfish][INFO] Starting refinement of breakpoint evidence clusters
2025-09-15 20:24:53.374 wdl.w:ptcp.w:call-sawfish-44.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:53][sawfish][INFO] Finished refining all breakpoint evidence clusters
2025-09-15 20:24:53.374 wdl.w:ptcp.w:call-sawfish-44.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:53][sawfish][INFO] Writing all contig alignments to bam file: 'm84036_250809_035451_s4.bc2141_sawfish_discover/contig.alignment.bam'
2025-09-15 20:24:53.374 wdl.w:ptcp.w:call-sawfish-44.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:53][sawfish][INFO] Writing candidate structural variants to file: 'm84036_250809_035451_s4.bc2141_sawfish_discover/candidate.sv.bcf'
2025-09-15 20:24:53.374 wdl.w:ptcp.w:call-sawfish-44.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:53][sawfish][INFO] Writing run statistics to file: 'm84036_250809_035451_s4.bc2141_sawfish_discover/run.stats.json'
2025-09-15 20:24:53.375 wdl.w:ptcp.w:call-sawfish-44.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:53][sawfish][INFO] sawfish completed. Total Runtime: 00:00:03.391
2025-09-15 20:24:53.390 wdl.w:ptcp.w:call-paraphase-61.t:call-run_paraphase NOTICE done
2025-09-15 20:24:53.395 wdl.w:ptcp.w:call-paraphase-61 NOTICE finish :: job: "call-run_paraphase"
2025-09-15 20:24:53.395 wdl.w:ptcp.w:call-paraphase-61 INFO output :: job: "call-run_paraphase", values: {"havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-61/call-run_paraphase/out/m84036_250809_035451_s4.bc2158.havanno.json", "paraphase_vcfs": [], "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-61/call-run_paraphase/out/m84036_250809_035451_s4.bc2158_paraphase/m84036_250809_035451_s4.bc2158.paraphase.json", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-61/call-run_paraphase/out/m84036_250809_035451_s4.bc2158_paraphase/m84036_250809_035451_s4.bc2158.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-61/call-run_paraphase/out/m84036_250809_035451_s4.bc2158_paraphase/m84036_250809_035451_s4.bc2158.paraphase.bam"}
2025-09-15 20:24:53.396 wdl.w:ptcp.w:call-paraphase-61 NOTICE ready :: job: "call-call_f8", callee: "call_f8"
2025-09-15 20:24:53.396 wdl.w:ptcp.w:call-paraphase-61 INFO input :: job: "call-call_f8", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "out_prefix": "m84036_250809_035451_s4.bc2158", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-61/call-run_paraphase/out/m84036_250809_035451_s4.bc2158_paraphase/m84036_250809_035451_s4.bc2158.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-61/call-run_paraphase/out/m84036_250809_035451_s4.bc2158_paraphase/m84036_250809_035451_s4.bc2158.paraphase.bam", "sex": "F"}
2025-09-15 20:24:53.397 wdl.w:ptcp.w:call-paraphase-61 INFO visit :: node: "output-havanno_json", values: {"havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-61/call-run_paraphase/out/m84036_250809_035451_s4.bc2158.havanno.json"}
2025-09-15 20:24:53.397 wdl.w:ptcp.w:call-paraphase-61 INFO visit :: node: "output-paraphase_bam", values: {"paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-61/call-run_paraphase/out/m84036_250809_035451_s4.bc2158_paraphase/m84036_250809_035451_s4.bc2158.paraphase.bam"}
2025-09-15 20:24:53.397 wdl.w:ptcp.w:call-paraphase-61 INFO visit :: node: "output-paraphase_bam_bai", values: {"paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-61/call-run_paraphase/out/m84036_250809_035451_s4.bc2158_paraphase/m84036_250809_035451_s4.bc2158.paraphase.bam.bai"}
2025-09-15 20:24:53.397 wdl.w:ptcp.w:call-paraphase-61 INFO visit :: node: "output-paraphase_json", values: {"paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-61/call-run_paraphase/out/m84036_250809_035451_s4.bc2158_paraphase/m84036_250809_035451_s4.bc2158.paraphase.json"}
2025-09-15 20:24:53.397 wdl.w:ptcp.w:call-paraphase-61 INFO visit :: node: "output-paraphase_vcfs", values: {"paraphase_vcfs": []}
2025-09-15 20:24:53.401 wdl.w:ptcp.w:call-trgt-69.t:call-get_reads_overlapping_repeats NOTICE task setup :: name: "get_reads_overlapping_repeats", source: "./trgt.wdl", line: 182, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-69/call-get_reads_overlapping_repeats", thread: 140608773551680
2025-09-15 20:24:53.417 wdl.w:ptcp.w:call-trgt-48.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:51 [ERROR] - No reads found for TRID=PRTS_ARX
2025-09-15 20:24:53.417 wdl.w:ptcp.w:call-trgt-48.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:51 [ERROR] - No reads found for TRID=EIEE1_ARX
2025-09-15 20:24:53.422 wdl.w:ptcp.w:call-trgt-69.t:call-get_reads_overlapping_repeats INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:53.422 wdl.w:ptcp.w:call-trgt-69.t:call-get_reads_overlapping_repeats INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:53.422 wdl.w:ptcp.w:call-trgt-69.t:call-get_reads_overlapping_repeats INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2166.mapped.bam.bai"
2025-09-15 20:24:53.422 wdl.w:ptcp.w:call-trgt-69.t:call-get_reads_overlapping_repeats INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2166.mapped.bam"
2025-09-15 20:24:53.422 wdl.w:ptcp.w:call-trgt-69.t:call-get_reads_overlapping_repeats INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2166"
2025-09-15 20:24:53.422 wdl.w:ptcp.w:call-trgt-69.t:call-get_reads_overlapping_repeats INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:53.422 wdl.w:ptcp.w:call-trgt-69.t:call-get_reads_overlapping_repeats INFO eval :: name: "expand_size", value: 3000
2025-09-15 20:24:53.423 wdl.w:ptcp.w:call-trgt-69.t:call-get_reads_overlapping_repeats INFO eval :: name: "threads", value: 1
2025-09-15 20:24:53.423 wdl.w:ptcp.w:call-trgt-69.t:call-get_reads_overlapping_repeats INFO eval :: name: "expanded_bed_name", value: "m84036_250809_035451_s4.bc2166.expanded.bed"
2025-09-15 20:24:53.423 wdl.w:ptcp.w:call-trgt-69.t:call-get_reads_overlapping_repeats INFO eval :: name: "disk_size", value: 11
2025-09-15 20:24:53.423 wdl.w:ptcp.w:call-trgt-69.t:call-get_reads_overlapping_repeats INFO eval :: name: "output_name", value: "m84036_250809_035451_s4.bc2166.repeats.bam"
2025-09-15 20:24:53.423 wdl.w:ptcp.w:call-trgt-69.t:call-get_reads_overlapping_repeats INFO eval :: name: "index_name", value: "m84036_250809_035451_s4.bc2166.repeats.bam.bai"
2025-09-15 20:24:53.423 wdl.w:ptcp.w:call-trgt-69.t:call-get_reads_overlapping_repeats INFO eval :: name: "output_name_with_index", value: "m84036_250809_035451_s4.bc2166.repeats.bam##idx##m84036_250809_035451_s4.bc2166.repeats.bam.bai"
2025-09-15 20:24:53.424 wdl.w:ptcp.w:call-trgt-69.t:call-get_reads_overlapping_repeats INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:53.424 wdl.w:ptcp.w:call-trgt-69.t:call-get_reads_overlapping_repeats WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:53.424 wdl.w:ptcp.w:call-trgt-69.t:call-get_reads_overlapping_repeats INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:53.424 wdl.w:ptcp.w:call-trgt-69.t:call-get_reads_overlapping_repeats INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:53.484 wdl.w:ptcp.w:call-trgt-69.t:call-get_reads_overlapping_repeats INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 9, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-69/call-get_reads_overlapping_repeats/_singularity_tmpdir__y2b2arj"
2025-09-15 20:24:53.484 wdl.w:ptcp.w:call-trgt-69.t:call-get_reads_overlapping_repeats INFO Slurm invocation: srun --job-name call-get_reads_overlapping_repeats --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-69/call-get_reads_overlapping_repeats/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-69/call-get_reads_overlapping_repeats/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-69/call-get_reads_overlapping_repeats/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-69/call-get_reads_overlapping_repeats/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-69/out/m84036_250809_035451_s4.bc2166.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2166.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-69/out/m84036_250809_035451_s4.bc2166.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2166.mapped.bam:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-69/call-get_reads_overlapping_repeats/_singularity_tmpdir__y2b2arj/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-69/call-get_reads_overlapping_repeats/_singularity_tmpdir__y2b2arj/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:53.506 wdl.w:ptcp.w:call-trgt-48.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:52 [ERROR] - No reads found for TRID=PRTS_ARX
2025-09-15 20:24:53.507 wdl.w:ptcp.w:call-trgt-48.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:52 [ERROR] - No reads found for TRID=EIEE1_ARX
2025-09-15 20:24:53.507 wdl.w:ptcp.w:call-trgt-69.t:call-get_reads_overlapping_repeats NOTICE slurm_singularity run :: pid: 1203456, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-69/call-get_reads_overlapping_repeats/slurm_singularity.log.txt"
2025-09-15 20:24:53.527 wdl.w:ptcp.w:call-trgt-48.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:52 [ERROR] - No reads found for TRID=PRTS_ARX
2025-09-15 20:24:53.527 wdl.w:ptcp.w:call-trgt-48.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:52 [ERROR] - No reads found for TRID=EIEE1_ARX
2025-09-15 20:24:53.585 wdl.w:ptcp.w:call-trgt-48.t:call-trgt_plot_meth_allele INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2145.meth_allele.trgt_plots.zip"
2025-09-15 20:24:53.681 wdl.w:ptcp.w:call-trgt-48.t:call-trgt_plot_meth_allele NOTICE done
2025-09-15 20:24:53.686 wdl.w:ptcp.w:call-trgt-48 NOTICE finish :: job: "call-trgt_plot_meth_allele"
2025-09-15 20:24:53.686 wdl.w:ptcp.w:call-trgt-48 INFO output :: job: "call-trgt_plot_meth_allele", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-48/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2145.meth_allele.trgt_plots.zip"}
2025-09-15 20:24:53.687 wdl.w:ptcp.w:call-trgt-48 INFO visit :: node: "output-images_meth_allele", values: {"images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-48/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2145.meth_allele.trgt_plots.zip"}
2025-09-15 20:24:53.692 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_plot_meth_allele NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-59/call-trgt_plot_meth_allele", thread: 140610895857216
2025-09-15 20:24:53.712 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:53 [ERROR] - No reads found for TRID=SCA37_DAB1
2025-09-15 20:24:53.712 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:53 [ERROR] - No reads found for TRID=OPDM_ABCD3
2025-09-15 20:24:53.712 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_plot_meth_allele INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:53.712 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:53 [ERROR] - No reads found for TRID=NIID_NOTCH2NLC
2025-09-15 20:24:53.712 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_plot_meth_allele INFO input :: name: "waterfall", value: false
2025-09-15 20:24:53.712 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:53 [ERROR] - No reads found for TRID=SCA2_ATXN2
2025-09-15 20:24:53.712 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_plot_meth_allele INFO input :: name: "methylation", value: true
2025-09-15 20:24:53.712 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:53 [ERROR] - No reads found for TRID=OPDM4_RILPL1
2025-09-15 20:24:53.713 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_plot_meth_allele INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:53.713 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:53 [ERROR] - No reads found for TRID=SCA8_ATXN8OS
2025-09-15 20:24:53.713 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_plot_meth_allele INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:53.713 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:53 [ERROR] - No reads found for TRID=OPMD_PABPN1
2025-09-15 20:24:53.713 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_plot_meth_allele INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:53.713 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_plot_meth_allele INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2156.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:53.713 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_plot_meth_allele INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2156.trgt.sorted.spanning.bam"
2025-09-15 20:24:53.713 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_plot_meth_allele INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2156.trgt.vcf"
2025-09-15 20:24:53.713 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_plot_meth_allele INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2156"
2025-09-15 20:24:53.714 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_plot_meth_allele INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:53.714 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_plot_meth_allele INFO eval :: name: "plot_type", value: "allele"
2025-09-15 20:24:53.714 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_plot_meth_allele INFO eval :: name: "show", value: "meth"
2025-09-15 20:24:53.714 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_plot_meth_allele INFO eval :: name: "threads", value: 1
2025-09-15 20:24:53.714 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_plot_meth_allele INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:53.714 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_plot_meth_allele INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2156.meth_allele"
2025-09-15 20:24:53.715 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_plot_meth_allele INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:53.715 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_plot_meth_allele WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:53.715 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_plot_meth_allele INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:53.715 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_plot_meth_allele INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:53.719 wdl.w:ptcp.t:call-tar_outputs-08.slurm_singularity INFO srun: job 51797821 queued and waiting for resources
2025-09-15 20:24:53.719 wdl.w:ptcp.t:call-tar_outputs-08.slurm_singularity INFO srun: job 51797821 has been allocated resources
2025-09-15 20:24:53.719 wdl.w:ptcp.t:call-tar_outputs-08.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:53.725 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_meth_allele.slurm_singularity INFO srun: job 51797822 queued and waiting for resources
2025-09-15 20:24:53.726 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_meth_allele.slurm_singularity INFO srun: job 51797822 has been allocated resources
2025-09-15 20:24:53.726 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_meth_allele.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:53.777 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_plot_meth_allele INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-59/call-trgt_plot_meth_allele/_singularity_tmpdir_nj_dsp79"
2025-09-15 20:24:53.778 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_plot_meth_allele INFO Slurm invocation: srun --job-name call-trgt_plot_meth_allele --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-59/call-trgt_plot_meth_allele/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-59/call-trgt_plot_meth_allele/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-59/call-trgt_plot_meth_allele/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-59/call-trgt_plot_meth_allele/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-59/call-trgt_genotype/out/m84036_250809_035451_s4.bc2156.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2156.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-59/call-trgt_genotype/out/m84036_250809_035451_s4.bc2156.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2156.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-59/call-trgt_genotype/out/m84036_250809_035451_s4.bc2156.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2156.trgt.sorted.spanning.bam:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-59/call-trgt_plot_meth_allele/_singularity_tmpdir_nj_dsp79/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-59/call-trgt_plot_meth_allele/_singularity_tmpdir_nj_dsp79/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:53.794 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_plot_meth_allele NOTICE slurm_singularity run :: pid: 1203469, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-59/call-trgt_plot_meth_allele/slurm_singularity.log.txt"
2025-09-15 20:24:53.800 wdl.w:ptcp.w:call-paraphase-58.t:call-run_paraphase.stderr VERBOSE INFO:root:Processing sample m84036_250809_035451_s4.bc2155 at 2025-09-15 20:24:49.208002...
2025-09-15 20:24:53.801 wdl.w:ptcp.w:call-paraphase-58.t:call-run_paraphase.stderr VERBOSE INFO:root:Checking sample sex at 2025-09-15 20:24:49.208791...
2025-09-15 20:24:53.801 wdl.w:ptcp.w:call-paraphase-58.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for gba for sample m84036_250809_035451_s4.bc2155 at 2025-09-15 20:24:49.257098...
2025-09-15 20:24:53.801 wdl.w:ptcp.w:call-paraphase-58.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for gba for sample m84036_250809_035451_s4.bc2155 at 2025-09-15 20:24:49.257606...
2025-09-15 20:24:53.801 wdl.w:ptcp.w:call-paraphase-58.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for cyp21 for sample m84036_250809_035451_s4.bc2155 at 2025-09-15 20:24:49.257018...
2025-09-15 20:24:53.801 wdl.w:ptcp.w:call-paraphase-58.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for cyp21 for sample m84036_250809_035451_s4.bc2155 at 2025-09-15 20:24:49.257706...
2025-09-15 20:24:53.801 wdl.w:ptcp.w:call-paraphase-58.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for smn1 for sample m84036_250809_035451_s4.bc2155 at 2025-09-15 20:24:49.257246...
2025-09-15 20:24:53.801 wdl.w:ptcp.w:call-paraphase-58.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for smn1 for sample m84036_250809_035451_s4.bc2155 at 2025-09-15 20:24:49.257869...
2025-09-15 20:24:53.801 wdl.w:ptcp.w:call-paraphase-58.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for hba for sample m84036_250809_035451_s4.bc2155 at 2025-09-15 20:24:49.258959...
2025-09-15 20:24:53.801 wdl.w:ptcp.w:call-paraphase-58.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for hba for sample m84036_250809_035451_s4.bc2155 at 2025-09-15 20:24:49.259414...
2025-09-15 20:24:53.877 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:53 [ERROR] - No reads found for TRID=SCA37_DAB1
2025-09-15 20:24:53.878 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:53 [ERROR] - No reads found for TRID=OPDM_ABCD3
2025-09-15 20:24:53.878 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:53 [ERROR] - No reads found for TRID=NIID_NOTCH2NLC
2025-09-15 20:24:53.878 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:53 [ERROR] - No reads found for TRID=SCA2_ATXN2
2025-09-15 20:24:53.878 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:53 [ERROR] - No reads found for TRID=OPDM4_RILPL1
2025-09-15 20:24:53.878 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:53 [ERROR] - No reads found for TRID=SCA8_ATXN8OS
2025-09-15 20:24:53.878 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:53 [ERROR] - No reads found for TRID=OPMD_PABPN1
2025-09-15 20:24:53.878 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:53 [ERROR] - No reads found for TRID=SCA27B_FGF14
2025-09-15 20:24:53.885 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO srun: job 51797823 queued and waiting for resources
2025-09-15 20:24:53.885 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO srun: job 51797823 has been allocated resources
2025-09-15 20:24:53.885 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:54.052 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:53 [ERROR] - No reads found for TRID=SCA37_DAB1
2025-09-15 20:24:54.052 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:53 [ERROR] - No reads found for TRID=OPDM_ABCD3
2025-09-15 20:24:54.052 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:53 [ERROR] - No reads found for TRID=NIID_NOTCH2NLC
2025-09-15 20:24:54.052 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:53 [ERROR] - No reads found for TRID=SCA2_ATXN2
2025-09-15 20:24:54.052 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:54 [ERROR] - No reads found for TRID=OPDM4_RILPL1
2025-09-15 20:24:54.059 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_motifs_allele.slurm_singularity INFO srun: job 51797824 queued and waiting for resources
2025-09-15 20:24:54.059 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_motifs_allele.slurm_singularity INFO srun: job 51797824 has been allocated resources
2025-09-15 20:24:54.059 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_motifs_allele.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:54.129 wdl.w:ptcp.t:call-tar_outputs-08 INFO output :: name: "sample_tarball", value: "m84036_250809_035451_s4.bc2105.tar"
2025-09-15 20:24:54.197 wdl.w:ptcp.t:call-tar_outputs-08 NOTICE done
2025-09-15 20:24:54.201 wdl.w:ptcp NOTICE finish :: job: "call-tar_outputs-08"
2025-09-15 20:24:54.202 wdl.w:ptcp INFO output :: job: "call-tar_outputs-08", values: {"sample_tarball": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-08/out/m84036_250809_035451_s4.bc2105.tar"}
2025-09-15 20:24:54.206 wdl.w:ptcp.w:call-paraphase-23.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for rpgr for sample m84036_250809_035451_s4.bc2120 at 2025-09-15 20:24:48.821844...
2025-09-15 20:24:54.206 wdl.w:ptcp.w:call-paraphase-23.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for rpgr for sample m84036_250809_035451_s4.bc2120 at 2025-09-15 20:24:49.255387...
2025-09-15 20:24:54.206 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_plot_meth_waterfall NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-59/call-trgt_plot_meth_waterfall", thread: 140610912642624
2025-09-15 20:24:54.227 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_plot_meth_waterfall INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:54.227 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_plot_meth_waterfall INFO input :: name: "waterfall", value: true
2025-09-15 20:24:54.227 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_plot_meth_waterfall INFO input :: name: "methylation", value: true
2025-09-15 20:24:54.227 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_plot_meth_waterfall INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:54.227 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_plot_meth_waterfall INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:54.227 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_plot_meth_waterfall INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:54.227 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_plot_meth_waterfall INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2156.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:54.227 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_plot_meth_waterfall INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2156.trgt.sorted.spanning.bam"
2025-09-15 20:24:54.227 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_plot_meth_waterfall INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2156.trgt.vcf"
2025-09-15 20:24:54.227 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_plot_meth_waterfall INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2156"
2025-09-15 20:24:54.227 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_plot_meth_waterfall INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:54.228 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_plot_meth_waterfall INFO eval :: name: "plot_type", value: "waterfall"
2025-09-15 20:24:54.228 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_plot_meth_waterfall INFO eval :: name: "show", value: "meth"
2025-09-15 20:24:54.228 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_plot_meth_waterfall INFO eval :: name: "threads", value: 1
2025-09-15 20:24:54.228 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_plot_meth_waterfall INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:54.228 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_plot_meth_waterfall INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2156.meth_waterfall"
2025-09-15 20:24:54.228 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_plot_meth_waterfall INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:54.228 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_plot_meth_waterfall WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:54.229 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_plot_meth_waterfall INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:54.229 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_plot_meth_waterfall INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:54.254 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:54 [ERROR] - No reads found for TRID=SCA37_DAB1
2025-09-15 20:24:54.260 wdl.w:ptcp.w:call-trgt-57.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:53 [ERROR] - No reads found for TRID=PRTS_ARX
2025-09-15 20:24:54.260 wdl.w:ptcp.w:call-trgt-57.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:53 [ERROR] - No reads found for TRID=EIEE1_ARX
2025-09-15 20:24:54.264 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO srun: job 51797825 queued and waiting for resources
2025-09-15 20:24:54.264 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO srun: job 51797825 has been allocated resources
2025-09-15 20:24:54.264 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:54.302 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_plot_meth_waterfall INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-59/call-trgt_plot_meth_waterfall/_singularity_tmpdir_e0xunvqp"
2025-09-15 20:24:54.302 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_plot_meth_waterfall INFO Slurm invocation: srun --job-name call-trgt_plot_meth_waterfall --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-59/call-trgt_plot_meth_waterfall/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-59/call-trgt_plot_meth_waterfall/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-59/call-trgt_plot_meth_waterfall/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-59/call-trgt_plot_meth_waterfall/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-59/call-trgt_genotype/out/m84036_250809_035451_s4.bc2156.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2156.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-59/call-trgt_genotype/out/m84036_250809_035451_s4.bc2156.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2156.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-59/call-trgt_genotype/out/m84036_250809_035451_s4.bc2156.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2156.trgt.sorted.spanning.bam:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-59/call-trgt_plot_meth_waterfall/_singularity_tmpdir_e0xunvqp/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-59/call-trgt_plot_meth_waterfall/_singularity_tmpdir_e0xunvqp/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:54.325 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_plot_meth_waterfall NOTICE slurm_singularity run :: pid: 1203477, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-59/call-trgt_plot_meth_waterfall/slurm_singularity.log.txt"
2025-09-15 20:24:54.518 wdl.w:ptcp.w:call-trgt-69.t:call-get_reads_overlapping_repeats.slurm_singularity INFO srun: job 51797826 queued and waiting for resources
2025-09-15 20:24:54.518 wdl.w:ptcp.w:call-trgt-69.t:call-get_reads_overlapping_repeats.slurm_singularity INFO srun: job 51797826 has been allocated resources
2025-09-15 20:24:54.518 wdl.w:ptcp.w:call-trgt-69.t:call-get_reads_overlapping_repeats.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:54.649 wdl.w:ptcp.w:call-trgt-48.t:call-trgt_plot_motifs_allele INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2145.motifs_allele.trgt_plots.zip"
2025-09-15 20:24:54.747 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:53 [ERROR] - No reads found for TRID=SCA27B_FGF14
2025-09-15 20:24:54.758 wdl.w:ptcp.w:call-trgt-48.t:call-trgt_plot_motifs_allele NOTICE done
2025-09-15 20:24:54.762 wdl.w:ptcp.w:call-trgt-48 NOTICE finish :: job: "call-trgt_plot_motifs_allele"
2025-09-15 20:24:54.763 wdl.w:ptcp.w:call-trgt-48 INFO output :: job: "call-trgt_plot_motifs_allele", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-48/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2145.motifs_allele.trgt_plots.zip"}
2025-09-15 20:24:54.763 wdl.w:ptcp.w:call-trgt-48 INFO visit :: node: "output-images_motifs_allele", values: {"images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-48/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2145.motifs_allele.trgt_plots.zip"}
2025-09-15 20:24:54.767 wdl.w:ptcp.w:call-trgt-69.t:call-trgt_genotype NOTICE task setup :: name: "trgt_genotype", source: "./trgt.wdl", line: 272, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-69/call-trgt_genotype", thread: 140607137760832
2025-09-15 20:24:54.784 wdl.w:ptcp.w:call-trgt-69.t:call-trgt_genotype INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:54.784 wdl.w:ptcp.w:call-trgt-69.t:call-trgt_genotype INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:54.785 wdl.w:ptcp.w:call-trgt-69.t:call-trgt_genotype INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:54.785 wdl.w:ptcp.w:call-trgt-69.t:call-trgt_genotype INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:54.785 wdl.w:ptcp.w:call-trgt-69.t:call-trgt_genotype INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2166.mapped.bam.bai"
2025-09-15 20:24:54.785 wdl.w:ptcp.w:call-trgt-69.t:call-trgt_genotype INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2166.mapped.bam"
2025-09-15 20:24:54.785 wdl.w:ptcp.w:call-trgt-69.t:call-trgt_genotype INFO input :: name: "sex", value: "F"
2025-09-15 20:24:54.785 wdl.w:ptcp.w:call-trgt-69.t:call-trgt_genotype INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2166"
2025-09-15 20:24:54.785 wdl.w:ptcp.w:call-trgt-69.t:call-trgt_genotype INFO eval :: name: "mem_gb", value: 16
2025-09-15 20:24:54.785 wdl.w:ptcp.w:call-trgt-69.t:call-trgt_genotype INFO eval :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2166.trgt"
2025-09-15 20:24:54.785 wdl.w:ptcp.w:call-trgt-69.t:call-trgt_genotype INFO eval :: name: "threads", value: 8
2025-09-15 20:24:54.786 wdl.w:ptcp.w:call-trgt-69.t:call-trgt_genotype INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:54.786 wdl.w:ptcp.w:call-trgt-69.t:call-trgt_genotype INFO eval :: name: "karyotype", value: "XX"
2025-09-15 20:24:54.786 wdl.w:ptcp.w:call-trgt-69.t:call-trgt_genotype INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 8, memory_reservation: 16000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:54.786 wdl.w:ptcp.w:call-trgt-69.t:call-trgt_genotype WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:54.787 wdl.w:ptcp.w:call-trgt-69.t:call-trgt_genotype INFO provisioned :: seconds_waited: 0, cpu: 8, mem_bytes: 16000000000
2025-09-15 20:24:54.787 wdl.w:ptcp.w:call-trgt-69.t:call-trgt_genotype INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:54.797 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:54 [ERROR] - No reads found for TRID=OPDM_ABCD3
2025-09-15 20:24:54.797 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:54 [ERROR] - No reads found for TRID=SCA37_DAB1
2025-09-15 20:24:54.797 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:54 [ERROR] - No reads found for TRID=SCA2_ATXN2
2025-09-15 20:24:54.797 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:54 [ERROR] - No reads found for TRID=OPDM4_RILPL1
2025-09-15 20:24:54.797 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:54 [ERROR] - No reads found for TRID=SCA27B_FGF14
2025-09-15 20:24:54.804 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_plot_meth_allele.slurm_singularity INFO srun: job 51797827 queued and waiting for resources
2025-09-15 20:24:54.804 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_plot_meth_allele.slurm_singularity INFO srun: job 51797827 has been allocated resources
2025-09-15 20:24:54.804 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_plot_meth_allele.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:54.843 wdl.w:ptcp.w:call-trgt-69.t:call-trgt_genotype INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 11, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-69/call-trgt_genotype/_singularity_tmpdir_adf24_ef"
2025-09-15 20:24:54.843 wdl.w:ptcp.w:call-trgt-69.t:call-trgt_genotype INFO Slurm invocation: srun --job-name call-trgt_genotype --partition compute,compute9 --cpus-per-task 8 --mem 15259M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-69/call-trgt_genotype/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-69/call-trgt_genotype/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-69/call-trgt_genotype/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-69/call-trgt_genotype/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-69/out/m84036_250809_035451_s4.bc2166.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2166.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-69/out/m84036_250809_035451_s4.bc2166.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2166.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-69/call-trgt_genotype/_singularity_tmpdir_adf24_ef/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-69/call-trgt_genotype/_singularity_tmpdir_adf24_ef/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:54.857 wdl.w:ptcp.w:call-trgt-69.t:call-trgt_genotype NOTICE slurm_singularity run :: pid: 1203485, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-69/call-trgt_genotype/slurm_singularity.log.txt"
2025-09-15 20:24:55.069 wdl.w:ptcp.w:call-paraphase-06.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for cyp21 for sample m84036_250809_035451_s4.bc2103 at 2025-09-15 20:24:31.481347...
2025-09-15 20:24:55.069 wdl.w:ptcp.w:call-paraphase-06.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for cyp21 for sample m84036_250809_035451_s4.bc2103 at 2025-09-15 20:24:32.693050...
2025-09-15 20:24:55.069 wdl.w:ptcp.w:call-paraphase-06.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for gba for sample m84036_250809_035451_s4.bc2103 at 2025-09-15 20:24:34.627819...
2025-09-15 20:24:55.069 wdl.w:ptcp.w:call-paraphase-06.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for gba for sample m84036_250809_035451_s4.bc2103 at 2025-09-15 20:24:35.310829...
2025-09-15 20:24:55.069 wdl.w:ptcp.w:call-paraphase-06.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for hbb for sample m84036_250809_035451_s4.bc2103 at 2025-09-15 20:24:51.279807...
2025-09-15 20:24:55.069 wdl.w:ptcp.w:call-paraphase-06.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for hbb for sample m84036_250809_035451_s4.bc2103 at 2025-09-15 20:24:51.279973...
2025-09-15 20:24:55.191 wdl.w:ptcp.w:call-trgt-48.t:call-trgt_plot_meth_waterfall INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2145.meth_waterfall.trgt_plots.zip"
2025-09-15 20:24:55.204 wdl.w:ptcp.w:call-paraphase-19.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for hbb for sample m84036_250809_035451_s4.bc2116 at 2025-09-15 20:24:40.757237...
2025-09-15 20:24:55.204 wdl.w:ptcp.w:call-paraphase-19.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for hbb for sample m84036_250809_035451_s4.bc2116 at 2025-09-15 20:24:46.339301...
2025-09-15 20:24:55.204 wdl.w:ptcp.w:call-paraphase-19.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for hbb for sample m84036_250809_035451_s4.bc2116 at 2025-09-15 20:24:46.661467...
2025-09-15 20:24:55.272 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:54 [ERROR] - No reads found for TRID=OPDM_ABCD3
2025-09-15 20:24:55.312 wdl.w:ptcp.w:call-trgt-48.t:call-trgt_plot_meth_waterfall NOTICE done
2025-09-15 20:24:55.317 wdl.w:ptcp.w:call-trgt-48 NOTICE finish :: job: "call-trgt_plot_meth_waterfall"
2025-09-15 20:24:55.317 wdl.w:ptcp.w:call-trgt-48 INFO output :: job: "call-trgt_plot_meth_waterfall", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-48/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2145.meth_waterfall.trgt_plots.zip"}
2025-09-15 20:24:55.317 wdl.w:ptcp.w:call-trgt-48 INFO visit :: node: "output-images_meth_waterfall", values: {"images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-48/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2145.meth_waterfall.trgt_plots.zip"}
2025-09-15 20:24:55.322 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_plot_motifs_allele NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-59/call-trgt_plot_motifs_allele", thread: 140607674631744
2025-09-15 20:24:55.327 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:55 [ERROR] - No reads found for TRID=OPDM_ABCD3
2025-09-15 20:24:55.336 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO srun: job 51797828 queued and waiting for resources
2025-09-15 20:24:55.336 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO srun: job 51797828 has been allocated resources
2025-09-15 20:24:55.336 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:55.343 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_plot_motifs_allele INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:55.343 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_plot_motifs_allele INFO input :: name: "waterfall", value: false
2025-09-15 20:24:55.343 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_plot_motifs_allele INFO input :: name: "methylation", value: false
2025-09-15 20:24:55.343 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_plot_motifs_allele INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:55.344 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_plot_motifs_allele INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:55.344 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_plot_motifs_allele INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:55.344 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_plot_motifs_allele INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2156.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:55.344 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_plot_motifs_allele INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2156.trgt.sorted.spanning.bam"
2025-09-15 20:24:55.344 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_plot_motifs_allele INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2156.trgt.vcf"
2025-09-15 20:24:55.344 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_plot_motifs_allele INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2156"
2025-09-15 20:24:55.344 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_plot_motifs_allele INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:55.344 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_plot_motifs_allele INFO eval :: name: "plot_type", value: "allele"
2025-09-15 20:24:55.344 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_plot_motifs_allele INFO eval :: name: "show", value: "motifs"
2025-09-15 20:24:55.344 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_plot_motifs_allele INFO eval :: name: "threads", value: 1
2025-09-15 20:24:55.345 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_plot_motifs_allele INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:55.345 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_plot_motifs_allele INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2156.motifs_allele"
2025-09-15 20:24:55.345 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_plot_motifs_allele INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:55.345 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_plot_motifs_allele WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:55.346 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_plot_motifs_allele INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:55.346 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_plot_motifs_allele INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:55.424 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_plot_motifs_allele INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-59/call-trgt_plot_motifs_allele/_singularity_tmpdir_5w6ray1k"
2025-09-15 20:24:55.424 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_plot_motifs_allele INFO Slurm invocation: srun --job-name call-trgt_plot_motifs_allele --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-59/call-trgt_plot_motifs_allele/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-59/call-trgt_plot_motifs_allele/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-59/call-trgt_plot_motifs_allele/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-59/call-trgt_plot_motifs_allele/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-59/call-trgt_genotype/out/m84036_250809_035451_s4.bc2156.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2156.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-59/call-trgt_genotype/out/m84036_250809_035451_s4.bc2156.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2156.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-59/call-trgt_genotype/out/m84036_250809_035451_s4.bc2156.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2156.trgt.sorted.spanning.bam:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-59/call-trgt_plot_motifs_allele/_singularity_tmpdir_5w6ray1k/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-59/call-trgt_plot_motifs_allele/_singularity_tmpdir_5w6ray1k/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:55.444 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_plot_motifs_allele NOTICE slurm_singularity run :: pid: 1203493, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-59/call-trgt_plot_motifs_allele/slurm_singularity.log.txt"
2025-09-15 20:24:55.527 wdl.w:ptcp.w:call-paraphase-69.t:call-run_paraphase INFO output :: name: "paraphase_bam", value: "m84036_250809_035451_s4.bc2166_paraphase/m84036_250809_035451_s4.bc2166.paraphase.bam"
2025-09-15 20:24:55.533 wdl.w:ptcp.w:call-paraphase-69.t:call-run_paraphase INFO output :: name: "paraphase_bam_bai", value: "m84036_250809_035451_s4.bc2166_paraphase/m84036_250809_035451_s4.bc2166.paraphase.bam.bai"
2025-09-15 20:24:55.535 wdl.w:ptcp.w:call-paraphase-69.t:call-run_paraphase INFO output :: name: "paraphase_json", value: "m84036_250809_035451_s4.bc2166_paraphase/m84036_250809_035451_s4.bc2166.paraphase.json"
2025-09-15 20:24:55.537 wdl.w:ptcp.w:call-paraphase-69.t:call-run_paraphase INFO output :: name: "paraphase_vcfs", value: []
2025-09-15 20:24:55.537 wdl.w:ptcp.w:call-paraphase-69.t:call-run_paraphase INFO output :: name: "havanno_json", value: "m84036_250809_035451_s4.bc2166.havanno.json"
2025-09-15 20:24:55.587 wdl.w:ptcp.w:call-sawfish-07.t:call-run_sawfish INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2104_sawfish/m84036_250809_035451_s4.bc2104.sv.vcf.gz"
2025-09-15 20:24:55.589 wdl.w:ptcp.w:call-trgt-41.t:call-trgt_plot_motifs_allele INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2138.motifs_allele.trgt_plots.zip"
2025-09-15 20:24:55.594 wdl.w:ptcp.w:call-sawfish-07.t:call-run_sawfish INFO output :: name: "vcf_tbi", value: "m84036_250809_035451_s4.bc2104_sawfish/m84036_250809_035451_s4.bc2104.sv.vcf.gz.tbi"
2025-09-15 20:24:55.595 wdl.w:ptcp.w:call-sawfish-07.t:call-run_sawfish INFO output :: name: "minimap2_bam", value: "m84036_250809_035451_s4.bc2104.minimap2.bam"
2025-09-15 20:24:55.597 wdl.w:ptcp.w:call-sawfish-07.t:call-run_sawfish INFO output :: name: "minimap2_bam_bai", value: "m84036_250809_035451_s4.bc2104.minimap2.bam.bai"
2025-09-15 20:24:55.610 wdl.w:ptcp.w:call-sawfish-46.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:50][sawfish][INFO] Starting sawfish 2.0.3
2025-09-15 20:24:55.611 wdl.w:ptcp.w:call-sawfish-46.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:50][sawfish][INFO] cmdline: sawfish discover --disable-cnv --threads 16 --ref /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa --bam m84036_250809_035451_s4.bc2143.minimap2.bam --output-dir m84036_250809_035451_s4.bc2143_sawfish_discover
2025-09-15 20:24:55.611 wdl.w:ptcp.w:call-sawfish-46.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:50][sawfish][INFO] Running on 16 threads
2025-09-15 20:24:55.611 wdl.w:ptcp.w:call-sawfish-46.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:50][sawfish][INFO] Writing discover settings to file: 'm84036_250809_035451_s4.bc2143_sawfish_discover/discover.settings.json'
2025-09-15 20:24:55.611 wdl.w:ptcp.w:call-sawfish-46.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:50][sawfish][INFO] Reading reference genome from file '/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa'
2025-09-15 20:24:55.611 wdl.w:ptcp.w:call-sawfish-46.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:53][sawfish][INFO] Processing alignment file '/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2143.minimap2.bam'
2025-09-15 20:24:55.611 wdl.w:ptcp.w:call-sawfish-46.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:53][sawfish][INFO] Finished processing all alignments
2025-09-15 20:24:55.611 wdl.w:ptcp.w:call-sawfish-46.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:53][sawfish][INFO] Writing depth bins to binary file: 'm84036_250809_035451_s4.bc2143_sawfish_discover/depth.mpack'
2025-09-15 20:24:55.611 wdl.w:ptcp.w:call-sawfish-46.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:53][sawfish][INFO] Writing max sv depth genome regions to bed file: 'm84036_250809_035451_s4.bc2143_sawfish_discover/max.depth.bed'
2025-09-15 20:24:55.611 wdl.w:ptcp.w:call-sawfish-46.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:53][sawfish][INFO] Completing breakpoint observation clustering
2025-09-15 20:24:55.611 wdl.w:ptcp.w:call-sawfish-46.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:53][sawfish][INFO] Finished breakpoint observation clustering
2025-09-15 20:24:55.611 wdl.w:ptcp.w:call-sawfish-46.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:53][sawfish][INFO] Consolidating adjacent indel candidates
2025-09-15 20:24:55.611 wdl.w:ptcp.w:call-sawfish-46.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:53][sawfish][INFO] Finding large insertion candidates
2025-09-15 20:24:55.611 wdl.w:ptcp.w:call-sawfish-46.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:53][sawfish][INFO] Writing breakpoint_cluster debug bed file: 'm84036_250809_035451_s4.bc2143_sawfish_discover/debug.breakpoint_clusters.bed'
2025-09-15 20:24:55.612 wdl.w:ptcp.w:call-sawfish-46.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:53][sawfish][INFO] Refining SV Candidates
2025-09-15 20:24:55.612 wdl.w:ptcp.w:call-sawfish-46.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:53][sawfish][INFO] Writing debug assembly region bed file: 'm84036_250809_035451_s4.bc2143_sawfish_discover/assembly.regions.bed'
2025-09-15 20:24:55.612 wdl.w:ptcp.w:call-sawfish-46.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:53][sawfish][INFO] Starting refinement of breakpoint evidence clusters
2025-09-15 20:24:55.612 wdl.w:ptcp.w:call-sawfish-46.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:53][sawfish][INFO] Finished refining all breakpoint evidence clusters
2025-09-15 20:24:55.612 wdl.w:ptcp.w:call-sawfish-46.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:53][sawfish][INFO] Writing all contig alignments to bam file: 'm84036_250809_035451_s4.bc2143_sawfish_discover/contig.alignment.bam'
2025-09-15 20:24:55.612 wdl.w:ptcp.w:call-sawfish-46.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:53][sawfish][INFO] Writing candidate structural variants to file: 'm84036_250809_035451_s4.bc2143_sawfish_discover/candidate.sv.bcf'
2025-09-15 20:24:55.613 wdl.w:ptcp.w:call-sawfish-46.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:53][sawfish][INFO] Writing run statistics to file: 'm84036_250809_035451_s4.bc2143_sawfish_discover/run.stats.json'
2025-09-15 20:24:55.613 wdl.w:ptcp.w:call-sawfish-46.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:53][sawfish][INFO] sawfish completed. Total Runtime: 00:00:03.627
2025-09-15 20:24:55.662 wdl.w:ptcp.w:call-paraphase-69.t:call-run_paraphase NOTICE done
2025-09-15 20:24:55.669 wdl.w:ptcp.w:call-paraphase-69 NOTICE finish :: job: "call-run_paraphase"
2025-09-15 20:24:55.669 wdl.w:ptcp.w:call-paraphase-69 INFO output :: job: "call-run_paraphase", values: {"havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-69/call-run_paraphase/out/m84036_250809_035451_s4.bc2166.havanno.json", "paraphase_vcfs": [], "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-69/call-run_paraphase/out/m84036_250809_035451_s4.bc2166_paraphase/m84036_250809_035451_s4.bc2166.paraphase.json", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-69/call-run_paraphase/out/m84036_250809_035451_s4.bc2166_paraphase/m84036_250809_035451_s4.bc2166.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-69/call-run_paraphase/out/m84036_250809_035451_s4.bc2166_paraphase/m84036_250809_035451_s4.bc2166.paraphase.bam"}
2025-09-15 20:24:55.670 wdl.w:ptcp.w:call-paraphase-69 NOTICE ready :: job: "call-call_f8", callee: "call_f8"
2025-09-15 20:24:55.670 wdl.w:ptcp.w:call-paraphase-69 INFO input :: job: "call-call_f8", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "out_prefix": "m84036_250809_035451_s4.bc2166", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-69/call-run_paraphase/out/m84036_250809_035451_s4.bc2166_paraphase/m84036_250809_035451_s4.bc2166.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-69/call-run_paraphase/out/m84036_250809_035451_s4.bc2166_paraphase/m84036_250809_035451_s4.bc2166.paraphase.bam", "sex": "F"}
2025-09-15 20:24:55.671 wdl.w:ptcp.w:call-paraphase-69 INFO visit :: node: "output-havanno_json", values: {"havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-69/call-run_paraphase/out/m84036_250809_035451_s4.bc2166.havanno.json"}
2025-09-15 20:24:55.671 wdl.w:ptcp.w:call-paraphase-69 INFO visit :: node: "output-paraphase_bam", values: {"paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-69/call-run_paraphase/out/m84036_250809_035451_s4.bc2166_paraphase/m84036_250809_035451_s4.bc2166.paraphase.bam"}
2025-09-15 20:24:55.671 wdl.w:ptcp.w:call-paraphase-69 INFO visit :: node: "output-paraphase_bam_bai", values: {"paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-69/call-run_paraphase/out/m84036_250809_035451_s4.bc2166_paraphase/m84036_250809_035451_s4.bc2166.paraphase.bam.bai"}
2025-09-15 20:24:55.671 wdl.w:ptcp.w:call-paraphase-69 INFO visit :: node: "output-paraphase_json", values: {"paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-69/call-run_paraphase/out/m84036_250809_035451_s4.bc2166_paraphase/m84036_250809_035451_s4.bc2166.paraphase.json"}
2025-09-15 20:24:55.671 wdl.w:ptcp.w:call-paraphase-69 INFO visit :: node: "output-paraphase_vcfs", values: {"paraphase_vcfs": []}
2025-09-15 20:24:55.675 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_plot_motifs_waterfall NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-59/call-trgt_plot_motifs_waterfall", thread: 140613571819072
2025-09-15 20:24:55.694 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_plot_motifs_waterfall INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:55.694 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_plot_motifs_waterfall INFO input :: name: "waterfall", value: true
2025-09-15 20:24:55.694 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_plot_motifs_waterfall INFO input :: name: "methylation", value: false
2025-09-15 20:24:55.694 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_plot_motifs_waterfall INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:55.694 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_plot_motifs_waterfall INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:55.694 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_plot_motifs_waterfall INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:55.694 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_plot_motifs_waterfall INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2156.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:55.694 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_plot_motifs_waterfall INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2156.trgt.sorted.spanning.bam"
2025-09-15 20:24:55.695 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_plot_motifs_waterfall INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2156.trgt.vcf"
2025-09-15 20:24:55.695 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_plot_motifs_waterfall INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2156"
2025-09-15 20:24:55.695 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:55.695 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "plot_type", value: "waterfall"
2025-09-15 20:24:55.695 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "show", value: "motifs"
2025-09-15 20:24:55.695 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "threads", value: 1
2025-09-15 20:24:55.696 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:55.696 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2156.motifs_waterfall"
2025-09-15 20:24:55.696 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_plot_motifs_waterfall INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:55.697 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_plot_motifs_waterfall WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:55.697 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_plot_motifs_waterfall INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:55.697 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_plot_motifs_waterfall INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:55.732 wdl.w:ptcp.w:call-trgt-41.t:call-trgt_plot_motifs_allele NOTICE done
2025-09-15 20:24:55.738 wdl.w:ptcp.w:call-trgt-41 NOTICE finish :: job: "call-trgt_plot_motifs_allele"
2025-09-15 20:24:55.738 wdl.w:ptcp.w:call-trgt-41 INFO output :: job: "call-trgt_plot_motifs_allele", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-41/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2138.motifs_allele.trgt_plots.zip"}
2025-09-15 20:24:55.739 wdl.w:ptcp.w:call-trgt-41 INFO visit :: node: "output-images_motifs_allele", values: {"images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-41/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2138.motifs_allele.trgt_plots.zip"}
2025-09-15 20:24:55.750 wdl.w:ptcp.w:call-paraphase-60.t:call-run_paraphase NOTICE task setup :: name: "run_paraphase", source: "./paraphase.wdl", line: 127, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-60/call-run_paraphase", thread: 140608211502656
2025-09-15 20:24:55.753 wdl.w:ptcp.w:call-sawfish-07.t:call-run_sawfish NOTICE done
2025-09-15 20:24:55.760 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:53 [ERROR] - No reads found for TRID=SCA3_ATXN3
2025-09-15 20:24:55.760 wdl.w:ptcp.w:call-sawfish-07 NOTICE finish :: job: "call-run_sawfish"
2025-09-15 20:24:55.760 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:53 [ERROR] - No reads found for TRID=SCA31_BEAN1
2025-09-15 20:24:55.761 wdl.w:ptcp.w:call-sawfish-07 INFO output :: job: "call-run_sawfish", values: {"minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-07/call-run_sawfish/out/m84036_250809_035451_s4.bc2104.minimap2.bam.bai", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-07/call-run_sawfish/out/m84036_250809_035451_s4.bc2104.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-07/call-run_sawfish/out/m84036_250809_035451_s4.bc2104_sawfish/m84036_250809_035451_s4.bc2104.sv.vcf.gz.tbi", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-07/call-run_sawfish/out/m84036_250809_035451_s4.bc2104_sawfish/m84036_250809_035451_s4.bc2104.sv.vcf.gz"}
2025-09-15 20:24:55.761 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:53 [ERROR] - No reads found for TRID=SCA4_ZFHX3
2025-09-15 20:24:55.761 wdl.w:ptcp.w:call-sawfish-07 INFO visit :: node: "output-minimap2_bam", values: {"minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-07/call-run_sawfish/out/m84036_250809_035451_s4.bc2104.minimap2.bam"}
2025-09-15 20:24:55.761 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:53 [ERROR] - No reads found for TRID=HDL2_JPH3
2025-09-15 20:24:55.761 wdl.w:ptcp.w:call-sawfish-07 INFO visit :: node: "output-minimap2_bam_bai", values: {"minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-07/call-run_sawfish/out/m84036_250809_035451_s4.bc2104.minimap2.bam.bai"}
2025-09-15 20:24:55.762 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:53 [ERROR] - No reads found for TRID=SCA6_CACNA1A
2025-09-15 20:24:55.762 wdl.w:ptcp.w:call-sawfish-07 INFO visit :: node: "output-vcf", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-07/call-run_sawfish/out/m84036_250809_035451_s4.bc2104_sawfish/m84036_250809_035451_s4.bc2104.sv.vcf.gz"}
2025-09-15 20:24:55.762 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:53 [ERROR] - No reads found for TRID=FECD3_TCF4
2025-09-15 20:24:55.762 wdl.w:ptcp.w:call-sawfish-07 INFO visit :: node: "output-vcf_tbi", values: {"vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-07/call-run_sawfish/out/m84036_250809_035451_s4.bc2104_sawfish/m84036_250809_035451_s4.bc2104.sv.vcf.gz.tbi"}
2025-09-15 20:24:55.762 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:54 [ERROR] - No reads found for TRID=OPDM2_GIPC1
2025-09-15 20:24:55.762 wdl.w:ptcp.w:call-sawfish-07 INFO visit :: node: "outputs", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-07/call-run_sawfish/out/m84036_250809_035451_s4.bc2104_sawfish/m84036_250809_035451_s4.bc2104.sv.vcf.gz", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-07/call-run_sawfish/out/m84036_250809_035451_s4.bc2104.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-07/call-run_sawfish/out/m84036_250809_035451_s4.bc2104_sawfish/m84036_250809_035451_s4.bc2104.sv.vcf.gz.tbi", "minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-07/call-run_sawfish/out/m84036_250809_035451_s4.bc2104.minimap2.bam.bai"}
2025-09-15 20:24:55.763 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:54 [ERROR] - No reads found for TRID=DM1_DMPK
2025-09-15 20:24:55.763 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:54 [ERROR] - No reads found for TRID=FRA2A_AFF3
2025-09-15 20:24:55.763 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:54 [ERROR] - No reads found for TRID=SD5_HOXD13
2025-09-15 20:24:55.763 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:54 [ERROR] - No reads found for TRID=SCA36_NOP56
2025-09-15 20:24:55.763 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:54 [ERROR] - No reads found for TRID=CJD_PRNP
2025-09-15 20:24:55.763 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:54 [ERROR] - No reads found for TRID=EPM1_CSTB
2025-09-15 20:24:55.764 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:54 [ERROR] - No reads found for TRID=SCA10_ATXN10
2025-09-15 20:24:55.764 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:54 [ERROR] - No reads found for TRID=SCA7_ATXN7
2025-09-15 20:24:55.764 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:54 [ERROR] - No reads found for TRID=DM2_CNBP
2025-09-15 20:24:55.764 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:54 [ERROR] - No reads found for TRID=HD_HTT
2025-09-15 20:24:55.764 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:54 [ERROR] - No reads found for TRID=CCHS_PHOX2B
2025-09-15 20:24:55.764 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:54 [ERROR] - No reads found for TRID=SCA12_PPP2R2B
2025-09-15 20:24:55.764 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:54 [ERROR] - No reads found for TRID=SCA1_ATXN1
2025-09-15 20:24:55.769 wdl.w:ptcp.w:call-trgt-49.t:call-trgt_plot_meth_allele NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-49/call-trgt_plot_meth_allele", thread: 140613060126272
2025-09-15 20:24:55.772 wdl.w:ptcp.w:call-trgt-64.t:call-get_reads_overlapping_repeats INFO output :: name: "reads_overlapping_repeats", value: "m84036_250809_035451_s4.bc2161.repeats.bam"
2025-09-15 20:24:55.777 wdl.w:ptcp.w:call-trgt-64.t:call-get_reads_overlapping_repeats INFO output :: name: "reads_overlapping_repeats_bai", value: "m84036_250809_035451_s4.bc2161.repeats.bam.bai"
2025-09-15 20:24:55.779 wdl.w:ptcp.w:call-paraphase-60.t:call-run_paraphase INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:55.779 wdl.w:ptcp.w:call-paraphase-60.t:call-run_paraphase INFO input :: name: "annotation_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf"
2025-09-15 20:24:55.779 wdl.w:ptcp.w:call-paraphase-60.t:call-run_paraphase INFO input :: name: "genome_version", value: "38"
2025-09-15 20:24:55.779 wdl.w:ptcp.w:call-paraphase-60.t:call-run_paraphase INFO input :: name: "config_file", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/paraphase_config.GRCh38.yaml"
2025-09-15 20:24:55.779 wdl.w:ptcp.w:call-paraphase-60.t:call-run_paraphase INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:55.779 wdl.w:ptcp.w:call-paraphase-60.t:call-run_paraphase INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:55.779 wdl.w:ptcp.w:call-paraphase-60.t:call-run_paraphase INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2157.mapped.bam.bai"
2025-09-15 20:24:55.780 wdl.w:ptcp.w:call-paraphase-60.t:call-run_paraphase INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2157.mapped.bam"
2025-09-15 20:24:55.780 wdl.w:ptcp.w:call-paraphase-60.t:call-run_paraphase INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2157"
2025-09-15 20:24:55.780 wdl.w:ptcp.w:call-paraphase-60.t:call-run_paraphase INFO eval :: name: "threads", value: 4
2025-09-15 20:24:55.780 wdl.w:ptcp.w:call-paraphase-60.t:call-run_paraphase INFO eval :: name: "mem_gb", value: 8
2025-09-15 20:24:55.780 wdl.w:ptcp.w:call-paraphase-60.t:call-run_paraphase INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:55.780 wdl.w:ptcp.w:call-paraphase-60.t:call-run_paraphase INFO eval :: name: "out_dir", value: "m84036_250809_035451_s4.bc2157_paraphase"
2025-09-15 20:24:55.781 wdl.w:ptcp.w:call-paraphase-60.t:call-run_paraphase INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 4, memory_reservation: 8000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:55.781 wdl.w:ptcp.w:call-paraphase-60.t:call-run_paraphase WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:55.781 wdl.w:ptcp.w:call-paraphase-60.t:call-run_paraphase INFO provisioned :: seconds_waited: 0, cpu: 4, mem_bytes: 8000000000
2025-09-15 20:24:55.781 wdl.w:ptcp.w:call-paraphase-60.t:call-run_paraphase INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:55.789 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_plot_motifs_waterfall INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-59/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_8yagm_3r"
2025-09-15 20:24:55.789 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_plot_motifs_waterfall INFO Slurm invocation: srun --job-name call-trgt_plot_motifs_waterfall --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-59/call-trgt_plot_motifs_waterfall/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-59/call-trgt_plot_motifs_waterfall/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-59/call-trgt_plot_motifs_waterfall/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-59/call-trgt_plot_motifs_waterfall/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-59/call-trgt_genotype/out/m84036_250809_035451_s4.bc2156.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2156.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-59/call-trgt_genotype/out/m84036_250809_035451_s4.bc2156.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2156.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-59/call-trgt_genotype/out/m84036_250809_035451_s4.bc2156.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2156.trgt.sorted.spanning.bam:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-59/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_8yagm_3r/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-59/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_8yagm_3r/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:55.794 wdl.w:ptcp.w:call-trgt-49.t:call-trgt_plot_meth_allele INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:55.794 wdl.w:ptcp.w:call-trgt-49.t:call-trgt_plot_meth_allele INFO input :: name: "waterfall", value: false
2025-09-15 20:24:55.794 wdl.w:ptcp.w:call-trgt-49.t:call-trgt_plot_meth_allele INFO input :: name: "methylation", value: true
2025-09-15 20:24:55.795 wdl.w:ptcp.w:call-trgt-49.t:call-trgt_plot_meth_allele INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:55.795 wdl.w:ptcp.w:call-trgt-49.t:call-trgt_plot_meth_allele INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:55.795 wdl.w:ptcp.w:call-trgt-49.t:call-trgt_plot_meth_allele INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:55.795 wdl.w:ptcp.w:call-trgt-49.t:call-trgt_plot_meth_allele INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2146.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:55.795 wdl.w:ptcp.w:call-trgt-49.t:call-trgt_plot_meth_allele INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2146.trgt.sorted.spanning.bam"
2025-09-15 20:24:55.795 wdl.w:ptcp.w:call-trgt-49.t:call-trgt_plot_meth_allele INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2146.trgt.vcf"
2025-09-15 20:24:55.795 wdl.w:ptcp.w:call-trgt-49.t:call-trgt_plot_meth_allele INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2146"
2025-09-15 20:24:55.796 wdl.w:ptcp.w:call-trgt-49.t:call-trgt_plot_meth_allele INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:55.796 wdl.w:ptcp.w:call-trgt-49.t:call-trgt_plot_meth_allele INFO eval :: name: "plot_type", value: "allele"
2025-09-15 20:24:55.796 wdl.w:ptcp.w:call-trgt-49.t:call-trgt_plot_meth_allele INFO eval :: name: "show", value: "meth"
2025-09-15 20:24:55.796 wdl.w:ptcp.w:call-trgt-49.t:call-trgt_plot_meth_allele INFO eval :: name: "threads", value: 1
2025-09-15 20:24:55.796 wdl.w:ptcp.w:call-trgt-49.t:call-trgt_plot_meth_allele INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:55.797 wdl.w:ptcp.w:call-trgt-49.t:call-trgt_plot_meth_allele INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2146.meth_allele"
2025-09-15 20:24:55.797 wdl.w:ptcp.w:call-trgt-49.t:call-trgt_plot_meth_allele INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:55.797 wdl.w:ptcp.w:call-trgt-49.t:call-trgt_plot_meth_allele WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:55.797 wdl.w:ptcp.w:call-trgt-49.t:call-trgt_plot_meth_allele INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:55.798 wdl.w:ptcp.w:call-trgt-49.t:call-trgt_plot_meth_allele INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:55.827 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_plot_motifs_waterfall NOTICE slurm_singularity run :: pid: 1203504, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-59/call-trgt_plot_motifs_waterfall/slurm_singularity.log.txt"
2025-09-15 20:24:55.827 wdl.w:ptcp.w:call-sawfish-07 NOTICE done
2025-09-15 20:24:55.834 wdl.w:ptcp NOTICE finish :: job: "call-sawfish-07"
2025-09-15 20:24:55.834 wdl.w:ptcp INFO output :: job: "call-sawfish-07", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-07/out/m84036_250809_035451_s4.bc2104_sawfish/m84036_250809_035451_s4.bc2104.sv.vcf.gz", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-07/out/m84036_250809_035451_s4.bc2104.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-07/out/m84036_250809_035451_s4.bc2104_sawfish/m84036_250809_035451_s4.bc2104.sv.vcf.gz.tbi", "minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-07/out/m84036_250809_035451_s4.bc2104.minimap2.bam.bai"}
2025-09-15 20:24:55.843 wdl.w:ptcp.w:call-sawfish-74 NOTICE workflow start :: name: "sawfish", source: "./sawfish.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-74"
2025-09-15 20:24:55.860 wdl.w:ptcp.w:call-sawfish-74 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:24:55.860 wdl.w:ptcp.w:call-sawfish-74 INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:24:55.860 wdl.w:ptcp.w:call-sawfish-74 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-74/out/m84036_250809_035451_s4.bc2171.mapped.bam"}
2025-09-15 20:24:55.861 wdl.w:ptcp.w:call-sawfish-74 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-74/out/m84036_250809_035451_s4.bc2171.mapped.bam.bai"}
2025-09-15 20:24:55.861 wdl.w:ptcp.w:call-sawfish-74 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:24:55.861 wdl.w:ptcp.w:call-sawfish-74 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:24:55.861 wdl.w:ptcp.w:call-sawfish-74 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2171"}
2025-09-15 20:24:55.861 wdl.w:ptcp.w:call-sawfish-74 NOTICE ready :: job: "call-run_sawfish", callee: "run_sawfish"
2025-09-15 20:24:55.861 wdl.w:ptcp.w:call-sawfish-74 INFO input :: job: "call-run_sawfish", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-74/out/m84036_250809_035451_s4.bc2171.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-74/out/m84036_250809_035451_s4.bc2171.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2171"}
2025-09-15 20:24:55.861 wdl.w:ptcp.w:call-trgt-64.t:call-get_reads_overlapping_repeats NOTICE done
2025-09-15 20:24:55.864 wdl.w:ptcp.w:call-paraphase-60.t:call-run_paraphase INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-60/call-run_paraphase/_singularity_tmpdir_b9_b6ebj"
2025-09-15 20:24:55.864 wdl.w:ptcp.w:call-paraphase-60.t:call-run_paraphase INFO Slurm invocation: srun --job-name call-run_paraphase --partition compute,compute9 --cpus-per-task 4 --mem 7629M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-60/call-run_paraphase/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-60/call-run_paraphase/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-60/call-run_paraphase/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-60/call-run_paraphase/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-60/out/m84036_250809_035451_s4.bc2157.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2157.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-60/out/m84036_250809_035451_s4.bc2157.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2157.mapped.bam:ro --bind /ptcp/meta/variant_list/variant_list.GRCh38.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf:ro --bind /ptcp/meta/paraphase/paraphase_config.GRCh38.yaml:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/paraphase_config.GRCh38.yaml:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-60/call-run_paraphase/_singularity_tmpdir_b9_b6ebj/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-60/call-run_paraphase/_singularity_tmpdir_b9_b6ebj/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:55.866 wdl.w:ptcp.w:call-trgt-64 NOTICE finish :: job: "call-get_reads_overlapping_repeats"
2025-09-15 20:24:55.867 wdl.w:ptcp.w:call-trgt-64 INFO output :: job: "call-get_reads_overlapping_repeats", values: {"reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-64/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2161.repeats.bam.bai", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-64/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2161.repeats.bam"}
2025-09-15 20:24:55.867 wdl.w:ptcp.w:call-trgt-64 INFO visit :: node: "output-reads_overlapping_repeats", values: {"reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-64/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2161.repeats.bam"}
2025-09-15 20:24:55.867 wdl.w:ptcp.w:call-trgt-64 INFO visit :: node: "output-reads_overlapping_repeats_bai", values: {"reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-64/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2161.repeats.bam.bai"}
2025-09-15 20:24:55.869 wdl.w:ptcp.w:call-trgt-69.t:call-trgt_genotype.slurm_singularity INFO srun: job 51797829 queued and waiting for resources
2025-09-15 20:24:55.869 wdl.w:ptcp.w:call-trgt-69.t:call-trgt_genotype.slurm_singularity INFO srun: job 51797829 has been allocated resources
2025-09-15 20:24:55.869 wdl.w:ptcp.w:call-trgt-69.t:call-trgt_genotype.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:55.874 wdl.w:ptcp.w:call-trgt-49.t:call-trgt_plot_meth_waterfall NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-49/call-trgt_plot_meth_waterfall", thread: 140609838900800
2025-09-15 20:24:55.884 wdl.w:ptcp.w:call-trgt-49.t:call-trgt_plot_meth_allele INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-49/call-trgt_plot_meth_allele/_singularity_tmpdir_zi8pxth7"
2025-09-15 20:24:55.884 wdl.w:ptcp.w:call-trgt-49.t:call-trgt_plot_meth_allele INFO Slurm invocation: srun --job-name call-trgt_plot_meth_allele --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-49/call-trgt_plot_meth_allele/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-49/call-trgt_plot_meth_allele/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-49/call-trgt_plot_meth_allele/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-49/call-trgt_plot_meth_allele/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-49/call-trgt_genotype/out/m84036_250809_035451_s4.bc2146.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2146.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-49/call-trgt_genotype/out/m84036_250809_035451_s4.bc2146.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2146.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-49/call-trgt_genotype/out/m84036_250809_035451_s4.bc2146.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2146.trgt.sorted.spanning.bam:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-49/call-trgt_plot_meth_allele/_singularity_tmpdir_zi8pxth7/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-49/call-trgt_plot_meth_allele/_singularity_tmpdir_zi8pxth7/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:55.884 wdl.w:ptcp.w:call-paraphase-60.t:call-run_paraphase NOTICE slurm_singularity run :: pid: 1203507, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-60/call-run_paraphase/slurm_singularity.log.txt"
2025-09-15 20:24:55.891 wdl.w:ptcp.w:call-trgt-49.t:call-trgt_plot_meth_waterfall INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:55.891 wdl.w:ptcp.w:call-trgt-49.t:call-trgt_plot_meth_waterfall INFO input :: name: "waterfall", value: true
2025-09-15 20:24:55.891 wdl.w:ptcp.w:call-trgt-49.t:call-trgt_plot_meth_waterfall INFO input :: name: "methylation", value: true
2025-09-15 20:24:55.891 wdl.w:ptcp.w:call-trgt-49.t:call-trgt_plot_meth_waterfall INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:55.891 wdl.w:ptcp.w:call-trgt-49.t:call-trgt_plot_meth_waterfall INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:55.891 wdl.w:ptcp.w:call-trgt-49.t:call-trgt_plot_meth_waterfall INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:55.891 wdl.w:ptcp.w:call-trgt-49.t:call-trgt_plot_meth_waterfall INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2146.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:55.891 wdl.w:ptcp.w:call-trgt-49.t:call-trgt_plot_meth_waterfall INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2146.trgt.sorted.spanning.bam"
2025-09-15 20:24:55.891 wdl.w:ptcp.w:call-trgt-49.t:call-trgt_plot_meth_waterfall INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2146.trgt.vcf"
2025-09-15 20:24:55.891 wdl.w:ptcp.w:call-trgt-49.t:call-trgt_plot_meth_waterfall INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2146"
2025-09-15 20:24:55.891 wdl.w:ptcp.w:call-trgt-49.t:call-trgt_plot_meth_waterfall INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:55.892 wdl.w:ptcp.w:call-trgt-49.t:call-trgt_plot_meth_waterfall INFO eval :: name: "plot_type", value: "waterfall"
2025-09-15 20:24:55.892 wdl.w:ptcp.w:call-trgt-49.t:call-trgt_plot_meth_waterfall INFO eval :: name: "show", value: "meth"
2025-09-15 20:24:55.892 wdl.w:ptcp.w:call-trgt-49.t:call-trgt_plot_meth_waterfall INFO eval :: name: "threads", value: 1
2025-09-15 20:24:55.892 wdl.w:ptcp.w:call-trgt-49.t:call-trgt_plot_meth_allele NOTICE slurm_singularity run :: pid: 1203513, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-49/call-trgt_plot_meth_allele/slurm_singularity.log.txt"
2025-09-15 20:24:55.892 wdl.w:ptcp.w:call-trgt-49.t:call-trgt_plot_meth_waterfall INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:55.892 wdl.w:ptcp.w:call-trgt-49.t:call-trgt_plot_meth_waterfall INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2146.meth_waterfall"
2025-09-15 20:24:55.893 wdl.w:ptcp.w:call-trgt-49.t:call-trgt_plot_meth_waterfall INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:55.893 wdl.w:ptcp.w:call-trgt-49.t:call-trgt_plot_meth_waterfall WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:55.893 wdl.w:ptcp.w:call-trgt-49.t:call-trgt_plot_meth_waterfall INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:55.893 wdl.w:ptcp.w:call-trgt-49.t:call-trgt_plot_meth_waterfall INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:55.904 wdl.w:ptcp.w:call-paraphase-67.t:call-run_paraphase.stderr VERBOSE INFO:root:Processing sample m84036_250809_035451_s4.bc2164 at 2025-09-15 20:24:51.781740...
2025-09-15 20:24:55.904 wdl.w:ptcp.w:call-paraphase-67.t:call-run_paraphase.stderr VERBOSE INFO:root:Checking sample sex at 2025-09-15 20:24:51.782499...
2025-09-15 20:24:55.905 wdl.w:ptcp.w:call-paraphase-67.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for cyp21 for sample m84036_250809_035451_s4.bc2164 at 2025-09-15 20:24:51.821429...
2025-09-15 20:24:55.905 wdl.w:ptcp.w:call-paraphase-67.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for cyp21 for sample m84036_250809_035451_s4.bc2164 at 2025-09-15 20:24:51.821824...
2025-09-15 20:24:55.905 wdl.w:ptcp.w:call-paraphase-67.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for smn1 for sample m84036_250809_035451_s4.bc2164 at 2025-09-15 20:24:51.822735...
2025-09-15 20:24:55.905 wdl.w:ptcp.w:call-paraphase-67.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for smn1 for sample m84036_250809_035451_s4.bc2164 at 2025-09-15 20:24:51.823091...
2025-09-15 20:24:55.905 wdl.w:ptcp.w:call-paraphase-67.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for gba for sample m84036_250809_035451_s4.bc2164 at 2025-09-15 20:24:51.822826...
2025-09-15 20:24:55.905 wdl.w:ptcp.w:call-paraphase-67.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for gba for sample m84036_250809_035451_s4.bc2164 at 2025-09-15 20:24:51.823189...
2025-09-15 20:24:55.905 wdl.w:ptcp.w:call-paraphase-67.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for hba for sample m84036_250809_035451_s4.bc2164 at 2025-09-15 20:24:51.823837...
2025-09-15 20:24:55.905 wdl.w:ptcp.w:call-paraphase-67.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for hba for sample m84036_250809_035451_s4.bc2164 at 2025-09-15 20:24:51.824191...
2025-09-15 20:24:55.949 wdl.w:ptcp.w:call-trgt-40.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:55 [ERROR] - No reads found for TRID=PRTS_ARX
2025-09-15 20:24:55.949 wdl.w:ptcp.w:call-trgt-40.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:55 [ERROR] - No reads found for TRID=EIEE1_ARX
2025-09-15 20:24:55.950 wdl.w:ptcp.w:call-sawfish-45.t:call-run_sawfish INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2142_sawfish/m84036_250809_035451_s4.bc2142.sv.vcf.gz"
2025-09-15 20:24:55.955 wdl.w:ptcp.w:call-sawfish-45.t:call-run_sawfish INFO output :: name: "vcf_tbi", value: "m84036_250809_035451_s4.bc2142_sawfish/m84036_250809_035451_s4.bc2142.sv.vcf.gz.tbi"
2025-09-15 20:24:55.956 wdl.w:ptcp.w:call-sawfish-45.t:call-run_sawfish INFO output :: name: "minimap2_bam", value: "m84036_250809_035451_s4.bc2142.minimap2.bam"
2025-09-15 20:24:55.957 wdl.w:ptcp.w:call-sawfish-45.t:call-run_sawfish INFO output :: name: "minimap2_bam_bai", value: "m84036_250809_035451_s4.bc2142.minimap2.bam.bai"
2025-09-15 20:24:55.968 wdl.w:ptcp.w:call-trgt-49.t:call-trgt_plot_meth_waterfall INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-49/call-trgt_plot_meth_waterfall/_singularity_tmpdir_k3iz0_hi"
2025-09-15 20:24:55.968 wdl.w:ptcp.w:call-trgt-49.t:call-trgt_plot_meth_waterfall INFO Slurm invocation: srun --job-name call-trgt_plot_meth_waterfall --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-49/call-trgt_plot_meth_waterfall/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-49/call-trgt_plot_meth_waterfall/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-49/call-trgt_plot_meth_waterfall/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-49/call-trgt_plot_meth_waterfall/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-49/call-trgt_genotype/out/m84036_250809_035451_s4.bc2146.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2146.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-49/call-trgt_genotype/out/m84036_250809_035451_s4.bc2146.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2146.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-49/call-trgt_genotype/out/m84036_250809_035451_s4.bc2146.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2146.trgt.sorted.spanning.bam:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-49/call-trgt_plot_meth_waterfall/_singularity_tmpdir_k3iz0_hi/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-49/call-trgt_plot_meth_waterfall/_singularity_tmpdir_k3iz0_hi/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:55.991 wdl.w:ptcp.w:call-trgt-49.t:call-trgt_plot_meth_waterfall NOTICE slurm_singularity run :: pid: 1203516, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-49/call-trgt_plot_meth_waterfall/slurm_singularity.log.txt"
2025-09-15 20:24:55.995 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:54 [ERROR] - No reads found for TRID=SCA17_TBP
2025-09-15 20:24:55.996 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:54 [ERROR] - No reads found for TRID=OPDM1_LRP12
2025-09-15 20:24:55.996 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:54 [ERROR] - No reads found for TRID=FAME1_SAMD12
2025-09-15 20:24:55.996 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:54 [ERROR] - No reads found for TRID=FTDALS1_C9orf72
2025-09-15 20:24:56.010 wdl.w:ptcp.w:call-paraphase-54.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for hba for sample m84036_250809_035451_s4.bc2151 at 2025-09-15 20:24:44.131588...
2025-09-15 20:24:56.010 wdl.w:ptcp.w:call-paraphase-54.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for smn1 for sample m84036_250809_035451_s4.bc2151 at 2025-09-15 20:24:44.199480...
2025-09-15 20:24:56.010 wdl.w:ptcp.w:call-paraphase-54.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for gba for sample m84036_250809_035451_s4.bc2151 at 2025-09-15 20:24:44.469260...
2025-09-15 20:24:56.011 wdl.w:ptcp.w:call-paraphase-54.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for cyp21 for sample m84036_250809_035451_s4.bc2151 at 2025-09-15 20:24:44.861163...
2025-09-15 20:24:56.011 wdl.w:ptcp.w:call-paraphase-54.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for smn1 for sample m84036_250809_035451_s4.bc2151 at 2025-09-15 20:24:52.854309...
2025-09-15 20:24:56.011 wdl.w:ptcp.w:call-paraphase-54.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning to gene2 region for smn1 for sample m84036_250809_035451_s4.bc2151 at 2025-09-15 20:24:53.439018...
2025-09-15 20:24:56.030 wdl.w:ptcp.w:call-trgt-40.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:54 [ERROR] - No reads found for TRID=PRTS_ARX
2025-09-15 20:24:56.030 wdl.w:ptcp.w:call-trgt-40.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:54 [ERROR] - No reads found for TRID=EIEE1_ARX
2025-09-15 20:24:56.050 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_meth_allele INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2151.meth_allele.trgt_plots.zip"
2025-09-15 20:24:56.117 wdl.w:ptcp.w:call-sawfish-45.t:call-run_sawfish NOTICE done
2025-09-15 20:24:56.124 wdl.w:ptcp.w:call-sawfish-45 NOTICE finish :: job: "call-run_sawfish"
2025-09-15 20:24:56.124 wdl.w:ptcp.w:call-sawfish-45 INFO output :: job: "call-run_sawfish", values: {"minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-45/call-run_sawfish/out/m84036_250809_035451_s4.bc2142.minimap2.bam.bai", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-45/call-run_sawfish/out/m84036_250809_035451_s4.bc2142.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-45/call-run_sawfish/out/m84036_250809_035451_s4.bc2142_sawfish/m84036_250809_035451_s4.bc2142.sv.vcf.gz.tbi", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-45/call-run_sawfish/out/m84036_250809_035451_s4.bc2142_sawfish/m84036_250809_035451_s4.bc2142.sv.vcf.gz"}
2025-09-15 20:24:56.125 wdl.w:ptcp.w:call-sawfish-45 INFO visit :: node: "output-minimap2_bam", values: {"minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-45/call-run_sawfish/out/m84036_250809_035451_s4.bc2142.minimap2.bam"}
2025-09-15 20:24:56.125 wdl.w:ptcp.w:call-sawfish-45 INFO visit :: node: "output-minimap2_bam_bai", values: {"minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-45/call-run_sawfish/out/m84036_250809_035451_s4.bc2142.minimap2.bam.bai"}
2025-09-15 20:24:56.125 wdl.w:ptcp.w:call-sawfish-45 INFO visit :: node: "output-vcf", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-45/call-run_sawfish/out/m84036_250809_035451_s4.bc2142_sawfish/m84036_250809_035451_s4.bc2142.sv.vcf.gz"}
2025-09-15 20:24:56.125 wdl.w:ptcp.w:call-sawfish-45 INFO visit :: node: "output-vcf_tbi", values: {"vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-45/call-run_sawfish/out/m84036_250809_035451_s4.bc2142_sawfish/m84036_250809_035451_s4.bc2142.sv.vcf.gz.tbi"}
2025-09-15 20:24:56.125 wdl.w:ptcp.w:call-sawfish-45 INFO visit :: node: "outputs", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-45/call-run_sawfish/out/m84036_250809_035451_s4.bc2142_sawfish/m84036_250809_035451_s4.bc2142.sv.vcf.gz", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-45/call-run_sawfish/out/m84036_250809_035451_s4.bc2142.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-45/call-run_sawfish/out/m84036_250809_035451_s4.bc2142_sawfish/m84036_250809_035451_s4.bc2142.sv.vcf.gz.tbi", "minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-45/call-run_sawfish/out/m84036_250809_035451_s4.bc2142.minimap2.bam.bai"}
2025-09-15 20:24:56.126 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_meth_allele NOTICE done
2025-09-15 20:24:56.130 wdl.w:ptcp.w:call-trgt-49.t:call-trgt_plot_motifs_allele NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-49/call-trgt_plot_motifs_allele", thread: 140609813722688
2025-09-15 20:24:56.132 wdl.w:ptcp.w:call-trgt-54 NOTICE finish :: job: "call-trgt_plot_meth_allele"
2025-09-15 20:24:56.132 wdl.w:ptcp.w:call-trgt-54 INFO output :: job: "call-trgt_plot_meth_allele", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-54/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2151.meth_allele.trgt_plots.zip"}
2025-09-15 20:24:56.132 wdl.w:ptcp.w:call-trgt-54 INFO visit :: node: "output-images_meth_allele", values: {"images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-54/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2151.meth_allele.trgt_plots.zip"}
2025-09-15 20:24:56.140 wdl.w:ptcp.w:call-trgt-49.t:call-trgt_plot_motifs_waterfall NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-49/call-trgt_plot_motifs_waterfall", thread: 140607649453632
2025-09-15 20:24:56.149 wdl.w:ptcp.w:call-trgt-49.t:call-trgt_plot_motifs_allele INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:56.149 wdl.w:ptcp.w:call-trgt-49.t:call-trgt_plot_motifs_allele INFO input :: name: "waterfall", value: false
2025-09-15 20:24:56.149 wdl.w:ptcp.w:call-trgt-49.t:call-trgt_plot_motifs_allele INFO input :: name: "methylation", value: false
2025-09-15 20:24:56.149 wdl.w:ptcp.w:call-trgt-49.t:call-trgt_plot_motifs_allele INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:56.150 wdl.w:ptcp.w:call-trgt-49.t:call-trgt_plot_motifs_allele INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:56.150 wdl.w:ptcp.w:call-trgt-49.t:call-trgt_plot_motifs_allele INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:56.150 wdl.w:ptcp.w:call-trgt-49.t:call-trgt_plot_motifs_allele INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2146.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:56.150 wdl.w:ptcp.w:call-trgt-49.t:call-trgt_plot_motifs_allele INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2146.trgt.sorted.spanning.bam"
2025-09-15 20:24:56.150 wdl.w:ptcp.w:call-trgt-49.t:call-trgt_plot_motifs_allele INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2146.trgt.vcf"
2025-09-15 20:24:56.150 wdl.w:ptcp.w:call-trgt-49.t:call-trgt_plot_motifs_allele INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2146"
2025-09-15 20:24:56.152 wdl.w:ptcp.w:call-trgt-49.t:call-trgt_plot_motifs_allele INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:56.153 wdl.w:ptcp.w:call-trgt-49.t:call-trgt_plot_motifs_allele INFO eval :: name: "plot_type", value: "allele"
2025-09-15 20:24:56.153 wdl.w:ptcp.w:call-trgt-49.t:call-trgt_plot_motifs_allele INFO eval :: name: "show", value: "motifs"
2025-09-15 20:24:56.153 wdl.w:ptcp.w:call-trgt-49.t:call-trgt_plot_motifs_allele INFO eval :: name: "threads", value: 1
2025-09-15 20:24:56.154 wdl.w:ptcp.w:call-trgt-49.t:call-trgt_plot_motifs_allele INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:56.154 wdl.w:ptcp.w:call-trgt-49.t:call-trgt_plot_motifs_allele INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2146.motifs_allele"
2025-09-15 20:24:56.155 wdl.w:ptcp.w:call-trgt-49.t:call-trgt_plot_motifs_allele INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:56.155 wdl.w:ptcp.w:call-trgt-49.t:call-trgt_plot_motifs_allele WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:56.156 wdl.w:ptcp.w:call-trgt-49.t:call-trgt_plot_motifs_allele INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:56.156 wdl.w:ptcp.w:call-trgt-49.t:call-trgt_plot_motifs_allele INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:56.162 wdl.w:ptcp.w:call-trgt-49.t:call-trgt_plot_motifs_waterfall INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:56.162 wdl.w:ptcp.w:call-trgt-49.t:call-trgt_plot_motifs_waterfall INFO input :: name: "waterfall", value: true
2025-09-15 20:24:56.162 wdl.w:ptcp.w:call-trgt-49.t:call-trgt_plot_motifs_waterfall INFO input :: name: "methylation", value: false
2025-09-15 20:24:56.163 wdl.w:ptcp.w:call-trgt-49.t:call-trgt_plot_motifs_waterfall INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:56.163 wdl.w:ptcp.w:call-trgt-49.t:call-trgt_plot_motifs_waterfall INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:56.163 wdl.w:ptcp.w:call-trgt-49.t:call-trgt_plot_motifs_waterfall INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:56.163 wdl.w:ptcp.w:call-trgt-49.t:call-trgt_plot_motifs_waterfall INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2146.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:56.163 wdl.w:ptcp.w:call-trgt-49.t:call-trgt_plot_motifs_waterfall INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2146.trgt.sorted.spanning.bam"
2025-09-15 20:24:56.163 wdl.w:ptcp.w:call-trgt-49.t:call-trgt_plot_motifs_waterfall INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2146.trgt.vcf"
2025-09-15 20:24:56.163 wdl.w:ptcp.w:call-trgt-49.t:call-trgt_plot_motifs_waterfall INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2146"
2025-09-15 20:24:56.163 wdl.w:ptcp.w:call-trgt-49.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:56.164 wdl.w:ptcp.w:call-trgt-49.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "plot_type", value: "waterfall"
2025-09-15 20:24:56.164 wdl.w:ptcp.w:call-trgt-49.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "show", value: "motifs"
2025-09-15 20:24:56.164 wdl.w:ptcp.w:call-trgt-49.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "threads", value: 1
2025-09-15 20:24:56.164 wdl.w:ptcp.w:call-trgt-49.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:56.164 wdl.w:ptcp.w:call-trgt-49.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2146.motifs_waterfall"
2025-09-15 20:24:56.165 wdl.w:ptcp.w:call-trgt-49.t:call-trgt_plot_motifs_waterfall INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:56.165 wdl.w:ptcp.w:call-trgt-49.t:call-trgt_plot_motifs_waterfall WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:56.165 wdl.w:ptcp.w:call-trgt-49.t:call-trgt_plot_motifs_waterfall INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:56.165 wdl.w:ptcp.w:call-trgt-49.t:call-trgt_plot_motifs_waterfall INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:56.177 wdl.w:ptcp.w:call-trgt-40.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:55 [ERROR] - No reads found for TRID=PRTS_ARX
2025-09-15 20:24:56.177 wdl.w:ptcp.w:call-trgt-40.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:55 [ERROR] - No reads found for TRID=EIEE1_ARX
2025-09-15 20:24:56.186 wdl.w:ptcp.w:call-trgt-41.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:53 [ERROR] - No reads found for TRID=EIEE1_ARX
2025-09-15 20:24:56.186 wdl.w:ptcp.w:call-sawfish-45 NOTICE done
2025-09-15 20:24:56.198 wdl.w:ptcp NOTICE finish :: job: "call-sawfish-45"
2025-09-15 20:24:56.198 wdl.w:ptcp INFO output :: job: "call-sawfish-45", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-45/out/m84036_250809_035451_s4.bc2142_sawfish/m84036_250809_035451_s4.bc2142.sv.vcf.gz", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-45/out/m84036_250809_035451_s4.bc2142.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-45/out/m84036_250809_035451_s4.bc2142_sawfish/m84036_250809_035451_s4.bc2142.sv.vcf.gz.tbi", "minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-45/out/m84036_250809_035451_s4.bc2142.minimap2.bam.bai"}
2025-09-15 20:24:56.198 wdl.w:ptcp NOTICE ready :: job: "call-tar_outputs-45", callee: "tar_outputs"
2025-09-15 20:24:56.199 wdl.w:ptcp INFO input :: job: "call-tar_outputs-45", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "sawfish_vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-45/out/m84036_250809_035451_s4.bc2142_sawfish/m84036_250809_035451_s4.bc2142.sv.vcf.gz.tbi", "sawfish_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-45/out/m84036_250809_035451_s4.bc2142_sawfish/m84036_250809_035451_s4.bc2142.sv.vcf.gz", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-45/out/m84036_250809_035451_s4.bc2142.f8inversion.json", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-45/out/m84036_250809_035451_s4.bc2142_paraphase/m84036_250809_035451_s4.bc2142.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-45/out/m84036_250809_035451_s4.bc2142_paraphase/m84036_250809_035451_s4.bc2142.paraphase.bam", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-45/out/m84036_250809_035451_s4.bc2142_paraphase/m84036_250809_035451_s4.bc2142.paraphase.json", "trgt_spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-45/out/m84036_250809_035451_s4.bc2142.trgt.sorted.spanning.bam.bai", "trgt_spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-45/out/m84036_250809_035451_s4.bc2142.trgt.sorted.spanning.bam", "trgt_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-45/out/m84036_250809_035451_s4.bc2142.trgt.vcf", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-45/out/m84036_250809_035451_s4.bc2142.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-45/out/m84036_250809_035451_s4.bc2142.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2142"}
2025-09-15 20:24:56.208 wdl.w:ptcp.w:call-trgt-74 NOTICE workflow start :: name: "trgt", source: "./trgt.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-74"
2025-09-15 20:24:56.227 wdl.w:ptcp.w:call-trgt-74 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:24:56.227 wdl.w:ptcp.w:call-trgt-74 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-74/out/m84036_250809_035451_s4.bc2171.mapped.bam"}
2025-09-15 20:24:56.227 wdl.w:ptcp.w:call-trgt-74 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-74/out/m84036_250809_035451_s4.bc2171.mapped.bam.bai"}
2025-09-15 20:24:56.227 wdl.w:ptcp.w:call-trgt-74 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:24:56.228 wdl.w:ptcp.w:call-trgt-74 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:24:56.228 wdl.w:ptcp.w:call-trgt-74 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2171"}
2025-09-15 20:24:56.228 wdl.w:ptcp.w:call-trgt-74 INFO visit :: node: "decl-sex", values: {"sex": "F"}
2025-09-15 20:24:56.228 wdl.w:ptcp.w:call-trgt-74 INFO visit :: node: "decl-trgt_bed", values: {"trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"}
2025-09-15 20:24:56.228 wdl.w:ptcp.w:call-trgt-74 NOTICE ready :: job: "call-get_reads_overlapping_repeats", callee: "get_reads_overlapping_repeats"
2025-09-15 20:24:56.228 wdl.w:ptcp.w:call-trgt-74 INFO input :: job: "call-get_reads_overlapping_repeats", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-74/out/m84036_250809_035451_s4.bc2171.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-74/out/m84036_250809_035451_s4.bc2171.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2171"}
2025-09-15 20:24:56.230 wdl.w:ptcp.w:call-trgt-74 NOTICE ready :: job: "call-trgt_genotype", callee: "trgt_genotype"
2025-09-15 20:24:56.230 wdl.w:ptcp.w:call-trgt-74 INFO input :: job: "call-trgt_genotype", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-74/out/m84036_250809_035451_s4.bc2171.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-74/out/m84036_250809_035451_s4.bc2171.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2171"}
2025-09-15 20:24:56.253 wdl.w:ptcp.w:call-trgt-49.t:call-trgt_plot_motifs_allele INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-49/call-trgt_plot_motifs_allele/_singularity_tmpdir_q_fs17_r"
2025-09-15 20:24:56.253 wdl.w:ptcp.w:call-trgt-49.t:call-trgt_plot_motifs_allele INFO Slurm invocation: srun --job-name call-trgt_plot_motifs_allele --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-49/call-trgt_plot_motifs_allele/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-49/call-trgt_plot_motifs_allele/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-49/call-trgt_plot_motifs_allele/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-49/call-trgt_plot_motifs_allele/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-49/call-trgt_genotype/out/m84036_250809_035451_s4.bc2146.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2146.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-49/call-trgt_genotype/out/m84036_250809_035451_s4.bc2146.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2146.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-49/call-trgt_genotype/out/m84036_250809_035451_s4.bc2146.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2146.trgt.sorted.spanning.bam:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-49/call-trgt_plot_motifs_allele/_singularity_tmpdir_q_fs17_r/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-49/call-trgt_plot_motifs_allele/_singularity_tmpdir_q_fs17_r/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:56.261 wdl.w:ptcp.w:call-trgt-57.t:call-trgt_plot_meth_allele INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2154.meth_allele.trgt_plots.zip"
2025-09-15 20:24:56.271 wdl.w:ptcp.w:call-trgt-49.t:call-trgt_plot_motifs_waterfall INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-49/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_a4v6rml8"
2025-09-15 20:24:56.271 wdl.w:ptcp.w:call-trgt-49.t:call-trgt_plot_motifs_waterfall INFO Slurm invocation: srun --job-name call-trgt_plot_motifs_waterfall --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-49/call-trgt_plot_motifs_waterfall/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-49/call-trgt_plot_motifs_waterfall/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-49/call-trgt_plot_motifs_waterfall/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-49/call-trgt_plot_motifs_waterfall/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-49/call-trgt_genotype/out/m84036_250809_035451_s4.bc2146.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2146.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-49/call-trgt_genotype/out/m84036_250809_035451_s4.bc2146.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2146.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-49/call-trgt_genotype/out/m84036_250809_035451_s4.bc2146.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2146.trgt.sorted.spanning.bam:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-49/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_a4v6rml8/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-49/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_a4v6rml8/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:56.284 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:54 [ERROR] - No reads found for TRID=NIID_NOTCH2NLC
2025-09-15 20:24:56.284 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:54 [ERROR] - No reads found for TRID=SCA2_ATXN2
2025-09-15 20:24:56.284 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:54 [ERROR] - No reads found for TRID=OPDM4_RILPL1
2025-09-15 20:24:56.284 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:54 [ERROR] - No reads found for TRID=SCA8_ATXN8OS
2025-09-15 20:24:56.284 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:54 [ERROR] - No reads found for TRID=OPMD_PABPN1
2025-09-15 20:24:56.284 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:54 [ERROR] - No reads found for TRID=SCA27B_FGF14
2025-09-15 20:24:56.284 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:54 [ERROR] - No reads found for TRID=SCA3_ATXN3
2025-09-15 20:24:56.284 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:54 [ERROR] - No reads found for TRID=SCA31_BEAN1
2025-09-15 20:24:56.284 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:54 [ERROR] - No reads found for TRID=SCA4_ZFHX3
2025-09-15 20:24:56.284 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:54 [ERROR] - No reads found for TRID=HDL2_JPH3
2025-09-15 20:24:56.284 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:54 [ERROR] - No reads found for TRID=SCA6_CACNA1A
2025-09-15 20:24:56.284 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:54 [ERROR] - No reads found for TRID=FECD3_TCF4
2025-09-15 20:24:56.285 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:54 [ERROR] - No reads found for TRID=OPDM2_GIPC1
2025-09-15 20:24:56.285 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:54 [ERROR] - No reads found for TRID=DM1_DMPK
2025-09-15 20:24:56.285 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:55 [ERROR] - No reads found for TRID=FRA2A_AFF3
2025-09-15 20:24:56.285 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:55 [ERROR] - No reads found for TRID=SD5_HOXD13
2025-09-15 20:24:56.285 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:55 [ERROR] - No reads found for TRID=SCA36_NOP56
2025-09-15 20:24:56.285 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:55 [ERROR] - No reads found for TRID=CJD_PRNP
2025-09-15 20:24:56.285 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:55 [ERROR] - No reads found for TRID=EPM1_CSTB
2025-09-15 20:24:56.290 wdl.w:ptcp.w:call-trgt-49.t:call-trgt_plot_motifs_waterfall NOTICE slurm_singularity run :: pid: 1203537, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-49/call-trgt_plot_motifs_waterfall/slurm_singularity.log.txt"
2025-09-15 20:24:56.292 wdl.w:ptcp.w:call-trgt-49.t:call-trgt_plot_motifs_allele NOTICE slurm_singularity run :: pid: 1203536, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-49/call-trgt_plot_motifs_allele/slurm_singularity.log.txt"
2025-09-15 20:24:56.306 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_motifs_allele INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2151.motifs_allele.trgt_plots.zip"
2025-09-15 20:24:56.385 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_meth_waterfall INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2151.meth_waterfall.trgt_plots.zip"
2025-09-15 20:24:56.389 wdl.w:ptcp.w:call-paraphase-64.t:call-run_paraphase INFO output :: name: "paraphase_bam", value: "m84036_250809_035451_s4.bc2161_paraphase/m84036_250809_035451_s4.bc2161.paraphase.bam"
2025-09-15 20:24:56.396 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_motifs_allele NOTICE done
2025-09-15 20:24:56.396 wdl.w:ptcp.w:call-paraphase-64.t:call-run_paraphase INFO output :: name: "paraphase_bam_bai", value: "m84036_250809_035451_s4.bc2161_paraphase/m84036_250809_035451_s4.bc2161.paraphase.bam.bai"
2025-09-15 20:24:56.398 wdl.w:ptcp.w:call-paraphase-64.t:call-run_paraphase INFO output :: name: "paraphase_json", value: "m84036_250809_035451_s4.bc2161_paraphase/m84036_250809_035451_s4.bc2161.paraphase.json"
2025-09-15 20:24:56.400 wdl.w:ptcp.w:call-paraphase-64.t:call-run_paraphase INFO output :: name: "paraphase_vcfs", value: []
2025-09-15 20:24:56.400 wdl.w:ptcp.w:call-paraphase-64.t:call-run_paraphase INFO output :: name: "havanno_json", value: "m84036_250809_035451_s4.bc2161.havanno.json"
2025-09-15 20:24:56.402 wdl.w:ptcp.w:call-trgt-54 NOTICE finish :: job: "call-trgt_plot_motifs_allele"
2025-09-15 20:24:56.402 wdl.w:ptcp.w:call-trgt-54 INFO output :: job: "call-trgt_plot_motifs_allele", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-54/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2151.motifs_allele.trgt_plots.zip"}
2025-09-15 20:24:56.402 wdl.w:ptcp.w:call-trgt-54 INFO visit :: node: "output-images_motifs_allele", values: {"images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-54/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2151.motifs_allele.trgt_plots.zip"}
2025-09-15 20:24:56.410 wdl.w:ptcp.w:call-sawfish-60.t:call-run_sawfish NOTICE task setup :: name: "run_sawfish", source: "./sawfish.wdl", line: 83, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-60/call-run_sawfish", thread: 140609302029888
2025-09-15 20:24:56.411 wdl.w:ptcp.w:call-trgt-57.t:call-trgt_plot_meth_allele NOTICE done
2025-09-15 20:24:56.416 wdl.w:ptcp.w:call-trgt-57 NOTICE finish :: job: "call-trgt_plot_meth_allele"
2025-09-15 20:24:56.416 wdl.w:ptcp.w:call-trgt-57 INFO output :: job: "call-trgt_plot_meth_allele", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-57/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2154.meth_allele.trgt_plots.zip"}
2025-09-15 20:24:56.417 wdl.w:ptcp.w:call-trgt-57 INFO visit :: node: "output-images_meth_allele", values: {"images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-57/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2154.meth_allele.trgt_plots.zip"}
2025-09-15 20:24:56.424 wdl.w:ptcp.w:call-trgt-60.t:call-get_reads_overlapping_repeats NOTICE task setup :: name: "get_reads_overlapping_repeats", source: "./trgt.wdl", line: 182, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-60/call-get_reads_overlapping_repeats", thread: 140610367379008
2025-09-15 20:24:56.430 wdl.w:ptcp.w:call-sawfish-60.t:call-run_sawfish INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:56.430 wdl.w:ptcp.w:call-sawfish-60.t:call-run_sawfish INFO input :: name: "genome_version", value: "38"
2025-09-15 20:24:56.430 wdl.w:ptcp.w:call-sawfish-60.t:call-run_sawfish INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:56.430 wdl.w:ptcp.w:call-sawfish-60.t:call-run_sawfish INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:56.430 wdl.w:ptcp.w:call-sawfish-60.t:call-run_sawfish INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2157.mapped.bam.bai"
2025-09-15 20:24:56.430 wdl.w:ptcp.w:call-sawfish-60.t:call-run_sawfish INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2157.mapped.bam"
2025-09-15 20:24:56.430 wdl.w:ptcp.w:call-sawfish-60.t:call-run_sawfish INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2157"
2025-09-15 20:24:56.431 wdl.w:ptcp.w:call-sawfish-60.t:call-run_sawfish INFO eval :: name: "mem_gb", value: 32
2025-09-15 20:24:56.431 wdl.w:ptcp.w:call-sawfish-60.t:call-run_sawfish INFO eval :: name: "threads", value: 16
2025-09-15 20:24:56.431 wdl.w:ptcp.w:call-sawfish-60.t:call-run_sawfish INFO eval :: name: "disk_size", value: 30
2025-09-15 20:24:56.431 wdl.w:ptcp.w:call-sawfish-60.t:call-run_sawfish INFO eval :: name: "discover_dirname", value: "m84036_250809_035451_s4.bc2157_sawfish_discover"
2025-09-15 20:24:56.431 wdl.w:ptcp.w:call-sawfish-60.t:call-run_sawfish INFO eval :: name: "call_dirname", value: "m84036_250809_035451_s4.bc2157_sawfish"
2025-09-15 20:24:56.431 wdl.w:ptcp.w:call-sawfish-60.t:call-run_sawfish INFO eval :: name: "minimap2_bam_filename", value: "m84036_250809_035451_s4.bc2157.minimap2.bam"
2025-09-15 20:24:56.432 wdl.w:ptcp.w:call-sawfish-60.t:call-run_sawfish INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 16, memory_reservation: 32000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:56.432 wdl.w:ptcp.w:call-sawfish-60.t:call-run_sawfish WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:56.432 wdl.w:ptcp.w:call-sawfish-60.t:call-run_sawfish INFO provisioned :: seconds_waited: 0, cpu: 16, mem_bytes: 32000000000
2025-09-15 20:24:56.433 wdl.w:ptcp.w:call-sawfish-60.t:call-run_sawfish INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:56.447 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:56 [ERROR] - No reads found for TRID=OPDM_ABCD3
2025-09-15 20:24:56.447 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:56 [ERROR] - No reads found for TRID=SCA37_DAB1
2025-09-15 20:24:56.447 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:56 [ERROR] - No reads found for TRID=SCA2_ATXN2
2025-09-15 20:24:56.447 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:56 [ERROR] - No reads found for TRID=OPDM4_RILPL1
2025-09-15 20:24:56.447 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:56 [ERROR] - No reads found for TRID=SCA27B_FGF14
2025-09-15 20:24:56.447 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:56 [ERROR] - No reads found for TRID=OPMD_PABPN1
2025-09-15 20:24:56.447 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:56 [ERROR] - No reads found for TRID=SCA31_BEAN1
2025-09-15 20:24:56.447 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:56 [ERROR] - No reads found for TRID=SCA4_ZFHX3
2025-09-15 20:24:56.448 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:56 [ERROR] - No reads found for TRID=HDL2_JPH3
2025-09-15 20:24:56.448 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:56 [ERROR] - No reads found for TRID=FECD3_TCF4
2025-09-15 20:24:56.448 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:56 [ERROR] - No reads found for TRID=SCA6_CACNA1A
2025-09-15 20:24:56.448 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:56 [ERROR] - No reads found for TRID=OPDM2_GIPC1
2025-09-15 20:24:56.450 wdl.w:ptcp.w:call-trgt-60.t:call-get_reads_overlapping_repeats INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:56.450 wdl.w:ptcp.w:call-trgt-60.t:call-get_reads_overlapping_repeats INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:56.450 wdl.w:ptcp.w:call-trgt-60.t:call-get_reads_overlapping_repeats INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2157.mapped.bam.bai"
2025-09-15 20:24:56.450 wdl.w:ptcp.w:call-trgt-60.t:call-get_reads_overlapping_repeats INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2157.mapped.bam"
2025-09-15 20:24:56.450 wdl.w:ptcp.w:call-trgt-60.t:call-get_reads_overlapping_repeats INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2157"
2025-09-15 20:24:56.450 wdl.w:ptcp.w:call-trgt-60.t:call-get_reads_overlapping_repeats INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:56.450 wdl.w:ptcp.w:call-trgt-60.t:call-get_reads_overlapping_repeats INFO eval :: name: "expand_size", value: 3000
2025-09-15 20:24:56.450 wdl.w:ptcp.w:call-trgt-60.t:call-get_reads_overlapping_repeats INFO eval :: name: "threads", value: 1
2025-09-15 20:24:56.451 wdl.w:ptcp.w:call-trgt-60.t:call-get_reads_overlapping_repeats INFO eval :: name: "expanded_bed_name", value: "m84036_250809_035451_s4.bc2157.expanded.bed"
2025-09-15 20:24:56.451 wdl.w:ptcp.w:call-trgt-60.t:call-get_reads_overlapping_repeats INFO eval :: name: "disk_size", value: 11
2025-09-15 20:24:56.451 wdl.w:ptcp.w:call-trgt-60.t:call-get_reads_overlapping_repeats INFO eval :: name: "output_name", value: "m84036_250809_035451_s4.bc2157.repeats.bam"
2025-09-15 20:24:56.451 wdl.w:ptcp.w:call-trgt-60.t:call-get_reads_overlapping_repeats INFO eval :: name: "index_name", value: "m84036_250809_035451_s4.bc2157.repeats.bam.bai"
2025-09-15 20:24:56.451 wdl.w:ptcp.w:call-trgt-60.t:call-get_reads_overlapping_repeats INFO eval :: name: "output_name_with_index", value: "m84036_250809_035451_s4.bc2157.repeats.bam##idx##m84036_250809_035451_s4.bc2157.repeats.bam.bai"
2025-09-15 20:24:56.451 wdl.w:ptcp.w:call-trgt-60.t:call-get_reads_overlapping_repeats INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:56.451 wdl.w:ptcp.w:call-trgt-60.t:call-get_reads_overlapping_repeats WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:56.452 wdl.w:ptcp.w:call-trgt-60.t:call-get_reads_overlapping_repeats INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:56.452 wdl.w:ptcp.w:call-trgt-60.t:call-get_reads_overlapping_repeats INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:56.468 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_plot_motifs_allele.slurm_singularity INFO srun: job 51797830 queued and waiting for resources
2025-09-15 20:24:56.468 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_plot_motifs_allele.slurm_singularity INFO srun: job 51797830 has been allocated resources
2025-09-15 20:24:56.468 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_plot_motifs_allele.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:56.489 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_meth_waterfall NOTICE done
2025-09-15 20:24:56.488 wdl.w:ptcp.w:call-sawfish-51.t:call-run_sawfish INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2148_sawfish/m84036_250809_035451_s4.bc2148.sv.vcf.gz"
2025-09-15 20:24:56.496 wdl.w:ptcp.w:call-trgt-54 NOTICE finish :: job: "call-trgt_plot_meth_waterfall"
2025-09-15 20:24:56.496 wdl.w:ptcp.w:call-trgt-54 INFO output :: job: "call-trgt_plot_meth_waterfall", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-54/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2151.meth_waterfall.trgt_plots.zip"}
2025-09-15 20:24:56.496 wdl.w:ptcp.w:call-trgt-54 INFO visit :: node: "output-images_meth_waterfall", values: {"images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-54/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2151.meth_waterfall.trgt_plots.zip"}
2025-09-15 20:24:56.499 wdl.w:ptcp.w:call-sawfish-51.t:call-run_sawfish INFO output :: name: "vcf_tbi", value: "m84036_250809_035451_s4.bc2148_sawfish/m84036_250809_035451_s4.bc2148.sv.vcf.gz.tbi"
2025-09-15 20:24:56.500 wdl.w:ptcp.w:call-sawfish-51.t:call-run_sawfish INFO output :: name: "minimap2_bam", value: "m84036_250809_035451_s4.bc2148.minimap2.bam"
2025-09-15 20:24:56.502 wdl.w:ptcp.w:call-sawfish-51.t:call-run_sawfish INFO output :: name: "minimap2_bam_bai", value: "m84036_250809_035451_s4.bc2148.minimap2.bam.bai"
2025-09-15 20:24:56.506 wdl.w:ptcp.w:call-trgt-60.t:call-trgt_genotype NOTICE task setup :: name: "trgt_genotype", source: "./trgt.wdl", line: 272, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-60/call-trgt_genotype", thread: 140612481291840
2025-09-15 20:24:56.527 wdl.w:ptcp.w:call-sawfish-60.t:call-run_sawfish INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 10, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-60/call-run_sawfish/_singularity_tmpdir_2ftbz3mc"
2025-09-15 20:24:56.527 wdl.w:ptcp.w:call-trgt-40.t:call-trgt_plot_motifs_allele INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2137.motifs_allele.trgt_plots.zip"
2025-09-15 20:24:56.528 wdl.w:ptcp.w:call-sawfish-60.t:call-run_sawfish INFO Slurm invocation: srun --job-name call-run_sawfish --partition compute,compute9 --cpus-per-task 16 --mem 30518M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-60/call-run_sawfish/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-60/call-run_sawfish/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-60/call-run_sawfish/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-60/call-run_sawfish/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-60/out/m84036_250809_035451_s4.bc2157.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2157.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-60/out/m84036_250809_035451_s4.bc2157.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2157.mapped.bam:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-60/call-run_sawfish/_singularity_tmpdir_2ftbz3mc/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-60/call-run_sawfish/_singularity_tmpdir_2ftbz3mc/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:56.536 wdl.w:ptcp.w:call-trgt-60.t:call-trgt_genotype INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:56.536 wdl.w:ptcp.w:call-trgt-60.t:call-trgt_genotype INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:56.536 wdl.w:ptcp.w:call-trgt-60.t:call-trgt_genotype INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:56.536 wdl.w:ptcp.w:call-trgt-60.t:call-trgt_genotype INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:56.536 wdl.w:ptcp.w:call-trgt-60.t:call-trgt_genotype INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2157.mapped.bam.bai"
2025-09-15 20:24:56.536 wdl.w:ptcp.w:call-trgt-60.t:call-trgt_genotype INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2157.mapped.bam"
2025-09-15 20:24:56.536 wdl.w:ptcp.w:call-trgt-60.t:call-trgt_genotype INFO input :: name: "sex", value: "F"
2025-09-15 20:24:56.536 wdl.w:ptcp.w:call-trgt-60.t:call-trgt_genotype INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2157"
2025-09-15 20:24:56.537 wdl.w:ptcp.w:call-trgt-60.t:call-trgt_genotype INFO eval :: name: "mem_gb", value: 16
2025-09-15 20:24:56.537 wdl.w:ptcp.w:call-trgt-60.t:call-trgt_genotype INFO eval :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2157.trgt"
2025-09-15 20:24:56.537 wdl.w:ptcp.w:call-trgt-60.t:call-trgt_genotype INFO eval :: name: "threads", value: 8
2025-09-15 20:24:56.537 wdl.w:ptcp.w:call-trgt-60.t:call-trgt_genotype INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:56.537 wdl.w:ptcp.w:call-trgt-60.t:call-trgt_genotype INFO eval :: name: "karyotype", value: "XX"
2025-09-15 20:24:56.538 wdl.w:ptcp.w:call-trgt-60.t:call-trgt_genotype INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 8, memory_reservation: 16000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:56.538 wdl.w:ptcp.w:call-trgt-60.t:call-trgt_genotype WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:56.538 wdl.w:ptcp.w:call-trgt-60.t:call-trgt_genotype INFO provisioned :: seconds_waited: 0, cpu: 8, mem_bytes: 16000000000
2025-09-15 20:24:56.538 wdl.w:ptcp.w:call-trgt-60.t:call-trgt_genotype INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:56.540 wdl.w:ptcp.w:call-trgt-60.t:call-get_reads_overlapping_repeats INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 9, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-60/call-get_reads_overlapping_repeats/_singularity_tmpdir_u3jmmmzh"
2025-09-15 20:24:56.541 wdl.w:ptcp.w:call-trgt-60.t:call-get_reads_overlapping_repeats INFO Slurm invocation: srun --job-name call-get_reads_overlapping_repeats --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-60/call-get_reads_overlapping_repeats/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-60/call-get_reads_overlapping_repeats/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-60/call-get_reads_overlapping_repeats/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-60/call-get_reads_overlapping_repeats/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-60/out/m84036_250809_035451_s4.bc2157.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2157.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-60/out/m84036_250809_035451_s4.bc2157.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2157.mapped.bam:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-60/call-get_reads_overlapping_repeats/_singularity_tmpdir_u3jmmmzh/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-60/call-get_reads_overlapping_repeats/_singularity_tmpdir_u3jmmmzh/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:56.544 wdl.w:ptcp.w:call-paraphase-64.t:call-run_paraphase NOTICE done
2025-09-15 20:24:56.557 wdl.w:ptcp.w:call-paraphase-64 NOTICE finish :: job: "call-run_paraphase"
2025-09-15 20:24:56.557 wdl.w:ptcp.w:call-paraphase-64 INFO output :: job: "call-run_paraphase", values: {"havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-64/call-run_paraphase/out/m84036_250809_035451_s4.bc2161.havanno.json", "paraphase_vcfs": [], "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-64/call-run_paraphase/out/m84036_250809_035451_s4.bc2161_paraphase/m84036_250809_035451_s4.bc2161.paraphase.json", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-64/call-run_paraphase/out/m84036_250809_035451_s4.bc2161_paraphase/m84036_250809_035451_s4.bc2161.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-64/call-run_paraphase/out/m84036_250809_035451_s4.bc2161_paraphase/m84036_250809_035451_s4.bc2161.paraphase.bam"}
2025-09-15 20:24:56.558 wdl.w:ptcp.w:call-paraphase-64 NOTICE ready :: job: "call-call_f8", callee: "call_f8"
2025-09-15 20:24:56.558 wdl.w:ptcp.w:call-paraphase-64 INFO input :: job: "call-call_f8", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "out_prefix": "m84036_250809_035451_s4.bc2161", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-64/call-run_paraphase/out/m84036_250809_035451_s4.bc2161_paraphase/m84036_250809_035451_s4.bc2161.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-64/call-run_paraphase/out/m84036_250809_035451_s4.bc2161_paraphase/m84036_250809_035451_s4.bc2161.paraphase.bam", "sex": "F"}
2025-09-15 20:24:56.559 wdl.w:ptcp.w:call-paraphase-64 INFO visit :: node: "output-havanno_json", values: {"havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-64/call-run_paraphase/out/m84036_250809_035451_s4.bc2161.havanno.json"}
2025-09-15 20:24:56.559 wdl.w:ptcp.w:call-paraphase-64 INFO visit :: node: "output-paraphase_bam", values: {"paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-64/call-run_paraphase/out/m84036_250809_035451_s4.bc2161_paraphase/m84036_250809_035451_s4.bc2161.paraphase.bam"}
2025-09-15 20:24:56.560 wdl.w:ptcp.w:call-paraphase-64 INFO visit :: node: "output-paraphase_bam_bai", values: {"paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-64/call-run_paraphase/out/m84036_250809_035451_s4.bc2161_paraphase/m84036_250809_035451_s4.bc2161.paraphase.bam.bai"}
2025-09-15 20:24:56.560 wdl.w:ptcp.w:call-paraphase-64 INFO visit :: node: "output-paraphase_json", values: {"paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-64/call-run_paraphase/out/m84036_250809_035451_s4.bc2161_paraphase/m84036_250809_035451_s4.bc2161.paraphase.json"}
2025-09-15 20:24:56.560 wdl.w:ptcp.w:call-paraphase-64 INFO visit :: node: "output-paraphase_vcfs", values: {"paraphase_vcfs": []}
2025-09-15 20:24:56.561 wdl.w:ptcp.w:call-paraphase-59.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for hba for sample m84036_250809_035451_s4.bc2156 at 2025-09-15 20:24:43.659591...
2025-09-15 20:24:56.562 wdl.w:ptcp.w:call-paraphase-59.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for smn1 for sample m84036_250809_035451_s4.bc2156 at 2025-09-15 20:24:44.151503...
2025-09-15 20:24:56.562 wdl.w:ptcp.w:call-paraphase-59.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for gba for sample m84036_250809_035451_s4.bc2156 at 2025-09-15 20:24:44.233340...
2025-09-15 20:24:56.562 wdl.w:ptcp.w:call-paraphase-59.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for cyp21 for sample m84036_250809_035451_s4.bc2156 at 2025-09-15 20:24:45.143109...
2025-09-15 20:24:56.562 wdl.w:ptcp.w:call-trgt-60.t:call-get_reads_overlapping_repeats NOTICE slurm_singularity run :: pid: 1203555, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-60/call-get_reads_overlapping_repeats/slurm_singularity.log.txt"
2025-09-15 20:24:56.562 wdl.w:ptcp.w:call-paraphase-59.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for smn1 for sample m84036_250809_035451_s4.bc2156 at 2025-09-15 20:24:54.454518...
2025-09-15 20:24:56.562 wdl.w:ptcp.w:call-sawfish-60.t:call-run_sawfish NOTICE slurm_singularity run :: pid: 1203554, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-60/call-run_sawfish/slurm_singularity.log.txt"
2025-09-15 20:24:56.562 wdl.w:ptcp.w:call-paraphase-59.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning to gene2 region for smn1 for sample m84036_250809_035451_s4.bc2156 at 2025-09-15 20:24:55.024153...
2025-09-15 20:24:56.566 wdl.w:ptcp.t:call-tar_outputs-01 NOTICE task setup :: name: "tar_outputs", source: "./common.wdl", line: 279, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-01", thread: 140607112582720
2025-09-15 20:24:56.602 wdl.w:ptcp.t:call-tar_outputs-01 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:56.602 wdl.w:ptcp.t:call-tar_outputs-01 INFO input :: name: "sawfish_vcf_tbi", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2098.sv.vcf.gz.tbi"
2025-09-15 20:24:56.602 wdl.w:ptcp.t:call-tar_outputs-01 INFO input :: name: "sawfish_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2098.sv.vcf.gz"
2025-09-15 20:24:56.602 wdl.w:ptcp.t:call-tar_outputs-01 INFO input :: name: "f8_json", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2098.f8inversion.json"
2025-09-15 20:24:56.602 wdl.w:ptcp.t:call-tar_outputs-01 INFO input :: name: "paraphase_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2098.paraphase.bam.bai"
2025-09-15 20:24:56.602 wdl.w:ptcp.t:call-tar_outputs-01 INFO input :: name: "paraphase_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2098.paraphase.bam"
2025-09-15 20:24:56.602 wdl.w:ptcp.t:call-tar_outputs-01 INFO input :: name: "paraphase_json", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2098.paraphase.json"
2025-09-15 20:24:56.602 wdl.w:ptcp.t:call-tar_outputs-01 INFO input :: name: "trgt_spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2098.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:56.602 wdl.w:ptcp.t:call-tar_outputs-01 INFO input :: name: "trgt_spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2098.trgt.sorted.spanning.bam"
2025-09-15 20:24:56.602 wdl.w:ptcp.t:call-tar_outputs-01 INFO input :: name: "trgt_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2098.trgt.vcf"
2025-09-15 20:24:56.602 wdl.w:ptcp.t:call-tar_outputs-01 INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2098.mapped.bam.bai"
2025-09-15 20:24:56.602 wdl.w:ptcp.t:call-tar_outputs-01 INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2098.mapped.bam"
2025-09-15 20:24:56.602 wdl.w:ptcp.t:call-tar_outputs-01 INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2098"
2025-09-15 20:24:56.603 wdl.w:ptcp.t:call-tar_outputs-01 INFO eval :: name: "threads", value: 1
2025-09-15 20:24:56.603 wdl.w:ptcp.t:call-tar_outputs-01 INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:56.603 wdl.w:ptcp.t:call-tar_outputs-01 INFO eval :: name: "disk_size", value: 6
2025-09-15 20:24:56.603 wdl.w:ptcp.t:call-tar_outputs-01 INFO eval :: name: "output_tarball", value: "m84036_250809_035451_s4.bc2098.tar"
2025-09-15 20:24:56.604 wdl.w:ptcp.t:call-tar_outputs-01 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:56.604 wdl.w:ptcp.t:call-tar_outputs-01 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:56.604 wdl.w:ptcp.t:call-tar_outputs-01 INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:56.604 wdl.w:ptcp.t:call-tar_outputs-01 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:56.622 wdl.w:ptcp.w:call-trgt-41.t:call-trgt_plot_meth_allele INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2138.meth_allele.trgt_plots.zip"
2025-09-15 20:24:56.639 wdl.w:ptcp.w:call-trgt-60.t:call-trgt_genotype INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 11, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-60/call-trgt_genotype/_singularity_tmpdir_9h335xht"
2025-09-15 20:24:56.639 wdl.w:ptcp.w:call-trgt-60.t:call-trgt_genotype INFO Slurm invocation: srun --job-name call-trgt_genotype --partition compute,compute9 --cpus-per-task 8 --mem 15259M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-60/call-trgt_genotype/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-60/call-trgt_genotype/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-60/call-trgt_genotype/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-60/call-trgt_genotype/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-60/out/m84036_250809_035451_s4.bc2157.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2157.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-60/out/m84036_250809_035451_s4.bc2157.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2157.mapped.bam:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-60/call-trgt_genotype/_singularity_tmpdir_9h335xht/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-60/call-trgt_genotype/_singularity_tmpdir_9h335xht/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:56.663 wdl.w:ptcp.w:call-trgt-60.t:call-trgt_genotype NOTICE slurm_singularity run :: pid: 1203559, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-60/call-trgt_genotype/slurm_singularity.log.txt"
2025-09-15 20:24:56.684 wdl.w:ptcp.w:call-sawfish-51.t:call-run_sawfish NOTICE done
2025-09-15 20:24:56.690 wdl.w:ptcp.w:call-trgt-40.t:call-trgt_plot_motifs_allele NOTICE done
2025-09-15 20:24:56.691 wdl.w:ptcp.w:call-sawfish-51 NOTICE finish :: job: "call-run_sawfish"
2025-09-15 20:24:56.691 wdl.w:ptcp.w:call-sawfish-51 INFO output :: job: "call-run_sawfish", values: {"minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-51/call-run_sawfish/out/m84036_250809_035451_s4.bc2148.minimap2.bam.bai", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-51/call-run_sawfish/out/m84036_250809_035451_s4.bc2148.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-51/call-run_sawfish/out/m84036_250809_035451_s4.bc2148_sawfish/m84036_250809_035451_s4.bc2148.sv.vcf.gz.tbi", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-51/call-run_sawfish/out/m84036_250809_035451_s4.bc2148_sawfish/m84036_250809_035451_s4.bc2148.sv.vcf.gz"}
2025-09-15 20:24:56.692 wdl.w:ptcp.w:call-sawfish-51 INFO visit :: node: "output-minimap2_bam", values: {"minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-51/call-run_sawfish/out/m84036_250809_035451_s4.bc2148.minimap2.bam"}
2025-09-15 20:24:56.692 wdl.w:ptcp.w:call-sawfish-51 INFO visit :: node: "output-minimap2_bam_bai", values: {"minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-51/call-run_sawfish/out/m84036_250809_035451_s4.bc2148.minimap2.bam.bai"}
2025-09-15 20:24:56.692 wdl.w:ptcp.w:call-sawfish-51 INFO visit :: node: "output-vcf", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-51/call-run_sawfish/out/m84036_250809_035451_s4.bc2148_sawfish/m84036_250809_035451_s4.bc2148.sv.vcf.gz"}
2025-09-15 20:24:56.692 wdl.w:ptcp.w:call-sawfish-51 INFO visit :: node: "output-vcf_tbi", values: {"vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-51/call-run_sawfish/out/m84036_250809_035451_s4.bc2148_sawfish/m84036_250809_035451_s4.bc2148.sv.vcf.gz.tbi"}
2025-09-15 20:24:56.692 wdl.w:ptcp.w:call-sawfish-51 INFO visit :: node: "outputs", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-51/call-run_sawfish/out/m84036_250809_035451_s4.bc2148_sawfish/m84036_250809_035451_s4.bc2148.sv.vcf.gz", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-51/call-run_sawfish/out/m84036_250809_035451_s4.bc2148.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-51/call-run_sawfish/out/m84036_250809_035451_s4.bc2148_sawfish/m84036_250809_035451_s4.bc2148.sv.vcf.gz.tbi", "minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-51/call-run_sawfish/out/m84036_250809_035451_s4.bc2148.minimap2.bam.bai"}
2025-09-15 20:24:56.698 wdl.w:ptcp.w:call-paraphase-65.t:call-run_paraphase NOTICE task setup :: name: "run_paraphase", source: "./paraphase.wdl", line: 127, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-65/call-run_paraphase", thread: 140608739980864
2025-09-15 20:24:56.713 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:55 [ERROR] - No reads found for TRID=SCA10_ATXN10
2025-09-15 20:24:56.713 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:55 [ERROR] - No reads found for TRID=SCA7_ATXN7
2025-09-15 20:24:56.713 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:55 [ERROR] - No reads found for TRID=DM2_CNBP
2025-09-15 20:24:56.713 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:55 [ERROR] - No reads found for TRID=HD_HTT
2025-09-15 20:24:56.713 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:55 [ERROR] - No reads found for TRID=CCHS_PHOX2B
2025-09-15 20:24:56.714 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:55 [ERROR] - No reads found for TRID=SCA12_PPP2R2B
2025-09-15 20:24:56.714 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:55 [ERROR] - No reads found for TRID=SCA1_ATXN1
2025-09-15 20:24:56.714 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:55 [ERROR] - No reads found for TRID=SCA17_TBP
2025-09-15 20:24:56.714 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:55 [ERROR] - No reads found for TRID=OPDM1_LRP12
2025-09-15 20:24:56.714 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:55 [ERROR] - No reads found for TRID=FAME1_SAMD12
2025-09-15 20:24:56.714 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:55 [ERROR] - No reads found for TRID=FTDALS1_C9orf72
2025-09-15 20:24:56.721 wdl.w:ptcp.w:call-paraphase-65.t:call-run_paraphase INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:56.721 wdl.w:ptcp.w:call-paraphase-65.t:call-run_paraphase INFO input :: name: "annotation_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf"
2025-09-15 20:24:56.721 wdl.w:ptcp.w:call-paraphase-65.t:call-run_paraphase INFO input :: name: "genome_version", value: "38"
2025-09-15 20:24:56.721 wdl.w:ptcp.w:call-paraphase-65.t:call-run_paraphase INFO input :: name: "config_file", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/paraphase_config.GRCh38.yaml"
2025-09-15 20:24:56.721 wdl.w:ptcp.w:call-paraphase-65.t:call-run_paraphase INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:56.721 wdl.w:ptcp.w:call-paraphase-65.t:call-run_paraphase INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:56.721 wdl.w:ptcp.w:call-paraphase-65.t:call-run_paraphase INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2162.mapped.bam.bai"
2025-09-15 20:24:56.721 wdl.w:ptcp.w:call-paraphase-65.t:call-run_paraphase INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2162.mapped.bam"
2025-09-15 20:24:56.721 wdl.w:ptcp.w:call-paraphase-65.t:call-run_paraphase INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2162"
2025-09-15 20:24:56.723 wdl.w:ptcp.w:call-paraphase-65.t:call-run_paraphase INFO eval :: name: "threads", value: 4
2025-09-15 20:24:56.724 wdl.w:ptcp.w:call-trgt-40 NOTICE finish :: job: "call-trgt_plot_motifs_allele"
2025-09-15 20:24:56.724 wdl.w:ptcp.w:call-paraphase-65.t:call-run_paraphase INFO eval :: name: "mem_gb", value: 8
2025-09-15 20:24:56.724 wdl.w:ptcp.w:call-trgt-40 INFO output :: job: "call-trgt_plot_motifs_allele", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-40/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2137.motifs_allele.trgt_plots.zip"}
2025-09-15 20:24:56.725 wdl.w:ptcp.w:call-paraphase-65.t:call-run_paraphase INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:56.725 wdl.w:ptcp.w:call-trgt-40 INFO visit :: node: "output-images_motifs_allele", values: {"images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-40/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2137.motifs_allele.trgt_plots.zip"}
2025-09-15 20:24:56.726 wdl.w:ptcp.w:call-paraphase-65.t:call-run_paraphase INFO eval :: name: "out_dir", value: "m84036_250809_035451_s4.bc2162_paraphase"
2025-09-15 20:24:56.726 wdl.w:ptcp.t:call-tar_outputs-01 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 17, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-01/_singularity_tmpdir_u3l5q1ts"
2025-09-15 20:24:56.726 wdl.w:ptcp.t:call-tar_outputs-01 INFO Slurm invocation: srun --job-name call-tar_outputs-01 --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-01/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-01/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-01/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-01/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-01/out/m84036_250809_035451_s4.bc2098_paraphase/m84036_250809_035451_s4.bc2098.paraphase.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2098.paraphase.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-01/out/m84036_250809_035451_s4.bc2098_paraphase/m84036_250809_035451_s4.bc2098.paraphase.json:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2098.paraphase.json:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-01/out/m84036_250809_035451_s4.bc2098_paraphase/m84036_250809_035451_s4.bc2098.paraphase.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2098.paraphase.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-01/out/m84036_250809_035451_s4.bc2098.f8inversion.json:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2098.f8inversion.json:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-01/out/m84036_250809_035451_s4.bc2098.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2098.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-01/out/m84036_250809_035451_s4.bc2098.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2098.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-01/out/m84036_250809_035451_s4.bc2098.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2098.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-01/out/m84036_250809_035451_s4.bc2098.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2098.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-01/out/m84036_250809_035451_s4.bc2098.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2098.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-01/out/m84036_250809_035451_s4.bc2098_sawfish/m84036_250809_035451_s4.bc2098.sv.vcf.gz.tbi:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2098.sv.vcf.gz.tbi:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-01/out/m84036_250809_035451_s4.bc2098_sawfish/m84036_250809_035451_s4.bc2098.sv.vcf.gz:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2098.sv.vcf.gz:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-01/_singularity_tmpdir_u3l5q1ts/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-01/_singularity_tmpdir_u3l5q1ts/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:56.727 wdl.w:ptcp.w:call-paraphase-65.t:call-run_paraphase INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 4, memory_reservation: 8000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:56.727 wdl.w:ptcp.w:call-paraphase-65.t:call-run_paraphase WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:56.729 wdl.w:ptcp.w:call-paraphase-65.t:call-run_paraphase INFO provisioned :: seconds_waited: 0, cpu: 4, mem_bytes: 8000000000
2025-09-15 20:24:56.729 wdl.w:ptcp.w:call-paraphase-65.t:call-run_paraphase INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:56.735 wdl.w:ptcp.t:call-tar_outputs-32 NOTICE task setup :: name: "tar_outputs", source: "./common.wdl", line: 279, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-32", thread: 140609285244480
2025-09-15 20:24:56.748 wdl.w:ptcp.t:call-tar_outputs-01 NOTICE slurm_singularity run :: pid: 1203566, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-01/slurm_singularity.log.txt"
2025-09-15 20:24:56.752 wdl.w:ptcp.w:call-sawfish-51 NOTICE done
2025-09-15 20:24:56.760 wdl.w:ptcp NOTICE finish :: job: "call-sawfish-51"
2025-09-15 20:24:56.761 wdl.w:ptcp INFO output :: job: "call-sawfish-51", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-51/out/m84036_250809_035451_s4.bc2148_sawfish/m84036_250809_035451_s4.bc2148.sv.vcf.gz", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-51/out/m84036_250809_035451_s4.bc2148.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-51/out/m84036_250809_035451_s4.bc2148_sawfish/m84036_250809_035451_s4.bc2148.sv.vcf.gz.tbi", "minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-51/out/m84036_250809_035451_s4.bc2148.minimap2.bam.bai"}
2025-09-15 20:24:56.765 wdl.w:ptcp.t:call-tar_outputs-32 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:56.765 wdl.w:ptcp.t:call-tar_outputs-32 INFO input :: name: "sawfish_vcf_tbi", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2129.sv.vcf.gz.tbi"
2025-09-15 20:24:56.766 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_motifs_waterfall INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2151.motifs_waterfall.trgt_plots.zip"
2025-09-15 20:24:56.766 wdl.w:ptcp.t:call-tar_outputs-32 INFO input :: name: "sawfish_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2129.sv.vcf.gz"
2025-09-15 20:24:56.766 wdl.w:ptcp.t:call-tar_outputs-32 INFO input :: name: "f8_json", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2129.f8inversion.json"
2025-09-15 20:24:56.766 wdl.w:ptcp.t:call-tar_outputs-32 INFO input :: name: "paraphase_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2129.paraphase.bam.bai"
2025-09-15 20:24:56.766 wdl.w:ptcp.t:call-tar_outputs-32 INFO input :: name: "paraphase_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2129.paraphase.bam"
2025-09-15 20:24:56.766 wdl.w:ptcp.t:call-tar_outputs-32 INFO input :: name: "paraphase_json", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2129.paraphase.json"
2025-09-15 20:24:56.766 wdl.w:ptcp.t:call-tar_outputs-32 INFO input :: name: "trgt_spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2129.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:56.766 wdl.w:ptcp.t:call-tar_outputs-32 INFO input :: name: "trgt_spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2129.trgt.sorted.spanning.bam"
2025-09-15 20:24:56.766 wdl.w:ptcp.t:call-tar_outputs-32 INFO input :: name: "trgt_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2129.trgt.vcf"
2025-09-15 20:24:56.766 wdl.w:ptcp.t:call-tar_outputs-32 INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2129.mapped.bam.bai"
2025-09-15 20:24:56.766 wdl.w:ptcp.t:call-tar_outputs-32 INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2129.mapped.bam"
2025-09-15 20:24:56.766 wdl.w:ptcp.t:call-tar_outputs-32 INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2129"
2025-09-15 20:24:56.767 wdl.w:ptcp.t:call-tar_outputs-32 INFO eval :: name: "threads", value: 1
2025-09-15 20:24:56.767 wdl.w:ptcp.t:call-tar_outputs-32 INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:56.767 wdl.w:ptcp.t:call-tar_outputs-32 INFO eval :: name: "disk_size", value: 6
2025-09-15 20:24:56.767 wdl.w:ptcp.t:call-tar_outputs-32 INFO eval :: name: "output_tarball", value: "m84036_250809_035451_s4.bc2129.tar"
2025-09-15 20:24:56.768 wdl.w:ptcp.t:call-tar_outputs-32 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:56.768 wdl.w:ptcp.t:call-tar_outputs-32 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:56.768 wdl.w:ptcp.t:call-tar_outputs-32 INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:56.768 wdl.w:ptcp.t:call-tar_outputs-32 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:56.769 wdl.w:ptcp.w:call-paraphase-78 NOTICE workflow start :: name: "paraphase", source: "./paraphase.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-78"
2025-09-15 20:24:56.782 wdl.w:ptcp.w:call-trgt-41.t:call-trgt_plot_meth_allele NOTICE done
2025-09-15 20:24:56.788 wdl.w:ptcp.w:call-trgt-41 NOTICE finish :: job: "call-trgt_plot_meth_allele"
2025-09-15 20:24:56.788 wdl.w:ptcp.w:call-trgt-41 INFO output :: job: "call-trgt_plot_meth_allele", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-41/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2138.meth_allele.trgt_plots.zip"}
2025-09-15 20:24:56.788 wdl.w:ptcp.w:call-trgt-41 INFO visit :: node: "output-images_meth_allele", values: {"images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-41/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2138.meth_allele.trgt_plots.zip"}
2025-09-15 20:24:56.792 wdl.w:ptcp.w:call-paraphase-78 INFO visit :: node: "decl-annotation_vcf", values: {"annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf"}
2025-09-15 20:24:56.792 wdl.w:ptcp.w:call-paraphase-78 INFO visit :: node: "decl-config_file", values: {"config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml"}
2025-09-15 20:24:56.792 wdl.w:ptcp.w:call-paraphase-78 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:24:56.792 wdl.w:ptcp.w:call-paraphase-78 INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:24:56.792 wdl.w:ptcp.w:call-paraphase-78 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-78/out/m84036_250809_035451_s4.bc2175.mapped.bam"}
2025-09-15 20:24:56.792 wdl.w:ptcp.w:call-paraphase-78 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-78/out/m84036_250809_035451_s4.bc2175.mapped.bam.bai"}
2025-09-15 20:24:56.792 wdl.w:ptcp.w:call-paraphase-78 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:24:56.792 wdl.w:ptcp.w:call-paraphase-78 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:24:56.793 wdl.w:ptcp.w:call-paraphase-78 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2175"}
2025-09-15 20:24:56.793 wdl.w:ptcp.w:call-paraphase-78 INFO visit :: node: "decl-sex", values: {"sex": "F"}
2025-09-15 20:24:56.793 wdl.w:ptcp.w:call-paraphase-78 NOTICE ready :: job: "call-run_paraphase", callee: "run_paraphase"
2025-09-15 20:24:56.793 wdl.w:ptcp.w:call-paraphase-78 INFO input :: job: "call-run_paraphase", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf", "genome_version": "38", "config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-78/out/m84036_250809_035451_s4.bc2175.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-78/out/m84036_250809_035451_s4.bc2175.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2175"}
2025-09-15 20:24:56.795 wdl.w:ptcp.w:call-sawfish-65.t:call-run_sawfish NOTICE task setup :: name: "run_sawfish", source: "./sawfish.wdl", line: 83, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-65/call-run_sawfish", thread: 140609310422592
2025-09-15 20:24:56.814 wdl.w:ptcp.w:call-sawfish-65.t:call-run_sawfish INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:56.814 wdl.w:ptcp.w:call-sawfish-65.t:call-run_sawfish INFO input :: name: "genome_version", value: "38"
2025-09-15 20:24:56.814 wdl.w:ptcp.w:call-sawfish-65.t:call-run_sawfish INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:56.814 wdl.w:ptcp.w:call-sawfish-65.t:call-run_sawfish INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:56.814 wdl.w:ptcp.w:call-sawfish-65.t:call-run_sawfish INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2162.mapped.bam.bai"
2025-09-15 20:24:56.814 wdl.w:ptcp.w:call-sawfish-65.t:call-run_sawfish INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2162.mapped.bam"
2025-09-15 20:24:56.815 wdl.w:ptcp.w:call-sawfish-65.t:call-run_sawfish INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2162"
2025-09-15 20:24:56.815 wdl.w:ptcp.w:call-sawfish-65.t:call-run_sawfish INFO eval :: name: "mem_gb", value: 32
2025-09-15 20:24:56.815 wdl.w:ptcp.w:call-sawfish-65.t:call-run_sawfish INFO eval :: name: "threads", value: 16
2025-09-15 20:24:56.815 wdl.w:ptcp.w:call-sawfish-65.t:call-run_sawfish INFO eval :: name: "disk_size", value: 30
2025-09-15 20:24:56.815 wdl.w:ptcp.w:call-sawfish-65.t:call-run_sawfish INFO eval :: name: "discover_dirname", value: "m84036_250809_035451_s4.bc2162_sawfish_discover"
2025-09-15 20:24:56.815 wdl.w:ptcp.w:call-sawfish-65.t:call-run_sawfish INFO eval :: name: "call_dirname", value: "m84036_250809_035451_s4.bc2162_sawfish"
2025-09-15 20:24:56.815 wdl.w:ptcp.w:call-sawfish-65.t:call-run_sawfish INFO eval :: name: "minimap2_bam_filename", value: "m84036_250809_035451_s4.bc2162.minimap2.bam"
2025-09-15 20:24:56.816 wdl.w:ptcp.w:call-sawfish-65.t:call-run_sawfish INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 16, memory_reservation: 32000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:56.816 wdl.w:ptcp.w:call-sawfish-65.t:call-run_sawfish WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:56.816 wdl.w:ptcp.w:call-sawfish-65.t:call-run_sawfish INFO provisioned :: seconds_waited: 0, cpu: 16, mem_bytes: 32000000000
2025-09-15 20:24:56.816 wdl.w:ptcp.w:call-sawfish-65.t:call-run_sawfish INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:56.823 wdl.w:ptcp.w:call-paraphase-65.t:call-run_paraphase INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-65/call-run_paraphase/_singularity_tmpdir_ahtrcxxq"
2025-09-15 20:24:56.823 wdl.w:ptcp.w:call-paraphase-65.t:call-run_paraphase INFO Slurm invocation: srun --job-name call-run_paraphase --partition compute,compute9 --cpus-per-task 4 --mem 7629M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-65/call-run_paraphase/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-65/call-run_paraphase/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-65/call-run_paraphase/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-65/call-run_paraphase/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/paraphase/paraphase_config.GRCh38.yaml:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/paraphase_config.GRCh38.yaml:ro --bind /ptcp/meta/variant_list/variant_list.GRCh38.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-65/out/m84036_250809_035451_s4.bc2162.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2162.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-65/out/m84036_250809_035451_s4.bc2162.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2162.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-65/call-run_paraphase/_singularity_tmpdir_ahtrcxxq/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-65/call-run_paraphase/_singularity_tmpdir_ahtrcxxq/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:56.831 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:56 [ERROR] - No reads found for TRID=OPDM_ABCD3
2025-09-15 20:24:56.831 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:56 [ERROR] - No reads found for TRID=SCA37_DAB1
2025-09-15 20:24:56.832 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:56 [ERROR] - No reads found for TRID=SCA2_ATXN2
2025-09-15 20:24:56.832 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:56 [ERROR] - No reads found for TRID=OPDM4_RILPL1
2025-09-15 20:24:56.832 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:56 [ERROR] - No reads found for TRID=SCA27B_FGF14
2025-09-15 20:24:56.832 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:56 [ERROR] - No reads found for TRID=OPMD_PABPN1
2025-09-15 20:24:56.832 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:56 [ERROR] - No reads found for TRID=SCA31_BEAN1
2025-09-15 20:24:56.832 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:56 [ERROR] - No reads found for TRID=SCA4_ZFHX3
2025-09-15 20:24:56.832 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:56 [ERROR] - No reads found for TRID=HDL2_JPH3
2025-09-15 20:24:56.832 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:56 [ERROR] - No reads found for TRID=FECD3_TCF4
2025-09-15 20:24:56.832 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:56 [ERROR] - No reads found for TRID=SCA6_CACNA1A
2025-09-15 20:24:56.832 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:56 [ERROR] - No reads found for TRID=OPDM2_GIPC1
2025-09-15 20:24:56.832 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:56 [ERROR] - No reads found for TRID=FRA2A_AFF3
2025-09-15 20:24:56.832 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:56 [ERROR] - No reads found for TRID=SCA3_ATXN3
2025-09-15 20:24:56.832 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:56 [ERROR] - No reads found for TRID=SCA36_NOP56
2025-09-15 20:24:56.843 wdl.w:ptcp.w:call-paraphase-65.t:call-run_paraphase NOTICE slurm_singularity run :: pid: 1203579, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-65/call-run_paraphase/slurm_singularity.log.txt"
2025-09-15 20:24:56.844 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO srun: job 51797831 queued and waiting for resources
2025-09-15 20:24:56.844 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO srun: job 51797831 has been allocated resources
2025-09-15 20:24:56.844 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:56.867 wdl.w:ptcp.w:call-trgt-54.t:call-trgt_plot_motifs_waterfall NOTICE done
2025-09-15 20:24:56.873 wdl.w:ptcp.w:call-trgt-54 NOTICE finish :: job: "call-trgt_plot_motifs_waterfall"
2025-09-15 20:24:56.874 wdl.w:ptcp.w:call-trgt-54 INFO output :: job: "call-trgt_plot_motifs_waterfall", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-54/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2151.motifs_waterfall.trgt_plots.zip"}
2025-09-15 20:24:56.874 wdl.w:ptcp.w:call-trgt-54 INFO visit :: node: "output-images_motifs_waterfall", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-54/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2151.motifs_waterfall.trgt_plots.zip"}
2025-09-15 20:24:56.874 wdl.w:ptcp.w:call-trgt-54 INFO visit :: node: "outputs", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-54/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2151.motifs_waterfall.trgt_plots.zip", "images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-54/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2151.meth_allele.trgt_plots.zip", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-54/call-trgt_genotype/out/m84036_250809_035451_s4.bc2151.trgt.sorted.spanning.bam.bai", "images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-54/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2151.motifs_allele.trgt_plots.zip", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-54/call-trgt_genotype/out/m84036_250809_035451_s4.bc2151.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-54/call-trgt_genotype/out/m84036_250809_035451_s4.bc2151.trgt.vcf", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-54/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2151.repeats.bam", "images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-54/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2151.meth_waterfall.trgt_plots.zip", "reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-54/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2151.repeats.bam.bai"}
2025-09-15 20:24:56.883 wdl.w:ptcp.w:call-trgt-65.t:call-get_reads_overlapping_repeats NOTICE task setup :: name: "get_reads_overlapping_repeats", source: "./trgt.wdl", line: 182, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-65/call-get_reads_overlapping_repeats", thread: 140607683024448
2025-09-15 20:24:56.898 wdl.w:ptcp.w:call-sawfish-65.t:call-run_sawfish INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 10, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-65/call-run_sawfish/_singularity_tmpdir_f9sfv72e"
2025-09-15 20:24:56.898 wdl.w:ptcp.w:call-sawfish-65.t:call-run_sawfish INFO Slurm invocation: srun --job-name call-run_sawfish --partition compute,compute9 --cpus-per-task 16 --mem 30518M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-65/call-run_sawfish/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-65/call-run_sawfish/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-65/call-run_sawfish/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-65/call-run_sawfish/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-65/out/m84036_250809_035451_s4.bc2162.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2162.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-65/out/m84036_250809_035451_s4.bc2162.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2162.mapped.bam:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-65/call-run_sawfish/_singularity_tmpdir_f9sfv72e/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-65/call-run_sawfish/_singularity_tmpdir_f9sfv72e/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:56.900 wdl.w:ptcp.t:call-tar_outputs-32 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 17, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-32/_singularity_tmpdir_ikwhfqp_"
2025-09-15 20:24:56.901 wdl.w:ptcp.w:call-paraphase-60.t:call-run_paraphase.slurm_singularity INFO srun: job 51797832 queued and waiting for resources
2025-09-15 20:24:56.901 wdl.w:ptcp.t:call-tar_outputs-32 INFO Slurm invocation: srun --job-name call-tar_outputs-32 --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-32/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-32/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-32/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-32/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-32/out/m84036_250809_035451_s4.bc2129.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2129.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-32/out/m84036_250809_035451_s4.bc2129.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2129.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-32/out/m84036_250809_035451_s4.bc2129_sawfish/m84036_250809_035451_s4.bc2129.sv.vcf.gz.tbi:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2129.sv.vcf.gz.tbi:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-32/out/m84036_250809_035451_s4.bc2129_sawfish/m84036_250809_035451_s4.bc2129.sv.vcf.gz:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2129.sv.vcf.gz:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-32/out/m84036_250809_035451_s4.bc2129.f8inversion.json:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2129.f8inversion.json:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-32/out/m84036_250809_035451_s4.bc2129_paraphase/m84036_250809_035451_s4.bc2129.paraphase.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2129.paraphase.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-32/out/m84036_250809_035451_s4.bc2129_paraphase/m84036_250809_035451_s4.bc2129.paraphase.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2129.paraphase.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-32/out/m84036_250809_035451_s4.bc2129_paraphase/m84036_250809_035451_s4.bc2129.paraphase.json:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2129.paraphase.json:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-32/out/m84036_250809_035451_s4.bc2129.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2129.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-32/out/m84036_250809_035451_s4.bc2129.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2129.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-32/out/m84036_250809_035451_s4.bc2129.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2129.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-32/_singularity_tmpdir_ikwhfqp_/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-32/_singularity_tmpdir_ikwhfqp_/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:56.901 wdl.w:ptcp.w:call-paraphase-60.t:call-run_paraphase.slurm_singularity INFO srun: job 51797832 has been allocated resources
2025-09-15 20:24:56.902 wdl.w:ptcp.w:call-paraphase-60.t:call-run_paraphase.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:56.906 wdl.w:ptcp.w:call-trgt-49.t:call-trgt_plot_meth_allele.slurm_singularity INFO srun: job 51797833 queued and waiting for resources
2025-09-15 20:24:56.906 wdl.w:ptcp.w:call-trgt-49.t:call-trgt_plot_meth_allele.slurm_singularity INFO srun: job 51797833 has been allocated resources
2025-09-15 20:24:56.907 wdl.w:ptcp.w:call-trgt-49.t:call-trgt_plot_meth_allele.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:56.907 wdl.w:ptcp.w:call-trgt-65.t:call-get_reads_overlapping_repeats INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:56.908 wdl.w:ptcp.w:call-trgt-65.t:call-get_reads_overlapping_repeats INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:56.908 wdl.w:ptcp.w:call-trgt-65.t:call-get_reads_overlapping_repeats INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2162.mapped.bam.bai"
2025-09-15 20:24:56.908 wdl.w:ptcp.w:call-trgt-65.t:call-get_reads_overlapping_repeats INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2162.mapped.bam"
2025-09-15 20:24:56.908 wdl.w:ptcp.w:call-trgt-65.t:call-get_reads_overlapping_repeats INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2162"
2025-09-15 20:24:56.908 wdl.w:ptcp.w:call-trgt-65.t:call-get_reads_overlapping_repeats INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:56.908 wdl.w:ptcp.w:call-trgt-65.t:call-get_reads_overlapping_repeats INFO eval :: name: "expand_size", value: 3000
2025-09-15 20:24:56.908 wdl.w:ptcp.w:call-trgt-65.t:call-get_reads_overlapping_repeats INFO eval :: name: "threads", value: 1
2025-09-15 20:24:56.909 wdl.w:ptcp.w:call-trgt-65.t:call-get_reads_overlapping_repeats INFO eval :: name: "expanded_bed_name", value: "m84036_250809_035451_s4.bc2162.expanded.bed"
2025-09-15 20:24:56.909 wdl.w:ptcp.w:call-trgt-65.t:call-get_reads_overlapping_repeats INFO eval :: name: "disk_size", value: 11
2025-09-15 20:24:56.909 wdl.w:ptcp.w:call-trgt-65.t:call-get_reads_overlapping_repeats INFO eval :: name: "output_name", value: "m84036_250809_035451_s4.bc2162.repeats.bam"
2025-09-15 20:24:56.909 wdl.w:ptcp.w:call-trgt-65.t:call-get_reads_overlapping_repeats INFO eval :: name: "index_name", value: "m84036_250809_035451_s4.bc2162.repeats.bam.bai"
2025-09-15 20:24:56.909 wdl.w:ptcp.w:call-trgt-65.t:call-get_reads_overlapping_repeats INFO eval :: name: "output_name_with_index", value: "m84036_250809_035451_s4.bc2162.repeats.bam##idx##m84036_250809_035451_s4.bc2162.repeats.bam.bai"
2025-09-15 20:24:56.910 wdl.w:ptcp.w:call-trgt-65.t:call-get_reads_overlapping_repeats INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:56.910 wdl.w:ptcp.w:call-trgt-65.t:call-get_reads_overlapping_repeats WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:56.910 wdl.w:ptcp.w:call-trgt-65.t:call-get_reads_overlapping_repeats INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:56.910 wdl.w:ptcp.w:call-trgt-65.t:call-get_reads_overlapping_repeats INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:56.925 wdl.w:ptcp.t:call-tar_outputs-32 NOTICE slurm_singularity run :: pid: 1203592, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-32/slurm_singularity.log.txt"
2025-09-15 20:24:56.925 wdl.w:ptcp.w:call-sawfish-65.t:call-run_sawfish NOTICE slurm_singularity run :: pid: 1203591, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-65/call-run_sawfish/slurm_singularity.log.txt"
2025-09-15 20:24:56.966 wdl.w:ptcp.w:call-trgt-65.t:call-get_reads_overlapping_repeats INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 9, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-65/call-get_reads_overlapping_repeats/_singularity_tmpdir_oa2sbt2q"
2025-09-15 20:24:56.966 wdl.w:ptcp.w:call-trgt-65.t:call-get_reads_overlapping_repeats INFO Slurm invocation: srun --job-name call-get_reads_overlapping_repeats --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-65/call-get_reads_overlapping_repeats/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-65/call-get_reads_overlapping_repeats/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-65/call-get_reads_overlapping_repeats/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-65/call-get_reads_overlapping_repeats/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-65/out/m84036_250809_035451_s4.bc2162.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2162.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-65/out/m84036_250809_035451_s4.bc2162.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2162.mapped.bam:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-65/call-get_reads_overlapping_repeats/_singularity_tmpdir_oa2sbt2q/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-65/call-get_reads_overlapping_repeats/_singularity_tmpdir_oa2sbt2q/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:56.973 wdl.w:ptcp.w:call-trgt-54 NOTICE done
2025-09-15 20:24:56.978 wdl.w:ptcp NOTICE finish :: job: "call-trgt-54"
2025-09-15 20:24:56.978 wdl.w:ptcp INFO output :: job: "call-trgt-54", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-54/out/m84036_250809_035451_s4.bc2151.motifs_waterfall.trgt_plots.zip", "images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-54/out/m84036_250809_035451_s4.bc2151.meth_allele.trgt_plots.zip", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-54/out/m84036_250809_035451_s4.bc2151.trgt.sorted.spanning.bam.bai", "images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-54/out/m84036_250809_035451_s4.bc2151.motifs_allele.trgt_plots.zip", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-54/out/m84036_250809_035451_s4.bc2151.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-54/out/m84036_250809_035451_s4.bc2151.trgt.vcf", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-54/out/m84036_250809_035451_s4.bc2151.repeats.bam", "images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-54/out/m84036_250809_035451_s4.bc2151.meth_waterfall.trgt_plots.zip", "reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-54/out/m84036_250809_035451_s4.bc2151.repeats.bam.bai"}
2025-09-15 20:24:56.982 wdl.w:ptcp.w:call-trgt-65.t:call-get_reads_overlapping_repeats NOTICE slurm_singularity run :: pid: 1203595, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-65/call-get_reads_overlapping_repeats/slurm_singularity.log.txt"
2025-09-15 20:24:56.983 wdl.w:ptcp.w:call-sawfish-78 NOTICE workflow start :: name: "sawfish", source: "./sawfish.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-78"
2025-09-15 20:24:57.000 wdl.w:ptcp.w:call-sawfish-78 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:24:57.000 wdl.w:ptcp.w:call-sawfish-78 INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:24:57.001 wdl.w:ptcp.w:call-sawfish-78 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-78/out/m84036_250809_035451_s4.bc2175.mapped.bam"}
2025-09-15 20:24:57.001 wdl.w:ptcp.w:call-sawfish-78 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-78/out/m84036_250809_035451_s4.bc2175.mapped.bam.bai"}
2025-09-15 20:24:57.001 wdl.w:ptcp.w:call-sawfish-78 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:24:57.001 wdl.w:ptcp.w:call-sawfish-78 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:24:57.001 wdl.w:ptcp.w:call-sawfish-78 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2175"}
2025-09-15 20:24:57.001 wdl.w:ptcp.w:call-sawfish-78 NOTICE ready :: job: "call-run_sawfish", callee: "run_sawfish"
2025-09-15 20:24:57.001 wdl.w:ptcp.w:call-sawfish-78 INFO input :: job: "call-run_sawfish", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-78/out/m84036_250809_035451_s4.bc2175.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-78/out/m84036_250809_035451_s4.bc2175.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2175"}
2025-09-15 20:24:57.007 wdl.w:ptcp.w:call-trgt-49.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO srun: job 51797834 queued and waiting for resources
2025-09-15 20:24:57.008 wdl.w:ptcp.w:call-trgt-49.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO srun: job 51797834 has been allocated resources
2025-09-15 20:24:57.008 wdl.w:ptcp.w:call-trgt-49.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:57.300 wdl.w:ptcp.w:call-trgt-49.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO srun: job 51797835 queued and waiting for resources
2025-09-15 20:24:57.301 wdl.w:ptcp.w:call-trgt-49.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO srun: job 51797835 has been allocated resources
2025-09-15 20:24:57.301 wdl.w:ptcp.w:call-trgt-49.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:57.303 wdl.w:ptcp.w:call-trgt-49.t:call-trgt_plot_motifs_allele.slurm_singularity INFO srun: job 51797836 queued and waiting for resources
2025-09-15 20:24:57.303 wdl.w:ptcp.w:call-trgt-49.t:call-trgt_plot_motifs_allele.slurm_singularity INFO srun: job 51797836 has been allocated resources
2025-09-15 20:24:57.303 wdl.w:ptcp.w:call-trgt-49.t:call-trgt_plot_motifs_allele.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:57.392 wdl.w:ptcp.w:call-paraphase-11.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for cyp21 for sample m84036_250809_035451_s4.bc2108 at 2025-09-15 20:24:11.926747...
2025-09-15 20:24:57.393 wdl.w:ptcp.w:call-paraphase-11.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for cyp21 for sample m84036_250809_035451_s4.bc2108 at 2025-09-15 20:24:12.730602...
2025-09-15 20:24:57.393 wdl.w:ptcp.w:call-paraphase-11.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for hba for sample m84036_250809_035451_s4.bc2108 at 2025-09-15 20:24:19.580587...
2025-09-15 20:24:57.393 wdl.w:ptcp.w:call-paraphase-11.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for hba for sample m84036_250809_035451_s4.bc2108 at 2025-09-15 20:24:19.971406...
2025-09-15 20:24:57.393 wdl.w:ptcp.w:call-paraphase-11.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for gba for sample m84036_250809_035451_s4.bc2108 at 2025-09-15 20:24:32.463944...
2025-09-15 20:24:57.393 wdl.w:ptcp.w:call-paraphase-11.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for gba for sample m84036_250809_035451_s4.bc2108 at 2025-09-15 20:24:33.008467...
2025-09-15 20:24:57.393 wdl.w:ptcp.w:call-paraphase-11.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for hbb for sample m84036_250809_035451_s4.bc2108 at 2025-09-15 20:24:37.453231...
2025-09-15 20:24:57.393 wdl.w:ptcp.w:call-paraphase-11.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for hbb for sample m84036_250809_035451_s4.bc2108 at 2025-09-15 20:24:37.453393...
2025-09-15 20:24:57.393 wdl.w:ptcp.w:call-paraphase-11.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for hbb for sample m84036_250809_035451_s4.bc2108 at 2025-09-15 20:24:38.611666...
2025-09-15 20:24:57.393 wdl.w:ptcp.w:call-paraphase-11.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for hbb for sample m84036_250809_035451_s4.bc2108 at 2025-09-15 20:24:43.490032...
2025-09-15 20:24:57.555 wdl.w:ptcp.w:call-sawfish-44.t:call-run_sawfish INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2141_sawfish/m84036_250809_035451_s4.bc2141.sv.vcf.gz"
2025-09-15 20:24:57.560 wdl.w:ptcp.w:call-sawfish-44.t:call-run_sawfish INFO output :: name: "vcf_tbi", value: "m84036_250809_035451_s4.bc2141_sawfish/m84036_250809_035451_s4.bc2141.sv.vcf.gz.tbi"
2025-09-15 20:24:57.561 wdl.w:ptcp.w:call-sawfish-44.t:call-run_sawfish INFO output :: name: "minimap2_bam", value: "m84036_250809_035451_s4.bc2141.minimap2.bam"
2025-09-15 20:24:57.564 wdl.w:ptcp.w:call-sawfish-44.t:call-run_sawfish INFO output :: name: "minimap2_bam_bai", value: "m84036_250809_035451_s4.bc2141.minimap2.bam.bai"
2025-09-15 20:24:57.566 wdl.w:ptcp.w:call-sawfish-60.t:call-run_sawfish.stderr VERBOSE [M::bam2fq_mainloop] discarded 0 singletons
2025-09-15 20:24:57.566 wdl.w:ptcp.w:call-sawfish-60.t:call-run_sawfish.stderr VERBOSE [M::bam2fq_mainloop] processed 0 reads
2025-09-15 20:24:57.578 wdl.w:ptcp.w:call-trgt-60.t:call-get_reads_overlapping_repeats.slurm_singularity INFO srun: job 51797838 queued and waiting for resources
2025-09-15 20:24:57.578 wdl.w:ptcp.w:call-trgt-60.t:call-get_reads_overlapping_repeats.slurm_singularity INFO srun: job 51797838 has been allocated resources
2025-09-15 20:24:57.578 wdl.w:ptcp.w:call-trgt-60.t:call-get_reads_overlapping_repeats.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:57.581 wdl.w:ptcp.w:call-sawfish-60.t:call-run_sawfish.slurm_singularity INFO srun: job 51797837 queued and waiting for resources
2025-09-15 20:24:57.581 wdl.w:ptcp.w:call-sawfish-60.t:call-run_sawfish.slurm_singularity INFO srun: job 51797837 has been allocated resources
2025-09-15 20:24:57.581 wdl.w:ptcp.w:call-sawfish-60.t:call-run_sawfish.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:57.646 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_plot_meth_allele INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2156.meth_allele.trgt_plots.zip"
2025-09-15 20:24:57.675 wdl.w:ptcp.w:call-trgt-57.t:call-trgt_plot_motifs_allele INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2154.motifs_allele.trgt_plots.zip"
2025-09-15 20:24:57.678 wdl.w:ptcp.w:call-trgt-60.t:call-trgt_genotype.slurm_singularity INFO srun: job 51797839 queued and waiting for resources
2025-09-15 20:24:57.678 wdl.w:ptcp.w:call-trgt-60.t:call-trgt_genotype.slurm_singularity INFO srun: job 51797839 has been allocated resources
2025-09-15 20:24:57.678 wdl.w:ptcp.w:call-trgt-60.t:call-trgt_genotype.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:57.692 wdl.w:ptcp.w:call-trgt-41.t:call-trgt_plot_motifs_waterfall INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2138.motifs_waterfall.trgt_plots.zip"
2025-09-15 20:24:57.716 wdl.w:ptcp.w:call-sawfish-44.t:call-run_sawfish NOTICE done
2025-09-15 20:24:57.723 wdl.w:ptcp.w:call-sawfish-44 NOTICE finish :: job: "call-run_sawfish"
2025-09-15 20:24:57.723 wdl.w:ptcp.w:call-sawfish-44 INFO output :: job: "call-run_sawfish", values: {"minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-44/call-run_sawfish/out/m84036_250809_035451_s4.bc2141.minimap2.bam.bai", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-44/call-run_sawfish/out/m84036_250809_035451_s4.bc2141.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-44/call-run_sawfish/out/m84036_250809_035451_s4.bc2141_sawfish/m84036_250809_035451_s4.bc2141.sv.vcf.gz.tbi", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-44/call-run_sawfish/out/m84036_250809_035451_s4.bc2141_sawfish/m84036_250809_035451_s4.bc2141.sv.vcf.gz"}
2025-09-15 20:24:57.723 wdl.w:ptcp.w:call-sawfish-44 INFO visit :: node: "output-minimap2_bam", values: {"minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-44/call-run_sawfish/out/m84036_250809_035451_s4.bc2141.minimap2.bam"}
2025-09-15 20:24:57.723 wdl.w:ptcp.w:call-sawfish-44 INFO visit :: node: "output-minimap2_bam_bai", values: {"minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-44/call-run_sawfish/out/m84036_250809_035451_s4.bc2141.minimap2.bam.bai"}
2025-09-15 20:24:57.723 wdl.w:ptcp.w:call-sawfish-44 INFO visit :: node: "output-vcf", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-44/call-run_sawfish/out/m84036_250809_035451_s4.bc2141_sawfish/m84036_250809_035451_s4.bc2141.sv.vcf.gz"}
2025-09-15 20:24:57.723 wdl.w:ptcp.w:call-sawfish-44 INFO visit :: node: "output-vcf_tbi", values: {"vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-44/call-run_sawfish/out/m84036_250809_035451_s4.bc2141_sawfish/m84036_250809_035451_s4.bc2141.sv.vcf.gz.tbi"}
2025-09-15 20:24:57.724 wdl.w:ptcp.w:call-sawfish-44 INFO visit :: node: "outputs", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-44/call-run_sawfish/out/m84036_250809_035451_s4.bc2141_sawfish/m84036_250809_035451_s4.bc2141.sv.vcf.gz", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-44/call-run_sawfish/out/m84036_250809_035451_s4.bc2141.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-44/call-run_sawfish/out/m84036_250809_035451_s4.bc2141_sawfish/m84036_250809_035451_s4.bc2141.sv.vcf.gz.tbi", "minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-44/call-run_sawfish/out/m84036_250809_035451_s4.bc2141.minimap2.bam.bai"}
2025-09-15 20:24:57.730 wdl.w:ptcp.w:call-trgt-65.t:call-trgt_genotype NOTICE task setup :: name: "trgt_genotype", source: "./trgt.wdl", line: 272, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-65/call-trgt_genotype", thread: 140610358986304
2025-09-15 20:24:57.735 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_plot_meth_allele NOTICE done
2025-09-15 20:24:57.742 wdl.w:ptcp.w:call-trgt-59 NOTICE finish :: job: "call-trgt_plot_meth_allele"
2025-09-15 20:24:57.742 wdl.w:ptcp.w:call-trgt-59 INFO output :: job: "call-trgt_plot_meth_allele", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-59/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2156.meth_allele.trgt_plots.zip"}
2025-09-15 20:24:57.742 wdl.w:ptcp.w:call-trgt-59 INFO visit :: node: "output-images_meth_allele", values: {"images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-59/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2156.meth_allele.trgt_plots.zip"}
2025-09-15 20:24:57.749 wdl.w:ptcp.w:call-trgt-65.t:call-trgt_genotype INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:57.749 wdl.w:ptcp.w:call-trgt-65.t:call-trgt_genotype INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:57.749 wdl.w:ptcp.w:call-trgt-65.t:call-trgt_genotype INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:57.749 wdl.w:ptcp.w:call-trgt-65.t:call-trgt_genotype INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:57.749 wdl.w:ptcp.w:call-trgt-65.t:call-trgt_genotype INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2162.mapped.bam.bai"
2025-09-15 20:24:57.749 wdl.w:ptcp.w:call-trgt-65.t:call-trgt_genotype INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2162.mapped.bam"
2025-09-15 20:24:57.749 wdl.w:ptcp.w:call-trgt-65.t:call-trgt_genotype INFO input :: name: "sex", value: "F"
2025-09-15 20:24:57.749 wdl.w:ptcp.w:call-trgt-65.t:call-trgt_genotype INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2162"
2025-09-15 20:24:57.750 wdl.w:ptcp.w:call-trgt-65.t:call-trgt_genotype INFO eval :: name: "mem_gb", value: 16
2025-09-15 20:24:57.750 wdl.w:ptcp.w:call-trgt-65.t:call-trgt_genotype INFO eval :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2162.trgt"
2025-09-15 20:24:57.750 wdl.w:ptcp.w:call-trgt-65.t:call-trgt_genotype INFO eval :: name: "threads", value: 8
2025-09-15 20:24:57.750 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_meth_allele NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-55/call-trgt_plot_meth_allele", thread: 140610895857216
2025-09-15 20:24:57.751 wdl.w:ptcp.w:call-trgt-65.t:call-trgt_genotype INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:57.752 wdl.w:ptcp.w:call-trgt-65.t:call-trgt_genotype INFO eval :: name: "karyotype", value: "XX"
2025-09-15 20:24:57.752 wdl.w:ptcp.w:call-trgt-65.t:call-trgt_genotype INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 8, memory_reservation: 16000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:57.752 wdl.w:ptcp.w:call-trgt-65.t:call-trgt_genotype WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:57.753 wdl.w:ptcp.w:call-trgt-65.t:call-trgt_genotype INFO provisioned :: seconds_waited: 0, cpu: 8, mem_bytes: 16000000000
2025-09-15 20:24:57.753 wdl.w:ptcp.w:call-trgt-65.t:call-trgt_genotype INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:57.753 wdl.w:ptcp.t:call-tar_outputs-01.stderr VERBOSE tar: Removing leading `/' from member names
2025-09-15 20:24:57.753 wdl.w:ptcp.t:call-tar_outputs-01.stderr VERBOSE tar: Removing leading `/' from hard link targets
2025-09-15 20:24:57.766 wdl.w:ptcp.t:call-tar_outputs-01.slurm_singularity INFO srun: job 51797840 queued and waiting for resources
2025-09-15 20:24:57.767 wdl.w:ptcp.t:call-tar_outputs-01.slurm_singularity INFO srun: job 51797840 has been allocated resources
2025-09-15 20:24:57.767 wdl.w:ptcp.t:call-tar_outputs-01.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:57.775 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_meth_allele INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:57.775 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_meth_allele INFO input :: name: "waterfall", value: false
2025-09-15 20:24:57.775 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_meth_allele INFO input :: name: "methylation", value: true
2025-09-15 20:24:57.775 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_meth_allele INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:57.775 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_meth_allele INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:57.776 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_meth_allele INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:57.776 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_meth_allele INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2152.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:57.776 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_meth_allele INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2152.trgt.sorted.spanning.bam"
2025-09-15 20:24:57.776 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_meth_allele INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2152.trgt.vcf"
2025-09-15 20:24:57.776 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_meth_allele INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2152"
2025-09-15 20:24:57.776 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_meth_allele INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:57.776 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_meth_allele INFO eval :: name: "plot_type", value: "allele"
2025-09-15 20:24:57.777 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_meth_allele INFO eval :: name: "show", value: "meth"
2025-09-15 20:24:57.777 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_meth_allele INFO eval :: name: "threads", value: 1
2025-09-15 20:24:57.777 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_meth_allele INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:57.777 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_meth_allele INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2152.meth_allele"
2025-09-15 20:24:57.779 wdl.w:ptcp.w:call-sawfish-44 NOTICE done
2025-09-15 20:24:57.780 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_meth_allele INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:57.780 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_meth_allele WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:57.781 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_meth_allele INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:57.781 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_meth_allele INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:57.787 wdl.w:ptcp NOTICE finish :: job: "call-sawfish-44"
2025-09-15 20:24:57.787 wdl.w:ptcp INFO output :: job: "call-sawfish-44", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-44/out/m84036_250809_035451_s4.bc2141_sawfish/m84036_250809_035451_s4.bc2141.sv.vcf.gz", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-44/out/m84036_250809_035451_s4.bc2141.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-44/out/m84036_250809_035451_s4.bc2141_sawfish/m84036_250809_035451_s4.bc2141.sv.vcf.gz.tbi", "minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-44/out/m84036_250809_035451_s4.bc2141.minimap2.bam.bai"}
2025-09-15 20:24:57.788 wdl.w:ptcp NOTICE ready :: job: "call-tar_outputs-44", callee: "tar_outputs"
2025-09-15 20:24:57.788 wdl.w:ptcp INFO input :: job: "call-tar_outputs-44", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "sawfish_vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-44/out/m84036_250809_035451_s4.bc2141_sawfish/m84036_250809_035451_s4.bc2141.sv.vcf.gz.tbi", "sawfish_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-44/out/m84036_250809_035451_s4.bc2141_sawfish/m84036_250809_035451_s4.bc2141.sv.vcf.gz", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-44/out/m84036_250809_035451_s4.bc2141.f8inversion.json", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-44/out/m84036_250809_035451_s4.bc2141_paraphase/m84036_250809_035451_s4.bc2141.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-44/out/m84036_250809_035451_s4.bc2141_paraphase/m84036_250809_035451_s4.bc2141.paraphase.bam", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-44/out/m84036_250809_035451_s4.bc2141_paraphase/m84036_250809_035451_s4.bc2141.paraphase.json", "trgt_spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-44/out/m84036_250809_035451_s4.bc2141.trgt.sorted.spanning.bam.bai", "trgt_spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-44/out/m84036_250809_035451_s4.bc2141.trgt.sorted.spanning.bam", "trgt_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-44/out/m84036_250809_035451_s4.bc2141.trgt.vcf", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-44/out/m84036_250809_035451_s4.bc2141.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-44/out/m84036_250809_035451_s4.bc2141.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2141"}
2025-09-15 20:24:57.799 wdl.w:ptcp.w:call-trgt-78 NOTICE workflow start :: name: "trgt", source: "./trgt.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-78"
2025-09-15 20:24:57.818 wdl.w:ptcp.w:call-trgt-78 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:24:57.819 wdl.w:ptcp.w:call-trgt-78 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-78/out/m84036_250809_035451_s4.bc2175.mapped.bam"}
2025-09-15 20:24:57.819 wdl.w:ptcp.w:call-trgt-78 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-78/out/m84036_250809_035451_s4.bc2175.mapped.bam.bai"}
2025-09-15 20:24:57.819 wdl.w:ptcp.w:call-trgt-78 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:24:57.819 wdl.w:ptcp.w:call-trgt-78 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:24:57.819 wdl.w:ptcp.w:call-trgt-78 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2175"}
2025-09-15 20:24:57.819 wdl.w:ptcp.w:call-trgt-41.t:call-trgt_plot_meth_waterfall INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2138.meth_waterfall.trgt_plots.zip"
2025-09-15 20:24:57.820 wdl.w:ptcp.w:call-trgt-78 INFO visit :: node: "decl-sex", values: {"sex": "F"}
2025-09-15 20:24:57.820 wdl.w:ptcp.w:call-trgt-78 INFO visit :: node: "decl-trgt_bed", values: {"trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"}
2025-09-15 20:24:57.820 wdl.w:ptcp.w:call-trgt-78 NOTICE ready :: job: "call-get_reads_overlapping_repeats", callee: "get_reads_overlapping_repeats"
2025-09-15 20:24:57.820 wdl.w:ptcp.w:call-trgt-78 INFO input :: job: "call-get_reads_overlapping_repeats", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-78/out/m84036_250809_035451_s4.bc2175.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-78/out/m84036_250809_035451_s4.bc2175.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2175"}
2025-09-15 20:24:57.821 wdl.w:ptcp.w:call-trgt-78 NOTICE ready :: job: "call-trgt_genotype", callee: "trgt_genotype"
2025-09-15 20:24:57.821 wdl.w:ptcp.w:call-trgt-78 INFO input :: job: "call-trgt_genotype", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-78/out/m84036_250809_035451_s4.bc2175.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-78/out/m84036_250809_035451_s4.bc2175.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2175"}
2025-09-15 20:24:57.841 wdl.w:ptcp.w:call-trgt-65.t:call-trgt_genotype INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 11, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-65/call-trgt_genotype/_singularity_tmpdir_xaahswr6"
2025-09-15 20:24:57.841 wdl.w:ptcp.w:call-trgt-65.t:call-trgt_genotype INFO Slurm invocation: srun --job-name call-trgt_genotype --partition compute,compute9 --cpus-per-task 8 --mem 15259M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-65/call-trgt_genotype/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-65/call-trgt_genotype/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-65/call-trgt_genotype/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-65/call-trgt_genotype/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-65/out/m84036_250809_035451_s4.bc2162.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2162.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-65/out/m84036_250809_035451_s4.bc2162.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2162.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-65/call-trgt_genotype/_singularity_tmpdir_xaahswr6/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-65/call-trgt_genotype/_singularity_tmpdir_xaahswr6/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:57.842 wdl.w:ptcp.w:call-trgt-57.t:call-trgt_plot_motifs_allele NOTICE done
2025-09-15 20:24:57.848 wdl.w:ptcp.w:call-trgt-57 NOTICE finish :: job: "call-trgt_plot_motifs_allele"
2025-09-15 20:24:57.848 wdl.w:ptcp.w:call-trgt-57 INFO output :: job: "call-trgt_plot_motifs_allele", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-57/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2154.motifs_allele.trgt_plots.zip"}
2025-09-15 20:24:57.848 wdl.w:ptcp.w:call-trgt-57 INFO visit :: node: "output-images_motifs_allele", values: {"images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-57/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2154.motifs_allele.trgt_plots.zip"}
2025-09-15 20:24:57.854 wdl.w:ptcp.w:call-paraphase-65.t:call-run_paraphase.slurm_singularity INFO srun: job 51797841 queued and waiting for resources
2025-09-15 20:24:57.855 wdl.w:ptcp.w:call-paraphase-65.t:call-run_paraphase.slurm_singularity INFO srun: job 51797841 has been allocated resources
2025-09-15 20:24:57.855 wdl.w:ptcp.w:call-paraphase-65.t:call-run_paraphase.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:57.858 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_meth_waterfall NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-55/call-trgt_plot_meth_waterfall", thread: 140613068518976
2025-09-15 20:24:57.859 wdl.w:ptcp.w:call-trgt-41.t:call-trgt_plot_motifs_waterfall NOTICE done
2025-09-15 20:24:57.864 wdl.w:ptcp.w:call-trgt-41 NOTICE finish :: job: "call-trgt_plot_motifs_waterfall"
2025-09-15 20:24:57.864 wdl.w:ptcp.w:call-trgt-41 INFO output :: job: "call-trgt_plot_motifs_waterfall", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-41/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2138.motifs_waterfall.trgt_plots.zip"}
2025-09-15 20:24:57.865 wdl.w:ptcp.w:call-trgt-41 INFO visit :: node: "output-images_motifs_waterfall", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-41/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2138.motifs_waterfall.trgt_plots.zip"}
2025-09-15 20:24:57.875 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_meth_allele INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-55/call-trgt_plot_meth_allele/_singularity_tmpdir_d8mwn25e"
2025-09-15 20:24:57.875 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_meth_allele INFO Slurm invocation: srun --job-name call-trgt_plot_meth_allele --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-55/call-trgt_plot_meth_allele/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-55/call-trgt_plot_meth_allele/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-55/call-trgt_plot_meth_allele/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-55/call-trgt_plot_meth_allele/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-55/call-trgt_genotype/out/m84036_250809_035451_s4.bc2152.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2152.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-55/call-trgt_genotype/out/m84036_250809_035451_s4.bc2152.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2152.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-55/call-trgt_genotype/out/m84036_250809_035451_s4.bc2152.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2152.trgt.sorted.spanning.bam:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-55/call-trgt_plot_meth_allele/_singularity_tmpdir_d8mwn25e/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-55/call-trgt_plot_meth_allele/_singularity_tmpdir_d8mwn25e/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:57.875 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_motifs_allele NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-55/call-trgt_plot_motifs_allele", thread: 140608236680768
2025-09-15 20:24:57.878 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_meth_waterfall INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:57.878 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_meth_waterfall INFO input :: name: "waterfall", value: true
2025-09-15 20:24:57.878 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_meth_waterfall INFO input :: name: "methylation", value: true
2025-09-15 20:24:57.878 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_meth_waterfall INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:57.878 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_meth_waterfall INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:57.878 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_meth_waterfall INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:57.878 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_meth_waterfall INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2152.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:57.878 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_meth_waterfall INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2152.trgt.sorted.spanning.bam"
2025-09-15 20:24:57.878 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_meth_waterfall INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2152.trgt.vcf"
2025-09-15 20:24:57.878 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_meth_waterfall INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2152"
2025-09-15 20:24:57.880 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_meth_waterfall INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:57.880 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_meth_waterfall INFO eval :: name: "plot_type", value: "waterfall"
2025-09-15 20:24:57.881 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_meth_waterfall INFO eval :: name: "show", value: "meth"
2025-09-15 20:24:57.881 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_meth_waterfall INFO eval :: name: "threads", value: 1
2025-09-15 20:24:57.882 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_meth_waterfall INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:57.882 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_meth_waterfall INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2152.meth_waterfall"
2025-09-15 20:24:57.882 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_meth_waterfall INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:57.882 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_meth_waterfall WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:57.883 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_meth_waterfall INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:57.883 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_meth_waterfall INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:57.892 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_meth_allele NOTICE slurm_singularity run :: pid: 1203619, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-55/call-trgt_plot_meth_allele/slurm_singularity.log.txt"
2025-09-15 20:24:57.892 wdl.w:ptcp.w:call-trgt-65.t:call-trgt_genotype NOTICE slurm_singularity run :: pid: 1203618, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-65/call-trgt_genotype/slurm_singularity.log.txt"
2025-09-15 20:24:57.893 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_motifs_allele INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:57.893 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_motifs_allele INFO input :: name: "waterfall", value: false
2025-09-15 20:24:57.893 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_motifs_allele INFO input :: name: "methylation", value: false
2025-09-15 20:24:57.893 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_motifs_allele INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:57.893 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_motifs_allele INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:57.893 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_motifs_allele INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:57.893 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_motifs_allele INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2152.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:57.894 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_motifs_allele INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2152.trgt.sorted.spanning.bam"
2025-09-15 20:24:57.894 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_motifs_allele INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2152.trgt.vcf"
2025-09-15 20:24:57.894 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_motifs_allele INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2152"
2025-09-15 20:24:57.894 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_motifs_allele INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:57.894 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_motifs_allele INFO eval :: name: "plot_type", value: "allele"
2025-09-15 20:24:57.895 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_motifs_allele INFO eval :: name: "show", value: "motifs"
2025-09-15 20:24:57.895 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_motifs_allele INFO eval :: name: "threads", value: 1
2025-09-15 20:24:57.895 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_motifs_allele INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:57.895 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_motifs_allele INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2152.motifs_allele"
2025-09-15 20:24:57.895 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_motifs_allele INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:57.896 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_motifs_allele WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:57.896 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_motifs_allele INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:57.896 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_motifs_allele INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:57.937 wdl.w:ptcp.t:call-tar_outputs-01 INFO output :: name: "sample_tarball", value: "m84036_250809_035451_s4.bc2098.tar"
2025-09-15 20:24:57.938 wdl.w:ptcp.t:call-tar_outputs-32.slurm_singularity INFO srun: job 51797842 queued and waiting for resources
2025-09-15 20:24:57.938 wdl.w:ptcp.t:call-tar_outputs-32.slurm_singularity INFO srun: job 51797842 has been allocated resources
2025-09-15 20:24:57.938 wdl.w:ptcp.w:call-sawfish-65.t:call-run_sawfish.slurm_singularity INFO srun: job 51797843 queued and waiting for resources
2025-09-15 20:24:57.939 wdl.w:ptcp.t:call-tar_outputs-32.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:57.939 wdl.w:ptcp.w:call-sawfish-65.t:call-run_sawfish.slurm_singularity INFO srun: job 51797843 has been allocated resources
2025-09-15 20:24:57.939 wdl.w:ptcp.w:call-sawfish-65.t:call-run_sawfish.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:57.939 wdl.w:ptcp.w:call-sawfish-65.t:call-run_sawfish.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:24:57.974 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_meth_waterfall INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-55/call-trgt_plot_meth_waterfall/_singularity_tmpdir_gebc7i8x"
2025-09-15 20:24:57.974 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_meth_waterfall INFO Slurm invocation: srun --job-name call-trgt_plot_meth_waterfall --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-55/call-trgt_plot_meth_waterfall/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-55/call-trgt_plot_meth_waterfall/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-55/call-trgt_plot_meth_waterfall/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-55/call-trgt_plot_meth_waterfall/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-55/call-trgt_genotype/out/m84036_250809_035451_s4.bc2152.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2152.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-55/call-trgt_genotype/out/m84036_250809_035451_s4.bc2152.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2152.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-55/call-trgt_genotype/out/m84036_250809_035451_s4.bc2152.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2152.trgt.sorted.spanning.bam:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-55/call-trgt_plot_meth_waterfall/_singularity_tmpdir_gebc7i8x/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-55/call-trgt_plot_meth_waterfall/_singularity_tmpdir_gebc7i8x/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:57.980 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_motifs_allele INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-55/call-trgt_plot_motifs_allele/_singularity_tmpdir_aex9hy67"
2025-09-15 20:24:57.980 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_motifs_allele INFO Slurm invocation: srun --job-name call-trgt_plot_motifs_allele --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-55/call-trgt_plot_motifs_allele/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-55/call-trgt_plot_motifs_allele/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-55/call-trgt_plot_motifs_allele/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-55/call-trgt_plot_motifs_allele/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-55/call-trgt_genotype/out/m84036_250809_035451_s4.bc2152.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2152.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-55/call-trgt_genotype/out/m84036_250809_035451_s4.bc2152.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2152.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-55/call-trgt_genotype/out/m84036_250809_035451_s4.bc2152.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2152.trgt.sorted.spanning.bam:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-55/call-trgt_plot_motifs_allele/_singularity_tmpdir_aex9hy67/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-55/call-trgt_plot_motifs_allele/_singularity_tmpdir_aex9hy67/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:57.993 wdl.w:ptcp.w:call-trgt-41.t:call-trgt_plot_meth_waterfall NOTICE done
2025-09-15 20:24:57.993 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_meth_waterfall NOTICE slurm_singularity run :: pid: 1203622, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-55/call-trgt_plot_meth_waterfall/slurm_singularity.log.txt"
2025-09-15 20:24:57.993 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_motifs_allele NOTICE slurm_singularity run :: pid: 1203623, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-55/call-trgt_plot_motifs_allele/slurm_singularity.log.txt"
2025-09-15 20:24:57.995 wdl.w:ptcp.w:call-trgt-65.t:call-get_reads_overlapping_repeats.slurm_singularity INFO srun: job 51797844 queued and waiting for resources
2025-09-15 20:24:57.995 wdl.w:ptcp.w:call-trgt-65.t:call-get_reads_overlapping_repeats.slurm_singularity INFO srun: job 51797844 has been allocated resources
2025-09-15 20:24:57.995 wdl.w:ptcp.w:call-trgt-65.t:call-get_reads_overlapping_repeats.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:57.996 wdl.w:ptcp.w:call-trgt-65.t:call-get_reads_overlapping_repeats.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:24:57.998 wdl.w:ptcp.w:call-trgt-41 NOTICE finish :: job: "call-trgt_plot_meth_waterfall"
2025-09-15 20:24:57.998 wdl.w:ptcp.w:call-trgt-41 INFO output :: job: "call-trgt_plot_meth_waterfall", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-41/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2138.meth_waterfall.trgt_plots.zip"}
2025-09-15 20:24:57.999 wdl.w:ptcp.w:call-trgt-41 INFO visit :: node: "output-images_meth_waterfall", values: {"images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-41/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2138.meth_waterfall.trgt_plots.zip"}
2025-09-15 20:24:57.999 wdl.w:ptcp.w:call-trgt-41 INFO visit :: node: "outputs", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-41/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2138.motifs_waterfall.trgt_plots.zip", "images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-41/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2138.meth_allele.trgt_plots.zip", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-41/call-trgt_genotype/out/m84036_250809_035451_s4.bc2138.trgt.sorted.spanning.bam.bai", "images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-41/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2138.motifs_allele.trgt_plots.zip", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-41/call-trgt_genotype/out/m84036_250809_035451_s4.bc2138.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-41/call-trgt_genotype/out/m84036_250809_035451_s4.bc2138.trgt.vcf", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-41/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2138.repeats.bam", "images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-41/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2138.meth_waterfall.trgt_plots.zip", "reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-41/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2138.repeats.bam.bai"}
2025-09-15 20:24:58.003 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_motifs_waterfall NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-55/call-trgt_plot_motifs_waterfall", thread: 140611944420928
2025-09-15 20:24:58.010 wdl.w:ptcp.t:call-tar_outputs-01 NOTICE done
2025-09-15 20:24:58.015 wdl.w:ptcp NOTICE finish :: job: "call-tar_outputs-01"
2025-09-15 20:24:58.015 wdl.w:ptcp INFO output :: job: "call-tar_outputs-01", values: {"sample_tarball": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-01/out/m84036_250809_035451_s4.bc2098.tar"}
2025-09-15 20:24:58.024 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_motifs_waterfall INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:58.024 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_motifs_waterfall INFO input :: name: "waterfall", value: true
2025-09-15 20:24:58.024 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_motifs_waterfall INFO input :: name: "methylation", value: false
2025-09-15 20:24:58.024 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_motifs_waterfall INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:58.024 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_motifs_waterfall INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:58.024 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_motifs_waterfall INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:58.024 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_motifs_waterfall INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2152.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:58.024 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_motifs_waterfall INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2152.trgt.sorted.spanning.bam"
2025-09-15 20:24:58.024 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_motifs_waterfall INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2152.trgt.vcf"
2025-09-15 20:24:58.024 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_motifs_waterfall INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2152"
2025-09-15 20:24:58.025 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:58.024 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_plot_meth_allele NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-43/call-trgt_plot_meth_allele", thread: 140607112582720
2025-09-15 20:24:58.025 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "plot_type", value: "waterfall"
2025-09-15 20:24:58.025 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "show", value: "motifs"
2025-09-15 20:24:58.026 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "threads", value: 1
2025-09-15 20:24:58.026 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:58.026 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2152.motifs_waterfall"
2025-09-15 20:24:58.026 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_motifs_waterfall INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:58.027 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_motifs_waterfall WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:58.027 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_motifs_waterfall INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:58.027 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_motifs_waterfall INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:58.040 wdl.w:ptcp.w:call-paraphase-62.t:call-run_paraphase.stderr VERBOSE INFO:root:Processing sample m84036_250809_035451_s4.bc2159 at 2025-09-15 20:24:46.933629...
2025-09-15 20:24:58.042 wdl.w:ptcp.w:call-paraphase-62.t:call-run_paraphase.stderr VERBOSE INFO:root:Checking sample sex at 2025-09-15 20:24:46.935876...
2025-09-15 20:24:58.042 wdl.w:ptcp.w:call-paraphase-62.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for cyp21 for sample m84036_250809_035451_s4.bc2159 at 2025-09-15 20:24:47.029714...
2025-09-15 20:24:58.042 wdl.w:ptcp.w:call-paraphase-62.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for cyp21 for sample m84036_250809_035451_s4.bc2159 at 2025-09-15 20:24:47.030125...
2025-09-15 20:24:58.042 wdl.w:ptcp.w:call-paraphase-62.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for smn1 for sample m84036_250809_035451_s4.bc2159 at 2025-09-15 20:24:47.029857...
2025-09-15 20:24:58.042 wdl.w:ptcp.w:call-paraphase-62.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for smn1 for sample m84036_250809_035451_s4.bc2159 at 2025-09-15 20:24:47.030252...
2025-09-15 20:24:58.042 wdl.w:ptcp.w:call-paraphase-62.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for hba for sample m84036_250809_035451_s4.bc2159 at 2025-09-15 20:24:47.029999...
2025-09-15 20:24:58.042 wdl.w:ptcp.w:call-paraphase-62.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for gba for sample m84036_250809_035451_s4.bc2159 at 2025-09-15 20:24:47.030007...
2025-09-15 20:24:58.042 wdl.w:ptcp.w:call-paraphase-62.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for hba for sample m84036_250809_035451_s4.bc2159 at 2025-09-15 20:24:47.030384...
2025-09-15 20:24:58.042 wdl.w:ptcp.w:call-paraphase-62.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for gba for sample m84036_250809_035451_s4.bc2159 at 2025-09-15 20:24:47.030421...
2025-09-15 20:24:58.064 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_plot_meth_allele INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:58.064 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_plot_meth_allele INFO input :: name: "waterfall", value: false
2025-09-15 20:24:58.065 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_plot_meth_allele INFO input :: name: "methylation", value: true
2025-09-15 20:24:58.065 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_plot_meth_allele INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:58.065 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_plot_meth_allele INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:58.065 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_plot_meth_allele INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:58.065 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_plot_meth_allele INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2140.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:58.065 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_plot_meth_allele INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2140.trgt.sorted.spanning.bam"
2025-09-15 20:24:58.065 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_plot_meth_allele INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2140.trgt.vcf"
2025-09-15 20:24:58.065 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_plot_meth_allele INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2140"
2025-09-15 20:24:58.065 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_plot_meth_allele INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:58.065 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_plot_meth_allele INFO eval :: name: "plot_type", value: "allele"
2025-09-15 20:24:58.065 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_plot_meth_allele INFO eval :: name: "show", value: "meth"
2025-09-15 20:24:58.066 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_plot_meth_allele INFO eval :: name: "threads", value: 1
2025-09-15 20:24:58.066 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_plot_meth_allele INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:58.066 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_plot_meth_allele INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2140.meth_allele"
2025-09-15 20:24:58.066 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_plot_meth_allele INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:58.067 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_plot_meth_allele WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:58.067 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_plot_meth_allele INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:58.067 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_plot_meth_allele INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:58.124 wdl.w:ptcp.w:call-trgt-41 NOTICE done
2025-09-15 20:24:58.134 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_motifs_waterfall INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-55/call-trgt_plot_motifs_waterfall/_singularity_tmpdir__z7x5ldr"
2025-09-15 20:24:58.135 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_motifs_waterfall INFO Slurm invocation: srun --job-name call-trgt_plot_motifs_waterfall --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-55/call-trgt_plot_motifs_waterfall/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-55/call-trgt_plot_motifs_waterfall/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-55/call-trgt_plot_motifs_waterfall/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-55/call-trgt_plot_motifs_waterfall/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-55/call-trgt_genotype/out/m84036_250809_035451_s4.bc2152.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2152.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-55/call-trgt_genotype/out/m84036_250809_035451_s4.bc2152.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2152.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-55/call-trgt_genotype/out/m84036_250809_035451_s4.bc2152.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2152.trgt.sorted.spanning.bam:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-55/call-trgt_plot_motifs_waterfall/_singularity_tmpdir__z7x5ldr/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-55/call-trgt_plot_motifs_waterfall/_singularity_tmpdir__z7x5ldr/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:58.159 wdl.w:ptcp NOTICE finish :: job: "call-trgt-41"
2025-09-15 20:24:58.159 wdl.w:ptcp INFO output :: job: "call-trgt-41", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-41/out/m84036_250809_035451_s4.bc2138.motifs_waterfall.trgt_plots.zip", "images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-41/out/m84036_250809_035451_s4.bc2138.meth_allele.trgt_plots.zip", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-41/out/m84036_250809_035451_s4.bc2138.trgt.sorted.spanning.bam.bai", "images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-41/out/m84036_250809_035451_s4.bc2138.motifs_allele.trgt_plots.zip", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-41/out/m84036_250809_035451_s4.bc2138.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-41/out/m84036_250809_035451_s4.bc2138.trgt.vcf", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-41/out/m84036_250809_035451_s4.bc2138.repeats.bam", "images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-41/out/m84036_250809_035451_s4.bc2138.meth_waterfall.trgt_plots.zip", "reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-41/out/m84036_250809_035451_s4.bc2138.repeats.bam.bai"}
2025-09-15 20:24:58.165 wdl.w:ptcp.w:call-paraphase-84 NOTICE workflow start :: name: "paraphase", source: "./paraphase.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-84"
2025-09-15 20:24:58.167 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_plot_meth_allele INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-43/call-trgt_plot_meth_allele/_singularity_tmpdir_c6m5kduu"
2025-09-15 20:24:58.168 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_plot_meth_allele INFO Slurm invocation: srun --job-name call-trgt_plot_meth_allele --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-43/call-trgt_plot_meth_allele/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-43/call-trgt_plot_meth_allele/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-43/call-trgt_plot_meth_allele/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-43/call-trgt_plot_meth_allele/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-43/call-trgt_genotype/out/m84036_250809_035451_s4.bc2140.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2140.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-43/call-trgt_genotype/out/m84036_250809_035451_s4.bc2140.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2140.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-43/call-trgt_genotype/out/m84036_250809_035451_s4.bc2140.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2140.trgt.sorted.spanning.bam.bai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-43/call-trgt_plot_meth_allele/_singularity_tmpdir_c6m5kduu/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-43/call-trgt_plot_meth_allele/_singularity_tmpdir_c6m5kduu/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:58.175 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_motifs_waterfall NOTICE slurm_singularity run :: pid: 1203626, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-55/call-trgt_plot_motifs_waterfall/slurm_singularity.log.txt"
2025-09-15 20:24:58.175 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_plot_meth_allele NOTICE slurm_singularity run :: pid: 1203627, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-43/call-trgt_plot_meth_allele/slurm_singularity.log.txt"
2025-09-15 20:24:58.181 wdl.w:ptcp.w:call-paraphase-84 INFO visit :: node: "decl-annotation_vcf", values: {"annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf"}
2025-09-15 20:24:58.182 wdl.w:ptcp.w:call-paraphase-84 INFO visit :: node: "decl-config_file", values: {"config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml"}
2025-09-15 20:24:58.182 wdl.w:ptcp.w:call-paraphase-84 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:24:58.182 wdl.w:ptcp.w:call-paraphase-84 INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:24:58.182 wdl.w:ptcp.w:call-paraphase-84 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-84/out/m84036_250809_035451_s4.bc2181.mapped.bam"}
2025-09-15 20:24:58.182 wdl.w:ptcp.w:call-paraphase-84 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-84/out/m84036_250809_035451_s4.bc2181.mapped.bam.bai"}
2025-09-15 20:24:58.182 wdl.w:ptcp.w:call-paraphase-84 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:24:58.182 wdl.w:ptcp.w:call-paraphase-84 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:24:58.182 wdl.w:ptcp.w:call-paraphase-84 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2181"}
2025-09-15 20:24:58.182 wdl.w:ptcp.w:call-paraphase-84 INFO visit :: node: "decl-sex", values: {"sex": "F"}
2025-09-15 20:24:58.182 wdl.w:ptcp.w:call-paraphase-84 NOTICE ready :: job: "call-run_paraphase", callee: "run_paraphase"
2025-09-15 20:24:58.183 wdl.w:ptcp.w:call-paraphase-84 INFO input :: job: "call-run_paraphase", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf", "genome_version": "38", "config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-84/out/m84036_250809_035451_s4.bc2181.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-84/out/m84036_250809_035451_s4.bc2181.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2181"}
2025-09-15 20:24:58.204 wdl.w:ptcp.w:call-sawfish-11.t:call-run_sawfish.stderr VERBOSE [M::mm_mapopt_update::77.877*1.72] mid_occ = 136
2025-09-15 20:24:58.204 wdl.w:ptcp.w:call-sawfish-11.t:call-run_sawfish.stderr VERBOSE [M::mm_idx_stat] kmer size: 19; skip: 19; is_hpc: 0; #seq: 195
2025-09-15 20:24:58.204 wdl.w:ptcp.w:call-sawfish-11.t:call-run_sawfish.stderr VERBOSE [M::mm_idx_stat::83.006*1.68] distinct minimizers: 214664461 (92.23% are singletons); average occurrences: 1.372; average spacing: 10.529; total length: 3099922541
2025-09-15 20:24:58.204 wdl.w:ptcp.w:call-sawfish-11.t:call-run_sawfish.stderr VERBOSE [M::bam2fq_mainloop] discarded 0 singletons
2025-09-15 20:24:58.204 wdl.w:ptcp.w:call-sawfish-11.t:call-run_sawfish.stderr VERBOSE [M::bam2fq_mainloop] processed 262 reads
2025-09-15 20:24:58.204 wdl.w:ptcp.w:call-sawfish-11.t:call-run_sawfish.stderr VERBOSE [M::worker_pipeline::83.581*1.68] mapped 262 sequences
2025-09-15 20:24:58.204 wdl.w:ptcp.w:call-sawfish-11.t:call-run_sawfish.stderr VERBOSE [M::main] Version: 2.26-r1175
2025-09-15 20:24:58.204 wdl.w:ptcp.w:call-sawfish-11.t:call-run_sawfish.stderr VERBOSE [M::main] CMD: /opt/pacbio/smrttools/install/smrtlink-release_25.1.0.257715/bundles/smrttools/install/smrttools-release_25.1.0.257715/private/thirdparty/minimap2/minimap2_2.26-pacbio2/binwrap/../../../../../private/thirdparty/minimap2/minimap2_2.26-pacbio2/bin/minimap2 -a -y -x map-hifi -Y -E 1,0 /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa -
2025-09-15 20:24:58.204 wdl.w:ptcp.w:call-sawfish-11.t:call-run_sawfish.stderr VERBOSE [M::main] Real time: 83.776 sec; CPU: 140.776 sec; Peak RSS: 11.886 GB
2025-09-15 20:24:58.368 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:55 [ERROR] - No reads found for TRID=SCA37_DAB1
2025-09-15 20:24:58.369 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:55 [ERROR] - No reads found for TRID=SCA2_ATXN2
2025-09-15 20:24:58.369 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:55 [ERROR] - No reads found for TRID=OPDM4_RILPL1
2025-09-15 20:24:58.369 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:55 [ERROR] - No reads found for TRID=SCA27B_FGF14
2025-09-15 20:24:58.369 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:55 [ERROR] - No reads found for TRID=OPMD_PABPN1
2025-09-15 20:24:58.369 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:55 [ERROR] - No reads found for TRID=SCA31_BEAN1
2025-09-15 20:24:58.369 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:55 [ERROR] - No reads found for TRID=SCA4_ZFHX3
2025-09-15 20:24:58.369 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:55 [ERROR] - No reads found for TRID=HDL2_JPH3
2025-09-15 20:24:58.369 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:55 [ERROR] - No reads found for TRID=FECD3_TCF4
2025-09-15 20:24:58.369 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:55 [ERROR] - No reads found for TRID=SCA6_CACNA1A
2025-09-15 20:24:58.369 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:55 [ERROR] - No reads found for TRID=OPDM2_GIPC1
2025-09-15 20:24:58.369 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:55 [ERROR] - No reads found for TRID=FRA2A_AFF3
2025-09-15 20:24:58.369 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:55 [ERROR] - No reads found for TRID=SCA3_ATXN3
2025-09-15 20:24:58.369 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:56 [ERROR] - No reads found for TRID=SCA36_NOP56
2025-09-15 20:24:58.369 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:56 [ERROR] - No reads found for TRID=CJD_PRNP
2025-09-15 20:24:58.369 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:56 [ERROR] - No reads found for TRID=EPM1_CSTB
2025-09-15 20:24:58.369 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:56 [ERROR] - No reads found for TRID=DM1_DMPK
2025-09-15 20:24:58.369 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:56 [ERROR] - No reads found for TRID=SCA7_ATXN7
2025-09-15 20:24:58.370 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:56 [ERROR] - No reads found for TRID=SD5_HOXD13
2025-09-15 20:24:58.370 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:56 [ERROR] - No reads found for TRID=HD_HTT
2025-09-15 20:24:58.370 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:56 [ERROR] - No reads found for TRID=CCHS_PHOX2B
2025-09-15 20:24:58.370 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:56 [ERROR] - No reads found for TRID=SCA1_ATXN1
2025-09-15 20:24:58.370 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:56 [ERROR] - No reads found for TRID=SCA12_PPP2R2B
2025-09-15 20:24:58.370 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:56 [ERROR] - No reads found for TRID=OPDM1_LRP12
2025-09-15 20:24:58.370 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:56 [ERROR] - No reads found for TRID=FAME1_SAMD12
2025-09-15 20:24:58.370 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:56 [ERROR] - No reads found for TRID=FTDALS1_C9orf72
2025-09-15 20:24:58.420 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_plot_motifs_allele INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2156.motifs_allele.trgt_plots.zip"
2025-09-15 20:24:58.442 wdl.w:ptcp.w:call-trgt-40.t:call-trgt_plot_motifs_waterfall INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2137.motifs_waterfall.trgt_plots.zip"
2025-09-15 20:24:58.510 wdl.w:ptcp.w:call-paraphase-43.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for hba for sample m84036_250809_035451_s4.bc2140 at 2025-09-15 20:24:46.981679...
2025-09-15 20:24:58.511 wdl.w:ptcp.w:call-paraphase-43.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for smn1 for sample m84036_250809_035451_s4.bc2140 at 2025-09-15 20:24:47.241583...
2025-09-15 20:24:58.511 wdl.w:ptcp.w:call-paraphase-43.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for gba for sample m84036_250809_035451_s4.bc2140 at 2025-09-15 20:24:47.459497...
2025-09-15 20:24:58.511 wdl.w:ptcp.w:call-paraphase-43.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for cyp21 for sample m84036_250809_035451_s4.bc2140 at 2025-09-15 20:24:47.814075...
2025-09-15 20:24:58.511 wdl.w:ptcp.w:call-paraphase-43.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for smn1 for sample m84036_250809_035451_s4.bc2140 at 2025-09-15 20:24:57.541536...
2025-09-15 20:24:58.512 wdl.w:ptcp.w:call-paraphase-43.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning to gene2 region for smn1 for sample m84036_250809_035451_s4.bc2140 at 2025-09-15 20:24:58.091130...
2025-09-15 20:24:58.536 wdl.w:ptcp.t:call-tar_outputs-32 INFO output :: name: "sample_tarball", value: "m84036_250809_035451_s4.bc2129.tar"
2025-09-15 20:24:58.540 wdl.w:ptcp.w:call-trgt-40.t:call-trgt_plot_meth_allele INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2137.meth_allele.trgt_plots.zip"
2025-09-15 20:24:58.563 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_plot_motifs_allele NOTICE done
2025-09-15 20:24:58.569 wdl.w:ptcp.w:call-trgt-59 NOTICE finish :: job: "call-trgt_plot_motifs_allele"
2025-09-15 20:24:58.569 wdl.w:ptcp.w:call-trgt-59 INFO output :: job: "call-trgt_plot_motifs_allele", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-59/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2156.motifs_allele.trgt_plots.zip"}
2025-09-15 20:24:58.570 wdl.w:ptcp.w:call-trgt-59 INFO visit :: node: "output-images_motifs_allele", values: {"images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-59/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2156.motifs_allele.trgt_plots.zip"}
2025-09-15 20:24:58.581 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_plot_meth_waterfall NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-43/call-trgt_plot_meth_waterfall", thread: 140607674631744
2025-09-15 20:24:58.612 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_plot_meth_waterfall INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:58.612 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_plot_meth_waterfall INFO input :: name: "waterfall", value: true
2025-09-15 20:24:58.612 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_plot_meth_waterfall INFO input :: name: "methylation", value: true
2025-09-15 20:24:58.612 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_plot_meth_waterfall INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:58.612 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_plot_meth_waterfall INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:58.612 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_plot_meth_waterfall INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:58.612 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_plot_meth_waterfall INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2140.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:58.612 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_plot_meth_waterfall INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2140.trgt.sorted.spanning.bam"
2025-09-15 20:24:58.612 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_plot_meth_waterfall INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2140.trgt.vcf"
2025-09-15 20:24:58.612 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_plot_meth_waterfall INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2140"
2025-09-15 20:24:58.613 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_plot_meth_waterfall INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:58.613 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_plot_meth_waterfall INFO eval :: name: "plot_type", value: "waterfall"
2025-09-15 20:24:58.613 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_plot_meth_waterfall INFO eval :: name: "show", value: "meth"
2025-09-15 20:24:58.613 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_plot_meth_waterfall INFO eval :: name: "threads", value: 1
2025-09-15 20:24:58.613 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_plot_meth_waterfall INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:58.614 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_plot_meth_waterfall INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2140.meth_waterfall"
2025-09-15 20:24:58.614 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_plot_meth_waterfall INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:58.614 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_plot_meth_waterfall WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:58.615 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_plot_meth_waterfall INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:58.615 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_plot_meth_waterfall INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:58.632 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_plot_motifs_waterfall INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2156.motifs_waterfall.trgt_plots.zip"
2025-09-15 20:24:58.632 wdl.w:ptcp.w:call-paraphase-55.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for hba for sample m84036_250809_035451_s4.bc2152 at 2025-09-15 20:24:46.401132...
2025-09-15 20:24:58.633 wdl.w:ptcp.w:call-paraphase-55.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for smn1 for sample m84036_250809_035451_s4.bc2152 at 2025-09-15 20:24:46.954429...
2025-09-15 20:24:58.633 wdl.w:ptcp.w:call-paraphase-55.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for gba for sample m84036_250809_035451_s4.bc2152 at 2025-09-15 20:24:47.100631...
2025-09-15 20:24:58.633 wdl.w:ptcp.w:call-paraphase-55.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for cyp21 for sample m84036_250809_035451_s4.bc2152 at 2025-09-15 20:24:47.573603...
2025-09-15 20:24:58.633 wdl.w:ptcp.w:call-paraphase-55.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for smn1 for sample m84036_250809_035451_s4.bc2152 at 2025-09-15 20:24:55.769809...
2025-09-15 20:24:58.633 wdl.w:ptcp.w:call-paraphase-55.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning to gene2 region for smn1 for sample m84036_250809_035451_s4.bc2152 at 2025-09-15 20:24:56.389575...
2025-09-15 20:24:58.667 wdl.w:ptcp.t:call-tar_outputs-32 NOTICE done
2025-09-15 20:24:58.667 wdl.w:ptcp.w:call-sawfish-46.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:53][sawfish][INFO] Starting sawfish 2.0.3
2025-09-15 20:24:58.668 wdl.w:ptcp.w:call-sawfish-46.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:53][sawfish][INFO] cmdline: sawfish joint-call --threads 16 --sample m84036_250809_035451_s4.bc2143_sawfish_discover --output-dir m84036_250809_035451_s4.bc2143_sawfish
2025-09-15 20:24:58.668 wdl.w:ptcp.w:call-sawfish-46.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:53][sawfish][INFO] Running on 16 threads
2025-09-15 20:24:58.668 wdl.w:ptcp.w:call-sawfish-46.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:53][sawfish][INFO] Reading reference genome from file '/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa'
2025-09-15 20:24:58.668 wdl.w:ptcp.w:call-sawfish-46.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:56][sawfish][INFO] Reading sawfish-discover results from 1 samples
2025-09-15 20:24:58.668 wdl.w:ptcp.w:call-sawfish-46.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:57][sawfish][INFO] Writing depth track to bigwig file: 'm84036_250809_035451_s4.bc2143_sawfish/samples/sample0001_UnknownSampleName/depth.bw'
2025-09-15 20:24:58.668 wdl.w:ptcp.w:call-sawfish-46.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:57][sawfish][INFO] Merging SV haplotypes
2025-09-15 20:24:58.668 wdl.w:ptcp.w:call-sawfish-46.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:57][sawfish][INFO] Finished merging SV haplotypes across samples
2025-09-15 20:24:58.668 wdl.w:ptcp.w:call-sawfish-46.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:57][sawfish][INFO] Writing merged contig alignments to bam file: 'm84036_250809_035451_s4.bc2143_sawfish/contig.alignment.bam'
2025-09-15 20:24:58.668 wdl.w:ptcp.w:call-sawfish-46.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:57][sawfish][INFO] Starting SV candidate cluster genotyping
2025-09-15 20:24:58.669 wdl.w:ptcp.w:call-sawfish-46.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:58][sawfish][INFO] Finished genotyping all SV candidate clusters
2025-09-15 20:24:58.669 wdl.w:ptcp.w:call-sawfish-46.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:58][sawfish][INFO] Starting joint CNV/SV refinement
2025-09-15 20:24:58.669 wdl.w:ptcp.w:call-sawfish-46.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:58][sawfish][INFO] Merged 0 CNVs into corresponding breakpoint-based SVs
2025-09-15 20:24:58.669 wdl.w:ptcp.w:call-sawfish-46.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:58][sawfish][INFO] Writing genotyped structural variants to file: 'm84036_250809_035451_s4.bc2143_sawfish/genotyped.sv.vcf.gz'
2025-09-15 20:24:58.669 wdl.w:ptcp.w:call-sawfish-46.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:58][sawfish][INFO] Writing run statistics to file: 'm84036_250809_035451_s4.bc2143_sawfish/run.stats.json'
2025-09-15 20:24:58.669 wdl.w:ptcp.w:call-sawfish-46.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:58][sawfish][INFO] sawfish completed. Total Runtime: 00:00:04.122
2025-09-15 20:24:58.673 wdl.w:ptcp NOTICE finish :: job: "call-tar_outputs-32"
2025-09-15 20:24:58.673 wdl.w:ptcp INFO output :: job: "call-tar_outputs-32", values: {"sample_tarball": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-32/out/m84036_250809_035451_s4.bc2129.tar"}
2025-09-15 20:24:58.677 wdl.w:ptcp.w:call-trgt-40.t:call-trgt_plot_motifs_waterfall NOTICE done
2025-09-15 20:24:58.682 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_plot_motifs_allele NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-43/call-trgt_plot_motifs_allele", thread: 140609285244480
2025-09-15 20:24:58.683 wdl.w:ptcp.w:call-trgt-40 NOTICE finish :: job: "call-trgt_plot_motifs_waterfall"
2025-09-15 20:24:58.683 wdl.w:ptcp.w:call-trgt-40 INFO output :: job: "call-trgt_plot_motifs_waterfall", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-40/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2137.motifs_waterfall.trgt_plots.zip"}
2025-09-15 20:24:58.685 wdl.w:ptcp.w:call-trgt-40 INFO visit :: node: "output-images_motifs_waterfall", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-40/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2137.motifs_waterfall.trgt_plots.zip"}
2025-09-15 20:24:58.694 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_plot_motifs_waterfall NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-43/call-trgt_plot_motifs_waterfall", thread: 140609847293504
2025-09-15 20:24:58.704 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_plot_motifs_allele INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:58.704 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_plot_motifs_allele INFO input :: name: "waterfall", value: false
2025-09-15 20:24:58.705 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_plot_motifs_allele INFO input :: name: "methylation", value: false
2025-09-15 20:24:58.705 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_plot_motifs_allele INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:58.705 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_plot_motifs_allele INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:58.705 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_plot_motifs_allele INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:58.705 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_plot_motifs_allele INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2140.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:58.705 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_plot_motifs_allele INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2140.trgt.sorted.spanning.bam"
2025-09-15 20:24:58.705 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_plot_motifs_allele INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2140.trgt.vcf"
2025-09-15 20:24:58.705 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_plot_motifs_allele INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2140"
2025-09-15 20:24:58.705 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_plot_motifs_allele INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:58.706 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_plot_motifs_allele INFO eval :: name: "plot_type", value: "allele"
2025-09-15 20:24:58.707 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_plot_motifs_allele INFO eval :: name: "show", value: "motifs"
2025-09-15 20:24:58.707 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_plot_motifs_allele INFO eval :: name: "threads", value: 1
2025-09-15 20:24:58.707 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_plot_motifs_allele INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:58.707 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_plot_motifs_allele INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2140.motifs_allele"
2025-09-15 20:24:58.708 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_plot_motifs_allele INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:58.709 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_plot_motifs_allele WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:58.710 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_plot_motifs_allele INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:58.710 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_plot_motifs_allele INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:58.720 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_plot_motifs_waterfall INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:58.720 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_plot_motifs_waterfall INFO input :: name: "waterfall", value: true
2025-09-15 20:24:58.721 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_plot_motifs_waterfall INFO input :: name: "methylation", value: false
2025-09-15 20:24:58.721 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_plot_motifs_waterfall INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:58.721 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_plot_motifs_waterfall INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:58.721 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_plot_motifs_waterfall INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:58.721 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_plot_motifs_waterfall INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2140.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:58.721 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_plot_motifs_waterfall INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2140.trgt.sorted.spanning.bam"
2025-09-15 20:24:58.721 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_plot_motifs_waterfall INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2140.trgt.vcf"
2025-09-15 20:24:58.721 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_plot_motifs_waterfall INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2140"
2025-09-15 20:24:58.721 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:58.721 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "plot_type", value: "waterfall"
2025-09-15 20:24:58.722 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "show", value: "motifs"
2025-09-15 20:24:58.722 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "threads", value: 1
2025-09-15 20:24:58.722 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:58.722 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2140.motifs_waterfall"
2025-09-15 20:24:58.722 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_plot_motifs_waterfall INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:58.723 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_plot_motifs_waterfall WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:58.723 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_plot_motifs_waterfall INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:58.723 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_plot_motifs_waterfall INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:58.724 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_plot_meth_waterfall INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-43/call-trgt_plot_meth_waterfall/_singularity_tmpdir_icugs70a"
2025-09-15 20:24:58.725 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_plot_meth_waterfall INFO Slurm invocation: srun --job-name call-trgt_plot_meth_waterfall --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-43/call-trgt_plot_meth_waterfall/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-43/call-trgt_plot_meth_waterfall/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-43/call-trgt_plot_meth_waterfall/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-43/call-trgt_plot_meth_waterfall/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-43/call-trgt_genotype/out/m84036_250809_035451_s4.bc2140.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2140.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-43/call-trgt_genotype/out/m84036_250809_035451_s4.bc2140.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2140.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-43/call-trgt_genotype/out/m84036_250809_035451_s4.bc2140.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2140.trgt.sorted.spanning.bam.bai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-43/call-trgt_plot_meth_waterfall/_singularity_tmpdir_icugs70a/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-43/call-trgt_plot_meth_waterfall/_singularity_tmpdir_icugs70a/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:58.728 wdl.w:ptcp.w:call-sawfish-46.t:call-run_sawfish INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2143_sawfish/m84036_250809_035451_s4.bc2143.sv.vcf.gz"
2025-09-15 20:24:58.734 wdl.w:ptcp.w:call-sawfish-46.t:call-run_sawfish INFO output :: name: "vcf_tbi", value: "m84036_250809_035451_s4.bc2143_sawfish/m84036_250809_035451_s4.bc2143.sv.vcf.gz.tbi"
2025-09-15 20:24:58.737 wdl.w:ptcp.w:call-sawfish-46.t:call-run_sawfish INFO output :: name: "minimap2_bam", value: "m84036_250809_035451_s4.bc2143.minimap2.bam"
2025-09-15 20:24:58.740 wdl.w:ptcp.w:call-sawfish-46.t:call-run_sawfish INFO output :: name: "minimap2_bam_bai", value: "m84036_250809_035451_s4.bc2143.minimap2.bam.bai"
2025-09-15 20:24:58.750 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_plot_motifs_waterfall NOTICE done
2025-09-15 20:24:58.754 wdl.w:ptcp.w:call-trgt-40.t:call-trgt_plot_meth_allele NOTICE done
2025-09-15 20:24:58.757 wdl.w:ptcp.w:call-trgt-59 NOTICE finish :: job: "call-trgt_plot_motifs_waterfall"
2025-09-15 20:24:58.758 wdl.w:ptcp.w:call-trgt-59 INFO output :: job: "call-trgt_plot_motifs_waterfall", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-59/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2156.motifs_waterfall.trgt_plots.zip"}
2025-09-15 20:24:58.758 wdl.w:ptcp.w:call-trgt-59 INFO visit :: node: "output-images_motifs_waterfall", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-59/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2156.motifs_waterfall.trgt_plots.zip"}
2025-09-15 20:24:58.759 wdl.w:ptcp.w:call-trgt-40 NOTICE finish :: job: "call-trgt_plot_meth_allele"
2025-09-15 20:24:58.759 wdl.w:ptcp.w:call-trgt-40 INFO output :: job: "call-trgt_plot_meth_allele", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-40/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2137.meth_allele.trgt_plots.zip"}
2025-09-15 20:24:58.759 wdl.w:ptcp.w:call-trgt-40 INFO visit :: node: "output-images_meth_allele", values: {"images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-40/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2137.meth_allele.trgt_plots.zip"}
2025-09-15 20:24:58.769 wdl.w:ptcp.w:call-paraphase-71.t:call-run_paraphase NOTICE task setup :: name: "run_paraphase", source: "./paraphase.wdl", line: 127, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-71/call-run_paraphase", thread: 140613571819072
2025-09-15 20:24:58.771 wdl.w:ptcp.w:call-trgt-53.t:call-trgt_plot_meth_allele NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-53/call-trgt_plot_meth_allele", thread: 140611415942720
2025-09-15 20:24:58.772 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_plot_meth_waterfall NOTICE slurm_singularity run :: pid: 1203666, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-43/call-trgt_plot_meth_waterfall/slurm_singularity.log.txt"
2025-09-15 20:24:58.798 wdl.w:ptcp.w:call-paraphase-71.t:call-run_paraphase INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:58.799 wdl.w:ptcp.w:call-paraphase-71.t:call-run_paraphase INFO input :: name: "annotation_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf"
2025-09-15 20:24:58.799 wdl.w:ptcp.w:call-paraphase-71.t:call-run_paraphase INFO input :: name: "genome_version", value: "38"
2025-09-15 20:24:58.799 wdl.w:ptcp.w:call-paraphase-71.t:call-run_paraphase INFO input :: name: "config_file", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/paraphase_config.GRCh38.yaml"
2025-09-15 20:24:58.799 wdl.w:ptcp.w:call-paraphase-71.t:call-run_paraphase INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:58.799 wdl.w:ptcp.w:call-paraphase-71.t:call-run_paraphase INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:58.799 wdl.w:ptcp.w:call-paraphase-71.t:call-run_paraphase INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2168.mapped.bam.bai"
2025-09-15 20:24:58.799 wdl.w:ptcp.w:call-paraphase-71.t:call-run_paraphase INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2168.mapped.bam"
2025-09-15 20:24:58.799 wdl.w:ptcp.w:call-paraphase-71.t:call-run_paraphase INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2168"
2025-09-15 20:24:58.799 wdl.w:ptcp.w:call-paraphase-71.t:call-run_paraphase INFO eval :: name: "threads", value: 4
2025-09-15 20:24:58.800 wdl.w:ptcp.w:call-paraphase-71.t:call-run_paraphase INFO eval :: name: "mem_gb", value: 8
2025-09-15 20:24:58.800 wdl.w:ptcp.w:call-paraphase-71.t:call-run_paraphase INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:58.800 wdl.w:ptcp.w:call-paraphase-71.t:call-run_paraphase INFO eval :: name: "out_dir", value: "m84036_250809_035451_s4.bc2168_paraphase"
2025-09-15 20:24:58.801 wdl.w:ptcp.w:call-paraphase-71.t:call-run_paraphase INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 4, memory_reservation: 8000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:58.801 wdl.w:ptcp.w:call-paraphase-71.t:call-run_paraphase WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:58.801 wdl.w:ptcp.w:call-paraphase-71.t:call-run_paraphase INFO provisioned :: seconds_waited: 0, cpu: 4, mem_bytes: 8000000000
2025-09-15 20:24:58.802 wdl.w:ptcp.w:call-paraphase-71.t:call-run_paraphase INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:58.803 wdl.w:ptcp.w:call-trgt-53.t:call-trgt_plot_meth_allele INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:58.803 wdl.w:ptcp.w:call-trgt-53.t:call-trgt_plot_meth_allele INFO input :: name: "waterfall", value: false
2025-09-15 20:24:58.803 wdl.w:ptcp.w:call-trgt-53.t:call-trgt_plot_meth_allele INFO input :: name: "methylation", value: true
2025-09-15 20:24:58.803 wdl.w:ptcp.w:call-trgt-53.t:call-trgt_plot_meth_allele INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:58.803 wdl.w:ptcp.w:call-trgt-53.t:call-trgt_plot_meth_allele INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:58.803 wdl.w:ptcp.w:call-trgt-53.t:call-trgt_plot_meth_allele INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:58.803 wdl.w:ptcp.w:call-trgt-53.t:call-trgt_plot_meth_allele INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2150.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:58.803 wdl.w:ptcp.w:call-trgt-53.t:call-trgt_plot_meth_allele INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2150.trgt.sorted.spanning.bam"
2025-09-15 20:24:58.803 wdl.w:ptcp.w:call-trgt-53.t:call-trgt_plot_meth_allele INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2150.trgt.vcf"
2025-09-15 20:24:58.803 wdl.w:ptcp.w:call-trgt-53.t:call-trgt_plot_meth_allele INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2150"
2025-09-15 20:24:58.803 wdl.w:ptcp.w:call-trgt-53.t:call-trgt_plot_meth_allele INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:58.804 wdl.w:ptcp.w:call-trgt-53.t:call-trgt_plot_meth_allele INFO eval :: name: "plot_type", value: "allele"
2025-09-15 20:24:58.804 wdl.w:ptcp.w:call-trgt-53.t:call-trgt_plot_meth_allele INFO eval :: name: "show", value: "meth"
2025-09-15 20:24:58.804 wdl.w:ptcp.w:call-trgt-53.t:call-trgt_plot_meth_allele INFO eval :: name: "threads", value: 1
2025-09-15 20:24:58.804 wdl.w:ptcp.w:call-trgt-53.t:call-trgt_plot_meth_allele INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:58.804 wdl.w:ptcp.w:call-trgt-53.t:call-trgt_plot_meth_allele INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2150.meth_allele"
2025-09-15 20:24:58.804 wdl.w:ptcp.w:call-trgt-53.t:call-trgt_plot_meth_allele INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:58.805 wdl.w:ptcp.w:call-trgt-53.t:call-trgt_plot_meth_allele WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:58.805 wdl.w:ptcp.w:call-trgt-53.t:call-trgt_plot_meth_allele INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:58.805 wdl.w:ptcp.w:call-trgt-53.t:call-trgt_plot_meth_allele INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:58.811 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_plot_motifs_allele INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-43/call-trgt_plot_motifs_allele/_singularity_tmpdir_e307utkh"
2025-09-15 20:24:58.811 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_plot_motifs_allele INFO Slurm invocation: srun --job-name call-trgt_plot_motifs_allele --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-43/call-trgt_plot_motifs_allele/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-43/call-trgt_plot_motifs_allele/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-43/call-trgt_plot_motifs_allele/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-43/call-trgt_plot_motifs_allele/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-43/call-trgt_genotype/out/m84036_250809_035451_s4.bc2140.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2140.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-43/call-trgt_genotype/out/m84036_250809_035451_s4.bc2140.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2140.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-43/call-trgt_genotype/out/m84036_250809_035451_s4.bc2140.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2140.trgt.sorted.spanning.bam.bai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-43/call-trgt_plot_motifs_allele/_singularity_tmpdir_e307utkh/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-43/call-trgt_plot_motifs_allele/_singularity_tmpdir_e307utkh/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:58.829 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_plot_motifs_waterfall INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-43/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_sw03au2o"
2025-09-15 20:24:58.830 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_plot_motifs_waterfall INFO Slurm invocation: srun --job-name call-trgt_plot_motifs_waterfall --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-43/call-trgt_plot_motifs_waterfall/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-43/call-trgt_plot_motifs_waterfall/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-43/call-trgt_plot_motifs_waterfall/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-43/call-trgt_plot_motifs_waterfall/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-43/call-trgt_genotype/out/m84036_250809_035451_s4.bc2140.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2140.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-43/call-trgt_genotype/out/m84036_250809_035451_s4.bc2140.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2140.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-43/call-trgt_genotype/out/m84036_250809_035451_s4.bc2140.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2140.trgt.sorted.spanning.bam.bai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-43/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_sw03au2o/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-43/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_sw03au2o/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:58.841 wdl.w:ptcp.w:call-trgt-57.t:call-trgt_plot_motifs_waterfall INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2154.motifs_waterfall.trgt_plots.zip"
2025-09-15 20:24:58.849 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_plot_motifs_waterfall NOTICE slurm_singularity run :: pid: 1203670, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-43/call-trgt_plot_motifs_waterfall/slurm_singularity.log.txt"
2025-09-15 20:24:58.852 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_plot_motifs_allele NOTICE slurm_singularity run :: pid: 1203669, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-43/call-trgt_plot_motifs_allele/slurm_singularity.log.txt"
2025-09-15 20:24:58.898 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:58 [ERROR] - No reads found for TRID=SCA37_DAB1
2025-09-15 20:24:58.898 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:58 [ERROR] - No reads found for TRID=OPDM_ABCD3
2025-09-15 20:24:58.898 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:58 [ERROR] - No reads found for TRID=DRPLA_ATN1
2025-09-15 20:24:58.898 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:58 [ERROR] - No reads found for TRID=SCA2_ATXN2
2025-09-15 20:24:58.898 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:58 [ERROR] - No reads found for TRID=OPDM4_RILPL1
2025-09-15 20:24:58.898 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:58 [ERROR] - No reads found for TRID=NIID_NOTCH2NLC
2025-09-15 20:24:58.898 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:58 [ERROR] - No reads found for TRID=SCA8_ATXN8OS
2025-09-15 20:24:58.907 wdl.w:ptcp.w:call-trgt-53.t:call-trgt_plot_meth_allele INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-53/call-trgt_plot_meth_allele/_singularity_tmpdir_92v7la7e"
2025-09-15 20:24:58.908 wdl.w:ptcp.w:call-trgt-53.t:call-trgt_plot_meth_allele INFO Slurm invocation: srun --job-name call-trgt_plot_meth_allele --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-53/call-trgt_plot_meth_allele/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-53/call-trgt_plot_meth_allele/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-53/call-trgt_plot_meth_allele/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-53/call-trgt_plot_meth_allele/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-53/call-trgt_genotype/out/m84036_250809_035451_s4.bc2150.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2150.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-53/call-trgt_genotype/out/m84036_250809_035451_s4.bc2150.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2150.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-53/call-trgt_genotype/out/m84036_250809_035451_s4.bc2150.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2150.trgt.vcf:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-53/call-trgt_plot_meth_allele/_singularity_tmpdir_92v7la7e/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-53/call-trgt_plot_meth_allele/_singularity_tmpdir_92v7la7e/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:58.909 wdl.w:ptcp.w:call-trgt-65.t:call-trgt_genotype.slurm_singularity INFO srun: job 51797845 queued and waiting for resources
2025-09-15 20:24:58.910 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_meth_allele.slurm_singularity INFO srun: job 51797846 queued and waiting for resources
2025-09-15 20:24:58.910 wdl.w:ptcp.w:call-trgt-65.t:call-trgt_genotype.slurm_singularity INFO srun: job 51797845 has been allocated resources
2025-09-15 20:24:58.910 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_meth_allele.slurm_singularity INFO srun: job 51797846 has been allocated resources
2025-09-15 20:24:58.911 wdl.w:ptcp.w:call-trgt-65.t:call-trgt_genotype.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:58.911 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_meth_allele.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:58.911 wdl.w:ptcp.w:call-trgt-65.t:call-trgt_genotype.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:24:58.911 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_meth_allele.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:24:58.918 wdl.w:ptcp.w:call-paraphase-71.t:call-run_paraphase INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-71/call-run_paraphase/_singularity_tmpdir_8bxuj2xf"
2025-09-15 20:24:58.918 wdl.w:ptcp.w:call-paraphase-71.t:call-run_paraphase INFO Slurm invocation: srun --job-name call-run_paraphase --partition compute,compute9 --cpus-per-task 4 --mem 7629M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-71/call-run_paraphase/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-71/call-run_paraphase/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-71/call-run_paraphase/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-71/call-run_paraphase/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-71/out/m84036_250809_035451_s4.bc2168.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2168.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-71/out/m84036_250809_035451_s4.bc2168.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2168.mapped.bam:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/variant_list/variant_list.GRCh38.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf:ro --bind /ptcp/meta/paraphase/paraphase_config.GRCh38.yaml:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/paraphase_config.GRCh38.yaml:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-71/call-run_paraphase/_singularity_tmpdir_8bxuj2xf/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-71/call-run_paraphase/_singularity_tmpdir_8bxuj2xf/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:58.931 wdl.w:ptcp.w:call-trgt-53.t:call-trgt_plot_meth_allele NOTICE slurm_singularity run :: pid: 1203673, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-53/call-trgt_plot_meth_allele/slurm_singularity.log.txt"
2025-09-15 20:24:58.931 wdl.w:ptcp.w:call-paraphase-71.t:call-run_paraphase NOTICE slurm_singularity run :: pid: 1203675, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-71/call-run_paraphase/slurm_singularity.log.txt"
2025-09-15 20:24:58.937 wdl.w:ptcp.w:call-sawfish-46.t:call-run_sawfish NOTICE done
2025-09-15 20:24:58.944 wdl.w:ptcp.w:call-sawfish-46 NOTICE finish :: job: "call-run_sawfish"
2025-09-15 20:24:58.944 wdl.w:ptcp.w:call-sawfish-46 INFO output :: job: "call-run_sawfish", values: {"minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-46/call-run_sawfish/out/m84036_250809_035451_s4.bc2143.minimap2.bam.bai", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-46/call-run_sawfish/out/m84036_250809_035451_s4.bc2143.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-46/call-run_sawfish/out/m84036_250809_035451_s4.bc2143_sawfish/m84036_250809_035451_s4.bc2143.sv.vcf.gz.tbi", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-46/call-run_sawfish/out/m84036_250809_035451_s4.bc2143_sawfish/m84036_250809_035451_s4.bc2143.sv.vcf.gz"}
2025-09-15 20:24:58.944 wdl.w:ptcp.w:call-sawfish-46 INFO visit :: node: "output-minimap2_bam", values: {"minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-46/call-run_sawfish/out/m84036_250809_035451_s4.bc2143.minimap2.bam"}
2025-09-15 20:24:58.944 wdl.w:ptcp.w:call-sawfish-46 INFO visit :: node: "output-minimap2_bam_bai", values: {"minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-46/call-run_sawfish/out/m84036_250809_035451_s4.bc2143.minimap2.bam.bai"}
2025-09-15 20:24:58.945 wdl.w:ptcp.w:call-sawfish-46 INFO visit :: node: "output-vcf", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-46/call-run_sawfish/out/m84036_250809_035451_s4.bc2143_sawfish/m84036_250809_035451_s4.bc2143.sv.vcf.gz"}
2025-09-15 20:24:58.945 wdl.w:ptcp.w:call-sawfish-46 INFO visit :: node: "output-vcf_tbi", values: {"vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-46/call-run_sawfish/out/m84036_250809_035451_s4.bc2143_sawfish/m84036_250809_035451_s4.bc2143.sv.vcf.gz.tbi"}
2025-09-15 20:24:58.945 wdl.w:ptcp.w:call-sawfish-46 INFO visit :: node: "outputs", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-46/call-run_sawfish/out/m84036_250809_035451_s4.bc2143_sawfish/m84036_250809_035451_s4.bc2143.sv.vcf.gz", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-46/call-run_sawfish/out/m84036_250809_035451_s4.bc2143.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-46/call-run_sawfish/out/m84036_250809_035451_s4.bc2143_sawfish/m84036_250809_035451_s4.bc2143.sv.vcf.gz.tbi", "minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-46/call-run_sawfish/out/m84036_250809_035451_s4.bc2143.minimap2.bam.bai"}
2025-09-15 20:24:58.949 wdl.w:ptcp.w:call-trgt-53.t:call-trgt_plot_meth_waterfall NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-53/call-trgt_plot_meth_waterfall", thread: 140612506469952
2025-09-15 20:24:58.967 wdl.w:ptcp.w:call-trgt-53.t:call-trgt_plot_meth_waterfall INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:58.968 wdl.w:ptcp.w:call-trgt-53.t:call-trgt_plot_meth_waterfall INFO input :: name: "waterfall", value: true
2025-09-15 20:24:58.968 wdl.w:ptcp.w:call-trgt-53.t:call-trgt_plot_meth_waterfall INFO input :: name: "methylation", value: true
2025-09-15 20:24:58.968 wdl.w:ptcp.w:call-trgt-53.t:call-trgt_plot_meth_waterfall INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:58.968 wdl.w:ptcp.w:call-trgt-53.t:call-trgt_plot_meth_waterfall INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:58.968 wdl.w:ptcp.w:call-trgt-53.t:call-trgt_plot_meth_waterfall INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:58.968 wdl.w:ptcp.w:call-trgt-53.t:call-trgt_plot_meth_waterfall INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2150.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:58.968 wdl.w:ptcp.w:call-trgt-53.t:call-trgt_plot_meth_waterfall INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2150.trgt.sorted.spanning.bam"
2025-09-15 20:24:58.968 wdl.w:ptcp.w:call-trgt-53.t:call-trgt_plot_meth_waterfall INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2150.trgt.vcf"
2025-09-15 20:24:58.968 wdl.w:ptcp.w:call-trgt-53.t:call-trgt_plot_meth_waterfall INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2150"
2025-09-15 20:24:58.968 wdl.w:ptcp.w:call-trgt-53.t:call-trgt_plot_meth_waterfall INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:58.969 wdl.w:ptcp.w:call-trgt-53.t:call-trgt_plot_meth_waterfall INFO eval :: name: "plot_type", value: "waterfall"
2025-09-15 20:24:58.969 wdl.w:ptcp.w:call-trgt-53.t:call-trgt_plot_meth_waterfall INFO eval :: name: "show", value: "meth"
2025-09-15 20:24:58.969 wdl.w:ptcp.w:call-trgt-53.t:call-trgt_plot_meth_waterfall INFO eval :: name: "threads", value: 1
2025-09-15 20:24:58.969 wdl.w:ptcp.w:call-trgt-53.t:call-trgt_plot_meth_waterfall INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:58.969 wdl.w:ptcp.w:call-trgt-53.t:call-trgt_plot_meth_waterfall INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2150.meth_waterfall"
2025-09-15 20:24:58.969 wdl.w:ptcp.w:call-trgt-53.t:call-trgt_plot_meth_waterfall INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:58.970 wdl.w:ptcp.w:call-trgt-53.t:call-trgt_plot_meth_waterfall WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:58.970 wdl.w:ptcp.w:call-trgt-53.t:call-trgt_plot_meth_waterfall INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:58.970 wdl.w:ptcp.w:call-trgt-53.t:call-trgt_plot_meth_waterfall INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:59.005 wdl.w:ptcp.w:call-sawfish-46 NOTICE done
2025-09-15 20:24:59.009 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_motifs_allele.slurm_singularity INFO srun: job 51797848 queued and waiting for resources
2025-09-15 20:24:59.009 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_motifs_allele.slurm_singularity INFO srun: job 51797848 has been allocated resources
2025-09-15 20:24:59.009 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_motifs_allele.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:59.009 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_motifs_allele.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:24:59.009 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO srun: job 51797847 queued and waiting for resources
2025-09-15 20:24:59.009 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO srun: job 51797847 has been allocated resources
2025-09-15 20:24:59.009 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:59.010 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:24:59.010 wdl.w:ptcp.w:call-trgt-57.t:call-trgt_plot_motifs_waterfall NOTICE done
2025-09-15 20:24:59.012 wdl.w:ptcp NOTICE finish :: job: "call-sawfish-46"
2025-09-15 20:24:59.012 wdl.w:ptcp INFO output :: job: "call-sawfish-46", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-46/out/m84036_250809_035451_s4.bc2143_sawfish/m84036_250809_035451_s4.bc2143.sv.vcf.gz", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-46/out/m84036_250809_035451_s4.bc2143.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-46/out/m84036_250809_035451_s4.bc2143_sawfish/m84036_250809_035451_s4.bc2143.sv.vcf.gz.tbi", "minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-46/out/m84036_250809_035451_s4.bc2143.minimap2.bam.bai"}
2025-09-15 20:24:59.015 wdl.w:ptcp.w:call-trgt-40.t:call-trgt_plot_meth_waterfall INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2137.meth_waterfall.trgt_plots.zip"
2025-09-15 20:24:59.016 wdl.w:ptcp.w:call-trgt-57 NOTICE finish :: job: "call-trgt_plot_motifs_waterfall"
2025-09-15 20:24:59.016 wdl.w:ptcp.w:call-trgt-57 INFO output :: job: "call-trgt_plot_motifs_waterfall", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-57/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2154.motifs_waterfall.trgt_plots.zip"}
2025-09-15 20:24:59.017 wdl.w:ptcp.w:call-trgt-57 INFO visit :: node: "output-images_motifs_waterfall", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-57/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2154.motifs_waterfall.trgt_plots.zip"}
2025-09-15 20:24:59.020 wdl.w:ptcp.w:call-sawfish-18.t:call-run_sawfish.stderr VERBOSE [M::mm_idx_gen::73.129*1.79] sorted minimizers
2025-09-15 20:24:59.020 wdl.w:ptcp.w:call-sawfish-18.t:call-run_sawfish.stderr VERBOSE [M::main::73.130*1.79] loaded/built the index for 195 target sequence(s)
2025-09-15 20:24:59.020 wdl.w:ptcp.w:call-sawfish-18.t:call-run_sawfish.stderr VERBOSE [M::mm_mapopt_update::79.702*1.72] mid_occ = 136
2025-09-15 20:24:59.020 wdl.w:ptcp.w:call-sawfish-18.t:call-run_sawfish.stderr VERBOSE [M::mm_idx_stat] kmer size: 19; skip: 19; is_hpc: 0; #seq: 195
2025-09-15 20:24:59.021 wdl.w:ptcp.w:call-sawfish-18.t:call-run_sawfish.stderr VERBOSE [M::mm_idx_stat::84.848*1.68] distinct minimizers: 214664461 (92.23% are singletons); average occurrences: 1.372; average spacing: 10.529; total length: 3099922541
2025-09-15 20:24:59.021 wdl.w:ptcp.w:call-sawfish-18.t:call-run_sawfish.stderr VERBOSE [M::bam2fq_mainloop] discarded 0 singletons
2025-09-15 20:24:59.021 wdl.w:ptcp.w:call-sawfish-18.t:call-run_sawfish.stderr VERBOSE [M::bam2fq_mainloop] processed 288 reads
2025-09-15 20:24:59.021 wdl.w:ptcp.w:call-sawfish-18.t:call-run_sawfish.stderr VERBOSE [M::worker_pipeline::85.533*1.68] mapped 288 sequences
2025-09-15 20:24:59.021 wdl.w:ptcp.w:call-sawfish-18.t:call-run_sawfish.stderr VERBOSE [M::main] Version: 2.26-r1175
2025-09-15 20:24:59.021 wdl.w:ptcp.w:call-sawfish-18.t:call-run_sawfish.stderr VERBOSE [M::main] CMD: /opt/pacbio/smrttools/install/smrtlink-release_25.1.0.257715/bundles/smrttools/install/smrttools-release_25.1.0.257715/private/thirdparty/minimap2/minimap2_2.26-pacbio2/binwrap/../../../../../private/thirdparty/minimap2/minimap2_2.26-pacbio2/bin/minimap2 -a -y -x map-hifi -Y -E 1,0 /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa -
2025-09-15 20:24:59.021 wdl.w:ptcp.w:call-sawfish-18.t:call-run_sawfish.stderr VERBOSE [M::main] Real time: 85.956 sec; CPU: 144.245 sec; Peak RSS: 11.886 GB
2025-09-15 20:24:59.022 wdl.w:ptcp.w:call-sawfish-84 NOTICE workflow start :: name: "sawfish", source: "./sawfish.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-84"
2025-09-15 20:24:59.037 wdl.w:ptcp.w:call-sawfish-84 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:24:59.038 wdl.w:ptcp.w:call-sawfish-84 INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:24:59.038 wdl.w:ptcp.w:call-sawfish-84 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-84/out/m84036_250809_035451_s4.bc2181.mapped.bam"}
2025-09-15 20:24:59.038 wdl.w:ptcp.w:call-sawfish-84 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-84/out/m84036_250809_035451_s4.bc2181.mapped.bam.bai"}
2025-09-15 20:24:59.038 wdl.w:ptcp.w:call-sawfish-84 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:24:59.038 wdl.w:ptcp.w:call-sawfish-84 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:24:59.038 wdl.w:ptcp.w:call-sawfish-84 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2181"}
2025-09-15 20:24:59.038 wdl.w:ptcp.w:call-sawfish-84 NOTICE ready :: job: "call-run_sawfish", callee: "run_sawfish"
2025-09-15 20:24:59.038 wdl.w:ptcp.w:call-sawfish-84 INFO input :: job: "call-run_sawfish", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-84/out/m84036_250809_035451_s4.bc2181.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-84/out/m84036_250809_035451_s4.bc2181.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2181"}
2025-09-15 20:24:59.041 wdl.w:ptcp.w:call-trgt-53.t:call-trgt_plot_motifs_allele NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-53/call-trgt_plot_motifs_allele", thread: 140610870679104
2025-09-15 20:24:59.049 wdl.w:ptcp.w:call-sawfish-10.t:call-run_sawfish.stderr VERBOSE [M::mm_idx_gen::74.250*1.83] sorted minimizers
2025-09-15 20:24:59.049 wdl.w:ptcp.w:call-sawfish-10.t:call-run_sawfish.stderr VERBOSE [M::main::74.252*1.83] loaded/built the index for 195 target sequence(s)
2025-09-15 20:24:59.054 wdl.w:ptcp.w:call-paraphase-10.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for hba for sample m84036_250809_035451_s4.bc2107 at 2025-09-15 20:24:44.915672...
2025-09-15 20:24:59.055 wdl.w:ptcp.w:call-paraphase-10.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for hba for sample m84036_250809_035451_s4.bc2107 at 2025-09-15 20:24:45.557582...
2025-09-15 20:24:59.063 wdl.w:ptcp.w:call-trgt-53.t:call-trgt_plot_motifs_allele INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:59.064 wdl.w:ptcp.w:call-trgt-53.t:call-trgt_plot_motifs_allele INFO input :: name: "waterfall", value: false
2025-09-15 20:24:59.064 wdl.w:ptcp.w:call-trgt-53.t:call-trgt_plot_motifs_allele INFO input :: name: "methylation", value: false
2025-09-15 20:24:59.064 wdl.w:ptcp.w:call-trgt-53.t:call-trgt_plot_motifs_allele INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:59.064 wdl.w:ptcp.w:call-trgt-53.t:call-trgt_plot_motifs_allele INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:59.064 wdl.w:ptcp.w:call-trgt-53.t:call-trgt_plot_motifs_allele INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:59.064 wdl.w:ptcp.w:call-trgt-53.t:call-trgt_plot_motifs_allele INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2150.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:59.064 wdl.w:ptcp.w:call-trgt-53.t:call-trgt_plot_motifs_allele INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2150.trgt.sorted.spanning.bam"
2025-09-15 20:24:59.064 wdl.w:ptcp.w:call-trgt-53.t:call-trgt_plot_motifs_allele INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2150.trgt.vcf"
2025-09-15 20:24:59.064 wdl.w:ptcp.w:call-trgt-53.t:call-trgt_plot_motifs_allele INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2150"
2025-09-15 20:24:59.064 wdl.w:ptcp.w:call-trgt-53.t:call-trgt_plot_motifs_allele INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:59.064 wdl.w:ptcp.w:call-trgt-53.t:call-trgt_plot_motifs_allele INFO eval :: name: "plot_type", value: "allele"
2025-09-15 20:24:59.065 wdl.w:ptcp.w:call-trgt-53.t:call-trgt_plot_motifs_allele INFO eval :: name: "show", value: "motifs"
2025-09-15 20:24:59.065 wdl.w:ptcp.w:call-trgt-53.t:call-trgt_plot_motifs_allele INFO eval :: name: "threads", value: 1
2025-09-15 20:24:59.065 wdl.w:ptcp.w:call-trgt-53.t:call-trgt_plot_motifs_allele INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:59.065 wdl.w:ptcp.w:call-trgt-53.t:call-trgt_plot_motifs_allele INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2150.motifs_allele"
2025-09-15 20:24:59.065 wdl.w:ptcp.w:call-trgt-53.t:call-trgt_plot_motifs_allele INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:59.066 wdl.w:ptcp.w:call-trgt-53.t:call-trgt_plot_motifs_allele WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:59.066 wdl.w:ptcp.w:call-trgt-53.t:call-trgt_plot_motifs_allele INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:59.066 wdl.w:ptcp.w:call-trgt-53.t:call-trgt_plot_motifs_allele INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:59.073 wdl.w:ptcp.w:call-trgt-53.t:call-trgt_plot_meth_waterfall INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-53/call-trgt_plot_meth_waterfall/_singularity_tmpdir_jm4zzn6b"
2025-09-15 20:24:59.073 wdl.w:ptcp.w:call-trgt-53.t:call-trgt_plot_meth_waterfall INFO Slurm invocation: srun --job-name call-trgt_plot_meth_waterfall --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-53/call-trgt_plot_meth_waterfall/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-53/call-trgt_plot_meth_waterfall/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-53/call-trgt_plot_meth_waterfall/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-53/call-trgt_plot_meth_waterfall/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-53/call-trgt_genotype/out/m84036_250809_035451_s4.bc2150.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2150.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-53/call-trgt_genotype/out/m84036_250809_035451_s4.bc2150.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2150.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-53/call-trgt_genotype/out/m84036_250809_035451_s4.bc2150.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2150.trgt.vcf:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-53/call-trgt_plot_meth_waterfall/_singularity_tmpdir_jm4zzn6b/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-53/call-trgt_plot_meth_waterfall/_singularity_tmpdir_jm4zzn6b/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:59.113 wdl.w:ptcp.w:call-trgt-53.t:call-trgt_plot_meth_waterfall NOTICE slurm_singularity run :: pid: 1203693, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-53/call-trgt_plot_meth_waterfall/slurm_singularity.log.txt"
2025-09-15 20:24:59.148 wdl.w:ptcp.w:call-trgt-53.t:call-trgt_plot_motifs_allele INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-53/call-trgt_plot_motifs_allele/_singularity_tmpdir_mc5x0xuw"
2025-09-15 20:24:59.148 wdl.w:ptcp.w:call-trgt-53.t:call-trgt_plot_motifs_allele INFO Slurm invocation: srun --job-name call-trgt_plot_motifs_allele --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-53/call-trgt_plot_motifs_allele/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-53/call-trgt_plot_motifs_allele/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-53/call-trgt_plot_motifs_allele/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-53/call-trgt_plot_motifs_allele/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-53/call-trgt_genotype/out/m84036_250809_035451_s4.bc2150.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2150.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-53/call-trgt_genotype/out/m84036_250809_035451_s4.bc2150.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2150.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-53/call-trgt_genotype/out/m84036_250809_035451_s4.bc2150.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2150.trgt.vcf:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-53/call-trgt_plot_motifs_allele/_singularity_tmpdir_mc5x0xuw/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-53/call-trgt_plot_motifs_allele/_singularity_tmpdir_mc5x0xuw/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:59.154 wdl.w:ptcp.w:call-trgt-40.t:call-trgt_plot_meth_waterfall NOTICE done
2025-09-15 20:24:59.157 wdl.w:ptcp.w:call-trgt-40 NOTICE finish :: job: "call-trgt_plot_meth_waterfall"
2025-09-15 20:24:59.157 wdl.w:ptcp.w:call-trgt-40 INFO output :: job: "call-trgt_plot_meth_waterfall", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-40/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2137.meth_waterfall.trgt_plots.zip"}
2025-09-15 20:24:59.158 wdl.w:ptcp.w:call-trgt-40 INFO visit :: node: "output-images_meth_waterfall", values: {"images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-40/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2137.meth_waterfall.trgt_plots.zip"}
2025-09-15 20:24:59.158 wdl.w:ptcp.w:call-trgt-40 INFO visit :: node: "outputs", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-40/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2137.motifs_waterfall.trgt_plots.zip", "images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-40/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2137.meth_allele.trgt_plots.zip", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-40/call-trgt_genotype/out/m84036_250809_035451_s4.bc2137.trgt.sorted.spanning.bam.bai", "images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-40/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2137.motifs_allele.trgt_plots.zip", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-40/call-trgt_genotype/out/m84036_250809_035451_s4.bc2137.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-40/call-trgt_genotype/out/m84036_250809_035451_s4.bc2137.trgt.vcf", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-40/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2137.repeats.bam", "images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-40/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2137.meth_waterfall.trgt_plots.zip", "reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-40/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2137.repeats.bam.bai"}
2025-09-15 20:24:59.163 wdl.w:ptcp.w:call-trgt-53.t:call-trgt_plot_motifs_waterfall NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-53/call-trgt_plot_motifs_waterfall", thread: 140611961206336
2025-09-15 20:24:59.165 wdl.w:ptcp.w:call-trgt-53.t:call-trgt_plot_motifs_allele NOTICE slurm_singularity run :: pid: 1203711, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-53/call-trgt_plot_motifs_allele/slurm_singularity.log.txt"
2025-09-15 20:24:59.178 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:58 [ERROR] - No reads found for TRID=SCA37_DAB1
2025-09-15 20:24:59.178 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:59 [ERROR] - No reads found for TRID=OPDM_ABCD3
2025-09-15 20:24:59.178 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:59 [ERROR] - No reads found for TRID=DRPLA_ATN1
2025-09-15 20:24:59.179 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:59 [ERROR] - No reads found for TRID=SCA2_ATXN2
2025-09-15 20:24:59.179 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:58 [ERROR] - No reads found for TRID=OPDM_ABCD3
2025-09-15 20:24:59.179 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:58 [ERROR] - No reads found for TRID=SCA37_DAB1
2025-09-15 20:24:59.179 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:59 [ERROR] - No reads found for TRID=NIID_NOTCH2NLC
2025-09-15 20:24:59.179 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:59 [ERROR] - No reads found for TRID=DRPLA_ATN1
2025-09-15 20:24:59.180 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:59 [ERROR] - No reads found for TRID=SCA2_ATXN2
2025-09-15 20:24:59.182 wdl.w:ptcp.w:call-trgt-53.t:call-trgt_plot_motifs_waterfall INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:59.182 wdl.w:ptcp.w:call-trgt-53.t:call-trgt_plot_motifs_waterfall INFO input :: name: "waterfall", value: true
2025-09-15 20:24:59.182 wdl.w:ptcp.w:call-trgt-53.t:call-trgt_plot_motifs_waterfall INFO input :: name: "methylation", value: false
2025-09-15 20:24:59.182 wdl.w:ptcp.w:call-trgt-53.t:call-trgt_plot_motifs_waterfall INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:59.182 wdl.w:ptcp.w:call-trgt-53.t:call-trgt_plot_motifs_waterfall INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:59.182 wdl.w:ptcp.w:call-trgt-53.t:call-trgt_plot_motifs_waterfall INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:59.182 wdl.w:ptcp.w:call-trgt-53.t:call-trgt_plot_motifs_waterfall INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2150.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:59.182 wdl.w:ptcp.w:call-trgt-53.t:call-trgt_plot_motifs_waterfall INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2150.trgt.sorted.spanning.bam"
2025-09-15 20:24:59.182 wdl.w:ptcp.w:call-trgt-53.t:call-trgt_plot_motifs_waterfall INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2150.trgt.vcf"
2025-09-15 20:24:59.182 wdl.w:ptcp.w:call-trgt-53.t:call-trgt_plot_motifs_waterfall INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2150"
2025-09-15 20:24:59.182 wdl.w:ptcp.w:call-trgt-53.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:59.183 wdl.w:ptcp.w:call-trgt-53.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "plot_type", value: "waterfall"
2025-09-15 20:24:59.183 wdl.w:ptcp.w:call-trgt-53.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "show", value: "motifs"
2025-09-15 20:24:59.183 wdl.w:ptcp.w:call-trgt-53.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "threads", value: 1
2025-09-15 20:24:59.183 wdl.w:ptcp.w:call-trgt-53.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:59.183 wdl.w:ptcp.w:call-trgt-53.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2150.motifs_waterfall"
2025-09-15 20:24:59.183 wdl.w:ptcp.w:call-trgt-53.t:call-trgt_plot_motifs_waterfall INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:59.184 wdl.w:ptcp.w:call-trgt-53.t:call-trgt_plot_motifs_waterfall WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:59.184 wdl.w:ptcp.w:call-trgt-53.t:call-trgt_plot_motifs_waterfall INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:59.184 wdl.w:ptcp.w:call-trgt-53.t:call-trgt_plot_motifs_waterfall INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:59.190 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO srun: job 51797849 queued and waiting for resources
2025-09-15 20:24:59.191 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO srun: job 51797849 has been allocated resources
2025-09-15 20:24:59.191 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:59.191 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:24:59.201 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_plot_meth_waterfall INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2156.meth_waterfall.trgt_plots.zip"
2025-09-15 20:24:59.202 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_plot_meth_allele.slurm_singularity INFO srun: job 51797850 queued and waiting for resources
2025-09-15 20:24:59.202 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_plot_meth_allele.slurm_singularity INFO srun: job 51797850 has been allocated resources
2025-09-15 20:24:59.202 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_plot_meth_allele.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:59.202 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_plot_meth_allele.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:24:59.256 wdl.w:ptcp.w:call-trgt-40 NOTICE done
2025-09-15 20:24:59.261 wdl.w:ptcp NOTICE finish :: job: "call-trgt-40"
2025-09-15 20:24:59.261 wdl.w:ptcp INFO output :: job: "call-trgt-40", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-40/out/m84036_250809_035451_s4.bc2137.motifs_waterfall.trgt_plots.zip", "images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-40/out/m84036_250809_035451_s4.bc2137.meth_allele.trgt_plots.zip", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-40/out/m84036_250809_035451_s4.bc2137.trgt.sorted.spanning.bam.bai", "images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-40/out/m84036_250809_035451_s4.bc2137.motifs_allele.trgt_plots.zip", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-40/out/m84036_250809_035451_s4.bc2137.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-40/out/m84036_250809_035451_s4.bc2137.trgt.vcf", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-40/out/m84036_250809_035451_s4.bc2137.repeats.bam", "images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-40/out/m84036_250809_035451_s4.bc2137.meth_waterfall.trgt_plots.zip", "reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-40/out/m84036_250809_035451_s4.bc2137.repeats.bam.bai"}
2025-09-15 20:24:59.269 wdl.w:ptcp.w:call-trgt-53.t:call-trgt_plot_motifs_waterfall INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-53/call-trgt_plot_motifs_waterfall/_singularity_tmpdir__i4vdbhf"
2025-09-15 20:24:59.269 wdl.w:ptcp.w:call-trgt-53.t:call-trgt_plot_motifs_waterfall INFO Slurm invocation: srun --job-name call-trgt_plot_motifs_waterfall --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-53/call-trgt_plot_motifs_waterfall/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-53/call-trgt_plot_motifs_waterfall/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-53/call-trgt_plot_motifs_waterfall/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-53/call-trgt_plot_motifs_waterfall/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-53/call-trgt_genotype/out/m84036_250809_035451_s4.bc2150.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2150.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-53/call-trgt_genotype/out/m84036_250809_035451_s4.bc2150.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2150.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-53/call-trgt_genotype/out/m84036_250809_035451_s4.bc2150.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2150.trgt.vcf:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-53/call-trgt_plot_motifs_waterfall/_singularity_tmpdir__i4vdbhf/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-53/call-trgt_plot_motifs_waterfall/_singularity_tmpdir__i4vdbhf/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:59.271 wdl.w:ptcp.w:call-trgt-84 NOTICE workflow start :: name: "trgt", source: "./trgt.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-84"
2025-09-15 20:24:59.288 wdl.w:ptcp.w:call-trgt-84 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:24:59.288 wdl.w:ptcp.w:call-trgt-84 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-84/out/m84036_250809_035451_s4.bc2181.mapped.bam"}
2025-09-15 20:24:59.288 wdl.w:ptcp.w:call-trgt-84 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-84/out/m84036_250809_035451_s4.bc2181.mapped.bam.bai"}
2025-09-15 20:24:59.288 wdl.w:ptcp.w:call-trgt-84 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:24:59.288 wdl.w:ptcp.w:call-trgt-84 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:24:59.288 wdl.w:ptcp.w:call-trgt-84 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2181"}
2025-09-15 20:24:59.288 wdl.w:ptcp.w:call-trgt-84 INFO visit :: node: "decl-sex", values: {"sex": "F"}
2025-09-15 20:24:59.288 wdl.w:ptcp.w:call-trgt-84 INFO visit :: node: "decl-trgt_bed", values: {"trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"}
2025-09-15 20:24:59.289 wdl.w:ptcp.w:call-trgt-84 NOTICE ready :: job: "call-get_reads_overlapping_repeats", callee: "get_reads_overlapping_repeats"
2025-09-15 20:24:59.289 wdl.w:ptcp.w:call-trgt-84 INFO input :: job: "call-get_reads_overlapping_repeats", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-84/out/m84036_250809_035451_s4.bc2181.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-84/out/m84036_250809_035451_s4.bc2181.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2181"}
2025-09-15 20:24:59.289 wdl.w:ptcp.w:call-trgt-84 NOTICE ready :: job: "call-trgt_genotype", callee: "trgt_genotype"
2025-09-15 20:24:59.290 wdl.w:ptcp.w:call-trgt-84 INFO input :: job: "call-trgt_genotype", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-84/out/m84036_250809_035451_s4.bc2181.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-84/out/m84036_250809_035451_s4.bc2181.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2181"}
2025-09-15 20:24:59.292 wdl.w:ptcp.w:call-trgt-53.t:call-trgt_plot_motifs_waterfall NOTICE slurm_singularity run :: pid: 1203713, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-53/call-trgt_plot_motifs_waterfall/slurm_singularity.log.txt"
2025-09-15 20:24:59.300 wdl.w:ptcp.w:call-trgt-59.t:call-trgt_plot_meth_waterfall NOTICE done
2025-09-15 20:24:59.311 wdl.w:ptcp.w:call-trgt-59 NOTICE finish :: job: "call-trgt_plot_meth_waterfall"
2025-09-15 20:24:59.311 wdl.w:ptcp.w:call-trgt-59 INFO output :: job: "call-trgt_plot_meth_waterfall", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-59/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2156.meth_waterfall.trgt_plots.zip"}
2025-09-15 20:24:59.311 wdl.w:ptcp.w:call-trgt-59 INFO visit :: node: "output-images_meth_waterfall", values: {"images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-59/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2156.meth_waterfall.trgt_plots.zip"}
2025-09-15 20:24:59.311 wdl.w:ptcp.w:call-trgt-59 INFO visit :: node: "outputs", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-59/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2156.motifs_waterfall.trgt_plots.zip", "images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-59/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2156.meth_allele.trgt_plots.zip", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-59/call-trgt_genotype/out/m84036_250809_035451_s4.bc2156.trgt.sorted.spanning.bam.bai", "images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-59/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2156.motifs_allele.trgt_plots.zip", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-59/call-trgt_genotype/out/m84036_250809_035451_s4.bc2156.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-59/call-trgt_genotype/out/m84036_250809_035451_s4.bc2156.trgt.vcf", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-59/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2156.repeats.bam", "images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-59/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2156.meth_waterfall.trgt_plots.zip", "reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-59/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2156.repeats.bam.bai"}
2025-09-15 20:24:59.317 wdl.w:ptcp.w:call-trgt-56.t:call-trgt_plot_meth_allele NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-56/call-trgt_plot_meth_allele", thread: 140610912642624
2025-09-15 20:24:59.390 wdl.w:ptcp.w:call-trgt-56.t:call-trgt_plot_meth_allele INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:59.391 wdl.w:ptcp.w:call-trgt-56.t:call-trgt_plot_meth_allele INFO input :: name: "waterfall", value: false
2025-09-15 20:24:59.391 wdl.w:ptcp.w:call-trgt-56.t:call-trgt_plot_meth_allele INFO input :: name: "methylation", value: true
2025-09-15 20:24:59.391 wdl.w:ptcp.w:call-trgt-56.t:call-trgt_plot_meth_allele INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:59.391 wdl.w:ptcp.w:call-trgt-56.t:call-trgt_plot_meth_allele INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:59.391 wdl.w:ptcp.w:call-trgt-56.t:call-trgt_plot_meth_allele INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:59.391 wdl.w:ptcp.w:call-trgt-56.t:call-trgt_plot_meth_allele INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2153.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:59.391 wdl.w:ptcp.w:call-trgt-56.t:call-trgt_plot_meth_allele INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2153.trgt.sorted.spanning.bam"
2025-09-15 20:24:59.391 wdl.w:ptcp.w:call-trgt-56.t:call-trgt_plot_meth_allele INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2153.trgt.vcf"
2025-09-15 20:24:59.391 wdl.w:ptcp.w:call-trgt-56.t:call-trgt_plot_meth_allele INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2153"
2025-09-15 20:24:59.391 wdl.w:ptcp.w:call-trgt-56.t:call-trgt_plot_meth_allele INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:59.392 wdl.w:ptcp.w:call-trgt-56.t:call-trgt_plot_meth_allele INFO eval :: name: "plot_type", value: "allele"
2025-09-15 20:24:59.392 wdl.w:ptcp.w:call-trgt-56.t:call-trgt_plot_meth_allele INFO eval :: name: "show", value: "meth"
2025-09-15 20:24:59.392 wdl.w:ptcp.w:call-trgt-56.t:call-trgt_plot_meth_allele INFO eval :: name: "threads", value: 1
2025-09-15 20:24:59.392 wdl.w:ptcp.w:call-trgt-56.t:call-trgt_plot_meth_allele INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:59.392 wdl.w:ptcp.w:call-trgt-56.t:call-trgt_plot_meth_allele INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2153.meth_allele"
2025-09-15 20:24:59.392 wdl.w:ptcp.w:call-trgt-56.t:call-trgt_plot_meth_allele INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:59.393 wdl.w:ptcp.w:call-trgt-56.t:call-trgt_plot_meth_allele WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:59.393 wdl.w:ptcp.w:call-trgt-56.t:call-trgt_plot_meth_allele INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:59.393 wdl.w:ptcp.w:call-trgt-56.t:call-trgt_plot_meth_allele INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:59.427 wdl.w:ptcp.w:call-trgt-57.t:call-trgt_plot_meth_waterfall INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2154.meth_waterfall.trgt_plots.zip"
2025-09-15 20:24:59.466 wdl.w:ptcp.w:call-trgt-59 NOTICE done
2025-09-15 20:24:59.472 wdl.w:ptcp NOTICE finish :: job: "call-trgt-59"
2025-09-15 20:24:59.473 wdl.w:ptcp INFO output :: job: "call-trgt-59", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-59/out/m84036_250809_035451_s4.bc2156.motifs_waterfall.trgt_plots.zip", "images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-59/out/m84036_250809_035451_s4.bc2156.meth_allele.trgt_plots.zip", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-59/out/m84036_250809_035451_s4.bc2156.trgt.sorted.spanning.bam.bai", "images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-59/out/m84036_250809_035451_s4.bc2156.motifs_allele.trgt_plots.zip", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-59/out/m84036_250809_035451_s4.bc2156.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-59/out/m84036_250809_035451_s4.bc2156.trgt.vcf", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-59/out/m84036_250809_035451_s4.bc2156.repeats.bam", "images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-59/out/m84036_250809_035451_s4.bc2156.meth_waterfall.trgt_plots.zip", "reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-59/out/m84036_250809_035451_s4.bc2156.repeats.bam.bai"}
2025-09-15 20:24:59.481 wdl.w:ptcp.w:call-paraphase-76 NOTICE workflow start :: name: "paraphase", source: "./paraphase.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-76"
2025-09-15 20:24:59.483 wdl.w:ptcp.w:call-trgt-56.t:call-trgt_plot_meth_allele INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-56/call-trgt_plot_meth_allele/_singularity_tmpdir_9juepi20"
2025-09-15 20:24:59.483 wdl.w:ptcp.w:call-trgt-56.t:call-trgt_plot_meth_allele INFO Slurm invocation: srun --job-name call-trgt_plot_meth_allele --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-56/call-trgt_plot_meth_allele/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-56/call-trgt_plot_meth_allele/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-56/call-trgt_plot_meth_allele/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-56/call-trgt_plot_meth_allele/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-56/call-trgt_genotype/out/m84036_250809_035451_s4.bc2153.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2153.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-56/call-trgt_genotype/out/m84036_250809_035451_s4.bc2153.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2153.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-56/call-trgt_genotype/out/m84036_250809_035451_s4.bc2153.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2153.trgt.sorted.spanning.bam.bai:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-56/call-trgt_plot_meth_allele/_singularity_tmpdir_9juepi20/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-56/call-trgt_plot_meth_allele/_singularity_tmpdir_9juepi20/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:59.487 wdl.w:ptcp.w:call-trgt-69.t:call-get_reads_overlapping_repeats INFO output :: name: "reads_overlapping_repeats", value: "m84036_250809_035451_s4.bc2166.repeats.bam"
2025-09-15 20:24:59.491 wdl.w:ptcp.w:call-trgt-69.t:call-get_reads_overlapping_repeats INFO output :: name: "reads_overlapping_repeats_bai", value: "m84036_250809_035451_s4.bc2166.repeats.bam.bai"
2025-09-15 20:24:59.498 wdl.w:ptcp.w:call-paraphase-76 INFO visit :: node: "decl-annotation_vcf", values: {"annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf"}
2025-09-15 20:24:59.498 wdl.w:ptcp.w:call-paraphase-76 INFO visit :: node: "decl-config_file", values: {"config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml"}
2025-09-15 20:24:59.499 wdl.w:ptcp.w:call-paraphase-76 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:24:59.499 wdl.w:ptcp.w:call-paraphase-76 INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:24:59.499 wdl.w:ptcp.w:call-paraphase-76 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-76/out/m84036_250809_035451_s4.bc2173.mapped.bam"}
2025-09-15 20:24:59.499 wdl.w:ptcp.w:call-paraphase-76 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-76/out/m84036_250809_035451_s4.bc2173.mapped.bam.bai"}
2025-09-15 20:24:59.499 wdl.w:ptcp.w:call-paraphase-76 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:24:59.499 wdl.w:ptcp.w:call-paraphase-76 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:24:59.499 wdl.w:ptcp.w:call-paraphase-76 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2173"}
2025-09-15 20:24:59.499 wdl.w:ptcp.w:call-paraphase-76 INFO visit :: node: "decl-sex", values: {"sex": "F"}
2025-09-15 20:24:59.499 wdl.w:ptcp.w:call-paraphase-76 NOTICE ready :: job: "call-run_paraphase", callee: "run_paraphase"
2025-09-15 20:24:59.500 wdl.w:ptcp.w:call-paraphase-76 INFO input :: job: "call-run_paraphase", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf", "genome_version": "38", "config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-76/out/m84036_250809_035451_s4.bc2173.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-76/out/m84036_250809_035451_s4.bc2173.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2173"}
2025-09-15 20:24:59.508 wdl.w:ptcp.w:call-trgt-56.t:call-trgt_plot_meth_allele NOTICE slurm_singularity run :: pid: 1203727, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-56/call-trgt_plot_meth_allele/slurm_singularity.log.txt"
2025-09-15 20:24:59.565 wdl.w:ptcp.w:call-trgt-69.t:call-get_reads_overlapping_repeats NOTICE done
2025-09-15 20:24:59.570 wdl.w:ptcp.w:call-trgt-69 NOTICE finish :: job: "call-get_reads_overlapping_repeats"
2025-09-15 20:24:59.570 wdl.w:ptcp.w:call-trgt-69 INFO output :: job: "call-get_reads_overlapping_repeats", values: {"reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-69/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2166.repeats.bam.bai", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-69/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2166.repeats.bam"}
2025-09-15 20:24:59.571 wdl.w:ptcp.w:call-trgt-69 INFO visit :: node: "output-reads_overlapping_repeats", values: {"reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-69/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2166.repeats.bam"}
2025-09-15 20:24:59.571 wdl.w:ptcp.w:call-trgt-69 INFO visit :: node: "output-reads_overlapping_repeats_bai", values: {"reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-69/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2166.repeats.bam.bai"}
2025-09-15 20:24:59.577 wdl.w:ptcp.w:call-trgt-57.t:call-trgt_plot_meth_waterfall NOTICE done
2025-09-15 20:24:59.578 wdl.w:ptcp.w:call-trgt-56.t:call-trgt_plot_meth_waterfall NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-56/call-trgt_plot_meth_waterfall", thread: 140608773551680
2025-09-15 20:24:59.603 wdl.w:ptcp.w:call-trgt-56.t:call-trgt_plot_meth_waterfall INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:59.603 wdl.w:ptcp.w:call-trgt-56.t:call-trgt_plot_meth_waterfall INFO input :: name: "waterfall", value: true
2025-09-15 20:24:59.603 wdl.w:ptcp.w:call-trgt-56.t:call-trgt_plot_meth_waterfall INFO input :: name: "methylation", value: true
2025-09-15 20:24:59.603 wdl.w:ptcp.w:call-trgt-56.t:call-trgt_plot_meth_waterfall INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:59.603 wdl.w:ptcp.w:call-trgt-56.t:call-trgt_plot_meth_waterfall INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:59.603 wdl.w:ptcp.w:call-trgt-56.t:call-trgt_plot_meth_waterfall INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:59.604 wdl.w:ptcp.w:call-trgt-56.t:call-trgt_plot_meth_waterfall INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2153.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:59.604 wdl.w:ptcp.w:call-trgt-56.t:call-trgt_plot_meth_waterfall INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2153.trgt.sorted.spanning.bam"
2025-09-15 20:24:59.604 wdl.w:ptcp.w:call-trgt-56.t:call-trgt_plot_meth_waterfall INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2153.trgt.vcf"
2025-09-15 20:24:59.604 wdl.w:ptcp.w:call-trgt-56.t:call-trgt_plot_meth_waterfall INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2153"
2025-09-15 20:24:59.604 wdl.w:ptcp.w:call-trgt-56.t:call-trgt_plot_meth_waterfall INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:59.604 wdl.w:ptcp.w:call-trgt-56.t:call-trgt_plot_meth_waterfall INFO eval :: name: "plot_type", value: "waterfall"
2025-09-15 20:24:59.604 wdl.w:ptcp.w:call-trgt-56.t:call-trgt_plot_meth_waterfall INFO eval :: name: "show", value: "meth"
2025-09-15 20:24:59.604 wdl.w:ptcp.w:call-trgt-56.t:call-trgt_plot_meth_waterfall INFO eval :: name: "threads", value: 1
2025-09-15 20:24:59.604 wdl.w:ptcp.w:call-trgt-56.t:call-trgt_plot_meth_waterfall INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:59.604 wdl.w:ptcp.w:call-trgt-56.t:call-trgt_plot_meth_waterfall INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2153.meth_waterfall"
2025-09-15 20:24:59.605 wdl.w:ptcp.w:call-trgt-56.t:call-trgt_plot_meth_waterfall INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:59.605 wdl.w:ptcp.w:call-trgt-56.t:call-trgt_plot_meth_waterfall WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:59.605 wdl.w:ptcp.w:call-trgt-56.t:call-trgt_plot_meth_waterfall INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:59.605 wdl.w:ptcp.w:call-trgt-56.t:call-trgt_plot_meth_waterfall INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:59.618 wdl.w:ptcp.w:call-trgt-57 NOTICE finish :: job: "call-trgt_plot_meth_waterfall"
2025-09-15 20:24:59.618 wdl.w:ptcp.w:call-trgt-57 INFO output :: job: "call-trgt_plot_meth_waterfall", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-57/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2154.meth_waterfall.trgt_plots.zip"}
2025-09-15 20:24:59.618 wdl.w:ptcp.w:call-trgt-57 INFO visit :: node: "output-images_meth_waterfall", values: {"images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-57/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2154.meth_waterfall.trgt_plots.zip"}
2025-09-15 20:24:59.618 wdl.w:ptcp.w:call-trgt-57 INFO visit :: node: "outputs", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-57/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2154.motifs_waterfall.trgt_plots.zip", "images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-57/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2154.meth_allele.trgt_plots.zip", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-57/call-trgt_genotype/out/m84036_250809_035451_s4.bc2154.trgt.sorted.spanning.bam.bai", "images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-57/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2154.motifs_allele.trgt_plots.zip", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-57/call-trgt_genotype/out/m84036_250809_035451_s4.bc2154.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-57/call-trgt_genotype/out/m84036_250809_035451_s4.bc2154.trgt.vcf", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-57/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2154.repeats.bam", "images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-57/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2154.meth_waterfall.trgt_plots.zip", "reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-57/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2154.repeats.bam.bai"}
2025-09-15 20:24:59.624 wdl.w:ptcp.w:call-trgt-56.t:call-trgt_plot_motifs_allele NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-56/call-trgt_plot_motifs_allele", thread: 140607691417152
2025-09-15 20:24:59.642 wdl.w:ptcp.w:call-trgt-56.t:call-trgt_plot_motifs_allele INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:59.643 wdl.w:ptcp.w:call-trgt-56.t:call-trgt_plot_motifs_allele INFO input :: name: "waterfall", value: false
2025-09-15 20:24:59.643 wdl.w:ptcp.w:call-trgt-56.t:call-trgt_plot_motifs_allele INFO input :: name: "methylation", value: false
2025-09-15 20:24:59.643 wdl.w:ptcp.w:call-trgt-56.t:call-trgt_plot_motifs_allele INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:59.643 wdl.w:ptcp.w:call-trgt-56.t:call-trgt_plot_motifs_allele INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:59.643 wdl.w:ptcp.w:call-trgt-56.t:call-trgt_plot_motifs_allele INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:59.643 wdl.w:ptcp.w:call-trgt-56.t:call-trgt_plot_motifs_allele INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2153.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:59.643 wdl.w:ptcp.w:call-trgt-56.t:call-trgt_plot_motifs_allele INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2153.trgt.sorted.spanning.bam"
2025-09-15 20:24:59.643 wdl.w:ptcp.w:call-trgt-56.t:call-trgt_plot_motifs_allele INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2153.trgt.vcf"
2025-09-15 20:24:59.643 wdl.w:ptcp.w:call-trgt-56.t:call-trgt_plot_motifs_allele INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2153"
2025-09-15 20:24:59.643 wdl.w:ptcp.w:call-trgt-56.t:call-trgt_plot_motifs_allele INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:59.644 wdl.w:ptcp.w:call-trgt-56.t:call-trgt_plot_motifs_allele INFO eval :: name: "plot_type", value: "allele"
2025-09-15 20:24:59.644 wdl.w:ptcp.w:call-trgt-56.t:call-trgt_plot_motifs_allele INFO eval :: name: "show", value: "motifs"
2025-09-15 20:24:59.644 wdl.w:ptcp.w:call-trgt-56.t:call-trgt_plot_motifs_allele INFO eval :: name: "threads", value: 1
2025-09-15 20:24:59.644 wdl.w:ptcp.w:call-trgt-56.t:call-trgt_plot_motifs_allele INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:59.644 wdl.w:ptcp.w:call-trgt-56.t:call-trgt_plot_motifs_allele INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2153.motifs_allele"
2025-09-15 20:24:59.644 wdl.w:ptcp.w:call-trgt-56.t:call-trgt_plot_motifs_allele INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:59.645 wdl.w:ptcp.w:call-trgt-56.t:call-trgt_plot_motifs_allele WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:59.645 wdl.w:ptcp.w:call-trgt-56.t:call-trgt_plot_motifs_allele INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:59.645 wdl.w:ptcp.w:call-trgt-56.t:call-trgt_plot_motifs_allele INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:59.681 wdl.w:ptcp.w:call-trgt-56.t:call-trgt_plot_meth_waterfall INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-56/call-trgt_plot_meth_waterfall/_singularity_tmpdir_jy1n8wb1"
2025-09-15 20:24:59.682 wdl.w:ptcp.w:call-trgt-56.t:call-trgt_plot_meth_waterfall INFO Slurm invocation: srun --job-name call-trgt_plot_meth_waterfall --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-56/call-trgt_plot_meth_waterfall/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-56/call-trgt_plot_meth_waterfall/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-56/call-trgt_plot_meth_waterfall/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-56/call-trgt_plot_meth_waterfall/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-56/call-trgt_genotype/out/m84036_250809_035451_s4.bc2153.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2153.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-56/call-trgt_genotype/out/m84036_250809_035451_s4.bc2153.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2153.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-56/call-trgt_genotype/out/m84036_250809_035451_s4.bc2153.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2153.trgt.sorted.spanning.bam.bai:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-56/call-trgt_plot_meth_waterfall/_singularity_tmpdir_jy1n8wb1/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-56/call-trgt_plot_meth_waterfall/_singularity_tmpdir_jy1n8wb1/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:59.697 wdl.w:ptcp.w:call-trgt-56.t:call-trgt_plot_meth_waterfall NOTICE slurm_singularity run :: pid: 1203790, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-56/call-trgt_plot_meth_waterfall/slurm_singularity.log.txt"
2025-09-15 20:24:59.721 wdl.w:ptcp.w:call-trgt-56.t:call-trgt_plot_motifs_allele INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-56/call-trgt_plot_motifs_allele/_singularity_tmpdir_09rfxae0"
2025-09-15 20:24:59.722 wdl.w:ptcp.w:call-trgt-56.t:call-trgt_plot_motifs_allele INFO Slurm invocation: srun --job-name call-trgt_plot_motifs_allele --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-56/call-trgt_plot_motifs_allele/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-56/call-trgt_plot_motifs_allele/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-56/call-trgt_plot_motifs_allele/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-56/call-trgt_plot_motifs_allele/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-56/call-trgt_genotype/out/m84036_250809_035451_s4.bc2153.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2153.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-56/call-trgt_genotype/out/m84036_250809_035451_s4.bc2153.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2153.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-56/call-trgt_genotype/out/m84036_250809_035451_s4.bc2153.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2153.trgt.sorted.spanning.bam.bai:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-56/call-trgt_plot_motifs_allele/_singularity_tmpdir_09rfxae0/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-56/call-trgt_plot_motifs_allele/_singularity_tmpdir_09rfxae0/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:59.722 wdl.w:ptcp.w:call-trgt-57 NOTICE done
2025-09-15 20:24:59.723 wdl.w:ptcp.w:call-trgt-69.t:call-trgt_genotype INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2166.trgt.vcf"
2025-09-15 20:24:59.726 wdl.w:ptcp NOTICE finish :: job: "call-trgt-57"
2025-09-15 20:24:59.726 wdl.w:ptcp INFO output :: job: "call-trgt-57", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-57/out/m84036_250809_035451_s4.bc2154.motifs_waterfall.trgt_plots.zip", "images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-57/out/m84036_250809_035451_s4.bc2154.meth_allele.trgt_plots.zip", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-57/out/m84036_250809_035451_s4.bc2154.trgt.sorted.spanning.bam.bai", "images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-57/out/m84036_250809_035451_s4.bc2154.motifs_allele.trgt_plots.zip", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-57/out/m84036_250809_035451_s4.bc2154.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-57/out/m84036_250809_035451_s4.bc2154.trgt.vcf", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-57/out/m84036_250809_035451_s4.bc2154.repeats.bam", "images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-57/out/m84036_250809_035451_s4.bc2154.meth_waterfall.trgt_plots.zip", "reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-57/out/m84036_250809_035451_s4.bc2154.repeats.bam.bai"}
2025-09-15 20:24:59.727 wdl.w:ptcp.w:call-trgt-69.t:call-trgt_genotype INFO output :: name: "spanning_bam", value: "m84036_250809_035451_s4.bc2166.trgt.sorted.spanning.bam"
2025-09-15 20:24:59.730 wdl.w:ptcp.w:call-trgt-69.t:call-trgt_genotype INFO output :: name: "spanning_bam_bai", value: "m84036_250809_035451_s4.bc2166.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:59.731 wdl.w:ptcp.w:call-sawfish-76 NOTICE workflow start :: name: "sawfish", source: "./sawfish.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-76"
2025-09-15 20:24:59.734 wdl.w:ptcp.w:call-trgt-56.t:call-trgt_plot_motifs_allele NOTICE slurm_singularity run :: pid: 1203801, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-56/call-trgt_plot_motifs_allele/slurm_singularity.log.txt"
2025-09-15 20:24:59.744 wdl.w:ptcp.w:call-sawfish-76 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:24:59.745 wdl.w:ptcp.w:call-sawfish-76 INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:24:59.745 wdl.w:ptcp.w:call-sawfish-76 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-76/out/m84036_250809_035451_s4.bc2173.mapped.bam"}
2025-09-15 20:24:59.745 wdl.w:ptcp.w:call-sawfish-76 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-76/out/m84036_250809_035451_s4.bc2173.mapped.bam.bai"}
2025-09-15 20:24:59.745 wdl.w:ptcp.w:call-sawfish-76 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:24:59.745 wdl.w:ptcp.w:call-sawfish-76 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:24:59.745 wdl.w:ptcp.w:call-sawfish-76 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2173"}
2025-09-15 20:24:59.745 wdl.w:ptcp.w:call-sawfish-76 NOTICE ready :: job: "call-run_sawfish", callee: "run_sawfish"
2025-09-15 20:24:59.745 wdl.w:ptcp.w:call-sawfish-76 INFO input :: job: "call-run_sawfish", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-76/out/m84036_250809_035451_s4.bc2173.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-76/out/m84036_250809_035451_s4.bc2173.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2173"}
2025-09-15 20:24:59.775 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:59 [ERROR] - No reads found for TRID=OPDM_ABCD3
2025-09-15 20:24:59.775 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:59 [ERROR] - No reads found for TRID=SCA37_DAB1
2025-09-15 20:24:59.775 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:59 [ERROR] - No reads found for TRID=NIID_NOTCH2NLC
2025-09-15 20:24:59.775 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:59 [ERROR] - No reads found for TRID=DRPLA_ATN1
2025-09-15 20:24:59.784 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO srun: job 51797851 queued and waiting for resources
2025-09-15 20:24:59.784 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO srun: job 51797851 has been allocated resources
2025-09-15 20:24:59.784 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:59.798 wdl.w:ptcp.w:call-trgt-69.t:call-trgt_genotype NOTICE done
2025-09-15 20:24:59.803 wdl.w:ptcp.w:call-trgt-69 NOTICE finish :: job: "call-trgt_genotype"
2025-09-15 20:24:59.803 wdl.w:ptcp.w:call-trgt-69 INFO output :: job: "call-trgt_genotype", values: {"spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-69/call-trgt_genotype/out/m84036_250809_035451_s4.bc2166.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-69/call-trgt_genotype/out/m84036_250809_035451_s4.bc2166.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-69/call-trgt_genotype/out/m84036_250809_035451_s4.bc2166.trgt.vcf"}
2025-09-15 20:24:59.804 wdl.w:ptcp.w:call-trgt-69 NOTICE ready :: job: "call-trgt_plot_meth_allele", callee: "trgt_plot"
2025-09-15 20:24:59.804 wdl.w:ptcp.w:call-trgt-69 INFO input :: job: "call-trgt_plot_meth_allele", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": false, "methylation": true, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-69/call-trgt_genotype/out/m84036_250809_035451_s4.bc2166.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-69/call-trgt_genotype/out/m84036_250809_035451_s4.bc2166.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-69/call-trgt_genotype/out/m84036_250809_035451_s4.bc2166.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2166"}
2025-09-15 20:24:59.806 wdl.w:ptcp.w:call-trgt-69 NOTICE ready :: job: "call-trgt_plot_meth_waterfall", callee: "trgt_plot"
2025-09-15 20:24:59.806 wdl.w:ptcp.w:call-trgt-69 INFO input :: job: "call-trgt_plot_meth_waterfall", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": true, "methylation": true, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-69/call-trgt_genotype/out/m84036_250809_035451_s4.bc2166.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-69/call-trgt_genotype/out/m84036_250809_035451_s4.bc2166.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-69/call-trgt_genotype/out/m84036_250809_035451_s4.bc2166.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2166"}
2025-09-15 20:24:59.807 wdl.w:ptcp.w:call-trgt-69 NOTICE ready :: job: "call-trgt_plot_motifs_allele", callee: "trgt_plot"
2025-09-15 20:24:59.807 wdl.w:ptcp.w:call-trgt-69 INFO input :: job: "call-trgt_plot_motifs_allele", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": false, "methylation": false, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-69/call-trgt_genotype/out/m84036_250809_035451_s4.bc2166.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-69/call-trgt_genotype/out/m84036_250809_035451_s4.bc2166.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-69/call-trgt_genotype/out/m84036_250809_035451_s4.bc2166.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2166"}
2025-09-15 20:24:59.808 wdl.w:ptcp.w:call-trgt-69 NOTICE ready :: job: "call-trgt_plot_motifs_waterfall", callee: "trgt_plot"
2025-09-15 20:24:59.808 wdl.w:ptcp.w:call-trgt-69 INFO input :: job: "call-trgt_plot_motifs_waterfall", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": true, "methylation": false, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-69/call-trgt_genotype/out/m84036_250809_035451_s4.bc2166.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-69/call-trgt_genotype/out/m84036_250809_035451_s4.bc2166.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-69/call-trgt_genotype/out/m84036_250809_035451_s4.bc2166.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2166"}
2025-09-15 20:24:59.808 wdl.w:ptcp.w:call-trgt-69 INFO visit :: node: "output-spanning_bam", values: {"spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-69/call-trgt_genotype/out/m84036_250809_035451_s4.bc2166.trgt.sorted.spanning.bam"}
2025-09-15 20:24:59.808 wdl.w:ptcp.w:call-trgt-69 INFO visit :: node: "output-spanning_bam_bai", values: {"spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-69/call-trgt_genotype/out/m84036_250809_035451_s4.bc2166.trgt.sorted.spanning.bam.bai"}
2025-09-15 20:24:59.808 wdl.w:ptcp.w:call-trgt-69 INFO visit :: node: "output-vcf", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-69/call-trgt_genotype/out/m84036_250809_035451_s4.bc2166.trgt.vcf"}
2025-09-15 20:24:59.809 wdl.w:ptcp.w:call-trgt-56.t:call-trgt_plot_motifs_waterfall NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-56/call-trgt_plot_motifs_waterfall", thread: 140607137760832
2025-09-15 20:24:59.825 wdl.w:ptcp.w:call-trgt-56.t:call-trgt_plot_motifs_waterfall INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:24:59.825 wdl.w:ptcp.w:call-trgt-56.t:call-trgt_plot_motifs_waterfall INFO input :: name: "waterfall", value: true
2025-09-15 20:24:59.825 wdl.w:ptcp.w:call-trgt-56.t:call-trgt_plot_motifs_waterfall INFO input :: name: "methylation", value: false
2025-09-15 20:24:59.825 wdl.w:ptcp.w:call-trgt-56.t:call-trgt_plot_motifs_waterfall INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:24:59.825 wdl.w:ptcp.w:call-trgt-56.t:call-trgt_plot_motifs_waterfall INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:24:59.825 wdl.w:ptcp.w:call-trgt-56.t:call-trgt_plot_motifs_waterfall INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:24:59.825 wdl.w:ptcp.w:call-trgt-56.t:call-trgt_plot_motifs_waterfall INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2153.trgt.sorted.spanning.bam.bai"
2025-09-15 20:24:59.825 wdl.w:ptcp.w:call-trgt-56.t:call-trgt_plot_motifs_waterfall INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2153.trgt.sorted.spanning.bam"
2025-09-15 20:24:59.825 wdl.w:ptcp.w:call-trgt-56.t:call-trgt_plot_motifs_waterfall INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2153.trgt.vcf"
2025-09-15 20:24:59.825 wdl.w:ptcp.w:call-trgt-56.t:call-trgt_plot_motifs_waterfall INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2153"
2025-09-15 20:24:59.826 wdl.w:ptcp.w:call-trgt-56.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:24:59.826 wdl.w:ptcp.w:call-trgt-56.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "plot_type", value: "waterfall"
2025-09-15 20:24:59.826 wdl.w:ptcp.w:call-trgt-56.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "show", value: "motifs"
2025-09-15 20:24:59.826 wdl.w:ptcp.w:call-trgt-56.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "threads", value: 1
2025-09-15 20:24:59.826 wdl.w:ptcp.w:call-trgt-56.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "disk_size", value: 27
2025-09-15 20:24:59.826 wdl.w:ptcp.w:call-trgt-56.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2153.motifs_waterfall"
2025-09-15 20:24:59.827 wdl.w:ptcp.w:call-trgt-56.t:call-trgt_plot_motifs_waterfall INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:24:59.827 wdl.w:ptcp.w:call-trgt-56.t:call-trgt_plot_motifs_waterfall WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:24:59.827 wdl.w:ptcp.w:call-trgt-56.t:call-trgt_plot_motifs_waterfall INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:24:59.827 wdl.w:ptcp.w:call-trgt-56.t:call-trgt_plot_motifs_waterfall INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:24:59.851 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:59 [ERROR] - No reads found for TRID=OPDM_ABCD3
2025-09-15 20:24:59.852 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:59 [ERROR] - No reads found for TRID=SCA37_DAB1
2025-09-15 20:24:59.852 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:59 [ERROR] - No reads found for TRID=NIID_NOTCH2NLC
2025-09-15 20:24:59.852 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:59 [ERROR] - No reads found for TRID=DRPLA_ATN1
2025-09-15 20:24:59.852 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:59 [ERROR] - No reads found for TRID=SCA2_ATXN2
2025-09-15 20:24:59.852 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:24:59 [ERROR] - No reads found for TRID=OPDM4_RILPL1
2025-09-15 20:24:59.855 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:59 [ERROR] - No reads found for TRID=OPDM_ABCD3
2025-09-15 20:24:59.855 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:59 [ERROR] - No reads found for TRID=SCA37_DAB1
2025-09-15 20:24:59.855 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:59 [ERROR] - No reads found for TRID=NIID_NOTCH2NLC
2025-09-15 20:24:59.855 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:59 [ERROR] - No reads found for TRID=DRPLA_ATN1
2025-09-15 20:24:59.855 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:59 [ERROR] - No reads found for TRID=SCA2_ATXN2
2025-09-15 20:24:59.855 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:59 [ERROR] - No reads found for TRID=OPDM4_RILPL1
2025-09-15 20:24:59.855 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:59 [ERROR] - No reads found for TRID=SCA8_ATXN8OS
2025-09-15 20:24:59.855 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:59 [ERROR] - No reads found for TRID=OPMD_PABPN1
2025-09-15 20:24:59.862 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO srun: job 51797852 queued and waiting for resources
2025-09-15 20:24:59.862 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO srun: job 51797852 has been allocated resources
2025-09-15 20:24:59.863 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:59.865 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_plot_motifs_allele.slurm_singularity INFO srun: job 51797853 queued and waiting for resources
2025-09-15 20:24:59.865 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_plot_motifs_allele.slurm_singularity INFO srun: job 51797853 has been allocated resources
2025-09-15 20:24:59.865 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_plot_motifs_allele.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:59.894 wdl.w:ptcp.w:call-trgt-56.t:call-trgt_plot_motifs_waterfall INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-56/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_wci6lpic"
2025-09-15 20:24:59.894 wdl.w:ptcp.w:call-trgt-56.t:call-trgt_plot_motifs_waterfall INFO Slurm invocation: srun --job-name call-trgt_plot_motifs_waterfall --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-56/call-trgt_plot_motifs_waterfall/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-56/call-trgt_plot_motifs_waterfall/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-56/call-trgt_plot_motifs_waterfall/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-56/call-trgt_plot_motifs_waterfall/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-56/call-trgt_genotype/out/m84036_250809_035451_s4.bc2153.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2153.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-56/call-trgt_genotype/out/m84036_250809_035451_s4.bc2153.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2153.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-56/call-trgt_genotype/out/m84036_250809_035451_s4.bc2153.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2153.trgt.sorted.spanning.bam.bai:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-56/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_wci6lpic/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-56/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_wci6lpic/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:24:59.913 wdl.w:ptcp.w:call-trgt-56.t:call-trgt_plot_motifs_waterfall NOTICE slurm_singularity run :: pid: 1203817, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-56/call-trgt_plot_motifs_waterfall/slurm_singularity.log.txt"
2025-09-15 20:24:59.919 wdl.w:ptcp.w:call-trgt-48.t:call-trgt_plot_motifs_waterfall INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2145.motifs_waterfall.trgt_plots.zip"
2025-09-15 20:24:59.943 wdl.w:ptcp.w:call-trgt-49.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:58 [ERROR] - No reads found for TRID=PRTS_ARX
2025-09-15 20:24:59.943 wdl.w:ptcp.w:call-trgt-49.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:24:58 [ERROR] - No reads found for TRID=EIEE1_ARX
2025-09-15 20:24:59.944 wdl.w:ptcp.w:call-trgt-53.t:call-trgt_plot_meth_allele.slurm_singularity INFO srun: job 51797854 queued and waiting for resources
2025-09-15 20:24:59.944 wdl.w:ptcp.w:call-trgt-53.t:call-trgt_plot_meth_allele.slurm_singularity INFO srun: job 51797854 has been allocated resources
2025-09-15 20:24:59.944 wdl.w:ptcp.w:call-trgt-53.t:call-trgt_plot_meth_allele.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:24:59.946 wdl.w:ptcp.w:call-paraphase-71.t:call-run_paraphase.slurm_singularity INFO srun: job 51797855 queued and waiting for resources
2025-09-15 20:24:59.946 wdl.w:ptcp.w:call-paraphase-71.t:call-run_paraphase.slurm_singularity INFO srun: job 51797855 has been allocated resources
2025-09-15 20:24:59.946 wdl.w:ptcp.w:call-paraphase-71.t:call-run_paraphase.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:00.036 wdl.w:ptcp.w:call-trgt-48.t:call-trgt_plot_motifs_waterfall NOTICE done
2025-09-15 20:25:00.042 wdl.w:ptcp.w:call-trgt-48 NOTICE finish :: job: "call-trgt_plot_motifs_waterfall"
2025-09-15 20:25:00.043 wdl.w:ptcp.w:call-trgt-48 INFO output :: job: "call-trgt_plot_motifs_waterfall", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-48/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2145.motifs_waterfall.trgt_plots.zip"}
2025-09-15 20:25:00.043 wdl.w:ptcp.w:call-trgt-48 INFO visit :: node: "output-images_motifs_waterfall", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-48/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2145.motifs_waterfall.trgt_plots.zip"}
2025-09-15 20:25:00.043 wdl.w:ptcp.w:call-trgt-48 INFO visit :: node: "outputs", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-48/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2145.motifs_waterfall.trgt_plots.zip", "images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-48/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2145.meth_allele.trgt_plots.zip", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-48/call-trgt_genotype/out/m84036_250809_035451_s4.bc2145.trgt.sorted.spanning.bam.bai", "images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-48/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2145.motifs_allele.trgt_plots.zip", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-48/call-trgt_genotype/out/m84036_250809_035451_s4.bc2145.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-48/call-trgt_genotype/out/m84036_250809_035451_s4.bc2145.trgt.vcf", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-48/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2145.repeats.bam", "images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-48/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2145.meth_waterfall.trgt_plots.zip", "reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-48/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2145.repeats.bam.bai"}
2025-09-15 20:25:00.052 wdl.w:ptcp.t:call-tar_outputs-33 NOTICE task setup :: name: "tar_outputs", source: "./common.wdl", line: 279, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-33", thread: 140608203109952
2025-09-15 20:25:00.095 wdl.w:ptcp.t:call-tar_outputs-33 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:00.095 wdl.w:ptcp.t:call-tar_outputs-33 INFO input :: name: "sawfish_vcf_tbi", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2130.sv.vcf.gz.tbi"
2025-09-15 20:25:00.096 wdl.w:ptcp.t:call-tar_outputs-33 INFO input :: name: "sawfish_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2130.sv.vcf.gz"
2025-09-15 20:25:00.096 wdl.w:ptcp.t:call-tar_outputs-33 INFO input :: name: "f8_json", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2130.f8inversion.json"
2025-09-15 20:25:00.096 wdl.w:ptcp.t:call-tar_outputs-33 INFO input :: name: "paraphase_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2130.paraphase.bam.bai"
2025-09-15 20:25:00.096 wdl.w:ptcp.t:call-tar_outputs-33 INFO input :: name: "paraphase_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2130.paraphase.bam"
2025-09-15 20:25:00.096 wdl.w:ptcp.t:call-tar_outputs-33 INFO input :: name: "paraphase_json", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2130.paraphase.json"
2025-09-15 20:25:00.096 wdl.w:ptcp.t:call-tar_outputs-33 INFO input :: name: "trgt_spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2130.trgt.sorted.spanning.bam.bai"
2025-09-15 20:25:00.096 wdl.w:ptcp.t:call-tar_outputs-33 INFO input :: name: "trgt_spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2130.trgt.sorted.spanning.bam"
2025-09-15 20:25:00.096 wdl.w:ptcp.t:call-tar_outputs-33 INFO input :: name: "trgt_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2130.trgt.vcf"
2025-09-15 20:25:00.096 wdl.w:ptcp.t:call-tar_outputs-33 INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2130.mapped.bam.bai"
2025-09-15 20:25:00.096 wdl.w:ptcp.t:call-tar_outputs-33 INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2130.mapped.bam"
2025-09-15 20:25:00.096 wdl.w:ptcp.t:call-tar_outputs-33 INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2130"
2025-09-15 20:25:00.096 wdl.w:ptcp.t:call-tar_outputs-33 INFO eval :: name: "threads", value: 1
2025-09-15 20:25:00.097 wdl.w:ptcp.t:call-tar_outputs-33 INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:25:00.097 wdl.w:ptcp.t:call-tar_outputs-33 INFO eval :: name: "disk_size", value: 6
2025-09-15 20:25:00.097 wdl.w:ptcp.t:call-tar_outputs-33 INFO eval :: name: "output_tarball", value: "m84036_250809_035451_s4.bc2130.tar"
2025-09-15 20:25:00.100 wdl.w:ptcp.t:call-tar_outputs-33 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:00.100 wdl.w:ptcp.t:call-tar_outputs-33 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:00.100 wdl.w:ptcp.t:call-tar_outputs-33 INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:25:00.100 wdl.w:ptcp.t:call-tar_outputs-33 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:00.127 wdl.w:ptcp.w:call-trgt-53.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO srun: job 51797856 queued and waiting for resources
2025-09-15 20:25:00.127 wdl.w:ptcp.w:call-trgt-53.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO srun: job 51797856 has been allocated resources
2025-09-15 20:25:00.127 wdl.w:ptcp.w:call-trgt-53.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:00.180 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_meth_allele INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2152.meth_allele.trgt_plots.zip"
2025-09-15 20:25:00.181 wdl.w:ptcp.w:call-trgt-53.t:call-trgt_plot_motifs_allele.slurm_singularity INFO srun: job 51797857 queued and waiting for resources
2025-09-15 20:25:00.181 wdl.w:ptcp.w:call-trgt-53.t:call-trgt_plot_motifs_allele.slurm_singularity INFO srun: job 51797857 has been allocated resources
2025-09-15 20:25:00.181 wdl.w:ptcp.w:call-trgt-53.t:call-trgt_plot_motifs_allele.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:00.215 wdl.w:ptcp.w:call-trgt-60.t:call-trgt_genotype INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2157.trgt.vcf"
2025-09-15 20:25:00.219 wdl.w:ptcp.w:call-trgt-48 NOTICE done
2025-09-15 20:25:00.223 wdl.w:ptcp.w:call-trgt-60.t:call-trgt_genotype INFO output :: name: "spanning_bam", value: "m84036_250809_035451_s4.bc2157.trgt.sorted.spanning.bam"
2025-09-15 20:25:00.225 wdl.w:ptcp.w:call-trgt-60.t:call-trgt_genotype INFO output :: name: "spanning_bam_bai", value: "m84036_250809_035451_s4.bc2157.trgt.sorted.spanning.bam.bai"
2025-09-15 20:25:00.225 wdl.w:ptcp NOTICE finish :: job: "call-trgt-48"
2025-09-15 20:25:00.225 wdl.w:ptcp INFO output :: job: "call-trgt-48", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-48/out/m84036_250809_035451_s4.bc2145.motifs_waterfall.trgt_plots.zip", "images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-48/out/m84036_250809_035451_s4.bc2145.meth_allele.trgt_plots.zip", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-48/out/m84036_250809_035451_s4.bc2145.trgt.sorted.spanning.bam.bai", "images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-48/out/m84036_250809_035451_s4.bc2145.motifs_allele.trgt_plots.zip", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-48/out/m84036_250809_035451_s4.bc2145.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-48/out/m84036_250809_035451_s4.bc2145.trgt.vcf", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-48/out/m84036_250809_035451_s4.bc2145.repeats.bam", "images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-48/out/m84036_250809_035451_s4.bc2145.meth_waterfall.trgt_plots.zip", "reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-48/out/m84036_250809_035451_s4.bc2145.repeats.bam.bai"}
2025-09-15 20:25:00.236 wdl.w:ptcp.w:call-trgt-76 NOTICE workflow start :: name: "trgt", source: "./trgt.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-76"
2025-09-15 20:25:00.258 wdl.w:ptcp.w:call-trgt-76 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:25:00.258 wdl.w:ptcp.w:call-trgt-76 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-76/out/m84036_250809_035451_s4.bc2173.mapped.bam"}
2025-09-15 20:25:00.258 wdl.w:ptcp.w:call-trgt-76 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-76/out/m84036_250809_035451_s4.bc2173.mapped.bam.bai"}
2025-09-15 20:25:00.258 wdl.w:ptcp.w:call-trgt-76 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:25:00.258 wdl.w:ptcp.w:call-trgt-76 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:25:00.259 wdl.w:ptcp.w:call-trgt-76 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2173"}
2025-09-15 20:25:00.259 wdl.w:ptcp.w:call-trgt-76 INFO visit :: node: "decl-sex", values: {"sex": "F"}
2025-09-15 20:25:00.259 wdl.w:ptcp.w:call-trgt-76 INFO visit :: node: "decl-trgt_bed", values: {"trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"}
2025-09-15 20:25:00.259 wdl.w:ptcp.w:call-trgt-76 NOTICE ready :: job: "call-get_reads_overlapping_repeats", callee: "get_reads_overlapping_repeats"
2025-09-15 20:25:00.259 wdl.w:ptcp.w:call-trgt-76 INFO input :: job: "call-get_reads_overlapping_repeats", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-76/out/m84036_250809_035451_s4.bc2173.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-76/out/m84036_250809_035451_s4.bc2173.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2173"}
2025-09-15 20:25:00.260 wdl.w:ptcp.w:call-trgt-76 NOTICE ready :: job: "call-trgt_genotype", callee: "trgt_genotype"
2025-09-15 20:25:00.260 wdl.w:ptcp.w:call-trgt-76 INFO input :: job: "call-trgt_genotype", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-76/out/m84036_250809_035451_s4.bc2173.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-76/out/m84036_250809_035451_s4.bc2173.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2173"}
2025-09-15 20:25:00.274 wdl.w:ptcp.t:call-tar_outputs-33 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 17, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-33/_singularity_tmpdir_lvca188_"
2025-09-15 20:25:00.274 wdl.w:ptcp.t:call-tar_outputs-33 INFO Slurm invocation: srun --job-name call-tar_outputs-33 --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-33/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-33/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-33/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-33/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-33/out/m84036_250809_035451_s4.bc2130.f8inversion.json:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2130.f8inversion.json:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-33/out/m84036_250809_035451_s4.bc2130_paraphase/m84036_250809_035451_s4.bc2130.paraphase.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2130.paraphase.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-33/out/m84036_250809_035451_s4.bc2130_paraphase/m84036_250809_035451_s4.bc2130.paraphase.json:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2130.paraphase.json:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-33/out/m84036_250809_035451_s4.bc2130_paraphase/m84036_250809_035451_s4.bc2130.paraphase.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2130.paraphase.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-33/out/m84036_250809_035451_s4.bc2130_sawfish/m84036_250809_035451_s4.bc2130.sv.vcf.gz:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2130.sv.vcf.gz:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-33/out/m84036_250809_035451_s4.bc2130_sawfish/m84036_250809_035451_s4.bc2130.sv.vcf.gz.tbi:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2130.sv.vcf.gz.tbi:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-33/out/m84036_250809_035451_s4.bc2130.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2130.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-33/out/m84036_250809_035451_s4.bc2130.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2130.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-33/out/m84036_250809_035451_s4.bc2130.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2130.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-33/out/m84036_250809_035451_s4.bc2130.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2130.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-33/out/m84036_250809_035451_s4.bc2130.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2130.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-33/_singularity_tmpdir_lvca188_/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-33/_singularity_tmpdir_lvca188_/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:00.281 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_meth_allele NOTICE done
2025-09-15 20:25:00.305 wdl.w:ptcp.w:call-trgt-53.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO srun: job 51797858 queued and waiting for resources
2025-09-15 20:25:00.305 wdl.w:ptcp.w:call-trgt-53.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO srun: job 51797858 has been allocated resources
2025-09-15 20:25:00.305 wdl.w:ptcp.w:call-trgt-53.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:00.306 wdl.w:ptcp.t:call-tar_outputs-33 NOTICE slurm_singularity run :: pid: 1203951, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-33/slurm_singularity.log.txt"
2025-09-15 20:25:00.331 wdl.w:ptcp.w:call-trgt-60.t:call-trgt_genotype NOTICE done
2025-09-15 20:25:00.336 wdl.w:ptcp.w:call-trgt-60 NOTICE finish :: job: "call-trgt_genotype"
2025-09-15 20:25:00.336 wdl.w:ptcp.w:call-trgt-60 INFO output :: job: "call-trgt_genotype", values: {"spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-60/call-trgt_genotype/out/m84036_250809_035451_s4.bc2157.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-60/call-trgt_genotype/out/m84036_250809_035451_s4.bc2157.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-60/call-trgt_genotype/out/m84036_250809_035451_s4.bc2157.trgt.vcf"}
2025-09-15 20:25:00.337 wdl.w:ptcp.w:call-trgt-60 NOTICE ready :: job: "call-trgt_plot_meth_allele", callee: "trgt_plot"
2025-09-15 20:25:00.337 wdl.w:ptcp.w:call-trgt-60 INFO input :: job: "call-trgt_plot_meth_allele", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": false, "methylation": true, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-60/call-trgt_genotype/out/m84036_250809_035451_s4.bc2157.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-60/call-trgt_genotype/out/m84036_250809_035451_s4.bc2157.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-60/call-trgt_genotype/out/m84036_250809_035451_s4.bc2157.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2157"}
2025-09-15 20:25:00.338 wdl.w:ptcp.w:call-trgt-60 NOTICE ready :: job: "call-trgt_plot_meth_waterfall", callee: "trgt_plot"
2025-09-15 20:25:00.338 wdl.w:ptcp.w:call-trgt-60 INFO input :: job: "call-trgt_plot_meth_waterfall", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": true, "methylation": true, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-60/call-trgt_genotype/out/m84036_250809_035451_s4.bc2157.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-60/call-trgt_genotype/out/m84036_250809_035451_s4.bc2157.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-60/call-trgt_genotype/out/m84036_250809_035451_s4.bc2157.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2157"}
2025-09-15 20:25:00.339 wdl.w:ptcp.w:call-trgt-60 NOTICE ready :: job: "call-trgt_plot_motifs_allele", callee: "trgt_plot"
2025-09-15 20:25:00.339 wdl.w:ptcp.w:call-trgt-60 INFO input :: job: "call-trgt_plot_motifs_allele", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": false, "methylation": false, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-60/call-trgt_genotype/out/m84036_250809_035451_s4.bc2157.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-60/call-trgt_genotype/out/m84036_250809_035451_s4.bc2157.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-60/call-trgt_genotype/out/m84036_250809_035451_s4.bc2157.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2157"}
2025-09-15 20:25:00.339 wdl.w:ptcp.w:call-trgt-60 NOTICE ready :: job: "call-trgt_plot_motifs_waterfall", callee: "trgt_plot"
2025-09-15 20:25:00.339 wdl.w:ptcp.w:call-trgt-60 INFO input :: job: "call-trgt_plot_motifs_waterfall", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": true, "methylation": false, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-60/call-trgt_genotype/out/m84036_250809_035451_s4.bc2157.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-60/call-trgt_genotype/out/m84036_250809_035451_s4.bc2157.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-60/call-trgt_genotype/out/m84036_250809_035451_s4.bc2157.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2157"}
2025-09-15 20:25:00.340 wdl.w:ptcp.w:call-trgt-60 INFO visit :: node: "output-spanning_bam", values: {"spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-60/call-trgt_genotype/out/m84036_250809_035451_s4.bc2157.trgt.sorted.spanning.bam"}
2025-09-15 20:25:00.340 wdl.w:ptcp.w:call-trgt-60 INFO visit :: node: "output-spanning_bam_bai", values: {"spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-60/call-trgt_genotype/out/m84036_250809_035451_s4.bc2157.trgt.sorted.spanning.bam.bai"}
2025-09-15 20:25:00.340 wdl.w:ptcp.w:call-trgt-60 INFO visit :: node: "output-vcf", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-60/call-trgt_genotype/out/m84036_250809_035451_s4.bc2157.trgt.vcf"}
2025-09-15 20:25:00.341 wdl.w:ptcp.w:call-sawfish-71.t:call-run_sawfish NOTICE task setup :: name: "run_sawfish", source: "./sawfish.wdl", line: 83, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-71/call-run_sawfish", thread: 140612481291840
2025-09-15 20:25:00.356 wdl.w:ptcp.w:call-sawfish-71.t:call-run_sawfish INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:00.356 wdl.w:ptcp.w:call-sawfish-71.t:call-run_sawfish INFO input :: name: "genome_version", value: "38"
2025-09-15 20:25:00.356 wdl.w:ptcp.w:call-sawfish-71.t:call-run_sawfish INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:25:00.356 wdl.w:ptcp.w:call-sawfish-71.t:call-run_sawfish INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:25:00.357 wdl.w:ptcp.w:call-sawfish-71.t:call-run_sawfish INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2168.mapped.bam.bai"
2025-09-15 20:25:00.357 wdl.w:ptcp.w:call-sawfish-71.t:call-run_sawfish INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2168.mapped.bam"
2025-09-15 20:25:00.357 wdl.w:ptcp.w:call-sawfish-71.t:call-run_sawfish INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2168"
2025-09-15 20:25:00.357 wdl.w:ptcp.w:call-sawfish-71.t:call-run_sawfish INFO eval :: name: "mem_gb", value: 32
2025-09-15 20:25:00.357 wdl.w:ptcp.w:call-sawfish-71.t:call-run_sawfish INFO eval :: name: "threads", value: 16
2025-09-15 20:25:00.357 wdl.w:ptcp.w:call-sawfish-71.t:call-run_sawfish INFO eval :: name: "disk_size", value: 30
2025-09-15 20:25:00.357 wdl.w:ptcp.w:call-sawfish-71.t:call-run_sawfish INFO eval :: name: "discover_dirname", value: "m84036_250809_035451_s4.bc2168_sawfish_discover"
2025-09-15 20:25:00.357 wdl.w:ptcp.w:call-sawfish-71.t:call-run_sawfish INFO eval :: name: "call_dirname", value: "m84036_250809_035451_s4.bc2168_sawfish"
2025-09-15 20:25:00.357 wdl.w:ptcp.w:call-sawfish-71.t:call-run_sawfish INFO eval :: name: "minimap2_bam_filename", value: "m84036_250809_035451_s4.bc2168.minimap2.bam"
2025-09-15 20:25:00.358 wdl.w:ptcp.w:call-sawfish-71.t:call-run_sawfish INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 16, memory_reservation: 32000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:00.358 wdl.w:ptcp.w:call-sawfish-71.t:call-run_sawfish WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:00.358 wdl.w:ptcp.w:call-sawfish-71.t:call-run_sawfish INFO provisioned :: seconds_waited: 0, cpu: 16, mem_bytes: 32000000000
2025-09-15 20:25:00.358 wdl.w:ptcp.w:call-sawfish-71.t:call-run_sawfish INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:00.377 wdl.w:ptcp.w:call-trgt-55 NOTICE finish :: job: "call-trgt_plot_meth_allele"
2025-09-15 20:25:00.377 wdl.w:ptcp.w:call-trgt-55 INFO output :: job: "call-trgt_plot_meth_allele", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-55/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2152.meth_allele.trgt_plots.zip"}
2025-09-15 20:25:00.378 wdl.w:ptcp.w:call-trgt-55 INFO visit :: node: "output-images_meth_allele", values: {"images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-55/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2152.meth_allele.trgt_plots.zip"}
2025-09-15 20:25:00.385 wdl.w:ptcp.w:call-trgt-71.t:call-get_reads_overlapping_repeats NOTICE task setup :: name: "get_reads_overlapping_repeats", source: "./trgt.wdl", line: 182, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-71/call-get_reads_overlapping_repeats", thread: 140610895857216
2025-09-15 20:25:00.390 wdl.w:ptcp.w:call-trgt-49.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:25:00 [ERROR] - No reads found for TRID=PRTS_ARX
2025-09-15 20:25:00.390 wdl.w:ptcp.w:call-trgt-49.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:25:00 [ERROR] - No reads found for TRID=EIEE1_ARX
2025-09-15 20:25:00.404 wdl.w:ptcp.w:call-trgt-71.t:call-get_reads_overlapping_repeats INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:00.405 wdl.w:ptcp.w:call-trgt-71.t:call-get_reads_overlapping_repeats INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:25:00.405 wdl.w:ptcp.w:call-trgt-71.t:call-get_reads_overlapping_repeats INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2168.mapped.bam.bai"
2025-09-15 20:25:00.405 wdl.w:ptcp.w:call-trgt-71.t:call-get_reads_overlapping_repeats INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2168.mapped.bam"
2025-09-15 20:25:00.405 wdl.w:ptcp.w:call-trgt-71.t:call-get_reads_overlapping_repeats INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2168"
2025-09-15 20:25:00.405 wdl.w:ptcp.w:call-trgt-71.t:call-get_reads_overlapping_repeats INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:25:00.405 wdl.w:ptcp.w:call-trgt-71.t:call-get_reads_overlapping_repeats INFO eval :: name: "expand_size", value: 3000
2025-09-15 20:25:00.405 wdl.w:ptcp.w:call-trgt-71.t:call-get_reads_overlapping_repeats INFO eval :: name: "threads", value: 1
2025-09-15 20:25:00.405 wdl.w:ptcp.w:call-trgt-71.t:call-get_reads_overlapping_repeats INFO eval :: name: "expanded_bed_name", value: "m84036_250809_035451_s4.bc2168.expanded.bed"
2025-09-15 20:25:00.406 wdl.w:ptcp.w:call-trgt-71.t:call-get_reads_overlapping_repeats INFO eval :: name: "disk_size", value: 11
2025-09-15 20:25:00.406 wdl.w:ptcp.w:call-trgt-71.t:call-get_reads_overlapping_repeats INFO eval :: name: "output_name", value: "m84036_250809_035451_s4.bc2168.repeats.bam"
2025-09-15 20:25:00.406 wdl.w:ptcp.w:call-trgt-71.t:call-get_reads_overlapping_repeats INFO eval :: name: "index_name", value: "m84036_250809_035451_s4.bc2168.repeats.bam.bai"
2025-09-15 20:25:00.406 wdl.w:ptcp.w:call-trgt-71.t:call-get_reads_overlapping_repeats INFO eval :: name: "output_name_with_index", value: "m84036_250809_035451_s4.bc2168.repeats.bam##idx##m84036_250809_035451_s4.bc2168.repeats.bam.bai"
2025-09-15 20:25:00.406 wdl.w:ptcp.w:call-trgt-71.t:call-get_reads_overlapping_repeats INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:00.406 wdl.w:ptcp.w:call-trgt-71.t:call-get_reads_overlapping_repeats WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:00.407 wdl.w:ptcp.w:call-trgt-71.t:call-get_reads_overlapping_repeats INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:25:00.407 wdl.w:ptcp.w:call-trgt-71.t:call-get_reads_overlapping_repeats INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:00.413 wdl.w:ptcp.w:call-sawfish-71.t:call-run_sawfish INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 10, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-71/call-run_sawfish/_singularity_tmpdir_qc2vvozh"
2025-09-15 20:25:00.413 wdl.w:ptcp.w:call-sawfish-71.t:call-run_sawfish INFO Slurm invocation: srun --job-name call-run_sawfish --partition compute,compute9 --cpus-per-task 16 --mem 30518M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-71/call-run_sawfish/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-71/call-run_sawfish/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-71/call-run_sawfish/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-71/call-run_sawfish/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-71/out/m84036_250809_035451_s4.bc2168.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2168.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-71/out/m84036_250809_035451_s4.bc2168.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2168.mapped.bam:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-71/call-run_sawfish/_singularity_tmpdir_qc2vvozh/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-71/call-run_sawfish/_singularity_tmpdir_qc2vvozh/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:00.432 wdl.w:ptcp.w:call-sawfish-71.t:call-run_sawfish NOTICE slurm_singularity run :: pid: 1204055, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-71/call-run_sawfish/slurm_singularity.log.txt"
2025-09-15 20:25:00.455 wdl.w:ptcp.w:call-trgt-71.t:call-get_reads_overlapping_repeats INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 9, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-71/call-get_reads_overlapping_repeats/_singularity_tmpdir_sh0a65tf"
2025-09-15 20:25:00.455 wdl.w:ptcp.w:call-trgt-71.t:call-get_reads_overlapping_repeats INFO Slurm invocation: srun --job-name call-get_reads_overlapping_repeats --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-71/call-get_reads_overlapping_repeats/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-71/call-get_reads_overlapping_repeats/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-71/call-get_reads_overlapping_repeats/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-71/call-get_reads_overlapping_repeats/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-71/out/m84036_250809_035451_s4.bc2168.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2168.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-71/out/m84036_250809_035451_s4.bc2168.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2168.mapped.bam:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-71/call-get_reads_overlapping_repeats/_singularity_tmpdir_sh0a65tf/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-71/call-get_reads_overlapping_repeats/_singularity_tmpdir_sh0a65tf/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:00.464 wdl.w:ptcp.w:call-trgt-71.t:call-get_reads_overlapping_repeats NOTICE slurm_singularity run :: pid: 1204090, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-71/call-get_reads_overlapping_repeats/slurm_singularity.log.txt"
2025-09-15 20:25:00.508 wdl.w:ptcp.w:call-paraphase-50.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for hba for sample m84036_250809_035451_s4.bc2147 at 2025-09-15 20:24:36.417648...
2025-09-15 20:25:00.509 wdl.w:ptcp.w:call-paraphase-50.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for smn1 for sample m84036_250809_035451_s4.bc2147 at 2025-09-15 20:24:36.817534...
2025-09-15 20:25:00.509 wdl.w:ptcp.w:call-paraphase-50.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for gba for sample m84036_250809_035451_s4.bc2147 at 2025-09-15 20:24:36.892205...
2025-09-15 20:25:00.509 wdl.w:ptcp.w:call-paraphase-50.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for cyp21 for sample m84036_250809_035451_s4.bc2147 at 2025-09-15 20:24:37.323984...
2025-09-15 20:25:00.509 wdl.w:ptcp.w:call-paraphase-50.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for smn1 for sample m84036_250809_035451_s4.bc2147 at 2025-09-15 20:24:49.799727...
2025-09-15 20:25:00.509 wdl.w:ptcp.w:call-paraphase-50.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning to gene2 region for smn1 for sample m84036_250809_035451_s4.bc2147 at 2025-09-15 20:24:50.231054...
2025-09-15 20:25:00.519 wdl.w:ptcp.w:call-trgt-56.t:call-trgt_plot_meth_allele.slurm_singularity INFO srun: job 51797859 queued and waiting for resources
2025-09-15 20:25:00.520 wdl.w:ptcp.w:call-trgt-56.t:call-trgt_plot_meth_allele.slurm_singularity INFO srun: job 51797859 has been allocated resources
2025-09-15 20:25:00.520 wdl.w:ptcp.w:call-trgt-56.t:call-trgt_plot_meth_allele.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:00.643 wdl.w:ptcp.w:call-sawfish-16.t:call-run_sawfish INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2113_sawfish/m84036_250809_035451_s4.bc2113.sv.vcf.gz"
2025-09-15 20:25:00.649 wdl.w:ptcp.w:call-sawfish-16.t:call-run_sawfish INFO output :: name: "vcf_tbi", value: "m84036_250809_035451_s4.bc2113_sawfish/m84036_250809_035451_s4.bc2113.sv.vcf.gz.tbi"
2025-09-15 20:25:00.651 wdl.w:ptcp.w:call-sawfish-16.t:call-run_sawfish INFO output :: name: "minimap2_bam", value: "m84036_250809_035451_s4.bc2113.minimap2.bam"
2025-09-15 20:25:00.653 wdl.w:ptcp.w:call-sawfish-16.t:call-run_sawfish INFO output :: name: "minimap2_bam_bai", value: "m84036_250809_035451_s4.bc2113.minimap2.bam.bai"
2025-09-15 20:25:00.706 wdl.w:ptcp.w:call-trgt-56.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO srun: job 51797860 queued and waiting for resources
2025-09-15 20:25:00.706 wdl.w:ptcp.w:call-trgt-56.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO srun: job 51797860 has been allocated resources
2025-09-15 20:25:00.707 wdl.w:ptcp.w:call-trgt-56.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:00.744 wdl.w:ptcp.w:call-trgt-56.t:call-trgt_plot_motifs_allele.slurm_singularity INFO srun: job 51797861 queued and waiting for resources
2025-09-15 20:25:00.744 wdl.w:ptcp.w:call-trgt-56.t:call-trgt_plot_motifs_allele.slurm_singularity INFO srun: job 51797861 has been allocated resources
2025-09-15 20:25:00.744 wdl.w:ptcp.w:call-trgt-56.t:call-trgt_plot_motifs_allele.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:00.777 wdl.w:ptcp.w:call-sawfish-16.t:call-run_sawfish NOTICE done
2025-09-15 20:25:00.783 wdl.w:ptcp.w:call-sawfish-16 NOTICE finish :: job: "call-run_sawfish"
2025-09-15 20:25:00.783 wdl.w:ptcp.w:call-sawfish-16 INFO output :: job: "call-run_sawfish", values: {"minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-16/call-run_sawfish/out/m84036_250809_035451_s4.bc2113.minimap2.bam.bai", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-16/call-run_sawfish/out/m84036_250809_035451_s4.bc2113.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-16/call-run_sawfish/out/m84036_250809_035451_s4.bc2113_sawfish/m84036_250809_035451_s4.bc2113.sv.vcf.gz.tbi", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-16/call-run_sawfish/out/m84036_250809_035451_s4.bc2113_sawfish/m84036_250809_035451_s4.bc2113.sv.vcf.gz"}
2025-09-15 20:25:00.783 wdl.w:ptcp.w:call-sawfish-16 INFO visit :: node: "output-minimap2_bam", values: {"minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-16/call-run_sawfish/out/m84036_250809_035451_s4.bc2113.minimap2.bam"}
2025-09-15 20:25:00.783 wdl.w:ptcp.w:call-sawfish-16 INFO visit :: node: "output-minimap2_bam_bai", values: {"minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-16/call-run_sawfish/out/m84036_250809_035451_s4.bc2113.minimap2.bam.bai"}
2025-09-15 20:25:00.783 wdl.w:ptcp.w:call-sawfish-16 INFO visit :: node: "output-vcf", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-16/call-run_sawfish/out/m84036_250809_035451_s4.bc2113_sawfish/m84036_250809_035451_s4.bc2113.sv.vcf.gz"}
2025-09-15 20:25:00.783 wdl.w:ptcp.w:call-sawfish-16 INFO visit :: node: "output-vcf_tbi", values: {"vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-16/call-run_sawfish/out/m84036_250809_035451_s4.bc2113_sawfish/m84036_250809_035451_s4.bc2113.sv.vcf.gz.tbi"}
2025-09-15 20:25:00.784 wdl.w:ptcp.w:call-sawfish-16 INFO visit :: node: "outputs", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-16/call-run_sawfish/out/m84036_250809_035451_s4.bc2113_sawfish/m84036_250809_035451_s4.bc2113.sv.vcf.gz", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-16/call-run_sawfish/out/m84036_250809_035451_s4.bc2113.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-16/call-run_sawfish/out/m84036_250809_035451_s4.bc2113_sawfish/m84036_250809_035451_s4.bc2113.sv.vcf.gz.tbi", "minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-16/call-run_sawfish/out/m84036_250809_035451_s4.bc2113.minimap2.bam.bai"}
2025-09-15 20:25:00.788 wdl.w:ptcp.w:call-trgt-71.t:call-trgt_genotype NOTICE task setup :: name: "trgt_genotype", source: "./trgt.wdl", line: 272, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-71/call-trgt_genotype", thread: 140611457906240
2025-09-15 20:25:00.812 wdl.w:ptcp.w:call-trgt-71.t:call-trgt_genotype INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:00.812 wdl.w:ptcp.w:call-trgt-71.t:call-trgt_genotype INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:25:00.813 wdl.w:ptcp.w:call-trgt-71.t:call-trgt_genotype INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:25:00.813 wdl.w:ptcp.w:call-trgt-71.t:call-trgt_genotype INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:25:00.813 wdl.w:ptcp.w:call-trgt-71.t:call-trgt_genotype INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2168.mapped.bam.bai"
2025-09-15 20:25:00.813 wdl.w:ptcp.w:call-trgt-71.t:call-trgt_genotype INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2168.mapped.bam"
2025-09-15 20:25:00.813 wdl.w:ptcp.w:call-trgt-71.t:call-trgt_genotype INFO input :: name: "sex", value: "F"
2025-09-15 20:25:00.813 wdl.w:ptcp.w:call-trgt-71.t:call-trgt_genotype INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2168"
2025-09-15 20:25:00.813 wdl.w:ptcp.w:call-trgt-71.t:call-trgt_genotype INFO eval :: name: "mem_gb", value: 16
2025-09-15 20:25:00.813 wdl.w:ptcp.w:call-trgt-71.t:call-trgt_genotype INFO eval :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2168.trgt"
2025-09-15 20:25:00.813 wdl.w:ptcp.w:call-trgt-71.t:call-trgt_genotype INFO eval :: name: "threads", value: 8
2025-09-15 20:25:00.814 wdl.w:ptcp.w:call-trgt-71.t:call-trgt_genotype INFO eval :: name: "disk_size", value: 27
2025-09-15 20:25:00.814 wdl.w:ptcp.w:call-trgt-71.t:call-trgt_genotype INFO eval :: name: "karyotype", value: "XX"
2025-09-15 20:25:00.814 wdl.w:ptcp.w:call-trgt-71.t:call-trgt_genotype INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 8, memory_reservation: 16000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:00.814 wdl.w:ptcp.w:call-trgt-71.t:call-trgt_genotype WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:00.814 wdl.w:ptcp.w:call-trgt-71.t:call-trgt_genotype INFO provisioned :: seconds_waited: 0, cpu: 8, mem_bytes: 16000000000
2025-09-15 20:25:00.815 wdl.w:ptcp.w:call-trgt-71.t:call-trgt_genotype INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:00.827 wdl.w:ptcp.w:call-sawfish-16 NOTICE done
2025-09-15 20:25:00.835 wdl.w:ptcp NOTICE finish :: job: "call-sawfish-16"
2025-09-15 20:25:00.836 wdl.w:ptcp INFO output :: job: "call-sawfish-16", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-16/out/m84036_250809_035451_s4.bc2113_sawfish/m84036_250809_035451_s4.bc2113.sv.vcf.gz", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-16/out/m84036_250809_035451_s4.bc2113.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-16/out/m84036_250809_035451_s4.bc2113_sawfish/m84036_250809_035451_s4.bc2113.sv.vcf.gz.tbi", "minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-16/out/m84036_250809_035451_s4.bc2113.minimap2.bam.bai"}
2025-09-15 20:25:00.836 wdl.w:ptcp NOTICE ready :: job: "call-tar_outputs-16", callee: "tar_outputs"
2025-09-15 20:25:00.837 wdl.w:ptcp INFO input :: job: "call-tar_outputs-16", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "sawfish_vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-16/out/m84036_250809_035451_s4.bc2113_sawfish/m84036_250809_035451_s4.bc2113.sv.vcf.gz.tbi", "sawfish_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-16/out/m84036_250809_035451_s4.bc2113_sawfish/m84036_250809_035451_s4.bc2113.sv.vcf.gz", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-16/out/m84036_250809_035451_s4.bc2113.f8inversion.json", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-16/out/m84036_250809_035451_s4.bc2113_paraphase/m84036_250809_035451_s4.bc2113.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-16/out/m84036_250809_035451_s4.bc2113_paraphase/m84036_250809_035451_s4.bc2113.paraphase.bam", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-16/out/m84036_250809_035451_s4.bc2113_paraphase/m84036_250809_035451_s4.bc2113.paraphase.json", "trgt_spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-16/out/m84036_250809_035451_s4.bc2113.trgt.sorted.spanning.bam.bai", "trgt_spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-16/out/m84036_250809_035451_s4.bc2113.trgt.sorted.spanning.bam", "trgt_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-16/out/m84036_250809_035451_s4.bc2113.trgt.vcf", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-16/out/m84036_250809_035451_s4.bc2113.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-16/out/m84036_250809_035451_s4.bc2113.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2113"}
2025-09-15 20:25:00.847 wdl.w:ptcp.w:call-paraphase-77 NOTICE workflow start :: name: "paraphase", source: "./paraphase.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-77"
2025-09-15 20:25:00.865 wdl.w:ptcp.w:call-paraphase-77 INFO visit :: node: "decl-annotation_vcf", values: {"annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf"}
2025-09-15 20:25:00.866 wdl.w:ptcp.w:call-paraphase-77 INFO visit :: node: "decl-config_file", values: {"config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml"}
2025-09-15 20:25:00.866 wdl.w:ptcp.w:call-paraphase-77 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:25:00.866 wdl.w:ptcp.w:call-paraphase-77 INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:25:00.866 wdl.w:ptcp.w:call-paraphase-77 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-77/out/m84036_250809_035451_s4.bc2174.mapped.bam"}
2025-09-15 20:25:00.866 wdl.w:ptcp.w:call-paraphase-77 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-77/out/m84036_250809_035451_s4.bc2174.mapped.bam.bai"}
2025-09-15 20:25:00.866 wdl.w:ptcp.w:call-paraphase-77 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:25:00.866 wdl.w:ptcp.w:call-paraphase-77 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:25:00.866 wdl.w:ptcp.w:call-paraphase-77 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2174"}
2025-09-15 20:25:00.866 wdl.w:ptcp.w:call-paraphase-77 INFO visit :: node: "decl-sex", values: {"sex": "F"}
2025-09-15 20:25:00.866 wdl.w:ptcp.w:call-paraphase-77 NOTICE ready :: job: "call-run_paraphase", callee: "run_paraphase"
2025-09-15 20:25:00.867 wdl.w:ptcp.w:call-paraphase-77 INFO input :: job: "call-run_paraphase", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf", "genome_version": "38", "config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-77/out/m84036_250809_035451_s4.bc2174.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-77/out/m84036_250809_035451_s4.bc2174.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2174"}
2025-09-15 20:25:00.878 wdl.w:ptcp.w:call-trgt-60.t:call-get_reads_overlapping_repeats INFO output :: name: "reads_overlapping_repeats", value: "m84036_250809_035451_s4.bc2157.repeats.bam"
2025-09-15 20:25:00.884 wdl.w:ptcp.w:call-trgt-60.t:call-get_reads_overlapping_repeats INFO output :: name: "reads_overlapping_repeats_bai", value: "m84036_250809_035451_s4.bc2157.repeats.bam.bai"
2025-09-15 20:25:00.886 wdl.w:ptcp.w:call-trgt-71.t:call-trgt_genotype INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 11, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-71/call-trgt_genotype/_singularity_tmpdir_jjwt0uad"
2025-09-15 20:25:00.886 wdl.w:ptcp.w:call-trgt-71.t:call-trgt_genotype INFO Slurm invocation: srun --job-name call-trgt_genotype --partition compute,compute9 --cpus-per-task 8 --mem 15259M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-71/call-trgt_genotype/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-71/call-trgt_genotype/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-71/call-trgt_genotype/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-71/call-trgt_genotype/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-71/out/m84036_250809_035451_s4.bc2168.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2168.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-71/out/m84036_250809_035451_s4.bc2168.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2168.mapped.bam:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-71/call-trgt_genotype/_singularity_tmpdir_jjwt0uad/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-71/call-trgt_genotype/_singularity_tmpdir_jjwt0uad/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:00.915 wdl.w:ptcp.w:call-trgt-71.t:call-trgt_genotype NOTICE slurm_singularity run :: pid: 1204338, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-71/call-trgt_genotype/slurm_singularity.log.txt"
2025-09-15 20:25:00.919 wdl.w:ptcp.w:call-sawfish-25.t:call-run_sawfish INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2122_sawfish/m84036_250809_035451_s4.bc2122.sv.vcf.gz"
2025-09-15 20:25:00.926 wdl.w:ptcp.w:call-sawfish-25.t:call-run_sawfish INFO output :: name: "vcf_tbi", value: "m84036_250809_035451_s4.bc2122_sawfish/m84036_250809_035451_s4.bc2122.sv.vcf.gz.tbi"
2025-09-15 20:25:00.927 wdl.w:ptcp.w:call-trgt-56.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO srun: job 51797862 queued and waiting for resources
2025-09-15 20:25:00.927 wdl.w:ptcp.w:call-trgt-56.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO srun: job 51797862 has been allocated resources
2025-09-15 20:25:00.927 wdl.w:ptcp.w:call-trgt-56.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:00.928 wdl.w:ptcp.w:call-sawfish-25.t:call-run_sawfish INFO output :: name: "minimap2_bam", value: "m84036_250809_035451_s4.bc2122.minimap2.bam"
2025-09-15 20:25:00.930 wdl.w:ptcp.w:call-sawfish-25.t:call-run_sawfish INFO output :: name: "minimap2_bam_bai", value: "m84036_250809_035451_s4.bc2122.minimap2.bam.bai"
2025-09-15 20:25:00.951 wdl.w:ptcp.w:call-trgt-60.t:call-get_reads_overlapping_repeats NOTICE done
2025-09-15 20:25:00.956 wdl.w:ptcp.w:call-trgt-60 NOTICE finish :: job: "call-get_reads_overlapping_repeats"
2025-09-15 20:25:00.956 wdl.w:ptcp.w:call-trgt-60 INFO output :: job: "call-get_reads_overlapping_repeats", values: {"reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-60/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2157.repeats.bam.bai", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-60/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2157.repeats.bam"}
2025-09-15 20:25:00.957 wdl.w:ptcp.w:call-trgt-60 INFO visit :: node: "output-reads_overlapping_repeats", values: {"reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-60/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2157.repeats.bam"}
2025-09-15 20:25:00.957 wdl.w:ptcp.w:call-trgt-60 INFO visit :: node: "output-reads_overlapping_repeats_bai", values: {"reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-60/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2157.repeats.bam.bai"}
2025-09-15 20:25:00.965 wdl.w:ptcp.t:call-tar_outputs-20 NOTICE task setup :: name: "tar_outputs", source: "./common.wdl", line: 279, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-20", thread: 140610367379008
2025-09-15 20:25:00.978 wdl.w:ptcp.w:call-sawfish-65.t:call-run_sawfish.stderr VERBOSE [M::bam2fq_mainloop] discarded 0 singletons
2025-09-15 20:25:00.978 wdl.w:ptcp.w:call-sawfish-65.t:call-run_sawfish.stderr VERBOSE [M::bam2fq_mainloop] processed 0 reads
2025-09-15 20:25:00.992 wdl.w:ptcp.t:call-tar_outputs-20 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:00.992 wdl.w:ptcp.t:call-tar_outputs-20 INFO input :: name: "sawfish_vcf_tbi", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2117.sv.vcf.gz.tbi"
2025-09-15 20:25:00.992 wdl.w:ptcp.t:call-tar_outputs-20 INFO input :: name: "sawfish_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2117.sv.vcf.gz"
2025-09-15 20:25:00.992 wdl.w:ptcp.t:call-tar_outputs-20 INFO input :: name: "f8_json", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2117.f8inversion.json"
2025-09-15 20:25:00.992 wdl.w:ptcp.t:call-tar_outputs-20 INFO input :: name: "paraphase_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2117.paraphase.bam.bai"
2025-09-15 20:25:00.992 wdl.w:ptcp.t:call-tar_outputs-20 INFO input :: name: "paraphase_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2117.paraphase.bam"
2025-09-15 20:25:00.992 wdl.w:ptcp.t:call-tar_outputs-20 INFO input :: name: "paraphase_json", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2117.paraphase.json"
2025-09-15 20:25:00.992 wdl.w:ptcp.t:call-tar_outputs-20 INFO input :: name: "trgt_spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2117.trgt.sorted.spanning.bam.bai"
2025-09-15 20:25:00.992 wdl.w:ptcp.t:call-tar_outputs-20 INFO input :: name: "trgt_spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2117.trgt.sorted.spanning.bam"
2025-09-15 20:25:00.992 wdl.w:ptcp.t:call-tar_outputs-20 INFO input :: name: "trgt_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2117.trgt.vcf"
2025-09-15 20:25:00.992 wdl.w:ptcp.t:call-tar_outputs-20 INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2117.mapped.bam.bai"
2025-09-15 20:25:00.992 wdl.w:ptcp.t:call-tar_outputs-20 INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2117.mapped.bam"
2025-09-15 20:25:00.992 wdl.w:ptcp.t:call-tar_outputs-20 INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2117"
2025-09-15 20:25:00.992 wdl.w:ptcp.t:call-tar_outputs-20 INFO eval :: name: "threads", value: 1
2025-09-15 20:25:00.993 wdl.w:ptcp.t:call-tar_outputs-20 INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:25:00.993 wdl.w:ptcp.t:call-tar_outputs-20 INFO eval :: name: "disk_size", value: 6
2025-09-15 20:25:00.993 wdl.w:ptcp.t:call-tar_outputs-20 INFO eval :: name: "output_tarball", value: "m84036_250809_035451_s4.bc2117.tar"
2025-09-15 20:25:00.993 wdl.w:ptcp.t:call-tar_outputs-20 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:00.993 wdl.w:ptcp.t:call-tar_outputs-20 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:00.994 wdl.w:ptcp.t:call-tar_outputs-20 INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:25:00.994 wdl.w:ptcp.t:call-tar_outputs-20 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:01.068 wdl.w:ptcp.w:call-sawfish-25.t:call-run_sawfish NOTICE done
2025-09-15 20:25:01.075 wdl.w:ptcp.w:call-sawfish-25 NOTICE finish :: job: "call-run_sawfish"
2025-09-15 20:25:01.075 wdl.w:ptcp.w:call-sawfish-25 INFO output :: job: "call-run_sawfish", values: {"minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-25/call-run_sawfish/out/m84036_250809_035451_s4.bc2122.minimap2.bam.bai", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-25/call-run_sawfish/out/m84036_250809_035451_s4.bc2122.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-25/call-run_sawfish/out/m84036_250809_035451_s4.bc2122_sawfish/m84036_250809_035451_s4.bc2122.sv.vcf.gz.tbi", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-25/call-run_sawfish/out/m84036_250809_035451_s4.bc2122_sawfish/m84036_250809_035451_s4.bc2122.sv.vcf.gz"}
2025-09-15 20:25:01.076 wdl.w:ptcp.w:call-sawfish-25 INFO visit :: node: "output-minimap2_bam", values: {"minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-25/call-run_sawfish/out/m84036_250809_035451_s4.bc2122.minimap2.bam"}
2025-09-15 20:25:01.076 wdl.w:ptcp.w:call-sawfish-25 INFO visit :: node: "output-minimap2_bam_bai", values: {"minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-25/call-run_sawfish/out/m84036_250809_035451_s4.bc2122.minimap2.bam.bai"}
2025-09-15 20:25:01.076 wdl.w:ptcp.w:call-sawfish-25 INFO visit :: node: "output-vcf", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-25/call-run_sawfish/out/m84036_250809_035451_s4.bc2122_sawfish/m84036_250809_035451_s4.bc2122.sv.vcf.gz"}
2025-09-15 20:25:01.076 wdl.w:ptcp.w:call-sawfish-25 INFO visit :: node: "output-vcf_tbi", values: {"vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-25/call-run_sawfish/out/m84036_250809_035451_s4.bc2122_sawfish/m84036_250809_035451_s4.bc2122.sv.vcf.gz.tbi"}
2025-09-15 20:25:01.076 wdl.w:ptcp.w:call-sawfish-25 INFO visit :: node: "outputs", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-25/call-run_sawfish/out/m84036_250809_035451_s4.bc2122_sawfish/m84036_250809_035451_s4.bc2122.sv.vcf.gz", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-25/call-run_sawfish/out/m84036_250809_035451_s4.bc2122.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-25/call-run_sawfish/out/m84036_250809_035451_s4.bc2122_sawfish/m84036_250809_035451_s4.bc2122.sv.vcf.gz.tbi", "minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-25/call-run_sawfish/out/m84036_250809_035451_s4.bc2122.minimap2.bam.bai"}
2025-09-15 20:25:01.084 wdl.w:ptcp.w:call-paraphase-68.t:call-run_paraphase NOTICE task setup :: name: "run_paraphase", source: "./paraphase.wdl", line: 127, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-68/call-run_paraphase", thread: 140609830508096
2025-09-15 20:25:01.102 wdl.w:ptcp.t:call-tar_outputs-20 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 17, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-20/_singularity_tmpdir_8gwiflt5"
2025-09-15 20:25:01.102 wdl.w:ptcp.t:call-tar_outputs-20 INFO Slurm invocation: srun --job-name call-tar_outputs-20 --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-20/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-20/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-20/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-20/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-20/out/m84036_250809_035451_s4.bc2117_paraphase/m84036_250809_035451_s4.bc2117.paraphase.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2117.paraphase.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-20/out/m84036_250809_035451_s4.bc2117_paraphase/m84036_250809_035451_s4.bc2117.paraphase.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2117.paraphase.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-20/out/m84036_250809_035451_s4.bc2117_paraphase/m84036_250809_035451_s4.bc2117.paraphase.json:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2117.paraphase.json:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-20/out/m84036_250809_035451_s4.bc2117.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2117.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-20/out/m84036_250809_035451_s4.bc2117.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2117.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-20/out/m84036_250809_035451_s4.bc2117.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2117.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-20/out/m84036_250809_035451_s4.bc2117.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2117.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-20/out/m84036_250809_035451_s4.bc2117.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2117.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-20/out/m84036_250809_035451_s4.bc2117_sawfish/m84036_250809_035451_s4.bc2117.sv.vcf.gz:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2117.sv.vcf.gz:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-20/out/m84036_250809_035451_s4.bc2117_sawfish/m84036_250809_035451_s4.bc2117.sv.vcf.gz.tbi:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2117.sv.vcf.gz.tbi:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-20/out/m84036_250809_035451_s4.bc2117.f8inversion.json:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2117.f8inversion.json:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-20/_singularity_tmpdir_8gwiflt5/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-20/_singularity_tmpdir_8gwiflt5/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:01.113 wdl.w:ptcp.w:call-paraphase-68.t:call-run_paraphase INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:01.113 wdl.w:ptcp.w:call-paraphase-68.t:call-run_paraphase INFO input :: name: "annotation_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf"
2025-09-15 20:25:01.113 wdl.w:ptcp.w:call-paraphase-68.t:call-run_paraphase INFO input :: name: "genome_version", value: "38"
2025-09-15 20:25:01.113 wdl.w:ptcp.w:call-paraphase-68.t:call-run_paraphase INFO input :: name: "config_file", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/paraphase_config.GRCh38.yaml"
2025-09-15 20:25:01.113 wdl.w:ptcp.w:call-paraphase-68.t:call-run_paraphase INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:25:01.113 wdl.w:ptcp.w:call-paraphase-68.t:call-run_paraphase INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:25:01.113 wdl.w:ptcp.w:call-paraphase-68.t:call-run_paraphase INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2165.mapped.bam.bai"
2025-09-15 20:25:01.113 wdl.w:ptcp.w:call-paraphase-68.t:call-run_paraphase INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2165.mapped.bam"
2025-09-15 20:25:01.113 wdl.w:ptcp.w:call-paraphase-68.t:call-run_paraphase INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2165"
2025-09-15 20:25:01.114 wdl.w:ptcp.w:call-paraphase-68.t:call-run_paraphase INFO eval :: name: "threads", value: 4
2025-09-15 20:25:01.114 wdl.w:ptcp.w:call-paraphase-68.t:call-run_paraphase INFO eval :: name: "mem_gb", value: 8
2025-09-15 20:25:01.114 wdl.w:ptcp.w:call-paraphase-68.t:call-run_paraphase INFO eval :: name: "disk_size", value: 27
2025-09-15 20:25:01.114 wdl.w:ptcp.w:call-paraphase-68.t:call-run_paraphase INFO eval :: name: "out_dir", value: "m84036_250809_035451_s4.bc2165_paraphase"
2025-09-15 20:25:01.114 wdl.w:ptcp.w:call-paraphase-68.t:call-run_paraphase INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 4, memory_reservation: 8000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:01.115 wdl.w:ptcp.w:call-paraphase-68.t:call-run_paraphase WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:01.115 wdl.w:ptcp.w:call-paraphase-68.t:call-run_paraphase INFO provisioned :: seconds_waited: 0, cpu: 4, mem_bytes: 8000000000
2025-09-15 20:25:01.115 wdl.w:ptcp.w:call-paraphase-68.t:call-run_paraphase INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:01.134 wdl.w:ptcp.t:call-tar_outputs-20 NOTICE slurm_singularity run :: pid: 1204340, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-20/slurm_singularity.log.txt"
2025-09-15 20:25:01.150 wdl.w:ptcp.w:call-sawfish-25 NOTICE done
2025-09-15 20:25:01.158 wdl.w:ptcp NOTICE finish :: job: "call-sawfish-25"
2025-09-15 20:25:01.158 wdl.w:ptcp INFO output :: job: "call-sawfish-25", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-25/out/m84036_250809_035451_s4.bc2122_sawfish/m84036_250809_035451_s4.bc2122.sv.vcf.gz", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-25/out/m84036_250809_035451_s4.bc2122.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-25/out/m84036_250809_035451_s4.bc2122_sawfish/m84036_250809_035451_s4.bc2122.sv.vcf.gz.tbi", "minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-25/out/m84036_250809_035451_s4.bc2122.minimap2.bam.bai"}
2025-09-15 20:25:01.159 wdl.w:ptcp NOTICE ready :: job: "call-tar_outputs-25", callee: "tar_outputs"
2025-09-15 20:25:01.159 wdl.w:ptcp INFO input :: job: "call-tar_outputs-25", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "sawfish_vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-25/out/m84036_250809_035451_s4.bc2122_sawfish/m84036_250809_035451_s4.bc2122.sv.vcf.gz.tbi", "sawfish_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-25/out/m84036_250809_035451_s4.bc2122_sawfish/m84036_250809_035451_s4.bc2122.sv.vcf.gz", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-25/out/m84036_250809_035451_s4.bc2122.f8inversion.json", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-25/out/m84036_250809_035451_s4.bc2122_paraphase/m84036_250809_035451_s4.bc2122.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-25/out/m84036_250809_035451_s4.bc2122_paraphase/m84036_250809_035451_s4.bc2122.paraphase.bam", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-25/out/m84036_250809_035451_s4.bc2122_paraphase/m84036_250809_035451_s4.bc2122.paraphase.json", "trgt_spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-25/out/m84036_250809_035451_s4.bc2122.trgt.sorted.spanning.bam.bai", "trgt_spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-25/out/m84036_250809_035451_s4.bc2122.trgt.sorted.spanning.bam", "trgt_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-25/out/m84036_250809_035451_s4.bc2122.trgt.vcf", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-25/out/m84036_250809_035451_s4.bc2122.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-25/out/m84036_250809_035451_s4.bc2122.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2122"}
2025-09-15 20:25:01.167 wdl.w:ptcp.w:call-sawfish-77 NOTICE workflow start :: name: "sawfish", source: "./sawfish.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-77"
2025-09-15 20:25:01.181 wdl.w:ptcp.w:call-sawfish-77 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:25:01.181 wdl.w:ptcp.w:call-sawfish-77 INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:25:01.181 wdl.w:ptcp.w:call-sawfish-77 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-77/out/m84036_250809_035451_s4.bc2174.mapped.bam"}
2025-09-15 20:25:01.182 wdl.w:ptcp.w:call-sawfish-77 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-77/out/m84036_250809_035451_s4.bc2174.mapped.bam.bai"}
2025-09-15 20:25:01.182 wdl.w:ptcp.w:call-sawfish-77 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:25:01.182 wdl.w:ptcp.w:call-sawfish-77 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:25:01.182 wdl.w:ptcp.w:call-sawfish-77 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2174"}
2025-09-15 20:25:01.182 wdl.w:ptcp.w:call-sawfish-77 NOTICE ready :: job: "call-run_sawfish", callee: "run_sawfish"
2025-09-15 20:25:01.182 wdl.w:ptcp.w:call-sawfish-77 INFO input :: job: "call-run_sawfish", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-77/out/m84036_250809_035451_s4.bc2174.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-77/out/m84036_250809_035451_s4.bc2174.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2174"}
2025-09-15 20:25:01.220 wdl.w:ptcp.w:call-paraphase-68.t:call-run_paraphase INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-68/call-run_paraphase/_singularity_tmpdir_6ml7n388"
2025-09-15 20:25:01.220 wdl.w:ptcp.w:call-paraphase-68.t:call-run_paraphase INFO Slurm invocation: srun --job-name call-run_paraphase --partition compute,compute9 --cpus-per-task 4 --mem 7629M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-68/call-run_paraphase/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-68/call-run_paraphase/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-68/call-run_paraphase/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-68/call-run_paraphase/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-68/out/m84036_250809_035451_s4.bc2165.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2165.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-68/out/m84036_250809_035451_s4.bc2165.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2165.mapped.bam.bai:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/variant_list/variant_list.GRCh38.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf:ro --bind /ptcp/meta/paraphase/paraphase_config.GRCh38.yaml:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/paraphase_config.GRCh38.yaml:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-68/call-run_paraphase/_singularity_tmpdir_6ml7n388/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-68/call-run_paraphase/_singularity_tmpdir_6ml7n388/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:01.232 wdl.w:ptcp.w:call-paraphase-68.t:call-run_paraphase NOTICE slurm_singularity run :: pid: 1204342, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-68/call-run_paraphase/slurm_singularity.log.txt"
2025-09-15 20:25:01.318 wdl.w:ptcp.t:call-tar_outputs-33.slurm_singularity INFO srun: job 51797863 queued and waiting for resources
2025-09-15 20:25:01.319 wdl.w:ptcp.t:call-tar_outputs-33.slurm_singularity INFO srun: job 51797863 has been allocated resources
2025-09-15 20:25:01.319 wdl.w:ptcp.t:call-tar_outputs-33.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:01.439 wdl.w:ptcp.w:call-sawfish-71.t:call-run_sawfish.slurm_singularity INFO srun: job 51797864 queued and waiting for resources
2025-09-15 20:25:01.440 wdl.w:ptcp.w:call-sawfish-71.t:call-run_sawfish.slurm_singularity INFO srun: job 51797864 has been allocated resources
2025-09-15 20:25:01.440 wdl.w:ptcp.w:call-sawfish-71.t:call-run_sawfish.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:01.440 wdl.w:ptcp.w:call-sawfish-71.t:call-run_sawfish.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:25:01.451 wdl.w:ptcp.w:call-paraphase-26.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for hbb for sample m84036_250809_035451_s4.bc2123 at 2025-09-15 20:24:54.367252...
2025-09-15 20:25:01.451 wdl.w:ptcp.w:call-paraphase-26.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for hbb for sample m84036_250809_035451_s4.bc2123 at 2025-09-15 20:24:54.368284...
2025-09-15 20:25:01.451 wdl.w:ptcp.w:call-paraphase-26.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for hbb for sample m84036_250809_035451_s4.bc2123 at 2025-09-15 20:24:55.574702...
2025-09-15 20:25:01.472 wdl.w:ptcp.w:call-trgt-71.t:call-get_reads_overlapping_repeats.slurm_singularity INFO srun: job 51797865 queued and waiting for resources
2025-09-15 20:25:01.472 wdl.w:ptcp.w:call-trgt-71.t:call-get_reads_overlapping_repeats.slurm_singularity INFO srun: job 51797865 has been allocated resources
2025-09-15 20:25:01.472 wdl.w:ptcp.w:call-trgt-71.t:call-get_reads_overlapping_repeats.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:01.472 wdl.w:ptcp.w:call-trgt-71.t:call-get_reads_overlapping_repeats.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:25:01.507 wdl.w:ptcp.w:call-trgt-71.t:call-get_reads_overlapping_repeats INFO output :: name: "reads_overlapping_repeats", value: "m84036_250809_035451_s4.bc2168.repeats.bam"
2025-09-15 20:25:01.511 wdl.w:ptcp.w:call-trgt-71.t:call-get_reads_overlapping_repeats INFO output :: name: "reads_overlapping_repeats_bai", value: "m84036_250809_035451_s4.bc2168.repeats.bam.bai"
2025-09-15 20:25:01.536 wdl.w:ptcp.t:call-tar_outputs-33 INFO output :: name: "sample_tarball", value: "m84036_250809_035451_s4.bc2130.tar"
2025-09-15 20:25:01.582 wdl.w:ptcp.w:call-trgt-71.t:call-get_reads_overlapping_repeats NOTICE done
2025-09-15 20:25:01.587 wdl.w:ptcp.w:call-trgt-71 NOTICE finish :: job: "call-get_reads_overlapping_repeats"
2025-09-15 20:25:01.588 wdl.w:ptcp.w:call-trgt-71 INFO output :: job: "call-get_reads_overlapping_repeats", values: {"reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-71/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2168.repeats.bam.bai", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-71/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2168.repeats.bam"}
2025-09-15 20:25:01.588 wdl.w:ptcp.w:call-trgt-71 INFO visit :: node: "output-reads_overlapping_repeats", values: {"reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-71/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2168.repeats.bam"}
2025-09-15 20:25:01.588 wdl.w:ptcp.w:call-trgt-71 INFO visit :: node: "output-reads_overlapping_repeats_bai", values: {"reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-71/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2168.repeats.bam.bai"}
2025-09-15 20:25:01.598 wdl.w:ptcp.t:call-tar_outputs-13 NOTICE task setup :: name: "tar_outputs", source: "./common.wdl", line: 279, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-13", thread: 140610895857216
2025-09-15 20:25:01.614 wdl.w:ptcp.t:call-tar_outputs-33 NOTICE done
2025-09-15 20:25:01.619 wdl.w:ptcp NOTICE finish :: job: "call-tar_outputs-33"
2025-09-15 20:25:01.619 wdl.w:ptcp INFO output :: job: "call-tar_outputs-33", values: {"sample_tarball": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-33/out/m84036_250809_035451_s4.bc2130.tar"}
2025-09-15 20:25:01.626 wdl.w:ptcp.w:call-sawfish-68.t:call-run_sawfish NOTICE task setup :: name: "run_sawfish", source: "./sawfish.wdl", line: 83, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-68/call-run_sawfish", thread: 140608203109952
2025-09-15 20:25:01.626 wdl.w:ptcp.t:call-tar_outputs-13 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:01.626 wdl.w:ptcp.t:call-tar_outputs-13 INFO input :: name: "sawfish_vcf_tbi", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2110.sv.vcf.gz.tbi"
2025-09-15 20:25:01.626 wdl.w:ptcp.t:call-tar_outputs-13 INFO input :: name: "sawfish_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2110.sv.vcf.gz"
2025-09-15 20:25:01.627 wdl.w:ptcp.t:call-tar_outputs-13 INFO input :: name: "f8_json", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2110.f8inversion.json"
2025-09-15 20:25:01.627 wdl.w:ptcp.t:call-tar_outputs-13 INFO input :: name: "paraphase_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2110.paraphase.bam.bai"
2025-09-15 20:25:01.627 wdl.w:ptcp.t:call-tar_outputs-13 INFO input :: name: "paraphase_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2110.paraphase.bam"
2025-09-15 20:25:01.627 wdl.w:ptcp.t:call-tar_outputs-13 INFO input :: name: "paraphase_json", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2110.paraphase.json"
2025-09-15 20:25:01.627 wdl.w:ptcp.t:call-tar_outputs-13 INFO input :: name: "trgt_spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2110.trgt.sorted.spanning.bam.bai"
2025-09-15 20:25:01.627 wdl.w:ptcp.t:call-tar_outputs-13 INFO input :: name: "trgt_spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2110.trgt.sorted.spanning.bam"
2025-09-15 20:25:01.627 wdl.w:ptcp.t:call-tar_outputs-13 INFO input :: name: "trgt_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2110.trgt.vcf"
2025-09-15 20:25:01.627 wdl.w:ptcp.t:call-tar_outputs-13 INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2110.mapped.bam.bai"
2025-09-15 20:25:01.627 wdl.w:ptcp.t:call-tar_outputs-13 INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2110.mapped.bam"
2025-09-15 20:25:01.627 wdl.w:ptcp.t:call-tar_outputs-13 INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2110"
2025-09-15 20:25:01.627 wdl.w:ptcp.t:call-tar_outputs-13 INFO eval :: name: "threads", value: 1
2025-09-15 20:25:01.627 wdl.w:ptcp.t:call-tar_outputs-13 INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:25:01.628 wdl.w:ptcp.t:call-tar_outputs-13 INFO eval :: name: "disk_size", value: 6
2025-09-15 20:25:01.628 wdl.w:ptcp.t:call-tar_outputs-13 INFO eval :: name: "output_tarball", value: "m84036_250809_035451_s4.bc2110.tar"
2025-09-15 20:25:01.628 wdl.w:ptcp.t:call-tar_outputs-13 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:01.628 wdl.w:ptcp.t:call-tar_outputs-13 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:01.629 wdl.w:ptcp.t:call-tar_outputs-13 INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:25:01.629 wdl.w:ptcp.t:call-tar_outputs-13 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:01.645 wdl.w:ptcp.w:call-sawfish-68.t:call-run_sawfish INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:01.645 wdl.w:ptcp.w:call-sawfish-68.t:call-run_sawfish INFO input :: name: "genome_version", value: "38"
2025-09-15 20:25:01.645 wdl.w:ptcp.w:call-sawfish-68.t:call-run_sawfish INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:25:01.645 wdl.w:ptcp.w:call-sawfish-68.t:call-run_sawfish INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:25:01.645 wdl.w:ptcp.w:call-sawfish-68.t:call-run_sawfish INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2165.mapped.bam.bai"
2025-09-15 20:25:01.645 wdl.w:ptcp.w:call-sawfish-68.t:call-run_sawfish INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2165.mapped.bam"
2025-09-15 20:25:01.645 wdl.w:ptcp.w:call-sawfish-68.t:call-run_sawfish INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2165"
2025-09-15 20:25:01.646 wdl.w:ptcp.w:call-sawfish-68.t:call-run_sawfish INFO eval :: name: "mem_gb", value: 32
2025-09-15 20:25:01.646 wdl.w:ptcp.w:call-sawfish-68.t:call-run_sawfish INFO eval :: name: "threads", value: 16
2025-09-15 20:25:01.646 wdl.w:ptcp.w:call-sawfish-68.t:call-run_sawfish INFO eval :: name: "disk_size", value: 30
2025-09-15 20:25:01.646 wdl.w:ptcp.w:call-sawfish-68.t:call-run_sawfish INFO eval :: name: "discover_dirname", value: "m84036_250809_035451_s4.bc2165_sawfish_discover"
2025-09-15 20:25:01.646 wdl.w:ptcp.w:call-sawfish-68.t:call-run_sawfish INFO eval :: name: "call_dirname", value: "m84036_250809_035451_s4.bc2165_sawfish"
2025-09-15 20:25:01.646 wdl.w:ptcp.w:call-sawfish-68.t:call-run_sawfish INFO eval :: name: "minimap2_bam_filename", value: "m84036_250809_035451_s4.bc2165.minimap2.bam"
2025-09-15 20:25:01.647 wdl.w:ptcp.w:call-sawfish-68.t:call-run_sawfish INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 16, memory_reservation: 32000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:01.647 wdl.w:ptcp.w:call-sawfish-68.t:call-run_sawfish WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:01.647 wdl.w:ptcp.w:call-sawfish-68.t:call-run_sawfish INFO provisioned :: seconds_waited: 0, cpu: 16, mem_bytes: 32000000000
2025-09-15 20:25:01.647 wdl.w:ptcp.w:call-sawfish-68.t:call-run_sawfish INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:01.650 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_plot_motifs_allele INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2140.motifs_allele.trgt_plots.zip"
2025-09-15 20:25:01.703 wdl.w:ptcp.w:call-trgt-49.t:call-trgt_plot_meth_allele INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2146.meth_allele.trgt_plots.zip"
2025-09-15 20:25:01.732 wdl.w:ptcp.w:call-sawfish-68.t:call-run_sawfish INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 10, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-68/call-run_sawfish/_singularity_tmpdir_ajvhec8w"
2025-09-15 20:25:01.732 wdl.w:ptcp.w:call-sawfish-68.t:call-run_sawfish INFO Slurm invocation: srun --job-name call-run_sawfish --partition compute,compute9 --cpus-per-task 16 --mem 30518M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-68/call-run_sawfish/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-68/call-run_sawfish/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-68/call-run_sawfish/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-68/call-run_sawfish/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-68/out/m84036_250809_035451_s4.bc2165.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2165.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-68/out/m84036_250809_035451_s4.bc2165.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2165.mapped.bam.bai:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-68/call-run_sawfish/_singularity_tmpdir_ajvhec8w/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-68/call-run_sawfish/_singularity_tmpdir_ajvhec8w/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:01.757 wdl.w:ptcp.w:call-sawfish-24.t:call-run_sawfish INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2121_sawfish/m84036_250809_035451_s4.bc2121.sv.vcf.gz"
2025-09-15 20:25:01.762 wdl.w:ptcp.w:call-sawfish-68.t:call-run_sawfish NOTICE slurm_singularity run :: pid: 1204366, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-68/call-run_sawfish/slurm_singularity.log.txt"
2025-09-15 20:25:01.762 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_plot_motifs_allele NOTICE done
2025-09-15 20:25:01.764 wdl.w:ptcp.w:call-sawfish-24.t:call-run_sawfish INFO output :: name: "vcf_tbi", value: "m84036_250809_035451_s4.bc2121_sawfish/m84036_250809_035451_s4.bc2121.sv.vcf.gz.tbi"
2025-09-15 20:25:01.766 wdl.w:ptcp.w:call-sawfish-24.t:call-run_sawfish INFO output :: name: "minimap2_bam", value: "m84036_250809_035451_s4.bc2121.minimap2.bam"
2025-09-15 20:25:01.766 wdl.w:ptcp.t:call-tar_outputs-13 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 17, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-13/_singularity_tmpdir_j94s2cuc"
2025-09-15 20:25:01.766 wdl.w:ptcp.t:call-tar_outputs-13 INFO Slurm invocation: srun --job-name call-tar_outputs-13 --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-13/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-13/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-13/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-13/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-13/out/m84036_250809_035451_s4.bc2110.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2110.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-13/out/m84036_250809_035451_s4.bc2110.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2110.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-13/out/m84036_250809_035451_s4.bc2110.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2110.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-13/out/m84036_250809_035451_s4.bc2110_sawfish/m84036_250809_035451_s4.bc2110.sv.vcf.gz:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2110.sv.vcf.gz:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-13/out/m84036_250809_035451_s4.bc2110_sawfish/m84036_250809_035451_s4.bc2110.sv.vcf.gz.tbi:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2110.sv.vcf.gz.tbi:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-13/out/m84036_250809_035451_s4.bc2110.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2110.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-13/out/m84036_250809_035451_s4.bc2110.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2110.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-13/out/m84036_250809_035451_s4.bc2110_paraphase/m84036_250809_035451_s4.bc2110.paraphase.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2110.paraphase.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-13/out/m84036_250809_035451_s4.bc2110_paraphase/m84036_250809_035451_s4.bc2110.paraphase.json:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2110.paraphase.json:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-13/out/m84036_250809_035451_s4.bc2110_paraphase/m84036_250809_035451_s4.bc2110.paraphase.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2110.paraphase.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-13/out/m84036_250809_035451_s4.bc2110.f8inversion.json:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2110.f8inversion.json:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-13/_singularity_tmpdir_j94s2cuc/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-13/_singularity_tmpdir_j94s2cuc/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:01.767 wdl.w:ptcp.w:call-trgt-43 NOTICE finish :: job: "call-trgt_plot_motifs_allele"
2025-09-15 20:25:01.768 wdl.w:ptcp.w:call-sawfish-24.t:call-run_sawfish INFO output :: name: "minimap2_bam_bai", value: "m84036_250809_035451_s4.bc2121.minimap2.bam.bai"
2025-09-15 20:25:01.768 wdl.w:ptcp.w:call-trgt-43 INFO output :: job: "call-trgt_plot_motifs_allele", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-43/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2140.motifs_allele.trgt_plots.zip"}
2025-09-15 20:25:01.768 wdl.w:ptcp.w:call-trgt-43 INFO visit :: node: "output-images_motifs_allele", values: {"images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-43/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2140.motifs_allele.trgt_plots.zip"}
2025-09-15 20:25:01.774 wdl.w:ptcp.t:call-tar_outputs-05 NOTICE task setup :: name: "tar_outputs", source: "./common.wdl", line: 279, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-05", thread: 140609285244480
2025-09-15 20:25:01.783 wdl.w:ptcp.t:call-tar_outputs-13 NOTICE slurm_singularity run :: pid: 1204367, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-13/slurm_singularity.log.txt"
2025-09-15 20:25:01.799 wdl.w:ptcp.t:call-tar_outputs-05 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:01.799 wdl.w:ptcp.t:call-tar_outputs-05 INFO input :: name: "sawfish_vcf_tbi", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2102.sv.vcf.gz.tbi"
2025-09-15 20:25:01.800 wdl.w:ptcp.t:call-tar_outputs-05 INFO input :: name: "sawfish_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2102.sv.vcf.gz"
2025-09-15 20:25:01.800 wdl.w:ptcp.t:call-tar_outputs-05 INFO input :: name: "f8_json", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2102.f8inversion.json"
2025-09-15 20:25:01.800 wdl.w:ptcp.t:call-tar_outputs-05 INFO input :: name: "paraphase_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2102.paraphase.bam.bai"
2025-09-15 20:25:01.800 wdl.w:ptcp.t:call-tar_outputs-05 INFO input :: name: "paraphase_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2102.paraphase.bam"
2025-09-15 20:25:01.800 wdl.w:ptcp.t:call-tar_outputs-05 INFO input :: name: "paraphase_json", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2102.paraphase.json"
2025-09-15 20:25:01.800 wdl.w:ptcp.t:call-tar_outputs-05 INFO input :: name: "trgt_spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2102.trgt.sorted.spanning.bam.bai"
2025-09-15 20:25:01.800 wdl.w:ptcp.t:call-tar_outputs-05 INFO input :: name: "trgt_spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2102.trgt.sorted.spanning.bam"
2025-09-15 20:25:01.800 wdl.w:ptcp.t:call-tar_outputs-05 INFO input :: name: "trgt_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2102.trgt.vcf"
2025-09-15 20:25:01.800 wdl.w:ptcp.t:call-tar_outputs-05 INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2102.mapped.bam.bai"
2025-09-15 20:25:01.800 wdl.w:ptcp.t:call-tar_outputs-05 INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2102.mapped.bam"
2025-09-15 20:25:01.800 wdl.w:ptcp.t:call-tar_outputs-05 INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2102"
2025-09-15 20:25:01.800 wdl.w:ptcp.t:call-tar_outputs-05 INFO eval :: name: "threads", value: 1
2025-09-15 20:25:01.800 wdl.w:ptcp.t:call-tar_outputs-05 INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:25:01.801 wdl.w:ptcp.t:call-tar_outputs-05 INFO eval :: name: "disk_size", value: 6
2025-09-15 20:25:01.801 wdl.w:ptcp.t:call-tar_outputs-05 INFO eval :: name: "output_tarball", value: "m84036_250809_035451_s4.bc2102.tar"
2025-09-15 20:25:01.801 wdl.w:ptcp.t:call-tar_outputs-05 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:01.801 wdl.w:ptcp.t:call-tar_outputs-05 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:01.801 wdl.w:ptcp.t:call-tar_outputs-05 INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:25:01.802 wdl.w:ptcp.t:call-tar_outputs-05 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:01.841 wdl.w:ptcp.w:call-trgt-65.t:call-trgt_genotype INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2162.trgt.vcf"
2025-09-15 20:25:01.845 wdl.w:ptcp.w:call-trgt-65.t:call-trgt_genotype INFO output :: name: "spanning_bam", value: "m84036_250809_035451_s4.bc2162.trgt.sorted.spanning.bam"
2025-09-15 20:25:01.847 wdl.w:ptcp.w:call-trgt-65.t:call-trgt_genotype INFO output :: name: "spanning_bam_bai", value: "m84036_250809_035451_s4.bc2162.trgt.sorted.spanning.bam.bai"
2025-09-15 20:25:01.882 wdl.w:ptcp.w:call-trgt-49.t:call-trgt_plot_meth_allele NOTICE done
2025-09-15 20:25:01.887 wdl.w:ptcp.w:call-trgt-49 NOTICE finish :: job: "call-trgt_plot_meth_allele"
2025-09-15 20:25:01.887 wdl.w:ptcp.w:call-trgt-49 INFO output :: job: "call-trgt_plot_meth_allele", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-49/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2146.meth_allele.trgt_plots.zip"}
2025-09-15 20:25:01.888 wdl.w:ptcp.w:call-trgt-49 INFO visit :: node: "output-images_meth_allele", values: {"images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-49/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2146.meth_allele.trgt_plots.zip"}
2025-09-15 20:25:01.894 wdl.w:ptcp.w:call-trgt-68.t:call-get_reads_overlapping_repeats NOTICE task setup :: name: "get_reads_overlapping_repeats", source: "./trgt.wdl", line: 182, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-68/call-get_reads_overlapping_repeats", thread: 140613060126272
2025-09-15 20:25:01.914 wdl.w:ptcp.w:call-trgt-68.t:call-get_reads_overlapping_repeats INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:01.914 wdl.w:ptcp.w:call-trgt-68.t:call-get_reads_overlapping_repeats INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:25:01.914 wdl.w:ptcp.w:call-trgt-68.t:call-get_reads_overlapping_repeats INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2165.mapped.bam.bai"
2025-09-15 20:25:01.914 wdl.w:ptcp.w:call-trgt-68.t:call-get_reads_overlapping_repeats INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2165.mapped.bam"
2025-09-15 20:25:01.914 wdl.w:ptcp.w:call-trgt-68.t:call-get_reads_overlapping_repeats INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2165"
2025-09-15 20:25:01.914 wdl.w:ptcp.w:call-trgt-68.t:call-get_reads_overlapping_repeats INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:25:01.914 wdl.w:ptcp.w:call-trgt-68.t:call-get_reads_overlapping_repeats INFO eval :: name: "expand_size", value: 3000
2025-09-15 20:25:01.914 wdl.w:ptcp.w:call-trgt-68.t:call-get_reads_overlapping_repeats INFO eval :: name: "threads", value: 1
2025-09-15 20:25:01.914 wdl.w:ptcp.w:call-trgt-68.t:call-get_reads_overlapping_repeats INFO eval :: name: "expanded_bed_name", value: "m84036_250809_035451_s4.bc2165.expanded.bed"
2025-09-15 20:25:01.915 wdl.w:ptcp.w:call-trgt-68.t:call-get_reads_overlapping_repeats INFO eval :: name: "disk_size", value: 11
2025-09-15 20:25:01.915 wdl.w:ptcp.w:call-trgt-68.t:call-get_reads_overlapping_repeats INFO eval :: name: "output_name", value: "m84036_250809_035451_s4.bc2165.repeats.bam"
2025-09-15 20:25:01.915 wdl.w:ptcp.w:call-trgt-68.t:call-get_reads_overlapping_repeats INFO eval :: name: "index_name", value: "m84036_250809_035451_s4.bc2165.repeats.bam.bai"
2025-09-15 20:25:01.915 wdl.w:ptcp.w:call-trgt-68.t:call-get_reads_overlapping_repeats INFO eval :: name: "output_name_with_index", value: "m84036_250809_035451_s4.bc2165.repeats.bam##idx##m84036_250809_035451_s4.bc2165.repeats.bam.bai"
2025-09-15 20:25:01.916 wdl.w:ptcp.w:call-trgt-68.t:call-get_reads_overlapping_repeats INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:01.916 wdl.w:ptcp.w:call-trgt-68.t:call-get_reads_overlapping_repeats WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:01.916 wdl.w:ptcp.w:call-trgt-68.t:call-get_reads_overlapping_repeats INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:25:01.916 wdl.w:ptcp.w:call-trgt-68.t:call-get_reads_overlapping_repeats INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:01.929 wdl.w:ptcp.w:call-trgt-71.t:call-trgt_genotype.slurm_singularity INFO srun: job 51797866 queued and waiting for resources
2025-09-15 20:25:01.929 wdl.w:ptcp.w:call-trgt-71.t:call-trgt_genotype.slurm_singularity INFO srun: job 51797866 has been allocated resources
2025-09-15 20:25:01.929 wdl.w:ptcp.w:call-trgt-71.t:call-trgt_genotype.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:01.930 wdl.w:ptcp.t:call-tar_outputs-05 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 17, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-05/_singularity_tmpdir_k8c9i9l9"
2025-09-15 20:25:01.930 wdl.w:ptcp.t:call-tar_outputs-05 INFO Slurm invocation: srun --job-name call-tar_outputs-05 --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-05/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-05/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-05/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-05/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-05/out/m84036_250809_035451_s4.bc2102_paraphase/m84036_250809_035451_s4.bc2102.paraphase.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2102.paraphase.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-05/out/m84036_250809_035451_s4.bc2102_paraphase/m84036_250809_035451_s4.bc2102.paraphase.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2102.paraphase.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-05/out/m84036_250809_035451_s4.bc2102_paraphase/m84036_250809_035451_s4.bc2102.paraphase.json:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2102.paraphase.json:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-05/out/m84036_250809_035451_s4.bc2102.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2102.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-05/out/m84036_250809_035451_s4.bc2102.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2102.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-05/out/m84036_250809_035451_s4.bc2102.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2102.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-05/out/m84036_250809_035451_s4.bc2102_sawfish/m84036_250809_035451_s4.bc2102.sv.vcf.gz:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2102.sv.vcf.gz:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-05/out/m84036_250809_035451_s4.bc2102_sawfish/m84036_250809_035451_s4.bc2102.sv.vcf.gz.tbi:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2102.sv.vcf.gz.tbi:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-05/out/m84036_250809_035451_s4.bc2102.f8inversion.json:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2102.f8inversion.json:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-05/out/m84036_250809_035451_s4.bc2102.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2102.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-05/out/m84036_250809_035451_s4.bc2102.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2102.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-05/_singularity_tmpdir_k8c9i9l9/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-05/_singularity_tmpdir_k8c9i9l9/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:01.937 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_motifs_waterfall INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2152.motifs_waterfall.trgt_plots.zip"
2025-09-15 20:25:01.938 wdl.w:ptcp.w:call-sawfish-24.t:call-run_sawfish NOTICE done
2025-09-15 20:25:01.946 wdl.w:ptcp.w:call-sawfish-24 NOTICE finish :: job: "call-run_sawfish"
2025-09-15 20:25:01.946 wdl.w:ptcp.w:call-trgt-65.t:call-trgt_genotype NOTICE done
2025-09-15 20:25:01.946 wdl.w:ptcp.w:call-sawfish-24 INFO output :: job: "call-run_sawfish", values: {"minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-24/call-run_sawfish/out/m84036_250809_035451_s4.bc2121.minimap2.bam.bai", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-24/call-run_sawfish/out/m84036_250809_035451_s4.bc2121.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-24/call-run_sawfish/out/m84036_250809_035451_s4.bc2121_sawfish/m84036_250809_035451_s4.bc2121.sv.vcf.gz.tbi", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-24/call-run_sawfish/out/m84036_250809_035451_s4.bc2121_sawfish/m84036_250809_035451_s4.bc2121.sv.vcf.gz"}
2025-09-15 20:25:01.947 wdl.w:ptcp.w:call-sawfish-24 INFO visit :: node: "output-minimap2_bam", values: {"minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-24/call-run_sawfish/out/m84036_250809_035451_s4.bc2121.minimap2.bam"}
2025-09-15 20:25:01.947 wdl.w:ptcp.w:call-sawfish-24 INFO visit :: node: "output-minimap2_bam_bai", values: {"minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-24/call-run_sawfish/out/m84036_250809_035451_s4.bc2121.minimap2.bam.bai"}
2025-09-15 20:25:01.947 wdl.w:ptcp.w:call-sawfish-24 INFO visit :: node: "output-vcf", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-24/call-run_sawfish/out/m84036_250809_035451_s4.bc2121_sawfish/m84036_250809_035451_s4.bc2121.sv.vcf.gz"}
2025-09-15 20:25:01.947 wdl.w:ptcp.w:call-sawfish-24 INFO visit :: node: "output-vcf_tbi", values: {"vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-24/call-run_sawfish/out/m84036_250809_035451_s4.bc2121_sawfish/m84036_250809_035451_s4.bc2121.sv.vcf.gz.tbi"}
2025-09-15 20:25:01.947 wdl.w:ptcp.w:call-sawfish-24 INFO visit :: node: "outputs", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-24/call-run_sawfish/out/m84036_250809_035451_s4.bc2121_sawfish/m84036_250809_035451_s4.bc2121.sv.vcf.gz", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-24/call-run_sawfish/out/m84036_250809_035451_s4.bc2121.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-24/call-run_sawfish/out/m84036_250809_035451_s4.bc2121_sawfish/m84036_250809_035451_s4.bc2121.sv.vcf.gz.tbi", "minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-24/call-run_sawfish/out/m84036_250809_035451_s4.bc2121.minimap2.bam.bai"}
2025-09-15 20:25:01.954 wdl.w:ptcp.w:call-trgt-68.t:call-trgt_genotype NOTICE task setup :: name: "trgt_genotype", source: "./trgt.wdl", line: 272, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-68/call-trgt_genotype", thread: 140609276851776
2025-09-15 20:25:01.959 wdl.w:ptcp.t:call-tar_outputs-05 NOTICE slurm_singularity run :: pid: 1204381, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-05/slurm_singularity.log.txt"
2025-09-15 20:25:01.974 wdl.w:ptcp.w:call-trgt-65 NOTICE finish :: job: "call-trgt_genotype"
2025-09-15 20:25:01.974 wdl.w:ptcp.w:call-trgt-65 INFO output :: job: "call-trgt_genotype", values: {"spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-65/call-trgt_genotype/out/m84036_250809_035451_s4.bc2162.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-65/call-trgt_genotype/out/m84036_250809_035451_s4.bc2162.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-65/call-trgt_genotype/out/m84036_250809_035451_s4.bc2162.trgt.vcf"}
2025-09-15 20:25:01.975 wdl.w:ptcp.w:call-trgt-65 NOTICE ready :: job: "call-trgt_plot_meth_allele", callee: "trgt_plot"
2025-09-15 20:25:01.975 wdl.w:ptcp.w:call-trgt-65 INFO input :: job: "call-trgt_plot_meth_allele", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": false, "methylation": true, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-65/call-trgt_genotype/out/m84036_250809_035451_s4.bc2162.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-65/call-trgt_genotype/out/m84036_250809_035451_s4.bc2162.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-65/call-trgt_genotype/out/m84036_250809_035451_s4.bc2162.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2162"}
2025-09-15 20:25:01.977 wdl.w:ptcp.w:call-trgt-65 NOTICE ready :: job: "call-trgt_plot_meth_waterfall", callee: "trgt_plot"
2025-09-15 20:25:01.977 wdl.w:ptcp.w:call-trgt-65 INFO input :: job: "call-trgt_plot_meth_waterfall", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": true, "methylation": true, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-65/call-trgt_genotype/out/m84036_250809_035451_s4.bc2162.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-65/call-trgt_genotype/out/m84036_250809_035451_s4.bc2162.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-65/call-trgt_genotype/out/m84036_250809_035451_s4.bc2162.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2162"}
2025-09-15 20:25:01.978 wdl.w:ptcp.w:call-trgt-65 NOTICE ready :: job: "call-trgt_plot_motifs_allele", callee: "trgt_plot"
2025-09-15 20:25:01.979 wdl.w:ptcp.w:call-trgt-65 INFO input :: job: "call-trgt_plot_motifs_allele", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": false, "methylation": false, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-65/call-trgt_genotype/out/m84036_250809_035451_s4.bc2162.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-65/call-trgt_genotype/out/m84036_250809_035451_s4.bc2162.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-65/call-trgt_genotype/out/m84036_250809_035451_s4.bc2162.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2162"}
2025-09-15 20:25:01.979 wdl.w:ptcp.w:call-trgt-65 NOTICE ready :: job: "call-trgt_plot_motifs_waterfall", callee: "trgt_plot"
2025-09-15 20:25:01.980 wdl.w:ptcp.w:call-trgt-65 INFO input :: job: "call-trgt_plot_motifs_waterfall", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": true, "methylation": false, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-65/call-trgt_genotype/out/m84036_250809_035451_s4.bc2162.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-65/call-trgt_genotype/out/m84036_250809_035451_s4.bc2162.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-65/call-trgt_genotype/out/m84036_250809_035451_s4.bc2162.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2162"}
2025-09-15 20:25:01.980 wdl.w:ptcp.w:call-trgt-65 INFO visit :: node: "output-spanning_bam", values: {"spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-65/call-trgt_genotype/out/m84036_250809_035451_s4.bc2162.trgt.sorted.spanning.bam"}
2025-09-15 20:25:01.980 wdl.w:ptcp.w:call-trgt-65 INFO visit :: node: "output-spanning_bam_bai", values: {"spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-65/call-trgt_genotype/out/m84036_250809_035451_s4.bc2162.trgt.sorted.spanning.bam.bai"}
2025-09-15 20:25:01.981 wdl.w:ptcp.w:call-trgt-65 INFO visit :: node: "output-vcf", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-65/call-trgt_genotype/out/m84036_250809_035451_s4.bc2162.trgt.vcf"}
2025-09-15 20:25:01.985 wdl.w:ptcp.w:call-trgt-68.t:call-trgt_genotype INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:01.985 wdl.w:ptcp.w:call-trgt-68.t:call-trgt_genotype INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:25:01.985 wdl.w:ptcp.w:call-trgt-68.t:call-trgt_genotype INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:25:01.985 wdl.w:ptcp.w:call-trgt-68.t:call-trgt_genotype INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:25:01.985 wdl.w:ptcp.w:call-trgt-68.t:call-trgt_genotype INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2165.mapped.bam.bai"
2025-09-15 20:25:01.984 wdl.w:ptcp.w:call-paraphase-66.t:call-run_paraphase NOTICE task setup :: name: "run_paraphase", source: "./paraphase.wdl", line: 127, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-66/call-run_paraphase", thread: 140610358986304
2025-09-15 20:25:01.985 wdl.w:ptcp.w:call-trgt-68.t:call-trgt_genotype INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2165.mapped.bam"
2025-09-15 20:25:01.987 wdl.w:ptcp.w:call-trgt-68.t:call-trgt_genotype INFO input :: name: "sex", value: "F"
2025-09-15 20:25:01.987 wdl.w:ptcp.w:call-trgt-68.t:call-trgt_genotype INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2165"
2025-09-15 20:25:01.988 wdl.w:ptcp.w:call-trgt-68.t:call-trgt_genotype INFO eval :: name: "mem_gb", value: 16
2025-09-15 20:25:01.988 wdl.w:ptcp.w:call-trgt-68.t:call-trgt_genotype INFO eval :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2165.trgt"
2025-09-15 20:25:01.988 wdl.w:ptcp.w:call-trgt-68.t:call-trgt_genotype INFO eval :: name: "threads", value: 8
2025-09-15 20:25:01.988 wdl.w:ptcp.w:call-trgt-68.t:call-trgt_genotype INFO eval :: name: "disk_size", value: 27
2025-09-15 20:25:01.988 wdl.w:ptcp.w:call-trgt-68.t:call-trgt_genotype INFO eval :: name: "karyotype", value: "XX"
2025-09-15 20:25:01.989 wdl.w:ptcp.w:call-trgt-68.t:call-trgt_genotype INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 8, memory_reservation: 16000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:01.989 wdl.w:ptcp.w:call-trgt-68.t:call-trgt_genotype WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:01.989 wdl.w:ptcp.w:call-trgt-68.t:call-trgt_genotype INFO provisioned :: seconds_waited: 0, cpu: 8, mem_bytes: 16000000000
2025-09-15 20:25:01.990 wdl.w:ptcp.w:call-trgt-68.t:call-trgt_genotype INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:02.006 wdl.w:ptcp.w:call-sawfish-24 NOTICE done
2025-09-15 20:25:02.008 wdl.w:ptcp.w:call-paraphase-66.t:call-run_paraphase INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:02.009 wdl.w:ptcp.w:call-paraphase-66.t:call-run_paraphase INFO input :: name: "annotation_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf"
2025-09-15 20:25:02.009 wdl.w:ptcp.w:call-paraphase-66.t:call-run_paraphase INFO input :: name: "genome_version", value: "38"
2025-09-15 20:25:02.009 wdl.w:ptcp.w:call-paraphase-66.t:call-run_paraphase INFO input :: name: "config_file", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/paraphase_config.GRCh38.yaml"
2025-09-15 20:25:02.009 wdl.w:ptcp.w:call-paraphase-66.t:call-run_paraphase INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:25:02.009 wdl.w:ptcp.w:call-paraphase-66.t:call-run_paraphase INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:25:02.009 wdl.w:ptcp.w:call-paraphase-66.t:call-run_paraphase INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2163.mapped.bam.bai"
2025-09-15 20:25:02.009 wdl.w:ptcp.w:call-paraphase-66.t:call-run_paraphase INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2163.mapped.bam"
2025-09-15 20:25:02.009 wdl.w:ptcp.w:call-paraphase-66.t:call-run_paraphase INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2163"
2025-09-15 20:25:02.010 wdl.w:ptcp.w:call-paraphase-66.t:call-run_paraphase INFO eval :: name: "threads", value: 4
2025-09-15 20:25:02.010 wdl.w:ptcp.w:call-paraphase-66.t:call-run_paraphase INFO eval :: name: "mem_gb", value: 8
2025-09-15 20:25:02.010 wdl.w:ptcp.w:call-paraphase-66.t:call-run_paraphase INFO eval :: name: "disk_size", value: 27
2025-09-15 20:25:02.010 wdl.w:ptcp.w:call-paraphase-66.t:call-run_paraphase INFO eval :: name: "out_dir", value: "m84036_250809_035451_s4.bc2163_paraphase"
2025-09-15 20:25:02.011 wdl.w:ptcp.w:call-paraphase-66.t:call-run_paraphase INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 4, memory_reservation: 8000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:02.011 wdl.w:ptcp.w:call-paraphase-66.t:call-run_paraphase WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:02.011 wdl.w:ptcp.w:call-paraphase-66.t:call-run_paraphase INFO provisioned :: seconds_waited: 0, cpu: 4, mem_bytes: 8000000000
2025-09-15 20:25:02.011 wdl.w:ptcp.w:call-paraphase-66.t:call-run_paraphase INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:02.013 wdl.w:ptcp NOTICE finish :: job: "call-sawfish-24"
2025-09-15 20:25:02.013 wdl.w:ptcp INFO output :: job: "call-sawfish-24", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-24/out/m84036_250809_035451_s4.bc2121_sawfish/m84036_250809_035451_s4.bc2121.sv.vcf.gz", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-24/out/m84036_250809_035451_s4.bc2121.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-24/out/m84036_250809_035451_s4.bc2121_sawfish/m84036_250809_035451_s4.bc2121.sv.vcf.gz.tbi", "minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-24/out/m84036_250809_035451_s4.bc2121.minimap2.bam.bai"}
2025-09-15 20:25:02.014 wdl.w:ptcp NOTICE ready :: job: "call-tar_outputs-24", callee: "tar_outputs"
2025-09-15 20:25:02.014 wdl.w:ptcp INFO input :: job: "call-tar_outputs-24", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "sawfish_vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-24/out/m84036_250809_035451_s4.bc2121_sawfish/m84036_250809_035451_s4.bc2121.sv.vcf.gz.tbi", "sawfish_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-24/out/m84036_250809_035451_s4.bc2121_sawfish/m84036_250809_035451_s4.bc2121.sv.vcf.gz", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-24/out/m84036_250809_035451_s4.bc2121.f8inversion.json", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-24/out/m84036_250809_035451_s4.bc2121_paraphase/m84036_250809_035451_s4.bc2121.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-24/out/m84036_250809_035451_s4.bc2121_paraphase/m84036_250809_035451_s4.bc2121.paraphase.bam", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-24/out/m84036_250809_035451_s4.bc2121_paraphase/m84036_250809_035451_s4.bc2121.paraphase.json", "trgt_spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-24/out/m84036_250809_035451_s4.bc2121.trgt.sorted.spanning.bam.bai", "trgt_spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-24/out/m84036_250809_035451_s4.bc2121.trgt.sorted.spanning.bam", "trgt_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-24/out/m84036_250809_035451_s4.bc2121.trgt.vcf", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-24/out/m84036_250809_035451_s4.bc2121.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-24/out/m84036_250809_035451_s4.bc2121.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2121"}
2025-09-15 20:25:02.017 wdl.w:ptcp.w:call-trgt-68.t:call-get_reads_overlapping_repeats INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 9, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-68/call-get_reads_overlapping_repeats/_singularity_tmpdir_frxbjfiq"
2025-09-15 20:25:02.017 wdl.w:ptcp.w:call-trgt-68.t:call-get_reads_overlapping_repeats INFO Slurm invocation: srun --job-name call-get_reads_overlapping_repeats --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-68/call-get_reads_overlapping_repeats/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-68/call-get_reads_overlapping_repeats/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-68/call-get_reads_overlapping_repeats/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-68/call-get_reads_overlapping_repeats/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-68/out/m84036_250809_035451_s4.bc2165.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2165.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-68/out/m84036_250809_035451_s4.bc2165.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2165.mapped.bam:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-68/call-get_reads_overlapping_repeats/_singularity_tmpdir_frxbjfiq/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-68/call-get_reads_overlapping_repeats/_singularity_tmpdir_frxbjfiq/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:02.024 wdl.w:ptcp.w:call-trgt-77 NOTICE workflow start :: name: "trgt", source: "./trgt.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-77"
2025-09-15 20:25:02.040 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_motifs_waterfall NOTICE done
2025-09-15 20:25:02.042 wdl.w:ptcp.w:call-trgt-68.t:call-get_reads_overlapping_repeats NOTICE slurm_singularity run :: pid: 1204384, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-68/call-get_reads_overlapping_repeats/slurm_singularity.log.txt"
2025-09-15 20:25:02.044 wdl.w:ptcp.w:call-trgt-77 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:25:02.044 wdl.w:ptcp.w:call-trgt-77 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-77/out/m84036_250809_035451_s4.bc2174.mapped.bam"}
2025-09-15 20:25:02.044 wdl.w:ptcp.w:call-trgt-77 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-77/out/m84036_250809_035451_s4.bc2174.mapped.bam.bai"}
2025-09-15 20:25:02.044 wdl.w:ptcp.w:call-trgt-77 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:25:02.044 wdl.w:ptcp.w:call-trgt-77 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:25:02.044 wdl.w:ptcp.w:call-trgt-77 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2174"}
2025-09-15 20:25:02.044 wdl.w:ptcp.w:call-trgt-77 INFO visit :: node: "decl-sex", values: {"sex": "F"}
2025-09-15 20:25:02.044 wdl.w:ptcp.w:call-trgt-77 INFO visit :: node: "decl-trgt_bed", values: {"trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"}
2025-09-15 20:25:02.045 wdl.w:ptcp.w:call-trgt-77 NOTICE ready :: job: "call-get_reads_overlapping_repeats", callee: "get_reads_overlapping_repeats"
2025-09-15 20:25:02.045 wdl.w:ptcp.w:call-trgt-77 INFO input :: job: "call-get_reads_overlapping_repeats", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-77/out/m84036_250809_035451_s4.bc2174.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-77/out/m84036_250809_035451_s4.bc2174.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2174"}
2025-09-15 20:25:02.046 wdl.w:ptcp.w:call-trgt-55 NOTICE finish :: job: "call-trgt_plot_motifs_waterfall"
2025-09-15 20:25:02.046 wdl.w:ptcp.w:call-trgt-55 INFO output :: job: "call-trgt_plot_motifs_waterfall", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-55/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2152.motifs_waterfall.trgt_plots.zip"}
2025-09-15 20:25:02.046 wdl.w:ptcp.w:call-trgt-77 NOTICE ready :: job: "call-trgt_genotype", callee: "trgt_genotype"
2025-09-15 20:25:02.046 wdl.w:ptcp.w:call-trgt-55 INFO visit :: node: "output-images_motifs_waterfall", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-55/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2152.motifs_waterfall.trgt_plots.zip"}
2025-09-15 20:25:02.046 wdl.w:ptcp.w:call-trgt-77 INFO input :: job: "call-trgt_genotype", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-77/out/m84036_250809_035451_s4.bc2174.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-77/out/m84036_250809_035451_s4.bc2174.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2174"}
2025-09-15 20:25:02.051 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:59 [ERROR] - No reads found for TRID=SCA37_DAB1
2025-09-15 20:25:02.051 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:25:00 [ERROR] - No reads found for TRID=OPDM_ABCD3
2025-09-15 20:25:02.051 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:25:00 [ERROR] - No reads found for TRID=DRPLA_ATN1
2025-09-15 20:25:02.051 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:25:00 [ERROR] - No reads found for TRID=SCA2_ATXN2
2025-09-15 20:25:02.051 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:25:00 [ERROR] - No reads found for TRID=OPDM4_RILPL1
2025-09-15 20:25:02.051 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:25:00 [ERROR] - No reads found for TRID=NIID_NOTCH2NLC
2025-09-15 20:25:02.051 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:25:00 [ERROR] - No reads found for TRID=SCA8_ATXN8OS
2025-09-15 20:25:02.051 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:25:00 [ERROR] - No reads found for TRID=OPMD_PABPN1
2025-09-15 20:25:02.051 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:25:00 [ERROR] - No reads found for TRID=SCA3_ATXN3
2025-09-15 20:25:02.051 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:25:00 [ERROR] - No reads found for TRID=SCA31_BEAN1
2025-09-15 20:25:02.051 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:25:01 [ERROR] - No reads found for TRID=SCA4_ZFHX3
2025-09-15 20:25:02.052 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:25:01 [ERROR] - No reads found for TRID=SCA27B_FGF14
2025-09-15 20:25:02.052 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:24:59 [ERROR] - No reads found for TRID=SCA37_DAB1
2025-09-15 20:25:02.052 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:25:01 [ERROR] - No reads found for TRID=HDL2_JPH3
2025-09-15 20:25:02.052 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:25:00 [ERROR] - No reads found for TRID=OPDM_ABCD3
2025-09-15 20:25:02.052 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:25:01 [ERROR] - No reads found for TRID=SCA6_CACNA1A
2025-09-15 20:25:02.052 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:25:00 [ERROR] - No reads found for TRID=DRPLA_ATN1
2025-09-15 20:25:02.052 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:25:01 [ERROR] - No reads found for TRID=FRA2A_AFF3
2025-09-15 20:25:02.052 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:25:00 [ERROR] - No reads found for TRID=SCA2_ATXN2
2025-09-15 20:25:02.052 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:25:01 [ERROR] - No reads found for TRID=DM1_DMPK
2025-09-15 20:25:02.053 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:25:00 [ERROR] - No reads found for TRID=OPDM4_RILPL1
2025-09-15 20:25:02.053 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:25:01 [ERROR] - No reads found for TRID=OPDM2_GIPC1
2025-09-15 20:25:02.053 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:25:00 [ERROR] - No reads found for TRID=NIID_NOTCH2NLC
2025-09-15 20:25:02.053 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:25:00 [ERROR] - No reads found for TRID=SCA8_ATXN8OS
2025-09-15 20:25:02.053 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:25:00 [ERROR] - No reads found for TRID=OPMD_PABPN1
2025-09-15 20:25:02.053 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:25:00 [ERROR] - No reads found for TRID=SCA3_ATXN3
2025-09-15 20:25:02.053 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:25:00 [ERROR] - No reads found for TRID=SCA31_BEAN1
2025-09-15 20:25:02.053 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:25:01 [ERROR] - No reads found for TRID=SCA4_ZFHX3
2025-09-15 20:25:02.053 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:25:01 [ERROR] - No reads found for TRID=SCA27B_FGF14
2025-09-15 20:25:02.053 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:25:01 [ERROR] - No reads found for TRID=HDL2_JPH3
2025-09-15 20:25:02.053 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:25:01 [ERROR] - No reads found for TRID=SCA6_CACNA1A
2025-09-15 20:25:02.053 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:25:01 [ERROR] - No reads found for TRID=FRA2A_AFF3
2025-09-15 20:25:02.053 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:25:01 [ERROR] - No reads found for TRID=DM1_DMPK
2025-09-15 20:25:02.053 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:25:01 [ERROR] - No reads found for TRID=OPDM2_GIPC1
2025-09-15 20:25:02.054 wdl.w:ptcp.t:call-tar_outputs-21 NOTICE task setup :: name: "tar_outputs", source: "./common.wdl", line: 279, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-21", thread: 140611944420928
2025-09-15 20:25:02.060 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_plot_meth_allele INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2140.meth_allele.trgt_plots.zip"
2025-09-15 20:25:02.080 wdl.w:ptcp.w:call-trgt-68.t:call-trgt_genotype INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 11, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-68/call-trgt_genotype/_singularity_tmpdir_l2zsvqly"
2025-09-15 20:25:02.080 wdl.w:ptcp.w:call-trgt-68.t:call-trgt_genotype INFO Slurm invocation: srun --job-name call-trgt_genotype --partition compute,compute9 --cpus-per-task 8 --mem 15259M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-68/call-trgt_genotype/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-68/call-trgt_genotype/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-68/call-trgt_genotype/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-68/call-trgt_genotype/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-68/out/m84036_250809_035451_s4.bc2165.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2165.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-68/out/m84036_250809_035451_s4.bc2165.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2165.mapped.bam.bai:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-68/call-trgt_genotype/_singularity_tmpdir_l2zsvqly/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-68/call-trgt_genotype/_singularity_tmpdir_l2zsvqly/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:02.082 wdl.w:ptcp.t:call-tar_outputs-21 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:02.083 wdl.w:ptcp.t:call-tar_outputs-21 INFO input :: name: "sawfish_vcf_tbi", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2118.sv.vcf.gz.tbi"
2025-09-15 20:25:02.083 wdl.w:ptcp.t:call-tar_outputs-21 INFO input :: name: "sawfish_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2118.sv.vcf.gz"
2025-09-15 20:25:02.083 wdl.w:ptcp.t:call-tar_outputs-21 INFO input :: name: "f8_json", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2118.f8inversion.json"
2025-09-15 20:25:02.083 wdl.w:ptcp.t:call-tar_outputs-21 INFO input :: name: "paraphase_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2118.paraphase.bam.bai"
2025-09-15 20:25:02.083 wdl.w:ptcp.t:call-tar_outputs-21 INFO input :: name: "paraphase_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2118.paraphase.bam"
2025-09-15 20:25:02.083 wdl.w:ptcp.t:call-tar_outputs-21 INFO input :: name: "paraphase_json", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2118.paraphase.json"
2025-09-15 20:25:02.083 wdl.w:ptcp.t:call-tar_outputs-21 INFO input :: name: "trgt_spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2118.trgt.sorted.spanning.bam.bai"
2025-09-15 20:25:02.083 wdl.w:ptcp.t:call-tar_outputs-21 INFO input :: name: "trgt_spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2118.trgt.sorted.spanning.bam"
2025-09-15 20:25:02.083 wdl.w:ptcp.t:call-tar_outputs-21 INFO input :: name: "trgt_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2118.trgt.vcf"
2025-09-15 20:25:02.083 wdl.w:ptcp.t:call-tar_outputs-21 INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2118.mapped.bam.bai"
2025-09-15 20:25:02.083 wdl.w:ptcp.t:call-tar_outputs-21 INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2118.mapped.bam"
2025-09-15 20:25:02.083 wdl.w:ptcp.t:call-tar_outputs-21 INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2118"
2025-09-15 20:25:02.083 wdl.w:ptcp.t:call-tar_outputs-21 INFO eval :: name: "threads", value: 1
2025-09-15 20:25:02.083 wdl.w:ptcp.t:call-tar_outputs-21 INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:25:02.084 wdl.w:ptcp.t:call-tar_outputs-21 INFO eval :: name: "disk_size", value: 6
2025-09-15 20:25:02.084 wdl.w:ptcp.t:call-tar_outputs-21 INFO eval :: name: "output_tarball", value: "m84036_250809_035451_s4.bc2118.tar"
2025-09-15 20:25:02.084 wdl.w:ptcp.t:call-tar_outputs-21 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:02.085 wdl.w:ptcp.t:call-tar_outputs-21 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:02.085 wdl.w:ptcp.t:call-tar_outputs-21 INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:25:02.085 wdl.w:ptcp.t:call-tar_outputs-21 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:02.100 wdl.w:ptcp.w:call-trgt-68.t:call-trgt_genotype NOTICE slurm_singularity run :: pid: 1204386, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-68/call-trgt_genotype/slurm_singularity.log.txt"
2025-09-15 20:25:02.111 wdl.w:ptcp.w:call-paraphase-63.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for hba for sample m84036_250809_035451_s4.bc2160 at 2025-09-15 20:24:42.168596...
2025-09-15 20:25:02.112 wdl.w:ptcp.w:call-paraphase-63.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for smn1 for sample m84036_250809_035451_s4.bc2160 at 2025-09-15 20:24:42.436088...
2025-09-15 20:25:02.112 wdl.w:ptcp.w:call-paraphase-63.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for gba for sample m84036_250809_035451_s4.bc2160 at 2025-09-15 20:24:42.704958...
2025-09-15 20:25:02.112 wdl.w:ptcp.w:call-paraphase-63.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for cyp21 for sample m84036_250809_035451_s4.bc2160 at 2025-09-15 20:24:44.046233...
2025-09-15 20:25:02.116 wdl.w:ptcp.w:call-paraphase-66.t:call-run_paraphase INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-66/call-run_paraphase/_singularity_tmpdir_qxvprwce"
2025-09-15 20:25:02.117 wdl.w:ptcp.w:call-paraphase-66.t:call-run_paraphase INFO Slurm invocation: srun --job-name call-run_paraphase --partition compute,compute9 --cpus-per-task 4 --mem 7629M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-66/call-run_paraphase/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-66/call-run_paraphase/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-66/call-run_paraphase/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-66/call-run_paraphase/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-66/out/m84036_250809_035451_s4.bc2163.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2163.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-66/out/m84036_250809_035451_s4.bc2163.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2163.mapped.bam.bai:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/variant_list/variant_list.GRCh38.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf:ro --bind /ptcp/meta/paraphase/paraphase_config.GRCh38.yaml:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/paraphase_config.GRCh38.yaml:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-66/call-run_paraphase/_singularity_tmpdir_qxvprwce/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-66/call-run_paraphase/_singularity_tmpdir_qxvprwce/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:02.134 wdl.w:ptcp.w:call-paraphase-66.t:call-run_paraphase NOTICE slurm_singularity run :: pid: 1204388, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-66/call-run_paraphase/slurm_singularity.log.txt"
2025-09-15 20:25:02.146 wdl.w:ptcp.w:call-sawfish-10.t:call-run_sawfish.stderr VERBOSE [M::mm_mapopt_update::83.742*1.73] mid_occ = 136
2025-09-15 20:25:02.147 wdl.w:ptcp.w:call-sawfish-10.t:call-run_sawfish.stderr VERBOSE [M::mm_idx_stat] kmer size: 19; skip: 19; is_hpc: 0; #seq: 195
2025-09-15 20:25:02.147 wdl.w:ptcp.w:call-sawfish-10.t:call-run_sawfish.stderr VERBOSE [M::mm_idx_stat::89.957*1.68] distinct minimizers: 214664461 (92.23% are singletons); average occurrences: 1.372; average spacing: 10.529; total length: 3099922541
2025-09-15 20:25:02.147 wdl.w:ptcp.w:call-sawfish-10.t:call-run_sawfish.stderr VERBOSE [M::bam2fq_mainloop] discarded 0 singletons
2025-09-15 20:25:02.147 wdl.w:ptcp.w:call-sawfish-10.t:call-run_sawfish.stderr VERBOSE [M::bam2fq_mainloop] processed 486 reads
2025-09-15 20:25:02.152 wdl.w:ptcp.t:call-tar_outputs-20.slurm_singularity INFO srun: job 51797867 queued and waiting for resources
2025-09-15 20:25:02.152 wdl.w:ptcp.t:call-tar_outputs-20.slurm_singularity INFO srun: job 51797867 has been allocated resources
2025-09-15 20:25:02.152 wdl.w:ptcp.t:call-tar_outputs-20.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:02.172 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_plot_meth_allele NOTICE done
2025-09-15 20:25:02.178 wdl.w:ptcp.w:call-trgt-43 NOTICE finish :: job: "call-trgt_plot_meth_allele"
2025-09-15 20:25:02.178 wdl.w:ptcp.w:call-trgt-43 INFO output :: job: "call-trgt_plot_meth_allele", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-43/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2140.meth_allele.trgt_plots.zip"}
2025-09-15 20:25:02.178 wdl.w:ptcp.w:call-trgt-43 INFO visit :: node: "output-images_meth_allele", values: {"images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-43/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2140.meth_allele.trgt_plots.zip"}
2025-09-15 20:25:02.186 wdl.w:ptcp.w:call-sawfish-66.t:call-run_sawfish NOTICE task setup :: name: "run_sawfish", source: "./sawfish.wdl", line: 83, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-66/call-run_sawfish", thread: 140607112582720
2025-09-15 20:25:02.202 wdl.w:ptcp.w:call-sawfish-66.t:call-run_sawfish INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:02.202 wdl.w:ptcp.w:call-sawfish-66.t:call-run_sawfish INFO input :: name: "genome_version", value: "38"
2025-09-15 20:25:02.202 wdl.w:ptcp.w:call-sawfish-66.t:call-run_sawfish INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:25:02.202 wdl.w:ptcp.w:call-sawfish-66.t:call-run_sawfish INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:25:02.202 wdl.w:ptcp.w:call-sawfish-66.t:call-run_sawfish INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2163.mapped.bam.bai"
2025-09-15 20:25:02.203 wdl.w:ptcp.w:call-sawfish-66.t:call-run_sawfish INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2163.mapped.bam"
2025-09-15 20:25:02.203 wdl.w:ptcp.w:call-sawfish-66.t:call-run_sawfish INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2163"
2025-09-15 20:25:02.203 wdl.w:ptcp.w:call-sawfish-66.t:call-run_sawfish INFO eval :: name: "mem_gb", value: 32
2025-09-15 20:25:02.203 wdl.w:ptcp.w:call-sawfish-66.t:call-run_sawfish INFO eval :: name: "threads", value: 16
2025-09-15 20:25:02.203 wdl.w:ptcp.w:call-sawfish-66.t:call-run_sawfish INFO eval :: name: "disk_size", value: 30
2025-09-15 20:25:02.203 wdl.w:ptcp.w:call-sawfish-66.t:call-run_sawfish INFO eval :: name: "discover_dirname", value: "m84036_250809_035451_s4.bc2163_sawfish_discover"
2025-09-15 20:25:02.203 wdl.w:ptcp.w:call-sawfish-66.t:call-run_sawfish INFO eval :: name: "call_dirname", value: "m84036_250809_035451_s4.bc2163_sawfish"
2025-09-15 20:25:02.204 wdl.w:ptcp.w:call-sawfish-66.t:call-run_sawfish INFO eval :: name: "minimap2_bam_filename", value: "m84036_250809_035451_s4.bc2163.minimap2.bam"
2025-09-15 20:25:02.204 wdl.w:ptcp.w:call-sawfish-66.t:call-run_sawfish INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 16, memory_reservation: 32000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:02.204 wdl.w:ptcp.w:call-sawfish-66.t:call-run_sawfish WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:02.204 wdl.w:ptcp.w:call-sawfish-66.t:call-run_sawfish INFO provisioned :: seconds_waited: 0, cpu: 16, mem_bytes: 32000000000
2025-09-15 20:25:02.205 wdl.w:ptcp.w:call-sawfish-66.t:call-run_sawfish INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:02.217 wdl.w:ptcp.t:call-tar_outputs-21 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 17, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-21/_singularity_tmpdir_609q3fnf"
2025-09-15 20:25:02.217 wdl.w:ptcp.t:call-tar_outputs-21 INFO Slurm invocation: srun --job-name call-tar_outputs-21 --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-21/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-21/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-21/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-21/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-21/out/m84036_250809_035451_s4.bc2118_paraphase/m84036_250809_035451_s4.bc2118.paraphase.json:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2118.paraphase.json:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-21/out/m84036_250809_035451_s4.bc2118_paraphase/m84036_250809_035451_s4.bc2118.paraphase.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2118.paraphase.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-21/out/m84036_250809_035451_s4.bc2118_paraphase/m84036_250809_035451_s4.bc2118.paraphase.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2118.paraphase.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-21/out/m84036_250809_035451_s4.bc2118.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2118.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-21/out/m84036_250809_035451_s4.bc2118.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2118.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-21/out/m84036_250809_035451_s4.bc2118.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2118.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-21/out/m84036_250809_035451_s4.bc2118.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2118.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-21/out/m84036_250809_035451_s4.bc2118.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2118.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-21/out/m84036_250809_035451_s4.bc2118_sawfish/m84036_250809_035451_s4.bc2118.sv.vcf.gz.tbi:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2118.sv.vcf.gz.tbi:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-21/out/m84036_250809_035451_s4.bc2118_sawfish/m84036_250809_035451_s4.bc2118.sv.vcf.gz:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2118.sv.vcf.gz:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-21/out/m84036_250809_035451_s4.bc2118.f8inversion.json:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2118.f8inversion.json:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-21/_singularity_tmpdir_609q3fnf/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-21/_singularity_tmpdir_609q3fnf/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:02.243 wdl.w:ptcp.w:call-paraphase-68.t:call-run_paraphase.slurm_singularity INFO srun: job 51797868 queued and waiting for resources
2025-09-15 20:25:02.244 wdl.w:ptcp.w:call-paraphase-68.t:call-run_paraphase.slurm_singularity INFO srun: job 51797868 has been allocated resources
2025-09-15 20:25:02.244 wdl.w:ptcp.w:call-paraphase-68.t:call-run_paraphase.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:02.246 wdl.w:ptcp.t:call-tar_outputs-21 NOTICE slurm_singularity run :: pid: 1204410, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-21/slurm_singularity.log.txt"
2025-09-15 20:25:02.269 wdl.w:ptcp.w:call-sawfish-66.t:call-run_sawfish INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 10, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-66/call-run_sawfish/_singularity_tmpdir_baqktycl"
2025-09-15 20:25:02.269 wdl.w:ptcp.w:call-sawfish-66.t:call-run_sawfish INFO Slurm invocation: srun --job-name call-run_sawfish --partition compute,compute9 --cpus-per-task 16 --mem 30518M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-66/call-run_sawfish/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-66/call-run_sawfish/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-66/call-run_sawfish/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-66/call-run_sawfish/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-66/out/m84036_250809_035451_s4.bc2163.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2163.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-66/out/m84036_250809_035451_s4.bc2163.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2163.mapped.bam.bai:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-66/call-run_sawfish/_singularity_tmpdir_baqktycl/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-66/call-run_sawfish/_singularity_tmpdir_baqktycl/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:02.280 wdl.w:ptcp.w:call-sawfish-19.t:call-run_sawfish.stderr VERBOSE [M::mm_mapopt_update::83.727*1.73] mid_occ = 136
2025-09-15 20:25:02.280 wdl.w:ptcp.w:call-sawfish-19.t:call-run_sawfish.stderr VERBOSE [M::mm_idx_stat] kmer size: 19; skip: 19; is_hpc: 0; #seq: 195
2025-09-15 20:25:02.281 wdl.w:ptcp.w:call-sawfish-19.t:call-run_sawfish.stderr VERBOSE [M::mm_idx_stat::89.754*1.68] distinct minimizers: 214664461 (92.23% are singletons); average occurrences: 1.372; average spacing: 10.529; total length: 3099922541
2025-09-15 20:25:02.281 wdl.w:ptcp.w:call-sawfish-19.t:call-run_sawfish.stderr VERBOSE [M::bam2fq_mainloop] discarded 0 singletons
2025-09-15 20:25:02.281 wdl.w:ptcp.w:call-sawfish-19.t:call-run_sawfish.stderr VERBOSE [M::bam2fq_mainloop] processed 252 reads
2025-09-15 20:25:02.289 wdl.w:ptcp.w:call-sawfish-66.t:call-run_sawfish NOTICE slurm_singularity run :: pid: 1204412, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-66/call-run_sawfish/slurm_singularity.log.txt"
2025-09-15 20:25:02.609 wdl.w:ptcp.t:call-tar_outputs-20 INFO output :: name: "sample_tarball", value: "m84036_250809_035451_s4.bc2117.tar"
2025-09-15 20:25:02.616 wdl.w:ptcp.w:call-paraphase-15.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for rpgr for sample m84036_250809_035451_s4.bc2112 at 2025-09-15 20:24:49.445280...
2025-09-15 20:25:02.618 wdl.w:ptcp.w:call-paraphase-15.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for rpgr for sample m84036_250809_035451_s4.bc2112 at 2025-09-15 20:24:49.445886...
2025-09-15 20:25:02.618 wdl.w:ptcp.w:call-paraphase-15.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for rpgr for sample m84036_250809_035451_s4.bc2112 at 2025-09-15 20:24:51.781226...
2025-09-15 20:25:02.618 wdl.w:ptcp.w:call-paraphase-15.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for rpgr for sample m84036_250809_035451_s4.bc2112 at 2025-09-15 20:24:52.651775...
2025-09-15 20:25:02.619 wdl.w:ptcp.w:call-paraphase-15.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for rpgr for sample m84036_250809_035451_s4.bc2112 at 2025-09-15 20:24:52.784000...
2025-09-15 20:25:02.648 wdl.w:ptcp.w:call-trgt-71.t:call-trgt_genotype INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2168.trgt.vcf"
2025-09-15 20:25:02.651 wdl.w:ptcp.w:call-trgt-71.t:call-trgt_genotype INFO output :: name: "spanning_bam", value: "m84036_250809_035451_s4.bc2168.trgt.sorted.spanning.bam"
2025-09-15 20:25:02.653 wdl.w:ptcp.w:call-trgt-71.t:call-trgt_genotype INFO output :: name: "spanning_bam_bai", value: "m84036_250809_035451_s4.bc2168.trgt.sorted.spanning.bam.bai"
2025-09-15 20:25:02.679 wdl.w:ptcp.t:call-tar_outputs-20 NOTICE done
2025-09-15 20:25:02.684 wdl.w:ptcp NOTICE finish :: job: "call-tar_outputs-20"
2025-09-15 20:25:02.684 wdl.w:ptcp INFO output :: job: "call-tar_outputs-20", values: {"sample_tarball": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-20/out/m84036_250809_035451_s4.bc2117.tar"}
2025-09-15 20:25:02.691 wdl.w:ptcp.w:call-trgt-66.t:call-get_reads_overlapping_repeats NOTICE task setup :: name: "get_reads_overlapping_repeats", source: "./trgt.wdl", line: 182, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-66/call-get_reads_overlapping_repeats", thread: 140610367379008
2025-09-15 20:25:02.711 wdl.w:ptcp.w:call-trgt-66.t:call-get_reads_overlapping_repeats INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:02.711 wdl.w:ptcp.w:call-trgt-66.t:call-get_reads_overlapping_repeats INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:25:02.712 wdl.w:ptcp.w:call-trgt-66.t:call-get_reads_overlapping_repeats INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2163.mapped.bam.bai"
2025-09-15 20:25:02.712 wdl.w:ptcp.w:call-trgt-66.t:call-get_reads_overlapping_repeats INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2163.mapped.bam"
2025-09-15 20:25:02.712 wdl.w:ptcp.w:call-trgt-66.t:call-get_reads_overlapping_repeats INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2163"
2025-09-15 20:25:02.712 wdl.w:ptcp.w:call-trgt-66.t:call-get_reads_overlapping_repeats INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:25:02.712 wdl.w:ptcp.w:call-trgt-66.t:call-get_reads_overlapping_repeats INFO eval :: name: "expand_size", value: 3000
2025-09-15 20:25:02.712 wdl.w:ptcp.w:call-trgt-66.t:call-get_reads_overlapping_repeats INFO eval :: name: "threads", value: 1
2025-09-15 20:25:02.712 wdl.w:ptcp.w:call-trgt-66.t:call-get_reads_overlapping_repeats INFO eval :: name: "expanded_bed_name", value: "m84036_250809_035451_s4.bc2163.expanded.bed"
2025-09-15 20:25:02.713 wdl.w:ptcp.w:call-trgt-66.t:call-get_reads_overlapping_repeats INFO eval :: name: "disk_size", value: 11
2025-09-15 20:25:02.713 wdl.w:ptcp.w:call-trgt-66.t:call-get_reads_overlapping_repeats INFO eval :: name: "output_name", value: "m84036_250809_035451_s4.bc2163.repeats.bam"
2025-09-15 20:25:02.713 wdl.w:ptcp.w:call-trgt-66.t:call-get_reads_overlapping_repeats INFO eval :: name: "index_name", value: "m84036_250809_035451_s4.bc2163.repeats.bam.bai"
2025-09-15 20:25:02.713 wdl.w:ptcp.w:call-trgt-66.t:call-get_reads_overlapping_repeats INFO eval :: name: "output_name_with_index", value: "m84036_250809_035451_s4.bc2163.repeats.bam##idx##m84036_250809_035451_s4.bc2163.repeats.bam.bai"
2025-09-15 20:25:02.713 wdl.w:ptcp.w:call-trgt-66.t:call-get_reads_overlapping_repeats INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:02.713 wdl.w:ptcp.w:call-trgt-66.t:call-get_reads_overlapping_repeats WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:02.714 wdl.w:ptcp.w:call-trgt-66.t:call-get_reads_overlapping_repeats INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:25:02.714 wdl.w:ptcp.w:call-trgt-66.t:call-get_reads_overlapping_repeats INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:02.742 wdl.w:ptcp.w:call-trgt-71.t:call-trgt_genotype NOTICE done
2025-09-15 20:25:02.747 wdl.w:ptcp.w:call-trgt-71 NOTICE finish :: job: "call-trgt_genotype"
2025-09-15 20:25:02.747 wdl.w:ptcp.w:call-trgt-71 INFO output :: job: "call-trgt_genotype", values: {"spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-71/call-trgt_genotype/out/m84036_250809_035451_s4.bc2168.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-71/call-trgt_genotype/out/m84036_250809_035451_s4.bc2168.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-71/call-trgt_genotype/out/m84036_250809_035451_s4.bc2168.trgt.vcf"}
2025-09-15 20:25:02.748 wdl.w:ptcp.w:call-trgt-71 NOTICE ready :: job: "call-trgt_plot_meth_allele", callee: "trgt_plot"
2025-09-15 20:25:02.748 wdl.w:ptcp.w:call-trgt-71 INFO input :: job: "call-trgt_plot_meth_allele", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": false, "methylation": true, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-71/call-trgt_genotype/out/m84036_250809_035451_s4.bc2168.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-71/call-trgt_genotype/out/m84036_250809_035451_s4.bc2168.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-71/call-trgt_genotype/out/m84036_250809_035451_s4.bc2168.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2168"}
2025-09-15 20:25:02.749 wdl.w:ptcp.w:call-trgt-71 NOTICE ready :: job: "call-trgt_plot_meth_waterfall", callee: "trgt_plot"
2025-09-15 20:25:02.749 wdl.w:ptcp.w:call-trgt-71 INFO input :: job: "call-trgt_plot_meth_waterfall", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": true, "methylation": true, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-71/call-trgt_genotype/out/m84036_250809_035451_s4.bc2168.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-71/call-trgt_genotype/out/m84036_250809_035451_s4.bc2168.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-71/call-trgt_genotype/out/m84036_250809_035451_s4.bc2168.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2168"}
2025-09-15 20:25:02.750 wdl.w:ptcp.w:call-trgt-71 NOTICE ready :: job: "call-trgt_plot_motifs_allele", callee: "trgt_plot"
2025-09-15 20:25:02.750 wdl.w:ptcp.w:call-trgt-71 INFO input :: job: "call-trgt_plot_motifs_allele", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": false, "methylation": false, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-71/call-trgt_genotype/out/m84036_250809_035451_s4.bc2168.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-71/call-trgt_genotype/out/m84036_250809_035451_s4.bc2168.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-71/call-trgt_genotype/out/m84036_250809_035451_s4.bc2168.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2168"}
2025-09-15 20:25:02.751 wdl.w:ptcp.w:call-trgt-71 NOTICE ready :: job: "call-trgt_plot_motifs_waterfall", callee: "trgt_plot"
2025-09-15 20:25:02.751 wdl.w:ptcp.w:call-trgt-71 INFO input :: job: "call-trgt_plot_motifs_waterfall", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": true, "methylation": false, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-71/call-trgt_genotype/out/m84036_250809_035451_s4.bc2168.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-71/call-trgt_genotype/out/m84036_250809_035451_s4.bc2168.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-71/call-trgt_genotype/out/m84036_250809_035451_s4.bc2168.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2168"}
2025-09-15 20:25:02.752 wdl.w:ptcp.w:call-trgt-71 INFO visit :: node: "output-spanning_bam", values: {"spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-71/call-trgt_genotype/out/m84036_250809_035451_s4.bc2168.trgt.sorted.spanning.bam"}
2025-09-15 20:25:02.752 wdl.w:ptcp.w:call-trgt-71 INFO visit :: node: "output-spanning_bam_bai", values: {"spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-71/call-trgt_genotype/out/m84036_250809_035451_s4.bc2168.trgt.sorted.spanning.bam.bai"}
2025-09-15 20:25:02.752 wdl.w:ptcp.w:call-trgt-71 INFO visit :: node: "output-vcf", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-71/call-trgt_genotype/out/m84036_250809_035451_s4.bc2168.trgt.vcf"}
2025-09-15 20:25:02.753 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_genotype NOTICE task setup :: name: "trgt_genotype", source: "./trgt.wdl", line: 272, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-66/call-trgt_genotype", thread: 140611457906240
2025-09-15 20:25:02.758 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_plot_motifs_waterfall INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2140.motifs_waterfall.trgt_plots.zip"
2025-09-15 20:25:02.764 wdl.w:ptcp.w:call-sawfish-68.t:call-run_sawfish.stderr VERBOSE [M::bam2fq_mainloop] discarded 0 singletons
2025-09-15 20:25:02.764 wdl.w:ptcp.w:call-sawfish-68.t:call-run_sawfish.stderr VERBOSE [M::bam2fq_mainloop] processed 0 reads
2025-09-15 20:25:02.770 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_genotype INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:02.770 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_genotype INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:25:02.770 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_genotype INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:25:02.770 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_genotype INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:25:02.770 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_genotype INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2163.mapped.bam.bai"
2025-09-15 20:25:02.770 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_genotype INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2163.mapped.bam"
2025-09-15 20:25:02.770 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_genotype INFO input :: name: "sex", value: "F"
2025-09-15 20:25:02.771 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_genotype INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2163"
2025-09-15 20:25:02.771 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_genotype INFO eval :: name: "mem_gb", value: 16
2025-09-15 20:25:02.771 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_genotype INFO eval :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2163.trgt"
2025-09-15 20:25:02.771 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_genotype INFO eval :: name: "threads", value: 8
2025-09-15 20:25:02.771 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_genotype INFO eval :: name: "disk_size", value: 27
2025-09-15 20:25:02.771 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_genotype INFO eval :: name: "karyotype", value: "XX"
2025-09-15 20:25:02.772 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_genotype INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 8, memory_reservation: 16000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:02.772 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_genotype WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:02.772 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_genotype INFO provisioned :: seconds_waited: 0, cpu: 8, mem_bytes: 16000000000
2025-09-15 20:25:02.772 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_genotype INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:02.773 wdl.w:ptcp.w:call-sawfish-68.t:call-run_sawfish.slurm_singularity INFO srun: job 51797869 queued and waiting for resources
2025-09-15 20:25:02.773 wdl.w:ptcp.w:call-sawfish-68.t:call-run_sawfish.slurm_singularity INFO srun: job 51797869 has been allocated resources
2025-09-15 20:25:02.773 wdl.w:ptcp.w:call-sawfish-68.t:call-run_sawfish.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:02.773 wdl.w:ptcp.w:call-sawfish-68.t:call-run_sawfish.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:25:02.776 wdl.w:ptcp.w:call-trgt-66.t:call-get_reads_overlapping_repeats INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 9, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-66/call-get_reads_overlapping_repeats/_singularity_tmpdir_3gn8jkt1"
2025-09-15 20:25:02.776 wdl.w:ptcp.w:call-trgt-66.t:call-get_reads_overlapping_repeats INFO Slurm invocation: srun --job-name call-get_reads_overlapping_repeats --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-66/call-get_reads_overlapping_repeats/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-66/call-get_reads_overlapping_repeats/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-66/call-get_reads_overlapping_repeats/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-66/call-get_reads_overlapping_repeats/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-66/out/m84036_250809_035451_s4.bc2163.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2163.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-66/out/m84036_250809_035451_s4.bc2163.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2163.mapped.bam.bai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-66/call-get_reads_overlapping_repeats/_singularity_tmpdir_3gn8jkt1/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-66/call-get_reads_overlapping_repeats/_singularity_tmpdir_3gn8jkt1/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:02.793 wdl.w:ptcp.t:call-tar_outputs-13.slurm_singularity INFO srun: job 51797870 queued and waiting for resources
2025-09-15 20:25:02.794 wdl.w:ptcp.t:call-tar_outputs-13.slurm_singularity INFO srun: job 51797870 has been allocated resources
2025-09-15 20:25:02.794 wdl.w:ptcp.t:call-tar_outputs-13.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:02.807 wdl.w:ptcp.w:call-trgt-66.t:call-get_reads_overlapping_repeats NOTICE slurm_singularity run :: pid: 1204427, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-66/call-get_reads_overlapping_repeats/slurm_singularity.log.txt"
2025-09-15 20:25:02.824 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:59 [ERROR] - No reads found for TRID=SCA2_ATXN2
2025-09-15 20:25:02.824 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:59 [ERROR] - No reads found for TRID=OPDM4_RILPL1
2025-09-15 20:25:02.824 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:59 [ERROR] - No reads found for TRID=SCA8_ATXN8OS
2025-09-15 20:25:02.825 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:59 [ERROR] - No reads found for TRID=OPMD_PABPN1
2025-09-15 20:25:02.825 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:24:59 [ERROR] - No reads found for TRID=SCA27B_FGF14
2025-09-15 20:25:02.825 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:25:00 [ERROR] - No reads found for TRID=SCA3_ATXN3
2025-09-15 20:25:02.825 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:25:00 [ERROR] - No reads found for TRID=SCA31_BEAN1
2025-09-15 20:25:02.825 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:25:00 [ERROR] - No reads found for TRID=SCA4_ZFHX3
2025-09-15 20:25:02.825 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:25:00 [ERROR] - No reads found for TRID=HDL2_JPH3
2025-09-15 20:25:02.825 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:25:00 [ERROR] - No reads found for TRID=SCA6_CACNA1A
2025-09-15 20:25:02.825 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:25:00 [ERROR] - No reads found for TRID=OPDM2_GIPC1
2025-09-15 20:25:02.825 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:25:00 [ERROR] - No reads found for TRID=DM1_DMPK
2025-09-15 20:25:02.825 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:25:00 [ERROR] - No reads found for TRID=FRA2A_AFF3
2025-09-15 20:25:02.825 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:25:00 [ERROR] - No reads found for TRID=SD5_HOXD13
2025-09-15 20:25:02.825 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:25:00 [ERROR] - No reads found for TRID=SCA36_NOP56
2025-09-15 20:25:02.825 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:25:00 [ERROR] - No reads found for TRID=CJD_PRNP
2025-09-15 20:25:02.825 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:25:00 [ERROR] - No reads found for TRID=EPM1_CSTB
2025-09-15 20:25:02.825 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:25:01 [ERROR] - No reads found for TRID=SCA7_ATXN7
2025-09-15 20:25:02.825 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:25:01 [ERROR] - No reads found for TRID=CCHS_PHOX2B
2025-09-15 20:25:02.825 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:25:01 [ERROR] - No reads found for TRID=SCA12_PPP2R2B
2025-09-15 20:25:02.825 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:25:01 [ERROR] - No reads found for TRID=SCA1_ATXN1
2025-09-15 20:25:02.826 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:25:01 [ERROR] - No reads found for TRID=OPDM1_LRP12
2025-09-15 20:25:02.826 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:25:01 [ERROR] - No reads found for TRID=FAME1_SAMD12
2025-09-15 20:25:02.826 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:25:01 [ERROR] - No reads found for TRID=FTDALS1_C9orf72
2025-09-15 20:25:02.845 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_plot_motifs_waterfall NOTICE done
2025-09-15 20:25:02.846 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_genotype INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 11, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-66/call-trgt_genotype/_singularity_tmpdir_rxb_emvt"
2025-09-15 20:25:02.846 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_genotype INFO Slurm invocation: srun --job-name call-trgt_genotype --partition compute,compute9 --cpus-per-task 8 --mem 15259M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-66/call-trgt_genotype/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-66/call-trgt_genotype/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-66/call-trgt_genotype/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-66/call-trgt_genotype/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-66/out/m84036_250809_035451_s4.bc2163.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2163.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-66/out/m84036_250809_035451_s4.bc2163.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2163.mapped.bam.bai:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-66/call-trgt_genotype/_singularity_tmpdir_rxb_emvt/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-66/call-trgt_genotype/_singularity_tmpdir_rxb_emvt/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:02.849 wdl.w:ptcp.w:call-trgt-43 NOTICE finish :: job: "call-trgt_plot_motifs_waterfall"
2025-09-15 20:25:02.849 wdl.w:ptcp.w:call-trgt-43 INFO output :: job: "call-trgt_plot_motifs_waterfall", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-43/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2140.motifs_waterfall.trgt_plots.zip"}
2025-09-15 20:25:02.849 wdl.w:ptcp.w:call-trgt-43 INFO visit :: node: "output-images_motifs_waterfall", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-43/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2140.motifs_waterfall.trgt_plots.zip"}
2025-09-15 20:25:02.855 wdl.w:ptcp.w:call-paraphase-57.t:call-call_f8 NOTICE task setup :: name: "call_f8", source: "./paraphase.wdl", line: 232, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-57/call-call_f8", thread: 140609847293504
2025-09-15 20:25:02.860 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_genotype NOTICE slurm_singularity run :: pid: 1204435, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-66/call-trgt_genotype/slurm_singularity.log.txt"
2025-09-15 20:25:02.873 wdl.w:ptcp.w:call-paraphase-57.t:call-call_f8 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:02.873 wdl.w:ptcp.w:call-paraphase-57.t:call-call_f8 INFO input :: name: "genome_version", value: "38"
2025-09-15 20:25:02.873 wdl.w:ptcp.w:call-paraphase-57.t:call-call_f8 INFO input :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2154"
2025-09-15 20:25:02.873 wdl.w:ptcp.w:call-paraphase-57.t:call-call_f8 INFO input :: name: "paraphase_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2154.paraphase.bam.bai"
2025-09-15 20:25:02.873 wdl.w:ptcp.w:call-paraphase-57.t:call-call_f8 INFO input :: name: "paraphase_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2154.paraphase.bam"
2025-09-15 20:25:02.873 wdl.w:ptcp.w:call-paraphase-57.t:call-call_f8 INFO input :: name: "sex", value: "F"
2025-09-15 20:25:02.874 wdl.w:ptcp.w:call-paraphase-57.t:call-call_f8 INFO eval :: name: "threads", value: 1
2025-09-15 20:25:02.874 wdl.w:ptcp.w:call-paraphase-57.t:call-call_f8 INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:25:02.874 wdl.w:ptcp.w:call-paraphase-57.t:call-call_f8 INFO eval :: name: "disk_size", value: 11
2025-09-15 20:25:02.874 wdl.w:ptcp.w:call-paraphase-57.t:call-call_f8 INFO eval :: name: "sample_sex", value: "F"
2025-09-15 20:25:02.874 wdl.w:ptcp.w:call-paraphase-57.t:call-call_f8 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:02.874 wdl.w:ptcp.w:call-paraphase-57.t:call-call_f8 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:02.875 wdl.w:ptcp.w:call-paraphase-57.t:call-call_f8 INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:25:02.875 wdl.w:ptcp.w:call-paraphase-57.t:call-call_f8 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:02.891 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_plot_meth_waterfall INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2140.meth_waterfall.trgt_plots.zip"
2025-09-15 20:25:02.925 wdl.w:ptcp.w:call-paraphase-57.t:call-call_f8 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 8, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-57/call-call_f8/_singularity_tmpdir_uwyvx69d"
2025-09-15 20:25:02.926 wdl.w:ptcp.w:call-paraphase-57.t:call-call_f8 INFO Slurm invocation: srun --job-name call-call_f8 --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-57/call-call_f8/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-57/call-call_f8/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-57/call-call_f8/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-57/call-call_f8/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-57/call-run_paraphase/out/m84036_250809_035451_s4.bc2154_paraphase/m84036_250809_035451_s4.bc2154.paraphase.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2154.paraphase.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-57/call-run_paraphase/out/m84036_250809_035451_s4.bc2154_paraphase/m84036_250809_035451_s4.bc2154.paraphase.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2154.paraphase.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-57/call-call_f8/_singularity_tmpdir_uwyvx69d/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-57/call-call_f8/_singularity_tmpdir_uwyvx69d/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:02.939 wdl.w:ptcp.w:call-paraphase-57.t:call-call_f8 NOTICE slurm_singularity run :: pid: 1204442, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-57/call-call_f8/slurm_singularity.log.txt"
2025-09-15 20:25:02.962 wdl.w:ptcp.w:call-trgt-43.t:call-trgt_plot_meth_waterfall NOTICE done
2025-09-15 20:25:02.968 wdl.w:ptcp.w:call-trgt-43 NOTICE finish :: job: "call-trgt_plot_meth_waterfall"
2025-09-15 20:25:02.968 wdl.w:ptcp.w:call-trgt-43 INFO output :: job: "call-trgt_plot_meth_waterfall", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-43/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2140.meth_waterfall.trgt_plots.zip"}
2025-09-15 20:25:02.968 wdl.w:ptcp.w:call-trgt-43 INFO visit :: node: "output-images_meth_waterfall", values: {"images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-43/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2140.meth_waterfall.trgt_plots.zip"}
2025-09-15 20:25:02.968 wdl.w:ptcp.w:call-trgt-43 INFO visit :: node: "outputs", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-43/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2140.motifs_waterfall.trgt_plots.zip", "images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-43/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2140.meth_allele.trgt_plots.zip", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-43/call-trgt_genotype/out/m84036_250809_035451_s4.bc2140.trgt.sorted.spanning.bam.bai", "images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-43/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2140.motifs_allele.trgt_plots.zip", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-43/call-trgt_genotype/out/m84036_250809_035451_s4.bc2140.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-43/call-trgt_genotype/out/m84036_250809_035451_s4.bc2140.trgt.vcf", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-43/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2140.repeats.bam", "images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-43/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2140.meth_waterfall.trgt_plots.zip", "reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-43/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2140.repeats.bam.bai"}
2025-09-15 20:25:02.972 wdl.w:ptcp.t:call-tar_outputs-05.slurm_singularity INFO srun: job 51797871 queued and waiting for resources
2025-09-15 20:25:02.972 wdl.w:ptcp.t:call-tar_outputs-05.slurm_singularity INFO srun: job 51797871 has been allocated resources
2025-09-15 20:25:02.972 wdl.w:ptcp.t:call-tar_outputs-05.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:02.978 wdl.w:ptcp.w:call-paraphase-49.t:call-call_f8 NOTICE task setup :: name: "call_f8", source: "./paraphase.wdl", line: 232, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-49/call-call_f8", thread: 140607674631744
2025-09-15 20:25:03.001 wdl.w:ptcp.w:call-paraphase-49.t:call-call_f8 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:03.001 wdl.w:ptcp.w:call-paraphase-49.t:call-call_f8 INFO input :: name: "genome_version", value: "38"
2025-09-15 20:25:03.001 wdl.w:ptcp.w:call-paraphase-49.t:call-call_f8 INFO input :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2146"
2025-09-15 20:25:03.001 wdl.w:ptcp.w:call-paraphase-49.t:call-call_f8 INFO input :: name: "paraphase_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2146.paraphase.bam.bai"
2025-09-15 20:25:03.001 wdl.w:ptcp.w:call-paraphase-49.t:call-call_f8 INFO input :: name: "paraphase_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2146.paraphase.bam"
2025-09-15 20:25:03.001 wdl.w:ptcp.w:call-paraphase-49.t:call-call_f8 INFO input :: name: "sex", value: "F"
2025-09-15 20:25:03.002 wdl.w:ptcp.w:call-paraphase-49.t:call-call_f8 INFO eval :: name: "threads", value: 1
2025-09-15 20:25:03.002 wdl.w:ptcp.w:call-paraphase-49.t:call-call_f8 INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:25:03.002 wdl.w:ptcp.w:call-paraphase-49.t:call-call_f8 INFO eval :: name: "disk_size", value: 11
2025-09-15 20:25:03.002 wdl.w:ptcp.w:call-paraphase-49.t:call-call_f8 INFO eval :: name: "sample_sex", value: "F"
2025-09-15 20:25:03.002 wdl.w:ptcp.w:call-paraphase-49.t:call-call_f8 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:03.003 wdl.w:ptcp.w:call-paraphase-49.t:call-call_f8 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:03.003 wdl.w:ptcp.w:call-paraphase-49.t:call-call_f8 INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:25:03.003 wdl.w:ptcp.w:call-paraphase-49.t:call-call_f8 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:03.031 wdl.w:ptcp.w:call-trgt-53.t:call-trgt_plot_motifs_allele INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2150.motifs_allele.trgt_plots.zip"
2025-09-15 20:25:03.052 wdl.w:ptcp.w:call-trgt-68.t:call-get_reads_overlapping_repeats.slurm_singularity INFO srun: job 51797872 queued and waiting for resources
2025-09-15 20:25:03.053 wdl.w:ptcp.w:call-trgt-68.t:call-get_reads_overlapping_repeats.slurm_singularity INFO srun: job 51797872 has been allocated resources
2025-09-15 20:25:03.053 wdl.w:ptcp.w:call-trgt-68.t:call-get_reads_overlapping_repeats.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:03.058 wdl.w:ptcp.w:call-paraphase-49.t:call-call_f8 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 8, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-49/call-call_f8/_singularity_tmpdir_2zz28u56"
2025-09-15 20:25:03.058 wdl.w:ptcp.w:call-paraphase-49.t:call-call_f8 INFO Slurm invocation: srun --job-name call-call_f8 --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-49/call-call_f8/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-49/call-call_f8/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-49/call-call_f8/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-49/call-call_f8/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-49/call-run_paraphase/out/m84036_250809_035451_s4.bc2146_paraphase/m84036_250809_035451_s4.bc2146.paraphase.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2146.paraphase.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-49/call-run_paraphase/out/m84036_250809_035451_s4.bc2146_paraphase/m84036_250809_035451_s4.bc2146.paraphase.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2146.paraphase.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-49/call-call_f8/_singularity_tmpdir_2zz28u56/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-49/call-call_f8/_singularity_tmpdir_2zz28u56/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:03.067 wdl.w:ptcp.w:call-trgt-43 NOTICE done
2025-09-15 20:25:03.071 wdl.w:ptcp NOTICE finish :: job: "call-trgt-43"
2025-09-15 20:25:03.071 wdl.w:ptcp INFO output :: job: "call-trgt-43", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-43/out/m84036_250809_035451_s4.bc2140.motifs_waterfall.trgt_plots.zip", "images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-43/out/m84036_250809_035451_s4.bc2140.meth_allele.trgt_plots.zip", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-43/out/m84036_250809_035451_s4.bc2140.trgt.sorted.spanning.bam.bai", "images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-43/out/m84036_250809_035451_s4.bc2140.motifs_allele.trgt_plots.zip", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-43/out/m84036_250809_035451_s4.bc2140.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-43/out/m84036_250809_035451_s4.bc2140.trgt.vcf", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-43/out/m84036_250809_035451_s4.bc2140.repeats.bam", "images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-43/out/m84036_250809_035451_s4.bc2140.meth_waterfall.trgt_plots.zip", "reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-43/out/m84036_250809_035451_s4.bc2140.repeats.bam.bai"}
2025-09-15 20:25:03.077 wdl.w:ptcp.w:call-paraphase-49.t:call-call_f8 NOTICE slurm_singularity run :: pid: 1204451, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-49/call-call_f8/slurm_singularity.log.txt"
2025-09-15 20:25:03.077 wdl.w:ptcp.w:call-paraphase-75 NOTICE workflow start :: name: "paraphase", source: "./paraphase.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-75"
2025-09-15 20:25:03.098 wdl.w:ptcp.w:call-paraphase-75 INFO visit :: node: "decl-annotation_vcf", values: {"annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf"}
2025-09-15 20:25:03.098 wdl.w:ptcp.w:call-paraphase-75 INFO visit :: node: "decl-config_file", values: {"config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml"}
2025-09-15 20:25:03.099 wdl.w:ptcp.w:call-paraphase-75 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:25:03.099 wdl.w:ptcp.w:call-paraphase-75 INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:25:03.099 wdl.w:ptcp.w:call-paraphase-75 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-75/out/m84036_250809_035451_s4.bc2172.mapped.bam"}
2025-09-15 20:25:03.099 wdl.w:ptcp.w:call-paraphase-75 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-75/out/m84036_250809_035451_s4.bc2172.mapped.bam.bai"}
2025-09-15 20:25:03.099 wdl.w:ptcp.w:call-paraphase-75 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:25:03.099 wdl.w:ptcp.w:call-paraphase-75 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:25:03.099 wdl.w:ptcp.w:call-paraphase-75 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2172"}
2025-09-15 20:25:03.099 wdl.w:ptcp.w:call-paraphase-75 INFO visit :: node: "decl-sex", values: {"sex": "F"}
2025-09-15 20:25:03.100 wdl.w:ptcp.w:call-paraphase-75 NOTICE ready :: job: "call-run_paraphase", callee: "run_paraphase"
2025-09-15 20:25:03.100 wdl.w:ptcp.w:call-paraphase-75 INFO input :: job: "call-run_paraphase", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf", "genome_version": "38", "config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-75/out/m84036_250809_035451_s4.bc2172.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-75/out/m84036_250809_035451_s4.bc2172.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2172"}
2025-09-15 20:25:03.112 wdl.w:ptcp.w:call-trgt-68.t:call-trgt_genotype.slurm_singularity INFO srun: job 51797873 queued and waiting for resources
2025-09-15 20:25:03.113 wdl.w:ptcp.w:call-trgt-68.t:call-trgt_genotype.slurm_singularity INFO srun: job 51797873 has been allocated resources
2025-09-15 20:25:03.113 wdl.w:ptcp.w:call-trgt-68.t:call-trgt_genotype.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:03.147 wdl.w:ptcp.w:call-paraphase-66.t:call-run_paraphase.slurm_singularity INFO srun: job 51797874 queued and waiting for resources
2025-09-15 20:25:03.147 wdl.w:ptcp.w:call-paraphase-66.t:call-run_paraphase.slurm_singularity INFO srun: job 51797874 has been allocated resources
2025-09-15 20:25:03.147 wdl.w:ptcp.w:call-paraphase-66.t:call-run_paraphase.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:03.167 wdl.w:ptcp.w:call-trgt-53.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:25:02 [ERROR] - No reads found for TRID=PRTS_ARX
2025-09-15 20:25:03.167 wdl.w:ptcp.w:call-trgt-53.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:25:02 [ERROR] - No reads found for TRID=EIEE1_ARX
2025-09-15 20:25:03.185 wdl.w:ptcp.w:call-sawfish-37.t:call-run_sawfish INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2134_sawfish/m84036_250809_035451_s4.bc2134.sv.vcf.gz"
2025-09-15 20:25:03.188 wdl.w:ptcp.w:call-trgt-53.t:call-trgt_plot_motifs_allele NOTICE done
2025-09-15 20:25:03.190 wdl.w:ptcp.w:call-sawfish-37.t:call-run_sawfish INFO output :: name: "vcf_tbi", value: "m84036_250809_035451_s4.bc2134_sawfish/m84036_250809_035451_s4.bc2134.sv.vcf.gz.tbi"
2025-09-15 20:25:03.191 wdl.w:ptcp.w:call-sawfish-37.t:call-run_sawfish INFO output :: name: "minimap2_bam", value: "m84036_250809_035451_s4.bc2134.minimap2.bam"
2025-09-15 20:25:03.193 wdl.w:ptcp.w:call-sawfish-37.t:call-run_sawfish INFO output :: name: "minimap2_bam_bai", value: "m84036_250809_035451_s4.bc2134.minimap2.bam.bai"
2025-09-15 20:25:03.196 wdl.w:ptcp.w:call-trgt-53 NOTICE finish :: job: "call-trgt_plot_motifs_allele"
2025-09-15 20:25:03.196 wdl.w:ptcp.w:call-trgt-53 INFO output :: job: "call-trgt_plot_motifs_allele", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-53/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2150.motifs_allele.trgt_plots.zip"}
2025-09-15 20:25:03.197 wdl.w:ptcp.w:call-trgt-53 INFO visit :: node: "output-images_motifs_allele", values: {"images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-53/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2150.motifs_allele.trgt_plots.zip"}
2025-09-15 20:25:03.201 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_plot_meth_allele NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-42/call-trgt_plot_meth_allele", thread: 140610870679104
2025-09-15 20:25:03.233 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_plot_meth_allele INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:03.233 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_plot_meth_allele INFO input :: name: "waterfall", value: false
2025-09-15 20:25:03.233 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_plot_meth_allele INFO input :: name: "methylation", value: true
2025-09-15 20:25:03.233 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_plot_meth_allele INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:25:03.233 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_plot_meth_allele INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:25:03.234 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_plot_meth_allele INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:25:03.234 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_plot_meth_allele INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2139.trgt.sorted.spanning.bam.bai"
2025-09-15 20:25:03.234 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_plot_meth_allele INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2139.trgt.sorted.spanning.bam"
2025-09-15 20:25:03.234 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_plot_meth_allele INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2139.trgt.vcf"
2025-09-15 20:25:03.234 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_plot_meth_allele INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2139"
2025-09-15 20:25:03.234 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_plot_meth_allele INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:25:03.234 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_plot_meth_allele INFO eval :: name: "plot_type", value: "allele"
2025-09-15 20:25:03.234 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_plot_meth_allele INFO eval :: name: "show", value: "meth"
2025-09-15 20:25:03.234 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_plot_meth_allele INFO eval :: name: "threads", value: 1
2025-09-15 20:25:03.235 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_plot_meth_allele INFO eval :: name: "disk_size", value: 27
2025-09-15 20:25:03.235 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_plot_meth_allele INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2139.meth_allele"
2025-09-15 20:25:03.235 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_plot_meth_allele INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:03.235 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_plot_meth_allele WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:03.236 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_plot_meth_allele INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:25:03.237 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_plot_meth_allele INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:03.260 wdl.w:ptcp.t:call-tar_outputs-21.slurm_singularity INFO srun: job 51797875 queued and waiting for resources
2025-09-15 20:25:03.260 wdl.w:ptcp.t:call-tar_outputs-21.slurm_singularity INFO srun: job 51797875 has been allocated resources
2025-09-15 20:25:03.260 wdl.w:ptcp.t:call-tar_outputs-21.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:03.302 wdl.w:ptcp.w:call-sawfish-66.t:call-run_sawfish.slurm_singularity INFO srun: job 51797876 queued and waiting for resources
2025-09-15 20:25:03.303 wdl.w:ptcp.w:call-sawfish-66.t:call-run_sawfish.slurm_singularity INFO srun: job 51797876 has been allocated resources
2025-09-15 20:25:03.303 wdl.w:ptcp.w:call-sawfish-66.t:call-run_sawfish.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:03.303 wdl.w:ptcp.w:call-sawfish-66.t:call-run_sawfish.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:25:03.318 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_plot_meth_allele INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-42/call-trgt_plot_meth_allele/_singularity_tmpdir_zx_lxybd"
2025-09-15 20:25:03.318 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_plot_meth_allele INFO Slurm invocation: srun --job-name call-trgt_plot_meth_allele --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-42/call-trgt_plot_meth_allele/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-42/call-trgt_plot_meth_allele/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-42/call-trgt_plot_meth_allele/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-42/call-trgt_plot_meth_allele/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-42/call-trgt_genotype/out/m84036_250809_035451_s4.bc2139.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2139.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-42/call-trgt_genotype/out/m84036_250809_035451_s4.bc2139.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2139.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-42/call-trgt_genotype/out/m84036_250809_035451_s4.bc2139.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2139.trgt.sorted.spanning.bam:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-42/call-trgt_plot_meth_allele/_singularity_tmpdir_zx_lxybd/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-42/call-trgt_plot_meth_allele/_singularity_tmpdir_zx_lxybd/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:03.328 wdl.w:ptcp.w:call-sawfish-37.t:call-run_sawfish NOTICE done
2025-09-15 20:25:03.343 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_plot_meth_allele NOTICE slurm_singularity run :: pid: 1204453, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-42/call-trgt_plot_meth_allele/slurm_singularity.log.txt"
2025-09-15 20:25:03.345 wdl.w:ptcp.w:call-sawfish-37 NOTICE finish :: job: "call-run_sawfish"
2025-09-15 20:25:03.345 wdl.w:ptcp.w:call-trgt-53.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:25:02 [ERROR] - No reads found for TRID=PRTS_ARX
2025-09-15 20:25:03.346 wdl.w:ptcp.w:call-sawfish-37 INFO output :: job: "call-run_sawfish", values: {"minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-37/call-run_sawfish/out/m84036_250809_035451_s4.bc2134.minimap2.bam.bai", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-37/call-run_sawfish/out/m84036_250809_035451_s4.bc2134.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-37/call-run_sawfish/out/m84036_250809_035451_s4.bc2134_sawfish/m84036_250809_035451_s4.bc2134.sv.vcf.gz.tbi", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-37/call-run_sawfish/out/m84036_250809_035451_s4.bc2134_sawfish/m84036_250809_035451_s4.bc2134.sv.vcf.gz"}
2025-09-15 20:25:03.346 wdl.w:ptcp.w:call-trgt-53.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:25:02 [ERROR] - No reads found for TRID=EIEE1_ARX
2025-09-15 20:25:03.346 wdl.w:ptcp.w:call-sawfish-37 INFO visit :: node: "output-minimap2_bam", values: {"minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-37/call-run_sawfish/out/m84036_250809_035451_s4.bc2134.minimap2.bam"}
2025-09-15 20:25:03.347 wdl.w:ptcp.w:call-sawfish-37 INFO visit :: node: "output-minimap2_bam_bai", values: {"minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-37/call-run_sawfish/out/m84036_250809_035451_s4.bc2134.minimap2.bam.bai"}
2025-09-15 20:25:03.347 wdl.w:ptcp.w:call-sawfish-37 INFO visit :: node: "output-vcf", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-37/call-run_sawfish/out/m84036_250809_035451_s4.bc2134_sawfish/m84036_250809_035451_s4.bc2134.sv.vcf.gz"}
2025-09-15 20:25:03.347 wdl.w:ptcp.w:call-sawfish-37 INFO visit :: node: "output-vcf_tbi", values: {"vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-37/call-run_sawfish/out/m84036_250809_035451_s4.bc2134_sawfish/m84036_250809_035451_s4.bc2134.sv.vcf.gz.tbi"}
2025-09-15 20:25:03.347 wdl.w:ptcp.w:call-sawfish-37 INFO visit :: node: "outputs", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-37/call-run_sawfish/out/m84036_250809_035451_s4.bc2134_sawfish/m84036_250809_035451_s4.bc2134.sv.vcf.gz", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-37/call-run_sawfish/out/m84036_250809_035451_s4.bc2134.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-37/call-run_sawfish/out/m84036_250809_035451_s4.bc2134_sawfish/m84036_250809_035451_s4.bc2134.sv.vcf.gz.tbi", "minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-37/call-run_sawfish/out/m84036_250809_035451_s4.bc2134.minimap2.bam.bai"}
2025-09-15 20:25:03.355 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_plot_meth_waterfall NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-42/call-trgt_plot_meth_waterfall", thread: 140609260066368
2025-09-15 20:25:03.380 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_plot_meth_waterfall INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:03.380 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_plot_meth_waterfall INFO input :: name: "waterfall", value: true
2025-09-15 20:25:03.380 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_plot_meth_waterfall INFO input :: name: "methylation", value: true
2025-09-15 20:25:03.380 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_plot_meth_waterfall INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:25:03.380 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_plot_meth_waterfall INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:25:03.380 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_plot_meth_waterfall INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:25:03.380 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_plot_meth_waterfall INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2139.trgt.sorted.spanning.bam.bai"
2025-09-15 20:25:03.380 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_plot_meth_waterfall INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2139.trgt.sorted.spanning.bam"
2025-09-15 20:25:03.380 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_plot_meth_waterfall INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2139.trgt.vcf"
2025-09-15 20:25:03.380 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_plot_meth_waterfall INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2139"
2025-09-15 20:25:03.380 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_plot_meth_waterfall INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:25:03.380 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_plot_meth_waterfall INFO eval :: name: "plot_type", value: "waterfall"
2025-09-15 20:25:03.381 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_plot_meth_waterfall INFO eval :: name: "show", value: "meth"
2025-09-15 20:25:03.381 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_plot_meth_waterfall INFO eval :: name: "threads", value: 1
2025-09-15 20:25:03.381 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_plot_meth_waterfall INFO eval :: name: "disk_size", value: 27
2025-09-15 20:25:03.381 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_plot_meth_waterfall INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2139.meth_waterfall"
2025-09-15 20:25:03.381 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_plot_meth_waterfall INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:03.382 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_plot_meth_waterfall WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:03.382 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_plot_meth_waterfall INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:25:03.382 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_plot_meth_waterfall INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:03.393 wdl.w:ptcp.w:call-sawfish-37 NOTICE done
2025-09-15 20:25:03.399 wdl.w:ptcp NOTICE finish :: job: "call-sawfish-37"
2025-09-15 20:25:03.400 wdl.w:ptcp INFO output :: job: "call-sawfish-37", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-37/out/m84036_250809_035451_s4.bc2134_sawfish/m84036_250809_035451_s4.bc2134.sv.vcf.gz", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-37/out/m84036_250809_035451_s4.bc2134.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-37/out/m84036_250809_035451_s4.bc2134_sawfish/m84036_250809_035451_s4.bc2134.sv.vcf.gz.tbi", "minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-37/out/m84036_250809_035451_s4.bc2134.minimap2.bam.bai"}
2025-09-15 20:25:03.400 wdl.w:ptcp NOTICE ready :: job: "call-tar_outputs-37", callee: "tar_outputs"
2025-09-15 20:25:03.401 wdl.w:ptcp INFO input :: job: "call-tar_outputs-37", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "sawfish_vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-37/out/m84036_250809_035451_s4.bc2134_sawfish/m84036_250809_035451_s4.bc2134.sv.vcf.gz.tbi", "sawfish_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-37/out/m84036_250809_035451_s4.bc2134_sawfish/m84036_250809_035451_s4.bc2134.sv.vcf.gz", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-37/out/m84036_250809_035451_s4.bc2134.f8inversion.json", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-37/out/m84036_250809_035451_s4.bc2134_paraphase/m84036_250809_035451_s4.bc2134.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-37/out/m84036_250809_035451_s4.bc2134_paraphase/m84036_250809_035451_s4.bc2134.paraphase.bam", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-37/out/m84036_250809_035451_s4.bc2134_paraphase/m84036_250809_035451_s4.bc2134.paraphase.json", "trgt_spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-37/out/m84036_250809_035451_s4.bc2134.trgt.sorted.spanning.bam.bai", "trgt_spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-37/out/m84036_250809_035451_s4.bc2134.trgt.sorted.spanning.bam", "trgt_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-37/out/m84036_250809_035451_s4.bc2134.trgt.vcf", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-37/out/m84036_250809_035451_s4.bc2134.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-37/out/m84036_250809_035451_s4.bc2134.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2134"}
2025-09-15 20:25:03.405 wdl.w:ptcp.w:call-sawfish-75 NOTICE workflow start :: name: "sawfish", source: "./sawfish.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-75"
2025-09-15 20:25:03.424 wdl.w:ptcp.w:call-sawfish-75 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:25:03.424 wdl.w:ptcp.w:call-sawfish-75 INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:25:03.424 wdl.w:ptcp.w:call-sawfish-75 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-75/out/m84036_250809_035451_s4.bc2172.mapped.bam"}
2025-09-15 20:25:03.424 wdl.w:ptcp.w:call-sawfish-75 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-75/out/m84036_250809_035451_s4.bc2172.mapped.bam.bai"}
2025-09-15 20:25:03.424 wdl.w:ptcp.w:call-sawfish-75 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:25:03.424 wdl.w:ptcp.w:call-sawfish-75 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:25:03.424 wdl.w:ptcp.w:call-sawfish-75 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2172"}
2025-09-15 20:25:03.425 wdl.w:ptcp.w:call-sawfish-75 NOTICE ready :: job: "call-run_sawfish", callee: "run_sawfish"
2025-09-15 20:25:03.425 wdl.w:ptcp.w:call-sawfish-75 INFO input :: job: "call-run_sawfish", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-75/out/m84036_250809_035451_s4.bc2172.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-75/out/m84036_250809_035451_s4.bc2172.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2172"}
2025-09-15 20:25:03.447 wdl.w:ptcp.t:call-tar_outputs-05 INFO output :: name: "sample_tarball", value: "m84036_250809_035451_s4.bc2102.tar"
2025-09-15 20:25:03.460 wdl.w:ptcp.w:call-sawfish-36.t:call-run_sawfish INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2133_sawfish/m84036_250809_035451_s4.bc2133.sv.vcf.gz"
2025-09-15 20:25:03.464 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_plot_meth_waterfall INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-42/call-trgt_plot_meth_waterfall/_singularity_tmpdir_2qinej41"
2025-09-15 20:25:03.465 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_plot_meth_waterfall INFO Slurm invocation: srun --job-name call-trgt_plot_meth_waterfall --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-42/call-trgt_plot_meth_waterfall/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-42/call-trgt_plot_meth_waterfall/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-42/call-trgt_plot_meth_waterfall/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-42/call-trgt_plot_meth_waterfall/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-42/call-trgt_genotype/out/m84036_250809_035451_s4.bc2139.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2139.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-42/call-trgt_genotype/out/m84036_250809_035451_s4.bc2139.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2139.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-42/call-trgt_genotype/out/m84036_250809_035451_s4.bc2139.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2139.trgt.sorted.spanning.bam:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-42/call-trgt_plot_meth_waterfall/_singularity_tmpdir_2qinej41/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-42/call-trgt_plot_meth_waterfall/_singularity_tmpdir_2qinej41/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:03.467 wdl.w:ptcp.w:call-sawfish-36.t:call-run_sawfish INFO output :: name: "vcf_tbi", value: "m84036_250809_035451_s4.bc2133_sawfish/m84036_250809_035451_s4.bc2133.sv.vcf.gz.tbi"
2025-09-15 20:25:03.469 wdl.w:ptcp.w:call-sawfish-36.t:call-run_sawfish INFO output :: name: "minimap2_bam", value: "m84036_250809_035451_s4.bc2133.minimap2.bam"
2025-09-15 20:25:03.471 wdl.w:ptcp.w:call-trgt-49.t:call-trgt_plot_motifs_allele INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2146.motifs_allele.trgt_plots.zip"
2025-09-15 20:25:03.472 wdl.w:ptcp.w:call-sawfish-36.t:call-run_sawfish INFO output :: name: "minimap2_bam_bai", value: "m84036_250809_035451_s4.bc2133.minimap2.bam.bai"
2025-09-15 20:25:03.488 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_plot_meth_waterfall NOTICE slurm_singularity run :: pid: 1204468, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-42/call-trgt_plot_meth_waterfall/slurm_singularity.log.txt"
2025-09-15 20:25:03.515 wdl.w:ptcp.t:call-tar_outputs-05 NOTICE done
2025-09-15 20:25:03.519 wdl.w:ptcp NOTICE finish :: job: "call-tar_outputs-05"
2025-09-15 20:25:03.519 wdl.w:ptcp INFO output :: job: "call-tar_outputs-05", values: {"sample_tarball": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-05/out/m84036_250809_035451_s4.bc2102.tar"}
2025-09-15 20:25:03.530 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_plot_motifs_allele NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-42/call-trgt_plot_motifs_allele", thread: 140609285244480
2025-09-15 20:25:03.550 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_plot_motifs_allele INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:03.550 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_plot_motifs_allele INFO input :: name: "waterfall", value: false
2025-09-15 20:25:03.550 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_plot_motifs_allele INFO input :: name: "methylation", value: false
2025-09-15 20:25:03.550 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_plot_motifs_allele INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:25:03.550 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_plot_motifs_allele INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:25:03.550 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_plot_motifs_allele INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:25:03.550 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_plot_motifs_allele INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2139.trgt.sorted.spanning.bam.bai"
2025-09-15 20:25:03.550 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_plot_motifs_allele INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2139.trgt.sorted.spanning.bam"
2025-09-15 20:25:03.550 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_plot_motifs_allele INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2139.trgt.vcf"
2025-09-15 20:25:03.551 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_plot_motifs_allele INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2139"
2025-09-15 20:25:03.551 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_plot_motifs_allele INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:25:03.551 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_plot_motifs_allele INFO eval :: name: "plot_type", value: "allele"
2025-09-15 20:25:03.551 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_plot_motifs_allele INFO eval :: name: "show", value: "motifs"
2025-09-15 20:25:03.551 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_plot_motifs_allele INFO eval :: name: "threads", value: 1
2025-09-15 20:25:03.551 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_plot_motifs_allele INFO eval :: name: "disk_size", value: 27
2025-09-15 20:25:03.552 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_plot_motifs_allele INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2139.motifs_allele"
2025-09-15 20:25:03.552 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_plot_motifs_allele INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:03.552 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_plot_motifs_allele WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:03.553 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_plot_motifs_allele INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:25:03.553 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_plot_motifs_allele INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:03.554 wdl.w:ptcp.w:call-trgt-56.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:02 [ERROR] - No reads found for TRID=PRTS_ARX
2025-09-15 20:25:03.554 wdl.w:ptcp.w:call-trgt-56.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:02 [ERROR] - No reads found for TRID=EIEE1_ARX
2025-09-15 20:25:03.612 wdl.w:ptcp.w:call-trgt-49.t:call-trgt_plot_motifs_allele NOTICE done
2025-09-15 20:25:03.617 wdl.w:ptcp.w:call-trgt-49 NOTICE finish :: job: "call-trgt_plot_motifs_allele"
2025-09-15 20:25:03.617 wdl.w:ptcp.w:call-trgt-49 INFO output :: job: "call-trgt_plot_motifs_allele", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-49/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2146.motifs_allele.trgt_plots.zip"}
2025-09-15 20:25:03.617 wdl.w:ptcp.w:call-trgt-49 INFO visit :: node: "output-images_motifs_allele", values: {"images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-49/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2146.motifs_allele.trgt_plots.zip"}
2025-09-15 20:25:03.624 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_plot_motifs_waterfall NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-42/call-trgt_plot_motifs_waterfall", thread: 140609813722688
2025-09-15 20:25:03.632 wdl.w:ptcp.w:call-sawfish-36.t:call-run_sawfish NOTICE done
2025-09-15 20:25:03.645 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_plot_motifs_allele INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-42/call-trgt_plot_motifs_allele/_singularity_tmpdir_g5lwcuee"
2025-09-15 20:25:03.646 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_plot_motifs_allele INFO Slurm invocation: srun --job-name call-trgt_plot_motifs_allele --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-42/call-trgt_plot_motifs_allele/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-42/call-trgt_plot_motifs_allele/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-42/call-trgt_plot_motifs_allele/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-42/call-trgt_plot_motifs_allele/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-42/call-trgt_genotype/out/m84036_250809_035451_s4.bc2139.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2139.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-42/call-trgt_genotype/out/m84036_250809_035451_s4.bc2139.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2139.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-42/call-trgt_genotype/out/m84036_250809_035451_s4.bc2139.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2139.trgt.sorted.spanning.bam:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-42/call-trgt_plot_motifs_allele/_singularity_tmpdir_g5lwcuee/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-42/call-trgt_plot_motifs_allele/_singularity_tmpdir_g5lwcuee/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:03.648 wdl.w:ptcp.w:call-sawfish-36 NOTICE finish :: job: "call-run_sawfish"
2025-09-15 20:25:03.649 wdl.w:ptcp.w:call-sawfish-36 INFO output :: job: "call-run_sawfish", values: {"minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-36/call-run_sawfish/out/m84036_250809_035451_s4.bc2133.minimap2.bam.bai", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-36/call-run_sawfish/out/m84036_250809_035451_s4.bc2133.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-36/call-run_sawfish/out/m84036_250809_035451_s4.bc2133_sawfish/m84036_250809_035451_s4.bc2133.sv.vcf.gz.tbi", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-36/call-run_sawfish/out/m84036_250809_035451_s4.bc2133_sawfish/m84036_250809_035451_s4.bc2133.sv.vcf.gz"}
2025-09-15 20:25:03.649 wdl.w:ptcp.w:call-sawfish-36 INFO visit :: node: "output-minimap2_bam", values: {"minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-36/call-run_sawfish/out/m84036_250809_035451_s4.bc2133.minimap2.bam"}
2025-09-15 20:25:03.649 wdl.w:ptcp.w:call-sawfish-36 INFO visit :: node: "output-minimap2_bam_bai", values: {"minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-36/call-run_sawfish/out/m84036_250809_035451_s4.bc2133.minimap2.bam.bai"}
2025-09-15 20:25:03.649 wdl.w:ptcp.w:call-sawfish-36 INFO visit :: node: "output-vcf", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-36/call-run_sawfish/out/m84036_250809_035451_s4.bc2133_sawfish/m84036_250809_035451_s4.bc2133.sv.vcf.gz"}
2025-09-15 20:25:03.649 wdl.w:ptcp.w:call-sawfish-36 INFO visit :: node: "output-vcf_tbi", values: {"vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-36/call-run_sawfish/out/m84036_250809_035451_s4.bc2133_sawfish/m84036_250809_035451_s4.bc2133.sv.vcf.gz.tbi"}
2025-09-15 20:25:03.649 wdl.w:ptcp.w:call-sawfish-36 INFO visit :: node: "outputs", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-36/call-run_sawfish/out/m84036_250809_035451_s4.bc2133_sawfish/m84036_250809_035451_s4.bc2133.sv.vcf.gz", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-36/call-run_sawfish/out/m84036_250809_035451_s4.bc2133.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-36/call-run_sawfish/out/m84036_250809_035451_s4.bc2133_sawfish/m84036_250809_035451_s4.bc2133.sv.vcf.gz.tbi", "minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-36/call-run_sawfish/out/m84036_250809_035451_s4.bc2133.minimap2.bam.bai"}
2025-09-15 20:25:03.650 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_plot_motifs_waterfall INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:03.650 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_plot_motifs_waterfall INFO input :: name: "waterfall", value: true
2025-09-15 20:25:03.650 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_plot_motifs_waterfall INFO input :: name: "methylation", value: false
2025-09-15 20:25:03.650 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_plot_motifs_waterfall INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:25:03.650 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_plot_motifs_waterfall INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:25:03.651 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_plot_motifs_waterfall INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:25:03.651 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_plot_motifs_waterfall INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2139.trgt.sorted.spanning.bam.bai"
2025-09-15 20:25:03.651 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_plot_motifs_waterfall INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2139.trgt.sorted.spanning.bam"
2025-09-15 20:25:03.651 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_plot_motifs_waterfall INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2139.trgt.vcf"
2025-09-15 20:25:03.651 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_plot_motifs_waterfall INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2139"
2025-09-15 20:25:03.651 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:25:03.651 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "plot_type", value: "waterfall"
2025-09-15 20:25:03.652 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "show", value: "motifs"
2025-09-15 20:25:03.652 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "threads", value: 1
2025-09-15 20:25:03.652 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "disk_size", value: 27
2025-09-15 20:25:03.652 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2139.motifs_waterfall"
2025-09-15 20:25:03.653 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_plot_motifs_waterfall INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:03.653 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_plot_motifs_waterfall WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:03.653 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_plot_motifs_waterfall INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:25:03.653 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_plot_motifs_waterfall INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:03.656 wdl.w:ptcp.w:call-trgt-58.t:call-trgt_plot_meth_allele NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-58/call-trgt_plot_meth_allele", thread: 140611424335424
2025-09-15 20:25:03.671 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_plot_motifs_allele NOTICE slurm_singularity run :: pid: 1204470, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-42/call-trgt_plot_motifs_allele/slurm_singularity.log.txt"
2025-09-15 20:25:03.676 wdl.w:ptcp.w:call-trgt-58.t:call-trgt_plot_meth_allele INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:03.676 wdl.w:ptcp.w:call-trgt-58.t:call-trgt_plot_meth_allele INFO input :: name: "waterfall", value: false
2025-09-15 20:25:03.676 wdl.w:ptcp.w:call-trgt-58.t:call-trgt_plot_meth_allele INFO input :: name: "methylation", value: true
2025-09-15 20:25:03.676 wdl.w:ptcp.w:call-trgt-58.t:call-trgt_plot_meth_allele INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:25:03.676 wdl.w:ptcp.w:call-trgt-58.t:call-trgt_plot_meth_allele INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:25:03.676 wdl.w:ptcp.w:call-trgt-58.t:call-trgt_plot_meth_allele INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:25:03.677 wdl.w:ptcp.w:call-trgt-58.t:call-trgt_plot_meth_allele INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2155.trgt.sorted.spanning.bam.bai"
2025-09-15 20:25:03.677 wdl.w:ptcp.w:call-trgt-58.t:call-trgt_plot_meth_allele INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2155.trgt.sorted.spanning.bam"
2025-09-15 20:25:03.677 wdl.w:ptcp.w:call-trgt-58.t:call-trgt_plot_meth_allele INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2155.trgt.vcf"
2025-09-15 20:25:03.677 wdl.w:ptcp.w:call-trgt-58.t:call-trgt_plot_meth_allele INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2155"
2025-09-15 20:25:03.678 wdl.w:ptcp.w:call-trgt-58.t:call-trgt_plot_meth_allele INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:25:03.679 wdl.w:ptcp.w:call-trgt-58.t:call-trgt_plot_meth_allele INFO eval :: name: "plot_type", value: "allele"
2025-09-15 20:25:03.679 wdl.w:ptcp.w:call-trgt-58.t:call-trgt_plot_meth_allele INFO eval :: name: "show", value: "meth"
2025-09-15 20:25:03.679 wdl.w:ptcp.w:call-trgt-58.t:call-trgt_plot_meth_allele INFO eval :: name: "threads", value: 1
2025-09-15 20:25:03.679 wdl.w:ptcp.w:call-trgt-58.t:call-trgt_plot_meth_allele INFO eval :: name: "disk_size", value: 27
2025-09-15 20:25:03.679 wdl.w:ptcp.w:call-trgt-58.t:call-trgt_plot_meth_allele INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2155.meth_allele"
2025-09-15 20:25:03.680 wdl.w:ptcp.w:call-trgt-58.t:call-trgt_plot_meth_allele INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:03.680 wdl.w:ptcp.w:call-trgt-58.t:call-trgt_plot_meth_allele WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:03.680 wdl.w:ptcp.w:call-trgt-58.t:call-trgt_plot_meth_allele INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:25:03.680 wdl.w:ptcp.w:call-trgt-58.t:call-trgt_plot_meth_allele INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:03.708 wdl.w:ptcp.w:call-sawfish-36 NOTICE done
2025-09-15 20:25:03.716 wdl.w:ptcp NOTICE finish :: job: "call-sawfish-36"
2025-09-15 20:25:03.716 wdl.w:ptcp INFO output :: job: "call-sawfish-36", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-36/out/m84036_250809_035451_s4.bc2133_sawfish/m84036_250809_035451_s4.bc2133.sv.vcf.gz", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-36/out/m84036_250809_035451_s4.bc2133.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-36/out/m84036_250809_035451_s4.bc2133_sawfish/m84036_250809_035451_s4.bc2133.sv.vcf.gz.tbi", "minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-36/out/m84036_250809_035451_s4.bc2133.minimap2.bam.bai"}
2025-09-15 20:25:03.717 wdl.w:ptcp NOTICE ready :: job: "call-tar_outputs-36", callee: "tar_outputs"
2025-09-15 20:25:03.717 wdl.w:ptcp INFO input :: job: "call-tar_outputs-36", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "sawfish_vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-36/out/m84036_250809_035451_s4.bc2133_sawfish/m84036_250809_035451_s4.bc2133.sv.vcf.gz.tbi", "sawfish_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-36/out/m84036_250809_035451_s4.bc2133_sawfish/m84036_250809_035451_s4.bc2133.sv.vcf.gz", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-36/out/m84036_250809_035451_s4.bc2133.f8inversion.json", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-36/out/m84036_250809_035451_s4.bc2133_paraphase/m84036_250809_035451_s4.bc2133.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-36/out/m84036_250809_035451_s4.bc2133_paraphase/m84036_250809_035451_s4.bc2133.paraphase.bam", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-36/out/m84036_250809_035451_s4.bc2133_paraphase/m84036_250809_035451_s4.bc2133.paraphase.json", "trgt_spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-36/out/m84036_250809_035451_s4.bc2133.trgt.sorted.spanning.bam.bai", "trgt_spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-36/out/m84036_250809_035451_s4.bc2133.trgt.sorted.spanning.bam", "trgt_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-36/out/m84036_250809_035451_s4.bc2133.trgt.vcf", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-36/out/m84036_250809_035451_s4.bc2133.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-36/out/m84036_250809_035451_s4.bc2133.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2133"}
2025-09-15 20:25:03.731 wdl.w:ptcp.w:call-trgt-75 NOTICE workflow start :: name: "trgt", source: "./trgt.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-75"
2025-09-15 20:25:03.751 wdl.w:ptcp.w:call-trgt-75 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:25:03.752 wdl.w:ptcp.w:call-trgt-75 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-75/out/m84036_250809_035451_s4.bc2172.mapped.bam"}
2025-09-15 20:25:03.752 wdl.w:ptcp.w:call-trgt-75 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-75/out/m84036_250809_035451_s4.bc2172.mapped.bam.bai"}
2025-09-15 20:25:03.752 wdl.w:ptcp.w:call-trgt-75 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:25:03.752 wdl.w:ptcp.w:call-trgt-75 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:25:03.752 wdl.w:ptcp.w:call-trgt-75 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2172"}
2025-09-15 20:25:03.752 wdl.w:ptcp.w:call-trgt-75 INFO visit :: node: "decl-sex", values: {"sex": "F"}
2025-09-15 20:25:03.752 wdl.w:ptcp.w:call-trgt-75 INFO visit :: node: "decl-trgt_bed", values: {"trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"}
2025-09-15 20:25:03.752 wdl.w:ptcp.w:call-trgt-75 NOTICE ready :: job: "call-get_reads_overlapping_repeats", callee: "get_reads_overlapping_repeats"
2025-09-15 20:25:03.752 wdl.w:ptcp.w:call-trgt-75 INFO input :: job: "call-get_reads_overlapping_repeats", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-75/out/m84036_250809_035451_s4.bc2172.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-75/out/m84036_250809_035451_s4.bc2172.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2172"}
2025-09-15 20:25:03.753 wdl.w:ptcp.w:call-trgt-75 NOTICE ready :: job: "call-trgt_genotype", callee: "trgt_genotype"
2025-09-15 20:25:03.753 wdl.w:ptcp.w:call-trgt-75 INFO input :: job: "call-trgt_genotype", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-75/out/m84036_250809_035451_s4.bc2172.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-75/out/m84036_250809_035451_s4.bc2172.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2172"}
2025-09-15 20:25:03.754 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_plot_motifs_waterfall INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-42/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_v5nukp6m"
2025-09-15 20:25:03.755 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_plot_motifs_waterfall INFO Slurm invocation: srun --job-name call-trgt_plot_motifs_waterfall --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-42/call-trgt_plot_motifs_waterfall/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-42/call-trgt_plot_motifs_waterfall/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-42/call-trgt_plot_motifs_waterfall/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-42/call-trgt_plot_motifs_waterfall/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-42/call-trgt_genotype/out/m84036_250809_035451_s4.bc2139.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2139.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-42/call-trgt_genotype/out/m84036_250809_035451_s4.bc2139.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2139.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-42/call-trgt_genotype/out/m84036_250809_035451_s4.bc2139.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2139.trgt.sorted.spanning.bam:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-42/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_v5nukp6m/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-42/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_v5nukp6m/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:03.767 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_plot_motifs_waterfall NOTICE slurm_singularity run :: pid: 1204472, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-42/call-trgt_plot_motifs_waterfall/slurm_singularity.log.txt"
2025-09-15 20:25:03.771 wdl.w:ptcp.w:call-trgt-58.t:call-trgt_plot_meth_allele INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-58/call-trgt_plot_meth_allele/_singularity_tmpdir_uu40y78t"
2025-09-15 20:25:03.771 wdl.w:ptcp.w:call-trgt-58.t:call-trgt_plot_meth_allele INFO Slurm invocation: srun --job-name call-trgt_plot_meth_allele --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-58/call-trgt_plot_meth_allele/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-58/call-trgt_plot_meth_allele/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-58/call-trgt_plot_meth_allele/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-58/call-trgt_plot_meth_allele/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-58/call-trgt_genotype/out/m84036_250809_035451_s4.bc2155.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2155.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-58/call-trgt_genotype/out/m84036_250809_035451_s4.bc2155.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2155.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-58/call-trgt_genotype/out/m84036_250809_035451_s4.bc2155.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2155.trgt.sorted.spanning.bam:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-58/call-trgt_plot_meth_allele/_singularity_tmpdir_uu40y78t/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-58/call-trgt_plot_meth_allele/_singularity_tmpdir_uu40y78t/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:03.779 wdl.w:ptcp.w:call-trgt-58.t:call-trgt_plot_meth_allele NOTICE slurm_singularity run :: pid: 1204473, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-58/call-trgt_plot_meth_allele/slurm_singularity.log.txt"
2025-09-15 20:25:03.781 wdl.w:ptcp.w:call-trgt-56.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:25:02 [ERROR] - No reads found for TRID=PRTS_ARX
2025-09-15 20:25:03.781 wdl.w:ptcp.w:call-trgt-56.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:25:02 [ERROR] - No reads found for TRID=EIEE1_ARX
2025-09-15 20:25:03.816 wdl.w:ptcp.w:call-trgt-66.t:call-get_reads_overlapping_repeats.slurm_singularity INFO srun: job 51797877 queued and waiting for resources
2025-09-15 20:25:03.816 wdl.w:ptcp.w:call-trgt-66.t:call-get_reads_overlapping_repeats.slurm_singularity INFO srun: job 51797877 has been allocated resources
2025-09-15 20:25:03.816 wdl.w:ptcp.w:call-trgt-66.t:call-get_reads_overlapping_repeats.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:03.869 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_genotype.slurm_singularity INFO srun: job 51797878 queued and waiting for resources
2025-09-15 20:25:03.870 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_genotype.slurm_singularity INFO srun: job 51797878 has been allocated resources
2025-09-15 20:25:03.870 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_genotype.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:03.872 wdl.w:ptcp.t:call-tar_outputs-21 INFO output :: name: "sample_tarball", value: "m84036_250809_035451_s4.bc2118.tar"
2025-09-15 20:25:03.941 wdl.w:ptcp.t:call-tar_outputs-21 NOTICE done
2025-09-15 20:25:03.946 wdl.w:ptcp NOTICE finish :: job: "call-tar_outputs-21"
2025-09-15 20:25:03.946 wdl.w:ptcp INFO output :: job: "call-tar_outputs-21", values: {"sample_tarball": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-21/out/m84036_250809_035451_s4.bc2118.tar"}
2025-09-15 20:25:03.947 wdl.w:ptcp.w:call-paraphase-57.t:call-call_f8.slurm_singularity INFO srun: job 51797879 queued and waiting for resources
2025-09-15 20:25:03.947 wdl.w:ptcp.w:call-paraphase-57.t:call-call_f8.slurm_singularity INFO srun: job 51797879 has been allocated resources
2025-09-15 20:25:03.947 wdl.w:ptcp.w:call-paraphase-57.t:call-call_f8.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:03.952 wdl.w:ptcp.w:call-trgt-58.t:call-trgt_plot_meth_waterfall NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-58/call-trgt_plot_meth_waterfall", thread: 140611944420928
2025-09-15 20:25:03.968 wdl.w:ptcp.w:call-trgt-58.t:call-trgt_plot_meth_waterfall INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:03.968 wdl.w:ptcp.w:call-trgt-58.t:call-trgt_plot_meth_waterfall INFO input :: name: "waterfall", value: true
2025-09-15 20:25:03.968 wdl.w:ptcp.w:call-trgt-58.t:call-trgt_plot_meth_waterfall INFO input :: name: "methylation", value: true
2025-09-15 20:25:03.968 wdl.w:ptcp.w:call-trgt-58.t:call-trgt_plot_meth_waterfall INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:25:03.968 wdl.w:ptcp.w:call-trgt-58.t:call-trgt_plot_meth_waterfall INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:25:03.968 wdl.w:ptcp.w:call-trgt-58.t:call-trgt_plot_meth_waterfall INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:25:03.968 wdl.w:ptcp.w:call-trgt-58.t:call-trgt_plot_meth_waterfall INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2155.trgt.sorted.spanning.bam.bai"
2025-09-15 20:25:03.968 wdl.w:ptcp.w:call-trgt-58.t:call-trgt_plot_meth_waterfall INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2155.trgt.sorted.spanning.bam"
2025-09-15 20:25:03.969 wdl.w:ptcp.w:call-trgt-58.t:call-trgt_plot_meth_waterfall INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2155.trgt.vcf"
2025-09-15 20:25:03.969 wdl.w:ptcp.w:call-trgt-58.t:call-trgt_plot_meth_waterfall INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2155"
2025-09-15 20:25:03.969 wdl.w:ptcp.w:call-trgt-58.t:call-trgt_plot_meth_waterfall INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:25:03.969 wdl.w:ptcp.w:call-trgt-58.t:call-trgt_plot_meth_waterfall INFO eval :: name: "plot_type", value: "waterfall"
2025-09-15 20:25:03.969 wdl.w:ptcp.w:call-trgt-58.t:call-trgt_plot_meth_waterfall INFO eval :: name: "show", value: "meth"
2025-09-15 20:25:03.969 wdl.w:ptcp.w:call-trgt-58.t:call-trgt_plot_meth_waterfall INFO eval :: name: "threads", value: 1
2025-09-15 20:25:03.970 wdl.w:ptcp.w:call-trgt-58.t:call-trgt_plot_meth_waterfall INFO eval :: name: "disk_size", value: 27
2025-09-15 20:25:03.970 wdl.w:ptcp.w:call-trgt-58.t:call-trgt_plot_meth_waterfall INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2155.meth_waterfall"
2025-09-15 20:25:03.970 wdl.w:ptcp.w:call-trgt-58.t:call-trgt_plot_meth_waterfall INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:03.970 wdl.w:ptcp.w:call-trgt-58.t:call-trgt_plot_meth_waterfall WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:03.970 wdl.w:ptcp.w:call-trgt-58.t:call-trgt_plot_meth_waterfall INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:25:03.971 wdl.w:ptcp.w:call-trgt-58.t:call-trgt_plot_meth_waterfall INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:04.042 wdl.w:ptcp.w:call-trgt-58.t:call-trgt_plot_meth_waterfall INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-58/call-trgt_plot_meth_waterfall/_singularity_tmpdir_yoa6o9fi"
2025-09-15 20:25:04.042 wdl.w:ptcp.w:call-trgt-58.t:call-trgt_plot_meth_waterfall INFO Slurm invocation: srun --job-name call-trgt_plot_meth_waterfall --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-58/call-trgt_plot_meth_waterfall/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-58/call-trgt_plot_meth_waterfall/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-58/call-trgt_plot_meth_waterfall/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-58/call-trgt_plot_meth_waterfall/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-58/call-trgt_genotype/out/m84036_250809_035451_s4.bc2155.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2155.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-58/call-trgt_genotype/out/m84036_250809_035451_s4.bc2155.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2155.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-58/call-trgt_genotype/out/m84036_250809_035451_s4.bc2155.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2155.trgt.sorted.spanning.bam:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-58/call-trgt_plot_meth_waterfall/_singularity_tmpdir_yoa6o9fi/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-58/call-trgt_plot_meth_waterfall/_singularity_tmpdir_yoa6o9fi/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:04.047 wdl.w:ptcp.w:call-trgt-65.t:call-get_reads_overlapping_repeats INFO output :: name: "reads_overlapping_repeats", value: "m84036_250809_035451_s4.bc2162.repeats.bam"
2025-09-15 20:25:04.051 wdl.w:ptcp.w:call-trgt-65.t:call-get_reads_overlapping_repeats INFO output :: name: "reads_overlapping_repeats_bai", value: "m84036_250809_035451_s4.bc2162.repeats.bam.bai"
2025-09-15 20:25:04.074 wdl.w:ptcp.w:call-trgt-66.t:call-get_reads_overlapping_repeats INFO output :: name: "reads_overlapping_repeats", value: "m84036_250809_035451_s4.bc2163.repeats.bam"
2025-09-15 20:25:04.076 wdl.w:ptcp.w:call-trgt-58.t:call-trgt_plot_meth_waterfall NOTICE slurm_singularity run :: pid: 1204500, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-58/call-trgt_plot_meth_waterfall/slurm_singularity.log.txt"
2025-09-15 20:25:04.077 wdl.w:ptcp.w:call-trgt-66.t:call-get_reads_overlapping_repeats INFO output :: name: "reads_overlapping_repeats_bai", value: "m84036_250809_035451_s4.bc2163.repeats.bam.bai"
2025-09-15 20:25:04.089 wdl.w:ptcp.w:call-paraphase-49.t:call-call_f8.slurm_singularity INFO srun: job 51797880 queued and waiting for resources
2025-09-15 20:25:04.089 wdl.w:ptcp.w:call-paraphase-49.t:call-call_f8.slurm_singularity INFO srun: job 51797880 has been allocated resources
2025-09-15 20:25:04.089 wdl.w:ptcp.w:call-paraphase-49.t:call-call_f8.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:04.104 wdl.w:ptcp.w:call-sawfish-38.t:call-run_sawfish INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2135_sawfish/m84036_250809_035451_s4.bc2135.sv.vcf.gz"
2025-09-15 20:25:04.111 wdl.w:ptcp.w:call-sawfish-38.t:call-run_sawfish INFO output :: name: "vcf_tbi", value: "m84036_250809_035451_s4.bc2135_sawfish/m84036_250809_035451_s4.bc2135.sv.vcf.gz.tbi"
2025-09-15 20:25:04.112 wdl.w:ptcp.w:call-sawfish-38.t:call-run_sawfish INFO output :: name: "minimap2_bam", value: "m84036_250809_035451_s4.bc2135.minimap2.bam"
2025-09-15 20:25:04.114 wdl.w:ptcp.w:call-sawfish-38.t:call-run_sawfish INFO output :: name: "minimap2_bam_bai", value: "m84036_250809_035451_s4.bc2135.minimap2.bam.bai"
2025-09-15 20:25:04.132 wdl.w:ptcp.w:call-trgt-65.t:call-get_reads_overlapping_repeats NOTICE done
2025-09-15 20:25:04.138 wdl.w:ptcp.w:call-trgt-65 NOTICE finish :: job: "call-get_reads_overlapping_repeats"
2025-09-15 20:25:04.138 wdl.w:ptcp.w:call-trgt-65 INFO output :: job: "call-get_reads_overlapping_repeats", values: {"reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-65/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2162.repeats.bam.bai", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-65/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2162.repeats.bam"}
2025-09-15 20:25:04.139 wdl.w:ptcp.w:call-trgt-65 INFO visit :: node: "output-reads_overlapping_repeats", values: {"reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-65/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2162.repeats.bam"}
2025-09-15 20:25:04.139 wdl.w:ptcp.w:call-trgt-65 INFO visit :: node: "output-reads_overlapping_repeats_bai", values: {"reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-65/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2162.repeats.bam.bai"}
2025-09-15 20:25:04.146 wdl.w:ptcp.w:call-trgt-58.t:call-trgt_plot_motifs_allele NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-58/call-trgt_plot_motifs_allele", thread: 140607683024448
2025-09-15 20:25:04.157 wdl.w:ptcp.w:call-trgt-66.t:call-get_reads_overlapping_repeats NOTICE done
2025-09-15 20:25:04.163 wdl.w:ptcp.w:call-trgt-66 NOTICE finish :: job: "call-get_reads_overlapping_repeats"
2025-09-15 20:25:04.164 wdl.w:ptcp.w:call-trgt-66 INFO output :: job: "call-get_reads_overlapping_repeats", values: {"reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-66/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2163.repeats.bam.bai", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-66/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2163.repeats.bam"}
2025-09-15 20:25:04.164 wdl.w:ptcp.w:call-trgt-66 INFO visit :: node: "output-reads_overlapping_repeats", values: {"reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-66/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2163.repeats.bam"}
2025-09-15 20:25:04.165 wdl.w:ptcp.w:call-trgt-66 INFO visit :: node: "output-reads_overlapping_repeats_bai", values: {"reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-66/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2163.repeats.bam.bai"}
2025-09-15 20:25:04.172 wdl.w:ptcp.w:call-trgt-58.t:call-trgt_plot_motifs_allele INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:04.172 wdl.w:ptcp.w:call-trgt-58.t:call-trgt_plot_motifs_allele INFO input :: name: "waterfall", value: false
2025-09-15 20:25:04.172 wdl.w:ptcp.w:call-trgt-58.t:call-trgt_plot_motifs_allele INFO input :: name: "methylation", value: false
2025-09-15 20:25:04.172 wdl.w:ptcp.w:call-trgt-58.t:call-trgt_plot_motifs_allele INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:25:04.172 wdl.w:ptcp.w:call-trgt-58.t:call-trgt_plot_motifs_allele INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:25:04.172 wdl.w:ptcp.w:call-trgt-58.t:call-trgt_plot_motifs_allele INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:25:04.172 wdl.w:ptcp.w:call-trgt-58.t:call-trgt_plot_motifs_allele INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2155.trgt.sorted.spanning.bam.bai"
2025-09-15 20:25:04.172 wdl.w:ptcp.w:call-trgt-58.t:call-trgt_plot_motifs_allele INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2155.trgt.sorted.spanning.bam"
2025-09-15 20:25:04.173 wdl.w:ptcp.w:call-trgt-58.t:call-trgt_plot_motifs_allele INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2155.trgt.vcf"
2025-09-15 20:25:04.173 wdl.w:ptcp.w:call-trgt-58.t:call-trgt_plot_motifs_allele INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2155"
2025-09-15 20:25:04.173 wdl.w:ptcp.w:call-trgt-58.t:call-trgt_plot_motifs_allele INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:25:04.173 wdl.w:ptcp.w:call-trgt-58.t:call-trgt_plot_motifs_allele INFO eval :: name: "plot_type", value: "allele"
2025-09-15 20:25:04.173 wdl.w:ptcp.w:call-trgt-58.t:call-trgt_plot_motifs_allele INFO eval :: name: "show", value: "motifs"
2025-09-15 20:25:04.173 wdl.w:ptcp.w:call-trgt-58.t:call-trgt_plot_motifs_waterfall NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-58/call-trgt_plot_motifs_waterfall", thread: 140610367379008
2025-09-15 20:25:04.173 wdl.w:ptcp.w:call-trgt-58.t:call-trgt_plot_motifs_allele INFO eval :: name: "threads", value: 1
2025-09-15 20:25:04.174 wdl.w:ptcp.w:call-trgt-58.t:call-trgt_plot_motifs_allele INFO eval :: name: "disk_size", value: 27
2025-09-15 20:25:04.174 wdl.w:ptcp.w:call-trgt-58.t:call-trgt_plot_motifs_allele INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2155.motifs_allele"
2025-09-15 20:25:04.175 wdl.w:ptcp.w:call-trgt-58.t:call-trgt_plot_motifs_allele INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:04.175 wdl.w:ptcp.w:call-trgt-58.t:call-trgt_plot_motifs_allele WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:04.175 wdl.w:ptcp.w:call-trgt-58.t:call-trgt_plot_motifs_allele INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:25:04.176 wdl.w:ptcp.w:call-trgt-58.t:call-trgt_plot_motifs_allele INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:04.195 wdl.w:ptcp.w:call-trgt-58.t:call-trgt_plot_motifs_waterfall INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:04.196 wdl.w:ptcp.w:call-trgt-58.t:call-trgt_plot_motifs_waterfall INFO input :: name: "waterfall", value: true
2025-09-15 20:25:04.196 wdl.w:ptcp.w:call-trgt-58.t:call-trgt_plot_motifs_waterfall INFO input :: name: "methylation", value: false
2025-09-15 20:25:04.196 wdl.w:ptcp.w:call-trgt-58.t:call-trgt_plot_motifs_waterfall INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:25:04.196 wdl.w:ptcp.w:call-trgt-58.t:call-trgt_plot_motifs_waterfall INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:25:04.196 wdl.w:ptcp.w:call-trgt-58.t:call-trgt_plot_motifs_waterfall INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:25:04.196 wdl.w:ptcp.w:call-trgt-58.t:call-trgt_plot_motifs_waterfall INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2155.trgt.sorted.spanning.bam.bai"
2025-09-15 20:25:04.196 wdl.w:ptcp.w:call-trgt-58.t:call-trgt_plot_motifs_waterfall INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2155.trgt.sorted.spanning.bam"
2025-09-15 20:25:04.196 wdl.w:ptcp.w:call-trgt-58.t:call-trgt_plot_motifs_waterfall INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2155.trgt.vcf"
2025-09-15 20:25:04.196 wdl.w:ptcp.w:call-trgt-58.t:call-trgt_plot_motifs_waterfall INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2155"
2025-09-15 20:25:04.196 wdl.w:ptcp.w:call-trgt-58.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:25:04.196 wdl.w:ptcp.w:call-trgt-58.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "plot_type", value: "waterfall"
2025-09-15 20:25:04.197 wdl.w:ptcp.w:call-trgt-58.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "show", value: "motifs"
2025-09-15 20:25:04.197 wdl.w:ptcp.w:call-trgt-58.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "threads", value: 1
2025-09-15 20:25:04.197 wdl.w:ptcp.w:call-trgt-58.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "disk_size", value: 27
2025-09-15 20:25:04.197 wdl.w:ptcp.w:call-trgt-58.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2155.motifs_waterfall"
2025-09-15 20:25:04.197 wdl.w:ptcp.w:call-trgt-58.t:call-trgt_plot_motifs_waterfall INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:04.198 wdl.w:ptcp.w:call-trgt-58.t:call-trgt_plot_motifs_waterfall WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:04.198 wdl.w:ptcp.w:call-trgt-58.t:call-trgt_plot_motifs_waterfall INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:25:04.198 wdl.w:ptcp.w:call-trgt-58.t:call-trgt_plot_motifs_waterfall INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:04.207 wdl.w:ptcp.w:call-paraphase-06.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for hbb for sample m84036_250809_035451_s4.bc2103 at 2025-09-15 20:24:52.321006...
2025-09-15 20:25:04.207 wdl.w:ptcp.w:call-paraphase-06.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for hbb for sample m84036_250809_035451_s4.bc2103 at 2025-09-15 20:24:56.002153...
2025-09-15 20:25:04.207 wdl.w:ptcp.w:call-paraphase-06.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for hbb for sample m84036_250809_035451_s4.bc2103 at 2025-09-15 20:24:56.331770...
2025-09-15 20:25:04.220 wdl.w:ptcp.w:call-paraphase-57.t:call-call_f8 INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2154.f8inversion.vcf"
2025-09-15 20:25:04.225 wdl.w:ptcp.w:call-paraphase-57.t:call-call_f8 INFO output :: name: "json", value: "m84036_250809_035451_s4.bc2154.f8inversion.json"
2025-09-15 20:25:04.268 wdl.w:ptcp.w:call-trgt-58.t:call-trgt_plot_motifs_allele INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-58/call-trgt_plot_motifs_allele/_singularity_tmpdir_7ih15b6i"
2025-09-15 20:25:04.268 wdl.w:ptcp.w:call-trgt-58.t:call-trgt_plot_motifs_allele INFO Slurm invocation: srun --job-name call-trgt_plot_motifs_allele --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-58/call-trgt_plot_motifs_allele/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-58/call-trgt_plot_motifs_allele/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-58/call-trgt_plot_motifs_allele/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-58/call-trgt_plot_motifs_allele/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-58/call-trgt_genotype/out/m84036_250809_035451_s4.bc2155.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2155.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-58/call-trgt_genotype/out/m84036_250809_035451_s4.bc2155.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2155.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-58/call-trgt_genotype/out/m84036_250809_035451_s4.bc2155.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2155.trgt.sorted.spanning.bam:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-58/call-trgt_plot_motifs_allele/_singularity_tmpdir_7ih15b6i/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-58/call-trgt_plot_motifs_allele/_singularity_tmpdir_7ih15b6i/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:04.288 wdl.w:ptcp.w:call-trgt-58.t:call-trgt_plot_motifs_waterfall INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-58/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_k6yvtnp0"
2025-09-15 20:25:04.288 wdl.w:ptcp.w:call-trgt-58.t:call-trgt_plot_motifs_waterfall INFO Slurm invocation: srun --job-name call-trgt_plot_motifs_waterfall --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-58/call-trgt_plot_motifs_waterfall/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-58/call-trgt_plot_motifs_waterfall/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-58/call-trgt_plot_motifs_waterfall/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-58/call-trgt_plot_motifs_waterfall/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-58/call-trgt_genotype/out/m84036_250809_035451_s4.bc2155.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2155.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-58/call-trgt_genotype/out/m84036_250809_035451_s4.bc2155.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2155.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-58/call-trgt_genotype/out/m84036_250809_035451_s4.bc2155.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2155.trgt.sorted.spanning.bam:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-58/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_k6yvtnp0/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-58/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_k6yvtnp0/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:04.289 wdl.w:ptcp.w:call-sawfish-38.t:call-run_sawfish NOTICE done
2025-09-15 20:25:04.295 wdl.w:ptcp.w:call-trgt-58.t:call-trgt_plot_motifs_allele NOTICE slurm_singularity run :: pid: 1204508, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-58/call-trgt_plot_motifs_allele/slurm_singularity.log.txt"
2025-09-15 20:25:04.296 wdl.w:ptcp.w:call-paraphase-57.t:call-call_f8 NOTICE done
2025-09-15 20:25:04.300 wdl.w:ptcp.w:call-trgt-58.t:call-trgt_plot_motifs_waterfall NOTICE slurm_singularity run :: pid: 1204509, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-58/call-trgt_plot_motifs_waterfall/slurm_singularity.log.txt"
2025-09-15 20:25:04.318 wdl.w:ptcp.w:call-paraphase-57 NOTICE finish :: job: "call-call_f8"
2025-09-15 20:25:04.318 wdl.w:ptcp.w:call-paraphase-57 INFO output :: job: "call-call_f8", values: {"json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-57/call-call_f8/out/m84036_250809_035451_s4.bc2154.f8inversion.json", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-57/call-call_f8/out/m84036_250809_035451_s4.bc2154.f8inversion.vcf"}
2025-09-15 20:25:04.318 wdl.w:ptcp.w:call-paraphase-57 INFO visit :: node: "output-f8_json", values: {"f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-57/call-call_f8/out/m84036_250809_035451_s4.bc2154.f8inversion.json"}
2025-09-15 20:25:04.318 wdl.w:ptcp.w:call-paraphase-57 INFO visit :: node: "output-f8_vcf", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-57/call-call_f8/out/m84036_250809_035451_s4.bc2154.f8inversion.vcf"}
2025-09-15 20:25:04.319 wdl.w:ptcp.w:call-paraphase-57 INFO visit :: node: "outputs", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-57/call-call_f8/out/m84036_250809_035451_s4.bc2154.f8inversion.vcf", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-57/call-run_paraphase/out/m84036_250809_035451_s4.bc2154_paraphase/m84036_250809_035451_s4.bc2154.paraphase.json", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-57/call-run_paraphase/out/m84036_250809_035451_s4.bc2154_paraphase/m84036_250809_035451_s4.bc2154.paraphase.bam", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-57/call-run_paraphase/out/m84036_250809_035451_s4.bc2154_paraphase/m84036_250809_035451_s4.bc2154.paraphase.bam.bai", "paraphase_vcfs": [], "havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-57/call-run_paraphase/out/m84036_250809_035451_s4.bc2154.havanno.json", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-57/call-call_f8/out/m84036_250809_035451_s4.bc2154.f8inversion.json"}
2025-09-15 20:25:04.325 wdl.w:ptcp.w:call-paraphase-48.t:call-call_f8 NOTICE task setup :: name: "call_f8", source: "./paraphase.wdl", line: 232, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-48/call-call_f8", thread: 140609847293504
2025-09-15 20:25:04.332 wdl.w:ptcp.w:call-sawfish-38 NOTICE finish :: job: "call-run_sawfish"
2025-09-15 20:25:04.332 wdl.w:ptcp.w:call-sawfish-38 INFO output :: job: "call-run_sawfish", values: {"minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-38/call-run_sawfish/out/m84036_250809_035451_s4.bc2135.minimap2.bam.bai", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-38/call-run_sawfish/out/m84036_250809_035451_s4.bc2135.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-38/call-run_sawfish/out/m84036_250809_035451_s4.bc2135_sawfish/m84036_250809_035451_s4.bc2135.sv.vcf.gz.tbi", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-38/call-run_sawfish/out/m84036_250809_035451_s4.bc2135_sawfish/m84036_250809_035451_s4.bc2135.sv.vcf.gz"}
2025-09-15 20:25:04.332 wdl.w:ptcp.w:call-sawfish-38 INFO visit :: node: "output-minimap2_bam", values: {"minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-38/call-run_sawfish/out/m84036_250809_035451_s4.bc2135.minimap2.bam"}
2025-09-15 20:25:04.333 wdl.w:ptcp.w:call-sawfish-38 INFO visit :: node: "output-minimap2_bam_bai", values: {"minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-38/call-run_sawfish/out/m84036_250809_035451_s4.bc2135.minimap2.bam.bai"}
2025-09-15 20:25:04.333 wdl.w:ptcp.w:call-sawfish-38 INFO visit :: node: "output-vcf", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-38/call-run_sawfish/out/m84036_250809_035451_s4.bc2135_sawfish/m84036_250809_035451_s4.bc2135.sv.vcf.gz"}
2025-09-15 20:25:04.333 wdl.w:ptcp.w:call-sawfish-38 INFO visit :: node: "output-vcf_tbi", values: {"vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-38/call-run_sawfish/out/m84036_250809_035451_s4.bc2135_sawfish/m84036_250809_035451_s4.bc2135.sv.vcf.gz.tbi"}
2025-09-15 20:25:04.333 wdl.w:ptcp.w:call-sawfish-38 INFO visit :: node: "outputs", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-38/call-run_sawfish/out/m84036_250809_035451_s4.bc2135_sawfish/m84036_250809_035451_s4.bc2135.sv.vcf.gz", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-38/call-run_sawfish/out/m84036_250809_035451_s4.bc2135.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-38/call-run_sawfish/out/m84036_250809_035451_s4.bc2135_sawfish/m84036_250809_035451_s4.bc2135.sv.vcf.gz.tbi", "minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-38/call-run_sawfish/out/m84036_250809_035451_s4.bc2135.minimap2.bam.bai"}
2025-09-15 20:25:04.339 wdl.w:ptcp.w:call-paraphase-70.t:call-run_paraphase NOTICE task setup :: name: "run_paraphase", source: "./paraphase.wdl", line: 127, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-70/call-run_paraphase", thread: 140609796937280
2025-09-15 20:25:04.347 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:04 [ERROR] - No reads found for TRID=SCA37_DAB1
2025-09-15 20:25:04.348 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:04 [ERROR] - No reads found for TRID=OPDM_ABCD3
2025-09-15 20:25:04.348 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:04 [ERROR] - No reads found for TRID=NIID_NOTCH2NLC
2025-09-15 20:25:04.348 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:04 [ERROR] - No reads found for TRID=SCA2_ATXN2
2025-09-15 20:25:04.348 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:04 [ERROR] - No reads found for TRID=OPDM4_RILPL1
2025-09-15 20:25:04.348 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:04 [ERROR] - No reads found for TRID=SCA27B_FGF14
2025-09-15 20:25:04.349 wdl.w:ptcp.w:call-paraphase-48.t:call-call_f8 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:04.349 wdl.w:ptcp.w:call-paraphase-48.t:call-call_f8 INFO input :: name: "genome_version", value: "38"
2025-09-15 20:25:04.349 wdl.w:ptcp.w:call-paraphase-48.t:call-call_f8 INFO input :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2145"
2025-09-15 20:25:04.349 wdl.w:ptcp.w:call-paraphase-48.t:call-call_f8 INFO input :: name: "paraphase_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2145.paraphase.bam.bai"
2025-09-15 20:25:04.349 wdl.w:ptcp.w:call-paraphase-48.t:call-call_f8 INFO input :: name: "paraphase_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2145.paraphase.bam"
2025-09-15 20:25:04.349 wdl.w:ptcp.w:call-paraphase-48.t:call-call_f8 INFO input :: name: "sex", value: "F"
2025-09-15 20:25:04.350 wdl.w:ptcp.w:call-paraphase-48.t:call-call_f8 INFO eval :: name: "threads", value: 1
2025-09-15 20:25:04.350 wdl.w:ptcp.w:call-paraphase-48.t:call-call_f8 INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:25:04.350 wdl.w:ptcp.w:call-paraphase-48.t:call-call_f8 INFO eval :: name: "disk_size", value: 11
2025-09-15 20:25:04.350 wdl.w:ptcp.w:call-paraphase-48.t:call-call_f8 INFO eval :: name: "sample_sex", value: "F"
2025-09-15 20:25:04.351 wdl.w:ptcp.w:call-paraphase-48.t:call-call_f8 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:04.351 wdl.w:ptcp.w:call-paraphase-48.t:call-call_f8 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:04.351 wdl.w:ptcp.w:call-paraphase-48.t:call-call_f8 INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:25:04.352 wdl.w:ptcp.w:call-paraphase-48.t:call-call_f8 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:04.365 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_plot_meth_allele.slurm_singularity INFO srun: job 51797881 queued and waiting for resources
2025-09-15 20:25:04.365 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_plot_meth_allele.slurm_singularity INFO srun: job 51797881 has been allocated resources
2025-09-15 20:25:04.365 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_plot_meth_allele.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:04.374 wdl.w:ptcp.w:call-paraphase-70.t:call-run_paraphase INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:04.374 wdl.w:ptcp.w:call-paraphase-70.t:call-run_paraphase INFO input :: name: "annotation_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf"
2025-09-15 20:25:04.374 wdl.w:ptcp.w:call-paraphase-70.t:call-run_paraphase INFO input :: name: "genome_version", value: "38"
2025-09-15 20:25:04.374 wdl.w:ptcp.w:call-paraphase-70.t:call-run_paraphase INFO input :: name: "config_file", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/paraphase_config.GRCh38.yaml"
2025-09-15 20:25:04.374 wdl.w:ptcp.w:call-paraphase-70.t:call-run_paraphase INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:25:04.374 wdl.w:ptcp.w:call-paraphase-70.t:call-run_paraphase INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:25:04.374 wdl.w:ptcp.w:call-paraphase-70.t:call-run_paraphase INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2167.mapped.bam.bai"
2025-09-15 20:25:04.375 wdl.w:ptcp.w:call-paraphase-70.t:call-run_paraphase INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2167.mapped.bam"
2025-09-15 20:25:04.375 wdl.w:ptcp.w:call-paraphase-70.t:call-run_paraphase INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2167"
2025-09-15 20:25:04.375 wdl.w:ptcp.w:call-paraphase-70.t:call-run_paraphase INFO eval :: name: "threads", value: 4
2025-09-15 20:25:04.375 wdl.w:ptcp.w:call-paraphase-70.t:call-run_paraphase INFO eval :: name: "mem_gb", value: 8
2025-09-15 20:25:04.375 wdl.w:ptcp.w:call-paraphase-70.t:call-run_paraphase INFO eval :: name: "disk_size", value: 27
2025-09-15 20:25:04.376 wdl.w:ptcp.w:call-paraphase-70.t:call-run_paraphase INFO eval :: name: "out_dir", value: "m84036_250809_035451_s4.bc2167_paraphase"
2025-09-15 20:25:04.376 wdl.w:ptcp.w:call-paraphase-70.t:call-run_paraphase INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 4, memory_reservation: 8000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:04.376 wdl.w:ptcp.w:call-paraphase-70.t:call-run_paraphase WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:04.377 wdl.w:ptcp.w:call-paraphase-70.t:call-run_paraphase INFO provisioned :: seconds_waited: 0, cpu: 4, mem_bytes: 8000000000
2025-09-15 20:25:04.377 wdl.w:ptcp.w:call-paraphase-70.t:call-run_paraphase INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:04.389 wdl.w:ptcp.w:call-sawfish-38 NOTICE done
2025-09-15 20:25:04.396 wdl.w:ptcp NOTICE finish :: job: "call-sawfish-38"
2025-09-15 20:25:04.397 wdl.w:ptcp INFO output :: job: "call-sawfish-38", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-38/out/m84036_250809_035451_s4.bc2135_sawfish/m84036_250809_035451_s4.bc2135.sv.vcf.gz", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-38/out/m84036_250809_035451_s4.bc2135.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-38/out/m84036_250809_035451_s4.bc2135_sawfish/m84036_250809_035451_s4.bc2135.sv.vcf.gz.tbi", "minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-38/out/m84036_250809_035451_s4.bc2135.minimap2.bam.bai"}
2025-09-15 20:25:04.399 wdl.w:ptcp.w:call-paraphase-57 NOTICE done
2025-09-15 20:25:04.404 wdl.w:ptcp.w:call-paraphase-81 NOTICE workflow start :: name: "paraphase", source: "./paraphase.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-81"
2025-09-15 20:25:04.409 wdl.w:ptcp.w:call-paraphase-48.t:call-call_f8 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 8, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-48/call-call_f8/_singularity_tmpdir_ang7pmie"
2025-09-15 20:25:04.409 wdl.w:ptcp.w:call-paraphase-48.t:call-call_f8 INFO Slurm invocation: srun --job-name call-call_f8 --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-48/call-call_f8/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-48/call-call_f8/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-48/call-call_f8/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-48/call-call_f8/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-48/call-run_paraphase/out/m84036_250809_035451_s4.bc2145_paraphase/m84036_250809_035451_s4.bc2145.paraphase.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2145.paraphase.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-48/call-run_paraphase/out/m84036_250809_035451_s4.bc2145_paraphase/m84036_250809_035451_s4.bc2145.paraphase.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2145.paraphase.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-48/call-call_f8/_singularity_tmpdir_ang7pmie/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-48/call-call_f8/_singularity_tmpdir_ang7pmie/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:04.418 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_genotype INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2163.trgt.vcf"
2025-09-15 20:25:04.419 wdl.w:ptcp.w:call-paraphase-81 INFO visit :: node: "decl-annotation_vcf", values: {"annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf"}
2025-09-15 20:25:04.420 wdl.w:ptcp.w:call-paraphase-81 INFO visit :: node: "decl-config_file", values: {"config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml"}
2025-09-15 20:25:04.420 wdl.w:ptcp.w:call-paraphase-81 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:25:04.420 wdl.w:ptcp.w:call-paraphase-81 INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:25:04.420 wdl.w:ptcp.w:call-paraphase-81 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-81/out/m84036_250809_035451_s4.bc2178.mapped.bam"}
2025-09-15 20:25:04.420 wdl.w:ptcp.w:call-paraphase-81 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-81/out/m84036_250809_035451_s4.bc2178.mapped.bam.bai"}
2025-09-15 20:25:04.420 wdl.w:ptcp.w:call-paraphase-81 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:25:04.420 wdl.w:ptcp.w:call-paraphase-81 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:25:04.420 wdl.w:ptcp.w:call-paraphase-81 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2178"}
2025-09-15 20:25:04.420 wdl.w:ptcp.w:call-paraphase-81 INFO visit :: node: "decl-sex", values: {"sex": "F"}
2025-09-15 20:25:04.422 wdl.w:ptcp.w:call-paraphase-81 NOTICE ready :: job: "call-run_paraphase", callee: "run_paraphase"
2025-09-15 20:25:04.422 wdl.w:ptcp.w:call-paraphase-81 INFO input :: job: "call-run_paraphase", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf", "genome_version": "38", "config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-81/out/m84036_250809_035451_s4.bc2178.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-81/out/m84036_250809_035451_s4.bc2178.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2178"}
2025-09-15 20:25:04.424 wdl.w:ptcp NOTICE finish :: job: "call-paraphase-57"
2025-09-15 20:25:04.424 wdl.w:ptcp INFO output :: job: "call-paraphase-57", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-57/out/m84036_250809_035451_s4.bc2154.f8inversion.vcf", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-57/out/m84036_250809_035451_s4.bc2154_paraphase/m84036_250809_035451_s4.bc2154.paraphase.json", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-57/out/m84036_250809_035451_s4.bc2154_paraphase/m84036_250809_035451_s4.bc2154.paraphase.bam", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-57/out/m84036_250809_035451_s4.bc2154_paraphase/m84036_250809_035451_s4.bc2154.paraphase.bam.bai", "paraphase_vcfs": [], "havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-57/out/m84036_250809_035451_s4.bc2154.havanno.json", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-57/out/m84036_250809_035451_s4.bc2154.f8inversion.json"}
2025-09-15 20:25:04.425 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_genotype INFO output :: name: "spanning_bam", value: "m84036_250809_035451_s4.bc2163.trgt.sorted.spanning.bam"
2025-09-15 20:25:04.426 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_genotype INFO output :: name: "spanning_bam_bai", value: "m84036_250809_035451_s4.bc2163.trgt.sorted.spanning.bam.bai"
2025-09-15 20:25:04.431 wdl.w:ptcp.w:call-sawfish-81 NOTICE workflow start :: name: "sawfish", source: "./sawfish.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-81"
2025-09-15 20:25:04.436 wdl.w:ptcp.w:call-paraphase-48.t:call-call_f8 NOTICE slurm_singularity run :: pid: 1204523, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-48/call-call_f8/slurm_singularity.log.txt"
2025-09-15 20:25:04.447 wdl.w:ptcp.w:call-sawfish-81 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:25:04.447 wdl.w:ptcp.w:call-sawfish-81 INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:25:04.447 wdl.w:ptcp.w:call-sawfish-81 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-81/out/m84036_250809_035451_s4.bc2178.mapped.bam"}
2025-09-15 20:25:04.447 wdl.w:ptcp.w:call-sawfish-81 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-81/out/m84036_250809_035451_s4.bc2178.mapped.bam.bai"}
2025-09-15 20:25:04.447 wdl.w:ptcp.w:call-sawfish-81 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:25:04.448 wdl.w:ptcp.w:call-sawfish-81 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:25:04.448 wdl.w:ptcp.w:call-sawfish-81 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2178"}
2025-09-15 20:25:04.448 wdl.w:ptcp.w:call-sawfish-81 NOTICE ready :: job: "call-run_sawfish", callee: "run_sawfish"
2025-09-15 20:25:04.448 wdl.w:ptcp.w:call-sawfish-81 INFO input :: job: "call-run_sawfish", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-81/out/m84036_250809_035451_s4.bc2178.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-81/out/m84036_250809_035451_s4.bc2178.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2178"}
2025-09-15 20:25:04.459 wdl.w:ptcp.w:call-paraphase-70.t:call-run_paraphase INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-70/call-run_paraphase/_singularity_tmpdir_2q2_7d4p"
2025-09-15 20:25:04.459 wdl.w:ptcp.w:call-paraphase-70.t:call-run_paraphase INFO Slurm invocation: srun --job-name call-run_paraphase --partition compute,compute9 --cpus-per-task 4 --mem 7629M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-70/call-run_paraphase/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-70/call-run_paraphase/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-70/call-run_paraphase/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-70/call-run_paraphase/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-70/out/m84036_250809_035451_s4.bc2167.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2167.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-70/out/m84036_250809_035451_s4.bc2167.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2167.mapped.bam:ro --bind /ptcp/meta/variant_list/variant_list.GRCh38.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf:ro --bind /ptcp/meta/paraphase/paraphase_config.GRCh38.yaml:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/paraphase_config.GRCh38.yaml:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-70/call-run_paraphase/_singularity_tmpdir_2q2_7d4p/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-70/call-run_paraphase/_singularity_tmpdir_2q2_7d4p/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:04.475 wdl.w:ptcp.w:call-paraphase-70.t:call-run_paraphase NOTICE slurm_singularity run :: pid: 1204531, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-70/call-run_paraphase/slurm_singularity.log.txt"
2025-09-15 20:25:04.502 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO srun: job 51797882 queued and waiting for resources
2025-09-15 20:25:04.502 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO srun: job 51797882 has been allocated resources
2025-09-15 20:25:04.503 wdl.w:ptcp.w:call-paraphase-49.t:call-call_f8 INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2146.f8inversion.vcf"
2025-09-15 20:25:04.503 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:04.508 wdl.w:ptcp.w:call-paraphase-49.t:call-call_f8 INFO output :: name: "json", value: "m84036_250809_035451_s4.bc2146.f8inversion.json"
2025-09-15 20:25:04.509 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_genotype NOTICE done
2025-09-15 20:25:04.517 wdl.w:ptcp.w:call-trgt-66 NOTICE finish :: job: "call-trgt_genotype"
2025-09-15 20:25:04.517 wdl.w:ptcp.w:call-trgt-66 INFO output :: job: "call-trgt_genotype", values: {"spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-66/call-trgt_genotype/out/m84036_250809_035451_s4.bc2163.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-66/call-trgt_genotype/out/m84036_250809_035451_s4.bc2163.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-66/call-trgt_genotype/out/m84036_250809_035451_s4.bc2163.trgt.vcf"}
2025-09-15 20:25:04.518 wdl.w:ptcp.w:call-trgt-66 NOTICE ready :: job: "call-trgt_plot_meth_allele", callee: "trgt_plot"
2025-09-15 20:25:04.518 wdl.w:ptcp.w:call-trgt-66 INFO input :: job: "call-trgt_plot_meth_allele", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": false, "methylation": true, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-66/call-trgt_genotype/out/m84036_250809_035451_s4.bc2163.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-66/call-trgt_genotype/out/m84036_250809_035451_s4.bc2163.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-66/call-trgt_genotype/out/m84036_250809_035451_s4.bc2163.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2163"}
2025-09-15 20:25:04.519 wdl.w:ptcp.w:call-trgt-66 NOTICE ready :: job: "call-trgt_plot_meth_waterfall", callee: "trgt_plot"
2025-09-15 20:25:04.519 wdl.w:ptcp.w:call-trgt-66 INFO input :: job: "call-trgt_plot_meth_waterfall", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": true, "methylation": true, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-66/call-trgt_genotype/out/m84036_250809_035451_s4.bc2163.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-66/call-trgt_genotype/out/m84036_250809_035451_s4.bc2163.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-66/call-trgt_genotype/out/m84036_250809_035451_s4.bc2163.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2163"}
2025-09-15 20:25:04.520 wdl.w:ptcp.w:call-trgt-66 NOTICE ready :: job: "call-trgt_plot_motifs_allele", callee: "trgt_plot"
2025-09-15 20:25:04.520 wdl.w:ptcp.w:call-trgt-66 INFO input :: job: "call-trgt_plot_motifs_allele", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": false, "methylation": false, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-66/call-trgt_genotype/out/m84036_250809_035451_s4.bc2163.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-66/call-trgt_genotype/out/m84036_250809_035451_s4.bc2163.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-66/call-trgt_genotype/out/m84036_250809_035451_s4.bc2163.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2163"}
2025-09-15 20:25:04.521 wdl.w:ptcp.w:call-trgt-66 NOTICE ready :: job: "call-trgt_plot_motifs_waterfall", callee: "trgt_plot"
2025-09-15 20:25:04.521 wdl.w:ptcp.w:call-trgt-66 INFO input :: job: "call-trgt_plot_motifs_waterfall", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": true, "methylation": false, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-66/call-trgt_genotype/out/m84036_250809_035451_s4.bc2163.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-66/call-trgt_genotype/out/m84036_250809_035451_s4.bc2163.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-66/call-trgt_genotype/out/m84036_250809_035451_s4.bc2163.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2163"}
2025-09-15 20:25:04.522 wdl.w:ptcp.w:call-trgt-66 INFO visit :: node: "output-spanning_bam", values: {"spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-66/call-trgt_genotype/out/m84036_250809_035451_s4.bc2163.trgt.sorted.spanning.bam"}
2025-09-15 20:25:04.523 wdl.w:ptcp.w:call-trgt-66 INFO visit :: node: "output-spanning_bam_bai", values: {"spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-66/call-trgt_genotype/out/m84036_250809_035451_s4.bc2163.trgt.sorted.spanning.bam.bai"}
2025-09-15 20:25:04.523 wdl.w:ptcp.w:call-trgt-66 INFO visit :: node: "output-vcf", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-66/call-trgt_genotype/out/m84036_250809_035451_s4.bc2163.trgt.vcf"}
2025-09-15 20:25:04.527 wdl.w:ptcp.w:call-sawfish-70.t:call-run_sawfish NOTICE task setup :: name: "run_sawfish", source: "./sawfish.wdl", line: 83, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-70/call-run_sawfish", thread: 140611457906240
2025-09-15 20:25:04.545 wdl.w:ptcp.w:call-sawfish-70.t:call-run_sawfish INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:04.545 wdl.w:ptcp.w:call-sawfish-70.t:call-run_sawfish INFO input :: name: "genome_version", value: "38"
2025-09-15 20:25:04.545 wdl.w:ptcp.w:call-sawfish-70.t:call-run_sawfish INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:25:04.545 wdl.w:ptcp.w:call-sawfish-70.t:call-run_sawfish INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:25:04.545 wdl.w:ptcp.w:call-sawfish-70.t:call-run_sawfish INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2167.mapped.bam.bai"
2025-09-15 20:25:04.545 wdl.w:ptcp.w:call-sawfish-70.t:call-run_sawfish INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2167.mapped.bam"
2025-09-15 20:25:04.546 wdl.w:ptcp.w:call-sawfish-70.t:call-run_sawfish INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2167"
2025-09-15 20:25:04.546 wdl.w:ptcp.w:call-sawfish-70.t:call-run_sawfish INFO eval :: name: "mem_gb", value: 32
2025-09-15 20:25:04.546 wdl.w:ptcp.w:call-sawfish-70.t:call-run_sawfish INFO eval :: name: "threads", value: 16
2025-09-15 20:25:04.546 wdl.w:ptcp.w:call-sawfish-70.t:call-run_sawfish INFO eval :: name: "disk_size", value: 30
2025-09-15 20:25:04.546 wdl.w:ptcp.w:call-sawfish-70.t:call-run_sawfish INFO eval :: name: "discover_dirname", value: "m84036_250809_035451_s4.bc2167_sawfish_discover"
2025-09-15 20:25:04.547 wdl.w:ptcp.w:call-sawfish-70.t:call-run_sawfish INFO eval :: name: "call_dirname", value: "m84036_250809_035451_s4.bc2167_sawfish"
2025-09-15 20:25:04.547 wdl.w:ptcp.w:call-sawfish-70.t:call-run_sawfish INFO eval :: name: "minimap2_bam_filename", value: "m84036_250809_035451_s4.bc2167.minimap2.bam"
2025-09-15 20:25:04.547 wdl.w:ptcp.w:call-sawfish-70.t:call-run_sawfish INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 16, memory_reservation: 32000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:04.547 wdl.w:ptcp.w:call-sawfish-70.t:call-run_sawfish WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:04.548 wdl.w:ptcp.w:call-sawfish-70.t:call-run_sawfish INFO provisioned :: seconds_waited: 0, cpu: 16, mem_bytes: 32000000000
2025-09-15 20:25:04.548 wdl.w:ptcp.w:call-sawfish-70.t:call-run_sawfish INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:04.560 wdl.w:ptcp.w:call-trgt-56.t:call-trgt_plot_motifs_allele INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2153.motifs_allele.trgt_plots.zip"
2025-09-15 20:25:04.588 wdl.w:ptcp.w:call-paraphase-49.t:call-call_f8 NOTICE done
2025-09-15 20:25:04.595 wdl.w:ptcp.w:call-paraphase-49 NOTICE finish :: job: "call-call_f8"
2025-09-15 20:25:04.595 wdl.w:ptcp.w:call-paraphase-49 INFO output :: job: "call-call_f8", values: {"json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-49/call-call_f8/out/m84036_250809_035451_s4.bc2146.f8inversion.json", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-49/call-call_f8/out/m84036_250809_035451_s4.bc2146.f8inversion.vcf"}
2025-09-15 20:25:04.595 wdl.w:ptcp.w:call-paraphase-49 INFO visit :: node: "output-f8_json", values: {"f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-49/call-call_f8/out/m84036_250809_035451_s4.bc2146.f8inversion.json"}
2025-09-15 20:25:04.596 wdl.w:ptcp.w:call-paraphase-49 INFO visit :: node: "output-f8_vcf", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-49/call-call_f8/out/m84036_250809_035451_s4.bc2146.f8inversion.vcf"}
2025-09-15 20:25:04.596 wdl.w:ptcp.w:call-paraphase-49 INFO visit :: node: "outputs", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-49/call-call_f8/out/m84036_250809_035451_s4.bc2146.f8inversion.vcf", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-49/call-run_paraphase/out/m84036_250809_035451_s4.bc2146_paraphase/m84036_250809_035451_s4.bc2146.paraphase.json", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-49/call-run_paraphase/out/m84036_250809_035451_s4.bc2146_paraphase/m84036_250809_035451_s4.bc2146.paraphase.bam", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-49/call-run_paraphase/out/m84036_250809_035451_s4.bc2146_paraphase/m84036_250809_035451_s4.bc2146.paraphase.bam.bai", "paraphase_vcfs": [], "havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-49/call-run_paraphase/out/m84036_250809_035451_s4.bc2146.havanno.json", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-49/call-call_f8/out/m84036_250809_035451_s4.bc2146.f8inversion.json"}
2025-09-15 20:25:04.602 wdl.w:ptcp.t:call-tar_outputs-00 NOTICE task setup :: name: "tar_outputs", source: "./common.wdl", line: 279, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-00", thread: 140607674631744
2025-09-15 20:25:04.620 wdl.w:ptcp.w:call-sawfish-70.t:call-run_sawfish INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 10, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-70/call-run_sawfish/_singularity_tmpdir_hcd_kfy1"
2025-09-15 20:25:04.620 wdl.w:ptcp.w:call-sawfish-70.t:call-run_sawfish INFO Slurm invocation: srun --job-name call-run_sawfish --partition compute,compute9 --cpus-per-task 16 --mem 30518M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-70/call-run_sawfish/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-70/call-run_sawfish/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-70/call-run_sawfish/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-70/call-run_sawfish/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-70/out/m84036_250809_035451_s4.bc2167.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2167.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-70/out/m84036_250809_035451_s4.bc2167.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2167.mapped.bam:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-70/call-run_sawfish/_singularity_tmpdir_hcd_kfy1/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-70/call-run_sawfish/_singularity_tmpdir_hcd_kfy1/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:04.627 wdl.w:ptcp.t:call-tar_outputs-00 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:04.627 wdl.w:ptcp.t:call-tar_outputs-00 INFO input :: name: "sawfish_vcf_tbi", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2097.sv.vcf.gz.tbi"
2025-09-15 20:25:04.627 wdl.w:ptcp.t:call-tar_outputs-00 INFO input :: name: "sawfish_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2097.sv.vcf.gz"
2025-09-15 20:25:04.627 wdl.w:ptcp.t:call-tar_outputs-00 INFO input :: name: "f8_json", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2097.f8inversion.json"
2025-09-15 20:25:04.627 wdl.w:ptcp.t:call-tar_outputs-00 INFO input :: name: "paraphase_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2097.paraphase.bam.bai"
2025-09-15 20:25:04.627 wdl.w:ptcp.t:call-tar_outputs-00 INFO input :: name: "paraphase_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2097.paraphase.bam"
2025-09-15 20:25:04.627 wdl.w:ptcp.t:call-tar_outputs-00 INFO input :: name: "paraphase_json", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2097.paraphase.json"
2025-09-15 20:25:04.627 wdl.w:ptcp.t:call-tar_outputs-00 INFO input :: name: "trgt_spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2097.trgt.sorted.spanning.bam.bai"
2025-09-15 20:25:04.628 wdl.w:ptcp.t:call-tar_outputs-00 INFO input :: name: "trgt_spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2097.trgt.sorted.spanning.bam"
2025-09-15 20:25:04.628 wdl.w:ptcp.t:call-tar_outputs-00 INFO input :: name: "trgt_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2097.trgt.vcf"
2025-09-15 20:25:04.628 wdl.w:ptcp.t:call-tar_outputs-00 INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2097.mapped.bam.bai"
2025-09-15 20:25:04.628 wdl.w:ptcp.t:call-tar_outputs-00 INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2097.mapped.bam"
2025-09-15 20:25:04.628 wdl.w:ptcp.t:call-tar_outputs-00 INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2097"
2025-09-15 20:25:04.628 wdl.w:ptcp.t:call-tar_outputs-00 INFO eval :: name: "threads", value: 1
2025-09-15 20:25:04.628 wdl.w:ptcp.t:call-tar_outputs-00 INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:25:04.629 wdl.w:ptcp.t:call-tar_outputs-00 INFO eval :: name: "disk_size", value: 6
2025-09-15 20:25:04.629 wdl.w:ptcp.t:call-tar_outputs-00 INFO eval :: name: "output_tarball", value: "m84036_250809_035451_s4.bc2097.tar"
2025-09-15 20:25:04.630 wdl.w:ptcp.t:call-tar_outputs-00 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:04.630 wdl.w:ptcp.t:call-tar_outputs-00 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:04.630 wdl.w:ptcp.t:call-tar_outputs-00 INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:25:04.630 wdl.w:ptcp.t:call-tar_outputs-00 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:04.642 wdl.w:ptcp.w:call-sawfish-70.t:call-run_sawfish NOTICE slurm_singularity run :: pid: 1204534, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-70/call-run_sawfish/slurm_singularity.log.txt"
2025-09-15 20:25:04.674 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:25:04 [ERROR] - No reads found for TRID=SCA37_DAB1
2025-09-15 20:25:04.674 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:25:04 [ERROR] - No reads found for TRID=OPDM_ABCD3
2025-09-15 20:25:04.674 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:25:04 [ERROR] - No reads found for TRID=NIID_NOTCH2NLC
2025-09-15 20:25:04.675 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:25:04 [ERROR] - No reads found for TRID=SCA2_ATXN2
2025-09-15 20:25:04.686 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_plot_motifs_allele.slurm_singularity INFO srun: job 51797883 queued and waiting for resources
2025-09-15 20:25:04.687 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_plot_motifs_allele.slurm_singularity INFO srun: job 51797883 has been allocated resources
2025-09-15 20:25:04.687 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_plot_motifs_allele.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:04.688 wdl.w:ptcp.w:call-paraphase-49 NOTICE done
2025-09-15 20:25:04.693 wdl.w:ptcp NOTICE finish :: job: "call-paraphase-49"
2025-09-15 20:25:04.694 wdl.w:ptcp INFO output :: job: "call-paraphase-49", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-49/out/m84036_250809_035451_s4.bc2146.f8inversion.vcf", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-49/out/m84036_250809_035451_s4.bc2146_paraphase/m84036_250809_035451_s4.bc2146.paraphase.json", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-49/out/m84036_250809_035451_s4.bc2146_paraphase/m84036_250809_035451_s4.bc2146.paraphase.bam", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-49/out/m84036_250809_035451_s4.bc2146_paraphase/m84036_250809_035451_s4.bc2146.paraphase.bam.bai", "paraphase_vcfs": [], "havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-49/out/m84036_250809_035451_s4.bc2146.havanno.json", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-49/out/m84036_250809_035451_s4.bc2146.f8inversion.json"}
2025-09-15 20:25:04.701 wdl.w:ptcp.w:call-trgt-81 NOTICE workflow start :: name: "trgt", source: "./trgt.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-81"
2025-09-15 20:25:04.710 wdl.w:ptcp.w:call-trgt-56.t:call-trgt_plot_motifs_allele NOTICE done
2025-09-15 20:25:04.716 wdl.w:ptcp.w:call-trgt-56 NOTICE finish :: job: "call-trgt_plot_motifs_allele"
2025-09-15 20:25:04.716 wdl.w:ptcp.w:call-trgt-56 INFO output :: job: "call-trgt_plot_motifs_allele", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-56/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2153.motifs_allele.trgt_plots.zip"}
2025-09-15 20:25:04.717 wdl.w:ptcp.w:call-trgt-56 INFO visit :: node: "output-images_motifs_allele", values: {"images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-56/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2153.motifs_allele.trgt_plots.zip"}
2025-09-15 20:25:04.723 wdl.w:ptcp.w:call-trgt-81 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:25:04.724 wdl.w:ptcp.w:call-trgt-81 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-81/out/m84036_250809_035451_s4.bc2178.mapped.bam"}
2025-09-15 20:25:04.724 wdl.w:ptcp.w:call-trgt-81 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-81/out/m84036_250809_035451_s4.bc2178.mapped.bam.bai"}
2025-09-15 20:25:04.724 wdl.w:ptcp.w:call-trgt-81 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:25:04.724 wdl.w:ptcp.w:call-trgt-81 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:25:04.724 wdl.w:ptcp.w:call-trgt-81 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2178"}
2025-09-15 20:25:04.724 wdl.w:ptcp.w:call-trgt-70.t:call-get_reads_overlapping_repeats NOTICE task setup :: name: "get_reads_overlapping_repeats", source: "./trgt.wdl", line: 182, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-70/call-get_reads_overlapping_repeats", thread: 140607691417152
2025-09-15 20:25:04.724 wdl.w:ptcp.w:call-trgt-81 INFO visit :: node: "decl-sex", values: {"sex": "F"}
2025-09-15 20:25:04.724 wdl.w:ptcp.w:call-trgt-81 INFO visit :: node: "decl-trgt_bed", values: {"trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"}
2025-09-15 20:25:04.725 wdl.w:ptcp.w:call-trgt-81 NOTICE ready :: job: "call-get_reads_overlapping_repeats", callee: "get_reads_overlapping_repeats"
2025-09-15 20:25:04.725 wdl.w:ptcp.w:call-trgt-81 INFO input :: job: "call-get_reads_overlapping_repeats", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-81/out/m84036_250809_035451_s4.bc2178.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-81/out/m84036_250809_035451_s4.bc2178.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2178"}
2025-09-15 20:25:04.726 wdl.w:ptcp.w:call-trgt-81 NOTICE ready :: job: "call-trgt_genotype", callee: "trgt_genotype"
2025-09-15 20:25:04.726 wdl.w:ptcp.w:call-trgt-81 INFO input :: job: "call-trgt_genotype", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-81/out/m84036_250809_035451_s4.bc2178.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-81/out/m84036_250809_035451_s4.bc2178.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2178"}
2025-09-15 20:25:04.744 wdl.w:ptcp.w:call-trgt-70.t:call-get_reads_overlapping_repeats INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:04.744 wdl.w:ptcp.w:call-trgt-70.t:call-get_reads_overlapping_repeats INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:25:04.744 wdl.w:ptcp.w:call-trgt-70.t:call-get_reads_overlapping_repeats INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2167.mapped.bam.bai"
2025-09-15 20:25:04.744 wdl.w:ptcp.w:call-trgt-70.t:call-get_reads_overlapping_repeats INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2167.mapped.bam"
2025-09-15 20:25:04.745 wdl.w:ptcp.w:call-trgt-70.t:call-get_reads_overlapping_repeats INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2167"
2025-09-15 20:25:04.745 wdl.w:ptcp.w:call-trgt-70.t:call-get_reads_overlapping_repeats INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:25:04.745 wdl.w:ptcp.w:call-trgt-70.t:call-get_reads_overlapping_repeats INFO eval :: name: "expand_size", value: 3000
2025-09-15 20:25:04.745 wdl.w:ptcp.w:call-trgt-70.t:call-get_reads_overlapping_repeats INFO eval :: name: "threads", value: 1
2025-09-15 20:25:04.745 wdl.w:ptcp.w:call-trgt-70.t:call-get_reads_overlapping_repeats INFO eval :: name: "expanded_bed_name", value: "m84036_250809_035451_s4.bc2167.expanded.bed"
2025-09-15 20:25:04.745 wdl.w:ptcp.w:call-trgt-70.t:call-get_reads_overlapping_repeats INFO eval :: name: "disk_size", value: 11
2025-09-15 20:25:04.745 wdl.w:ptcp.w:call-trgt-70.t:call-get_reads_overlapping_repeats INFO eval :: name: "output_name", value: "m84036_250809_035451_s4.bc2167.repeats.bam"
2025-09-15 20:25:04.746 wdl.w:ptcp.w:call-trgt-70.t:call-get_reads_overlapping_repeats INFO eval :: name: "index_name", value: "m84036_250809_035451_s4.bc2167.repeats.bam.bai"
2025-09-15 20:25:04.746 wdl.w:ptcp.w:call-trgt-70.t:call-get_reads_overlapping_repeats INFO eval :: name: "output_name_with_index", value: "m84036_250809_035451_s4.bc2167.repeats.bam##idx##m84036_250809_035451_s4.bc2167.repeats.bam.bai"
2025-09-15 20:25:04.746 wdl.w:ptcp.w:call-trgt-70.t:call-get_reads_overlapping_repeats INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:04.746 wdl.w:ptcp.w:call-trgt-70.t:call-get_reads_overlapping_repeats WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:04.746 wdl.w:ptcp.w:call-trgt-70.t:call-get_reads_overlapping_repeats INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:25:04.747 wdl.w:ptcp.w:call-trgt-70.t:call-get_reads_overlapping_repeats INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:04.755 wdl.w:ptcp.t:call-tar_outputs-00 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 17, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-00/_singularity_tmpdir_5va6ytq5"
2025-09-15 20:25:04.755 wdl.w:ptcp.t:call-tar_outputs-00 INFO Slurm invocation: srun --job-name call-tar_outputs-00 --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-00/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-00/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-00/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-00/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-00/out/m84036_250809_035451_s4.bc2097_paraphase/m84036_250809_035451_s4.bc2097.paraphase.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2097.paraphase.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-00/out/m84036_250809_035451_s4.bc2097_paraphase/m84036_250809_035451_s4.bc2097.paraphase.json:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2097.paraphase.json:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-00/out/m84036_250809_035451_s4.bc2097_paraphase/m84036_250809_035451_s4.bc2097.paraphase.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2097.paraphase.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-00/out/m84036_250809_035451_s4.bc2097_sawfish/m84036_250809_035451_s4.bc2097.sv.vcf.gz:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2097.sv.vcf.gz:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-00/out/m84036_250809_035451_s4.bc2097_sawfish/m84036_250809_035451_s4.bc2097.sv.vcf.gz.tbi:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2097.sv.vcf.gz.tbi:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-00/out/m84036_250809_035451_s4.bc2097.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2097.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-00/out/m84036_250809_035451_s4.bc2097.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2097.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-00/out/m84036_250809_035451_s4.bc2097.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2097.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-00/out/m84036_250809_035451_s4.bc2097.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2097.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-00/out/m84036_250809_035451_s4.bc2097.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2097.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-00/out/m84036_250809_035451_s4.bc2097.f8inversion.json:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2097.f8inversion.json:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-00/_singularity_tmpdir_5va6ytq5/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-00/_singularity_tmpdir_5va6ytq5/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:04.769 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:25:04 [ERROR] - No reads found for TRID=SCA37_DAB1
2025-09-15 20:25:04.770 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:25:04 [ERROR] - No reads found for TRID=OPDM_ABCD3
2025-09-15 20:25:04.770 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:25:04 [ERROR] - No reads found for TRID=NIID_NOTCH2NLC
2025-09-15 20:25:04.775 wdl.w:ptcp.t:call-tar_outputs-00 NOTICE slurm_singularity run :: pid: 1204536, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-00/slurm_singularity.log.txt"
2025-09-15 20:25:04.780 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO srun: job 51797884 queued and waiting for resources
2025-09-15 20:25:04.780 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO srun: job 51797884 has been allocated resources
2025-09-15 20:25:04.780 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:04.782 wdl.w:ptcp.w:call-trgt-58.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:04 [ERROR] - No reads found for TRID=SCA37_DAB1
2025-09-15 20:25:04.782 wdl.w:ptcp.w:call-trgt-58.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:04 [ERROR] - No reads found for TRID=OPDM_ABCD3
2025-09-15 20:25:04.782 wdl.w:ptcp.w:call-trgt-58.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:04 [ERROR] - No reads found for TRID=NIID_NOTCH2NLC
2025-09-15 20:25:04.782 wdl.w:ptcp.w:call-trgt-58.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:04 [ERROR] - No reads found for TRID=DRPLA_ATN1
2025-09-15 20:25:04.782 wdl.w:ptcp.w:call-trgt-58.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:04 [ERROR] - No reads found for TRID=SCA2_ATXN2
2025-09-15 20:25:04.782 wdl.w:ptcp.w:call-trgt-58.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:04 [ERROR] - No reads found for TRID=OPDM4_RILPL1
2025-09-15 20:25:04.782 wdl.w:ptcp.w:call-trgt-58.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:04 [ERROR] - No reads found for TRID=SCA27B_FGF14
2025-09-15 20:25:04.782 wdl.w:ptcp.w:call-trgt-58.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:04 [ERROR] - No reads found for TRID=SCA3_ATXN3
2025-09-15 20:25:04.782 wdl.w:ptcp.w:call-trgt-58.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:04 [ERROR] - No reads found for TRID=SCA31_BEAN1
2025-09-15 20:25:04.791 wdl.w:ptcp.w:call-trgt-58.t:call-trgt_plot_meth_allele.slurm_singularity INFO srun: job 51797885 queued and waiting for resources
2025-09-15 20:25:04.791 wdl.w:ptcp.w:call-trgt-58.t:call-trgt_plot_meth_allele.slurm_singularity INFO srun: job 51797885 has been allocated resources
2025-09-15 20:25:04.791 wdl.w:ptcp.w:call-trgt-58.t:call-trgt_plot_meth_allele.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:04.802 wdl.w:ptcp.w:call-trgt-70.t:call-get_reads_overlapping_repeats INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 9, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-70/call-get_reads_overlapping_repeats/_singularity_tmpdir_dw4rpeci"
2025-09-15 20:25:04.803 wdl.w:ptcp.w:call-trgt-70.t:call-get_reads_overlapping_repeats INFO Slurm invocation: srun --job-name call-get_reads_overlapping_repeats --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-70/call-get_reads_overlapping_repeats/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-70/call-get_reads_overlapping_repeats/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-70/call-get_reads_overlapping_repeats/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-70/call-get_reads_overlapping_repeats/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-70/out/m84036_250809_035451_s4.bc2167.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2167.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-70/out/m84036_250809_035451_s4.bc2167.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2167.mapped.bam:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-70/call-get_reads_overlapping_repeats/_singularity_tmpdir_dw4rpeci/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-70/call-get_reads_overlapping_repeats/_singularity_tmpdir_dw4rpeci/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:04.813 wdl.w:ptcp.w:call-trgt-70.t:call-get_reads_overlapping_repeats NOTICE slurm_singularity run :: pid: 1204538, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-70/call-get_reads_overlapping_repeats/slurm_singularity.log.txt"
2025-09-15 20:25:04.990 wdl.w:ptcp.w:call-trgt-56.t:call-trgt_plot_meth_allele INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2153.meth_allele.trgt_plots.zip"
2025-09-15 20:25:05.077 wdl.w:ptcp.w:call-trgt-58.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:25:04 [ERROR] - No reads found for TRID=SCA37_DAB1
2025-09-15 20:25:05.078 wdl.w:ptcp.w:call-trgt-58.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:25:04 [ERROR] - No reads found for TRID=OPDM_ABCD3
2025-09-15 20:25:05.078 wdl.w:ptcp.w:call-trgt-58.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:25:04 [ERROR] - No reads found for TRID=NIID_NOTCH2NLC
2025-09-15 20:25:05.078 wdl.w:ptcp.w:call-trgt-58.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:25:04 [ERROR] - No reads found for TRID=DRPLA_ATN1
2025-09-15 20:25:05.078 wdl.w:ptcp.w:call-trgt-58.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:25:04 [ERROR] - No reads found for TRID=SCA2_ATXN2
2025-09-15 20:25:05.078 wdl.w:ptcp.w:call-trgt-58.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:25:04 [ERROR] - No reads found for TRID=OPDM4_RILPL1
2025-09-15 20:25:05.078 wdl.w:ptcp.w:call-trgt-58.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:25:04 [ERROR] - No reads found for TRID=SCA27B_FGF14
2025-09-15 20:25:05.078 wdl.w:ptcp.w:call-trgt-58.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:25:04 [ERROR] - No reads found for TRID=SCA3_ATXN3
2025-09-15 20:25:05.078 wdl.w:ptcp.w:call-trgt-58.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:25:05 [ERROR] - No reads found for TRID=SCA31_BEAN1
2025-09-15 20:25:05.087 wdl.w:ptcp.w:call-trgt-58.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO srun: job 51797886 queued and waiting for resources
2025-09-15 20:25:05.087 wdl.w:ptcp.w:call-trgt-58.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO srun: job 51797886 has been allocated resources
2025-09-15 20:25:05.087 wdl.w:ptcp.w:call-trgt-58.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:05.099 wdl.w:ptcp.w:call-trgt-56.t:call-trgt_plot_meth_allele NOTICE done
2025-09-15 20:25:05.103 wdl.w:ptcp.w:call-trgt-56 NOTICE finish :: job: "call-trgt_plot_meth_allele"
2025-09-15 20:25:05.103 wdl.w:ptcp.w:call-trgt-56 INFO output :: job: "call-trgt_plot_meth_allele", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-56/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2153.meth_allele.trgt_plots.zip"}
2025-09-15 20:25:05.104 wdl.w:ptcp.w:call-trgt-56 INFO visit :: node: "output-images_meth_allele", values: {"images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-56/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2153.meth_allele.trgt_plots.zip"}
2025-09-15 20:25:05.106 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:25:02 [ERROR] - No reads found for TRID=SD5_HOXD13
2025-09-15 20:25:05.106 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:25:02 [ERROR] - No reads found for TRID=SCA36_NOP56
2025-09-15 20:25:05.106 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:25:02 [ERROR] - No reads found for TRID=CJD_PRNP
2025-09-15 20:25:05.106 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:25:02 [ERROR] - No reads found for TRID=EPM1_CSTB
2025-09-15 20:25:05.106 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:25:02 [ERROR] - No reads found for TRID=SCA10_ATXN10
2025-09-15 20:25:05.106 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:25:03 [ERROR] - No reads found for TRID=SCA7_ATXN7
2025-09-15 20:25:05.106 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:25:03 [ERROR] - No reads found for TRID=CCHS_PHOX2B
2025-09-15 20:25:05.107 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:25:03 [ERROR] - No reads found for TRID=SCA1_ATXN1
2025-09-15 20:25:05.107 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:25:03 [ERROR] - No reads found for TRID=SCA12_PPP2R2B
2025-09-15 20:25:05.107 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:25:03 [ERROR] - No reads found for TRID=SCA17_TBP
2025-09-15 20:25:05.107 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:25:03 [ERROR] - No reads found for TRID=OPDM1_LRP12
2025-09-15 20:25:05.107 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:25:03 [ERROR] - No reads found for TRID=FTDALS1_C9orf72
2025-09-15 20:25:05.107 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:25:04 [ERROR] - No reads found for TRID=FAME1_SAMD12
2025-09-15 20:25:05.107 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:25:04 [ERROR] - No reads found for TRID=SBMA_AR
2025-09-15 20:25:05.109 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_genotype NOTICE task setup :: name: "trgt_genotype", source: "./trgt.wdl", line: 272, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-70/call-trgt_genotype", thread: 140610912642624
2025-09-15 20:25:05.127 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_genotype INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:05.127 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_genotype INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:25:05.127 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:25:02 [ERROR] - No reads found for TRID=SD5_HOXD13
2025-09-15 20:25:05.128 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_genotype INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:25:05.128 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:25:02 [ERROR] - No reads found for TRID=SCA36_NOP56
2025-09-15 20:25:05.128 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_genotype INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:25:05.128 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:25:02 [ERROR] - No reads found for TRID=CJD_PRNP
2025-09-15 20:25:05.128 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_genotype INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2167.mapped.bam.bai"
2025-09-15 20:25:05.128 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:25:02 [ERROR] - No reads found for TRID=EPM1_CSTB
2025-09-15 20:25:05.128 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_genotype INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2167.mapped.bam"
2025-09-15 20:25:05.128 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:25:02 [ERROR] - No reads found for TRID=SCA10_ATXN10
2025-09-15 20:25:05.128 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_genotype INFO input :: name: "sex", value: "F"
2025-09-15 20:25:05.129 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:25:03 [ERROR] - No reads found for TRID=SCA7_ATXN7
2025-09-15 20:25:05.129 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_genotype INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2167"
2025-09-15 20:25:05.129 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:25:03 [ERROR] - No reads found for TRID=CCHS_PHOX2B
2025-09-15 20:25:05.129 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_genotype INFO eval :: name: "mem_gb", value: 16
2025-09-15 20:25:05.129 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:25:03 [ERROR] - No reads found for TRID=SCA1_ATXN1
2025-09-15 20:25:05.129 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_genotype INFO eval :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2167.trgt"
2025-09-15 20:25:05.129 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:25:03 [ERROR] - No reads found for TRID=SCA12_PPP2R2B
2025-09-15 20:25:05.130 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_genotype INFO eval :: name: "threads", value: 8
2025-09-15 20:25:05.130 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:25:03 [ERROR] - No reads found for TRID=SCA17_TBP
2025-09-15 20:25:05.130 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:25:03 [ERROR] - No reads found for TRID=OPDM1_LRP12
2025-09-15 20:25:05.130 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_genotype INFO eval :: name: "disk_size", value: 27
2025-09-15 20:25:05.130 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:25:03 [ERROR] - No reads found for TRID=FTDALS1_C9orf72
2025-09-15 20:25:05.130 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:25:04 [ERROR] - No reads found for TRID=FAME1_SAMD12
2025-09-15 20:25:05.130 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_genotype INFO eval :: name: "karyotype", value: "XX"
2025-09-15 20:25:05.131 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:25:04 [ERROR] - No reads found for TRID=SBMA_AR
2025-09-15 20:25:05.131 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_genotype INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 8, memory_reservation: 16000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:05.131 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_genotype WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:05.132 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_genotype INFO provisioned :: seconds_waited: 0, cpu: 8, mem_bytes: 16000000000
2025-09-15 20:25:05.132 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_genotype INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:05.160 wdl.w:ptcp.w:call-paraphase-63.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for smn1 for sample m84036_250809_035451_s4.bc2160 at 2025-09-15 20:25:02.935281...
2025-09-15 20:25:05.160 wdl.w:ptcp.w:call-paraphase-63.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning to gene2 region for smn1 for sample m84036_250809_035451_s4.bc2160 at 2025-09-15 20:25:03.678199...
2025-09-15 20:25:05.205 wdl.w:ptcp.w:call-sawfish-10.t:call-run_sawfish.stderr VERBOSE [M::worker_pipeline::90.901*1.69] mapped 486 sequences
2025-09-15 20:25:05.205 wdl.w:ptcp.w:call-sawfish-10.t:call-run_sawfish.stderr VERBOSE [M::main] Version: 2.26-r1175
2025-09-15 20:25:05.205 wdl.w:ptcp.w:call-sawfish-10.t:call-run_sawfish.stderr VERBOSE [M::main] CMD: /opt/pacbio/smrttools/install/smrtlink-release_25.1.0.257715/bundles/smrttools/install/smrttools-release_25.1.0.257715/private/thirdparty/minimap2/minimap2_2.26-pacbio2/binwrap/../../../../../private/thirdparty/minimap2/minimap2_2.26-pacbio2/bin/minimap2 -a -y -x map-hifi -Y -E 1,0 /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa -
2025-09-15 20:25:05.205 wdl.w:ptcp.w:call-sawfish-10.t:call-run_sawfish.stderr VERBOSE [M::main] Real time: 91.326 sec; CPU: 153.791 sec; Peak RSS: 11.886 GB
2025-09-15 20:25:05.209 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_genotype INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 11, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-70/call-trgt_genotype/_singularity_tmpdir__viync09"
2025-09-15 20:25:05.209 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_genotype INFO Slurm invocation: srun --job-name call-trgt_genotype --partition compute,compute9 --cpus-per-task 8 --mem 15259M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-70/call-trgt_genotype/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-70/call-trgt_genotype/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-70/call-trgt_genotype/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-70/call-trgt_genotype/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-70/out/m84036_250809_035451_s4.bc2167.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2167.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-70/out/m84036_250809_035451_s4.bc2167.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2167.mapped.bam:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-70/call-trgt_genotype/_singularity_tmpdir__viync09/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-70/call-trgt_genotype/_singularity_tmpdir__viync09/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:05.238 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_genotype NOTICE slurm_singularity run :: pid: 1204561, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-70/call-trgt_genotype/slurm_singularity.log.txt"
2025-09-15 20:25:05.298 wdl.w:ptcp.w:call-trgt-58.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:25:04 [ERROR] - No reads found for TRID=SCA37_DAB1
2025-09-15 20:25:05.298 wdl.w:ptcp.w:call-trgt-58.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:25:05 [ERROR] - No reads found for TRID=OPDM_ABCD3
2025-09-15 20:25:05.298 wdl.w:ptcp.w:call-trgt-58.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:25:05 [ERROR] - No reads found for TRID=NIID_NOTCH2NLC
2025-09-15 20:25:05.298 wdl.w:ptcp.w:call-trgt-58.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:25:05 [ERROR] - No reads found for TRID=DRPLA_ATN1
2025-09-15 20:25:05.298 wdl.w:ptcp.w:call-trgt-58.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:25:05 [ERROR] - No reads found for TRID=SCA2_ATXN2
2025-09-15 20:25:05.302 wdl.w:ptcp.w:call-trgt-58.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:25:04 [ERROR] - No reads found for TRID=SCA37_DAB1
2025-09-15 20:25:05.302 wdl.w:ptcp.w:call-trgt-58.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:25:04 [ERROR] - No reads found for TRID=OPDM_ABCD3
2025-09-15 20:25:05.302 wdl.w:ptcp.w:call-trgt-58.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:25:04 [ERROR] - No reads found for TRID=NIID_NOTCH2NLC
2025-09-15 20:25:05.302 wdl.w:ptcp.w:call-trgt-58.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:25:04 [ERROR] - No reads found for TRID=DRPLA_ATN1
2025-09-15 20:25:05.302 wdl.w:ptcp.w:call-trgt-58.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:25:04 [ERROR] - No reads found for TRID=SCA2_ATXN2
2025-09-15 20:25:05.302 wdl.w:ptcp.w:call-trgt-58.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:25:05 [ERROR] - No reads found for TRID=OPDM4_RILPL1
2025-09-15 20:25:05.302 wdl.w:ptcp.w:call-trgt-58.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:25:05 [ERROR] - No reads found for TRID=SCA27B_FGF14
2025-09-15 20:25:05.302 wdl.w:ptcp.w:call-trgt-58.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:25:05 [ERROR] - No reads found for TRID=SCA3_ATXN3
2025-09-15 20:25:05.302 wdl.w:ptcp.w:call-trgt-58.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:25:05 [ERROR] - No reads found for TRID=SCA31_BEAN1
2025-09-15 20:25:05.302 wdl.w:ptcp.w:call-trgt-58.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:25:05 [ERROR] - No reads found for TRID=SCA4_ZFHX3
2025-09-15 20:25:05.307 wdl.w:ptcp.w:call-trgt-58.t:call-trgt_plot_motifs_allele.slurm_singularity INFO srun: job 51797887 queued and waiting for resources
2025-09-15 20:25:05.307 wdl.w:ptcp.w:call-trgt-58.t:call-trgt_plot_motifs_allele.slurm_singularity INFO srun: job 51797887 has been allocated resources
2025-09-15 20:25:05.307 wdl.w:ptcp.w:call-trgt-58.t:call-trgt_plot_motifs_allele.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:05.311 wdl.w:ptcp.w:call-trgt-58.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO srun: job 51797888 queued and waiting for resources
2025-09-15 20:25:05.311 wdl.w:ptcp.w:call-trgt-58.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO srun: job 51797888 has been allocated resources
2025-09-15 20:25:05.311 wdl.w:ptcp.w:call-trgt-58.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:05.334 wdl.w:ptcp.w:call-sawfish-19.t:call-run_sawfish.stderr VERBOSE [M::worker_pipeline::90.328*1.69] mapped 252 sequences
2025-09-15 20:25:05.334 wdl.w:ptcp.w:call-sawfish-19.t:call-run_sawfish.stderr VERBOSE [M::main] Version: 2.26-r1175
2025-09-15 20:25:05.334 wdl.w:ptcp.w:call-sawfish-19.t:call-run_sawfish.stderr VERBOSE [M::main] CMD: /opt/pacbio/smrttools/install/smrtlink-release_25.1.0.257715/bundles/smrttools/install/smrttools-release_25.1.0.257715/private/thirdparty/minimap2/minimap2_2.26-pacbio2/binwrap/../../../../../private/thirdparty/minimap2/minimap2_2.26-pacbio2/bin/minimap2 -a -y -x map-hifi -Y -E 1,0 /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa -
2025-09-15 20:25:05.334 wdl.w:ptcp.w:call-sawfish-19.t:call-run_sawfish.stderr VERBOSE [M::main] Real time: 90.762 sec; CPU: 152.723 sec; Peak RSS: 11.886 GB
2025-09-15 20:25:05.376 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:04 [ERROR] - No reads found for TRID=OPMD_PABPN1
2025-09-15 20:25:05.438 wdl.w:ptcp.w:call-paraphase-48.t:call-call_f8.stderr VERBOSE 2025-09-15 20:25:05,285 INFO  Started analysis for m84036_250809_035451_s4.bc2145 at 2025-09-15 20:25:05.285320...
2025-09-15 20:25:05.438 wdl.w:ptcp.w:call-paraphase-48.t:call-call_f8.stderr VERBOSE 2025-09-15 20:25:05,330 INFO  Completed analysis for m84036_250809_035451_s4.bc2145
2025-09-15 20:25:05.445 wdl.w:ptcp.w:call-paraphase-48.t:call-call_f8.slurm_singularity INFO srun: job 51797889 queued and waiting for resources
2025-09-15 20:25:05.446 wdl.w:ptcp.w:call-paraphase-48.t:call-call_f8.slurm_singularity INFO srun: job 51797889 has been allocated resources
2025-09-15 20:25:05.446 wdl.w:ptcp.w:call-paraphase-48.t:call-call_f8.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:05.484 wdl.w:ptcp.w:call-paraphase-70.t:call-run_paraphase.slurm_singularity INFO srun: job 51797890 queued and waiting for resources
2025-09-15 20:25:05.484 wdl.w:ptcp.w:call-paraphase-70.t:call-run_paraphase.slurm_singularity INFO srun: job 51797890 has been allocated resources
2025-09-15 20:25:05.484 wdl.w:ptcp.w:call-paraphase-70.t:call-run_paraphase.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:05.526 wdl.w:ptcp.w:call-paraphase-48.t:call-call_f8 INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2145.f8inversion.vcf"
2025-09-15 20:25:05.529 wdl.w:ptcp.w:call-paraphase-48.t:call-call_f8 INFO output :: name: "json", value: "m84036_250809_035451_s4.bc2145.f8inversion.json"
2025-09-15 20:25:05.599 wdl.w:ptcp.w:call-paraphase-48.t:call-call_f8 NOTICE done
2025-09-15 20:25:05.604 wdl.w:ptcp.w:call-paraphase-48 NOTICE finish :: job: "call-call_f8"
2025-09-15 20:25:05.605 wdl.w:ptcp.w:call-paraphase-48 INFO output :: job: "call-call_f8", values: {"json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-48/call-call_f8/out/m84036_250809_035451_s4.bc2145.f8inversion.json", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-48/call-call_f8/out/m84036_250809_035451_s4.bc2145.f8inversion.vcf"}
2025-09-15 20:25:05.605 wdl.w:ptcp.w:call-paraphase-48 INFO visit :: node: "output-f8_json", values: {"f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-48/call-call_f8/out/m84036_250809_035451_s4.bc2145.f8inversion.json"}
2025-09-15 20:25:05.605 wdl.w:ptcp.w:call-paraphase-48 INFO visit :: node: "output-f8_vcf", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-48/call-call_f8/out/m84036_250809_035451_s4.bc2145.f8inversion.vcf"}
2025-09-15 20:25:05.605 wdl.w:ptcp.w:call-paraphase-48 INFO visit :: node: "outputs", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-48/call-call_f8/out/m84036_250809_035451_s4.bc2145.f8inversion.vcf", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-48/call-run_paraphase/out/m84036_250809_035451_s4.bc2145_paraphase/m84036_250809_035451_s4.bc2145.paraphase.json", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-48/call-run_paraphase/out/m84036_250809_035451_s4.bc2145_paraphase/m84036_250809_035451_s4.bc2145.paraphase.bam", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-48/call-run_paraphase/out/m84036_250809_035451_s4.bc2145_paraphase/m84036_250809_035451_s4.bc2145.paraphase.bam.bai", "paraphase_vcfs": [], "havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-48/call-run_paraphase/out/m84036_250809_035451_s4.bc2145.havanno.json", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-48/call-call_f8/out/m84036_250809_035451_s4.bc2145.f8inversion.json"}
2025-09-15 20:25:05.607 wdl.w:ptcp.w:call-paraphase-39.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for hba for sample m84036_250809_035451_s4.bc2136 at 2025-09-15 20:24:40.742957...
2025-09-15 20:25:05.608 wdl.w:ptcp.w:call-paraphase-39.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for smn1 for sample m84036_250809_035451_s4.bc2136 at 2025-09-15 20:24:40.830961...
2025-09-15 20:25:05.608 wdl.w:ptcp.w:call-paraphase-39.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for gba for sample m84036_250809_035451_s4.bc2136 at 2025-09-15 20:24:41.250476...
2025-09-15 20:25:05.609 wdl.w:ptcp.w:call-paraphase-39.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for cyp21 for sample m84036_250809_035451_s4.bc2136 at 2025-09-15 20:24:41.979761...
2025-09-15 20:25:05.609 wdl.w:ptcp.w:call-paraphase-39.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for smn1 for sample m84036_250809_035451_s4.bc2136 at 2025-09-15 20:24:54.826066...
2025-09-15 20:25:05.609 wdl.w:ptcp.w:call-paraphase-39.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning to gene2 region for smn1 for sample m84036_250809_035451_s4.bc2136 at 2025-09-15 20:24:55.225931...
2025-09-15 20:25:05.615 wdl.w:ptcp.w:call-paraphase-79.t:call-run_paraphase NOTICE task setup :: name: "run_paraphase", source: "./paraphase.wdl", line: 127, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-79/call-run_paraphase", thread: 140609847293504
2025-09-15 20:25:05.628 wdl.w:ptcp.w:call-trgt-53.t:call-trgt_plot_motifs_waterfall INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2150.motifs_waterfall.trgt_plots.zip"
2025-09-15 20:25:05.636 wdl.w:ptcp.t:call-tar_outputs-13 INFO command stdout unused; consider output `File cmd_out = stdout()` or redirect command to stderr log >&2 :: stdout_file: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-13/stdout.txt"
2025-09-15 20:25:05.636 wdl.w:ptcp.t:call-tar_outputs-13 INFO output :: name: "sample_tarball", value: "m84036_250809_035451_s4.bc2110.tar"
2025-09-15 20:25:05.639 wdl.w:ptcp.w:call-paraphase-79.t:call-run_paraphase INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:05.640 wdl.w:ptcp.w:call-paraphase-79.t:call-run_paraphase INFO input :: name: "annotation_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf"
2025-09-15 20:25:05.640 wdl.w:ptcp.w:call-paraphase-79.t:call-run_paraphase INFO input :: name: "genome_version", value: "38"
2025-09-15 20:25:05.640 wdl.w:ptcp.w:call-paraphase-79.t:call-run_paraphase INFO input :: name: "config_file", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/paraphase_config.GRCh38.yaml"
2025-09-15 20:25:05.640 wdl.w:ptcp.w:call-paraphase-79.t:call-run_paraphase INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:25:05.640 wdl.w:ptcp.w:call-paraphase-79.t:call-run_paraphase INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:25:05.640 wdl.w:ptcp.w:call-paraphase-79.t:call-run_paraphase INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2176.mapped.bam.bai"
2025-09-15 20:25:05.640 wdl.w:ptcp.w:call-paraphase-79.t:call-run_paraphase INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2176.mapped.bam"
2025-09-15 20:25:05.640 wdl.w:ptcp.w:call-paraphase-79.t:call-run_paraphase INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2176"
2025-09-15 20:25:05.641 wdl.w:ptcp.w:call-paraphase-79.t:call-run_paraphase INFO eval :: name: "threads", value: 4
2025-09-15 20:25:05.641 wdl.w:ptcp.w:call-paraphase-79.t:call-run_paraphase INFO eval :: name: "mem_gb", value: 8
2025-09-15 20:25:05.641 wdl.w:ptcp.w:call-paraphase-79.t:call-run_paraphase INFO eval :: name: "disk_size", value: 27
2025-09-15 20:25:05.641 wdl.w:ptcp.w:call-paraphase-79.t:call-run_paraphase INFO eval :: name: "out_dir", value: "m84036_250809_035451_s4.bc2176_paraphase"
2025-09-15 20:25:05.642 wdl.w:ptcp.w:call-paraphase-79.t:call-run_paraphase INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 4, memory_reservation: 8000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:05.642 wdl.w:ptcp.w:call-paraphase-79.t:call-run_paraphase WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:05.643 wdl.w:ptcp.w:call-paraphase-79.t:call-run_paraphase INFO provisioned :: seconds_waited: 0, cpu: 4, mem_bytes: 8000000000
2025-09-15 20:25:05.643 wdl.w:ptcp.w:call-paraphase-79.t:call-run_paraphase INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:05.657 wdl.w:ptcp.w:call-sawfish-70.t:call-run_sawfish.slurm_singularity INFO srun: job 51797891 queued and waiting for resources
2025-09-15 20:25:05.657 wdl.w:ptcp.w:call-sawfish-70.t:call-run_sawfish.slurm_singularity INFO srun: job 51797891 has been allocated resources
2025-09-15 20:25:05.657 wdl.w:ptcp.w:call-sawfish-70.t:call-run_sawfish.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:05.657 wdl.w:ptcp.w:call-sawfish-70.t:call-run_sawfish.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:25:05.691 wdl.w:ptcp.w:call-trgt-53.t:call-trgt_plot_meth_waterfall INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2150.meth_waterfall.trgt_plots.zip"
2025-09-15 20:25:05.701 wdl.w:ptcp.w:call-paraphase-48 NOTICE done
2025-09-15 20:25:05.708 wdl.w:ptcp NOTICE finish :: job: "call-paraphase-48"
2025-09-15 20:25:05.708 wdl.w:ptcp INFO output :: job: "call-paraphase-48", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-48/out/m84036_250809_035451_s4.bc2145.f8inversion.vcf", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-48/out/m84036_250809_035451_s4.bc2145_paraphase/m84036_250809_035451_s4.bc2145.paraphase.json", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-48/out/m84036_250809_035451_s4.bc2145_paraphase/m84036_250809_035451_s4.bc2145.paraphase.bam", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-48/out/m84036_250809_035451_s4.bc2145_paraphase/m84036_250809_035451_s4.bc2145.paraphase.bam.bai", "paraphase_vcfs": [], "havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-48/out/m84036_250809_035451_s4.bc2145.havanno.json", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-48/out/m84036_250809_035451_s4.bc2145.f8inversion.json"}
2025-09-15 20:25:05.721 wdl.w:ptcp.w:call-paraphase-72 NOTICE workflow start :: name: "paraphase", source: "./paraphase.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-72"
2025-09-15 20:25:05.744 wdl.w:ptcp.w:call-paraphase-72 INFO visit :: node: "decl-annotation_vcf", values: {"annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf"}
2025-09-15 20:25:05.744 wdl.w:ptcp.w:call-paraphase-72 INFO visit :: node: "decl-config_file", values: {"config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml"}
2025-09-15 20:25:05.744 wdl.w:ptcp.w:call-paraphase-72 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:25:05.744 wdl.w:ptcp.w:call-paraphase-72 INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:25:05.745 wdl.w:ptcp.w:call-paraphase-72 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-72/out/m84036_250809_035451_s4.bc2169.mapped.bam"}
2025-09-15 20:25:05.745 wdl.w:ptcp.w:call-paraphase-72 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-72/out/m84036_250809_035451_s4.bc2169.mapped.bam.bai"}
2025-09-15 20:25:05.745 wdl.w:ptcp.w:call-paraphase-72 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:25:05.745 wdl.w:ptcp.w:call-paraphase-72 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:25:05.745 wdl.w:ptcp.w:call-paraphase-72 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2169"}
2025-09-15 20:25:05.745 wdl.w:ptcp.w:call-paraphase-72 INFO visit :: node: "decl-sex", values: {"sex": "F"}
2025-09-15 20:25:05.745 wdl.w:ptcp.w:call-paraphase-72 NOTICE ready :: job: "call-run_paraphase", callee: "run_paraphase"
2025-09-15 20:25:05.745 wdl.w:ptcp.w:call-paraphase-72 INFO input :: job: "call-run_paraphase", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf", "genome_version": "38", "config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-72/out/m84036_250809_035451_s4.bc2169.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-72/out/m84036_250809_035451_s4.bc2169.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2169"}
2025-09-15 20:25:05.760 wdl.w:ptcp.t:call-tar_outputs-13 NOTICE done
2025-09-15 20:25:05.767 wdl.w:ptcp.w:call-paraphase-79.t:call-run_paraphase INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-79/call-run_paraphase/_singularity_tmpdir_xdvgyex4"
2025-09-15 20:25:05.767 wdl.w:ptcp.w:call-paraphase-79.t:call-run_paraphase INFO Slurm invocation: srun --job-name call-run_paraphase --partition compute,compute9 --cpus-per-task 4 --mem 7629M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-79/call-run_paraphase/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-79/call-run_paraphase/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-79/call-run_paraphase/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-79/call-run_paraphase/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-79/out/m84036_250809_035451_s4.bc2176.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2176.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-79/out/m84036_250809_035451_s4.bc2176.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2176.mapped.bam:ro --bind /ptcp/meta/variant_list/variant_list.GRCh38.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf:ro --bind /ptcp/meta/paraphase/paraphase_config.GRCh38.yaml:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/paraphase_config.GRCh38.yaml:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-79/call-run_paraphase/_singularity_tmpdir_xdvgyex4/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-79/call-run_paraphase/_singularity_tmpdir_xdvgyex4/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:05.782 wdl.w:ptcp NOTICE finish :: job: "call-tar_outputs-13"
2025-09-15 20:25:05.782 wdl.w:ptcp INFO output :: job: "call-tar_outputs-13", values: {"sample_tarball": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-13/out/m84036_250809_035451_s4.bc2110.tar"}
2025-09-15 20:25:05.787 wdl.w:ptcp.w:call-paraphase-65.t:call-run_paraphase INFO output :: name: "paraphase_bam", value: "m84036_250809_035451_s4.bc2162_paraphase/m84036_250809_035451_s4.bc2162.paraphase.bam"
2025-09-15 20:25:05.788 wdl.w:ptcp.t:call-tar_outputs-00.slurm_singularity INFO srun: job 51797892 queued and waiting for resources
2025-09-15 20:25:05.789 wdl.w:ptcp.t:call-tar_outputs-00.slurm_singularity INFO srun: job 51797892 has been allocated resources
2025-09-15 20:25:05.789 wdl.w:ptcp.t:call-tar_outputs-00.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:05.789 wdl.w:ptcp.t:call-tar_outputs-00.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:25:05.790 wdl.w:ptcp.w:call-paraphase-56.t:call-call_f8 NOTICE task setup :: name: "call_f8", source: "./paraphase.wdl", line: 232, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-56/call-call_f8", thread: 140610895857216
2025-09-15 20:25:05.797 wdl.w:ptcp.w:call-paraphase-65.t:call-run_paraphase INFO output :: name: "paraphase_bam_bai", value: "m84036_250809_035451_s4.bc2162_paraphase/m84036_250809_035451_s4.bc2162.paraphase.bam.bai"
2025-09-15 20:25:05.799 wdl.w:ptcp.w:call-paraphase-65.t:call-run_paraphase INFO output :: name: "paraphase_json", value: "m84036_250809_035451_s4.bc2162_paraphase/m84036_250809_035451_s4.bc2162.paraphase.json"
2025-09-15 20:25:05.801 wdl.w:ptcp.w:call-paraphase-65.t:call-run_paraphase INFO output :: name: "paraphase_vcfs", value: []
2025-09-15 20:25:05.802 wdl.w:ptcp.w:call-paraphase-65.t:call-run_paraphase INFO output :: name: "havanno_json", value: "m84036_250809_035451_s4.bc2162.havanno.json"
2025-09-15 20:25:05.807 wdl.w:ptcp.w:call-trgt-53.t:call-trgt_plot_motifs_waterfall NOTICE done
2025-09-15 20:25:05.812 wdl.w:ptcp.w:call-trgt-53 NOTICE finish :: job: "call-trgt_plot_motifs_waterfall"
2025-09-15 20:25:05.813 wdl.w:ptcp.w:call-paraphase-56.t:call-call_f8 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:05.813 wdl.w:ptcp.w:call-trgt-53 INFO output :: job: "call-trgt_plot_motifs_waterfall", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-53/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2150.motifs_waterfall.trgt_plots.zip"}
2025-09-15 20:25:05.813 wdl.w:ptcp.w:call-paraphase-79.t:call-run_paraphase NOTICE slurm_singularity run :: pid: 1204575, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-79/call-run_paraphase/slurm_singularity.log.txt"
2025-09-15 20:25:05.813 wdl.w:ptcp.w:call-paraphase-56.t:call-call_f8 INFO input :: name: "genome_version", value: "38"
2025-09-15 20:25:05.814 wdl.w:ptcp.w:call-trgt-53 INFO visit :: node: "output-images_motifs_waterfall", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-53/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2150.motifs_waterfall.trgt_plots.zip"}
2025-09-15 20:25:05.814 wdl.w:ptcp.w:call-paraphase-56.t:call-call_f8 INFO input :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2153"
2025-09-15 20:25:05.814 wdl.w:ptcp.w:call-paraphase-56.t:call-call_f8 INFO input :: name: "paraphase_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2153.paraphase.bam.bai"
2025-09-15 20:25:05.814 wdl.w:ptcp.w:call-paraphase-56.t:call-call_f8 INFO input :: name: "paraphase_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2153.paraphase.bam"
2025-09-15 20:25:05.814 wdl.w:ptcp.w:call-paraphase-56.t:call-call_f8 INFO input :: name: "sex", value: "F"
2025-09-15 20:25:05.814 wdl.w:ptcp.w:call-paraphase-56.t:call-call_f8 INFO eval :: name: "threads", value: 1
2025-09-15 20:25:05.814 wdl.w:ptcp.w:call-paraphase-56.t:call-call_f8 INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:25:05.815 wdl.w:ptcp.w:call-paraphase-56.t:call-call_f8 INFO eval :: name: "disk_size", value: 11
2025-09-15 20:25:05.815 wdl.w:ptcp.w:call-paraphase-56.t:call-call_f8 INFO eval :: name: "sample_sex", value: "F"
2025-09-15 20:25:05.815 wdl.w:ptcp.w:call-paraphase-56.t:call-call_f8 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:05.815 wdl.w:ptcp.w:call-paraphase-56.t:call-call_f8 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:05.816 wdl.w:ptcp.w:call-paraphase-56.t:call-call_f8 INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:25:05.816 wdl.w:ptcp.w:call-paraphase-56.t:call-call_f8 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:05.819 wdl.w:ptcp.w:call-trgt-67.t:call-trgt_plot_meth_allele NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-67/call-trgt_plot_meth_allele", thread: 140611961206336
2025-09-15 20:25:05.830 wdl.w:ptcp.w:call-trgt-70.t:call-get_reads_overlapping_repeats.slurm_singularity INFO srun: job 51797893 queued and waiting for resources
2025-09-15 20:25:05.830 wdl.w:ptcp.w:call-trgt-70.t:call-get_reads_overlapping_repeats.slurm_singularity INFO srun: job 51797893 has been allocated resources
2025-09-15 20:25:05.830 wdl.w:ptcp.w:call-trgt-70.t:call-get_reads_overlapping_repeats.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:05.830 wdl.w:ptcp.w:call-trgt-70.t:call-get_reads_overlapping_repeats.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:25:05.843 wdl.w:ptcp.w:call-trgt-67.t:call-trgt_plot_meth_allele INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:05.843 wdl.w:ptcp.w:call-trgt-67.t:call-trgt_plot_meth_allele INFO input :: name: "waterfall", value: false
2025-09-15 20:25:05.843 wdl.w:ptcp.w:call-trgt-67.t:call-trgt_plot_meth_allele INFO input :: name: "methylation", value: true
2025-09-15 20:25:05.843 wdl.w:ptcp.w:call-trgt-67.t:call-trgt_plot_meth_allele INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:25:05.843 wdl.w:ptcp.w:call-trgt-67.t:call-trgt_plot_meth_allele INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:25:05.843 wdl.w:ptcp.w:call-trgt-67.t:call-trgt_plot_meth_allele INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:25:05.843 wdl.w:ptcp.w:call-trgt-67.t:call-trgt_plot_meth_allele INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2164.trgt.sorted.spanning.bam.bai"
2025-09-15 20:25:05.843 wdl.w:ptcp.w:call-trgt-67.t:call-trgt_plot_meth_allele INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2164.trgt.sorted.spanning.bam"
2025-09-15 20:25:05.843 wdl.w:ptcp.w:call-trgt-67.t:call-trgt_plot_meth_allele INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2164.trgt.vcf"
2025-09-15 20:25:05.843 wdl.w:ptcp.w:call-trgt-67.t:call-trgt_plot_meth_allele INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2164"
2025-09-15 20:25:05.844 wdl.w:ptcp.w:call-trgt-67.t:call-trgt_plot_meth_allele INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:25:05.844 wdl.w:ptcp.w:call-trgt-67.t:call-trgt_plot_meth_allele INFO eval :: name: "plot_type", value: "allele"
2025-09-15 20:25:05.844 wdl.w:ptcp.w:call-trgt-67.t:call-trgt_plot_meth_allele INFO eval :: name: "show", value: "meth"
2025-09-15 20:25:05.844 wdl.w:ptcp.w:call-trgt-67.t:call-trgt_plot_meth_allele INFO eval :: name: "threads", value: 1
2025-09-15 20:25:05.845 wdl.w:ptcp.w:call-trgt-67.t:call-trgt_plot_meth_allele INFO eval :: name: "disk_size", value: 27
2025-09-15 20:25:05.845 wdl.w:ptcp.w:call-trgt-67.t:call-trgt_plot_meth_allele INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2164.meth_allele"
2025-09-15 20:25:05.845 wdl.w:ptcp.w:call-trgt-67.t:call-trgt_plot_meth_allele INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:05.845 wdl.w:ptcp.w:call-trgt-67.t:call-trgt_plot_meth_allele WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:05.846 wdl.w:ptcp.w:call-trgt-67.t:call-trgt_plot_meth_allele INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:25:05.846 wdl.w:ptcp.w:call-trgt-67.t:call-trgt_plot_meth_allele INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:05.860 wdl.w:ptcp.w:call-trgt-53.t:call-trgt_plot_meth_waterfall NOTICE done
2025-09-15 20:25:05.875 wdl.w:ptcp.w:call-paraphase-56.t:call-call_f8 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 8, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-56/call-call_f8/_singularity_tmpdir_mp7chod0"
2025-09-15 20:25:05.875 wdl.w:ptcp.w:call-paraphase-56.t:call-call_f8 INFO Slurm invocation: srun --job-name call-call_f8 --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-56/call-call_f8/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-56/call-call_f8/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-56/call-call_f8/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-56/call-call_f8/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-56/call-run_paraphase/out/m84036_250809_035451_s4.bc2153_paraphase/m84036_250809_035451_s4.bc2153.paraphase.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2153.paraphase.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-56/call-run_paraphase/out/m84036_250809_035451_s4.bc2153_paraphase/m84036_250809_035451_s4.bc2153.paraphase.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2153.paraphase.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-56/call-call_f8/_singularity_tmpdir_mp7chod0/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-56/call-call_f8/_singularity_tmpdir_mp7chod0/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:05.877 wdl.w:ptcp.w:call-trgt-70.t:call-get_reads_overlapping_repeats INFO output :: name: "reads_overlapping_repeats", value: "m84036_250809_035451_s4.bc2167.repeats.bam"
2025-09-15 20:25:05.880 wdl.w:ptcp.w:call-trgt-70.t:call-get_reads_overlapping_repeats INFO output :: name: "reads_overlapping_repeats_bai", value: "m84036_250809_035451_s4.bc2167.repeats.bam.bai"
2025-09-15 20:25:05.896 wdl.w:ptcp.w:call-paraphase-56.t:call-call_f8 NOTICE slurm_singularity run :: pid: 1204579, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-56/call-call_f8/slurm_singularity.log.txt"
2025-09-15 20:25:05.912 wdl.w:ptcp.w:call-paraphase-65.t:call-run_paraphase NOTICE done
2025-09-15 20:25:05.919 wdl.w:ptcp.w:call-paraphase-65 NOTICE finish :: job: "call-run_paraphase"
2025-09-15 20:25:05.919 wdl.w:ptcp.w:call-paraphase-65 INFO output :: job: "call-run_paraphase", values: {"havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-65/call-run_paraphase/out/m84036_250809_035451_s4.bc2162.havanno.json", "paraphase_vcfs": [], "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-65/call-run_paraphase/out/m84036_250809_035451_s4.bc2162_paraphase/m84036_250809_035451_s4.bc2162.paraphase.json", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-65/call-run_paraphase/out/m84036_250809_035451_s4.bc2162_paraphase/m84036_250809_035451_s4.bc2162.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-65/call-run_paraphase/out/m84036_250809_035451_s4.bc2162_paraphase/m84036_250809_035451_s4.bc2162.paraphase.bam"}
2025-09-15 20:25:05.920 wdl.w:ptcp.w:call-paraphase-65 NOTICE ready :: job: "call-call_f8", callee: "call_f8"
2025-09-15 20:25:05.921 wdl.w:ptcp.w:call-trgt-53 NOTICE finish :: job: "call-trgt_plot_meth_waterfall"
2025-09-15 20:25:05.921 wdl.w:ptcp.w:call-paraphase-65 INFO input :: job: "call-call_f8", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "out_prefix": "m84036_250809_035451_s4.bc2162", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-65/call-run_paraphase/out/m84036_250809_035451_s4.bc2162_paraphase/m84036_250809_035451_s4.bc2162.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-65/call-run_paraphase/out/m84036_250809_035451_s4.bc2162_paraphase/m84036_250809_035451_s4.bc2162.paraphase.bam", "sex": "F"}
2025-09-15 20:25:05.921 wdl.w:ptcp.w:call-trgt-53 INFO output :: job: "call-trgt_plot_meth_waterfall", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-53/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2150.meth_waterfall.trgt_plots.zip"}
2025-09-15 20:25:05.921 wdl.w:ptcp.w:call-trgt-53 INFO visit :: node: "output-images_meth_waterfall", values: {"images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-53/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2150.meth_waterfall.trgt_plots.zip"}
2025-09-15 20:25:05.921 wdl.w:ptcp.w:call-trgt-67.t:call-trgt_plot_meth_allele INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-67/call-trgt_plot_meth_allele/_singularity_tmpdir_09m5odl3"
2025-09-15 20:25:05.922 wdl.w:ptcp.w:call-trgt-67.t:call-trgt_plot_meth_allele INFO Slurm invocation: srun --job-name call-trgt_plot_meth_allele --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-67/call-trgt_plot_meth_allele/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-67/call-trgt_plot_meth_allele/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-67/call-trgt_plot_meth_allele/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-67/call-trgt_plot_meth_allele/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-67/call-trgt_genotype/out/m84036_250809_035451_s4.bc2164.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2164.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-67/call-trgt_genotype/out/m84036_250809_035451_s4.bc2164.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2164.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-67/call-trgt_genotype/out/m84036_250809_035451_s4.bc2164.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2164.trgt.vcf:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-67/call-trgt_plot_meth_allele/_singularity_tmpdir_09m5odl3/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-67/call-trgt_plot_meth_allele/_singularity_tmpdir_09m5odl3/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:05.923 wdl.w:ptcp.w:call-paraphase-65 INFO visit :: node: "output-havanno_json", values: {"havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-65/call-run_paraphase/out/m84036_250809_035451_s4.bc2162.havanno.json"}
2025-09-15 20:25:05.924 wdl.w:ptcp.w:call-paraphase-65 INFO visit :: node: "output-paraphase_bam", values: {"paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-65/call-run_paraphase/out/m84036_250809_035451_s4.bc2162_paraphase/m84036_250809_035451_s4.bc2162.paraphase.bam"}
2025-09-15 20:25:05.924 wdl.w:ptcp.w:call-paraphase-65 INFO visit :: node: "output-paraphase_bam_bai", values: {"paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-65/call-run_paraphase/out/m84036_250809_035451_s4.bc2162_paraphase/m84036_250809_035451_s4.bc2162.paraphase.bam.bai"}
2025-09-15 20:25:05.924 wdl.w:ptcp.w:call-paraphase-65 INFO visit :: node: "output-paraphase_json", values: {"paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-65/call-run_paraphase/out/m84036_250809_035451_s4.bc2162_paraphase/m84036_250809_035451_s4.bc2162.paraphase.json"}
2025-09-15 20:25:05.925 wdl.w:ptcp.w:call-paraphase-65 INFO visit :: node: "output-paraphase_vcfs", values: {"paraphase_vcfs": []}
2025-09-15 20:25:05.929 wdl.w:ptcp.w:call-trgt-67.t:call-trgt_plot_meth_waterfall NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-67/call-trgt_plot_meth_waterfall", thread: 140608739980864
2025-09-15 20:25:05.931 wdl.w:ptcp.w:call-trgt-67.t:call-trgt_plot_motifs_allele NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-67/call-trgt_plot_motifs_allele", thread: 140612506469952
2025-09-15 20:25:05.937 wdl.w:ptcp.w:call-trgt-67.t:call-trgt_plot_meth_allele NOTICE slurm_singularity run :: pid: 1204586, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-67/call-trgt_plot_meth_allele/slurm_singularity.log.txt"
2025-09-15 20:25:05.954 wdl.w:ptcp.w:call-trgt-67.t:call-trgt_plot_meth_waterfall INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:05.954 wdl.w:ptcp.w:call-trgt-67.t:call-trgt_plot_meth_waterfall INFO input :: name: "waterfall", value: true
2025-09-15 20:25:05.954 wdl.w:ptcp.w:call-trgt-67.t:call-trgt_plot_meth_waterfall INFO input :: name: "methylation", value: true
2025-09-15 20:25:05.954 wdl.w:ptcp.w:call-trgt-67.t:call-trgt_plot_meth_waterfall INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:25:05.954 wdl.w:ptcp.w:call-trgt-67.t:call-trgt_plot_meth_waterfall INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:25:05.954 wdl.w:ptcp.w:call-trgt-67.t:call-trgt_plot_meth_waterfall INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:25:05.954 wdl.w:ptcp.w:call-trgt-67.t:call-trgt_plot_meth_waterfall INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2164.trgt.sorted.spanning.bam.bai"
2025-09-15 20:25:05.954 wdl.w:ptcp.w:call-trgt-67.t:call-trgt_plot_meth_waterfall INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2164.trgt.sorted.spanning.bam"
2025-09-15 20:25:05.955 wdl.w:ptcp.w:call-trgt-67.t:call-trgt_plot_meth_waterfall INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2164.trgt.vcf"
2025-09-15 20:25:05.955 wdl.w:ptcp.w:call-trgt-67.t:call-trgt_plot_meth_waterfall INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2164"
2025-09-15 20:25:05.955 wdl.w:ptcp.w:call-trgt-67.t:call-trgt_plot_meth_waterfall INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:25:05.955 wdl.w:ptcp.w:call-trgt-67.t:call-trgt_plot_meth_waterfall INFO eval :: name: "plot_type", value: "waterfall"
2025-09-15 20:25:05.955 wdl.w:ptcp.w:call-trgt-67.t:call-trgt_plot_meth_waterfall INFO eval :: name: "show", value: "meth"
2025-09-15 20:25:05.955 wdl.w:ptcp.w:call-trgt-67.t:call-trgt_plot_meth_waterfall INFO eval :: name: "threads", value: 1
2025-09-15 20:25:05.955 wdl.w:ptcp.w:call-trgt-67.t:call-trgt_plot_meth_waterfall INFO eval :: name: "disk_size", value: 27
2025-09-15 20:25:05.955 wdl.w:ptcp.w:call-trgt-67.t:call-trgt_plot_meth_waterfall INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2164.meth_waterfall"
2025-09-15 20:25:05.956 wdl.w:ptcp.w:call-trgt-67.t:call-trgt_plot_meth_waterfall INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:05.956 wdl.w:ptcp.w:call-trgt-67.t:call-trgt_plot_meth_waterfall WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:05.956 wdl.w:ptcp.w:call-trgt-67.t:call-trgt_plot_meth_waterfall INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:25:05.956 wdl.w:ptcp.w:call-trgt-67.t:call-trgt_plot_meth_waterfall INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:05.958 wdl.w:ptcp.w:call-trgt-67.t:call-trgt_plot_motifs_allele INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:05.958 wdl.w:ptcp.w:call-trgt-67.t:call-trgt_plot_motifs_allele INFO input :: name: "waterfall", value: false
2025-09-15 20:25:05.959 wdl.w:ptcp.w:call-trgt-67.t:call-trgt_plot_motifs_allele INFO input :: name: "methylation", value: false
2025-09-15 20:25:05.959 wdl.w:ptcp.w:call-trgt-67.t:call-trgt_plot_motifs_allele INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:25:05.959 wdl.w:ptcp.w:call-trgt-67.t:call-trgt_plot_motifs_allele INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:25:05.959 wdl.w:ptcp.w:call-trgt-67.t:call-trgt_plot_motifs_allele INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:25:05.959 wdl.w:ptcp.w:call-trgt-67.t:call-trgt_plot_motifs_allele INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2164.trgt.sorted.spanning.bam.bai"
2025-09-15 20:25:05.959 wdl.w:ptcp.w:call-trgt-67.t:call-trgt_plot_motifs_allele INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2164.trgt.sorted.spanning.bam"
2025-09-15 20:25:05.959 wdl.w:ptcp.w:call-trgt-67.t:call-trgt_plot_motifs_allele INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2164.trgt.vcf"
2025-09-15 20:25:05.959 wdl.w:ptcp.w:call-trgt-70.t:call-get_reads_overlapping_repeats NOTICE done
2025-09-15 20:25:05.959 wdl.w:ptcp.w:call-trgt-67.t:call-trgt_plot_motifs_allele INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2164"
2025-09-15 20:25:05.959 wdl.w:ptcp.w:call-trgt-67.t:call-trgt_plot_motifs_allele INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:25:05.959 wdl.w:ptcp.w:call-trgt-67.t:call-trgt_plot_motifs_allele INFO eval :: name: "plot_type", value: "allele"
2025-09-15 20:25:05.959 wdl.w:ptcp.w:call-trgt-67.t:call-trgt_plot_motifs_allele INFO eval :: name: "show", value: "motifs"
2025-09-15 20:25:05.960 wdl.w:ptcp.w:call-trgt-67.t:call-trgt_plot_motifs_allele INFO eval :: name: "threads", value: 1
2025-09-15 20:25:05.960 wdl.w:ptcp.w:call-trgt-67.t:call-trgt_plot_motifs_allele INFO eval :: name: "disk_size", value: 27
2025-09-15 20:25:05.960 wdl.w:ptcp.w:call-trgt-67.t:call-trgt_plot_motifs_allele INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2164.motifs_allele"
2025-09-15 20:25:05.960 wdl.w:ptcp.w:call-trgt-67.t:call-trgt_plot_motifs_allele INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:05.960 wdl.w:ptcp.w:call-trgt-67.t:call-trgt_plot_motifs_allele WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:05.961 wdl.w:ptcp.w:call-trgt-67.t:call-trgt_plot_motifs_allele INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:25:05.961 wdl.w:ptcp.w:call-trgt-67.t:call-trgt_plot_motifs_allele INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:05.962 wdl.w:ptcp.t:call-tar_outputs-00 INFO output :: name: "sample_tarball", value: "m84036_250809_035451_s4.bc2097.tar"
2025-09-15 20:25:05.983 wdl.w:ptcp.w:call-trgt-70 NOTICE finish :: job: "call-get_reads_overlapping_repeats"
2025-09-15 20:25:05.983 wdl.w:ptcp.w:call-trgt-70 INFO output :: job: "call-get_reads_overlapping_repeats", values: {"reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-70/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2167.repeats.bam.bai", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-70/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2167.repeats.bam"}
2025-09-15 20:25:05.983 wdl.w:ptcp.w:call-trgt-70 INFO visit :: node: "output-reads_overlapping_repeats", values: {"reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-70/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2167.repeats.bam"}
2025-09-15 20:25:05.983 wdl.w:ptcp.w:call-trgt-70 INFO visit :: node: "output-reads_overlapping_repeats_bai", values: {"reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-70/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2167.repeats.bam.bai"}
2025-09-15 20:25:05.991 wdl.w:ptcp.w:call-trgt-67.t:call-trgt_plot_motifs_waterfall NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-67/call-trgt_plot_motifs_waterfall", thread: 140607691417152
2025-09-15 20:25:06.012 wdl.w:ptcp.w:call-trgt-67.t:call-trgt_plot_motifs_waterfall INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:06.012 wdl.w:ptcp.w:call-trgt-67.t:call-trgt_plot_motifs_waterfall INFO input :: name: "waterfall", value: true
2025-09-15 20:25:06.012 wdl.w:ptcp.w:call-trgt-67.t:call-trgt_plot_motifs_waterfall INFO input :: name: "methylation", value: false
2025-09-15 20:25:06.012 wdl.w:ptcp.w:call-trgt-67.t:call-trgt_plot_motifs_waterfall INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:25:06.012 wdl.w:ptcp.w:call-trgt-67.t:call-trgt_plot_motifs_waterfall INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:25:06.012 wdl.w:ptcp.w:call-trgt-67.t:call-trgt_plot_motifs_waterfall INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:25:06.012 wdl.w:ptcp.w:call-trgt-67.t:call-trgt_plot_motifs_waterfall INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2164.trgt.sorted.spanning.bam.bai"
2025-09-15 20:25:06.012 wdl.w:ptcp.w:call-trgt-67.t:call-trgt_plot_motifs_waterfall INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2164.trgt.sorted.spanning.bam"
2025-09-15 20:25:06.012 wdl.w:ptcp.w:call-trgt-67.t:call-trgt_plot_motifs_waterfall INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2164.trgt.vcf"
2025-09-15 20:25:06.012 wdl.w:ptcp.w:call-trgt-67.t:call-trgt_plot_motifs_waterfall INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2164"
2025-09-15 20:25:06.013 wdl.w:ptcp.w:call-trgt-67.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:25:06.013 wdl.w:ptcp.w:call-trgt-67.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "plot_type", value: "waterfall"
2025-09-15 20:25:06.013 wdl.w:ptcp.w:call-trgt-67.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "show", value: "motifs"
2025-09-15 20:25:06.013 wdl.w:ptcp.w:call-trgt-67.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "threads", value: 1
2025-09-15 20:25:06.013 wdl.w:ptcp.w:call-trgt-67.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "disk_size", value: 27
2025-09-15 20:25:06.013 wdl.w:ptcp.w:call-trgt-67.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2164.motifs_waterfall"
2025-09-15 20:25:06.014 wdl.w:ptcp.w:call-trgt-67.t:call-trgt_plot_motifs_waterfall INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:06.014 wdl.w:ptcp.w:call-trgt-67.t:call-trgt_plot_motifs_waterfall WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:06.014 wdl.w:ptcp.w:call-trgt-67.t:call-trgt_plot_motifs_waterfall INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:25:06.014 wdl.w:ptcp.w:call-trgt-67.t:call-trgt_plot_motifs_waterfall INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:06.038 wdl.w:ptcp.w:call-paraphase-60.t:call-run_paraphase.stderr VERBOSE INFO:root:Processing sample m84036_250809_035451_s4.bc2157 at 2025-09-15 20:25:02.759996...
2025-09-15 20:25:06.039 wdl.w:ptcp.w:call-paraphase-60.t:call-run_paraphase.stderr VERBOSE INFO:root:Checking sample sex at 2025-09-15 20:25:02.761972...
2025-09-15 20:25:06.039 wdl.w:ptcp.w:call-paraphase-60.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for cyp21 for sample m84036_250809_035451_s4.bc2157 at 2025-09-15 20:25:02.819446...
2025-09-15 20:25:06.039 wdl.w:ptcp.w:call-paraphase-60.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for cyp21 for sample m84036_250809_035451_s4.bc2157 at 2025-09-15 20:25:02.819952...
2025-09-15 20:25:06.039 wdl.w:ptcp.w:call-paraphase-60.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for smn1 for sample m84036_250809_035451_s4.bc2157 at 2025-09-15 20:25:02.820997...
2025-09-15 20:25:06.039 wdl.w:ptcp.w:call-paraphase-60.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for smn1 for sample m84036_250809_035451_s4.bc2157 at 2025-09-15 20:25:02.821404...
2025-09-15 20:25:06.040 wdl.w:ptcp.w:call-paraphase-60.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for gba for sample m84036_250809_035451_s4.bc2157 at 2025-09-15 20:25:02.821381...
2025-09-15 20:25:06.040 wdl.w:ptcp.w:call-paraphase-60.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for hba for sample m84036_250809_035451_s4.bc2157 at 2025-09-15 20:25:02.821394...
2025-09-15 20:25:06.040 wdl.w:ptcp.w:call-paraphase-60.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for gba for sample m84036_250809_035451_s4.bc2157 at 2025-09-15 20:25:02.821976...
2025-09-15 20:25:06.040 wdl.w:ptcp.w:call-paraphase-60.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for hba for sample m84036_250809_035451_s4.bc2157 at 2025-09-15 20:25:02.821979...
2025-09-15 20:25:06.040 wdl.w:ptcp.w:call-paraphase-60.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for cyp21 for sample m84036_250809_035451_s4.bc2157 at 2025-09-15 20:25:03.413992...
2025-09-15 20:25:06.040 wdl.w:ptcp.w:call-paraphase-60.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for gba for sample m84036_250809_035451_s4.bc2157 at 2025-09-15 20:25:03.432819...
2025-09-15 20:25:06.040 wdl.w:ptcp.w:call-paraphase-60.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for hba for sample m84036_250809_035451_s4.bc2157 at 2025-09-15 20:25:03.445611...
2025-09-15 20:25:06.040 wdl.w:ptcp.w:call-paraphase-60.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for smn1 for sample m84036_250809_035451_s4.bc2157 at 2025-09-15 20:25:03.463505...
2025-09-15 20:25:06.040 wdl.w:ptcp.w:call-paraphase-60.t:call-run_paraphase.stderr VERBOSE WARNING:root:This region does not appear to have coverage. Will not attempt to phase haplotypes.
2025-09-15 20:25:06.040 wdl.w:ptcp.w:call-paraphase-60.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for cyp21 for sample m84036_250809_035451_s4.bc2157 at 2025-09-15 20:25:03.502190...
2025-09-15 20:25:06.040 wdl.w:ptcp.w:call-paraphase-60.t:call-run_paraphase.stderr VERBOSE WARNING:root:This region does not appear to have coverage. Will not attempt to phase haplotypes.
2025-09-15 20:25:06.040 wdl.w:ptcp.w:call-paraphase-60.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for hba for sample m84036_250809_035451_s4.bc2157 at 2025-09-15 20:25:03.505140...
2025-09-15 20:25:06.040 wdl.w:ptcp.w:call-paraphase-60.t:call-run_paraphase.stderr VERBOSE WARNING:root:This region does not appear to have coverage. Will not attempt to phase haplotypes.
2025-09-15 20:25:06.040 wdl.w:ptcp.w:call-paraphase-60.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for gba for sample m84036_250809_035451_s4.bc2157 at 2025-09-15 20:25:03.526373...
2025-09-15 20:25:06.040 wdl.w:ptcp.w:call-paraphase-60.t:call-run_paraphase.stderr VERBOSE WARNING:root:This region does not appear to have coverage. Will not attempt to phase haplotypes.
2025-09-15 20:25:06.040 wdl.w:ptcp.w:call-paraphase-60.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for smn1 for sample m84036_250809_035451_s4.bc2157 at 2025-09-15 20:25:03.598604...
2025-09-15 20:25:06.041 wdl.w:ptcp.w:call-paraphase-60.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for hba for sample m84036_250809_035451_s4.bc2157 at 2025-09-15 20:25:03.815650...
2025-09-15 20:25:06.041 wdl.w:ptcp.w:call-paraphase-60.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for hbb for sample m84036_250809_035451_s4.bc2157 at 2025-09-15 20:25:03.823606...
2025-09-15 20:25:06.041 wdl.w:ptcp.w:call-paraphase-60.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for hbb for sample m84036_250809_035451_s4.bc2157 at 2025-09-15 20:25:03.823686...
2025-09-15 20:25:06.041 wdl.w:ptcp.w:call-paraphase-60.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for cyp21 for sample m84036_250809_035451_s4.bc2157 at 2025-09-15 20:25:03.880240...
2025-09-15 20:25:06.041 wdl.w:ptcp.w:call-paraphase-60.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for f8inv22 for sample m84036_250809_035451_s4.bc2157 at 2025-09-15 20:25:03.885109...
2025-09-15 20:25:06.041 wdl.w:ptcp.w:call-paraphase-60.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for f8inv22 for sample m84036_250809_035451_s4.bc2157 at 2025-09-15 20:25:03.885175...
2025-09-15 20:25:06.041 wdl.w:ptcp.w:call-paraphase-60.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for gba for sample m84036_250809_035451_s4.bc2157 at 2025-09-15 20:25:03.906517...
2025-09-15 20:25:06.041 wdl.w:ptcp.w:call-paraphase-60.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for rpgr for sample m84036_250809_035451_s4.bc2157 at 2025-09-15 20:25:03.918182...
2025-09-15 20:25:06.041 wdl.w:ptcp.w:call-paraphase-60.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for rpgr for sample m84036_250809_035451_s4.bc2157 at 2025-09-15 20:25:03.918249...
2025-09-15 20:25:06.041 wdl.w:ptcp.w:call-paraphase-60.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning to gene2 region for smn1 for sample m84036_250809_035451_s4.bc2157 at 2025-09-15 20:25:03.942040...
2025-09-15 20:25:06.041 wdl.w:ptcp.w:call-paraphase-60.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for hbb for sample m84036_250809_035451_s4.bc2157 at 2025-09-15 20:25:04.335878...
2025-09-15 20:25:06.041 wdl.w:ptcp.w:call-paraphase-60.t:call-run_paraphase.stderr VERBOSE WARNING:root:This region does not appear to have coverage. Will not attempt to phase haplotypes.
2025-09-15 20:25:06.041 wdl.w:ptcp.w:call-paraphase-60.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for f8inv22 for sample m84036_250809_035451_s4.bc2157 at 2025-09-15 20:25:04.399578...
2025-09-15 20:25:06.041 wdl.w:ptcp.w:call-paraphase-60.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for hbb for sample m84036_250809_035451_s4.bc2157 at 2025-09-15 20:25:04.399870...
2025-09-15 20:25:06.041 wdl.w:ptcp.w:call-paraphase-60.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for rpgr for sample m84036_250809_035451_s4.bc2157 at 2025-09-15 20:25:04.435524...
2025-09-15 20:25:06.041 wdl.w:ptcp.w:call-paraphase-60.t:call-run_paraphase.stderr VERBOSE WARNING:root:This region does not appear to have coverage. Will not attempt to phase haplotypes.
2025-09-15 20:25:06.041 wdl.w:ptcp.w:call-paraphase-60.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for f8inv22 for sample m84036_250809_035451_s4.bc2157 at 2025-09-15 20:25:04.446464...
2025-09-15 20:25:06.041 wdl.w:ptcp.w:call-paraphase-60.t:call-run_paraphase.stderr VERBOSE WARNING:root:This region does not appear to have coverage. Will not attempt to phase haplotypes.
2025-09-15 20:25:06.042 wdl.w:ptcp.w:call-paraphase-60.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for rpgr for sample m84036_250809_035451_s4.bc2157 at 2025-09-15 20:25:04.514103...
2025-09-15 20:25:06.042 wdl.w:ptcp.w:call-paraphase-60.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for hbb for sample m84036_250809_035451_s4.bc2157 at 2025-09-15 20:25:04.837234...
2025-09-15 20:25:06.042 wdl.w:ptcp.w:call-paraphase-60.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for f8inv22 for sample m84036_250809_035451_s4.bc2157 at 2025-09-15 20:25:04.958970...
2025-09-15 20:25:06.042 wdl.w:ptcp.w:call-paraphase-60.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for smn1 for sample m84036_250809_035451_s4.bc2157 at 2025-09-15 20:25:04.973055...
2025-09-15 20:25:06.042 wdl.w:ptcp.w:call-paraphase-60.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for rpgr for sample m84036_250809_035451_s4.bc2157 at 2025-09-15 20:25:05.006752...
2025-09-15 20:25:06.042 wdl.w:ptcp.t:call-tar_outputs-00 NOTICE done
2025-09-15 20:25:06.042 wdl.w:ptcp.w:call-paraphase-60.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for f8inv1 for sample m84036_250809_035451_s4.bc2157 at 2025-09-15 20:25:05.046666...
2025-09-15 20:25:06.042 wdl.w:ptcp.w:call-paraphase-60.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for f8inv1 for sample m84036_250809_035451_s4.bc2157 at 2025-09-15 20:25:05.046831...
2025-09-15 20:25:06.042 wdl.w:ptcp.w:call-paraphase-60.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for f8inv1 for sample m84036_250809_035451_s4.bc2157 at 2025-09-15 20:25:05.479753...
2025-09-15 20:25:06.042 wdl.w:ptcp.w:call-paraphase-60.t:call-run_paraphase.stderr VERBOSE WARNING:root:This region does not appear to have coverage. Will not attempt to phase haplotypes.
2025-09-15 20:25:06.042 wdl.w:ptcp.w:call-paraphase-60.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for f8inv1 for sample m84036_250809_035451_s4.bc2157 at 2025-09-15 20:25:05.530378...
2025-09-15 20:25:06.042 wdl.w:ptcp.w:call-paraphase-60.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for f8inv1 for sample m84036_250809_035451_s4.bc2157 at 2025-09-15 20:25:05.760416...
2025-09-15 20:25:06.044 wdl.w:ptcp.w:call-trgt-67.t:call-trgt_plot_meth_waterfall INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-67/call-trgt_plot_meth_waterfall/_singularity_tmpdir_5r35gsek"
2025-09-15 20:25:06.045 wdl.w:ptcp.w:call-trgt-67.t:call-trgt_plot_meth_waterfall INFO Slurm invocation: srun --job-name call-trgt_plot_meth_waterfall --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-67/call-trgt_plot_meth_waterfall/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-67/call-trgt_plot_meth_waterfall/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-67/call-trgt_plot_meth_waterfall/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-67/call-trgt_plot_meth_waterfall/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-67/call-trgt_genotype/out/m84036_250809_035451_s4.bc2164.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2164.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-67/call-trgt_genotype/out/m84036_250809_035451_s4.bc2164.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2164.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-67/call-trgt_genotype/out/m84036_250809_035451_s4.bc2164.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2164.trgt.vcf:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-67/call-trgt_plot_meth_waterfall/_singularity_tmpdir_5r35gsek/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-67/call-trgt_plot_meth_waterfall/_singularity_tmpdir_5r35gsek/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:06.048 wdl.w:ptcp NOTICE finish :: job: "call-tar_outputs-00"
2025-09-15 20:25:06.048 wdl.w:ptcp INFO output :: job: "call-tar_outputs-00", values: {"sample_tarball": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-00/out/m84036_250809_035451_s4.bc2097.tar"}
2025-09-15 20:25:06.050 wdl.w:ptcp.w:call-trgt-67.t:call-trgt_plot_motifs_allele INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-67/call-trgt_plot_motifs_allele/_singularity_tmpdir_62qryzge"
2025-09-15 20:25:06.051 wdl.w:ptcp.w:call-trgt-67.t:call-trgt_plot_motifs_allele INFO Slurm invocation: srun --job-name call-trgt_plot_motifs_allele --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-67/call-trgt_plot_motifs_allele/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-67/call-trgt_plot_motifs_allele/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-67/call-trgt_plot_motifs_allele/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-67/call-trgt_plot_motifs_allele/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-67/call-trgt_genotype/out/m84036_250809_035451_s4.bc2164.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2164.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-67/call-trgt_genotype/out/m84036_250809_035451_s4.bc2164.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2164.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-67/call-trgt_genotype/out/m84036_250809_035451_s4.bc2164.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2164.trgt.vcf:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-67/call-trgt_plot_motifs_allele/_singularity_tmpdir_62qryzge/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-67/call-trgt_plot_motifs_allele/_singularity_tmpdir_62qryzge/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:06.056 wdl.w:ptcp.w:call-paraphase-22.t:call-call_f8 NOTICE task setup :: name: "call_f8", source: "./paraphase.wdl", line: 232, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-22/call-call_f8", thread: 140607674631744
2025-09-15 20:25:06.070 wdl.w:ptcp.w:call-trgt-67.t:call-trgt_plot_meth_waterfall NOTICE slurm_singularity run :: pid: 1204593, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-67/call-trgt_plot_meth_waterfall/slurm_singularity.log.txt"
2025-09-15 20:25:06.070 wdl.w:ptcp.w:call-trgt-67.t:call-trgt_plot_motifs_allele NOTICE slurm_singularity run :: pid: 1204594, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-67/call-trgt_plot_motifs_allele/slurm_singularity.log.txt"
2025-09-15 20:25:06.076 wdl.w:ptcp.w:call-paraphase-22.t:call-call_f8 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:06.076 wdl.w:ptcp.w:call-paraphase-22.t:call-call_f8 INFO input :: name: "genome_version", value: "38"
2025-09-15 20:25:06.076 wdl.w:ptcp.w:call-paraphase-22.t:call-call_f8 INFO input :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2119"
2025-09-15 20:25:06.077 wdl.w:ptcp.w:call-paraphase-22.t:call-call_f8 INFO input :: name: "paraphase_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2119.paraphase.bam.bai"
2025-09-15 20:25:06.077 wdl.w:ptcp.w:call-paraphase-22.t:call-call_f8 INFO input :: name: "paraphase_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2119.paraphase.bam"
2025-09-15 20:25:06.077 wdl.w:ptcp.w:call-paraphase-22.t:call-call_f8 INFO input :: name: "sex", value: "F"
2025-09-15 20:25:06.077 wdl.w:ptcp.w:call-paraphase-22.t:call-call_f8 INFO eval :: name: "threads", value: 1
2025-09-15 20:25:06.077 wdl.w:ptcp.w:call-paraphase-22.t:call-call_f8 INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:25:06.077 wdl.w:ptcp.w:call-paraphase-22.t:call-call_f8 INFO eval :: name: "disk_size", value: 11
2025-09-15 20:25:06.077 wdl.w:ptcp.w:call-paraphase-22.t:call-call_f8 INFO eval :: name: "sample_sex", value: "F"
2025-09-15 20:25:06.078 wdl.w:ptcp.w:call-paraphase-22.t:call-call_f8 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:06.078 wdl.w:ptcp.w:call-paraphase-22.t:call-call_f8 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:06.078 wdl.w:ptcp.w:call-paraphase-22.t:call-call_f8 INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:25:06.078 wdl.w:ptcp.w:call-paraphase-22.t:call-call_f8 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:06.096 wdl.w:ptcp.w:call-trgt-67.t:call-trgt_plot_motifs_waterfall INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-67/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_h00nhhzv"
2025-09-15 20:25:06.097 wdl.w:ptcp.w:call-trgt-67.t:call-trgt_plot_motifs_waterfall INFO Slurm invocation: srun --job-name call-trgt_plot_motifs_waterfall --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-67/call-trgt_plot_motifs_waterfall/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-67/call-trgt_plot_motifs_waterfall/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-67/call-trgt_plot_motifs_waterfall/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-67/call-trgt_plot_motifs_waterfall/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-67/call-trgt_genotype/out/m84036_250809_035451_s4.bc2164.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2164.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-67/call-trgt_genotype/out/m84036_250809_035451_s4.bc2164.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2164.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-67/call-trgt_genotype/out/m84036_250809_035451_s4.bc2164.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2164.trgt.vcf:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-67/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_h00nhhzv/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-67/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_h00nhhzv/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:06.116 wdl.w:ptcp.w:call-trgt-67.t:call-trgt_plot_motifs_waterfall NOTICE slurm_singularity run :: pid: 1204597, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-67/call-trgt_plot_motifs_waterfall/slurm_singularity.log.txt"
2025-09-15 20:25:06.124 wdl.w:ptcp.w:call-paraphase-22.t:call-call_f8 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 8, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-22/call-call_f8/_singularity_tmpdir_uhm5mifx"
2025-09-15 20:25:06.124 wdl.w:ptcp.w:call-paraphase-22.t:call-call_f8 INFO Slurm invocation: srun --job-name call-call_f8 --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-22/call-call_f8/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-22/call-call_f8/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-22/call-call_f8/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-22/call-call_f8/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-22/call-run_paraphase/out/m84036_250809_035451_s4.bc2119_paraphase/m84036_250809_035451_s4.bc2119.paraphase.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2119.paraphase.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-22/call-run_paraphase/out/m84036_250809_035451_s4.bc2119_paraphase/m84036_250809_035451_s4.bc2119.paraphase.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2119.paraphase.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-22/call-call_f8/_singularity_tmpdir_uhm5mifx/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-22/call-call_f8/_singularity_tmpdir_uhm5mifx/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:06.139 wdl.w:ptcp.w:call-paraphase-22.t:call-call_f8 NOTICE slurm_singularity run :: pid: 1204602, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-22/call-call_f8/slurm_singularity.log.txt"
2025-09-15 20:25:06.161 wdl.w:ptcp.w:call-trgt-49.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:25:01 [ERROR] - No reads found for TRID=PRTS_ARX
2025-09-15 20:25:06.161 wdl.w:ptcp.w:call-trgt-49.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:25:01 [ERROR] - No reads found for TRID=EIEE1_ARX
2025-09-15 20:25:06.165 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_motifs_allele INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2152.motifs_allele.trgt_plots.zip"
2025-09-15 20:25:06.248 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_meth_waterfall INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2152.meth_waterfall.trgt_plots.zip"
2025-09-15 20:25:06.251 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_motifs_allele NOTICE done
2025-09-15 20:25:06.253 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_genotype.slurm_singularity INFO srun: job 51797894 queued and waiting for resources
2025-09-15 20:25:06.253 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_genotype.slurm_singularity INFO srun: job 51797894 has been allocated resources
2025-09-15 20:25:06.253 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_genotype.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:06.257 wdl.w:ptcp.w:call-trgt-55 NOTICE finish :: job: "call-trgt_plot_motifs_allele"
2025-09-15 20:25:06.258 wdl.w:ptcp.w:call-trgt-55 INFO output :: job: "call-trgt_plot_motifs_allele", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-55/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2152.motifs_allele.trgt_plots.zip"}
2025-09-15 20:25:06.258 wdl.w:ptcp.w:call-trgt-55 INFO visit :: node: "output-images_motifs_allele", values: {"images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-55/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2152.motifs_allele.trgt_plots.zip"}
2025-09-15 20:25:06.263 wdl.w:ptcp.w:call-sawfish-79.t:call-run_sawfish NOTICE task setup :: name: "run_sawfish", source: "./sawfish.wdl", line: 83, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-79/call-run_sawfish", thread: 140608236680768
2025-09-15 20:25:06.283 wdl.w:ptcp.w:call-sawfish-79.t:call-run_sawfish INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:06.283 wdl.w:ptcp.w:call-sawfish-79.t:call-run_sawfish INFO input :: name: "genome_version", value: "38"
2025-09-15 20:25:06.283 wdl.w:ptcp.w:call-sawfish-79.t:call-run_sawfish INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:25:06.283 wdl.w:ptcp.w:call-sawfish-79.t:call-run_sawfish INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:25:06.283 wdl.w:ptcp.w:call-sawfish-79.t:call-run_sawfish INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2176.mapped.bam.bai"
2025-09-15 20:25:06.283 wdl.w:ptcp.w:call-sawfish-79.t:call-run_sawfish INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2176.mapped.bam"
2025-09-15 20:25:06.283 wdl.w:ptcp.w:call-sawfish-79.t:call-run_sawfish INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2176"
2025-09-15 20:25:06.283 wdl.w:ptcp.w:call-sawfish-79.t:call-run_sawfish INFO eval :: name: "mem_gb", value: 32
2025-09-15 20:25:06.283 wdl.w:ptcp.w:call-sawfish-79.t:call-run_sawfish INFO eval :: name: "threads", value: 16
2025-09-15 20:25:06.284 wdl.w:ptcp.w:call-sawfish-79.t:call-run_sawfish INFO eval :: name: "disk_size", value: 30
2025-09-15 20:25:06.284 wdl.w:ptcp.w:call-sawfish-79.t:call-run_sawfish INFO eval :: name: "discover_dirname", value: "m84036_250809_035451_s4.bc2176_sawfish_discover"
2025-09-15 20:25:06.284 wdl.w:ptcp.w:call-sawfish-79.t:call-run_sawfish INFO eval :: name: "call_dirname", value: "m84036_250809_035451_s4.bc2176_sawfish"
2025-09-15 20:25:06.284 wdl.w:ptcp.w:call-sawfish-79.t:call-run_sawfish INFO eval :: name: "minimap2_bam_filename", value: "m84036_250809_035451_s4.bc2176.minimap2.bam"
2025-09-15 20:25:06.285 wdl.w:ptcp.w:call-sawfish-79.t:call-run_sawfish INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 16, memory_reservation: 32000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:06.285 wdl.w:ptcp.w:call-sawfish-79.t:call-run_sawfish WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:06.286 wdl.w:ptcp.w:call-sawfish-79.t:call-run_sawfish INFO provisioned :: seconds_waited: 0, cpu: 16, mem_bytes: 32000000000
2025-09-15 20:25:06.286 wdl.w:ptcp.w:call-sawfish-79.t:call-run_sawfish INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:06.322 wdl.w:ptcp.w:call-trgt-55.t:call-trgt_plot_meth_waterfall NOTICE done
2025-09-15 20:25:06.328 wdl.w:ptcp.w:call-trgt-55 NOTICE finish :: job: "call-trgt_plot_meth_waterfall"
2025-09-15 20:25:06.328 wdl.w:ptcp.w:call-trgt-55 INFO output :: job: "call-trgt_plot_meth_waterfall", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-55/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2152.meth_waterfall.trgt_plots.zip"}
2025-09-15 20:25:06.328 wdl.w:ptcp.w:call-trgt-55 INFO visit :: node: "output-images_meth_waterfall", values: {"images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-55/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2152.meth_waterfall.trgt_plots.zip"}
2025-09-15 20:25:06.328 wdl.w:ptcp.w:call-trgt-55 INFO visit :: node: "outputs", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-55/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2152.motifs_waterfall.trgt_plots.zip", "images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-55/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2152.meth_allele.trgt_plots.zip", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-55/call-trgt_genotype/out/m84036_250809_035451_s4.bc2152.trgt.sorted.spanning.bam.bai", "images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-55/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2152.motifs_allele.trgt_plots.zip", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-55/call-trgt_genotype/out/m84036_250809_035451_s4.bc2152.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-55/call-trgt_genotype/out/m84036_250809_035451_s4.bc2152.trgt.vcf", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-55/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2152.repeats.bam", "images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-55/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2152.meth_waterfall.trgt_plots.zip", "reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-55/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2152.repeats.bam.bai"}
2025-09-15 20:25:06.337 wdl.w:ptcp.w:call-paraphase-40.t:call-call_f8 NOTICE task setup :: name: "call_f8", source: "./paraphase.wdl", line: 232, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-40/call-call_f8", thread: 140613068518976
2025-09-15 20:25:06.361 wdl.w:ptcp.w:call-sawfish-79.t:call-run_sawfish INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 10, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-79/call-run_sawfish/_singularity_tmpdir_7rec8ro0"
2025-09-15 20:25:06.362 wdl.w:ptcp.w:call-sawfish-79.t:call-run_sawfish INFO Slurm invocation: srun --job-name call-run_sawfish --partition compute,compute9 --cpus-per-task 16 --mem 30518M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-79/call-run_sawfish/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-79/call-run_sawfish/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-79/call-run_sawfish/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-79/call-run_sawfish/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-79/out/m84036_250809_035451_s4.bc2176.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2176.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-79/out/m84036_250809_035451_s4.bc2176.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2176.mapped.bam:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-79/call-run_sawfish/_singularity_tmpdir_7rec8ro0/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-79/call-run_sawfish/_singularity_tmpdir_7rec8ro0/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:06.366 wdl.w:ptcp.w:call-paraphase-40.t:call-call_f8 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:06.366 wdl.w:ptcp.w:call-paraphase-40.t:call-call_f8 INFO input :: name: "genome_version", value: "38"
2025-09-15 20:25:06.366 wdl.w:ptcp.w:call-paraphase-40.t:call-call_f8 INFO input :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2137"
2025-09-15 20:25:06.366 wdl.w:ptcp.w:call-paraphase-40.t:call-call_f8 INFO input :: name: "paraphase_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2137.paraphase.bam.bai"
2025-09-15 20:25:06.367 wdl.w:ptcp.w:call-paraphase-40.t:call-call_f8 INFO input :: name: "paraphase_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2137.paraphase.bam"
2025-09-15 20:25:06.367 wdl.w:ptcp.w:call-paraphase-40.t:call-call_f8 INFO input :: name: "sex", value: "F"
2025-09-15 20:25:06.367 wdl.w:ptcp.w:call-paraphase-40.t:call-call_f8 INFO eval :: name: "threads", value: 1
2025-09-15 20:25:06.367 wdl.w:ptcp.w:call-paraphase-40.t:call-call_f8 INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:25:06.367 wdl.w:ptcp.w:call-paraphase-40.t:call-call_f8 INFO eval :: name: "disk_size", value: 11
2025-09-15 20:25:06.367 wdl.w:ptcp.w:call-paraphase-40.t:call-call_f8 INFO eval :: name: "sample_sex", value: "F"
2025-09-15 20:25:06.368 wdl.w:ptcp.w:call-paraphase-40.t:call-call_f8 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:06.368 wdl.w:ptcp.w:call-paraphase-40.t:call-call_f8 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:06.368 wdl.w:ptcp.w:call-paraphase-40.t:call-call_f8 INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:25:06.368 wdl.w:ptcp.w:call-paraphase-40.t:call-call_f8 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:06.382 wdl.w:ptcp.w:call-trgt-49.t:call-trgt_plot_motifs_waterfall INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2146.motifs_waterfall.trgt_plots.zip"
2025-09-15 20:25:06.388 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:04 [ERROR] - No reads found for TRID=SCA8_ATXN8OS
2025-09-15 20:25:06.389 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:04 [ERROR] - No reads found for TRID=SCA3_ATXN3
2025-09-15 20:25:06.389 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:04 [ERROR] - No reads found for TRID=SCA31_BEAN1
2025-09-15 20:25:06.389 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:04 [ERROR] - No reads found for TRID=HDL2_JPH3
2025-09-15 20:25:06.389 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:04 [ERROR] - No reads found for TRID=SCA4_ZFHX3
2025-09-15 20:25:06.389 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:04 [ERROR] - No reads found for TRID=SCA6_CACNA1A
2025-09-15 20:25:06.389 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:04 [ERROR] - No reads found for TRID=FECD3_TCF4
2025-09-15 20:25:06.389 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:04 [ERROR] - No reads found for TRID=SD5_HOXD13
2025-09-15 20:25:06.389 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:04 [ERROR] - No reads found for TRID=OPDM2_GIPC1
2025-09-15 20:25:06.389 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:04 [ERROR] - No reads found for TRID=FRA2A_AFF3
2025-09-15 20:25:06.389 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:04 [ERROR] - No reads found for TRID=SCA10_ATXN10
2025-09-15 20:25:06.389 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:04 [ERROR] - No reads found for TRID=SCA7_ATXN7
2025-09-15 20:25:06.390 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:04 [ERROR] - No reads found for TRID=EPM1_CSTB
2025-09-15 20:25:06.390 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:04 [ERROR] - No reads found for TRID=SCA36_NOP56
2025-09-15 20:25:06.390 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:05 [ERROR] - No reads found for TRID=CJD_PRNP
2025-09-15 20:25:06.390 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:05 [ERROR] - No reads found for TRID=SCA12_PPP2R2B
2025-09-15 20:25:06.390 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:05 [ERROR] - No reads found for TRID=OPDM1_LRP12
2025-09-15 20:25:06.390 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:05 [ERROR] - No reads found for TRID=FAME1_SAMD12
2025-09-15 20:25:06.390 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:05 [ERROR] - No reads found for TRID=SCA1_ATXN1
2025-09-15 20:25:06.398 wdl.w:ptcp.w:call-trgt-49.t:call-trgt_plot_meth_waterfall INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2146.meth_waterfall.trgt_plots.zip"
2025-09-15 20:25:06.413 wdl.w:ptcp.w:call-sawfish-79.t:call-run_sawfish NOTICE slurm_singularity run :: pid: 1204630, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-79/call-run_sawfish/slurm_singularity.log.txt"
2025-09-15 20:25:06.428 wdl.w:ptcp.w:call-paraphase-40.t:call-call_f8 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 8, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-40/call-call_f8/_singularity_tmpdir_nlzb_450"
2025-09-15 20:25:06.428 wdl.w:ptcp.w:call-paraphase-40.t:call-call_f8 INFO Slurm invocation: srun --job-name call-call_f8 --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-40/call-call_f8/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-40/call-call_f8/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-40/call-call_f8/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-40/call-call_f8/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-40/call-run_paraphase/out/m84036_250809_035451_s4.bc2137_paraphase/m84036_250809_035451_s4.bc2137.paraphase.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2137.paraphase.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-40/call-run_paraphase/out/m84036_250809_035451_s4.bc2137_paraphase/m84036_250809_035451_s4.bc2137.paraphase.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2137.paraphase.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-40/call-call_f8/_singularity_tmpdir_nlzb_450/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-40/call-call_f8/_singularity_tmpdir_nlzb_450/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:06.441 wdl.w:ptcp.w:call-paraphase-40.t:call-call_f8 NOTICE slurm_singularity run :: pid: 1204632, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-40/call-call_f8/slurm_singularity.log.txt"
2025-09-15 20:25:06.464 wdl.w:ptcp.w:call-trgt-55 NOTICE done
2025-09-15 20:25:06.469 wdl.w:ptcp NOTICE finish :: job: "call-trgt-55"
2025-09-15 20:25:06.469 wdl.w:ptcp INFO output :: job: "call-trgt-55", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-55/out/m84036_250809_035451_s4.bc2152.motifs_waterfall.trgt_plots.zip", "images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-55/out/m84036_250809_035451_s4.bc2152.meth_allele.trgt_plots.zip", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-55/out/m84036_250809_035451_s4.bc2152.trgt.sorted.spanning.bam.bai", "images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-55/out/m84036_250809_035451_s4.bc2152.motifs_allele.trgt_plots.zip", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-55/out/m84036_250809_035451_s4.bc2152.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-55/out/m84036_250809_035451_s4.bc2152.trgt.vcf", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-55/out/m84036_250809_035451_s4.bc2152.repeats.bam", "images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-55/out/m84036_250809_035451_s4.bc2152.meth_waterfall.trgt_plots.zip", "reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-55/out/m84036_250809_035451_s4.bc2152.repeats.bam.bai"}
2025-09-15 20:25:06.476 wdl.w:ptcp.w:call-sawfish-72 NOTICE workflow start :: name: "sawfish", source: "./sawfish.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-72"
2025-09-15 20:25:06.493 wdl.w:ptcp.w:call-sawfish-72 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:25:06.494 wdl.w:ptcp.w:call-sawfish-72 INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:25:06.494 wdl.w:ptcp.w:call-sawfish-72 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-72/out/m84036_250809_035451_s4.bc2169.mapped.bam"}
2025-09-15 20:25:06.494 wdl.w:ptcp.w:call-sawfish-72 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-72/out/m84036_250809_035451_s4.bc2169.mapped.bam.bai"}
2025-09-15 20:25:06.494 wdl.w:ptcp.w:call-sawfish-72 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:25:06.494 wdl.w:ptcp.w:call-sawfish-72 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:25:06.494 wdl.w:ptcp.w:call-sawfish-72 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2169"}
2025-09-15 20:25:06.495 wdl.w:ptcp.w:call-sawfish-72 NOTICE ready :: job: "call-run_sawfish", callee: "run_sawfish"
2025-09-15 20:25:06.495 wdl.w:ptcp.w:call-sawfish-72 INFO input :: job: "call-run_sawfish", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-72/out/m84036_250809_035451_s4.bc2169.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-72/out/m84036_250809_035451_s4.bc2169.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2169"}
2025-09-15 20:25:06.513 wdl.w:ptcp.w:call-trgt-49.t:call-trgt_plot_motifs_waterfall NOTICE done
2025-09-15 20:25:06.518 wdl.w:ptcp.w:call-trgt-49 NOTICE finish :: job: "call-trgt_plot_motifs_waterfall"
2025-09-15 20:25:06.518 wdl.w:ptcp.w:call-trgt-49 INFO output :: job: "call-trgt_plot_motifs_waterfall", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-49/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2146.motifs_waterfall.trgt_plots.zip"}
2025-09-15 20:25:06.519 wdl.w:ptcp.w:call-trgt-49 INFO visit :: node: "output-images_motifs_waterfall", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-49/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2146.motifs_waterfall.trgt_plots.zip"}
2025-09-15 20:25:06.526 wdl.w:ptcp.w:call-paraphase-53.t:call-call_f8 NOTICE task setup :: name: "call_f8", source: "./paraphase.wdl", line: 232, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-53/call-call_f8", thread: 140607649453632
2025-09-15 20:25:06.552 wdl.w:ptcp.w:call-paraphase-53.t:call-call_f8 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:06.552 wdl.w:ptcp.w:call-paraphase-53.t:call-call_f8 INFO input :: name: "genome_version", value: "38"
2025-09-15 20:25:06.552 wdl.w:ptcp.w:call-paraphase-53.t:call-call_f8 INFO input :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2150"
2025-09-15 20:25:06.552 wdl.w:ptcp.w:call-paraphase-53.t:call-call_f8 INFO input :: name: "paraphase_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2150.paraphase.bam.bai"
2025-09-15 20:25:06.552 wdl.w:ptcp.w:call-paraphase-53.t:call-call_f8 INFO input :: name: "paraphase_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2150.paraphase.bam"
2025-09-15 20:25:06.552 wdl.w:ptcp.w:call-paraphase-53.t:call-call_f8 INFO input :: name: "sex", value: "F"
2025-09-15 20:25:06.553 wdl.w:ptcp.w:call-paraphase-53.t:call-call_f8 INFO eval :: name: "threads", value: 1
2025-09-15 20:25:06.553 wdl.w:ptcp.w:call-paraphase-53.t:call-call_f8 INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:25:06.553 wdl.w:ptcp.w:call-paraphase-53.t:call-call_f8 INFO eval :: name: "disk_size", value: 11
2025-09-15 20:25:06.553 wdl.w:ptcp.w:call-paraphase-53.t:call-call_f8 INFO eval :: name: "sample_sex", value: "F"
2025-09-15 20:25:06.553 wdl.w:ptcp.w:call-paraphase-53.t:call-call_f8 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:06.554 wdl.w:ptcp.w:call-paraphase-53.t:call-call_f8 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:06.554 wdl.w:ptcp.w:call-paraphase-53.t:call-call_f8 INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:25:06.554 wdl.w:ptcp.w:call-paraphase-53.t:call-call_f8 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:06.558 wdl.w:ptcp.w:call-trgt-49.t:call-trgt_plot_meth_waterfall NOTICE done
2025-09-15 20:25:06.563 wdl.w:ptcp.w:call-trgt-49 NOTICE finish :: job: "call-trgt_plot_meth_waterfall"
2025-09-15 20:25:06.563 wdl.w:ptcp.w:call-trgt-49 INFO output :: job: "call-trgt_plot_meth_waterfall", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-49/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2146.meth_waterfall.trgt_plots.zip"}
2025-09-15 20:25:06.563 wdl.w:ptcp.w:call-trgt-49 INFO visit :: node: "output-images_meth_waterfall", values: {"images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-49/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2146.meth_waterfall.trgt_plots.zip"}
2025-09-15 20:25:06.564 wdl.w:ptcp.w:call-trgt-49 INFO visit :: node: "outputs", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-49/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2146.motifs_waterfall.trgt_plots.zip", "images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-49/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2146.meth_allele.trgt_plots.zip", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-49/call-trgt_genotype/out/m84036_250809_035451_s4.bc2146.trgt.sorted.spanning.bam.bai", "images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-49/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2146.motifs_allele.trgt_plots.zip", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-49/call-trgt_genotype/out/m84036_250809_035451_s4.bc2146.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-49/call-trgt_genotype/out/m84036_250809_035451_s4.bc2146.trgt.vcf", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-49/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2146.repeats.bam", "images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-49/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2146.meth_waterfall.trgt_plots.zip", "reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-49/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2146.repeats.bam.bai"}
2025-09-15 20:25:06.568 wdl.w:ptcp.w:call-paraphase-41.t:call-call_f8 NOTICE task setup :: name: "call_f8", source: "./paraphase.wdl", line: 232, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-41/call-call_f8", thread: 140609838900800
2025-09-15 20:25:06.592 wdl.w:ptcp.w:call-paraphase-41.t:call-call_f8 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:06.593 wdl.w:ptcp.w:call-paraphase-41.t:call-call_f8 INFO input :: name: "genome_version", value: "38"
2025-09-15 20:25:06.593 wdl.w:ptcp.w:call-paraphase-41.t:call-call_f8 INFO input :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2138"
2025-09-15 20:25:06.593 wdl.w:ptcp.w:call-paraphase-41.t:call-call_f8 INFO input :: name: "paraphase_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2138.paraphase.bam.bai"
2025-09-15 20:25:06.593 wdl.w:ptcp.w:call-paraphase-41.t:call-call_f8 INFO input :: name: "paraphase_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2138.paraphase.bam"
2025-09-15 20:25:06.593 wdl.w:ptcp.w:call-paraphase-41.t:call-call_f8 INFO input :: name: "sex", value: "F"
2025-09-15 20:25:06.593 wdl.w:ptcp.w:call-paraphase-41.t:call-call_f8 INFO eval :: name: "threads", value: 1
2025-09-15 20:25:06.593 wdl.w:ptcp.w:call-paraphase-41.t:call-call_f8 INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:25:06.593 wdl.w:ptcp.w:call-paraphase-41.t:call-call_f8 INFO eval :: name: "disk_size", value: 11
2025-09-15 20:25:06.593 wdl.w:ptcp.w:call-paraphase-41.t:call-call_f8 INFO eval :: name: "sample_sex", value: "F"
2025-09-15 20:25:06.594 wdl.w:ptcp.w:call-paraphase-41.t:call-call_f8 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:06.594 wdl.w:ptcp.w:call-paraphase-41.t:call-call_f8 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:06.594 wdl.w:ptcp.w:call-paraphase-41.t:call-call_f8 INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:25:06.594 wdl.w:ptcp.w:call-paraphase-41.t:call-call_f8 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:06.598 wdl.w:ptcp.w:call-sawfish-17.t:call-run_sawfish.stderr VERBOSE [M::mm_idx_gen::60.165*1.56] collected minimizers
2025-09-15 20:25:06.599 wdl.w:ptcp.w:call-sawfish-17.t:call-run_sawfish.stderr VERBOSE [M::mm_idx_gen::71.483*1.78] sorted minimizers
2025-09-15 20:25:06.600 wdl.w:ptcp.w:call-sawfish-17.t:call-run_sawfish.stderr VERBOSE [M::main::71.484*1.78] loaded/built the index for 195 target sequence(s)
2025-09-15 20:25:06.600 wdl.w:ptcp.w:call-sawfish-17.t:call-run_sawfish.stderr VERBOSE [M::mm_mapopt_update::77.726*1.72] mid_occ = 136
2025-09-15 20:25:06.600 wdl.w:ptcp.w:call-sawfish-17.t:call-run_sawfish.stderr VERBOSE [M::mm_idx_stat] kmer size: 19; skip: 19; is_hpc: 0; #seq: 195
2025-09-15 20:25:06.600 wdl.w:ptcp.w:call-sawfish-17.t:call-run_sawfish.stderr VERBOSE [M::mm_idx_stat::82.841*1.68] distinct minimizers: 214664461 (92.23% are singletons); average occurrences: 1.372; average spacing: 10.529; total length: 3099922541
2025-09-15 20:25:06.600 wdl.w:ptcp.w:call-sawfish-17.t:call-run_sawfish.stderr VERBOSE [M::main] Version: 2.26-r1175
2025-09-15 20:25:06.600 wdl.w:ptcp.w:call-sawfish-17.t:call-run_sawfish.stderr VERBOSE [M::main] CMD: /opt/pacbio/smrttools/install/smrtlink-release_25.1.0.257715/bundles/smrttools/install/smrttools-release_25.1.0.257715/private/thirdparty/minimap2/minimap2_2.26-pacbio2/binwrap/../../../../../private/thirdparty/minimap2/minimap2_2.26-pacbio2/bin/minimap2 -a -y -x map-hifi -Y -E 1,0 /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa -
2025-09-15 20:25:06.600 wdl.w:ptcp.w:call-sawfish-17.t:call-run_sawfish.stderr VERBOSE [M::main] Real time: 83.262 sec; CPU: 139.210 sec; Peak RSS: 11.886 GB
2025-09-15 20:25:06.600 wdl.w:ptcp.w:call-sawfish-17.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:54][sawfish][INFO] Starting sawfish 2.0.3
2025-09-15 20:25:06.600 wdl.w:ptcp.w:call-sawfish-17.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:54][sawfish][INFO] cmdline: sawfish discover --disable-cnv --threads 16 --ref /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa --bam m84036_250809_035451_s4.bc2114.minimap2.bam --output-dir m84036_250809_035451_s4.bc2114_sawfish_discover
2025-09-15 20:25:06.600 wdl.w:ptcp.w:call-sawfish-17.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:54][sawfish][INFO] Running on 16 threads
2025-09-15 20:25:06.600 wdl.w:ptcp.w:call-sawfish-17.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:54][sawfish][INFO] Writing discover settings to file: 'm84036_250809_035451_s4.bc2114_sawfish_discover/discover.settings.json'
2025-09-15 20:25:06.600 wdl.w:ptcp.w:call-sawfish-17.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:54][sawfish][INFO] Reading reference genome from file '/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa'
2025-09-15 20:25:06.600 wdl.w:ptcp.w:call-sawfish-17.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:00][sawfish][INFO] Processing alignment file '/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2114.minimap2.bam'
2025-09-15 20:25:06.600 wdl.w:ptcp.w:call-sawfish-17.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:00][sawfish][INFO] Finished processing all alignments
2025-09-15 20:25:06.600 wdl.w:ptcp.w:call-sawfish-17.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:01][sawfish][INFO] Writing depth bins to binary file: 'm84036_250809_035451_s4.bc2114_sawfish_discover/depth.mpack'
2025-09-15 20:25:06.600 wdl.w:ptcp.w:call-sawfish-17.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:01][sawfish][INFO] Writing max sv depth genome regions to bed file: 'm84036_250809_035451_s4.bc2114_sawfish_discover/max.depth.bed'
2025-09-15 20:25:06.601 wdl.w:ptcp.w:call-sawfish-17.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:01][sawfish][INFO] Completing breakpoint observation clustering
2025-09-15 20:25:06.601 wdl.w:ptcp.w:call-sawfish-17.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:01][sawfish][INFO] Finished breakpoint observation clustering
2025-09-15 20:25:06.601 wdl.w:ptcp.w:call-sawfish-17.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:01][sawfish][INFO] Consolidating adjacent indel candidates
2025-09-15 20:25:06.601 wdl.w:ptcp.w:call-sawfish-17.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:01][sawfish][INFO] Finding large insertion candidates
2025-09-15 20:25:06.601 wdl.w:ptcp.w:call-sawfish-17.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:01][sawfish][INFO] Writing breakpoint_cluster debug bed file: 'm84036_250809_035451_s4.bc2114_sawfish_discover/debug.breakpoint_clusters.bed'
2025-09-15 20:25:06.601 wdl.w:ptcp.w:call-sawfish-17.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:01][sawfish][INFO] Refining SV Candidates
2025-09-15 20:25:06.601 wdl.w:ptcp.w:call-sawfish-17.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:01][sawfish][INFO] Writing debug assembly region bed file: 'm84036_250809_035451_s4.bc2114_sawfish_discover/assembly.regions.bed'
2025-09-15 20:25:06.601 wdl.w:ptcp.w:call-sawfish-17.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:01][sawfish][INFO] Starting refinement of breakpoint evidence clusters
2025-09-15 20:25:06.601 wdl.w:ptcp.w:call-sawfish-17.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:01][sawfish][INFO] Finished refining all breakpoint evidence clusters
2025-09-15 20:25:06.601 wdl.w:ptcp.w:call-sawfish-17.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:01][sawfish][INFO] Writing all contig alignments to bam file: 'm84036_250809_035451_s4.bc2114_sawfish_discover/contig.alignment.bam'
2025-09-15 20:25:06.601 wdl.w:ptcp.w:call-sawfish-17.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:01][sawfish][INFO] Writing candidate structural variants to file: 'm84036_250809_035451_s4.bc2114_sawfish_discover/candidate.sv.bcf'
2025-09-15 20:25:06.601 wdl.w:ptcp.w:call-sawfish-17.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:01][sawfish][INFO] Writing run statistics to file: 'm84036_250809_035451_s4.bc2114_sawfish_discover/run.stats.json'
2025-09-15 20:25:06.601 wdl.w:ptcp.w:call-sawfish-17.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:01][sawfish][INFO] sawfish completed. Total Runtime: 00:00:06.296
2025-09-15 20:25:06.604 wdl.w:ptcp.w:call-paraphase-53.t:call-call_f8 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 8, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-53/call-call_f8/_singularity_tmpdir_viocskk7"
2025-09-15 20:25:06.604 wdl.w:ptcp.w:call-paraphase-53.t:call-call_f8 INFO Slurm invocation: srun --job-name call-call_f8 --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-53/call-call_f8/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-53/call-call_f8/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-53/call-call_f8/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-53/call-call_f8/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-53/call-run_paraphase/out/m84036_250809_035451_s4.bc2150_paraphase/m84036_250809_035451_s4.bc2150.paraphase.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2150.paraphase.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-53/call-run_paraphase/out/m84036_250809_035451_s4.bc2150_paraphase/m84036_250809_035451_s4.bc2150.paraphase.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2150.paraphase.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-53/call-call_f8/_singularity_tmpdir_viocskk7/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-53/call-call_f8/_singularity_tmpdir_viocskk7/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:06.616 wdl.w:ptcp.w:call-trgt-58.t:call-trgt_plot_meth_allele INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2155.meth_allele.trgt_plots.zip"
2025-09-15 20:25:06.630 wdl.w:ptcp.w:call-paraphase-53.t:call-call_f8 NOTICE slurm_singularity run :: pid: 1204646, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-53/call-call_f8/slurm_singularity.log.txt"
2025-09-15 20:25:06.647 wdl.w:ptcp.w:call-paraphase-41.t:call-call_f8 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 8, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-41/call-call_f8/_singularity_tmpdir_x1dtx6q5"
2025-09-15 20:25:06.647 wdl.w:ptcp.w:call-paraphase-41.t:call-call_f8 INFO Slurm invocation: srun --job-name call-call_f8 --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-41/call-call_f8/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-41/call-call_f8/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-41/call-call_f8/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-41/call-call_f8/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-41/call-run_paraphase/out/m84036_250809_035451_s4.bc2138_paraphase/m84036_250809_035451_s4.bc2138.paraphase.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2138.paraphase.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-41/call-run_paraphase/out/m84036_250809_035451_s4.bc2138_paraphase/m84036_250809_035451_s4.bc2138.paraphase.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2138.paraphase.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-41/call-call_f8/_singularity_tmpdir_x1dtx6q5/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-41/call-call_f8/_singularity_tmpdir_x1dtx6q5/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:06.659 wdl.w:ptcp.w:call-paraphase-41.t:call-call_f8 NOTICE slurm_singularity run :: pid: 1204648, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-41/call-call_f8/slurm_singularity.log.txt"
2025-09-15 20:25:06.672 wdl.w:ptcp.w:call-sawfish-26.t:call-run_sawfish INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2123_sawfish/m84036_250809_035451_s4.bc2123.sv.vcf.gz"
2025-09-15 20:25:06.677 wdl.w:ptcp.w:call-sawfish-26.t:call-run_sawfish INFO output :: name: "vcf_tbi", value: "m84036_250809_035451_s4.bc2123_sawfish/m84036_250809_035451_s4.bc2123.sv.vcf.gz.tbi"
2025-09-15 20:25:06.678 wdl.w:ptcp.w:call-sawfish-26.t:call-run_sawfish INFO output :: name: "minimap2_bam", value: "m84036_250809_035451_s4.bc2123.minimap2.bam"
2025-09-15 20:25:06.680 wdl.w:ptcp.w:call-sawfish-26.t:call-run_sawfish INFO output :: name: "minimap2_bam_bai", value: "m84036_250809_035451_s4.bc2123.minimap2.bam.bai"
2025-09-15 20:25:06.682 wdl.w:ptcp.w:call-trgt-49 NOTICE done
2025-09-15 20:25:06.688 wdl.w:ptcp NOTICE finish :: job: "call-trgt-49"
2025-09-15 20:25:06.688 wdl.w:ptcp INFO output :: job: "call-trgt-49", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-49/out/m84036_250809_035451_s4.bc2146.motifs_waterfall.trgt_plots.zip", "images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-49/out/m84036_250809_035451_s4.bc2146.meth_allele.trgt_plots.zip", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-49/out/m84036_250809_035451_s4.bc2146.trgt.sorted.spanning.bam.bai", "images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-49/out/m84036_250809_035451_s4.bc2146.motifs_allele.trgt_plots.zip", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-49/out/m84036_250809_035451_s4.bc2146.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-49/out/m84036_250809_035451_s4.bc2146.trgt.vcf", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-49/out/m84036_250809_035451_s4.bc2146.repeats.bam", "images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-49/out/m84036_250809_035451_s4.bc2146.meth_waterfall.trgt_plots.zip", "reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-49/out/m84036_250809_035451_s4.bc2146.repeats.bam.bai"}
2025-09-15 20:25:06.696 wdl.w:ptcp.w:call-trgt-72 NOTICE workflow start :: name: "trgt", source: "./trgt.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-72"
2025-09-15 20:25:06.706 wdl.w:ptcp.w:call-trgt-58.t:call-trgt_plot_meth_allele NOTICE done
2025-09-15 20:25:06.713 wdl.w:ptcp.w:call-trgt-72 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:25:06.713 wdl.w:ptcp.w:call-trgt-72 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-72/out/m84036_250809_035451_s4.bc2169.mapped.bam"}
2025-09-15 20:25:06.713 wdl.w:ptcp.w:call-trgt-72 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-72/out/m84036_250809_035451_s4.bc2169.mapped.bam.bai"}
2025-09-15 20:25:06.713 wdl.w:ptcp.w:call-trgt-72 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:25:06.713 wdl.w:ptcp.w:call-trgt-72 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:25:06.713 wdl.w:ptcp.w:call-trgt-72 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2169"}
2025-09-15 20:25:06.714 wdl.w:ptcp.w:call-trgt-72 INFO visit :: node: "decl-sex", values: {"sex": "F"}
2025-09-15 20:25:06.714 wdl.w:ptcp.w:call-trgt-72 INFO visit :: node: "decl-trgt_bed", values: {"trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"}
2025-09-15 20:25:06.714 wdl.w:ptcp.w:call-trgt-72 NOTICE ready :: job: "call-get_reads_overlapping_repeats", callee: "get_reads_overlapping_repeats"
2025-09-15 20:25:06.714 wdl.w:ptcp.w:call-trgt-72 INFO input :: job: "call-get_reads_overlapping_repeats", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-72/out/m84036_250809_035451_s4.bc2169.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-72/out/m84036_250809_035451_s4.bc2169.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2169"}
2025-09-15 20:25:06.715 wdl.w:ptcp.w:call-trgt-72 NOTICE ready :: job: "call-trgt_genotype", callee: "trgt_genotype"
2025-09-15 20:25:06.715 wdl.w:ptcp.w:call-trgt-72 INFO input :: job: "call-trgt_genotype", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-72/out/m84036_250809_035451_s4.bc2169.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-72/out/m84036_250809_035451_s4.bc2169.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2169"}
2025-09-15 20:25:06.716 wdl.w:ptcp.w:call-trgt-58 NOTICE finish :: job: "call-trgt_plot_meth_allele"
2025-09-15 20:25:06.716 wdl.w:ptcp.w:call-trgt-58 INFO output :: job: "call-trgt_plot_meth_allele", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-58/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2155.meth_allele.trgt_plots.zip"}
2025-09-15 20:25:06.716 wdl.w:ptcp.w:call-trgt-58 INFO visit :: node: "output-images_meth_allele", values: {"images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-58/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2155.meth_allele.trgt_plots.zip"}
2025-09-15 20:25:06.725 wdl.w:ptcp.w:call-trgt-79.t:call-get_reads_overlapping_repeats NOTICE task setup :: name: "get_reads_overlapping_repeats", source: "./trgt.wdl", line: 182, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-79/call-get_reads_overlapping_repeats", thread: 140611424335424
2025-09-15 20:25:06.744 wdl.w:ptcp.w:call-trgt-79.t:call-get_reads_overlapping_repeats INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:06.744 wdl.w:ptcp.w:call-trgt-79.t:call-get_reads_overlapping_repeats INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:25:06.744 wdl.w:ptcp.w:call-trgt-79.t:call-get_reads_overlapping_repeats INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2176.mapped.bam.bai"
2025-09-15 20:25:06.744 wdl.w:ptcp.w:call-trgt-79.t:call-get_reads_overlapping_repeats INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2176.mapped.bam"
2025-09-15 20:25:06.744 wdl.w:ptcp.w:call-trgt-79.t:call-get_reads_overlapping_repeats INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2176"
2025-09-15 20:25:06.744 wdl.w:ptcp.w:call-trgt-79.t:call-get_reads_overlapping_repeats INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:25:06.744 wdl.w:ptcp.w:call-trgt-79.t:call-get_reads_overlapping_repeats INFO eval :: name: "expand_size", value: 3000
2025-09-15 20:25:06.744 wdl.w:ptcp.w:call-trgt-79.t:call-get_reads_overlapping_repeats INFO eval :: name: "threads", value: 1
2025-09-15 20:25:06.745 wdl.w:ptcp.w:call-trgt-79.t:call-get_reads_overlapping_repeats INFO eval :: name: "expanded_bed_name", value: "m84036_250809_035451_s4.bc2176.expanded.bed"
2025-09-15 20:25:06.745 wdl.w:ptcp.w:call-trgt-79.t:call-get_reads_overlapping_repeats INFO eval :: name: "disk_size", value: 11
2025-09-15 20:25:06.745 wdl.w:ptcp.w:call-trgt-79.t:call-get_reads_overlapping_repeats INFO eval :: name: "output_name", value: "m84036_250809_035451_s4.bc2176.repeats.bam"
2025-09-15 20:25:06.745 wdl.w:ptcp.w:call-trgt-79.t:call-get_reads_overlapping_repeats INFO eval :: name: "index_name", value: "m84036_250809_035451_s4.bc2176.repeats.bam.bai"
2025-09-15 20:25:06.745 wdl.w:ptcp.w:call-trgt-79.t:call-get_reads_overlapping_repeats INFO eval :: name: "output_name_with_index", value: "m84036_250809_035451_s4.bc2176.repeats.bam##idx##m84036_250809_035451_s4.bc2176.repeats.bam.bai"
2025-09-15 20:25:06.745 wdl.w:ptcp.w:call-trgt-79.t:call-get_reads_overlapping_repeats INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:06.745 wdl.w:ptcp.w:call-trgt-79.t:call-get_reads_overlapping_repeats WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:06.746 wdl.w:ptcp.w:call-trgt-79.t:call-get_reads_overlapping_repeats INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:25:06.746 wdl.w:ptcp.w:call-trgt-79.t:call-get_reads_overlapping_repeats INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:06.761 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_plot_motifs_allele INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2139.motifs_allele.trgt_plots.zip"
2025-09-15 20:25:06.775 wdl.w:ptcp.w:call-trgt-68.t:call-trgt_genotype INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2165.trgt.vcf"
2025-09-15 20:25:06.782 wdl.w:ptcp.w:call-trgt-68.t:call-trgt_genotype INFO output :: name: "spanning_bam", value: "m84036_250809_035451_s4.bc2165.trgt.sorted.spanning.bam"
2025-09-15 20:25:06.784 wdl.w:ptcp.w:call-trgt-68.t:call-trgt_genotype INFO output :: name: "spanning_bam_bai", value: "m84036_250809_035451_s4.bc2165.trgt.sorted.spanning.bam.bai"
2025-09-15 20:25:06.830 wdl.w:ptcp.w:call-trgt-79.t:call-get_reads_overlapping_repeats INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 9, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-79/call-get_reads_overlapping_repeats/_singularity_tmpdir_kgalo6uq"
2025-09-15 20:25:06.830 wdl.w:ptcp.w:call-trgt-79.t:call-get_reads_overlapping_repeats INFO Slurm invocation: srun --job-name call-get_reads_overlapping_repeats --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-79/call-get_reads_overlapping_repeats/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-79/call-get_reads_overlapping_repeats/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-79/call-get_reads_overlapping_repeats/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-79/call-get_reads_overlapping_repeats/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-79/out/m84036_250809_035451_s4.bc2176.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2176.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-79/out/m84036_250809_035451_s4.bc2176.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2176.mapped.bam:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-79/call-get_reads_overlapping_repeats/_singularity_tmpdir_kgalo6uq/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-79/call-get_reads_overlapping_repeats/_singularity_tmpdir_kgalo6uq/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:06.833 wdl.w:ptcp.w:call-paraphase-79.t:call-run_paraphase.slurm_singularity INFO srun: job 51797895 queued and waiting for resources
2025-09-15 20:25:06.833 wdl.w:ptcp.w:call-paraphase-79.t:call-run_paraphase.slurm_singularity INFO srun: job 51797895 has been allocated resources
2025-09-15 20:25:06.833 wdl.w:ptcp.w:call-paraphase-79.t:call-run_paraphase.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:06.858 wdl.w:ptcp.w:call-sawfish-26.t:call-run_sawfish NOTICE done
2025-09-15 20:25:06.859 wdl.w:ptcp.w:call-trgt-79.t:call-get_reads_overlapping_repeats NOTICE slurm_singularity run :: pid: 1204666, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-79/call-get_reads_overlapping_repeats/slurm_singularity.log.txt"
2025-09-15 20:25:06.866 wdl.w:ptcp.w:call-sawfish-26 NOTICE finish :: job: "call-run_sawfish"
2025-09-15 20:25:06.866 wdl.w:ptcp.w:call-sawfish-26 INFO output :: job: "call-run_sawfish", values: {"minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-26/call-run_sawfish/out/m84036_250809_035451_s4.bc2123.minimap2.bam.bai", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-26/call-run_sawfish/out/m84036_250809_035451_s4.bc2123.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-26/call-run_sawfish/out/m84036_250809_035451_s4.bc2123_sawfish/m84036_250809_035451_s4.bc2123.sv.vcf.gz.tbi", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-26/call-run_sawfish/out/m84036_250809_035451_s4.bc2123_sawfish/m84036_250809_035451_s4.bc2123.sv.vcf.gz"}
2025-09-15 20:25:06.866 wdl.w:ptcp.w:call-sawfish-26 INFO visit :: node: "output-minimap2_bam", values: {"minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-26/call-run_sawfish/out/m84036_250809_035451_s4.bc2123.minimap2.bam"}
2025-09-15 20:25:06.866 wdl.w:ptcp.w:call-sawfish-26 INFO visit :: node: "output-minimap2_bam_bai", values: {"minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-26/call-run_sawfish/out/m84036_250809_035451_s4.bc2123.minimap2.bam.bai"}
2025-09-15 20:25:06.867 wdl.w:ptcp.w:call-sawfish-26 INFO visit :: node: "output-vcf", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-26/call-run_sawfish/out/m84036_250809_035451_s4.bc2123_sawfish/m84036_250809_035451_s4.bc2123.sv.vcf.gz"}
2025-09-15 20:25:06.867 wdl.w:ptcp.w:call-sawfish-26 INFO visit :: node: "output-vcf_tbi", values: {"vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-26/call-run_sawfish/out/m84036_250809_035451_s4.bc2123_sawfish/m84036_250809_035451_s4.bc2123.sv.vcf.gz.tbi"}
2025-09-15 20:25:06.867 wdl.w:ptcp.w:call-sawfish-26 INFO visit :: node: "outputs", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-26/call-run_sawfish/out/m84036_250809_035451_s4.bc2123_sawfish/m84036_250809_035451_s4.bc2123.sv.vcf.gz", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-26/call-run_sawfish/out/m84036_250809_035451_s4.bc2123.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-26/call-run_sawfish/out/m84036_250809_035451_s4.bc2123_sawfish/m84036_250809_035451_s4.bc2123.sv.vcf.gz.tbi", "minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-26/call-run_sawfish/out/m84036_250809_035451_s4.bc2123.minimap2.bam.bai"}
2025-09-15 20:25:06.875 wdl.w:ptcp.w:call-trgt-79.t:call-trgt_genotype NOTICE task setup :: name: "trgt_genotype", source: "./trgt.wdl", line: 272, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-79/call-trgt_genotype", thread: 140613588604480
2025-09-15 20:25:06.879 wdl.w:ptcp.w:call-trgt-58.t:call-trgt_plot_meth_waterfall INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2155.meth_waterfall.trgt_plots.zip"
2025-09-15 20:25:06.880 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_plot_meth_allele INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2139.meth_allele.trgt_plots.zip"
2025-09-15 20:25:06.880 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_plot_motifs_allele NOTICE done
2025-09-15 20:25:06.892 wdl.w:ptcp.w:call-trgt-68.t:call-trgt_genotype NOTICE done
2025-09-15 20:25:06.894 wdl.w:ptcp.w:call-trgt-53.t:call-trgt_plot_meth_allele INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2150.meth_allele.trgt_plots.zip"
2025-09-15 20:25:06.896 wdl.w:ptcp.w:call-trgt-42 NOTICE finish :: job: "call-trgt_plot_motifs_allele"
2025-09-15 20:25:06.896 wdl.w:ptcp.w:call-trgt-42 INFO output :: job: "call-trgt_plot_motifs_allele", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-42/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2139.motifs_allele.trgt_plots.zip"}
2025-09-15 20:25:06.896 wdl.w:ptcp.w:call-trgt-42 INFO visit :: node: "output-images_motifs_allele", values: {"images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-42/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2139.motifs_allele.trgt_plots.zip"}
2025-09-15 20:25:06.900 wdl.w:ptcp.w:call-trgt-68 NOTICE finish :: job: "call-trgt_genotype"
2025-09-15 20:25:06.900 wdl.w:ptcp.w:call-trgt-68 INFO output :: job: "call-trgt_genotype", values: {"spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-68/call-trgt_genotype/out/m84036_250809_035451_s4.bc2165.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-68/call-trgt_genotype/out/m84036_250809_035451_s4.bc2165.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-68/call-trgt_genotype/out/m84036_250809_035451_s4.bc2165.trgt.vcf"}
2025-09-15 20:25:06.900 wdl.w:ptcp.w:call-trgt-68 NOTICE ready :: job: "call-trgt_plot_meth_allele", callee: "trgt_plot"
2025-09-15 20:25:06.901 wdl.w:ptcp.w:call-trgt-68 INFO input :: job: "call-trgt_plot_meth_allele", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": false, "methylation": true, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-68/call-trgt_genotype/out/m84036_250809_035451_s4.bc2165.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-68/call-trgt_genotype/out/m84036_250809_035451_s4.bc2165.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-68/call-trgt_genotype/out/m84036_250809_035451_s4.bc2165.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2165"}
2025-09-15 20:25:06.901 wdl.w:ptcp.w:call-trgt-68 NOTICE ready :: job: "call-trgt_plot_meth_waterfall", callee: "trgt_plot"
2025-09-15 20:25:06.902 wdl.w:ptcp.w:call-trgt-68 INFO input :: job: "call-trgt_plot_meth_waterfall", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": true, "methylation": true, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-68/call-trgt_genotype/out/m84036_250809_035451_s4.bc2165.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-68/call-trgt_genotype/out/m84036_250809_035451_s4.bc2165.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-68/call-trgt_genotype/out/m84036_250809_035451_s4.bc2165.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2165"}
2025-09-15 20:25:06.902 wdl.w:ptcp.w:call-trgt-68 NOTICE ready :: job: "call-trgt_plot_motifs_allele", callee: "trgt_plot"
2025-09-15 20:25:06.903 wdl.w:ptcp.w:call-trgt-79.t:call-trgt_genotype INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:06.903 wdl.w:ptcp.w:call-trgt-68 INFO input :: job: "call-trgt_plot_motifs_allele", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": false, "methylation": false, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-68/call-trgt_genotype/out/m84036_250809_035451_s4.bc2165.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-68/call-trgt_genotype/out/m84036_250809_035451_s4.bc2165.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-68/call-trgt_genotype/out/m84036_250809_035451_s4.bc2165.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2165"}
2025-09-15 20:25:06.903 wdl.w:ptcp.w:call-trgt-79.t:call-trgt_genotype INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:25:06.903 wdl.w:ptcp.w:call-trgt-79.t:call-trgt_genotype INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:25:06.903 wdl.w:ptcp.w:call-trgt-79.t:call-trgt_genotype INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:25:06.903 wdl.w:ptcp.w:call-trgt-79.t:call-trgt_genotype INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2176.mapped.bam.bai"
2025-09-15 20:25:06.904 wdl.w:ptcp.w:call-trgt-79.t:call-trgt_genotype INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2176.mapped.bam"
2025-09-15 20:25:06.904 wdl.w:ptcp.w:call-trgt-68 NOTICE ready :: job: "call-trgt_plot_motifs_waterfall", callee: "trgt_plot"
2025-09-15 20:25:06.904 wdl.w:ptcp.w:call-trgt-79.t:call-trgt_genotype INFO input :: name: "sex", value: "F"
2025-09-15 20:25:06.904 wdl.w:ptcp.w:call-trgt-68 INFO input :: job: "call-trgt_plot_motifs_waterfall", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": true, "methylation": false, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-68/call-trgt_genotype/out/m84036_250809_035451_s4.bc2165.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-68/call-trgt_genotype/out/m84036_250809_035451_s4.bc2165.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-68/call-trgt_genotype/out/m84036_250809_035451_s4.bc2165.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2165"}
2025-09-15 20:25:06.905 wdl.w:ptcp.w:call-trgt-79.t:call-trgt_genotype INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2176"
2025-09-15 20:25:06.905 wdl.w:ptcp.w:call-trgt-79.t:call-trgt_genotype INFO eval :: name: "mem_gb", value: 16
2025-09-15 20:25:06.905 wdl.w:ptcp.w:call-trgt-79.t:call-trgt_genotype INFO eval :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2176.trgt"
2025-09-15 20:25:06.905 wdl.w:ptcp.w:call-trgt-79.t:call-trgt_genotype INFO eval :: name: "threads", value: 8
2025-09-15 20:25:06.905 wdl.w:ptcp.w:call-trgt-68 INFO visit :: node: "output-spanning_bam", values: {"spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-68/call-trgt_genotype/out/m84036_250809_035451_s4.bc2165.trgt.sorted.spanning.bam"}
2025-09-15 20:25:06.905 wdl.w:ptcp.w:call-paraphase-73.t:call-run_paraphase NOTICE task setup :: name: "run_paraphase", source: "./paraphase.wdl", line: 127, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-73/call-run_paraphase", thread: 140609285244480
2025-09-15 20:25:06.906 wdl.w:ptcp.w:call-trgt-68 INFO visit :: node: "output-spanning_bam_bai", values: {"spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-68/call-trgt_genotype/out/m84036_250809_035451_s4.bc2165.trgt.sorted.spanning.bam.bai"}
2025-09-15 20:25:06.906 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_genotype INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2167.trgt.vcf"
2025-09-15 20:25:06.906 wdl.w:ptcp.w:call-trgt-68 INFO visit :: node: "output-vcf", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-68/call-trgt_genotype/out/m84036_250809_035451_s4.bc2165.trgt.vcf"}
2025-09-15 20:25:06.906 wdl.w:ptcp.w:call-trgt-79.t:call-trgt_genotype INFO eval :: name: "disk_size", value: 27
2025-09-15 20:25:06.907 wdl.w:ptcp.w:call-trgt-79.t:call-trgt_genotype INFO eval :: name: "karyotype", value: "XX"
2025-09-15 20:25:06.907 wdl.w:ptcp.w:call-trgt-79.t:call-trgt_genotype INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 8, memory_reservation: 16000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:06.908 wdl.w:ptcp.w:call-trgt-79.t:call-trgt_genotype WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:06.908 wdl.w:ptcp.w:call-trgt-79.t:call-trgt_genotype INFO provisioned :: seconds_waited: 0, cpu: 8, mem_bytes: 16000000000
2025-09-15 20:25:06.908 wdl.w:ptcp.w:call-trgt-79.t:call-trgt_genotype INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:06.909 wdl.w:ptcp.w:call-paraphase-56.t:call-call_f8.slurm_singularity INFO srun: job 51797896 queued and waiting for resources
2025-09-15 20:25:06.909 wdl.w:ptcp.w:call-paraphase-56.t:call-call_f8.slurm_singularity INFO srun: job 51797896 has been allocated resources
2025-09-15 20:25:06.909 wdl.w:ptcp.w:call-paraphase-56.t:call-call_f8.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:06.910 wdl.w:ptcp.w:call-sawfish-73.t:call-run_sawfish NOTICE task setup :: name: "run_sawfish", source: "./sawfish.wdl", line: 83, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-73/call-run_sawfish", thread: 140609276851776
2025-09-15 20:25:06.912 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_genotype INFO output :: name: "spanning_bam", value: "m84036_250809_035451_s4.bc2167.trgt.sorted.spanning.bam"
2025-09-15 20:25:06.914 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_genotype INFO output :: name: "spanning_bam_bai", value: "m84036_250809_035451_s4.bc2167.trgt.sorted.spanning.bam.bai"
2025-09-15 20:25:06.939 wdl.w:ptcp.w:call-paraphase-73.t:call-run_paraphase INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:06.939 wdl.w:ptcp.w:call-paraphase-73.t:call-run_paraphase INFO input :: name: "annotation_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf"
2025-09-15 20:25:06.939 wdl.w:ptcp.w:call-sawfish-73.t:call-run_sawfish INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:06.939 wdl.w:ptcp.w:call-paraphase-73.t:call-run_paraphase INFO input :: name: "genome_version", value: "38"
2025-09-15 20:25:06.940 wdl.w:ptcp.w:call-sawfish-73.t:call-run_sawfish INFO input :: name: "genome_version", value: "38"
2025-09-15 20:25:06.940 wdl.w:ptcp.w:call-paraphase-73.t:call-run_paraphase INFO input :: name: "config_file", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/paraphase_config.GRCh38.yaml"
2025-09-15 20:25:06.940 wdl.w:ptcp.w:call-sawfish-73.t:call-run_sawfish INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:25:06.940 wdl.w:ptcp.w:call-paraphase-73.t:call-run_paraphase INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:25:06.940 wdl.w:ptcp.w:call-sawfish-73.t:call-run_sawfish INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:25:06.940 wdl.w:ptcp.w:call-paraphase-73.t:call-run_paraphase INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:25:06.940 wdl.w:ptcp.w:call-sawfish-73.t:call-run_sawfish INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2170.mapped.bam.bai"
2025-09-15 20:25:06.940 wdl.w:ptcp.w:call-paraphase-73.t:call-run_paraphase INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2170.mapped.bam.bai"
2025-09-15 20:25:06.940 wdl.w:ptcp.w:call-sawfish-73.t:call-run_sawfish INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2170.mapped.bam"
2025-09-15 20:25:06.940 wdl.w:ptcp.w:call-paraphase-73.t:call-run_paraphase INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2170.mapped.bam"
2025-09-15 20:25:06.940 wdl.w:ptcp.w:call-sawfish-73.t:call-run_sawfish INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2170"
2025-09-15 20:25:06.941 wdl.w:ptcp.w:call-paraphase-73.t:call-run_paraphase INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2170"
2025-09-15 20:25:06.941 wdl.w:ptcp.w:call-sawfish-73.t:call-run_sawfish INFO eval :: name: "mem_gb", value: 32
2025-09-15 20:25:06.941 wdl.w:ptcp.w:call-paraphase-73.t:call-run_paraphase INFO eval :: name: "threads", value: 4
2025-09-15 20:25:06.941 wdl.w:ptcp.w:call-sawfish-73.t:call-run_sawfish INFO eval :: name: "threads", value: 16
2025-09-15 20:25:06.941 wdl.w:ptcp.w:call-paraphase-73.t:call-run_paraphase INFO eval :: name: "mem_gb", value: 8
2025-09-15 20:25:06.942 wdl.w:ptcp.w:call-sawfish-73.t:call-run_sawfish INFO eval :: name: "disk_size", value: 30
2025-09-15 20:25:06.942 wdl.w:ptcp.w:call-paraphase-73.t:call-run_paraphase INFO eval :: name: "disk_size", value: 27
2025-09-15 20:25:06.942 wdl.w:ptcp.w:call-trgt-67.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:06 [ERROR] - No reads found for TRID=SCA37_DAB1
2025-09-15 20:25:06.943 wdl.w:ptcp.w:call-sawfish-73.t:call-run_sawfish INFO eval :: name: "discover_dirname", value: "m84036_250809_035451_s4.bc2170_sawfish_discover"
2025-09-15 20:25:06.943 wdl.w:ptcp.w:call-paraphase-73.t:call-run_paraphase INFO eval :: name: "out_dir", value: "m84036_250809_035451_s4.bc2170_paraphase"
2025-09-15 20:25:06.943 wdl.w:ptcp.w:call-trgt-67.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:06 [ERROR] - No reads found for TRID=SCA2_ATXN2
2025-09-15 20:25:06.943 wdl.w:ptcp.w:call-sawfish-73.t:call-run_sawfish INFO eval :: name: "call_dirname", value: "m84036_250809_035451_s4.bc2170_sawfish"
2025-09-15 20:25:06.944 wdl.w:ptcp.w:call-trgt-67.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:06 [ERROR] - No reads found for TRID=NIID_NOTCH2NLC
2025-09-15 20:25:06.944 wdl.w:ptcp.w:call-sawfish-73.t:call-run_sawfish INFO eval :: name: "minimap2_bam_filename", value: "m84036_250809_035451_s4.bc2170.minimap2.bam"
2025-09-15 20:25:06.944 wdl.w:ptcp.w:call-paraphase-73.t:call-run_paraphase INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 4, memory_reservation: 8000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:06.944 wdl.w:ptcp.w:call-trgt-67.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:06 [ERROR] - No reads found for TRID=SCA8_ATXN8OS
2025-09-15 20:25:06.945 wdl.w:ptcp.w:call-paraphase-73.t:call-run_paraphase WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:06.945 wdl.w:ptcp.w:call-trgt-67.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:06 [ERROR] - No reads found for TRID=OPDM4_RILPL1
2025-09-15 20:25:06.945 wdl.w:ptcp.w:call-sawfish-73.t:call-run_sawfish INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 16, memory_reservation: 32000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:06.945 wdl.w:ptcp.w:call-trgt-67.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:06 [ERROR] - No reads found for TRID=OPMD_PABPN1
2025-09-15 20:25:06.945 wdl.w:ptcp.w:call-sawfish-73.t:call-run_sawfish WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:06.946 wdl.w:ptcp.w:call-trgt-67.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:06 [ERROR] - No reads found for TRID=SCA3_ATXN3
2025-09-15 20:25:06.946 wdl.w:ptcp.w:call-trgt-67.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:06 [ERROR] - No reads found for TRID=SCA31_BEAN1
2025-09-15 20:25:06.946 wdl.w:ptcp.w:call-trgt-67.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:06 [ERROR] - No reads found for TRID=SCA4_ZFHX3
2025-09-15 20:25:06.947 wdl.w:ptcp.w:call-trgt-67.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:06 [ERROR] - No reads found for TRID=HDL2_JPH3
2025-09-15 20:25:06.947 wdl.w:ptcp.w:call-paraphase-73.t:call-run_paraphase INFO provisioned :: seconds_waited: 0, cpu: 4, mem_bytes: 8000000000
2025-09-15 20:25:06.947 wdl.w:ptcp.w:call-paraphase-73.t:call-run_paraphase INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:06.947 wdl.w:ptcp.w:call-sawfish-73.t:call-run_sawfish INFO provisioned :: seconds_waited: 0, cpu: 16, mem_bytes: 32000000000
2025-09-15 20:25:06.947 wdl.w:ptcp.w:call-sawfish-73.t:call-run_sawfish INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:06.950 wdl.w:ptcp.w:call-sawfish-26 NOTICE done
2025-09-15 20:25:06.957 wdl.w:ptcp NOTICE finish :: job: "call-sawfish-26"
2025-09-15 20:25:06.957 wdl.w:ptcp INFO output :: job: "call-sawfish-26", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-26/out/m84036_250809_035451_s4.bc2123_sawfish/m84036_250809_035451_s4.bc2123.sv.vcf.gz", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-26/out/m84036_250809_035451_s4.bc2123.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-26/out/m84036_250809_035451_s4.bc2123_sawfish/m84036_250809_035451_s4.bc2123.sv.vcf.gz.tbi", "minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-26/out/m84036_250809_035451_s4.bc2123.minimap2.bam.bai"}
2025-09-15 20:25:06.962 wdl.w:ptcp.w:call-trgt-67.t:call-trgt_plot_meth_allele.slurm_singularity INFO srun: job 51797897 queued and waiting for resources
2025-09-15 20:25:06.962 wdl.w:ptcp.w:call-trgt-67.t:call-trgt_plot_meth_allele.slurm_singularity INFO srun: job 51797897 has been allocated resources
2025-09-15 20:25:06.963 wdl.w:ptcp.w:call-trgt-67.t:call-trgt_plot_meth_allele.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:06.967 wdl.w:ptcp.w:call-paraphase-80 NOTICE workflow start :: name: "paraphase", source: "./paraphase.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-80"
2025-09-15 20:25:06.989 wdl.w:ptcp.w:call-paraphase-80 INFO visit :: node: "decl-annotation_vcf", values: {"annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf"}
2025-09-15 20:25:06.989 wdl.w:ptcp.w:call-paraphase-80 INFO visit :: node: "decl-config_file", values: {"config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml"}
2025-09-15 20:25:06.990 wdl.w:ptcp.w:call-paraphase-80 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:25:06.990 wdl.w:ptcp.w:call-paraphase-80 INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:25:06.990 wdl.w:ptcp.w:call-paraphase-80 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-80/out/m84036_250809_035451_s4.bc2177.mapped.bam"}
2025-09-15 20:25:06.990 wdl.w:ptcp.w:call-paraphase-80 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-80/out/m84036_250809_035451_s4.bc2177.mapped.bam.bai"}
2025-09-15 20:25:06.991 wdl.w:ptcp.w:call-paraphase-80 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:25:06.991 wdl.w:ptcp.w:call-paraphase-80 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:25:06.991 wdl.w:ptcp.w:call-paraphase-80 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2177"}
2025-09-15 20:25:06.991 wdl.w:ptcp.w:call-paraphase-80 INFO visit :: node: "decl-sex", values: {"sex": "F"}
2025-09-15 20:25:06.991 wdl.w:ptcp.w:call-paraphase-80 NOTICE ready :: job: "call-run_paraphase", callee: "run_paraphase"
2025-09-15 20:25:06.991 wdl.w:ptcp.w:call-paraphase-80 INFO input :: job: "call-run_paraphase", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf", "genome_version": "38", "config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-80/out/m84036_250809_035451_s4.bc2177.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-80/out/m84036_250809_035451_s4.bc2177.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2177"}
2025-09-15 20:25:07.008 wdl.w:ptcp.w:call-trgt-58.t:call-trgt_plot_meth_waterfall NOTICE done
2025-09-15 20:25:07.008 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_plot_meth_allele NOTICE done
2025-09-15 20:25:07.014 wdl.w:ptcp.w:call-trgt-58 NOTICE finish :: job: "call-trgt_plot_meth_waterfall"
2025-09-15 20:25:07.014 wdl.w:ptcp.w:call-trgt-58 INFO output :: job: "call-trgt_plot_meth_waterfall", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-58/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2155.meth_waterfall.trgt_plots.zip"}
2025-09-15 20:25:07.015 wdl.w:ptcp.w:call-trgt-58 INFO visit :: node: "output-images_meth_waterfall", values: {"images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-58/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2155.meth_waterfall.trgt_plots.zip"}
2025-09-15 20:25:07.016 wdl.w:ptcp.w:call-trgt-42 NOTICE finish :: job: "call-trgt_plot_meth_allele"
2025-09-15 20:25:07.016 wdl.w:ptcp.w:call-trgt-42 INFO output :: job: "call-trgt_plot_meth_allele", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-42/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2139.meth_allele.trgt_plots.zip"}
2025-09-15 20:25:07.016 wdl.w:ptcp.w:call-trgt-42 INFO visit :: node: "output-images_meth_allele", values: {"images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-42/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2139.meth_allele.trgt_plots.zip"}
2025-09-15 20:25:07.020 wdl.w:ptcp.w:call-trgt-79.t:call-trgt_genotype INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 11, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-79/call-trgt_genotype/_singularity_tmpdir_4grirx4f"
2025-09-15 20:25:07.020 wdl.w:ptcp.w:call-trgt-79.t:call-trgt_genotype INFO Slurm invocation: srun --job-name call-trgt_genotype --partition compute,compute9 --cpus-per-task 8 --mem 15259M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-79/call-trgt_genotype/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-79/call-trgt_genotype/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-79/call-trgt_genotype/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-79/call-trgt_genotype/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-79/out/m84036_250809_035451_s4.bc2176.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2176.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-79/out/m84036_250809_035451_s4.bc2176.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2176.mapped.bam:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-79/call-trgt_genotype/_singularity_tmpdir_4grirx4f/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-79/call-trgt_genotype/_singularity_tmpdir_4grirx4f/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:07.024 wdl.w:ptcp.w:call-trgt-73.t:call-get_reads_overlapping_repeats NOTICE task setup :: name: "get_reads_overlapping_repeats", source: "./trgt.wdl", line: 182, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-73/call-get_reads_overlapping_repeats", thread: 140611944420928
2025-09-15 20:25:07.028 wdl.w:ptcp.w:call-trgt-73.t:call-trgt_genotype NOTICE task setup :: name: "trgt_genotype", source: "./trgt.wdl", line: 272, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-73/call-trgt_genotype", thread: 140610870679104
2025-09-15 20:25:07.035 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_genotype NOTICE done
2025-09-15 20:25:07.041 wdl.w:ptcp.w:call-sawfish-73.t:call-run_sawfish INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 10, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-73/call-run_sawfish/_singularity_tmpdir_04gx_g6b"
2025-09-15 20:25:07.042 wdl.w:ptcp.w:call-sawfish-73.t:call-run_sawfish INFO Slurm invocation: srun --job-name call-run_sawfish --partition compute,compute9 --cpus-per-task 16 --mem 30518M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-73/call-run_sawfish/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-73/call-run_sawfish/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-73/call-run_sawfish/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-73/call-run_sawfish/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-73/out/m84036_250809_035451_s4.bc2170.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2170.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-73/out/m84036_250809_035451_s4.bc2170.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2170.mapped.bam:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-73/call-run_sawfish/_singularity_tmpdir_04gx_g6b/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-73/call-run_sawfish/_singularity_tmpdir_04gx_g6b/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:07.053 wdl.w:ptcp.w:call-trgt-73.t:call-get_reads_overlapping_repeats INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:07.055 wdl.w:ptcp.w:call-trgt-73.t:call-get_reads_overlapping_repeats INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:25:07.055 wdl.w:ptcp.w:call-trgt-73.t:call-get_reads_overlapping_repeats INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2170.mapped.bam.bai"
2025-09-15 20:25:07.055 wdl.w:ptcp.w:call-trgt-73.t:call-get_reads_overlapping_repeats INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2170.mapped.bam"
2025-09-15 20:25:07.055 wdl.w:ptcp.w:call-trgt-73.t:call-get_reads_overlapping_repeats INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2170"
2025-09-15 20:25:07.056 wdl.w:ptcp.w:call-paraphase-73.t:call-run_paraphase INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-73/call-run_paraphase/_singularity_tmpdir_m9yisliv"
2025-09-15 20:25:07.056 wdl.w:ptcp.w:call-paraphase-73.t:call-run_paraphase INFO Slurm invocation: srun --job-name call-run_paraphase --partition compute,compute9 --cpus-per-task 4 --mem 7629M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-73/call-run_paraphase/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-73/call-run_paraphase/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-73/call-run_paraphase/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-73/call-run_paraphase/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-73/out/m84036_250809_035451_s4.bc2170.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2170.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-73/out/m84036_250809_035451_s4.bc2170.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2170.mapped.bam:ro --bind /ptcp/meta/variant_list/variant_list.GRCh38.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf:ro --bind /ptcp/meta/paraphase/paraphase_config.GRCh38.yaml:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/paraphase_config.GRCh38.yaml:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-73/call-run_paraphase/_singularity_tmpdir_m9yisliv/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-73/call-run_paraphase/_singularity_tmpdir_m9yisliv/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:07.055 wdl.w:ptcp.w:call-trgt-73.t:call-get_reads_overlapping_repeats INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:25:07.056 wdl.w:ptcp.w:call-trgt-73.t:call-trgt_genotype INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:07.054 wdl.w:ptcp.w:call-trgt-70 NOTICE finish :: job: "call-trgt_genotype"
2025-09-15 20:25:07.058 wdl.w:ptcp.w:call-trgt-73.t:call-get_reads_overlapping_repeats INFO eval :: name: "expand_size", value: 3000
2025-09-15 20:25:07.058 wdl.w:ptcp.w:call-paraphase-22.t:call-call_f8.stderr VERBOSE 2025-09-15 20:25:06,918 INFO  Started analysis for m84036_250809_035451_s4.bc2119 at 2025-09-15 20:25:06.918515...
2025-09-15 20:25:07.059 wdl.w:ptcp.w:call-trgt-73.t:call-trgt_genotype INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:25:07.060 wdl.w:ptcp.w:call-trgt-70 INFO output :: job: "call-trgt_genotype", values: {"spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-70/call-trgt_genotype/out/m84036_250809_035451_s4.bc2167.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-70/call-trgt_genotype/out/m84036_250809_035451_s4.bc2167.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-70/call-trgt_genotype/out/m84036_250809_035451_s4.bc2167.trgt.vcf"}
2025-09-15 20:25:07.060 wdl.w:ptcp.w:call-paraphase-22.t:call-call_f8.stderr VERBOSE 2025-09-15 20:25:06,979 INFO  Completed analysis for m84036_250809_035451_s4.bc2119
2025-09-15 20:25:07.060 wdl.w:ptcp.w:call-trgt-73.t:call-trgt_genotype INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:25:07.061 wdl.w:ptcp.w:call-trgt-70 NOTICE ready :: job: "call-trgt_plot_meth_allele", callee: "trgt_plot"
2025-09-15 20:25:07.060 wdl.w:ptcp.w:call-trgt-73.t:call-get_reads_overlapping_repeats INFO eval :: name: "threads", value: 1
2025-09-15 20:25:07.061 wdl.w:ptcp.w:call-trgt-73.t:call-trgt_genotype INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:25:07.061 wdl.w:ptcp.w:call-trgt-70 INFO input :: job: "call-trgt_plot_meth_allele", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": false, "methylation": true, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-70/call-trgt_genotype/out/m84036_250809_035451_s4.bc2167.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-70/call-trgt_genotype/out/m84036_250809_035451_s4.bc2167.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-70/call-trgt_genotype/out/m84036_250809_035451_s4.bc2167.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2167"}
2025-09-15 20:25:07.062 wdl.w:ptcp.w:call-trgt-73.t:call-get_reads_overlapping_repeats INFO eval :: name: "expanded_bed_name", value: "m84036_250809_035451_s4.bc2170.expanded.bed"
2025-09-15 20:25:07.062 wdl.w:ptcp.w:call-trgt-73.t:call-trgt_genotype INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2170.mapped.bam.bai"
2025-09-15 20:25:07.062 wdl.w:ptcp.w:call-trgt-73.t:call-get_reads_overlapping_repeats INFO eval :: name: "disk_size", value: 11
2025-09-15 20:25:07.062 wdl.w:ptcp.w:call-trgt-73.t:call-trgt_genotype INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2170.mapped.bam"
2025-09-15 20:25:07.062 wdl.w:ptcp.w:call-trgt-73.t:call-get_reads_overlapping_repeats INFO eval :: name: "output_name", value: "m84036_250809_035451_s4.bc2170.repeats.bam"
2025-09-15 20:25:07.062 wdl.w:ptcp.w:call-trgt-73.t:call-trgt_genotype INFO input :: name: "sex", value: "F"
2025-09-15 20:25:07.063 wdl.w:ptcp.w:call-trgt-73.t:call-get_reads_overlapping_repeats INFO eval :: name: "index_name", value: "m84036_250809_035451_s4.bc2170.repeats.bam.bai"
2025-09-15 20:25:07.063 wdl.w:ptcp.w:call-trgt-73.t:call-trgt_genotype INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2170"
2025-09-15 20:25:07.063 wdl.w:ptcp.w:call-trgt-73.t:call-get_reads_overlapping_repeats INFO eval :: name: "output_name_with_index", value: "m84036_250809_035451_s4.bc2170.repeats.bam##idx##m84036_250809_035451_s4.bc2170.repeats.bam.bai"
2025-09-15 20:25:07.063 wdl.w:ptcp.w:call-trgt-73.t:call-trgt_genotype INFO eval :: name: "mem_gb", value: 16
2025-09-15 20:25:07.063 wdl.w:ptcp.w:call-trgt-70 NOTICE ready :: job: "call-trgt_plot_meth_waterfall", callee: "trgt_plot"
2025-09-15 20:25:07.064 wdl.w:ptcp.w:call-trgt-79.t:call-trgt_genotype NOTICE slurm_singularity run :: pid: 1204675, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-79/call-trgt_genotype/slurm_singularity.log.txt"
2025-09-15 20:25:07.064 wdl.w:ptcp.w:call-trgt-70 INFO input :: job: "call-trgt_plot_meth_waterfall", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": true, "methylation": true, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-70/call-trgt_genotype/out/m84036_250809_035451_s4.bc2167.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-70/call-trgt_genotype/out/m84036_250809_035451_s4.bc2167.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-70/call-trgt_genotype/out/m84036_250809_035451_s4.bc2167.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2167"}
2025-09-15 20:25:07.065 wdl.w:ptcp.w:call-trgt-73.t:call-get_reads_overlapping_repeats INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:07.064 wdl.w:ptcp.w:call-trgt-73.t:call-trgt_genotype INFO eval :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2170.trgt"
2025-09-15 20:25:07.065 wdl.w:ptcp.w:call-sawfish-73.t:call-run_sawfish NOTICE slurm_singularity run :: pid: 1204677, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-73/call-run_sawfish/slurm_singularity.log.txt"
2025-09-15 20:25:07.066 wdl.w:ptcp.w:call-trgt-70 NOTICE ready :: job: "call-trgt_plot_motifs_allele", callee: "trgt_plot"
2025-09-15 20:25:07.067 wdl.w:ptcp.w:call-trgt-70 INFO input :: job: "call-trgt_plot_motifs_allele", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": false, "methylation": false, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-70/call-trgt_genotype/out/m84036_250809_035451_s4.bc2167.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-70/call-trgt_genotype/out/m84036_250809_035451_s4.bc2167.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-70/call-trgt_genotype/out/m84036_250809_035451_s4.bc2167.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2167"}
2025-09-15 20:25:07.067 wdl.w:ptcp.w:call-trgt-70 NOTICE ready :: job: "call-trgt_plot_motifs_waterfall", callee: "trgt_plot"
2025-09-15 20:25:07.067 wdl.w:ptcp.w:call-trgt-70 INFO input :: job: "call-trgt_plot_motifs_waterfall", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": true, "methylation": false, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-70/call-trgt_genotype/out/m84036_250809_035451_s4.bc2167.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-70/call-trgt_genotype/out/m84036_250809_035451_s4.bc2167.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-70/call-trgt_genotype/out/m84036_250809_035451_s4.bc2167.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2167"}
2025-09-15 20:25:07.068 wdl.w:ptcp.w:call-trgt-70 INFO visit :: node: "output-spanning_bam", values: {"spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-70/call-trgt_genotype/out/m84036_250809_035451_s4.bc2167.trgt.sorted.spanning.bam"}
2025-09-15 20:25:07.068 wdl.w:ptcp.w:call-trgt-70 INFO visit :: node: "output-spanning_bam_bai", values: {"spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-70/call-trgt_genotype/out/m84036_250809_035451_s4.bc2167.trgt.sorted.spanning.bam.bai"}
2025-09-15 20:25:07.068 wdl.w:ptcp.w:call-trgt-70 INFO visit :: node: "output-vcf", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-70/call-trgt_genotype/out/m84036_250809_035451_s4.bc2167.trgt.vcf"}
2025-09-15 20:25:07.068 wdl.w:ptcp.w:call-sawfish-27.t:call-run_sawfish INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2124_sawfish/m84036_250809_035451_s4.bc2124.sv.vcf.gz"
2025-09-15 20:25:07.065 wdl.w:ptcp.w:call-trgt-73.t:call-get_reads_overlapping_repeats WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:07.065 wdl.w:ptcp.w:call-trgt-73.t:call-trgt_genotype INFO eval :: name: "threads", value: 8
2025-09-15 20:25:07.070 wdl.w:ptcp.w:call-trgt-73.t:call-trgt_genotype INFO eval :: name: "disk_size", value: 27
2025-09-15 20:25:07.070 wdl.w:ptcp.w:call-trgt-73.t:call-get_reads_overlapping_repeats INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:25:07.071 wdl.w:ptcp.w:call-trgt-73.t:call-trgt_genotype INFO eval :: name: "karyotype", value: "XX"
2025-09-15 20:25:07.071 wdl.w:ptcp.w:call-trgt-73.t:call-get_reads_overlapping_repeats INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:07.071 wdl.w:ptcp.w:call-trgt-73.t:call-trgt_genotype INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 8, memory_reservation: 16000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:07.071 wdl.w:ptcp.w:call-trgt-73.t:call-trgt_genotype WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:07.072 wdl.w:ptcp.w:call-trgt-73.t:call-trgt_genotype INFO provisioned :: seconds_waited: 0, cpu: 8, mem_bytes: 16000000000
2025-09-15 20:25:07.072 wdl.w:ptcp.w:call-trgt-73.t:call-trgt_genotype INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:07.075 wdl.w:ptcp.w:call-trgt-67.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:25:06 [ERROR] - No reads found for TRID=SCA37_DAB1
2025-09-15 20:25:07.076 wdl.w:ptcp.w:call-trgt-67.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:25:06 [ERROR] - No reads found for TRID=SCA2_ATXN2
2025-09-15 20:25:07.076 wdl.w:ptcp.w:call-trgt-67.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:25:06 [ERROR] - No reads found for TRID=NIID_NOTCH2NLC
2025-09-15 20:25:07.076 wdl.w:ptcp.w:call-trgt-67.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:25:06 [ERROR] - No reads found for TRID=SCA8_ATXN8OS
2025-09-15 20:25:07.076 wdl.w:ptcp.w:call-trgt-67.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:25:06 [ERROR] - No reads found for TRID=OPDM4_RILPL1
2025-09-15 20:25:07.076 wdl.w:ptcp.w:call-trgt-67.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:25:06 [ERROR] - No reads found for TRID=SCA37_DAB1
2025-09-15 20:25:07.076 wdl.w:ptcp.w:call-trgt-67.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:25:06 [ERROR] - No reads found for TRID=OPMD_PABPN1
2025-09-15 20:25:07.076 wdl.w:ptcp.w:call-trgt-67.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:25:06 [ERROR] - No reads found for TRID=SCA2_ATXN2
2025-09-15 20:25:07.076 wdl.w:ptcp.w:call-trgt-67.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:25:07 [ERROR] - No reads found for TRID=SCA3_ATXN3
2025-09-15 20:25:07.076 wdl.w:ptcp.w:call-trgt-67.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:25:06 [ERROR] - No reads found for TRID=NIID_NOTCH2NLC
2025-09-15 20:25:07.076 wdl.w:ptcp.w:call-trgt-67.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:25:07 [ERROR] - No reads found for TRID=SCA31_BEAN1
2025-09-15 20:25:07.076 wdl.w:ptcp.w:call-trgt-67.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:25:06 [ERROR] - No reads found for TRID=SCA8_ATXN8OS
2025-09-15 20:25:07.076 wdl.w:ptcp.w:call-trgt-67.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:25:07 [ERROR] - No reads found for TRID=SCA4_ZFHX3
2025-09-15 20:25:07.077 wdl.w:ptcp.w:call-trgt-67.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:25:06 [ERROR] - No reads found for TRID=OPDM4_RILPL1
2025-09-15 20:25:07.077 wdl.w:ptcp.w:call-trgt-67.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:25:06 [ERROR] - No reads found for TRID=OPMD_PABPN1
2025-09-15 20:25:07.077 wdl.w:ptcp.w:call-trgt-67.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:25:06 [ERROR] - No reads found for TRID=SCA3_ATXN3
2025-09-15 20:25:07.077 wdl.w:ptcp.w:call-trgt-67.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:25:07 [ERROR] - No reads found for TRID=SCA31_BEAN1
2025-09-15 20:25:07.077 wdl.w:ptcp.w:call-trgt-67.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:25:07 [ERROR] - No reads found for TRID=SCA4_ZFHX3
2025-09-15 20:25:07.077 wdl.w:ptcp.w:call-sawfish-27.t:call-run_sawfish INFO output :: name: "vcf_tbi", value: "m84036_250809_035451_s4.bc2124_sawfish/m84036_250809_035451_s4.bc2124.sv.vcf.gz.tbi"
2025-09-15 20:25:07.079 wdl.w:ptcp.w:call-sawfish-27.t:call-run_sawfish INFO output :: name: "minimap2_bam", value: "m84036_250809_035451_s4.bc2124.minimap2.bam"
2025-09-15 20:25:07.081 wdl.w:ptcp.w:call-sawfish-27.t:call-run_sawfish INFO output :: name: "minimap2_bam_bai", value: "m84036_250809_035451_s4.bc2124.minimap2.bam.bai"
2025-09-15 20:25:07.082 wdl.w:ptcp.w:call-trgt-53.t:call-trgt_plot_meth_allele NOTICE done
2025-09-15 20:25:07.082 wdl.w:ptcp.w:call-trgt-61.t:call-trgt_plot_meth_allele NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-61/call-trgt_plot_meth_allele", thread: 140610912642624
2025-09-15 20:25:07.085 wdl.w:ptcp.w:call-paraphase-73.t:call-run_paraphase NOTICE slurm_singularity run :: pid: 1204678, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-73/call-run_paraphase/slurm_singularity.log.txt"
2025-09-15 20:25:07.087 wdl.w:ptcp.w:call-paraphase-22.t:call-call_f8.slurm_singularity INFO srun: job 51797901 queued and waiting for resources
2025-09-15 20:25:07.087 wdl.w:ptcp.w:call-paraphase-22.t:call-call_f8.slurm_singularity INFO srun: job 51797901 has been allocated resources
2025-09-15 20:25:07.087 wdl.w:ptcp.w:call-paraphase-22.t:call-call_f8.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:07.087 wdl.w:ptcp.w:call-paraphase-22.t:call-call_f8.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:25:07.092 wdl.w:ptcp.w:call-trgt-53 NOTICE finish :: job: "call-trgt_plot_meth_allele"
2025-09-15 20:25:07.092 wdl.w:ptcp.w:call-trgt-53 INFO output :: job: "call-trgt_plot_meth_allele", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-53/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2150.meth_allele.trgt_plots.zip"}
2025-09-15 20:25:07.092 wdl.w:ptcp.w:call-trgt-53 INFO visit :: node: "output-images_meth_allele", values: {"images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-53/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2150.meth_allele.trgt_plots.zip"}
2025-09-15 20:25:07.092 wdl.w:ptcp.w:call-trgt-53 INFO visit :: node: "outputs", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-53/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2150.motifs_waterfall.trgt_plots.zip", "images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-53/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2150.meth_allele.trgt_plots.zip", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-53/call-trgt_genotype/out/m84036_250809_035451_s4.bc2150.trgt.sorted.spanning.bam.bai", "images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-53/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2150.motifs_allele.trgt_plots.zip", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-53/call-trgt_genotype/out/m84036_250809_035451_s4.bc2150.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-53/call-trgt_genotype/out/m84036_250809_035451_s4.bc2150.trgt.vcf", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-53/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2150.repeats.bam", "images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-53/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2150.meth_waterfall.trgt_plots.zip", "reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-53/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2150.repeats.bam.bai"}
2025-09-15 20:25:07.096 wdl.w:ptcp.w:call-trgt-67.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO srun: job 51797899 queued and waiting for resources
2025-09-15 20:25:07.096 wdl.w:ptcp.w:call-trgt-67.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO srun: job 51797899 has been allocated resources
2025-09-15 20:25:07.096 wdl.w:ptcp.w:call-trgt-67.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:07.097 wdl.w:ptcp.w:call-trgt-56.t:call-trgt_plot_motifs_waterfall INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2153.motifs_waterfall.trgt_plots.zip"
2025-09-15 20:25:07.103 wdl.w:ptcp.w:call-trgt-67.t:call-trgt_plot_motifs_allele.slurm_singularity INFO srun: job 51797898 queued and waiting for resources
2025-09-15 20:25:07.103 wdl.w:ptcp.w:call-trgt-67.t:call-trgt_plot_motifs_allele.slurm_singularity INFO srun: job 51797898 has been allocated resources
2025-09-15 20:25:07.103 wdl.w:ptcp.w:call-trgt-67.t:call-trgt_plot_motifs_allele.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:07.104 wdl.w:ptcp.w:call-trgt-61.t:call-trgt_plot_meth_waterfall NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-61/call-trgt_plot_meth_waterfall", thread: 140611415942720
2025-09-15 20:25:07.115 wdl.w:ptcp.w:call-trgt-61.t:call-trgt_plot_meth_allele INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:07.115 wdl.w:ptcp.w:call-trgt-61.t:call-trgt_plot_meth_allele INFO input :: name: "waterfall", value: false
2025-09-15 20:25:07.115 wdl.w:ptcp.w:call-trgt-61.t:call-trgt_plot_meth_allele INFO input :: name: "methylation", value: true
2025-09-15 20:25:07.116 wdl.w:ptcp.w:call-trgt-61.t:call-trgt_plot_meth_allele INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:25:07.116 wdl.w:ptcp.w:call-trgt-61.t:call-trgt_plot_meth_allele INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:25:07.116 wdl.w:ptcp.w:call-trgt-61.t:call-trgt_plot_meth_allele INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:25:07.116 wdl.w:ptcp.w:call-trgt-61.t:call-trgt_plot_meth_allele INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2158.trgt.sorted.spanning.bam.bai"
2025-09-15 20:25:07.116 wdl.w:ptcp.w:call-trgt-61.t:call-trgt_plot_meth_allele INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2158.trgt.sorted.spanning.bam"
2025-09-15 20:25:07.116 wdl.w:ptcp.w:call-trgt-61.t:call-trgt_plot_meth_allele INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2158.trgt.vcf"
2025-09-15 20:25:07.116 wdl.w:ptcp.w:call-trgt-61.t:call-trgt_plot_meth_allele INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2158"
2025-09-15 20:25:07.116 wdl.w:ptcp.w:call-trgt-61.t:call-trgt_plot_meth_allele INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:25:07.116 wdl.w:ptcp.w:call-trgt-61.t:call-trgt_plot_meth_allele INFO eval :: name: "plot_type", value: "allele"
2025-09-15 20:25:07.116 wdl.w:ptcp.w:call-trgt-61.t:call-trgt_plot_meth_allele INFO eval :: name: "show", value: "meth"
2025-09-15 20:25:07.116 wdl.w:ptcp.w:call-trgt-61.t:call-trgt_plot_meth_allele INFO eval :: name: "threads", value: 1
2025-09-15 20:25:07.117 wdl.w:ptcp.w:call-trgt-61.t:call-trgt_plot_meth_allele INFO eval :: name: "disk_size", value: 27
2025-09-15 20:25:07.117 wdl.w:ptcp.w:call-trgt-61.t:call-trgt_plot_meth_allele INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2158.meth_allele"
2025-09-15 20:25:07.119 wdl.w:ptcp.w:call-trgt-61.t:call-trgt_plot_meth_allele INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:07.120 wdl.w:ptcp.w:call-trgt-61.t:call-trgt_plot_meth_allele WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:07.120 wdl.w:ptcp.w:call-trgt-67.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:25:06 [ERROR] - No reads found for TRID=SCA37_DAB1
2025-09-15 20:25:07.120 wdl.w:ptcp.w:call-trgt-67.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:25:06 [ERROR] - No reads found for TRID=SCA2_ATXN2
2025-09-15 20:25:07.120 wdl.w:ptcp.w:call-trgt-67.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:25:06 [ERROR] - No reads found for TRID=NIID_NOTCH2NLC
2025-09-15 20:25:07.121 wdl.w:ptcp.w:call-trgt-67.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:25:06 [ERROR] - No reads found for TRID=SCA8_ATXN8OS
2025-09-15 20:25:07.121 wdl.w:ptcp.w:call-trgt-67.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:25:06 [ERROR] - No reads found for TRID=OPDM4_RILPL1
2025-09-15 20:25:07.121 wdl.w:ptcp.w:call-trgt-67.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:25:06 [ERROR] - No reads found for TRID=OPMD_PABPN1
2025-09-15 20:25:07.121 wdl.w:ptcp.w:call-trgt-61.t:call-trgt_plot_meth_allele INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:25:07.122 wdl.w:ptcp.w:call-trgt-67.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:25:06 [ERROR] - No reads found for TRID=SCA3_ATXN3
2025-09-15 20:25:07.122 wdl.w:ptcp.w:call-trgt-61.t:call-trgt_plot_meth_allele INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:07.122 wdl.w:ptcp.w:call-trgt-67.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:25:06 [ERROR] - No reads found for TRID=SCA31_BEAN1
2025-09-15 20:25:07.122 wdl.w:ptcp.w:call-trgt-67.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:25:06 [ERROR] - No reads found for TRID=SCA4_ZFHX3
2025-09-15 20:25:07.122 wdl.w:ptcp.w:call-trgt-67.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:25:06 [ERROR] - No reads found for TRID=HDL2_JPH3
2025-09-15 20:25:07.123 wdl.w:ptcp.w:call-trgt-67.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:25:06 [ERROR] - No reads found for TRID=SCA27B_FGF14
2025-09-15 20:25:07.123 wdl.w:ptcp.w:call-trgt-67.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:25:06 [ERROR] - No reads found for TRID=SCA6_CACNA1A
2025-09-15 20:25:07.123 wdl.w:ptcp.w:call-trgt-67.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:25:06 [ERROR] - No reads found for TRID=OPDM_ABCD3
2025-09-15 20:25:07.123 wdl.w:ptcp.w:call-trgt-67.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:25:06 [ERROR] - No reads found for TRID=FRA2A_AFF3
2025-09-15 20:25:07.123 wdl.w:ptcp.w:call-trgt-67.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:25:06 [ERROR] - No reads found for TRID=SCA36_NOP56
2025-09-15 20:25:07.123 wdl.w:ptcp.w:call-trgt-67.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:25:06 [ERROR] - No reads found for TRID=EPM1_CSTB
2025-09-15 20:25:07.123 wdl.w:ptcp.w:call-trgt-67.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:25:07 [ERROR] - No reads found for TRID=CJD_PRNP
2025-09-15 20:25:07.124 wdl.w:ptcp.w:call-trgt-67.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:25:07 [ERROR] - No reads found for TRID=SCA7_ATXN7
2025-09-15 20:25:07.124 wdl.w:ptcp.w:call-trgt-67.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:25:07 [ERROR] - No reads found for TRID=HD_HTT
2025-09-15 20:25:07.136 wdl.w:ptcp.w:call-trgt-61.t:call-trgt_plot_meth_waterfall INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:07.136 wdl.w:ptcp.w:call-trgt-61.t:call-trgt_plot_meth_waterfall INFO input :: name: "waterfall", value: true
2025-09-15 20:25:07.136 wdl.w:ptcp.w:call-trgt-61.t:call-trgt_plot_meth_waterfall INFO input :: name: "methylation", value: true
2025-09-15 20:25:07.136 wdl.w:ptcp.w:call-trgt-61.t:call-trgt_plot_meth_waterfall INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:25:07.136 wdl.w:ptcp.w:call-trgt-61.t:call-trgt_plot_meth_waterfall INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:25:07.136 wdl.w:ptcp.w:call-trgt-61.t:call-trgt_plot_meth_waterfall INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:25:07.136 wdl.w:ptcp.w:call-trgt-61.t:call-trgt_plot_meth_waterfall INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2158.trgt.sorted.spanning.bam.bai"
2025-09-15 20:25:07.136 wdl.w:ptcp.w:call-trgt-61.t:call-trgt_plot_meth_waterfall INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2158.trgt.sorted.spanning.bam"
2025-09-15 20:25:07.136 wdl.w:ptcp.w:call-trgt-61.t:call-trgt_plot_meth_waterfall INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2158.trgt.vcf"
2025-09-15 20:25:07.136 wdl.w:ptcp.w:call-trgt-61.t:call-trgt_plot_meth_waterfall INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2158"
2025-09-15 20:25:07.137 wdl.w:ptcp.w:call-trgt-61.t:call-trgt_plot_meth_waterfall INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:25:07.137 wdl.w:ptcp.w:call-trgt-61.t:call-trgt_plot_meth_waterfall INFO eval :: name: "plot_type", value: "waterfall"
2025-09-15 20:25:07.137 wdl.w:ptcp.w:call-trgt-61.t:call-trgt_plot_meth_waterfall INFO eval :: name: "show", value: "meth"
2025-09-15 20:25:07.137 wdl.w:ptcp.w:call-trgt-61.t:call-trgt_plot_meth_waterfall INFO eval :: name: "threads", value: 1
2025-09-15 20:25:07.137 wdl.w:ptcp.w:call-trgt-61.t:call-trgt_plot_meth_waterfall INFO eval :: name: "disk_size", value: 27
2025-09-15 20:25:07.137 wdl.w:ptcp.w:call-trgt-61.t:call-trgt_plot_meth_waterfall INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2158.meth_waterfall"
2025-09-15 20:25:07.138 wdl.w:ptcp.w:call-trgt-61.t:call-trgt_plot_meth_waterfall INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:07.138 wdl.w:ptcp.w:call-trgt-61.t:call-trgt_plot_meth_waterfall WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:07.138 wdl.w:ptcp.w:call-trgt-61.t:call-trgt_plot_meth_waterfall INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:25:07.139 wdl.w:ptcp.w:call-trgt-61.t:call-trgt_plot_meth_waterfall INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:07.142 wdl.w:ptcp.w:call-trgt-67.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO srun: job 51797900 queued and waiting for resources
2025-09-15 20:25:07.142 wdl.w:ptcp.w:call-trgt-67.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO srun: job 51797900 has been allocated resources
2025-09-15 20:25:07.142 wdl.w:ptcp.w:call-trgt-67.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:07.142 wdl.w:ptcp.w:call-trgt-67.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:25:07.149 wdl.w:ptcp.w:call-paraphase-22.t:call-call_f8 INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2119.f8inversion.vcf"
2025-09-15 20:25:07.157 wdl.w:ptcp.w:call-paraphase-22.t:call-call_f8 INFO output :: name: "json", value: "m84036_250809_035451_s4.bc2119.f8inversion.json"
2025-09-15 20:25:07.163 wdl.w:ptcp.w:call-paraphase-60.t:call-run_paraphase INFO output :: name: "paraphase_bam", value: "m84036_250809_035451_s4.bc2157_paraphase/m84036_250809_035451_s4.bc2157.paraphase.bam"
2025-09-15 20:25:07.170 wdl.w:ptcp.w:call-paraphase-60.t:call-run_paraphase INFO output :: name: "paraphase_bam_bai", value: "m84036_250809_035451_s4.bc2157_paraphase/m84036_250809_035451_s4.bc2157.paraphase.bam.bai"
2025-09-15 20:25:07.173 wdl.w:ptcp.w:call-paraphase-60.t:call-run_paraphase INFO output :: name: "paraphase_json", value: "m84036_250809_035451_s4.bc2157_paraphase/m84036_250809_035451_s4.bc2157.paraphase.json"
2025-09-15 20:25:07.176 wdl.w:ptcp.w:call-paraphase-60.t:call-run_paraphase INFO output :: name: "paraphase_vcfs", value: []
2025-09-15 20:25:07.176 wdl.w:ptcp.w:call-paraphase-60.t:call-run_paraphase INFO output :: name: "havanno_json", value: "m84036_250809_035451_s4.bc2157.havanno.json"
2025-09-15 20:25:07.177 wdl.w:ptcp.w:call-trgt-58.t:call-trgt_plot_motifs_waterfall INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2155.motifs_waterfall.trgt_plots.zip"
2025-09-15 20:25:07.185 wdl.w:ptcp.w:call-trgt-73.t:call-get_reads_overlapping_repeats INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 9, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-73/call-get_reads_overlapping_repeats/_singularity_tmpdir_6mx00eb_"
2025-09-15 20:25:07.185 wdl.w:ptcp.w:call-trgt-73.t:call-get_reads_overlapping_repeats INFO Slurm invocation: srun --job-name call-get_reads_overlapping_repeats --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-73/call-get_reads_overlapping_repeats/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-73/call-get_reads_overlapping_repeats/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-73/call-get_reads_overlapping_repeats/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-73/call-get_reads_overlapping_repeats/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-73/out/m84036_250809_035451_s4.bc2170.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2170.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-73/out/m84036_250809_035451_s4.bc2170.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2170.mapped.bam:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-73/call-get_reads_overlapping_repeats/_singularity_tmpdir_6mx00eb_/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-73/call-get_reads_overlapping_repeats/_singularity_tmpdir_6mx00eb_/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:07.217 wdl.w:ptcp.w:call-trgt-73.t:call-trgt_genotype INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 11, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-73/call-trgt_genotype/_singularity_tmpdir_4sar61y6"
2025-09-15 20:25:07.217 wdl.w:ptcp.w:call-trgt-73.t:call-trgt_genotype INFO Slurm invocation: srun --job-name call-trgt_genotype --partition compute,compute9 --cpus-per-task 8 --mem 15259M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-73/call-trgt_genotype/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-73/call-trgt_genotype/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-73/call-trgt_genotype/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-73/call-trgt_genotype/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-73/out/m84036_250809_035451_s4.bc2170.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2170.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-73/out/m84036_250809_035451_s4.bc2170.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2170.mapped.bam:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-73/call-trgt_genotype/_singularity_tmpdir_4sar61y6/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-73/call-trgt_genotype/_singularity_tmpdir_4sar61y6/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:07.223 wdl.w:ptcp.w:call-paraphase-62.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for hba for sample m84036_250809_035451_s4.bc2159 at 2025-09-15 20:24:50.275556...
2025-09-15 20:25:07.224 wdl.w:ptcp.w:call-paraphase-62.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for smn1 for sample m84036_250809_035451_s4.bc2159 at 2025-09-15 20:24:50.353843...
2025-09-15 20:25:07.224 wdl.w:ptcp.w:call-paraphase-62.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for gba for sample m84036_250809_035451_s4.bc2159 at 2025-09-15 20:24:50.517461...
2025-09-15 20:25:07.225 wdl.w:ptcp.w:call-paraphase-62.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for cyp21 for sample m84036_250809_035451_s4.bc2159 at 2025-09-15 20:24:51.904629...
2025-09-15 20:25:07.225 wdl.w:ptcp.w:call-paraphase-62.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for smn1 for sample m84036_250809_035451_s4.bc2159 at 2025-09-15 20:25:03.630106...
2025-09-15 20:25:07.225 wdl.w:ptcp.w:call-paraphase-62.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning to gene2 region for smn1 for sample m84036_250809_035451_s4.bc2159 at 2025-09-15 20:25:04.499014...
2025-09-15 20:25:07.245 wdl.w:ptcp.w:call-sawfish-14.t:call-run_sawfish.stderr VERBOSE [M::mm_idx_gen::85.565*1.86] sorted minimizers
2025-09-15 20:25:07.247 wdl.w:ptcp.w:call-sawfish-14.t:call-run_sawfish.stderr VERBOSE [M::main::85.569*1.86] loaded/built the index for 195 target sequence(s)
2025-09-15 20:25:07.248 wdl.w:ptcp.w:call-sawfish-14.t:call-run_sawfish.stderr VERBOSE [M::mm_mapopt_update::94.896*1.78] mid_occ = 136
2025-09-15 20:25:07.248 wdl.w:ptcp.w:call-sawfish-14.t:call-run_sawfish.stderr VERBOSE [M::mm_idx_stat] kmer size: 19; skip: 19; is_hpc: 0; #seq: 195
2025-09-15 20:25:07.248 wdl.w:ptcp.w:call-sawfish-14.t:call-run_sawfish.stderr VERBOSE [M::mm_idx_stat::102.430*1.72] distinct minimizers: 214664461 (92.23% are singletons); average occurrences: 1.372; average spacing: 10.529; total length: 3099922541
2025-09-15 20:25:07.248 wdl.w:ptcp.w:call-sawfish-14.t:call-run_sawfish.stderr VERBOSE [M::bam2fq_mainloop] discarded 0 singletons
2025-09-15 20:25:07.248 wdl.w:ptcp.w:call-sawfish-14.t:call-run_sawfish.stderr VERBOSE [M::bam2fq_mainloop] processed 295 reads
2025-09-15 20:25:07.248 wdl.w:ptcp.w:call-sawfish-14.t:call-run_sawfish.stderr VERBOSE [M::worker_pipeline::103.166*1.72] mapped 295 sequences
2025-09-15 20:25:07.248 wdl.w:ptcp.w:call-sawfish-14.t:call-run_sawfish.stderr VERBOSE [M::main] Version: 2.26-r1175
2025-09-15 20:25:07.248 wdl.w:ptcp.w:call-sawfish-14.t:call-run_sawfish.stderr VERBOSE [M::main] CMD: /opt/pacbio/smrttools/install/smrtlink-release_25.1.0.257715/bundles/smrttools/install/smrttools-release_25.1.0.257715/private/thirdparty/minimap2/minimap2_2.26-pacbio2/binwrap/../../../../../private/thirdparty/minimap2/minimap2_2.26-pacbio2/bin/minimap2 -a -y -x map-hifi -Y -E 1,0 /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa -
2025-09-15 20:25:07.248 wdl.w:ptcp.w:call-sawfish-14.t:call-run_sawfish.stderr VERBOSE [M::main] Real time: 103.883 sec; CPU: 178.461 sec; Peak RSS: 11.886 GB
2025-09-15 20:25:07.248 wdl.w:ptcp.w:call-sawfish-14.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:46][sawfish][INFO] Starting sawfish 2.0.3
2025-09-15 20:25:07.248 wdl.w:ptcp.w:call-sawfish-14.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:46][sawfish][INFO] cmdline: sawfish discover --disable-cnv --threads 16 --ref /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa --bam m84036_250809_035451_s4.bc2111.minimap2.bam --output-dir m84036_250809_035451_s4.bc2111_sawfish_discover
2025-09-15 20:25:07.248 wdl.w:ptcp.w:call-sawfish-14.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:46][sawfish][INFO] Running on 16 threads
2025-09-15 20:25:07.248 wdl.w:ptcp.w:call-sawfish-14.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:46][sawfish][INFO] Writing discover settings to file: 'm84036_250809_035451_s4.bc2111_sawfish_discover/discover.settings.json'
2025-09-15 20:25:07.249 wdl.w:ptcp.w:call-sawfish-14.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:46][sawfish][INFO] Reading reference genome from file '/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa'
2025-09-15 20:25:07.249 wdl.w:ptcp.w:call-sawfish-14.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:57][sawfish][INFO] Processing alignment file '/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2111.minimap2.bam'
2025-09-15 20:25:07.252 wdl.w:ptcp.w:call-sawfish-14.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:57][sawfish][INFO] Finished processing all alignments
2025-09-15 20:25:07.252 wdl.w:ptcp.w:call-sawfish-14.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:57][sawfish][INFO] Writing depth bins to binary file: 'm84036_250809_035451_s4.bc2111_sawfish_discover/depth.mpack'
2025-09-15 20:25:07.252 wdl.w:ptcp.w:call-sawfish-14.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:58][sawfish][INFO] Writing max sv depth genome regions to bed file: 'm84036_250809_035451_s4.bc2111_sawfish_discover/max.depth.bed'
2025-09-15 20:25:07.252 wdl.w:ptcp.w:call-sawfish-14.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:58][sawfish][INFO] Completing breakpoint observation clustering
2025-09-15 20:25:07.252 wdl.w:ptcp.w:call-sawfish-14.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:58][sawfish][INFO] Finished breakpoint observation clustering
2025-09-15 20:25:07.252 wdl.w:ptcp.w:call-sawfish-14.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:58][sawfish][INFO] Consolidating adjacent indel candidates
2025-09-15 20:25:07.252 wdl.w:ptcp.w:call-sawfish-14.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:58][sawfish][INFO] Finding large insertion candidates
2025-09-15 20:25:07.252 wdl.w:ptcp.w:call-sawfish-14.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:58][sawfish][INFO] Writing breakpoint_cluster debug bed file: 'm84036_250809_035451_s4.bc2111_sawfish_discover/debug.breakpoint_clusters.bed'
2025-09-15 20:25:07.252 wdl.w:ptcp.w:call-sawfish-14.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:58][sawfish][INFO] Refining SV Candidates
2025-09-15 20:25:07.252 wdl.w:ptcp.w:call-sawfish-14.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:58][sawfish][INFO] Writing debug assembly region bed file: 'm84036_250809_035451_s4.bc2111_sawfish_discover/assembly.regions.bed'
2025-09-15 20:25:07.252 wdl.w:ptcp.w:call-sawfish-14.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:58][sawfish][INFO] Starting refinement of breakpoint evidence clusters
2025-09-15 20:25:07.252 wdl.w:ptcp.w:call-sawfish-14.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:59][sawfish][INFO] Finished refining all breakpoint evidence clusters
2025-09-15 20:25:07.252 wdl.w:ptcp.w:call-sawfish-14.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:59][sawfish][INFO] Writing all contig alignments to bam file: 'm84036_250809_035451_s4.bc2111_sawfish_discover/contig.alignment.bam'
2025-09-15 20:25:07.252 wdl.w:ptcp.w:call-sawfish-14.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:59][sawfish][INFO] Writing candidate structural variants to file: 'm84036_250809_035451_s4.bc2111_sawfish_discover/candidate.sv.bcf'
2025-09-15 20:25:07.252 wdl.w:ptcp.w:call-sawfish-14.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:59][sawfish][INFO] Writing run statistics to file: 'm84036_250809_035451_s4.bc2111_sawfish_discover/run.stats.json'
2025-09-15 20:25:07.253 wdl.w:ptcp.w:call-sawfish-14.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:00][sawfish][INFO] sawfish completed. Total Runtime: 00:00:13.847
2025-09-15 20:25:07.258 wdl.w:ptcp.w:call-trgt-73.t:call-get_reads_overlapping_repeats NOTICE slurm_singularity run :: pid: 1204700, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-73/call-get_reads_overlapping_repeats/slurm_singularity.log.txt"
2025-09-15 20:25:07.258 wdl.w:ptcp.w:call-trgt-73.t:call-trgt_genotype NOTICE slurm_singularity run :: pid: 1204701, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-73/call-trgt_genotype/slurm_singularity.log.txt"
2025-09-15 20:25:07.260 wdl.w:ptcp.w:call-trgt-61.t:call-trgt_plot_meth_allele INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-61/call-trgt_plot_meth_allele/_singularity_tmpdir_kknkts93"
2025-09-15 20:25:07.261 wdl.w:ptcp.w:call-trgt-61.t:call-trgt_plot_meth_allele INFO Slurm invocation: srun --job-name call-trgt_plot_meth_allele --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-61/call-trgt_plot_meth_allele/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-61/call-trgt_plot_meth_allele/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-61/call-trgt_plot_meth_allele/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-61/call-trgt_plot_meth_allele/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-61/call-trgt_genotype/out/m84036_250809_035451_s4.bc2158.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2158.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-61/call-trgt_genotype/out/m84036_250809_035451_s4.bc2158.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2158.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-61/call-trgt_genotype/out/m84036_250809_035451_s4.bc2158.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2158.trgt.sorted.spanning.bam:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-61/call-trgt_plot_meth_allele/_singularity_tmpdir_kknkts93/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-61/call-trgt_plot_meth_allele/_singularity_tmpdir_kknkts93/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:07.268 wdl.w:ptcp.w:call-trgt-53 NOTICE done
2025-09-15 20:25:07.271 wdl.w:ptcp.w:call-paraphase-22.t:call-call_f8 NOTICE done
2025-09-15 20:25:07.272 wdl.w:ptcp NOTICE finish :: job: "call-trgt-53"
2025-09-15 20:25:07.272 wdl.w:ptcp INFO output :: job: "call-trgt-53", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-53/out/m84036_250809_035451_s4.bc2150.motifs_waterfall.trgt_plots.zip", "images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-53/out/m84036_250809_035451_s4.bc2150.meth_allele.trgt_plots.zip", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-53/out/m84036_250809_035451_s4.bc2150.trgt.sorted.spanning.bam.bai", "images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-53/out/m84036_250809_035451_s4.bc2150.motifs_allele.trgt_plots.zip", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-53/out/m84036_250809_035451_s4.bc2150.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-53/out/m84036_250809_035451_s4.bc2150.trgt.vcf", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-53/out/m84036_250809_035451_s4.bc2150.repeats.bam", "images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-53/out/m84036_250809_035451_s4.bc2150.meth_waterfall.trgt_plots.zip", "reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-53/out/m84036_250809_035451_s4.bc2150.repeats.bam.bai"}
2025-09-15 20:25:07.275 wdl.w:ptcp.w:call-paraphase-56.t:call-call_f8 INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2153.f8inversion.vcf"
2025-09-15 20:25:07.278 wdl.w:ptcp.w:call-paraphase-22 NOTICE finish :: job: "call-call_f8"
2025-09-15 20:25:07.278 wdl.w:ptcp.w:call-paraphase-22 INFO output :: job: "call-call_f8", values: {"json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-22/call-call_f8/out/m84036_250809_035451_s4.bc2119.f8inversion.json", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-22/call-call_f8/out/m84036_250809_035451_s4.bc2119.f8inversion.vcf"}
2025-09-15 20:25:07.278 wdl.w:ptcp.w:call-paraphase-22 INFO visit :: node: "output-f8_json", values: {"f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-22/call-call_f8/out/m84036_250809_035451_s4.bc2119.f8inversion.json"}
2025-09-15 20:25:07.278 wdl.w:ptcp.w:call-paraphase-22 INFO visit :: node: "output-f8_vcf", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-22/call-call_f8/out/m84036_250809_035451_s4.bc2119.f8inversion.vcf"}
2025-09-15 20:25:07.279 wdl.w:ptcp.w:call-paraphase-22 INFO visit :: node: "outputs", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-22/call-call_f8/out/m84036_250809_035451_s4.bc2119.f8inversion.vcf", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-22/call-run_paraphase/out/m84036_250809_035451_s4.bc2119_paraphase/m84036_250809_035451_s4.bc2119.paraphase.json", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-22/call-run_paraphase/out/m84036_250809_035451_s4.bc2119_paraphase/m84036_250809_035451_s4.bc2119.paraphase.bam", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-22/call-run_paraphase/out/m84036_250809_035451_s4.bc2119_paraphase/m84036_250809_035451_s4.bc2119.paraphase.bam.bai", "paraphase_vcfs": ["/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-22/call-run_paraphase/out/m84036_250809_035451_s4.bc2119_paraphase/m84036_250809_035451_s4.bc2119_paraphase_vcfs/m84036_250809_035451_s4.bc2119_cyp21.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-22/call-run_paraphase/out/m84036_250809_035451_s4.bc2119_paraphase/m84036_250809_035451_s4.bc2119_paraphase_vcfs/m84036_250809_035451_s4.bc2119_f8inv1.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-22/call-run_paraphase/out/m84036_250809_035451_s4.bc2119_paraphase/m84036_250809_035451_s4.bc2119_paraphase_vcfs/m84036_250809_035451_s4.bc2119_f8inv22.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-22/call-run_paraphase/out/m84036_250809_035451_s4.bc2119_paraphase/m84036_250809_035451_s4.bc2119_paraphase_vcfs/m84036_250809_035451_s4.bc2119_gba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-22/call-run_paraphase/out/m84036_250809_035451_s4.bc2119_paraphase/m84036_250809_035451_s4.bc2119_paraphase_vcfs/m84036_250809_035451_s4.bc2119_hba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-22/call-run_paraphase/out/m84036_250809_035451_s4.bc2119_paraphase/m84036_250809_035451_s4.bc2119_paraphase_vcfs/m84036_250809_035451_s4.bc2119_hbb.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-22/call-run_paraphase/out/m84036_250809_035451_s4.bc2119_paraphase/m84036_250809_035451_s4.bc2119_paraphase_vcfs/m84036_250809_035451_s4.bc2119_rpgr.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-22/call-run_paraphase/out/m84036_250809_035451_s4.bc2119_paraphase/m84036_250809_035451_s4.bc2119_paraphase_vcfs/m84036_250809_035451_s4.bc2119_smn1.vcf"], "havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-22/call-run_paraphase/out/m84036_250809_035451_s4.bc2119.havanno.json", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-22/call-call_f8/out/m84036_250809_035451_s4.bc2119.f8inversion.json"}
2025-09-15 20:25:07.279 wdl.w:ptcp.w:call-sawfish-80 NOTICE workflow start :: name: "sawfish", source: "./sawfish.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-80"
2025-09-15 20:25:07.281 wdl.w:ptcp.w:call-paraphase-56.t:call-call_f8 INFO output :: name: "json", value: "m84036_250809_035451_s4.bc2153.f8inversion.json"
2025-09-15 20:25:07.281 wdl.w:ptcp.w:call-trgt-61.t:call-trgt_plot_meth_waterfall INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-61/call-trgt_plot_meth_waterfall/_singularity_tmpdir_xvtamvab"
2025-09-15 20:25:07.281 wdl.w:ptcp.w:call-trgt-61.t:call-trgt_plot_meth_waterfall INFO Slurm invocation: srun --job-name call-trgt_plot_meth_waterfall --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-61/call-trgt_plot_meth_waterfall/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-61/call-trgt_plot_meth_waterfall/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-61/call-trgt_plot_meth_waterfall/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-61/call-trgt_plot_meth_waterfall/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-61/call-trgt_genotype/out/m84036_250809_035451_s4.bc2158.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2158.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-61/call-trgt_genotype/out/m84036_250809_035451_s4.bc2158.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2158.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-61/call-trgt_genotype/out/m84036_250809_035451_s4.bc2158.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2158.trgt.sorted.spanning.bam:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-61/call-trgt_plot_meth_waterfall/_singularity_tmpdir_xvtamvab/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-61/call-trgt_plot_meth_waterfall/_singularity_tmpdir_xvtamvab/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:07.286 wdl.w:ptcp.w:call-trgt-61.t:call-trgt_plot_motifs_allele NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-61/call-trgt_plot_motifs_allele", thread: 140607674631744
2025-09-15 20:25:07.297 wdl.w:ptcp.w:call-trgt-61.t:call-trgt_plot_meth_waterfall NOTICE slurm_singularity run :: pid: 1204706, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-61/call-trgt_plot_meth_waterfall/slurm_singularity.log.txt"
2025-09-15 20:25:07.297 wdl.w:ptcp.w:call-trgt-61.t:call-trgt_plot_meth_allele NOTICE slurm_singularity run :: pid: 1204703, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-61/call-trgt_plot_meth_allele/slurm_singularity.log.txt"
2025-09-15 20:25:07.299 wdl.w:ptcp.w:call-sawfish-80 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:25:07.300 wdl.w:ptcp.w:call-sawfish-80 INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:25:07.300 wdl.w:ptcp.w:call-sawfish-80 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-80/out/m84036_250809_035451_s4.bc2177.mapped.bam"}
2025-09-15 20:25:07.300 wdl.w:ptcp.w:call-sawfish-80 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-80/out/m84036_250809_035451_s4.bc2177.mapped.bam.bai"}
2025-09-15 20:25:07.301 wdl.w:ptcp.w:call-sawfish-80 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:25:07.301 wdl.w:ptcp.w:call-sawfish-80 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:25:07.301 wdl.w:ptcp.w:call-sawfish-80 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2177"}
2025-09-15 20:25:07.301 wdl.w:ptcp.w:call-sawfish-80 NOTICE ready :: job: "call-run_sawfish", callee: "run_sawfish"
2025-09-15 20:25:07.302 wdl.w:ptcp.w:call-sawfish-80 INFO input :: job: "call-run_sawfish", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-80/out/m84036_250809_035451_s4.bc2177.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-80/out/m84036_250809_035451_s4.bc2177.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2177"}
2025-09-15 20:25:07.313 wdl.w:ptcp.w:call-trgt-61.t:call-trgt_plot_motifs_allele INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:07.314 wdl.w:ptcp.w:call-trgt-61.t:call-trgt_plot_motifs_allele INFO input :: name: "waterfall", value: false
2025-09-15 20:25:07.314 wdl.w:ptcp.w:call-trgt-61.t:call-trgt_plot_motifs_allele INFO input :: name: "methylation", value: false
2025-09-15 20:25:07.314 wdl.w:ptcp.w:call-trgt-61.t:call-trgt_plot_motifs_allele INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:25:07.314 wdl.w:ptcp.w:call-trgt-61.t:call-trgt_plot_motifs_allele INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:25:07.314 wdl.w:ptcp.w:call-trgt-61.t:call-trgt_plot_motifs_allele INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:25:07.314 wdl.w:ptcp.w:call-trgt-61.t:call-trgt_plot_motifs_allele INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2158.trgt.sorted.spanning.bam.bai"
2025-09-15 20:25:07.314 wdl.w:ptcp.w:call-trgt-61.t:call-trgt_plot_motifs_allele INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2158.trgt.sorted.spanning.bam"
2025-09-15 20:25:07.314 wdl.w:ptcp.w:call-trgt-61.t:call-trgt_plot_motifs_allele INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2158.trgt.vcf"
2025-09-15 20:25:07.314 wdl.w:ptcp.w:call-trgt-61.t:call-trgt_plot_motifs_allele INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2158"
2025-09-15 20:25:07.315 wdl.w:ptcp.w:call-trgt-61.t:call-trgt_plot_motifs_allele INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:25:07.315 wdl.w:ptcp.w:call-trgt-61.t:call-trgt_plot_motifs_allele INFO eval :: name: "plot_type", value: "allele"
2025-09-15 20:25:07.315 wdl.w:ptcp.w:call-trgt-61.t:call-trgt_plot_motifs_allele INFO eval :: name: "show", value: "motifs"
2025-09-15 20:25:07.315 wdl.w:ptcp.w:call-trgt-61.t:call-trgt_plot_motifs_allele INFO eval :: name: "threads", value: 1
2025-09-15 20:25:07.315 wdl.w:ptcp.w:call-trgt-61.t:call-trgt_plot_motifs_allele INFO eval :: name: "disk_size", value: 27
2025-09-15 20:25:07.315 wdl.w:ptcp.w:call-trgt-61.t:call-trgt_plot_motifs_allele INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2158.motifs_allele"
2025-09-15 20:25:07.316 wdl.w:ptcp.w:call-trgt-61.t:call-trgt_plot_motifs_allele INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:07.316 wdl.w:ptcp.w:call-trgt-61.t:call-trgt_plot_motifs_allele WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:07.317 wdl.w:ptcp.w:call-trgt-61.t:call-trgt_plot_motifs_allele INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:25:07.317 wdl.w:ptcp.w:call-trgt-61.t:call-trgt_plot_motifs_allele INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:07.322 wdl.w:ptcp.w:call-trgt-58.t:call-trgt_plot_motifs_waterfall NOTICE done
2025-09-15 20:25:07.322 wdl.w:ptcp.w:call-sawfish-27.t:call-run_sawfish NOTICE done
2025-09-15 20:25:07.326 wdl.w:ptcp.w:call-trgt-56.t:call-trgt_plot_motifs_waterfall NOTICE done
2025-09-15 20:25:07.328 wdl.w:ptcp.w:call-trgt-58 NOTICE finish :: job: "call-trgt_plot_motifs_waterfall"
2025-09-15 20:25:07.328 wdl.w:ptcp.w:call-trgt-58 INFO output :: job: "call-trgt_plot_motifs_waterfall", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-58/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2155.motifs_waterfall.trgt_plots.zip"}
2025-09-15 20:25:07.329 wdl.w:ptcp.w:call-sawfish-27 NOTICE finish :: job: "call-run_sawfish"
2025-09-15 20:25:07.329 wdl.w:ptcp.w:call-trgt-58 INFO visit :: node: "output-images_motifs_waterfall", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-58/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2155.motifs_waterfall.trgt_plots.zip"}
2025-09-15 20:25:07.329 wdl.w:ptcp.w:call-paraphase-60.t:call-run_paraphase NOTICE done
2025-09-15 20:25:07.329 wdl.w:ptcp.w:call-sawfish-27 INFO output :: job: "call-run_sawfish", values: {"minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-27/call-run_sawfish/out/m84036_250809_035451_s4.bc2124.minimap2.bam.bai", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-27/call-run_sawfish/out/m84036_250809_035451_s4.bc2124.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-27/call-run_sawfish/out/m84036_250809_035451_s4.bc2124_sawfish/m84036_250809_035451_s4.bc2124.sv.vcf.gz.tbi", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-27/call-run_sawfish/out/m84036_250809_035451_s4.bc2124_sawfish/m84036_250809_035451_s4.bc2124.sv.vcf.gz"}
2025-09-15 20:25:07.330 wdl.w:ptcp.w:call-sawfish-27 INFO visit :: node: "output-minimap2_bam", values: {"minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-27/call-run_sawfish/out/m84036_250809_035451_s4.bc2124.minimap2.bam"}
2025-09-15 20:25:07.331 wdl.w:ptcp.w:call-sawfish-27 INFO visit :: node: "output-minimap2_bam_bai", values: {"minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-27/call-run_sawfish/out/m84036_250809_035451_s4.bc2124.minimap2.bam.bai"}
2025-09-15 20:25:07.331 wdl.w:ptcp.w:call-sawfish-27 INFO visit :: node: "output-vcf", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-27/call-run_sawfish/out/m84036_250809_035451_s4.bc2124_sawfish/m84036_250809_035451_s4.bc2124.sv.vcf.gz"}
2025-09-15 20:25:07.331 wdl.w:ptcp.w:call-sawfish-27 INFO visit :: node: "output-vcf_tbi", values: {"vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-27/call-run_sawfish/out/m84036_250809_035451_s4.bc2124_sawfish/m84036_250809_035451_s4.bc2124.sv.vcf.gz.tbi"}
2025-09-15 20:25:07.331 wdl.w:ptcp.w:call-sawfish-27 INFO visit :: node: "outputs", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-27/call-run_sawfish/out/m84036_250809_035451_s4.bc2124_sawfish/m84036_250809_035451_s4.bc2124.sv.vcf.gz", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-27/call-run_sawfish/out/m84036_250809_035451_s4.bc2124.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-27/call-run_sawfish/out/m84036_250809_035451_s4.bc2124_sawfish/m84036_250809_035451_s4.bc2124.sv.vcf.gz.tbi", "minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-27/call-run_sawfish/out/m84036_250809_035451_s4.bc2124.minimap2.bam.bai"}
2025-09-15 20:25:07.336 wdl.w:ptcp.w:call-trgt-56 NOTICE finish :: job: "call-trgt_plot_motifs_waterfall"
2025-09-15 20:25:07.336 wdl.w:ptcp.w:call-trgt-56 INFO output :: job: "call-trgt_plot_motifs_waterfall", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-56/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2153.motifs_waterfall.trgt_plots.zip"}
2025-09-15 20:25:07.336 wdl.w:ptcp.w:call-trgt-56 INFO visit :: node: "output-images_motifs_waterfall", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-56/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2153.motifs_waterfall.trgt_plots.zip"}
2025-09-15 20:25:07.337 wdl.w:ptcp.w:call-paraphase-60 NOTICE finish :: job: "call-run_paraphase"
2025-09-15 20:25:07.337 wdl.w:ptcp.w:call-paraphase-60 INFO output :: job: "call-run_paraphase", values: {"havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-60/call-run_paraphase/out/m84036_250809_035451_s4.bc2157.havanno.json", "paraphase_vcfs": [], "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-60/call-run_paraphase/out/m84036_250809_035451_s4.bc2157_paraphase/m84036_250809_035451_s4.bc2157.paraphase.json", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-60/call-run_paraphase/out/m84036_250809_035451_s4.bc2157_paraphase/m84036_250809_035451_s4.bc2157.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-60/call-run_paraphase/out/m84036_250809_035451_s4.bc2157_paraphase/m84036_250809_035451_s4.bc2157.paraphase.bam"}
2025-09-15 20:25:07.338 wdl.w:ptcp.w:call-paraphase-60 NOTICE ready :: job: "call-call_f8", callee: "call_f8"
2025-09-15 20:25:07.338 wdl.w:ptcp.w:call-paraphase-60 INFO input :: job: "call-call_f8", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "out_prefix": "m84036_250809_035451_s4.bc2157", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-60/call-run_paraphase/out/m84036_250809_035451_s4.bc2157_paraphase/m84036_250809_035451_s4.bc2157.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-60/call-run_paraphase/out/m84036_250809_035451_s4.bc2157_paraphase/m84036_250809_035451_s4.bc2157.paraphase.bam", "sex": "F"}
2025-09-15 20:25:07.340 wdl.w:ptcp.w:call-paraphase-60 INFO visit :: node: "output-havanno_json", values: {"havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-60/call-run_paraphase/out/m84036_250809_035451_s4.bc2157.havanno.json"}
2025-09-15 20:25:07.340 wdl.w:ptcp.w:call-paraphase-60 INFO visit :: node: "output-paraphase_bam", values: {"paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-60/call-run_paraphase/out/m84036_250809_035451_s4.bc2157_paraphase/m84036_250809_035451_s4.bc2157.paraphase.bam"}
2025-09-15 20:25:07.340 wdl.w:ptcp.w:call-paraphase-60 INFO visit :: node: "output-paraphase_bam_bai", values: {"paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-60/call-run_paraphase/out/m84036_250809_035451_s4.bc2157_paraphase/m84036_250809_035451_s4.bc2157.paraphase.bam.bai"}
2025-09-15 20:25:07.340 wdl.w:ptcp.w:call-paraphase-60 INFO visit :: node: "output-paraphase_json", values: {"paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-60/call-run_paraphase/out/m84036_250809_035451_s4.bc2157_paraphase/m84036_250809_035451_s4.bc2157.paraphase.json"}
2025-09-15 20:25:07.339 wdl.w:ptcp.w:call-paraphase-74.t:call-run_paraphase NOTICE task setup :: name: "run_paraphase", source: "./paraphase.wdl", line: 127, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-74/call-run_paraphase", thread: 140613018162752
2025-09-15 20:25:07.340 wdl.w:ptcp.w:call-paraphase-60 INFO visit :: node: "output-paraphase_vcfs", values: {"paraphase_vcfs": []}
2025-09-15 20:25:07.345 wdl.w:ptcp.w:call-trgt-64.t:call-trgt_plot_meth_allele NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-64/call-trgt_plot_meth_allele", thread: 140607137760832
2025-09-15 20:25:07.348 wdl.w:ptcp.w:call-trgt-64.t:call-trgt_plot_meth_waterfall NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-64/call-trgt_plot_meth_waterfall", thread: 140608211502656
2025-09-15 20:25:07.349 wdl.w:ptcp.w:call-sawfish-11.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:55][sawfish][INFO] Starting sawfish 2.0.3
2025-09-15 20:25:07.349 wdl.w:ptcp.w:call-sawfish-11.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:55][sawfish][INFO] cmdline: sawfish discover --disable-cnv --threads 16 --ref /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa --bam m84036_250809_035451_s4.bc2108.minimap2.bam --output-dir m84036_250809_035451_s4.bc2108_sawfish_discover
2025-09-15 20:25:07.350 wdl.w:ptcp.w:call-sawfish-11.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:55][sawfish][INFO] Running on 16 threads
2025-09-15 20:25:07.350 wdl.w:ptcp.w:call-sawfish-11.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:55][sawfish][INFO] Writing discover settings to file: 'm84036_250809_035451_s4.bc2108_sawfish_discover/discover.settings.json'
2025-09-15 20:25:07.350 wdl.w:ptcp.w:call-sawfish-11.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:55][sawfish][INFO] Reading reference genome from file '/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa'
2025-09-15 20:25:07.350 wdl.w:ptcp.w:call-sawfish-11.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:01][sawfish][INFO] Processing alignment file '/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2108.minimap2.bam'
2025-09-15 20:25:07.350 wdl.w:ptcp.w:call-sawfish-11.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:01][sawfish][INFO] Finished processing all alignments
2025-09-15 20:25:07.350 wdl.w:ptcp.w:call-sawfish-11.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:01][sawfish][INFO] Writing depth bins to binary file: 'm84036_250809_035451_s4.bc2108_sawfish_discover/depth.mpack'
2025-09-15 20:25:07.350 wdl.w:ptcp.w:call-sawfish-11.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:02][sawfish][INFO] Writing max sv depth genome regions to bed file: 'm84036_250809_035451_s4.bc2108_sawfish_discover/max.depth.bed'
2025-09-15 20:25:07.350 wdl.w:ptcp.w:call-sawfish-11.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:02][sawfish][INFO] Completing breakpoint observation clustering
2025-09-15 20:25:07.350 wdl.w:ptcp.w:call-sawfish-11.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:02][sawfish][INFO] Finished breakpoint observation clustering
2025-09-15 20:25:07.350 wdl.w:ptcp.w:call-sawfish-11.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:02][sawfish][INFO] Consolidating adjacent indel candidates
2025-09-15 20:25:07.350 wdl.w:ptcp.w:call-sawfish-11.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:02][sawfish][INFO] Finding large insertion candidates
2025-09-15 20:25:07.350 wdl.w:ptcp.w:call-sawfish-11.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:02][sawfish][INFO] Writing breakpoint_cluster debug bed file: 'm84036_250809_035451_s4.bc2108_sawfish_discover/debug.breakpoint_clusters.bed'
2025-09-15 20:25:07.350 wdl.w:ptcp.w:call-sawfish-11.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:02][sawfish][INFO] Refining SV Candidates
2025-09-15 20:25:07.350 wdl.w:ptcp.w:call-sawfish-11.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:02][sawfish][INFO] Writing debug assembly region bed file: 'm84036_250809_035451_s4.bc2108_sawfish_discover/assembly.regions.bed'
2025-09-15 20:25:07.350 wdl.w:ptcp.w:call-sawfish-11.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:02][sawfish][INFO] Starting refinement of breakpoint evidence clusters
2025-09-15 20:25:07.351 wdl.w:ptcp.w:call-sawfish-11.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:03][sawfish][INFO] Finished refining all breakpoint evidence clusters
2025-09-15 20:25:07.351 wdl.w:ptcp.w:call-sawfish-11.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:03][sawfish][INFO] Writing all contig alignments to bam file: 'm84036_250809_035451_s4.bc2108_sawfish_discover/contig.alignment.bam'
2025-09-15 20:25:07.351 wdl.w:ptcp.w:call-sawfish-11.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:03][sawfish][INFO] Writing candidate structural variants to file: 'm84036_250809_035451_s4.bc2108_sawfish_discover/candidate.sv.bcf'
2025-09-15 20:25:07.351 wdl.w:ptcp.w:call-sawfish-11.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:03][sawfish][INFO] Writing run statistics to file: 'm84036_250809_035451_s4.bc2108_sawfish_discover/run.stats.json'
2025-09-15 20:25:07.351 wdl.w:ptcp.w:call-sawfish-11.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:03][sawfish][INFO] sawfish completed. Total Runtime: 00:00:07.427
2025-09-15 20:25:07.357 wdl.w:ptcp.w:call-trgt-61.t:call-trgt_plot_motifs_waterfall NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-61/call-trgt_plot_motifs_waterfall", thread: 140610367379008
2025-09-15 20:25:07.370 wdl.w:ptcp.w:call-paraphase-74.t:call-run_paraphase INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:07.370 wdl.w:ptcp.w:call-paraphase-74.t:call-run_paraphase INFO input :: name: "annotation_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf"
2025-09-15 20:25:07.370 wdl.w:ptcp.w:call-paraphase-74.t:call-run_paraphase INFO input :: name: "genome_version", value: "38"
2025-09-15 20:25:07.370 wdl.w:ptcp.w:call-paraphase-74.t:call-run_paraphase INFO input :: name: "config_file", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/paraphase_config.GRCh38.yaml"
2025-09-15 20:25:07.370 wdl.w:ptcp.w:call-paraphase-74.t:call-run_paraphase INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:25:07.370 wdl.w:ptcp.w:call-paraphase-74.t:call-run_paraphase INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:25:07.371 wdl.w:ptcp.w:call-paraphase-74.t:call-run_paraphase INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2171.mapped.bam.bai"
2025-09-15 20:25:07.371 wdl.w:ptcp.w:call-paraphase-74.t:call-run_paraphase INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2171.mapped.bam"
2025-09-15 20:25:07.371 wdl.w:ptcp.w:call-paraphase-74.t:call-run_paraphase INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2171"
2025-09-15 20:25:07.371 wdl.w:ptcp.w:call-paraphase-74.t:call-run_paraphase INFO eval :: name: "threads", value: 4
2025-09-15 20:25:07.371 wdl.w:ptcp.w:call-paraphase-74.t:call-run_paraphase INFO eval :: name: "mem_gb", value: 8
2025-09-15 20:25:07.372 wdl.w:ptcp.w:call-paraphase-74.t:call-run_paraphase INFO eval :: name: "disk_size", value: 27
2025-09-15 20:25:07.372 wdl.w:ptcp.w:call-paraphase-74.t:call-run_paraphase INFO eval :: name: "out_dir", value: "m84036_250809_035451_s4.bc2171_paraphase"
2025-09-15 20:25:07.373 wdl.w:ptcp.w:call-paraphase-74.t:call-run_paraphase INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 4, memory_reservation: 8000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:07.373 wdl.w:ptcp.w:call-paraphase-74.t:call-run_paraphase WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:07.374 wdl.w:ptcp.w:call-paraphase-74.t:call-run_paraphase INFO provisioned :: seconds_waited: 0, cpu: 4, mem_bytes: 8000000000
2025-09-15 20:25:07.374 wdl.w:ptcp.w:call-paraphase-74.t:call-run_paraphase INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:07.374 wdl.w:ptcp.w:call-trgt-64.t:call-trgt_plot_meth_allele INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:07.375 wdl.w:ptcp.w:call-trgt-64.t:call-trgt_plot_meth_allele INFO input :: name: "waterfall", value: false
2025-09-15 20:25:07.375 wdl.w:ptcp.w:call-trgt-64.t:call-trgt_plot_meth_waterfall INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:07.375 wdl.w:ptcp.w:call-trgt-64.t:call-trgt_plot_meth_allele INFO input :: name: "methylation", value: true
2025-09-15 20:25:07.376 wdl.w:ptcp.w:call-trgt-64.t:call-trgt_plot_meth_waterfall INFO input :: name: "waterfall", value: true
2025-09-15 20:25:07.376 wdl.w:ptcp.w:call-trgt-64.t:call-trgt_plot_meth_allele INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:25:07.376 wdl.w:ptcp.w:call-trgt-64.t:call-trgt_plot_meth_waterfall INFO input :: name: "methylation", value: true
2025-09-15 20:25:07.376 wdl.w:ptcp.w:call-trgt-64.t:call-trgt_plot_meth_allele INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:25:07.376 wdl.w:ptcp.w:call-trgt-64.t:call-trgt_plot_meth_waterfall INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:25:07.376 wdl.w:ptcp.w:call-trgt-64.t:call-trgt_plot_meth_allele INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:25:07.376 wdl.w:ptcp.w:call-trgt-64.t:call-trgt_plot_meth_waterfall INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:25:07.376 wdl.w:ptcp.w:call-trgt-64.t:call-trgt_plot_meth_allele INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2161.trgt.sorted.spanning.bam.bai"
2025-09-15 20:25:07.376 wdl.w:ptcp.w:call-paraphase-56.t:call-call_f8 NOTICE done
2025-09-15 20:25:07.377 wdl.w:ptcp.w:call-trgt-64.t:call-trgt_plot_meth_waterfall INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:25:07.377 wdl.w:ptcp.w:call-trgt-64.t:call-trgt_plot_meth_allele INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2161.trgt.sorted.spanning.bam"
2025-09-15 20:25:07.377 wdl.w:ptcp.w:call-trgt-64.t:call-trgt_plot_meth_waterfall INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2161.trgt.sorted.spanning.bam.bai"
2025-09-15 20:25:07.377 wdl.w:ptcp.w:call-trgt-64.t:call-trgt_plot_meth_allele INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2161.trgt.vcf"
2025-09-15 20:25:07.377 wdl.w:ptcp.w:call-trgt-64.t:call-trgt_plot_meth_waterfall INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2161.trgt.sorted.spanning.bam"
2025-09-15 20:25:07.377 wdl.w:ptcp.w:call-trgt-64.t:call-trgt_plot_meth_allele INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2161"
2025-09-15 20:25:07.377 wdl.w:ptcp.w:call-trgt-64.t:call-trgt_plot_meth_waterfall INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2161.trgt.vcf"
2025-09-15 20:25:07.378 wdl.w:ptcp.w:call-trgt-64.t:call-trgt_plot_meth_allele INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:25:07.378 wdl.w:ptcp.w:call-trgt-64.t:call-trgt_plot_meth_waterfall INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2161"
2025-09-15 20:25:07.378 wdl.w:ptcp.w:call-trgt-64.t:call-trgt_plot_meth_allele INFO eval :: name: "plot_type", value: "allele"
2025-09-15 20:25:07.378 wdl.w:ptcp.w:call-trgt-64.t:call-trgt_plot_meth_waterfall INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:25:07.378 wdl.w:ptcp.w:call-trgt-64.t:call-trgt_plot_meth_allele INFO eval :: name: "show", value: "meth"
2025-09-15 20:25:07.378 wdl.w:ptcp.w:call-trgt-64.t:call-trgt_plot_meth_waterfall INFO eval :: name: "plot_type", value: "waterfall"
2025-09-15 20:25:07.378 wdl.w:ptcp.w:call-trgt-64.t:call-trgt_plot_meth_allele INFO eval :: name: "threads", value: 1
2025-09-15 20:25:07.379 wdl.w:ptcp.w:call-trgt-64.t:call-trgt_plot_meth_waterfall INFO eval :: name: "show", value: "meth"
2025-09-15 20:25:07.379 wdl.w:ptcp.w:call-trgt-64.t:call-trgt_plot_meth_waterfall INFO eval :: name: "threads", value: 1
2025-09-15 20:25:07.379 wdl.w:ptcp.w:call-trgt-64.t:call-trgt_plot_meth_allele INFO eval :: name: "disk_size", value: 27
2025-09-15 20:25:07.379 wdl.w:ptcp.w:call-trgt-64.t:call-trgt_plot_meth_allele INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2161.meth_allele"
2025-09-15 20:25:07.379 wdl.w:ptcp.w:call-trgt-64.t:call-trgt_plot_meth_waterfall INFO eval :: name: "disk_size", value: 27
2025-09-15 20:25:07.380 wdl.w:ptcp.w:call-trgt-61.t:call-trgt_plot_motifs_waterfall INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:07.380 wdl.w:ptcp.w:call-trgt-64.t:call-trgt_plot_meth_allele INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:07.380 wdl.w:ptcp.w:call-trgt-64.t:call-trgt_plot_meth_waterfall INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2161.meth_waterfall"
2025-09-15 20:25:07.380 wdl.w:ptcp.w:call-trgt-61.t:call-trgt_plot_motifs_waterfall INFO input :: name: "waterfall", value: true
2025-09-15 20:25:07.381 wdl.w:ptcp.w:call-trgt-64.t:call-trgt_plot_meth_allele WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:07.381 wdl.w:ptcp.w:call-trgt-64.t:call-trgt_plot_meth_waterfall INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:07.381 wdl.w:ptcp.w:call-trgt-61.t:call-trgt_plot_motifs_waterfall INFO input :: name: "methylation", value: false
2025-09-15 20:25:07.381 wdl.w:ptcp.w:call-trgt-64.t:call-trgt_plot_meth_waterfall WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:07.382 wdl.w:ptcp.w:call-trgt-61.t:call-trgt_plot_motifs_waterfall INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:25:07.382 wdl.w:ptcp.w:call-trgt-61.t:call-trgt_plot_motifs_waterfall INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:25:07.382 wdl.w:ptcp.w:call-trgt-61.t:call-trgt_plot_motifs_waterfall INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:25:07.382 wdl.w:ptcp.w:call-paraphase-56 NOTICE finish :: job: "call-call_f8"
2025-09-15 20:25:07.383 wdl.w:ptcp.w:call-trgt-61.t:call-trgt_plot_motifs_waterfall INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2158.trgt.sorted.spanning.bam.bai"
2025-09-15 20:25:07.383 wdl.w:ptcp.w:call-paraphase-56 INFO output :: job: "call-call_f8", values: {"json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-56/call-call_f8/out/m84036_250809_035451_s4.bc2153.f8inversion.json", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-56/call-call_f8/out/m84036_250809_035451_s4.bc2153.f8inversion.vcf"}
2025-09-15 20:25:07.383 wdl.w:ptcp.w:call-trgt-64.t:call-trgt_plot_meth_allele INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:25:07.383 wdl.w:ptcp.w:call-trgt-61.t:call-trgt_plot_motifs_waterfall INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2158.trgt.sorted.spanning.bam"
2025-09-15 20:25:07.383 wdl.w:ptcp.w:call-paraphase-56 INFO visit :: node: "output-f8_json", values: {"f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-56/call-call_f8/out/m84036_250809_035451_s4.bc2153.f8inversion.json"}
2025-09-15 20:25:07.384 wdl.w:ptcp.w:call-trgt-64.t:call-trgt_plot_meth_allele INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:07.384 wdl.w:ptcp.w:call-trgt-64.t:call-trgt_plot_meth_waterfall INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:25:07.384 wdl.w:ptcp.w:call-trgt-61.t:call-trgt_plot_motifs_waterfall INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2158.trgt.vcf"
2025-09-15 20:25:07.384 wdl.w:ptcp.w:call-paraphase-56 INFO visit :: node: "output-f8_vcf", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-56/call-call_f8/out/m84036_250809_035451_s4.bc2153.f8inversion.vcf"}
2025-09-15 20:25:07.384 wdl.w:ptcp.w:call-trgt-64.t:call-trgt_plot_meth_waterfall INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:07.384 wdl.w:ptcp.w:call-trgt-61.t:call-trgt_plot_motifs_waterfall INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2158"
2025-09-15 20:25:07.385 wdl.w:ptcp.w:call-paraphase-56 INFO visit :: node: "outputs", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-56/call-call_f8/out/m84036_250809_035451_s4.bc2153.f8inversion.vcf", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-56/call-run_paraphase/out/m84036_250809_035451_s4.bc2153_paraphase/m84036_250809_035451_s4.bc2153.paraphase.json", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-56/call-run_paraphase/out/m84036_250809_035451_s4.bc2153_paraphase/m84036_250809_035451_s4.bc2153.paraphase.bam", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-56/call-run_paraphase/out/m84036_250809_035451_s4.bc2153_paraphase/m84036_250809_035451_s4.bc2153.paraphase.bam.bai", "paraphase_vcfs": [], "havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-56/call-run_paraphase/out/m84036_250809_035451_s4.bc2153.havanno.json", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-56/call-call_f8/out/m84036_250809_035451_s4.bc2153.f8inversion.json"}
2025-09-15 20:25:07.385 wdl.w:ptcp.w:call-trgt-61.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:25:07.385 wdl.w:ptcp.w:call-trgt-61.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "plot_type", value: "waterfall"
2025-09-15 20:25:07.385 wdl.w:ptcp.w:call-trgt-61.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "show", value: "motifs"
2025-09-15 20:25:07.385 wdl.w:ptcp.w:call-trgt-61.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "threads", value: 1
2025-09-15 20:25:07.386 wdl.w:ptcp.w:call-trgt-61.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "disk_size", value: 27
2025-09-15 20:25:07.386 wdl.w:ptcp.w:call-trgt-61.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2158.motifs_waterfall"
2025-09-15 20:25:07.386 wdl.w:ptcp.w:call-trgt-61.t:call-trgt_plot_motifs_waterfall INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:07.386 wdl.w:ptcp.w:call-trgt-61.t:call-trgt_plot_motifs_waterfall WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:07.387 wdl.w:ptcp.w:call-trgt-61.t:call-trgt_plot_motifs_waterfall INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:25:07.387 wdl.w:ptcp.w:call-trgt-61.t:call-trgt_plot_motifs_waterfall INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:07.394 wdl.w:ptcp.w:call-trgt-64.t:call-trgt_plot_motifs_allele NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-64/call-trgt_plot_motifs_allele", thread: 140610895857216
2025-09-15 20:25:07.417 wdl.w:ptcp.w:call-sawfish-27 NOTICE done
2025-09-15 20:25:07.422 wdl.w:ptcp.w:call-trgt-64.t:call-trgt_plot_motifs_allele INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:07.423 wdl.w:ptcp.w:call-trgt-64.t:call-trgt_plot_motifs_allele INFO input :: name: "waterfall", value: false
2025-09-15 20:25:07.423 wdl.w:ptcp.w:call-trgt-64.t:call-trgt_plot_motifs_allele INFO input :: name: "methylation", value: false
2025-09-15 20:25:07.423 wdl.w:ptcp.w:call-trgt-64.t:call-trgt_plot_motifs_allele INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:25:07.423 wdl.w:ptcp.w:call-trgt-64.t:call-trgt_plot_motifs_allele INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:25:07.423 wdl.w:ptcp.w:call-trgt-64.t:call-trgt_plot_motifs_allele INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:25:07.423 wdl.w:ptcp.w:call-trgt-64.t:call-trgt_plot_motifs_allele INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2161.trgt.sorted.spanning.bam.bai"
2025-09-15 20:25:07.423 wdl.w:ptcp.w:call-trgt-64.t:call-trgt_plot_motifs_allele INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2161.trgt.sorted.spanning.bam"
2025-09-15 20:25:07.424 wdl.w:ptcp.w:call-trgt-64.t:call-trgt_plot_motifs_allele INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2161.trgt.vcf"
2025-09-15 20:25:07.424 wdl.w:ptcp.w:call-trgt-64.t:call-trgt_plot_motifs_allele INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2161"
2025-09-15 20:25:07.424 wdl.w:ptcp.w:call-trgt-64.t:call-trgt_plot_motifs_allele INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:25:07.424 wdl.w:ptcp.w:call-trgt-64.t:call-trgt_plot_motifs_allele INFO eval :: name: "plot_type", value: "allele"
2025-09-15 20:25:07.424 wdl.w:ptcp.w:call-trgt-64.t:call-trgt_plot_motifs_allele INFO eval :: name: "show", value: "motifs"
2025-09-15 20:25:07.424 wdl.w:ptcp NOTICE finish :: job: "call-sawfish-27"
2025-09-15 20:25:07.425 wdl.w:ptcp.w:call-trgt-64.t:call-trgt_plot_motifs_allele INFO eval :: name: "threads", value: 1
2025-09-15 20:25:07.425 wdl.w:ptcp INFO output :: job: "call-sawfish-27", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-27/out/m84036_250809_035451_s4.bc2124_sawfish/m84036_250809_035451_s4.bc2124.sv.vcf.gz", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-27/out/m84036_250809_035451_s4.bc2124.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-27/out/m84036_250809_035451_s4.bc2124_sawfish/m84036_250809_035451_s4.bc2124.sv.vcf.gz.tbi", "minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-27/out/m84036_250809_035451_s4.bc2124.minimap2.bam.bai"}
2025-09-15 20:25:07.426 wdl.w:ptcp.w:call-trgt-64.t:call-trgt_plot_motifs_allele INFO eval :: name: "disk_size", value: 27
2025-09-15 20:25:07.426 wdl.w:ptcp.w:call-trgt-64.t:call-trgt_plot_motifs_allele INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2161.motifs_allele"
2025-09-15 20:25:07.426 wdl.w:ptcp.w:call-trgt-64.t:call-trgt_plot_motifs_allele INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:07.426 wdl.w:ptcp.w:call-trgt-64.t:call-trgt_plot_motifs_allele WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:07.426 wdl.w:ptcp.w:call-trgt-64.t:call-trgt_plot_motifs_allele INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:25:07.427 wdl.w:ptcp.w:call-trgt-64.t:call-trgt_plot_motifs_allele INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:07.436 wdl.w:ptcp.w:call-sawfish-79.t:call-run_sawfish.slurm_singularity INFO srun: job 51797902 queued and waiting for resources
2025-09-15 20:25:07.436 wdl.w:ptcp.w:call-sawfish-79.t:call-run_sawfish.slurm_singularity INFO srun: job 51797902 has been allocated resources
2025-09-15 20:25:07.436 wdl.w:ptcp.w:call-sawfish-79.t:call-run_sawfish.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:07.436 wdl.w:ptcp.w:call-sawfish-79.t:call-run_sawfish.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:25:07.437 wdl.w:ptcp.w:call-trgt-80 NOTICE workflow start :: name: "trgt", source: "./trgt.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-80"
2025-09-15 20:25:07.510 wdl.w:ptcp.w:call-paraphase-40.t:call-call_f8.slurm_singularity INFO srun: job 51797903 queued and waiting for resources
2025-09-15 20:25:07.510 wdl.w:ptcp.w:call-paraphase-40.t:call-call_f8.slurm_singularity INFO srun: job 51797903 has been allocated resources
2025-09-15 20:25:07.510 wdl.w:ptcp.w:call-paraphase-40.t:call-call_f8.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:07.510 wdl.w:ptcp.w:call-paraphase-40.t:call-call_f8.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:25:07.511 wdl.w:ptcp.w:call-trgt-80 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:25:07.512 wdl.w:ptcp.w:call-trgt-80 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-80/out/m84036_250809_035451_s4.bc2177.mapped.bam"}
2025-09-15 20:25:07.512 wdl.w:ptcp.w:call-trgt-80 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-80/out/m84036_250809_035451_s4.bc2177.mapped.bam.bai"}
2025-09-15 20:25:07.512 wdl.w:ptcp.w:call-trgt-80 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:25:07.512 wdl.w:ptcp.w:call-trgt-80 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:25:07.512 wdl.w:ptcp.w:call-trgt-80 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2177"}
2025-09-15 20:25:07.512 wdl.w:ptcp.w:call-trgt-80 INFO visit :: node: "decl-sex", values: {"sex": "F"}
2025-09-15 20:25:07.512 wdl.w:ptcp.w:call-trgt-80 INFO visit :: node: "decl-trgt_bed", values: {"trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"}
2025-09-15 20:25:07.512 wdl.w:ptcp.w:call-trgt-80 NOTICE ready :: job: "call-get_reads_overlapping_repeats", callee: "get_reads_overlapping_repeats"
2025-09-15 20:25:07.512 wdl.w:ptcp.w:call-trgt-80 INFO input :: job: "call-get_reads_overlapping_repeats", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-80/out/m84036_250809_035451_s4.bc2177.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-80/out/m84036_250809_035451_s4.bc2177.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2177"}
2025-09-15 20:25:07.514 wdl.w:ptcp.w:call-trgt-80 NOTICE ready :: job: "call-trgt_genotype", callee: "trgt_genotype"
2025-09-15 20:25:07.514 wdl.w:ptcp.w:call-trgt-61.t:call-trgt_plot_motifs_allele INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-61/call-trgt_plot_motifs_allele/_singularity_tmpdir_31x4gjmz"
2025-09-15 20:25:07.514 wdl.w:ptcp.w:call-trgt-80 INFO input :: job: "call-trgt_genotype", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-80/out/m84036_250809_035451_s4.bc2177.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-80/out/m84036_250809_035451_s4.bc2177.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2177"}
2025-09-15 20:25:07.514 wdl.w:ptcp.w:call-trgt-61.t:call-trgt_plot_motifs_allele INFO Slurm invocation: srun --job-name call-trgt_plot_motifs_allele --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-61/call-trgt_plot_motifs_allele/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-61/call-trgt_plot_motifs_allele/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-61/call-trgt_plot_motifs_allele/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-61/call-trgt_plot_motifs_allele/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-61/call-trgt_genotype/out/m84036_250809_035451_s4.bc2158.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2158.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-61/call-trgt_genotype/out/m84036_250809_035451_s4.bc2158.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2158.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-61/call-trgt_genotype/out/m84036_250809_035451_s4.bc2158.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2158.trgt.sorted.spanning.bam:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-61/call-trgt_plot_motifs_allele/_singularity_tmpdir_31x4gjmz/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-61/call-trgt_plot_motifs_allele/_singularity_tmpdir_31x4gjmz/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:07.519 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_plot_motifs_waterfall INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2139.motifs_waterfall.trgt_plots.zip"
2025-09-15 20:25:07.540 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:25:04 [ERROR] - No reads found for TRID=SCA37_DAB1
2025-09-15 20:25:07.540 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:25:04 [ERROR] - No reads found for TRID=OPDM_ABCD3
2025-09-15 20:25:07.541 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:25:05 [ERROR] - No reads found for TRID=NIID_NOTCH2NLC
2025-09-15 20:25:07.541 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:25:05 [ERROR] - No reads found for TRID=SCA2_ATXN2
2025-09-15 20:25:07.541 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:25:05 [ERROR] - No reads found for TRID=OPDM4_RILPL1
2025-09-15 20:25:07.541 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:25:05 [ERROR] - No reads found for TRID=SCA27B_FGF14
2025-09-15 20:25:07.541 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:25:05 [ERROR] - No reads found for TRID=OPMD_PABPN1
2025-09-15 20:25:07.541 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:25:05 [ERROR] - No reads found for TRID=SCA8_ATXN8OS
2025-09-15 20:25:07.541 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:25:05 [ERROR] - No reads found for TRID=SCA3_ATXN3
2025-09-15 20:25:07.541 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:25:05 [ERROR] - No reads found for TRID=SCA31_BEAN1
2025-09-15 20:25:07.541 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:25:05 [ERROR] - No reads found for TRID=HDL2_JPH3
2025-09-15 20:25:07.541 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:25:05 [ERROR] - No reads found for TRID=SCA4_ZFHX3
2025-09-15 20:25:07.542 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:25:05 [ERROR] - No reads found for TRID=SCA6_CACNA1A
2025-09-15 20:25:07.542 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:25:06 [ERROR] - No reads found for TRID=FECD3_TCF4
2025-09-15 20:25:07.542 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:25:06 [ERROR] - No reads found for TRID=SD5_HOXD13
2025-09-15 20:25:07.542 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:25:06 [ERROR] - No reads found for TRID=OPDM2_GIPC1
2025-09-15 20:25:07.542 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:25:06 [ERROR] - No reads found for TRID=FRA2A_AFF3
2025-09-15 20:25:07.542 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:25:06 [ERROR] - No reads found for TRID=SCA10_ATXN10
2025-09-15 20:25:07.542 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:25:06 [ERROR] - No reads found for TRID=SCA7_ATXN7
2025-09-15 20:25:07.542 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:25:06 [ERROR] - No reads found for TRID=EPM1_CSTB
2025-09-15 20:25:07.542 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:25:06 [ERROR] - No reads found for TRID=SCA36_NOP56
2025-09-15 20:25:07.542 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:25:06 [ERROR] - No reads found for TRID=CJD_PRNP
2025-09-15 20:25:07.542 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:25:06 [ERROR] - No reads found for TRID=SCA12_PPP2R2B
2025-09-15 20:25:07.542 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:25:06 [ERROR] - No reads found for TRID=OPDM1_LRP12
2025-09-15 20:25:07.542 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:25:06 [ERROR] - No reads found for TRID=FAME1_SAMD12
2025-09-15 20:25:07.542 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:25:06 [ERROR] - No reads found for TRID=SCA1_ATXN1
2025-09-15 20:25:07.544 wdl.w:ptcp.w:call-paraphase-22 NOTICE done
2025-09-15 20:25:07.549 wdl.w:ptcp NOTICE finish :: job: "call-paraphase-22"
2025-09-15 20:25:07.549 wdl.w:ptcp INFO output :: job: "call-paraphase-22", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-22/out/m84036_250809_035451_s4.bc2119.f8inversion.vcf", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-22/out/m84036_250809_035451_s4.bc2119_paraphase/m84036_250809_035451_s4.bc2119.paraphase.json", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-22/out/m84036_250809_035451_s4.bc2119_paraphase/m84036_250809_035451_s4.bc2119.paraphase.bam", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-22/out/m84036_250809_035451_s4.bc2119_paraphase/m84036_250809_035451_s4.bc2119.paraphase.bam.bai", "paraphase_vcfs": ["/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-22/out/m84036_250809_035451_s4.bc2119_paraphase/m84036_250809_035451_s4.bc2119_paraphase_vcfs/m84036_250809_035451_s4.bc2119_cyp21.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-22/out/m84036_250809_035451_s4.bc2119_paraphase/m84036_250809_035451_s4.bc2119_paraphase_vcfs/m84036_250809_035451_s4.bc2119_f8inv1.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-22/out/m84036_250809_035451_s4.bc2119_paraphase/m84036_250809_035451_s4.bc2119_paraphase_vcfs/m84036_250809_035451_s4.bc2119_f8inv22.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-22/out/m84036_250809_035451_s4.bc2119_paraphase/m84036_250809_035451_s4.bc2119_paraphase_vcfs/m84036_250809_035451_s4.bc2119_gba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-22/out/m84036_250809_035451_s4.bc2119_paraphase/m84036_250809_035451_s4.bc2119_paraphase_vcfs/m84036_250809_035451_s4.bc2119_hba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-22/out/m84036_250809_035451_s4.bc2119_paraphase/m84036_250809_035451_s4.bc2119_paraphase_vcfs/m84036_250809_035451_s4.bc2119_hbb.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-22/out/m84036_250809_035451_s4.bc2119_paraphase/m84036_250809_035451_s4.bc2119_paraphase_vcfs/m84036_250809_035451_s4.bc2119_rpgr.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-22/out/m84036_250809_035451_s4.bc2119_paraphase/m84036_250809_035451_s4.bc2119_paraphase_vcfs/m84036_250809_035451_s4.bc2119_smn1.vcf"], "havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-22/out/m84036_250809_035451_s4.bc2119.havanno.json", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-22/out/m84036_250809_035451_s4.bc2119.f8inversion.json"}
2025-09-15 20:25:07.550 wdl.w:ptcp NOTICE ready :: job: "call-tar_outputs-22", callee: "tar_outputs"
2025-09-15 20:25:07.551 wdl.w:ptcp INFO input :: job: "call-tar_outputs-22", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "sawfish_vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-22/out/m84036_250809_035451_s4.bc2119_sawfish/m84036_250809_035451_s4.bc2119.sv.vcf.gz.tbi", "sawfish_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-22/out/m84036_250809_035451_s4.bc2119_sawfish/m84036_250809_035451_s4.bc2119.sv.vcf.gz", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-22/out/m84036_250809_035451_s4.bc2119.f8inversion.json", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-22/out/m84036_250809_035451_s4.bc2119_paraphase/m84036_250809_035451_s4.bc2119.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-22/out/m84036_250809_035451_s4.bc2119_paraphase/m84036_250809_035451_s4.bc2119.paraphase.bam", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-22/out/m84036_250809_035451_s4.bc2119_paraphase/m84036_250809_035451_s4.bc2119.paraphase.json", "trgt_spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-22/out/m84036_250809_035451_s4.bc2119.trgt.sorted.spanning.bam.bai", "trgt_spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-22/out/m84036_250809_035451_s4.bc2119.trgt.sorted.spanning.bam", "trgt_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-22/out/m84036_250809_035451_s4.bc2119.trgt.vcf", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-22/out/m84036_250809_035451_s4.bc2119.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-22/out/m84036_250809_035451_s4.bc2119.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2119"}
2025-09-15 20:25:07.560 wdl.w:ptcp.w:call-paraphase-74.t:call-run_paraphase INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-74/call-run_paraphase/_singularity_tmpdir_x04lvdff"
2025-09-15 20:25:07.560 wdl.w:ptcp.w:call-paraphase-74.t:call-run_paraphase INFO Slurm invocation: srun --job-name call-run_paraphase --partition compute,compute9 --cpus-per-task 4 --mem 7629M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-74/call-run_paraphase/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-74/call-run_paraphase/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-74/call-run_paraphase/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-74/call-run_paraphase/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-74/out/m84036_250809_035451_s4.bc2171.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2171.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-74/out/m84036_250809_035451_s4.bc2171.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2171.mapped.bam:ro --bind /ptcp/meta/variant_list/variant_list.GRCh38.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf:ro --bind /ptcp/meta/paraphase/paraphase_config.GRCh38.yaml:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/paraphase_config.GRCh38.yaml:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-74/call-run_paraphase/_singularity_tmpdir_x04lvdff/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-74/call-run_paraphase/_singularity_tmpdir_x04lvdff/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:07.560 wdl.w:ptcp.w:call-paraphase-85 NOTICE workflow start :: name: "paraphase", source: "./paraphase.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-85"
2025-09-15 20:25:07.567 wdl.w:ptcp.w:call-paraphase-56 NOTICE done
2025-09-15 20:25:07.572 wdl.w:ptcp NOTICE finish :: job: "call-paraphase-56"
2025-09-15 20:25:07.572 wdl.w:ptcp INFO output :: job: "call-paraphase-56", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-56/out/m84036_250809_035451_s4.bc2153.f8inversion.vcf", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-56/out/m84036_250809_035451_s4.bc2153_paraphase/m84036_250809_035451_s4.bc2153.paraphase.json", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-56/out/m84036_250809_035451_s4.bc2153_paraphase/m84036_250809_035451_s4.bc2153.paraphase.bam", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-56/out/m84036_250809_035451_s4.bc2153_paraphase/m84036_250809_035451_s4.bc2153.paraphase.bam.bai", "paraphase_vcfs": [], "havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-56/out/m84036_250809_035451_s4.bc2153.havanno.json", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-56/out/m84036_250809_035451_s4.bc2153.f8inversion.json"}
2025-09-15 20:25:07.577 wdl.w:ptcp.w:call-trgt-64.t:call-trgt_plot_meth_waterfall INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-64/call-trgt_plot_meth_waterfall/_singularity_tmpdir_ti7gzcnr"
2025-09-15 20:25:07.577 wdl.w:ptcp.w:call-trgt-64.t:call-trgt_plot_meth_waterfall INFO Slurm invocation: srun --job-name call-trgt_plot_meth_waterfall --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-64/call-trgt_plot_meth_waterfall/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-64/call-trgt_plot_meth_waterfall/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-64/call-trgt_plot_meth_waterfall/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-64/call-trgt_plot_meth_waterfall/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-64/call-trgt_genotype/out/m84036_250809_035451_s4.bc2161.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2161.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-64/call-trgt_genotype/out/m84036_250809_035451_s4.bc2161.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2161.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-64/call-trgt_genotype/out/m84036_250809_035451_s4.bc2161.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2161.trgt.sorted.spanning.bam:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-64/call-trgt_plot_meth_waterfall/_singularity_tmpdir_ti7gzcnr/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-64/call-trgt_plot_meth_waterfall/_singularity_tmpdir_ti7gzcnr/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:07.583 wdl.w:ptcp.w:call-trgt-61.t:call-trgt_plot_motifs_waterfall INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-61/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_s0j9xgba"
2025-09-15 20:25:07.583 wdl.w:ptcp.w:call-trgt-61.t:call-trgt_plot_motifs_waterfall INFO Slurm invocation: srun --job-name call-trgt_plot_motifs_waterfall --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-61/call-trgt_plot_motifs_waterfall/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-61/call-trgt_plot_motifs_waterfall/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-61/call-trgt_plot_motifs_waterfall/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-61/call-trgt_plot_motifs_waterfall/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-61/call-trgt_genotype/out/m84036_250809_035451_s4.bc2158.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2158.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-61/call-trgt_genotype/out/m84036_250809_035451_s4.bc2158.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2158.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-61/call-trgt_genotype/out/m84036_250809_035451_s4.bc2158.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2158.trgt.sorted.spanning.bam:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-61/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_s0j9xgba/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-61/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_s0j9xgba/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:07.584 wdl.w:ptcp.w:call-sawfish-85 NOTICE workflow start :: name: "sawfish", source: "./sawfish.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-85"
2025-09-15 20:25:07.582 wdl.w:ptcp.w:call-trgt-64.t:call-trgt_plot_meth_allele INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-64/call-trgt_plot_meth_allele/_singularity_tmpdir_v6v0qvnl"
2025-09-15 20:25:07.587 wdl.w:ptcp.w:call-paraphase-85 INFO visit :: node: "decl-annotation_vcf", values: {"annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf"}
2025-09-15 20:25:07.588 wdl.w:ptcp.w:call-trgt-64.t:call-trgt_plot_meth_allele INFO Slurm invocation: srun --job-name call-trgt_plot_meth_allele --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-64/call-trgt_plot_meth_allele/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-64/call-trgt_plot_meth_allele/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-64/call-trgt_plot_meth_allele/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-64/call-trgt_plot_meth_allele/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-64/call-trgt_genotype/out/m84036_250809_035451_s4.bc2161.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2161.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-64/call-trgt_genotype/out/m84036_250809_035451_s4.bc2161.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2161.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-64/call-trgt_genotype/out/m84036_250809_035451_s4.bc2161.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2161.trgt.sorted.spanning.bam:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-64/call-trgt_plot_meth_allele/_singularity_tmpdir_v6v0qvnl/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-64/call-trgt_plot_meth_allele/_singularity_tmpdir_v6v0qvnl/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:07.588 wdl.w:ptcp.w:call-paraphase-85 INFO visit :: node: "decl-config_file", values: {"config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml"}
2025-09-15 20:25:07.588 wdl.w:ptcp.w:call-paraphase-85 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:25:07.588 wdl.w:ptcp.w:call-paraphase-85 INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:25:07.588 wdl.w:ptcp.w:call-paraphase-85 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-85/out/m84036_250809_035451_s4.bc2182.mapped.bam"}
2025-09-15 20:25:07.590 wdl.w:ptcp.w:call-paraphase-85 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-85/out/m84036_250809_035451_s4.bc2182.mapped.bam.bai"}
2025-09-15 20:25:07.591 wdl.w:ptcp.w:call-paraphase-85 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:25:07.591 wdl.w:ptcp.w:call-paraphase-85 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:25:07.591 wdl.w:ptcp.w:call-paraphase-85 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2182"}
2025-09-15 20:25:07.592 wdl.w:ptcp.w:call-paraphase-85 INFO visit :: node: "decl-sex", values: {"sex": "F"}
2025-09-15 20:25:07.592 wdl.w:ptcp.w:call-paraphase-85 NOTICE ready :: job: "call-run_paraphase", callee: "run_paraphase"
2025-09-15 20:25:07.592 wdl.w:ptcp.w:call-paraphase-85 INFO input :: job: "call-run_paraphase", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf", "genome_version": "38", "config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-85/out/m84036_250809_035451_s4.bc2182.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-85/out/m84036_250809_035451_s4.bc2182.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2182"}
2025-09-15 20:25:07.594 wdl.w:ptcp.w:call-trgt-61.t:call-trgt_plot_motifs_allele NOTICE slurm_singularity run :: pid: 1204730, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-61/call-trgt_plot_motifs_allele/slurm_singularity.log.txt"
2025-09-15 20:25:07.594 wdl.w:ptcp.w:call-paraphase-74.t:call-run_paraphase NOTICE slurm_singularity run :: pid: 1204732, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-74/call-run_paraphase/slurm_singularity.log.txt"
2025-09-15 20:25:07.597 wdl.w:ptcp.w:call-trgt-64.t:call-trgt_plot_meth_allele NOTICE slurm_singularity run :: pid: 1204735, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-64/call-trgt_plot_meth_allele/slurm_singularity.log.txt"
2025-09-15 20:25:07.599 wdl.w:ptcp.w:call-trgt-64.t:call-trgt_plot_meth_waterfall NOTICE slurm_singularity run :: pid: 1204733, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-64/call-trgt_plot_meth_waterfall/slurm_singularity.log.txt"
2025-09-15 20:25:07.600 wdl.w:ptcp.w:call-trgt-61.t:call-trgt_plot_motifs_waterfall NOTICE slurm_singularity run :: pid: 1204734, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-61/call-trgt_plot_motifs_waterfall/slurm_singularity.log.txt"
2025-09-15 20:25:07.607 wdl.w:ptcp.w:call-sawfish-85 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:25:07.607 wdl.w:ptcp.w:call-sawfish-85 INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:25:07.608 wdl.w:ptcp.w:call-sawfish-85 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-85/out/m84036_250809_035451_s4.bc2182.mapped.bam"}
2025-09-15 20:25:07.608 wdl.w:ptcp.w:call-sawfish-85 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-85/out/m84036_250809_035451_s4.bc2182.mapped.bam.bai"}
2025-09-15 20:25:07.608 wdl.w:ptcp.w:call-sawfish-85 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:25:07.608 wdl.w:ptcp.w:call-sawfish-85 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:25:07.608 wdl.w:ptcp.w:call-sawfish-85 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2182"}
2025-09-15 20:25:07.608 wdl.w:ptcp.w:call-sawfish-85 NOTICE ready :: job: "call-run_sawfish", callee: "run_sawfish"
2025-09-15 20:25:07.608 wdl.w:ptcp.w:call-sawfish-85 INFO input :: job: "call-run_sawfish", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-85/out/m84036_250809_035451_s4.bc2182.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-85/out/m84036_250809_035451_s4.bc2182.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2182"}
2025-09-15 20:25:07.609 wdl.w:ptcp.w:call-trgt-64.t:call-trgt_plot_motifs_allele INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-64/call-trgt_plot_motifs_allele/_singularity_tmpdir_3a0_4grc"
2025-09-15 20:25:07.609 wdl.w:ptcp.w:call-trgt-64.t:call-trgt_plot_motifs_allele INFO Slurm invocation: srun --job-name call-trgt_plot_motifs_allele --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-64/call-trgt_plot_motifs_allele/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-64/call-trgt_plot_motifs_allele/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-64/call-trgt_plot_motifs_allele/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-64/call-trgt_plot_motifs_allele/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-64/call-trgt_genotype/out/m84036_250809_035451_s4.bc2161.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2161.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-64/call-trgt_genotype/out/m84036_250809_035451_s4.bc2161.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2161.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-64/call-trgt_genotype/out/m84036_250809_035451_s4.bc2161.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2161.trgt.sorted.spanning.bam:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-64/call-trgt_plot_motifs_allele/_singularity_tmpdir_3a0_4grc/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-64/call-trgt_plot_motifs_allele/_singularity_tmpdir_3a0_4grc/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:07.610 wdl.w:ptcp.w:call-trgt-58.t:call-trgt_plot_motifs_allele INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2155.motifs_allele.trgt_plots.zip"
2025-09-15 20:25:07.638 wdl.w:ptcp.w:call-trgt-64.t:call-trgt_plot_motifs_allele NOTICE slurm_singularity run :: pid: 1204741, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-64/call-trgt_plot_motifs_allele/slurm_singularity.log.txt"
2025-09-15 20:25:07.649 wdl.w:ptcp.w:call-paraphase-53.t:call-call_f8.slurm_singularity INFO srun: job 51797904 queued and waiting for resources
2025-09-15 20:25:07.649 wdl.w:ptcp.w:call-paraphase-53.t:call-call_f8.slurm_singularity INFO srun: job 51797904 has been allocated resources
2025-09-15 20:25:07.649 wdl.w:ptcp.w:call-paraphase-53.t:call-call_f8.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:07.657 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_plot_motifs_waterfall NOTICE done
2025-09-15 20:25:07.664 wdl.w:ptcp.w:call-trgt-42 NOTICE finish :: job: "call-trgt_plot_motifs_waterfall"
2025-09-15 20:25:07.664 wdl.w:ptcp.w:call-trgt-42 INFO output :: job: "call-trgt_plot_motifs_waterfall", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-42/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2139.motifs_waterfall.trgt_plots.zip"}
2025-09-15 20:25:07.664 wdl.w:ptcp.w:call-trgt-42 INFO visit :: node: "output-images_motifs_waterfall", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-42/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2139.motifs_waterfall.trgt_plots.zip"}
2025-09-15 20:25:07.672 wdl.w:ptcp.w:call-paraphase-41.t:call-call_f8.slurm_singularity INFO srun: job 51797905 queued and waiting for resources
2025-09-15 20:25:07.672 wdl.w:ptcp.w:call-paraphase-41.t:call-call_f8.slurm_singularity INFO srun: job 51797905 has been allocated resources
2025-09-15 20:25:07.672 wdl.w:ptcp.w:call-paraphase-41.t:call-call_f8.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:07.673 wdl.w:ptcp.w:call-trgt-64.t:call-trgt_plot_motifs_waterfall NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-64/call-trgt_plot_motifs_waterfall", thread: 140609813722688
2025-09-15 20:25:07.697 wdl.w:ptcp.w:call-trgt-64.t:call-trgt_plot_motifs_waterfall INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:07.698 wdl.w:ptcp.w:call-trgt-64.t:call-trgt_plot_motifs_waterfall INFO input :: name: "waterfall", value: true
2025-09-15 20:25:07.698 wdl.w:ptcp.w:call-trgt-64.t:call-trgt_plot_motifs_waterfall INFO input :: name: "methylation", value: false
2025-09-15 20:25:07.698 wdl.w:ptcp.w:call-trgt-64.t:call-trgt_plot_motifs_waterfall INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:25:07.698 wdl.w:ptcp.w:call-trgt-64.t:call-trgt_plot_motifs_waterfall INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:25:07.698 wdl.w:ptcp.w:call-trgt-64.t:call-trgt_plot_motifs_waterfall INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:25:07.698 wdl.w:ptcp.w:call-trgt-64.t:call-trgt_plot_motifs_waterfall INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2161.trgt.sorted.spanning.bam.bai"
2025-09-15 20:25:07.698 wdl.w:ptcp.w:call-trgt-64.t:call-trgt_plot_motifs_waterfall INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2161.trgt.sorted.spanning.bam"
2025-09-15 20:25:07.698 wdl.w:ptcp.w:call-trgt-64.t:call-trgt_plot_motifs_waterfall INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2161.trgt.vcf"
2025-09-15 20:25:07.698 wdl.w:ptcp.w:call-trgt-64.t:call-trgt_plot_motifs_waterfall INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2161"
2025-09-15 20:25:07.698 wdl.w:ptcp.w:call-trgt-64.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:25:07.699 wdl.w:ptcp.w:call-trgt-64.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "plot_type", value: "waterfall"
2025-09-15 20:25:07.699 wdl.w:ptcp.w:call-trgt-64.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "show", value: "motifs"
2025-09-15 20:25:07.699 wdl.w:ptcp.w:call-trgt-64.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "threads", value: 1
2025-09-15 20:25:07.699 wdl.w:ptcp.w:call-trgt-64.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "disk_size", value: 27
2025-09-15 20:25:07.699 wdl.w:ptcp.w:call-trgt-64.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2161.motifs_waterfall"
2025-09-15 20:25:07.700 wdl.w:ptcp.w:call-trgt-64.t:call-trgt_plot_motifs_waterfall INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:07.700 wdl.w:ptcp.w:call-trgt-64.t:call-trgt_plot_motifs_waterfall WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:07.700 wdl.w:ptcp.w:call-trgt-64.t:call-trgt_plot_motifs_waterfall INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:25:07.700 wdl.w:ptcp.w:call-trgt-64.t:call-trgt_plot_motifs_waterfall INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:07.728 wdl.w:ptcp.w:call-trgt-79.t:call-get_reads_overlapping_repeats.slurm_singularity INFO srun: job 51797906 queued and waiting for resources
2025-09-15 20:25:07.728 wdl.w:ptcp.w:call-trgt-79.t:call-get_reads_overlapping_repeats.slurm_singularity INFO srun: job 51797906 has been allocated resources
2025-09-15 20:25:07.728 wdl.w:ptcp.w:call-trgt-79.t:call-get_reads_overlapping_repeats.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:07.747 wdl.w:ptcp.w:call-trgt-58.t:call-trgt_plot_motifs_allele NOTICE done
2025-09-15 20:25:07.755 wdl.w:ptcp.w:call-trgt-58 NOTICE finish :: job: "call-trgt_plot_motifs_allele"
2025-09-15 20:25:07.755 wdl.w:ptcp.w:call-trgt-58 INFO output :: job: "call-trgt_plot_motifs_allele", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-58/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2155.motifs_allele.trgt_plots.zip"}
2025-09-15 20:25:07.755 wdl.w:ptcp.w:call-trgt-58 INFO visit :: node: "output-images_motifs_allele", values: {"images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-58/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2155.motifs_allele.trgt_plots.zip"}
2025-09-15 20:25:07.755 wdl.w:ptcp.w:call-trgt-58 INFO visit :: node: "outputs", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-58/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2155.motifs_waterfall.trgt_plots.zip", "images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-58/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2155.meth_allele.trgt_plots.zip", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-58/call-trgt_genotype/out/m84036_250809_035451_s4.bc2155.trgt.sorted.spanning.bam.bai", "images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-58/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2155.motifs_allele.trgt_plots.zip", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-58/call-trgt_genotype/out/m84036_250809_035451_s4.bc2155.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-58/call-trgt_genotype/out/m84036_250809_035451_s4.bc2155.trgt.vcf", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-58/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2155.repeats.bam", "images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-58/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2155.meth_waterfall.trgt_plots.zip", "reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-58/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2155.repeats.bam.bai"}
2025-09-15 20:25:07.767 wdl.w:ptcp.w:call-paraphase-61.t:call-call_f8 NOTICE task setup :: name: "call_f8", source: "./paraphase.wdl", line: 232, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-61/call-call_f8", thread: 140607683024448
2025-09-15 20:25:07.786 wdl.w:ptcp.w:call-trgt-79.t:call-get_reads_overlapping_repeats INFO output :: name: "reads_overlapping_repeats", value: "m84036_250809_035451_s4.bc2176.repeats.bam"
2025-09-15 20:25:07.790 wdl.w:ptcp.w:call-trgt-79.t:call-get_reads_overlapping_repeats INFO output :: name: "reads_overlapping_repeats_bai", value: "m84036_250809_035451_s4.bc2176.repeats.bam.bai"
2025-09-15 20:25:07.800 wdl.w:ptcp.w:call-paraphase-61.t:call-call_f8 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:07.800 wdl.w:ptcp.w:call-paraphase-61.t:call-call_f8 INFO input :: name: "genome_version", value: "38"
2025-09-15 20:25:07.800 wdl.w:ptcp.w:call-paraphase-61.t:call-call_f8 INFO input :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2158"
2025-09-15 20:25:07.800 wdl.w:ptcp.w:call-paraphase-61.t:call-call_f8 INFO input :: name: "paraphase_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2158.paraphase.bam.bai"
2025-09-15 20:25:07.800 wdl.w:ptcp.w:call-paraphase-61.t:call-call_f8 INFO input :: name: "paraphase_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2158.paraphase.bam"
2025-09-15 20:25:07.800 wdl.w:ptcp.w:call-paraphase-61.t:call-call_f8 INFO input :: name: "sex", value: "F"
2025-09-15 20:25:07.801 wdl.w:ptcp.w:call-paraphase-61.t:call-call_f8 INFO eval :: name: "threads", value: 1
2025-09-15 20:25:07.801 wdl.w:ptcp.w:call-paraphase-61.t:call-call_f8 INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:25:07.801 wdl.w:ptcp.w:call-paraphase-61.t:call-call_f8 INFO eval :: name: "disk_size", value: 11
2025-09-15 20:25:07.802 wdl.w:ptcp.w:call-paraphase-61.t:call-call_f8 INFO eval :: name: "sample_sex", value: "F"
2025-09-15 20:25:07.803 wdl.w:ptcp.w:call-paraphase-61.t:call-call_f8 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:07.803 wdl.w:ptcp.w:call-paraphase-61.t:call-call_f8 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:07.803 wdl.w:ptcp.w:call-paraphase-61.t:call-call_f8 INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:25:07.803 wdl.w:ptcp.w:call-paraphase-61.t:call-call_f8 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:07.820 wdl.w:ptcp.w:call-trgt-64.t:call-trgt_plot_motifs_waterfall INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-64/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_jfhtot9j"
2025-09-15 20:25:07.820 wdl.w:ptcp.w:call-trgt-64.t:call-trgt_plot_motifs_waterfall INFO Slurm invocation: srun --job-name call-trgt_plot_motifs_waterfall --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-64/call-trgt_plot_motifs_waterfall/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-64/call-trgt_plot_motifs_waterfall/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-64/call-trgt_plot_motifs_waterfall/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-64/call-trgt_plot_motifs_waterfall/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-64/call-trgt_genotype/out/m84036_250809_035451_s4.bc2161.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2161.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-64/call-trgt_genotype/out/m84036_250809_035451_s4.bc2161.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2161.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-64/call-trgt_genotype/out/m84036_250809_035451_s4.bc2161.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2161.trgt.sorted.spanning.bam:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-64/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_jfhtot9j/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-64/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_jfhtot9j/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:07.863 wdl.w:ptcp.w:call-paraphase-40.t:call-call_f8 INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2137.f8inversion.vcf"
2025-09-15 20:25:07.870 wdl.w:ptcp.w:call-paraphase-61.t:call-call_f8 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 8, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-61/call-call_f8/_singularity_tmpdir_0vp4gfuv"
2025-09-15 20:25:07.870 wdl.w:ptcp.w:call-paraphase-61.t:call-call_f8 INFO Slurm invocation: srun --job-name call-call_f8 --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-61/call-call_f8/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-61/call-call_f8/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-61/call-call_f8/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-61/call-call_f8/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-61/call-run_paraphase/out/m84036_250809_035451_s4.bc2158_paraphase/m84036_250809_035451_s4.bc2158.paraphase.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2158.paraphase.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-61/call-run_paraphase/out/m84036_250809_035451_s4.bc2158_paraphase/m84036_250809_035451_s4.bc2158.paraphase.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2158.paraphase.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-61/call-call_f8/_singularity_tmpdir_0vp4gfuv/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-61/call-call_f8/_singularity_tmpdir_0vp4gfuv/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:07.871 wdl.w:ptcp.w:call-paraphase-40.t:call-call_f8 INFO output :: name: "json", value: "m84036_250809_035451_s4.bc2137.f8inversion.json"
2025-09-15 20:25:07.877 wdl.w:ptcp.w:call-trgt-64.t:call-trgt_plot_motifs_waterfall NOTICE slurm_singularity run :: pid: 1204775, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-64/call-trgt_plot_motifs_waterfall/slurm_singularity.log.txt"
2025-09-15 20:25:07.878 wdl.w:ptcp.w:call-paraphase-61.t:call-call_f8 NOTICE slurm_singularity run :: pid: 1204776, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-61/call-call_f8/slurm_singularity.log.txt"
2025-09-15 20:25:07.882 wdl.w:ptcp.w:call-trgt-79.t:call-get_reads_overlapping_repeats NOTICE done
2025-09-15 20:25:07.886 wdl.w:ptcp.w:call-trgt-79 NOTICE finish :: job: "call-get_reads_overlapping_repeats"
2025-09-15 20:25:07.886 wdl.w:ptcp.w:call-trgt-79 INFO output :: job: "call-get_reads_overlapping_repeats", values: {"reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-79/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2176.repeats.bam.bai", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-79/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2176.repeats.bam"}
2025-09-15 20:25:07.887 wdl.w:ptcp.w:call-trgt-79 INFO visit :: node: "output-reads_overlapping_repeats", values: {"reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-79/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2176.repeats.bam"}
2025-09-15 20:25:07.887 wdl.w:ptcp.w:call-trgt-58 NOTICE done
2025-09-15 20:25:07.887 wdl.w:ptcp.w:call-trgt-79 INFO visit :: node: "output-reads_overlapping_repeats_bai", values: {"reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-79/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2176.repeats.bam.bai"}
2025-09-15 20:25:07.892 wdl.w:ptcp NOTICE finish :: job: "call-trgt-58"
2025-09-15 20:25:07.892 wdl.w:ptcp INFO output :: job: "call-trgt-58", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-58/out/m84036_250809_035451_s4.bc2155.motifs_waterfall.trgt_plots.zip", "images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-58/out/m84036_250809_035451_s4.bc2155.meth_allele.trgt_plots.zip", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-58/out/m84036_250809_035451_s4.bc2155.trgt.sorted.spanning.bam.bai", "images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-58/out/m84036_250809_035451_s4.bc2155.motifs_allele.trgt_plots.zip", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-58/out/m84036_250809_035451_s4.bc2155.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-58/out/m84036_250809_035451_s4.bc2155.trgt.vcf", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-58/out/m84036_250809_035451_s4.bc2155.repeats.bam", "images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-58/out/m84036_250809_035451_s4.bc2155.meth_waterfall.trgt_plots.zip", "reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-58/out/m84036_250809_035451_s4.bc2155.repeats.bam.bai"}
2025-09-15 20:25:07.893 wdl.w:ptcp.w:call-paraphase-69.t:call-call_f8 NOTICE task setup :: name: "call_f8", source: "./paraphase.wdl", line: 232, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-69/call-call_f8", thread: 140611424335424
2025-09-15 20:25:07.898 wdl.w:ptcp.w:call-trgt-85 NOTICE workflow start :: name: "trgt", source: "./trgt.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-85"
2025-09-15 20:25:07.915 wdl.w:ptcp.w:call-trgt-85 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:25:07.915 wdl.w:ptcp.w:call-trgt-85 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-85/out/m84036_250809_035451_s4.bc2182.mapped.bam"}
2025-09-15 20:25:07.915 wdl.w:ptcp.w:call-trgt-85 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-85/out/m84036_250809_035451_s4.bc2182.mapped.bam.bai"}
2025-09-15 20:25:07.915 wdl.w:ptcp.w:call-trgt-85 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:25:07.915 wdl.w:ptcp.w:call-trgt-85 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:25:07.915 wdl.w:ptcp.w:call-trgt-85 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2182"}
2025-09-15 20:25:07.915 wdl.w:ptcp.w:call-trgt-85 INFO visit :: node: "decl-sex", values: {"sex": "F"}
2025-09-15 20:25:07.915 wdl.w:ptcp.w:call-trgt-85 INFO visit :: node: "decl-trgt_bed", values: {"trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"}
2025-09-15 20:25:07.916 wdl.w:ptcp.w:call-trgt-85 NOTICE ready :: job: "call-get_reads_overlapping_repeats", callee: "get_reads_overlapping_repeats"
2025-09-15 20:25:07.916 wdl.w:ptcp.w:call-trgt-85 INFO input :: job: "call-get_reads_overlapping_repeats", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-85/out/m84036_250809_035451_s4.bc2182.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-85/out/m84036_250809_035451_s4.bc2182.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2182"}
2025-09-15 20:25:07.917 wdl.w:ptcp.w:call-trgt-85 NOTICE ready :: job: "call-trgt_genotype", callee: "trgt_genotype"
2025-09-15 20:25:07.917 wdl.w:ptcp.w:call-trgt-85 INFO input :: job: "call-trgt_genotype", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-85/out/m84036_250809_035451_s4.bc2182.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-85/out/m84036_250809_035451_s4.bc2182.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2182"}
2025-09-15 20:25:07.919 wdl.w:ptcp.w:call-paraphase-69.t:call-call_f8 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:07.919 wdl.w:ptcp.w:call-paraphase-69.t:call-call_f8 INFO input :: name: "genome_version", value: "38"
2025-09-15 20:25:07.919 wdl.w:ptcp.w:call-paraphase-69.t:call-call_f8 INFO input :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2166"
2025-09-15 20:25:07.919 wdl.w:ptcp.w:call-paraphase-69.t:call-call_f8 INFO input :: name: "paraphase_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2166.paraphase.bam.bai"
2025-09-15 20:25:07.919 wdl.w:ptcp.w:call-paraphase-69.t:call-call_f8 INFO input :: name: "paraphase_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2166.paraphase.bam"
2025-09-15 20:25:07.919 wdl.w:ptcp.w:call-paraphase-69.t:call-call_f8 INFO input :: name: "sex", value: "F"
2025-09-15 20:25:07.919 wdl.w:ptcp.w:call-paraphase-69.t:call-call_f8 INFO eval :: name: "threads", value: 1
2025-09-15 20:25:07.920 wdl.w:ptcp.w:call-paraphase-69.t:call-call_f8 INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:25:07.920 wdl.w:ptcp.w:call-paraphase-69.t:call-call_f8 INFO eval :: name: "disk_size", value: 11
2025-09-15 20:25:07.920 wdl.w:ptcp.w:call-paraphase-69.t:call-call_f8 INFO eval :: name: "sample_sex", value: "F"
2025-09-15 20:25:07.920 wdl.w:ptcp.w:call-paraphase-69.t:call-call_f8 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:07.920 wdl.w:ptcp.w:call-paraphase-69.t:call-call_f8 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:07.921 wdl.w:ptcp.w:call-paraphase-69.t:call-call_f8 INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:25:07.921 wdl.w:ptcp.w:call-paraphase-69.t:call-call_f8 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:07.942 wdl.w:ptcp.w:call-paraphase-40.t:call-call_f8 NOTICE done
2025-09-15 20:25:07.947 wdl.w:ptcp.w:call-paraphase-40 NOTICE finish :: job: "call-call_f8"
2025-09-15 20:25:07.948 wdl.w:ptcp.w:call-paraphase-40 INFO output :: job: "call-call_f8", values: {"json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-40/call-call_f8/out/m84036_250809_035451_s4.bc2137.f8inversion.json", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-40/call-call_f8/out/m84036_250809_035451_s4.bc2137.f8inversion.vcf"}
2025-09-15 20:25:07.948 wdl.w:ptcp.w:call-paraphase-40 INFO visit :: node: "output-f8_json", values: {"f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-40/call-call_f8/out/m84036_250809_035451_s4.bc2137.f8inversion.json"}
2025-09-15 20:25:07.948 wdl.w:ptcp.w:call-paraphase-40 INFO visit :: node: "output-f8_vcf", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-40/call-call_f8/out/m84036_250809_035451_s4.bc2137.f8inversion.vcf"}
2025-09-15 20:25:07.948 wdl.w:ptcp.w:call-paraphase-40 INFO visit :: node: "outputs", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-40/call-call_f8/out/m84036_250809_035451_s4.bc2137.f8inversion.vcf", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-40/call-run_paraphase/out/m84036_250809_035451_s4.bc2137_paraphase/m84036_250809_035451_s4.bc2137.paraphase.json", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-40/call-run_paraphase/out/m84036_250809_035451_s4.bc2137_paraphase/m84036_250809_035451_s4.bc2137.paraphase.bam", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-40/call-run_paraphase/out/m84036_250809_035451_s4.bc2137_paraphase/m84036_250809_035451_s4.bc2137.paraphase.bam.bai", "paraphase_vcfs": [], "havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-40/call-run_paraphase/out/m84036_250809_035451_s4.bc2137.havanno.json", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-40/call-call_f8/out/m84036_250809_035451_s4.bc2137.f8inversion.json"}
2025-09-15 20:25:07.957 wdl.w:ptcp.w:call-sawfish-74.t:call-run_sawfish NOTICE task setup :: name: "run_sawfish", source: "./sawfish.wdl", line: 83, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-74/call-run_sawfish", thread: 140613068518976
2025-09-15 20:25:07.968 wdl.w:ptcp.w:call-paraphase-69.t:call-call_f8 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 8, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-69/call-call_f8/_singularity_tmpdir_st5me5pn"
2025-09-15 20:25:07.969 wdl.w:ptcp.w:call-paraphase-69.t:call-call_f8 INFO Slurm invocation: srun --job-name call-call_f8 --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-69/call-call_f8/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-69/call-call_f8/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-69/call-call_f8/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-69/call-call_f8/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-69/call-run_paraphase/out/m84036_250809_035451_s4.bc2166_paraphase/m84036_250809_035451_s4.bc2166.paraphase.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2166.paraphase.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-69/call-run_paraphase/out/m84036_250809_035451_s4.bc2166_paraphase/m84036_250809_035451_s4.bc2166.paraphase.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2166.paraphase.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-69/call-call_f8/_singularity_tmpdir_st5me5pn/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-69/call-call_f8/_singularity_tmpdir_st5me5pn/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:07.984 wdl.w:ptcp.w:call-sawfish-74.t:call-run_sawfish INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:07.984 wdl.w:ptcp.w:call-sawfish-74.t:call-run_sawfish INFO input :: name: "genome_version", value: "38"
2025-09-15 20:25:07.985 wdl.w:ptcp.w:call-sawfish-74.t:call-run_sawfish INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:25:07.985 wdl.w:ptcp.w:call-sawfish-74.t:call-run_sawfish INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:25:07.985 wdl.w:ptcp.w:call-sawfish-74.t:call-run_sawfish INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2171.mapped.bam.bai"
2025-09-15 20:25:07.985 wdl.w:ptcp.w:call-sawfish-74.t:call-run_sawfish INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2171.mapped.bam"
2025-09-15 20:25:07.985 wdl.w:ptcp.w:call-sawfish-74.t:call-run_sawfish INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2171"
2025-09-15 20:25:07.985 wdl.w:ptcp.w:call-sawfish-74.t:call-run_sawfish INFO eval :: name: "mem_gb", value: 32
2025-09-15 20:25:07.985 wdl.w:ptcp.w:call-sawfish-74.t:call-run_sawfish INFO eval :: name: "threads", value: 16
2025-09-15 20:25:07.985 wdl.w:ptcp.w:call-sawfish-74.t:call-run_sawfish INFO eval :: name: "disk_size", value: 30
2025-09-15 20:25:07.985 wdl.w:ptcp.w:call-sawfish-74.t:call-run_sawfish INFO eval :: name: "discover_dirname", value: "m84036_250809_035451_s4.bc2171_sawfish_discover"
2025-09-15 20:25:07.986 wdl.w:ptcp.w:call-sawfish-74.t:call-run_sawfish INFO eval :: name: "call_dirname", value: "m84036_250809_035451_s4.bc2171_sawfish"
2025-09-15 20:25:07.986 wdl.w:ptcp.w:call-sawfish-74.t:call-run_sawfish INFO eval :: name: "minimap2_bam_filename", value: "m84036_250809_035451_s4.bc2171.minimap2.bam"
2025-09-15 20:25:07.986 wdl.w:ptcp.w:call-sawfish-74.t:call-run_sawfish INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 16, memory_reservation: 32000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:07.986 wdl.w:ptcp.w:call-sawfish-74.t:call-run_sawfish WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:07.987 wdl.w:ptcp.w:call-sawfish-74.t:call-run_sawfish INFO provisioned :: seconds_waited: 0, cpu: 16, mem_bytes: 32000000000
2025-09-15 20:25:07.987 wdl.w:ptcp.w:call-sawfish-74.t:call-run_sawfish INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:07.994 wdl.w:ptcp.w:call-paraphase-69.t:call-call_f8 NOTICE slurm_singularity run :: pid: 1204790, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-69/call-call_f8/slurm_singularity.log.txt"
2025-09-15 20:25:08.007 wdl.w:ptcp.w:call-paraphase-41.t:call-call_f8 INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2138.f8inversion.vcf"
2025-09-15 20:25:08.010 wdl.w:ptcp.w:call-paraphase-41.t:call-call_f8 INFO output :: name: "json", value: "m84036_250809_035451_s4.bc2138.f8inversion.json"
2025-09-15 20:25:08.020 wdl.w:ptcp.w:call-paraphase-40 NOTICE done
2025-09-15 20:25:08.035 wdl.w:ptcp NOTICE finish :: job: "call-paraphase-40"
2025-09-15 20:25:08.036 wdl.w:ptcp INFO output :: job: "call-paraphase-40", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-40/out/m84036_250809_035451_s4.bc2137.f8inversion.vcf", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-40/out/m84036_250809_035451_s4.bc2137_paraphase/m84036_250809_035451_s4.bc2137.paraphase.json", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-40/out/m84036_250809_035451_s4.bc2137_paraphase/m84036_250809_035451_s4.bc2137.paraphase.bam", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-40/out/m84036_250809_035451_s4.bc2137_paraphase/m84036_250809_035451_s4.bc2137.paraphase.bam.bai", "paraphase_vcfs": [], "havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-40/out/m84036_250809_035451_s4.bc2137.havanno.json", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-40/out/m84036_250809_035451_s4.bc2137.f8inversion.json"}
2025-09-15 20:25:08.043 wdl.w:ptcp.w:call-paraphase-92 NOTICE workflow start :: name: "paraphase", source: "./paraphase.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-92"
2025-09-15 20:25:08.050 wdl.w:ptcp.w:call-sawfish-74.t:call-run_sawfish INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 10, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-74/call-run_sawfish/_singularity_tmpdir_jsx3siqd"
2025-09-15 20:25:08.051 wdl.w:ptcp.w:call-sawfish-74.t:call-run_sawfish INFO Slurm invocation: srun --job-name call-run_sawfish --partition compute,compute9 --cpus-per-task 16 --mem 30518M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-74/call-run_sawfish/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-74/call-run_sawfish/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-74/call-run_sawfish/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-74/call-run_sawfish/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-74/out/m84036_250809_035451_s4.bc2171.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2171.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-74/out/m84036_250809_035451_s4.bc2171.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2171.mapped.bam:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-74/call-run_sawfish/_singularity_tmpdir_jsx3siqd/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-74/call-run_sawfish/_singularity_tmpdir_jsx3siqd/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:08.060 wdl.w:ptcp.w:call-paraphase-92 INFO visit :: node: "decl-annotation_vcf", values: {"annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf"}
2025-09-15 20:25:08.060 wdl.w:ptcp.w:call-paraphase-92 INFO visit :: node: "decl-config_file", values: {"config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml"}
2025-09-15 20:25:08.060 wdl.w:ptcp.w:call-paraphase-92 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:25:08.060 wdl.w:ptcp.w:call-paraphase-92 INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:25:08.060 wdl.w:ptcp.w:call-paraphase-92 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-92/out/m84036_250809_035451_s4.bc2189.mapped.bam"}
2025-09-15 20:25:08.060 wdl.w:ptcp.w:call-paraphase-92 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-92/out/m84036_250809_035451_s4.bc2189.mapped.bam.bai"}
2025-09-15 20:25:08.061 wdl.w:ptcp.w:call-paraphase-92 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:25:08.061 wdl.w:ptcp.w:call-paraphase-92 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:25:08.061 wdl.w:ptcp.w:call-paraphase-92 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2189"}
2025-09-15 20:25:08.061 wdl.w:ptcp.w:call-paraphase-92 INFO visit :: node: "decl-sex", values: {"sex": "F"}
2025-09-15 20:25:08.061 wdl.w:ptcp.w:call-paraphase-92 NOTICE ready :: job: "call-run_paraphase", callee: "run_paraphase"
2025-09-15 20:25:08.061 wdl.w:ptcp.w:call-paraphase-92 INFO input :: job: "call-run_paraphase", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf", "genome_version": "38", "config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-92/out/m84036_250809_035451_s4.bc2189.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-92/out/m84036_250809_035451_s4.bc2189.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2189"}
2025-09-15 20:25:08.062 wdl.w:ptcp.w:call-sawfish-74.t:call-run_sawfish NOTICE slurm_singularity run :: pid: 1204793, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-74/call-run_sawfish/slurm_singularity.log.txt"
2025-09-15 20:25:08.067 wdl.w:ptcp.w:call-trgt-79.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:25:07 [INFO] - Running trgt-4.0.0-429afcd [genotype]
2025-09-15 20:25:08.067 wdl.w:ptcp.w:call-trgt-79.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:25:07 [WARN] - FRAXE_AFF2: Filtered out 7 impure reads
2025-09-15 20:25:08.067 wdl.w:ptcp.w:call-trgt-79.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:25:07 [WARN] - FXS_FMR1: Filtered out 2 impure reads
2025-09-15 20:25:08.067 wdl.w:ptcp.w:call-trgt-79.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:25:07 [INFO] - Total execution time: 123.41ms
2025-09-15 20:25:08.067 wdl.w:ptcp.w:call-trgt-79.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:25:07 [INFO] - trgt end
2025-09-15 20:25:08.068 wdl.w:ptcp.w:call-sawfish-73.t:call-run_sawfish.stderr VERBOSE [M::bam2fq_mainloop] discarded 0 singletons
2025-09-15 20:25:08.068 wdl.w:ptcp.w:call-sawfish-73.t:call-run_sawfish.stderr VERBOSE [M::bam2fq_mainloop] processed 1 reads
2025-09-15 20:25:08.075 wdl.w:ptcp.w:call-trgt-79.t:call-trgt_genotype.slurm_singularity INFO srun: job 51797907 queued and waiting for resources
2025-09-15 20:25:08.075 wdl.w:ptcp.w:call-trgt-79.t:call-trgt_genotype.slurm_singularity INFO srun: job 51797907 has been allocated resources
2025-09-15 20:25:08.075 wdl.w:ptcp.w:call-trgt-79.t:call-trgt_genotype.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:08.083 wdl.w:ptcp.w:call-sawfish-73.t:call-run_sawfish.slurm_singularity INFO srun: job 51797908 queued and waiting for resources
2025-09-15 20:25:08.083 wdl.w:ptcp.w:call-sawfish-73.t:call-run_sawfish.slurm_singularity INFO srun: job 51797908 has been allocated resources
2025-09-15 20:25:08.083 wdl.w:ptcp.w:call-sawfish-73.t:call-run_sawfish.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:08.088 wdl.w:ptcp.w:call-paraphase-41.t:call-call_f8 NOTICE done
2025-09-15 20:25:08.093 wdl.w:ptcp.w:call-paraphase-41 NOTICE finish :: job: "call-call_f8"
2025-09-15 20:25:08.094 wdl.w:ptcp.w:call-paraphase-41 INFO output :: job: "call-call_f8", values: {"json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-41/call-call_f8/out/m84036_250809_035451_s4.bc2138.f8inversion.json", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-41/call-call_f8/out/m84036_250809_035451_s4.bc2138.f8inversion.vcf"}
2025-09-15 20:25:08.094 wdl.w:ptcp.w:call-paraphase-41 INFO visit :: node: "output-f8_json", values: {"f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-41/call-call_f8/out/m84036_250809_035451_s4.bc2138.f8inversion.json"}
2025-09-15 20:25:08.094 wdl.w:ptcp.w:call-paraphase-41 INFO visit :: node: "output-f8_vcf", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-41/call-call_f8/out/m84036_250809_035451_s4.bc2138.f8inversion.vcf"}
2025-09-15 20:25:08.094 wdl.w:ptcp.w:call-paraphase-41 INFO visit :: node: "outputs", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-41/call-call_f8/out/m84036_250809_035451_s4.bc2138.f8inversion.vcf", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-41/call-run_paraphase/out/m84036_250809_035451_s4.bc2138_paraphase/m84036_250809_035451_s4.bc2138.paraphase.json", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-41/call-run_paraphase/out/m84036_250809_035451_s4.bc2138_paraphase/m84036_250809_035451_s4.bc2138.paraphase.bam", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-41/call-run_paraphase/out/m84036_250809_035451_s4.bc2138_paraphase/m84036_250809_035451_s4.bc2138.paraphase.bam.bai", "paraphase_vcfs": [], "havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-41/call-run_paraphase/out/m84036_250809_035451_s4.bc2138.havanno.json", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-41/call-call_f8/out/m84036_250809_035451_s4.bc2138.f8inversion.json"}
2025-09-15 20:25:08.097 wdl.w:ptcp.w:call-paraphase-73.t:call-run_paraphase.slurm_singularity INFO srun: job 51797909 queued and waiting for resources
2025-09-15 20:25:08.097 wdl.w:ptcp.w:call-paraphase-73.t:call-run_paraphase.slurm_singularity INFO srun: job 51797909 has been allocated resources
2025-09-15 20:25:08.097 wdl.w:ptcp.w:call-paraphase-73.t:call-run_paraphase.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:08.102 wdl.w:ptcp.t:call-tar_outputs-45 NOTICE task setup :: name: "tar_outputs", source: "./common.wdl", line: 279, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-45", thread: 140609838900800
2025-09-15 20:25:08.125 wdl.w:ptcp.w:call-paraphase-53.t:call-call_f8 INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2150.f8inversion.vcf"
2025-09-15 20:25:08.131 wdl.w:ptcp.w:call-paraphase-53.t:call-call_f8 INFO output :: name: "json", value: "m84036_250809_035451_s4.bc2150.f8inversion.json"
2025-09-15 20:25:08.137 wdl.w:ptcp.t:call-tar_outputs-45 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:08.138 wdl.w:ptcp.t:call-tar_outputs-45 INFO input :: name: "sawfish_vcf_tbi", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2142.sv.vcf.gz.tbi"
2025-09-15 20:25:08.138 wdl.w:ptcp.t:call-tar_outputs-45 INFO input :: name: "sawfish_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2142.sv.vcf.gz"
2025-09-15 20:25:08.138 wdl.w:ptcp.t:call-tar_outputs-45 INFO input :: name: "f8_json", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2142.f8inversion.json"
2025-09-15 20:25:08.138 wdl.w:ptcp.t:call-tar_outputs-45 INFO input :: name: "paraphase_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2142.paraphase.bam.bai"
2025-09-15 20:25:08.138 wdl.w:ptcp.t:call-tar_outputs-45 INFO input :: name: "paraphase_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2142.paraphase.bam"
2025-09-15 20:25:08.138 wdl.w:ptcp.t:call-tar_outputs-45 INFO input :: name: "paraphase_json", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2142.paraphase.json"
2025-09-15 20:25:08.138 wdl.w:ptcp.t:call-tar_outputs-45 INFO input :: name: "trgt_spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2142.trgt.sorted.spanning.bam.bai"
2025-09-15 20:25:08.138 wdl.w:ptcp.t:call-tar_outputs-45 INFO input :: name: "trgt_spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2142.trgt.sorted.spanning.bam"
2025-09-15 20:25:08.138 wdl.w:ptcp.t:call-tar_outputs-45 INFO input :: name: "trgt_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2142.trgt.vcf"
2025-09-15 20:25:08.138 wdl.w:ptcp.t:call-tar_outputs-45 INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2142.mapped.bam.bai"
2025-09-15 20:25:08.138 wdl.w:ptcp.t:call-tar_outputs-45 INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2142.mapped.bam"
2025-09-15 20:25:08.138 wdl.w:ptcp.t:call-tar_outputs-45 INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2142"
2025-09-15 20:25:08.139 wdl.w:ptcp.t:call-tar_outputs-45 INFO eval :: name: "threads", value: 1
2025-09-15 20:25:08.139 wdl.w:ptcp.t:call-tar_outputs-45 INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:25:08.139 wdl.w:ptcp.t:call-tar_outputs-45 INFO eval :: name: "disk_size", value: 6
2025-09-15 20:25:08.139 wdl.w:ptcp.t:call-tar_outputs-45 INFO eval :: name: "output_tarball", value: "m84036_250809_035451_s4.bc2142.tar"
2025-09-15 20:25:08.140 wdl.w:ptcp.t:call-tar_outputs-45 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:08.140 wdl.w:ptcp.t:call-tar_outputs-45 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:08.141 wdl.w:ptcp.t:call-tar_outputs-45 INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:25:08.141 wdl.w:ptcp.t:call-tar_outputs-45 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:08.147 wdl.w:ptcp.w:call-trgt-79.t:call-trgt_genotype INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2176.trgt.vcf"
2025-09-15 20:25:08.151 wdl.w:ptcp.w:call-trgt-79.t:call-trgt_genotype INFO output :: name: "spanning_bam", value: "m84036_250809_035451_s4.bc2176.trgt.sorted.spanning.bam"
2025-09-15 20:25:08.153 wdl.w:ptcp.w:call-trgt-79.t:call-trgt_genotype INFO output :: name: "spanning_bam_bai", value: "m84036_250809_035451_s4.bc2176.trgt.sorted.spanning.bam.bai"
2025-09-15 20:25:08.161 wdl.w:ptcp.w:call-sawfish-18.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:57][sawfish][INFO] Starting sawfish 2.0.3
2025-09-15 20:25:08.161 wdl.w:ptcp.w:call-sawfish-18.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:57][sawfish][INFO] cmdline: sawfish discover --disable-cnv --threads 16 --ref /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa --bam m84036_250809_035451_s4.bc2115.minimap2.bam --output-dir m84036_250809_035451_s4.bc2115_sawfish_discover
2025-09-15 20:25:08.161 wdl.w:ptcp.w:call-sawfish-18.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:57][sawfish][INFO] Running on 16 threads
2025-09-15 20:25:08.161 wdl.w:ptcp.w:call-sawfish-18.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:57][sawfish][INFO] Writing discover settings to file: 'm84036_250809_035451_s4.bc2115_sawfish_discover/discover.settings.json'
2025-09-15 20:25:08.161 wdl.w:ptcp.w:call-sawfish-18.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:24:57][sawfish][INFO] Reading reference genome from file '/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa'
2025-09-15 20:25:08.161 wdl.w:ptcp.w:call-sawfish-18.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:05][sawfish][INFO] Processing alignment file '/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2115.minimap2.bam'
2025-09-15 20:25:08.161 wdl.w:ptcp.w:call-sawfish-18.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:05][sawfish][INFO] Finished processing all alignments
2025-09-15 20:25:08.161 wdl.w:ptcp.w:call-sawfish-18.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:05][sawfish][INFO] Writing depth bins to binary file: 'm84036_250809_035451_s4.bc2115_sawfish_discover/depth.mpack'
2025-09-15 20:25:08.161 wdl.w:ptcp.w:call-sawfish-18.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:05][sawfish][INFO] Writing max sv depth genome regions to bed file: 'm84036_250809_035451_s4.bc2115_sawfish_discover/max.depth.bed'
2025-09-15 20:25:08.162 wdl.w:ptcp.w:call-sawfish-18.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:05][sawfish][INFO] Completing breakpoint observation clustering
2025-09-15 20:25:08.162 wdl.w:ptcp.w:call-sawfish-18.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:05][sawfish][INFO] Finished breakpoint observation clustering
2025-09-15 20:25:08.162 wdl.w:ptcp.w:call-sawfish-18.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:05][sawfish][INFO] Consolidating adjacent indel candidates
2025-09-15 20:25:08.162 wdl.w:ptcp.w:call-sawfish-18.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:05][sawfish][INFO] Finding large insertion candidates
2025-09-15 20:25:08.162 wdl.w:ptcp.w:call-sawfish-18.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:05][sawfish][INFO] Writing breakpoint_cluster debug bed file: 'm84036_250809_035451_s4.bc2115_sawfish_discover/debug.breakpoint_clusters.bed'
2025-09-15 20:25:08.162 wdl.w:ptcp.w:call-sawfish-18.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:05][sawfish][INFO] Refining SV Candidates
2025-09-15 20:25:08.162 wdl.w:ptcp.w:call-sawfish-18.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:05][sawfish][INFO] Writing debug assembly region bed file: 'm84036_250809_035451_s4.bc2115_sawfish_discover/assembly.regions.bed'
2025-09-15 20:25:08.162 wdl.w:ptcp.w:call-sawfish-18.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:05][sawfish][INFO] Starting refinement of breakpoint evidence clusters
2025-09-15 20:25:08.162 wdl.w:ptcp.w:call-sawfish-18.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:06][sawfish][INFO] Finished refining all breakpoint evidence clusters
2025-09-15 20:25:08.162 wdl.w:ptcp.w:call-sawfish-18.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:06][sawfish][INFO] Writing all contig alignments to bam file: 'm84036_250809_035451_s4.bc2115_sawfish_discover/contig.alignment.bam'
2025-09-15 20:25:08.162 wdl.w:ptcp.w:call-sawfish-18.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:06][sawfish][INFO] Writing candidate structural variants to file: 'm84036_250809_035451_s4.bc2115_sawfish_discover/candidate.sv.bcf'
2025-09-15 20:25:08.162 wdl.w:ptcp.w:call-sawfish-18.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:06][sawfish][INFO] Writing run statistics to file: 'm84036_250809_035451_s4.bc2115_sawfish_discover/run.stats.json'
2025-09-15 20:25:08.162 wdl.w:ptcp.w:call-sawfish-18.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:07][sawfish][INFO] sawfish completed. Total Runtime: 00:00:09.341
2025-09-15 20:25:08.183 wdl.w:ptcp.w:call-paraphase-41 NOTICE done
2025-09-15 20:25:08.189 wdl.w:ptcp NOTICE finish :: job: "call-paraphase-41"
2025-09-15 20:25:08.189 wdl.w:ptcp INFO output :: job: "call-paraphase-41", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-41/out/m84036_250809_035451_s4.bc2138.f8inversion.vcf", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-41/out/m84036_250809_035451_s4.bc2138_paraphase/m84036_250809_035451_s4.bc2138.paraphase.json", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-41/out/m84036_250809_035451_s4.bc2138_paraphase/m84036_250809_035451_s4.bc2138.paraphase.bam", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-41/out/m84036_250809_035451_s4.bc2138_paraphase/m84036_250809_035451_s4.bc2138.paraphase.bam.bai", "paraphase_vcfs": [], "havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-41/out/m84036_250809_035451_s4.bc2138.havanno.json", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-41/out/m84036_250809_035451_s4.bc2138.f8inversion.json"}
2025-09-15 20:25:08.196 wdl.w:ptcp.w:call-sawfish-92 NOTICE workflow start :: name: "sawfish", source: "./sawfish.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-92"
2025-09-15 20:25:08.212 wdl.w:ptcp.w:call-sawfish-92 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:25:08.212 wdl.w:ptcp.w:call-sawfish-92 INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:25:08.212 wdl.w:ptcp.w:call-sawfish-92 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-92/out/m84036_250809_035451_s4.bc2189.mapped.bam"}
2025-09-15 20:25:08.212 wdl.w:ptcp.w:call-sawfish-92 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-92/out/m84036_250809_035451_s4.bc2189.mapped.bam.bai"}
2025-09-15 20:25:08.212 wdl.w:ptcp.w:call-sawfish-92 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:25:08.213 wdl.w:ptcp.w:call-sawfish-92 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:25:08.213 wdl.w:ptcp.w:call-sawfish-92 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2189"}
2025-09-15 20:25:08.213 wdl.w:ptcp.w:call-sawfish-92 NOTICE ready :: job: "call-run_sawfish", callee: "run_sawfish"
2025-09-15 20:25:08.213 wdl.w:ptcp.w:call-sawfish-92 INFO input :: job: "call-run_sawfish", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-92/out/m84036_250809_035451_s4.bc2189.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-92/out/m84036_250809_035451_s4.bc2189.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2189"}
2025-09-15 20:25:08.239 wdl.w:ptcp.w:call-paraphase-53.t:call-call_f8 NOTICE done
2025-09-15 20:25:08.245 wdl.w:ptcp.w:call-paraphase-53 NOTICE finish :: job: "call-call_f8"
2025-09-15 20:25:08.245 wdl.w:ptcp.w:call-paraphase-53 INFO output :: job: "call-call_f8", values: {"json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-53/call-call_f8/out/m84036_250809_035451_s4.bc2150.f8inversion.json", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-53/call-call_f8/out/m84036_250809_035451_s4.bc2150.f8inversion.vcf"}
2025-09-15 20:25:08.245 wdl.w:ptcp.w:call-paraphase-53 INFO visit :: node: "output-f8_json", values: {"f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-53/call-call_f8/out/m84036_250809_035451_s4.bc2150.f8inversion.json"}
2025-09-15 20:25:08.245 wdl.w:ptcp.w:call-paraphase-53 INFO visit :: node: "output-f8_vcf", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-53/call-call_f8/out/m84036_250809_035451_s4.bc2150.f8inversion.vcf"}
2025-09-15 20:25:08.245 wdl.w:ptcp.w:call-paraphase-53 INFO visit :: node: "outputs", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-53/call-call_f8/out/m84036_250809_035451_s4.bc2150.f8inversion.vcf", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-53/call-run_paraphase/out/m84036_250809_035451_s4.bc2150_paraphase/m84036_250809_035451_s4.bc2150.paraphase.json", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-53/call-run_paraphase/out/m84036_250809_035451_s4.bc2150_paraphase/m84036_250809_035451_s4.bc2150.paraphase.bam", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-53/call-run_paraphase/out/m84036_250809_035451_s4.bc2150_paraphase/m84036_250809_035451_s4.bc2150.paraphase.bam.bai", "paraphase_vcfs": [], "havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-53/call-run_paraphase/out/m84036_250809_035451_s4.bc2150.havanno.json", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-53/call-call_f8/out/m84036_250809_035451_s4.bc2150.f8inversion.json"}
2025-09-15 20:25:08.263 wdl.w:ptcp.w:call-trgt-74.t:call-get_reads_overlapping_repeats NOTICE task setup :: name: "get_reads_overlapping_repeats", source: "./trgt.wdl", line: 182, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-74/call-get_reads_overlapping_repeats", thread: 140607649453632
2025-09-15 20:25:08.288 wdl.w:ptcp.w:call-trgt-73.t:call-trgt_genotype.slurm_singularity INFO srun: job 51797910 queued and waiting for resources
2025-09-15 20:25:08.288 wdl.w:ptcp.w:call-trgt-73.t:call-trgt_genotype.slurm_singularity INFO srun: job 51797910 has been allocated resources
2025-09-15 20:25:08.289 wdl.w:ptcp.w:call-trgt-73.t:call-trgt_genotype.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:08.289 wdl.w:ptcp.w:call-trgt-73.t:call-get_reads_overlapping_repeats.slurm_singularity INFO srun: job 51797911 queued and waiting for resources
2025-09-15 20:25:08.289 wdl.w:ptcp.w:call-trgt-73.t:call-get_reads_overlapping_repeats.slurm_singularity INFO srun: job 51797911 has been allocated resources
2025-09-15 20:25:08.289 wdl.w:ptcp.w:call-trgt-73.t:call-get_reads_overlapping_repeats.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:08.296 wdl.w:ptcp.w:call-trgt-74.t:call-get_reads_overlapping_repeats INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:08.296 wdl.w:ptcp.w:call-trgt-74.t:call-get_reads_overlapping_repeats INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:25:08.296 wdl.w:ptcp.w:call-trgt-74.t:call-get_reads_overlapping_repeats INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2171.mapped.bam.bai"
2025-09-15 20:25:08.296 wdl.w:ptcp.w:call-trgt-74.t:call-get_reads_overlapping_repeats INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2171.mapped.bam"
2025-09-15 20:25:08.296 wdl.w:ptcp.w:call-trgt-74.t:call-get_reads_overlapping_repeats INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2171"
2025-09-15 20:25:08.296 wdl.w:ptcp.w:call-trgt-74.t:call-get_reads_overlapping_repeats INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:25:08.296 wdl.w:ptcp.w:call-trgt-74.t:call-get_reads_overlapping_repeats INFO eval :: name: "expand_size", value: 3000
2025-09-15 20:25:08.296 wdl.w:ptcp.w:call-trgt-74.t:call-get_reads_overlapping_repeats INFO eval :: name: "threads", value: 1
2025-09-15 20:25:08.297 wdl.w:ptcp.w:call-trgt-74.t:call-get_reads_overlapping_repeats INFO eval :: name: "expanded_bed_name", value: "m84036_250809_035451_s4.bc2171.expanded.bed"
2025-09-15 20:25:08.297 wdl.w:ptcp.w:call-trgt-74.t:call-get_reads_overlapping_repeats INFO eval :: name: "disk_size", value: 11
2025-09-15 20:25:08.297 wdl.w:ptcp.w:call-trgt-74.t:call-get_reads_overlapping_repeats INFO eval :: name: "output_name", value: "m84036_250809_035451_s4.bc2171.repeats.bam"
2025-09-15 20:25:08.297 wdl.w:ptcp.w:call-trgt-74.t:call-get_reads_overlapping_repeats INFO eval :: name: "index_name", value: "m84036_250809_035451_s4.bc2171.repeats.bam.bai"
2025-09-15 20:25:08.297 wdl.w:ptcp.w:call-trgt-74.t:call-get_reads_overlapping_repeats INFO eval :: name: "output_name_with_index", value: "m84036_250809_035451_s4.bc2171.repeats.bam##idx##m84036_250809_035451_s4.bc2171.repeats.bam.bai"
2025-09-15 20:25:08.297 wdl.w:ptcp.w:call-trgt-74.t:call-get_reads_overlapping_repeats INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:08.298 wdl.w:ptcp.w:call-trgt-74.t:call-get_reads_overlapping_repeats WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:08.298 wdl.w:ptcp.w:call-trgt-74.t:call-get_reads_overlapping_repeats INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:25:08.298 wdl.w:ptcp.w:call-trgt-74.t:call-get_reads_overlapping_repeats INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:08.308 wdl.w:ptcp.w:call-trgt-79.t:call-trgt_genotype NOTICE done
2025-09-15 20:25:08.315 wdl.w:ptcp.w:call-trgt-79 NOTICE finish :: job: "call-trgt_genotype"
2025-09-15 20:25:08.315 wdl.w:ptcp.w:call-trgt-79 INFO output :: job: "call-trgt_genotype", values: {"spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-79/call-trgt_genotype/out/m84036_250809_035451_s4.bc2176.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-79/call-trgt_genotype/out/m84036_250809_035451_s4.bc2176.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-79/call-trgt_genotype/out/m84036_250809_035451_s4.bc2176.trgt.vcf"}
2025-09-15 20:25:08.316 wdl.w:ptcp.w:call-trgt-79 NOTICE ready :: job: "call-trgt_plot_meth_allele", callee: "trgt_plot"
2025-09-15 20:25:08.316 wdl.w:ptcp.w:call-trgt-67.t:call-trgt_plot_motifs_waterfall INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2164.motifs_waterfall.trgt_plots.zip"
2025-09-15 20:25:08.317 wdl.w:ptcp.w:call-trgt-79 INFO input :: job: "call-trgt_plot_meth_allele", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": false, "methylation": true, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-79/call-trgt_genotype/out/m84036_250809_035451_s4.bc2176.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-79/call-trgt_genotype/out/m84036_250809_035451_s4.bc2176.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-79/call-trgt_genotype/out/m84036_250809_035451_s4.bc2176.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2176"}
2025-09-15 20:25:08.319 wdl.w:ptcp.w:call-trgt-79 NOTICE ready :: job: "call-trgt_plot_meth_waterfall", callee: "trgt_plot"
2025-09-15 20:25:08.319 wdl.w:ptcp.w:call-trgt-79 INFO input :: job: "call-trgt_plot_meth_waterfall", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": true, "methylation": true, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-79/call-trgt_genotype/out/m84036_250809_035451_s4.bc2176.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-79/call-trgt_genotype/out/m84036_250809_035451_s4.bc2176.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-79/call-trgt_genotype/out/m84036_250809_035451_s4.bc2176.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2176"}
2025-09-15 20:25:08.320 wdl.w:ptcp.w:call-trgt-79 NOTICE ready :: job: "call-trgt_plot_motifs_allele", callee: "trgt_plot"
2025-09-15 20:25:08.320 wdl.w:ptcp.w:call-trgt-79 INFO input :: job: "call-trgt_plot_motifs_allele", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": false, "methylation": false, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-79/call-trgt_genotype/out/m84036_250809_035451_s4.bc2176.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-79/call-trgt_genotype/out/m84036_250809_035451_s4.bc2176.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-79/call-trgt_genotype/out/m84036_250809_035451_s4.bc2176.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2176"}
2025-09-15 20:25:08.320 wdl.w:ptcp.t:call-tar_outputs-45 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 17, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-45/_singularity_tmpdir_0qxdh6oh"
2025-09-15 20:25:08.321 wdl.w:ptcp.t:call-tar_outputs-45 INFO Slurm invocation: srun --job-name call-tar_outputs-45 --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-45/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-45/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-45/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-45/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-45/out/m84036_250809_035451_s4.bc2142.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2142.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-45/out/m84036_250809_035451_s4.bc2142.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2142.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-45/out/m84036_250809_035451_s4.bc2142.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2142.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-45/out/m84036_250809_035451_s4.bc2142.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2142.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-45/out/m84036_250809_035451_s4.bc2142.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2142.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-45/out/m84036_250809_035451_s4.bc2142_sawfish/m84036_250809_035451_s4.bc2142.sv.vcf.gz.tbi:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2142.sv.vcf.gz.tbi:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-45/out/m84036_250809_035451_s4.bc2142_sawfish/m84036_250809_035451_s4.bc2142.sv.vcf.gz:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2142.sv.vcf.gz:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-45/out/m84036_250809_035451_s4.bc2142.f8inversion.json:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2142.f8inversion.json:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-45/out/m84036_250809_035451_s4.bc2142_paraphase/m84036_250809_035451_s4.bc2142.paraphase.json:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2142.paraphase.json:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-45/out/m84036_250809_035451_s4.bc2142_paraphase/m84036_250809_035451_s4.bc2142.paraphase.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2142.paraphase.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-45/out/m84036_250809_035451_s4.bc2142_paraphase/m84036_250809_035451_s4.bc2142.paraphase.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2142.paraphase.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-45/_singularity_tmpdir_0qxdh6oh/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-45/_singularity_tmpdir_0qxdh6oh/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:08.321 wdl.w:ptcp.w:call-trgt-79 NOTICE ready :: job: "call-trgt_plot_motifs_waterfall", callee: "trgt_plot"
2025-09-15 20:25:08.322 wdl.w:ptcp.w:call-trgt-61.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO srun: job 51797912 queued and waiting for resources
2025-09-15 20:25:08.322 wdl.w:ptcp.w:call-trgt-61.t:call-trgt_plot_meth_allele.slurm_singularity INFO srun: job 51797913 queued and waiting for resources
2025-09-15 20:25:08.324 wdl.w:ptcp.w:call-trgt-79 INFO input :: job: "call-trgt_plot_motifs_waterfall", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": true, "methylation": false, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-79/call-trgt_genotype/out/m84036_250809_035451_s4.bc2176.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-79/call-trgt_genotype/out/m84036_250809_035451_s4.bc2176.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-79/call-trgt_genotype/out/m84036_250809_035451_s4.bc2176.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2176"}
2025-09-15 20:25:08.324 wdl.w:ptcp.w:call-trgt-61.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO srun: job 51797912 has been allocated resources
2025-09-15 20:25:08.324 wdl.w:ptcp.w:call-trgt-61.t:call-trgt_plot_meth_allele.slurm_singularity INFO srun: job 51797913 has been allocated resources
2025-09-15 20:25:08.324 wdl.w:ptcp.w:call-trgt-61.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:08.325 wdl.w:ptcp.w:call-trgt-61.t:call-trgt_plot_meth_allele.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:08.325 wdl.w:ptcp.w:call-trgt-79 INFO visit :: node: "output-spanning_bam", values: {"spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-79/call-trgt_genotype/out/m84036_250809_035451_s4.bc2176.trgt.sorted.spanning.bam"}
2025-09-15 20:25:08.325 wdl.w:ptcp.w:call-trgt-79 INFO visit :: node: "output-spanning_bam_bai", values: {"spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-79/call-trgt_genotype/out/m84036_250809_035451_s4.bc2176.trgt.sorted.spanning.bam.bai"}
2025-09-15 20:25:08.325 wdl.w:ptcp.w:call-trgt-79 INFO visit :: node: "output-vcf", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-79/call-trgt_genotype/out/m84036_250809_035451_s4.bc2176.trgt.vcf"}
2025-09-15 20:25:08.333 wdl.w:ptcp.w:call-trgt-74.t:call-trgt_genotype NOTICE task setup :: name: "trgt_genotype", source: "./trgt.wdl", line: 272, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-74/call-trgt_genotype", thread: 140613588604480
2025-09-15 20:25:08.356 wdl.w:ptcp.w:call-trgt-74.t:call-trgt_genotype INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:08.356 wdl.w:ptcp.w:call-trgt-74.t:call-trgt_genotype INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:25:08.356 wdl.w:ptcp.w:call-trgt-74.t:call-trgt_genotype INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:25:08.357 wdl.w:ptcp.w:call-trgt-74.t:call-trgt_genotype INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:25:08.357 wdl.w:ptcp.w:call-trgt-74.t:call-trgt_genotype INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2171.mapped.bam.bai"
2025-09-15 20:25:08.357 wdl.w:ptcp.w:call-trgt-74.t:call-trgt_genotype INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2171.mapped.bam"
2025-09-15 20:25:08.357 wdl.w:ptcp.w:call-trgt-74.t:call-trgt_genotype INFO input :: name: "sex", value: "F"
2025-09-15 20:25:08.357 wdl.w:ptcp.w:call-trgt-74.t:call-trgt_genotype INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2171"
2025-09-15 20:25:08.357 wdl.w:ptcp.w:call-trgt-74.t:call-trgt_genotype INFO eval :: name: "mem_gb", value: 16
2025-09-15 20:25:08.357 wdl.w:ptcp.w:call-trgt-74.t:call-trgt_genotype INFO eval :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2171.trgt"
2025-09-15 20:25:08.357 wdl.w:ptcp.w:call-trgt-74.t:call-trgt_genotype INFO eval :: name: "threads", value: 8
2025-09-15 20:25:08.357 wdl.w:ptcp.w:call-trgt-74.t:call-trgt_genotype INFO eval :: name: "disk_size", value: 27
2025-09-15 20:25:08.358 wdl.w:ptcp.w:call-trgt-74.t:call-trgt_genotype INFO eval :: name: "karyotype", value: "XX"
2025-09-15 20:25:08.358 wdl.w:ptcp.w:call-trgt-74.t:call-trgt_genotype INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 8, memory_reservation: 16000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:08.358 wdl.w:ptcp.w:call-trgt-74.t:call-trgt_genotype WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:08.359 wdl.w:ptcp.w:call-trgt-74.t:call-trgt_genotype INFO provisioned :: seconds_waited: 0, cpu: 8, mem_bytes: 16000000000
2025-09-15 20:25:08.359 wdl.w:ptcp.w:call-trgt-74.t:call-trgt_genotype INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:08.362 wdl.w:ptcp.w:call-paraphase-53 NOTICE done
2025-09-15 20:25:08.385 wdl.w:ptcp.t:call-tar_outputs-45 NOTICE slurm_singularity run :: pid: 1204807, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-45/slurm_singularity.log.txt"
2025-09-15 20:25:08.390 wdl.w:ptcp NOTICE finish :: job: "call-paraphase-53"
2025-09-15 20:25:08.391 wdl.w:ptcp INFO output :: job: "call-paraphase-53", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-53/out/m84036_250809_035451_s4.bc2150.f8inversion.vcf", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-53/out/m84036_250809_035451_s4.bc2150_paraphase/m84036_250809_035451_s4.bc2150.paraphase.json", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-53/out/m84036_250809_035451_s4.bc2150_paraphase/m84036_250809_035451_s4.bc2150.paraphase.bam", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-53/out/m84036_250809_035451_s4.bc2150_paraphase/m84036_250809_035451_s4.bc2150.paraphase.bam.bai", "paraphase_vcfs": [], "havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-53/out/m84036_250809_035451_s4.bc2150.havanno.json", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-53/out/m84036_250809_035451_s4.bc2150.f8inversion.json"}
2025-09-15 20:25:08.398 wdl.w:ptcp.w:call-trgt-74.t:call-get_reads_overlapping_repeats INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 9, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-74/call-get_reads_overlapping_repeats/_singularity_tmpdir_q0wv4qht"
2025-09-15 20:25:08.398 wdl.w:ptcp.w:call-trgt-74.t:call-get_reads_overlapping_repeats INFO Slurm invocation: srun --job-name call-get_reads_overlapping_repeats --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-74/call-get_reads_overlapping_repeats/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-74/call-get_reads_overlapping_repeats/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-74/call-get_reads_overlapping_repeats/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-74/call-get_reads_overlapping_repeats/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-74/out/m84036_250809_035451_s4.bc2171.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2171.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-74/out/m84036_250809_035451_s4.bc2171.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2171.mapped.bam:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-74/call-get_reads_overlapping_repeats/_singularity_tmpdir_q0wv4qht/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-74/call-get_reads_overlapping_repeats/_singularity_tmpdir_q0wv4qht/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:08.399 wdl.w:ptcp.w:call-trgt-92 NOTICE workflow start :: name: "trgt", source: "./trgt.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-92"
2025-09-15 20:25:08.409 wdl.w:ptcp.w:call-trgt-74.t:call-get_reads_overlapping_repeats NOTICE slurm_singularity run :: pid: 1204810, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-74/call-get_reads_overlapping_repeats/slurm_singularity.log.txt"
2025-09-15 20:25:08.422 wdl.w:ptcp.w:call-trgt-92 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:25:08.422 wdl.w:ptcp.w:call-trgt-92 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-92/out/m84036_250809_035451_s4.bc2189.mapped.bam"}
2025-09-15 20:25:08.422 wdl.w:ptcp.w:call-trgt-92 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-92/out/m84036_250809_035451_s4.bc2189.mapped.bam.bai"}
2025-09-15 20:25:08.422 wdl.w:ptcp.w:call-trgt-92 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:25:08.422 wdl.w:ptcp.w:call-trgt-92 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:25:08.422 wdl.w:ptcp.w:call-trgt-92 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2189"}
2025-09-15 20:25:08.422 wdl.w:ptcp.w:call-trgt-92 INFO visit :: node: "decl-sex", values: {"sex": "F"}
2025-09-15 20:25:08.422 wdl.w:ptcp.w:call-trgt-92 INFO visit :: node: "decl-trgt_bed", values: {"trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"}
2025-09-15 20:25:08.423 wdl.w:ptcp.w:call-trgt-92 NOTICE ready :: job: "call-get_reads_overlapping_repeats", callee: "get_reads_overlapping_repeats"
2025-09-15 20:25:08.423 wdl.w:ptcp.w:call-trgt-92 INFO input :: job: "call-get_reads_overlapping_repeats", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-92/out/m84036_250809_035451_s4.bc2189.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-92/out/m84036_250809_035451_s4.bc2189.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2189"}
2025-09-15 20:25:08.424 wdl.w:ptcp.w:call-trgt-92 NOTICE ready :: job: "call-trgt_genotype", callee: "trgt_genotype"
2025-09-15 20:25:08.424 wdl.w:ptcp.w:call-trgt-92 INFO input :: job: "call-trgt_genotype", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-92/out/m84036_250809_035451_s4.bc2189.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-92/out/m84036_250809_035451_s4.bc2189.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2189"}
2025-09-15 20:25:08.452 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_plot_meth_waterfall INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2139.meth_waterfall.trgt_plots.zip"
2025-09-15 20:25:08.457 wdl.w:ptcp.w:call-trgt-74.t:call-trgt_genotype INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 11, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-74/call-trgt_genotype/_singularity_tmpdir_ppby9bpa"
2025-09-15 20:25:08.457 wdl.w:ptcp.w:call-trgt-74.t:call-trgt_genotype INFO Slurm invocation: srun --job-name call-trgt_genotype --partition compute,compute9 --cpus-per-task 8 --mem 15259M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-74/call-trgt_genotype/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-74/call-trgt_genotype/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-74/call-trgt_genotype/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-74/call-trgt_genotype/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-74/out/m84036_250809_035451_s4.bc2171.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2171.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-74/out/m84036_250809_035451_s4.bc2171.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2171.mapped.bam:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-74/call-trgt_genotype/_singularity_tmpdir_ppby9bpa/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-74/call-trgt_genotype/_singularity_tmpdir_ppby9bpa/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:08.464 wdl.w:ptcp.w:call-trgt-67.t:call-trgt_plot_motifs_waterfall NOTICE done
2025-09-15 20:25:08.475 wdl.w:ptcp.w:call-trgt-74.t:call-trgt_genotype NOTICE slurm_singularity run :: pid: 1204812, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-74/call-trgt_genotype/slurm_singularity.log.txt"
2025-09-15 20:25:08.510 wdl.w:ptcp.w:call-trgt-67 NOTICE finish :: job: "call-trgt_plot_motifs_waterfall"
2025-09-15 20:25:08.510 wdl.w:ptcp.w:call-trgt-67 INFO output :: job: "call-trgt_plot_motifs_waterfall", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-67/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2164.motifs_waterfall.trgt_plots.zip"}
2025-09-15 20:25:08.511 wdl.w:ptcp.w:call-trgt-67 INFO visit :: node: "output-images_motifs_waterfall", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-67/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2164.motifs_waterfall.trgt_plots.zip"}
2025-09-15 20:25:08.521 wdl.w:ptcp.w:call-paraphase-64.t:call-call_f8 NOTICE task setup :: name: "call_f8", source: "./paraphase.wdl", line: 232, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-64/call-call_f8", thread: 140607691417152
2025-09-15 20:25:08.544 wdl.w:ptcp.w:call-paraphase-64.t:call-call_f8 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:08.544 wdl.w:ptcp.w:call-paraphase-64.t:call-call_f8 INFO input :: name: "genome_version", value: "38"
2025-09-15 20:25:08.544 wdl.w:ptcp.w:call-paraphase-64.t:call-call_f8 INFO input :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2161"
2025-09-15 20:25:08.544 wdl.w:ptcp.w:call-paraphase-64.t:call-call_f8 INFO input :: name: "paraphase_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2161.paraphase.bam.bai"
2025-09-15 20:25:08.544 wdl.w:ptcp.w:call-paraphase-64.t:call-call_f8 INFO input :: name: "paraphase_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2161.paraphase.bam"
2025-09-15 20:25:08.544 wdl.w:ptcp.w:call-paraphase-64.t:call-call_f8 INFO input :: name: "sex", value: "F"
2025-09-15 20:25:08.544 wdl.w:ptcp.w:call-paraphase-64.t:call-call_f8 INFO eval :: name: "threads", value: 1
2025-09-15 20:25:08.545 wdl.w:ptcp.w:call-paraphase-64.t:call-call_f8 INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:25:08.545 wdl.w:ptcp.w:call-paraphase-64.t:call-call_f8 INFO eval :: name: "disk_size", value: 11
2025-09-15 20:25:08.545 wdl.w:ptcp.w:call-paraphase-64.t:call-call_f8 INFO eval :: name: "sample_sex", value: "F"
2025-09-15 20:25:08.545 wdl.w:ptcp.w:call-paraphase-64.t:call-call_f8 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:08.545 wdl.w:ptcp.w:call-paraphase-64.t:call-call_f8 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:08.546 wdl.w:ptcp.w:call-paraphase-64.t:call-call_f8 INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:25:08.546 wdl.w:ptcp.w:call-paraphase-64.t:call-call_f8 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:08.564 wdl.w:ptcp.w:call-trgt-42.t:call-trgt_plot_meth_waterfall NOTICE done
2025-09-15 20:25:08.570 wdl.w:ptcp.w:call-trgt-42 NOTICE finish :: job: "call-trgt_plot_meth_waterfall"
2025-09-15 20:25:08.571 wdl.w:ptcp.w:call-trgt-42 INFO output :: job: "call-trgt_plot_meth_waterfall", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-42/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2139.meth_waterfall.trgt_plots.zip"}
2025-09-15 20:25:08.571 wdl.w:ptcp.w:call-trgt-42 INFO visit :: node: "output-images_meth_waterfall", values: {"images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-42/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2139.meth_waterfall.trgt_plots.zip"}
2025-09-15 20:25:08.571 wdl.w:ptcp.w:call-trgt-42 INFO visit :: node: "outputs", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-42/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2139.motifs_waterfall.trgt_plots.zip", "images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-42/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2139.meth_allele.trgt_plots.zip", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-42/call-trgt_genotype/out/m84036_250809_035451_s4.bc2139.trgt.sorted.spanning.bam.bai", "images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-42/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2139.motifs_allele.trgt_plots.zip", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-42/call-trgt_genotype/out/m84036_250809_035451_s4.bc2139.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-42/call-trgt_genotype/out/m84036_250809_035451_s4.bc2139.trgt.vcf", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-42/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2139.repeats.bam", "images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-42/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2139.meth_waterfall.trgt_plots.zip", "reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-42/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2139.repeats.bam.bai"}
2025-09-15 20:25:08.582 wdl.w:ptcp.w:call-paraphase-78.t:call-run_paraphase NOTICE task setup :: name: "run_paraphase", source: "./paraphase.wdl", line: 127, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-78/call-run_paraphase", thread: 140609260066368
2025-09-15 20:25:08.608 wdl.w:ptcp.w:call-paraphase-78.t:call-run_paraphase INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:08.608 wdl.w:ptcp.w:call-paraphase-78.t:call-run_paraphase INFO input :: name: "annotation_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf"
2025-09-15 20:25:08.608 wdl.w:ptcp.w:call-paraphase-78.t:call-run_paraphase INFO input :: name: "genome_version", value: "38"
2025-09-15 20:25:08.608 wdl.w:ptcp.w:call-paraphase-78.t:call-run_paraphase INFO input :: name: "config_file", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/paraphase_config.GRCh38.yaml"
2025-09-15 20:25:08.608 wdl.w:ptcp.w:call-paraphase-78.t:call-run_paraphase INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:25:08.608 wdl.w:ptcp.w:call-paraphase-78.t:call-run_paraphase INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:25:08.608 wdl.w:ptcp.w:call-paraphase-78.t:call-run_paraphase INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2175.mapped.bam.bai"
2025-09-15 20:25:08.608 wdl.w:ptcp.w:call-paraphase-78.t:call-run_paraphase INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2175.mapped.bam"
2025-09-15 20:25:08.608 wdl.w:ptcp.w:call-paraphase-78.t:call-run_paraphase INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2175"
2025-09-15 20:25:08.609 wdl.w:ptcp.w:call-paraphase-78.t:call-run_paraphase INFO eval :: name: "threads", value: 4
2025-09-15 20:25:08.609 wdl.w:ptcp.w:call-paraphase-78.t:call-run_paraphase INFO eval :: name: "mem_gb", value: 8
2025-09-15 20:25:08.609 wdl.w:ptcp.w:call-paraphase-78.t:call-run_paraphase INFO eval :: name: "disk_size", value: 27
2025-09-15 20:25:08.609 wdl.w:ptcp.w:call-paraphase-78.t:call-run_paraphase INFO eval :: name: "out_dir", value: "m84036_250809_035451_s4.bc2175_paraphase"
2025-09-15 20:25:08.609 wdl.w:ptcp.w:call-paraphase-78.t:call-run_paraphase INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 4, memory_reservation: 8000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:08.610 wdl.w:ptcp.w:call-paraphase-78.t:call-run_paraphase WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:08.610 wdl.w:ptcp.w:call-paraphase-78.t:call-run_paraphase INFO provisioned :: seconds_waited: 0, cpu: 4, mem_bytes: 8000000000
2025-09-15 20:25:08.610 wdl.w:ptcp.w:call-paraphase-78.t:call-run_paraphase INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:08.608 wdl.w:ptcp.w:call-paraphase-47.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for smn1 for sample m84036_250809_035451_s4.bc2144 at 2025-09-15 20:24:46.727624...
2025-09-15 20:25:08.610 wdl.w:ptcp.w:call-paraphase-47.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for hba for sample m84036_250809_035451_s4.bc2144 at 2025-09-15 20:24:57.126262...
2025-09-15 20:25:08.611 wdl.w:ptcp.w:call-paraphase-47.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for hba for sample m84036_250809_035451_s4.bc2144 at 2025-09-15 20:24:57.569986...
2025-09-15 20:25:08.611 wdl.w:ptcp.w:call-paraphase-47.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for cyp21 for sample m84036_250809_035451_s4.bc2144 at 2025-09-15 20:24:58.382169...
2025-09-15 20:25:08.611 wdl.w:ptcp.w:call-paraphase-47.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for cyp21 for sample m84036_250809_035451_s4.bc2144 at 2025-09-15 20:24:59.485495...
2025-09-15 20:25:08.611 wdl.w:ptcp.w:call-paraphase-47.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for gba for sample m84036_250809_035451_s4.bc2144 at 2025-09-15 20:25:05.130330...
2025-09-15 20:25:08.611 wdl.w:ptcp.w:call-paraphase-47.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for gba for sample m84036_250809_035451_s4.bc2144 at 2025-09-15 20:25:05.785076...
2025-09-15 20:25:08.611 wdl.w:ptcp.w:call-paraphase-47.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for f8inv1 for sample m84036_250809_035451_s4.bc2144 at 2025-09-15 20:25:07.973883...
2025-09-15 20:25:08.611 wdl.w:ptcp.w:call-paraphase-47.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for f8inv1 for sample m84036_250809_035451_s4.bc2144 at 2025-09-15 20:25:07.974092...
2025-09-15 20:25:08.618 wdl.w:ptcp.w:call-paraphase-64.t:call-call_f8 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 8, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-64/call-call_f8/_singularity_tmpdir_ukld3ecp"
2025-09-15 20:25:08.618 wdl.w:ptcp.w:call-trgt-61.t:call-trgt_plot_motifs_allele.slurm_singularity INFO srun: job 51797918 queued and waiting for resources
2025-09-15 20:25:08.618 wdl.w:ptcp.w:call-paraphase-64.t:call-call_f8 INFO Slurm invocation: srun --job-name call-call_f8 --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-64/call-call_f8/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-64/call-call_f8/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-64/call-call_f8/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-64/call-call_f8/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-64/call-run_paraphase/out/m84036_250809_035451_s4.bc2161_paraphase/m84036_250809_035451_s4.bc2161.paraphase.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2161.paraphase.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-64/call-run_paraphase/out/m84036_250809_035451_s4.bc2161_paraphase/m84036_250809_035451_s4.bc2161.paraphase.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2161.paraphase.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-64/call-call_f8/_singularity_tmpdir_ukld3ecp/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-64/call-call_f8/_singularity_tmpdir_ukld3ecp/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:08.618 wdl.w:ptcp.w:call-paraphase-74.t:call-run_paraphase.slurm_singularity INFO srun: job 51797919 queued and waiting for resources
2025-09-15 20:25:08.618 wdl.w:ptcp.w:call-trgt-61.t:call-trgt_plot_motifs_allele.slurm_singularity INFO srun: job 51797918 has been allocated resources
2025-09-15 20:25:08.618 wdl.w:ptcp.w:call-paraphase-74.t:call-run_paraphase.slurm_singularity INFO srun: job 51797919 has been allocated resources
2025-09-15 20:25:08.618 wdl.w:ptcp.w:call-trgt-61.t:call-trgt_plot_motifs_allele.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:08.618 wdl.w:ptcp.w:call-paraphase-74.t:call-run_paraphase.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:08.621 wdl.w:ptcp.w:call-paraphase-74.t:call-run_paraphase.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:25:08.627 wdl.w:ptcp.w:call-trgt-64.t:call-trgt_plot_meth_allele.slurm_singularity INFO srun: job 51797920 queued and waiting for resources
2025-09-15 20:25:08.627 wdl.w:ptcp.w:call-trgt-64.t:call-trgt_plot_meth_allele.slurm_singularity INFO srun: job 51797920 has been allocated resources
2025-09-15 20:25:08.627 wdl.w:ptcp.w:call-trgt-64.t:call-trgt_plot_meth_allele.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:08.627 wdl.w:ptcp.w:call-trgt-64.t:call-trgt_plot_meth_allele.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:25:08.632 wdl.w:ptcp.w:call-trgt-61.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO srun: job 51797921 queued and waiting for resources
2025-09-15 20:25:08.632 wdl.w:ptcp.w:call-trgt-61.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO srun: job 51797921 has been allocated resources
2025-09-15 20:25:08.632 wdl.w:ptcp.w:call-trgt-61.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:08.632 wdl.w:ptcp.w:call-trgt-61.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:25:08.634 wdl.w:ptcp.w:call-trgt-64.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO srun: job 51797917 queued and waiting for resources
2025-09-15 20:25:08.634 wdl.w:ptcp.w:call-trgt-64.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO srun: job 51797917 has been allocated resources
2025-09-15 20:25:08.635 wdl.w:ptcp.w:call-trgt-64.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:08.643 wdl.w:ptcp.w:call-sawfish-17.t:call-run_sawfish INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2114_sawfish/m84036_250809_035451_s4.bc2114.sv.vcf.gz"
2025-09-15 20:25:08.651 wdl.w:ptcp.w:call-sawfish-17.t:call-run_sawfish INFO output :: name: "vcf_tbi", value: "m84036_250809_035451_s4.bc2114_sawfish/m84036_250809_035451_s4.bc2114.sv.vcf.gz.tbi"
2025-09-15 20:25:08.654 wdl.w:ptcp.w:call-sawfish-17.t:call-run_sawfish INFO output :: name: "minimap2_bam", value: "m84036_250809_035451_s4.bc2114.minimap2.bam"
2025-09-15 20:25:08.657 wdl.w:ptcp.w:call-sawfish-17.t:call-run_sawfish INFO output :: name: "minimap2_bam_bai", value: "m84036_250809_035451_s4.bc2114.minimap2.bam.bai"
2025-09-15 20:25:08.657 wdl.w:ptcp.w:call-trgt-64.t:call-trgt_plot_motifs_allele.slurm_singularity INFO srun: job 51797922 queued and waiting for resources
2025-09-15 20:25:08.657 wdl.w:ptcp.w:call-trgt-64.t:call-trgt_plot_motifs_allele.slurm_singularity INFO srun: job 51797922 has been allocated resources
2025-09-15 20:25:08.658 wdl.w:ptcp.w:call-trgt-64.t:call-trgt_plot_motifs_allele.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:08.673 wdl.w:ptcp.w:call-paraphase-64.t:call-call_f8 NOTICE slurm_singularity run :: pid: 1204831, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-64/call-call_f8/slurm_singularity.log.txt"
2025-09-15 20:25:08.693 wdl.w:ptcp.w:call-paraphase-68.t:call-run_paraphase INFO output :: name: "paraphase_bam", value: "m84036_250809_035451_s4.bc2165_paraphase/m84036_250809_035451_s4.bc2165.paraphase.bam"
2025-09-15 20:25:08.701 wdl.w:ptcp.w:call-paraphase-68.t:call-run_paraphase INFO output :: name: "paraphase_bam_bai", value: "m84036_250809_035451_s4.bc2165_paraphase/m84036_250809_035451_s4.bc2165.paraphase.bam.bai"
2025-09-15 20:25:08.703 wdl.w:ptcp.w:call-paraphase-68.t:call-run_paraphase INFO output :: name: "paraphase_json", value: "m84036_250809_035451_s4.bc2165_paraphase/m84036_250809_035451_s4.bc2165.paraphase.json"
2025-09-15 20:25:08.706 wdl.w:ptcp.w:call-paraphase-68.t:call-run_paraphase INFO output :: name: "paraphase_vcfs", value: []
2025-09-15 20:25:08.706 wdl.w:ptcp.w:call-paraphase-68.t:call-run_paraphase INFO output :: name: "havanno_json", value: "m84036_250809_035451_s4.bc2165.havanno.json"
2025-09-15 20:25:08.708 wdl.w:ptcp.w:call-trgt-42 NOTICE done
2025-09-15 20:25:08.714 wdl.w:ptcp NOTICE finish :: job: "call-trgt-42"
2025-09-15 20:25:08.714 wdl.w:ptcp INFO output :: job: "call-trgt-42", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-42/out/m84036_250809_035451_s4.bc2139.motifs_waterfall.trgt_plots.zip", "images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-42/out/m84036_250809_035451_s4.bc2139.meth_allele.trgt_plots.zip", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-42/out/m84036_250809_035451_s4.bc2139.trgt.sorted.spanning.bam.bai", "images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-42/out/m84036_250809_035451_s4.bc2139.motifs_allele.trgt_plots.zip", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-42/out/m84036_250809_035451_s4.bc2139.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-42/out/m84036_250809_035451_s4.bc2139.trgt.vcf", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-42/out/m84036_250809_035451_s4.bc2139.repeats.bam", "images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-42/out/m84036_250809_035451_s4.bc2139.meth_waterfall.trgt_plots.zip", "reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-42/out/m84036_250809_035451_s4.bc2139.repeats.bam.bai"}
2025-09-15 20:25:08.723 wdl.w:ptcp.w:call-paraphase-91 NOTICE workflow start :: name: "paraphase", source: "./paraphase.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-91"
2025-09-15 20:25:08.740 wdl.w:ptcp.w:call-paraphase-78.t:call-run_paraphase INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-78/call-run_paraphase/_singularity_tmpdir_f6d3bdrq"
2025-09-15 20:25:08.741 wdl.w:ptcp.w:call-paraphase-78.t:call-run_paraphase INFO Slurm invocation: srun --job-name call-run_paraphase --partition compute,compute9 --cpus-per-task 4 --mem 7629M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-78/call-run_paraphase/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-78/call-run_paraphase/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-78/call-run_paraphase/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-78/call-run_paraphase/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-78/out/m84036_250809_035451_s4.bc2175.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2175.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-78/out/m84036_250809_035451_s4.bc2175.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2175.mapped.bam:ro --bind /ptcp/meta/variant_list/variant_list.GRCh38.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf:ro --bind /ptcp/meta/paraphase/paraphase_config.GRCh38.yaml:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/paraphase_config.GRCh38.yaml:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-78/call-run_paraphase/_singularity_tmpdir_f6d3bdrq/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-78/call-run_paraphase/_singularity_tmpdir_f6d3bdrq/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:08.744 wdl.w:ptcp.w:call-paraphase-91 INFO visit :: node: "decl-annotation_vcf", values: {"annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf"}
2025-09-15 20:25:08.745 wdl.w:ptcp.w:call-paraphase-91 INFO visit :: node: "decl-config_file", values: {"config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml"}
2025-09-15 20:25:08.745 wdl.w:ptcp.w:call-paraphase-91 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:25:08.745 wdl.w:ptcp.w:call-paraphase-91 INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:25:08.745 wdl.w:ptcp.w:call-paraphase-91 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-91/out/m84036_250809_035451_s4.bc2188.mapped.bam"}
2025-09-15 20:25:08.745 wdl.w:ptcp.w:call-paraphase-91 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-91/out/m84036_250809_035451_s4.bc2188.mapped.bam.bai"}
2025-09-15 20:25:08.745 wdl.w:ptcp.w:call-paraphase-91 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:25:08.745 wdl.w:ptcp.w:call-paraphase-91 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:25:08.745 wdl.w:ptcp.w:call-paraphase-91 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2188"}
2025-09-15 20:25:08.745 wdl.w:ptcp.w:call-paraphase-91 INFO visit :: node: "decl-sex", values: {"sex": "F"}
2025-09-15 20:25:08.746 wdl.w:ptcp.w:call-paraphase-91 NOTICE ready :: job: "call-run_paraphase", callee: "run_paraphase"
2025-09-15 20:25:08.746 wdl.w:ptcp.w:call-paraphase-91 INFO input :: job: "call-run_paraphase", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf", "genome_version": "38", "config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-91/out/m84036_250809_035451_s4.bc2188.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-91/out/m84036_250809_035451_s4.bc2188.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2188"}
2025-09-15 20:25:08.775 wdl.w:ptcp.w:call-paraphase-78.t:call-run_paraphase NOTICE slurm_singularity run :: pid: 1204835, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-78/call-run_paraphase/slurm_singularity.log.txt"
2025-09-15 20:25:08.816 wdl.w:ptcp.w:call-trgt-67.t:call-trgt_plot_meth_allele INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2164.meth_allele.trgt_plots.zip"
2025-09-15 20:25:08.861 wdl.w:ptcp.w:call-paraphase-68.t:call-run_paraphase NOTICE done
2025-09-15 20:25:08.869 wdl.w:ptcp.w:call-paraphase-68 NOTICE finish :: job: "call-run_paraphase"
2025-09-15 20:25:08.869 wdl.w:ptcp.w:call-paraphase-68 INFO output :: job: "call-run_paraphase", values: {"havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-68/call-run_paraphase/out/m84036_250809_035451_s4.bc2165.havanno.json", "paraphase_vcfs": [], "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-68/call-run_paraphase/out/m84036_250809_035451_s4.bc2165_paraphase/m84036_250809_035451_s4.bc2165.paraphase.json", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-68/call-run_paraphase/out/m84036_250809_035451_s4.bc2165_paraphase/m84036_250809_035451_s4.bc2165.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-68/call-run_paraphase/out/m84036_250809_035451_s4.bc2165_paraphase/m84036_250809_035451_s4.bc2165.paraphase.bam"}
2025-09-15 20:25:08.870 wdl.w:ptcp.w:call-paraphase-68 NOTICE ready :: job: "call-call_f8", callee: "call_f8"
2025-09-15 20:25:08.870 wdl.w:ptcp.w:call-paraphase-68 INFO input :: job: "call-call_f8", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "out_prefix": "m84036_250809_035451_s4.bc2165", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-68/call-run_paraphase/out/m84036_250809_035451_s4.bc2165_paraphase/m84036_250809_035451_s4.bc2165.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-68/call-run_paraphase/out/m84036_250809_035451_s4.bc2165_paraphase/m84036_250809_035451_s4.bc2165.paraphase.bam", "sex": "F"}
2025-09-15 20:25:08.871 wdl.w:ptcp.w:call-paraphase-68 INFO visit :: node: "output-havanno_json", values: {"havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-68/call-run_paraphase/out/m84036_250809_035451_s4.bc2165.havanno.json"}
2025-09-15 20:25:08.871 wdl.w:ptcp.w:call-paraphase-68 INFO visit :: node: "output-paraphase_bam", values: {"paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-68/call-run_paraphase/out/m84036_250809_035451_s4.bc2165_paraphase/m84036_250809_035451_s4.bc2165.paraphase.bam"}
2025-09-15 20:25:08.871 wdl.w:ptcp.w:call-paraphase-68 INFO visit :: node: "output-paraphase_bam_bai", values: {"paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-68/call-run_paraphase/out/m84036_250809_035451_s4.bc2165_paraphase/m84036_250809_035451_s4.bc2165.paraphase.bam.bai"}
2025-09-15 20:25:08.871 wdl.w:ptcp.w:call-paraphase-68 INFO visit :: node: "output-paraphase_json", values: {"paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-68/call-run_paraphase/out/m84036_250809_035451_s4.bc2165_paraphase/m84036_250809_035451_s4.bc2165.paraphase.json"}
2025-09-15 20:25:08.871 wdl.w:ptcp.w:call-paraphase-68 INFO visit :: node: "output-paraphase_vcfs", values: {"paraphase_vcfs": []}
2025-09-15 20:25:08.882 wdl.w:ptcp.w:call-sawfish-17.t:call-run_sawfish NOTICE done
2025-09-15 20:25:08.882 wdl.w:ptcp.w:call-paraphase-61.t:call-call_f8.stderr VERBOSE 2025-09-15 20:25:08,795 INFO  Started analysis for m84036_250809_035451_s4.bc2158 at 2025-09-15 20:25:08.794983...
2025-09-15 20:25:08.883 wdl.w:ptcp.w:call-paraphase-61.t:call-call_f8.stderr VERBOSE 2025-09-15 20:25:08,821 INFO  Completed analysis for m84036_250809_035451_s4.bc2158
2025-09-15 20:25:08.882 wdl.w:ptcp.w:call-sawfish-78.t:call-run_sawfish NOTICE task setup :: name: "run_sawfish", source: "./sawfish.wdl", line: 83, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-78/call-run_sawfish", thread: 140609830508096
2025-09-15 20:25:08.898 wdl.w:ptcp.w:call-trgt-64.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO srun: job 51797927 queued and waiting for resources
2025-09-15 20:25:08.898 wdl.w:ptcp.w:call-trgt-64.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO srun: job 51797927 has been allocated resources
2025-09-15 20:25:08.898 wdl.w:ptcp.w:call-trgt-64.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:08.899 wdl.w:ptcp.w:call-paraphase-61.t:call-call_f8.slurm_singularity INFO srun: job 51797928 queued and waiting for resources
2025-09-15 20:25:08.899 wdl.w:ptcp.w:call-paraphase-61.t:call-call_f8.slurm_singularity INFO srun: job 51797928 has been allocated resources
2025-09-15 20:25:08.899 wdl.w:ptcp.w:call-paraphase-61.t:call-call_f8.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:08.908 wdl.w:ptcp.w:call-sawfish-17 NOTICE finish :: job: "call-run_sawfish"
2025-09-15 20:25:08.908 wdl.w:ptcp.w:call-sawfish-17 INFO output :: job: "call-run_sawfish", values: {"minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-17/call-run_sawfish/out/m84036_250809_035451_s4.bc2114.minimap2.bam.bai", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-17/call-run_sawfish/out/m84036_250809_035451_s4.bc2114.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-17/call-run_sawfish/out/m84036_250809_035451_s4.bc2114_sawfish/m84036_250809_035451_s4.bc2114.sv.vcf.gz.tbi", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-17/call-run_sawfish/out/m84036_250809_035451_s4.bc2114_sawfish/m84036_250809_035451_s4.bc2114.sv.vcf.gz"}
2025-09-15 20:25:08.908 wdl.w:ptcp.w:call-sawfish-17 INFO visit :: node: "output-minimap2_bam", values: {"minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-17/call-run_sawfish/out/m84036_250809_035451_s4.bc2114.minimap2.bam"}
2025-09-15 20:25:08.909 wdl.w:ptcp.w:call-sawfish-17 INFO visit :: node: "output-minimap2_bam_bai", values: {"minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-17/call-run_sawfish/out/m84036_250809_035451_s4.bc2114.minimap2.bam.bai"}
2025-09-15 20:25:08.909 wdl.w:ptcp.w:call-sawfish-17 INFO visit :: node: "output-vcf", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-17/call-run_sawfish/out/m84036_250809_035451_s4.bc2114_sawfish/m84036_250809_035451_s4.bc2114.sv.vcf.gz"}
2025-09-15 20:25:08.909 wdl.w:ptcp.w:call-sawfish-17 INFO visit :: node: "output-vcf_tbi", values: {"vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-17/call-run_sawfish/out/m84036_250809_035451_s4.bc2114_sawfish/m84036_250809_035451_s4.bc2114.sv.vcf.gz.tbi"}
2025-09-15 20:25:08.909 wdl.w:ptcp.w:call-sawfish-17 INFO visit :: node: "outputs", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-17/call-run_sawfish/out/m84036_250809_035451_s4.bc2114_sawfish/m84036_250809_035451_s4.bc2114.sv.vcf.gz", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-17/call-run_sawfish/out/m84036_250809_035451_s4.bc2114.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-17/call-run_sawfish/out/m84036_250809_035451_s4.bc2114_sawfish/m84036_250809_035451_s4.bc2114.sv.vcf.gz.tbi", "minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-17/call-run_sawfish/out/m84036_250809_035451_s4.bc2114.minimap2.bam.bai"}
2025-09-15 20:25:08.910 wdl.w:ptcp.w:call-sawfish-78.t:call-run_sawfish INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:08.910 wdl.w:ptcp.w:call-sawfish-78.t:call-run_sawfish INFO input :: name: "genome_version", value: "38"
2025-09-15 20:25:08.910 wdl.w:ptcp.w:call-sawfish-78.t:call-run_sawfish INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:25:08.910 wdl.w:ptcp.w:call-sawfish-78.t:call-run_sawfish INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:25:08.910 wdl.w:ptcp.w:call-sawfish-78.t:call-run_sawfish INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2175.mapped.bam.bai"
2025-09-15 20:25:08.910 wdl.w:ptcp.w:call-sawfish-78.t:call-run_sawfish INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2175.mapped.bam"
2025-09-15 20:25:08.910 wdl.w:ptcp.w:call-sawfish-78.t:call-run_sawfish INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2175"
2025-09-15 20:25:08.910 wdl.w:ptcp.w:call-sawfish-78.t:call-run_sawfish INFO eval :: name: "mem_gb", value: 32
2025-09-15 20:25:08.910 wdl.w:ptcp.w:call-sawfish-78.t:call-run_sawfish INFO eval :: name: "threads", value: 16
2025-09-15 20:25:08.910 wdl.w:ptcp.w:call-sawfish-78.t:call-run_sawfish INFO eval :: name: "disk_size", value: 30
2025-09-15 20:25:08.911 wdl.w:ptcp.w:call-sawfish-78.t:call-run_sawfish INFO eval :: name: "discover_dirname", value: "m84036_250809_035451_s4.bc2175_sawfish_discover"
2025-09-15 20:25:08.911 wdl.w:ptcp.w:call-sawfish-78.t:call-run_sawfish INFO eval :: name: "call_dirname", value: "m84036_250809_035451_s4.bc2175_sawfish"
2025-09-15 20:25:08.911 wdl.w:ptcp.w:call-sawfish-78.t:call-run_sawfish INFO eval :: name: "minimap2_bam_filename", value: "m84036_250809_035451_s4.bc2175.minimap2.bam"
2025-09-15 20:25:08.911 wdl.w:ptcp.w:call-sawfish-78.t:call-run_sawfish INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 16, memory_reservation: 32000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:08.911 wdl.w:ptcp.w:call-sawfish-78.t:call-run_sawfish WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:08.912 wdl.w:ptcp.w:call-sawfish-78.t:call-run_sawfish INFO provisioned :: seconds_waited: 0, cpu: 16, mem_bytes: 32000000000
2025-09-15 20:25:08.912 wdl.w:ptcp.w:call-sawfish-78.t:call-run_sawfish INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:08.917 wdl.w:ptcp.t:call-tar_outputs-44 NOTICE task setup :: name: "tar_outputs", source: "./common.wdl", line: 279, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-44", thread: 140610375771712
2025-09-15 20:25:08.942 wdl.w:ptcp.w:call-sawfish-28.t:call-run_sawfish INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2125_sawfish/m84036_250809_035451_s4.bc2125.sv.vcf.gz"
2025-09-15 20:25:08.949 wdl.w:ptcp.w:call-sawfish-28.t:call-run_sawfish INFO output :: name: "vcf_tbi", value: "m84036_250809_035451_s4.bc2125_sawfish/m84036_250809_035451_s4.bc2125.sv.vcf.gz.tbi"
2025-09-15 20:25:08.952 wdl.w:ptcp.w:call-sawfish-28.t:call-run_sawfish INFO output :: name: "minimap2_bam", value: "m84036_250809_035451_s4.bc2125.minimap2.bam"
2025-09-15 20:25:08.954 wdl.w:ptcp.w:call-sawfish-28.t:call-run_sawfish INFO output :: name: "minimap2_bam_bai", value: "m84036_250809_035451_s4.bc2125.minimap2.bam.bai"
2025-09-15 20:25:08.958 wdl.w:ptcp.t:call-tar_outputs-44 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:08.958 wdl.w:ptcp.t:call-tar_outputs-44 INFO input :: name: "sawfish_vcf_tbi", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2141.sv.vcf.gz.tbi"
2025-09-15 20:25:08.958 wdl.w:ptcp.t:call-tar_outputs-44 INFO input :: name: "sawfish_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2141.sv.vcf.gz"
2025-09-15 20:25:08.958 wdl.w:ptcp.t:call-tar_outputs-44 INFO input :: name: "f8_json", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2141.f8inversion.json"
2025-09-15 20:25:08.958 wdl.w:ptcp.t:call-tar_outputs-44 INFO input :: name: "paraphase_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2141.paraphase.bam.bai"
2025-09-15 20:25:08.958 wdl.w:ptcp.t:call-tar_outputs-44 INFO input :: name: "paraphase_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2141.paraphase.bam"
2025-09-15 20:25:08.958 wdl.w:ptcp.t:call-tar_outputs-44 INFO input :: name: "paraphase_json", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2141.paraphase.json"
2025-09-15 20:25:08.958 wdl.w:ptcp.t:call-tar_outputs-44 INFO input :: name: "trgt_spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2141.trgt.sorted.spanning.bam.bai"
2025-09-15 20:25:08.958 wdl.w:ptcp.t:call-tar_outputs-44 INFO input :: name: "trgt_spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2141.trgt.sorted.spanning.bam"
2025-09-15 20:25:08.958 wdl.w:ptcp.t:call-tar_outputs-44 INFO input :: name: "trgt_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2141.trgt.vcf"
2025-09-15 20:25:08.958 wdl.w:ptcp.t:call-tar_outputs-44 INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2141.mapped.bam.bai"
2025-09-15 20:25:08.959 wdl.w:ptcp.t:call-tar_outputs-44 INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2141.mapped.bam"
2025-09-15 20:25:08.959 wdl.w:ptcp.t:call-tar_outputs-44 INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2141"
2025-09-15 20:25:08.959 wdl.w:ptcp.t:call-tar_outputs-44 INFO eval :: name: "threads", value: 1
2025-09-15 20:25:08.959 wdl.w:ptcp.t:call-tar_outputs-44 INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:25:08.959 wdl.w:ptcp.t:call-tar_outputs-44 INFO eval :: name: "disk_size", value: 6
2025-09-15 20:25:08.959 wdl.w:ptcp.t:call-tar_outputs-44 INFO eval :: name: "output_tarball", value: "m84036_250809_035451_s4.bc2141.tar"
2025-09-15 20:25:08.960 wdl.w:ptcp.t:call-tar_outputs-44 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:08.960 wdl.w:ptcp.t:call-tar_outputs-44 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:08.960 wdl.w:ptcp.t:call-tar_outputs-44 INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:25:08.960 wdl.w:ptcp.t:call-tar_outputs-44 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:08.963 wdl.w:ptcp.w:call-trgt-67.t:call-trgt_plot_meth_allele NOTICE done
2025-09-15 20:25:08.969 wdl.w:ptcp.w:call-trgt-67 NOTICE finish :: job: "call-trgt_plot_meth_allele"
2025-09-15 20:25:08.969 wdl.w:ptcp.w:call-trgt-67 INFO output :: job: "call-trgt_plot_meth_allele", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-67/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2164.meth_allele.trgt_plots.zip"}
2025-09-15 20:25:08.969 wdl.w:ptcp.w:call-trgt-67 INFO visit :: node: "output-images_meth_allele", values: {"images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-67/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2164.meth_allele.trgt_plots.zip"}
2025-09-15 20:25:08.980 wdl.w:ptcp.w:call-sawfish-17 NOTICE done
2025-09-15 20:25:08.979 wdl.w:ptcp.w:call-trgt-78.t:call-get_reads_overlapping_repeats NOTICE task setup :: name: "get_reads_overlapping_repeats", source: "./trgt.wdl", line: 182, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-78/call-get_reads_overlapping_repeats", thread: 140611961206336
2025-09-15 20:25:08.997 wdl.w:ptcp.w:call-sawfish-78.t:call-run_sawfish INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 10, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-78/call-run_sawfish/_singularity_tmpdir_kwhcmd7z"
2025-09-15 20:25:08.997 wdl.w:ptcp.w:call-sawfish-78.t:call-run_sawfish INFO Slurm invocation: srun --job-name call-run_sawfish --partition compute,compute9 --cpus-per-task 16 --mem 30518M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-78/call-run_sawfish/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-78/call-run_sawfish/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-78/call-run_sawfish/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-78/call-run_sawfish/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-78/out/m84036_250809_035451_s4.bc2175.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2175.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-78/out/m84036_250809_035451_s4.bc2175.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2175.mapped.bam:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-78/call-run_sawfish/_singularity_tmpdir_kwhcmd7z/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-78/call-run_sawfish/_singularity_tmpdir_kwhcmd7z/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:09.005 wdl.w:ptcp.w:call-trgt-78.t:call-get_reads_overlapping_repeats INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:09.005 wdl.w:ptcp.w:call-trgt-78.t:call-get_reads_overlapping_repeats INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:25:09.005 wdl.w:ptcp.w:call-trgt-78.t:call-get_reads_overlapping_repeats INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2175.mapped.bam.bai"
2025-09-15 20:25:09.005 wdl.w:ptcp.w:call-trgt-78.t:call-get_reads_overlapping_repeats INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2175.mapped.bam"
2025-09-15 20:25:09.005 wdl.w:ptcp.w:call-trgt-78.t:call-get_reads_overlapping_repeats INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2175"
2025-09-15 20:25:09.006 wdl.w:ptcp.w:call-trgt-78.t:call-get_reads_overlapping_repeats INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:25:09.006 wdl.w:ptcp.w:call-trgt-78.t:call-get_reads_overlapping_repeats INFO eval :: name: "expand_size", value: 3000
2025-09-15 20:25:09.006 wdl.w:ptcp.w:call-trgt-78.t:call-get_reads_overlapping_repeats INFO eval :: name: "threads", value: 1
2025-09-15 20:25:09.006 wdl.w:ptcp.w:call-trgt-78.t:call-get_reads_overlapping_repeats INFO eval :: name: "expanded_bed_name", value: "m84036_250809_035451_s4.bc2175.expanded.bed"
2025-09-15 20:25:09.006 wdl.w:ptcp.w:call-trgt-78.t:call-get_reads_overlapping_repeats INFO eval :: name: "disk_size", value: 11
2025-09-15 20:25:09.006 wdl.w:ptcp.w:call-trgt-78.t:call-get_reads_overlapping_repeats INFO eval :: name: "output_name", value: "m84036_250809_035451_s4.bc2175.repeats.bam"
2025-09-15 20:25:09.006 wdl.w:ptcp.w:call-trgt-78.t:call-get_reads_overlapping_repeats INFO eval :: name: "index_name", value: "m84036_250809_035451_s4.bc2175.repeats.bam.bai"
2025-09-15 20:25:09.007 wdl.w:ptcp.w:call-trgt-78.t:call-get_reads_overlapping_repeats INFO eval :: name: "output_name_with_index", value: "m84036_250809_035451_s4.bc2175.repeats.bam##idx##m84036_250809_035451_s4.bc2175.repeats.bam.bai"
2025-09-15 20:25:09.007 wdl.w:ptcp.w:call-trgt-78.t:call-get_reads_overlapping_repeats INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:09.007 wdl.w:ptcp.w:call-trgt-78.t:call-get_reads_overlapping_repeats WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:09.007 wdl.w:ptcp.w:call-trgt-78.t:call-get_reads_overlapping_repeats INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:25:09.008 wdl.w:ptcp.w:call-trgt-78.t:call-get_reads_overlapping_repeats INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:09.008 wdl.w:ptcp.w:call-paraphase-69.t:call-call_f8.slurm_singularity INFO srun: job 51797933 queued and waiting for resources
2025-09-15 20:25:09.008 wdl.w:ptcp.w:call-paraphase-69.t:call-call_f8.slurm_singularity INFO srun: job 51797933 has been allocated resources
2025-09-15 20:25:09.008 wdl.w:ptcp.w:call-paraphase-69.t:call-call_f8.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:09.015 wdl.w:ptcp NOTICE finish :: job: "call-sawfish-17"
2025-09-15 20:25:09.015 wdl.w:ptcp INFO output :: job: "call-sawfish-17", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-17/out/m84036_250809_035451_s4.bc2114_sawfish/m84036_250809_035451_s4.bc2114.sv.vcf.gz", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-17/out/m84036_250809_035451_s4.bc2114.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-17/out/m84036_250809_035451_s4.bc2114_sawfish/m84036_250809_035451_s4.bc2114.sv.vcf.gz.tbi", "minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-17/out/m84036_250809_035451_s4.bc2114.minimap2.bam.bai"}
2025-09-15 20:25:09.016 wdl.w:ptcp NOTICE ready :: job: "call-tar_outputs-17", callee: "tar_outputs"
2025-09-15 20:25:09.016 wdl.w:ptcp INFO input :: job: "call-tar_outputs-17", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "sawfish_vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-17/out/m84036_250809_035451_s4.bc2114_sawfish/m84036_250809_035451_s4.bc2114.sv.vcf.gz.tbi", "sawfish_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-17/out/m84036_250809_035451_s4.bc2114_sawfish/m84036_250809_035451_s4.bc2114.sv.vcf.gz", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-17/out/m84036_250809_035451_s4.bc2114.f8inversion.json", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-17/out/m84036_250809_035451_s4.bc2114_paraphase/m84036_250809_035451_s4.bc2114.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-17/out/m84036_250809_035451_s4.bc2114_paraphase/m84036_250809_035451_s4.bc2114.paraphase.bam", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-17/out/m84036_250809_035451_s4.bc2114_paraphase/m84036_250809_035451_s4.bc2114.paraphase.json", "trgt_spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-17/out/m84036_250809_035451_s4.bc2114.trgt.sorted.spanning.bam.bai", "trgt_spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-17/out/m84036_250809_035451_s4.bc2114.trgt.sorted.spanning.bam", "trgt_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-17/out/m84036_250809_035451_s4.bc2114.trgt.vcf", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-17/out/m84036_250809_035451_s4.bc2114.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-17/out/m84036_250809_035451_s4.bc2114.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2114"}
2025-09-15 20:25:09.024 wdl.w:ptcp.w:call-sawfish-91 NOTICE workflow start :: name: "sawfish", source: "./sawfish.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-91"
2025-09-15 20:25:09.033 wdl.w:ptcp.w:call-paraphase-61.t:call-call_f8 INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2158.f8inversion.vcf"
2025-09-15 20:25:09.034 wdl.w:ptcp.w:call-sawfish-78.t:call-run_sawfish NOTICE slurm_singularity run :: pid: 1204848, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-78/call-run_sawfish/slurm_singularity.log.txt"
2025-09-15 20:25:09.038 wdl.w:ptcp.w:call-paraphase-61.t:call-call_f8 INFO output :: name: "json", value: "m84036_250809_035451_s4.bc2158.f8inversion.json"
2025-09-15 20:25:09.044 wdl.w:ptcp.w:call-sawfish-91 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:25:09.045 wdl.w:ptcp.w:call-sawfish-91 INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:25:09.045 wdl.w:ptcp.w:call-sawfish-91 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-91/out/m84036_250809_035451_s4.bc2188.mapped.bam"}
2025-09-15 20:25:09.045 wdl.w:ptcp.w:call-sawfish-91 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-91/out/m84036_250809_035451_s4.bc2188.mapped.bam.bai"}
2025-09-15 20:25:09.045 wdl.w:ptcp.w:call-sawfish-91 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:25:09.045 wdl.w:ptcp.w:call-sawfish-91 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:25:09.045 wdl.w:ptcp.w:call-sawfish-91 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2188"}
2025-09-15 20:25:09.047 wdl.w:ptcp.w:call-sawfish-91 NOTICE ready :: job: "call-run_sawfish", callee: "run_sawfish"
2025-09-15 20:25:09.048 wdl.w:ptcp.w:call-sawfish-91 INFO input :: job: "call-run_sawfish", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-91/out/m84036_250809_035451_s4.bc2188.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-91/out/m84036_250809_035451_s4.bc2188.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2188"}
2025-09-15 20:25:09.076 wdl.w:ptcp.w:call-sawfish-74.t:call-run_sawfish.slurm_singularity INFO srun: job 51797934 queued and waiting for resources
2025-09-15 20:25:09.076 wdl.w:ptcp.w:call-sawfish-74.t:call-run_sawfish.slurm_singularity INFO srun: job 51797934 has been allocated resources
2025-09-15 20:25:09.076 wdl.w:ptcp.w:call-sawfish-74.t:call-run_sawfish.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:09.076 wdl.w:ptcp.w:call-sawfish-74.t:call-run_sawfish.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:25:09.087 wdl.w:ptcp.w:call-trgt-78.t:call-get_reads_overlapping_repeats INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 9, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-78/call-get_reads_overlapping_repeats/_singularity_tmpdir_hstnxanc"
2025-09-15 20:25:09.087 wdl.w:ptcp.w:call-trgt-78.t:call-get_reads_overlapping_repeats INFO Slurm invocation: srun --job-name call-get_reads_overlapping_repeats --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-78/call-get_reads_overlapping_repeats/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-78/call-get_reads_overlapping_repeats/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-78/call-get_reads_overlapping_repeats/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-78/call-get_reads_overlapping_repeats/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-78/out/m84036_250809_035451_s4.bc2175.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2175.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-78/out/m84036_250809_035451_s4.bc2175.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2175.mapped.bam:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-78/call-get_reads_overlapping_repeats/_singularity_tmpdir_hstnxanc/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-78/call-get_reads_overlapping_repeats/_singularity_tmpdir_hstnxanc/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:09.095 wdl.w:ptcp.w:call-paraphase-71.t:call-run_paraphase.stderr VERBOSE INFO:root:Processing sample m84036_250809_035451_s4.bc2168 at 2025-09-15 20:25:03.609981...
2025-09-15 20:25:09.096 wdl.w:ptcp.w:call-paraphase-71.t:call-run_paraphase.stderr VERBOSE INFO:root:Checking sample sex at 2025-09-15 20:25:03.610697...
2025-09-15 20:25:09.096 wdl.w:ptcp.w:call-paraphase-71.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for cyp21 for sample m84036_250809_035451_s4.bc2168 at 2025-09-15 20:25:03.639801...
2025-09-15 20:25:09.096 wdl.w:ptcp.w:call-paraphase-71.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for cyp21 for sample m84036_250809_035451_s4.bc2168 at 2025-09-15 20:25:03.640197...
2025-09-15 20:25:09.096 wdl.w:ptcp.w:call-paraphase-71.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for smn1 for sample m84036_250809_035451_s4.bc2168 at 2025-09-15 20:25:03.640049...
2025-09-15 20:25:09.097 wdl.w:ptcp.w:call-paraphase-71.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for smn1 for sample m84036_250809_035451_s4.bc2168 at 2025-09-15 20:25:03.640412...
2025-09-15 20:25:09.097 wdl.w:ptcp.w:call-paraphase-71.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for gba for sample m84036_250809_035451_s4.bc2168 at 2025-09-15 20:25:03.641314...
2025-09-15 20:25:09.097 wdl.w:ptcp.w:call-paraphase-71.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for hba for sample m84036_250809_035451_s4.bc2168 at 2025-09-15 20:25:03.641313...
2025-09-15 20:25:09.097 wdl.w:ptcp.w:call-paraphase-71.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for gba for sample m84036_250809_035451_s4.bc2168 at 2025-09-15 20:25:03.641663...
2025-09-15 20:25:09.097 wdl.w:ptcp.w:call-paraphase-71.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for hba for sample m84036_250809_035451_s4.bc2168 at 2025-09-15 20:25:03.641668...
2025-09-15 20:25:09.115 wdl.w:ptcp.w:call-trgt-78.t:call-get_reads_overlapping_repeats NOTICE slurm_singularity run :: pid: 1204856, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-78/call-get_reads_overlapping_repeats/slurm_singularity.log.txt"
2025-09-15 20:25:09.124 wdl.w:ptcp.t:call-tar_outputs-44 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 17, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-44/_singularity_tmpdir_ih8patr4"
2025-09-15 20:25:09.125 wdl.w:ptcp.t:call-tar_outputs-44 INFO Slurm invocation: srun --job-name call-tar_outputs-44 --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-44/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-44/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-44/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-44/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-44/out/m84036_250809_035451_s4.bc2141.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2141.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-44/out/m84036_250809_035451_s4.bc2141.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2141.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-44/out/m84036_250809_035451_s4.bc2141.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2141.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-44/out/m84036_250809_035451_s4.bc2141.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2141.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-44/out/m84036_250809_035451_s4.bc2141.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2141.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-44/out/m84036_250809_035451_s4.bc2141_sawfish/m84036_250809_035451_s4.bc2141.sv.vcf.gz.tbi:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2141.sv.vcf.gz.tbi:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-44/out/m84036_250809_035451_s4.bc2141_sawfish/m84036_250809_035451_s4.bc2141.sv.vcf.gz:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2141.sv.vcf.gz:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-44/out/m84036_250809_035451_s4.bc2141_paraphase/m84036_250809_035451_s4.bc2141.paraphase.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2141.paraphase.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-44/out/m84036_250809_035451_s4.bc2141_paraphase/m84036_250809_035451_s4.bc2141.paraphase.json:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2141.paraphase.json:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-44/out/m84036_250809_035451_s4.bc2141_paraphase/m84036_250809_035451_s4.bc2141.paraphase.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2141.paraphase.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-44/out/m84036_250809_035451_s4.bc2141.f8inversion.json:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2141.f8inversion.json:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-44/_singularity_tmpdir_ih8patr4/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-44/_singularity_tmpdir_ih8patr4/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:09.143 wdl.w:ptcp.t:call-tar_outputs-44 NOTICE slurm_singularity run :: pid: 1204858, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-44/slurm_singularity.log.txt"
2025-09-15 20:25:09.149 wdl.w:ptcp.w:call-paraphase-61.t:call-call_f8 NOTICE done
2025-09-15 20:25:09.155 wdl.w:ptcp.w:call-paraphase-61 NOTICE finish :: job: "call-call_f8"
2025-09-15 20:25:09.155 wdl.w:ptcp.w:call-paraphase-61 INFO output :: job: "call-call_f8", values: {"json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-61/call-call_f8/out/m84036_250809_035451_s4.bc2158.f8inversion.json", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-61/call-call_f8/out/m84036_250809_035451_s4.bc2158.f8inversion.vcf"}
2025-09-15 20:25:09.156 wdl.w:ptcp.w:call-paraphase-61 INFO visit :: node: "output-f8_json", values: {"f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-61/call-call_f8/out/m84036_250809_035451_s4.bc2158.f8inversion.json"}
2025-09-15 20:25:09.156 wdl.w:ptcp.w:call-paraphase-61 INFO visit :: node: "output-f8_vcf", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-61/call-call_f8/out/m84036_250809_035451_s4.bc2158.f8inversion.vcf"}
2025-09-15 20:25:09.156 wdl.w:ptcp.w:call-paraphase-61 INFO visit :: node: "outputs", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-61/call-call_f8/out/m84036_250809_035451_s4.bc2158.f8inversion.vcf", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-61/call-run_paraphase/out/m84036_250809_035451_s4.bc2158_paraphase/m84036_250809_035451_s4.bc2158.paraphase.json", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-61/call-run_paraphase/out/m84036_250809_035451_s4.bc2158_paraphase/m84036_250809_035451_s4.bc2158.paraphase.bam", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-61/call-run_paraphase/out/m84036_250809_035451_s4.bc2158_paraphase/m84036_250809_035451_s4.bc2158.paraphase.bam.bai", "paraphase_vcfs": [], "havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-61/call-run_paraphase/out/m84036_250809_035451_s4.bc2158.havanno.json", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-61/call-call_f8/out/m84036_250809_035451_s4.bc2158.f8inversion.json"}
2025-09-15 20:25:09.161 wdl.w:ptcp.w:call-sawfish-28.t:call-run_sawfish NOTICE done
2025-09-15 20:25:09.165 wdl.w:ptcp.w:call-trgt-78.t:call-trgt_genotype NOTICE task setup :: name: "trgt_genotype", source: "./trgt.wdl", line: 272, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-78/call-trgt_genotype", thread: 140607683024448
2025-09-15 20:25:09.166 wdl.w:ptcp.w:call-sawfish-28 NOTICE finish :: job: "call-run_sawfish"
2025-09-15 20:25:09.166 wdl.w:ptcp.w:call-sawfish-28 INFO output :: job: "call-run_sawfish", values: {"minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-28/call-run_sawfish/out/m84036_250809_035451_s4.bc2125.minimap2.bam.bai", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-28/call-run_sawfish/out/m84036_250809_035451_s4.bc2125.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-28/call-run_sawfish/out/m84036_250809_035451_s4.bc2125_sawfish/m84036_250809_035451_s4.bc2125.sv.vcf.gz.tbi", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-28/call-run_sawfish/out/m84036_250809_035451_s4.bc2125_sawfish/m84036_250809_035451_s4.bc2125.sv.vcf.gz"}
2025-09-15 20:25:09.167 wdl.w:ptcp.w:call-sawfish-28 INFO visit :: node: "output-minimap2_bam", values: {"minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-28/call-run_sawfish/out/m84036_250809_035451_s4.bc2125.minimap2.bam"}
2025-09-15 20:25:09.167 wdl.w:ptcp.w:call-sawfish-28 INFO visit :: node: "output-minimap2_bam_bai", values: {"minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-28/call-run_sawfish/out/m84036_250809_035451_s4.bc2125.minimap2.bam.bai"}
2025-09-15 20:25:09.167 wdl.w:ptcp.w:call-sawfish-28 INFO visit :: node: "output-vcf", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-28/call-run_sawfish/out/m84036_250809_035451_s4.bc2125_sawfish/m84036_250809_035451_s4.bc2125.sv.vcf.gz"}
2025-09-15 20:25:09.167 wdl.w:ptcp.w:call-sawfish-28 INFO visit :: node: "output-vcf_tbi", values: {"vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-28/call-run_sawfish/out/m84036_250809_035451_s4.bc2125_sawfish/m84036_250809_035451_s4.bc2125.sv.vcf.gz.tbi"}
2025-09-15 20:25:09.167 wdl.w:ptcp.w:call-sawfish-28 INFO visit :: node: "outputs", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-28/call-run_sawfish/out/m84036_250809_035451_s4.bc2125_sawfish/m84036_250809_035451_s4.bc2125.sv.vcf.gz", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-28/call-run_sawfish/out/m84036_250809_035451_s4.bc2125.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-28/call-run_sawfish/out/m84036_250809_035451_s4.bc2125_sawfish/m84036_250809_035451_s4.bc2125.sv.vcf.gz.tbi", "minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-28/call-run_sawfish/out/m84036_250809_035451_s4.bc2125.minimap2.bam.bai"}
2025-09-15 20:25:09.173 wdl.w:ptcp.w:call-paraphase-84.t:call-run_paraphase NOTICE task setup :: name: "run_paraphase", source: "./paraphase.wdl", line: 127, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-84/call-run_paraphase", thread: 140613034948160
2025-09-15 20:25:09.179 wdl.w:ptcp.w:call-trgt-68.t:call-get_reads_overlapping_repeats INFO output :: name: "reads_overlapping_repeats", value: "m84036_250809_035451_s4.bc2165.repeats.bam"
2025-09-15 20:25:09.182 wdl.w:ptcp.w:call-trgt-78.t:call-trgt_genotype INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:09.182 wdl.w:ptcp.w:call-trgt-78.t:call-trgt_genotype INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:25:09.183 wdl.w:ptcp.w:call-trgt-78.t:call-trgt_genotype INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:25:09.183 wdl.w:ptcp.w:call-trgt-78.t:call-trgt_genotype INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:25:09.183 wdl.w:ptcp.w:call-trgt-78.t:call-trgt_genotype INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2175.mapped.bam.bai"
2025-09-15 20:25:09.183 wdl.w:ptcp.w:call-trgt-78.t:call-trgt_genotype INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2175.mapped.bam"
2025-09-15 20:25:09.183 wdl.w:ptcp.w:call-trgt-78.t:call-trgt_genotype INFO input :: name: "sex", value: "F"
2025-09-15 20:25:09.183 wdl.w:ptcp.w:call-trgt-78.t:call-trgt_genotype INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2175"
2025-09-15 20:25:09.183 wdl.w:ptcp.w:call-trgt-78.t:call-trgt_genotype INFO eval :: name: "mem_gb", value: 16
2025-09-15 20:25:09.183 wdl.w:ptcp.w:call-trgt-78.t:call-trgt_genotype INFO eval :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2175.trgt"
2025-09-15 20:25:09.184 wdl.w:ptcp.w:call-trgt-78.t:call-trgt_genotype INFO eval :: name: "threads", value: 8
2025-09-15 20:25:09.184 wdl.w:ptcp.w:call-trgt-78.t:call-trgt_genotype INFO eval :: name: "disk_size", value: 27
2025-09-15 20:25:09.185 wdl.w:ptcp.w:call-trgt-78.t:call-trgt_genotype INFO eval :: name: "karyotype", value: "XX"
2025-09-15 20:25:09.185 wdl.w:ptcp.w:call-trgt-68.t:call-get_reads_overlapping_repeats INFO output :: name: "reads_overlapping_repeats_bai", value: "m84036_250809_035451_s4.bc2165.repeats.bam.bai"
2025-09-15 20:25:09.186 wdl.w:ptcp.w:call-trgt-78.t:call-trgt_genotype INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 8, memory_reservation: 16000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:09.186 wdl.w:ptcp.w:call-trgt-78.t:call-trgt_genotype WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:09.188 wdl.w:ptcp.w:call-trgt-78.t:call-trgt_genotype INFO provisioned :: seconds_waited: 0, cpu: 8, mem_bytes: 16000000000
2025-09-15 20:25:09.188 wdl.w:ptcp.w:call-trgt-78.t:call-trgt_genotype INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:09.198 wdl.w:ptcp.w:call-paraphase-84.t:call-run_paraphase INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:09.198 wdl.w:ptcp.w:call-paraphase-84.t:call-run_paraphase INFO input :: name: "annotation_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf"
2025-09-15 20:25:09.198 wdl.w:ptcp.w:call-paraphase-84.t:call-run_paraphase INFO input :: name: "genome_version", value: "38"
2025-09-15 20:25:09.198 wdl.w:ptcp.w:call-paraphase-84.t:call-run_paraphase INFO input :: name: "config_file", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/paraphase_config.GRCh38.yaml"
2025-09-15 20:25:09.198 wdl.w:ptcp.w:call-paraphase-84.t:call-run_paraphase INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:25:09.199 wdl.w:ptcp.w:call-paraphase-84.t:call-run_paraphase INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:25:09.199 wdl.w:ptcp.w:call-paraphase-84.t:call-run_paraphase INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2181.mapped.bam.bai"
2025-09-15 20:25:09.199 wdl.w:ptcp.w:call-paraphase-84.t:call-run_paraphase INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2181.mapped.bam"
2025-09-15 20:25:09.199 wdl.w:ptcp.w:call-paraphase-84.t:call-run_paraphase INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2181"
2025-09-15 20:25:09.199 wdl.w:ptcp.w:call-paraphase-84.t:call-run_paraphase INFO eval :: name: "threads", value: 4
2025-09-15 20:25:09.199 wdl.w:ptcp.w:call-paraphase-84.t:call-run_paraphase INFO eval :: name: "mem_gb", value: 8
2025-09-15 20:25:09.200 wdl.w:ptcp.w:call-paraphase-84.t:call-run_paraphase INFO eval :: name: "disk_size", value: 27
2025-09-15 20:25:09.200 wdl.w:ptcp.w:call-paraphase-84.t:call-run_paraphase INFO eval :: name: "out_dir", value: "m84036_250809_035451_s4.bc2181_paraphase"
2025-09-15 20:25:09.200 wdl.w:ptcp.w:call-paraphase-84.t:call-run_paraphase INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 4, memory_reservation: 8000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:09.200 wdl.w:ptcp.w:call-paraphase-84.t:call-run_paraphase WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:09.201 wdl.w:ptcp.w:call-paraphase-84.t:call-run_paraphase INFO provisioned :: seconds_waited: 0, cpu: 4, mem_bytes: 8000000000
2025-09-15 20:25:09.202 wdl.w:ptcp.w:call-paraphase-84.t:call-run_paraphase INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:09.226 wdl.w:ptcp.w:call-sawfish-28 NOTICE done
2025-09-15 20:25:09.232 wdl.w:ptcp NOTICE finish :: job: "call-sawfish-28"
2025-09-15 20:25:09.232 wdl.w:ptcp INFO output :: job: "call-sawfish-28", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-28/out/m84036_250809_035451_s4.bc2125_sawfish/m84036_250809_035451_s4.bc2125.sv.vcf.gz", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-28/out/m84036_250809_035451_s4.bc2125.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-28/out/m84036_250809_035451_s4.bc2125_sawfish/m84036_250809_035451_s4.bc2125.sv.vcf.gz.tbi", "minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-28/out/m84036_250809_035451_s4.bc2125.minimap2.bam.bai"}
2025-09-15 20:25:09.233 wdl.w:ptcp NOTICE ready :: job: "call-tar_outputs-28", callee: "tar_outputs"
2025-09-15 20:25:09.233 wdl.w:ptcp INFO input :: job: "call-tar_outputs-28", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "sawfish_vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-28/out/m84036_250809_035451_s4.bc2125_sawfish/m84036_250809_035451_s4.bc2125.sv.vcf.gz.tbi", "sawfish_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-28/out/m84036_250809_035451_s4.bc2125_sawfish/m84036_250809_035451_s4.bc2125.sv.vcf.gz", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-28/out/m84036_250809_035451_s4.bc2125.f8inversion.json", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-28/out/m84036_250809_035451_s4.bc2125_paraphase/m84036_250809_035451_s4.bc2125.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-28/out/m84036_250809_035451_s4.bc2125_paraphase/m84036_250809_035451_s4.bc2125.paraphase.bam", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-28/out/m84036_250809_035451_s4.bc2125_paraphase/m84036_250809_035451_s4.bc2125.paraphase.json", "trgt_spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-28/out/m84036_250809_035451_s4.bc2125.trgt.sorted.spanning.bam.bai", "trgt_spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-28/out/m84036_250809_035451_s4.bc2125.trgt.sorted.spanning.bam", "trgt_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-28/out/m84036_250809_035451_s4.bc2125.trgt.vcf", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-28/out/m84036_250809_035451_s4.bc2125.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-28/out/m84036_250809_035451_s4.bc2125.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2125"}
2025-09-15 20:25:09.235 wdl.w:ptcp.w:call-paraphase-61 NOTICE done
2025-09-15 20:25:09.244 wdl.w:ptcp.w:call-trgt-91 NOTICE workflow start :: name: "trgt", source: "./trgt.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-91"
2025-09-15 20:25:09.261 wdl.w:ptcp.w:call-trgt-91 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:25:09.261 wdl.w:ptcp.w:call-trgt-91 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-91/out/m84036_250809_035451_s4.bc2188.mapped.bam"}
2025-09-15 20:25:09.261 wdl.w:ptcp.w:call-trgt-91 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-91/out/m84036_250809_035451_s4.bc2188.mapped.bam.bai"}
2025-09-15 20:25:09.261 wdl.w:ptcp.w:call-trgt-91 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:25:09.261 wdl.w:ptcp.w:call-trgt-91 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:25:09.262 wdl.w:ptcp NOTICE finish :: job: "call-paraphase-61"
2025-09-15 20:25:09.262 wdl.w:ptcp.w:call-trgt-91 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2188"}
2025-09-15 20:25:09.262 wdl.w:ptcp INFO output :: job: "call-paraphase-61", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-61/out/m84036_250809_035451_s4.bc2158.f8inversion.vcf", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-61/out/m84036_250809_035451_s4.bc2158_paraphase/m84036_250809_035451_s4.bc2158.paraphase.json", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-61/out/m84036_250809_035451_s4.bc2158_paraphase/m84036_250809_035451_s4.bc2158.paraphase.bam", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-61/out/m84036_250809_035451_s4.bc2158_paraphase/m84036_250809_035451_s4.bc2158.paraphase.bam.bai", "paraphase_vcfs": [], "havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-61/out/m84036_250809_035451_s4.bc2158.havanno.json", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-61/out/m84036_250809_035451_s4.bc2158.f8inversion.json"}
2025-09-15 20:25:09.262 wdl.w:ptcp.w:call-trgt-91 INFO visit :: node: "decl-sex", values: {"sex": "F"}
2025-09-15 20:25:09.263 wdl.w:ptcp.w:call-trgt-91 INFO visit :: node: "decl-trgt_bed", values: {"trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"}
2025-09-15 20:25:09.263 wdl.w:ptcp.w:call-trgt-91 NOTICE ready :: job: "call-get_reads_overlapping_repeats", callee: "get_reads_overlapping_repeats"
2025-09-15 20:25:09.263 wdl.w:ptcp.w:call-trgt-91 INFO input :: job: "call-get_reads_overlapping_repeats", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-91/out/m84036_250809_035451_s4.bc2188.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-91/out/m84036_250809_035451_s4.bc2188.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2188"}
2025-09-15 20:25:09.264 wdl.w:ptcp.w:call-trgt-91 NOTICE ready :: job: "call-trgt_genotype", callee: "trgt_genotype"
2025-09-15 20:25:09.264 wdl.w:ptcp.w:call-trgt-91 INFO input :: job: "call-trgt_genotype", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-91/out/m84036_250809_035451_s4.bc2188.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-91/out/m84036_250809_035451_s4.bc2188.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2188"}
2025-09-15 20:25:09.264 wdl.w:ptcp.w:call-trgt-78.t:call-trgt_genotype INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 11, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-78/call-trgt_genotype/_singularity_tmpdir_s53zrtdy"
2025-09-15 20:25:09.264 wdl.w:ptcp.w:call-trgt-78.t:call-trgt_genotype INFO Slurm invocation: srun --job-name call-trgt_genotype --partition compute,compute9 --cpus-per-task 8 --mem 15259M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-78/call-trgt_genotype/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-78/call-trgt_genotype/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-78/call-trgt_genotype/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-78/call-trgt_genotype/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-78/out/m84036_250809_035451_s4.bc2175.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2175.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-78/out/m84036_250809_035451_s4.bc2175.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2175.mapped.bam:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-78/call-trgt_genotype/_singularity_tmpdir_s53zrtdy/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-78/call-trgt_genotype/_singularity_tmpdir_s53zrtdy/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:09.267 wdl.w:ptcp.w:call-trgt-68.t:call-get_reads_overlapping_repeats NOTICE done
2025-09-15 20:25:09.269 wdl.w:ptcp.w:call-paraphase-87 NOTICE workflow start :: name: "paraphase", source: "./paraphase.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-87"
2025-09-15 20:25:09.272 wdl.w:ptcp.w:call-trgt-68 NOTICE finish :: job: "call-get_reads_overlapping_repeats"
2025-09-15 20:25:09.273 wdl.w:ptcp.w:call-trgt-68 INFO output :: job: "call-get_reads_overlapping_repeats", values: {"reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-68/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2165.repeats.bam.bai", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-68/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2165.repeats.bam"}
2025-09-15 20:25:09.273 wdl.w:ptcp.w:call-trgt-68 INFO visit :: node: "output-reads_overlapping_repeats", values: {"reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-68/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2165.repeats.bam"}
2025-09-15 20:25:09.273 wdl.w:ptcp.w:call-trgt-68 INFO visit :: node: "output-reads_overlapping_repeats_bai", values: {"reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-68/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2165.repeats.bam.bai"}
2025-09-15 20:25:09.281 wdl.w:ptcp.w:call-sawfish-84.t:call-run_sawfish NOTICE task setup :: name: "run_sawfish", source: "./sawfish.wdl", line: 83, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-84/call-run_sawfish", thread: 140613060126272
2025-09-15 20:25:09.283 wdl.w:ptcp.w:call-trgt-78.t:call-trgt_genotype NOTICE slurm_singularity run :: pid: 1204860, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-78/call-trgt_genotype/slurm_singularity.log.txt"
2025-09-15 20:25:09.284 wdl.w:ptcp.w:call-paraphase-87 INFO visit :: node: "decl-annotation_vcf", values: {"annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf"}
2025-09-15 20:25:09.285 wdl.w:ptcp.w:call-paraphase-87 INFO visit :: node: "decl-config_file", values: {"config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml"}
2025-09-15 20:25:09.285 wdl.w:ptcp.w:call-paraphase-87 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:25:09.285 wdl.w:ptcp.w:call-paraphase-87 INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:25:09.285 wdl.w:ptcp.w:call-paraphase-87 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-87/out/m84036_250809_035451_s4.bc2184.mapped.bam"}
2025-09-15 20:25:09.285 wdl.w:ptcp.w:call-paraphase-87 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-87/out/m84036_250809_035451_s4.bc2184.mapped.bam.bai"}
2025-09-15 20:25:09.285 wdl.w:ptcp.w:call-paraphase-87 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:25:09.285 wdl.w:ptcp.w:call-paraphase-87 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:25:09.285 wdl.w:ptcp.w:call-paraphase-87 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2184"}
2025-09-15 20:25:09.285 wdl.w:ptcp.w:call-paraphase-87 INFO visit :: node: "decl-sex", values: {"sex": "F"}
2025-09-15 20:25:09.286 wdl.w:ptcp.w:call-paraphase-87 NOTICE ready :: job: "call-run_paraphase", callee: "run_paraphase"
2025-09-15 20:25:09.286 wdl.w:ptcp.w:call-paraphase-87 INFO input :: job: "call-run_paraphase", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf", "genome_version": "38", "config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-87/out/m84036_250809_035451_s4.bc2184.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-87/out/m84036_250809_035451_s4.bc2184.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2184"}
2025-09-15 20:25:09.290 wdl.w:ptcp.w:call-paraphase-84.t:call-run_paraphase INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-84/call-run_paraphase/_singularity_tmpdir_yqcwk6v4"
2025-09-15 20:25:09.290 wdl.w:ptcp.w:call-paraphase-84.t:call-run_paraphase INFO Slurm invocation: srun --job-name call-run_paraphase --partition compute,compute9 --cpus-per-task 4 --mem 7629M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-84/call-run_paraphase/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-84/call-run_paraphase/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-84/call-run_paraphase/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-84/call-run_paraphase/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-84/out/m84036_250809_035451_s4.bc2181.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2181.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-84/out/m84036_250809_035451_s4.bc2181.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2181.mapped.bam:ro --bind /ptcp/meta/variant_list/variant_list.GRCh38.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf:ro --bind /ptcp/meta/paraphase/paraphase_config.GRCh38.yaml:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/paraphase_config.GRCh38.yaml:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-84/call-run_paraphase/_singularity_tmpdir_yqcwk6v4/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-84/call-run_paraphase/_singularity_tmpdir_yqcwk6v4/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:09.298 wdl.w:ptcp.w:call-sawfish-84.t:call-run_sawfish INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:09.298 wdl.w:ptcp.w:call-sawfish-84.t:call-run_sawfish INFO input :: name: "genome_version", value: "38"
2025-09-15 20:25:09.298 wdl.w:ptcp.w:call-sawfish-84.t:call-run_sawfish INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:25:09.298 wdl.w:ptcp.w:call-sawfish-84.t:call-run_sawfish INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:25:09.298 wdl.w:ptcp.w:call-sawfish-84.t:call-run_sawfish INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2181.mapped.bam.bai"
2025-09-15 20:25:09.298 wdl.w:ptcp.w:call-sawfish-84.t:call-run_sawfish INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2181.mapped.bam"
2025-09-15 20:25:09.299 wdl.w:ptcp.w:call-sawfish-84.t:call-run_sawfish INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2181"
2025-09-15 20:25:09.299 wdl.w:ptcp.w:call-sawfish-84.t:call-run_sawfish INFO eval :: name: "mem_gb", value: 32
2025-09-15 20:25:09.299 wdl.w:ptcp.w:call-sawfish-84.t:call-run_sawfish INFO eval :: name: "threads", value: 16
2025-09-15 20:25:09.299 wdl.w:ptcp.w:call-sawfish-84.t:call-run_sawfish INFO eval :: name: "disk_size", value: 30
2025-09-15 20:25:09.301 wdl.w:ptcp.w:call-sawfish-84.t:call-run_sawfish INFO eval :: name: "discover_dirname", value: "m84036_250809_035451_s4.bc2181_sawfish_discover"
2025-09-15 20:25:09.302 wdl.w:ptcp.w:call-sawfish-84.t:call-run_sawfish INFO eval :: name: "call_dirname", value: "m84036_250809_035451_s4.bc2181_sawfish"
2025-09-15 20:25:09.302 wdl.w:ptcp.w:call-sawfish-84.t:call-run_sawfish INFO eval :: name: "minimap2_bam_filename", value: "m84036_250809_035451_s4.bc2181.minimap2.bam"
2025-09-15 20:25:09.302 wdl.w:ptcp.w:call-sawfish-84.t:call-run_sawfish INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 16, memory_reservation: 32000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:09.302 wdl.w:ptcp.w:call-sawfish-84.t:call-run_sawfish WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:09.303 wdl.w:ptcp.w:call-sawfish-84.t:call-run_sawfish INFO provisioned :: seconds_waited: 0, cpu: 16, mem_bytes: 32000000000
2025-09-15 20:25:09.303 wdl.w:ptcp.w:call-sawfish-84.t:call-run_sawfish INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:09.308 wdl.w:ptcp.w:call-paraphase-84.t:call-run_paraphase NOTICE slurm_singularity run :: pid: 1204862, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-84/call-run_paraphase/slurm_singularity.log.txt"
2025-09-15 20:25:09.363 wdl.w:ptcp.w:call-trgt-67.t:call-trgt_plot_motifs_allele INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2164.motifs_allele.trgt_plots.zip"
2025-09-15 20:25:09.376 wdl.w:ptcp.w:call-sawfish-84.t:call-run_sawfish INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 10, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-84/call-run_sawfish/_singularity_tmpdir_pcwj0pe7"
2025-09-15 20:25:09.376 wdl.w:ptcp.w:call-sawfish-84.t:call-run_sawfish INFO Slurm invocation: srun --job-name call-run_sawfish --partition compute,compute9 --cpus-per-task 16 --mem 30518M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-84/call-run_sawfish/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-84/call-run_sawfish/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-84/call-run_sawfish/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-84/call-run_sawfish/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-84/out/m84036_250809_035451_s4.bc2181.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2181.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-84/out/m84036_250809_035451_s4.bc2181.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2181.mapped.bam:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-84/call-run_sawfish/_singularity_tmpdir_pcwj0pe7/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-84/call-run_sawfish/_singularity_tmpdir_pcwj0pe7/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:09.378 wdl.w:ptcp.w:call-paraphase-69.t:call-call_f8 INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2166.f8inversion.vcf"
2025-09-15 20:25:09.383 wdl.w:ptcp.w:call-paraphase-69.t:call-call_f8 INFO output :: name: "json", value: "m84036_250809_035451_s4.bc2166.f8inversion.json"
2025-09-15 20:25:09.399 wdl.w:ptcp.t:call-tar_outputs-45.slurm_singularity INFO srun: job 51797935 queued and waiting for resources
2025-09-15 20:25:09.399 wdl.w:ptcp.t:call-tar_outputs-45.slurm_singularity INFO srun: job 51797935 has been allocated resources
2025-09-15 20:25:09.399 wdl.w:ptcp.t:call-tar_outputs-45.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:09.406 wdl.w:ptcp.w:call-sawfish-84.t:call-run_sawfish NOTICE slurm_singularity run :: pid: 1204887, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-84/call-run_sawfish/slurm_singularity.log.txt"
2025-09-15 20:25:09.423 wdl.w:ptcp.w:call-trgt-74.t:call-get_reads_overlapping_repeats.slurm_singularity INFO srun: job 51797936 queued and waiting for resources
2025-09-15 20:25:09.423 wdl.w:ptcp.w:call-trgt-74.t:call-get_reads_overlapping_repeats.slurm_singularity INFO srun: job 51797936 has been allocated resources
2025-09-15 20:25:09.423 wdl.w:ptcp.w:call-trgt-67.t:call-trgt_plot_meth_waterfall INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2164.meth_waterfall.trgt_plots.zip"
2025-09-15 20:25:09.424 wdl.w:ptcp.w:call-trgt-74.t:call-get_reads_overlapping_repeats.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:09.465 wdl.w:ptcp.w:call-trgt-67.t:call-trgt_plot_motifs_allele NOTICE done
2025-09-15 20:25:09.469 wdl.w:ptcp.w:call-paraphase-69.t:call-call_f8 NOTICE done
2025-09-15 20:25:09.470 wdl.w:ptcp.w:call-trgt-67 NOTICE finish :: job: "call-trgt_plot_motifs_allele"
2025-09-15 20:25:09.471 wdl.w:ptcp.w:call-trgt-67 INFO output :: job: "call-trgt_plot_motifs_allele", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-67/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2164.motifs_allele.trgt_plots.zip"}
2025-09-15 20:25:09.471 wdl.w:ptcp.w:call-trgt-67 INFO visit :: node: "output-images_motifs_allele", values: {"images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-67/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2164.motifs_allele.trgt_plots.zip"}
2025-09-15 20:25:09.476 wdl.w:ptcp.w:call-trgt-84.t:call-get_reads_overlapping_repeats NOTICE task setup :: name: "get_reads_overlapping_repeats", source: "./trgt.wdl", line: 182, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-84/call-get_reads_overlapping_repeats", thread: 140612506469952
2025-09-15 20:25:09.478 wdl.w:ptcp.w:call-trgt-74.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:25:09 [INFO] - Running trgt-4.0.0-429afcd [genotype]
2025-09-15 20:25:09.478 wdl.w:ptcp.w:call-trgt-74.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:25:09 [WARN] - EIEE1_ARX: Filtered out 2 impure reads
2025-09-15 20:25:09.478 wdl.w:ptcp.w:call-trgt-74.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:25:09 [WARN] - PRTS_ARX: Filtered out 3 impure reads
2025-09-15 20:25:09.478 wdl.w:ptcp.w:call-trgt-74.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:25:09 [WARN] - FXS_FMR1: Filtered out 6 impure reads
2025-09-15 20:25:09.478 wdl.w:ptcp.w:call-trgt-74.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:25:09 [WARN] - FRAXE_AFF2: Filtered out 17 impure reads
2025-09-15 20:25:09.478 wdl.w:ptcp.w:call-trgt-74.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:25:09 [WARN] - FRDA_FXN: Filtered out 3 impure reads
2025-09-15 20:25:09.478 wdl.w:ptcp.w:call-trgt-74.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:25:09 [INFO] - Total execution time: 283.55ms
2025-09-15 20:25:09.478 wdl.w:ptcp.w:call-trgt-74.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:25:09 [INFO] - trgt end
2025-09-15 20:25:09.481 wdl.w:ptcp.w:call-paraphase-69 NOTICE finish :: job: "call-call_f8"
2025-09-15 20:25:09.482 wdl.w:ptcp.w:call-paraphase-69 INFO output :: job: "call-call_f8", values: {"json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-69/call-call_f8/out/m84036_250809_035451_s4.bc2166.f8inversion.json", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-69/call-call_f8/out/m84036_250809_035451_s4.bc2166.f8inversion.vcf"}
2025-09-15 20:25:09.482 wdl.w:ptcp.w:call-paraphase-69 INFO visit :: node: "output-f8_json", values: {"f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-69/call-call_f8/out/m84036_250809_035451_s4.bc2166.f8inversion.json"}
2025-09-15 20:25:09.482 wdl.w:ptcp.w:call-paraphase-69 INFO visit :: node: "output-f8_vcf", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-69/call-call_f8/out/m84036_250809_035451_s4.bc2166.f8inversion.vcf"}
2025-09-15 20:25:09.482 wdl.w:ptcp.w:call-paraphase-69 INFO visit :: node: "outputs", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-69/call-call_f8/out/m84036_250809_035451_s4.bc2166.f8inversion.vcf", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-69/call-run_paraphase/out/m84036_250809_035451_s4.bc2166_paraphase/m84036_250809_035451_s4.bc2166.paraphase.json", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-69/call-run_paraphase/out/m84036_250809_035451_s4.bc2166_paraphase/m84036_250809_035451_s4.bc2166.paraphase.bam", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-69/call-run_paraphase/out/m84036_250809_035451_s4.bc2166_paraphase/m84036_250809_035451_s4.bc2166.paraphase.bam.bai", "paraphase_vcfs": [], "havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-69/call-run_paraphase/out/m84036_250809_035451_s4.bc2166.havanno.json", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-69/call-call_f8/out/m84036_250809_035451_s4.bc2166.f8inversion.json"}
2025-09-15 20:25:09.489 wdl.w:ptcp.w:call-trgt-84.t:call-trgt_genotype NOTICE task setup :: name: "trgt_genotype", source: "./trgt.wdl", line: 272, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-84/call-trgt_genotype", thread: 140611424335424
2025-09-15 20:25:09.490 wdl.w:ptcp.w:call-trgt-74.t:call-trgt_genotype.slurm_singularity INFO srun: job 51797937 queued and waiting for resources
2025-09-15 20:25:09.490 wdl.w:ptcp.w:call-trgt-74.t:call-trgt_genotype.slurm_singularity INFO srun: job 51797937 has been allocated resources
2025-09-15 20:25:09.491 wdl.w:ptcp.w:call-trgt-74.t:call-trgt_genotype.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:09.498 wdl.w:ptcp.w:call-trgt-84.t:call-get_reads_overlapping_repeats INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:09.499 wdl.w:ptcp.w:call-trgt-84.t:call-get_reads_overlapping_repeats INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:25:09.499 wdl.w:ptcp.w:call-trgt-84.t:call-get_reads_overlapping_repeats INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2181.mapped.bam.bai"
2025-09-15 20:25:09.499 wdl.w:ptcp.w:call-trgt-84.t:call-get_reads_overlapping_repeats INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2181.mapped.bam"
2025-09-15 20:25:09.499 wdl.w:ptcp.w:call-trgt-84.t:call-get_reads_overlapping_repeats INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2181"
2025-09-15 20:25:09.499 wdl.w:ptcp.w:call-trgt-84.t:call-get_reads_overlapping_repeats INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:25:09.499 wdl.w:ptcp.w:call-trgt-84.t:call-get_reads_overlapping_repeats INFO eval :: name: "expand_size", value: 3000
2025-09-15 20:25:09.499 wdl.w:ptcp.w:call-trgt-84.t:call-get_reads_overlapping_repeats INFO eval :: name: "threads", value: 1
2025-09-15 20:25:09.499 wdl.w:ptcp.w:call-trgt-84.t:call-get_reads_overlapping_repeats INFO eval :: name: "expanded_bed_name", value: "m84036_250809_035451_s4.bc2181.expanded.bed"
2025-09-15 20:25:09.500 wdl.w:ptcp.w:call-trgt-84.t:call-get_reads_overlapping_repeats INFO eval :: name: "disk_size", value: 11
2025-09-15 20:25:09.500 wdl.w:ptcp.w:call-trgt-84.t:call-get_reads_overlapping_repeats INFO eval :: name: "output_name", value: "m84036_250809_035451_s4.bc2181.repeats.bam"
2025-09-15 20:25:09.500 wdl.w:ptcp.w:call-trgt-84.t:call-get_reads_overlapping_repeats INFO eval :: name: "index_name", value: "m84036_250809_035451_s4.bc2181.repeats.bam.bai"
2025-09-15 20:25:09.501 wdl.w:ptcp.w:call-trgt-84.t:call-get_reads_overlapping_repeats INFO eval :: name: "output_name_with_index", value: "m84036_250809_035451_s4.bc2181.repeats.bam##idx##m84036_250809_035451_s4.bc2181.repeats.bam.bai"
2025-09-15 20:25:09.501 wdl.w:ptcp.w:call-trgt-84.t:call-get_reads_overlapping_repeats INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:09.501 wdl.w:ptcp.w:call-trgt-84.t:call-get_reads_overlapping_repeats WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:09.502 wdl.w:ptcp.w:call-trgt-84.t:call-get_reads_overlapping_repeats INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:25:09.502 wdl.w:ptcp.w:call-trgt-84.t:call-get_reads_overlapping_repeats INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:09.509 wdl.w:ptcp.w:call-trgt-84.t:call-trgt_genotype INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:09.509 wdl.w:ptcp.w:call-trgt-84.t:call-trgt_genotype INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:25:09.510 wdl.w:ptcp.w:call-trgt-84.t:call-trgt_genotype INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:25:09.510 wdl.w:ptcp.w:call-trgt-84.t:call-trgt_genotype INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:25:09.510 wdl.w:ptcp.w:call-trgt-84.t:call-trgt_genotype INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2181.mapped.bam.bai"
2025-09-15 20:25:09.510 wdl.w:ptcp.w:call-trgt-84.t:call-trgt_genotype INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2181.mapped.bam"
2025-09-15 20:25:09.510 wdl.w:ptcp.w:call-trgt-84.t:call-trgt_genotype INFO input :: name: "sex", value: "F"
2025-09-15 20:25:09.510 wdl.w:ptcp.w:call-trgt-84.t:call-trgt_genotype INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2181"
2025-09-15 20:25:09.510 wdl.w:ptcp.w:call-trgt-84.t:call-trgt_genotype INFO eval :: name: "mem_gb", value: 16
2025-09-15 20:25:09.510 wdl.w:ptcp.w:call-trgt-84.t:call-trgt_genotype INFO eval :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2181.trgt"
2025-09-15 20:25:09.510 wdl.w:ptcp.w:call-trgt-84.t:call-trgt_genotype INFO eval :: name: "threads", value: 8
2025-09-15 20:25:09.511 wdl.w:ptcp.w:call-trgt-84.t:call-trgt_genotype INFO eval :: name: "disk_size", value: 27
2025-09-15 20:25:09.511 wdl.w:ptcp.w:call-trgt-84.t:call-trgt_genotype INFO eval :: name: "karyotype", value: "XX"
2025-09-15 20:25:09.511 wdl.w:ptcp.w:call-trgt-84.t:call-trgt_genotype INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 8, memory_reservation: 16000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:09.512 wdl.w:ptcp.w:call-trgt-84.t:call-trgt_genotype WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:09.512 wdl.w:ptcp.w:call-trgt-84.t:call-trgt_genotype INFO provisioned :: seconds_waited: 0, cpu: 8, mem_bytes: 16000000000
2025-09-15 20:25:09.512 wdl.w:ptcp.w:call-trgt-84.t:call-trgt_genotype INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:09.535 wdl.w:ptcp.w:call-trgt-67.t:call-trgt_plot_meth_waterfall NOTICE done
2025-09-15 20:25:09.540 wdl.w:ptcp.w:call-trgt-67 NOTICE finish :: job: "call-trgt_plot_meth_waterfall"
2025-09-15 20:25:09.541 wdl.w:ptcp.w:call-trgt-67 INFO output :: job: "call-trgt_plot_meth_waterfall", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-67/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2164.meth_waterfall.trgt_plots.zip"}
2025-09-15 20:25:09.541 wdl.w:ptcp.w:call-trgt-67 INFO visit :: node: "output-images_meth_waterfall", values: {"images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-67/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2164.meth_waterfall.trgt_plots.zip"}
2025-09-15 20:25:09.541 wdl.w:ptcp.w:call-trgt-67 INFO visit :: node: "outputs", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-67/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2164.motifs_waterfall.trgt_plots.zip", "images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-67/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2164.meth_allele.trgt_plots.zip", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-67/call-trgt_genotype/out/m84036_250809_035451_s4.bc2164.trgt.sorted.spanning.bam.bai", "images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-67/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2164.motifs_allele.trgt_plots.zip", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-67/call-trgt_genotype/out/m84036_250809_035451_s4.bc2164.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-67/call-trgt_genotype/out/m84036_250809_035451_s4.bc2164.trgt.vcf", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-67/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2164.repeats.bam", "images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-67/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2164.meth_waterfall.trgt_plots.zip", "reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-67/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2164.repeats.bam.bai"}
2025-09-15 20:25:09.552 wdl.w:ptcp.w:call-paraphase-76.t:call-run_paraphase NOTICE task setup :: name: "run_paraphase", source: "./paraphase.wdl", line: 127, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-76/call-run_paraphase", thread: 140608739980864
2025-09-15 20:25:09.563 wdl.w:ptcp.w:call-paraphase-69 NOTICE done
2025-09-15 20:25:09.569 wdl.w:ptcp NOTICE finish :: job: "call-paraphase-69"
2025-09-15 20:25:09.569 wdl.w:ptcp INFO output :: job: "call-paraphase-69", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-69/out/m84036_250809_035451_s4.bc2166.f8inversion.vcf", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-69/out/m84036_250809_035451_s4.bc2166_paraphase/m84036_250809_035451_s4.bc2166.paraphase.json", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-69/out/m84036_250809_035451_s4.bc2166_paraphase/m84036_250809_035451_s4.bc2166.paraphase.bam", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-69/out/m84036_250809_035451_s4.bc2166_paraphase/m84036_250809_035451_s4.bc2166.paraphase.bam.bai", "paraphase_vcfs": [], "havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-69/out/m84036_250809_035451_s4.bc2166.havanno.json", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-69/out/m84036_250809_035451_s4.bc2166.f8inversion.json"}
2025-09-15 20:25:09.575 wdl.w:ptcp.w:call-sawfish-87 NOTICE workflow start :: name: "sawfish", source: "./sawfish.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-87"
2025-09-15 20:25:09.579 wdl.w:ptcp.w:call-trgt-84.t:call-get_reads_overlapping_repeats INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 9, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-84/call-get_reads_overlapping_repeats/_singularity_tmpdir_nljne5n2"
2025-09-15 20:25:09.579 wdl.w:ptcp.w:call-trgt-84.t:call-get_reads_overlapping_repeats INFO Slurm invocation: srun --job-name call-get_reads_overlapping_repeats --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-84/call-get_reads_overlapping_repeats/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-84/call-get_reads_overlapping_repeats/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-84/call-get_reads_overlapping_repeats/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-84/call-get_reads_overlapping_repeats/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-84/out/m84036_250809_035451_s4.bc2181.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2181.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-84/out/m84036_250809_035451_s4.bc2181.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2181.mapped.bam:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-84/call-get_reads_overlapping_repeats/_singularity_tmpdir_nljne5n2/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-84/call-get_reads_overlapping_repeats/_singularity_tmpdir_nljne5n2/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:09.581 wdl.w:ptcp.w:call-paraphase-76.t:call-run_paraphase INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:09.582 wdl.w:ptcp.w:call-paraphase-76.t:call-run_paraphase INFO input :: name: "annotation_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf"
2025-09-15 20:25:09.583 wdl.w:ptcp.w:call-paraphase-76.t:call-run_paraphase INFO input :: name: "genome_version", value: "38"
2025-09-15 20:25:09.583 wdl.w:ptcp.w:call-paraphase-76.t:call-run_paraphase INFO input :: name: "config_file", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/paraphase_config.GRCh38.yaml"
2025-09-15 20:25:09.583 wdl.w:ptcp.w:call-paraphase-76.t:call-run_paraphase INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:25:09.583 wdl.w:ptcp.w:call-paraphase-76.t:call-run_paraphase INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:25:09.583 wdl.w:ptcp.w:call-paraphase-76.t:call-run_paraphase INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2173.mapped.bam.bai"
2025-09-15 20:25:09.583 wdl.w:ptcp.w:call-paraphase-76.t:call-run_paraphase INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2173.mapped.bam"
2025-09-15 20:25:09.583 wdl.w:ptcp.w:call-paraphase-76.t:call-run_paraphase INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2173"
2025-09-15 20:25:09.584 wdl.w:ptcp.w:call-paraphase-76.t:call-run_paraphase INFO eval :: name: "threads", value: 4
2025-09-15 20:25:09.584 wdl.w:ptcp.w:call-paraphase-76.t:call-run_paraphase INFO eval :: name: "mem_gb", value: 8
2025-09-15 20:25:09.584 wdl.w:ptcp.w:call-paraphase-76.t:call-run_paraphase INFO eval :: name: "disk_size", value: 27
2025-09-15 20:25:09.584 wdl.w:ptcp.w:call-paraphase-76.t:call-run_paraphase INFO eval :: name: "out_dir", value: "m84036_250809_035451_s4.bc2173_paraphase"
2025-09-15 20:25:09.585 wdl.w:ptcp.w:call-paraphase-76.t:call-run_paraphase INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 4, memory_reservation: 8000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:09.585 wdl.w:ptcp.w:call-paraphase-76.t:call-run_paraphase WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:09.586 wdl.w:ptcp.w:call-paraphase-76.t:call-run_paraphase INFO provisioned :: seconds_waited: 0, cpu: 4, mem_bytes: 8000000000
2025-09-15 20:25:09.586 wdl.w:ptcp.w:call-paraphase-76.t:call-run_paraphase INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:09.592 wdl.w:ptcp.w:call-sawfish-87 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:25:09.592 wdl.w:ptcp.w:call-sawfish-87 INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:25:09.592 wdl.w:ptcp.w:call-sawfish-87 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-87/out/m84036_250809_035451_s4.bc2184.mapped.bam"}
2025-09-15 20:25:09.592 wdl.w:ptcp.w:call-sawfish-87 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-87/out/m84036_250809_035451_s4.bc2184.mapped.bam.bai"}
2025-09-15 20:25:09.592 wdl.w:ptcp.w:call-sawfish-87 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:25:09.592 wdl.w:ptcp.w:call-sawfish-87 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:25:09.592 wdl.w:ptcp.w:call-sawfish-87 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2184"}
2025-09-15 20:25:09.592 wdl.w:ptcp.w:call-sawfish-87 NOTICE ready :: job: "call-run_sawfish", callee: "run_sawfish"
2025-09-15 20:25:09.592 wdl.w:ptcp.w:call-sawfish-87 INFO input :: job: "call-run_sawfish", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-87/out/m84036_250809_035451_s4.bc2184.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-87/out/m84036_250809_035451_s4.bc2184.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2184"}
2025-09-15 20:25:09.597 wdl.w:ptcp.w:call-trgt-84.t:call-trgt_genotype INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 11, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-84/call-trgt_genotype/_singularity_tmpdir_6s2vs_85"
2025-09-15 20:25:09.597 wdl.w:ptcp.w:call-trgt-84.t:call-trgt_genotype INFO Slurm invocation: srun --job-name call-trgt_genotype --partition compute,compute9 --cpus-per-task 8 --mem 15259M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-84/call-trgt_genotype/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-84/call-trgt_genotype/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-84/call-trgt_genotype/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-84/call-trgt_genotype/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-84/out/m84036_250809_035451_s4.bc2181.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2181.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-84/out/m84036_250809_035451_s4.bc2181.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2181.mapped.bam:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-84/call-trgt_genotype/_singularity_tmpdir_6s2vs_85/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-84/call-trgt_genotype/_singularity_tmpdir_6s2vs_85/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:09.614 wdl.w:ptcp.w:call-trgt-84.t:call-get_reads_overlapping_repeats NOTICE slurm_singularity run :: pid: 1204889, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-84/call-get_reads_overlapping_repeats/slurm_singularity.log.txt"
2025-09-15 20:25:09.614 wdl.w:ptcp.w:call-trgt-84.t:call-trgt_genotype NOTICE slurm_singularity run :: pid: 1204890, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-84/call-trgt_genotype/slurm_singularity.log.txt"
2025-09-15 20:25:09.644 wdl.w:ptcp.w:call-trgt-67 NOTICE done
2025-09-15 20:25:09.647 wdl.w:ptcp.w:call-paraphase-50.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for smn1 for sample m84036_250809_035451_s4.bc2147 at 2025-09-15 20:24:51.813877...
2025-09-15 20:25:09.647 wdl.w:ptcp.w:call-paraphase-50.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for cyp21 for sample m84036_250809_035451_s4.bc2147 at 2025-09-15 20:25:00.012552...
2025-09-15 20:25:09.648 wdl.w:ptcp.w:call-paraphase-50.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for cyp21 for sample m84036_250809_035451_s4.bc2147 at 2025-09-15 20:25:00.805612...
2025-09-15 20:25:09.648 wdl.w:ptcp.w:call-paraphase-50.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for hba for sample m84036_250809_035451_s4.bc2147 at 2025-09-15 20:25:02.911264...
2025-09-15 20:25:09.648 wdl.w:ptcp.w:call-paraphase-50.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for hba for sample m84036_250809_035451_s4.bc2147 at 2025-09-15 20:25:03.295921...
2025-09-15 20:25:09.650 wdl.w:ptcp NOTICE finish :: job: "call-trgt-67"
2025-09-15 20:25:09.650 wdl.w:ptcp INFO output :: job: "call-trgt-67", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-67/out/m84036_250809_035451_s4.bc2164.motifs_waterfall.trgt_plots.zip", "images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-67/out/m84036_250809_035451_s4.bc2164.meth_allele.trgt_plots.zip", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-67/out/m84036_250809_035451_s4.bc2164.trgt.sorted.spanning.bam.bai", "images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-67/out/m84036_250809_035451_s4.bc2164.motifs_allele.trgt_plots.zip", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-67/out/m84036_250809_035451_s4.bc2164.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-67/out/m84036_250809_035451_s4.bc2164.trgt.vcf", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-67/out/m84036_250809_035451_s4.bc2164.repeats.bam", "images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-67/out/m84036_250809_035451_s4.bc2164.meth_waterfall.trgt_plots.zip", "reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-67/out/m84036_250809_035451_s4.bc2164.repeats.bam.bai"}
2025-09-15 20:25:09.662 wdl.w:ptcp.w:call-trgt-87 NOTICE workflow start :: name: "trgt", source: "./trgt.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-87"
2025-09-15 20:25:09.668 wdl.w:ptcp.w:call-paraphase-76.t:call-run_paraphase INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-76/call-run_paraphase/_singularity_tmpdir_n15nt4hu"
2025-09-15 20:25:09.668 wdl.w:ptcp.w:call-paraphase-76.t:call-run_paraphase INFO Slurm invocation: srun --job-name call-run_paraphase --partition compute,compute9 --cpus-per-task 4 --mem 7629M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-76/call-run_paraphase/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-76/call-run_paraphase/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-76/call-run_paraphase/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-76/call-run_paraphase/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-76/out/m84036_250809_035451_s4.bc2173.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2173.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-76/out/m84036_250809_035451_s4.bc2173.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2173.mapped.bam:ro --bind /ptcp/meta/variant_list/variant_list.GRCh38.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf:ro --bind /ptcp/meta/paraphase/paraphase_config.GRCh38.yaml:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/paraphase_config.GRCh38.yaml:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-76/call-run_paraphase/_singularity_tmpdir_n15nt4hu/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-76/call-run_paraphase/_singularity_tmpdir_n15nt4hu/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:09.669 wdl.w:ptcp.t:call-tar_outputs-45 INFO output :: name: "sample_tarball", value: "m84036_250809_035451_s4.bc2142.tar"
2025-09-15 20:25:09.678 wdl.w:ptcp.w:call-trgt-87 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:25:09.678 wdl.w:ptcp.w:call-trgt-87 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-87/out/m84036_250809_035451_s4.bc2184.mapped.bam"}
2025-09-15 20:25:09.678 wdl.w:ptcp.w:call-trgt-87 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-87/out/m84036_250809_035451_s4.bc2184.mapped.bam.bai"}
2025-09-15 20:25:09.678 wdl.w:ptcp.w:call-trgt-87 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:25:09.678 wdl.w:ptcp.w:call-trgt-87 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:25:09.678 wdl.w:ptcp.w:call-trgt-87 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2184"}
2025-09-15 20:25:09.679 wdl.w:ptcp.w:call-trgt-87 INFO visit :: node: "decl-sex", values: {"sex": "F"}
2025-09-15 20:25:09.679 wdl.w:ptcp.w:call-trgt-87 INFO visit :: node: "decl-trgt_bed", values: {"trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"}
2025-09-15 20:25:09.679 wdl.w:ptcp.w:call-trgt-87 NOTICE ready :: job: "call-get_reads_overlapping_repeats", callee: "get_reads_overlapping_repeats"
2025-09-15 20:25:09.679 wdl.w:ptcp.w:call-trgt-87 INFO input :: job: "call-get_reads_overlapping_repeats", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-87/out/m84036_250809_035451_s4.bc2184.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-87/out/m84036_250809_035451_s4.bc2184.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2184"}
2025-09-15 20:25:09.680 wdl.w:ptcp.w:call-trgt-87 NOTICE ready :: job: "call-trgt_genotype", callee: "trgt_genotype"
2025-09-15 20:25:09.680 wdl.w:ptcp.w:call-trgt-87 INFO input :: job: "call-trgt_genotype", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-87/out/m84036_250809_035451_s4.bc2184.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-87/out/m84036_250809_035451_s4.bc2184.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2184"}
2025-09-15 20:25:09.684 wdl.w:ptcp.w:call-paraphase-64.t:call-call_f8.slurm_singularity INFO srun: job 51797938 queued and waiting for resources
2025-09-15 20:25:09.685 wdl.w:ptcp.w:call-paraphase-64.t:call-call_f8.slurm_singularity INFO srun: job 51797938 has been allocated resources
2025-09-15 20:25:09.685 wdl.w:ptcp.w:call-paraphase-64.t:call-call_f8.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:09.698 wdl.w:ptcp.w:call-paraphase-76.t:call-run_paraphase NOTICE slurm_singularity run :: pid: 1204955, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-76/call-run_paraphase/slurm_singularity.log.txt"
2025-09-15 20:25:09.735 wdl.w:ptcp.t:call-tar_outputs-45 NOTICE done
2025-09-15 20:25:09.739 wdl.w:ptcp NOTICE finish :: job: "call-tar_outputs-45"
2025-09-15 20:25:09.739 wdl.w:ptcp INFO output :: job: "call-tar_outputs-45", values: {"sample_tarball": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-45/out/m84036_250809_035451_s4.bc2142.tar"}
2025-09-15 20:25:09.745 wdl.w:ptcp.w:call-sawfish-76.t:call-run_sawfish NOTICE task setup :: name: "run_sawfish", source: "./sawfish.wdl", line: 83, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-76/call-run_sawfish", thread: 140609838900800
2025-09-15 20:25:09.749 wdl.w:ptcp.w:call-trgt-74.t:call-trgt_genotype INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2171.trgt.vcf"
2025-09-15 20:25:09.753 wdl.w:ptcp.w:call-trgt-74.t:call-trgt_genotype INFO output :: name: "spanning_bam", value: "m84036_250809_035451_s4.bc2171.trgt.sorted.spanning.bam"
2025-09-15 20:25:09.754 wdl.w:ptcp.w:call-trgt-74.t:call-trgt_genotype INFO output :: name: "spanning_bam_bai", value: "m84036_250809_035451_s4.bc2171.trgt.sorted.spanning.bam.bai"
2025-09-15 20:25:09.764 wdl.w:ptcp.w:call-sawfish-76.t:call-run_sawfish INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:09.764 wdl.w:ptcp.w:call-sawfish-76.t:call-run_sawfish INFO input :: name: "genome_version", value: "38"
2025-09-15 20:25:09.764 wdl.w:ptcp.w:call-sawfish-76.t:call-run_sawfish INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:25:09.765 wdl.w:ptcp.w:call-sawfish-76.t:call-run_sawfish INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:25:09.765 wdl.w:ptcp.w:call-sawfish-76.t:call-run_sawfish INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2173.mapped.bam.bai"
2025-09-15 20:25:09.765 wdl.w:ptcp.w:call-sawfish-76.t:call-run_sawfish INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2173.mapped.bam"
2025-09-15 20:25:09.765 wdl.w:ptcp.w:call-sawfish-76.t:call-run_sawfish INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2173"
2025-09-15 20:25:09.765 wdl.w:ptcp.w:call-sawfish-76.t:call-run_sawfish INFO eval :: name: "mem_gb", value: 32
2025-09-15 20:25:09.765 wdl.w:ptcp.w:call-sawfish-76.t:call-run_sawfish INFO eval :: name: "threads", value: 16
2025-09-15 20:25:09.766 wdl.w:ptcp.w:call-sawfish-76.t:call-run_sawfish INFO eval :: name: "disk_size", value: 30
2025-09-15 20:25:09.766 wdl.w:ptcp.w:call-sawfish-76.t:call-run_sawfish INFO eval :: name: "discover_dirname", value: "m84036_250809_035451_s4.bc2173_sawfish_discover"
2025-09-15 20:25:09.766 wdl.w:ptcp.w:call-sawfish-76.t:call-run_sawfish INFO eval :: name: "call_dirname", value: "m84036_250809_035451_s4.bc2173_sawfish"
2025-09-15 20:25:09.766 wdl.w:ptcp.w:call-sawfish-76.t:call-run_sawfish INFO eval :: name: "minimap2_bam_filename", value: "m84036_250809_035451_s4.bc2173.minimap2.bam"
2025-09-15 20:25:09.766 wdl.w:ptcp.w:call-sawfish-76.t:call-run_sawfish INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 16, memory_reservation: 32000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:09.767 wdl.w:ptcp.w:call-sawfish-76.t:call-run_sawfish WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:09.767 wdl.w:ptcp.w:call-sawfish-76.t:call-run_sawfish INFO provisioned :: seconds_waited: 0, cpu: 16, mem_bytes: 32000000000
2025-09-15 20:25:09.767 wdl.w:ptcp.w:call-sawfish-76.t:call-run_sawfish INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:09.790 wdl.w:ptcp.w:call-paraphase-78.t:call-run_paraphase.slurm_singularity INFO srun: job 51797939 queued and waiting for resources
2025-09-15 20:25:09.790 wdl.w:ptcp.w:call-paraphase-78.t:call-run_paraphase.slurm_singularity INFO srun: job 51797939 has been allocated resources
2025-09-15 20:25:09.790 wdl.w:ptcp.w:call-paraphase-78.t:call-run_paraphase.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:09.844 wdl.w:ptcp.w:call-trgt-74.t:call-trgt_genotype NOTICE done
2025-09-15 20:25:09.846 wdl.w:ptcp.w:call-sawfish-76.t:call-run_sawfish INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 10, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-76/call-run_sawfish/_singularity_tmpdir_5aohrdf1"
2025-09-15 20:25:09.846 wdl.w:ptcp.w:call-sawfish-76.t:call-run_sawfish INFO Slurm invocation: srun --job-name call-run_sawfish --partition compute,compute9 --cpus-per-task 16 --mem 30518M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-76/call-run_sawfish/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-76/call-run_sawfish/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-76/call-run_sawfish/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-76/call-run_sawfish/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-76/out/m84036_250809_035451_s4.bc2173.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2173.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-76/out/m84036_250809_035451_s4.bc2173.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2173.mapped.bam:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-76/call-run_sawfish/_singularity_tmpdir_5aohrdf1/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-76/call-run_sawfish/_singularity_tmpdir_5aohrdf1/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:09.848 wdl.w:ptcp.w:call-trgt-74 NOTICE finish :: job: "call-trgt_genotype"
2025-09-15 20:25:09.849 wdl.w:ptcp.w:call-trgt-74 INFO output :: job: "call-trgt_genotype", values: {"spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-74/call-trgt_genotype/out/m84036_250809_035451_s4.bc2171.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-74/call-trgt_genotype/out/m84036_250809_035451_s4.bc2171.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-74/call-trgt_genotype/out/m84036_250809_035451_s4.bc2171.trgt.vcf"}
2025-09-15 20:25:09.851 wdl.w:ptcp.w:call-trgt-74 NOTICE ready :: job: "call-trgt_plot_meth_allele", callee: "trgt_plot"
2025-09-15 20:25:09.851 wdl.w:ptcp.w:call-trgt-74 INFO input :: job: "call-trgt_plot_meth_allele", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": false, "methylation": true, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-74/call-trgt_genotype/out/m84036_250809_035451_s4.bc2171.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-74/call-trgt_genotype/out/m84036_250809_035451_s4.bc2171.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-74/call-trgt_genotype/out/m84036_250809_035451_s4.bc2171.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2171"}
2025-09-15 20:25:09.853 wdl.w:ptcp.w:call-trgt-74 NOTICE ready :: job: "call-trgt_plot_meth_waterfall", callee: "trgt_plot"
2025-09-15 20:25:09.853 wdl.w:ptcp.w:call-trgt-74 INFO input :: job: "call-trgt_plot_meth_waterfall", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": true, "methylation": true, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-74/call-trgt_genotype/out/m84036_250809_035451_s4.bc2171.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-74/call-trgt_genotype/out/m84036_250809_035451_s4.bc2171.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-74/call-trgt_genotype/out/m84036_250809_035451_s4.bc2171.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2171"}
2025-09-15 20:25:09.853 wdl.w:ptcp.w:call-trgt-74 NOTICE ready :: job: "call-trgt_plot_motifs_allele", callee: "trgt_plot"
2025-09-15 20:25:09.853 wdl.w:ptcp.w:call-trgt-74 INFO input :: job: "call-trgt_plot_motifs_allele", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": false, "methylation": false, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-74/call-trgt_genotype/out/m84036_250809_035451_s4.bc2171.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-74/call-trgt_genotype/out/m84036_250809_035451_s4.bc2171.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-74/call-trgt_genotype/out/m84036_250809_035451_s4.bc2171.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2171"}
2025-09-15 20:25:09.854 wdl.w:ptcp.w:call-trgt-74 NOTICE ready :: job: "call-trgt_plot_motifs_waterfall", callee: "trgt_plot"
2025-09-15 20:25:09.854 wdl.w:ptcp.w:call-trgt-74 INFO input :: job: "call-trgt_plot_motifs_waterfall", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": true, "methylation": false, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-74/call-trgt_genotype/out/m84036_250809_035451_s4.bc2171.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-74/call-trgt_genotype/out/m84036_250809_035451_s4.bc2171.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-74/call-trgt_genotype/out/m84036_250809_035451_s4.bc2171.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2171"}
2025-09-15 20:25:09.855 wdl.w:ptcp.w:call-trgt-74 INFO visit :: node: "output-spanning_bam", values: {"spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-74/call-trgt_genotype/out/m84036_250809_035451_s4.bc2171.trgt.sorted.spanning.bam"}
2025-09-15 20:25:09.855 wdl.w:ptcp.w:call-trgt-74 INFO visit :: node: "output-spanning_bam_bai", values: {"spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-74/call-trgt_genotype/out/m84036_250809_035451_s4.bc2171.trgt.sorted.spanning.bam.bai"}
2025-09-15 20:25:09.855 wdl.w:ptcp.w:call-trgt-74 INFO visit :: node: "output-vcf", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-74/call-trgt_genotype/out/m84036_250809_035451_s4.bc2171.trgt.vcf"}
2025-09-15 20:25:09.856 wdl.w:ptcp.w:call-trgt-69.t:call-trgt_plot_meth_allele NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-69/call-trgt_plot_meth_allele", thread: 140613588604480
2025-09-15 20:25:09.858 wdl.w:ptcp.w:call-trgt-56.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:25:05 [ERROR] - No reads found for TRID=PRTS_ARX
2025-09-15 20:25:09.859 wdl.w:ptcp.w:call-trgt-56.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:25:05 [ERROR] - No reads found for TRID=EIEE1_ARX
2025-09-15 20:25:09.876 wdl.w:ptcp.w:call-sawfish-76.t:call-run_sawfish NOTICE slurm_singularity run :: pid: 1204980, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-76/call-run_sawfish/slurm_singularity.log.txt"
2025-09-15 20:25:09.880 wdl.w:ptcp.w:call-trgt-69.t:call-trgt_plot_meth_allele INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:09.880 wdl.w:ptcp.w:call-trgt-69.t:call-trgt_plot_meth_allele INFO input :: name: "waterfall", value: false
2025-09-15 20:25:09.880 wdl.w:ptcp.w:call-trgt-69.t:call-trgt_plot_meth_allele INFO input :: name: "methylation", value: true
2025-09-15 20:25:09.881 wdl.w:ptcp.w:call-trgt-69.t:call-trgt_plot_meth_allele INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:25:09.881 wdl.w:ptcp.w:call-trgt-69.t:call-trgt_plot_meth_allele INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:25:09.881 wdl.w:ptcp.w:call-trgt-69.t:call-trgt_plot_meth_allele INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:25:09.881 wdl.w:ptcp.w:call-trgt-69.t:call-trgt_plot_meth_allele INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2166.trgt.sorted.spanning.bam.bai"
2025-09-15 20:25:09.881 wdl.w:ptcp.w:call-trgt-69.t:call-trgt_plot_meth_allele INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2166.trgt.sorted.spanning.bam"
2025-09-15 20:25:09.881 wdl.w:ptcp.w:call-trgt-69.t:call-trgt_plot_meth_allele INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2166.trgt.vcf"
2025-09-15 20:25:09.881 wdl.w:ptcp.w:call-trgt-69.t:call-trgt_plot_meth_allele INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2166"
2025-09-15 20:25:09.881 wdl.w:ptcp.w:call-trgt-69.t:call-trgt_plot_meth_allele INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:25:09.881 wdl.w:ptcp.w:call-trgt-69.t:call-trgt_plot_meth_allele INFO eval :: name: "plot_type", value: "allele"
2025-09-15 20:25:09.881 wdl.w:ptcp.w:call-trgt-69.t:call-trgt_plot_meth_allele INFO eval :: name: "show", value: "meth"
2025-09-15 20:25:09.881 wdl.w:ptcp.w:call-trgt-69.t:call-trgt_plot_meth_allele INFO eval :: name: "threads", value: 1
2025-09-15 20:25:09.882 wdl.w:ptcp.w:call-trgt-69.t:call-trgt_plot_meth_allele INFO eval :: name: "disk_size", value: 27
2025-09-15 20:25:09.882 wdl.w:ptcp.w:call-trgt-69.t:call-trgt_plot_meth_allele INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2166.meth_allele"
2025-09-15 20:25:09.882 wdl.w:ptcp.w:call-trgt-69.t:call-trgt_plot_meth_allele INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:09.882 wdl.w:ptcp.w:call-trgt-69.t:call-trgt_plot_meth_allele WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:09.883 wdl.w:ptcp.w:call-trgt-69.t:call-trgt_plot_meth_allele INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:25:09.883 wdl.w:ptcp.w:call-trgt-69.t:call-trgt_plot_meth_allele INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:09.945 wdl.w:ptcp.w:call-trgt-69.t:call-trgt_plot_meth_allele INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-69/call-trgt_plot_meth_allele/_singularity_tmpdir_wgb4cmlg"
2025-09-15 20:25:09.946 wdl.w:ptcp.w:call-trgt-69.t:call-trgt_plot_meth_allele INFO Slurm invocation: srun --job-name call-trgt_plot_meth_allele --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-69/call-trgt_plot_meth_allele/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-69/call-trgt_plot_meth_allele/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-69/call-trgt_plot_meth_allele/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-69/call-trgt_plot_meth_allele/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-69/call-trgt_genotype/out/m84036_250809_035451_s4.bc2166.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2166.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-69/call-trgt_genotype/out/m84036_250809_035451_s4.bc2166.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2166.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-69/call-trgt_genotype/out/m84036_250809_035451_s4.bc2166.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2166.trgt.vcf:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-69/call-trgt_plot_meth_allele/_singularity_tmpdir_wgb4cmlg/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-69/call-trgt_plot_meth_allele/_singularity_tmpdir_wgb4cmlg/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:09.960 wdl.w:ptcp.w:call-trgt-69.t:call-trgt_plot_meth_allele NOTICE slurm_singularity run :: pid: 1204984, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-69/call-trgt_plot_meth_allele/slurm_singularity.log.txt"
2025-09-15 20:25:09.977 wdl.w:ptcp.w:call-trgt-74.t:call-get_reads_overlapping_repeats INFO output :: name: "reads_overlapping_repeats", value: "m84036_250809_035451_s4.bc2171.repeats.bam"
2025-09-15 20:25:09.980 wdl.w:ptcp.w:call-trgt-74.t:call-get_reads_overlapping_repeats INFO output :: name: "reads_overlapping_repeats_bai", value: "m84036_250809_035451_s4.bc2171.repeats.bam.bai"
2025-09-15 20:25:10.045 wdl.w:ptcp.w:call-sawfish-78.t:call-run_sawfish.slurm_singularity INFO srun: job 51797940 queued and waiting for resources
2025-09-15 20:25:10.045 wdl.w:ptcp.w:call-sawfish-78.t:call-run_sawfish.slurm_singularity INFO srun: job 51797940 has been allocated resources
2025-09-15 20:25:10.045 wdl.w:ptcp.w:call-sawfish-78.t:call-run_sawfish.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:10.051 wdl.w:ptcp.w:call-trgt-74.t:call-get_reads_overlapping_repeats NOTICE done
2025-09-15 20:25:10.058 wdl.w:ptcp.w:call-trgt-74 NOTICE finish :: job: "call-get_reads_overlapping_repeats"
2025-09-15 20:25:10.058 wdl.w:ptcp.w:call-trgt-74 INFO output :: job: "call-get_reads_overlapping_repeats", values: {"reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-74/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2171.repeats.bam.bai", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-74/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2171.repeats.bam"}
2025-09-15 20:25:10.059 wdl.w:ptcp.w:call-trgt-74 INFO visit :: node: "output-reads_overlapping_repeats", values: {"reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-74/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2171.repeats.bam"}
2025-09-15 20:25:10.059 wdl.w:ptcp.w:call-trgt-74 INFO visit :: node: "output-reads_overlapping_repeats_bai", values: {"reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-74/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2171.repeats.bam.bai"}
2025-09-15 20:25:10.065 wdl.w:ptcp.w:call-trgt-69.t:call-trgt_plot_meth_waterfall NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-69/call-trgt_plot_meth_waterfall", thread: 140607649453632
2025-09-15 20:25:10.084 wdl.w:ptcp.w:call-trgt-69.t:call-trgt_plot_meth_waterfall INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:10.084 wdl.w:ptcp.w:call-trgt-69.t:call-trgt_plot_meth_waterfall INFO input :: name: "waterfall", value: true
2025-09-15 20:25:10.084 wdl.w:ptcp.w:call-trgt-69.t:call-trgt_plot_meth_waterfall INFO input :: name: "methylation", value: true
2025-09-15 20:25:10.084 wdl.w:ptcp.w:call-trgt-69.t:call-trgt_plot_meth_waterfall INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:25:10.084 wdl.w:ptcp.w:call-trgt-69.t:call-trgt_plot_meth_waterfall INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:25:10.084 wdl.w:ptcp.w:call-trgt-69.t:call-trgt_plot_meth_waterfall INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:25:10.084 wdl.w:ptcp.w:call-trgt-69.t:call-trgt_plot_meth_waterfall INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2166.trgt.sorted.spanning.bam.bai"
2025-09-15 20:25:10.084 wdl.w:ptcp.w:call-trgt-69.t:call-trgt_plot_meth_waterfall INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2166.trgt.sorted.spanning.bam"
2025-09-15 20:25:10.084 wdl.w:ptcp.w:call-trgt-69.t:call-trgt_plot_meth_waterfall INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2166.trgt.vcf"
2025-09-15 20:25:10.084 wdl.w:ptcp.w:call-trgt-69.t:call-trgt_plot_meth_waterfall INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2166"
2025-09-15 20:25:10.085 wdl.w:ptcp.w:call-trgt-69.t:call-trgt_plot_meth_waterfall INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:25:10.085 wdl.w:ptcp.w:call-trgt-69.t:call-trgt_plot_meth_waterfall INFO eval :: name: "plot_type", value: "waterfall"
2025-09-15 20:25:10.085 wdl.w:ptcp.w:call-trgt-69.t:call-trgt_plot_meth_waterfall INFO eval :: name: "show", value: "meth"
2025-09-15 20:25:10.085 wdl.w:ptcp.w:call-trgt-69.t:call-trgt_plot_meth_waterfall INFO eval :: name: "threads", value: 1
2025-09-15 20:25:10.085 wdl.w:ptcp.w:call-trgt-69.t:call-trgt_plot_meth_waterfall INFO eval :: name: "disk_size", value: 27
2025-09-15 20:25:10.085 wdl.w:ptcp.w:call-trgt-69.t:call-trgt_plot_meth_waterfall INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2166.meth_waterfall"
2025-09-15 20:25:10.086 wdl.w:ptcp.w:call-trgt-69.t:call-trgt_plot_meth_waterfall INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:10.086 wdl.w:ptcp.w:call-trgt-69.t:call-trgt_plot_meth_waterfall WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:10.086 wdl.w:ptcp.w:call-trgt-69.t:call-trgt_plot_meth_waterfall INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:25:10.086 wdl.w:ptcp.w:call-trgt-69.t:call-trgt_plot_meth_waterfall INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:10.102 wdl.w:ptcp.w:call-paraphase-64.t:call-call_f8 INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2161.f8inversion.vcf"
2025-09-15 20:25:10.105 wdl.w:ptcp.w:call-paraphase-64.t:call-call_f8 INFO output :: name: "json", value: "m84036_250809_035451_s4.bc2161.f8inversion.json"
2025-09-15 20:25:10.126 wdl.w:ptcp.w:call-trgt-78.t:call-get_reads_overlapping_repeats.slurm_singularity INFO srun: job 51797941 queued and waiting for resources
2025-09-15 20:25:10.127 wdl.w:ptcp.w:call-trgt-78.t:call-get_reads_overlapping_repeats.slurm_singularity INFO srun: job 51797941 has been allocated resources
2025-09-15 20:25:10.127 wdl.w:ptcp.w:call-trgt-78.t:call-get_reads_overlapping_repeats.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:10.147 wdl.w:ptcp.t:call-tar_outputs-44.stderr VERBOSE tar: Removing leading `/' from member names
2025-09-15 20:25:10.147 wdl.w:ptcp.t:call-tar_outputs-44.stderr VERBOSE tar: Removing leading `/' from hard link targets
2025-09-15 20:25:10.158 wdl.w:ptcp.t:call-tar_outputs-44.slurm_singularity INFO srun: job 51797942 queued and waiting for resources
2025-09-15 20:25:10.158 wdl.w:ptcp.t:call-tar_outputs-44.slurm_singularity INFO srun: job 51797942 has been allocated resources
2025-09-15 20:25:10.158 wdl.w:ptcp.t:call-tar_outputs-44.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:10.169 wdl.w:ptcp.w:call-trgt-69.t:call-trgt_plot_meth_waterfall INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-69/call-trgt_plot_meth_waterfall/_singularity_tmpdir_bt7f0bwi"
2025-09-15 20:25:10.170 wdl.w:ptcp.w:call-trgt-69.t:call-trgt_plot_meth_waterfall INFO Slurm invocation: srun --job-name call-trgt_plot_meth_waterfall --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-69/call-trgt_plot_meth_waterfall/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-69/call-trgt_plot_meth_waterfall/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-69/call-trgt_plot_meth_waterfall/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-69/call-trgt_plot_meth_waterfall/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-69/call-trgt_genotype/out/m84036_250809_035451_s4.bc2166.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2166.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-69/call-trgt_genotype/out/m84036_250809_035451_s4.bc2166.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2166.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-69/call-trgt_genotype/out/m84036_250809_035451_s4.bc2166.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2166.trgt.vcf:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-69/call-trgt_plot_meth_waterfall/_singularity_tmpdir_bt7f0bwi/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-69/call-trgt_plot_meth_waterfall/_singularity_tmpdir_bt7f0bwi/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:10.172 wdl.w:ptcp.w:call-paraphase-64.t:call-call_f8 NOTICE done
2025-09-15 20:25:10.178 wdl.w:ptcp.w:call-paraphase-64 NOTICE finish :: job: "call-call_f8"
2025-09-15 20:25:10.179 wdl.w:ptcp.w:call-paraphase-64 INFO output :: job: "call-call_f8", values: {"json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-64/call-call_f8/out/m84036_250809_035451_s4.bc2161.f8inversion.json", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-64/call-call_f8/out/m84036_250809_035451_s4.bc2161.f8inversion.vcf"}
2025-09-15 20:25:10.179 wdl.w:ptcp.w:call-paraphase-64 INFO visit :: node: "output-f8_json", values: {"f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-64/call-call_f8/out/m84036_250809_035451_s4.bc2161.f8inversion.json"}
2025-09-15 20:25:10.179 wdl.w:ptcp.w:call-paraphase-64 INFO visit :: node: "output-f8_vcf", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-64/call-call_f8/out/m84036_250809_035451_s4.bc2161.f8inversion.vcf"}
2025-09-15 20:25:10.179 wdl.w:ptcp.w:call-paraphase-64 INFO visit :: node: "outputs", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-64/call-call_f8/out/m84036_250809_035451_s4.bc2161.f8inversion.vcf", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-64/call-run_paraphase/out/m84036_250809_035451_s4.bc2161_paraphase/m84036_250809_035451_s4.bc2161.paraphase.json", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-64/call-run_paraphase/out/m84036_250809_035451_s4.bc2161_paraphase/m84036_250809_035451_s4.bc2161.paraphase.bam", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-64/call-run_paraphase/out/m84036_250809_035451_s4.bc2161_paraphase/m84036_250809_035451_s4.bc2161.paraphase.bam.bai", "paraphase_vcfs": [], "havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-64/call-run_paraphase/out/m84036_250809_035451_s4.bc2161.havanno.json", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-64/call-call_f8/out/m84036_250809_035451_s4.bc2161.f8inversion.json"}
2025-09-15 20:25:10.184 wdl.w:ptcp.w:call-trgt-69.t:call-trgt_plot_motifs_allele NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-69/call-trgt_plot_motifs_allele", thread: 140607691417152
2025-09-15 20:25:10.196 wdl.w:ptcp.w:call-trgt-69.t:call-trgt_plot_meth_waterfall NOTICE slurm_singularity run :: pid: 1205042, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-69/call-trgt_plot_meth_waterfall/slurm_singularity.log.txt"
2025-09-15 20:25:10.200 wdl.w:ptcp.w:call-trgt-69.t:call-trgt_plot_motifs_allele INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:10.201 wdl.w:ptcp.w:call-trgt-69.t:call-trgt_plot_motifs_allele INFO input :: name: "waterfall", value: false
2025-09-15 20:25:10.201 wdl.w:ptcp.w:call-trgt-69.t:call-trgt_plot_motifs_allele INFO input :: name: "methylation", value: false
2025-09-15 20:25:10.201 wdl.w:ptcp.w:call-trgt-69.t:call-trgt_plot_motifs_allele INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:25:10.201 wdl.w:ptcp.w:call-trgt-69.t:call-trgt_plot_motifs_allele INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:25:10.201 wdl.w:ptcp.w:call-trgt-69.t:call-trgt_plot_motifs_allele INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:25:10.201 wdl.w:ptcp.w:call-trgt-69.t:call-trgt_plot_motifs_allele INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2166.trgt.sorted.spanning.bam.bai"
2025-09-15 20:25:10.201 wdl.w:ptcp.w:call-trgt-69.t:call-trgt_plot_motifs_allele INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2166.trgt.sorted.spanning.bam"
2025-09-15 20:25:10.201 wdl.w:ptcp.w:call-trgt-69.t:call-trgt_plot_motifs_allele INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2166.trgt.vcf"
2025-09-15 20:25:10.201 wdl.w:ptcp.w:call-trgt-69.t:call-trgt_plot_motifs_allele INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2166"
2025-09-15 20:25:10.201 wdl.w:ptcp.w:call-trgt-69.t:call-trgt_plot_motifs_allele INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:25:10.201 wdl.w:ptcp.w:call-trgt-69.t:call-trgt_plot_motifs_allele INFO eval :: name: "plot_type", value: "allele"
2025-09-15 20:25:10.202 wdl.w:ptcp.w:call-trgt-69.t:call-trgt_plot_motifs_allele INFO eval :: name: "show", value: "motifs"
2025-09-15 20:25:10.202 wdl.w:ptcp.w:call-trgt-69.t:call-trgt_plot_motifs_allele INFO eval :: name: "threads", value: 1
2025-09-15 20:25:10.202 wdl.w:ptcp.w:call-trgt-69.t:call-trgt_plot_motifs_allele INFO eval :: name: "disk_size", value: 27
2025-09-15 20:25:10.202 wdl.w:ptcp.w:call-trgt-69.t:call-trgt_plot_motifs_allele INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2166.motifs_allele"
2025-09-15 20:25:10.202 wdl.w:ptcp.w:call-trgt-69.t:call-trgt_plot_motifs_allele INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:10.202 wdl.w:ptcp.w:call-trgt-69.t:call-trgt_plot_motifs_allele WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:10.203 wdl.w:ptcp.w:call-trgt-69.t:call-trgt_plot_motifs_allele INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:25:10.203 wdl.w:ptcp.w:call-trgt-69.t:call-trgt_plot_motifs_allele INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:10.251 wdl.w:ptcp.w:call-paraphase-64 NOTICE done
2025-09-15 20:25:10.257 wdl.w:ptcp NOTICE finish :: job: "call-paraphase-64"
2025-09-15 20:25:10.258 wdl.w:ptcp INFO output :: job: "call-paraphase-64", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-64/out/m84036_250809_035451_s4.bc2161.f8inversion.vcf", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-64/out/m84036_250809_035451_s4.bc2161_paraphase/m84036_250809_035451_s4.bc2161.paraphase.json", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-64/out/m84036_250809_035451_s4.bc2161_paraphase/m84036_250809_035451_s4.bc2161.paraphase.bam", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-64/out/m84036_250809_035451_s4.bc2161_paraphase/m84036_250809_035451_s4.bc2161.paraphase.bam.bai", "paraphase_vcfs": [], "havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-64/out/m84036_250809_035451_s4.bc2161.havanno.json", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-64/out/m84036_250809_035451_s4.bc2161.f8inversion.json"}
2025-09-15 20:25:10.267 wdl.w:ptcp.w:call-paraphase-89 NOTICE workflow start :: name: "paraphase", source: "./paraphase.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-89"
2025-09-15 20:25:10.269 wdl.w:ptcp.t:call-tar_outputs-44 INFO output :: name: "sample_tarball", value: "m84036_250809_035451_s4.bc2141.tar"
2025-09-15 20:25:10.282 wdl.w:ptcp.w:call-paraphase-89 INFO visit :: node: "decl-annotation_vcf", values: {"annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf"}
2025-09-15 20:25:10.282 wdl.w:ptcp.w:call-paraphase-89 INFO visit :: node: "decl-config_file", values: {"config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml"}
2025-09-15 20:25:10.282 wdl.w:ptcp.w:call-paraphase-89 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:25:10.282 wdl.w:ptcp.w:call-paraphase-89 INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:25:10.282 wdl.w:ptcp.w:call-paraphase-89 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-89/out/m84036_250809_035451_s4.bc2186.mapped.bam"}
2025-09-15 20:25:10.282 wdl.w:ptcp.w:call-paraphase-89 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-89/out/m84036_250809_035451_s4.bc2186.mapped.bam.bai"}
2025-09-15 20:25:10.282 wdl.w:ptcp.w:call-paraphase-89 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:25:10.282 wdl.w:ptcp.w:call-paraphase-89 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:25:10.282 wdl.w:ptcp.w:call-paraphase-89 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2186"}
2025-09-15 20:25:10.283 wdl.w:ptcp.w:call-paraphase-89 INFO visit :: node: "decl-sex", values: {"sex": "F"}
2025-09-15 20:25:10.284 wdl.w:ptcp.w:call-paraphase-89 NOTICE ready :: job: "call-run_paraphase", callee: "run_paraphase"
2025-09-15 20:25:10.285 wdl.w:ptcp.w:call-paraphase-89 INFO input :: job: "call-run_paraphase", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf", "genome_version": "38", "config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-89/out/m84036_250809_035451_s4.bc2186.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-89/out/m84036_250809_035451_s4.bc2186.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2186"}
2025-09-15 20:25:10.287 wdl.w:ptcp.w:call-trgt-78.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:25:09 [INFO] - Running trgt-4.0.0-429afcd [genotype]
2025-09-15 20:25:10.287 wdl.w:ptcp.w:call-trgt-78.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:25:09 [WARN] - PRTS_ARX: Filtered out 6 impure reads
2025-09-15 20:25:10.287 wdl.w:ptcp.w:call-trgt-78.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:25:09 [WARN] - FXS_FMR1: Filtered out 12 impure reads
2025-09-15 20:25:10.287 wdl.w:ptcp.w:call-trgt-78.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:25:09 [WARN] - EIEE1_ARX: Filtered out 4 impure reads
2025-09-15 20:25:10.288 wdl.w:ptcp.w:call-trgt-78.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:25:09 [WARN] - FRAXE_AFF2: Filtered out 10 impure reads
2025-09-15 20:25:10.288 wdl.w:ptcp.w:call-trgt-78.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:25:10 [WARN] - FRDA_FXN: Filtered out 4 impure reads
2025-09-15 20:25:10.288 wdl.w:ptcp.w:call-trgt-78.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:25:10 [INFO] - Total execution time: 267.95ms
2025-09-15 20:25:10.288 wdl.w:ptcp.w:call-trgt-78.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:25:10 [INFO] - trgt end
2025-09-15 20:25:10.293 wdl.w:ptcp.w:call-trgt-69.t:call-trgt_plot_motifs_allele INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-69/call-trgt_plot_motifs_allele/_singularity_tmpdir_vfm3vvl4"
2025-09-15 20:25:10.293 wdl.w:ptcp.w:call-trgt-69.t:call-trgt_plot_motifs_allele INFO Slurm invocation: srun --job-name call-trgt_plot_motifs_allele --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-69/call-trgt_plot_motifs_allele/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-69/call-trgt_plot_motifs_allele/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-69/call-trgt_plot_motifs_allele/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-69/call-trgt_plot_motifs_allele/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-69/call-trgt_genotype/out/m84036_250809_035451_s4.bc2166.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2166.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-69/call-trgt_genotype/out/m84036_250809_035451_s4.bc2166.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2166.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-69/call-trgt_genotype/out/m84036_250809_035451_s4.bc2166.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2166.trgt.vcf:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-69/call-trgt_plot_motifs_allele/_singularity_tmpdir_vfm3vvl4/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-69/call-trgt_plot_motifs_allele/_singularity_tmpdir_vfm3vvl4/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:10.296 wdl.w:ptcp.w:call-trgt-78.t:call-trgt_genotype.slurm_singularity INFO srun: job 51797943 queued and waiting for resources
2025-09-15 20:25:10.296 wdl.w:ptcp.w:call-trgt-78.t:call-trgt_genotype.slurm_singularity INFO srun: job 51797943 has been allocated resources
2025-09-15 20:25:10.296 wdl.w:ptcp.w:call-trgt-78.t:call-trgt_genotype.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:10.313 wdl.w:ptcp.w:call-trgt-69.t:call-trgt_plot_motifs_allele NOTICE slurm_singularity run :: pid: 1205099, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-69/call-trgt_plot_motifs_allele/slurm_singularity.log.txt"
2025-09-15 20:25:10.331 wdl.w:ptcp.w:call-paraphase-84.t:call-run_paraphase.slurm_singularity INFO srun: job 51797944 queued and waiting for resources
2025-09-15 20:25:10.331 wdl.w:ptcp.w:call-paraphase-84.t:call-run_paraphase.slurm_singularity INFO srun: job 51797944 has been allocated resources
2025-09-15 20:25:10.331 wdl.w:ptcp.w:call-paraphase-84.t:call-run_paraphase.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:10.349 wdl.w:ptcp.t:call-tar_outputs-44 NOTICE done
2025-09-15 20:25:10.353 wdl.w:ptcp NOTICE finish :: job: "call-tar_outputs-44"
2025-09-15 20:25:10.353 wdl.w:ptcp INFO output :: job: "call-tar_outputs-44", values: {"sample_tarball": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-44/out/m84036_250809_035451_s4.bc2141.tar"}
2025-09-15 20:25:10.361 wdl.w:ptcp.w:call-trgt-69.t:call-trgt_plot_motifs_waterfall NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-69/call-trgt_plot_motifs_waterfall", thread: 140610375771712
2025-09-15 20:25:10.378 wdl.w:ptcp.w:call-trgt-69.t:call-trgt_plot_motifs_waterfall INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:10.378 wdl.w:ptcp.w:call-trgt-69.t:call-trgt_plot_motifs_waterfall INFO input :: name: "waterfall", value: true
2025-09-15 20:25:10.378 wdl.w:ptcp.w:call-trgt-69.t:call-trgt_plot_motifs_waterfall INFO input :: name: "methylation", value: false
2025-09-15 20:25:10.378 wdl.w:ptcp.w:call-trgt-69.t:call-trgt_plot_motifs_waterfall INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:25:10.378 wdl.w:ptcp.w:call-trgt-69.t:call-trgt_plot_motifs_waterfall INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:25:10.378 wdl.w:ptcp.w:call-trgt-69.t:call-trgt_plot_motifs_waterfall INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:25:10.378 wdl.w:ptcp.w:call-trgt-69.t:call-trgt_plot_motifs_waterfall INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2166.trgt.sorted.spanning.bam.bai"
2025-09-15 20:25:10.378 wdl.w:ptcp.w:call-trgt-69.t:call-trgt_plot_motifs_waterfall INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2166.trgt.sorted.spanning.bam"
2025-09-15 20:25:10.378 wdl.w:ptcp.w:call-trgt-69.t:call-trgt_plot_motifs_waterfall INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2166.trgt.vcf"
2025-09-15 20:25:10.378 wdl.w:ptcp.w:call-trgt-69.t:call-trgt_plot_motifs_waterfall INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2166"
2025-09-15 20:25:10.379 wdl.w:ptcp.w:call-trgt-69.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:25:10.379 wdl.w:ptcp.w:call-trgt-69.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "plot_type", value: "waterfall"
2025-09-15 20:25:10.379 wdl.w:ptcp.w:call-trgt-69.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "show", value: "motifs"
2025-09-15 20:25:10.379 wdl.w:ptcp.w:call-trgt-69.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "threads", value: 1
2025-09-15 20:25:10.379 wdl.w:ptcp.w:call-trgt-69.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "disk_size", value: 27
2025-09-15 20:25:10.379 wdl.w:ptcp.w:call-trgt-69.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2166.motifs_waterfall"
2025-09-15 20:25:10.380 wdl.w:ptcp.w:call-trgt-69.t:call-trgt_plot_motifs_waterfall INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:10.380 wdl.w:ptcp.w:call-trgt-69.t:call-trgt_plot_motifs_waterfall WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:10.380 wdl.w:ptcp.w:call-trgt-69.t:call-trgt_plot_motifs_waterfall INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:25:10.380 wdl.w:ptcp.w:call-trgt-69.t:call-trgt_plot_motifs_waterfall INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:10.409 wdl.w:ptcp.w:call-sawfish-84.t:call-run_sawfish.stderr VERBOSE [M::bam2fq_mainloop] discarded 0 singletons
2025-09-15 20:25:10.409 wdl.w:ptcp.w:call-sawfish-84.t:call-run_sawfish.stderr VERBOSE [M::bam2fq_mainloop] processed 1 reads
2025-09-15 20:25:10.427 wdl.w:ptcp.w:call-sawfish-84.t:call-run_sawfish.slurm_singularity INFO srun: job 51797945 queued and waiting for resources
2025-09-15 20:25:10.427 wdl.w:ptcp.w:call-sawfish-84.t:call-run_sawfish.slurm_singularity INFO srun: job 51797945 has been allocated resources
2025-09-15 20:25:10.428 wdl.w:ptcp.w:call-sawfish-84.t:call-run_sawfish.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:10.428 wdl.w:ptcp.w:call-sawfish-84.t:call-run_sawfish.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:25:10.454 wdl.w:ptcp.w:call-trgt-69.t:call-trgt_plot_motifs_waterfall INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-69/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_d_ip9htc"
2025-09-15 20:25:10.454 wdl.w:ptcp.w:call-trgt-69.t:call-trgt_plot_motifs_waterfall INFO Slurm invocation: srun --job-name call-trgt_plot_motifs_waterfall --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-69/call-trgt_plot_motifs_waterfall/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-69/call-trgt_plot_motifs_waterfall/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-69/call-trgt_plot_motifs_waterfall/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-69/call-trgt_plot_motifs_waterfall/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-69/call-trgt_genotype/out/m84036_250809_035451_s4.bc2166.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2166.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-69/call-trgt_genotype/out/m84036_250809_035451_s4.bc2166.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2166.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-69/call-trgt_genotype/out/m84036_250809_035451_s4.bc2166.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2166.trgt.vcf:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-69/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_d_ip9htc/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-69/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_d_ip9htc/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:10.464 wdl.w:ptcp.w:call-trgt-78.t:call-trgt_genotype INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2175.trgt.vcf"
2025-09-15 20:25:10.470 wdl.w:ptcp.w:call-trgt-78.t:call-trgt_genotype INFO output :: name: "spanning_bam", value: "m84036_250809_035451_s4.bc2175.trgt.sorted.spanning.bam"
2025-09-15 20:25:10.471 wdl.w:ptcp.w:call-trgt-78.t:call-trgt_genotype INFO output :: name: "spanning_bam_bai", value: "m84036_250809_035451_s4.bc2175.trgt.sorted.spanning.bam.bai"
2025-09-15 20:25:10.475 wdl.w:ptcp.w:call-trgt-69.t:call-trgt_plot_motifs_waterfall NOTICE slurm_singularity run :: pid: 1205107, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-69/call-trgt_plot_motifs_waterfall/slurm_singularity.log.txt"
2025-09-15 20:25:10.545 wdl.w:ptcp.w:call-trgt-78.t:call-get_reads_overlapping_repeats INFO output :: name: "reads_overlapping_repeats", value: "m84036_250809_035451_s4.bc2175.repeats.bam"
2025-09-15 20:25:10.554 wdl.w:ptcp.w:call-trgt-78.t:call-get_reads_overlapping_repeats INFO output :: name: "reads_overlapping_repeats_bai", value: "m84036_250809_035451_s4.bc2175.repeats.bam.bai"
2025-09-15 20:25:10.561 wdl.w:ptcp.w:call-trgt-78.t:call-trgt_genotype NOTICE done
2025-09-15 20:25:10.567 wdl.w:ptcp.w:call-trgt-78 NOTICE finish :: job: "call-trgt_genotype"
2025-09-15 20:25:10.567 wdl.w:ptcp.w:call-trgt-78 INFO output :: job: "call-trgt_genotype", values: {"spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-78/call-trgt_genotype/out/m84036_250809_035451_s4.bc2175.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-78/call-trgt_genotype/out/m84036_250809_035451_s4.bc2175.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-78/call-trgt_genotype/out/m84036_250809_035451_s4.bc2175.trgt.vcf"}
2025-09-15 20:25:10.568 wdl.w:ptcp.w:call-trgt-78 NOTICE ready :: job: "call-trgt_plot_meth_allele", callee: "trgt_plot"
2025-09-15 20:25:10.568 wdl.w:ptcp.w:call-trgt-78 INFO input :: job: "call-trgt_plot_meth_allele", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": false, "methylation": true, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-78/call-trgt_genotype/out/m84036_250809_035451_s4.bc2175.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-78/call-trgt_genotype/out/m84036_250809_035451_s4.bc2175.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-78/call-trgt_genotype/out/m84036_250809_035451_s4.bc2175.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2175"}
2025-09-15 20:25:10.569 wdl.w:ptcp.w:call-trgt-78 NOTICE ready :: job: "call-trgt_plot_meth_waterfall", callee: "trgt_plot"
2025-09-15 20:25:10.569 wdl.w:ptcp.w:call-trgt-78 INFO input :: job: "call-trgt_plot_meth_waterfall", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": true, "methylation": true, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-78/call-trgt_genotype/out/m84036_250809_035451_s4.bc2175.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-78/call-trgt_genotype/out/m84036_250809_035451_s4.bc2175.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-78/call-trgt_genotype/out/m84036_250809_035451_s4.bc2175.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2175"}
2025-09-15 20:25:10.570 wdl.w:ptcp.w:call-trgt-78 NOTICE ready :: job: "call-trgt_plot_motifs_allele", callee: "trgt_plot"
2025-09-15 20:25:10.570 wdl.w:ptcp.w:call-trgt-78 INFO input :: job: "call-trgt_plot_motifs_allele", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": false, "methylation": false, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-78/call-trgt_genotype/out/m84036_250809_035451_s4.bc2175.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-78/call-trgt_genotype/out/m84036_250809_035451_s4.bc2175.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-78/call-trgt_genotype/out/m84036_250809_035451_s4.bc2175.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2175"}
2025-09-15 20:25:10.571 wdl.w:ptcp.w:call-trgt-78 NOTICE ready :: job: "call-trgt_plot_motifs_waterfall", callee: "trgt_plot"
2025-09-15 20:25:10.571 wdl.w:ptcp.w:call-trgt-78 INFO input :: job: "call-trgt_plot_motifs_waterfall", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": true, "methylation": false, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-78/call-trgt_genotype/out/m84036_250809_035451_s4.bc2175.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-78/call-trgt_genotype/out/m84036_250809_035451_s4.bc2175.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-78/call-trgt_genotype/out/m84036_250809_035451_s4.bc2175.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2175"}
2025-09-15 20:25:10.571 wdl.w:ptcp.w:call-trgt-78 INFO visit :: node: "output-spanning_bam", values: {"spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-78/call-trgt_genotype/out/m84036_250809_035451_s4.bc2175.trgt.sorted.spanning.bam"}
2025-09-15 20:25:10.572 wdl.w:ptcp.w:call-trgt-78 INFO visit :: node: "output-spanning_bam_bai", values: {"spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-78/call-trgt_genotype/out/m84036_250809_035451_s4.bc2175.trgt.sorted.spanning.bam.bai"}
2025-09-15 20:25:10.572 wdl.w:ptcp.w:call-trgt-78 INFO visit :: node: "output-vcf", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-78/call-trgt_genotype/out/m84036_250809_035451_s4.bc2175.trgt.vcf"}
2025-09-15 20:25:10.576 wdl.w:ptcp.w:call-trgt-76.t:call-get_reads_overlapping_repeats NOTICE task setup :: name: "get_reads_overlapping_repeats", source: "./trgt.wdl", line: 182, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-76/call-get_reads_overlapping_repeats", thread: 140607683024448
2025-09-15 20:25:10.594 wdl.w:ptcp.w:call-paraphase-26.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for hbb for sample m84036_250809_035451_s4.bc2123 at 2025-09-15 20:25:01.242869...
2025-09-15 20:25:10.594 wdl.w:ptcp.w:call-paraphase-26.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for hbb for sample m84036_250809_035451_s4.bc2123 at 2025-09-15 20:25:01.527962...
2025-09-15 20:25:10.597 wdl.w:ptcp.w:call-trgt-76.t:call-get_reads_overlapping_repeats INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:10.597 wdl.w:ptcp.w:call-trgt-76.t:call-get_reads_overlapping_repeats INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:25:10.597 wdl.w:ptcp.w:call-trgt-76.t:call-get_reads_overlapping_repeats INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2173.mapped.bam.bai"
2025-09-15 20:25:10.597 wdl.w:ptcp.w:call-trgt-76.t:call-get_reads_overlapping_repeats INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2173.mapped.bam"
2025-09-15 20:25:10.597 wdl.w:ptcp.w:call-trgt-76.t:call-get_reads_overlapping_repeats INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2173"
2025-09-15 20:25:10.597 wdl.w:ptcp.w:call-trgt-76.t:call-get_reads_overlapping_repeats INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:25:10.597 wdl.w:ptcp.w:call-trgt-76.t:call-get_reads_overlapping_repeats INFO eval :: name: "expand_size", value: 3000
2025-09-15 20:25:10.597 wdl.w:ptcp.w:call-trgt-76.t:call-get_reads_overlapping_repeats INFO eval :: name: "threads", value: 1
2025-09-15 20:25:10.598 wdl.w:ptcp.w:call-trgt-76.t:call-get_reads_overlapping_repeats INFO eval :: name: "expanded_bed_name", value: "m84036_250809_035451_s4.bc2173.expanded.bed"
2025-09-15 20:25:10.598 wdl.w:ptcp.w:call-trgt-76.t:call-get_reads_overlapping_repeats INFO eval :: name: "disk_size", value: 11
2025-09-15 20:25:10.598 wdl.w:ptcp.w:call-trgt-76.t:call-get_reads_overlapping_repeats INFO eval :: name: "output_name", value: "m84036_250809_035451_s4.bc2173.repeats.bam"
2025-09-15 20:25:10.598 wdl.w:ptcp.w:call-trgt-76.t:call-get_reads_overlapping_repeats INFO eval :: name: "index_name", value: "m84036_250809_035451_s4.bc2173.repeats.bam.bai"
2025-09-15 20:25:10.598 wdl.w:ptcp.w:call-trgt-76.t:call-get_reads_overlapping_repeats INFO eval :: name: "output_name_with_index", value: "m84036_250809_035451_s4.bc2173.repeats.bam##idx##m84036_250809_035451_s4.bc2173.repeats.bam.bai"
2025-09-15 20:25:10.598 wdl.w:ptcp.w:call-trgt-76.t:call-get_reads_overlapping_repeats INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:10.599 wdl.w:ptcp.w:call-trgt-76.t:call-get_reads_overlapping_repeats WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:10.599 wdl.w:ptcp.w:call-trgt-76.t:call-get_reads_overlapping_repeats INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:25:10.599 wdl.w:ptcp.w:call-trgt-76.t:call-get_reads_overlapping_repeats INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:10.628 wdl.w:ptcp.w:call-trgt-84.t:call-trgt_genotype.slurm_singularity INFO srun: job 51797947 queued and waiting for resources
2025-09-15 20:25:10.628 wdl.w:ptcp.w:call-trgt-84.t:call-trgt_genotype.slurm_singularity INFO srun: job 51797947 has been allocated resources
2025-09-15 20:25:10.628 wdl.w:ptcp.w:call-trgt-84.t:call-trgt_genotype.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:10.630 wdl.w:ptcp.w:call-trgt-84.t:call-get_reads_overlapping_repeats.slurm_singularity INFO srun: job 51797946 queued and waiting for resources
2025-09-15 20:25:10.630 wdl.w:ptcp.w:call-trgt-84.t:call-get_reads_overlapping_repeats.slurm_singularity INFO srun: job 51797946 has been allocated resources
2025-09-15 20:25:10.630 wdl.w:ptcp.w:call-trgt-84.t:call-get_reads_overlapping_repeats.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:10.640 wdl.w:ptcp.w:call-trgt-78.t:call-get_reads_overlapping_repeats NOTICE done
2025-09-15 20:25:10.645 wdl.w:ptcp.w:call-trgt-78 NOTICE finish :: job: "call-get_reads_overlapping_repeats"
2025-09-15 20:25:10.645 wdl.w:ptcp.w:call-trgt-78 INFO output :: job: "call-get_reads_overlapping_repeats", values: {"reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-78/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2175.repeats.bam.bai", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-78/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2175.repeats.bam"}
2025-09-15 20:25:10.645 wdl.w:ptcp.w:call-trgt-78 INFO visit :: node: "output-reads_overlapping_repeats", values: {"reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-78/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2175.repeats.bam"}
2025-09-15 20:25:10.646 wdl.w:ptcp.w:call-trgt-78 INFO visit :: node: "output-reads_overlapping_repeats_bai", values: {"reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-78/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2175.repeats.bam.bai"}
2025-09-15 20:25:10.652 wdl.w:ptcp.w:call-trgt-76.t:call-trgt_genotype NOTICE task setup :: name: "trgt_genotype", source: "./trgt.wdl", line: 272, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-76/call-trgt_genotype", thread: 140611961206336
2025-09-15 20:25:10.675 wdl.w:ptcp.w:call-trgt-76.t:call-get_reads_overlapping_repeats INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 9, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-76/call-get_reads_overlapping_repeats/_singularity_tmpdir_qdsjjnky"
2025-09-15 20:25:10.675 wdl.w:ptcp.w:call-trgt-76.t:call-get_reads_overlapping_repeats INFO Slurm invocation: srun --job-name call-get_reads_overlapping_repeats --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-76/call-get_reads_overlapping_repeats/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-76/call-get_reads_overlapping_repeats/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-76/call-get_reads_overlapping_repeats/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-76/call-get_reads_overlapping_repeats/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-76/out/m84036_250809_035451_s4.bc2173.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2173.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-76/out/m84036_250809_035451_s4.bc2173.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2173.mapped.bam:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-76/call-get_reads_overlapping_repeats/_singularity_tmpdir_qdsjjnky/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-76/call-get_reads_overlapping_repeats/_singularity_tmpdir_qdsjjnky/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:10.685 wdl.w:ptcp.w:call-trgt-76.t:call-trgt_genotype INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:10.685 wdl.w:ptcp.w:call-trgt-76.t:call-trgt_genotype INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:25:10.685 wdl.w:ptcp.w:call-trgt-76.t:call-trgt_genotype INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:25:10.685 wdl.w:ptcp.w:call-trgt-76.t:call-trgt_genotype INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:25:10.685 wdl.w:ptcp.w:call-trgt-76.t:call-trgt_genotype INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2173.mapped.bam.bai"
2025-09-15 20:25:10.685 wdl.w:ptcp.w:call-trgt-76.t:call-trgt_genotype INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2173.mapped.bam"
2025-09-15 20:25:10.685 wdl.w:ptcp.w:call-trgt-76.t:call-trgt_genotype INFO input :: name: "sex", value: "F"
2025-09-15 20:25:10.685 wdl.w:ptcp.w:call-trgt-76.t:call-trgt_genotype INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2173"
2025-09-15 20:25:10.686 wdl.w:ptcp.w:call-trgt-76.t:call-trgt_genotype INFO eval :: name: "mem_gb", value: 16
2025-09-15 20:25:10.686 wdl.w:ptcp.w:call-trgt-76.t:call-trgt_genotype INFO eval :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2173.trgt"
2025-09-15 20:25:10.686 wdl.w:ptcp.w:call-trgt-76.t:call-trgt_genotype INFO eval :: name: "threads", value: 8
2025-09-15 20:25:10.686 wdl.w:ptcp.w:call-trgt-76.t:call-trgt_genotype INFO eval :: name: "disk_size", value: 27
2025-09-15 20:25:10.686 wdl.w:ptcp.w:call-trgt-76.t:call-trgt_genotype INFO eval :: name: "karyotype", value: "XX"
2025-09-15 20:25:10.687 wdl.w:ptcp.w:call-trgt-76.t:call-trgt_genotype INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 8, memory_reservation: 16000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:10.687 wdl.w:ptcp.w:call-trgt-76.t:call-trgt_genotype WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:10.688 wdl.w:ptcp.w:call-trgt-76.t:call-trgt_genotype INFO provisioned :: seconds_waited: 0, cpu: 8, mem_bytes: 16000000000
2025-09-15 20:25:10.689 wdl.w:ptcp.w:call-trgt-76.t:call-trgt_genotype INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:10.708 wdl.w:ptcp.w:call-trgt-76.t:call-get_reads_overlapping_repeats NOTICE slurm_singularity run :: pid: 1205115, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-76/call-get_reads_overlapping_repeats/slurm_singularity.log.txt"
2025-09-15 20:25:10.712 wdl.w:ptcp.w:call-paraphase-76.t:call-run_paraphase.slurm_singularity INFO srun: job 51797948 queued and waiting for resources
2025-09-15 20:25:10.712 wdl.w:ptcp.w:call-paraphase-76.t:call-run_paraphase.slurm_singularity INFO srun: job 51797948 has been allocated resources
2025-09-15 20:25:10.712 wdl.w:ptcp.w:call-paraphase-76.t:call-run_paraphase.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:10.754 wdl.w:ptcp.w:call-trgt-76.t:call-trgt_genotype INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 11, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-76/call-trgt_genotype/_singularity_tmpdir_2wod0ruw"
2025-09-15 20:25:10.754 wdl.w:ptcp.w:call-trgt-76.t:call-trgt_genotype INFO Slurm invocation: srun --job-name call-trgt_genotype --partition compute,compute9 --cpus-per-task 8 --mem 15259M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-76/call-trgt_genotype/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-76/call-trgt_genotype/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-76/call-trgt_genotype/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-76/call-trgt_genotype/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-76/out/m84036_250809_035451_s4.bc2173.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2173.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-76/out/m84036_250809_035451_s4.bc2173.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2173.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-76/call-trgt_genotype/_singularity_tmpdir_2wod0ruw/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-76/call-trgt_genotype/_singularity_tmpdir_2wod0ruw/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:10.766 wdl.w:ptcp.w:call-trgt-76.t:call-trgt_genotype NOTICE slurm_singularity run :: pid: 1205117, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-76/call-trgt_genotype/slurm_singularity.log.txt"
2025-09-15 20:25:10.880 wdl.w:ptcp.w:call-sawfish-76.t:call-run_sawfish.stderr VERBOSE [M::bam2fq_mainloop] discarded 0 singletons
2025-09-15 20:25:10.880 wdl.w:ptcp.w:call-sawfish-76.t:call-run_sawfish.stderr VERBOSE [M::bam2fq_mainloop] processed 1 reads
2025-09-15 20:25:10.891 wdl.w:ptcp.w:call-sawfish-76.t:call-run_sawfish.slurm_singularity INFO srun: job 51797949 queued and waiting for resources
2025-09-15 20:25:10.891 wdl.w:ptcp.w:call-sawfish-76.t:call-run_sawfish.slurm_singularity INFO srun: job 51797949 has been allocated resources
2025-09-15 20:25:10.891 wdl.w:ptcp.w:call-sawfish-76.t:call-run_sawfish.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:10.891 wdl.w:ptcp.w:call-sawfish-76.t:call-run_sawfish.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:25:10.967 wdl.w:ptcp.w:call-trgt-69.t:call-trgt_plot_meth_allele.slurm_singularity INFO srun: job 51797950 queued and waiting for resources
2025-09-15 20:25:10.967 wdl.w:ptcp.w:call-trgt-69.t:call-trgt_plot_meth_allele.slurm_singularity INFO srun: job 51797950 has been allocated resources
2025-09-15 20:25:10.967 wdl.w:ptcp.w:call-trgt-69.t:call-trgt_plot_meth_allele.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:11.203 wdl.w:ptcp.w:call-trgt-69.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO srun: job 51797951 queued and waiting for resources
2025-09-15 20:25:11.203 wdl.w:ptcp.w:call-trgt-69.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO srun: job 51797951 has been allocated resources
2025-09-15 20:25:11.203 wdl.w:ptcp.w:call-trgt-69.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:11.239 wdl.w:ptcp.w:call-sawfish-11.t:call-run_sawfish INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2108_sawfish/m84036_250809_035451_s4.bc2108.sv.vcf.gz"
2025-09-15 20:25:11.244 wdl.w:ptcp.w:call-sawfish-11.t:call-run_sawfish INFO output :: name: "vcf_tbi", value: "m84036_250809_035451_s4.bc2108_sawfish/m84036_250809_035451_s4.bc2108.sv.vcf.gz.tbi"
2025-09-15 20:25:11.246 wdl.w:ptcp.w:call-sawfish-11.t:call-run_sawfish INFO output :: name: "minimap2_bam", value: "m84036_250809_035451_s4.bc2108.minimap2.bam"
2025-09-15 20:25:11.247 wdl.w:ptcp.w:call-sawfish-11.t:call-run_sawfish INFO output :: name: "minimap2_bam_bai", value: "m84036_250809_035451_s4.bc2108.minimap2.bam.bai"
2025-09-15 20:25:11.325 wdl.w:ptcp.w:call-trgt-69.t:call-trgt_plot_motifs_allele.slurm_singularity INFO srun: job 51797952 queued and waiting for resources
2025-09-15 20:25:11.326 wdl.w:ptcp.w:call-trgt-69.t:call-trgt_plot_motifs_allele.slurm_singularity INFO srun: job 51797952 has been allocated resources
2025-09-15 20:25:11.326 wdl.w:ptcp.w:call-trgt-69.t:call-trgt_plot_motifs_allele.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:11.369 wdl.w:ptcp.w:call-trgt-61.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:10 [ERROR] - No reads found for TRID=PRTS_ARX
2025-09-15 20:25:11.370 wdl.w:ptcp.w:call-trgt-61.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:11 [ERROR] - No reads found for TRID=EIEE1_ARX
2025-09-15 20:25:11.385 wdl.w:ptcp.w:call-sawfish-11.t:call-run_sawfish NOTICE done
2025-09-15 20:25:11.486 wdl.w:ptcp.w:call-trgt-69.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO srun: job 51797953 queued and waiting for resources
2025-09-15 20:25:11.486 wdl.w:ptcp.w:call-trgt-69.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO srun: job 51797953 has been allocated resources
2025-09-15 20:25:11.486 wdl.w:ptcp.w:call-trgt-69.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:11.581 wdl.w:ptcp.w:call-paraphase-18.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for cyp21 for sample m84036_250809_035451_s4.bc2115 at 2025-09-15 20:24:23.293996...
2025-09-15 20:25:11.582 wdl.w:ptcp.w:call-paraphase-18.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for cyp21 for sample m84036_250809_035451_s4.bc2115 at 2025-09-15 20:24:24.120623...
2025-09-15 20:25:11.582 wdl.w:ptcp.w:call-paraphase-18.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for hba for sample m84036_250809_035451_s4.bc2115 at 2025-09-15 20:24:26.004236...
2025-09-15 20:25:11.582 wdl.w:ptcp.w:call-paraphase-18.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for hba for sample m84036_250809_035451_s4.bc2115 at 2025-09-15 20:24:26.431261...
2025-09-15 20:25:11.582 wdl.w:ptcp.w:call-paraphase-18.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for gba for sample m84036_250809_035451_s4.bc2115 at 2025-09-15 20:24:39.253790...
2025-09-15 20:25:11.582 wdl.w:ptcp.w:call-paraphase-18.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for gba for sample m84036_250809_035451_s4.bc2115 at 2025-09-15 20:24:39.790333...
2025-09-15 20:25:11.582 wdl.w:ptcp.w:call-paraphase-18.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for hbb for sample m84036_250809_035451_s4.bc2115 at 2025-09-15 20:24:49.645710...
2025-09-15 20:25:11.582 wdl.w:ptcp.w:call-paraphase-18.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for hbb for sample m84036_250809_035451_s4.bc2115 at 2025-09-15 20:24:49.645886...
2025-09-15 20:25:11.582 wdl.w:ptcp.w:call-paraphase-18.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for hbb for sample m84036_250809_035451_s4.bc2115 at 2025-09-15 20:24:51.052206...
2025-09-15 20:25:11.582 wdl.w:ptcp.w:call-paraphase-18.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for hbb for sample m84036_250809_035451_s4.bc2115 at 2025-09-15 20:24:57.909432...
2025-09-15 20:25:11.583 wdl.w:ptcp.w:call-paraphase-18.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for hbb for sample m84036_250809_035451_s4.bc2115 at 2025-09-15 20:24:58.239966...
2025-09-15 20:25:11.644 wdl.w:ptcp.w:call-trgt-56.t:call-trgt_plot_meth_waterfall INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2153.meth_waterfall.trgt_plots.zip"
2025-09-15 20:25:11.665 wdl.w:ptcp.w:call-paraphase-74.t:call-run_paraphase.stderr VERBOSE INFO:root:Processing sample m84036_250809_035451_s4.bc2171 at 2025-09-15 20:25:11.349734...
2025-09-15 20:25:11.666 wdl.w:ptcp.w:call-paraphase-74.t:call-run_paraphase.stderr VERBOSE INFO:root:Checking sample sex at 2025-09-15 20:25:11.350759...
2025-09-15 20:25:11.666 wdl.w:ptcp.w:call-paraphase-74.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for cyp21 for sample m84036_250809_035451_s4.bc2171 at 2025-09-15 20:25:11.393917...
2025-09-15 20:25:11.666 wdl.w:ptcp.w:call-paraphase-74.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for cyp21 for sample m84036_250809_035451_s4.bc2171 at 2025-09-15 20:25:11.394216...
2025-09-15 20:25:11.666 wdl.w:ptcp.w:call-paraphase-74.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for smn1 for sample m84036_250809_035451_s4.bc2171 at 2025-09-15 20:25:11.394010...
2025-09-15 20:25:11.666 wdl.w:ptcp.w:call-paraphase-74.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for gba for sample m84036_250809_035451_s4.bc2171 at 2025-09-15 20:25:11.394059...
2025-09-15 20:25:11.666 wdl.w:ptcp.w:call-paraphase-74.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for smn1 for sample m84036_250809_035451_s4.bc2171 at 2025-09-15 20:25:11.394265...
2025-09-15 20:25:11.666 wdl.w:ptcp.w:call-paraphase-74.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for hba for sample m84036_250809_035451_s4.bc2171 at 2025-09-15 20:25:11.394098...
2025-09-15 20:25:11.666 wdl.w:ptcp.w:call-paraphase-74.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for gba for sample m84036_250809_035451_s4.bc2171 at 2025-09-15 20:25:11.394305...
2025-09-15 20:25:11.666 wdl.w:ptcp.w:call-paraphase-74.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for hba for sample m84036_250809_035451_s4.bc2171 at 2025-09-15 20:25:11.394334...
2025-09-15 20:25:11.671 wdl.w:ptcp.w:call-trgt-61.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:25:10 [ERROR] - No reads found for TRID=PRTS_ARX
2025-09-15 20:25:11.671 wdl.w:ptcp.w:call-trgt-61.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:25:10 [ERROR] - No reads found for TRID=EIEE1_ARX
2025-09-15 20:25:11.682 wdl.w:ptcp.w:call-trgt-64.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:09 [ERROR] - No reads found for TRID=PRTS_ARX
2025-09-15 20:25:11.683 wdl.w:ptcp.w:call-trgt-64.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:09 [ERROR] - No reads found for TRID=EIEE1_ARX
2025-09-15 20:25:11.699 wdl.w:ptcp.w:call-trgt-64.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:25:10 [ERROR] - No reads found for TRID=PRTS_ARX
2025-09-15 20:25:11.699 wdl.w:ptcp.w:call-trgt-64.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:25:10 [ERROR] - No reads found for TRID=EIEE1_ARX
2025-09-15 20:25:11.702 wdl.w:ptcp.w:call-paraphase-47.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for hbb for sample m84036_250809_035451_s4.bc2144 at 2025-09-15 20:25:09.030251...
2025-09-15 20:25:11.702 wdl.w:ptcp.w:call-paraphase-47.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for hbb for sample m84036_250809_035451_s4.bc2144 at 2025-09-15 20:25:09.030446...
2025-09-15 20:25:11.724 wdl.w:ptcp.w:call-trgt-76.t:call-get_reads_overlapping_repeats.slurm_singularity INFO srun: job 51797954 queued and waiting for resources
2025-09-15 20:25:11.724 wdl.w:ptcp.w:call-trgt-76.t:call-get_reads_overlapping_repeats.slurm_singularity INFO srun: job 51797954 has been allocated resources
2025-09-15 20:25:11.724 wdl.w:ptcp.w:call-trgt-76.t:call-get_reads_overlapping_repeats.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:11.765 wdl.w:ptcp.w:call-trgt-56.t:call-trgt_plot_meth_waterfall NOTICE done
2025-09-15 20:25:11.772 wdl.w:ptcp.w:call-trgt-56 NOTICE finish :: job: "call-trgt_plot_meth_waterfall"
2025-09-15 20:25:11.772 wdl.w:ptcp.w:call-trgt-56 INFO output :: job: "call-trgt_plot_meth_waterfall", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-56/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2153.meth_waterfall.trgt_plots.zip"}
2025-09-15 20:25:11.772 wdl.w:ptcp.w:call-trgt-56 INFO visit :: node: "output-images_meth_waterfall", values: {"images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-56/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2153.meth_waterfall.trgt_plots.zip"}
2025-09-15 20:25:11.772 wdl.w:ptcp.w:call-trgt-56 INFO visit :: node: "outputs", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-56/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2153.motifs_waterfall.trgt_plots.zip", "images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-56/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2153.meth_allele.trgt_plots.zip", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-56/call-trgt_genotype/out/m84036_250809_035451_s4.bc2153.trgt.sorted.spanning.bam.bai", "images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-56/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2153.motifs_allele.trgt_plots.zip", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-56/call-trgt_genotype/out/m84036_250809_035451_s4.bc2153.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-56/call-trgt_genotype/out/m84036_250809_035451_s4.bc2153.trgt.vcf", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-56/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2153.repeats.bam", "images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-56/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2153.meth_waterfall.trgt_plots.zip", "reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-56/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2153.repeats.bam.bai"}
2025-09-15 20:25:11.777 wdl.w:ptcp.w:call-trgt-76.t:call-trgt_genotype.slurm_singularity INFO srun: job 51797955 queued and waiting for resources
2025-09-15 20:25:11.777 wdl.w:ptcp.w:call-trgt-76.t:call-trgt_genotype.slurm_singularity INFO srun: job 51797955 has been allocated resources
2025-09-15 20:25:11.777 wdl.w:ptcp.w:call-trgt-76.t:call-trgt_genotype.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:11.778 wdl.w:ptcp.w:call-trgt-60.t:call-trgt_plot_meth_allele NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-60/call-trgt_plot_meth_allele", thread: 140608773551680
2025-09-15 20:25:11.800 wdl.w:ptcp.w:call-trgt-60.t:call-trgt_plot_meth_allele INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:11.801 wdl.w:ptcp.w:call-trgt-60.t:call-trgt_plot_meth_allele INFO input :: name: "waterfall", value: false
2025-09-15 20:25:11.801 wdl.w:ptcp.w:call-trgt-60.t:call-trgt_plot_meth_allele INFO input :: name: "methylation", value: true
2025-09-15 20:25:11.801 wdl.w:ptcp.w:call-trgt-60.t:call-trgt_plot_meth_allele INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:25:11.801 wdl.w:ptcp.w:call-trgt-60.t:call-trgt_plot_meth_allele INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:25:11.801 wdl.w:ptcp.w:call-trgt-60.t:call-trgt_plot_meth_allele INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:25:11.801 wdl.w:ptcp.w:call-trgt-60.t:call-trgt_plot_meth_allele INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2157.trgt.sorted.spanning.bam.bai"
2025-09-15 20:25:11.801 wdl.w:ptcp.w:call-trgt-60.t:call-trgt_plot_meth_allele INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2157.trgt.sorted.spanning.bam"
2025-09-15 20:25:11.801 wdl.w:ptcp.w:call-trgt-60.t:call-trgt_plot_meth_allele INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2157.trgt.vcf"
2025-09-15 20:25:11.801 wdl.w:ptcp.w:call-trgt-60.t:call-trgt_plot_meth_allele INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2157"
2025-09-15 20:25:11.801 wdl.w:ptcp.w:call-trgt-60.t:call-trgt_plot_meth_allele INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:25:11.802 wdl.w:ptcp.w:call-trgt-60.t:call-trgt_plot_meth_allele INFO eval :: name: "plot_type", value: "allele"
2025-09-15 20:25:11.802 wdl.w:ptcp.w:call-trgt-60.t:call-trgt_plot_meth_allele INFO eval :: name: "show", value: "meth"
2025-09-15 20:25:11.802 wdl.w:ptcp.w:call-trgt-60.t:call-trgt_plot_meth_allele INFO eval :: name: "threads", value: 1
2025-09-15 20:25:11.802 wdl.w:ptcp.w:call-trgt-60.t:call-trgt_plot_meth_allele INFO eval :: name: "disk_size", value: 27
2025-09-15 20:25:11.802 wdl.w:ptcp.w:call-trgt-60.t:call-trgt_plot_meth_allele INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2157.meth_allele"
2025-09-15 20:25:11.803 wdl.w:ptcp.w:call-trgt-60.t:call-trgt_plot_meth_allele INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:11.803 wdl.w:ptcp.w:call-trgt-60.t:call-trgt_plot_meth_allele WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:11.803 wdl.w:ptcp.w:call-trgt-60.t:call-trgt_plot_meth_allele INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:25:11.803 wdl.w:ptcp.w:call-trgt-60.t:call-trgt_plot_meth_allele INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:11.863 wdl.w:ptcp.w:call-sawfish-11 NOTICE finish :: job: "call-run_sawfish"
2025-09-15 20:25:11.863 wdl.w:ptcp.w:call-sawfish-11 INFO output :: job: "call-run_sawfish", values: {"minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-11/call-run_sawfish/out/m84036_250809_035451_s4.bc2108.minimap2.bam.bai", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-11/call-run_sawfish/out/m84036_250809_035451_s4.bc2108.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-11/call-run_sawfish/out/m84036_250809_035451_s4.bc2108_sawfish/m84036_250809_035451_s4.bc2108.sv.vcf.gz.tbi", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-11/call-run_sawfish/out/m84036_250809_035451_s4.bc2108_sawfish/m84036_250809_035451_s4.bc2108.sv.vcf.gz"}
2025-09-15 20:25:11.863 wdl.w:ptcp.w:call-sawfish-11 INFO visit :: node: "output-minimap2_bam", values: {"minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-11/call-run_sawfish/out/m84036_250809_035451_s4.bc2108.minimap2.bam"}
2025-09-15 20:25:11.864 wdl.w:ptcp.w:call-sawfish-11 INFO visit :: node: "output-minimap2_bam_bai", values: {"minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-11/call-run_sawfish/out/m84036_250809_035451_s4.bc2108.minimap2.bam.bai"}
2025-09-15 20:25:11.864 wdl.w:ptcp.w:call-sawfish-11 INFO visit :: node: "output-vcf", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-11/call-run_sawfish/out/m84036_250809_035451_s4.bc2108_sawfish/m84036_250809_035451_s4.bc2108.sv.vcf.gz"}
2025-09-15 20:25:11.864 wdl.w:ptcp.w:call-sawfish-11 INFO visit :: node: "output-vcf_tbi", values: {"vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-11/call-run_sawfish/out/m84036_250809_035451_s4.bc2108_sawfish/m84036_250809_035451_s4.bc2108.sv.vcf.gz.tbi"}
2025-09-15 20:25:11.864 wdl.w:ptcp.w:call-sawfish-11 INFO visit :: node: "outputs", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-11/call-run_sawfish/out/m84036_250809_035451_s4.bc2108_sawfish/m84036_250809_035451_s4.bc2108.sv.vcf.gz", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-11/call-run_sawfish/out/m84036_250809_035451_s4.bc2108.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-11/call-run_sawfish/out/m84036_250809_035451_s4.bc2108_sawfish/m84036_250809_035451_s4.bc2108.sv.vcf.gz.tbi", "minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-11/call-run_sawfish/out/m84036_250809_035451_s4.bc2108.minimap2.bam.bai"}
2025-09-15 20:25:11.869 wdl.w:ptcp.w:call-trgt-56 NOTICE done
2025-09-15 20:25:11.871 wdl.w:ptcp.w:call-trgt-60.t:call-trgt_plot_meth_waterfall NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-60/call-trgt_plot_meth_waterfall", thread: 140611969599040
2025-09-15 20:25:11.873 wdl.w:ptcp NOTICE finish :: job: "call-trgt-56"
2025-09-15 20:25:11.874 wdl.w:ptcp INFO output :: job: "call-trgt-56", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-56/out/m84036_250809_035451_s4.bc2153.motifs_waterfall.trgt_plots.zip", "images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-56/out/m84036_250809_035451_s4.bc2153.meth_allele.trgt_plots.zip", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-56/out/m84036_250809_035451_s4.bc2153.trgt.sorted.spanning.bam.bai", "images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-56/out/m84036_250809_035451_s4.bc2153.motifs_allele.trgt_plots.zip", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-56/out/m84036_250809_035451_s4.bc2153.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-56/out/m84036_250809_035451_s4.bc2153.trgt.vcf", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-56/out/m84036_250809_035451_s4.bc2153.repeats.bam", "images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-56/out/m84036_250809_035451_s4.bc2153.meth_waterfall.trgt_plots.zip", "reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-56/out/m84036_250809_035451_s4.bc2153.repeats.bam.bai"}
2025-09-15 20:25:11.881 wdl.w:ptcp.w:call-sawfish-89 NOTICE workflow start :: name: "sawfish", source: "./sawfish.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-89"
2025-09-15 20:25:11.901 wdl.w:ptcp.w:call-trgt-60.t:call-trgt_plot_meth_waterfall INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:11.901 wdl.w:ptcp.w:call-trgt-60.t:call-trgt_plot_meth_waterfall INFO input :: name: "waterfall", value: true
2025-09-15 20:25:11.901 wdl.w:ptcp.w:call-trgt-60.t:call-trgt_plot_meth_waterfall INFO input :: name: "methylation", value: true
2025-09-15 20:25:11.901 wdl.w:ptcp.w:call-trgt-60.t:call-trgt_plot_meth_waterfall INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:25:11.901 wdl.w:ptcp.w:call-trgt-60.t:call-trgt_plot_meth_waterfall INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:25:11.901 wdl.w:ptcp.w:call-trgt-60.t:call-trgt_plot_meth_waterfall INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:25:11.901 wdl.w:ptcp.w:call-trgt-60.t:call-trgt_plot_meth_waterfall INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2157.trgt.sorted.spanning.bam.bai"
2025-09-15 20:25:11.901 wdl.w:ptcp.w:call-trgt-60.t:call-trgt_plot_meth_waterfall INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2157.trgt.sorted.spanning.bam"
2025-09-15 20:25:11.901 wdl.w:ptcp.w:call-trgt-60.t:call-trgt_plot_meth_waterfall INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2157.trgt.vcf"
2025-09-15 20:25:11.901 wdl.w:ptcp.w:call-trgt-60.t:call-trgt_plot_meth_waterfall INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2157"
2025-09-15 20:25:11.902 wdl.w:ptcp.w:call-trgt-60.t:call-trgt_plot_meth_waterfall INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:25:11.902 wdl.w:ptcp.w:call-trgt-60.t:call-trgt_plot_meth_waterfall INFO eval :: name: "plot_type", value: "waterfall"
2025-09-15 20:25:11.903 wdl.w:ptcp.w:call-trgt-60.t:call-trgt_plot_meth_waterfall INFO eval :: name: "show", value: "meth"
2025-09-15 20:25:11.903 wdl.w:ptcp.w:call-trgt-60.t:call-trgt_plot_meth_waterfall INFO eval :: name: "threads", value: 1
2025-09-15 20:25:11.904 wdl.w:ptcp.w:call-trgt-60.t:call-trgt_plot_meth_waterfall INFO eval :: name: "disk_size", value: 27
2025-09-15 20:25:11.904 wdl.w:ptcp.w:call-trgt-60.t:call-trgt_plot_meth_waterfall INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2157.meth_waterfall"
2025-09-15 20:25:11.904 wdl.w:ptcp.w:call-trgt-60.t:call-trgt_plot_meth_waterfall INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:11.905 wdl.w:ptcp.w:call-trgt-60.t:call-trgt_plot_meth_waterfall WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:11.905 wdl.w:ptcp.w:call-trgt-60.t:call-trgt_plot_meth_waterfall INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:25:11.905 wdl.w:ptcp.w:call-trgt-60.t:call-trgt_plot_meth_waterfall INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:11.913 wdl.w:ptcp.w:call-sawfish-89 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:25:11.913 wdl.w:ptcp.w:call-sawfish-89 INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:25:11.913 wdl.w:ptcp.w:call-sawfish-89 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-89/out/m84036_250809_035451_s4.bc2186.mapped.bam"}
2025-09-15 20:25:11.913 wdl.w:ptcp.w:call-sawfish-89 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-89/out/m84036_250809_035451_s4.bc2186.mapped.bam.bai"}
2025-09-15 20:25:11.914 wdl.w:ptcp.w:call-sawfish-89 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:25:11.914 wdl.w:ptcp.w:call-sawfish-89 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:25:11.914 wdl.w:ptcp.w:call-sawfish-89 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2186"}
2025-09-15 20:25:11.914 wdl.w:ptcp.w:call-sawfish-89 NOTICE ready :: job: "call-run_sawfish", callee: "run_sawfish"
2025-09-15 20:25:11.914 wdl.w:ptcp.w:call-sawfish-89 INFO input :: job: "call-run_sawfish", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-89/out/m84036_250809_035451_s4.bc2186.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-89/out/m84036_250809_035451_s4.bc2186.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2186"}
2025-09-15 20:25:11.914 wdl.w:ptcp.w:call-trgt-60.t:call-trgt_plot_meth_allele INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-60/call-trgt_plot_meth_allele/_singularity_tmpdir_tk9vs3aq"
2025-09-15 20:25:11.914 wdl.w:ptcp.w:call-trgt-60.t:call-trgt_plot_meth_allele INFO Slurm invocation: srun --job-name call-trgt_plot_meth_allele --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-60/call-trgt_plot_meth_allele/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-60/call-trgt_plot_meth_allele/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-60/call-trgt_plot_meth_allele/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-60/call-trgt_plot_meth_allele/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-60/call-trgt_genotype/out/m84036_250809_035451_s4.bc2157.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2157.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-60/call-trgt_genotype/out/m84036_250809_035451_s4.bc2157.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2157.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-60/call-trgt_genotype/out/m84036_250809_035451_s4.bc2157.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2157.trgt.sorted.spanning.bam.bai:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-60/call-trgt_plot_meth_allele/_singularity_tmpdir_tk9vs3aq/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-60/call-trgt_plot_meth_allele/_singularity_tmpdir_tk9vs3aq/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:11.929 wdl.w:ptcp.w:call-sawfish-11 NOTICE done
2025-09-15 20:25:11.929 wdl.w:ptcp.w:call-trgt-64.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:25:11 [ERROR] - No reads found for TRID=PRTS_ARX
2025-09-15 20:25:11.930 wdl.w:ptcp.w:call-trgt-64.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:25:11 [ERROR] - No reads found for TRID=EIEE1_ARX
2025-09-15 20:25:11.937 wdl.w:ptcp NOTICE finish :: job: "call-sawfish-11"
2025-09-15 20:25:11.937 wdl.w:ptcp INFO output :: job: "call-sawfish-11", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-11/out/m84036_250809_035451_s4.bc2108_sawfish/m84036_250809_035451_s4.bc2108.sv.vcf.gz", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-11/out/m84036_250809_035451_s4.bc2108.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-11/out/m84036_250809_035451_s4.bc2108_sawfish/m84036_250809_035451_s4.bc2108.sv.vcf.gz.tbi", "minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-11/out/m84036_250809_035451_s4.bc2108.minimap2.bam.bai"}
2025-09-15 20:25:11.944 wdl.w:ptcp.w:call-trgt-89 NOTICE workflow start :: name: "trgt", source: "./trgt.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-89"
2025-09-15 20:25:11.955 wdl.w:ptcp.w:call-trgt-60.t:call-trgt_plot_meth_allele NOTICE slurm_singularity run :: pid: 1205132, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-60/call-trgt_plot_meth_allele/slurm_singularity.log.txt"
2025-09-15 20:25:11.964 wdl.w:ptcp.w:call-trgt-89 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:25:11.964 wdl.w:ptcp.w:call-trgt-89 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-89/out/m84036_250809_035451_s4.bc2186.mapped.bam"}
2025-09-15 20:25:11.964 wdl.w:ptcp.w:call-trgt-89 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-89/out/m84036_250809_035451_s4.bc2186.mapped.bam.bai"}
2025-09-15 20:25:11.964 wdl.w:ptcp.w:call-trgt-89 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:25:11.964 wdl.w:ptcp.w:call-trgt-89 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:25:11.964 wdl.w:ptcp.w:call-trgt-89 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2186"}
2025-09-15 20:25:11.964 wdl.w:ptcp.w:call-trgt-89 INFO visit :: node: "decl-sex", values: {"sex": "F"}
2025-09-15 20:25:11.964 wdl.w:ptcp.w:call-trgt-89 INFO visit :: node: "decl-trgt_bed", values: {"trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"}
2025-09-15 20:25:11.965 wdl.w:ptcp.w:call-trgt-89 NOTICE ready :: job: "call-get_reads_overlapping_repeats", callee: "get_reads_overlapping_repeats"
2025-09-15 20:25:11.965 wdl.w:ptcp.w:call-trgt-89 INFO input :: job: "call-get_reads_overlapping_repeats", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-89/out/m84036_250809_035451_s4.bc2186.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-89/out/m84036_250809_035451_s4.bc2186.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2186"}
2025-09-15 20:25:11.965 wdl.w:ptcp.w:call-trgt-89 NOTICE ready :: job: "call-trgt_genotype", callee: "trgt_genotype"
2025-09-15 20:25:11.966 wdl.w:ptcp.w:call-trgt-89 INFO input :: job: "call-trgt_genotype", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-89/out/m84036_250809_035451_s4.bc2186.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-89/out/m84036_250809_035451_s4.bc2186.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2186"}
2025-09-15 20:25:11.979 wdl.w:ptcp.w:call-trgt-60.t:call-trgt_plot_meth_waterfall INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-60/call-trgt_plot_meth_waterfall/_singularity_tmpdir_lk7uvt4n"
2025-09-15 20:25:11.980 wdl.w:ptcp.w:call-trgt-60.t:call-trgt_plot_meth_waterfall INFO Slurm invocation: srun --job-name call-trgt_plot_meth_waterfall --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-60/call-trgt_plot_meth_waterfall/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-60/call-trgt_plot_meth_waterfall/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-60/call-trgt_plot_meth_waterfall/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-60/call-trgt_plot_meth_waterfall/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-60/call-trgt_genotype/out/m84036_250809_035451_s4.bc2157.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2157.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-60/call-trgt_genotype/out/m84036_250809_035451_s4.bc2157.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2157.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-60/call-trgt_genotype/out/m84036_250809_035451_s4.bc2157.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2157.trgt.sorted.spanning.bam.bai:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-60/call-trgt_plot_meth_waterfall/_singularity_tmpdir_lk7uvt4n/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-60/call-trgt_plot_meth_waterfall/_singularity_tmpdir_lk7uvt4n/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:11.991 wdl.w:ptcp.w:call-trgt-60.t:call-trgt_plot_meth_waterfall NOTICE slurm_singularity run :: pid: 1205134, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-60/call-trgt_plot_meth_waterfall/slurm_singularity.log.txt"
2025-09-15 20:25:12.198 wdl.w:ptcp.w:call-trgt-64.t:call-trgt_plot_meth_allele INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2161.meth_allele.trgt_plots.zip"
2025-09-15 20:25:12.307 wdl.w:ptcp.w:call-trgt-64.t:call-trgt_plot_meth_allele NOTICE done
2025-09-15 20:25:12.311 wdl.w:ptcp.w:call-trgt-64 NOTICE finish :: job: "call-trgt_plot_meth_allele"
2025-09-15 20:25:12.312 wdl.w:ptcp.w:call-trgt-64 INFO output :: job: "call-trgt_plot_meth_allele", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-64/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2161.meth_allele.trgt_plots.zip"}
2025-09-15 20:25:12.312 wdl.w:ptcp.w:call-trgt-64 INFO visit :: node: "output-images_meth_allele", values: {"images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-64/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2161.meth_allele.trgt_plots.zip"}
2025-09-15 20:25:12.317 wdl.w:ptcp.w:call-trgt-60.t:call-trgt_plot_motifs_allele NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-60/call-trgt_plot_motifs_allele", thread: 140607137760832
2025-09-15 20:25:12.327 wdl.w:ptcp.w:call-paraphase-66.t:call-run_paraphase.stderr VERBOSE INFO:root:Processing sample m84036_250809_035451_s4.bc2163 at 2025-09-15 20:25:08.695016...
2025-09-15 20:25:12.328 wdl.w:ptcp.w:call-paraphase-66.t:call-run_paraphase.stderr VERBOSE INFO:root:Checking sample sex at 2025-09-15 20:25:08.696020...
2025-09-15 20:25:12.328 wdl.w:ptcp.w:call-paraphase-66.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for smn1 for sample m84036_250809_035451_s4.bc2163 at 2025-09-15 20:25:08.740417...
2025-09-15 20:25:12.328 wdl.w:ptcp.w:call-paraphase-66.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for cyp21 for sample m84036_250809_035451_s4.bc2163 at 2025-09-15 20:25:08.740355...
2025-09-15 20:25:12.328 wdl.w:ptcp.w:call-paraphase-66.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for cyp21 for sample m84036_250809_035451_s4.bc2163 at 2025-09-15 20:25:08.740905...
2025-09-15 20:25:12.328 wdl.w:ptcp.w:call-paraphase-66.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for smn1 for sample m84036_250809_035451_s4.bc2163 at 2025-09-15 20:25:08.740905...
2025-09-15 20:25:12.328 wdl.w:ptcp.w:call-paraphase-66.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for gba for sample m84036_250809_035451_s4.bc2163 at 2025-09-15 20:25:08.742113...
2025-09-15 20:25:12.328 wdl.w:ptcp.w:call-paraphase-66.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for hba for sample m84036_250809_035451_s4.bc2163 at 2025-09-15 20:25:08.742113...
2025-09-15 20:25:12.329 wdl.w:ptcp.w:call-paraphase-66.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for gba for sample m84036_250809_035451_s4.bc2163 at 2025-09-15 20:25:08.742612...
2025-09-15 20:25:12.329 wdl.w:ptcp.w:call-paraphase-66.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for hba for sample m84036_250809_035451_s4.bc2163 at 2025-09-15 20:25:08.742613...
2025-09-15 20:25:12.353 wdl.w:ptcp.w:call-trgt-60.t:call-trgt_plot_motifs_allele INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:12.353 wdl.w:ptcp.w:call-trgt-60.t:call-trgt_plot_motifs_allele INFO input :: name: "waterfall", value: false
2025-09-15 20:25:12.353 wdl.w:ptcp.w:call-trgt-60.t:call-trgt_plot_motifs_allele INFO input :: name: "methylation", value: false
2025-09-15 20:25:12.353 wdl.w:ptcp.w:call-trgt-60.t:call-trgt_plot_motifs_allele INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:25:12.353 wdl.w:ptcp.w:call-trgt-60.t:call-trgt_plot_motifs_allele INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:25:12.353 wdl.w:ptcp.w:call-trgt-60.t:call-trgt_plot_motifs_allele INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:25:12.353 wdl.w:ptcp.w:call-trgt-60.t:call-trgt_plot_motifs_allele INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2157.trgt.sorted.spanning.bam.bai"
2025-09-15 20:25:12.353 wdl.w:ptcp.w:call-trgt-60.t:call-trgt_plot_motifs_allele INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2157.trgt.sorted.spanning.bam"
2025-09-15 20:25:12.353 wdl.w:ptcp.w:call-trgt-60.t:call-trgt_plot_motifs_allele INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2157.trgt.vcf"
2025-09-15 20:25:12.353 wdl.w:ptcp.w:call-trgt-60.t:call-trgt_plot_motifs_allele INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2157"
2025-09-15 20:25:12.354 wdl.w:ptcp.w:call-trgt-60.t:call-trgt_plot_motifs_allele INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:25:12.354 wdl.w:ptcp.w:call-trgt-60.t:call-trgt_plot_motifs_allele INFO eval :: name: "plot_type", value: "allele"
2025-09-15 20:25:12.354 wdl.w:ptcp.w:call-trgt-60.t:call-trgt_plot_motifs_allele INFO eval :: name: "show", value: "motifs"
2025-09-15 20:25:12.354 wdl.w:ptcp.w:call-trgt-60.t:call-trgt_plot_motifs_allele INFO eval :: name: "threads", value: 1
2025-09-15 20:25:12.354 wdl.w:ptcp.w:call-trgt-60.t:call-trgt_plot_motifs_allele INFO eval :: name: "disk_size", value: 27
2025-09-15 20:25:12.354 wdl.w:ptcp.w:call-trgt-60.t:call-trgt_plot_motifs_allele INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2157.motifs_allele"
2025-09-15 20:25:12.355 wdl.w:ptcp.w:call-trgt-60.t:call-trgt_plot_motifs_allele INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:12.355 wdl.w:ptcp.w:call-trgt-60.t:call-trgt_plot_motifs_allele WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:12.355 wdl.w:ptcp.w:call-trgt-60.t:call-trgt_plot_motifs_allele INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:25:12.355 wdl.w:ptcp.w:call-trgt-60.t:call-trgt_plot_motifs_allele INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:12.422 wdl.w:ptcp.w:call-trgt-64.t:call-trgt_plot_motifs_allele INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2161.motifs_allele.trgt_plots.zip"
2025-09-15 20:25:12.445 wdl.w:ptcp.w:call-trgt-60.t:call-trgt_plot_motifs_allele INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-60/call-trgt_plot_motifs_allele/_singularity_tmpdir_hl539mg4"
2025-09-15 20:25:12.446 wdl.w:ptcp.w:call-trgt-60.t:call-trgt_plot_motifs_allele INFO Slurm invocation: srun --job-name call-trgt_plot_motifs_allele --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-60/call-trgt_plot_motifs_allele/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-60/call-trgt_plot_motifs_allele/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-60/call-trgt_plot_motifs_allele/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-60/call-trgt_plot_motifs_allele/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-60/call-trgt_genotype/out/m84036_250809_035451_s4.bc2157.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2157.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-60/call-trgt_genotype/out/m84036_250809_035451_s4.bc2157.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2157.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-60/call-trgt_genotype/out/m84036_250809_035451_s4.bc2157.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2157.trgt.sorted.spanning.bam.bai:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-60/call-trgt_plot_motifs_allele/_singularity_tmpdir_hl539mg4/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-60/call-trgt_plot_motifs_allele/_singularity_tmpdir_hl539mg4/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:12.472 wdl.w:ptcp.w:call-trgt-60.t:call-trgt_plot_motifs_allele NOTICE slurm_singularity run :: pid: 1205148, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-60/call-trgt_plot_motifs_allele/slurm_singularity.log.txt"
2025-09-15 20:25:12.516 wdl.w:ptcp.w:call-trgt-61.t:call-trgt_plot_motifs_allele INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2158.motifs_allele.trgt_plots.zip"
2025-09-15 20:25:12.545 wdl.w:ptcp.w:call-trgt-64.t:call-trgt_plot_motifs_allele NOTICE done
2025-09-15 20:25:12.552 wdl.w:ptcp.w:call-trgt-64 NOTICE finish :: job: "call-trgt_plot_motifs_allele"
2025-09-15 20:25:12.552 wdl.w:ptcp.w:call-trgt-64 INFO output :: job: "call-trgt_plot_motifs_allele", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-64/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2161.motifs_allele.trgt_plots.zip"}
2025-09-15 20:25:12.552 wdl.w:ptcp.w:call-trgt-64 INFO visit :: node: "output-images_motifs_allele", values: {"images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-64/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2161.motifs_allele.trgt_plots.zip"}
2025-09-15 20:25:12.558 wdl.w:ptcp.w:call-trgt-60.t:call-trgt_plot_motifs_waterfall NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-60/call-trgt_plot_motifs_waterfall", thread: 140610895857216
2025-09-15 20:25:12.586 wdl.w:ptcp.w:call-trgt-60.t:call-trgt_plot_motifs_waterfall INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:12.587 wdl.w:ptcp.w:call-trgt-60.t:call-trgt_plot_motifs_waterfall INFO input :: name: "waterfall", value: true
2025-09-15 20:25:12.587 wdl.w:ptcp.w:call-trgt-60.t:call-trgt_plot_motifs_waterfall INFO input :: name: "methylation", value: false
2025-09-15 20:25:12.587 wdl.w:ptcp.w:call-trgt-60.t:call-trgt_plot_motifs_waterfall INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:25:12.587 wdl.w:ptcp.w:call-trgt-60.t:call-trgt_plot_motifs_waterfall INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:25:12.587 wdl.w:ptcp.w:call-trgt-60.t:call-trgt_plot_motifs_waterfall INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:25:12.587 wdl.w:ptcp.w:call-trgt-60.t:call-trgt_plot_motifs_waterfall INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2157.trgt.sorted.spanning.bam.bai"
2025-09-15 20:25:12.587 wdl.w:ptcp.w:call-trgt-60.t:call-trgt_plot_motifs_waterfall INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2157.trgt.sorted.spanning.bam"
2025-09-15 20:25:12.587 wdl.w:ptcp.w:call-trgt-60.t:call-trgt_plot_motifs_waterfall INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2157.trgt.vcf"
2025-09-15 20:25:12.587 wdl.w:ptcp.w:call-trgt-60.t:call-trgt_plot_motifs_waterfall INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2157"
2025-09-15 20:25:12.588 wdl.w:ptcp.w:call-trgt-60.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:25:12.588 wdl.w:ptcp.w:call-trgt-60.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "plot_type", value: "waterfall"
2025-09-15 20:25:12.588 wdl.w:ptcp.w:call-trgt-60.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "show", value: "motifs"
2025-09-15 20:25:12.588 wdl.w:ptcp.w:call-trgt-60.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "threads", value: 1
2025-09-15 20:25:12.588 wdl.w:ptcp.w:call-trgt-60.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "disk_size", value: 27
2025-09-15 20:25:12.588 wdl.w:ptcp.w:call-trgt-60.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2157.motifs_waterfall"
2025-09-15 20:25:12.589 wdl.w:ptcp.w:call-trgt-60.t:call-trgt_plot_motifs_waterfall INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:12.589 wdl.w:ptcp.w:call-trgt-60.t:call-trgt_plot_motifs_waterfall WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:12.589 wdl.w:ptcp.w:call-trgt-60.t:call-trgt_plot_motifs_waterfall INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:25:12.589 wdl.w:ptcp.w:call-trgt-60.t:call-trgt_plot_motifs_waterfall INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:12.639 wdl.w:ptcp.w:call-trgt-61.t:call-trgt_plot_motifs_allele NOTICE done
2025-09-15 20:25:12.644 wdl.w:ptcp.w:call-trgt-61 NOTICE finish :: job: "call-trgt_plot_motifs_allele"
2025-09-15 20:25:12.645 wdl.w:ptcp.w:call-trgt-61 INFO output :: job: "call-trgt_plot_motifs_allele", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-61/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2158.motifs_allele.trgt_plots.zip"}
2025-09-15 20:25:12.645 wdl.w:ptcp.w:call-trgt-61 INFO visit :: node: "output-images_motifs_allele", values: {"images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-61/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2158.motifs_allele.trgt_plots.zip"}
2025-09-15 20:25:12.652 wdl.w:ptcp.t:call-tar_outputs-16 NOTICE task setup :: name: "tar_outputs", source: "./common.wdl", line: 279, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-16", thread: 140607674631744
2025-09-15 20:25:12.664 wdl.w:ptcp.w:call-trgt-60.t:call-trgt_plot_motifs_waterfall INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-60/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_e3hegkmw"
2025-09-15 20:25:12.664 wdl.w:ptcp.w:call-trgt-60.t:call-trgt_plot_motifs_waterfall INFO Slurm invocation: srun --job-name call-trgt_plot_motifs_waterfall --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-60/call-trgt_plot_motifs_waterfall/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-60/call-trgt_plot_motifs_waterfall/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-60/call-trgt_plot_motifs_waterfall/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-60/call-trgt_plot_motifs_waterfall/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-60/call-trgt_genotype/out/m84036_250809_035451_s4.bc2157.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2157.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-60/call-trgt_genotype/out/m84036_250809_035451_s4.bc2157.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2157.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-60/call-trgt_genotype/out/m84036_250809_035451_s4.bc2157.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2157.trgt.sorted.spanning.bam.bai:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-60/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_e3hegkmw/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-60/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_e3hegkmw/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:12.675 wdl.w:ptcp.w:call-trgt-60.t:call-trgt_plot_motifs_waterfall NOTICE slurm_singularity run :: pid: 1205151, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-60/call-trgt_plot_motifs_waterfall/slurm_singularity.log.txt"
2025-09-15 20:25:12.682 wdl.w:ptcp.t:call-tar_outputs-16 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:12.682 wdl.w:ptcp.t:call-tar_outputs-16 INFO input :: name: "sawfish_vcf_tbi", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2113.sv.vcf.gz.tbi"
2025-09-15 20:25:12.682 wdl.w:ptcp.t:call-tar_outputs-16 INFO input :: name: "sawfish_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2113.sv.vcf.gz"
2025-09-15 20:25:12.682 wdl.w:ptcp.t:call-tar_outputs-16 INFO input :: name: "f8_json", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2113.f8inversion.json"
2025-09-15 20:25:12.682 wdl.w:ptcp.t:call-tar_outputs-16 INFO input :: name: "paraphase_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2113.paraphase.bam.bai"
2025-09-15 20:25:12.682 wdl.w:ptcp.t:call-tar_outputs-16 INFO input :: name: "paraphase_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2113.paraphase.bam"
2025-09-15 20:25:12.682 wdl.w:ptcp.t:call-tar_outputs-16 INFO input :: name: "paraphase_json", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2113.paraphase.json"
2025-09-15 20:25:12.682 wdl.w:ptcp.t:call-tar_outputs-16 INFO input :: name: "trgt_spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2113.trgt.sorted.spanning.bam.bai"
2025-09-15 20:25:12.682 wdl.w:ptcp.t:call-tar_outputs-16 INFO input :: name: "trgt_spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2113.trgt.sorted.spanning.bam"
2025-09-15 20:25:12.683 wdl.w:ptcp.t:call-tar_outputs-16 INFO input :: name: "trgt_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2113.trgt.vcf"
2025-09-15 20:25:12.683 wdl.w:ptcp.t:call-tar_outputs-16 INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2113.mapped.bam.bai"
2025-09-15 20:25:12.683 wdl.w:ptcp.t:call-tar_outputs-16 INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2113.mapped.bam"
2025-09-15 20:25:12.683 wdl.w:ptcp.t:call-tar_outputs-16 INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2113"
2025-09-15 20:25:12.683 wdl.w:ptcp.t:call-tar_outputs-16 INFO eval :: name: "threads", value: 1
2025-09-15 20:25:12.683 wdl.w:ptcp.t:call-tar_outputs-16 INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:25:12.683 wdl.w:ptcp.t:call-tar_outputs-16 INFO eval :: name: "disk_size", value: 6
2025-09-15 20:25:12.683 wdl.w:ptcp.t:call-tar_outputs-16 INFO eval :: name: "output_tarball", value: "m84036_250809_035451_s4.bc2113.tar"
2025-09-15 20:25:12.684 wdl.w:ptcp.t:call-tar_outputs-16 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:12.684 wdl.w:ptcp.t:call-tar_outputs-16 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:12.684 wdl.w:ptcp.t:call-tar_outputs-16 INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:25:12.684 wdl.w:ptcp.t:call-tar_outputs-16 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:12.775 wdl.w:ptcp.t:call-tar_outputs-16 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 17, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-16/_singularity_tmpdir_m5lhdoxe"
2025-09-15 20:25:12.775 wdl.w:ptcp.t:call-tar_outputs-16 INFO Slurm invocation: srun --job-name call-tar_outputs-16 --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-16/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-16/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-16/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-16/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-16/out/m84036_250809_035451_s4.bc2113.f8inversion.json:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2113.f8inversion.json:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-16/out/m84036_250809_035451_s4.bc2113.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2113.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-16/out/m84036_250809_035451_s4.bc2113.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2113.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-16/out/m84036_250809_035451_s4.bc2113_paraphase/m84036_250809_035451_s4.bc2113.paraphase.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2113.paraphase.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-16/out/m84036_250809_035451_s4.bc2113_paraphase/m84036_250809_035451_s4.bc2113.paraphase.json:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2113.paraphase.json:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-16/out/m84036_250809_035451_s4.bc2113_paraphase/m84036_250809_035451_s4.bc2113.paraphase.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2113.paraphase.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-16/out/m84036_250809_035451_s4.bc2113.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2113.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-16/out/m84036_250809_035451_s4.bc2113.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2113.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-16/out/m84036_250809_035451_s4.bc2113.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2113.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-16/out/m84036_250809_035451_s4.bc2113_sawfish/m84036_250809_035451_s4.bc2113.sv.vcf.gz.tbi:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2113.sv.vcf.gz.tbi:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-16/out/m84036_250809_035451_s4.bc2113_sawfish/m84036_250809_035451_s4.bc2113.sv.vcf.gz:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2113.sv.vcf.gz:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-16/_singularity_tmpdir_m5lhdoxe/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-16/_singularity_tmpdir_m5lhdoxe/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:12.783 wdl.w:ptcp.t:call-tar_outputs-16 NOTICE slurm_singularity run :: pid: 1205153, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-16/slurm_singularity.log.txt"
2025-09-15 20:25:12.961 wdl.w:ptcp.w:call-trgt-60.t:call-trgt_plot_meth_allele.slurm_singularity INFO srun: job 51797956 queued and waiting for resources
2025-09-15 20:25:12.962 wdl.w:ptcp.w:call-trgt-60.t:call-trgt_plot_meth_allele.slurm_singularity INFO srun: job 51797956 has been allocated resources
2025-09-15 20:25:12.962 wdl.w:ptcp.w:call-trgt-60.t:call-trgt_plot_meth_allele.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:12.998 wdl.w:ptcp.w:call-trgt-60.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO srun: job 51797957 queued and waiting for resources
2025-09-15 20:25:12.999 wdl.w:ptcp.w:call-trgt-60.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO srun: job 51797957 has been allocated resources
2025-09-15 20:25:12.999 wdl.w:ptcp.w:call-trgt-60.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:13.481 wdl.w:ptcp.w:call-trgt-60.t:call-trgt_plot_motifs_allele.slurm_singularity INFO srun: job 51797958 queued and waiting for resources
2025-09-15 20:25:13.593 wdl.w:ptcp.w:call-paraphase-46.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for cyp21 for sample m84036_250809_035451_s4.bc2143 at 2025-09-15 20:24:47.693838...
2025-09-15 20:25:13.593 wdl.w:ptcp.w:call-paraphase-46.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for cyp21 for sample m84036_250809_035451_s4.bc2143 at 2025-09-15 20:24:48.596340...
2025-09-15 20:25:13.593 wdl.w:ptcp.w:call-paraphase-46.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for hba for sample m84036_250809_035451_s4.bc2143 at 2025-09-15 20:24:50.603045...
2025-09-15 20:25:13.593 wdl.w:ptcp.w:call-paraphase-46.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for hba for sample m84036_250809_035451_s4.bc2143 at 2025-09-15 20:24:51.047785...
2025-09-15 20:25:13.593 wdl.w:ptcp.w:call-paraphase-46.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for gba for sample m84036_250809_035451_s4.bc2143 at 2025-09-15 20:25:00.718672...
2025-09-15 20:25:13.593 wdl.w:ptcp.w:call-paraphase-46.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for gba for sample m84036_250809_035451_s4.bc2143 at 2025-09-15 20:25:01.270807...
2025-09-15 20:25:13.593 wdl.w:ptcp.w:call-paraphase-46.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for f8inv1 for sample m84036_250809_035451_s4.bc2143 at 2025-09-15 20:25:04.853511...
2025-09-15 20:25:13.593 wdl.w:ptcp.w:call-paraphase-46.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for f8inv1 for sample m84036_250809_035451_s4.bc2143 at 2025-09-15 20:25:04.854278...
2025-09-15 20:25:13.593 wdl.w:ptcp.w:call-paraphase-46.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for f8inv1 for sample m84036_250809_035451_s4.bc2143 at 2025-09-15 20:25:06.741278...
2025-09-15 20:25:13.593 wdl.w:ptcp.w:call-paraphase-46.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for hbb for sample m84036_250809_035451_s4.bc2143 at 2025-09-15 20:25:11.041077...
2025-09-15 20:25:13.593 wdl.w:ptcp.w:call-paraphase-46.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for hbb for sample m84036_250809_035451_s4.bc2143 at 2025-09-15 20:25:11.042388...
2025-09-15 20:25:13.663 wdl.w:ptcp.w:call-trgt-84.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:25:10 [INFO] - Running trgt-4.0.0-429afcd [genotype]
2025-09-15 20:25:13.664 wdl.w:ptcp.w:call-trgt-84.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:25:10 [WARN] - OPDM_ABCD3: Filtered out 7 impure reads
2025-09-15 20:25:13.664 wdl.w:ptcp.w:call-trgt-84.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:25:10 [WARN] - SCA37_DAB1: Filtered out 9 impure reads
2025-09-15 20:25:13.664 wdl.w:ptcp.w:call-trgt-84.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:25:10 [WARN] - NIID_NOTCH2NLC: Filtered out 13 impure reads
2025-09-15 20:25:13.664 wdl.w:ptcp.w:call-trgt-84.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:25:10 [WARN] - SCA2_ATXN2: Filtered out 18 impure reads
2025-09-15 20:25:13.664 wdl.w:ptcp.w:call-trgt-84.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:25:10 [WARN] - DRPLA_ATN1: Filtered out 33 impure reads
2025-09-15 20:25:13.664 wdl.w:ptcp.w:call-trgt-84.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:25:10 [WARN] - OPDM4_RILPL1: Filtered out 5 impure reads
2025-09-15 20:25:13.664 wdl.w:ptcp.w:call-trgt-84.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:25:10 [WARN] - SCA8_ATXN8OS: Filtered out 17 impure reads
2025-09-15 20:25:13.664 wdl.w:ptcp.w:call-trgt-84.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:25:10 [WARN] - SCA3_ATXN3: Filtered out 20 impure reads
2025-09-15 20:25:13.664 wdl.w:ptcp.w:call-trgt-84.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:25:10 [WARN] - OPMD_PABPN1: Filtered out 15 impure reads
2025-09-15 20:25:13.664 wdl.w:ptcp.w:call-trgt-84.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:25:10 [WARN] - SCA31_BEAN1: Filtered out 8 impure reads
2025-09-15 20:25:13.664 wdl.w:ptcp.w:call-trgt-84.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:25:10 [WARN] - SCA27B_FGF14: Filtered out 27 impure reads
2025-09-15 20:25:13.664 wdl.w:ptcp.w:call-trgt-84.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:25:11 [WARN] - HDL2_JPH3: Filtered out 17 impure reads
2025-09-15 20:25:13.664 wdl.w:ptcp.w:call-trgt-84.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:25:11 [WARN] - SCA4_ZFHX3: Filtered out 27 impure reads
2025-09-15 20:25:13.664 wdl.w:ptcp.w:call-trgt-84.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:25:11 [WARN] - FECD3_TCF4: Filtered out 24 impure reads
2025-09-15 20:25:13.664 wdl.w:ptcp.w:call-trgt-84.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:25:11 [WARN] - DM1_DMPK: Filtered out 28 impure reads
2025-09-15 20:25:13.664 wdl.w:ptcp.w:call-trgt-84.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:25:11 [WARN] - SCA6_CACNA1A: Filtered out 18 impure reads
2025-09-15 20:25:13.665 wdl.w:ptcp.w:call-trgt-84.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:25:11 [WARN] - OPDM2_GIPC1: Filtered out 18 impure reads
2025-09-15 20:25:13.665 wdl.w:ptcp.w:call-trgt-84.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:25:11 [WARN] - FRA2A_AFF3: Filtered out 9 impure reads
2025-09-15 20:25:13.665 wdl.w:ptcp.w:call-trgt-84.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:25:12 [WARN] - CJD_PRNP: Filtered out 15 impure reads
2025-09-15 20:25:13.665 wdl.w:ptcp.w:call-trgt-84.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:25:12 [WARN] - SD5_HOXD13: Filtered out 16 impure reads
2025-09-15 20:25:13.665 wdl.w:ptcp.w:call-trgt-84.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:25:12 [WARN] - SCA10_ATXN10: Filtered out 13 impure reads
2025-09-15 20:25:13.665 wdl.w:ptcp.w:call-trgt-84.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:25:12 [WARN] - EPM1_CSTB: Filtered out 14 impure reads
2025-09-15 20:25:13.665 wdl.w:ptcp.w:call-trgt-84.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:25:12 [WARN] - SCA36_NOP56: Filtered out 21 impure reads
2025-09-15 20:25:13.665 wdl.w:ptcp.w:call-trgt-84.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:25:12 [WARN] - SCA7_ATXN7: Filtered out 16 impure reads
2025-09-15 20:25:13.665 wdl.w:ptcp.w:call-trgt-84.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:25:12 [WARN] - CCHS_PHOX2B: Filtered out 1 impure reads
2025-09-15 20:25:13.665 wdl.w:ptcp.w:call-trgt-84.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:25:12 [WARN] - DM2_CNBP: Filtered out 3 impure reads
2025-09-15 20:25:13.665 wdl.w:ptcp.w:call-trgt-84.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:25:12 [WARN] - SCA12_PPP2R2B: Filtered out 16 impure reads
2025-09-15 20:25:13.665 wdl.w:ptcp.w:call-trgt-84.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:25:12 [WARN] - FAME1_SAMD12: Filtered out 17 impure reads
2025-09-15 20:25:13.665 wdl.w:ptcp.w:call-trgt-84.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:25:12 [WARN] - HD_HTT: Filtered out 15 impure reads
2025-09-15 20:25:13.665 wdl.w:ptcp.w:call-trgt-84.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:25:12 [WARN] - CANVAS_RFC1: Filtered out 3 impure reads
2025-09-15 20:25:13.665 wdl.w:ptcp.w:call-trgt-84.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:25:12 [WARN] - SCA17_TBP: Filtered out 5 impure reads
2025-09-15 20:25:13.665 wdl.w:ptcp.w:call-trgt-84.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:25:12 [WARN] - OPDM1_LRP12: Filtered out 9 impure reads
2025-09-15 20:25:13.665 wdl.w:ptcp.w:call-trgt-84.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:25:12 [WARN] - SBMA_AR: Filtered out 17 impure reads
2025-09-15 20:25:13.665 wdl.w:ptcp.w:call-trgt-84.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:25:12 [WARN] - SCA1_ATXN1: Filtered out 25 impure reads
2025-09-15 20:25:13.665 wdl.w:ptcp.w:call-trgt-84.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:25:13 [WARN] - FXS_FMR1: Filtered out 2 impure reads
2025-09-15 20:25:13.665 wdl.w:ptcp.w:call-trgt-84.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:25:13 [WARN] - FRAXE_AFF2: Filtered out 13 impure reads
2025-09-15 20:25:13.666 wdl.w:ptcp.w:call-trgt-84.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:25:13 [WARN] - FRDA_FXN: Filtered out 3 impure reads
2025-09-15 20:25:13.666 wdl.w:ptcp.w:call-trgt-84.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:25:13 [WARN] - FTDALS1_C9orf72: Filtered out 18 impure reads
2025-09-15 20:25:13.666 wdl.w:ptcp.w:call-trgt-84.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:25:13 [INFO] - Total execution time: 3.41s
2025-09-15 20:25:13.666 wdl.w:ptcp.w:call-trgt-84.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:25:13 [INFO] - trgt end
2025-09-15 20:25:13.682 wdl.w:ptcp.w:call-trgt-60.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO srun: job 51797959 queued and waiting for resources
2025-09-15 20:25:13.791 wdl.w:ptcp.t:call-tar_outputs-16.slurm_singularity INFO srun: job 51797960 queued and waiting for resources
2025-09-15 20:25:14.047 wdl.w:ptcp.w:call-trgt-73.t:call-trgt_genotype INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2170.trgt.vcf"
2025-09-15 20:25:14.050 wdl.w:ptcp.w:call-trgt-73.t:call-trgt_genotype INFO output :: name: "spanning_bam", value: "m84036_250809_035451_s4.bc2170.trgt.sorted.spanning.bam"
2025-09-15 20:25:14.051 wdl.w:ptcp.w:call-trgt-73.t:call-trgt_genotype INFO output :: name: "spanning_bam_bai", value: "m84036_250809_035451_s4.bc2170.trgt.sorted.spanning.bam.bai"
2025-09-15 20:25:14.122 wdl.w:ptcp.w:call-trgt-73.t:call-trgt_genotype NOTICE done
2025-09-15 20:25:14.127 wdl.w:ptcp.w:call-trgt-73 NOTICE finish :: job: "call-trgt_genotype"
2025-09-15 20:25:14.127 wdl.w:ptcp.w:call-trgt-73 INFO output :: job: "call-trgt_genotype", values: {"spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-73/call-trgt_genotype/out/m84036_250809_035451_s4.bc2170.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-73/call-trgt_genotype/out/m84036_250809_035451_s4.bc2170.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-73/call-trgt_genotype/out/m84036_250809_035451_s4.bc2170.trgt.vcf"}
2025-09-15 20:25:14.127 wdl.w:ptcp.w:call-trgt-73 NOTICE ready :: job: "call-trgt_plot_meth_allele", callee: "trgt_plot"
2025-09-15 20:25:14.127 wdl.w:ptcp.w:call-trgt-73 INFO input :: job: "call-trgt_plot_meth_allele", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": false, "methylation": true, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-73/call-trgt_genotype/out/m84036_250809_035451_s4.bc2170.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-73/call-trgt_genotype/out/m84036_250809_035451_s4.bc2170.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-73/call-trgt_genotype/out/m84036_250809_035451_s4.bc2170.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2170"}
2025-09-15 20:25:14.128 wdl.w:ptcp.w:call-trgt-73 NOTICE ready :: job: "call-trgt_plot_meth_waterfall", callee: "trgt_plot"
2025-09-15 20:25:14.128 wdl.w:ptcp.w:call-trgt-73 INFO input :: job: "call-trgt_plot_meth_waterfall", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": true, "methylation": true, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-73/call-trgt_genotype/out/m84036_250809_035451_s4.bc2170.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-73/call-trgt_genotype/out/m84036_250809_035451_s4.bc2170.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-73/call-trgt_genotype/out/m84036_250809_035451_s4.bc2170.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2170"}
2025-09-15 20:25:14.129 wdl.w:ptcp.w:call-trgt-73 NOTICE ready :: job: "call-trgt_plot_motifs_allele", callee: "trgt_plot"
2025-09-15 20:25:14.129 wdl.w:ptcp.w:call-trgt-73 INFO input :: job: "call-trgt_plot_motifs_allele", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": false, "methylation": false, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-73/call-trgt_genotype/out/m84036_250809_035451_s4.bc2170.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-73/call-trgt_genotype/out/m84036_250809_035451_s4.bc2170.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-73/call-trgt_genotype/out/m84036_250809_035451_s4.bc2170.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2170"}
2025-09-15 20:25:14.130 wdl.w:ptcp.w:call-trgt-73 NOTICE ready :: job: "call-trgt_plot_motifs_waterfall", callee: "trgt_plot"
2025-09-15 20:25:14.130 wdl.w:ptcp.w:call-trgt-73 INFO input :: job: "call-trgt_plot_motifs_waterfall", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": true, "methylation": false, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-73/call-trgt_genotype/out/m84036_250809_035451_s4.bc2170.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-73/call-trgt_genotype/out/m84036_250809_035451_s4.bc2170.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-73/call-trgt_genotype/out/m84036_250809_035451_s4.bc2170.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2170"}
2025-09-15 20:25:14.131 wdl.w:ptcp.w:call-trgt-73 INFO visit :: node: "output-spanning_bam", values: {"spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-73/call-trgt_genotype/out/m84036_250809_035451_s4.bc2170.trgt.sorted.spanning.bam"}
2025-09-15 20:25:14.131 wdl.w:ptcp.w:call-trgt-73 INFO visit :: node: "output-spanning_bam_bai", values: {"spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-73/call-trgt_genotype/out/m84036_250809_035451_s4.bc2170.trgt.sorted.spanning.bam.bai"}
2025-09-15 20:25:14.131 wdl.w:ptcp.w:call-trgt-73 INFO visit :: node: "output-vcf", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-73/call-trgt_genotype/out/m84036_250809_035451_s4.bc2170.trgt.vcf"}
2025-09-15 20:25:14.134 wdl.w:ptcp.w:call-trgt-84.t:call-trgt_genotype INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2181.trgt.vcf"
2025-09-15 20:25:14.135 wdl.w:ptcp.w:call-paraphase-77.t:call-run_paraphase NOTICE task setup :: name: "run_paraphase", source: "./paraphase.wdl", line: 127, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-77/call-run_paraphase", thread: 140610870679104
2025-09-15 20:25:14.136 wdl.w:ptcp.w:call-trgt-84.t:call-get_reads_overlapping_repeats INFO output :: name: "reads_overlapping_repeats", value: "m84036_250809_035451_s4.bc2181.repeats.bam"
2025-09-15 20:25:14.138 wdl.w:ptcp.w:call-trgt-84.t:call-trgt_genotype INFO output :: name: "spanning_bam", value: "m84036_250809_035451_s4.bc2181.trgt.sorted.spanning.bam"
2025-09-15 20:25:14.140 wdl.w:ptcp.w:call-trgt-84.t:call-trgt_genotype INFO output :: name: "spanning_bam_bai", value: "m84036_250809_035451_s4.bc2181.trgt.sorted.spanning.bam.bai"
2025-09-15 20:25:14.141 wdl.w:ptcp.w:call-trgt-84.t:call-get_reads_overlapping_repeats INFO output :: name: "reads_overlapping_repeats_bai", value: "m84036_250809_035451_s4.bc2181.repeats.bam.bai"
2025-09-15 20:25:14.154 wdl.w:ptcp.w:call-paraphase-77.t:call-run_paraphase INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:14.154 wdl.w:ptcp.w:call-paraphase-77.t:call-run_paraphase INFO input :: name: "annotation_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf"
2025-09-15 20:25:14.154 wdl.w:ptcp.w:call-paraphase-77.t:call-run_paraphase INFO input :: name: "genome_version", value: "38"
2025-09-15 20:25:14.154 wdl.w:ptcp.w:call-paraphase-77.t:call-run_paraphase INFO input :: name: "config_file", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/paraphase_config.GRCh38.yaml"
2025-09-15 20:25:14.154 wdl.w:ptcp.w:call-paraphase-77.t:call-run_paraphase INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:25:14.154 wdl.w:ptcp.w:call-paraphase-77.t:call-run_paraphase INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:25:14.154 wdl.w:ptcp.w:call-paraphase-77.t:call-run_paraphase INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2174.mapped.bam.bai"
2025-09-15 20:25:14.154 wdl.w:ptcp.w:call-paraphase-77.t:call-run_paraphase INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2174.mapped.bam"
2025-09-15 20:25:14.154 wdl.w:ptcp.w:call-paraphase-77.t:call-run_paraphase INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2174"
2025-09-15 20:25:14.154 wdl.w:ptcp.w:call-paraphase-77.t:call-run_paraphase INFO eval :: name: "threads", value: 4
2025-09-15 20:25:14.155 wdl.w:ptcp.w:call-paraphase-77.t:call-run_paraphase INFO eval :: name: "mem_gb", value: 8
2025-09-15 20:25:14.155 wdl.w:ptcp.w:call-paraphase-77.t:call-run_paraphase INFO eval :: name: "disk_size", value: 27
2025-09-15 20:25:14.155 wdl.w:ptcp.w:call-paraphase-77.t:call-run_paraphase INFO eval :: name: "out_dir", value: "m84036_250809_035451_s4.bc2174_paraphase"
2025-09-15 20:25:14.155 wdl.w:ptcp.w:call-paraphase-77.t:call-run_paraphase INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 4, memory_reservation: 8000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:14.155 wdl.w:ptcp.w:call-paraphase-77.t:call-run_paraphase WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:14.156 wdl.w:ptcp.w:call-paraphase-77.t:call-run_paraphase INFO provisioned :: seconds_waited: 0, cpu: 4, mem_bytes: 8000000000
2025-09-15 20:25:14.156 wdl.w:ptcp.w:call-paraphase-77.t:call-run_paraphase INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:14.216 wdl.w:ptcp.w:call-trgt-73.t:call-get_reads_overlapping_repeats INFO output :: name: "reads_overlapping_repeats", value: "m84036_250809_035451_s4.bc2170.repeats.bam"
2025-09-15 20:25:14.221 wdl.w:ptcp.w:call-trgt-73.t:call-get_reads_overlapping_repeats INFO output :: name: "reads_overlapping_repeats_bai", value: "m84036_250809_035451_s4.bc2170.repeats.bam.bai"
2025-09-15 20:25:14.223 wdl.w:ptcp.w:call-trgt-84.t:call-get_reads_overlapping_repeats NOTICE done
2025-09-15 20:25:14.228 wdl.w:ptcp.w:call-trgt-84 NOTICE finish :: job: "call-get_reads_overlapping_repeats"
2025-09-15 20:25:14.228 wdl.w:ptcp.w:call-trgt-84 INFO output :: job: "call-get_reads_overlapping_repeats", values: {"reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-84/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2181.repeats.bam.bai", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-84/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2181.repeats.bam"}
2025-09-15 20:25:14.229 wdl.w:ptcp.w:call-trgt-84 INFO visit :: node: "output-reads_overlapping_repeats", values: {"reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-84/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2181.repeats.bam"}
2025-09-15 20:25:14.229 wdl.w:ptcp.w:call-trgt-84 INFO visit :: node: "output-reads_overlapping_repeats_bai", values: {"reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-84/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2181.repeats.bam.bai"}
2025-09-15 20:25:14.235 wdl.w:ptcp.w:call-trgt-84.t:call-trgt_genotype NOTICE done
2025-09-15 20:25:14.236 wdl.w:ptcp.t:call-tar_outputs-25 NOTICE task setup :: name: "tar_outputs", source: "./common.wdl", line: 279, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-25", thread: 140612506469952
2025-09-15 20:25:14.237 wdl.w:ptcp.w:call-paraphase-77.t:call-run_paraphase INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-77/call-run_paraphase/_singularity_tmpdir_4_lwhv7j"
2025-09-15 20:25:14.238 wdl.w:ptcp.w:call-paraphase-77.t:call-run_paraphase INFO Slurm invocation: srun --job-name call-run_paraphase --partition compute,compute9 --cpus-per-task 4 --mem 7629M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-77/call-run_paraphase/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-77/call-run_paraphase/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-77/call-run_paraphase/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-77/call-run_paraphase/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/variant_list/variant_list.GRCh38.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-77/out/m84036_250809_035451_s4.bc2174.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2174.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-77/out/m84036_250809_035451_s4.bc2174.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2174.mapped.bam.bai:ro --bind /ptcp/meta/paraphase/paraphase_config.GRCh38.yaml:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/paraphase_config.GRCh38.yaml:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-77/call-run_paraphase/_singularity_tmpdir_4_lwhv7j/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-77/call-run_paraphase/_singularity_tmpdir_4_lwhv7j/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:14.239 wdl.w:ptcp.w:call-trgt-84 NOTICE finish :: job: "call-trgt_genotype"
2025-09-15 20:25:14.240 wdl.w:ptcp.w:call-trgt-84 INFO output :: job: "call-trgt_genotype", values: {"spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-84/call-trgt_genotype/out/m84036_250809_035451_s4.bc2181.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-84/call-trgt_genotype/out/m84036_250809_035451_s4.bc2181.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-84/call-trgt_genotype/out/m84036_250809_035451_s4.bc2181.trgt.vcf"}
2025-09-15 20:25:14.241 wdl.w:ptcp.w:call-trgt-84 NOTICE ready :: job: "call-trgt_plot_meth_allele", callee: "trgt_plot"
2025-09-15 20:25:14.241 wdl.w:ptcp.w:call-trgt-84 INFO input :: job: "call-trgt_plot_meth_allele", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": false, "methylation": true, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-84/call-trgt_genotype/out/m84036_250809_035451_s4.bc2181.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-84/call-trgt_genotype/out/m84036_250809_035451_s4.bc2181.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-84/call-trgt_genotype/out/m84036_250809_035451_s4.bc2181.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2181"}
2025-09-15 20:25:14.243 wdl.w:ptcp.w:call-trgt-84 NOTICE ready :: job: "call-trgt_plot_meth_waterfall", callee: "trgt_plot"
2025-09-15 20:25:14.243 wdl.w:ptcp.w:call-trgt-84 INFO input :: job: "call-trgt_plot_meth_waterfall", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": true, "methylation": true, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-84/call-trgt_genotype/out/m84036_250809_035451_s4.bc2181.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-84/call-trgt_genotype/out/m84036_250809_035451_s4.bc2181.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-84/call-trgt_genotype/out/m84036_250809_035451_s4.bc2181.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2181"}
2025-09-15 20:25:14.244 wdl.w:ptcp.w:call-trgt-84 NOTICE ready :: job: "call-trgt_plot_motifs_allele", callee: "trgt_plot"
2025-09-15 20:25:14.244 wdl.w:ptcp.w:call-trgt-84 INFO input :: job: "call-trgt_plot_motifs_allele", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": false, "methylation": false, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-84/call-trgt_genotype/out/m84036_250809_035451_s4.bc2181.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-84/call-trgt_genotype/out/m84036_250809_035451_s4.bc2181.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-84/call-trgt_genotype/out/m84036_250809_035451_s4.bc2181.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2181"}
2025-09-15 20:25:14.244 wdl.w:ptcp.w:call-trgt-84 NOTICE ready :: job: "call-trgt_plot_motifs_waterfall", callee: "trgt_plot"
2025-09-15 20:25:14.244 wdl.w:ptcp.w:call-trgt-84 INFO input :: job: "call-trgt_plot_motifs_waterfall", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": true, "methylation": false, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-84/call-trgt_genotype/out/m84036_250809_035451_s4.bc2181.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-84/call-trgt_genotype/out/m84036_250809_035451_s4.bc2181.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-84/call-trgt_genotype/out/m84036_250809_035451_s4.bc2181.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2181"}
2025-09-15 20:25:14.245 wdl.w:ptcp.w:call-trgt-84 INFO visit :: node: "output-spanning_bam", values: {"spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-84/call-trgt_genotype/out/m84036_250809_035451_s4.bc2181.trgt.sorted.spanning.bam"}
2025-09-15 20:25:14.245 wdl.w:ptcp.w:call-trgt-84 INFO visit :: node: "output-spanning_bam_bai", values: {"spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-84/call-trgt_genotype/out/m84036_250809_035451_s4.bc2181.trgt.sorted.spanning.bam.bai"}
2025-09-15 20:25:14.245 wdl.w:ptcp.w:call-trgt-84 INFO visit :: node: "output-vcf", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-84/call-trgt_genotype/out/m84036_250809_035451_s4.bc2181.trgt.vcf"}
2025-09-15 20:25:14.247 wdl.w:ptcp.w:call-sawfish-77.t:call-run_sawfish NOTICE task setup :: name: "run_sawfish", source: "./sawfish.wdl", line: 83, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-77/call-run_sawfish", thread: 140611424335424
2025-09-15 20:25:14.264 wdl.w:ptcp.t:call-tar_outputs-25 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:14.264 wdl.w:ptcp.t:call-tar_outputs-25 INFO input :: name: "sawfish_vcf_tbi", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2122.sv.vcf.gz.tbi"
2025-09-15 20:25:14.264 wdl.w:ptcp.t:call-tar_outputs-25 INFO input :: name: "sawfish_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2122.sv.vcf.gz"
2025-09-15 20:25:14.264 wdl.w:ptcp.t:call-tar_outputs-25 INFO input :: name: "f8_json", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2122.f8inversion.json"
2025-09-15 20:25:14.264 wdl.w:ptcp.t:call-tar_outputs-25 INFO input :: name: "paraphase_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2122.paraphase.bam.bai"
2025-09-15 20:25:14.264 wdl.w:ptcp.t:call-tar_outputs-25 INFO input :: name: "paraphase_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2122.paraphase.bam"
2025-09-15 20:25:14.264 wdl.w:ptcp.t:call-tar_outputs-25 INFO input :: name: "paraphase_json", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2122.paraphase.json"
2025-09-15 20:25:14.264 wdl.w:ptcp.t:call-tar_outputs-25 INFO input :: name: "trgt_spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2122.trgt.sorted.spanning.bam.bai"
2025-09-15 20:25:14.264 wdl.w:ptcp.t:call-tar_outputs-25 INFO input :: name: "trgt_spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2122.trgt.sorted.spanning.bam"
2025-09-15 20:25:14.265 wdl.w:ptcp.t:call-tar_outputs-25 INFO input :: name: "trgt_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2122.trgt.vcf"
2025-09-15 20:25:14.265 wdl.w:ptcp.t:call-tar_outputs-25 INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2122.mapped.bam.bai"
2025-09-15 20:25:14.265 wdl.w:ptcp.t:call-tar_outputs-25 INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2122.mapped.bam"
2025-09-15 20:25:14.265 wdl.w:ptcp.t:call-tar_outputs-25 INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2122"
2025-09-15 20:25:14.265 wdl.w:ptcp.t:call-tar_outputs-25 INFO eval :: name: "threads", value: 1
2025-09-15 20:25:14.265 wdl.w:ptcp.t:call-tar_outputs-25 INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:25:14.265 wdl.w:ptcp.t:call-tar_outputs-25 INFO eval :: name: "disk_size", value: 6
2025-09-15 20:25:14.265 wdl.w:ptcp.t:call-tar_outputs-25 INFO eval :: name: "output_tarball", value: "m84036_250809_035451_s4.bc2122.tar"
2025-09-15 20:25:14.266 wdl.w:ptcp.t:call-tar_outputs-25 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:14.266 wdl.w:ptcp.w:call-sawfish-77.t:call-run_sawfish INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:14.266 wdl.w:ptcp.t:call-tar_outputs-25 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:14.266 wdl.w:ptcp.w:call-sawfish-77.t:call-run_sawfish INFO input :: name: "genome_version", value: "38"
2025-09-15 20:25:14.267 wdl.w:ptcp.w:call-sawfish-77.t:call-run_sawfish INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:25:14.267 wdl.w:ptcp.w:call-sawfish-77.t:call-run_sawfish INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:25:14.267 wdl.w:ptcp.w:call-sawfish-77.t:call-run_sawfish INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2174.mapped.bam.bai"
2025-09-15 20:25:14.267 wdl.w:ptcp.w:call-sawfish-77.t:call-run_sawfish INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2174.mapped.bam"
2025-09-15 20:25:14.267 wdl.w:ptcp.w:call-sawfish-77.t:call-run_sawfish INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2174"
2025-09-15 20:25:14.268 wdl.w:ptcp.w:call-sawfish-77.t:call-run_sawfish INFO eval :: name: "mem_gb", value: 32
2025-09-15 20:25:14.268 wdl.w:ptcp.w:call-sawfish-77.t:call-run_sawfish INFO eval :: name: "threads", value: 16
2025-09-15 20:25:14.268 wdl.w:ptcp.t:call-tar_outputs-25 INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:25:14.268 wdl.w:ptcp.t:call-tar_outputs-25 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:14.268 wdl.w:ptcp.w:call-sawfish-77.t:call-run_sawfish INFO eval :: name: "disk_size", value: 30
2025-09-15 20:25:14.270 wdl.w:ptcp.w:call-sawfish-77.t:call-run_sawfish INFO eval :: name: "discover_dirname", value: "m84036_250809_035451_s4.bc2174_sawfish_discover"
2025-09-15 20:25:14.270 wdl.w:ptcp.w:call-sawfish-77.t:call-run_sawfish INFO eval :: name: "call_dirname", value: "m84036_250809_035451_s4.bc2174_sawfish"
2025-09-15 20:25:14.270 wdl.w:ptcp.w:call-sawfish-77.t:call-run_sawfish INFO eval :: name: "minimap2_bam_filename", value: "m84036_250809_035451_s4.bc2174.minimap2.bam"
2025-09-15 20:25:14.271 wdl.w:ptcp.w:call-sawfish-77.t:call-run_sawfish INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 16, memory_reservation: 32000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:14.271 wdl.w:ptcp.w:call-sawfish-77.t:call-run_sawfish WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:14.271 wdl.w:ptcp.w:call-sawfish-77.t:call-run_sawfish INFO provisioned :: seconds_waited: 0, cpu: 16, mem_bytes: 32000000000
2025-09-15 20:25:14.271 wdl.w:ptcp.w:call-sawfish-77.t:call-run_sawfish INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:14.276 wdl.w:ptcp.w:call-paraphase-77.t:call-run_paraphase NOTICE slurm_singularity run :: pid: 1205174, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-77/call-run_paraphase/slurm_singularity.log.txt"
2025-09-15 20:25:14.300 wdl.w:ptcp.w:call-trgt-73.t:call-get_reads_overlapping_repeats NOTICE done
2025-09-15 20:25:14.305 wdl.w:ptcp.w:call-trgt-73 NOTICE finish :: job: "call-get_reads_overlapping_repeats"
2025-09-15 20:25:14.305 wdl.w:ptcp.w:call-trgt-73 INFO output :: job: "call-get_reads_overlapping_repeats", values: {"reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-73/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2170.repeats.bam.bai", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-73/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2170.repeats.bam"}
2025-09-15 20:25:14.305 wdl.w:ptcp.w:call-trgt-73 INFO visit :: node: "output-reads_overlapping_repeats", values: {"reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-73/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2170.repeats.bam"}
2025-09-15 20:25:14.306 wdl.w:ptcp.w:call-trgt-73 INFO visit :: node: "output-reads_overlapping_repeats_bai", values: {"reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-73/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2170.repeats.bam.bai"}
2025-09-15 20:25:14.315 wdl.w:ptcp.w:call-trgt-65.t:call-trgt_plot_meth_allele NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-65/call-trgt_plot_meth_allele", thread: 140611944420928
2025-09-15 20:25:14.339 wdl.w:ptcp.w:call-trgt-65.t:call-trgt_plot_meth_allele INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:14.339 wdl.w:ptcp.w:call-trgt-65.t:call-trgt_plot_meth_allele INFO input :: name: "waterfall", value: false
2025-09-15 20:25:14.339 wdl.w:ptcp.w:call-trgt-65.t:call-trgt_plot_meth_allele INFO input :: name: "methylation", value: true
2025-09-15 20:25:14.339 wdl.w:ptcp.w:call-trgt-65.t:call-trgt_plot_meth_allele INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:25:14.339 wdl.w:ptcp.w:call-trgt-65.t:call-trgt_plot_meth_allele INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:25:14.339 wdl.w:ptcp.w:call-trgt-65.t:call-trgt_plot_meth_allele INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:25:14.339 wdl.w:ptcp.w:call-trgt-65.t:call-trgt_plot_meth_allele INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2162.trgt.sorted.spanning.bam.bai"
2025-09-15 20:25:14.339 wdl.w:ptcp.w:call-trgt-65.t:call-trgt_plot_meth_allele INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2162.trgt.sorted.spanning.bam"
2025-09-15 20:25:14.339 wdl.w:ptcp.w:call-trgt-65.t:call-trgt_plot_meth_allele INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2162.trgt.vcf"
2025-09-15 20:25:14.340 wdl.w:ptcp.w:call-trgt-65.t:call-trgt_plot_meth_allele INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2162"
2025-09-15 20:25:14.340 wdl.w:ptcp.w:call-trgt-65.t:call-trgt_plot_meth_allele INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:25:14.340 wdl.w:ptcp.w:call-trgt-65.t:call-trgt_plot_meth_allele INFO eval :: name: "plot_type", value: "allele"
2025-09-15 20:25:14.340 wdl.w:ptcp.w:call-trgt-65.t:call-trgt_plot_meth_allele INFO eval :: name: "show", value: "meth"
2025-09-15 20:25:14.340 wdl.w:ptcp.w:call-trgt-65.t:call-trgt_plot_meth_allele INFO eval :: name: "threads", value: 1
2025-09-15 20:25:14.340 wdl.w:ptcp.w:call-trgt-65.t:call-trgt_plot_meth_allele INFO eval :: name: "disk_size", value: 27
2025-09-15 20:25:14.340 wdl.w:ptcp.w:call-trgt-65.t:call-trgt_plot_meth_allele INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2162.meth_allele"
2025-09-15 20:25:14.341 wdl.w:ptcp.w:call-trgt-65.t:call-trgt_plot_meth_allele INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:14.341 wdl.w:ptcp.w:call-trgt-65.t:call-trgt_plot_meth_allele WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:14.341 wdl.w:ptcp.w:call-trgt-65.t:call-trgt_plot_meth_allele INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:25:14.341 wdl.w:ptcp.w:call-trgt-65.t:call-trgt_plot_meth_allele INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:14.348 wdl.w:ptcp.w:call-sawfish-77.t:call-run_sawfish INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 10, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-77/call-run_sawfish/_singularity_tmpdir_q63g7j2j"
2025-09-15 20:25:14.349 wdl.w:ptcp.w:call-sawfish-77.t:call-run_sawfish INFO Slurm invocation: srun --job-name call-run_sawfish --partition compute,compute9 --cpus-per-task 16 --mem 30518M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-77/call-run_sawfish/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-77/call-run_sawfish/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-77/call-run_sawfish/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-77/call-run_sawfish/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-77/out/m84036_250809_035451_s4.bc2174.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2174.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-77/out/m84036_250809_035451_s4.bc2174.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2174.mapped.bam.bai:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-77/call-run_sawfish/_singularity_tmpdir_q63g7j2j/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-77/call-run_sawfish/_singularity_tmpdir_q63g7j2j/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:14.356 wdl.w:ptcp.w:call-trgt-69.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:25:13 [ERROR] - No reads found for TRID=PRTS_ARX
2025-09-15 20:25:14.356 wdl.w:ptcp.w:call-trgt-69.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:25:13 [ERROR] - No reads found for TRID=EIEE1_ARX
2025-09-15 20:25:14.373 wdl.w:ptcp.w:call-sawfish-77.t:call-run_sawfish NOTICE slurm_singularity run :: pid: 1205176, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-77/call-run_sawfish/slurm_singularity.log.txt"
2025-09-15 20:25:14.378 wdl.w:ptcp.t:call-tar_outputs-25 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 17, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-25/_singularity_tmpdir_jvhtofug"
2025-09-15 20:25:14.378 wdl.w:ptcp.t:call-tar_outputs-25 INFO Slurm invocation: srun --job-name call-tar_outputs-25 --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-25/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-25/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-25/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-25/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-25/out/m84036_250809_035451_s4.bc2122.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2122.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-25/out/m84036_250809_035451_s4.bc2122.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2122.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-25/out/m84036_250809_035451_s4.bc2122.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2122.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-25/out/m84036_250809_035451_s4.bc2122_sawfish/m84036_250809_035451_s4.bc2122.sv.vcf.gz:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2122.sv.vcf.gz:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-25/out/m84036_250809_035451_s4.bc2122_sawfish/m84036_250809_035451_s4.bc2122.sv.vcf.gz.tbi:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2122.sv.vcf.gz.tbi:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-25/out/m84036_250809_035451_s4.bc2122_paraphase/m84036_250809_035451_s4.bc2122.paraphase.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2122.paraphase.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-25/out/m84036_250809_035451_s4.bc2122_paraphase/m84036_250809_035451_s4.bc2122.paraphase.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2122.paraphase.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-25/out/m84036_250809_035451_s4.bc2122_paraphase/m84036_250809_035451_s4.bc2122.paraphase.json:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2122.paraphase.json:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-25/out/m84036_250809_035451_s4.bc2122.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2122.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-25/out/m84036_250809_035451_s4.bc2122.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2122.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-25/out/m84036_250809_035451_s4.bc2122.f8inversion.json:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2122.f8inversion.json:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-25/_singularity_tmpdir_jvhtofug/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-25/_singularity_tmpdir_jvhtofug/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:14.386 wdl.w:ptcp.t:call-tar_outputs-25 NOTICE slurm_singularity run :: pid: 1205177, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-25/slurm_singularity.log.txt"
2025-09-15 20:25:14.404 wdl.w:ptcp.w:call-sawfish-10.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:03][sawfish][INFO] Starting sawfish 2.0.3
2025-09-15 20:25:14.404 wdl.w:ptcp.w:call-sawfish-10.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:03][sawfish][INFO] cmdline: sawfish discover --disable-cnv --threads 16 --ref /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa --bam m84036_250809_035451_s4.bc2107.minimap2.bam --output-dir m84036_250809_035451_s4.bc2107_sawfish_discover
2025-09-15 20:25:14.404 wdl.w:ptcp.w:call-sawfish-10.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:03][sawfish][INFO] Running on 16 threads
2025-09-15 20:25:14.404 wdl.w:ptcp.w:call-sawfish-10.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:03][sawfish][INFO] Writing discover settings to file: 'm84036_250809_035451_s4.bc2107_sawfish_discover/discover.settings.json'
2025-09-15 20:25:14.404 wdl.w:ptcp.w:call-sawfish-10.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:03][sawfish][INFO] Reading reference genome from file '/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa'
2025-09-15 20:25:14.404 wdl.w:ptcp.w:call-sawfish-10.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:10][sawfish][INFO] Processing alignment file '/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2107.minimap2.bam'
2025-09-15 20:25:14.404 wdl.w:ptcp.w:call-sawfish-10.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:10][sawfish][INFO] Finished processing all alignments
2025-09-15 20:25:14.404 wdl.w:ptcp.w:call-sawfish-10.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:10][sawfish][INFO] Writing depth bins to binary file: 'm84036_250809_035451_s4.bc2107_sawfish_discover/depth.mpack'
2025-09-15 20:25:14.404 wdl.w:ptcp.w:call-sawfish-10.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:10][sawfish][INFO] Writing max sv depth genome regions to bed file: 'm84036_250809_035451_s4.bc2107_sawfish_discover/max.depth.bed'
2025-09-15 20:25:14.404 wdl.w:ptcp.w:call-sawfish-10.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:10][sawfish][INFO] Completing breakpoint observation clustering
2025-09-15 20:25:14.404 wdl.w:ptcp.w:call-sawfish-10.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:10][sawfish][INFO] Finished breakpoint observation clustering
2025-09-15 20:25:14.404 wdl.w:ptcp.w:call-sawfish-10.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:10][sawfish][INFO] Consolidating adjacent indel candidates
2025-09-15 20:25:14.404 wdl.w:ptcp.w:call-sawfish-10.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:10][sawfish][INFO] Finding large insertion candidates
2025-09-15 20:25:14.404 wdl.w:ptcp.w:call-sawfish-10.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:10][sawfish][INFO] Writing breakpoint_cluster debug bed file: 'm84036_250809_035451_s4.bc2107_sawfish_discover/debug.breakpoint_clusters.bed'
2025-09-15 20:25:14.405 wdl.w:ptcp.w:call-sawfish-10.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:10][sawfish][INFO] Refining SV Candidates
2025-09-15 20:25:14.405 wdl.w:ptcp.w:call-sawfish-10.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:10][sawfish][INFO] Writing debug assembly region bed file: 'm84036_250809_035451_s4.bc2107_sawfish_discover/assembly.regions.bed'
2025-09-15 20:25:14.405 wdl.w:ptcp.w:call-sawfish-10.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:10][sawfish][INFO] Starting refinement of breakpoint evidence clusters
2025-09-15 20:25:14.405 wdl.w:ptcp.w:call-sawfish-10.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:11][sawfish][INFO] Finished refining all breakpoint evidence clusters
2025-09-15 20:25:14.405 wdl.w:ptcp.w:call-sawfish-10.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:11][sawfish][INFO] Writing all contig alignments to bam file: 'm84036_250809_035451_s4.bc2107_sawfish_discover/contig.alignment.bam'
2025-09-15 20:25:14.405 wdl.w:ptcp.w:call-sawfish-10.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:11][sawfish][INFO] Writing candidate structural variants to file: 'm84036_250809_035451_s4.bc2107_sawfish_discover/candidate.sv.bcf'
2025-09-15 20:25:14.405 wdl.w:ptcp.w:call-sawfish-10.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:11][sawfish][INFO] Writing run statistics to file: 'm84036_250809_035451_s4.bc2107_sawfish_discover/run.stats.json'
2025-09-15 20:25:14.405 wdl.w:ptcp.w:call-sawfish-10.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:11][sawfish][INFO] sawfish completed. Total Runtime: 00:00:08.512
2025-09-15 20:25:14.429 wdl.w:ptcp.w:call-trgt-65.t:call-trgt_plot_meth_allele INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-65/call-trgt_plot_meth_allele/_singularity_tmpdir_0bfysyaq"
2025-09-15 20:25:14.429 wdl.w:ptcp.w:call-trgt-65.t:call-trgt_plot_meth_allele INFO Slurm invocation: srun --job-name call-trgt_plot_meth_allele --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-65/call-trgt_plot_meth_allele/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-65/call-trgt_plot_meth_allele/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-65/call-trgt_plot_meth_allele/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-65/call-trgt_plot_meth_allele/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-65/call-trgt_genotype/out/m84036_250809_035451_s4.bc2162.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2162.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-65/call-trgt_genotype/out/m84036_250809_035451_s4.bc2162.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2162.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-65/call-trgt_genotype/out/m84036_250809_035451_s4.bc2162.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2162.trgt.vcf:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-65/call-trgt_plot_meth_allele/_singularity_tmpdir_0bfysyaq/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-65/call-trgt_plot_meth_allele/_singularity_tmpdir_0bfysyaq/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:14.440 wdl.w:ptcp.w:call-trgt-65.t:call-trgt_plot_meth_allele NOTICE slurm_singularity run :: pid: 1205180, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-65/call-trgt_plot_meth_allele/slurm_singularity.log.txt"
2025-09-15 20:25:14.493 wdl.w:ptcp.w:call-sawfish-19.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:02][sawfish][INFO] Starting sawfish 2.0.3
2025-09-15 20:25:14.493 wdl.w:ptcp.w:call-sawfish-19.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:02][sawfish][INFO] cmdline: sawfish discover --disable-cnv --threads 16 --ref /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa --bam m84036_250809_035451_s4.bc2116.minimap2.bam --output-dir m84036_250809_035451_s4.bc2116_sawfish_discover
2025-09-15 20:25:14.494 wdl.w:ptcp.w:call-sawfish-19.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:02][sawfish][INFO] Running on 16 threads
2025-09-15 20:25:14.494 wdl.w:ptcp.w:call-sawfish-19.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:02][sawfish][INFO] Writing discover settings to file: 'm84036_250809_035451_s4.bc2116_sawfish_discover/discover.settings.json'
2025-09-15 20:25:14.494 wdl.w:ptcp.w:call-sawfish-19.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:02][sawfish][INFO] Reading reference genome from file '/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa'
2025-09-15 20:25:14.494 wdl.w:ptcp.w:call-sawfish-19.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:08][sawfish][INFO] Processing alignment file '/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2116.minimap2.bam'
2025-09-15 20:25:14.494 wdl.w:ptcp.w:call-sawfish-19.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:08][sawfish][INFO] Finished processing all alignments
2025-09-15 20:25:14.494 wdl.w:ptcp.w:call-sawfish-19.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:08][sawfish][INFO] Writing depth bins to binary file: 'm84036_250809_035451_s4.bc2116_sawfish_discover/depth.mpack'
2025-09-15 20:25:14.494 wdl.w:ptcp.w:call-sawfish-19.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:08][sawfish][INFO] Writing max sv depth genome regions to bed file: 'm84036_250809_035451_s4.bc2116_sawfish_discover/max.depth.bed'
2025-09-15 20:25:14.494 wdl.w:ptcp.w:call-sawfish-19.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:08][sawfish][INFO] Completing breakpoint observation clustering
2025-09-15 20:25:14.494 wdl.w:ptcp.w:call-sawfish-19.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:08][sawfish][INFO] Finished breakpoint observation clustering
2025-09-15 20:25:14.494 wdl.w:ptcp.w:call-sawfish-19.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:08][sawfish][INFO] Consolidating adjacent indel candidates
2025-09-15 20:25:14.494 wdl.w:ptcp.w:call-sawfish-19.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:08][sawfish][INFO] Finding large insertion candidates
2025-09-15 20:25:14.494 wdl.w:ptcp.w:call-sawfish-19.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:08][sawfish][INFO] Writing breakpoint_cluster debug bed file: 'm84036_250809_035451_s4.bc2116_sawfish_discover/debug.breakpoint_clusters.bed'
2025-09-15 20:25:14.494 wdl.w:ptcp.w:call-sawfish-19.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:08][sawfish][INFO] Refining SV Candidates
2025-09-15 20:25:14.494 wdl.w:ptcp.w:call-sawfish-19.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:08][sawfish][INFO] Writing debug assembly region bed file: 'm84036_250809_035451_s4.bc2116_sawfish_discover/assembly.regions.bed'
2025-09-15 20:25:14.495 wdl.w:ptcp.w:call-trgt-60.t:call-trgt_plot_motifs_allele.slurm_singularity INFO srun: job 51797958 has been allocated resources
2025-09-15 20:25:14.495 wdl.w:ptcp.w:call-sawfish-19.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:08][sawfish][INFO] Starting refinement of breakpoint evidence clusters
2025-09-15 20:25:14.495 wdl.w:ptcp.w:call-trgt-60.t:call-trgt_plot_motifs_allele.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:14.495 wdl.w:ptcp.w:call-sawfish-19.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:09][sawfish][INFO] Finished refining all breakpoint evidence clusters
2025-09-15 20:25:14.495 wdl.w:ptcp.w:call-sawfish-19.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:09][sawfish][INFO] Writing all contig alignments to bam file: 'm84036_250809_035451_s4.bc2116_sawfish_discover/contig.alignment.bam'
2025-09-15 20:25:14.495 wdl.w:ptcp.w:call-sawfish-19.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:09][sawfish][INFO] Writing candidate structural variants to file: 'm84036_250809_035451_s4.bc2116_sawfish_discover/candidate.sv.bcf'
2025-09-15 20:25:14.495 wdl.w:ptcp.w:call-sawfish-19.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:09][sawfish][INFO] Writing run statistics to file: 'm84036_250809_035451_s4.bc2116_sawfish_discover/run.stats.json'
2025-09-15 20:25:14.495 wdl.w:ptcp.w:call-sawfish-19.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:10][sawfish][INFO] sawfish completed. Total Runtime: 00:00:07.462
2025-09-15 20:25:14.619 wdl.w:ptcp.w:call-paraphase-70.t:call-run_paraphase.stderr VERBOSE INFO:root:Processing sample m84036_250809_035451_s4.bc2167 at 2025-09-15 20:25:10.810912...
2025-09-15 20:25:14.620 wdl.w:ptcp.w:call-paraphase-70.t:call-run_paraphase.stderr VERBOSE INFO:root:Checking sample sex at 2025-09-15 20:25:10.811578...
2025-09-15 20:25:14.620 wdl.w:ptcp.w:call-paraphase-70.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for smn1 for sample m84036_250809_035451_s4.bc2167 at 2025-09-15 20:25:10.851672...
2025-09-15 20:25:14.620 wdl.w:ptcp.w:call-paraphase-70.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for cyp21 for sample m84036_250809_035451_s4.bc2167 at 2025-09-15 20:25:10.851553...
2025-09-15 20:25:14.620 wdl.w:ptcp.w:call-paraphase-70.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for smn1 for sample m84036_250809_035451_s4.bc2167 at 2025-09-15 20:25:10.852072...
2025-09-15 20:25:14.620 wdl.w:ptcp.w:call-paraphase-70.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for cyp21 for sample m84036_250809_035451_s4.bc2167 at 2025-09-15 20:25:10.852084...
2025-09-15 20:25:14.620 wdl.w:ptcp.w:call-paraphase-70.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for gba for sample m84036_250809_035451_s4.bc2167 at 2025-09-15 20:25:10.851952...
2025-09-15 20:25:14.620 wdl.w:ptcp.w:call-paraphase-70.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for gba for sample m84036_250809_035451_s4.bc2167 at 2025-09-15 20:25:10.852438...
2025-09-15 20:25:14.620 wdl.w:ptcp.w:call-paraphase-70.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for hba for sample m84036_250809_035451_s4.bc2167 at 2025-09-15 20:25:10.852899...
2025-09-15 20:25:14.620 wdl.w:ptcp.w:call-paraphase-70.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for hba for sample m84036_250809_035451_s4.bc2167 at 2025-09-15 20:25:10.853256...
2025-09-15 20:25:14.622 wdl.w:ptcp.w:call-sawfish-14.t:call-run_sawfish INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2111_sawfish/m84036_250809_035451_s4.bc2111.sv.vcf.gz"
2025-09-15 20:25:14.628 wdl.w:ptcp.w:call-sawfish-14.t:call-run_sawfish INFO output :: name: "vcf_tbi", value: "m84036_250809_035451_s4.bc2111_sawfish/m84036_250809_035451_s4.bc2111.sv.vcf.gz.tbi"
2025-09-15 20:25:14.629 wdl.w:ptcp.w:call-sawfish-14.t:call-run_sawfish INFO output :: name: "minimap2_bam", value: "m84036_250809_035451_s4.bc2111.minimap2.bam"
2025-09-15 20:25:14.631 wdl.w:ptcp.w:call-sawfish-14.t:call-run_sawfish INFO output :: name: "minimap2_bam_bai", value: "m84036_250809_035451_s4.bc2111.minimap2.bam.bai"
2025-09-15 20:25:14.691 wdl.w:ptcp.w:call-trgt-60.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO srun: job 51797959 has been allocated resources
2025-09-15 20:25:14.691 wdl.w:ptcp.w:call-trgt-60.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:14.761 wdl.w:ptcp.w:call-paraphase-39.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for smn1 for sample m84036_250809_035451_s4.bc2136 at 2025-09-15 20:24:56.878955...
2025-09-15 20:25:14.761 wdl.w:ptcp.w:call-paraphase-39.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for cyp21 for sample m84036_250809_035451_s4.bc2136 at 2025-09-15 20:25:08.529734...
2025-09-15 20:25:14.761 wdl.w:ptcp.w:call-paraphase-39.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for cyp21 for sample m84036_250809_035451_s4.bc2136 at 2025-09-15 20:25:09.153659...
2025-09-15 20:25:14.776 wdl.w:ptcp.w:call-sawfish-14.t:call-run_sawfish NOTICE done
2025-09-15 20:25:14.781 wdl.w:ptcp.w:call-sawfish-14 NOTICE finish :: job: "call-run_sawfish"
2025-09-15 20:25:14.781 wdl.w:ptcp.w:call-sawfish-14 INFO output :: job: "call-run_sawfish", values: {"minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-14/call-run_sawfish/out/m84036_250809_035451_s4.bc2111.minimap2.bam.bai", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-14/call-run_sawfish/out/m84036_250809_035451_s4.bc2111.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-14/call-run_sawfish/out/m84036_250809_035451_s4.bc2111_sawfish/m84036_250809_035451_s4.bc2111.sv.vcf.gz.tbi", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-14/call-run_sawfish/out/m84036_250809_035451_s4.bc2111_sawfish/m84036_250809_035451_s4.bc2111.sv.vcf.gz"}
2025-09-15 20:25:14.782 wdl.w:ptcp.w:call-sawfish-14 INFO visit :: node: "output-minimap2_bam", values: {"minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-14/call-run_sawfish/out/m84036_250809_035451_s4.bc2111.minimap2.bam"}
2025-09-15 20:25:14.782 wdl.w:ptcp.w:call-sawfish-14 INFO visit :: node: "output-minimap2_bam_bai", values: {"minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-14/call-run_sawfish/out/m84036_250809_035451_s4.bc2111.minimap2.bam.bai"}
2025-09-15 20:25:14.782 wdl.w:ptcp.w:call-sawfish-14 INFO visit :: node: "output-vcf", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-14/call-run_sawfish/out/m84036_250809_035451_s4.bc2111_sawfish/m84036_250809_035451_s4.bc2111.sv.vcf.gz"}
2025-09-15 20:25:14.782 wdl.w:ptcp.w:call-sawfish-14 INFO visit :: node: "output-vcf_tbi", values: {"vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-14/call-run_sawfish/out/m84036_250809_035451_s4.bc2111_sawfish/m84036_250809_035451_s4.bc2111.sv.vcf.gz.tbi"}
2025-09-15 20:25:14.782 wdl.w:ptcp.w:call-sawfish-14 INFO visit :: node: "outputs", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-14/call-run_sawfish/out/m84036_250809_035451_s4.bc2111_sawfish/m84036_250809_035451_s4.bc2111.sv.vcf.gz", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-14/call-run_sawfish/out/m84036_250809_035451_s4.bc2111.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-14/call-run_sawfish/out/m84036_250809_035451_s4.bc2111_sawfish/m84036_250809_035451_s4.bc2111.sv.vcf.gz.tbi", "minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-14/call-run_sawfish/out/m84036_250809_035451_s4.bc2111.minimap2.bam.bai"}
2025-09-15 20:25:14.789 wdl.w:ptcp.w:call-trgt-65.t:call-trgt_plot_meth_waterfall NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-65/call-trgt_plot_meth_waterfall", thread: 140606575711808
2025-09-15 20:25:14.804 wdl.w:ptcp.t:call-tar_outputs-16.slurm_singularity INFO srun: job 51797960 has been allocated resources
2025-09-15 20:25:14.804 wdl.w:ptcp.t:call-tar_outputs-16.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:14.822 wdl.w:ptcp.w:call-trgt-65.t:call-trgt_plot_meth_waterfall INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:14.822 wdl.w:ptcp.w:call-trgt-65.t:call-trgt_plot_meth_waterfall INFO input :: name: "waterfall", value: true
2025-09-15 20:25:14.822 wdl.w:ptcp.w:call-trgt-65.t:call-trgt_plot_meth_waterfall INFO input :: name: "methylation", value: true
2025-09-15 20:25:14.822 wdl.w:ptcp.w:call-trgt-65.t:call-trgt_plot_meth_waterfall INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:25:14.822 wdl.w:ptcp.w:call-trgt-65.t:call-trgt_plot_meth_waterfall INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:25:14.822 wdl.w:ptcp.w:call-trgt-65.t:call-trgt_plot_meth_waterfall INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:25:14.823 wdl.w:ptcp.w:call-trgt-65.t:call-trgt_plot_meth_waterfall INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2162.trgt.sorted.spanning.bam.bai"
2025-09-15 20:25:14.823 wdl.w:ptcp.w:call-trgt-65.t:call-trgt_plot_meth_waterfall INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2162.trgt.sorted.spanning.bam"
2025-09-15 20:25:14.823 wdl.w:ptcp.w:call-trgt-65.t:call-trgt_plot_meth_waterfall INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2162.trgt.vcf"
2025-09-15 20:25:14.823 wdl.w:ptcp.w:call-trgt-65.t:call-trgt_plot_meth_waterfall INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2162"
2025-09-15 20:25:14.823 wdl.w:ptcp.w:call-trgt-65.t:call-trgt_plot_meth_waterfall INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:25:14.823 wdl.w:ptcp.w:call-trgt-65.t:call-trgt_plot_meth_waterfall INFO eval :: name: "plot_type", value: "waterfall"
2025-09-15 20:25:14.823 wdl.w:ptcp.w:call-trgt-65.t:call-trgt_plot_meth_waterfall INFO eval :: name: "show", value: "meth"
2025-09-15 20:25:14.823 wdl.w:ptcp.w:call-trgt-65.t:call-trgt_plot_meth_waterfall INFO eval :: name: "threads", value: 1
2025-09-15 20:25:14.824 wdl.w:ptcp.w:call-trgt-65.t:call-trgt_plot_meth_waterfall INFO eval :: name: "disk_size", value: 27
2025-09-15 20:25:14.824 wdl.w:ptcp.w:call-trgt-65.t:call-trgt_plot_meth_waterfall INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2162.meth_waterfall"
2025-09-15 20:25:14.824 wdl.w:ptcp.w:call-trgt-65.t:call-trgt_plot_meth_waterfall INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:14.824 wdl.w:ptcp.w:call-trgt-65.t:call-trgt_plot_meth_waterfall WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:14.825 wdl.w:ptcp.w:call-trgt-65.t:call-trgt_plot_meth_waterfall INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:25:14.825 wdl.w:ptcp.w:call-trgt-65.t:call-trgt_plot_meth_waterfall INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:14.834 wdl.w:ptcp.w:call-sawfish-14 NOTICE done
2025-09-15 20:25:14.841 wdl.w:ptcp NOTICE finish :: job: "call-sawfish-14"
2025-09-15 20:25:14.841 wdl.w:ptcp INFO output :: job: "call-sawfish-14", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-14/out/m84036_250809_035451_s4.bc2111_sawfish/m84036_250809_035451_s4.bc2111.sv.vcf.gz", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-14/out/m84036_250809_035451_s4.bc2111.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-14/out/m84036_250809_035451_s4.bc2111_sawfish/m84036_250809_035451_s4.bc2111.sv.vcf.gz.tbi", "minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-14/out/m84036_250809_035451_s4.bc2111.minimap2.bam.bai"}
2025-09-15 20:25:14.846 wdl.w:ptcp.w:call-paraphase-82 NOTICE workflow start :: name: "paraphase", source: "./paraphase.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-82"
2025-09-15 20:25:14.868 wdl.w:ptcp.w:call-paraphase-82 INFO visit :: node: "decl-annotation_vcf", values: {"annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf"}
2025-09-15 20:25:14.868 wdl.w:ptcp.w:call-paraphase-82 INFO visit :: node: "decl-config_file", values: {"config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml"}
2025-09-15 20:25:14.868 wdl.w:ptcp.w:call-paraphase-82 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:25:14.868 wdl.w:ptcp.w:call-paraphase-82 INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:25:14.868 wdl.w:ptcp.w:call-paraphase-82 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-82/out/m84036_250809_035451_s4.bc2179.mapped.bam"}
2025-09-15 20:25:14.868 wdl.w:ptcp.w:call-paraphase-82 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-82/out/m84036_250809_035451_s4.bc2179.mapped.bam.bai"}
2025-09-15 20:25:14.869 wdl.w:ptcp.w:call-paraphase-82 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:25:14.869 wdl.w:ptcp.w:call-paraphase-82 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:25:14.869 wdl.w:ptcp.w:call-paraphase-82 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2179"}
2025-09-15 20:25:14.869 wdl.w:ptcp.w:call-paraphase-82 INFO visit :: node: "decl-sex", values: {"sex": "F"}
2025-09-15 20:25:14.869 wdl.w:ptcp.w:call-paraphase-82 NOTICE ready :: job: "call-run_paraphase", callee: "run_paraphase"
2025-09-15 20:25:14.869 wdl.w:ptcp.w:call-paraphase-82 INFO input :: job: "call-run_paraphase", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf", "genome_version": "38", "config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-82/out/m84036_250809_035451_s4.bc2179.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-82/out/m84036_250809_035451_s4.bc2179.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2179"}
2025-09-15 20:25:14.899 wdl.w:ptcp.w:call-trgt-65.t:call-trgt_plot_meth_waterfall INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-65/call-trgt_plot_meth_waterfall/_singularity_tmpdir_v_l0g6t0"
2025-09-15 20:25:14.899 wdl.w:ptcp.w:call-trgt-65.t:call-trgt_plot_meth_waterfall INFO Slurm invocation: srun --job-name call-trgt_plot_meth_waterfall --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-65/call-trgt_plot_meth_waterfall/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-65/call-trgt_plot_meth_waterfall/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-65/call-trgt_plot_meth_waterfall/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-65/call-trgt_plot_meth_waterfall/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-65/call-trgt_genotype/out/m84036_250809_035451_s4.bc2162.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2162.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-65/call-trgt_genotype/out/m84036_250809_035451_s4.bc2162.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2162.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-65/call-trgt_genotype/out/m84036_250809_035451_s4.bc2162.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2162.trgt.vcf:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-65/call-trgt_plot_meth_waterfall/_singularity_tmpdir_v_l0g6t0/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-65/call-trgt_plot_meth_waterfall/_singularity_tmpdir_v_l0g6t0/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:14.926 wdl.w:ptcp.w:call-trgt-65.t:call-trgt_plot_meth_waterfall NOTICE slurm_singularity run :: pid: 1205204, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-65/call-trgt_plot_meth_waterfall/slurm_singularity.log.txt"
2025-09-15 20:25:14.995 wdl.w:ptcp.w:call-trgt-61.t:call-trgt_plot_motifs_waterfall INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2158.motifs_waterfall.trgt_plots.zip"
2025-09-15 20:25:15.105 wdl.w:ptcp.w:call-trgt-61.t:call-trgt_plot_motifs_waterfall NOTICE done
2025-09-15 20:25:15.110 wdl.w:ptcp.w:call-trgt-61 NOTICE finish :: job: "call-trgt_plot_motifs_waterfall"
2025-09-15 20:25:15.110 wdl.w:ptcp.w:call-trgt-61 INFO output :: job: "call-trgt_plot_motifs_waterfall", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-61/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2158.motifs_waterfall.trgt_plots.zip"}
2025-09-15 20:25:15.110 wdl.w:ptcp.w:call-trgt-61 INFO visit :: node: "output-images_motifs_waterfall", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-61/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2158.motifs_waterfall.trgt_plots.zip"}
2025-09-15 20:25:15.112 wdl.w:ptcp.t:call-tar_outputs-16 INFO output :: name: "sample_tarball", value: "m84036_250809_035451_s4.bc2113.tar"
2025-09-15 20:25:15.119 wdl.w:ptcp.w:call-trgt-65.t:call-trgt_plot_motifs_allele NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-65/call-trgt_plot_motifs_allele", thread: 140610367379008
2025-09-15 20:25:15.134 wdl.w:ptcp.w:call-trgt-64.t:call-trgt_plot_motifs_waterfall INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2161.motifs_waterfall.trgt_plots.zip"
2025-09-15 20:25:15.136 wdl.w:ptcp.w:call-trgt-65.t:call-trgt_plot_motifs_allele INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:15.137 wdl.w:ptcp.w:call-trgt-65.t:call-trgt_plot_motifs_allele INFO input :: name: "waterfall", value: false
2025-09-15 20:25:15.137 wdl.w:ptcp.w:call-trgt-65.t:call-trgt_plot_motifs_allele INFO input :: name: "methylation", value: false
2025-09-15 20:25:15.137 wdl.w:ptcp.w:call-trgt-65.t:call-trgt_plot_motifs_allele INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:25:15.137 wdl.w:ptcp.w:call-trgt-65.t:call-trgt_plot_motifs_allele INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:25:15.137 wdl.w:ptcp.w:call-trgt-65.t:call-trgt_plot_motifs_allele INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:25:15.137 wdl.w:ptcp.w:call-trgt-65.t:call-trgt_plot_motifs_allele INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2162.trgt.sorted.spanning.bam.bai"
2025-09-15 20:25:15.137 wdl.w:ptcp.w:call-trgt-65.t:call-trgt_plot_motifs_allele INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2162.trgt.sorted.spanning.bam"
2025-09-15 20:25:15.137 wdl.w:ptcp.w:call-trgt-65.t:call-trgt_plot_motifs_allele INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2162.trgt.vcf"
2025-09-15 20:25:15.137 wdl.w:ptcp.w:call-trgt-65.t:call-trgt_plot_motifs_allele INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2162"
2025-09-15 20:25:15.137 wdl.w:ptcp.w:call-trgt-65.t:call-trgt_plot_motifs_allele INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:25:15.138 wdl.w:ptcp.w:call-trgt-65.t:call-trgt_plot_motifs_allele INFO eval :: name: "plot_type", value: "allele"
2025-09-15 20:25:15.138 wdl.w:ptcp.w:call-trgt-65.t:call-trgt_plot_motifs_allele INFO eval :: name: "show", value: "motifs"
2025-09-15 20:25:15.138 wdl.w:ptcp.w:call-trgt-65.t:call-trgt_plot_motifs_allele INFO eval :: name: "threads", value: 1
2025-09-15 20:25:15.138 wdl.w:ptcp.w:call-trgt-65.t:call-trgt_plot_motifs_allele INFO eval :: name: "disk_size", value: 27
2025-09-15 20:25:15.138 wdl.w:ptcp.w:call-trgt-65.t:call-trgt_plot_motifs_allele INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2162.motifs_allele"
2025-09-15 20:25:15.139 wdl.w:ptcp.w:call-trgt-65.t:call-trgt_plot_motifs_allele INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:15.139 wdl.w:ptcp.w:call-trgt-65.t:call-trgt_plot_motifs_allele WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:15.139 wdl.w:ptcp.w:call-trgt-69.t:call-trgt_plot_motifs_allele INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2166.motifs_allele.trgt_plots.zip"
2025-09-15 20:25:15.140 wdl.w:ptcp.w:call-trgt-65.t:call-trgt_plot_motifs_allele INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:25:15.140 wdl.w:ptcp.w:call-trgt-65.t:call-trgt_plot_motifs_allele INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:15.209 wdl.w:ptcp.t:call-tar_outputs-16 NOTICE done
2025-09-15 20:25:15.215 wdl.w:ptcp NOTICE finish :: job: "call-tar_outputs-16"
2025-09-15 20:25:15.216 wdl.w:ptcp INFO output :: job: "call-tar_outputs-16", values: {"sample_tarball": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-16/out/m84036_250809_035451_s4.bc2113.tar"}
2025-09-15 20:25:15.230 wdl.w:ptcp.w:call-trgt-65.t:call-trgt_plot_motifs_waterfall NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-65/call-trgt_plot_motifs_waterfall", thread: 140607674631744
2025-09-15 20:25:15.244 wdl.w:ptcp.w:call-trgt-65.t:call-trgt_plot_motifs_allele INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-65/call-trgt_plot_motifs_allele/_singularity_tmpdir_wd6mm2br"
2025-09-15 20:25:15.244 wdl.w:ptcp.w:call-trgt-65.t:call-trgt_plot_motifs_allele INFO Slurm invocation: srun --job-name call-trgt_plot_motifs_allele --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-65/call-trgt_plot_motifs_allele/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-65/call-trgt_plot_motifs_allele/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-65/call-trgt_plot_motifs_allele/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-65/call-trgt_plot_motifs_allele/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-65/call-trgt_genotype/out/m84036_250809_035451_s4.bc2162.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2162.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-65/call-trgt_genotype/out/m84036_250809_035451_s4.bc2162.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2162.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-65/call-trgt_genotype/out/m84036_250809_035451_s4.bc2162.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2162.trgt.vcf:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-65/call-trgt_plot_motifs_allele/_singularity_tmpdir_wd6mm2br/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-65/call-trgt_plot_motifs_allele/_singularity_tmpdir_wd6mm2br/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:15.256 wdl.w:ptcp.w:call-trgt-65.t:call-trgt_plot_motifs_waterfall INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:15.256 wdl.w:ptcp.w:call-trgt-65.t:call-trgt_plot_motifs_waterfall INFO input :: name: "waterfall", value: true
2025-09-15 20:25:15.256 wdl.w:ptcp.w:call-trgt-65.t:call-trgt_plot_motifs_waterfall INFO input :: name: "methylation", value: false
2025-09-15 20:25:15.256 wdl.w:ptcp.w:call-trgt-65.t:call-trgt_plot_motifs_waterfall INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:25:15.256 wdl.w:ptcp.w:call-trgt-65.t:call-trgt_plot_motifs_waterfall INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:25:15.256 wdl.w:ptcp.w:call-trgt-65.t:call-trgt_plot_motifs_waterfall INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:25:15.257 wdl.w:ptcp.w:call-trgt-65.t:call-trgt_plot_motifs_waterfall INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2162.trgt.sorted.spanning.bam.bai"
2025-09-15 20:25:15.257 wdl.w:ptcp.w:call-trgt-65.t:call-trgt_plot_motifs_waterfall INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2162.trgt.sorted.spanning.bam"
2025-09-15 20:25:15.257 wdl.w:ptcp.w:call-trgt-65.t:call-trgt_plot_motifs_waterfall INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2162.trgt.vcf"
2025-09-15 20:25:15.257 wdl.w:ptcp.w:call-trgt-65.t:call-trgt_plot_motifs_waterfall INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2162"
2025-09-15 20:25:15.257 wdl.w:ptcp.w:call-trgt-65.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:25:15.257 wdl.w:ptcp.w:call-trgt-65.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "plot_type", value: "waterfall"
2025-09-15 20:25:15.257 wdl.w:ptcp.w:call-trgt-65.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "show", value: "motifs"
2025-09-15 20:25:15.257 wdl.w:ptcp.w:call-trgt-65.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "threads", value: 1
2025-09-15 20:25:15.257 wdl.w:ptcp.w:call-trgt-65.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "disk_size", value: 27
2025-09-15 20:25:15.258 wdl.w:ptcp.w:call-trgt-65.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2162.motifs_waterfall"
2025-09-15 20:25:15.258 wdl.w:ptcp.w:call-trgt-65.t:call-trgt_plot_motifs_waterfall INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:15.258 wdl.w:ptcp.w:call-trgt-65.t:call-trgt_plot_motifs_waterfall WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:15.258 wdl.w:ptcp.w:call-trgt-65.t:call-trgt_plot_motifs_waterfall INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:25:15.258 wdl.w:ptcp.w:call-trgt-65.t:call-trgt_plot_motifs_waterfall INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:15.265 wdl.w:ptcp.w:call-trgt-65.t:call-trgt_plot_motifs_allele NOTICE slurm_singularity run :: pid: 1205215, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-65/call-trgt_plot_motifs_allele/slurm_singularity.log.txt"
2025-09-15 20:25:15.301 wdl.w:ptcp.w:call-paraphase-77.t:call-run_paraphase.slurm_singularity INFO srun: job 51797961 queued and waiting for resources
2025-09-15 20:25:15.301 wdl.w:ptcp.w:call-paraphase-77.t:call-run_paraphase.slurm_singularity INFO srun: job 51797961 has been allocated resources
2025-09-15 20:25:15.301 wdl.w:ptcp.w:call-paraphase-77.t:call-run_paraphase.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:15.322 wdl.w:ptcp.w:call-trgt-69.t:call-trgt_plot_motifs_allele NOTICE done
2025-09-15 20:25:15.329 wdl.w:ptcp.w:call-trgt-64.t:call-trgt_plot_motifs_waterfall NOTICE done
2025-09-15 20:25:15.329 wdl.w:ptcp.w:call-trgt-69 NOTICE finish :: job: "call-trgt_plot_motifs_allele"
2025-09-15 20:25:15.330 wdl.w:ptcp.w:call-trgt-69 INFO output :: job: "call-trgt_plot_motifs_allele", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-69/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2166.motifs_allele.trgt_plots.zip"}
2025-09-15 20:25:15.330 wdl.w:ptcp.w:call-trgt-69 INFO visit :: node: "output-images_motifs_allele", values: {"images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-69/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2166.motifs_allele.trgt_plots.zip"}
2025-09-15 20:25:15.334 wdl.w:ptcp.w:call-trgt-64 NOTICE finish :: job: "call-trgt_plot_motifs_waterfall"
2025-09-15 20:25:15.335 wdl.w:ptcp.w:call-trgt-64 INFO output :: job: "call-trgt_plot_motifs_waterfall", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-64/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2161.motifs_waterfall.trgt_plots.zip"}
2025-09-15 20:25:15.335 wdl.w:ptcp.w:call-trgt-64 INFO visit :: node: "output-images_motifs_waterfall", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-64/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2161.motifs_waterfall.trgt_plots.zip"}
2025-09-15 20:25:15.341 wdl.w:ptcp.t:call-tar_outputs-24 NOTICE task setup :: name: "tar_outputs", source: "./common.wdl", line: 279, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-24", thread: 140607691417152
2025-09-15 20:25:15.343 wdl.w:ptcp.w:call-trgt-77.t:call-get_reads_overlapping_repeats NOTICE task setup :: name: "get_reads_overlapping_repeats", source: "./trgt.wdl", line: 182, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-77/call-get_reads_overlapping_repeats", thread: 140609813722688
2025-09-15 20:25:15.362 wdl.w:ptcp.w:call-trgt-65.t:call-trgt_plot_motifs_waterfall INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-65/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_nm04x0zq"
2025-09-15 20:25:15.362 wdl.w:ptcp.w:call-trgt-65.t:call-trgt_plot_motifs_waterfall INFO Slurm invocation: srun --job-name call-trgt_plot_motifs_waterfall --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-65/call-trgt_plot_motifs_waterfall/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-65/call-trgt_plot_motifs_waterfall/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-65/call-trgt_plot_motifs_waterfall/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-65/call-trgt_plot_motifs_waterfall/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-65/call-trgt_genotype/out/m84036_250809_035451_s4.bc2162.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2162.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-65/call-trgt_genotype/out/m84036_250809_035451_s4.bc2162.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2162.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-65/call-trgt_genotype/out/m84036_250809_035451_s4.bc2162.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2162.trgt.vcf:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-65/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_nm04x0zq/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-65/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_nm04x0zq/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:15.363 wdl.w:ptcp.w:call-trgt-77.t:call-get_reads_overlapping_repeats INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:15.365 wdl.w:ptcp.w:call-trgt-77.t:call-get_reads_overlapping_repeats INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:25:15.366 wdl.w:ptcp.w:call-trgt-77.t:call-get_reads_overlapping_repeats INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2174.mapped.bam.bai"
2025-09-15 20:25:15.366 wdl.w:ptcp.w:call-trgt-77.t:call-get_reads_overlapping_repeats INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2174.mapped.bam"
2025-09-15 20:25:15.366 wdl.w:ptcp.w:call-trgt-77.t:call-get_reads_overlapping_repeats INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2174"
2025-09-15 20:25:15.366 wdl.w:ptcp.w:call-trgt-77.t:call-get_reads_overlapping_repeats INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:25:15.366 wdl.w:ptcp.w:call-trgt-77.t:call-get_reads_overlapping_repeats INFO eval :: name: "expand_size", value: 3000
2025-09-15 20:25:15.366 wdl.w:ptcp.w:call-trgt-77.t:call-get_reads_overlapping_repeats INFO eval :: name: "threads", value: 1
2025-09-15 20:25:15.367 wdl.w:ptcp.w:call-trgt-77.t:call-get_reads_overlapping_repeats INFO eval :: name: "expanded_bed_name", value: "m84036_250809_035451_s4.bc2174.expanded.bed"
2025-09-15 20:25:15.367 wdl.w:ptcp.w:call-trgt-77.t:call-get_reads_overlapping_repeats INFO eval :: name: "disk_size", value: 11
2025-09-15 20:25:15.367 wdl.w:ptcp.w:call-trgt-77.t:call-get_reads_overlapping_repeats INFO eval :: name: "output_name", value: "m84036_250809_035451_s4.bc2174.repeats.bam"
2025-09-15 20:25:15.367 wdl.w:ptcp.w:call-trgt-77.t:call-get_reads_overlapping_repeats INFO eval :: name: "index_name", value: "m84036_250809_035451_s4.bc2174.repeats.bam.bai"
2025-09-15 20:25:15.367 wdl.w:ptcp.w:call-trgt-77.t:call-get_reads_overlapping_repeats INFO eval :: name: "output_name_with_index", value: "m84036_250809_035451_s4.bc2174.repeats.bam##idx##m84036_250809_035451_s4.bc2174.repeats.bam.bai"
2025-09-15 20:25:15.366 wdl.w:ptcp.t:call-tar_outputs-24 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:15.368 wdl.w:ptcp.t:call-tar_outputs-24 INFO input :: name: "sawfish_vcf_tbi", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2121.sv.vcf.gz.tbi"
2025-09-15 20:25:15.367 wdl.w:ptcp.w:call-trgt-77.t:call-get_reads_overlapping_repeats INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:15.368 wdl.w:ptcp.t:call-tar_outputs-24 INFO input :: name: "sawfish_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2121.sv.vcf.gz"
2025-09-15 20:25:15.368 wdl.w:ptcp.w:call-trgt-77.t:call-get_reads_overlapping_repeats WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:15.368 wdl.w:ptcp.t:call-tar_outputs-24 INFO input :: name: "f8_json", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2121.f8inversion.json"
2025-09-15 20:25:15.368 wdl.w:ptcp.t:call-tar_outputs-24 INFO input :: name: "paraphase_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2121.paraphase.bam.bai"
2025-09-15 20:25:15.368 wdl.w:ptcp.t:call-tar_outputs-24 INFO input :: name: "paraphase_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2121.paraphase.bam"
2025-09-15 20:25:15.368 wdl.w:ptcp.t:call-tar_outputs-24 INFO input :: name: "paraphase_json", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2121.paraphase.json"
2025-09-15 20:25:15.368 wdl.w:ptcp.w:call-trgt-77.t:call-get_reads_overlapping_repeats INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:25:15.368 wdl.w:ptcp.t:call-tar_outputs-24 INFO input :: name: "trgt_spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2121.trgt.sorted.spanning.bam.bai"
2025-09-15 20:25:15.369 wdl.w:ptcp.w:call-trgt-77.t:call-get_reads_overlapping_repeats INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:15.369 wdl.w:ptcp.t:call-tar_outputs-24 INFO input :: name: "trgt_spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2121.trgt.sorted.spanning.bam"
2025-09-15 20:25:15.369 wdl.w:ptcp.t:call-tar_outputs-24 INFO input :: name: "trgt_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2121.trgt.vcf"
2025-09-15 20:25:15.369 wdl.w:ptcp.t:call-tar_outputs-24 INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2121.mapped.bam.bai"
2025-09-15 20:25:15.369 wdl.w:ptcp.t:call-tar_outputs-24 INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2121.mapped.bam"
2025-09-15 20:25:15.369 wdl.w:ptcp.t:call-tar_outputs-24 INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2121"
2025-09-15 20:25:15.369 wdl.w:ptcp.t:call-tar_outputs-24 INFO eval :: name: "threads", value: 1
2025-09-15 20:25:15.369 wdl.w:ptcp.t:call-tar_outputs-24 INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:25:15.369 wdl.w:ptcp.t:call-tar_outputs-24 INFO eval :: name: "disk_size", value: 6
2025-09-15 20:25:15.369 wdl.w:ptcp.t:call-tar_outputs-24 INFO eval :: name: "output_tarball", value: "m84036_250809_035451_s4.bc2121.tar"
2025-09-15 20:25:15.370 wdl.w:ptcp.t:call-tar_outputs-24 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:15.370 wdl.w:ptcp.t:call-tar_outputs-24 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:15.370 wdl.w:ptcp.t:call-tar_outputs-24 INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:25:15.370 wdl.w:ptcp.t:call-tar_outputs-24 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:15.376 wdl.w:ptcp.w:call-sawfish-77.t:call-run_sawfish.stderr VERBOSE [M::bam2fq_mainloop] discarded 0 singletons
2025-09-15 20:25:15.376 wdl.w:ptcp.w:call-sawfish-77.t:call-run_sawfish.stderr VERBOSE [M::bam2fq_mainloop] processed 0 reads
2025-09-15 20:25:15.389 wdl.w:ptcp.w:call-sawfish-77.t:call-run_sawfish.slurm_singularity INFO srun: job 51797962 queued and waiting for resources
2025-09-15 20:25:15.389 wdl.w:ptcp.w:call-sawfish-77.t:call-run_sawfish.slurm_singularity INFO srun: job 51797962 has been allocated resources
2025-09-15 20:25:15.389 wdl.w:ptcp.w:call-sawfish-77.t:call-run_sawfish.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:15.391 wdl.w:ptcp.w:call-trgt-65.t:call-trgt_plot_motifs_waterfall NOTICE slurm_singularity run :: pid: 1205217, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-65/call-trgt_plot_motifs_waterfall/slurm_singularity.log.txt"
2025-09-15 20:25:15.400 wdl.w:ptcp.t:call-tar_outputs-25.slurm_singularity INFO srun: job 51797963 queued and waiting for resources
2025-09-15 20:25:15.400 wdl.w:ptcp.t:call-tar_outputs-25.slurm_singularity INFO srun: job 51797963 has been allocated resources
2025-09-15 20:25:15.400 wdl.w:ptcp.t:call-tar_outputs-25.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:15.443 wdl.w:ptcp.w:call-trgt-77.t:call-get_reads_overlapping_repeats INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 9, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-77/call-get_reads_overlapping_repeats/_singularity_tmpdir_iwu28wvm"
2025-09-15 20:25:15.443 wdl.w:ptcp.w:call-trgt-77.t:call-get_reads_overlapping_repeats INFO Slurm invocation: srun --job-name call-get_reads_overlapping_repeats --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-77/call-get_reads_overlapping_repeats/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-77/call-get_reads_overlapping_repeats/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-77/call-get_reads_overlapping_repeats/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-77/call-get_reads_overlapping_repeats/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-77/out/m84036_250809_035451_s4.bc2174.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2174.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-77/out/m84036_250809_035451_s4.bc2174.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2174.mapped.bam.bai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-77/call-get_reads_overlapping_repeats/_singularity_tmpdir_iwu28wvm/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-77/call-get_reads_overlapping_repeats/_singularity_tmpdir_iwu28wvm/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:15.452 wdl.w:ptcp.w:call-trgt-65.t:call-trgt_plot_meth_allele.slurm_singularity INFO srun: job 51797964 queued and waiting for resources
2025-09-15 20:25:15.452 wdl.w:ptcp.w:call-trgt-65.t:call-trgt_plot_meth_allele.slurm_singularity INFO srun: job 51797964 has been allocated resources
2025-09-15 20:25:15.452 wdl.w:ptcp.w:call-trgt-65.t:call-trgt_plot_meth_allele.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:15.461 wdl.w:ptcp.w:call-trgt-77.t:call-get_reads_overlapping_repeats NOTICE slurm_singularity run :: pid: 1205220, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-77/call-get_reads_overlapping_repeats/slurm_singularity.log.txt"
2025-09-15 20:25:15.494 wdl.w:ptcp.w:call-trgt-61.t:call-trgt_plot_meth_allele INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2158.meth_allele.trgt_plots.zip"
2025-09-15 20:25:15.496 wdl.w:ptcp.t:call-tar_outputs-24 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 17, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-24/_singularity_tmpdir_7u2x03d_"
2025-09-15 20:25:15.496 wdl.w:ptcp.t:call-tar_outputs-24 INFO Slurm invocation: srun --job-name call-tar_outputs-24 --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-24/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-24/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-24/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-24/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-24/out/m84036_250809_035451_s4.bc2121_paraphase/m84036_250809_035451_s4.bc2121.paraphase.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2121.paraphase.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-24/out/m84036_250809_035451_s4.bc2121_paraphase/m84036_250809_035451_s4.bc2121.paraphase.json:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2121.paraphase.json:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-24/out/m84036_250809_035451_s4.bc2121_paraphase/m84036_250809_035451_s4.bc2121.paraphase.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2121.paraphase.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-24/out/m84036_250809_035451_s4.bc2121_sawfish/m84036_250809_035451_s4.bc2121.sv.vcf.gz.tbi:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2121.sv.vcf.gz.tbi:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-24/out/m84036_250809_035451_s4.bc2121_sawfish/m84036_250809_035451_s4.bc2121.sv.vcf.gz:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2121.sv.vcf.gz:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-24/out/m84036_250809_035451_s4.bc2121.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2121.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-24/out/m84036_250809_035451_s4.bc2121.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2121.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-24/out/m84036_250809_035451_s4.bc2121.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2121.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-24/out/m84036_250809_035451_s4.bc2121.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2121.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-24/out/m84036_250809_035451_s4.bc2121.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2121.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-24/out/m84036_250809_035451_s4.bc2121.f8inversion.json:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2121.f8inversion.json:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-24/_singularity_tmpdir_7u2x03d_/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-24/_singularity_tmpdir_7u2x03d_/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:15.511 wdl.w:ptcp.t:call-tar_outputs-24 NOTICE slurm_singularity run :: pid: 1205232, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-24/slurm_singularity.log.txt"
2025-09-15 20:25:15.590 wdl.w:ptcp.w:call-trgt-61.t:call-trgt_plot_meth_allele NOTICE done
2025-09-15 20:25:15.598 wdl.w:ptcp.w:call-trgt-61 NOTICE finish :: job: "call-trgt_plot_meth_allele"
2025-09-15 20:25:15.598 wdl.w:ptcp.w:call-trgt-61 INFO output :: job: "call-trgt_plot_meth_allele", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-61/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2158.meth_allele.trgt_plots.zip"}
2025-09-15 20:25:15.598 wdl.w:ptcp.w:call-trgt-61 INFO visit :: node: "output-images_meth_allele", values: {"images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-61/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2158.meth_allele.trgt_plots.zip"}
2025-09-15 20:25:15.603 wdl.w:ptcp.w:call-trgt-77.t:call-trgt_genotype NOTICE task setup :: name: "trgt_genotype", source: "./trgt.wdl", line: 272, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-77/call-trgt_genotype", thread: 140610912642624
2025-09-15 20:25:15.622 wdl.w:ptcp.w:call-trgt-77.t:call-trgt_genotype INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:15.622 wdl.w:ptcp.w:call-trgt-77.t:call-trgt_genotype INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:25:15.622 wdl.w:ptcp.w:call-trgt-77.t:call-trgt_genotype INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:25:15.622 wdl.w:ptcp.w:call-trgt-77.t:call-trgt_genotype INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:25:15.622 wdl.w:ptcp.w:call-trgt-77.t:call-trgt_genotype INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2174.mapped.bam.bai"
2025-09-15 20:25:15.622 wdl.w:ptcp.w:call-trgt-77.t:call-trgt_genotype INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2174.mapped.bam"
2025-09-15 20:25:15.622 wdl.w:ptcp.w:call-trgt-77.t:call-trgt_genotype INFO input :: name: "sex", value: "F"
2025-09-15 20:25:15.622 wdl.w:ptcp.w:call-trgt-77.t:call-trgt_genotype INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2174"
2025-09-15 20:25:15.624 wdl.w:ptcp.w:call-trgt-77.t:call-trgt_genotype INFO eval :: name: "mem_gb", value: 16
2025-09-15 20:25:15.624 wdl.w:ptcp.w:call-trgt-77.t:call-trgt_genotype INFO eval :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2174.trgt"
2025-09-15 20:25:15.624 wdl.w:ptcp.w:call-trgt-77.t:call-trgt_genotype INFO eval :: name: "threads", value: 8
2025-09-15 20:25:15.625 wdl.w:ptcp.w:call-trgt-77.t:call-trgt_genotype INFO eval :: name: "disk_size", value: 27
2025-09-15 20:25:15.625 wdl.w:ptcp.w:call-trgt-77.t:call-trgt_genotype INFO eval :: name: "karyotype", value: "XX"
2025-09-15 20:25:15.625 wdl.w:ptcp.w:call-trgt-77.t:call-trgt_genotype INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 8, memory_reservation: 16000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:15.625 wdl.w:ptcp.w:call-trgt-77.t:call-trgt_genotype WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:15.625 wdl.w:ptcp.w:call-trgt-77.t:call-trgt_genotype INFO provisioned :: seconds_waited: 0, cpu: 8, mem_bytes: 16000000000
2025-09-15 20:25:15.626 wdl.w:ptcp.w:call-trgt-77.t:call-trgt_genotype INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:15.691 wdl.w:ptcp.w:call-trgt-77.t:call-trgt_genotype INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 11, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-77/call-trgt_genotype/_singularity_tmpdir_et4jklkj"
2025-09-15 20:25:15.691 wdl.w:ptcp.w:call-trgt-77.t:call-trgt_genotype INFO Slurm invocation: srun --job-name call-trgt_genotype --partition compute,compute9 --cpus-per-task 8 --mem 15259M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-77/call-trgt_genotype/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-77/call-trgt_genotype/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-77/call-trgt_genotype/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-77/call-trgt_genotype/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-77/out/m84036_250809_035451_s4.bc2174.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2174.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-77/out/m84036_250809_035451_s4.bc2174.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2174.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-77/call-trgt_genotype/_singularity_tmpdir_et4jklkj/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-77/call-trgt_genotype/_singularity_tmpdir_et4jklkj/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:15.704 wdl.w:ptcp.w:call-trgt-77.t:call-trgt_genotype NOTICE slurm_singularity run :: pid: 1205234, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-77/call-trgt_genotype/slurm_singularity.log.txt"
2025-09-15 20:25:15.935 wdl.w:ptcp.w:call-trgt-65.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO srun: job 51797965 queued and waiting for resources
2025-09-15 20:25:15.935 wdl.w:ptcp.w:call-trgt-65.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO srun: job 51797965 has been allocated resources
2025-09-15 20:25:15.935 wdl.w:ptcp.w:call-trgt-65.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:15.965 wdl.w:ptcp.w:call-paraphase-79.t:call-run_paraphase.stderr VERBOSE INFO:root:Processing sample m84036_250809_035451_s4.bc2176 at 2025-09-15 20:25:11.811099...
2025-09-15 20:25:15.966 wdl.w:ptcp.w:call-paraphase-79.t:call-run_paraphase.stderr VERBOSE INFO:root:Checking sample sex at 2025-09-15 20:25:11.813261...
2025-09-15 20:25:15.966 wdl.w:ptcp.w:call-paraphase-79.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for cyp21 for sample m84036_250809_035451_s4.bc2176 at 2025-09-15 20:25:11.853858...
2025-09-15 20:25:15.966 wdl.w:ptcp.w:call-paraphase-79.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for smn1 for sample m84036_250809_035451_s4.bc2176 at 2025-09-15 20:25:11.854110...
2025-09-15 20:25:15.966 wdl.w:ptcp.w:call-paraphase-79.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for smn1 for sample m84036_250809_035451_s4.bc2176 at 2025-09-15 20:25:11.854582...
2025-09-15 20:25:15.966 wdl.w:ptcp.w:call-paraphase-79.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for cyp21 for sample m84036_250809_035451_s4.bc2176 at 2025-09-15 20:25:11.854573...
2025-09-15 20:25:15.966 wdl.w:ptcp.w:call-paraphase-79.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for gba for sample m84036_250809_035451_s4.bc2176 at 2025-09-15 20:25:11.854409...
2025-09-15 20:25:15.966 wdl.w:ptcp.w:call-paraphase-79.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for hba for sample m84036_250809_035451_s4.bc2176 at 2025-09-15 20:25:11.854441...
2025-09-15 20:25:15.966 wdl.w:ptcp.w:call-paraphase-79.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for gba for sample m84036_250809_035451_s4.bc2176 at 2025-09-15 20:25:11.855076...
2025-09-15 20:25:15.966 wdl.w:ptcp.w:call-paraphase-79.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for hba for sample m84036_250809_035451_s4.bc2176 at 2025-09-15 20:25:11.855078...
2025-09-15 20:25:15.986 wdl.w:ptcp.w:call-trgt-60.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:15 [ERROR] - No reads found for TRID=PRTS_ARX
2025-09-15 20:25:15.987 wdl.w:ptcp.w:call-trgt-60.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:15 [ERROR] - No reads found for TRID=EIEE1_ARX
2025-09-15 20:25:16.031 wdl.w:ptcp.w:call-trgt-60.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:25:15 [ERROR] - No reads found for TRID=PRTS_ARX
2025-09-15 20:25:16.031 wdl.w:ptcp.w:call-trgt-60.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:25:15 [ERROR] - No reads found for TRID=EIEE1_ARX
2025-09-15 20:25:16.057 wdl.w:ptcp.t:call-tar_outputs-25 INFO output :: name: "sample_tarball", value: "m84036_250809_035451_s4.bc2122.tar"
2025-09-15 20:25:16.107 wdl.w:ptcp.t:call-tar_outputs-25 NOTICE done
2025-09-15 20:25:16.111 wdl.w:ptcp NOTICE finish :: job: "call-tar_outputs-25"
2025-09-15 20:25:16.111 wdl.w:ptcp INFO output :: job: "call-tar_outputs-25", values: {"sample_tarball": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-25/out/m84036_250809_035451_s4.bc2122.tar"}
2025-09-15 20:25:16.115 wdl.w:ptcp.w:call-trgt-71.t:call-trgt_plot_meth_allele NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-71/call-trgt_plot_meth_allele", thread: 140612506469952
2025-09-15 20:25:16.132 wdl.w:ptcp.w:call-trgt-71.t:call-trgt_plot_meth_allele INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:16.132 wdl.w:ptcp.w:call-trgt-71.t:call-trgt_plot_meth_allele INFO input :: name: "waterfall", value: false
2025-09-15 20:25:16.132 wdl.w:ptcp.w:call-trgt-71.t:call-trgt_plot_meth_allele INFO input :: name: "methylation", value: true
2025-09-15 20:25:16.132 wdl.w:ptcp.w:call-trgt-71.t:call-trgt_plot_meth_allele INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:25:16.132 wdl.w:ptcp.w:call-trgt-71.t:call-trgt_plot_meth_allele INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:25:16.132 wdl.w:ptcp.w:call-trgt-71.t:call-trgt_plot_meth_allele INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:25:16.132 wdl.w:ptcp.w:call-trgt-71.t:call-trgt_plot_meth_allele INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2168.trgt.sorted.spanning.bam.bai"
2025-09-15 20:25:16.132 wdl.w:ptcp.w:call-trgt-71.t:call-trgt_plot_meth_allele INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2168.trgt.sorted.spanning.bam"
2025-09-15 20:25:16.132 wdl.w:ptcp.w:call-trgt-71.t:call-trgt_plot_meth_allele INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2168.trgt.vcf"
2025-09-15 20:25:16.132 wdl.w:ptcp.w:call-trgt-71.t:call-trgt_plot_meth_allele INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2168"
2025-09-15 20:25:16.133 wdl.w:ptcp.w:call-trgt-71.t:call-trgt_plot_meth_allele INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:25:16.133 wdl.w:ptcp.w:call-trgt-71.t:call-trgt_plot_meth_allele INFO eval :: name: "plot_type", value: "allele"
2025-09-15 20:25:16.133 wdl.w:ptcp.w:call-trgt-71.t:call-trgt_plot_meth_allele INFO eval :: name: "show", value: "meth"
2025-09-15 20:25:16.133 wdl.w:ptcp.w:call-trgt-71.t:call-trgt_plot_meth_allele INFO eval :: name: "threads", value: 1
2025-09-15 20:25:16.133 wdl.w:ptcp.w:call-trgt-71.t:call-trgt_plot_meth_allele INFO eval :: name: "disk_size", value: 27
2025-09-15 20:25:16.133 wdl.w:ptcp.w:call-trgt-71.t:call-trgt_plot_meth_allele INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2168.meth_allele"
2025-09-15 20:25:16.134 wdl.w:ptcp.w:call-trgt-71.t:call-trgt_plot_meth_allele INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:16.134 wdl.w:ptcp.w:call-trgt-71.t:call-trgt_plot_meth_allele WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:16.134 wdl.w:ptcp.w:call-trgt-71.t:call-trgt_plot_meth_allele INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:25:16.134 wdl.w:ptcp.w:call-trgt-71.t:call-trgt_plot_meth_allele INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:16.193 wdl.w:ptcp.w:call-trgt-71.t:call-trgt_plot_meth_allele INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-71/call-trgt_plot_meth_allele/_singularity_tmpdir_hloh0gi5"
2025-09-15 20:25:16.193 wdl.w:ptcp.w:call-trgt-71.t:call-trgt_plot_meth_allele INFO Slurm invocation: srun --job-name call-trgt_plot_meth_allele --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-71/call-trgt_plot_meth_allele/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-71/call-trgt_plot_meth_allele/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-71/call-trgt_plot_meth_allele/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-71/call-trgt_plot_meth_allele/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-71/call-trgt_genotype/out/m84036_250809_035451_s4.bc2168.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2168.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-71/call-trgt_genotype/out/m84036_250809_035451_s4.bc2168.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2168.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-71/call-trgt_genotype/out/m84036_250809_035451_s4.bc2168.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2168.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-71/call-trgt_plot_meth_allele/_singularity_tmpdir_hloh0gi5/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-71/call-trgt_plot_meth_allele/_singularity_tmpdir_hloh0gi5/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:16.211 wdl.w:ptcp.w:call-trgt-71.t:call-trgt_plot_meth_allele NOTICE slurm_singularity run :: pid: 1205252, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-71/call-trgt_plot_meth_allele/slurm_singularity.log.txt"
2025-09-15 20:25:16.278 wdl.w:ptcp.w:call-trgt-65.t:call-trgt_plot_motifs_allele.slurm_singularity INFO srun: job 51797966 queued and waiting for resources
2025-09-15 20:25:16.278 wdl.w:ptcp.w:call-trgt-65.t:call-trgt_plot_motifs_allele.slurm_singularity INFO srun: job 51797966 has been allocated resources
2025-09-15 20:25:16.278 wdl.w:ptcp.w:call-trgt-65.t:call-trgt_plot_motifs_allele.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:16.404 wdl.w:ptcp.w:call-trgt-65.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO srun: job 51797967 queued and waiting for resources
2025-09-15 20:25:16.404 wdl.w:ptcp.w:call-trgt-65.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO srun: job 51797967 has been allocated resources
2025-09-15 20:25:16.404 wdl.w:ptcp.w:call-trgt-65.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:16.472 wdl.w:ptcp.w:call-trgt-77.t:call-get_reads_overlapping_repeats.slurm_singularity INFO srun: job 51797968 queued and waiting for resources
2025-09-15 20:25:16.472 wdl.w:ptcp.w:call-trgt-77.t:call-get_reads_overlapping_repeats.slurm_singularity INFO srun: job 51797968 has been allocated resources
2025-09-15 20:25:16.472 wdl.w:ptcp.w:call-trgt-77.t:call-get_reads_overlapping_repeats.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:16.521 wdl.w:ptcp.t:call-tar_outputs-24.slurm_singularity INFO srun: job 51797969 queued and waiting for resources
2025-09-15 20:25:16.521 wdl.w:ptcp.t:call-tar_outputs-24.slurm_singularity INFO srun: job 51797969 has been allocated resources
2025-09-15 20:25:16.521 wdl.w:ptcp.t:call-tar_outputs-24.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:16.530 wdl.w:ptcp.w:call-paraphase-73.t:call-run_paraphase INFO output :: name: "paraphase_bam", value: "m84036_250809_035451_s4.bc2170_paraphase/m84036_250809_035451_s4.bc2170.paraphase.bam"
2025-09-15 20:25:16.537 wdl.w:ptcp.w:call-paraphase-73.t:call-run_paraphase INFO output :: name: "paraphase_bam_bai", value: "m84036_250809_035451_s4.bc2170_paraphase/m84036_250809_035451_s4.bc2170.paraphase.bam.bai"
2025-09-15 20:25:16.538 wdl.w:ptcp.w:call-paraphase-73.t:call-run_paraphase INFO output :: name: "paraphase_json", value: "m84036_250809_035451_s4.bc2170_paraphase/m84036_250809_035451_s4.bc2170.paraphase.json"
2025-09-15 20:25:16.539 wdl.w:ptcp.w:call-paraphase-73.t:call-run_paraphase INFO output :: name: "paraphase_vcfs", value: []
2025-09-15 20:25:16.539 wdl.w:ptcp.w:call-paraphase-73.t:call-run_paraphase INFO output :: name: "havanno_json", value: "m84036_250809_035451_s4.bc2170.havanno.json"
2025-09-15 20:25:16.619 wdl.w:ptcp.w:call-paraphase-73.t:call-run_paraphase NOTICE done
2025-09-15 20:25:16.625 wdl.w:ptcp.w:call-paraphase-73 NOTICE finish :: job: "call-run_paraphase"
2025-09-15 20:25:16.626 wdl.w:ptcp.w:call-paraphase-73 INFO output :: job: "call-run_paraphase", values: {"havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-73/call-run_paraphase/out/m84036_250809_035451_s4.bc2170.havanno.json", "paraphase_vcfs": [], "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-73/call-run_paraphase/out/m84036_250809_035451_s4.bc2170_paraphase/m84036_250809_035451_s4.bc2170.paraphase.json", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-73/call-run_paraphase/out/m84036_250809_035451_s4.bc2170_paraphase/m84036_250809_035451_s4.bc2170.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-73/call-run_paraphase/out/m84036_250809_035451_s4.bc2170_paraphase/m84036_250809_035451_s4.bc2170.paraphase.bam"}
2025-09-15 20:25:16.626 wdl.w:ptcp.w:call-paraphase-73 NOTICE ready :: job: "call-call_f8", callee: "call_f8"
2025-09-15 20:25:16.626 wdl.w:ptcp.w:call-paraphase-73 INFO input :: job: "call-call_f8", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "out_prefix": "m84036_250809_035451_s4.bc2170", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-73/call-run_paraphase/out/m84036_250809_035451_s4.bc2170_paraphase/m84036_250809_035451_s4.bc2170.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-73/call-run_paraphase/out/m84036_250809_035451_s4.bc2170_paraphase/m84036_250809_035451_s4.bc2170.paraphase.bam", "sex": "F"}
2025-09-15 20:25:16.627 wdl.w:ptcp.w:call-paraphase-73 INFO visit :: node: "output-havanno_json", values: {"havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-73/call-run_paraphase/out/m84036_250809_035451_s4.bc2170.havanno.json"}
2025-09-15 20:25:16.627 wdl.w:ptcp.w:call-paraphase-73 INFO visit :: node: "output-paraphase_bam", values: {"paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-73/call-run_paraphase/out/m84036_250809_035451_s4.bc2170_paraphase/m84036_250809_035451_s4.bc2170.paraphase.bam"}
2025-09-15 20:25:16.627 wdl.w:ptcp.w:call-paraphase-73 INFO visit :: node: "output-paraphase_bam_bai", values: {"paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-73/call-run_paraphase/out/m84036_250809_035451_s4.bc2170_paraphase/m84036_250809_035451_s4.bc2170.paraphase.bam.bai"}
2025-09-15 20:25:16.627 wdl.w:ptcp.w:call-paraphase-73 INFO visit :: node: "output-paraphase_json", values: {"paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-73/call-run_paraphase/out/m84036_250809_035451_s4.bc2170_paraphase/m84036_250809_035451_s4.bc2170.paraphase.json"}
2025-09-15 20:25:16.627 wdl.w:ptcp.w:call-paraphase-73 INFO visit :: node: "output-paraphase_vcfs", values: {"paraphase_vcfs": []}
2025-09-15 20:25:16.632 wdl.w:ptcp.w:call-trgt-71.t:call-trgt_plot_meth_waterfall NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-71/call-trgt_plot_meth_waterfall", thread: 140609285244480
2025-09-15 20:25:16.646 wdl.w:ptcp.w:call-trgt-76.t:call-get_reads_overlapping_repeats INFO output :: name: "reads_overlapping_repeats", value: "m84036_250809_035451_s4.bc2173.repeats.bam"
2025-09-15 20:25:16.652 wdl.w:ptcp.w:call-trgt-76.t:call-get_reads_overlapping_repeats INFO output :: name: "reads_overlapping_repeats_bai", value: "m84036_250809_035451_s4.bc2173.repeats.bam.bai"
2025-09-15 20:25:16.654 wdl.w:ptcp.w:call-trgt-71.t:call-trgt_plot_meth_waterfall INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:16.654 wdl.w:ptcp.w:call-trgt-71.t:call-trgt_plot_meth_waterfall INFO input :: name: "waterfall", value: true
2025-09-15 20:25:16.654 wdl.w:ptcp.w:call-trgt-71.t:call-trgt_plot_meth_waterfall INFO input :: name: "methylation", value: true
2025-09-15 20:25:16.654 wdl.w:ptcp.w:call-trgt-71.t:call-trgt_plot_meth_waterfall INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:25:16.654 wdl.w:ptcp.w:call-trgt-71.t:call-trgt_plot_meth_waterfall INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:25:16.654 wdl.w:ptcp.w:call-trgt-71.t:call-trgt_plot_meth_waterfall INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:25:16.654 wdl.w:ptcp.w:call-trgt-71.t:call-trgt_plot_meth_waterfall INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2168.trgt.sorted.spanning.bam.bai"
2025-09-15 20:25:16.654 wdl.w:ptcp.w:call-trgt-71.t:call-trgt_plot_meth_waterfall INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2168.trgt.sorted.spanning.bam"
2025-09-15 20:25:16.654 wdl.w:ptcp.w:call-trgt-71.t:call-trgt_plot_meth_waterfall INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2168.trgt.vcf"
2025-09-15 20:25:16.654 wdl.w:ptcp.w:call-trgt-71.t:call-trgt_plot_meth_waterfall INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2168"
2025-09-15 20:25:16.655 wdl.w:ptcp.w:call-trgt-71.t:call-trgt_plot_meth_waterfall INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:25:16.655 wdl.w:ptcp.w:call-trgt-71.t:call-trgt_plot_meth_waterfall INFO eval :: name: "plot_type", value: "waterfall"
2025-09-15 20:25:16.655 wdl.w:ptcp.w:call-trgt-71.t:call-trgt_plot_meth_waterfall INFO eval :: name: "show", value: "meth"
2025-09-15 20:25:16.655 wdl.w:ptcp.w:call-trgt-71.t:call-trgt_plot_meth_waterfall INFO eval :: name: "threads", value: 1
2025-09-15 20:25:16.655 wdl.w:ptcp.w:call-trgt-71.t:call-trgt_plot_meth_waterfall INFO eval :: name: "disk_size", value: 27
2025-09-15 20:25:16.655 wdl.w:ptcp.w:call-trgt-71.t:call-trgt_plot_meth_waterfall INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2168.meth_waterfall"
2025-09-15 20:25:16.656 wdl.w:ptcp.w:call-trgt-71.t:call-trgt_plot_meth_waterfall INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:16.656 wdl.w:ptcp.w:call-trgt-71.t:call-trgt_plot_meth_waterfall WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:16.656 wdl.w:ptcp.w:call-trgt-71.t:call-trgt_plot_meth_waterfall INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:25:16.657 wdl.w:ptcp.w:call-trgt-71.t:call-trgt_plot_meth_waterfall INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:16.715 wdl.w:ptcp.w:call-trgt-77.t:call-trgt_genotype.slurm_singularity INFO srun: job 51797970 queued and waiting for resources
2025-09-15 20:25:16.715 wdl.w:ptcp.w:call-trgt-77.t:call-trgt_genotype.slurm_singularity INFO srun: job 51797970 has been allocated resources
2025-09-15 20:25:16.716 wdl.w:ptcp.w:call-trgt-77.t:call-trgt_genotype.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:16.731 wdl.w:ptcp.w:call-trgt-71.t:call-trgt_plot_meth_waterfall INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-71/call-trgt_plot_meth_waterfall/_singularity_tmpdir_0zqqp0bu"
2025-09-15 20:25:16.731 wdl.w:ptcp.w:call-trgt-71.t:call-trgt_plot_meth_waterfall INFO Slurm invocation: srun --job-name call-trgt_plot_meth_waterfall --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-71/call-trgt_plot_meth_waterfall/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-71/call-trgt_plot_meth_waterfall/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-71/call-trgt_plot_meth_waterfall/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-71/call-trgt_plot_meth_waterfall/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-71/call-trgt_genotype/out/m84036_250809_035451_s4.bc2168.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2168.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-71/call-trgt_genotype/out/m84036_250809_035451_s4.bc2168.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2168.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-71/call-trgt_genotype/out/m84036_250809_035451_s4.bc2168.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2168.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-71/call-trgt_plot_meth_waterfall/_singularity_tmpdir_0zqqp0bu/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-71/call-trgt_plot_meth_waterfall/_singularity_tmpdir_0zqqp0bu/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:16.735 wdl.w:ptcp.w:call-trgt-76.t:call-get_reads_overlapping_repeats NOTICE done
2025-09-15 20:25:16.739 wdl.w:ptcp.w:call-trgt-76 NOTICE finish :: job: "call-get_reads_overlapping_repeats"
2025-09-15 20:25:16.739 wdl.w:ptcp.w:call-trgt-76 INFO output :: job: "call-get_reads_overlapping_repeats", values: {"reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-76/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2173.repeats.bam.bai", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-76/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2173.repeats.bam"}
2025-09-15 20:25:16.739 wdl.w:ptcp.w:call-trgt-76 INFO visit :: node: "output-reads_overlapping_repeats", values: {"reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-76/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2173.repeats.bam"}
2025-09-15 20:25:16.740 wdl.w:ptcp.w:call-trgt-76 INFO visit :: node: "output-reads_overlapping_repeats_bai", values: {"reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-76/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2173.repeats.bam.bai"}
2025-09-15 20:25:16.744 wdl.w:ptcp.w:call-trgt-71.t:call-trgt_plot_motifs_allele NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-71/call-trgt_plot_motifs_allele", thread: 140607683024448
2025-09-15 20:25:16.753 wdl.w:ptcp.w:call-paraphase-03.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for f8inv1 for sample m84036_250809_035451_s4.bc2100 at 2025-09-15 20:24:29.185279...
2025-09-15 20:25:16.754 wdl.w:ptcp.w:call-trgt-71.t:call-trgt_plot_meth_waterfall NOTICE slurm_singularity run :: pid: 1205261, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-71/call-trgt_plot_meth_waterfall/slurm_singularity.log.txt"
2025-09-15 20:25:16.755 wdl.w:ptcp.w:call-paraphase-03.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for f8inv1 for sample m84036_250809_035451_s4.bc2100 at 2025-09-15 20:24:34.509893...
2025-09-15 20:25:16.755 wdl.w:ptcp.w:call-paraphase-03.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for f8inv1 for sample m84036_250809_035451_s4.bc2100 at 2025-09-15 20:24:34.905919...
2025-09-15 20:25:16.755 wdl.w:ptcp.w:call-paraphase-03.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for hba for sample m84036_250809_035451_s4.bc2100 at 2025-09-15 20:24:37.970078...
2025-09-15 20:25:16.755 wdl.w:ptcp.w:call-paraphase-03.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for hba for sample m84036_250809_035451_s4.bc2100 at 2025-09-15 20:24:38.529721...
2025-09-15 20:25:16.756 wdl.w:ptcp.w:call-paraphase-03.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for cyp21 for sample m84036_250809_035451_s4.bc2100 at 2025-09-15 20:24:39.914907...
2025-09-15 20:25:16.756 wdl.w:ptcp.w:call-paraphase-03.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for cyp21 for sample m84036_250809_035451_s4.bc2100 at 2025-09-15 20:24:41.184510...
2025-09-15 20:25:16.756 wdl.w:ptcp.w:call-paraphase-03.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for gba for sample m84036_250809_035451_s4.bc2100 at 2025-09-15 20:24:44.145297...
2025-09-15 20:25:16.756 wdl.w:ptcp.w:call-paraphase-03.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for gba for sample m84036_250809_035451_s4.bc2100 at 2025-09-15 20:24:44.764034...
2025-09-15 20:25:16.762 wdl.w:ptcp.w:call-trgt-71.t:call-trgt_plot_motifs_allele INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:16.763 wdl.w:ptcp.w:call-trgt-71.t:call-trgt_plot_motifs_allele INFO input :: name: "waterfall", value: false
2025-09-15 20:25:16.763 wdl.w:ptcp.w:call-trgt-71.t:call-trgt_plot_motifs_allele INFO input :: name: "methylation", value: false
2025-09-15 20:25:16.763 wdl.w:ptcp.w:call-trgt-71.t:call-trgt_plot_motifs_allele INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:25:16.763 wdl.w:ptcp.w:call-trgt-71.t:call-trgt_plot_motifs_allele INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:25:16.763 wdl.w:ptcp.w:call-trgt-71.t:call-trgt_plot_motifs_allele INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:25:16.763 wdl.w:ptcp.w:call-trgt-71.t:call-trgt_plot_motifs_allele INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2168.trgt.sorted.spanning.bam.bai"
2025-09-15 20:25:16.763 wdl.w:ptcp.w:call-trgt-71.t:call-trgt_plot_motifs_allele INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2168.trgt.sorted.spanning.bam"
2025-09-15 20:25:16.763 wdl.w:ptcp.w:call-trgt-71.t:call-trgt_plot_motifs_allele INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2168.trgt.vcf"
2025-09-15 20:25:16.763 wdl.w:ptcp.w:call-trgt-71.t:call-trgt_plot_motifs_allele INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2168"
2025-09-15 20:25:16.763 wdl.w:ptcp.w:call-trgt-71.t:call-trgt_plot_motifs_allele INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:25:16.764 wdl.w:ptcp.w:call-trgt-71.t:call-trgt_plot_motifs_allele INFO eval :: name: "plot_type", value: "allele"
2025-09-15 20:25:16.764 wdl.w:ptcp.w:call-trgt-71.t:call-trgt_plot_motifs_allele INFO eval :: name: "show", value: "motifs"
2025-09-15 20:25:16.764 wdl.w:ptcp.w:call-trgt-71.t:call-trgt_plot_motifs_allele INFO eval :: name: "threads", value: 1
2025-09-15 20:25:16.764 wdl.w:ptcp.w:call-trgt-71.t:call-trgt_plot_motifs_allele INFO eval :: name: "disk_size", value: 27
2025-09-15 20:25:16.764 wdl.w:ptcp.w:call-trgt-71.t:call-trgt_plot_motifs_allele INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2168.motifs_allele"
2025-09-15 20:25:16.764 wdl.w:ptcp.w:call-trgt-71.t:call-trgt_plot_motifs_allele INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:16.765 wdl.w:ptcp.w:call-trgt-71.t:call-trgt_plot_motifs_allele WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:16.765 wdl.w:ptcp.w:call-trgt-71.t:call-trgt_plot_motifs_allele INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:25:16.765 wdl.w:ptcp.w:call-trgt-71.t:call-trgt_plot_motifs_allele INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:16.837 wdl.w:ptcp.w:call-trgt-71.t:call-trgt_plot_motifs_allele INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-71/call-trgt_plot_motifs_allele/_singularity_tmpdir_jj726j6i"
2025-09-15 20:25:16.838 wdl.w:ptcp.w:call-trgt-71.t:call-trgt_plot_motifs_allele INFO Slurm invocation: srun --job-name call-trgt_plot_motifs_allele --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-71/call-trgt_plot_motifs_allele/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-71/call-trgt_plot_motifs_allele/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-71/call-trgt_plot_motifs_allele/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-71/call-trgt_plot_motifs_allele/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-71/call-trgt_genotype/out/m84036_250809_035451_s4.bc2168.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2168.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-71/call-trgt_genotype/out/m84036_250809_035451_s4.bc2168.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2168.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-71/call-trgt_genotype/out/m84036_250809_035451_s4.bc2168.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2168.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-71/call-trgt_plot_motifs_allele/_singularity_tmpdir_jj726j6i/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-71/call-trgt_plot_motifs_allele/_singularity_tmpdir_jj726j6i/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:16.851 wdl.w:ptcp.w:call-trgt-71.t:call-trgt_plot_motifs_allele NOTICE slurm_singularity run :: pid: 1205263, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-71/call-trgt_plot_motifs_allele/slurm_singularity.log.txt"
2025-09-15 20:25:17.108 wdl.w:ptcp.w:call-sawfish-18.t:call-run_sawfish INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2115_sawfish/m84036_250809_035451_s4.bc2115.sv.vcf.gz"
2025-09-15 20:25:17.111 wdl.w:ptcp.w:call-sawfish-18.t:call-run_sawfish INFO output :: name: "vcf_tbi", value: "m84036_250809_035451_s4.bc2115_sawfish/m84036_250809_035451_s4.bc2115.sv.vcf.gz.tbi"
2025-09-15 20:25:17.113 wdl.w:ptcp.w:call-sawfish-18.t:call-run_sawfish INFO output :: name: "minimap2_bam", value: "m84036_250809_035451_s4.bc2115.minimap2.bam"
2025-09-15 20:25:17.115 wdl.w:ptcp.w:call-sawfish-18.t:call-run_sawfish INFO output :: name: "minimap2_bam_bai", value: "m84036_250809_035451_s4.bc2115.minimap2.bam.bai"
2025-09-15 20:25:17.132 wdl.w:ptcp.t:call-tar_outputs-24 INFO output :: name: "sample_tarball", value: "m84036_250809_035451_s4.bc2121.tar"
2025-09-15 20:25:17.203 wdl.w:ptcp.t:call-tar_outputs-24 NOTICE done
2025-09-15 20:25:17.207 wdl.w:ptcp NOTICE finish :: job: "call-tar_outputs-24"
2025-09-15 20:25:17.207 wdl.w:ptcp INFO output :: job: "call-tar_outputs-24", values: {"sample_tarball": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-24/out/m84036_250809_035451_s4.bc2121.tar"}
2025-09-15 20:25:17.211 wdl.w:ptcp.w:call-trgt-76.t:call-trgt_genotype INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2173.trgt.vcf"
2025-09-15 20:25:17.213 wdl.w:ptcp.w:call-trgt-71.t:call-trgt_plot_motifs_waterfall NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-71/call-trgt_plot_motifs_waterfall", thread: 140607691417152
2025-09-15 20:25:17.215 wdl.w:ptcp.w:call-trgt-71.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:17 [ERROR] - No reads found for TRID=SCA37_DAB1
2025-09-15 20:25:17.215 wdl.w:ptcp.w:call-trgt-71.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:17 [ERROR] - No reads found for TRID=NIID_NOTCH2NLC
2025-09-15 20:25:17.215 wdl.w:ptcp.w:call-trgt-71.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:17 [ERROR] - No reads found for TRID=OPDM_ABCD3
2025-09-15 20:25:17.215 wdl.w:ptcp.w:call-trgt-71.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:17 [ERROR] - No reads found for TRID=DRPLA_ATN1
2025-09-15 20:25:17.215 wdl.w:ptcp.w:call-trgt-71.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:17 [ERROR] - No reads found for TRID=OPDM4_RILPL1
2025-09-15 20:25:17.216 wdl.w:ptcp.w:call-trgt-76.t:call-trgt_genotype INFO output :: name: "spanning_bam", value: "m84036_250809_035451_s4.bc2173.trgt.sorted.spanning.bam"
2025-09-15 20:25:17.219 wdl.w:ptcp.w:call-trgt-76.t:call-trgt_genotype INFO output :: name: "spanning_bam_bai", value: "m84036_250809_035451_s4.bc2173.trgt.sorted.spanning.bam.bai"
2025-09-15 20:25:17.228 wdl.w:ptcp.w:call-trgt-71.t:call-trgt_plot_meth_allele.slurm_singularity INFO srun: job 51797971 queued and waiting for resources
2025-09-15 20:25:17.228 wdl.w:ptcp.w:call-trgt-71.t:call-trgt_plot_meth_allele.slurm_singularity INFO srun: job 51797971 has been allocated resources
2025-09-15 20:25:17.228 wdl.w:ptcp.w:call-trgt-71.t:call-trgt_plot_meth_allele.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:17.233 wdl.w:ptcp.w:call-trgt-71.t:call-trgt_plot_motifs_waterfall INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:17.233 wdl.w:ptcp.w:call-trgt-71.t:call-trgt_plot_motifs_waterfall INFO input :: name: "waterfall", value: true
2025-09-15 20:25:17.233 wdl.w:ptcp.w:call-trgt-71.t:call-trgt_plot_motifs_waterfall INFO input :: name: "methylation", value: false
2025-09-15 20:25:17.233 wdl.w:ptcp.w:call-trgt-71.t:call-trgt_plot_motifs_waterfall INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:25:17.234 wdl.w:ptcp.w:call-trgt-71.t:call-trgt_plot_motifs_waterfall INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:25:17.234 wdl.w:ptcp.w:call-trgt-71.t:call-trgt_plot_motifs_waterfall INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:25:17.234 wdl.w:ptcp.w:call-trgt-71.t:call-trgt_plot_motifs_waterfall INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2168.trgt.sorted.spanning.bam.bai"
2025-09-15 20:25:17.234 wdl.w:ptcp.w:call-trgt-71.t:call-trgt_plot_motifs_waterfall INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2168.trgt.sorted.spanning.bam"
2025-09-15 20:25:17.234 wdl.w:ptcp.w:call-trgt-71.t:call-trgt_plot_motifs_waterfall INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2168.trgt.vcf"
2025-09-15 20:25:17.234 wdl.w:ptcp.w:call-trgt-71.t:call-trgt_plot_motifs_waterfall INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2168"
2025-09-15 20:25:17.234 wdl.w:ptcp.w:call-trgt-71.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:25:17.234 wdl.w:ptcp.w:call-trgt-71.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "plot_type", value: "waterfall"
2025-09-15 20:25:17.234 wdl.w:ptcp.w:call-trgt-71.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "show", value: "motifs"
2025-09-15 20:25:17.234 wdl.w:ptcp.w:call-trgt-71.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "threads", value: 1
2025-09-15 20:25:17.235 wdl.w:ptcp.w:call-trgt-71.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "disk_size", value: 27
2025-09-15 20:25:17.235 wdl.w:ptcp.w:call-trgt-71.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2168.motifs_waterfall"
2025-09-15 20:25:17.236 wdl.w:ptcp.w:call-trgt-71.t:call-trgt_plot_motifs_waterfall INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:17.236 wdl.w:ptcp.w:call-trgt-71.t:call-trgt_plot_motifs_waterfall WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:17.236 wdl.w:ptcp.w:call-trgt-71.t:call-trgt_plot_motifs_waterfall INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:25:17.236 wdl.w:ptcp.w:call-trgt-71.t:call-trgt_plot_motifs_waterfall INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:17.281 wdl.w:ptcp.w:call-sawfish-18.t:call-run_sawfish NOTICE done
2025-09-15 20:25:17.289 wdl.w:ptcp.w:call-sawfish-18 NOTICE finish :: job: "call-run_sawfish"
2025-09-15 20:25:17.289 wdl.w:ptcp.w:call-sawfish-18 INFO output :: job: "call-run_sawfish", values: {"minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-18/call-run_sawfish/out/m84036_250809_035451_s4.bc2115.minimap2.bam.bai", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-18/call-run_sawfish/out/m84036_250809_035451_s4.bc2115.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-18/call-run_sawfish/out/m84036_250809_035451_s4.bc2115_sawfish/m84036_250809_035451_s4.bc2115.sv.vcf.gz.tbi", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-18/call-run_sawfish/out/m84036_250809_035451_s4.bc2115_sawfish/m84036_250809_035451_s4.bc2115.sv.vcf.gz"}
2025-09-15 20:25:17.290 wdl.w:ptcp.w:call-sawfish-18 INFO visit :: node: "output-minimap2_bam", values: {"minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-18/call-run_sawfish/out/m84036_250809_035451_s4.bc2115.minimap2.bam"}
2025-09-15 20:25:17.290 wdl.w:ptcp.w:call-sawfish-18 INFO visit :: node: "output-minimap2_bam_bai", values: {"minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-18/call-run_sawfish/out/m84036_250809_035451_s4.bc2115.minimap2.bam.bai"}
2025-09-15 20:25:17.290 wdl.w:ptcp.w:call-sawfish-18 INFO visit :: node: "output-vcf", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-18/call-run_sawfish/out/m84036_250809_035451_s4.bc2115_sawfish/m84036_250809_035451_s4.bc2115.sv.vcf.gz"}
2025-09-15 20:25:17.290 wdl.w:ptcp.w:call-sawfish-18 INFO visit :: node: "output-vcf_tbi", values: {"vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-18/call-run_sawfish/out/m84036_250809_035451_s4.bc2115_sawfish/m84036_250809_035451_s4.bc2115.sv.vcf.gz.tbi"}
2025-09-15 20:25:17.290 wdl.w:ptcp.w:call-sawfish-18 INFO visit :: node: "outputs", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-18/call-run_sawfish/out/m84036_250809_035451_s4.bc2115_sawfish/m84036_250809_035451_s4.bc2115.sv.vcf.gz", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-18/call-run_sawfish/out/m84036_250809_035451_s4.bc2115.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-18/call-run_sawfish/out/m84036_250809_035451_s4.bc2115_sawfish/m84036_250809_035451_s4.bc2115.sv.vcf.gz.tbi", "minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-18/call-run_sawfish/out/m84036_250809_035451_s4.bc2115.minimap2.bam.bai"}
2025-09-15 20:25:17.298 wdl.w:ptcp.w:call-paraphase-75.t:call-run_paraphase NOTICE task setup :: name: "run_paraphase", source: "./paraphase.wdl", line: 127, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-75/call-run_paraphase", thread: 140612514862656
2025-09-15 20:25:17.313 wdl.w:ptcp.w:call-trgt-76.t:call-trgt_genotype NOTICE done
2025-09-15 20:25:17.318 wdl.w:ptcp.w:call-trgt-76 NOTICE finish :: job: "call-trgt_genotype"
2025-09-15 20:25:17.318 wdl.w:ptcp.w:call-trgt-76 INFO output :: job: "call-trgt_genotype", values: {"spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-76/call-trgt_genotype/out/m84036_250809_035451_s4.bc2173.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-76/call-trgt_genotype/out/m84036_250809_035451_s4.bc2173.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-76/call-trgt_genotype/out/m84036_250809_035451_s4.bc2173.trgt.vcf"}
2025-09-15 20:25:17.319 wdl.w:ptcp.w:call-trgt-76 NOTICE ready :: job: "call-trgt_plot_meth_allele", callee: "trgt_plot"
2025-09-15 20:25:17.319 wdl.w:ptcp.w:call-trgt-76 INFO input :: job: "call-trgt_plot_meth_allele", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": false, "methylation": true, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-76/call-trgt_genotype/out/m84036_250809_035451_s4.bc2173.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-76/call-trgt_genotype/out/m84036_250809_035451_s4.bc2173.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-76/call-trgt_genotype/out/m84036_250809_035451_s4.bc2173.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2173"}
2025-09-15 20:25:17.320 wdl.w:ptcp.w:call-trgt-76 NOTICE ready :: job: "call-trgt_plot_meth_waterfall", callee: "trgt_plot"
2025-09-15 20:25:17.320 wdl.w:ptcp.w:call-paraphase-75.t:call-run_paraphase INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:17.321 wdl.w:ptcp.w:call-trgt-76 INFO input :: job: "call-trgt_plot_meth_waterfall", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": true, "methylation": true, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-76/call-trgt_genotype/out/m84036_250809_035451_s4.bc2173.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-76/call-trgt_genotype/out/m84036_250809_035451_s4.bc2173.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-76/call-trgt_genotype/out/m84036_250809_035451_s4.bc2173.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2173"}
2025-09-15 20:25:17.321 wdl.w:ptcp.w:call-paraphase-75.t:call-run_paraphase INFO input :: name: "annotation_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf"
2025-09-15 20:25:17.321 wdl.w:ptcp.w:call-paraphase-75.t:call-run_paraphase INFO input :: name: "genome_version", value: "38"
2025-09-15 20:25:17.321 wdl.w:ptcp.w:call-paraphase-75.t:call-run_paraphase INFO input :: name: "config_file", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/paraphase_config.GRCh38.yaml"
2025-09-15 20:25:17.321 wdl.w:ptcp.w:call-paraphase-75.t:call-run_paraphase INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:25:17.321 wdl.w:ptcp.w:call-paraphase-75.t:call-run_paraphase INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:25:17.321 wdl.w:ptcp.w:call-paraphase-75.t:call-run_paraphase INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2172.mapped.bam.bai"
2025-09-15 20:25:17.321 wdl.w:ptcp.w:call-paraphase-75.t:call-run_paraphase INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2172.mapped.bam"
2025-09-15 20:25:17.321 wdl.w:ptcp.w:call-paraphase-75.t:call-run_paraphase INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2172"
2025-09-15 20:25:17.322 wdl.w:ptcp.w:call-trgt-76 NOTICE ready :: job: "call-trgt_plot_motifs_allele", callee: "trgt_plot"
2025-09-15 20:25:17.322 wdl.w:ptcp.w:call-paraphase-75.t:call-run_paraphase INFO eval :: name: "threads", value: 4
2025-09-15 20:25:17.322 wdl.w:ptcp.w:call-trgt-76 INFO input :: job: "call-trgt_plot_motifs_allele", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": false, "methylation": false, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-76/call-trgt_genotype/out/m84036_250809_035451_s4.bc2173.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-76/call-trgt_genotype/out/m84036_250809_035451_s4.bc2173.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-76/call-trgt_genotype/out/m84036_250809_035451_s4.bc2173.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2173"}
2025-09-15 20:25:17.322 wdl.w:ptcp.w:call-paraphase-75.t:call-run_paraphase INFO eval :: name: "mem_gb", value: 8
2025-09-15 20:25:17.322 wdl.w:ptcp.w:call-trgt-71.t:call-trgt_plot_motifs_waterfall INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-71/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_od3k0slw"
2025-09-15 20:25:17.323 wdl.w:ptcp.w:call-trgt-76 NOTICE ready :: job: "call-trgt_plot_motifs_waterfall", callee: "trgt_plot"
2025-09-15 20:25:17.323 wdl.w:ptcp.w:call-trgt-71.t:call-trgt_plot_motifs_waterfall INFO Slurm invocation: srun --job-name call-trgt_plot_motifs_waterfall --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-71/call-trgt_plot_motifs_waterfall/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-71/call-trgt_plot_motifs_waterfall/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-71/call-trgt_plot_motifs_waterfall/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-71/call-trgt_plot_motifs_waterfall/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-71/call-trgt_genotype/out/m84036_250809_035451_s4.bc2168.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2168.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-71/call-trgt_genotype/out/m84036_250809_035451_s4.bc2168.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2168.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-71/call-trgt_genotype/out/m84036_250809_035451_s4.bc2168.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2168.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-71/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_od3k0slw/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-71/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_od3k0slw/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:17.323 wdl.w:ptcp.w:call-paraphase-75.t:call-run_paraphase INFO eval :: name: "disk_size", value: 27
2025-09-15 20:25:17.324 wdl.w:ptcp.w:call-trgt-76 INFO input :: job: "call-trgt_plot_motifs_waterfall", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": true, "methylation": false, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-76/call-trgt_genotype/out/m84036_250809_035451_s4.bc2173.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-76/call-trgt_genotype/out/m84036_250809_035451_s4.bc2173.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-76/call-trgt_genotype/out/m84036_250809_035451_s4.bc2173.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2173"}
2025-09-15 20:25:17.324 wdl.w:ptcp.w:call-paraphase-75.t:call-run_paraphase INFO eval :: name: "out_dir", value: "m84036_250809_035451_s4.bc2172_paraphase"
2025-09-15 20:25:17.325 wdl.w:ptcp.w:call-trgt-76 INFO visit :: node: "output-spanning_bam", values: {"spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-76/call-trgt_genotype/out/m84036_250809_035451_s4.bc2173.trgt.sorted.spanning.bam"}
2025-09-15 20:25:17.325 wdl.w:ptcp.w:call-paraphase-75.t:call-run_paraphase INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 4, memory_reservation: 8000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:17.326 wdl.w:ptcp.w:call-trgt-76 INFO visit :: node: "output-spanning_bam_bai", values: {"spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-76/call-trgt_genotype/out/m84036_250809_035451_s4.bc2173.trgt.sorted.spanning.bam.bai"}
2025-09-15 20:25:17.326 wdl.w:ptcp.w:call-trgt-76 INFO visit :: node: "output-vcf", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-76/call-trgt_genotype/out/m84036_250809_035451_s4.bc2173.trgt.vcf"}
2025-09-15 20:25:17.326 wdl.w:ptcp.w:call-paraphase-75.t:call-run_paraphase WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:17.327 wdl.w:ptcp.w:call-paraphase-75.t:call-run_paraphase INFO provisioned :: seconds_waited: 0, cpu: 4, mem_bytes: 8000000000
2025-09-15 20:25:17.327 wdl.w:ptcp.w:call-paraphase-75.t:call-run_paraphase INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:17.340 wdl.w:ptcp.t:call-tar_outputs-37 NOTICE task setup :: name: "tar_outputs", source: "./common.wdl", line: 279, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-37", thread: 140611961206336
2025-09-15 20:25:17.341 wdl.w:ptcp.w:call-sawfish-18 NOTICE done
2025-09-15 20:25:17.348 wdl.w:ptcp NOTICE finish :: job: "call-sawfish-18"
2025-09-15 20:25:17.348 wdl.w:ptcp INFO output :: job: "call-sawfish-18", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-18/out/m84036_250809_035451_s4.bc2115_sawfish/m84036_250809_035451_s4.bc2115.sv.vcf.gz", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-18/out/m84036_250809_035451_s4.bc2115.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-18/out/m84036_250809_035451_s4.bc2115_sawfish/m84036_250809_035451_s4.bc2115.sv.vcf.gz.tbi", "minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-18/out/m84036_250809_035451_s4.bc2115.minimap2.bam.bai"}
2025-09-15 20:25:17.349 wdl.w:ptcp.w:call-trgt-71.t:call-trgt_plot_motifs_waterfall NOTICE slurm_singularity run :: pid: 1205278, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-71/call-trgt_plot_motifs_waterfall/slurm_singularity.log.txt"
2025-09-15 20:25:17.355 wdl.w:ptcp.w:call-sawfish-82 NOTICE workflow start :: name: "sawfish", source: "./sawfish.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-82"
2025-09-15 20:25:17.369 wdl.w:ptcp.t:call-tar_outputs-37 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:17.369 wdl.w:ptcp.t:call-tar_outputs-37 INFO input :: name: "sawfish_vcf_tbi", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2134.sv.vcf.gz.tbi"
2025-09-15 20:25:17.369 wdl.w:ptcp.t:call-tar_outputs-37 INFO input :: name: "sawfish_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2134.sv.vcf.gz"
2025-09-15 20:25:17.369 wdl.w:ptcp.t:call-tar_outputs-37 INFO input :: name: "f8_json", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2134.f8inversion.json"
2025-09-15 20:25:17.370 wdl.w:ptcp.t:call-tar_outputs-37 INFO input :: name: "paraphase_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2134.paraphase.bam.bai"
2025-09-15 20:25:17.370 wdl.w:ptcp.t:call-tar_outputs-37 INFO input :: name: "paraphase_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2134.paraphase.bam"
2025-09-15 20:25:17.370 wdl.w:ptcp.t:call-tar_outputs-37 INFO input :: name: "paraphase_json", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2134.paraphase.json"
2025-09-15 20:25:17.370 wdl.w:ptcp.t:call-tar_outputs-37 INFO input :: name: "trgt_spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2134.trgt.sorted.spanning.bam.bai"
2025-09-15 20:25:17.370 wdl.w:ptcp.t:call-tar_outputs-37 INFO input :: name: "trgt_spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2134.trgt.sorted.spanning.bam"
2025-09-15 20:25:17.370 wdl.w:ptcp.t:call-tar_outputs-37 INFO input :: name: "trgt_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2134.trgt.vcf"
2025-09-15 20:25:17.370 wdl.w:ptcp.t:call-tar_outputs-37 INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2134.mapped.bam.bai"
2025-09-15 20:25:17.370 wdl.w:ptcp.t:call-tar_outputs-37 INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2134.mapped.bam"
2025-09-15 20:25:17.370 wdl.w:ptcp.t:call-tar_outputs-37 INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2134"
2025-09-15 20:25:17.371 wdl.w:ptcp.t:call-tar_outputs-37 INFO eval :: name: "threads", value: 1
2025-09-15 20:25:17.371 wdl.w:ptcp.t:call-tar_outputs-37 INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:25:17.371 wdl.w:ptcp.t:call-tar_outputs-37 INFO eval :: name: "disk_size", value: 6
2025-09-15 20:25:17.372 wdl.w:ptcp.t:call-tar_outputs-37 INFO eval :: name: "output_tarball", value: "m84036_250809_035451_s4.bc2134.tar"
2025-09-15 20:25:17.373 wdl.w:ptcp.t:call-tar_outputs-37 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:17.374 wdl.w:ptcp.t:call-tar_outputs-37 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:17.374 wdl.w:ptcp.t:call-tar_outputs-37 INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:25:17.374 wdl.w:ptcp.t:call-tar_outputs-37 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:17.375 wdl.w:ptcp.w:call-sawfish-82 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:25:17.375 wdl.w:ptcp.w:call-sawfish-82 INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:25:17.376 wdl.w:ptcp.w:call-sawfish-82 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-82/out/m84036_250809_035451_s4.bc2179.mapped.bam"}
2025-09-15 20:25:17.376 wdl.w:ptcp.w:call-sawfish-82 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-82/out/m84036_250809_035451_s4.bc2179.mapped.bam.bai"}
2025-09-15 20:25:17.376 wdl.w:ptcp.w:call-sawfish-82 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:25:17.376 wdl.w:ptcp.w:call-sawfish-82 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:25:17.376 wdl.w:ptcp.w:call-sawfish-82 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2179"}
2025-09-15 20:25:17.376 wdl.w:ptcp.w:call-sawfish-82 NOTICE ready :: job: "call-run_sawfish", callee: "run_sawfish"
2025-09-15 20:25:17.376 wdl.w:ptcp.w:call-sawfish-82 INFO input :: job: "call-run_sawfish", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-82/out/m84036_250809_035451_s4.bc2179.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-82/out/m84036_250809_035451_s4.bc2179.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2179"}
2025-09-15 20:25:17.405 wdl.w:ptcp.w:call-paraphase-75.t:call-run_paraphase INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-75/call-run_paraphase/_singularity_tmpdir_yiwzlans"
2025-09-15 20:25:17.405 wdl.w:ptcp.w:call-paraphase-75.t:call-run_paraphase INFO Slurm invocation: srun --job-name call-run_paraphase --partition compute,compute9 --cpus-per-task 4 --mem 7629M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-75/call-run_paraphase/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-75/call-run_paraphase/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-75/call-run_paraphase/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-75/call-run_paraphase/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-75/out/m84036_250809_035451_s4.bc2172.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2172.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-75/out/m84036_250809_035451_s4.bc2172.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2172.mapped.bam.bai:ro --bind /ptcp/meta/variant_list/variant_list.GRCh38.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf:ro --bind /ptcp/meta/paraphase/paraphase_config.GRCh38.yaml:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/paraphase_config.GRCh38.yaml:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-75/call-run_paraphase/_singularity_tmpdir_yiwzlans/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-75/call-run_paraphase/_singularity_tmpdir_yiwzlans/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:17.419 wdl.w:ptcp.w:call-paraphase-75.t:call-run_paraphase NOTICE slurm_singularity run :: pid: 1205280, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-75/call-run_paraphase/slurm_singularity.log.txt"
2025-09-15 20:25:17.447 wdl.w:ptcp.w:call-paraphase-54.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for smn1 for sample m84036_250809_035451_s4.bc2151 at 2025-09-15 20:24:54.952898...
2025-09-15 20:25:17.448 wdl.w:ptcp.w:call-paraphase-54.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for cyp21 for sample m84036_250809_035451_s4.bc2151 at 2025-09-15 20:25:02.411726...
2025-09-15 20:25:17.448 wdl.w:ptcp.w:call-paraphase-54.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for cyp21 for sample m84036_250809_035451_s4.bc2151 at 2025-09-15 20:25:03.025277...
2025-09-15 20:25:17.448 wdl.w:ptcp.w:call-paraphase-54.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for hba for sample m84036_250809_035451_s4.bc2151 at 2025-09-15 20:25:05.463454...
2025-09-15 20:25:17.448 wdl.w:ptcp.w:call-paraphase-54.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for hba for sample m84036_250809_035451_s4.bc2151 at 2025-09-15 20:25:05.730006...
2025-09-15 20:25:17.449 wdl.w:ptcp.w:call-paraphase-54.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for f8inv1 for sample m84036_250809_035451_s4.bc2151 at 2025-09-15 20:25:07.857595...
2025-09-15 20:25:17.449 wdl.w:ptcp.w:call-paraphase-54.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for f8inv1 for sample m84036_250809_035451_s4.bc2151 at 2025-09-15 20:25:07.857752...
2025-09-15 20:25:17.449 wdl.w:ptcp.w:call-paraphase-54.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for f8inv1 for sample m84036_250809_035451_s4.bc2151 at 2025-09-15 20:25:08.854512...
2025-09-15 20:25:17.449 wdl.w:ptcp.w:call-paraphase-54.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for gba for sample m84036_250809_035451_s4.bc2151 at 2025-09-15 20:25:10.090264...
2025-09-15 20:25:17.449 wdl.w:ptcp.w:call-paraphase-54.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for gba for sample m84036_250809_035451_s4.bc2151 at 2025-09-15 20:25:10.574841...
2025-09-15 20:25:17.449 wdl.w:ptcp.w:call-paraphase-54.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for f8inv1 for sample m84036_250809_035451_s4.bc2151 at 2025-09-15 20:25:11.442802...
2025-09-15 20:25:17.449 wdl.w:ptcp.w:call-paraphase-54.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for f8inv1 for sample m84036_250809_035451_s4.bc2151 at 2025-09-15 20:25:11.807799...
2025-09-15 20:25:17.449 wdl.w:ptcp.w:call-paraphase-54.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for hbb for sample m84036_250809_035451_s4.bc2151 at 2025-09-15 20:25:12.270075...
2025-09-15 20:25:17.449 wdl.w:ptcp.w:call-paraphase-54.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for hbb for sample m84036_250809_035451_s4.bc2151 at 2025-09-15 20:25:12.270238...
2025-09-15 20:25:17.449 wdl.w:ptcp.w:call-paraphase-54.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for hbb for sample m84036_250809_035451_s4.bc2151 at 2025-09-15 20:25:13.090559...
2025-09-15 20:25:17.449 wdl.w:ptcp.w:call-paraphase-54.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for hbb for sample m84036_250809_035451_s4.bc2151 at 2025-09-15 20:25:15.202024...
2025-09-15 20:25:17.449 wdl.w:ptcp.w:call-paraphase-54.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for hbb for sample m84036_250809_035451_s4.bc2151 at 2025-09-15 20:25:15.455350...
2025-09-15 20:25:17.464 wdl.w:ptcp.w:call-trgt-61.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:25:12 [ERROR] - No reads found for TRID=PRTS_ARX
2025-09-15 20:25:17.465 wdl.w:ptcp.w:call-trgt-61.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:25:12 [ERROR] - No reads found for TRID=EIEE1_ARX
2025-09-15 20:25:17.494 wdl.w:ptcp.t:call-tar_outputs-37 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 17, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-37/_singularity_tmpdir_glkwalii"
2025-09-15 20:25:17.494 wdl.w:ptcp.t:call-tar_outputs-37 INFO Slurm invocation: srun --job-name call-tar_outputs-37 --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-37/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-37/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-37/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-37/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-37/out/m84036_250809_035451_s4.bc2134.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2134.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-37/out/m84036_250809_035451_s4.bc2134.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2134.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-37/out/m84036_250809_035451_s4.bc2134_sawfish/m84036_250809_035451_s4.bc2134.sv.vcf.gz:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2134.sv.vcf.gz:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-37/out/m84036_250809_035451_s4.bc2134_sawfish/m84036_250809_035451_s4.bc2134.sv.vcf.gz.tbi:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2134.sv.vcf.gz.tbi:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-37/out/m84036_250809_035451_s4.bc2134.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2134.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-37/out/m84036_250809_035451_s4.bc2134.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2134.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-37/out/m84036_250809_035451_s4.bc2134.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2134.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-37/out/m84036_250809_035451_s4.bc2134_paraphase/m84036_250809_035451_s4.bc2134.paraphase.json:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2134.paraphase.json:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-37/out/m84036_250809_035451_s4.bc2134_paraphase/m84036_250809_035451_s4.bc2134.paraphase.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2134.paraphase.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-37/out/m84036_250809_035451_s4.bc2134_paraphase/m84036_250809_035451_s4.bc2134.paraphase.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2134.paraphase.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-37/out/m84036_250809_035451_s4.bc2134.f8inversion.json:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2134.f8inversion.json:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-37/_singularity_tmpdir_glkwalii/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-37/_singularity_tmpdir_glkwalii/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:17.508 wdl.w:ptcp.t:call-tar_outputs-37 NOTICE slurm_singularity run :: pid: 1205282, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-37/slurm_singularity.log.txt"
2025-09-15 20:25:17.763 wdl.w:ptcp.w:call-trgt-71.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO srun: job 51797972 queued and waiting for resources
2025-09-15 20:25:17.763 wdl.w:ptcp.w:call-trgt-71.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO srun: job 51797972 has been allocated resources
2025-09-15 20:25:17.764 wdl.w:ptcp.w:call-trgt-71.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:17.777 wdl.w:ptcp.w:call-trgt-64.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:25:17 [ERROR] - No reads found for TRID=PRTS_ARX
2025-09-15 20:25:17.777 wdl.w:ptcp.w:call-trgt-64.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:25:17 [ERROR] - No reads found for TRID=EIEE1_ARX
2025-09-15 20:25:17.854 wdl.w:ptcp.w:call-trgt-71.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:25:17 [ERROR] - No reads found for TRID=SCA37_DAB1
2025-09-15 20:25:17.854 wdl.w:ptcp.w:call-trgt-71.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:25:17 [ERROR] - No reads found for TRID=NIID_NOTCH2NLC
2025-09-15 20:25:17.854 wdl.w:ptcp.w:call-trgt-71.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:25:17 [ERROR] - No reads found for TRID=OPDM_ABCD3
2025-09-15 20:25:17.854 wdl.w:ptcp.w:call-trgt-71.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:25:17 [ERROR] - No reads found for TRID=DRPLA_ATN1
2025-09-15 20:25:17.854 wdl.w:ptcp.w:call-trgt-71.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:25:17 [ERROR] - No reads found for TRID=OPDM4_RILPL1
2025-09-15 20:25:17.865 wdl.w:ptcp.w:call-trgt-71.t:call-trgt_plot_motifs_allele.slurm_singularity INFO srun: job 51797973 queued and waiting for resources
2025-09-15 20:25:17.865 wdl.w:ptcp.w:call-trgt-71.t:call-trgt_plot_motifs_allele.slurm_singularity INFO srun: job 51797973 has been allocated resources
2025-09-15 20:25:17.865 wdl.w:ptcp.w:call-trgt-71.t:call-trgt_plot_motifs_allele.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:17.957 wdl.w:ptcp.w:call-paraphase-59.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for smn1 for sample m84036_250809_035451_s4.bc2156 at 2025-09-15 20:24:57.288117...
2025-09-15 20:25:17.958 wdl.w:ptcp.w:call-paraphase-59.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for hba for sample m84036_250809_035451_s4.bc2156 at 2025-09-15 20:25:08.799264...
2025-09-15 20:25:17.958 wdl.w:ptcp.w:call-paraphase-59.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for hba for sample m84036_250809_035451_s4.bc2156 at 2025-09-15 20:25:09.206125...
2025-09-15 20:25:17.958 wdl.w:ptcp.w:call-paraphase-59.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for cyp21 for sample m84036_250809_035451_s4.bc2156 at 2025-09-15 20:25:13.259386...
2025-09-15 20:25:17.958 wdl.w:ptcp.w:call-paraphase-59.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for cyp21 for sample m84036_250809_035451_s4.bc2156 at 2025-09-15 20:25:14.041784...
2025-09-15 20:25:18.271 wdl.w:ptcp.w:call-sawfish-19.t:call-run_sawfish INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2116_sawfish/m84036_250809_035451_s4.bc2116.sv.vcf.gz"
2025-09-15 20:25:18.277 wdl.w:ptcp.w:call-sawfish-19.t:call-run_sawfish INFO output :: name: "vcf_tbi", value: "m84036_250809_035451_s4.bc2116_sawfish/m84036_250809_035451_s4.bc2116.sv.vcf.gz.tbi"
2025-09-15 20:25:18.278 wdl.w:ptcp.w:call-sawfish-19.t:call-run_sawfish INFO output :: name: "minimap2_bam", value: "m84036_250809_035451_s4.bc2116.minimap2.bam"
2025-09-15 20:25:18.280 wdl.w:ptcp.w:call-sawfish-19.t:call-run_sawfish INFO output :: name: "minimap2_bam_bai", value: "m84036_250809_035451_s4.bc2116.minimap2.bam.bai"
2025-09-15 20:25:18.349 wdl.w:ptcp.w:call-trgt-61.t:call-trgt_plot_meth_waterfall INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2158.meth_waterfall.trgt_plots.zip"
2025-09-15 20:25:18.371 wdl.w:ptcp.w:call-trgt-71.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO srun: job 51797974 queued and waiting for resources
2025-09-15 20:25:18.371 wdl.w:ptcp.w:call-trgt-71.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO srun: job 51797974 has been allocated resources
2025-09-15 20:25:18.371 wdl.w:ptcp.w:call-trgt-71.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:18.439 wdl.w:ptcp.w:call-paraphase-75.t:call-run_paraphase.slurm_singularity INFO srun: job 51797975 queued and waiting for resources
2025-09-15 20:25:18.439 wdl.w:ptcp.w:call-paraphase-75.t:call-run_paraphase.slurm_singularity INFO srun: job 51797975 has been allocated resources
2025-09-15 20:25:18.439 wdl.w:ptcp.w:call-paraphase-75.t:call-run_paraphase.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:18.486 wdl.w:ptcp.w:call-sawfish-19.t:call-run_sawfish NOTICE done
2025-09-15 20:25:18.487 wdl.w:ptcp.w:call-trgt-65.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:17 [ERROR] - No reads found for TRID=PRTS_ARX
2025-09-15 20:25:18.488 wdl.w:ptcp.w:call-trgt-65.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:17 [ERROR] - No reads found for TRID=EIEE1_ARX
2025-09-15 20:25:18.500 wdl.w:ptcp.w:call-sawfish-19 NOTICE finish :: job: "call-run_sawfish"
2025-09-15 20:25:18.500 wdl.w:ptcp.w:call-sawfish-19 INFO output :: job: "call-run_sawfish", values: {"minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-19/call-run_sawfish/out/m84036_250809_035451_s4.bc2116.minimap2.bam.bai", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-19/call-run_sawfish/out/m84036_250809_035451_s4.bc2116.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-19/call-run_sawfish/out/m84036_250809_035451_s4.bc2116_sawfish/m84036_250809_035451_s4.bc2116.sv.vcf.gz.tbi", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-19/call-run_sawfish/out/m84036_250809_035451_s4.bc2116_sawfish/m84036_250809_035451_s4.bc2116.sv.vcf.gz"}
2025-09-15 20:25:18.500 wdl.w:ptcp.w:call-sawfish-19 INFO visit :: node: "output-minimap2_bam", values: {"minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-19/call-run_sawfish/out/m84036_250809_035451_s4.bc2116.minimap2.bam"}
2025-09-15 20:25:18.500 wdl.w:ptcp.w:call-sawfish-19 INFO visit :: node: "output-minimap2_bam_bai", values: {"minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-19/call-run_sawfish/out/m84036_250809_035451_s4.bc2116.minimap2.bam.bai"}
2025-09-15 20:25:18.500 wdl.w:ptcp.w:call-sawfish-19 INFO visit :: node: "output-vcf", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-19/call-run_sawfish/out/m84036_250809_035451_s4.bc2116_sawfish/m84036_250809_035451_s4.bc2116.sv.vcf.gz"}
2025-09-15 20:25:18.501 wdl.w:ptcp.w:call-sawfish-19 INFO visit :: node: "output-vcf_tbi", values: {"vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-19/call-run_sawfish/out/m84036_250809_035451_s4.bc2116_sawfish/m84036_250809_035451_s4.bc2116.sv.vcf.gz.tbi"}
2025-09-15 20:25:18.501 wdl.w:ptcp.w:call-sawfish-19 INFO visit :: node: "outputs", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-19/call-run_sawfish/out/m84036_250809_035451_s4.bc2116_sawfish/m84036_250809_035451_s4.bc2116.sv.vcf.gz", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-19/call-run_sawfish/out/m84036_250809_035451_s4.bc2116.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-19/call-run_sawfish/out/m84036_250809_035451_s4.bc2116_sawfish/m84036_250809_035451_s4.bc2116.sv.vcf.gz.tbi", "minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-19/call-run_sawfish/out/m84036_250809_035451_s4.bc2116.minimap2.bam.bai"}
2025-09-15 20:25:18.510 wdl.w:ptcp.w:call-sawfish-75.t:call-run_sawfish NOTICE task setup :: name: "run_sawfish", source: "./sawfish.wdl", line: 83, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-75/call-run_sawfish", thread: 140612523255360
2025-09-15 20:25:18.529 wdl.w:ptcp.t:call-tar_outputs-37.slurm_singularity INFO srun: job 51797976 queued and waiting for resources
2025-09-15 20:25:18.529 wdl.w:ptcp.t:call-tar_outputs-37.slurm_singularity INFO srun: job 51797976 has been allocated resources
2025-09-15 20:25:18.529 wdl.w:ptcp.t:call-tar_outputs-37.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:18.535 wdl.w:ptcp.w:call-sawfish-75.t:call-run_sawfish INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:18.535 wdl.w:ptcp.w:call-sawfish-75.t:call-run_sawfish INFO input :: name: "genome_version", value: "38"
2025-09-15 20:25:18.535 wdl.w:ptcp.w:call-sawfish-75.t:call-run_sawfish INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:25:18.535 wdl.w:ptcp.w:call-sawfish-75.t:call-run_sawfish INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:25:18.535 wdl.w:ptcp.w:call-sawfish-75.t:call-run_sawfish INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2172.mapped.bam.bai"
2025-09-15 20:25:18.535 wdl.w:ptcp.w:call-sawfish-75.t:call-run_sawfish INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2172.mapped.bam"
2025-09-15 20:25:18.535 wdl.w:ptcp.w:call-sawfish-75.t:call-run_sawfish INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2172"
2025-09-15 20:25:18.536 wdl.w:ptcp.w:call-sawfish-75.t:call-run_sawfish INFO eval :: name: "mem_gb", value: 32
2025-09-15 20:25:18.536 wdl.w:ptcp.w:call-sawfish-75.t:call-run_sawfish INFO eval :: name: "threads", value: 16
2025-09-15 20:25:18.536 wdl.w:ptcp.w:call-sawfish-75.t:call-run_sawfish INFO eval :: name: "disk_size", value: 30
2025-09-15 20:25:18.536 wdl.w:ptcp.w:call-sawfish-75.t:call-run_sawfish INFO eval :: name: "discover_dirname", value: "m84036_250809_035451_s4.bc2172_sawfish_discover"
2025-09-15 20:25:18.537 wdl.w:ptcp.w:call-sawfish-75.t:call-run_sawfish INFO eval :: name: "call_dirname", value: "m84036_250809_035451_s4.bc2172_sawfish"
2025-09-15 20:25:18.537 wdl.w:ptcp.w:call-sawfish-75.t:call-run_sawfish INFO eval :: name: "minimap2_bam_filename", value: "m84036_250809_035451_s4.bc2172.minimap2.bam"
2025-09-15 20:25:18.537 wdl.w:ptcp.w:call-sawfish-75.t:call-run_sawfish INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 16, memory_reservation: 32000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:18.538 wdl.w:ptcp.w:call-sawfish-75.t:call-run_sawfish WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:18.538 wdl.w:ptcp.w:call-sawfish-75.t:call-run_sawfish INFO provisioned :: seconds_waited: 0, cpu: 16, mem_bytes: 32000000000
2025-09-15 20:25:18.538 wdl.w:ptcp.w:call-sawfish-75.t:call-run_sawfish INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:18.544 wdl.w:ptcp.w:call-trgt-61.t:call-trgt_plot_meth_waterfall NOTICE done
2025-09-15 20:25:18.551 wdl.w:ptcp.w:call-trgt-61 NOTICE finish :: job: "call-trgt_plot_meth_waterfall"
2025-09-15 20:25:18.551 wdl.w:ptcp.w:call-trgt-61 INFO output :: job: "call-trgt_plot_meth_waterfall", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-61/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2158.meth_waterfall.trgt_plots.zip"}
2025-09-15 20:25:18.551 wdl.w:ptcp.w:call-trgt-61 INFO visit :: node: "output-images_meth_waterfall", values: {"images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-61/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2158.meth_waterfall.trgt_plots.zip"}
2025-09-15 20:25:18.552 wdl.w:ptcp.w:call-trgt-61 INFO visit :: node: "outputs", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-61/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2158.motifs_waterfall.trgt_plots.zip", "images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-61/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2158.meth_allele.trgt_plots.zip", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-61/call-trgt_genotype/out/m84036_250809_035451_s4.bc2158.trgt.sorted.spanning.bam.bai", "images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-61/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2158.motifs_allele.trgt_plots.zip", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-61/call-trgt_genotype/out/m84036_250809_035451_s4.bc2158.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-61/call-trgt_genotype/out/m84036_250809_035451_s4.bc2158.trgt.vcf", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-61/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2158.repeats.bam", "images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-61/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2158.meth_waterfall.trgt_plots.zip", "reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-61/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2158.repeats.bam.bai"}
2025-09-15 20:25:18.566 wdl.w:ptcp.t:call-tar_outputs-36 NOTICE task setup :: name: "tar_outputs", source: "./common.wdl", line: 279, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-36", thread: 140611415942720
2025-09-15 20:25:18.573 wdl.w:ptcp.w:call-sawfish-19 NOTICE done
2025-09-15 20:25:18.581 wdl.w:ptcp NOTICE finish :: job: "call-sawfish-19"
2025-09-15 20:25:18.582 wdl.w:ptcp INFO output :: job: "call-sawfish-19", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-19/out/m84036_250809_035451_s4.bc2116_sawfish/m84036_250809_035451_s4.bc2116.sv.vcf.gz", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-19/out/m84036_250809_035451_s4.bc2116.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-19/out/m84036_250809_035451_s4.bc2116_sawfish/m84036_250809_035451_s4.bc2116.sv.vcf.gz.tbi", "minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-19/out/m84036_250809_035451_s4.bc2116.minimap2.bam.bai"}
2025-09-15 20:25:18.592 wdl.w:ptcp.w:call-trgt-82 NOTICE workflow start :: name: "trgt", source: "./trgt.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-82"
2025-09-15 20:25:18.606 wdl.w:ptcp.t:call-tar_outputs-36 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:18.606 wdl.w:ptcp.t:call-tar_outputs-36 INFO input :: name: "sawfish_vcf_tbi", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2133.sv.vcf.gz.tbi"
2025-09-15 20:25:18.606 wdl.w:ptcp.t:call-tar_outputs-36 INFO input :: name: "sawfish_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2133.sv.vcf.gz"
2025-09-15 20:25:18.606 wdl.w:ptcp.t:call-tar_outputs-36 INFO input :: name: "f8_json", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2133.f8inversion.json"
2025-09-15 20:25:18.606 wdl.w:ptcp.t:call-tar_outputs-36 INFO input :: name: "paraphase_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2133.paraphase.bam.bai"
2025-09-15 20:25:18.606 wdl.w:ptcp.t:call-tar_outputs-36 INFO input :: name: "paraphase_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2133.paraphase.bam"
2025-09-15 20:25:18.606 wdl.w:ptcp.t:call-tar_outputs-36 INFO input :: name: "paraphase_json", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2133.paraphase.json"
2025-09-15 20:25:18.606 wdl.w:ptcp.t:call-tar_outputs-36 INFO input :: name: "trgt_spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2133.trgt.sorted.spanning.bam.bai"
2025-09-15 20:25:18.607 wdl.w:ptcp.t:call-tar_outputs-36 INFO input :: name: "trgt_spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2133.trgt.sorted.spanning.bam"
2025-09-15 20:25:18.607 wdl.w:ptcp.t:call-tar_outputs-36 INFO input :: name: "trgt_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2133.trgt.vcf"
2025-09-15 20:25:18.607 wdl.w:ptcp.t:call-tar_outputs-36 INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2133.mapped.bam.bai"
2025-09-15 20:25:18.607 wdl.w:ptcp.t:call-tar_outputs-36 INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2133.mapped.bam"
2025-09-15 20:25:18.607 wdl.w:ptcp.t:call-tar_outputs-36 INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2133"
2025-09-15 20:25:18.607 wdl.w:ptcp.t:call-tar_outputs-36 INFO eval :: name: "threads", value: 1
2025-09-15 20:25:18.607 wdl.w:ptcp.t:call-tar_outputs-36 INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:25:18.607 wdl.w:ptcp.t:call-tar_outputs-36 INFO eval :: name: "disk_size", value: 6
2025-09-15 20:25:18.607 wdl.w:ptcp.t:call-tar_outputs-36 INFO eval :: name: "output_tarball", value: "m84036_250809_035451_s4.bc2133.tar"
2025-09-15 20:25:18.608 wdl.w:ptcp.t:call-tar_outputs-36 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:18.608 wdl.w:ptcp.t:call-tar_outputs-36 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:18.608 wdl.w:ptcp.t:call-tar_outputs-36 INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:25:18.608 wdl.w:ptcp.t:call-tar_outputs-36 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:18.617 wdl.w:ptcp.w:call-trgt-82 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:25:18.617 wdl.w:ptcp.w:call-trgt-82 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-82/out/m84036_250809_035451_s4.bc2179.mapped.bam"}
2025-09-15 20:25:18.617 wdl.w:ptcp.w:call-trgt-82 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-82/out/m84036_250809_035451_s4.bc2179.mapped.bam.bai"}
2025-09-15 20:25:18.617 wdl.w:ptcp.w:call-trgt-82 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:25:18.618 wdl.w:ptcp.w:call-trgt-82 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:25:18.618 wdl.w:ptcp.w:call-trgt-82 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2179"}
2025-09-15 20:25:18.618 wdl.w:ptcp.w:call-trgt-82 INFO visit :: node: "decl-sex", values: {"sex": "F"}
2025-09-15 20:25:18.618 wdl.w:ptcp.w:call-trgt-82 INFO visit :: node: "decl-trgt_bed", values: {"trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"}
2025-09-15 20:25:18.618 wdl.w:ptcp.w:call-trgt-82 NOTICE ready :: job: "call-get_reads_overlapping_repeats", callee: "get_reads_overlapping_repeats"
2025-09-15 20:25:18.618 wdl.w:ptcp.w:call-trgt-82 INFO input :: job: "call-get_reads_overlapping_repeats", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-82/out/m84036_250809_035451_s4.bc2179.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-82/out/m84036_250809_035451_s4.bc2179.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2179"}
2025-09-15 20:25:18.619 wdl.w:ptcp.w:call-trgt-82 NOTICE ready :: job: "call-trgt_genotype", callee: "trgt_genotype"
2025-09-15 20:25:18.619 wdl.w:ptcp.w:call-trgt-82 INFO input :: job: "call-trgt_genotype", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-82/out/m84036_250809_035451_s4.bc2179.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-82/out/m84036_250809_035451_s4.bc2179.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2179"}
2025-09-15 20:25:18.638 wdl.w:ptcp.w:call-sawfish-75.t:call-run_sawfish INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 10, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-75/call-run_sawfish/_singularity_tmpdir_x9zipyhq"
2025-09-15 20:25:18.638 wdl.w:ptcp.w:call-sawfish-75.t:call-run_sawfish INFO Slurm invocation: srun --job-name call-run_sawfish --partition compute,compute9 --cpus-per-task 16 --mem 30518M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-75/call-run_sawfish/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-75/call-run_sawfish/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-75/call-run_sawfish/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-75/call-run_sawfish/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-75/out/m84036_250809_035451_s4.bc2172.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2172.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-75/out/m84036_250809_035451_s4.bc2172.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2172.mapped.bam.bai:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-75/call-run_sawfish/_singularity_tmpdir_x9zipyhq/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-75/call-run_sawfish/_singularity_tmpdir_x9zipyhq/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:18.650 wdl.w:ptcp.w:call-trgt-60.t:call-trgt_plot_meth_waterfall INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2157.meth_waterfall.trgt_plots.zip"
2025-09-15 20:25:18.687 wdl.w:ptcp.w:call-sawfish-75.t:call-run_sawfish NOTICE slurm_singularity run :: pid: 1205302, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-75/call-run_sawfish/slurm_singularity.log.txt"
2025-09-15 20:25:18.695 wdl.w:ptcp.w:call-trgt-61 NOTICE done
2025-09-15 20:25:18.700 wdl.w:ptcp NOTICE finish :: job: "call-trgt-61"
2025-09-15 20:25:18.700 wdl.w:ptcp INFO output :: job: "call-trgt-61", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-61/out/m84036_250809_035451_s4.bc2158.motifs_waterfall.trgt_plots.zip", "images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-61/out/m84036_250809_035451_s4.bc2158.meth_allele.trgt_plots.zip", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-61/out/m84036_250809_035451_s4.bc2158.trgt.sorted.spanning.bam.bai", "images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-61/out/m84036_250809_035451_s4.bc2158.motifs_allele.trgt_plots.zip", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-61/out/m84036_250809_035451_s4.bc2158.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-61/out/m84036_250809_035451_s4.bc2158.trgt.vcf", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-61/out/m84036_250809_035451_s4.bc2158.repeats.bam", "images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-61/out/m84036_250809_035451_s4.bc2158.meth_waterfall.trgt_plots.zip", "reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-61/out/m84036_250809_035451_s4.bc2158.repeats.bam.bai"}
2025-09-15 20:25:18.708 wdl.w:ptcp.w:call-paraphase-93 NOTICE workflow start :: name: "paraphase", source: "./paraphase.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-93"
2025-09-15 20:25:18.728 wdl.w:ptcp.w:call-paraphase-93 INFO visit :: node: "decl-annotation_vcf", values: {"annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf"}
2025-09-15 20:25:18.729 wdl.w:ptcp.w:call-paraphase-93 INFO visit :: node: "decl-config_file", values: {"config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml"}
2025-09-15 20:25:18.729 wdl.w:ptcp.w:call-paraphase-93 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:25:18.729 wdl.w:ptcp.w:call-paraphase-93 INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:25:18.729 wdl.w:ptcp.w:call-paraphase-93 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-93/out/m84036_250809_035451_s4.bc2190.mapped.bam"}
2025-09-15 20:25:18.729 wdl.w:ptcp.w:call-paraphase-93 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-93/out/m84036_250809_035451_s4.bc2190.mapped.bam.bai"}
2025-09-15 20:25:18.729 wdl.w:ptcp.w:call-paraphase-93 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:25:18.729 wdl.w:ptcp.w:call-paraphase-93 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:25:18.729 wdl.w:ptcp.w:call-paraphase-93 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2190"}
2025-09-15 20:25:18.729 wdl.w:ptcp.w:call-paraphase-93 INFO visit :: node: "decl-sex", values: {"sex": "F"}
2025-09-15 20:25:18.730 wdl.w:ptcp.w:call-paraphase-93 NOTICE ready :: job: "call-run_paraphase", callee: "run_paraphase"
2025-09-15 20:25:18.730 wdl.w:ptcp.w:call-paraphase-93 INFO input :: job: "call-run_paraphase", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf", "genome_version": "38", "config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-93/out/m84036_250809_035451_s4.bc2190.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-93/out/m84036_250809_035451_s4.bc2190.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2190"}
2025-09-15 20:25:18.761 wdl.w:ptcp.t:call-tar_outputs-36 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 17, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-36/_singularity_tmpdir_2iaz7606"
2025-09-15 20:25:18.761 wdl.w:ptcp.t:call-tar_outputs-36 INFO Slurm invocation: srun --job-name call-tar_outputs-36 --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-36/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-36/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-36/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-36/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-36/out/m84036_250809_035451_s4.bc2133.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2133.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-36/out/m84036_250809_035451_s4.bc2133.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2133.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-36/out/m84036_250809_035451_s4.bc2133.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2133.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-36/out/m84036_250809_035451_s4.bc2133.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2133.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-36/out/m84036_250809_035451_s4.bc2133.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2133.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-36/out/m84036_250809_035451_s4.bc2133.f8inversion.json:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2133.f8inversion.json:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-36/out/m84036_250809_035451_s4.bc2133_paraphase/m84036_250809_035451_s4.bc2133.paraphase.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2133.paraphase.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-36/out/m84036_250809_035451_s4.bc2133_paraphase/m84036_250809_035451_s4.bc2133.paraphase.json:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2133.paraphase.json:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-36/out/m84036_250809_035451_s4.bc2133_paraphase/m84036_250809_035451_s4.bc2133.paraphase.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2133.paraphase.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-36/out/m84036_250809_035451_s4.bc2133_sawfish/m84036_250809_035451_s4.bc2133.sv.vcf.gz:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2133.sv.vcf.gz:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-36/out/m84036_250809_035451_s4.bc2133_sawfish/m84036_250809_035451_s4.bc2133.sv.vcf.gz.tbi:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2133.sv.vcf.gz.tbi:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-36/_singularity_tmpdir_2iaz7606/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-36/_singularity_tmpdir_2iaz7606/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:18.762 wdl.w:ptcp.w:call-paraphase-11.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for hbb for sample m84036_250809_035451_s4.bc2108 at 2025-09-15 20:24:43.781098...
2025-09-15 20:25:18.782 wdl.w:ptcp.t:call-tar_outputs-36 NOTICE slurm_singularity run :: pid: 1205304, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-36/slurm_singularity.log.txt"
2025-09-15 20:25:18.788 wdl.w:ptcp.w:call-paraphase-50.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for gba for sample m84036_250809_035451_s4.bc2147 at 2025-09-15 20:25:11.113134...
2025-09-15 20:25:18.788 wdl.w:ptcp.w:call-paraphase-50.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for gba for sample m84036_250809_035451_s4.bc2147 at 2025-09-15 20:25:11.578998...
2025-09-15 20:25:18.788 wdl.w:ptcp.w:call-paraphase-50.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for hbb for sample m84036_250809_035451_s4.bc2147 at 2025-09-15 20:25:16.925351...
2025-09-15 20:25:18.789 wdl.w:ptcp.w:call-paraphase-50.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for hbb for sample m84036_250809_035451_s4.bc2147 at 2025-09-15 20:25:16.925499...
2025-09-15 20:25:18.789 wdl.w:ptcp.w:call-paraphase-50.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for f8inv1 for sample m84036_250809_035451_s4.bc2147 at 2025-09-15 20:25:17.866268...
2025-09-15 20:25:18.789 wdl.w:ptcp.w:call-paraphase-50.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for f8inv1 for sample m84036_250809_035451_s4.bc2147 at 2025-09-15 20:25:17.866447...
2025-09-15 20:25:18.820 wdl.w:ptcp.w:call-trgt-60.t:call-trgt_plot_meth_waterfall NOTICE done
2025-09-15 20:25:18.855 wdl.w:ptcp.w:call-paraphase-84.t:call-run_paraphase INFO output :: name: "paraphase_bam", value: "m84036_250809_035451_s4.bc2181_paraphase/m84036_250809_035451_s4.bc2181.paraphase.bam"
2025-09-15 20:25:18.859 wdl.w:ptcp.w:call-paraphase-84.t:call-run_paraphase INFO output :: name: "paraphase_bam_bai", value: "m84036_250809_035451_s4.bc2181_paraphase/m84036_250809_035451_s4.bc2181.paraphase.bam.bai"
2025-09-15 20:25:18.860 wdl.w:ptcp.w:call-paraphase-84.t:call-run_paraphase INFO output :: name: "paraphase_json", value: "m84036_250809_035451_s4.bc2181_paraphase/m84036_250809_035451_s4.bc2181.paraphase.json"
2025-09-15 20:25:18.861 wdl.w:ptcp.w:call-paraphase-84.t:call-run_paraphase INFO output :: name: "paraphase_vcfs", value: []
2025-09-15 20:25:18.861 wdl.w:ptcp.w:call-paraphase-84.t:call-run_paraphase INFO output :: name: "havanno_json", value: "m84036_250809_035451_s4.bc2181.havanno.json"
2025-09-15 20:25:18.886 wdl.w:ptcp.w:call-trgt-60 NOTICE finish :: job: "call-trgt_plot_meth_waterfall"
2025-09-15 20:25:18.886 wdl.w:ptcp.w:call-trgt-60 INFO output :: job: "call-trgt_plot_meth_waterfall", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-60/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2157.meth_waterfall.trgt_plots.zip"}
2025-09-15 20:25:18.887 wdl.w:ptcp.w:call-trgt-60 INFO visit :: node: "output-images_meth_waterfall", values: {"images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-60/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2157.meth_waterfall.trgt_plots.zip"}
2025-09-15 20:25:18.894 wdl.w:ptcp.w:call-trgt-75.t:call-get_reads_overlapping_repeats NOTICE task setup :: name: "get_reads_overlapping_repeats", source: "./trgt.wdl", line: 182, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-75/call-get_reads_overlapping_repeats", thread: 140611969599040
2025-09-15 20:25:18.916 wdl.w:ptcp.w:call-trgt-75.t:call-get_reads_overlapping_repeats INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:18.916 wdl.w:ptcp.w:call-trgt-75.t:call-get_reads_overlapping_repeats INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:25:18.916 wdl.w:ptcp.w:call-trgt-75.t:call-get_reads_overlapping_repeats INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2172.mapped.bam.bai"
2025-09-15 20:25:18.916 wdl.w:ptcp.w:call-trgt-75.t:call-get_reads_overlapping_repeats INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2172.mapped.bam"
2025-09-15 20:25:18.916 wdl.w:ptcp.w:call-trgt-75.t:call-get_reads_overlapping_repeats INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2172"
2025-09-15 20:25:18.917 wdl.w:ptcp.w:call-trgt-75.t:call-get_reads_overlapping_repeats INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:25:18.917 wdl.w:ptcp.w:call-trgt-75.t:call-get_reads_overlapping_repeats INFO eval :: name: "expand_size", value: 3000
2025-09-15 20:25:18.917 wdl.w:ptcp.w:call-trgt-75.t:call-get_reads_overlapping_repeats INFO eval :: name: "threads", value: 1
2025-09-15 20:25:18.917 wdl.w:ptcp.w:call-trgt-75.t:call-get_reads_overlapping_repeats INFO eval :: name: "expanded_bed_name", value: "m84036_250809_035451_s4.bc2172.expanded.bed"
2025-09-15 20:25:18.917 wdl.w:ptcp.w:call-trgt-75.t:call-get_reads_overlapping_repeats INFO eval :: name: "disk_size", value: 11
2025-09-15 20:25:18.918 wdl.w:ptcp.w:call-trgt-75.t:call-get_reads_overlapping_repeats INFO eval :: name: "output_name", value: "m84036_250809_035451_s4.bc2172.repeats.bam"
2025-09-15 20:25:18.918 wdl.w:ptcp.w:call-trgt-75.t:call-get_reads_overlapping_repeats INFO eval :: name: "index_name", value: "m84036_250809_035451_s4.bc2172.repeats.bam.bai"
2025-09-15 20:25:18.918 wdl.w:ptcp.w:call-trgt-75.t:call-get_reads_overlapping_repeats INFO eval :: name: "output_name_with_index", value: "m84036_250809_035451_s4.bc2172.repeats.bam##idx##m84036_250809_035451_s4.bc2172.repeats.bam.bai"
2025-09-15 20:25:18.918 wdl.w:ptcp.w:call-trgt-75.t:call-get_reads_overlapping_repeats INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:18.918 wdl.w:ptcp.w:call-trgt-75.t:call-get_reads_overlapping_repeats WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:18.919 wdl.w:ptcp.w:call-trgt-75.t:call-get_reads_overlapping_repeats INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:25:18.919 wdl.w:ptcp.w:call-trgt-75.t:call-get_reads_overlapping_repeats INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:18.933 wdl.w:ptcp.w:call-paraphase-78.t:call-run_paraphase.stderr VERBOSE INFO:root:Processing sample m84036_250809_035451_s4.bc2175 at 2025-09-15 20:25:14.761067...
2025-09-15 20:25:18.934 wdl.w:ptcp.w:call-paraphase-78.t:call-run_paraphase.stderr VERBOSE INFO:root:Checking sample sex at 2025-09-15 20:25:14.761962...
2025-09-15 20:25:18.934 wdl.w:ptcp.w:call-paraphase-78.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for cyp21 for sample m84036_250809_035451_s4.bc2175 at 2025-09-15 20:25:14.814455...
2025-09-15 20:25:18.934 wdl.w:ptcp.w:call-paraphase-78.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for cyp21 for sample m84036_250809_035451_s4.bc2175 at 2025-09-15 20:25:14.815149...
2025-09-15 20:25:18.934 wdl.w:ptcp.w:call-paraphase-78.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for smn1 for sample m84036_250809_035451_s4.bc2175 at 2025-09-15 20:25:14.814693...
2025-09-15 20:25:18.935 wdl.w:ptcp.w:call-paraphase-78.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for hba for sample m84036_250809_035451_s4.bc2175 at 2025-09-15 20:25:14.814789...
2025-09-15 20:25:18.935 wdl.w:ptcp.w:call-paraphase-78.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for gba for sample m84036_250809_035451_s4.bc2175 at 2025-09-15 20:25:14.814776...
2025-09-15 20:25:18.935 wdl.w:ptcp.w:call-paraphase-78.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for smn1 for sample m84036_250809_035451_s4.bc2175 at 2025-09-15 20:25:14.815354...
2025-09-15 20:25:18.935 wdl.w:ptcp.w:call-paraphase-78.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for hba for sample m84036_250809_035451_s4.bc2175 at 2025-09-15 20:25:14.815383...
2025-09-15 20:25:18.935 wdl.w:ptcp.w:call-paraphase-78.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for gba for sample m84036_250809_035451_s4.bc2175 at 2025-09-15 20:25:14.815390...
2025-09-15 20:25:18.974 wdl.w:ptcp.w:call-paraphase-84.t:call-run_paraphase NOTICE done
2025-09-15 20:25:18.984 wdl.w:ptcp.w:call-paraphase-84 NOTICE finish :: job: "call-run_paraphase"
2025-09-15 20:25:18.985 wdl.w:ptcp.w:call-paraphase-84 INFO output :: job: "call-run_paraphase", values: {"havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-84/call-run_paraphase/out/m84036_250809_035451_s4.bc2181.havanno.json", "paraphase_vcfs": [], "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-84/call-run_paraphase/out/m84036_250809_035451_s4.bc2181_paraphase/m84036_250809_035451_s4.bc2181.paraphase.json", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-84/call-run_paraphase/out/m84036_250809_035451_s4.bc2181_paraphase/m84036_250809_035451_s4.bc2181.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-84/call-run_paraphase/out/m84036_250809_035451_s4.bc2181_paraphase/m84036_250809_035451_s4.bc2181.paraphase.bam"}
2025-09-15 20:25:18.985 wdl.w:ptcp.w:call-paraphase-84 NOTICE ready :: job: "call-call_f8", callee: "call_f8"
2025-09-15 20:25:18.985 wdl.w:ptcp.w:call-paraphase-84 INFO input :: job: "call-call_f8", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "out_prefix": "m84036_250809_035451_s4.bc2181", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-84/call-run_paraphase/out/m84036_250809_035451_s4.bc2181_paraphase/m84036_250809_035451_s4.bc2181.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-84/call-run_paraphase/out/m84036_250809_035451_s4.bc2181_paraphase/m84036_250809_035451_s4.bc2181.paraphase.bam", "sex": "F"}
2025-09-15 20:25:18.986 wdl.w:ptcp.w:call-paraphase-84 INFO visit :: node: "output-havanno_json", values: {"havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-84/call-run_paraphase/out/m84036_250809_035451_s4.bc2181.havanno.json"}
2025-09-15 20:25:18.987 wdl.w:ptcp.w:call-paraphase-84 INFO visit :: node: "output-paraphase_bam", values: {"paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-84/call-run_paraphase/out/m84036_250809_035451_s4.bc2181_paraphase/m84036_250809_035451_s4.bc2181.paraphase.bam"}
2025-09-15 20:25:18.987 wdl.w:ptcp.w:call-paraphase-84 INFO visit :: node: "output-paraphase_bam_bai", values: {"paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-84/call-run_paraphase/out/m84036_250809_035451_s4.bc2181_paraphase/m84036_250809_035451_s4.bc2181.paraphase.bam.bai"}
2025-09-15 20:25:18.987 wdl.w:ptcp.w:call-paraphase-84 INFO visit :: node: "output-paraphase_json", values: {"paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-84/call-run_paraphase/out/m84036_250809_035451_s4.bc2181_paraphase/m84036_250809_035451_s4.bc2181.paraphase.json"}
2025-09-15 20:25:18.987 wdl.w:ptcp.w:call-paraphase-84 INFO visit :: node: "output-paraphase_vcfs", values: {"paraphase_vcfs": []}
2025-09-15 20:25:18.987 wdl.w:ptcp.w:call-trgt-75.t:call-get_reads_overlapping_repeats INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 9, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-75/call-get_reads_overlapping_repeats/_singularity_tmpdir_x97_c2k9"
2025-09-15 20:25:18.987 wdl.w:ptcp.w:call-trgt-75.t:call-get_reads_overlapping_repeats INFO Slurm invocation: srun --job-name call-get_reads_overlapping_repeats --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-75/call-get_reads_overlapping_repeats/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-75/call-get_reads_overlapping_repeats/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-75/call-get_reads_overlapping_repeats/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-75/call-get_reads_overlapping_repeats/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-75/out/m84036_250809_035451_s4.bc2172.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2172.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-75/out/m84036_250809_035451_s4.bc2172.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2172.mapped.bam.bai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-75/call-get_reads_overlapping_repeats/_singularity_tmpdir_x97_c2k9/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-75/call-get_reads_overlapping_repeats/_singularity_tmpdir_x97_c2k9/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:18.993 wdl.w:ptcp.w:call-trgt-75.t:call-trgt_genotype NOTICE task setup :: name: "trgt_genotype", source: "./trgt.wdl", line: 272, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-75/call-trgt_genotype", thread: 140613034948160
2025-09-15 20:25:19.007 wdl.w:ptcp.w:call-trgt-75.t:call-get_reads_overlapping_repeats NOTICE slurm_singularity run :: pid: 1205318, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-75/call-get_reads_overlapping_repeats/slurm_singularity.log.txt"
2025-09-15 20:25:19.012 wdl.w:ptcp.w:call-trgt-75.t:call-trgt_genotype INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:19.012 wdl.w:ptcp.w:call-trgt-75.t:call-trgt_genotype INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:25:19.012 wdl.w:ptcp.w:call-trgt-75.t:call-trgt_genotype INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:25:19.012 wdl.w:ptcp.w:call-trgt-75.t:call-trgt_genotype INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:25:19.013 wdl.w:ptcp.w:call-trgt-75.t:call-trgt_genotype INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2172.mapped.bam.bai"
2025-09-15 20:25:19.013 wdl.w:ptcp.w:call-trgt-75.t:call-trgt_genotype INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2172.mapped.bam"
2025-09-15 20:25:19.013 wdl.w:ptcp.w:call-trgt-75.t:call-trgt_genotype INFO input :: name: "sex", value: "F"
2025-09-15 20:25:19.013 wdl.w:ptcp.w:call-trgt-75.t:call-trgt_genotype INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2172"
2025-09-15 20:25:19.013 wdl.w:ptcp.w:call-trgt-75.t:call-trgt_genotype INFO eval :: name: "mem_gb", value: 16
2025-09-15 20:25:19.013 wdl.w:ptcp.w:call-trgt-75.t:call-trgt_genotype INFO eval :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2172.trgt"
2025-09-15 20:25:19.013 wdl.w:ptcp.w:call-trgt-75.t:call-trgt_genotype INFO eval :: name: "threads", value: 8
2025-09-15 20:25:19.013 wdl.w:ptcp.w:call-trgt-75.t:call-trgt_genotype INFO eval :: name: "disk_size", value: 27
2025-09-15 20:25:19.013 wdl.w:ptcp.w:call-trgt-75.t:call-trgt_genotype INFO eval :: name: "karyotype", value: "XX"
2025-09-15 20:25:19.014 wdl.w:ptcp.w:call-trgt-75.t:call-trgt_genotype INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 8, memory_reservation: 16000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:19.014 wdl.w:ptcp.w:call-trgt-75.t:call-trgt_genotype WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:19.014 wdl.w:ptcp.w:call-trgt-75.t:call-trgt_genotype INFO provisioned :: seconds_waited: 0, cpu: 8, mem_bytes: 16000000000
2025-09-15 20:25:19.014 wdl.w:ptcp.w:call-trgt-75.t:call-trgt_genotype INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:19.072 wdl.w:ptcp.w:call-trgt-75.t:call-trgt_genotype INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 11, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-75/call-trgt_genotype/_singularity_tmpdir_h3le78ub"
2025-09-15 20:25:19.072 wdl.w:ptcp.w:call-trgt-75.t:call-trgt_genotype INFO Slurm invocation: srun --job-name call-trgt_genotype --partition compute,compute9 --cpus-per-task 8 --mem 15259M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-75/call-trgt_genotype/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-75/call-trgt_genotype/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-75/call-trgt_genotype/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-75/call-trgt_genotype/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-75/out/m84036_250809_035451_s4.bc2172.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2172.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-75/out/m84036_250809_035451_s4.bc2172.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2172.mapped.bam.bai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-75/call-trgt_genotype/_singularity_tmpdir_h3le78ub/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-75/call-trgt_genotype/_singularity_tmpdir_h3le78ub/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:19.073 wdl.w:ptcp.w:call-paraphase-76.t:call-run_paraphase INFO output :: name: "paraphase_bam", value: "m84036_250809_035451_s4.bc2173_paraphase/m84036_250809_035451_s4.bc2173.paraphase.bam"
2025-09-15 20:25:19.078 wdl.w:ptcp.w:call-paraphase-76.t:call-run_paraphase INFO output :: name: "paraphase_bam_bai", value: "m84036_250809_035451_s4.bc2173_paraphase/m84036_250809_035451_s4.bc2173.paraphase.bam.bai"
2025-09-15 20:25:19.079 wdl.w:ptcp.w:call-paraphase-76.t:call-run_paraphase INFO output :: name: "paraphase_json", value: "m84036_250809_035451_s4.bc2173_paraphase/m84036_250809_035451_s4.bc2173.paraphase.json"
2025-09-15 20:25:19.081 wdl.w:ptcp.w:call-paraphase-76.t:call-run_paraphase INFO output :: name: "paraphase_vcfs", value: []
2025-09-15 20:25:19.082 wdl.w:ptcp.w:call-paraphase-76.t:call-run_paraphase INFO output :: name: "havanno_json", value: "m84036_250809_035451_s4.bc2173.havanno.json"
2025-09-15 20:25:19.084 wdl.w:ptcp.w:call-trgt-75.t:call-trgt_genotype NOTICE slurm_singularity run :: pid: 1205320, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-75/call-trgt_genotype/slurm_singularity.log.txt"
2025-09-15 20:25:19.163 wdl.w:ptcp.w:call-paraphase-76.t:call-run_paraphase NOTICE done
2025-09-15 20:25:19.170 wdl.w:ptcp.w:call-paraphase-76 NOTICE finish :: job: "call-run_paraphase"
2025-09-15 20:25:19.170 wdl.w:ptcp.w:call-paraphase-76 INFO output :: job: "call-run_paraphase", values: {"havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-76/call-run_paraphase/out/m84036_250809_035451_s4.bc2173.havanno.json", "paraphase_vcfs": [], "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-76/call-run_paraphase/out/m84036_250809_035451_s4.bc2173_paraphase/m84036_250809_035451_s4.bc2173.paraphase.json", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-76/call-run_paraphase/out/m84036_250809_035451_s4.bc2173_paraphase/m84036_250809_035451_s4.bc2173.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-76/call-run_paraphase/out/m84036_250809_035451_s4.bc2173_paraphase/m84036_250809_035451_s4.bc2173.paraphase.bam"}
2025-09-15 20:25:19.171 wdl.w:ptcp.w:call-paraphase-76 NOTICE ready :: job: "call-call_f8", callee: "call_f8"
2025-09-15 20:25:19.171 wdl.w:ptcp.w:call-paraphase-76 INFO input :: job: "call-call_f8", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "out_prefix": "m84036_250809_035451_s4.bc2173", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-76/call-run_paraphase/out/m84036_250809_035451_s4.bc2173_paraphase/m84036_250809_035451_s4.bc2173.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-76/call-run_paraphase/out/m84036_250809_035451_s4.bc2173_paraphase/m84036_250809_035451_s4.bc2173.paraphase.bam", "sex": "F"}
2025-09-15 20:25:19.172 wdl.w:ptcp.w:call-paraphase-76 INFO visit :: node: "output-havanno_json", values: {"havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-76/call-run_paraphase/out/m84036_250809_035451_s4.bc2173.havanno.json"}
2025-09-15 20:25:19.172 wdl.w:ptcp.w:call-paraphase-76 INFO visit :: node: "output-paraphase_bam", values: {"paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-76/call-run_paraphase/out/m84036_250809_035451_s4.bc2173_paraphase/m84036_250809_035451_s4.bc2173.paraphase.bam"}
2025-09-15 20:25:19.172 wdl.w:ptcp.w:call-paraphase-76 INFO visit :: node: "output-paraphase_bam_bai", values: {"paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-76/call-run_paraphase/out/m84036_250809_035451_s4.bc2173_paraphase/m84036_250809_035451_s4.bc2173.paraphase.bam.bai"}
2025-09-15 20:25:19.172 wdl.w:ptcp.w:call-paraphase-76 INFO visit :: node: "output-paraphase_json", values: {"paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-76/call-run_paraphase/out/m84036_250809_035451_s4.bc2173_paraphase/m84036_250809_035451_s4.bc2173.paraphase.json"}
2025-09-15 20:25:19.172 wdl.w:ptcp.w:call-paraphase-76 INFO visit :: node: "output-paraphase_vcfs", values: {"paraphase_vcfs": []}
2025-09-15 20:25:19.178 wdl.w:ptcp.w:call-paraphase-81.t:call-run_paraphase NOTICE task setup :: name: "run_paraphase", source: "./paraphase.wdl", line: 127, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-81/call-run_paraphase", thread: 140608739980864
2025-09-15 20:25:19.198 wdl.w:ptcp.t:call-tar_outputs-37 INFO output :: name: "sample_tarball", value: "m84036_250809_035451_s4.bc2134.tar"
2025-09-15 20:25:19.199 wdl.w:ptcp.w:call-paraphase-81.t:call-run_paraphase INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:19.199 wdl.w:ptcp.w:call-paraphase-81.t:call-run_paraphase INFO input :: name: "annotation_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf"
2025-09-15 20:25:19.199 wdl.w:ptcp.w:call-paraphase-81.t:call-run_paraphase INFO input :: name: "genome_version", value: "38"
2025-09-15 20:25:19.199 wdl.w:ptcp.w:call-paraphase-81.t:call-run_paraphase INFO input :: name: "config_file", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/paraphase_config.GRCh38.yaml"
2025-09-15 20:25:19.199 wdl.w:ptcp.w:call-paraphase-81.t:call-run_paraphase INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:25:19.199 wdl.w:ptcp.w:call-paraphase-81.t:call-run_paraphase INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:25:19.199 wdl.w:ptcp.w:call-paraphase-81.t:call-run_paraphase INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2178.mapped.bam.bai"
2025-09-15 20:25:19.199 wdl.w:ptcp.w:call-paraphase-81.t:call-run_paraphase INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2178.mapped.bam"
2025-09-15 20:25:19.199 wdl.w:ptcp.w:call-paraphase-81.t:call-run_paraphase INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2178"
2025-09-15 20:25:19.199 wdl.w:ptcp.w:call-paraphase-81.t:call-run_paraphase INFO eval :: name: "threads", value: 4
2025-09-15 20:25:19.199 wdl.w:ptcp.w:call-paraphase-81.t:call-run_paraphase INFO eval :: name: "mem_gb", value: 8
2025-09-15 20:25:19.200 wdl.w:ptcp.w:call-paraphase-81.t:call-run_paraphase INFO eval :: name: "disk_size", value: 27
2025-09-15 20:25:19.200 wdl.w:ptcp.w:call-paraphase-81.t:call-run_paraphase INFO eval :: name: "out_dir", value: "m84036_250809_035451_s4.bc2178_paraphase"
2025-09-15 20:25:19.202 wdl.w:ptcp.w:call-paraphase-81.t:call-run_paraphase INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 4, memory_reservation: 8000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:19.202 wdl.w:ptcp.w:call-paraphase-81.t:call-run_paraphase WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:19.202 wdl.w:ptcp.w:call-paraphase-81.t:call-run_paraphase INFO provisioned :: seconds_waited: 0, cpu: 4, mem_bytes: 8000000000
2025-09-15 20:25:19.202 wdl.w:ptcp.w:call-paraphase-81.t:call-run_paraphase INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:19.219 wdl.w:ptcp.w:call-trgt-69.t:call-trgt_plot_meth_waterfall INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2166.meth_waterfall.trgt_plots.zip"
2025-09-15 20:25:19.277 wdl.w:ptcp.t:call-tar_outputs-37 NOTICE done
2025-09-15 20:25:19.282 wdl.w:ptcp NOTICE finish :: job: "call-tar_outputs-37"
2025-09-15 20:25:19.282 wdl.w:ptcp INFO output :: job: "call-tar_outputs-37", values: {"sample_tarball": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-37/out/m84036_250809_035451_s4.bc2134.tar"}
2025-09-15 20:25:19.285 wdl.w:ptcp.w:call-paraphase-81.t:call-run_paraphase INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-81/call-run_paraphase/_singularity_tmpdir_wqn1m4zk"
2025-09-15 20:25:19.285 wdl.w:ptcp.w:call-paraphase-81.t:call-run_paraphase INFO Slurm invocation: srun --job-name call-run_paraphase --partition compute,compute9 --cpus-per-task 4 --mem 7629M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-81/call-run_paraphase/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-81/call-run_paraphase/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-81/call-run_paraphase/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-81/call-run_paraphase/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-81/out/m84036_250809_035451_s4.bc2178.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2178.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-81/out/m84036_250809_035451_s4.bc2178.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2178.mapped.bam.bai:ro --bind /ptcp/meta/variant_list/variant_list.GRCh38.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf:ro --bind /ptcp/meta/paraphase/paraphase_config.GRCh38.yaml:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/paraphase_config.GRCh38.yaml:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-81/call-run_paraphase/_singularity_tmpdir_wqn1m4zk/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-81/call-run_paraphase/_singularity_tmpdir_wqn1m4zk/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:19.287 wdl.w:ptcp.w:call-sawfish-81.t:call-run_sawfish NOTICE task setup :: name: "run_sawfish", source: "./sawfish.wdl", line: 83, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-81/call-run_sawfish", thread: 140611961206336
2025-09-15 20:25:19.303 wdl.w:ptcp.w:call-paraphase-81.t:call-run_paraphase NOTICE slurm_singularity run :: pid: 1205335, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-81/call-run_paraphase/slurm_singularity.log.txt"
2025-09-15 20:25:19.308 wdl.w:ptcp.w:call-sawfish-81.t:call-run_sawfish INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:19.308 wdl.w:ptcp.w:call-sawfish-81.t:call-run_sawfish INFO input :: name: "genome_version", value: "38"
2025-09-15 20:25:19.308 wdl.w:ptcp.w:call-sawfish-81.t:call-run_sawfish INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:25:19.308 wdl.w:ptcp.w:call-sawfish-81.t:call-run_sawfish INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:25:19.308 wdl.w:ptcp.w:call-sawfish-81.t:call-run_sawfish INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2178.mapped.bam.bai"
2025-09-15 20:25:19.308 wdl.w:ptcp.w:call-sawfish-81.t:call-run_sawfish INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2178.mapped.bam"
2025-09-15 20:25:19.308 wdl.w:ptcp.w:call-sawfish-81.t:call-run_sawfish INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2178"
2025-09-15 20:25:19.309 wdl.w:ptcp.w:call-sawfish-81.t:call-run_sawfish INFO eval :: name: "mem_gb", value: 32
2025-09-15 20:25:19.309 wdl.w:ptcp.w:call-sawfish-81.t:call-run_sawfish INFO eval :: name: "threads", value: 16
2025-09-15 20:25:19.309 wdl.w:ptcp.w:call-sawfish-81.t:call-run_sawfish INFO eval :: name: "disk_size", value: 30
2025-09-15 20:25:19.309 wdl.w:ptcp.w:call-sawfish-81.t:call-run_sawfish INFO eval :: name: "discover_dirname", value: "m84036_250809_035451_s4.bc2178_sawfish_discover"
2025-09-15 20:25:19.309 wdl.w:ptcp.w:call-sawfish-81.t:call-run_sawfish INFO eval :: name: "call_dirname", value: "m84036_250809_035451_s4.bc2178_sawfish"
2025-09-15 20:25:19.309 wdl.w:ptcp.w:call-sawfish-81.t:call-run_sawfish INFO eval :: name: "minimap2_bam_filename", value: "m84036_250809_035451_s4.bc2178.minimap2.bam"
2025-09-15 20:25:19.310 wdl.w:ptcp.w:call-sawfish-81.t:call-run_sawfish INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 16, memory_reservation: 32000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:19.310 wdl.w:ptcp.w:call-sawfish-81.t:call-run_sawfish WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:19.310 wdl.w:ptcp.w:call-sawfish-81.t:call-run_sawfish INFO provisioned :: seconds_waited: 0, cpu: 16, mem_bytes: 32000000000
2025-09-15 20:25:19.311 wdl.w:ptcp.w:call-sawfish-81.t:call-run_sawfish INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:19.318 wdl.w:ptcp.w:call-trgt-65.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:25:18 [ERROR] - No reads found for TRID=PRTS_ARX
2025-09-15 20:25:19.318 wdl.w:ptcp.w:call-trgt-65.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:25:18 [ERROR] - No reads found for TRID=EIEE1_ARX
2025-09-15 20:25:19.339 wdl.w:ptcp.w:call-trgt-71.t:call-trgt_plot_meth_allele INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2168.meth_allele.trgt_plots.zip"
2025-09-15 20:25:19.355 wdl.w:ptcp.w:call-trgt-69.t:call-trgt_plot_meth_waterfall NOTICE done
2025-09-15 20:25:19.360 wdl.w:ptcp.w:call-trgt-69 NOTICE finish :: job: "call-trgt_plot_meth_waterfall"
2025-09-15 20:25:19.360 wdl.w:ptcp.w:call-trgt-69 INFO output :: job: "call-trgt_plot_meth_waterfall", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-69/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2166.meth_waterfall.trgt_plots.zip"}
2025-09-15 20:25:19.360 wdl.w:ptcp.w:call-trgt-69 INFO visit :: node: "output-images_meth_waterfall", values: {"images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-69/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2166.meth_waterfall.trgt_plots.zip"}
2025-09-15 20:25:19.369 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_plot_meth_allele NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-66/call-trgt_plot_meth_allele", thread: 140607649453632
2025-09-15 20:25:19.376 wdl.w:ptcp.w:call-sawfish-81.t:call-run_sawfish INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 10, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-81/call-run_sawfish/_singularity_tmpdir_amp9ymbl"
2025-09-15 20:25:19.376 wdl.w:ptcp.w:call-sawfish-81.t:call-run_sawfish INFO Slurm invocation: srun --job-name call-run_sawfish --partition compute,compute9 --cpus-per-task 16 --mem 30518M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-81/call-run_sawfish/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-81/call-run_sawfish/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-81/call-run_sawfish/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-81/call-run_sawfish/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-81/out/m84036_250809_035451_s4.bc2178.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2178.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-81/out/m84036_250809_035451_s4.bc2178.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2178.mapped.bam.bai:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-81/call-run_sawfish/_singularity_tmpdir_amp9ymbl/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-81/call-run_sawfish/_singularity_tmpdir_amp9ymbl/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:19.392 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_plot_meth_allele INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:19.392 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_plot_meth_allele INFO input :: name: "waterfall", value: false
2025-09-15 20:25:19.392 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_plot_meth_allele INFO input :: name: "methylation", value: true
2025-09-15 20:25:19.392 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_plot_meth_allele INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:25:19.392 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_plot_meth_allele INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:25:19.392 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_plot_meth_allele INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:25:19.392 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_plot_meth_allele INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2163.trgt.sorted.spanning.bam.bai"
2025-09-15 20:25:19.392 wdl.w:ptcp.w:call-sawfish-81.t:call-run_sawfish NOTICE slurm_singularity run :: pid: 1205337, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-81/call-run_sawfish/slurm_singularity.log.txt"
2025-09-15 20:25:19.393 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_plot_meth_allele INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2163.trgt.sorted.spanning.bam"
2025-09-15 20:25:19.393 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_plot_meth_allele INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2163.trgt.vcf"
2025-09-15 20:25:19.393 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_plot_meth_allele INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2163"
2025-09-15 20:25:19.393 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_plot_meth_allele INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:25:19.393 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_plot_meth_allele INFO eval :: name: "plot_type", value: "allele"
2025-09-15 20:25:19.394 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_plot_meth_allele INFO eval :: name: "show", value: "meth"
2025-09-15 20:25:19.394 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_plot_meth_allele INFO eval :: name: "threads", value: 1
2025-09-15 20:25:19.394 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_plot_meth_allele INFO eval :: name: "disk_size", value: 27
2025-09-15 20:25:19.394 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_plot_meth_allele INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2163.meth_allele"
2025-09-15 20:25:19.394 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_plot_meth_allele INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:19.395 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_plot_meth_allele WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:19.395 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_plot_meth_allele INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:25:19.395 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_plot_meth_allele INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:19.422 wdl.w:ptcp.w:call-trgt-71.t:call-trgt_plot_meth_allele NOTICE done
2025-09-15 20:25:19.428 wdl.w:ptcp.w:call-trgt-71 NOTICE finish :: job: "call-trgt_plot_meth_allele"
2025-09-15 20:25:19.428 wdl.w:ptcp.w:call-trgt-71 INFO output :: job: "call-trgt_plot_meth_allele", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-71/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2168.meth_allele.trgt_plots.zip"}
2025-09-15 20:25:19.428 wdl.w:ptcp.w:call-trgt-71 INFO visit :: node: "output-images_meth_allele", values: {"images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-71/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2168.meth_allele.trgt_plots.zip"}
2025-09-15 20:25:19.433 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_plot_meth_waterfall NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-66/call-trgt_plot_meth_waterfall", thread: 140612506469952
2025-09-15 20:25:19.451 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_plot_meth_waterfall INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:19.451 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_plot_meth_waterfall INFO input :: name: "waterfall", value: true
2025-09-15 20:25:19.451 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_plot_meth_waterfall INFO input :: name: "methylation", value: true
2025-09-15 20:25:19.451 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_plot_meth_waterfall INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:25:19.451 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_plot_meth_waterfall INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:25:19.451 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_plot_meth_waterfall INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:25:19.452 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_plot_meth_waterfall INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2163.trgt.sorted.spanning.bam.bai"
2025-09-15 20:25:19.452 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_plot_meth_waterfall INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2163.trgt.sorted.spanning.bam"
2025-09-15 20:25:19.452 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_plot_meth_waterfall INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2163.trgt.vcf"
2025-09-15 20:25:19.452 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_plot_meth_waterfall INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2163"
2025-09-15 20:25:19.452 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_plot_meth_waterfall INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:25:19.452 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_plot_meth_waterfall INFO eval :: name: "plot_type", value: "waterfall"
2025-09-15 20:25:19.452 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_plot_meth_waterfall INFO eval :: name: "show", value: "meth"
2025-09-15 20:25:19.452 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_plot_meth_waterfall INFO eval :: name: "threads", value: 1
2025-09-15 20:25:19.453 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_plot_meth_waterfall INFO eval :: name: "disk_size", value: 27
2025-09-15 20:25:19.453 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_plot_meth_waterfall INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2163.meth_waterfall"
2025-09-15 20:25:19.453 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_plot_meth_waterfall INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:19.453 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_plot_meth_waterfall WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:19.454 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_plot_meth_waterfall INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:25:19.454 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_plot_meth_waterfall INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:19.476 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_plot_meth_allele INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-66/call-trgt_plot_meth_allele/_singularity_tmpdir_uam62mss"
2025-09-15 20:25:19.476 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_plot_meth_allele INFO Slurm invocation: srun --job-name call-trgt_plot_meth_allele --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-66/call-trgt_plot_meth_allele/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-66/call-trgt_plot_meth_allele/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-66/call-trgt_plot_meth_allele/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-66/call-trgt_plot_meth_allele/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-66/call-trgt_genotype/out/m84036_250809_035451_s4.bc2163.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2163.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-66/call-trgt_genotype/out/m84036_250809_035451_s4.bc2163.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2163.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-66/call-trgt_genotype/out/m84036_250809_035451_s4.bc2163.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2163.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-66/call-trgt_plot_meth_allele/_singularity_tmpdir_uam62mss/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-66/call-trgt_plot_meth_allele/_singularity_tmpdir_uam62mss/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:19.492 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_plot_meth_allele NOTICE slurm_singularity run :: pid: 1205339, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-66/call-trgt_plot_meth_allele/slurm_singularity.log.txt"
2025-09-15 20:25:19.536 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_plot_meth_waterfall INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-66/call-trgt_plot_meth_waterfall/_singularity_tmpdir_8dy_x98v"
2025-09-15 20:25:19.537 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_plot_meth_waterfall INFO Slurm invocation: srun --job-name call-trgt_plot_meth_waterfall --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-66/call-trgt_plot_meth_waterfall/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-66/call-trgt_plot_meth_waterfall/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-66/call-trgt_plot_meth_waterfall/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-66/call-trgt_plot_meth_waterfall/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-66/call-trgt_genotype/out/m84036_250809_035451_s4.bc2163.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2163.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-66/call-trgt_genotype/out/m84036_250809_035451_s4.bc2163.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2163.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-66/call-trgt_genotype/out/m84036_250809_035451_s4.bc2163.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2163.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-66/call-trgt_plot_meth_waterfall/_singularity_tmpdir_8dy_x98v/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-66/call-trgt_plot_meth_waterfall/_singularity_tmpdir_8dy_x98v/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:19.547 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_plot_meth_waterfall NOTICE slurm_singularity run :: pid: 1205342, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-66/call-trgt_plot_meth_waterfall/slurm_singularity.log.txt"
2025-09-15 20:25:19.594 wdl.w:ptcp.w:call-trgt-69.t:call-trgt_plot_motifs_waterfall INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2166.motifs_waterfall.trgt_plots.zip"
2025-09-15 20:25:19.643 wdl.w:ptcp.w:call-trgt-60.t:call-trgt_plot_motifs_allele INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2157.motifs_allele.trgt_plots.zip"
2025-09-15 20:25:19.698 wdl.w:ptcp.w:call-sawfish-75.t:call-run_sawfish.slurm_singularity INFO srun: job 51797977 queued and waiting for resources
2025-09-15 20:25:19.699 wdl.w:ptcp.w:call-sawfish-75.t:call-run_sawfish.slurm_singularity INFO srun: job 51797977 has been allocated resources
2025-09-15 20:25:19.699 wdl.w:ptcp.w:call-sawfish-75.t:call-run_sawfish.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:19.718 wdl.w:ptcp.w:call-trgt-69.t:call-trgt_plot_motifs_waterfall NOTICE done
2025-09-15 20:25:19.724 wdl.w:ptcp.w:call-trgt-69 NOTICE finish :: job: "call-trgt_plot_motifs_waterfall"
2025-09-15 20:25:19.724 wdl.w:ptcp.w:call-trgt-69 INFO output :: job: "call-trgt_plot_motifs_waterfall", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-69/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2166.motifs_waterfall.trgt_plots.zip"}
2025-09-15 20:25:19.725 wdl.w:ptcp.w:call-trgt-69 INFO visit :: node: "output-images_motifs_waterfall", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-69/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2166.motifs_waterfall.trgt_plots.zip"}
2025-09-15 20:25:19.732 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_plot_motifs_allele NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-66/call-trgt_plot_motifs_allele", thread: 140610375771712
2025-09-15 20:25:19.752 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_plot_motifs_allele INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:19.752 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_plot_motifs_allele INFO input :: name: "waterfall", value: false
2025-09-15 20:25:19.752 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_plot_motifs_allele INFO input :: name: "methylation", value: false
2025-09-15 20:25:19.753 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_plot_motifs_allele INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:25:19.753 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_plot_motifs_allele INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:25:19.753 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_plot_motifs_allele INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:25:19.753 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_plot_motifs_allele INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2163.trgt.sorted.spanning.bam.bai"
2025-09-15 20:25:19.753 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_plot_motifs_allele INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2163.trgt.sorted.spanning.bam"
2025-09-15 20:25:19.753 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_plot_motifs_allele INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2163.trgt.vcf"
2025-09-15 20:25:19.753 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_plot_motifs_allele INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2163"
2025-09-15 20:25:19.753 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_plot_motifs_allele INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:25:19.754 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_plot_motifs_allele INFO eval :: name: "plot_type", value: "allele"
2025-09-15 20:25:19.754 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_plot_motifs_allele INFO eval :: name: "show", value: "motifs"
2025-09-15 20:25:19.754 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_plot_motifs_allele INFO eval :: name: "threads", value: 1
2025-09-15 20:25:19.754 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_plot_motifs_allele INFO eval :: name: "disk_size", value: 27
2025-09-15 20:25:19.754 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_plot_motifs_allele INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2163.motifs_allele"
2025-09-15 20:25:19.755 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_plot_motifs_allele INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:19.755 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_plot_motifs_allele WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:19.755 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_plot_motifs_allele INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:25:19.755 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_plot_motifs_allele INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:19.771 wdl.w:ptcp.w:call-trgt-60.t:call-trgt_plot_motifs_allele NOTICE done
2025-09-15 20:25:19.776 wdl.w:ptcp.w:call-trgt-60 NOTICE finish :: job: "call-trgt_plot_motifs_allele"
2025-09-15 20:25:19.777 wdl.w:ptcp.w:call-trgt-60 INFO output :: job: "call-trgt_plot_motifs_allele", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-60/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2157.motifs_allele.trgt_plots.zip"}
2025-09-15 20:25:19.777 wdl.w:ptcp.w:call-trgt-60 INFO visit :: node: "output-images_motifs_allele", values: {"images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-60/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2157.motifs_allele.trgt_plots.zip"}
2025-09-15 20:25:19.784 wdl.w:ptcp.t:call-tar_outputs-36.stderr VERBOSE tar: Removing leading `/' from member names
2025-09-15 20:25:19.785 wdl.w:ptcp.t:call-tar_outputs-36.stderr VERBOSE tar: Removing leading `/' from hard link targets
2025-09-15 20:25:19.785 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_plot_motifs_waterfall NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-66/call-trgt_plot_motifs_waterfall", thread: 140607137760832
2025-09-15 20:25:19.795 wdl.w:ptcp.t:call-tar_outputs-36.slurm_singularity INFO srun: job 51797978 queued and waiting for resources
2025-09-15 20:25:19.795 wdl.w:ptcp.t:call-tar_outputs-36.slurm_singularity INFO srun: job 51797978 has been allocated resources
2025-09-15 20:25:19.796 wdl.w:ptcp.t:call-tar_outputs-36.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:19.820 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_plot_motifs_waterfall INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:19.820 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_plot_motifs_waterfall INFO input :: name: "waterfall", value: true
2025-09-15 20:25:19.820 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_plot_motifs_waterfall INFO input :: name: "methylation", value: false
2025-09-15 20:25:19.820 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_plot_motifs_waterfall INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:25:19.820 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_plot_motifs_waterfall INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:25:19.820 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_plot_motifs_waterfall INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:25:19.820 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_plot_motifs_waterfall INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2163.trgt.sorted.spanning.bam.bai"
2025-09-15 20:25:19.820 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_plot_motifs_waterfall INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2163.trgt.sorted.spanning.bam"
2025-09-15 20:25:19.820 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_plot_motifs_waterfall INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2163.trgt.vcf"
2025-09-15 20:25:19.821 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_plot_motifs_waterfall INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2163"
2025-09-15 20:25:19.821 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:25:19.821 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "plot_type", value: "waterfall"
2025-09-15 20:25:19.821 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "show", value: "motifs"
2025-09-15 20:25:19.821 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "threads", value: 1
2025-09-15 20:25:19.821 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "disk_size", value: 27
2025-09-15 20:25:19.821 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2163.motifs_waterfall"
2025-09-15 20:25:19.822 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_plot_motifs_waterfall INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:19.822 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_plot_motifs_waterfall WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:19.822 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_plot_motifs_waterfall INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:25:19.822 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_plot_motifs_waterfall INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:19.840 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_plot_motifs_allele INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-66/call-trgt_plot_motifs_allele/_singularity_tmpdir_x0ub_h82"
2025-09-15 20:25:19.840 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_plot_motifs_allele INFO Slurm invocation: srun --job-name call-trgt_plot_motifs_allele --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-66/call-trgt_plot_motifs_allele/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-66/call-trgt_plot_motifs_allele/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-66/call-trgt_plot_motifs_allele/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-66/call-trgt_plot_motifs_allele/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-66/call-trgt_genotype/out/m84036_250809_035451_s4.bc2163.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2163.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-66/call-trgt_genotype/out/m84036_250809_035451_s4.bc2163.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2163.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-66/call-trgt_genotype/out/m84036_250809_035451_s4.bc2163.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2163.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-66/call-trgt_plot_motifs_allele/_singularity_tmpdir_x0ub_h82/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-66/call-trgt_plot_motifs_allele/_singularity_tmpdir_x0ub_h82/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:19.860 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_plot_motifs_allele NOTICE slurm_singularity run :: pid: 1205433, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-66/call-trgt_plot_motifs_allele/slurm_singularity.log.txt"
2025-09-15 20:25:19.891 wdl.w:ptcp.w:call-paraphase-43.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for smn1 for sample m84036_250809_035451_s4.bc2140 at 2025-09-15 20:25:00.167366...
2025-09-15 20:25:19.892 wdl.w:ptcp.w:call-paraphase-43.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for cyp21 for sample m84036_250809_035451_s4.bc2140 at 2025-09-15 20:25:11.340293...
2025-09-15 20:25:19.892 wdl.w:ptcp.w:call-paraphase-43.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for cyp21 for sample m84036_250809_035451_s4.bc2140 at 2025-09-15 20:25:12.030356...
2025-09-15 20:25:19.892 wdl.w:ptcp.w:call-paraphase-43.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for hba for sample m84036_250809_035451_s4.bc2140 at 2025-09-15 20:25:16.890627...
2025-09-15 20:25:19.892 wdl.w:ptcp.w:call-paraphase-43.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for hba for sample m84036_250809_035451_s4.bc2140 at 2025-09-15 20:25:17.258609...
2025-09-15 20:25:19.892 wdl.w:ptcp.w:call-paraphase-43.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for f8inv1 for sample m84036_250809_035451_s4.bc2140 at 2025-09-15 20:25:18.027633...
2025-09-15 20:25:19.893 wdl.w:ptcp.w:call-paraphase-43.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for f8inv1 for sample m84036_250809_035451_s4.bc2140 at 2025-09-15 20:25:18.027779...
2025-09-15 20:25:19.895 wdl.w:ptcp.w:call-trgt-71.t:call-trgt_plot_motifs_allele INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2168.motifs_allele.trgt_plots.zip"
2025-09-15 20:25:19.901 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_plot_motifs_waterfall INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-66/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_200n25te"
2025-09-15 20:25:19.901 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_plot_motifs_waterfall INFO Slurm invocation: srun --job-name call-trgt_plot_motifs_waterfall --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-66/call-trgt_plot_motifs_waterfall/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-66/call-trgt_plot_motifs_waterfall/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-66/call-trgt_plot_motifs_waterfall/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-66/call-trgt_plot_motifs_waterfall/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-66/call-trgt_genotype/out/m84036_250809_035451_s4.bc2163.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2163.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-66/call-trgt_genotype/out/m84036_250809_035451_s4.bc2163.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2163.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-66/call-trgt_genotype/out/m84036_250809_035451_s4.bc2163.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2163.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-66/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_200n25te/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-66/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_200n25te/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:19.915 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_plot_motifs_waterfall NOTICE slurm_singularity run :: pid: 1205436, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-66/call-trgt_plot_motifs_waterfall/slurm_singularity.log.txt"
2025-09-15 20:25:19.973 wdl.w:ptcp.w:call-trgt-71.t:call-trgt_plot_motifs_allele NOTICE done
2025-09-15 20:25:19.979 wdl.w:ptcp.w:call-trgt-71 NOTICE finish :: job: "call-trgt_plot_motifs_allele"
2025-09-15 20:25:19.979 wdl.w:ptcp.w:call-trgt-71 INFO output :: job: "call-trgt_plot_motifs_allele", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-71/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2168.motifs_allele.trgt_plots.zip"}
2025-09-15 20:25:19.979 wdl.w:ptcp.w:call-trgt-71 INFO visit :: node: "output-images_motifs_allele", values: {"images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-71/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2168.motifs_allele.trgt_plots.zip"}
2025-09-15 20:25:19.986 wdl.w:ptcp.w:call-trgt-81.t:call-get_reads_overlapping_repeats NOTICE task setup :: name: "get_reads_overlapping_repeats", source: "./trgt.wdl", line: 182, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-81/call-get_reads_overlapping_repeats", thread: 140607683024448
2025-09-15 20:25:19.998 wdl.w:ptcp.w:call-trgt-60.t:call-trgt_plot_meth_allele INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2157.meth_allele.trgt_plots.zip"
2025-09-15 20:25:20.007 wdl.w:ptcp.w:call-paraphase-55.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for smn1 for sample m84036_250809_035451_s4.bc2152 at 2025-09-15 20:24:57.802548...
2025-09-15 20:25:20.008 wdl.w:ptcp.w:call-paraphase-55.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for cyp21 for sample m84036_250809_035451_s4.bc2152 at 2025-09-15 20:25:06.069545...
2025-09-15 20:25:20.008 wdl.w:ptcp.w:call-paraphase-55.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for cyp21 for sample m84036_250809_035451_s4.bc2152 at 2025-09-15 20:25:06.971538...
2025-09-15 20:25:20.008 wdl.w:ptcp.w:call-paraphase-55.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for f8inv1 for sample m84036_250809_035451_s4.bc2152 at 2025-09-15 20:25:09.378316...
2025-09-15 20:25:20.008 wdl.w:ptcp.w:call-paraphase-55.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for f8inv1 for sample m84036_250809_035451_s4.bc2152 at 2025-09-15 20:25:09.379438...
2025-09-15 20:25:20.008 wdl.w:ptcp.w:call-paraphase-55.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for hba for sample m84036_250809_035451_s4.bc2152 at 2025-09-15 20:25:09.514895...
2025-09-15 20:25:20.008 wdl.w:ptcp.w:call-paraphase-55.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for hba for sample m84036_250809_035451_s4.bc2152 at 2025-09-15 20:25:09.953254...
2025-09-15 20:25:20.008 wdl.w:ptcp.w:call-paraphase-55.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for f8inv1 for sample m84036_250809_035451_s4.bc2152 at 2025-09-15 20:25:10.433200...
2025-09-15 20:25:20.008 wdl.w:ptcp.w:call-trgt-81.t:call-get_reads_overlapping_repeats INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:20.009 wdl.w:ptcp.w:call-paraphase-55.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for gba for sample m84036_250809_035451_s4.bc2152 at 2025-09-15 20:25:12.579640...
2025-09-15 20:25:20.009 wdl.w:ptcp.w:call-trgt-81.t:call-get_reads_overlapping_repeats INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:25:20.009 wdl.w:ptcp.w:call-paraphase-55.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for gba for sample m84036_250809_035451_s4.bc2152 at 2025-09-15 20:25:13.060814...
2025-09-15 20:25:20.009 wdl.w:ptcp.w:call-trgt-81.t:call-get_reads_overlapping_repeats INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2178.mapped.bam.bai"
2025-09-15 20:25:20.009 wdl.w:ptcp.w:call-paraphase-55.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for f8inv1 for sample m84036_250809_035451_s4.bc2152 at 2025-09-15 20:25:13.070211...
2025-09-15 20:25:20.009 wdl.w:ptcp.w:call-trgt-81.t:call-get_reads_overlapping_repeats INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2178.mapped.bam"
2025-09-15 20:25:20.009 wdl.w:ptcp.w:call-paraphase-55.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for f8inv1 for sample m84036_250809_035451_s4.bc2152 at 2025-09-15 20:25:13.580539...
2025-09-15 20:25:20.009 wdl.w:ptcp.w:call-trgt-81.t:call-get_reads_overlapping_repeats INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2178"
2025-09-15 20:25:20.009 wdl.w:ptcp.w:call-paraphase-55.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for hbb for sample m84036_250809_035451_s4.bc2152 at 2025-09-15 20:25:16.371772...
2025-09-15 20:25:20.010 wdl.w:ptcp.w:call-trgt-81.t:call-get_reads_overlapping_repeats INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:25:20.010 wdl.w:ptcp.w:call-paraphase-55.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for hbb for sample m84036_250809_035451_s4.bc2152 at 2025-09-15 20:25:16.371924...
2025-09-15 20:25:20.010 wdl.w:ptcp.w:call-trgt-81.t:call-get_reads_overlapping_repeats INFO eval :: name: "expand_size", value: 3000
2025-09-15 20:25:20.010 wdl.w:ptcp.w:call-trgt-81.t:call-get_reads_overlapping_repeats INFO eval :: name: "threads", value: 1
2025-09-15 20:25:20.010 wdl.w:ptcp.w:call-trgt-81.t:call-get_reads_overlapping_repeats INFO eval :: name: "expanded_bed_name", value: "m84036_250809_035451_s4.bc2178.expanded.bed"
2025-09-15 20:25:20.010 wdl.w:ptcp.w:call-trgt-81.t:call-get_reads_overlapping_repeats INFO eval :: name: "disk_size", value: 11
2025-09-15 20:25:20.011 wdl.w:ptcp.w:call-trgt-81.t:call-get_reads_overlapping_repeats INFO eval :: name: "output_name", value: "m84036_250809_035451_s4.bc2178.repeats.bam"
2025-09-15 20:25:20.011 wdl.w:ptcp.w:call-trgt-81.t:call-get_reads_overlapping_repeats INFO eval :: name: "index_name", value: "m84036_250809_035451_s4.bc2178.repeats.bam.bai"
2025-09-15 20:25:20.011 wdl.w:ptcp.w:call-trgt-81.t:call-get_reads_overlapping_repeats INFO eval :: name: "output_name_with_index", value: "m84036_250809_035451_s4.bc2178.repeats.bam##idx##m84036_250809_035451_s4.bc2178.repeats.bam.bai"
2025-09-15 20:25:20.011 wdl.w:ptcp.w:call-trgt-81.t:call-get_reads_overlapping_repeats INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:20.011 wdl.w:ptcp.w:call-trgt-81.t:call-get_reads_overlapping_repeats WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:20.012 wdl.w:ptcp.w:call-trgt-81.t:call-get_reads_overlapping_repeats INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:25:20.012 wdl.w:ptcp.w:call-trgt-81.t:call-get_reads_overlapping_repeats INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:20.023 wdl.w:ptcp.w:call-trgt-75.t:call-get_reads_overlapping_repeats.slurm_singularity INFO srun: job 51797979 queued and waiting for resources
2025-09-15 20:25:20.023 wdl.w:ptcp.w:call-trgt-75.t:call-get_reads_overlapping_repeats.slurm_singularity INFO srun: job 51797979 has been allocated resources
2025-09-15 20:25:20.023 wdl.w:ptcp.w:call-trgt-75.t:call-get_reads_overlapping_repeats.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:20.025 wdl.w:ptcp.t:call-tar_outputs-36 INFO output :: name: "sample_tarball", value: "m84036_250809_035451_s4.bc2133.tar"
2025-09-15 20:25:20.079 wdl.w:ptcp.w:call-trgt-81.t:call-get_reads_overlapping_repeats INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 9, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-81/call-get_reads_overlapping_repeats/_singularity_tmpdir_k52ftbwe"
2025-09-15 20:25:20.080 wdl.w:ptcp.w:call-trgt-81.t:call-get_reads_overlapping_repeats INFO Slurm invocation: srun --job-name call-get_reads_overlapping_repeats --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-81/call-get_reads_overlapping_repeats/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-81/call-get_reads_overlapping_repeats/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-81/call-get_reads_overlapping_repeats/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-81/call-get_reads_overlapping_repeats/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-81/out/m84036_250809_035451_s4.bc2178.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2178.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-81/out/m84036_250809_035451_s4.bc2178.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2178.mapped.bam.bai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-81/call-get_reads_overlapping_repeats/_singularity_tmpdir_k52ftbwe/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-81/call-get_reads_overlapping_repeats/_singularity_tmpdir_k52ftbwe/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:20.096 wdl.w:ptcp.w:call-trgt-75.t:call-trgt_genotype.slurm_singularity INFO srun: job 51797980 queued and waiting for resources
2025-09-15 20:25:20.096 wdl.w:ptcp.w:call-trgt-75.t:call-trgt_genotype.slurm_singularity INFO srun: job 51797980 has been allocated resources
2025-09-15 20:25:20.097 wdl.w:ptcp.w:call-trgt-75.t:call-trgt_genotype.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:20.104 wdl.w:ptcp.t:call-tar_outputs-36 NOTICE done
2025-09-15 20:25:20.107 wdl.w:ptcp.w:call-trgt-81.t:call-get_reads_overlapping_repeats NOTICE slurm_singularity run :: pid: 1205449, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-81/call-get_reads_overlapping_repeats/slurm_singularity.log.txt"
2025-09-15 20:25:20.108 wdl.w:ptcp NOTICE finish :: job: "call-tar_outputs-36"
2025-09-15 20:25:20.108 wdl.w:ptcp INFO output :: job: "call-tar_outputs-36", values: {"sample_tarball": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-36/out/m84036_250809_035451_s4.bc2133.tar"}
2025-09-15 20:25:20.116 wdl.w:ptcp.w:call-trgt-81.t:call-trgt_genotype NOTICE task setup :: name: "trgt_genotype", source: "./trgt.wdl", line: 272, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-81/call-trgt_genotype", thread: 140611415942720
2025-09-15 20:25:20.132 wdl.w:ptcp.w:call-trgt-60.t:call-trgt_plot_meth_allele NOTICE done
2025-09-15 20:25:20.133 wdl.w:ptcp.w:call-trgt-81.t:call-trgt_genotype INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:20.133 wdl.w:ptcp.w:call-trgt-81.t:call-trgt_genotype INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:25:20.133 wdl.w:ptcp.w:call-trgt-81.t:call-trgt_genotype INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:25:20.133 wdl.w:ptcp.w:call-trgt-81.t:call-trgt_genotype INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:25:20.133 wdl.w:ptcp.w:call-trgt-81.t:call-trgt_genotype INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2178.mapped.bam.bai"
2025-09-15 20:25:20.133 wdl.w:ptcp.w:call-trgt-81.t:call-trgt_genotype INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2178.mapped.bam"
2025-09-15 20:25:20.133 wdl.w:ptcp.w:call-trgt-81.t:call-trgt_genotype INFO input :: name: "sex", value: "F"
2025-09-15 20:25:20.133 wdl.w:ptcp.w:call-trgt-81.t:call-trgt_genotype INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2178"
2025-09-15 20:25:20.134 wdl.w:ptcp.w:call-trgt-81.t:call-trgt_genotype INFO eval :: name: "mem_gb", value: 16
2025-09-15 20:25:20.134 wdl.w:ptcp.w:call-trgt-81.t:call-trgt_genotype INFO eval :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2178.trgt"
2025-09-15 20:25:20.134 wdl.w:ptcp.w:call-trgt-81.t:call-trgt_genotype INFO eval :: name: "threads", value: 8
2025-09-15 20:25:20.134 wdl.w:ptcp.w:call-trgt-81.t:call-trgt_genotype INFO eval :: name: "disk_size", value: 27
2025-09-15 20:25:20.134 wdl.w:ptcp.w:call-trgt-81.t:call-trgt_genotype INFO eval :: name: "karyotype", value: "XX"
2025-09-15 20:25:20.135 wdl.w:ptcp.w:call-trgt-81.t:call-trgt_genotype INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 8, memory_reservation: 16000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:20.135 wdl.w:ptcp.w:call-trgt-81.t:call-trgt_genotype WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:20.135 wdl.w:ptcp.w:call-trgt-81.t:call-trgt_genotype INFO provisioned :: seconds_waited: 0, cpu: 8, mem_bytes: 16000000000
2025-09-15 20:25:20.136 wdl.w:ptcp.w:call-trgt-81.t:call-trgt_genotype INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:20.137 wdl.w:ptcp.w:call-trgt-60 NOTICE finish :: job: "call-trgt_plot_meth_allele"
2025-09-15 20:25:20.137 wdl.w:ptcp.w:call-trgt-60 INFO output :: job: "call-trgt_plot_meth_allele", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-60/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2157.meth_allele.trgt_plots.zip"}
2025-09-15 20:25:20.137 wdl.w:ptcp.w:call-trgt-60 INFO visit :: node: "output-images_meth_allele", values: {"images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-60/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2157.meth_allele.trgt_plots.zip"}
2025-09-15 20:25:20.143 wdl.w:ptcp.w:call-paraphase-72.t:call-run_paraphase NOTICE task setup :: name: "run_paraphase", source: "./paraphase.wdl", line: 127, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-72/call-run_paraphase", thread: 140608773551680
2025-09-15 20:25:20.163 wdl.w:ptcp.w:call-paraphase-72.t:call-run_paraphase INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:20.163 wdl.w:ptcp.w:call-paraphase-72.t:call-run_paraphase INFO input :: name: "annotation_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf"
2025-09-15 20:25:20.163 wdl.w:ptcp.w:call-paraphase-72.t:call-run_paraphase INFO input :: name: "genome_version", value: "38"
2025-09-15 20:25:20.163 wdl.w:ptcp.w:call-paraphase-72.t:call-run_paraphase INFO input :: name: "config_file", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/paraphase_config.GRCh38.yaml"
2025-09-15 20:25:20.163 wdl.w:ptcp.w:call-paraphase-72.t:call-run_paraphase INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:25:20.163 wdl.w:ptcp.w:call-paraphase-72.t:call-run_paraphase INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:25:20.164 wdl.w:ptcp.w:call-paraphase-72.t:call-run_paraphase INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2169.mapped.bam.bai"
2025-09-15 20:25:20.164 wdl.w:ptcp.w:call-paraphase-72.t:call-run_paraphase INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2169.mapped.bam"
2025-09-15 20:25:20.164 wdl.w:ptcp.w:call-paraphase-72.t:call-run_paraphase INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2169"
2025-09-15 20:25:20.164 wdl.w:ptcp.w:call-paraphase-72.t:call-run_paraphase INFO eval :: name: "threads", value: 4
2025-09-15 20:25:20.164 wdl.w:ptcp.w:call-paraphase-72.t:call-run_paraphase INFO eval :: name: "mem_gb", value: 8
2025-09-15 20:25:20.164 wdl.w:ptcp.w:call-paraphase-72.t:call-run_paraphase INFO eval :: name: "disk_size", value: 27
2025-09-15 20:25:20.164 wdl.w:ptcp.w:call-paraphase-72.t:call-run_paraphase INFO eval :: name: "out_dir", value: "m84036_250809_035451_s4.bc2169_paraphase"
2025-09-15 20:25:20.165 wdl.w:ptcp.w:call-paraphase-72.t:call-run_paraphase INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 4, memory_reservation: 8000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:20.165 wdl.w:ptcp.w:call-paraphase-72.t:call-run_paraphase WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:20.165 wdl.w:ptcp.w:call-paraphase-72.t:call-run_paraphase INFO provisioned :: seconds_waited: 0, cpu: 4, mem_bytes: 8000000000
2025-09-15 20:25:20.165 wdl.w:ptcp.w:call-paraphase-72.t:call-run_paraphase INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:20.197 wdl.w:ptcp.w:call-trgt-81.t:call-trgt_genotype INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 11, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-81/call-trgt_genotype/_singularity_tmpdir_hjc2nxou"
2025-09-15 20:25:20.197 wdl.w:ptcp.w:call-trgt-81.t:call-trgt_genotype INFO Slurm invocation: srun --job-name call-trgt_genotype --partition compute,compute9 --cpus-per-task 8 --mem 15259M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-81/call-trgt_genotype/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-81/call-trgt_genotype/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-81/call-trgt_genotype/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-81/call-trgt_genotype/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-81/out/m84036_250809_035451_s4.bc2178.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2178.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-81/out/m84036_250809_035451_s4.bc2178.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2178.mapped.bam.bai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-81/call-trgt_genotype/_singularity_tmpdir_hjc2nxou/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-81/call-trgt_genotype/_singularity_tmpdir_hjc2nxou/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:20.210 wdl.w:ptcp.w:call-trgt-81.t:call-trgt_genotype NOTICE slurm_singularity run :: pid: 1205451, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-81/call-trgt_genotype/slurm_singularity.log.txt"
2025-09-15 20:25:20.234 wdl.w:ptcp.w:call-paraphase-72.t:call-run_paraphase INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-72/call-run_paraphase/_singularity_tmpdir_gnqkkmyu"
2025-09-15 20:25:20.234 wdl.w:ptcp.w:call-paraphase-72.t:call-run_paraphase INFO Slurm invocation: srun --job-name call-run_paraphase --partition compute,compute9 --cpus-per-task 4 --mem 7629M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-72/call-run_paraphase/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-72/call-run_paraphase/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-72/call-run_paraphase/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-72/call-run_paraphase/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-72/out/m84036_250809_035451_s4.bc2169.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2169.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-72/out/m84036_250809_035451_s4.bc2169.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2169.mapped.bam.bai:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/variant_list/variant_list.GRCh38.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf:ro --bind /ptcp/meta/paraphase/paraphase_config.GRCh38.yaml:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/paraphase_config.GRCh38.yaml:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-72/call-run_paraphase/_singularity_tmpdir_gnqkkmyu/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-72/call-run_paraphase/_singularity_tmpdir_gnqkkmyu/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:20.243 wdl.w:ptcp.w:call-paraphase-72.t:call-run_paraphase NOTICE slurm_singularity run :: pid: 1205453, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-72/call-run_paraphase/slurm_singularity.log.txt"
2025-09-15 20:25:20.312 wdl.w:ptcp.w:call-paraphase-81.t:call-run_paraphase.slurm_singularity INFO srun: job 51797981 queued and waiting for resources
2025-09-15 20:25:20.312 wdl.w:ptcp.w:call-paraphase-81.t:call-run_paraphase.slurm_singularity INFO srun: job 51797981 has been allocated resources
2025-09-15 20:25:20.312 wdl.w:ptcp.w:call-paraphase-81.t:call-run_paraphase.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:20.333 wdl.w:ptcp.w:call-trgt-75.t:call-get_reads_overlapping_repeats INFO output :: name: "reads_overlapping_repeats", value: "m84036_250809_035451_s4.bc2172.repeats.bam"
2025-09-15 20:25:20.336 wdl.w:ptcp.w:call-trgt-75.t:call-get_reads_overlapping_repeats INFO output :: name: "reads_overlapping_repeats_bai", value: "m84036_250809_035451_s4.bc2172.repeats.bam.bai"
2025-09-15 20:25:20.397 wdl.w:ptcp.w:call-sawfish-81.t:call-run_sawfish.stderr VERBOSE [M::bam2fq_mainloop] discarded 0 singletons
2025-09-15 20:25:20.397 wdl.w:ptcp.w:call-sawfish-81.t:call-run_sawfish.stderr VERBOSE [M::bam2fq_mainloop] processed 1 reads
2025-09-15 20:25:20.407 wdl.w:ptcp.w:call-sawfish-81.t:call-run_sawfish.slurm_singularity INFO srun: job 51797982 queued and waiting for resources
2025-09-15 20:25:20.407 wdl.w:ptcp.w:call-sawfish-81.t:call-run_sawfish.slurm_singularity INFO srun: job 51797982 has been allocated resources
2025-09-15 20:25:20.407 wdl.w:ptcp.w:call-sawfish-81.t:call-run_sawfish.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:20.454 wdl.w:ptcp.w:call-trgt-75.t:call-get_reads_overlapping_repeats NOTICE done
2025-09-15 20:25:20.458 wdl.w:ptcp.w:call-trgt-75 NOTICE finish :: job: "call-get_reads_overlapping_repeats"
2025-09-15 20:25:20.458 wdl.w:ptcp.w:call-trgt-75 INFO output :: job: "call-get_reads_overlapping_repeats", values: {"reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-75/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2172.repeats.bam.bai", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-75/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2172.repeats.bam"}
2025-09-15 20:25:20.459 wdl.w:ptcp.w:call-trgt-75 INFO visit :: node: "output-reads_overlapping_repeats", values: {"reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-75/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2172.repeats.bam"}
2025-09-15 20:25:20.459 wdl.w:ptcp.w:call-trgt-75 INFO visit :: node: "output-reads_overlapping_repeats_bai", values: {"reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-75/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2172.repeats.bam.bai"}
2025-09-15 20:25:20.463 wdl.w:ptcp.w:call-paraphase-65.t:call-call_f8 NOTICE task setup :: name: "call_f8", source: "./paraphase.wdl", line: 232, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-65/call-call_f8", thread: 140611969599040
2025-09-15 20:25:20.485 wdl.w:ptcp.w:call-paraphase-65.t:call-call_f8 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:20.485 wdl.w:ptcp.w:call-paraphase-65.t:call-call_f8 INFO input :: name: "genome_version", value: "38"
2025-09-15 20:25:20.485 wdl.w:ptcp.w:call-paraphase-65.t:call-call_f8 INFO input :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2162"
2025-09-15 20:25:20.485 wdl.w:ptcp.w:call-paraphase-65.t:call-call_f8 INFO input :: name: "paraphase_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2162.paraphase.bam.bai"
2025-09-15 20:25:20.485 wdl.w:ptcp.w:call-paraphase-65.t:call-call_f8 INFO input :: name: "paraphase_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2162.paraphase.bam"
2025-09-15 20:25:20.485 wdl.w:ptcp.w:call-paraphase-65.t:call-call_f8 INFO input :: name: "sex", value: "F"
2025-09-15 20:25:20.485 wdl.w:ptcp.w:call-paraphase-65.t:call-call_f8 INFO eval :: name: "threads", value: 1
2025-09-15 20:25:20.485 wdl.w:ptcp.w:call-paraphase-65.t:call-call_f8 INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:25:20.485 wdl.w:ptcp.w:call-paraphase-65.t:call-call_f8 INFO eval :: name: "disk_size", value: 11
2025-09-15 20:25:20.486 wdl.w:ptcp.w:call-paraphase-65.t:call-call_f8 INFO eval :: name: "sample_sex", value: "F"
2025-09-15 20:25:20.486 wdl.w:ptcp.w:call-paraphase-65.t:call-call_f8 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:20.486 wdl.w:ptcp.w:call-paraphase-65.t:call-call_f8 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:20.486 wdl.w:ptcp.w:call-paraphase-65.t:call-call_f8 INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:25:20.487 wdl.w:ptcp.w:call-paraphase-65.t:call-call_f8 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:20.488 wdl.w:ptcp.w:call-paraphase-10.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for cyp21 for sample m84036_250809_035451_s4.bc2107 at 2025-09-15 20:24:49.970387...
2025-09-15 20:25:20.488 wdl.w:ptcp.w:call-paraphase-10.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for cyp21 for sample m84036_250809_035451_s4.bc2107 at 2025-09-15 20:24:51.349942...
2025-09-15 20:25:20.488 wdl.w:ptcp.w:call-paraphase-10.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for gba for sample m84036_250809_035451_s4.bc2107 at 2025-09-15 20:25:02.875524...
2025-09-15 20:25:20.488 wdl.w:ptcp.w:call-paraphase-10.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for gba for sample m84036_250809_035451_s4.bc2107 at 2025-09-15 20:25:03.657443...
2025-09-15 20:25:20.497 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:20 [ERROR] - No reads found for TRID=SCA37_DAB1
2025-09-15 20:25:20.510 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_plot_meth_allele.slurm_singularity INFO srun: job 51797983 queued and waiting for resources
2025-09-15 20:25:20.510 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_plot_meth_allele.slurm_singularity INFO srun: job 51797983 has been allocated resources
2025-09-15 20:25:20.510 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_plot_meth_allele.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:20.544 wdl.w:ptcp.w:call-paraphase-65.t:call-call_f8 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 8, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-65/call-call_f8/_singularity_tmpdir_zdx_hp34"
2025-09-15 20:25:20.544 wdl.w:ptcp.w:call-paraphase-65.t:call-call_f8 INFO Slurm invocation: srun --job-name call-call_f8 --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-65/call-call_f8/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-65/call-call_f8/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-65/call-call_f8/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-65/call-call_f8/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-65/call-run_paraphase/out/m84036_250809_035451_s4.bc2162_paraphase/m84036_250809_035451_s4.bc2162.paraphase.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2162.paraphase.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-65/call-run_paraphase/out/m84036_250809_035451_s4.bc2162_paraphase/m84036_250809_035451_s4.bc2162.paraphase.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2162.paraphase.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-65/call-call_f8/_singularity_tmpdir_zdx_hp34/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-65/call-call_f8/_singularity_tmpdir_zdx_hp34/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:20.550 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:25:20 [ERROR] - No reads found for TRID=SCA37_DAB1
2025-09-15 20:25:20.551 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:25:20 [ERROR] - No reads found for TRID=NIID_NOTCH2NLC
2025-09-15 20:25:20.551 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:25:20 [ERROR] - No reads found for TRID=OPDM_ABCD3
2025-09-15 20:25:20.551 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:25:20 [ERROR] - No reads found for TRID=SCA2_ATXN2
2025-09-15 20:25:20.551 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:25:20 [ERROR] - No reads found for TRID=SCA27B_FGF14
2025-09-15 20:25:20.551 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:25:20 [ERROR] - No reads found for TRID=SCA3_ATXN3
2025-09-15 20:25:20.551 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:25:20 [ERROR] - No reads found for TRID=OPMD_PABPN1
2025-09-15 20:25:20.558 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO srun: job 51797984 queued and waiting for resources
2025-09-15 20:25:20.559 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO srun: job 51797984 has been allocated resources
2025-09-15 20:25:20.559 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:20.586 wdl.w:ptcp.w:call-paraphase-65.t:call-call_f8 NOTICE slurm_singularity run :: pid: 1205471, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-65/call-call_f8/slurm_singularity.log.txt"
2025-09-15 20:25:20.741 wdl.w:ptcp.w:call-trgt-71.t:call-trgt_plot_meth_waterfall INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2168.meth_waterfall.trgt_plots.zip"
2025-09-15 20:25:20.787 wdl.w:ptcp.w:call-trgt-75.t:call-trgt_genotype INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2172.trgt.vcf"
2025-09-15 20:25:20.789 wdl.w:ptcp.w:call-paraphase-74.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for hba for sample m84036_250809_035451_s4.bc2171 at 2025-09-15 20:25:13.419357...
2025-09-15 20:25:20.790 wdl.w:ptcp.w:call-paraphase-74.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for smn1 for sample m84036_250809_035451_s4.bc2171 at 2025-09-15 20:25:13.905810...
2025-09-15 20:25:20.790 wdl.w:ptcp.w:call-paraphase-74.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for gba for sample m84036_250809_035451_s4.bc2171 at 2025-09-15 20:25:13.929068...
2025-09-15 20:25:20.790 wdl.w:ptcp.w:call-paraphase-74.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for cyp21 for sample m84036_250809_035451_s4.bc2171 at 2025-09-15 20:25:14.607062...
2025-09-15 20:25:20.791 wdl.w:ptcp.w:call-trgt-75.t:call-trgt_genotype INFO output :: name: "spanning_bam", value: "m84036_250809_035451_s4.bc2172.trgt.sorted.spanning.bam"
2025-09-15 20:25:20.792 wdl.w:ptcp.w:call-trgt-75.t:call-trgt_genotype INFO output :: name: "spanning_bam_bai", value: "m84036_250809_035451_s4.bc2172.trgt.sorted.spanning.bam.bai"
2025-09-15 20:25:20.820 wdl.w:ptcp.w:call-trgt-71.t:call-trgt_plot_meth_waterfall NOTICE done
2025-09-15 20:25:20.826 wdl.w:ptcp.w:call-trgt-71 NOTICE finish :: job: "call-trgt_plot_meth_waterfall"
2025-09-15 20:25:20.826 wdl.w:ptcp.w:call-trgt-71 INFO output :: job: "call-trgt_plot_meth_waterfall", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-71/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2168.meth_waterfall.trgt_plots.zip"}
2025-09-15 20:25:20.826 wdl.w:ptcp.w:call-trgt-71 INFO visit :: node: "output-images_meth_waterfall", values: {"images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-71/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2168.meth_waterfall.trgt_plots.zip"}
2025-09-15 20:25:20.833 wdl.w:ptcp.w:call-sawfish-72.t:call-run_sawfish NOTICE task setup :: name: "run_sawfish", source: "./sawfish.wdl", line: 83, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-72/call-run_sawfish", thread: 140609285244480
2025-09-15 20:25:20.856 wdl.w:ptcp.w:call-sawfish-72.t:call-run_sawfish INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:20.856 wdl.w:ptcp.w:call-sawfish-72.t:call-run_sawfish INFO input :: name: "genome_version", value: "38"
2025-09-15 20:25:20.856 wdl.w:ptcp.w:call-sawfish-72.t:call-run_sawfish INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:25:20.856 wdl.w:ptcp.w:call-sawfish-72.t:call-run_sawfish INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:25:20.856 wdl.w:ptcp.w:call-sawfish-72.t:call-run_sawfish INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2169.mapped.bam.bai"
2025-09-15 20:25:20.856 wdl.w:ptcp.w:call-sawfish-72.t:call-run_sawfish INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2169.mapped.bam"
2025-09-15 20:25:20.856 wdl.w:ptcp.w:call-sawfish-72.t:call-run_sawfish INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2169"
2025-09-15 20:25:20.856 wdl.w:ptcp.w:call-sawfish-72.t:call-run_sawfish INFO eval :: name: "mem_gb", value: 32
2025-09-15 20:25:20.856 wdl.w:ptcp.w:call-sawfish-72.t:call-run_sawfish INFO eval :: name: "threads", value: 16
2025-09-15 20:25:20.857 wdl.w:ptcp.w:call-sawfish-72.t:call-run_sawfish INFO eval :: name: "disk_size", value: 30
2025-09-15 20:25:20.857 wdl.w:ptcp.w:call-sawfish-72.t:call-run_sawfish INFO eval :: name: "discover_dirname", value: "m84036_250809_035451_s4.bc2169_sawfish_discover"
2025-09-15 20:25:20.857 wdl.w:ptcp.w:call-sawfish-72.t:call-run_sawfish INFO eval :: name: "call_dirname", value: "m84036_250809_035451_s4.bc2169_sawfish"
2025-09-15 20:25:20.857 wdl.w:ptcp.w:call-sawfish-72.t:call-run_sawfish INFO eval :: name: "minimap2_bam_filename", value: "m84036_250809_035451_s4.bc2169.minimap2.bam"
2025-09-15 20:25:20.857 wdl.w:ptcp.w:call-sawfish-72.t:call-run_sawfish INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 16, memory_reservation: 32000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:20.857 wdl.w:ptcp.w:call-sawfish-72.t:call-run_sawfish WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:20.858 wdl.w:ptcp.w:call-sawfish-72.t:call-run_sawfish INFO provisioned :: seconds_waited: 0, cpu: 16, mem_bytes: 32000000000
2025-09-15 20:25:20.858 wdl.w:ptcp.w:call-sawfish-72.t:call-run_sawfish INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:20.863 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:25:20 [ERROR] - No reads found for TRID=SCA37_DAB1
2025-09-15 20:25:20.863 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:25:20 [ERROR] - No reads found for TRID=NIID_NOTCH2NLC
2025-09-15 20:25:20.863 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:25:20 [ERROR] - No reads found for TRID=OPDM_ABCD3
2025-09-15 20:25:20.863 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:25:20 [ERROR] - No reads found for TRID=SCA2_ATXN2
2025-09-15 20:25:20.864 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:25:20 [ERROR] - No reads found for TRID=SCA27B_FGF14
2025-09-15 20:25:20.875 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_plot_motifs_allele.slurm_singularity INFO srun: job 51797985 queued and waiting for resources
2025-09-15 20:25:20.875 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_plot_motifs_allele.slurm_singularity INFO srun: job 51797985 has been allocated resources
2025-09-15 20:25:20.875 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_plot_motifs_allele.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:20.885 wdl.w:ptcp.w:call-trgt-75.t:call-trgt_genotype NOTICE done
2025-09-15 20:25:20.917 wdl.w:ptcp.w:call-trgt-75 NOTICE finish :: job: "call-trgt_genotype"
2025-09-15 20:25:20.917 wdl.w:ptcp.w:call-trgt-75 INFO output :: job: "call-trgt_genotype", values: {"spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-75/call-trgt_genotype/out/m84036_250809_035451_s4.bc2172.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-75/call-trgt_genotype/out/m84036_250809_035451_s4.bc2172.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-75/call-trgt_genotype/out/m84036_250809_035451_s4.bc2172.trgt.vcf"}
2025-09-15 20:25:20.918 wdl.w:ptcp.w:call-trgt-75 NOTICE ready :: job: "call-trgt_plot_meth_allele", callee: "trgt_plot"
2025-09-15 20:25:20.918 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:25:20 [ERROR] - No reads found for TRID=SCA37_DAB1
2025-09-15 20:25:20.918 wdl.w:ptcp.w:call-trgt-75 INFO input :: job: "call-trgt_plot_meth_allele", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": false, "methylation": true, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-75/call-trgt_genotype/out/m84036_250809_035451_s4.bc2172.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-75/call-trgt_genotype/out/m84036_250809_035451_s4.bc2172.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-75/call-trgt_genotype/out/m84036_250809_035451_s4.bc2172.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2172"}
2025-09-15 20:25:20.918 wdl.w:ptcp.w:call-sawfish-72.t:call-run_sawfish INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 10, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-72/call-run_sawfish/_singularity_tmpdir_7l9uc0ub"
2025-09-15 20:25:20.918 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:25:20 [ERROR] - No reads found for TRID=NIID_NOTCH2NLC
2025-09-15 20:25:20.918 wdl.w:ptcp.w:call-sawfish-72.t:call-run_sawfish INFO Slurm invocation: srun --job-name call-run_sawfish --partition compute,compute9 --cpus-per-task 16 --mem 30518M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-72/call-run_sawfish/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-72/call-run_sawfish/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-72/call-run_sawfish/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-72/call-run_sawfish/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-72/out/m84036_250809_035451_s4.bc2169.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2169.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-72/out/m84036_250809_035451_s4.bc2169.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2169.mapped.bam.bai:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-72/call-run_sawfish/_singularity_tmpdir_7l9uc0ub/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-72/call-run_sawfish/_singularity_tmpdir_7l9uc0ub/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:20.918 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:25:20 [ERROR] - No reads found for TRID=OPDM_ABCD3
2025-09-15 20:25:20.925 wdl.w:ptcp.w:call-trgt-75 NOTICE ready :: job: "call-trgt_plot_meth_waterfall", callee: "trgt_plot"
2025-09-15 20:25:20.925 wdl.w:ptcp.w:call-trgt-75 INFO input :: job: "call-trgt_plot_meth_waterfall", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": true, "methylation": true, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-75/call-trgt_genotype/out/m84036_250809_035451_s4.bc2172.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-75/call-trgt_genotype/out/m84036_250809_035451_s4.bc2172.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-75/call-trgt_genotype/out/m84036_250809_035451_s4.bc2172.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2172"}
2025-09-15 20:25:20.925 wdl.w:ptcp.w:call-trgt-72.t:call-get_reads_overlapping_repeats NOTICE task setup :: name: "get_reads_overlapping_repeats", source: "./trgt.wdl", line: 182, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-72/call-get_reads_overlapping_repeats", thread: 140613034948160
2025-09-15 20:25:20.926 wdl.w:ptcp.w:call-trgt-75 NOTICE ready :: job: "call-trgt_plot_motifs_allele", callee: "trgt_plot"
2025-09-15 20:25:20.927 wdl.w:ptcp.w:call-trgt-75 INFO input :: job: "call-trgt_plot_motifs_allele", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": false, "methylation": false, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-75/call-trgt_genotype/out/m84036_250809_035451_s4.bc2172.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-75/call-trgt_genotype/out/m84036_250809_035451_s4.bc2172.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-75/call-trgt_genotype/out/m84036_250809_035451_s4.bc2172.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2172"}
2025-09-15 20:25:20.927 wdl.w:ptcp.w:call-trgt-75 NOTICE ready :: job: "call-trgt_plot_motifs_waterfall", callee: "trgt_plot"
2025-09-15 20:25:20.927 wdl.w:ptcp.w:call-trgt-75 INFO input :: job: "call-trgt_plot_motifs_waterfall", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": true, "methylation": false, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-75/call-trgt_genotype/out/m84036_250809_035451_s4.bc2172.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-75/call-trgt_genotype/out/m84036_250809_035451_s4.bc2172.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-75/call-trgt_genotype/out/m84036_250809_035451_s4.bc2172.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2172"}
2025-09-15 20:25:20.928 wdl.w:ptcp.w:call-trgt-75 INFO visit :: node: "output-spanning_bam", values: {"spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-75/call-trgt_genotype/out/m84036_250809_035451_s4.bc2172.trgt.sorted.spanning.bam"}
2025-09-15 20:25:20.928 wdl.w:ptcp.w:call-trgt-75 INFO visit :: node: "output-spanning_bam_bai", values: {"spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-75/call-trgt_genotype/out/m84036_250809_035451_s4.bc2172.trgt.sorted.spanning.bam.bai"}
2025-09-15 20:25:20.928 wdl.w:ptcp.w:call-trgt-75 INFO visit :: node: "output-vcf", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-75/call-trgt_genotype/out/m84036_250809_035451_s4.bc2172.trgt.vcf"}
2025-09-15 20:25:20.930 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO srun: job 51797986 queued and waiting for resources
2025-09-15 20:25:20.930 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO srun: job 51797986 has been allocated resources
2025-09-15 20:25:20.930 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:20.947 wdl.w:ptcp.w:call-trgt-72.t:call-get_reads_overlapping_repeats INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:20.948 wdl.w:ptcp.w:call-trgt-72.t:call-get_reads_overlapping_repeats INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:25:20.948 wdl.w:ptcp.w:call-trgt-72.t:call-get_reads_overlapping_repeats INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2169.mapped.bam.bai"
2025-09-15 20:25:20.948 wdl.w:ptcp.w:call-trgt-72.t:call-get_reads_overlapping_repeats INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2169.mapped.bam"
2025-09-15 20:25:20.948 wdl.w:ptcp.w:call-trgt-72.t:call-get_reads_overlapping_repeats INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2169"
2025-09-15 20:25:20.948 wdl.w:ptcp.w:call-trgt-72.t:call-get_reads_overlapping_repeats INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:25:20.948 wdl.w:ptcp.w:call-trgt-72.t:call-get_reads_overlapping_repeats INFO eval :: name: "expand_size", value: 3000
2025-09-15 20:25:20.948 wdl.w:ptcp.w:call-trgt-72.t:call-get_reads_overlapping_repeats INFO eval :: name: "threads", value: 1
2025-09-15 20:25:20.948 wdl.w:ptcp.w:call-trgt-72.t:call-get_reads_overlapping_repeats INFO eval :: name: "expanded_bed_name", value: "m84036_250809_035451_s4.bc2169.expanded.bed"
2025-09-15 20:25:20.948 wdl.w:ptcp.w:call-trgt-72.t:call-get_reads_overlapping_repeats INFO eval :: name: "disk_size", value: 11
2025-09-15 20:25:20.948 wdl.w:ptcp.w:call-trgt-72.t:call-get_reads_overlapping_repeats INFO eval :: name: "output_name", value: "m84036_250809_035451_s4.bc2169.repeats.bam"
2025-09-15 20:25:20.949 wdl.w:ptcp.w:call-trgt-72.t:call-get_reads_overlapping_repeats INFO eval :: name: "index_name", value: "m84036_250809_035451_s4.bc2169.repeats.bam.bai"
2025-09-15 20:25:20.949 wdl.w:ptcp.w:call-trgt-72.t:call-get_reads_overlapping_repeats INFO eval :: name: "output_name_with_index", value: "m84036_250809_035451_s4.bc2169.repeats.bam##idx##m84036_250809_035451_s4.bc2169.repeats.bam.bai"
2025-09-15 20:25:20.949 wdl.w:ptcp.w:call-trgt-72.t:call-get_reads_overlapping_repeats INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:20.949 wdl.w:ptcp.w:call-trgt-72.t:call-get_reads_overlapping_repeats WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:20.949 wdl.w:ptcp.w:call-trgt-72.t:call-get_reads_overlapping_repeats INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:25:20.949 wdl.w:ptcp.w:call-trgt-72.t:call-get_reads_overlapping_repeats INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:20.953 wdl.w:ptcp.w:call-sawfish-72.t:call-run_sawfish NOTICE slurm_singularity run :: pid: 1205480, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-72/call-run_sawfish/slurm_singularity.log.txt"
2025-09-15 20:25:21.009 wdl.w:ptcp.w:call-trgt-72.t:call-get_reads_overlapping_repeats INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 9, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-72/call-get_reads_overlapping_repeats/_singularity_tmpdir_39jkjzrw"
2025-09-15 20:25:21.010 wdl.w:ptcp.w:call-trgt-72.t:call-get_reads_overlapping_repeats INFO Slurm invocation: srun --job-name call-get_reads_overlapping_repeats --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-72/call-get_reads_overlapping_repeats/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-72/call-get_reads_overlapping_repeats/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-72/call-get_reads_overlapping_repeats/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-72/call-get_reads_overlapping_repeats/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-72/out/m84036_250809_035451_s4.bc2169.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2169.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-72/out/m84036_250809_035451_s4.bc2169.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2169.mapped.bam.bai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-72/call-get_reads_overlapping_repeats/_singularity_tmpdir_39jkjzrw/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-72/call-get_reads_overlapping_repeats/_singularity_tmpdir_39jkjzrw/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:21.021 wdl.w:ptcp.w:call-trgt-72.t:call-get_reads_overlapping_repeats NOTICE slurm_singularity run :: pid: 1205488, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-72/call-get_reads_overlapping_repeats/slurm_singularity.log.txt"
2025-09-15 20:25:21.064 wdl.w:ptcp.w:call-trgt-71.t:call-trgt_plot_motifs_waterfall INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2168.motifs_waterfall.trgt_plots.zip"
2025-09-15 20:25:21.099 wdl.w:ptcp.w:call-trgt-65.t:call-trgt_plot_motifs_allele INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2162.motifs_allele.trgt_plots.zip"
2025-09-15 20:25:21.119 wdl.w:ptcp.w:call-trgt-81.t:call-get_reads_overlapping_repeats.slurm_singularity INFO srun: job 51797987 queued and waiting for resources
2025-09-15 20:25:21.119 wdl.w:ptcp.w:call-trgt-81.t:call-get_reads_overlapping_repeats.slurm_singularity INFO srun: job 51797987 has been allocated resources
2025-09-15 20:25:21.119 wdl.w:ptcp.w:call-trgt-81.t:call-get_reads_overlapping_repeats.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:21.155 wdl.w:ptcp.w:call-trgt-71.t:call-trgt_plot_motifs_waterfall NOTICE done
2025-09-15 20:25:21.160 wdl.w:ptcp.w:call-trgt-71 NOTICE finish :: job: "call-trgt_plot_motifs_waterfall"
2025-09-15 20:25:21.161 wdl.w:ptcp.w:call-trgt-71 INFO output :: job: "call-trgt_plot_motifs_waterfall", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-71/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2168.motifs_waterfall.trgt_plots.zip"}
2025-09-15 20:25:21.161 wdl.w:ptcp.w:call-trgt-71 INFO visit :: node: "output-images_motifs_waterfall", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-71/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2168.motifs_waterfall.trgt_plots.zip"}
2025-09-15 20:25:21.161 wdl.w:ptcp.w:call-trgt-71 INFO visit :: node: "outputs", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-71/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2168.motifs_waterfall.trgt_plots.zip", "images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-71/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2168.meth_allele.trgt_plots.zip", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-71/call-trgt_genotype/out/m84036_250809_035451_s4.bc2168.trgt.sorted.spanning.bam.bai", "images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-71/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2168.motifs_allele.trgt_plots.zip", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-71/call-trgt_genotype/out/m84036_250809_035451_s4.bc2168.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-71/call-trgt_genotype/out/m84036_250809_035451_s4.bc2168.trgt.vcf", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-71/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2168.repeats.bam", "images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-71/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2168.meth_waterfall.trgt_plots.zip", "reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-71/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2168.repeats.bam.bai"}
2025-09-15 20:25:21.169 wdl.w:ptcp.w:call-trgt-72.t:call-trgt_genotype NOTICE task setup :: name: "trgt_genotype", source: "./trgt.wdl", line: 272, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-72/call-trgt_genotype", thread: 140607691417152
2025-09-15 20:25:21.189 wdl.w:ptcp.w:call-trgt-72.t:call-trgt_genotype INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:21.189 wdl.w:ptcp.w:call-trgt-72.t:call-trgt_genotype INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:25:21.189 wdl.w:ptcp.w:call-trgt-72.t:call-trgt_genotype INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:25:21.189 wdl.w:ptcp.w:call-trgt-72.t:call-trgt_genotype INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:25:21.189 wdl.w:ptcp.w:call-trgt-72.t:call-trgt_genotype INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2169.mapped.bam.bai"
2025-09-15 20:25:21.189 wdl.w:ptcp.w:call-trgt-72.t:call-trgt_genotype INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2169.mapped.bam"
2025-09-15 20:25:21.189 wdl.w:ptcp.w:call-trgt-72.t:call-trgt_genotype INFO input :: name: "sex", value: "F"
2025-09-15 20:25:21.189 wdl.w:ptcp.w:call-trgt-72.t:call-trgt_genotype INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2169"
2025-09-15 20:25:21.189 wdl.w:ptcp.w:call-trgt-72.t:call-trgt_genotype INFO eval :: name: "mem_gb", value: 16
2025-09-15 20:25:21.189 wdl.w:ptcp.w:call-trgt-72.t:call-trgt_genotype INFO eval :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2169.trgt"
2025-09-15 20:25:21.190 wdl.w:ptcp.w:call-trgt-72.t:call-trgt_genotype INFO eval :: name: "threads", value: 8
2025-09-15 20:25:21.190 wdl.w:ptcp.w:call-trgt-72.t:call-trgt_genotype INFO eval :: name: "disk_size", value: 27
2025-09-15 20:25:21.190 wdl.w:ptcp.w:call-trgt-72.t:call-trgt_genotype INFO eval :: name: "karyotype", value: "XX"
2025-09-15 20:25:21.191 wdl.w:ptcp.w:call-trgt-72.t:call-trgt_genotype INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 8, memory_reservation: 16000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:21.191 wdl.w:ptcp.w:call-trgt-72.t:call-trgt_genotype WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:21.191 wdl.w:ptcp.w:call-trgt-72.t:call-trgt_genotype INFO provisioned :: seconds_waited: 0, cpu: 8, mem_bytes: 16000000000
2025-09-15 20:25:21.191 wdl.w:ptcp.w:call-trgt-72.t:call-trgt_genotype INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:21.197 wdl.w:ptcp.w:call-trgt-65.t:call-trgt_plot_meth_allele INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2162.meth_allele.trgt_plots.zip"
2025-09-15 20:25:21.198 wdl.w:ptcp.w:call-sawfish-10.t:call-run_sawfish INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2107_sawfish/m84036_250809_035451_s4.bc2107.sv.vcf.gz"
2025-09-15 20:25:21.204 wdl.w:ptcp.w:call-sawfish-10.t:call-run_sawfish INFO output :: name: "vcf_tbi", value: "m84036_250809_035451_s4.bc2107_sawfish/m84036_250809_035451_s4.bc2107.sv.vcf.gz.tbi"
2025-09-15 20:25:21.206 wdl.w:ptcp.w:call-sawfish-10.t:call-run_sawfish INFO output :: name: "minimap2_bam", value: "m84036_250809_035451_s4.bc2107.minimap2.bam"
2025-09-15 20:25:21.207 wdl.w:ptcp.w:call-sawfish-10.t:call-run_sawfish INFO output :: name: "minimap2_bam_bai", value: "m84036_250809_035451_s4.bc2107.minimap2.bam.bai"
2025-09-15 20:25:21.224 wdl.w:ptcp.w:call-trgt-81.t:call-trgt_genotype.slurm_singularity INFO srun: job 51797988 queued and waiting for resources
2025-09-15 20:25:21.224 wdl.w:ptcp.w:call-trgt-81.t:call-trgt_genotype.slurm_singularity INFO srun: job 51797988 has been allocated resources
2025-09-15 20:25:21.224 wdl.w:ptcp.w:call-trgt-81.t:call-trgt_genotype.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:21.254 wdl.w:ptcp.w:call-trgt-65.t:call-trgt_plot_motifs_allele NOTICE done
2025-09-15 20:25:21.254 wdl.w:ptcp.w:call-paraphase-72.t:call-run_paraphase.slurm_singularity INFO srun: job 51797989 queued and waiting for resources
2025-09-15 20:25:21.255 wdl.w:ptcp.w:call-paraphase-72.t:call-run_paraphase.slurm_singularity INFO srun: job 51797989 has been allocated resources
2025-09-15 20:25:21.255 wdl.w:ptcp.w:call-paraphase-72.t:call-run_paraphase.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:21.260 wdl.w:ptcp.w:call-trgt-65 NOTICE finish :: job: "call-trgt_plot_motifs_allele"
2025-09-15 20:25:21.260 wdl.w:ptcp.w:call-trgt-65 INFO output :: job: "call-trgt_plot_motifs_allele", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-65/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2162.motifs_allele.trgt_plots.zip"}
2025-09-15 20:25:21.261 wdl.w:ptcp.w:call-trgt-65 INFO visit :: node: "output-images_motifs_allele", values: {"images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-65/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2162.motifs_allele.trgt_plots.zip"}
2025-09-15 20:25:21.267 wdl.w:ptcp.w:call-trgt-68.t:call-trgt_plot_meth_allele NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-68/call-trgt_plot_meth_allele", thread: 140610367379008
2025-09-15 20:25:21.280 wdl.w:ptcp.w:call-trgt-72.t:call-trgt_genotype INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 11, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-72/call-trgt_genotype/_singularity_tmpdir_dw6qtaw2"
2025-09-15 20:25:21.280 wdl.w:ptcp.w:call-trgt-72.t:call-trgt_genotype INFO Slurm invocation: srun --job-name call-trgt_genotype --partition compute,compute9 --cpus-per-task 8 --mem 15259M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-72/call-trgt_genotype/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-72/call-trgt_genotype/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-72/call-trgt_genotype/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-72/call-trgt_genotype/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-72/out/m84036_250809_035451_s4.bc2169.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2169.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-72/out/m84036_250809_035451_s4.bc2169.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2169.mapped.bam.bai:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-72/call-trgt_genotype/_singularity_tmpdir_dw6qtaw2/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-72/call-trgt_genotype/_singularity_tmpdir_dw6qtaw2/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:21.304 wdl.w:ptcp.w:call-trgt-71 NOTICE done
2025-09-15 20:25:21.309 wdl.w:ptcp.w:call-trgt-72.t:call-trgt_genotype NOTICE slurm_singularity run :: pid: 1205498, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-72/call-trgt_genotype/slurm_singularity.log.txt"
2025-09-15 20:25:21.310 wdl.w:ptcp.w:call-trgt-68.t:call-trgt_plot_meth_allele INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:21.310 wdl.w:ptcp.w:call-trgt-68.t:call-trgt_plot_meth_allele INFO input :: name: "waterfall", value: false
2025-09-15 20:25:21.310 wdl.w:ptcp.w:call-trgt-68.t:call-trgt_plot_meth_allele INFO input :: name: "methylation", value: true
2025-09-15 20:25:21.310 wdl.w:ptcp.w:call-trgt-68.t:call-trgt_plot_meth_allele INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:25:21.310 wdl.w:ptcp.w:call-trgt-68.t:call-trgt_plot_meth_allele INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:25:21.310 wdl.w:ptcp.w:call-trgt-68.t:call-trgt_plot_meth_allele INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:25:21.310 wdl.w:ptcp.w:call-trgt-68.t:call-trgt_plot_meth_allele INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2165.trgt.sorted.spanning.bam.bai"
2025-09-15 20:25:21.310 wdl.w:ptcp.w:call-trgt-68.t:call-trgt_plot_meth_allele INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2165.trgt.sorted.spanning.bam"
2025-09-15 20:25:21.310 wdl.w:ptcp.w:call-trgt-68.t:call-trgt_plot_meth_allele INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2165.trgt.vcf"
2025-09-15 20:25:21.310 wdl.w:ptcp.w:call-trgt-68.t:call-trgt_plot_meth_allele INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2165"
2025-09-15 20:25:21.311 wdl.w:ptcp.w:call-trgt-68.t:call-trgt_plot_meth_allele INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:25:21.311 wdl.w:ptcp.w:call-trgt-68.t:call-trgt_plot_meth_allele INFO eval :: name: "plot_type", value: "allele"
2025-09-15 20:25:21.311 wdl.w:ptcp.w:call-trgt-68.t:call-trgt_plot_meth_allele INFO eval :: name: "show", value: "meth"
2025-09-15 20:25:21.311 wdl.w:ptcp.w:call-trgt-68.t:call-trgt_plot_meth_allele INFO eval :: name: "threads", value: 1
2025-09-15 20:25:21.311 wdl.w:ptcp.w:call-trgt-68.t:call-trgt_plot_meth_allele INFO eval :: name: "disk_size", value: 27
2025-09-15 20:25:21.312 wdl.w:ptcp.w:call-trgt-68.t:call-trgt_plot_meth_allele INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2165.meth_allele"
2025-09-15 20:25:21.312 wdl.w:ptcp.w:call-trgt-68.t:call-trgt_plot_meth_allele INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:21.312 wdl.w:ptcp.w:call-trgt-68.t:call-trgt_plot_meth_allele WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:21.312 wdl.w:ptcp.w:call-trgt-68.t:call-trgt_plot_meth_allele INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:25:21.313 wdl.w:ptcp.w:call-trgt-68.t:call-trgt_plot_meth_allele INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:21.321 wdl.w:ptcp NOTICE finish :: job: "call-trgt-71"
2025-09-15 20:25:21.322 wdl.w:ptcp INFO output :: job: "call-trgt-71", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-71/out/m84036_250809_035451_s4.bc2168.motifs_waterfall.trgt_plots.zip", "images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-71/out/m84036_250809_035451_s4.bc2168.meth_allele.trgt_plots.zip", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-71/out/m84036_250809_035451_s4.bc2168.trgt.sorted.spanning.bam.bai", "images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-71/out/m84036_250809_035451_s4.bc2168.motifs_allele.trgt_plots.zip", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-71/out/m84036_250809_035451_s4.bc2168.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-71/out/m84036_250809_035451_s4.bc2168.trgt.vcf", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-71/out/m84036_250809_035451_s4.bc2168.repeats.bam", "images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-71/out/m84036_250809_035451_s4.bc2168.meth_waterfall.trgt_plots.zip", "reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-71/out/m84036_250809_035451_s4.bc2168.repeats.bam.bai"}
2025-09-15 20:25:21.330 wdl.w:ptcp.w:call-sawfish-93 NOTICE workflow start :: name: "sawfish", source: "./sawfish.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-93"
2025-09-15 20:25:21.347 wdl.w:ptcp.w:call-sawfish-93 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:25:21.348 wdl.w:ptcp.w:call-sawfish-93 INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:25:21.348 wdl.w:ptcp.w:call-sawfish-93 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-93/out/m84036_250809_035451_s4.bc2190.mapped.bam"}
2025-09-15 20:25:21.348 wdl.w:ptcp.w:call-sawfish-93 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-93/out/m84036_250809_035451_s4.bc2190.mapped.bam.bai"}
2025-09-15 20:25:21.348 wdl.w:ptcp.w:call-sawfish-93 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:25:21.348 wdl.w:ptcp.w:call-sawfish-93 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:25:21.348 wdl.w:ptcp.w:call-sawfish-93 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2190"}
2025-09-15 20:25:21.348 wdl.w:ptcp.w:call-sawfish-93 NOTICE ready :: job: "call-run_sawfish", callee: "run_sawfish"
2025-09-15 20:25:21.348 wdl.w:ptcp.w:call-sawfish-93 INFO input :: job: "call-run_sawfish", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-93/out/m84036_250809_035451_s4.bc2190.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-93/out/m84036_250809_035451_s4.bc2190.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2190"}
2025-09-15 20:25:21.351 wdl.w:ptcp.w:call-trgt-65.t:call-trgt_plot_meth_allele NOTICE done
2025-09-15 20:25:21.355 wdl.w:ptcp.w:call-trgt-65 NOTICE finish :: job: "call-trgt_plot_meth_allele"
2025-09-15 20:25:21.356 wdl.w:ptcp.w:call-trgt-65 INFO output :: job: "call-trgt_plot_meth_allele", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-65/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2162.meth_allele.trgt_plots.zip"}
2025-09-15 20:25:21.356 wdl.w:ptcp.w:call-trgt-65 INFO visit :: node: "output-images_meth_allele", values: {"images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-65/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2162.meth_allele.trgt_plots.zip"}
2025-09-15 20:25:21.361 wdl.w:ptcp.w:call-trgt-68.t:call-trgt_plot_meth_waterfall NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-68/call-trgt_plot_meth_waterfall", thread: 140611944420928
2025-09-15 20:25:21.381 wdl.w:ptcp.w:call-trgt-68.t:call-trgt_plot_meth_waterfall INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:21.381 wdl.w:ptcp.w:call-trgt-68.t:call-trgt_plot_meth_waterfall INFO input :: name: "waterfall", value: true
2025-09-15 20:25:21.382 wdl.w:ptcp.w:call-trgt-68.t:call-trgt_plot_meth_waterfall INFO input :: name: "methylation", value: true
2025-09-15 20:25:21.382 wdl.w:ptcp.w:call-trgt-68.t:call-trgt_plot_meth_waterfall INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:25:21.382 wdl.w:ptcp.w:call-trgt-68.t:call-trgt_plot_meth_waterfall INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:25:21.382 wdl.w:ptcp.w:call-trgt-68.t:call-trgt_plot_meth_waterfall INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:25:21.382 wdl.w:ptcp.w:call-trgt-68.t:call-trgt_plot_meth_waterfall INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2165.trgt.sorted.spanning.bam.bai"
2025-09-15 20:25:21.382 wdl.w:ptcp.w:call-trgt-68.t:call-trgt_plot_meth_waterfall INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2165.trgt.sorted.spanning.bam"
2025-09-15 20:25:21.382 wdl.w:ptcp.w:call-trgt-68.t:call-trgt_plot_meth_waterfall INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2165.trgt.vcf"
2025-09-15 20:25:21.382 wdl.w:ptcp.w:call-trgt-68.t:call-trgt_plot_meth_waterfall INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2165"
2025-09-15 20:25:21.382 wdl.w:ptcp.w:call-trgt-68.t:call-trgt_plot_meth_waterfall INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:25:21.383 wdl.w:ptcp.w:call-trgt-68.t:call-trgt_plot_meth_waterfall INFO eval :: name: "plot_type", value: "waterfall"
2025-09-15 20:25:21.383 wdl.w:ptcp.w:call-trgt-68.t:call-trgt_plot_meth_waterfall INFO eval :: name: "show", value: "meth"
2025-09-15 20:25:21.383 wdl.w:ptcp.w:call-trgt-68.t:call-trgt_plot_meth_waterfall INFO eval :: name: "threads", value: 1
2025-09-15 20:25:21.383 wdl.w:ptcp.w:call-trgt-68.t:call-trgt_plot_meth_waterfall INFO eval :: name: "disk_size", value: 27
2025-09-15 20:25:21.383 wdl.w:ptcp.w:call-trgt-68.t:call-trgt_plot_meth_waterfall INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2165.meth_waterfall"
2025-09-15 20:25:21.383 wdl.w:ptcp.w:call-trgt-68.t:call-trgt_plot_meth_waterfall INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:21.383 wdl.w:ptcp.w:call-trgt-68.t:call-trgt_plot_meth_waterfall WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:21.384 wdl.w:ptcp.w:call-trgt-68.t:call-trgt_plot_meth_waterfall INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:25:21.384 wdl.w:ptcp.w:call-trgt-68.t:call-trgt_plot_meth_waterfall INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:21.395 wdl.w:ptcp.w:call-trgt-68.t:call-trgt_plot_meth_allele INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-68/call-trgt_plot_meth_allele/_singularity_tmpdir_0sr0iuhh"
2025-09-15 20:25:21.395 wdl.w:ptcp.w:call-trgt-68.t:call-trgt_plot_meth_allele INFO Slurm invocation: srun --job-name call-trgt_plot_meth_allele --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-68/call-trgt_plot_meth_allele/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-68/call-trgt_plot_meth_allele/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-68/call-trgt_plot_meth_allele/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-68/call-trgt_plot_meth_allele/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-68/call-trgt_genotype/out/m84036_250809_035451_s4.bc2165.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2165.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-68/call-trgt_genotype/out/m84036_250809_035451_s4.bc2165.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2165.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-68/call-trgt_genotype/out/m84036_250809_035451_s4.bc2165.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2165.trgt.sorted.spanning.bam.bai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-68/call-trgt_plot_meth_allele/_singularity_tmpdir_0sr0iuhh/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-68/call-trgt_plot_meth_allele/_singularity_tmpdir_0sr0iuhh/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:21.406 wdl.w:ptcp.w:call-sawfish-10.t:call-run_sawfish NOTICE done
2025-09-15 20:25:21.410 wdl.w:ptcp.w:call-trgt-68.t:call-trgt_plot_meth_allele NOTICE slurm_singularity run :: pid: 1205500, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-68/call-trgt_plot_meth_allele/slurm_singularity.log.txt"
2025-09-15 20:25:21.411 wdl.w:ptcp.w:call-sawfish-10 NOTICE finish :: job: "call-run_sawfish"
2025-09-15 20:25:21.411 wdl.w:ptcp.w:call-sawfish-10 INFO output :: job: "call-run_sawfish", values: {"minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-10/call-run_sawfish/out/m84036_250809_035451_s4.bc2107.minimap2.bam.bai", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-10/call-run_sawfish/out/m84036_250809_035451_s4.bc2107.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-10/call-run_sawfish/out/m84036_250809_035451_s4.bc2107_sawfish/m84036_250809_035451_s4.bc2107.sv.vcf.gz.tbi", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-10/call-run_sawfish/out/m84036_250809_035451_s4.bc2107_sawfish/m84036_250809_035451_s4.bc2107.sv.vcf.gz"}
2025-09-15 20:25:21.411 wdl.w:ptcp.w:call-sawfish-10 INFO visit :: node: "output-minimap2_bam", values: {"minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-10/call-run_sawfish/out/m84036_250809_035451_s4.bc2107.minimap2.bam"}
2025-09-15 20:25:21.411 wdl.w:ptcp.w:call-sawfish-10 INFO visit :: node: "output-minimap2_bam_bai", values: {"minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-10/call-run_sawfish/out/m84036_250809_035451_s4.bc2107.minimap2.bam.bai"}
2025-09-15 20:25:21.411 wdl.w:ptcp.w:call-sawfish-10 INFO visit :: node: "output-vcf", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-10/call-run_sawfish/out/m84036_250809_035451_s4.bc2107_sawfish/m84036_250809_035451_s4.bc2107.sv.vcf.gz"}
2025-09-15 20:25:21.411 wdl.w:ptcp.w:call-sawfish-10 INFO visit :: node: "output-vcf_tbi", values: {"vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-10/call-run_sawfish/out/m84036_250809_035451_s4.bc2107_sawfish/m84036_250809_035451_s4.bc2107.sv.vcf.gz.tbi"}
2025-09-15 20:25:21.412 wdl.w:ptcp.w:call-sawfish-10 INFO visit :: node: "outputs", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-10/call-run_sawfish/out/m84036_250809_035451_s4.bc2107_sawfish/m84036_250809_035451_s4.bc2107.sv.vcf.gz", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-10/call-run_sawfish/out/m84036_250809_035451_s4.bc2107.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-10/call-run_sawfish/out/m84036_250809_035451_s4.bc2107_sawfish/m84036_250809_035451_s4.bc2107.sv.vcf.gz.tbi", "minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-10/call-run_sawfish/out/m84036_250809_035451_s4.bc2107.minimap2.bam.bai"}
2025-09-15 20:25:21.418 wdl.w:ptcp.w:call-trgt-68.t:call-trgt_plot_motifs_allele NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-68/call-trgt_plot_motifs_allele", thread: 140611441120832
2025-09-15 20:25:21.440 wdl.w:ptcp.w:call-trgt-68.t:call-trgt_plot_motifs_allele INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:21.440 wdl.w:ptcp.w:call-trgt-68.t:call-trgt_plot_motifs_allele INFO input :: name: "waterfall", value: false
2025-09-15 20:25:21.440 wdl.w:ptcp.w:call-trgt-68.t:call-trgt_plot_motifs_allele INFO input :: name: "methylation", value: false
2025-09-15 20:25:21.440 wdl.w:ptcp.w:call-trgt-68.t:call-trgt_plot_motifs_allele INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:25:21.440 wdl.w:ptcp.w:call-trgt-68.t:call-trgt_plot_motifs_allele INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:25:21.440 wdl.w:ptcp.w:call-trgt-68.t:call-trgt_plot_motifs_allele INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:25:21.440 wdl.w:ptcp.w:call-trgt-68.t:call-trgt_plot_motifs_allele INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2165.trgt.sorted.spanning.bam.bai"
2025-09-15 20:25:21.440 wdl.w:ptcp.w:call-trgt-68.t:call-trgt_plot_motifs_allele INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2165.trgt.sorted.spanning.bam"
2025-09-15 20:25:21.440 wdl.w:ptcp.w:call-trgt-68.t:call-trgt_plot_motifs_allele INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2165.trgt.vcf"
2025-09-15 20:25:21.440 wdl.w:ptcp.w:call-trgt-68.t:call-trgt_plot_motifs_allele INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2165"
2025-09-15 20:25:21.440 wdl.w:ptcp.w:call-trgt-68.t:call-trgt_plot_motifs_allele INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:25:21.441 wdl.w:ptcp.w:call-trgt-68.t:call-trgt_plot_motifs_allele INFO eval :: name: "plot_type", value: "allele"
2025-09-15 20:25:21.441 wdl.w:ptcp.w:call-trgt-68.t:call-trgt_plot_motifs_allele INFO eval :: name: "show", value: "motifs"
2025-09-15 20:25:21.441 wdl.w:ptcp.w:call-trgt-68.t:call-trgt_plot_motifs_allele INFO eval :: name: "threads", value: 1
2025-09-15 20:25:21.441 wdl.w:ptcp.w:call-trgt-68.t:call-trgt_plot_motifs_allele INFO eval :: name: "disk_size", value: 27
2025-09-15 20:25:21.441 wdl.w:ptcp.w:call-trgt-68.t:call-trgt_plot_motifs_allele INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2165.motifs_allele"
2025-09-15 20:25:21.441 wdl.w:ptcp.w:call-trgt-68.t:call-trgt_plot_motifs_allele INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:21.441 wdl.w:ptcp.w:call-trgt-68.t:call-trgt_plot_motifs_allele WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:21.442 wdl.w:ptcp.w:call-trgt-68.t:call-trgt_plot_motifs_allele INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:25:21.442 wdl.w:ptcp.w:call-trgt-68.t:call-trgt_plot_motifs_allele INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:21.465 wdl.w:ptcp.w:call-trgt-68.t:call-trgt_plot_meth_waterfall INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-68/call-trgt_plot_meth_waterfall/_singularity_tmpdir_oba3w2jn"
2025-09-15 20:25:21.465 wdl.w:ptcp.w:call-trgt-68.t:call-trgt_plot_meth_waterfall INFO Slurm invocation: srun --job-name call-trgt_plot_meth_waterfall --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-68/call-trgt_plot_meth_waterfall/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-68/call-trgt_plot_meth_waterfall/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-68/call-trgt_plot_meth_waterfall/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-68/call-trgt_plot_meth_waterfall/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-68/call-trgt_genotype/out/m84036_250809_035451_s4.bc2165.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2165.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-68/call-trgt_genotype/out/m84036_250809_035451_s4.bc2165.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2165.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-68/call-trgt_genotype/out/m84036_250809_035451_s4.bc2165.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2165.trgt.sorted.spanning.bam.bai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-68/call-trgt_plot_meth_waterfall/_singularity_tmpdir_oba3w2jn/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-68/call-trgt_plot_meth_waterfall/_singularity_tmpdir_oba3w2jn/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:21.479 wdl.w:ptcp.w:call-trgt-68.t:call-trgt_plot_meth_waterfall NOTICE slurm_singularity run :: pid: 1205507, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-68/call-trgt_plot_meth_waterfall/slurm_singularity.log.txt"
2025-09-15 20:25:21.479 wdl.w:ptcp.w:call-sawfish-10 NOTICE done
2025-09-15 20:25:21.488 wdl.w:ptcp NOTICE finish :: job: "call-sawfish-10"
2025-09-15 20:25:21.488 wdl.w:ptcp INFO output :: job: "call-sawfish-10", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-10/out/m84036_250809_035451_s4.bc2107_sawfish/m84036_250809_035451_s4.bc2107.sv.vcf.gz", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-10/out/m84036_250809_035451_s4.bc2107.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-10/out/m84036_250809_035451_s4.bc2107_sawfish/m84036_250809_035451_s4.bc2107.sv.vcf.gz.tbi", "minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-10/out/m84036_250809_035451_s4.bc2107.minimap2.bam.bai"}
2025-09-15 20:25:21.501 wdl.w:ptcp.w:call-trgt-93 NOTICE workflow start :: name: "trgt", source: "./trgt.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-93"
2025-09-15 20:25:21.521 wdl.w:ptcp.w:call-trgt-93 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:25:21.522 wdl.w:ptcp.w:call-trgt-93 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-93/out/m84036_250809_035451_s4.bc2190.mapped.bam"}
2025-09-15 20:25:21.522 wdl.w:ptcp.w:call-trgt-93 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-93/out/m84036_250809_035451_s4.bc2190.mapped.bam.bai"}
2025-09-15 20:25:21.522 wdl.w:ptcp.w:call-trgt-93 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:25:21.522 wdl.w:ptcp.w:call-trgt-93 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:25:21.522 wdl.w:ptcp.w:call-trgt-93 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2190"}
2025-09-15 20:25:21.522 wdl.w:ptcp.w:call-trgt-93 INFO visit :: node: "decl-sex", values: {"sex": "F"}
2025-09-15 20:25:21.522 wdl.w:ptcp.w:call-trgt-93 INFO visit :: node: "decl-trgt_bed", values: {"trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"}
2025-09-15 20:25:21.522 wdl.w:ptcp.w:call-trgt-93 NOTICE ready :: job: "call-get_reads_overlapping_repeats", callee: "get_reads_overlapping_repeats"
2025-09-15 20:25:21.523 wdl.w:ptcp.w:call-trgt-93 INFO input :: job: "call-get_reads_overlapping_repeats", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-93/out/m84036_250809_035451_s4.bc2190.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-93/out/m84036_250809_035451_s4.bc2190.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2190"}
2025-09-15 20:25:21.524 wdl.w:ptcp.w:call-trgt-93 NOTICE ready :: job: "call-trgt_genotype", callee: "trgt_genotype"
2025-09-15 20:25:21.524 wdl.w:ptcp.w:call-trgt-93 INFO input :: job: "call-trgt_genotype", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-93/out/m84036_250809_035451_s4.bc2190.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-93/out/m84036_250809_035451_s4.bc2190.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2190"}
2025-09-15 20:25:21.531 wdl.w:ptcp.w:call-trgt-68.t:call-trgt_plot_motifs_allele INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-68/call-trgt_plot_motifs_allele/_singularity_tmpdir_gknmhfaw"
2025-09-15 20:25:21.531 wdl.w:ptcp.w:call-trgt-68.t:call-trgt_plot_motifs_allele INFO Slurm invocation: srun --job-name call-trgt_plot_motifs_allele --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-68/call-trgt_plot_motifs_allele/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-68/call-trgt_plot_motifs_allele/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-68/call-trgt_plot_motifs_allele/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-68/call-trgt_plot_motifs_allele/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-68/call-trgt_genotype/out/m84036_250809_035451_s4.bc2165.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2165.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-68/call-trgt_genotype/out/m84036_250809_035451_s4.bc2165.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2165.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-68/call-trgt_genotype/out/m84036_250809_035451_s4.bc2165.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2165.trgt.sorted.spanning.bam.bai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-68/call-trgt_plot_motifs_allele/_singularity_tmpdir_gknmhfaw/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-68/call-trgt_plot_motifs_allele/_singularity_tmpdir_gknmhfaw/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:21.545 wdl.w:ptcp.w:call-trgt-77.t:call-trgt_genotype INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2174.trgt.vcf"
2025-09-15 20:25:21.548 wdl.w:ptcp.w:call-trgt-77.t:call-trgt_genotype INFO output :: name: "spanning_bam", value: "m84036_250809_035451_s4.bc2174.trgt.sorted.spanning.bam"
2025-09-15 20:25:21.550 wdl.w:ptcp.w:call-trgt-77.t:call-trgt_genotype INFO output :: name: "spanning_bam_bai", value: "m84036_250809_035451_s4.bc2174.trgt.sorted.spanning.bam.bai"
2025-09-15 20:25:21.550 wdl.w:ptcp.w:call-trgt-68.t:call-trgt_plot_motifs_allele NOTICE slurm_singularity run :: pid: 1205516, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-68/call-trgt_plot_motifs_allele/slurm_singularity.log.txt"
2025-09-15 20:25:21.552 wdl.w:ptcp.w:call-trgt-60.t:call-trgt_plot_motifs_waterfall INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2157.motifs_waterfall.trgt_plots.zip"
2025-09-15 20:25:21.597 wdl.w:ptcp.w:call-paraphase-65.t:call-call_f8.slurm_singularity INFO srun: job 51797990 queued and waiting for resources
2025-09-15 20:25:21.597 wdl.w:ptcp.w:call-paraphase-65.t:call-call_f8.slurm_singularity INFO srun: job 51797990 has been allocated resources
2025-09-15 20:25:21.597 wdl.w:ptcp.w:call-paraphase-65.t:call-call_f8.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:21.645 wdl.w:ptcp.w:call-trgt-77.t:call-trgt_genotype NOTICE done
2025-09-15 20:25:21.651 wdl.w:ptcp.w:call-trgt-77 NOTICE finish :: job: "call-trgt_genotype"
2025-09-15 20:25:21.651 wdl.w:ptcp.w:call-trgt-77 INFO output :: job: "call-trgt_genotype", values: {"spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-77/call-trgt_genotype/out/m84036_250809_035451_s4.bc2174.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-77/call-trgt_genotype/out/m84036_250809_035451_s4.bc2174.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-77/call-trgt_genotype/out/m84036_250809_035451_s4.bc2174.trgt.vcf"}
2025-09-15 20:25:21.652 wdl.w:ptcp.w:call-trgt-77 NOTICE ready :: job: "call-trgt_plot_meth_allele", callee: "trgt_plot"
2025-09-15 20:25:21.652 wdl.w:ptcp.w:call-trgt-77 INFO input :: job: "call-trgt_plot_meth_allele", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": false, "methylation": true, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-77/call-trgt_genotype/out/m84036_250809_035451_s4.bc2174.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-77/call-trgt_genotype/out/m84036_250809_035451_s4.bc2174.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-77/call-trgt_genotype/out/m84036_250809_035451_s4.bc2174.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2174"}
2025-09-15 20:25:21.653 wdl.w:ptcp.w:call-trgt-77 NOTICE ready :: job: "call-trgt_plot_meth_waterfall", callee: "trgt_plot"
2025-09-15 20:25:21.653 wdl.w:ptcp.w:call-trgt-77 INFO input :: job: "call-trgt_plot_meth_waterfall", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": true, "methylation": true, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-77/call-trgt_genotype/out/m84036_250809_035451_s4.bc2174.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-77/call-trgt_genotype/out/m84036_250809_035451_s4.bc2174.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-77/call-trgt_genotype/out/m84036_250809_035451_s4.bc2174.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2174"}
2025-09-15 20:25:21.654 wdl.w:ptcp.w:call-trgt-77 NOTICE ready :: job: "call-trgt_plot_motifs_allele", callee: "trgt_plot"
2025-09-15 20:25:21.654 wdl.w:ptcp.w:call-trgt-77 INFO input :: job: "call-trgt_plot_motifs_allele", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": false, "methylation": false, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-77/call-trgt_genotype/out/m84036_250809_035451_s4.bc2174.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-77/call-trgt_genotype/out/m84036_250809_035451_s4.bc2174.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-77/call-trgt_genotype/out/m84036_250809_035451_s4.bc2174.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2174"}
2025-09-15 20:25:21.655 wdl.w:ptcp.w:call-trgt-77 NOTICE ready :: job: "call-trgt_plot_motifs_waterfall", callee: "trgt_plot"
2025-09-15 20:25:21.655 wdl.w:ptcp.w:call-trgt-77 INFO input :: job: "call-trgt_plot_motifs_waterfall", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": true, "methylation": false, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-77/call-trgt_genotype/out/m84036_250809_035451_s4.bc2174.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-77/call-trgt_genotype/out/m84036_250809_035451_s4.bc2174.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-77/call-trgt_genotype/out/m84036_250809_035451_s4.bc2174.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2174"}
2025-09-15 20:25:21.655 wdl.w:ptcp.w:call-trgt-77 INFO visit :: node: "output-spanning_bam", values: {"spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-77/call-trgt_genotype/out/m84036_250809_035451_s4.bc2174.trgt.sorted.spanning.bam"}
2025-09-15 20:25:21.655 wdl.w:ptcp.w:call-trgt-77 INFO visit :: node: "output-spanning_bam_bai", values: {"spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-77/call-trgt_genotype/out/m84036_250809_035451_s4.bc2174.trgt.sorted.spanning.bam.bai"}
2025-09-15 20:25:21.655 wdl.w:ptcp.w:call-trgt-77 INFO visit :: node: "output-vcf", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-77/call-trgt_genotype/out/m84036_250809_035451_s4.bc2174.trgt.vcf"}
2025-09-15 20:25:21.657 wdl.w:ptcp.w:call-trgt-68.t:call-trgt_plot_motifs_waterfall NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-68/call-trgt_plot_motifs_waterfall", thread: 140610912642624
2025-09-15 20:25:21.675 wdl.w:ptcp.w:call-trgt-68.t:call-trgt_plot_motifs_waterfall INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:21.675 wdl.w:ptcp.w:call-trgt-68.t:call-trgt_plot_motifs_waterfall INFO input :: name: "waterfall", value: true
2025-09-15 20:25:21.675 wdl.w:ptcp.w:call-trgt-68.t:call-trgt_plot_motifs_waterfall INFO input :: name: "methylation", value: false
2025-09-15 20:25:21.675 wdl.w:ptcp.w:call-trgt-68.t:call-trgt_plot_motifs_waterfall INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:25:21.675 wdl.w:ptcp.w:call-trgt-68.t:call-trgt_plot_motifs_waterfall INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:25:21.675 wdl.w:ptcp.w:call-trgt-68.t:call-trgt_plot_motifs_waterfall INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:25:21.675 wdl.w:ptcp.w:call-trgt-68.t:call-trgt_plot_motifs_waterfall INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2165.trgt.sorted.spanning.bam.bai"
2025-09-15 20:25:21.675 wdl.w:ptcp.w:call-trgt-68.t:call-trgt_plot_motifs_waterfall INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2165.trgt.sorted.spanning.bam"
2025-09-15 20:25:21.675 wdl.w:ptcp.w:call-trgt-68.t:call-trgt_plot_motifs_waterfall INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2165.trgt.vcf"
2025-09-15 20:25:21.675 wdl.w:ptcp.w:call-trgt-68.t:call-trgt_plot_motifs_waterfall INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2165"
2025-09-15 20:25:21.676 wdl.w:ptcp.w:call-trgt-68.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:25:21.676 wdl.w:ptcp.w:call-trgt-68.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "plot_type", value: "waterfall"
2025-09-15 20:25:21.676 wdl.w:ptcp.w:call-trgt-68.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "show", value: "motifs"
2025-09-15 20:25:21.676 wdl.w:ptcp.w:call-trgt-68.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "threads", value: 1
2025-09-15 20:25:21.676 wdl.w:ptcp.w:call-trgt-68.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "disk_size", value: 27
2025-09-15 20:25:21.676 wdl.w:ptcp.w:call-trgt-68.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2165.motifs_waterfall"
2025-09-15 20:25:21.676 wdl.w:ptcp.w:call-trgt-68.t:call-trgt_plot_motifs_waterfall INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:21.677 wdl.w:ptcp.w:call-trgt-68.t:call-trgt_plot_motifs_waterfall WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:21.677 wdl.w:ptcp.w:call-trgt-60.t:call-trgt_plot_motifs_waterfall NOTICE done
2025-09-15 20:25:21.677 wdl.w:ptcp.w:call-trgt-68.t:call-trgt_plot_motifs_waterfall INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:25:21.677 wdl.w:ptcp.w:call-trgt-68.t:call-trgt_plot_motifs_waterfall INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:21.682 wdl.w:ptcp.w:call-trgt-60 NOTICE finish :: job: "call-trgt_plot_motifs_waterfall"
2025-09-15 20:25:21.682 wdl.w:ptcp.w:call-trgt-60 INFO output :: job: "call-trgt_plot_motifs_waterfall", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-60/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2157.motifs_waterfall.trgt_plots.zip"}
2025-09-15 20:25:21.682 wdl.w:ptcp.w:call-trgt-60 INFO visit :: node: "output-images_motifs_waterfall", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-60/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2157.motifs_waterfall.trgt_plots.zip"}
2025-09-15 20:25:21.682 wdl.w:ptcp.w:call-trgt-60 INFO visit :: node: "outputs", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-60/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2157.motifs_waterfall.trgt_plots.zip", "images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-60/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2157.meth_allele.trgt_plots.zip", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-60/call-trgt_genotype/out/m84036_250809_035451_s4.bc2157.trgt.sorted.spanning.bam.bai", "images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-60/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2157.motifs_allele.trgt_plots.zip", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-60/call-trgt_genotype/out/m84036_250809_035451_s4.bc2157.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-60/call-trgt_genotype/out/m84036_250809_035451_s4.bc2157.trgt.vcf", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-60/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2157.repeats.bam", "images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-60/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2157.meth_waterfall.trgt_plots.zip", "reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-60/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2157.repeats.bam.bai"}
2025-09-15 20:25:21.693 wdl.w:ptcp.w:call-paraphase-80.t:call-run_paraphase NOTICE task setup :: name: "run_paraphase", source: "./paraphase.wdl", line: 127, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-80/call-run_paraphase", thread: 140610895857216
2025-09-15 20:25:21.718 wdl.w:ptcp.w:call-paraphase-80.t:call-run_paraphase INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:21.718 wdl.w:ptcp.w:call-paraphase-80.t:call-run_paraphase INFO input :: name: "annotation_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf"
2025-09-15 20:25:21.718 wdl.w:ptcp.w:call-paraphase-80.t:call-run_paraphase INFO input :: name: "genome_version", value: "38"
2025-09-15 20:25:21.718 wdl.w:ptcp.w:call-paraphase-80.t:call-run_paraphase INFO input :: name: "config_file", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/paraphase_config.GRCh38.yaml"
2025-09-15 20:25:21.718 wdl.w:ptcp.w:call-paraphase-80.t:call-run_paraphase INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:25:21.718 wdl.w:ptcp.w:call-paraphase-80.t:call-run_paraphase INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:25:21.719 wdl.w:ptcp.w:call-paraphase-80.t:call-run_paraphase INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2177.mapped.bam.bai"
2025-09-15 20:25:21.719 wdl.w:ptcp.w:call-paraphase-80.t:call-run_paraphase INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2177.mapped.bam"
2025-09-15 20:25:21.719 wdl.w:ptcp.w:call-paraphase-80.t:call-run_paraphase INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2177"
2025-09-15 20:25:21.719 wdl.w:ptcp.w:call-paraphase-80.t:call-run_paraphase INFO eval :: name: "threads", value: 4
2025-09-15 20:25:21.719 wdl.w:ptcp.w:call-paraphase-80.t:call-run_paraphase INFO eval :: name: "mem_gb", value: 8
2025-09-15 20:25:21.719 wdl.w:ptcp.w:call-paraphase-80.t:call-run_paraphase INFO eval :: name: "disk_size", value: 27
2025-09-15 20:25:21.719 wdl.w:ptcp.w:call-paraphase-80.t:call-run_paraphase INFO eval :: name: "out_dir", value: "m84036_250809_035451_s4.bc2177_paraphase"
2025-09-15 20:25:21.720 wdl.w:ptcp.w:call-paraphase-80.t:call-run_paraphase INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 4, memory_reservation: 8000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:21.720 wdl.w:ptcp.w:call-paraphase-80.t:call-run_paraphase WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:21.720 wdl.w:ptcp.w:call-paraphase-80.t:call-run_paraphase INFO provisioned :: seconds_waited: 0, cpu: 4, mem_bytes: 8000000000
2025-09-15 20:25:21.720 wdl.w:ptcp.w:call-paraphase-80.t:call-run_paraphase INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:21.765 wdl.w:ptcp.w:call-trgt-68.t:call-trgt_plot_motifs_waterfall INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-68/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_nk3v_if5"
2025-09-15 20:25:21.765 wdl.w:ptcp.w:call-trgt-68.t:call-trgt_plot_motifs_waterfall INFO Slurm invocation: srun --job-name call-trgt_plot_motifs_waterfall --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-68/call-trgt_plot_motifs_waterfall/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-68/call-trgt_plot_motifs_waterfall/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-68/call-trgt_plot_motifs_waterfall/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-68/call-trgt_plot_motifs_waterfall/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-68/call-trgt_genotype/out/m84036_250809_035451_s4.bc2165.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2165.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-68/call-trgt_genotype/out/m84036_250809_035451_s4.bc2165.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2165.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-68/call-trgt_genotype/out/m84036_250809_035451_s4.bc2165.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2165.trgt.sorted.spanning.bam.bai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-68/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_nk3v_if5/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-68/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_nk3v_if5/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:21.782 wdl.w:ptcp.w:call-trgt-60 NOTICE done
2025-09-15 20:25:21.782 wdl.w:ptcp.w:call-trgt-68.t:call-trgt_plot_motifs_waterfall NOTICE slurm_singularity run :: pid: 1205518, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-68/call-trgt_plot_motifs_waterfall/slurm_singularity.log.txt"
2025-09-15 20:25:21.786 wdl.w:ptcp NOTICE finish :: job: "call-trgt-60"
2025-09-15 20:25:21.786 wdl.w:ptcp INFO output :: job: "call-trgt-60", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-60/out/m84036_250809_035451_s4.bc2157.motifs_waterfall.trgt_plots.zip", "images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-60/out/m84036_250809_035451_s4.bc2157.meth_allele.trgt_plots.zip", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-60/out/m84036_250809_035451_s4.bc2157.trgt.sorted.spanning.bam.bai", "images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-60/out/m84036_250809_035451_s4.bc2157.motifs_allele.trgt_plots.zip", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-60/out/m84036_250809_035451_s4.bc2157.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-60/out/m84036_250809_035451_s4.bc2157.trgt.vcf", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-60/out/m84036_250809_035451_s4.bc2157.repeats.bam", "images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-60/out/m84036_250809_035451_s4.bc2157.meth_waterfall.trgt_plots.zip", "reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-60/out/m84036_250809_035451_s4.bc2157.repeats.bam.bai"}
2025-09-15 20:25:21.791 wdl.w:ptcp.w:call-paraphase-95 NOTICE workflow start :: name: "paraphase", source: "./paraphase.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-95"
2025-09-15 20:25:21.808 wdl.w:ptcp.w:call-paraphase-95 INFO visit :: node: "decl-annotation_vcf", values: {"annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf"}
2025-09-15 20:25:21.808 wdl.w:ptcp.w:call-paraphase-95 INFO visit :: node: "decl-config_file", values: {"config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml"}
2025-09-15 20:25:21.808 wdl.w:ptcp.w:call-paraphase-95 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:25:21.808 wdl.w:ptcp.w:call-paraphase-95 INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:25:21.808 wdl.w:ptcp.w:call-paraphase-95 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-95/out/m84036_250809_035451_s4.bc2192.mapped.bam"}
2025-09-15 20:25:21.808 wdl.w:ptcp.w:call-paraphase-95 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-95/out/m84036_250809_035451_s4.bc2192.mapped.bam.bai"}
2025-09-15 20:25:21.808 wdl.w:ptcp.w:call-paraphase-95 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:25:21.808 wdl.w:ptcp.w:call-paraphase-95 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:25:21.808 wdl.w:ptcp.w:call-paraphase-95 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2192"}
2025-09-15 20:25:21.808 wdl.w:ptcp.w:call-paraphase-95 INFO visit :: node: "decl-sex", values: {"sex": "F"}
2025-09-15 20:25:21.809 wdl.w:ptcp.w:call-paraphase-95 NOTICE ready :: job: "call-run_paraphase", callee: "run_paraphase"
2025-09-15 20:25:21.809 wdl.w:ptcp.w:call-paraphase-95 INFO input :: job: "call-run_paraphase", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf", "genome_version": "38", "config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-95/out/m84036_250809_035451_s4.bc2192.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-95/out/m84036_250809_035451_s4.bc2192.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2192"}
2025-09-15 20:25:21.816 wdl.w:ptcp.w:call-paraphase-80.t:call-run_paraphase INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-80/call-run_paraphase/_singularity_tmpdir_5_u4jh8n"
2025-09-15 20:25:21.816 wdl.w:ptcp.w:call-paraphase-80.t:call-run_paraphase INFO Slurm invocation: srun --job-name call-run_paraphase --partition compute,compute9 --cpus-per-task 4 --mem 7629M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-80/call-run_paraphase/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-80/call-run_paraphase/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-80/call-run_paraphase/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-80/call-run_paraphase/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-80/out/m84036_250809_035451_s4.bc2177.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2177.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-80/out/m84036_250809_035451_s4.bc2177.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2177.mapped.bam.bai:ro --bind /ptcp/meta/variant_list/variant_list.GRCh38.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf:ro --bind /ptcp/meta/paraphase/paraphase_config.GRCh38.yaml:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/paraphase_config.GRCh38.yaml:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-80/call-run_paraphase/_singularity_tmpdir_5_u4jh8n/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-80/call-run_paraphase/_singularity_tmpdir_5_u4jh8n/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:21.831 wdl.w:ptcp.w:call-paraphase-80.t:call-run_paraphase NOTICE slurm_singularity run :: pid: 1205521, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-80/call-run_paraphase/slurm_singularity.log.txt"
2025-09-15 20:25:21.843 wdl.w:ptcp.w:call-paraphase-38.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for hba for sample m84036_250809_035451_s4.bc2135 at 2025-09-15 20:24:45.000046...
2025-09-15 20:25:21.845 wdl.w:ptcp.w:call-paraphase-38.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for hba for sample m84036_250809_035451_s4.bc2135 at 2025-09-15 20:24:45.449210...
2025-09-15 20:25:21.845 wdl.w:ptcp.w:call-paraphase-38.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for cyp21 for sample m84036_250809_035451_s4.bc2135 at 2025-09-15 20:24:46.413551...
2025-09-15 20:25:21.845 wdl.w:ptcp.w:call-paraphase-38.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for cyp21 for sample m84036_250809_035451_s4.bc2135 at 2025-09-15 20:24:47.153579...
2025-09-15 20:25:21.845 wdl.w:ptcp.w:call-paraphase-38.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for gba for sample m84036_250809_035451_s4.bc2135 at 2025-09-15 20:25:01.769666...
2025-09-15 20:25:21.845 wdl.w:ptcp.w:call-paraphase-38.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for gba for sample m84036_250809_035451_s4.bc2135 at 2025-09-15 20:25:02.263054...
2025-09-15 20:25:21.845 wdl.w:ptcp.w:call-paraphase-38.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for f8inv1 for sample m84036_250809_035451_s4.bc2135 at 2025-09-15 20:25:10.032606...
2025-09-15 20:25:21.845 wdl.w:ptcp.w:call-paraphase-38.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for f8inv1 for sample m84036_250809_035451_s4.bc2135 at 2025-09-15 20:25:10.032851...
2025-09-15 20:25:21.845 wdl.w:ptcp.w:call-paraphase-38.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for hbb for sample m84036_250809_035451_s4.bc2135 at 2025-09-15 20:25:10.095513...
2025-09-15 20:25:21.845 wdl.w:ptcp.w:call-paraphase-38.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for hbb for sample m84036_250809_035451_s4.bc2135 at 2025-09-15 20:25:10.095662...
2025-09-15 20:25:21.845 wdl.w:ptcp.w:call-paraphase-38.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for hbb for sample m84036_250809_035451_s4.bc2135 at 2025-09-15 20:25:11.722746...
2025-09-15 20:25:21.845 wdl.w:ptcp.w:call-paraphase-38.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for f8inv1 for sample m84036_250809_035451_s4.bc2135 at 2025-09-15 20:25:11.952260...
2025-09-15 20:25:21.845 wdl.w:ptcp.w:call-paraphase-38.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for hbb for sample m84036_250809_035451_s4.bc2135 at 2025-09-15 20:25:14.921487...
2025-09-15 20:25:21.845 wdl.w:ptcp.w:call-paraphase-38.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for hbb for sample m84036_250809_035451_s4.bc2135 at 2025-09-15 20:25:15.215740...
2025-09-15 20:25:21.845 wdl.w:ptcp.w:call-paraphase-38.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for f8inv1 for sample m84036_250809_035451_s4.bc2135 at 2025-09-15 20:25:16.298981...
2025-09-15 20:25:21.845 wdl.w:ptcp.w:call-paraphase-38.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for f8inv1 for sample m84036_250809_035451_s4.bc2135 at 2025-09-15 20:25:16.716172...
2025-09-15 20:25:21.865 wdl.w:ptcp.w:call-paraphase-65.t:call-call_f8 INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2162.f8inversion.vcf"
2025-09-15 20:25:21.868 wdl.w:ptcp.w:call-paraphase-65.t:call-call_f8 INFO output :: name: "json", value: "m84036_250809_035451_s4.bc2162.f8inversion.json"
2025-09-15 20:25:21.926 wdl.w:ptcp.w:call-paraphase-65.t:call-call_f8 NOTICE done
2025-09-15 20:25:21.933 wdl.w:ptcp.w:call-paraphase-65 NOTICE finish :: job: "call-call_f8"
2025-09-15 20:25:21.933 wdl.w:ptcp.w:call-paraphase-65 INFO output :: job: "call-call_f8", values: {"json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-65/call-call_f8/out/m84036_250809_035451_s4.bc2162.f8inversion.json", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-65/call-call_f8/out/m84036_250809_035451_s4.bc2162.f8inversion.vcf"}
2025-09-15 20:25:21.933 wdl.w:ptcp.w:call-paraphase-65 INFO visit :: node: "output-f8_json", values: {"f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-65/call-call_f8/out/m84036_250809_035451_s4.bc2162.f8inversion.json"}
2025-09-15 20:25:21.933 wdl.w:ptcp.w:call-paraphase-65 INFO visit :: node: "output-f8_vcf", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-65/call-call_f8/out/m84036_250809_035451_s4.bc2162.f8inversion.vcf"}
2025-09-15 20:25:21.933 wdl.w:ptcp.w:call-paraphase-65 INFO visit :: node: "outputs", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-65/call-call_f8/out/m84036_250809_035451_s4.bc2162.f8inversion.vcf", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-65/call-run_paraphase/out/m84036_250809_035451_s4.bc2162_paraphase/m84036_250809_035451_s4.bc2162.paraphase.json", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-65/call-run_paraphase/out/m84036_250809_035451_s4.bc2162_paraphase/m84036_250809_035451_s4.bc2162.paraphase.bam", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-65/call-run_paraphase/out/m84036_250809_035451_s4.bc2162_paraphase/m84036_250809_035451_s4.bc2162.paraphase.bam.bai", "paraphase_vcfs": [], "havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-65/call-run_paraphase/out/m84036_250809_035451_s4.bc2162.havanno.json", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-65/call-call_f8/out/m84036_250809_035451_s4.bc2162.f8inversion.json"}
2025-09-15 20:25:21.937 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:25:20 [ERROR] - No reads found for TRID=SCA2_ATXN2
2025-09-15 20:25:21.939 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_plot_meth_allele NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-70/call-trgt_plot_meth_allele", thread: 140611969599040
2025-09-15 20:25:21.955 wdl.w:ptcp.w:call-sawfish-72.t:call-run_sawfish.stderr VERBOSE [M::bam2fq_mainloop] discarded 0 singletons
2025-09-15 20:25:21.955 wdl.w:ptcp.w:call-sawfish-72.t:call-run_sawfish.stderr VERBOSE [M::bam2fq_mainloop] processed 1 reads
2025-09-15 20:25:21.964 wdl.w:ptcp.w:call-sawfish-72.t:call-run_sawfish.slurm_singularity INFO srun: job 51797991 queued and waiting for resources
2025-09-15 20:25:21.964 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_plot_meth_allele INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:21.965 wdl.w:ptcp.w:call-sawfish-72.t:call-run_sawfish.slurm_singularity INFO srun: job 51797991 has been allocated resources
2025-09-15 20:25:21.965 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_plot_meth_allele INFO input :: name: "waterfall", value: false
2025-09-15 20:25:21.965 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_plot_meth_allele INFO input :: name: "methylation", value: true
2025-09-15 20:25:21.965 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_plot_meth_allele INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:25:21.965 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_plot_meth_allele INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:25:21.965 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_plot_meth_allele INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:25:21.965 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_plot_meth_allele INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2167.trgt.sorted.spanning.bam.bai"
2025-09-15 20:25:21.965 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_plot_meth_allele INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2167.trgt.sorted.spanning.bam"
2025-09-15 20:25:21.965 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_plot_meth_allele INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2167.trgt.vcf"
2025-09-15 20:25:21.965 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_plot_meth_allele INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2167"
2025-09-15 20:25:21.966 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_plot_meth_allele INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:25:21.966 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_plot_meth_allele INFO eval :: name: "plot_type", value: "allele"
2025-09-15 20:25:21.966 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_plot_meth_allele INFO eval :: name: "show", value: "meth"
2025-09-15 20:25:21.966 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_plot_meth_allele INFO eval :: name: "threads", value: 1
2025-09-15 20:25:21.966 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_plot_meth_allele INFO eval :: name: "disk_size", value: 27
2025-09-15 20:25:21.966 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_plot_meth_allele INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2167.meth_allele"
2025-09-15 20:25:21.967 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_plot_meth_allele INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:21.967 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_plot_meth_allele WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:21.967 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_plot_meth_allele INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:25:21.967 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_plot_meth_allele INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:22.017 wdl.w:ptcp.w:call-paraphase-65 NOTICE done
2025-09-15 20:25:22.023 wdl.w:ptcp NOTICE finish :: job: "call-paraphase-65"
2025-09-15 20:25:22.023 wdl.w:ptcp INFO output :: job: "call-paraphase-65", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-65/out/m84036_250809_035451_s4.bc2162.f8inversion.vcf", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-65/out/m84036_250809_035451_s4.bc2162_paraphase/m84036_250809_035451_s4.bc2162.paraphase.json", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-65/out/m84036_250809_035451_s4.bc2162_paraphase/m84036_250809_035451_s4.bc2162.paraphase.bam", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-65/out/m84036_250809_035451_s4.bc2162_paraphase/m84036_250809_035451_s4.bc2162.paraphase.bam.bai", "paraphase_vcfs": [], "havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-65/out/m84036_250809_035451_s4.bc2162.havanno.json", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-65/out/m84036_250809_035451_s4.bc2162.f8inversion.json"}
2025-09-15 20:25:22.030 wdl.w:ptcp.w:call-sawfish-95 NOTICE workflow start :: name: "sawfish", source: "./sawfish.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-95"
2025-09-15 20:25:22.031 wdl.w:ptcp.w:call-trgt-72.t:call-get_reads_overlapping_repeats.slurm_singularity INFO srun: job 51797992 queued and waiting for resources
2025-09-15 20:25:22.031 wdl.w:ptcp.w:call-trgt-72.t:call-get_reads_overlapping_repeats.slurm_singularity INFO srun: job 51797992 has been allocated resources
2025-09-15 20:25:22.031 wdl.w:ptcp.w:call-trgt-72.t:call-get_reads_overlapping_repeats.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:22.047 wdl.w:ptcp.w:call-sawfish-95 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:25:22.047 wdl.w:ptcp.w:call-sawfish-95 INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:25:22.047 wdl.w:ptcp.w:call-sawfish-95 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-95/out/m84036_250809_035451_s4.bc2192.mapped.bam"}
2025-09-15 20:25:22.047 wdl.w:ptcp.w:call-sawfish-95 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-95/out/m84036_250809_035451_s4.bc2192.mapped.bam.bai"}
2025-09-15 20:25:22.047 wdl.w:ptcp.w:call-sawfish-95 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:25:22.047 wdl.w:ptcp.w:call-sawfish-95 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:25:22.048 wdl.w:ptcp.w:call-sawfish-95 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2192"}
2025-09-15 20:25:22.048 wdl.w:ptcp.w:call-sawfish-95 NOTICE ready :: job: "call-run_sawfish", callee: "run_sawfish"
2025-09-15 20:25:22.048 wdl.w:ptcp.w:call-sawfish-95 INFO input :: job: "call-run_sawfish", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-95/out/m84036_250809_035451_s4.bc2192.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-95/out/m84036_250809_035451_s4.bc2192.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2192"}
2025-09-15 20:25:22.073 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_plot_meth_allele INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-70/call-trgt_plot_meth_allele/_singularity_tmpdir_umq5ucqt"
2025-09-15 20:25:22.073 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_plot_meth_allele INFO Slurm invocation: srun --job-name call-trgt_plot_meth_allele --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-70/call-trgt_plot_meth_allele/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-70/call-trgt_plot_meth_allele/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-70/call-trgt_plot_meth_allele/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-70/call-trgt_plot_meth_allele/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-70/call-trgt_genotype/out/m84036_250809_035451_s4.bc2167.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2167.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-70/call-trgt_genotype/out/m84036_250809_035451_s4.bc2167.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2167.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-70/call-trgt_genotype/out/m84036_250809_035451_s4.bc2167.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2167.trgt.sorted.spanning.bam.bai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-70/call-trgt_plot_meth_allele/_singularity_tmpdir_umq5ucqt/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-70/call-trgt_plot_meth_allele/_singularity_tmpdir_umq5ucqt/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:22.087 wdl.w:ptcp.w:call-paraphase-77.t:call-run_paraphase INFO output :: name: "paraphase_bam", value: "m84036_250809_035451_s4.bc2174_paraphase/m84036_250809_035451_s4.bc2174.paraphase.bam"
2025-09-15 20:25:22.094 wdl.w:ptcp.w:call-paraphase-77.t:call-run_paraphase INFO output :: name: "paraphase_bam_bai", value: "m84036_250809_035451_s4.bc2174_paraphase/m84036_250809_035451_s4.bc2174.paraphase.bam.bai"
2025-09-15 20:25:22.097 wdl.w:ptcp.w:call-paraphase-77.t:call-run_paraphase INFO output :: name: "paraphase_json", value: "m84036_250809_035451_s4.bc2174_paraphase/m84036_250809_035451_s4.bc2174.paraphase.json"
2025-09-15 20:25:22.099 wdl.w:ptcp.w:call-paraphase-77.t:call-run_paraphase INFO output :: name: "paraphase_vcfs", value: []
2025-09-15 20:25:22.099 wdl.w:ptcp.w:call-paraphase-77.t:call-run_paraphase INFO output :: name: "havanno_json", value: "m84036_250809_035451_s4.bc2174.havanno.json"
2025-09-15 20:25:22.108 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_plot_meth_allele NOTICE slurm_singularity run :: pid: 1205544, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-70/call-trgt_plot_meth_allele/slurm_singularity.log.txt"
2025-09-15 20:25:22.180 wdl.w:ptcp.w:call-paraphase-77.t:call-run_paraphase NOTICE done
2025-09-15 20:25:22.186 wdl.w:ptcp.w:call-paraphase-77 NOTICE finish :: job: "call-run_paraphase"
2025-09-15 20:25:22.186 wdl.w:ptcp.w:call-paraphase-77 INFO output :: job: "call-run_paraphase", values: {"havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-77/call-run_paraphase/out/m84036_250809_035451_s4.bc2174.havanno.json", "paraphase_vcfs": [], "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-77/call-run_paraphase/out/m84036_250809_035451_s4.bc2174_paraphase/m84036_250809_035451_s4.bc2174.paraphase.json", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-77/call-run_paraphase/out/m84036_250809_035451_s4.bc2174_paraphase/m84036_250809_035451_s4.bc2174.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-77/call-run_paraphase/out/m84036_250809_035451_s4.bc2174_paraphase/m84036_250809_035451_s4.bc2174.paraphase.bam"}
2025-09-15 20:25:22.186 wdl.w:ptcp.w:call-paraphase-77 NOTICE ready :: job: "call-call_f8", callee: "call_f8"
2025-09-15 20:25:22.187 wdl.w:ptcp.w:call-paraphase-77 INFO input :: job: "call-call_f8", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "out_prefix": "m84036_250809_035451_s4.bc2174", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-77/call-run_paraphase/out/m84036_250809_035451_s4.bc2174_paraphase/m84036_250809_035451_s4.bc2174.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-77/call-run_paraphase/out/m84036_250809_035451_s4.bc2174_paraphase/m84036_250809_035451_s4.bc2174.paraphase.bam", "sex": "F"}
2025-09-15 20:25:22.188 wdl.w:ptcp.w:call-paraphase-77 INFO visit :: node: "output-havanno_json", values: {"havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-77/call-run_paraphase/out/m84036_250809_035451_s4.bc2174.havanno.json"}
2025-09-15 20:25:22.188 wdl.w:ptcp.w:call-paraphase-77 INFO visit :: node: "output-paraphase_bam", values: {"paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-77/call-run_paraphase/out/m84036_250809_035451_s4.bc2174_paraphase/m84036_250809_035451_s4.bc2174.paraphase.bam"}
2025-09-15 20:25:22.188 wdl.w:ptcp.w:call-paraphase-77 INFO visit :: node: "output-paraphase_bam_bai", values: {"paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-77/call-run_paraphase/out/m84036_250809_035451_s4.bc2174_paraphase/m84036_250809_035451_s4.bc2174.paraphase.bam.bai"}
2025-09-15 20:25:22.188 wdl.w:ptcp.w:call-paraphase-77 INFO visit :: node: "output-paraphase_json", values: {"paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-77/call-run_paraphase/out/m84036_250809_035451_s4.bc2174_paraphase/m84036_250809_035451_s4.bc2174.paraphase.json"}
2025-09-15 20:25:22.188 wdl.w:ptcp.w:call-paraphase-77 INFO visit :: node: "output-paraphase_vcfs", values: {"paraphase_vcfs": []}
2025-09-15 20:25:22.191 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_plot_meth_waterfall NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-70/call-trgt_plot_meth_waterfall", thread: 140610870679104
2025-09-15 20:25:22.207 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_plot_meth_waterfall INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:22.207 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_plot_meth_waterfall INFO input :: name: "waterfall", value: true
2025-09-15 20:25:22.207 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_plot_meth_waterfall INFO input :: name: "methylation", value: true
2025-09-15 20:25:22.207 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_plot_meth_waterfall INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:25:22.207 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_plot_meth_waterfall INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:25:22.207 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_plot_meth_waterfall INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:25:22.208 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_plot_meth_waterfall INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2167.trgt.sorted.spanning.bam.bai"
2025-09-15 20:25:22.208 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_plot_meth_waterfall INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2167.trgt.sorted.spanning.bam"
2025-09-15 20:25:22.208 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_plot_meth_waterfall INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2167.trgt.vcf"
2025-09-15 20:25:22.208 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_plot_meth_waterfall INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2167"
2025-09-15 20:25:22.208 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_plot_meth_waterfall INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:25:22.208 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_plot_meth_waterfall INFO eval :: name: "plot_type", value: "waterfall"
2025-09-15 20:25:22.208 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_plot_meth_waterfall INFO eval :: name: "show", value: "meth"
2025-09-15 20:25:22.208 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_plot_meth_waterfall INFO eval :: name: "threads", value: 1
2025-09-15 20:25:22.208 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_plot_meth_waterfall INFO eval :: name: "disk_size", value: 27
2025-09-15 20:25:22.208 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_plot_meth_waterfall INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2167.meth_waterfall"
2025-09-15 20:25:22.209 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_plot_meth_waterfall INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:22.209 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_plot_meth_waterfall WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:22.209 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_plot_meth_waterfall INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:25:22.209 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_plot_meth_waterfall INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:22.281 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_plot_meth_waterfall INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-70/call-trgt_plot_meth_waterfall/_singularity_tmpdir_czbbq_xw"
2025-09-15 20:25:22.281 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_plot_meth_waterfall INFO Slurm invocation: srun --job-name call-trgt_plot_meth_waterfall --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-70/call-trgt_plot_meth_waterfall/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-70/call-trgt_plot_meth_waterfall/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-70/call-trgt_plot_meth_waterfall/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-70/call-trgt_plot_meth_waterfall/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-70/call-trgt_genotype/out/m84036_250809_035451_s4.bc2167.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2167.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-70/call-trgt_genotype/out/m84036_250809_035451_s4.bc2167.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2167.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-70/call-trgt_genotype/out/m84036_250809_035451_s4.bc2167.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2167.trgt.sorted.spanning.bam.bai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-70/call-trgt_plot_meth_waterfall/_singularity_tmpdir_czbbq_xw/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-70/call-trgt_plot_meth_waterfall/_singularity_tmpdir_czbbq_xw/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:22.291 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_plot_meth_waterfall NOTICE slurm_singularity run :: pid: 1205546, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-70/call-trgt_plot_meth_waterfall/slurm_singularity.log.txt"
2025-09-15 20:25:22.327 wdl.w:ptcp.w:call-trgt-72.t:call-trgt_genotype.slurm_singularity INFO srun: job 51797993 queued and waiting for resources
2025-09-15 20:25:22.327 wdl.w:ptcp.w:call-trgt-72.t:call-trgt_genotype.slurm_singularity INFO srun: job 51797993 has been allocated resources
2025-09-15 20:25:22.327 wdl.w:ptcp.w:call-trgt-72.t:call-trgt_genotype.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:22.417 wdl.w:ptcp.w:call-trgt-68.t:call-trgt_plot_meth_allele.slurm_singularity INFO srun: job 51797994 queued and waiting for resources
2025-09-15 20:25:22.417 wdl.w:ptcp.w:call-trgt-68.t:call-trgt_plot_meth_allele.slurm_singularity INFO srun: job 51797994 has been allocated resources
2025-09-15 20:25:22.417 wdl.w:ptcp.w:call-trgt-68.t:call-trgt_plot_meth_allele.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:22.486 wdl.w:ptcp.w:call-trgt-68.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO srun: job 51797995 queued and waiting for resources
2025-09-15 20:25:22.486 wdl.w:ptcp.w:call-trgt-68.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO srun: job 51797995 has been allocated resources
2025-09-15 20:25:22.487 wdl.w:ptcp.w:call-trgt-68.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:22.560 wdl.w:ptcp.w:call-trgt-68.t:call-trgt_plot_motifs_allele.slurm_singularity INFO srun: job 51797996 queued and waiting for resources
2025-09-15 20:25:22.560 wdl.w:ptcp.w:call-trgt-68.t:call-trgt_plot_motifs_allele.slurm_singularity INFO srun: job 51797996 has been allocated resources
2025-09-15 20:25:22.560 wdl.w:ptcp.w:call-trgt-68.t:call-trgt_plot_motifs_allele.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:22.724 wdl.w:ptcp.w:call-trgt-77.t:call-get_reads_overlapping_repeats INFO output :: name: "reads_overlapping_repeats", value: "m84036_250809_035451_s4.bc2174.repeats.bam"
2025-09-15 20:25:22.729 wdl.w:ptcp.w:call-trgt-77.t:call-get_reads_overlapping_repeats INFO output :: name: "reads_overlapping_repeats_bai", value: "m84036_250809_035451_s4.bc2174.repeats.bam.bai"
2025-09-15 20:25:22.744 wdl.w:ptcp.w:call-paraphase-46.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for f8inv1 for sample m84036_250809_035451_s4.bc2143 at 2025-09-15 20:25:11.476607...
2025-09-15 20:25:22.744 wdl.w:ptcp.w:call-paraphase-46.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for f8inv1 for sample m84036_250809_035451_s4.bc2143 at 2025-09-15 20:25:12.359170...
2025-09-15 20:25:22.744 wdl.w:ptcp.w:call-paraphase-46.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for hbb for sample m84036_250809_035451_s4.bc2143 at 2025-09-15 20:25:12.718246...
2025-09-15 20:25:22.744 wdl.w:ptcp.w:call-paraphase-46.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for hbb for sample m84036_250809_035451_s4.bc2143 at 2025-09-15 20:25:17.076707...
2025-09-15 20:25:22.744 wdl.w:ptcp.w:call-paraphase-46.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for hbb for sample m84036_250809_035451_s4.bc2143 at 2025-09-15 20:25:17.563232...
2025-09-15 20:25:22.798 wdl.w:ptcp.w:call-trgt-68.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO srun: job 51797997 queued and waiting for resources
2025-09-15 20:25:22.799 wdl.w:ptcp.w:call-trgt-68.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO srun: job 51797997 has been allocated resources
2025-09-15 20:25:22.799 wdl.w:ptcp.w:call-trgt-68.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:22.812 wdl.w:ptcp.w:call-trgt-77.t:call-get_reads_overlapping_repeats NOTICE done
2025-09-15 20:25:22.817 wdl.w:ptcp.w:call-trgt-77 NOTICE finish :: job: "call-get_reads_overlapping_repeats"
2025-09-15 20:25:22.817 wdl.w:ptcp.w:call-trgt-77 INFO output :: job: "call-get_reads_overlapping_repeats", values: {"reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-77/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2174.repeats.bam.bai", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-77/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2174.repeats.bam"}
2025-09-15 20:25:22.818 wdl.w:ptcp.w:call-trgt-77 INFO visit :: node: "output-reads_overlapping_repeats", values: {"reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-77/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2174.repeats.bam"}
2025-09-15 20:25:22.818 wdl.w:ptcp.w:call-trgt-77 INFO visit :: node: "output-reads_overlapping_repeats_bai", values: {"reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-77/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2174.repeats.bam.bai"}
2025-09-15 20:25:22.827 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_plot_motifs_allele NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-70/call-trgt_plot_motifs_allele", thread: 140609813722688
2025-09-15 20:25:22.847 wdl.w:ptcp.w:call-paraphase-80.t:call-run_paraphase.slurm_singularity INFO srun: job 51797998 queued and waiting for resources
2025-09-15 20:25:22.847 wdl.w:ptcp.w:call-paraphase-80.t:call-run_paraphase.slurm_singularity INFO srun: job 51797998 has been allocated resources
2025-09-15 20:25:22.847 wdl.w:ptcp.w:call-paraphase-80.t:call-run_paraphase.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:22.857 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_plot_motifs_allele INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:22.857 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_plot_motifs_allele INFO input :: name: "waterfall", value: false
2025-09-15 20:25:22.857 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_plot_motifs_allele INFO input :: name: "methylation", value: false
2025-09-15 20:25:22.857 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_plot_motifs_allele INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:25:22.857 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_plot_motifs_allele INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:25:22.857 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_plot_motifs_allele INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:25:22.857 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_plot_motifs_allele INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2167.trgt.sorted.spanning.bam.bai"
2025-09-15 20:25:22.857 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_plot_motifs_allele INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2167.trgt.sorted.spanning.bam"
2025-09-15 20:25:22.857 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_plot_motifs_allele INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2167.trgt.vcf"
2025-09-15 20:25:22.858 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_plot_motifs_allele INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2167"
2025-09-15 20:25:22.858 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_plot_motifs_allele INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:25:22.858 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_plot_motifs_allele INFO eval :: name: "plot_type", value: "allele"
2025-09-15 20:25:22.858 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_plot_motifs_allele INFO eval :: name: "show", value: "motifs"
2025-09-15 20:25:22.858 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_plot_motifs_allele INFO eval :: name: "threads", value: 1
2025-09-15 20:25:22.858 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_plot_motifs_allele INFO eval :: name: "disk_size", value: 27
2025-09-15 20:25:22.858 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_plot_motifs_allele INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2167.motifs_allele"
2025-09-15 20:25:22.859 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_plot_motifs_allele INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:22.859 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_plot_motifs_allele WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:22.859 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_plot_motifs_allele INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:25:22.859 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_plot_motifs_allele INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:22.929 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_plot_meth_waterfall INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2163.meth_waterfall.trgt_plots.zip"
2025-09-15 20:25:22.933 wdl.w:ptcp.w:call-paraphase-43.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for f8inv1 for sample m84036_250809_035451_s4.bc2140 at 2025-09-15 20:25:19.111986...
2025-09-15 20:25:22.933 wdl.w:ptcp.w:call-paraphase-43.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for gba for sample m84036_250809_035451_s4.bc2140 at 2025-09-15 20:25:19.515201...
2025-09-15 20:25:22.933 wdl.w:ptcp.w:call-paraphase-43.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for gba for sample m84036_250809_035451_s4.bc2140 at 2025-09-15 20:25:20.027035...
2025-09-15 20:25:22.952 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:25:21 [ERROR] - No reads found for TRID=SCA27B_FGF14
2025-09-15 20:25:22.952 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:25:21 [ERROR] - No reads found for TRID=SCA3_ATXN3
2025-09-15 20:25:22.952 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:25:21 [ERROR] - No reads found for TRID=OPMD_PABPN1
2025-09-15 20:25:22.952 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:25:21 [ERROR] - No reads found for TRID=SCA4_ZFHX3
2025-09-15 20:25:22.952 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:25:21 [ERROR] - No reads found for TRID=HDL2_JPH3
2025-09-15 20:25:22.952 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:25:21 [ERROR] - No reads found for TRID=OPDM4_RILPL1
2025-09-15 20:25:22.952 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:25:21 [ERROR] - No reads found for TRID=SCA6_CACNA1A
2025-09-15 20:25:22.952 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:25:21 [ERROR] - No reads found for TRID=OPDM2_GIPC1
2025-09-15 20:25:22.952 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:25:21 [ERROR] - No reads found for TRID=DM1_DMPK
2025-09-15 20:25:22.952 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:25:21 [ERROR] - No reads found for TRID=SCA31_BEAN1
2025-09-15 20:25:22.952 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:25:21 [ERROR] - No reads found for TRID=SD5_HOXD13
2025-09-15 20:25:22.952 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:25:21 [ERROR] - No reads found for TRID=SCA36_NOP56
2025-09-15 20:25:22.952 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:25:21 [ERROR] - No reads found for TRID=CJD_PRNP
2025-09-15 20:25:22.953 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:25:21 [ERROR] - No reads found for TRID=EPM1_CSTB
2025-09-15 20:25:22.953 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:25:21 [ERROR] - No reads found for TRID=SCA10_ATXN10
2025-09-15 20:25:22.953 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:25:21 [ERROR] - No reads found for TRID=SCA7_ATXN7
2025-09-15 20:25:22.953 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:25:21 [ERROR] - No reads found for TRID=HD_HTT
2025-09-15 20:25:22.953 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:25:21 [ERROR] - No reads found for TRID=FRA2A_AFF3
2025-09-15 20:25:22.953 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:25:21 [ERROR] - No reads found for TRID=CCHS_PHOX2B
2025-09-15 20:25:22.953 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:25:21 [ERROR] - No reads found for TRID=SCA12_PPP2R2B
2025-09-15 20:25:22.976 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_plot_motifs_allele INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-70/call-trgt_plot_motifs_allele/_singularity_tmpdir_jf4swclq"
2025-09-15 20:25:22.976 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_plot_motifs_allele INFO Slurm invocation: srun --job-name call-trgt_plot_motifs_allele --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-70/call-trgt_plot_motifs_allele/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-70/call-trgt_plot_motifs_allele/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-70/call-trgt_plot_motifs_allele/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-70/call-trgt_plot_motifs_allele/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-70/call-trgt_genotype/out/m84036_250809_035451_s4.bc2167.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2167.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-70/call-trgt_genotype/out/m84036_250809_035451_s4.bc2167.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2167.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-70/call-trgt_genotype/out/m84036_250809_035451_s4.bc2167.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2167.trgt.sorted.spanning.bam.bai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-70/call-trgt_plot_motifs_allele/_singularity_tmpdir_jf4swclq/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-70/call-trgt_plot_motifs_allele/_singularity_tmpdir_jf4swclq/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:23.016 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_plot_motifs_allele NOTICE slurm_singularity run :: pid: 1205560, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-70/call-trgt_plot_motifs_allele/slurm_singularity.log.txt"
2025-09-15 20:25:23.042 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_plot_meth_waterfall NOTICE done
2025-09-15 20:25:23.048 wdl.w:ptcp.w:call-trgt-66 NOTICE finish :: job: "call-trgt_plot_meth_waterfall"
2025-09-15 20:25:23.048 wdl.w:ptcp.w:call-trgt-66 INFO output :: job: "call-trgt_plot_meth_waterfall", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-66/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2163.meth_waterfall.trgt_plots.zip"}
2025-09-15 20:25:23.048 wdl.w:ptcp.w:call-trgt-66 INFO visit :: node: "output-images_meth_waterfall", values: {"images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-66/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2163.meth_waterfall.trgt_plots.zip"}
2025-09-15 20:25:23.056 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_plot_motifs_waterfall NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-70/call-trgt_plot_motifs_waterfall", thread: 140612506469952
2025-09-15 20:25:23.058 wdl.w:ptcp.w:call-paraphase-55.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for hbb for sample m84036_250809_035451_s4.bc2152 at 2025-09-15 20:25:17.228809...
2025-09-15 20:25:23.058 wdl.w:ptcp.w:call-paraphase-55.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for hbb for sample m84036_250809_035451_s4.bc2152 at 2025-09-15 20:25:19.189763...
2025-09-15 20:25:23.058 wdl.w:ptcp.w:call-paraphase-55.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for hbb for sample m84036_250809_035451_s4.bc2152 at 2025-09-15 20:25:19.534738...
2025-09-15 20:25:23.074 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_plot_motifs_waterfall INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:23.074 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_plot_motifs_waterfall INFO input :: name: "waterfall", value: true
2025-09-15 20:25:23.074 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_plot_motifs_waterfall INFO input :: name: "methylation", value: false
2025-09-15 20:25:23.074 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_plot_motifs_waterfall INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:25:23.074 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_plot_motifs_waterfall INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:25:23.074 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_plot_motifs_waterfall INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:25:23.074 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_plot_motifs_waterfall INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2167.trgt.sorted.spanning.bam.bai"
2025-09-15 20:25:23.075 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_plot_motifs_waterfall INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2167.trgt.sorted.spanning.bam"
2025-09-15 20:25:23.075 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_plot_motifs_waterfall INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2167.trgt.vcf"
2025-09-15 20:25:23.075 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_plot_motifs_waterfall INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2167"
2025-09-15 20:25:23.075 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:25:23.075 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "plot_type", value: "waterfall"
2025-09-15 20:25:23.075 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "show", value: "motifs"
2025-09-15 20:25:23.075 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "threads", value: 1
2025-09-15 20:25:23.076 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "disk_size", value: 27
2025-09-15 20:25:23.076 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2167.motifs_waterfall"
2025-09-15 20:25:23.076 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_plot_motifs_waterfall INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:23.076 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_plot_motifs_waterfall WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:23.076 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_plot_motifs_waterfall INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:25:23.077 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_plot_motifs_waterfall INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:23.078 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_plot_motifs_allele INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2163.motifs_allele.trgt_plots.zip"
2025-09-15 20:25:23.122 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_plot_meth_allele.slurm_singularity INFO srun: job 51797999 queued and waiting for resources
2025-09-15 20:25:23.122 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_plot_meth_allele.slurm_singularity INFO srun: job 51797999 has been allocated resources
2025-09-15 20:25:23.122 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_plot_meth_allele.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:23.154 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_plot_motifs_waterfall INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-70/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_biepgjol"
2025-09-15 20:25:23.154 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_plot_motifs_waterfall INFO Slurm invocation: srun --job-name call-trgt_plot_motifs_waterfall --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-70/call-trgt_plot_motifs_waterfall/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-70/call-trgt_plot_motifs_waterfall/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-70/call-trgt_plot_motifs_waterfall/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-70/call-trgt_plot_motifs_waterfall/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-70/call-trgt_genotype/out/m84036_250809_035451_s4.bc2167.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2167.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-70/call-trgt_genotype/out/m84036_250809_035451_s4.bc2167.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2167.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-70/call-trgt_genotype/out/m84036_250809_035451_s4.bc2167.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2167.trgt.sorted.spanning.bam.bai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-70/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_biepgjol/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-70/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_biepgjol/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:23.159 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_plot_motifs_allele NOTICE done
2025-09-15 20:25:23.164 wdl.w:ptcp.w:call-trgt-66 NOTICE finish :: job: "call-trgt_plot_motifs_allele"
2025-09-15 20:25:23.164 wdl.w:ptcp.w:call-trgt-66 INFO output :: job: "call-trgt_plot_motifs_allele", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-66/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2163.motifs_allele.trgt_plots.zip"}
2025-09-15 20:25:23.165 wdl.w:ptcp.w:call-trgt-66 INFO visit :: node: "output-images_motifs_allele", values: {"images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-66/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2163.motifs_allele.trgt_plots.zip"}
2025-09-15 20:25:23.171 wdl.w:ptcp.w:call-sawfish-80.t:call-run_sawfish NOTICE task setup :: name: "run_sawfish", source: "./sawfish.wdl", line: 83, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-80/call-run_sawfish", thread: 140610375771712
2025-09-15 20:25:23.172 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_plot_motifs_waterfall NOTICE slurm_singularity run :: pid: 1205568, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-70/call-trgt_plot_motifs_waterfall/slurm_singularity.log.txt"
2025-09-15 20:25:23.186 wdl.w:ptcp.w:call-sawfish-80.t:call-run_sawfish INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:23.186 wdl.w:ptcp.w:call-sawfish-80.t:call-run_sawfish INFO input :: name: "genome_version", value: "38"
2025-09-15 20:25:23.186 wdl.w:ptcp.w:call-sawfish-80.t:call-run_sawfish INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:25:23.186 wdl.w:ptcp.w:call-sawfish-80.t:call-run_sawfish INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:25:23.186 wdl.w:ptcp.w:call-sawfish-80.t:call-run_sawfish INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2177.mapped.bam.bai"
2025-09-15 20:25:23.187 wdl.w:ptcp.w:call-sawfish-80.t:call-run_sawfish INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2177.mapped.bam"
2025-09-15 20:25:23.187 wdl.w:ptcp.w:call-sawfish-80.t:call-run_sawfish INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2177"
2025-09-15 20:25:23.187 wdl.w:ptcp.w:call-sawfish-80.t:call-run_sawfish INFO eval :: name: "mem_gb", value: 32
2025-09-15 20:25:23.187 wdl.w:ptcp.w:call-sawfish-80.t:call-run_sawfish INFO eval :: name: "threads", value: 16
2025-09-15 20:25:23.187 wdl.w:ptcp.w:call-sawfish-80.t:call-run_sawfish INFO eval :: name: "disk_size", value: 30
2025-09-15 20:25:23.188 wdl.w:ptcp.w:call-sawfish-80.t:call-run_sawfish INFO eval :: name: "discover_dirname", value: "m84036_250809_035451_s4.bc2177_sawfish_discover"
2025-09-15 20:25:23.188 wdl.w:ptcp.w:call-sawfish-80.t:call-run_sawfish INFO eval :: name: "call_dirname", value: "m84036_250809_035451_s4.bc2177_sawfish"
2025-09-15 20:25:23.188 wdl.w:ptcp.w:call-sawfish-80.t:call-run_sawfish INFO eval :: name: "minimap2_bam_filename", value: "m84036_250809_035451_s4.bc2177.minimap2.bam"
2025-09-15 20:25:23.188 wdl.w:ptcp.w:call-sawfish-80.t:call-run_sawfish INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 16, memory_reservation: 32000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:23.188 wdl.w:ptcp.w:call-sawfish-80.t:call-run_sawfish WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:23.189 wdl.w:ptcp.w:call-sawfish-80.t:call-run_sawfish INFO provisioned :: seconds_waited: 0, cpu: 16, mem_bytes: 32000000000
2025-09-15 20:25:23.189 wdl.w:ptcp.w:call-sawfish-80.t:call-run_sawfish INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:23.242 wdl.w:ptcp.w:call-sawfish-80.t:call-run_sawfish INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 10, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-80/call-run_sawfish/_singularity_tmpdir_r6ax_tq6"
2025-09-15 20:25:23.242 wdl.w:ptcp.w:call-sawfish-80.t:call-run_sawfish INFO Slurm invocation: srun --job-name call-run_sawfish --partition compute,compute9 --cpus-per-task 16 --mem 30518M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-80/call-run_sawfish/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-80/call-run_sawfish/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-80/call-run_sawfish/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-80/call-run_sawfish/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-80/out/m84036_250809_035451_s4.bc2177.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2177.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-80/out/m84036_250809_035451_s4.bc2177.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2177.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-80/call-run_sawfish/_singularity_tmpdir_r6ax_tq6/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-80/call-run_sawfish/_singularity_tmpdir_r6ax_tq6/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:23.254 wdl.w:ptcp.w:call-sawfish-80.t:call-run_sawfish NOTICE slurm_singularity run :: pid: 1205570, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-80/call-run_sawfish/slurm_singularity.log.txt"
2025-09-15 20:25:23.298 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO srun: job 51798000 queued and waiting for resources
2025-09-15 20:25:23.298 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO srun: job 51798000 has been allocated resources
2025-09-15 20:25:23.298 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:23.513 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:20 [ERROR] - No reads found for TRID=NIID_NOTCH2NLC
2025-09-15 20:25:23.513 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:20 [ERROR] - No reads found for TRID=OPDM_ABCD3
2025-09-15 20:25:23.513 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:20 [ERROR] - No reads found for TRID=SCA2_ATXN2
2025-09-15 20:25:23.513 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:20 [ERROR] - No reads found for TRID=SCA27B_FGF14
2025-09-15 20:25:23.513 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:20 [ERROR] - No reads found for TRID=SCA3_ATXN3
2025-09-15 20:25:23.513 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:20 [ERROR] - No reads found for TRID=OPMD_PABPN1
2025-09-15 20:25:23.513 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:20 [ERROR] - No reads found for TRID=SCA4_ZFHX3
2025-09-15 20:25:23.514 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:20 [ERROR] - No reads found for TRID=HDL2_JPH3
2025-09-15 20:25:23.514 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:20 [ERROR] - No reads found for TRID=OPDM4_RILPL1
2025-09-15 20:25:23.514 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:20 [ERROR] - No reads found for TRID=SCA6_CACNA1A
2025-09-15 20:25:23.514 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:20 [ERROR] - No reads found for TRID=OPDM2_GIPC1
2025-09-15 20:25:23.514 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:21 [ERROR] - No reads found for TRID=DM1_DMPK
2025-09-15 20:25:23.514 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:21 [ERROR] - No reads found for TRID=SCA31_BEAN1
2025-09-15 20:25:23.514 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:21 [ERROR] - No reads found for TRID=SD5_HOXD13
2025-09-15 20:25:23.514 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:21 [ERROR] - No reads found for TRID=SCA36_NOP56
2025-09-15 20:25:23.514 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:21 [ERROR] - No reads found for TRID=CJD_PRNP
2025-09-15 20:25:23.514 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:21 [ERROR] - No reads found for TRID=EPM1_CSTB
2025-09-15 20:25:23.514 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:21 [ERROR] - No reads found for TRID=SCA10_ATXN10
2025-09-15 20:25:23.514 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:21 [ERROR] - No reads found for TRID=SCA7_ATXN7
2025-09-15 20:25:23.514 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:21 [ERROR] - No reads found for TRID=HD_HTT
2025-09-15 20:25:23.514 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:21 [ERROR] - No reads found for TRID=FRA2A_AFF3
2025-09-15 20:25:23.514 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:21 [ERROR] - No reads found for TRID=CCHS_PHOX2B
2025-09-15 20:25:23.514 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:21 [ERROR] - No reads found for TRID=SCA12_PPP2R2B
2025-09-15 20:25:23.515 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:21 [ERROR] - No reads found for TRID=SCA1_ATXN1
2025-09-15 20:25:23.515 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:21 [ERROR] - No reads found for TRID=OPDM1_LRP12
2025-09-15 20:25:23.515 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:21 [ERROR] - No reads found for TRID=FAME1_SAMD12
2025-09-15 20:25:23.585 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_plot_meth_allele INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2163.meth_allele.trgt_plots.zip"
2025-09-15 20:25:23.662 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_plot_meth_allele NOTICE done
2025-09-15 20:25:23.684 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:25:21 [ERROR] - No reads found for TRID=SCA1_ATXN1
2025-09-15 20:25:23.685 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:25:21 [ERROR] - No reads found for TRID=OPDM1_LRP12
2025-09-15 20:25:23.685 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:25:22 [ERROR] - No reads found for TRID=FAME1_SAMD12
2025-09-15 20:25:23.708 wdl.w:ptcp.w:call-trgt-66 NOTICE finish :: job: "call-trgt_plot_meth_allele"
2025-09-15 20:25:23.708 wdl.w:ptcp.w:call-trgt-66 INFO output :: job: "call-trgt_plot_meth_allele", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-66/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2163.meth_allele.trgt_plots.zip"}
2025-09-15 20:25:23.709 wdl.w:ptcp.w:call-trgt-66 INFO visit :: node: "output-images_meth_allele", values: {"images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-66/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2163.meth_allele.trgt_plots.zip"}
2025-09-15 20:25:23.713 wdl.w:ptcp.w:call-paraphase-60.t:call-call_f8 NOTICE task setup :: name: "call_f8", source: "./paraphase.wdl", line: 232, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-60/call-call_f8", thread: 140607649453632
2025-09-15 20:25:23.723 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_plot_motifs_waterfall INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2163.motifs_waterfall.trgt_plots.zip"
2025-09-15 20:25:23.737 wdl.w:ptcp.w:call-paraphase-60.t:call-call_f8 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:23.737 wdl.w:ptcp.w:call-paraphase-60.t:call-call_f8 INFO input :: name: "genome_version", value: "38"
2025-09-15 20:25:23.737 wdl.w:ptcp.w:call-paraphase-60.t:call-call_f8 INFO input :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2157"
2025-09-15 20:25:23.737 wdl.w:ptcp.w:call-paraphase-60.t:call-call_f8 INFO input :: name: "paraphase_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2157.paraphase.bam.bai"
2025-09-15 20:25:23.737 wdl.w:ptcp.w:call-paraphase-60.t:call-call_f8 INFO input :: name: "paraphase_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2157.paraphase.bam"
2025-09-15 20:25:23.737 wdl.w:ptcp.w:call-paraphase-60.t:call-call_f8 INFO input :: name: "sex", value: "F"
2025-09-15 20:25:23.738 wdl.w:ptcp.w:call-paraphase-60.t:call-call_f8 INFO eval :: name: "threads", value: 1
2025-09-15 20:25:23.738 wdl.w:ptcp.w:call-paraphase-60.t:call-call_f8 INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:25:23.738 wdl.w:ptcp.w:call-paraphase-60.t:call-call_f8 INFO eval :: name: "disk_size", value: 11
2025-09-15 20:25:23.738 wdl.w:ptcp.w:call-paraphase-60.t:call-call_f8 INFO eval :: name: "sample_sex", value: "F"
2025-09-15 20:25:23.738 wdl.w:ptcp.w:call-paraphase-60.t:call-call_f8 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:23.739 wdl.w:ptcp.w:call-paraphase-60.t:call-call_f8 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:23.739 wdl.w:ptcp.w:call-paraphase-60.t:call-call_f8 INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:25:23.739 wdl.w:ptcp.w:call-paraphase-60.t:call-call_f8 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:23.801 wdl.w:ptcp.w:call-paraphase-60.t:call-call_f8 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 8, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-60/call-call_f8/_singularity_tmpdir_crr0s2kr"
2025-09-15 20:25:23.802 wdl.w:ptcp.w:call-paraphase-60.t:call-call_f8 INFO Slurm invocation: srun --job-name call-call_f8 --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-60/call-call_f8/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-60/call-call_f8/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-60/call-call_f8/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-60/call-call_f8/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-60/call-run_paraphase/out/m84036_250809_035451_s4.bc2157_paraphase/m84036_250809_035451_s4.bc2157.paraphase.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2157.paraphase.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-60/call-run_paraphase/out/m84036_250809_035451_s4.bc2157_paraphase/m84036_250809_035451_s4.bc2157.paraphase.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2157.paraphase.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-60/call-call_f8/_singularity_tmpdir_crr0s2kr/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-60/call-call_f8/_singularity_tmpdir_crr0s2kr/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:23.820 wdl.w:ptcp.w:call-paraphase-60.t:call-call_f8 NOTICE slurm_singularity run :: pid: 1205585, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-60/call-call_f8/slurm_singularity.log.txt"
2025-09-15 20:25:23.828 wdl.w:ptcp.w:call-trgt-66.t:call-trgt_plot_motifs_waterfall NOTICE done
2025-09-15 20:25:23.841 wdl.w:ptcp.w:call-trgt-65.t:call-trgt_plot_meth_waterfall INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2162.meth_waterfall.trgt_plots.zip"
2025-09-15 20:25:23.876 wdl.w:ptcp.w:call-trgt-66 NOTICE finish :: job: "call-trgt_plot_motifs_waterfall"
2025-09-15 20:25:23.876 wdl.w:ptcp.w:call-trgt-66 INFO output :: job: "call-trgt_plot_motifs_waterfall", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-66/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2163.motifs_waterfall.trgt_plots.zip"}
2025-09-15 20:25:23.877 wdl.w:ptcp.w:call-trgt-66 INFO visit :: node: "output-images_motifs_waterfall", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-66/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2163.motifs_waterfall.trgt_plots.zip"}
2025-09-15 20:25:23.877 wdl.w:ptcp.w:call-trgt-66 INFO visit :: node: "outputs", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-66/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2163.motifs_waterfall.trgt_plots.zip", "images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-66/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2163.meth_allele.trgt_plots.zip", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-66/call-trgt_genotype/out/m84036_250809_035451_s4.bc2163.trgt.sorted.spanning.bam.bai", "images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-66/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2163.motifs_allele.trgt_plots.zip", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-66/call-trgt_genotype/out/m84036_250809_035451_s4.bc2163.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-66/call-trgt_genotype/out/m84036_250809_035451_s4.bc2163.trgt.vcf", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-66/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2163.repeats.bam", "images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-66/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2163.meth_waterfall.trgt_plots.zip", "reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-66/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2163.repeats.bam.bai"}
2025-09-15 20:25:23.884 wdl.w:ptcp.w:call-trgt-80.t:call-get_reads_overlapping_repeats NOTICE task setup :: name: "get_reads_overlapping_repeats", source: "./trgt.wdl", line: 182, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-80/call-get_reads_overlapping_repeats", thread: 140607137760832
2025-09-15 20:25:23.900 wdl.w:ptcp.w:call-paraphase-39.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for hba for sample m84036_250809_035451_s4.bc2136 at 2025-09-15 20:25:10.980179...
2025-09-15 20:25:23.900 wdl.w:ptcp.w:call-paraphase-39.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for hba for sample m84036_250809_035451_s4.bc2136 at 2025-09-15 20:25:11.260405...
2025-09-15 20:25:23.900 wdl.w:ptcp.w:call-paraphase-39.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for gba for sample m84036_250809_035451_s4.bc2136 at 2025-09-15 20:25:18.495663...
2025-09-15 20:25:23.900 wdl.w:ptcp.w:call-paraphase-39.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for gba for sample m84036_250809_035451_s4.bc2136 at 2025-09-15 20:25:18.910186...
2025-09-15 20:25:23.900 wdl.w:ptcp.w:call-paraphase-39.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for f8inv1 for sample m84036_250809_035451_s4.bc2136 at 2025-09-15 20:25:22.733436...
2025-09-15 20:25:23.901 wdl.w:ptcp.w:call-paraphase-39.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for f8inv1 for sample m84036_250809_035451_s4.bc2136 at 2025-09-15 20:25:22.733661...
2025-09-15 20:25:23.911 wdl.w:ptcp.w:call-trgt-80.t:call-get_reads_overlapping_repeats INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:23.911 wdl.w:ptcp.w:call-trgt-80.t:call-get_reads_overlapping_repeats INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:25:23.911 wdl.w:ptcp.w:call-trgt-80.t:call-get_reads_overlapping_repeats INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2177.mapped.bam.bai"
2025-09-15 20:25:23.911 wdl.w:ptcp.w:call-trgt-80.t:call-get_reads_overlapping_repeats INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2177.mapped.bam"
2025-09-15 20:25:23.911 wdl.w:ptcp.w:call-trgt-80.t:call-get_reads_overlapping_repeats INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2177"
2025-09-15 20:25:23.911 wdl.w:ptcp.w:call-trgt-80.t:call-get_reads_overlapping_repeats INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:25:23.911 wdl.w:ptcp.w:call-trgt-80.t:call-get_reads_overlapping_repeats INFO eval :: name: "expand_size", value: 3000
2025-09-15 20:25:23.911 wdl.w:ptcp.w:call-trgt-80.t:call-get_reads_overlapping_repeats INFO eval :: name: "threads", value: 1
2025-09-15 20:25:23.912 wdl.w:ptcp.w:call-trgt-80.t:call-get_reads_overlapping_repeats INFO eval :: name: "expanded_bed_name", value: "m84036_250809_035451_s4.bc2177.expanded.bed"
2025-09-15 20:25:23.912 wdl.w:ptcp.w:call-trgt-80.t:call-get_reads_overlapping_repeats INFO eval :: name: "disk_size", value: 11
2025-09-15 20:25:23.912 wdl.w:ptcp.w:call-trgt-80.t:call-get_reads_overlapping_repeats INFO eval :: name: "output_name", value: "m84036_250809_035451_s4.bc2177.repeats.bam"
2025-09-15 20:25:23.912 wdl.w:ptcp.w:call-trgt-80.t:call-get_reads_overlapping_repeats INFO eval :: name: "index_name", value: "m84036_250809_035451_s4.bc2177.repeats.bam.bai"
2025-09-15 20:25:23.912 wdl.w:ptcp.w:call-trgt-80.t:call-get_reads_overlapping_repeats INFO eval :: name: "output_name_with_index", value: "m84036_250809_035451_s4.bc2177.repeats.bam##idx##m84036_250809_035451_s4.bc2177.repeats.bam.bai"
2025-09-15 20:25:23.914 wdl.w:ptcp.w:call-trgt-80.t:call-get_reads_overlapping_repeats INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:23.914 wdl.w:ptcp.w:call-trgt-80.t:call-get_reads_overlapping_repeats WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:23.915 wdl.w:ptcp.w:call-trgt-80.t:call-get_reads_overlapping_repeats INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:25:23.915 wdl.w:ptcp.w:call-trgt-80.t:call-get_reads_overlapping_repeats INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:23.964 wdl.w:ptcp.w:call-paraphase-15.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for f8inv22 for sample m84036_250809_035451_s4.bc2112 at 2025-09-15 20:25:22.669708...
2025-09-15 20:25:23.964 wdl.w:ptcp.w:call-paraphase-15.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for f8inv22 for sample m84036_250809_035451_s4.bc2112 at 2025-09-15 20:25:22.670790...
2025-09-15 20:25:23.976 wdl.w:ptcp.w:call-trgt-80.t:call-get_reads_overlapping_repeats INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 9, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-80/call-get_reads_overlapping_repeats/_singularity_tmpdir_i6w3izcb"
2025-09-15 20:25:23.976 wdl.w:ptcp.w:call-trgt-80.t:call-get_reads_overlapping_repeats INFO Slurm invocation: srun --job-name call-get_reads_overlapping_repeats --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-80/call-get_reads_overlapping_repeats/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-80/call-get_reads_overlapping_repeats/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-80/call-get_reads_overlapping_repeats/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-80/call-get_reads_overlapping_repeats/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-80/out/m84036_250809_035451_s4.bc2177.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2177.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-80/out/m84036_250809_035451_s4.bc2177.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2177.mapped.bam.bai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-80/call-get_reads_overlapping_repeats/_singularity_tmpdir_i6w3izcb/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-80/call-get_reads_overlapping_repeats/_singularity_tmpdir_i6w3izcb/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:23.995 wdl.w:ptcp.w:call-trgt-66 NOTICE done
2025-09-15 20:25:23.996 wdl.w:ptcp.w:call-trgt-80.t:call-get_reads_overlapping_repeats NOTICE slurm_singularity run :: pid: 1205587, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-80/call-get_reads_overlapping_repeats/slurm_singularity.log.txt"
2025-09-15 20:25:24.001 wdl.w:ptcp NOTICE finish :: job: "call-trgt-66"
2025-09-15 20:25:24.001 wdl.w:ptcp INFO output :: job: "call-trgt-66", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-66/out/m84036_250809_035451_s4.bc2163.motifs_waterfall.trgt_plots.zip", "images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-66/out/m84036_250809_035451_s4.bc2163.meth_allele.trgt_plots.zip", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-66/out/m84036_250809_035451_s4.bc2163.trgt.sorted.spanning.bam.bai", "images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-66/out/m84036_250809_035451_s4.bc2163.motifs_allele.trgt_plots.zip", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-66/out/m84036_250809_035451_s4.bc2163.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-66/out/m84036_250809_035451_s4.bc2163.trgt.vcf", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-66/out/m84036_250809_035451_s4.bc2163.repeats.bam", "images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-66/out/m84036_250809_035451_s4.bc2163.meth_waterfall.trgt_plots.zip", "reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-66/out/m84036_250809_035451_s4.bc2163.repeats.bam.bai"}
2025-09-15 20:25:24.002 wdl.w:ptcp.w:call-paraphase-35.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for f8inv1 for sample m84036_250809_035451_s4.bc2132 at 2025-09-15 20:24:40.320789...
2025-09-15 20:25:24.002 wdl.w:ptcp.w:call-paraphase-35.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for f8inv1 for sample m84036_250809_035451_s4.bc2132 at 2025-09-15 20:24:46.995584...
2025-09-15 20:25:24.002 wdl.w:ptcp.w:call-paraphase-35.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for f8inv1 for sample m84036_250809_035451_s4.bc2132 at 2025-09-15 20:24:47.407473...
2025-09-15 20:25:24.008 wdl.w:ptcp.w:call-trgt-95 NOTICE workflow start :: name: "trgt", source: "./trgt.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-95"
2025-09-15 20:25:24.021 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:25:23 [ERROR] - No reads found for TRID=SCA2_ATXN2
2025-09-15 20:25:24.021 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:25:23 [ERROR] - No reads found for TRID=DRPLA_ATN1
2025-09-15 20:25:24.021 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:25:23 [ERROR] - No reads found for TRID=OPDM4_RILPL1
2025-09-15 20:25:24.021 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:25:23 [ERROR] - No reads found for TRID=SCA37_DAB1
2025-09-15 20:25:24.021 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:25:23 [ERROR] - No reads found for TRID=NIID_NOTCH2NLC
2025-09-15 20:25:24.021 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:25:23 [ERROR] - No reads found for TRID=OPDM_ABCD3
2025-09-15 20:25:24.021 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:25:23 [ERROR] - No reads found for TRID=SCA27B_FGF14
2025-09-15 20:25:24.021 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:25:23 [ERROR] - No reads found for TRID=SCA3_ATXN3
2025-09-15 20:25:24.022 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:25:23 [ERROR] - No reads found for TRID=SCA4_ZFHX3
2025-09-15 20:25:24.022 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:25:24 [ERROR] - No reads found for TRID=HDL2_JPH3
2025-09-15 20:25:24.027 wdl.w:ptcp.w:call-trgt-95 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:25:24.027 wdl.w:ptcp.w:call-trgt-95 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-95/out/m84036_250809_035451_s4.bc2192.mapped.bam"}
2025-09-15 20:25:24.027 wdl.w:ptcp.w:call-trgt-95 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-95/out/m84036_250809_035451_s4.bc2192.mapped.bam.bai"}
2025-09-15 20:25:24.027 wdl.w:ptcp.w:call-trgt-95 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:25:24.027 wdl.w:ptcp.w:call-trgt-95 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:25:24.027 wdl.w:ptcp.w:call-trgt-95 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2192"}
2025-09-15 20:25:24.028 wdl.w:ptcp.w:call-trgt-95 INFO visit :: node: "decl-sex", values: {"sex": "F"}
2025-09-15 20:25:24.028 wdl.w:ptcp.w:call-trgt-95 INFO visit :: node: "decl-trgt_bed", values: {"trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"}
2025-09-15 20:25:24.028 wdl.w:ptcp.w:call-trgt-95 NOTICE ready :: job: "call-get_reads_overlapping_repeats", callee: "get_reads_overlapping_repeats"
2025-09-15 20:25:24.028 wdl.w:ptcp.w:call-trgt-95 INFO input :: job: "call-get_reads_overlapping_repeats", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-95/out/m84036_250809_035451_s4.bc2192.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-95/out/m84036_250809_035451_s4.bc2192.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2192"}
2025-09-15 20:25:24.029 wdl.w:ptcp.w:call-trgt-95 NOTICE ready :: job: "call-trgt_genotype", callee: "trgt_genotype"
2025-09-15 20:25:24.029 wdl.w:ptcp.w:call-trgt-95 INFO input :: job: "call-trgt_genotype", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-95/out/m84036_250809_035451_s4.bc2192.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-95/out/m84036_250809_035451_s4.bc2192.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2192"}
2025-09-15 20:25:24.032 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_plot_motifs_allele.slurm_singularity INFO srun: job 51798002 queued and waiting for resources
2025-09-15 20:25:24.033 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_plot_motifs_allele.slurm_singularity INFO srun: job 51798002 has been allocated resources
2025-09-15 20:25:24.033 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_plot_motifs_allele.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:24.039 wdl.w:ptcp.w:call-trgt-65.t:call-trgt_plot_meth_waterfall NOTICE done
2025-09-15 20:25:24.045 wdl.w:ptcp.w:call-trgt-65 NOTICE finish :: job: "call-trgt_plot_meth_waterfall"
2025-09-15 20:25:24.045 wdl.w:ptcp.w:call-trgt-65 INFO output :: job: "call-trgt_plot_meth_waterfall", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-65/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2162.meth_waterfall.trgt_plots.zip"}
2025-09-15 20:25:24.045 wdl.w:ptcp.w:call-trgt-65 INFO visit :: node: "output-images_meth_waterfall", values: {"images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-65/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2162.meth_waterfall.trgt_plots.zip"}
2025-09-15 20:25:24.052 wdl.w:ptcp.w:call-trgt-80.t:call-trgt_genotype NOTICE task setup :: name: "trgt_genotype", source: "./trgt.wdl", line: 272, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-80/call-trgt_genotype", thread: 140606575711808
2025-09-15 20:25:24.074 wdl.w:ptcp.w:call-trgt-80.t:call-trgt_genotype INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:24.075 wdl.w:ptcp.w:call-trgt-80.t:call-trgt_genotype INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:25:24.075 wdl.w:ptcp.w:call-trgt-80.t:call-trgt_genotype INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:25:24.075 wdl.w:ptcp.w:call-trgt-80.t:call-trgt_genotype INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:25:24.075 wdl.w:ptcp.w:call-trgt-80.t:call-trgt_genotype INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2177.mapped.bam.bai"
2025-09-15 20:25:24.075 wdl.w:ptcp.w:call-trgt-80.t:call-trgt_genotype INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2177.mapped.bam"
2025-09-15 20:25:24.075 wdl.w:ptcp.w:call-trgt-80.t:call-trgt_genotype INFO input :: name: "sex", value: "F"
2025-09-15 20:25:24.075 wdl.w:ptcp.w:call-trgt-80.t:call-trgt_genotype INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2177"
2025-09-15 20:25:24.075 wdl.w:ptcp.w:call-trgt-80.t:call-trgt_genotype INFO eval :: name: "mem_gb", value: 16
2025-09-15 20:25:24.076 wdl.w:ptcp.w:call-trgt-80.t:call-trgt_genotype INFO eval :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2177.trgt"
2025-09-15 20:25:24.076 wdl.w:ptcp.w:call-trgt-80.t:call-trgt_genotype INFO eval :: name: "threads", value: 8
2025-09-15 20:25:24.076 wdl.w:ptcp.w:call-trgt-80.t:call-trgt_genotype INFO eval :: name: "disk_size", value: 27
2025-09-15 20:25:24.076 wdl.w:ptcp.w:call-trgt-80.t:call-trgt_genotype INFO eval :: name: "karyotype", value: "XX"
2025-09-15 20:25:24.076 wdl.w:ptcp.w:call-trgt-80.t:call-trgt_genotype INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 8, memory_reservation: 16000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:24.076 wdl.w:ptcp.w:call-trgt-80.t:call-trgt_genotype WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:24.077 wdl.w:ptcp.w:call-trgt-80.t:call-trgt_genotype INFO provisioned :: seconds_waited: 0, cpu: 8, mem_bytes: 16000000000
2025-09-15 20:25:24.077 wdl.w:ptcp.w:call-trgt-80.t:call-trgt_genotype INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:24.092 wdl.w:ptcp.w:call-trgt-65.t:call-trgt_plot_motifs_waterfall INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2162.motifs_waterfall.trgt_plots.zip"
2025-09-15 20:25:24.146 wdl.w:ptcp.w:call-trgt-80.t:call-trgt_genotype INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 11, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-80/call-trgt_genotype/_singularity_tmpdir_kngr27yb"
2025-09-15 20:25:24.146 wdl.w:ptcp.w:call-trgt-80.t:call-trgt_genotype INFO Slurm invocation: srun --job-name call-trgt_genotype --partition compute,compute9 --cpus-per-task 8 --mem 15259M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-80/call-trgt_genotype/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-80/call-trgt_genotype/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-80/call-trgt_genotype/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-80/call-trgt_genotype/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-80/out/m84036_250809_035451_s4.bc2177.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2177.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-80/out/m84036_250809_035451_s4.bc2177.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2177.mapped.bam.bai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-80/call-trgt_genotype/_singularity_tmpdir_kngr27yb/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-80/call-trgt_genotype/_singularity_tmpdir_kngr27yb/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:24.164 wdl.w:ptcp.w:call-trgt-80.t:call-trgt_genotype NOTICE slurm_singularity run :: pid: 1205595, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-80/call-trgt_genotype/slurm_singularity.log.txt"
2025-09-15 20:25:24.180 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO srun: job 51798003 queued and waiting for resources
2025-09-15 20:25:24.180 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO srun: job 51798003 has been allocated resources
2025-09-15 20:25:24.181 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:24.219 wdl.w:ptcp.w:call-trgt-65.t:call-trgt_plot_motifs_waterfall NOTICE done
2025-09-15 20:25:24.224 wdl.w:ptcp.w:call-trgt-65 NOTICE finish :: job: "call-trgt_plot_motifs_waterfall"
2025-09-15 20:25:24.224 wdl.w:ptcp.w:call-trgt-65 INFO output :: job: "call-trgt_plot_motifs_waterfall", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-65/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2162.motifs_waterfall.trgt_plots.zip"}
2025-09-15 20:25:24.224 wdl.w:ptcp.w:call-trgt-65 INFO visit :: node: "output-images_motifs_waterfall", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-65/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2162.motifs_waterfall.trgt_plots.zip"}
2025-09-15 20:25:24.225 wdl.w:ptcp.w:call-trgt-65 INFO visit :: node: "outputs", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-65/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2162.motifs_waterfall.trgt_plots.zip", "images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-65/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2162.meth_allele.trgt_plots.zip", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-65/call-trgt_genotype/out/m84036_250809_035451_s4.bc2162.trgt.sorted.spanning.bam.bai", "images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-65/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2162.motifs_allele.trgt_plots.zip", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-65/call-trgt_genotype/out/m84036_250809_035451_s4.bc2162.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-65/call-trgt_genotype/out/m84036_250809_035451_s4.bc2162.trgt.vcf", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-65/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2162.repeats.bam", "images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-65/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2162.meth_waterfall.trgt_plots.zip", "reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-65/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2162.repeats.bam.bai"}
2025-09-15 20:25:24.230 wdl.w:ptcp.t:call-tar_outputs-22 NOTICE task setup :: name: "tar_outputs", source: "./common.wdl", line: 279, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-22", thread: 140607674631744
2025-09-15 20:25:24.257 wdl.w:ptcp.t:call-tar_outputs-22 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:24.257 wdl.w:ptcp.t:call-tar_outputs-22 INFO input :: name: "sawfish_vcf_tbi", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2119.sv.vcf.gz.tbi"
2025-09-15 20:25:24.257 wdl.w:ptcp.t:call-tar_outputs-22 INFO input :: name: "sawfish_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2119.sv.vcf.gz"
2025-09-15 20:25:24.257 wdl.w:ptcp.t:call-tar_outputs-22 INFO input :: name: "f8_json", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2119.f8inversion.json"
2025-09-15 20:25:24.257 wdl.w:ptcp.t:call-tar_outputs-22 INFO input :: name: "paraphase_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2119.paraphase.bam.bai"
2025-09-15 20:25:24.257 wdl.w:ptcp.t:call-tar_outputs-22 INFO input :: name: "paraphase_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2119.paraphase.bam"
2025-09-15 20:25:24.257 wdl.w:ptcp.t:call-tar_outputs-22 INFO input :: name: "paraphase_json", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2119.paraphase.json"
2025-09-15 20:25:24.258 wdl.w:ptcp.t:call-tar_outputs-22 INFO input :: name: "trgt_spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2119.trgt.sorted.spanning.bam.bai"
2025-09-15 20:25:24.258 wdl.w:ptcp.t:call-tar_outputs-22 INFO input :: name: "trgt_spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2119.trgt.sorted.spanning.bam"
2025-09-15 20:25:24.258 wdl.w:ptcp.t:call-tar_outputs-22 INFO input :: name: "trgt_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2119.trgt.vcf"
2025-09-15 20:25:24.258 wdl.w:ptcp.t:call-tar_outputs-22 INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2119.mapped.bam.bai"
2025-09-15 20:25:24.258 wdl.w:ptcp.t:call-tar_outputs-22 INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2119.mapped.bam"
2025-09-15 20:25:24.258 wdl.w:ptcp.t:call-tar_outputs-22 INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2119"
2025-09-15 20:25:24.258 wdl.w:ptcp.t:call-tar_outputs-22 INFO eval :: name: "threads", value: 1
2025-09-15 20:25:24.258 wdl.w:ptcp.t:call-tar_outputs-22 INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:25:24.258 wdl.w:ptcp.t:call-tar_outputs-22 INFO eval :: name: "disk_size", value: 6
2025-09-15 20:25:24.259 wdl.w:ptcp.t:call-tar_outputs-22 INFO eval :: name: "output_tarball", value: "m84036_250809_035451_s4.bc2119.tar"
2025-09-15 20:25:24.259 wdl.w:ptcp.w:call-sawfish-80.t:call-run_sawfish.stderr VERBOSE [M::bam2fq_mainloop] discarded 0 singletons
2025-09-15 20:25:24.259 wdl.w:ptcp.w:call-sawfish-80.t:call-run_sawfish.stderr VERBOSE [M::bam2fq_mainloop] processed 0 reads
2025-09-15 20:25:24.259 wdl.w:ptcp.t:call-tar_outputs-22 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:24.259 wdl.w:ptcp.t:call-tar_outputs-22 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:24.260 wdl.w:ptcp.t:call-tar_outputs-22 INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:25:24.260 wdl.w:ptcp.t:call-tar_outputs-22 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:24.267 wdl.w:ptcp.w:call-sawfish-80.t:call-run_sawfish.slurm_singularity INFO srun: job 51798004 queued and waiting for resources
2025-09-15 20:25:24.267 wdl.w:ptcp.w:call-sawfish-80.t:call-run_sawfish.slurm_singularity INFO srun: job 51798004 has been allocated resources
2025-09-15 20:25:24.267 wdl.w:ptcp.w:call-sawfish-80.t:call-run_sawfish.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:24.324 wdl.w:ptcp.w:call-trgt-65 NOTICE done
2025-09-15 20:25:24.330 wdl.w:ptcp NOTICE finish :: job: "call-trgt-65"
2025-09-15 20:25:24.330 wdl.w:ptcp INFO output :: job: "call-trgt-65", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-65/out/m84036_250809_035451_s4.bc2162.motifs_waterfall.trgt_plots.zip", "images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-65/out/m84036_250809_035451_s4.bc2162.meth_allele.trgt_plots.zip", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-65/out/m84036_250809_035451_s4.bc2162.trgt.sorted.spanning.bam.bai", "images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-65/out/m84036_250809_035451_s4.bc2162.motifs_allele.trgt_plots.zip", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-65/out/m84036_250809_035451_s4.bc2162.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-65/out/m84036_250809_035451_s4.bc2162.trgt.vcf", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-65/out/m84036_250809_035451_s4.bc2162.repeats.bam", "images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-65/out/m84036_250809_035451_s4.bc2162.meth_waterfall.trgt_plots.zip", "reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-65/out/m84036_250809_035451_s4.bc2162.repeats.bam.bai"}
2025-09-15 20:25:24.337 wdl.w:ptcp.w:call-paraphase-94 NOTICE workflow start :: name: "paraphase", source: "./paraphase.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-94"
2025-09-15 20:25:24.356 wdl.w:ptcp.w:call-paraphase-94 INFO visit :: node: "decl-annotation_vcf", values: {"annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf"}
2025-09-15 20:25:24.356 wdl.w:ptcp.w:call-paraphase-94 INFO visit :: node: "decl-config_file", values: {"config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml"}
2025-09-15 20:25:24.357 wdl.w:ptcp.w:call-paraphase-94 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:25:24.357 wdl.w:ptcp.w:call-paraphase-94 INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:25:24.357 wdl.w:ptcp.w:call-paraphase-94 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-94/out/m84036_250809_035451_s4.bc2191.mapped.bam"}
2025-09-15 20:25:24.357 wdl.w:ptcp.w:call-paraphase-94 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-94/out/m84036_250809_035451_s4.bc2191.mapped.bam.bai"}
2025-09-15 20:25:24.357 wdl.w:ptcp.w:call-paraphase-94 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:25:24.357 wdl.w:ptcp.w:call-paraphase-94 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:25:24.357 wdl.w:ptcp.w:call-paraphase-94 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2191"}
2025-09-15 20:25:24.357 wdl.w:ptcp.w:call-paraphase-94 INFO visit :: node: "decl-sex", values: {"sex": "F"}
2025-09-15 20:25:24.357 wdl.w:ptcp.w:call-paraphase-94 NOTICE ready :: job: "call-run_paraphase", callee: "run_paraphase"
2025-09-15 20:25:24.358 wdl.w:ptcp.w:call-paraphase-94 INFO input :: job: "call-run_paraphase", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf", "genome_version": "38", "config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-94/out/m84036_250809_035451_s4.bc2191.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-94/out/m84036_250809_035451_s4.bc2191.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2191"}
2025-09-15 20:25:24.368 wdl.w:ptcp.t:call-tar_outputs-22 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 17, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-22/_singularity_tmpdir_dddu66cy"
2025-09-15 20:25:24.368 wdl.w:ptcp.t:call-tar_outputs-22 INFO Slurm invocation: srun --job-name call-tar_outputs-22 --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-22/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-22/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-22/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-22/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-22/out/m84036_250809_035451_s4.bc2119.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2119.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-22/out/m84036_250809_035451_s4.bc2119.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2119.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-22/out/m84036_250809_035451_s4.bc2119.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2119.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-22/out/m84036_250809_035451_s4.bc2119.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2119.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-22/out/m84036_250809_035451_s4.bc2119.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2119.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-22/out/m84036_250809_035451_s4.bc2119_paraphase/m84036_250809_035451_s4.bc2119.paraphase.json:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2119.paraphase.json:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-22/out/m84036_250809_035451_s4.bc2119_paraphase/m84036_250809_035451_s4.bc2119.paraphase.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2119.paraphase.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-22/out/m84036_250809_035451_s4.bc2119_paraphase/m84036_250809_035451_s4.bc2119.paraphase.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2119.paraphase.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-22/out/m84036_250809_035451_s4.bc2119_sawfish/m84036_250809_035451_s4.bc2119.sv.vcf.gz.tbi:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2119.sv.vcf.gz.tbi:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-22/out/m84036_250809_035451_s4.bc2119_sawfish/m84036_250809_035451_s4.bc2119.sv.vcf.gz:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2119.sv.vcf.gz:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-22/out/m84036_250809_035451_s4.bc2119.f8inversion.json:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2119.f8inversion.json:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-22/_singularity_tmpdir_dddu66cy/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-22/_singularity_tmpdir_dddu66cy/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:24.380 wdl.w:ptcp.t:call-tar_outputs-22 NOTICE slurm_singularity run :: pid: 1205597, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-22/slurm_singularity.log.txt"
2025-09-15 20:25:24.827 wdl.w:ptcp.w:call-paraphase-60.t:call-call_f8.slurm_singularity INFO srun: job 51798005 queued and waiting for resources
2025-09-15 20:25:24.828 wdl.w:ptcp.w:call-paraphase-60.t:call-call_f8.slurm_singularity INFO srun: job 51798005 has been allocated resources
2025-09-15 20:25:24.828 wdl.w:ptcp.w:call-paraphase-60.t:call-call_f8.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:25.006 wdl.w:ptcp.w:call-trgt-80.t:call-get_reads_overlapping_repeats.slurm_singularity INFO srun: job 51798006 queued and waiting for resources
2025-09-15 20:25:25.087 wdl.w:ptcp.w:call-paraphase-60.t:call-call_f8 INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2157.f8inversion.vcf"
2025-09-15 20:25:25.091 wdl.w:ptcp.w:call-paraphase-60.t:call-call_f8 INFO output :: name: "json", value: "m84036_250809_035451_s4.bc2157.f8inversion.json"
2025-09-15 20:25:25.111 wdl.w:ptcp.w:call-paraphase-79.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for smn1 for sample m84036_250809_035451_s4.bc2176 at 2025-09-15 20:25:12.687303...
2025-09-15 20:25:25.112 wdl.w:ptcp.w:call-paraphase-79.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for hba for sample m84036_250809_035451_s4.bc2176 at 2025-09-15 20:25:12.782602...
2025-09-15 20:25:25.112 wdl.w:ptcp.w:call-paraphase-79.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for cyp21 for sample m84036_250809_035451_s4.bc2176 at 2025-09-15 20:25:12.911671...
2025-09-15 20:25:25.112 wdl.w:ptcp.w:call-paraphase-79.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for gba for sample m84036_250809_035451_s4.bc2176 at 2025-09-15 20:25:13.231343...
2025-09-15 20:25:25.112 wdl.w:ptcp.w:call-paraphase-79.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for cyp21 for sample m84036_250809_035451_s4.bc2176 at 2025-09-15 20:25:22.373583...
2025-09-15 20:25:25.112 wdl.w:ptcp.w:call-paraphase-79.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for cyp21 for sample m84036_250809_035451_s4.bc2176 at 2025-09-15 20:25:22.723327...
2025-09-15 20:25:25.112 wdl.w:ptcp.w:call-paraphase-79.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for smn1 for sample m84036_250809_035451_s4.bc2176 at 2025-09-15 20:25:22.732726...
2025-09-15 20:25:25.112 wdl.w:ptcp.w:call-paraphase-79.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning to gene2 region for smn1 for sample m84036_250809_035451_s4.bc2176 at 2025-09-15 20:25:22.880968...
2025-09-15 20:25:25.153 wdl.w:ptcp.w:call-paraphase-60.t:call-call_f8 NOTICE done
2025-09-15 20:25:25.158 wdl.w:ptcp.w:call-paraphase-60 NOTICE finish :: job: "call-call_f8"
2025-09-15 20:25:25.159 wdl.w:ptcp.w:call-paraphase-60 INFO output :: job: "call-call_f8", values: {"json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-60/call-call_f8/out/m84036_250809_035451_s4.bc2157.f8inversion.json", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-60/call-call_f8/out/m84036_250809_035451_s4.bc2157.f8inversion.vcf"}
2025-09-15 20:25:25.159 wdl.w:ptcp.w:call-paraphase-60 INFO visit :: node: "output-f8_json", values: {"f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-60/call-call_f8/out/m84036_250809_035451_s4.bc2157.f8inversion.json"}
2025-09-15 20:25:25.159 wdl.w:ptcp.w:call-paraphase-60 INFO visit :: node: "output-f8_vcf", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-60/call-call_f8/out/m84036_250809_035451_s4.bc2157.f8inversion.vcf"}
2025-09-15 20:25:25.159 wdl.w:ptcp.w:call-paraphase-60 INFO visit :: node: "outputs", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-60/call-call_f8/out/m84036_250809_035451_s4.bc2157.f8inversion.vcf", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-60/call-run_paraphase/out/m84036_250809_035451_s4.bc2157_paraphase/m84036_250809_035451_s4.bc2157.paraphase.json", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-60/call-run_paraphase/out/m84036_250809_035451_s4.bc2157_paraphase/m84036_250809_035451_s4.bc2157.paraphase.bam", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-60/call-run_paraphase/out/m84036_250809_035451_s4.bc2157_paraphase/m84036_250809_035451_s4.bc2157.paraphase.bam.bai", "paraphase_vcfs": [], "havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-60/call-run_paraphase/out/m84036_250809_035451_s4.bc2157.havanno.json", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-60/call-call_f8/out/m84036_250809_035451_s4.bc2157.f8inversion.json"}
2025-09-15 20:25:25.164 wdl.w:ptcp.w:call-paraphase-85.t:call-run_paraphase NOTICE task setup :: name: "run_paraphase", source: "./paraphase.wdl", line: 127, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-85/call-run_paraphase", thread: 140607649453632
2025-09-15 20:25:25.179 wdl.w:ptcp.w:call-trgt-80.t:call-trgt_genotype.slurm_singularity INFO srun: job 51798007 queued and waiting for resources
2025-09-15 20:25:25.179 wdl.w:ptcp.w:call-trgt-80.t:call-trgt_genotype.slurm_singularity INFO srun: job 51798007 has been allocated resources
2025-09-15 20:25:25.179 wdl.w:ptcp.w:call-trgt-80.t:call-trgt_genotype.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:25.187 wdl.w:ptcp.w:call-paraphase-85.t:call-run_paraphase INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:25.187 wdl.w:ptcp.w:call-paraphase-85.t:call-run_paraphase INFO input :: name: "annotation_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf"
2025-09-15 20:25:25.187 wdl.w:ptcp.w:call-paraphase-85.t:call-run_paraphase INFO input :: name: "genome_version", value: "38"
2025-09-15 20:25:25.187 wdl.w:ptcp.w:call-paraphase-85.t:call-run_paraphase INFO input :: name: "config_file", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/paraphase_config.GRCh38.yaml"
2025-09-15 20:25:25.187 wdl.w:ptcp.w:call-paraphase-85.t:call-run_paraphase INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:25:25.187 wdl.w:ptcp.w:call-paraphase-85.t:call-run_paraphase INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:25:25.187 wdl.w:ptcp.w:call-paraphase-85.t:call-run_paraphase INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2182.mapped.bam.bai"
2025-09-15 20:25:25.187 wdl.w:ptcp.w:call-paraphase-85.t:call-run_paraphase INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2182.mapped.bam"
2025-09-15 20:25:25.188 wdl.w:ptcp.w:call-paraphase-85.t:call-run_paraphase INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2182"
2025-09-15 20:25:25.188 wdl.w:ptcp.w:call-paraphase-85.t:call-run_paraphase INFO eval :: name: "threads", value: 4
2025-09-15 20:25:25.188 wdl.w:ptcp.w:call-paraphase-85.t:call-run_paraphase INFO eval :: name: "mem_gb", value: 8
2025-09-15 20:25:25.189 wdl.w:ptcp.w:call-paraphase-85.t:call-run_paraphase INFO eval :: name: "disk_size", value: 27
2025-09-15 20:25:25.189 wdl.w:ptcp.w:call-paraphase-85.t:call-run_paraphase INFO eval :: name: "out_dir", value: "m84036_250809_035451_s4.bc2182_paraphase"
2025-09-15 20:25:25.189 wdl.w:ptcp.w:call-paraphase-85.t:call-run_paraphase INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 4, memory_reservation: 8000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:25.189 wdl.w:ptcp.w:call-paraphase-85.t:call-run_paraphase WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:25.190 wdl.w:ptcp.w:call-paraphase-85.t:call-run_paraphase INFO provisioned :: seconds_waited: 0, cpu: 4, mem_bytes: 8000000000
2025-09-15 20:25:25.190 wdl.w:ptcp.w:call-paraphase-85.t:call-run_paraphase INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:25.228 wdl.w:ptcp.w:call-paraphase-60 NOTICE done
2025-09-15 20:25:25.233 wdl.w:ptcp NOTICE finish :: job: "call-paraphase-60"
2025-09-15 20:25:25.234 wdl.w:ptcp INFO output :: job: "call-paraphase-60", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-60/out/m84036_250809_035451_s4.bc2157.f8inversion.vcf", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-60/out/m84036_250809_035451_s4.bc2157_paraphase/m84036_250809_035451_s4.bc2157.paraphase.json", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-60/out/m84036_250809_035451_s4.bc2157_paraphase/m84036_250809_035451_s4.bc2157.paraphase.bam", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-60/out/m84036_250809_035451_s4.bc2157_paraphase/m84036_250809_035451_s4.bc2157.paraphase.bam.bai", "paraphase_vcfs": [], "havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-60/out/m84036_250809_035451_s4.bc2157.havanno.json", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-60/out/m84036_250809_035451_s4.bc2157.f8inversion.json"}
2025-09-15 20:25:25.239 wdl.w:ptcp.w:call-sawfish-94 NOTICE workflow start :: name: "sawfish", source: "./sawfish.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-94"
2025-09-15 20:25:25.253 wdl.w:ptcp.w:call-sawfish-94 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:25:25.253 wdl.w:ptcp.w:call-sawfish-94 INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:25:25.253 wdl.w:ptcp.w:call-sawfish-94 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-94/out/m84036_250809_035451_s4.bc2191.mapped.bam"}
2025-09-15 20:25:25.253 wdl.w:ptcp.w:call-sawfish-94 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-94/out/m84036_250809_035451_s4.bc2191.mapped.bam.bai"}
2025-09-15 20:25:25.254 wdl.w:ptcp.w:call-sawfish-94 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:25:25.254 wdl.w:ptcp.w:call-sawfish-94 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:25:25.254 wdl.w:ptcp.w:call-sawfish-94 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2191"}
2025-09-15 20:25:25.254 wdl.w:ptcp.w:call-sawfish-94 NOTICE ready :: job: "call-run_sawfish", callee: "run_sawfish"
2025-09-15 20:25:25.254 wdl.w:ptcp.w:call-sawfish-94 INFO input :: job: "call-run_sawfish", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-94/out/m84036_250809_035451_s4.bc2191.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-94/out/m84036_250809_035451_s4.bc2191.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2191"}
2025-09-15 20:25:25.258 wdl.w:ptcp.w:call-paraphase-85.t:call-run_paraphase INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-85/call-run_paraphase/_singularity_tmpdir_uqaqlr11"
2025-09-15 20:25:25.258 wdl.w:ptcp.w:call-paraphase-85.t:call-run_paraphase INFO Slurm invocation: srun --job-name call-run_paraphase --partition compute,compute9 --cpus-per-task 4 --mem 7629M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-85/call-run_paraphase/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-85/call-run_paraphase/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-85/call-run_paraphase/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-85/call-run_paraphase/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-85/out/m84036_250809_035451_s4.bc2182.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2182.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-85/out/m84036_250809_035451_s4.bc2182.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2182.mapped.bam:ro --bind /ptcp/meta/variant_list/variant_list.GRCh38.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf:ro --bind /ptcp/meta/paraphase/paraphase_config.GRCh38.yaml:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/paraphase_config.GRCh38.yaml:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-85/call-run_paraphase/_singularity_tmpdir_uqaqlr11/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-85/call-run_paraphase/_singularity_tmpdir_uqaqlr11/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:25.277 wdl.w:ptcp.w:call-paraphase-85.t:call-run_paraphase NOTICE slurm_singularity run :: pid: 1205616, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-85/call-run_paraphase/slurm_singularity.log.txt"
2025-09-15 20:25:25.388 wdl.w:ptcp.t:call-tar_outputs-22.slurm_singularity INFO srun: job 51798008 queued and waiting for resources
2025-09-15 20:25:25.388 wdl.w:ptcp.t:call-tar_outputs-22.slurm_singularity INFO srun: job 51798008 has been allocated resources
2025-09-15 20:25:25.388 wdl.w:ptcp.t:call-tar_outputs-22.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:25.441 wdl.w:ptcp.w:call-trgt-68.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:24 [ERROR] - No reads found for TRID=PRTS_ARX
2025-09-15 20:25:25.441 wdl.w:ptcp.w:call-trgt-68.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:24 [ERROR] - No reads found for TRID=EIEE1_ARX
2025-09-15 20:25:25.589 wdl.w:ptcp.w:call-trgt-68.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:25:24 [ERROR] - No reads found for TRID=PRTS_ARX
2025-09-15 20:25:25.589 wdl.w:ptcp.w:call-trgt-68.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:25:24 [ERROR] - No reads found for TRID=EIEE1_ARX
2025-09-15 20:25:25.642 wdl.w:ptcp.w:call-paraphase-07.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for cyp21 for sample m84036_250809_035451_s4.bc2104 at 2025-09-15 20:24:45.493701...
2025-09-15 20:25:25.642 wdl.w:ptcp.w:call-paraphase-07.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for cyp21 for sample m84036_250809_035451_s4.bc2104 at 2025-09-15 20:24:47.220155...
2025-09-15 20:25:25.642 wdl.w:ptcp.w:call-paraphase-07.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for gba for sample m84036_250809_035451_s4.bc2104 at 2025-09-15 20:25:14.123375...
2025-09-15 20:25:25.643 wdl.w:ptcp.w:call-paraphase-07.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for gba for sample m84036_250809_035451_s4.bc2104 at 2025-09-15 20:25:15.116390...
2025-09-15 20:25:25.643 wdl.w:ptcp.w:call-paraphase-07.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for hbb for sample m84036_250809_035451_s4.bc2104 at 2025-09-15 20:25:16.811605...
2025-09-15 20:25:25.643 wdl.w:ptcp.w:call-paraphase-07.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for hbb for sample m84036_250809_035451_s4.bc2104 at 2025-09-15 20:25:16.811780...
2025-09-15 20:25:25.643 wdl.w:ptcp.w:call-paraphase-07.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for hbb for sample m84036_250809_035451_s4.bc2104 at 2025-09-15 20:25:18.558639...
2025-09-15 20:25:25.705 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_plot_motifs_allele INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2167.motifs_allele.trgt_plots.zip"
2025-09-15 20:25:25.770 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_plot_motifs_allele NOTICE done
2025-09-15 20:25:25.774 wdl.w:ptcp.w:call-trgt-70 NOTICE finish :: job: "call-trgt_plot_motifs_allele"
2025-09-15 20:25:25.775 wdl.w:ptcp.w:call-trgt-70 INFO output :: job: "call-trgt_plot_motifs_allele", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-70/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2167.motifs_allele.trgt_plots.zip"}
2025-09-15 20:25:25.775 wdl.w:ptcp.w:call-trgt-70 INFO visit :: node: "output-images_motifs_allele", values: {"images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-70/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2167.motifs_allele.trgt_plots.zip"}
2025-09-15 20:25:25.780 wdl.w:ptcp.w:call-sawfish-85.t:call-run_sawfish NOTICE task setup :: name: "run_sawfish", source: "./sawfish.wdl", line: 83, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-85/call-run_sawfish", thread: 140609813722688
2025-09-15 20:25:25.798 wdl.w:ptcp.w:call-sawfish-85.t:call-run_sawfish INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:25.798 wdl.w:ptcp.w:call-sawfish-85.t:call-run_sawfish INFO input :: name: "genome_version", value: "38"
2025-09-15 20:25:25.798 wdl.w:ptcp.w:call-sawfish-85.t:call-run_sawfish INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:25:25.798 wdl.w:ptcp.w:call-sawfish-85.t:call-run_sawfish INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:25:25.798 wdl.w:ptcp.w:call-sawfish-85.t:call-run_sawfish INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2182.mapped.bam.bai"
2025-09-15 20:25:25.798 wdl.w:ptcp.w:call-sawfish-85.t:call-run_sawfish INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2182.mapped.bam"
2025-09-15 20:25:25.798 wdl.w:ptcp.w:call-sawfish-85.t:call-run_sawfish INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2182"
2025-09-15 20:25:25.798 wdl.w:ptcp.w:call-sawfish-85.t:call-run_sawfish INFO eval :: name: "mem_gb", value: 32
2025-09-15 20:25:25.799 wdl.w:ptcp.w:call-sawfish-85.t:call-run_sawfish INFO eval :: name: "threads", value: 16
2025-09-15 20:25:25.799 wdl.w:ptcp.w:call-sawfish-85.t:call-run_sawfish INFO eval :: name: "disk_size", value: 30
2025-09-15 20:25:25.799 wdl.w:ptcp.w:call-sawfish-85.t:call-run_sawfish INFO eval :: name: "discover_dirname", value: "m84036_250809_035451_s4.bc2182_sawfish_discover"
2025-09-15 20:25:25.799 wdl.w:ptcp.w:call-sawfish-85.t:call-run_sawfish INFO eval :: name: "call_dirname", value: "m84036_250809_035451_s4.bc2182_sawfish"
2025-09-15 20:25:25.799 wdl.w:ptcp.w:call-sawfish-85.t:call-run_sawfish INFO eval :: name: "minimap2_bam_filename", value: "m84036_250809_035451_s4.bc2182.minimap2.bam"
2025-09-15 20:25:25.799 wdl.w:ptcp.w:call-sawfish-85.t:call-run_sawfish INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 16, memory_reservation: 32000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:25.799 wdl.w:ptcp.w:call-sawfish-85.t:call-run_sawfish WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:25.800 wdl.w:ptcp.w:call-sawfish-85.t:call-run_sawfish INFO provisioned :: seconds_waited: 0, cpu: 16, mem_bytes: 32000000000
2025-09-15 20:25:25.800 wdl.w:ptcp.w:call-sawfish-85.t:call-run_sawfish INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:25.846 wdl.w:ptcp.w:call-trgt-68.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:25:25 [ERROR] - No reads found for TRID=PRTS_ARX
2025-09-15 20:25:25.846 wdl.w:ptcp.w:call-trgt-68.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:25:25 [ERROR] - No reads found for TRID=EIEE1_ARX
2025-09-15 20:25:25.861 wdl.w:ptcp.w:call-sawfish-85.t:call-run_sawfish INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 10, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-85/call-run_sawfish/_singularity_tmpdir_6jgub2ph"
2025-09-15 20:25:25.861 wdl.w:ptcp.w:call-sawfish-85.t:call-run_sawfish INFO Slurm invocation: srun --job-name call-run_sawfish --partition compute,compute9 --cpus-per-task 16 --mem 30518M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-85/call-run_sawfish/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-85/call-run_sawfish/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-85/call-run_sawfish/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-85/call-run_sawfish/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-85/out/m84036_250809_035451_s4.bc2182.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2182.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-85/out/m84036_250809_035451_s4.bc2182.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2182.mapped.bam:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-85/call-run_sawfish/_singularity_tmpdir_6jgub2ph/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-85/call-run_sawfish/_singularity_tmpdir_6jgub2ph/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:25.883 wdl.w:ptcp.w:call-sawfish-85.t:call-run_sawfish NOTICE slurm_singularity run :: pid: 1205625, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-85/call-run_sawfish/slurm_singularity.log.txt"
2025-09-15 20:25:25.965 wdl.w:ptcp.w:call-sawfish-43.t:call-run_sawfish.stderr VERBOSE [M::mm_idx_gen::35.386*1.42] collected minimizers
2025-09-15 20:25:25.965 wdl.w:ptcp.w:call-sawfish-43.t:call-run_sawfish.stderr VERBOSE [M::mm_idx_gen::42.260*1.66] sorted minimizers
2025-09-15 20:25:25.965 wdl.w:ptcp.w:call-sawfish-43.t:call-run_sawfish.stderr VERBOSE [M::main::42.260*1.66] loaded/built the index for 195 target sequence(s)
2025-09-15 20:25:25.965 wdl.w:ptcp.w:call-sawfish-43.t:call-run_sawfish.stderr VERBOSE [M::mm_mapopt_update::45.329*1.62] mid_occ = 136
2025-09-15 20:25:25.966 wdl.w:ptcp.w:call-sawfish-43.t:call-run_sawfish.stderr VERBOSE [M::mm_idx_stat] kmer size: 19; skip: 19; is_hpc: 0; #seq: 195
2025-09-15 20:25:26.018 wdl.w:ptcp.w:call-trgt-80.t:call-get_reads_overlapping_repeats.slurm_singularity INFO srun: job 51798006 has been allocated resources
2025-09-15 20:25:26.018 wdl.w:ptcp.w:call-trgt-80.t:call-get_reads_overlapping_repeats.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:26.037 wdl.w:ptcp.w:call-sawfish-55.t:call-run_sawfish.stderr VERBOSE [M::mm_idx_gen::35.240*1.42] collected minimizers
2025-09-15 20:25:26.038 wdl.w:ptcp.w:call-sawfish-55.t:call-run_sawfish.stderr VERBOSE [M::mm_idx_gen::42.093*1.67] sorted minimizers
2025-09-15 20:25:26.038 wdl.w:ptcp.w:call-sawfish-55.t:call-run_sawfish.stderr VERBOSE [M::main::42.093*1.67] loaded/built the index for 195 target sequence(s)
2025-09-15 20:25:26.038 wdl.w:ptcp.w:call-sawfish-55.t:call-run_sawfish.stderr VERBOSE [M::mm_mapopt_update::45.153*1.62] mid_occ = 136
2025-09-15 20:25:26.038 wdl.w:ptcp.w:call-sawfish-55.t:call-run_sawfish.stderr VERBOSE [M::mm_idx_stat] kmer size: 19; skip: 19; is_hpc: 0; #seq: 195
2025-09-15 20:25:26.160 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:23 [ERROR] - No reads found for TRID=SCA2_ATXN2
2025-09-15 20:25:26.160 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:23 [ERROR] - No reads found for TRID=DRPLA_ATN1
2025-09-15 20:25:26.160 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:23 [ERROR] - No reads found for TRID=OPDM4_RILPL1
2025-09-15 20:25:26.160 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:23 [ERROR] - No reads found for TRID=SCA37_DAB1
2025-09-15 20:25:26.160 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:23 [ERROR] - No reads found for TRID=NIID_NOTCH2NLC
2025-09-15 20:25:26.160 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:23 [ERROR] - No reads found for TRID=OPDM_ABCD3
2025-09-15 20:25:26.161 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:23 [ERROR] - No reads found for TRID=SCA27B_FGF14
2025-09-15 20:25:26.161 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:23 [ERROR] - No reads found for TRID=SCA3_ATXN3
2025-09-15 20:25:26.161 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:23 [ERROR] - No reads found for TRID=SCA4_ZFHX3
2025-09-15 20:25:26.161 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:23 [ERROR] - No reads found for TRID=HDL2_JPH3
2025-09-15 20:25:26.161 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:23 [ERROR] - No reads found for TRID=SCA31_BEAN1
2025-09-15 20:25:26.161 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:23 [ERROR] - No reads found for TRID=SCA6_CACNA1A
2025-09-15 20:25:26.161 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:23 [ERROR] - No reads found for TRID=OPDM2_GIPC1
2025-09-15 20:25:26.161 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:24 [ERROR] - No reads found for TRID=FRA2A_AFF3
2025-09-15 20:25:26.161 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:24 [ERROR] - No reads found for TRID=SD5_HOXD13
2025-09-15 20:25:26.161 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:24 [ERROR] - No reads found for TRID=SCA36_NOP56
2025-09-15 20:25:26.161 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:24 [ERROR] - No reads found for TRID=DM1_DMPK
2025-09-15 20:25:26.161 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:24 [ERROR] - No reads found for TRID=EPM1_CSTB
2025-09-15 20:25:26.161 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:24 [ERROR] - No reads found for TRID=SCA7_ATXN7
2025-09-15 20:25:26.161 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:24 [ERROR] - No reads found for TRID=CJD_PRNP
2025-09-15 20:25:26.161 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:24 [ERROR] - No reads found for TRID=SCA12_PPP2R2B
2025-09-15 20:25:26.161 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:24 [ERROR] - No reads found for TRID=SCA1_ATXN1
2025-09-15 20:25:26.161 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:24 [ERROR] - No reads found for TRID=CCHS_PHOX2B
2025-09-15 20:25:26.161 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:24 [ERROR] - No reads found for TRID=FAME1_SAMD12
2025-09-15 20:25:26.162 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:24 [ERROR] - No reads found for TRID=FTDALS1_C9orf72
2025-09-15 20:25:26.162 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:24 [ERROR] - No reads found for TRID=OPDM1_LRP12
2025-09-15 20:25:26.162 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:24 [ERROR] - No reads found for TRID=SBMA_AR
2025-09-15 20:25:26.186 wdl.w:ptcp.w:call-trgt-81.t:call-get_reads_overlapping_repeats INFO output :: name: "reads_overlapping_repeats", value: "m84036_250809_035451_s4.bc2178.repeats.bam"
2025-09-15 20:25:26.190 wdl.w:ptcp.w:call-trgt-81.t:call-get_reads_overlapping_repeats INFO output :: name: "reads_overlapping_repeats_bai", value: "m84036_250809_035451_s4.bc2178.repeats.bam.bai"
2025-09-15 20:25:26.246 wdl.w:ptcp.w:call-trgt-81.t:call-get_reads_overlapping_repeats NOTICE done
2025-09-15 20:25:26.250 wdl.w:ptcp.w:call-trgt-81 NOTICE finish :: job: "call-get_reads_overlapping_repeats"
2025-09-15 20:25:26.250 wdl.w:ptcp.w:call-trgt-81 INFO output :: job: "call-get_reads_overlapping_repeats", values: {"reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-81/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2178.repeats.bam.bai", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-81/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2178.repeats.bam"}
2025-09-15 20:25:26.251 wdl.w:ptcp.w:call-trgt-81 INFO visit :: node: "output-reads_overlapping_repeats", values: {"reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-81/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2178.repeats.bam"}
2025-09-15 20:25:26.251 wdl.w:ptcp.w:call-trgt-81 INFO visit :: node: "output-reads_overlapping_repeats_bai", values: {"reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-81/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2178.repeats.bam.bai"}
2025-09-15 20:25:26.254 wdl.w:ptcp.w:call-trgt-85.t:call-get_reads_overlapping_repeats NOTICE task setup :: name: "get_reads_overlapping_repeats", source: "./trgt.wdl", line: 182, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-85/call-get_reads_overlapping_repeats", thread: 140607683024448
2025-09-15 20:25:26.272 wdl.w:ptcp.w:call-trgt-85.t:call-get_reads_overlapping_repeats INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:26.272 wdl.w:ptcp.w:call-trgt-85.t:call-get_reads_overlapping_repeats INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:25:26.272 wdl.w:ptcp.w:call-trgt-85.t:call-get_reads_overlapping_repeats INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2182.mapped.bam.bai"
2025-09-15 20:25:26.272 wdl.w:ptcp.w:call-trgt-85.t:call-get_reads_overlapping_repeats INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2182.mapped.bam"
2025-09-15 20:25:26.272 wdl.w:ptcp.w:call-trgt-85.t:call-get_reads_overlapping_repeats INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2182"
2025-09-15 20:25:26.272 wdl.w:ptcp.w:call-trgt-85.t:call-get_reads_overlapping_repeats INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:25:26.272 wdl.w:ptcp.w:call-trgt-85.t:call-get_reads_overlapping_repeats INFO eval :: name: "expand_size", value: 3000
2025-09-15 20:25:26.273 wdl.w:ptcp.w:call-trgt-85.t:call-get_reads_overlapping_repeats INFO eval :: name: "threads", value: 1
2025-09-15 20:25:26.273 wdl.w:ptcp.w:call-trgt-85.t:call-get_reads_overlapping_repeats INFO eval :: name: "expanded_bed_name", value: "m84036_250809_035451_s4.bc2182.expanded.bed"
2025-09-15 20:25:26.273 wdl.w:ptcp.w:call-trgt-85.t:call-get_reads_overlapping_repeats INFO eval :: name: "disk_size", value: 11
2025-09-15 20:25:26.273 wdl.w:ptcp.w:call-trgt-85.t:call-get_reads_overlapping_repeats INFO eval :: name: "output_name", value: "m84036_250809_035451_s4.bc2182.repeats.bam"
2025-09-15 20:25:26.273 wdl.w:ptcp.w:call-trgt-85.t:call-get_reads_overlapping_repeats INFO eval :: name: "index_name", value: "m84036_250809_035451_s4.bc2182.repeats.bam.bai"
2025-09-15 20:25:26.273 wdl.w:ptcp.w:call-trgt-85.t:call-get_reads_overlapping_repeats INFO eval :: name: "output_name_with_index", value: "m84036_250809_035451_s4.bc2182.repeats.bam##idx##m84036_250809_035451_s4.bc2182.repeats.bam.bai"
2025-09-15 20:25:26.275 wdl.w:ptcp.w:call-trgt-85.t:call-get_reads_overlapping_repeats INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:26.275 wdl.w:ptcp.w:call-trgt-85.t:call-get_reads_overlapping_repeats WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:26.276 wdl.w:ptcp.w:call-trgt-85.t:call-get_reads_overlapping_repeats INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:25:26.276 wdl.w:ptcp.w:call-trgt-85.t:call-get_reads_overlapping_repeats INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:26.287 wdl.w:ptcp.w:call-paraphase-85.t:call-run_paraphase.slurm_singularity INFO srun: job 51798009 queued and waiting for resources
2025-09-15 20:25:26.287 wdl.w:ptcp.w:call-paraphase-85.t:call-run_paraphase.slurm_singularity INFO srun: job 51798009 has been allocated resources
2025-09-15 20:25:26.287 wdl.w:ptcp.w:call-paraphase-85.t:call-run_paraphase.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:26.305 wdl.w:ptcp.t:call-tar_outputs-22 INFO output :: name: "sample_tarball", value: "m84036_250809_035451_s4.bc2119.tar"
2025-09-15 20:25:26.333 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_plot_meth_allele INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2167.meth_allele.trgt_plots.zip"
2025-09-15 20:25:26.334 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:25:23 [ERROR] - No reads found for TRID=SCA2_ATXN2
2025-09-15 20:25:26.334 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:25:23 [ERROR] - No reads found for TRID=DRPLA_ATN1
2025-09-15 20:25:26.334 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:25:23 [ERROR] - No reads found for TRID=OPDM4_RILPL1
2025-09-15 20:25:26.334 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:25:24 [ERROR] - No reads found for TRID=SCA37_DAB1
2025-09-15 20:25:26.334 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:25:24 [ERROR] - No reads found for TRID=NIID_NOTCH2NLC
2025-09-15 20:25:26.334 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:25:24 [ERROR] - No reads found for TRID=OPDM_ABCD3
2025-09-15 20:25:26.334 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:25:24 [ERROR] - No reads found for TRID=SCA27B_FGF14
2025-09-15 20:25:26.334 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:25:24 [ERROR] - No reads found for TRID=SCA3_ATXN3
2025-09-15 20:25:26.334 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:25:24 [ERROR] - No reads found for TRID=SCA4_ZFHX3
2025-09-15 20:25:26.334 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:25:24 [ERROR] - No reads found for TRID=HDL2_JPH3
2025-09-15 20:25:26.334 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:25:24 [ERROR] - No reads found for TRID=SCA31_BEAN1
2025-09-15 20:25:26.335 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:25:24 [ERROR] - No reads found for TRID=SCA6_CACNA1A
2025-09-15 20:25:26.335 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:25:25 [ERROR] - No reads found for TRID=OPDM2_GIPC1
2025-09-15 20:25:26.335 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:25:25 [ERROR] - No reads found for TRID=FRA2A_AFF3
2025-09-15 20:25:26.335 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:25:25 [ERROR] - No reads found for TRID=SD5_HOXD13
2025-09-15 20:25:26.335 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:25:25 [ERROR] - No reads found for TRID=SCA36_NOP56
2025-09-15 20:25:26.335 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:25:25 [ERROR] - No reads found for TRID=DM1_DMPK
2025-09-15 20:25:26.335 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:25:25 [ERROR] - No reads found for TRID=EPM1_CSTB
2025-09-15 20:25:26.335 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:25:25 [ERROR] - No reads found for TRID=SCA7_ATXN7
2025-09-15 20:25:26.335 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:25:25 [ERROR] - No reads found for TRID=CJD_PRNP
2025-09-15 20:25:26.335 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:25:26 [ERROR] - No reads found for TRID=SCA12_PPP2R2B
2025-09-15 20:25:26.335 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:25:26 [ERROR] - No reads found for TRID=SCA1_ATXN1
2025-09-15 20:25:26.335 wdl.w:ptcp.w:call-trgt-85.t:call-get_reads_overlapping_repeats INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 9, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-85/call-get_reads_overlapping_repeats/_singularity_tmpdir_u_lxsg3s"
2025-09-15 20:25:26.335 wdl.w:ptcp.w:call-trgt-85.t:call-get_reads_overlapping_repeats INFO Slurm invocation: srun --job-name call-get_reads_overlapping_repeats --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-85/call-get_reads_overlapping_repeats/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-85/call-get_reads_overlapping_repeats/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-85/call-get_reads_overlapping_repeats/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-85/call-get_reads_overlapping_repeats/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-85/out/m84036_250809_035451_s4.bc2182.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2182.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-85/out/m84036_250809_035451_s4.bc2182.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2182.mapped.bam:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-85/call-get_reads_overlapping_repeats/_singularity_tmpdir_u_lxsg3s/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-85/call-get_reads_overlapping_repeats/_singularity_tmpdir_u_lxsg3s/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:26.368 wdl.w:ptcp.w:call-trgt-85.t:call-get_reads_overlapping_repeats NOTICE slurm_singularity run :: pid: 1205635, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-85/call-get_reads_overlapping_repeats/slurm_singularity.log.txt"
2025-09-15 20:25:26.377 wdl.w:ptcp.t:call-tar_outputs-22 NOTICE done
2025-09-15 20:25:26.381 wdl.w:ptcp NOTICE finish :: job: "call-tar_outputs-22"
2025-09-15 20:25:26.382 wdl.w:ptcp INFO output :: job: "call-tar_outputs-22", values: {"sample_tarball": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-22/out/m84036_250809_035451_s4.bc2119.tar"}
2025-09-15 20:25:26.388 wdl.w:ptcp.w:call-trgt-85.t:call-trgt_genotype NOTICE task setup :: name: "trgt_genotype", source: "./trgt.wdl", line: 272, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-85/call-trgt_genotype", thread: 140607674631744
2025-09-15 20:25:26.406 wdl.w:ptcp.w:call-trgt-85.t:call-trgt_genotype INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:26.406 wdl.w:ptcp.w:call-trgt-85.t:call-trgt_genotype INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:25:26.406 wdl.w:ptcp.w:call-trgt-85.t:call-trgt_genotype INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:25:26.407 wdl.w:ptcp.w:call-trgt-85.t:call-trgt_genotype INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:25:26.407 wdl.w:ptcp.w:call-trgt-85.t:call-trgt_genotype INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2182.mapped.bam.bai"
2025-09-15 20:25:26.407 wdl.w:ptcp.w:call-trgt-85.t:call-trgt_genotype INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2182.mapped.bam"
2025-09-15 20:25:26.407 wdl.w:ptcp.w:call-trgt-85.t:call-trgt_genotype INFO input :: name: "sex", value: "F"
2025-09-15 20:25:26.407 wdl.w:ptcp.w:call-trgt-85.t:call-trgt_genotype INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2182"
2025-09-15 20:25:26.407 wdl.w:ptcp.w:call-trgt-85.t:call-trgt_genotype INFO eval :: name: "mem_gb", value: 16
2025-09-15 20:25:26.407 wdl.w:ptcp.w:call-trgt-85.t:call-trgt_genotype INFO eval :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2182.trgt"
2025-09-15 20:25:26.408 wdl.w:ptcp.w:call-trgt-85.t:call-trgt_genotype INFO eval :: name: "threads", value: 8
2025-09-15 20:25:26.408 wdl.w:ptcp.w:call-trgt-85.t:call-trgt_genotype INFO eval :: name: "disk_size", value: 27
2025-09-15 20:25:26.408 wdl.w:ptcp.w:call-trgt-85.t:call-trgt_genotype INFO eval :: name: "karyotype", value: "XX"
2025-09-15 20:25:26.408 wdl.w:ptcp.w:call-trgt-85.t:call-trgt_genotype INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 8, memory_reservation: 16000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:26.408 wdl.w:ptcp.w:call-trgt-85.t:call-trgt_genotype WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:26.409 wdl.w:ptcp.w:call-trgt-85.t:call-trgt_genotype INFO provisioned :: seconds_waited: 0, cpu: 8, mem_bytes: 16000000000
2025-09-15 20:25:26.409 wdl.w:ptcp.w:call-trgt-85.t:call-trgt_genotype INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:26.421 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_plot_meth_allele NOTICE done
2025-09-15 20:25:26.426 wdl.w:ptcp.w:call-trgt-70 NOTICE finish :: job: "call-trgt_plot_meth_allele"
2025-09-15 20:25:26.427 wdl.w:ptcp.w:call-trgt-70 INFO output :: job: "call-trgt_plot_meth_allele", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-70/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2167.meth_allele.trgt_plots.zip"}
2025-09-15 20:25:26.427 wdl.w:ptcp.w:call-trgt-70 INFO visit :: node: "output-images_meth_allele", values: {"images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-70/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2167.meth_allele.trgt_plots.zip"}
2025-09-15 20:25:26.433 wdl.w:ptcp.w:call-paraphase-92.t:call-run_paraphase NOTICE task setup :: name: "run_paraphase", source: "./paraphase.wdl", line: 127, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-92/call-run_paraphase", thread: 140611969599040
2025-09-15 20:25:26.452 wdl.w:ptcp.w:call-paraphase-92.t:call-run_paraphase INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:26.452 wdl.w:ptcp.w:call-paraphase-92.t:call-run_paraphase INFO input :: name: "annotation_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf"
2025-09-15 20:25:26.452 wdl.w:ptcp.w:call-paraphase-92.t:call-run_paraphase INFO input :: name: "genome_version", value: "38"
2025-09-15 20:25:26.452 wdl.w:ptcp.w:call-paraphase-92.t:call-run_paraphase INFO input :: name: "config_file", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/paraphase_config.GRCh38.yaml"
2025-09-15 20:25:26.452 wdl.w:ptcp.w:call-paraphase-92.t:call-run_paraphase INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:25:26.452 wdl.w:ptcp.w:call-paraphase-92.t:call-run_paraphase INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:25:26.452 wdl.w:ptcp.w:call-paraphase-92.t:call-run_paraphase INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2189.mapped.bam.bai"
2025-09-15 20:25:26.452 wdl.w:ptcp.w:call-paraphase-92.t:call-run_paraphase INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2189.mapped.bam"
2025-09-15 20:25:26.452 wdl.w:ptcp.w:call-paraphase-92.t:call-run_paraphase INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2189"
2025-09-15 20:25:26.453 wdl.w:ptcp.w:call-paraphase-92.t:call-run_paraphase INFO eval :: name: "threads", value: 4
2025-09-15 20:25:26.453 wdl.w:ptcp.w:call-paraphase-92.t:call-run_paraphase INFO eval :: name: "mem_gb", value: 8
2025-09-15 20:25:26.453 wdl.w:ptcp.w:call-paraphase-92.t:call-run_paraphase INFO eval :: name: "disk_size", value: 27
2025-09-15 20:25:26.453 wdl.w:ptcp.w:call-paraphase-92.t:call-run_paraphase INFO eval :: name: "out_dir", value: "m84036_250809_035451_s4.bc2189_paraphase"
2025-09-15 20:25:26.453 wdl.w:ptcp.w:call-paraphase-92.t:call-run_paraphase INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 4, memory_reservation: 8000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:26.454 wdl.w:ptcp.w:call-paraphase-92.t:call-run_paraphase WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:26.454 wdl.w:ptcp.w:call-paraphase-92.t:call-run_paraphase INFO provisioned :: seconds_waited: 0, cpu: 4, mem_bytes: 8000000000
2025-09-15 20:25:26.454 wdl.w:ptcp.w:call-paraphase-92.t:call-run_paraphase INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:26.465 wdl.w:ptcp.w:call-trgt-85.t:call-trgt_genotype INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 11, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-85/call-trgt_genotype/_singularity_tmpdir_7fxinl00"
2025-09-15 20:25:26.465 wdl.w:ptcp.w:call-trgt-85.t:call-trgt_genotype INFO Slurm invocation: srun --job-name call-trgt_genotype --partition compute,compute9 --cpus-per-task 8 --mem 15259M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-85/call-trgt_genotype/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-85/call-trgt_genotype/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-85/call-trgt_genotype/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-85/call-trgt_genotype/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-85/out/m84036_250809_035451_s4.bc2182.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2182.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-85/out/m84036_250809_035451_s4.bc2182.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2182.mapped.bam:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-85/call-trgt_genotype/_singularity_tmpdir_7fxinl00/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-85/call-trgt_genotype/_singularity_tmpdir_7fxinl00/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:26.476 wdl.w:ptcp.w:call-trgt-85.t:call-trgt_genotype NOTICE slurm_singularity run :: pid: 1205637, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-85/call-trgt_genotype/slurm_singularity.log.txt"
2025-09-15 20:25:26.521 wdl.w:ptcp.w:call-paraphase-92.t:call-run_paraphase INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-92/call-run_paraphase/_singularity_tmpdir_7ctilnda"
2025-09-15 20:25:26.521 wdl.w:ptcp.w:call-paraphase-92.t:call-run_paraphase INFO Slurm invocation: srun --job-name call-run_paraphase --partition compute,compute9 --cpus-per-task 4 --mem 7629M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-92/call-run_paraphase/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-92/call-run_paraphase/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-92/call-run_paraphase/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-92/call-run_paraphase/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-92/out/m84036_250809_035451_s4.bc2189.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2189.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-92/out/m84036_250809_035451_s4.bc2189.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2189.mapped.bam.bai:ro --bind /ptcp/meta/variant_list/variant_list.GRCh38.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf:ro --bind /ptcp/meta/paraphase/paraphase_config.GRCh38.yaml:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/paraphase_config.GRCh38.yaml:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-92/call-run_paraphase/_singularity_tmpdir_7ctilnda/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-92/call-run_paraphase/_singularity_tmpdir_7ctilnda/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:26.530 wdl.w:ptcp.w:call-paraphase-92.t:call-run_paraphase NOTICE slurm_singularity run :: pid: 1205639, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-92/call-run_paraphase/slurm_singularity.log.txt"
2025-09-15 20:25:26.614 wdl.w:ptcp.w:call-trgt-81.t:call-trgt_genotype INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2178.trgt.vcf"
2025-09-15 20:25:26.618 wdl.w:ptcp.w:call-trgt-81.t:call-trgt_genotype INFO output :: name: "spanning_bam", value: "m84036_250809_035451_s4.bc2178.trgt.sorted.spanning.bam"
2025-09-15 20:25:26.619 wdl.w:ptcp.w:call-trgt-81.t:call-trgt_genotype INFO output :: name: "spanning_bam_bai", value: "m84036_250809_035451_s4.bc2178.trgt.sorted.spanning.bam.bai"
2025-09-15 20:25:26.701 wdl.w:ptcp.w:call-trgt-81.t:call-trgt_genotype NOTICE done
2025-09-15 20:25:26.706 wdl.w:ptcp.w:call-trgt-81 NOTICE finish :: job: "call-trgt_genotype"
2025-09-15 20:25:26.706 wdl.w:ptcp.w:call-trgt-81 INFO output :: job: "call-trgt_genotype", values: {"spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-81/call-trgt_genotype/out/m84036_250809_035451_s4.bc2178.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-81/call-trgt_genotype/out/m84036_250809_035451_s4.bc2178.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-81/call-trgt_genotype/out/m84036_250809_035451_s4.bc2178.trgt.vcf"}
2025-09-15 20:25:26.707 wdl.w:ptcp.w:call-trgt-81 NOTICE ready :: job: "call-trgt_plot_meth_allele", callee: "trgt_plot"
2025-09-15 20:25:26.707 wdl.w:ptcp.w:call-trgt-81 INFO input :: job: "call-trgt_plot_meth_allele", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": false, "methylation": true, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-81/call-trgt_genotype/out/m84036_250809_035451_s4.bc2178.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-81/call-trgt_genotype/out/m84036_250809_035451_s4.bc2178.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-81/call-trgt_genotype/out/m84036_250809_035451_s4.bc2178.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2178"}
2025-09-15 20:25:26.709 wdl.w:ptcp.w:call-trgt-81 NOTICE ready :: job: "call-trgt_plot_meth_waterfall", callee: "trgt_plot"
2025-09-15 20:25:26.709 wdl.w:ptcp.w:call-trgt-81 INFO input :: job: "call-trgt_plot_meth_waterfall", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": true, "methylation": true, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-81/call-trgt_genotype/out/m84036_250809_035451_s4.bc2178.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-81/call-trgt_genotype/out/m84036_250809_035451_s4.bc2178.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-81/call-trgt_genotype/out/m84036_250809_035451_s4.bc2178.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2178"}
2025-09-15 20:25:26.710 wdl.w:ptcp.w:call-trgt-81 NOTICE ready :: job: "call-trgt_plot_motifs_allele", callee: "trgt_plot"
2025-09-15 20:25:26.710 wdl.w:ptcp.w:call-trgt-81 INFO input :: job: "call-trgt_plot_motifs_allele", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": false, "methylation": false, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-81/call-trgt_genotype/out/m84036_250809_035451_s4.bc2178.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-81/call-trgt_genotype/out/m84036_250809_035451_s4.bc2178.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-81/call-trgt_genotype/out/m84036_250809_035451_s4.bc2178.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2178"}
2025-09-15 20:25:26.711 wdl.w:ptcp.w:call-trgt-81 NOTICE ready :: job: "call-trgt_plot_motifs_waterfall", callee: "trgt_plot"
2025-09-15 20:25:26.711 wdl.w:ptcp.w:call-trgt-81 INFO input :: job: "call-trgt_plot_motifs_waterfall", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": true, "methylation": false, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-81/call-trgt_genotype/out/m84036_250809_035451_s4.bc2178.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-81/call-trgt_genotype/out/m84036_250809_035451_s4.bc2178.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-81/call-trgt_genotype/out/m84036_250809_035451_s4.bc2178.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2178"}
2025-09-15 20:25:26.712 wdl.w:ptcp.w:call-trgt-81 INFO visit :: node: "output-spanning_bam", values: {"spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-81/call-trgt_genotype/out/m84036_250809_035451_s4.bc2178.trgt.sorted.spanning.bam"}
2025-09-15 20:25:26.712 wdl.w:ptcp.w:call-trgt-81 INFO visit :: node: "output-spanning_bam_bai", values: {"spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-81/call-trgt_genotype/out/m84036_250809_035451_s4.bc2178.trgt.sorted.spanning.bam.bai"}
2025-09-15 20:25:26.712 wdl.w:ptcp.w:call-trgt-81 INFO visit :: node: "output-vcf", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-81/call-trgt_genotype/out/m84036_250809_035451_s4.bc2178.trgt.vcf"}
2025-09-15 20:25:26.713 wdl.w:ptcp.w:call-sawfish-92.t:call-run_sawfish NOTICE task setup :: name: "run_sawfish", source: "./sawfish.wdl", line: 83, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-92/call-run_sawfish", thread: 140611415942720
2025-09-15 20:25:26.721 wdl.w:ptcp.w:call-trgt-72.t:call-trgt_genotype INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2169.trgt.vcf"
2025-09-15 20:25:26.724 wdl.w:ptcp.w:call-trgt-72.t:call-trgt_genotype INFO output :: name: "spanning_bam", value: "m84036_250809_035451_s4.bc2169.trgt.sorted.spanning.bam"
2025-09-15 20:25:26.726 wdl.w:ptcp.w:call-trgt-72.t:call-trgt_genotype INFO output :: name: "spanning_bam_bai", value: "m84036_250809_035451_s4.bc2169.trgt.sorted.spanning.bam.bai"
2025-09-15 20:25:26.732 wdl.w:ptcp.w:call-sawfish-92.t:call-run_sawfish INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:26.732 wdl.w:ptcp.w:call-sawfish-92.t:call-run_sawfish INFO input :: name: "genome_version", value: "38"
2025-09-15 20:25:26.732 wdl.w:ptcp.w:call-sawfish-92.t:call-run_sawfish INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:25:26.732 wdl.w:ptcp.w:call-sawfish-92.t:call-run_sawfish INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:25:26.732 wdl.w:ptcp.w:call-sawfish-92.t:call-run_sawfish INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2189.mapped.bam.bai"
2025-09-15 20:25:26.732 wdl.w:ptcp.w:call-sawfish-92.t:call-run_sawfish INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2189.mapped.bam"
2025-09-15 20:25:26.732 wdl.w:ptcp.w:call-sawfish-92.t:call-run_sawfish INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2189"
2025-09-15 20:25:26.733 wdl.w:ptcp.w:call-sawfish-92.t:call-run_sawfish INFO eval :: name: "mem_gb", value: 32
2025-09-15 20:25:26.733 wdl.w:ptcp.w:call-sawfish-92.t:call-run_sawfish INFO eval :: name: "threads", value: 16
2025-09-15 20:25:26.733 wdl.w:ptcp.w:call-sawfish-92.t:call-run_sawfish INFO eval :: name: "disk_size", value: 30
2025-09-15 20:25:26.733 wdl.w:ptcp.w:call-sawfish-92.t:call-run_sawfish INFO eval :: name: "discover_dirname", value: "m84036_250809_035451_s4.bc2189_sawfish_discover"
2025-09-15 20:25:26.733 wdl.w:ptcp.w:call-sawfish-92.t:call-run_sawfish INFO eval :: name: "call_dirname", value: "m84036_250809_035451_s4.bc2189_sawfish"
2025-09-15 20:25:26.733 wdl.w:ptcp.w:call-sawfish-92.t:call-run_sawfish INFO eval :: name: "minimap2_bam_filename", value: "m84036_250809_035451_s4.bc2189.minimap2.bam"
2025-09-15 20:25:26.734 wdl.w:ptcp.w:call-sawfish-92.t:call-run_sawfish INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 16, memory_reservation: 32000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:26.734 wdl.w:ptcp.w:call-sawfish-92.t:call-run_sawfish WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:26.734 wdl.w:ptcp.w:call-sawfish-92.t:call-run_sawfish INFO provisioned :: seconds_waited: 0, cpu: 16, mem_bytes: 32000000000
2025-09-15 20:25:26.735 wdl.w:ptcp.w:call-sawfish-92.t:call-run_sawfish INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:26.787 wdl.w:ptcp.w:call-sawfish-92.t:call-run_sawfish INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 10, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-92/call-run_sawfish/_singularity_tmpdir_6rew87uj"
2025-09-15 20:25:26.787 wdl.w:ptcp.w:call-sawfish-92.t:call-run_sawfish INFO Slurm invocation: srun --job-name call-run_sawfish --partition compute,compute9 --cpus-per-task 16 --mem 30518M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-92/call-run_sawfish/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-92/call-run_sawfish/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-92/call-run_sawfish/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-92/call-run_sawfish/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-92/out/m84036_250809_035451_s4.bc2189.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2189.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-92/out/m84036_250809_035451_s4.bc2189.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2189.mapped.bam.bai:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-92/call-run_sawfish/_singularity_tmpdir_6rew87uj/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-92/call-run_sawfish/_singularity_tmpdir_6rew87uj/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:26.804 wdl.w:ptcp.w:call-sawfish-92.t:call-run_sawfish NOTICE slurm_singularity run :: pid: 1205658, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-92/call-run_sawfish/slurm_singularity.log.txt"
2025-09-15 20:25:26.805 wdl.w:ptcp.w:call-trgt-72.t:call-trgt_genotype NOTICE done
2025-09-15 20:25:26.810 wdl.w:ptcp.w:call-trgt-72 NOTICE finish :: job: "call-trgt_genotype"
2025-09-15 20:25:26.811 wdl.w:ptcp.w:call-trgt-72 INFO output :: job: "call-trgt_genotype", values: {"spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-72/call-trgt_genotype/out/m84036_250809_035451_s4.bc2169.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-72/call-trgt_genotype/out/m84036_250809_035451_s4.bc2169.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-72/call-trgt_genotype/out/m84036_250809_035451_s4.bc2169.trgt.vcf"}
2025-09-15 20:25:26.811 wdl.w:ptcp.w:call-trgt-72 NOTICE ready :: job: "call-trgt_plot_meth_allele", callee: "trgt_plot"
2025-09-15 20:25:26.811 wdl.w:ptcp.w:call-trgt-72 INFO input :: job: "call-trgt_plot_meth_allele", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": false, "methylation": true, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-72/call-trgt_genotype/out/m84036_250809_035451_s4.bc2169.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-72/call-trgt_genotype/out/m84036_250809_035451_s4.bc2169.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-72/call-trgt_genotype/out/m84036_250809_035451_s4.bc2169.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2169"}
2025-09-15 20:25:26.812 wdl.w:ptcp.w:call-trgt-72 NOTICE ready :: job: "call-trgt_plot_meth_waterfall", callee: "trgt_plot"
2025-09-15 20:25:26.812 wdl.w:ptcp.w:call-trgt-72 INFO input :: job: "call-trgt_plot_meth_waterfall", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": true, "methylation": true, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-72/call-trgt_genotype/out/m84036_250809_035451_s4.bc2169.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-72/call-trgt_genotype/out/m84036_250809_035451_s4.bc2169.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-72/call-trgt_genotype/out/m84036_250809_035451_s4.bc2169.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2169"}
2025-09-15 20:25:26.813 wdl.w:ptcp.w:call-trgt-72 NOTICE ready :: job: "call-trgt_plot_motifs_allele", callee: "trgt_plot"
2025-09-15 20:25:26.814 wdl.w:ptcp.w:call-trgt-72 INFO input :: job: "call-trgt_plot_motifs_allele", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": false, "methylation": false, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-72/call-trgt_genotype/out/m84036_250809_035451_s4.bc2169.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-72/call-trgt_genotype/out/m84036_250809_035451_s4.bc2169.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-72/call-trgt_genotype/out/m84036_250809_035451_s4.bc2169.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2169"}
2025-09-15 20:25:26.814 wdl.w:ptcp.w:call-trgt-72 NOTICE ready :: job: "call-trgt_plot_motifs_waterfall", callee: "trgt_plot"
2025-09-15 20:25:26.815 wdl.w:ptcp.w:call-trgt-72 INFO input :: job: "call-trgt_plot_motifs_waterfall", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": true, "methylation": false, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-72/call-trgt_genotype/out/m84036_250809_035451_s4.bc2169.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-72/call-trgt_genotype/out/m84036_250809_035451_s4.bc2169.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-72/call-trgt_genotype/out/m84036_250809_035451_s4.bc2169.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2169"}
2025-09-15 20:25:26.815 wdl.w:ptcp.w:call-trgt-72 INFO visit :: node: "output-spanning_bam", values: {"spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-72/call-trgt_genotype/out/m84036_250809_035451_s4.bc2169.trgt.sorted.spanning.bam"}
2025-09-15 20:25:26.815 wdl.w:ptcp.w:call-trgt-72 INFO visit :: node: "output-spanning_bam_bai", values: {"spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-72/call-trgt_genotype/out/m84036_250809_035451_s4.bc2169.trgt.sorted.spanning.bam.bai"}
2025-09-15 20:25:26.815 wdl.w:ptcp.w:call-trgt-72 INFO visit :: node: "output-vcf", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-72/call-trgt_genotype/out/m84036_250809_035451_s4.bc2169.trgt.vcf"}
2025-09-15 20:25:26.817 wdl.w:ptcp.w:call-trgt-79.t:call-trgt_plot_meth_allele NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-79/call-trgt_plot_meth_allele", thread: 140607691417152
2025-09-15 20:25:26.839 wdl.w:ptcp.w:call-trgt-79.t:call-trgt_plot_meth_allele INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:26.840 wdl.w:ptcp.w:call-trgt-79.t:call-trgt_plot_meth_allele INFO input :: name: "waterfall", value: false
2025-09-15 20:25:26.840 wdl.w:ptcp.w:call-trgt-79.t:call-trgt_plot_meth_allele INFO input :: name: "methylation", value: true
2025-09-15 20:25:26.840 wdl.w:ptcp.w:call-trgt-79.t:call-trgt_plot_meth_allele INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:25:26.840 wdl.w:ptcp.w:call-trgt-79.t:call-trgt_plot_meth_allele INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:25:26.840 wdl.w:ptcp.w:call-trgt-79.t:call-trgt_plot_meth_allele INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:25:26.840 wdl.w:ptcp.w:call-trgt-79.t:call-trgt_plot_meth_allele INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2176.trgt.sorted.spanning.bam.bai"
2025-09-15 20:25:26.840 wdl.w:ptcp.w:call-trgt-79.t:call-trgt_plot_meth_allele INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2176.trgt.sorted.spanning.bam"
2025-09-15 20:25:26.840 wdl.w:ptcp.w:call-trgt-79.t:call-trgt_plot_meth_allele INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2176.trgt.vcf"
2025-09-15 20:25:26.840 wdl.w:ptcp.w:call-trgt-79.t:call-trgt_plot_meth_allele INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2176"
2025-09-15 20:25:26.841 wdl.w:ptcp.w:call-trgt-79.t:call-trgt_plot_meth_allele INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:25:26.841 wdl.w:ptcp.w:call-trgt-79.t:call-trgt_plot_meth_allele INFO eval :: name: "plot_type", value: "allele"
2025-09-15 20:25:26.841 wdl.w:ptcp.w:call-trgt-79.t:call-trgt_plot_meth_allele INFO eval :: name: "show", value: "meth"
2025-09-15 20:25:26.841 wdl.w:ptcp.w:call-trgt-79.t:call-trgt_plot_meth_allele INFO eval :: name: "threads", value: 1
2025-09-15 20:25:26.841 wdl.w:ptcp.w:call-trgt-79.t:call-trgt_plot_meth_allele INFO eval :: name: "disk_size", value: 27
2025-09-15 20:25:26.841 wdl.w:ptcp.w:call-trgt-79.t:call-trgt_plot_meth_allele INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2176.meth_allele"
2025-09-15 20:25:26.842 wdl.w:ptcp.w:call-trgt-79.t:call-trgt_plot_meth_allele INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:26.842 wdl.w:ptcp.w:call-trgt-79.t:call-trgt_plot_meth_allele WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:26.842 wdl.w:ptcp.w:call-trgt-79.t:call-trgt_plot_meth_allele INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:25:26.842 wdl.w:ptcp.w:call-trgt-79.t:call-trgt_plot_meth_allele INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:26.890 wdl.w:ptcp.w:call-sawfish-85.t:call-run_sawfish.stderr VERBOSE [M::bam2fq_mainloop] discarded 0 singletons
2025-09-15 20:25:26.890 wdl.w:ptcp.w:call-sawfish-85.t:call-run_sawfish.stderr VERBOSE [M::bam2fq_mainloop] processed 0 reads
2025-09-15 20:25:26.901 wdl.w:ptcp.w:call-sawfish-85.t:call-run_sawfish.slurm_singularity INFO srun: job 51798010 queued and waiting for resources
2025-09-15 20:25:26.902 wdl.w:ptcp.w:call-sawfish-85.t:call-run_sawfish.slurm_singularity INFO srun: job 51798010 has been allocated resources
2025-09-15 20:25:26.929 wdl.w:ptcp.w:call-trgt-68.t:call-trgt_plot_motifs_allele INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2165.motifs_allele.trgt_plots.zip"
2025-09-15 20:25:26.937 wdl.w:ptcp.w:call-trgt-79.t:call-trgt_plot_meth_allele INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-79/call-trgt_plot_meth_allele/_singularity_tmpdir_hk9i6dvg"
2025-09-15 20:25:26.937 wdl.w:ptcp.w:call-trgt-79.t:call-trgt_plot_meth_allele INFO Slurm invocation: srun --job-name call-trgt_plot_meth_allele --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-79/call-trgt_plot_meth_allele/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-79/call-trgt_plot_meth_allele/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-79/call-trgt_plot_meth_allele/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-79/call-trgt_plot_meth_allele/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-79/call-trgt_genotype/out/m84036_250809_035451_s4.bc2176.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2176.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-79/call-trgt_genotype/out/m84036_250809_035451_s4.bc2176.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2176.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-79/call-trgt_genotype/out/m84036_250809_035451_s4.bc2176.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2176.trgt.sorted.spanning.bam.bai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-79/call-trgt_plot_meth_allele/_singularity_tmpdir_hk9i6dvg/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-79/call-trgt_plot_meth_allele/_singularity_tmpdir_hk9i6dvg/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:26.961 wdl.w:ptcp.w:call-trgt-79.t:call-trgt_plot_meth_allele NOTICE slurm_singularity run :: pid: 1205666, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-79/call-trgt_plot_meth_allele/slurm_singularity.log.txt"
2025-09-15 20:25:27.026 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_plot_motifs_waterfall INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2167.motifs_waterfall.trgt_plots.zip"
2025-09-15 20:25:27.075 wdl.w:ptcp.w:call-trgt-68.t:call-trgt_plot_motifs_allele NOTICE done
2025-09-15 20:25:27.081 wdl.w:ptcp.w:call-trgt-68 NOTICE finish :: job: "call-trgt_plot_motifs_allele"
2025-09-15 20:25:27.081 wdl.w:ptcp.w:call-trgt-68 INFO output :: job: "call-trgt_plot_motifs_allele", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-68/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2165.motifs_allele.trgt_plots.zip"}
2025-09-15 20:25:27.081 wdl.w:ptcp.w:call-trgt-68 INFO visit :: node: "output-images_motifs_allele", values: {"images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-68/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2165.motifs_allele.trgt_plots.zip"}
2025-09-15 20:25:27.088 wdl.w:ptcp.w:call-trgt-79.t:call-trgt_plot_meth_waterfall NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-79/call-trgt_plot_meth_waterfall", thread: 140611441120832
2025-09-15 20:25:27.095 wdl.w:ptcp.w:call-paraphase-59.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for gba for sample m84036_250809_035451_s4.bc2156 at 2025-09-15 20:25:20.062763...
2025-09-15 20:25:27.095 wdl.w:ptcp.w:call-paraphase-59.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for gba for sample m84036_250809_035451_s4.bc2156 at 2025-09-15 20:25:20.556675...
2025-09-15 20:25:27.095 wdl.w:ptcp.w:call-paraphase-59.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for hbb for sample m84036_250809_035451_s4.bc2156 at 2025-09-15 20:25:23.425172...
2025-09-15 20:25:27.095 wdl.w:ptcp.w:call-paraphase-59.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for hbb for sample m84036_250809_035451_s4.bc2156 at 2025-09-15 20:25:23.425336...
2025-09-15 20:25:27.096 wdl.w:ptcp.w:call-paraphase-59.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for hbb for sample m84036_250809_035451_s4.bc2156 at 2025-09-15 20:25:24.269487...
2025-09-15 20:25:27.104 wdl.w:ptcp.w:call-trgt-79.t:call-trgt_plot_meth_waterfall INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:27.104 wdl.w:ptcp.w:call-trgt-79.t:call-trgt_plot_meth_waterfall INFO input :: name: "waterfall", value: true
2025-09-15 20:25:27.104 wdl.w:ptcp.w:call-trgt-79.t:call-trgt_plot_meth_waterfall INFO input :: name: "methylation", value: true
2025-09-15 20:25:27.104 wdl.w:ptcp.w:call-trgt-79.t:call-trgt_plot_meth_waterfall INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:25:27.104 wdl.w:ptcp.w:call-trgt-79.t:call-trgt_plot_meth_waterfall INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:25:27.104 wdl.w:ptcp.w:call-trgt-79.t:call-trgt_plot_meth_waterfall INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:25:27.104 wdl.w:ptcp.w:call-trgt-79.t:call-trgt_plot_meth_waterfall INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2176.trgt.sorted.spanning.bam.bai"
2025-09-15 20:25:27.104 wdl.w:ptcp.w:call-trgt-79.t:call-trgt_plot_meth_waterfall INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2176.trgt.sorted.spanning.bam"
2025-09-15 20:25:27.104 wdl.w:ptcp.w:call-trgt-79.t:call-trgt_plot_meth_waterfall INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2176.trgt.vcf"
2025-09-15 20:25:27.104 wdl.w:ptcp.w:call-trgt-79.t:call-trgt_plot_meth_waterfall INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2176"
2025-09-15 20:25:27.105 wdl.w:ptcp.w:call-trgt-79.t:call-trgt_plot_meth_waterfall INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:25:27.105 wdl.w:ptcp.w:call-trgt-79.t:call-trgt_plot_meth_waterfall INFO eval :: name: "plot_type", value: "waterfall"
2025-09-15 20:25:27.105 wdl.w:ptcp.w:call-trgt-79.t:call-trgt_plot_meth_waterfall INFO eval :: name: "show", value: "meth"
2025-09-15 20:25:27.105 wdl.w:ptcp.w:call-trgt-79.t:call-trgt_plot_meth_waterfall INFO eval :: name: "threads", value: 1
2025-09-15 20:25:27.105 wdl.w:ptcp.w:call-trgt-79.t:call-trgt_plot_meth_waterfall INFO eval :: name: "disk_size", value: 27
2025-09-15 20:25:27.105 wdl.w:ptcp.w:call-trgt-79.t:call-trgt_plot_meth_waterfall INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2176.meth_waterfall"
2025-09-15 20:25:27.106 wdl.w:ptcp.w:call-trgt-79.t:call-trgt_plot_meth_waterfall INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:27.106 wdl.w:ptcp.w:call-trgt-79.t:call-trgt_plot_meth_waterfall WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:27.106 wdl.w:ptcp.w:call-trgt-79.t:call-trgt_plot_meth_waterfall INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:25:27.106 wdl.w:ptcp.w:call-trgt-79.t:call-trgt_plot_meth_waterfall INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:27.109 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_plot_motifs_waterfall NOTICE done
2025-09-15 20:25:27.115 wdl.w:ptcp.w:call-trgt-70 NOTICE finish :: job: "call-trgt_plot_motifs_waterfall"
2025-09-15 20:25:27.115 wdl.w:ptcp.w:call-trgt-70 INFO output :: job: "call-trgt_plot_motifs_waterfall", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-70/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2167.motifs_waterfall.trgt_plots.zip"}
2025-09-15 20:25:27.115 wdl.w:ptcp.w:call-trgt-70 INFO visit :: node: "output-images_motifs_waterfall", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-70/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2167.motifs_waterfall.trgt_plots.zip"}
2025-09-15 20:25:27.122 wdl.w:ptcp.w:call-trgt-79.t:call-trgt_plot_motifs_allele NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-79/call-trgt_plot_motifs_allele", thread: 140612506469952
2025-09-15 20:25:27.139 wdl.w:ptcp.w:call-trgt-79.t:call-trgt_plot_motifs_allele INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:27.139 wdl.w:ptcp.w:call-trgt-79.t:call-trgt_plot_motifs_allele INFO input :: name: "waterfall", value: false
2025-09-15 20:25:27.139 wdl.w:ptcp.w:call-trgt-79.t:call-trgt_plot_motifs_allele INFO input :: name: "methylation", value: false
2025-09-15 20:25:27.139 wdl.w:ptcp.w:call-trgt-79.t:call-trgt_plot_motifs_allele INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:25:27.139 wdl.w:ptcp.w:call-trgt-79.t:call-trgt_plot_motifs_allele INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:25:27.139 wdl.w:ptcp.w:call-trgt-79.t:call-trgt_plot_motifs_allele INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:25:27.139 wdl.w:ptcp.w:call-trgt-79.t:call-trgt_plot_motifs_allele INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2176.trgt.sorted.spanning.bam.bai"
2025-09-15 20:25:27.139 wdl.w:ptcp.w:call-trgt-79.t:call-trgt_plot_motifs_allele INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2176.trgt.sorted.spanning.bam"
2025-09-15 20:25:27.139 wdl.w:ptcp.w:call-trgt-79.t:call-trgt_plot_motifs_allele INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2176.trgt.vcf"
2025-09-15 20:25:27.139 wdl.w:ptcp.w:call-trgt-79.t:call-trgt_plot_motifs_allele INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2176"
2025-09-15 20:25:27.140 wdl.w:ptcp.w:call-trgt-79.t:call-trgt_plot_motifs_allele INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:25:27.140 wdl.w:ptcp.w:call-trgt-79.t:call-trgt_plot_motifs_allele INFO eval :: name: "plot_type", value: "allele"
2025-09-15 20:25:27.140 wdl.w:ptcp.w:call-trgt-79.t:call-trgt_plot_motifs_allele INFO eval :: name: "show", value: "motifs"
2025-09-15 20:25:27.140 wdl.w:ptcp.w:call-trgt-79.t:call-trgt_plot_motifs_allele INFO eval :: name: "threads", value: 1
2025-09-15 20:25:27.140 wdl.w:ptcp.w:call-trgt-79.t:call-trgt_plot_motifs_allele INFO eval :: name: "disk_size", value: 27
2025-09-15 20:25:27.140 wdl.w:ptcp.w:call-trgt-79.t:call-trgt_plot_motifs_allele INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2176.motifs_allele"
2025-09-15 20:25:27.141 wdl.w:ptcp.w:call-trgt-79.t:call-trgt_plot_motifs_allele INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:27.141 wdl.w:ptcp.w:call-trgt-79.t:call-trgt_plot_motifs_allele WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:27.141 wdl.w:ptcp.w:call-trgt-79.t:call-trgt_plot_motifs_allele INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:25:27.141 wdl.w:ptcp.w:call-trgt-79.t:call-trgt_plot_motifs_allele INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:27.184 wdl.w:ptcp.w:call-trgt-79.t:call-trgt_plot_meth_waterfall INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-79/call-trgt_plot_meth_waterfall/_singularity_tmpdir_26b10d4g"
2025-09-15 20:25:27.184 wdl.w:ptcp.w:call-trgt-79.t:call-trgt_plot_meth_waterfall INFO Slurm invocation: srun --job-name call-trgt_plot_meth_waterfall --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-79/call-trgt_plot_meth_waterfall/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-79/call-trgt_plot_meth_waterfall/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-79/call-trgt_plot_meth_waterfall/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-79/call-trgt_plot_meth_waterfall/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-79/call-trgt_genotype/out/m84036_250809_035451_s4.bc2176.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2176.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-79/call-trgt_genotype/out/m84036_250809_035451_s4.bc2176.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2176.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-79/call-trgt_genotype/out/m84036_250809_035451_s4.bc2176.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2176.trgt.sorted.spanning.bam.bai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-79/call-trgt_plot_meth_waterfall/_singularity_tmpdir_26b10d4g/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-79/call-trgt_plot_meth_waterfall/_singularity_tmpdir_26b10d4g/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:27.200 wdl.w:ptcp.w:call-trgt-79.t:call-trgt_plot_meth_waterfall NOTICE slurm_singularity run :: pid: 1205669, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-79/call-trgt_plot_meth_waterfall/slurm_singularity.log.txt"
2025-09-15 20:25:27.210 wdl.w:ptcp.w:call-trgt-79.t:call-trgt_plot_motifs_allele INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-79/call-trgt_plot_motifs_allele/_singularity_tmpdir_6vnh28lk"
2025-09-15 20:25:27.210 wdl.w:ptcp.w:call-trgt-79.t:call-trgt_plot_motifs_allele INFO Slurm invocation: srun --job-name call-trgt_plot_motifs_allele --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-79/call-trgt_plot_motifs_allele/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-79/call-trgt_plot_motifs_allele/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-79/call-trgt_plot_motifs_allele/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-79/call-trgt_plot_motifs_allele/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-79/call-trgt_genotype/out/m84036_250809_035451_s4.bc2176.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2176.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-79/call-trgt_genotype/out/m84036_250809_035451_s4.bc2176.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2176.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-79/call-trgt_genotype/out/m84036_250809_035451_s4.bc2176.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2176.trgt.sorted.spanning.bam.bai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-79/call-trgt_plot_motifs_allele/_singularity_tmpdir_6vnh28lk/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-79/call-trgt_plot_motifs_allele/_singularity_tmpdir_6vnh28lk/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:27.217 wdl.w:ptcp.w:call-trgt-79.t:call-trgt_plot_motifs_allele NOTICE slurm_singularity run :: pid: 1205671, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-79/call-trgt_plot_motifs_allele/slurm_singularity.log.txt"
2025-09-15 20:25:27.378 wdl.w:ptcp.w:call-trgt-85.t:call-get_reads_overlapping_repeats.slurm_singularity INFO srun: job 51798011 queued and waiting for resources
2025-09-15 20:25:27.379 wdl.w:ptcp.w:call-trgt-85.t:call-get_reads_overlapping_repeats.slurm_singularity INFO srun: job 51798011 has been allocated resources
2025-09-15 20:25:27.379 wdl.w:ptcp.w:call-trgt-85.t:call-get_reads_overlapping_repeats.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:27.482 wdl.w:ptcp.w:call-trgt-85.t:call-trgt_genotype.slurm_singularity INFO srun: job 51798012 queued and waiting for resources
2025-09-15 20:25:27.483 wdl.w:ptcp.w:call-trgt-85.t:call-trgt_genotype.slurm_singularity INFO srun: job 51798012 has been allocated resources
2025-09-15 20:25:27.483 wdl.w:ptcp.w:call-trgt-85.t:call-trgt_genotype.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:27.539 wdl.w:ptcp.w:call-paraphase-92.t:call-run_paraphase.slurm_singularity INFO srun: job 51798013 queued and waiting for resources
2025-09-15 20:25:27.540 wdl.w:ptcp.w:call-paraphase-92.t:call-run_paraphase.slurm_singularity INFO srun: job 51798013 has been allocated resources
2025-09-15 20:25:27.540 wdl.w:ptcp.w:call-paraphase-92.t:call-run_paraphase.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:27.570 wdl.w:ptcp.w:call-paraphase-75.t:call-run_paraphase.stderr VERBOSE INFO:root:Processing sample m84036_250809_035451_s4.bc2172 at 2025-09-15 20:25:26.490264...
2025-09-15 20:25:27.570 wdl.w:ptcp.w:call-paraphase-75.t:call-run_paraphase.stderr VERBOSE INFO:root:Checking sample sex at 2025-09-15 20:25:26.492968...
2025-09-15 20:25:27.571 wdl.w:ptcp.w:call-paraphase-75.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for smn1 for sample m84036_250809_035451_s4.bc2172 at 2025-09-15 20:25:26.591668...
2025-09-15 20:25:27.571 wdl.w:ptcp.w:call-paraphase-75.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for smn1 for sample m84036_250809_035451_s4.bc2172 at 2025-09-15 20:25:26.592384...
2025-09-15 20:25:27.571 wdl.w:ptcp.w:call-paraphase-75.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for cyp21 for sample m84036_250809_035451_s4.bc2172 at 2025-09-15 20:25:26.591717...
2025-09-15 20:25:27.571 wdl.w:ptcp.w:call-paraphase-75.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for cyp21 for sample m84036_250809_035451_s4.bc2172 at 2025-09-15 20:25:26.592598...
2025-09-15 20:25:27.571 wdl.w:ptcp.w:call-paraphase-75.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for gba for sample m84036_250809_035451_s4.bc2172 at 2025-09-15 20:25:26.592251...
2025-09-15 20:25:27.571 wdl.w:ptcp.w:call-paraphase-75.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for gba for sample m84036_250809_035451_s4.bc2172 at 2025-09-15 20:25:26.593077...
2025-09-15 20:25:27.571 wdl.w:ptcp.w:call-paraphase-75.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for hba for sample m84036_250809_035451_s4.bc2172 at 2025-09-15 20:25:26.593760...
2025-09-15 20:25:27.571 wdl.w:ptcp.w:call-paraphase-75.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for hba for sample m84036_250809_035451_s4.bc2172 at 2025-09-15 20:25:26.594332...
2025-09-15 20:25:27.806 wdl.w:ptcp.w:call-sawfish-92.t:call-run_sawfish.stderr VERBOSE [M::bam2fq_mainloop] discarded 0 singletons
2025-09-15 20:25:27.806 wdl.w:ptcp.w:call-sawfish-92.t:call-run_sawfish.stderr VERBOSE [M::bam2fq_mainloop] processed 0 reads
2025-09-15 20:25:27.814 wdl.w:ptcp.w:call-sawfish-92.t:call-run_sawfish.slurm_singularity INFO srun: job 51798014 queued and waiting for resources
2025-09-15 20:25:27.814 wdl.w:ptcp.w:call-sawfish-92.t:call-run_sawfish.slurm_singularity INFO srun: job 51798014 has been allocated resources
2025-09-15 20:25:27.814 wdl.w:ptcp.w:call-sawfish-92.t:call-run_sawfish.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:27.814 wdl.w:ptcp.w:call-sawfish-92.t:call-run_sawfish.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:25:27.866 wdl.w:ptcp.w:call-trgt-64.t:call-trgt_plot_meth_waterfall INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2161.meth_waterfall.trgt_plots.zip"
2025-09-15 20:25:27.978 wdl.w:ptcp.w:call-trgt-79.t:call-trgt_plot_meth_allele.slurm_singularity INFO srun: job 51798015 queued and waiting for resources
2025-09-15 20:25:27.978 wdl.w:ptcp.w:call-trgt-79.t:call-trgt_plot_meth_allele.slurm_singularity INFO srun: job 51798015 has been allocated resources
2025-09-15 20:25:27.988 wdl.w:ptcp.w:call-trgt-64.t:call-trgt_plot_meth_waterfall NOTICE done
2025-09-15 20:25:27.993 wdl.w:ptcp.w:call-trgt-64 NOTICE finish :: job: "call-trgt_plot_meth_waterfall"
2025-09-15 20:25:27.993 wdl.w:ptcp.w:call-trgt-64 INFO output :: job: "call-trgt_plot_meth_waterfall", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-64/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2161.meth_waterfall.trgt_plots.zip"}
2025-09-15 20:25:27.993 wdl.w:ptcp.w:call-trgt-64 INFO visit :: node: "output-images_meth_waterfall", values: {"images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-64/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2161.meth_waterfall.trgt_plots.zip"}
2025-09-15 20:25:27.993 wdl.w:ptcp.w:call-trgt-64 INFO visit :: node: "outputs", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-64/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2161.motifs_waterfall.trgt_plots.zip", "images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-64/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2161.meth_allele.trgt_plots.zip", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-64/call-trgt_genotype/out/m84036_250809_035451_s4.bc2161.trgt.sorted.spanning.bam.bai", "images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-64/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2161.motifs_allele.trgt_plots.zip", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-64/call-trgt_genotype/out/m84036_250809_035451_s4.bc2161.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-64/call-trgt_genotype/out/m84036_250809_035451_s4.bc2161.trgt.vcf", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-64/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2161.repeats.bam", "images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-64/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2161.meth_waterfall.trgt_plots.zip", "reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-64/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2161.repeats.bam.bai"}
2025-09-15 20:25:27.999 wdl.w:ptcp.w:call-trgt-79.t:call-trgt_plot_motifs_waterfall NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-79/call-trgt_plot_motifs_waterfall", thread: 140608211502656
2025-09-15 20:25:28.021 wdl.w:ptcp.w:call-trgt-79.t:call-trgt_plot_motifs_waterfall INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:28.021 wdl.w:ptcp.w:call-trgt-79.t:call-trgt_plot_motifs_waterfall INFO input :: name: "waterfall", value: true
2025-09-15 20:25:28.021 wdl.w:ptcp.w:call-trgt-79.t:call-trgt_plot_motifs_waterfall INFO input :: name: "methylation", value: false
2025-09-15 20:25:28.021 wdl.w:ptcp.w:call-trgt-79.t:call-trgt_plot_motifs_waterfall INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:25:28.021 wdl.w:ptcp.w:call-trgt-79.t:call-trgt_plot_motifs_waterfall INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:25:28.021 wdl.w:ptcp.w:call-trgt-79.t:call-trgt_plot_motifs_waterfall INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:25:28.021 wdl.w:ptcp.w:call-trgt-79.t:call-trgt_plot_motifs_waterfall INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2176.trgt.sorted.spanning.bam.bai"
2025-09-15 20:25:28.021 wdl.w:ptcp.w:call-trgt-79.t:call-trgt_plot_motifs_waterfall INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2176.trgt.sorted.spanning.bam"
2025-09-15 20:25:28.021 wdl.w:ptcp.w:call-trgt-79.t:call-trgt_plot_motifs_waterfall INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2176.trgt.vcf"
2025-09-15 20:25:28.021 wdl.w:ptcp.w:call-trgt-79.t:call-trgt_plot_motifs_waterfall INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2176"
2025-09-15 20:25:28.022 wdl.w:ptcp.w:call-trgt-79.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:25:28.022 wdl.w:ptcp.w:call-trgt-79.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "plot_type", value: "waterfall"
2025-09-15 20:25:28.022 wdl.w:ptcp.w:call-trgt-79.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "show", value: "motifs"
2025-09-15 20:25:28.022 wdl.w:ptcp.w:call-trgt-79.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "threads", value: 1
2025-09-15 20:25:28.022 wdl.w:ptcp.w:call-trgt-79.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "disk_size", value: 27
2025-09-15 20:25:28.022 wdl.w:ptcp.w:call-trgt-79.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2176.motifs_waterfall"
2025-09-15 20:25:28.023 wdl.w:ptcp.w:call-trgt-79.t:call-trgt_plot_motifs_waterfall INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:28.023 wdl.w:ptcp.w:call-trgt-79.t:call-trgt_plot_motifs_waterfall WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:28.023 wdl.w:ptcp.w:call-trgt-79.t:call-trgt_plot_motifs_waterfall INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:25:28.023 wdl.w:ptcp.w:call-trgt-79.t:call-trgt_plot_motifs_waterfall INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:28.084 wdl.w:ptcp.w:call-trgt-72.t:call-get_reads_overlapping_repeats INFO output :: name: "reads_overlapping_repeats", value: "m84036_250809_035451_s4.bc2169.repeats.bam"
2025-09-15 20:25:28.089 wdl.w:ptcp.w:call-trgt-72.t:call-get_reads_overlapping_repeats INFO output :: name: "reads_overlapping_repeats_bai", value: "m84036_250809_035451_s4.bc2169.repeats.bam.bai"
2025-09-15 20:25:28.090 wdl.w:ptcp.w:call-trgt-68.t:call-trgt_plot_meth_allele INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2165.meth_allele.trgt_plots.zip"
2025-09-15 20:25:28.104 wdl.w:ptcp.w:call-trgt-64 NOTICE done
2025-09-15 20:25:28.109 wdl.w:ptcp NOTICE finish :: job: "call-trgt-64"
2025-09-15 20:25:28.109 wdl.w:ptcp INFO output :: job: "call-trgt-64", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-64/out/m84036_250809_035451_s4.bc2161.motifs_waterfall.trgt_plots.zip", "images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-64/out/m84036_250809_035451_s4.bc2161.meth_allele.trgt_plots.zip", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-64/out/m84036_250809_035451_s4.bc2161.trgt.sorted.spanning.bam.bai", "images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-64/out/m84036_250809_035451_s4.bc2161.motifs_allele.trgt_plots.zip", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-64/out/m84036_250809_035451_s4.bc2161.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-64/out/m84036_250809_035451_s4.bc2161.trgt.vcf", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-64/out/m84036_250809_035451_s4.bc2161.repeats.bam", "images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-64/out/m84036_250809_035451_s4.bc2161.meth_waterfall.trgt_plots.zip", "reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-64/out/m84036_250809_035451_s4.bc2161.repeats.bam.bai"}
2025-09-15 20:25:28.116 wdl.w:ptcp.w:call-trgt-94 NOTICE workflow start :: name: "trgt", source: "./trgt.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-94"
2025-09-15 20:25:28.119 wdl.w:ptcp.w:call-trgt-79.t:call-trgt_plot_motifs_waterfall INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-79/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_2u6btuw1"
2025-09-15 20:25:28.119 wdl.w:ptcp.w:call-trgt-79.t:call-trgt_plot_motifs_waterfall INFO Slurm invocation: srun --job-name call-trgt_plot_motifs_waterfall --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-79/call-trgt_plot_motifs_waterfall/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-79/call-trgt_plot_motifs_waterfall/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-79/call-trgt_plot_motifs_waterfall/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-79/call-trgt_plot_motifs_waterfall/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-79/call-trgt_genotype/out/m84036_250809_035451_s4.bc2176.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2176.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-79/call-trgt_genotype/out/m84036_250809_035451_s4.bc2176.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2176.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-79/call-trgt_genotype/out/m84036_250809_035451_s4.bc2176.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2176.trgt.sorted.spanning.bam.bai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-79/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_2u6btuw1/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-79/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_2u6btuw1/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:28.134 wdl.w:ptcp.w:call-trgt-94 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:25:28.134 wdl.w:ptcp.w:call-trgt-94 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-94/out/m84036_250809_035451_s4.bc2191.mapped.bam"}
2025-09-15 20:25:28.134 wdl.w:ptcp.w:call-trgt-94 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-94/out/m84036_250809_035451_s4.bc2191.mapped.bam.bai"}
2025-09-15 20:25:28.135 wdl.w:ptcp.w:call-trgt-94 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:25:28.135 wdl.w:ptcp.w:call-trgt-94 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:25:28.135 wdl.w:ptcp.w:call-trgt-94 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2191"}
2025-09-15 20:25:28.135 wdl.w:ptcp.w:call-trgt-94 INFO visit :: node: "decl-sex", values: {"sex": "F"}
2025-09-15 20:25:28.135 wdl.w:ptcp.w:call-trgt-94 INFO visit :: node: "decl-trgt_bed", values: {"trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"}
2025-09-15 20:25:28.135 wdl.w:ptcp.w:call-trgt-94 NOTICE ready :: job: "call-get_reads_overlapping_repeats", callee: "get_reads_overlapping_repeats"
2025-09-15 20:25:28.135 wdl.w:ptcp.w:call-trgt-94 INFO input :: job: "call-get_reads_overlapping_repeats", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-94/out/m84036_250809_035451_s4.bc2191.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-94/out/m84036_250809_035451_s4.bc2191.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2191"}
2025-09-15 20:25:28.137 wdl.w:ptcp.w:call-trgt-94 NOTICE ready :: job: "call-trgt_genotype", callee: "trgt_genotype"
2025-09-15 20:25:28.137 wdl.w:ptcp.w:call-trgt-94 INFO input :: job: "call-trgt_genotype", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-94/out/m84036_250809_035451_s4.bc2191.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-94/out/m84036_250809_035451_s4.bc2191.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2191"}
2025-09-15 20:25:28.146 wdl.w:ptcp.w:call-paraphase-79.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for smn1 for sample m84036_250809_035451_s4.bc2176 at 2025-09-15 20:25:23.631935...
2025-09-15 20:25:28.147 wdl.w:ptcp.w:call-paraphase-79.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for f8inv1 for sample m84036_250809_035451_s4.bc2176 at 2025-09-15 20:25:26.093428...
2025-09-15 20:25:28.147 wdl.w:ptcp.w:call-paraphase-79.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for f8inv1 for sample m84036_250809_035451_s4.bc2176 at 2025-09-15 20:25:26.095208...
2025-09-15 20:25:28.159 wdl.w:ptcp.w:call-trgt-79.t:call-trgt_plot_motifs_waterfall NOTICE slurm_singularity run :: pid: 1205691, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-79/call-trgt_plot_motifs_waterfall/slurm_singularity.log.txt"
2025-09-15 20:25:28.177 wdl.w:ptcp.w:call-trgt-72.t:call-get_reads_overlapping_repeats NOTICE done
2025-09-15 20:25:28.181 wdl.w:ptcp.w:call-trgt-72 NOTICE finish :: job: "call-get_reads_overlapping_repeats"
2025-09-15 20:25:28.181 wdl.w:ptcp.w:call-trgt-72 INFO output :: job: "call-get_reads_overlapping_repeats", values: {"reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-72/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2169.repeats.bam.bai", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-72/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2169.repeats.bam"}
2025-09-15 20:25:28.181 wdl.w:ptcp.w:call-trgt-72 INFO visit :: node: "output-reads_overlapping_repeats", values: {"reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-72/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2169.repeats.bam"}
2025-09-15 20:25:28.182 wdl.w:ptcp.w:call-trgt-72 INFO visit :: node: "output-reads_overlapping_repeats_bai", values: {"reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-72/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2169.repeats.bam.bai"}
2025-09-15 20:25:28.188 wdl.w:ptcp.w:call-trgt-92.t:call-get_reads_overlapping_repeats NOTICE task setup :: name: "get_reads_overlapping_repeats", source: "./trgt.wdl", line: 182, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-92/call-get_reads_overlapping_repeats", thread: 140613034948160
2025-09-15 20:25:28.207 wdl.w:ptcp.w:call-trgt-92.t:call-get_reads_overlapping_repeats INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:28.207 wdl.w:ptcp.w:call-trgt-92.t:call-get_reads_overlapping_repeats INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:25:28.207 wdl.w:ptcp.w:call-trgt-92.t:call-get_reads_overlapping_repeats INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2189.mapped.bam.bai"
2025-09-15 20:25:28.207 wdl.w:ptcp.w:call-trgt-92.t:call-get_reads_overlapping_repeats INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2189.mapped.bam"
2025-09-15 20:25:28.207 wdl.w:ptcp.w:call-trgt-92.t:call-get_reads_overlapping_repeats INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2189"
2025-09-15 20:25:28.207 wdl.w:ptcp.w:call-trgt-92.t:call-get_reads_overlapping_repeats INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:25:28.208 wdl.w:ptcp.w:call-trgt-92.t:call-get_reads_overlapping_repeats INFO eval :: name: "expand_size", value: 3000
2025-09-15 20:25:28.208 wdl.w:ptcp.w:call-trgt-92.t:call-get_reads_overlapping_repeats INFO eval :: name: "threads", value: 1
2025-09-15 20:25:28.208 wdl.w:ptcp.w:call-trgt-92.t:call-get_reads_overlapping_repeats INFO eval :: name: "expanded_bed_name", value: "m84036_250809_035451_s4.bc2189.expanded.bed"
2025-09-15 20:25:28.208 wdl.w:ptcp.w:call-trgt-92.t:call-get_reads_overlapping_repeats INFO eval :: name: "disk_size", value: 11
2025-09-15 20:25:28.208 wdl.w:ptcp.w:call-trgt-92.t:call-get_reads_overlapping_repeats INFO eval :: name: "output_name", value: "m84036_250809_035451_s4.bc2189.repeats.bam"
2025-09-15 20:25:28.208 wdl.w:ptcp.w:call-trgt-92.t:call-get_reads_overlapping_repeats INFO eval :: name: "index_name", value: "m84036_250809_035451_s4.bc2189.repeats.bam.bai"
2025-09-15 20:25:28.208 wdl.w:ptcp.w:call-trgt-92.t:call-get_reads_overlapping_repeats INFO eval :: name: "output_name_with_index", value: "m84036_250809_035451_s4.bc2189.repeats.bam##idx##m84036_250809_035451_s4.bc2189.repeats.bam.bai"
2025-09-15 20:25:28.209 wdl.w:ptcp.w:call-trgt-92.t:call-get_reads_overlapping_repeats INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:28.209 wdl.w:ptcp.w:call-trgt-92.t:call-get_reads_overlapping_repeats WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:28.209 wdl.w:ptcp.w:call-trgt-92.t:call-get_reads_overlapping_repeats INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:25:28.209 wdl.w:ptcp.w:call-trgt-92.t:call-get_reads_overlapping_repeats INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:28.213 wdl.w:ptcp.w:call-trgt-79.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO srun: job 51798016 queued and waiting for resources
2025-09-15 20:25:28.213 wdl.w:ptcp.w:call-trgt-79.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO srun: job 51798016 has been allocated resources
2025-09-15 20:25:28.213 wdl.w:ptcp.w:call-trgt-79.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:28.235 wdl.w:ptcp.w:call-trgt-79.t:call-trgt_plot_motifs_allele.slurm_singularity INFO srun: job 51798017 queued and waiting for resources
2025-09-15 20:25:28.236 wdl.w:ptcp.w:call-trgt-79.t:call-trgt_plot_motifs_allele.slurm_singularity INFO srun: job 51798017 has been allocated resources
2025-09-15 20:25:28.236 wdl.w:ptcp.w:call-trgt-79.t:call-trgt_plot_motifs_allele.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:28.244 wdl.w:ptcp.w:call-trgt-68.t:call-trgt_plot_meth_allele NOTICE done
2025-09-15 20:25:28.249 wdl.w:ptcp.w:call-trgt-68 NOTICE finish :: job: "call-trgt_plot_meth_allele"
2025-09-15 20:25:28.249 wdl.w:ptcp.w:call-trgt-68 INFO output :: job: "call-trgt_plot_meth_allele", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-68/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2165.meth_allele.trgt_plots.zip"}
2025-09-15 20:25:28.249 wdl.w:ptcp.w:call-trgt-68 INFO visit :: node: "output-images_meth_allele", values: {"images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-68/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2165.meth_allele.trgt_plots.zip"}
2025-09-15 20:25:28.256 wdl.w:ptcp.w:call-trgt-92.t:call-trgt_genotype NOTICE task setup :: name: "trgt_genotype", source: "./trgt.wdl", line: 272, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-92/call-trgt_genotype", thread: 140610367379008
2025-09-15 20:25:28.277 wdl.w:ptcp.w:call-trgt-92.t:call-trgt_genotype INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:28.277 wdl.w:ptcp.w:call-trgt-92.t:call-trgt_genotype INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:25:28.277 wdl.w:ptcp.w:call-trgt-92.t:call-trgt_genotype INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:25:28.277 wdl.w:ptcp.w:call-trgt-92.t:call-trgt_genotype INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:25:28.278 wdl.w:ptcp.w:call-trgt-92.t:call-trgt_genotype INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2189.mapped.bam.bai"
2025-09-15 20:25:28.278 wdl.w:ptcp.w:call-trgt-92.t:call-trgt_genotype INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2189.mapped.bam"
2025-09-15 20:25:28.278 wdl.w:ptcp.w:call-trgt-92.t:call-trgt_genotype INFO input :: name: "sex", value: "F"
2025-09-15 20:25:28.278 wdl.w:ptcp.w:call-trgt-92.t:call-trgt_genotype INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2189"
2025-09-15 20:25:28.278 wdl.w:ptcp.w:call-trgt-92.t:call-trgt_genotype INFO eval :: name: "mem_gb", value: 16
2025-09-15 20:25:28.278 wdl.w:ptcp.w:call-trgt-92.t:call-trgt_genotype INFO eval :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2189.trgt"
2025-09-15 20:25:28.278 wdl.w:ptcp.w:call-trgt-92.t:call-trgt_genotype INFO eval :: name: "threads", value: 8
2025-09-15 20:25:28.279 wdl.w:ptcp.w:call-trgt-92.t:call-trgt_genotype INFO eval :: name: "disk_size", value: 27
2025-09-15 20:25:28.279 wdl.w:ptcp.w:call-trgt-92.t:call-trgt_genotype INFO eval :: name: "karyotype", value: "XX"
2025-09-15 20:25:28.279 wdl.w:ptcp.w:call-trgt-92.t:call-trgt_genotype INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 8, memory_reservation: 16000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:28.279 wdl.w:ptcp.w:call-trgt-92.t:call-trgt_genotype WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:28.279 wdl.w:ptcp.w:call-trgt-92.t:call-trgt_genotype INFO provisioned :: seconds_waited: 0, cpu: 8, mem_bytes: 16000000000
2025-09-15 20:25:28.279 wdl.w:ptcp.w:call-trgt-92.t:call-trgt_genotype INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:28.280 wdl.w:ptcp.w:call-trgt-92.t:call-get_reads_overlapping_repeats INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 9, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-92/call-get_reads_overlapping_repeats/_singularity_tmpdir_gzc5nh8w"
2025-09-15 20:25:28.281 wdl.w:ptcp.w:call-trgt-92.t:call-get_reads_overlapping_repeats INFO Slurm invocation: srun --job-name call-get_reads_overlapping_repeats --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-92/call-get_reads_overlapping_repeats/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-92/call-get_reads_overlapping_repeats/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-92/call-get_reads_overlapping_repeats/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-92/call-get_reads_overlapping_repeats/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-92/out/m84036_250809_035451_s4.bc2189.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2189.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-92/out/m84036_250809_035451_s4.bc2189.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2189.mapped.bam.bai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-92/call-get_reads_overlapping_repeats/_singularity_tmpdir_gzc5nh8w/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-92/call-get_reads_overlapping_repeats/_singularity_tmpdir_gzc5nh8w/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:28.304 wdl.w:ptcp.w:call-trgt-92.t:call-get_reads_overlapping_repeats NOTICE slurm_singularity run :: pid: 1205693, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-92/call-get_reads_overlapping_repeats/slurm_singularity.log.txt"
2025-09-15 20:25:28.357 wdl.w:ptcp.w:call-trgt-92.t:call-trgt_genotype INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 11, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-92/call-trgt_genotype/_singularity_tmpdir_jbxhvhrm"
2025-09-15 20:25:28.357 wdl.w:ptcp.w:call-trgt-92.t:call-trgt_genotype INFO Slurm invocation: srun --job-name call-trgt_genotype --partition compute,compute9 --cpus-per-task 8 --mem 15259M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-92/call-trgt_genotype/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-92/call-trgt_genotype/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-92/call-trgt_genotype/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-92/call-trgt_genotype/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-92/out/m84036_250809_035451_s4.bc2189.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2189.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-92/out/m84036_250809_035451_s4.bc2189.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2189.mapped.bam.bai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-92/call-trgt_genotype/_singularity_tmpdir_jbxhvhrm/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-92/call-trgt_genotype/_singularity_tmpdir_jbxhvhrm/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:28.367 wdl.w:ptcp.w:call-trgt-92.t:call-trgt_genotype NOTICE slurm_singularity run :: pid: 1205695, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-92/call-trgt_genotype/slurm_singularity.log.txt"
2025-09-15 20:25:28.628 wdl.w:ptcp.w:call-paraphase-62.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for smn1 for sample m84036_250809_035451_s4.bc2159 at 2025-09-15 20:25:07.417867...
2025-09-15 20:25:28.821 wdl.w:ptcp.w:call-paraphase-81.t:call-run_paraphase INFO output :: name: "paraphase_bam", value: "m84036_250809_035451_s4.bc2178_paraphase/m84036_250809_035451_s4.bc2178.paraphase.bam"
2025-09-15 20:25:28.828 wdl.w:ptcp.w:call-paraphase-81.t:call-run_paraphase INFO output :: name: "paraphase_bam_bai", value: "m84036_250809_035451_s4.bc2178_paraphase/m84036_250809_035451_s4.bc2178.paraphase.bam.bai"
2025-09-15 20:25:28.829 wdl.w:ptcp.w:call-paraphase-81.t:call-run_paraphase INFO output :: name: "paraphase_json", value: "m84036_250809_035451_s4.bc2178_paraphase/m84036_250809_035451_s4.bc2178.paraphase.json"
2025-09-15 20:25:28.831 wdl.w:ptcp.w:call-paraphase-81.t:call-run_paraphase INFO output :: name: "paraphase_vcfs", value: []
2025-09-15 20:25:28.831 wdl.w:ptcp.w:call-paraphase-81.t:call-run_paraphase INFO output :: name: "havanno_json", value: "m84036_250809_035451_s4.bc2178.havanno.json"
2025-09-15 20:25:28.854 wdl.w:ptcp.w:call-trgt-68.t:call-trgt_plot_motifs_waterfall INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2165.motifs_waterfall.trgt_plots.zip"
2025-09-15 20:25:28.929 wdl.w:ptcp.w:call-paraphase-81.t:call-run_paraphase NOTICE done
2025-09-15 20:25:28.935 wdl.w:ptcp.w:call-paraphase-81 NOTICE finish :: job: "call-run_paraphase"
2025-09-15 20:25:28.936 wdl.w:ptcp.w:call-paraphase-81 INFO output :: job: "call-run_paraphase", values: {"havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-81/call-run_paraphase/out/m84036_250809_035451_s4.bc2178.havanno.json", "paraphase_vcfs": [], "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-81/call-run_paraphase/out/m84036_250809_035451_s4.bc2178_paraphase/m84036_250809_035451_s4.bc2178.paraphase.json", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-81/call-run_paraphase/out/m84036_250809_035451_s4.bc2178_paraphase/m84036_250809_035451_s4.bc2178.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-81/call-run_paraphase/out/m84036_250809_035451_s4.bc2178_paraphase/m84036_250809_035451_s4.bc2178.paraphase.bam"}
2025-09-15 20:25:28.936 wdl.w:ptcp.w:call-paraphase-81 NOTICE ready :: job: "call-call_f8", callee: "call_f8"
2025-09-15 20:25:28.936 wdl.w:ptcp.w:call-paraphase-81 INFO input :: job: "call-call_f8", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "out_prefix": "m84036_250809_035451_s4.bc2178", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-81/call-run_paraphase/out/m84036_250809_035451_s4.bc2178_paraphase/m84036_250809_035451_s4.bc2178.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-81/call-run_paraphase/out/m84036_250809_035451_s4.bc2178_paraphase/m84036_250809_035451_s4.bc2178.paraphase.bam", "sex": "F"}
2025-09-15 20:25:28.938 wdl.w:ptcp.w:call-paraphase-81 INFO visit :: node: "output-havanno_json", values: {"havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-81/call-run_paraphase/out/m84036_250809_035451_s4.bc2178.havanno.json"}
2025-09-15 20:25:28.938 wdl.w:ptcp.w:call-paraphase-81 INFO visit :: node: "output-paraphase_bam", values: {"paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-81/call-run_paraphase/out/m84036_250809_035451_s4.bc2178_paraphase/m84036_250809_035451_s4.bc2178.paraphase.bam"}
2025-09-15 20:25:28.938 wdl.w:ptcp.w:call-paraphase-81 INFO visit :: node: "output-paraphase_bam_bai", values: {"paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-81/call-run_paraphase/out/m84036_250809_035451_s4.bc2178_paraphase/m84036_250809_035451_s4.bc2178.paraphase.bam.bai"}
2025-09-15 20:25:28.938 wdl.w:ptcp.w:call-paraphase-81 INFO visit :: node: "output-paraphase_json", values: {"paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-81/call-run_paraphase/out/m84036_250809_035451_s4.bc2178_paraphase/m84036_250809_035451_s4.bc2178.paraphase.json"}
2025-09-15 20:25:28.938 wdl.w:ptcp.w:call-paraphase-81 INFO visit :: node: "output-paraphase_vcfs", values: {"paraphase_vcfs": []}
2025-09-15 20:25:28.943 wdl.w:ptcp.w:call-paraphase-91.t:call-run_paraphase NOTICE task setup :: name: "run_paraphase", source: "./paraphase.wdl", line: 127, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-91/call-run_paraphase", thread: 140608739980864
2025-09-15 20:25:28.963 wdl.w:ptcp.w:call-paraphase-91.t:call-run_paraphase INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:28.963 wdl.w:ptcp.w:call-paraphase-91.t:call-run_paraphase INFO input :: name: "annotation_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf"
2025-09-15 20:25:28.963 wdl.w:ptcp.w:call-paraphase-91.t:call-run_paraphase INFO input :: name: "genome_version", value: "38"
2025-09-15 20:25:28.963 wdl.w:ptcp.w:call-paraphase-91.t:call-run_paraphase INFO input :: name: "config_file", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/paraphase_config.GRCh38.yaml"
2025-09-15 20:25:28.963 wdl.w:ptcp.w:call-paraphase-91.t:call-run_paraphase INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:25:28.963 wdl.w:ptcp.w:call-paraphase-91.t:call-run_paraphase INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:25:28.963 wdl.w:ptcp.w:call-paraphase-91.t:call-run_paraphase INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2188.mapped.bam.bai"
2025-09-15 20:25:28.963 wdl.w:ptcp.w:call-paraphase-91.t:call-run_paraphase INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2188.mapped.bam"
2025-09-15 20:25:28.963 wdl.w:ptcp.w:call-paraphase-91.t:call-run_paraphase INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2188"
2025-09-15 20:25:28.964 wdl.w:ptcp.w:call-paraphase-91.t:call-run_paraphase INFO eval :: name: "threads", value: 4
2025-09-15 20:25:28.964 wdl.w:ptcp.w:call-paraphase-91.t:call-run_paraphase INFO eval :: name: "mem_gb", value: 8
2025-09-15 20:25:28.964 wdl.w:ptcp.w:call-paraphase-91.t:call-run_paraphase INFO eval :: name: "disk_size", value: 27
2025-09-15 20:25:28.964 wdl.w:ptcp.w:call-paraphase-91.t:call-run_paraphase INFO eval :: name: "out_dir", value: "m84036_250809_035451_s4.bc2188_paraphase"
2025-09-15 20:25:28.964 wdl.w:ptcp.w:call-paraphase-91.t:call-run_paraphase INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 4, memory_reservation: 8000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:28.965 wdl.w:ptcp.w:call-paraphase-91.t:call-run_paraphase WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:28.965 wdl.w:ptcp.w:call-paraphase-91.t:call-run_paraphase INFO provisioned :: seconds_waited: 0, cpu: 4, mem_bytes: 8000000000
2025-09-15 20:25:28.965 wdl.w:ptcp.w:call-paraphase-91.t:call-run_paraphase INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:28.985 wdl.w:ptcp.w:call-trgt-68.t:call-trgt_plot_motifs_waterfall NOTICE done
2025-09-15 20:25:28.990 wdl.w:ptcp.w:call-trgt-68 NOTICE finish :: job: "call-trgt_plot_motifs_waterfall"
2025-09-15 20:25:28.991 wdl.w:ptcp.w:call-trgt-68 INFO output :: job: "call-trgt_plot_motifs_waterfall", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-68/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2165.motifs_waterfall.trgt_plots.zip"}
2025-09-15 20:25:28.991 wdl.w:ptcp.w:call-trgt-68 INFO visit :: node: "output-images_motifs_waterfall", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-68/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2165.motifs_waterfall.trgt_plots.zip"}
2025-09-15 20:25:28.998 wdl.w:ptcp.w:call-trgt-79.t:call-trgt_plot_meth_allele.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:29.001 wdl.w:ptcp.w:call-paraphase-68.t:call-call_f8 NOTICE task setup :: name: "call_f8", source: "./paraphase.wdl", line: 232, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-68/call-call_f8", thread: 140610912642624
2025-09-15 20:25:29.011 wdl.w:ptcp.w:call-sawfish-43.t:call-run_sawfish.stderr VERBOSE [M::mm_idx_stat::47.974*1.58] distinct minimizers: 214664461 (92.23% are singletons); average occurrences: 1.372; average spacing: 10.529; total length: 3099922541
2025-09-15 20:25:29.011 wdl.w:ptcp.w:call-sawfish-43.t:call-run_sawfish.stderr VERBOSE [M::bam2fq_mainloop] discarded 0 singletons
2025-09-15 20:25:29.011 wdl.w:ptcp.w:call-sawfish-43.t:call-run_sawfish.stderr VERBOSE [M::bam2fq_mainloop] processed 277 reads
2025-09-15 20:25:29.021 wdl.w:ptcp.w:call-paraphase-68.t:call-call_f8 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:29.022 wdl.w:ptcp.w:call-paraphase-68.t:call-call_f8 INFO input :: name: "genome_version", value: "38"
2025-09-15 20:25:29.022 wdl.w:ptcp.w:call-paraphase-68.t:call-call_f8 INFO input :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2165"
2025-09-15 20:25:29.022 wdl.w:ptcp.w:call-paraphase-68.t:call-call_f8 INFO input :: name: "paraphase_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2165.paraphase.bam.bai"
2025-09-15 20:25:29.022 wdl.w:ptcp.w:call-paraphase-68.t:call-call_f8 INFO input :: name: "paraphase_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2165.paraphase.bam"
2025-09-15 20:25:29.022 wdl.w:ptcp.w:call-paraphase-68.t:call-call_f8 INFO input :: name: "sex", value: "F"
2025-09-15 20:25:29.022 wdl.w:ptcp.w:call-paraphase-68.t:call-call_f8 INFO eval :: name: "threads", value: 1
2025-09-15 20:25:29.022 wdl.w:ptcp.w:call-paraphase-68.t:call-call_f8 INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:25:29.022 wdl.w:ptcp.w:call-paraphase-68.t:call-call_f8 INFO eval :: name: "disk_size", value: 11
2025-09-15 20:25:29.022 wdl.w:ptcp.w:call-paraphase-68.t:call-call_f8 INFO eval :: name: "sample_sex", value: "F"
2025-09-15 20:25:29.023 wdl.w:ptcp.w:call-paraphase-68.t:call-call_f8 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:29.023 wdl.w:ptcp.w:call-paraphase-68.t:call-call_f8 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:29.023 wdl.w:ptcp.w:call-paraphase-68.t:call-call_f8 INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:25:29.023 wdl.w:ptcp.w:call-paraphase-68.t:call-call_f8 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:29.049 wdl.w:ptcp.w:call-paraphase-91.t:call-run_paraphase INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-91/call-run_paraphase/_singularity_tmpdir_036zg14_"
2025-09-15 20:25:29.049 wdl.w:ptcp.w:call-paraphase-91.t:call-run_paraphase INFO Slurm invocation: srun --job-name call-run_paraphase --partition compute,compute9 --cpus-per-task 4 --mem 7629M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-91/call-run_paraphase/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-91/call-run_paraphase/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-91/call-run_paraphase/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-91/call-run_paraphase/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-91/out/m84036_250809_035451_s4.bc2188.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2188.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-91/out/m84036_250809_035451_s4.bc2188.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2188.mapped.bam:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/variant_list/variant_list.GRCh38.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf:ro --bind /ptcp/meta/paraphase/paraphase_config.GRCh38.yaml:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/paraphase_config.GRCh38.yaml:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-91/call-run_paraphase/_singularity_tmpdir_036zg14_/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-91/call-run_paraphase/_singularity_tmpdir_036zg14_/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:29.081 wdl.w:ptcp.w:call-sawfish-55.t:call-run_sawfish.stderr VERBOSE [M::mm_idx_stat::47.796*1.59] distinct minimizers: 214664461 (92.23% are singletons); average occurrences: 1.372; average spacing: 10.529; total length: 3099922541
2025-09-15 20:25:29.081 wdl.w:ptcp.w:call-sawfish-55.t:call-run_sawfish.stderr VERBOSE [M::bam2fq_mainloop] discarded 0 singletons
2025-09-15 20:25:29.081 wdl.w:ptcp.w:call-sawfish-55.t:call-run_sawfish.stderr VERBOSE [M::bam2fq_mainloop] processed 162 reads
2025-09-15 20:25:29.081 wdl.w:ptcp.w:call-sawfish-55.t:call-run_sawfish.stderr VERBOSE [M::worker_pipeline::48.010*1.59] mapped 162 sequences
2025-09-15 20:25:29.081 wdl.w:ptcp.w:call-sawfish-55.t:call-run_sawfish.stderr VERBOSE [M::main] Version: 2.26-r1175
2025-09-15 20:25:29.081 wdl.w:ptcp.w:call-paraphase-68.t:call-call_f8 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 8, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-68/call-call_f8/_singularity_tmpdir_8rscqqyr"
2025-09-15 20:25:29.081 wdl.w:ptcp.w:call-sawfish-55.t:call-run_sawfish.stderr VERBOSE [M::main] CMD: /opt/pacbio/smrttools/install/smrtlink-release_25.1.0.257715/bundles/smrttools/install/smrttools-release_25.1.0.257715/private/thirdparty/minimap2/minimap2_2.26-pacbio2/binwrap/../../../../../private/thirdparty/minimap2/minimap2_2.26-pacbio2/bin/minimap2 -a -y -x map-hifi -Y -E 1,0 /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa -
2025-09-15 20:25:29.081 wdl.w:ptcp.w:call-paraphase-68.t:call-call_f8 INFO Slurm invocation: srun --job-name call-call_f8 --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-68/call-call_f8/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-68/call-call_f8/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-68/call-call_f8/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-68/call-call_f8/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-68/call-run_paraphase/out/m84036_250809_035451_s4.bc2165_paraphase/m84036_250809_035451_s4.bc2165.paraphase.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2165.paraphase.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-68/call-run_paraphase/out/m84036_250809_035451_s4.bc2165_paraphase/m84036_250809_035451_s4.bc2165.paraphase.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2165.paraphase.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-68/call-call_f8/_singularity_tmpdir_8rscqqyr/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-68/call-call_f8/_singularity_tmpdir_8rscqqyr/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:29.082 wdl.w:ptcp.w:call-sawfish-55.t:call-run_sawfish.stderr VERBOSE [M::main] Real time: 48.277 sec; CPU: 76.532 sec; Peak RSS: 11.886 GB
2025-09-15 20:25:29.089 wdl.w:ptcp.w:call-paraphase-91.t:call-run_paraphase NOTICE slurm_singularity run :: pid: 1205714, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-91/call-run_paraphase/slurm_singularity.log.txt"
2025-09-15 20:25:29.090 wdl.w:ptcp.w:call-paraphase-68.t:call-call_f8 NOTICE slurm_singularity run :: pid: 1205715, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-68/call-call_f8/slurm_singularity.log.txt"
2025-09-15 20:25:29.172 wdl.w:ptcp.w:call-trgt-79.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO srun: job 51798018 queued and waiting for resources
2025-09-15 20:25:29.172 wdl.w:ptcp.w:call-trgt-79.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO srun: job 51798018 has been allocated resources
2025-09-15 20:25:29.172 wdl.w:ptcp.w:call-trgt-79.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:29.206 wdl.w:ptcp.w:call-paraphase-80.t:call-run_paraphase INFO output :: name: "paraphase_bam", value: "m84036_250809_035451_s4.bc2177_paraphase/m84036_250809_035451_s4.bc2177.paraphase.bam"
2025-09-15 20:25:29.211 wdl.w:ptcp.w:call-paraphase-80.t:call-run_paraphase INFO output :: name: "paraphase_bam_bai", value: "m84036_250809_035451_s4.bc2177_paraphase/m84036_250809_035451_s4.bc2177.paraphase.bam.bai"
2025-09-15 20:25:29.213 wdl.w:ptcp.w:call-paraphase-80.t:call-run_paraphase INFO output :: name: "paraphase_json", value: "m84036_250809_035451_s4.bc2177_paraphase/m84036_250809_035451_s4.bc2177.paraphase.json"
2025-09-15 20:25:29.215 wdl.w:ptcp.w:call-paraphase-80.t:call-run_paraphase INFO output :: name: "paraphase_vcfs", value: []
2025-09-15 20:25:29.215 wdl.w:ptcp.w:call-paraphase-80.t:call-run_paraphase INFO output :: name: "havanno_json", value: "m84036_250809_035451_s4.bc2177.havanno.json"
2025-09-15 20:25:29.230 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_plot_meth_waterfall INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2167.meth_waterfall.trgt_plots.zip"
2025-09-15 20:25:29.315 wdl.w:ptcp.w:call-trgt-92.t:call-get_reads_overlapping_repeats.slurm_singularity INFO srun: job 51798019 queued and waiting for resources
2025-09-15 20:25:29.315 wdl.w:ptcp.w:call-trgt-92.t:call-get_reads_overlapping_repeats.slurm_singularity INFO srun: job 51798019 has been allocated resources
2025-09-15 20:25:29.315 wdl.w:ptcp.w:call-trgt-92.t:call-get_reads_overlapping_repeats.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:29.325 wdl.w:ptcp.w:call-paraphase-80.t:call-run_paraphase NOTICE done
2025-09-15 20:25:29.326 wdl.w:ptcp.w:call-trgt-70.t:call-trgt_plot_meth_waterfall NOTICE done
2025-09-15 20:25:29.331 wdl.w:ptcp.w:call-trgt-70 NOTICE finish :: job: "call-trgt_plot_meth_waterfall"
2025-09-15 20:25:29.332 wdl.w:ptcp.w:call-trgt-70 INFO output :: job: "call-trgt_plot_meth_waterfall", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-70/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2167.meth_waterfall.trgt_plots.zip"}
2025-09-15 20:25:29.332 wdl.w:ptcp.w:call-trgt-70 INFO visit :: node: "output-images_meth_waterfall", values: {"images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-70/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2167.meth_waterfall.trgt_plots.zip"}
2025-09-15 20:25:29.332 wdl.w:ptcp.w:call-trgt-70 INFO visit :: node: "outputs", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-70/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2167.motifs_waterfall.trgt_plots.zip", "images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-70/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2167.meth_allele.trgt_plots.zip", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-70/call-trgt_genotype/out/m84036_250809_035451_s4.bc2167.trgt.sorted.spanning.bam.bai", "images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-70/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2167.motifs_allele.trgt_plots.zip", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-70/call-trgt_genotype/out/m84036_250809_035451_s4.bc2167.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-70/call-trgt_genotype/out/m84036_250809_035451_s4.bc2167.trgt.vcf", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-70/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2167.repeats.bam", "images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-70/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2167.meth_waterfall.trgt_plots.zip", "reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-70/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2167.repeats.bam.bai"}
2025-09-15 20:25:29.338 wdl.w:ptcp.t:call-tar_outputs-17 NOTICE task setup :: name: "tar_outputs", source: "./common.wdl", line: 279, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-17", thread: 140610870679104
2025-09-15 20:25:29.359 wdl.w:ptcp.w:call-paraphase-80 NOTICE finish :: job: "call-run_paraphase"
2025-09-15 20:25:29.359 wdl.w:ptcp.w:call-paraphase-80 INFO output :: job: "call-run_paraphase", values: {"havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-80/call-run_paraphase/out/m84036_250809_035451_s4.bc2177.havanno.json", "paraphase_vcfs": [], "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-80/call-run_paraphase/out/m84036_250809_035451_s4.bc2177_paraphase/m84036_250809_035451_s4.bc2177.paraphase.json", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-80/call-run_paraphase/out/m84036_250809_035451_s4.bc2177_paraphase/m84036_250809_035451_s4.bc2177.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-80/call-run_paraphase/out/m84036_250809_035451_s4.bc2177_paraphase/m84036_250809_035451_s4.bc2177.paraphase.bam"}
2025-09-15 20:25:29.360 wdl.w:ptcp.w:call-paraphase-80 NOTICE ready :: job: "call-call_f8", callee: "call_f8"
2025-09-15 20:25:29.360 wdl.w:ptcp.w:call-paraphase-80 INFO input :: job: "call-call_f8", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "out_prefix": "m84036_250809_035451_s4.bc2177", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-80/call-run_paraphase/out/m84036_250809_035451_s4.bc2177_paraphase/m84036_250809_035451_s4.bc2177.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-80/call-run_paraphase/out/m84036_250809_035451_s4.bc2177_paraphase/m84036_250809_035451_s4.bc2177.paraphase.bam", "sex": "F"}
2025-09-15 20:25:29.362 wdl.w:ptcp.w:call-paraphase-80 INFO visit :: node: "output-havanno_json", values: {"havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-80/call-run_paraphase/out/m84036_250809_035451_s4.bc2177.havanno.json"}
2025-09-15 20:25:29.362 wdl.w:ptcp.w:call-paraphase-80 INFO visit :: node: "output-paraphase_bam", values: {"paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-80/call-run_paraphase/out/m84036_250809_035451_s4.bc2177_paraphase/m84036_250809_035451_s4.bc2177.paraphase.bam"}
2025-09-15 20:25:29.362 wdl.w:ptcp.w:call-paraphase-80 INFO visit :: node: "output-paraphase_bam_bai", values: {"paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-80/call-run_paraphase/out/m84036_250809_035451_s4.bc2177_paraphase/m84036_250809_035451_s4.bc2177.paraphase.bam.bai"}
2025-09-15 20:25:29.362 wdl.w:ptcp.w:call-paraphase-80 INFO visit :: node: "output-paraphase_json", values: {"paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-80/call-run_paraphase/out/m84036_250809_035451_s4.bc2177_paraphase/m84036_250809_035451_s4.bc2177.paraphase.json"}
2025-09-15 20:25:29.362 wdl.w:ptcp.w:call-paraphase-80 INFO visit :: node: "output-paraphase_vcfs", values: {"paraphase_vcfs": []}
2025-09-15 20:25:29.364 wdl.w:ptcp.t:call-tar_outputs-17 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:29.364 wdl.w:ptcp.t:call-tar_outputs-17 INFO input :: name: "sawfish_vcf_tbi", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2114.sv.vcf.gz.tbi"
2025-09-15 20:25:29.364 wdl.w:ptcp.t:call-tar_outputs-17 INFO input :: name: "sawfish_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2114.sv.vcf.gz"
2025-09-15 20:25:29.364 wdl.w:ptcp.t:call-tar_outputs-17 INFO input :: name: "f8_json", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2114.f8inversion.json"
2025-09-15 20:25:29.365 wdl.w:ptcp.t:call-tar_outputs-17 INFO input :: name: "paraphase_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2114.paraphase.bam.bai"
2025-09-15 20:25:29.365 wdl.w:ptcp.t:call-tar_outputs-17 INFO input :: name: "paraphase_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2114.paraphase.bam"
2025-09-15 20:25:29.365 wdl.w:ptcp.t:call-tar_outputs-17 INFO input :: name: "paraphase_json", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2114.paraphase.json"
2025-09-15 20:25:29.365 wdl.w:ptcp.t:call-tar_outputs-17 INFO input :: name: "trgt_spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2114.trgt.sorted.spanning.bam.bai"
2025-09-15 20:25:29.365 wdl.w:ptcp.t:call-tar_outputs-17 INFO input :: name: "trgt_spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2114.trgt.sorted.spanning.bam"
2025-09-15 20:25:29.365 wdl.w:ptcp.t:call-tar_outputs-17 INFO input :: name: "trgt_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2114.trgt.vcf"
2025-09-15 20:25:29.365 wdl.w:ptcp.t:call-tar_outputs-17 INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2114.mapped.bam.bai"
2025-09-15 20:25:29.365 wdl.w:ptcp.t:call-tar_outputs-17 INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2114.mapped.bam"
2025-09-15 20:25:29.365 wdl.w:ptcp.t:call-tar_outputs-17 INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2114"
2025-09-15 20:25:29.365 wdl.w:ptcp.t:call-tar_outputs-17 INFO eval :: name: "threads", value: 1
2025-09-15 20:25:29.365 wdl.w:ptcp.t:call-tar_outputs-17 INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:25:29.366 wdl.w:ptcp.t:call-tar_outputs-17 INFO eval :: name: "disk_size", value: 6
2025-09-15 20:25:29.366 wdl.w:ptcp.t:call-tar_outputs-17 INFO eval :: name: "output_tarball", value: "m84036_250809_035451_s4.bc2114.tar"
2025-09-15 20:25:29.366 wdl.w:ptcp.t:call-tar_outputs-17 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:29.366 wdl.w:ptcp.t:call-tar_outputs-17 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:29.366 wdl.w:ptcp.w:call-sawfish-91.t:call-run_sawfish NOTICE task setup :: name: "run_sawfish", source: "./sawfish.wdl", line: 83, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-91/call-run_sawfish", thread: 140610895857216
2025-09-15 20:25:29.367 wdl.w:ptcp.t:call-tar_outputs-17 INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:25:29.367 wdl.w:ptcp.t:call-tar_outputs-17 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:29.378 wdl.w:ptcp.w:call-trgt-92.t:call-trgt_genotype.slurm_singularity INFO srun: job 51798020 queued and waiting for resources
2025-09-15 20:25:29.378 wdl.w:ptcp.w:call-trgt-92.t:call-trgt_genotype.slurm_singularity INFO srun: job 51798020 has been allocated resources
2025-09-15 20:25:29.378 wdl.w:ptcp.w:call-trgt-92.t:call-trgt_genotype.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:29.392 wdl.w:ptcp.w:call-sawfish-91.t:call-run_sawfish INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:29.392 wdl.w:ptcp.w:call-sawfish-91.t:call-run_sawfish INFO input :: name: "genome_version", value: "38"
2025-09-15 20:25:29.392 wdl.w:ptcp.w:call-sawfish-91.t:call-run_sawfish INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:25:29.392 wdl.w:ptcp.w:call-sawfish-91.t:call-run_sawfish INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:25:29.392 wdl.w:ptcp.w:call-sawfish-91.t:call-run_sawfish INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2188.mapped.bam.bai"
2025-09-15 20:25:29.392 wdl.w:ptcp.w:call-sawfish-91.t:call-run_sawfish INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2188.mapped.bam"
2025-09-15 20:25:29.392 wdl.w:ptcp.w:call-sawfish-91.t:call-run_sawfish INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2188"
2025-09-15 20:25:29.394 wdl.w:ptcp.w:call-sawfish-91.t:call-run_sawfish INFO eval :: name: "mem_gb", value: 32
2025-09-15 20:25:29.395 wdl.w:ptcp.w:call-sawfish-91.t:call-run_sawfish INFO eval :: name: "threads", value: 16
2025-09-15 20:25:29.395 wdl.w:ptcp.w:call-sawfish-91.t:call-run_sawfish INFO eval :: name: "disk_size", value: 30
2025-09-15 20:25:29.395 wdl.w:ptcp.w:call-sawfish-91.t:call-run_sawfish INFO eval :: name: "discover_dirname", value: "m84036_250809_035451_s4.bc2188_sawfish_discover"
2025-09-15 20:25:29.395 wdl.w:ptcp.w:call-sawfish-91.t:call-run_sawfish INFO eval :: name: "call_dirname", value: "m84036_250809_035451_s4.bc2188_sawfish"
2025-09-15 20:25:29.395 wdl.w:ptcp.w:call-sawfish-91.t:call-run_sawfish INFO eval :: name: "minimap2_bam_filename", value: "m84036_250809_035451_s4.bc2188.minimap2.bam"
2025-09-15 20:25:29.396 wdl.w:ptcp.w:call-sawfish-91.t:call-run_sawfish INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 16, memory_reservation: 32000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:29.396 wdl.w:ptcp.w:call-sawfish-91.t:call-run_sawfish WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:29.396 wdl.w:ptcp.w:call-sawfish-91.t:call-run_sawfish INFO provisioned :: seconds_waited: 0, cpu: 16, mem_bytes: 32000000000
2025-09-15 20:25:29.396 wdl.w:ptcp.w:call-sawfish-91.t:call-run_sawfish INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:29.445 wdl.w:ptcp.w:call-trgt-70 NOTICE done
2025-09-15 20:25:29.449 wdl.w:ptcp NOTICE finish :: job: "call-trgt-70"
2025-09-15 20:25:29.450 wdl.w:ptcp INFO output :: job: "call-trgt-70", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-70/out/m84036_250809_035451_s4.bc2167.motifs_waterfall.trgt_plots.zip", "images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-70/out/m84036_250809_035451_s4.bc2167.meth_allele.trgt_plots.zip", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-70/out/m84036_250809_035451_s4.bc2167.trgt.sorted.spanning.bam.bai", "images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-70/out/m84036_250809_035451_s4.bc2167.motifs_allele.trgt_plots.zip", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-70/out/m84036_250809_035451_s4.bc2167.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-70/out/m84036_250809_035451_s4.bc2167.trgt.vcf", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-70/out/m84036_250809_035451_s4.bc2167.repeats.bam", "images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-70/out/m84036_250809_035451_s4.bc2167.meth_waterfall.trgt_plots.zip", "reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-70/out/m84036_250809_035451_s4.bc2167.repeats.bam.bai"}
2025-09-15 20:25:29.457 wdl.w:ptcp.w:call-paraphase-90 NOTICE workflow start :: name: "paraphase", source: "./paraphase.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-90"
2025-09-15 20:25:29.471 wdl.w:ptcp.w:call-paraphase-90 INFO visit :: node: "decl-annotation_vcf", values: {"annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf"}
2025-09-15 20:25:29.472 wdl.w:ptcp.w:call-paraphase-90 INFO visit :: node: "decl-config_file", values: {"config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml"}
2025-09-15 20:25:29.472 wdl.w:ptcp.w:call-paraphase-90 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:25:29.472 wdl.w:ptcp.w:call-paraphase-90 INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:25:29.472 wdl.w:ptcp.w:call-paraphase-90 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-90/out/m84036_250809_035451_s4.bc2187.mapped.bam"}
2025-09-15 20:25:29.472 wdl.w:ptcp.w:call-paraphase-90 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-90/out/m84036_250809_035451_s4.bc2187.mapped.bam.bai"}
2025-09-15 20:25:29.472 wdl.w:ptcp.w:call-paraphase-90 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:25:29.472 wdl.w:ptcp.w:call-paraphase-90 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:25:29.472 wdl.w:ptcp.w:call-paraphase-90 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2187"}
2025-09-15 20:25:29.472 wdl.w:ptcp.w:call-paraphase-90 INFO visit :: node: "decl-sex", values: {"sex": "F"}
2025-09-15 20:25:29.472 wdl.w:ptcp.w:call-paraphase-90 NOTICE ready :: job: "call-run_paraphase", callee: "run_paraphase"
2025-09-15 20:25:29.473 wdl.w:ptcp.w:call-paraphase-90 INFO input :: job: "call-run_paraphase", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf", "genome_version": "38", "config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-90/out/m84036_250809_035451_s4.bc2187.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-90/out/m84036_250809_035451_s4.bc2187.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2187"}
2025-09-15 20:25:29.473 wdl.w:ptcp.w:call-sawfish-91.t:call-run_sawfish INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 10, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-91/call-run_sawfish/_singularity_tmpdir_pi30uu1z"
2025-09-15 20:25:29.474 wdl.w:ptcp.w:call-sawfish-91.t:call-run_sawfish INFO Slurm invocation: srun --job-name call-run_sawfish --partition compute,compute9 --cpus-per-task 16 --mem 30518M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-91/call-run_sawfish/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-91/call-run_sawfish/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-91/call-run_sawfish/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-91/call-run_sawfish/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-91/out/m84036_250809_035451_s4.bc2188.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2188.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-91/out/m84036_250809_035451_s4.bc2188.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2188.mapped.bam:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-91/call-run_sawfish/_singularity_tmpdir_pi30uu1z/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-91/call-run_sawfish/_singularity_tmpdir_pi30uu1z/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:29.483 wdl.w:ptcp.t:call-tar_outputs-17 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 17, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-17/_singularity_tmpdir_3jc_oc3f"
2025-09-15 20:25:29.483 wdl.w:ptcp.t:call-tar_outputs-17 INFO Slurm invocation: srun --job-name call-tar_outputs-17 --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-17/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-17/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-17/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-17/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-17/out/m84036_250809_035451_s4.bc2114_paraphase/m84036_250809_035451_s4.bc2114.paraphase.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2114.paraphase.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-17/out/m84036_250809_035451_s4.bc2114_paraphase/m84036_250809_035451_s4.bc2114.paraphase.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2114.paraphase.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-17/out/m84036_250809_035451_s4.bc2114_paraphase/m84036_250809_035451_s4.bc2114.paraphase.json:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2114.paraphase.json:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-17/out/m84036_250809_035451_s4.bc2114.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2114.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-17/out/m84036_250809_035451_s4.bc2114.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2114.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-17/out/m84036_250809_035451_s4.bc2114.f8inversion.json:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2114.f8inversion.json:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-17/out/m84036_250809_035451_s4.bc2114.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2114.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-17/out/m84036_250809_035451_s4.bc2114.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2114.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-17/out/m84036_250809_035451_s4.bc2114.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2114.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-17/out/m84036_250809_035451_s4.bc2114_sawfish/m84036_250809_035451_s4.bc2114.sv.vcf.gz:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2114.sv.vcf.gz:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-17/out/m84036_250809_035451_s4.bc2114_sawfish/m84036_250809_035451_s4.bc2114.sv.vcf.gz.tbi:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2114.sv.vcf.gz.tbi:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-17/_singularity_tmpdir_3jc_oc3f/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-17/_singularity_tmpdir_3jc_oc3f/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:29.496 wdl.w:ptcp.w:call-sawfish-91.t:call-run_sawfish NOTICE slurm_singularity run :: pid: 1205730, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-91/call-run_sawfish/slurm_singularity.log.txt"
2025-09-15 20:25:29.497 wdl.w:ptcp.t:call-tar_outputs-17 NOTICE slurm_singularity run :: pid: 1205731, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-17/slurm_singularity.log.txt"
2025-09-15 20:25:29.955 wdl.w:ptcp.w:call-paraphase-74.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for smn1 for sample m84036_250809_035451_s4.bc2171 at 2025-09-15 20:25:23.954365...
2025-09-15 20:25:29.956 wdl.w:ptcp.w:call-paraphase-74.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning to gene2 region for smn1 for sample m84036_250809_035451_s4.bc2171 at 2025-09-15 20:25:24.456117...
2025-09-15 20:25:30.067 wdl.w:ptcp.w:call-trgt-80.t:call-trgt_genotype INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2177.trgt.vcf"
2025-09-15 20:25:30.072 wdl.w:ptcp.w:call-trgt-80.t:call-trgt_genotype INFO output :: name: "spanning_bam", value: "m84036_250809_035451_s4.bc2177.trgt.sorted.spanning.bam"
2025-09-15 20:25:30.073 wdl.w:ptcp.w:call-trgt-80.t:call-trgt_genotype INFO output :: name: "spanning_bam_bai", value: "m84036_250809_035451_s4.bc2177.trgt.sorted.spanning.bam.bai"
2025-09-15 20:25:30.102 wdl.w:ptcp.w:call-paraphase-68.t:call-call_f8.slurm_singularity INFO srun: job 51798022 queued and waiting for resources
2025-09-15 20:25:30.103 wdl.w:ptcp.w:call-paraphase-68.t:call-call_f8.slurm_singularity INFO srun: job 51798022 has been allocated resources
2025-09-15 20:25:30.103 wdl.w:ptcp.w:call-paraphase-68.t:call-call_f8.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:30.103 wdl.w:ptcp.w:call-paraphase-91.t:call-run_paraphase.slurm_singularity INFO srun: job 51798021 queued and waiting for resources
2025-09-15 20:25:30.103 wdl.w:ptcp.w:call-paraphase-91.t:call-run_paraphase.slurm_singularity INFO srun: job 51798021 has been allocated resources
2025-09-15 20:25:30.103 wdl.w:ptcp.w:call-paraphase-91.t:call-run_paraphase.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:30.157 wdl.w:ptcp.w:call-trgt-80.t:call-trgt_genotype NOTICE done
2025-09-15 20:25:30.162 wdl.w:ptcp.w:call-trgt-80 NOTICE finish :: job: "call-trgt_genotype"
2025-09-15 20:25:30.162 wdl.w:ptcp.w:call-trgt-80 INFO output :: job: "call-trgt_genotype", values: {"spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-80/call-trgt_genotype/out/m84036_250809_035451_s4.bc2177.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-80/call-trgt_genotype/out/m84036_250809_035451_s4.bc2177.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-80/call-trgt_genotype/out/m84036_250809_035451_s4.bc2177.trgt.vcf"}
2025-09-15 20:25:30.162 wdl.w:ptcp.w:call-trgt-80 NOTICE ready :: job: "call-trgt_plot_meth_allele", callee: "trgt_plot"
2025-09-15 20:25:30.162 wdl.w:ptcp.w:call-trgt-80 INFO input :: job: "call-trgt_plot_meth_allele", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": false, "methylation": true, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-80/call-trgt_genotype/out/m84036_250809_035451_s4.bc2177.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-80/call-trgt_genotype/out/m84036_250809_035451_s4.bc2177.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-80/call-trgt_genotype/out/m84036_250809_035451_s4.bc2177.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2177"}
2025-09-15 20:25:30.163 wdl.w:ptcp.w:call-trgt-80 NOTICE ready :: job: "call-trgt_plot_meth_waterfall", callee: "trgt_plot"
2025-09-15 20:25:30.163 wdl.w:ptcp.w:call-trgt-80 INFO input :: job: "call-trgt_plot_meth_waterfall", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": true, "methylation": true, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-80/call-trgt_genotype/out/m84036_250809_035451_s4.bc2177.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-80/call-trgt_genotype/out/m84036_250809_035451_s4.bc2177.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-80/call-trgt_genotype/out/m84036_250809_035451_s4.bc2177.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2177"}
2025-09-15 20:25:30.164 wdl.w:ptcp.w:call-trgt-80 NOTICE ready :: job: "call-trgt_plot_motifs_allele", callee: "trgt_plot"
2025-09-15 20:25:30.164 wdl.w:ptcp.w:call-trgt-80 INFO input :: job: "call-trgt_plot_motifs_allele", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": false, "methylation": false, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-80/call-trgt_genotype/out/m84036_250809_035451_s4.bc2177.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-80/call-trgt_genotype/out/m84036_250809_035451_s4.bc2177.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-80/call-trgt_genotype/out/m84036_250809_035451_s4.bc2177.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2177"}
2025-09-15 20:25:30.165 wdl.w:ptcp.w:call-trgt-80 NOTICE ready :: job: "call-trgt_plot_motifs_waterfall", callee: "trgt_plot"
2025-09-15 20:25:30.165 wdl.w:ptcp.w:call-trgt-80 INFO input :: job: "call-trgt_plot_motifs_waterfall", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": true, "methylation": false, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-80/call-trgt_genotype/out/m84036_250809_035451_s4.bc2177.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-80/call-trgt_genotype/out/m84036_250809_035451_s4.bc2177.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-80/call-trgt_genotype/out/m84036_250809_035451_s4.bc2177.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2177"}
2025-09-15 20:25:30.166 wdl.w:ptcp.w:call-trgt-80 INFO visit :: node: "output-spanning_bam", values: {"spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-80/call-trgt_genotype/out/m84036_250809_035451_s4.bc2177.trgt.sorted.spanning.bam"}
2025-09-15 20:25:30.166 wdl.w:ptcp.w:call-trgt-80 INFO visit :: node: "output-spanning_bam_bai", values: {"spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-80/call-trgt_genotype/out/m84036_250809_035451_s4.bc2177.trgt.sorted.spanning.bam.bai"}
2025-09-15 20:25:30.166 wdl.w:ptcp.w:call-trgt-80 INFO visit :: node: "output-vcf", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-80/call-trgt_genotype/out/m84036_250809_035451_s4.bc2177.trgt.vcf"}
2025-09-15 20:25:30.167 wdl.w:ptcp.t:call-tar_outputs-28 NOTICE task setup :: name: "tar_outputs", source: "./common.wdl", line: 279, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-28", thread: 140606575711808
2025-09-15 20:25:30.197 wdl.w:ptcp.t:call-tar_outputs-28 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:30.198 wdl.w:ptcp.t:call-tar_outputs-28 INFO input :: name: "sawfish_vcf_tbi", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2125.sv.vcf.gz.tbi"
2025-09-15 20:25:30.198 wdl.w:ptcp.t:call-tar_outputs-28 INFO input :: name: "sawfish_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2125.sv.vcf.gz"
2025-09-15 20:25:30.198 wdl.w:ptcp.t:call-tar_outputs-28 INFO input :: name: "f8_json", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2125.f8inversion.json"
2025-09-15 20:25:30.198 wdl.w:ptcp.t:call-tar_outputs-28 INFO input :: name: "paraphase_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2125.paraphase.bam.bai"
2025-09-15 20:25:30.198 wdl.w:ptcp.t:call-tar_outputs-28 INFO input :: name: "paraphase_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2125.paraphase.bam"
2025-09-15 20:25:30.198 wdl.w:ptcp.t:call-tar_outputs-28 INFO input :: name: "paraphase_json", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2125.paraphase.json"
2025-09-15 20:25:30.198 wdl.w:ptcp.t:call-tar_outputs-28 INFO input :: name: "trgt_spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2125.trgt.sorted.spanning.bam.bai"
2025-09-15 20:25:30.198 wdl.w:ptcp.t:call-tar_outputs-28 INFO input :: name: "trgt_spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2125.trgt.sorted.spanning.bam"
2025-09-15 20:25:30.198 wdl.w:ptcp.t:call-tar_outputs-28 INFO input :: name: "trgt_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2125.trgt.vcf"
2025-09-15 20:25:30.198 wdl.w:ptcp.t:call-tar_outputs-28 INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2125.mapped.bam.bai"
2025-09-15 20:25:30.198 wdl.w:ptcp.t:call-tar_outputs-28 INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2125.mapped.bam"
2025-09-15 20:25:30.198 wdl.w:ptcp.t:call-tar_outputs-28 INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2125"
2025-09-15 20:25:30.198 wdl.w:ptcp.t:call-tar_outputs-28 INFO eval :: name: "threads", value: 1
2025-09-15 20:25:30.198 wdl.w:ptcp.t:call-tar_outputs-28 INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:25:30.199 wdl.w:ptcp.t:call-tar_outputs-28 INFO eval :: name: "disk_size", value: 6
2025-09-15 20:25:30.199 wdl.w:ptcp.t:call-tar_outputs-28 INFO eval :: name: "output_tarball", value: "m84036_250809_035451_s4.bc2125.tar"
2025-09-15 20:25:30.199 wdl.w:ptcp.t:call-tar_outputs-28 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:30.199 wdl.w:ptcp.t:call-tar_outputs-28 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:30.200 wdl.w:ptcp.t:call-tar_outputs-28 INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:25:30.200 wdl.w:ptcp.t:call-tar_outputs-28 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:30.281 wdl.w:ptcp.t:call-tar_outputs-28 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 17, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-28/_singularity_tmpdir_iw7pxyjk"
2025-09-15 20:25:30.281 wdl.w:ptcp.t:call-tar_outputs-28 INFO Slurm invocation: srun --job-name call-tar_outputs-28 --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-28/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-28/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-28/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-28/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-28/out/m84036_250809_035451_s4.bc2125_paraphase/m84036_250809_035451_s4.bc2125.paraphase.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2125.paraphase.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-28/out/m84036_250809_035451_s4.bc2125_paraphase/m84036_250809_035451_s4.bc2125.paraphase.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2125.paraphase.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-28/out/m84036_250809_035451_s4.bc2125_paraphase/m84036_250809_035451_s4.bc2125.paraphase.json:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2125.paraphase.json:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-28/out/m84036_250809_035451_s4.bc2125.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2125.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-28/out/m84036_250809_035451_s4.bc2125.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2125.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-28/out/m84036_250809_035451_s4.bc2125.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2125.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-28/out/m84036_250809_035451_s4.bc2125.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2125.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-28/out/m84036_250809_035451_s4.bc2125.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2125.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-28/out/m84036_250809_035451_s4.bc2125_sawfish/m84036_250809_035451_s4.bc2125.sv.vcf.gz:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2125.sv.vcf.gz:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-28/out/m84036_250809_035451_s4.bc2125_sawfish/m84036_250809_035451_s4.bc2125.sv.vcf.gz.tbi:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2125.sv.vcf.gz.tbi:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-28/out/m84036_250809_035451_s4.bc2125.f8inversion.json:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2125.f8inversion.json:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-28/_singularity_tmpdir_iw7pxyjk/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-28/_singularity_tmpdir_iw7pxyjk/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:30.298 wdl.w:ptcp.t:call-tar_outputs-28 NOTICE slurm_singularity run :: pid: 1205812, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-28/slurm_singularity.log.txt"
2025-09-15 20:25:30.367 wdl.w:ptcp.w:call-paraphase-72.t:call-run_paraphase.stderr VERBOSE INFO:root:Processing sample m84036_250809_035451_s4.bc2169 at 2025-09-15 20:25:28.847079...
2025-09-15 20:25:30.368 wdl.w:ptcp.w:call-paraphase-72.t:call-run_paraphase.stderr VERBOSE INFO:root:Checking sample sex at 2025-09-15 20:25:28.848717...
2025-09-15 20:25:30.368 wdl.w:ptcp.w:call-paraphase-72.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for cyp21 for sample m84036_250809_035451_s4.bc2169 at 2025-09-15 20:25:28.923554...
2025-09-15 20:25:30.368 wdl.w:ptcp.w:call-paraphase-72.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for cyp21 for sample m84036_250809_035451_s4.bc2169 at 2025-09-15 20:25:28.924281...
2025-09-15 20:25:30.368 wdl.w:ptcp.w:call-paraphase-72.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for smn1 for sample m84036_250809_035451_s4.bc2169 at 2025-09-15 20:25:28.924066...
2025-09-15 20:25:30.368 wdl.w:ptcp.w:call-paraphase-72.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for smn1 for sample m84036_250809_035451_s4.bc2169 at 2025-09-15 20:25:28.924941...
2025-09-15 20:25:30.368 wdl.w:ptcp.w:call-paraphase-72.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for gba for sample m84036_250809_035451_s4.bc2169 at 2025-09-15 20:25:28.924283...
2025-09-15 20:25:30.368 wdl.w:ptcp.w:call-paraphase-72.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for gba for sample m84036_250809_035451_s4.bc2169 at 2025-09-15 20:25:28.925114...
2025-09-15 20:25:30.368 wdl.w:ptcp.w:call-paraphase-72.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for hba for sample m84036_250809_035451_s4.bc2169 at 2025-09-15 20:25:28.925670...
2025-09-15 20:25:30.369 wdl.w:ptcp.w:call-paraphase-72.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for hba for sample m84036_250809_035451_s4.bc2169 at 2025-09-15 20:25:28.926246...
2025-09-15 20:25:30.369 wdl.w:ptcp.w:call-paraphase-72.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for cyp21 for sample m84036_250809_035451_s4.bc2169 at 2025-09-15 20:25:29.599794...
2025-09-15 20:25:30.369 wdl.w:ptcp.w:call-paraphase-72.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for hba for sample m84036_250809_035451_s4.bc2169 at 2025-09-15 20:25:29.618832...
2025-09-15 20:25:30.369 wdl.w:ptcp.w:call-paraphase-72.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for gba for sample m84036_250809_035451_s4.bc2169 at 2025-09-15 20:25:29.633552...
2025-09-15 20:25:30.369 wdl.w:ptcp.w:call-paraphase-72.t:call-run_paraphase.stderr VERBOSE WARNING:root:This region does not appear to have coverage. Will not attempt to phase haplotypes.
2025-09-15 20:25:30.369 wdl.w:ptcp.w:call-paraphase-72.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for cyp21 for sample m84036_250809_035451_s4.bc2169 at 2025-09-15 20:25:29.676730...
2025-09-15 20:25:30.369 wdl.w:ptcp.w:call-paraphase-72.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for smn1 for sample m84036_250809_035451_s4.bc2169 at 2025-09-15 20:25:29.699054...
2025-09-15 20:25:30.369 wdl.w:ptcp.w:call-paraphase-72.t:call-run_paraphase.stderr VERBOSE WARNING:root:This region does not appear to have coverage. Will not attempt to phase haplotypes.
2025-09-15 20:25:30.369 wdl.w:ptcp.w:call-paraphase-72.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for hba for sample m84036_250809_035451_s4.bc2169 at 2025-09-15 20:25:29.705244...
2025-09-15 20:25:30.369 wdl.w:ptcp.w:call-paraphase-72.t:call-run_paraphase.stderr VERBOSE WARNING:root:This region does not appear to have coverage. Will not attempt to phase haplotypes.
2025-09-15 20:25:30.369 wdl.w:ptcp.w:call-paraphase-72.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for gba for sample m84036_250809_035451_s4.bc2169 at 2025-09-15 20:25:29.734221...
2025-09-15 20:25:30.369 wdl.w:ptcp.w:call-paraphase-72.t:call-run_paraphase.stderr VERBOSE WARNING:root:This region does not appear to have coverage. Will not attempt to phase haplotypes.
2025-09-15 20:25:30.369 wdl.w:ptcp.w:call-paraphase-72.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for smn1 for sample m84036_250809_035451_s4.bc2169 at 2025-09-15 20:25:29.841950...
2025-09-15 20:25:30.369 wdl.w:ptcp.w:call-paraphase-72.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for cyp21 for sample m84036_250809_035451_s4.bc2169 at 2025-09-15 20:25:30.051630...
2025-09-15 20:25:30.369 wdl.w:ptcp.w:call-paraphase-72.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for f8inv22 for sample m84036_250809_035451_s4.bc2169 at 2025-09-15 20:25:30.055278...
2025-09-15 20:25:30.369 wdl.w:ptcp.w:call-paraphase-72.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for f8inv22 for sample m84036_250809_035451_s4.bc2169 at 2025-09-15 20:25:30.055509...
2025-09-15 20:25:30.369 wdl.w:ptcp.w:call-paraphase-72.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for hba for sample m84036_250809_035451_s4.bc2169 at 2025-09-15 20:25:30.105228...
2025-09-15 20:25:30.369 wdl.w:ptcp.w:call-paraphase-72.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for hbb for sample m84036_250809_035451_s4.bc2169 at 2025-09-15 20:25:30.110142...
2025-09-15 20:25:30.369 wdl.w:ptcp.w:call-paraphase-72.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for hbb for sample m84036_250809_035451_s4.bc2169 at 2025-09-15 20:25:30.110435...
2025-09-15 20:25:30.369 wdl.w:ptcp.w:call-paraphase-72.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for gba for sample m84036_250809_035451_s4.bc2169 at 2025-09-15 20:25:30.145904...
2025-09-15 20:25:30.370 wdl.w:ptcp.w:call-paraphase-72.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for rpgr for sample m84036_250809_035451_s4.bc2169 at 2025-09-15 20:25:30.149796...
2025-09-15 20:25:30.370 wdl.w:ptcp.w:call-paraphase-72.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for rpgr for sample m84036_250809_035451_s4.bc2169 at 2025-09-15 20:25:30.151092...
2025-09-15 20:25:30.370 wdl.w:ptcp.w:call-paraphase-72.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning to gene2 region for smn1 for sample m84036_250809_035451_s4.bc2169 at 2025-09-15 20:25:30.227976...
2025-09-15 20:25:30.479 wdl.w:ptcp.w:call-paraphase-68.t:call-call_f8 INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2165.f8inversion.vcf"
2025-09-15 20:25:30.483 wdl.w:ptcp.w:call-paraphase-68.t:call-call_f8 INFO output :: name: "json", value: "m84036_250809_035451_s4.bc2165.f8inversion.json"
2025-09-15 20:25:30.511 wdl.w:ptcp.w:call-sawfish-91.t:call-run_sawfish.slurm_singularity INFO srun: job 51798023 queued and waiting for resources
2025-09-15 20:25:30.511 wdl.w:ptcp.w:call-sawfish-91.t:call-run_sawfish.slurm_singularity INFO srun: job 51798023 has been allocated resources
2025-09-15 20:25:30.511 wdl.w:ptcp.w:call-sawfish-91.t:call-run_sawfish.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:30.511 wdl.w:ptcp.w:call-sawfish-91.t:call-run_sawfish.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:25:30.513 wdl.w:ptcp.t:call-tar_outputs-17.slurm_singularity INFO srun: job 51798024 queued and waiting for resources
2025-09-15 20:25:30.513 wdl.w:ptcp.t:call-tar_outputs-17.slurm_singularity INFO srun: job 51798024 has been allocated resources
2025-09-15 20:25:30.513 wdl.w:ptcp.t:call-tar_outputs-17.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:30.513 wdl.w:ptcp.t:call-tar_outputs-17.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:25:30.551 wdl.w:ptcp.w:call-paraphase-68.t:call-call_f8 NOTICE done
2025-09-15 20:25:30.569 wdl.w:ptcp.w:call-paraphase-68 NOTICE finish :: job: "call-call_f8"
2025-09-15 20:25:30.569 wdl.w:ptcp.w:call-paraphase-68 INFO output :: job: "call-call_f8", values: {"json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-68/call-call_f8/out/m84036_250809_035451_s4.bc2165.f8inversion.json", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-68/call-call_f8/out/m84036_250809_035451_s4.bc2165.f8inversion.vcf"}
2025-09-15 20:25:30.569 wdl.w:ptcp.w:call-paraphase-68 INFO visit :: node: "output-f8_json", values: {"f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-68/call-call_f8/out/m84036_250809_035451_s4.bc2165.f8inversion.json"}
2025-09-15 20:25:30.569 wdl.w:ptcp.w:call-paraphase-68 INFO visit :: node: "output-f8_vcf", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-68/call-call_f8/out/m84036_250809_035451_s4.bc2165.f8inversion.vcf"}
2025-09-15 20:25:30.570 wdl.w:ptcp.w:call-paraphase-68 INFO visit :: node: "outputs", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-68/call-call_f8/out/m84036_250809_035451_s4.bc2165.f8inversion.vcf", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-68/call-run_paraphase/out/m84036_250809_035451_s4.bc2165_paraphase/m84036_250809_035451_s4.bc2165.paraphase.json", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-68/call-run_paraphase/out/m84036_250809_035451_s4.bc2165_paraphase/m84036_250809_035451_s4.bc2165.paraphase.bam", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-68/call-run_paraphase/out/m84036_250809_035451_s4.bc2165_paraphase/m84036_250809_035451_s4.bc2165.paraphase.bam.bai", "paraphase_vcfs": [], "havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-68/call-run_paraphase/out/m84036_250809_035451_s4.bc2165.havanno.json", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-68/call-call_f8/out/m84036_250809_035451_s4.bc2165.f8inversion.json"}
2025-09-15 20:25:30.577 wdl.w:ptcp.w:call-trgt-91.t:call-get_reads_overlapping_repeats NOTICE task setup :: name: "get_reads_overlapping_repeats", source: "./trgt.wdl", line: 182, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-91/call-get_reads_overlapping_repeats", thread: 140610912642624
2025-09-15 20:25:30.600 wdl.w:ptcp.w:call-trgt-91.t:call-get_reads_overlapping_repeats INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:30.600 wdl.w:ptcp.w:call-trgt-91.t:call-get_reads_overlapping_repeats INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:25:30.600 wdl.w:ptcp.w:call-trgt-91.t:call-get_reads_overlapping_repeats INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2188.mapped.bam.bai"
2025-09-15 20:25:30.600 wdl.w:ptcp.w:call-trgt-91.t:call-get_reads_overlapping_repeats INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2188.mapped.bam"
2025-09-15 20:25:30.600 wdl.w:ptcp.w:call-trgt-91.t:call-get_reads_overlapping_repeats INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2188"
2025-09-15 20:25:30.600 wdl.w:ptcp.w:call-trgt-91.t:call-get_reads_overlapping_repeats INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:25:30.600 wdl.w:ptcp.w:call-trgt-91.t:call-get_reads_overlapping_repeats INFO eval :: name: "expand_size", value: 3000
2025-09-15 20:25:30.600 wdl.w:ptcp.w:call-trgt-91.t:call-get_reads_overlapping_repeats INFO eval :: name: "threads", value: 1
2025-09-15 20:25:30.601 wdl.w:ptcp.w:call-trgt-91.t:call-get_reads_overlapping_repeats INFO eval :: name: "expanded_bed_name", value: "m84036_250809_035451_s4.bc2188.expanded.bed"
2025-09-15 20:25:30.601 wdl.w:ptcp.w:call-trgt-91.t:call-get_reads_overlapping_repeats INFO eval :: name: "disk_size", value: 11
2025-09-15 20:25:30.601 wdl.w:ptcp.w:call-trgt-91.t:call-get_reads_overlapping_repeats INFO eval :: name: "output_name", value: "m84036_250809_035451_s4.bc2188.repeats.bam"
2025-09-15 20:25:30.601 wdl.w:ptcp.w:call-trgt-91.t:call-get_reads_overlapping_repeats INFO eval :: name: "index_name", value: "m84036_250809_035451_s4.bc2188.repeats.bam.bai"
2025-09-15 20:25:30.601 wdl.w:ptcp.w:call-trgt-91.t:call-get_reads_overlapping_repeats INFO eval :: name: "output_name_with_index", value: "m84036_250809_035451_s4.bc2188.repeats.bam##idx##m84036_250809_035451_s4.bc2188.repeats.bam.bai"
2025-09-15 20:25:30.602 wdl.w:ptcp.w:call-trgt-91.t:call-get_reads_overlapping_repeats INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:30.602 wdl.w:ptcp.w:call-trgt-91.t:call-get_reads_overlapping_repeats WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:30.602 wdl.w:ptcp.w:call-trgt-91.t:call-get_reads_overlapping_repeats INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:25:30.603 wdl.w:ptcp.w:call-trgt-91.t:call-get_reads_overlapping_repeats INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:30.613 wdl.w:ptcp.w:call-trgt-79.t:call-trgt_plot_meth_waterfall INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2176.meth_waterfall.trgt_plots.zip"
2025-09-15 20:25:30.647 wdl.w:ptcp.w:call-paraphase-68 NOTICE done
2025-09-15 20:25:30.653 wdl.w:ptcp NOTICE finish :: job: "call-paraphase-68"
2025-09-15 20:25:30.653 wdl.w:ptcp INFO output :: job: "call-paraphase-68", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-68/out/m84036_250809_035451_s4.bc2165.f8inversion.vcf", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-68/out/m84036_250809_035451_s4.bc2165_paraphase/m84036_250809_035451_s4.bc2165.paraphase.json", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-68/out/m84036_250809_035451_s4.bc2165_paraphase/m84036_250809_035451_s4.bc2165.paraphase.bam", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-68/out/m84036_250809_035451_s4.bc2165_paraphase/m84036_250809_035451_s4.bc2165.paraphase.bam.bai", "paraphase_vcfs": [], "havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-68/out/m84036_250809_035451_s4.bc2165.havanno.json", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-68/out/m84036_250809_035451_s4.bc2165.f8inversion.json"}
2025-09-15 20:25:30.660 wdl.w:ptcp.w:call-sawfish-90 NOTICE workflow start :: name: "sawfish", source: "./sawfish.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-90"
2025-09-15 20:25:30.665 wdl.w:ptcp.w:call-trgt-91.t:call-get_reads_overlapping_repeats INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 9, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-91/call-get_reads_overlapping_repeats/_singularity_tmpdir_3z8mx4gn"
2025-09-15 20:25:30.665 wdl.w:ptcp.w:call-trgt-91.t:call-get_reads_overlapping_repeats INFO Slurm invocation: srun --job-name call-get_reads_overlapping_repeats --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-91/call-get_reads_overlapping_repeats/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-91/call-get_reads_overlapping_repeats/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-91/call-get_reads_overlapping_repeats/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-91/call-get_reads_overlapping_repeats/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-91/out/m84036_250809_035451_s4.bc2188.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2188.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-91/out/m84036_250809_035451_s4.bc2188.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2188.mapped.bam:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-91/call-get_reads_overlapping_repeats/_singularity_tmpdir_3z8mx4gn/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-91/call-get_reads_overlapping_repeats/_singularity_tmpdir_3z8mx4gn/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:30.676 wdl.w:ptcp.w:call-sawfish-90 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:25:30.676 wdl.w:ptcp.w:call-sawfish-90 INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:25:30.676 wdl.w:ptcp.w:call-sawfish-90 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-90/out/m84036_250809_035451_s4.bc2187.mapped.bam"}
2025-09-15 20:25:30.676 wdl.w:ptcp.w:call-sawfish-90 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-90/out/m84036_250809_035451_s4.bc2187.mapped.bam.bai"}
2025-09-15 20:25:30.676 wdl.w:ptcp.w:call-sawfish-90 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:25:30.677 wdl.w:ptcp.w:call-sawfish-90 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:25:30.677 wdl.w:ptcp.w:call-sawfish-90 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2187"}
2025-09-15 20:25:30.677 wdl.w:ptcp.w:call-sawfish-90 NOTICE ready :: job: "call-run_sawfish", callee: "run_sawfish"
2025-09-15 20:25:30.677 wdl.w:ptcp.w:call-sawfish-90 INFO input :: job: "call-run_sawfish", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-90/out/m84036_250809_035451_s4.bc2187.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-90/out/m84036_250809_035451_s4.bc2187.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2187"}
2025-09-15 20:25:30.688 wdl.w:ptcp.w:call-trgt-91.t:call-get_reads_overlapping_repeats NOTICE slurm_singularity run :: pid: 1205821, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-91/call-get_reads_overlapping_repeats/slurm_singularity.log.txt"
2025-09-15 20:25:30.706 wdl.w:ptcp.w:call-trgt-79.t:call-trgt_plot_meth_waterfall NOTICE done
2025-09-15 20:25:30.710 wdl.w:ptcp.w:call-trgt-79 NOTICE finish :: job: "call-trgt_plot_meth_waterfall"
2025-09-15 20:25:30.710 wdl.w:ptcp.w:call-trgt-79 INFO output :: job: "call-trgt_plot_meth_waterfall", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-79/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2176.meth_waterfall.trgt_plots.zip"}
2025-09-15 20:25:30.711 wdl.w:ptcp.w:call-trgt-79 INFO visit :: node: "output-images_meth_waterfall", values: {"images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-79/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2176.meth_waterfall.trgt_plots.zip"}
2025-09-15 20:25:30.717 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_genotype NOTICE task setup :: name: "trgt_genotype", source: "./trgt.wdl", line: 272, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-91/call-trgt_genotype", thread: 140611441120832
2025-09-15 20:25:30.735 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_genotype INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:30.735 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_genotype INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:25:30.735 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_genotype INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:25:30.735 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_genotype INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:25:30.736 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_genotype INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2188.mapped.bam.bai"
2025-09-15 20:25:30.736 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_genotype INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2188.mapped.bam"
2025-09-15 20:25:30.736 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_genotype INFO input :: name: "sex", value: "F"
2025-09-15 20:25:30.736 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_genotype INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2188"
2025-09-15 20:25:30.736 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_genotype INFO eval :: name: "mem_gb", value: 16
2025-09-15 20:25:30.736 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_genotype INFO eval :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2188.trgt"
2025-09-15 20:25:30.736 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_genotype INFO eval :: name: "threads", value: 8
2025-09-15 20:25:30.737 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_genotype INFO eval :: name: "disk_size", value: 27
2025-09-15 20:25:30.737 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_genotype INFO eval :: name: "karyotype", value: "XX"
2025-09-15 20:25:30.737 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_genotype INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 8, memory_reservation: 16000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:30.737 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_genotype WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:30.737 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_genotype INFO provisioned :: seconds_waited: 0, cpu: 8, mem_bytes: 16000000000
2025-09-15 20:25:30.738 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_genotype INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:30.783 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_genotype INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 11, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-91/call-trgt_genotype/_singularity_tmpdir_k2y4ie3z"
2025-09-15 20:25:30.783 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_genotype INFO Slurm invocation: srun --job-name call-trgt_genotype --partition compute,compute9 --cpus-per-task 8 --mem 15259M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-91/call-trgt_genotype/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-91/call-trgt_genotype/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-91/call-trgt_genotype/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-91/call-trgt_genotype/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-91/out/m84036_250809_035451_s4.bc2188.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2188.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-91/out/m84036_250809_035451_s4.bc2188.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2188.mapped.bam:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-91/call-trgt_genotype/_singularity_tmpdir_k2y4ie3z/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-91/call-trgt_genotype/_singularity_tmpdir_k2y4ie3z/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:30.793 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_genotype NOTICE slurm_singularity run :: pid: 1205824, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-91/call-trgt_genotype/slurm_singularity.log.txt"
2025-09-15 20:25:30.815 wdl.w:ptcp.t:call-tar_outputs-17 INFO output :: name: "sample_tarball", value: "m84036_250809_035451_s4.bc2114.tar"
2025-09-15 20:25:30.875 wdl.w:ptcp.t:call-tar_outputs-17 NOTICE done
2025-09-15 20:25:30.882 wdl.w:ptcp NOTICE finish :: job: "call-tar_outputs-17"
2025-09-15 20:25:30.882 wdl.w:ptcp INFO output :: job: "call-tar_outputs-17", values: {"sample_tarball": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-17/out/m84036_250809_035451_s4.bc2114.tar"}
2025-09-15 20:25:30.888 wdl.w:ptcp.w:call-paraphase-87.t:call-run_paraphase NOTICE task setup :: name: "run_paraphase", source: "./paraphase.wdl", line: 127, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-87/call-run_paraphase", thread: 140610870679104
2025-09-15 20:25:30.913 wdl.w:ptcp.w:call-paraphase-87.t:call-run_paraphase INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:30.913 wdl.w:ptcp.w:call-paraphase-87.t:call-run_paraphase INFO input :: name: "annotation_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf"
2025-09-15 20:25:30.913 wdl.w:ptcp.w:call-paraphase-87.t:call-run_paraphase INFO input :: name: "genome_version", value: "38"
2025-09-15 20:25:30.913 wdl.w:ptcp.w:call-paraphase-87.t:call-run_paraphase INFO input :: name: "config_file", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/paraphase_config.GRCh38.yaml"
2025-09-15 20:25:30.913 wdl.w:ptcp.w:call-paraphase-87.t:call-run_paraphase INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:25:30.913 wdl.w:ptcp.w:call-paraphase-87.t:call-run_paraphase INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:25:30.913 wdl.w:ptcp.w:call-paraphase-87.t:call-run_paraphase INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2184.mapped.bam.bai"
2025-09-15 20:25:30.913 wdl.w:ptcp.w:call-paraphase-87.t:call-run_paraphase INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2184.mapped.bam"
2025-09-15 20:25:30.914 wdl.w:ptcp.w:call-paraphase-87.t:call-run_paraphase INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2184"
2025-09-15 20:25:30.914 wdl.w:ptcp.w:call-paraphase-87.t:call-run_paraphase INFO eval :: name: "threads", value: 4
2025-09-15 20:25:30.914 wdl.w:ptcp.w:call-paraphase-87.t:call-run_paraphase INFO eval :: name: "mem_gb", value: 8
2025-09-15 20:25:30.914 wdl.w:ptcp.w:call-paraphase-87.t:call-run_paraphase INFO eval :: name: "disk_size", value: 27
2025-09-15 20:25:30.914 wdl.w:ptcp.w:call-paraphase-87.t:call-run_paraphase INFO eval :: name: "out_dir", value: "m84036_250809_035451_s4.bc2184_paraphase"
2025-09-15 20:25:30.915 wdl.w:ptcp.w:call-paraphase-87.t:call-run_paraphase INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 4, memory_reservation: 8000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:30.915 wdl.w:ptcp.w:call-paraphase-87.t:call-run_paraphase WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:30.915 wdl.w:ptcp.w:call-paraphase-87.t:call-run_paraphase INFO provisioned :: seconds_waited: 0, cpu: 4, mem_bytes: 8000000000
2025-09-15 20:25:30.915 wdl.w:ptcp.w:call-paraphase-87.t:call-run_paraphase INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:30.933 wdl.w:ptcp.w:call-trgt-79.t:call-trgt_plot_motifs_allele INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2176.motifs_allele.trgt_plots.zip"
2025-09-15 20:25:30.941 wdl.w:ptcp.w:call-trgt-80.t:call-get_reads_overlapping_repeats INFO output :: name: "reads_overlapping_repeats", value: "m84036_250809_035451_s4.bc2177.repeats.bam"
2025-09-15 20:25:30.944 wdl.w:ptcp.w:call-trgt-80.t:call-get_reads_overlapping_repeats INFO output :: name: "reads_overlapping_repeats_bai", value: "m84036_250809_035451_s4.bc2177.repeats.bam.bai"
2025-09-15 20:25:30.999 wdl.w:ptcp.w:call-paraphase-87.t:call-run_paraphase INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-87/call-run_paraphase/_singularity_tmpdir_8j24n_fg"
2025-09-15 20:25:30.999 wdl.w:ptcp.w:call-paraphase-87.t:call-run_paraphase INFO Slurm invocation: srun --job-name call-run_paraphase --partition compute,compute9 --cpus-per-task 4 --mem 7629M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-87/call-run_paraphase/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-87/call-run_paraphase/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-87/call-run_paraphase/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-87/call-run_paraphase/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-87/out/m84036_250809_035451_s4.bc2184.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2184.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-87/out/m84036_250809_035451_s4.bc2184.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2184.mapped.bam.bai:ro --bind /ptcp/meta/variant_list/variant_list.GRCh38.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf:ro --bind /ptcp/meta/paraphase/paraphase_config.GRCh38.yaml:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/paraphase_config.GRCh38.yaml:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-87/call-run_paraphase/_singularity_tmpdir_8j24n_fg/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-87/call-run_paraphase/_singularity_tmpdir_8j24n_fg/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:31.015 wdl.w:ptcp.w:call-paraphase-87.t:call-run_paraphase NOTICE slurm_singularity run :: pid: 1205838, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-87/call-run_paraphase/slurm_singularity.log.txt"
2025-09-15 20:25:31.019 wdl.w:ptcp.w:call-trgt-79.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:29 [ERROR] - No reads found for TRID=DRPLA_ATN1
2025-09-15 20:25:31.019 wdl.w:ptcp.w:call-trgt-79.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:29 [ERROR] - No reads found for TRID=OPDM_ABCD3
2025-09-15 20:25:31.019 wdl.w:ptcp.w:call-trgt-79.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:30 [ERROR] - No reads found for TRID=SCA2_ATXN2
2025-09-15 20:25:31.019 wdl.w:ptcp.w:call-trgt-79.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:30 [ERROR] - No reads found for TRID=OPDM4_RILPL1
2025-09-15 20:25:31.019 wdl.w:ptcp.w:call-trgt-79.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:30 [ERROR] - No reads found for TRID=NIID_NOTCH2NLC
2025-09-15 20:25:31.019 wdl.w:ptcp.w:call-trgt-79.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:31 [ERROR] - No reads found for TRID=SCA8_ATXN8OS
2025-09-15 20:25:31.020 wdl.w:ptcp.w:call-trgt-79.t:call-trgt_plot_motifs_allele NOTICE done
2025-09-15 20:25:31.027 wdl.w:ptcp.w:call-trgt-79 NOTICE finish :: job: "call-trgt_plot_motifs_allele"
2025-09-15 20:25:31.027 wdl.w:ptcp.w:call-trgt-79 INFO output :: job: "call-trgt_plot_motifs_allele", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-79/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2176.motifs_allele.trgt_plots.zip"}
2025-09-15 20:25:31.027 wdl.w:ptcp.w:call-trgt-79 INFO visit :: node: "output-images_motifs_allele", values: {"images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-79/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2176.motifs_allele.trgt_plots.zip"}
2025-09-15 20:25:31.033 wdl.w:ptcp.w:call-sawfish-87.t:call-run_sawfish NOTICE task setup :: name: "run_sawfish", source: "./sawfish.wdl", line: 83, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-87/call-run_sawfish", thread: 140612506469952
2025-09-15 20:25:31.035 wdl.w:ptcp.w:call-trgt-80.t:call-get_reads_overlapping_repeats NOTICE done
2025-09-15 20:25:31.040 wdl.w:ptcp.w:call-trgt-80 NOTICE finish :: job: "call-get_reads_overlapping_repeats"
2025-09-15 20:25:31.040 wdl.w:ptcp.w:call-trgt-80 INFO output :: job: "call-get_reads_overlapping_repeats", values: {"reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-80/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2177.repeats.bam.bai", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-80/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2177.repeats.bam"}
2025-09-15 20:25:31.041 wdl.w:ptcp.w:call-trgt-80 INFO visit :: node: "output-reads_overlapping_repeats", values: {"reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-80/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2177.repeats.bam"}
2025-09-15 20:25:31.041 wdl.w:ptcp.w:call-trgt-80 INFO visit :: node: "output-reads_overlapping_repeats_bai", values: {"reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-80/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2177.repeats.bam.bai"}
2025-09-15 20:25:31.047 wdl.w:ptcp.w:call-trgt-87.t:call-get_reads_overlapping_repeats NOTICE task setup :: name: "get_reads_overlapping_repeats", source: "./trgt.wdl", line: 182, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-87/call-get_reads_overlapping_repeats", thread: 140607137760832
2025-09-15 20:25:31.054 wdl.w:ptcp.w:call-sawfish-87.t:call-run_sawfish INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:31.054 wdl.w:ptcp.w:call-sawfish-87.t:call-run_sawfish INFO input :: name: "genome_version", value: "38"
2025-09-15 20:25:31.054 wdl.w:ptcp.w:call-sawfish-87.t:call-run_sawfish INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:25:31.054 wdl.w:ptcp.w:call-sawfish-87.t:call-run_sawfish INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:25:31.054 wdl.w:ptcp.w:call-sawfish-87.t:call-run_sawfish INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2184.mapped.bam.bai"
2025-09-15 20:25:31.054 wdl.w:ptcp.w:call-sawfish-87.t:call-run_sawfish INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2184.mapped.bam"
2025-09-15 20:25:31.054 wdl.w:ptcp.w:call-sawfish-87.t:call-run_sawfish INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2184"
2025-09-15 20:25:31.054 wdl.w:ptcp.w:call-sawfish-87.t:call-run_sawfish INFO eval :: name: "mem_gb", value: 32
2025-09-15 20:25:31.054 wdl.w:ptcp.w:call-sawfish-87.t:call-run_sawfish INFO eval :: name: "threads", value: 16
2025-09-15 20:25:31.054 wdl.w:ptcp.w:call-sawfish-87.t:call-run_sawfish INFO eval :: name: "disk_size", value: 30
2025-09-15 20:25:31.055 wdl.w:ptcp.w:call-sawfish-87.t:call-run_sawfish INFO eval :: name: "discover_dirname", value: "m84036_250809_035451_s4.bc2184_sawfish_discover"
2025-09-15 20:25:31.055 wdl.w:ptcp.w:call-sawfish-87.t:call-run_sawfish INFO eval :: name: "call_dirname", value: "m84036_250809_035451_s4.bc2184_sawfish"
2025-09-15 20:25:31.055 wdl.w:ptcp.w:call-sawfish-87.t:call-run_sawfish INFO eval :: name: "minimap2_bam_filename", value: "m84036_250809_035451_s4.bc2184.minimap2.bam"
2025-09-15 20:25:31.057 wdl.w:ptcp.w:call-sawfish-87.t:call-run_sawfish INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 16, memory_reservation: 32000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:31.057 wdl.w:ptcp.w:call-sawfish-87.t:call-run_sawfish WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:31.058 wdl.w:ptcp.w:call-sawfish-87.t:call-run_sawfish INFO provisioned :: seconds_waited: 0, cpu: 16, mem_bytes: 32000000000
2025-09-15 20:25:31.058 wdl.w:ptcp.w:call-sawfish-87.t:call-run_sawfish INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:31.065 wdl.w:ptcp.w:call-trgt-87.t:call-get_reads_overlapping_repeats INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:31.066 wdl.w:ptcp.w:call-trgt-87.t:call-get_reads_overlapping_repeats INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:25:31.066 wdl.w:ptcp.w:call-trgt-87.t:call-get_reads_overlapping_repeats INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2184.mapped.bam.bai"
2025-09-15 20:25:31.066 wdl.w:ptcp.w:call-trgt-87.t:call-get_reads_overlapping_repeats INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2184.mapped.bam"
2025-09-15 20:25:31.066 wdl.w:ptcp.w:call-trgt-87.t:call-get_reads_overlapping_repeats INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2184"
2025-09-15 20:25:31.066 wdl.w:ptcp.w:call-trgt-87.t:call-get_reads_overlapping_repeats INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:25:31.066 wdl.w:ptcp.w:call-trgt-87.t:call-get_reads_overlapping_repeats INFO eval :: name: "expand_size", value: 3000
2025-09-15 20:25:31.066 wdl.w:ptcp.w:call-trgt-87.t:call-get_reads_overlapping_repeats INFO eval :: name: "threads", value: 1
2025-09-15 20:25:31.066 wdl.w:ptcp.w:call-trgt-87.t:call-get_reads_overlapping_repeats INFO eval :: name: "expanded_bed_name", value: "m84036_250809_035451_s4.bc2184.expanded.bed"
2025-09-15 20:25:31.066 wdl.w:ptcp.w:call-trgt-87.t:call-get_reads_overlapping_repeats INFO eval :: name: "disk_size", value: 11
2025-09-15 20:25:31.067 wdl.w:ptcp.w:call-trgt-87.t:call-get_reads_overlapping_repeats INFO eval :: name: "output_name", value: "m84036_250809_035451_s4.bc2184.repeats.bam"
2025-09-15 20:25:31.067 wdl.w:ptcp.w:call-trgt-87.t:call-get_reads_overlapping_repeats INFO eval :: name: "index_name", value: "m84036_250809_035451_s4.bc2184.repeats.bam.bai"
2025-09-15 20:25:31.067 wdl.w:ptcp.w:call-trgt-87.t:call-get_reads_overlapping_repeats INFO eval :: name: "output_name_with_index", value: "m84036_250809_035451_s4.bc2184.repeats.bam##idx##m84036_250809_035451_s4.bc2184.repeats.bam.bai"
2025-09-15 20:25:31.067 wdl.w:ptcp.w:call-trgt-87.t:call-get_reads_overlapping_repeats INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:31.067 wdl.w:ptcp.w:call-trgt-87.t:call-get_reads_overlapping_repeats WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:31.067 wdl.w:ptcp.w:call-trgt-87.t:call-get_reads_overlapping_repeats INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:25:31.068 wdl.w:ptcp.w:call-trgt-87.t:call-get_reads_overlapping_repeats INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:31.127 wdl.w:ptcp.w:call-sawfish-87.t:call-run_sawfish INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 10, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-87/call-run_sawfish/_singularity_tmpdir_szzv0ji8"
2025-09-15 20:25:31.127 wdl.w:ptcp.w:call-sawfish-87.t:call-run_sawfish INFO Slurm invocation: srun --job-name call-run_sawfish --partition compute,compute9 --cpus-per-task 16 --mem 30518M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-87/call-run_sawfish/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-87/call-run_sawfish/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-87/call-run_sawfish/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-87/call-run_sawfish/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-87/out/m84036_250809_035451_s4.bc2184.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2184.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-87/out/m84036_250809_035451_s4.bc2184.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2184.mapped.bam.bai:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-87/call-run_sawfish/_singularity_tmpdir_szzv0ji8/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-87/call-run_sawfish/_singularity_tmpdir_szzv0ji8/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:31.141 wdl.w:ptcp.w:call-trgt-87.t:call-get_reads_overlapping_repeats INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 9, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-87/call-get_reads_overlapping_repeats/_singularity_tmpdir_qp8bxft6"
2025-09-15 20:25:31.141 wdl.w:ptcp.w:call-trgt-87.t:call-get_reads_overlapping_repeats INFO Slurm invocation: srun --job-name call-get_reads_overlapping_repeats --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-87/call-get_reads_overlapping_repeats/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-87/call-get_reads_overlapping_repeats/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-87/call-get_reads_overlapping_repeats/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-87/call-get_reads_overlapping_repeats/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-87/out/m84036_250809_035451_s4.bc2184.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2184.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-87/out/m84036_250809_035451_s4.bc2184.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2184.mapped.bam.bai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-87/call-get_reads_overlapping_repeats/_singularity_tmpdir_qp8bxft6/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-87/call-get_reads_overlapping_repeats/_singularity_tmpdir_qp8bxft6/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:31.148 wdl.w:ptcp.w:call-trgt-87.t:call-get_reads_overlapping_repeats NOTICE slurm_singularity run :: pid: 1205841, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-87/call-get_reads_overlapping_repeats/slurm_singularity.log.txt"
2025-09-15 20:25:31.148 wdl.w:ptcp.w:call-sawfish-87.t:call-run_sawfish NOTICE slurm_singularity run :: pid: 1205840, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-87/call-run_sawfish/slurm_singularity.log.txt"
2025-09-15 20:25:31.299 wdl.w:ptcp.t:call-tar_outputs-28.stderr VERBOSE tar: Removing leading `/' from member names
2025-09-15 20:25:31.300 wdl.w:ptcp.t:call-tar_outputs-28.stderr VERBOSE tar: Removing leading `/' from hard link targets
2025-09-15 20:25:31.306 wdl.w:ptcp.t:call-tar_outputs-28.slurm_singularity INFO srun: job 51798025 queued and waiting for resources
2025-09-15 20:25:31.306 wdl.w:ptcp.t:call-tar_outputs-28.slurm_singularity INFO srun: job 51798025 has been allocated resources
2025-09-15 20:25:31.306 wdl.w:ptcp.t:call-tar_outputs-28.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:31.462 wdl.w:ptcp.t:call-tar_outputs-28 INFO output :: name: "sample_tarball", value: "m84036_250809_035451_s4.bc2125.tar"
2025-09-15 20:25:31.509 wdl.w:ptcp.t:call-tar_outputs-28 NOTICE done
2025-09-15 20:25:31.513 wdl.w:ptcp NOTICE finish :: job: "call-tar_outputs-28"
2025-09-15 20:25:31.513 wdl.w:ptcp INFO output :: job: "call-tar_outputs-28", values: {"sample_tarball": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-28/out/m84036_250809_035451_s4.bc2125.tar"}
2025-09-15 20:25:31.518 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_genotype NOTICE task setup :: name: "trgt_genotype", source: "./trgt.wdl", line: 272, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-87/call-trgt_genotype", thread: 140606575711808
2025-09-15 20:25:31.534 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_genotype INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:31.534 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_genotype INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:25:31.534 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_genotype INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:25:31.534 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_genotype INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:25:31.534 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_genotype INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2184.mapped.bam.bai"
2025-09-15 20:25:31.534 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_genotype INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2184.mapped.bam"
2025-09-15 20:25:31.534 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_genotype INFO input :: name: "sex", value: "F"
2025-09-15 20:25:31.535 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_genotype INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2184"
2025-09-15 20:25:31.535 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_genotype INFO eval :: name: "mem_gb", value: 16
2025-09-15 20:25:31.535 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_genotype INFO eval :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2184.trgt"
2025-09-15 20:25:31.535 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_genotype INFO eval :: name: "threads", value: 8
2025-09-15 20:25:31.535 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_genotype INFO eval :: name: "disk_size", value: 27
2025-09-15 20:25:31.535 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_genotype INFO eval :: name: "karyotype", value: "XX"
2025-09-15 20:25:31.536 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_genotype INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 8, memory_reservation: 16000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:31.536 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_genotype WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:31.536 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_genotype INFO provisioned :: seconds_waited: 0, cpu: 8, mem_bytes: 16000000000
2025-09-15 20:25:31.536 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_genotype INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:31.593 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_genotype INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 11, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-87/call-trgt_genotype/_singularity_tmpdir_vvvcfkw8"
2025-09-15 20:25:31.593 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_genotype INFO Slurm invocation: srun --job-name call-trgt_genotype --partition compute,compute9 --cpus-per-task 8 --mem 15259M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-87/call-trgt_genotype/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-87/call-trgt_genotype/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-87/call-trgt_genotype/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-87/call-trgt_genotype/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-87/out/m84036_250809_035451_s4.bc2184.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2184.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-87/out/m84036_250809_035451_s4.bc2184.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2184.mapped.bam.bai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-87/call-trgt_genotype/_singularity_tmpdir_vvvcfkw8/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-87/call-trgt_genotype/_singularity_tmpdir_vvvcfkw8/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:31.595 wdl.w:ptcp.w:call-trgt-68.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:25:27 [ERROR] - No reads found for TRID=PRTS_ARX
2025-09-15 20:25:31.596 wdl.w:ptcp.w:call-trgt-68.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:25:27 [ERROR] - No reads found for TRID=EIEE1_ARX
2025-09-15 20:25:31.609 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_genotype NOTICE slurm_singularity run :: pid: 1205860, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-87/call-trgt_genotype/slurm_singularity.log.txt"
2025-09-15 20:25:31.699 wdl.w:ptcp.w:call-trgt-91.t:call-get_reads_overlapping_repeats.slurm_singularity INFO srun: job 51798026 queued and waiting for resources
2025-09-15 20:25:31.699 wdl.w:ptcp.w:call-trgt-91.t:call-get_reads_overlapping_repeats.slurm_singularity INFO srun: job 51798026 has been allocated resources
2025-09-15 20:25:31.699 wdl.w:ptcp.w:call-trgt-91.t:call-get_reads_overlapping_repeats.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:31.715 wdl.w:ptcp.w:call-trgt-79.t:call-trgt_plot_motifs_waterfall INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2176.motifs_waterfall.trgt_plots.zip"
2025-09-15 20:25:31.774 wdl.w:ptcp.w:call-trgt-79.t:call-trgt_plot_motifs_waterfall NOTICE done
2025-09-15 20:25:31.779 wdl.w:ptcp.w:call-trgt-79 NOTICE finish :: job: "call-trgt_plot_motifs_waterfall"
2025-09-15 20:25:31.779 wdl.w:ptcp.w:call-trgt-79 INFO output :: job: "call-trgt_plot_motifs_waterfall", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-79/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2176.motifs_waterfall.trgt_plots.zip"}
2025-09-15 20:25:31.780 wdl.w:ptcp.w:call-trgt-79 INFO visit :: node: "output-images_motifs_waterfall", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-79/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2176.motifs_waterfall.trgt_plots.zip"}
2025-09-15 20:25:31.784 wdl.w:ptcp.w:call-trgt-74.t:call-trgt_plot_meth_allele NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-74/call-trgt_plot_meth_allele", thread: 140608211502656
2025-09-15 20:25:31.800 wdl.w:ptcp.w:call-trgt-74.t:call-trgt_plot_meth_allele INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:31.800 wdl.w:ptcp.w:call-trgt-74.t:call-trgt_plot_meth_allele INFO input :: name: "waterfall", value: false
2025-09-15 20:25:31.801 wdl.w:ptcp.w:call-trgt-74.t:call-trgt_plot_meth_allele INFO input :: name: "methylation", value: true
2025-09-15 20:25:31.801 wdl.w:ptcp.w:call-trgt-74.t:call-trgt_plot_meth_allele INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:25:31.801 wdl.w:ptcp.w:call-trgt-74.t:call-trgt_plot_meth_allele INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:25:31.801 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_genotype.slurm_singularity INFO srun: job 51798027 queued and waiting for resources
2025-09-15 20:25:31.801 wdl.w:ptcp.w:call-trgt-74.t:call-trgt_plot_meth_allele INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:25:31.801 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_genotype.slurm_singularity INFO srun: job 51798027 has been allocated resources
2025-09-15 20:25:31.801 wdl.w:ptcp.w:call-trgt-74.t:call-trgt_plot_meth_allele INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2171.trgt.sorted.spanning.bam.bai"
2025-09-15 20:25:31.801 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_genotype.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:31.801 wdl.w:ptcp.w:call-trgt-74.t:call-trgt_plot_meth_allele INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2171.trgt.sorted.spanning.bam"
2025-09-15 20:25:31.801 wdl.w:ptcp.w:call-trgt-74.t:call-trgt_plot_meth_allele INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2171.trgt.vcf"
2025-09-15 20:25:31.801 wdl.w:ptcp.w:call-trgt-74.t:call-trgt_plot_meth_allele INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2171"
2025-09-15 20:25:31.802 wdl.w:ptcp.w:call-trgt-74.t:call-trgt_plot_meth_allele INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:25:31.802 wdl.w:ptcp.w:call-trgt-74.t:call-trgt_plot_meth_allele INFO eval :: name: "plot_type", value: "allele"
2025-09-15 20:25:31.802 wdl.w:ptcp.w:call-trgt-74.t:call-trgt_plot_meth_allele INFO eval :: name: "show", value: "meth"
2025-09-15 20:25:31.802 wdl.w:ptcp.w:call-trgt-74.t:call-trgt_plot_meth_allele INFO eval :: name: "threads", value: 1
2025-09-15 20:25:31.802 wdl.w:ptcp.w:call-trgt-74.t:call-trgt_plot_meth_allele INFO eval :: name: "disk_size", value: 27
2025-09-15 20:25:31.802 wdl.w:ptcp.w:call-trgt-74.t:call-trgt_plot_meth_allele INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2171.meth_allele"
2025-09-15 20:25:31.803 wdl.w:ptcp.w:call-trgt-74.t:call-trgt_plot_meth_allele INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:31.803 wdl.w:ptcp.w:call-trgt-74.t:call-trgt_plot_meth_allele WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:31.803 wdl.w:ptcp.w:call-trgt-74.t:call-trgt_plot_meth_allele INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:25:31.803 wdl.w:ptcp.w:call-trgt-74.t:call-trgt_plot_meth_allele INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:31.857 wdl.w:ptcp.w:call-trgt-74.t:call-trgt_plot_meth_allele INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-74/call-trgt_plot_meth_allele/_singularity_tmpdir_lpsjlqol"
2025-09-15 20:25:31.857 wdl.w:ptcp.w:call-trgt-74.t:call-trgt_plot_meth_allele INFO Slurm invocation: srun --job-name call-trgt_plot_meth_allele --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-74/call-trgt_plot_meth_allele/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-74/call-trgt_plot_meth_allele/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-74/call-trgt_plot_meth_allele/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-74/call-trgt_plot_meth_allele/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-74/call-trgt_genotype/out/m84036_250809_035451_s4.bc2171.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2171.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-74/call-trgt_genotype/out/m84036_250809_035451_s4.bc2171.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2171.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-74/call-trgt_genotype/out/m84036_250809_035451_s4.bc2171.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2171.trgt.vcf:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-74/call-trgt_plot_meth_allele/_singularity_tmpdir_lpsjlqol/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-74/call-trgt_plot_meth_allele/_singularity_tmpdir_lpsjlqol/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:31.881 wdl.w:ptcp.w:call-trgt-74.t:call-trgt_plot_meth_allele NOTICE slurm_singularity run :: pid: 1205869, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-74/call-trgt_plot_meth_allele/slurm_singularity.log.txt"
2025-09-15 20:25:31.907 wdl.w:ptcp.w:call-trgt-68.t:call-trgt_plot_meth_waterfall INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2165.meth_waterfall.trgt_plots.zip"
2025-09-15 20:25:32.025 wdl.w:ptcp.w:call-paraphase-87.t:call-run_paraphase.slurm_singularity INFO srun: job 51798028 queued and waiting for resources
2025-09-15 20:25:32.025 wdl.w:ptcp.w:call-paraphase-87.t:call-run_paraphase.slurm_singularity INFO srun: job 51798028 has been allocated resources
2025-09-15 20:25:32.025 wdl.w:ptcp.w:call-paraphase-87.t:call-run_paraphase.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:32.027 wdl.w:ptcp.w:call-trgt-68.t:call-trgt_plot_meth_waterfall NOTICE done
2025-09-15 20:25:32.049 wdl.w:ptcp.w:call-sawfish-43.t:call-run_sawfish.stderr VERBOSE [M::worker_pipeline::48.325*1.59] mapped 277 sequences
2025-09-15 20:25:32.050 wdl.w:ptcp.w:call-sawfish-43.t:call-run_sawfish.stderr VERBOSE [M::main] Version: 2.26-r1175
2025-09-15 20:25:32.050 wdl.w:ptcp.w:call-sawfish-43.t:call-run_sawfish.stderr VERBOSE [M::main] CMD: /opt/pacbio/smrttools/install/smrtlink-release_25.1.0.257715/bundles/smrttools/install/smrttools-release_25.1.0.257715/private/thirdparty/minimap2/minimap2_2.26-pacbio2/binwrap/../../../../../private/thirdparty/minimap2/minimap2_2.26-pacbio2/bin/minimap2 -a -y -x map-hifi -Y -E 1,0 /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa -
2025-09-15 20:25:32.050 wdl.w:ptcp.w:call-sawfish-43.t:call-run_sawfish.stderr VERBOSE [M::main] Real time: 48.603 sec; CPU: 77.003 sec; Peak RSS: 11.886 GB
2025-09-15 20:25:32.066 wdl.w:ptcp.w:call-trgt-68 NOTICE finish :: job: "call-trgt_plot_meth_waterfall"
2025-09-15 20:25:32.066 wdl.w:ptcp.w:call-trgt-68 INFO output :: job: "call-trgt_plot_meth_waterfall", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-68/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2165.meth_waterfall.trgt_plots.zip"}
2025-09-15 20:25:32.066 wdl.w:ptcp.w:call-trgt-68 INFO visit :: node: "output-images_meth_waterfall", values: {"images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-68/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2165.meth_waterfall.trgt_plots.zip"}
2025-09-15 20:25:32.066 wdl.w:ptcp.w:call-trgt-68 INFO visit :: node: "outputs", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-68/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2165.motifs_waterfall.trgt_plots.zip", "images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-68/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2165.meth_allele.trgt_plots.zip", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-68/call-trgt_genotype/out/m84036_250809_035451_s4.bc2165.trgt.sorted.spanning.bam.bai", "images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-68/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2165.motifs_allele.trgt_plots.zip", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-68/call-trgt_genotype/out/m84036_250809_035451_s4.bc2165.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-68/call-trgt_genotype/out/m84036_250809_035451_s4.bc2165.trgt.vcf", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-68/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2165.repeats.bam", "images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-68/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2165.meth_waterfall.trgt_plots.zip", "reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-68/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2165.repeats.bam.bai"}
2025-09-15 20:25:32.073 wdl.w:ptcp.w:call-trgt-74.t:call-trgt_plot_meth_waterfall NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-74/call-trgt_plot_meth_waterfall", thread: 140611944420928
2025-09-15 20:25:32.092 wdl.w:ptcp.w:call-trgt-74.t:call-trgt_plot_meth_waterfall INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:32.092 wdl.w:ptcp.w:call-trgt-74.t:call-trgt_plot_meth_waterfall INFO input :: name: "waterfall", value: true
2025-09-15 20:25:32.092 wdl.w:ptcp.w:call-trgt-74.t:call-trgt_plot_meth_waterfall INFO input :: name: "methylation", value: true
2025-09-15 20:25:32.092 wdl.w:ptcp.w:call-trgt-74.t:call-trgt_plot_meth_waterfall INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:25:32.092 wdl.w:ptcp.w:call-trgt-74.t:call-trgt_plot_meth_waterfall INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:25:32.092 wdl.w:ptcp.w:call-trgt-74.t:call-trgt_plot_meth_waterfall INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:25:32.092 wdl.w:ptcp.w:call-trgt-74.t:call-trgt_plot_meth_waterfall INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2171.trgt.sorted.spanning.bam.bai"
2025-09-15 20:25:32.092 wdl.w:ptcp.w:call-trgt-74.t:call-trgt_plot_meth_waterfall INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2171.trgt.sorted.spanning.bam"
2025-09-15 20:25:32.092 wdl.w:ptcp.w:call-trgt-74.t:call-trgt_plot_meth_waterfall INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2171.trgt.vcf"
2025-09-15 20:25:32.092 wdl.w:ptcp.w:call-trgt-74.t:call-trgt_plot_meth_waterfall INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2171"
2025-09-15 20:25:32.093 wdl.w:ptcp.w:call-trgt-74.t:call-trgt_plot_meth_waterfall INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:25:32.093 wdl.w:ptcp.w:call-trgt-74.t:call-trgt_plot_meth_waterfall INFO eval :: name: "plot_type", value: "waterfall"
2025-09-15 20:25:32.093 wdl.w:ptcp.w:call-trgt-74.t:call-trgt_plot_meth_waterfall INFO eval :: name: "show", value: "meth"
2025-09-15 20:25:32.093 wdl.w:ptcp.w:call-trgt-74.t:call-trgt_plot_meth_waterfall INFO eval :: name: "threads", value: 1
2025-09-15 20:25:32.093 wdl.w:ptcp.w:call-trgt-74.t:call-trgt_plot_meth_waterfall INFO eval :: name: "disk_size", value: 27
2025-09-15 20:25:32.093 wdl.w:ptcp.w:call-trgt-74.t:call-trgt_plot_meth_waterfall INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2171.meth_waterfall"
2025-09-15 20:25:32.094 wdl.w:ptcp.w:call-trgt-74.t:call-trgt_plot_meth_waterfall INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:32.094 wdl.w:ptcp.w:call-trgt-74.t:call-trgt_plot_meth_waterfall WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:32.094 wdl.w:ptcp.w:call-trgt-74.t:call-trgt_plot_meth_waterfall INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:25:32.094 wdl.w:ptcp.w:call-trgt-74.t:call-trgt_plot_meth_waterfall INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:32.106 wdl.w:ptcp.w:call-paraphase-43.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for f8inv1 for sample m84036_250809_035451_s4.bc2140 at 2025-09-15 20:25:22.519980...
2025-09-15 20:25:32.106 wdl.w:ptcp.w:call-paraphase-43.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for f8inv1 for sample m84036_250809_035451_s4.bc2140 at 2025-09-15 20:25:23.105873...
2025-09-15 20:25:32.106 wdl.w:ptcp.w:call-paraphase-43.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for hbb for sample m84036_250809_035451_s4.bc2140 at 2025-09-15 20:25:28.305854...
2025-09-15 20:25:32.106 wdl.w:ptcp.w:call-paraphase-43.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for hbb for sample m84036_250809_035451_s4.bc2140 at 2025-09-15 20:25:28.306057...
2025-09-15 20:25:32.107 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_genotype INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2188.trgt.vcf"
2025-09-15 20:25:32.112 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_genotype INFO output :: name: "spanning_bam", value: "m84036_250809_035451_s4.bc2188.trgt.sorted.spanning.bam"
2025-09-15 20:25:32.113 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_genotype INFO output :: name: "spanning_bam_bai", value: "m84036_250809_035451_s4.bc2188.trgt.sorted.spanning.bam.bai"
2025-09-15 20:25:32.165 wdl.w:ptcp.w:call-sawfish-87.t:call-run_sawfish.slurm_singularity INFO srun: job 51798030 queued and waiting for resources
2025-09-15 20:25:32.165 wdl.w:ptcp.w:call-sawfish-87.t:call-run_sawfish.slurm_singularity INFO srun: job 51798030 has been allocated resources
2025-09-15 20:25:32.165 wdl.w:ptcp.w:call-sawfish-87.t:call-run_sawfish.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:32.165 wdl.w:ptcp.w:call-sawfish-87.t:call-run_sawfish.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:25:32.171 wdl.w:ptcp.w:call-trgt-87.t:call-get_reads_overlapping_repeats.slurm_singularity INFO srun: job 51798029 queued and waiting for resources
2025-09-15 20:25:32.171 wdl.w:ptcp.w:call-trgt-87.t:call-get_reads_overlapping_repeats.slurm_singularity INFO srun: job 51798029 has been allocated resources
2025-09-15 20:25:32.171 wdl.w:ptcp.w:call-trgt-87.t:call-get_reads_overlapping_repeats.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:32.180 wdl.w:ptcp.w:call-trgt-68 NOTICE done
2025-09-15 20:25:32.185 wdl.w:ptcp NOTICE finish :: job: "call-trgt-68"
2025-09-15 20:25:32.185 wdl.w:ptcp INFO output :: job: "call-trgt-68", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-68/out/m84036_250809_035451_s4.bc2165.motifs_waterfall.trgt_plots.zip", "images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-68/out/m84036_250809_035451_s4.bc2165.meth_allele.trgt_plots.zip", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-68/out/m84036_250809_035451_s4.bc2165.trgt.sorted.spanning.bam.bai", "images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-68/out/m84036_250809_035451_s4.bc2165.motifs_allele.trgt_plots.zip", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-68/out/m84036_250809_035451_s4.bc2165.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-68/out/m84036_250809_035451_s4.bc2165.trgt.vcf", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-68/out/m84036_250809_035451_s4.bc2165.repeats.bam", "images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-68/out/m84036_250809_035451_s4.bc2165.meth_waterfall.trgt_plots.zip", "reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-68/out/m84036_250809_035451_s4.bc2165.repeats.bam.bai"}
2025-09-15 20:25:32.187 wdl.w:ptcp.w:call-trgt-74.t:call-trgt_plot_meth_waterfall INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-74/call-trgt_plot_meth_waterfall/_singularity_tmpdir_i1kycu8j"
2025-09-15 20:25:32.187 wdl.w:ptcp.w:call-trgt-74.t:call-trgt_plot_meth_waterfall INFO Slurm invocation: srun --job-name call-trgt_plot_meth_waterfall --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-74/call-trgt_plot_meth_waterfall/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-74/call-trgt_plot_meth_waterfall/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-74/call-trgt_plot_meth_waterfall/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-74/call-trgt_plot_meth_waterfall/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-74/call-trgt_genotype/out/m84036_250809_035451_s4.bc2171.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2171.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-74/call-trgt_genotype/out/m84036_250809_035451_s4.bc2171.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2171.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-74/call-trgt_genotype/out/m84036_250809_035451_s4.bc2171.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2171.trgt.vcf:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-74/call-trgt_plot_meth_waterfall/_singularity_tmpdir_i1kycu8j/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-74/call-trgt_plot_meth_waterfall/_singularity_tmpdir_i1kycu8j/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:32.192 wdl.w:ptcp.w:call-trgt-90 NOTICE workflow start :: name: "trgt", source: "./trgt.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-90"
2025-09-15 20:25:32.209 wdl.w:ptcp.w:call-trgt-90 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:25:32.209 wdl.w:ptcp.w:call-trgt-90 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-90/out/m84036_250809_035451_s4.bc2187.mapped.bam"}
2025-09-15 20:25:32.209 wdl.w:ptcp.w:call-trgt-90 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-90/out/m84036_250809_035451_s4.bc2187.mapped.bam.bai"}
2025-09-15 20:25:32.209 wdl.w:ptcp.w:call-trgt-90 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:25:32.209 wdl.w:ptcp.w:call-trgt-90 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:25:32.209 wdl.w:ptcp.w:call-trgt-90 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2187"}
2025-09-15 20:25:32.209 wdl.w:ptcp.w:call-trgt-90 INFO visit :: node: "decl-sex", values: {"sex": "F"}
2025-09-15 20:25:32.209 wdl.w:ptcp.w:call-trgt-90 INFO visit :: node: "decl-trgt_bed", values: {"trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"}
2025-09-15 20:25:32.209 wdl.w:ptcp.w:call-trgt-90 NOTICE ready :: job: "call-get_reads_overlapping_repeats", callee: "get_reads_overlapping_repeats"
2025-09-15 20:25:32.209 wdl.w:ptcp.w:call-trgt-90 INFO input :: job: "call-get_reads_overlapping_repeats", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-90/out/m84036_250809_035451_s4.bc2187.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-90/out/m84036_250809_035451_s4.bc2187.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2187"}
2025-09-15 20:25:32.210 wdl.w:ptcp.w:call-trgt-90 NOTICE ready :: job: "call-trgt_genotype", callee: "trgt_genotype"
2025-09-15 20:25:32.210 wdl.w:ptcp.w:call-trgt-90 INFO input :: job: "call-trgt_genotype", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-90/out/m84036_250809_035451_s4.bc2187.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-90/out/m84036_250809_035451_s4.bc2187.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2187"}
2025-09-15 20:25:32.214 wdl.w:ptcp.w:call-trgt-69.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:23 [ERROR] - No reads found for TRID=PRTS_ARX
2025-09-15 20:25:32.214 wdl.w:ptcp.w:call-trgt-69.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:23 [ERROR] - No reads found for TRID=EIEE1_ARX
2025-09-15 20:25:32.215 wdl.w:ptcp.w:call-trgt-74.t:call-trgt_plot_meth_waterfall NOTICE slurm_singularity run :: pid: 1205878, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-74/call-trgt_plot_meth_waterfall/slurm_singularity.log.txt"
2025-09-15 20:25:32.216 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_genotype NOTICE done
2025-09-15 20:25:32.223 wdl.w:ptcp.w:call-trgt-91 NOTICE finish :: job: "call-trgt_genotype"
2025-09-15 20:25:32.223 wdl.w:ptcp.w:call-trgt-91 INFO output :: job: "call-trgt_genotype", values: {"spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-91/call-trgt_genotype/out/m84036_250809_035451_s4.bc2188.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-91/call-trgt_genotype/out/m84036_250809_035451_s4.bc2188.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-91/call-trgt_genotype/out/m84036_250809_035451_s4.bc2188.trgt.vcf"}
2025-09-15 20:25:32.224 wdl.w:ptcp.w:call-trgt-91 NOTICE ready :: job: "call-trgt_plot_meth_allele", callee: "trgt_plot"
2025-09-15 20:25:32.224 wdl.w:ptcp.w:call-trgt-91 INFO input :: job: "call-trgt_plot_meth_allele", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": false, "methylation": true, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-91/call-trgt_genotype/out/m84036_250809_035451_s4.bc2188.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-91/call-trgt_genotype/out/m84036_250809_035451_s4.bc2188.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-91/call-trgt_genotype/out/m84036_250809_035451_s4.bc2188.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2188"}
2025-09-15 20:25:32.225 wdl.w:ptcp.w:call-trgt-91 NOTICE ready :: job: "call-trgt_plot_meth_waterfall", callee: "trgt_plot"
2025-09-15 20:25:32.225 wdl.w:ptcp.w:call-trgt-91 INFO input :: job: "call-trgt_plot_meth_waterfall", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": true, "methylation": true, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-91/call-trgt_genotype/out/m84036_250809_035451_s4.bc2188.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-91/call-trgt_genotype/out/m84036_250809_035451_s4.bc2188.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-91/call-trgt_genotype/out/m84036_250809_035451_s4.bc2188.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2188"}
2025-09-15 20:25:32.226 wdl.w:ptcp.w:call-trgt-91 NOTICE ready :: job: "call-trgt_plot_motifs_allele", callee: "trgt_plot"
2025-09-15 20:25:32.226 wdl.w:ptcp.w:call-trgt-91 INFO input :: job: "call-trgt_plot_motifs_allele", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": false, "methylation": false, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-91/call-trgt_genotype/out/m84036_250809_035451_s4.bc2188.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-91/call-trgt_genotype/out/m84036_250809_035451_s4.bc2188.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-91/call-trgt_genotype/out/m84036_250809_035451_s4.bc2188.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2188"}
2025-09-15 20:25:32.227 wdl.w:ptcp.w:call-trgt-91 NOTICE ready :: job: "call-trgt_plot_motifs_waterfall", callee: "trgt_plot"
2025-09-15 20:25:32.227 wdl.w:ptcp.w:call-trgt-91 INFO input :: job: "call-trgt_plot_motifs_waterfall", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": true, "methylation": false, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-91/call-trgt_genotype/out/m84036_250809_035451_s4.bc2188.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-91/call-trgt_genotype/out/m84036_250809_035451_s4.bc2188.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-91/call-trgt_genotype/out/m84036_250809_035451_s4.bc2188.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2188"}
2025-09-15 20:25:32.228 wdl.w:ptcp.w:call-trgt-91 INFO visit :: node: "output-spanning_bam", values: {"spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-91/call-trgt_genotype/out/m84036_250809_035451_s4.bc2188.trgt.sorted.spanning.bam"}
2025-09-15 20:25:32.228 wdl.w:ptcp.w:call-trgt-91 INFO visit :: node: "output-spanning_bam_bai", values: {"spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-91/call-trgt_genotype/out/m84036_250809_035451_s4.bc2188.trgt.sorted.spanning.bam.bai"}
2025-09-15 20:25:32.228 wdl.w:ptcp.w:call-trgt-91 INFO visit :: node: "output-vcf", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-91/call-trgt_genotype/out/m84036_250809_035451_s4.bc2188.trgt.vcf"}
2025-09-15 20:25:32.231 wdl.w:ptcp.w:call-trgt-74.t:call-trgt_plot_motifs_allele NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-74/call-trgt_plot_motifs_allele", thread: 140611441120832
2025-09-15 20:25:32.247 wdl.w:ptcp.w:call-trgt-74.t:call-trgt_plot_motifs_allele INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:32.247 wdl.w:ptcp.w:call-trgt-74.t:call-trgt_plot_motifs_allele INFO input :: name: "waterfall", value: false
2025-09-15 20:25:32.247 wdl.w:ptcp.w:call-trgt-74.t:call-trgt_plot_motifs_allele INFO input :: name: "methylation", value: false
2025-09-15 20:25:32.247 wdl.w:ptcp.w:call-trgt-74.t:call-trgt_plot_motifs_allele INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:25:32.247 wdl.w:ptcp.w:call-trgt-74.t:call-trgt_plot_motifs_allele INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:25:32.248 wdl.w:ptcp.w:call-trgt-74.t:call-trgt_plot_motifs_allele INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:25:32.248 wdl.w:ptcp.w:call-trgt-74.t:call-trgt_plot_motifs_allele INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2171.trgt.sorted.spanning.bam.bai"
2025-09-15 20:25:32.248 wdl.w:ptcp.w:call-trgt-74.t:call-trgt_plot_motifs_allele INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2171.trgt.sorted.spanning.bam"
2025-09-15 20:25:32.248 wdl.w:ptcp.w:call-trgt-74.t:call-trgt_plot_motifs_allele INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2171.trgt.vcf"
2025-09-15 20:25:32.248 wdl.w:ptcp.w:call-trgt-74.t:call-trgt_plot_motifs_allele INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2171"
2025-09-15 20:25:32.248 wdl.w:ptcp.w:call-trgt-74.t:call-trgt_plot_motifs_allele INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:25:32.248 wdl.w:ptcp.w:call-trgt-74.t:call-trgt_plot_motifs_allele INFO eval :: name: "plot_type", value: "allele"
2025-09-15 20:25:32.248 wdl.w:ptcp.w:call-trgt-74.t:call-trgt_plot_motifs_allele INFO eval :: name: "show", value: "motifs"
2025-09-15 20:25:32.248 wdl.w:ptcp.w:call-trgt-74.t:call-trgt_plot_motifs_allele INFO eval :: name: "threads", value: 1
2025-09-15 20:25:32.249 wdl.w:ptcp.w:call-trgt-74.t:call-trgt_plot_motifs_allele INFO eval :: name: "disk_size", value: 27
2025-09-15 20:25:32.249 wdl.w:ptcp.w:call-trgt-74.t:call-trgt_plot_motifs_allele INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2171.motifs_allele"
2025-09-15 20:25:32.249 wdl.w:ptcp.w:call-trgt-74.t:call-trgt_plot_motifs_allele INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:32.249 wdl.w:ptcp.w:call-trgt-74.t:call-trgt_plot_motifs_allele WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:32.249 wdl.w:ptcp.w:call-trgt-74.t:call-trgt_plot_motifs_allele INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:25:32.250 wdl.w:ptcp.w:call-trgt-74.t:call-trgt_plot_motifs_allele INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:32.258 wdl.w:ptcp.w:call-trgt-91.t:call-get_reads_overlapping_repeats INFO output :: name: "reads_overlapping_repeats", value: "m84036_250809_035451_s4.bc2188.repeats.bam"
2025-09-15 20:25:32.260 wdl.w:ptcp.w:call-trgt-91.t:call-get_reads_overlapping_repeats INFO output :: name: "reads_overlapping_repeats_bai", value: "m84036_250809_035451_s4.bc2188.repeats.bam.bai"
2025-09-15 20:25:32.323 wdl.w:ptcp.w:call-trgt-74.t:call-trgt_plot_motifs_allele INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-74/call-trgt_plot_motifs_allele/_singularity_tmpdir_drqpzv74"
2025-09-15 20:25:32.323 wdl.w:ptcp.w:call-trgt-74.t:call-trgt_plot_motifs_allele INFO Slurm invocation: srun --job-name call-trgt_plot_motifs_allele --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-74/call-trgt_plot_motifs_allele/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-74/call-trgt_plot_motifs_allele/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-74/call-trgt_plot_motifs_allele/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-74/call-trgt_plot_motifs_allele/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-74/call-trgt_genotype/out/m84036_250809_035451_s4.bc2171.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2171.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-74/call-trgt_genotype/out/m84036_250809_035451_s4.bc2171.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2171.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-74/call-trgt_genotype/out/m84036_250809_035451_s4.bc2171.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2171.trgt.vcf:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-74/call-trgt_plot_motifs_allele/_singularity_tmpdir_drqpzv74/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-74/call-trgt_plot_motifs_allele/_singularity_tmpdir_drqpzv74/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:32.328 wdl.w:ptcp.w:call-trgt-91.t:call-get_reads_overlapping_repeats NOTICE done
2025-09-15 20:25:32.331 wdl.w:ptcp.w:call-trgt-91 NOTICE finish :: job: "call-get_reads_overlapping_repeats"
2025-09-15 20:25:32.331 wdl.w:ptcp.w:call-trgt-91 INFO output :: job: "call-get_reads_overlapping_repeats", values: {"reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-91/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2188.repeats.bam.bai", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-91/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2188.repeats.bam"}
2025-09-15 20:25:32.332 wdl.w:ptcp.w:call-trgt-91 INFO visit :: node: "output-reads_overlapping_repeats", values: {"reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-91/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2188.repeats.bam"}
2025-09-15 20:25:32.332 wdl.w:ptcp.w:call-trgt-91 INFO visit :: node: "output-reads_overlapping_repeats_bai", values: {"reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-91/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2188.repeats.bam.bai"}
2025-09-15 20:25:32.337 wdl.w:ptcp.w:call-trgt-74.t:call-trgt_plot_motifs_waterfall NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-74/call-trgt_plot_motifs_waterfall", thread: 140610912642624
2025-09-15 20:25:32.338 wdl.w:ptcp.w:call-trgt-74.t:call-trgt_plot_motifs_allele NOTICE slurm_singularity run :: pid: 1205880, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-74/call-trgt_plot_motifs_allele/slurm_singularity.log.txt"
2025-09-15 20:25:32.355 wdl.w:ptcp.w:call-trgt-74.t:call-trgt_plot_motifs_waterfall INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:32.355 wdl.w:ptcp.w:call-trgt-74.t:call-trgt_plot_motifs_waterfall INFO input :: name: "waterfall", value: true
2025-09-15 20:25:32.356 wdl.w:ptcp.w:call-trgt-74.t:call-trgt_plot_motifs_waterfall INFO input :: name: "methylation", value: false
2025-09-15 20:25:32.356 wdl.w:ptcp.w:call-trgt-74.t:call-trgt_plot_motifs_waterfall INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:25:32.356 wdl.w:ptcp.w:call-trgt-74.t:call-trgt_plot_motifs_waterfall INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:25:32.356 wdl.w:ptcp.w:call-trgt-74.t:call-trgt_plot_motifs_waterfall INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:25:32.356 wdl.w:ptcp.w:call-trgt-74.t:call-trgt_plot_motifs_waterfall INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2171.trgt.sorted.spanning.bam.bai"
2025-09-15 20:25:32.356 wdl.w:ptcp.w:call-trgt-74.t:call-trgt_plot_motifs_waterfall INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2171.trgt.sorted.spanning.bam"
2025-09-15 20:25:32.356 wdl.w:ptcp.w:call-trgt-74.t:call-trgt_plot_motifs_waterfall INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2171.trgt.vcf"
2025-09-15 20:25:32.356 wdl.w:ptcp.w:call-trgt-74.t:call-trgt_plot_motifs_waterfall INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2171"
2025-09-15 20:25:32.356 wdl.w:ptcp.w:call-trgt-74.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:25:32.356 wdl.w:ptcp.w:call-trgt-74.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "plot_type", value: "waterfall"
2025-09-15 20:25:32.357 wdl.w:ptcp.w:call-trgt-74.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "show", value: "motifs"
2025-09-15 20:25:32.357 wdl.w:ptcp.w:call-trgt-74.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "threads", value: 1
2025-09-15 20:25:32.357 wdl.w:ptcp.w:call-trgt-74.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "disk_size", value: 27
2025-09-15 20:25:32.357 wdl.w:ptcp.w:call-trgt-74.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2171.motifs_waterfall"
2025-09-15 20:25:32.357 wdl.w:ptcp.w:call-trgt-74.t:call-trgt_plot_motifs_waterfall INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:32.357 wdl.w:ptcp.w:call-trgt-74.t:call-trgt_plot_motifs_waterfall WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:32.358 wdl.w:ptcp.w:call-trgt-74.t:call-trgt_plot_motifs_waterfall INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:25:32.358 wdl.w:ptcp.w:call-trgt-74.t:call-trgt_plot_motifs_waterfall INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:32.422 wdl.w:ptcp.w:call-trgt-74.t:call-trgt_plot_motifs_waterfall INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-74/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_ogfjtw4d"
2025-09-15 20:25:32.422 wdl.w:ptcp.w:call-trgt-74.t:call-trgt_plot_motifs_waterfall INFO Slurm invocation: srun --job-name call-trgt_plot_motifs_waterfall --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-74/call-trgt_plot_motifs_waterfall/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-74/call-trgt_plot_motifs_waterfall/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-74/call-trgt_plot_motifs_waterfall/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-74/call-trgt_plot_motifs_waterfall/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-74/call-trgt_genotype/out/m84036_250809_035451_s4.bc2171.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2171.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-74/call-trgt_genotype/out/m84036_250809_035451_s4.bc2171.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2171.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-74/call-trgt_genotype/out/m84036_250809_035451_s4.bc2171.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2171.trgt.vcf:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-74/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_ogfjtw4d/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-74/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_ogfjtw4d/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:32.427 wdl.w:ptcp.w:call-trgt-69.t:call-trgt_plot_meth_allele INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2166.meth_allele.trgt_plots.zip"
2025-09-15 20:25:32.438 wdl.w:ptcp.w:call-trgt-74.t:call-trgt_plot_motifs_waterfall NOTICE slurm_singularity run :: pid: 1205893, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-74/call-trgt_plot_motifs_waterfall/slurm_singularity.log.txt"
2025-09-15 20:25:32.530 wdl.w:ptcp.w:call-trgt-69.t:call-trgt_plot_meth_allele NOTICE done
2025-09-15 20:25:32.537 wdl.w:ptcp.w:call-trgt-69 NOTICE finish :: job: "call-trgt_plot_meth_allele"
2025-09-15 20:25:32.537 wdl.w:ptcp.w:call-trgt-69 INFO output :: job: "call-trgt_plot_meth_allele", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-69/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2166.meth_allele.trgt_plots.zip"}
2025-09-15 20:25:32.538 wdl.w:ptcp.w:call-trgt-69 INFO visit :: node: "output-images_meth_allele", values: {"images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-69/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2166.meth_allele.trgt_plots.zip"}
2025-09-15 20:25:32.538 wdl.w:ptcp.w:call-trgt-69 INFO visit :: node: "outputs", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-69/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2166.motifs_waterfall.trgt_plots.zip", "images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-69/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2166.meth_allele.trgt_plots.zip", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-69/call-trgt_genotype/out/m84036_250809_035451_s4.bc2166.trgt.sorted.spanning.bam.bai", "images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-69/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2166.motifs_allele.trgt_plots.zip", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-69/call-trgt_genotype/out/m84036_250809_035451_s4.bc2166.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-69/call-trgt_genotype/out/m84036_250809_035451_s4.bc2166.trgt.vcf", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-69/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2166.repeats.bam", "images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-69/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2166.meth_waterfall.trgt_plots.zip", "reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-69/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2166.repeats.bam.bai"}
2025-09-15 20:25:32.544 wdl.w:ptcp.w:call-paraphase-89.t:call-run_paraphase NOTICE task setup :: name: "run_paraphase", source: "./paraphase.wdl", line: 127, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-89/call-run_paraphase", thread: 140613588604480
2025-09-15 20:25:32.564 wdl.w:ptcp.w:call-paraphase-89.t:call-run_paraphase INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:32.564 wdl.w:ptcp.w:call-paraphase-89.t:call-run_paraphase INFO input :: name: "annotation_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf"
2025-09-15 20:25:32.564 wdl.w:ptcp.w:call-paraphase-89.t:call-run_paraphase INFO input :: name: "genome_version", value: "38"
2025-09-15 20:25:32.564 wdl.w:ptcp.w:call-paraphase-89.t:call-run_paraphase INFO input :: name: "config_file", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/paraphase_config.GRCh38.yaml"
2025-09-15 20:25:32.564 wdl.w:ptcp.w:call-paraphase-89.t:call-run_paraphase INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:25:32.564 wdl.w:ptcp.w:call-paraphase-89.t:call-run_paraphase INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:25:32.564 wdl.w:ptcp.w:call-paraphase-89.t:call-run_paraphase INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2186.mapped.bam.bai"
2025-09-15 20:25:32.564 wdl.w:ptcp.w:call-paraphase-89.t:call-run_paraphase INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2186.mapped.bam"
2025-09-15 20:25:32.564 wdl.w:ptcp.w:call-paraphase-89.t:call-run_paraphase INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2186"
2025-09-15 20:25:32.564 wdl.w:ptcp.w:call-paraphase-89.t:call-run_paraphase INFO eval :: name: "threads", value: 4
2025-09-15 20:25:32.565 wdl.w:ptcp.w:call-paraphase-89.t:call-run_paraphase INFO eval :: name: "mem_gb", value: 8
2025-09-15 20:25:32.565 wdl.w:ptcp.w:call-paraphase-89.t:call-run_paraphase INFO eval :: name: "disk_size", value: 27
2025-09-15 20:25:32.565 wdl.w:ptcp.w:call-paraphase-89.t:call-run_paraphase INFO eval :: name: "out_dir", value: "m84036_250809_035451_s4.bc2186_paraphase"
2025-09-15 20:25:32.565 wdl.w:ptcp.w:call-paraphase-89.t:call-run_paraphase INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 4, memory_reservation: 8000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:32.565 wdl.w:ptcp.w:call-paraphase-89.t:call-run_paraphase WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:32.566 wdl.w:ptcp.w:call-paraphase-89.t:call-run_paraphase INFO provisioned :: seconds_waited: 0, cpu: 4, mem_bytes: 8000000000
2025-09-15 20:25:32.566 wdl.w:ptcp.w:call-paraphase-89.t:call-run_paraphase INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:32.591 wdl.w:ptcp.w:call-paraphase-31.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for rpgr for sample m84036_250809_035451_s4.bc2128 at 2025-09-15 20:24:43.839279...
2025-09-15 20:25:32.592 wdl.w:ptcp.w:call-paraphase-31.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for rpgr for sample m84036_250809_035451_s4.bc2128 at 2025-09-15 20:24:44.866470...
2025-09-15 20:25:32.592 wdl.w:ptcp.w:call-paraphase-31.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for rpgr for sample m84036_250809_035451_s4.bc2128 at 2025-09-15 20:24:45.039089...
2025-09-15 20:25:32.592 wdl.w:ptcp.w:call-paraphase-31.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for f8inv22 for sample m84036_250809_035451_s4.bc2128 at 2025-09-15 20:25:31.737425...
2025-09-15 20:25:32.592 wdl.w:ptcp.w:call-paraphase-31.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for f8inv22 for sample m84036_250809_035451_s4.bc2128 at 2025-09-15 20:25:31.738099...
2025-09-15 20:25:32.620 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_genotype.slurm_singularity INFO srun: job 51798031 queued and waiting for resources
2025-09-15 20:25:32.620 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_genotype.slurm_singularity INFO srun: job 51798031 has been allocated resources
2025-09-15 20:25:32.620 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_genotype.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:32.620 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_genotype.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:25:32.642 wdl.w:ptcp.w:call-paraphase-89.t:call-run_paraphase INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-89/call-run_paraphase/_singularity_tmpdir_lf5elt9m"
2025-09-15 20:25:32.642 wdl.w:ptcp.w:call-paraphase-89.t:call-run_paraphase INFO Slurm invocation: srun --job-name call-run_paraphase --partition compute,compute9 --cpus-per-task 4 --mem 7629M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-89/call-run_paraphase/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-89/call-run_paraphase/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-89/call-run_paraphase/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-89/call-run_paraphase/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-89/out/m84036_250809_035451_s4.bc2186.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2186.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-89/out/m84036_250809_035451_s4.bc2186.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2186.mapped.bam:ro --bind /ptcp/meta/variant_list/variant_list.GRCh38.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf:ro --bind /ptcp/meta/paraphase/paraphase_config.GRCh38.yaml:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/paraphase_config.GRCh38.yaml:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-89/call-run_paraphase/_singularity_tmpdir_lf5elt9m/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-89/call-run_paraphase/_singularity_tmpdir_lf5elt9m/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:32.659 wdl.w:ptcp.w:call-trgt-69 NOTICE done
2025-09-15 20:25:32.665 wdl.w:ptcp NOTICE finish :: job: "call-trgt-69"
2025-09-15 20:25:32.665 wdl.w:ptcp INFO output :: job: "call-trgt-69", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-69/out/m84036_250809_035451_s4.bc2166.motifs_waterfall.trgt_plots.zip", "images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-69/out/m84036_250809_035451_s4.bc2166.meth_allele.trgt_plots.zip", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-69/out/m84036_250809_035451_s4.bc2166.trgt.sorted.spanning.bam.bai", "images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-69/out/m84036_250809_035451_s4.bc2166.motifs_allele.trgt_plots.zip", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-69/out/m84036_250809_035451_s4.bc2166.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-69/out/m84036_250809_035451_s4.bc2166.trgt.vcf", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-69/out/m84036_250809_035451_s4.bc2166.repeats.bam", "images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-69/out/m84036_250809_035451_s4.bc2166.meth_waterfall.trgt_plots.zip", "reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-69/out/m84036_250809_035451_s4.bc2166.repeats.bam.bai"}
2025-09-15 20:25:32.666 wdl.w:ptcp.w:call-paraphase-89.t:call-run_paraphase NOTICE slurm_singularity run :: pid: 1205896, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-89/call-run_paraphase/slurm_singularity.log.txt"
2025-09-15 20:25:32.671 wdl.w:ptcp.w:call-paraphase-86 NOTICE workflow start :: name: "paraphase", source: "./paraphase.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-86"
2025-09-15 20:25:32.689 wdl.w:ptcp.w:call-paraphase-86 INFO visit :: node: "decl-annotation_vcf", values: {"annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf"}
2025-09-15 20:25:32.689 wdl.w:ptcp.w:call-paraphase-86 INFO visit :: node: "decl-config_file", values: {"config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml"}
2025-09-15 20:25:32.689 wdl.w:ptcp.w:call-paraphase-86 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:25:32.689 wdl.w:ptcp.w:call-paraphase-86 INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:25:32.689 wdl.w:ptcp.w:call-paraphase-86 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-86/out/m84036_250809_035451_s4.bc2183.mapped.bam"}
2025-09-15 20:25:32.689 wdl.w:ptcp.w:call-paraphase-86 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-86/out/m84036_250809_035451_s4.bc2183.mapped.bam.bai"}
2025-09-15 20:25:32.689 wdl.w:ptcp.w:call-paraphase-86 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:25:32.689 wdl.w:ptcp.w:call-paraphase-86 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:25:32.689 wdl.w:ptcp.w:call-paraphase-86 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2183"}
2025-09-15 20:25:32.689 wdl.w:ptcp.w:call-paraphase-86 INFO visit :: node: "decl-sex", values: {"sex": "F"}
2025-09-15 20:25:32.690 wdl.w:ptcp.w:call-paraphase-86 NOTICE ready :: job: "call-run_paraphase", callee: "run_paraphase"
2025-09-15 20:25:32.690 wdl.w:ptcp.w:call-paraphase-86 INFO input :: job: "call-run_paraphase", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf", "genome_version": "38", "config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-86/out/m84036_250809_035451_s4.bc2183.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-86/out/m84036_250809_035451_s4.bc2183.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2183"}
2025-09-15 20:25:32.707 wdl.w:ptcp.w:call-trgt-85.t:call-trgt_genotype INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2182.trgt.vcf"
2025-09-15 20:25:32.712 wdl.w:ptcp.w:call-trgt-85.t:call-trgt_genotype INFO output :: name: "spanning_bam", value: "m84036_250809_035451_s4.bc2182.trgt.sorted.spanning.bam"
2025-09-15 20:25:32.714 wdl.w:ptcp.w:call-trgt-85.t:call-trgt_genotype INFO output :: name: "spanning_bam_bai", value: "m84036_250809_035451_s4.bc2182.trgt.sorted.spanning.bam.bai"
2025-09-15 20:25:32.731 wdl.w:ptcp.w:call-trgt-87.t:call-get_reads_overlapping_repeats INFO output :: name: "reads_overlapping_repeats", value: "m84036_250809_035451_s4.bc2184.repeats.bam"
2025-09-15 20:25:32.735 wdl.w:ptcp.w:call-trgt-87.t:call-get_reads_overlapping_repeats INFO output :: name: "reads_overlapping_repeats_bai", value: "m84036_250809_035451_s4.bc2184.repeats.bam.bai"
2025-09-15 20:25:32.791 wdl.w:ptcp.w:call-trgt-85.t:call-trgt_genotype NOTICE done
2025-09-15 20:25:32.795 wdl.w:ptcp.w:call-trgt-87.t:call-get_reads_overlapping_repeats NOTICE done
2025-09-15 20:25:32.797 wdl.w:ptcp.w:call-trgt-85 NOTICE finish :: job: "call-trgt_genotype"
2025-09-15 20:25:32.797 wdl.w:ptcp.w:call-trgt-85 INFO output :: job: "call-trgt_genotype", values: {"spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-85/call-trgt_genotype/out/m84036_250809_035451_s4.bc2182.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-85/call-trgt_genotype/out/m84036_250809_035451_s4.bc2182.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-85/call-trgt_genotype/out/m84036_250809_035451_s4.bc2182.trgt.vcf"}
2025-09-15 20:25:32.798 wdl.w:ptcp.w:call-trgt-85 NOTICE ready :: job: "call-trgt_plot_meth_allele", callee: "trgt_plot"
2025-09-15 20:25:32.798 wdl.w:ptcp.w:call-trgt-85 INFO input :: job: "call-trgt_plot_meth_allele", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": false, "methylation": true, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-85/call-trgt_genotype/out/m84036_250809_035451_s4.bc2182.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-85/call-trgt_genotype/out/m84036_250809_035451_s4.bc2182.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-85/call-trgt_genotype/out/m84036_250809_035451_s4.bc2182.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2182"}
2025-09-15 20:25:32.799 wdl.w:ptcp.w:call-trgt-85 NOTICE ready :: job: "call-trgt_plot_meth_waterfall", callee: "trgt_plot"
2025-09-15 20:25:32.799 wdl.w:ptcp.w:call-trgt-85 INFO input :: job: "call-trgt_plot_meth_waterfall", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": true, "methylation": true, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-85/call-trgt_genotype/out/m84036_250809_035451_s4.bc2182.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-85/call-trgt_genotype/out/m84036_250809_035451_s4.bc2182.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-85/call-trgt_genotype/out/m84036_250809_035451_s4.bc2182.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2182"}
2025-09-15 20:25:32.800 wdl.w:ptcp.w:call-trgt-85 NOTICE ready :: job: "call-trgt_plot_motifs_allele", callee: "trgt_plot"
2025-09-15 20:25:32.800 wdl.w:ptcp.w:call-trgt-85 INFO input :: job: "call-trgt_plot_motifs_allele", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": false, "methylation": false, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-85/call-trgt_genotype/out/m84036_250809_035451_s4.bc2182.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-85/call-trgt_genotype/out/m84036_250809_035451_s4.bc2182.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-85/call-trgt_genotype/out/m84036_250809_035451_s4.bc2182.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2182"}
2025-09-15 20:25:32.801 wdl.w:ptcp.w:call-trgt-85 NOTICE ready :: job: "call-trgt_plot_motifs_waterfall", callee: "trgt_plot"
2025-09-15 20:25:32.801 wdl.w:ptcp.w:call-trgt-85 INFO input :: job: "call-trgt_plot_motifs_waterfall", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": true, "methylation": false, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-85/call-trgt_genotype/out/m84036_250809_035451_s4.bc2182.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-85/call-trgt_genotype/out/m84036_250809_035451_s4.bc2182.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-85/call-trgt_genotype/out/m84036_250809_035451_s4.bc2182.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2182"}
2025-09-15 20:25:32.801 wdl.w:ptcp.w:call-trgt-85 INFO visit :: node: "output-spanning_bam", values: {"spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-85/call-trgt_genotype/out/m84036_250809_035451_s4.bc2182.trgt.sorted.spanning.bam"}
2025-09-15 20:25:32.801 wdl.w:ptcp.w:call-trgt-85 INFO visit :: node: "output-spanning_bam_bai", values: {"spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-85/call-trgt_genotype/out/m84036_250809_035451_s4.bc2182.trgt.sorted.spanning.bam.bai"}
2025-09-15 20:25:32.801 wdl.w:ptcp.w:call-trgt-85 INFO visit :: node: "output-vcf", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-85/call-trgt_genotype/out/m84036_250809_035451_s4.bc2182.trgt.vcf"}
2025-09-15 20:25:32.805 wdl.w:ptcp.w:call-trgt-78.t:call-trgt_plot_meth_allele NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-78/call-trgt_plot_meth_allele", thread: 140607674631744
2025-09-15 20:25:32.821 wdl.w:ptcp.w:call-trgt-78.t:call-trgt_plot_meth_allele INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:32.821 wdl.w:ptcp.w:call-trgt-78.t:call-trgt_plot_meth_allele INFO input :: name: "waterfall", value: false
2025-09-15 20:25:32.821 wdl.w:ptcp.w:call-trgt-78.t:call-trgt_plot_meth_allele INFO input :: name: "methylation", value: true
2025-09-15 20:25:32.821 wdl.w:ptcp.w:call-trgt-78.t:call-trgt_plot_meth_allele INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:25:32.821 wdl.w:ptcp.w:call-trgt-78.t:call-trgt_plot_meth_allele INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:25:32.822 wdl.w:ptcp.w:call-trgt-78.t:call-trgt_plot_meth_allele INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:25:32.822 wdl.w:ptcp.w:call-trgt-78.t:call-trgt_plot_meth_allele INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2175.trgt.sorted.spanning.bam.bai"
2025-09-15 20:25:32.822 wdl.w:ptcp.w:call-trgt-78.t:call-trgt_plot_meth_allele INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2175.trgt.sorted.spanning.bam"
2025-09-15 20:25:32.822 wdl.w:ptcp.w:call-trgt-78.t:call-trgt_plot_meth_allele INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2175.trgt.vcf"
2025-09-15 20:25:32.822 wdl.w:ptcp.w:call-trgt-78.t:call-trgt_plot_meth_allele INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2175"
2025-09-15 20:25:32.822 wdl.w:ptcp.w:call-trgt-78.t:call-trgt_plot_meth_allele INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:25:32.822 wdl.w:ptcp.w:call-trgt-78.t:call-trgt_plot_meth_allele INFO eval :: name: "plot_type", value: "allele"
2025-09-15 20:25:32.822 wdl.w:ptcp.w:call-trgt-78.t:call-trgt_plot_meth_allele INFO eval :: name: "show", value: "meth"
2025-09-15 20:25:32.822 wdl.w:ptcp.w:call-trgt-78.t:call-trgt_plot_meth_allele INFO eval :: name: "threads", value: 1
2025-09-15 20:25:32.823 wdl.w:ptcp.w:call-trgt-78.t:call-trgt_plot_meth_allele INFO eval :: name: "disk_size", value: 27
2025-09-15 20:25:32.823 wdl.w:ptcp.w:call-trgt-78.t:call-trgt_plot_meth_allele INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2175.meth_allele"
2025-09-15 20:25:32.823 wdl.w:ptcp.w:call-trgt-78.t:call-trgt_plot_meth_allele INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:32.823 wdl.w:ptcp.w:call-trgt-78.t:call-trgt_plot_meth_allele WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:32.823 wdl.w:ptcp.w:call-trgt-78.t:call-trgt_plot_meth_allele INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:25:32.824 wdl.w:ptcp.w:call-trgt-78.t:call-trgt_plot_meth_allele INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:32.846 wdl.w:ptcp.w:call-trgt-87 NOTICE finish :: job: "call-get_reads_overlapping_repeats"
2025-09-15 20:25:32.846 wdl.w:ptcp.w:call-trgt-87 INFO output :: job: "call-get_reads_overlapping_repeats", values: {"reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-87/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2184.repeats.bam.bai", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-87/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2184.repeats.bam"}
2025-09-15 20:25:32.846 wdl.w:ptcp.w:call-trgt-87 INFO visit :: node: "output-reads_overlapping_repeats", values: {"reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-87/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2184.repeats.bam"}
2025-09-15 20:25:32.846 wdl.w:ptcp.w:call-trgt-87 INFO visit :: node: "output-reads_overlapping_repeats_bai", values: {"reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-87/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2184.repeats.bam.bai"}
2025-09-15 20:25:32.852 wdl.w:ptcp.w:call-trgt-78.t:call-trgt_plot_meth_waterfall NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-78/call-trgt_plot_meth_waterfall", thread: 140607137760832
2025-09-15 20:25:32.872 wdl.w:ptcp.w:call-trgt-78.t:call-trgt_plot_meth_waterfall INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:32.872 wdl.w:ptcp.w:call-trgt-78.t:call-trgt_plot_meth_waterfall INFO input :: name: "waterfall", value: true
2025-09-15 20:25:32.872 wdl.w:ptcp.w:call-trgt-78.t:call-trgt_plot_meth_waterfall INFO input :: name: "methylation", value: true
2025-09-15 20:25:32.872 wdl.w:ptcp.w:call-trgt-78.t:call-trgt_plot_meth_waterfall INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:25:32.872 wdl.w:ptcp.w:call-trgt-78.t:call-trgt_plot_meth_waterfall INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:25:32.872 wdl.w:ptcp.w:call-trgt-78.t:call-trgt_plot_meth_waterfall INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:25:32.872 wdl.w:ptcp.w:call-trgt-78.t:call-trgt_plot_meth_waterfall INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2175.trgt.sorted.spanning.bam.bai"
2025-09-15 20:25:32.872 wdl.w:ptcp.w:call-trgt-78.t:call-trgt_plot_meth_waterfall INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2175.trgt.sorted.spanning.bam"
2025-09-15 20:25:32.872 wdl.w:ptcp.w:call-trgt-78.t:call-trgt_plot_meth_waterfall INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2175.trgt.vcf"
2025-09-15 20:25:32.873 wdl.w:ptcp.w:call-trgt-78.t:call-trgt_plot_meth_waterfall INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2175"
2025-09-15 20:25:32.873 wdl.w:ptcp.w:call-trgt-78.t:call-trgt_plot_meth_waterfall INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:25:32.873 wdl.w:ptcp.w:call-trgt-78.t:call-trgt_plot_meth_waterfall INFO eval :: name: "plot_type", value: "waterfall"
2025-09-15 20:25:32.873 wdl.w:ptcp.w:call-trgt-78.t:call-trgt_plot_meth_waterfall INFO eval :: name: "show", value: "meth"
2025-09-15 20:25:32.873 wdl.w:ptcp.w:call-trgt-78.t:call-trgt_plot_meth_waterfall INFO eval :: name: "threads", value: 1
2025-09-15 20:25:32.873 wdl.w:ptcp.w:call-trgt-78.t:call-trgt_plot_meth_waterfall INFO eval :: name: "disk_size", value: 27
2025-09-15 20:25:32.873 wdl.w:ptcp.w:call-trgt-78.t:call-trgt_plot_meth_waterfall INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2175.meth_waterfall"
2025-09-15 20:25:32.874 wdl.w:ptcp.w:call-trgt-78.t:call-trgt_plot_meth_waterfall INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:32.874 wdl.w:ptcp.w:call-trgt-78.t:call-trgt_plot_meth_waterfall WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:32.874 wdl.w:ptcp.w:call-trgt-78.t:call-trgt_plot_meth_waterfall INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:25:32.874 wdl.w:ptcp.w:call-trgt-78.t:call-trgt_plot_meth_waterfall INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:32.885 wdl.w:ptcp.w:call-trgt-74.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:32 [ERROR] - No reads found for TRID=SCA37_DAB1
2025-09-15 20:25:32.885 wdl.w:ptcp.w:call-trgt-74.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:32 [ERROR] - No reads found for TRID=OPDM_ABCD3
2025-09-15 20:25:32.885 wdl.w:ptcp.w:call-trgt-74.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:32 [ERROR] - No reads found for TRID=NIID_NOTCH2NLC
2025-09-15 20:25:32.885 wdl.w:ptcp.w:call-trgt-74.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:32 [ERROR] - No reads found for TRID=SCA2_ATXN2
2025-09-15 20:25:32.894 wdl.w:ptcp.w:call-trgt-74.t:call-trgt_plot_meth_allele.slurm_singularity INFO srun: job 51798032 queued and waiting for resources
2025-09-15 20:25:32.894 wdl.w:ptcp.w:call-trgt-74.t:call-trgt_plot_meth_allele.slurm_singularity INFO srun: job 51798032 has been allocated resources
2025-09-15 20:25:32.894 wdl.w:ptcp.w:call-trgt-74.t:call-trgt_plot_meth_allele.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:32.903 wdl.w:ptcp.w:call-trgt-78.t:call-trgt_plot_meth_allele INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-78/call-trgt_plot_meth_allele/_singularity_tmpdir_w2fa0j90"
2025-09-15 20:25:32.903 wdl.w:ptcp.w:call-trgt-78.t:call-trgt_plot_meth_allele INFO Slurm invocation: srun --job-name call-trgt_plot_meth_allele --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-78/call-trgt_plot_meth_allele/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-78/call-trgt_plot_meth_allele/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-78/call-trgt_plot_meth_allele/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-78/call-trgt_plot_meth_allele/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-78/call-trgt_genotype/out/m84036_250809_035451_s4.bc2175.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2175.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-78/call-trgt_genotype/out/m84036_250809_035451_s4.bc2175.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2175.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-78/call-trgt_genotype/out/m84036_250809_035451_s4.bc2175.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2175.trgt.sorted.spanning.bam.bai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-78/call-trgt_plot_meth_allele/_singularity_tmpdir_w2fa0j90/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-78/call-trgt_plot_meth_allele/_singularity_tmpdir_w2fa0j90/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:32.922 wdl.w:ptcp.w:call-trgt-78.t:call-trgt_plot_meth_allele NOTICE slurm_singularity run :: pid: 1205904, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-78/call-trgt_plot_meth_allele/slurm_singularity.log.txt"
2025-09-15 20:25:32.958 wdl.w:ptcp.w:call-trgt-78.t:call-trgt_plot_meth_waterfall INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-78/call-trgt_plot_meth_waterfall/_singularity_tmpdir_q59d_8rm"
2025-09-15 20:25:32.958 wdl.w:ptcp.w:call-trgt-78.t:call-trgt_plot_meth_waterfall INFO Slurm invocation: srun --job-name call-trgt_plot_meth_waterfall --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-78/call-trgt_plot_meth_waterfall/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-78/call-trgt_plot_meth_waterfall/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-78/call-trgt_plot_meth_waterfall/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-78/call-trgt_plot_meth_waterfall/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-78/call-trgt_genotype/out/m84036_250809_035451_s4.bc2175.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2175.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-78/call-trgt_genotype/out/m84036_250809_035451_s4.bc2175.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2175.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-78/call-trgt_genotype/out/m84036_250809_035451_s4.bc2175.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2175.trgt.sorted.spanning.bam.bai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-78/call-trgt_plot_meth_waterfall/_singularity_tmpdir_q59d_8rm/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-78/call-trgt_plot_meth_waterfall/_singularity_tmpdir_q59d_8rm/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:32.966 wdl.w:ptcp.w:call-trgt-78.t:call-trgt_plot_meth_waterfall NOTICE slurm_singularity run :: pid: 1205906, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-78/call-trgt_plot_meth_waterfall/slurm_singularity.log.txt"
2025-09-15 20:25:32.999 wdl.w:ptcp.w:call-paraphase-74.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for smn1 for sample m84036_250809_035451_s4.bc2171 at 2025-09-15 20:25:26.590388...
2025-09-15 20:25:33.052 wdl.w:ptcp.w:call-paraphase-39.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for f8inv1 for sample m84036_250809_035451_s4.bc2136 at 2025-09-15 20:25:24.516248...
2025-09-15 20:25:33.052 wdl.w:ptcp.w:call-paraphase-39.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for f8inv1 for sample m84036_250809_035451_s4.bc2136 at 2025-09-15 20:25:28.473242...
2025-09-15 20:25:33.052 wdl.w:ptcp.w:call-paraphase-39.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for hbb for sample m84036_250809_035451_s4.bc2136 at 2025-09-15 20:25:28.682401...
2025-09-15 20:25:33.053 wdl.w:ptcp.w:call-paraphase-39.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for hbb for sample m84036_250809_035451_s4.bc2136 at 2025-09-15 20:25:28.682598...
2025-09-15 20:25:33.217 wdl.w:ptcp.w:call-trgt-74.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:25:33 [ERROR] - No reads found for TRID=SCA37_DAB1
2025-09-15 20:25:33.217 wdl.w:ptcp.w:call-trgt-74.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:25:33 [ERROR] - No reads found for TRID=OPDM_ABCD3
2025-09-15 20:25:33.225 wdl.w:ptcp.w:call-trgt-74.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO srun: job 51798033 queued and waiting for resources
2025-09-15 20:25:33.225 wdl.w:ptcp.w:call-trgt-74.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO srun: job 51798033 has been allocated resources
2025-09-15 20:25:33.225 wdl.w:ptcp.w:call-trgt-74.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:33.325 wdl.w:ptcp.w:call-trgt-85.t:call-get_reads_overlapping_repeats INFO output :: name: "reads_overlapping_repeats", value: "m84036_250809_035451_s4.bc2182.repeats.bam"
2025-09-15 20:25:33.328 wdl.w:ptcp.w:call-trgt-85.t:call-get_reads_overlapping_repeats INFO output :: name: "reads_overlapping_repeats_bai", value: "m84036_250809_035451_s4.bc2182.repeats.bam.bai"
2025-09-15 20:25:33.348 wdl.w:ptcp.w:call-trgt-74.t:call-trgt_plot_motifs_allele.slurm_singularity INFO srun: job 51798034 queued and waiting for resources
2025-09-15 20:25:33.348 wdl.w:ptcp.w:call-trgt-74.t:call-trgt_plot_motifs_allele.slurm_singularity INFO srun: job 51798034 has been allocated resources
2025-09-15 20:25:33.348 wdl.w:ptcp.w:call-trgt-74.t:call-trgt_plot_motifs_allele.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:33.390 wdl.w:ptcp.w:call-trgt-85.t:call-get_reads_overlapping_repeats NOTICE done
2025-09-15 20:25:33.394 wdl.w:ptcp.w:call-trgt-85 NOTICE finish :: job: "call-get_reads_overlapping_repeats"
2025-09-15 20:25:33.394 wdl.w:ptcp.w:call-trgt-85 INFO output :: job: "call-get_reads_overlapping_repeats", values: {"reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-85/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2182.repeats.bam.bai", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-85/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2182.repeats.bam"}
2025-09-15 20:25:33.394 wdl.w:ptcp.w:call-trgt-85 INFO visit :: node: "output-reads_overlapping_repeats", values: {"reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-85/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2182.repeats.bam"}
2025-09-15 20:25:33.395 wdl.w:ptcp.w:call-trgt-85 INFO visit :: node: "output-reads_overlapping_repeats_bai", values: {"reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-85/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2182.repeats.bam.bai"}
2025-09-15 20:25:33.399 wdl.w:ptcp.w:call-trgt-78.t:call-trgt_plot_motifs_allele NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-78/call-trgt_plot_motifs_allele", thread: 140607683024448
2025-09-15 20:25:33.406 wdl.w:ptcp.w:call-paraphase-72.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for f8inv22 for sample m84036_250809_035451_s4.bc2169 at 2025-09-15 20:25:30.572068...
2025-09-15 20:25:33.406 wdl.w:ptcp.w:call-paraphase-72.t:call-run_paraphase.stderr VERBOSE WARNING:root:This region does not appear to have coverage. Will not attempt to phase haplotypes.
2025-09-15 20:25:33.406 wdl.w:ptcp.w:call-paraphase-72.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for f8inv22 for sample m84036_250809_035451_s4.bc2169 at 2025-09-15 20:25:30.686297...
2025-09-15 20:25:33.406 wdl.w:ptcp.w:call-paraphase-72.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for hbb for sample m84036_250809_035451_s4.bc2169 at 2025-09-15 20:25:30.691145...
2025-09-15 20:25:33.406 wdl.w:ptcp.w:call-paraphase-72.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for rpgr for sample m84036_250809_035451_s4.bc2169 at 2025-09-15 20:25:30.706092...
2025-09-15 20:25:33.406 wdl.w:ptcp.w:call-paraphase-72.t:call-run_paraphase.stderr VERBOSE WARNING:root:This region does not appear to have coverage. Will not attempt to phase haplotypes.
2025-09-15 20:25:33.406 wdl.w:ptcp.w:call-paraphase-72.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for hbb for sample m84036_250809_035451_s4.bc2169 at 2025-09-15 20:25:30.791977...
2025-09-15 20:25:33.406 wdl.w:ptcp.w:call-paraphase-72.t:call-run_paraphase.stderr VERBOSE WARNING:root:This region does not appear to have coverage. Will not attempt to phase haplotypes.
2025-09-15 20:25:33.406 wdl.w:ptcp.w:call-paraphase-72.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for rpgr for sample m84036_250809_035451_s4.bc2169 at 2025-09-15 20:25:30.833334...
2025-09-15 20:25:33.407 wdl.w:ptcp.w:call-paraphase-72.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for f8inv22 for sample m84036_250809_035451_s4.bc2169 at 2025-09-15 20:25:31.204698...
2025-09-15 20:25:33.407 wdl.w:ptcp.w:call-paraphase-72.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for smn1 for sample m84036_250809_035451_s4.bc2169 at 2025-09-15 20:25:31.272650...
2025-09-15 20:25:33.407 wdl.w:ptcp.w:call-paraphase-72.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for hbb for sample m84036_250809_035451_s4.bc2169 at 2025-09-15 20:25:31.335943...
2025-09-15 20:25:33.407 wdl.w:ptcp.w:call-paraphase-72.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for f8inv1 for sample m84036_250809_035451_s4.bc2169 at 2025-09-15 20:25:31.353883...
2025-09-15 20:25:33.407 wdl.w:ptcp.w:call-paraphase-72.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for f8inv1 for sample m84036_250809_035451_s4.bc2169 at 2025-09-15 20:25:31.354115...
2025-09-15 20:25:33.407 wdl.w:ptcp.w:call-paraphase-72.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for rpgr for sample m84036_250809_035451_s4.bc2169 at 2025-09-15 20:25:31.392873...
2025-09-15 20:25:33.408 wdl.w:ptcp.w:call-paraphase-72.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for f8inv1 for sample m84036_250809_035451_s4.bc2169 at 2025-09-15 20:25:31.805124...
2025-09-15 20:25:33.408 wdl.w:ptcp.w:call-paraphase-72.t:call-run_paraphase.stderr VERBOSE WARNING:root:This region does not appear to have coverage. Will not attempt to phase haplotypes.
2025-09-15 20:25:33.408 wdl.w:ptcp.w:call-paraphase-72.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for f8inv1 for sample m84036_250809_035451_s4.bc2169 at 2025-09-15 20:25:31.896430...
2025-09-15 20:25:33.408 wdl.w:ptcp.w:call-paraphase-72.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for f8inv1 for sample m84036_250809_035451_s4.bc2169 at 2025-09-15 20:25:32.206734...
2025-09-15 20:25:33.408 wdl.w:ptcp.w:call-paraphase-72.t:call-run_paraphase.stderr VERBOSE INFO:root:Merging all bams for sample m84036_250809_035451_s4.bc2169 at 2025-09-15 20:25:32.231545...
2025-09-15 20:25:33.408 wdl.w:ptcp.w:call-paraphase-72.t:call-run_paraphase.stderr VERBOSE INFO:root:Writing to json for sample m84036_250809_035451_s4.bc2169 at 2025-09-15 20:25:32.612885...
2025-09-15 20:25:33.409 wdl.w:ptcp.w:call-paraphase-72.t:call-run_paraphase.stderr VERBOSE INFO:root:Completed Paraphase analysis at 2025-09-15 20:25:33.008120...
2025-09-15 20:25:33.414 wdl.w:ptcp.w:call-trgt-78.t:call-trgt_plot_motifs_allele INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:33.414 wdl.w:ptcp.w:call-trgt-78.t:call-trgt_plot_motifs_allele INFO input :: name: "waterfall", value: false
2025-09-15 20:25:33.414 wdl.w:ptcp.w:call-trgt-78.t:call-trgt_plot_motifs_allele INFO input :: name: "methylation", value: false
2025-09-15 20:25:33.414 wdl.w:ptcp.w:call-trgt-78.t:call-trgt_plot_motifs_allele INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:25:33.414 wdl.w:ptcp.w:call-trgt-78.t:call-trgt_plot_motifs_allele INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:25:33.414 wdl.w:ptcp.w:call-trgt-78.t:call-trgt_plot_motifs_allele INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:25:33.414 wdl.w:ptcp.w:call-trgt-78.t:call-trgt_plot_motifs_allele INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2175.trgt.sorted.spanning.bam.bai"
2025-09-15 20:25:33.414 wdl.w:ptcp.w:call-trgt-78.t:call-trgt_plot_motifs_allele INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2175.trgt.sorted.spanning.bam"
2025-09-15 20:25:33.414 wdl.w:ptcp.w:call-trgt-78.t:call-trgt_plot_motifs_allele INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2175.trgt.vcf"
2025-09-15 20:25:33.415 wdl.w:ptcp.w:call-trgt-78.t:call-trgt_plot_motifs_allele INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2175"
2025-09-15 20:25:33.415 wdl.w:ptcp.w:call-trgt-78.t:call-trgt_plot_motifs_allele INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:25:33.415 wdl.w:ptcp.w:call-trgt-78.t:call-trgt_plot_motifs_allele INFO eval :: name: "plot_type", value: "allele"
2025-09-15 20:25:33.415 wdl.w:ptcp.w:call-trgt-78.t:call-trgt_plot_motifs_allele INFO eval :: name: "show", value: "motifs"
2025-09-15 20:25:33.415 wdl.w:ptcp.w:call-trgt-78.t:call-trgt_plot_motifs_allele INFO eval :: name: "threads", value: 1
2025-09-15 20:25:33.415 wdl.w:ptcp.w:call-trgt-78.t:call-trgt_plot_motifs_allele INFO eval :: name: "disk_size", value: 27
2025-09-15 20:25:33.415 wdl.w:ptcp.w:call-trgt-78.t:call-trgt_plot_motifs_allele INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2175.motifs_allele"
2025-09-15 20:25:33.416 wdl.w:ptcp.w:call-trgt-78.t:call-trgt_plot_motifs_allele INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:33.416 wdl.w:ptcp.w:call-trgt-78.t:call-trgt_plot_motifs_allele WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:33.416 wdl.w:ptcp.w:call-trgt-78.t:call-trgt_plot_motifs_allele INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:25:33.416 wdl.w:ptcp.w:call-trgt-78.t:call-trgt_plot_motifs_allele INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:33.441 wdl.w:ptcp.w:call-trgt-74.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:25:33 [ERROR] - No reads found for TRID=SCA37_DAB1
2025-09-15 20:25:33.441 wdl.w:ptcp.w:call-trgt-74.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:25:33 [ERROR] - No reads found for TRID=OPDM_ABCD3
2025-09-15 20:25:33.441 wdl.w:ptcp.w:call-trgt-74.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:25:33 [ERROR] - No reads found for TRID=NIID_NOTCH2NLC
2025-09-15 20:25:33.441 wdl.w:ptcp.w:call-trgt-74.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:25:33 [ERROR] - No reads found for TRID=SCA2_ATXN2
2025-09-15 20:25:33.441 wdl.w:ptcp.w:call-trgt-74.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:25:33 [ERROR] - No reads found for TRID=SCA27B_FGF14
2025-09-15 20:25:33.441 wdl.w:ptcp.w:call-trgt-74.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:25:33 [ERROR] - No reads found for TRID=OPDM4_RILPL1
2025-09-15 20:25:33.449 wdl.w:ptcp.w:call-trgt-74.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO srun: job 51798035 queued and waiting for resources
2025-09-15 20:25:33.449 wdl.w:ptcp.w:call-trgt-74.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO srun: job 51798035 has been allocated resources
2025-09-15 20:25:33.449 wdl.w:ptcp.w:call-trgt-74.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:33.473 wdl.w:ptcp.w:call-trgt-78.t:call-trgt_plot_motifs_allele INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-78/call-trgt_plot_motifs_allele/_singularity_tmpdir_vcwr7vwu"
2025-09-15 20:25:33.473 wdl.w:ptcp.w:call-trgt-78.t:call-trgt_plot_motifs_allele INFO Slurm invocation: srun --job-name call-trgt_plot_motifs_allele --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-78/call-trgt_plot_motifs_allele/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-78/call-trgt_plot_motifs_allele/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-78/call-trgt_plot_motifs_allele/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-78/call-trgt_plot_motifs_allele/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-78/call-trgt_genotype/out/m84036_250809_035451_s4.bc2175.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2175.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-78/call-trgt_genotype/out/m84036_250809_035451_s4.bc2175.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2175.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-78/call-trgt_genotype/out/m84036_250809_035451_s4.bc2175.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2175.trgt.sorted.spanning.bam.bai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-78/call-trgt_plot_motifs_allele/_singularity_tmpdir_vcwr7vwu/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-78/call-trgt_plot_motifs_allele/_singularity_tmpdir_vcwr7vwu/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:33.497 wdl.w:ptcp.w:call-trgt-78.t:call-trgt_plot_motifs_allele NOTICE slurm_singularity run :: pid: 1205924, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-78/call-trgt_plot_motifs_allele/slurm_singularity.log.txt"
2025-09-15 20:25:33.651 wdl.w:ptcp.w:call-paraphase-02.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for hba for sample m84036_250809_035451_s4.bc2099 at 2025-09-15 20:24:55.110385...
2025-09-15 20:25:33.652 wdl.w:ptcp.w:call-paraphase-02.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for hba for sample m84036_250809_035451_s4.bc2099 at 2025-09-15 20:24:55.788456...
2025-09-15 20:25:33.652 wdl.w:ptcp.w:call-paraphase-02.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for cyp21 for sample m84036_250809_035451_s4.bc2099 at 2025-09-15 20:25:08.770329...
2025-09-15 20:25:33.652 wdl.w:ptcp.w:call-paraphase-02.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for cyp21 for sample m84036_250809_035451_s4.bc2099 at 2025-09-15 20:25:10.100233...
2025-09-15 20:25:33.652 wdl.w:ptcp.w:call-paraphase-02.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for gba for sample m84036_250809_035451_s4.bc2099 at 2025-09-15 20:25:21.136701...
2025-09-15 20:25:33.652 wdl.w:ptcp.w:call-paraphase-02.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for gba for sample m84036_250809_035451_s4.bc2099 at 2025-09-15 20:25:21.904893...
2025-09-15 20:25:33.673 wdl.w:ptcp.w:call-paraphase-89.t:call-run_paraphase.slurm_singularity INFO srun: job 51798036 queued and waiting for resources
2025-09-15 20:25:33.673 wdl.w:ptcp.w:call-paraphase-89.t:call-run_paraphase.slurm_singularity INFO srun: job 51798036 has been allocated resources
2025-09-15 20:25:33.673 wdl.w:ptcp.w:call-paraphase-89.t:call-run_paraphase.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:33.685 wdl.w:ptcp.w:call-paraphase-66.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for gba for sample m84036_250809_035451_s4.bc2163 at 2025-09-15 20:25:14.012594...
2025-09-15 20:25:33.686 wdl.w:ptcp.w:call-paraphase-66.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for hba for sample m84036_250809_035451_s4.bc2163 at 2025-09-15 20:25:15.032770...
2025-09-15 20:25:33.686 wdl.w:ptcp.w:call-paraphase-66.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for smn1 for sample m84036_250809_035451_s4.bc2163 at 2025-09-15 20:25:15.086488...
2025-09-15 20:25:33.686 wdl.w:ptcp.w:call-paraphase-66.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for cyp21 for sample m84036_250809_035451_s4.bc2163 at 2025-09-15 20:25:17.227700...
2025-09-15 20:25:33.926 wdl.w:ptcp.w:call-paraphase-72.t:call-run_paraphase INFO output :: name: "paraphase_bam", value: "m84036_250809_035451_s4.bc2169_paraphase/m84036_250809_035451_s4.bc2169.paraphase.bam"
2025-09-15 20:25:33.931 wdl.w:ptcp.w:call-trgt-78.t:call-trgt_plot_meth_allele.slurm_singularity INFO srun: job 51798037 queued and waiting for resources
2025-09-15 20:25:33.931 wdl.w:ptcp.w:call-trgt-78.t:call-trgt_plot_meth_allele.slurm_singularity INFO srun: job 51798037 has been allocated resources
2025-09-15 20:25:33.931 wdl.w:ptcp.w:call-trgt-78.t:call-trgt_plot_meth_allele.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:33.932 wdl.w:ptcp.w:call-paraphase-72.t:call-run_paraphase INFO output :: name: "paraphase_bam_bai", value: "m84036_250809_035451_s4.bc2169_paraphase/m84036_250809_035451_s4.bc2169.paraphase.bam.bai"
2025-09-15 20:25:33.933 wdl.w:ptcp.w:call-paraphase-72.t:call-run_paraphase INFO output :: name: "paraphase_json", value: "m84036_250809_035451_s4.bc2169_paraphase/m84036_250809_035451_s4.bc2169.paraphase.json"
2025-09-15 20:25:33.935 wdl.w:ptcp.w:call-paraphase-72.t:call-run_paraphase INFO output :: name: "paraphase_vcfs", value: []
2025-09-15 20:25:33.935 wdl.w:ptcp.w:call-paraphase-72.t:call-run_paraphase INFO output :: name: "havanno_json", value: "m84036_250809_035451_s4.bc2169.havanno.json"
2025-09-15 20:25:33.951 wdl.w:ptcp.w:call-paraphase-51.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for hba for sample m84036_250809_035451_s4.bc2148 at 2025-09-15 20:25:00.453453...
2025-09-15 20:25:33.952 wdl.w:ptcp.w:call-paraphase-51.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for hba for sample m84036_250809_035451_s4.bc2148 at 2025-09-15 20:25:00.955723...
2025-09-15 20:25:33.952 wdl.w:ptcp.w:call-paraphase-51.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for cyp21 for sample m84036_250809_035451_s4.bc2148 at 2025-09-15 20:25:03.334932...
2025-09-15 20:25:33.952 wdl.w:ptcp.w:call-paraphase-51.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for cyp21 for sample m84036_250809_035451_s4.bc2148 at 2025-09-15 20:25:04.557604...
2025-09-15 20:25:33.952 wdl.w:ptcp.w:call-paraphase-51.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for f8inv1 for sample m84036_250809_035451_s4.bc2148 at 2025-09-15 20:25:28.679833...
2025-09-15 20:25:33.952 wdl.w:ptcp.w:call-paraphase-51.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for f8inv1 for sample m84036_250809_035451_s4.bc2148 at 2025-09-15 20:25:28.682128...
2025-09-15 20:25:33.952 wdl.w:ptcp.w:call-paraphase-51.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for f8inv1 for sample m84036_250809_035451_s4.bc2148 at 2025-09-15 20:25:31.284756...
2025-09-15 20:25:33.952 wdl.w:ptcp.w:call-paraphase-51.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for hbb for sample m84036_250809_035451_s4.bc2148 at 2025-09-15 20:25:31.991569...
2025-09-15 20:25:33.952 wdl.w:ptcp.w:call-paraphase-51.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for hbb for sample m84036_250809_035451_s4.bc2148 at 2025-09-15 20:25:31.993063...
2025-09-15 20:25:33.967 wdl.w:ptcp.w:call-trgt-78.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:25:33 [ERROR] - No reads found for TRID=NIID_NOTCH2NLC
2025-09-15 20:25:33.968 wdl.w:ptcp.w:call-trgt-78.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:25:33 [ERROR] - No reads found for TRID=OPDM_ABCD3
2025-09-15 20:25:33.977 wdl.w:ptcp.w:call-trgt-78.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO srun: job 51798038 queued and waiting for resources
2025-09-15 20:25:33.977 wdl.w:ptcp.w:call-trgt-78.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO srun: job 51798038 has been allocated resources
2025-09-15 20:25:33.977 wdl.w:ptcp.w:call-trgt-78.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:34.030 wdl.w:ptcp.w:call-paraphase-72.t:call-run_paraphase NOTICE done
2025-09-15 20:25:34.035 wdl.w:ptcp.w:call-paraphase-72 NOTICE finish :: job: "call-run_paraphase"
2025-09-15 20:25:34.036 wdl.w:ptcp.w:call-paraphase-72 INFO output :: job: "call-run_paraphase", values: {"havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-72/call-run_paraphase/out/m84036_250809_035451_s4.bc2169.havanno.json", "paraphase_vcfs": [], "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-72/call-run_paraphase/out/m84036_250809_035451_s4.bc2169_paraphase/m84036_250809_035451_s4.bc2169.paraphase.json", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-72/call-run_paraphase/out/m84036_250809_035451_s4.bc2169_paraphase/m84036_250809_035451_s4.bc2169.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-72/call-run_paraphase/out/m84036_250809_035451_s4.bc2169_paraphase/m84036_250809_035451_s4.bc2169.paraphase.bam"}
2025-09-15 20:25:34.036 wdl.w:ptcp.w:call-paraphase-72 NOTICE ready :: job: "call-call_f8", callee: "call_f8"
2025-09-15 20:25:34.036 wdl.w:ptcp.w:call-paraphase-72 INFO input :: job: "call-call_f8", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "out_prefix": "m84036_250809_035451_s4.bc2169", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-72/call-run_paraphase/out/m84036_250809_035451_s4.bc2169_paraphase/m84036_250809_035451_s4.bc2169.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-72/call-run_paraphase/out/m84036_250809_035451_s4.bc2169_paraphase/m84036_250809_035451_s4.bc2169.paraphase.bam", "sex": "F"}
2025-09-15 20:25:34.037 wdl.w:ptcp.w:call-paraphase-72 INFO visit :: node: "output-havanno_json", values: {"havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-72/call-run_paraphase/out/m84036_250809_035451_s4.bc2169.havanno.json"}
2025-09-15 20:25:34.037 wdl.w:ptcp.w:call-paraphase-72 INFO visit :: node: "output-paraphase_bam", values: {"paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-72/call-run_paraphase/out/m84036_250809_035451_s4.bc2169_paraphase/m84036_250809_035451_s4.bc2169.paraphase.bam"}
2025-09-15 20:25:34.037 wdl.w:ptcp.w:call-paraphase-72 INFO visit :: node: "output-paraphase_bam_bai", values: {"paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-72/call-run_paraphase/out/m84036_250809_035451_s4.bc2169_paraphase/m84036_250809_035451_s4.bc2169.paraphase.bam.bai"}
2025-09-15 20:25:34.037 wdl.w:ptcp.w:call-paraphase-72 INFO visit :: node: "output-paraphase_json", values: {"paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-72/call-run_paraphase/out/m84036_250809_035451_s4.bc2169_paraphase/m84036_250809_035451_s4.bc2169.paraphase.json"}
2025-09-15 20:25:34.038 wdl.w:ptcp.w:call-paraphase-72 INFO visit :: node: "output-paraphase_vcfs", values: {"paraphase_vcfs": []}
2025-09-15 20:25:34.040 wdl.w:ptcp.w:call-trgt-78.t:call-trgt_plot_motifs_waterfall NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-78/call-trgt_plot_motifs_waterfall", thread: 140608773551680
2025-09-15 20:25:34.058 wdl.w:ptcp.w:call-trgt-78.t:call-trgt_plot_motifs_waterfall INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:34.058 wdl.w:ptcp.w:call-trgt-78.t:call-trgt_plot_motifs_waterfall INFO input :: name: "waterfall", value: true
2025-09-15 20:25:34.058 wdl.w:ptcp.w:call-trgt-78.t:call-trgt_plot_motifs_waterfall INFO input :: name: "methylation", value: false
2025-09-15 20:25:34.058 wdl.w:ptcp.w:call-trgt-78.t:call-trgt_plot_motifs_waterfall INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:25:34.058 wdl.w:ptcp.w:call-trgt-78.t:call-trgt_plot_motifs_waterfall INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:25:34.058 wdl.w:ptcp.w:call-trgt-78.t:call-trgt_plot_motifs_waterfall INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:25:34.058 wdl.w:ptcp.w:call-trgt-78.t:call-trgt_plot_motifs_waterfall INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2175.trgt.sorted.spanning.bam.bai"
2025-09-15 20:25:34.058 wdl.w:ptcp.w:call-trgt-78.t:call-trgt_plot_motifs_waterfall INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2175.trgt.sorted.spanning.bam"
2025-09-15 20:25:34.058 wdl.w:ptcp.w:call-trgt-78.t:call-trgt_plot_motifs_waterfall INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2175.trgt.vcf"
2025-09-15 20:25:34.058 wdl.w:ptcp.w:call-trgt-78.t:call-trgt_plot_motifs_waterfall INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2175"
2025-09-15 20:25:34.058 wdl.w:ptcp.w:call-trgt-78.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:25:34.059 wdl.w:ptcp.w:call-trgt-78.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "plot_type", value: "waterfall"
2025-09-15 20:25:34.059 wdl.w:ptcp.w:call-trgt-78.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "show", value: "motifs"
2025-09-15 20:25:34.059 wdl.w:ptcp.w:call-trgt-78.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "threads", value: 1
2025-09-15 20:25:34.059 wdl.w:ptcp.w:call-trgt-78.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "disk_size", value: 27
2025-09-15 20:25:34.059 wdl.w:ptcp.w:call-trgt-78.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2175.motifs_waterfall"
2025-09-15 20:25:34.059 wdl.w:ptcp.w:call-trgt-78.t:call-trgt_plot_motifs_waterfall INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:34.060 wdl.w:ptcp.w:call-trgt-78.t:call-trgt_plot_motifs_waterfall WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:34.060 wdl.w:ptcp.w:call-trgt-78.t:call-trgt_plot_motifs_waterfall INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:25:34.060 wdl.w:ptcp.w:call-trgt-78.t:call-trgt_plot_motifs_waterfall INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:34.063 wdl.w:ptcp.w:call-trgt-79.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:31 [ERROR] - No reads found for TRID=SCA37_DAB1
2025-09-15 20:25:34.063 wdl.w:ptcp.w:call-trgt-79.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:31 [ERROR] - No reads found for TRID=OPMD_PABPN1
2025-09-15 20:25:34.063 wdl.w:ptcp.w:call-trgt-79.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:31 [ERROR] - No reads found for TRID=SCA3_ATXN3
2025-09-15 20:25:34.063 wdl.w:ptcp.w:call-trgt-79.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:32 [ERROR] - No reads found for TRID=SCA31_BEAN1
2025-09-15 20:25:34.063 wdl.w:ptcp.w:call-trgt-79.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:32 [ERROR] - No reads found for TRID=SCA4_ZFHX3
2025-09-15 20:25:34.063 wdl.w:ptcp.w:call-trgt-79.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:32 [ERROR] - No reads found for TRID=HDL2_JPH3
2025-09-15 20:25:34.063 wdl.w:ptcp.w:call-trgt-79.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:32 [ERROR] - No reads found for TRID=FECD3_TCF4
2025-09-15 20:25:34.063 wdl.w:ptcp.w:call-trgt-79.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:33 [ERROR] - No reads found for TRID=SCA6_CACNA1A
2025-09-15 20:25:34.063 wdl.w:ptcp.w:call-trgt-79.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:33 [ERROR] - No reads found for TRID=OPDM2_GIPC1
2025-09-15 20:25:34.063 wdl.w:ptcp.w:call-trgt-79.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:33 [ERROR] - No reads found for TRID=DM1_DMPK
2025-09-15 20:25:34.129 wdl.w:ptcp.w:call-trgt-78.t:call-trgt_plot_motifs_waterfall INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-78/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_du9bmaj1"
2025-09-15 20:25:34.129 wdl.w:ptcp.w:call-trgt-78.t:call-trgt_plot_motifs_waterfall INFO Slurm invocation: srun --job-name call-trgt_plot_motifs_waterfall --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-78/call-trgt_plot_motifs_waterfall/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-78/call-trgt_plot_motifs_waterfall/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-78/call-trgt_plot_motifs_waterfall/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-78/call-trgt_plot_motifs_waterfall/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-78/call-trgt_genotype/out/m84036_250809_035451_s4.bc2175.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2175.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-78/call-trgt_genotype/out/m84036_250809_035451_s4.bc2175.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2175.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-78/call-trgt_genotype/out/m84036_250809_035451_s4.bc2175.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2175.trgt.sorted.spanning.bam.bai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-78/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_du9bmaj1/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-78/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_du9bmaj1/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:34.154 wdl.w:ptcp.w:call-trgt-78.t:call-trgt_plot_motifs_waterfall NOTICE slurm_singularity run :: pid: 1205932, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-78/call-trgt_plot_motifs_waterfall/slurm_singularity.log.txt"
2025-09-15 20:25:34.383 wdl.w:ptcp.w:call-trgt-92.t:call-trgt_genotype INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2189.trgt.vcf"
2025-09-15 20:25:34.387 wdl.w:ptcp.w:call-trgt-92.t:call-trgt_genotype INFO output :: name: "spanning_bam", value: "m84036_250809_035451_s4.bc2189.trgt.sorted.spanning.bam"
2025-09-15 20:25:34.389 wdl.w:ptcp.w:call-trgt-92.t:call-trgt_genotype INFO output :: name: "spanning_bam_bai", value: "m84036_250809_035451_s4.bc2189.trgt.sorted.spanning.bam.bai"
2025-09-15 20:25:34.452 wdl.w:ptcp.w:call-trgt-92.t:call-trgt_genotype NOTICE done
2025-09-15 20:25:34.493 wdl.w:ptcp.w:call-trgt-92 NOTICE finish :: job: "call-trgt_genotype"
2025-09-15 20:25:34.493 wdl.w:ptcp.w:call-trgt-92 INFO output :: job: "call-trgt_genotype", values: {"spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-92/call-trgt_genotype/out/m84036_250809_035451_s4.bc2189.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-92/call-trgt_genotype/out/m84036_250809_035451_s4.bc2189.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-92/call-trgt_genotype/out/m84036_250809_035451_s4.bc2189.trgt.vcf"}
2025-09-15 20:25:34.493 wdl.w:ptcp.w:call-trgt-92 NOTICE ready :: job: "call-trgt_plot_meth_allele", callee: "trgt_plot"
2025-09-15 20:25:34.494 wdl.w:ptcp.w:call-trgt-92 INFO input :: job: "call-trgt_plot_meth_allele", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": false, "methylation": true, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-92/call-trgt_genotype/out/m84036_250809_035451_s4.bc2189.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-92/call-trgt_genotype/out/m84036_250809_035451_s4.bc2189.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-92/call-trgt_genotype/out/m84036_250809_035451_s4.bc2189.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2189"}
2025-09-15 20:25:34.495 wdl.w:ptcp.w:call-trgt-92 NOTICE ready :: job: "call-trgt_plot_meth_waterfall", callee: "trgt_plot"
2025-09-15 20:25:34.495 wdl.w:ptcp.w:call-trgt-92 INFO input :: job: "call-trgt_plot_meth_waterfall", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": true, "methylation": true, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-92/call-trgt_genotype/out/m84036_250809_035451_s4.bc2189.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-92/call-trgt_genotype/out/m84036_250809_035451_s4.bc2189.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-92/call-trgt_genotype/out/m84036_250809_035451_s4.bc2189.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2189"}
2025-09-15 20:25:34.496 wdl.w:ptcp.w:call-trgt-92 NOTICE ready :: job: "call-trgt_plot_motifs_allele", callee: "trgt_plot"
2025-09-15 20:25:34.496 wdl.w:ptcp.w:call-trgt-92 INFO input :: job: "call-trgt_plot_motifs_allele", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": false, "methylation": false, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-92/call-trgt_genotype/out/m84036_250809_035451_s4.bc2189.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-92/call-trgt_genotype/out/m84036_250809_035451_s4.bc2189.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-92/call-trgt_genotype/out/m84036_250809_035451_s4.bc2189.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2189"}
2025-09-15 20:25:34.497 wdl.w:ptcp.w:call-trgt-92 NOTICE ready :: job: "call-trgt_plot_motifs_waterfall", callee: "trgt_plot"
2025-09-15 20:25:34.497 wdl.w:ptcp.w:call-trgt-92 INFO input :: job: "call-trgt_plot_motifs_waterfall", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": true, "methylation": false, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-92/call-trgt_genotype/out/m84036_250809_035451_s4.bc2189.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-92/call-trgt_genotype/out/m84036_250809_035451_s4.bc2189.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-92/call-trgt_genotype/out/m84036_250809_035451_s4.bc2189.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2189"}
2025-09-15 20:25:34.498 wdl.w:ptcp.w:call-trgt-92 INFO visit :: node: "output-spanning_bam", values: {"spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-92/call-trgt_genotype/out/m84036_250809_035451_s4.bc2189.trgt.sorted.spanning.bam"}
2025-09-15 20:25:34.498 wdl.w:ptcp.w:call-trgt-92 INFO visit :: node: "output-spanning_bam_bai", values: {"spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-92/call-trgt_genotype/out/m84036_250809_035451_s4.bc2189.trgt.sorted.spanning.bam.bai"}
2025-09-15 20:25:34.498 wdl.w:ptcp.w:call-trgt-92 INFO visit :: node: "output-vcf", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-92/call-trgt_genotype/out/m84036_250809_035451_s4.bc2189.trgt.vcf"}
2025-09-15 20:25:34.503 wdl.w:ptcp.w:call-sawfish-89.t:call-run_sawfish NOTICE task setup :: name: "run_sawfish", source: "./sawfish.wdl", line: 83, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-89/call-run_sawfish", thread: 140610367379008
2025-09-15 20:25:34.509 wdl.w:ptcp.w:call-trgt-78.t:call-trgt_plot_motifs_allele.slurm_singularity INFO srun: job 51798039 queued and waiting for resources
2025-09-15 20:25:34.509 wdl.w:ptcp.w:call-trgt-78.t:call-trgt_plot_motifs_allele.slurm_singularity INFO srun: job 51798039 has been allocated resources
2025-09-15 20:25:34.509 wdl.w:ptcp.w:call-trgt-78.t:call-trgt_plot_motifs_allele.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:34.520 wdl.w:ptcp.w:call-sawfish-89.t:call-run_sawfish INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:34.520 wdl.w:ptcp.w:call-sawfish-89.t:call-run_sawfish INFO input :: name: "genome_version", value: "38"
2025-09-15 20:25:34.520 wdl.w:ptcp.w:call-sawfish-89.t:call-run_sawfish INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:25:34.520 wdl.w:ptcp.w:call-sawfish-89.t:call-run_sawfish INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:25:34.520 wdl.w:ptcp.w:call-sawfish-89.t:call-run_sawfish INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2186.mapped.bam.bai"
2025-09-15 20:25:34.520 wdl.w:ptcp.w:call-sawfish-89.t:call-run_sawfish INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2186.mapped.bam"
2025-09-15 20:25:34.520 wdl.w:ptcp.w:call-sawfish-89.t:call-run_sawfish INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2186"
2025-09-15 20:25:34.520 wdl.w:ptcp.w:call-sawfish-89.t:call-run_sawfish INFO eval :: name: "mem_gb", value: 32
2025-09-15 20:25:34.520 wdl.w:ptcp.w:call-sawfish-89.t:call-run_sawfish INFO eval :: name: "threads", value: 16
2025-09-15 20:25:34.521 wdl.w:ptcp.w:call-sawfish-89.t:call-run_sawfish INFO eval :: name: "disk_size", value: 30
2025-09-15 20:25:34.521 wdl.w:ptcp.w:call-sawfish-89.t:call-run_sawfish INFO eval :: name: "discover_dirname", value: "m84036_250809_035451_s4.bc2186_sawfish_discover"
2025-09-15 20:25:34.521 wdl.w:ptcp.w:call-sawfish-89.t:call-run_sawfish INFO eval :: name: "call_dirname", value: "m84036_250809_035451_s4.bc2186_sawfish"
2025-09-15 20:25:34.521 wdl.w:ptcp.w:call-sawfish-89.t:call-run_sawfish INFO eval :: name: "minimap2_bam_filename", value: "m84036_250809_035451_s4.bc2186.minimap2.bam"
2025-09-15 20:25:34.523 wdl.w:ptcp.w:call-sawfish-89.t:call-run_sawfish INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 16, memory_reservation: 32000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:34.523 wdl.w:ptcp.w:call-sawfish-89.t:call-run_sawfish WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:34.523 wdl.w:ptcp.w:call-sawfish-89.t:call-run_sawfish INFO provisioned :: seconds_waited: 0, cpu: 16, mem_bytes: 32000000000
2025-09-15 20:25:34.523 wdl.w:ptcp.w:call-sawfish-89.t:call-run_sawfish INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:34.574 wdl.w:ptcp.w:call-sawfish-89.t:call-run_sawfish INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 10, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-89/call-run_sawfish/_singularity_tmpdir_7wwfukwo"
2025-09-15 20:25:34.575 wdl.w:ptcp.w:call-sawfish-89.t:call-run_sawfish INFO Slurm invocation: srun --job-name call-run_sawfish --partition compute,compute9 --cpus-per-task 16 --mem 30518M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-89/call-run_sawfish/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-89/call-run_sawfish/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-89/call-run_sawfish/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-89/call-run_sawfish/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-89/out/m84036_250809_035451_s4.bc2186.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2186.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-89/out/m84036_250809_035451_s4.bc2186.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2186.mapped.bam:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-89/call-run_sawfish/_singularity_tmpdir_7wwfukwo/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-89/call-run_sawfish/_singularity_tmpdir_7wwfukwo/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:34.587 wdl.w:ptcp.w:call-sawfish-89.t:call-run_sawfish NOTICE slurm_singularity run :: pid: 1205940, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-89/call-run_sawfish/slurm_singularity.log.txt"
2025-09-15 20:25:34.698 wdl.w:ptcp.w:call-paraphase-30.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for rpgr for sample m84036_250809_035451_s4.bc2127 at 2025-09-15 20:25:33.737949...
2025-09-15 20:25:34.699 wdl.w:ptcp.w:call-paraphase-30.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for rpgr for sample m84036_250809_035451_s4.bc2127 at 2025-09-15 20:25:33.739095...
2025-09-15 20:25:35.088 wdl.w:ptcp.w:call-sawfish-43.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:29][sawfish][INFO] Starting sawfish 2.0.3
2025-09-15 20:25:35.088 wdl.w:ptcp.w:call-sawfish-43.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:29][sawfish][INFO] cmdline: sawfish discover --disable-cnv --threads 16 --ref /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa --bam m84036_250809_035451_s4.bc2140.minimap2.bam --output-dir m84036_250809_035451_s4.bc2140_sawfish_discover
2025-09-15 20:25:35.088 wdl.w:ptcp.w:call-sawfish-43.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:29][sawfish][INFO] Running on 16 threads
2025-09-15 20:25:35.088 wdl.w:ptcp.w:call-sawfish-43.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:29][sawfish][INFO] Writing discover settings to file: 'm84036_250809_035451_s4.bc2140_sawfish_discover/discover.settings.json'
2025-09-15 20:25:35.088 wdl.w:ptcp.w:call-sawfish-43.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:29][sawfish][INFO] Reading reference genome from file '/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa'
2025-09-15 20:25:35.089 wdl.w:ptcp.w:call-sawfish-43.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:32][sawfish][INFO] Processing alignment file '/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2140.minimap2.bam'
2025-09-15 20:25:35.089 wdl.w:ptcp.w:call-sawfish-43.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:32][sawfish][INFO] Finished processing all alignments
2025-09-15 20:25:35.089 wdl.w:ptcp.w:call-sawfish-43.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:32][sawfish][INFO] Writing depth bins to binary file: 'm84036_250809_035451_s4.bc2140_sawfish_discover/depth.mpack'
2025-09-15 20:25:35.089 wdl.w:ptcp.w:call-sawfish-43.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:33][sawfish][INFO] Writing max sv depth genome regions to bed file: 'm84036_250809_035451_s4.bc2140_sawfish_discover/max.depth.bed'
2025-09-15 20:25:35.089 wdl.w:ptcp.w:call-sawfish-43.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:33][sawfish][INFO] Completing breakpoint observation clustering
2025-09-15 20:25:35.089 wdl.w:ptcp.w:call-sawfish-43.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:33][sawfish][INFO] Finished breakpoint observation clustering
2025-09-15 20:25:35.089 wdl.w:ptcp.w:call-sawfish-43.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:33][sawfish][INFO] Consolidating adjacent indel candidates
2025-09-15 20:25:35.089 wdl.w:ptcp.w:call-sawfish-43.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:33][sawfish][INFO] Finding large insertion candidates
2025-09-15 20:25:35.089 wdl.w:ptcp.w:call-sawfish-43.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:33][sawfish][INFO] Writing breakpoint_cluster debug bed file: 'm84036_250809_035451_s4.bc2140_sawfish_discover/debug.breakpoint_clusters.bed'
2025-09-15 20:25:35.089 wdl.w:ptcp.w:call-sawfish-43.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:33][sawfish][INFO] Refining SV Candidates
2025-09-15 20:25:35.089 wdl.w:ptcp.w:call-sawfish-43.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:33][sawfish][INFO] Writing debug assembly region bed file: 'm84036_250809_035451_s4.bc2140_sawfish_discover/assembly.regions.bed'
2025-09-15 20:25:35.089 wdl.w:ptcp.w:call-sawfish-43.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:33][sawfish][INFO] Starting refinement of breakpoint evidence clusters
2025-09-15 20:25:35.089 wdl.w:ptcp.w:call-sawfish-43.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:33][sawfish][INFO] Finished refining all breakpoint evidence clusters
2025-09-15 20:25:35.089 wdl.w:ptcp.w:call-sawfish-43.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:33][sawfish][INFO] Writing all contig alignments to bam file: 'm84036_250809_035451_s4.bc2140_sawfish_discover/contig.alignment.bam'
2025-09-15 20:25:35.090 wdl.w:ptcp.w:call-sawfish-43.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:33][sawfish][INFO] Writing candidate structural variants to file: 'm84036_250809_035451_s4.bc2140_sawfish_discover/candidate.sv.bcf'
2025-09-15 20:25:35.090 wdl.w:ptcp.w:call-sawfish-43.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:33][sawfish][INFO] Writing run statistics to file: 'm84036_250809_035451_s4.bc2140_sawfish_discover/run.stats.json'
2025-09-15 20:25:35.090 wdl.w:ptcp.w:call-sawfish-43.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:33][sawfish][INFO] sawfish completed. Total Runtime: 00:00:04.359
2025-09-15 20:25:35.113 wdl.w:ptcp.w:call-paraphase-92.t:call-run_paraphase INFO output :: name: "paraphase_bam", value: "m84036_250809_035451_s4.bc2189_paraphase/m84036_250809_035451_s4.bc2189.paraphase.bam"
2025-09-15 20:25:35.119 wdl.w:ptcp.w:call-paraphase-92.t:call-run_paraphase INFO output :: name: "paraphase_bam_bai", value: "m84036_250809_035451_s4.bc2189_paraphase/m84036_250809_035451_s4.bc2189.paraphase.bam.bai"
2025-09-15 20:25:35.121 wdl.w:ptcp.w:call-paraphase-92.t:call-run_paraphase INFO output :: name: "paraphase_json", value: "m84036_250809_035451_s4.bc2189_paraphase/m84036_250809_035451_s4.bc2189.paraphase.json"
2025-09-15 20:25:35.123 wdl.w:ptcp.w:call-paraphase-92.t:call-run_paraphase INFO output :: name: "paraphase_vcfs", value: []
2025-09-15 20:25:35.123 wdl.w:ptcp.w:call-paraphase-92.t:call-run_paraphase INFO output :: name: "havanno_json", value: "m84036_250809_035451_s4.bc2189.havanno.json"
2025-09-15 20:25:35.141 wdl.w:ptcp.w:call-trgt-92.t:call-get_reads_overlapping_repeats INFO output :: name: "reads_overlapping_repeats", value: "m84036_250809_035451_s4.bc2189.repeats.bam"
2025-09-15 20:25:35.145 wdl.w:ptcp.w:call-trgt-92.t:call-get_reads_overlapping_repeats INFO output :: name: "reads_overlapping_repeats_bai", value: "m84036_250809_035451_s4.bc2189.repeats.bam.bai"
2025-09-15 20:25:35.157 wdl.w:ptcp.w:call-trgt-78.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:25:35 [ERROR] - No reads found for TRID=NIID_NOTCH2NLC
2025-09-15 20:25:35.167 wdl.w:ptcp.w:call-trgt-78.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO srun: job 51798040 queued and waiting for resources
2025-09-15 20:25:35.167 wdl.w:ptcp.w:call-trgt-78.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO srun: job 51798040 has been allocated resources
2025-09-15 20:25:35.167 wdl.w:ptcp.w:call-trgt-78.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:35.223 wdl.w:ptcp.w:call-trgt-92.t:call-get_reads_overlapping_repeats NOTICE done
2025-09-15 20:25:35.228 wdl.w:ptcp.w:call-trgt-92 NOTICE finish :: job: "call-get_reads_overlapping_repeats"
2025-09-15 20:25:35.228 wdl.w:ptcp.w:call-trgt-92 INFO output :: job: "call-get_reads_overlapping_repeats", values: {"reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-92/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2189.repeats.bam.bai", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-92/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2189.repeats.bam"}
2025-09-15 20:25:35.229 wdl.w:ptcp.w:call-trgt-92 INFO visit :: node: "output-reads_overlapping_repeats", values: {"reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-92/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2189.repeats.bam"}
2025-09-15 20:25:35.229 wdl.w:ptcp.w:call-trgt-92 INFO visit :: node: "output-reads_overlapping_repeats_bai", values: {"reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-92/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2189.repeats.bam.bai"}
2025-09-15 20:25:35.234 wdl.w:ptcp.w:call-trgt-89.t:call-get_reads_overlapping_repeats NOTICE task setup :: name: "get_reads_overlapping_repeats", source: "./trgt.wdl", line: 182, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-89/call-get_reads_overlapping_repeats", thread: 140613034948160
2025-09-15 20:25:35.236 wdl.w:ptcp.w:call-paraphase-92.t:call-run_paraphase NOTICE done
2025-09-15 20:25:35.242 wdl.w:ptcp.w:call-paraphase-92 NOTICE finish :: job: "call-run_paraphase"
2025-09-15 20:25:35.242 wdl.w:ptcp.w:call-paraphase-92 INFO output :: job: "call-run_paraphase", values: {"havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-92/call-run_paraphase/out/m84036_250809_035451_s4.bc2189.havanno.json", "paraphase_vcfs": [], "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-92/call-run_paraphase/out/m84036_250809_035451_s4.bc2189_paraphase/m84036_250809_035451_s4.bc2189.paraphase.json", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-92/call-run_paraphase/out/m84036_250809_035451_s4.bc2189_paraphase/m84036_250809_035451_s4.bc2189.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-92/call-run_paraphase/out/m84036_250809_035451_s4.bc2189_paraphase/m84036_250809_035451_s4.bc2189.paraphase.bam"}
2025-09-15 20:25:35.242 wdl.w:ptcp.w:call-paraphase-92 NOTICE ready :: job: "call-call_f8", callee: "call_f8"
2025-09-15 20:25:35.242 wdl.w:ptcp.w:call-paraphase-92 INFO input :: job: "call-call_f8", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "out_prefix": "m84036_250809_035451_s4.bc2189", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-92/call-run_paraphase/out/m84036_250809_035451_s4.bc2189_paraphase/m84036_250809_035451_s4.bc2189.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-92/call-run_paraphase/out/m84036_250809_035451_s4.bc2189_paraphase/m84036_250809_035451_s4.bc2189.paraphase.bam", "sex": "F"}
2025-09-15 20:25:35.243 wdl.w:ptcp.w:call-paraphase-92 INFO visit :: node: "output-havanno_json", values: {"havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-92/call-run_paraphase/out/m84036_250809_035451_s4.bc2189.havanno.json"}
2025-09-15 20:25:35.244 wdl.w:ptcp.w:call-paraphase-92 INFO visit :: node: "output-paraphase_bam", values: {"paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-92/call-run_paraphase/out/m84036_250809_035451_s4.bc2189_paraphase/m84036_250809_035451_s4.bc2189.paraphase.bam"}
2025-09-15 20:25:35.244 wdl.w:ptcp.w:call-paraphase-92 INFO visit :: node: "output-paraphase_bam_bai", values: {"paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-92/call-run_paraphase/out/m84036_250809_035451_s4.bc2189_paraphase/m84036_250809_035451_s4.bc2189.paraphase.bam.bai"}
2025-09-15 20:25:35.244 wdl.w:ptcp.w:call-paraphase-92 INFO visit :: node: "output-paraphase_json", values: {"paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-92/call-run_paraphase/out/m84036_250809_035451_s4.bc2189_paraphase/m84036_250809_035451_s4.bc2189.paraphase.json"}
2025-09-15 20:25:35.244 wdl.w:ptcp.w:call-paraphase-92 INFO visit :: node: "output-paraphase_vcfs", values: {"paraphase_vcfs": []}
2025-09-15 20:25:35.248 wdl.w:ptcp.w:call-trgt-89.t:call-trgt_genotype NOTICE task setup :: name: "trgt_genotype", source: "./trgt.wdl", line: 272, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-89/call-trgt_genotype", thread: 140611969599040
2025-09-15 20:25:35.253 wdl.w:ptcp.w:call-trgt-89.t:call-get_reads_overlapping_repeats INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:35.253 wdl.w:ptcp.w:call-trgt-89.t:call-get_reads_overlapping_repeats INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:25:35.253 wdl.w:ptcp.w:call-trgt-89.t:call-get_reads_overlapping_repeats INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2186.mapped.bam.bai"
2025-09-15 20:25:35.253 wdl.w:ptcp.w:call-trgt-89.t:call-get_reads_overlapping_repeats INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2186.mapped.bam"
2025-09-15 20:25:35.253 wdl.w:ptcp.w:call-trgt-89.t:call-get_reads_overlapping_repeats INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2186"
2025-09-15 20:25:35.254 wdl.w:ptcp.w:call-trgt-89.t:call-get_reads_overlapping_repeats INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:25:35.254 wdl.w:ptcp.w:call-trgt-89.t:call-get_reads_overlapping_repeats INFO eval :: name: "expand_size", value: 3000
2025-09-15 20:25:35.254 wdl.w:ptcp.w:call-trgt-89.t:call-get_reads_overlapping_repeats INFO eval :: name: "threads", value: 1
2025-09-15 20:25:35.254 wdl.w:ptcp.w:call-trgt-89.t:call-get_reads_overlapping_repeats INFO eval :: name: "expanded_bed_name", value: "m84036_250809_035451_s4.bc2186.expanded.bed"
2025-09-15 20:25:35.254 wdl.w:ptcp.w:call-trgt-89.t:call-get_reads_overlapping_repeats INFO eval :: name: "disk_size", value: 11
2025-09-15 20:25:35.254 wdl.w:ptcp.w:call-trgt-89.t:call-get_reads_overlapping_repeats INFO eval :: name: "output_name", value: "m84036_250809_035451_s4.bc2186.repeats.bam"
2025-09-15 20:25:35.254 wdl.w:ptcp.w:call-trgt-89.t:call-get_reads_overlapping_repeats INFO eval :: name: "index_name", value: "m84036_250809_035451_s4.bc2186.repeats.bam.bai"
2025-09-15 20:25:35.254 wdl.w:ptcp.w:call-trgt-89.t:call-get_reads_overlapping_repeats INFO eval :: name: "output_name_with_index", value: "m84036_250809_035451_s4.bc2186.repeats.bam##idx##m84036_250809_035451_s4.bc2186.repeats.bam.bai"
2025-09-15 20:25:35.255 wdl.w:ptcp.w:call-trgt-89.t:call-get_reads_overlapping_repeats INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:35.255 wdl.w:ptcp.w:call-trgt-89.t:call-get_reads_overlapping_repeats WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:35.255 wdl.w:ptcp.w:call-trgt-89.t:call-get_reads_overlapping_repeats INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:25:35.255 wdl.w:ptcp.w:call-trgt-89.t:call-get_reads_overlapping_repeats INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:35.267 wdl.w:ptcp.w:call-trgt-89.t:call-trgt_genotype INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:35.267 wdl.w:ptcp.w:call-trgt-89.t:call-trgt_genotype INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:25:35.267 wdl.w:ptcp.w:call-trgt-89.t:call-trgt_genotype INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:25:35.267 wdl.w:ptcp.w:call-trgt-89.t:call-trgt_genotype INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:25:35.267 wdl.w:ptcp.w:call-trgt-89.t:call-trgt_genotype INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2186.mapped.bam.bai"
2025-09-15 20:25:35.267 wdl.w:ptcp.w:call-trgt-89.t:call-trgt_genotype INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2186.mapped.bam"
2025-09-15 20:25:35.267 wdl.w:ptcp.w:call-trgt-89.t:call-trgt_genotype INFO input :: name: "sex", value: "F"
2025-09-15 20:25:35.267 wdl.w:ptcp.w:call-trgt-89.t:call-trgt_genotype INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2186"
2025-09-15 20:25:35.268 wdl.w:ptcp.w:call-trgt-89.t:call-trgt_genotype INFO eval :: name: "mem_gb", value: 16
2025-09-15 20:25:35.268 wdl.w:ptcp.w:call-trgt-89.t:call-trgt_genotype INFO eval :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2186.trgt"
2025-09-15 20:25:35.268 wdl.w:ptcp.w:call-trgt-89.t:call-trgt_genotype INFO eval :: name: "threads", value: 8
2025-09-15 20:25:35.268 wdl.w:ptcp.w:call-trgt-89.t:call-trgt_genotype INFO eval :: name: "disk_size", value: 27
2025-09-15 20:25:35.268 wdl.w:ptcp.w:call-trgt-89.t:call-trgt_genotype INFO eval :: name: "karyotype", value: "XX"
2025-09-15 20:25:35.269 wdl.w:ptcp.w:call-trgt-89.t:call-trgt_genotype INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 8, memory_reservation: 16000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:35.269 wdl.w:ptcp.w:call-trgt-89.t:call-trgt_genotype WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:35.269 wdl.w:ptcp.w:call-trgt-89.t:call-trgt_genotype INFO provisioned :: seconds_waited: 0, cpu: 8, mem_bytes: 16000000000
2025-09-15 20:25:35.269 wdl.w:ptcp.w:call-trgt-89.t:call-trgt_genotype INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:35.307 wdl.w:ptcp.w:call-trgt-89.t:call-get_reads_overlapping_repeats INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 9, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-89/call-get_reads_overlapping_repeats/_singularity_tmpdir_gf9pwhn2"
2025-09-15 20:25:35.307 wdl.w:ptcp.w:call-trgt-89.t:call-get_reads_overlapping_repeats INFO Slurm invocation: srun --job-name call-get_reads_overlapping_repeats --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-89/call-get_reads_overlapping_repeats/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-89/call-get_reads_overlapping_repeats/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-89/call-get_reads_overlapping_repeats/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-89/call-get_reads_overlapping_repeats/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-89/out/m84036_250809_035451_s4.bc2186.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2186.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-89/out/m84036_250809_035451_s4.bc2186.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2186.mapped.bam:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-89/call-get_reads_overlapping_repeats/_singularity_tmpdir_gf9pwhn2/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-89/call-get_reads_overlapping_repeats/_singularity_tmpdir_gf9pwhn2/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:35.331 wdl.w:ptcp.w:call-trgt-89.t:call-get_reads_overlapping_repeats NOTICE slurm_singularity run :: pid: 1205949, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-89/call-get_reads_overlapping_repeats/slurm_singularity.log.txt"
2025-09-15 20:25:35.335 wdl.w:ptcp.w:call-trgt-89.t:call-trgt_genotype INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 11, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-89/call-trgt_genotype/_singularity_tmpdir__qx4m5i4"
2025-09-15 20:25:35.335 wdl.w:ptcp.w:call-trgt-89.t:call-trgt_genotype INFO Slurm invocation: srun --job-name call-trgt_genotype --partition compute,compute9 --cpus-per-task 8 --mem 15259M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-89/call-trgt_genotype/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-89/call-trgt_genotype/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-89/call-trgt_genotype/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-89/call-trgt_genotype/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-89/out/m84036_250809_035451_s4.bc2186.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2186.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-89/out/m84036_250809_035451_s4.bc2186.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2186.mapped.bam:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-89/call-trgt_genotype/_singularity_tmpdir__qx4m5i4/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-89/call-trgt_genotype/_singularity_tmpdir__qx4m5i4/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:35.342 wdl.w:ptcp.w:call-trgt-89.t:call-trgt_genotype NOTICE slurm_singularity run :: pid: 1205950, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-89/call-trgt_genotype/slurm_singularity.log.txt"
2025-09-15 20:25:35.406 wdl.w:ptcp.w:call-paraphase-85.t:call-run_paraphase.stderr VERBOSE INFO:root:Processing sample m84036_250809_035451_s4.bc2182 at 2025-09-15 20:25:33.694637...
2025-09-15 20:25:35.407 wdl.w:ptcp.w:call-paraphase-85.t:call-run_paraphase.stderr VERBOSE INFO:root:Checking sample sex at 2025-09-15 20:25:33.697946...
2025-09-15 20:25:35.407 wdl.w:ptcp.w:call-paraphase-85.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for cyp21 for sample m84036_250809_035451_s4.bc2182 at 2025-09-15 20:25:33.794751...
2025-09-15 20:25:35.407 wdl.w:ptcp.w:call-paraphase-85.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for cyp21 for sample m84036_250809_035451_s4.bc2182 at 2025-09-15 20:25:33.795409...
2025-09-15 20:25:35.407 wdl.w:ptcp.w:call-paraphase-85.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for smn1 for sample m84036_250809_035451_s4.bc2182 at 2025-09-15 20:25:33.794981...
2025-09-15 20:25:35.407 wdl.w:ptcp.w:call-paraphase-85.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for smn1 for sample m84036_250809_035451_s4.bc2182 at 2025-09-15 20:25:33.795553...
2025-09-15 20:25:35.407 wdl.w:ptcp.w:call-paraphase-85.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for gba for sample m84036_250809_035451_s4.bc2182 at 2025-09-15 20:25:33.795130...
2025-09-15 20:25:35.407 wdl.w:ptcp.w:call-paraphase-85.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for gba for sample m84036_250809_035451_s4.bc2182 at 2025-09-15 20:25:33.795704...
2025-09-15 20:25:35.407 wdl.w:ptcp.w:call-paraphase-85.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for hba for sample m84036_250809_035451_s4.bc2182 at 2025-09-15 20:25:33.796651...
2025-09-15 20:25:35.407 wdl.w:ptcp.w:call-paraphase-85.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for hba for sample m84036_250809_035451_s4.bc2182 at 2025-09-15 20:25:33.797173...
2025-09-15 20:25:35.407 wdl.w:ptcp.w:call-paraphase-85.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for cyp21 for sample m84036_250809_035451_s4.bc2182 at 2025-09-15 20:25:34.435433...
2025-09-15 20:25:35.407 wdl.w:ptcp.w:call-paraphase-85.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for hba for sample m84036_250809_035451_s4.bc2182 at 2025-09-15 20:25:34.452051...
2025-09-15 20:25:35.407 wdl.w:ptcp.w:call-paraphase-85.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for smn1 for sample m84036_250809_035451_s4.bc2182 at 2025-09-15 20:25:34.465332...
2025-09-15 20:25:35.407 wdl.w:ptcp.w:call-paraphase-85.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for gba for sample m84036_250809_035451_s4.bc2182 at 2025-09-15 20:25:34.496789...
2025-09-15 20:25:35.407 wdl.w:ptcp.w:call-paraphase-85.t:call-run_paraphase.stderr VERBOSE WARNING:root:This region does not appear to have coverage. Will not attempt to phase haplotypes.
2025-09-15 20:25:35.407 wdl.w:ptcp.w:call-paraphase-85.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for cyp21 for sample m84036_250809_035451_s4.bc2182 at 2025-09-15 20:25:34.506930...
2025-09-15 20:25:35.407 wdl.w:ptcp.w:call-paraphase-85.t:call-run_paraphase.stderr VERBOSE WARNING:root:This region does not appear to have coverage. Will not attempt to phase haplotypes.
2025-09-15 20:25:35.407 wdl.w:ptcp.w:call-paraphase-85.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for hba for sample m84036_250809_035451_s4.bc2182 at 2025-09-15 20:25:34.517810...
2025-09-15 20:25:35.407 wdl.w:ptcp.w:call-paraphase-85.t:call-run_paraphase.stderr VERBOSE WARNING:root:This region does not appear to have coverage. Will not attempt to phase haplotypes.
2025-09-15 20:25:35.408 wdl.w:ptcp.w:call-paraphase-85.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for smn1 for sample m84036_250809_035451_s4.bc2182 at 2025-09-15 20:25:34.606466...
2025-09-15 20:25:35.408 wdl.w:ptcp.w:call-paraphase-85.t:call-run_paraphase.stderr VERBOSE WARNING:root:This region does not appear to have coverage. Will not attempt to phase haplotypes.
2025-09-15 20:25:35.408 wdl.w:ptcp.w:call-paraphase-85.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for gba for sample m84036_250809_035451_s4.bc2182 at 2025-09-15 20:25:34.684514...
2025-09-15 20:25:35.408 wdl.w:ptcp.w:call-paraphase-85.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for cyp21 for sample m84036_250809_035451_s4.bc2182 at 2025-09-15 20:25:35.097942...
2025-09-15 20:25:35.408 wdl.w:ptcp.w:call-paraphase-85.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for f8inv22 for sample m84036_250809_035451_s4.bc2182 at 2025-09-15 20:25:35.107659...
2025-09-15 20:25:35.408 wdl.w:ptcp.w:call-paraphase-85.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for f8inv22 for sample m84036_250809_035451_s4.bc2182 at 2025-09-15 20:25:35.107845...
2025-09-15 20:25:35.408 wdl.w:ptcp.w:call-paraphase-85.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for hba for sample m84036_250809_035451_s4.bc2182 at 2025-09-15 20:25:35.153229...
2025-09-15 20:25:35.408 wdl.w:ptcp.w:call-paraphase-85.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for hbb for sample m84036_250809_035451_s4.bc2182 at 2025-09-15 20:25:35.163397...
2025-09-15 20:25:35.408 wdl.w:ptcp.w:call-paraphase-85.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for hbb for sample m84036_250809_035451_s4.bc2182 at 2025-09-15 20:25:35.163690...
2025-09-15 20:25:35.408 wdl.w:ptcp.w:call-paraphase-85.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning to gene2 region for smn1 for sample m84036_250809_035451_s4.bc2182 at 2025-09-15 20:25:35.219809...
2025-09-15 20:25:35.408 wdl.w:ptcp.w:call-paraphase-85.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for gba for sample m84036_250809_035451_s4.bc2182 at 2025-09-15 20:25:35.292655...
2025-09-15 20:25:35.408 wdl.w:ptcp.w:call-paraphase-85.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for rpgr for sample m84036_250809_035451_s4.bc2182 at 2025-09-15 20:25:35.305878...
2025-09-15 20:25:35.408 wdl.w:ptcp.w:call-paraphase-85.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for rpgr for sample m84036_250809_035451_s4.bc2182 at 2025-09-15 20:25:35.306179...
2025-09-15 20:25:35.426 wdl.w:ptcp.w:call-paraphase-15.t:call-run_paraphase INFO output :: name: "paraphase_bam", value: "m84036_250809_035451_s4.bc2112_paraphase/m84036_250809_035451_s4.bc2112.paraphase.bam"
2025-09-15 20:25:35.429 wdl.w:ptcp.w:call-paraphase-15.t:call-run_paraphase INFO output :: name: "paraphase_bam_bai", value: "m84036_250809_035451_s4.bc2112_paraphase/m84036_250809_035451_s4.bc2112.paraphase.bam.bai"
2025-09-15 20:25:35.431 wdl.w:ptcp.w:call-paraphase-15.t:call-run_paraphase INFO output :: name: "paraphase_json", value: "m84036_250809_035451_s4.bc2112_paraphase/m84036_250809_035451_s4.bc2112.paraphase.json"
2025-09-15 20:25:35.434 wdl.w:ptcp.w:call-trgt-74.t:call-trgt_plot_meth_allele INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2171.meth_allele.trgt_plots.zip"
2025-09-15 20:25:35.435 wdl.w:ptcp.w:call-paraphase-15.t:call-run_paraphase INFO output :: name: "paraphase_vcfs", value: ["/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2112_paraphase/m84036_250809_035451_s4.bc2112_paraphase_vcfs/m84036_250809_035451_s4.bc2112_cyp21.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2112_paraphase/m84036_250809_035451_s4.bc2112_paraphase_vcfs/m84036_250809_035451_s4.bc2112_f8inv1.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2112_paraphase/m84036_250809_035451_s4.bc2112_paraphase_vcfs/m84036_250809_035451_s4.bc2112_f8inv22.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2112_paraphase/m84036_250809_035451_s4.bc2112_paraphase_vcfs/m84036_250809_035451_s4.bc2112_gba.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2112_paraphase/m84036_250809_035451_s4.bc2112_paraphase_vcfs/m84036_250809_035451_s4.bc2112_hba.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2112_paraphase/m84036_250809_035451_s4.bc2112_paraphase_vcfs/m84036_250809_035451_s4.bc2112_hbb.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2112_paraphase/m84036_250809_035451_s4.bc2112_paraphase_vcfs/m84036_250809_035451_s4.bc2112_rpgr.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2112_paraphase/m84036_250809_035451_s4.bc2112_paraphase_vcfs/m84036_250809_035451_s4.bc2112_smn1.vcf"]
2025-09-15 20:25:35.439 wdl.w:ptcp.w:call-paraphase-15.t:call-run_paraphase INFO output :: name: "havanno_json", value: "m84036_250809_035451_s4.bc2112.havanno.json"
2025-09-15 20:25:35.518 wdl.w:ptcp.w:call-trgt-74.t:call-trgt_plot_meth_allele NOTICE done
2025-09-15 20:25:35.524 wdl.w:ptcp.w:call-trgt-74 NOTICE finish :: job: "call-trgt_plot_meth_allele"
2025-09-15 20:25:35.524 wdl.w:ptcp.w:call-trgt-74 INFO output :: job: "call-trgt_plot_meth_allele", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-74/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2171.meth_allele.trgt_plots.zip"}
2025-09-15 20:25:35.525 wdl.w:ptcp.w:call-trgt-74 INFO visit :: node: "output-images_meth_allele", values: {"images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-74/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2171.meth_allele.trgt_plots.zip"}
2025-09-15 20:25:35.531 wdl.w:ptcp.w:call-trgt-73.t:call-trgt_plot_meth_allele NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-73/call-trgt_plot_meth_allele", thread: 140608211502656
2025-09-15 20:25:35.551 wdl.w:ptcp.w:call-trgt-73.t:call-trgt_plot_meth_allele INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:35.551 wdl.w:ptcp.w:call-trgt-73.t:call-trgt_plot_meth_allele INFO input :: name: "waterfall", value: false
2025-09-15 20:25:35.551 wdl.w:ptcp.w:call-trgt-73.t:call-trgt_plot_meth_allele INFO input :: name: "methylation", value: true
2025-09-15 20:25:35.551 wdl.w:ptcp.w:call-trgt-73.t:call-trgt_plot_meth_allele INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:25:35.551 wdl.w:ptcp.w:call-trgt-73.t:call-trgt_plot_meth_allele INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:25:35.552 wdl.w:ptcp.w:call-trgt-73.t:call-trgt_plot_meth_allele INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:25:35.552 wdl.w:ptcp.w:call-trgt-73.t:call-trgt_plot_meth_allele INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2170.trgt.sorted.spanning.bam.bai"
2025-09-15 20:25:35.552 wdl.w:ptcp.w:call-trgt-73.t:call-trgt_plot_meth_allele INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2170.trgt.sorted.spanning.bam"
2025-09-15 20:25:35.552 wdl.w:ptcp.w:call-trgt-73.t:call-trgt_plot_meth_allele INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2170.trgt.vcf"
2025-09-15 20:25:35.552 wdl.w:ptcp.w:call-trgt-73.t:call-trgt_plot_meth_allele INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2170"
2025-09-15 20:25:35.552 wdl.w:ptcp.w:call-trgt-73.t:call-trgt_plot_meth_allele INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:25:35.552 wdl.w:ptcp.w:call-trgt-73.t:call-trgt_plot_meth_allele INFO eval :: name: "plot_type", value: "allele"
2025-09-15 20:25:35.552 wdl.w:ptcp.w:call-trgt-73.t:call-trgt_plot_meth_allele INFO eval :: name: "show", value: "meth"
2025-09-15 20:25:35.553 wdl.w:ptcp.w:call-trgt-73.t:call-trgt_plot_meth_allele INFO eval :: name: "threads", value: 1
2025-09-15 20:25:35.553 wdl.w:ptcp.w:call-trgt-73.t:call-trgt_plot_meth_allele INFO eval :: name: "disk_size", value: 27
2025-09-15 20:25:35.553 wdl.w:ptcp.w:call-trgt-73.t:call-trgt_plot_meth_allele INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2170.meth_allele"
2025-09-15 20:25:35.553 wdl.w:ptcp.w:call-trgt-73.t:call-trgt_plot_meth_allele INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:35.553 wdl.w:ptcp.w:call-trgt-73.t:call-trgt_plot_meth_allele WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:35.554 wdl.w:ptcp.w:call-trgt-73.t:call-trgt_plot_meth_allele INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:25:35.554 wdl.w:ptcp.w:call-trgt-73.t:call-trgt_plot_meth_allele INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:35.585 wdl.w:ptcp.w:call-trgt-74.t:call-trgt_plot_motifs_waterfall INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2171.motifs_waterfall.trgt_plots.zip"
2025-09-15 20:25:35.591 wdl.w:ptcp.w:call-sawfish-89.t:call-run_sawfish.stderr VERBOSE [M::bam2fq_mainloop] discarded 0 singletons
2025-09-15 20:25:35.591 wdl.w:ptcp.w:call-sawfish-89.t:call-run_sawfish.stderr VERBOSE [M::bam2fq_mainloop] processed 0 reads
2025-09-15 20:25:35.602 wdl.w:ptcp.w:call-sawfish-89.t:call-run_sawfish.slurm_singularity INFO srun: job 51798041 queued and waiting for resources
2025-09-15 20:25:35.603 wdl.w:ptcp.w:call-sawfish-89.t:call-run_sawfish.slurm_singularity INFO srun: job 51798041 has been allocated resources
2025-09-15 20:25:35.603 wdl.w:ptcp.w:call-sawfish-89.t:call-run_sawfish.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:35.632 wdl.w:ptcp.w:call-trgt-73.t:call-trgt_plot_meth_allele INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-73/call-trgt_plot_meth_allele/_singularity_tmpdir_69eikyma"
2025-09-15 20:25:35.632 wdl.w:ptcp.w:call-trgt-73.t:call-trgt_plot_meth_allele INFO Slurm invocation: srun --job-name call-trgt_plot_meth_allele --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-73/call-trgt_plot_meth_allele/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-73/call-trgt_plot_meth_allele/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-73/call-trgt_plot_meth_allele/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-73/call-trgt_plot_meth_allele/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-73/call-trgt_genotype/out/m84036_250809_035451_s4.bc2170.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2170.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-73/call-trgt_genotype/out/m84036_250809_035451_s4.bc2170.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2170.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-73/call-trgt_genotype/out/m84036_250809_035451_s4.bc2170.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2170.trgt.vcf:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-73/call-trgt_plot_meth_allele/_singularity_tmpdir_69eikyma/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-73/call-trgt_plot_meth_allele/_singularity_tmpdir_69eikyma/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:35.636 wdl.w:ptcp.w:call-paraphase-15.t:call-run_paraphase NOTICE done
2025-09-15 20:25:35.642 wdl.w:ptcp.w:call-paraphase-15 NOTICE finish :: job: "call-run_paraphase"
2025-09-15 20:25:35.643 wdl.w:ptcp.w:call-paraphase-15 INFO output :: job: "call-run_paraphase", values: {"havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-15/call-run_paraphase/out/m84036_250809_035451_s4.bc2112.havanno.json", "paraphase_vcfs": ["/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-15/call-run_paraphase/out/m84036_250809_035451_s4.bc2112_paraphase/m84036_250809_035451_s4.bc2112_paraphase_vcfs/m84036_250809_035451_s4.bc2112_cyp21.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-15/call-run_paraphase/out/m84036_250809_035451_s4.bc2112_paraphase/m84036_250809_035451_s4.bc2112_paraphase_vcfs/m84036_250809_035451_s4.bc2112_f8inv1.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-15/call-run_paraphase/out/m84036_250809_035451_s4.bc2112_paraphase/m84036_250809_035451_s4.bc2112_paraphase_vcfs/m84036_250809_035451_s4.bc2112_f8inv22.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-15/call-run_paraphase/out/m84036_250809_035451_s4.bc2112_paraphase/m84036_250809_035451_s4.bc2112_paraphase_vcfs/m84036_250809_035451_s4.bc2112_gba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-15/call-run_paraphase/out/m84036_250809_035451_s4.bc2112_paraphase/m84036_250809_035451_s4.bc2112_paraphase_vcfs/m84036_250809_035451_s4.bc2112_hba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-15/call-run_paraphase/out/m84036_250809_035451_s4.bc2112_paraphase/m84036_250809_035451_s4.bc2112_paraphase_vcfs/m84036_250809_035451_s4.bc2112_hbb.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-15/call-run_paraphase/out/m84036_250809_035451_s4.bc2112_paraphase/m84036_250809_035451_s4.bc2112_paraphase_vcfs/m84036_250809_035451_s4.bc2112_rpgr.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-15/call-run_paraphase/out/m84036_250809_035451_s4.bc2112_paraphase/m84036_250809_035451_s4.bc2112_paraphase_vcfs/m84036_250809_035451_s4.bc2112_smn1.vcf"], "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-15/call-run_paraphase/out/m84036_250809_035451_s4.bc2112_paraphase/m84036_250809_035451_s4.bc2112.paraphase.json", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-15/call-run_paraphase/out/m84036_250809_035451_s4.bc2112_paraphase/m84036_250809_035451_s4.bc2112.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-15/call-run_paraphase/out/m84036_250809_035451_s4.bc2112_paraphase/m84036_250809_035451_s4.bc2112.paraphase.bam"}
2025-09-15 20:25:35.643 wdl.w:ptcp.w:call-paraphase-15 NOTICE ready :: job: "call-call_f8", callee: "call_f8"
2025-09-15 20:25:35.644 wdl.w:ptcp.w:call-paraphase-15 INFO input :: job: "call-call_f8", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "out_prefix": "m84036_250809_035451_s4.bc2112", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-15/call-run_paraphase/out/m84036_250809_035451_s4.bc2112_paraphase/m84036_250809_035451_s4.bc2112.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-15/call-run_paraphase/out/m84036_250809_035451_s4.bc2112_paraphase/m84036_250809_035451_s4.bc2112.paraphase.bam", "sex": "F"}
2025-09-15 20:25:35.644 wdl.w:ptcp.w:call-paraphase-15 INFO visit :: node: "output-havanno_json", values: {"havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-15/call-run_paraphase/out/m84036_250809_035451_s4.bc2112.havanno.json"}
2025-09-15 20:25:35.644 wdl.w:ptcp.w:call-paraphase-15 INFO visit :: node: "output-paraphase_bam", values: {"paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-15/call-run_paraphase/out/m84036_250809_035451_s4.bc2112_paraphase/m84036_250809_035451_s4.bc2112.paraphase.bam"}
2025-09-15 20:25:35.644 wdl.w:ptcp.w:call-paraphase-15 INFO visit :: node: "output-paraphase_bam_bai", values: {"paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-15/call-run_paraphase/out/m84036_250809_035451_s4.bc2112_paraphase/m84036_250809_035451_s4.bc2112.paraphase.bam.bai"}
2025-09-15 20:25:35.645 wdl.w:ptcp.w:call-paraphase-15 INFO visit :: node: "output-paraphase_json", values: {"paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-15/call-run_paraphase/out/m84036_250809_035451_s4.bc2112_paraphase/m84036_250809_035451_s4.bc2112.paraphase.json"}
2025-09-15 20:25:35.645 wdl.w:ptcp.w:call-paraphase-15 INFO visit :: node: "output-paraphase_vcfs", values: {"paraphase_vcfs": ["/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-15/call-run_paraphase/out/m84036_250809_035451_s4.bc2112_paraphase/m84036_250809_035451_s4.bc2112_paraphase_vcfs/m84036_250809_035451_s4.bc2112_cyp21.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-15/call-run_paraphase/out/m84036_250809_035451_s4.bc2112_paraphase/m84036_250809_035451_s4.bc2112_paraphase_vcfs/m84036_250809_035451_s4.bc2112_f8inv1.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-15/call-run_paraphase/out/m84036_250809_035451_s4.bc2112_paraphase/m84036_250809_035451_s4.bc2112_paraphase_vcfs/m84036_250809_035451_s4.bc2112_f8inv22.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-15/call-run_paraphase/out/m84036_250809_035451_s4.bc2112_paraphase/m84036_250809_035451_s4.bc2112_paraphase_vcfs/m84036_250809_035451_s4.bc2112_gba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-15/call-run_paraphase/out/m84036_250809_035451_s4.bc2112_paraphase/m84036_250809_035451_s4.bc2112_paraphase_vcfs/m84036_250809_035451_s4.bc2112_hba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-15/call-run_paraphase/out/m84036_250809_035451_s4.bc2112_paraphase/m84036_250809_035451_s4.bc2112_paraphase_vcfs/m84036_250809_035451_s4.bc2112_hbb.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-15/call-run_paraphase/out/m84036_250809_035451_s4.bc2112_paraphase/m84036_250809_035451_s4.bc2112_paraphase_vcfs/m84036_250809_035451_s4.bc2112_rpgr.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-15/call-run_paraphase/out/m84036_250809_035451_s4.bc2112_paraphase/m84036_250809_035451_s4.bc2112_paraphase_vcfs/m84036_250809_035451_s4.bc2112_smn1.vcf"]}
2025-09-15 20:25:35.648 wdl.w:ptcp.w:call-trgt-73.t:call-trgt_plot_meth_waterfall NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-73/call-trgt_plot_meth_waterfall", thread: 140613563426368
2025-09-15 20:25:35.652 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:25:34 [INFO] - Running trgt-4.0.0-429afcd [genotype]
2025-09-15 20:25:35.653 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:25:34 [WARN] - PRTS_ARX: Filtered out 2 impure reads
2025-09-15 20:25:35.653 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:25:34 [WARN] - EIEE1_ARX: Filtered out 2 impure reads
2025-09-15 20:25:35.653 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:25:34 [WARN] - FXS_FMR1: Filtered out 4 impure reads
2025-09-15 20:25:35.653 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:25:34 [WARN] - FRDA_FXN: Filtered out 4 impure reads
2025-09-15 20:25:35.653 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:25:34 [WARN] - FRAXE_AFF2: Filtered out 18 impure reads
2025-09-15 20:25:35.653 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:25:35 [INFO] - Total execution time: 804.11ms
2025-09-15 20:25:35.653 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_genotype.stderr VERBOSE 2025-09-15 20:25:35 [INFO] - trgt end
2025-09-15 20:25:35.665 wdl.w:ptcp.w:call-trgt-73.t:call-trgt_plot_meth_allele NOTICE slurm_singularity run :: pid: 1205966, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-73/call-trgt_plot_meth_allele/slurm_singularity.log.txt"
2025-09-15 20:25:35.671 wdl.w:ptcp.w:call-trgt-73.t:call-trgt_plot_meth_waterfall INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:35.672 wdl.w:ptcp.w:call-trgt-73.t:call-trgt_plot_meth_waterfall INFO input :: name: "waterfall", value: true
2025-09-15 20:25:35.672 wdl.w:ptcp.w:call-trgt-73.t:call-trgt_plot_meth_waterfall INFO input :: name: "methylation", value: true
2025-09-15 20:25:35.672 wdl.w:ptcp.w:call-trgt-73.t:call-trgt_plot_meth_waterfall INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:25:35.672 wdl.w:ptcp.w:call-trgt-73.t:call-trgt_plot_meth_waterfall INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:25:35.672 wdl.w:ptcp.w:call-trgt-73.t:call-trgt_plot_meth_waterfall INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:25:35.672 wdl.w:ptcp.w:call-trgt-73.t:call-trgt_plot_meth_waterfall INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2170.trgt.sorted.spanning.bam.bai"
2025-09-15 20:25:35.672 wdl.w:ptcp.w:call-trgt-73.t:call-trgt_plot_meth_waterfall INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2170.trgt.sorted.spanning.bam"
2025-09-15 20:25:35.672 wdl.w:ptcp.w:call-trgt-73.t:call-trgt_plot_meth_waterfall INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2170.trgt.vcf"
2025-09-15 20:25:35.672 wdl.w:ptcp.w:call-trgt-73.t:call-trgt_plot_meth_waterfall INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2170"
2025-09-15 20:25:35.672 wdl.w:ptcp.w:call-trgt-73.t:call-trgt_plot_meth_waterfall INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:25:35.673 wdl.w:ptcp.w:call-trgt-73.t:call-trgt_plot_meth_waterfall INFO eval :: name: "plot_type", value: "waterfall"
2025-09-15 20:25:35.673 wdl.w:ptcp.w:call-trgt-73.t:call-trgt_plot_meth_waterfall INFO eval :: name: "show", value: "meth"
2025-09-15 20:25:35.673 wdl.w:ptcp.w:call-trgt-73.t:call-trgt_plot_meth_waterfall INFO eval :: name: "threads", value: 1
2025-09-15 20:25:35.673 wdl.w:ptcp.w:call-trgt-73.t:call-trgt_plot_meth_waterfall INFO eval :: name: "disk_size", value: 27
2025-09-15 20:25:35.674 wdl.w:ptcp.w:call-trgt-73.t:call-trgt_plot_meth_waterfall INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2170.meth_waterfall"
2025-09-15 20:25:35.674 wdl.w:ptcp.w:call-trgt-73.t:call-trgt_plot_meth_waterfall INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:35.674 wdl.w:ptcp.w:call-trgt-73.t:call-trgt_plot_meth_waterfall WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:35.674 wdl.w:ptcp.w:call-trgt-73.t:call-trgt_plot_meth_waterfall INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:25:35.674 wdl.w:ptcp.w:call-trgt-73.t:call-trgt_plot_meth_waterfall INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:35.690 wdl.w:ptcp.w:call-trgt-74.t:call-trgt_plot_motifs_waterfall NOTICE done
2025-09-15 20:25:35.696 wdl.w:ptcp.w:call-trgt-74 NOTICE finish :: job: "call-trgt_plot_motifs_waterfall"
2025-09-15 20:25:35.697 wdl.w:ptcp.w:call-trgt-74 INFO output :: job: "call-trgt_plot_motifs_waterfall", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-74/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2171.motifs_waterfall.trgt_plots.zip"}
2025-09-15 20:25:35.697 wdl.w:ptcp.w:call-trgt-74 INFO visit :: node: "output-images_motifs_waterfall", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-74/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2171.motifs_waterfall.trgt_plots.zip"}
2025-09-15 20:25:35.705 wdl.w:ptcp.w:call-trgt-73.t:call-trgt_plot_motifs_allele NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-73/call-trgt_plot_motifs_allele", thread: 140610912642624
2025-09-15 20:25:35.726 wdl.w:ptcp.w:call-trgt-73.t:call-trgt_plot_motifs_allele INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:35.726 wdl.w:ptcp.w:call-trgt-73.t:call-trgt_plot_motifs_allele INFO input :: name: "waterfall", value: false
2025-09-15 20:25:35.726 wdl.w:ptcp.w:call-trgt-73.t:call-trgt_plot_motifs_allele INFO input :: name: "methylation", value: false
2025-09-15 20:25:35.726 wdl.w:ptcp.w:call-trgt-73.t:call-trgt_plot_motifs_allele INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:25:35.726 wdl.w:ptcp.w:call-trgt-73.t:call-trgt_plot_motifs_allele INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:25:35.726 wdl.w:ptcp.w:call-trgt-73.t:call-trgt_plot_motifs_allele INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:25:35.726 wdl.w:ptcp.w:call-trgt-73.t:call-trgt_plot_motifs_allele INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2170.trgt.sorted.spanning.bam.bai"
2025-09-15 20:25:35.726 wdl.w:ptcp.w:call-trgt-73.t:call-trgt_plot_motifs_allele INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2170.trgt.sorted.spanning.bam"
2025-09-15 20:25:35.727 wdl.w:ptcp.w:call-trgt-73.t:call-trgt_plot_motifs_allele INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2170.trgt.vcf"
2025-09-15 20:25:35.727 wdl.w:ptcp.w:call-trgt-73.t:call-trgt_plot_motifs_allele INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2170"
2025-09-15 20:25:35.727 wdl.w:ptcp.w:call-trgt-73.t:call-trgt_plot_motifs_allele INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:25:35.727 wdl.w:ptcp.w:call-trgt-73.t:call-trgt_plot_motifs_allele INFO eval :: name: "plot_type", value: "allele"
2025-09-15 20:25:35.727 wdl.w:ptcp.w:call-trgt-73.t:call-trgt_plot_motifs_allele INFO eval :: name: "show", value: "motifs"
2025-09-15 20:25:35.727 wdl.w:ptcp.w:call-trgt-73.t:call-trgt_plot_motifs_allele INFO eval :: name: "threads", value: 1
2025-09-15 20:25:35.728 wdl.w:ptcp.w:call-trgt-73.t:call-trgt_plot_motifs_allele INFO eval :: name: "disk_size", value: 27
2025-09-15 20:25:35.728 wdl.w:ptcp.w:call-trgt-73.t:call-trgt_plot_motifs_allele INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2170.motifs_allele"
2025-09-15 20:25:35.728 wdl.w:ptcp.w:call-trgt-73.t:call-trgt_plot_motifs_allele INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:35.728 wdl.w:ptcp.w:call-trgt-73.t:call-trgt_plot_motifs_allele WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:35.728 wdl.w:ptcp.w:call-trgt-73.t:call-trgt_plot_motifs_allele INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:25:35.729 wdl.w:ptcp.w:call-trgt-73.t:call-trgt_plot_motifs_allele INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:35.761 wdl.w:ptcp.w:call-trgt-73.t:call-trgt_plot_meth_waterfall INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-73/call-trgt_plot_meth_waterfall/_singularity_tmpdir_b88zk04h"
2025-09-15 20:25:35.762 wdl.w:ptcp.w:call-trgt-73.t:call-trgt_plot_meth_waterfall INFO Slurm invocation: srun --job-name call-trgt_plot_meth_waterfall --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-73/call-trgt_plot_meth_waterfall/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-73/call-trgt_plot_meth_waterfall/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-73/call-trgt_plot_meth_waterfall/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-73/call-trgt_plot_meth_waterfall/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-73/call-trgt_genotype/out/m84036_250809_035451_s4.bc2170.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2170.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-73/call-trgt_genotype/out/m84036_250809_035451_s4.bc2170.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2170.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-73/call-trgt_genotype/out/m84036_250809_035451_s4.bc2170.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2170.trgt.vcf:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-73/call-trgt_plot_meth_waterfall/_singularity_tmpdir_b88zk04h/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-73/call-trgt_plot_meth_waterfall/_singularity_tmpdir_b88zk04h/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:35.776 wdl.w:ptcp.w:call-trgt-73.t:call-trgt_plot_meth_waterfall NOTICE slurm_singularity run :: pid: 1205971, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-73/call-trgt_plot_meth_waterfall/slurm_singularity.log.txt"
2025-09-15 20:25:35.789 wdl.w:ptcp.w:call-paraphase-42.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for hba for sample m84036_250809_035451_s4.bc2139 at 2025-09-15 20:24:49.290982...
2025-09-15 20:25:35.790 wdl.w:ptcp.w:call-paraphase-42.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for smn1 for sample m84036_250809_035451_s4.bc2139 at 2025-09-15 20:24:49.751650...
2025-09-15 20:25:35.790 wdl.w:ptcp.w:call-paraphase-42.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for gba for sample m84036_250809_035451_s4.bc2139 at 2025-09-15 20:24:50.206730...
2025-09-15 20:25:35.791 wdl.w:ptcp.w:call-paraphase-42.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for cyp21 for sample m84036_250809_035451_s4.bc2139 at 2025-09-15 20:24:50.922834...
2025-09-15 20:25:35.791 wdl.w:ptcp.w:call-paraphase-42.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for smn1 for sample m84036_250809_035451_s4.bc2139 at 2025-09-15 20:25:12.990204...
2025-09-15 20:25:35.791 wdl.w:ptcp.w:call-paraphase-42.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning to gene2 region for smn1 for sample m84036_250809_035451_s4.bc2139 at 2025-09-15 20:25:13.544506...
2025-09-15 20:25:35.791 wdl.w:ptcp.w:call-paraphase-42.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for smn1 for sample m84036_250809_035451_s4.bc2139 at 2025-09-15 20:25:16.549725...
2025-09-15 20:25:35.811 wdl.w:ptcp.w:call-trgt-73.t:call-trgt_plot_motifs_allele INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-73/call-trgt_plot_motifs_allele/_singularity_tmpdir_1n0yv9py"
2025-09-15 20:25:35.812 wdl.w:ptcp.w:call-trgt-73.t:call-trgt_plot_motifs_allele INFO Slurm invocation: srun --job-name call-trgt_plot_motifs_allele --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-73/call-trgt_plot_motifs_allele/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-73/call-trgt_plot_motifs_allele/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-73/call-trgt_plot_motifs_allele/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-73/call-trgt_plot_motifs_allele/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-73/call-trgt_genotype/out/m84036_250809_035451_s4.bc2170.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2170.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-73/call-trgt_genotype/out/m84036_250809_035451_s4.bc2170.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2170.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-73/call-trgt_genotype/out/m84036_250809_035451_s4.bc2170.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2170.trgt.vcf:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-73/call-trgt_plot_motifs_allele/_singularity_tmpdir_1n0yv9py/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-73/call-trgt_plot_motifs_allele/_singularity_tmpdir_1n0yv9py/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:35.821 wdl.w:ptcp.w:call-trgt-73.t:call-trgt_plot_motifs_allele NOTICE slurm_singularity run :: pid: 1205976, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-73/call-trgt_plot_motifs_allele/slurm_singularity.log.txt"
2025-09-15 20:25:35.825 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_genotype INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2184.trgt.vcf"
2025-09-15 20:25:35.828 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_genotype INFO output :: name: "spanning_bam", value: "m84036_250809_035451_s4.bc2184.trgt.sorted.spanning.bam"
2025-09-15 20:25:35.829 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_genotype INFO output :: name: "spanning_bam_bai", value: "m84036_250809_035451_s4.bc2184.trgt.sorted.spanning.bam.bai"
2025-09-15 20:25:35.893 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_genotype NOTICE done
2025-09-15 20:25:35.898 wdl.w:ptcp.w:call-trgt-87 NOTICE finish :: job: "call-trgt_genotype"
2025-09-15 20:25:35.898 wdl.w:ptcp.w:call-trgt-87 INFO output :: job: "call-trgt_genotype", values: {"spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-87/call-trgt_genotype/out/m84036_250809_035451_s4.bc2184.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-87/call-trgt_genotype/out/m84036_250809_035451_s4.bc2184.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-87/call-trgt_genotype/out/m84036_250809_035451_s4.bc2184.trgt.vcf"}
2025-09-15 20:25:35.899 wdl.w:ptcp.w:call-trgt-87 NOTICE ready :: job: "call-trgt_plot_meth_allele", callee: "trgt_plot"
2025-09-15 20:25:35.899 wdl.w:ptcp.w:call-trgt-87 INFO input :: job: "call-trgt_plot_meth_allele", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": false, "methylation": true, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-87/call-trgt_genotype/out/m84036_250809_035451_s4.bc2184.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-87/call-trgt_genotype/out/m84036_250809_035451_s4.bc2184.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-87/call-trgt_genotype/out/m84036_250809_035451_s4.bc2184.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2184"}
2025-09-15 20:25:35.900 wdl.w:ptcp.w:call-trgt-87 NOTICE ready :: job: "call-trgt_plot_meth_waterfall", callee: "trgt_plot"
2025-09-15 20:25:35.900 wdl.w:ptcp.w:call-trgt-87 INFO input :: job: "call-trgt_plot_meth_waterfall", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": true, "methylation": true, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-87/call-trgt_genotype/out/m84036_250809_035451_s4.bc2184.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-87/call-trgt_genotype/out/m84036_250809_035451_s4.bc2184.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-87/call-trgt_genotype/out/m84036_250809_035451_s4.bc2184.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2184"}
2025-09-15 20:25:35.901 wdl.w:ptcp.w:call-trgt-87 NOTICE ready :: job: "call-trgt_plot_motifs_allele", callee: "trgt_plot"
2025-09-15 20:25:35.901 wdl.w:ptcp.w:call-trgt-87 INFO input :: job: "call-trgt_plot_motifs_allele", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": false, "methylation": false, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-87/call-trgt_genotype/out/m84036_250809_035451_s4.bc2184.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-87/call-trgt_genotype/out/m84036_250809_035451_s4.bc2184.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-87/call-trgt_genotype/out/m84036_250809_035451_s4.bc2184.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2184"}
2025-09-15 20:25:35.902 wdl.w:ptcp.w:call-trgt-87 NOTICE ready :: job: "call-trgt_plot_motifs_waterfall", callee: "trgt_plot"
2025-09-15 20:25:35.902 wdl.w:ptcp.w:call-trgt-87 INFO input :: job: "call-trgt_plot_motifs_waterfall", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": true, "methylation": false, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-87/call-trgt_genotype/out/m84036_250809_035451_s4.bc2184.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-87/call-trgt_genotype/out/m84036_250809_035451_s4.bc2184.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-87/call-trgt_genotype/out/m84036_250809_035451_s4.bc2184.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2184"}
2025-09-15 20:25:35.902 wdl.w:ptcp.w:call-trgt-87 INFO visit :: node: "output-spanning_bam", values: {"spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-87/call-trgt_genotype/out/m84036_250809_035451_s4.bc2184.trgt.sorted.spanning.bam"}
2025-09-15 20:25:35.902 wdl.w:ptcp.w:call-trgt-87 INFO visit :: node: "output-spanning_bam_bai", values: {"spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-87/call-trgt_genotype/out/m84036_250809_035451_s4.bc2184.trgt.sorted.spanning.bam.bai"}
2025-09-15 20:25:35.902 wdl.w:ptcp.w:call-trgt-87 INFO visit :: node: "output-vcf", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-87/call-trgt_genotype/out/m84036_250809_035451_s4.bc2184.trgt.vcf"}
2025-09-15 20:25:35.904 wdl.w:ptcp.w:call-trgt-73.t:call-trgt_plot_motifs_waterfall NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-73/call-trgt_plot_motifs_waterfall", thread: 140606575711808
2025-09-15 20:25:35.916 wdl.w:ptcp.w:call-paraphase-70.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for smn1 for sample m84036_250809_035451_s4.bc2167 at 2025-09-15 20:25:14.192912...
2025-09-15 20:25:35.917 wdl.w:ptcp.w:call-paraphase-70.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for hba for sample m84036_250809_035451_s4.bc2167 at 2025-09-15 20:25:14.365989...
2025-09-15 20:25:35.917 wdl.w:ptcp.w:call-paraphase-70.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for gba for sample m84036_250809_035451_s4.bc2167 at 2025-09-15 20:25:14.576669...
2025-09-15 20:25:35.917 wdl.w:ptcp.w:call-paraphase-70.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for cyp21 for sample m84036_250809_035451_s4.bc2167 at 2025-09-15 20:25:16.287398...
2025-09-15 20:25:35.917 wdl.w:ptcp.w:call-paraphase-70.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for smn1 for sample m84036_250809_035451_s4.bc2167 at 2025-09-15 20:25:32.544587...
2025-09-15 20:25:35.917 wdl.w:ptcp.w:call-paraphase-70.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning to gene2 region for smn1 for sample m84036_250809_035451_s4.bc2167 at 2025-09-15 20:25:32.980096...
2025-09-15 20:25:35.920 wdl.w:ptcp.w:call-trgt-73.t:call-trgt_plot_motifs_waterfall INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:35.920 wdl.w:ptcp.w:call-trgt-73.t:call-trgt_plot_motifs_waterfall INFO input :: name: "waterfall", value: true
2025-09-15 20:25:35.920 wdl.w:ptcp.w:call-trgt-73.t:call-trgt_plot_motifs_waterfall INFO input :: name: "methylation", value: false
2025-09-15 20:25:35.921 wdl.w:ptcp.w:call-trgt-73.t:call-trgt_plot_motifs_waterfall INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:25:35.921 wdl.w:ptcp.w:call-trgt-73.t:call-trgt_plot_motifs_waterfall INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:25:35.921 wdl.w:ptcp.w:call-trgt-73.t:call-trgt_plot_motifs_waterfall INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:25:35.921 wdl.w:ptcp.w:call-trgt-73.t:call-trgt_plot_motifs_waterfall INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2170.trgt.sorted.spanning.bam.bai"
2025-09-15 20:25:35.921 wdl.w:ptcp.w:call-trgt-73.t:call-trgt_plot_motifs_waterfall INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2170.trgt.sorted.spanning.bam"
2025-09-15 20:25:35.921 wdl.w:ptcp.w:call-trgt-73.t:call-trgt_plot_motifs_waterfall INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2170.trgt.vcf"
2025-09-15 20:25:35.921 wdl.w:ptcp.w:call-trgt-73.t:call-trgt_plot_motifs_waterfall INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2170"
2025-09-15 20:25:35.921 wdl.w:ptcp.w:call-trgt-73.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:25:35.921 wdl.w:ptcp.w:call-trgt-73.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "plot_type", value: "waterfall"
2025-09-15 20:25:35.921 wdl.w:ptcp.w:call-trgt-73.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "show", value: "motifs"
2025-09-15 20:25:35.922 wdl.w:ptcp.w:call-trgt-73.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "threads", value: 1
2025-09-15 20:25:35.922 wdl.w:ptcp.w:call-trgt-73.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "disk_size", value: 27
2025-09-15 20:25:35.922 wdl.w:ptcp.w:call-trgt-73.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2170.motifs_waterfall"
2025-09-15 20:25:35.922 wdl.w:ptcp.w:call-trgt-73.t:call-trgt_plot_motifs_waterfall INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:35.922 wdl.w:ptcp.w:call-trgt-73.t:call-trgt_plot_motifs_waterfall WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:35.923 wdl.w:ptcp.w:call-trgt-73.t:call-trgt_plot_motifs_waterfall INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:25:35.923 wdl.w:ptcp.w:call-trgt-73.t:call-trgt_plot_motifs_waterfall INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:36.004 wdl.w:ptcp.w:call-trgt-73.t:call-trgt_plot_motifs_waterfall INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-73/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_ucg_ytbs"
2025-09-15 20:25:36.004 wdl.w:ptcp.w:call-trgt-73.t:call-trgt_plot_motifs_waterfall INFO Slurm invocation: srun --job-name call-trgt_plot_motifs_waterfall --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-73/call-trgt_plot_motifs_waterfall/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-73/call-trgt_plot_motifs_waterfall/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-73/call-trgt_plot_motifs_waterfall/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-73/call-trgt_plot_motifs_waterfall/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-73/call-trgt_genotype/out/m84036_250809_035451_s4.bc2170.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2170.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-73/call-trgt_genotype/out/m84036_250809_035451_s4.bc2170.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2170.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-73/call-trgt_genotype/out/m84036_250809_035451_s4.bc2170.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2170.trgt.vcf:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-73/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_ucg_ytbs/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-73/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_ucg_ytbs/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:36.011 wdl.w:ptcp.w:call-trgt-74.t:call-trgt_plot_meth_waterfall INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2171.meth_waterfall.trgt_plots.zip"
2025-09-15 20:25:36.025 wdl.w:ptcp.w:call-trgt-73.t:call-trgt_plot_motifs_waterfall NOTICE slurm_singularity run :: pid: 1205989, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-73/call-trgt_plot_motifs_waterfall/slurm_singularity.log.txt"
2025-09-15 20:25:36.086 wdl.w:ptcp.w:call-trgt-74.t:call-trgt_plot_meth_waterfall NOTICE done
2025-09-15 20:25:36.091 wdl.w:ptcp.w:call-trgt-74 NOTICE finish :: job: "call-trgt_plot_meth_waterfall"
2025-09-15 20:25:36.091 wdl.w:ptcp.w:call-trgt-74 INFO output :: job: "call-trgt_plot_meth_waterfall", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-74/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2171.meth_waterfall.trgt_plots.zip"}
2025-09-15 20:25:36.091 wdl.w:ptcp.w:call-trgt-74 INFO visit :: node: "output-images_meth_waterfall", values: {"images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-74/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2171.meth_waterfall.trgt_plots.zip"}
2025-09-15 20:25:36.098 wdl.w:ptcp.w:call-trgt-84.t:call-trgt_plot_meth_allele NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-84/call-trgt_plot_meth_allele", thread: 140611944420928
2025-09-15 20:25:36.124 wdl.w:ptcp.w:call-trgt-84.t:call-trgt_plot_meth_allele INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:36.124 wdl.w:ptcp.w:call-trgt-84.t:call-trgt_plot_meth_allele INFO input :: name: "waterfall", value: false
2025-09-15 20:25:36.124 wdl.w:ptcp.w:call-trgt-84.t:call-trgt_plot_meth_allele INFO input :: name: "methylation", value: true
2025-09-15 20:25:36.124 wdl.w:ptcp.w:call-trgt-84.t:call-trgt_plot_meth_allele INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:25:36.124 wdl.w:ptcp.w:call-trgt-84.t:call-trgt_plot_meth_allele INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:25:36.124 wdl.w:ptcp.w:call-trgt-84.t:call-trgt_plot_meth_allele INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:25:36.125 wdl.w:ptcp.w:call-trgt-84.t:call-trgt_plot_meth_allele INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2181.trgt.sorted.spanning.bam.bai"
2025-09-15 20:25:36.125 wdl.w:ptcp.w:call-trgt-84.t:call-trgt_plot_meth_allele INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2181.trgt.sorted.spanning.bam"
2025-09-15 20:25:36.125 wdl.w:ptcp.w:call-trgt-84.t:call-trgt_plot_meth_allele INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2181.trgt.vcf"
2025-09-15 20:25:36.125 wdl.w:ptcp.w:call-trgt-84.t:call-trgt_plot_meth_allele INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2181"
2025-09-15 20:25:36.125 wdl.w:ptcp.w:call-trgt-84.t:call-trgt_plot_meth_allele INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:25:36.125 wdl.w:ptcp.w:call-trgt-84.t:call-trgt_plot_meth_allele INFO eval :: name: "plot_type", value: "allele"
2025-09-15 20:25:36.125 wdl.w:ptcp.w:call-trgt-84.t:call-trgt_plot_meth_allele INFO eval :: name: "show", value: "meth"
2025-09-15 20:25:36.125 wdl.w:ptcp.w:call-trgt-84.t:call-trgt_plot_meth_allele INFO eval :: name: "threads", value: 1
2025-09-15 20:25:36.125 wdl.w:ptcp.w:call-trgt-84.t:call-trgt_plot_meth_allele INFO eval :: name: "disk_size", value: 27
2025-09-15 20:25:36.126 wdl.w:ptcp.w:call-trgt-84.t:call-trgt_plot_meth_allele INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2181.meth_allele"
2025-09-15 20:25:36.126 wdl.w:ptcp.w:call-trgt-84.t:call-trgt_plot_meth_allele INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:36.126 wdl.w:ptcp.w:call-trgt-84.t:call-trgt_plot_meth_allele WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:36.126 wdl.w:ptcp.w:call-trgt-84.t:call-trgt_plot_meth_allele INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:25:36.126 wdl.w:ptcp.w:call-trgt-84.t:call-trgt_plot_meth_allele INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:36.195 wdl.w:ptcp.w:call-trgt-84.t:call-trgt_plot_meth_allele INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-84/call-trgt_plot_meth_allele/_singularity_tmpdir_ifljt6ef"
2025-09-15 20:25:36.195 wdl.w:ptcp.w:call-trgt-84.t:call-trgt_plot_meth_allele INFO Slurm invocation: srun --job-name call-trgt_plot_meth_allele --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-84/call-trgt_plot_meth_allele/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-84/call-trgt_plot_meth_allele/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-84/call-trgt_plot_meth_allele/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-84/call-trgt_plot_meth_allele/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-84/call-trgt_genotype/out/m84036_250809_035451_s4.bc2181.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2181.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-84/call-trgt_genotype/out/m84036_250809_035451_s4.bc2181.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2181.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-84/call-trgt_genotype/out/m84036_250809_035451_s4.bc2181.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2181.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-84/call-trgt_plot_meth_allele/_singularity_tmpdir_ifljt6ef/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-84/call-trgt_plot_meth_allele/_singularity_tmpdir_ifljt6ef/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:36.211 wdl.w:ptcp.w:call-trgt-84.t:call-trgt_plot_meth_allele NOTICE slurm_singularity run :: pid: 1205991, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-84/call-trgt_plot_meth_allele/slurm_singularity.log.txt"
2025-09-15 20:25:36.228 wdl.w:ptcp.w:call-paraphase-59.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for hbb for sample m84036_250809_035451_s4.bc2156 at 2025-09-15 20:25:27.245795...
2025-09-15 20:25:36.228 wdl.w:ptcp.w:call-paraphase-59.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for hbb for sample m84036_250809_035451_s4.bc2156 at 2025-09-15 20:25:27.491045...
2025-09-15 20:25:36.264 wdl.w:ptcp.w:call-trgt-78.t:call-trgt_plot_meth_waterfall INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2175.meth_waterfall.trgt_plots.zip"
2025-09-15 20:25:36.331 wdl.w:ptcp.w:call-trgt-78.t:call-trgt_plot_meth_waterfall NOTICE done
2025-09-15 20:25:36.337 wdl.w:ptcp.w:call-trgt-78 NOTICE finish :: job: "call-trgt_plot_meth_waterfall"
2025-09-15 20:25:36.337 wdl.w:ptcp.w:call-trgt-78 INFO output :: job: "call-trgt_plot_meth_waterfall", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-78/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2175.meth_waterfall.trgt_plots.zip"}
2025-09-15 20:25:36.337 wdl.w:ptcp.w:call-trgt-78 INFO visit :: node: "output-images_meth_waterfall", values: {"images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-78/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2175.meth_waterfall.trgt_plots.zip"}
2025-09-15 20:25:36.339 wdl.w:ptcp.w:call-trgt-89.t:call-get_reads_overlapping_repeats.slurm_singularity INFO srun: job 51798042 queued and waiting for resources
2025-09-15 20:25:36.339 wdl.w:ptcp.w:call-trgt-89.t:call-get_reads_overlapping_repeats.slurm_singularity INFO srun: job 51798042 has been allocated resources
2025-09-15 20:25:36.339 wdl.w:ptcp.w:call-trgt-89.t:call-get_reads_overlapping_repeats.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:36.345 wdl.w:ptcp.w:call-trgt-84.t:call-trgt_plot_meth_waterfall NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-84/call-trgt_plot_meth_waterfall", thread: 140607137760832
2025-09-15 20:25:36.353 wdl.w:ptcp.w:call-trgt-89.t:call-trgt_genotype.slurm_singularity INFO srun: job 51798043 queued and waiting for resources
2025-09-15 20:25:36.354 wdl.w:ptcp.w:call-trgt-89.t:call-trgt_genotype.slurm_singularity INFO srun: job 51798043 has been allocated resources
2025-09-15 20:25:36.354 wdl.w:ptcp.w:call-trgt-89.t:call-trgt_genotype.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:36.364 wdl.w:ptcp.w:call-trgt-84.t:call-trgt_plot_meth_waterfall INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:36.364 wdl.w:ptcp.w:call-trgt-84.t:call-trgt_plot_meth_waterfall INFO input :: name: "waterfall", value: true
2025-09-15 20:25:36.364 wdl.w:ptcp.w:call-trgt-84.t:call-trgt_plot_meth_waterfall INFO input :: name: "methylation", value: true
2025-09-15 20:25:36.364 wdl.w:ptcp.w:call-trgt-84.t:call-trgt_plot_meth_waterfall INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:25:36.364 wdl.w:ptcp.w:call-trgt-84.t:call-trgt_plot_meth_waterfall INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:25:36.364 wdl.w:ptcp.w:call-trgt-84.t:call-trgt_plot_meth_waterfall INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:25:36.364 wdl.w:ptcp.w:call-trgt-84.t:call-trgt_plot_meth_waterfall INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2181.trgt.sorted.spanning.bam.bai"
2025-09-15 20:25:36.364 wdl.w:ptcp.w:call-trgt-84.t:call-trgt_plot_meth_waterfall INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2181.trgt.sorted.spanning.bam"
2025-09-15 20:25:36.364 wdl.w:ptcp.w:call-trgt-84.t:call-trgt_plot_meth_waterfall INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2181.trgt.vcf"
2025-09-15 20:25:36.364 wdl.w:ptcp.w:call-trgt-84.t:call-trgt_plot_meth_waterfall INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2181"
2025-09-15 20:25:36.365 wdl.w:ptcp.w:call-trgt-84.t:call-trgt_plot_meth_waterfall INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:25:36.365 wdl.w:ptcp.w:call-trgt-84.t:call-trgt_plot_meth_waterfall INFO eval :: name: "plot_type", value: "waterfall"
2025-09-15 20:25:36.365 wdl.w:ptcp.w:call-trgt-84.t:call-trgt_plot_meth_waterfall INFO eval :: name: "show", value: "meth"
2025-09-15 20:25:36.365 wdl.w:ptcp.w:call-trgt-84.t:call-trgt_plot_meth_waterfall INFO eval :: name: "threads", value: 1
2025-09-15 20:25:36.365 wdl.w:ptcp.w:call-trgt-84.t:call-trgt_plot_meth_waterfall INFO eval :: name: "disk_size", value: 27
2025-09-15 20:25:36.365 wdl.w:ptcp.w:call-trgt-84.t:call-trgt_plot_meth_waterfall INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2181.meth_waterfall"
2025-09-15 20:25:36.366 wdl.w:ptcp.w:call-trgt-84.t:call-trgt_plot_meth_waterfall INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:36.366 wdl.w:ptcp.w:call-trgt-84.t:call-trgt_plot_meth_waterfall WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:36.366 wdl.w:ptcp.w:call-trgt-84.t:call-trgt_plot_meth_waterfall INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:25:36.366 wdl.w:ptcp.w:call-trgt-84.t:call-trgt_plot_meth_waterfall INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:36.379 wdl.w:ptcp.w:call-trgt-74.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:25:34 [ERROR] - No reads found for TRID=SCA37_DAB1
2025-09-15 20:25:36.379 wdl.w:ptcp.w:call-trgt-74.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:25:35 [ERROR] - No reads found for TRID=OPDM_ABCD3
2025-09-15 20:25:36.379 wdl.w:ptcp.w:call-trgt-74.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:25:35 [ERROR] - No reads found for TRID=NIID_NOTCH2NLC
2025-09-15 20:25:36.379 wdl.w:ptcp.w:call-trgt-74.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:25:35 [ERROR] - No reads found for TRID=SCA2_ATXN2
2025-09-15 20:25:36.379 wdl.w:ptcp.w:call-trgt-74.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:25:36 [ERROR] - No reads found for TRID=SCA27B_FGF14
2025-09-15 20:25:36.379 wdl.w:ptcp.w:call-trgt-74.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:25:36 [ERROR] - No reads found for TRID=OPDM4_RILPL1
2025-09-15 20:25:36.443 wdl.w:ptcp.w:call-trgt-84.t:call-trgt_plot_meth_waterfall INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-84/call-trgt_plot_meth_waterfall/_singularity_tmpdir_n_k7jp50"
2025-09-15 20:25:36.443 wdl.w:ptcp.w:call-trgt-84.t:call-trgt_plot_meth_waterfall INFO Slurm invocation: srun --job-name call-trgt_plot_meth_waterfall --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-84/call-trgt_plot_meth_waterfall/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-84/call-trgt_plot_meth_waterfall/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-84/call-trgt_plot_meth_waterfall/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-84/call-trgt_plot_meth_waterfall/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-84/call-trgt_genotype/out/m84036_250809_035451_s4.bc2181.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2181.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-84/call-trgt_genotype/out/m84036_250809_035451_s4.bc2181.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2181.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-84/call-trgt_genotype/out/m84036_250809_035451_s4.bc2181.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2181.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-84/call-trgt_plot_meth_waterfall/_singularity_tmpdir_n_k7jp50/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-84/call-trgt_plot_meth_waterfall/_singularity_tmpdir_n_k7jp50/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:36.460 wdl.w:ptcp.w:call-trgt-84.t:call-trgt_plot_meth_waterfall NOTICE slurm_singularity run :: pid: 1206004, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-84/call-trgt_plot_meth_waterfall/slurm_singularity.log.txt"
2025-09-15 20:25:36.674 wdl.w:ptcp.w:call-trgt-73.t:call-trgt_plot_meth_allele.slurm_singularity INFO srun: job 51798044 queued and waiting for resources
2025-09-15 20:25:36.675 wdl.w:ptcp.w:call-trgt-73.t:call-trgt_plot_meth_allele.slurm_singularity INFO srun: job 51798044 has been allocated resources
2025-09-15 20:25:36.675 wdl.w:ptcp.w:call-trgt-73.t:call-trgt_plot_meth_allele.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:36.786 wdl.w:ptcp.w:call-trgt-73.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO srun: job 51798045 queued and waiting for resources
2025-09-15 20:25:36.786 wdl.w:ptcp.w:call-trgt-73.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO srun: job 51798045 has been allocated resources
2025-09-15 20:25:36.786 wdl.w:ptcp.w:call-trgt-73.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:36.832 wdl.w:ptcp.w:call-trgt-73.t:call-trgt_plot_motifs_allele.slurm_singularity INFO srun: job 51798046 queued and waiting for resources
2025-09-15 20:25:36.832 wdl.w:ptcp.w:call-trgt-73.t:call-trgt_plot_motifs_allele.slurm_singularity INFO srun: job 51798046 has been allocated resources
2025-09-15 20:25:36.832 wdl.w:ptcp.w:call-trgt-73.t:call-trgt_plot_motifs_allele.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:36.857 wdl.w:ptcp.w:call-trgt-78.t:call-trgt_plot_motifs_allele INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2175.motifs_allele.trgt_plots.zip"
2025-09-15 20:25:36.922 wdl.w:ptcp.w:call-trgt-78.t:call-trgt_plot_motifs_allele NOTICE done
2025-09-15 20:25:36.927 wdl.w:ptcp.w:call-trgt-78 NOTICE finish :: job: "call-trgt_plot_motifs_allele"
2025-09-15 20:25:36.927 wdl.w:ptcp.w:call-trgt-78 INFO output :: job: "call-trgt_plot_motifs_allele", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-78/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2175.motifs_allele.trgt_plots.zip"}
2025-09-15 20:25:36.927 wdl.w:ptcp.w:call-trgt-78 INFO visit :: node: "output-images_motifs_allele", values: {"images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-78/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2175.motifs_allele.trgt_plots.zip"}
2025-09-15 20:25:36.933 wdl.w:ptcp.w:call-trgt-84.t:call-trgt_plot_motifs_allele NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-84/call-trgt_plot_motifs_allele", thread: 140607683024448
2025-09-15 20:25:36.954 wdl.w:ptcp.w:call-trgt-84.t:call-trgt_plot_motifs_allele INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:36.954 wdl.w:ptcp.w:call-trgt-84.t:call-trgt_plot_motifs_allele INFO input :: name: "waterfall", value: false
2025-09-15 20:25:36.954 wdl.w:ptcp.w:call-trgt-84.t:call-trgt_plot_motifs_allele INFO input :: name: "methylation", value: false
2025-09-15 20:25:36.954 wdl.w:ptcp.w:call-trgt-84.t:call-trgt_plot_motifs_allele INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:25:36.954 wdl.w:ptcp.w:call-trgt-84.t:call-trgt_plot_motifs_allele INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:25:36.954 wdl.w:ptcp.w:call-trgt-84.t:call-trgt_plot_motifs_allele INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:25:36.954 wdl.w:ptcp.w:call-trgt-84.t:call-trgt_plot_motifs_allele INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2181.trgt.sorted.spanning.bam.bai"
2025-09-15 20:25:36.954 wdl.w:ptcp.w:call-trgt-84.t:call-trgt_plot_motifs_allele INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2181.trgt.sorted.spanning.bam"
2025-09-15 20:25:36.955 wdl.w:ptcp.w:call-trgt-84.t:call-trgt_plot_motifs_allele INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2181.trgt.vcf"
2025-09-15 20:25:36.955 wdl.w:ptcp.w:call-trgt-84.t:call-trgt_plot_motifs_allele INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2181"
2025-09-15 20:25:36.955 wdl.w:ptcp.w:call-trgt-84.t:call-trgt_plot_motifs_allele INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:25:36.955 wdl.w:ptcp.w:call-trgt-84.t:call-trgt_plot_motifs_allele INFO eval :: name: "plot_type", value: "allele"
2025-09-15 20:25:36.955 wdl.w:ptcp.w:call-trgt-84.t:call-trgt_plot_motifs_allele INFO eval :: name: "show", value: "motifs"
2025-09-15 20:25:36.955 wdl.w:ptcp.w:call-trgt-84.t:call-trgt_plot_motifs_allele INFO eval :: name: "threads", value: 1
2025-09-15 20:25:36.955 wdl.w:ptcp.w:call-trgt-84.t:call-trgt_plot_motifs_allele INFO eval :: name: "disk_size", value: 27
2025-09-15 20:25:36.955 wdl.w:ptcp.w:call-trgt-84.t:call-trgt_plot_motifs_allele INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2181.motifs_allele"
2025-09-15 20:25:36.956 wdl.w:ptcp.w:call-trgt-84.t:call-trgt_plot_motifs_allele INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:36.956 wdl.w:ptcp.w:call-trgt-84.t:call-trgt_plot_motifs_allele WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:36.956 wdl.w:ptcp.w:call-trgt-84.t:call-trgt_plot_motifs_allele INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:25:36.956 wdl.w:ptcp.w:call-trgt-84.t:call-trgt_plot_motifs_allele INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:36.960 wdl.w:ptcp.w:call-trgt-78.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:34 [ERROR] - No reads found for TRID=NIID_NOTCH2NLC
2025-09-15 20:25:36.960 wdl.w:ptcp.w:call-trgt-78.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:34 [ERROR] - No reads found for TRID=OPDM_ABCD3
2025-09-15 20:25:36.960 wdl.w:ptcp.w:call-trgt-78.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:34 [ERROR] - No reads found for TRID=OPDM4_RILPL1
2025-09-15 20:25:36.960 wdl.w:ptcp.w:call-trgt-78.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:34 [ERROR] - No reads found for TRID=SCA8_ATXN8OS
2025-09-15 20:25:36.960 wdl.w:ptcp.w:call-trgt-78.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:34 [ERROR] - No reads found for TRID=SCA37_DAB1
2025-09-15 20:25:36.961 wdl.w:ptcp.w:call-trgt-78.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:34 [ERROR] - No reads found for TRID=SCA2_ATXN2
2025-09-15 20:25:36.961 wdl.w:ptcp.w:call-trgt-78.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:34 [ERROR] - No reads found for TRID=DRPLA_ATN1
2025-09-15 20:25:36.961 wdl.w:ptcp.w:call-trgt-78.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:34 [ERROR] - No reads found for TRID=SCA27B_FGF14
2025-09-15 20:25:36.961 wdl.w:ptcp.w:call-trgt-78.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:34 [ERROR] - No reads found for TRID=SCA3_ATXN3
2025-09-15 20:25:36.961 wdl.w:ptcp.w:call-trgt-78.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:34 [ERROR] - No reads found for TRID=SCA31_BEAN1
2025-09-15 20:25:36.961 wdl.w:ptcp.w:call-trgt-78.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:34 [ERROR] - No reads found for TRID=OPMD_PABPN1
2025-09-15 20:25:36.961 wdl.w:ptcp.w:call-trgt-78.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:34 [ERROR] - No reads found for TRID=HDL2_JPH3
2025-09-15 20:25:36.961 wdl.w:ptcp.w:call-trgt-78.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:34 [ERROR] - No reads found for TRID=SCA4_ZFHX3
2025-09-15 20:25:36.961 wdl.w:ptcp.w:call-trgt-78.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:34 [ERROR] - No reads found for TRID=SCA6_CACNA1A
2025-09-15 20:25:36.961 wdl.w:ptcp.w:call-trgt-78.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:34 [ERROR] - No reads found for TRID=FRA2A_AFF3
2025-09-15 20:25:36.961 wdl.w:ptcp.w:call-trgt-78.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:34 [ERROR] - No reads found for TRID=OPDM2_GIPC1
2025-09-15 20:25:36.961 wdl.w:ptcp.w:call-trgt-78.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:35 [ERROR] - No reads found for TRID=SD5_HOXD13
2025-09-15 20:25:36.961 wdl.w:ptcp.w:call-trgt-78.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:35 [ERROR] - No reads found for TRID=CJD_PRNP
2025-09-15 20:25:36.961 wdl.w:ptcp.w:call-trgt-78.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:35 [ERROR] - No reads found for TRID=EPM1_CSTB
2025-09-15 20:25:36.961 wdl.w:ptcp.w:call-trgt-78.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:35 [ERROR] - No reads found for TRID=DM1_DMPK
2025-09-15 20:25:36.961 wdl.w:ptcp.w:call-trgt-78.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:35 [ERROR] - No reads found for TRID=SCA7_ATXN7
2025-09-15 20:25:36.961 wdl.w:ptcp.w:call-trgt-78.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:35 [ERROR] - No reads found for TRID=SCA10_ATXN10
2025-09-15 20:25:36.961 wdl.w:ptcp.w:call-trgt-78.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:35 [ERROR] - No reads found for TRID=CCHS_PHOX2B
2025-09-15 20:25:36.962 wdl.w:ptcp.w:call-trgt-78.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:35 [ERROR] - No reads found for TRID=SCA12_PPP2R2B
2025-09-15 20:25:36.962 wdl.w:ptcp.w:call-trgt-78.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:35 [ERROR] - No reads found for TRID=SCA36_NOP56
2025-09-15 20:25:36.962 wdl.w:ptcp.w:call-trgt-78.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:35 [ERROR] - No reads found for TRID=SCA1_ATXN1
2025-09-15 20:25:36.962 wdl.w:ptcp.w:call-trgt-78.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:35 [ERROR] - No reads found for TRID=HD_HTT
2025-09-15 20:25:36.962 wdl.w:ptcp.w:call-trgt-78.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:35 [ERROR] - No reads found for TRID=FAME1_SAMD12
2025-09-15 20:25:37.035 wdl.w:ptcp.w:call-trgt-73.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO srun: job 51798047 queued and waiting for resources
2025-09-15 20:25:37.035 wdl.w:ptcp.w:call-trgt-73.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO srun: job 51798047 has been allocated resources
2025-09-15 20:25:37.035 wdl.w:ptcp.w:call-trgt-73.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:37.045 wdl.w:ptcp.w:call-trgt-84.t:call-trgt_plot_motifs_allele INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-84/call-trgt_plot_motifs_allele/_singularity_tmpdir_qn3qebxr"
2025-09-15 20:25:37.045 wdl.w:ptcp.w:call-trgt-84.t:call-trgt_plot_motifs_allele INFO Slurm invocation: srun --job-name call-trgt_plot_motifs_allele --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-84/call-trgt_plot_motifs_allele/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-84/call-trgt_plot_motifs_allele/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-84/call-trgt_plot_motifs_allele/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-84/call-trgt_plot_motifs_allele/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-84/call-trgt_genotype/out/m84036_250809_035451_s4.bc2181.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2181.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-84/call-trgt_genotype/out/m84036_250809_035451_s4.bc2181.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2181.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-84/call-trgt_genotype/out/m84036_250809_035451_s4.bc2181.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2181.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-84/call-trgt_plot_motifs_allele/_singularity_tmpdir_qn3qebxr/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-84/call-trgt_plot_motifs_allele/_singularity_tmpdir_qn3qebxr/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:37.046 wdl.w:ptcp.w:call-trgt-78.t:call-trgt_plot_meth_allele INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2175.meth_allele.trgt_plots.zip"
2025-09-15 20:25:37.068 wdl.w:ptcp.w:call-trgt-84.t:call-trgt_plot_motifs_allele NOTICE slurm_singularity run :: pid: 1206013, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-84/call-trgt_plot_motifs_allele/slurm_singularity.log.txt"
2025-09-15 20:25:37.120 wdl.w:ptcp.w:call-trgt-79.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:34 [ERROR] - No reads found for TRID=FRA2A_AFF3
2025-09-15 20:25:37.121 wdl.w:ptcp.w:call-trgt-79.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:34 [ERROR] - No reads found for TRID=SD5_HOXD13
2025-09-15 20:25:37.121 wdl.w:ptcp.w:call-trgt-79.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:34 [ERROR] - No reads found for TRID=SCA36_NOP56
2025-09-15 20:25:37.121 wdl.w:ptcp.w:call-trgt-79.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:35 [ERROR] - No reads found for TRID=CJD_PRNP
2025-09-15 20:25:37.121 wdl.w:ptcp.w:call-trgt-79.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:35 [ERROR] - No reads found for TRID=EPM1_CSTB
2025-09-15 20:25:37.121 wdl.w:ptcp.w:call-trgt-79.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:35 [ERROR] - No reads found for TRID=SCA10_ATXN10
2025-09-15 20:25:37.121 wdl.w:ptcp.w:call-trgt-79.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:36 [ERROR] - No reads found for TRID=SCA7_ATXN7
2025-09-15 20:25:37.121 wdl.w:ptcp.w:call-trgt-79.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:36 [ERROR] - No reads found for TRID=DM2_CNBP
2025-09-15 20:25:37.121 wdl.w:ptcp.w:call-trgt-79.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:36 [ERROR] - No reads found for TRID=SCA27B_FGF14
2025-09-15 20:25:37.121 wdl.w:ptcp.w:call-trgt-79.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:36 [ERROR] - No reads found for TRID=CCHS_PHOX2B
2025-09-15 20:25:37.128 wdl.w:ptcp.w:call-trgt-78.t:call-trgt_plot_meth_allele NOTICE done
2025-09-15 20:25:37.133 wdl.w:ptcp.w:call-trgt-78 NOTICE finish :: job: "call-trgt_plot_meth_allele"
2025-09-15 20:25:37.133 wdl.w:ptcp.w:call-trgt-78 INFO output :: job: "call-trgt_plot_meth_allele", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-78/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2175.meth_allele.trgt_plots.zip"}
2025-09-15 20:25:37.134 wdl.w:ptcp.w:call-trgt-78 INFO visit :: node: "output-images_meth_allele", values: {"images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-78/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2175.meth_allele.trgt_plots.zip"}
2025-09-15 20:25:37.139 wdl.w:ptcp.w:call-trgt-84.t:call-trgt_plot_motifs_waterfall NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-84/call-trgt_plot_motifs_waterfall", thread: 140607674631744
2025-09-15 20:25:37.156 wdl.w:ptcp.w:call-trgt-84.t:call-trgt_plot_motifs_waterfall INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:37.156 wdl.w:ptcp.w:call-trgt-84.t:call-trgt_plot_motifs_waterfall INFO input :: name: "waterfall", value: true
2025-09-15 20:25:37.156 wdl.w:ptcp.w:call-trgt-84.t:call-trgt_plot_motifs_waterfall INFO input :: name: "methylation", value: false
2025-09-15 20:25:37.156 wdl.w:ptcp.w:call-trgt-84.t:call-trgt_plot_motifs_waterfall INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:25:37.156 wdl.w:ptcp.w:call-trgt-84.t:call-trgt_plot_motifs_waterfall INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:25:37.156 wdl.w:ptcp.w:call-trgt-84.t:call-trgt_plot_motifs_waterfall INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:25:37.156 wdl.w:ptcp.w:call-trgt-84.t:call-trgt_plot_motifs_waterfall INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2181.trgt.sorted.spanning.bam.bai"
2025-09-15 20:25:37.156 wdl.w:ptcp.w:call-trgt-84.t:call-trgt_plot_motifs_waterfall INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2181.trgt.sorted.spanning.bam"
2025-09-15 20:25:37.156 wdl.w:ptcp.w:call-trgt-84.t:call-trgt_plot_motifs_waterfall INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2181.trgt.vcf"
2025-09-15 20:25:37.156 wdl.w:ptcp.w:call-trgt-84.t:call-trgt_plot_motifs_waterfall INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2181"
2025-09-15 20:25:37.157 wdl.w:ptcp.w:call-trgt-84.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:25:37.157 wdl.w:ptcp.w:call-trgt-84.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "plot_type", value: "waterfall"
2025-09-15 20:25:37.157 wdl.w:ptcp.w:call-trgt-84.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "show", value: "motifs"
2025-09-15 20:25:37.157 wdl.w:ptcp.w:call-trgt-84.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "threads", value: 1
2025-09-15 20:25:37.157 wdl.w:ptcp.w:call-trgt-84.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "disk_size", value: 27
2025-09-15 20:25:37.157 wdl.w:ptcp.w:call-trgt-84.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2181.motifs_waterfall"
2025-09-15 20:25:37.158 wdl.w:ptcp.w:call-trgt-84.t:call-trgt_plot_motifs_waterfall INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:37.158 wdl.w:ptcp.w:call-trgt-84.t:call-trgt_plot_motifs_waterfall WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:37.158 wdl.w:ptcp.w:call-trgt-84.t:call-trgt_plot_motifs_waterfall INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:25:37.158 wdl.w:ptcp.w:call-trgt-84.t:call-trgt_plot_motifs_waterfall INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:37.220 wdl.w:ptcp.w:call-trgt-84.t:call-trgt_plot_meth_allele.slurm_singularity INFO srun: job 51798048 queued and waiting for resources
2025-09-15 20:25:37.221 wdl.w:ptcp.w:call-trgt-84.t:call-trgt_plot_meth_allele.slurm_singularity INFO srun: job 51798048 has been allocated resources
2025-09-15 20:25:37.221 wdl.w:ptcp.w:call-trgt-84.t:call-trgt_plot_meth_allele.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:37.226 wdl.w:ptcp.w:call-trgt-84.t:call-trgt_plot_motifs_waterfall INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-84/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_2lrm_6xq"
2025-09-15 20:25:37.226 wdl.w:ptcp.w:call-trgt-84.t:call-trgt_plot_motifs_waterfall INFO Slurm invocation: srun --job-name call-trgt_plot_motifs_waterfall --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-84/call-trgt_plot_motifs_waterfall/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-84/call-trgt_plot_motifs_waterfall/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-84/call-trgt_plot_motifs_waterfall/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-84/call-trgt_plot_motifs_waterfall/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-84/call-trgt_genotype/out/m84036_250809_035451_s4.bc2181.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2181.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-84/call-trgt_genotype/out/m84036_250809_035451_s4.bc2181.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2181.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-84/call-trgt_genotype/out/m84036_250809_035451_s4.bc2181.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2181.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-84/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_2lrm_6xq/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-84/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_2lrm_6xq/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:37.241 wdl.w:ptcp.w:call-trgt-84.t:call-trgt_plot_motifs_waterfall NOTICE slurm_singularity run :: pid: 1206015, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-84/call-trgt_plot_motifs_waterfall/slurm_singularity.log.txt"
2025-09-15 20:25:37.288 wdl.w:ptcp.w:call-paraphase-79.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for f8inv1 for sample m84036_250809_035451_s4.bc2176 at 2025-09-15 20:25:26.959087...
2025-09-15 20:25:37.289 wdl.w:ptcp.w:call-paraphase-79.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for hba for sample m84036_250809_035451_s4.bc2176 at 2025-09-15 20:25:27.932909...
2025-09-15 20:25:37.289 wdl.w:ptcp.w:call-paraphase-79.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for hba for sample m84036_250809_035451_s4.bc2176 at 2025-09-15 20:25:28.385883...
2025-09-15 20:25:37.289 wdl.w:ptcp.w:call-paraphase-79.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for f8inv1 for sample m84036_250809_035451_s4.bc2176 at 2025-09-15 20:25:29.905657...
2025-09-15 20:25:37.289 wdl.w:ptcp.w:call-paraphase-79.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for f8inv1 for sample m84036_250809_035451_s4.bc2176 at 2025-09-15 20:25:30.139105...
2025-09-15 20:25:37.289 wdl.w:ptcp.w:call-paraphase-79.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for hbb for sample m84036_250809_035451_s4.bc2176 at 2025-09-15 20:25:35.847079...
2025-09-15 20:25:37.289 wdl.w:ptcp.w:call-paraphase-79.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for hbb for sample m84036_250809_035451_s4.bc2176 at 2025-09-15 20:25:35.847434...
2025-09-15 20:25:37.467 wdl.w:ptcp.w:call-trgt-84.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO srun: job 51798049 queued and waiting for resources
2025-09-15 20:25:37.467 wdl.w:ptcp.w:call-trgt-84.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO srun: job 51798049 has been allocated resources
2025-09-15 20:25:37.467 wdl.w:ptcp.w:call-trgt-84.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:37.710 wdl.w:ptcp.w:call-trgt-78.t:call-trgt_plot_motifs_waterfall INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2175.motifs_waterfall.trgt_plots.zip"
2025-09-15 20:25:37.785 wdl.w:ptcp.w:call-trgt-78.t:call-trgt_plot_motifs_waterfall NOTICE done
2025-09-15 20:25:37.790 wdl.w:ptcp.w:call-trgt-78 NOTICE finish :: job: "call-trgt_plot_motifs_waterfall"
2025-09-15 20:25:37.790 wdl.w:ptcp.w:call-trgt-78 INFO output :: job: "call-trgt_plot_motifs_waterfall", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-78/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2175.motifs_waterfall.trgt_plots.zip"}
2025-09-15 20:25:37.790 wdl.w:ptcp.w:call-trgt-78 INFO visit :: node: "output-images_motifs_waterfall", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-78/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2175.motifs_waterfall.trgt_plots.zip"}
2025-09-15 20:25:37.790 wdl.w:ptcp.w:call-trgt-78 INFO visit :: node: "outputs", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-78/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2175.motifs_waterfall.trgt_plots.zip", "images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-78/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2175.meth_allele.trgt_plots.zip", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-78/call-trgt_genotype/out/m84036_250809_035451_s4.bc2175.trgt.sorted.spanning.bam.bai", "images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-78/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2175.motifs_allele.trgt_plots.zip", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-78/call-trgt_genotype/out/m84036_250809_035451_s4.bc2175.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-78/call-trgt_genotype/out/m84036_250809_035451_s4.bc2175.trgt.vcf", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-78/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2175.repeats.bam", "images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-78/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2175.meth_waterfall.trgt_plots.zip", "reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-78/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2175.repeats.bam.bai"}
2025-09-15 20:25:37.798 wdl.w:ptcp.w:call-paraphase-82.t:call-run_paraphase NOTICE task setup :: name: "run_paraphase", source: "./paraphase.wdl", line: 127, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-82/call-run_paraphase", thread: 140608773551680
2025-09-15 20:25:37.821 wdl.w:ptcp.w:call-paraphase-82.t:call-run_paraphase INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:37.821 wdl.w:ptcp.w:call-paraphase-82.t:call-run_paraphase INFO input :: name: "annotation_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf"
2025-09-15 20:25:37.821 wdl.w:ptcp.w:call-paraphase-82.t:call-run_paraphase INFO input :: name: "genome_version", value: "38"
2025-09-15 20:25:37.822 wdl.w:ptcp.w:call-paraphase-82.t:call-run_paraphase INFO input :: name: "config_file", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/paraphase_config.GRCh38.yaml"
2025-09-15 20:25:37.822 wdl.w:ptcp.w:call-paraphase-82.t:call-run_paraphase INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:25:37.822 wdl.w:ptcp.w:call-paraphase-82.t:call-run_paraphase INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:25:37.822 wdl.w:ptcp.w:call-paraphase-82.t:call-run_paraphase INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2179.mapped.bam.bai"
2025-09-15 20:25:37.822 wdl.w:ptcp.w:call-paraphase-82.t:call-run_paraphase INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2179.mapped.bam"
2025-09-15 20:25:37.822 wdl.w:ptcp.w:call-paraphase-82.t:call-run_paraphase INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2179"
2025-09-15 20:25:37.822 wdl.w:ptcp.w:call-paraphase-82.t:call-run_paraphase INFO eval :: name: "threads", value: 4
2025-09-15 20:25:37.823 wdl.w:ptcp.w:call-paraphase-82.t:call-run_paraphase INFO eval :: name: "mem_gb", value: 8
2025-09-15 20:25:37.823 wdl.w:ptcp.w:call-paraphase-82.t:call-run_paraphase INFO eval :: name: "disk_size", value: 27
2025-09-15 20:25:37.823 wdl.w:ptcp.w:call-paraphase-82.t:call-run_paraphase INFO eval :: name: "out_dir", value: "m84036_250809_035451_s4.bc2179_paraphase"
2025-09-15 20:25:37.824 wdl.w:ptcp.w:call-paraphase-82.t:call-run_paraphase INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 4, memory_reservation: 8000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:37.824 wdl.w:ptcp.w:call-paraphase-82.t:call-run_paraphase WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:37.824 wdl.w:ptcp.w:call-paraphase-82.t:call-run_paraphase INFO provisioned :: seconds_waited: 0, cpu: 4, mem_bytes: 8000000000
2025-09-15 20:25:37.824 wdl.w:ptcp.w:call-paraphase-82.t:call-run_paraphase INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:37.889 wdl.w:ptcp.w:call-trgt-78 NOTICE done
2025-09-15 20:25:37.894 wdl.w:ptcp.w:call-paraphase-82.t:call-run_paraphase INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-82/call-run_paraphase/_singularity_tmpdir_gx8_cpnl"
2025-09-15 20:25:37.894 wdl.w:ptcp.w:call-paraphase-82.t:call-run_paraphase INFO Slurm invocation: srun --job-name call-run_paraphase --partition compute,compute9 --cpus-per-task 4 --mem 7629M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-82/call-run_paraphase/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-82/call-run_paraphase/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-82/call-run_paraphase/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-82/call-run_paraphase/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-82/out/m84036_250809_035451_s4.bc2179.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2179.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-82/out/m84036_250809_035451_s4.bc2179.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2179.mapped.bam.bai:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/variant_list/variant_list.GRCh38.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf:ro --bind /ptcp/meta/paraphase/paraphase_config.GRCh38.yaml:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/paraphase_config.GRCh38.yaml:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-82/call-run_paraphase/_singularity_tmpdir_gx8_cpnl/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-82/call-run_paraphase/_singularity_tmpdir_gx8_cpnl/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:37.896 wdl.w:ptcp NOTICE finish :: job: "call-trgt-78"
2025-09-15 20:25:37.898 wdl.w:ptcp INFO output :: job: "call-trgt-78", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-78/out/m84036_250809_035451_s4.bc2175.motifs_waterfall.trgt_plots.zip", "images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-78/out/m84036_250809_035451_s4.bc2175.meth_allele.trgt_plots.zip", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-78/out/m84036_250809_035451_s4.bc2175.trgt.sorted.spanning.bam.bai", "images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-78/out/m84036_250809_035451_s4.bc2175.motifs_allele.trgt_plots.zip", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-78/out/m84036_250809_035451_s4.bc2175.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-78/out/m84036_250809_035451_s4.bc2175.trgt.vcf", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-78/out/m84036_250809_035451_s4.bc2175.repeats.bam", "images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-78/out/m84036_250809_035451_s4.bc2175.meth_waterfall.trgt_plots.zip", "reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-78/out/m84036_250809_035451_s4.bc2175.repeats.bam.bai"}
2025-09-15 20:25:37.907 wdl.w:ptcp.w:call-sawfish-86 NOTICE workflow start :: name: "sawfish", source: "./sawfish.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-86"
2025-09-15 20:25:37.912 wdl.w:ptcp.w:call-paraphase-82.t:call-run_paraphase NOTICE slurm_singularity run :: pid: 1206028, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-82/call-run_paraphase/slurm_singularity.log.txt"
2025-09-15 20:25:37.922 wdl.w:ptcp.w:call-sawfish-86 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:25:37.922 wdl.w:ptcp.w:call-sawfish-86 INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:25:37.922 wdl.w:ptcp.w:call-sawfish-86 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-86/out/m84036_250809_035451_s4.bc2183.mapped.bam"}
2025-09-15 20:25:37.922 wdl.w:ptcp.w:call-sawfish-86 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-86/out/m84036_250809_035451_s4.bc2183.mapped.bam.bai"}
2025-09-15 20:25:37.922 wdl.w:ptcp.w:call-sawfish-86 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:25:37.922 wdl.w:ptcp.w:call-sawfish-86 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:25:37.922 wdl.w:ptcp.w:call-sawfish-86 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2183"}
2025-09-15 20:25:37.922 wdl.w:ptcp.w:call-sawfish-86 NOTICE ready :: job: "call-run_sawfish", callee: "run_sawfish"
2025-09-15 20:25:37.922 wdl.w:ptcp.w:call-sawfish-86 INFO input :: job: "call-run_sawfish", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-86/out/m84036_250809_035451_s4.bc2183.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-86/out/m84036_250809_035451_s4.bc2183.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2183"}
2025-09-15 20:25:38.071 wdl.w:ptcp.w:call-paraphase-03.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for hbb for sample m84036_250809_035451_s4.bc2100 at 2025-09-15 20:25:37.120670...
2025-09-15 20:25:38.072 wdl.w:ptcp.w:call-paraphase-03.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for hbb for sample m84036_250809_035451_s4.bc2100 at 2025-09-15 20:25:37.120869...
2025-09-15 20:25:38.079 wdl.w:ptcp.w:call-trgt-84.t:call-trgt_plot_motifs_allele.slurm_singularity INFO srun: job 51798050 queued and waiting for resources
2025-09-15 20:25:38.080 wdl.w:ptcp.w:call-trgt-84.t:call-trgt_plot_motifs_allele.slurm_singularity INFO srun: job 51798050 has been allocated resources
2025-09-15 20:25:38.080 wdl.w:ptcp.w:call-trgt-84.t:call-trgt_plot_motifs_allele.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:38.131 wdl.w:ptcp.w:call-sawfish-55.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:29][sawfish][INFO] Starting sawfish 2.0.3
2025-09-15 20:25:38.131 wdl.w:ptcp.w:call-sawfish-55.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:29][sawfish][INFO] cmdline: sawfish discover --disable-cnv --threads 16 --ref /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa --bam m84036_250809_035451_s4.bc2152.minimap2.bam --output-dir m84036_250809_035451_s4.bc2152_sawfish_discover
2025-09-15 20:25:38.131 wdl.w:ptcp.w:call-sawfish-55.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:29][sawfish][INFO] Running on 16 threads
2025-09-15 20:25:38.131 wdl.w:ptcp.w:call-sawfish-55.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:29][sawfish][INFO] Writing discover settings to file: 'm84036_250809_035451_s4.bc2152_sawfish_discover/discover.settings.json'
2025-09-15 20:25:38.132 wdl.w:ptcp.w:call-sawfish-55.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:29][sawfish][INFO] Reading reference genome from file '/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa'
2025-09-15 20:25:38.132 wdl.w:ptcp.w:call-sawfish-55.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:32][sawfish][INFO] Processing alignment file '/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2152.minimap2.bam'
2025-09-15 20:25:38.132 wdl.w:ptcp.w:call-sawfish-55.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:32][sawfish][INFO] Finished processing all alignments
2025-09-15 20:25:38.132 wdl.w:ptcp.w:call-sawfish-55.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:32][sawfish][INFO] Writing depth bins to binary file: 'm84036_250809_035451_s4.bc2152_sawfish_discover/depth.mpack'
2025-09-15 20:25:38.132 wdl.w:ptcp.w:call-sawfish-55.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:32][sawfish][INFO] Writing max sv depth genome regions to bed file: 'm84036_250809_035451_s4.bc2152_sawfish_discover/max.depth.bed'
2025-09-15 20:25:38.132 wdl.w:ptcp.w:call-sawfish-55.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:32][sawfish][INFO] Completing breakpoint observation clustering
2025-09-15 20:25:38.132 wdl.w:ptcp.w:call-sawfish-55.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:32][sawfish][INFO] Finished breakpoint observation clustering
2025-09-15 20:25:38.132 wdl.w:ptcp.w:call-sawfish-55.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:32][sawfish][INFO] Consolidating adjacent indel candidates
2025-09-15 20:25:38.132 wdl.w:ptcp.w:call-sawfish-55.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:32][sawfish][INFO] Finding large insertion candidates
2025-09-15 20:25:38.132 wdl.w:ptcp.w:call-sawfish-55.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:32][sawfish][INFO] Writing breakpoint_cluster debug bed file: 'm84036_250809_035451_s4.bc2152_sawfish_discover/debug.breakpoint_clusters.bed'
2025-09-15 20:25:38.132 wdl.w:ptcp.w:call-sawfish-55.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:32][sawfish][INFO] Refining SV Candidates
2025-09-15 20:25:38.132 wdl.w:ptcp.w:call-sawfish-55.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:32][sawfish][INFO] Writing debug assembly region bed file: 'm84036_250809_035451_s4.bc2152_sawfish_discover/assembly.regions.bed'
2025-09-15 20:25:38.132 wdl.w:ptcp.w:call-sawfish-55.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:32][sawfish][INFO] Starting refinement of breakpoint evidence clusters
2025-09-15 20:25:38.132 wdl.w:ptcp.w:call-sawfish-55.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:33][sawfish][INFO] Finished refining all breakpoint evidence clusters
2025-09-15 20:25:38.132 wdl.w:ptcp.w:call-sawfish-55.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:33][sawfish][INFO] Writing all contig alignments to bam file: 'm84036_250809_035451_s4.bc2152_sawfish_discover/contig.alignment.bam'
2025-09-15 20:25:38.132 wdl.w:ptcp.w:call-sawfish-55.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:33][sawfish][INFO] Writing candidate structural variants to file: 'm84036_250809_035451_s4.bc2152_sawfish_discover/candidate.sv.bcf'
2025-09-15 20:25:38.132 wdl.w:ptcp.w:call-sawfish-55.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:33][sawfish][INFO] Writing run statistics to file: 'm84036_250809_035451_s4.bc2152_sawfish_discover/run.stats.json'
2025-09-15 20:25:38.132 wdl.w:ptcp.w:call-sawfish-55.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:33][sawfish][INFO] sawfish completed. Total Runtime: 00:00:04.271
2025-09-15 20:25:38.133 wdl.w:ptcp.w:call-sawfish-55.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:33][sawfish][INFO] Starting sawfish 2.0.3
2025-09-15 20:25:38.133 wdl.w:ptcp.w:call-sawfish-55.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:33][sawfish][INFO] cmdline: sawfish joint-call --threads 16 --sample m84036_250809_035451_s4.bc2152_sawfish_discover --output-dir m84036_250809_035451_s4.bc2152_sawfish
2025-09-15 20:25:38.133 wdl.w:ptcp.w:call-sawfish-55.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:33][sawfish][INFO] Running on 16 threads
2025-09-15 20:25:38.133 wdl.w:ptcp.w:call-sawfish-55.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:33][sawfish][INFO] Reading reference genome from file '/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa'
2025-09-15 20:25:38.133 wdl.w:ptcp.w:call-sawfish-55.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:36][sawfish][INFO] Reading sawfish-discover results from 1 samples
2025-09-15 20:25:38.133 wdl.w:ptcp.w:call-sawfish-55.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:37][sawfish][INFO] Writing depth track to bigwig file: 'm84036_250809_035451_s4.bc2152_sawfish/samples/sample0001_UnknownSampleName/depth.bw'
2025-09-15 20:25:38.133 wdl.w:ptcp.w:call-sawfish-55.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:37][sawfish][INFO] Merging SV haplotypes
2025-09-15 20:25:38.133 wdl.w:ptcp.w:call-sawfish-55.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:37][sawfish][INFO] Finished merging SV haplotypes across samples
2025-09-15 20:25:38.133 wdl.w:ptcp.w:call-sawfish-55.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:37][sawfish][INFO] Writing merged contig alignments to bam file: 'm84036_250809_035451_s4.bc2152_sawfish/contig.alignment.bam'
2025-09-15 20:25:38.133 wdl.w:ptcp.w:call-sawfish-55.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:37][sawfish][INFO] Starting SV candidate cluster genotyping
2025-09-15 20:25:38.133 wdl.w:ptcp.w:call-sawfish-55.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:37][sawfish][INFO] Finished genotyping all SV candidate clusters
2025-09-15 20:25:38.133 wdl.w:ptcp.w:call-sawfish-55.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:37][sawfish][INFO] Starting joint CNV/SV refinement
2025-09-15 20:25:38.133 wdl.w:ptcp.w:call-sawfish-55.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:37][sawfish][INFO] Merged 0 CNVs into corresponding breakpoint-based SVs
2025-09-15 20:25:38.133 wdl.w:ptcp.w:call-sawfish-55.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:37][sawfish][INFO] Writing genotyped structural variants to file: 'm84036_250809_035451_s4.bc2152_sawfish/genotyped.sv.vcf.gz'
2025-09-15 20:25:38.133 wdl.w:ptcp.w:call-sawfish-55.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:37][sawfish][INFO] Writing run statistics to file: 'm84036_250809_035451_s4.bc2152_sawfish/run.stats.json'
2025-09-15 20:25:38.133 wdl.w:ptcp.w:call-sawfish-55.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:37][sawfish][INFO] sawfish completed. Total Runtime: 00:00:04.606
2025-09-15 20:25:38.179 wdl.w:ptcp.w:call-paraphase-23.t:call-run_paraphase INFO output :: name: "paraphase_bam", value: "m84036_250809_035451_s4.bc2120_paraphase/m84036_250809_035451_s4.bc2120.paraphase.bam"
2025-09-15 20:25:38.184 wdl.w:ptcp.w:call-paraphase-23.t:call-run_paraphase INFO output :: name: "paraphase_bam_bai", value: "m84036_250809_035451_s4.bc2120_paraphase/m84036_250809_035451_s4.bc2120.paraphase.bam.bai"
2025-09-15 20:25:38.185 wdl.w:ptcp.w:call-paraphase-23.t:call-run_paraphase INFO output :: name: "paraphase_json", value: "m84036_250809_035451_s4.bc2120_paraphase/m84036_250809_035451_s4.bc2120.paraphase.json"
2025-09-15 20:25:38.185 wdl.w:ptcp.w:call-sawfish-55.t:call-run_sawfish INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2152_sawfish/m84036_250809_035451_s4.bc2152.sv.vcf.gz"
2025-09-15 20:25:38.189 wdl.w:ptcp.w:call-paraphase-23.t:call-run_paraphase INFO output :: name: "paraphase_vcfs", value: ["/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2120_paraphase/m84036_250809_035451_s4.bc2120_paraphase_vcfs/m84036_250809_035451_s4.bc2120_cyp21.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2120_paraphase/m84036_250809_035451_s4.bc2120_paraphase_vcfs/m84036_250809_035451_s4.bc2120_f8inv1.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2120_paraphase/m84036_250809_035451_s4.bc2120_paraphase_vcfs/m84036_250809_035451_s4.bc2120_f8inv22.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2120_paraphase/m84036_250809_035451_s4.bc2120_paraphase_vcfs/m84036_250809_035451_s4.bc2120_gba.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2120_paraphase/m84036_250809_035451_s4.bc2120_paraphase_vcfs/m84036_250809_035451_s4.bc2120_hba.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2120_paraphase/m84036_250809_035451_s4.bc2120_paraphase_vcfs/m84036_250809_035451_s4.bc2120_hbb.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2120_paraphase/m84036_250809_035451_s4.bc2120_paraphase_vcfs/m84036_250809_035451_s4.bc2120_rpgr.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2120_paraphase/m84036_250809_035451_s4.bc2120_paraphase_vcfs/m84036_250809_035451_s4.bc2120_smn1.vcf"]
2025-09-15 20:25:38.190 wdl.w:ptcp.w:call-sawfish-55.t:call-run_sawfish INFO output :: name: "vcf_tbi", value: "m84036_250809_035451_s4.bc2152_sawfish/m84036_250809_035451_s4.bc2152.sv.vcf.gz.tbi"
2025-09-15 20:25:38.191 wdl.w:ptcp.w:call-sawfish-55.t:call-run_sawfish INFO output :: name: "minimap2_bam", value: "m84036_250809_035451_s4.bc2152.minimap2.bam"
2025-09-15 20:25:38.193 wdl.w:ptcp.w:call-sawfish-55.t:call-run_sawfish INFO output :: name: "minimap2_bam_bai", value: "m84036_250809_035451_s4.bc2152.minimap2.bam.bai"
2025-09-15 20:25:38.193 wdl.w:ptcp.w:call-paraphase-23.t:call-run_paraphase INFO output :: name: "havanno_json", value: "m84036_250809_035451_s4.bc2120.havanno.json"
2025-09-15 20:25:38.266 wdl.w:ptcp.w:call-trgt-84.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO srun: job 51798051 queued and waiting for resources
2025-09-15 20:25:38.266 wdl.w:ptcp.w:call-trgt-84.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO srun: job 51798051 has been allocated resources
2025-09-15 20:25:38.266 wdl.w:ptcp.w:call-trgt-84.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:38.378 wdl.w:ptcp.w:call-sawfish-55.t:call-run_sawfish NOTICE done
2025-09-15 20:25:38.386 wdl.w:ptcp.w:call-sawfish-55 NOTICE finish :: job: "call-run_sawfish"
2025-09-15 20:25:38.386 wdl.w:ptcp.w:call-sawfish-55 INFO output :: job: "call-run_sawfish", values: {"minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-55/call-run_sawfish/out/m84036_250809_035451_s4.bc2152.minimap2.bam.bai", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-55/call-run_sawfish/out/m84036_250809_035451_s4.bc2152.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-55/call-run_sawfish/out/m84036_250809_035451_s4.bc2152_sawfish/m84036_250809_035451_s4.bc2152.sv.vcf.gz.tbi", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-55/call-run_sawfish/out/m84036_250809_035451_s4.bc2152_sawfish/m84036_250809_035451_s4.bc2152.sv.vcf.gz"}
2025-09-15 20:25:38.386 wdl.w:ptcp.w:call-sawfish-55 INFO visit :: node: "output-minimap2_bam", values: {"minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-55/call-run_sawfish/out/m84036_250809_035451_s4.bc2152.minimap2.bam"}
2025-09-15 20:25:38.386 wdl.w:ptcp.w:call-sawfish-55 INFO visit :: node: "output-minimap2_bam_bai", values: {"minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-55/call-run_sawfish/out/m84036_250809_035451_s4.bc2152.minimap2.bam.bai"}
2025-09-15 20:25:38.387 wdl.w:ptcp.w:call-sawfish-55 INFO visit :: node: "output-vcf", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-55/call-run_sawfish/out/m84036_250809_035451_s4.bc2152_sawfish/m84036_250809_035451_s4.bc2152.sv.vcf.gz"}
2025-09-15 20:25:38.387 wdl.w:ptcp.w:call-sawfish-55 INFO visit :: node: "output-vcf_tbi", values: {"vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-55/call-run_sawfish/out/m84036_250809_035451_s4.bc2152_sawfish/m84036_250809_035451_s4.bc2152.sv.vcf.gz.tbi"}
2025-09-15 20:25:38.387 wdl.w:ptcp.w:call-sawfish-55 INFO visit :: node: "outputs", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-55/call-run_sawfish/out/m84036_250809_035451_s4.bc2152_sawfish/m84036_250809_035451_s4.bc2152.sv.vcf.gz", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-55/call-run_sawfish/out/m84036_250809_035451_s4.bc2152.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-55/call-run_sawfish/out/m84036_250809_035451_s4.bc2152_sawfish/m84036_250809_035451_s4.bc2152.sv.vcf.gz.tbi", "minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-55/call-run_sawfish/out/m84036_250809_035451_s4.bc2152.minimap2.bam.bai"}
2025-09-15 20:25:38.396 wdl.w:ptcp.w:call-paraphase-73.t:call-call_f8 NOTICE task setup :: name: "call_f8", source: "./paraphase.wdl", line: 232, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-73/call-call_f8", thread: 140608186324544
2025-09-15 20:25:38.424 wdl.w:ptcp.w:call-paraphase-73.t:call-call_f8 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:38.424 wdl.w:ptcp.w:call-paraphase-73.t:call-call_f8 INFO input :: name: "genome_version", value: "38"
2025-09-15 20:25:38.424 wdl.w:ptcp.w:call-paraphase-73.t:call-call_f8 INFO input :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2170"
2025-09-15 20:25:38.424 wdl.w:ptcp.w:call-paraphase-73.t:call-call_f8 INFO input :: name: "paraphase_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2170.paraphase.bam.bai"
2025-09-15 20:25:38.424 wdl.w:ptcp.w:call-paraphase-73.t:call-call_f8 INFO input :: name: "paraphase_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2170.paraphase.bam"
2025-09-15 20:25:38.424 wdl.w:ptcp.w:call-paraphase-73.t:call-call_f8 INFO input :: name: "sex", value: "F"
2025-09-15 20:25:38.424 wdl.w:ptcp.w:call-paraphase-73.t:call-call_f8 INFO eval :: name: "threads", value: 1
2025-09-15 20:25:38.424 wdl.w:ptcp.w:call-paraphase-73.t:call-call_f8 INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:25:38.425 wdl.w:ptcp.w:call-paraphase-73.t:call-call_f8 INFO eval :: name: "disk_size", value: 11
2025-09-15 20:25:38.425 wdl.w:ptcp.w:call-paraphase-73.t:call-call_f8 INFO eval :: name: "sample_sex", value: "F"
2025-09-15 20:25:38.425 wdl.w:ptcp.w:call-paraphase-73.t:call-call_f8 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:38.425 wdl.w:ptcp.w:call-paraphase-73.t:call-call_f8 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:38.426 wdl.w:ptcp.w:call-paraphase-73.t:call-call_f8 INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:25:38.426 wdl.w:ptcp.w:call-paraphase-73.t:call-call_f8 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:38.448 wdl.w:ptcp.w:call-paraphase-85.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for f8inv22 for sample m84036_250809_035451_s4.bc2182 at 2025-09-15 20:25:35.868147...
2025-09-15 20:25:38.449 wdl.w:ptcp.w:call-paraphase-85.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for hbb for sample m84036_250809_035451_s4.bc2182 at 2025-09-15 20:25:35.926066...
2025-09-15 20:25:38.449 wdl.w:ptcp.w:call-paraphase-85.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for rpgr for sample m84036_250809_035451_s4.bc2182 at 2025-09-15 20:25:36.018370...
2025-09-15 20:25:38.449 wdl.w:ptcp.w:call-paraphase-85.t:call-run_paraphase.stderr VERBOSE WARNING:root:This region does not appear to have coverage. Will not attempt to phase haplotypes.
2025-09-15 20:25:38.449 wdl.w:ptcp.w:call-paraphase-85.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for f8inv22 for sample m84036_250809_035451_s4.bc2182 at 2025-09-15 20:25:36.028894...
2025-09-15 20:25:38.449 wdl.w:ptcp.w:call-paraphase-85.t:call-run_paraphase.stderr VERBOSE WARNING:root:This region does not appear to have coverage. Will not attempt to phase haplotypes.
2025-09-15 20:25:38.449 wdl.w:ptcp.w:call-paraphase-85.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for hbb for sample m84036_250809_035451_s4.bc2182 at 2025-09-15 20:25:36.047703...
2025-09-15 20:25:38.449 wdl.w:ptcp.w:call-paraphase-85.t:call-run_paraphase.stderr VERBOSE WARNING:root:This region does not appear to have coverage. Will not attempt to phase haplotypes.
2025-09-15 20:25:38.449 wdl.w:ptcp.w:call-paraphase-85.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for rpgr for sample m84036_250809_035451_s4.bc2182 at 2025-09-15 20:25:36.126291...
2025-09-15 20:25:38.449 wdl.w:ptcp.w:call-paraphase-85.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for smn1 for sample m84036_250809_035451_s4.bc2182 at 2025-09-15 20:25:36.434285...
2025-09-15 20:25:38.449 wdl.w:ptcp.w:call-paraphase-85.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for f8inv22 for sample m84036_250809_035451_s4.bc2182 at 2025-09-15 20:25:36.440545...
2025-09-15 20:25:38.449 wdl.w:ptcp.w:call-paraphase-85.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for hbb for sample m84036_250809_035451_s4.bc2182 at 2025-09-15 20:25:36.472114...
2025-09-15 20:25:38.449 wdl.w:ptcp.w:call-paraphase-85.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for rpgr for sample m84036_250809_035451_s4.bc2182 at 2025-09-15 20:25:36.502843...
2025-09-15 20:25:38.449 wdl.w:ptcp.w:call-paraphase-85.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for f8inv1 for sample m84036_250809_035451_s4.bc2182 at 2025-09-15 20:25:36.514164...
2025-09-15 20:25:38.450 wdl.w:ptcp.w:call-paraphase-85.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for f8inv1 for sample m84036_250809_035451_s4.bc2182 at 2025-09-15 20:25:36.514407...
2025-09-15 20:25:38.450 wdl.w:ptcp.w:call-paraphase-85.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for f8inv1 for sample m84036_250809_035451_s4.bc2182 at 2025-09-15 20:25:36.982408...
2025-09-15 20:25:38.450 wdl.w:ptcp.w:call-paraphase-85.t:call-run_paraphase.stderr VERBOSE WARNING:root:This region does not appear to have coverage. Will not attempt to phase haplotypes.
2025-09-15 20:25:38.450 wdl.w:ptcp.w:call-paraphase-85.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for f8inv1 for sample m84036_250809_035451_s4.bc2182 at 2025-09-15 20:25:37.065368...
2025-09-15 20:25:38.450 wdl.w:ptcp.w:call-paraphase-85.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for f8inv1 for sample m84036_250809_035451_s4.bc2182 at 2025-09-15 20:25:37.389301...
2025-09-15 20:25:38.464 wdl.w:ptcp.w:call-sawfish-55 NOTICE done
2025-09-15 20:25:38.470 wdl.w:ptcp NOTICE finish :: job: "call-sawfish-55"
2025-09-15 20:25:38.471 wdl.w:ptcp INFO output :: job: "call-sawfish-55", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-55/out/m84036_250809_035451_s4.bc2152_sawfish/m84036_250809_035451_s4.bc2152.sv.vcf.gz", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-55/out/m84036_250809_035451_s4.bc2152.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-55/out/m84036_250809_035451_s4.bc2152_sawfish/m84036_250809_035451_s4.bc2152.sv.vcf.gz.tbi", "minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-55/out/m84036_250809_035451_s4.bc2152.minimap2.bam.bai"}
2025-09-15 20:25:38.471 wdl.w:ptcp.w:call-paraphase-23.t:call-run_paraphase NOTICE done
2025-09-15 20:25:38.477 wdl.w:ptcp.w:call-trgt-86 NOTICE workflow start :: name: "trgt", source: "./trgt.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-86"
2025-09-15 20:25:38.478 wdl.w:ptcp.w:call-paraphase-23 NOTICE finish :: job: "call-run_paraphase"
2025-09-15 20:25:38.478 wdl.w:ptcp.w:call-paraphase-23 INFO output :: job: "call-run_paraphase", values: {"havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-23/call-run_paraphase/out/m84036_250809_035451_s4.bc2120.havanno.json", "paraphase_vcfs": ["/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-23/call-run_paraphase/out/m84036_250809_035451_s4.bc2120_paraphase/m84036_250809_035451_s4.bc2120_paraphase_vcfs/m84036_250809_035451_s4.bc2120_cyp21.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-23/call-run_paraphase/out/m84036_250809_035451_s4.bc2120_paraphase/m84036_250809_035451_s4.bc2120_paraphase_vcfs/m84036_250809_035451_s4.bc2120_f8inv1.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-23/call-run_paraphase/out/m84036_250809_035451_s4.bc2120_paraphase/m84036_250809_035451_s4.bc2120_paraphase_vcfs/m84036_250809_035451_s4.bc2120_f8inv22.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-23/call-run_paraphase/out/m84036_250809_035451_s4.bc2120_paraphase/m84036_250809_035451_s4.bc2120_paraphase_vcfs/m84036_250809_035451_s4.bc2120_gba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-23/call-run_paraphase/out/m84036_250809_035451_s4.bc2120_paraphase/m84036_250809_035451_s4.bc2120_paraphase_vcfs/m84036_250809_035451_s4.bc2120_hba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-23/call-run_paraphase/out/m84036_250809_035451_s4.bc2120_paraphase/m84036_250809_035451_s4.bc2120_paraphase_vcfs/m84036_250809_035451_s4.bc2120_hbb.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-23/call-run_paraphase/out/m84036_250809_035451_s4.bc2120_paraphase/m84036_250809_035451_s4.bc2120_paraphase_vcfs/m84036_250809_035451_s4.bc2120_rpgr.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-23/call-run_paraphase/out/m84036_250809_035451_s4.bc2120_paraphase/m84036_250809_035451_s4.bc2120_paraphase_vcfs/m84036_250809_035451_s4.bc2120_smn1.vcf"], "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-23/call-run_paraphase/out/m84036_250809_035451_s4.bc2120_paraphase/m84036_250809_035451_s4.bc2120.paraphase.json", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-23/call-run_paraphase/out/m84036_250809_035451_s4.bc2120_paraphase/m84036_250809_035451_s4.bc2120.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-23/call-run_paraphase/out/m84036_250809_035451_s4.bc2120_paraphase/m84036_250809_035451_s4.bc2120.paraphase.bam"}
2025-09-15 20:25:38.479 wdl.w:ptcp.w:call-paraphase-23 NOTICE ready :: job: "call-call_f8", callee: "call_f8"
2025-09-15 20:25:38.479 wdl.w:ptcp.w:call-paraphase-23 INFO input :: job: "call-call_f8", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "out_prefix": "m84036_250809_035451_s4.bc2120", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-23/call-run_paraphase/out/m84036_250809_035451_s4.bc2120_paraphase/m84036_250809_035451_s4.bc2120.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-23/call-run_paraphase/out/m84036_250809_035451_s4.bc2120_paraphase/m84036_250809_035451_s4.bc2120.paraphase.bam", "sex": "F"}
2025-09-15 20:25:38.480 wdl.w:ptcp.w:call-paraphase-23 INFO visit :: node: "output-havanno_json", values: {"havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-23/call-run_paraphase/out/m84036_250809_035451_s4.bc2120.havanno.json"}
2025-09-15 20:25:38.480 wdl.w:ptcp.w:call-paraphase-23 INFO visit :: node: "output-paraphase_bam", values: {"paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-23/call-run_paraphase/out/m84036_250809_035451_s4.bc2120_paraphase/m84036_250809_035451_s4.bc2120.paraphase.bam"}
2025-09-15 20:25:38.480 wdl.w:ptcp.w:call-paraphase-23 INFO visit :: node: "output-paraphase_bam_bai", values: {"paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-23/call-run_paraphase/out/m84036_250809_035451_s4.bc2120_paraphase/m84036_250809_035451_s4.bc2120.paraphase.bam.bai"}
2025-09-15 20:25:38.480 wdl.w:ptcp.w:call-paraphase-23 INFO visit :: node: "output-paraphase_json", values: {"paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-23/call-run_paraphase/out/m84036_250809_035451_s4.bc2120_paraphase/m84036_250809_035451_s4.bc2120.paraphase.json"}
2025-09-15 20:25:38.480 wdl.w:ptcp.w:call-paraphase-23 INFO visit :: node: "output-paraphase_vcfs", values: {"paraphase_vcfs": ["/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-23/call-run_paraphase/out/m84036_250809_035451_s4.bc2120_paraphase/m84036_250809_035451_s4.bc2120_paraphase_vcfs/m84036_250809_035451_s4.bc2120_cyp21.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-23/call-run_paraphase/out/m84036_250809_035451_s4.bc2120_paraphase/m84036_250809_035451_s4.bc2120_paraphase_vcfs/m84036_250809_035451_s4.bc2120_f8inv1.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-23/call-run_paraphase/out/m84036_250809_035451_s4.bc2120_paraphase/m84036_250809_035451_s4.bc2120_paraphase_vcfs/m84036_250809_035451_s4.bc2120_f8inv22.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-23/call-run_paraphase/out/m84036_250809_035451_s4.bc2120_paraphase/m84036_250809_035451_s4.bc2120_paraphase_vcfs/m84036_250809_035451_s4.bc2120_gba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-23/call-run_paraphase/out/m84036_250809_035451_s4.bc2120_paraphase/m84036_250809_035451_s4.bc2120_paraphase_vcfs/m84036_250809_035451_s4.bc2120_hba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-23/call-run_paraphase/out/m84036_250809_035451_s4.bc2120_paraphase/m84036_250809_035451_s4.bc2120_paraphase_vcfs/m84036_250809_035451_s4.bc2120_hbb.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-23/call-run_paraphase/out/m84036_250809_035451_s4.bc2120_paraphase/m84036_250809_035451_s4.bc2120_paraphase_vcfs/m84036_250809_035451_s4.bc2120_rpgr.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-23/call-run_paraphase/out/m84036_250809_035451_s4.bc2120_paraphase/m84036_250809_035451_s4.bc2120_paraphase_vcfs/m84036_250809_035451_s4.bc2120_smn1.vcf"]}
2025-09-15 20:25:38.487 wdl.w:ptcp.w:call-trgt-76.t:call-trgt_plot_meth_allele NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-76/call-trgt_plot_meth_allele", thread: 140611977991744
2025-09-15 20:25:38.498 wdl.w:ptcp.w:call-trgt-86 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:25:38.498 wdl.w:ptcp.w:call-trgt-86 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-86/out/m84036_250809_035451_s4.bc2183.mapped.bam"}
2025-09-15 20:25:38.498 wdl.w:ptcp.w:call-trgt-86 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-86/out/m84036_250809_035451_s4.bc2183.mapped.bam.bai"}
2025-09-15 20:25:38.498 wdl.w:ptcp.w:call-trgt-86 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:25:38.498 wdl.w:ptcp.w:call-trgt-86 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:25:38.498 wdl.w:ptcp.w:call-trgt-86 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2183"}
2025-09-15 20:25:38.498 wdl.w:ptcp.w:call-trgt-86 INFO visit :: node: "decl-sex", values: {"sex": "F"}
2025-09-15 20:25:38.498 wdl.w:ptcp.w:call-trgt-86 INFO visit :: node: "decl-trgt_bed", values: {"trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"}
2025-09-15 20:25:38.498 wdl.w:ptcp.w:call-trgt-86 NOTICE ready :: job: "call-get_reads_overlapping_repeats", callee: "get_reads_overlapping_repeats"
2025-09-15 20:25:38.499 wdl.w:ptcp.w:call-trgt-86 INFO input :: job: "call-get_reads_overlapping_repeats", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-86/out/m84036_250809_035451_s4.bc2183.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-86/out/m84036_250809_035451_s4.bc2183.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2183"}
2025-09-15 20:25:38.499 wdl.w:ptcp.w:call-trgt-86 NOTICE ready :: job: "call-trgt_genotype", callee: "trgt_genotype"
2025-09-15 20:25:38.500 wdl.w:ptcp.w:call-trgt-86 INFO input :: job: "call-trgt_genotype", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-86/out/m84036_250809_035451_s4.bc2183.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-86/out/m84036_250809_035451_s4.bc2183.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2183"}
2025-09-15 20:25:38.500 wdl.w:ptcp.w:call-paraphase-73.t:call-call_f8 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 8, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-73/call-call_f8/_singularity_tmpdir_ulaufy4v"
2025-09-15 20:25:38.500 wdl.w:ptcp.w:call-paraphase-73.t:call-call_f8 INFO Slurm invocation: srun --job-name call-call_f8 --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-73/call-call_f8/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-73/call-call_f8/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-73/call-call_f8/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-73/call-call_f8/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-73/call-run_paraphase/out/m84036_250809_035451_s4.bc2170_paraphase/m84036_250809_035451_s4.bc2170.paraphase.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2170.paraphase.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-73/call-run_paraphase/out/m84036_250809_035451_s4.bc2170_paraphase/m84036_250809_035451_s4.bc2170.paraphase.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2170.paraphase.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-73/call-call_f8/_singularity_tmpdir_ulaufy4v/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-73/call-call_f8/_singularity_tmpdir_ulaufy4v/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:38.568 wdl.w:ptcp.w:call-paraphase-73.t:call-call_f8 NOTICE slurm_singularity run :: pid: 1206037, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-73/call-call_f8/slurm_singularity.log.txt"
2025-09-15 20:25:38.569 wdl.w:ptcp.w:call-trgt-76.t:call-trgt_plot_meth_allele INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:38.569 wdl.w:ptcp.w:call-trgt-76.t:call-trgt_plot_meth_allele INFO input :: name: "waterfall", value: false
2025-09-15 20:25:38.569 wdl.w:ptcp.w:call-trgt-76.t:call-trgt_plot_meth_allele INFO input :: name: "methylation", value: true
2025-09-15 20:25:38.569 wdl.w:ptcp.w:call-trgt-76.t:call-trgt_plot_meth_allele INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:25:38.569 wdl.w:ptcp.w:call-trgt-76.t:call-trgt_plot_meth_allele INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:25:38.569 wdl.w:ptcp.w:call-trgt-76.t:call-trgt_plot_meth_allele INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:25:38.569 wdl.w:ptcp.w:call-trgt-76.t:call-trgt_plot_meth_allele INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2173.trgt.sorted.spanning.bam.bai"
2025-09-15 20:25:38.569 wdl.w:ptcp.w:call-trgt-76.t:call-trgt_plot_meth_allele INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2173.trgt.sorted.spanning.bam"
2025-09-15 20:25:38.569 wdl.w:ptcp.w:call-trgt-76.t:call-trgt_plot_meth_allele INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2173.trgt.vcf"
2025-09-15 20:25:38.570 wdl.w:ptcp.w:call-trgt-76.t:call-trgt_plot_meth_allele INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2173"
2025-09-15 20:25:38.570 wdl.w:ptcp.w:call-trgt-76.t:call-trgt_plot_meth_allele INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:25:38.570 wdl.w:ptcp.w:call-trgt-76.t:call-trgt_plot_meth_allele INFO eval :: name: "plot_type", value: "allele"
2025-09-15 20:25:38.570 wdl.w:ptcp.w:call-trgt-76.t:call-trgt_plot_meth_allele INFO eval :: name: "show", value: "meth"
2025-09-15 20:25:38.570 wdl.w:ptcp.w:call-trgt-76.t:call-trgt_plot_meth_allele INFO eval :: name: "threads", value: 1
2025-09-15 20:25:38.570 wdl.w:ptcp.w:call-trgt-76.t:call-trgt_plot_meth_allele INFO eval :: name: "disk_size", value: 27
2025-09-15 20:25:38.570 wdl.w:ptcp.w:call-trgt-76.t:call-trgt_plot_meth_allele INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2173.meth_allele"
2025-09-15 20:25:38.571 wdl.w:ptcp.w:call-trgt-76.t:call-trgt_plot_meth_allele INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:38.571 wdl.w:ptcp.w:call-trgt-76.t:call-trgt_plot_meth_allele WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:38.571 wdl.w:ptcp.w:call-trgt-76.t:call-trgt_plot_meth_allele INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:25:38.571 wdl.w:ptcp.w:call-trgt-76.t:call-trgt_plot_meth_allele INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:38.667 wdl.w:ptcp.w:call-trgt-76.t:call-trgt_plot_meth_allele INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-76/call-trgt_plot_meth_allele/_singularity_tmpdir_shanfxcx"
2025-09-15 20:25:38.667 wdl.w:ptcp.w:call-trgt-76.t:call-trgt_plot_meth_allele INFO Slurm invocation: srun --job-name call-trgt_plot_meth_allele --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-76/call-trgt_plot_meth_allele/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-76/call-trgt_plot_meth_allele/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-76/call-trgt_plot_meth_allele/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-76/call-trgt_plot_meth_allele/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-76/call-trgt_genotype/out/m84036_250809_035451_s4.bc2173.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2173.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-76/call-trgt_genotype/out/m84036_250809_035451_s4.bc2173.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2173.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-76/call-trgt_genotype/out/m84036_250809_035451_s4.bc2173.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2173.trgt.vcf:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-76/call-trgt_plot_meth_allele/_singularity_tmpdir_shanfxcx/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-76/call-trgt_plot_meth_allele/_singularity_tmpdir_shanfxcx/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:38.679 wdl.w:ptcp.w:call-trgt-76.t:call-trgt_plot_meth_allele NOTICE slurm_singularity run :: pid: 1206039, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-76/call-trgt_plot_meth_allele/slurm_singularity.log.txt"
2025-09-15 20:25:38.919 wdl.w:ptcp.w:call-paraphase-82.t:call-run_paraphase.slurm_singularity INFO srun: job 51798052 queued and waiting for resources
2025-09-15 20:25:38.919 wdl.w:ptcp.w:call-paraphase-82.t:call-run_paraphase.slurm_singularity INFO srun: job 51798052 has been allocated resources
2025-09-15 20:25:38.919 wdl.w:ptcp.w:call-paraphase-82.t:call-run_paraphase.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:38.957 wdl.w:ptcp.w:call-sawfish-43.t:call-run_sawfish INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2140_sawfish/m84036_250809_035451_s4.bc2140.sv.vcf.gz"
2025-09-15 20:25:38.961 wdl.w:ptcp.w:call-sawfish-43.t:call-run_sawfish INFO output :: name: "vcf_tbi", value: "m84036_250809_035451_s4.bc2140_sawfish/m84036_250809_035451_s4.bc2140.sv.vcf.gz.tbi"
2025-09-15 20:25:38.962 wdl.w:ptcp.w:call-sawfish-43.t:call-run_sawfish INFO output :: name: "minimap2_bam", value: "m84036_250809_035451_s4.bc2140.minimap2.bam"
2025-09-15 20:25:38.964 wdl.w:ptcp.w:call-sawfish-43.t:call-run_sawfish INFO output :: name: "minimap2_bam_bai", value: "m84036_250809_035451_s4.bc2140.minimap2.bam.bai"
2025-09-15 20:25:38.995 wdl.w:ptcp.w:call-sawfish-69.t:call-run_sawfish.stderr VERBOSE [M::mm_idx_gen::33.716*1.45] collected minimizers
2025-09-15 20:25:38.996 wdl.w:ptcp.w:call-sawfish-69.t:call-run_sawfish.stderr VERBOSE [M::mm_idx_gen::40.576*1.71] sorted minimizers
2025-09-15 20:25:38.996 wdl.w:ptcp.w:call-sawfish-69.t:call-run_sawfish.stderr VERBOSE [M::main::40.576*1.71] loaded/built the index for 195 target sequence(s)
2025-09-15 20:25:38.997 wdl.w:ptcp.w:call-sawfish-69.t:call-run_sawfish.stderr VERBOSE [M::mm_mapopt_update::43.606*1.66] mid_occ = 136
2025-09-15 20:25:38.997 wdl.w:ptcp.w:call-sawfish-69.t:call-run_sawfish.stderr VERBOSE [M::mm_idx_stat] kmer size: 19; skip: 19; is_hpc: 0; #seq: 195
2025-09-15 20:25:38.997 wdl.w:ptcp.w:call-sawfish-69.t:call-run_sawfish.stderr VERBOSE [M::mm_idx_stat::46.246*1.62] distinct minimizers: 214664461 (92.23% are singletons); average occurrences: 1.372; average spacing: 10.529; total length: 3099922541
2025-09-15 20:25:38.997 wdl.w:ptcp.w:call-sawfish-69.t:call-run_sawfish.stderr VERBOSE [M::main] Version: 2.26-r1175
2025-09-15 20:25:38.997 wdl.w:ptcp.w:call-sawfish-69.t:call-run_sawfish.stderr VERBOSE [M::main] CMD: /opt/pacbio/smrttools/install/smrtlink-release_25.1.0.257715/bundles/smrttools/install/smrttools-release_25.1.0.257715/private/thirdparty/minimap2/minimap2_2.26-pacbio2/binwrap/../../../../../private/thirdparty/minimap2/minimap2_2.26-pacbio2/bin/minimap2 -a -y -x map-hifi -Y -E 1,0 /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa -
2025-09-15 20:25:38.997 wdl.w:ptcp.w:call-sawfish-69.t:call-run_sawfish.stderr VERBOSE [M::main] Real time: 46.529 sec; CPU: 75.106 sec; Peak RSS: 11.886 GB
2025-09-15 20:25:39.093 wdl.w:ptcp.w:call-sawfish-43.t:call-run_sawfish NOTICE done
2025-09-15 20:25:39.124 wdl.w:ptcp.w:call-sawfish-43 NOTICE finish :: job: "call-run_sawfish"
2025-09-15 20:25:39.124 wdl.w:ptcp.w:call-sawfish-43 INFO output :: job: "call-run_sawfish", values: {"minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-43/call-run_sawfish/out/m84036_250809_035451_s4.bc2140.minimap2.bam.bai", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-43/call-run_sawfish/out/m84036_250809_035451_s4.bc2140.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-43/call-run_sawfish/out/m84036_250809_035451_s4.bc2140_sawfish/m84036_250809_035451_s4.bc2140.sv.vcf.gz.tbi", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-43/call-run_sawfish/out/m84036_250809_035451_s4.bc2140_sawfish/m84036_250809_035451_s4.bc2140.sv.vcf.gz"}
2025-09-15 20:25:39.124 wdl.w:ptcp.w:call-sawfish-43 INFO visit :: node: "output-minimap2_bam", values: {"minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-43/call-run_sawfish/out/m84036_250809_035451_s4.bc2140.minimap2.bam"}
2025-09-15 20:25:39.125 wdl.w:ptcp.w:call-sawfish-43 INFO visit :: node: "output-minimap2_bam_bai", values: {"minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-43/call-run_sawfish/out/m84036_250809_035451_s4.bc2140.minimap2.bam.bai"}
2025-09-15 20:25:39.125 wdl.w:ptcp.w:call-sawfish-43 INFO visit :: node: "output-vcf", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-43/call-run_sawfish/out/m84036_250809_035451_s4.bc2140_sawfish/m84036_250809_035451_s4.bc2140.sv.vcf.gz"}
2025-09-15 20:25:39.125 wdl.w:ptcp.w:call-sawfish-43 INFO visit :: node: "output-vcf_tbi", values: {"vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-43/call-run_sawfish/out/m84036_250809_035451_s4.bc2140_sawfish/m84036_250809_035451_s4.bc2140.sv.vcf.gz.tbi"}
2025-09-15 20:25:39.125 wdl.w:ptcp.w:call-sawfish-43 INFO visit :: node: "outputs", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-43/call-run_sawfish/out/m84036_250809_035451_s4.bc2140_sawfish/m84036_250809_035451_s4.bc2140.sv.vcf.gz", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-43/call-run_sawfish/out/m84036_250809_035451_s4.bc2140.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-43/call-run_sawfish/out/m84036_250809_035451_s4.bc2140_sawfish/m84036_250809_035451_s4.bc2140.sv.vcf.gz.tbi", "minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-43/call-run_sawfish/out/m84036_250809_035451_s4.bc2140.minimap2.bam.bai"}
2025-09-15 20:25:39.132 wdl.w:ptcp.w:call-trgt-76.t:call-trgt_plot_meth_waterfall NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-76/call-trgt_plot_meth_waterfall", thread: 140607120975424
2025-09-15 20:25:39.149 wdl.w:ptcp.w:call-trgt-76.t:call-trgt_plot_meth_waterfall INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:39.149 wdl.w:ptcp.w:call-trgt-76.t:call-trgt_plot_meth_waterfall INFO input :: name: "waterfall", value: true
2025-09-15 20:25:39.149 wdl.w:ptcp.w:call-trgt-76.t:call-trgt_plot_meth_waterfall INFO input :: name: "methylation", value: true
2025-09-15 20:25:39.149 wdl.w:ptcp.w:call-trgt-76.t:call-trgt_plot_meth_waterfall INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:25:39.149 wdl.w:ptcp.w:call-trgt-76.t:call-trgt_plot_meth_waterfall INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:25:39.149 wdl.w:ptcp.w:call-trgt-76.t:call-trgt_plot_meth_waterfall INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:25:39.149 wdl.w:ptcp.w:call-trgt-76.t:call-trgt_plot_meth_waterfall INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2173.trgt.sorted.spanning.bam.bai"
2025-09-15 20:25:39.150 wdl.w:ptcp.w:call-trgt-76.t:call-trgt_plot_meth_waterfall INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2173.trgt.sorted.spanning.bam"
2025-09-15 20:25:39.150 wdl.w:ptcp.w:call-trgt-76.t:call-trgt_plot_meth_waterfall INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2173.trgt.vcf"
2025-09-15 20:25:39.150 wdl.w:ptcp.w:call-trgt-76.t:call-trgt_plot_meth_waterfall INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2173"
2025-09-15 20:25:39.150 wdl.w:ptcp.w:call-trgt-76.t:call-trgt_plot_meth_waterfall INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:25:39.150 wdl.w:ptcp.w:call-trgt-76.t:call-trgt_plot_meth_waterfall INFO eval :: name: "plot_type", value: "waterfall"
2025-09-15 20:25:39.150 wdl.w:ptcp.w:call-trgt-76.t:call-trgt_plot_meth_waterfall INFO eval :: name: "show", value: "meth"
2025-09-15 20:25:39.150 wdl.w:ptcp.w:call-trgt-76.t:call-trgt_plot_meth_waterfall INFO eval :: name: "threads", value: 1
2025-09-15 20:25:39.150 wdl.w:ptcp.w:call-trgt-76.t:call-trgt_plot_meth_waterfall INFO eval :: name: "disk_size", value: 27
2025-09-15 20:25:39.151 wdl.w:ptcp.w:call-trgt-76.t:call-trgt_plot_meth_waterfall INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2173.meth_waterfall"
2025-09-15 20:25:39.151 wdl.w:ptcp.w:call-trgt-76.t:call-trgt_plot_meth_waterfall INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:39.151 wdl.w:ptcp.w:call-trgt-76.t:call-trgt_plot_meth_waterfall WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:39.152 wdl.w:ptcp.w:call-trgt-76.t:call-trgt_plot_meth_waterfall INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:25:39.152 wdl.w:ptcp.w:call-trgt-76.t:call-trgt_plot_meth_waterfall INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:39.176 wdl.w:ptcp.w:call-sawfish-43 NOTICE done
2025-09-15 20:25:39.183 wdl.w:ptcp NOTICE finish :: job: "call-sawfish-43"
2025-09-15 20:25:39.183 wdl.w:ptcp INFO output :: job: "call-sawfish-43", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-43/out/m84036_250809_035451_s4.bc2140_sawfish/m84036_250809_035451_s4.bc2140.sv.vcf.gz", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-43/out/m84036_250809_035451_s4.bc2140.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-43/out/m84036_250809_035451_s4.bc2140_sawfish/m84036_250809_035451_s4.bc2140.sv.vcf.gz.tbi", "minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-43/out/m84036_250809_035451_s4.bc2140.minimap2.bam.bai"}
2025-09-15 20:25:39.192 wdl.w:ptcp.w:call-paraphase-88 NOTICE workflow start :: name: "paraphase", source: "./paraphase.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-88"
2025-09-15 20:25:39.207 wdl.w:ptcp.w:call-paraphase-88 INFO visit :: node: "decl-annotation_vcf", values: {"annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf"}
2025-09-15 20:25:39.207 wdl.w:ptcp.w:call-paraphase-88 INFO visit :: node: "decl-config_file", values: {"config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml"}
2025-09-15 20:25:39.207 wdl.w:ptcp.w:call-paraphase-88 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:25:39.207 wdl.w:ptcp.w:call-paraphase-88 INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:25:39.207 wdl.w:ptcp.w:call-paraphase-88 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-88/out/m84036_250809_035451_s4.bc2185.mapped.bam"}
2025-09-15 20:25:39.207 wdl.w:ptcp.w:call-paraphase-88 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-88/out/m84036_250809_035451_s4.bc2185.mapped.bam.bai"}
2025-09-15 20:25:39.207 wdl.w:ptcp.w:call-paraphase-88 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:25:39.208 wdl.w:ptcp.w:call-paraphase-88 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:25:39.208 wdl.w:ptcp.w:call-paraphase-88 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2185"}
2025-09-15 20:25:39.208 wdl.w:ptcp.w:call-paraphase-88 INFO visit :: node: "decl-sex", values: {"sex": "F"}
2025-09-15 20:25:39.208 wdl.w:ptcp.w:call-paraphase-88 NOTICE ready :: job: "call-run_paraphase", callee: "run_paraphase"
2025-09-15 20:25:39.208 wdl.w:ptcp.w:call-paraphase-88 INFO input :: job: "call-run_paraphase", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf", "genome_version": "38", "config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-88/out/m84036_250809_035451_s4.bc2185.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-88/out/m84036_250809_035451_s4.bc2185.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2185"}
2025-09-15 20:25:39.215 wdl.w:ptcp.w:call-paraphase-85.t:call-run_paraphase INFO output :: name: "paraphase_bam", value: "m84036_250809_035451_s4.bc2182_paraphase/m84036_250809_035451_s4.bc2182.paraphase.bam"
2025-09-15 20:25:39.221 wdl.w:ptcp.w:call-paraphase-85.t:call-run_paraphase INFO output :: name: "paraphase_bam_bai", value: "m84036_250809_035451_s4.bc2182_paraphase/m84036_250809_035451_s4.bc2182.paraphase.bam.bai"
2025-09-15 20:25:39.223 wdl.w:ptcp.w:call-paraphase-85.t:call-run_paraphase INFO output :: name: "paraphase_json", value: "m84036_250809_035451_s4.bc2182_paraphase/m84036_250809_035451_s4.bc2182.paraphase.json"
2025-09-15 20:25:39.224 wdl.w:ptcp.w:call-paraphase-85.t:call-run_paraphase INFO output :: name: "paraphase_vcfs", value: []
2025-09-15 20:25:39.225 wdl.w:ptcp.w:call-paraphase-85.t:call-run_paraphase INFO output :: name: "havanno_json", value: "m84036_250809_035451_s4.bc2182.havanno.json"
2025-09-15 20:25:39.234 wdl.w:ptcp.w:call-trgt-76.t:call-trgt_plot_meth_waterfall INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-76/call-trgt_plot_meth_waterfall/_singularity_tmpdir_mfw629it"
2025-09-15 20:25:39.234 wdl.w:ptcp.w:call-trgt-76.t:call-trgt_plot_meth_waterfall INFO Slurm invocation: srun --job-name call-trgt_plot_meth_waterfall --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-76/call-trgt_plot_meth_waterfall/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-76/call-trgt_plot_meth_waterfall/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-76/call-trgt_plot_meth_waterfall/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-76/call-trgt_plot_meth_waterfall/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-76/call-trgt_genotype/out/m84036_250809_035451_s4.bc2173.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2173.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-76/call-trgt_genotype/out/m84036_250809_035451_s4.bc2173.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2173.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-76/call-trgt_genotype/out/m84036_250809_035451_s4.bc2173.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2173.trgt.vcf:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-76/call-trgt_plot_meth_waterfall/_singularity_tmpdir_mfw629it/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-76/call-trgt_plot_meth_waterfall/_singularity_tmpdir_mfw629it/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:39.255 wdl.w:ptcp.w:call-trgt-76.t:call-trgt_plot_meth_waterfall NOTICE slurm_singularity run :: pid: 1206064, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-76/call-trgt_plot_meth_waterfall/slurm_singularity.log.txt"
2025-09-15 20:25:39.257 wdl.w:ptcp.w:call-paraphase-91.t:call-run_paraphase.stderr VERBOSE INFO:root:Processing sample m84036_250809_035451_s4.bc2188 at 2025-09-15 20:25:35.572502...
2025-09-15 20:25:39.257 wdl.w:ptcp.w:call-paraphase-91.t:call-run_paraphase.stderr VERBOSE INFO:root:Checking sample sex at 2025-09-15 20:25:35.573988...
2025-09-15 20:25:39.258 wdl.w:ptcp.w:call-paraphase-91.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for smn1 for sample m84036_250809_035451_s4.bc2188 at 2025-09-15 20:25:35.638136...
2025-09-15 20:25:39.258 wdl.w:ptcp.w:call-paraphase-91.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for smn1 for sample m84036_250809_035451_s4.bc2188 at 2025-09-15 20:25:35.638689...
2025-09-15 20:25:39.258 wdl.w:ptcp.w:call-paraphase-91.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for cyp21 for sample m84036_250809_035451_s4.bc2188 at 2025-09-15 20:25:35.638118...
2025-09-15 20:25:39.258 wdl.w:ptcp.w:call-paraphase-91.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for cyp21 for sample m84036_250809_035451_s4.bc2188 at 2025-09-15 20:25:35.638801...
2025-09-15 20:25:39.258 wdl.w:ptcp.w:call-paraphase-91.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for gba for sample m84036_250809_035451_s4.bc2188 at 2025-09-15 20:25:35.638499...
2025-09-15 20:25:39.258 wdl.w:ptcp.w:call-paraphase-91.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for gba for sample m84036_250809_035451_s4.bc2188 at 2025-09-15 20:25:35.639132...
2025-09-15 20:25:39.258 wdl.w:ptcp.w:call-paraphase-91.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for hba for sample m84036_250809_035451_s4.bc2188 at 2025-09-15 20:25:35.639767...
2025-09-15 20:25:39.258 wdl.w:ptcp.w:call-paraphase-91.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for hba for sample m84036_250809_035451_s4.bc2188 at 2025-09-15 20:25:35.640255...
2025-09-15 20:25:39.332 wdl.w:ptcp.w:call-paraphase-85.t:call-run_paraphase NOTICE done
2025-09-15 20:25:39.340 wdl.w:ptcp.w:call-paraphase-85 NOTICE finish :: job: "call-run_paraphase"
2025-09-15 20:25:39.340 wdl.w:ptcp.w:call-paraphase-85 INFO output :: job: "call-run_paraphase", values: {"havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-85/call-run_paraphase/out/m84036_250809_035451_s4.bc2182.havanno.json", "paraphase_vcfs": [], "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-85/call-run_paraphase/out/m84036_250809_035451_s4.bc2182_paraphase/m84036_250809_035451_s4.bc2182.paraphase.json", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-85/call-run_paraphase/out/m84036_250809_035451_s4.bc2182_paraphase/m84036_250809_035451_s4.bc2182.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-85/call-run_paraphase/out/m84036_250809_035451_s4.bc2182_paraphase/m84036_250809_035451_s4.bc2182.paraphase.bam"}
2025-09-15 20:25:39.341 wdl.w:ptcp.w:call-paraphase-85 NOTICE ready :: job: "call-call_f8", callee: "call_f8"
2025-09-15 20:25:39.341 wdl.w:ptcp.w:call-paraphase-85 INFO input :: job: "call-call_f8", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "out_prefix": "m84036_250809_035451_s4.bc2182", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-85/call-run_paraphase/out/m84036_250809_035451_s4.bc2182_paraphase/m84036_250809_035451_s4.bc2182.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-85/call-run_paraphase/out/m84036_250809_035451_s4.bc2182_paraphase/m84036_250809_035451_s4.bc2182.paraphase.bam", "sex": "F"}
2025-09-15 20:25:39.342 wdl.w:ptcp.w:call-paraphase-85 INFO visit :: node: "output-havanno_json", values: {"havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-85/call-run_paraphase/out/m84036_250809_035451_s4.bc2182.havanno.json"}
2025-09-15 20:25:39.342 wdl.w:ptcp.w:call-paraphase-85 INFO visit :: node: "output-paraphase_bam", values: {"paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-85/call-run_paraphase/out/m84036_250809_035451_s4.bc2182_paraphase/m84036_250809_035451_s4.bc2182.paraphase.bam"}
2025-09-15 20:25:39.342 wdl.w:ptcp.w:call-paraphase-85 INFO visit :: node: "output-paraphase_bam_bai", values: {"paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-85/call-run_paraphase/out/m84036_250809_035451_s4.bc2182_paraphase/m84036_250809_035451_s4.bc2182.paraphase.bam.bai"}
2025-09-15 20:25:39.342 wdl.w:ptcp.w:call-paraphase-85 INFO visit :: node: "output-paraphase_json", values: {"paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-85/call-run_paraphase/out/m84036_250809_035451_s4.bc2182_paraphase/m84036_250809_035451_s4.bc2182.paraphase.json"}
2025-09-15 20:25:39.342 wdl.w:ptcp.w:call-paraphase-85 INFO visit :: node: "output-paraphase_vcfs", values: {"paraphase_vcfs": []}
2025-09-15 20:25:39.345 wdl.w:ptcp.w:call-trgt-76.t:call-trgt_plot_motifs_allele NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-76/call-trgt_plot_motifs_allele", thread: 140607649453632
2025-09-15 20:25:39.366 wdl.w:ptcp.w:call-trgt-76.t:call-trgt_plot_motifs_allele INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:39.366 wdl.w:ptcp.w:call-trgt-76.t:call-trgt_plot_motifs_allele INFO input :: name: "waterfall", value: false
2025-09-15 20:25:39.366 wdl.w:ptcp.w:call-trgt-76.t:call-trgt_plot_motifs_allele INFO input :: name: "methylation", value: false
2025-09-15 20:25:39.366 wdl.w:ptcp.w:call-trgt-76.t:call-trgt_plot_motifs_allele INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:25:39.366 wdl.w:ptcp.w:call-trgt-76.t:call-trgt_plot_motifs_allele INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:25:39.366 wdl.w:ptcp.w:call-trgt-76.t:call-trgt_plot_motifs_allele INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:25:39.366 wdl.w:ptcp.w:call-trgt-76.t:call-trgt_plot_motifs_allele INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2173.trgt.sorted.spanning.bam.bai"
2025-09-15 20:25:39.366 wdl.w:ptcp.w:call-trgt-76.t:call-trgt_plot_motifs_allele INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2173.trgt.sorted.spanning.bam"
2025-09-15 20:25:39.366 wdl.w:ptcp.w:call-trgt-76.t:call-trgt_plot_motifs_allele INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2173.trgt.vcf"
2025-09-15 20:25:39.366 wdl.w:ptcp.w:call-trgt-76.t:call-trgt_plot_motifs_allele INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2173"
2025-09-15 20:25:39.366 wdl.w:ptcp.w:call-trgt-76.t:call-trgt_plot_motifs_allele INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:25:39.367 wdl.w:ptcp.w:call-trgt-76.t:call-trgt_plot_motifs_allele INFO eval :: name: "plot_type", value: "allele"
2025-09-15 20:25:39.367 wdl.w:ptcp.w:call-trgt-76.t:call-trgt_plot_motifs_allele INFO eval :: name: "show", value: "motifs"
2025-09-15 20:25:39.367 wdl.w:ptcp.w:call-trgt-76.t:call-trgt_plot_motifs_allele INFO eval :: name: "threads", value: 1
2025-09-15 20:25:39.367 wdl.w:ptcp.w:call-trgt-76.t:call-trgt_plot_motifs_allele INFO eval :: name: "disk_size", value: 27
2025-09-15 20:25:39.367 wdl.w:ptcp.w:call-trgt-76.t:call-trgt_plot_motifs_allele INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2173.motifs_allele"
2025-09-15 20:25:39.367 wdl.w:ptcp.w:call-trgt-76.t:call-trgt_plot_motifs_allele INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:39.367 wdl.w:ptcp.w:call-trgt-76.t:call-trgt_plot_motifs_allele WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:39.368 wdl.w:ptcp.w:call-trgt-76.t:call-trgt_plot_motifs_allele INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:25:39.368 wdl.w:ptcp.w:call-trgt-76.t:call-trgt_plot_motifs_allele INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:39.429 wdl.w:ptcp.w:call-trgt-76.t:call-trgt_plot_motifs_allele INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-76/call-trgt_plot_motifs_allele/_singularity_tmpdir_scxzuwdq"
2025-09-15 20:25:39.429 wdl.w:ptcp.w:call-trgt-76.t:call-trgt_plot_motifs_allele INFO Slurm invocation: srun --job-name call-trgt_plot_motifs_allele --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-76/call-trgt_plot_motifs_allele/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-76/call-trgt_plot_motifs_allele/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-76/call-trgt_plot_motifs_allele/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-76/call-trgt_plot_motifs_allele/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-76/call-trgt_genotype/out/m84036_250809_035451_s4.bc2173.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2173.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-76/call-trgt_genotype/out/m84036_250809_035451_s4.bc2173.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2173.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-76/call-trgt_genotype/out/m84036_250809_035451_s4.bc2173.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2173.trgt.vcf:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-76/call-trgt_plot_motifs_allele/_singularity_tmpdir_scxzuwdq/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-76/call-trgt_plot_motifs_allele/_singularity_tmpdir_scxzuwdq/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:39.441 wdl.w:ptcp.w:call-trgt-74.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:25:37 [ERROR] - No reads found for TRID=SCA31_BEAN1
2025-09-15 20:25:39.441 wdl.w:ptcp.w:call-trgt-74.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:25:37 [ERROR] - No reads found for TRID=HDL2_JPH3
2025-09-15 20:25:39.441 wdl.w:ptcp.w:call-trgt-74.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:25:37 [ERROR] - No reads found for TRID=FECD3_TCF4
2025-09-15 20:25:39.442 wdl.w:ptcp.w:call-trgt-74.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:25:38 [ERROR] - No reads found for TRID=SCA4_ZFHX3
2025-09-15 20:25:39.442 wdl.w:ptcp.w:call-trgt-74.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:25:38 [ERROR] - No reads found for TRID=OPDM2_GIPC1
2025-09-15 20:25:39.442 wdl.w:ptcp.w:call-trgt-74.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:25:38 [ERROR] - No reads found for TRID=SD5_HOXD13
2025-09-15 20:25:39.442 wdl.w:ptcp.w:call-trgt-74.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:25:39 [ERROR] - No reads found for TRID=SCA36_NOP56
2025-09-15 20:25:39.442 wdl.w:ptcp.w:call-trgt-74.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:25:39 [ERROR] - No reads found for TRID=CJD_PRNP
2025-09-15 20:25:39.442 wdl.w:ptcp.w:call-trgt-74.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:25:39 [ERROR] - No reads found for TRID=EPM1_CSTB
2025-09-15 20:25:39.445 wdl.w:ptcp.w:call-trgt-76.t:call-trgt_plot_motifs_allele NOTICE slurm_singularity run :: pid: 1206135, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-76/call-trgt_plot_motifs_allele/slurm_singularity.log.txt"
2025-09-15 20:25:39.450 wdl.w:ptcp.w:call-paraphase-58.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for hba for sample m84036_250809_035451_s4.bc2155 at 2025-09-15 20:24:53.935803...
2025-09-15 20:25:39.450 wdl.w:ptcp.w:call-paraphase-58.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for smn1 for sample m84036_250809_035451_s4.bc2155 at 2025-09-15 20:24:55.579072...
2025-09-15 20:25:39.450 wdl.w:ptcp.w:call-paraphase-58.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for gba for sample m84036_250809_035451_s4.bc2155 at 2025-09-15 20:24:56.566063...
2025-09-15 20:25:39.450 wdl.w:ptcp.w:call-paraphase-58.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for cyp21 for sample m84036_250809_035451_s4.bc2155 at 2025-09-15 20:24:56.676911...
2025-09-15 20:25:39.450 wdl.w:ptcp.w:call-paraphase-58.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for smn1 for sample m84036_250809_035451_s4.bc2155 at 2025-09-15 20:25:22.890286...
2025-09-15 20:25:39.451 wdl.w:ptcp.w:call-paraphase-58.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning to gene2 region for smn1 for sample m84036_250809_035451_s4.bc2155 at 2025-09-15 20:25:23.850646...
2025-09-15 20:25:39.577 wdl.w:ptcp.w:call-paraphase-73.t:call-call_f8.slurm_singularity INFO srun: job 51798053 queued and waiting for resources
2025-09-15 20:25:39.577 wdl.w:ptcp.w:call-paraphase-73.t:call-call_f8.slurm_singularity INFO srun: job 51798053 has been allocated resources
2025-09-15 20:25:39.577 wdl.w:ptcp.w:call-paraphase-73.t:call-call_f8.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:39.686 wdl.w:ptcp.w:call-trgt-76.t:call-trgt_plot_meth_allele.slurm_singularity INFO srun: job 51798054 queued and waiting for resources
2025-09-15 20:25:39.686 wdl.w:ptcp.w:call-trgt-76.t:call-trgt_plot_meth_allele.slurm_singularity INFO srun: job 51798054 has been allocated resources
2025-09-15 20:25:39.686 wdl.w:ptcp.w:call-trgt-76.t:call-trgt_plot_meth_allele.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:39.715 wdl.w:ptcp.w:call-trgt-73.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:38 [ERROR] - No reads found for TRID=PRTS_ARX
2025-09-15 20:25:39.715 wdl.w:ptcp.w:call-trgt-73.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:38 [ERROR] - No reads found for TRID=EIEE1_ARX
2025-09-15 20:25:39.861 wdl.w:ptcp.w:call-trgt-73.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:25:38 [ERROR] - No reads found for TRID=PRTS_ARX
2025-09-15 20:25:39.862 wdl.w:ptcp.w:call-trgt-73.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:25:39 [ERROR] - No reads found for TRID=EIEE1_ARX
2025-09-15 20:25:40.177 wdl.w:ptcp.w:call-trgt-79.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:37 [ERROR] - No reads found for TRID=SCA12_PPP2R2B
2025-09-15 20:25:40.177 wdl.w:ptcp.w:call-trgt-79.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:37 [ERROR] - No reads found for TRID=CANVAS_RFC1
2025-09-15 20:25:40.177 wdl.w:ptcp.w:call-trgt-79.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:37 [ERROR] - No reads found for TRID=SCA1_ATXN1
2025-09-15 20:25:40.177 wdl.w:ptcp.w:call-trgt-79.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:38 [ERROR] - No reads found for TRID=OPDM1_LRP12
2025-09-15 20:25:40.177 wdl.w:ptcp.w:call-trgt-79.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:38 [ERROR] - No reads found for TRID=FAME1_SAMD12
2025-09-15 20:25:40.178 wdl.w:ptcp.w:call-trgt-79.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:39 [ERROR] - No reads found for TRID=FTDALS1_C9orf72
2025-09-15 20:25:40.189 wdl.w:ptcp.w:call-paraphase-73.t:call-call_f8 INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2170.f8inversion.vcf"
2025-09-15 20:25:40.192 wdl.w:ptcp.w:call-paraphase-73.t:call-call_f8 INFO output :: name: "json", value: "m84036_250809_035451_s4.bc2170.f8inversion.json"
2025-09-15 20:25:40.259 wdl.w:ptcp.w:call-trgt-84.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:38 [ERROR] - No reads found for TRID=PRTS_ARX
2025-09-15 20:25:40.259 wdl.w:ptcp.w:call-trgt-84.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:38 [ERROR] - No reads found for TRID=EIEE1_ARX
2025-09-15 20:25:40.269 wdl.w:ptcp.w:call-trgt-76.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO srun: job 51798055 queued and waiting for resources
2025-09-15 20:25:40.269 wdl.w:ptcp.w:call-trgt-76.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO srun: job 51798055 has been allocated resources
2025-09-15 20:25:40.269 wdl.w:ptcp.w:call-trgt-76.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:40.292 wdl.w:ptcp.w:call-paraphase-73.t:call-call_f8 NOTICE done
2025-09-15 20:25:40.298 wdl.w:ptcp.w:call-paraphase-73 NOTICE finish :: job: "call-call_f8"
2025-09-15 20:25:40.298 wdl.w:ptcp.w:call-paraphase-73 INFO output :: job: "call-call_f8", values: {"json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-73/call-call_f8/out/m84036_250809_035451_s4.bc2170.f8inversion.json", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-73/call-call_f8/out/m84036_250809_035451_s4.bc2170.f8inversion.vcf"}
2025-09-15 20:25:40.298 wdl.w:ptcp.w:call-paraphase-73 INFO visit :: node: "output-f8_json", values: {"f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-73/call-call_f8/out/m84036_250809_035451_s4.bc2170.f8inversion.json"}
2025-09-15 20:25:40.298 wdl.w:ptcp.w:call-paraphase-73 INFO visit :: node: "output-f8_vcf", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-73/call-call_f8/out/m84036_250809_035451_s4.bc2170.f8inversion.vcf"}
2025-09-15 20:25:40.299 wdl.w:ptcp.w:call-paraphase-73 INFO visit :: node: "outputs", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-73/call-call_f8/out/m84036_250809_035451_s4.bc2170.f8inversion.vcf", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-73/call-run_paraphase/out/m84036_250809_035451_s4.bc2170_paraphase/m84036_250809_035451_s4.bc2170.paraphase.json", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-73/call-run_paraphase/out/m84036_250809_035451_s4.bc2170_paraphase/m84036_250809_035451_s4.bc2170.paraphase.bam", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-73/call-run_paraphase/out/m84036_250809_035451_s4.bc2170_paraphase/m84036_250809_035451_s4.bc2170.paraphase.bam.bai", "paraphase_vcfs": [], "havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-73/call-run_paraphase/out/m84036_250809_035451_s4.bc2170.havanno.json", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-73/call-call_f8/out/m84036_250809_035451_s4.bc2170.f8inversion.json"}
2025-09-15 20:25:40.310 wdl.w:ptcp.w:call-trgt-76.t:call-trgt_plot_motifs_waterfall NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-76/call-trgt_plot_motifs_waterfall", thread: 140608186324544
2025-09-15 20:25:40.330 wdl.w:ptcp.w:call-trgt-76.t:call-trgt_plot_motifs_waterfall INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:40.330 wdl.w:ptcp.w:call-trgt-76.t:call-trgt_plot_motifs_waterfall INFO input :: name: "waterfall", value: true
2025-09-15 20:25:40.330 wdl.w:ptcp.w:call-trgt-76.t:call-trgt_plot_motifs_waterfall INFO input :: name: "methylation", value: false
2025-09-15 20:25:40.330 wdl.w:ptcp.w:call-trgt-76.t:call-trgt_plot_motifs_waterfall INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:25:40.330 wdl.w:ptcp.w:call-trgt-76.t:call-trgt_plot_motifs_waterfall INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:25:40.330 wdl.w:ptcp.w:call-trgt-76.t:call-trgt_plot_motifs_waterfall INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:25:40.330 wdl.w:ptcp.w:call-trgt-76.t:call-trgt_plot_motifs_waterfall INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2173.trgt.sorted.spanning.bam.bai"
2025-09-15 20:25:40.330 wdl.w:ptcp.w:call-trgt-76.t:call-trgt_plot_motifs_waterfall INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2173.trgt.sorted.spanning.bam"
2025-09-15 20:25:40.330 wdl.w:ptcp.w:call-trgt-76.t:call-trgt_plot_motifs_waterfall INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2173.trgt.vcf"
2025-09-15 20:25:40.330 wdl.w:ptcp.w:call-trgt-76.t:call-trgt_plot_motifs_waterfall INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2173"
2025-09-15 20:25:40.331 wdl.w:ptcp.w:call-trgt-76.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:25:40.331 wdl.w:ptcp.w:call-trgt-76.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "plot_type", value: "waterfall"
2025-09-15 20:25:40.331 wdl.w:ptcp.w:call-trgt-76.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "show", value: "motifs"
2025-09-15 20:25:40.331 wdl.w:ptcp.w:call-trgt-76.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "threads", value: 1
2025-09-15 20:25:40.331 wdl.w:ptcp.w:call-trgt-76.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "disk_size", value: 27
2025-09-15 20:25:40.331 wdl.w:ptcp.w:call-trgt-76.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2173.motifs_waterfall"
2025-09-15 20:25:40.332 wdl.w:ptcp.w:call-trgt-76.t:call-trgt_plot_motifs_waterfall INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:40.332 wdl.w:ptcp.w:call-trgt-76.t:call-trgt_plot_motifs_waterfall WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:40.332 wdl.w:ptcp.w:call-trgt-76.t:call-trgt_plot_motifs_waterfall INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:25:40.332 wdl.w:ptcp.w:call-trgt-76.t:call-trgt_plot_motifs_waterfall INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:40.376 wdl.w:ptcp.w:call-paraphase-73 NOTICE done
2025-09-15 20:25:40.383 wdl.w:ptcp NOTICE finish :: job: "call-paraphase-73"
2025-09-15 20:25:40.383 wdl.w:ptcp INFO output :: job: "call-paraphase-73", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-73/out/m84036_250809_035451_s4.bc2170.f8inversion.vcf", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-73/out/m84036_250809_035451_s4.bc2170_paraphase/m84036_250809_035451_s4.bc2170.paraphase.json", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-73/out/m84036_250809_035451_s4.bc2170_paraphase/m84036_250809_035451_s4.bc2170.paraphase.bam", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-73/out/m84036_250809_035451_s4.bc2170_paraphase/m84036_250809_035451_s4.bc2170.paraphase.bam.bai", "paraphase_vcfs": [], "havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-73/out/m84036_250809_035451_s4.bc2170.havanno.json", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-73/out/m84036_250809_035451_s4.bc2170.f8inversion.json"}
2025-09-15 20:25:40.388 wdl.w:ptcp.w:call-sawfish-88 NOTICE workflow start :: name: "sawfish", source: "./sawfish.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-88"
2025-09-15 20:25:40.403 wdl.w:ptcp.w:call-trgt-76.t:call-trgt_plot_motifs_waterfall INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-76/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_o83adxp1"
2025-09-15 20:25:40.403 wdl.w:ptcp.w:call-trgt-76.t:call-trgt_plot_motifs_waterfall INFO Slurm invocation: srun --job-name call-trgt_plot_motifs_waterfall --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-76/call-trgt_plot_motifs_waterfall/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-76/call-trgt_plot_motifs_waterfall/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-76/call-trgt_plot_motifs_waterfall/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-76/call-trgt_plot_motifs_waterfall/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-76/call-trgt_genotype/out/m84036_250809_035451_s4.bc2173.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2173.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-76/call-trgt_genotype/out/m84036_250809_035451_s4.bc2173.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2173.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-76/call-trgt_genotype/out/m84036_250809_035451_s4.bc2173.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2173.trgt.vcf:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-76/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_o83adxp1/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-76/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_o83adxp1/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:40.404 wdl.w:ptcp.w:call-sawfish-88 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:25:40.405 wdl.w:ptcp.w:call-sawfish-88 INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:25:40.405 wdl.w:ptcp.w:call-sawfish-88 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-88/out/m84036_250809_035451_s4.bc2185.mapped.bam"}
2025-09-15 20:25:40.405 wdl.w:ptcp.w:call-sawfish-88 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-88/out/m84036_250809_035451_s4.bc2185.mapped.bam.bai"}
2025-09-15 20:25:40.406 wdl.w:ptcp.w:call-sawfish-88 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:25:40.406 wdl.w:ptcp.w:call-sawfish-88 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:25:40.406 wdl.w:ptcp.w:call-sawfish-88 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2185"}
2025-09-15 20:25:40.406 wdl.w:ptcp.w:call-sawfish-88 NOTICE ready :: job: "call-run_sawfish", callee: "run_sawfish"
2025-09-15 20:25:40.406 wdl.w:ptcp.w:call-sawfish-88 INFO input :: job: "call-run_sawfish", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-88/out/m84036_250809_035451_s4.bc2185.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-88/out/m84036_250809_035451_s4.bc2185.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2185"}
2025-09-15 20:25:40.432 wdl.w:ptcp.w:call-trgt-76.t:call-trgt_plot_motifs_waterfall NOTICE slurm_singularity run :: pid: 1206151, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-76/call-trgt_plot_motifs_waterfall/slurm_singularity.log.txt"
2025-09-15 20:25:40.453 wdl.w:ptcp.w:call-trgt-76.t:call-trgt_plot_motifs_allele.slurm_singularity INFO srun: job 51798056 queued and waiting for resources
2025-09-15 20:25:40.453 wdl.w:ptcp.w:call-trgt-76.t:call-trgt_plot_motifs_allele.slurm_singularity INFO srun: job 51798056 has been allocated resources
2025-09-15 20:25:40.453 wdl.w:ptcp.w:call-trgt-76.t:call-trgt_plot_motifs_allele.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:40.880 wdl.w:ptcp.w:call-sawfish-42.t:call-run_sawfish INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2139_sawfish/m84036_250809_035451_s4.bc2139.sv.vcf.gz"
2025-09-15 20:25:40.885 wdl.w:ptcp.w:call-sawfish-42.t:call-run_sawfish INFO output :: name: "vcf_tbi", value: "m84036_250809_035451_s4.bc2139_sawfish/m84036_250809_035451_s4.bc2139.sv.vcf.gz.tbi"
2025-09-15 20:25:40.888 wdl.w:ptcp.w:call-sawfish-42.t:call-run_sawfish INFO output :: name: "minimap2_bam", value: "m84036_250809_035451_s4.bc2139.minimap2.bam"
2025-09-15 20:25:40.890 wdl.w:ptcp.w:call-sawfish-42.t:call-run_sawfish INFO output :: name: "minimap2_bam_bai", value: "m84036_250809_035451_s4.bc2139.minimap2.bam.bai"
2025-09-15 20:25:41.050 wdl.w:ptcp.w:call-trgt-79.t:call-trgt_plot_meth_allele INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2176.meth_allele.trgt_plots.zip"
2025-09-15 20:25:41.057 wdl.w:ptcp.w:call-sawfish-42.t:call-run_sawfish NOTICE done
2025-09-15 20:25:41.064 wdl.w:ptcp.w:call-sawfish-42 NOTICE finish :: job: "call-run_sawfish"
2025-09-15 20:25:41.065 wdl.w:ptcp.w:call-sawfish-42 INFO output :: job: "call-run_sawfish", values: {"minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-42/call-run_sawfish/out/m84036_250809_035451_s4.bc2139.minimap2.bam.bai", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-42/call-run_sawfish/out/m84036_250809_035451_s4.bc2139.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-42/call-run_sawfish/out/m84036_250809_035451_s4.bc2139_sawfish/m84036_250809_035451_s4.bc2139.sv.vcf.gz.tbi", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-42/call-run_sawfish/out/m84036_250809_035451_s4.bc2139_sawfish/m84036_250809_035451_s4.bc2139.sv.vcf.gz"}
2025-09-15 20:25:41.065 wdl.w:ptcp.w:call-sawfish-42 INFO visit :: node: "output-minimap2_bam", values: {"minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-42/call-run_sawfish/out/m84036_250809_035451_s4.bc2139.minimap2.bam"}
2025-09-15 20:25:41.065 wdl.w:ptcp.w:call-sawfish-42 INFO visit :: node: "output-minimap2_bam_bai", values: {"minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-42/call-run_sawfish/out/m84036_250809_035451_s4.bc2139.minimap2.bam.bai"}
2025-09-15 20:25:41.065 wdl.w:ptcp.w:call-sawfish-42 INFO visit :: node: "output-vcf", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-42/call-run_sawfish/out/m84036_250809_035451_s4.bc2139_sawfish/m84036_250809_035451_s4.bc2139.sv.vcf.gz"}
2025-09-15 20:25:41.065 wdl.w:ptcp.w:call-sawfish-42 INFO visit :: node: "output-vcf_tbi", values: {"vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-42/call-run_sawfish/out/m84036_250809_035451_s4.bc2139_sawfish/m84036_250809_035451_s4.bc2139.sv.vcf.gz.tbi"}
2025-09-15 20:25:41.065 wdl.w:ptcp.w:call-sawfish-42 INFO visit :: node: "outputs", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-42/call-run_sawfish/out/m84036_250809_035451_s4.bc2139_sawfish/m84036_250809_035451_s4.bc2139.sv.vcf.gz", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-42/call-run_sawfish/out/m84036_250809_035451_s4.bc2139.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-42/call-run_sawfish/out/m84036_250809_035451_s4.bc2139_sawfish/m84036_250809_035451_s4.bc2139.sv.vcf.gz.tbi", "minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-42/call-run_sawfish/out/m84036_250809_035451_s4.bc2139.minimap2.bam.bai"}
2025-09-15 20:25:41.073 wdl.w:ptcp.w:call-sawfish-82.t:call-run_sawfish NOTICE task setup :: name: "run_sawfish", source: "./sawfish.wdl", line: 83, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-82/call-run_sawfish", thread: 140607146153536
2025-09-15 20:25:41.091 wdl.w:ptcp.w:call-sawfish-82.t:call-run_sawfish INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:41.091 wdl.w:ptcp.w:call-sawfish-82.t:call-run_sawfish INFO input :: name: "genome_version", value: "38"
2025-09-15 20:25:41.091 wdl.w:ptcp.w:call-sawfish-82.t:call-run_sawfish INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:25:41.091 wdl.w:ptcp.w:call-sawfish-82.t:call-run_sawfish INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:25:41.091 wdl.w:ptcp.w:call-sawfish-82.t:call-run_sawfish INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2179.mapped.bam.bai"
2025-09-15 20:25:41.091 wdl.w:ptcp.w:call-sawfish-82.t:call-run_sawfish INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2179.mapped.bam"
2025-09-15 20:25:41.091 wdl.w:ptcp.w:call-sawfish-82.t:call-run_sawfish INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2179"
2025-09-15 20:25:41.091 wdl.w:ptcp.w:call-sawfish-82.t:call-run_sawfish INFO eval :: name: "mem_gb", value: 32
2025-09-15 20:25:41.091 wdl.w:ptcp.w:call-sawfish-82.t:call-run_sawfish INFO eval :: name: "threads", value: 16
2025-09-15 20:25:41.092 wdl.w:ptcp.w:call-sawfish-82.t:call-run_sawfish INFO eval :: name: "disk_size", value: 30
2025-09-15 20:25:41.092 wdl.w:ptcp.w:call-sawfish-82.t:call-run_sawfish INFO eval :: name: "discover_dirname", value: "m84036_250809_035451_s4.bc2179_sawfish_discover"
2025-09-15 20:25:41.092 wdl.w:ptcp.w:call-sawfish-82.t:call-run_sawfish INFO eval :: name: "call_dirname", value: "m84036_250809_035451_s4.bc2179_sawfish"
2025-09-15 20:25:41.092 wdl.w:ptcp.w:call-sawfish-82.t:call-run_sawfish INFO eval :: name: "minimap2_bam_filename", value: "m84036_250809_035451_s4.bc2179.minimap2.bam"
2025-09-15 20:25:41.093 wdl.w:ptcp.w:call-sawfish-82.t:call-run_sawfish INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 16, memory_reservation: 32000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:41.093 wdl.w:ptcp.w:call-sawfish-82.t:call-run_sawfish WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:41.094 wdl.w:ptcp.w:call-sawfish-82.t:call-run_sawfish INFO provisioned :: seconds_waited: 0, cpu: 16, mem_bytes: 32000000000
2025-09-15 20:25:41.094 wdl.w:ptcp.w:call-sawfish-82.t:call-run_sawfish INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:41.124 wdl.w:ptcp.w:call-sawfish-42 NOTICE done
2025-09-15 20:25:41.126 wdl.w:ptcp.w:call-trgt-84.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:25:40 [ERROR] - No reads found for TRID=PRTS_ARX
2025-09-15 20:25:41.126 wdl.w:ptcp.w:call-trgt-84.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:25:40 [ERROR] - No reads found for TRID=EIEE1_ARX
2025-09-15 20:25:41.135 wdl.w:ptcp NOTICE finish :: job: "call-sawfish-42"
2025-09-15 20:25:41.133 wdl.w:ptcp.w:call-paraphase-87.t:call-run_paraphase.stderr VERBOSE INFO:root:Processing sample m84036_250809_035451_s4.bc2184 at 2025-09-15 20:25:35.928436...
2025-09-15 20:25:41.135 wdl.w:ptcp INFO output :: job: "call-sawfish-42", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-42/out/m84036_250809_035451_s4.bc2139_sawfish/m84036_250809_035451_s4.bc2139.sv.vcf.gz", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-42/out/m84036_250809_035451_s4.bc2139.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-42/out/m84036_250809_035451_s4.bc2139_sawfish/m84036_250809_035451_s4.bc2139.sv.vcf.gz.tbi", "minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-42/out/m84036_250809_035451_s4.bc2139.minimap2.bam.bai"}
2025-09-15 20:25:41.135 wdl.w:ptcp.w:call-paraphase-87.t:call-run_paraphase.stderr VERBOSE INFO:root:Checking sample sex at 2025-09-15 20:25:35.929155...
2025-09-15 20:25:41.136 wdl.w:ptcp.w:call-paraphase-87.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for cyp21 for sample m84036_250809_035451_s4.bc2184 at 2025-09-15 20:25:35.967917...
2025-09-15 20:25:41.136 wdl.w:ptcp.w:call-paraphase-87.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for cyp21 for sample m84036_250809_035451_s4.bc2184 at 2025-09-15 20:25:35.968397...
2025-09-15 20:25:41.136 wdl.w:ptcp.w:call-paraphase-87.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for gba for sample m84036_250809_035451_s4.bc2184 at 2025-09-15 20:25:35.969686...
2025-09-15 20:25:41.136 wdl.w:ptcp.w:call-paraphase-87.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for smn1 for sample m84036_250809_035451_s4.bc2184 at 2025-09-15 20:25:35.969702...
2025-09-15 20:25:41.137 wdl.w:ptcp.w:call-paraphase-87.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for smn1 for sample m84036_250809_035451_s4.bc2184 at 2025-09-15 20:25:35.970141...
2025-09-15 20:25:41.137 wdl.w:ptcp.w:call-paraphase-87.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for gba for sample m84036_250809_035451_s4.bc2184 at 2025-09-15 20:25:35.970127...
2025-09-15 20:25:41.137 wdl.w:ptcp.w:call-paraphase-87.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for hba for sample m84036_250809_035451_s4.bc2184 at 2025-09-15 20:25:35.970207...
2025-09-15 20:25:41.137 wdl.w:ptcp.w:call-paraphase-87.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for hba for sample m84036_250809_035451_s4.bc2184 at 2025-09-15 20:25:35.970641...
2025-09-15 20:25:41.146 wdl.w:ptcp.w:call-trgt-88 NOTICE workflow start :: name: "trgt", source: "./trgt.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-88"
2025-09-15 20:25:41.159 wdl.w:ptcp.w:call-trgt-84.t:call-trgt_plot_meth_allele INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2181.meth_allele.trgt_plots.zip"
2025-09-15 20:25:41.161 wdl.w:ptcp.w:call-trgt-88 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:25:41.162 wdl.w:ptcp.w:call-trgt-88 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-88/out/m84036_250809_035451_s4.bc2185.mapped.bam"}
2025-09-15 20:25:41.162 wdl.w:ptcp.w:call-trgt-88 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-88/out/m84036_250809_035451_s4.bc2185.mapped.bam.bai"}
2025-09-15 20:25:41.162 wdl.w:ptcp.w:call-trgt-88 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:25:41.162 wdl.w:ptcp.w:call-trgt-88 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:25:41.162 wdl.w:ptcp.w:call-trgt-88 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2185"}
2025-09-15 20:25:41.162 wdl.w:ptcp.w:call-trgt-88 INFO visit :: node: "decl-sex", values: {"sex": "F"}
2025-09-15 20:25:41.162 wdl.w:ptcp.w:call-trgt-88 INFO visit :: node: "decl-trgt_bed", values: {"trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"}
2025-09-15 20:25:41.162 wdl.w:ptcp.w:call-trgt-88 NOTICE ready :: job: "call-get_reads_overlapping_repeats", callee: "get_reads_overlapping_repeats"
2025-09-15 20:25:41.163 wdl.w:ptcp.w:call-trgt-88 INFO input :: job: "call-get_reads_overlapping_repeats", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-88/out/m84036_250809_035451_s4.bc2185.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-88/out/m84036_250809_035451_s4.bc2185.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2185"}
2025-09-15 20:25:41.164 wdl.w:ptcp.w:call-trgt-88 NOTICE ready :: job: "call-trgt_genotype", callee: "trgt_genotype"
2025-09-15 20:25:41.164 wdl.w:ptcp.w:call-trgt-88 INFO input :: job: "call-trgt_genotype", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-88/out/m84036_250809_035451_s4.bc2185.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-88/out/m84036_250809_035451_s4.bc2185.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2185"}
2025-09-15 20:25:41.179 wdl.w:ptcp.w:call-trgt-79.t:call-trgt_plot_meth_allele NOTICE done
2025-09-15 20:25:41.184 wdl.w:ptcp.w:call-trgt-79 NOTICE finish :: job: "call-trgt_plot_meth_allele"
2025-09-15 20:25:41.185 wdl.w:ptcp.w:call-trgt-79 INFO output :: job: "call-trgt_plot_meth_allele", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-79/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2176.meth_allele.trgt_plots.zip"}
2025-09-15 20:25:41.185 wdl.w:ptcp.w:call-trgt-79 INFO visit :: node: "output-images_meth_allele", values: {"images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-79/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2176.meth_allele.trgt_plots.zip"}
2025-09-15 20:25:41.185 wdl.w:ptcp.w:call-trgt-79 INFO visit :: node: "outputs", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-79/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2176.motifs_waterfall.trgt_plots.zip", "images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-79/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2176.meth_allele.trgt_plots.zip", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-79/call-trgt_genotype/out/m84036_250809_035451_s4.bc2176.trgt.sorted.spanning.bam.bai", "images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-79/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2176.motifs_allele.trgt_plots.zip", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-79/call-trgt_genotype/out/m84036_250809_035451_s4.bc2176.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-79/call-trgt_genotype/out/m84036_250809_035451_s4.bc2176.trgt.vcf", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-79/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2176.repeats.bam", "images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-79/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2176.meth_waterfall.trgt_plots.zip", "reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-79/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2176.repeats.bam.bai"}
2025-09-15 20:25:41.193 wdl.w:ptcp.w:call-sawfish-82.t:call-run_sawfish INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 10, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-82/call-run_sawfish/_singularity_tmpdir_tfq0ffeh"
2025-09-15 20:25:41.193 wdl.w:ptcp.w:call-sawfish-82.t:call-run_sawfish INFO Slurm invocation: srun --job-name call-run_sawfish --partition compute,compute9 --cpus-per-task 16 --mem 30518M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-82/call-run_sawfish/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-82/call-run_sawfish/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-82/call-run_sawfish/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-82/call-run_sawfish/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-82/out/m84036_250809_035451_s4.bc2179.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2179.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-82/out/m84036_250809_035451_s4.bc2179.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2179.mapped.bam.bai:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-82/call-run_sawfish/_singularity_tmpdir_tfq0ffeh/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-82/call-run_sawfish/_singularity_tmpdir_tfq0ffeh/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:41.194 wdl.w:ptcp.w:call-trgt-82.t:call-get_reads_overlapping_repeats NOTICE task setup :: name: "get_reads_overlapping_repeats", source: "./trgt.wdl", line: 182, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-82/call-get_reads_overlapping_repeats", thread: 140607691417152
2025-09-15 20:25:41.217 wdl.w:ptcp.w:call-trgt-82.t:call-get_reads_overlapping_repeats INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:41.217 wdl.w:ptcp.w:call-trgt-82.t:call-get_reads_overlapping_repeats INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:25:41.217 wdl.w:ptcp.w:call-trgt-82.t:call-get_reads_overlapping_repeats INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2179.mapped.bam.bai"
2025-09-15 20:25:41.217 wdl.w:ptcp.w:call-trgt-82.t:call-get_reads_overlapping_repeats INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2179.mapped.bam"
2025-09-15 20:25:41.217 wdl.w:ptcp.w:call-trgt-82.t:call-get_reads_overlapping_repeats INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2179"
2025-09-15 20:25:41.217 wdl.w:ptcp.w:call-trgt-82.t:call-get_reads_overlapping_repeats INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:25:41.217 wdl.w:ptcp.w:call-trgt-82.t:call-get_reads_overlapping_repeats INFO eval :: name: "expand_size", value: 3000
2025-09-15 20:25:41.217 wdl.w:ptcp.w:call-trgt-82.t:call-get_reads_overlapping_repeats INFO eval :: name: "threads", value: 1
2025-09-15 20:25:41.217 wdl.w:ptcp.w:call-trgt-82.t:call-get_reads_overlapping_repeats INFO eval :: name: "expanded_bed_name", value: "m84036_250809_035451_s4.bc2179.expanded.bed"
2025-09-15 20:25:41.218 wdl.w:ptcp.w:call-trgt-82.t:call-get_reads_overlapping_repeats INFO eval :: name: "disk_size", value: 11
2025-09-15 20:25:41.218 wdl.w:ptcp.w:call-trgt-82.t:call-get_reads_overlapping_repeats INFO eval :: name: "output_name", value: "m84036_250809_035451_s4.bc2179.repeats.bam"
2025-09-15 20:25:41.218 wdl.w:ptcp.w:call-trgt-82.t:call-get_reads_overlapping_repeats INFO eval :: name: "index_name", value: "m84036_250809_035451_s4.bc2179.repeats.bam.bai"
2025-09-15 20:25:41.218 wdl.w:ptcp.w:call-trgt-82.t:call-get_reads_overlapping_repeats INFO eval :: name: "output_name_with_index", value: "m84036_250809_035451_s4.bc2179.repeats.bam##idx##m84036_250809_035451_s4.bc2179.repeats.bam.bai"
2025-09-15 20:25:41.218 wdl.w:ptcp.w:call-trgt-82.t:call-get_reads_overlapping_repeats INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:41.219 wdl.w:ptcp.w:call-trgt-82.t:call-get_reads_overlapping_repeats WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:41.219 wdl.w:ptcp.w:call-trgt-82.t:call-get_reads_overlapping_repeats INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:25:41.219 wdl.w:ptcp.w:call-trgt-82.t:call-get_reads_overlapping_repeats INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:41.245 wdl.w:ptcp.w:call-sawfish-82.t:call-run_sawfish NOTICE slurm_singularity run :: pid: 1206163, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-82/call-run_sawfish/slurm_singularity.log.txt"
2025-09-15 20:25:41.276 wdl.w:ptcp.w:call-trgt-82.t:call-get_reads_overlapping_repeats INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 9, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-82/call-get_reads_overlapping_repeats/_singularity_tmpdir_kswud2ua"
2025-09-15 20:25:41.277 wdl.w:ptcp.w:call-trgt-82.t:call-get_reads_overlapping_repeats INFO Slurm invocation: srun --job-name call-get_reads_overlapping_repeats --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-82/call-get_reads_overlapping_repeats/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-82/call-get_reads_overlapping_repeats/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-82/call-get_reads_overlapping_repeats/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-82/call-get_reads_overlapping_repeats/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-82/out/m84036_250809_035451_s4.bc2179.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2179.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-82/out/m84036_250809_035451_s4.bc2179.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2179.mapped.bam.bai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-82/call-get_reads_overlapping_repeats/_singularity_tmpdir_kswud2ua/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-82/call-get_reads_overlapping_repeats/_singularity_tmpdir_kswud2ua/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:41.280 wdl.w:ptcp.w:call-trgt-89.t:call-trgt_genotype INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2186.trgt.vcf"
2025-09-15 20:25:41.284 wdl.w:ptcp.w:call-trgt-89.t:call-trgt_genotype INFO output :: name: "spanning_bam", value: "m84036_250809_035451_s4.bc2186.trgt.sorted.spanning.bam"
2025-09-15 20:25:41.286 wdl.w:ptcp.w:call-trgt-89.t:call-trgt_genotype INFO output :: name: "spanning_bam_bai", value: "m84036_250809_035451_s4.bc2186.trgt.sorted.spanning.bam.bai"
2025-09-15 20:25:41.295 wdl.w:ptcp.w:call-trgt-82.t:call-get_reads_overlapping_repeats NOTICE slurm_singularity run :: pid: 1206165, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-82/call-get_reads_overlapping_repeats/slurm_singularity.log.txt"
2025-09-15 20:25:41.296 wdl.w:ptcp.w:call-trgt-79 NOTICE done
2025-09-15 20:25:41.303 wdl.w:ptcp NOTICE finish :: job: "call-trgt-79"
2025-09-15 20:25:41.303 wdl.w:ptcp INFO output :: job: "call-trgt-79", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-79/out/m84036_250809_035451_s4.bc2176.motifs_waterfall.trgt_plots.zip", "images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-79/out/m84036_250809_035451_s4.bc2176.meth_allele.trgt_plots.zip", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-79/out/m84036_250809_035451_s4.bc2176.trgt.sorted.spanning.bam.bai", "images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-79/out/m84036_250809_035451_s4.bc2176.motifs_allele.trgt_plots.zip", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-79/out/m84036_250809_035451_s4.bc2176.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-79/out/m84036_250809_035451_s4.bc2176.trgt.vcf", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-79/out/m84036_250809_035451_s4.bc2176.repeats.bam", "images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-79/out/m84036_250809_035451_s4.bc2176.meth_waterfall.trgt_plots.zip", "reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-79/out/m84036_250809_035451_s4.bc2176.repeats.bam.bai"}
2025-09-15 20:25:41.309 wdl.w:ptcp.w:call-paraphase-83 NOTICE workflow start :: name: "paraphase", source: "./paraphase.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-83"
2025-09-15 20:25:41.328 wdl.w:ptcp.w:call-paraphase-83 INFO visit :: node: "decl-annotation_vcf", values: {"annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf"}
2025-09-15 20:25:41.329 wdl.w:ptcp.w:call-paraphase-83 INFO visit :: node: "decl-config_file", values: {"config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml"}
2025-09-15 20:25:41.329 wdl.w:ptcp.w:call-paraphase-83 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:25:41.329 wdl.w:ptcp.w:call-paraphase-83 INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:25:41.329 wdl.w:ptcp.w:call-paraphase-83 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-83/out/m84036_250809_035451_s4.bc2180.mapped.bam"}
2025-09-15 20:25:41.329 wdl.w:ptcp.w:call-paraphase-83 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-83/out/m84036_250809_035451_s4.bc2180.mapped.bam.bai"}
2025-09-15 20:25:41.329 wdl.w:ptcp.w:call-paraphase-83 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:25:41.329 wdl.w:ptcp.w:call-paraphase-83 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:25:41.330 wdl.w:ptcp.w:call-paraphase-83 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2180"}
2025-09-15 20:25:41.330 wdl.w:ptcp.w:call-paraphase-83 INFO visit :: node: "decl-sex", values: {"sex": "F"}
2025-09-15 20:25:41.330 wdl.w:ptcp.w:call-paraphase-83 NOTICE ready :: job: "call-run_paraphase", callee: "run_paraphase"
2025-09-15 20:25:41.330 wdl.w:ptcp.w:call-paraphase-83 INFO input :: job: "call-run_paraphase", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "annotation_vcf": "/ptcp/meta/variant_list/variant_list.GRCh38.vcf", "genome_version": "38", "config_file": "/ptcp/meta/paraphase/paraphase_config.GRCh38.yaml", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-83/out/m84036_250809_035451_s4.bc2180.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-83/out/m84036_250809_035451_s4.bc2180.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2180"}
2025-09-15 20:25:41.363 wdl.w:ptcp.w:call-trgt-84.t:call-trgt_plot_meth_allele NOTICE done
2025-09-15 20:25:41.368 wdl.w:ptcp.w:call-trgt-84 NOTICE finish :: job: "call-trgt_plot_meth_allele"
2025-09-15 20:25:41.368 wdl.w:ptcp.w:call-trgt-84 INFO output :: job: "call-trgt_plot_meth_allele", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-84/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2181.meth_allele.trgt_plots.zip"}
2025-09-15 20:25:41.368 wdl.w:ptcp.w:call-trgt-84 INFO visit :: node: "output-images_meth_allele", values: {"images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-84/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2181.meth_allele.trgt_plots.zip"}
2025-09-15 20:25:41.373 wdl.w:ptcp.w:call-trgt-82.t:call-trgt_genotype NOTICE task setup :: name: "trgt_genotype", source: "./trgt.wdl", line: 272, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-82/call-trgt_genotype", thread: 140611944420928
2025-09-15 20:25:41.385 wdl.w:ptcp.w:call-trgt-89.t:call-trgt_genotype NOTICE done
2025-09-15 20:25:41.389 wdl.w:ptcp.w:call-trgt-82.t:call-trgt_genotype INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:41.389 wdl.w:ptcp.w:call-trgt-82.t:call-trgt_genotype INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:25:41.389 wdl.w:ptcp.w:call-trgt-82.t:call-trgt_genotype INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:25:41.389 wdl.w:ptcp.w:call-trgt-82.t:call-trgt_genotype INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:25:41.390 wdl.w:ptcp.w:call-trgt-82.t:call-trgt_genotype INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2179.mapped.bam.bai"
2025-09-15 20:25:41.390 wdl.w:ptcp.w:call-trgt-82.t:call-trgt_genotype INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2179.mapped.bam"
2025-09-15 20:25:41.390 wdl.w:ptcp.w:call-trgt-82.t:call-trgt_genotype INFO input :: name: "sex", value: "F"
2025-09-15 20:25:41.390 wdl.w:ptcp.w:call-trgt-82.t:call-trgt_genotype INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2179"
2025-09-15 20:25:41.390 wdl.w:ptcp.w:call-trgt-82.t:call-trgt_genotype INFO eval :: name: "mem_gb", value: 16
2025-09-15 20:25:41.390 wdl.w:ptcp.w:call-trgt-82.t:call-trgt_genotype INFO eval :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2179.trgt"
2025-09-15 20:25:41.390 wdl.w:ptcp.w:call-trgt-82.t:call-trgt_genotype INFO eval :: name: "threads", value: 8
2025-09-15 20:25:41.390 wdl.w:ptcp.w:call-trgt-82.t:call-trgt_genotype INFO eval :: name: "disk_size", value: 27
2025-09-15 20:25:41.390 wdl.w:ptcp.w:call-trgt-82.t:call-trgt_genotype INFO eval :: name: "karyotype", value: "XX"
2025-09-15 20:25:41.391 wdl.w:ptcp.w:call-trgt-82.t:call-trgt_genotype INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 8, memory_reservation: 16000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:41.391 wdl.w:ptcp.w:call-trgt-82.t:call-trgt_genotype WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:41.391 wdl.w:ptcp.w:call-trgt-82.t:call-trgt_genotype INFO provisioned :: seconds_waited: 0, cpu: 8, mem_bytes: 16000000000
2025-09-15 20:25:41.391 wdl.w:ptcp.w:call-trgt-82.t:call-trgt_genotype INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:41.392 wdl.w:ptcp.w:call-trgt-89 NOTICE finish :: job: "call-trgt_genotype"
2025-09-15 20:25:41.392 wdl.w:ptcp.w:call-trgt-89 INFO output :: job: "call-trgt_genotype", values: {"spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-89/call-trgt_genotype/out/m84036_250809_035451_s4.bc2186.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-89/call-trgt_genotype/out/m84036_250809_035451_s4.bc2186.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-89/call-trgt_genotype/out/m84036_250809_035451_s4.bc2186.trgt.vcf"}
2025-09-15 20:25:41.392 wdl.w:ptcp.w:call-trgt-89 NOTICE ready :: job: "call-trgt_plot_meth_allele", callee: "trgt_plot"
2025-09-15 20:25:41.392 wdl.w:ptcp.w:call-trgt-89 INFO input :: job: "call-trgt_plot_meth_allele", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": false, "methylation": true, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-89/call-trgt_genotype/out/m84036_250809_035451_s4.bc2186.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-89/call-trgt_genotype/out/m84036_250809_035451_s4.bc2186.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-89/call-trgt_genotype/out/m84036_250809_035451_s4.bc2186.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2186"}
2025-09-15 20:25:41.394 wdl.w:ptcp.w:call-trgt-89 NOTICE ready :: job: "call-trgt_plot_meth_waterfall", callee: "trgt_plot"
2025-09-15 20:25:41.394 wdl.w:ptcp.w:call-trgt-89 INFO input :: job: "call-trgt_plot_meth_waterfall", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": true, "methylation": true, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-89/call-trgt_genotype/out/m84036_250809_035451_s4.bc2186.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-89/call-trgt_genotype/out/m84036_250809_035451_s4.bc2186.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-89/call-trgt_genotype/out/m84036_250809_035451_s4.bc2186.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2186"}
2025-09-15 20:25:41.395 wdl.w:ptcp.w:call-trgt-89 NOTICE ready :: job: "call-trgt_plot_motifs_allele", callee: "trgt_plot"
2025-09-15 20:25:41.395 wdl.w:ptcp.w:call-trgt-89 INFO input :: job: "call-trgt_plot_motifs_allele", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": false, "methylation": false, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-89/call-trgt_genotype/out/m84036_250809_035451_s4.bc2186.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-89/call-trgt_genotype/out/m84036_250809_035451_s4.bc2186.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-89/call-trgt_genotype/out/m84036_250809_035451_s4.bc2186.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2186"}
2025-09-15 20:25:41.396 wdl.w:ptcp.w:call-trgt-89 NOTICE ready :: job: "call-trgt_plot_motifs_waterfall", callee: "trgt_plot"
2025-09-15 20:25:41.396 wdl.w:ptcp.w:call-trgt-89 INFO input :: job: "call-trgt_plot_motifs_waterfall", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": true, "methylation": false, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-89/call-trgt_genotype/out/m84036_250809_035451_s4.bc2186.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-89/call-trgt_genotype/out/m84036_250809_035451_s4.bc2186.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-89/call-trgt_genotype/out/m84036_250809_035451_s4.bc2186.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2186"}
2025-09-15 20:25:41.396 wdl.w:ptcp.w:call-trgt-89 INFO visit :: node: "output-spanning_bam", values: {"spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-89/call-trgt_genotype/out/m84036_250809_035451_s4.bc2186.trgt.sorted.spanning.bam"}
2025-09-15 20:25:41.396 wdl.w:ptcp.w:call-trgt-89 INFO visit :: node: "output-spanning_bam_bai", values: {"spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-89/call-trgt_genotype/out/m84036_250809_035451_s4.bc2186.trgt.sorted.spanning.bam.bai"}
2025-09-15 20:25:41.396 wdl.w:ptcp.w:call-trgt-89 INFO visit :: node: "output-vcf", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-89/call-trgt_genotype/out/m84036_250809_035451_s4.bc2186.trgt.vcf"}
2025-09-15 20:25:41.399 wdl.w:ptcp.w:call-paraphase-93.t:call-run_paraphase NOTICE task setup :: name: "run_paraphase", source: "./paraphase.wdl", line: 127, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-93/call-run_paraphase", thread: 140611969599040
2025-09-15 20:25:41.424 wdl.w:ptcp.w:call-paraphase-93.t:call-run_paraphase INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:41.425 wdl.w:ptcp.w:call-paraphase-93.t:call-run_paraphase INFO input :: name: "annotation_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf"
2025-09-15 20:25:41.425 wdl.w:ptcp.w:call-paraphase-93.t:call-run_paraphase INFO input :: name: "genome_version", value: "38"
2025-09-15 20:25:41.425 wdl.w:ptcp.w:call-paraphase-93.t:call-run_paraphase INFO input :: name: "config_file", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/paraphase_config.GRCh38.yaml"
2025-09-15 20:25:41.425 wdl.w:ptcp.w:call-paraphase-93.t:call-run_paraphase INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:25:41.425 wdl.w:ptcp.w:call-paraphase-93.t:call-run_paraphase INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:25:41.425 wdl.w:ptcp.w:call-paraphase-93.t:call-run_paraphase INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2190.mapped.bam.bai"
2025-09-15 20:25:41.425 wdl.w:ptcp.w:call-paraphase-93.t:call-run_paraphase INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2190.mapped.bam"
2025-09-15 20:25:41.425 wdl.w:ptcp.w:call-paraphase-93.t:call-run_paraphase INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2190"
2025-09-15 20:25:41.425 wdl.w:ptcp.w:call-paraphase-93.t:call-run_paraphase INFO eval :: name: "threads", value: 4
2025-09-15 20:25:41.425 wdl.w:ptcp.w:call-paraphase-93.t:call-run_paraphase INFO eval :: name: "mem_gb", value: 8
2025-09-15 20:25:41.425 wdl.w:ptcp.w:call-paraphase-93.t:call-run_paraphase INFO eval :: name: "disk_size", value: 27
2025-09-15 20:25:41.426 wdl.w:ptcp.w:call-paraphase-93.t:call-run_paraphase INFO eval :: name: "out_dir", value: "m84036_250809_035451_s4.bc2190_paraphase"
2025-09-15 20:25:41.426 wdl.w:ptcp.w:call-paraphase-93.t:call-run_paraphase INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 4, memory_reservation: 8000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:41.426 wdl.w:ptcp.w:call-paraphase-93.t:call-run_paraphase WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:41.427 wdl.w:ptcp.w:call-paraphase-93.t:call-run_paraphase INFO provisioned :: seconds_waited: 0, cpu: 4, mem_bytes: 8000000000
2025-09-15 20:25:41.427 wdl.w:ptcp.w:call-paraphase-93.t:call-run_paraphase INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:41.445 wdl.w:ptcp.w:call-trgt-76.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO srun: job 51798057 queued and waiting for resources
2025-09-15 20:25:41.445 wdl.w:ptcp.w:call-trgt-76.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO srun: job 51798057 has been allocated resources
2025-09-15 20:25:41.445 wdl.w:ptcp.w:call-trgt-76.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:41.487 wdl.w:ptcp.w:call-trgt-82.t:call-trgt_genotype INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 11, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-82/call-trgt_genotype/_singularity_tmpdir_pdnxx8ea"
2025-09-15 20:25:41.487 wdl.w:ptcp.w:call-trgt-82.t:call-trgt_genotype INFO Slurm invocation: srun --job-name call-trgt_genotype --partition compute,compute9 --cpus-per-task 8 --mem 15259M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-82/call-trgt_genotype/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-82/call-trgt_genotype/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-82/call-trgt_genotype/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-82/call-trgt_genotype/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-82/out/m84036_250809_035451_s4.bc2179.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2179.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-82/out/m84036_250809_035451_s4.bc2179.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2179.mapped.bam.bai:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-82/call-trgt_genotype/_singularity_tmpdir_pdnxx8ea/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-82/call-trgt_genotype/_singularity_tmpdir_pdnxx8ea/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:41.504 wdl.w:ptcp.w:call-paraphase-93.t:call-run_paraphase INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-93/call-run_paraphase/_singularity_tmpdir_e2bigw0i"
2025-09-15 20:25:41.504 wdl.w:ptcp.w:call-paraphase-93.t:call-run_paraphase INFO Slurm invocation: srun --job-name call-run_paraphase --partition compute,compute9 --cpus-per-task 4 --mem 7629M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-93/call-run_paraphase/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-93/call-run_paraphase/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-93/call-run_paraphase/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-93/call-run_paraphase/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-93/out/m84036_250809_035451_s4.bc2190.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2190.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-93/out/m84036_250809_035451_s4.bc2190.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2190.mapped.bam.bai:ro --bind /ptcp/meta/variant_list/variant_list.GRCh38.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf:ro --bind /ptcp/meta/paraphase/paraphase_config.GRCh38.yaml:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/paraphase_config.GRCh38.yaml:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-93/call-run_paraphase/_singularity_tmpdir_e2bigw0i/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-93/call-run_paraphase/_singularity_tmpdir_e2bigw0i/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:41.509 wdl.w:ptcp.w:call-trgt-82.t:call-trgt_genotype NOTICE slurm_singularity run :: pid: 1206167, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-82/call-trgt_genotype/slurm_singularity.log.txt"
2025-09-15 20:25:41.511 wdl.w:ptcp.w:call-paraphase-93.t:call-run_paraphase NOTICE slurm_singularity run :: pid: 1206168, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-93/call-run_paraphase/slurm_singularity.log.txt"
2025-09-15 20:25:41.616 wdl.w:ptcp.w:call-paraphase-67.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for hba for sample m84036_250809_035451_s4.bc2164 at 2025-09-15 20:24:55.226422...
2025-09-15 20:25:41.617 wdl.w:ptcp.w:call-paraphase-67.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for smn1 for sample m84036_250809_035451_s4.bc2164 at 2025-09-15 20:24:56.066019...
2025-09-15 20:25:41.617 wdl.w:ptcp.w:call-paraphase-67.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for gba for sample m84036_250809_035451_s4.bc2164 at 2025-09-15 20:24:56.358001...
2025-09-15 20:25:41.617 wdl.w:ptcp.w:call-paraphase-67.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for cyp21 for sample m84036_250809_035451_s4.bc2164 at 2025-09-15 20:24:58.207266...
2025-09-15 20:25:41.617 wdl.w:ptcp.w:call-paraphase-67.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for smn1 for sample m84036_250809_035451_s4.bc2164 at 2025-09-15 20:25:18.736176...
2025-09-15 20:25:41.617 wdl.w:ptcp.w:call-paraphase-67.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning to gene2 region for smn1 for sample m84036_250809_035451_s4.bc2164 at 2025-09-15 20:25:20.116518...
2025-09-15 20:25:41.617 wdl.w:ptcp.w:call-paraphase-67.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for smn1 for sample m84036_250809_035451_s4.bc2164 at 2025-09-15 20:25:24.333066...
2025-09-15 20:25:41.739 wdl.w:ptcp.w:call-trgt-73.t:call-trgt_plot_motifs_allele INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2170.motifs_allele.trgt_plots.zip"
2025-09-15 20:25:41.862 wdl.w:ptcp.w:call-trgt-73.t:call-trgt_plot_motifs_allele NOTICE done
2025-09-15 20:25:41.867 wdl.w:ptcp.w:call-trgt-73 NOTICE finish :: job: "call-trgt_plot_motifs_allele"
2025-09-15 20:25:41.867 wdl.w:ptcp.w:call-trgt-73 INFO output :: job: "call-trgt_plot_motifs_allele", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-73/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2170.motifs_allele.trgt_plots.zip"}
2025-09-15 20:25:41.868 wdl.w:ptcp.w:call-trgt-73 INFO visit :: node: "output-images_motifs_allele", values: {"images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-73/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2170.motifs_allele.trgt_plots.zip"}
2025-09-15 20:25:41.873 wdl.w:ptcp.w:call-paraphase-84.t:call-call_f8 NOTICE task setup :: name: "call_f8", source: "./paraphase.wdl", line: 232, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-84/call-call_f8", thread: 140610912642624
2025-09-15 20:25:41.891 wdl.w:ptcp.w:call-paraphase-84.t:call-call_f8 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:41.891 wdl.w:ptcp.w:call-paraphase-84.t:call-call_f8 INFO input :: name: "genome_version", value: "38"
2025-09-15 20:25:41.891 wdl.w:ptcp.w:call-paraphase-84.t:call-call_f8 INFO input :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2181"
2025-09-15 20:25:41.891 wdl.w:ptcp.w:call-paraphase-84.t:call-call_f8 INFO input :: name: "paraphase_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2181.paraphase.bam.bai"
2025-09-15 20:25:41.891 wdl.w:ptcp.w:call-paraphase-84.t:call-call_f8 INFO input :: name: "paraphase_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2181.paraphase.bam"
2025-09-15 20:25:41.891 wdl.w:ptcp.w:call-paraphase-84.t:call-call_f8 INFO input :: name: "sex", value: "F"
2025-09-15 20:25:41.892 wdl.w:ptcp.w:call-paraphase-84.t:call-call_f8 INFO eval :: name: "threads", value: 1
2025-09-15 20:25:41.892 wdl.w:ptcp.w:call-paraphase-84.t:call-call_f8 INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:25:41.892 wdl.w:ptcp.w:call-paraphase-84.t:call-call_f8 INFO eval :: name: "disk_size", value: 11
2025-09-15 20:25:41.892 wdl.w:ptcp.w:call-paraphase-84.t:call-call_f8 INFO eval :: name: "sample_sex", value: "F"
2025-09-15 20:25:41.892 wdl.w:ptcp.w:call-paraphase-84.t:call-call_f8 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:41.892 wdl.w:ptcp.w:call-paraphase-84.t:call-call_f8 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:41.893 wdl.w:ptcp.w:call-paraphase-84.t:call-call_f8 INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:25:41.893 wdl.w:ptcp.w:call-paraphase-84.t:call-call_f8 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:41.927 wdl.w:ptcp.w:call-paraphase-84.t:call-call_f8 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 8, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-84/call-call_f8/_singularity_tmpdir_ekoclj3p"
2025-09-15 20:25:41.927 wdl.w:ptcp.w:call-paraphase-84.t:call-call_f8 INFO Slurm invocation: srun --job-name call-call_f8 --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-84/call-call_f8/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-84/call-call_f8/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-84/call-call_f8/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-84/call-call_f8/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-84/call-run_paraphase/out/m84036_250809_035451_s4.bc2181_paraphase/m84036_250809_035451_s4.bc2181.paraphase.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2181.paraphase.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-84/call-run_paraphase/out/m84036_250809_035451_s4.bc2181_paraphase/m84036_250809_035451_s4.bc2181.paraphase.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2181.paraphase.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-84/call-call_f8/_singularity_tmpdir_ekoclj3p/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-84/call-call_f8/_singularity_tmpdir_ekoclj3p/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:41.944 wdl.w:ptcp.w:call-paraphase-84.t:call-call_f8 NOTICE slurm_singularity run :: pid: 1206192, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-84/call-call_f8/slurm_singularity.log.txt"
2025-09-15 20:25:42.126 wdl.w:ptcp.w:call-paraphase-74.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for hba for sample m84036_250809_035451_s4.bc2171 at 2025-09-15 20:25:41.479642...
2025-09-15 20:25:42.256 wdl.w:ptcp.w:call-sawfish-82.t:call-run_sawfish.slurm_singularity INFO srun: job 51798058 queued and waiting for resources
2025-09-15 20:25:42.256 wdl.w:ptcp.w:call-sawfish-82.t:call-run_sawfish.slurm_singularity INFO srun: job 51798058 has been allocated resources
2025-09-15 20:25:42.256 wdl.w:ptcp.w:call-sawfish-82.t:call-run_sawfish.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:42.256 wdl.w:ptcp.w:call-sawfish-82.t:call-run_sawfish.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:25:42.306 wdl.w:ptcp.w:call-trgt-82.t:call-get_reads_overlapping_repeats.slurm_singularity INFO srun: job 51798059 queued and waiting for resources
2025-09-15 20:25:42.306 wdl.w:ptcp.w:call-trgt-82.t:call-get_reads_overlapping_repeats.slurm_singularity INFO srun: job 51798059 has been allocated resources
2025-09-15 20:25:42.306 wdl.w:ptcp.w:call-trgt-82.t:call-get_reads_overlapping_repeats.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:42.307 wdl.w:ptcp.w:call-trgt-82.t:call-get_reads_overlapping_repeats.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:25:42.349 wdl.w:ptcp.w:call-trgt-74.t:call-trgt_plot_motifs_allele INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2171.motifs_allele.trgt_plots.zip"
2025-09-15 20:25:42.441 wdl.w:ptcp.w:call-trgt-74.t:call-trgt_plot_motifs_allele NOTICE done
2025-09-15 20:25:42.446 wdl.w:ptcp.w:call-trgt-74 NOTICE finish :: job: "call-trgt_plot_motifs_allele"
2025-09-15 20:25:42.447 wdl.w:ptcp.w:call-trgt-74 INFO output :: job: "call-trgt_plot_motifs_allele", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-74/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2171.motifs_allele.trgt_plots.zip"}
2025-09-15 20:25:42.447 wdl.w:ptcp.w:call-trgt-74 INFO visit :: node: "output-images_motifs_allele", values: {"images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-74/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2171.motifs_allele.trgt_plots.zip"}
2025-09-15 20:25:42.447 wdl.w:ptcp.w:call-trgt-74 INFO visit :: node: "outputs", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-74/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2171.motifs_waterfall.trgt_plots.zip", "images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-74/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2171.meth_allele.trgt_plots.zip", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-74/call-trgt_genotype/out/m84036_250809_035451_s4.bc2171.trgt.sorted.spanning.bam.bai", "images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-74/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2171.motifs_allele.trgt_plots.zip", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-74/call-trgt_genotype/out/m84036_250809_035451_s4.bc2171.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-74/call-trgt_genotype/out/m84036_250809_035451_s4.bc2171.trgt.vcf", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-74/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2171.repeats.bam", "images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-74/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2171.meth_waterfall.trgt_plots.zip", "reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-74/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2171.repeats.bam.bai"}
2025-09-15 20:25:42.453 wdl.w:ptcp.w:call-paraphase-76.t:call-call_f8 NOTICE task setup :: name: "call_f8", source: "./paraphase.wdl", line: 232, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-76/call-call_f8", thread: 140611441120832
2025-09-15 20:25:42.473 wdl.w:ptcp.w:call-paraphase-76.t:call-call_f8 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:42.474 wdl.w:ptcp.w:call-paraphase-76.t:call-call_f8 INFO input :: name: "genome_version", value: "38"
2025-09-15 20:25:42.474 wdl.w:ptcp.w:call-paraphase-76.t:call-call_f8 INFO input :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2173"
2025-09-15 20:25:42.474 wdl.w:ptcp.w:call-paraphase-76.t:call-call_f8 INFO input :: name: "paraphase_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2173.paraphase.bam.bai"
2025-09-15 20:25:42.474 wdl.w:ptcp.w:call-paraphase-76.t:call-call_f8 INFO input :: name: "paraphase_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2173.paraphase.bam"
2025-09-15 20:25:42.474 wdl.w:ptcp.w:call-paraphase-76.t:call-call_f8 INFO input :: name: "sex", value: "F"
2025-09-15 20:25:42.474 wdl.w:ptcp.w:call-paraphase-76.t:call-call_f8 INFO eval :: name: "threads", value: 1
2025-09-15 20:25:42.474 wdl.w:ptcp.w:call-paraphase-76.t:call-call_f8 INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:25:42.474 wdl.w:ptcp.w:call-paraphase-76.t:call-call_f8 INFO eval :: name: "disk_size", value: 11
2025-09-15 20:25:42.475 wdl.w:ptcp.w:call-paraphase-76.t:call-call_f8 INFO eval :: name: "sample_sex", value: "F"
2025-09-15 20:25:42.475 wdl.w:ptcp.w:call-paraphase-76.t:call-call_f8 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:42.475 wdl.w:ptcp.w:call-paraphase-76.t:call-call_f8 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:42.475 wdl.w:ptcp.w:call-paraphase-76.t:call-call_f8 INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:25:42.476 wdl.w:ptcp.w:call-paraphase-76.t:call-call_f8 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:42.496 wdl.w:ptcp.w:call-trgt-73.t:call-trgt_plot_meth_allele INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2170.meth_allele.trgt_plots.zip"
2025-09-15 20:25:42.526 wdl.w:ptcp.w:call-paraphase-93.t:call-run_paraphase.slurm_singularity INFO srun: job 51798061 queued and waiting for resources
2025-09-15 20:25:42.526 wdl.w:ptcp.w:call-paraphase-93.t:call-run_paraphase.slurm_singularity INFO srun: job 51798061 has been allocated resources
2025-09-15 20:25:42.526 wdl.w:ptcp.w:call-paraphase-93.t:call-run_paraphase.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:42.526 wdl.w:ptcp.w:call-paraphase-93.t:call-run_paraphase.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:25:42.527 wdl.w:ptcp.w:call-trgt-82.t:call-trgt_genotype.slurm_singularity INFO srun: job 51798060 queued and waiting for resources
2025-09-15 20:25:42.527 wdl.w:ptcp.w:call-trgt-82.t:call-trgt_genotype.slurm_singularity INFO srun: job 51798060 has been allocated resources
2025-09-15 20:25:42.527 wdl.w:ptcp.w:call-trgt-82.t:call-trgt_genotype.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:42.527 wdl.w:ptcp.w:call-trgt-82.t:call-trgt_genotype.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:25:42.539 wdl.w:ptcp.w:call-paraphase-76.t:call-call_f8 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 8, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-76/call-call_f8/_singularity_tmpdir_yvp65594"
2025-09-15 20:25:42.539 wdl.w:ptcp.w:call-paraphase-76.t:call-call_f8 INFO Slurm invocation: srun --job-name call-call_f8 --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-76/call-call_f8/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-76/call-call_f8/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-76/call-call_f8/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-76/call-call_f8/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-76/call-run_paraphase/out/m84036_250809_035451_s4.bc2173_paraphase/m84036_250809_035451_s4.bc2173.paraphase.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2173.paraphase.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-76/call-run_paraphase/out/m84036_250809_035451_s4.bc2173_paraphase/m84036_250809_035451_s4.bc2173.paraphase.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2173.paraphase.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-76/call-call_f8/_singularity_tmpdir_yvp65594/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-76/call-call_f8/_singularity_tmpdir_yvp65594/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:42.558 wdl.w:ptcp.w:call-trgt-74 NOTICE done
2025-09-15 20:25:42.566 wdl.w:ptcp.w:call-paraphase-76.t:call-call_f8 NOTICE slurm_singularity run :: pid: 1206201, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-76/call-call_f8/slurm_singularity.log.txt"
2025-09-15 20:25:42.627 wdl.w:ptcp.w:call-trgt-82.t:call-get_reads_overlapping_repeats INFO output :: name: "reads_overlapping_repeats", value: "m84036_250809_035451_s4.bc2179.repeats.bam"
2025-09-15 20:25:42.631 wdl.w:ptcp.w:call-trgt-82.t:call-get_reads_overlapping_repeats INFO output :: name: "reads_overlapping_repeats_bai", value: "m84036_250809_035451_s4.bc2179.repeats.bam.bai"
2025-09-15 20:25:42.635 wdl.w:ptcp.w:call-trgt-73.t:call-trgt_plot_meth_allele NOTICE done
2025-09-15 20:25:42.641 wdl.w:ptcp.w:call-trgt-73 NOTICE finish :: job: "call-trgt_plot_meth_allele"
2025-09-15 20:25:42.642 wdl.w:ptcp.w:call-trgt-73 INFO output :: job: "call-trgt_plot_meth_allele", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-73/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2170.meth_allele.trgt_plots.zip"}
2025-09-15 20:25:42.642 wdl.w:ptcp.w:call-trgt-73 INFO visit :: node: "output-images_meth_allele", values: {"images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-73/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2170.meth_allele.trgt_plots.zip"}
2025-09-15 20:25:42.647 wdl.w:ptcp.w:call-trgt-75.t:call-trgt_plot_meth_allele NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-75/call-trgt_plot_meth_allele", thread: 140608211502656
2025-09-15 20:25:42.668 wdl.w:ptcp.w:call-trgt-75.t:call-trgt_plot_meth_allele INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:42.668 wdl.w:ptcp.w:call-trgt-75.t:call-trgt_plot_meth_allele INFO input :: name: "waterfall", value: false
2025-09-15 20:25:42.668 wdl.w:ptcp.w:call-trgt-75.t:call-trgt_plot_meth_allele INFO input :: name: "methylation", value: true
2025-09-15 20:25:42.668 wdl.w:ptcp.w:call-trgt-75.t:call-trgt_plot_meth_allele INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:25:42.668 wdl.w:ptcp.w:call-trgt-75.t:call-trgt_plot_meth_allele INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:25:42.668 wdl.w:ptcp.w:call-trgt-75.t:call-trgt_plot_meth_allele INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:25:42.668 wdl.w:ptcp.w:call-trgt-75.t:call-trgt_plot_meth_allele INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2172.trgt.sorted.spanning.bam.bai"
2025-09-15 20:25:42.668 wdl.w:ptcp.w:call-trgt-75.t:call-trgt_plot_meth_allele INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2172.trgt.sorted.spanning.bam"
2025-09-15 20:25:42.669 wdl.w:ptcp.w:call-trgt-75.t:call-trgt_plot_meth_allele INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2172.trgt.vcf"
2025-09-15 20:25:42.669 wdl.w:ptcp.w:call-trgt-75.t:call-trgt_plot_meth_allele INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2172"
2025-09-15 20:25:42.669 wdl.w:ptcp.w:call-trgt-75.t:call-trgt_plot_meth_allele INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:25:42.669 wdl.w:ptcp.w:call-trgt-75.t:call-trgt_plot_meth_allele INFO eval :: name: "plot_type", value: "allele"
2025-09-15 20:25:42.669 wdl.w:ptcp.w:call-trgt-75.t:call-trgt_plot_meth_allele INFO eval :: name: "show", value: "meth"
2025-09-15 20:25:42.669 wdl.w:ptcp.w:call-trgt-75.t:call-trgt_plot_meth_allele INFO eval :: name: "threads", value: 1
2025-09-15 20:25:42.669 wdl.w:ptcp.w:call-trgt-75.t:call-trgt_plot_meth_allele INFO eval :: name: "disk_size", value: 27
2025-09-15 20:25:42.670 wdl.w:ptcp.w:call-trgt-75.t:call-trgt_plot_meth_allele INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2172.meth_allele"
2025-09-15 20:25:42.670 wdl.w:ptcp.w:call-trgt-75.t:call-trgt_plot_meth_allele INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:42.670 wdl.w:ptcp.w:call-trgt-75.t:call-trgt_plot_meth_allele WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:42.670 wdl.w:ptcp.w:call-trgt-75.t:call-trgt_plot_meth_allele INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:25:42.671 wdl.w:ptcp.w:call-trgt-75.t:call-trgt_plot_meth_allele INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:42.672 wdl.w:ptcp NOTICE finish :: job: "call-trgt-74"
2025-09-15 20:25:42.673 wdl.w:ptcp INFO output :: job: "call-trgt-74", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-74/out/m84036_250809_035451_s4.bc2171.motifs_waterfall.trgt_plots.zip", "images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-74/out/m84036_250809_035451_s4.bc2171.meth_allele.trgt_plots.zip", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-74/out/m84036_250809_035451_s4.bc2171.trgt.sorted.spanning.bam.bai", "images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-74/out/m84036_250809_035451_s4.bc2171.motifs_allele.trgt_plots.zip", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-74/out/m84036_250809_035451_s4.bc2171.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-74/out/m84036_250809_035451_s4.bc2171.trgt.vcf", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-74/out/m84036_250809_035451_s4.bc2171.repeats.bam", "images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-74/out/m84036_250809_035451_s4.bc2171.meth_waterfall.trgt_plots.zip", "reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-74/out/m84036_250809_035451_s4.bc2171.repeats.bam.bai"}
2025-09-15 20:25:42.680 wdl.w:ptcp.w:call-sawfish-83 NOTICE workflow start :: name: "sawfish", source: "./sawfish.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-83"
2025-09-15 20:25:42.699 wdl.w:ptcp.w:call-sawfish-83 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:25:42.699 wdl.w:ptcp.w:call-sawfish-83 INFO visit :: node: "decl-genome_version", values: {"genome_version": "38"}
2025-09-15 20:25:42.700 wdl.w:ptcp.w:call-sawfish-83 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-83/out/m84036_250809_035451_s4.bc2180.mapped.bam"}
2025-09-15 20:25:42.700 wdl.w:ptcp.w:call-sawfish-83 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-83/out/m84036_250809_035451_s4.bc2180.mapped.bam.bai"}
2025-09-15 20:25:42.700 wdl.w:ptcp.w:call-sawfish-83 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:25:42.700 wdl.w:ptcp.w:call-sawfish-83 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:25:42.700 wdl.w:ptcp.w:call-sawfish-83 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2180"}
2025-09-15 20:25:42.700 wdl.w:ptcp.w:call-sawfish-83 NOTICE ready :: job: "call-run_sawfish", callee: "run_sawfish"
2025-09-15 20:25:42.700 wdl.w:ptcp.w:call-sawfish-83 INFO input :: job: "call-run_sawfish", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-83/out/m84036_250809_035451_s4.bc2180.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-83/out/m84036_250809_035451_s4.bc2180.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2180"}
2025-09-15 20:25:42.702 wdl.w:ptcp.w:call-trgt-82.t:call-get_reads_overlapping_repeats NOTICE done
2025-09-15 20:25:42.707 wdl.w:ptcp.w:call-trgt-82 NOTICE finish :: job: "call-get_reads_overlapping_repeats"
2025-09-15 20:25:42.707 wdl.w:ptcp.w:call-trgt-82 INFO output :: job: "call-get_reads_overlapping_repeats", values: {"reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-82/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2179.repeats.bam.bai", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-82/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2179.repeats.bam"}
2025-09-15 20:25:42.708 wdl.w:ptcp.w:call-trgt-82 INFO visit :: node: "output-reads_overlapping_repeats", values: {"reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-82/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2179.repeats.bam"}
2025-09-15 20:25:42.708 wdl.w:ptcp.w:call-trgt-82 INFO visit :: node: "output-reads_overlapping_repeats_bai", values: {"reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-82/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2179.repeats.bam.bai"}
2025-09-15 20:25:42.714 wdl.w:ptcp.w:call-trgt-75.t:call-trgt_plot_meth_waterfall NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-75/call-trgt_plot_meth_waterfall", thread: 140607691417152
2025-09-15 20:25:42.719 wdl.w:ptcp.w:call-trgt-76.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:41 [ERROR] - No reads found for TRID=PRTS_ARX
2025-09-15 20:25:42.719 wdl.w:ptcp.w:call-trgt-76.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:41 [ERROR] - No reads found for TRID=EIEE1_ARX
2025-09-15 20:25:42.733 wdl.w:ptcp.w:call-trgt-75.t:call-trgt_plot_meth_waterfall INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:42.733 wdl.w:ptcp.w:call-trgt-75.t:call-trgt_plot_meth_waterfall INFO input :: name: "waterfall", value: true
2025-09-15 20:25:42.733 wdl.w:ptcp.w:call-trgt-75.t:call-trgt_plot_meth_waterfall INFO input :: name: "methylation", value: true
2025-09-15 20:25:42.733 wdl.w:ptcp.w:call-trgt-75.t:call-trgt_plot_meth_waterfall INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:25:42.733 wdl.w:ptcp.w:call-trgt-75.t:call-trgt_plot_meth_waterfall INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:25:42.733 wdl.w:ptcp.w:call-trgt-75.t:call-trgt_plot_meth_waterfall INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:25:42.733 wdl.w:ptcp.w:call-trgt-75.t:call-trgt_plot_meth_waterfall INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2172.trgt.sorted.spanning.bam.bai"
2025-09-15 20:25:42.733 wdl.w:ptcp.w:call-trgt-75.t:call-trgt_plot_meth_waterfall INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2172.trgt.sorted.spanning.bam"
2025-09-15 20:25:42.733 wdl.w:ptcp.w:call-trgt-75.t:call-trgt_plot_meth_waterfall INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2172.trgt.vcf"
2025-09-15 20:25:42.733 wdl.w:ptcp.w:call-trgt-75.t:call-trgt_plot_meth_waterfall INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2172"
2025-09-15 20:25:42.734 wdl.w:ptcp.w:call-trgt-75.t:call-trgt_plot_meth_waterfall INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:25:42.734 wdl.w:ptcp.w:call-trgt-75.t:call-trgt_plot_meth_waterfall INFO eval :: name: "plot_type", value: "waterfall"
2025-09-15 20:25:42.734 wdl.w:ptcp.w:call-trgt-75.t:call-trgt_plot_meth_waterfall INFO eval :: name: "show", value: "meth"
2025-09-15 20:25:42.734 wdl.w:ptcp.w:call-trgt-75.t:call-trgt_plot_meth_waterfall INFO eval :: name: "threads", value: 1
2025-09-15 20:25:42.734 wdl.w:ptcp.w:call-trgt-75.t:call-trgt_plot_meth_waterfall INFO eval :: name: "disk_size", value: 27
2025-09-15 20:25:42.734 wdl.w:ptcp.w:call-trgt-75.t:call-trgt_plot_meth_waterfall INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2172.meth_waterfall"
2025-09-15 20:25:42.735 wdl.w:ptcp.w:call-trgt-75.t:call-trgt_plot_meth_waterfall INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:42.735 wdl.w:ptcp.w:call-trgt-75.t:call-trgt_plot_meth_waterfall WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:42.735 wdl.w:ptcp.w:call-trgt-75.t:call-trgt_plot_meth_waterfall INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:25:42.735 wdl.w:ptcp.w:call-trgt-75.t:call-trgt_plot_meth_waterfall INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:42.766 wdl.w:ptcp.w:call-trgt-75.t:call-trgt_plot_meth_allele INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-75/call-trgt_plot_meth_allele/_singularity_tmpdir_m250wdw1"
2025-09-15 20:25:42.766 wdl.w:ptcp.w:call-trgt-75.t:call-trgt_plot_meth_allele INFO Slurm invocation: srun --job-name call-trgt_plot_meth_allele --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-75/call-trgt_plot_meth_allele/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-75/call-trgt_plot_meth_allele/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-75/call-trgt_plot_meth_allele/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-75/call-trgt_plot_meth_allele/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-75/call-trgt_genotype/out/m84036_250809_035451_s4.bc2172.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2172.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-75/call-trgt_genotype/out/m84036_250809_035451_s4.bc2172.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2172.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-75/call-trgt_genotype/out/m84036_250809_035451_s4.bc2172.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2172.trgt.vcf:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-75/call-trgt_plot_meth_allele/_singularity_tmpdir_m250wdw1/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-75/call-trgt_plot_meth_allele/_singularity_tmpdir_m250wdw1/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:42.775 wdl.w:ptcp.w:call-paraphase-02.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for hbb for sample m84036_250809_035451_s4.bc2099 at 2025-09-15 20:25:37.119442...
2025-09-15 20:25:42.775 wdl.w:ptcp.w:call-paraphase-02.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for hbb for sample m84036_250809_035451_s4.bc2099 at 2025-09-15 20:25:37.120637...
2025-09-15 20:25:42.775 wdl.w:ptcp.w:call-paraphase-02.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for hbb for sample m84036_250809_035451_s4.bc2099 at 2025-09-15 20:25:38.421434...
2025-09-15 20:25:42.778 wdl.w:ptcp.w:call-paraphase-89.t:call-run_paraphase.stderr VERBOSE INFO:root:Processing sample m84036_250809_035451_s4.bc2186 at 2025-09-15 20:25:40.996150...
2025-09-15 20:25:42.779 wdl.w:ptcp.w:call-paraphase-89.t:call-run_paraphase.stderr VERBOSE INFO:root:Checking sample sex at 2025-09-15 20:25:40.999060...
2025-09-15 20:25:42.780 wdl.w:ptcp.w:call-paraphase-89.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for smn1 for sample m84036_250809_035451_s4.bc2186 at 2025-09-15 20:25:41.092825...
2025-09-15 20:25:42.780 wdl.w:ptcp.w:call-paraphase-89.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for gba for sample m84036_250809_035451_s4.bc2186 at 2025-09-15 20:25:41.092965...
2025-09-15 20:25:42.780 wdl.w:ptcp.w:call-paraphase-89.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for smn1 for sample m84036_250809_035451_s4.bc2186 at 2025-09-15 20:25:41.093550...
2025-09-15 20:25:42.780 wdl.w:ptcp.w:call-paraphase-89.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for gba for sample m84036_250809_035451_s4.bc2186 at 2025-09-15 20:25:41.093576...
2025-09-15 20:25:42.780 wdl.w:ptcp.w:call-paraphase-89.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for cyp21 for sample m84036_250809_035451_s4.bc2186 at 2025-09-15 20:25:41.092810...
2025-09-15 20:25:42.780 wdl.w:ptcp.w:call-paraphase-89.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for cyp21 for sample m84036_250809_035451_s4.bc2186 at 2025-09-15 20:25:41.093709...
2025-09-15 20:25:42.780 wdl.w:ptcp.w:call-paraphase-89.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for hba for sample m84036_250809_035451_s4.bc2186 at 2025-09-15 20:25:41.093300...
2025-09-15 20:25:42.781 wdl.w:ptcp.w:call-paraphase-89.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for hba for sample m84036_250809_035451_s4.bc2186 at 2025-09-15 20:25:41.094062...
2025-09-15 20:25:42.781 wdl.w:ptcp.w:call-paraphase-89.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for gba for sample m84036_250809_035451_s4.bc2186 at 2025-09-15 20:25:41.823435...
2025-09-15 20:25:42.781 wdl.w:ptcp.w:call-paraphase-89.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for hba for sample m84036_250809_035451_s4.bc2186 at 2025-09-15 20:25:41.848548...
2025-09-15 20:25:42.781 wdl.w:ptcp.w:call-paraphase-89.t:call-run_paraphase.stderr VERBOSE WARNING:root:This region does not appear to have coverage. Will not attempt to phase haplotypes.
2025-09-15 20:25:42.781 wdl.w:ptcp.w:call-paraphase-89.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for hba for sample m84036_250809_035451_s4.bc2186 at 2025-09-15 20:25:41.905173...
2025-09-15 20:25:42.781 wdl.w:ptcp.w:call-paraphase-89.t:call-run_paraphase.stderr VERBOSE WARNING:root:This region does not appear to have coverage. Will not attempt to phase haplotypes.
2025-09-15 20:25:42.781 wdl.w:ptcp.w:call-paraphase-89.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for gba for sample m84036_250809_035451_s4.bc2186 at 2025-09-15 20:25:41.912038...
2025-09-15 20:25:42.781 wdl.w:ptcp.w:call-paraphase-89.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for cyp21 for sample m84036_250809_035451_s4.bc2186 at 2025-09-15 20:25:41.912858...
2025-09-15 20:25:42.781 wdl.w:ptcp.w:call-paraphase-89.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for smn1 for sample m84036_250809_035451_s4.bc2186 at 2025-09-15 20:25:41.935422...
2025-09-15 20:25:42.781 wdl.w:ptcp.w:call-paraphase-89.t:call-run_paraphase.stderr VERBOSE WARNING:root:This region does not appear to have coverage. Will not attempt to phase haplotypes.
2025-09-15 20:25:42.781 wdl.w:ptcp.w:call-paraphase-89.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for cyp21 for sample m84036_250809_035451_s4.bc2186 at 2025-09-15 20:25:42.039581...
2025-09-15 20:25:42.781 wdl.w:ptcp.w:call-paraphase-89.t:call-run_paraphase.stderr VERBOSE WARNING:root:This region does not appear to have coverage. Will not attempt to phase haplotypes.
2025-09-15 20:25:42.781 wdl.w:ptcp.w:call-paraphase-89.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for smn1 for sample m84036_250809_035451_s4.bc2186 at 2025-09-15 20:25:42.112273...
2025-09-15 20:25:42.781 wdl.w:ptcp.w:call-paraphase-89.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for hba for sample m84036_250809_035451_s4.bc2186 at 2025-09-15 20:25:42.414040...
2025-09-15 20:25:42.781 wdl.w:ptcp.w:call-paraphase-89.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for hbb for sample m84036_250809_035451_s4.bc2186 at 2025-09-15 20:25:42.421144...
2025-09-15 20:25:42.782 wdl.w:ptcp.w:call-paraphase-89.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for hbb for sample m84036_250809_035451_s4.bc2186 at 2025-09-15 20:25:42.421401...
2025-09-15 20:25:42.782 wdl.w:ptcp.w:call-paraphase-89.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for gba for sample m84036_250809_035451_s4.bc2186 at 2025-09-15 20:25:42.514235...
2025-09-15 20:25:42.782 wdl.w:ptcp.w:call-paraphase-89.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for rpgr for sample m84036_250809_035451_s4.bc2186 at 2025-09-15 20:25:42.528357...
2025-09-15 20:25:42.782 wdl.w:ptcp.w:call-paraphase-89.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for rpgr for sample m84036_250809_035451_s4.bc2186 at 2025-09-15 20:25:42.528657...
2025-09-15 20:25:42.782 wdl.w:ptcp.w:call-paraphase-89.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for cyp21 for sample m84036_250809_035451_s4.bc2186 at 2025-09-15 20:25:42.575499...
2025-09-15 20:25:42.782 wdl.w:ptcp.w:call-paraphase-89.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for f8inv22 for sample m84036_250809_035451_s4.bc2186 at 2025-09-15 20:25:42.591173...
2025-09-15 20:25:42.782 wdl.w:ptcp.w:call-paraphase-89.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for f8inv22 for sample m84036_250809_035451_s4.bc2186 at 2025-09-15 20:25:42.591470...
2025-09-15 20:25:42.782 wdl.w:ptcp.w:call-paraphase-89.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning to gene2 region for smn1 for sample m84036_250809_035451_s4.bc2186 at 2025-09-15 20:25:42.666398...
2025-09-15 20:25:42.793 wdl.w:ptcp.w:call-trgt-75.t:call-trgt_plot_meth_allele NOTICE slurm_singularity run :: pid: 1206209, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-75/call-trgt_plot_meth_allele/slurm_singularity.log.txt"
2025-09-15 20:25:42.806 wdl.w:ptcp.w:call-paraphase-66.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for smn1 for sample m84036_250809_035451_s4.bc2163 at 2025-09-15 20:25:38.732478...
2025-09-15 20:25:42.806 wdl.w:ptcp.w:call-paraphase-66.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning to gene2 region for smn1 for sample m84036_250809_035451_s4.bc2163 at 2025-09-15 20:25:39.603891...
2025-09-15 20:25:42.819 wdl.w:ptcp.w:call-trgt-75.t:call-trgt_plot_meth_waterfall INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-75/call-trgt_plot_meth_waterfall/_singularity_tmpdir_zoiut_70"
2025-09-15 20:25:42.819 wdl.w:ptcp.w:call-trgt-75.t:call-trgt_plot_meth_waterfall INFO Slurm invocation: srun --job-name call-trgt_plot_meth_waterfall --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-75/call-trgt_plot_meth_waterfall/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-75/call-trgt_plot_meth_waterfall/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-75/call-trgt_plot_meth_waterfall/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-75/call-trgt_plot_meth_waterfall/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-75/call-trgt_genotype/out/m84036_250809_035451_s4.bc2172.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2172.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-75/call-trgt_genotype/out/m84036_250809_035451_s4.bc2172.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2172.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-75/call-trgt_genotype/out/m84036_250809_035451_s4.bc2172.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2172.trgt.vcf:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-75/call-trgt_plot_meth_waterfall/_singularity_tmpdir_zoiut_70/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-75/call-trgt_plot_meth_waterfall/_singularity_tmpdir_zoiut_70/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:42.835 wdl.w:ptcp.w:call-trgt-75.t:call-trgt_plot_meth_waterfall NOTICE slurm_singularity run :: pid: 1206211, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-75/call-trgt_plot_meth_waterfall/slurm_singularity.log.txt"
2025-09-15 20:25:42.950 wdl.w:ptcp.w:call-paraphase-84.t:call-call_f8.slurm_singularity INFO srun: job 51798062 queued and waiting for resources
2025-09-15 20:25:42.951 wdl.w:ptcp.w:call-paraphase-84.t:call-call_f8.slurm_singularity INFO srun: job 51798062 has been allocated resources
2025-09-15 20:25:42.951 wdl.w:ptcp.w:call-paraphase-84.t:call-call_f8.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:43.122 wdl.w:ptcp.w:call-trgt-82.t:call-trgt_genotype INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2179.trgt.vcf"
2025-09-15 20:25:43.125 wdl.w:ptcp.w:call-trgt-82.t:call-trgt_genotype INFO output :: name: "spanning_bam", value: "m84036_250809_035451_s4.bc2179.trgt.sorted.spanning.bam"
2025-09-15 20:25:43.126 wdl.w:ptcp.w:call-trgt-82.t:call-trgt_genotype INFO output :: name: "spanning_bam_bai", value: "m84036_250809_035451_s4.bc2179.trgt.sorted.spanning.bam.bai"
2025-09-15 20:25:43.201 wdl.w:ptcp.w:call-trgt-82.t:call-trgt_genotype NOTICE done
2025-09-15 20:25:43.236 wdl.w:ptcp.w:call-trgt-82 NOTICE finish :: job: "call-trgt_genotype"
2025-09-15 20:25:43.236 wdl.w:ptcp.w:call-trgt-82 INFO output :: job: "call-trgt_genotype", values: {"spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-82/call-trgt_genotype/out/m84036_250809_035451_s4.bc2179.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-82/call-trgt_genotype/out/m84036_250809_035451_s4.bc2179.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-82/call-trgt_genotype/out/m84036_250809_035451_s4.bc2179.trgt.vcf"}
2025-09-15 20:25:43.237 wdl.w:ptcp.w:call-trgt-82 NOTICE ready :: job: "call-trgt_plot_meth_allele", callee: "trgt_plot"
2025-09-15 20:25:43.237 wdl.w:ptcp.w:call-trgt-82 INFO input :: job: "call-trgt_plot_meth_allele", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": false, "methylation": true, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-82/call-trgt_genotype/out/m84036_250809_035451_s4.bc2179.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-82/call-trgt_genotype/out/m84036_250809_035451_s4.bc2179.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-82/call-trgt_genotype/out/m84036_250809_035451_s4.bc2179.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2179"}
2025-09-15 20:25:43.238 wdl.w:ptcp.w:call-trgt-82 NOTICE ready :: job: "call-trgt_plot_meth_waterfall", callee: "trgt_plot"
2025-09-15 20:25:43.239 wdl.w:ptcp.w:call-trgt-82 INFO input :: job: "call-trgt_plot_meth_waterfall", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": true, "methylation": true, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-82/call-trgt_genotype/out/m84036_250809_035451_s4.bc2179.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-82/call-trgt_genotype/out/m84036_250809_035451_s4.bc2179.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-82/call-trgt_genotype/out/m84036_250809_035451_s4.bc2179.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2179"}
2025-09-15 20:25:43.240 wdl.w:ptcp.w:call-trgt-82 NOTICE ready :: job: "call-trgt_plot_motifs_allele", callee: "trgt_plot"
2025-09-15 20:25:43.240 wdl.w:ptcp.w:call-trgt-82 INFO input :: job: "call-trgt_plot_motifs_allele", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": false, "methylation": false, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-82/call-trgt_genotype/out/m84036_250809_035451_s4.bc2179.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-82/call-trgt_genotype/out/m84036_250809_035451_s4.bc2179.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-82/call-trgt_genotype/out/m84036_250809_035451_s4.bc2179.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2179"}
2025-09-15 20:25:43.241 wdl.w:ptcp.w:call-trgt-82 NOTICE ready :: job: "call-trgt_plot_motifs_waterfall", callee: "trgt_plot"
2025-09-15 20:25:43.241 wdl.w:ptcp.w:call-trgt-82 INFO input :: job: "call-trgt_plot_motifs_waterfall", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": true, "methylation": false, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-82/call-trgt_genotype/out/m84036_250809_035451_s4.bc2179.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-82/call-trgt_genotype/out/m84036_250809_035451_s4.bc2179.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-82/call-trgt_genotype/out/m84036_250809_035451_s4.bc2179.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2179"}
2025-09-15 20:25:43.241 wdl.w:ptcp.w:call-trgt-82 INFO visit :: node: "output-spanning_bam", values: {"spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-82/call-trgt_genotype/out/m84036_250809_035451_s4.bc2179.trgt.sorted.spanning.bam"}
2025-09-15 20:25:43.241 wdl.w:ptcp.w:call-trgt-82 INFO visit :: node: "output-spanning_bam_bai", values: {"spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-82/call-trgt_genotype/out/m84036_250809_035451_s4.bc2179.trgt.sorted.spanning.bam.bai"}
2025-09-15 20:25:43.241 wdl.w:ptcp.w:call-trgt-82 INFO visit :: node: "output-vcf", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-82/call-trgt_genotype/out/m84036_250809_035451_s4.bc2179.trgt.vcf"}
2025-09-15 20:25:43.247 wdl.w:ptcp.w:call-trgt-75.t:call-trgt_plot_motifs_allele NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-75/call-trgt_plot_motifs_allele", thread: 140611944420928
2025-09-15 20:25:43.252 wdl.w:ptcp.w:call-trgt-89.t:call-get_reads_overlapping_repeats INFO output :: name: "reads_overlapping_repeats", value: "m84036_250809_035451_s4.bc2186.repeats.bam"
2025-09-15 20:25:43.255 wdl.w:ptcp.w:call-trgt-89.t:call-get_reads_overlapping_repeats INFO output :: name: "reads_overlapping_repeats_bai", value: "m84036_250809_035451_s4.bc2186.repeats.bam.bai"
2025-09-15 20:25:43.271 wdl.w:ptcp.w:call-trgt-75.t:call-trgt_plot_motifs_allele INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:43.271 wdl.w:ptcp.w:call-trgt-75.t:call-trgt_plot_motifs_allele INFO input :: name: "waterfall", value: false
2025-09-15 20:25:43.271 wdl.w:ptcp.w:call-trgt-75.t:call-trgt_plot_motifs_allele INFO input :: name: "methylation", value: false
2025-09-15 20:25:43.271 wdl.w:ptcp.w:call-trgt-75.t:call-trgt_plot_motifs_allele INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:25:43.272 wdl.w:ptcp.w:call-trgt-75.t:call-trgt_plot_motifs_allele INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:25:43.272 wdl.w:ptcp.w:call-trgt-75.t:call-trgt_plot_motifs_allele INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:25:43.272 wdl.w:ptcp.w:call-trgt-75.t:call-trgt_plot_motifs_allele INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2172.trgt.sorted.spanning.bam.bai"
2025-09-15 20:25:43.272 wdl.w:ptcp.w:call-trgt-75.t:call-trgt_plot_motifs_allele INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2172.trgt.sorted.spanning.bam"
2025-09-15 20:25:43.272 wdl.w:ptcp.w:call-trgt-75.t:call-trgt_plot_motifs_allele INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2172.trgt.vcf"
2025-09-15 20:25:43.272 wdl.w:ptcp.w:call-trgt-75.t:call-trgt_plot_motifs_allele INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2172"
2025-09-15 20:25:43.272 wdl.w:ptcp.w:call-trgt-75.t:call-trgt_plot_motifs_allele INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:25:43.272 wdl.w:ptcp.w:call-trgt-75.t:call-trgt_plot_motifs_allele INFO eval :: name: "plot_type", value: "allele"
2025-09-15 20:25:43.272 wdl.w:ptcp.w:call-trgt-75.t:call-trgt_plot_motifs_allele INFO eval :: name: "show", value: "motifs"
2025-09-15 20:25:43.272 wdl.w:ptcp.w:call-trgt-75.t:call-trgt_plot_motifs_allele INFO eval :: name: "threads", value: 1
2025-09-15 20:25:43.272 wdl.w:ptcp.w:call-trgt-75.t:call-trgt_plot_motifs_allele INFO eval :: name: "disk_size", value: 27
2025-09-15 20:25:43.273 wdl.w:ptcp.w:call-trgt-75.t:call-trgt_plot_motifs_allele INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2172.motifs_allele"
2025-09-15 20:25:43.273 wdl.w:ptcp.w:call-trgt-75.t:call-trgt_plot_motifs_allele INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:43.273 wdl.w:ptcp.w:call-trgt-75.t:call-trgt_plot_motifs_allele WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:43.274 wdl.w:ptcp.w:call-trgt-75.t:call-trgt_plot_motifs_allele INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:25:43.274 wdl.w:ptcp.w:call-trgt-75.t:call-trgt_plot_motifs_allele INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:43.338 wdl.w:ptcp.w:call-trgt-89.t:call-get_reads_overlapping_repeats NOTICE done
2025-09-15 20:25:43.342 wdl.w:ptcp.w:call-trgt-89 NOTICE finish :: job: "call-get_reads_overlapping_repeats"
2025-09-15 20:25:43.343 wdl.w:ptcp.w:call-trgt-89 INFO output :: job: "call-get_reads_overlapping_repeats", values: {"reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-89/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2186.repeats.bam.bai", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-89/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2186.repeats.bam"}
2025-09-15 20:25:43.343 wdl.w:ptcp.w:call-trgt-89 INFO visit :: node: "output-reads_overlapping_repeats", values: {"reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-89/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2186.repeats.bam"}
2025-09-15 20:25:43.343 wdl.w:ptcp.w:call-trgt-89 INFO visit :: node: "output-reads_overlapping_repeats_bai", values: {"reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-89/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2186.repeats.bam.bai"}
2025-09-15 20:25:43.348 wdl.w:ptcp.w:call-trgt-84.t:call-trgt_plot_motifs_allele INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2181.motifs_allele.trgt_plots.zip"
2025-09-15 20:25:43.354 wdl.w:ptcp.w:call-trgt-75.t:call-trgt_plot_motifs_waterfall NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-75/call-trgt_plot_motifs_waterfall", thread: 140613034948160
2025-09-15 20:25:43.382 wdl.w:ptcp.w:call-trgt-75.t:call-trgt_plot_motifs_allele INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-75/call-trgt_plot_motifs_allele/_singularity_tmpdir_pjpxpjjo"
2025-09-15 20:25:43.382 wdl.w:ptcp.w:call-trgt-75.t:call-trgt_plot_motifs_allele INFO Slurm invocation: srun --job-name call-trgt_plot_motifs_allele --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-75/call-trgt_plot_motifs_allele/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-75/call-trgt_plot_motifs_allele/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-75/call-trgt_plot_motifs_allele/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-75/call-trgt_plot_motifs_allele/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-75/call-trgt_genotype/out/m84036_250809_035451_s4.bc2172.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2172.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-75/call-trgt_genotype/out/m84036_250809_035451_s4.bc2172.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2172.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-75/call-trgt_genotype/out/m84036_250809_035451_s4.bc2172.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2172.trgt.vcf:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-75/call-trgt_plot_motifs_allele/_singularity_tmpdir_pjpxpjjo/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-75/call-trgt_plot_motifs_allele/_singularity_tmpdir_pjpxpjjo/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:43.403 wdl.w:ptcp.w:call-trgt-75.t:call-trgt_plot_motifs_allele NOTICE slurm_singularity run :: pid: 1206227, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-75/call-trgt_plot_motifs_allele/slurm_singularity.log.txt"
2025-09-15 20:25:43.410 wdl.w:ptcp.w:call-trgt-75.t:call-trgt_plot_motifs_waterfall INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:43.410 wdl.w:ptcp.w:call-trgt-75.t:call-trgt_plot_motifs_waterfall INFO input :: name: "waterfall", value: true
2025-09-15 20:25:43.410 wdl.w:ptcp.w:call-trgt-75.t:call-trgt_plot_motifs_waterfall INFO input :: name: "methylation", value: false
2025-09-15 20:25:43.410 wdl.w:ptcp.w:call-trgt-75.t:call-trgt_plot_motifs_waterfall INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:25:43.410 wdl.w:ptcp.w:call-trgt-75.t:call-trgt_plot_motifs_waterfall INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:25:43.410 wdl.w:ptcp.w:call-trgt-75.t:call-trgt_plot_motifs_waterfall INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:25:43.410 wdl.w:ptcp.w:call-trgt-75.t:call-trgt_plot_motifs_waterfall INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2172.trgt.sorted.spanning.bam.bai"
2025-09-15 20:25:43.410 wdl.w:ptcp.w:call-trgt-75.t:call-trgt_plot_motifs_waterfall INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2172.trgt.sorted.spanning.bam"
2025-09-15 20:25:43.410 wdl.w:ptcp.w:call-trgt-75.t:call-trgt_plot_motifs_waterfall INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2172.trgt.vcf"
2025-09-15 20:25:43.410 wdl.w:ptcp.w:call-trgt-75.t:call-trgt_plot_motifs_waterfall INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2172"
2025-09-15 20:25:43.411 wdl.w:ptcp.w:call-trgt-75.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:25:43.411 wdl.w:ptcp.w:call-trgt-75.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "plot_type", value: "waterfall"
2025-09-15 20:25:43.411 wdl.w:ptcp.w:call-trgt-75.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "show", value: "motifs"
2025-09-15 20:25:43.411 wdl.w:ptcp.w:call-trgt-75.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "threads", value: 1
2025-09-15 20:25:43.411 wdl.w:ptcp.w:call-trgt-75.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "disk_size", value: 27
2025-09-15 20:25:43.411 wdl.w:ptcp.w:call-trgt-75.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2172.motifs_waterfall"
2025-09-15 20:25:43.412 wdl.w:ptcp.w:call-trgt-75.t:call-trgt_plot_motifs_waterfall INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:43.412 wdl.w:ptcp.w:call-trgt-75.t:call-trgt_plot_motifs_waterfall WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:43.412 wdl.w:ptcp.w:call-trgt-75.t:call-trgt_plot_motifs_waterfall INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:25:43.412 wdl.w:ptcp.w:call-trgt-75.t:call-trgt_plot_motifs_waterfall INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:43.420 wdl.w:ptcp.w:call-paraphase-84.t:call-call_f8 INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2181.f8inversion.vcf"
2025-09-15 20:25:43.423 wdl.w:ptcp.w:call-paraphase-84.t:call-call_f8 INFO output :: name: "json", value: "m84036_250809_035451_s4.bc2181.f8inversion.json"
2025-09-15 20:25:43.485 wdl.w:ptcp.w:call-trgt-76.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:25:42 [ERROR] - No reads found for TRID=PRTS_ARX
2025-09-15 20:25:43.485 wdl.w:ptcp.w:call-trgt-76.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:25:42 [ERROR] - No reads found for TRID=EIEE1_ARX
2025-09-15 20:25:43.486 wdl.w:ptcp.w:call-trgt-84.t:call-trgt_plot_motifs_allele NOTICE done
2025-09-15 20:25:43.495 wdl.w:ptcp.w:call-trgt-75.t:call-trgt_plot_motifs_waterfall INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-75/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_zlsorpjs"
2025-09-15 20:25:43.496 wdl.w:ptcp.w:call-trgt-75.t:call-trgt_plot_motifs_waterfall INFO Slurm invocation: srun --job-name call-trgt_plot_motifs_waterfall --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-75/call-trgt_plot_motifs_waterfall/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-75/call-trgt_plot_motifs_waterfall/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-75/call-trgt_plot_motifs_waterfall/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-75/call-trgt_plot_motifs_waterfall/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-75/call-trgt_genotype/out/m84036_250809_035451_s4.bc2172.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2172.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-75/call-trgt_genotype/out/m84036_250809_035451_s4.bc2172.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2172.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-75/call-trgt_genotype/out/m84036_250809_035451_s4.bc2172.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2172.trgt.vcf:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-75/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_zlsorpjs/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-75/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_zlsorpjs/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:43.516 wdl.w:ptcp.w:call-paraphase-84.t:call-call_f8 NOTICE done
2025-09-15 20:25:43.517 wdl.w:ptcp.w:call-trgt-75.t:call-trgt_plot_motifs_waterfall NOTICE slurm_singularity run :: pid: 1206229, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-75/call-trgt_plot_motifs_waterfall/slurm_singularity.log.txt"
2025-09-15 20:25:43.522 wdl.w:ptcp.w:call-paraphase-84 NOTICE finish :: job: "call-call_f8"
2025-09-15 20:25:43.523 wdl.w:ptcp.w:call-paraphase-84 INFO output :: job: "call-call_f8", values: {"json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-84/call-call_f8/out/m84036_250809_035451_s4.bc2181.f8inversion.json", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-84/call-call_f8/out/m84036_250809_035451_s4.bc2181.f8inversion.vcf"}
2025-09-15 20:25:43.523 wdl.w:ptcp.w:call-paraphase-84 INFO visit :: node: "output-f8_json", values: {"f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-84/call-call_f8/out/m84036_250809_035451_s4.bc2181.f8inversion.json"}
2025-09-15 20:25:43.523 wdl.w:ptcp.w:call-paraphase-84 INFO visit :: node: "output-f8_vcf", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-84/call-call_f8/out/m84036_250809_035451_s4.bc2181.f8inversion.vcf"}
2025-09-15 20:25:43.523 wdl.w:ptcp.w:call-paraphase-84 INFO visit :: node: "outputs", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-84/call-call_f8/out/m84036_250809_035451_s4.bc2181.f8inversion.vcf", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-84/call-run_paraphase/out/m84036_250809_035451_s4.bc2181_paraphase/m84036_250809_035451_s4.bc2181.paraphase.json", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-84/call-run_paraphase/out/m84036_250809_035451_s4.bc2181_paraphase/m84036_250809_035451_s4.bc2181.paraphase.bam", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-84/call-run_paraphase/out/m84036_250809_035451_s4.bc2181_paraphase/m84036_250809_035451_s4.bc2181.paraphase.bam.bai", "paraphase_vcfs": [], "havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-84/call-run_paraphase/out/m84036_250809_035451_s4.bc2181.havanno.json", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-84/call-call_f8/out/m84036_250809_035451_s4.bc2181.f8inversion.json"}
2025-09-15 20:25:43.525 wdl.w:ptcp.w:call-trgt-84 NOTICE finish :: job: "call-trgt_plot_motifs_allele"
2025-09-15 20:25:43.525 wdl.w:ptcp.w:call-trgt-84 INFO output :: job: "call-trgt_plot_motifs_allele", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-84/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2181.motifs_allele.trgt_plots.zip"}
2025-09-15 20:25:43.526 wdl.w:ptcp.w:call-trgt-84 INFO visit :: node: "output-images_motifs_allele", values: {"images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-84/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2181.motifs_allele.trgt_plots.zip"}
2025-09-15 20:25:43.529 wdl.w:ptcp.w:call-sawfish-93.t:call-run_sawfish NOTICE task setup :: name: "run_sawfish", source: "./sawfish.wdl", line: 83, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-93/call-run_sawfish", thread: 140610912642624
2025-09-15 20:25:43.531 wdl.w:ptcp.w:call-trgt-93.t:call-get_reads_overlapping_repeats NOTICE task setup :: name: "get_reads_overlapping_repeats", source: "./trgt.wdl", line: 182, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-93/call-get_reads_overlapping_repeats", thread: 140607683024448
2025-09-15 20:25:43.550 wdl.w:ptcp.w:call-sawfish-93.t:call-run_sawfish INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:43.550 wdl.w:ptcp.w:call-sawfish-93.t:call-run_sawfish INFO input :: name: "genome_version", value: "38"
2025-09-15 20:25:43.550 wdl.w:ptcp.w:call-sawfish-93.t:call-run_sawfish INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:25:43.550 wdl.w:ptcp.w:call-sawfish-93.t:call-run_sawfish INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:25:43.550 wdl.w:ptcp.w:call-sawfish-93.t:call-run_sawfish INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2190.mapped.bam.bai"
2025-09-15 20:25:43.550 wdl.w:ptcp.w:call-sawfish-93.t:call-run_sawfish INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2190.mapped.bam"
2025-09-15 20:25:43.550 wdl.w:ptcp.w:call-sawfish-93.t:call-run_sawfish INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2190"
2025-09-15 20:25:43.551 wdl.w:ptcp.w:call-sawfish-93.t:call-run_sawfish INFO eval :: name: "mem_gb", value: 32
2025-09-15 20:25:43.551 wdl.w:ptcp.w:call-sawfish-93.t:call-run_sawfish INFO eval :: name: "threads", value: 16
2025-09-15 20:25:43.552 wdl.w:ptcp.w:call-sawfish-93.t:call-run_sawfish INFO eval :: name: "disk_size", value: 30
2025-09-15 20:25:43.552 wdl.w:ptcp.w:call-sawfish-93.t:call-run_sawfish INFO eval :: name: "discover_dirname", value: "m84036_250809_035451_s4.bc2190_sawfish_discover"
2025-09-15 20:25:43.552 wdl.w:ptcp.w:call-sawfish-93.t:call-run_sawfish INFO eval :: name: "call_dirname", value: "m84036_250809_035451_s4.bc2190_sawfish"
2025-09-15 20:25:43.552 wdl.w:ptcp.w:call-sawfish-93.t:call-run_sawfish INFO eval :: name: "minimap2_bam_filename", value: "m84036_250809_035451_s4.bc2190.minimap2.bam"
2025-09-15 20:25:43.553 wdl.w:ptcp.w:call-sawfish-93.t:call-run_sawfish INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 16, memory_reservation: 32000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:43.553 wdl.w:ptcp.w:call-sawfish-93.t:call-run_sawfish WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:43.553 wdl.w:ptcp.w:call-sawfish-93.t:call-run_sawfish INFO provisioned :: seconds_waited: 0, cpu: 16, mem_bytes: 32000000000
2025-09-15 20:25:43.553 wdl.w:ptcp.w:call-sawfish-93.t:call-run_sawfish INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:43.555 wdl.w:ptcp.w:call-trgt-93.t:call-get_reads_overlapping_repeats INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:43.555 wdl.w:ptcp.w:call-trgt-93.t:call-get_reads_overlapping_repeats INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:25:43.555 wdl.w:ptcp.w:call-trgt-93.t:call-get_reads_overlapping_repeats INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2190.mapped.bam.bai"
2025-09-15 20:25:43.555 wdl.w:ptcp.w:call-trgt-93.t:call-get_reads_overlapping_repeats INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2190.mapped.bam"
2025-09-15 20:25:43.555 wdl.w:ptcp.w:call-trgt-93.t:call-get_reads_overlapping_repeats INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2190"
2025-09-15 20:25:43.555 wdl.w:ptcp.w:call-trgt-93.t:call-get_reads_overlapping_repeats INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:25:43.555 wdl.w:ptcp.w:call-trgt-93.t:call-get_reads_overlapping_repeats INFO eval :: name: "expand_size", value: 3000
2025-09-15 20:25:43.556 wdl.w:ptcp.w:call-trgt-93.t:call-get_reads_overlapping_repeats INFO eval :: name: "threads", value: 1
2025-09-15 20:25:43.556 wdl.w:ptcp.w:call-trgt-93.t:call-get_reads_overlapping_repeats INFO eval :: name: "expanded_bed_name", value: "m84036_250809_035451_s4.bc2190.expanded.bed"
2025-09-15 20:25:43.556 wdl.w:ptcp.w:call-trgt-93.t:call-get_reads_overlapping_repeats INFO eval :: name: "disk_size", value: 11
2025-09-15 20:25:43.556 wdl.w:ptcp.w:call-trgt-93.t:call-get_reads_overlapping_repeats INFO eval :: name: "output_name", value: "m84036_250809_035451_s4.bc2190.repeats.bam"
2025-09-15 20:25:43.556 wdl.w:ptcp.w:call-trgt-93.t:call-get_reads_overlapping_repeats INFO eval :: name: "index_name", value: "m84036_250809_035451_s4.bc2190.repeats.bam.bai"
2025-09-15 20:25:43.556 wdl.w:ptcp.w:call-trgt-93.t:call-get_reads_overlapping_repeats INFO eval :: name: "output_name_with_index", value: "m84036_250809_035451_s4.bc2190.repeats.bam##idx##m84036_250809_035451_s4.bc2190.repeats.bam.bai"
2025-09-15 20:25:43.556 wdl.w:ptcp.w:call-trgt-93.t:call-get_reads_overlapping_repeats INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:43.556 wdl.w:ptcp.w:call-trgt-93.t:call-get_reads_overlapping_repeats WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:43.557 wdl.w:ptcp.w:call-trgt-93.t:call-get_reads_overlapping_repeats INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:25:43.557 wdl.w:ptcp.w:call-trgt-93.t:call-get_reads_overlapping_repeats INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:43.584 wdl.w:ptcp.w:call-paraphase-76.t:call-call_f8.slurm_singularity INFO srun: job 51798063 queued and waiting for resources
2025-09-15 20:25:43.584 wdl.w:ptcp.w:call-paraphase-76.t:call-call_f8.slurm_singularity INFO srun: job 51798063 has been allocated resources
2025-09-15 20:25:43.584 wdl.w:ptcp.w:call-paraphase-76.t:call-call_f8.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:43.600 wdl.w:ptcp.w:call-paraphase-84 NOTICE done
2025-09-15 20:25:43.609 wdl.w:ptcp.w:call-trgt-93.t:call-get_reads_overlapping_repeats INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 9, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-93/call-get_reads_overlapping_repeats/_singularity_tmpdir_ji_93u_g"
2025-09-15 20:25:43.609 wdl.w:ptcp.w:call-trgt-93.t:call-get_reads_overlapping_repeats INFO Slurm invocation: srun --job-name call-get_reads_overlapping_repeats --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-93/call-get_reads_overlapping_repeats/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-93/call-get_reads_overlapping_repeats/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-93/call-get_reads_overlapping_repeats/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-93/call-get_reads_overlapping_repeats/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-93/out/m84036_250809_035451_s4.bc2190.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2190.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-93/out/m84036_250809_035451_s4.bc2190.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2190.mapped.bam.bai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-93/call-get_reads_overlapping_repeats/_singularity_tmpdir_ji_93u_g/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-93/call-get_reads_overlapping_repeats/_singularity_tmpdir_ji_93u_g/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:43.615 wdl.w:ptcp.w:call-sawfish-93.t:call-run_sawfish INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 10, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-93/call-run_sawfish/_singularity_tmpdir_gy1v_i0f"
2025-09-15 20:25:43.615 wdl.w:ptcp.w:call-sawfish-93.t:call-run_sawfish INFO Slurm invocation: srun --job-name call-run_sawfish --partition compute,compute9 --cpus-per-task 16 --mem 30518M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-93/call-run_sawfish/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-93/call-run_sawfish/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-93/call-run_sawfish/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-93/call-run_sawfish/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-93/out/m84036_250809_035451_s4.bc2190.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2190.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-93/out/m84036_250809_035451_s4.bc2190.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2190.mapped.bam.bai:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-93/call-run_sawfish/_singularity_tmpdir_gy1v_i0f/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-93/call-run_sawfish/_singularity_tmpdir_gy1v_i0f/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:43.626 wdl.w:ptcp NOTICE finish :: job: "call-paraphase-84"
2025-09-15 20:25:43.626 wdl.w:ptcp INFO output :: job: "call-paraphase-84", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-84/out/m84036_250809_035451_s4.bc2181.f8inversion.vcf", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-84/out/m84036_250809_035451_s4.bc2181_paraphase/m84036_250809_035451_s4.bc2181.paraphase.json", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-84/out/m84036_250809_035451_s4.bc2181_paraphase/m84036_250809_035451_s4.bc2181.paraphase.bam", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-84/out/m84036_250809_035451_s4.bc2181_paraphase/m84036_250809_035451_s4.bc2181.paraphase.bam.bai", "paraphase_vcfs": [], "havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-84/out/m84036_250809_035451_s4.bc2181.havanno.json", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-84/out/m84036_250809_035451_s4.bc2181.f8inversion.json"}
2025-09-15 20:25:43.628 wdl.w:ptcp.w:call-trgt-93.t:call-get_reads_overlapping_repeats NOTICE slurm_singularity run :: pid: 1206231, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-93/call-get_reads_overlapping_repeats/slurm_singularity.log.txt"
2025-09-15 20:25:43.628 wdl.w:ptcp.w:call-sawfish-93.t:call-run_sawfish NOTICE slurm_singularity run :: pid: 1206232, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-93/call-run_sawfish/slurm_singularity.log.txt"
2025-09-15 20:25:43.631 wdl.w:ptcp.w:call-trgt-83 NOTICE workflow start :: name: "trgt", source: "./trgt.wdl", line: 3, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-83"
2025-09-15 20:25:43.648 wdl.w:ptcp.w:call-trgt-83 INFO visit :: node: "decl-docker_smrttools", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}
2025-09-15 20:25:43.649 wdl.w:ptcp.w:call-trgt-83 INFO visit :: node: "decl-mapped_bam", values: {"mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-83/out/m84036_250809_035451_s4.bc2180.mapped.bam"}
2025-09-15 20:25:43.649 wdl.w:ptcp.w:call-trgt-83 INFO visit :: node: "decl-mapped_bam_bai", values: {"mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-83/out/m84036_250809_035451_s4.bc2180.mapped.bam.bai"}
2025-09-15 20:25:43.649 wdl.w:ptcp.w:call-trgt-83 INFO visit :: node: "decl-ref_fasta", values: {"ref_fasta": "/meta/refs/hg38.fa"}
2025-09-15 20:25:43.649 wdl.w:ptcp.w:call-trgt-83 INFO visit :: node: "decl-ref_index", values: {"ref_index": "/meta/refs/hg38.fa.fai"}
2025-09-15 20:25:43.649 wdl.w:ptcp.w:call-trgt-83 INFO visit :: node: "decl-sample_name", values: {"sample_name": "m84036_250809_035451_s4.bc2180"}
2025-09-15 20:25:43.649 wdl.w:ptcp.w:call-trgt-83 INFO visit :: node: "decl-sex", values: {"sex": "F"}
2025-09-15 20:25:43.649 wdl.w:ptcp.w:call-trgt-83 INFO visit :: node: "decl-trgt_bed", values: {"trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"}
2025-09-15 20:25:43.649 wdl.w:ptcp.w:call-trgt-83 NOTICE ready :: job: "call-get_reads_overlapping_repeats", callee: "get_reads_overlapping_repeats"
2025-09-15 20:25:43.650 wdl.w:ptcp.w:call-trgt-83 INFO input :: job: "call-get_reads_overlapping_repeats", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-83/out/m84036_250809_035451_s4.bc2180.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-83/out/m84036_250809_035451_s4.bc2180.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2180"}
2025-09-15 20:25:43.650 wdl.w:ptcp.w:call-trgt-83 NOTICE ready :: job: "call-trgt_genotype", callee: "trgt_genotype"
2025-09-15 20:25:43.650 wdl.w:ptcp.w:call-trgt-83 INFO input :: job: "call-trgt_genotype", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-83/out/m84036_250809_035451_s4.bc2180.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-83/out/m84036_250809_035451_s4.bc2180.mapped.bam", "sex": "F", "sample_name": "m84036_250809_035451_s4.bc2180"}
2025-09-15 20:25:43.795 wdl.w:ptcp.w:call-trgt-75.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:43 [ERROR] - No reads found for TRID=OPDM_ABCD3
2025-09-15 20:25:43.805 wdl.w:ptcp.w:call-trgt-75.t:call-trgt_plot_meth_allele.slurm_singularity INFO srun: job 51798064 queued and waiting for resources
2025-09-15 20:25:43.805 wdl.w:ptcp.w:call-trgt-75.t:call-trgt_plot_meth_allele.slurm_singularity INFO srun: job 51798064 has been allocated resources
2025-09-15 20:25:43.805 wdl.w:ptcp.w:call-trgt-75.t:call-trgt_plot_meth_allele.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:43.838 wdl.w:ptcp.w:call-trgt-75.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:25:43 [ERROR] - No reads found for TRID=OPDM_ABCD3
2025-09-15 20:25:43.838 wdl.w:ptcp.w:call-trgt-75.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:25:43 [ERROR] - No reads found for TRID=SCA37_DAB1
2025-09-15 20:25:43.838 wdl.w:ptcp.w:call-trgt-75.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:25:43 [ERROR] - No reads found for TRID=SCA2_ATXN2
2025-09-15 20:25:43.838 wdl.w:ptcp.w:call-trgt-75.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:25:43 [ERROR] - No reads found for TRID=NIID_NOTCH2NLC
2025-09-15 20:25:43.838 wdl.w:ptcp.w:call-trgt-75.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:25:43 [ERROR] - No reads found for TRID=SCA27B_FGF14
2025-09-15 20:25:43.848 wdl.w:ptcp.w:call-trgt-75.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO srun: job 51798065 queued and waiting for resources
2025-09-15 20:25:43.848 wdl.w:ptcp.w:call-trgt-75.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO srun: job 51798065 has been allocated resources
2025-09-15 20:25:43.848 wdl.w:ptcp.w:call-trgt-75.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:43.852 wdl.w:ptcp.w:call-paraphase-76.t:call-call_f8 INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2173.f8inversion.vcf"
2025-09-15 20:25:43.856 wdl.w:ptcp.w:call-paraphase-76.t:call-call_f8 INFO output :: name: "json", value: "m84036_250809_035451_s4.bc2173.f8inversion.json"
2025-09-15 20:25:43.946 wdl.w:ptcp.w:call-paraphase-76.t:call-call_f8 NOTICE done
2025-09-15 20:25:43.958 wdl.w:ptcp.w:call-paraphase-76 NOTICE finish :: job: "call-call_f8"
2025-09-15 20:25:43.958 wdl.w:ptcp.w:call-paraphase-76 INFO output :: job: "call-call_f8", values: {"json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-76/call-call_f8/out/m84036_250809_035451_s4.bc2173.f8inversion.json", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-76/call-call_f8/out/m84036_250809_035451_s4.bc2173.f8inversion.vcf"}
2025-09-15 20:25:43.958 wdl.w:ptcp.w:call-paraphase-76 INFO visit :: node: "output-f8_json", values: {"f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-76/call-call_f8/out/m84036_250809_035451_s4.bc2173.f8inversion.json"}
2025-09-15 20:25:43.958 wdl.w:ptcp.w:call-paraphase-76 INFO visit :: node: "output-f8_vcf", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-76/call-call_f8/out/m84036_250809_035451_s4.bc2173.f8inversion.vcf"}
2025-09-15 20:25:43.958 wdl.w:ptcp.w:call-paraphase-76 INFO visit :: node: "outputs", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-76/call-call_f8/out/m84036_250809_035451_s4.bc2173.f8inversion.vcf", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-76/call-run_paraphase/out/m84036_250809_035451_s4.bc2173_paraphase/m84036_250809_035451_s4.bc2173.paraphase.json", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-76/call-run_paraphase/out/m84036_250809_035451_s4.bc2173_paraphase/m84036_250809_035451_s4.bc2173.paraphase.bam", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-76/call-run_paraphase/out/m84036_250809_035451_s4.bc2173_paraphase/m84036_250809_035451_s4.bc2173.paraphase.bam.bai", "paraphase_vcfs": [], "havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-76/call-run_paraphase/out/m84036_250809_035451_s4.bc2173.havanno.json", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-76/call-call_f8/out/m84036_250809_035451_s4.bc2173.f8inversion.json"}
2025-09-15 20:25:43.964 wdl.w:ptcp.w:call-trgt-93.t:call-trgt_genotype NOTICE task setup :: name: "trgt_genotype", source: "./trgt.wdl", line: 272, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-93/call-trgt_genotype", thread: 140611441120832
2025-09-15 20:25:43.981 wdl.w:ptcp.w:call-trgt-93.t:call-trgt_genotype INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:43.981 wdl.w:ptcp.w:call-trgt-93.t:call-trgt_genotype INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:25:43.981 wdl.w:ptcp.w:call-trgt-93.t:call-trgt_genotype INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:25:43.981 wdl.w:ptcp.w:call-trgt-93.t:call-trgt_genotype INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:25:43.981 wdl.w:ptcp.w:call-trgt-93.t:call-trgt_genotype INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2190.mapped.bam.bai"
2025-09-15 20:25:43.981 wdl.w:ptcp.w:call-trgt-93.t:call-trgt_genotype INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2190.mapped.bam"
2025-09-15 20:25:43.981 wdl.w:ptcp.w:call-trgt-93.t:call-trgt_genotype INFO input :: name: "sex", value: "F"
2025-09-15 20:25:43.981 wdl.w:ptcp.w:call-trgt-93.t:call-trgt_genotype INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2190"
2025-09-15 20:25:43.981 wdl.w:ptcp.w:call-trgt-93.t:call-trgt_genotype INFO eval :: name: "mem_gb", value: 16
2025-09-15 20:25:43.982 wdl.w:ptcp.w:call-trgt-93.t:call-trgt_genotype INFO eval :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2190.trgt"
2025-09-15 20:25:43.982 wdl.w:ptcp.w:call-trgt-93.t:call-trgt_genotype INFO eval :: name: "threads", value: 8
2025-09-15 20:25:43.982 wdl.w:ptcp.w:call-trgt-93.t:call-trgt_genotype INFO eval :: name: "disk_size", value: 27
2025-09-15 20:25:43.982 wdl.w:ptcp.w:call-trgt-93.t:call-trgt_genotype INFO eval :: name: "karyotype", value: "XX"
2025-09-15 20:25:43.982 wdl.w:ptcp.w:call-trgt-93.t:call-trgt_genotype INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 8, memory_reservation: 16000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:43.983 wdl.w:ptcp.w:call-trgt-93.t:call-trgt_genotype WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:43.983 wdl.w:ptcp.w:call-trgt-93.t:call-trgt_genotype INFO provisioned :: seconds_waited: 0, cpu: 8, mem_bytes: 16000000000
2025-09-15 20:25:43.983 wdl.w:ptcp.w:call-trgt-93.t:call-trgt_genotype INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:44.028 wdl.w:ptcp.w:call-paraphase-76 NOTICE done
2025-09-15 20:25:44.035 wdl.w:ptcp NOTICE finish :: job: "call-paraphase-76"
2025-09-15 20:25:44.035 wdl.w:ptcp INFO output :: job: "call-paraphase-76", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-76/out/m84036_250809_035451_s4.bc2173.f8inversion.vcf", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-76/out/m84036_250809_035451_s4.bc2173_paraphase/m84036_250809_035451_s4.bc2173.paraphase.json", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-76/out/m84036_250809_035451_s4.bc2173_paraphase/m84036_250809_035451_s4.bc2173.paraphase.bam", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-76/out/m84036_250809_035451_s4.bc2173_paraphase/m84036_250809_035451_s4.bc2173.paraphase.bam.bai", "paraphase_vcfs": [], "havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-76/out/m84036_250809_035451_s4.bc2173.havanno.json", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-76/out/m84036_250809_035451_s4.bc2173.f8inversion.json"}
2025-09-15 20:25:44.053 wdl.w:ptcp.w:call-trgt-93.t:call-trgt_genotype INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 11, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-93/call-trgt_genotype/_singularity_tmpdir_6ohy8wv0"
2025-09-15 20:25:44.053 wdl.w:ptcp.w:call-trgt-93.t:call-trgt_genotype INFO Slurm invocation: srun --job-name call-trgt_genotype --partition compute,compute9 --cpus-per-task 8 --mem 15259M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-93/call-trgt_genotype/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-93/call-trgt_genotype/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-93/call-trgt_genotype/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-93/call-trgt_genotype/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-93/out/m84036_250809_035451_s4.bc2190.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2190.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-93/out/m84036_250809_035451_s4.bc2190.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2190.mapped.bam.bai:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-93/call-trgt_genotype/_singularity_tmpdir_6ohy8wv0/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-93/call-trgt_genotype/_singularity_tmpdir_6ohy8wv0/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:44.080 wdl.w:ptcp.w:call-trgt-93.t:call-trgt_genotype NOTICE slurm_singularity run :: pid: 1206256, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-93/call-trgt_genotype/slurm_singularity.log.txt"
2025-09-15 20:25:44.405 wdl.w:ptcp.w:call-trgt-75.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:25:44 [ERROR] - No reads found for TRID=OPDM_ABCD3
2025-09-15 20:25:44.414 wdl.w:ptcp.w:call-trgt-75.t:call-trgt_plot_motifs_allele.slurm_singularity INFO srun: job 51798066 queued and waiting for resources
2025-09-15 20:25:44.415 wdl.w:ptcp.w:call-trgt-75.t:call-trgt_plot_motifs_allele.slurm_singularity INFO srun: job 51798066 has been allocated resources
2025-09-15 20:25:44.415 wdl.w:ptcp.w:call-trgt-75.t:call-trgt_plot_motifs_allele.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:44.451 wdl.w:ptcp.w:call-paraphase-55.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for rpgr for sample m84036_250809_035451_s4.bc2152 at 2025-09-15 20:25:34.541171...
2025-09-15 20:25:44.451 wdl.w:ptcp.w:call-paraphase-55.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for rpgr for sample m84036_250809_035451_s4.bc2152 at 2025-09-15 20:25:34.541331...
2025-09-15 20:25:44.525 wdl.w:ptcp.w:call-trgt-75.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO srun: job 51798067 queued and waiting for resources
2025-09-15 20:25:44.525 wdl.w:ptcp.w:call-trgt-75.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO srun: job 51798067 has been allocated resources
2025-09-15 20:25:44.526 wdl.w:ptcp.w:call-trgt-75.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:44.631 wdl.w:ptcp.w:call-sawfish-93.t:call-run_sawfish.stderr VERBOSE [M::bam2fq_mainloop] discarded 0 singletons
2025-09-15 20:25:44.631 wdl.w:ptcp.w:call-sawfish-93.t:call-run_sawfish.stderr VERBOSE [M::bam2fq_mainloop] processed 0 reads
2025-09-15 20:25:44.637 wdl.w:ptcp.w:call-sawfish-93.t:call-run_sawfish.slurm_singularity INFO srun: job 51798069 queued and waiting for resources
2025-09-15 20:25:44.637 wdl.w:ptcp.w:call-sawfish-93.t:call-run_sawfish.slurm_singularity INFO srun: job 51798069 has been allocated resources
2025-09-15 20:25:44.637 wdl.w:ptcp.w:call-sawfish-93.t:call-run_sawfish.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:44.637 wdl.w:ptcp.w:call-sawfish-93.t:call-run_sawfish.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:25:44.639 wdl.w:ptcp.w:call-trgt-93.t:call-get_reads_overlapping_repeats.slurm_singularity INFO srun: job 51798068 queued and waiting for resources
2025-09-15 20:25:44.639 wdl.w:ptcp.w:call-trgt-93.t:call-get_reads_overlapping_repeats.slurm_singularity INFO srun: job 51798068 has been allocated resources
2025-09-15 20:25:44.639 wdl.w:ptcp.w:call-trgt-93.t:call-get_reads_overlapping_repeats.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:44.917 wdl.w:ptcp.w:call-paraphase-42.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for hba for sample m84036_250809_035451_s4.bc2139 at 2025-09-15 20:25:38.972977...
2025-09-15 20:25:44.917 wdl.w:ptcp.w:call-paraphase-42.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for hba for sample m84036_250809_035451_s4.bc2139 at 2025-09-15 20:25:39.417818...
2025-09-15 20:25:44.951 wdl.w:ptcp.w:call-trgt-76.t:call-trgt_plot_meth_allele INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2173.meth_allele.trgt_plots.zip"
2025-09-15 20:25:45.053 wdl.w:ptcp.w:call-trgt-76.t:call-trgt_plot_meth_allele NOTICE done
2025-09-15 20:25:45.058 wdl.w:ptcp.w:call-trgt-76 NOTICE finish :: job: "call-trgt_plot_meth_allele"
2025-09-15 20:25:45.059 wdl.w:ptcp.w:call-trgt-76 INFO output :: job: "call-trgt_plot_meth_allele", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-76/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2173.meth_allele.trgt_plots.zip"}
2025-09-15 20:25:45.059 wdl.w:ptcp.w:call-trgt-76 INFO visit :: node: "output-images_meth_allele", values: {"images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-76/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2173.meth_allele.trgt_plots.zip"}
2025-09-15 20:25:45.064 wdl.w:ptcp.w:call-trgt-77.t:call-trgt_plot_meth_allele NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-77/call-trgt_plot_meth_allele", thread: 140611977991744
2025-09-15 20:25:45.077 wdl.w:ptcp.w:call-trgt-76.t:call-trgt_plot_motifs_allele INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2173.motifs_allele.trgt_plots.zip"
2025-09-15 20:25:45.086 wdl.w:ptcp.w:call-trgt-77.t:call-trgt_plot_meth_allele INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:45.086 wdl.w:ptcp.w:call-trgt-77.t:call-trgt_plot_meth_allele INFO input :: name: "waterfall", value: false
2025-09-15 20:25:45.086 wdl.w:ptcp.w:call-trgt-77.t:call-trgt_plot_meth_allele INFO input :: name: "methylation", value: true
2025-09-15 20:25:45.086 wdl.w:ptcp.w:call-trgt-77.t:call-trgt_plot_meth_allele INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:25:45.086 wdl.w:ptcp.w:call-trgt-77.t:call-trgt_plot_meth_allele INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:25:45.087 wdl.w:ptcp.w:call-trgt-77.t:call-trgt_plot_meth_allele INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:25:45.087 wdl.w:ptcp.w:call-trgt-77.t:call-trgt_plot_meth_allele INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2174.trgt.sorted.spanning.bam.bai"
2025-09-15 20:25:45.087 wdl.w:ptcp.w:call-trgt-77.t:call-trgt_plot_meth_allele INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2174.trgt.sorted.spanning.bam"
2025-09-15 20:25:45.087 wdl.w:ptcp.w:call-trgt-77.t:call-trgt_plot_meth_allele INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2174.trgt.vcf"
2025-09-15 20:25:45.087 wdl.w:ptcp.w:call-trgt-77.t:call-trgt_plot_meth_allele INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2174"
2025-09-15 20:25:45.087 wdl.w:ptcp.w:call-trgt-77.t:call-trgt_plot_meth_allele INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:25:45.087 wdl.w:ptcp.w:call-trgt-77.t:call-trgt_plot_meth_allele INFO eval :: name: "plot_type", value: "allele"
2025-09-15 20:25:45.087 wdl.w:ptcp.w:call-trgt-77.t:call-trgt_plot_meth_allele INFO eval :: name: "show", value: "meth"
2025-09-15 20:25:45.087 wdl.w:ptcp.w:call-trgt-77.t:call-trgt_plot_meth_allele INFO eval :: name: "threads", value: 1
2025-09-15 20:25:45.087 wdl.w:ptcp.w:call-trgt-77.t:call-trgt_plot_meth_allele INFO eval :: name: "disk_size", value: 27
2025-09-15 20:25:45.088 wdl.w:ptcp.w:call-trgt-77.t:call-trgt_plot_meth_allele INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2174.meth_allele"
2025-09-15 20:25:45.088 wdl.w:ptcp.w:call-trgt-77.t:call-trgt_plot_meth_allele INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:45.088 wdl.w:ptcp.w:call-trgt-77.t:call-trgt_plot_meth_allele WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:45.088 wdl.w:ptcp.w:call-trgt-77.t:call-trgt_plot_meth_allele INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:25:45.089 wdl.w:ptcp.w:call-trgt-77.t:call-trgt_plot_meth_allele INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:45.093 wdl.w:ptcp.w:call-trgt-93.t:call-trgt_genotype.slurm_singularity INFO srun: job 51798070 queued and waiting for resources
2025-09-15 20:25:45.093 wdl.w:ptcp.w:call-trgt-93.t:call-trgt_genotype.slurm_singularity INFO srun: job 51798070 has been allocated resources
2025-09-15 20:25:45.093 wdl.w:ptcp.w:call-trgt-93.t:call-trgt_genotype.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:45.169 wdl.w:ptcp.w:call-trgt-77.t:call-trgt_plot_meth_allele INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-77/call-trgt_plot_meth_allele/_singularity_tmpdir___cf16hd"
2025-09-15 20:25:45.169 wdl.w:ptcp.w:call-trgt-77.t:call-trgt_plot_meth_allele INFO Slurm invocation: srun --job-name call-trgt_plot_meth_allele --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-77/call-trgt_plot_meth_allele/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-77/call-trgt_plot_meth_allele/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-77/call-trgt_plot_meth_allele/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-77/call-trgt_plot_meth_allele/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-77/call-trgt_genotype/out/m84036_250809_035451_s4.bc2174.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2174.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-77/call-trgt_genotype/out/m84036_250809_035451_s4.bc2174.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2174.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-77/call-trgt_genotype/out/m84036_250809_035451_s4.bc2174.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2174.trgt.vcf:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-77/call-trgt_plot_meth_allele/_singularity_tmpdir___cf16hd/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-77/call-trgt_plot_meth_allele/_singularity_tmpdir___cf16hd/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:45.193 wdl.w:ptcp.w:call-trgt-77.t:call-trgt_plot_meth_allele NOTICE slurm_singularity run :: pid: 1206265, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-77/call-trgt_plot_meth_allele/slurm_singularity.log.txt"
2025-09-15 20:25:45.207 wdl.w:ptcp.w:call-trgt-76.t:call-trgt_plot_motifs_allele NOTICE done
2025-09-15 20:25:45.213 wdl.w:ptcp.w:call-trgt-76 NOTICE finish :: job: "call-trgt_plot_motifs_allele"
2025-09-15 20:25:45.213 wdl.w:ptcp.w:call-trgt-76 INFO output :: job: "call-trgt_plot_motifs_allele", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-76/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2173.motifs_allele.trgt_plots.zip"}
2025-09-15 20:25:45.214 wdl.w:ptcp.w:call-trgt-76 INFO visit :: node: "output-images_motifs_allele", values: {"images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-76/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2173.motifs_allele.trgt_plots.zip"}
2025-09-15 20:25:45.235 wdl.w:ptcp.w:call-trgt-77.t:call-trgt_plot_meth_waterfall NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-77/call-trgt_plot_meth_waterfall", thread: 140607649453632
2025-09-15 20:25:45.252 wdl.w:ptcp.w:call-trgt-77.t:call-trgt_plot_meth_waterfall INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:45.252 wdl.w:ptcp.w:call-trgt-77.t:call-trgt_plot_meth_waterfall INFO input :: name: "waterfall", value: true
2025-09-15 20:25:45.252 wdl.w:ptcp.w:call-trgt-77.t:call-trgt_plot_meth_waterfall INFO input :: name: "methylation", value: true
2025-09-15 20:25:45.252 wdl.w:ptcp.w:call-trgt-77.t:call-trgt_plot_meth_waterfall INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:25:45.252 wdl.w:ptcp.w:call-trgt-77.t:call-trgt_plot_meth_waterfall INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:25:45.252 wdl.w:ptcp.w:call-trgt-77.t:call-trgt_plot_meth_waterfall INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:25:45.252 wdl.w:ptcp.w:call-trgt-77.t:call-trgt_plot_meth_waterfall INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2174.trgt.sorted.spanning.bam.bai"
2025-09-15 20:25:45.252 wdl.w:ptcp.w:call-trgt-77.t:call-trgt_plot_meth_waterfall INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2174.trgt.sorted.spanning.bam"
2025-09-15 20:25:45.252 wdl.w:ptcp.w:call-trgt-77.t:call-trgt_plot_meth_waterfall INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2174.trgt.vcf"
2025-09-15 20:25:45.252 wdl.w:ptcp.w:call-trgt-77.t:call-trgt_plot_meth_waterfall INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2174"
2025-09-15 20:25:45.253 wdl.w:ptcp.w:call-trgt-77.t:call-trgt_plot_meth_waterfall INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:25:45.253 wdl.w:ptcp.w:call-trgt-77.t:call-trgt_plot_meth_waterfall INFO eval :: name: "plot_type", value: "waterfall"
2025-09-15 20:25:45.253 wdl.w:ptcp.w:call-trgt-77.t:call-trgt_plot_meth_waterfall INFO eval :: name: "show", value: "meth"
2025-09-15 20:25:45.253 wdl.w:ptcp.w:call-trgt-77.t:call-trgt_plot_meth_waterfall INFO eval :: name: "threads", value: 1
2025-09-15 20:25:45.253 wdl.w:ptcp.w:call-trgt-77.t:call-trgt_plot_meth_waterfall INFO eval :: name: "disk_size", value: 27
2025-09-15 20:25:45.253 wdl.w:ptcp.w:call-trgt-77.t:call-trgt_plot_meth_waterfall INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2174.meth_waterfall"
2025-09-15 20:25:45.254 wdl.w:ptcp.w:call-trgt-77.t:call-trgt_plot_meth_waterfall INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:45.254 wdl.w:ptcp.w:call-trgt-77.t:call-trgt_plot_meth_waterfall WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:45.254 wdl.w:ptcp.w:call-trgt-77.t:call-trgt_plot_meth_waterfall INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:25:45.254 wdl.w:ptcp.w:call-trgt-77.t:call-trgt_plot_meth_waterfall INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:45.318 wdl.w:ptcp.w:call-paraphase-35.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for rpgr for sample m84036_250809_035451_s4.bc2132 at 2025-09-15 20:25:38.452271...
2025-09-15 20:25:45.318 wdl.w:ptcp.w:call-paraphase-35.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for rpgr for sample m84036_250809_035451_s4.bc2132 at 2025-09-15 20:25:38.452977...
2025-09-15 20:25:45.318 wdl.w:ptcp.w:call-paraphase-35.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for rpgr for sample m84036_250809_035451_s4.bc2132 at 2025-09-15 20:25:40.567241...
2025-09-15 20:25:45.318 wdl.w:ptcp.w:call-paraphase-35.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for rpgr for sample m84036_250809_035451_s4.bc2132 at 2025-09-15 20:25:41.698204...
2025-09-15 20:25:45.319 wdl.w:ptcp.w:call-paraphase-35.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for rpgr for sample m84036_250809_035451_s4.bc2132 at 2025-09-15 20:25:41.837533...
2025-09-15 20:25:45.321 wdl.w:ptcp.w:call-trgt-77.t:call-trgt_plot_meth_waterfall INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-77/call-trgt_plot_meth_waterfall/_singularity_tmpdir_idsfqpwx"
2025-09-15 20:25:45.321 wdl.w:ptcp.w:call-trgt-77.t:call-trgt_plot_meth_waterfall INFO Slurm invocation: srun --job-name call-trgt_plot_meth_waterfall --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-77/call-trgt_plot_meth_waterfall/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-77/call-trgt_plot_meth_waterfall/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-77/call-trgt_plot_meth_waterfall/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-77/call-trgt_plot_meth_waterfall/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-77/call-trgt_genotype/out/m84036_250809_035451_s4.bc2174.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2174.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-77/call-trgt_genotype/out/m84036_250809_035451_s4.bc2174.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2174.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-77/call-trgt_genotype/out/m84036_250809_035451_s4.bc2174.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2174.trgt.vcf:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-77/call-trgt_plot_meth_waterfall/_singularity_tmpdir_idsfqpwx/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-77/call-trgt_plot_meth_waterfall/_singularity_tmpdir_idsfqpwx/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:45.332 wdl.w:ptcp.w:call-trgt-77.t:call-trgt_plot_meth_waterfall NOTICE slurm_singularity run :: pid: 1206267, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-77/call-trgt_plot_meth_waterfall/slurm_singularity.log.txt"
2025-09-15 20:25:45.713 wdl.w:ptcp.w:call-trgt-73.t:call-trgt_plot_motifs_waterfall INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2170.motifs_waterfall.trgt_plots.zip"
2025-09-15 20:25:45.716 wdl.w:ptcp.w:call-trgt-84.t:call-trgt_plot_motifs_waterfall INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2181.motifs_waterfall.trgt_plots.zip"
2025-09-15 20:25:45.828 wdl.w:ptcp.w:call-paraphase-89.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for hbb for sample m84036_250809_035451_s4.bc2186 at 2025-09-15 20:25:43.110114...
2025-09-15 20:25:45.828 wdl.w:ptcp.w:call-paraphase-89.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for rpgr for sample m84036_250809_035451_s4.bc2186 at 2025-09-15 20:25:43.168338...
2025-09-15 20:25:45.828 wdl.w:ptcp.w:call-paraphase-89.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for f8inv22 for sample m84036_250809_035451_s4.bc2186 at 2025-09-15 20:25:43.207803...
2025-09-15 20:25:45.828 wdl.w:ptcp.w:call-paraphase-89.t:call-run_paraphase.stderr VERBOSE WARNING:root:This region does not appear to have coverage. Will not attempt to phase haplotypes.
2025-09-15 20:25:45.828 wdl.w:ptcp.w:call-paraphase-89.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for hbb for sample m84036_250809_035451_s4.bc2186 at 2025-09-15 20:25:43.228530...
2025-09-15 20:25:45.828 wdl.w:ptcp.w:call-paraphase-89.t:call-run_paraphase.stderr VERBOSE WARNING:root:This region does not appear to have coverage. Will not attempt to phase haplotypes.
2025-09-15 20:25:45.828 wdl.w:ptcp.w:call-paraphase-89.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for rpgr for sample m84036_250809_035451_s4.bc2186 at 2025-09-15 20:25:43.265811...
2025-09-15 20:25:45.828 wdl.w:ptcp.w:call-paraphase-89.t:call-run_paraphase.stderr VERBOSE WARNING:root:This region does not appear to have coverage. Will not attempt to phase haplotypes.
2025-09-15 20:25:45.828 wdl.w:ptcp.w:call-paraphase-89.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for f8inv22 for sample m84036_250809_035451_s4.bc2186 at 2025-09-15 20:25:43.291047...
2025-09-15 20:25:45.828 wdl.w:ptcp.w:call-paraphase-89.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for hbb for sample m84036_250809_035451_s4.bc2186 at 2025-09-15 20:25:43.680219...
2025-09-15 20:25:45.828 wdl.w:ptcp.w:call-paraphase-89.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for rpgr for sample m84036_250809_035451_s4.bc2186 at 2025-09-15 20:25:43.743745...
2025-09-15 20:25:45.829 wdl.w:ptcp.w:call-paraphase-89.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for f8inv22 for sample m84036_250809_035451_s4.bc2186 at 2025-09-15 20:25:43.787176...
2025-09-15 20:25:45.829 wdl.w:ptcp.w:call-paraphase-89.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for smn1 for sample m84036_250809_035451_s4.bc2186 at 2025-09-15 20:25:43.809704...
2025-09-15 20:25:45.829 wdl.w:ptcp.w:call-paraphase-89.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for f8inv1 for sample m84036_250809_035451_s4.bc2186 at 2025-09-15 20:25:43.897135...
2025-09-15 20:25:45.829 wdl.w:ptcp.w:call-paraphase-89.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for f8inv1 for sample m84036_250809_035451_s4.bc2186 at 2025-09-15 20:25:43.897479...
2025-09-15 20:25:45.829 wdl.w:ptcp.w:call-paraphase-89.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for f8inv1 for sample m84036_250809_035451_s4.bc2186 at 2025-09-15 20:25:44.421728...
2025-09-15 20:25:45.829 wdl.w:ptcp.w:call-paraphase-89.t:call-run_paraphase.stderr VERBOSE WARNING:root:This region does not appear to have coverage. Will not attempt to phase haplotypes.
2025-09-15 20:25:45.829 wdl.w:ptcp.w:call-paraphase-89.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for f8inv1 for sample m84036_250809_035451_s4.bc2186 at 2025-09-15 20:25:44.451367...
2025-09-15 20:25:45.829 wdl.w:ptcp.w:call-paraphase-89.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for f8inv1 for sample m84036_250809_035451_s4.bc2186 at 2025-09-15 20:25:44.653565...
2025-09-15 20:25:45.852 wdl.w:ptcp.w:call-trgt-84.t:call-trgt_plot_motifs_waterfall NOTICE done
2025-09-15 20:25:45.860 wdl.w:ptcp.w:call-trgt-84 NOTICE finish :: job: "call-trgt_plot_motifs_waterfall"
2025-09-15 20:25:45.860 wdl.w:ptcp.w:call-trgt-84 INFO output :: job: "call-trgt_plot_motifs_waterfall", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-84/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2181.motifs_waterfall.trgt_plots.zip"}
2025-09-15 20:25:45.860 wdl.w:ptcp.w:call-trgt-84 INFO visit :: node: "output-images_motifs_waterfall", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-84/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2181.motifs_waterfall.trgt_plots.zip"}
2025-09-15 20:25:45.868 wdl.w:ptcp.w:call-trgt-77.t:call-trgt_plot_motifs_allele NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-77/call-trgt_plot_motifs_allele", thread: 140607674631744
2025-09-15 20:25:45.877 wdl.w:ptcp.w:call-trgt-73.t:call-trgt_plot_motifs_waterfall NOTICE done
2025-09-15 20:25:45.895 wdl.w:ptcp.w:call-trgt-73 NOTICE finish :: job: "call-trgt_plot_motifs_waterfall"
2025-09-15 20:25:45.895 wdl.w:ptcp.w:call-trgt-73 INFO output :: job: "call-trgt_plot_motifs_waterfall", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-73/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2170.motifs_waterfall.trgt_plots.zip"}
2025-09-15 20:25:45.895 wdl.w:ptcp.w:call-trgt-73 INFO visit :: node: "output-images_motifs_waterfall", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-73/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2170.motifs_waterfall.trgt_plots.zip"}
2025-09-15 20:25:45.901 wdl.w:ptcp.w:call-trgt-77.t:call-trgt_plot_motifs_allele INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:45.901 wdl.w:ptcp.w:call-trgt-77.t:call-trgt_plot_motifs_allele INFO input :: name: "waterfall", value: false
2025-09-15 20:25:45.901 wdl.w:ptcp.w:call-trgt-77.t:call-trgt_plot_motifs_allele INFO input :: name: "methylation", value: false
2025-09-15 20:25:45.901 wdl.w:ptcp.w:call-trgt-77.t:call-trgt_plot_motifs_allele INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:25:45.901 wdl.w:ptcp.w:call-trgt-77.t:call-trgt_plot_motifs_allele INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:25:45.901 wdl.w:ptcp.w:call-trgt-77.t:call-trgt_plot_motifs_allele INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:25:45.901 wdl.w:ptcp.w:call-trgt-77.t:call-trgt_plot_motifs_allele INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2174.trgt.sorted.spanning.bam.bai"
2025-09-15 20:25:45.901 wdl.w:ptcp.w:call-trgt-77.t:call-trgt_plot_motifs_allele INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2174.trgt.sorted.spanning.bam"
2025-09-15 20:25:45.901 wdl.w:ptcp.w:call-trgt-77.t:call-trgt_plot_motifs_allele INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2174.trgt.vcf"
2025-09-15 20:25:45.902 wdl.w:ptcp.w:call-trgt-77.t:call-trgt_plot_motifs_allele INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2174"
2025-09-15 20:25:45.902 wdl.w:ptcp.w:call-trgt-77.t:call-trgt_plot_motifs_allele INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:25:45.902 wdl.w:ptcp.w:call-trgt-77.t:call-trgt_plot_motifs_allele INFO eval :: name: "plot_type", value: "allele"
2025-09-15 20:25:45.902 wdl.w:ptcp.w:call-trgt-77.t:call-trgt_plot_motifs_allele INFO eval :: name: "show", value: "motifs"
2025-09-15 20:25:45.902 wdl.w:ptcp.w:call-trgt-77.t:call-trgt_plot_motifs_allele INFO eval :: name: "threads", value: 1
2025-09-15 20:25:45.902 wdl.w:ptcp.w:call-trgt-77.t:call-trgt_plot_motifs_allele INFO eval :: name: "disk_size", value: 27
2025-09-15 20:25:45.902 wdl.w:ptcp.w:call-trgt-77.t:call-trgt_plot_motifs_allele INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2174.motifs_allele"
2025-09-15 20:25:45.903 wdl.w:ptcp.w:call-trgt-77.t:call-trgt_plot_motifs_allele INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:45.903 wdl.w:ptcp.w:call-trgt-77.t:call-trgt_plot_motifs_allele WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:45.903 wdl.w:ptcp.w:call-trgt-77.t:call-trgt_plot_motifs_allele INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:25:45.903 wdl.w:ptcp.w:call-trgt-77.t:call-trgt_plot_motifs_allele INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:45.912 wdl.w:ptcp.w:call-trgt-73.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:25:43 [ERROR] - No reads found for TRID=PRTS_ARX
2025-09-15 20:25:45.912 wdl.w:ptcp.w:call-trgt-73.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:25:43 [ERROR] - No reads found for TRID=EIEE1_ARX
2025-09-15 20:25:45.914 wdl.w:ptcp.w:call-trgt-77.t:call-trgt_plot_motifs_waterfall NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-77/call-trgt_plot_motifs_waterfall", thread: 140606575711808
2025-09-15 20:25:45.924 wdl.w:ptcp.w:call-trgt-84.t:call-trgt_plot_meth_waterfall INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2181.meth_waterfall.trgt_plots.zip"
2025-09-15 20:25:45.939 wdl.w:ptcp.w:call-trgt-77.t:call-trgt_plot_motifs_waterfall INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:45.939 wdl.w:ptcp.w:call-trgt-77.t:call-trgt_plot_motifs_waterfall INFO input :: name: "waterfall", value: true
2025-09-15 20:25:45.939 wdl.w:ptcp.w:call-trgt-77.t:call-trgt_plot_motifs_waterfall INFO input :: name: "methylation", value: false
2025-09-15 20:25:45.939 wdl.w:ptcp.w:call-trgt-77.t:call-trgt_plot_motifs_waterfall INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:25:45.939 wdl.w:ptcp.w:call-trgt-77.t:call-trgt_plot_motifs_waterfall INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:25:45.939 wdl.w:ptcp.w:call-trgt-77.t:call-trgt_plot_motifs_waterfall INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:25:45.939 wdl.w:ptcp.w:call-trgt-77.t:call-trgt_plot_motifs_waterfall INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2174.trgt.sorted.spanning.bam.bai"
2025-09-15 20:25:45.939 wdl.w:ptcp.w:call-trgt-77.t:call-trgt_plot_motifs_waterfall INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2174.trgt.sorted.spanning.bam"
2025-09-15 20:25:45.939 wdl.w:ptcp.w:call-trgt-77.t:call-trgt_plot_motifs_waterfall INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2174.trgt.vcf"
2025-09-15 20:25:45.940 wdl.w:ptcp.w:call-trgt-77.t:call-trgt_plot_motifs_waterfall INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2174"
2025-09-15 20:25:45.940 wdl.w:ptcp.w:call-trgt-77.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:25:45.940 wdl.w:ptcp.w:call-trgt-77.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "plot_type", value: "waterfall"
2025-09-15 20:25:45.940 wdl.w:ptcp.w:call-trgt-77.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "show", value: "motifs"
2025-09-15 20:25:45.940 wdl.w:ptcp.w:call-trgt-77.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "threads", value: 1
2025-09-15 20:25:45.940 wdl.w:ptcp.w:call-trgt-77.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "disk_size", value: 27
2025-09-15 20:25:45.941 wdl.w:ptcp.w:call-trgt-77.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2174.motifs_waterfall"
2025-09-15 20:25:45.941 wdl.w:ptcp.w:call-trgt-77.t:call-trgt_plot_motifs_waterfall INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:45.941 wdl.w:ptcp.w:call-trgt-77.t:call-trgt_plot_motifs_waterfall WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:45.941 wdl.w:ptcp.w:call-trgt-77.t:call-trgt_plot_motifs_waterfall INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:25:45.942 wdl.w:ptcp.w:call-trgt-77.t:call-trgt_plot_motifs_waterfall INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:45.982 wdl.w:ptcp.w:call-trgt-75.t:call-trgt_plot_meth_waterfall INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2172.meth_waterfall.trgt_plots.zip"
2025-09-15 20:25:45.996 wdl.w:ptcp.w:call-trgt-77.t:call-trgt_plot_motifs_allele INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-77/call-trgt_plot_motifs_allele/_singularity_tmpdir_2507w0a7"
2025-09-15 20:25:45.997 wdl.w:ptcp.w:call-trgt-77.t:call-trgt_plot_motifs_allele INFO Slurm invocation: srun --job-name call-trgt_plot_motifs_allele --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-77/call-trgt_plot_motifs_allele/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-77/call-trgt_plot_motifs_allele/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-77/call-trgt_plot_motifs_allele/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-77/call-trgt_plot_motifs_allele/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-77/call-trgt_genotype/out/m84036_250809_035451_s4.bc2174.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2174.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-77/call-trgt_genotype/out/m84036_250809_035451_s4.bc2174.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2174.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-77/call-trgt_genotype/out/m84036_250809_035451_s4.bc2174.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2174.trgt.vcf:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-77/call-trgt_plot_motifs_allele/_singularity_tmpdir_2507w0a7/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-77/call-trgt_plot_motifs_allele/_singularity_tmpdir_2507w0a7/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:46.020 wdl.w:ptcp.w:call-trgt-77.t:call-trgt_plot_motifs_allele NOTICE slurm_singularity run :: pid: 1206283, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-77/call-trgt_plot_motifs_allele/slurm_singularity.log.txt"
2025-09-15 20:25:46.032 wdl.w:ptcp.w:call-trgt-77.t:call-trgt_plot_motifs_waterfall INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-77/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_i5hmsgf0"
2025-09-15 20:25:46.032 wdl.w:ptcp.w:call-trgt-77.t:call-trgt_plot_motifs_waterfall INFO Slurm invocation: srun --job-name call-trgt_plot_motifs_waterfall --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-77/call-trgt_plot_motifs_waterfall/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-77/call-trgt_plot_motifs_waterfall/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-77/call-trgt_plot_motifs_waterfall/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-77/call-trgt_plot_motifs_waterfall/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-77/call-trgt_genotype/out/m84036_250809_035451_s4.bc2174.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2174.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-77/call-trgt_genotype/out/m84036_250809_035451_s4.bc2174.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2174.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-77/call-trgt_genotype/out/m84036_250809_035451_s4.bc2174.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2174.trgt.vcf:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-77/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_i5hmsgf0/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-77/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_i5hmsgf0/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:46.041 wdl.w:ptcp.w:call-trgt-77.t:call-trgt_plot_motifs_waterfall NOTICE slurm_singularity run :: pid: 1206285, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-77/call-trgt_plot_motifs_waterfall/slurm_singularity.log.txt"
2025-09-15 20:25:46.060 wdl.w:ptcp.w:call-trgt-75.t:call-trgt_plot_meth_waterfall NOTICE done
2025-09-15 20:25:46.067 wdl.w:ptcp.w:call-trgt-75 NOTICE finish :: job: "call-trgt_plot_meth_waterfall"
2025-09-15 20:25:46.068 wdl.w:ptcp.w:call-trgt-75 INFO output :: job: "call-trgt_plot_meth_waterfall", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-75/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2172.meth_waterfall.trgt_plots.zip"}
2025-09-15 20:25:46.068 wdl.w:ptcp.w:call-trgt-75 INFO visit :: node: "output-images_meth_waterfall", values: {"images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-75/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2172.meth_waterfall.trgt_plots.zip"}
2025-09-15 20:25:46.071 wdl.w:ptcp.w:call-trgt-84.t:call-trgt_plot_meth_waterfall NOTICE done
2025-09-15 20:25:46.073 wdl.w:ptcp.w:call-paraphase-95.t:call-run_paraphase NOTICE task setup :: name: "run_paraphase", source: "./paraphase.wdl", line: 127, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-95/call-run_paraphase", thread: 140607691417152
2025-09-15 20:25:46.076 wdl.w:ptcp.w:call-trgt-84 NOTICE finish :: job: "call-trgt_plot_meth_waterfall"
2025-09-15 20:25:46.077 wdl.w:ptcp.w:call-trgt-84 INFO output :: job: "call-trgt_plot_meth_waterfall", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-84/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2181.meth_waterfall.trgt_plots.zip"}
2025-09-15 20:25:46.077 wdl.w:ptcp.w:call-trgt-84 INFO visit :: node: "output-images_meth_waterfall", values: {"images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-84/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2181.meth_waterfall.trgt_plots.zip"}
2025-09-15 20:25:46.077 wdl.w:ptcp.w:call-trgt-84 INFO visit :: node: "outputs", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-84/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2181.motifs_waterfall.trgt_plots.zip", "images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-84/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2181.meth_allele.trgt_plots.zip", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-84/call-trgt_genotype/out/m84036_250809_035451_s4.bc2181.trgt.sorted.spanning.bam.bai", "images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-84/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2181.motifs_allele.trgt_plots.zip", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-84/call-trgt_genotype/out/m84036_250809_035451_s4.bc2181.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-84/call-trgt_genotype/out/m84036_250809_035451_s4.bc2181.trgt.vcf", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-84/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2181.repeats.bam", "images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-84/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2181.meth_waterfall.trgt_plots.zip", "reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-84/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2181.repeats.bam.bai"}
2025-09-15 20:25:46.083 wdl.w:ptcp.w:call-sawfish-95.t:call-run_sawfish NOTICE task setup :: name: "run_sawfish", source: "./sawfish.wdl", line: 83, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-95/call-run_sawfish", thread: 140607137760832
2025-09-15 20:25:46.091 wdl.w:ptcp.w:call-paraphase-95.t:call-run_paraphase INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:46.091 wdl.w:ptcp.w:call-paraphase-95.t:call-run_paraphase INFO input :: name: "annotation_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf"
2025-09-15 20:25:46.091 wdl.w:ptcp.w:call-paraphase-95.t:call-run_paraphase INFO input :: name: "genome_version", value: "38"
2025-09-15 20:25:46.091 wdl.w:ptcp.w:call-paraphase-95.t:call-run_paraphase INFO input :: name: "config_file", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/paraphase_config.GRCh38.yaml"
2025-09-15 20:25:46.091 wdl.w:ptcp.w:call-paraphase-95.t:call-run_paraphase INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:25:46.091 wdl.w:ptcp.w:call-paraphase-95.t:call-run_paraphase INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:25:46.091 wdl.w:ptcp.w:call-paraphase-95.t:call-run_paraphase INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2192.mapped.bam.bai"
2025-09-15 20:25:46.091 wdl.w:ptcp.w:call-paraphase-95.t:call-run_paraphase INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2192.mapped.bam"
2025-09-15 20:25:46.092 wdl.w:ptcp.w:call-paraphase-95.t:call-run_paraphase INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2192"
2025-09-15 20:25:46.093 wdl.w:ptcp.w:call-paraphase-95.t:call-run_paraphase INFO eval :: name: "threads", value: 4
2025-09-15 20:25:46.093 wdl.w:ptcp.w:call-paraphase-95.t:call-run_paraphase INFO eval :: name: "mem_gb", value: 8
2025-09-15 20:25:46.094 wdl.w:ptcp.w:call-paraphase-95.t:call-run_paraphase INFO eval :: name: "disk_size", value: 27
2025-09-15 20:25:46.094 wdl.w:ptcp.w:call-paraphase-95.t:call-run_paraphase INFO eval :: name: "out_dir", value: "m84036_250809_035451_s4.bc2192_paraphase"
2025-09-15 20:25:46.094 wdl.w:ptcp.w:call-paraphase-95.t:call-run_paraphase INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 4, memory_reservation: 8000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:46.094 wdl.w:ptcp.w:call-paraphase-95.t:call-run_paraphase WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:46.095 wdl.w:ptcp.w:call-paraphase-95.t:call-run_paraphase INFO provisioned :: seconds_waited: 0, cpu: 4, mem_bytes: 8000000000
2025-09-15 20:25:46.095 wdl.w:ptcp.w:call-paraphase-95.t:call-run_paraphase INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:46.108 wdl.w:ptcp.w:call-sawfish-95.t:call-run_sawfish INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:46.108 wdl.w:ptcp.w:call-sawfish-95.t:call-run_sawfish INFO input :: name: "genome_version", value: "38"
2025-09-15 20:25:46.108 wdl.w:ptcp.w:call-sawfish-95.t:call-run_sawfish INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:25:46.108 wdl.w:ptcp.w:call-sawfish-95.t:call-run_sawfish INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:25:46.108 wdl.w:ptcp.w:call-sawfish-95.t:call-run_sawfish INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2192.mapped.bam.bai"
2025-09-15 20:25:46.108 wdl.w:ptcp.w:call-sawfish-95.t:call-run_sawfish INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2192.mapped.bam"
2025-09-15 20:25:46.108 wdl.w:ptcp.w:call-sawfish-95.t:call-run_sawfish INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2192"
2025-09-15 20:25:46.109 wdl.w:ptcp.w:call-sawfish-95.t:call-run_sawfish INFO eval :: name: "mem_gb", value: 32
2025-09-15 20:25:46.109 wdl.w:ptcp.w:call-sawfish-95.t:call-run_sawfish INFO eval :: name: "threads", value: 16
2025-09-15 20:25:46.109 wdl.w:ptcp.w:call-sawfish-95.t:call-run_sawfish INFO eval :: name: "disk_size", value: 30
2025-09-15 20:25:46.109 wdl.w:ptcp.w:call-sawfish-95.t:call-run_sawfish INFO eval :: name: "discover_dirname", value: "m84036_250809_035451_s4.bc2192_sawfish_discover"
2025-09-15 20:25:46.109 wdl.w:ptcp.w:call-sawfish-95.t:call-run_sawfish INFO eval :: name: "call_dirname", value: "m84036_250809_035451_s4.bc2192_sawfish"
2025-09-15 20:25:46.109 wdl.w:ptcp.w:call-sawfish-95.t:call-run_sawfish INFO eval :: name: "minimap2_bam_filename", value: "m84036_250809_035451_s4.bc2192.minimap2.bam"
2025-09-15 20:25:46.110 wdl.w:ptcp.w:call-sawfish-95.t:call-run_sawfish INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 16, memory_reservation: 32000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:46.110 wdl.w:ptcp.w:call-sawfish-95.t:call-run_sawfish WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:46.110 wdl.w:ptcp.w:call-sawfish-95.t:call-run_sawfish INFO provisioned :: seconds_waited: 0, cpu: 16, mem_bytes: 32000000000
2025-09-15 20:25:46.110 wdl.w:ptcp.w:call-sawfish-95.t:call-run_sawfish INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:46.147 wdl.w:ptcp.w:call-trgt-75.t:call-trgt_plot_meth_allele INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2172.meth_allele.trgt_plots.zip"
2025-09-15 20:25:46.177 wdl.w:ptcp.w:call-trgt-84 NOTICE done
2025-09-15 20:25:46.178 wdl.w:ptcp.w:call-paraphase-95.t:call-run_paraphase INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-95/call-run_paraphase/_singularity_tmpdir_owv6acha"
2025-09-15 20:25:46.178 wdl.w:ptcp.w:call-paraphase-95.t:call-run_paraphase INFO Slurm invocation: srun --job-name call-run_paraphase --partition compute,compute9 --cpus-per-task 4 --mem 7629M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-95/call-run_paraphase/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-95/call-run_paraphase/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-95/call-run_paraphase/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-95/call-run_paraphase/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-95/out/m84036_250809_035451_s4.bc2192.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2192.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-95/out/m84036_250809_035451_s4.bc2192.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2192.mapped.bam.bai:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/variant_list/variant_list.GRCh38.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf:ro --bind /ptcp/meta/paraphase/paraphase_config.GRCh38.yaml:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/paraphase_config.GRCh38.yaml:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-95/call-run_paraphase/_singularity_tmpdir_owv6acha/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-95/call-run_paraphase/_singularity_tmpdir_owv6acha/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:46.182 wdl.w:ptcp NOTICE finish :: job: "call-trgt-84"
2025-09-15 20:25:46.182 wdl.w:ptcp INFO output :: job: "call-trgt-84", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-84/out/m84036_250809_035451_s4.bc2181.motifs_waterfall.trgt_plots.zip", "images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-84/out/m84036_250809_035451_s4.bc2181.meth_allele.trgt_plots.zip", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-84/out/m84036_250809_035451_s4.bc2181.trgt.sorted.spanning.bam.bai", "images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-84/out/m84036_250809_035451_s4.bc2181.motifs_allele.trgt_plots.zip", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-84/out/m84036_250809_035451_s4.bc2181.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-84/out/m84036_250809_035451_s4.bc2181.trgt.vcf", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-84/out/m84036_250809_035451_s4.bc2181.repeats.bam", "images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-84/out/m84036_250809_035451_s4.bc2181.meth_waterfall.trgt_plots.zip", "reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-84/out/m84036_250809_035451_s4.bc2181.repeats.bam.bai"}
2025-09-15 20:25:46.186 wdl.w:ptcp.w:call-sawfish-95.t:call-run_sawfish INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 10, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-95/call-run_sawfish/_singularity_tmpdir_mx24zy_c"
2025-09-15 20:25:46.186 wdl.w:ptcp.w:call-sawfish-95.t:call-run_sawfish INFO Slurm invocation: srun --job-name call-run_sawfish --partition compute,compute9 --cpus-per-task 16 --mem 30518M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-95/call-run_sawfish/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-95/call-run_sawfish/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-95/call-run_sawfish/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-95/call-run_sawfish/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-95/out/m84036_250809_035451_s4.bc2192.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2192.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-95/out/m84036_250809_035451_s4.bc2192.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2192.mapped.bam:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-95/call-run_sawfish/_singularity_tmpdir_mx24zy_c/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-95/call-run_sawfish/_singularity_tmpdir_mx24zy_c/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:46.198 wdl.w:ptcp.w:call-paraphase-95.t:call-run_paraphase NOTICE slurm_singularity run :: pid: 1206298, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-95/call-run_paraphase/slurm_singularity.log.txt"
2025-09-15 20:25:46.198 wdl.w:ptcp.w:call-sawfish-95.t:call-run_sawfish NOTICE slurm_singularity run :: pid: 1206299, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-95/call-run_sawfish/slurm_singularity.log.txt"
2025-09-15 20:25:46.204 wdl.w:ptcp.w:call-trgt-77.t:call-trgt_plot_meth_allele.slurm_singularity INFO srun: job 51798071 queued and waiting for resources
2025-09-15 20:25:46.204 wdl.w:ptcp.w:call-trgt-77.t:call-trgt_plot_meth_allele.slurm_singularity INFO srun: job 51798071 has been allocated resources
2025-09-15 20:25:46.204 wdl.w:ptcp.w:call-trgt-77.t:call-trgt_plot_meth_allele.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:46.230 wdl.w:ptcp.w:call-trgt-75.t:call-trgt_plot_meth_allele NOTICE done
2025-09-15 20:25:46.236 wdl.w:ptcp.w:call-trgt-75 NOTICE finish :: job: "call-trgt_plot_meth_allele"
2025-09-15 20:25:46.236 wdl.w:ptcp.w:call-trgt-75 INFO output :: job: "call-trgt_plot_meth_allele", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-75/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2172.meth_allele.trgt_plots.zip"}
2025-09-15 20:25:46.236 wdl.w:ptcp.w:call-trgt-75 INFO visit :: node: "output-images_meth_allele", values: {"images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-75/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2172.meth_allele.trgt_plots.zip"}
2025-09-15 20:25:46.247 wdl.w:ptcp.w:call-paraphase-77.t:call-call_f8 NOTICE task setup :: name: "call_f8", source: "./paraphase.wdl", line: 232, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-77/call-call_f8", thread: 140608211502656
2025-09-15 20:25:46.273 wdl.w:ptcp.w:call-paraphase-77.t:call-call_f8 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:46.273 wdl.w:ptcp.w:call-paraphase-77.t:call-call_f8 INFO input :: name: "genome_version", value: "38"
2025-09-15 20:25:46.273 wdl.w:ptcp.w:call-paraphase-77.t:call-call_f8 INFO input :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2174"
2025-09-15 20:25:46.273 wdl.w:ptcp.w:call-paraphase-77.t:call-call_f8 INFO input :: name: "paraphase_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2174.paraphase.bam.bai"
2025-09-15 20:25:46.273 wdl.w:ptcp.w:call-paraphase-77.t:call-call_f8 INFO input :: name: "paraphase_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2174.paraphase.bam"
2025-09-15 20:25:46.274 wdl.w:ptcp.w:call-paraphase-77.t:call-call_f8 INFO input :: name: "sex", value: "F"
2025-09-15 20:25:46.274 wdl.w:ptcp.w:call-paraphase-77.t:call-call_f8 INFO eval :: name: "threads", value: 1
2025-09-15 20:25:46.274 wdl.w:ptcp.w:call-paraphase-77.t:call-call_f8 INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:25:46.274 wdl.w:ptcp.w:call-paraphase-77.t:call-call_f8 INFO eval :: name: "disk_size", value: 11
2025-09-15 20:25:46.274 wdl.w:ptcp.w:call-paraphase-77.t:call-call_f8 INFO eval :: name: "sample_sex", value: "F"
2025-09-15 20:25:46.275 wdl.w:ptcp.w:call-paraphase-77.t:call-call_f8 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:46.275 wdl.w:ptcp.w:call-paraphase-77.t:call-call_f8 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:46.275 wdl.w:ptcp.w:call-paraphase-77.t:call-call_f8 INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:25:46.275 wdl.w:ptcp.w:call-paraphase-77.t:call-call_f8 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:46.314 wdl.w:ptcp.w:call-paraphase-77.t:call-call_f8 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 8, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-77/call-call_f8/_singularity_tmpdir_5ybkprkr"
2025-09-15 20:25:46.314 wdl.w:ptcp.w:call-paraphase-77.t:call-call_f8 INFO Slurm invocation: srun --job-name call-call_f8 --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-77/call-call_f8/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-77/call-call_f8/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-77/call-call_f8/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-77/call-call_f8/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-77/call-run_paraphase/out/m84036_250809_035451_s4.bc2174_paraphase/m84036_250809_035451_s4.bc2174.paraphase.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2174.paraphase.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-77/call-run_paraphase/out/m84036_250809_035451_s4.bc2174_paraphase/m84036_250809_035451_s4.bc2174.paraphase.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2174.paraphase.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-77/call-call_f8/_singularity_tmpdir_5ybkprkr/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-77/call-call_f8/_singularity_tmpdir_5ybkprkr/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:46.330 wdl.w:ptcp.w:call-paraphase-77.t:call-call_f8 NOTICE slurm_singularity run :: pid: 1206302, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-77/call-call_f8/slurm_singularity.log.txt"
2025-09-15 20:25:46.341 wdl.w:ptcp.w:call-trgt-77.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO srun: job 51798072 queued and waiting for resources
2025-09-15 20:25:46.341 wdl.w:ptcp.w:call-trgt-77.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO srun: job 51798072 has been allocated resources
2025-09-15 20:25:46.341 wdl.w:ptcp.w:call-trgt-77.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:46.440 wdl.w:ptcp.w:call-paraphase-79.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for hbb for sample m84036_250809_035451_s4.bc2176 at 2025-09-15 20:25:37.014058...
2025-09-15 20:25:46.440 wdl.w:ptcp.w:call-paraphase-79.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for gba for sample m84036_250809_035451_s4.bc2176 at 2025-09-15 20:25:37.642895...
2025-09-15 20:25:46.440 wdl.w:ptcp.w:call-paraphase-79.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for gba for sample m84036_250809_035451_s4.bc2176 at 2025-09-15 20:25:37.903516...
2025-09-15 20:25:46.440 wdl.w:ptcp.w:call-paraphase-79.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for hbb for sample m84036_250809_035451_s4.bc2176 at 2025-09-15 20:25:40.521629...
2025-09-15 20:25:46.440 wdl.w:ptcp.w:call-paraphase-79.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for hbb for sample m84036_250809_035451_s4.bc2176 at 2025-09-15 20:25:40.758648...
2025-09-15 20:25:46.697 wdl.w:ptcp.w:call-sawfish-65.t:call-run_sawfish.stderr VERBOSE [M::mm_idx_gen::33.713*1.45] collected minimizers
2025-09-15 20:25:46.698 wdl.w:ptcp.w:call-sawfish-65.t:call-run_sawfish.stderr VERBOSE [M::mm_idx_gen::40.618*1.71] sorted minimizers
2025-09-15 20:25:46.698 wdl.w:ptcp.w:call-sawfish-65.t:call-run_sawfish.stderr VERBOSE [M::main::40.618*1.71] loaded/built the index for 195 target sequence(s)
2025-09-15 20:25:46.698 wdl.w:ptcp.w:call-sawfish-65.t:call-run_sawfish.stderr VERBOSE [M::mm_mapopt_update::43.693*1.66] mid_occ = 136
2025-09-15 20:25:46.698 wdl.w:ptcp.w:call-sawfish-65.t:call-run_sawfish.stderr VERBOSE [M::mm_idx_stat] kmer size: 19; skip: 19; is_hpc: 0; #seq: 195
2025-09-15 20:25:46.698 wdl.w:ptcp.w:call-sawfish-65.t:call-run_sawfish.stderr VERBOSE [M::mm_idx_stat::46.372*1.62] distinct minimizers: 214664461 (92.23% are singletons); average occurrences: 1.372; average spacing: 10.529; total length: 3099922541
2025-09-15 20:25:46.699 wdl.w:ptcp.w:call-sawfish-65.t:call-run_sawfish.stderr VERBOSE [M::main] Version: 2.26-r1175
2025-09-15 20:25:46.699 wdl.w:ptcp.w:call-sawfish-65.t:call-run_sawfish.stderr VERBOSE [M::main] CMD: /opt/pacbio/smrttools/install/smrtlink-release_25.1.0.257715/bundles/smrttools/install/smrttools-release_25.1.0.257715/private/thirdparty/minimap2/minimap2_2.26-pacbio2/binwrap/../../../../../private/thirdparty/minimap2/minimap2_2.26-pacbio2/bin/minimap2 -a -y -x map-hifi -Y -E 1,0 /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa -
2025-09-15 20:25:46.699 wdl.w:ptcp.w:call-sawfish-65.t:call-run_sawfish.stderr VERBOSE [M::main] Real time: 46.700 sec; CPU: 75.298 sec; Peak RSS: 11.885 GB
2025-09-15 20:25:46.753 wdl.w:ptcp.w:call-trgt-75.t:call-trgt_plot_motifs_waterfall INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2172.motifs_waterfall.trgt_plots.zip"
2025-09-15 20:25:46.800 wdl.w:ptcp.w:call-trgt-75.t:call-trgt_plot_motifs_allele INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2172.motifs_allele.trgt_plots.zip"
2025-09-15 20:25:46.825 wdl.w:ptcp.w:call-trgt-75.t:call-trgt_plot_motifs_waterfall NOTICE done
2025-09-15 20:25:46.831 wdl.w:ptcp.w:call-trgt-75 NOTICE finish :: job: "call-trgt_plot_motifs_waterfall"
2025-09-15 20:25:46.831 wdl.w:ptcp.w:call-trgt-75 INFO output :: job: "call-trgt_plot_motifs_waterfall", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-75/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2172.motifs_waterfall.trgt_plots.zip"}
2025-09-15 20:25:46.831 wdl.w:ptcp.w:call-trgt-75 INFO visit :: node: "output-images_motifs_waterfall", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-75/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2172.motifs_waterfall.trgt_plots.zip"}
2025-09-15 20:25:46.838 wdl.w:ptcp.w:call-trgt-95.t:call-get_reads_overlapping_repeats NOTICE task setup :: name: "get_reads_overlapping_repeats", source: "./trgt.wdl", line: 182, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-95/call-get_reads_overlapping_repeats", thread: 140613034948160
2025-09-15 20:25:46.869 wdl.w:ptcp.w:call-trgt-95.t:call-get_reads_overlapping_repeats INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:46.870 wdl.w:ptcp.w:call-trgt-95.t:call-get_reads_overlapping_repeats INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:25:46.870 wdl.w:ptcp.w:call-trgt-95.t:call-get_reads_overlapping_repeats INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2192.mapped.bam.bai"
2025-09-15 20:25:46.870 wdl.w:ptcp.w:call-trgt-95.t:call-get_reads_overlapping_repeats INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2192.mapped.bam"
2025-09-15 20:25:46.870 wdl.w:ptcp.w:call-trgt-95.t:call-get_reads_overlapping_repeats INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2192"
2025-09-15 20:25:46.870 wdl.w:ptcp.w:call-trgt-95.t:call-get_reads_overlapping_repeats INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:25:46.870 wdl.w:ptcp.w:call-trgt-95.t:call-get_reads_overlapping_repeats INFO eval :: name: "expand_size", value: 3000
2025-09-15 20:25:46.870 wdl.w:ptcp.w:call-trgt-95.t:call-get_reads_overlapping_repeats INFO eval :: name: "threads", value: 1
2025-09-15 20:25:46.870 wdl.w:ptcp.w:call-trgt-95.t:call-get_reads_overlapping_repeats INFO eval :: name: "expanded_bed_name", value: "m84036_250809_035451_s4.bc2192.expanded.bed"
2025-09-15 20:25:46.871 wdl.w:ptcp.w:call-trgt-95.t:call-get_reads_overlapping_repeats INFO eval :: name: "disk_size", value: 11
2025-09-15 20:25:46.871 wdl.w:ptcp.w:call-trgt-95.t:call-get_reads_overlapping_repeats INFO eval :: name: "output_name", value: "m84036_250809_035451_s4.bc2192.repeats.bam"
2025-09-15 20:25:46.871 wdl.w:ptcp.w:call-trgt-95.t:call-get_reads_overlapping_repeats INFO eval :: name: "index_name", value: "m84036_250809_035451_s4.bc2192.repeats.bam.bai"
2025-09-15 20:25:46.871 wdl.w:ptcp.w:call-trgt-95.t:call-get_reads_overlapping_repeats INFO eval :: name: "output_name_with_index", value: "m84036_250809_035451_s4.bc2192.repeats.bam##idx##m84036_250809_035451_s4.bc2192.repeats.bam.bai"
2025-09-15 20:25:46.871 wdl.w:ptcp.w:call-trgt-95.t:call-get_reads_overlapping_repeats INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:46.871 wdl.w:ptcp.w:call-trgt-95.t:call-get_reads_overlapping_repeats WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:46.872 wdl.w:ptcp.w:call-trgt-95.t:call-get_reads_overlapping_repeats INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:25:46.872 wdl.w:ptcp.w:call-trgt-95.t:call-get_reads_overlapping_repeats INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:46.874 wdl.w:ptcp.w:call-trgt-75.t:call-trgt_plot_motifs_allele NOTICE done
2025-09-15 20:25:46.880 wdl.w:ptcp.w:call-trgt-75 NOTICE finish :: job: "call-trgt_plot_motifs_allele"
2025-09-15 20:25:46.880 wdl.w:ptcp.w:call-trgt-75 INFO output :: job: "call-trgt_plot_motifs_allele", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-75/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2172.motifs_allele.trgt_plots.zip"}
2025-09-15 20:25:46.880 wdl.w:ptcp.w:call-trgt-75 INFO visit :: node: "output-images_motifs_allele", values: {"images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-75/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2172.motifs_allele.trgt_plots.zip"}
2025-09-15 20:25:46.880 wdl.w:ptcp.w:call-trgt-75 INFO visit :: node: "outputs", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-75/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2172.motifs_waterfall.trgt_plots.zip", "images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-75/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2172.meth_allele.trgt_plots.zip", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-75/call-trgt_genotype/out/m84036_250809_035451_s4.bc2172.trgt.sorted.spanning.bam.bai", "images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-75/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2172.motifs_allele.trgt_plots.zip", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-75/call-trgt_genotype/out/m84036_250809_035451_s4.bc2172.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-75/call-trgt_genotype/out/m84036_250809_035451_s4.bc2172.trgt.vcf", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-75/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2172.repeats.bam", "images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-75/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2172.meth_waterfall.trgt_plots.zip", "reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-75/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2172.repeats.bam.bai"}
2025-09-15 20:25:46.885 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_genotype NOTICE task setup :: name: "trgt_genotype", source: "./trgt.wdl", line: 272, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-95/call-trgt_genotype", thread: 140611944420928
2025-09-15 20:25:46.905 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_genotype INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:46.905 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_genotype INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:25:46.905 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_genotype INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:25:46.905 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_genotype INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:25:46.905 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_genotype INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2192.mapped.bam.bai"
2025-09-15 20:25:46.905 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_genotype INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2192.mapped.bam"
2025-09-15 20:25:46.905 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_genotype INFO input :: name: "sex", value: "F"
2025-09-15 20:25:46.905 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_genotype INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2192"
2025-09-15 20:25:46.906 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_genotype INFO eval :: name: "mem_gb", value: 16
2025-09-15 20:25:46.906 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_genotype INFO eval :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2192.trgt"
2025-09-15 20:25:46.906 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_genotype INFO eval :: name: "threads", value: 8
2025-09-15 20:25:46.906 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_genotype INFO eval :: name: "disk_size", value: 27
2025-09-15 20:25:46.906 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_genotype INFO eval :: name: "karyotype", value: "XX"
2025-09-15 20:25:46.906 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_genotype INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 8, memory_reservation: 16000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:46.907 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_genotype WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:46.907 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_genotype INFO provisioned :: seconds_waited: 0, cpu: 8, mem_bytes: 16000000000
2025-09-15 20:25:46.907 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_genotype INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:46.933 wdl.w:ptcp.w:call-trgt-95.t:call-get_reads_overlapping_repeats INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 9, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-95/call-get_reads_overlapping_repeats/_singularity_tmpdir_uh0dq1hg"
2025-09-15 20:25:46.933 wdl.w:ptcp.w:call-trgt-95.t:call-get_reads_overlapping_repeats INFO Slurm invocation: srun --job-name call-get_reads_overlapping_repeats --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-95/call-get_reads_overlapping_repeats/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-95/call-get_reads_overlapping_repeats/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-95/call-get_reads_overlapping_repeats/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-95/call-get_reads_overlapping_repeats/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-95/out/m84036_250809_035451_s4.bc2192.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2192.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-95/out/m84036_250809_035451_s4.bc2192.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2192.mapped.bam:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-95/call-get_reads_overlapping_repeats/_singularity_tmpdir_uh0dq1hg/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-95/call-get_reads_overlapping_repeats/_singularity_tmpdir_uh0dq1hg/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:46.962 wdl.w:ptcp.w:call-trgt-95.t:call-get_reads_overlapping_repeats NOTICE slurm_singularity run :: pid: 1206321, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-95/call-get_reads_overlapping_repeats/slurm_singularity.log.txt"
2025-09-15 20:25:46.975 wdl.w:ptcp.w:call-trgt-75 NOTICE done
2025-09-15 20:25:46.977 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_genotype INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 11, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-95/call-trgt_genotype/_singularity_tmpdir_86_c2xpj"
2025-09-15 20:25:46.978 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_genotype INFO Slurm invocation: srun --job-name call-trgt_genotype --partition compute,compute9 --cpus-per-task 8 --mem 15259M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-95/call-trgt_genotype/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-95/call-trgt_genotype/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-95/call-trgt_genotype/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-95/call-trgt_genotype/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-95/out/m84036_250809_035451_s4.bc2192.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2192.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-95/out/m84036_250809_035451_s4.bc2192.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2192.mapped.bam.bai:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-95/call-trgt_genotype/_singularity_tmpdir_86_c2xpj/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-95/call-trgt_genotype/_singularity_tmpdir_86_c2xpj/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:46.981 wdl.w:ptcp NOTICE finish :: job: "call-trgt-75"
2025-09-15 20:25:46.981 wdl.w:ptcp INFO output :: job: "call-trgt-75", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-75/out/m84036_250809_035451_s4.bc2172.motifs_waterfall.trgt_plots.zip", "images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-75/out/m84036_250809_035451_s4.bc2172.meth_allele.trgt_plots.zip", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-75/out/m84036_250809_035451_s4.bc2172.trgt.sorted.spanning.bam.bai", "images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-75/out/m84036_250809_035451_s4.bc2172.motifs_allele.trgt_plots.zip", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-75/out/m84036_250809_035451_s4.bc2172.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-75/out/m84036_250809_035451_s4.bc2172.trgt.vcf", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-75/out/m84036_250809_035451_s4.bc2172.repeats.bam", "images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-75/out/m84036_250809_035451_s4.bc2172.meth_waterfall.trgt_plots.zip", "reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-75/out/m84036_250809_035451_s4.bc2172.repeats.bam.bai"}
2025-09-15 20:25:46.986 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_genotype NOTICE slurm_singularity run :: pid: 1206324, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-95/call-trgt_genotype/slurm_singularity.log.txt"
2025-09-15 20:25:47.010 wdl.w:ptcp.w:call-paraphase-89.t:call-run_paraphase INFO output :: name: "paraphase_bam", value: "m84036_250809_035451_s4.bc2186_paraphase/m84036_250809_035451_s4.bc2186.paraphase.bam"
2025-09-15 20:25:47.015 wdl.w:ptcp.w:call-paraphase-89.t:call-run_paraphase INFO output :: name: "paraphase_bam_bai", value: "m84036_250809_035451_s4.bc2186_paraphase/m84036_250809_035451_s4.bc2186.paraphase.bam.bai"
2025-09-15 20:25:47.017 wdl.w:ptcp.w:call-paraphase-89.t:call-run_paraphase INFO output :: name: "paraphase_json", value: "m84036_250809_035451_s4.bc2186_paraphase/m84036_250809_035451_s4.bc2186.paraphase.json"
2025-09-15 20:25:47.018 wdl.w:ptcp.w:call-paraphase-89.t:call-run_paraphase INFO output :: name: "paraphase_vcfs", value: []
2025-09-15 20:25:47.018 wdl.w:ptcp.w:call-paraphase-89.t:call-run_paraphase INFO output :: name: "havanno_json", value: "m84036_250809_035451_s4.bc2186.havanno.json"
2025-09-15 20:25:47.028 wdl.w:ptcp.w:call-trgt-77.t:call-trgt_plot_motifs_allele.slurm_singularity INFO srun: job 51798073 queued and waiting for resources
2025-09-15 20:25:47.028 wdl.w:ptcp.w:call-trgt-77.t:call-trgt_plot_motifs_allele.slurm_singularity INFO srun: job 51798073 has been allocated resources
2025-09-15 20:25:47.028 wdl.w:ptcp.w:call-trgt-77.t:call-trgt_plot_motifs_allele.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:47.052 wdl.w:ptcp.w:call-trgt-77.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO srun: job 51798074 queued and waiting for resources
2025-09-15 20:25:47.052 wdl.w:ptcp.w:call-trgt-77.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO srun: job 51798074 has been allocated resources
2025-09-15 20:25:47.052 wdl.w:ptcp.w:call-trgt-77.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:47.112 wdl.w:ptcp.w:call-paraphase-89.t:call-run_paraphase NOTICE done
2025-09-15 20:25:47.118 wdl.w:ptcp.w:call-paraphase-89 NOTICE finish :: job: "call-run_paraphase"
2025-09-15 20:25:47.118 wdl.w:ptcp.w:call-paraphase-89 INFO output :: job: "call-run_paraphase", values: {"havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-89/call-run_paraphase/out/m84036_250809_035451_s4.bc2186.havanno.json", "paraphase_vcfs": [], "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-89/call-run_paraphase/out/m84036_250809_035451_s4.bc2186_paraphase/m84036_250809_035451_s4.bc2186.paraphase.json", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-89/call-run_paraphase/out/m84036_250809_035451_s4.bc2186_paraphase/m84036_250809_035451_s4.bc2186.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-89/call-run_paraphase/out/m84036_250809_035451_s4.bc2186_paraphase/m84036_250809_035451_s4.bc2186.paraphase.bam"}
2025-09-15 20:25:47.119 wdl.w:ptcp.w:call-paraphase-89 NOTICE ready :: job: "call-call_f8", callee: "call_f8"
2025-09-15 20:25:47.119 wdl.w:ptcp.w:call-paraphase-89 INFO input :: job: "call-call_f8", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "out_prefix": "m84036_250809_035451_s4.bc2186", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-89/call-run_paraphase/out/m84036_250809_035451_s4.bc2186_paraphase/m84036_250809_035451_s4.bc2186.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-89/call-run_paraphase/out/m84036_250809_035451_s4.bc2186_paraphase/m84036_250809_035451_s4.bc2186.paraphase.bam", "sex": "F"}
2025-09-15 20:25:47.120 wdl.w:ptcp.w:call-paraphase-89 INFO visit :: node: "output-havanno_json", values: {"havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-89/call-run_paraphase/out/m84036_250809_035451_s4.bc2186.havanno.json"}
2025-09-15 20:25:47.120 wdl.w:ptcp.w:call-paraphase-89 INFO visit :: node: "output-paraphase_bam", values: {"paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-89/call-run_paraphase/out/m84036_250809_035451_s4.bc2186_paraphase/m84036_250809_035451_s4.bc2186.paraphase.bam"}
2025-09-15 20:25:47.120 wdl.w:ptcp.w:call-paraphase-89 INFO visit :: node: "output-paraphase_bam_bai", values: {"paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-89/call-run_paraphase/out/m84036_250809_035451_s4.bc2186_paraphase/m84036_250809_035451_s4.bc2186.paraphase.bam.bai"}
2025-09-15 20:25:47.120 wdl.w:ptcp.w:call-paraphase-89 INFO visit :: node: "output-paraphase_json", values: {"paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-89/call-run_paraphase/out/m84036_250809_035451_s4.bc2186_paraphase/m84036_250809_035451_s4.bc2186.paraphase.json"}
2025-09-15 20:25:47.120 wdl.w:ptcp.w:call-paraphase-89 INFO visit :: node: "output-paraphase_vcfs", values: {"paraphase_vcfs": []}
2025-09-15 20:25:47.125 wdl.w:ptcp.w:call-paraphase-94.t:call-run_paraphase NOTICE task setup :: name: "run_paraphase", source: "./paraphase.wdl", line: 127, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-94/call-run_paraphase", thread: 140613588604480
2025-09-15 20:25:47.142 wdl.w:ptcp.w:call-paraphase-94.t:call-run_paraphase INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:47.142 wdl.w:ptcp.w:call-paraphase-94.t:call-run_paraphase INFO input :: name: "annotation_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf"
2025-09-15 20:25:47.142 wdl.w:ptcp.w:call-paraphase-94.t:call-run_paraphase INFO input :: name: "genome_version", value: "38"
2025-09-15 20:25:47.142 wdl.w:ptcp.w:call-paraphase-94.t:call-run_paraphase INFO input :: name: "config_file", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/paraphase_config.GRCh38.yaml"
2025-09-15 20:25:47.142 wdl.w:ptcp.w:call-paraphase-94.t:call-run_paraphase INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:25:47.142 wdl.w:ptcp.w:call-paraphase-94.t:call-run_paraphase INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:25:47.142 wdl.w:ptcp.w:call-paraphase-94.t:call-run_paraphase INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2191.mapped.bam.bai"
2025-09-15 20:25:47.143 wdl.w:ptcp.w:call-paraphase-94.t:call-run_paraphase INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2191.mapped.bam"
2025-09-15 20:25:47.143 wdl.w:ptcp.w:call-paraphase-94.t:call-run_paraphase INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2191"
2025-09-15 20:25:47.143 wdl.w:ptcp.w:call-paraphase-94.t:call-run_paraphase INFO eval :: name: "threads", value: 4
2025-09-15 20:25:47.143 wdl.w:ptcp.w:call-paraphase-94.t:call-run_paraphase INFO eval :: name: "mem_gb", value: 8
2025-09-15 20:25:47.143 wdl.w:ptcp.w:call-paraphase-94.t:call-run_paraphase INFO eval :: name: "disk_size", value: 27
2025-09-15 20:25:47.143 wdl.w:ptcp.w:call-paraphase-94.t:call-run_paraphase INFO eval :: name: "out_dir", value: "m84036_250809_035451_s4.bc2191_paraphase"
2025-09-15 20:25:47.144 wdl.w:ptcp.w:call-paraphase-94.t:call-run_paraphase INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 4, memory_reservation: 8000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:47.144 wdl.w:ptcp.w:call-paraphase-94.t:call-run_paraphase WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:47.144 wdl.w:ptcp.w:call-paraphase-94.t:call-run_paraphase INFO provisioned :: seconds_waited: 0, cpu: 4, mem_bytes: 8000000000
2025-09-15 20:25:47.144 wdl.w:ptcp.w:call-paraphase-94.t:call-run_paraphase INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:47.209 wdl.w:ptcp.w:call-sawfish-95.t:call-run_sawfish.slurm_singularity INFO srun: job 51798075 queued and waiting for resources
2025-09-15 20:25:47.209 wdl.w:ptcp.w:call-sawfish-95.t:call-run_sawfish.slurm_singularity INFO srun: job 51798075 has been allocated resources
2025-09-15 20:25:47.209 wdl.w:ptcp.w:call-sawfish-95.t:call-run_sawfish.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:47.209 wdl.w:ptcp.w:call-sawfish-95.t:call-run_sawfish.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:25:47.212 wdl.w:ptcp.w:call-paraphase-95.t:call-run_paraphase.slurm_singularity INFO srun: job 51798076 queued and waiting for resources
2025-09-15 20:25:47.212 wdl.w:ptcp.w:call-paraphase-95.t:call-run_paraphase.slurm_singularity INFO srun: job 51798076 has been allocated resources
2025-09-15 20:25:47.212 wdl.w:ptcp.w:call-paraphase-95.t:call-run_paraphase.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:47.212 wdl.w:ptcp.w:call-paraphase-95.t:call-run_paraphase.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:25:47.213 wdl.w:ptcp.w:call-paraphase-94.t:call-run_paraphase INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-94/call-run_paraphase/_singularity_tmpdir_icsrg09x"
2025-09-15 20:25:47.213 wdl.w:ptcp.w:call-paraphase-94.t:call-run_paraphase INFO Slurm invocation: srun --job-name call-run_paraphase --partition compute,compute9 --cpus-per-task 4 --mem 7629M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-94/call-run_paraphase/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-94/call-run_paraphase/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-94/call-run_paraphase/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-94/call-run_paraphase/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-94/out/m84036_250809_035451_s4.bc2191.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2191.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-94/out/m84036_250809_035451_s4.bc2191.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2191.mapped.bam.bai:ro --bind /ptcp/meta/variant_list/variant_list.GRCh38.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf:ro --bind /ptcp/meta/paraphase/paraphase_config.GRCh38.yaml:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/paraphase_config.GRCh38.yaml:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-94/call-run_paraphase/_singularity_tmpdir_icsrg09x/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-94/call-run_paraphase/_singularity_tmpdir_icsrg09x/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:47.235 wdl.w:ptcp.w:call-paraphase-94.t:call-run_paraphase NOTICE slurm_singularity run :: pid: 1206336, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-94/call-run_paraphase/slurm_singularity.log.txt"
2025-09-15 20:25:47.332 wdl.w:ptcp.w:call-paraphase-77.t:call-call_f8.stderr VERBOSE 2025-09-15 20:25:47,281 INFO  Started analysis for m84036_250809_035451_s4.bc2174 at 2025-09-15 20:25:47.281805...
2025-09-15 20:25:47.332 wdl.w:ptcp.w:call-paraphase-77.t:call-call_f8.stderr VERBOSE 2025-09-15 20:25:47,303 INFO  Completed analysis for m84036_250809_035451_s4.bc2174
2025-09-15 20:25:47.339 wdl.w:ptcp.w:call-paraphase-77.t:call-call_f8.slurm_singularity INFO srun: job 51798077 queued and waiting for resources
2025-09-15 20:25:47.339 wdl.w:ptcp.w:call-paraphase-77.t:call-call_f8.slurm_singularity INFO srun: job 51798077 has been allocated resources
2025-09-15 20:25:47.339 wdl.w:ptcp.w:call-paraphase-77.t:call-call_f8.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:47.339 wdl.w:ptcp.w:call-paraphase-77.t:call-call_f8.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:25:47.453 wdl.w:ptcp.w:call-paraphase-77.t:call-call_f8 INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2174.f8inversion.vcf"
2025-09-15 20:25:47.456 wdl.w:ptcp.w:call-paraphase-77.t:call-call_f8 INFO output :: name: "json", value: "m84036_250809_035451_s4.bc2174.f8inversion.json"
2025-09-15 20:25:47.479 wdl.w:ptcp.w:call-paraphase-55.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for rpgr for sample m84036_250809_035451_s4.bc2152 at 2025-09-15 20:25:35.470602...
2025-09-15 20:25:47.480 wdl.w:ptcp.w:call-paraphase-55.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for rpgr for sample m84036_250809_035451_s4.bc2152 at 2025-09-15 20:25:36.135185...
2025-09-15 20:25:47.480 wdl.w:ptcp.w:call-paraphase-55.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for rpgr for sample m84036_250809_035451_s4.bc2152 at 2025-09-15 20:25:36.285163...
2025-09-15 20:25:47.517 wdl.w:ptcp.w:call-paraphase-77.t:call-call_f8 NOTICE done
2025-09-15 20:25:47.522 wdl.w:ptcp.w:call-paraphase-77 NOTICE finish :: job: "call-call_f8"
2025-09-15 20:25:47.523 wdl.w:ptcp.w:call-paraphase-77 INFO output :: job: "call-call_f8", values: {"json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-77/call-call_f8/out/m84036_250809_035451_s4.bc2174.f8inversion.json", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-77/call-call_f8/out/m84036_250809_035451_s4.bc2174.f8inversion.vcf"}
2025-09-15 20:25:47.523 wdl.w:ptcp.w:call-paraphase-77 INFO visit :: node: "output-f8_json", values: {"f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-77/call-call_f8/out/m84036_250809_035451_s4.bc2174.f8inversion.json"}
2025-09-15 20:25:47.523 wdl.w:ptcp.w:call-paraphase-77 INFO visit :: node: "output-f8_vcf", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-77/call-call_f8/out/m84036_250809_035451_s4.bc2174.f8inversion.vcf"}
2025-09-15 20:25:47.523 wdl.w:ptcp.w:call-paraphase-77 INFO visit :: node: "outputs", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-77/call-call_f8/out/m84036_250809_035451_s4.bc2174.f8inversion.vcf", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-77/call-run_paraphase/out/m84036_250809_035451_s4.bc2174_paraphase/m84036_250809_035451_s4.bc2174.paraphase.json", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-77/call-run_paraphase/out/m84036_250809_035451_s4.bc2174_paraphase/m84036_250809_035451_s4.bc2174.paraphase.bam", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-77/call-run_paraphase/out/m84036_250809_035451_s4.bc2174_paraphase/m84036_250809_035451_s4.bc2174.paraphase.bam.bai", "paraphase_vcfs": [], "havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-77/call-run_paraphase/out/m84036_250809_035451_s4.bc2174.havanno.json", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-77/call-call_f8/out/m84036_250809_035451_s4.bc2174.f8inversion.json"}
2025-09-15 20:25:47.528 wdl.w:ptcp.w:call-sawfish-94.t:call-run_sawfish NOTICE task setup :: name: "run_sawfish", source: "./sawfish.wdl", line: 83, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-94/call-run_sawfish", thread: 140608211502656
2025-09-15 20:25:47.546 wdl.w:ptcp.w:call-sawfish-94.t:call-run_sawfish INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:47.546 wdl.w:ptcp.w:call-sawfish-94.t:call-run_sawfish INFO input :: name: "genome_version", value: "38"
2025-09-15 20:25:47.546 wdl.w:ptcp.w:call-sawfish-94.t:call-run_sawfish INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:25:47.546 wdl.w:ptcp.w:call-sawfish-94.t:call-run_sawfish INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:25:47.546 wdl.w:ptcp.w:call-sawfish-94.t:call-run_sawfish INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2191.mapped.bam.bai"
2025-09-15 20:25:47.546 wdl.w:ptcp.w:call-sawfish-94.t:call-run_sawfish INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2191.mapped.bam"
2025-09-15 20:25:47.546 wdl.w:ptcp.w:call-sawfish-94.t:call-run_sawfish INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2191"
2025-09-15 20:25:47.547 wdl.w:ptcp.w:call-sawfish-94.t:call-run_sawfish INFO eval :: name: "mem_gb", value: 32
2025-09-15 20:25:47.547 wdl.w:ptcp.w:call-sawfish-94.t:call-run_sawfish INFO eval :: name: "threads", value: 16
2025-09-15 20:25:47.547 wdl.w:ptcp.w:call-sawfish-94.t:call-run_sawfish INFO eval :: name: "disk_size", value: 30
2025-09-15 20:25:47.547 wdl.w:ptcp.w:call-sawfish-94.t:call-run_sawfish INFO eval :: name: "discover_dirname", value: "m84036_250809_035451_s4.bc2191_sawfish_discover"
2025-09-15 20:25:47.547 wdl.w:ptcp.w:call-sawfish-94.t:call-run_sawfish INFO eval :: name: "call_dirname", value: "m84036_250809_035451_s4.bc2191_sawfish"
2025-09-15 20:25:47.547 wdl.w:ptcp.w:call-sawfish-94.t:call-run_sawfish INFO eval :: name: "minimap2_bam_filename", value: "m84036_250809_035451_s4.bc2191.minimap2.bam"
2025-09-15 20:25:47.548 wdl.w:ptcp.w:call-sawfish-94.t:call-run_sawfish INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 16, memory_reservation: 32000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:47.548 wdl.w:ptcp.w:call-sawfish-94.t:call-run_sawfish WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:47.548 wdl.w:ptcp.w:call-sawfish-94.t:call-run_sawfish INFO provisioned :: seconds_waited: 0, cpu: 16, mem_bytes: 32000000000
2025-09-15 20:25:47.548 wdl.w:ptcp.w:call-sawfish-94.t:call-run_sawfish INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:47.586 wdl.w:ptcp.w:call-paraphase-77 NOTICE done
2025-09-15 20:25:47.608 wdl.w:ptcp.w:call-sawfish-94.t:call-run_sawfish INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 10, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-94/call-run_sawfish/_singularity_tmpdir_tw0nkgic"
2025-09-15 20:25:47.608 wdl.w:ptcp.w:call-sawfish-94.t:call-run_sawfish INFO Slurm invocation: srun --job-name call-run_sawfish --partition compute,compute9 --cpus-per-task 16 --mem 30518M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-94/call-run_sawfish/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-94/call-run_sawfish/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-94/call-run_sawfish/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-94/call-run_sawfish/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-94/out/m84036_250809_035451_s4.bc2191.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2191.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-94/out/m84036_250809_035451_s4.bc2191.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2191.mapped.bam.bai:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-94/call-run_sawfish/_singularity_tmpdir_tw0nkgic/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-94/call-run_sawfish/_singularity_tmpdir_tw0nkgic/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:47.617 wdl.w:ptcp NOTICE finish :: job: "call-paraphase-77"
2025-09-15 20:25:47.617 wdl.w:ptcp INFO output :: job: "call-paraphase-77", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-77/out/m84036_250809_035451_s4.bc2174.f8inversion.vcf", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-77/out/m84036_250809_035451_s4.bc2174_paraphase/m84036_250809_035451_s4.bc2174.paraphase.json", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-77/out/m84036_250809_035451_s4.bc2174_paraphase/m84036_250809_035451_s4.bc2174.paraphase.bam", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-77/out/m84036_250809_035451_s4.bc2174_paraphase/m84036_250809_035451_s4.bc2174.paraphase.bam.bai", "paraphase_vcfs": [], "havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-77/out/m84036_250809_035451_s4.bc2174.havanno.json", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-77/out/m84036_250809_035451_s4.bc2174.f8inversion.json"}
2025-09-15 20:25:47.623 wdl.w:ptcp.w:call-sawfish-94.t:call-run_sawfish NOTICE slurm_singularity run :: pid: 1206344, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-94/call-run_sawfish/slurm_singularity.log.txt"
2025-09-15 20:25:47.781 wdl.w:ptcp.w:call-trgt-93.t:call-trgt_genotype INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2190.trgt.vcf"
2025-09-15 20:25:47.785 wdl.w:ptcp.w:call-trgt-93.t:call-trgt_genotype INFO output :: name: "spanning_bam", value: "m84036_250809_035451_s4.bc2190.trgt.sorted.spanning.bam"
2025-09-15 20:25:47.787 wdl.w:ptcp.w:call-trgt-93.t:call-trgt_genotype INFO output :: name: "spanning_bam_bai", value: "m84036_250809_035451_s4.bc2190.trgt.sorted.spanning.bam.bai"
2025-09-15 20:25:47.862 wdl.w:ptcp.w:call-trgt-93.t:call-trgt_genotype NOTICE done
2025-09-15 20:25:47.877 wdl.w:ptcp.w:call-trgt-93 NOTICE finish :: job: "call-trgt_genotype"
2025-09-15 20:25:47.878 wdl.w:ptcp.w:call-trgt-93 INFO output :: job: "call-trgt_genotype", values: {"spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-93/call-trgt_genotype/out/m84036_250809_035451_s4.bc2190.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-93/call-trgt_genotype/out/m84036_250809_035451_s4.bc2190.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-93/call-trgt_genotype/out/m84036_250809_035451_s4.bc2190.trgt.vcf"}
2025-09-15 20:25:47.880 wdl.w:ptcp.w:call-trgt-93 NOTICE ready :: job: "call-trgt_plot_meth_allele", callee: "trgt_plot"
2025-09-15 20:25:47.880 wdl.w:ptcp.w:call-trgt-93 INFO input :: job: "call-trgt_plot_meth_allele", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": false, "methylation": true, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-93/call-trgt_genotype/out/m84036_250809_035451_s4.bc2190.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-93/call-trgt_genotype/out/m84036_250809_035451_s4.bc2190.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-93/call-trgt_genotype/out/m84036_250809_035451_s4.bc2190.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2190"}
2025-09-15 20:25:47.881 wdl.w:ptcp.w:call-trgt-93 NOTICE ready :: job: "call-trgt_plot_meth_waterfall", callee: "trgt_plot"
2025-09-15 20:25:47.881 wdl.w:ptcp.w:call-trgt-93 INFO input :: job: "call-trgt_plot_meth_waterfall", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": true, "methylation": true, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-93/call-trgt_genotype/out/m84036_250809_035451_s4.bc2190.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-93/call-trgt_genotype/out/m84036_250809_035451_s4.bc2190.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-93/call-trgt_genotype/out/m84036_250809_035451_s4.bc2190.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2190"}
2025-09-15 20:25:47.882 wdl.w:ptcp.w:call-trgt-93 NOTICE ready :: job: "call-trgt_plot_motifs_allele", callee: "trgt_plot"
2025-09-15 20:25:47.882 wdl.w:ptcp.w:call-trgt-93 INFO input :: job: "call-trgt_plot_motifs_allele", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": false, "methylation": false, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-93/call-trgt_genotype/out/m84036_250809_035451_s4.bc2190.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-93/call-trgt_genotype/out/m84036_250809_035451_s4.bc2190.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-93/call-trgt_genotype/out/m84036_250809_035451_s4.bc2190.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2190"}
2025-09-15 20:25:47.883 wdl.w:ptcp.w:call-trgt-93 NOTICE ready :: job: "call-trgt_plot_motifs_waterfall", callee: "trgt_plot"
2025-09-15 20:25:47.883 wdl.w:ptcp.w:call-trgt-93 INFO input :: job: "call-trgt_plot_motifs_waterfall", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": true, "methylation": false, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-93/call-trgt_genotype/out/m84036_250809_035451_s4.bc2190.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-93/call-trgt_genotype/out/m84036_250809_035451_s4.bc2190.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-93/call-trgt_genotype/out/m84036_250809_035451_s4.bc2190.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2190"}
2025-09-15 20:25:47.883 wdl.w:ptcp.w:call-trgt-93 INFO visit :: node: "output-spanning_bam", values: {"spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-93/call-trgt_genotype/out/m84036_250809_035451_s4.bc2190.trgt.sorted.spanning.bam"}
2025-09-15 20:25:47.883 wdl.w:ptcp.w:call-trgt-93 INFO visit :: node: "output-spanning_bam_bai", values: {"spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-93/call-trgt_genotype/out/m84036_250809_035451_s4.bc2190.trgt.sorted.spanning.bam.bai"}
2025-09-15 20:25:47.883 wdl.w:ptcp.w:call-trgt-93 INFO visit :: node: "output-vcf", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-93/call-trgt_genotype/out/m84036_250809_035451_s4.bc2190.trgt.vcf"}
2025-09-15 20:25:47.885 wdl.w:ptcp.w:call-trgt-81.t:call-trgt_plot_meth_allele NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-81/call-trgt_plot_meth_allele", thread: 140611441120832
2025-09-15 20:25:47.903 wdl.w:ptcp.w:call-trgt-81.t:call-trgt_plot_meth_allele INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:47.904 wdl.w:ptcp.w:call-trgt-81.t:call-trgt_plot_meth_allele INFO input :: name: "waterfall", value: false
2025-09-15 20:25:47.904 wdl.w:ptcp.w:call-trgt-81.t:call-trgt_plot_meth_allele INFO input :: name: "methylation", value: true
2025-09-15 20:25:47.904 wdl.w:ptcp.w:call-trgt-81.t:call-trgt_plot_meth_allele INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:25:47.904 wdl.w:ptcp.w:call-trgt-81.t:call-trgt_plot_meth_allele INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:25:47.904 wdl.w:ptcp.w:call-trgt-81.t:call-trgt_plot_meth_allele INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:25:47.904 wdl.w:ptcp.w:call-trgt-81.t:call-trgt_plot_meth_allele INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2178.trgt.sorted.spanning.bam.bai"
2025-09-15 20:25:47.904 wdl.w:ptcp.w:call-trgt-81.t:call-trgt_plot_meth_allele INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2178.trgt.sorted.spanning.bam"
2025-09-15 20:25:47.904 wdl.w:ptcp.w:call-trgt-81.t:call-trgt_plot_meth_allele INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2178.trgt.vcf"
2025-09-15 20:25:47.904 wdl.w:ptcp.w:call-trgt-81.t:call-trgt_plot_meth_allele INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2178"
2025-09-15 20:25:47.904 wdl.w:ptcp.w:call-trgt-81.t:call-trgt_plot_meth_allele INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:25:47.905 wdl.w:ptcp.w:call-trgt-81.t:call-trgt_plot_meth_allele INFO eval :: name: "plot_type", value: "allele"
2025-09-15 20:25:47.905 wdl.w:ptcp.w:call-trgt-81.t:call-trgt_plot_meth_allele INFO eval :: name: "show", value: "meth"
2025-09-15 20:25:47.905 wdl.w:ptcp.w:call-trgt-81.t:call-trgt_plot_meth_allele INFO eval :: name: "threads", value: 1
2025-09-15 20:25:47.905 wdl.w:ptcp.w:call-trgt-81.t:call-trgt_plot_meth_allele INFO eval :: name: "disk_size", value: 27
2025-09-15 20:25:47.905 wdl.w:ptcp.w:call-trgt-81.t:call-trgt_plot_meth_allele INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2178.meth_allele"
2025-09-15 20:25:47.906 wdl.w:ptcp.w:call-trgt-81.t:call-trgt_plot_meth_allele INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:47.906 wdl.w:ptcp.w:call-trgt-81.t:call-trgt_plot_meth_allele WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:47.906 wdl.w:ptcp.w:call-trgt-81.t:call-trgt_plot_meth_allele INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:25:47.906 wdl.w:ptcp.w:call-trgt-81.t:call-trgt_plot_meth_allele INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:47.975 wdl.w:ptcp.w:call-trgt-95.t:call-get_reads_overlapping_repeats.slurm_singularity INFO srun: job 51798078 queued and waiting for resources
2025-09-15 20:25:47.975 wdl.w:ptcp.w:call-trgt-95.t:call-get_reads_overlapping_repeats.slurm_singularity INFO srun: job 51798078 has been allocated resources
2025-09-15 20:25:47.975 wdl.w:ptcp.w:call-trgt-95.t:call-get_reads_overlapping_repeats.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:47.977 wdl.w:ptcp.w:call-trgt-81.t:call-trgt_plot_meth_allele INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-81/call-trgt_plot_meth_allele/_singularity_tmpdir_nguqo0h1"
2025-09-15 20:25:47.978 wdl.w:ptcp.w:call-trgt-81.t:call-trgt_plot_meth_allele INFO Slurm invocation: srun --job-name call-trgt_plot_meth_allele --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-81/call-trgt_plot_meth_allele/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-81/call-trgt_plot_meth_allele/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-81/call-trgt_plot_meth_allele/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-81/call-trgt_plot_meth_allele/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-81/call-trgt_genotype/out/m84036_250809_035451_s4.bc2178.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2178.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-81/call-trgt_genotype/out/m84036_250809_035451_s4.bc2178.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2178.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-81/call-trgt_genotype/out/m84036_250809_035451_s4.bc2178.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2178.trgt.sorted.spanning.bam.bai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-81/call-trgt_plot_meth_allele/_singularity_tmpdir_nguqo0h1/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-81/call-trgt_plot_meth_allele/_singularity_tmpdir_nguqo0h1/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:47.991 wdl.w:ptcp.w:call-trgt-81.t:call-trgt_plot_meth_allele NOTICE slurm_singularity run :: pid: 1206352, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-81/call-trgt_plot_meth_allele/slurm_singularity.log.txt"
2025-09-15 20:25:47.994 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_genotype.slurm_singularity INFO srun: job 51798079 queued and waiting for resources
2025-09-15 20:25:47.994 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_genotype.slurm_singularity INFO srun: job 51798079 has been allocated resources
2025-09-15 20:25:47.994 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_genotype.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:48.018 wdl.w:ptcp.w:call-paraphase-82.t:call-run_paraphase.stderr VERBOSE INFO:root:Processing sample m84036_250809_035451_s4.bc2179 at 2025-09-15 20:25:46.880226...
2025-09-15 20:25:48.019 wdl.w:ptcp.w:call-paraphase-82.t:call-run_paraphase.stderr VERBOSE INFO:root:Checking sample sex at 2025-09-15 20:25:46.882413...
2025-09-15 20:25:48.019 wdl.w:ptcp.w:call-paraphase-82.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for gba for sample m84036_250809_035451_s4.bc2179 at 2025-09-15 20:25:46.979423...
2025-09-15 20:25:48.019 wdl.w:ptcp.w:call-paraphase-82.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for gba for sample m84036_250809_035451_s4.bc2179 at 2025-09-15 20:25:46.980174...
2025-09-15 20:25:48.019 wdl.w:ptcp.w:call-paraphase-82.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for cyp21 for sample m84036_250809_035451_s4.bc2179 at 2025-09-15 20:25:46.979349...
2025-09-15 20:25:48.019 wdl.w:ptcp.w:call-paraphase-82.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for cyp21 for sample m84036_250809_035451_s4.bc2179 at 2025-09-15 20:25:46.980337...
2025-09-15 20:25:48.019 wdl.w:ptcp.w:call-paraphase-82.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for smn1 for sample m84036_250809_035451_s4.bc2179 at 2025-09-15 20:25:46.979631...
2025-09-15 20:25:48.020 wdl.w:ptcp.w:call-paraphase-82.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for smn1 for sample m84036_250809_035451_s4.bc2179 at 2025-09-15 20:25:46.980496...
2025-09-15 20:25:48.020 wdl.w:ptcp.w:call-paraphase-82.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for hba for sample m84036_250809_035451_s4.bc2179 at 2025-09-15 20:25:46.982024...
2025-09-15 20:25:48.020 wdl.w:ptcp.w:call-paraphase-82.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for hba for sample m84036_250809_035451_s4.bc2179 at 2025-09-15 20:25:46.982669...
2025-09-15 20:25:48.117 wdl.w:ptcp.w:call-sawfish-69.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:37][sawfish][INFO] Starting sawfish 2.0.3
2025-09-15 20:25:48.118 wdl.w:ptcp.w:call-sawfish-69.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:37][sawfish][INFO] cmdline: sawfish discover --disable-cnv --threads 16 --ref /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa --bam m84036_250809_035451_s4.bc2166.minimap2.bam --output-dir m84036_250809_035451_s4.bc2166_sawfish_discover
2025-09-15 20:25:48.118 wdl.w:ptcp.w:call-sawfish-69.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:37][sawfish][INFO] Running on 16 threads
2025-09-15 20:25:48.118 wdl.w:ptcp.w:call-sawfish-69.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:37][sawfish][INFO] Writing discover settings to file: 'm84036_250809_035451_s4.bc2166_sawfish_discover/discover.settings.json'
2025-09-15 20:25:48.118 wdl.w:ptcp.w:call-sawfish-69.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:37][sawfish][INFO] Reading reference genome from file '/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa'
2025-09-15 20:25:48.118 wdl.w:ptcp.w:call-sawfish-69.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:43][sawfish][INFO] Processing alignment file '/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2166.minimap2.bam'
2025-09-15 20:25:48.118 wdl.w:ptcp.w:call-sawfish-69.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:43][sawfish][INFO] Finished processing all alignments
2025-09-15 20:25:48.118 wdl.w:ptcp.w:call-sawfish-69.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:43][sawfish][INFO] Writing depth bins to binary file: 'm84036_250809_035451_s4.bc2166_sawfish_discover/depth.mpack'
2025-09-15 20:25:48.118 wdl.w:ptcp.w:call-sawfish-69.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:43][sawfish][INFO] Writing max sv depth genome regions to bed file: 'm84036_250809_035451_s4.bc2166_sawfish_discover/max.depth.bed'
2025-09-15 20:25:48.118 wdl.w:ptcp.w:call-sawfish-69.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:43][sawfish][INFO] Completing breakpoint observation clustering
2025-09-15 20:25:48.118 wdl.w:ptcp.w:call-sawfish-69.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:43][sawfish][INFO] Finished breakpoint observation clustering
2025-09-15 20:25:48.118 wdl.w:ptcp.w:call-sawfish-69.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:43][sawfish][INFO] Consolidating adjacent indel candidates
2025-09-15 20:25:48.118 wdl.w:ptcp.w:call-sawfish-69.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:43][sawfish][INFO] Finding large insertion candidates
2025-09-15 20:25:48.119 wdl.w:ptcp.w:call-sawfish-69.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:43][sawfish][INFO] Writing breakpoint_cluster debug bed file: 'm84036_250809_035451_s4.bc2166_sawfish_discover/debug.breakpoint_clusters.bed'
2025-09-15 20:25:48.119 wdl.w:ptcp.w:call-sawfish-69.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:43][sawfish][INFO] Refining SV Candidates
2025-09-15 20:25:48.119 wdl.w:ptcp.w:call-sawfish-69.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:43][sawfish][INFO] Writing debug assembly region bed file: 'm84036_250809_035451_s4.bc2166_sawfish_discover/assembly.regions.bed'
2025-09-15 20:25:48.119 wdl.w:ptcp.w:call-sawfish-69.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:43][sawfish][INFO] Starting refinement of breakpoint evidence clusters
2025-09-15 20:25:48.119 wdl.w:ptcp.w:call-sawfish-69.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:43][sawfish][INFO] Finished refining all breakpoint evidence clusters
2025-09-15 20:25:48.119 wdl.w:ptcp.w:call-sawfish-69.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:43][sawfish][INFO] Writing all contig alignments to bam file: 'm84036_250809_035451_s4.bc2166_sawfish_discover/contig.alignment.bam'
2025-09-15 20:25:48.119 wdl.w:ptcp.w:call-sawfish-69.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:43][sawfish][INFO] Writing candidate structural variants to file: 'm84036_250809_035451_s4.bc2166_sawfish_discover/candidate.sv.bcf'
2025-09-15 20:25:48.119 wdl.w:ptcp.w:call-sawfish-69.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:43][sawfish][INFO] Writing run statistics to file: 'm84036_250809_035451_s4.bc2166_sawfish_discover/run.stats.json'
2025-09-15 20:25:48.119 wdl.w:ptcp.w:call-sawfish-69.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:43][sawfish][INFO] sawfish completed. Total Runtime: 00:00:06.416
2025-09-15 20:25:48.129 wdl.w:ptcp.w:call-trgt-76.t:call-trgt_plot_meth_waterfall INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2173.meth_waterfall.trgt_plots.zip"
2025-09-15 20:25:48.235 wdl.w:ptcp.w:call-trgt-76.t:call-trgt_plot_meth_waterfall NOTICE done
2025-09-15 20:25:48.242 wdl.w:ptcp.w:call-trgt-76 NOTICE finish :: job: "call-trgt_plot_meth_waterfall"
2025-09-15 20:25:48.242 wdl.w:ptcp.w:call-trgt-76 INFO output :: job: "call-trgt_plot_meth_waterfall", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-76/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2173.meth_waterfall.trgt_plots.zip"}
2025-09-15 20:25:48.242 wdl.w:ptcp.w:call-trgt-76 INFO visit :: node: "output-images_meth_waterfall", values: {"images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-76/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2173.meth_waterfall.trgt_plots.zip"}
2025-09-15 20:25:48.250 wdl.w:ptcp.w:call-paraphase-94.t:call-run_paraphase.slurm_singularity INFO srun: job 51798080 queued and waiting for resources
2025-09-15 20:25:48.250 wdl.w:ptcp.w:call-paraphase-94.t:call-run_paraphase.slurm_singularity INFO srun: job 51798080 has been allocated resources
2025-09-15 20:25:48.250 wdl.w:ptcp.w:call-paraphase-94.t:call-run_paraphase.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:48.255 wdl.w:ptcp.w:call-trgt-81.t:call-trgt_plot_meth_waterfall NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-81/call-trgt_plot_meth_waterfall", thread: 140607120975424
2025-09-15 20:25:48.278 wdl.w:ptcp.w:call-trgt-81.t:call-trgt_plot_meth_waterfall INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:48.278 wdl.w:ptcp.w:call-trgt-81.t:call-trgt_plot_meth_waterfall INFO input :: name: "waterfall", value: true
2025-09-15 20:25:48.278 wdl.w:ptcp.w:call-trgt-81.t:call-trgt_plot_meth_waterfall INFO input :: name: "methylation", value: true
2025-09-15 20:25:48.279 wdl.w:ptcp.w:call-trgt-81.t:call-trgt_plot_meth_waterfall INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:25:48.279 wdl.w:ptcp.w:call-trgt-81.t:call-trgt_plot_meth_waterfall INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:25:48.279 wdl.w:ptcp.w:call-trgt-81.t:call-trgt_plot_meth_waterfall INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:25:48.279 wdl.w:ptcp.w:call-trgt-81.t:call-trgt_plot_meth_waterfall INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2178.trgt.sorted.spanning.bam.bai"
2025-09-15 20:25:48.279 wdl.w:ptcp.w:call-trgt-81.t:call-trgt_plot_meth_waterfall INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2178.trgt.sorted.spanning.bam"
2025-09-15 20:25:48.279 wdl.w:ptcp.w:call-trgt-81.t:call-trgt_plot_meth_waterfall INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2178.trgt.vcf"
2025-09-15 20:25:48.279 wdl.w:ptcp.w:call-trgt-81.t:call-trgt_plot_meth_waterfall INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2178"
2025-09-15 20:25:48.279 wdl.w:ptcp.w:call-trgt-81.t:call-trgt_plot_meth_waterfall INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:25:48.279 wdl.w:ptcp.w:call-trgt-81.t:call-trgt_plot_meth_waterfall INFO eval :: name: "plot_type", value: "waterfall"
2025-09-15 20:25:48.279 wdl.w:ptcp.w:call-trgt-81.t:call-trgt_plot_meth_waterfall INFO eval :: name: "show", value: "meth"
2025-09-15 20:25:48.279 wdl.w:ptcp.w:call-trgt-81.t:call-trgt_plot_meth_waterfall INFO eval :: name: "threads", value: 1
2025-09-15 20:25:48.280 wdl.w:ptcp.w:call-trgt-81.t:call-trgt_plot_meth_waterfall INFO eval :: name: "disk_size", value: 27
2025-09-15 20:25:48.280 wdl.w:ptcp.w:call-trgt-81.t:call-trgt_plot_meth_waterfall INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2178.meth_waterfall"
2025-09-15 20:25:48.280 wdl.w:ptcp.w:call-trgt-81.t:call-trgt_plot_meth_waterfall INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:48.280 wdl.w:ptcp.w:call-trgt-81.t:call-trgt_plot_meth_waterfall WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:48.281 wdl.w:ptcp.w:call-trgt-81.t:call-trgt_plot_meth_waterfall INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:25:48.281 wdl.w:ptcp.w:call-trgt-81.t:call-trgt_plot_meth_waterfall INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:48.363 wdl.w:ptcp.w:call-trgt-81.t:call-trgt_plot_meth_waterfall INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-81/call-trgt_plot_meth_waterfall/_singularity_tmpdir_p8ijpm9l"
2025-09-15 20:25:48.363 wdl.w:ptcp.w:call-trgt-81.t:call-trgt_plot_meth_waterfall INFO Slurm invocation: srun --job-name call-trgt_plot_meth_waterfall --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-81/call-trgt_plot_meth_waterfall/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-81/call-trgt_plot_meth_waterfall/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-81/call-trgt_plot_meth_waterfall/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-81/call-trgt_plot_meth_waterfall/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-81/call-trgt_genotype/out/m84036_250809_035451_s4.bc2178.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2178.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-81/call-trgt_genotype/out/m84036_250809_035451_s4.bc2178.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2178.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-81/call-trgt_genotype/out/m84036_250809_035451_s4.bc2178.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2178.trgt.sorted.spanning.bam.bai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-81/call-trgt_plot_meth_waterfall/_singularity_tmpdir_p8ijpm9l/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-81/call-trgt_plot_meth_waterfall/_singularity_tmpdir_p8ijpm9l/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:48.394 wdl.w:ptcp.w:call-trgt-81.t:call-trgt_plot_meth_waterfall NOTICE slurm_singularity run :: pid: 1206360, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-81/call-trgt_plot_meth_waterfall/slurm_singularity.log.txt"
2025-09-15 20:25:48.414 wdl.w:ptcp.w:call-sawfish-68.t:call-run_sawfish.stderr VERBOSE [M::mm_idx_gen::34.025*1.49] collected minimizers
2025-09-15 20:25:48.415 wdl.w:ptcp.w:call-sawfish-68.t:call-run_sawfish.stderr VERBOSE [M::mm_idx_gen::40.997*1.74] sorted minimizers
2025-09-15 20:25:48.415 wdl.w:ptcp.w:call-sawfish-68.t:call-run_sawfish.stderr VERBOSE [M::main::40.998*1.74] loaded/built the index for 195 target sequence(s)
2025-09-15 20:25:48.632 wdl.w:ptcp.w:call-sawfish-94.t:call-run_sawfish.slurm_singularity INFO srun: job 51798081 queued and waiting for resources
2025-09-15 20:25:48.632 wdl.w:ptcp.w:call-sawfish-94.t:call-run_sawfish.slurm_singularity INFO srun: job 51798081 has been allocated resources
2025-09-15 20:25:48.632 wdl.w:ptcp.w:call-sawfish-94.t:call-run_sawfish.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:48.632 wdl.w:ptcp.w:call-sawfish-94.t:call-run_sawfish.slurm_singularity INFO WARNING: Could not find any nv libraries on this host!
2025-09-15 20:25:48.722 wdl.w:ptcp.w:call-trgt-93.t:call-get_reads_overlapping_repeats INFO output :: name: "reads_overlapping_repeats", value: "m84036_250809_035451_s4.bc2190.repeats.bam"
2025-09-15 20:25:48.725 wdl.w:ptcp.w:call-trgt-93.t:call-get_reads_overlapping_repeats INFO output :: name: "reads_overlapping_repeats_bai", value: "m84036_250809_035451_s4.bc2190.repeats.bam.bai"
2025-09-15 20:25:48.781 wdl.w:ptcp.w:call-trgt-93.t:call-get_reads_overlapping_repeats NOTICE done
2025-09-15 20:25:48.786 wdl.w:ptcp.w:call-trgt-93 NOTICE finish :: job: "call-get_reads_overlapping_repeats"
2025-09-15 20:25:48.786 wdl.w:ptcp.w:call-trgt-93 INFO output :: job: "call-get_reads_overlapping_repeats", values: {"reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-93/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2190.repeats.bam.bai", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-93/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2190.repeats.bam"}
2025-09-15 20:25:48.786 wdl.w:ptcp.w:call-trgt-93 INFO visit :: node: "output-reads_overlapping_repeats", values: {"reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-93/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2190.repeats.bam"}
2025-09-15 20:25:48.786 wdl.w:ptcp.w:call-trgt-93 INFO visit :: node: "output-reads_overlapping_repeats_bai", values: {"reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-93/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2190.repeats.bam.bai"}
2025-09-15 20:25:48.792 wdl.w:ptcp.w:call-trgt-81.t:call-trgt_plot_motifs_allele NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-81/call-trgt_plot_motifs_allele", thread: 140607683024448
2025-09-15 20:25:48.809 wdl.w:ptcp.w:call-trgt-81.t:call-trgt_plot_motifs_allele INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:48.809 wdl.w:ptcp.w:call-trgt-81.t:call-trgt_plot_motifs_allele INFO input :: name: "waterfall", value: false
2025-09-15 20:25:48.809 wdl.w:ptcp.w:call-trgt-81.t:call-trgt_plot_motifs_allele INFO input :: name: "methylation", value: false
2025-09-15 20:25:48.809 wdl.w:ptcp.w:call-trgt-81.t:call-trgt_plot_motifs_allele INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:25:48.809 wdl.w:ptcp.w:call-trgt-81.t:call-trgt_plot_motifs_allele INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:25:48.809 wdl.w:ptcp.w:call-trgt-81.t:call-trgt_plot_motifs_allele INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:25:48.809 wdl.w:ptcp.w:call-trgt-81.t:call-trgt_plot_motifs_allele INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2178.trgt.sorted.spanning.bam.bai"
2025-09-15 20:25:48.809 wdl.w:ptcp.w:call-trgt-81.t:call-trgt_plot_motifs_allele INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2178.trgt.sorted.spanning.bam"
2025-09-15 20:25:48.809 wdl.w:ptcp.w:call-trgt-81.t:call-trgt_plot_motifs_allele INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2178.trgt.vcf"
2025-09-15 20:25:48.809 wdl.w:ptcp.w:call-trgt-81.t:call-trgt_plot_motifs_allele INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2178"
2025-09-15 20:25:48.810 wdl.w:ptcp.w:call-trgt-81.t:call-trgt_plot_motifs_allele INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:25:48.810 wdl.w:ptcp.w:call-trgt-81.t:call-trgt_plot_motifs_allele INFO eval :: name: "plot_type", value: "allele"
2025-09-15 20:25:48.810 wdl.w:ptcp.w:call-trgt-81.t:call-trgt_plot_motifs_allele INFO eval :: name: "show", value: "motifs"
2025-09-15 20:25:48.810 wdl.w:ptcp.w:call-trgt-81.t:call-trgt_plot_motifs_allele INFO eval :: name: "threads", value: 1
2025-09-15 20:25:48.810 wdl.w:ptcp.w:call-trgt-81.t:call-trgt_plot_motifs_allele INFO eval :: name: "disk_size", value: 27
2025-09-15 20:25:48.810 wdl.w:ptcp.w:call-trgt-81.t:call-trgt_plot_motifs_allele INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2178.motifs_allele"
2025-09-15 20:25:48.811 wdl.w:ptcp.w:call-trgt-81.t:call-trgt_plot_motifs_allele INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:48.811 wdl.w:ptcp.w:call-trgt-81.t:call-trgt_plot_motifs_allele WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:48.811 wdl.w:ptcp.w:call-trgt-81.t:call-trgt_plot_motifs_allele INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:25:48.811 wdl.w:ptcp.w:call-trgt-81.t:call-trgt_plot_motifs_allele INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:48.829 wdl.w:ptcp.w:call-paraphase-75.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for smn1 for sample m84036_250809_035451_s4.bc2172 at 2025-09-15 20:25:31.235753...
2025-09-15 20:25:48.829 wdl.w:ptcp.w:call-paraphase-75.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for hba for sample m84036_250809_035451_s4.bc2172 at 2025-09-15 20:25:31.564643...
2025-09-15 20:25:48.829 wdl.w:ptcp.w:call-paraphase-75.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for gba for sample m84036_250809_035451_s4.bc2172 at 2025-09-15 20:25:32.386387...
2025-09-15 20:25:48.829 wdl.w:ptcp.w:call-paraphase-75.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for cyp21 for sample m84036_250809_035451_s4.bc2172 at 2025-09-15 20:25:34.219708...
2025-09-15 20:25:48.883 wdl.w:ptcp.w:call-trgt-81.t:call-trgt_plot_motifs_allele INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-81/call-trgt_plot_motifs_allele/_singularity_tmpdir_c4bai8p3"
2025-09-15 20:25:48.883 wdl.w:ptcp.w:call-trgt-81.t:call-trgt_plot_motifs_allele INFO Slurm invocation: srun --job-name call-trgt_plot_motifs_allele --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-81/call-trgt_plot_motifs_allele/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-81/call-trgt_plot_motifs_allele/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-81/call-trgt_plot_motifs_allele/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-81/call-trgt_plot_motifs_allele/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-81/call-trgt_genotype/out/m84036_250809_035451_s4.bc2178.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2178.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-81/call-trgt_genotype/out/m84036_250809_035451_s4.bc2178.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2178.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-81/call-trgt_genotype/out/m84036_250809_035451_s4.bc2178.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2178.trgt.sorted.spanning.bam.bai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-81/call-trgt_plot_motifs_allele/_singularity_tmpdir_c4bai8p3/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-81/call-trgt_plot_motifs_allele/_singularity_tmpdir_c4bai8p3/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:48.904 wdl.w:ptcp.w:call-trgt-81.t:call-trgt_plot_motifs_allele NOTICE slurm_singularity run :: pid: 1206368, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-81/call-trgt_plot_motifs_allele/slurm_singularity.log.txt"
2025-09-15 20:25:49.002 wdl.w:ptcp.w:call-trgt-81.t:call-trgt_plot_meth_allele.slurm_singularity INFO srun: job 51798082 queued and waiting for resources
2025-09-15 20:25:49.003 wdl.w:ptcp.w:call-trgt-81.t:call-trgt_plot_meth_allele.slurm_singularity INFO srun: job 51798082 has been allocated resources
2025-09-15 20:25:49.003 wdl.w:ptcp.w:call-trgt-81.t:call-trgt_plot_meth_allele.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:49.029 wdl.w:ptcp.w:call-paraphase-93.t:call-run_paraphase INFO output :: name: "paraphase_bam", value: "m84036_250809_035451_s4.bc2190_paraphase/m84036_250809_035451_s4.bc2190.paraphase.bam"
2025-09-15 20:25:49.035 wdl.w:ptcp.w:call-paraphase-93.t:call-run_paraphase INFO output :: name: "paraphase_bam_bai", value: "m84036_250809_035451_s4.bc2190_paraphase/m84036_250809_035451_s4.bc2190.paraphase.bam.bai"
2025-09-15 20:25:49.036 wdl.w:ptcp.w:call-paraphase-93.t:call-run_paraphase INFO output :: name: "paraphase_json", value: "m84036_250809_035451_s4.bc2190_paraphase/m84036_250809_035451_s4.bc2190.paraphase.json"
2025-09-15 20:25:49.038 wdl.w:ptcp.w:call-paraphase-93.t:call-run_paraphase INFO output :: name: "paraphase_vcfs", value: []
2025-09-15 20:25:49.038 wdl.w:ptcp.w:call-paraphase-93.t:call-run_paraphase INFO output :: name: "havanno_json", value: "m84036_250809_035451_s4.bc2190.havanno.json"
2025-09-15 20:25:49.088 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_genotype INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2192.trgt.vcf"
2025-09-15 20:25:49.091 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_genotype INFO output :: name: "spanning_bam", value: "m84036_250809_035451_s4.bc2192.trgt.sorted.spanning.bam"
2025-09-15 20:25:49.092 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_genotype INFO output :: name: "spanning_bam_bai", value: "m84036_250809_035451_s4.bc2192.trgt.sorted.spanning.bam.bai"
2025-09-15 20:25:49.134 wdl.w:ptcp.w:call-paraphase-93.t:call-run_paraphase NOTICE done
2025-09-15 20:25:49.140 wdl.w:ptcp.w:call-paraphase-93 NOTICE finish :: job: "call-run_paraphase"
2025-09-15 20:25:49.140 wdl.w:ptcp.w:call-paraphase-93 INFO output :: job: "call-run_paraphase", values: {"havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-93/call-run_paraphase/out/m84036_250809_035451_s4.bc2190.havanno.json", "paraphase_vcfs": [], "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-93/call-run_paraphase/out/m84036_250809_035451_s4.bc2190_paraphase/m84036_250809_035451_s4.bc2190.paraphase.json", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-93/call-run_paraphase/out/m84036_250809_035451_s4.bc2190_paraphase/m84036_250809_035451_s4.bc2190.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-93/call-run_paraphase/out/m84036_250809_035451_s4.bc2190_paraphase/m84036_250809_035451_s4.bc2190.paraphase.bam"}
2025-09-15 20:25:49.141 wdl.w:ptcp.w:call-paraphase-93 NOTICE ready :: job: "call-call_f8", callee: "call_f8"
2025-09-15 20:25:49.141 wdl.w:ptcp.w:call-paraphase-93 INFO input :: job: "call-call_f8", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "out_prefix": "m84036_250809_035451_s4.bc2190", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-93/call-run_paraphase/out/m84036_250809_035451_s4.bc2190_paraphase/m84036_250809_035451_s4.bc2190.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-93/call-run_paraphase/out/m84036_250809_035451_s4.bc2190_paraphase/m84036_250809_035451_s4.bc2190.paraphase.bam", "sex": "F"}
2025-09-15 20:25:49.142 wdl.w:ptcp.w:call-paraphase-93 INFO visit :: node: "output-havanno_json", values: {"havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-93/call-run_paraphase/out/m84036_250809_035451_s4.bc2190.havanno.json"}
2025-09-15 20:25:49.142 wdl.w:ptcp.w:call-paraphase-93 INFO visit :: node: "output-paraphase_bam", values: {"paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-93/call-run_paraphase/out/m84036_250809_035451_s4.bc2190_paraphase/m84036_250809_035451_s4.bc2190.paraphase.bam"}
2025-09-15 20:25:49.142 wdl.w:ptcp.w:call-paraphase-93 INFO visit :: node: "output-paraphase_bam_bai", values: {"paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-93/call-run_paraphase/out/m84036_250809_035451_s4.bc2190_paraphase/m84036_250809_035451_s4.bc2190.paraphase.bam.bai"}
2025-09-15 20:25:49.142 wdl.w:ptcp.w:call-paraphase-93 INFO visit :: node: "output-paraphase_json", values: {"paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-93/call-run_paraphase/out/m84036_250809_035451_s4.bc2190_paraphase/m84036_250809_035451_s4.bc2190.paraphase.json"}
2025-09-15 20:25:49.142 wdl.w:ptcp.w:call-paraphase-93 INFO visit :: node: "output-paraphase_vcfs", values: {"paraphase_vcfs": []}
2025-09-15 20:25:49.146 wdl.w:ptcp.w:call-trgt-81.t:call-trgt_plot_motifs_waterfall NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-81/call-trgt_plot_motifs_waterfall", thread: 140611969599040
2025-09-15 20:25:49.164 wdl.w:ptcp.w:call-trgt-81.t:call-trgt_plot_motifs_waterfall INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:49.164 wdl.w:ptcp.w:call-trgt-81.t:call-trgt_plot_motifs_waterfall INFO input :: name: "waterfall", value: true
2025-09-15 20:25:49.164 wdl.w:ptcp.w:call-trgt-81.t:call-trgt_plot_motifs_waterfall INFO input :: name: "methylation", value: false
2025-09-15 20:25:49.164 wdl.w:ptcp.w:call-trgt-81.t:call-trgt_plot_motifs_waterfall INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:25:49.164 wdl.w:ptcp.w:call-trgt-81.t:call-trgt_plot_motifs_waterfall INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:25:49.164 wdl.w:ptcp.w:call-trgt-81.t:call-trgt_plot_motifs_waterfall INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:25:49.164 wdl.w:ptcp.w:call-trgt-81.t:call-trgt_plot_motifs_waterfall INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2178.trgt.sorted.spanning.bam.bai"
2025-09-15 20:25:49.164 wdl.w:ptcp.w:call-trgt-81.t:call-trgt_plot_motifs_waterfall INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2178.trgt.sorted.spanning.bam"
2025-09-15 20:25:49.164 wdl.w:ptcp.w:call-trgt-81.t:call-trgt_plot_motifs_waterfall INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2178.trgt.vcf"
2025-09-15 20:25:49.164 wdl.w:ptcp.w:call-trgt-81.t:call-trgt_plot_motifs_waterfall INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2178"
2025-09-15 20:25:49.165 wdl.w:ptcp.w:call-trgt-81.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:25:49.165 wdl.w:ptcp.w:call-trgt-81.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "plot_type", value: "waterfall"
2025-09-15 20:25:49.165 wdl.w:ptcp.w:call-trgt-81.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "show", value: "motifs"
2025-09-15 20:25:49.165 wdl.w:ptcp.w:call-trgt-81.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "threads", value: 1
2025-09-15 20:25:49.165 wdl.w:ptcp.w:call-trgt-81.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "disk_size", value: 27
2025-09-15 20:25:49.165 wdl.w:ptcp.w:call-trgt-81.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2178.motifs_waterfall"
2025-09-15 20:25:49.166 wdl.w:ptcp.w:call-trgt-81.t:call-trgt_plot_motifs_waterfall INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:49.166 wdl.w:ptcp.w:call-trgt-81.t:call-trgt_plot_motifs_waterfall WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:49.166 wdl.w:ptcp.w:call-trgt-81.t:call-trgt_plot_motifs_waterfall INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:25:49.166 wdl.w:ptcp.w:call-trgt-81.t:call-trgt_plot_motifs_waterfall INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:49.167 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_genotype NOTICE done
2025-09-15 20:25:49.175 wdl.w:ptcp.w:call-trgt-95 NOTICE finish :: job: "call-trgt_genotype"
2025-09-15 20:25:49.175 wdl.w:ptcp.w:call-trgt-95 INFO output :: job: "call-trgt_genotype", values: {"spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-95/call-trgt_genotype/out/m84036_250809_035451_s4.bc2192.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-95/call-trgt_genotype/out/m84036_250809_035451_s4.bc2192.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-95/call-trgt_genotype/out/m84036_250809_035451_s4.bc2192.trgt.vcf"}
2025-09-15 20:25:49.175 wdl.w:ptcp.w:call-trgt-95 NOTICE ready :: job: "call-trgt_plot_meth_allele", callee: "trgt_plot"
2025-09-15 20:25:49.175 wdl.w:ptcp.w:call-trgt-95 INFO input :: job: "call-trgt_plot_meth_allele", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": false, "methylation": true, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-95/call-trgt_genotype/out/m84036_250809_035451_s4.bc2192.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-95/call-trgt_genotype/out/m84036_250809_035451_s4.bc2192.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-95/call-trgt_genotype/out/m84036_250809_035451_s4.bc2192.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2192"}
2025-09-15 20:25:49.176 wdl.w:ptcp.w:call-trgt-95 NOTICE ready :: job: "call-trgt_plot_meth_waterfall", callee: "trgt_plot"
2025-09-15 20:25:49.176 wdl.w:ptcp.w:call-trgt-95 INFO input :: job: "call-trgt_plot_meth_waterfall", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": true, "methylation": true, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-95/call-trgt_genotype/out/m84036_250809_035451_s4.bc2192.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-95/call-trgt_genotype/out/m84036_250809_035451_s4.bc2192.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-95/call-trgt_genotype/out/m84036_250809_035451_s4.bc2192.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2192"}
2025-09-15 20:25:49.177 wdl.w:ptcp.w:call-trgt-95 NOTICE ready :: job: "call-trgt_plot_motifs_allele", callee: "trgt_plot"
2025-09-15 20:25:49.177 wdl.w:ptcp.w:call-trgt-95 INFO input :: job: "call-trgt_plot_motifs_allele", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": false, "methylation": false, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-95/call-trgt_genotype/out/m84036_250809_035451_s4.bc2192.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-95/call-trgt_genotype/out/m84036_250809_035451_s4.bc2192.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-95/call-trgt_genotype/out/m84036_250809_035451_s4.bc2192.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2192"}
2025-09-15 20:25:49.178 wdl.w:ptcp.w:call-trgt-95 NOTICE ready :: job: "call-trgt_plot_motifs_waterfall", callee: "trgt_plot"
2025-09-15 20:25:49.178 wdl.w:ptcp.w:call-trgt-95 INFO input :: job: "call-trgt_plot_motifs_waterfall", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": true, "methylation": false, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-95/call-trgt_genotype/out/m84036_250809_035451_s4.bc2192.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-95/call-trgt_genotype/out/m84036_250809_035451_s4.bc2192.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-95/call-trgt_genotype/out/m84036_250809_035451_s4.bc2192.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2192"}
2025-09-15 20:25:49.179 wdl.w:ptcp.w:call-trgt-95 INFO visit :: node: "output-spanning_bam", values: {"spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-95/call-trgt_genotype/out/m84036_250809_035451_s4.bc2192.trgt.sorted.spanning.bam"}
2025-09-15 20:25:49.179 wdl.w:ptcp.w:call-trgt-95 INFO visit :: node: "output-spanning_bam_bai", values: {"spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-95/call-trgt_genotype/out/m84036_250809_035451_s4.bc2192.trgt.sorted.spanning.bam.bai"}
2025-09-15 20:25:49.179 wdl.w:ptcp.w:call-trgt-95 INFO visit :: node: "output-vcf", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-95/call-trgt_genotype/out/m84036_250809_035451_s4.bc2192.trgt.vcf"}
2025-09-15 20:25:49.182 wdl.w:ptcp.w:call-trgt-72.t:call-trgt_plot_meth_allele NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-72/call-trgt_plot_meth_allele", thread: 140611944420928
2025-09-15 20:25:49.204 wdl.w:ptcp.w:call-trgt-72.t:call-trgt_plot_meth_allele INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:49.204 wdl.w:ptcp.w:call-trgt-72.t:call-trgt_plot_meth_allele INFO input :: name: "waterfall", value: false
2025-09-15 20:25:49.204 wdl.w:ptcp.w:call-trgt-72.t:call-trgt_plot_meth_allele INFO input :: name: "methylation", value: true
2025-09-15 20:25:49.204 wdl.w:ptcp.w:call-trgt-72.t:call-trgt_plot_meth_allele INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:25:49.204 wdl.w:ptcp.w:call-trgt-72.t:call-trgt_plot_meth_allele INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:25:49.204 wdl.w:ptcp.w:call-trgt-72.t:call-trgt_plot_meth_allele INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:25:49.204 wdl.w:ptcp.w:call-trgt-72.t:call-trgt_plot_meth_allele INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2169.trgt.sorted.spanning.bam.bai"
2025-09-15 20:25:49.204 wdl.w:ptcp.w:call-trgt-72.t:call-trgt_plot_meth_allele INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2169.trgt.sorted.spanning.bam"
2025-09-15 20:25:49.205 wdl.w:ptcp.w:call-trgt-72.t:call-trgt_plot_meth_allele INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2169.trgt.vcf"
2025-09-15 20:25:49.205 wdl.w:ptcp.w:call-trgt-72.t:call-trgt_plot_meth_allele INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2169"
2025-09-15 20:25:49.205 wdl.w:ptcp.w:call-trgt-72.t:call-trgt_plot_meth_allele INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:25:49.205 wdl.w:ptcp.w:call-trgt-72.t:call-trgt_plot_meth_allele INFO eval :: name: "plot_type", value: "allele"
2025-09-15 20:25:49.205 wdl.w:ptcp.w:call-trgt-72.t:call-trgt_plot_meth_allele INFO eval :: name: "show", value: "meth"
2025-09-15 20:25:49.205 wdl.w:ptcp.w:call-trgt-72.t:call-trgt_plot_meth_allele INFO eval :: name: "threads", value: 1
2025-09-15 20:25:49.205 wdl.w:ptcp.w:call-trgt-72.t:call-trgt_plot_meth_allele INFO eval :: name: "disk_size", value: 27
2025-09-15 20:25:49.205 wdl.w:ptcp.w:call-trgt-72.t:call-trgt_plot_meth_allele INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2169.meth_allele"
2025-09-15 20:25:49.206 wdl.w:ptcp.w:call-trgt-72.t:call-trgt_plot_meth_allele INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:49.206 wdl.w:ptcp.w:call-trgt-72.t:call-trgt_plot_meth_allele WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:49.206 wdl.w:ptcp.w:call-trgt-72.t:call-trgt_plot_meth_allele INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:25:49.206 wdl.w:ptcp.w:call-trgt-72.t:call-trgt_plot_meth_allele INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:49.237 wdl.w:ptcp.w:call-trgt-77.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:48 [ERROR] - No reads found for TRID=PRTS_ARX
2025-09-15 20:25:49.238 wdl.w:ptcp.w:call-trgt-77.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:48 [ERROR] - No reads found for TRID=EIEE1_ARX
2025-09-15 20:25:49.243 wdl.w:ptcp.w:call-trgt-81.t:call-trgt_plot_motifs_waterfall INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-81/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_m1pst1av"
2025-09-15 20:25:49.244 wdl.w:ptcp.w:call-trgt-81.t:call-trgt_plot_motifs_waterfall INFO Slurm invocation: srun --job-name call-trgt_plot_motifs_waterfall --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-81/call-trgt_plot_motifs_waterfall/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-81/call-trgt_plot_motifs_waterfall/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-81/call-trgt_plot_motifs_waterfall/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-81/call-trgt_plot_motifs_waterfall/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-81/call-trgt_genotype/out/m84036_250809_035451_s4.bc2178.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2178.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-81/call-trgt_genotype/out/m84036_250809_035451_s4.bc2178.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2178.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-81/call-trgt_genotype/out/m84036_250809_035451_s4.bc2178.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2178.trgt.sorted.spanning.bam.bai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-81/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_m1pst1av/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-81/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_m1pst1av/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:49.264 wdl.w:ptcp.w:call-trgt-81.t:call-trgt_plot_motifs_waterfall NOTICE slurm_singularity run :: pid: 1206377, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-81/call-trgt_plot_motifs_waterfall/slurm_singularity.log.txt"
2025-09-15 20:25:49.288 wdl.w:ptcp.w:call-trgt-72.t:call-trgt_plot_meth_allele INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-72/call-trgt_plot_meth_allele/_singularity_tmpdir_ns1gpwnl"
2025-09-15 20:25:49.288 wdl.w:ptcp.w:call-trgt-72.t:call-trgt_plot_meth_allele INFO Slurm invocation: srun --job-name call-trgt_plot_meth_allele --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-72/call-trgt_plot_meth_allele/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-72/call-trgt_plot_meth_allele/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-72/call-trgt_plot_meth_allele/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-72/call-trgt_plot_meth_allele/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-72/call-trgt_genotype/out/m84036_250809_035451_s4.bc2169.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2169.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-72/call-trgt_genotype/out/m84036_250809_035451_s4.bc2169.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2169.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-72/call-trgt_genotype/out/m84036_250809_035451_s4.bc2169.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2169.trgt.vcf:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-72/call-trgt_plot_meth_allele/_singularity_tmpdir_ns1gpwnl/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-72/call-trgt_plot_meth_allele/_singularity_tmpdir_ns1gpwnl/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:49.297 wdl.w:ptcp.w:call-trgt-72.t:call-trgt_plot_meth_allele NOTICE slurm_singularity run :: pid: 1206379, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-72/call-trgt_plot_meth_allele/slurm_singularity.log.txt"
2025-09-15 20:25:49.395 wdl.w:ptcp.w:call-trgt-95.t:call-get_reads_overlapping_repeats INFO output :: name: "reads_overlapping_repeats", value: "m84036_250809_035451_s4.bc2192.repeats.bam"
2025-09-15 20:25:49.398 wdl.w:ptcp.w:call-trgt-95.t:call-get_reads_overlapping_repeats INFO output :: name: "reads_overlapping_repeats_bai", value: "m84036_250809_035451_s4.bc2192.repeats.bam.bai"
2025-09-15 20:25:49.404 wdl.w:ptcp.w:call-trgt-81.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO srun: job 51798083 queued and waiting for resources
2025-09-15 20:25:49.404 wdl.w:ptcp.w:call-trgt-81.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO srun: job 51798083 has been allocated resources
2025-09-15 20:25:49.405 wdl.w:ptcp.w:call-trgt-81.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:49.458 wdl.w:ptcp.w:call-trgt-95.t:call-get_reads_overlapping_repeats NOTICE done
2025-09-15 20:25:49.462 wdl.w:ptcp.w:call-trgt-95 NOTICE finish :: job: "call-get_reads_overlapping_repeats"
2025-09-15 20:25:49.462 wdl.w:ptcp.w:call-trgt-95 INFO output :: job: "call-get_reads_overlapping_repeats", values: {"reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-95/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2192.repeats.bam.bai", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-95/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2192.repeats.bam"}
2025-09-15 20:25:49.463 wdl.w:ptcp.w:call-trgt-95 INFO visit :: node: "output-reads_overlapping_repeats", values: {"reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-95/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2192.repeats.bam"}
2025-09-15 20:25:49.463 wdl.w:ptcp.w:call-trgt-95 INFO visit :: node: "output-reads_overlapping_repeats_bai", values: {"reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-95/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2192.repeats.bam.bai"}
2025-09-15 20:25:49.470 wdl.w:ptcp.w:call-trgt-72.t:call-trgt_plot_meth_waterfall NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-72/call-trgt_plot_meth_waterfall", thread: 140613034948160
2025-09-15 20:25:49.492 wdl.w:ptcp.w:call-trgt-72.t:call-trgt_plot_meth_waterfall INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:49.492 wdl.w:ptcp.w:call-trgt-72.t:call-trgt_plot_meth_waterfall INFO input :: name: "waterfall", value: true
2025-09-15 20:25:49.492 wdl.w:ptcp.w:call-trgt-72.t:call-trgt_plot_meth_waterfall INFO input :: name: "methylation", value: true
2025-09-15 20:25:49.492 wdl.w:ptcp.w:call-trgt-72.t:call-trgt_plot_meth_waterfall INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:25:49.492 wdl.w:ptcp.w:call-trgt-72.t:call-trgt_plot_meth_waterfall INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:25:49.492 wdl.w:ptcp.w:call-trgt-72.t:call-trgt_plot_meth_waterfall INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:25:49.492 wdl.w:ptcp.w:call-trgt-72.t:call-trgt_plot_meth_waterfall INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2169.trgt.sorted.spanning.bam.bai"
2025-09-15 20:25:49.492 wdl.w:ptcp.w:call-trgt-72.t:call-trgt_plot_meth_waterfall INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2169.trgt.sorted.spanning.bam"
2025-09-15 20:25:49.492 wdl.w:ptcp.w:call-trgt-72.t:call-trgt_plot_meth_waterfall INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2169.trgt.vcf"
2025-09-15 20:25:49.492 wdl.w:ptcp.w:call-trgt-72.t:call-trgt_plot_meth_waterfall INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2169"
2025-09-15 20:25:49.493 wdl.w:ptcp.w:call-trgt-72.t:call-trgt_plot_meth_waterfall INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:25:49.493 wdl.w:ptcp.w:call-trgt-72.t:call-trgt_plot_meth_waterfall INFO eval :: name: "plot_type", value: "waterfall"
2025-09-15 20:25:49.493 wdl.w:ptcp.w:call-trgt-72.t:call-trgt_plot_meth_waterfall INFO eval :: name: "show", value: "meth"
2025-09-15 20:25:49.493 wdl.w:ptcp.w:call-trgt-72.t:call-trgt_plot_meth_waterfall INFO eval :: name: "threads", value: 1
2025-09-15 20:25:49.493 wdl.w:ptcp.w:call-trgt-72.t:call-trgt_plot_meth_waterfall INFO eval :: name: "disk_size", value: 27
2025-09-15 20:25:49.493 wdl.w:ptcp.w:call-trgt-72.t:call-trgt_plot_meth_waterfall INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2169.meth_waterfall"
2025-09-15 20:25:49.494 wdl.w:ptcp.w:call-trgt-72.t:call-trgt_plot_meth_waterfall INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:49.494 wdl.w:ptcp.w:call-trgt-72.t:call-trgt_plot_meth_waterfall WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:49.494 wdl.w:ptcp.w:call-trgt-72.t:call-trgt_plot_meth_waterfall INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:25:49.494 wdl.w:ptcp.w:call-trgt-72.t:call-trgt_plot_meth_waterfall INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:49.556 wdl.w:ptcp.w:call-trgt-72.t:call-trgt_plot_meth_waterfall INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-72/call-trgt_plot_meth_waterfall/_singularity_tmpdir_5thibsg7"
2025-09-15 20:25:49.556 wdl.w:ptcp.w:call-trgt-72.t:call-trgt_plot_meth_waterfall INFO Slurm invocation: srun --job-name call-trgt_plot_meth_waterfall --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-72/call-trgt_plot_meth_waterfall/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-72/call-trgt_plot_meth_waterfall/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-72/call-trgt_plot_meth_waterfall/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-72/call-trgt_plot_meth_waterfall/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-72/call-trgt_genotype/out/m84036_250809_035451_s4.bc2169.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2169.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-72/call-trgt_genotype/out/m84036_250809_035451_s4.bc2169.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2169.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-72/call-trgt_genotype/out/m84036_250809_035451_s4.bc2169.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2169.trgt.vcf:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-72/call-trgt_plot_meth_waterfall/_singularity_tmpdir_5thibsg7/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-72/call-trgt_plot_meth_waterfall/_singularity_tmpdir_5thibsg7/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:49.567 wdl.w:ptcp.w:call-trgt-72.t:call-trgt_plot_meth_waterfall NOTICE slurm_singularity run :: pid: 1206392, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-72/call-trgt_plot_meth_waterfall/slurm_singularity.log.txt"
2025-09-15 20:25:49.901 wdl.w:ptcp.w:call-trgt-76.t:call-trgt_plot_motifs_waterfall INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2173.motifs_waterfall.trgt_plots.zip"
2025-09-15 20:25:49.918 wdl.w:ptcp.w:call-trgt-81.t:call-trgt_plot_motifs_allele.slurm_singularity INFO srun: job 51798084 queued and waiting for resources
2025-09-15 20:25:49.918 wdl.w:ptcp.w:call-trgt-81.t:call-trgt_plot_motifs_allele.slurm_singularity INFO srun: job 51798084 has been allocated resources
2025-09-15 20:25:49.918 wdl.w:ptcp.w:call-trgt-81.t:call-trgt_plot_motifs_allele.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:50.018 wdl.w:ptcp.w:call-trgt-76.t:call-trgt_plot_motifs_waterfall NOTICE done
2025-09-15 20:25:50.023 wdl.w:ptcp.w:call-trgt-76 NOTICE finish :: job: "call-trgt_plot_motifs_waterfall"
2025-09-15 20:25:50.023 wdl.w:ptcp.w:call-trgt-76 INFO output :: job: "call-trgt_plot_motifs_waterfall", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-76/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2173.motifs_waterfall.trgt_plots.zip"}
2025-09-15 20:25:50.023 wdl.w:ptcp.w:call-trgt-76 INFO visit :: node: "output-images_motifs_waterfall", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-76/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2173.motifs_waterfall.trgt_plots.zip"}
2025-09-15 20:25:50.023 wdl.w:ptcp.w:call-trgt-76 INFO visit :: node: "outputs", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-76/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2173.motifs_waterfall.trgt_plots.zip", "images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-76/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2173.meth_allele.trgt_plots.zip", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-76/call-trgt_genotype/out/m84036_250809_035451_s4.bc2173.trgt.sorted.spanning.bam.bai", "images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-76/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2173.motifs_allele.trgt_plots.zip", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-76/call-trgt_genotype/out/m84036_250809_035451_s4.bc2173.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-76/call-trgt_genotype/out/m84036_250809_035451_s4.bc2173.trgt.vcf", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-76/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2173.repeats.bam", "images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-76/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2173.meth_waterfall.trgt_plots.zip", "reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-76/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2173.repeats.bam.bai"}
2025-09-15 20:25:50.027 wdl.w:ptcp.w:call-trgt-72.t:call-trgt_plot_motifs_allele NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-72/call-trgt_plot_motifs_allele", thread: 140608186324544
2025-09-15 20:25:50.043 wdl.w:ptcp.w:call-trgt-72.t:call-trgt_plot_motifs_allele INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:50.044 wdl.w:ptcp.w:call-trgt-72.t:call-trgt_plot_motifs_allele INFO input :: name: "waterfall", value: false
2025-09-15 20:25:50.044 wdl.w:ptcp.w:call-trgt-72.t:call-trgt_plot_motifs_allele INFO input :: name: "methylation", value: false
2025-09-15 20:25:50.044 wdl.w:ptcp.w:call-trgt-72.t:call-trgt_plot_motifs_allele INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:25:50.044 wdl.w:ptcp.w:call-trgt-72.t:call-trgt_plot_motifs_allele INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:25:50.044 wdl.w:ptcp.w:call-trgt-72.t:call-trgt_plot_motifs_allele INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:25:50.044 wdl.w:ptcp.w:call-trgt-72.t:call-trgt_plot_motifs_allele INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2169.trgt.sorted.spanning.bam.bai"
2025-09-15 20:25:50.044 wdl.w:ptcp.w:call-trgt-72.t:call-trgt_plot_motifs_allele INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2169.trgt.sorted.spanning.bam"
2025-09-15 20:25:50.044 wdl.w:ptcp.w:call-trgt-72.t:call-trgt_plot_motifs_allele INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2169.trgt.vcf"
2025-09-15 20:25:50.044 wdl.w:ptcp.w:call-trgt-72.t:call-trgt_plot_motifs_allele INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2169"
2025-09-15 20:25:50.046 wdl.w:ptcp.w:call-trgt-72.t:call-trgt_plot_motifs_allele INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:25:50.046 wdl.w:ptcp.w:call-trgt-72.t:call-trgt_plot_motifs_allele INFO eval :: name: "plot_type", value: "allele"
2025-09-15 20:25:50.046 wdl.w:ptcp.w:call-trgt-72.t:call-trgt_plot_motifs_allele INFO eval :: name: "show", value: "motifs"
2025-09-15 20:25:50.046 wdl.w:ptcp.w:call-trgt-72.t:call-trgt_plot_motifs_allele INFO eval :: name: "threads", value: 1
2025-09-15 20:25:50.046 wdl.w:ptcp.w:call-trgt-72.t:call-trgt_plot_motifs_allele INFO eval :: name: "disk_size", value: 27
2025-09-15 20:25:50.046 wdl.w:ptcp.w:call-trgt-72.t:call-trgt_plot_motifs_allele INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2169.motifs_allele"
2025-09-15 20:25:50.047 wdl.w:ptcp.w:call-trgt-72.t:call-trgt_plot_motifs_allele INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:50.047 wdl.w:ptcp.w:call-trgt-72.t:call-trgt_plot_motifs_allele WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:50.047 wdl.w:ptcp.w:call-trgt-72.t:call-trgt_plot_motifs_allele INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:25:50.047 wdl.w:ptcp.w:call-trgt-72.t:call-trgt_plot_motifs_allele INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:50.125 wdl.w:ptcp.w:call-trgt-76 NOTICE done
2025-09-15 20:25:50.128 wdl.w:ptcp.w:call-trgt-72.t:call-trgt_plot_motifs_allele INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-72/call-trgt_plot_motifs_allele/_singularity_tmpdir_13cea56b"
2025-09-15 20:25:50.128 wdl.w:ptcp.w:call-trgt-72.t:call-trgt_plot_motifs_allele INFO Slurm invocation: srun --job-name call-trgt_plot_motifs_allele --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-72/call-trgt_plot_motifs_allele/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-72/call-trgt_plot_motifs_allele/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-72/call-trgt_plot_motifs_allele/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-72/call-trgt_plot_motifs_allele/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-72/call-trgt_genotype/out/m84036_250809_035451_s4.bc2169.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2169.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-72/call-trgt_genotype/out/m84036_250809_035451_s4.bc2169.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2169.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-72/call-trgt_genotype/out/m84036_250809_035451_s4.bc2169.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2169.trgt.vcf:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-72/call-trgt_plot_motifs_allele/_singularity_tmpdir_13cea56b/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-72/call-trgt_plot_motifs_allele/_singularity_tmpdir_13cea56b/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:50.130 wdl.w:ptcp NOTICE finish :: job: "call-trgt-76"
2025-09-15 20:25:50.130 wdl.w:ptcp INFO output :: job: "call-trgt-76", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-76/out/m84036_250809_035451_s4.bc2173.motifs_waterfall.trgt_plots.zip", "images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-76/out/m84036_250809_035451_s4.bc2173.meth_allele.trgt_plots.zip", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-76/out/m84036_250809_035451_s4.bc2173.trgt.sorted.spanning.bam.bai", "images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-76/out/m84036_250809_035451_s4.bc2173.motifs_allele.trgt_plots.zip", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-76/out/m84036_250809_035451_s4.bc2173.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-76/out/m84036_250809_035451_s4.bc2173.trgt.vcf", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-76/out/m84036_250809_035451_s4.bc2173.repeats.bam", "images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-76/out/m84036_250809_035451_s4.bc2173.meth_waterfall.trgt_plots.zip", "reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-76/out/m84036_250809_035451_s4.bc2173.repeats.bam.bai"}
2025-09-15 20:25:50.139 wdl.w:ptcp.w:call-trgt-72.t:call-trgt_plot_motifs_allele NOTICE slurm_singularity run :: pid: 1206468, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-72/call-trgt_plot_motifs_allele/slurm_singularity.log.txt"
2025-09-15 20:25:50.192 wdl.w:ptcp.w:call-trgt-73.t:call-trgt_plot_meth_waterfall INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2170.meth_waterfall.trgt_plots.zip"
2025-09-15 20:25:50.274 wdl.w:ptcp.w:call-trgt-81.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO srun: job 51798085 queued and waiting for resources
2025-09-15 20:25:50.274 wdl.w:ptcp.w:call-trgt-81.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO srun: job 51798085 has been allocated resources
2025-09-15 20:25:50.274 wdl.w:ptcp.w:call-trgt-81.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:50.310 wdl.w:ptcp.w:call-trgt-72.t:call-trgt_plot_meth_allele.slurm_singularity INFO srun: job 51798086 queued and waiting for resources
2025-09-15 20:25:50.310 wdl.w:ptcp.w:call-trgt-72.t:call-trgt_plot_meth_allele.slurm_singularity INFO srun: job 51798086 has been allocated resources
2025-09-15 20:25:50.310 wdl.w:ptcp.w:call-trgt-72.t:call-trgt_plot_meth_allele.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:50.322 wdl.w:ptcp.w:call-trgt-73.t:call-trgt_plot_meth_waterfall NOTICE done
2025-09-15 20:25:50.327 wdl.w:ptcp.w:call-trgt-73 NOTICE finish :: job: "call-trgt_plot_meth_waterfall"
2025-09-15 20:25:50.327 wdl.w:ptcp.w:call-trgt-73 INFO output :: job: "call-trgt_plot_meth_waterfall", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-73/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2170.meth_waterfall.trgt_plots.zip"}
2025-09-15 20:25:50.328 wdl.w:ptcp.w:call-trgt-73 INFO visit :: node: "output-images_meth_waterfall", values: {"images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-73/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2170.meth_waterfall.trgt_plots.zip"}
2025-09-15 20:25:50.328 wdl.w:ptcp.w:call-trgt-73 INFO visit :: node: "outputs", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-73/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2170.motifs_waterfall.trgt_plots.zip", "images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-73/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2170.meth_allele.trgt_plots.zip", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-73/call-trgt_genotype/out/m84036_250809_035451_s4.bc2170.trgt.sorted.spanning.bam.bai", "images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-73/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2170.motifs_allele.trgt_plots.zip", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-73/call-trgt_genotype/out/m84036_250809_035451_s4.bc2170.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-73/call-trgt_genotype/out/m84036_250809_035451_s4.bc2170.trgt.vcf", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-73/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2170.repeats.bam", "images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-73/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2170.meth_waterfall.trgt_plots.zip", "reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-73/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2170.repeats.bam.bai"}
2025-09-15 20:25:50.334 wdl.w:ptcp.w:call-trgt-72.t:call-trgt_plot_motifs_waterfall NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-72/call-trgt_plot_motifs_waterfall", thread: 140613563426368
2025-09-15 20:25:50.355 wdl.w:ptcp.w:call-trgt-72.t:call-trgt_plot_motifs_waterfall INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:50.355 wdl.w:ptcp.w:call-trgt-72.t:call-trgt_plot_motifs_waterfall INFO input :: name: "waterfall", value: true
2025-09-15 20:25:50.355 wdl.w:ptcp.w:call-trgt-72.t:call-trgt_plot_motifs_waterfall INFO input :: name: "methylation", value: false
2025-09-15 20:25:50.355 wdl.w:ptcp.w:call-trgt-72.t:call-trgt_plot_motifs_waterfall INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:25:50.355 wdl.w:ptcp.w:call-trgt-72.t:call-trgt_plot_motifs_waterfall INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:25:50.355 wdl.w:ptcp.w:call-trgt-72.t:call-trgt_plot_motifs_waterfall INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:25:50.355 wdl.w:ptcp.w:call-trgt-72.t:call-trgt_plot_motifs_waterfall INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2169.trgt.sorted.spanning.bam.bai"
2025-09-15 20:25:50.355 wdl.w:ptcp.w:call-trgt-72.t:call-trgt_plot_motifs_waterfall INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2169.trgt.sorted.spanning.bam"
2025-09-15 20:25:50.355 wdl.w:ptcp.w:call-trgt-72.t:call-trgt_plot_motifs_waterfall INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2169.trgt.vcf"
2025-09-15 20:25:50.355 wdl.w:ptcp.w:call-trgt-72.t:call-trgt_plot_motifs_waterfall INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2169"
2025-09-15 20:25:50.356 wdl.w:ptcp.w:call-trgt-72.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:25:50.356 wdl.w:ptcp.w:call-trgt-72.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "plot_type", value: "waterfall"
2025-09-15 20:25:50.356 wdl.w:ptcp.w:call-trgt-72.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "show", value: "motifs"
2025-09-15 20:25:50.356 wdl.w:ptcp.w:call-trgt-72.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "threads", value: 1
2025-09-15 20:25:50.356 wdl.w:ptcp.w:call-trgt-72.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "disk_size", value: 27
2025-09-15 20:25:50.356 wdl.w:ptcp.w:call-trgt-72.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2169.motifs_waterfall"
2025-09-15 20:25:50.357 wdl.w:ptcp.w:call-trgt-72.t:call-trgt_plot_motifs_waterfall INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:50.357 wdl.w:ptcp.w:call-trgt-72.t:call-trgt_plot_motifs_waterfall WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:50.357 wdl.w:ptcp.w:call-trgt-72.t:call-trgt_plot_motifs_waterfall INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:25:50.357 wdl.w:ptcp.w:call-trgt-72.t:call-trgt_plot_motifs_waterfall INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:50.363 wdl.w:ptcp.w:call-sawfish-69.t:call-run_sawfish INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2166_sawfish/m84036_250809_035451_s4.bc2166.sv.vcf.gz"
2025-09-15 20:25:50.368 wdl.w:ptcp.w:call-sawfish-69.t:call-run_sawfish INFO output :: name: "vcf_tbi", value: "m84036_250809_035451_s4.bc2166_sawfish/m84036_250809_035451_s4.bc2166.sv.vcf.gz.tbi"
2025-09-15 20:25:50.370 wdl.w:ptcp.w:call-sawfish-69.t:call-run_sawfish INFO output :: name: "minimap2_bam", value: "m84036_250809_035451_s4.bc2166.minimap2.bam"
2025-09-15 20:25:50.371 wdl.w:ptcp.w:call-sawfish-69.t:call-run_sawfish INFO output :: name: "minimap2_bam_bai", value: "m84036_250809_035451_s4.bc2166.minimap2.bam.bai"
2025-09-15 20:25:50.435 wdl.w:ptcp.w:call-trgt-73 NOTICE done
2025-09-15 20:25:50.437 wdl.w:ptcp.w:call-trgt-72.t:call-trgt_plot_motifs_waterfall INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-72/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_i_hf8s6q"
2025-09-15 20:25:50.437 wdl.w:ptcp.w:call-trgt-72.t:call-trgt_plot_motifs_waterfall INFO Slurm invocation: srun --job-name call-trgt_plot_motifs_waterfall --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-72/call-trgt_plot_motifs_waterfall/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-72/call-trgt_plot_motifs_waterfall/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-72/call-trgt_plot_motifs_waterfall/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-72/call-trgt_plot_motifs_waterfall/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-72/call-trgt_genotype/out/m84036_250809_035451_s4.bc2169.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2169.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-72/call-trgt_genotype/out/m84036_250809_035451_s4.bc2169.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2169.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-72/call-trgt_genotype/out/m84036_250809_035451_s4.bc2169.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2169.trgt.vcf:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-72/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_i_hf8s6q/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-72/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_i_hf8s6q/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:50.440 wdl.w:ptcp NOTICE finish :: job: "call-trgt-73"
2025-09-15 20:25:50.440 wdl.w:ptcp INFO output :: job: "call-trgt-73", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-73/out/m84036_250809_035451_s4.bc2170.motifs_waterfall.trgt_plots.zip", "images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-73/out/m84036_250809_035451_s4.bc2170.meth_allele.trgt_plots.zip", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-73/out/m84036_250809_035451_s4.bc2170.trgt.sorted.spanning.bam.bai", "images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-73/out/m84036_250809_035451_s4.bc2170.motifs_allele.trgt_plots.zip", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-73/out/m84036_250809_035451_s4.bc2170.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-73/out/m84036_250809_035451_s4.bc2170.trgt.vcf", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-73/out/m84036_250809_035451_s4.bc2170.repeats.bam", "images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-73/out/m84036_250809_035451_s4.bc2170.meth_waterfall.trgt_plots.zip", "reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-73/out/m84036_250809_035451_s4.bc2170.repeats.bam.bai"}
2025-09-15 20:25:50.457 wdl.w:ptcp.w:call-trgt-72.t:call-trgt_plot_motifs_waterfall NOTICE slurm_singularity run :: pid: 1206476, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-72/call-trgt_plot_motifs_waterfall/slurm_singularity.log.txt"
2025-09-15 20:25:50.515 wdl.w:ptcp.w:call-sawfish-69.t:call-run_sawfish NOTICE done
2025-09-15 20:25:50.522 wdl.w:ptcp.w:call-sawfish-69 NOTICE finish :: job: "call-run_sawfish"
2025-09-15 20:25:50.522 wdl.w:ptcp.w:call-sawfish-69 INFO output :: job: "call-run_sawfish", values: {"minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-69/call-run_sawfish/out/m84036_250809_035451_s4.bc2166.minimap2.bam.bai", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-69/call-run_sawfish/out/m84036_250809_035451_s4.bc2166.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-69/call-run_sawfish/out/m84036_250809_035451_s4.bc2166_sawfish/m84036_250809_035451_s4.bc2166.sv.vcf.gz.tbi", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-69/call-run_sawfish/out/m84036_250809_035451_s4.bc2166_sawfish/m84036_250809_035451_s4.bc2166.sv.vcf.gz"}
2025-09-15 20:25:50.522 wdl.w:ptcp.w:call-sawfish-69 INFO visit :: node: "output-minimap2_bam", values: {"minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-69/call-run_sawfish/out/m84036_250809_035451_s4.bc2166.minimap2.bam"}
2025-09-15 20:25:50.522 wdl.w:ptcp.w:call-sawfish-69 INFO visit :: node: "output-minimap2_bam_bai", values: {"minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-69/call-run_sawfish/out/m84036_250809_035451_s4.bc2166.minimap2.bam.bai"}
2025-09-15 20:25:50.523 wdl.w:ptcp.w:call-sawfish-69 INFO visit :: node: "output-vcf", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-69/call-run_sawfish/out/m84036_250809_035451_s4.bc2166_sawfish/m84036_250809_035451_s4.bc2166.sv.vcf.gz"}
2025-09-15 20:25:50.523 wdl.w:ptcp.w:call-sawfish-69 INFO visit :: node: "output-vcf_tbi", values: {"vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-69/call-run_sawfish/out/m84036_250809_035451_s4.bc2166_sawfish/m84036_250809_035451_s4.bc2166.sv.vcf.gz.tbi"}
2025-09-15 20:25:50.523 wdl.w:ptcp.w:call-sawfish-69 INFO visit :: node: "outputs", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-69/call-run_sawfish/out/m84036_250809_035451_s4.bc2166_sawfish/m84036_250809_035451_s4.bc2166.sv.vcf.gz", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-69/call-run_sawfish/out/m84036_250809_035451_s4.bc2166.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-69/call-run_sawfish/out/m84036_250809_035451_s4.bc2166_sawfish/m84036_250809_035451_s4.bc2166.sv.vcf.gz.tbi", "minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-69/call-run_sawfish/out/m84036_250809_035451_s4.bc2166.minimap2.bam.bai"}
2025-09-15 20:25:50.529 wdl.w:ptcp.w:call-trgt-94.t:call-get_reads_overlapping_repeats NOTICE task setup :: name: "get_reads_overlapping_repeats", source: "./trgt.wdl", line: 182, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-94/call-get_reads_overlapping_repeats", thread: 140610342200896
2025-09-15 20:25:50.547 wdl.w:ptcp.w:call-trgt-94.t:call-get_reads_overlapping_repeats INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:50.547 wdl.w:ptcp.w:call-trgt-94.t:call-get_reads_overlapping_repeats INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:25:50.547 wdl.w:ptcp.w:call-trgt-94.t:call-get_reads_overlapping_repeats INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2191.mapped.bam.bai"
2025-09-15 20:25:50.547 wdl.w:ptcp.w:call-trgt-94.t:call-get_reads_overlapping_repeats INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2191.mapped.bam"
2025-09-15 20:25:50.547 wdl.w:ptcp.w:call-trgt-94.t:call-get_reads_overlapping_repeats INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2191"
2025-09-15 20:25:50.547 wdl.w:ptcp.w:call-trgt-94.t:call-get_reads_overlapping_repeats INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:25:50.548 wdl.w:ptcp.w:call-trgt-94.t:call-get_reads_overlapping_repeats INFO eval :: name: "expand_size", value: 3000
2025-09-15 20:25:50.548 wdl.w:ptcp.w:call-trgt-94.t:call-get_reads_overlapping_repeats INFO eval :: name: "threads", value: 1
2025-09-15 20:25:50.548 wdl.w:ptcp.w:call-trgt-94.t:call-get_reads_overlapping_repeats INFO eval :: name: "expanded_bed_name", value: "m84036_250809_035451_s4.bc2191.expanded.bed"
2025-09-15 20:25:50.548 wdl.w:ptcp.w:call-trgt-94.t:call-get_reads_overlapping_repeats INFO eval :: name: "disk_size", value: 11
2025-09-15 20:25:50.548 wdl.w:ptcp.w:call-trgt-94.t:call-get_reads_overlapping_repeats INFO eval :: name: "output_name", value: "m84036_250809_035451_s4.bc2191.repeats.bam"
2025-09-15 20:25:50.548 wdl.w:ptcp.w:call-trgt-94.t:call-get_reads_overlapping_repeats INFO eval :: name: "index_name", value: "m84036_250809_035451_s4.bc2191.repeats.bam.bai"
2025-09-15 20:25:50.548 wdl.w:ptcp.w:call-trgt-94.t:call-get_reads_overlapping_repeats INFO eval :: name: "output_name_with_index", value: "m84036_250809_035451_s4.bc2191.repeats.bam##idx##m84036_250809_035451_s4.bc2191.repeats.bam.bai"
2025-09-15 20:25:50.548 wdl.w:ptcp.w:call-trgt-94.t:call-get_reads_overlapping_repeats INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:50.549 wdl.w:ptcp.w:call-trgt-94.t:call-get_reads_overlapping_repeats WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:50.549 wdl.w:ptcp.w:call-trgt-94.t:call-get_reads_overlapping_repeats INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:25:50.549 wdl.w:ptcp.w:call-trgt-94.t:call-get_reads_overlapping_repeats INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:50.575 wdl.w:ptcp.w:call-sawfish-69 NOTICE done
2025-09-15 20:25:50.579 wdl.w:ptcp.w:call-trgt-72.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO srun: job 51798087 queued and waiting for resources
2025-09-15 20:25:50.580 wdl.w:ptcp.w:call-trgt-72.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO srun: job 51798087 has been allocated resources
2025-09-15 20:25:50.580 wdl.w:ptcp.w:call-trgt-72.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:50.582 wdl.w:ptcp NOTICE finish :: job: "call-sawfish-69"
2025-09-15 20:25:50.582 wdl.w:ptcp INFO output :: job: "call-sawfish-69", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-69/out/m84036_250809_035451_s4.bc2166_sawfish/m84036_250809_035451_s4.bc2166.sv.vcf.gz", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-69/out/m84036_250809_035451_s4.bc2166.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-69/out/m84036_250809_035451_s4.bc2166_sawfish/m84036_250809_035451_s4.bc2166.sv.vcf.gz.tbi", "minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-69/out/m84036_250809_035451_s4.bc2166.minimap2.bam.bai"}
2025-09-15 20:25:50.583 wdl.w:ptcp NOTICE ready :: job: "call-tar_outputs-69", callee: "tar_outputs"
2025-09-15 20:25:50.583 wdl.w:ptcp INFO input :: job: "call-tar_outputs-69", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "sawfish_vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-69/out/m84036_250809_035451_s4.bc2166_sawfish/m84036_250809_035451_s4.bc2166.sv.vcf.gz.tbi", "sawfish_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-69/out/m84036_250809_035451_s4.bc2166_sawfish/m84036_250809_035451_s4.bc2166.sv.vcf.gz", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-69/out/m84036_250809_035451_s4.bc2166.f8inversion.json", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-69/out/m84036_250809_035451_s4.bc2166_paraphase/m84036_250809_035451_s4.bc2166.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-69/out/m84036_250809_035451_s4.bc2166_paraphase/m84036_250809_035451_s4.bc2166.paraphase.bam", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-69/out/m84036_250809_035451_s4.bc2166_paraphase/m84036_250809_035451_s4.bc2166.paraphase.json", "trgt_spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-69/out/m84036_250809_035451_s4.bc2166.trgt.sorted.spanning.bam.bai", "trgt_spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-69/out/m84036_250809_035451_s4.bc2166.trgt.sorted.spanning.bam", "trgt_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-69/out/m84036_250809_035451_s4.bc2166.trgt.vcf", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-69/out/m84036_250809_035451_s4.bc2166.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-69/out/m84036_250809_035451_s4.bc2166.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2166"}
2025-09-15 20:25:50.598 wdl.w:ptcp.w:call-trgt-94.t:call-get_reads_overlapping_repeats INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 9, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-94/call-get_reads_overlapping_repeats/_singularity_tmpdir_fd4uqwg2"
2025-09-15 20:25:50.598 wdl.w:ptcp.w:call-trgt-94.t:call-get_reads_overlapping_repeats INFO Slurm invocation: srun --job-name call-get_reads_overlapping_repeats --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-94/call-get_reads_overlapping_repeats/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-94/call-get_reads_overlapping_repeats/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-94/call-get_reads_overlapping_repeats/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-94/call-get_reads_overlapping_repeats/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-94/out/m84036_250809_035451_s4.bc2191.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2191.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-94/out/m84036_250809_035451_s4.bc2191.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2191.mapped.bam.bai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-94/call-get_reads_overlapping_repeats/_singularity_tmpdir_fd4uqwg2/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-94/call-get_reads_overlapping_repeats/_singularity_tmpdir_fd4uqwg2/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:50.608 wdl.w:ptcp.w:call-trgt-94.t:call-get_reads_overlapping_repeats NOTICE slurm_singularity run :: pid: 1206478, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-94/call-get_reads_overlapping_repeats/slurm_singularity.log.txt"
2025-09-15 20:25:50.829 wdl.w:ptcp.w:call-paraphase-63.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for smn1 for sample m84036_250809_035451_s4.bc2160 at 2025-09-15 20:25:07.640381...
2025-09-15 20:25:51.146 wdl.w:ptcp.w:call-trgt-72.t:call-trgt_plot_motifs_allele.slurm_singularity INFO srun: job 51798088 queued and waiting for resources
2025-09-15 20:25:51.146 wdl.w:ptcp.w:call-trgt-72.t:call-trgt_plot_motifs_allele.slurm_singularity INFO srun: job 51798088 has been allocated resources
2025-09-15 20:25:51.147 wdl.w:ptcp.w:call-trgt-72.t:call-trgt_plot_motifs_allele.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:51.236 wdl.w:ptcp.w:call-paraphase-74.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for hba for sample m84036_250809_035451_s4.bc2171 at 2025-09-15 20:25:42.303980...
2025-09-15 20:25:51.236 wdl.w:ptcp.w:call-paraphase-74.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for cyp21 for sample m84036_250809_035451_s4.bc2171 at 2025-09-15 20:25:44.060285...
2025-09-15 20:25:51.236 wdl.w:ptcp.w:call-paraphase-74.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for cyp21 for sample m84036_250809_035451_s4.bc2171 at 2025-09-15 20:25:45.083736...
2025-09-15 20:25:51.275 wdl.w:ptcp.w:call-trgt-77.t:call-trgt_plot_meth_allele INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2174.meth_allele.trgt_plots.zip"
2025-09-15 20:25:51.307 wdl.w:ptcp.w:call-paraphase-31.t:call-run_paraphase INFO output :: name: "paraphase_bam", value: "m84036_250809_035451_s4.bc2128_paraphase/m84036_250809_035451_s4.bc2128.paraphase.bam"
2025-09-15 20:25:51.311 wdl.w:ptcp.w:call-paraphase-31.t:call-run_paraphase INFO output :: name: "paraphase_bam_bai", value: "m84036_250809_035451_s4.bc2128_paraphase/m84036_250809_035451_s4.bc2128.paraphase.bam.bai"
2025-09-15 20:25:51.314 wdl.w:ptcp.w:call-paraphase-31.t:call-run_paraphase INFO output :: name: "paraphase_json", value: "m84036_250809_035451_s4.bc2128_paraphase/m84036_250809_035451_s4.bc2128.paraphase.json"
2025-09-15 20:25:51.321 wdl.w:ptcp.w:call-paraphase-31.t:call-run_paraphase INFO output :: name: "paraphase_vcfs", value: ["/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2128_paraphase/m84036_250809_035451_s4.bc2128_paraphase_vcfs/m84036_250809_035451_s4.bc2128_cyp21.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2128_paraphase/m84036_250809_035451_s4.bc2128_paraphase_vcfs/m84036_250809_035451_s4.bc2128_f8inv1.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2128_paraphase/m84036_250809_035451_s4.bc2128_paraphase_vcfs/m84036_250809_035451_s4.bc2128_f8inv22.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2128_paraphase/m84036_250809_035451_s4.bc2128_paraphase_vcfs/m84036_250809_035451_s4.bc2128_gba.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2128_paraphase/m84036_250809_035451_s4.bc2128_paraphase_vcfs/m84036_250809_035451_s4.bc2128_hba.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2128_paraphase/m84036_250809_035451_s4.bc2128_paraphase_vcfs/m84036_250809_035451_s4.bc2128_hbb.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2128_paraphase/m84036_250809_035451_s4.bc2128_paraphase_vcfs/m84036_250809_035451_s4.bc2128_rpgr.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2128_paraphase/m84036_250809_035451_s4.bc2128_paraphase_vcfs/m84036_250809_035451_s4.bc2128_smn1.vcf"]
2025-09-15 20:25:51.325 wdl.w:ptcp.w:call-paraphase-31.t:call-run_paraphase INFO output :: name: "havanno_json", value: "m84036_250809_035451_s4.bc2128.havanno.json"
2025-09-15 20:25:51.410 wdl.w:ptcp.w:call-trgt-77.t:call-trgt_plot_meth_allele NOTICE done
2025-09-15 20:25:51.416 wdl.w:ptcp.w:call-trgt-77 NOTICE finish :: job: "call-trgt_plot_meth_allele"
2025-09-15 20:25:51.416 wdl.w:ptcp.w:call-trgt-77 INFO output :: job: "call-trgt_plot_meth_allele", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-77/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2174.meth_allele.trgt_plots.zip"}
2025-09-15 20:25:51.416 wdl.w:ptcp.w:call-trgt-77 INFO visit :: node: "output-images_meth_allele", values: {"images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-77/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2174.meth_allele.trgt_plots.zip"}
2025-09-15 20:25:51.422 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_genotype NOTICE task setup :: name: "trgt_genotype", source: "./trgt.wdl", line: 272, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-94/call-trgt_genotype", thread: 140611977991744
2025-09-15 20:25:51.440 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_genotype INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:51.441 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_genotype INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:25:51.441 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_genotype INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:25:51.441 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_genotype INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:25:51.441 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_genotype INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2191.mapped.bam.bai"
2025-09-15 20:25:51.441 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_genotype INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2191.mapped.bam"
2025-09-15 20:25:51.441 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_genotype INFO input :: name: "sex", value: "F"
2025-09-15 20:25:51.441 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_genotype INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2191"
2025-09-15 20:25:51.441 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_genotype INFO eval :: name: "mem_gb", value: 16
2025-09-15 20:25:51.441 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_genotype INFO eval :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2191.trgt"
2025-09-15 20:25:51.442 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_genotype INFO eval :: name: "threads", value: 8
2025-09-15 20:25:51.442 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_genotype INFO eval :: name: "disk_size", value: 27
2025-09-15 20:25:51.442 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_genotype INFO eval :: name: "karyotype", value: "XX"
2025-09-15 20:25:51.442 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_genotype INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 8, memory_reservation: 16000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:51.442 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_genotype WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:51.443 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_genotype INFO provisioned :: seconds_waited: 0, cpu: 8, mem_bytes: 16000000000
2025-09-15 20:25:51.443 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_genotype INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:51.457 wdl.w:ptcp.w:call-sawfish-68.t:call-run_sawfish.stderr VERBOSE [M::mm_mapopt_update::44.076*1.69] mid_occ = 136
2025-09-15 20:25:51.457 wdl.w:ptcp.w:call-sawfish-68.t:call-run_sawfish.stderr VERBOSE [M::mm_idx_stat] kmer size: 19; skip: 19; is_hpc: 0; #seq: 195
2025-09-15 20:25:51.457 wdl.w:ptcp.w:call-sawfish-68.t:call-run_sawfish.stderr VERBOSE [M::mm_idx_stat::46.768*1.65] distinct minimizers: 214664461 (92.23% are singletons); average occurrences: 1.372; average spacing: 10.529; total length: 3099922541
2025-09-15 20:25:51.457 wdl.w:ptcp.w:call-sawfish-68.t:call-run_sawfish.stderr VERBOSE [M::main] Version: 2.26-r1175
2025-09-15 20:25:51.457 wdl.w:ptcp.w:call-sawfish-68.t:call-run_sawfish.stderr VERBOSE [M::main] CMD: /opt/pacbio/smrttools/install/smrtlink-release_25.1.0.257715/bundles/smrttools/install/smrttools-release_25.1.0.257715/private/thirdparty/minimap2/minimap2_2.26-pacbio2/binwrap/../../../../../private/thirdparty/minimap2/minimap2_2.26-pacbio2/bin/minimap2 -a -y -x map-hifi -Y -E 1,0 /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa -
2025-09-15 20:25:51.457 wdl.w:ptcp.w:call-sawfish-68.t:call-run_sawfish.stderr VERBOSE [M::main] Real time: 47.064 sec; CPU: 77.356 sec; Peak RSS: 11.886 GB
2025-09-15 20:25:51.472 wdl.w:ptcp.w:call-trgt-72.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO srun: job 51798089 queued and waiting for resources
2025-09-15 20:25:51.472 wdl.w:ptcp.w:call-trgt-72.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO srun: job 51798089 has been allocated resources
2025-09-15 20:25:51.472 wdl.w:ptcp.w:call-trgt-72.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:51.523 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_genotype INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 11, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-94/call-trgt_genotype/_singularity_tmpdir_u9vae_ox"
2025-09-15 20:25:51.523 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_genotype INFO Slurm invocation: srun --job-name call-trgt_genotype --partition compute,compute9 --cpus-per-task 8 --mem 15259M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-94/call-trgt_genotype/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-94/call-trgt_genotype/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-94/call-trgt_genotype/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-94/call-trgt_genotype/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-94/out/m84036_250809_035451_s4.bc2191.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2191.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-94/out/m84036_250809_035451_s4.bc2191.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2191.mapped.bam.bai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-94/call-trgt_genotype/_singularity_tmpdir_u9vae_ox/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-94/call-trgt_genotype/_singularity_tmpdir_u9vae_ox/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:51.530 wdl.w:ptcp.w:call-paraphase-31.t:call-run_paraphase NOTICE done
2025-09-15 20:25:51.535 wdl.w:ptcp.w:call-paraphase-31 NOTICE finish :: job: "call-run_paraphase"
2025-09-15 20:25:51.535 wdl.w:ptcp.w:call-paraphase-31 INFO output :: job: "call-run_paraphase", values: {"havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-31/call-run_paraphase/out/m84036_250809_035451_s4.bc2128.havanno.json", "paraphase_vcfs": ["/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-31/call-run_paraphase/out/m84036_250809_035451_s4.bc2128_paraphase/m84036_250809_035451_s4.bc2128_paraphase_vcfs/m84036_250809_035451_s4.bc2128_cyp21.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-31/call-run_paraphase/out/m84036_250809_035451_s4.bc2128_paraphase/m84036_250809_035451_s4.bc2128_paraphase_vcfs/m84036_250809_035451_s4.bc2128_f8inv1.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-31/call-run_paraphase/out/m84036_250809_035451_s4.bc2128_paraphase/m84036_250809_035451_s4.bc2128_paraphase_vcfs/m84036_250809_035451_s4.bc2128_f8inv22.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-31/call-run_paraphase/out/m84036_250809_035451_s4.bc2128_paraphase/m84036_250809_035451_s4.bc2128_paraphase_vcfs/m84036_250809_035451_s4.bc2128_gba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-31/call-run_paraphase/out/m84036_250809_035451_s4.bc2128_paraphase/m84036_250809_035451_s4.bc2128_paraphase_vcfs/m84036_250809_035451_s4.bc2128_hba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-31/call-run_paraphase/out/m84036_250809_035451_s4.bc2128_paraphase/m84036_250809_035451_s4.bc2128_paraphase_vcfs/m84036_250809_035451_s4.bc2128_hbb.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-31/call-run_paraphase/out/m84036_250809_035451_s4.bc2128_paraphase/m84036_250809_035451_s4.bc2128_paraphase_vcfs/m84036_250809_035451_s4.bc2128_rpgr.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-31/call-run_paraphase/out/m84036_250809_035451_s4.bc2128_paraphase/m84036_250809_035451_s4.bc2128_paraphase_vcfs/m84036_250809_035451_s4.bc2128_smn1.vcf"], "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-31/call-run_paraphase/out/m84036_250809_035451_s4.bc2128_paraphase/m84036_250809_035451_s4.bc2128.paraphase.json", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-31/call-run_paraphase/out/m84036_250809_035451_s4.bc2128_paraphase/m84036_250809_035451_s4.bc2128.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-31/call-run_paraphase/out/m84036_250809_035451_s4.bc2128_paraphase/m84036_250809_035451_s4.bc2128.paraphase.bam"}
2025-09-15 20:25:51.536 wdl.w:ptcp.w:call-paraphase-31 NOTICE ready :: job: "call-call_f8", callee: "call_f8"
2025-09-15 20:25:51.536 wdl.w:ptcp.w:call-paraphase-31 INFO input :: job: "call-call_f8", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "out_prefix": "m84036_250809_035451_s4.bc2128", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-31/call-run_paraphase/out/m84036_250809_035451_s4.bc2128_paraphase/m84036_250809_035451_s4.bc2128.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-31/call-run_paraphase/out/m84036_250809_035451_s4.bc2128_paraphase/m84036_250809_035451_s4.bc2128.paraphase.bam", "sex": "F"}
2025-09-15 20:25:51.537 wdl.w:ptcp.w:call-paraphase-31 INFO visit :: node: "output-havanno_json", values: {"havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-31/call-run_paraphase/out/m84036_250809_035451_s4.bc2128.havanno.json"}
2025-09-15 20:25:51.538 wdl.w:ptcp.w:call-paraphase-31 INFO visit :: node: "output-paraphase_bam", values: {"paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-31/call-run_paraphase/out/m84036_250809_035451_s4.bc2128_paraphase/m84036_250809_035451_s4.bc2128.paraphase.bam"}
2025-09-15 20:25:51.538 wdl.w:ptcp.w:call-paraphase-31 INFO visit :: node: "output-paraphase_bam_bai", values: {"paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-31/call-run_paraphase/out/m84036_250809_035451_s4.bc2128_paraphase/m84036_250809_035451_s4.bc2128.paraphase.bam.bai"}
2025-09-15 20:25:51.538 wdl.w:ptcp.w:call-paraphase-31 INFO visit :: node: "output-paraphase_json", values: {"paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-31/call-run_paraphase/out/m84036_250809_035451_s4.bc2128_paraphase/m84036_250809_035451_s4.bc2128.paraphase.json"}
2025-09-15 20:25:51.539 wdl.w:ptcp.w:call-paraphase-31 INFO visit :: node: "output-paraphase_vcfs", values: {"paraphase_vcfs": ["/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-31/call-run_paraphase/out/m84036_250809_035451_s4.bc2128_paraphase/m84036_250809_035451_s4.bc2128_paraphase_vcfs/m84036_250809_035451_s4.bc2128_cyp21.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-31/call-run_paraphase/out/m84036_250809_035451_s4.bc2128_paraphase/m84036_250809_035451_s4.bc2128_paraphase_vcfs/m84036_250809_035451_s4.bc2128_f8inv1.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-31/call-run_paraphase/out/m84036_250809_035451_s4.bc2128_paraphase/m84036_250809_035451_s4.bc2128_paraphase_vcfs/m84036_250809_035451_s4.bc2128_f8inv22.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-31/call-run_paraphase/out/m84036_250809_035451_s4.bc2128_paraphase/m84036_250809_035451_s4.bc2128_paraphase_vcfs/m84036_250809_035451_s4.bc2128_gba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-31/call-run_paraphase/out/m84036_250809_035451_s4.bc2128_paraphase/m84036_250809_035451_s4.bc2128_paraphase_vcfs/m84036_250809_035451_s4.bc2128_hba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-31/call-run_paraphase/out/m84036_250809_035451_s4.bc2128_paraphase/m84036_250809_035451_s4.bc2128_paraphase_vcfs/m84036_250809_035451_s4.bc2128_hbb.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-31/call-run_paraphase/out/m84036_250809_035451_s4.bc2128_paraphase/m84036_250809_035451_s4.bc2128_paraphase_vcfs/m84036_250809_035451_s4.bc2128_rpgr.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-31/call-run_paraphase/out/m84036_250809_035451_s4.bc2128_paraphase/m84036_250809_035451_s4.bc2128_paraphase_vcfs/m84036_250809_035451_s4.bc2128_smn1.vcf"]}
2025-09-15 20:25:51.541 wdl.w:ptcp.w:call-paraphase-81.t:call-call_f8 NOTICE task setup :: name: "call_f8", source: "./paraphase.wdl", line: 232, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-81/call-call_f8", thread: 140611432728128
2025-09-15 20:25:51.560 wdl.w:ptcp.w:call-paraphase-81.t:call-call_f8 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:51.560 wdl.w:ptcp.w:call-paraphase-81.t:call-call_f8 INFO input :: name: "genome_version", value: "38"
2025-09-15 20:25:51.560 wdl.w:ptcp.w:call-paraphase-81.t:call-call_f8 INFO input :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2178"
2025-09-15 20:25:51.560 wdl.w:ptcp.w:call-paraphase-81.t:call-call_f8 INFO input :: name: "paraphase_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2178.paraphase.bam.bai"
2025-09-15 20:25:51.560 wdl.w:ptcp.w:call-paraphase-81.t:call-call_f8 INFO input :: name: "paraphase_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2178.paraphase.bam"
2025-09-15 20:25:51.561 wdl.w:ptcp.w:call-paraphase-81.t:call-call_f8 INFO input :: name: "sex", value: "F"
2025-09-15 20:25:51.561 wdl.w:ptcp.w:call-paraphase-81.t:call-call_f8 INFO eval :: name: "threads", value: 1
2025-09-15 20:25:51.561 wdl.w:ptcp.w:call-paraphase-81.t:call-call_f8 INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:25:51.561 wdl.w:ptcp.w:call-paraphase-81.t:call-call_f8 INFO eval :: name: "disk_size", value: 11
2025-09-15 20:25:51.561 wdl.w:ptcp.w:call-paraphase-81.t:call-call_f8 INFO eval :: name: "sample_sex", value: "F"
2025-09-15 20:25:51.562 wdl.w:ptcp.w:call-paraphase-81.t:call-call_f8 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:51.562 wdl.w:ptcp.w:call-paraphase-81.t:call-call_f8 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:51.562 wdl.w:ptcp.w:call-paraphase-81.t:call-call_f8 INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:25:51.562 wdl.w:ptcp.w:call-paraphase-81.t:call-call_f8 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:51.564 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_genotype NOTICE slurm_singularity run :: pid: 1206492, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-94/call-trgt_genotype/slurm_singularity.log.txt"
2025-09-15 20:25:51.605 wdl.w:ptcp.w:call-paraphase-81.t:call-call_f8 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 8, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-81/call-call_f8/_singularity_tmpdir_8cee84km"
2025-09-15 20:25:51.605 wdl.w:ptcp.w:call-paraphase-81.t:call-call_f8 INFO Slurm invocation: srun --job-name call-call_f8 --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-81/call-call_f8/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-81/call-call_f8/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-81/call-call_f8/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-81/call-call_f8/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-81/call-run_paraphase/out/m84036_250809_035451_s4.bc2178_paraphase/m84036_250809_035451_s4.bc2178.paraphase.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2178.paraphase.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-81/call-run_paraphase/out/m84036_250809_035451_s4.bc2178_paraphase/m84036_250809_035451_s4.bc2178.paraphase.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2178.paraphase.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-81/call-call_f8/_singularity_tmpdir_8cee84km/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-81/call-call_f8/_singularity_tmpdir_8cee84km/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:51.618 wdl.w:ptcp.w:call-paraphase-81.t:call-call_f8 NOTICE slurm_singularity run :: pid: 1206494, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-81/call-call_f8/slurm_singularity.log.txt"
2025-09-15 20:25:51.619 wdl.w:ptcp.w:call-trgt-94.t:call-get_reads_overlapping_repeats.slurm_singularity INFO srun: job 51798090 queued and waiting for resources
2025-09-15 20:25:51.619 wdl.w:ptcp.w:call-trgt-94.t:call-get_reads_overlapping_repeats.slurm_singularity INFO srun: job 51798090 has been allocated resources
2025-09-15 20:25:51.619 wdl.w:ptcp.w:call-trgt-94.t:call-get_reads_overlapping_repeats.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:51.885 wdl.w:ptcp.w:call-paraphase-02.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for hbb for sample m84036_250809_035451_s4.bc2099 at 2025-09-15 20:25:44.290169...
2025-09-15 20:25:51.886 wdl.w:ptcp.w:call-paraphase-02.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for hbb for sample m84036_250809_035451_s4.bc2099 at 2025-09-15 20:25:44.777869...
2025-09-15 20:25:52.382 wdl.w:ptcp.w:call-trgt-94.t:call-get_reads_overlapping_repeats INFO output :: name: "reads_overlapping_repeats", value: "m84036_250809_035451_s4.bc2191.repeats.bam"
2025-09-15 20:25:52.385 wdl.w:ptcp.w:call-trgt-94.t:call-get_reads_overlapping_repeats INFO output :: name: "reads_overlapping_repeats_bai", value: "m84036_250809_035451_s4.bc2191.repeats.bam.bai"
2025-09-15 20:25:52.449 wdl.w:ptcp.w:call-trgt-94.t:call-get_reads_overlapping_repeats NOTICE done
2025-09-15 20:25:52.453 wdl.w:ptcp.w:call-trgt-94 NOTICE finish :: job: "call-get_reads_overlapping_repeats"
2025-09-15 20:25:52.453 wdl.w:ptcp.w:call-trgt-94 INFO output :: job: "call-get_reads_overlapping_repeats", values: {"reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-94/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2191.repeats.bam.bai", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-94/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2191.repeats.bam"}
2025-09-15 20:25:52.454 wdl.w:ptcp.w:call-trgt-94 INFO visit :: node: "output-reads_overlapping_repeats", values: {"reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-94/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2191.repeats.bam"}
2025-09-15 20:25:52.454 wdl.w:ptcp.w:call-trgt-94 INFO visit :: node: "output-reads_overlapping_repeats_bai", values: {"reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-94/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2191.repeats.bam.bai"}
2025-09-15 20:25:52.461 wdl.w:ptcp.w:call-paraphase-80.t:call-call_f8 NOTICE task setup :: name: "call_f8", source: "./paraphase.wdl", line: 232, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-80/call-call_f8", thread: 140610342200896
2025-09-15 20:25:52.487 wdl.w:ptcp.w:call-paraphase-80.t:call-call_f8 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:52.487 wdl.w:ptcp.w:call-paraphase-80.t:call-call_f8 INFO input :: name: "genome_version", value: "38"
2025-09-15 20:25:52.487 wdl.w:ptcp.w:call-paraphase-80.t:call-call_f8 INFO input :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2177"
2025-09-15 20:25:52.487 wdl.w:ptcp.w:call-paraphase-80.t:call-call_f8 INFO input :: name: "paraphase_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2177.paraphase.bam.bai"
2025-09-15 20:25:52.487 wdl.w:ptcp.w:call-paraphase-80.t:call-call_f8 INFO input :: name: "paraphase_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2177.paraphase.bam"
2025-09-15 20:25:52.487 wdl.w:ptcp.w:call-paraphase-80.t:call-call_f8 INFO input :: name: "sex", value: "F"
2025-09-15 20:25:52.487 wdl.w:ptcp.w:call-paraphase-80.t:call-call_f8 INFO eval :: name: "threads", value: 1
2025-09-15 20:25:52.487 wdl.w:ptcp.w:call-paraphase-80.t:call-call_f8 INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:25:52.488 wdl.w:ptcp.w:call-paraphase-80.t:call-call_f8 INFO eval :: name: "disk_size", value: 11
2025-09-15 20:25:52.488 wdl.w:ptcp.w:call-paraphase-80.t:call-call_f8 INFO eval :: name: "sample_sex", value: "F"
2025-09-15 20:25:52.488 wdl.w:ptcp.w:call-paraphase-80.t:call-call_f8 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:52.488 wdl.w:ptcp.w:call-paraphase-80.t:call-call_f8 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:52.488 wdl.w:ptcp.w:call-paraphase-80.t:call-call_f8 INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:25:52.489 wdl.w:ptcp.w:call-paraphase-80.t:call-call_f8 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:52.537 wdl.w:ptcp.w:call-paraphase-80.t:call-call_f8 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 8, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-80/call-call_f8/_singularity_tmpdir_e6vhu8mj"
2025-09-15 20:25:52.537 wdl.w:ptcp.w:call-paraphase-80.t:call-call_f8 INFO Slurm invocation: srun --job-name call-call_f8 --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-80/call-call_f8/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-80/call-call_f8/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-80/call-call_f8/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-80/call-call_f8/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-80/call-run_paraphase/out/m84036_250809_035451_s4.bc2177_paraphase/m84036_250809_035451_s4.bc2177.paraphase.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2177.paraphase.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-80/call-run_paraphase/out/m84036_250809_035451_s4.bc2177_paraphase/m84036_250809_035451_s4.bc2177.paraphase.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2177.paraphase.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-80/call-call_f8/_singularity_tmpdir_e6vhu8mj/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-80/call-call_f8/_singularity_tmpdir_e6vhu8mj/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:52.550 wdl.w:ptcp.w:call-paraphase-80.t:call-call_f8 NOTICE slurm_singularity run :: pid: 1206507, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-80/call-call_f8/slurm_singularity.log.txt"
2025-09-15 20:25:52.573 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_genotype.slurm_singularity INFO srun: job 51798091 queued and waiting for resources
2025-09-15 20:25:52.573 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_genotype.slurm_singularity INFO srun: job 51798091 has been allocated resources
2025-09-15 20:25:52.573 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_genotype.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:52.627 wdl.w:ptcp.w:call-paraphase-81.t:call-call_f8.slurm_singularity INFO srun: job 51798092 queued and waiting for resources
2025-09-15 20:25:52.627 wdl.w:ptcp.w:call-paraphase-81.t:call-call_f8.slurm_singularity INFO srun: job 51798092 has been allocated resources
2025-09-15 20:25:52.627 wdl.w:ptcp.w:call-paraphase-81.t:call-call_f8.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:53.037 wdl.w:ptcp.w:call-sawfish-47.t:call-run_sawfish INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2144_sawfish/m84036_250809_035451_s4.bc2144.sv.vcf.gz"
2025-09-15 20:25:53.042 wdl.w:ptcp.w:call-sawfish-47.t:call-run_sawfish INFO output :: name: "vcf_tbi", value: "m84036_250809_035451_s4.bc2144_sawfish/m84036_250809_035451_s4.bc2144.sv.vcf.gz.tbi"
2025-09-15 20:25:53.043 wdl.w:ptcp.w:call-sawfish-47.t:call-run_sawfish INFO output :: name: "minimap2_bam", value: "m84036_250809_035451_s4.bc2144.minimap2.bam"
2025-09-15 20:25:53.044 wdl.w:ptcp.w:call-sawfish-47.t:call-run_sawfish INFO output :: name: "minimap2_bam_bai", value: "m84036_250809_035451_s4.bc2144.minimap2.bam.bai"
2025-09-15 20:25:53.193 wdl.w:ptcp.w:call-sawfish-47.t:call-run_sawfish NOTICE done
2025-09-15 20:25:53.202 wdl.w:ptcp.w:call-sawfish-47 NOTICE finish :: job: "call-run_sawfish"
2025-09-15 20:25:53.202 wdl.w:ptcp.w:call-sawfish-47 INFO output :: job: "call-run_sawfish", values: {"minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-47/call-run_sawfish/out/m84036_250809_035451_s4.bc2144.minimap2.bam.bai", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-47/call-run_sawfish/out/m84036_250809_035451_s4.bc2144.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-47/call-run_sawfish/out/m84036_250809_035451_s4.bc2144_sawfish/m84036_250809_035451_s4.bc2144.sv.vcf.gz.tbi", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-47/call-run_sawfish/out/m84036_250809_035451_s4.bc2144_sawfish/m84036_250809_035451_s4.bc2144.sv.vcf.gz"}
2025-09-15 20:25:53.202 wdl.w:ptcp.w:call-sawfish-47 INFO visit :: node: "output-minimap2_bam", values: {"minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-47/call-run_sawfish/out/m84036_250809_035451_s4.bc2144.minimap2.bam"}
2025-09-15 20:25:53.203 wdl.w:ptcp.w:call-sawfish-47 INFO visit :: node: "output-minimap2_bam_bai", values: {"minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-47/call-run_sawfish/out/m84036_250809_035451_s4.bc2144.minimap2.bam.bai"}
2025-09-15 20:25:53.203 wdl.w:ptcp.w:call-sawfish-47 INFO visit :: node: "output-vcf", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-47/call-run_sawfish/out/m84036_250809_035451_s4.bc2144_sawfish/m84036_250809_035451_s4.bc2144.sv.vcf.gz"}
2025-09-15 20:25:53.203 wdl.w:ptcp.w:call-sawfish-47 INFO visit :: node: "output-vcf_tbi", values: {"vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-47/call-run_sawfish/out/m84036_250809_035451_s4.bc2144_sawfish/m84036_250809_035451_s4.bc2144.sv.vcf.gz.tbi"}
2025-09-15 20:25:53.203 wdl.w:ptcp.w:call-sawfish-47 INFO visit :: node: "outputs", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-47/call-run_sawfish/out/m84036_250809_035451_s4.bc2144_sawfish/m84036_250809_035451_s4.bc2144.sv.vcf.gz", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-47/call-run_sawfish/out/m84036_250809_035451_s4.bc2144.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-47/call-run_sawfish/out/m84036_250809_035451_s4.bc2144_sawfish/m84036_250809_035451_s4.bc2144.sv.vcf.gz.tbi", "minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-47/call-run_sawfish/out/m84036_250809_035451_s4.bc2144.minimap2.bam.bai"}
2025-09-15 20:25:53.211 wdl.w:ptcp.w:call-paraphase-90.t:call-run_paraphase NOTICE task setup :: name: "run_paraphase", source: "./paraphase.wdl", line: 127, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-90/call-run_paraphase", thread: 140607699809856
2025-09-15 20:25:53.233 wdl.w:ptcp.w:call-paraphase-90.t:call-run_paraphase INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:53.233 wdl.w:ptcp.w:call-paraphase-90.t:call-run_paraphase INFO input :: name: "annotation_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf"
2025-09-15 20:25:53.234 wdl.w:ptcp.w:call-paraphase-90.t:call-run_paraphase INFO input :: name: "genome_version", value: "38"
2025-09-15 20:25:53.234 wdl.w:ptcp.w:call-paraphase-90.t:call-run_paraphase INFO input :: name: "config_file", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/paraphase_config.GRCh38.yaml"
2025-09-15 20:25:53.234 wdl.w:ptcp.w:call-paraphase-90.t:call-run_paraphase INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:25:53.234 wdl.w:ptcp.w:call-paraphase-90.t:call-run_paraphase INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:25:53.234 wdl.w:ptcp.w:call-paraphase-90.t:call-run_paraphase INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2187.mapped.bam.bai"
2025-09-15 20:25:53.234 wdl.w:ptcp.w:call-paraphase-90.t:call-run_paraphase INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2187.mapped.bam"
2025-09-15 20:25:53.234 wdl.w:ptcp.w:call-paraphase-90.t:call-run_paraphase INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2187"
2025-09-15 20:25:53.236 wdl.w:ptcp.w:call-paraphase-90.t:call-run_paraphase INFO eval :: name: "threads", value: 4
2025-09-15 20:25:53.236 wdl.w:ptcp.w:call-paraphase-90.t:call-run_paraphase INFO eval :: name: "mem_gb", value: 8
2025-09-15 20:25:53.236 wdl.w:ptcp.w:call-paraphase-90.t:call-run_paraphase INFO eval :: name: "disk_size", value: 27
2025-09-15 20:25:53.236 wdl.w:ptcp.w:call-paraphase-90.t:call-run_paraphase INFO eval :: name: "out_dir", value: "m84036_250809_035451_s4.bc2187_paraphase"
2025-09-15 20:25:53.236 wdl.w:ptcp.w:call-paraphase-90.t:call-run_paraphase INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 4, memory_reservation: 8000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:53.237 wdl.w:ptcp.w:call-paraphase-90.t:call-run_paraphase WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:53.237 wdl.w:ptcp.w:call-paraphase-90.t:call-run_paraphase INFO provisioned :: seconds_waited: 0, cpu: 4, mem_bytes: 8000000000
2025-09-15 20:25:53.237 wdl.w:ptcp.w:call-paraphase-90.t:call-run_paraphase INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:53.279 wdl.w:ptcp.w:call-sawfish-47 NOTICE done
2025-09-15 20:25:53.284 wdl.w:ptcp NOTICE finish :: job: "call-sawfish-47"
2025-09-15 20:25:53.284 wdl.w:ptcp INFO output :: job: "call-sawfish-47", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-47/out/m84036_250809_035451_s4.bc2144_sawfish/m84036_250809_035451_s4.bc2144.sv.vcf.gz", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-47/out/m84036_250809_035451_s4.bc2144.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-47/out/m84036_250809_035451_s4.bc2144_sawfish/m84036_250809_035451_s4.bc2144.sv.vcf.gz.tbi", "minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-47/out/m84036_250809_035451_s4.bc2144.minimap2.bam.bai"}
2025-09-15 20:25:53.315 wdl.w:ptcp.w:call-paraphase-90.t:call-run_paraphase INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-90/call-run_paraphase/_singularity_tmpdir_w6vseare"
2025-09-15 20:25:53.315 wdl.w:ptcp.w:call-paraphase-90.t:call-run_paraphase INFO Slurm invocation: srun --job-name call-run_paraphase --partition compute,compute9 --cpus-per-task 4 --mem 7629M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-90/call-run_paraphase/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-90/call-run_paraphase/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-90/call-run_paraphase/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-90/call-run_paraphase/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-90/out/m84036_250809_035451_s4.bc2187.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2187.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-90/out/m84036_250809_035451_s4.bc2187.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2187.mapped.bam.bai:ro --bind /ptcp/meta/variant_list/variant_list.GRCh38.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf:ro --bind /ptcp/meta/paraphase/paraphase_config.GRCh38.yaml:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/paraphase_config.GRCh38.yaml:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-90/call-run_paraphase/_singularity_tmpdir_w6vseare/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-90/call-run_paraphase/_singularity_tmpdir_w6vseare/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:53.329 wdl.w:ptcp.w:call-paraphase-90.t:call-run_paraphase NOTICE slurm_singularity run :: pid: 1206515, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-90/call-run_paraphase/slurm_singularity.log.txt"
2025-09-15 20:25:53.350 wdl.w:ptcp.w:call-trgt-72.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:51 [ERROR] - No reads found for TRID=PRTS_ARX
2025-09-15 20:25:53.350 wdl.w:ptcp.w:call-trgt-72.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:51 [ERROR] - No reads found for TRID=EIEE1_ARX
2025-09-15 20:25:53.418 wdl.w:ptcp.w:call-paraphase-43.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for hbb for sample m84036_250809_035451_s4.bc2140 at 2025-09-15 20:25:29.326858...
2025-09-15 20:25:53.418 wdl.w:ptcp.w:call-paraphase-43.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for hbb for sample m84036_250809_035451_s4.bc2140 at 2025-09-15 20:25:31.603317...
2025-09-15 20:25:53.418 wdl.w:ptcp.w:call-paraphase-43.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for hbb for sample m84036_250809_035451_s4.bc2140 at 2025-09-15 20:25:31.847049...
2025-09-15 20:25:53.554 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_genotype INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2191.trgt.vcf"
2025-09-15 20:25:53.555 wdl.w:ptcp.w:call-paraphase-81.t:call-call_f8 INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2178.f8inversion.vcf"
2025-09-15 20:25:53.558 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_genotype INFO output :: name: "spanning_bam", value: "m84036_250809_035451_s4.bc2191.trgt.sorted.spanning.bam"
2025-09-15 20:25:53.559 wdl.w:ptcp.w:call-paraphase-81.t:call-call_f8 INFO output :: name: "json", value: "m84036_250809_035451_s4.bc2178.f8inversion.json"
2025-09-15 20:25:53.560 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_genotype INFO output :: name: "spanning_bam_bai", value: "m84036_250809_035451_s4.bc2191.trgt.sorted.spanning.bam.bai"
2025-09-15 20:25:53.561 wdl.w:ptcp.w:call-paraphase-80.t:call-call_f8.slurm_singularity INFO srun: job 51798093 queued and waiting for resources
2025-09-15 20:25:53.561 wdl.w:ptcp.w:call-paraphase-80.t:call-call_f8.slurm_singularity INFO srun: job 51798093 has been allocated resources
2025-09-15 20:25:53.561 wdl.w:ptcp.w:call-paraphase-80.t:call-call_f8.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:53.625 wdl.w:ptcp.w:call-paraphase-81.t:call-call_f8 NOTICE done
2025-09-15 20:25:53.632 wdl.w:ptcp.w:call-paraphase-81 NOTICE finish :: job: "call-call_f8"
2025-09-15 20:25:53.632 wdl.w:ptcp.w:call-paraphase-81 INFO output :: job: "call-call_f8", values: {"json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-81/call-call_f8/out/m84036_250809_035451_s4.bc2178.f8inversion.json", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-81/call-call_f8/out/m84036_250809_035451_s4.bc2178.f8inversion.vcf"}
2025-09-15 20:25:53.632 wdl.w:ptcp.w:call-paraphase-81 INFO visit :: node: "output-f8_json", values: {"f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-81/call-call_f8/out/m84036_250809_035451_s4.bc2178.f8inversion.json"}
2025-09-15 20:25:53.632 wdl.w:ptcp.w:call-paraphase-81 INFO visit :: node: "output-f8_vcf", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-81/call-call_f8/out/m84036_250809_035451_s4.bc2178.f8inversion.vcf"}
2025-09-15 20:25:53.633 wdl.w:ptcp.w:call-paraphase-81 INFO visit :: node: "outputs", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-81/call-call_f8/out/m84036_250809_035451_s4.bc2178.f8inversion.vcf", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-81/call-run_paraphase/out/m84036_250809_035451_s4.bc2178_paraphase/m84036_250809_035451_s4.bc2178.paraphase.json", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-81/call-run_paraphase/out/m84036_250809_035451_s4.bc2178_paraphase/m84036_250809_035451_s4.bc2178.paraphase.bam", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-81/call-run_paraphase/out/m84036_250809_035451_s4.bc2178_paraphase/m84036_250809_035451_s4.bc2178.paraphase.bam.bai", "paraphase_vcfs": [], "havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-81/call-run_paraphase/out/m84036_250809_035451_s4.bc2178.havanno.json", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-81/call-call_f8/out/m84036_250809_035451_s4.bc2178.f8inversion.json"}
2025-09-15 20:25:53.639 wdl.w:ptcp.w:call-trgt-80.t:call-trgt_plot_meth_allele NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-80/call-trgt_plot_meth_allele", thread: 140611432728128
2025-09-15 20:25:53.653 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_genotype NOTICE done
2025-09-15 20:25:53.658 wdl.w:ptcp.w:call-trgt-94 NOTICE finish :: job: "call-trgt_genotype"
2025-09-15 20:25:53.658 wdl.w:ptcp.w:call-trgt-94 INFO output :: job: "call-trgt_genotype", values: {"spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-94/call-trgt_genotype/out/m84036_250809_035451_s4.bc2191.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-94/call-trgt_genotype/out/m84036_250809_035451_s4.bc2191.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-94/call-trgt_genotype/out/m84036_250809_035451_s4.bc2191.trgt.vcf"}
2025-09-15 20:25:53.659 wdl.w:ptcp.w:call-trgt-94 NOTICE ready :: job: "call-trgt_plot_meth_allele", callee: "trgt_plot"
2025-09-15 20:25:53.659 wdl.w:ptcp.w:call-trgt-94 INFO input :: job: "call-trgt_plot_meth_allele", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": false, "methylation": true, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-94/call-trgt_genotype/out/m84036_250809_035451_s4.bc2191.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-94/call-trgt_genotype/out/m84036_250809_035451_s4.bc2191.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-94/call-trgt_genotype/out/m84036_250809_035451_s4.bc2191.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2191"}
2025-09-15 20:25:53.660 wdl.w:ptcp.w:call-trgt-94 NOTICE ready :: job: "call-trgt_plot_meth_waterfall", callee: "trgt_plot"
2025-09-15 20:25:53.660 wdl.w:ptcp.w:call-trgt-94 INFO input :: job: "call-trgt_plot_meth_waterfall", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": true, "methylation": true, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-94/call-trgt_genotype/out/m84036_250809_035451_s4.bc2191.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-94/call-trgt_genotype/out/m84036_250809_035451_s4.bc2191.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-94/call-trgt_genotype/out/m84036_250809_035451_s4.bc2191.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2191"}
2025-09-15 20:25:53.661 wdl.w:ptcp.w:call-trgt-94 NOTICE ready :: job: "call-trgt_plot_motifs_allele", callee: "trgt_plot"
2025-09-15 20:25:53.661 wdl.w:ptcp.w:call-trgt-94 INFO input :: job: "call-trgt_plot_motifs_allele", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": false, "methylation": false, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-94/call-trgt_genotype/out/m84036_250809_035451_s4.bc2191.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-94/call-trgt_genotype/out/m84036_250809_035451_s4.bc2191.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-94/call-trgt_genotype/out/m84036_250809_035451_s4.bc2191.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2191"}
2025-09-15 20:25:53.662 wdl.w:ptcp.w:call-trgt-94 NOTICE ready :: job: "call-trgt_plot_motifs_waterfall", callee: "trgt_plot"
2025-09-15 20:25:53.662 wdl.w:ptcp.w:call-trgt-94 INFO input :: job: "call-trgt_plot_motifs_waterfall", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": true, "methylation": false, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-94/call-trgt_genotype/out/m84036_250809_035451_s4.bc2191.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-94/call-trgt_genotype/out/m84036_250809_035451_s4.bc2191.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-94/call-trgt_genotype/out/m84036_250809_035451_s4.bc2191.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2191"}
2025-09-15 20:25:53.663 wdl.w:ptcp.w:call-trgt-94 INFO visit :: node: "output-spanning_bam", values: {"spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-94/call-trgt_genotype/out/m84036_250809_035451_s4.bc2191.trgt.sorted.spanning.bam"}
2025-09-15 20:25:53.663 wdl.w:ptcp.w:call-trgt-94 INFO visit :: node: "output-spanning_bam_bai", values: {"spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-94/call-trgt_genotype/out/m84036_250809_035451_s4.bc2191.trgt.sorted.spanning.bam.bai"}
2025-09-15 20:25:53.664 wdl.w:ptcp.w:call-trgt-94 INFO visit :: node: "output-vcf", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-94/call-trgt_genotype/out/m84036_250809_035451_s4.bc2191.trgt.vcf"}
2025-09-15 20:25:53.671 wdl.w:ptcp.w:call-trgt-80.t:call-trgt_plot_meth_allele INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:53.671 wdl.w:ptcp.w:call-trgt-80.t:call-trgt_plot_meth_allele INFO input :: name: "waterfall", value: false
2025-09-15 20:25:53.671 wdl.w:ptcp.w:call-trgt-80.t:call-trgt_plot_meth_allele INFO input :: name: "methylation", value: true
2025-09-15 20:25:53.671 wdl.w:ptcp.w:call-trgt-80.t:call-trgt_plot_meth_allele INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:25:53.671 wdl.w:ptcp.w:call-trgt-80.t:call-trgt_plot_meth_allele INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:25:53.671 wdl.w:ptcp.w:call-trgt-80.t:call-trgt_plot_meth_allele INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:25:53.671 wdl.w:ptcp.w:call-trgt-80.t:call-trgt_plot_meth_allele INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2177.trgt.sorted.spanning.bam.bai"
2025-09-15 20:25:53.671 wdl.w:ptcp.w:call-trgt-80.t:call-trgt_plot_meth_allele INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2177.trgt.sorted.spanning.bam"
2025-09-15 20:25:53.671 wdl.w:ptcp.w:call-trgt-80.t:call-trgt_plot_meth_allele INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2177.trgt.vcf"
2025-09-15 20:25:53.672 wdl.w:ptcp.w:call-trgt-80.t:call-trgt_plot_meth_allele INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2177"
2025-09-15 20:25:53.672 wdl.w:ptcp.w:call-trgt-80.t:call-trgt_plot_meth_allele INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:25:53.672 wdl.w:ptcp.w:call-trgt-80.t:call-trgt_plot_meth_allele INFO eval :: name: "plot_type", value: "allele"
2025-09-15 20:25:53.672 wdl.w:ptcp.w:call-trgt-80.t:call-trgt_plot_meth_allele INFO eval :: name: "show", value: "meth"
2025-09-15 20:25:53.672 wdl.w:ptcp.w:call-trgt-80.t:call-trgt_plot_meth_allele INFO eval :: name: "threads", value: 1
2025-09-15 20:25:53.672 wdl.w:ptcp.w:call-trgt-80.t:call-trgt_plot_meth_allele INFO eval :: name: "disk_size", value: 27
2025-09-15 20:25:53.672 wdl.w:ptcp.w:call-trgt-80.t:call-trgt_plot_meth_allele INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2177.meth_allele"
2025-09-15 20:25:53.673 wdl.w:ptcp.w:call-trgt-80.t:call-trgt_plot_meth_allele INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:53.673 wdl.w:ptcp.w:call-trgt-80.t:call-trgt_plot_meth_allele WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:53.674 wdl.w:ptcp.w:call-trgt-80.t:call-trgt_plot_meth_allele INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:25:53.674 wdl.w:ptcp.w:call-trgt-80.t:call-trgt_plot_meth_allele INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:53.674 wdl.w:ptcp.w:call-trgt-80.t:call-trgt_plot_meth_waterfall NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-80/call-trgt_plot_meth_waterfall", thread: 140611977991744
2025-09-15 20:25:53.702 wdl.w:ptcp.w:call-trgt-80.t:call-trgt_plot_meth_waterfall INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:53.702 wdl.w:ptcp.w:call-trgt-80.t:call-trgt_plot_meth_waterfall INFO input :: name: "waterfall", value: true
2025-09-15 20:25:53.702 wdl.w:ptcp.w:call-trgt-80.t:call-trgt_plot_meth_waterfall INFO input :: name: "methylation", value: true
2025-09-15 20:25:53.702 wdl.w:ptcp.w:call-trgt-80.t:call-trgt_plot_meth_waterfall INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:25:53.702 wdl.w:ptcp.w:call-trgt-80.t:call-trgt_plot_meth_waterfall INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:25:53.702 wdl.w:ptcp.w:call-trgt-80.t:call-trgt_plot_meth_waterfall INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:25:53.702 wdl.w:ptcp.w:call-trgt-80.t:call-trgt_plot_meth_waterfall INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2177.trgt.sorted.spanning.bam.bai"
2025-09-15 20:25:53.703 wdl.w:ptcp.w:call-trgt-80.t:call-trgt_plot_meth_waterfall INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2177.trgt.sorted.spanning.bam"
2025-09-15 20:25:53.703 wdl.w:ptcp.w:call-trgt-80.t:call-trgt_plot_meth_waterfall INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2177.trgt.vcf"
2025-09-15 20:25:53.703 wdl.w:ptcp.w:call-trgt-80.t:call-trgt_plot_meth_waterfall INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2177"
2025-09-15 20:25:53.703 wdl.w:ptcp.w:call-trgt-80.t:call-trgt_plot_meth_waterfall INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:25:53.703 wdl.w:ptcp.w:call-trgt-80.t:call-trgt_plot_meth_waterfall INFO eval :: name: "plot_type", value: "waterfall"
2025-09-15 20:25:53.703 wdl.w:ptcp.w:call-trgt-80.t:call-trgt_plot_meth_waterfall INFO eval :: name: "show", value: "meth"
2025-09-15 20:25:53.703 wdl.w:ptcp.w:call-trgt-80.t:call-trgt_plot_meth_waterfall INFO eval :: name: "threads", value: 1
2025-09-15 20:25:53.703 wdl.w:ptcp.w:call-trgt-80.t:call-trgt_plot_meth_waterfall INFO eval :: name: "disk_size", value: 27
2025-09-15 20:25:53.704 wdl.w:ptcp.w:call-trgt-80.t:call-trgt_plot_meth_waterfall INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2177.meth_waterfall"
2025-09-15 20:25:53.704 wdl.w:ptcp.w:call-trgt-80.t:call-trgt_plot_meth_waterfall INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:53.704 wdl.w:ptcp.w:call-trgt-80.t:call-trgt_plot_meth_waterfall WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:53.704 wdl.w:ptcp.w:call-trgt-80.t:call-trgt_plot_meth_waterfall INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:25:53.704 wdl.w:ptcp.w:call-trgt-80.t:call-trgt_plot_meth_waterfall INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:53.718 wdl.w:ptcp.w:call-paraphase-81 NOTICE done
2025-09-15 20:25:53.735 wdl.w:ptcp NOTICE finish :: job: "call-paraphase-81"
2025-09-15 20:25:53.735 wdl.w:ptcp INFO output :: job: "call-paraphase-81", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-81/out/m84036_250809_035451_s4.bc2178.f8inversion.vcf", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-81/out/m84036_250809_035451_s4.bc2178_paraphase/m84036_250809_035451_s4.bc2178.paraphase.json", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-81/out/m84036_250809_035451_s4.bc2178_paraphase/m84036_250809_035451_s4.bc2178.paraphase.bam", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-81/out/m84036_250809_035451_s4.bc2178_paraphase/m84036_250809_035451_s4.bc2178.paraphase.bam.bai", "paraphase_vcfs": [], "havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-81/out/m84036_250809_035451_s4.bc2178.havanno.json", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-81/out/m84036_250809_035451_s4.bc2178.f8inversion.json"}
2025-09-15 20:25:53.746 wdl.w:ptcp.w:call-trgt-80.t:call-trgt_plot_meth_allele INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-80/call-trgt_plot_meth_allele/_singularity_tmpdir__ip7begb"
2025-09-15 20:25:53.746 wdl.w:ptcp.w:call-trgt-80.t:call-trgt_plot_meth_allele INFO Slurm invocation: srun --job-name call-trgt_plot_meth_allele --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-80/call-trgt_plot_meth_allele/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-80/call-trgt_plot_meth_allele/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-80/call-trgt_plot_meth_allele/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-80/call-trgt_plot_meth_allele/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-80/call-trgt_genotype/out/m84036_250809_035451_s4.bc2177.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2177.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-80/call-trgt_genotype/out/m84036_250809_035451_s4.bc2177.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2177.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-80/call-trgt_genotype/out/m84036_250809_035451_s4.bc2177.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2177.trgt.vcf:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-80/call-trgt_plot_meth_allele/_singularity_tmpdir__ip7begb/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-80/call-trgt_plot_meth_allele/_singularity_tmpdir__ip7begb/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:53.769 wdl.w:ptcp.w:call-trgt-80.t:call-trgt_plot_meth_allele NOTICE slurm_singularity run :: pid: 1206524, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-80/call-trgt_plot_meth_allele/slurm_singularity.log.txt"
2025-09-15 20:25:53.779 wdl.w:ptcp.w:call-trgt-80.t:call-trgt_plot_meth_waterfall INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-80/call-trgt_plot_meth_waterfall/_singularity_tmpdir_lx9kd4xw"
2025-09-15 20:25:53.779 wdl.w:ptcp.w:call-trgt-80.t:call-trgt_plot_meth_waterfall INFO Slurm invocation: srun --job-name call-trgt_plot_meth_waterfall --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-80/call-trgt_plot_meth_waterfall/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-80/call-trgt_plot_meth_waterfall/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-80/call-trgt_plot_meth_waterfall/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-80/call-trgt_plot_meth_waterfall/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-80/call-trgt_genotype/out/m84036_250809_035451_s4.bc2177.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2177.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-80/call-trgt_genotype/out/m84036_250809_035451_s4.bc2177.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2177.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-80/call-trgt_genotype/out/m84036_250809_035451_s4.bc2177.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2177.trgt.vcf:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-80/call-trgt_plot_meth_waterfall/_singularity_tmpdir_lx9kd4xw/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-80/call-trgt_plot_meth_waterfall/_singularity_tmpdir_lx9kd4xw/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:53.786 wdl.w:ptcp.w:call-trgt-80.t:call-trgt_plot_meth_waterfall NOTICE slurm_singularity run :: pid: 1206526, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-80/call-trgt_plot_meth_waterfall/slurm_singularity.log.txt"
2025-09-15 20:25:54.001 wdl.w:ptcp.w:call-trgt-77.t:call-trgt_plot_meth_waterfall INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2174.meth_waterfall.trgt_plots.zip"
2025-09-15 20:25:54.031 wdl.w:ptcp.w:call-paraphase-42.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for cyp21 for sample m84036_250809_035451_s4.bc2139 at 2025-09-15 20:25:43.470361...
2025-09-15 20:25:54.032 wdl.w:ptcp.w:call-paraphase-42.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for cyp21 for sample m84036_250809_035451_s4.bc2139 at 2025-09-15 20:25:44.596562...
2025-09-15 20:25:54.084 wdl.w:ptcp.w:call-sawfish-52.t:call-run_sawfish INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2149_sawfish/m84036_250809_035451_s4.bc2149.sv.vcf.gz"
2025-09-15 20:25:54.093 wdl.w:ptcp.w:call-sawfish-52.t:call-run_sawfish INFO output :: name: "vcf_tbi", value: "m84036_250809_035451_s4.bc2149_sawfish/m84036_250809_035451_s4.bc2149.sv.vcf.gz.tbi"
2025-09-15 20:25:54.094 wdl.w:ptcp.w:call-paraphase-80.t:call-call_f8 INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2177.f8inversion.vcf"
2025-09-15 20:25:54.095 wdl.w:ptcp.w:call-sawfish-52.t:call-run_sawfish INFO output :: name: "minimap2_bam", value: "m84036_250809_035451_s4.bc2149.minimap2.bam"
2025-09-15 20:25:54.096 wdl.w:ptcp.w:call-sawfish-52.t:call-run_sawfish INFO output :: name: "minimap2_bam_bai", value: "m84036_250809_035451_s4.bc2149.minimap2.bam.bai"
2025-09-15 20:25:54.097 wdl.w:ptcp.w:call-paraphase-80.t:call-call_f8 INFO output :: name: "json", value: "m84036_250809_035451_s4.bc2177.f8inversion.json"
2025-09-15 20:25:54.126 wdl.w:ptcp.w:call-trgt-77.t:call-trgt_plot_meth_waterfall NOTICE done
2025-09-15 20:25:54.166 wdl.w:ptcp.w:call-paraphase-80.t:call-call_f8 NOTICE done
2025-09-15 20:25:54.173 wdl.w:ptcp.w:call-paraphase-80 NOTICE finish :: job: "call-call_f8"
2025-09-15 20:25:54.174 wdl.w:ptcp.w:call-paraphase-80 INFO output :: job: "call-call_f8", values: {"json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-80/call-call_f8/out/m84036_250809_035451_s4.bc2177.f8inversion.json", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-80/call-call_f8/out/m84036_250809_035451_s4.bc2177.f8inversion.vcf"}
2025-09-15 20:25:54.174 wdl.w:ptcp.w:call-paraphase-80 INFO visit :: node: "output-f8_json", values: {"f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-80/call-call_f8/out/m84036_250809_035451_s4.bc2177.f8inversion.json"}
2025-09-15 20:25:54.174 wdl.w:ptcp.w:call-paraphase-80 INFO visit :: node: "output-f8_vcf", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-80/call-call_f8/out/m84036_250809_035451_s4.bc2177.f8inversion.vcf"}
2025-09-15 20:25:54.174 wdl.w:ptcp.w:call-paraphase-80 INFO visit :: node: "outputs", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-80/call-call_f8/out/m84036_250809_035451_s4.bc2177.f8inversion.vcf", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-80/call-run_paraphase/out/m84036_250809_035451_s4.bc2177_paraphase/m84036_250809_035451_s4.bc2177.paraphase.json", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-80/call-run_paraphase/out/m84036_250809_035451_s4.bc2177_paraphase/m84036_250809_035451_s4.bc2177.paraphase.bam", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-80/call-run_paraphase/out/m84036_250809_035451_s4.bc2177_paraphase/m84036_250809_035451_s4.bc2177.paraphase.bam.bai", "paraphase_vcfs": [], "havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-80/call-run_paraphase/out/m84036_250809_035451_s4.bc2177.havanno.json", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-80/call-call_f8/out/m84036_250809_035451_s4.bc2177.f8inversion.json"}
2025-09-15 20:25:54.179 wdl.w:ptcp.w:call-trgt-72.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:25:53 [ERROR] - No reads found for TRID=PRTS_ARX
2025-09-15 20:25:54.179 wdl.w:ptcp.w:call-trgt-72.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:25:53 [ERROR] - No reads found for TRID=EIEE1_ARX
2025-09-15 20:25:54.180 wdl.w:ptcp.w:call-trgt-77 NOTICE finish :: job: "call-trgt_plot_meth_waterfall"
2025-09-15 20:25:54.180 wdl.w:ptcp.w:call-trgt-77 INFO output :: job: "call-trgt_plot_meth_waterfall", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-77/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2174.meth_waterfall.trgt_plots.zip"}
2025-09-15 20:25:54.181 wdl.w:ptcp.w:call-trgt-77 INFO visit :: node: "output-images_meth_waterfall", values: {"images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-77/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2174.meth_waterfall.trgt_plots.zip"}
2025-09-15 20:25:54.183 wdl.w:ptcp.w:call-trgt-80.t:call-trgt_plot_motifs_allele NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-80/call-trgt_plot_motifs_allele", thread: 140610342200896
2025-09-15 20:25:54.192 wdl.w:ptcp.w:call-trgt-80.t:call-trgt_plot_motifs_waterfall NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-80/call-trgt_plot_motifs_waterfall", thread: 140607649453632
2025-09-15 20:25:54.201 wdl.w:ptcp.w:call-trgt-80.t:call-trgt_plot_motifs_allele INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:54.201 wdl.w:ptcp.w:call-trgt-80.t:call-trgt_plot_motifs_allele INFO input :: name: "waterfall", value: false
2025-09-15 20:25:54.201 wdl.w:ptcp.w:call-trgt-80.t:call-trgt_plot_motifs_allele INFO input :: name: "methylation", value: false
2025-09-15 20:25:54.201 wdl.w:ptcp.w:call-trgt-80.t:call-trgt_plot_motifs_allele INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:25:54.201 wdl.w:ptcp.w:call-trgt-80.t:call-trgt_plot_motifs_allele INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:25:54.201 wdl.w:ptcp.w:call-trgt-80.t:call-trgt_plot_motifs_allele INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:25:54.202 wdl.w:ptcp.w:call-trgt-80.t:call-trgt_plot_motifs_allele INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2177.trgt.sorted.spanning.bam.bai"
2025-09-15 20:25:54.202 wdl.w:ptcp.w:call-trgt-80.t:call-trgt_plot_motifs_allele INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2177.trgt.sorted.spanning.bam"
2025-09-15 20:25:54.202 wdl.w:ptcp.w:call-trgt-80.t:call-trgt_plot_motifs_allele INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2177.trgt.vcf"
2025-09-15 20:25:54.202 wdl.w:ptcp.w:call-trgt-80.t:call-trgt_plot_motifs_allele INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2177"
2025-09-15 20:25:54.202 wdl.w:ptcp.w:call-trgt-80.t:call-trgt_plot_motifs_allele INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:25:54.202 wdl.w:ptcp.w:call-trgt-80.t:call-trgt_plot_motifs_allele INFO eval :: name: "plot_type", value: "allele"
2025-09-15 20:25:54.203 wdl.w:ptcp.w:call-trgt-80.t:call-trgt_plot_motifs_allele INFO eval :: name: "show", value: "motifs"
2025-09-15 20:25:54.203 wdl.w:ptcp.w:call-trgt-80.t:call-trgt_plot_motifs_allele INFO eval :: name: "threads", value: 1
2025-09-15 20:25:54.203 wdl.w:ptcp.w:call-trgt-80.t:call-trgt_plot_motifs_allele INFO eval :: name: "disk_size", value: 27
2025-09-15 20:25:54.203 wdl.w:ptcp.w:call-trgt-80.t:call-trgt_plot_motifs_allele INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2177.motifs_allele"
2025-09-15 20:25:54.204 wdl.w:ptcp.w:call-trgt-80.t:call-trgt_plot_motifs_allele INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:54.204 wdl.w:ptcp.w:call-trgt-80.t:call-trgt_plot_motifs_allele WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:54.205 wdl.w:ptcp.w:call-trgt-80.t:call-trgt_plot_motifs_allele INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:25:54.205 wdl.w:ptcp.w:call-trgt-80.t:call-trgt_plot_motifs_allele INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:54.210 wdl.w:ptcp.w:call-trgt-80.t:call-trgt_plot_motifs_waterfall INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:54.210 wdl.w:ptcp.w:call-trgt-80.t:call-trgt_plot_motifs_waterfall INFO input :: name: "waterfall", value: true
2025-09-15 20:25:54.210 wdl.w:ptcp.w:call-trgt-80.t:call-trgt_plot_motifs_waterfall INFO input :: name: "methylation", value: false
2025-09-15 20:25:54.210 wdl.w:ptcp.w:call-trgt-80.t:call-trgt_plot_motifs_waterfall INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:25:54.210 wdl.w:ptcp.w:call-trgt-80.t:call-trgt_plot_motifs_waterfall INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:25:54.210 wdl.w:ptcp.w:call-trgt-80.t:call-trgt_plot_motifs_waterfall INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:25:54.210 wdl.w:ptcp.w:call-trgt-80.t:call-trgt_plot_motifs_waterfall INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2177.trgt.sorted.spanning.bam.bai"
2025-09-15 20:25:54.210 wdl.w:ptcp.w:call-trgt-80.t:call-trgt_plot_motifs_waterfall INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2177.trgt.sorted.spanning.bam"
2025-09-15 20:25:54.211 wdl.w:ptcp.w:call-trgt-80.t:call-trgt_plot_motifs_waterfall INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2177.trgt.vcf"
2025-09-15 20:25:54.211 wdl.w:ptcp.w:call-trgt-80.t:call-trgt_plot_motifs_waterfall INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2177"
2025-09-15 20:25:54.211 wdl.w:ptcp.w:call-trgt-80.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:25:54.211 wdl.w:ptcp.w:call-trgt-80.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "plot_type", value: "waterfall"
2025-09-15 20:25:54.211 wdl.w:ptcp.w:call-trgt-80.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "show", value: "motifs"
2025-09-15 20:25:54.211 wdl.w:ptcp.w:call-trgt-80.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "threads", value: 1
2025-09-15 20:25:54.211 wdl.w:ptcp.w:call-trgt-80.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "disk_size", value: 27
2025-09-15 20:25:54.212 wdl.w:ptcp.w:call-trgt-80.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2177.motifs_waterfall"
2025-09-15 20:25:54.212 wdl.w:ptcp.w:call-trgt-80.t:call-trgt_plot_motifs_waterfall INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:54.212 wdl.w:ptcp.w:call-trgt-80.t:call-trgt_plot_motifs_waterfall WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:54.212 wdl.w:ptcp.w:call-trgt-80.t:call-trgt_plot_motifs_waterfall INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:25:54.213 wdl.w:ptcp.w:call-trgt-80.t:call-trgt_plot_motifs_waterfall INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:54.261 wdl.w:ptcp.w:call-sawfish-52.t:call-run_sawfish NOTICE done
2025-09-15 20:25:54.268 wdl.w:ptcp.w:call-sawfish-52 NOTICE finish :: job: "call-run_sawfish"
2025-09-15 20:25:54.268 wdl.w:ptcp.w:call-sawfish-52 INFO output :: job: "call-run_sawfish", values: {"minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-52/call-run_sawfish/out/m84036_250809_035451_s4.bc2149.minimap2.bam.bai", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-52/call-run_sawfish/out/m84036_250809_035451_s4.bc2149.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-52/call-run_sawfish/out/m84036_250809_035451_s4.bc2149_sawfish/m84036_250809_035451_s4.bc2149.sv.vcf.gz.tbi", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-52/call-run_sawfish/out/m84036_250809_035451_s4.bc2149_sawfish/m84036_250809_035451_s4.bc2149.sv.vcf.gz"}
2025-09-15 20:25:54.269 wdl.w:ptcp.w:call-sawfish-52 INFO visit :: node: "output-minimap2_bam", values: {"minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-52/call-run_sawfish/out/m84036_250809_035451_s4.bc2149.minimap2.bam"}
2025-09-15 20:25:54.269 wdl.w:ptcp.w:call-sawfish-52 INFO visit :: node: "output-minimap2_bam_bai", values: {"minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-52/call-run_sawfish/out/m84036_250809_035451_s4.bc2149.minimap2.bam.bai"}
2025-09-15 20:25:54.269 wdl.w:ptcp.w:call-sawfish-52 INFO visit :: node: "output-vcf", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-52/call-run_sawfish/out/m84036_250809_035451_s4.bc2149_sawfish/m84036_250809_035451_s4.bc2149.sv.vcf.gz"}
2025-09-15 20:25:54.269 wdl.w:ptcp.w:call-sawfish-52 INFO visit :: node: "output-vcf_tbi", values: {"vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-52/call-run_sawfish/out/m84036_250809_035451_s4.bc2149_sawfish/m84036_250809_035451_s4.bc2149.sv.vcf.gz.tbi"}
2025-09-15 20:25:54.269 wdl.w:ptcp.w:call-sawfish-52 INFO visit :: node: "outputs", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-52/call-run_sawfish/out/m84036_250809_035451_s4.bc2149_sawfish/m84036_250809_035451_s4.bc2149.sv.vcf.gz", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-52/call-run_sawfish/out/m84036_250809_035451_s4.bc2149.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-52/call-run_sawfish/out/m84036_250809_035451_s4.bc2149_sawfish/m84036_250809_035451_s4.bc2149.sv.vcf.gz.tbi", "minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-52/call-run_sawfish/out/m84036_250809_035451_s4.bc2149.minimap2.bam.bai"}
2025-09-15 20:25:54.273 wdl.w:ptcp.w:call-paraphase-80 NOTICE done
2025-09-15 20:25:54.280 wdl.w:ptcp.w:call-sawfish-90.t:call-run_sawfish NOTICE task setup :: name: "run_sawfish", source: "./sawfish.wdl", line: 83, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-90/call-run_sawfish", thread: 140607666239040
2025-09-15 20:25:54.281 wdl.w:ptcp NOTICE finish :: job: "call-paraphase-80"
2025-09-15 20:25:54.282 wdl.w:ptcp INFO output :: job: "call-paraphase-80", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-80/out/m84036_250809_035451_s4.bc2177.f8inversion.vcf", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-80/out/m84036_250809_035451_s4.bc2177_paraphase/m84036_250809_035451_s4.bc2177.paraphase.json", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-80/out/m84036_250809_035451_s4.bc2177_paraphase/m84036_250809_035451_s4.bc2177.paraphase.bam", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-80/out/m84036_250809_035451_s4.bc2177_paraphase/m84036_250809_035451_s4.bc2177.paraphase.bam.bai", "paraphase_vcfs": [], "havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-80/out/m84036_250809_035451_s4.bc2177.havanno.json", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-80/out/m84036_250809_035451_s4.bc2177.f8inversion.json"}
2025-09-15 20:25:54.306 wdl.w:ptcp.w:call-trgt-80.t:call-trgt_plot_motifs_waterfall INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-80/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_wf0xuutg"
2025-09-15 20:25:54.307 wdl.w:ptcp.w:call-sawfish-90.t:call-run_sawfish INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:54.307 wdl.w:ptcp.w:call-trgt-80.t:call-trgt_plot_motifs_waterfall INFO Slurm invocation: srun --job-name call-trgt_plot_motifs_waterfall --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-80/call-trgt_plot_motifs_waterfall/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-80/call-trgt_plot_motifs_waterfall/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-80/call-trgt_plot_motifs_waterfall/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-80/call-trgt_plot_motifs_waterfall/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-80/call-trgt_genotype/out/m84036_250809_035451_s4.bc2177.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2177.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-80/call-trgt_genotype/out/m84036_250809_035451_s4.bc2177.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2177.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-80/call-trgt_genotype/out/m84036_250809_035451_s4.bc2177.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2177.trgt.vcf:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-80/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_wf0xuutg/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-80/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_wf0xuutg/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:54.307 wdl.w:ptcp.w:call-sawfish-90.t:call-run_sawfish INFO input :: name: "genome_version", value: "38"
2025-09-15 20:25:54.307 wdl.w:ptcp.w:call-sawfish-90.t:call-run_sawfish INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:25:54.307 wdl.w:ptcp.w:call-sawfish-90.t:call-run_sawfish INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:25:54.307 wdl.w:ptcp.w:call-sawfish-90.t:call-run_sawfish INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2187.mapped.bam.bai"
2025-09-15 20:25:54.307 wdl.w:ptcp.w:call-sawfish-90.t:call-run_sawfish INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2187.mapped.bam"
2025-09-15 20:25:54.309 wdl.w:ptcp.w:call-sawfish-90.t:call-run_sawfish INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2187"
2025-09-15 20:25:54.310 wdl.w:ptcp.w:call-sawfish-90.t:call-run_sawfish INFO eval :: name: "mem_gb", value: 32
2025-09-15 20:25:54.310 wdl.w:ptcp.w:call-sawfish-90.t:call-run_sawfish INFO eval :: name: "threads", value: 16
2025-09-15 20:25:54.310 wdl.w:ptcp.w:call-sawfish-90.t:call-run_sawfish INFO eval :: name: "disk_size", value: 30
2025-09-15 20:25:54.310 wdl.w:ptcp.w:call-sawfish-90.t:call-run_sawfish INFO eval :: name: "discover_dirname", value: "m84036_250809_035451_s4.bc2187_sawfish_discover"
2025-09-15 20:25:54.310 wdl.w:ptcp.w:call-sawfish-90.t:call-run_sawfish INFO eval :: name: "call_dirname", value: "m84036_250809_035451_s4.bc2187_sawfish"
2025-09-15 20:25:54.310 wdl.w:ptcp.w:call-sawfish-90.t:call-run_sawfish INFO eval :: name: "minimap2_bam_filename", value: "m84036_250809_035451_s4.bc2187.minimap2.bam"
2025-09-15 20:25:54.311 wdl.w:ptcp.w:call-sawfish-90.t:call-run_sawfish INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 16, memory_reservation: 32000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:54.311 wdl.w:ptcp.w:call-sawfish-90.t:call-run_sawfish WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:54.312 wdl.w:ptcp.w:call-sawfish-90.t:call-run_sawfish INFO provisioned :: seconds_waited: 0, cpu: 16, mem_bytes: 32000000000
2025-09-15 20:25:54.312 wdl.w:ptcp.w:call-sawfish-90.t:call-run_sawfish INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:54.312 wdl.w:ptcp.w:call-trgt-80.t:call-trgt_plot_motifs_allele INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-80/call-trgt_plot_motifs_allele/_singularity_tmpdir_61koxyd3"
2025-09-15 20:25:54.312 wdl.w:ptcp.w:call-trgt-80.t:call-trgt_plot_motifs_allele INFO Slurm invocation: srun --job-name call-trgt_plot_motifs_allele --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-80/call-trgt_plot_motifs_allele/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-80/call-trgt_plot_motifs_allele/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-80/call-trgt_plot_motifs_allele/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-80/call-trgt_plot_motifs_allele/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-80/call-trgt_genotype/out/m84036_250809_035451_s4.bc2177.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2177.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-80/call-trgt_genotype/out/m84036_250809_035451_s4.bc2177.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2177.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-80/call-trgt_genotype/out/m84036_250809_035451_s4.bc2177.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2177.trgt.vcf:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-80/call-trgt_plot_motifs_allele/_singularity_tmpdir_61koxyd3/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-80/call-trgt_plot_motifs_allele/_singularity_tmpdir_61koxyd3/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:54.331 wdl.w:ptcp.w:call-sawfish-52 NOTICE done
2025-09-15 20:25:54.332 wdl.w:ptcp.w:call-trgt-80.t:call-trgt_plot_motifs_allele NOTICE slurm_singularity run :: pid: 1206542, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-80/call-trgt_plot_motifs_allele/slurm_singularity.log.txt"
2025-09-15 20:25:54.332 wdl.w:ptcp.w:call-trgt-80.t:call-trgt_plot_motifs_waterfall NOTICE slurm_singularity run :: pid: 1206541, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-80/call-trgt_plot_motifs_waterfall/slurm_singularity.log.txt"
2025-09-15 20:25:54.338 wdl.w:ptcp NOTICE finish :: job: "call-sawfish-52"
2025-09-15 20:25:54.338 wdl.w:ptcp INFO output :: job: "call-sawfish-52", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-52/out/m84036_250809_035451_s4.bc2149_sawfish/m84036_250809_035451_s4.bc2149.sv.vcf.gz", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-52/out/m84036_250809_035451_s4.bc2149.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-52/out/m84036_250809_035451_s4.bc2149_sawfish/m84036_250809_035451_s4.bc2149.sv.vcf.gz.tbi", "minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-52/out/m84036_250809_035451_s4.bc2149.minimap2.bam.bai"}
2025-09-15 20:25:54.339 wdl.w:ptcp NOTICE ready :: job: "call-tar_outputs-52", callee: "tar_outputs"
2025-09-15 20:25:54.339 wdl.w:ptcp INFO input :: job: "call-tar_outputs-52", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "sawfish_vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-52/out/m84036_250809_035451_s4.bc2149_sawfish/m84036_250809_035451_s4.bc2149.sv.vcf.gz.tbi", "sawfish_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-52/out/m84036_250809_035451_s4.bc2149_sawfish/m84036_250809_035451_s4.bc2149.sv.vcf.gz", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-52/out/m84036_250809_035451_s4.bc2149.f8inversion.json", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-52/out/m84036_250809_035451_s4.bc2149_paraphase/m84036_250809_035451_s4.bc2149.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-52/out/m84036_250809_035451_s4.bc2149_paraphase/m84036_250809_035451_s4.bc2149.paraphase.bam", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-52/out/m84036_250809_035451_s4.bc2149_paraphase/m84036_250809_035451_s4.bc2149.paraphase.json", "trgt_spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-52/out/m84036_250809_035451_s4.bc2149.trgt.sorted.spanning.bam.bai", "trgt_spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-52/out/m84036_250809_035451_s4.bc2149.trgt.sorted.spanning.bam", "trgt_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-52/out/m84036_250809_035451_s4.bc2149.trgt.vcf", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-52/out/m84036_250809_035451_s4.bc2149.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-52/out/m84036_250809_035451_s4.bc2149.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2149"}
2025-09-15 20:25:54.341 wdl.w:ptcp.w:call-paraphase-90.t:call-run_paraphase.slurm_singularity INFO srun: job 51798094 queued and waiting for resources
2025-09-15 20:25:54.342 wdl.w:ptcp.w:call-paraphase-90.t:call-run_paraphase.slurm_singularity INFO srun: job 51798094 has been allocated resources
2025-09-15 20:25:54.342 wdl.w:ptcp.w:call-paraphase-90.t:call-run_paraphase.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:54.383 wdl.w:ptcp.w:call-sawfish-90.t:call-run_sawfish INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 10, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-90/call-run_sawfish/_singularity_tmpdir_dstpazx_"
2025-09-15 20:25:54.383 wdl.w:ptcp.w:call-sawfish-90.t:call-run_sawfish INFO Slurm invocation: srun --job-name call-run_sawfish --partition compute,compute9 --cpus-per-task 16 --mem 30518M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-90/call-run_sawfish/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-90/call-run_sawfish/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-90/call-run_sawfish/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-90/call-run_sawfish/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-90/out/m84036_250809_035451_s4.bc2187.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2187.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-90/out/m84036_250809_035451_s4.bc2187.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2187.mapped.bam.bai:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-90/call-run_sawfish/_singularity_tmpdir_dstpazx_/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-90/call-run_sawfish/_singularity_tmpdir_dstpazx_/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:54.387 wdl.w:ptcp.w:call-paraphase-39.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for f8inv1 for sample m84036_250809_035451_s4.bc2136 at 2025-09-15 20:25:28.771120...
2025-09-15 20:25:54.387 wdl.w:ptcp.w:call-paraphase-39.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for hbb for sample m84036_250809_035451_s4.bc2136 at 2025-09-15 20:25:29.621058...
2025-09-15 20:25:54.387 wdl.w:ptcp.w:call-paraphase-39.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for hbb for sample m84036_250809_035451_s4.bc2136 at 2025-09-15 20:25:32.708602...
2025-09-15 20:25:54.387 wdl.w:ptcp.w:call-paraphase-39.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for hbb for sample m84036_250809_035451_s4.bc2136 at 2025-09-15 20:25:32.931664...
2025-09-15 20:25:54.402 wdl.w:ptcp.w:call-sawfish-90.t:call-run_sawfish NOTICE slurm_singularity run :: pid: 1206545, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-90/call-run_sawfish/slurm_singularity.log.txt"
2025-09-15 20:25:54.496 wdl.w:ptcp.w:call-sawfish-68.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:50][sawfish][INFO] Starting sawfish 2.0.3
2025-09-15 20:25:54.496 wdl.w:ptcp.w:call-sawfish-68.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:50][sawfish][INFO] cmdline: sawfish discover --disable-cnv --threads 16 --ref /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa --bam m84036_250809_035451_s4.bc2165.minimap2.bam --output-dir m84036_250809_035451_s4.bc2165_sawfish_discover
2025-09-15 20:25:54.496 wdl.w:ptcp.w:call-sawfish-68.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:50][sawfish][INFO] Running on 16 threads
2025-09-15 20:25:54.496 wdl.w:ptcp.w:call-sawfish-68.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:50][sawfish][INFO] Writing discover settings to file: 'm84036_250809_035451_s4.bc2165_sawfish_discover/discover.settings.json'
2025-09-15 20:25:54.496 wdl.w:ptcp.w:call-sawfish-68.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:50][sawfish][INFO] Reading reference genome from file '/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa'
2025-09-15 20:25:54.496 wdl.w:ptcp.w:call-sawfish-68.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:53][sawfish][INFO] Processing alignment file '/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2165.minimap2.bam'
2025-09-15 20:25:54.496 wdl.w:ptcp.w:call-sawfish-68.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:53][sawfish][INFO] Finished processing all alignments
2025-09-15 20:25:54.496 wdl.w:ptcp.w:call-sawfish-68.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:53][sawfish][INFO] Writing depth bins to binary file: 'm84036_250809_035451_s4.bc2165_sawfish_discover/depth.mpack'
2025-09-15 20:25:54.496 wdl.w:ptcp.w:call-sawfish-68.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:53][sawfish][INFO] Writing max sv depth genome regions to bed file: 'm84036_250809_035451_s4.bc2165_sawfish_discover/max.depth.bed'
2025-09-15 20:25:54.497 wdl.w:ptcp.w:call-sawfish-68.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:53][sawfish][INFO] Completing breakpoint observation clustering
2025-09-15 20:25:54.497 wdl.w:ptcp.w:call-sawfish-68.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:53][sawfish][INFO] Finished breakpoint observation clustering
2025-09-15 20:25:54.497 wdl.w:ptcp.w:call-sawfish-68.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:53][sawfish][INFO] Consolidating adjacent indel candidates
2025-09-15 20:25:54.497 wdl.w:ptcp.w:call-sawfish-68.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:53][sawfish][INFO] Finding large insertion candidates
2025-09-15 20:25:54.497 wdl.w:ptcp.w:call-sawfish-68.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:53][sawfish][INFO] Writing breakpoint_cluster debug bed file: 'm84036_250809_035451_s4.bc2165_sawfish_discover/debug.breakpoint_clusters.bed'
2025-09-15 20:25:54.497 wdl.w:ptcp.w:call-sawfish-68.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:53][sawfish][INFO] Refining SV Candidates
2025-09-15 20:25:54.497 wdl.w:ptcp.w:call-sawfish-68.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:53][sawfish][INFO] Writing debug assembly region bed file: 'm84036_250809_035451_s4.bc2165_sawfish_discover/assembly.regions.bed'
2025-09-15 20:25:54.497 wdl.w:ptcp.w:call-sawfish-68.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:53][sawfish][INFO] Starting refinement of breakpoint evidence clusters
2025-09-15 20:25:54.497 wdl.w:ptcp.w:call-sawfish-68.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:53][sawfish][INFO] Finished refining all breakpoint evidence clusters
2025-09-15 20:25:54.497 wdl.w:ptcp.w:call-sawfish-68.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:53][sawfish][INFO] Writing all contig alignments to bam file: 'm84036_250809_035451_s4.bc2165_sawfish_discover/contig.alignment.bam'
2025-09-15 20:25:54.497 wdl.w:ptcp.w:call-sawfish-68.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:53][sawfish][INFO] Writing candidate structural variants to file: 'm84036_250809_035451_s4.bc2165_sawfish_discover/candidate.sv.bcf'
2025-09-15 20:25:54.497 wdl.w:ptcp.w:call-sawfish-68.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:53][sawfish][INFO] Writing run statistics to file: 'm84036_250809_035451_s4.bc2165_sawfish_discover/run.stats.json'
2025-09-15 20:25:54.497 wdl.w:ptcp.w:call-sawfish-68.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:53][sawfish][INFO] sawfish completed. Total Runtime: 00:00:03.548
2025-09-15 20:25:54.678 wdl.w:ptcp.w:call-sawfish-40.t:call-run_sawfish INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2137_sawfish/m84036_250809_035451_s4.bc2137.sv.vcf.gz"
2025-09-15 20:25:54.683 wdl.w:ptcp.w:call-sawfish-40.t:call-run_sawfish INFO output :: name: "vcf_tbi", value: "m84036_250809_035451_s4.bc2137_sawfish/m84036_250809_035451_s4.bc2137.sv.vcf.gz.tbi"
2025-09-15 20:25:54.684 wdl.w:ptcp.w:call-sawfish-40.t:call-run_sawfish INFO output :: name: "minimap2_bam", value: "m84036_250809_035451_s4.bc2137.minimap2.bam"
2025-09-15 20:25:54.685 wdl.w:ptcp.w:call-sawfish-40.t:call-run_sawfish INFO output :: name: "minimap2_bam_bai", value: "m84036_250809_035451_s4.bc2137.minimap2.bam.bai"
2025-09-15 20:25:54.782 wdl.w:ptcp.w:call-trgt-80.t:call-trgt_plot_meth_allele.slurm_singularity INFO srun: job 51798095 queued and waiting for resources
2025-09-15 20:25:54.782 wdl.w:ptcp.w:call-trgt-80.t:call-trgt_plot_meth_allele.slurm_singularity INFO srun: job 51798095 has been allocated resources
2025-09-15 20:25:54.782 wdl.w:ptcp.w:call-trgt-80.t:call-trgt_plot_meth_allele.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:54.795 wdl.w:ptcp.w:call-trgt-80.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO srun: job 51798096 queued and waiting for resources
2025-09-15 20:25:54.795 wdl.w:ptcp.w:call-trgt-80.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO srun: job 51798096 has been allocated resources
2025-09-15 20:25:54.795 wdl.w:ptcp.w:call-trgt-80.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:54.804 wdl.w:ptcp.w:call-sawfish-40.t:call-run_sawfish NOTICE done
2025-09-15 20:25:54.815 wdl.w:ptcp.w:call-sawfish-40 NOTICE finish :: job: "call-run_sawfish"
2025-09-15 20:25:54.815 wdl.w:ptcp.w:call-sawfish-40 INFO output :: job: "call-run_sawfish", values: {"minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-40/call-run_sawfish/out/m84036_250809_035451_s4.bc2137.minimap2.bam.bai", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-40/call-run_sawfish/out/m84036_250809_035451_s4.bc2137.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-40/call-run_sawfish/out/m84036_250809_035451_s4.bc2137_sawfish/m84036_250809_035451_s4.bc2137.sv.vcf.gz.tbi", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-40/call-run_sawfish/out/m84036_250809_035451_s4.bc2137_sawfish/m84036_250809_035451_s4.bc2137.sv.vcf.gz"}
2025-09-15 20:25:54.815 wdl.w:ptcp.w:call-sawfish-40 INFO visit :: node: "output-minimap2_bam", values: {"minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-40/call-run_sawfish/out/m84036_250809_035451_s4.bc2137.minimap2.bam"}
2025-09-15 20:25:54.816 wdl.w:ptcp.w:call-sawfish-40 INFO visit :: node: "output-minimap2_bam_bai", values: {"minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-40/call-run_sawfish/out/m84036_250809_035451_s4.bc2137.minimap2.bam.bai"}
2025-09-15 20:25:54.816 wdl.w:ptcp.w:call-sawfish-40 INFO visit :: node: "output-vcf", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-40/call-run_sawfish/out/m84036_250809_035451_s4.bc2137_sawfish/m84036_250809_035451_s4.bc2137.sv.vcf.gz"}
2025-09-15 20:25:54.816 wdl.w:ptcp.w:call-sawfish-40 INFO visit :: node: "output-vcf_tbi", values: {"vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-40/call-run_sawfish/out/m84036_250809_035451_s4.bc2137_sawfish/m84036_250809_035451_s4.bc2137.sv.vcf.gz.tbi"}
2025-09-15 20:25:54.816 wdl.w:ptcp.w:call-sawfish-40 INFO visit :: node: "outputs", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-40/call-run_sawfish/out/m84036_250809_035451_s4.bc2137_sawfish/m84036_250809_035451_s4.bc2137.sv.vcf.gz", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-40/call-run_sawfish/out/m84036_250809_035451_s4.bc2137.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-40/call-run_sawfish/out/m84036_250809_035451_s4.bc2137_sawfish/m84036_250809_035451_s4.bc2137.sv.vcf.gz.tbi", "minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-40/call-run_sawfish/out/m84036_250809_035451_s4.bc2137.minimap2.bam.bai"}
2025-09-15 20:25:54.819 wdl.w:ptcp.w:call-paraphase-71.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for hba for sample m84036_250809_035451_s4.bc2168 at 2025-09-15 20:25:07.536948...
2025-09-15 20:25:54.820 wdl.w:ptcp.w:call-paraphase-71.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for smn1 for sample m84036_250809_035451_s4.bc2168 at 2025-09-15 20:25:07.997716...
2025-09-15 20:25:54.821 wdl.w:ptcp.w:call-paraphase-71.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for gba for sample m84036_250809_035451_s4.bc2168 at 2025-09-15 20:25:08.215158...
2025-09-15 20:25:54.821 wdl.w:ptcp.w:call-paraphase-71.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for cyp21 for sample m84036_250809_035451_s4.bc2168 at 2025-09-15 20:25:09.563005...
2025-09-15 20:25:54.821 wdl.w:ptcp.w:call-paraphase-71.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for smn1 for sample m84036_250809_035451_s4.bc2168 at 2025-09-15 20:25:31.860929...
2025-09-15 20:25:54.821 wdl.w:ptcp.w:call-paraphase-71.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning to gene2 region for smn1 for sample m84036_250809_035451_s4.bc2168 at 2025-09-15 20:25:33.262251...
2025-09-15 20:25:54.822 wdl.w:ptcp.w:call-trgt-90.t:call-get_reads_overlapping_repeats NOTICE task setup :: name: "get_reads_overlapping_repeats", source: "./trgt.wdl", line: 182, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-90/call-get_reads_overlapping_repeats", thread: 140608748373568
2025-09-15 20:25:54.840 wdl.w:ptcp.w:call-trgt-90.t:call-get_reads_overlapping_repeats INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:54.841 wdl.w:ptcp.w:call-trgt-90.t:call-get_reads_overlapping_repeats INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:25:54.841 wdl.w:ptcp.w:call-trgt-90.t:call-get_reads_overlapping_repeats INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2187.mapped.bam.bai"
2025-09-15 20:25:54.841 wdl.w:ptcp.w:call-trgt-90.t:call-get_reads_overlapping_repeats INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2187.mapped.bam"
2025-09-15 20:25:54.841 wdl.w:ptcp.w:call-trgt-90.t:call-get_reads_overlapping_repeats INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2187"
2025-09-15 20:25:54.841 wdl.w:ptcp.w:call-trgt-90.t:call-get_reads_overlapping_repeats INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:25:54.841 wdl.w:ptcp.w:call-trgt-90.t:call-get_reads_overlapping_repeats INFO eval :: name: "expand_size", value: 3000
2025-09-15 20:25:54.841 wdl.w:ptcp.w:call-trgt-90.t:call-get_reads_overlapping_repeats INFO eval :: name: "threads", value: 1
2025-09-15 20:25:54.841 wdl.w:ptcp.w:call-trgt-90.t:call-get_reads_overlapping_repeats INFO eval :: name: "expanded_bed_name", value: "m84036_250809_035451_s4.bc2187.expanded.bed"
2025-09-15 20:25:54.842 wdl.w:ptcp.w:call-trgt-90.t:call-get_reads_overlapping_repeats INFO eval :: name: "disk_size", value: 11
2025-09-15 20:25:54.842 wdl.w:ptcp.w:call-trgt-90.t:call-get_reads_overlapping_repeats INFO eval :: name: "output_name", value: "m84036_250809_035451_s4.bc2187.repeats.bam"
2025-09-15 20:25:54.842 wdl.w:ptcp.w:call-trgt-90.t:call-get_reads_overlapping_repeats INFO eval :: name: "index_name", value: "m84036_250809_035451_s4.bc2187.repeats.bam.bai"
2025-09-15 20:25:54.842 wdl.w:ptcp.w:call-trgt-90.t:call-get_reads_overlapping_repeats INFO eval :: name: "output_name_with_index", value: "m84036_250809_035451_s4.bc2187.repeats.bam##idx##m84036_250809_035451_s4.bc2187.repeats.bam.bai"
2025-09-15 20:25:54.842 wdl.w:ptcp.w:call-trgt-90.t:call-get_reads_overlapping_repeats INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:54.842 wdl.w:ptcp.w:call-trgt-90.t:call-get_reads_overlapping_repeats WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:54.843 wdl.w:ptcp.w:call-trgt-90.t:call-get_reads_overlapping_repeats INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:25:54.843 wdl.w:ptcp.w:call-trgt-90.t:call-get_reads_overlapping_repeats INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:54.860 wdl.w:ptcp.w:call-sawfish-40 NOTICE done
2025-09-15 20:25:54.866 wdl.w:ptcp NOTICE finish :: job: "call-sawfish-40"
2025-09-15 20:25:54.866 wdl.w:ptcp INFO output :: job: "call-sawfish-40", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-40/out/m84036_250809_035451_s4.bc2137_sawfish/m84036_250809_035451_s4.bc2137.sv.vcf.gz", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-40/out/m84036_250809_035451_s4.bc2137.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-40/out/m84036_250809_035451_s4.bc2137_sawfish/m84036_250809_035451_s4.bc2137.sv.vcf.gz.tbi", "minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-40/out/m84036_250809_035451_s4.bc2137.minimap2.bam.bai"}
2025-09-15 20:25:54.867 wdl.w:ptcp NOTICE ready :: job: "call-tar_outputs-40", callee: "tar_outputs"
2025-09-15 20:25:54.867 wdl.w:ptcp INFO input :: job: "call-tar_outputs-40", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "sawfish_vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-40/out/m84036_250809_035451_s4.bc2137_sawfish/m84036_250809_035451_s4.bc2137.sv.vcf.gz.tbi", "sawfish_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-40/out/m84036_250809_035451_s4.bc2137_sawfish/m84036_250809_035451_s4.bc2137.sv.vcf.gz", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-40/out/m84036_250809_035451_s4.bc2137.f8inversion.json", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-40/out/m84036_250809_035451_s4.bc2137_paraphase/m84036_250809_035451_s4.bc2137.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-40/out/m84036_250809_035451_s4.bc2137_paraphase/m84036_250809_035451_s4.bc2137.paraphase.bam", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-40/out/m84036_250809_035451_s4.bc2137_paraphase/m84036_250809_035451_s4.bc2137.paraphase.json", "trgt_spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-40/out/m84036_250809_035451_s4.bc2137.trgt.sorted.spanning.bam.bai", "trgt_spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-40/out/m84036_250809_035451_s4.bc2137.trgt.sorted.spanning.bam", "trgt_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-40/out/m84036_250809_035451_s4.bc2137.trgt.vcf", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-40/out/m84036_250809_035451_s4.bc2137.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-40/out/m84036_250809_035451_s4.bc2137.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2137"}
2025-09-15 20:25:54.894 wdl.w:ptcp.w:call-trgt-90.t:call-get_reads_overlapping_repeats INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 9, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-90/call-get_reads_overlapping_repeats/_singularity_tmpdir_cx9hlbnu"
2025-09-15 20:25:54.894 wdl.w:ptcp.w:call-trgt-90.t:call-get_reads_overlapping_repeats INFO Slurm invocation: srun --job-name call-get_reads_overlapping_repeats --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-90/call-get_reads_overlapping_repeats/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-90/call-get_reads_overlapping_repeats/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-90/call-get_reads_overlapping_repeats/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-90/call-get_reads_overlapping_repeats/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-90/out/m84036_250809_035451_s4.bc2187.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2187.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-90/out/m84036_250809_035451_s4.bc2187.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2187.mapped.bam.bai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-90/call-get_reads_overlapping_repeats/_singularity_tmpdir_cx9hlbnu/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-90/call-get_reads_overlapping_repeats/_singularity_tmpdir_cx9hlbnu/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:54.917 wdl.w:ptcp.w:call-trgt-90.t:call-get_reads_overlapping_repeats NOTICE slurm_singularity run :: pid: 1206563, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-90/call-get_reads_overlapping_repeats/slurm_singularity.log.txt"
2025-09-15 20:25:55.076 wdl.w:ptcp.w:call-trgt-72.t:call-trgt_plot_meth_allele INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2169.meth_allele.trgt_plots.zip"
2025-09-15 20:25:55.192 wdl.w:ptcp.w:call-trgt-72.t:call-trgt_plot_meth_allele NOTICE done
2025-09-15 20:25:55.196 wdl.w:ptcp.w:call-trgt-72 NOTICE finish :: job: "call-trgt_plot_meth_allele"
2025-09-15 20:25:55.197 wdl.w:ptcp.w:call-trgt-72 INFO output :: job: "call-trgt_plot_meth_allele", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-72/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2169.meth_allele.trgt_plots.zip"}
2025-09-15 20:25:55.197 wdl.w:ptcp.w:call-trgt-72 INFO visit :: node: "output-images_meth_allele", values: {"images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-72/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2169.meth_allele.trgt_plots.zip"}
2025-09-15 20:25:55.202 wdl.w:ptcp.w:call-trgt-90.t:call-trgt_genotype NOTICE task setup :: name: "trgt_genotype", source: "./trgt.wdl", line: 272, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-90/call-trgt_genotype", thread: 140611944420928
2025-09-15 20:25:55.218 wdl.w:ptcp.w:call-trgt-90.t:call-trgt_genotype INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:55.218 wdl.w:ptcp.w:call-trgt-90.t:call-trgt_genotype INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:25:55.218 wdl.w:ptcp.w:call-trgt-90.t:call-trgt_genotype INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:25:55.218 wdl.w:ptcp.w:call-trgt-90.t:call-trgt_genotype INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:25:55.218 wdl.w:ptcp.w:call-trgt-90.t:call-trgt_genotype INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2187.mapped.bam.bai"
2025-09-15 20:25:55.218 wdl.w:ptcp.w:call-trgt-90.t:call-trgt_genotype INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2187.mapped.bam"
2025-09-15 20:25:55.218 wdl.w:ptcp.w:call-trgt-90.t:call-trgt_genotype INFO input :: name: "sex", value: "F"
2025-09-15 20:25:55.218 wdl.w:ptcp.w:call-trgt-90.t:call-trgt_genotype INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2187"
2025-09-15 20:25:55.219 wdl.w:ptcp.w:call-trgt-90.t:call-trgt_genotype INFO eval :: name: "mem_gb", value: 16
2025-09-15 20:25:55.219 wdl.w:ptcp.w:call-trgt-90.t:call-trgt_genotype INFO eval :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2187.trgt"
2025-09-15 20:25:55.219 wdl.w:ptcp.w:call-trgt-90.t:call-trgt_genotype INFO eval :: name: "threads", value: 8
2025-09-15 20:25:55.219 wdl.w:ptcp.w:call-trgt-90.t:call-trgt_genotype INFO eval :: name: "disk_size", value: 27
2025-09-15 20:25:55.219 wdl.w:ptcp.w:call-trgt-90.t:call-trgt_genotype INFO eval :: name: "karyotype", value: "XX"
2025-09-15 20:25:55.220 wdl.w:ptcp.w:call-trgt-90.t:call-trgt_genotype INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 8, memory_reservation: 16000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:55.220 wdl.w:ptcp.w:call-trgt-90.t:call-trgt_genotype WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:55.220 wdl.w:ptcp.w:call-trgt-90.t:call-trgt_genotype INFO provisioned :: seconds_waited: 0, cpu: 8, mem_bytes: 16000000000
2025-09-15 20:25:55.220 wdl.w:ptcp.w:call-trgt-90.t:call-trgt_genotype INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:55.274 wdl.w:ptcp.w:call-paraphase-51.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for hbb for sample m84036_250809_035451_s4.bc2148 at 2025-09-15 20:25:33.844066...
2025-09-15 20:25:55.274 wdl.w:ptcp.w:call-paraphase-51.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for gba for sample m84036_250809_035451_s4.bc2148 at 2025-09-15 20:25:35.210033...
2025-09-15 20:25:55.275 wdl.w:ptcp.w:call-paraphase-51.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for gba for sample m84036_250809_035451_s4.bc2148 at 2025-09-15 20:25:36.207496...
2025-09-15 20:25:55.275 wdl.w:ptcp.w:call-paraphase-51.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for f8inv1 for sample m84036_250809_035451_s4.bc2148 at 2025-09-15 20:25:37.924339...
2025-09-15 20:25:55.275 wdl.w:ptcp.w:call-paraphase-51.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for f8inv1 for sample m84036_250809_035451_s4.bc2148 at 2025-09-15 20:25:38.400374...
2025-09-15 20:25:55.275 wdl.w:ptcp.w:call-paraphase-51.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for hbb for sample m84036_250809_035451_s4.bc2148 at 2025-09-15 20:25:38.467396...
2025-09-15 20:25:55.275 wdl.w:ptcp.w:call-paraphase-51.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for hbb for sample m84036_250809_035451_s4.bc2148 at 2025-09-15 20:25:39.015581...
2025-09-15 20:25:55.280 wdl.w:ptcp.w:call-trgt-90.t:call-trgt_genotype INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 11, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-90/call-trgt_genotype/_singularity_tmpdir_gucmq7rg"
2025-09-15 20:25:55.280 wdl.w:ptcp.w:call-trgt-90.t:call-trgt_genotype INFO Slurm invocation: srun --job-name call-trgt_genotype --partition compute,compute9 --cpus-per-task 8 --mem 15259M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-90/call-trgt_genotype/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-90/call-trgt_genotype/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-90/call-trgt_genotype/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-90/call-trgt_genotype/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-90/out/m84036_250809_035451_s4.bc2187.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2187.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-90/out/m84036_250809_035451_s4.bc2187.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2187.mapped.bam.bai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-90/call-trgt_genotype/_singularity_tmpdir_gucmq7rg/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-90/call-trgt_genotype/_singularity_tmpdir_gucmq7rg/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:55.294 wdl.w:ptcp.w:call-trgt-90.t:call-trgt_genotype NOTICE slurm_singularity run :: pid: 1206571, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-90/call-trgt_genotype/slurm_singularity.log.txt"
2025-09-15 20:25:55.341 wdl.w:ptcp.w:call-trgt-80.t:call-trgt_plot_motifs_allele.slurm_singularity INFO srun: job 51798097 queued and waiting for resources
2025-09-15 20:25:55.341 wdl.w:ptcp.w:call-trgt-80.t:call-trgt_plot_motifs_allele.slurm_singularity INFO srun: job 51798097 has been allocated resources
2025-09-15 20:25:55.341 wdl.w:ptcp.w:call-trgt-80.t:call-trgt_plot_motifs_allele.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:55.350 wdl.w:ptcp.w:call-trgt-80.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO srun: job 51798098 queued and waiting for resources
2025-09-15 20:25:55.350 wdl.w:ptcp.w:call-trgt-80.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO srun: job 51798098 has been allocated resources
2025-09-15 20:25:55.350 wdl.w:ptcp.w:call-trgt-80.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:55.413 wdl.w:ptcp.w:call-sawfish-90.t:call-run_sawfish.slurm_singularity INFO srun: job 51798099 queued and waiting for resources
2025-09-15 20:25:55.414 wdl.w:ptcp.w:call-sawfish-90.t:call-run_sawfish.slurm_singularity INFO srun: job 51798099 has been allocated resources
2025-09-15 20:25:55.576 wdl.w:ptcp.w:call-paraphase-79.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for f8inv22 for sample m84036_250809_035451_s4.bc2176 at 2025-09-15 20:25:51.360417...
2025-09-15 20:25:55.576 wdl.w:ptcp.w:call-paraphase-79.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for f8inv22 for sample m84036_250809_035451_s4.bc2176 at 2025-09-15 20:25:51.361423...
2025-09-15 20:25:55.820 wdl.w:ptcp.w:call-sawfish-65.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:45][sawfish][INFO] Starting sawfish 2.0.3
2025-09-15 20:25:55.820 wdl.w:ptcp.w:call-sawfish-65.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:45][sawfish][INFO] cmdline: sawfish discover --disable-cnv --threads 16 --ref /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa --bam m84036_250809_035451_s4.bc2162.minimap2.bam --output-dir m84036_250809_035451_s4.bc2162_sawfish_discover
2025-09-15 20:25:55.821 wdl.w:ptcp.w:call-sawfish-65.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:45][sawfish][INFO] Running on 16 threads
2025-09-15 20:25:55.821 wdl.w:ptcp.w:call-sawfish-65.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:45][sawfish][INFO] Writing discover settings to file: 'm84036_250809_035451_s4.bc2162_sawfish_discover/discover.settings.json'
2025-09-15 20:25:55.821 wdl.w:ptcp.w:call-sawfish-65.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:45][sawfish][INFO] Reading reference genome from file '/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa'
2025-09-15 20:25:55.821 wdl.w:ptcp.w:call-sawfish-65.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:49][sawfish][INFO] Processing alignment file '/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2162.minimap2.bam'
2025-09-15 20:25:55.821 wdl.w:ptcp.w:call-sawfish-65.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:49][sawfish][INFO] Finished processing all alignments
2025-09-15 20:25:55.821 wdl.w:ptcp.w:call-sawfish-65.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:49][sawfish][INFO] Writing depth bins to binary file: 'm84036_250809_035451_s4.bc2162_sawfish_discover/depth.mpack'
2025-09-15 20:25:55.821 wdl.w:ptcp.w:call-sawfish-65.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:49][sawfish][INFO] Writing max sv depth genome regions to bed file: 'm84036_250809_035451_s4.bc2162_sawfish_discover/max.depth.bed'
2025-09-15 20:25:55.821 wdl.w:ptcp.w:call-sawfish-65.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:49][sawfish][INFO] Completing breakpoint observation clustering
2025-09-15 20:25:55.821 wdl.w:ptcp.w:call-sawfish-65.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:49][sawfish][INFO] Finished breakpoint observation clustering
2025-09-15 20:25:55.821 wdl.w:ptcp.w:call-sawfish-65.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:49][sawfish][INFO] Consolidating adjacent indel candidates
2025-09-15 20:25:55.821 wdl.w:ptcp.w:call-sawfish-65.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:49][sawfish][INFO] Finding large insertion candidates
2025-09-15 20:25:55.821 wdl.w:ptcp.w:call-sawfish-65.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:49][sawfish][INFO] Writing breakpoint_cluster debug bed file: 'm84036_250809_035451_s4.bc2162_sawfish_discover/debug.breakpoint_clusters.bed'
2025-09-15 20:25:55.821 wdl.w:ptcp.w:call-sawfish-65.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:49][sawfish][INFO] Refining SV Candidates
2025-09-15 20:25:55.821 wdl.w:ptcp.w:call-sawfish-65.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:49][sawfish][INFO] Writing debug assembly region bed file: 'm84036_250809_035451_s4.bc2162_sawfish_discover/assembly.regions.bed'
2025-09-15 20:25:55.821 wdl.w:ptcp.w:call-sawfish-65.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:49][sawfish][INFO] Starting refinement of breakpoint evidence clusters
2025-09-15 20:25:55.821 wdl.w:ptcp.w:call-sawfish-65.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:49][sawfish][INFO] Finished refining all breakpoint evidence clusters
2025-09-15 20:25:55.821 wdl.w:ptcp.w:call-sawfish-65.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:49][sawfish][INFO] Writing all contig alignments to bam file: 'm84036_250809_035451_s4.bc2162_sawfish_discover/contig.alignment.bam'
2025-09-15 20:25:55.821 wdl.w:ptcp.w:call-sawfish-65.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:49][sawfish][INFO] Writing candidate structural variants to file: 'm84036_250809_035451_s4.bc2162_sawfish_discover/candidate.sv.bcf'
2025-09-15 20:25:55.821 wdl.w:ptcp.w:call-sawfish-65.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:49][sawfish][INFO] Writing run statistics to file: 'm84036_250809_035451_s4.bc2162_sawfish_discover/run.stats.json'
2025-09-15 20:25:55.822 wdl.w:ptcp.w:call-sawfish-65.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:49][sawfish][INFO] sawfish completed. Total Runtime: 00:00:04.309
2025-09-15 20:25:55.927 wdl.w:ptcp.w:call-trgt-90.t:call-get_reads_overlapping_repeats.slurm_singularity INFO srun: job 51798100 queued and waiting for resources
2025-09-15 20:25:55.927 wdl.w:ptcp.w:call-trgt-90.t:call-get_reads_overlapping_repeats.slurm_singularity INFO srun: job 51798100 has been allocated resources
2025-09-15 20:25:55.927 wdl.w:ptcp.w:call-trgt-90.t:call-get_reads_overlapping_repeats.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:56.113 wdl.w:ptcp.w:call-paraphase-34.t:call-run_paraphase INFO output :: name: "paraphase_bam", value: "m84036_250809_035451_s4.bc2131_paraphase/m84036_250809_035451_s4.bc2131.paraphase.bam"
2025-09-15 20:25:56.118 wdl.w:ptcp.w:call-paraphase-34.t:call-run_paraphase INFO output :: name: "paraphase_bam_bai", value: "m84036_250809_035451_s4.bc2131_paraphase/m84036_250809_035451_s4.bc2131.paraphase.bam.bai"
2025-09-15 20:25:56.119 wdl.w:ptcp.w:call-paraphase-34.t:call-run_paraphase INFO output :: name: "paraphase_json", value: "m84036_250809_035451_s4.bc2131_paraphase/m84036_250809_035451_s4.bc2131.paraphase.json"
2025-09-15 20:25:56.124 wdl.w:ptcp.w:call-paraphase-34.t:call-run_paraphase INFO output :: name: "paraphase_vcfs", value: ["/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2131_paraphase/m84036_250809_035451_s4.bc2131_paraphase_vcfs/m84036_250809_035451_s4.bc2131_cyp21.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2131_paraphase/m84036_250809_035451_s4.bc2131_paraphase_vcfs/m84036_250809_035451_s4.bc2131_f8inv1.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2131_paraphase/m84036_250809_035451_s4.bc2131_paraphase_vcfs/m84036_250809_035451_s4.bc2131_f8inv22.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2131_paraphase/m84036_250809_035451_s4.bc2131_paraphase_vcfs/m84036_250809_035451_s4.bc2131_gba.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2131_paraphase/m84036_250809_035451_s4.bc2131_paraphase_vcfs/m84036_250809_035451_s4.bc2131_hba.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2131_paraphase/m84036_250809_035451_s4.bc2131_paraphase_vcfs/m84036_250809_035451_s4.bc2131_hbb.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2131_paraphase/m84036_250809_035451_s4.bc2131_paraphase_vcfs/m84036_250809_035451_s4.bc2131_rpgr.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2131_paraphase/m84036_250809_035451_s4.bc2131_paraphase_vcfs/m84036_250809_035451_s4.bc2131_smn1.vcf"]
2025-09-15 20:25:56.127 wdl.w:ptcp.w:call-paraphase-34.t:call-run_paraphase INFO output :: name: "havanno_json", value: "m84036_250809_035451_s4.bc2131.havanno.json"
2025-09-15 20:25:56.136 wdl.w:ptcp.w:call-trgt-77.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:25:54 [ERROR] - No reads found for TRID=PRTS_ARX
2025-09-15 20:25:56.136 wdl.w:ptcp.w:call-trgt-77.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:25:54 [ERROR] - No reads found for TRID=EIEE1_ARX
2025-09-15 20:25:56.164 wdl.w:ptcp.w:call-trgt-77.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:25:52 [ERROR] - No reads found for TRID=PRTS_ARX
2025-09-15 20:25:56.164 wdl.w:ptcp.w:call-trgt-77.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:25:52 [ERROR] - No reads found for TRID=EIEE1_ARX
2025-09-15 20:25:56.297 wdl.w:ptcp.w:call-paraphase-34.t:call-run_paraphase NOTICE done
2025-09-15 20:25:56.304 wdl.w:ptcp.w:call-paraphase-34 NOTICE finish :: job: "call-run_paraphase"
2025-09-15 20:25:56.304 wdl.w:ptcp.w:call-paraphase-34 INFO output :: job: "call-run_paraphase", values: {"havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-34/call-run_paraphase/out/m84036_250809_035451_s4.bc2131.havanno.json", "paraphase_vcfs": ["/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-34/call-run_paraphase/out/m84036_250809_035451_s4.bc2131_paraphase/m84036_250809_035451_s4.bc2131_paraphase_vcfs/m84036_250809_035451_s4.bc2131_cyp21.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-34/call-run_paraphase/out/m84036_250809_035451_s4.bc2131_paraphase/m84036_250809_035451_s4.bc2131_paraphase_vcfs/m84036_250809_035451_s4.bc2131_f8inv1.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-34/call-run_paraphase/out/m84036_250809_035451_s4.bc2131_paraphase/m84036_250809_035451_s4.bc2131_paraphase_vcfs/m84036_250809_035451_s4.bc2131_f8inv22.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-34/call-run_paraphase/out/m84036_250809_035451_s4.bc2131_paraphase/m84036_250809_035451_s4.bc2131_paraphase_vcfs/m84036_250809_035451_s4.bc2131_gba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-34/call-run_paraphase/out/m84036_250809_035451_s4.bc2131_paraphase/m84036_250809_035451_s4.bc2131_paraphase_vcfs/m84036_250809_035451_s4.bc2131_hba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-34/call-run_paraphase/out/m84036_250809_035451_s4.bc2131_paraphase/m84036_250809_035451_s4.bc2131_paraphase_vcfs/m84036_250809_035451_s4.bc2131_hbb.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-34/call-run_paraphase/out/m84036_250809_035451_s4.bc2131_paraphase/m84036_250809_035451_s4.bc2131_paraphase_vcfs/m84036_250809_035451_s4.bc2131_rpgr.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-34/call-run_paraphase/out/m84036_250809_035451_s4.bc2131_paraphase/m84036_250809_035451_s4.bc2131_paraphase_vcfs/m84036_250809_035451_s4.bc2131_smn1.vcf"], "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-34/call-run_paraphase/out/m84036_250809_035451_s4.bc2131_paraphase/m84036_250809_035451_s4.bc2131.paraphase.json", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-34/call-run_paraphase/out/m84036_250809_035451_s4.bc2131_paraphase/m84036_250809_035451_s4.bc2131.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-34/call-run_paraphase/out/m84036_250809_035451_s4.bc2131_paraphase/m84036_250809_035451_s4.bc2131.paraphase.bam"}
2025-09-15 20:25:56.305 wdl.w:ptcp.w:call-paraphase-34 NOTICE ready :: job: "call-call_f8", callee: "call_f8"
2025-09-15 20:25:56.305 wdl.w:ptcp.w:call-paraphase-34 INFO input :: job: "call-call_f8", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "out_prefix": "m84036_250809_035451_s4.bc2131", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-34/call-run_paraphase/out/m84036_250809_035451_s4.bc2131_paraphase/m84036_250809_035451_s4.bc2131.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-34/call-run_paraphase/out/m84036_250809_035451_s4.bc2131_paraphase/m84036_250809_035451_s4.bc2131.paraphase.bam", "sex": "F"}
2025-09-15 20:25:56.306 wdl.w:ptcp.w:call-paraphase-34 INFO visit :: node: "output-havanno_json", values: {"havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-34/call-run_paraphase/out/m84036_250809_035451_s4.bc2131.havanno.json"}
2025-09-15 20:25:56.306 wdl.w:ptcp.w:call-paraphase-34 INFO visit :: node: "output-paraphase_bam", values: {"paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-34/call-run_paraphase/out/m84036_250809_035451_s4.bc2131_paraphase/m84036_250809_035451_s4.bc2131.paraphase.bam"}
2025-09-15 20:25:56.306 wdl.w:ptcp.w:call-paraphase-34 INFO visit :: node: "output-paraphase_bam_bai", values: {"paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-34/call-run_paraphase/out/m84036_250809_035451_s4.bc2131_paraphase/m84036_250809_035451_s4.bc2131.paraphase.bam.bai"}
2025-09-15 20:25:56.306 wdl.w:ptcp.w:call-paraphase-34 INFO visit :: node: "output-paraphase_json", values: {"paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-34/call-run_paraphase/out/m84036_250809_035451_s4.bc2131_paraphase/m84036_250809_035451_s4.bc2131.paraphase.json"}
2025-09-15 20:25:56.306 wdl.w:ptcp.w:call-paraphase-34 INFO visit :: node: "output-paraphase_vcfs", values: {"paraphase_vcfs": ["/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-34/call-run_paraphase/out/m84036_250809_035451_s4.bc2131_paraphase/m84036_250809_035451_s4.bc2131_paraphase_vcfs/m84036_250809_035451_s4.bc2131_cyp21.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-34/call-run_paraphase/out/m84036_250809_035451_s4.bc2131_paraphase/m84036_250809_035451_s4.bc2131_paraphase_vcfs/m84036_250809_035451_s4.bc2131_f8inv1.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-34/call-run_paraphase/out/m84036_250809_035451_s4.bc2131_paraphase/m84036_250809_035451_s4.bc2131_paraphase_vcfs/m84036_250809_035451_s4.bc2131_f8inv22.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-34/call-run_paraphase/out/m84036_250809_035451_s4.bc2131_paraphase/m84036_250809_035451_s4.bc2131_paraphase_vcfs/m84036_250809_035451_s4.bc2131_gba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-34/call-run_paraphase/out/m84036_250809_035451_s4.bc2131_paraphase/m84036_250809_035451_s4.bc2131_paraphase_vcfs/m84036_250809_035451_s4.bc2131_hba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-34/call-run_paraphase/out/m84036_250809_035451_s4.bc2131_paraphase/m84036_250809_035451_s4.bc2131_paraphase_vcfs/m84036_250809_035451_s4.bc2131_hbb.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-34/call-run_paraphase/out/m84036_250809_035451_s4.bc2131_paraphase/m84036_250809_035451_s4.bc2131_paraphase_vcfs/m84036_250809_035451_s4.bc2131_rpgr.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-34/call-run_paraphase/out/m84036_250809_035451_s4.bc2131_paraphase/m84036_250809_035451_s4.bc2131_paraphase_vcfs/m84036_250809_035451_s4.bc2131_smn1.vcf"]}
2025-09-15 20:25:56.311 wdl.w:ptcp.w:call-trgt-90.t:call-trgt_genotype.slurm_singularity INFO srun: job 51798101 queued and waiting for resources
2025-09-15 20:25:56.312 wdl.w:ptcp.w:call-trgt-90.t:call-trgt_genotype.slurm_singularity INFO srun: job 51798101 has been allocated resources
2025-09-15 20:25:56.312 wdl.w:ptcp.w:call-trgt-90.t:call-trgt_genotype.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:56.312 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_meth_allele NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-91/call-trgt_plot_meth_allele", thread: 140613043340864
2025-09-15 20:25:56.337 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_meth_allele INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:56.337 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_meth_allele INFO input :: name: "waterfall", value: false
2025-09-15 20:25:56.337 wdl.w:ptcp.w:call-paraphase-95.t:call-run_paraphase.stderr VERBOSE INFO:root:Processing sample m84036_250809_035451_s4.bc2192 at 2025-09-15 20:25:52.762124...
2025-09-15 20:25:56.338 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_meth_allele INFO input :: name: "methylation", value: true
2025-09-15 20:25:56.338 wdl.w:ptcp.w:call-paraphase-95.t:call-run_paraphase.stderr VERBOSE INFO:root:Checking sample sex at 2025-09-15 20:25:52.762988...
2025-09-15 20:25:56.338 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_meth_allele INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:25:56.338 wdl.w:ptcp.w:call-paraphase-95.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for cyp21 for sample m84036_250809_035451_s4.bc2192 at 2025-09-15 20:25:52.806226...
2025-09-15 20:25:56.338 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_meth_allele INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:25:56.338 wdl.w:ptcp.w:call-paraphase-95.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for smn1 for sample m84036_250809_035451_s4.bc2192 at 2025-09-15 20:25:52.806330...
2025-09-15 20:25:56.338 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_meth_allele INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:25:56.339 wdl.w:ptcp.w:call-paraphase-95.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for cyp21 for sample m84036_250809_035451_s4.bc2192 at 2025-09-15 20:25:52.806680...
2025-09-15 20:25:56.339 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_meth_allele INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2188.trgt.sorted.spanning.bam.bai"
2025-09-15 20:25:56.339 wdl.w:ptcp.w:call-paraphase-95.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for gba for sample m84036_250809_035451_s4.bc2192 at 2025-09-15 20:25:52.806378...
2025-09-15 20:25:56.339 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_meth_allele INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2188.trgt.sorted.spanning.bam"
2025-09-15 20:25:56.339 wdl.w:ptcp.w:call-paraphase-95.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for smn1 for sample m84036_250809_035451_s4.bc2192 at 2025-09-15 20:25:52.806724...
2025-09-15 20:25:56.339 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_meth_allele INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2188.trgt.vcf"
2025-09-15 20:25:56.339 wdl.w:ptcp.w:call-paraphase-95.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for hba for sample m84036_250809_035451_s4.bc2192 at 2025-09-15 20:25:52.806425...
2025-09-15 20:25:56.339 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_meth_allele INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2188"
2025-09-15 20:25:56.339 wdl.w:ptcp.w:call-paraphase-95.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for gba for sample m84036_250809_035451_s4.bc2192 at 2025-09-15 20:25:52.806744...
2025-09-15 20:25:56.340 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_meth_allele INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:25:56.340 wdl.w:ptcp.w:call-paraphase-95.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for hba for sample m84036_250809_035451_s4.bc2192 at 2025-09-15 20:25:52.806778...
2025-09-15 20:25:56.340 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_meth_allele INFO eval :: name: "plot_type", value: "allele"
2025-09-15 20:25:56.340 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_meth_allele INFO eval :: name: "show", value: "meth"
2025-09-15 20:25:56.340 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_meth_allele INFO eval :: name: "threads", value: 1
2025-09-15 20:25:56.341 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_meth_allele INFO eval :: name: "disk_size", value: 27
2025-09-15 20:25:56.341 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_meth_allele INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2188.meth_allele"
2025-09-15 20:25:56.341 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_meth_allele INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:56.341 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_meth_allele WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:56.342 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_meth_allele INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:25:56.342 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_meth_allele INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:56.347 wdl.w:ptcp.w:call-sawfish-64.t:call-run_sawfish INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2161_sawfish/m84036_250809_035451_s4.bc2161.sv.vcf.gz"
2025-09-15 20:25:56.355 wdl.w:ptcp.w:call-sawfish-64.t:call-run_sawfish INFO output :: name: "vcf_tbi", value: "m84036_250809_035451_s4.bc2161_sawfish/m84036_250809_035451_s4.bc2161.sv.vcf.gz.tbi"
2025-09-15 20:25:56.356 wdl.w:ptcp.w:call-sawfish-64.t:call-run_sawfish INFO output :: name: "minimap2_bam", value: "m84036_250809_035451_s4.bc2161.minimap2.bam"
2025-09-15 20:25:56.360 wdl.w:ptcp.w:call-sawfish-64.t:call-run_sawfish INFO output :: name: "minimap2_bam_bai", value: "m84036_250809_035451_s4.bc2161.minimap2.bam.bai"
2025-09-15 20:25:56.402 wdl.w:ptcp.w:call-trgt-72.t:call-trgt_plot_motifs_allele INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2169.motifs_allele.trgt_plots.zip"
2025-09-15 20:25:56.410 wdl.w:ptcp.w:call-trgt-77.t:call-trgt_plot_motifs_waterfall INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2174.motifs_waterfall.trgt_plots.zip"
2025-09-15 20:25:56.433 wdl.w:ptcp.w:call-sawfish-90.t:call-run_sawfish.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:56.472 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_meth_allele INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-91/call-trgt_plot_meth_allele/_singularity_tmpdir_nbdswvz6"
2025-09-15 20:25:56.472 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_meth_allele INFO Slurm invocation: srun --job-name call-trgt_plot_meth_allele --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-91/call-trgt_plot_meth_allele/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-91/call-trgt_plot_meth_allele/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-91/call-trgt_plot_meth_allele/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-91/call-trgt_plot_meth_allele/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-91/call-trgt_genotype/out/m84036_250809_035451_s4.bc2188.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2188.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-91/call-trgt_genotype/out/m84036_250809_035451_s4.bc2188.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2188.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-91/call-trgt_genotype/out/m84036_250809_035451_s4.bc2188.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2188.trgt.vcf:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-91/call-trgt_plot_meth_allele/_singularity_tmpdir_nbdswvz6/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-91/call-trgt_plot_meth_allele/_singularity_tmpdir_nbdswvz6/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:56.476 wdl.w:ptcp.w:call-trgt-90.t:call-get_reads_overlapping_repeats INFO output :: name: "reads_overlapping_repeats", value: "m84036_250809_035451_s4.bc2187.repeats.bam"
2025-09-15 20:25:56.483 wdl.w:ptcp.w:call-trgt-90.t:call-get_reads_overlapping_repeats INFO output :: name: "reads_overlapping_repeats_bai", value: "m84036_250809_035451_s4.bc2187.repeats.bam.bai"
2025-09-15 20:25:56.534 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_meth_allele NOTICE slurm_singularity run :: pid: 1206584, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-91/call-trgt_plot_meth_allele/slurm_singularity.log.txt"
2025-09-15 20:25:56.582 wdl.w:ptcp.w:call-trgt-90.t:call-get_reads_overlapping_repeats NOTICE done
2025-09-15 20:25:56.588 wdl.w:ptcp.w:call-trgt-90 NOTICE finish :: job: "call-get_reads_overlapping_repeats"
2025-09-15 20:25:56.589 wdl.w:ptcp.w:call-trgt-90 INFO output :: job: "call-get_reads_overlapping_repeats", values: {"reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-90/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2187.repeats.bam.bai", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-90/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2187.repeats.bam"}
2025-09-15 20:25:56.589 wdl.w:ptcp.w:call-trgt-90 INFO visit :: node: "output-reads_overlapping_repeats", values: {"reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-90/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2187.repeats.bam"}
2025-09-15 20:25:56.589 wdl.w:ptcp.w:call-trgt-90 INFO visit :: node: "output-reads_overlapping_repeats_bai", values: {"reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-90/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2187.repeats.bam.bai"}
2025-09-15 20:25:56.591 wdl.w:ptcp.w:call-sawfish-64.t:call-run_sawfish NOTICE done
2025-09-15 20:25:56.596 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_meth_waterfall NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-91/call-trgt_plot_meth_waterfall", thread: 140608748373568
2025-09-15 20:25:56.598 wdl.w:ptcp.w:call-trgt-72.t:call-trgt_plot_motifs_allele NOTICE done
2025-09-15 20:25:56.604 wdl.w:ptcp.w:call-trgt-72 NOTICE finish :: job: "call-trgt_plot_motifs_allele"
2025-09-15 20:25:56.604 wdl.w:ptcp.w:call-trgt-72 INFO output :: job: "call-trgt_plot_motifs_allele", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-72/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2169.motifs_allele.trgt_plots.zip"}
2025-09-15 20:25:56.604 wdl.w:ptcp.w:call-trgt-72 INFO visit :: node: "output-images_motifs_allele", values: {"images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-72/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2169.motifs_allele.trgt_plots.zip"}
2025-09-15 20:25:56.612 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_motifs_allele NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-91/call-trgt_plot_motifs_allele", thread: 140608186324544
2025-09-15 20:25:56.624 wdl.w:ptcp.w:call-trgt-77.t:call-trgt_plot_motifs_waterfall NOTICE done
2025-09-15 20:25:56.625 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_meth_waterfall INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:56.625 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_meth_waterfall INFO input :: name: "waterfall", value: true
2025-09-15 20:25:56.625 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_meth_waterfall INFO input :: name: "methylation", value: true
2025-09-15 20:25:56.625 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_meth_waterfall INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:25:56.626 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_meth_waterfall INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:25:56.626 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_meth_waterfall INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:25:56.626 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_meth_waterfall INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2188.trgt.sorted.spanning.bam.bai"
2025-09-15 20:25:56.626 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_meth_waterfall INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2188.trgt.sorted.spanning.bam"
2025-09-15 20:25:56.626 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_meth_waterfall INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2188.trgt.vcf"
2025-09-15 20:25:56.626 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_meth_waterfall INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2188"
2025-09-15 20:25:56.626 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_meth_waterfall INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:25:56.626 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_meth_waterfall INFO eval :: name: "plot_type", value: "waterfall"
2025-09-15 20:25:56.626 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_meth_waterfall INFO eval :: name: "show", value: "meth"
2025-09-15 20:25:56.626 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_meth_waterfall INFO eval :: name: "threads", value: 1
2025-09-15 20:25:56.627 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_meth_waterfall INFO eval :: name: "disk_size", value: 27
2025-09-15 20:25:56.627 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_meth_waterfall INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2188.meth_waterfall"
2025-09-15 20:25:56.627 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_meth_waterfall INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:56.627 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_meth_waterfall WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:56.628 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_meth_waterfall INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:25:56.628 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_meth_waterfall INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:56.629 wdl.w:ptcp.w:call-trgt-77 NOTICE finish :: job: "call-trgt_plot_motifs_waterfall"
2025-09-15 20:25:56.629 wdl.w:ptcp.w:call-trgt-77 INFO output :: job: "call-trgt_plot_motifs_waterfall", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-77/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2174.motifs_waterfall.trgt_plots.zip"}
2025-09-15 20:25:56.630 wdl.w:ptcp.w:call-trgt-77 INFO visit :: node: "output-images_motifs_waterfall", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-77/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2174.motifs_waterfall.trgt_plots.zip"}
2025-09-15 20:25:56.630 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_motifs_allele INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:56.630 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_motifs_allele INFO input :: name: "waterfall", value: false
2025-09-15 20:25:56.630 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_motifs_allele INFO input :: name: "methylation", value: false
2025-09-15 20:25:56.630 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_motifs_allele INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:25:56.630 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_motifs_allele INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:25:56.630 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_motifs_allele INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:25:56.631 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_motifs_allele INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2188.trgt.sorted.spanning.bam.bai"
2025-09-15 20:25:56.631 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_motifs_allele INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2188.trgt.sorted.spanning.bam"
2025-09-15 20:25:56.631 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_motifs_allele INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2188.trgt.vcf"
2025-09-15 20:25:56.631 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_motifs_allele INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2188"
2025-09-15 20:25:56.631 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_motifs_allele INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:25:56.631 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_motifs_allele INFO eval :: name: "plot_type", value: "allele"
2025-09-15 20:25:56.631 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_motifs_allele INFO eval :: name: "show", value: "motifs"
2025-09-15 20:25:56.631 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_motifs_allele INFO eval :: name: "threads", value: 1
2025-09-15 20:25:56.632 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_motifs_allele INFO eval :: name: "disk_size", value: 27
2025-09-15 20:25:56.632 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_motifs_allele INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2188.motifs_allele"
2025-09-15 20:25:56.632 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_motifs_allele INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:56.632 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_motifs_allele WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:56.632 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_motifs_allele INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:25:56.632 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_motifs_allele INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:56.634 wdl.w:ptcp.w:call-sawfish-64 NOTICE finish :: job: "call-run_sawfish"
2025-09-15 20:25:56.634 wdl.w:ptcp.w:call-sawfish-64 INFO output :: job: "call-run_sawfish", values: {"minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-64/call-run_sawfish/out/m84036_250809_035451_s4.bc2161.minimap2.bam.bai", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-64/call-run_sawfish/out/m84036_250809_035451_s4.bc2161.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-64/call-run_sawfish/out/m84036_250809_035451_s4.bc2161_sawfish/m84036_250809_035451_s4.bc2161.sv.vcf.gz.tbi", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-64/call-run_sawfish/out/m84036_250809_035451_s4.bc2161_sawfish/m84036_250809_035451_s4.bc2161.sv.vcf.gz"}
2025-09-15 20:25:56.634 wdl.w:ptcp.w:call-sawfish-64 INFO visit :: node: "output-minimap2_bam", values: {"minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-64/call-run_sawfish/out/m84036_250809_035451_s4.bc2161.minimap2.bam"}
2025-09-15 20:25:56.634 wdl.w:ptcp.w:call-sawfish-64 INFO visit :: node: "output-minimap2_bam_bai", values: {"minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-64/call-run_sawfish/out/m84036_250809_035451_s4.bc2161.minimap2.bam.bai"}
2025-09-15 20:25:56.634 wdl.w:ptcp.w:call-sawfish-64 INFO visit :: node: "output-vcf", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-64/call-run_sawfish/out/m84036_250809_035451_s4.bc2161_sawfish/m84036_250809_035451_s4.bc2161.sv.vcf.gz"}
2025-09-15 20:25:56.635 wdl.w:ptcp.w:call-sawfish-64 INFO visit :: node: "output-vcf_tbi", values: {"vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-64/call-run_sawfish/out/m84036_250809_035451_s4.bc2161_sawfish/m84036_250809_035451_s4.bc2161.sv.vcf.gz.tbi"}
2025-09-15 20:25:56.635 wdl.w:ptcp.w:call-sawfish-64 INFO visit :: node: "outputs", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-64/call-run_sawfish/out/m84036_250809_035451_s4.bc2161_sawfish/m84036_250809_035451_s4.bc2161.sv.vcf.gz", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-64/call-run_sawfish/out/m84036_250809_035451_s4.bc2161.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-64/call-run_sawfish/out/m84036_250809_035451_s4.bc2161_sawfish/m84036_250809_035451_s4.bc2161.sv.vcf.gz.tbi", "minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-64/call-run_sawfish/out/m84036_250809_035451_s4.bc2161.minimap2.bam.bai"}
2025-09-15 20:25:56.639 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_motifs_waterfall NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-91/call-trgt_plot_motifs_waterfall", thread: 140606575711808
2025-09-15 20:25:56.644 wdl.w:ptcp.w:call-paraphase-86.t:call-run_paraphase NOTICE task setup :: name: "run_paraphase", source: "./paraphase.wdl", line: 127, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-86/call-run_paraphase", thread: 140609268459072
2025-09-15 20:25:56.668 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_motifs_waterfall INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:56.668 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_motifs_waterfall INFO input :: name: "waterfall", value: true
2025-09-15 20:25:56.669 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_motifs_waterfall INFO input :: name: "methylation", value: false
2025-09-15 20:25:56.669 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_motifs_waterfall INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:25:56.669 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_motifs_waterfall INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:25:56.669 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_motifs_waterfall INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:25:56.669 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_motifs_waterfall INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2188.trgt.sorted.spanning.bam.bai"
2025-09-15 20:25:56.669 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_motifs_waterfall INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2188.trgt.sorted.spanning.bam"
2025-09-15 20:25:56.669 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_motifs_waterfall INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2188.trgt.vcf"
2025-09-15 20:25:56.669 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_motifs_waterfall INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2188"
2025-09-15 20:25:56.669 wdl.w:ptcp.w:call-paraphase-86.t:call-run_paraphase INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:56.669 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:25:56.669 wdl.w:ptcp.w:call-paraphase-86.t:call-run_paraphase INFO input :: name: "annotation_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf"
2025-09-15 20:25:56.670 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "plot_type", value: "waterfall"
2025-09-15 20:25:56.670 wdl.w:ptcp.w:call-paraphase-86.t:call-run_paraphase INFO input :: name: "genome_version", value: "38"
2025-09-15 20:25:56.670 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "show", value: "motifs"
2025-09-15 20:25:56.670 wdl.w:ptcp.w:call-paraphase-86.t:call-run_paraphase INFO input :: name: "config_file", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/paraphase_config.GRCh38.yaml"
2025-09-15 20:25:56.670 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "threads", value: 1
2025-09-15 20:25:56.670 wdl.w:ptcp.w:call-paraphase-86.t:call-run_paraphase INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:25:56.670 wdl.w:ptcp.w:call-paraphase-86.t:call-run_paraphase INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:25:56.670 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "disk_size", value: 27
2025-09-15 20:25:56.670 wdl.w:ptcp.w:call-paraphase-86.t:call-run_paraphase INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2183.mapped.bam.bai"
2025-09-15 20:25:56.671 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2188.motifs_waterfall"
2025-09-15 20:25:56.671 wdl.w:ptcp.w:call-paraphase-86.t:call-run_paraphase INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2183.mapped.bam"
2025-09-15 20:25:56.672 wdl.w:ptcp.w:call-paraphase-86.t:call-run_paraphase INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2183"
2025-09-15 20:25:56.673 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_motifs_waterfall INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:56.673 wdl.w:ptcp.w:call-paraphase-86.t:call-run_paraphase INFO eval :: name: "threads", value: 4
2025-09-15 20:25:56.673 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_motifs_waterfall WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:56.673 wdl.w:ptcp.w:call-paraphase-86.t:call-run_paraphase INFO eval :: name: "mem_gb", value: 8
2025-09-15 20:25:56.674 wdl.w:ptcp.w:call-paraphase-86.t:call-run_paraphase INFO eval :: name: "disk_size", value: 27
2025-09-15 20:25:56.674 wdl.w:ptcp.w:call-paraphase-86.t:call-run_paraphase INFO eval :: name: "out_dir", value: "m84036_250809_035451_s4.bc2183_paraphase"
2025-09-15 20:25:56.674 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_motifs_waterfall INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:25:56.674 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_motifs_waterfall INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:56.675 wdl.w:ptcp.w:call-paraphase-86.t:call-run_paraphase INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 4, memory_reservation: 8000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:56.675 wdl.w:ptcp.w:call-paraphase-86.t:call-run_paraphase WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:56.675 wdl.w:ptcp.w:call-paraphase-86.t:call-run_paraphase INFO provisioned :: seconds_waited: 0, cpu: 4, mem_bytes: 8000000000
2025-09-15 20:25:56.675 wdl.w:ptcp.w:call-paraphase-86.t:call-run_paraphase INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:56.703 wdl.w:ptcp.w:call-sawfish-64 NOTICE done
2025-09-15 20:25:56.721 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_meth_waterfall INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-91/call-trgt_plot_meth_waterfall/_singularity_tmpdir_1kznu_bl"
2025-09-15 20:25:56.721 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_meth_waterfall INFO Slurm invocation: srun --job-name call-trgt_plot_meth_waterfall --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-91/call-trgt_plot_meth_waterfall/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-91/call-trgt_plot_meth_waterfall/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-91/call-trgt_plot_meth_waterfall/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-91/call-trgt_plot_meth_waterfall/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-91/call-trgt_genotype/out/m84036_250809_035451_s4.bc2188.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2188.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-91/call-trgt_genotype/out/m84036_250809_035451_s4.bc2188.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2188.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-91/call-trgt_genotype/out/m84036_250809_035451_s4.bc2188.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2188.trgt.vcf:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-91/call-trgt_plot_meth_waterfall/_singularity_tmpdir_1kznu_bl/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-91/call-trgt_plot_meth_waterfall/_singularity_tmpdir_1kznu_bl/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:56.725 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_motifs_allele INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-91/call-trgt_plot_motifs_allele/_singularity_tmpdir_vfc08khz"
2025-09-15 20:25:56.730 wdl.w:ptcp NOTICE finish :: job: "call-sawfish-64"
2025-09-15 20:25:56.737 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_motifs_allele INFO Slurm invocation: srun --job-name call-trgt_plot_motifs_allele --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-91/call-trgt_plot_motifs_allele/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-91/call-trgt_plot_motifs_allele/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-91/call-trgt_plot_motifs_allele/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-91/call-trgt_plot_motifs_allele/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-91/call-trgt_genotype/out/m84036_250809_035451_s4.bc2188.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2188.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-91/call-trgt_genotype/out/m84036_250809_035451_s4.bc2188.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2188.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-91/call-trgt_genotype/out/m84036_250809_035451_s4.bc2188.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2188.trgt.vcf:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-91/call-trgt_plot_motifs_allele/_singularity_tmpdir_vfc08khz/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-91/call-trgt_plot_motifs_allele/_singularity_tmpdir_vfc08khz/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:56.739 wdl.w:ptcp INFO output :: job: "call-sawfish-64", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-64/out/m84036_250809_035451_s4.bc2161_sawfish/m84036_250809_035451_s4.bc2161.sv.vcf.gz", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-64/out/m84036_250809_035451_s4.bc2161.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-64/out/m84036_250809_035451_s4.bc2161_sawfish/m84036_250809_035451_s4.bc2161.sv.vcf.gz.tbi", "minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-64/out/m84036_250809_035451_s4.bc2161.minimap2.bam.bai"}
2025-09-15 20:25:56.740 wdl.w:ptcp NOTICE ready :: job: "call-tar_outputs-64", callee: "tar_outputs"
2025-09-15 20:25:56.740 wdl.w:ptcp INFO input :: job: "call-tar_outputs-64", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "sawfish_vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-64/out/m84036_250809_035451_s4.bc2161_sawfish/m84036_250809_035451_s4.bc2161.sv.vcf.gz.tbi", "sawfish_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-64/out/m84036_250809_035451_s4.bc2161_sawfish/m84036_250809_035451_s4.bc2161.sv.vcf.gz", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-64/out/m84036_250809_035451_s4.bc2161.f8inversion.json", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-64/out/m84036_250809_035451_s4.bc2161_paraphase/m84036_250809_035451_s4.bc2161.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-64/out/m84036_250809_035451_s4.bc2161_paraphase/m84036_250809_035451_s4.bc2161.paraphase.bam", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-64/out/m84036_250809_035451_s4.bc2161_paraphase/m84036_250809_035451_s4.bc2161.paraphase.json", "trgt_spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-64/out/m84036_250809_035451_s4.bc2161.trgt.sorted.spanning.bam.bai", "trgt_spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-64/out/m84036_250809_035451_s4.bc2161.trgt.sorted.spanning.bam", "trgt_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-64/out/m84036_250809_035451_s4.bc2161.trgt.vcf", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-64/out/m84036_250809_035451_s4.bc2161.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-64/out/m84036_250809_035451_s4.bc2161.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2161"}
2025-09-15 20:25:56.760 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_meth_waterfall NOTICE slurm_singularity run :: pid: 1206586, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-91/call-trgt_plot_meth_waterfall/slurm_singularity.log.txt"
2025-09-15 20:25:56.760 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_motifs_allele NOTICE slurm_singularity run :: pid: 1206587, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-91/call-trgt_plot_motifs_allele/slurm_singularity.log.txt"
2025-09-15 20:25:56.763 wdl.w:ptcp.w:call-paraphase-86.t:call-run_paraphase INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-86/call-run_paraphase/_singularity_tmpdir_w0z642vc"
2025-09-15 20:25:56.763 wdl.w:ptcp.w:call-paraphase-86.t:call-run_paraphase INFO Slurm invocation: srun --job-name call-run_paraphase --partition compute,compute9 --cpus-per-task 4 --mem 7629M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-86/call-run_paraphase/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-86/call-run_paraphase/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-86/call-run_paraphase/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-86/call-run_paraphase/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-86/out/m84036_250809_035451_s4.bc2183.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2183.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-86/out/m84036_250809_035451_s4.bc2183.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2183.mapped.bam:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/variant_list/variant_list.GRCh38.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf:ro --bind /ptcp/meta/paraphase/paraphase_config.GRCh38.yaml:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/paraphase_config.GRCh38.yaml:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-86/call-run_paraphase/_singularity_tmpdir_w0z642vc/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-86/call-run_paraphase/_singularity_tmpdir_w0z642vc/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:56.767 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_motifs_waterfall INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-91/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_a5c_6x_5"
2025-09-15 20:25:56.767 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_motifs_waterfall INFO Slurm invocation: srun --job-name call-trgt_plot_motifs_waterfall --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-91/call-trgt_plot_motifs_waterfall/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-91/call-trgt_plot_motifs_waterfall/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-91/call-trgt_plot_motifs_waterfall/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-91/call-trgt_plot_motifs_waterfall/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-91/call-trgt_genotype/out/m84036_250809_035451_s4.bc2188.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2188.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-91/call-trgt_genotype/out/m84036_250809_035451_s4.bc2188.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2188.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-91/call-trgt_genotype/out/m84036_250809_035451_s4.bc2188.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2188.trgt.vcf:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-91/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_a5c_6x_5/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-91/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_a5c_6x_5/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:56.774 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_motifs_waterfall NOTICE slurm_singularity run :: pid: 1206591, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-91/call-trgt_plot_motifs_waterfall/slurm_singularity.log.txt"
2025-09-15 20:25:56.774 wdl.w:ptcp.w:call-paraphase-86.t:call-run_paraphase NOTICE slurm_singularity run :: pid: 1206588, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-86/call-run_paraphase/slurm_singularity.log.txt"
2025-09-15 20:25:56.952 wdl.w:ptcp.w:call-trgt-77.t:call-trgt_plot_motifs_allele INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2174.motifs_allele.trgt_plots.zip"
2025-09-15 20:25:57.088 wdl.w:ptcp.w:call-trgt-77.t:call-trgt_plot_motifs_allele NOTICE done
2025-09-15 20:25:57.093 wdl.w:ptcp.w:call-trgt-77 NOTICE finish :: job: "call-trgt_plot_motifs_allele"
2025-09-15 20:25:57.094 wdl.w:ptcp.w:call-trgt-77 INFO output :: job: "call-trgt_plot_motifs_allele", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-77/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2174.motifs_allele.trgt_plots.zip"}
2025-09-15 20:25:57.094 wdl.w:ptcp.w:call-trgt-77 INFO visit :: node: "output-images_motifs_allele", values: {"images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-77/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2174.motifs_allele.trgt_plots.zip"}
2025-09-15 20:25:57.094 wdl.w:ptcp.w:call-trgt-77 INFO visit :: node: "outputs", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-77/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2174.motifs_waterfall.trgt_plots.zip", "images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-77/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2174.meth_allele.trgt_plots.zip", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-77/call-trgt_genotype/out/m84036_250809_035451_s4.bc2174.trgt.sorted.spanning.bam.bai", "images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-77/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2174.motifs_allele.trgt_plots.zip", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-77/call-trgt_genotype/out/m84036_250809_035451_s4.bc2174.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-77/call-trgt_genotype/out/m84036_250809_035451_s4.bc2174.trgt.vcf", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-77/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2174.repeats.bam", "images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-77/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2174.meth_waterfall.trgt_plots.zip", "reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-77/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2174.repeats.bam.bai"}
2025-09-15 20:25:57.100 wdl.w:ptcp.w:call-trgt-85.t:call-trgt_plot_meth_allele NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-85/call-trgt_plot_meth_allele", thread: 140607674631744
2025-09-15 20:25:57.119 wdl.w:ptcp.w:call-trgt-85.t:call-trgt_plot_meth_allele INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:57.119 wdl.w:ptcp.w:call-trgt-85.t:call-trgt_plot_meth_allele INFO input :: name: "waterfall", value: false
2025-09-15 20:25:57.119 wdl.w:ptcp.w:call-trgt-85.t:call-trgt_plot_meth_allele INFO input :: name: "methylation", value: true
2025-09-15 20:25:57.119 wdl.w:ptcp.w:call-trgt-85.t:call-trgt_plot_meth_allele INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:25:57.119 wdl.w:ptcp.w:call-trgt-85.t:call-trgt_plot_meth_allele INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:25:57.119 wdl.w:ptcp.w:call-trgt-85.t:call-trgt_plot_meth_allele INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:25:57.119 wdl.w:ptcp.w:call-trgt-85.t:call-trgt_plot_meth_allele INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2182.trgt.sorted.spanning.bam.bai"
2025-09-15 20:25:57.119 wdl.w:ptcp.w:call-trgt-85.t:call-trgt_plot_meth_allele INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2182.trgt.sorted.spanning.bam"
2025-09-15 20:25:57.119 wdl.w:ptcp.w:call-trgt-85.t:call-trgt_plot_meth_allele INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2182.trgt.vcf"
2025-09-15 20:25:57.120 wdl.w:ptcp.w:call-trgt-85.t:call-trgt_plot_meth_allele INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2182"
2025-09-15 20:25:57.120 wdl.w:ptcp.w:call-trgt-85.t:call-trgt_plot_meth_allele INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:25:57.120 wdl.w:ptcp.w:call-trgt-85.t:call-trgt_plot_meth_allele INFO eval :: name: "plot_type", value: "allele"
2025-09-15 20:25:57.120 wdl.w:ptcp.w:call-trgt-85.t:call-trgt_plot_meth_allele INFO eval :: name: "show", value: "meth"
2025-09-15 20:25:57.120 wdl.w:ptcp.w:call-trgt-85.t:call-trgt_plot_meth_allele INFO eval :: name: "threads", value: 1
2025-09-15 20:25:57.120 wdl.w:ptcp.w:call-trgt-85.t:call-trgt_plot_meth_allele INFO eval :: name: "disk_size", value: 27
2025-09-15 20:25:57.120 wdl.w:ptcp.w:call-trgt-85.t:call-trgt_plot_meth_allele INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2182.meth_allele"
2025-09-15 20:25:57.121 wdl.w:ptcp.w:call-trgt-85.t:call-trgt_plot_meth_allele INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:57.121 wdl.w:ptcp.w:call-trgt-85.t:call-trgt_plot_meth_allele WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:57.121 wdl.w:ptcp.w:call-trgt-85.t:call-trgt_plot_meth_allele INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:25:57.121 wdl.w:ptcp.w:call-trgt-85.t:call-trgt_plot_meth_allele INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:57.192 wdl.w:ptcp.w:call-trgt-77 NOTICE done
2025-09-15 20:25:57.197 wdl.w:ptcp NOTICE finish :: job: "call-trgt-77"
2025-09-15 20:25:57.197 wdl.w:ptcp INFO output :: job: "call-trgt-77", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-77/out/m84036_250809_035451_s4.bc2174.motifs_waterfall.trgt_plots.zip", "images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-77/out/m84036_250809_035451_s4.bc2174.meth_allele.trgt_plots.zip", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-77/out/m84036_250809_035451_s4.bc2174.trgt.sorted.spanning.bam.bai", "images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-77/out/m84036_250809_035451_s4.bc2174.motifs_allele.trgt_plots.zip", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-77/out/m84036_250809_035451_s4.bc2174.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-77/out/m84036_250809_035451_s4.bc2174.trgt.vcf", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-77/out/m84036_250809_035451_s4.bc2174.repeats.bam", "images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-77/out/m84036_250809_035451_s4.bc2174.meth_waterfall.trgt_plots.zip", "reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-77/out/m84036_250809_035451_s4.bc2174.repeats.bam.bai"}
2025-09-15 20:25:57.202 wdl.w:ptcp.w:call-trgt-85.t:call-trgt_plot_meth_allele INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-85/call-trgt_plot_meth_allele/_singularity_tmpdir_6vwla0gc"
2025-09-15 20:25:57.202 wdl.w:ptcp.w:call-trgt-85.t:call-trgt_plot_meth_allele INFO Slurm invocation: srun --job-name call-trgt_plot_meth_allele --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-85/call-trgt_plot_meth_allele/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-85/call-trgt_plot_meth_allele/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-85/call-trgt_plot_meth_allele/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-85/call-trgt_plot_meth_allele/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-85/call-trgt_genotype/out/m84036_250809_035451_s4.bc2182.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2182.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-85/call-trgt_genotype/out/m84036_250809_035451_s4.bc2182.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2182.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-85/call-trgt_genotype/out/m84036_250809_035451_s4.bc2182.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2182.trgt.sorted.spanning.bam:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-85/call-trgt_plot_meth_allele/_singularity_tmpdir_6vwla0gc/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-85/call-trgt_plot_meth_allele/_singularity_tmpdir_6vwla0gc/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:57.220 wdl.w:ptcp.w:call-paraphase-70.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for smn1 for sample m84036_250809_035451_s4.bc2167 at 2025-09-15 20:25:35.937152...
2025-09-15 20:25:57.230 wdl.w:ptcp.w:call-trgt-85.t:call-trgt_plot_meth_allele NOTICE slurm_singularity run :: pid: 1206620, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-85/call-trgt_plot_meth_allele/slurm_singularity.log.txt"
2025-09-15 20:25:57.444 wdl.w:ptcp.w:call-paraphase-94.t:call-run_paraphase.stderr VERBOSE INFO:root:Processing sample m84036_250809_035451_s4.bc2191 at 2025-09-15 20:25:54.165295...
2025-09-15 20:25:57.445 wdl.w:ptcp.w:call-paraphase-94.t:call-run_paraphase.stderr VERBOSE INFO:root:Checking sample sex at 2025-09-15 20:25:54.166206...
2025-09-15 20:25:57.445 wdl.w:ptcp.w:call-paraphase-94.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for cyp21 for sample m84036_250809_035451_s4.bc2191 at 2025-09-15 20:25:54.219488...
2025-09-15 20:25:57.445 wdl.w:ptcp.w:call-paraphase-94.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for cyp21 for sample m84036_250809_035451_s4.bc2191 at 2025-09-15 20:25:54.220028...
2025-09-15 20:25:57.445 wdl.w:ptcp.w:call-paraphase-94.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for smn1 for sample m84036_250809_035451_s4.bc2191 at 2025-09-15 20:25:54.219886...
2025-09-15 20:25:57.445 wdl.w:ptcp.w:call-paraphase-94.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for smn1 for sample m84036_250809_035451_s4.bc2191 at 2025-09-15 20:25:54.220370...
2025-09-15 20:25:57.445 wdl.w:ptcp.w:call-paraphase-94.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for gba for sample m84036_250809_035451_s4.bc2191 at 2025-09-15 20:25:54.221350...
2025-09-15 20:25:57.446 wdl.w:ptcp.w:call-paraphase-94.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for gba for sample m84036_250809_035451_s4.bc2191 at 2025-09-15 20:25:54.221841...
2025-09-15 20:25:57.446 wdl.w:ptcp.w:call-paraphase-94.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for hba for sample m84036_250809_035451_s4.bc2191 at 2025-09-15 20:25:54.222985...
2025-09-15 20:25:57.446 wdl.w:ptcp.w:call-paraphase-94.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for hba for sample m84036_250809_035451_s4.bc2191 at 2025-09-15 20:25:54.223460...
2025-09-15 20:25:57.455 wdl.w:ptcp.w:call-paraphase-47.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for f8inv1 for sample m84036_250809_035451_s4.bc2144 at 2025-09-15 20:25:09.063145...
2025-09-15 20:25:57.456 wdl.w:ptcp.w:call-paraphase-47.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for hbb for sample m84036_250809_035451_s4.bc2144 at 2025-09-15 20:25:09.883547...
2025-09-15 20:25:57.456 wdl.w:ptcp.w:call-paraphase-47.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for hbb for sample m84036_250809_035451_s4.bc2144 at 2025-09-15 20:25:12.144194...
2025-09-15 20:25:57.456 wdl.w:ptcp.w:call-paraphase-47.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for f8inv1 for sample m84036_250809_035451_s4.bc2144 at 2025-09-15 20:25:12.303659...
2025-09-15 20:25:57.456 wdl.w:ptcp.w:call-paraphase-47.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for hbb for sample m84036_250809_035451_s4.bc2144 at 2025-09-15 20:25:12.528383...
2025-09-15 20:25:57.456 wdl.w:ptcp.w:call-paraphase-47.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for f8inv1 for sample m84036_250809_035451_s4.bc2144 at 2025-09-15 20:25:12.683468...
2025-09-15 20:25:57.544 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_meth_allele.slurm_singularity INFO srun: job 51798102 queued and waiting for resources
2025-09-15 20:25:57.545 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_meth_allele.slurm_singularity INFO srun: job 51798102 has been allocated resources
2025-09-15 20:25:57.545 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_meth_allele.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:57.572 wdl.w:ptcp.w:call-paraphase-59.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for f8inv1 for sample m84036_250809_035451_s4.bc2156 at 2025-09-15 20:25:49.779710...
2025-09-15 20:25:57.572 wdl.w:ptcp.w:call-paraphase-59.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for f8inv1 for sample m84036_250809_035451_s4.bc2156 at 2025-09-15 20:25:49.779881...
2025-09-15 20:25:57.634 wdl.w:ptcp.w:call-trgt-90.t:call-trgt_genotype INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2187.trgt.vcf"
2025-09-15 20:25:57.636 wdl.w:ptcp.w:call-trgt-90.t:call-trgt_genotype INFO output :: name: "spanning_bam", value: "m84036_250809_035451_s4.bc2187.trgt.sorted.spanning.bam"
2025-09-15 20:25:57.637 wdl.w:ptcp.w:call-trgt-90.t:call-trgt_genotype INFO output :: name: "spanning_bam_bai", value: "m84036_250809_035451_s4.bc2187.trgt.sorted.spanning.bam.bai"
2025-09-15 20:25:57.709 wdl.w:ptcp.w:call-trgt-81.t:call-trgt_plot_meth_allele INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2178.meth_allele.trgt_plots.zip"
2025-09-15 20:25:57.715 wdl.w:ptcp.w:call-trgt-90.t:call-trgt_genotype NOTICE done
2025-09-15 20:25:57.733 wdl.w:ptcp.w:call-trgt-90 NOTICE finish :: job: "call-trgt_genotype"
2025-09-15 20:25:57.733 wdl.w:ptcp.w:call-trgt-90 INFO output :: job: "call-trgt_genotype", values: {"spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-90/call-trgt_genotype/out/m84036_250809_035451_s4.bc2187.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-90/call-trgt_genotype/out/m84036_250809_035451_s4.bc2187.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-90/call-trgt_genotype/out/m84036_250809_035451_s4.bc2187.trgt.vcf"}
2025-09-15 20:25:57.733 wdl.w:ptcp.w:call-trgt-90 NOTICE ready :: job: "call-trgt_plot_meth_allele", callee: "trgt_plot"
2025-09-15 20:25:57.733 wdl.w:ptcp.w:call-trgt-90 INFO input :: job: "call-trgt_plot_meth_allele", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": false, "methylation": true, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-90/call-trgt_genotype/out/m84036_250809_035451_s4.bc2187.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-90/call-trgt_genotype/out/m84036_250809_035451_s4.bc2187.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-90/call-trgt_genotype/out/m84036_250809_035451_s4.bc2187.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2187"}
2025-09-15 20:25:57.734 wdl.w:ptcp.w:call-trgt-90 NOTICE ready :: job: "call-trgt_plot_meth_waterfall", callee: "trgt_plot"
2025-09-15 20:25:57.734 wdl.w:ptcp.w:call-trgt-90 INFO input :: job: "call-trgt_plot_meth_waterfall", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": true, "methylation": true, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-90/call-trgt_genotype/out/m84036_250809_035451_s4.bc2187.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-90/call-trgt_genotype/out/m84036_250809_035451_s4.bc2187.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-90/call-trgt_genotype/out/m84036_250809_035451_s4.bc2187.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2187"}
2025-09-15 20:25:57.735 wdl.w:ptcp.w:call-trgt-90 NOTICE ready :: job: "call-trgt_plot_motifs_allele", callee: "trgt_plot"
2025-09-15 20:25:57.735 wdl.w:ptcp.w:call-trgt-90 INFO input :: job: "call-trgt_plot_motifs_allele", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": false, "methylation": false, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-90/call-trgt_genotype/out/m84036_250809_035451_s4.bc2187.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-90/call-trgt_genotype/out/m84036_250809_035451_s4.bc2187.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-90/call-trgt_genotype/out/m84036_250809_035451_s4.bc2187.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2187"}
2025-09-15 20:25:57.736 wdl.w:ptcp.w:call-trgt-90 NOTICE ready :: job: "call-trgt_plot_motifs_waterfall", callee: "trgt_plot"
2025-09-15 20:25:57.736 wdl.w:ptcp.w:call-trgt-90 INFO input :: job: "call-trgt_plot_motifs_waterfall", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": true, "methylation": false, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-90/call-trgt_genotype/out/m84036_250809_035451_s4.bc2187.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-90/call-trgt_genotype/out/m84036_250809_035451_s4.bc2187.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-90/call-trgt_genotype/out/m84036_250809_035451_s4.bc2187.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2187"}
2025-09-15 20:25:57.737 wdl.w:ptcp.w:call-trgt-90 INFO visit :: node: "output-spanning_bam", values: {"spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-90/call-trgt_genotype/out/m84036_250809_035451_s4.bc2187.trgt.sorted.spanning.bam"}
2025-09-15 20:25:57.737 wdl.w:ptcp.w:call-trgt-90 INFO visit :: node: "output-spanning_bam_bai", values: {"spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-90/call-trgt_genotype/out/m84036_250809_035451_s4.bc2187.trgt.sorted.spanning.bam.bai"}
2025-09-15 20:25:57.737 wdl.w:ptcp.w:call-trgt-90 INFO visit :: node: "output-vcf", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-90/call-trgt_genotype/out/m84036_250809_035451_s4.bc2187.trgt.vcf"}
2025-09-15 20:25:57.740 wdl.w:ptcp.w:call-trgt-85.t:call-trgt_plot_meth_waterfall NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-85/call-trgt_plot_meth_waterfall", thread: 140611944420928
2025-09-15 20:25:57.756 wdl.w:ptcp.w:call-trgt-85.t:call-trgt_plot_meth_waterfall INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:57.756 wdl.w:ptcp.w:call-trgt-85.t:call-trgt_plot_meth_waterfall INFO input :: name: "waterfall", value: true
2025-09-15 20:25:57.756 wdl.w:ptcp.w:call-trgt-85.t:call-trgt_plot_meth_waterfall INFO input :: name: "methylation", value: true
2025-09-15 20:25:57.756 wdl.w:ptcp.w:call-trgt-85.t:call-trgt_plot_meth_waterfall INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:25:57.756 wdl.w:ptcp.w:call-trgt-85.t:call-trgt_plot_meth_waterfall INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:25:57.756 wdl.w:ptcp.w:call-trgt-85.t:call-trgt_plot_meth_waterfall INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:25:57.756 wdl.w:ptcp.w:call-trgt-85.t:call-trgt_plot_meth_waterfall INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2182.trgt.sorted.spanning.bam.bai"
2025-09-15 20:25:57.757 wdl.w:ptcp.w:call-trgt-85.t:call-trgt_plot_meth_waterfall INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2182.trgt.sorted.spanning.bam"
2025-09-15 20:25:57.757 wdl.w:ptcp.w:call-trgt-85.t:call-trgt_plot_meth_waterfall INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2182.trgt.vcf"
2025-09-15 20:25:57.757 wdl.w:ptcp.w:call-trgt-85.t:call-trgt_plot_meth_waterfall INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2182"
2025-09-15 20:25:57.757 wdl.w:ptcp.w:call-trgt-85.t:call-trgt_plot_meth_waterfall INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:25:57.757 wdl.w:ptcp.w:call-trgt-85.t:call-trgt_plot_meth_waterfall INFO eval :: name: "plot_type", value: "waterfall"
2025-09-15 20:25:57.757 wdl.w:ptcp.w:call-trgt-85.t:call-trgt_plot_meth_waterfall INFO eval :: name: "show", value: "meth"
2025-09-15 20:25:57.757 wdl.w:ptcp.w:call-trgt-85.t:call-trgt_plot_meth_waterfall INFO eval :: name: "threads", value: 1
2025-09-15 20:25:57.757 wdl.w:ptcp.w:call-trgt-85.t:call-trgt_plot_meth_waterfall INFO eval :: name: "disk_size", value: 27
2025-09-15 20:25:57.758 wdl.w:ptcp.w:call-trgt-85.t:call-trgt_plot_meth_waterfall INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2182.meth_waterfall"
2025-09-15 20:25:57.758 wdl.w:ptcp.w:call-trgt-85.t:call-trgt_plot_meth_waterfall INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:57.758 wdl.w:ptcp.w:call-trgt-85.t:call-trgt_plot_meth_waterfall WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:57.758 wdl.w:ptcp.w:call-trgt-85.t:call-trgt_plot_meth_waterfall INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:25:57.759 wdl.w:ptcp.w:call-trgt-85.t:call-trgt_plot_meth_waterfall INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:57.766 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:25:57 [ERROR] - No reads found for TRID=NIID_NOTCH2NLC
2025-09-15 20:25:57.766 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:25:57 [ERROR] - No reads found for TRID=OPDM_ABCD3
2025-09-15 20:25:57.766 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:25:57 [ERROR] - No reads found for TRID=SCA2_ATXN2
2025-09-15 20:25:57.766 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:25:57 [ERROR] - No reads found for TRID=OPDM4_RILPL1
2025-09-15 20:25:57.766 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:25:57 [ERROR] - No reads found for TRID=SCA27B_FGF14
2025-09-15 20:25:57.766 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:25:57 [ERROR] - No reads found for TRID=OPMD_PABPN1
2025-09-15 20:25:57.766 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:25:57 [ERROR] - No reads found for TRID=SCA3_ATXN3
2025-09-15 20:25:57.766 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:25:57 [ERROR] - No reads found for TRID=SCA31_BEAN1
2025-09-15 20:25:57.766 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:25:57 [ERROR] - No reads found for TRID=NIID_NOTCH2NLC
2025-09-15 20:25:57.766 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:25:57 [ERROR] - No reads found for TRID=OPDM_ABCD3
2025-09-15 20:25:57.766 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:25:57 [ERROR] - No reads found for TRID=SCA2_ATXN2
2025-09-15 20:25:57.767 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:25:57 [ERROR] - No reads found for TRID=OPDM4_RILPL1
2025-09-15 20:25:57.767 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:25:57 [ERROR] - No reads found for TRID=SCA27B_FGF14
2025-09-15 20:25:57.767 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:25:57 [ERROR] - No reads found for TRID=OPMD_PABPN1
2025-09-15 20:25:57.767 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:25:57 [ERROR] - No reads found for TRID=SCA3_ATXN3
2025-09-15 20:25:57.779 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_motifs_allele.slurm_singularity INFO srun: job 51798103 queued and waiting for resources
2025-09-15 20:25:57.779 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_motifs_allele.slurm_singularity INFO srun: job 51798103 has been allocated resources
2025-09-15 20:25:57.779 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO srun: job 51798104 queued and waiting for resources
2025-09-15 20:25:57.779 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_motifs_allele.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:57.779 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO srun: job 51798104 has been allocated resources
2025-09-15 20:25:57.779 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:57.792 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO srun: job 51798105 queued and waiting for resources
2025-09-15 20:25:57.792 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO srun: job 51798105 has been allocated resources
2025-09-15 20:25:57.792 wdl.w:ptcp.w:call-paraphase-86.t:call-run_paraphase.slurm_singularity INFO srun: job 51798106 queued and waiting for resources
2025-09-15 20:25:57.792 wdl.w:ptcp.w:call-paraphase-86.t:call-run_paraphase.slurm_singularity INFO srun: job 51798106 has been allocated resources
2025-09-15 20:25:57.792 wdl.w:ptcp.w:call-paraphase-86.t:call-run_paraphase.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:57.818 wdl.w:ptcp.w:call-trgt-80.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:56 [ERROR] - No reads found for TRID=PRTS_ARX
2025-09-15 20:25:57.821 wdl.w:ptcp.w:call-trgt-81.t:call-trgt_plot_motifs_allele INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2178.motifs_allele.trgt_plots.zip"
2025-09-15 20:25:57.822 wdl.w:ptcp.w:call-trgt-80.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:56 [ERROR] - No reads found for TRID=EIEE1_ARX
2025-09-15 20:25:57.866 wdl.w:ptcp.w:call-trgt-85.t:call-trgt_plot_meth_waterfall INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-85/call-trgt_plot_meth_waterfall/_singularity_tmpdir_jome528l"
2025-09-15 20:25:57.867 wdl.w:ptcp.w:call-trgt-85.t:call-trgt_plot_meth_waterfall INFO Slurm invocation: srun --job-name call-trgt_plot_meth_waterfall --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-85/call-trgt_plot_meth_waterfall/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-85/call-trgt_plot_meth_waterfall/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-85/call-trgt_plot_meth_waterfall/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-85/call-trgt_plot_meth_waterfall/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-85/call-trgt_genotype/out/m84036_250809_035451_s4.bc2182.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2182.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-85/call-trgt_genotype/out/m84036_250809_035451_s4.bc2182.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2182.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-85/call-trgt_genotype/out/m84036_250809_035451_s4.bc2182.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2182.trgt.sorted.spanning.bam:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-85/call-trgt_plot_meth_waterfall/_singularity_tmpdir_jome528l/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-85/call-trgt_plot_meth_waterfall/_singularity_tmpdir_jome528l/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:57.892 wdl.w:ptcp.w:call-trgt-81.t:call-trgt_plot_meth_allele NOTICE done
2025-09-15 20:25:57.898 wdl.w:ptcp.w:call-trgt-81 NOTICE finish :: job: "call-trgt_plot_meth_allele"
2025-09-15 20:25:57.899 wdl.w:ptcp.w:call-trgt-81 INFO output :: job: "call-trgt_plot_meth_allele", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-81/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2178.meth_allele.trgt_plots.zip"}
2025-09-15 20:25:57.899 wdl.w:ptcp.w:call-trgt-81 INFO visit :: node: "output-images_meth_allele", values: {"images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-81/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2178.meth_allele.trgt_plots.zip"}
2025-09-15 20:25:57.906 wdl.w:ptcp.w:call-trgt-85.t:call-trgt_plot_motifs_allele NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-85/call-trgt_plot_motifs_allele", thread: 140611441120832
2025-09-15 20:25:57.913 wdl.w:ptcp.w:call-trgt-85.t:call-trgt_plot_meth_waterfall NOTICE slurm_singularity run :: pid: 1206630, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-85/call-trgt_plot_meth_waterfall/slurm_singularity.log.txt"
2025-09-15 20:25:57.925 wdl.w:ptcp.w:call-trgt-85.t:call-trgt_plot_motifs_allele INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:57.925 wdl.w:ptcp.w:call-trgt-85.t:call-trgt_plot_motifs_allele INFO input :: name: "waterfall", value: false
2025-09-15 20:25:57.925 wdl.w:ptcp.w:call-trgt-85.t:call-trgt_plot_motifs_allele INFO input :: name: "methylation", value: false
2025-09-15 20:25:57.925 wdl.w:ptcp.w:call-trgt-85.t:call-trgt_plot_motifs_allele INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:25:57.925 wdl.w:ptcp.w:call-trgt-85.t:call-trgt_plot_motifs_allele INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:25:57.925 wdl.w:ptcp.w:call-trgt-85.t:call-trgt_plot_motifs_allele INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:25:57.925 wdl.w:ptcp.w:call-trgt-85.t:call-trgt_plot_motifs_allele INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2182.trgt.sorted.spanning.bam.bai"
2025-09-15 20:25:57.925 wdl.w:ptcp.w:call-trgt-85.t:call-trgt_plot_motifs_allele INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2182.trgt.sorted.spanning.bam"
2025-09-15 20:25:57.925 wdl.w:ptcp.w:call-trgt-85.t:call-trgt_plot_motifs_allele INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2182.trgt.vcf"
2025-09-15 20:25:57.925 wdl.w:ptcp.w:call-trgt-85.t:call-trgt_plot_motifs_allele INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2182"
2025-09-15 20:25:57.926 wdl.w:ptcp.w:call-trgt-85.t:call-trgt_plot_motifs_allele INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:25:57.926 wdl.w:ptcp.w:call-trgt-85.t:call-trgt_plot_motifs_allele INFO eval :: name: "plot_type", value: "allele"
2025-09-15 20:25:57.926 wdl.w:ptcp.w:call-trgt-85.t:call-trgt_plot_motifs_allele INFO eval :: name: "show", value: "motifs"
2025-09-15 20:25:57.926 wdl.w:ptcp.w:call-trgt-85.t:call-trgt_plot_motifs_allele INFO eval :: name: "threads", value: 1
2025-09-15 20:25:57.926 wdl.w:ptcp.w:call-trgt-85.t:call-trgt_plot_motifs_allele INFO eval :: name: "disk_size", value: 27
2025-09-15 20:25:57.926 wdl.w:ptcp.w:call-trgt-85.t:call-trgt_plot_motifs_allele INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2182.motifs_allele"
2025-09-15 20:25:57.927 wdl.w:ptcp.w:call-trgt-85.t:call-trgt_plot_motifs_allele INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:57.927 wdl.w:ptcp.w:call-trgt-85.t:call-trgt_plot_motifs_allele WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:57.927 wdl.w:ptcp.w:call-trgt-85.t:call-trgt_plot_motifs_allele INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:25:57.927 wdl.w:ptcp.w:call-trgt-85.t:call-trgt_plot_motifs_allele INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:57.966 wdl.w:ptcp.w:call-trgt-81.t:call-trgt_plot_motifs_allele NOTICE done
2025-09-15 20:25:57.973 wdl.w:ptcp.w:call-trgt-81 NOTICE finish :: job: "call-trgt_plot_motifs_allele"
2025-09-15 20:25:57.973 wdl.w:ptcp.w:call-trgt-81 INFO output :: job: "call-trgt_plot_motifs_allele", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-81/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2178.motifs_allele.trgt_plots.zip"}
2025-09-15 20:25:57.973 wdl.w:ptcp.w:call-trgt-81 INFO visit :: node: "output-images_motifs_allele", values: {"images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-81/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2178.motifs_allele.trgt_plots.zip"}
2025-09-15 20:25:57.982 wdl.w:ptcp.w:call-trgt-85.t:call-trgt_plot_motifs_waterfall NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-85/call-trgt_plot_motifs_waterfall", thread: 140607683024448
2025-09-15 20:25:58.011 wdl.w:ptcp.w:call-trgt-85.t:call-trgt_plot_motifs_allele INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-85/call-trgt_plot_motifs_allele/_singularity_tmpdir_ht_3ejpc"
2025-09-15 20:25:58.011 wdl.w:ptcp.w:call-trgt-85.t:call-trgt_plot_motifs_allele INFO Slurm invocation: srun --job-name call-trgt_plot_motifs_allele --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-85/call-trgt_plot_motifs_allele/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-85/call-trgt_plot_motifs_allele/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-85/call-trgt_plot_motifs_allele/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-85/call-trgt_plot_motifs_allele/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-85/call-trgt_genotype/out/m84036_250809_035451_s4.bc2182.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2182.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-85/call-trgt_genotype/out/m84036_250809_035451_s4.bc2182.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2182.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-85/call-trgt_genotype/out/m84036_250809_035451_s4.bc2182.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2182.trgt.sorted.spanning.bam:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-85/call-trgt_plot_motifs_allele/_singularity_tmpdir_ht_3ejpc/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-85/call-trgt_plot_motifs_allele/_singularity_tmpdir_ht_3ejpc/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:58.013 wdl.w:ptcp.w:call-trgt-85.t:call-trgt_plot_motifs_waterfall INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:58.013 wdl.w:ptcp.w:call-trgt-85.t:call-trgt_plot_motifs_waterfall INFO input :: name: "waterfall", value: true
2025-09-15 20:25:58.013 wdl.w:ptcp.w:call-trgt-85.t:call-trgt_plot_motifs_waterfall INFO input :: name: "methylation", value: false
2025-09-15 20:25:58.013 wdl.w:ptcp.w:call-trgt-85.t:call-trgt_plot_motifs_waterfall INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:25:58.013 wdl.w:ptcp.w:call-trgt-85.t:call-trgt_plot_motifs_waterfall INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:25:58.013 wdl.w:ptcp.w:call-trgt-85.t:call-trgt_plot_motifs_waterfall INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:25:58.013 wdl.w:ptcp.w:call-trgt-85.t:call-trgt_plot_motifs_waterfall INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2182.trgt.sorted.spanning.bam.bai"
2025-09-15 20:25:58.013 wdl.w:ptcp.w:call-trgt-85.t:call-trgt_plot_motifs_waterfall INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2182.trgt.sorted.spanning.bam"
2025-09-15 20:25:58.014 wdl.w:ptcp.w:call-trgt-85.t:call-trgt_plot_motifs_waterfall INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2182.trgt.vcf"
2025-09-15 20:25:58.014 wdl.w:ptcp.w:call-trgt-85.t:call-trgt_plot_motifs_waterfall INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2182"
2025-09-15 20:25:58.014 wdl.w:ptcp.w:call-trgt-85.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:25:58.014 wdl.w:ptcp.w:call-trgt-85.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "plot_type", value: "waterfall"
2025-09-15 20:25:58.014 wdl.w:ptcp.w:call-trgt-85.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "show", value: "motifs"
2025-09-15 20:25:58.014 wdl.w:ptcp.w:call-trgt-85.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "threads", value: 1
2025-09-15 20:25:58.014 wdl.w:ptcp.w:call-trgt-85.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "disk_size", value: 27
2025-09-15 20:25:58.014 wdl.w:ptcp.w:call-trgt-85.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2182.motifs_waterfall"
2025-09-15 20:25:58.015 wdl.w:ptcp.w:call-trgt-85.t:call-trgt_plot_motifs_waterfall INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:58.015 wdl.w:ptcp.w:call-trgt-85.t:call-trgt_plot_motifs_waterfall WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:58.015 wdl.w:ptcp.w:call-trgt-85.t:call-trgt_plot_motifs_waterfall INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:25:58.015 wdl.w:ptcp.w:call-trgt-85.t:call-trgt_plot_motifs_waterfall INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:58.024 wdl.w:ptcp.w:call-trgt-85.t:call-trgt_plot_motifs_allele NOTICE slurm_singularity run :: pid: 1206632, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-85/call-trgt_plot_motifs_allele/slurm_singularity.log.txt"
2025-09-15 20:25:58.087 wdl.w:ptcp.w:call-trgt-85.t:call-trgt_plot_motifs_waterfall INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-85/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_qdi77lj3"
2025-09-15 20:25:58.087 wdl.w:ptcp.w:call-trgt-85.t:call-trgt_plot_motifs_waterfall INFO Slurm invocation: srun --job-name call-trgt_plot_motifs_waterfall --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-85/call-trgt_plot_motifs_waterfall/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-85/call-trgt_plot_motifs_waterfall/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-85/call-trgt_plot_motifs_waterfall/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-85/call-trgt_plot_motifs_waterfall/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-85/call-trgt_genotype/out/m84036_250809_035451_s4.bc2182.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2182.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-85/call-trgt_genotype/out/m84036_250809_035451_s4.bc2182.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2182.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-85/call-trgt_genotype/out/m84036_250809_035451_s4.bc2182.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2182.trgt.sorted.spanning.bam:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-85/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_qdi77lj3/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-85/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_qdi77lj3/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:58.095 wdl.w:ptcp.w:call-trgt-85.t:call-trgt_plot_motifs_waterfall NOTICE slurm_singularity run :: pid: 1206634, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-85/call-trgt_plot_motifs_waterfall/slurm_singularity.log.txt"
2025-09-15 20:25:58.242 wdl.w:ptcp.w:call-trgt-85.t:call-trgt_plot_meth_allele.slurm_singularity INFO srun: job 51798107 queued and waiting for resources
2025-09-15 20:25:58.242 wdl.w:ptcp.w:call-trgt-85.t:call-trgt_plot_meth_allele.slurm_singularity INFO srun: job 51798107 has been allocated resources
2025-09-15 20:25:58.242 wdl.w:ptcp.w:call-trgt-85.t:call-trgt_plot_meth_allele.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:58.344 wdl.w:ptcp.w:call-sawfish-53.t:call-run_sawfish INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2150_sawfish/m84036_250809_035451_s4.bc2150.sv.vcf.gz"
2025-09-15 20:25:58.352 wdl.w:ptcp.w:call-sawfish-53.t:call-run_sawfish INFO output :: name: "vcf_tbi", value: "m84036_250809_035451_s4.bc2150_sawfish/m84036_250809_035451_s4.bc2150.sv.vcf.gz.tbi"
2025-09-15 20:25:58.354 wdl.w:ptcp.w:call-sawfish-53.t:call-run_sawfish INFO output :: name: "minimap2_bam", value: "m84036_250809_035451_s4.bc2150.minimap2.bam"
2025-09-15 20:25:58.356 wdl.w:ptcp.w:call-sawfish-53.t:call-run_sawfish INFO output :: name: "minimap2_bam_bai", value: "m84036_250809_035451_s4.bc2150.minimap2.bam.bai"
2025-09-15 20:25:58.384 wdl.w:ptcp.w:call-trgt-80.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:25:56 [ERROR] - No reads found for TRID=PRTS_ARX
2025-09-15 20:25:58.384 wdl.w:ptcp.w:call-trgt-80.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:25:56 [ERROR] - No reads found for TRID=EIEE1_ARX
2025-09-15 20:25:58.605 wdl.w:ptcp.w:call-sawfish-53.t:call-run_sawfish NOTICE done
2025-09-15 20:25:58.610 wdl.w:ptcp.w:call-sawfish-53 NOTICE finish :: job: "call-run_sawfish"
2025-09-15 20:25:58.611 wdl.w:ptcp.w:call-sawfish-53 INFO output :: job: "call-run_sawfish", values: {"minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-53/call-run_sawfish/out/m84036_250809_035451_s4.bc2150.minimap2.bam.bai", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-53/call-run_sawfish/out/m84036_250809_035451_s4.bc2150.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-53/call-run_sawfish/out/m84036_250809_035451_s4.bc2150_sawfish/m84036_250809_035451_s4.bc2150.sv.vcf.gz.tbi", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-53/call-run_sawfish/out/m84036_250809_035451_s4.bc2150_sawfish/m84036_250809_035451_s4.bc2150.sv.vcf.gz"}
2025-09-15 20:25:58.611 wdl.w:ptcp.w:call-sawfish-53 INFO visit :: node: "output-minimap2_bam", values: {"minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-53/call-run_sawfish/out/m84036_250809_035451_s4.bc2150.minimap2.bam"}
2025-09-15 20:25:58.611 wdl.w:ptcp.w:call-sawfish-53 INFO visit :: node: "output-minimap2_bam_bai", values: {"minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-53/call-run_sawfish/out/m84036_250809_035451_s4.bc2150.minimap2.bam.bai"}
2025-09-15 20:25:58.611 wdl.w:ptcp.w:call-sawfish-53 INFO visit :: node: "output-vcf", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-53/call-run_sawfish/out/m84036_250809_035451_s4.bc2150_sawfish/m84036_250809_035451_s4.bc2150.sv.vcf.gz"}
2025-09-15 20:25:58.611 wdl.w:ptcp.w:call-sawfish-53 INFO visit :: node: "output-vcf_tbi", values: {"vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-53/call-run_sawfish/out/m84036_250809_035451_s4.bc2150_sawfish/m84036_250809_035451_s4.bc2150.sv.vcf.gz.tbi"}
2025-09-15 20:25:58.611 wdl.w:ptcp.w:call-sawfish-53 INFO visit :: node: "outputs", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-53/call-run_sawfish/out/m84036_250809_035451_s4.bc2150_sawfish/m84036_250809_035451_s4.bc2150.sv.vcf.gz", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-53/call-run_sawfish/out/m84036_250809_035451_s4.bc2150.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-53/call-run_sawfish/out/m84036_250809_035451_s4.bc2150_sawfish/m84036_250809_035451_s4.bc2150.sv.vcf.gz.tbi", "minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-53/call-run_sawfish/out/m84036_250809_035451_s4.bc2150.minimap2.bam.bai"}
2025-09-15 20:25:58.619 wdl.w:ptcp.w:call-paraphase-72.t:call-call_f8 NOTICE task setup :: name: "call_f8", source: "./paraphase.wdl", line: 232, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-72/call-call_f8", thread: 140606609282624
2025-09-15 20:25:58.642 wdl.w:ptcp.w:call-sawfish-49.t:call-run_sawfish INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2146_sawfish/m84036_250809_035451_s4.bc2146.sv.vcf.gz"
2025-09-15 20:25:58.645 wdl.w:ptcp.w:call-paraphase-72.t:call-call_f8 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:58.645 wdl.w:ptcp.w:call-paraphase-72.t:call-call_f8 INFO input :: name: "genome_version", value: "38"
2025-09-15 20:25:58.645 wdl.w:ptcp.w:call-paraphase-72.t:call-call_f8 INFO input :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2169"
2025-09-15 20:25:58.645 wdl.w:ptcp.w:call-paraphase-72.t:call-call_f8 INFO input :: name: "paraphase_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2169.paraphase.bam.bai"
2025-09-15 20:25:58.645 wdl.w:ptcp.w:call-paraphase-72.t:call-call_f8 INFO input :: name: "paraphase_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2169.paraphase.bam"
2025-09-15 20:25:58.645 wdl.w:ptcp.w:call-paraphase-72.t:call-call_f8 INFO input :: name: "sex", value: "F"
2025-09-15 20:25:58.645 wdl.w:ptcp.w:call-paraphase-72.t:call-call_f8 INFO eval :: name: "threads", value: 1
2025-09-15 20:25:58.645 wdl.w:ptcp.w:call-paraphase-72.t:call-call_f8 INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:25:58.646 wdl.w:ptcp.w:call-paraphase-72.t:call-call_f8 INFO eval :: name: "disk_size", value: 11
2025-09-15 20:25:58.646 wdl.w:ptcp.w:call-paraphase-72.t:call-call_f8 INFO eval :: name: "sample_sex", value: "F"
2025-09-15 20:25:58.646 wdl.w:ptcp.w:call-paraphase-72.t:call-call_f8 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:58.646 wdl.w:ptcp.w:call-paraphase-72.t:call-call_f8 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:58.647 wdl.w:ptcp.w:call-paraphase-72.t:call-call_f8 INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:25:58.647 wdl.w:ptcp.w:call-paraphase-72.t:call-call_f8 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:58.650 wdl.w:ptcp.w:call-sawfish-49.t:call-run_sawfish INFO output :: name: "vcf_tbi", value: "m84036_250809_035451_s4.bc2146_sawfish/m84036_250809_035451_s4.bc2146.sv.vcf.gz.tbi"
2025-09-15 20:25:58.651 wdl.w:ptcp.w:call-sawfish-49.t:call-run_sawfish INFO output :: name: "minimap2_bam", value: "m84036_250809_035451_s4.bc2146.minimap2.bam"
2025-09-15 20:25:58.654 wdl.w:ptcp.w:call-sawfish-49.t:call-run_sawfish INFO output :: name: "minimap2_bam_bai", value: "m84036_250809_035451_s4.bc2146.minimap2.bam.bai"
2025-09-15 20:25:58.683 wdl.w:ptcp.w:call-sawfish-53 NOTICE done
2025-09-15 20:25:58.692 wdl.w:ptcp NOTICE finish :: job: "call-sawfish-53"
2025-09-15 20:25:58.692 wdl.w:ptcp INFO output :: job: "call-sawfish-53", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-53/out/m84036_250809_035451_s4.bc2150_sawfish/m84036_250809_035451_s4.bc2150.sv.vcf.gz", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-53/out/m84036_250809_035451_s4.bc2150.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-53/out/m84036_250809_035451_s4.bc2150_sawfish/m84036_250809_035451_s4.bc2150.sv.vcf.gz.tbi", "minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-53/out/m84036_250809_035451_s4.bc2150.minimap2.bam.bai"}
2025-09-15 20:25:58.692 wdl.w:ptcp NOTICE ready :: job: "call-tar_outputs-53", callee: "tar_outputs"
2025-09-15 20:25:58.693 wdl.w:ptcp INFO input :: job: "call-tar_outputs-53", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "sawfish_vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-53/out/m84036_250809_035451_s4.bc2150_sawfish/m84036_250809_035451_s4.bc2150.sv.vcf.gz.tbi", "sawfish_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-53/out/m84036_250809_035451_s4.bc2150_sawfish/m84036_250809_035451_s4.bc2150.sv.vcf.gz", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-53/out/m84036_250809_035451_s4.bc2150.f8inversion.json", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-53/out/m84036_250809_035451_s4.bc2150_paraphase/m84036_250809_035451_s4.bc2150.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-53/out/m84036_250809_035451_s4.bc2150_paraphase/m84036_250809_035451_s4.bc2150.paraphase.bam", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-53/out/m84036_250809_035451_s4.bc2150_paraphase/m84036_250809_035451_s4.bc2150.paraphase.json", "trgt_spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-53/out/m84036_250809_035451_s4.bc2150.trgt.sorted.spanning.bam.bai", "trgt_spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-53/out/m84036_250809_035451_s4.bc2150.trgt.sorted.spanning.bam", "trgt_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-53/out/m84036_250809_035451_s4.bc2150.trgt.vcf", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-53/out/m84036_250809_035451_s4.bc2150.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-53/out/m84036_250809_035451_s4.bc2150.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2150"}
2025-09-15 20:25:58.704 wdl.w:ptcp.w:call-sawfish-68.t:call-run_sawfish INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2165_sawfish/m84036_250809_035451_s4.bc2165.sv.vcf.gz"
2025-09-15 20:25:58.710 wdl.w:ptcp.w:call-sawfish-68.t:call-run_sawfish INFO output :: name: "vcf_tbi", value: "m84036_250809_035451_s4.bc2165_sawfish/m84036_250809_035451_s4.bc2165.sv.vcf.gz.tbi"
2025-09-15 20:25:58.714 wdl.w:ptcp.w:call-sawfish-68.t:call-run_sawfish INFO output :: name: "minimap2_bam", value: "m84036_250809_035451_s4.bc2165.minimap2.bam"
2025-09-15 20:25:58.716 wdl.w:ptcp.w:call-sawfish-68.t:call-run_sawfish INFO output :: name: "minimap2_bam_bai", value: "m84036_250809_035451_s4.bc2165.minimap2.bam.bai"
2025-09-15 20:25:58.716 wdl.w:ptcp.w:call-paraphase-72.t:call-call_f8 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 8, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-72/call-call_f8/_singularity_tmpdir_6p3r7mwr"
2025-09-15 20:25:58.716 wdl.w:ptcp.w:call-paraphase-72.t:call-call_f8 INFO Slurm invocation: srun --job-name call-call_f8 --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-72/call-call_f8/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-72/call-call_f8/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-72/call-call_f8/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-72/call-call_f8/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-72/call-run_paraphase/out/m84036_250809_035451_s4.bc2169_paraphase/m84036_250809_035451_s4.bc2169.paraphase.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2169.paraphase.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-72/call-run_paraphase/out/m84036_250809_035451_s4.bc2169_paraphase/m84036_250809_035451_s4.bc2169.paraphase.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2169.paraphase.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-72/call-call_f8/_singularity_tmpdir_6p3r7mwr/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-72/call-call_f8/_singularity_tmpdir_6p3r7mwr/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:58.750 wdl.w:ptcp.w:call-paraphase-72.t:call-call_f8 NOTICE slurm_singularity run :: pid: 1206655, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-72/call-call_f8/slurm_singularity.log.txt"
2025-09-15 20:25:58.771 wdl.w:ptcp.w:call-trgt-72.t:call-trgt_plot_motifs_waterfall INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2169.motifs_waterfall.trgt_plots.zip"
2025-09-15 20:25:58.790 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:25:57 [ERROR] - No reads found for TRID=SCA31_BEAN1
2025-09-15 20:25:58.808 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:58.856 wdl.w:ptcp.w:call-sawfish-49.t:call-run_sawfish NOTICE done
2025-09-15 20:25:58.866 wdl.w:ptcp.w:call-sawfish-49 NOTICE finish :: job: "call-run_sawfish"
2025-09-15 20:25:58.866 wdl.w:ptcp.w:call-sawfish-49 INFO output :: job: "call-run_sawfish", values: {"minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-49/call-run_sawfish/out/m84036_250809_035451_s4.bc2146.minimap2.bam.bai", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-49/call-run_sawfish/out/m84036_250809_035451_s4.bc2146.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-49/call-run_sawfish/out/m84036_250809_035451_s4.bc2146_sawfish/m84036_250809_035451_s4.bc2146.sv.vcf.gz.tbi", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-49/call-run_sawfish/out/m84036_250809_035451_s4.bc2146_sawfish/m84036_250809_035451_s4.bc2146.sv.vcf.gz"}
2025-09-15 20:25:58.866 wdl.w:ptcp.w:call-sawfish-49 INFO visit :: node: "output-minimap2_bam", values: {"minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-49/call-run_sawfish/out/m84036_250809_035451_s4.bc2146.minimap2.bam"}
2025-09-15 20:25:58.866 wdl.w:ptcp.w:call-sawfish-49 INFO visit :: node: "output-minimap2_bam_bai", values: {"minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-49/call-run_sawfish/out/m84036_250809_035451_s4.bc2146.minimap2.bam.bai"}
2025-09-15 20:25:58.866 wdl.w:ptcp.w:call-sawfish-49 INFO visit :: node: "output-vcf", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-49/call-run_sawfish/out/m84036_250809_035451_s4.bc2146_sawfish/m84036_250809_035451_s4.bc2146.sv.vcf.gz"}
2025-09-15 20:25:58.866 wdl.w:ptcp.w:call-sawfish-49 INFO visit :: node: "output-vcf_tbi", values: {"vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-49/call-run_sawfish/out/m84036_250809_035451_s4.bc2146_sawfish/m84036_250809_035451_s4.bc2146.sv.vcf.gz.tbi"}
2025-09-15 20:25:58.866 wdl.w:ptcp.w:call-sawfish-49 INFO visit :: node: "outputs", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-49/call-run_sawfish/out/m84036_250809_035451_s4.bc2146_sawfish/m84036_250809_035451_s4.bc2146.sv.vcf.gz", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-49/call-run_sawfish/out/m84036_250809_035451_s4.bc2146.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-49/call-run_sawfish/out/m84036_250809_035451_s4.bc2146_sawfish/m84036_250809_035451_s4.bc2146.sv.vcf.gz.tbi", "minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-49/call-run_sawfish/out/m84036_250809_035451_s4.bc2146.minimap2.bam.bai"}
2025-09-15 20:25:58.878 wdl.w:ptcp.w:call-trgt-92.t:call-trgt_plot_meth_allele NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-92/call-trgt_plot_meth_allele", thread: 140610887464512
2025-09-15 20:25:58.914 wdl.w:ptcp.w:call-trgt-92.t:call-trgt_plot_meth_allele INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:58.914 wdl.w:ptcp.w:call-trgt-92.t:call-trgt_plot_meth_allele INFO input :: name: "waterfall", value: false
2025-09-15 20:25:58.914 wdl.w:ptcp.w:call-trgt-92.t:call-trgt_plot_meth_allele INFO input :: name: "methylation", value: true
2025-09-15 20:25:58.914 wdl.w:ptcp.w:call-trgt-92.t:call-trgt_plot_meth_allele INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:25:58.914 wdl.w:ptcp.w:call-trgt-92.t:call-trgt_plot_meth_allele INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:25:58.914 wdl.w:ptcp.w:call-trgt-92.t:call-trgt_plot_meth_allele INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:25:58.914 wdl.w:ptcp.w:call-trgt-92.t:call-trgt_plot_meth_allele INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2189.trgt.sorted.spanning.bam.bai"
2025-09-15 20:25:58.914 wdl.w:ptcp.w:call-trgt-92.t:call-trgt_plot_meth_allele INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2189.trgt.sorted.spanning.bam"
2025-09-15 20:25:58.914 wdl.w:ptcp.w:call-trgt-92.t:call-trgt_plot_meth_allele INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2189.trgt.vcf"
2025-09-15 20:25:58.914 wdl.w:ptcp.w:call-trgt-92.t:call-trgt_plot_meth_allele INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2189"
2025-09-15 20:25:58.915 wdl.w:ptcp.w:call-trgt-92.t:call-trgt_plot_meth_allele INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:25:58.915 wdl.w:ptcp.w:call-trgt-92.t:call-trgt_plot_meth_allele INFO eval :: name: "plot_type", value: "allele"
2025-09-15 20:25:58.915 wdl.w:ptcp.w:call-trgt-92.t:call-trgt_plot_meth_allele INFO eval :: name: "show", value: "meth"
2025-09-15 20:25:58.915 wdl.w:ptcp.w:call-trgt-92.t:call-trgt_plot_meth_allele INFO eval :: name: "threads", value: 1
2025-09-15 20:25:58.915 wdl.w:ptcp.w:call-trgt-92.t:call-trgt_plot_meth_allele INFO eval :: name: "disk_size", value: 27
2025-09-15 20:25:58.915 wdl.w:ptcp.w:call-trgt-92.t:call-trgt_plot_meth_allele INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2189.meth_allele"
2025-09-15 20:25:58.916 wdl.w:ptcp.w:call-trgt-92.t:call-trgt_plot_meth_allele INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:58.916 wdl.w:ptcp.w:call-trgt-92.t:call-trgt_plot_meth_allele WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:58.916 wdl.w:ptcp.w:call-trgt-92.t:call-trgt_plot_meth_allele INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:25:58.916 wdl.w:ptcp.w:call-trgt-92.t:call-trgt_plot_meth_allele INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:58.921 wdl.w:ptcp.w:call-sawfish-68.t:call-run_sawfish NOTICE done
2025-09-15 20:25:58.929 wdl.w:ptcp.w:call-sawfish-68 NOTICE finish :: job: "call-run_sawfish"
2025-09-15 20:25:58.929 wdl.w:ptcp.w:call-sawfish-68 INFO output :: job: "call-run_sawfish", values: {"minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-68/call-run_sawfish/out/m84036_250809_035451_s4.bc2165.minimap2.bam.bai", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-68/call-run_sawfish/out/m84036_250809_035451_s4.bc2165.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-68/call-run_sawfish/out/m84036_250809_035451_s4.bc2165_sawfish/m84036_250809_035451_s4.bc2165.sv.vcf.gz.tbi", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-68/call-run_sawfish/out/m84036_250809_035451_s4.bc2165_sawfish/m84036_250809_035451_s4.bc2165.sv.vcf.gz"}
2025-09-15 20:25:58.930 wdl.w:ptcp.w:call-trgt-85.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO srun: job 51798108 queued and waiting for resources
2025-09-15 20:25:58.930 wdl.w:ptcp.w:call-sawfish-68 INFO visit :: node: "output-minimap2_bam", values: {"minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-68/call-run_sawfish/out/m84036_250809_035451_s4.bc2165.minimap2.bam"}
2025-09-15 20:25:58.930 wdl.w:ptcp.w:call-trgt-85.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO srun: job 51798108 has been allocated resources
2025-09-15 20:25:58.930 wdl.w:ptcp.w:call-sawfish-68 INFO visit :: node: "output-minimap2_bam_bai", values: {"minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-68/call-run_sawfish/out/m84036_250809_035451_s4.bc2165.minimap2.bam.bai"}
2025-09-15 20:25:58.930 wdl.w:ptcp.w:call-trgt-85.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:58.931 wdl.w:ptcp.w:call-sawfish-68 INFO visit :: node: "output-vcf", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-68/call-run_sawfish/out/m84036_250809_035451_s4.bc2165_sawfish/m84036_250809_035451_s4.bc2165.sv.vcf.gz"}
2025-09-15 20:25:58.931 wdl.w:ptcp.w:call-sawfish-68 INFO visit :: node: "output-vcf_tbi", values: {"vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-68/call-run_sawfish/out/m84036_250809_035451_s4.bc2165_sawfish/m84036_250809_035451_s4.bc2165.sv.vcf.gz.tbi"}
2025-09-15 20:25:58.931 wdl.w:ptcp.w:call-sawfish-68 INFO visit :: node: "outputs", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-68/call-run_sawfish/out/m84036_250809_035451_s4.bc2165_sawfish/m84036_250809_035451_s4.bc2165.sv.vcf.gz", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-68/call-run_sawfish/out/m84036_250809_035451_s4.bc2165.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-68/call-run_sawfish/out/m84036_250809_035451_s4.bc2165_sawfish/m84036_250809_035451_s4.bc2165.sv.vcf.gz.tbi", "minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-68/call-run_sawfish/out/m84036_250809_035451_s4.bc2165.minimap2.bam.bai"}
2025-09-15 20:25:58.941 wdl.w:ptcp.w:call-trgt-92.t:call-trgt_plot_meth_waterfall NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-92/call-trgt_plot_meth_waterfall", thread: 140608203109952
2025-09-15 20:25:58.943 wdl.w:ptcp.w:call-sawfish-49 NOTICE done
2025-09-15 20:25:58.945 wdl.w:ptcp.w:call-trgt-72.t:call-trgt_plot_motifs_waterfall NOTICE done
2025-09-15 20:25:58.953 wdl.w:ptcp NOTICE finish :: job: "call-sawfish-49"
2025-09-15 20:25:58.953 wdl.w:ptcp INFO output :: job: "call-sawfish-49", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-49/out/m84036_250809_035451_s4.bc2146_sawfish/m84036_250809_035451_s4.bc2146.sv.vcf.gz", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-49/out/m84036_250809_035451_s4.bc2146.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-49/out/m84036_250809_035451_s4.bc2146_sawfish/m84036_250809_035451_s4.bc2146.sv.vcf.gz.tbi", "minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-49/out/m84036_250809_035451_s4.bc2146.minimap2.bam.bai"}
2025-09-15 20:25:58.954 wdl.w:ptcp NOTICE ready :: job: "call-tar_outputs-49", callee: "tar_outputs"
2025-09-15 20:25:58.954 wdl.w:ptcp INFO input :: job: "call-tar_outputs-49", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "sawfish_vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-49/out/m84036_250809_035451_s4.bc2146_sawfish/m84036_250809_035451_s4.bc2146.sv.vcf.gz.tbi", "sawfish_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-49/out/m84036_250809_035451_s4.bc2146_sawfish/m84036_250809_035451_s4.bc2146.sv.vcf.gz", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-49/out/m84036_250809_035451_s4.bc2146.f8inversion.json", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-49/out/m84036_250809_035451_s4.bc2146_paraphase/m84036_250809_035451_s4.bc2146.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-49/out/m84036_250809_035451_s4.bc2146_paraphase/m84036_250809_035451_s4.bc2146.paraphase.bam", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-49/out/m84036_250809_035451_s4.bc2146_paraphase/m84036_250809_035451_s4.bc2146.paraphase.json", "trgt_spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-49/out/m84036_250809_035451_s4.bc2146.trgt.sorted.spanning.bam.bai", "trgt_spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-49/out/m84036_250809_035451_s4.bc2146.trgt.sorted.spanning.bam", "trgt_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-49/out/m84036_250809_035451_s4.bc2146.trgt.vcf", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-49/out/m84036_250809_035451_s4.bc2146.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-49/out/m84036_250809_035451_s4.bc2146.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2146"}
2025-09-15 20:25:58.957 wdl.w:ptcp.w:call-trgt-72 NOTICE finish :: job: "call-trgt_plot_motifs_waterfall"
2025-09-15 20:25:58.957 wdl.w:ptcp.w:call-trgt-72 INFO output :: job: "call-trgt_plot_motifs_waterfall", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-72/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2169.motifs_waterfall.trgt_plots.zip"}
2025-09-15 20:25:58.957 wdl.w:ptcp.w:call-trgt-72 INFO visit :: node: "output-images_motifs_waterfall", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-72/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2169.motifs_waterfall.trgt_plots.zip"}
2025-09-15 20:25:58.965 wdl.w:ptcp.w:call-trgt-92.t:call-trgt_plot_meth_waterfall INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:58.965 wdl.w:ptcp.w:call-trgt-92.t:call-trgt_plot_meth_waterfall INFO input :: name: "waterfall", value: true
2025-09-15 20:25:58.965 wdl.w:ptcp.w:call-trgt-92.t:call-trgt_plot_meth_waterfall INFO input :: name: "methylation", value: true
2025-09-15 20:25:58.965 wdl.w:ptcp.w:call-trgt-92.t:call-trgt_plot_meth_waterfall INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:25:58.965 wdl.w:ptcp.w:call-trgt-92.t:call-trgt_plot_meth_waterfall INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:25:58.965 wdl.w:ptcp.w:call-trgt-92.t:call-trgt_plot_meth_waterfall INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:25:58.965 wdl.w:ptcp.w:call-trgt-92.t:call-trgt_plot_meth_waterfall INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2189.trgt.sorted.spanning.bam.bai"
2025-09-15 20:25:58.965 wdl.w:ptcp.w:call-trgt-92.t:call-trgt_plot_meth_waterfall INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2189.trgt.sorted.spanning.bam"
2025-09-15 20:25:58.965 wdl.w:ptcp.w:call-trgt-92.t:call-trgt_plot_meth_waterfall INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2189.trgt.vcf"
2025-09-15 20:25:58.965 wdl.w:ptcp.w:call-trgt-92.t:call-trgt_plot_meth_waterfall INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2189"
2025-09-15 20:25:58.966 wdl.w:ptcp.w:call-trgt-92.t:call-trgt_plot_meth_waterfall INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:25:58.966 wdl.w:ptcp.w:call-trgt-92.t:call-trgt_plot_meth_waterfall INFO eval :: name: "plot_type", value: "waterfall"
2025-09-15 20:25:58.966 wdl.w:ptcp.w:call-trgt-92.t:call-trgt_plot_meth_waterfall INFO eval :: name: "show", value: "meth"
2025-09-15 20:25:58.966 wdl.w:ptcp.w:call-trgt-92.t:call-trgt_plot_meth_waterfall INFO eval :: name: "threads", value: 1
2025-09-15 20:25:58.966 wdl.w:ptcp.w:call-trgt-92.t:call-trgt_plot_meth_waterfall INFO eval :: name: "disk_size", value: 27
2025-09-15 20:25:58.967 wdl.w:ptcp.w:call-trgt-92.t:call-trgt_plot_meth_waterfall INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2189.meth_waterfall"
2025-09-15 20:25:58.967 wdl.w:ptcp.w:call-trgt-92.t:call-trgt_plot_motifs_allele NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-92/call-trgt_plot_motifs_allele", thread: 140613563426368
2025-09-15 20:25:58.967 wdl.w:ptcp.w:call-trgt-92.t:call-trgt_plot_meth_waterfall INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:58.968 wdl.w:ptcp.w:call-trgt-92.t:call-trgt_plot_meth_waterfall WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:58.968 wdl.w:ptcp.w:call-trgt-92.t:call-trgt_plot_meth_waterfall INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:25:58.968 wdl.w:ptcp.w:call-trgt-92.t:call-trgt_plot_meth_waterfall INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:58.990 wdl.w:ptcp.w:call-trgt-92.t:call-trgt_plot_motifs_allele INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:58.990 wdl.w:ptcp.w:call-trgt-92.t:call-trgt_plot_motifs_allele INFO input :: name: "waterfall", value: false
2025-09-15 20:25:58.990 wdl.w:ptcp.w:call-trgt-92.t:call-trgt_plot_motifs_allele INFO input :: name: "methylation", value: false
2025-09-15 20:25:58.990 wdl.w:ptcp.w:call-trgt-92.t:call-trgt_plot_motifs_allele INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:25:58.990 wdl.w:ptcp.w:call-trgt-92.t:call-trgt_plot_motifs_allele INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:25:58.990 wdl.w:ptcp.w:call-trgt-92.t:call-trgt_plot_motifs_allele INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:25:58.990 wdl.w:ptcp.w:call-trgt-92.t:call-trgt_plot_motifs_allele INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2189.trgt.sorted.spanning.bam.bai"
2025-09-15 20:25:58.990 wdl.w:ptcp.w:call-trgt-92.t:call-trgt_plot_motifs_allele INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2189.trgt.sorted.spanning.bam"
2025-09-15 20:25:58.990 wdl.w:ptcp.w:call-trgt-92.t:call-trgt_plot_motifs_allele INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2189.trgt.vcf"
2025-09-15 20:25:58.991 wdl.w:ptcp.w:call-trgt-92.t:call-trgt_plot_motifs_allele INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2189"
2025-09-15 20:25:58.991 wdl.w:ptcp.w:call-trgt-92.t:call-trgt_plot_motifs_allele INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:25:58.991 wdl.w:ptcp.w:call-trgt-92.t:call-trgt_plot_motifs_allele INFO eval :: name: "plot_type", value: "allele"
2025-09-15 20:25:58.991 wdl.w:ptcp.w:call-trgt-92.t:call-trgt_plot_motifs_allele INFO eval :: name: "show", value: "motifs"
2025-09-15 20:25:58.991 wdl.w:ptcp.w:call-trgt-92.t:call-trgt_plot_motifs_allele INFO eval :: name: "threads", value: 1
2025-09-15 20:25:58.991 wdl.w:ptcp.w:call-trgt-92.t:call-trgt_plot_motifs_allele INFO eval :: name: "disk_size", value: 27
2025-09-15 20:25:58.991 wdl.w:ptcp.w:call-trgt-92.t:call-trgt_plot_motifs_allele INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2189.motifs_allele"
2025-09-15 20:25:58.992 wdl.w:ptcp.w:call-trgt-92.t:call-trgt_plot_motifs_allele INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:58.992 wdl.w:ptcp.w:call-trgt-92.t:call-trgt_plot_motifs_allele WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:58.992 wdl.w:ptcp.w:call-trgt-92.t:call-trgt_plot_motifs_allele INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:25:58.992 wdl.w:ptcp.w:call-trgt-92.t:call-trgt_plot_motifs_allele INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:58.996 wdl.w:ptcp.w:call-sawfish-68 NOTICE done
2025-09-15 20:25:59.004 wdl.w:ptcp NOTICE finish :: job: "call-sawfish-68"
2025-09-15 20:25:59.004 wdl.w:ptcp INFO output :: job: "call-sawfish-68", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-68/out/m84036_250809_035451_s4.bc2165_sawfish/m84036_250809_035451_s4.bc2165.sv.vcf.gz", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-68/out/m84036_250809_035451_s4.bc2165.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-68/out/m84036_250809_035451_s4.bc2165_sawfish/m84036_250809_035451_s4.bc2165.sv.vcf.gz.tbi", "minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-68/out/m84036_250809_035451_s4.bc2165.minimap2.bam.bai"}
2025-09-15 20:25:59.005 wdl.w:ptcp NOTICE ready :: job: "call-tar_outputs-68", callee: "tar_outputs"
2025-09-15 20:25:59.005 wdl.w:ptcp INFO input :: job: "call-tar_outputs-68", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "sawfish_vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-68/out/m84036_250809_035451_s4.bc2165_sawfish/m84036_250809_035451_s4.bc2165.sv.vcf.gz.tbi", "sawfish_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-68/out/m84036_250809_035451_s4.bc2165_sawfish/m84036_250809_035451_s4.bc2165.sv.vcf.gz", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-68/out/m84036_250809_035451_s4.bc2165.f8inversion.json", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-68/out/m84036_250809_035451_s4.bc2165_paraphase/m84036_250809_035451_s4.bc2165.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-68/out/m84036_250809_035451_s4.bc2165_paraphase/m84036_250809_035451_s4.bc2165.paraphase.bam", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-68/out/m84036_250809_035451_s4.bc2165_paraphase/m84036_250809_035451_s4.bc2165.paraphase.json", "trgt_spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-68/out/m84036_250809_035451_s4.bc2165.trgt.sorted.spanning.bam.bai", "trgt_spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-68/out/m84036_250809_035451_s4.bc2165.trgt.sorted.spanning.bam", "trgt_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-68/out/m84036_250809_035451_s4.bc2165.trgt.vcf", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-68/out/m84036_250809_035451_s4.bc2165.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-68/out/m84036_250809_035451_s4.bc2165.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2165"}
2025-09-15 20:25:59.013 wdl.w:ptcp.w:call-trgt-92.t:call-trgt_plot_meth_allele INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-92/call-trgt_plot_meth_allele/_singularity_tmpdir_7hqxkavi"
2025-09-15 20:25:59.013 wdl.w:ptcp.w:call-trgt-92.t:call-trgt_plot_meth_allele INFO Slurm invocation: srun --job-name call-trgt_plot_meth_allele --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-92/call-trgt_plot_meth_allele/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-92/call-trgt_plot_meth_allele/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-92/call-trgt_plot_meth_allele/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-92/call-trgt_plot_meth_allele/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-92/call-trgt_genotype/out/m84036_250809_035451_s4.bc2189.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2189.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-92/call-trgt_genotype/out/m84036_250809_035451_s4.bc2189.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2189.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-92/call-trgt_genotype/out/m84036_250809_035451_s4.bc2189.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2189.trgt.sorted.spanning.bam.bai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-92/call-trgt_plot_meth_allele/_singularity_tmpdir_7hqxkavi/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-92/call-trgt_plot_meth_allele/_singularity_tmpdir_7hqxkavi/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:59.037 wdl.w:ptcp.w:call-trgt-92.t:call-trgt_plot_meth_allele NOTICE slurm_singularity run :: pid: 1206657, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-92/call-trgt_plot_meth_allele/slurm_singularity.log.txt"
2025-09-15 20:25:59.039 wdl.w:ptcp.w:call-trgt-85.t:call-trgt_plot_motifs_allele.slurm_singularity INFO srun: job 51798109 queued and waiting for resources
2025-09-15 20:25:59.039 wdl.w:ptcp.w:call-trgt-85.t:call-trgt_plot_motifs_allele.slurm_singularity INFO srun: job 51798109 has been allocated resources
2025-09-15 20:25:59.039 wdl.w:ptcp.w:call-trgt-85.t:call-trgt_plot_motifs_allele.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:59.075 wdl.w:ptcp.w:call-trgt-92.t:call-trgt_plot_meth_waterfall INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-92/call-trgt_plot_meth_waterfall/_singularity_tmpdir_j40rg0z2"
2025-09-15 20:25:59.075 wdl.w:ptcp.w:call-trgt-92.t:call-trgt_plot_meth_waterfall INFO Slurm invocation: srun --job-name call-trgt_plot_meth_waterfall --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-92/call-trgt_plot_meth_waterfall/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-92/call-trgt_plot_meth_waterfall/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-92/call-trgt_plot_meth_waterfall/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-92/call-trgt_plot_meth_waterfall/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-92/call-trgt_genotype/out/m84036_250809_035451_s4.bc2189.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2189.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-92/call-trgt_genotype/out/m84036_250809_035451_s4.bc2189.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2189.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-92/call-trgt_genotype/out/m84036_250809_035451_s4.bc2189.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2189.trgt.sorted.spanning.bam.bai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-92/call-trgt_plot_meth_waterfall/_singularity_tmpdir_j40rg0z2/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-92/call-trgt_plot_meth_waterfall/_singularity_tmpdir_j40rg0z2/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:59.080 wdl.w:ptcp.w:call-trgt-92.t:call-trgt_plot_motifs_allele INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-92/call-trgt_plot_motifs_allele/_singularity_tmpdir_ge0m0ut4"
2025-09-15 20:25:59.080 wdl.w:ptcp.w:call-trgt-92.t:call-trgt_plot_motifs_allele INFO Slurm invocation: srun --job-name call-trgt_plot_motifs_allele --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-92/call-trgt_plot_motifs_allele/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-92/call-trgt_plot_motifs_allele/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-92/call-trgt_plot_motifs_allele/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-92/call-trgt_plot_motifs_allele/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-92/call-trgt_genotype/out/m84036_250809_035451_s4.bc2189.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2189.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-92/call-trgt_genotype/out/m84036_250809_035451_s4.bc2189.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2189.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-92/call-trgt_genotype/out/m84036_250809_035451_s4.bc2189.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2189.trgt.sorted.spanning.bam.bai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-92/call-trgt_plot_motifs_allele/_singularity_tmpdir_ge0m0ut4/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-92/call-trgt_plot_motifs_allele/_singularity_tmpdir_ge0m0ut4/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:59.089 wdl.w:ptcp.w:call-trgt-92.t:call-trgt_plot_motifs_allele NOTICE slurm_singularity run :: pid: 1206671, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-92/call-trgt_plot_motifs_allele/slurm_singularity.log.txt"
2025-09-15 20:25:59.089 wdl.w:ptcp.w:call-trgt-92.t:call-trgt_plot_meth_waterfall NOTICE slurm_singularity run :: pid: 1206670, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-92/call-trgt_plot_meth_waterfall/slurm_singularity.log.txt"
2025-09-15 20:25:59.105 wdl.w:ptcp.w:call-trgt-85.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO srun: job 51798110 queued and waiting for resources
2025-09-15 20:25:59.105 wdl.w:ptcp.w:call-trgt-85.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO srun: job 51798110 has been allocated resources
2025-09-15 20:25:59.105 wdl.w:ptcp.w:call-trgt-85.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:59.114 wdl.w:ptcp.w:call-trgt-80.t:call-trgt_plot_motifs_allele INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2177.motifs_allele.trgt_plots.zip"
2025-09-15 20:25:59.208 wdl.w:ptcp.w:call-trgt-80.t:call-trgt_plot_motifs_allele NOTICE done
2025-09-15 20:25:59.214 wdl.w:ptcp.w:call-trgt-80 NOTICE finish :: job: "call-trgt_plot_motifs_allele"
2025-09-15 20:25:59.214 wdl.w:ptcp.w:call-trgt-80 INFO output :: job: "call-trgt_plot_motifs_allele", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-80/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2177.motifs_allele.trgt_plots.zip"}
2025-09-15 20:25:59.214 wdl.w:ptcp.w:call-trgt-80 INFO visit :: node: "output-images_motifs_allele", values: {"images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-80/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2177.motifs_allele.trgt_plots.zip"}
2025-09-15 20:25:59.219 wdl.w:ptcp.w:call-trgt-92.t:call-trgt_plot_motifs_waterfall NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-92/call-trgt_plot_motifs_waterfall", thread: 140610342200896
2025-09-15 20:25:59.236 wdl.w:ptcp.w:call-trgt-92.t:call-trgt_plot_motifs_waterfall INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:59.236 wdl.w:ptcp.w:call-trgt-92.t:call-trgt_plot_motifs_waterfall INFO input :: name: "waterfall", value: true
2025-09-15 20:25:59.236 wdl.w:ptcp.w:call-trgt-92.t:call-trgt_plot_motifs_waterfall INFO input :: name: "methylation", value: false
2025-09-15 20:25:59.236 wdl.w:ptcp.w:call-trgt-92.t:call-trgt_plot_motifs_waterfall INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:25:59.237 wdl.w:ptcp.w:call-trgt-92.t:call-trgt_plot_motifs_waterfall INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:25:59.237 wdl.w:ptcp.w:call-trgt-92.t:call-trgt_plot_motifs_waterfall INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:25:59.237 wdl.w:ptcp.w:call-trgt-92.t:call-trgt_plot_motifs_waterfall INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2189.trgt.sorted.spanning.bam.bai"
2025-09-15 20:25:59.237 wdl.w:ptcp.w:call-trgt-92.t:call-trgt_plot_motifs_waterfall INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2189.trgt.sorted.spanning.bam"
2025-09-15 20:25:59.237 wdl.w:ptcp.w:call-trgt-92.t:call-trgt_plot_motifs_waterfall INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2189.trgt.vcf"
2025-09-15 20:25:59.237 wdl.w:ptcp.w:call-trgt-92.t:call-trgt_plot_motifs_waterfall INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2189"
2025-09-15 20:25:59.237 wdl.w:ptcp.w:call-trgt-92.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:25:59.237 wdl.w:ptcp.w:call-trgt-92.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "plot_type", value: "waterfall"
2025-09-15 20:25:59.237 wdl.w:ptcp.w:call-trgt-92.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "show", value: "motifs"
2025-09-15 20:25:59.237 wdl.w:ptcp.w:call-trgt-92.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "threads", value: 1
2025-09-15 20:25:59.238 wdl.w:ptcp.w:call-trgt-92.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "disk_size", value: 27
2025-09-15 20:25:59.238 wdl.w:ptcp.w:call-trgt-92.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2189.motifs_waterfall"
2025-09-15 20:25:59.238 wdl.w:ptcp.w:call-trgt-92.t:call-trgt_plot_motifs_waterfall INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:59.238 wdl.w:ptcp.w:call-trgt-92.t:call-trgt_plot_motifs_waterfall WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:59.239 wdl.w:ptcp.w:call-trgt-92.t:call-trgt_plot_motifs_waterfall INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:25:59.239 wdl.w:ptcp.w:call-trgt-92.t:call-trgt_plot_motifs_waterfall INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:59.302 wdl.w:ptcp.w:call-trgt-92.t:call-trgt_plot_motifs_waterfall INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-92/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_tip365di"
2025-09-15 20:25:59.303 wdl.w:ptcp.w:call-trgt-92.t:call-trgt_plot_motifs_waterfall INFO Slurm invocation: srun --job-name call-trgt_plot_motifs_waterfall --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-92/call-trgt_plot_motifs_waterfall/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-92/call-trgt_plot_motifs_waterfall/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-92/call-trgt_plot_motifs_waterfall/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-92/call-trgt_plot_motifs_waterfall/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-92/call-trgt_genotype/out/m84036_250809_035451_s4.bc2189.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2189.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-92/call-trgt_genotype/out/m84036_250809_035451_s4.bc2189.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2189.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-92/call-trgt_genotype/out/m84036_250809_035451_s4.bc2189.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2189.trgt.sorted.spanning.bam.bai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-92/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_tip365di/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-92/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_tip365di/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:59.319 wdl.w:ptcp.w:call-trgt-92.t:call-trgt_plot_motifs_waterfall NOTICE slurm_singularity run :: pid: 1206684, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-92/call-trgt_plot_motifs_waterfall/slurm_singularity.log.txt"
2025-09-15 20:25:59.395 wdl.w:ptcp.w:call-paraphase-95.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for smn1 for sample m84036_250809_035451_s4.bc2192 at 2025-09-15 20:25:54.950514...
2025-09-15 20:25:59.395 wdl.w:ptcp.w:call-paraphase-95.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for hba for sample m84036_250809_035451_s4.bc2192 at 2025-09-15 20:25:54.958888...
2025-09-15 20:25:59.395 wdl.w:ptcp.w:call-paraphase-95.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for gba for sample m84036_250809_035451_s4.bc2192 at 2025-09-15 20:25:55.757035...
2025-09-15 20:25:59.395 wdl.w:ptcp.w:call-paraphase-95.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for cyp21 for sample m84036_250809_035451_s4.bc2192 at 2025-09-15 20:25:56.822079...
2025-09-15 20:25:59.464 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_motifs_allele INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2188.motifs_allele.trgt_plots.zip"
2025-09-15 20:25:59.549 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_motifs_allele NOTICE done
2025-09-15 20:25:59.553 wdl.w:ptcp.w:call-trgt-91 NOTICE finish :: job: "call-trgt_plot_motifs_allele"
2025-09-15 20:25:59.554 wdl.w:ptcp.w:call-trgt-91 INFO output :: job: "call-trgt_plot_motifs_allele", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-91/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2188.motifs_allele.trgt_plots.zip"}
2025-09-15 20:25:59.554 wdl.w:ptcp.w:call-trgt-91 INFO visit :: node: "output-images_motifs_allele", values: {"images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-91/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2188.motifs_allele.trgt_plots.zip"}
2025-09-15 20:25:59.560 wdl.w:ptcp.w:call-paraphase-92.t:call-call_f8 NOTICE task setup :: name: "call_f8", source: "./paraphase.wdl", line: 232, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-92/call-call_f8", thread: 140608186324544
2025-09-15 20:25:59.579 wdl.w:ptcp.w:call-paraphase-92.t:call-call_f8 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:59.579 wdl.w:ptcp.w:call-paraphase-92.t:call-call_f8 INFO input :: name: "genome_version", value: "38"
2025-09-15 20:25:59.579 wdl.w:ptcp.w:call-paraphase-92.t:call-call_f8 INFO input :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2189"
2025-09-15 20:25:59.579 wdl.w:ptcp.w:call-paraphase-92.t:call-call_f8 INFO input :: name: "paraphase_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2189.paraphase.bam.bai"
2025-09-15 20:25:59.579 wdl.w:ptcp.w:call-paraphase-92.t:call-call_f8 INFO input :: name: "paraphase_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2189.paraphase.bam"
2025-09-15 20:25:59.579 wdl.w:ptcp.w:call-paraphase-92.t:call-call_f8 INFO input :: name: "sex", value: "F"
2025-09-15 20:25:59.579 wdl.w:ptcp.w:call-paraphase-92.t:call-call_f8 INFO eval :: name: "threads", value: 1
2025-09-15 20:25:59.580 wdl.w:ptcp.w:call-paraphase-92.t:call-call_f8 INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:25:59.580 wdl.w:ptcp.w:call-paraphase-92.t:call-call_f8 INFO eval :: name: "disk_size", value: 11
2025-09-15 20:25:59.580 wdl.w:ptcp.w:call-paraphase-92.t:call-call_f8 INFO eval :: name: "sample_sex", value: "F"
2025-09-15 20:25:59.580 wdl.w:ptcp.w:call-paraphase-92.t:call-call_f8 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:59.580 wdl.w:ptcp.w:call-paraphase-92.t:call-call_f8 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:59.581 wdl.w:ptcp.w:call-paraphase-92.t:call-call_f8 INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:25:59.581 wdl.w:ptcp.w:call-paraphase-92.t:call-call_f8 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:59.628 wdl.w:ptcp.w:call-paraphase-92.t:call-call_f8 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 8, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-92/call-call_f8/_singularity_tmpdir_r4bski1o"
2025-09-15 20:25:59.628 wdl.w:ptcp.w:call-paraphase-92.t:call-call_f8 INFO Slurm invocation: srun --job-name call-call_f8 --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-92/call-call_f8/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-92/call-call_f8/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-92/call-call_f8/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-92/call-call_f8/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-92/call-run_paraphase/out/m84036_250809_035451_s4.bc2189_paraphase/m84036_250809_035451_s4.bc2189.paraphase.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2189.paraphase.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-92/call-run_paraphase/out/m84036_250809_035451_s4.bc2189_paraphase/m84036_250809_035451_s4.bc2189.paraphase.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2189.paraphase.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-92/call-call_f8/_singularity_tmpdir_r4bski1o/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-92/call-call_f8/_singularity_tmpdir_r4bski1o/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:25:59.645 wdl.w:ptcp.w:call-paraphase-92.t:call-call_f8 NOTICE slurm_singularity run :: pid: 1206693, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-92/call-call_f8/slurm_singularity.log.txt"
2025-09-15 20:25:59.698 wdl.w:ptcp.w:call-trgt-72.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:25:56 [ERROR] - No reads found for TRID=PRTS_ARX
2025-09-15 20:25:59.698 wdl.w:ptcp.w:call-trgt-72.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:25:56 [ERROR] - No reads found for TRID=EIEE1_ARX
2025-09-15 20:25:59.760 wdl.w:ptcp.w:call-paraphase-72.t:call-call_f8.slurm_singularity INFO srun: job 51798111 queued and waiting for resources
2025-09-15 20:25:59.761 wdl.w:ptcp.w:call-paraphase-72.t:call-call_f8.slurm_singularity INFO srun: job 51798111 has been allocated resources
2025-09-15 20:25:59.761 wdl.w:ptcp.w:call-paraphase-72.t:call-call_f8.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:25:59.814 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:25:57 [ERROR] - No reads found for TRID=HDL2_JPH3
2025-09-15 20:25:59.814 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:25:57 [ERROR] - No reads found for TRID=FECD3_TCF4
2025-09-15 20:25:59.814 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:25:57 [ERROR] - No reads found for TRID=SCA6_CACNA1A
2025-09-15 20:25:59.814 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:25:57 [ERROR] - No reads found for TRID=OPDM2_GIPC1
2025-09-15 20:25:59.814 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:25:57 [ERROR] - No reads found for TRID=DM1_DMPK
2025-09-15 20:25:59.814 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:25:58 [ERROR] - No reads found for TRID=FRA2A_AFF3
2025-09-15 20:25:59.814 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:25:58 [ERROR] - No reads found for TRID=SCA4_ZFHX3
2025-09-15 20:25:59.814 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:25:58 [ERROR] - No reads found for TRID=CJD_PRNP
2025-09-15 20:25:59.814 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:25:58 [ERROR] - No reads found for TRID=EPM1_CSTB
2025-09-15 20:25:59.814 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:25:58 [ERROR] - No reads found for TRID=SD5_HOXD13
2025-09-15 20:25:59.815 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:25:58 [ERROR] - No reads found for TRID=SCA7_ATXN7
2025-09-15 20:25:59.815 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:25:58 [ERROR] - No reads found for TRID=SCA36_NOP56
2025-09-15 20:25:59.815 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:25:58 [ERROR] - No reads found for TRID=HD_HTT
2025-09-15 20:25:59.815 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:25:58 [ERROR] - No reads found for TRID=SCA10_ATXN10
2025-09-15 20:25:59.815 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:25:58 [ERROR] - No reads found for TRID=CCHS_PHOX2B
2025-09-15 20:25:59.815 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:25:58 [ERROR] - No reads found for TRID=SCA12_PPP2R2B
2025-09-15 20:25:59.815 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:25:58 [ERROR] - No reads found for TRID=CANVAS_RFC1
2025-09-15 20:25:59.815 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:25:58 [ERROR] - No reads found for TRID=OPDM1_LRP12
2025-09-15 20:25:59.815 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:25:58 [ERROR] - No reads found for TRID=FAME1_SAMD12
2025-09-15 20:25:59.815 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:25:58 [ERROR] - No reads found for TRID=FTDALS1_C9orf72
2025-09-15 20:25:59.822 wdl.w:ptcp.w:call-trgt-81.t:call-trgt_plot_motifs_waterfall INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2178.motifs_waterfall.trgt_plots.zip"
2025-09-15 20:25:59.938 wdl.w:ptcp.w:call-trgt-81.t:call-trgt_plot_motifs_waterfall NOTICE done
2025-09-15 20:25:59.947 wdl.w:ptcp.w:call-trgt-81 NOTICE finish :: job: "call-trgt_plot_motifs_waterfall"
2025-09-15 20:25:59.947 wdl.w:ptcp.w:call-trgt-81 INFO output :: job: "call-trgt_plot_motifs_waterfall", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-81/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2178.motifs_waterfall.trgt_plots.zip"}
2025-09-15 20:25:59.948 wdl.w:ptcp.w:call-trgt-81 INFO visit :: node: "output-images_motifs_waterfall", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-81/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2178.motifs_waterfall.trgt_plots.zip"}
2025-09-15 20:25:59.953 wdl.w:ptcp.w:call-paraphase-15.t:call-call_f8 NOTICE task setup :: name: "call_f8", source: "./paraphase.wdl", line: 232, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-15/call-call_f8", thread: 140611969599040
2025-09-15 20:25:59.975 wdl.w:ptcp.w:call-paraphase-15.t:call-call_f8 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:25:59.975 wdl.w:ptcp.w:call-paraphase-15.t:call-call_f8 INFO input :: name: "genome_version", value: "38"
2025-09-15 20:25:59.975 wdl.w:ptcp.w:call-paraphase-15.t:call-call_f8 INFO input :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2112"
2025-09-15 20:25:59.976 wdl.w:ptcp.w:call-paraphase-15.t:call-call_f8 INFO input :: name: "paraphase_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2112.paraphase.bam.bai"
2025-09-15 20:25:59.976 wdl.w:ptcp.w:call-paraphase-15.t:call-call_f8 INFO input :: name: "paraphase_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2112.paraphase.bam"
2025-09-15 20:25:59.976 wdl.w:ptcp.w:call-paraphase-15.t:call-call_f8 INFO input :: name: "sex", value: "F"
2025-09-15 20:25:59.976 wdl.w:ptcp.w:call-paraphase-15.t:call-call_f8 INFO eval :: name: "threads", value: 1
2025-09-15 20:25:59.976 wdl.w:ptcp.w:call-paraphase-15.t:call-call_f8 INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:25:59.976 wdl.w:ptcp.w:call-paraphase-15.t:call-call_f8 INFO eval :: name: "disk_size", value: 11
2025-09-15 20:25:59.977 wdl.w:ptcp.w:call-paraphase-15.t:call-call_f8 INFO eval :: name: "sample_sex", value: "F"
2025-09-15 20:25:59.977 wdl.w:ptcp.w:call-paraphase-15.t:call-call_f8 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:25:59.977 wdl.w:ptcp.w:call-paraphase-15.t:call-call_f8 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:25:59.977 wdl.w:ptcp.w:call-paraphase-15.t:call-call_f8 INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:25:59.977 wdl.w:ptcp.w:call-paraphase-15.t:call-call_f8 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:25:59.986 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_meth_waterfall INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2188.meth_waterfall.trgt_plots.zip"
2025-09-15 20:26:00.034 wdl.w:ptcp.w:call-paraphase-15.t:call-call_f8 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 8, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-15/call-call_f8/_singularity_tmpdir_tkn0xhd5"
2025-09-15 20:26:00.034 wdl.w:ptcp.w:call-paraphase-15.t:call-call_f8 INFO Slurm invocation: srun --job-name call-call_f8 --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-15/call-call_f8/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-15/call-call_f8/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-15/call-call_f8/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-15/call-call_f8/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-15/call-run_paraphase/out/m84036_250809_035451_s4.bc2112_paraphase/m84036_250809_035451_s4.bc2112.paraphase.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2112.paraphase.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-15/call-run_paraphase/out/m84036_250809_035451_s4.bc2112_paraphase/m84036_250809_035451_s4.bc2112.paraphase.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2112.paraphase.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-15/call-call_f8/_singularity_tmpdir_tkn0xhd5/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-15/call-call_f8/_singularity_tmpdir_tkn0xhd5/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:26:00.048 wdl.w:ptcp.w:call-trgt-92.t:call-trgt_plot_meth_allele.slurm_singularity INFO srun: job 51798112 queued and waiting for resources
2025-09-15 20:26:00.048 wdl.w:ptcp.w:call-trgt-92.t:call-trgt_plot_meth_allele.slurm_singularity INFO srun: job 51798112 has been allocated resources
2025-09-15 20:26:00.048 wdl.w:ptcp.w:call-trgt-92.t:call-trgt_plot_meth_allele.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:26:00.059 wdl.w:ptcp.w:call-paraphase-15.t:call-call_f8 NOTICE slurm_singularity run :: pid: 1206769, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-15/call-call_f8/slurm_singularity.log.txt"
2025-09-15 20:26:00.074 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_meth_waterfall NOTICE done
2025-09-15 20:26:00.079 wdl.w:ptcp.w:call-trgt-91 NOTICE finish :: job: "call-trgt_plot_meth_waterfall"
2025-09-15 20:26:00.080 wdl.w:ptcp.w:call-trgt-91 INFO output :: job: "call-trgt_plot_meth_waterfall", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-91/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2188.meth_waterfall.trgt_plots.zip"}
2025-09-15 20:26:00.080 wdl.w:ptcp.w:call-trgt-91 INFO visit :: node: "output-images_meth_waterfall", values: {"images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-91/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2188.meth_waterfall.trgt_plots.zip"}
2025-09-15 20:26:00.085 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_plot_meth_allele NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-87/call-trgt_plot_meth_allele", thread: 140608748373568
2025-09-15 20:26:00.102 wdl.w:ptcp.w:call-trgt-92.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO srun: job 51798113 queued and waiting for resources
2025-09-15 20:26:00.102 wdl.w:ptcp.w:call-trgt-92.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO srun: job 51798113 has been allocated resources
2025-09-15 20:26:00.102 wdl.w:ptcp.w:call-trgt-92.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:26:00.103 wdl.w:ptcp.w:call-trgt-92.t:call-trgt_plot_motifs_allele.slurm_singularity INFO srun: job 51798114 queued and waiting for resources
2025-09-15 20:26:00.103 wdl.w:ptcp.w:call-trgt-92.t:call-trgt_plot_motifs_allele.slurm_singularity INFO srun: job 51798114 has been allocated resources
2025-09-15 20:26:00.103 wdl.w:ptcp.w:call-trgt-92.t:call-trgt_plot_motifs_allele.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:26:00.107 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_plot_meth_allele INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:26:00.107 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_plot_meth_allele INFO input :: name: "waterfall", value: false
2025-09-15 20:26:00.107 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_plot_meth_allele INFO input :: name: "methylation", value: true
2025-09-15 20:26:00.107 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_plot_meth_allele INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:26:00.107 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_plot_meth_allele INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:26:00.107 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_plot_meth_allele INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:26:00.107 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_plot_meth_allele INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2184.trgt.sorted.spanning.bam.bai"
2025-09-15 20:26:00.107 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_plot_meth_allele INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2184.trgt.sorted.spanning.bam"
2025-09-15 20:26:00.107 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_plot_meth_allele INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2184.trgt.vcf"
2025-09-15 20:26:00.107 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_plot_meth_allele INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2184"
2025-09-15 20:26:00.109 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_plot_meth_allele INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:26:00.109 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_plot_meth_allele INFO eval :: name: "plot_type", value: "allele"
2025-09-15 20:26:00.109 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_plot_meth_allele INFO eval :: name: "show", value: "meth"
2025-09-15 20:26:00.109 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_plot_meth_allele INFO eval :: name: "threads", value: 1
2025-09-15 20:26:00.110 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_plot_meth_allele INFO eval :: name: "disk_size", value: 27
2025-09-15 20:26:00.110 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_plot_meth_allele INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2184.meth_allele"
2025-09-15 20:26:00.110 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_plot_meth_allele INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:26:00.110 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_plot_meth_allele WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:26:00.110 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_plot_meth_allele INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:26:00.111 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_plot_meth_allele INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:26:00.139 wdl.w:ptcp.w:call-trgt-80.t:call-trgt_plot_meth_allele INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2177.meth_allele.trgt_plots.zip"
2025-09-15 20:26:00.186 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_plot_meth_allele INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-87/call-trgt_plot_meth_allele/_singularity_tmpdir_6dangxev"
2025-09-15 20:26:00.186 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_plot_meth_allele INFO Slurm invocation: srun --job-name call-trgt_plot_meth_allele --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-87/call-trgt_plot_meth_allele/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-87/call-trgt_plot_meth_allele/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-87/call-trgt_plot_meth_allele/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-87/call-trgt_plot_meth_allele/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-87/call-trgt_genotype/out/m84036_250809_035451_s4.bc2184.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2184.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-87/call-trgt_genotype/out/m84036_250809_035451_s4.bc2184.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2184.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-87/call-trgt_genotype/out/m84036_250809_035451_s4.bc2184.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2184.trgt.vcf:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-87/call-trgt_plot_meth_allele/_singularity_tmpdir_6dangxev/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-87/call-trgt_plot_meth_allele/_singularity_tmpdir_6dangxev/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:26:00.210 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_plot_meth_allele NOTICE slurm_singularity run :: pid: 1206777, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-87/call-trgt_plot_meth_allele/slurm_singularity.log.txt"
2025-09-15 20:26:00.259 wdl.w:ptcp.w:call-trgt-80.t:call-trgt_plot_meth_allele NOTICE done
2025-09-15 20:26:00.264 wdl.w:ptcp.w:call-trgt-80 NOTICE finish :: job: "call-trgt_plot_meth_allele"
2025-09-15 20:26:00.264 wdl.w:ptcp.w:call-trgt-80 INFO output :: job: "call-trgt_plot_meth_allele", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-80/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2177.meth_allele.trgt_plots.zip"}
2025-09-15 20:26:00.264 wdl.w:ptcp.w:call-trgt-80 INFO visit :: node: "output-images_meth_allele", values: {"images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-80/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2177.meth_allele.trgt_plots.zip"}
2025-09-15 20:26:00.271 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_plot_meth_waterfall NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-87/call-trgt_plot_meth_waterfall", thread: 140611432728128
2025-09-15 20:26:00.328 wdl.w:ptcp.w:call-paraphase-72.t:call-call_f8 INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2169.f8inversion.vcf"
2025-09-15 20:26:00.333 wdl.w:ptcp.w:call-paraphase-72.t:call-call_f8 INFO output :: name: "json", value: "m84036_250809_035451_s4.bc2169.f8inversion.json"
2025-09-15 20:26:00.339 wdl.w:ptcp.w:call-trgt-92.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO srun: job 51798115 queued and waiting for resources
2025-09-15 20:26:00.339 wdl.w:ptcp.w:call-trgt-92.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO srun: job 51798115 has been allocated resources
2025-09-15 20:26:00.339 wdl.w:ptcp.w:call-trgt-92.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:26:00.346 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_plot_meth_waterfall INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:26:00.346 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_plot_meth_waterfall INFO input :: name: "waterfall", value: true
2025-09-15 20:26:00.346 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_plot_meth_waterfall INFO input :: name: "methylation", value: true
2025-09-15 20:26:00.346 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_plot_meth_waterfall INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:26:00.346 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_plot_meth_waterfall INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:26:00.346 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_plot_meth_waterfall INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:26:00.346 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_plot_meth_waterfall INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2184.trgt.sorted.spanning.bam.bai"
2025-09-15 20:26:00.346 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_plot_meth_waterfall INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2184.trgt.sorted.spanning.bam"
2025-09-15 20:26:00.346 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_plot_meth_waterfall INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2184.trgt.vcf"
2025-09-15 20:26:00.346 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_plot_meth_waterfall INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2184"
2025-09-15 20:26:00.347 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_plot_meth_waterfall INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:26:00.347 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_plot_meth_waterfall INFO eval :: name: "plot_type", value: "waterfall"
2025-09-15 20:26:00.347 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_plot_meth_waterfall INFO eval :: name: "show", value: "meth"
2025-09-15 20:26:00.347 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_plot_meth_waterfall INFO eval :: name: "threads", value: 1
2025-09-15 20:26:00.347 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_plot_meth_waterfall INFO eval :: name: "disk_size", value: 27
2025-09-15 20:26:00.347 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_plot_meth_waterfall INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2184.meth_waterfall"
2025-09-15 20:26:00.348 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_plot_meth_waterfall INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:26:00.348 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_plot_meth_waterfall WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:26:00.348 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_plot_meth_waterfall INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:26:00.348 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_plot_meth_waterfall INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:26:00.375 wdl.w:ptcp.w:call-paraphase-74.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for gba for sample m84036_250809_035451_s4.bc2171 at 2025-09-15 20:25:53.720644...
2025-09-15 20:26:00.375 wdl.w:ptcp.w:call-paraphase-74.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for gba for sample m84036_250809_035451_s4.bc2171 at 2025-09-15 20:25:54.254037...
2025-09-15 20:26:00.375 wdl.w:ptcp.w:call-paraphase-74.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for hbb for sample m84036_250809_035451_s4.bc2171 at 2025-09-15 20:25:58.157370...
2025-09-15 20:26:00.375 wdl.w:ptcp.w:call-paraphase-74.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for hbb for sample m84036_250809_035451_s4.bc2171 at 2025-09-15 20:25:58.157522...
2025-09-15 20:26:00.414 wdl.w:ptcp.w:call-paraphase-72.t:call-call_f8 NOTICE done
2025-09-15 20:26:00.432 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_plot_meth_waterfall INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-87/call-trgt_plot_meth_waterfall/_singularity_tmpdir_vruxaz_c"
2025-09-15 20:26:00.432 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_plot_meth_waterfall INFO Slurm invocation: srun --job-name call-trgt_plot_meth_waterfall --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-87/call-trgt_plot_meth_waterfall/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-87/call-trgt_plot_meth_waterfall/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-87/call-trgt_plot_meth_waterfall/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-87/call-trgt_plot_meth_waterfall/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-87/call-trgt_genotype/out/m84036_250809_035451_s4.bc2184.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2184.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-87/call-trgt_genotype/out/m84036_250809_035451_s4.bc2184.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2184.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-87/call-trgt_genotype/out/m84036_250809_035451_s4.bc2184.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2184.trgt.vcf:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-87/call-trgt_plot_meth_waterfall/_singularity_tmpdir_vruxaz_c/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-87/call-trgt_plot_meth_waterfall/_singularity_tmpdir_vruxaz_c/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:26:00.438 wdl.w:ptcp.w:call-paraphase-72 NOTICE finish :: job: "call-call_f8"
2025-09-15 20:26:00.439 wdl.w:ptcp.w:call-paraphase-72 INFO output :: job: "call-call_f8", values: {"json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-72/call-call_f8/out/m84036_250809_035451_s4.bc2169.f8inversion.json", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-72/call-call_f8/out/m84036_250809_035451_s4.bc2169.f8inversion.vcf"}
2025-09-15 20:26:00.439 wdl.w:ptcp.w:call-paraphase-72 INFO visit :: node: "output-f8_json", values: {"f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-72/call-call_f8/out/m84036_250809_035451_s4.bc2169.f8inversion.json"}
2025-09-15 20:26:00.439 wdl.w:ptcp.w:call-paraphase-72 INFO visit :: node: "output-f8_vcf", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-72/call-call_f8/out/m84036_250809_035451_s4.bc2169.f8inversion.vcf"}
2025-09-15 20:26:00.439 wdl.w:ptcp.w:call-paraphase-72 INFO visit :: node: "outputs", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-72/call-call_f8/out/m84036_250809_035451_s4.bc2169.f8inversion.vcf", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-72/call-run_paraphase/out/m84036_250809_035451_s4.bc2169_paraphase/m84036_250809_035451_s4.bc2169.paraphase.json", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-72/call-run_paraphase/out/m84036_250809_035451_s4.bc2169_paraphase/m84036_250809_035451_s4.bc2169.paraphase.bam", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-72/call-run_paraphase/out/m84036_250809_035451_s4.bc2169_paraphase/m84036_250809_035451_s4.bc2169.paraphase.bam.bai", "paraphase_vcfs": [], "havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-72/call-run_paraphase/out/m84036_250809_035451_s4.bc2169.havanno.json", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-72/call-call_f8/out/m84036_250809_035451_s4.bc2169.f8inversion.json"}
2025-09-15 20:26:00.446 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_plot_motifs_allele NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-87/call-trgt_plot_motifs_allele", thread: 140606609282624
2025-09-15 20:26:00.453 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_plot_meth_waterfall NOTICE slurm_singularity run :: pid: 1206785, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-87/call-trgt_plot_meth_waterfall/slurm_singularity.log.txt"
2025-09-15 20:26:00.467 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_plot_motifs_allele INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:26:00.467 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_plot_motifs_allele INFO input :: name: "waterfall", value: false
2025-09-15 20:26:00.467 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_plot_motifs_allele INFO input :: name: "methylation", value: false
2025-09-15 20:26:00.467 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_plot_motifs_allele INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:26:00.467 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_plot_motifs_allele INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:26:00.467 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_plot_motifs_allele INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:26:00.467 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_plot_motifs_allele INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2184.trgt.sorted.spanning.bam.bai"
2025-09-15 20:26:00.467 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_plot_motifs_allele INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2184.trgt.sorted.spanning.bam"
2025-09-15 20:26:00.467 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_plot_motifs_allele INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2184.trgt.vcf"
2025-09-15 20:26:00.468 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_plot_motifs_allele INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2184"
2025-09-15 20:26:00.468 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_plot_motifs_allele INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:26:00.468 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_plot_motifs_allele INFO eval :: name: "plot_type", value: "allele"
2025-09-15 20:26:00.468 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_plot_motifs_allele INFO eval :: name: "show", value: "motifs"
2025-09-15 20:26:00.468 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_plot_motifs_allele INFO eval :: name: "threads", value: 1
2025-09-15 20:26:00.468 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_plot_motifs_allele INFO eval :: name: "disk_size", value: 27
2025-09-15 20:26:00.469 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_plot_motifs_allele INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2184.motifs_allele"
2025-09-15 20:26:00.469 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_plot_motifs_allele INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:26:00.469 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_plot_motifs_allele WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:26:00.469 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_plot_motifs_allele INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:26:00.469 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_plot_motifs_allele INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:26:00.518 wdl.w:ptcp.w:call-paraphase-72 NOTICE done
2025-09-15 20:26:00.524 wdl.w:ptcp NOTICE finish :: job: "call-paraphase-72"
2025-09-15 20:26:00.525 wdl.w:ptcp INFO output :: job: "call-paraphase-72", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-72/out/m84036_250809_035451_s4.bc2169.f8inversion.vcf", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-72/out/m84036_250809_035451_s4.bc2169_paraphase/m84036_250809_035451_s4.bc2169.paraphase.json", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-72/out/m84036_250809_035451_s4.bc2169_paraphase/m84036_250809_035451_s4.bc2169.paraphase.bam", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-72/out/m84036_250809_035451_s4.bc2169_paraphase/m84036_250809_035451_s4.bc2169.paraphase.bam.bai", "paraphase_vcfs": [], "havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-72/out/m84036_250809_035451_s4.bc2169.havanno.json", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-72/out/m84036_250809_035451_s4.bc2169.f8inversion.json"}
2025-09-15 20:26:00.548 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_plot_motifs_allele INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-87/call-trgt_plot_motifs_allele/_singularity_tmpdir_5krkw22s"
2025-09-15 20:26:00.548 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_plot_motifs_allele INFO Slurm invocation: srun --job-name call-trgt_plot_motifs_allele --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-87/call-trgt_plot_motifs_allele/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-87/call-trgt_plot_motifs_allele/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-87/call-trgt_plot_motifs_allele/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-87/call-trgt_plot_motifs_allele/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-87/call-trgt_genotype/out/m84036_250809_035451_s4.bc2184.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2184.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-87/call-trgt_genotype/out/m84036_250809_035451_s4.bc2184.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2184.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-87/call-trgt_genotype/out/m84036_250809_035451_s4.bc2184.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2184.trgt.vcf:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-87/call-trgt_plot_motifs_allele/_singularity_tmpdir_5krkw22s/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-87/call-trgt_plot_motifs_allele/_singularity_tmpdir_5krkw22s/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:26:00.556 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_plot_motifs_allele NOTICE slurm_singularity run :: pid: 1206787, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-87/call-trgt_plot_motifs_allele/slurm_singularity.log.txt"
2025-09-15 20:26:00.589 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:57 [ERROR] - No reads found for TRID=NIID_NOTCH2NLC
2025-09-15 20:26:00.590 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:57 [ERROR] - No reads found for TRID=OPDM_ABCD3
2025-09-15 20:26:00.590 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:57 [ERROR] - No reads found for TRID=SCA2_ATXN2
2025-09-15 20:26:00.590 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:57 [ERROR] - No reads found for TRID=OPDM4_RILPL1
2025-09-15 20:26:00.590 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:57 [ERROR] - No reads found for TRID=SCA27B_FGF14
2025-09-15 20:26:00.590 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:57 [ERROR] - No reads found for TRID=OPMD_PABPN1
2025-09-15 20:26:00.590 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:57 [ERROR] - No reads found for TRID=SCA3_ATXN3
2025-09-15 20:26:00.590 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:58 [ERROR] - No reads found for TRID=SCA31_BEAN1
2025-09-15 20:26:00.590 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:58 [ERROR] - No reads found for TRID=HDL2_JPH3
2025-09-15 20:26:00.590 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:58 [ERROR] - No reads found for TRID=FECD3_TCF4
2025-09-15 20:26:00.590 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:58 [ERROR] - No reads found for TRID=SCA6_CACNA1A
2025-09-15 20:26:00.590 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:58 [ERROR] - No reads found for TRID=OPDM2_GIPC1
2025-09-15 20:26:00.590 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:58 [ERROR] - No reads found for TRID=DM1_DMPK
2025-09-15 20:26:00.590 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:58 [ERROR] - No reads found for TRID=FRA2A_AFF3
2025-09-15 20:26:00.590 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:58 [ERROR] - No reads found for TRID=SCA4_ZFHX3
2025-09-15 20:26:00.590 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:58 [ERROR] - No reads found for TRID=CJD_PRNP
2025-09-15 20:26:00.590 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:58 [ERROR] - No reads found for TRID=EPM1_CSTB
2025-09-15 20:26:00.591 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:58 [ERROR] - No reads found for TRID=SD5_HOXD13
2025-09-15 20:26:00.591 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:58 [ERROR] - No reads found for TRID=SCA7_ATXN7
2025-09-15 20:26:00.591 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:58 [ERROR] - No reads found for TRID=SCA36_NOP56
2025-09-15 20:26:00.591 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:58 [ERROR] - No reads found for TRID=HD_HTT
2025-09-15 20:26:00.591 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:58 [ERROR] - No reads found for TRID=SCA10_ATXN10
2025-09-15 20:26:00.591 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:58 [ERROR] - No reads found for TRID=CCHS_PHOX2B
2025-09-15 20:26:00.591 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:58 [ERROR] - No reads found for TRID=SCA12_PPP2R2B
2025-09-15 20:26:00.591 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:58 [ERROR] - No reads found for TRID=CANVAS_RFC1
2025-09-15 20:26:00.591 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:58 [ERROR] - No reads found for TRID=OPDM1_LRP12
2025-09-15 20:26:00.591 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:58 [ERROR] - No reads found for TRID=FAME1_SAMD12
2025-09-15 20:26:00.591 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:25:59 [ERROR] - No reads found for TRID=FTDALS1_C9orf72
2025-09-15 20:26:00.657 wdl.w:ptcp.w:call-paraphase-92.t:call-call_f8.slurm_singularity INFO srun: job 51798116 queued and waiting for resources
2025-09-15 20:26:00.657 wdl.w:ptcp.w:call-paraphase-92.t:call-call_f8.slurm_singularity INFO srun: job 51798116 has been allocated resources
2025-09-15 20:26:00.657 wdl.w:ptcp.w:call-paraphase-92.t:call-call_f8.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:26:00.755 wdl.w:ptcp.w:call-paraphase-58.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for smn1 for sample m84036_250809_035451_s4.bc2155 at 2025-09-15 20:25:28.461845...
2025-09-15 20:26:00.766 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_meth_allele INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2188.meth_allele.trgt_plots.zip"
2025-09-15 20:26:00.830 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:25:58 [ERROR] - No reads found for TRID=NIID_NOTCH2NLC
2025-09-15 20:26:00.830 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:25:58 [ERROR] - No reads found for TRID=OPDM_ABCD3
2025-09-15 20:26:00.831 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:25:58 [ERROR] - No reads found for TRID=SCA2_ATXN2
2025-09-15 20:26:00.831 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:25:58 [ERROR] - No reads found for TRID=OPDM4_RILPL1
2025-09-15 20:26:00.831 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:25:58 [ERROR] - No reads found for TRID=SCA27B_FGF14
2025-09-15 20:26:00.831 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:25:58 [ERROR] - No reads found for TRID=OPMD_PABPN1
2025-09-15 20:26:00.831 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:25:59 [ERROR] - No reads found for TRID=SCA3_ATXN3
2025-09-15 20:26:00.831 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:25:59 [ERROR] - No reads found for TRID=SCA31_BEAN1
2025-09-15 20:26:00.831 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:25:59 [ERROR] - No reads found for TRID=HDL2_JPH3
2025-09-15 20:26:00.831 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:25:59 [ERROR] - No reads found for TRID=FECD3_TCF4
2025-09-15 20:26:00.831 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:25:59 [ERROR] - No reads found for TRID=SCA6_CACNA1A
2025-09-15 20:26:00.831 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:25:59 [ERROR] - No reads found for TRID=OPDM2_GIPC1
2025-09-15 20:26:00.831 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:25:59 [ERROR] - No reads found for TRID=DM1_DMPK
2025-09-15 20:26:00.831 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:25:59 [ERROR] - No reads found for TRID=FRA2A_AFF3
2025-09-15 20:26:00.831 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:25:59 [ERROR] - No reads found for TRID=SCA4_ZFHX3
2025-09-15 20:26:00.831 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:25:59 [ERROR] - No reads found for TRID=CJD_PRNP
2025-09-15 20:26:00.831 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:25:59 [ERROR] - No reads found for TRID=EPM1_CSTB
2025-09-15 20:26:00.832 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:26:00 [ERROR] - No reads found for TRID=SD5_HOXD13
2025-09-15 20:26:00.832 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:26:00 [ERROR] - No reads found for TRID=SCA7_ATXN7
2025-09-15 20:26:00.832 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:26:00 [ERROR] - No reads found for TRID=SCA36_NOP56
2025-09-15 20:26:00.832 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:26:00 [ERROR] - No reads found for TRID=HD_HTT
2025-09-15 20:26:00.832 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:26:00 [ERROR] - No reads found for TRID=SCA10_ATXN10
2025-09-15 20:26:00.832 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:26:00 [ERROR] - No reads found for TRID=CCHS_PHOX2B
2025-09-15 20:26:00.832 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:26:00 [ERROR] - No reads found for TRID=SCA12_PPP2R2B
2025-09-15 20:26:00.837 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_meth_allele NOTICE done
2025-09-15 20:26:00.841 wdl.w:ptcp.w:call-trgt-91 NOTICE finish :: job: "call-trgt_plot_meth_allele"
2025-09-15 20:26:00.842 wdl.w:ptcp.w:call-trgt-91 INFO output :: job: "call-trgt_plot_meth_allele", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-91/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2188.meth_allele.trgt_plots.zip"}
2025-09-15 20:26:00.842 wdl.w:ptcp.w:call-trgt-91 INFO visit :: node: "output-images_meth_allele", values: {"images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-91/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2188.meth_allele.trgt_plots.zip"}
2025-09-15 20:26:00.849 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_plot_motifs_waterfall NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-87/call-trgt_plot_motifs_waterfall", thread: 140613043340864
2025-09-15 20:26:00.866 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_plot_motifs_waterfall INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:26:00.866 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_plot_motifs_waterfall INFO input :: name: "waterfall", value: true
2025-09-15 20:26:00.866 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_plot_motifs_waterfall INFO input :: name: "methylation", value: false
2025-09-15 20:26:00.866 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_plot_motifs_waterfall INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:26:00.866 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_plot_motifs_waterfall INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:26:00.866 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_plot_motifs_waterfall INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:26:00.866 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_plot_motifs_waterfall INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2184.trgt.sorted.spanning.bam.bai"
2025-09-15 20:26:00.866 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_plot_motifs_waterfall INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2184.trgt.sorted.spanning.bam"
2025-09-15 20:26:00.866 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_plot_motifs_waterfall INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2184.trgt.vcf"
2025-09-15 20:26:00.866 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_plot_motifs_waterfall INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2184"
2025-09-15 20:26:00.867 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:26:00.867 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "plot_type", value: "waterfall"
2025-09-15 20:26:00.867 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "show", value: "motifs"
2025-09-15 20:26:00.867 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "threads", value: 1
2025-09-15 20:26:00.867 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "disk_size", value: 27
2025-09-15 20:26:00.867 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2184.motifs_waterfall"
2025-09-15 20:26:00.868 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_plot_motifs_waterfall INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:26:00.868 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_plot_motifs_waterfall WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:26:00.868 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_plot_motifs_waterfall INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:26:00.868 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_plot_motifs_waterfall INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:26:00.932 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_plot_motifs_waterfall INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-87/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_s6b79p51"
2025-09-15 20:26:00.933 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_plot_motifs_waterfall INFO Slurm invocation: srun --job-name call-trgt_plot_motifs_waterfall --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-87/call-trgt_plot_motifs_waterfall/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-87/call-trgt_plot_motifs_waterfall/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-87/call-trgt_plot_motifs_waterfall/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-87/call-trgt_plot_motifs_waterfall/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-87/call-trgt_genotype/out/m84036_250809_035451_s4.bc2184.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2184.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-87/call-trgt_genotype/out/m84036_250809_035451_s4.bc2184.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2184.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-87/call-trgt_genotype/out/m84036_250809_035451_s4.bc2184.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2184.trgt.vcf:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-87/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_s6b79p51/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-87/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_s6b79p51/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:26:00.954 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_plot_motifs_waterfall NOTICE slurm_singularity run :: pid: 1206800, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-87/call-trgt_plot_motifs_waterfall/slurm_singularity.log.txt"
2025-09-15 20:26:01.019 wdl.w:ptcp.w:call-paraphase-92.t:call-call_f8 INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2189.f8inversion.vcf"
2025-09-15 20:26:01.022 wdl.w:ptcp.w:call-paraphase-92.t:call-call_f8 INFO output :: name: "json", value: "m84036_250809_035451_s4.bc2189.f8inversion.json"
2025-09-15 20:26:01.071 wdl.w:ptcp.w:call-paraphase-15.t:call-call_f8.slurm_singularity INFO srun: job 51798117 queued and waiting for resources
2025-09-15 20:26:01.072 wdl.w:ptcp.w:call-paraphase-15.t:call-call_f8.slurm_singularity INFO srun: job 51798117 has been allocated resources
2025-09-15 20:26:01.072 wdl.w:ptcp.w:call-paraphase-15.t:call-call_f8.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:26:01.087 wdl.w:ptcp.w:call-paraphase-92.t:call-call_f8 NOTICE done
2025-09-15 20:26:01.093 wdl.w:ptcp.w:call-paraphase-92 NOTICE finish :: job: "call-call_f8"
2025-09-15 20:26:01.093 wdl.w:ptcp.w:call-paraphase-92 INFO output :: job: "call-call_f8", values: {"json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-92/call-call_f8/out/m84036_250809_035451_s4.bc2189.f8inversion.json", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-92/call-call_f8/out/m84036_250809_035451_s4.bc2189.f8inversion.vcf"}
2025-09-15 20:26:01.093 wdl.w:ptcp.w:call-paraphase-92 INFO visit :: node: "output-f8_json", values: {"f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-92/call-call_f8/out/m84036_250809_035451_s4.bc2189.f8inversion.json"}
2025-09-15 20:26:01.093 wdl.w:ptcp.w:call-paraphase-92 INFO visit :: node: "output-f8_vcf", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-92/call-call_f8/out/m84036_250809_035451_s4.bc2189.f8inversion.vcf"}
2025-09-15 20:26:01.093 wdl.w:ptcp.w:call-paraphase-92 INFO visit :: node: "outputs", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-92/call-call_f8/out/m84036_250809_035451_s4.bc2189.f8inversion.vcf", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-92/call-run_paraphase/out/m84036_250809_035451_s4.bc2189_paraphase/m84036_250809_035451_s4.bc2189.paraphase.json", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-92/call-run_paraphase/out/m84036_250809_035451_s4.bc2189_paraphase/m84036_250809_035451_s4.bc2189.paraphase.bam", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-92/call-run_paraphase/out/m84036_250809_035451_s4.bc2189_paraphase/m84036_250809_035451_s4.bc2189.paraphase.bam.bai", "paraphase_vcfs": [], "havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-92/call-run_paraphase/out/m84036_250809_035451_s4.bc2189.havanno.json", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-92/call-call_f8/out/m84036_250809_035451_s4.bc2189.f8inversion.json"}
2025-09-15 20:26:01.100 wdl.w:ptcp.w:call-sawfish-86.t:call-run_sawfish NOTICE task setup :: name: "run_sawfish", source: "./sawfish.wdl", line: 83, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-86/call-run_sawfish", thread: 140608186324544
2025-09-15 20:26:01.131 wdl.w:ptcp.w:call-sawfish-86.t:call-run_sawfish INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:26:01.131 wdl.w:ptcp.w:call-sawfish-86.t:call-run_sawfish INFO input :: name: "genome_version", value: "38"
2025-09-15 20:26:01.131 wdl.w:ptcp.w:call-sawfish-86.t:call-run_sawfish INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:26:01.131 wdl.w:ptcp.w:call-sawfish-86.t:call-run_sawfish INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:26:01.131 wdl.w:ptcp.w:call-sawfish-86.t:call-run_sawfish INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2183.mapped.bam.bai"
2025-09-15 20:26:01.131 wdl.w:ptcp.w:call-sawfish-86.t:call-run_sawfish INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2183.mapped.bam"
2025-09-15 20:26:01.131 wdl.w:ptcp.w:call-sawfish-86.t:call-run_sawfish INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2183"
2025-09-15 20:26:01.131 wdl.w:ptcp.w:call-sawfish-86.t:call-run_sawfish INFO eval :: name: "mem_gb", value: 32
2025-09-15 20:26:01.132 wdl.w:ptcp.w:call-sawfish-86.t:call-run_sawfish INFO eval :: name: "threads", value: 16
2025-09-15 20:26:01.132 wdl.w:ptcp.w:call-sawfish-86.t:call-run_sawfish INFO eval :: name: "disk_size", value: 30
2025-09-15 20:26:01.132 wdl.w:ptcp.w:call-sawfish-86.t:call-run_sawfish INFO eval :: name: "discover_dirname", value: "m84036_250809_035451_s4.bc2183_sawfish_discover"
2025-09-15 20:26:01.132 wdl.w:ptcp.w:call-sawfish-86.t:call-run_sawfish INFO eval :: name: "call_dirname", value: "m84036_250809_035451_s4.bc2183_sawfish"
2025-09-15 20:26:01.132 wdl.w:ptcp.w:call-sawfish-86.t:call-run_sawfish INFO eval :: name: "minimap2_bam_filename", value: "m84036_250809_035451_s4.bc2183.minimap2.bam"
2025-09-15 20:26:01.132 wdl.w:ptcp.w:call-sawfish-86.t:call-run_sawfish INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 16, memory_reservation: 32000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:26:01.132 wdl.w:ptcp.w:call-sawfish-86.t:call-run_sawfish WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:26:01.133 wdl.w:ptcp.w:call-sawfish-86.t:call-run_sawfish INFO provisioned :: seconds_waited: 0, cpu: 16, mem_bytes: 32000000000
2025-09-15 20:26:01.133 wdl.w:ptcp.w:call-sawfish-86.t:call-run_sawfish INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:26:01.164 wdl.w:ptcp.w:call-paraphase-92 NOTICE done
2025-09-15 20:26:01.170 wdl.w:ptcp NOTICE finish :: job: "call-paraphase-92"
2025-09-15 20:26:01.170 wdl.w:ptcp INFO output :: job: "call-paraphase-92", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-92/out/m84036_250809_035451_s4.bc2189.f8inversion.vcf", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-92/out/m84036_250809_035451_s4.bc2189_paraphase/m84036_250809_035451_s4.bc2189.paraphase.json", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-92/out/m84036_250809_035451_s4.bc2189_paraphase/m84036_250809_035451_s4.bc2189.paraphase.bam", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-92/out/m84036_250809_035451_s4.bc2189_paraphase/m84036_250809_035451_s4.bc2189.paraphase.bam.bai", "paraphase_vcfs": [], "havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-92/out/m84036_250809_035451_s4.bc2189.havanno.json", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-92/out/m84036_250809_035451_s4.bc2189.f8inversion.json"}
2025-09-15 20:26:01.207 wdl.w:ptcp.w:call-sawfish-86.t:call-run_sawfish INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 10, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-86/call-run_sawfish/_singularity_tmpdir_k3b7_4_t"
2025-09-15 20:26:01.207 wdl.w:ptcp.w:call-sawfish-86.t:call-run_sawfish INFO Slurm invocation: srun --job-name call-run_sawfish --partition compute,compute9 --cpus-per-task 16 --mem 30518M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-86/call-run_sawfish/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-86/call-run_sawfish/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-86/call-run_sawfish/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-86/call-run_sawfish/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-86/out/m84036_250809_035451_s4.bc2183.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2183.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-86/out/m84036_250809_035451_s4.bc2183.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2183.mapped.bam:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-86/call-run_sawfish/_singularity_tmpdir_k3b7_4_t/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-86/call-run_sawfish/_singularity_tmpdir_k3b7_4_t/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:26:01.212 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:26:00 [ERROR] - No reads found for TRID=OPDM_ABCD3
2025-09-15 20:26:01.212 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:26:00 [ERROR] - No reads found for TRID=NIID_NOTCH2NLC
2025-09-15 20:26:01.212 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:26:00 [ERROR] - No reads found for TRID=DRPLA_ATN1
2025-09-15 20:26:01.212 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:26:01 [ERROR] - No reads found for TRID=SCA2_ATXN2
2025-09-15 20:26:01.212 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:26:01 [ERROR] - No reads found for TRID=OPDM4_RILPL1
2025-09-15 20:26:01.212 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:26:01 [ERROR] - No reads found for TRID=SCA8_ATXN8OS
2025-09-15 20:26:01.212 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:26:01 [ERROR] - No reads found for TRID=OPMD_PABPN1
2025-09-15 20:26:01.223 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_plot_meth_allele.slurm_singularity INFO srun: job 51798118 queued and waiting for resources
2025-09-15 20:26:01.223 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_plot_meth_allele.slurm_singularity INFO srun: job 51798118 has been allocated resources
2025-09-15 20:26:01.223 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_plot_meth_allele.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:26:01.224 wdl.w:ptcp.w:call-sawfish-86.t:call-run_sawfish NOTICE slurm_singularity run :: pid: 1206803, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-86/call-run_sawfish/slurm_singularity.log.txt"
2025-09-15 20:26:01.418 wdl.w:ptcp.w:call-trgt-81.t:call-trgt_plot_meth_waterfall INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2178.meth_waterfall.trgt_plots.zip"
2025-09-15 20:26:01.437 wdl.w:ptcp.w:call-paraphase-15.t:call-call_f8 INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2112.f8inversion.vcf"
2025-09-15 20:26:01.441 wdl.w:ptcp.w:call-paraphase-15.t:call-call_f8 INFO output :: name: "json", value: "m84036_250809_035451_s4.bc2112.f8inversion.json"
2025-09-15 20:26:01.469 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO srun: job 51798119 queued and waiting for resources
2025-09-15 20:26:01.470 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO srun: job 51798119 has been allocated resources
2025-09-15 20:26:01.470 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:26:01.513 wdl.w:ptcp.w:call-paraphase-15.t:call-call_f8 NOTICE done
2025-09-15 20:26:01.534 wdl.w:ptcp.w:call-paraphase-15 NOTICE finish :: job: "call-call_f8"
2025-09-15 20:26:01.534 wdl.w:ptcp.w:call-paraphase-15 INFO output :: job: "call-call_f8", values: {"json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-15/call-call_f8/out/m84036_250809_035451_s4.bc2112.f8inversion.json", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-15/call-call_f8/out/m84036_250809_035451_s4.bc2112.f8inversion.vcf"}
2025-09-15 20:26:01.534 wdl.w:ptcp.w:call-paraphase-15 INFO visit :: node: "output-f8_json", values: {"f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-15/call-call_f8/out/m84036_250809_035451_s4.bc2112.f8inversion.json"}
2025-09-15 20:26:01.535 wdl.w:ptcp.w:call-paraphase-15 INFO visit :: node: "output-f8_vcf", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-15/call-call_f8/out/m84036_250809_035451_s4.bc2112.f8inversion.vcf"}
2025-09-15 20:26:01.535 wdl.w:ptcp.w:call-paraphase-15 INFO visit :: node: "outputs", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-15/call-call_f8/out/m84036_250809_035451_s4.bc2112.f8inversion.vcf", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-15/call-run_paraphase/out/m84036_250809_035451_s4.bc2112_paraphase/m84036_250809_035451_s4.bc2112.paraphase.json", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-15/call-run_paraphase/out/m84036_250809_035451_s4.bc2112_paraphase/m84036_250809_035451_s4.bc2112.paraphase.bam", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-15/call-run_paraphase/out/m84036_250809_035451_s4.bc2112_paraphase/m84036_250809_035451_s4.bc2112.paraphase.bam.bai", "paraphase_vcfs": ["/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-15/call-run_paraphase/out/m84036_250809_035451_s4.bc2112_paraphase/m84036_250809_035451_s4.bc2112_paraphase_vcfs/m84036_250809_035451_s4.bc2112_cyp21.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-15/call-run_paraphase/out/m84036_250809_035451_s4.bc2112_paraphase/m84036_250809_035451_s4.bc2112_paraphase_vcfs/m84036_250809_035451_s4.bc2112_f8inv1.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-15/call-run_paraphase/out/m84036_250809_035451_s4.bc2112_paraphase/m84036_250809_035451_s4.bc2112_paraphase_vcfs/m84036_250809_035451_s4.bc2112_f8inv22.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-15/call-run_paraphase/out/m84036_250809_035451_s4.bc2112_paraphase/m84036_250809_035451_s4.bc2112_paraphase_vcfs/m84036_250809_035451_s4.bc2112_gba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-15/call-run_paraphase/out/m84036_250809_035451_s4.bc2112_paraphase/m84036_250809_035451_s4.bc2112_paraphase_vcfs/m84036_250809_035451_s4.bc2112_hba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-15/call-run_paraphase/out/m84036_250809_035451_s4.bc2112_paraphase/m84036_250809_035451_s4.bc2112_paraphase_vcfs/m84036_250809_035451_s4.bc2112_hbb.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-15/call-run_paraphase/out/m84036_250809_035451_s4.bc2112_paraphase/m84036_250809_035451_s4.bc2112_paraphase_vcfs/m84036_250809_035451_s4.bc2112_rpgr.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-15/call-run_paraphase/out/m84036_250809_035451_s4.bc2112_paraphase/m84036_250809_035451_s4.bc2112_paraphase_vcfs/m84036_250809_035451_s4.bc2112_smn1.vcf"], "havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-15/call-run_paraphase/out/m84036_250809_035451_s4.bc2112.havanno.json", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-15/call-call_f8/out/m84036_250809_035451_s4.bc2112.f8inversion.json"}
2025-09-15 20:26:01.541 wdl.w:ptcp.w:call-paraphase-23.t:call-call_f8 NOTICE task setup :: name: "call_f8", source: "./paraphase.wdl", line: 232, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-23/call-call_f8", thread: 140611969599040
2025-09-15 20:26:01.559 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:26:01 [ERROR] - No reads found for TRID=OPDM_ABCD3
2025-09-15 20:26:01.559 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:26:01 [ERROR] - No reads found for TRID=NIID_NOTCH2NLC
2025-09-15 20:26:01.559 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:26:01 [ERROR] - No reads found for TRID=DRPLA_ATN1
2025-09-15 20:26:01.560 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:26:01 [ERROR] - No reads found for TRID=SCA2_ATXN2
2025-09-15 20:26:01.560 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:26:01 [ERROR] - No reads found for TRID=OPDM4_RILPL1
2025-09-15 20:26:01.560 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:26:01 [ERROR] - No reads found for TRID=SCA8_ATXN8OS
2025-09-15 20:26:01.560 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:26:01 [ERROR] - No reads found for TRID=OPMD_PABPN1
2025-09-15 20:26:01.563 wdl.w:ptcp.w:call-trgt-81.t:call-trgt_plot_meth_waterfall NOTICE done
2025-09-15 20:26:01.564 wdl.w:ptcp.w:call-paraphase-23.t:call-call_f8 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:26:01.564 wdl.w:ptcp.w:call-paraphase-23.t:call-call_f8 INFO input :: name: "genome_version", value: "38"
2025-09-15 20:26:01.564 wdl.w:ptcp.w:call-paraphase-23.t:call-call_f8 INFO input :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2120"
2025-09-15 20:26:01.564 wdl.w:ptcp.w:call-paraphase-23.t:call-call_f8 INFO input :: name: "paraphase_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2120.paraphase.bam.bai"
2025-09-15 20:26:01.564 wdl.w:ptcp.w:call-paraphase-23.t:call-call_f8 INFO input :: name: "paraphase_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2120.paraphase.bam"
2025-09-15 20:26:01.564 wdl.w:ptcp.w:call-paraphase-23.t:call-call_f8 INFO input :: name: "sex", value: "F"
2025-09-15 20:26:01.564 wdl.w:ptcp.w:call-paraphase-23.t:call-call_f8 INFO eval :: name: "threads", value: 1
2025-09-15 20:26:01.564 wdl.w:ptcp.w:call-paraphase-23.t:call-call_f8 INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:26:01.565 wdl.w:ptcp.w:call-paraphase-23.t:call-call_f8 INFO eval :: name: "disk_size", value: 11
2025-09-15 20:26:01.565 wdl.w:ptcp.w:call-paraphase-23.t:call-call_f8 INFO eval :: name: "sample_sex", value: "F"
2025-09-15 20:26:01.565 wdl.w:ptcp.w:call-paraphase-23.t:call-call_f8 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:26:01.565 wdl.w:ptcp.w:call-paraphase-23.t:call-call_f8 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:26:01.566 wdl.w:ptcp.w:call-paraphase-23.t:call-call_f8 INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:26:01.566 wdl.w:ptcp.w:call-paraphase-23.t:call-call_f8 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:26:01.571 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_plot_motifs_allele.slurm_singularity INFO srun: job 51798120 queued and waiting for resources
2025-09-15 20:26:01.571 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_plot_motifs_allele.slurm_singularity INFO srun: job 51798120 has been allocated resources
2025-09-15 20:26:01.571 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_plot_motifs_allele.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:26:01.598 wdl.w:ptcp.w:call-trgt-81 NOTICE finish :: job: "call-trgt_plot_meth_waterfall"
2025-09-15 20:26:01.599 wdl.w:ptcp.w:call-trgt-81 INFO output :: job: "call-trgt_plot_meth_waterfall", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-81/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2178.meth_waterfall.trgt_plots.zip"}
2025-09-15 20:26:01.599 wdl.w:ptcp.w:call-trgt-81 INFO visit :: node: "output-images_meth_waterfall", values: {"images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-81/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2178.meth_waterfall.trgt_plots.zip"}
2025-09-15 20:26:01.599 wdl.w:ptcp.w:call-trgt-81 INFO visit :: node: "outputs", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-81/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2178.motifs_waterfall.trgt_plots.zip", "images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-81/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2178.meth_allele.trgt_plots.zip", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-81/call-trgt_genotype/out/m84036_250809_035451_s4.bc2178.trgt.sorted.spanning.bam.bai", "images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-81/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2178.motifs_allele.trgt_plots.zip", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-81/call-trgt_genotype/out/m84036_250809_035451_s4.bc2178.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-81/call-trgt_genotype/out/m84036_250809_035451_s4.bc2178.trgt.vcf", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-81/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2178.repeats.bam", "images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-81/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2178.meth_waterfall.trgt_plots.zip", "reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-81/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2178.repeats.bam.bai"}
2025-09-15 20:26:01.605 wdl.w:ptcp.w:call-trgt-86.t:call-get_reads_overlapping_repeats NOTICE task setup :: name: "get_reads_overlapping_repeats", source: "./trgt.wdl", line: 182, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-86/call-get_reads_overlapping_repeats", thread: 140607120975424
2025-09-15 20:26:01.618 wdl.w:ptcp.w:call-paraphase-23.t:call-call_f8 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 8, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-23/call-call_f8/_singularity_tmpdir_cwndrpmz"
2025-09-15 20:26:01.618 wdl.w:ptcp.w:call-paraphase-23.t:call-call_f8 INFO Slurm invocation: srun --job-name call-call_f8 --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-23/call-call_f8/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-23/call-call_f8/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-23/call-call_f8/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-23/call-call_f8/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-23/call-run_paraphase/out/m84036_250809_035451_s4.bc2120_paraphase/m84036_250809_035451_s4.bc2120.paraphase.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2120.paraphase.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-23/call-run_paraphase/out/m84036_250809_035451_s4.bc2120_paraphase/m84036_250809_035451_s4.bc2120.paraphase.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2120.paraphase.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-23/call-call_f8/_singularity_tmpdir_cwndrpmz/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-23/call-call_f8/_singularity_tmpdir_cwndrpmz/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:26:01.624 wdl.w:ptcp.w:call-trgt-86.t:call-get_reads_overlapping_repeats INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:26:01.624 wdl.w:ptcp.w:call-trgt-86.t:call-get_reads_overlapping_repeats INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:26:01.624 wdl.w:ptcp.w:call-trgt-86.t:call-get_reads_overlapping_repeats INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2183.mapped.bam.bai"
2025-09-15 20:26:01.625 wdl.w:ptcp.w:call-trgt-86.t:call-get_reads_overlapping_repeats INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2183.mapped.bam"
2025-09-15 20:26:01.625 wdl.w:ptcp.w:call-trgt-86.t:call-get_reads_overlapping_repeats INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2183"
2025-09-15 20:26:01.625 wdl.w:ptcp.w:call-trgt-86.t:call-get_reads_overlapping_repeats INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:26:01.625 wdl.w:ptcp.w:call-trgt-86.t:call-get_reads_overlapping_repeats INFO eval :: name: "expand_size", value: 3000
2025-09-15 20:26:01.625 wdl.w:ptcp.w:call-trgt-86.t:call-get_reads_overlapping_repeats INFO eval :: name: "threads", value: 1
2025-09-15 20:26:01.625 wdl.w:ptcp.w:call-trgt-86.t:call-get_reads_overlapping_repeats INFO eval :: name: "expanded_bed_name", value: "m84036_250809_035451_s4.bc2183.expanded.bed"
2025-09-15 20:26:01.625 wdl.w:ptcp.w:call-trgt-86.t:call-get_reads_overlapping_repeats INFO eval :: name: "disk_size", value: 11
2025-09-15 20:26:01.625 wdl.w:ptcp.w:call-trgt-86.t:call-get_reads_overlapping_repeats INFO eval :: name: "output_name", value: "m84036_250809_035451_s4.bc2183.repeats.bam"
2025-09-15 20:26:01.625 wdl.w:ptcp.w:call-trgt-86.t:call-get_reads_overlapping_repeats INFO eval :: name: "index_name", value: "m84036_250809_035451_s4.bc2183.repeats.bam.bai"
2025-09-15 20:26:01.625 wdl.w:ptcp.w:call-trgt-86.t:call-get_reads_overlapping_repeats INFO eval :: name: "output_name_with_index", value: "m84036_250809_035451_s4.bc2183.repeats.bam##idx##m84036_250809_035451_s4.bc2183.repeats.bam.bai"
2025-09-15 20:26:01.626 wdl.w:ptcp.w:call-trgt-86.t:call-get_reads_overlapping_repeats INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:26:01.626 wdl.w:ptcp.w:call-trgt-86.t:call-get_reads_overlapping_repeats WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:26:01.626 wdl.w:ptcp.w:call-trgt-86.t:call-get_reads_overlapping_repeats INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:26:01.626 wdl.w:ptcp.w:call-trgt-86.t:call-get_reads_overlapping_repeats INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:26:01.643 wdl.w:ptcp.w:call-paraphase-23.t:call-call_f8 NOTICE slurm_singularity run :: pid: 1206817, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-23/call-call_f8/slurm_singularity.log.txt"
2025-09-15 20:26:01.685 wdl.w:ptcp.w:call-paraphase-15 NOTICE done
2025-09-15 20:26:01.691 wdl.w:ptcp NOTICE finish :: job: "call-paraphase-15"
2025-09-15 20:26:01.691 wdl.w:ptcp INFO output :: job: "call-paraphase-15", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-15/out/m84036_250809_035451_s4.bc2112.f8inversion.vcf", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-15/out/m84036_250809_035451_s4.bc2112_paraphase/m84036_250809_035451_s4.bc2112.paraphase.json", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-15/out/m84036_250809_035451_s4.bc2112_paraphase/m84036_250809_035451_s4.bc2112.paraphase.bam", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-15/out/m84036_250809_035451_s4.bc2112_paraphase/m84036_250809_035451_s4.bc2112.paraphase.bam.bai", "paraphase_vcfs": ["/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-15/out/m84036_250809_035451_s4.bc2112_paraphase/m84036_250809_035451_s4.bc2112_paraphase_vcfs/m84036_250809_035451_s4.bc2112_cyp21.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-15/out/m84036_250809_035451_s4.bc2112_paraphase/m84036_250809_035451_s4.bc2112_paraphase_vcfs/m84036_250809_035451_s4.bc2112_f8inv1.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-15/out/m84036_250809_035451_s4.bc2112_paraphase/m84036_250809_035451_s4.bc2112_paraphase_vcfs/m84036_250809_035451_s4.bc2112_f8inv22.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-15/out/m84036_250809_035451_s4.bc2112_paraphase/m84036_250809_035451_s4.bc2112_paraphase_vcfs/m84036_250809_035451_s4.bc2112_gba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-15/out/m84036_250809_035451_s4.bc2112_paraphase/m84036_250809_035451_s4.bc2112_paraphase_vcfs/m84036_250809_035451_s4.bc2112_hba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-15/out/m84036_250809_035451_s4.bc2112_paraphase/m84036_250809_035451_s4.bc2112_paraphase_vcfs/m84036_250809_035451_s4.bc2112_hbb.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-15/out/m84036_250809_035451_s4.bc2112_paraphase/m84036_250809_035451_s4.bc2112_paraphase_vcfs/m84036_250809_035451_s4.bc2112_rpgr.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-15/out/m84036_250809_035451_s4.bc2112_paraphase/m84036_250809_035451_s4.bc2112_paraphase_vcfs/m84036_250809_035451_s4.bc2112_smn1.vcf"], "havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-15/out/m84036_250809_035451_s4.bc2112.havanno.json", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-15/out/m84036_250809_035451_s4.bc2112.f8inversion.json"}
2025-09-15 20:26:01.692 wdl.w:ptcp NOTICE ready :: job: "call-tar_outputs-15", callee: "tar_outputs"
2025-09-15 20:26:01.692 wdl.w:ptcp.w:call-trgt-86.t:call-get_reads_overlapping_repeats INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 9, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-86/call-get_reads_overlapping_repeats/_singularity_tmpdir_dchpsmeq"
2025-09-15 20:26:01.693 wdl.w:ptcp INFO input :: job: "call-tar_outputs-15", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "sawfish_vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-15/out/m84036_250809_035451_s4.bc2112_sawfish/m84036_250809_035451_s4.bc2112.sv.vcf.gz.tbi", "sawfish_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-15/out/m84036_250809_035451_s4.bc2112_sawfish/m84036_250809_035451_s4.bc2112.sv.vcf.gz", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-15/out/m84036_250809_035451_s4.bc2112.f8inversion.json", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-15/out/m84036_250809_035451_s4.bc2112_paraphase/m84036_250809_035451_s4.bc2112.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-15/out/m84036_250809_035451_s4.bc2112_paraphase/m84036_250809_035451_s4.bc2112.paraphase.bam", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-15/out/m84036_250809_035451_s4.bc2112_paraphase/m84036_250809_035451_s4.bc2112.paraphase.json", "trgt_spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-15/out/m84036_250809_035451_s4.bc2112.trgt.sorted.spanning.bam.bai", "trgt_spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-15/out/m84036_250809_035451_s4.bc2112.trgt.sorted.spanning.bam", "trgt_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-15/out/m84036_250809_035451_s4.bc2112.trgt.vcf", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-15/out/m84036_250809_035451_s4.bc2112.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-15/out/m84036_250809_035451_s4.bc2112.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2112"}
2025-09-15 20:26:01.693 wdl.w:ptcp.w:call-trgt-86.t:call-get_reads_overlapping_repeats INFO Slurm invocation: srun --job-name call-get_reads_overlapping_repeats --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-86/call-get_reads_overlapping_repeats/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-86/call-get_reads_overlapping_repeats/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-86/call-get_reads_overlapping_repeats/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-86/call-get_reads_overlapping_repeats/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-86/out/m84036_250809_035451_s4.bc2183.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2183.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-86/out/m84036_250809_035451_s4.bc2183.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2183.mapped.bam:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-86/call-get_reads_overlapping_repeats/_singularity_tmpdir_dchpsmeq/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-86/call-get_reads_overlapping_repeats/_singularity_tmpdir_dchpsmeq/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:26:01.701 wdl.w:ptcp.w:call-trgt-81 NOTICE done
2025-09-15 20:26:01.703 wdl.w:ptcp.w:call-trgt-86.t:call-get_reads_overlapping_repeats NOTICE slurm_singularity run :: pid: 1206820, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-86/call-get_reads_overlapping_repeats/slurm_singularity.log.txt"
2025-09-15 20:26:01.704 wdl.w:ptcp NOTICE finish :: job: "call-trgt-81"
2025-09-15 20:26:01.704 wdl.w:ptcp INFO output :: job: "call-trgt-81", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-81/out/m84036_250809_035451_s4.bc2178.motifs_waterfall.trgt_plots.zip", "images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-81/out/m84036_250809_035451_s4.bc2178.meth_allele.trgt_plots.zip", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-81/out/m84036_250809_035451_s4.bc2178.trgt.sorted.spanning.bam.bai", "images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-81/out/m84036_250809_035451_s4.bc2178.motifs_allele.trgt_plots.zip", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-81/out/m84036_250809_035451_s4.bc2178.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-81/out/m84036_250809_035451_s4.bc2178.trgt.vcf", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-81/out/m84036_250809_035451_s4.bc2178.repeats.bam", "images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-81/out/m84036_250809_035451_s4.bc2178.meth_waterfall.trgt_plots.zip", "reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-81/out/m84036_250809_035451_s4.bc2178.repeats.bam.bai"}
2025-09-15 20:26:01.772 wdl.w:ptcp.w:call-trgt-80.t:call-trgt_plot_meth_waterfall INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2177.meth_waterfall.trgt_plots.zip"
2025-09-15 20:26:01.881 wdl.w:ptcp.w:call-trgt-80.t:call-trgt_plot_meth_waterfall NOTICE done
2025-09-15 20:26:01.889 wdl.w:ptcp.w:call-trgt-80 NOTICE finish :: job: "call-trgt_plot_meth_waterfall"
2025-09-15 20:26:01.889 wdl.w:ptcp.w:call-trgt-80 INFO output :: job: "call-trgt_plot_meth_waterfall", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-80/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2177.meth_waterfall.trgt_plots.zip"}
2025-09-15 20:26:01.889 wdl.w:ptcp.w:call-trgt-80 INFO visit :: node: "output-images_meth_waterfall", values: {"images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-80/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2177.meth_waterfall.trgt_plots.zip"}
2025-09-15 20:26:01.895 wdl.w:ptcp.w:call-trgt-72.t:call-trgt_plot_meth_waterfall INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2169.meth_waterfall.trgt_plots.zip"
2025-09-15 20:26:01.896 wdl.w:ptcp.w:call-trgt-86.t:call-trgt_genotype NOTICE task setup :: name: "trgt_genotype", source: "./trgt.wdl", line: 272, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-86/call-trgt_genotype", thread: 140611977991744
2025-09-15 20:26:01.902 wdl.w:ptcp.w:call-trgt-80.t:call-trgt_plot_motifs_waterfall INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2177.motifs_waterfall.trgt_plots.zip"
2025-09-15 20:26:01.914 wdl.w:ptcp.w:call-trgt-86.t:call-trgt_genotype INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:26:01.914 wdl.w:ptcp.w:call-trgt-86.t:call-trgt_genotype INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:26:01.914 wdl.w:ptcp.w:call-trgt-86.t:call-trgt_genotype INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:26:01.914 wdl.w:ptcp.w:call-trgt-86.t:call-trgt_genotype INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:26:01.914 wdl.w:ptcp.w:call-trgt-86.t:call-trgt_genotype INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2183.mapped.bam.bai"
2025-09-15 20:26:01.914 wdl.w:ptcp.w:call-trgt-86.t:call-trgt_genotype INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2183.mapped.bam"
2025-09-15 20:26:01.914 wdl.w:ptcp.w:call-trgt-86.t:call-trgt_genotype INFO input :: name: "sex", value: "F"
2025-09-15 20:26:01.914 wdl.w:ptcp.w:call-trgt-86.t:call-trgt_genotype INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2183"
2025-09-15 20:26:01.914 wdl.w:ptcp.w:call-trgt-86.t:call-trgt_genotype INFO eval :: name: "mem_gb", value: 16
2025-09-15 20:26:01.915 wdl.w:ptcp.w:call-trgt-86.t:call-trgt_genotype INFO eval :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2183.trgt"
2025-09-15 20:26:01.915 wdl.w:ptcp.w:call-trgt-86.t:call-trgt_genotype INFO eval :: name: "threads", value: 8
2025-09-15 20:26:01.915 wdl.w:ptcp.w:call-trgt-86.t:call-trgt_genotype INFO eval :: name: "disk_size", value: 27
2025-09-15 20:26:01.915 wdl.w:ptcp.w:call-trgt-86.t:call-trgt_genotype INFO eval :: name: "karyotype", value: "XX"
2025-09-15 20:26:01.916 wdl.w:ptcp.w:call-trgt-86.t:call-trgt_genotype INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 8, memory_reservation: 16000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:26:01.916 wdl.w:ptcp.w:call-trgt-86.t:call-trgt_genotype WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:26:01.916 wdl.w:ptcp.w:call-trgt-86.t:call-trgt_genotype INFO provisioned :: seconds_waited: 0, cpu: 8, mem_bytes: 16000000000
2025-09-15 20:26:01.916 wdl.w:ptcp.w:call-trgt-86.t:call-trgt_genotype INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:26:01.972 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO srun: job 51798121 queued and waiting for resources
2025-09-15 20:26:01.972 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO srun: job 51798121 has been allocated resources
2025-09-15 20:26:01.972 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:26:01.995 wdl.w:ptcp.w:call-trgt-86.t:call-trgt_genotype INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 11, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-86/call-trgt_genotype/_singularity_tmpdir_djkol3na"
2025-09-15 20:26:01.995 wdl.w:ptcp.w:call-trgt-86.t:call-trgt_genotype INFO Slurm invocation: srun --job-name call-trgt_genotype --partition compute,compute9 --cpus-per-task 8 --mem 15259M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-86/call-trgt_genotype/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-86/call-trgt_genotype/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-86/call-trgt_genotype/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-86/call-trgt_genotype/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-86/out/m84036_250809_035451_s4.bc2183.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2183.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-86/out/m84036_250809_035451_s4.bc2183.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2183.mapped.bam:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-86/call-trgt_genotype/_singularity_tmpdir_djkol3na/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-86/call-trgt_genotype/_singularity_tmpdir_djkol3na/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:26:02.009 wdl.w:ptcp.w:call-trgt-86.t:call-trgt_genotype NOTICE slurm_singularity run :: pid: 1206834, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-86/call-trgt_genotype/slurm_singularity.log.txt"
2025-09-15 20:26:02.030 wdl.w:ptcp.w:call-trgt-72.t:call-trgt_plot_meth_waterfall NOTICE done
2025-09-15 20:26:02.034 wdl.w:ptcp.w:call-trgt-80.t:call-trgt_plot_motifs_waterfall NOTICE done
2025-09-15 20:26:02.035 wdl.w:ptcp.w:call-trgt-72 NOTICE finish :: job: "call-trgt_plot_meth_waterfall"
2025-09-15 20:26:02.036 wdl.w:ptcp.w:call-trgt-72 INFO output :: job: "call-trgt_plot_meth_waterfall", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-72/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2169.meth_waterfall.trgt_plots.zip"}
2025-09-15 20:26:02.036 wdl.w:ptcp.w:call-trgt-72 INFO visit :: node: "output-images_meth_waterfall", values: {"images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-72/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2169.meth_waterfall.trgt_plots.zip"}
2025-09-15 20:26:02.036 wdl.w:ptcp.w:call-trgt-72 INFO visit :: node: "outputs", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-72/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2169.motifs_waterfall.trgt_plots.zip", "images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-72/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2169.meth_allele.trgt_plots.zip", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-72/call-trgt_genotype/out/m84036_250809_035451_s4.bc2169.trgt.sorted.spanning.bam.bai", "images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-72/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2169.motifs_allele.trgt_plots.zip", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-72/call-trgt_genotype/out/m84036_250809_035451_s4.bc2169.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-72/call-trgt_genotype/out/m84036_250809_035451_s4.bc2169.trgt.vcf", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-72/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2169.repeats.bam", "images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-72/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2169.meth_waterfall.trgt_plots.zip", "reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-72/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2169.repeats.bam.bai"}
2025-09-15 20:26:02.040 wdl.w:ptcp.w:call-trgt-80 NOTICE finish :: job: "call-trgt_plot_motifs_waterfall"
2025-09-15 20:26:02.040 wdl.w:ptcp.w:call-trgt-80 INFO output :: job: "call-trgt_plot_motifs_waterfall", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-80/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2177.motifs_waterfall.trgt_plots.zip"}
2025-09-15 20:26:02.041 wdl.w:ptcp.w:call-trgt-80 INFO visit :: node: "output-images_motifs_waterfall", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-80/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2177.motifs_waterfall.trgt_plots.zip"}
2025-09-15 20:26:02.041 wdl.w:ptcp.w:call-trgt-80 INFO visit :: node: "outputs", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-80/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2177.motifs_waterfall.trgt_plots.zip", "images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-80/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2177.meth_allele.trgt_plots.zip", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-80/call-trgt_genotype/out/m84036_250809_035451_s4.bc2177.trgt.sorted.spanning.bam.bai", "images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-80/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2177.motifs_allele.trgt_plots.zip", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-80/call-trgt_genotype/out/m84036_250809_035451_s4.bc2177.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-80/call-trgt_genotype/out/m84036_250809_035451_s4.bc2177.trgt.vcf", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-80/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2177.repeats.bam", "images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-80/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2177.meth_waterfall.trgt_plots.zip", "reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-80/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2177.repeats.bam.bai"}
2025-09-15 20:26:02.045 wdl.w:ptcp.w:call-paraphase-88.t:call-run_paraphase NOTICE task setup :: name: "run_paraphase", source: "./paraphase.wdl", line: 127, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-88/call-run_paraphase", thread: 140613034948160
2025-09-15 20:26:02.049 wdl.w:ptcp.w:call-paraphase-85.t:call-call_f8 NOTICE task setup :: name: "call_f8", source: "./paraphase.wdl", line: 232, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-85/call-call_f8", thread: 140607649453632
2025-09-15 20:26:02.068 wdl.w:ptcp.w:call-paraphase-88.t:call-run_paraphase INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:26:02.068 wdl.w:ptcp.w:call-paraphase-88.t:call-run_paraphase INFO input :: name: "annotation_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf"
2025-09-15 20:26:02.068 wdl.w:ptcp.w:call-paraphase-88.t:call-run_paraphase INFO input :: name: "genome_version", value: "38"
2025-09-15 20:26:02.068 wdl.w:ptcp.w:call-paraphase-88.t:call-run_paraphase INFO input :: name: "config_file", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/paraphase_config.GRCh38.yaml"
2025-09-15 20:26:02.068 wdl.w:ptcp.w:call-paraphase-88.t:call-run_paraphase INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:26:02.068 wdl.w:ptcp.w:call-paraphase-88.t:call-run_paraphase INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:26:02.068 wdl.w:ptcp.w:call-paraphase-88.t:call-run_paraphase INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2185.mapped.bam.bai"
2025-09-15 20:26:02.068 wdl.w:ptcp.w:call-paraphase-88.t:call-run_paraphase INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2185.mapped.bam"
2025-09-15 20:26:02.068 wdl.w:ptcp.w:call-paraphase-88.t:call-run_paraphase INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2185"
2025-09-15 20:26:02.069 wdl.w:ptcp.w:call-paraphase-88.t:call-run_paraphase INFO eval :: name: "threads", value: 4
2025-09-15 20:26:02.069 wdl.w:ptcp.w:call-paraphase-88.t:call-run_paraphase INFO eval :: name: "mem_gb", value: 8
2025-09-15 20:26:02.069 wdl.w:ptcp.w:call-paraphase-88.t:call-run_paraphase INFO eval :: name: "disk_size", value: 27
2025-09-15 20:26:02.069 wdl.w:ptcp.w:call-paraphase-88.t:call-run_paraphase INFO eval :: name: "out_dir", value: "m84036_250809_035451_s4.bc2185_paraphase"
2025-09-15 20:26:02.070 wdl.w:ptcp.w:call-paraphase-88.t:call-run_paraphase INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 4, memory_reservation: 8000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:26:02.070 wdl.w:ptcp.w:call-paraphase-88.t:call-run_paraphase WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:26:02.071 wdl.w:ptcp.w:call-paraphase-85.t:call-call_f8 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:26:02.071 wdl.w:ptcp.w:call-paraphase-88.t:call-run_paraphase INFO provisioned :: seconds_waited: 0, cpu: 4, mem_bytes: 8000000000
2025-09-15 20:26:02.071 wdl.w:ptcp.w:call-paraphase-85.t:call-call_f8 INFO input :: name: "genome_version", value: "38"
2025-09-15 20:26:02.071 wdl.w:ptcp.w:call-paraphase-88.t:call-run_paraphase INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:26:02.071 wdl.w:ptcp.w:call-paraphase-85.t:call-call_f8 INFO input :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2182"
2025-09-15 20:26:02.071 wdl.w:ptcp.w:call-paraphase-85.t:call-call_f8 INFO input :: name: "paraphase_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2182.paraphase.bam.bai"
2025-09-15 20:26:02.071 wdl.w:ptcp.w:call-paraphase-85.t:call-call_f8 INFO input :: name: "paraphase_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2182.paraphase.bam"
2025-09-15 20:26:02.071 wdl.w:ptcp.w:call-paraphase-85.t:call-call_f8 INFO input :: name: "sex", value: "F"
2025-09-15 20:26:02.072 wdl.w:ptcp.w:call-paraphase-85.t:call-call_f8 INFO eval :: name: "threads", value: 1
2025-09-15 20:26:02.072 wdl.w:ptcp.w:call-paraphase-85.t:call-call_f8 INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:26:02.072 wdl.w:ptcp.w:call-paraphase-85.t:call-call_f8 INFO eval :: name: "disk_size", value: 11
2025-09-15 20:26:02.072 wdl.w:ptcp.w:call-paraphase-85.t:call-call_f8 INFO eval :: name: "sample_sex", value: "F"
2025-09-15 20:26:02.072 wdl.w:ptcp.w:call-paraphase-85.t:call-call_f8 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:26:02.073 wdl.w:ptcp.w:call-paraphase-85.t:call-call_f8 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:26:02.073 wdl.w:ptcp.w:call-paraphase-85.t:call-call_f8 INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:26:02.073 wdl.w:ptcp.w:call-paraphase-85.t:call-call_f8 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:26:02.086 wdl.w:ptcp.w:call-sawfish-65.t:call-run_sawfish INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2162_sawfish/m84036_250809_035451_s4.bc2162.sv.vcf.gz"
2025-09-15 20:26:02.094 wdl.w:ptcp.w:call-sawfish-65.t:call-run_sawfish INFO output :: name: "vcf_tbi", value: "m84036_250809_035451_s4.bc2162_sawfish/m84036_250809_035451_s4.bc2162.sv.vcf.gz.tbi"
2025-09-15 20:26:02.096 wdl.w:ptcp.w:call-sawfish-65.t:call-run_sawfish INFO output :: name: "minimap2_bam", value: "m84036_250809_035451_s4.bc2162.minimap2.bam"
2025-09-15 20:26:02.098 wdl.w:ptcp.w:call-sawfish-65.t:call-run_sawfish INFO output :: name: "minimap2_bam_bai", value: "m84036_250809_035451_s4.bc2162.minimap2.bam.bai"
2025-09-15 20:26:02.140 wdl.w:ptcp.w:call-paraphase-85.t:call-call_f8 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 8, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-85/call-call_f8/_singularity_tmpdir_s6orxbvs"
2025-09-15 20:26:02.141 wdl.w:ptcp.w:call-paraphase-85.t:call-call_f8 INFO Slurm invocation: srun --job-name call-call_f8 --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-85/call-call_f8/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-85/call-call_f8/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-85/call-call_f8/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-85/call-call_f8/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-85/call-run_paraphase/out/m84036_250809_035451_s4.bc2182_paraphase/m84036_250809_035451_s4.bc2182.paraphase.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2182.paraphase.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-85/call-run_paraphase/out/m84036_250809_035451_s4.bc2182_paraphase/m84036_250809_035451_s4.bc2182.paraphase.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2182.paraphase.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-85/call-call_f8/_singularity_tmpdir_s6orxbvs/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-85/call-call_f8/_singularity_tmpdir_s6orxbvs/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:26:02.142 wdl.w:ptcp.w:call-sawfish-48.t:call-run_sawfish INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2145_sawfish/m84036_250809_035451_s4.bc2145.sv.vcf.gz"
2025-09-15 20:26:02.151 wdl.w:ptcp.w:call-sawfish-48.t:call-run_sawfish INFO output :: name: "vcf_tbi", value: "m84036_250809_035451_s4.bc2145_sawfish/m84036_250809_035451_s4.bc2145.sv.vcf.gz.tbi"
2025-09-15 20:26:02.154 wdl.w:ptcp.w:call-trgt-72 NOTICE done
2025-09-15 20:26:02.153 wdl.w:ptcp.w:call-sawfish-48.t:call-run_sawfish INFO output :: name: "minimap2_bam", value: "m84036_250809_035451_s4.bc2145.minimap2.bam"
2025-09-15 20:26:02.156 wdl.w:ptcp.w:call-sawfish-48.t:call-run_sawfish INFO output :: name: "minimap2_bam_bai", value: "m84036_250809_035451_s4.bc2145.minimap2.bam.bai"
2025-09-15 20:26:02.158 wdl.w:ptcp NOTICE finish :: job: "call-trgt-72"
2025-09-15 20:26:02.158 wdl.w:ptcp INFO output :: job: "call-trgt-72", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-72/out/m84036_250809_035451_s4.bc2169.motifs_waterfall.trgt_plots.zip", "images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-72/out/m84036_250809_035451_s4.bc2169.meth_allele.trgt_plots.zip", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-72/out/m84036_250809_035451_s4.bc2169.trgt.sorted.spanning.bam.bai", "images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-72/out/m84036_250809_035451_s4.bc2169.motifs_allele.trgt_plots.zip", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-72/out/m84036_250809_035451_s4.bc2169.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-72/out/m84036_250809_035451_s4.bc2169.trgt.vcf", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-72/out/m84036_250809_035451_s4.bc2169.repeats.bam", "images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-72/out/m84036_250809_035451_s4.bc2169.meth_waterfall.trgt_plots.zip", "reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-72/out/m84036_250809_035451_s4.bc2169.repeats.bam.bai"}
2025-09-15 20:26:02.159 wdl.w:ptcp.w:call-sawfish-54.t:call-run_sawfish INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2151_sawfish/m84036_250809_035451_s4.bc2151.sv.vcf.gz"
2025-09-15 20:26:02.166 wdl.w:ptcp.w:call-sawfish-54.t:call-run_sawfish INFO output :: name: "vcf_tbi", value: "m84036_250809_035451_s4.bc2151_sawfish/m84036_250809_035451_s4.bc2151.sv.vcf.gz.tbi"
2025-09-15 20:26:02.167 wdl.w:ptcp.w:call-sawfish-54.t:call-run_sawfish INFO output :: name: "minimap2_bam", value: "m84036_250809_035451_s4.bc2151.minimap2.bam"
2025-09-15 20:26:02.169 wdl.w:ptcp.w:call-sawfish-54.t:call-run_sawfish INFO output :: name: "minimap2_bam_bai", value: "m84036_250809_035451_s4.bc2151.minimap2.bam.bai"
2025-09-15 20:26:02.170 wdl.w:ptcp.w:call-trgt-80 NOTICE done
2025-09-15 20:26:02.175 wdl.w:ptcp NOTICE finish :: job: "call-trgt-80"
2025-09-15 20:26:02.175 wdl.w:ptcp INFO output :: job: "call-trgt-80", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-80/out/m84036_250809_035451_s4.bc2177.motifs_waterfall.trgt_plots.zip", "images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-80/out/m84036_250809_035451_s4.bc2177.meth_allele.trgt_plots.zip", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-80/out/m84036_250809_035451_s4.bc2177.trgt.sorted.spanning.bam.bai", "images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-80/out/m84036_250809_035451_s4.bc2177.motifs_allele.trgt_plots.zip", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-80/out/m84036_250809_035451_s4.bc2177.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-80/out/m84036_250809_035451_s4.bc2177.trgt.vcf", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-80/out/m84036_250809_035451_s4.bc2177.repeats.bam", "images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-80/out/m84036_250809_035451_s4.bc2177.meth_waterfall.trgt_plots.zip", "reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-80/out/m84036_250809_035451_s4.bc2177.repeats.bam.bai"}
2025-09-15 20:26:02.178 wdl.w:ptcp.w:call-paraphase-88.t:call-run_paraphase INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-88/call-run_paraphase/_singularity_tmpdir_fr7tmih3"
2025-09-15 20:26:02.178 wdl.w:ptcp.w:call-paraphase-88.t:call-run_paraphase INFO Slurm invocation: srun --job-name call-run_paraphase --partition compute,compute9 --cpus-per-task 4 --mem 7629M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-88/call-run_paraphase/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-88/call-run_paraphase/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-88/call-run_paraphase/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-88/call-run_paraphase/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/variant_list/variant_list.GRCh38.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-88/out/m84036_250809_035451_s4.bc2185.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2185.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-88/out/m84036_250809_035451_s4.bc2185.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2185.mapped.bam:ro --bind /ptcp/meta/paraphase/paraphase_config.GRCh38.yaml:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/paraphase_config.GRCh38.yaml:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-88/call-run_paraphase/_singularity_tmpdir_fr7tmih3/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-88/call-run_paraphase/_singularity_tmpdir_fr7tmih3/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:26:02.184 wdl.w:ptcp.w:call-paraphase-85.t:call-call_f8 NOTICE slurm_singularity run :: pid: 1206845, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-85/call-call_f8/slurm_singularity.log.txt"
2025-09-15 20:26:02.189 wdl.w:ptcp.w:call-paraphase-88.t:call-run_paraphase NOTICE slurm_singularity run :: pid: 1206846, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-88/call-run_paraphase/slurm_singularity.log.txt"
2025-09-15 20:26:02.219 wdl.w:ptcp.w:call-sawfish-50.t:call-run_sawfish INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2147_sawfish/m84036_250809_035451_s4.bc2147.sv.vcf.gz"
2025-09-15 20:26:02.227 wdl.w:ptcp.w:call-sawfish-50.t:call-run_sawfish INFO output :: name: "vcf_tbi", value: "m84036_250809_035451_s4.bc2147_sawfish/m84036_250809_035451_s4.bc2147.sv.vcf.gz.tbi"
2025-09-15 20:26:02.228 wdl.w:ptcp.w:call-sawfish-50.t:call-run_sawfish INFO output :: name: "minimap2_bam", value: "m84036_250809_035451_s4.bc2147.minimap2.bam"
2025-09-15 20:26:02.230 wdl.w:ptcp.w:call-sawfish-50.t:call-run_sawfish INFO output :: name: "minimap2_bam_bai", value: "m84036_250809_035451_s4.bc2147.minimap2.bam.bai"
2025-09-15 20:26:02.240 wdl.w:ptcp.w:call-sawfish-86.t:call-run_sawfish.slurm_singularity INFO srun: job 51798122 queued and waiting for resources
2025-09-15 20:26:02.240 wdl.w:ptcp.w:call-sawfish-86.t:call-run_sawfish.slurm_singularity INFO srun: job 51798122 has been allocated resources
2025-09-15 20:26:02.241 wdl.w:ptcp.w:call-sawfish-86.t:call-run_sawfish.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:26:02.287 wdl.w:ptcp.w:call-sawfish-65.t:call-run_sawfish NOTICE done
2025-09-15 20:26:02.293 wdl.w:ptcp.w:call-sawfish-65 NOTICE finish :: job: "call-run_sawfish"
2025-09-15 20:26:02.294 wdl.w:ptcp.w:call-sawfish-65 INFO output :: job: "call-run_sawfish", values: {"minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-65/call-run_sawfish/out/m84036_250809_035451_s4.bc2162.minimap2.bam.bai", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-65/call-run_sawfish/out/m84036_250809_035451_s4.bc2162.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-65/call-run_sawfish/out/m84036_250809_035451_s4.bc2162_sawfish/m84036_250809_035451_s4.bc2162.sv.vcf.gz.tbi", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-65/call-run_sawfish/out/m84036_250809_035451_s4.bc2162_sawfish/m84036_250809_035451_s4.bc2162.sv.vcf.gz"}
2025-09-15 20:26:02.294 wdl.w:ptcp.w:call-sawfish-65 INFO visit :: node: "output-minimap2_bam", values: {"minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-65/call-run_sawfish/out/m84036_250809_035451_s4.bc2162.minimap2.bam"}
2025-09-15 20:26:02.294 wdl.w:ptcp.w:call-sawfish-65 INFO visit :: node: "output-minimap2_bam_bai", values: {"minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-65/call-run_sawfish/out/m84036_250809_035451_s4.bc2162.minimap2.bam.bai"}
2025-09-15 20:26:02.295 wdl.w:ptcp.w:call-sawfish-65 INFO visit :: node: "output-vcf", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-65/call-run_sawfish/out/m84036_250809_035451_s4.bc2162_sawfish/m84036_250809_035451_s4.bc2162.sv.vcf.gz"}
2025-09-15 20:26:02.295 wdl.w:ptcp.w:call-sawfish-65 INFO visit :: node: "output-vcf_tbi", values: {"vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-65/call-run_sawfish/out/m84036_250809_035451_s4.bc2162_sawfish/m84036_250809_035451_s4.bc2162.sv.vcf.gz.tbi"}
2025-09-15 20:26:02.295 wdl.w:ptcp.w:call-sawfish-65 INFO visit :: node: "outputs", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-65/call-run_sawfish/out/m84036_250809_035451_s4.bc2162_sawfish/m84036_250809_035451_s4.bc2162.sv.vcf.gz", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-65/call-run_sawfish/out/m84036_250809_035451_s4.bc2162.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-65/call-run_sawfish/out/m84036_250809_035451_s4.bc2162_sawfish/m84036_250809_035451_s4.bc2162.sv.vcf.gz.tbi", "minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-65/call-run_sawfish/out/m84036_250809_035451_s4.bc2162.minimap2.bam.bai"}
2025-09-15 20:26:02.302 wdl.w:ptcp.w:call-sawfish-88.t:call-run_sawfish NOTICE task setup :: name: "run_sawfish", source: "./sawfish.wdl", line: 83, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-88/call-run_sawfish", thread: 140609310422592
2025-09-15 20:26:02.326 wdl.w:ptcp.w:call-sawfish-88.t:call-run_sawfish INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:26:02.326 wdl.w:ptcp.w:call-sawfish-88.t:call-run_sawfish INFO input :: name: "genome_version", value: "38"
2025-09-15 20:26:02.326 wdl.w:ptcp.w:call-sawfish-88.t:call-run_sawfish INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:26:02.326 wdl.w:ptcp.w:call-sawfish-88.t:call-run_sawfish INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:26:02.326 wdl.w:ptcp.w:call-sawfish-88.t:call-run_sawfish INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2185.mapped.bam.bai"
2025-09-15 20:26:02.327 wdl.w:ptcp.w:call-sawfish-88.t:call-run_sawfish INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2185.mapped.bam"
2025-09-15 20:26:02.327 wdl.w:ptcp.w:call-sawfish-88.t:call-run_sawfish INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2185"
2025-09-15 20:26:02.327 wdl.w:ptcp.w:call-sawfish-88.t:call-run_sawfish INFO eval :: name: "mem_gb", value: 32
2025-09-15 20:26:02.327 wdl.w:ptcp.w:call-sawfish-88.t:call-run_sawfish INFO eval :: name: "threads", value: 16
2025-09-15 20:26:02.327 wdl.w:ptcp.w:call-sawfish-88.t:call-run_sawfish INFO eval :: name: "disk_size", value: 30
2025-09-15 20:26:02.328 wdl.w:ptcp.w:call-sawfish-88.t:call-run_sawfish INFO eval :: name: "discover_dirname", value: "m84036_250809_035451_s4.bc2185_sawfish_discover"
2025-09-15 20:26:02.328 wdl.w:ptcp.w:call-sawfish-88.t:call-run_sawfish INFO eval :: name: "call_dirname", value: "m84036_250809_035451_s4.bc2185_sawfish"
2025-09-15 20:26:02.328 wdl.w:ptcp.w:call-sawfish-88.t:call-run_sawfish INFO eval :: name: "minimap2_bam_filename", value: "m84036_250809_035451_s4.bc2185.minimap2.bam"
2025-09-15 20:26:02.328 wdl.w:ptcp.w:call-sawfish-88.t:call-run_sawfish INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 16, memory_reservation: 32000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:26:02.328 wdl.w:ptcp.w:call-sawfish-88.t:call-run_sawfish WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:26:02.329 wdl.w:ptcp.w:call-sawfish-88.t:call-run_sawfish INFO provisioned :: seconds_waited: 0, cpu: 16, mem_bytes: 32000000000
2025-09-15 20:26:02.329 wdl.w:ptcp.w:call-sawfish-88.t:call-run_sawfish INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:26:02.332 wdl.w:ptcp.w:call-sawfish-48.t:call-run_sawfish NOTICE done
2025-09-15 20:26:02.339 wdl.w:ptcp.w:call-sawfish-48 NOTICE finish :: job: "call-run_sawfish"
2025-09-15 20:26:02.339 wdl.w:ptcp.w:call-sawfish-48 INFO output :: job: "call-run_sawfish", values: {"minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-48/call-run_sawfish/out/m84036_250809_035451_s4.bc2145.minimap2.bam.bai", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-48/call-run_sawfish/out/m84036_250809_035451_s4.bc2145.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-48/call-run_sawfish/out/m84036_250809_035451_s4.bc2145_sawfish/m84036_250809_035451_s4.bc2145.sv.vcf.gz.tbi", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-48/call-run_sawfish/out/m84036_250809_035451_s4.bc2145_sawfish/m84036_250809_035451_s4.bc2145.sv.vcf.gz"}
2025-09-15 20:26:02.340 wdl.w:ptcp.w:call-sawfish-48 INFO visit :: node: "output-minimap2_bam", values: {"minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-48/call-run_sawfish/out/m84036_250809_035451_s4.bc2145.minimap2.bam"}
2025-09-15 20:26:02.340 wdl.w:ptcp.w:call-sawfish-48 INFO visit :: node: "output-minimap2_bam_bai", values: {"minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-48/call-run_sawfish/out/m84036_250809_035451_s4.bc2145.minimap2.bam.bai"}
2025-09-15 20:26:02.340 wdl.w:ptcp.w:call-sawfish-48 INFO visit :: node: "output-vcf", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-48/call-run_sawfish/out/m84036_250809_035451_s4.bc2145_sawfish/m84036_250809_035451_s4.bc2145.sv.vcf.gz"}
2025-09-15 20:26:02.340 wdl.w:ptcp.w:call-sawfish-48 INFO visit :: node: "output-vcf_tbi", values: {"vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-48/call-run_sawfish/out/m84036_250809_035451_s4.bc2145_sawfish/m84036_250809_035451_s4.bc2145.sv.vcf.gz.tbi"}
2025-09-15 20:26:02.340 wdl.w:ptcp.w:call-sawfish-48 INFO visit :: node: "outputs", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-48/call-run_sawfish/out/m84036_250809_035451_s4.bc2145_sawfish/m84036_250809_035451_s4.bc2145.sv.vcf.gz", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-48/call-run_sawfish/out/m84036_250809_035451_s4.bc2145.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-48/call-run_sawfish/out/m84036_250809_035451_s4.bc2145_sawfish/m84036_250809_035451_s4.bc2145.sv.vcf.gz.tbi", "minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-48/call-run_sawfish/out/m84036_250809_035451_s4.bc2145.minimap2.bam.bai"}
2025-09-15 20:26:02.341 wdl.w:ptcp.w:call-sawfish-54.t:call-run_sawfish NOTICE done
2025-09-15 20:26:02.348 wdl.w:ptcp.w:call-sawfish-54 NOTICE finish :: job: "call-run_sawfish"
2025-09-15 20:26:02.349 wdl.w:ptcp.w:call-sawfish-54 INFO output :: job: "call-run_sawfish", values: {"minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-54/call-run_sawfish/out/m84036_250809_035451_s4.bc2151.minimap2.bam.bai", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-54/call-run_sawfish/out/m84036_250809_035451_s4.bc2151.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-54/call-run_sawfish/out/m84036_250809_035451_s4.bc2151_sawfish/m84036_250809_035451_s4.bc2151.sv.vcf.gz.tbi", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-54/call-run_sawfish/out/m84036_250809_035451_s4.bc2151_sawfish/m84036_250809_035451_s4.bc2151.sv.vcf.gz"}
2025-09-15 20:26:02.348 wdl.w:ptcp.w:call-trgt-88.t:call-get_reads_overlapping_repeats NOTICE task setup :: name: "get_reads_overlapping_repeats", source: "./trgt.wdl", line: 182, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-88/call-get_reads_overlapping_repeats", thread: 140613580211776
2025-09-15 20:26:02.349 wdl.w:ptcp.w:call-sawfish-54 INFO visit :: node: "output-minimap2_bam", values: {"minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-54/call-run_sawfish/out/m84036_250809_035451_s4.bc2151.minimap2.bam"}
2025-09-15 20:26:02.349 wdl.w:ptcp.w:call-sawfish-54 INFO visit :: node: "output-minimap2_bam_bai", values: {"minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-54/call-run_sawfish/out/m84036_250809_035451_s4.bc2151.minimap2.bam.bai"}
2025-09-15 20:26:02.349 wdl.w:ptcp.w:call-sawfish-54 INFO visit :: node: "output-vcf", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-54/call-run_sawfish/out/m84036_250809_035451_s4.bc2151_sawfish/m84036_250809_035451_s4.bc2151.sv.vcf.gz"}
2025-09-15 20:26:02.350 wdl.w:ptcp.w:call-sawfish-54 INFO visit :: node: "output-vcf_tbi", values: {"vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-54/call-run_sawfish/out/m84036_250809_035451_s4.bc2151_sawfish/m84036_250809_035451_s4.bc2151.sv.vcf.gz.tbi"}
2025-09-15 20:26:02.350 wdl.w:ptcp.w:call-sawfish-54 INFO visit :: node: "outputs", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-54/call-run_sawfish/out/m84036_250809_035451_s4.bc2151_sawfish/m84036_250809_035451_s4.bc2151.sv.vcf.gz", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-54/call-run_sawfish/out/m84036_250809_035451_s4.bc2151.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-54/call-run_sawfish/out/m84036_250809_035451_s4.bc2151_sawfish/m84036_250809_035451_s4.bc2151.sv.vcf.gz.tbi", "minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-54/call-run_sawfish/out/m84036_250809_035451_s4.bc2151.minimap2.bam.bai"}
2025-09-15 20:26:02.360 wdl.w:ptcp.w:call-trgt-88.t:call-trgt_genotype NOTICE task setup :: name: "trgt_genotype", source: "./trgt.wdl", line: 272, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-88/call-trgt_genotype", thread: 140613823374912
2025-09-15 20:26:02.360 wdl.w:ptcp.w:call-sawfish-65 NOTICE done
2025-09-15 20:26:02.367 wdl.w:ptcp NOTICE finish :: job: "call-sawfish-65"
2025-09-15 20:26:02.367 wdl.w:ptcp INFO output :: job: "call-sawfish-65", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-65/out/m84036_250809_035451_s4.bc2162_sawfish/m84036_250809_035451_s4.bc2162.sv.vcf.gz", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-65/out/m84036_250809_035451_s4.bc2162.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-65/out/m84036_250809_035451_s4.bc2162_sawfish/m84036_250809_035451_s4.bc2162.sv.vcf.gz.tbi", "minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-65/out/m84036_250809_035451_s4.bc2162.minimap2.bam.bai"}
2025-09-15 20:26:02.368 wdl.w:ptcp NOTICE ready :: job: "call-tar_outputs-65", callee: "tar_outputs"
2025-09-15 20:26:02.368 wdl.w:ptcp INFO input :: job: "call-tar_outputs-65", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "sawfish_vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-65/out/m84036_250809_035451_s4.bc2162_sawfish/m84036_250809_035451_s4.bc2162.sv.vcf.gz.tbi", "sawfish_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-65/out/m84036_250809_035451_s4.bc2162_sawfish/m84036_250809_035451_s4.bc2162.sv.vcf.gz", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-65/out/m84036_250809_035451_s4.bc2162.f8inversion.json", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-65/out/m84036_250809_035451_s4.bc2162_paraphase/m84036_250809_035451_s4.bc2162.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-65/out/m84036_250809_035451_s4.bc2162_paraphase/m84036_250809_035451_s4.bc2162.paraphase.bam", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-65/out/m84036_250809_035451_s4.bc2162_paraphase/m84036_250809_035451_s4.bc2162.paraphase.json", "trgt_spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-65/out/m84036_250809_035451_s4.bc2162.trgt.sorted.spanning.bam.bai", "trgt_spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-65/out/m84036_250809_035451_s4.bc2162.trgt.sorted.spanning.bam", "trgt_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-65/out/m84036_250809_035451_s4.bc2162.trgt.vcf", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-65/out/m84036_250809_035451_s4.bc2162.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-65/out/m84036_250809_035451_s4.bc2162.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2162"}
2025-09-15 20:26:02.370 wdl.w:ptcp.w:call-trgt-88.t:call-get_reads_overlapping_repeats INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:26:02.370 wdl.w:ptcp.w:call-trgt-88.t:call-get_reads_overlapping_repeats INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:26:02.370 wdl.w:ptcp.w:call-trgt-88.t:call-get_reads_overlapping_repeats INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2185.mapped.bam.bai"
2025-09-15 20:26:02.371 wdl.w:ptcp.w:call-trgt-88.t:call-get_reads_overlapping_repeats INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2185.mapped.bam"
2025-09-15 20:26:02.371 wdl.w:ptcp.w:call-trgt-88.t:call-get_reads_overlapping_repeats INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2185"
2025-09-15 20:26:02.372 wdl.w:ptcp.w:call-trgt-88.t:call-get_reads_overlapping_repeats INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:26:02.373 wdl.w:ptcp.w:call-trgt-88.t:call-get_reads_overlapping_repeats INFO eval :: name: "expand_size", value: 3000
2025-09-15 20:26:02.373 wdl.w:ptcp.w:call-trgt-88.t:call-get_reads_overlapping_repeats INFO eval :: name: "threads", value: 1
2025-09-15 20:26:02.374 wdl.w:ptcp.w:call-trgt-88.t:call-get_reads_overlapping_repeats INFO eval :: name: "expanded_bed_name", value: "m84036_250809_035451_s4.bc2185.expanded.bed"
2025-09-15 20:26:02.374 wdl.w:ptcp.w:call-trgt-88.t:call-get_reads_overlapping_repeats INFO eval :: name: "disk_size", value: 11
2025-09-15 20:26:02.374 wdl.w:ptcp.w:call-trgt-88.t:call-get_reads_overlapping_repeats INFO eval :: name: "output_name", value: "m84036_250809_035451_s4.bc2185.repeats.bam"
2025-09-15 20:26:02.375 wdl.w:ptcp.w:call-trgt-88.t:call-get_reads_overlapping_repeats INFO eval :: name: "index_name", value: "m84036_250809_035451_s4.bc2185.repeats.bam.bai"
2025-09-15 20:26:02.375 wdl.w:ptcp.w:call-trgt-88.t:call-get_reads_overlapping_repeats INFO eval :: name: "output_name_with_index", value: "m84036_250809_035451_s4.bc2185.repeats.bam##idx##m84036_250809_035451_s4.bc2185.repeats.bam.bai"
2025-09-15 20:26:02.376 wdl.w:ptcp.w:call-trgt-88.t:call-get_reads_overlapping_repeats INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:26:02.377 wdl.w:ptcp.w:call-trgt-88.t:call-get_reads_overlapping_repeats WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:26:02.377 wdl.w:ptcp.w:call-trgt-88.t:call-get_reads_overlapping_repeats INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:26:02.377 wdl.w:ptcp.w:call-trgt-88.t:call-get_reads_overlapping_repeats INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:26:02.385 wdl.w:ptcp.w:call-trgt-88.t:call-trgt_genotype INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:26:02.385 wdl.w:ptcp.w:call-trgt-88.t:call-trgt_genotype INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:26:02.385 wdl.w:ptcp.w:call-trgt-88.t:call-trgt_genotype INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:26:02.385 wdl.w:ptcp.w:call-trgt-88.t:call-trgt_genotype INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:26:02.385 wdl.w:ptcp.w:call-trgt-88.t:call-trgt_genotype INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2185.mapped.bam.bai"
2025-09-15 20:26:02.385 wdl.w:ptcp.w:call-trgt-88.t:call-trgt_genotype INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2185.mapped.bam"
2025-09-15 20:26:02.385 wdl.w:ptcp.w:call-trgt-88.t:call-trgt_genotype INFO input :: name: "sex", value: "F"
2025-09-15 20:26:02.385 wdl.w:ptcp.w:call-trgt-88.t:call-trgt_genotype INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2185"
2025-09-15 20:26:02.386 wdl.w:ptcp.w:call-trgt-88.t:call-trgt_genotype INFO eval :: name: "mem_gb", value: 16
2025-09-15 20:26:02.386 wdl.w:ptcp.w:call-trgt-88.t:call-trgt_genotype INFO eval :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2185.trgt"
2025-09-15 20:26:02.386 wdl.w:ptcp.w:call-trgt-88.t:call-trgt_genotype INFO eval :: name: "threads", value: 8
2025-09-15 20:26:02.386 wdl.w:ptcp.w:call-trgt-88.t:call-trgt_genotype INFO eval :: name: "disk_size", value: 27
2025-09-15 20:26:02.386 wdl.w:ptcp.w:call-trgt-88.t:call-trgt_genotype INFO eval :: name: "karyotype", value: "XX"
2025-09-15 20:26:02.387 wdl.w:ptcp.w:call-trgt-88.t:call-trgt_genotype INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 8, memory_reservation: 16000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:26:02.387 wdl.w:ptcp.w:call-trgt-88.t:call-trgt_genotype WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:26:02.387 wdl.w:ptcp.w:call-trgt-88.t:call-trgt_genotype INFO provisioned :: seconds_waited: 0, cpu: 8, mem_bytes: 16000000000
2025-09-15 20:26:02.387 wdl.w:ptcp.w:call-trgt-88.t:call-trgt_genotype INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:26:02.414 wdl.w:ptcp.w:call-sawfish-88.t:call-run_sawfish INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 10, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-88/call-run_sawfish/_singularity_tmpdir_woo8xyd0"
2025-09-15 20:26:02.414 wdl.w:ptcp.w:call-sawfish-88.t:call-run_sawfish INFO Slurm invocation: srun --job-name call-run_sawfish --partition compute,compute9 --cpus-per-task 16 --mem 30518M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-88/call-run_sawfish/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-88/call-run_sawfish/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-88/call-run_sawfish/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-88/call-run_sawfish/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-88/out/m84036_250809_035451_s4.bc2185.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2185.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-88/out/m84036_250809_035451_s4.bc2185.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2185.mapped.bam:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-88/call-run_sawfish/_singularity_tmpdir_woo8xyd0/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-88/call-run_sawfish/_singularity_tmpdir_woo8xyd0/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:26:02.419 wdl.w:ptcp.w:call-sawfish-48 NOTICE done
2025-09-15 20:26:02.419 wdl.w:ptcp.w:call-sawfish-54 NOTICE done
2025-09-15 20:26:02.421 wdl.w:ptcp.w:call-sawfish-50.t:call-run_sawfish NOTICE done
2025-09-15 20:26:02.424 wdl.w:ptcp NOTICE finish :: job: "call-sawfish-48"
2025-09-15 20:26:02.424 wdl.w:ptcp INFO output :: job: "call-sawfish-48", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-48/out/m84036_250809_035451_s4.bc2145_sawfish/m84036_250809_035451_s4.bc2145.sv.vcf.gz", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-48/out/m84036_250809_035451_s4.bc2145.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-48/out/m84036_250809_035451_s4.bc2145_sawfish/m84036_250809_035451_s4.bc2145.sv.vcf.gz.tbi", "minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-48/out/m84036_250809_035451_s4.bc2145.minimap2.bam.bai"}
2025-09-15 20:26:02.425 wdl.w:ptcp NOTICE ready :: job: "call-tar_outputs-48", callee: "tar_outputs"
2025-09-15 20:26:02.425 wdl.w:ptcp INFO input :: job: "call-tar_outputs-48", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "sawfish_vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-48/out/m84036_250809_035451_s4.bc2145_sawfish/m84036_250809_035451_s4.bc2145.sv.vcf.gz.tbi", "sawfish_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-48/out/m84036_250809_035451_s4.bc2145_sawfish/m84036_250809_035451_s4.bc2145.sv.vcf.gz", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-48/out/m84036_250809_035451_s4.bc2145.f8inversion.json", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-48/out/m84036_250809_035451_s4.bc2145_paraphase/m84036_250809_035451_s4.bc2145.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-48/out/m84036_250809_035451_s4.bc2145_paraphase/m84036_250809_035451_s4.bc2145.paraphase.bam", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-48/out/m84036_250809_035451_s4.bc2145_paraphase/m84036_250809_035451_s4.bc2145.paraphase.json", "trgt_spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-48/out/m84036_250809_035451_s4.bc2145.trgt.sorted.spanning.bam.bai", "trgt_spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-48/out/m84036_250809_035451_s4.bc2145.trgt.sorted.spanning.bam", "trgt_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-48/out/m84036_250809_035451_s4.bc2145.trgt.vcf", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-48/out/m84036_250809_035451_s4.bc2145.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-48/out/m84036_250809_035451_s4.bc2145.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2145"}
2025-09-15 20:26:02.426 wdl.w:ptcp NOTICE finish :: job: "call-sawfish-54"
2025-09-15 20:26:02.426 wdl.w:ptcp INFO output :: job: "call-sawfish-54", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-54/out/m84036_250809_035451_s4.bc2151_sawfish/m84036_250809_035451_s4.bc2151.sv.vcf.gz", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-54/out/m84036_250809_035451_s4.bc2151.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-54/out/m84036_250809_035451_s4.bc2151_sawfish/m84036_250809_035451_s4.bc2151.sv.vcf.gz.tbi", "minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-54/out/m84036_250809_035451_s4.bc2151.minimap2.bam.bai"}
2025-09-15 20:26:02.429 wdl.w:ptcp.w:call-sawfish-50 NOTICE finish :: job: "call-run_sawfish"
2025-09-15 20:26:02.429 wdl.w:ptcp.w:call-sawfish-50 INFO output :: job: "call-run_sawfish", values: {"minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-50/call-run_sawfish/out/m84036_250809_035451_s4.bc2147.minimap2.bam.bai", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-50/call-run_sawfish/out/m84036_250809_035451_s4.bc2147.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-50/call-run_sawfish/out/m84036_250809_035451_s4.bc2147_sawfish/m84036_250809_035451_s4.bc2147.sv.vcf.gz.tbi", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-50/call-run_sawfish/out/m84036_250809_035451_s4.bc2147_sawfish/m84036_250809_035451_s4.bc2147.sv.vcf.gz"}
2025-09-15 20:26:02.429 wdl.w:ptcp.w:call-sawfish-50 INFO visit :: node: "output-minimap2_bam", values: {"minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-50/call-run_sawfish/out/m84036_250809_035451_s4.bc2147.minimap2.bam"}
2025-09-15 20:26:02.429 wdl.w:ptcp.w:call-sawfish-50 INFO visit :: node: "output-minimap2_bam_bai", values: {"minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-50/call-run_sawfish/out/m84036_250809_035451_s4.bc2147.minimap2.bam.bai"}
2025-09-15 20:26:02.430 wdl.w:ptcp.w:call-sawfish-50 INFO visit :: node: "output-vcf", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-50/call-run_sawfish/out/m84036_250809_035451_s4.bc2147_sawfish/m84036_250809_035451_s4.bc2147.sv.vcf.gz"}
2025-09-15 20:26:02.430 wdl.w:ptcp.w:call-sawfish-50 INFO visit :: node: "output-vcf_tbi", values: {"vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-50/call-run_sawfish/out/m84036_250809_035451_s4.bc2147_sawfish/m84036_250809_035451_s4.bc2147.sv.vcf.gz.tbi"}
2025-09-15 20:26:02.430 wdl.w:ptcp.w:call-sawfish-50 INFO visit :: node: "outputs", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-50/call-run_sawfish/out/m84036_250809_035451_s4.bc2147_sawfish/m84036_250809_035451_s4.bc2147.sv.vcf.gz", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-50/call-run_sawfish/out/m84036_250809_035451_s4.bc2147.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-50/call-run_sawfish/out/m84036_250809_035451_s4.bc2147_sawfish/m84036_250809_035451_s4.bc2147.sv.vcf.gz.tbi", "minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-50/call-run_sawfish/out/m84036_250809_035451_s4.bc2147.minimap2.bam.bai"}
2025-09-15 20:26:02.440 wdl.w:ptcp.w:call-paraphase-83.t:call-run_paraphase NOTICE task setup :: name: "run_paraphase", source: "./paraphase.wdl", line: 127, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-83/call-run_paraphase", thread: 140608228288064
2025-09-15 20:26:02.458 wdl.w:ptcp.w:call-trgt-88.t:call-get_reads_overlapping_repeats INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 9, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-88/call-get_reads_overlapping_repeats/_singularity_tmpdir_pyik56mf"
2025-09-15 20:26:02.458 wdl.w:ptcp.w:call-trgt-88.t:call-get_reads_overlapping_repeats INFO Slurm invocation: srun --job-name call-get_reads_overlapping_repeats --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-88/call-get_reads_overlapping_repeats/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-88/call-get_reads_overlapping_repeats/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-88/call-get_reads_overlapping_repeats/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-88/call-get_reads_overlapping_repeats/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-88/out/m84036_250809_035451_s4.bc2185.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2185.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-88/out/m84036_250809_035451_s4.bc2185.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2185.mapped.bam:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-88/call-get_reads_overlapping_repeats/_singularity_tmpdir_pyik56mf/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-88/call-get_reads_overlapping_repeats/_singularity_tmpdir_pyik56mf/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:26:02.466 wdl.w:ptcp.w:call-sawfish-88.t:call-run_sawfish NOTICE slurm_singularity run :: pid: 1206859, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-88/call-run_sawfish/slurm_singularity.log.txt"
2025-09-15 20:26:02.470 wdl.w:ptcp.w:call-trgt-88.t:call-get_reads_overlapping_repeats NOTICE slurm_singularity run :: pid: 1206860, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-88/call-get_reads_overlapping_repeats/slurm_singularity.log.txt"
2025-09-15 20:26:02.471 wdl.w:ptcp.w:call-paraphase-83.t:call-run_paraphase INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:26:02.472 wdl.w:ptcp.w:call-paraphase-83.t:call-run_paraphase INFO input :: name: "annotation_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf"
2025-09-15 20:26:02.472 wdl.w:ptcp.w:call-paraphase-83.t:call-run_paraphase INFO input :: name: "genome_version", value: "38"
2025-09-15 20:26:02.472 wdl.w:ptcp.w:call-paraphase-83.t:call-run_paraphase INFO input :: name: "config_file", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/paraphase_config.GRCh38.yaml"
2025-09-15 20:26:02.472 wdl.w:ptcp.w:call-paraphase-83.t:call-run_paraphase INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:26:02.472 wdl.w:ptcp.w:call-paraphase-83.t:call-run_paraphase INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:26:02.472 wdl.w:ptcp.w:call-paraphase-83.t:call-run_paraphase INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2180.mapped.bam.bai"
2025-09-15 20:26:02.472 wdl.w:ptcp.w:call-paraphase-83.t:call-run_paraphase INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2180.mapped.bam"
2025-09-15 20:26:02.472 wdl.w:ptcp.w:call-paraphase-83.t:call-run_paraphase INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2180"
2025-09-15 20:26:02.472 wdl.w:ptcp.w:call-paraphase-83.t:call-run_paraphase INFO eval :: name: "threads", value: 4
2025-09-15 20:26:02.472 wdl.w:ptcp.w:call-paraphase-83.t:call-run_paraphase INFO eval :: name: "mem_gb", value: 8
2025-09-15 20:26:02.473 wdl.w:ptcp.w:call-paraphase-83.t:call-run_paraphase INFO eval :: name: "disk_size", value: 27
2025-09-15 20:26:02.473 wdl.w:ptcp.w:call-paraphase-83.t:call-run_paraphase INFO eval :: name: "out_dir", value: "m84036_250809_035451_s4.bc2180_paraphase"
2025-09-15 20:26:02.473 wdl.w:ptcp.w:call-paraphase-83.t:call-run_paraphase INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 4, memory_reservation: 8000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:26:02.473 wdl.w:ptcp.w:call-paraphase-83.t:call-run_paraphase WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:26:02.474 wdl.w:ptcp.w:call-paraphase-83.t:call-run_paraphase INFO provisioned :: seconds_waited: 0, cpu: 4, mem_bytes: 8000000000
2025-09-15 20:26:02.474 wdl.w:ptcp.w:call-paraphase-83.t:call-run_paraphase INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:26:02.482 wdl.w:ptcp.w:call-paraphase-87.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for smn1 for sample m84036_250809_035451_s4.bc2184 at 2025-09-15 20:25:40.507892...
2025-09-15 20:26:02.484 wdl.w:ptcp.w:call-paraphase-87.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for hba for sample m84036_250809_035451_s4.bc2184 at 2025-09-15 20:25:41.243262...
2025-09-15 20:26:02.484 wdl.w:ptcp.w:call-paraphase-87.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for gba for sample m84036_250809_035451_s4.bc2184 at 2025-09-15 20:25:42.362952...
2025-09-15 20:26:02.484 wdl.w:ptcp.w:call-paraphase-87.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for cyp21 for sample m84036_250809_035451_s4.bc2184 at 2025-09-15 20:25:43.870352...
2025-09-15 20:26:02.484 wdl.w:ptcp.w:call-paraphase-87.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for smn1 for sample m84036_250809_035451_s4.bc2184 at 2025-09-15 20:25:53.529815...
2025-09-15 20:26:02.484 wdl.w:ptcp.w:call-paraphase-87.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning to gene2 region for smn1 for sample m84036_250809_035451_s4.bc2184 at 2025-09-15 20:25:53.901253...
2025-09-15 20:26:02.488 wdl.w:ptcp.w:call-trgt-88.t:call-trgt_genotype INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 11, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-88/call-trgt_genotype/_singularity_tmpdir_42td2v_h"
2025-09-15 20:26:02.488 wdl.w:ptcp.w:call-trgt-88.t:call-trgt_genotype INFO Slurm invocation: srun --job-name call-trgt_genotype --partition compute,compute9 --cpus-per-task 8 --mem 15259M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-88/call-trgt_genotype/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-88/call-trgt_genotype/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-88/call-trgt_genotype/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-88/call-trgt_genotype/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-88/out/m84036_250809_035451_s4.bc2185.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2185.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-88/out/m84036_250809_035451_s4.bc2185.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2185.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-88/call-trgt_genotype/_singularity_tmpdir_42td2v_h/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-88/call-trgt_genotype/_singularity_tmpdir_42td2v_h/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:26:02.494 wdl.w:ptcp.w:call-sawfish-50 NOTICE done
2025-09-15 20:26:02.499 wdl.w:ptcp NOTICE finish :: job: "call-sawfish-50"
2025-09-15 20:26:02.499 wdl.w:ptcp INFO output :: job: "call-sawfish-50", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-50/out/m84036_250809_035451_s4.bc2147_sawfish/m84036_250809_035451_s4.bc2147.sv.vcf.gz", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-50/out/m84036_250809_035451_s4.bc2147.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-50/out/m84036_250809_035451_s4.bc2147_sawfish/m84036_250809_035451_s4.bc2147.sv.vcf.gz.tbi", "minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-50/out/m84036_250809_035451_s4.bc2147.minimap2.bam.bai"}
2025-09-15 20:26:02.507 wdl.w:ptcp.w:call-trgt-88.t:call-trgt_genotype NOTICE slurm_singularity run :: pid: 1206863, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-88/call-trgt_genotype/slurm_singularity.log.txt"
2025-09-15 20:26:02.555 wdl.w:ptcp.w:call-paraphase-83.t:call-run_paraphase INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-83/call-run_paraphase/_singularity_tmpdir_f43f1bq1"
2025-09-15 20:26:02.555 wdl.w:ptcp.w:call-paraphase-83.t:call-run_paraphase INFO Slurm invocation: srun --job-name call-run_paraphase --partition compute,compute9 --cpus-per-task 4 --mem 7629M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-83/call-run_paraphase/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-83/call-run_paraphase/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-83/call-run_paraphase/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-83/call-run_paraphase/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/variant_list/variant_list.GRCh38.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-83/out/m84036_250809_035451_s4.bc2180.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2180.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-83/out/m84036_250809_035451_s4.bc2180.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2180.mapped.bam.bai:ro --bind /ptcp/meta/paraphase/paraphase_config.GRCh38.yaml:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/paraphase_config.GRCh38.yaml:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-83/call-run_paraphase/_singularity_tmpdir_f43f1bq1/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-83/call-run_paraphase/_singularity_tmpdir_f43f1bq1/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:26:02.557 wdl.w:ptcp.w:call-paraphase-43.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for rpgr for sample m84036_250809_035451_s4.bc2140 at 2025-09-15 20:25:58.202916...
2025-09-15 20:26:02.558 wdl.w:ptcp.w:call-paraphase-43.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for rpgr for sample m84036_250809_035451_s4.bc2140 at 2025-09-15 20:25:58.203087...
2025-09-15 20:26:02.567 wdl.w:ptcp.w:call-paraphase-83.t:call-run_paraphase NOTICE slurm_singularity run :: pid: 1206865, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-83/call-run_paraphase/slurm_singularity.log.txt"
2025-09-15 20:26:02.653 wdl.w:ptcp.w:call-paraphase-23.t:call-call_f8.slurm_singularity INFO srun: job 51798123 queued and waiting for resources
2025-09-15 20:26:02.653 wdl.w:ptcp.w:call-paraphase-23.t:call-call_f8.slurm_singularity INFO srun: job 51798123 has been allocated resources
2025-09-15 20:26:02.654 wdl.w:ptcp.w:call-paraphase-23.t:call-call_f8.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:26:02.711 wdl.w:ptcp.w:call-trgt-86.t:call-get_reads_overlapping_repeats.slurm_singularity INFO srun: job 51798124 queued and waiting for resources
2025-09-15 20:26:02.711 wdl.w:ptcp.w:call-trgt-86.t:call-get_reads_overlapping_repeats.slurm_singularity INFO srun: job 51798124 has been allocated resources
2025-09-15 20:26:02.711 wdl.w:ptcp.w:call-trgt-86.t:call-get_reads_overlapping_repeats.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:26:02.724 wdl.w:ptcp.w:call-sawfish-58.t:call-run_sawfish INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2155_sawfish/m84036_250809_035451_s4.bc2155.sv.vcf.gz"
2025-09-15 20:26:02.729 wdl.w:ptcp.w:call-sawfish-58.t:call-run_sawfish INFO output :: name: "vcf_tbi", value: "m84036_250809_035451_s4.bc2155_sawfish/m84036_250809_035451_s4.bc2155.sv.vcf.gz.tbi"
2025-09-15 20:26:02.730 wdl.w:ptcp.w:call-sawfish-58.t:call-run_sawfish INFO output :: name: "minimap2_bam", value: "m84036_250809_035451_s4.bc2155.minimap2.bam"
2025-09-15 20:26:02.731 wdl.w:ptcp.w:call-sawfish-58.t:call-run_sawfish INFO output :: name: "minimap2_bam_bai", value: "m84036_250809_035451_s4.bc2155.minimap2.bam.bai"
2025-09-15 20:26:02.844 wdl.w:ptcp.w:call-sawfish-58.t:call-run_sawfish NOTICE done
2025-09-15 20:26:02.909 wdl.w:ptcp.w:call-paraphase-23.t:call-call_f8 INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2120.f8inversion.vcf"
2025-09-15 20:26:02.912 wdl.w:ptcp.w:call-paraphase-23.t:call-call_f8 INFO output :: name: "json", value: "m84036_250809_035451_s4.bc2120.f8inversion.json"
2025-09-15 20:26:02.915 wdl.w:ptcp.w:call-sawfish-58 NOTICE finish :: job: "call-run_sawfish"
2025-09-15 20:26:02.915 wdl.w:ptcp.w:call-sawfish-58 INFO output :: job: "call-run_sawfish", values: {"minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-58/call-run_sawfish/out/m84036_250809_035451_s4.bc2155.minimap2.bam.bai", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-58/call-run_sawfish/out/m84036_250809_035451_s4.bc2155.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-58/call-run_sawfish/out/m84036_250809_035451_s4.bc2155_sawfish/m84036_250809_035451_s4.bc2155.sv.vcf.gz.tbi", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-58/call-run_sawfish/out/m84036_250809_035451_s4.bc2155_sawfish/m84036_250809_035451_s4.bc2155.sv.vcf.gz"}
2025-09-15 20:26:02.916 wdl.w:ptcp.w:call-sawfish-58 INFO visit :: node: "output-minimap2_bam", values: {"minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-58/call-run_sawfish/out/m84036_250809_035451_s4.bc2155.minimap2.bam"}
2025-09-15 20:26:02.916 wdl.w:ptcp.w:call-sawfish-58 INFO visit :: node: "output-minimap2_bam_bai", values: {"minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-58/call-run_sawfish/out/m84036_250809_035451_s4.bc2155.minimap2.bam.bai"}
2025-09-15 20:26:02.916 wdl.w:ptcp.w:call-sawfish-58 INFO visit :: node: "output-vcf", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-58/call-run_sawfish/out/m84036_250809_035451_s4.bc2155_sawfish/m84036_250809_035451_s4.bc2155.sv.vcf.gz"}
2025-09-15 20:26:02.916 wdl.w:ptcp.w:call-sawfish-58 INFO visit :: node: "output-vcf_tbi", values: {"vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-58/call-run_sawfish/out/m84036_250809_035451_s4.bc2155_sawfish/m84036_250809_035451_s4.bc2155.sv.vcf.gz.tbi"}
2025-09-15 20:26:02.916 wdl.w:ptcp.w:call-sawfish-58 INFO visit :: node: "outputs", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-58/call-run_sawfish/out/m84036_250809_035451_s4.bc2155_sawfish/m84036_250809_035451_s4.bc2155.sv.vcf.gz", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-58/call-run_sawfish/out/m84036_250809_035451_s4.bc2155.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-58/call-run_sawfish/out/m84036_250809_035451_s4.bc2155_sawfish/m84036_250809_035451_s4.bc2155.sv.vcf.gz.tbi", "minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-58/call-run_sawfish/out/m84036_250809_035451_s4.bc2155.minimap2.bam.bai"}
2025-09-15 20:26:02.927 wdl.w:ptcp.w:call-trgt-89.t:call-trgt_plot_meth_allele NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-89/call-trgt_plot_meth_allele", thread: 140611449513536
2025-09-15 20:26:02.949 wdl.w:ptcp.w:call-trgt-89.t:call-trgt_plot_meth_allele INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:26:02.949 wdl.w:ptcp.w:call-trgt-89.t:call-trgt_plot_meth_allele INFO input :: name: "waterfall", value: false
2025-09-15 20:26:02.950 wdl.w:ptcp.w:call-trgt-89.t:call-trgt_plot_meth_allele INFO input :: name: "methylation", value: true
2025-09-15 20:26:02.950 wdl.w:ptcp.w:call-trgt-89.t:call-trgt_plot_meth_allele INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:26:02.950 wdl.w:ptcp.w:call-trgt-89.t:call-trgt_plot_meth_allele INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:26:02.950 wdl.w:ptcp.w:call-trgt-89.t:call-trgt_plot_meth_allele INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:26:02.950 wdl.w:ptcp.w:call-trgt-89.t:call-trgt_plot_meth_allele INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2186.trgt.sorted.spanning.bam.bai"
2025-09-15 20:26:02.950 wdl.w:ptcp.w:call-trgt-89.t:call-trgt_plot_meth_allele INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2186.trgt.sorted.spanning.bam"
2025-09-15 20:26:02.950 wdl.w:ptcp.w:call-trgt-89.t:call-trgt_plot_meth_allele INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2186.trgt.vcf"
2025-09-15 20:26:02.950 wdl.w:ptcp.w:call-trgt-89.t:call-trgt_plot_meth_allele INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2186"
2025-09-15 20:26:02.950 wdl.w:ptcp.w:call-trgt-89.t:call-trgt_plot_meth_allele INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:26:02.951 wdl.w:ptcp.w:call-trgt-89.t:call-trgt_plot_meth_allele INFO eval :: name: "plot_type", value: "allele"
2025-09-15 20:26:02.951 wdl.w:ptcp.w:call-trgt-89.t:call-trgt_plot_meth_allele INFO eval :: name: "show", value: "meth"
2025-09-15 20:26:02.951 wdl.w:ptcp.w:call-trgt-89.t:call-trgt_plot_meth_allele INFO eval :: name: "threads", value: 1
2025-09-15 20:26:02.951 wdl.w:ptcp.w:call-trgt-89.t:call-trgt_plot_meth_allele INFO eval :: name: "disk_size", value: 27
2025-09-15 20:26:02.951 wdl.w:ptcp.w:call-trgt-89.t:call-trgt_plot_meth_allele INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2186.meth_allele"
2025-09-15 20:26:02.951 wdl.w:ptcp.w:call-trgt-89.t:call-trgt_plot_meth_allele INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:26:02.952 wdl.w:ptcp.w:call-trgt-89.t:call-trgt_plot_meth_allele WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:26:02.952 wdl.w:ptcp.w:call-trgt-89.t:call-trgt_plot_meth_allele INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:26:02.952 wdl.w:ptcp.w:call-trgt-89.t:call-trgt_plot_meth_allele INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:26:02.967 wdl.w:ptcp.w:call-sawfish-58 NOTICE done
2025-09-15 20:26:02.974 wdl.w:ptcp NOTICE finish :: job: "call-sawfish-58"
2025-09-15 20:26:02.974 wdl.w:ptcp INFO output :: job: "call-sawfish-58", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-58/out/m84036_250809_035451_s4.bc2155_sawfish/m84036_250809_035451_s4.bc2155.sv.vcf.gz", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-58/out/m84036_250809_035451_s4.bc2155.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-58/out/m84036_250809_035451_s4.bc2155_sawfish/m84036_250809_035451_s4.bc2155.sv.vcf.gz.tbi", "minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-58/out/m84036_250809_035451_s4.bc2155.minimap2.bam.bai"}
2025-09-15 20:26:03.001 wdl.w:ptcp.w:call-paraphase-23.t:call-call_f8 NOTICE done
2025-09-15 20:26:03.007 wdl.w:ptcp.w:call-paraphase-23 NOTICE finish :: job: "call-call_f8"
2025-09-15 20:26:03.007 wdl.w:ptcp.w:call-paraphase-23 INFO output :: job: "call-call_f8", values: {"json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-23/call-call_f8/out/m84036_250809_035451_s4.bc2120.f8inversion.json", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-23/call-call_f8/out/m84036_250809_035451_s4.bc2120.f8inversion.vcf"}
2025-09-15 20:26:03.007 wdl.w:ptcp.w:call-paraphase-23 INFO visit :: node: "output-f8_json", values: {"f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-23/call-call_f8/out/m84036_250809_035451_s4.bc2120.f8inversion.json"}
2025-09-15 20:26:03.008 wdl.w:ptcp.w:call-paraphase-23 INFO visit :: node: "output-f8_vcf", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-23/call-call_f8/out/m84036_250809_035451_s4.bc2120.f8inversion.vcf"}
2025-09-15 20:26:03.008 wdl.w:ptcp.w:call-paraphase-23 INFO visit :: node: "outputs", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-23/call-call_f8/out/m84036_250809_035451_s4.bc2120.f8inversion.vcf", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-23/call-run_paraphase/out/m84036_250809_035451_s4.bc2120_paraphase/m84036_250809_035451_s4.bc2120.paraphase.json", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-23/call-run_paraphase/out/m84036_250809_035451_s4.bc2120_paraphase/m84036_250809_035451_s4.bc2120.paraphase.bam", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-23/call-run_paraphase/out/m84036_250809_035451_s4.bc2120_paraphase/m84036_250809_035451_s4.bc2120.paraphase.bam.bai", "paraphase_vcfs": ["/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-23/call-run_paraphase/out/m84036_250809_035451_s4.bc2120_paraphase/m84036_250809_035451_s4.bc2120_paraphase_vcfs/m84036_250809_035451_s4.bc2120_cyp21.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-23/call-run_paraphase/out/m84036_250809_035451_s4.bc2120_paraphase/m84036_250809_035451_s4.bc2120_paraphase_vcfs/m84036_250809_035451_s4.bc2120_f8inv1.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-23/call-run_paraphase/out/m84036_250809_035451_s4.bc2120_paraphase/m84036_250809_035451_s4.bc2120_paraphase_vcfs/m84036_250809_035451_s4.bc2120_f8inv22.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-23/call-run_paraphase/out/m84036_250809_035451_s4.bc2120_paraphase/m84036_250809_035451_s4.bc2120_paraphase_vcfs/m84036_250809_035451_s4.bc2120_gba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-23/call-run_paraphase/out/m84036_250809_035451_s4.bc2120_paraphase/m84036_250809_035451_s4.bc2120_paraphase_vcfs/m84036_250809_035451_s4.bc2120_hba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-23/call-run_paraphase/out/m84036_250809_035451_s4.bc2120_paraphase/m84036_250809_035451_s4.bc2120_paraphase_vcfs/m84036_250809_035451_s4.bc2120_hbb.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-23/call-run_paraphase/out/m84036_250809_035451_s4.bc2120_paraphase/m84036_250809_035451_s4.bc2120_paraphase_vcfs/m84036_250809_035451_s4.bc2120_rpgr.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-23/call-run_paraphase/out/m84036_250809_035451_s4.bc2120_paraphase/m84036_250809_035451_s4.bc2120_paraphase_vcfs/m84036_250809_035451_s4.bc2120_smn1.vcf"], "havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-23/call-run_paraphase/out/m84036_250809_035451_s4.bc2120.havanno.json", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-23/call-call_f8/out/m84036_250809_035451_s4.bc2120.f8inversion.json"}
2025-09-15 20:26:03.014 wdl.w:ptcp.w:call-trgt-89.t:call-trgt_plot_meth_waterfall NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-89/call-trgt_plot_meth_waterfall", thread: 140611969599040
2025-09-15 20:26:03.022 wdl.w:ptcp.w:call-trgt-86.t:call-trgt_genotype.slurm_singularity INFO srun: job 51798125 queued and waiting for resources
2025-09-15 20:26:03.022 wdl.w:ptcp.w:call-trgt-86.t:call-trgt_genotype.slurm_singularity INFO srun: job 51798125 has been allocated resources
2025-09-15 20:26:03.022 wdl.w:ptcp.w:call-trgt-86.t:call-trgt_genotype.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:26:03.035 wdl.w:ptcp.w:call-trgt-89.t:call-trgt_plot_meth_waterfall INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:26:03.035 wdl.w:ptcp.w:call-trgt-89.t:call-trgt_plot_meth_waterfall INFO input :: name: "waterfall", value: true
2025-09-15 20:26:03.035 wdl.w:ptcp.w:call-trgt-89.t:call-trgt_plot_meth_waterfall INFO input :: name: "methylation", value: true
2025-09-15 20:26:03.035 wdl.w:ptcp.w:call-trgt-89.t:call-trgt_plot_meth_waterfall INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:26:03.035 wdl.w:ptcp.w:call-trgt-89.t:call-trgt_plot_meth_waterfall INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:26:03.035 wdl.w:ptcp.w:call-trgt-89.t:call-trgt_plot_meth_waterfall INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:26:03.035 wdl.w:ptcp.w:call-trgt-89.t:call-trgt_plot_meth_waterfall INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2186.trgt.sorted.spanning.bam.bai"
2025-09-15 20:26:03.035 wdl.w:ptcp.w:call-trgt-89.t:call-trgt_plot_meth_waterfall INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2186.trgt.sorted.spanning.bam"
2025-09-15 20:26:03.035 wdl.w:ptcp.w:call-trgt-89.t:call-trgt_plot_meth_waterfall INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2186.trgt.vcf"
2025-09-15 20:26:03.035 wdl.w:ptcp.w:call-trgt-89.t:call-trgt_plot_meth_waterfall INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2186"
2025-09-15 20:26:03.036 wdl.w:ptcp.w:call-trgt-89.t:call-trgt_plot_meth_waterfall INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:26:03.036 wdl.w:ptcp.w:call-trgt-89.t:call-trgt_plot_meth_waterfall INFO eval :: name: "plot_type", value: "waterfall"
2025-09-15 20:26:03.036 wdl.w:ptcp.w:call-trgt-89.t:call-trgt_plot_meth_waterfall INFO eval :: name: "show", value: "meth"
2025-09-15 20:26:03.036 wdl.w:ptcp.w:call-trgt-89.t:call-trgt_plot_meth_waterfall INFO eval :: name: "threads", value: 1
2025-09-15 20:26:03.036 wdl.w:ptcp.w:call-trgt-89.t:call-trgt_plot_meth_waterfall INFO eval :: name: "disk_size", value: 27
2025-09-15 20:26:03.036 wdl.w:ptcp.w:call-trgt-89.t:call-trgt_plot_meth_waterfall INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2186.meth_waterfall"
2025-09-15 20:26:03.037 wdl.w:ptcp.w:call-trgt-89.t:call-trgt_plot_meth_waterfall INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:26:03.037 wdl.w:ptcp.w:call-trgt-89.t:call-trgt_plot_meth_waterfall WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:26:03.037 wdl.w:ptcp.w:call-trgt-89.t:call-trgt_plot_meth_waterfall INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:26:03.038 wdl.w:ptcp.w:call-trgt-89.t:call-trgt_plot_meth_waterfall INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:26:03.042 wdl.w:ptcp.w:call-trgt-89.t:call-trgt_plot_meth_allele INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-89/call-trgt_plot_meth_allele/_singularity_tmpdir_icyqfb7e"
2025-09-15 20:26:03.043 wdl.w:ptcp.w:call-trgt-89.t:call-trgt_plot_meth_allele INFO Slurm invocation: srun --job-name call-trgt_plot_meth_allele --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-89/call-trgt_plot_meth_allele/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-89/call-trgt_plot_meth_allele/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-89/call-trgt_plot_meth_allele/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-89/call-trgt_plot_meth_allele/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-89/call-trgt_genotype/out/m84036_250809_035451_s4.bc2186.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2186.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-89/call-trgt_genotype/out/m84036_250809_035451_s4.bc2186.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2186.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-89/call-trgt_genotype/out/m84036_250809_035451_s4.bc2186.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2186.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-89/call-trgt_plot_meth_allele/_singularity_tmpdir_icyqfb7e/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-89/call-trgt_plot_meth_allele/_singularity_tmpdir_icyqfb7e/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:26:03.065 wdl.w:ptcp.w:call-trgt-89.t:call-trgt_plot_meth_allele NOTICE slurm_singularity run :: pid: 1206889, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-89/call-trgt_plot_meth_allele/slurm_singularity.log.txt"
2025-09-15 20:26:03.098 wdl.w:ptcp.w:call-trgt-92.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:26:02 [ERROR] - No reads found for TRID=PRTS_ARX
2025-09-15 20:26:03.098 wdl.w:ptcp.w:call-trgt-92.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:26:02 [ERROR] - No reads found for TRID=EIEE1_ARX
2025-09-15 20:26:03.097 wdl.w:ptcp.w:call-paraphase-54.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for rpgr for sample m84036_250809_035451_s4.bc2151 at 2025-09-15 20:25:39.233568...
2025-09-15 20:26:03.099 wdl.w:ptcp.w:call-paraphase-54.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for rpgr for sample m84036_250809_035451_s4.bc2151 at 2025-09-15 20:25:39.233736...
2025-09-15 20:26:03.106 wdl.w:ptcp.w:call-trgt-89.t:call-trgt_plot_meth_waterfall INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-89/call-trgt_plot_meth_waterfall/_singularity_tmpdir_koavevn8"
2025-09-15 20:26:03.106 wdl.w:ptcp.w:call-trgt-89.t:call-trgt_plot_meth_waterfall INFO Slurm invocation: srun --job-name call-trgt_plot_meth_waterfall --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-89/call-trgt_plot_meth_waterfall/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-89/call-trgt_plot_meth_waterfall/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-89/call-trgt_plot_meth_waterfall/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-89/call-trgt_plot_meth_waterfall/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-89/call-trgt_genotype/out/m84036_250809_035451_s4.bc2186.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2186.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-89/call-trgt_genotype/out/m84036_250809_035451_s4.bc2186.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2186.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-89/call-trgt_genotype/out/m84036_250809_035451_s4.bc2186.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2186.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-89/call-trgt_plot_meth_waterfall/_singularity_tmpdir_koavevn8/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-89/call-trgt_plot_meth_waterfall/_singularity_tmpdir_koavevn8/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:26:03.120 wdl.w:ptcp.w:call-trgt-89.t:call-trgt_plot_meth_waterfall NOTICE slurm_singularity run :: pid: 1206892, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-89/call-trgt_plot_meth_waterfall/slurm_singularity.log.txt"
2025-09-15 20:26:03.143 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_motifs_waterfall INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2188.motifs_waterfall.trgt_plots.zip"
2025-09-15 20:26:03.167 wdl.w:ptcp.w:call-paraphase-23 NOTICE done
2025-09-15 20:26:03.177 wdl.w:ptcp NOTICE finish :: job: "call-paraphase-23"
2025-09-15 20:26:03.177 wdl.w:ptcp INFO output :: job: "call-paraphase-23", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-23/out/m84036_250809_035451_s4.bc2120.f8inversion.vcf", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-23/out/m84036_250809_035451_s4.bc2120_paraphase/m84036_250809_035451_s4.bc2120.paraphase.json", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-23/out/m84036_250809_035451_s4.bc2120_paraphase/m84036_250809_035451_s4.bc2120.paraphase.bam", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-23/out/m84036_250809_035451_s4.bc2120_paraphase/m84036_250809_035451_s4.bc2120.paraphase.bam.bai", "paraphase_vcfs": ["/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-23/out/m84036_250809_035451_s4.bc2120_paraphase/m84036_250809_035451_s4.bc2120_paraphase_vcfs/m84036_250809_035451_s4.bc2120_cyp21.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-23/out/m84036_250809_035451_s4.bc2120_paraphase/m84036_250809_035451_s4.bc2120_paraphase_vcfs/m84036_250809_035451_s4.bc2120_f8inv1.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-23/out/m84036_250809_035451_s4.bc2120_paraphase/m84036_250809_035451_s4.bc2120_paraphase_vcfs/m84036_250809_035451_s4.bc2120_f8inv22.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-23/out/m84036_250809_035451_s4.bc2120_paraphase/m84036_250809_035451_s4.bc2120_paraphase_vcfs/m84036_250809_035451_s4.bc2120_gba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-23/out/m84036_250809_035451_s4.bc2120_paraphase/m84036_250809_035451_s4.bc2120_paraphase_vcfs/m84036_250809_035451_s4.bc2120_hba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-23/out/m84036_250809_035451_s4.bc2120_paraphase/m84036_250809_035451_s4.bc2120_paraphase_vcfs/m84036_250809_035451_s4.bc2120_hbb.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-23/out/m84036_250809_035451_s4.bc2120_paraphase/m84036_250809_035451_s4.bc2120_paraphase_vcfs/m84036_250809_035451_s4.bc2120_rpgr.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-23/out/m84036_250809_035451_s4.bc2120_paraphase/m84036_250809_035451_s4.bc2120_paraphase_vcfs/m84036_250809_035451_s4.bc2120_smn1.vcf"], "havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-23/out/m84036_250809_035451_s4.bc2120.havanno.json", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-23/out/m84036_250809_035451_s4.bc2120.f8inversion.json"}
2025-09-15 20:26:03.178 wdl.w:ptcp NOTICE ready :: job: "call-tar_outputs-23", callee: "tar_outputs"
2025-09-15 20:26:03.178 wdl.w:ptcp INFO input :: job: "call-tar_outputs-23", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "sawfish_vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-23/out/m84036_250809_035451_s4.bc2120_sawfish/m84036_250809_035451_s4.bc2120.sv.vcf.gz.tbi", "sawfish_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-23/out/m84036_250809_035451_s4.bc2120_sawfish/m84036_250809_035451_s4.bc2120.sv.vcf.gz", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-23/out/m84036_250809_035451_s4.bc2120.f8inversion.json", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-23/out/m84036_250809_035451_s4.bc2120_paraphase/m84036_250809_035451_s4.bc2120.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-23/out/m84036_250809_035451_s4.bc2120_paraphase/m84036_250809_035451_s4.bc2120.paraphase.bam", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-23/out/m84036_250809_035451_s4.bc2120_paraphase/m84036_250809_035451_s4.bc2120.paraphase.json", "trgt_spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-23/out/m84036_250809_035451_s4.bc2120.trgt.sorted.spanning.bam.bai", "trgt_spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-23/out/m84036_250809_035451_s4.bc2120.trgt.sorted.spanning.bam", "trgt_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-23/out/m84036_250809_035451_s4.bc2120.trgt.vcf", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-23/out/m84036_250809_035451_s4.bc2120.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-23/out/m84036_250809_035451_s4.bc2120.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2120"}
2025-09-15 20:26:03.180 wdl.w:ptcp.w:call-trgt-86.t:call-get_reads_overlapping_repeats INFO output :: name: "reads_overlapping_repeats", value: "m84036_250809_035451_s4.bc2183.repeats.bam"
2025-09-15 20:26:03.184 wdl.w:ptcp.w:call-trgt-86.t:call-get_reads_overlapping_repeats INFO output :: name: "reads_overlapping_repeats_bai", value: "m84036_250809_035451_s4.bc2183.repeats.bam.bai"
2025-09-15 20:26:03.198 wdl.w:ptcp.w:call-paraphase-85.t:call-call_f8.slurm_singularity INFO srun: job 51798126 queued and waiting for resources
2025-09-15 20:26:03.199 wdl.w:ptcp.w:call-paraphase-85.t:call-call_f8.slurm_singularity INFO srun: job 51798126 has been allocated resources
2025-09-15 20:26:03.199 wdl.w:ptcp.w:call-paraphase-85.t:call-call_f8.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:26:03.200 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_plot_motifs_allele INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2184.motifs_allele.trgt_plots.zip"
2025-09-15 20:26:03.200 wdl.w:ptcp.w:call-paraphase-88.t:call-run_paraphase.slurm_singularity INFO srun: job 51798127 queued and waiting for resources
2025-09-15 20:26:03.201 wdl.w:ptcp.w:call-paraphase-88.t:call-run_paraphase.slurm_singularity INFO srun: job 51798127 has been allocated resources
2025-09-15 20:26:03.201 wdl.w:ptcp.w:call-paraphase-88.t:call-run_paraphase.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:26:03.236 wdl.w:ptcp.w:call-trgt-91.t:call-trgt_plot_motifs_waterfall NOTICE done
2025-09-15 20:26:03.243 wdl.w:ptcp.w:call-trgt-91 NOTICE finish :: job: "call-trgt_plot_motifs_waterfall"
2025-09-15 20:26:03.243 wdl.w:ptcp.w:call-trgt-91 INFO output :: job: "call-trgt_plot_motifs_waterfall", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-91/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2188.motifs_waterfall.trgt_plots.zip"}
2025-09-15 20:26:03.243 wdl.w:ptcp.w:call-trgt-91 INFO visit :: node: "output-images_motifs_waterfall", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-91/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2188.motifs_waterfall.trgt_plots.zip"}
2025-09-15 20:26:03.244 wdl.w:ptcp.w:call-trgt-91 INFO visit :: node: "outputs", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-91/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2188.motifs_waterfall.trgt_plots.zip", "images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-91/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2188.meth_allele.trgt_plots.zip", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-91/call-trgt_genotype/out/m84036_250809_035451_s4.bc2188.trgt.sorted.spanning.bam.bai", "images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-91/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2188.motifs_allele.trgt_plots.zip", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-91/call-trgt_genotype/out/m84036_250809_035451_s4.bc2188.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-91/call-trgt_genotype/out/m84036_250809_035451_s4.bc2188.trgt.vcf", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-91/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2188.repeats.bam", "images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-91/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2188.meth_waterfall.trgt_plots.zip", "reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-91/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2188.repeats.bam.bai"}
2025-09-15 20:26:03.250 wdl.w:ptcp.w:call-trgt-89.t:call-trgt_plot_motifs_allele NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-89/call-trgt_plot_motifs_allele", thread: 140606575711808
2025-09-15 20:26:03.257 wdl.w:ptcp.w:call-trgt-86.t:call-get_reads_overlapping_repeats NOTICE done
2025-09-15 20:26:03.263 wdl.w:ptcp.w:call-trgt-86 NOTICE finish :: job: "call-get_reads_overlapping_repeats"
2025-09-15 20:26:03.264 wdl.w:ptcp.w:call-trgt-86 INFO output :: job: "call-get_reads_overlapping_repeats", values: {"reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-86/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2183.repeats.bam.bai", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-86/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2183.repeats.bam"}
2025-09-15 20:26:03.264 wdl.w:ptcp.w:call-trgt-86 INFO visit :: node: "output-reads_overlapping_repeats", values: {"reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-86/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2183.repeats.bam"}
2025-09-15 20:26:03.264 wdl.w:ptcp.w:call-trgt-86 INFO visit :: node: "output-reads_overlapping_repeats_bai", values: {"reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-86/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2183.repeats.bam.bai"}
2025-09-15 20:26:03.273 wdl.w:ptcp.w:call-trgt-89.t:call-trgt_plot_motifs_waterfall NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-89/call-trgt_plot_motifs_waterfall", thread: 140607120975424
2025-09-15 20:26:03.282 wdl.w:ptcp.w:call-trgt-89.t:call-trgt_plot_motifs_allele INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:26:03.282 wdl.w:ptcp.w:call-trgt-89.t:call-trgt_plot_motifs_allele INFO input :: name: "waterfall", value: false
2025-09-15 20:26:03.282 wdl.w:ptcp.w:call-trgt-89.t:call-trgt_plot_motifs_allele INFO input :: name: "methylation", value: false
2025-09-15 20:26:03.282 wdl.w:ptcp.w:call-trgt-89.t:call-trgt_plot_motifs_allele INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:26:03.282 wdl.w:ptcp.w:call-trgt-89.t:call-trgt_plot_motifs_allele INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:26:03.282 wdl.w:ptcp.w:call-trgt-89.t:call-trgt_plot_motifs_allele INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:26:03.283 wdl.w:ptcp.w:call-trgt-89.t:call-trgt_plot_motifs_allele INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2186.trgt.sorted.spanning.bam.bai"
2025-09-15 20:26:03.283 wdl.w:ptcp.w:call-trgt-89.t:call-trgt_plot_motifs_allele INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2186.trgt.sorted.spanning.bam"
2025-09-15 20:26:03.283 wdl.w:ptcp.w:call-trgt-89.t:call-trgt_plot_motifs_allele INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2186.trgt.vcf"
2025-09-15 20:26:03.283 wdl.w:ptcp.w:call-trgt-89.t:call-trgt_plot_motifs_allele INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2186"
2025-09-15 20:26:03.283 wdl.w:ptcp.w:call-trgt-89.t:call-trgt_plot_motifs_allele INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:26:03.283 wdl.w:ptcp.w:call-trgt-89.t:call-trgt_plot_motifs_allele INFO eval :: name: "plot_type", value: "allele"
2025-09-15 20:26:03.283 wdl.w:ptcp.w:call-trgt-89.t:call-trgt_plot_motifs_allele INFO eval :: name: "show", value: "motifs"
2025-09-15 20:26:03.283 wdl.w:ptcp.w:call-trgt-89.t:call-trgt_plot_motifs_allele INFO eval :: name: "threads", value: 1
2025-09-15 20:26:03.284 wdl.w:ptcp.w:call-trgt-89.t:call-trgt_plot_motifs_allele INFO eval :: name: "disk_size", value: 27
2025-09-15 20:26:03.284 wdl.w:ptcp.w:call-trgt-89.t:call-trgt_plot_motifs_allele INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2186.motifs_allele"
2025-09-15 20:26:03.284 wdl.w:ptcp.w:call-trgt-89.t:call-trgt_plot_motifs_allele INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:26:03.285 wdl.w:ptcp.w:call-trgt-89.t:call-trgt_plot_motifs_allele WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:26:03.288 wdl.w:ptcp.w:call-trgt-89.t:call-trgt_plot_motifs_allele INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:26:03.290 wdl.w:ptcp.w:call-trgt-89.t:call-trgt_plot_motifs_allele INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:26:03.295 wdl.w:ptcp.w:call-trgt-89.t:call-trgt_plot_motifs_waterfall INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:26:03.296 wdl.w:ptcp.w:call-trgt-89.t:call-trgt_plot_motifs_waterfall INFO input :: name: "waterfall", value: true
2025-09-15 20:26:03.296 wdl.w:ptcp.w:call-trgt-89.t:call-trgt_plot_motifs_waterfall INFO input :: name: "methylation", value: false
2025-09-15 20:26:03.296 wdl.w:ptcp.w:call-trgt-89.t:call-trgt_plot_motifs_waterfall INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:26:03.296 wdl.w:ptcp.w:call-trgt-89.t:call-trgt_plot_motifs_waterfall INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:26:03.296 wdl.w:ptcp.w:call-trgt-89.t:call-trgt_plot_motifs_waterfall INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:26:03.296 wdl.w:ptcp.w:call-trgt-89.t:call-trgt_plot_motifs_waterfall INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2186.trgt.sorted.spanning.bam.bai"
2025-09-15 20:26:03.296 wdl.w:ptcp.w:call-trgt-89.t:call-trgt_plot_motifs_waterfall INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2186.trgt.sorted.spanning.bam"
2025-09-15 20:26:03.296 wdl.w:ptcp.w:call-trgt-89.t:call-trgt_plot_motifs_waterfall INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2186.trgt.vcf"
2025-09-15 20:26:03.296 wdl.w:ptcp.w:call-trgt-89.t:call-trgt_plot_motifs_waterfall INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2186"
2025-09-15 20:26:03.296 wdl.w:ptcp.w:call-trgt-89.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:26:03.296 wdl.w:ptcp.w:call-trgt-89.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "plot_type", value: "waterfall"
2025-09-15 20:26:03.297 wdl.w:ptcp.w:call-trgt-89.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "show", value: "motifs"
2025-09-15 20:26:03.297 wdl.w:ptcp.w:call-trgt-89.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "threads", value: 1
2025-09-15 20:26:03.297 wdl.w:ptcp.w:call-trgt-89.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "disk_size", value: 27
2025-09-15 20:26:03.297 wdl.w:ptcp.w:call-trgt-89.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2186.motifs_waterfall"
2025-09-15 20:26:03.298 wdl.w:ptcp.w:call-trgt-89.t:call-trgt_plot_motifs_waterfall INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:26:03.298 wdl.w:ptcp.w:call-trgt-89.t:call-trgt_plot_motifs_waterfall WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:26:03.298 wdl.w:ptcp.w:call-trgt-89.t:call-trgt_plot_motifs_waterfall INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:26:03.298 wdl.w:ptcp.w:call-trgt-89.t:call-trgt_plot_motifs_waterfall INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:26:03.311 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_plot_motifs_allele NOTICE done
2025-09-15 20:26:03.315 wdl.w:ptcp.w:call-trgt-87 NOTICE finish :: job: "call-trgt_plot_motifs_allele"
2025-09-15 20:26:03.316 wdl.w:ptcp.w:call-trgt-87 INFO output :: job: "call-trgt_plot_motifs_allele", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-87/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2184.motifs_allele.trgt_plots.zip"}
2025-09-15 20:26:03.316 wdl.w:ptcp.w:call-trgt-87 INFO visit :: node: "output-images_motifs_allele", values: {"images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-87/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2184.motifs_allele.trgt_plots.zip"}
2025-09-15 20:26:03.326 wdl.w:ptcp.w:call-sawfish-83.t:call-run_sawfish NOTICE task setup :: name: "run_sawfish", source: "./sawfish.wdl", line: 83, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-83/call-run_sawfish", thread: 140606609282624
2025-09-15 20:26:03.350 wdl.w:ptcp.w:call-trgt-91 NOTICE done
2025-09-15 20:26:03.356 wdl.w:ptcp.w:call-sawfish-83.t:call-run_sawfish INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:26:03.356 wdl.w:ptcp.w:call-sawfish-83.t:call-run_sawfish INFO input :: name: "genome_version", value: "38"
2025-09-15 20:26:03.356 wdl.w:ptcp.w:call-sawfish-83.t:call-run_sawfish INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:26:03.356 wdl.w:ptcp.w:call-sawfish-83.t:call-run_sawfish INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:26:03.356 wdl.w:ptcp.w:call-sawfish-83.t:call-run_sawfish INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2180.mapped.bam.bai"
2025-09-15 20:26:03.356 wdl.w:ptcp.w:call-sawfish-83.t:call-run_sawfish INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2180.mapped.bam"
2025-09-15 20:26:03.356 wdl.w:ptcp.w:call-sawfish-83.t:call-run_sawfish INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2180"
2025-09-15 20:26:03.356 wdl.w:ptcp.w:call-sawfish-83.t:call-run_sawfish INFO eval :: name: "mem_gb", value: 32
2025-09-15 20:26:03.357 wdl.w:ptcp.w:call-sawfish-83.t:call-run_sawfish INFO eval :: name: "threads", value: 16
2025-09-15 20:26:03.357 wdl.w:ptcp.w:call-sawfish-83.t:call-run_sawfish INFO eval :: name: "disk_size", value: 30
2025-09-15 20:26:03.357 wdl.w:ptcp.w:call-sawfish-83.t:call-run_sawfish INFO eval :: name: "discover_dirname", value: "m84036_250809_035451_s4.bc2180_sawfish_discover"
2025-09-15 20:26:03.357 wdl.w:ptcp.w:call-sawfish-83.t:call-run_sawfish INFO eval :: name: "call_dirname", value: "m84036_250809_035451_s4.bc2180_sawfish"
2025-09-15 20:26:03.357 wdl.w:ptcp.w:call-sawfish-83.t:call-run_sawfish INFO eval :: name: "minimap2_bam_filename", value: "m84036_250809_035451_s4.bc2180.minimap2.bam"
2025-09-15 20:26:03.357 wdl.w:ptcp.w:call-sawfish-83.t:call-run_sawfish INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 16, memory_reservation: 32000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:26:03.357 wdl.w:ptcp.w:call-sawfish-83.t:call-run_sawfish WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:26:03.358 wdl.w:ptcp.w:call-sawfish-83.t:call-run_sawfish INFO provisioned :: seconds_waited: 0, cpu: 16, mem_bytes: 32000000000
2025-09-15 20:26:03.358 wdl.w:ptcp.w:call-sawfish-83.t:call-run_sawfish INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:26:03.367 wdl.w:ptcp NOTICE finish :: job: "call-trgt-91"
2025-09-15 20:26:03.367 wdl.w:ptcp INFO output :: job: "call-trgt-91", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-91/out/m84036_250809_035451_s4.bc2188.motifs_waterfall.trgt_plots.zip", "images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-91/out/m84036_250809_035451_s4.bc2188.meth_allele.trgt_plots.zip", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-91/out/m84036_250809_035451_s4.bc2188.trgt.sorted.spanning.bam.bai", "images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-91/out/m84036_250809_035451_s4.bc2188.motifs_allele.trgt_plots.zip", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-91/out/m84036_250809_035451_s4.bc2188.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-91/out/m84036_250809_035451_s4.bc2188.trgt.vcf", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-91/out/m84036_250809_035451_s4.bc2188.repeats.bam", "images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-91/out/m84036_250809_035451_s4.bc2188.meth_waterfall.trgt_plots.zip", "reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-91/out/m84036_250809_035451_s4.bc2188.repeats.bam.bai"}
2025-09-15 20:26:03.375 wdl.w:ptcp.w:call-trgt-89.t:call-trgt_plot_motifs_allele INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-89/call-trgt_plot_motifs_allele/_singularity_tmpdir_4k9sxj9m"
2025-09-15 20:26:03.375 wdl.w:ptcp.w:call-trgt-89.t:call-trgt_plot_motifs_allele INFO Slurm invocation: srun --job-name call-trgt_plot_motifs_allele --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-89/call-trgt_plot_motifs_allele/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-89/call-trgt_plot_motifs_allele/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-89/call-trgt_plot_motifs_allele/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-89/call-trgt_plot_motifs_allele/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-89/call-trgt_genotype/out/m84036_250809_035451_s4.bc2186.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2186.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-89/call-trgt_genotype/out/m84036_250809_035451_s4.bc2186.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2186.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-89/call-trgt_genotype/out/m84036_250809_035451_s4.bc2186.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2186.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-89/call-trgt_plot_motifs_allele/_singularity_tmpdir_4k9sxj9m/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-89/call-trgt_plot_motifs_allele/_singularity_tmpdir_4k9sxj9m/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:26:03.388 wdl.w:ptcp.w:call-trgt-89.t:call-trgt_plot_motifs_waterfall INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-89/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_cyaa0wep"
2025-09-15 20:26:03.389 wdl.w:ptcp.w:call-trgt-89.t:call-trgt_plot_motifs_waterfall INFO Slurm invocation: srun --job-name call-trgt_plot_motifs_waterfall --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-89/call-trgt_plot_motifs_waterfall/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-89/call-trgt_plot_motifs_waterfall/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-89/call-trgt_plot_motifs_waterfall/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-89/call-trgt_plot_motifs_waterfall/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-89/call-trgt_genotype/out/m84036_250809_035451_s4.bc2186.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2186.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-89/call-trgt_genotype/out/m84036_250809_035451_s4.bc2186.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2186.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-89/call-trgt_genotype/out/m84036_250809_035451_s4.bc2186.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2186.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-89/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_cyaa0wep/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-89/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_cyaa0wep/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:26:03.400 wdl.w:ptcp.w:call-trgt-89.t:call-trgt_plot_motifs_waterfall NOTICE slurm_singularity run :: pid: 1206902, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-89/call-trgt_plot_motifs_waterfall/slurm_singularity.log.txt"
2025-09-15 20:26:03.400 wdl.w:ptcp.w:call-trgt-89.t:call-trgt_plot_motifs_allele NOTICE slurm_singularity run :: pid: 1206901, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-89/call-trgt_plot_motifs_allele/slurm_singularity.log.txt"
2025-09-15 20:26:03.432 wdl.w:ptcp.w:call-sawfish-83.t:call-run_sawfish INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 10, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-83/call-run_sawfish/_singularity_tmpdir_39jaa48n"
2025-09-15 20:26:03.432 wdl.w:ptcp.w:call-sawfish-83.t:call-run_sawfish INFO Slurm invocation: srun --job-name call-run_sawfish --partition compute,compute9 --cpus-per-task 16 --mem 30518M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-83/call-run_sawfish/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-83/call-run_sawfish/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-83/call-run_sawfish/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-83/call-run_sawfish/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-83/out/m84036_250809_035451_s4.bc2180.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2180.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-83/out/m84036_250809_035451_s4.bc2180.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2180.mapped.bam.bai:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-83/call-run_sawfish/_singularity_tmpdir_39jaa48n/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-83/call-run_sawfish/_singularity_tmpdir_39jaa48n/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:26:03.449 wdl.w:ptcp.w:call-sawfish-83.t:call-run_sawfish NOTICE slurm_singularity run :: pid: 1206921, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-83/call-run_sawfish/slurm_singularity.log.txt"
2025-09-15 20:26:03.469 wdl.w:ptcp.w:call-sawfish-88.t:call-run_sawfish.stderr VERBOSE [M::bam2fq_mainloop] discarded 0 singletons
2025-09-15 20:26:03.469 wdl.w:ptcp.w:call-sawfish-88.t:call-run_sawfish.stderr VERBOSE [M::bam2fq_mainloop] processed 0 reads
2025-09-15 20:26:03.479 wdl.w:ptcp.w:call-sawfish-88.t:call-run_sawfish.slurm_singularity INFO srun: job 51798128 queued and waiting for resources
2025-09-15 20:26:03.479 wdl.w:ptcp.w:call-sawfish-88.t:call-run_sawfish.slurm_singularity INFO srun: job 51798128 has been allocated resources
2025-09-15 20:26:03.479 wdl.w:ptcp.w:call-sawfish-88.t:call-run_sawfish.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:26:03.483 wdl.w:ptcp.w:call-trgt-88.t:call-get_reads_overlapping_repeats.slurm_singularity INFO srun: job 51798129 queued and waiting for resources
2025-09-15 20:26:03.483 wdl.w:ptcp.w:call-trgt-88.t:call-get_reads_overlapping_repeats.slurm_singularity INFO srun: job 51798129 has been allocated resources
2025-09-15 20:26:03.483 wdl.w:ptcp.w:call-trgt-88.t:call-get_reads_overlapping_repeats.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:26:03.487 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_plot_meth_allele INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2184.meth_allele.trgt_plots.zip"
2025-09-15 20:26:03.486 wdl.w:ptcp.w:call-paraphase-90.t:call-run_paraphase.stderr VERBOSE INFO:root:Processing sample m84036_250809_035451_s4.bc2187 at 2025-09-15 20:25:58.925924...
2025-09-15 20:26:03.487 wdl.w:ptcp.w:call-paraphase-90.t:call-run_paraphase.stderr VERBOSE INFO:root:Checking sample sex at 2025-09-15 20:25:58.927510...
2025-09-15 20:26:03.487 wdl.w:ptcp.w:call-paraphase-90.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for smn1 for sample m84036_250809_035451_s4.bc2187 at 2025-09-15 20:25:58.977630...
2025-09-15 20:26:03.487 wdl.w:ptcp.w:call-paraphase-90.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for smn1 for sample m84036_250809_035451_s4.bc2187 at 2025-09-15 20:25:58.978102...
2025-09-15 20:26:03.488 wdl.w:ptcp.w:call-paraphase-90.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for cyp21 for sample m84036_250809_035451_s4.bc2187 at 2025-09-15 20:25:58.977712...
2025-09-15 20:26:03.488 wdl.w:ptcp.w:call-paraphase-90.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for cyp21 for sample m84036_250809_035451_s4.bc2187 at 2025-09-15 20:25:58.978338...
2025-09-15 20:26:03.488 wdl.w:ptcp.w:call-paraphase-90.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for gba for sample m84036_250809_035451_s4.bc2187 at 2025-09-15 20:25:58.978173...
2025-09-15 20:26:03.488 wdl.w:ptcp.w:call-paraphase-90.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for gba for sample m84036_250809_035451_s4.bc2187 at 2025-09-15 20:25:58.978745...
2025-09-15 20:26:03.488 wdl.w:ptcp.w:call-paraphase-90.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for hba for sample m84036_250809_035451_s4.bc2187 at 2025-09-15 20:25:58.979495...
2025-09-15 20:26:03.488 wdl.w:ptcp.w:call-paraphase-90.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for hba for sample m84036_250809_035451_s4.bc2187 at 2025-09-15 20:25:58.979873...
2025-09-15 20:26:03.522 wdl.w:ptcp.w:call-trgt-88.t:call-trgt_genotype.slurm_singularity INFO srun: job 51798130 queued and waiting for resources
2025-09-15 20:26:03.522 wdl.w:ptcp.w:call-trgt-88.t:call-trgt_genotype.slurm_singularity INFO srun: job 51798130 has been allocated resources
2025-09-15 20:26:03.522 wdl.w:ptcp.w:call-trgt-88.t:call-trgt_genotype.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:26:03.579 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_plot_meth_allele NOTICE done
2025-09-15 20:26:03.583 wdl.w:ptcp.w:call-paraphase-83.t:call-run_paraphase.slurm_singularity INFO srun: job 51798131 queued and waiting for resources
2025-09-15 20:26:03.583 wdl.w:ptcp.w:call-paraphase-83.t:call-run_paraphase.slurm_singularity INFO srun: job 51798131 has been allocated resources
2025-09-15 20:26:03.583 wdl.w:ptcp.w:call-paraphase-83.t:call-run_paraphase.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:26:03.585 wdl.w:ptcp.w:call-trgt-87 NOTICE finish :: job: "call-trgt_plot_meth_allele"
2025-09-15 20:26:03.585 wdl.w:ptcp.w:call-trgt-87 INFO output :: job: "call-trgt_plot_meth_allele", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-87/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2184.meth_allele.trgt_plots.zip"}
2025-09-15 20:26:03.586 wdl.w:ptcp.w:call-trgt-87 INFO visit :: node: "output-images_meth_allele", values: {"images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-87/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2184.meth_allele.trgt_plots.zip"}
2025-09-15 20:26:03.595 wdl.w:ptcp.w:call-trgt-82.t:call-trgt_plot_meth_allele NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-82/call-trgt_plot_meth_allele", thread: 140608748373568
2025-09-15 20:26:03.614 wdl.w:ptcp.w:call-trgt-82.t:call-trgt_plot_meth_allele INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:26:03.614 wdl.w:ptcp.w:call-trgt-82.t:call-trgt_plot_meth_allele INFO input :: name: "waterfall", value: false
2025-09-15 20:26:03.614 wdl.w:ptcp.w:call-trgt-82.t:call-trgt_plot_meth_allele INFO input :: name: "methylation", value: true
2025-09-15 20:26:03.614 wdl.w:ptcp.w:call-trgt-82.t:call-trgt_plot_meth_allele INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:26:03.614 wdl.w:ptcp.w:call-trgt-82.t:call-trgt_plot_meth_allele INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:26:03.614 wdl.w:ptcp.w:call-trgt-82.t:call-trgt_plot_meth_allele INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:26:03.614 wdl.w:ptcp.w:call-trgt-82.t:call-trgt_plot_meth_allele INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2179.trgt.sorted.spanning.bam.bai"
2025-09-15 20:26:03.614 wdl.w:ptcp.w:call-trgt-82.t:call-trgt_plot_meth_allele INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2179.trgt.sorted.spanning.bam"
2025-09-15 20:26:03.614 wdl.w:ptcp.w:call-trgt-82.t:call-trgt_plot_meth_allele INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2179.trgt.vcf"
2025-09-15 20:26:03.614 wdl.w:ptcp.w:call-trgt-82.t:call-trgt_plot_meth_allele INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2179"
2025-09-15 20:26:03.615 wdl.w:ptcp.w:call-trgt-82.t:call-trgt_plot_meth_allele INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:26:03.615 wdl.w:ptcp.w:call-trgt-82.t:call-trgt_plot_meth_allele INFO eval :: name: "plot_type", value: "allele"
2025-09-15 20:26:03.615 wdl.w:ptcp.w:call-trgt-82.t:call-trgt_plot_meth_allele INFO eval :: name: "show", value: "meth"
2025-09-15 20:26:03.615 wdl.w:ptcp.w:call-trgt-82.t:call-trgt_plot_meth_allele INFO eval :: name: "threads", value: 1
2025-09-15 20:26:03.615 wdl.w:ptcp.w:call-trgt-82.t:call-trgt_plot_meth_allele INFO eval :: name: "disk_size", value: 27
2025-09-15 20:26:03.616 wdl.w:ptcp.w:call-trgt-82.t:call-trgt_plot_meth_allele INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2179.meth_allele"
2025-09-15 20:26:03.616 wdl.w:ptcp.w:call-trgt-82.t:call-trgt_plot_meth_allele INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:26:03.616 wdl.w:ptcp.w:call-trgt-82.t:call-trgt_plot_meth_allele WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:26:03.616 wdl.w:ptcp.w:call-trgt-82.t:call-trgt_plot_meth_allele INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:26:03.616 wdl.w:ptcp.w:call-trgt-82.t:call-trgt_plot_meth_allele INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:26:03.685 wdl.w:ptcp.w:call-trgt-82.t:call-trgt_plot_meth_allele INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-82/call-trgt_plot_meth_allele/_singularity_tmpdir_w426ehpj"
2025-09-15 20:26:03.685 wdl.w:ptcp.w:call-trgt-82.t:call-trgt_plot_meth_allele INFO Slurm invocation: srun --job-name call-trgt_plot_meth_allele --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-82/call-trgt_plot_meth_allele/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-82/call-trgt_plot_meth_allele/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-82/call-trgt_plot_meth_allele/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-82/call-trgt_plot_meth_allele/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-82/call-trgt_genotype/out/m84036_250809_035451_s4.bc2179.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2179.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-82/call-trgt_genotype/out/m84036_250809_035451_s4.bc2179.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2179.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-82/call-trgt_genotype/out/m84036_250809_035451_s4.bc2179.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2179.trgt.sorted.spanning.bam.bai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-82/call-trgt_plot_meth_allele/_singularity_tmpdir_w426ehpj/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-82/call-trgt_plot_meth_allele/_singularity_tmpdir_w426ehpj/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:26:03.712 wdl.w:ptcp.w:call-trgt-82.t:call-trgt_plot_meth_allele NOTICE slurm_singularity run :: pid: 1206929, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-82/call-trgt_plot_meth_allele/slurm_singularity.log.txt"
2025-09-15 20:26:03.713 wdl.w:ptcp.w:call-paraphase-85.t:call-call_f8 INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2182.f8inversion.vcf"
2025-09-15 20:26:03.716 wdl.w:ptcp.w:call-paraphase-85.t:call-call_f8 INFO output :: name: "json", value: "m84036_250809_035451_s4.bc2182.f8inversion.json"
2025-09-15 20:26:03.737 wdl.w:ptcp.w:call-trgt-86.t:call-trgt_genotype INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2183.trgt.vcf"
2025-09-15 20:26:03.740 wdl.w:ptcp.w:call-trgt-86.t:call-trgt_genotype INFO output :: name: "spanning_bam", value: "m84036_250809_035451_s4.bc2183.trgt.sorted.spanning.bam"
2025-09-15 20:26:03.742 wdl.w:ptcp.w:call-trgt-86.t:call-trgt_genotype INFO output :: name: "spanning_bam_bai", value: "m84036_250809_035451_s4.bc2183.trgt.sorted.spanning.bam.bai"
2025-09-15 20:26:03.773 wdl.w:ptcp.w:call-paraphase-85.t:call-call_f8 NOTICE done
2025-09-15 20:26:03.779 wdl.w:ptcp.w:call-paraphase-85 NOTICE finish :: job: "call-call_f8"
2025-09-15 20:26:03.779 wdl.w:ptcp.w:call-paraphase-85 INFO output :: job: "call-call_f8", values: {"json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-85/call-call_f8/out/m84036_250809_035451_s4.bc2182.f8inversion.json", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-85/call-call_f8/out/m84036_250809_035451_s4.bc2182.f8inversion.vcf"}
2025-09-15 20:26:03.779 wdl.w:ptcp.w:call-paraphase-85 INFO visit :: node: "output-f8_json", values: {"f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-85/call-call_f8/out/m84036_250809_035451_s4.bc2182.f8inversion.json"}
2025-09-15 20:26:03.779 wdl.w:ptcp.w:call-paraphase-85 INFO visit :: node: "output-f8_vcf", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-85/call-call_f8/out/m84036_250809_035451_s4.bc2182.f8inversion.vcf"}
2025-09-15 20:26:03.780 wdl.w:ptcp.w:call-paraphase-85 INFO visit :: node: "outputs", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-85/call-call_f8/out/m84036_250809_035451_s4.bc2182.f8inversion.vcf", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-85/call-run_paraphase/out/m84036_250809_035451_s4.bc2182_paraphase/m84036_250809_035451_s4.bc2182.paraphase.json", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-85/call-run_paraphase/out/m84036_250809_035451_s4.bc2182_paraphase/m84036_250809_035451_s4.bc2182.paraphase.bam", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-85/call-run_paraphase/out/m84036_250809_035451_s4.bc2182_paraphase/m84036_250809_035451_s4.bc2182.paraphase.bam.bai", "paraphase_vcfs": [], "havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-85/call-run_paraphase/out/m84036_250809_035451_s4.bc2182.havanno.json", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-85/call-call_f8/out/m84036_250809_035451_s4.bc2182.f8inversion.json"}
2025-09-15 20:26:03.785 wdl.w:ptcp.w:call-trgt-82.t:call-trgt_plot_meth_waterfall NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-82/call-trgt_plot_meth_waterfall", thread: 140607649453632
2025-09-15 20:26:03.807 wdl.w:ptcp.w:call-trgt-82.t:call-trgt_plot_meth_waterfall INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:26:03.807 wdl.w:ptcp.w:call-trgt-82.t:call-trgt_plot_meth_waterfall INFO input :: name: "waterfall", value: true
2025-09-15 20:26:03.807 wdl.w:ptcp.w:call-trgt-82.t:call-trgt_plot_meth_waterfall INFO input :: name: "methylation", value: true
2025-09-15 20:26:03.807 wdl.w:ptcp.w:call-trgt-82.t:call-trgt_plot_meth_waterfall INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:26:03.808 wdl.w:ptcp.w:call-trgt-82.t:call-trgt_plot_meth_waterfall INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:26:03.808 wdl.w:ptcp.w:call-trgt-82.t:call-trgt_plot_meth_waterfall INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:26:03.808 wdl.w:ptcp.w:call-trgt-82.t:call-trgt_plot_meth_waterfall INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2179.trgt.sorted.spanning.bam.bai"
2025-09-15 20:26:03.808 wdl.w:ptcp.w:call-trgt-82.t:call-trgt_plot_meth_waterfall INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2179.trgt.sorted.spanning.bam"
2025-09-15 20:26:03.808 wdl.w:ptcp.w:call-trgt-82.t:call-trgt_plot_meth_waterfall INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2179.trgt.vcf"
2025-09-15 20:26:03.808 wdl.w:ptcp.w:call-trgt-82.t:call-trgt_plot_meth_waterfall INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2179"
2025-09-15 20:26:03.808 wdl.w:ptcp.w:call-trgt-82.t:call-trgt_plot_meth_waterfall INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:26:03.808 wdl.w:ptcp.w:call-trgt-82.t:call-trgt_plot_meth_waterfall INFO eval :: name: "plot_type", value: "waterfall"
2025-09-15 20:26:03.808 wdl.w:ptcp.w:call-trgt-82.t:call-trgt_plot_meth_waterfall INFO eval :: name: "show", value: "meth"
2025-09-15 20:26:03.808 wdl.w:ptcp.w:call-trgt-82.t:call-trgt_plot_meth_waterfall INFO eval :: name: "threads", value: 1
2025-09-15 20:26:03.809 wdl.w:ptcp.w:call-trgt-82.t:call-trgt_plot_meth_waterfall INFO eval :: name: "disk_size", value: 27
2025-09-15 20:26:03.809 wdl.w:ptcp.w:call-trgt-82.t:call-trgt_plot_meth_waterfall INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2179.meth_waterfall"
2025-09-15 20:26:03.809 wdl.w:ptcp.w:call-trgt-82.t:call-trgt_plot_meth_waterfall INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:26:03.809 wdl.w:ptcp.w:call-trgt-82.t:call-trgt_plot_meth_waterfall WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:26:03.810 wdl.w:ptcp.w:call-trgt-82.t:call-trgt_plot_meth_waterfall INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:26:03.810 wdl.w:ptcp.w:call-trgt-82.t:call-trgt_plot_meth_waterfall INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:26:03.819 wdl.w:ptcp.w:call-trgt-86.t:call-trgt_genotype NOTICE done
2025-09-15 20:26:03.824 wdl.w:ptcp.w:call-trgt-86 NOTICE finish :: job: "call-trgt_genotype"
2025-09-15 20:26:03.824 wdl.w:ptcp.w:call-trgt-86 INFO output :: job: "call-trgt_genotype", values: {"spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-86/call-trgt_genotype/out/m84036_250809_035451_s4.bc2183.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-86/call-trgt_genotype/out/m84036_250809_035451_s4.bc2183.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-86/call-trgt_genotype/out/m84036_250809_035451_s4.bc2183.trgt.vcf"}
2025-09-15 20:26:03.825 wdl.w:ptcp.w:call-trgt-86 NOTICE ready :: job: "call-trgt_plot_meth_allele", callee: "trgt_plot"
2025-09-15 20:26:03.825 wdl.w:ptcp.w:call-trgt-86 INFO input :: job: "call-trgt_plot_meth_allele", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": false, "methylation": true, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-86/call-trgt_genotype/out/m84036_250809_035451_s4.bc2183.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-86/call-trgt_genotype/out/m84036_250809_035451_s4.bc2183.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-86/call-trgt_genotype/out/m84036_250809_035451_s4.bc2183.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2183"}
2025-09-15 20:26:03.826 wdl.w:ptcp.w:call-trgt-86 NOTICE ready :: job: "call-trgt_plot_meth_waterfall", callee: "trgt_plot"
2025-09-15 20:26:03.827 wdl.w:ptcp.w:call-trgt-86 INFO input :: job: "call-trgt_plot_meth_waterfall", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": true, "methylation": true, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-86/call-trgt_genotype/out/m84036_250809_035451_s4.bc2183.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-86/call-trgt_genotype/out/m84036_250809_035451_s4.bc2183.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-86/call-trgt_genotype/out/m84036_250809_035451_s4.bc2183.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2183"}
2025-09-15 20:26:03.827 wdl.w:ptcp.w:call-trgt-86 NOTICE ready :: job: "call-trgt_plot_motifs_allele", callee: "trgt_plot"
2025-09-15 20:26:03.827 wdl.w:ptcp.w:call-trgt-86 INFO input :: job: "call-trgt_plot_motifs_allele", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": false, "methylation": false, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-86/call-trgt_genotype/out/m84036_250809_035451_s4.bc2183.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-86/call-trgt_genotype/out/m84036_250809_035451_s4.bc2183.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-86/call-trgt_genotype/out/m84036_250809_035451_s4.bc2183.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2183"}
2025-09-15 20:26:03.828 wdl.w:ptcp.w:call-trgt-86 NOTICE ready :: job: "call-trgt_plot_motifs_waterfall", callee: "trgt_plot"
2025-09-15 20:26:03.828 wdl.w:ptcp.w:call-trgt-86 INFO input :: job: "call-trgt_plot_motifs_waterfall", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": true, "methylation": false, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-86/call-trgt_genotype/out/m84036_250809_035451_s4.bc2183.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-86/call-trgt_genotype/out/m84036_250809_035451_s4.bc2183.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-86/call-trgt_genotype/out/m84036_250809_035451_s4.bc2183.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2183"}
2025-09-15 20:26:03.829 wdl.w:ptcp.w:call-trgt-86 INFO visit :: node: "output-spanning_bam", values: {"spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-86/call-trgt_genotype/out/m84036_250809_035451_s4.bc2183.trgt.sorted.spanning.bam"}
2025-09-15 20:26:03.829 wdl.w:ptcp.w:call-trgt-86 INFO visit :: node: "output-spanning_bam_bai", values: {"spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-86/call-trgt_genotype/out/m84036_250809_035451_s4.bc2183.trgt.sorted.spanning.bam.bai"}
2025-09-15 20:26:03.829 wdl.w:ptcp.w:call-trgt-86 INFO visit :: node: "output-vcf", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-86/call-trgt_genotype/out/m84036_250809_035451_s4.bc2183.trgt.vcf"}
2025-09-15 20:26:03.832 wdl.w:ptcp.w:call-trgt-82.t:call-trgt_plot_motifs_allele NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-82/call-trgt_plot_motifs_allele", thread: 140611977991744
2025-09-15 20:26:03.847 wdl.w:ptcp.w:call-trgt-82.t:call-trgt_plot_motifs_allele INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:26:03.848 wdl.w:ptcp.w:call-trgt-82.t:call-trgt_plot_motifs_allele INFO input :: name: "waterfall", value: false
2025-09-15 20:26:03.848 wdl.w:ptcp.w:call-trgt-82.t:call-trgt_plot_motifs_allele INFO input :: name: "methylation", value: false
2025-09-15 20:26:03.848 wdl.w:ptcp.w:call-trgt-82.t:call-trgt_plot_motifs_allele INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:26:03.848 wdl.w:ptcp.w:call-trgt-82.t:call-trgt_plot_motifs_allele INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:26:03.848 wdl.w:ptcp.w:call-trgt-82.t:call-trgt_plot_motifs_allele INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:26:03.848 wdl.w:ptcp.w:call-trgt-82.t:call-trgt_plot_motifs_allele INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2179.trgt.sorted.spanning.bam.bai"
2025-09-15 20:26:03.848 wdl.w:ptcp.w:call-trgt-82.t:call-trgt_plot_motifs_allele INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2179.trgt.sorted.spanning.bam"
2025-09-15 20:26:03.848 wdl.w:ptcp.w:call-trgt-82.t:call-trgt_plot_motifs_allele INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2179.trgt.vcf"
2025-09-15 20:26:03.848 wdl.w:ptcp.w:call-trgt-82.t:call-trgt_plot_motifs_allele INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2179"
2025-09-15 20:26:03.848 wdl.w:ptcp.w:call-trgt-82.t:call-trgt_plot_motifs_allele INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:26:03.848 wdl.w:ptcp.w:call-trgt-82.t:call-trgt_plot_motifs_allele INFO eval :: name: "plot_type", value: "allele"
2025-09-15 20:26:03.849 wdl.w:ptcp.w:call-trgt-82.t:call-trgt_plot_motifs_allele INFO eval :: name: "show", value: "motifs"
2025-09-15 20:26:03.849 wdl.w:ptcp.w:call-trgt-82.t:call-trgt_plot_motifs_allele INFO eval :: name: "threads", value: 1
2025-09-15 20:26:03.849 wdl.w:ptcp.w:call-trgt-82.t:call-trgt_plot_motifs_allele INFO eval :: name: "disk_size", value: 27
2025-09-15 20:26:03.849 wdl.w:ptcp.w:call-trgt-82.t:call-trgt_plot_motifs_allele INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2179.motifs_allele"
2025-09-15 20:26:03.849 wdl.w:ptcp.w:call-trgt-82.t:call-trgt_plot_motifs_allele INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:26:03.849 wdl.w:ptcp.w:call-trgt-82.t:call-trgt_plot_motifs_allele WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:26:03.850 wdl.w:ptcp.w:call-trgt-82.t:call-trgt_plot_motifs_allele INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:26:03.850 wdl.w:ptcp.w:call-trgt-82.t:call-trgt_plot_motifs_allele INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:26:03.851 wdl.w:ptcp.w:call-paraphase-85 NOTICE done
2025-09-15 20:26:03.856 wdl.w:ptcp NOTICE finish :: job: "call-paraphase-85"
2025-09-15 20:26:03.856 wdl.w:ptcp INFO output :: job: "call-paraphase-85", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-85/out/m84036_250809_035451_s4.bc2182.f8inversion.vcf", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-85/out/m84036_250809_035451_s4.bc2182_paraphase/m84036_250809_035451_s4.bc2182.paraphase.json", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-85/out/m84036_250809_035451_s4.bc2182_paraphase/m84036_250809_035451_s4.bc2182.paraphase.bam", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-85/out/m84036_250809_035451_s4.bc2182_paraphase/m84036_250809_035451_s4.bc2182.paraphase.bam.bai", "paraphase_vcfs": [], "havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-85/out/m84036_250809_035451_s4.bc2182.havanno.json", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-85/out/m84036_250809_035451_s4.bc2182.f8inversion.json"}
2025-09-15 20:26:03.885 wdl.w:ptcp.w:call-trgt-82.t:call-trgt_plot_meth_waterfall INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-82/call-trgt_plot_meth_waterfall/_singularity_tmpdir_v8k_wr9k"
2025-09-15 20:26:03.885 wdl.w:ptcp.w:call-trgt-82.t:call-trgt_plot_meth_waterfall INFO Slurm invocation: srun --job-name call-trgt_plot_meth_waterfall --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-82/call-trgt_plot_meth_waterfall/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-82/call-trgt_plot_meth_waterfall/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-82/call-trgt_plot_meth_waterfall/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-82/call-trgt_plot_meth_waterfall/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-82/call-trgt_genotype/out/m84036_250809_035451_s4.bc2179.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2179.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-82/call-trgt_genotype/out/m84036_250809_035451_s4.bc2179.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2179.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-82/call-trgt_genotype/out/m84036_250809_035451_s4.bc2179.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2179.trgt.sorted.spanning.bam.bai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-82/call-trgt_plot_meth_waterfall/_singularity_tmpdir_v8k_wr9k/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-82/call-trgt_plot_meth_waterfall/_singularity_tmpdir_v8k_wr9k/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:26:03.899 wdl.w:ptcp.w:call-trgt-82.t:call-trgt_plot_meth_waterfall NOTICE slurm_singularity run :: pid: 1206932, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-82/call-trgt_plot_meth_waterfall/slurm_singularity.log.txt"
2025-09-15 20:26:03.914 wdl.w:ptcp.w:call-trgt-82.t:call-trgt_plot_motifs_allele INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-82/call-trgt_plot_motifs_allele/_singularity_tmpdir_50jkchnx"
2025-09-15 20:26:03.914 wdl.w:ptcp.w:call-trgt-82.t:call-trgt_plot_motifs_allele INFO Slurm invocation: srun --job-name call-trgt_plot_motifs_allele --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-82/call-trgt_plot_motifs_allele/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-82/call-trgt_plot_motifs_allele/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-82/call-trgt_plot_motifs_allele/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-82/call-trgt_plot_motifs_allele/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-82/call-trgt_genotype/out/m84036_250809_035451_s4.bc2179.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2179.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-82/call-trgt_genotype/out/m84036_250809_035451_s4.bc2179.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2179.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-82/call-trgt_genotype/out/m84036_250809_035451_s4.bc2179.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2179.trgt.sorted.spanning.bam.bai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-82/call-trgt_plot_motifs_allele/_singularity_tmpdir_50jkchnx/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-82/call-trgt_plot_motifs_allele/_singularity_tmpdir_50jkchnx/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:26:03.921 wdl.w:ptcp.w:call-trgt-82.t:call-trgt_plot_motifs_allele NOTICE slurm_singularity run :: pid: 1206934, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-82/call-trgt_plot_motifs_allele/slurm_singularity.log.txt"
2025-09-15 20:26:04.033 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_plot_motifs_waterfall INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2184.motifs_waterfall.trgt_plots.zip"
2025-09-15 20:26:04.076 wdl.w:ptcp.w:call-trgt-89.t:call-trgt_plot_meth_allele.slurm_singularity INFO srun: job 51798132 queued and waiting for resources
2025-09-15 20:26:04.077 wdl.w:ptcp.w:call-trgt-89.t:call-trgt_plot_meth_allele.slurm_singularity INFO srun: job 51798132 has been allocated resources
2025-09-15 20:26:04.077 wdl.w:ptcp.w:call-trgt-89.t:call-trgt_plot_meth_allele.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:26:04.106 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_plot_motifs_waterfall NOTICE done
2025-09-15 20:26:04.110 wdl.w:ptcp.w:call-trgt-87 NOTICE finish :: job: "call-trgt_plot_motifs_waterfall"
2025-09-15 20:26:04.110 wdl.w:ptcp.w:call-trgt-87 INFO output :: job: "call-trgt_plot_motifs_waterfall", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-87/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2184.motifs_waterfall.trgt_plots.zip"}
2025-09-15 20:26:04.110 wdl.w:ptcp.w:call-trgt-87 INFO visit :: node: "output-images_motifs_waterfall", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-87/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2184.motifs_waterfall.trgt_plots.zip"}
2025-09-15 20:26:04.117 wdl.w:ptcp.w:call-trgt-82.t:call-trgt_plot_motifs_waterfall NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-82/call-trgt_plot_motifs_waterfall", thread: 140613043340864
2025-09-15 20:26:04.134 wdl.w:ptcp.w:call-trgt-89.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO srun: job 51798133 queued and waiting for resources
2025-09-15 20:26:04.134 wdl.w:ptcp.w:call-trgt-89.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO srun: job 51798133 has been allocated resources
2025-09-15 20:26:04.134 wdl.w:ptcp.w:call-trgt-89.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:26:04.141 wdl.w:ptcp.w:call-trgt-82.t:call-trgt_plot_motifs_waterfall INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:26:04.141 wdl.w:ptcp.w:call-trgt-82.t:call-trgt_plot_motifs_waterfall INFO input :: name: "waterfall", value: true
2025-09-15 20:26:04.141 wdl.w:ptcp.w:call-trgt-82.t:call-trgt_plot_motifs_waterfall INFO input :: name: "methylation", value: false
2025-09-15 20:26:04.141 wdl.w:ptcp.w:call-trgt-82.t:call-trgt_plot_motifs_waterfall INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:26:04.141 wdl.w:ptcp.w:call-trgt-82.t:call-trgt_plot_motifs_waterfall INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:26:04.141 wdl.w:ptcp.w:call-trgt-82.t:call-trgt_plot_motifs_waterfall INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:26:04.142 wdl.w:ptcp.w:call-trgt-82.t:call-trgt_plot_motifs_waterfall INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2179.trgt.sorted.spanning.bam.bai"
2025-09-15 20:26:04.142 wdl.w:ptcp.w:call-trgt-82.t:call-trgt_plot_motifs_waterfall INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2179.trgt.sorted.spanning.bam"
2025-09-15 20:26:04.142 wdl.w:ptcp.w:call-trgt-82.t:call-trgt_plot_motifs_waterfall INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2179.trgt.vcf"
2025-09-15 20:26:04.142 wdl.w:ptcp.w:call-trgt-82.t:call-trgt_plot_motifs_waterfall INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2179"
2025-09-15 20:26:04.142 wdl.w:ptcp.w:call-trgt-82.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:26:04.142 wdl.w:ptcp.w:call-trgt-82.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "plot_type", value: "waterfall"
2025-09-15 20:26:04.142 wdl.w:ptcp.w:call-trgt-82.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "show", value: "motifs"
2025-09-15 20:26:04.142 wdl.w:ptcp.w:call-trgt-82.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "threads", value: 1
2025-09-15 20:26:04.142 wdl.w:ptcp.w:call-trgt-82.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "disk_size", value: 27
2025-09-15 20:26:04.143 wdl.w:ptcp.w:call-trgt-82.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2179.motifs_waterfall"
2025-09-15 20:26:04.143 wdl.w:ptcp.w:call-trgt-82.t:call-trgt_plot_motifs_waterfall INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:26:04.143 wdl.w:ptcp.w:call-trgt-82.t:call-trgt_plot_motifs_waterfall WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:26:04.143 wdl.w:ptcp.w:call-trgt-82.t:call-trgt_plot_motifs_waterfall INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:26:04.144 wdl.w:ptcp.w:call-trgt-82.t:call-trgt_plot_motifs_waterfall INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:26:04.200 wdl.w:ptcp.w:call-sawfish-57.t:call-run_sawfish INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2154_sawfish/m84036_250809_035451_s4.bc2154.sv.vcf.gz"
2025-09-15 20:26:04.205 wdl.w:ptcp.w:call-sawfish-57.t:call-run_sawfish INFO output :: name: "vcf_tbi", value: "m84036_250809_035451_s4.bc2154_sawfish/m84036_250809_035451_s4.bc2154.sv.vcf.gz.tbi"
2025-09-15 20:26:04.206 wdl.w:ptcp.w:call-sawfish-57.t:call-run_sawfish INFO output :: name: "minimap2_bam", value: "m84036_250809_035451_s4.bc2154.minimap2.bam"
2025-09-15 20:26:04.207 wdl.w:ptcp.w:call-sawfish-57.t:call-run_sawfish INFO output :: name: "minimap2_bam_bai", value: "m84036_250809_035451_s4.bc2154.minimap2.bam.bai"
2025-09-15 20:26:04.233 wdl.w:ptcp.w:call-trgt-82.t:call-trgt_plot_motifs_waterfall INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-82/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_dmj79x5j"
2025-09-15 20:26:04.233 wdl.w:ptcp.w:call-trgt-82.t:call-trgt_plot_motifs_waterfall INFO Slurm invocation: srun --job-name call-trgt_plot_motifs_waterfall --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-82/call-trgt_plot_motifs_waterfall/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-82/call-trgt_plot_motifs_waterfall/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-82/call-trgt_plot_motifs_waterfall/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-82/call-trgt_plot_motifs_waterfall/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-82/call-trgt_genotype/out/m84036_250809_035451_s4.bc2179.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2179.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-82/call-trgt_genotype/out/m84036_250809_035451_s4.bc2179.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2179.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-82/call-trgt_genotype/out/m84036_250809_035451_s4.bc2179.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2179.trgt.sorted.spanning.bam.bai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-82/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_dmj79x5j/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-82/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_dmj79x5j/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:26:04.253 wdl.w:ptcp.w:call-trgt-82.t:call-trgt_plot_motifs_waterfall NOTICE slurm_singularity run :: pid: 1206953, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-82/call-trgt_plot_motifs_waterfall/slurm_singularity.log.txt"
2025-09-15 20:26:04.323 wdl.w:ptcp.w:call-sawfish-57.t:call-run_sawfish NOTICE done
2025-09-15 20:26:04.328 wdl.w:ptcp.w:call-sawfish-57 NOTICE finish :: job: "call-run_sawfish"
2025-09-15 20:26:04.329 wdl.w:ptcp.w:call-sawfish-57 INFO output :: job: "call-run_sawfish", values: {"minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-57/call-run_sawfish/out/m84036_250809_035451_s4.bc2154.minimap2.bam.bai", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-57/call-run_sawfish/out/m84036_250809_035451_s4.bc2154.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-57/call-run_sawfish/out/m84036_250809_035451_s4.bc2154_sawfish/m84036_250809_035451_s4.bc2154.sv.vcf.gz.tbi", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-57/call-run_sawfish/out/m84036_250809_035451_s4.bc2154_sawfish/m84036_250809_035451_s4.bc2154.sv.vcf.gz"}
2025-09-15 20:26:04.329 wdl.w:ptcp.w:call-sawfish-57 INFO visit :: node: "output-minimap2_bam", values: {"minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-57/call-run_sawfish/out/m84036_250809_035451_s4.bc2154.minimap2.bam"}
2025-09-15 20:26:04.329 wdl.w:ptcp.w:call-sawfish-57 INFO visit :: node: "output-minimap2_bam_bai", values: {"minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-57/call-run_sawfish/out/m84036_250809_035451_s4.bc2154.minimap2.bam.bai"}
2025-09-15 20:26:04.329 wdl.w:ptcp.w:call-sawfish-57 INFO visit :: node: "output-vcf", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-57/call-run_sawfish/out/m84036_250809_035451_s4.bc2154_sawfish/m84036_250809_035451_s4.bc2154.sv.vcf.gz"}
2025-09-15 20:26:04.329 wdl.w:ptcp.w:call-sawfish-57 INFO visit :: node: "output-vcf_tbi", values: {"vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-57/call-run_sawfish/out/m84036_250809_035451_s4.bc2154_sawfish/m84036_250809_035451_s4.bc2154.sv.vcf.gz.tbi"}
2025-09-15 20:26:04.329 wdl.w:ptcp.w:call-sawfish-57 INFO visit :: node: "outputs", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-57/call-run_sawfish/out/m84036_250809_035451_s4.bc2154_sawfish/m84036_250809_035451_s4.bc2154.sv.vcf.gz", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-57/call-run_sawfish/out/m84036_250809_035451_s4.bc2154.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-57/call-run_sawfish/out/m84036_250809_035451_s4.bc2154_sawfish/m84036_250809_035451_s4.bc2154.sv.vcf.gz.tbi", "minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-57/call-run_sawfish/out/m84036_250809_035451_s4.bc2154.minimap2.bam.bai"}
2025-09-15 20:26:04.334 wdl.w:ptcp.w:call-trgt-83.t:call-get_reads_overlapping_repeats NOTICE task setup :: name: "get_reads_overlapping_repeats", source: "./trgt.wdl", line: 182, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-83/call-get_reads_overlapping_repeats", thread: 140608731588160
2025-09-15 20:26:04.353 wdl.w:ptcp.w:call-trgt-83.t:call-get_reads_overlapping_repeats INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:26:04.353 wdl.w:ptcp.w:call-trgt-83.t:call-get_reads_overlapping_repeats INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:26:04.353 wdl.w:ptcp.w:call-trgt-83.t:call-get_reads_overlapping_repeats INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2180.mapped.bam.bai"
2025-09-15 20:26:04.353 wdl.w:ptcp.w:call-trgt-83.t:call-get_reads_overlapping_repeats INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2180.mapped.bam"
2025-09-15 20:26:04.353 wdl.w:ptcp.w:call-trgt-83.t:call-get_reads_overlapping_repeats INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2180"
2025-09-15 20:26:04.354 wdl.w:ptcp.w:call-trgt-83.t:call-get_reads_overlapping_repeats INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:26:04.354 wdl.w:ptcp.w:call-trgt-83.t:call-get_reads_overlapping_repeats INFO eval :: name: "expand_size", value: 3000
2025-09-15 20:26:04.354 wdl.w:ptcp.w:call-trgt-83.t:call-get_reads_overlapping_repeats INFO eval :: name: "threads", value: 1
2025-09-15 20:26:04.354 wdl.w:ptcp.w:call-trgt-83.t:call-get_reads_overlapping_repeats INFO eval :: name: "expanded_bed_name", value: "m84036_250809_035451_s4.bc2180.expanded.bed"
2025-09-15 20:26:04.354 wdl.w:ptcp.w:call-trgt-83.t:call-get_reads_overlapping_repeats INFO eval :: name: "disk_size", value: 11
2025-09-15 20:26:04.354 wdl.w:ptcp.w:call-trgt-83.t:call-get_reads_overlapping_repeats INFO eval :: name: "output_name", value: "m84036_250809_035451_s4.bc2180.repeats.bam"
2025-09-15 20:26:04.354 wdl.w:ptcp.w:call-trgt-83.t:call-get_reads_overlapping_repeats INFO eval :: name: "index_name", value: "m84036_250809_035451_s4.bc2180.repeats.bam.bai"
2025-09-15 20:26:04.354 wdl.w:ptcp.w:call-trgt-83.t:call-get_reads_overlapping_repeats INFO eval :: name: "output_name_with_index", value: "m84036_250809_035451_s4.bc2180.repeats.bam##idx##m84036_250809_035451_s4.bc2180.repeats.bam.bai"
2025-09-15 20:26:04.355 wdl.w:ptcp.w:call-trgt-83.t:call-get_reads_overlapping_repeats INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:26:04.355 wdl.w:ptcp.w:call-trgt-83.t:call-get_reads_overlapping_repeats WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:26:04.355 wdl.w:ptcp.w:call-trgt-83.t:call-get_reads_overlapping_repeats INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:26:04.355 wdl.w:ptcp.w:call-trgt-83.t:call-get_reads_overlapping_repeats INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:26:04.374 wdl.w:ptcp.w:call-sawfish-57 NOTICE done
2025-09-15 20:26:04.380 wdl.w:ptcp NOTICE finish :: job: "call-sawfish-57"
2025-09-15 20:26:04.380 wdl.w:ptcp INFO output :: job: "call-sawfish-57", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-57/out/m84036_250809_035451_s4.bc2154_sawfish/m84036_250809_035451_s4.bc2154.sv.vcf.gz", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-57/out/m84036_250809_035451_s4.bc2154.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-57/out/m84036_250809_035451_s4.bc2154_sawfish/m84036_250809_035451_s4.bc2154.sv.vcf.gz.tbi", "minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-57/out/m84036_250809_035451_s4.bc2154.minimap2.bam.bai"}
2025-09-15 20:26:04.381 wdl.w:ptcp NOTICE ready :: job: "call-tar_outputs-57", callee: "tar_outputs"
2025-09-15 20:26:04.381 wdl.w:ptcp INFO input :: job: "call-tar_outputs-57", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "sawfish_vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-57/out/m84036_250809_035451_s4.bc2154_sawfish/m84036_250809_035451_s4.bc2154.sv.vcf.gz.tbi", "sawfish_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-57/out/m84036_250809_035451_s4.bc2154_sawfish/m84036_250809_035451_s4.bc2154.sv.vcf.gz", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-57/out/m84036_250809_035451_s4.bc2154.f8inversion.json", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-57/out/m84036_250809_035451_s4.bc2154_paraphase/m84036_250809_035451_s4.bc2154.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-57/out/m84036_250809_035451_s4.bc2154_paraphase/m84036_250809_035451_s4.bc2154.paraphase.bam", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-57/out/m84036_250809_035451_s4.bc2154_paraphase/m84036_250809_035451_s4.bc2154.paraphase.json", "trgt_spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-57/out/m84036_250809_035451_s4.bc2154.trgt.sorted.spanning.bam.bai", "trgt_spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-57/out/m84036_250809_035451_s4.bc2154.trgt.sorted.spanning.bam", "trgt_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-57/out/m84036_250809_035451_s4.bc2154.trgt.vcf", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-57/out/m84036_250809_035451_s4.bc2154.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-57/out/m84036_250809_035451_s4.bc2154.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2154"}
2025-09-15 20:26:04.415 wdl.w:ptcp.w:call-trgt-89.t:call-trgt_plot_motifs_allele.slurm_singularity INFO srun: job 51798135 queued and waiting for resources
2025-09-15 20:26:04.415 wdl.w:ptcp.w:call-trgt-89.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO srun: job 51798134 queued and waiting for resources
2025-09-15 20:26:04.415 wdl.w:ptcp.w:call-trgt-89.t:call-trgt_plot_motifs_allele.slurm_singularity INFO srun: job 51798135 has been allocated resources
2025-09-15 20:26:04.415 wdl.w:ptcp.w:call-trgt-89.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO srun: job 51798134 has been allocated resources
2025-09-15 20:26:04.415 wdl.w:ptcp.w:call-trgt-89.t:call-trgt_plot_motifs_allele.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:26:04.415 wdl.w:ptcp.w:call-trgt-89.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:26:04.418 wdl.w:ptcp.w:call-trgt-83.t:call-get_reads_overlapping_repeats INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 9, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-83/call-get_reads_overlapping_repeats/_singularity_tmpdir_idz1pvjs"
2025-09-15 20:26:04.418 wdl.w:ptcp.w:call-trgt-83.t:call-get_reads_overlapping_repeats INFO Slurm invocation: srun --job-name call-get_reads_overlapping_repeats --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-83/call-get_reads_overlapping_repeats/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-83/call-get_reads_overlapping_repeats/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-83/call-get_reads_overlapping_repeats/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-83/call-get_reads_overlapping_repeats/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-83/out/m84036_250809_035451_s4.bc2180.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2180.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-83/out/m84036_250809_035451_s4.bc2180.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2180.mapped.bam.bai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-83/call-get_reads_overlapping_repeats/_singularity_tmpdir_idz1pvjs/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-83/call-get_reads_overlapping_repeats/_singularity_tmpdir_idz1pvjs/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:26:04.432 wdl.w:ptcp.w:call-trgt-83.t:call-get_reads_overlapping_repeats NOTICE slurm_singularity run :: pid: 1206962, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-83/call-get_reads_overlapping_repeats/slurm_singularity.log.txt"
2025-09-15 20:26:04.461 wdl.w:ptcp.w:call-sawfish-83.t:call-run_sawfish.slurm_singularity INFO srun: job 51798136 queued and waiting for resources
2025-09-15 20:26:04.462 wdl.w:ptcp.w:call-sawfish-83.t:call-run_sawfish.slurm_singularity INFO srun: job 51798136 has been allocated resources
2025-09-15 20:26:04.462 wdl.w:ptcp.w:call-sawfish-83.t:call-run_sawfish.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:26:04.461 wdl.w:ptcp.w:call-paraphase-50.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for hbb for sample m84036_250809_035451_s4.bc2147 at 2025-09-15 20:25:17.966773...
2025-09-15 20:26:04.462 wdl.w:ptcp.w:call-paraphase-50.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for f8inv1 for sample m84036_250809_035451_s4.bc2147 at 2025-09-15 20:25:19.191825...
2025-09-15 20:26:04.462 wdl.w:ptcp.w:call-paraphase-50.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for hbb for sample m84036_250809_035451_s4.bc2147 at 2025-09-15 20:25:20.656736...
2025-09-15 20:26:04.462 wdl.w:ptcp.w:call-paraphase-50.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for hbb for sample m84036_250809_035451_s4.bc2147 at 2025-09-15 20:25:20.891915...
2025-09-15 20:26:04.462 wdl.w:ptcp.w:call-paraphase-50.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for f8inv1 for sample m84036_250809_035451_s4.bc2147 at 2025-09-15 20:25:22.335332...
2025-09-15 20:26:04.463 wdl.w:ptcp.w:call-paraphase-50.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for f8inv1 for sample m84036_250809_035451_s4.bc2147 at 2025-09-15 20:25:22.594758...
2025-09-15 20:26:04.463 wdl.w:ptcp.w:call-paraphase-50.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for rpgr for sample m84036_250809_035451_s4.bc2147 at 2025-09-15 20:25:56.280928...
2025-09-15 20:26:04.463 wdl.w:ptcp.w:call-paraphase-50.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for rpgr for sample m84036_250809_035451_s4.bc2147 at 2025-09-15 20:25:56.281547...
2025-09-15 20:26:04.463 wdl.w:ptcp.w:call-paraphase-50.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for rpgr for sample m84036_250809_035451_s4.bc2147 at 2025-09-15 20:25:57.635907...
2025-09-15 20:26:04.463 wdl.w:ptcp.w:call-paraphase-50.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for rpgr for sample m84036_250809_035451_s4.bc2147 at 2025-09-15 20:25:58.626338...
2025-09-15 20:26:04.461 wdl.w:ptcp.w:call-sawfish-67.t:call-run_sawfish INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2164_sawfish/m84036_250809_035451_s4.bc2164.sv.vcf.gz"
2025-09-15 20:26:04.463 wdl.w:ptcp.w:call-paraphase-50.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for rpgr for sample m84036_250809_035451_s4.bc2147 at 2025-09-15 20:25:58.825586...
2025-09-15 20:26:04.468 wdl.w:ptcp.w:call-sawfish-67.t:call-run_sawfish INFO output :: name: "vcf_tbi", value: "m84036_250809_035451_s4.bc2164_sawfish/m84036_250809_035451_s4.bc2164.sv.vcf.gz.tbi"
2025-09-15 20:26:04.470 wdl.w:ptcp.w:call-sawfish-67.t:call-run_sawfish INFO output :: name: "minimap2_bam", value: "m84036_250809_035451_s4.bc2164.minimap2.bam"
2025-09-15 20:26:04.472 wdl.w:ptcp.w:call-sawfish-67.t:call-run_sawfish INFO output :: name: "minimap2_bam_bai", value: "m84036_250809_035451_s4.bc2164.minimap2.bam.bai"
2025-09-15 20:26:04.484 wdl.w:ptcp.w:call-paraphase-11.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for rpgr for sample m84036_250809_035451_s4.bc2108 at 2025-09-15 20:25:55.200547...
2025-09-15 20:26:04.485 wdl.w:ptcp.w:call-paraphase-11.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for rpgr for sample m84036_250809_035451_s4.bc2108 at 2025-09-15 20:25:55.201359...
2025-09-15 20:26:04.492 wdl.w:ptcp.w:call-sawfish-39.t:call-run_sawfish INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2136_sawfish/m84036_250809_035451_s4.bc2136.sv.vcf.gz"
2025-09-15 20:26:04.499 wdl.w:ptcp.w:call-sawfish-39.t:call-run_sawfish INFO output :: name: "vcf_tbi", value: "m84036_250809_035451_s4.bc2136_sawfish/m84036_250809_035451_s4.bc2136.sv.vcf.gz.tbi"
2025-09-15 20:26:04.500 wdl.w:ptcp.w:call-sawfish-39.t:call-run_sawfish INFO output :: name: "minimap2_bam", value: "m84036_250809_035451_s4.bc2136.minimap2.bam"
2025-09-15 20:26:04.501 wdl.w:ptcp.w:call-sawfish-39.t:call-run_sawfish INFO output :: name: "minimap2_bam_bai", value: "m84036_250809_035451_s4.bc2136.minimap2.bam.bai"
2025-09-15 20:26:04.518 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:26:01 [ERROR] - No reads found for TRID=OPDM_ABCD3
2025-09-15 20:26:04.518 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:26:01 [ERROR] - No reads found for TRID=NIID_NOTCH2NLC
2025-09-15 20:26:04.518 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:26:01 [ERROR] - No reads found for TRID=DRPLA_ATN1
2025-09-15 20:26:04.518 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:26:01 [ERROR] - No reads found for TRID=SCA2_ATXN2
2025-09-15 20:26:04.518 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:26:01 [ERROR] - No reads found for TRID=OPDM4_RILPL1
2025-09-15 20:26:04.518 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:26:01 [ERROR] - No reads found for TRID=SCA8_ATXN8OS
2025-09-15 20:26:04.518 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:26:01 [ERROR] - No reads found for TRID=OPMD_PABPN1
2025-09-15 20:26:04.518 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:26:01 [ERROR] - No reads found for TRID=SCA27B_FGF14
2025-09-15 20:26:04.518 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:26:01 [ERROR] - No reads found for TRID=SCA3_ATXN3
2025-09-15 20:26:04.519 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:26:01 [ERROR] - No reads found for TRID=SCA31_BEAN1
2025-09-15 20:26:04.519 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:26:02 [ERROR] - No reads found for TRID=SCA4_ZFHX3
2025-09-15 20:26:04.519 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:26:02 [ERROR] - No reads found for TRID=HDL2_JPH3
2025-09-15 20:26:04.519 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:26:02 [ERROR] - No reads found for TRID=FECD3_TCF4
2025-09-15 20:26:04.519 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:26:02 [ERROR] - No reads found for TRID=SCA6_CACNA1A
2025-09-15 20:26:04.519 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:26:02 [ERROR] - No reads found for TRID=OPDM2_GIPC1
2025-09-15 20:26:04.519 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:26:02 [ERROR] - No reads found for TRID=FRA2A_AFF3
2025-09-15 20:26:04.519 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:26:02 [ERROR] - No reads found for TRID=DM1_DMPK
2025-09-15 20:26:04.519 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:26:02 [ERROR] - No reads found for TRID=SD5_HOXD13
2025-09-15 20:26:04.519 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:26:02 [ERROR] - No reads found for TRID=SCA36_NOP56
2025-09-15 20:26:04.519 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:26:02 [ERROR] - No reads found for TRID=CJD_PRNP
2025-09-15 20:26:04.519 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:26:02 [ERROR] - No reads found for TRID=EPM1_CSTB
2025-09-15 20:26:04.519 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:26:02 [ERROR] - No reads found for TRID=SCA10_ATXN10
2025-09-15 20:26:04.519 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:26:02 [ERROR] - No reads found for TRID=CCHS_PHOX2B
2025-09-15 20:26:04.519 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:26:02 [ERROR] - No reads found for TRID=SCA12_PPP2R2B
2025-09-15 20:26:04.519 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:26:02 [ERROR] - No reads found for TRID=SCA1_ATXN1
2025-09-15 20:26:04.519 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:26:02 [ERROR] - No reads found for TRID=OPDM1_LRP12
2025-09-15 20:26:04.520 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:26:03 [ERROR] - No reads found for TRID=FAME1_SAMD12
2025-09-15 20:26:04.608 wdl.w:ptcp.w:call-trgt-92.t:call-trgt_plot_meth_allele INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2189.meth_allele.trgt_plots.zip"
2025-09-15 20:26:04.634 wdl.w:ptcp.w:call-sawfish-67.t:call-run_sawfish NOTICE done
2025-09-15 20:26:04.640 wdl.w:ptcp.w:call-sawfish-67 NOTICE finish :: job: "call-run_sawfish"
2025-09-15 20:26:04.640 wdl.w:ptcp.w:call-sawfish-67 INFO output :: job: "call-run_sawfish", values: {"minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-67/call-run_sawfish/out/m84036_250809_035451_s4.bc2164.minimap2.bam.bai", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-67/call-run_sawfish/out/m84036_250809_035451_s4.bc2164.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-67/call-run_sawfish/out/m84036_250809_035451_s4.bc2164_sawfish/m84036_250809_035451_s4.bc2164.sv.vcf.gz.tbi", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-67/call-run_sawfish/out/m84036_250809_035451_s4.bc2164_sawfish/m84036_250809_035451_s4.bc2164.sv.vcf.gz"}
2025-09-15 20:26:04.640 wdl.w:ptcp.w:call-sawfish-67 INFO visit :: node: "output-minimap2_bam", values: {"minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-67/call-run_sawfish/out/m84036_250809_035451_s4.bc2164.minimap2.bam"}
2025-09-15 20:26:04.641 wdl.w:ptcp.w:call-sawfish-67 INFO visit :: node: "output-minimap2_bam_bai", values: {"minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-67/call-run_sawfish/out/m84036_250809_035451_s4.bc2164.minimap2.bam.bai"}
2025-09-15 20:26:04.641 wdl.w:ptcp.w:call-sawfish-67 INFO visit :: node: "output-vcf", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-67/call-run_sawfish/out/m84036_250809_035451_s4.bc2164_sawfish/m84036_250809_035451_s4.bc2164.sv.vcf.gz"}
2025-09-15 20:26:04.641 wdl.w:ptcp.w:call-sawfish-67 INFO visit :: node: "output-vcf_tbi", values: {"vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-67/call-run_sawfish/out/m84036_250809_035451_s4.bc2164_sawfish/m84036_250809_035451_s4.bc2164.sv.vcf.gz.tbi"}
2025-09-15 20:26:04.641 wdl.w:ptcp.w:call-sawfish-67 INFO visit :: node: "outputs", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-67/call-run_sawfish/out/m84036_250809_035451_s4.bc2164_sawfish/m84036_250809_035451_s4.bc2164.sv.vcf.gz", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-67/call-run_sawfish/out/m84036_250809_035451_s4.bc2164.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-67/call-run_sawfish/out/m84036_250809_035451_s4.bc2164_sawfish/m84036_250809_035451_s4.bc2164.sv.vcf.gz.tbi", "minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-67/call-run_sawfish/out/m84036_250809_035451_s4.bc2164.minimap2.bam.bai"}
2025-09-15 20:26:04.642 wdl.w:ptcp.w:call-paraphase-78.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for smn1 for sample m84036_250809_035451_s4.bc2175 at 2025-09-15 20:25:18.116738...
2025-09-15 20:26:04.642 wdl.w:ptcp.w:call-paraphase-78.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for hba for sample m84036_250809_035451_s4.bc2175 at 2025-09-15 20:25:18.218036...
2025-09-15 20:26:04.642 wdl.w:ptcp.w:call-paraphase-78.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for gba for sample m84036_250809_035451_s4.bc2175 at 2025-09-15 20:25:19.461462...
2025-09-15 20:26:04.643 wdl.w:ptcp.w:call-paraphase-78.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for cyp21 for sample m84036_250809_035451_s4.bc2175 at 2025-09-15 20:25:20.781115...
2025-09-15 20:26:04.643 wdl.w:ptcp.w:call-paraphase-78.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for smn1 for sample m84036_250809_035451_s4.bc2175 at 2025-09-15 20:25:39.912063...
2025-09-15 20:26:04.643 wdl.w:ptcp.w:call-paraphase-78.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning to gene2 region for smn1 for sample m84036_250809_035451_s4.bc2175 at 2025-09-15 20:25:40.357095...
2025-09-15 20:26:04.643 wdl.w:ptcp.w:call-paraphase-78.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for smn1 for sample m84036_250809_035451_s4.bc2175 at 2025-09-15 20:25:42.349471...
2025-09-15 20:26:04.648 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_genotype NOTICE task setup :: name: "trgt_genotype", source: "./trgt.wdl", line: 272, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-83/call-trgt_genotype", thread: 140610879071808
2025-09-15 20:26:04.657 wdl.w:ptcp.w:call-sawfish-39.t:call-run_sawfish NOTICE done
2025-09-15 20:26:04.663 wdl.w:ptcp.w:call-sawfish-39 NOTICE finish :: job: "call-run_sawfish"
2025-09-15 20:26:04.664 wdl.w:ptcp.w:call-sawfish-39 INFO output :: job: "call-run_sawfish", values: {"minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-39/call-run_sawfish/out/m84036_250809_035451_s4.bc2136.minimap2.bam.bai", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-39/call-run_sawfish/out/m84036_250809_035451_s4.bc2136.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-39/call-run_sawfish/out/m84036_250809_035451_s4.bc2136_sawfish/m84036_250809_035451_s4.bc2136.sv.vcf.gz.tbi", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-39/call-run_sawfish/out/m84036_250809_035451_s4.bc2136_sawfish/m84036_250809_035451_s4.bc2136.sv.vcf.gz"}
2025-09-15 20:26:04.664 wdl.w:ptcp.w:call-sawfish-39 INFO visit :: node: "output-minimap2_bam", values: {"minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-39/call-run_sawfish/out/m84036_250809_035451_s4.bc2136.minimap2.bam"}
2025-09-15 20:26:04.664 wdl.w:ptcp.w:call-sawfish-39 INFO visit :: node: "output-minimap2_bam_bai", values: {"minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-39/call-run_sawfish/out/m84036_250809_035451_s4.bc2136.minimap2.bam.bai"}
2025-09-15 20:26:04.664 wdl.w:ptcp.w:call-sawfish-39 INFO visit :: node: "output-vcf", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-39/call-run_sawfish/out/m84036_250809_035451_s4.bc2136_sawfish/m84036_250809_035451_s4.bc2136.sv.vcf.gz"}
2025-09-15 20:26:04.665 wdl.w:ptcp.w:call-sawfish-39 INFO visit :: node: "output-vcf_tbi", values: {"vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-39/call-run_sawfish/out/m84036_250809_035451_s4.bc2136_sawfish/m84036_250809_035451_s4.bc2136.sv.vcf.gz.tbi"}
2025-09-15 20:26:04.665 wdl.w:ptcp.w:call-sawfish-39 INFO visit :: node: "outputs", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-39/call-run_sawfish/out/m84036_250809_035451_s4.bc2136_sawfish/m84036_250809_035451_s4.bc2136.sv.vcf.gz", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-39/call-run_sawfish/out/m84036_250809_035451_s4.bc2136.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-39/call-run_sawfish/out/m84036_250809_035451_s4.bc2136_sawfish/m84036_250809_035451_s4.bc2136.sv.vcf.gz.tbi", "minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-39/call-run_sawfish/out/m84036_250809_035451_s4.bc2136.minimap2.bam.bai"}
2025-09-15 20:26:04.670 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_genotype INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:26:04.670 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_genotype INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:26:04.670 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_genotype INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:26:04.671 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_genotype INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:26:04.671 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_genotype INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2180.mapped.bam.bai"
2025-09-15 20:26:04.671 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_genotype INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2180.mapped.bam"
2025-09-15 20:26:04.671 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_genotype INFO input :: name: "sex", value: "F"
2025-09-15 20:26:04.671 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_genotype INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2180"
2025-09-15 20:26:04.671 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_genotype INFO eval :: name: "mem_gb", value: 16
2025-09-15 20:26:04.671 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_genotype INFO eval :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2180.trgt"
2025-09-15 20:26:04.672 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_genotype INFO eval :: name: "threads", value: 8
2025-09-15 20:26:04.672 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_genotype INFO eval :: name: "disk_size", value: 27
2025-09-15 20:26:04.672 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_genotype INFO eval :: name: "karyotype", value: "XX"
2025-09-15 20:26:04.672 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_genotype INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 8, memory_reservation: 16000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:26:04.673 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_genotype WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:26:04.673 wdl.w:ptcp.w:call-paraphase-89.t:call-call_f8 NOTICE task setup :: name: "call_f8", source: "./paraphase.wdl", line: 232, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-89/call-call_f8", thread: 140607129368128
2025-09-15 20:26:04.674 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_genotype INFO provisioned :: seconds_waited: 0, cpu: 8, mem_bytes: 16000000000
2025-09-15 20:26:04.674 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_genotype INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:26:04.700 wdl.w:ptcp.w:call-paraphase-89.t:call-call_f8 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:26:04.700 wdl.w:ptcp.w:call-paraphase-89.t:call-call_f8 INFO input :: name: "genome_version", value: "38"
2025-09-15 20:26:04.700 wdl.w:ptcp.w:call-paraphase-89.t:call-call_f8 INFO input :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2186"
2025-09-15 20:26:04.700 wdl.w:ptcp.w:call-paraphase-89.t:call-call_f8 INFO input :: name: "paraphase_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2186.paraphase.bam.bai"
2025-09-15 20:26:04.700 wdl.w:ptcp.w:call-paraphase-89.t:call-call_f8 INFO input :: name: "paraphase_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2186.paraphase.bam"
2025-09-15 20:26:04.700 wdl.w:ptcp.w:call-paraphase-89.t:call-call_f8 INFO input :: name: "sex", value: "F"
2025-09-15 20:26:04.701 wdl.w:ptcp.w:call-paraphase-89.t:call-call_f8 INFO eval :: name: "threads", value: 1
2025-09-15 20:26:04.701 wdl.w:ptcp.w:call-paraphase-89.t:call-call_f8 INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:26:04.701 wdl.w:ptcp.w:call-paraphase-89.t:call-call_f8 INFO eval :: name: "disk_size", value: 11
2025-09-15 20:26:04.701 wdl.w:ptcp.w:call-paraphase-89.t:call-call_f8 INFO eval :: name: "sample_sex", value: "F"
2025-09-15 20:26:04.702 wdl.w:ptcp.w:call-paraphase-89.t:call-call_f8 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:26:04.702 wdl.w:ptcp.w:call-paraphase-89.t:call-call_f8 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:26:04.702 wdl.w:ptcp.w:call-paraphase-89.t:call-call_f8 INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:26:04.703 wdl.w:ptcp.w:call-paraphase-89.t:call-call_f8 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:26:04.705 wdl.w:ptcp.w:call-sawfish-67 NOTICE done
2025-09-15 20:26:04.705 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_plot_meth_waterfall INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2184.meth_waterfall.trgt_plots.zip"
2025-09-15 20:26:04.713 wdl.w:ptcp NOTICE finish :: job: "call-sawfish-67"
2025-09-15 20:26:04.713 wdl.w:ptcp INFO output :: job: "call-sawfish-67", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-67/out/m84036_250809_035451_s4.bc2164_sawfish/m84036_250809_035451_s4.bc2164.sv.vcf.gz", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-67/out/m84036_250809_035451_s4.bc2164.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-67/out/m84036_250809_035451_s4.bc2164_sawfish/m84036_250809_035451_s4.bc2164.sv.vcf.gz.tbi", "minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-67/out/m84036_250809_035451_s4.bc2164.minimap2.bam.bai"}
2025-09-15 20:26:04.735 wdl.w:ptcp.w:call-trgt-82.t:call-trgt_plot_meth_allele.slurm_singularity INFO srun: job 51798137 queued and waiting for resources
2025-09-15 20:26:04.735 wdl.w:ptcp.w:call-trgt-82.t:call-trgt_plot_meth_allele.slurm_singularity INFO srun: job 51798137 has been allocated resources
2025-09-15 20:26:04.735 wdl.w:ptcp.w:call-trgt-82.t:call-trgt_plot_meth_allele.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:26:04.746 wdl.w:ptcp.w:call-sawfish-39 NOTICE done
2025-09-15 20:26:04.753 wdl.w:ptcp NOTICE finish :: job: "call-sawfish-39"
2025-09-15 20:26:04.753 wdl.w:ptcp INFO output :: job: "call-sawfish-39", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-39/out/m84036_250809_035451_s4.bc2136_sawfish/m84036_250809_035451_s4.bc2136.sv.vcf.gz", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-39/out/m84036_250809_035451_s4.bc2136.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-39/out/m84036_250809_035451_s4.bc2136_sawfish/m84036_250809_035451_s4.bc2136.sv.vcf.gz.tbi", "minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-39/out/m84036_250809_035451_s4.bc2136.minimap2.bam.bai"}
2025-09-15 20:26:04.755 wdl.w:ptcp.w:call-trgt-92.t:call-trgt_plot_meth_allele NOTICE done
2025-09-15 20:26:04.760 wdl.w:ptcp.w:call-trgt-92 NOTICE finish :: job: "call-trgt_plot_meth_allele"
2025-09-15 20:26:04.761 wdl.w:ptcp.w:call-trgt-92 INFO output :: job: "call-trgt_plot_meth_allele", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-92/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2189.meth_allele.trgt_plots.zip"}
2025-09-15 20:26:04.761 wdl.w:ptcp.w:call-trgt-92 INFO visit :: node: "output-images_meth_allele", values: {"images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-92/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2189.meth_allele.trgt_plots.zip"}
2025-09-15 20:26:04.766 wdl.w:ptcp.w:call-paraphase-89.t:call-call_f8 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 8, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-89/call-call_f8/_singularity_tmpdir_iu0t86mr"
2025-09-15 20:26:04.766 wdl.w:ptcp.w:call-paraphase-89.t:call-call_f8 INFO Slurm invocation: srun --job-name call-call_f8 --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-89/call-call_f8/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-89/call-call_f8/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-89/call-call_f8/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-89/call-call_f8/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-89/call-run_paraphase/out/m84036_250809_035451_s4.bc2186_paraphase/m84036_250809_035451_s4.bc2186.paraphase.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2186.paraphase.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-89/call-run_paraphase/out/m84036_250809_035451_s4.bc2186_paraphase/m84036_250809_035451_s4.bc2186.paraphase.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2186.paraphase.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-89/call-call_f8/_singularity_tmpdir_iu0t86mr/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-89/call-call_f8/_singularity_tmpdir_iu0t86mr/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:26:04.769 wdl.w:ptcp.w:call-trgt-93.t:call-trgt_plot_meth_allele NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-93/call-trgt_plot_meth_allele", thread: 140610887464512
2025-09-15 20:26:04.770 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_genotype INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 11, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-83/call-trgt_genotype/_singularity_tmpdir_8tte5m7p"
2025-09-15 20:26:04.770 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_genotype INFO Slurm invocation: srun --job-name call-trgt_genotype --partition compute,compute9 --cpus-per-task 8 --mem 15259M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-83/call-trgt_genotype/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-83/call-trgt_genotype/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-83/call-trgt_genotype/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-83/call-trgt_genotype/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-83/out/m84036_250809_035451_s4.bc2180.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2180.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-83/out/m84036_250809_035451_s4.bc2180.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2180.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-83/call-trgt_genotype/_singularity_tmpdir_8tte5m7p/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-83/call-trgt_genotype/_singularity_tmpdir_8tte5m7p/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:26:04.788 wdl.w:ptcp.w:call-trgt-93.t:call-trgt_plot_meth_allele INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:26:04.788 wdl.w:ptcp.w:call-trgt-93.t:call-trgt_plot_meth_allele INFO input :: name: "waterfall", value: false
2025-09-15 20:26:04.788 wdl.w:ptcp.w:call-trgt-93.t:call-trgt_plot_meth_allele INFO input :: name: "methylation", value: true
2025-09-15 20:26:04.788 wdl.w:ptcp.w:call-trgt-93.t:call-trgt_plot_meth_allele INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:26:04.788 wdl.w:ptcp.w:call-trgt-93.t:call-trgt_plot_meth_allele INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:26:04.788 wdl.w:ptcp.w:call-trgt-93.t:call-trgt_plot_meth_allele INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:26:04.788 wdl.w:ptcp.w:call-trgt-93.t:call-trgt_plot_meth_allele INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2190.trgt.sorted.spanning.bam.bai"
2025-09-15 20:26:04.788 wdl.w:ptcp.w:call-trgt-93.t:call-trgt_plot_meth_allele INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2190.trgt.sorted.spanning.bam"
2025-09-15 20:26:04.788 wdl.w:ptcp.w:call-trgt-93.t:call-trgt_plot_meth_allele INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2190.trgt.vcf"
2025-09-15 20:26:04.788 wdl.w:ptcp.w:call-trgt-93.t:call-trgt_plot_meth_allele INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2190"
2025-09-15 20:26:04.789 wdl.w:ptcp.w:call-trgt-93.t:call-trgt_plot_meth_allele INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:26:04.789 wdl.w:ptcp.w:call-trgt-93.t:call-trgt_plot_meth_allele INFO eval :: name: "plot_type", value: "allele"
2025-09-15 20:26:04.789 wdl.w:ptcp.w:call-trgt-93.t:call-trgt_plot_meth_allele INFO eval :: name: "show", value: "meth"
2025-09-15 20:26:04.789 wdl.w:ptcp.w:call-trgt-93.t:call-trgt_plot_meth_allele INFO eval :: name: "threads", value: 1
2025-09-15 20:26:04.789 wdl.w:ptcp.w:call-trgt-93.t:call-trgt_plot_meth_allele INFO eval :: name: "disk_size", value: 27
2025-09-15 20:26:04.789 wdl.w:ptcp.w:call-trgt-93.t:call-trgt_plot_meth_allele INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2190.meth_allele"
2025-09-15 20:26:04.790 wdl.w:ptcp.w:call-trgt-93.t:call-trgt_plot_meth_allele INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:26:04.791 wdl.w:ptcp.w:call-trgt-93.t:call-trgt_plot_meth_allele WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:26:04.792 wdl.w:ptcp.w:call-trgt-93.t:call-trgt_plot_meth_allele INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:26:04.792 wdl.w:ptcp.w:call-trgt-93.t:call-trgt_plot_meth_allele INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:26:04.797 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_genotype NOTICE slurm_singularity run :: pid: 1206972, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-83/call-trgt_genotype/slurm_singularity.log.txt"
2025-09-15 20:26:04.797 wdl.w:ptcp.w:call-paraphase-89.t:call-call_f8 NOTICE slurm_singularity run :: pid: 1206971, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-89/call-call_f8/slurm_singularity.log.txt"
2025-09-15 20:26:04.812 wdl.w:ptcp.w:call-trgt-87.t:call-trgt_plot_meth_waterfall NOTICE done
2025-09-15 20:26:04.817 wdl.w:ptcp.w:call-trgt-87 NOTICE finish :: job: "call-trgt_plot_meth_waterfall"
2025-09-15 20:26:04.817 wdl.w:ptcp.w:call-trgt-87 INFO output :: job: "call-trgt_plot_meth_waterfall", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-87/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2184.meth_waterfall.trgt_plots.zip"}
2025-09-15 20:26:04.818 wdl.w:ptcp.w:call-trgt-87 INFO visit :: node: "output-images_meth_waterfall", values: {"images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-87/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2184.meth_waterfall.trgt_plots.zip"}
2025-09-15 20:26:04.818 wdl.w:ptcp.w:call-trgt-87 INFO visit :: node: "outputs", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-87/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2184.motifs_waterfall.trgt_plots.zip", "images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-87/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2184.meth_allele.trgt_plots.zip", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-87/call-trgt_genotype/out/m84036_250809_035451_s4.bc2184.trgt.sorted.spanning.bam.bai", "images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-87/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2184.motifs_allele.trgt_plots.zip", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-87/call-trgt_genotype/out/m84036_250809_035451_s4.bc2184.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-87/call-trgt_genotype/out/m84036_250809_035451_s4.bc2184.trgt.vcf", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-87/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2184.repeats.bam", "images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-87/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2184.meth_waterfall.trgt_plots.zip", "reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-87/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2184.repeats.bam.bai"}
2025-09-15 20:26:04.826 wdl.w:ptcp.w:call-trgt-93.t:call-trgt_plot_meth_waterfall NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-93/call-trgt_plot_meth_waterfall", thread: 140611432728128
2025-09-15 20:26:04.844 wdl.w:ptcp.w:call-trgt-93.t:call-trgt_plot_meth_waterfall INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:26:04.844 wdl.w:ptcp.w:call-trgt-93.t:call-trgt_plot_meth_waterfall INFO input :: name: "waterfall", value: true
2025-09-15 20:26:04.844 wdl.w:ptcp.w:call-trgt-93.t:call-trgt_plot_meth_waterfall INFO input :: name: "methylation", value: true
2025-09-15 20:26:04.844 wdl.w:ptcp.w:call-trgt-93.t:call-trgt_plot_meth_waterfall INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:26:04.844 wdl.w:ptcp.w:call-trgt-93.t:call-trgt_plot_meth_waterfall INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:26:04.844 wdl.w:ptcp.w:call-trgt-93.t:call-trgt_plot_meth_waterfall INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:26:04.844 wdl.w:ptcp.w:call-trgt-93.t:call-trgt_plot_meth_waterfall INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2190.trgt.sorted.spanning.bam.bai"
2025-09-15 20:26:04.844 wdl.w:ptcp.w:call-trgt-93.t:call-trgt_plot_meth_waterfall INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2190.trgt.sorted.spanning.bam"
2025-09-15 20:26:04.844 wdl.w:ptcp.w:call-trgt-93.t:call-trgt_plot_meth_waterfall INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2190.trgt.vcf"
2025-09-15 20:26:04.844 wdl.w:ptcp.w:call-trgt-93.t:call-trgt_plot_meth_waterfall INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2190"
2025-09-15 20:26:04.845 wdl.w:ptcp.w:call-trgt-93.t:call-trgt_plot_meth_waterfall INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:26:04.845 wdl.w:ptcp.w:call-trgt-93.t:call-trgt_plot_meth_waterfall INFO eval :: name: "plot_type", value: "waterfall"
2025-09-15 20:26:04.845 wdl.w:ptcp.w:call-trgt-93.t:call-trgt_plot_meth_waterfall INFO eval :: name: "show", value: "meth"
2025-09-15 20:26:04.845 wdl.w:ptcp.w:call-trgt-93.t:call-trgt_plot_meth_waterfall INFO eval :: name: "threads", value: 1
2025-09-15 20:26:04.845 wdl.w:ptcp.w:call-trgt-93.t:call-trgt_plot_meth_waterfall INFO eval :: name: "disk_size", value: 27
2025-09-15 20:26:04.846 wdl.w:ptcp.w:call-trgt-93.t:call-trgt_plot_meth_waterfall INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2190.meth_waterfall"
2025-09-15 20:26:04.846 wdl.w:ptcp.w:call-trgt-93.t:call-trgt_plot_meth_waterfall INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:26:04.846 wdl.w:ptcp.w:call-trgt-93.t:call-trgt_plot_meth_waterfall WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:26:04.846 wdl.w:ptcp.w:call-trgt-93.t:call-trgt_plot_meth_waterfall INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:26:04.847 wdl.w:ptcp.w:call-trgt-93.t:call-trgt_plot_meth_waterfall INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:26:04.867 wdl.w:ptcp.w:call-trgt-93.t:call-trgt_plot_meth_allele INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-93/call-trgt_plot_meth_allele/_singularity_tmpdir_wh51genn"
2025-09-15 20:26:04.867 wdl.w:ptcp.w:call-trgt-93.t:call-trgt_plot_meth_allele INFO Slurm invocation: srun --job-name call-trgt_plot_meth_allele --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-93/call-trgt_plot_meth_allele/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-93/call-trgt_plot_meth_allele/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-93/call-trgt_plot_meth_allele/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-93/call-trgt_plot_meth_allele/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-93/call-trgt_genotype/out/m84036_250809_035451_s4.bc2190.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2190.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-93/call-trgt_genotype/out/m84036_250809_035451_s4.bc2190.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2190.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-93/call-trgt_genotype/out/m84036_250809_035451_s4.bc2190.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2190.trgt.sorted.spanning.bam:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-93/call-trgt_plot_meth_allele/_singularity_tmpdir_wh51genn/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-93/call-trgt_plot_meth_allele/_singularity_tmpdir_wh51genn/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:26:04.882 wdl.w:ptcp.w:call-trgt-93.t:call-trgt_plot_meth_allele NOTICE slurm_singularity run :: pid: 1206976, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-93/call-trgt_plot_meth_allele/slurm_singularity.log.txt"
2025-09-15 20:26:04.902 wdl.w:ptcp.w:call-trgt-82.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:26:04 [ERROR] - No reads found for TRID=SCA37_DAB1
2025-09-15 20:26:04.902 wdl.w:ptcp.w:call-trgt-82.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:26:04 [ERROR] - No reads found for TRID=OPDM_ABCD3
2025-09-15 20:26:04.902 wdl.w:ptcp.w:call-trgt-82.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:26:04 [ERROR] - No reads found for TRID=NIID_NOTCH2NLC
2025-09-15 20:26:04.902 wdl.w:ptcp.w:call-trgt-82.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:26:04 [ERROR] - No reads found for TRID=DRPLA_ATN1
2025-09-15 20:26:04.902 wdl.w:ptcp.w:call-trgt-82.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:26:04 [ERROR] - No reads found for TRID=SCA2_ATXN2
2025-09-15 20:26:04.902 wdl.w:ptcp.w:call-trgt-82.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:26:04 [ERROR] - No reads found for TRID=OPDM4_RILPL1
2025-09-15 20:26:04.902 wdl.w:ptcp.w:call-trgt-82.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:26:04 [ERROR] - No reads found for TRID=SCA8_ATXN8OS
2025-09-15 20:26:04.902 wdl.w:ptcp.w:call-trgt-82.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:26:04 [ERROR] - No reads found for TRID=SCA27B_FGF14
2025-09-15 20:26:04.902 wdl.w:ptcp.w:call-trgt-82.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:26:04 [ERROR] - No reads found for TRID=OPMD_PABPN1
2025-09-15 20:26:04.902 wdl.w:ptcp.w:call-trgt-82.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:26:04 [ERROR] - No reads found for TRID=SCA31_BEAN1
2025-09-15 20:26:04.907 wdl.w:ptcp.w:call-trgt-87 NOTICE done
2025-09-15 20:26:04.913 wdl.w:ptcp NOTICE finish :: job: "call-trgt-87"
2025-09-15 20:26:04.913 wdl.w:ptcp INFO output :: job: "call-trgt-87", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-87/out/m84036_250809_035451_s4.bc2184.motifs_waterfall.trgt_plots.zip", "images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-87/out/m84036_250809_035451_s4.bc2184.meth_allele.trgt_plots.zip", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-87/out/m84036_250809_035451_s4.bc2184.trgt.sorted.spanning.bam.bai", "images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-87/out/m84036_250809_035451_s4.bc2184.motifs_allele.trgt_plots.zip", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-87/out/m84036_250809_035451_s4.bc2184.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-87/out/m84036_250809_035451_s4.bc2184.trgt.vcf", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-87/out/m84036_250809_035451_s4.bc2184.repeats.bam", "images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-87/out/m84036_250809_035451_s4.bc2184.meth_waterfall.trgt_plots.zip", "reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-87/out/m84036_250809_035451_s4.bc2184.repeats.bam.bai"}
2025-09-15 20:26:04.914 wdl.w:ptcp.w:call-trgt-82.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO srun: job 51798138 queued and waiting for resources
2025-09-15 20:26:04.914 wdl.w:ptcp.w:call-trgt-82.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO srun: job 51798138 has been allocated resources
2025-09-15 20:26:04.914 wdl.w:ptcp.w:call-trgt-82.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:26:04.920 wdl.w:ptcp.w:call-trgt-93.t:call-trgt_plot_meth_waterfall INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-93/call-trgt_plot_meth_waterfall/_singularity_tmpdir_i5ukmfuy"
2025-09-15 20:26:04.920 wdl.w:ptcp.w:call-trgt-93.t:call-trgt_plot_meth_waterfall INFO Slurm invocation: srun --job-name call-trgt_plot_meth_waterfall --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-93/call-trgt_plot_meth_waterfall/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-93/call-trgt_plot_meth_waterfall/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-93/call-trgt_plot_meth_waterfall/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-93/call-trgt_plot_meth_waterfall/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-93/call-trgt_genotype/out/m84036_250809_035451_s4.bc2190.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2190.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-93/call-trgt_genotype/out/m84036_250809_035451_s4.bc2190.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2190.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-93/call-trgt_genotype/out/m84036_250809_035451_s4.bc2190.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2190.trgt.sorted.spanning.bam:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-93/call-trgt_plot_meth_waterfall/_singularity_tmpdir_i5ukmfuy/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-93/call-trgt_plot_meth_waterfall/_singularity_tmpdir_i5ukmfuy/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:26:04.923 wdl.w:ptcp.w:call-trgt-82.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:26:04 [ERROR] - No reads found for TRID=SCA37_DAB1
2025-09-15 20:26:04.923 wdl.w:ptcp.w:call-trgt-82.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:26:04 [ERROR] - No reads found for TRID=OPDM_ABCD3
2025-09-15 20:26:04.923 wdl.w:ptcp.w:call-trgt-82.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:26:04 [ERROR] - No reads found for TRID=NIID_NOTCH2NLC
2025-09-15 20:26:04.923 wdl.w:ptcp.w:call-trgt-82.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:26:04 [ERROR] - No reads found for TRID=DRPLA_ATN1
2025-09-15 20:26:04.923 wdl.w:ptcp.w:call-trgt-82.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:26:04 [ERROR] - No reads found for TRID=SCA2_ATXN2
2025-09-15 20:26:04.923 wdl.w:ptcp.w:call-trgt-82.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:26:04 [ERROR] - No reads found for TRID=OPDM4_RILPL1
2025-09-15 20:26:04.923 wdl.w:ptcp.w:call-trgt-82.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:26:04 [ERROR] - No reads found for TRID=SCA8_ATXN8OS
2025-09-15 20:26:04.923 wdl.w:ptcp.w:call-trgt-82.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:26:04 [ERROR] - No reads found for TRID=SCA27B_FGF14
2025-09-15 20:26:04.923 wdl.w:ptcp.w:call-trgt-82.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:26:04 [ERROR] - No reads found for TRID=OPMD_PABPN1
2025-09-15 20:26:04.923 wdl.w:ptcp.w:call-trgt-82.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:26:04 [ERROR] - No reads found for TRID=SCA31_BEAN1
2025-09-15 20:26:04.931 wdl.w:ptcp.w:call-trgt-82.t:call-trgt_plot_motifs_allele.slurm_singularity INFO srun: job 51798139 queued and waiting for resources
2025-09-15 20:26:04.932 wdl.w:ptcp.w:call-trgt-82.t:call-trgt_plot_motifs_allele.slurm_singularity INFO srun: job 51798139 has been allocated resources
2025-09-15 20:26:04.932 wdl.w:ptcp.w:call-trgt-82.t:call-trgt_plot_motifs_allele.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:26:04.932 wdl.w:ptcp.w:call-trgt-93.t:call-trgt_plot_meth_waterfall NOTICE slurm_singularity run :: pid: 1206978, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-93/call-trgt_plot_meth_waterfall/slurm_singularity.log.txt"
2025-09-15 20:26:05.255 wdl.w:ptcp.w:call-trgt-82.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:26:05 [ERROR] - No reads found for TRID=SCA37_DAB1
2025-09-15 20:26:05.255 wdl.w:ptcp.w:call-trgt-82.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:26:05 [ERROR] - No reads found for TRID=OPDM_ABCD3
2025-09-15 20:26:05.255 wdl.w:ptcp.w:call-trgt-82.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:26:05 [ERROR] - No reads found for TRID=NIID_NOTCH2NLC
2025-09-15 20:26:05.255 wdl.w:ptcp.w:call-trgt-82.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:26:05 [ERROR] - No reads found for TRID=DRPLA_ATN1
2025-09-15 20:26:05.255 wdl.w:ptcp.w:call-trgt-82.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:26:05 [ERROR] - No reads found for TRID=SCA2_ATXN2
2025-09-15 20:26:05.255 wdl.w:ptcp.w:call-trgt-82.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:26:05 [ERROR] - No reads found for TRID=OPDM4_RILPL1
2025-09-15 20:26:05.262 wdl.w:ptcp.w:call-trgt-82.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO srun: job 51798140 queued and waiting for resources
2025-09-15 20:26:05.262 wdl.w:ptcp.w:call-trgt-82.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO srun: job 51798140 has been allocated resources
2025-09-15 20:26:05.262 wdl.w:ptcp.w:call-trgt-82.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:26:05.442 wdl.w:ptcp.w:call-trgt-83.t:call-get_reads_overlapping_repeats.slurm_singularity INFO srun: job 51798141 queued and waiting for resources
2025-09-15 20:26:05.442 wdl.w:ptcp.w:call-trgt-83.t:call-get_reads_overlapping_repeats.slurm_singularity INFO srun: job 51798141 has been allocated resources
2025-09-15 20:26:05.442 wdl.w:ptcp.w:call-trgt-83.t:call-get_reads_overlapping_repeats.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:26:05.539 wdl.w:ptcp.w:call-paraphase-87.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for smn1 for sample m84036_250809_035451_s4.bc2184 at 2025-09-15 20:25:56.544099...
2025-09-15 20:26:05.701 wdl.w:ptcp.w:call-trgt-83.t:call-get_reads_overlapping_repeats INFO output :: name: "reads_overlapping_repeats", value: "m84036_250809_035451_s4.bc2180.repeats.bam"
2025-09-15 20:26:05.704 wdl.w:ptcp.w:call-trgt-83.t:call-get_reads_overlapping_repeats INFO output :: name: "reads_overlapping_repeats_bai", value: "m84036_250809_035451_s4.bc2180.repeats.bam.bai"
2025-09-15 20:26:05.767 wdl.w:ptcp.w:call-trgt-83.t:call-get_reads_overlapping_repeats NOTICE done
2025-09-15 20:26:05.774 wdl.w:ptcp.w:call-trgt-83 NOTICE finish :: job: "call-get_reads_overlapping_repeats"
2025-09-15 20:26:05.774 wdl.w:ptcp.w:call-trgt-83 INFO output :: job: "call-get_reads_overlapping_repeats", values: {"reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-83/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2180.repeats.bam.bai", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-83/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2180.repeats.bam"}
2025-09-15 20:26:05.774 wdl.w:ptcp.w:call-trgt-83 INFO visit :: node: "output-reads_overlapping_repeats", values: {"reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-83/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2180.repeats.bam"}
2025-09-15 20:26:05.774 wdl.w:ptcp.w:call-trgt-83 INFO visit :: node: "output-reads_overlapping_repeats_bai", values: {"reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-83/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2180.repeats.bam.bai"}
2025-09-15 20:26:05.781 wdl.w:ptcp.w:call-trgt-93.t:call-trgt_plot_motifs_allele NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-93/call-trgt_plot_motifs_allele", thread: 140608731588160
2025-09-15 20:26:05.801 wdl.w:ptcp.w:call-trgt-93.t:call-trgt_plot_motifs_allele INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:26:05.801 wdl.w:ptcp.w:call-trgt-93.t:call-trgt_plot_motifs_allele INFO input :: name: "waterfall", value: false
2025-09-15 20:26:05.801 wdl.w:ptcp.w:call-trgt-93.t:call-trgt_plot_motifs_allele INFO input :: name: "methylation", value: false
2025-09-15 20:26:05.801 wdl.w:ptcp.w:call-trgt-93.t:call-trgt_plot_motifs_allele INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:26:05.801 wdl.w:ptcp.w:call-trgt-93.t:call-trgt_plot_motifs_allele INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:26:05.801 wdl.w:ptcp.w:call-trgt-93.t:call-trgt_plot_motifs_allele INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:26:05.801 wdl.w:ptcp.w:call-trgt-93.t:call-trgt_plot_motifs_allele INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2190.trgt.sorted.spanning.bam.bai"
2025-09-15 20:26:05.801 wdl.w:ptcp.w:call-trgt-93.t:call-trgt_plot_motifs_allele INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2190.trgt.sorted.spanning.bam"
2025-09-15 20:26:05.801 wdl.w:ptcp.w:call-trgt-93.t:call-trgt_plot_motifs_allele INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2190.trgt.vcf"
2025-09-15 20:26:05.801 wdl.w:ptcp.w:call-trgt-93.t:call-trgt_plot_motifs_allele INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2190"
2025-09-15 20:26:05.802 wdl.w:ptcp.w:call-trgt-93.t:call-trgt_plot_motifs_allele INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:26:05.802 wdl.w:ptcp.w:call-trgt-93.t:call-trgt_plot_motifs_allele INFO eval :: name: "plot_type", value: "allele"
2025-09-15 20:26:05.802 wdl.w:ptcp.w:call-trgt-93.t:call-trgt_plot_motifs_allele INFO eval :: name: "show", value: "motifs"
2025-09-15 20:26:05.802 wdl.w:ptcp.w:call-trgt-93.t:call-trgt_plot_motifs_allele INFO eval :: name: "threads", value: 1
2025-09-15 20:26:05.802 wdl.w:ptcp.w:call-trgt-93.t:call-trgt_plot_motifs_allele INFO eval :: name: "disk_size", value: 27
2025-09-15 20:26:05.802 wdl.w:ptcp.w:call-trgt-93.t:call-trgt_plot_motifs_allele INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2190.motifs_allele"
2025-09-15 20:26:05.803 wdl.w:ptcp.w:call-trgt-93.t:call-trgt_plot_motifs_allele INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:26:05.803 wdl.w:ptcp.w:call-trgt-93.t:call-trgt_plot_motifs_allele WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:26:05.803 wdl.w:ptcp.w:call-trgt-93.t:call-trgt_plot_motifs_allele INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:26:05.803 wdl.w:ptcp.w:call-trgt-93.t:call-trgt_plot_motifs_allele INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:26:05.810 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_genotype.slurm_singularity INFO srun: job 51798142 queued and waiting for resources
2025-09-15 20:26:05.810 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_genotype.slurm_singularity INFO srun: job 51798142 has been allocated resources
2025-09-15 20:26:05.810 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_genotype.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:26:05.813 wdl.w:ptcp.w:call-paraphase-89.t:call-call_f8.slurm_singularity INFO srun: job 51798143 queued and waiting for resources
2025-09-15 20:26:05.813 wdl.w:ptcp.w:call-paraphase-89.t:call-call_f8.slurm_singularity INFO srun: job 51798143 has been allocated resources
2025-09-15 20:26:05.813 wdl.w:ptcp.w:call-paraphase-89.t:call-call_f8.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:26:05.867 wdl.w:ptcp.w:call-trgt-93.t:call-trgt_plot_motifs_allele INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-93/call-trgt_plot_motifs_allele/_singularity_tmpdir_m75aeabv"
2025-09-15 20:26:05.867 wdl.w:ptcp.w:call-trgt-93.t:call-trgt_plot_motifs_allele INFO Slurm invocation: srun --job-name call-trgt_plot_motifs_allele --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-93/call-trgt_plot_motifs_allele/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-93/call-trgt_plot_motifs_allele/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-93/call-trgt_plot_motifs_allele/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-93/call-trgt_plot_motifs_allele/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-93/call-trgt_genotype/out/m84036_250809_035451_s4.bc2190.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2190.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-93/call-trgt_genotype/out/m84036_250809_035451_s4.bc2190.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2190.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-93/call-trgt_genotype/out/m84036_250809_035451_s4.bc2190.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2190.trgt.sorted.spanning.bam:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-93/call-trgt_plot_motifs_allele/_singularity_tmpdir_m75aeabv/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-93/call-trgt_plot_motifs_allele/_singularity_tmpdir_m75aeabv/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:26:05.885 wdl.w:ptcp.w:call-trgt-93.t:call-trgt_plot_motifs_allele NOTICE slurm_singularity run :: pid: 1207001, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-93/call-trgt_plot_motifs_allele/slurm_singularity.log.txt"
2025-09-15 20:26:05.893 wdl.w:ptcp.w:call-trgt-93.t:call-trgt_plot_meth_allele.slurm_singularity INFO srun: job 51798144 queued and waiting for resources
2025-09-15 20:26:05.893 wdl.w:ptcp.w:call-trgt-93.t:call-trgt_plot_meth_allele.slurm_singularity INFO srun: job 51798144 has been allocated resources
2025-09-15 20:26:05.893 wdl.w:ptcp.w:call-trgt-93.t:call-trgt_plot_meth_allele.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:26:05.941 wdl.w:ptcp.w:call-trgt-93.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO srun: job 51798145 queued and waiting for resources
2025-09-15 20:26:05.941 wdl.w:ptcp.w:call-trgt-93.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO srun: job 51798145 has been allocated resources
2025-09-15 20:26:05.941 wdl.w:ptcp.w:call-trgt-93.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:26:06.082 wdl.w:ptcp.w:call-paraphase-10.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for hbb for sample m84036_250809_035451_s4.bc2107 at 2025-09-15 20:25:59.870875...
2025-09-15 20:26:06.083 wdl.w:ptcp.w:call-paraphase-10.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for hbb for sample m84036_250809_035451_s4.bc2107 at 2025-09-15 20:25:59.872760...
2025-09-15 20:26:06.083 wdl.w:ptcp.w:call-paraphase-10.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for hbb for sample m84036_250809_035451_s4.bc2107 at 2025-09-15 20:26:01.668973...
2025-09-15 20:26:06.141 wdl.w:ptcp.w:call-paraphase-54.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for rpgr for sample m84036_250809_035451_s4.bc2151 at 2025-09-15 20:25:40.106960...
2025-09-15 20:26:06.141 wdl.w:ptcp.w:call-paraphase-54.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for rpgr for sample m84036_250809_035451_s4.bc2151 at 2025-09-15 20:25:40.786147...
2025-09-15 20:26:06.142 wdl.w:ptcp.w:call-paraphase-54.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for rpgr for sample m84036_250809_035451_s4.bc2151 at 2025-09-15 20:25:41.106138...
2025-09-15 20:26:06.142 wdl.w:ptcp.w:call-paraphase-54.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for f8inv22 for sample m84036_250809_035451_s4.bc2151 at 2025-09-15 20:26:03.106592...
2025-09-15 20:26:06.142 wdl.w:ptcp.w:call-paraphase-54.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for f8inv22 for sample m84036_250809_035451_s4.bc2151 at 2025-09-15 20:26:03.106740...
2025-09-15 20:26:06.605 wdl.w:ptcp.w:call-trgt-82.t:call-trgt_plot_motifs_allele INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2179.motifs_allele.trgt_plots.zip"
2025-09-15 20:26:06.624 wdl.w:ptcp.w:call-paraphase-47.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for rpgr for sample m84036_250809_035451_s4.bc2144 at 2025-09-15 20:26:05.007244...
2025-09-15 20:26:06.624 wdl.w:ptcp.w:call-paraphase-47.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for rpgr for sample m84036_250809_035451_s4.bc2144 at 2025-09-15 20:26:05.007436...
2025-09-15 20:26:06.669 wdl.w:ptcp.w:call-trgt-85.t:call-trgt_plot_motifs_allele INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2182.motifs_allele.trgt_plots.zip"
2025-09-15 20:26:06.676 wdl.w:ptcp.w:call-paraphase-89.t:call-call_f8 INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2186.f8inversion.vcf"
2025-09-15 20:26:06.682 wdl.w:ptcp.w:call-paraphase-89.t:call-call_f8 INFO output :: name: "json", value: "m84036_250809_035451_s4.bc2186.f8inversion.json"
2025-09-15 20:26:06.682 wdl.w:ptcp.w:call-trgt-82.t:call-trgt_plot_motifs_allele NOTICE done
2025-09-15 20:26:06.687 wdl.w:ptcp.w:call-trgt-82 NOTICE finish :: job: "call-trgt_plot_motifs_allele"
2025-09-15 20:26:06.687 wdl.w:ptcp.w:call-trgt-82 INFO output :: job: "call-trgt_plot_motifs_allele", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-82/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2179.motifs_allele.trgt_plots.zip"}
2025-09-15 20:26:06.688 wdl.w:ptcp.w:call-trgt-82 INFO visit :: node: "output-images_motifs_allele", values: {"images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-82/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2179.motifs_allele.trgt_plots.zip"}
2025-09-15 20:26:06.694 wdl.w:ptcp.w:call-trgt-93.t:call-trgt_plot_motifs_waterfall NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-93/call-trgt_plot_motifs_waterfall", thread: 140611977991744
2025-09-15 20:26:06.719 wdl.w:ptcp.w:call-trgt-93.t:call-trgt_plot_motifs_waterfall INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:26:06.719 wdl.w:ptcp.w:call-trgt-93.t:call-trgt_plot_motifs_waterfall INFO input :: name: "waterfall", value: true
2025-09-15 20:26:06.719 wdl.w:ptcp.w:call-trgt-93.t:call-trgt_plot_motifs_waterfall INFO input :: name: "methylation", value: false
2025-09-15 20:26:06.719 wdl.w:ptcp.w:call-trgt-93.t:call-trgt_plot_motifs_waterfall INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:26:06.719 wdl.w:ptcp.w:call-trgt-93.t:call-trgt_plot_motifs_waterfall INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:26:06.719 wdl.w:ptcp.w:call-trgt-93.t:call-trgt_plot_motifs_waterfall INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:26:06.719 wdl.w:ptcp.w:call-trgt-93.t:call-trgt_plot_motifs_waterfall INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2190.trgt.sorted.spanning.bam.bai"
2025-09-15 20:26:06.720 wdl.w:ptcp.w:call-trgt-93.t:call-trgt_plot_motifs_waterfall INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2190.trgt.sorted.spanning.bam"
2025-09-15 20:26:06.720 wdl.w:ptcp.w:call-trgt-93.t:call-trgt_plot_motifs_waterfall INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2190.trgt.vcf"
2025-09-15 20:26:06.720 wdl.w:ptcp.w:call-trgt-93.t:call-trgt_plot_motifs_waterfall INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2190"
2025-09-15 20:26:06.720 wdl.w:ptcp.w:call-trgt-93.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:26:06.720 wdl.w:ptcp.w:call-trgt-93.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "plot_type", value: "waterfall"
2025-09-15 20:26:06.720 wdl.w:ptcp.w:call-trgt-93.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "show", value: "motifs"
2025-09-15 20:26:06.720 wdl.w:ptcp.w:call-trgt-93.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "threads", value: 1
2025-09-15 20:26:06.721 wdl.w:ptcp.w:call-trgt-93.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "disk_size", value: 27
2025-09-15 20:26:06.721 wdl.w:ptcp.w:call-trgt-93.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2190.motifs_waterfall"
2025-09-15 20:26:06.721 wdl.w:ptcp.w:call-trgt-93.t:call-trgt_plot_motifs_waterfall INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:26:06.721 wdl.w:ptcp.w:call-trgt-93.t:call-trgt_plot_motifs_waterfall WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:26:06.722 wdl.w:ptcp.w:call-trgt-93.t:call-trgt_plot_motifs_waterfall INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:26:06.722 wdl.w:ptcp.w:call-trgt-93.t:call-trgt_plot_motifs_waterfall INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:26:06.762 wdl.w:ptcp.w:call-paraphase-89.t:call-call_f8 NOTICE done
2025-09-15 20:26:06.802 wdl.w:ptcp.w:call-trgt-93.t:call-trgt_plot_motifs_waterfall INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-93/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_0iw1mo03"
2025-09-15 20:26:06.803 wdl.w:ptcp.w:call-trgt-93.t:call-trgt_plot_motifs_waterfall INFO Slurm invocation: srun --job-name call-trgt_plot_motifs_waterfall --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-93/call-trgt_plot_motifs_waterfall/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-93/call-trgt_plot_motifs_waterfall/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-93/call-trgt_plot_motifs_waterfall/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-93/call-trgt_plot_motifs_waterfall/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-93/call-trgt_genotype/out/m84036_250809_035451_s4.bc2190.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2190.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-93/call-trgt_genotype/out/m84036_250809_035451_s4.bc2190.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2190.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-93/call-trgt_genotype/out/m84036_250809_035451_s4.bc2190.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2190.trgt.sorted.spanning.bam:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-93/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_0iw1mo03/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-93/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_0iw1mo03/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:26:06.804 wdl.w:ptcp.w:call-trgt-85.t:call-trgt_plot_motifs_allele NOTICE done
2025-09-15 20:26:06.808 wdl.w:ptcp.w:call-trgt-85 NOTICE finish :: job: "call-trgt_plot_motifs_allele"
2025-09-15 20:26:06.808 wdl.w:ptcp.w:call-trgt-85 INFO output :: job: "call-trgt_plot_motifs_allele", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-85/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2182.motifs_allele.trgt_plots.zip"}
2025-09-15 20:26:06.808 wdl.w:ptcp.w:call-trgt-85 INFO visit :: node: "output-images_motifs_allele", values: {"images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-85/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2182.motifs_allele.trgt_plots.zip"}
2025-09-15 20:26:06.816 wdl.w:ptcp.w:call-paraphase-93.t:call-call_f8 NOTICE task setup :: name: "call_f8", source: "./paraphase.wdl", line: 232, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-93/call-call_f8", thread: 140611441120832
2025-09-15 20:26:06.830 wdl.w:ptcp.w:call-paraphase-89 NOTICE finish :: job: "call-call_f8"
2025-09-15 20:26:06.831 wdl.w:ptcp.w:call-paraphase-89 INFO output :: job: "call-call_f8", values: {"json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-89/call-call_f8/out/m84036_250809_035451_s4.bc2186.f8inversion.json", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-89/call-call_f8/out/m84036_250809_035451_s4.bc2186.f8inversion.vcf"}
2025-09-15 20:26:06.832 wdl.w:ptcp.w:call-paraphase-89 INFO visit :: node: "output-f8_json", values: {"f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-89/call-call_f8/out/m84036_250809_035451_s4.bc2186.f8inversion.json"}
2025-09-15 20:26:06.832 wdl.w:ptcp.w:call-paraphase-89 INFO visit :: node: "output-f8_vcf", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-89/call-call_f8/out/m84036_250809_035451_s4.bc2186.f8inversion.vcf"}
2025-09-15 20:26:06.832 wdl.w:ptcp.w:call-paraphase-89 INFO visit :: node: "outputs", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-89/call-call_f8/out/m84036_250809_035451_s4.bc2186.f8inversion.vcf", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-89/call-run_paraphase/out/m84036_250809_035451_s4.bc2186_paraphase/m84036_250809_035451_s4.bc2186.paraphase.json", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-89/call-run_paraphase/out/m84036_250809_035451_s4.bc2186_paraphase/m84036_250809_035451_s4.bc2186.paraphase.bam", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-89/call-run_paraphase/out/m84036_250809_035451_s4.bc2186_paraphase/m84036_250809_035451_s4.bc2186.paraphase.bam.bai", "paraphase_vcfs": [], "havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-89/call-run_paraphase/out/m84036_250809_035451_s4.bc2186.havanno.json", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-89/call-call_f8/out/m84036_250809_035451_s4.bc2186.f8inversion.json"}
2025-09-15 20:26:06.835 wdl.w:ptcp.w:call-trgt-93.t:call-trgt_plot_motifs_waterfall NOTICE slurm_singularity run :: pid: 1207013, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-93/call-trgt_plot_motifs_waterfall/slurm_singularity.log.txt"
2025-09-15 20:26:06.837 wdl.w:ptcp.w:call-paraphase-93.t:call-call_f8 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:26:06.837 wdl.w:ptcp.w:call-paraphase-93.t:call-call_f8 INFO input :: name: "genome_version", value: "38"
2025-09-15 20:26:06.837 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_plot_meth_allele NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-95/call-trgt_plot_meth_allele", thread: 140607129368128
2025-09-15 20:26:06.838 wdl.w:ptcp.w:call-paraphase-93.t:call-call_f8 INFO input :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2190"
2025-09-15 20:26:06.838 wdl.w:ptcp.w:call-paraphase-93.t:call-call_f8 INFO input :: name: "paraphase_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2190.paraphase.bam.bai"
2025-09-15 20:26:06.838 wdl.w:ptcp.w:call-paraphase-93.t:call-call_f8 INFO input :: name: "paraphase_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2190.paraphase.bam"
2025-09-15 20:26:06.838 wdl.w:ptcp.w:call-paraphase-93.t:call-call_f8 INFO input :: name: "sex", value: "F"
2025-09-15 20:26:06.838 wdl.w:ptcp.w:call-paraphase-93.t:call-call_f8 INFO eval :: name: "threads", value: 1
2025-09-15 20:26:06.838 wdl.w:ptcp.w:call-paraphase-93.t:call-call_f8 INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:26:06.839 wdl.w:ptcp.w:call-paraphase-93.t:call-call_f8 INFO eval :: name: "disk_size", value: 11
2025-09-15 20:26:06.839 wdl.w:ptcp.w:call-paraphase-93.t:call-call_f8 INFO eval :: name: "sample_sex", value: "F"
2025-09-15 20:26:06.839 wdl.w:ptcp.w:call-paraphase-93.t:call-call_f8 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:26:06.839 wdl.w:ptcp.w:call-paraphase-93.t:call-call_f8 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:26:06.840 wdl.w:ptcp.w:call-paraphase-93.t:call-call_f8 INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:26:06.840 wdl.w:ptcp.w:call-paraphase-93.t:call-call_f8 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:26:06.849 wdl.w:ptcp.w:call-trgt-92.t:call-trgt_plot_motifs_waterfall INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2189.motifs_waterfall.trgt_plots.zip"
2025-09-15 20:26:06.863 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_plot_meth_allele INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:26:06.863 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_plot_meth_allele INFO input :: name: "waterfall", value: false
2025-09-15 20:26:06.863 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_plot_meth_allele INFO input :: name: "methylation", value: true
2025-09-15 20:26:06.863 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_plot_meth_allele INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:26:06.863 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_plot_meth_allele INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:26:06.863 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_plot_meth_allele INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:26:06.864 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_plot_meth_allele INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2192.trgt.sorted.spanning.bam.bai"
2025-09-15 20:26:06.864 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_plot_meth_allele INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2192.trgt.sorted.spanning.bam"
2025-09-15 20:26:06.864 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_plot_meth_allele INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2192.trgt.vcf"
2025-09-15 20:26:06.864 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_plot_meth_allele INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2192"
2025-09-15 20:26:06.864 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_plot_meth_allele INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:26:06.864 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_plot_meth_allele INFO eval :: name: "plot_type", value: "allele"
2025-09-15 20:26:06.864 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_plot_meth_allele INFO eval :: name: "show", value: "meth"
2025-09-15 20:26:06.864 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_plot_meth_allele INFO eval :: name: "threads", value: 1
2025-09-15 20:26:06.865 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_plot_meth_allele INFO eval :: name: "disk_size", value: 27
2025-09-15 20:26:06.865 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_plot_meth_allele INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2192.meth_allele"
2025-09-15 20:26:06.865 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_plot_meth_allele INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:26:06.865 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_plot_meth_allele WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:26:06.866 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_plot_meth_allele INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:26:06.866 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_plot_meth_allele INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:26:06.868 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_genotype INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2180.trgt.vcf"
2025-09-15 20:26:06.874 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_genotype INFO output :: name: "spanning_bam", value: "m84036_250809_035451_s4.bc2180.trgt.sorted.spanning.bam"
2025-09-15 20:26:06.875 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_genotype INFO output :: name: "spanning_bam_bai", value: "m84036_250809_035451_s4.bc2180.trgt.sorted.spanning.bam.bai"
2025-09-15 20:26:06.900 wdl.w:ptcp.w:call-trgt-93.t:call-trgt_plot_motifs_allele.slurm_singularity INFO srun: job 51798146 queued and waiting for resources
2025-09-15 20:26:06.901 wdl.w:ptcp.w:call-trgt-93.t:call-trgt_plot_motifs_allele.slurm_singularity INFO srun: job 51798146 has been allocated resources
2025-09-15 20:26:06.901 wdl.w:ptcp.w:call-trgt-93.t:call-trgt_plot_motifs_allele.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:26:06.901 wdl.w:ptcp.w:call-trgt-82.t:call-trgt_plot_meth_waterfall INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2179.meth_waterfall.trgt_plots.zip"
2025-09-15 20:26:06.902 wdl.w:ptcp.w:call-paraphase-93.t:call-call_f8 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 8, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-93/call-call_f8/_singularity_tmpdir_254jm_ox"
2025-09-15 20:26:06.903 wdl.w:ptcp.w:call-paraphase-93.t:call-call_f8 INFO Slurm invocation: srun --job-name call-call_f8 --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-93/call-call_f8/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-93/call-call_f8/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-93/call-call_f8/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-93/call-call_f8/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-93/call-run_paraphase/out/m84036_250809_035451_s4.bc2190_paraphase/m84036_250809_035451_s4.bc2190.paraphase.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2190.paraphase.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-93/call-run_paraphase/out/m84036_250809_035451_s4.bc2190_paraphase/m84036_250809_035451_s4.bc2190.paraphase.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2190.paraphase.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-93/call-call_f8/_singularity_tmpdir_254jm_ox/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-93/call-call_f8/_singularity_tmpdir_254jm_ox/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:26:06.913 wdl.w:ptcp.w:call-paraphase-86.t:call-run_paraphase.stderr VERBOSE INFO:root:Processing sample m84036_250809_035451_s4.bc2183 at 2025-09-15 20:26:03.354371...
2025-09-15 20:26:06.914 wdl.w:ptcp.w:call-paraphase-86.t:call-run_paraphase.stderr VERBOSE INFO:root:Checking sample sex at 2025-09-15 20:26:03.356259...
2025-09-15 20:26:06.915 wdl.w:ptcp.w:call-paraphase-86.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for cyp21 for sample m84036_250809_035451_s4.bc2183 at 2025-09-15 20:26:03.421495...
2025-09-15 20:26:06.915 wdl.w:ptcp.w:call-paraphase-86.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for cyp21 for sample m84036_250809_035451_s4.bc2183 at 2025-09-15 20:26:03.421938...
2025-09-15 20:26:06.915 wdl.w:ptcp.w:call-paraphase-86.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for smn1 for sample m84036_250809_035451_s4.bc2183 at 2025-09-15 20:26:03.421643...
2025-09-15 20:26:06.915 wdl.w:ptcp.w:call-paraphase-86.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for smn1 for sample m84036_250809_035451_s4.bc2183 at 2025-09-15 20:26:03.422024...
2025-09-15 20:26:06.915 wdl.w:ptcp.w:call-paraphase-86.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for gba for sample m84036_250809_035451_s4.bc2183 at 2025-09-15 20:26:03.421738...
2025-09-15 20:26:06.915 wdl.w:ptcp.w:call-paraphase-86.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for gba for sample m84036_250809_035451_s4.bc2183 at 2025-09-15 20:26:03.422098...
2025-09-15 20:26:06.915 wdl.w:ptcp.w:call-paraphase-86.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for hba for sample m84036_250809_035451_s4.bc2183 at 2025-09-15 20:26:03.421940...
2025-09-15 20:26:06.916 wdl.w:ptcp.w:call-paraphase-86.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for hba for sample m84036_250809_035451_s4.bc2183 at 2025-09-15 20:26:03.422287...
2025-09-15 20:26:06.931 wdl.w:ptcp.w:call-paraphase-89 NOTICE done
2025-09-15 20:26:06.933 wdl.w:ptcp.w:call-paraphase-93.t:call-call_f8 NOTICE slurm_singularity run :: pid: 1207022, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-93/call-call_f8/slurm_singularity.log.txt"
2025-09-15 20:26:06.937 wdl.w:ptcp NOTICE finish :: job: "call-paraphase-89"
2025-09-15 20:26:06.937 wdl.w:ptcp INFO output :: job: "call-paraphase-89", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-89/out/m84036_250809_035451_s4.bc2186.f8inversion.vcf", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-89/out/m84036_250809_035451_s4.bc2186_paraphase/m84036_250809_035451_s4.bc2186.paraphase.json", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-89/out/m84036_250809_035451_s4.bc2186_paraphase/m84036_250809_035451_s4.bc2186.paraphase.bam", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-89/out/m84036_250809_035451_s4.bc2186_paraphase/m84036_250809_035451_s4.bc2186.paraphase.bam.bai", "paraphase_vcfs": [], "havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-89/out/m84036_250809_035451_s4.bc2186.havanno.json", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-89/out/m84036_250809_035451_s4.bc2186.f8inversion.json"}
2025-09-15 20:26:06.956 wdl.w:ptcp.w:call-trgt-82.t:call-trgt_plot_motifs_waterfall INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2179.motifs_waterfall.trgt_plots.zip"
2025-09-15 20:26:06.983 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_plot_meth_allele INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-95/call-trgt_plot_meth_allele/_singularity_tmpdir_cj36mny5"
2025-09-15 20:26:06.984 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_plot_meth_allele INFO Slurm invocation: srun --job-name call-trgt_plot_meth_allele --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-95/call-trgt_plot_meth_allele/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-95/call-trgt_plot_meth_allele/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-95/call-trgt_plot_meth_allele/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-95/call-trgt_plot_meth_allele/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-95/call-trgt_genotype/out/m84036_250809_035451_s4.bc2192.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2192.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-95/call-trgt_genotype/out/m84036_250809_035451_s4.bc2192.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2192.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-95/call-trgt_genotype/out/m84036_250809_035451_s4.bc2192.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2192.trgt.vcf:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-95/call-trgt_plot_meth_allele/_singularity_tmpdir_cj36mny5/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-95/call-trgt_plot_meth_allele/_singularity_tmpdir_cj36mny5/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:26:07.000 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_plot_meth_allele NOTICE slurm_singularity run :: pid: 1207024, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-95/call-trgt_plot_meth_allele/slurm_singularity.log.txt"
2025-09-15 20:26:07.007 wdl.w:ptcp.w:call-trgt-82.t:call-trgt_plot_meth_waterfall NOTICE done
2025-09-15 20:26:07.009 wdl.w:ptcp.w:call-trgt-92.t:call-trgt_plot_motifs_waterfall NOTICE done
2025-09-15 20:26:07.012 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_genotype NOTICE done
2025-09-15 20:26:07.013 wdl.w:ptcp.w:call-trgt-82 NOTICE finish :: job: "call-trgt_plot_meth_waterfall"
2025-09-15 20:26:07.013 wdl.w:ptcp.w:call-trgt-82 INFO output :: job: "call-trgt_plot_meth_waterfall", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-82/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2179.meth_waterfall.trgt_plots.zip"}
2025-09-15 20:26:07.014 wdl.w:ptcp.w:call-trgt-82 INFO visit :: node: "output-images_meth_waterfall", values: {"images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-82/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2179.meth_waterfall.trgt_plots.zip"}
2025-09-15 20:26:07.014 wdl.w:ptcp.w:call-trgt-92 NOTICE finish :: job: "call-trgt_plot_motifs_waterfall"
2025-09-15 20:26:07.015 wdl.w:ptcp.w:call-trgt-92 INFO output :: job: "call-trgt_plot_motifs_waterfall", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-92/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2189.motifs_waterfall.trgt_plots.zip"}
2025-09-15 20:26:07.015 wdl.w:ptcp.w:call-trgt-92 INFO visit :: node: "output-images_motifs_waterfall", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-92/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2189.motifs_waterfall.trgt_plots.zip"}
2025-09-15 20:26:07.018 wdl.w:ptcp.w:call-trgt-83 NOTICE finish :: job: "call-trgt_genotype"
2025-09-15 20:26:07.019 wdl.w:ptcp.w:call-trgt-83 INFO output :: job: "call-trgt_genotype", values: {"spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-83/call-trgt_genotype/out/m84036_250809_035451_s4.bc2180.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-83/call-trgt_genotype/out/m84036_250809_035451_s4.bc2180.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-83/call-trgt_genotype/out/m84036_250809_035451_s4.bc2180.trgt.vcf"}
2025-09-15 20:26:07.019 wdl.w:ptcp.w:call-trgt-83 NOTICE ready :: job: "call-trgt_plot_meth_allele", callee: "trgt_plot"
2025-09-15 20:26:07.019 wdl.w:ptcp.w:call-trgt-83 INFO input :: job: "call-trgt_plot_meth_allele", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": false, "methylation": true, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-83/call-trgt_genotype/out/m84036_250809_035451_s4.bc2180.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-83/call-trgt_genotype/out/m84036_250809_035451_s4.bc2180.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-83/call-trgt_genotype/out/m84036_250809_035451_s4.bc2180.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2180"}
2025-09-15 20:26:07.020 wdl.w:ptcp.w:call-trgt-83 NOTICE ready :: job: "call-trgt_plot_meth_waterfall", callee: "trgt_plot"
2025-09-15 20:26:07.020 wdl.w:ptcp.w:call-trgt-83 INFO input :: job: "call-trgt_plot_meth_waterfall", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": true, "methylation": true, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-83/call-trgt_genotype/out/m84036_250809_035451_s4.bc2180.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-83/call-trgt_genotype/out/m84036_250809_035451_s4.bc2180.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-83/call-trgt_genotype/out/m84036_250809_035451_s4.bc2180.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2180"}
2025-09-15 20:26:07.021 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_plot_meth_waterfall NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-95/call-trgt_plot_meth_waterfall", thread: 140607649453632
2025-09-15 20:26:07.021 wdl.w:ptcp.w:call-trgt-83 NOTICE ready :: job: "call-trgt_plot_motifs_allele", callee: "trgt_plot"
2025-09-15 20:26:07.021 wdl.w:ptcp.w:call-trgt-83 INFO input :: job: "call-trgt_plot_motifs_allele", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": false, "methylation": false, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-83/call-trgt_genotype/out/m84036_250809_035451_s4.bc2180.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-83/call-trgt_genotype/out/m84036_250809_035451_s4.bc2180.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-83/call-trgt_genotype/out/m84036_250809_035451_s4.bc2180.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2180"}
2025-09-15 20:26:07.022 wdl.w:ptcp.w:call-trgt-83 NOTICE ready :: job: "call-trgt_plot_motifs_waterfall", callee: "trgt_plot"
2025-09-15 20:26:07.022 wdl.w:ptcp.w:call-trgt-83 INFO input :: job: "call-trgt_plot_motifs_waterfall", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": true, "methylation": false, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-83/call-trgt_genotype/out/m84036_250809_035451_s4.bc2180.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-83/call-trgt_genotype/out/m84036_250809_035451_s4.bc2180.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-83/call-trgt_genotype/out/m84036_250809_035451_s4.bc2180.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2180"}
2025-09-15 20:26:07.023 wdl.w:ptcp.w:call-trgt-83 INFO visit :: node: "output-spanning_bam", values: {"spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-83/call-trgt_genotype/out/m84036_250809_035451_s4.bc2180.trgt.sorted.spanning.bam"}
2025-09-15 20:26:07.023 wdl.w:ptcp.w:call-trgt-83 INFO visit :: node: "output-spanning_bam_bai", values: {"spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-83/call-trgt_genotype/out/m84036_250809_035451_s4.bc2180.trgt.sorted.spanning.bam.bai"}
2025-09-15 20:26:07.023 wdl.w:ptcp.w:call-trgt-83 INFO visit :: node: "output-vcf", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-83/call-trgt_genotype/out/m84036_250809_035451_s4.bc2180.trgt.vcf"}
2025-09-15 20:26:07.027 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_plot_motifs_allele NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-95/call-trgt_plot_motifs_allele", thread: 140610342200896
2025-09-15 20:26:07.028 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_plot_motifs_waterfall NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-95/call-trgt_plot_motifs_waterfall", thread: 140610879071808
2025-09-15 20:26:07.041 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_plot_meth_waterfall INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:26:07.042 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_plot_meth_waterfall INFO input :: name: "waterfall", value: true
2025-09-15 20:26:07.042 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_plot_meth_waterfall INFO input :: name: "methylation", value: true
2025-09-15 20:26:07.043 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_plot_meth_waterfall INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:26:07.043 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_plot_meth_waterfall INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:26:07.043 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_plot_meth_waterfall INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:26:07.043 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_plot_meth_waterfall INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2192.trgt.sorted.spanning.bam.bai"
2025-09-15 20:26:07.043 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_plot_meth_waterfall INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2192.trgt.sorted.spanning.bam"
2025-09-15 20:26:07.043 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_plot_meth_waterfall INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2192.trgt.vcf"
2025-09-15 20:26:07.044 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_plot_meth_waterfall INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2192"
2025-09-15 20:26:07.044 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_plot_meth_waterfall INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:26:07.044 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_plot_meth_waterfall INFO eval :: name: "plot_type", value: "waterfall"
2025-09-15 20:26:07.045 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_plot_meth_waterfall INFO eval :: name: "show", value: "meth"
2025-09-15 20:26:07.045 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_plot_meth_waterfall INFO eval :: name: "threads", value: 1
2025-09-15 20:26:07.045 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_plot_meth_waterfall INFO eval :: name: "disk_size", value: 27
2025-09-15 20:26:07.046 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_plot_meth_waterfall INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2192.meth_waterfall"
2025-09-15 20:26:07.046 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_plot_meth_waterfall INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:26:07.046 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_plot_meth_waterfall WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:26:07.047 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_plot_meth_waterfall INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:26:07.047 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_plot_meth_waterfall INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:26:07.049 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_plot_motifs_allele INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:26:07.049 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_plot_motifs_allele INFO input :: name: "waterfall", value: false
2025-09-15 20:26:07.049 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_plot_motifs_allele INFO input :: name: "methylation", value: false
2025-09-15 20:26:07.049 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_plot_motifs_allele INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:26:07.049 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_plot_motifs_allele INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:26:07.049 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_plot_motifs_allele INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:26:07.049 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_plot_motifs_allele INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2192.trgt.sorted.spanning.bam.bai"
2025-09-15 20:26:07.050 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_plot_motifs_allele INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2192.trgt.sorted.spanning.bam"
2025-09-15 20:26:07.050 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_plot_motifs_allele INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2192.trgt.vcf"
2025-09-15 20:26:07.050 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_plot_motifs_allele INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2192"
2025-09-15 20:26:07.050 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_plot_motifs_allele INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:26:07.050 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_plot_motifs_allele INFO eval :: name: "plot_type", value: "allele"
2025-09-15 20:26:07.050 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_plot_motifs_allele INFO eval :: name: "show", value: "motifs"
2025-09-15 20:26:07.050 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_plot_motifs_allele INFO eval :: name: "threads", value: 1
2025-09-15 20:26:07.050 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_plot_motifs_allele INFO eval :: name: "disk_size", value: 27
2025-09-15 20:26:07.050 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_plot_motifs_allele INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2192.motifs_allele"
2025-09-15 20:26:07.051 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_plot_motifs_allele INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:26:07.051 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_plot_motifs_allele WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:26:07.051 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_plot_motifs_allele INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:26:07.051 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_plot_motifs_allele INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:26:07.052 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_plot_motifs_waterfall INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:26:07.052 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_plot_motifs_waterfall INFO input :: name: "waterfall", value: true
2025-09-15 20:26:07.052 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_plot_motifs_waterfall INFO input :: name: "methylation", value: false
2025-09-15 20:26:07.052 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_plot_motifs_waterfall INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:26:07.052 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_plot_motifs_waterfall INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:26:07.052 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_plot_motifs_waterfall INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:26:07.052 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_plot_motifs_waterfall INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2192.trgt.sorted.spanning.bam.bai"
2025-09-15 20:26:07.052 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_plot_motifs_waterfall INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2192.trgt.sorted.spanning.bam"
2025-09-15 20:26:07.053 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_plot_motifs_waterfall INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2192.trgt.vcf"
2025-09-15 20:26:07.053 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_plot_motifs_waterfall INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2192"
2025-09-15 20:26:07.053 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:26:07.053 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "plot_type", value: "waterfall"
2025-09-15 20:26:07.053 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "show", value: "motifs"
2025-09-15 20:26:07.053 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "threads", value: 1
2025-09-15 20:26:07.053 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "disk_size", value: 27
2025-09-15 20:26:07.054 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2192.motifs_waterfall"
2025-09-15 20:26:07.054 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_plot_motifs_waterfall INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:26:07.054 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_plot_motifs_waterfall WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:26:07.054 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_plot_motifs_waterfall INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:26:07.054 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_plot_motifs_waterfall INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:26:07.058 wdl.w:ptcp.w:call-trgt-82.t:call-trgt_plot_motifs_waterfall NOTICE done
2025-09-15 20:26:07.104 wdl.w:ptcp.w:call-trgt-82 NOTICE finish :: job: "call-trgt_plot_motifs_waterfall"
2025-09-15 20:26:07.105 wdl.w:ptcp.w:call-trgt-82 INFO output :: job: "call-trgt_plot_motifs_waterfall", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-82/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2179.motifs_waterfall.trgt_plots.zip"}
2025-09-15 20:26:07.105 wdl.w:ptcp.w:call-trgt-82 INFO visit :: node: "output-images_motifs_waterfall", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-82/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2179.motifs_waterfall.trgt_plots.zip"}
2025-09-15 20:26:07.114 wdl.w:ptcp.t:call-tar_outputs-69 NOTICE task setup :: name: "tar_outputs", source: "./common.wdl", line: 279, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-69", thread: 140613043340864
2025-09-15 20:26:07.131 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_plot_meth_waterfall INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-95/call-trgt_plot_meth_waterfall/_singularity_tmpdir_qzrmi7rv"
2025-09-15 20:26:07.131 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_plot_meth_waterfall INFO Slurm invocation: srun --job-name call-trgt_plot_meth_waterfall --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-95/call-trgt_plot_meth_waterfall/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-95/call-trgt_plot_meth_waterfall/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-95/call-trgt_plot_meth_waterfall/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-95/call-trgt_plot_meth_waterfall/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-95/call-trgt_genotype/out/m84036_250809_035451_s4.bc2192.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2192.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-95/call-trgt_genotype/out/m84036_250809_035451_s4.bc2192.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2192.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-95/call-trgt_genotype/out/m84036_250809_035451_s4.bc2192.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2192.trgt.vcf:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-95/call-trgt_plot_meth_waterfall/_singularity_tmpdir_qzrmi7rv/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-95/call-trgt_plot_meth_waterfall/_singularity_tmpdir_qzrmi7rv/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:26:07.138 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_plot_motifs_allele INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-95/call-trgt_plot_motifs_allele/_singularity_tmpdir_wk9o7ova"
2025-09-15 20:26:07.139 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_plot_motifs_allele INFO Slurm invocation: srun --job-name call-trgt_plot_motifs_allele --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-95/call-trgt_plot_motifs_allele/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-95/call-trgt_plot_motifs_allele/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-95/call-trgt_plot_motifs_allele/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-95/call-trgt_plot_motifs_allele/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-95/call-trgt_genotype/out/m84036_250809_035451_s4.bc2192.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2192.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-95/call-trgt_genotype/out/m84036_250809_035451_s4.bc2192.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2192.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-95/call-trgt_genotype/out/m84036_250809_035451_s4.bc2192.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2192.trgt.vcf:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-95/call-trgt_plot_motifs_allele/_singularity_tmpdir_wk9o7ova/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-95/call-trgt_plot_motifs_allele/_singularity_tmpdir_wk9o7ova/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:26:07.145 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_plot_motifs_waterfall INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-95/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_s0cputvz"
2025-09-15 20:26:07.145 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_plot_motifs_waterfall INFO Slurm invocation: srun --job-name call-trgt_plot_motifs_waterfall --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-95/call-trgt_plot_motifs_waterfall/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-95/call-trgt_plot_motifs_waterfall/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-95/call-trgt_plot_motifs_waterfall/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-95/call-trgt_plot_motifs_waterfall/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-95/call-trgt_genotype/out/m84036_250809_035451_s4.bc2192.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2192.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-95/call-trgt_genotype/out/m84036_250809_035451_s4.bc2192.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2192.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-95/call-trgt_genotype/out/m84036_250809_035451_s4.bc2192.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2192.trgt.vcf:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-95/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_s0cputvz/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-95/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_s0cputvz/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:26:07.149 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_plot_meth_waterfall NOTICE slurm_singularity run :: pid: 1207026, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-95/call-trgt_plot_meth_waterfall/slurm_singularity.log.txt"
2025-09-15 20:26:07.150 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_plot_motifs_allele NOTICE slurm_singularity run :: pid: 1207027, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-95/call-trgt_plot_motifs_allele/slurm_singularity.log.txt"
2025-09-15 20:26:07.152 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_plot_motifs_waterfall NOTICE slurm_singularity run :: pid: 1207028, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-95/call-trgt_plot_motifs_waterfall/slurm_singularity.log.txt"
2025-09-15 20:26:07.159 wdl.w:ptcp.t:call-tar_outputs-69 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:26:07.160 wdl.w:ptcp.t:call-tar_outputs-69 INFO input :: name: "sawfish_vcf_tbi", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2166.sv.vcf.gz.tbi"
2025-09-15 20:26:07.160 wdl.w:ptcp.t:call-tar_outputs-69 INFO input :: name: "sawfish_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2166.sv.vcf.gz"
2025-09-15 20:26:07.160 wdl.w:ptcp.t:call-tar_outputs-69 INFO input :: name: "f8_json", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2166.f8inversion.json"
2025-09-15 20:26:07.160 wdl.w:ptcp.t:call-tar_outputs-69 INFO input :: name: "paraphase_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2166.paraphase.bam.bai"
2025-09-15 20:26:07.160 wdl.w:ptcp.t:call-tar_outputs-69 INFO input :: name: "paraphase_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2166.paraphase.bam"
2025-09-15 20:26:07.160 wdl.w:ptcp.t:call-tar_outputs-69 INFO input :: name: "paraphase_json", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2166.paraphase.json"
2025-09-15 20:26:07.160 wdl.w:ptcp.t:call-tar_outputs-69 INFO input :: name: "trgt_spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2166.trgt.sorted.spanning.bam.bai"
2025-09-15 20:26:07.160 wdl.w:ptcp.t:call-tar_outputs-69 INFO input :: name: "trgt_spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2166.trgt.sorted.spanning.bam"
2025-09-15 20:26:07.160 wdl.w:ptcp.t:call-tar_outputs-69 INFO input :: name: "trgt_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2166.trgt.vcf"
2025-09-15 20:26:07.160 wdl.w:ptcp.t:call-tar_outputs-69 INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2166.mapped.bam.bai"
2025-09-15 20:26:07.160 wdl.w:ptcp.t:call-tar_outputs-69 INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2166.mapped.bam"
2025-09-15 20:26:07.160 wdl.w:ptcp.t:call-tar_outputs-69 INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2166"
2025-09-15 20:26:07.160 wdl.w:ptcp.t:call-tar_outputs-69 INFO eval :: name: "threads", value: 1
2025-09-15 20:26:07.160 wdl.w:ptcp.t:call-tar_outputs-69 INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:26:07.161 wdl.w:ptcp.t:call-tar_outputs-69 INFO eval :: name: "disk_size", value: 6
2025-09-15 20:26:07.161 wdl.w:ptcp.t:call-tar_outputs-69 INFO eval :: name: "output_tarball", value: "m84036_250809_035451_s4.bc2166.tar"
2025-09-15 20:26:07.161 wdl.w:ptcp.t:call-tar_outputs-69 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:26:07.161 wdl.w:ptcp.t:call-tar_outputs-69 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:26:07.163 wdl.w:ptcp.t:call-tar_outputs-69 INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:26:07.164 wdl.w:ptcp.t:call-tar_outputs-69 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:26:07.262 wdl.w:ptcp.w:call-trgt-85.t:call-trgt_plot_meth_allele INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2182.meth_allele.trgt_plots.zip"
2025-09-15 20:26:07.264 wdl.w:ptcp.t:call-tar_outputs-69 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 17, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-69/_singularity_tmpdir_1jpvftf8"
2025-09-15 20:26:07.265 wdl.w:ptcp.t:call-tar_outputs-69 INFO Slurm invocation: srun --job-name call-tar_outputs-69 --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-69/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-69/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-69/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-69/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-69/out/m84036_250809_035451_s4.bc2166.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2166.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-69/out/m84036_250809_035451_s4.bc2166.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2166.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-69/out/m84036_250809_035451_s4.bc2166.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2166.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-69/out/m84036_250809_035451_s4.bc2166_sawfish/m84036_250809_035451_s4.bc2166.sv.vcf.gz.tbi:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2166.sv.vcf.gz.tbi:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-69/out/m84036_250809_035451_s4.bc2166_sawfish/m84036_250809_035451_s4.bc2166.sv.vcf.gz:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2166.sv.vcf.gz:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-69/out/m84036_250809_035451_s4.bc2166_paraphase/m84036_250809_035451_s4.bc2166.paraphase.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2166.paraphase.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-69/out/m84036_250809_035451_s4.bc2166_paraphase/m84036_250809_035451_s4.bc2166.paraphase.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2166.paraphase.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-69/out/m84036_250809_035451_s4.bc2166_paraphase/m84036_250809_035451_s4.bc2166.paraphase.json:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2166.paraphase.json:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-69/out/m84036_250809_035451_s4.bc2166.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2166.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-69/out/m84036_250809_035451_s4.bc2166.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2166.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-69/out/m84036_250809_035451_s4.bc2166.f8inversion.json:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2166.f8inversion.json:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-69/_singularity_tmpdir_1jpvftf8/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-69/_singularity_tmpdir_1jpvftf8/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:26:07.286 wdl.w:ptcp.t:call-tar_outputs-69 NOTICE slurm_singularity run :: pid: 1207058, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-69/slurm_singularity.log.txt"
2025-09-15 20:26:07.368 wdl.w:ptcp.w:call-trgt-82.t:call-trgt_plot_meth_allele INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2179.meth_allele.trgt_plots.zip"
2025-09-15 20:26:07.369 wdl.w:ptcp.w:call-trgt-85.t:call-trgt_plot_meth_allele NOTICE done
2025-09-15 20:26:07.375 wdl.w:ptcp.w:call-trgt-85 NOTICE finish :: job: "call-trgt_plot_meth_allele"
2025-09-15 20:26:07.375 wdl.w:ptcp.w:call-trgt-85 INFO output :: job: "call-trgt_plot_meth_allele", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-85/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2182.meth_allele.trgt_plots.zip"}
2025-09-15 20:26:07.375 wdl.w:ptcp.w:call-trgt-85 INFO visit :: node: "output-images_meth_allele", values: {"images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-85/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2182.meth_allele.trgt_plots.zip"}
2025-09-15 20:26:07.380 wdl.w:ptcp.w:call-paraphase-31.t:call-call_f8 NOTICE task setup :: name: "call_f8", source: "./paraphase.wdl", line: 232, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-31/call-call_f8", thread: 140607674631744
2025-09-15 20:26:07.403 wdl.w:ptcp.w:call-paraphase-31.t:call-call_f8 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:26:07.403 wdl.w:ptcp.w:call-paraphase-31.t:call-call_f8 INFO input :: name: "genome_version", value: "38"
2025-09-15 20:26:07.403 wdl.w:ptcp.w:call-paraphase-31.t:call-call_f8 INFO input :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2128"
2025-09-15 20:26:07.403 wdl.w:ptcp.w:call-paraphase-31.t:call-call_f8 INFO input :: name: "paraphase_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2128.paraphase.bam.bai"
2025-09-15 20:26:07.403 wdl.w:ptcp.w:call-paraphase-31.t:call-call_f8 INFO input :: name: "paraphase_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2128.paraphase.bam"
2025-09-15 20:26:07.403 wdl.w:ptcp.w:call-paraphase-31.t:call-call_f8 INFO input :: name: "sex", value: "F"
2025-09-15 20:26:07.403 wdl.w:ptcp.w:call-paraphase-31.t:call-call_f8 INFO eval :: name: "threads", value: 1
2025-09-15 20:26:07.403 wdl.w:ptcp.w:call-paraphase-31.t:call-call_f8 INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:26:07.404 wdl.w:ptcp.w:call-paraphase-31.t:call-call_f8 INFO eval :: name: "disk_size", value: 11
2025-09-15 20:26:07.404 wdl.w:ptcp.w:call-paraphase-31.t:call-call_f8 INFO eval :: name: "sample_sex", value: "F"
2025-09-15 20:26:07.404 wdl.w:ptcp.w:call-paraphase-31.t:call-call_f8 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:26:07.404 wdl.w:ptcp.w:call-paraphase-31.t:call-call_f8 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:26:07.404 wdl.w:ptcp.w:call-paraphase-31.t:call-call_f8 INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:26:07.405 wdl.w:ptcp.w:call-paraphase-31.t:call-call_f8 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:26:07.436 wdl.w:ptcp.w:call-trgt-82.t:call-trgt_plot_meth_allele NOTICE done
2025-09-15 20:26:07.440 wdl.w:ptcp.w:call-trgt-82 NOTICE finish :: job: "call-trgt_plot_meth_allele"
2025-09-15 20:26:07.440 wdl.w:ptcp.w:call-trgt-82 INFO output :: job: "call-trgt_plot_meth_allele", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-82/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2179.meth_allele.trgt_plots.zip"}
2025-09-15 20:26:07.441 wdl.w:ptcp.w:call-trgt-82 INFO visit :: node: "output-images_meth_allele", values: {"images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-82/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2179.meth_allele.trgt_plots.zip"}
2025-09-15 20:26:07.441 wdl.w:ptcp.w:call-trgt-82 INFO visit :: node: "outputs", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-82/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2179.motifs_waterfall.trgt_plots.zip", "images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-82/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2179.meth_allele.trgt_plots.zip", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-82/call-trgt_genotype/out/m84036_250809_035451_s4.bc2179.trgt.sorted.spanning.bam.bai", "images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-82/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2179.motifs_allele.trgt_plots.zip", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-82/call-trgt_genotype/out/m84036_250809_035451_s4.bc2179.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-82/call-trgt_genotype/out/m84036_250809_035451_s4.bc2179.trgt.vcf", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-82/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2179.repeats.bam", "images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-82/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2179.meth_waterfall.trgt_plots.zip", "reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-82/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2179.repeats.bam.bai"}
2025-09-15 20:26:07.448 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_meth_allele NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-94/call-trgt_plot_meth_allele", thread: 140608748373568
2025-09-15 20:26:07.451 wdl.w:ptcp.w:call-trgt-89.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:26:05 [ERROR] - No reads found for TRID=PRTS_ARX
2025-09-15 20:26:07.451 wdl.w:ptcp.w:call-trgt-89.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:26:05 [ERROR] - No reads found for TRID=EIEE1_ARX
2025-09-15 20:26:07.452 wdl.w:ptcp.w:call-paraphase-31.t:call-call_f8 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 8, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-31/call-call_f8/_singularity_tmpdir_acd0dep1"
2025-09-15 20:26:07.452 wdl.w:ptcp.w:call-paraphase-31.t:call-call_f8 INFO Slurm invocation: srun --job-name call-call_f8 --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-31/call-call_f8/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-31/call-call_f8/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-31/call-call_f8/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-31/call-call_f8/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-31/call-run_paraphase/out/m84036_250809_035451_s4.bc2128_paraphase/m84036_250809_035451_s4.bc2128.paraphase.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2128.paraphase.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-31/call-run_paraphase/out/m84036_250809_035451_s4.bc2128_paraphase/m84036_250809_035451_s4.bc2128.paraphase.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2128.paraphase.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-31/call-call_f8/_singularity_tmpdir_acd0dep1/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-31/call-call_f8/_singularity_tmpdir_acd0dep1/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:26:07.472 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_meth_allele INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:26:07.472 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_meth_allele INFO input :: name: "waterfall", value: false
2025-09-15 20:26:07.472 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_meth_allele INFO input :: name: "methylation", value: true
2025-09-15 20:26:07.472 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_meth_allele INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:26:07.472 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_meth_allele INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:26:07.472 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_meth_allele INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:26:07.472 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_meth_allele INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2191.trgt.sorted.spanning.bam.bai"
2025-09-15 20:26:07.472 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_meth_allele INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2191.trgt.sorted.spanning.bam"
2025-09-15 20:26:07.473 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_meth_allele INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2191.trgt.vcf"
2025-09-15 20:26:07.473 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_meth_allele INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2191"
2025-09-15 20:26:07.473 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_meth_allele INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:26:07.474 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_meth_allele INFO eval :: name: "plot_type", value: "allele"
2025-09-15 20:26:07.474 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_meth_allele INFO eval :: name: "show", value: "meth"
2025-09-15 20:26:07.474 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_meth_allele INFO eval :: name: "threads", value: 1
2025-09-15 20:26:07.474 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_meth_allele INFO eval :: name: "disk_size", value: 27
2025-09-15 20:26:07.474 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_meth_allele INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2191.meth_allele"
2025-09-15 20:26:07.475 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_meth_allele INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:26:07.475 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_meth_allele WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:26:07.475 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_meth_allele INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:26:07.476 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_meth_allele INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:26:07.479 wdl.w:ptcp.w:call-paraphase-31.t:call-call_f8 NOTICE slurm_singularity run :: pid: 1207066, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-31/call-call_f8/slurm_singularity.log.txt"
2025-09-15 20:26:07.522 wdl.w:ptcp.w:call-trgt-92.t:call-trgt_plot_motifs_allele INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2189.motifs_allele.trgt_plots.zip"
2025-09-15 20:26:07.564 wdl.w:ptcp.w:call-trgt-82 NOTICE done
2025-09-15 20:26:07.569 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_meth_allele INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-94/call-trgt_plot_meth_allele/_singularity_tmpdir_uk4nge1d"
2025-09-15 20:26:07.569 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_meth_allele INFO Slurm invocation: srun --job-name call-trgt_plot_meth_allele --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-94/call-trgt_plot_meth_allele/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-94/call-trgt_plot_meth_allele/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-94/call-trgt_plot_meth_allele/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-94/call-trgt_plot_meth_allele/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-94/call-trgt_genotype/out/m84036_250809_035451_s4.bc2191.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2191.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-94/call-trgt_genotype/out/m84036_250809_035451_s4.bc2191.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2191.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-94/call-trgt_genotype/out/m84036_250809_035451_s4.bc2191.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2191.trgt.sorted.spanning.bam:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-94/call-trgt_plot_meth_allele/_singularity_tmpdir_uk4nge1d/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-94/call-trgt_plot_meth_allele/_singularity_tmpdir_uk4nge1d/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:26:07.571 wdl.w:ptcp NOTICE finish :: job: "call-trgt-82"
2025-09-15 20:26:07.571 wdl.w:ptcp INFO output :: job: "call-trgt-82", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-82/out/m84036_250809_035451_s4.bc2179.motifs_waterfall.trgt_plots.zip", "images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-82/out/m84036_250809_035451_s4.bc2179.meth_allele.trgt_plots.zip", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-82/out/m84036_250809_035451_s4.bc2179.trgt.sorted.spanning.bam.bai", "images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-82/out/m84036_250809_035451_s4.bc2179.motifs_allele.trgt_plots.zip", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-82/out/m84036_250809_035451_s4.bc2179.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-82/out/m84036_250809_035451_s4.bc2179.trgt.vcf", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-82/out/m84036_250809_035451_s4.bc2179.repeats.bam", "images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-82/out/m84036_250809_035451_s4.bc2179.meth_waterfall.trgt_plots.zip", "reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-82/out/m84036_250809_035451_s4.bc2179.repeats.bam.bai"}
2025-09-15 20:26:07.589 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_meth_allele NOTICE slurm_singularity run :: pid: 1207069, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-94/call-trgt_plot_meth_allele/slurm_singularity.log.txt"
2025-09-15 20:26:07.637 wdl.w:ptcp.w:call-trgt-92.t:call-trgt_plot_motifs_allele NOTICE done
2025-09-15 20:26:07.641 wdl.w:ptcp.w:call-trgt-92 NOTICE finish :: job: "call-trgt_plot_motifs_allele"
2025-09-15 20:26:07.641 wdl.w:ptcp.w:call-trgt-92 INFO output :: job: "call-trgt_plot_motifs_allele", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-92/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2189.motifs_allele.trgt_plots.zip"}
2025-09-15 20:26:07.642 wdl.w:ptcp.w:call-trgt-92 INFO visit :: node: "output-images_motifs_allele", values: {"images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-92/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2189.motifs_allele.trgt_plots.zip"}
2025-09-15 20:26:07.644 wdl.w:ptcp.w:call-sawfish-72.t:call-run_sawfish.stderr VERBOSE [M::mm_idx_gen::35.442*1.39] collected minimizers
2025-09-15 20:26:07.648 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_meth_waterfall NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-94/call-trgt_plot_meth_waterfall", thread: 140613563426368
2025-09-15 20:26:07.669 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_meth_waterfall INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:26:07.669 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_meth_waterfall INFO input :: name: "waterfall", value: true
2025-09-15 20:26:07.669 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_meth_waterfall INFO input :: name: "methylation", value: true
2025-09-15 20:26:07.669 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_meth_waterfall INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:26:07.669 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_meth_waterfall INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:26:07.669 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_meth_waterfall INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:26:07.670 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_meth_waterfall INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2191.trgt.sorted.spanning.bam.bai"
2025-09-15 20:26:07.670 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_meth_waterfall INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2191.trgt.sorted.spanning.bam"
2025-09-15 20:26:07.670 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_meth_waterfall INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2191.trgt.vcf"
2025-09-15 20:26:07.670 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_meth_waterfall INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2191"
2025-09-15 20:26:07.670 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_meth_waterfall INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:26:07.670 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_meth_waterfall INFO eval :: name: "plot_type", value: "waterfall"
2025-09-15 20:26:07.670 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_meth_waterfall INFO eval :: name: "show", value: "meth"
2025-09-15 20:26:07.670 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_meth_waterfall INFO eval :: name: "threads", value: 1
2025-09-15 20:26:07.671 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_meth_waterfall INFO eval :: name: "disk_size", value: 27
2025-09-15 20:26:07.671 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_meth_waterfall INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2191.meth_waterfall"
2025-09-15 20:26:07.671 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_meth_waterfall INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:26:07.671 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_meth_waterfall WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:26:07.671 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_meth_waterfall INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:26:07.672 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_meth_waterfall INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:26:07.676 wdl.w:ptcp.w:call-trgt-89.t:call-trgt_plot_motifs_allele INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2186.motifs_allele.trgt_plots.zip"
2025-09-15 20:26:07.749 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_meth_waterfall INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-94/call-trgt_plot_meth_waterfall/_singularity_tmpdir_0_wlyrhg"
2025-09-15 20:26:07.749 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_meth_waterfall INFO Slurm invocation: srun --job-name call-trgt_plot_meth_waterfall --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-94/call-trgt_plot_meth_waterfall/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-94/call-trgt_plot_meth_waterfall/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-94/call-trgt_plot_meth_waterfall/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-94/call-trgt_plot_meth_waterfall/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-94/call-trgt_genotype/out/m84036_250809_035451_s4.bc2191.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2191.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-94/call-trgt_genotype/out/m84036_250809_035451_s4.bc2191.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2191.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-94/call-trgt_genotype/out/m84036_250809_035451_s4.bc2191.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2191.trgt.sorted.spanning.bam:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-94/call-trgt_plot_meth_waterfall/_singularity_tmpdir_0_wlyrhg/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-94/call-trgt_plot_meth_waterfall/_singularity_tmpdir_0_wlyrhg/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:26:07.771 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_meth_waterfall NOTICE slurm_singularity run :: pid: 1207077, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-94/call-trgt_plot_meth_waterfall/slurm_singularity.log.txt"
2025-09-15 20:26:07.805 wdl.w:ptcp.w:call-trgt-89.t:call-trgt_plot_motifs_allele NOTICE done
2025-09-15 20:26:07.810 wdl.w:ptcp.w:call-trgt-89 NOTICE finish :: job: "call-trgt_plot_motifs_allele"
2025-09-15 20:26:07.810 wdl.w:ptcp.w:call-trgt-89 INFO output :: job: "call-trgt_plot_motifs_allele", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-89/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2186.motifs_allele.trgt_plots.zip"}
2025-09-15 20:26:07.810 wdl.w:ptcp.w:call-trgt-89 INFO visit :: node: "output-images_motifs_allele", values: {"images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-89/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2186.motifs_allele.trgt_plots.zip"}
2025-09-15 20:26:07.815 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_motifs_allele NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-94/call-trgt_plot_motifs_allele", thread: 140606575711808
2025-09-15 20:26:07.831 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_motifs_allele INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:26:07.831 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_motifs_allele INFO input :: name: "waterfall", value: false
2025-09-15 20:26:07.831 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_motifs_allele INFO input :: name: "methylation", value: false
2025-09-15 20:26:07.831 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_motifs_allele INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:26:07.831 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_motifs_allele INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:26:07.831 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_motifs_allele INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:26:07.831 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_motifs_allele INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2191.trgt.sorted.spanning.bam.bai"
2025-09-15 20:26:07.831 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_motifs_allele INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2191.trgt.sorted.spanning.bam"
2025-09-15 20:26:07.831 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_motifs_allele INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2191.trgt.vcf"
2025-09-15 20:26:07.831 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_motifs_allele INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2191"
2025-09-15 20:26:07.832 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_motifs_allele INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:26:07.832 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_motifs_allele INFO eval :: name: "plot_type", value: "allele"
2025-09-15 20:26:07.832 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_motifs_allele INFO eval :: name: "show", value: "motifs"
2025-09-15 20:26:07.832 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_motifs_allele INFO eval :: name: "threads", value: 1
2025-09-15 20:26:07.832 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_motifs_allele INFO eval :: name: "disk_size", value: 27
2025-09-15 20:26:07.832 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_motifs_allele INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2191.motifs_allele"
2025-09-15 20:26:07.833 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_motifs_allele INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:26:07.833 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_motifs_allele WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:26:07.833 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_motifs_allele INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:26:07.833 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_motifs_allele INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:26:07.847 wdl.w:ptcp.w:call-trgt-93.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO srun: job 51798147 queued and waiting for resources
2025-09-15 20:26:07.847 wdl.w:ptcp.w:call-trgt-93.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO srun: job 51798147 has been allocated resources
2025-09-15 20:26:07.847 wdl.w:ptcp.w:call-trgt-93.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:26:07.878 wdl.w:ptcp.w:call-sawfish-41.t:call-run_sawfish INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2138_sawfish/m84036_250809_035451_s4.bc2138.sv.vcf.gz"
2025-09-15 20:26:07.884 wdl.w:ptcp.w:call-sawfish-41.t:call-run_sawfish INFO output :: name: "vcf_tbi", value: "m84036_250809_035451_s4.bc2138_sawfish/m84036_250809_035451_s4.bc2138.sv.vcf.gz.tbi"
2025-09-15 20:26:07.885 wdl.w:ptcp.w:call-sawfish-41.t:call-run_sawfish INFO output :: name: "minimap2_bam", value: "m84036_250809_035451_s4.bc2138.minimap2.bam"
2025-09-15 20:26:07.887 wdl.w:ptcp.w:call-sawfish-41.t:call-run_sawfish INFO output :: name: "minimap2_bam_bai", value: "m84036_250809_035451_s4.bc2138.minimap2.bam.bai"
2025-09-15 20:26:07.903 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_motifs_allele INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-94/call-trgt_plot_motifs_allele/_singularity_tmpdir_lbt243gt"
2025-09-15 20:26:07.904 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_motifs_allele INFO Slurm invocation: srun --job-name call-trgt_plot_motifs_allele --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-94/call-trgt_plot_motifs_allele/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-94/call-trgt_plot_motifs_allele/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-94/call-trgt_plot_motifs_allele/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-94/call-trgt_plot_motifs_allele/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-94/call-trgt_genotype/out/m84036_250809_035451_s4.bc2191.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2191.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-94/call-trgt_genotype/out/m84036_250809_035451_s4.bc2191.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2191.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-94/call-trgt_genotype/out/m84036_250809_035451_s4.bc2191.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2191.trgt.sorted.spanning.bam:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-94/call-trgt_plot_motifs_allele/_singularity_tmpdir_lbt243gt/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-94/call-trgt_plot_motifs_allele/_singularity_tmpdir_lbt243gt/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:26:07.923 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_motifs_allele NOTICE slurm_singularity run :: pid: 1207090, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-94/call-trgt_plot_motifs_allele/slurm_singularity.log.txt"
2025-09-15 20:26:07.943 wdl.w:ptcp.w:call-paraphase-93.t:call-call_f8.slurm_singularity INFO srun: job 51798148 queued and waiting for resources
2025-09-15 20:26:07.943 wdl.w:ptcp.w:call-paraphase-93.t:call-call_f8.slurm_singularity INFO srun: job 51798148 has been allocated resources
2025-09-15 20:26:07.943 wdl.w:ptcp.w:call-paraphase-93.t:call-call_f8.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:26:08.007 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:26:07 [ERROR] - No reads found for TRID=OPDM_ABCD3
2025-09-15 20:26:08.008 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:26:07 [ERROR] - No reads found for TRID=NIID_NOTCH2NLC
2025-09-15 20:26:08.008 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:26:07 [ERROR] - No reads found for TRID=SCA37_DAB1
2025-09-15 20:26:08.008 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:26:07 [ERROR] - No reads found for TRID=OPDM4_RILPL1
2025-09-15 20:26:08.008 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:26:07 [ERROR] - No reads found for TRID=DRPLA_ATN1
2025-09-15 20:26:08.008 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:26:07 [ERROR] - No reads found for TRID=SCA2_ATXN2
2025-09-15 20:26:08.013 wdl.w:ptcp.w:call-sawfish-41.t:call-run_sawfish NOTICE done
2025-09-15 20:26:08.016 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_plot_meth_allele.slurm_singularity INFO srun: job 51798149 queued and waiting for resources
2025-09-15 20:26:08.017 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_plot_meth_allele.slurm_singularity INFO srun: job 51798149 has been allocated resources
2025-09-15 20:26:08.017 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_plot_meth_allele.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:26:08.021 wdl.w:ptcp.w:call-sawfish-41 NOTICE finish :: job: "call-run_sawfish"
2025-09-15 20:26:08.021 wdl.w:ptcp.w:call-sawfish-41 INFO output :: job: "call-run_sawfish", values: {"minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-41/call-run_sawfish/out/m84036_250809_035451_s4.bc2138.minimap2.bam.bai", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-41/call-run_sawfish/out/m84036_250809_035451_s4.bc2138.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-41/call-run_sawfish/out/m84036_250809_035451_s4.bc2138_sawfish/m84036_250809_035451_s4.bc2138.sv.vcf.gz.tbi", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-41/call-run_sawfish/out/m84036_250809_035451_s4.bc2138_sawfish/m84036_250809_035451_s4.bc2138.sv.vcf.gz"}
2025-09-15 20:26:08.022 wdl.w:ptcp.w:call-sawfish-41 INFO visit :: node: "output-minimap2_bam", values: {"minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-41/call-run_sawfish/out/m84036_250809_035451_s4.bc2138.minimap2.bam"}
2025-09-15 20:26:08.022 wdl.w:ptcp.w:call-sawfish-41 INFO visit :: node: "output-minimap2_bam_bai", values: {"minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-41/call-run_sawfish/out/m84036_250809_035451_s4.bc2138.minimap2.bam.bai"}
2025-09-15 20:26:08.022 wdl.w:ptcp.w:call-sawfish-41 INFO visit :: node: "output-vcf", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-41/call-run_sawfish/out/m84036_250809_035451_s4.bc2138_sawfish/m84036_250809_035451_s4.bc2138.sv.vcf.gz"}
2025-09-15 20:26:08.022 wdl.w:ptcp.w:call-sawfish-41 INFO visit :: node: "output-vcf_tbi", values: {"vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-41/call-run_sawfish/out/m84036_250809_035451_s4.bc2138_sawfish/m84036_250809_035451_s4.bc2138.sv.vcf.gz.tbi"}
2025-09-15 20:26:08.022 wdl.w:ptcp.w:call-sawfish-41 INFO visit :: node: "outputs", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-41/call-run_sawfish/out/m84036_250809_035451_s4.bc2138_sawfish/m84036_250809_035451_s4.bc2138.sv.vcf.gz", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-41/call-run_sawfish/out/m84036_250809_035451_s4.bc2138.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-41/call-run_sawfish/out/m84036_250809_035451_s4.bc2138_sawfish/m84036_250809_035451_s4.bc2138.sv.vcf.gz.tbi", "minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-41/call-run_sawfish/out/m84036_250809_035451_s4.bc2138.minimap2.bam.bai"}
2025-09-15 20:26:08.028 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_motifs_waterfall NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-94/call-trgt_plot_motifs_waterfall", thread: 140608765158976
2025-09-15 20:26:08.046 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_motifs_waterfall INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:26:08.046 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_motifs_waterfall INFO input :: name: "waterfall", value: true
2025-09-15 20:26:08.047 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_motifs_waterfall INFO input :: name: "methylation", value: false
2025-09-15 20:26:08.047 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_motifs_waterfall INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:26:08.047 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_motifs_waterfall INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:26:08.047 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_motifs_waterfall INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:26:08.047 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_motifs_waterfall INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2191.trgt.sorted.spanning.bam.bai"
2025-09-15 20:26:08.047 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_motifs_waterfall INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2191.trgt.sorted.spanning.bam"
2025-09-15 20:26:08.047 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_motifs_waterfall INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2191.trgt.vcf"
2025-09-15 20:26:08.047 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_motifs_waterfall INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2191"
2025-09-15 20:26:08.047 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:26:08.047 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "plot_type", value: "waterfall"
2025-09-15 20:26:08.048 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "show", value: "motifs"
2025-09-15 20:26:08.048 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "threads", value: 1
2025-09-15 20:26:08.047 wdl.w:ptcp.w:call-trgt-85.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:26:05 [ERROR] - No reads found for TRID=PRTS_ARX
2025-09-15 20:26:08.048 wdl.w:ptcp.w:call-trgt-85.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:26:05 [ERROR] - No reads found for TRID=EIEE1_ARX
2025-09-15 20:26:08.048 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "disk_size", value: 27
2025-09-15 20:26:08.048 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2191.motifs_waterfall"
2025-09-15 20:26:08.048 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_motifs_waterfall INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:26:08.049 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_motifs_waterfall WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:26:08.049 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_motifs_waterfall INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:26:08.049 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_motifs_waterfall INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:26:08.071 wdl.w:ptcp.w:call-sawfish-41 NOTICE done
2025-09-15 20:26:08.117 wdl.w:ptcp NOTICE finish :: job: "call-sawfish-41"
2025-09-15 20:26:08.117 wdl.w:ptcp INFO output :: job: "call-sawfish-41", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-41/out/m84036_250809_035451_s4.bc2138_sawfish/m84036_250809_035451_s4.bc2138.sv.vcf.gz", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-41/out/m84036_250809_035451_s4.bc2138.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-41/out/m84036_250809_035451_s4.bc2138_sawfish/m84036_250809_035451_s4.bc2138.sv.vcf.gz.tbi", "minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-41/out/m84036_250809_035451_s4.bc2138.minimap2.bam.bai"}
2025-09-15 20:26:08.117 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_motifs_waterfall INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-94/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_arp46isr"
2025-09-15 20:26:08.118 wdl.w:ptcp NOTICE ready :: job: "call-tar_outputs-41", callee: "tar_outputs"
2025-09-15 20:26:08.118 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_motifs_waterfall INFO Slurm invocation: srun --job-name call-trgt_plot_motifs_waterfall --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-94/call-trgt_plot_motifs_waterfall/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-94/call-trgt_plot_motifs_waterfall/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-94/call-trgt_plot_motifs_waterfall/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-94/call-trgt_plot_motifs_waterfall/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-94/call-trgt_genotype/out/m84036_250809_035451_s4.bc2191.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2191.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-94/call-trgt_genotype/out/m84036_250809_035451_s4.bc2191.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2191.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-94/call-trgt_genotype/out/m84036_250809_035451_s4.bc2191.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2191.trgt.sorted.spanning.bam:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-94/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_arp46isr/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-94/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_arp46isr/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:26:08.118 wdl.w:ptcp INFO input :: job: "call-tar_outputs-41", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "sawfish_vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-41/out/m84036_250809_035451_s4.bc2138_sawfish/m84036_250809_035451_s4.bc2138.sv.vcf.gz.tbi", "sawfish_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-41/out/m84036_250809_035451_s4.bc2138_sawfish/m84036_250809_035451_s4.bc2138.sv.vcf.gz", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-41/out/m84036_250809_035451_s4.bc2138.f8inversion.json", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-41/out/m84036_250809_035451_s4.bc2138_paraphase/m84036_250809_035451_s4.bc2138.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-41/out/m84036_250809_035451_s4.bc2138_paraphase/m84036_250809_035451_s4.bc2138.paraphase.bam", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-41/out/m84036_250809_035451_s4.bc2138_paraphase/m84036_250809_035451_s4.bc2138.paraphase.json", "trgt_spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-41/out/m84036_250809_035451_s4.bc2138.trgt.sorted.spanning.bam.bai", "trgt_spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-41/out/m84036_250809_035451_s4.bc2138.trgt.sorted.spanning.bam", "trgt_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-41/out/m84036_250809_035451_s4.bc2138.trgt.vcf", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-41/out/m84036_250809_035451_s4.bc2138.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-41/out/m84036_250809_035451_s4.bc2138.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2138"}
2025-09-15 20:26:08.134 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_motifs_waterfall NOTICE slurm_singularity run :: pid: 1207092, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-94/call-trgt_plot_motifs_waterfall/slurm_singularity.log.txt"
2025-09-15 20:26:08.151 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:26:07 [ERROR] - No reads found for TRID=OPDM_ABCD3
2025-09-15 20:26:08.152 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:26:07 [ERROR] - No reads found for TRID=NIID_NOTCH2NLC
2025-09-15 20:26:08.152 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:26:08 [ERROR] - No reads found for TRID=SCA37_DAB1
2025-09-15 20:26:08.152 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:26:08 [ERROR] - No reads found for TRID=OPDM4_RILPL1
2025-09-15 20:26:08.152 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:26:07 [ERROR] - No reads found for TRID=OPDM_ABCD3
2025-09-15 20:26:08.152 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:26:08 [ERROR] - No reads found for TRID=DRPLA_ATN1
2025-09-15 20:26:08.152 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:26:07 [ERROR] - No reads found for TRID=NIID_NOTCH2NLC
2025-09-15 20:26:08.152 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:26:08 [ERROR] - No reads found for TRID=SCA37_DAB1
2025-09-15 20:26:08.152 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:26:08 [ERROR] - No reads found for TRID=OPDM4_RILPL1
2025-09-15 20:26:08.152 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:26:08 [ERROR] - No reads found for TRID=DRPLA_ATN1
2025-09-15 20:26:08.155 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:26:08 [ERROR] - No reads found for TRID=OPDM_ABCD3
2025-09-15 20:26:08.155 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:26:08 [ERROR] - No reads found for TRID=NIID_NOTCH2NLC
2025-09-15 20:26:08.161 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO srun: job 51798150 queued and waiting for resources
2025-09-15 20:26:08.161 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO srun: job 51798150 has been allocated resources
2025-09-15 20:26:08.161 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:26:08.162 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO srun: job 51798152 queued and waiting for resources
2025-09-15 20:26:08.163 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO srun: job 51798152 has been allocated resources
2025-09-15 20:26:08.163 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:26:08.164 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_plot_motifs_allele.slurm_singularity INFO srun: job 51798151 queued and waiting for resources
2025-09-15 20:26:08.165 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_plot_motifs_allele.slurm_singularity INFO srun: job 51798151 has been allocated resources
2025-09-15 20:26:08.165 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_plot_motifs_allele.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:26:08.237 wdl.w:ptcp.w:call-trgt-85.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:26:04 [ERROR] - No reads found for TRID=PRTS_ARX
2025-09-15 20:26:08.238 wdl.w:ptcp.w:call-trgt-85.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:26:04 [ERROR] - No reads found for TRID=EIEE1_ARX
2025-09-15 20:26:08.289 wdl.w:ptcp.t:call-tar_outputs-69.stderr VERBOSE tar: Removing leading `/' from member names
2025-09-15 20:26:08.290 wdl.w:ptcp.t:call-tar_outputs-69.stderr VERBOSE tar: Removing leading `/' from hard link targets
2025-09-15 20:26:08.300 wdl.w:ptcp.t:call-tar_outputs-69.slurm_singularity INFO srun: job 51798153 queued and waiting for resources
2025-09-15 20:26:08.300 wdl.w:ptcp.t:call-tar_outputs-69.slurm_singularity INFO srun: job 51798153 has been allocated resources
2025-09-15 20:26:08.300 wdl.w:ptcp.t:call-tar_outputs-69.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:26:08.337 wdl.w:ptcp.w:call-sawfish-59.t:call-run_sawfish INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2156_sawfish/m84036_250809_035451_s4.bc2156.sv.vcf.gz"
2025-09-15 20:26:08.345 wdl.w:ptcp.w:call-sawfish-59.t:call-run_sawfish INFO output :: name: "vcf_tbi", value: "m84036_250809_035451_s4.bc2156_sawfish/m84036_250809_035451_s4.bc2156.sv.vcf.gz.tbi"
2025-09-15 20:26:08.344 wdl.w:ptcp.w:call-paraphase-46.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for rpgr for sample m84036_250809_035451_s4.bc2143 at 2025-09-15 20:25:57.983993...
2025-09-15 20:26:08.346 wdl.w:ptcp.w:call-paraphase-46.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for rpgr for sample m84036_250809_035451_s4.bc2143 at 2025-09-15 20:25:57.985617...
2025-09-15 20:26:08.346 wdl.w:ptcp.w:call-paraphase-46.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for rpgr for sample m84036_250809_035451_s4.bc2143 at 2025-09-15 20:25:59.904711...
2025-09-15 20:26:08.346 wdl.w:ptcp.w:call-paraphase-46.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for rpgr for sample m84036_250809_035451_s4.bc2143 at 2025-09-15 20:26:00.940062...
2025-09-15 20:26:08.346 wdl.w:ptcp.w:call-paraphase-46.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for rpgr for sample m84036_250809_035451_s4.bc2143 at 2025-09-15 20:26:01.202111...
2025-09-15 20:26:08.347 wdl.w:ptcp.w:call-sawfish-59.t:call-run_sawfish INFO output :: name: "minimap2_bam", value: "m84036_250809_035451_s4.bc2156.minimap2.bam"
2025-09-15 20:26:08.350 wdl.w:ptcp.w:call-sawfish-59.t:call-run_sawfish INFO output :: name: "minimap2_bam_bai", value: "m84036_250809_035451_s4.bc2156.minimap2.bam.bai"
2025-09-15 20:26:08.427 wdl.w:ptcp.w:call-paraphase-93.t:call-call_f8 INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2190.f8inversion.vcf"
2025-09-15 20:26:08.434 wdl.w:ptcp.w:call-paraphase-93.t:call-call_f8 INFO output :: name: "json", value: "m84036_250809_035451_s4.bc2190.f8inversion.json"
2025-09-15 20:26:08.477 wdl.w:ptcp.t:call-tar_outputs-69 INFO output :: name: "sample_tarball", value: "m84036_250809_035451_s4.bc2166.tar"
2025-09-15 20:26:08.496 wdl.w:ptcp.w:call-paraphase-31.t:call-call_f8.slurm_singularity INFO srun: job 51798154 queued and waiting for resources
2025-09-15 20:26:08.496 wdl.w:ptcp.w:call-paraphase-31.t:call-call_f8.slurm_singularity INFO srun: job 51798154 has been allocated resources
2025-09-15 20:26:08.496 wdl.w:ptcp.w:call-paraphase-31.t:call-call_f8.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:26:08.521 wdl.w:ptcp.w:call-paraphase-95.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for smn1 for sample m84036_250809_035451_s4.bc2192 at 2025-09-15 20:26:06.924353...
2025-09-15 20:26:08.522 wdl.w:ptcp.w:call-paraphase-95.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning to gene2 region for smn1 for sample m84036_250809_035451_s4.bc2192 at 2025-09-15 20:26:07.261167...
2025-09-15 20:26:08.529 wdl.w:ptcp.w:call-paraphase-93.t:call-call_f8 NOTICE done
2025-09-15 20:26:08.535 wdl.w:ptcp.w:call-paraphase-93 NOTICE finish :: job: "call-call_f8"
2025-09-15 20:26:08.535 wdl.w:ptcp.w:call-paraphase-93 INFO output :: job: "call-call_f8", values: {"json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-93/call-call_f8/out/m84036_250809_035451_s4.bc2190.f8inversion.json", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-93/call-call_f8/out/m84036_250809_035451_s4.bc2190.f8inversion.vcf"}
2025-09-15 20:26:08.535 wdl.w:ptcp.w:call-paraphase-93 INFO visit :: node: "output-f8_json", values: {"f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-93/call-call_f8/out/m84036_250809_035451_s4.bc2190.f8inversion.json"}
2025-09-15 20:26:08.536 wdl.w:ptcp.w:call-paraphase-93 INFO visit :: node: "output-f8_vcf", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-93/call-call_f8/out/m84036_250809_035451_s4.bc2190.f8inversion.vcf"}
2025-09-15 20:26:08.536 wdl.w:ptcp.w:call-paraphase-93 INFO visit :: node: "outputs", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-93/call-call_f8/out/m84036_250809_035451_s4.bc2190.f8inversion.vcf", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-93/call-run_paraphase/out/m84036_250809_035451_s4.bc2190_paraphase/m84036_250809_035451_s4.bc2190.paraphase.json", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-93/call-run_paraphase/out/m84036_250809_035451_s4.bc2190_paraphase/m84036_250809_035451_s4.bc2190.paraphase.bam", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-93/call-run_paraphase/out/m84036_250809_035451_s4.bc2190_paraphase/m84036_250809_035451_s4.bc2190.paraphase.bam.bai", "paraphase_vcfs": [], "havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-93/call-run_paraphase/out/m84036_250809_035451_s4.bc2190.havanno.json", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-93/call-call_f8/out/m84036_250809_035451_s4.bc2190.f8inversion.json"}
2025-09-15 20:26:08.547 wdl.w:ptcp.t:call-tar_outputs-52 NOTICE task setup :: name: "tar_outputs", source: "./common.wdl", line: 279, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-52", thread: 140611441120832
2025-09-15 20:26:08.589 wdl.w:ptcp.t:call-tar_outputs-52 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:26:08.589 wdl.w:ptcp.t:call-tar_outputs-52 INFO input :: name: "sawfish_vcf_tbi", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2149.sv.vcf.gz.tbi"
2025-09-15 20:26:08.589 wdl.w:ptcp.t:call-tar_outputs-52 INFO input :: name: "sawfish_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2149.sv.vcf.gz"
2025-09-15 20:26:08.589 wdl.w:ptcp.t:call-tar_outputs-52 INFO input :: name: "f8_json", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2149.f8inversion.json"
2025-09-15 20:26:08.589 wdl.w:ptcp.t:call-tar_outputs-52 INFO input :: name: "paraphase_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2149.paraphase.bam.bai"
2025-09-15 20:26:08.589 wdl.w:ptcp.t:call-tar_outputs-52 INFO input :: name: "paraphase_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2149.paraphase.bam"
2025-09-15 20:26:08.589 wdl.w:ptcp.t:call-tar_outputs-52 INFO input :: name: "paraphase_json", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2149.paraphase.json"
2025-09-15 20:26:08.589 wdl.w:ptcp.t:call-tar_outputs-52 INFO input :: name: "trgt_spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2149.trgt.sorted.spanning.bam.bai"
2025-09-15 20:26:08.589 wdl.w:ptcp.t:call-tar_outputs-52 INFO input :: name: "trgt_spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2149.trgt.sorted.spanning.bam"
2025-09-15 20:26:08.589 wdl.w:ptcp.t:call-tar_outputs-52 INFO input :: name: "trgt_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2149.trgt.vcf"
2025-09-15 20:26:08.590 wdl.w:ptcp.t:call-tar_outputs-52 INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2149.mapped.bam.bai"
2025-09-15 20:26:08.590 wdl.w:ptcp.t:call-tar_outputs-52 INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2149.mapped.bam"
2025-09-15 20:26:08.590 wdl.w:ptcp.t:call-tar_outputs-52 INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2149"
2025-09-15 20:26:08.590 wdl.w:ptcp.t:call-tar_outputs-52 INFO eval :: name: "threads", value: 1
2025-09-15 20:26:08.590 wdl.w:ptcp.t:call-tar_outputs-52 INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:26:08.590 wdl.w:ptcp.t:call-tar_outputs-52 INFO eval :: name: "disk_size", value: 6
2025-09-15 20:26:08.590 wdl.w:ptcp.t:call-tar_outputs-69 NOTICE done
2025-09-15 20:26:08.590 wdl.w:ptcp.t:call-tar_outputs-52 INFO eval :: name: "output_tarball", value: "m84036_250809_035451_s4.bc2149.tar"
2025-09-15 20:26:08.591 wdl.w:ptcp.t:call-tar_outputs-52 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:26:08.591 wdl.w:ptcp.t:call-tar_outputs-52 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:26:08.591 wdl.w:ptcp.w:call-sawfish-59.t:call-run_sawfish NOTICE done
2025-09-15 20:26:08.592 wdl.w:ptcp.t:call-tar_outputs-52 INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:26:08.592 wdl.w:ptcp.t:call-tar_outputs-52 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:26:08.594 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:26:08 [ERROR] - No reads found for TRID=OPDM_ABCD3
2025-09-15 20:26:08.594 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:26:08 [ERROR] - No reads found for TRID=SCA37_DAB1
2025-09-15 20:26:08.594 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:26:08 [ERROR] - No reads found for TRID=NIID_NOTCH2NLC
2025-09-15 20:26:08.595 wdl.w:ptcp NOTICE finish :: job: "call-tar_outputs-69"
2025-09-15 20:26:08.596 wdl.w:ptcp INFO output :: job: "call-tar_outputs-69", values: {"sample_tarball": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-69/out/m84036_250809_035451_s4.bc2166.tar"}
2025-09-15 20:26:08.606 wdl.w:ptcp.t:call-tar_outputs-40 NOTICE task setup :: name: "tar_outputs", source: "./common.wdl", line: 279, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-40", thread: 140613043340864
2025-09-15 20:26:08.614 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_meth_allele.slurm_singularity INFO srun: job 51798155 queued and waiting for resources
2025-09-15 20:26:08.614 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_meth_allele.slurm_singularity INFO srun: job 51798155 has been allocated resources
2025-09-15 20:26:08.614 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_meth_allele.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:26:08.617 wdl.w:ptcp.w:call-sawfish-59 NOTICE finish :: job: "call-run_sawfish"
2025-09-15 20:26:08.618 wdl.w:ptcp.w:call-sawfish-59 INFO output :: job: "call-run_sawfish", values: {"minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-59/call-run_sawfish/out/m84036_250809_035451_s4.bc2156.minimap2.bam.bai", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-59/call-run_sawfish/out/m84036_250809_035451_s4.bc2156.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-59/call-run_sawfish/out/m84036_250809_035451_s4.bc2156_sawfish/m84036_250809_035451_s4.bc2156.sv.vcf.gz.tbi", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-59/call-run_sawfish/out/m84036_250809_035451_s4.bc2156_sawfish/m84036_250809_035451_s4.bc2156.sv.vcf.gz"}
2025-09-15 20:26:08.618 wdl.w:ptcp.w:call-sawfish-59 INFO visit :: node: "output-minimap2_bam", values: {"minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-59/call-run_sawfish/out/m84036_250809_035451_s4.bc2156.minimap2.bam"}
2025-09-15 20:26:08.618 wdl.w:ptcp.w:call-sawfish-59 INFO visit :: node: "output-minimap2_bam_bai", values: {"minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-59/call-run_sawfish/out/m84036_250809_035451_s4.bc2156.minimap2.bam.bai"}
2025-09-15 20:26:08.618 wdl.w:ptcp.w:call-sawfish-59 INFO visit :: node: "output-vcf", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-59/call-run_sawfish/out/m84036_250809_035451_s4.bc2156_sawfish/m84036_250809_035451_s4.bc2156.sv.vcf.gz"}
2025-09-15 20:26:08.618 wdl.w:ptcp.w:call-sawfish-59 INFO visit :: node: "output-vcf_tbi", values: {"vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-59/call-run_sawfish/out/m84036_250809_035451_s4.bc2156_sawfish/m84036_250809_035451_s4.bc2156.sv.vcf.gz.tbi"}
2025-09-15 20:26:08.618 wdl.w:ptcp.w:call-sawfish-59 INFO visit :: node: "outputs", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-59/call-run_sawfish/out/m84036_250809_035451_s4.bc2156_sawfish/m84036_250809_035451_s4.bc2156.sv.vcf.gz", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-59/call-run_sawfish/out/m84036_250809_035451_s4.bc2156.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-59/call-run_sawfish/out/m84036_250809_035451_s4.bc2156_sawfish/m84036_250809_035451_s4.bc2156.sv.vcf.gz.tbi", "minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-59/call-run_sawfish/out/m84036_250809_035451_s4.bc2156.minimap2.bam.bai"}
2025-09-15 20:26:08.628 wdl.w:ptcp.w:call-paraphase-34.t:call-call_f8 NOTICE task setup :: name: "call_f8", source: "./paraphase.wdl", line: 232, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-34/call-call_f8", thread: 140609822115392
2025-09-15 20:26:08.645 wdl.w:ptcp.w:call-paraphase-93 NOTICE done
2025-09-15 20:26:08.649 wdl.w:ptcp.t:call-tar_outputs-40 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:26:08.649 wdl.w:ptcp.t:call-tar_outputs-40 INFO input :: name: "sawfish_vcf_tbi", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2137.sv.vcf.gz.tbi"
2025-09-15 20:26:08.649 wdl.w:ptcp.t:call-tar_outputs-40 INFO input :: name: "sawfish_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2137.sv.vcf.gz"
2025-09-15 20:26:08.649 wdl.w:ptcp.t:call-tar_outputs-40 INFO input :: name: "f8_json", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2137.f8inversion.json"
2025-09-15 20:26:08.649 wdl.w:ptcp.t:call-tar_outputs-40 INFO input :: name: "paraphase_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2137.paraphase.bam.bai"
2025-09-15 20:26:08.649 wdl.w:ptcp.t:call-tar_outputs-40 INFO input :: name: "paraphase_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2137.paraphase.bam"
2025-09-15 20:26:08.649 wdl.w:ptcp.t:call-tar_outputs-40 INFO input :: name: "paraphase_json", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2137.paraphase.json"
2025-09-15 20:26:08.649 wdl.w:ptcp.t:call-tar_outputs-40 INFO input :: name: "trgt_spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2137.trgt.sorted.spanning.bam.bai"
2025-09-15 20:26:08.649 wdl.w:ptcp.t:call-tar_outputs-40 INFO input :: name: "trgt_spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2137.trgt.sorted.spanning.bam"
2025-09-15 20:26:08.649 wdl.w:ptcp.t:call-tar_outputs-40 INFO input :: name: "trgt_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2137.trgt.vcf"
2025-09-15 20:26:08.649 wdl.w:ptcp.t:call-tar_outputs-40 INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2137.mapped.bam.bai"
2025-09-15 20:26:08.649 wdl.w:ptcp.t:call-tar_outputs-40 INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2137.mapped.bam"
2025-09-15 20:26:08.649 wdl.w:ptcp.t:call-tar_outputs-40 INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2137"
2025-09-15 20:26:08.650 wdl.w:ptcp.t:call-tar_outputs-40 INFO eval :: name: "threads", value: 1
2025-09-15 20:26:08.650 wdl.w:ptcp.t:call-tar_outputs-40 INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:26:08.650 wdl.w:ptcp.t:call-tar_outputs-40 INFO eval :: name: "disk_size", value: 6
2025-09-15 20:26:08.650 wdl.w:ptcp.t:call-tar_outputs-40 INFO eval :: name: "output_tarball", value: "m84036_250809_035451_s4.bc2137.tar"
2025-09-15 20:26:08.650 wdl.w:ptcp.t:call-tar_outputs-40 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:26:08.651 wdl.w:ptcp.t:call-tar_outputs-40 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:26:08.651 wdl.w:ptcp.t:call-tar_outputs-40 INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:26:08.651 wdl.w:ptcp NOTICE finish :: job: "call-paraphase-93"
2025-09-15 20:26:08.651 wdl.w:ptcp.t:call-tar_outputs-40 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:26:08.652 wdl.w:ptcp INFO output :: job: "call-paraphase-93", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-93/out/m84036_250809_035451_s4.bc2190.f8inversion.vcf", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-93/out/m84036_250809_035451_s4.bc2190_paraphase/m84036_250809_035451_s4.bc2190.paraphase.json", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-93/out/m84036_250809_035451_s4.bc2190_paraphase/m84036_250809_035451_s4.bc2190.paraphase.bam", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-93/out/m84036_250809_035451_s4.bc2190_paraphase/m84036_250809_035451_s4.bc2190.paraphase.bam.bai", "paraphase_vcfs": [], "havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-93/out/m84036_250809_035451_s4.bc2190.havanno.json", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-93/out/m84036_250809_035451_s4.bc2190.f8inversion.json"}
2025-09-15 20:26:08.680 wdl.w:ptcp.w:call-paraphase-34.t:call-call_f8 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:26:08.680 wdl.w:ptcp.w:call-paraphase-34.t:call-call_f8 INFO input :: name: "genome_version", value: "38"
2025-09-15 20:26:08.680 wdl.w:ptcp.w:call-paraphase-34.t:call-call_f8 INFO input :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2131"
2025-09-15 20:26:08.680 wdl.w:ptcp.w:call-paraphase-34.t:call-call_f8 INFO input :: name: "paraphase_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2131.paraphase.bam.bai"
2025-09-15 20:26:08.681 wdl.w:ptcp.w:call-paraphase-34.t:call-call_f8 INFO input :: name: "paraphase_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2131.paraphase.bam"
2025-09-15 20:26:08.681 wdl.w:ptcp.w:call-paraphase-34.t:call-call_f8 INFO input :: name: "sex", value: "F"
2025-09-15 20:26:08.681 wdl.w:ptcp.w:call-paraphase-34.t:call-call_f8 INFO eval :: name: "threads", value: 1
2025-09-15 20:26:08.681 wdl.w:ptcp.w:call-paraphase-34.t:call-call_f8 INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:26:08.681 wdl.w:ptcp.w:call-paraphase-34.t:call-call_f8 INFO eval :: name: "disk_size", value: 11
2025-09-15 20:26:08.681 wdl.w:ptcp.w:call-paraphase-34.t:call-call_f8 INFO eval :: name: "sample_sex", value: "F"
2025-09-15 20:26:08.682 wdl.w:ptcp.w:call-paraphase-34.t:call-call_f8 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:26:08.682 wdl.w:ptcp.w:call-paraphase-34.t:call-call_f8 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:26:08.682 wdl.w:ptcp.w:call-paraphase-34.t:call-call_f8 INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:26:08.682 wdl.w:ptcp.w:call-paraphase-34.t:call-call_f8 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:26:08.688 wdl.w:ptcp.w:call-sawfish-59 NOTICE done
2025-09-15 20:26:08.695 wdl.w:ptcp NOTICE finish :: job: "call-sawfish-59"
2025-09-15 20:26:08.695 wdl.w:ptcp INFO output :: job: "call-sawfish-59", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-59/out/m84036_250809_035451_s4.bc2156_sawfish/m84036_250809_035451_s4.bc2156.sv.vcf.gz", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-59/out/m84036_250809_035451_s4.bc2156.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-59/out/m84036_250809_035451_s4.bc2156_sawfish/m84036_250809_035451_s4.bc2156.sv.vcf.gz.tbi", "minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-59/out/m84036_250809_035451_s4.bc2156.minimap2.bam.bai"}
2025-09-15 20:26:08.756 wdl.w:ptcp.w:call-sawfish-63.t:call-run_sawfish.stderr VERBOSE [M::mm_idx_gen::51.813*1.64] collected minimizers
2025-09-15 20:26:08.758 wdl.w:ptcp.w:call-sawfish-63.t:call-run_sawfish.stderr VERBOSE [M::mm_idx_gen::61.586*1.84] sorted minimizers
2025-09-15 20:26:08.758 wdl.w:ptcp.w:call-sawfish-63.t:call-run_sawfish.stderr VERBOSE [M::main::61.586*1.84] loaded/built the index for 195 target sequence(s)
2025-09-15 20:26:08.758 wdl.w:ptcp.w:call-sawfish-63.t:call-run_sawfish.stderr VERBOSE [M::mm_mapopt_update::72.752*1.71] mid_occ = 136
2025-09-15 20:26:08.758 wdl.w:ptcp.w:call-sawfish-63.t:call-run_sawfish.stderr VERBOSE [M::mm_idx_stat] kmer size: 19; skip: 19; is_hpc: 0; #seq: 195
2025-09-15 20:26:08.758 wdl.w:ptcp.w:call-sawfish-63.t:call-run_sawfish.stderr VERBOSE [M::mm_idx_stat::79.462*1.65] distinct minimizers: 214664461 (92.23% are singletons); average occurrences: 1.372; average spacing: 10.529; total length: 3099922541
2025-09-15 20:26:08.758 wdl.w:ptcp.w:call-sawfish-63.t:call-run_sawfish.stderr VERBOSE [M::bam2fq_mainloop] discarded 0 singletons
2025-09-15 20:26:08.758 wdl.w:ptcp.w:call-sawfish-63.t:call-run_sawfish.stderr VERBOSE [M::bam2fq_mainloop] processed 364 reads
2025-09-15 20:26:08.758 wdl.w:ptcp.w:call-sawfish-63.t:call-run_sawfish.stderr VERBOSE [M::worker_pipeline::80.260*1.66] mapped 364 sequences
2025-09-15 20:26:08.758 wdl.w:ptcp.w:call-sawfish-63.t:call-run_sawfish.stderr VERBOSE [M::main] Version: 2.26-r1175
2025-09-15 20:26:08.759 wdl.w:ptcp.w:call-sawfish-63.t:call-run_sawfish.stderr VERBOSE [M::main] CMD: /opt/pacbio/smrttools/install/smrtlink-release_25.1.0.257715/bundles/smrttools/install/smrttools-release_25.1.0.257715/private/thirdparty/minimap2/minimap2_2.26-pacbio2/binwrap/../../../../../private/thirdparty/minimap2/minimap2_2.26-pacbio2/bin/minimap2 -a -y -x map-hifi -Y -E 1,0 /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa -
2025-09-15 20:26:08.759 wdl.w:ptcp.w:call-sawfish-63.t:call-run_sawfish.stderr VERBOSE [M::main] Real time: 80.685 sec; CPU: 133.507 sec; Peak RSS: 11.887 GB
2025-09-15 20:26:08.759 wdl.w:ptcp.w:call-sawfish-63.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:55][sawfish][INFO] Starting sawfish 2.0.3
2025-09-15 20:26:08.759 wdl.w:ptcp.w:call-sawfish-63.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:55][sawfish][INFO] cmdline: sawfish discover --disable-cnv --threads 16 --ref /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa --bam m84036_250809_035451_s4.bc2160.minimap2.bam --output-dir m84036_250809_035451_s4.bc2160_sawfish_discover
2025-09-15 20:26:08.759 wdl.w:ptcp.w:call-sawfish-63.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:55][sawfish][INFO] Running on 16 threads
2025-09-15 20:26:08.759 wdl.w:ptcp.w:call-sawfish-63.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:55][sawfish][INFO] Writing discover settings to file: 'm84036_250809_035451_s4.bc2160_sawfish_discover/discover.settings.json'
2025-09-15 20:26:08.759 wdl.w:ptcp.w:call-sawfish-63.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:55][sawfish][INFO] Reading reference genome from file '/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa'
2025-09-15 20:26:08.759 wdl.w:ptcp.w:call-sawfish-63.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:03][sawfish][INFO] Processing alignment file '/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2160.minimap2.bam'
2025-09-15 20:26:08.759 wdl.w:ptcp.w:call-sawfish-63.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:03][sawfish][INFO] Finished processing all alignments
2025-09-15 20:26:08.759 wdl.w:ptcp.w:call-sawfish-63.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:03][sawfish][INFO] Writing depth bins to binary file: 'm84036_250809_035451_s4.bc2160_sawfish_discover/depth.mpack'
2025-09-15 20:26:08.759 wdl.w:ptcp.w:call-sawfish-63.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:03][sawfish][INFO] Writing max sv depth genome regions to bed file: 'm84036_250809_035451_s4.bc2160_sawfish_discover/max.depth.bed'
2025-09-15 20:26:08.759 wdl.w:ptcp.w:call-sawfish-63.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:03][sawfish][INFO] Completing breakpoint observation clustering
2025-09-15 20:26:08.759 wdl.w:ptcp.w:call-sawfish-63.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:03][sawfish][INFO] Finished breakpoint observation clustering
2025-09-15 20:26:08.759 wdl.w:ptcp.w:call-sawfish-63.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:03][sawfish][INFO] Consolidating adjacent indel candidates
2025-09-15 20:26:08.759 wdl.w:ptcp.w:call-sawfish-63.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:03][sawfish][INFO] Finding large insertion candidates
2025-09-15 20:26:08.759 wdl.w:ptcp.w:call-sawfish-63.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:03][sawfish][INFO] Writing breakpoint_cluster debug bed file: 'm84036_250809_035451_s4.bc2160_sawfish_discover/debug.breakpoint_clusters.bed'
2025-09-15 20:26:08.759 wdl.w:ptcp.w:call-sawfish-63.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:03][sawfish][INFO] Refining SV Candidates
2025-09-15 20:26:08.760 wdl.w:ptcp.w:call-sawfish-63.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:03][sawfish][INFO] Writing debug assembly region bed file: 'm84036_250809_035451_s4.bc2160_sawfish_discover/assembly.regions.bed'
2025-09-15 20:26:08.760 wdl.w:ptcp.w:call-sawfish-63.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:03][sawfish][INFO] Starting refinement of breakpoint evidence clusters
2025-09-15 20:26:08.760 wdl.w:ptcp.w:call-sawfish-63.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:04][sawfish][INFO] Finished refining all breakpoint evidence clusters
2025-09-15 20:26:08.760 wdl.w:ptcp.w:call-sawfish-63.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:04][sawfish][INFO] Writing all contig alignments to bam file: 'm84036_250809_035451_s4.bc2160_sawfish_discover/contig.alignment.bam'
2025-09-15 20:26:08.760 wdl.w:ptcp.w:call-sawfish-63.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:04][sawfish][INFO] Writing candidate structural variants to file: 'm84036_250809_035451_s4.bc2160_sawfish_discover/candidate.sv.bcf'
2025-09-15 20:26:08.760 wdl.w:ptcp.w:call-sawfish-63.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:04][sawfish][INFO] Writing run statistics to file: 'm84036_250809_035451_s4.bc2160_sawfish_discover/run.stats.json'
2025-09-15 20:26:08.760 wdl.w:ptcp.w:call-sawfish-63.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:04][sawfish][INFO] sawfish completed. Total Runtime: 00:00:09.106
2025-09-15 20:26:08.760 wdl.w:ptcp.w:call-sawfish-63.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:04][sawfish][INFO] Starting sawfish 2.0.3
2025-09-15 20:26:08.760 wdl.w:ptcp.w:call-sawfish-63.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:04][sawfish][INFO] cmdline: sawfish joint-call --threads 16 --sample m84036_250809_035451_s4.bc2160_sawfish_discover --output-dir m84036_250809_035451_s4.bc2160_sawfish
2025-09-15 20:26:08.760 wdl.w:ptcp.w:call-sawfish-63.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:04][sawfish][INFO] Running on 16 threads
2025-09-15 20:26:08.760 wdl.w:ptcp.w:call-sawfish-63.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:04][sawfish][INFO] Reading reference genome from file '/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa'
2025-09-15 20:26:08.768 wdl.w:ptcp.t:call-tar_outputs-52 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 17, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-52/_singularity_tmpdir_1j9035jb"
2025-09-15 20:26:08.769 wdl.w:ptcp.t:call-tar_outputs-52 INFO Slurm invocation: srun --job-name call-tar_outputs-52 --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-52/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-52/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-52/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-52/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-52/out/m84036_250809_035451_s4.bc2149.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2149.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-52/out/m84036_250809_035451_s4.bc2149.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2149.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-52/out/m84036_250809_035451_s4.bc2149.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2149.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-52/out/m84036_250809_035451_s4.bc2149.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2149.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-52/out/m84036_250809_035451_s4.bc2149.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2149.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-52/out/m84036_250809_035451_s4.bc2149_paraphase/m84036_250809_035451_s4.bc2149.paraphase.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2149.paraphase.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-52/out/m84036_250809_035451_s4.bc2149_paraphase/m84036_250809_035451_s4.bc2149.paraphase.json:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2149.paraphase.json:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-52/out/m84036_250809_035451_s4.bc2149_paraphase/m84036_250809_035451_s4.bc2149.paraphase.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2149.paraphase.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-52/out/m84036_250809_035451_s4.bc2149_sawfish/m84036_250809_035451_s4.bc2149.sv.vcf.gz:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2149.sv.vcf.gz:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-52/out/m84036_250809_035451_s4.bc2149_sawfish/m84036_250809_035451_s4.bc2149.sv.vcf.gz.tbi:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2149.sv.vcf.gz.tbi:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-52/out/m84036_250809_035451_s4.bc2149.f8inversion.json:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2149.f8inversion.json:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-52/_singularity_tmpdir_1j9035jb/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-52/_singularity_tmpdir_1j9035jb/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:26:08.782 wdl.w:ptcp.w:call-paraphase-34.t:call-call_f8 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 8, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-34/call-call_f8/_singularity_tmpdir_we2hfxbs"
2025-09-15 20:26:08.782 wdl.w:ptcp.w:call-paraphase-34.t:call-call_f8 INFO Slurm invocation: srun --job-name call-call_f8 --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-34/call-call_f8/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-34/call-call_f8/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-34/call-call_f8/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-34/call-call_f8/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-34/call-run_paraphase/out/m84036_250809_035451_s4.bc2131_paraphase/m84036_250809_035451_s4.bc2131.paraphase.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2131.paraphase.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-34/call-run_paraphase/out/m84036_250809_035451_s4.bc2131_paraphase/m84036_250809_035451_s4.bc2131.paraphase.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2131.paraphase.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-34/call-call_f8/_singularity_tmpdir_we2hfxbs/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-34/call-call_f8/_singularity_tmpdir_we2hfxbs/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:26:08.793 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO srun: job 51798156 queued and waiting for resources
2025-09-15 20:26:08.793 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO srun: job 51798156 has been allocated resources
2025-09-15 20:26:08.793 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:26:08.818 wdl.w:ptcp.w:call-paraphase-34.t:call-call_f8 NOTICE slurm_singularity run :: pid: 1207109, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-34/call-call_f8/slurm_singularity.log.txt"
2025-09-15 20:26:08.818 wdl.w:ptcp.t:call-tar_outputs-52 NOTICE slurm_singularity run :: pid: 1207108, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-52/slurm_singularity.log.txt"
2025-09-15 20:26:08.826 wdl.w:ptcp.t:call-tar_outputs-40 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 17, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-40/_singularity_tmpdir_v9mkpmfk"
2025-09-15 20:26:08.826 wdl.w:ptcp.t:call-tar_outputs-40 INFO Slurm invocation: srun --job-name call-tar_outputs-40 --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-40/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-40/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-40/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-40/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-40/out/m84036_250809_035451_s4.bc2137_sawfish/m84036_250809_035451_s4.bc2137.sv.vcf.gz:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2137.sv.vcf.gz:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-40/out/m84036_250809_035451_s4.bc2137_sawfish/m84036_250809_035451_s4.bc2137.sv.vcf.gz.tbi:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2137.sv.vcf.gz.tbi:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-40/out/m84036_250809_035451_s4.bc2137_paraphase/m84036_250809_035451_s4.bc2137.paraphase.json:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2137.paraphase.json:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-40/out/m84036_250809_035451_s4.bc2137_paraphase/m84036_250809_035451_s4.bc2137.paraphase.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2137.paraphase.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-40/out/m84036_250809_035451_s4.bc2137_paraphase/m84036_250809_035451_s4.bc2137.paraphase.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2137.paraphase.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-40/out/m84036_250809_035451_s4.bc2137.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2137.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-40/out/m84036_250809_035451_s4.bc2137.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2137.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-40/out/m84036_250809_035451_s4.bc2137.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2137.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-40/out/m84036_250809_035451_s4.bc2137.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2137.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-40/out/m84036_250809_035451_s4.bc2137.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2137.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-40/out/m84036_250809_035451_s4.bc2137.f8inversion.json:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2137.f8inversion.json:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-40/_singularity_tmpdir_v9mkpmfk/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-40/_singularity_tmpdir_v9mkpmfk/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:26:08.828 wdl.w:ptcp.w:call-trgt-85.t:call-trgt_plot_motifs_waterfall INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2182.motifs_waterfall.trgt_plots.zip"
2025-09-15 20:26:08.849 wdl.w:ptcp.t:call-tar_outputs-40 NOTICE slurm_singularity run :: pid: 1207112, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-40/slurm_singularity.log.txt"
2025-09-15 20:26:08.938 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_motifs_allele.slurm_singularity INFO srun: job 51798157 queued and waiting for resources
2025-09-15 20:26:08.938 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_motifs_allele.slurm_singularity INFO srun: job 51798157 has been allocated resources
2025-09-15 20:26:08.938 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_motifs_allele.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:26:08.980 wdl.w:ptcp.w:call-trgt-85.t:call-trgt_plot_motifs_waterfall NOTICE done
2025-09-15 20:26:08.985 wdl.w:ptcp.w:call-trgt-85 NOTICE finish :: job: "call-trgt_plot_motifs_waterfall"
2025-09-15 20:26:08.986 wdl.w:ptcp.w:call-trgt-85 INFO output :: job: "call-trgt_plot_motifs_waterfall", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-85/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2182.motifs_waterfall.trgt_plots.zip"}
2025-09-15 20:26:08.986 wdl.w:ptcp.w:call-trgt-85 INFO visit :: node: "output-images_motifs_waterfall", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-85/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2182.motifs_waterfall.trgt_plots.zip"}
2025-09-15 20:26:08.992 wdl.w:ptcp.t:call-tar_outputs-64 NOTICE task setup :: name: "tar_outputs", source: "./common.wdl", line: 279, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-64", thread: 140607683024448
2025-09-15 20:26:09.018 wdl.w:ptcp.t:call-tar_outputs-64 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:26:09.018 wdl.w:ptcp.t:call-tar_outputs-64 INFO input :: name: "sawfish_vcf_tbi", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2161.sv.vcf.gz.tbi"
2025-09-15 20:26:09.018 wdl.w:ptcp.t:call-tar_outputs-64 INFO input :: name: "sawfish_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2161.sv.vcf.gz"
2025-09-15 20:26:09.018 wdl.w:ptcp.t:call-tar_outputs-64 INFO input :: name: "f8_json", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2161.f8inversion.json"
2025-09-15 20:26:09.018 wdl.w:ptcp.t:call-tar_outputs-64 INFO input :: name: "paraphase_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2161.paraphase.bam.bai"
2025-09-15 20:26:09.018 wdl.w:ptcp.t:call-tar_outputs-64 INFO input :: name: "paraphase_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2161.paraphase.bam"
2025-09-15 20:26:09.018 wdl.w:ptcp.t:call-tar_outputs-64 INFO input :: name: "paraphase_json", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2161.paraphase.json"
2025-09-15 20:26:09.018 wdl.w:ptcp.t:call-tar_outputs-64 INFO input :: name: "trgt_spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2161.trgt.sorted.spanning.bam.bai"
2025-09-15 20:26:09.018 wdl.w:ptcp.t:call-tar_outputs-64 INFO input :: name: "trgt_spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2161.trgt.sorted.spanning.bam"
2025-09-15 20:26:09.018 wdl.w:ptcp.t:call-tar_outputs-64 INFO input :: name: "trgt_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2161.trgt.vcf"
2025-09-15 20:26:09.019 wdl.w:ptcp.t:call-tar_outputs-64 INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2161.mapped.bam.bai"
2025-09-15 20:26:09.019 wdl.w:ptcp.t:call-tar_outputs-64 INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2161.mapped.bam"
2025-09-15 20:26:09.019 wdl.w:ptcp.t:call-tar_outputs-64 INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2161"
2025-09-15 20:26:09.019 wdl.w:ptcp.t:call-tar_outputs-64 INFO eval :: name: "threads", value: 1
2025-09-15 20:26:09.019 wdl.w:ptcp.t:call-tar_outputs-64 INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:26:09.019 wdl.w:ptcp.t:call-tar_outputs-64 INFO eval :: name: "disk_size", value: 6
2025-09-15 20:26:09.019 wdl.w:ptcp.t:call-tar_outputs-64 INFO eval :: name: "output_tarball", value: "m84036_250809_035451_s4.bc2161.tar"
2025-09-15 20:26:09.020 wdl.w:ptcp.t:call-tar_outputs-64 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:26:09.020 wdl.w:ptcp.t:call-tar_outputs-64 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:26:09.020 wdl.w:ptcp.t:call-tar_outputs-64 INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:26:09.020 wdl.w:ptcp.t:call-tar_outputs-64 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:26:09.123 wdl.w:ptcp.w:call-trgt-88.t:call-trgt_genotype INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2185.trgt.vcf"
2025-09-15 20:26:09.127 wdl.w:ptcp.w:call-trgt-88.t:call-trgt_genotype INFO output :: name: "spanning_bam", value: "m84036_250809_035451_s4.bc2185.trgt.sorted.spanning.bam"
2025-09-15 20:26:09.129 wdl.w:ptcp.w:call-trgt-88.t:call-trgt_genotype INFO output :: name: "spanning_bam_bai", value: "m84036_250809_035451_s4.bc2185.trgt.sorted.spanning.bam.bai"
2025-09-15 20:26:09.144 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO srun: job 51798158 queued and waiting for resources
2025-09-15 20:26:09.144 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO srun: job 51798158 has been allocated resources
2025-09-15 20:26:09.145 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:26:09.155 wdl.w:ptcp.t:call-tar_outputs-64 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 17, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-64/_singularity_tmpdir_ayr5163v"
2025-09-15 20:26:09.156 wdl.w:ptcp.t:call-tar_outputs-64 INFO Slurm invocation: srun --job-name call-tar_outputs-64 --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-64/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-64/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-64/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-64/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-64/out/m84036_250809_035451_s4.bc2161.f8inversion.json:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2161.f8inversion.json:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-64/out/m84036_250809_035451_s4.bc2161_paraphase/m84036_250809_035451_s4.bc2161.paraphase.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2161.paraphase.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-64/out/m84036_250809_035451_s4.bc2161_paraphase/m84036_250809_035451_s4.bc2161.paraphase.json:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2161.paraphase.json:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-64/out/m84036_250809_035451_s4.bc2161_paraphase/m84036_250809_035451_s4.bc2161.paraphase.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2161.paraphase.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-64/out/m84036_250809_035451_s4.bc2161.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2161.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-64/out/m84036_250809_035451_s4.bc2161.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2161.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-64/out/m84036_250809_035451_s4.bc2161_sawfish/m84036_250809_035451_s4.bc2161.sv.vcf.gz:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2161.sv.vcf.gz:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-64/out/m84036_250809_035451_s4.bc2161_sawfish/m84036_250809_035451_s4.bc2161.sv.vcf.gz.tbi:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2161.sv.vcf.gz.tbi:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-64/out/m84036_250809_035451_s4.bc2161.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2161.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-64/out/m84036_250809_035451_s4.bc2161.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2161.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-64/out/m84036_250809_035451_s4.bc2161.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2161.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-64/_singularity_tmpdir_ayr5163v/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-64/_singularity_tmpdir_ayr5163v/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:26:09.167 wdl.w:ptcp.t:call-tar_outputs-64 NOTICE slurm_singularity run :: pid: 1207115, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-64/slurm_singularity.log.txt"
2025-09-15 20:26:09.170 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:26:08 [ERROR] - No reads found for TRID=SCA2_ATXN2
2025-09-15 20:26:09.228 wdl.w:ptcp.w:call-trgt-88.t:call-trgt_genotype NOTICE done
2025-09-15 20:26:09.234 wdl.w:ptcp.w:call-trgt-88 NOTICE finish :: job: "call-trgt_genotype"
2025-09-15 20:26:09.235 wdl.w:ptcp.w:call-trgt-88 INFO output :: job: "call-trgt_genotype", values: {"spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-88/call-trgt_genotype/out/m84036_250809_035451_s4.bc2185.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-88/call-trgt_genotype/out/m84036_250809_035451_s4.bc2185.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-88/call-trgt_genotype/out/m84036_250809_035451_s4.bc2185.trgt.vcf"}
2025-09-15 20:26:09.235 wdl.w:ptcp.w:call-trgt-88 NOTICE ready :: job: "call-trgt_plot_meth_allele", callee: "trgt_plot"
2025-09-15 20:26:09.235 wdl.w:ptcp.w:call-trgt-88 INFO input :: job: "call-trgt_plot_meth_allele", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": false, "methylation": true, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-88/call-trgt_genotype/out/m84036_250809_035451_s4.bc2185.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-88/call-trgt_genotype/out/m84036_250809_035451_s4.bc2185.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-88/call-trgt_genotype/out/m84036_250809_035451_s4.bc2185.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2185"}
2025-09-15 20:26:09.237 wdl.w:ptcp.w:call-trgt-88 NOTICE ready :: job: "call-trgt_plot_meth_waterfall", callee: "trgt_plot"
2025-09-15 20:26:09.237 wdl.w:ptcp.w:call-trgt-88 INFO input :: job: "call-trgt_plot_meth_waterfall", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": true, "methylation": true, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-88/call-trgt_genotype/out/m84036_250809_035451_s4.bc2185.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-88/call-trgt_genotype/out/m84036_250809_035451_s4.bc2185.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-88/call-trgt_genotype/out/m84036_250809_035451_s4.bc2185.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2185"}
2025-09-15 20:26:09.238 wdl.w:ptcp.w:call-trgt-88 NOTICE ready :: job: "call-trgt_plot_motifs_allele", callee: "trgt_plot"
2025-09-15 20:26:09.238 wdl.w:ptcp.w:call-trgt-88 INFO input :: job: "call-trgt_plot_motifs_allele", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": false, "methylation": false, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-88/call-trgt_genotype/out/m84036_250809_035451_s4.bc2185.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-88/call-trgt_genotype/out/m84036_250809_035451_s4.bc2185.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-88/call-trgt_genotype/out/m84036_250809_035451_s4.bc2185.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2185"}
2025-09-15 20:26:09.238 wdl.w:ptcp.w:call-trgt-88 NOTICE ready :: job: "call-trgt_plot_motifs_waterfall", callee: "trgt_plot"
2025-09-15 20:26:09.239 wdl.w:ptcp.w:call-trgt-88 INFO input :: job: "call-trgt_plot_motifs_waterfall", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "waterfall": true, "methylation": false, "trgt_bed": "/ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed", "ref_index": "/meta/refs/hg38.fa.fai", "ref_fasta": "/meta/refs/hg38.fa", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-88/call-trgt_genotype/out/m84036_250809_035451_s4.bc2185.trgt.sorted.spanning.bam.bai", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-88/call-trgt_genotype/out/m84036_250809_035451_s4.bc2185.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-88/call-trgt_genotype/out/m84036_250809_035451_s4.bc2185.trgt.vcf", "sample_name": "m84036_250809_035451_s4.bc2185"}
2025-09-15 20:26:09.239 wdl.w:ptcp.w:call-trgt-88 INFO visit :: node: "output-spanning_bam", values: {"spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-88/call-trgt_genotype/out/m84036_250809_035451_s4.bc2185.trgt.sorted.spanning.bam"}
2025-09-15 20:26:09.239 wdl.w:ptcp.w:call-trgt-88 INFO visit :: node: "output-spanning_bam_bai", values: {"spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-88/call-trgt_genotype/out/m84036_250809_035451_s4.bc2185.trgt.sorted.spanning.bam.bai"}
2025-09-15 20:26:09.239 wdl.w:ptcp.w:call-trgt-88 INFO visit :: node: "output-vcf", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-88/call-trgt_genotype/out/m84036_250809_035451_s4.bc2185.trgt.vcf"}
2025-09-15 20:26:09.239 wdl.w:ptcp.w:call-trgt-90.t:call-trgt_plot_meth_allele NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-90/call-trgt_plot_meth_allele", thread: 140613823374912
2025-09-15 20:26:09.243 wdl.w:ptcp.w:call-trgt-92.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:26:06 [ERROR] - No reads found for TRID=PRTS_ARX
2025-09-15 20:26:09.243 wdl.w:ptcp.w:call-trgt-92.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:26:06 [ERROR] - No reads found for TRID=EIEE1_ARX
2025-09-15 20:26:09.258 wdl.w:ptcp.w:call-trgt-90.t:call-trgt_plot_meth_allele INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:26:09.259 wdl.w:ptcp.w:call-trgt-90.t:call-trgt_plot_meth_allele INFO input :: name: "waterfall", value: false
2025-09-15 20:26:09.259 wdl.w:ptcp.w:call-trgt-90.t:call-trgt_plot_meth_allele INFO input :: name: "methylation", value: true
2025-09-15 20:26:09.259 wdl.w:ptcp.w:call-trgt-90.t:call-trgt_plot_meth_allele INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:26:09.259 wdl.w:ptcp.w:call-trgt-90.t:call-trgt_plot_meth_allele INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:26:09.259 wdl.w:ptcp.w:call-trgt-90.t:call-trgt_plot_meth_allele INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:26:09.259 wdl.w:ptcp.w:call-trgt-90.t:call-trgt_plot_meth_allele INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2187.trgt.sorted.spanning.bam.bai"
2025-09-15 20:26:09.259 wdl.w:ptcp.w:call-trgt-90.t:call-trgt_plot_meth_allele INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2187.trgt.sorted.spanning.bam"
2025-09-15 20:26:09.259 wdl.w:ptcp.w:call-trgt-90.t:call-trgt_plot_meth_allele INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2187.trgt.vcf"
2025-09-15 20:26:09.259 wdl.w:ptcp.w:call-trgt-90.t:call-trgt_plot_meth_allele INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2187"
2025-09-15 20:26:09.259 wdl.w:ptcp.w:call-trgt-90.t:call-trgt_plot_meth_allele INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:26:09.260 wdl.w:ptcp.w:call-trgt-90.t:call-trgt_plot_meth_allele INFO eval :: name: "plot_type", value: "allele"
2025-09-15 20:26:09.260 wdl.w:ptcp.w:call-trgt-90.t:call-trgt_plot_meth_allele INFO eval :: name: "show", value: "meth"
2025-09-15 20:26:09.260 wdl.w:ptcp.w:call-trgt-90.t:call-trgt_plot_meth_allele INFO eval :: name: "threads", value: 1
2025-09-15 20:26:09.260 wdl.w:ptcp.w:call-trgt-90.t:call-trgt_plot_meth_allele INFO eval :: name: "disk_size", value: 27
2025-09-15 20:26:09.260 wdl.w:ptcp.w:call-trgt-90.t:call-trgt_plot_meth_allele INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2187.meth_allele"
2025-09-15 20:26:09.260 wdl.w:ptcp.w:call-trgt-90.t:call-trgt_plot_meth_allele INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:26:09.261 wdl.w:ptcp.w:call-trgt-90.t:call-trgt_plot_meth_allele WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:26:09.261 wdl.w:ptcp.w:call-trgt-90.t:call-trgt_plot_meth_allele INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:26:09.261 wdl.w:ptcp.w:call-trgt-90.t:call-trgt_plot_meth_allele INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:26:09.296 wdl.w:ptcp.w:call-paraphase-82.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for smn1 for sample m84036_250809_035451_s4.bc2179 at 2025-09-15 20:25:51.203065...
2025-09-15 20:26:09.297 wdl.w:ptcp.w:call-paraphase-82.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for hba for sample m84036_250809_035451_s4.bc2179 at 2025-09-15 20:25:51.549016...
2025-09-15 20:26:09.297 wdl.w:ptcp.w:call-paraphase-82.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for gba for sample m84036_250809_035451_s4.bc2179 at 2025-09-15 20:25:52.524524...
2025-09-15 20:26:09.297 wdl.w:ptcp.w:call-paraphase-82.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for cyp21 for sample m84036_250809_035451_s4.bc2179 at 2025-09-15 20:25:53.857074...
2025-09-15 20:26:09.331 wdl.w:ptcp.w:call-trgt-90.t:call-trgt_plot_meth_allele INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-90/call-trgt_plot_meth_allele/_singularity_tmpdir_ikq5t6m1"
2025-09-15 20:26:09.331 wdl.w:ptcp.w:call-trgt-90.t:call-trgt_plot_meth_allele INFO Slurm invocation: srun --job-name call-trgt_plot_meth_allele --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-90/call-trgt_plot_meth_allele/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-90/call-trgt_plot_meth_allele/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-90/call-trgt_plot_meth_allele/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-90/call-trgt_plot_meth_allele/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-90/call-trgt_genotype/out/m84036_250809_035451_s4.bc2187.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2187.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-90/call-trgt_genotype/out/m84036_250809_035451_s4.bc2187.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2187.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-90/call-trgt_genotype/out/m84036_250809_035451_s4.bc2187.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2187.trgt.vcf:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-90/call-trgt_plot_meth_allele/_singularity_tmpdir_ikq5t6m1/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-90/call-trgt_plot_meth_allele/_singularity_tmpdir_ikq5t6m1/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:26:09.346 wdl.w:ptcp.w:call-trgt-90.t:call-trgt_plot_meth_allele NOTICE slurm_singularity run :: pid: 1207117, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-90/call-trgt_plot_meth_allele/slurm_singularity.log.txt"
2025-09-15 20:26:09.516 wdl.w:ptcp.w:call-paraphase-74.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for hbb for sample m84036_250809_035451_s4.bc2171 at 2025-09-15 20:25:59.101616...
2025-09-15 20:26:09.516 wdl.w:ptcp.w:call-paraphase-74.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for hbb for sample m84036_250809_035451_s4.bc2171 at 2025-09-15 20:26:02.347722...
2025-09-15 20:26:09.516 wdl.w:ptcp.w:call-paraphase-74.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for hbb for sample m84036_250809_035451_s4.bc2171 at 2025-09-15 20:26:02.667546...
2025-09-15 20:26:09.616 wdl.w:ptcp.w:call-paraphase-31.t:call-call_f8 INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2128.f8inversion.vcf"
2025-09-15 20:26:09.619 wdl.w:ptcp.w:call-paraphase-31.t:call-call_f8 INFO output :: name: "json", value: "m84036_250809_035451_s4.bc2128.f8inversion.json"
2025-09-15 20:26:09.679 wdl.w:ptcp.w:call-paraphase-31.t:call-call_f8 NOTICE done
2025-09-15 20:26:09.685 wdl.w:ptcp.w:call-paraphase-31 NOTICE finish :: job: "call-call_f8"
2025-09-15 20:26:09.685 wdl.w:ptcp.w:call-paraphase-31 INFO output :: job: "call-call_f8", values: {"json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-31/call-call_f8/out/m84036_250809_035451_s4.bc2128.f8inversion.json", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-31/call-call_f8/out/m84036_250809_035451_s4.bc2128.f8inversion.vcf"}
2025-09-15 20:26:09.685 wdl.w:ptcp.w:call-paraphase-31 INFO visit :: node: "output-f8_json", values: {"f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-31/call-call_f8/out/m84036_250809_035451_s4.bc2128.f8inversion.json"}
2025-09-15 20:26:09.685 wdl.w:ptcp.w:call-paraphase-31 INFO visit :: node: "output-f8_vcf", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-31/call-call_f8/out/m84036_250809_035451_s4.bc2128.f8inversion.vcf"}
2025-09-15 20:26:09.685 wdl.w:ptcp.w:call-paraphase-31 INFO visit :: node: "outputs", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-31/call-call_f8/out/m84036_250809_035451_s4.bc2128.f8inversion.vcf", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-31/call-run_paraphase/out/m84036_250809_035451_s4.bc2128_paraphase/m84036_250809_035451_s4.bc2128.paraphase.json", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-31/call-run_paraphase/out/m84036_250809_035451_s4.bc2128_paraphase/m84036_250809_035451_s4.bc2128.paraphase.bam", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-31/call-run_paraphase/out/m84036_250809_035451_s4.bc2128_paraphase/m84036_250809_035451_s4.bc2128.paraphase.bam.bai", "paraphase_vcfs": ["/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-31/call-run_paraphase/out/m84036_250809_035451_s4.bc2128_paraphase/m84036_250809_035451_s4.bc2128_paraphase_vcfs/m84036_250809_035451_s4.bc2128_cyp21.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-31/call-run_paraphase/out/m84036_250809_035451_s4.bc2128_paraphase/m84036_250809_035451_s4.bc2128_paraphase_vcfs/m84036_250809_035451_s4.bc2128_f8inv1.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-31/call-run_paraphase/out/m84036_250809_035451_s4.bc2128_paraphase/m84036_250809_035451_s4.bc2128_paraphase_vcfs/m84036_250809_035451_s4.bc2128_f8inv22.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-31/call-run_paraphase/out/m84036_250809_035451_s4.bc2128_paraphase/m84036_250809_035451_s4.bc2128_paraphase_vcfs/m84036_250809_035451_s4.bc2128_gba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-31/call-run_paraphase/out/m84036_250809_035451_s4.bc2128_paraphase/m84036_250809_035451_s4.bc2128_paraphase_vcfs/m84036_250809_035451_s4.bc2128_hba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-31/call-run_paraphase/out/m84036_250809_035451_s4.bc2128_paraphase/m84036_250809_035451_s4.bc2128_paraphase_vcfs/m84036_250809_035451_s4.bc2128_hbb.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-31/call-run_paraphase/out/m84036_250809_035451_s4.bc2128_paraphase/m84036_250809_035451_s4.bc2128_paraphase_vcfs/m84036_250809_035451_s4.bc2128_rpgr.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-31/call-run_paraphase/out/m84036_250809_035451_s4.bc2128_paraphase/m84036_250809_035451_s4.bc2128_paraphase_vcfs/m84036_250809_035451_s4.bc2128_smn1.vcf"], "havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-31/call-run_paraphase/out/m84036_250809_035451_s4.bc2128.havanno.json", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-31/call-call_f8/out/m84036_250809_035451_s4.bc2128.f8inversion.json"}
2025-09-15 20:26:09.694 wdl.w:ptcp.w:call-trgt-90.t:call-trgt_plot_meth_waterfall NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-90/call-trgt_plot_meth_waterfall", thread: 140607674631744
2025-09-15 20:26:09.715 wdl.w:ptcp.w:call-trgt-90.t:call-trgt_plot_meth_waterfall INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:26:09.715 wdl.w:ptcp.w:call-trgt-90.t:call-trgt_plot_meth_waterfall INFO input :: name: "waterfall", value: true
2025-09-15 20:26:09.715 wdl.w:ptcp.w:call-trgt-90.t:call-trgt_plot_meth_waterfall INFO input :: name: "methylation", value: true
2025-09-15 20:26:09.715 wdl.w:ptcp.w:call-trgt-90.t:call-trgt_plot_meth_waterfall INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:26:09.716 wdl.w:ptcp.w:call-trgt-90.t:call-trgt_plot_meth_waterfall INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:26:09.716 wdl.w:ptcp.w:call-trgt-90.t:call-trgt_plot_meth_waterfall INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:26:09.716 wdl.w:ptcp.w:call-trgt-90.t:call-trgt_plot_meth_waterfall INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2187.trgt.sorted.spanning.bam.bai"
2025-09-15 20:26:09.716 wdl.w:ptcp.w:call-trgt-90.t:call-trgt_plot_meth_waterfall INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2187.trgt.sorted.spanning.bam"
2025-09-15 20:26:09.716 wdl.w:ptcp.w:call-trgt-90.t:call-trgt_plot_meth_waterfall INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2187.trgt.vcf"
2025-09-15 20:26:09.716 wdl.w:ptcp.w:call-trgt-90.t:call-trgt_plot_meth_waterfall INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2187"
2025-09-15 20:26:09.716 wdl.w:ptcp.w:call-trgt-90.t:call-trgt_plot_meth_waterfall INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:26:09.716 wdl.w:ptcp.w:call-trgt-90.t:call-trgt_plot_meth_waterfall INFO eval :: name: "plot_type", value: "waterfall"
2025-09-15 20:26:09.716 wdl.w:ptcp.w:call-trgt-90.t:call-trgt_plot_meth_waterfall INFO eval :: name: "show", value: "meth"
2025-09-15 20:26:09.716 wdl.w:ptcp.w:call-trgt-90.t:call-trgt_plot_meth_waterfall INFO eval :: name: "threads", value: 1
2025-09-15 20:26:09.716 wdl.w:ptcp.w:call-trgt-90.t:call-trgt_plot_meth_waterfall INFO eval :: name: "disk_size", value: 27
2025-09-15 20:26:09.717 wdl.w:ptcp.w:call-trgt-90.t:call-trgt_plot_meth_waterfall INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2187.meth_waterfall"
2025-09-15 20:26:09.717 wdl.w:ptcp.w:call-trgt-90.t:call-trgt_plot_meth_waterfall INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:26:09.717 wdl.w:ptcp.w:call-trgt-90.t:call-trgt_plot_meth_waterfall WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:26:09.717 wdl.w:ptcp.w:call-trgt-90.t:call-trgt_plot_meth_waterfall INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:26:09.717 wdl.w:ptcp.w:call-trgt-90.t:call-trgt_plot_meth_waterfall INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:26:09.801 wdl.w:ptcp.w:call-trgt-90.t:call-trgt_plot_meth_waterfall INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-90/call-trgt_plot_meth_waterfall/_singularity_tmpdir_jh6rgk4w"
2025-09-15 20:26:09.801 wdl.w:ptcp.w:call-trgt-90.t:call-trgt_plot_meth_waterfall INFO Slurm invocation: srun --job-name call-trgt_plot_meth_waterfall --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-90/call-trgt_plot_meth_waterfall/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-90/call-trgt_plot_meth_waterfall/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-90/call-trgt_plot_meth_waterfall/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-90/call-trgt_plot_meth_waterfall/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-90/call-trgt_genotype/out/m84036_250809_035451_s4.bc2187.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2187.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-90/call-trgt_genotype/out/m84036_250809_035451_s4.bc2187.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2187.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-90/call-trgt_genotype/out/m84036_250809_035451_s4.bc2187.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2187.trgt.vcf:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-90/call-trgt_plot_meth_waterfall/_singularity_tmpdir_jh6rgk4w/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-90/call-trgt_plot_meth_waterfall/_singularity_tmpdir_jh6rgk4w/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:26:09.814 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_plot_meth_allele INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2192.meth_allele.trgt_plots.zip"
2025-09-15 20:26:09.832 wdl.w:ptcp.w:call-paraphase-34.t:call-call_f8.slurm_singularity INFO srun: job 51798160 queued and waiting for resources
2025-09-15 20:26:09.832 wdl.w:ptcp.w:call-paraphase-34.t:call-call_f8.slurm_singularity INFO srun: job 51798160 has been allocated resources
2025-09-15 20:26:09.832 wdl.w:ptcp.w:call-paraphase-34.t:call-call_f8.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:26:09.832 wdl.w:ptcp.t:call-tar_outputs-52.slurm_singularity INFO srun: job 51798159 queued and waiting for resources
2025-09-15 20:26:09.833 wdl.w:ptcp.t:call-tar_outputs-52.slurm_singularity INFO srun: job 51798159 has been allocated resources
2025-09-15 20:26:09.833 wdl.w:ptcp.t:call-tar_outputs-52.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:26:09.833 wdl.w:ptcp.w:call-trgt-90.t:call-trgt_plot_meth_waterfall NOTICE slurm_singularity run :: pid: 1207210, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-90/call-trgt_plot_meth_waterfall/slurm_singularity.log.txt"
2025-09-15 20:26:09.860 wdl.w:ptcp.t:call-tar_outputs-40.slurm_singularity INFO srun: job 51798161 queued and waiting for resources
2025-09-15 20:26:09.861 wdl.w:ptcp.t:call-tar_outputs-40.slurm_singularity INFO srun: job 51798161 has been allocated resources
2025-09-15 20:26:09.861 wdl.w:ptcp.t:call-tar_outputs-40.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:26:09.862 wdl.w:ptcp.w:call-paraphase-31 NOTICE done
2025-09-15 20:26:09.868 wdl.w:ptcp NOTICE finish :: job: "call-paraphase-31"
2025-09-15 20:26:09.868 wdl.w:ptcp INFO output :: job: "call-paraphase-31", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-31/out/m84036_250809_035451_s4.bc2128.f8inversion.vcf", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-31/out/m84036_250809_035451_s4.bc2128_paraphase/m84036_250809_035451_s4.bc2128.paraphase.json", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-31/out/m84036_250809_035451_s4.bc2128_paraphase/m84036_250809_035451_s4.bc2128.paraphase.bam", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-31/out/m84036_250809_035451_s4.bc2128_paraphase/m84036_250809_035451_s4.bc2128.paraphase.bam.bai", "paraphase_vcfs": ["/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-31/out/m84036_250809_035451_s4.bc2128_paraphase/m84036_250809_035451_s4.bc2128_paraphase_vcfs/m84036_250809_035451_s4.bc2128_cyp21.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-31/out/m84036_250809_035451_s4.bc2128_paraphase/m84036_250809_035451_s4.bc2128_paraphase_vcfs/m84036_250809_035451_s4.bc2128_f8inv1.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-31/out/m84036_250809_035451_s4.bc2128_paraphase/m84036_250809_035451_s4.bc2128_paraphase_vcfs/m84036_250809_035451_s4.bc2128_f8inv22.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-31/out/m84036_250809_035451_s4.bc2128_paraphase/m84036_250809_035451_s4.bc2128_paraphase_vcfs/m84036_250809_035451_s4.bc2128_gba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-31/out/m84036_250809_035451_s4.bc2128_paraphase/m84036_250809_035451_s4.bc2128_paraphase_vcfs/m84036_250809_035451_s4.bc2128_hba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-31/out/m84036_250809_035451_s4.bc2128_paraphase/m84036_250809_035451_s4.bc2128_paraphase_vcfs/m84036_250809_035451_s4.bc2128_hbb.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-31/out/m84036_250809_035451_s4.bc2128_paraphase/m84036_250809_035451_s4.bc2128_paraphase_vcfs/m84036_250809_035451_s4.bc2128_rpgr.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-31/out/m84036_250809_035451_s4.bc2128_paraphase/m84036_250809_035451_s4.bc2128_paraphase_vcfs/m84036_250809_035451_s4.bc2128_smn1.vcf"], "havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-31/out/m84036_250809_035451_s4.bc2128.havanno.json", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-31/out/m84036_250809_035451_s4.bc2128.f8inversion.json"}
2025-09-15 20:26:09.869 wdl.w:ptcp NOTICE ready :: job: "call-tar_outputs-31", callee: "tar_outputs"
2025-09-15 20:26:09.869 wdl.w:ptcp INFO input :: job: "call-tar_outputs-31", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "sawfish_vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-31/out/m84036_250809_035451_s4.bc2128_sawfish/m84036_250809_035451_s4.bc2128.sv.vcf.gz.tbi", "sawfish_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-31/out/m84036_250809_035451_s4.bc2128_sawfish/m84036_250809_035451_s4.bc2128.sv.vcf.gz", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-31/out/m84036_250809_035451_s4.bc2128.f8inversion.json", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-31/out/m84036_250809_035451_s4.bc2128_paraphase/m84036_250809_035451_s4.bc2128.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-31/out/m84036_250809_035451_s4.bc2128_paraphase/m84036_250809_035451_s4.bc2128.paraphase.bam", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-31/out/m84036_250809_035451_s4.bc2128_paraphase/m84036_250809_035451_s4.bc2128.paraphase.json", "trgt_spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-31/out/m84036_250809_035451_s4.bc2128.trgt.sorted.spanning.bam.bai", "trgt_spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-31/out/m84036_250809_035451_s4.bc2128.trgt.sorted.spanning.bam", "trgt_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-31/out/m84036_250809_035451_s4.bc2128.trgt.vcf", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-31/out/m84036_250809_035451_s4.bc2128.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-31/out/m84036_250809_035451_s4.bc2128.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2128"}
2025-09-15 20:26:09.885 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_plot_meth_allele NOTICE done
2025-09-15 20:26:09.894 wdl.w:ptcp.w:call-trgt-95 NOTICE finish :: job: "call-trgt_plot_meth_allele"
2025-09-15 20:26:09.895 wdl.w:ptcp.w:call-trgt-95 INFO output :: job: "call-trgt_plot_meth_allele", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-95/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2192.meth_allele.trgt_plots.zip"}
2025-09-15 20:26:09.895 wdl.w:ptcp.w:call-trgt-95 INFO visit :: node: "output-images_meth_allele", values: {"images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-95/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2192.meth_allele.trgt_plots.zip"}
2025-09-15 20:26:09.903 wdl.w:ptcp.w:call-trgt-90.t:call-trgt_plot_motifs_allele NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-90/call-trgt_plot_motifs_allele", thread: 140607129368128
2025-09-15 20:26:09.922 wdl.w:ptcp.w:call-trgt-90.t:call-trgt_plot_motifs_allele INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:26:09.922 wdl.w:ptcp.w:call-trgt-90.t:call-trgt_plot_motifs_allele INFO input :: name: "waterfall", value: false
2025-09-15 20:26:09.922 wdl.w:ptcp.w:call-trgt-90.t:call-trgt_plot_motifs_allele INFO input :: name: "methylation", value: false
2025-09-15 20:26:09.922 wdl.w:ptcp.w:call-trgt-90.t:call-trgt_plot_motifs_allele INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:26:09.922 wdl.w:ptcp.w:call-trgt-90.t:call-trgt_plot_motifs_allele INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:26:09.922 wdl.w:ptcp.w:call-trgt-90.t:call-trgt_plot_motifs_allele INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:26:09.922 wdl.w:ptcp.w:call-trgt-90.t:call-trgt_plot_motifs_allele INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2187.trgt.sorted.spanning.bam.bai"
2025-09-15 20:26:09.922 wdl.w:ptcp.w:call-trgt-90.t:call-trgt_plot_motifs_allele INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2187.trgt.sorted.spanning.bam"
2025-09-15 20:26:09.922 wdl.w:ptcp.w:call-trgt-90.t:call-trgt_plot_motifs_allele INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2187.trgt.vcf"
2025-09-15 20:26:09.922 wdl.w:ptcp.w:call-trgt-90.t:call-trgt_plot_motifs_allele INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2187"
2025-09-15 20:26:09.922 wdl.w:ptcp.w:call-trgt-90.t:call-trgt_plot_motifs_allele INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:26:09.923 wdl.w:ptcp.w:call-trgt-90.t:call-trgt_plot_motifs_allele INFO eval :: name: "plot_type", value: "allele"
2025-09-15 20:26:09.923 wdl.w:ptcp.w:call-trgt-90.t:call-trgt_plot_motifs_allele INFO eval :: name: "show", value: "motifs"
2025-09-15 20:26:09.923 wdl.w:ptcp.w:call-trgt-90.t:call-trgt_plot_motifs_allele INFO eval :: name: "threads", value: 1
2025-09-15 20:26:09.923 wdl.w:ptcp.w:call-trgt-90.t:call-trgt_plot_motifs_allele INFO eval :: name: "disk_size", value: 27
2025-09-15 20:26:09.923 wdl.w:ptcp.w:call-trgt-90.t:call-trgt_plot_motifs_allele INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2187.motifs_allele"
2025-09-15 20:26:09.923 wdl.w:ptcp.w:call-trgt-90.t:call-trgt_plot_motifs_allele INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:26:09.924 wdl.w:ptcp.w:call-trgt-90.t:call-trgt_plot_motifs_allele WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:26:09.924 wdl.w:ptcp.w:call-trgt-90.t:call-trgt_plot_motifs_allele INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:26:09.924 wdl.w:ptcp.w:call-trgt-90.t:call-trgt_plot_motifs_allele INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:26:09.930 wdl.w:ptcp.w:call-trgt-88.t:call-get_reads_overlapping_repeats INFO output :: name: "reads_overlapping_repeats", value: "m84036_250809_035451_s4.bc2185.repeats.bam"
2025-09-15 20:26:09.936 wdl.w:ptcp.w:call-trgt-88.t:call-get_reads_overlapping_repeats INFO output :: name: "reads_overlapping_repeats_bai", value: "m84036_250809_035451_s4.bc2185.repeats.bam.bai"
2025-09-15 20:26:09.944 wdl.w:ptcp.w:call-trgt-93.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:26:08 [ERROR] - No reads found for TRID=PRTS_ARX
2025-09-15 20:26:09.944 wdl.w:ptcp.w:call-trgt-93.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:26:08 [ERROR] - No reads found for TRID=EIEE1_ARX
2025-09-15 20:26:10.011 wdl.w:ptcp.w:call-trgt-90.t:call-trgt_plot_motifs_allele INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-90/call-trgt_plot_motifs_allele/_singularity_tmpdir_n48pqfvt"
2025-09-15 20:26:10.011 wdl.w:ptcp.w:call-trgt-90.t:call-trgt_plot_motifs_allele INFO Slurm invocation: srun --job-name call-trgt_plot_motifs_allele --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-90/call-trgt_plot_motifs_allele/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-90/call-trgt_plot_motifs_allele/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-90/call-trgt_plot_motifs_allele/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-90/call-trgt_plot_motifs_allele/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-90/call-trgt_genotype/out/m84036_250809_035451_s4.bc2187.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2187.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-90/call-trgt_genotype/out/m84036_250809_035451_s4.bc2187.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2187.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-90/call-trgt_genotype/out/m84036_250809_035451_s4.bc2187.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2187.trgt.vcf:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-90/call-trgt_plot_motifs_allele/_singularity_tmpdir_n48pqfvt/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-90/call-trgt_plot_motifs_allele/_singularity_tmpdir_n48pqfvt/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:26:10.025 wdl.w:ptcp.w:call-trgt-88.t:call-get_reads_overlapping_repeats NOTICE done
2025-09-15 20:26:10.033 wdl.w:ptcp.w:call-trgt-88 NOTICE finish :: job: "call-get_reads_overlapping_repeats"
2025-09-15 20:26:10.033 wdl.w:ptcp.w:call-trgt-88 INFO output :: job: "call-get_reads_overlapping_repeats", values: {"reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-88/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2185.repeats.bam.bai", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-88/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2185.repeats.bam"}
2025-09-15 20:26:10.033 wdl.w:ptcp.w:call-trgt-90.t:call-trgt_plot_motifs_allele NOTICE slurm_singularity run :: pid: 1207221, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-90/call-trgt_plot_motifs_allele/slurm_singularity.log.txt"
2025-09-15 20:26:10.033 wdl.w:ptcp.w:call-trgt-88 INFO visit :: node: "output-reads_overlapping_repeats", values: {"reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-88/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2185.repeats.bam"}
2025-09-15 20:26:10.034 wdl.w:ptcp.w:call-trgt-88 INFO visit :: node: "output-reads_overlapping_repeats_bai", values: {"reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-88/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2185.repeats.bam.bai"}
2025-09-15 20:26:10.039 wdl.w:ptcp.w:call-trgt-90.t:call-trgt_plot_motifs_waterfall NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-90/call-trgt_plot_motifs_waterfall", thread: 140613580211776
2025-09-15 20:26:10.060 wdl.w:ptcp.w:call-trgt-90.t:call-trgt_plot_motifs_waterfall INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:26:10.060 wdl.w:ptcp.w:call-trgt-90.t:call-trgt_plot_motifs_waterfall INFO input :: name: "waterfall", value: true
2025-09-15 20:26:10.060 wdl.w:ptcp.w:call-trgt-90.t:call-trgt_plot_motifs_waterfall INFO input :: name: "methylation", value: false
2025-09-15 20:26:10.060 wdl.w:ptcp.w:call-trgt-90.t:call-trgt_plot_motifs_waterfall INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:26:10.060 wdl.w:ptcp.w:call-trgt-90.t:call-trgt_plot_motifs_waterfall INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:26:10.060 wdl.w:ptcp.w:call-trgt-90.t:call-trgt_plot_motifs_waterfall INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:26:10.060 wdl.w:ptcp.w:call-trgt-90.t:call-trgt_plot_motifs_waterfall INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2187.trgt.sorted.spanning.bam.bai"
2025-09-15 20:26:10.060 wdl.w:ptcp.w:call-trgt-90.t:call-trgt_plot_motifs_waterfall INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2187.trgt.sorted.spanning.bam"
2025-09-15 20:26:10.060 wdl.w:ptcp.w:call-trgt-90.t:call-trgt_plot_motifs_waterfall INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2187.trgt.vcf"
2025-09-15 20:26:10.060 wdl.w:ptcp.w:call-trgt-90.t:call-trgt_plot_motifs_waterfall INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2187"
2025-09-15 20:26:10.060 wdl.w:ptcp.w:call-trgt-90.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:26:10.061 wdl.w:ptcp.w:call-trgt-90.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "plot_type", value: "waterfall"
2025-09-15 20:26:10.061 wdl.w:ptcp.w:call-trgt-90.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "show", value: "motifs"
2025-09-15 20:26:10.061 wdl.w:ptcp.w:call-trgt-90.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "threads", value: 1
2025-09-15 20:26:10.061 wdl.w:ptcp.w:call-trgt-90.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "disk_size", value: 27
2025-09-15 20:26:10.061 wdl.w:ptcp.w:call-trgt-90.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2187.motifs_waterfall"
2025-09-15 20:26:10.061 wdl.w:ptcp.w:call-trgt-90.t:call-trgt_plot_motifs_waterfall INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:26:10.062 wdl.w:ptcp.w:call-trgt-90.t:call-trgt_plot_motifs_waterfall WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:26:10.062 wdl.w:ptcp.w:call-trgt-90.t:call-trgt_plot_motifs_waterfall INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:26:10.062 wdl.w:ptcp.w:call-trgt-90.t:call-trgt_plot_motifs_waterfall INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:26:10.093 wdl.w:ptcp.w:call-trgt-85.t:call-trgt_plot_meth_waterfall INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2182.meth_waterfall.trgt_plots.zip"
2025-09-15 20:26:10.119 wdl.w:ptcp.w:call-paraphase-75.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for smn1 for sample m84036_250809_035451_s4.bc2172 at 2025-09-15 20:25:58.553790...
2025-09-15 20:26:10.119 wdl.w:ptcp.w:call-paraphase-75.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning to gene2 region for smn1 for sample m84036_250809_035451_s4.bc2172 at 2025-09-15 20:25:59.211246...
2025-09-15 20:26:10.119 wdl.w:ptcp.w:call-paraphase-75.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for smn1 for sample m84036_250809_035451_s4.bc2172 at 2025-09-15 20:26:02.236538...
2025-09-15 20:26:10.149 wdl.w:ptcp.w:call-trgt-90.t:call-trgt_plot_motifs_waterfall INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-90/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_ho4abnb_"
2025-09-15 20:26:10.150 wdl.w:ptcp.w:call-trgt-90.t:call-trgt_plot_motifs_waterfall INFO Slurm invocation: srun --job-name call-trgt_plot_motifs_waterfall --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-90/call-trgt_plot_motifs_waterfall/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-90/call-trgt_plot_motifs_waterfall/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-90/call-trgt_plot_motifs_waterfall/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-90/call-trgt_plot_motifs_waterfall/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-90/call-trgt_genotype/out/m84036_250809_035451_s4.bc2187.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2187.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-90/call-trgt_genotype/out/m84036_250809_035451_s4.bc2187.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2187.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-90/call-trgt_genotype/out/m84036_250809_035451_s4.bc2187.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2187.trgt.vcf:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-90/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_ho4abnb_/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-90/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_ho4abnb_/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:26:10.170 wdl.w:ptcp.w:call-trgt-90.t:call-trgt_plot_motifs_waterfall NOTICE slurm_singularity run :: pid: 1207231, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-90/call-trgt_plot_motifs_waterfall/slurm_singularity.log.txt"
2025-09-15 20:26:10.180 wdl.w:ptcp.t:call-tar_outputs-64.slurm_singularity INFO srun: job 51798162 queued and waiting for resources
2025-09-15 20:26:10.180 wdl.w:ptcp.t:call-tar_outputs-64.slurm_singularity INFO srun: job 51798162 has been allocated resources
2025-09-15 20:26:10.180 wdl.w:ptcp.t:call-tar_outputs-64.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:26:10.185 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:26:08 [ERROR] - No reads found for TRID=OPMD_PABPN1
2025-09-15 20:26:10.185 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:26:08 [ERROR] - No reads found for TRID=SCA31_BEAN1
2025-09-15 20:26:10.185 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:26:08 [ERROR] - No reads found for TRID=SCA4_ZFHX3
2025-09-15 20:26:10.185 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:26:08 [ERROR] - No reads found for TRID=SCA27B_FGF14
2025-09-15 20:26:10.185 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:26:08 [ERROR] - No reads found for TRID=FECD3_TCF4
2025-09-15 20:26:10.185 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:26:08 [ERROR] - No reads found for TRID=SCA6_CACNA1A
2025-09-15 20:26:10.185 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:26:08 [ERROR] - No reads found for TRID=OPDM2_GIPC1
2025-09-15 20:26:10.185 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:26:08 [ERROR] - No reads found for TRID=DM1_DMPK
2025-09-15 20:26:10.186 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:26:08 [ERROR] - No reads found for TRID=FRA2A_AFF3
2025-09-15 20:26:10.186 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:26:08 [ERROR] - No reads found for TRID=SD5_HOXD13
2025-09-15 20:26:10.186 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:26:08 [ERROR] - No reads found for TRID=SCA36_NOP56
2025-09-15 20:26:10.186 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:26:08 [ERROR] - No reads found for TRID=CJD_PRNP
2025-09-15 20:26:10.186 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:26:08 [ERROR] - No reads found for TRID=EPM1_CSTB
2025-09-15 20:26:10.186 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:26:08 [ERROR] - No reads found for TRID=SCA3_ATXN3
2025-09-15 20:26:10.186 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:26:08 [ERROR] - No reads found for TRID=HDL2_JPH3
2025-09-15 20:26:10.186 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:26:08 [ERROR] - No reads found for TRID=CANVAS_RFC1
2025-09-15 20:26:10.186 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:26:08 [ERROR] - No reads found for TRID=SCA12_PPP2R2B
2025-09-15 20:26:10.186 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:26:08 [ERROR] - No reads found for TRID=CCHS_PHOX2B
2025-09-15 20:26:10.186 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:26:08 [ERROR] - No reads found for TRID=HD_HTT
2025-09-15 20:26:10.186 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:26:09 [ERROR] - No reads found for TRID=DM2_CNBP
2025-09-15 20:26:10.186 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:26:09 [ERROR] - No reads found for TRID=FAME1_SAMD12
2025-09-15 20:26:10.186 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:26:09 [ERROR] - No reads found for TRID=FTDALS1_C9orf72
2025-09-15 20:26:10.186 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:26:09 [ERROR] - No reads found for TRID=OPDM1_LRP12
2025-09-15 20:26:10.187 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:26:09 [ERROR] - No reads found for TRID=SCA1_ATXN1
2025-09-15 20:26:10.215 wdl.w:ptcp.w:call-paraphase-88.t:call-run_paraphase INFO output :: name: "paraphase_bam", value: "m84036_250809_035451_s4.bc2185_paraphase/m84036_250809_035451_s4.bc2185.paraphase.bam"
2025-09-15 20:26:10.223 wdl.w:ptcp.w:call-paraphase-88.t:call-run_paraphase INFO output :: name: "paraphase_bam_bai", value: "m84036_250809_035451_s4.bc2185_paraphase/m84036_250809_035451_s4.bc2185.paraphase.bam.bai"
2025-09-15 20:26:10.224 wdl.w:ptcp.w:call-paraphase-88.t:call-run_paraphase INFO output :: name: "paraphase_json", value: "m84036_250809_035451_s4.bc2185_paraphase/m84036_250809_035451_s4.bc2185.paraphase.json"
2025-09-15 20:26:10.226 wdl.w:ptcp.w:call-paraphase-88.t:call-run_paraphase INFO output :: name: "paraphase_vcfs", value: []
2025-09-15 20:26:10.226 wdl.w:ptcp.w:call-paraphase-88.t:call-run_paraphase INFO output :: name: "havanno_json", value: "m84036_250809_035451_s4.bc2185.havanno.json"
2025-09-15 20:26:10.228 wdl.w:ptcp.w:call-trgt-85.t:call-trgt_plot_meth_waterfall NOTICE done
2025-09-15 20:26:10.233 wdl.w:ptcp.w:call-trgt-85 NOTICE finish :: job: "call-trgt_plot_meth_waterfall"
2025-09-15 20:26:10.234 wdl.w:ptcp.w:call-trgt-85 INFO output :: job: "call-trgt_plot_meth_waterfall", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-85/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2182.meth_waterfall.trgt_plots.zip"}
2025-09-15 20:26:10.234 wdl.w:ptcp.w:call-trgt-85 INFO visit :: node: "output-images_meth_waterfall", values: {"images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-85/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2182.meth_waterfall.trgt_plots.zip"}
2025-09-15 20:26:10.234 wdl.w:ptcp.w:call-trgt-85 INFO visit :: node: "outputs", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-85/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2182.motifs_waterfall.trgt_plots.zip", "images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-85/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2182.meth_allele.trgt_plots.zip", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-85/call-trgt_genotype/out/m84036_250809_035451_s4.bc2182.trgt.sorted.spanning.bam.bai", "images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-85/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2182.motifs_allele.trgt_plots.zip", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-85/call-trgt_genotype/out/m84036_250809_035451_s4.bc2182.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-85/call-trgt_genotype/out/m84036_250809_035451_s4.bc2182.trgt.vcf", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-85/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2182.repeats.bam", "images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-85/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2182.meth_waterfall.trgt_plots.zip", "reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-85/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2182.repeats.bam.bai"}
2025-09-15 20:26:10.240 wdl.w:ptcp.t:call-tar_outputs-53 NOTICE task setup :: name: "tar_outputs", source: "./common.wdl", line: 279, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-53", thread: 140611944420928
2025-09-15 20:26:10.280 wdl.w:ptcp.t:call-tar_outputs-53 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:26:10.280 wdl.w:ptcp.t:call-tar_outputs-53 INFO input :: name: "sawfish_vcf_tbi", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2150.sv.vcf.gz.tbi"
2025-09-15 20:26:10.280 wdl.w:ptcp.t:call-tar_outputs-53 INFO input :: name: "sawfish_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2150.sv.vcf.gz"
2025-09-15 20:26:10.280 wdl.w:ptcp.t:call-tar_outputs-53 INFO input :: name: "f8_json", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2150.f8inversion.json"
2025-09-15 20:26:10.280 wdl.w:ptcp.t:call-tar_outputs-53 INFO input :: name: "paraphase_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2150.paraphase.bam.bai"
2025-09-15 20:26:10.280 wdl.w:ptcp.t:call-tar_outputs-53 INFO input :: name: "paraphase_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2150.paraphase.bam"
2025-09-15 20:26:10.280 wdl.w:ptcp.t:call-tar_outputs-53 INFO input :: name: "paraphase_json", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2150.paraphase.json"
2025-09-15 20:26:10.280 wdl.w:ptcp.t:call-tar_outputs-53 INFO input :: name: "trgt_spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2150.trgt.sorted.spanning.bam.bai"
2025-09-15 20:26:10.280 wdl.w:ptcp.t:call-tar_outputs-53 INFO input :: name: "trgt_spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2150.trgt.sorted.spanning.bam"
2025-09-15 20:26:10.280 wdl.w:ptcp.t:call-tar_outputs-53 INFO input :: name: "trgt_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2150.trgt.vcf"
2025-09-15 20:26:10.280 wdl.w:ptcp.t:call-tar_outputs-53 INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2150.mapped.bam.bai"
2025-09-15 20:26:10.280 wdl.w:ptcp.t:call-tar_outputs-53 INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2150.mapped.bam"
2025-09-15 20:26:10.281 wdl.w:ptcp.t:call-tar_outputs-53 INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2150"
2025-09-15 20:26:10.281 wdl.w:ptcp.t:call-tar_outputs-53 INFO eval :: name: "threads", value: 1
2025-09-15 20:26:10.281 wdl.w:ptcp.t:call-tar_outputs-53 INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:26:10.281 wdl.w:ptcp.t:call-tar_outputs-53 INFO eval :: name: "disk_size", value: 6
2025-09-15 20:26:10.281 wdl.w:ptcp.t:call-tar_outputs-53 INFO eval :: name: "output_tarball", value: "m84036_250809_035451_s4.bc2150.tar"
2025-09-15 20:26:10.282 wdl.w:ptcp.t:call-tar_outputs-53 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:26:10.282 wdl.w:ptcp.t:call-tar_outputs-53 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:26:10.282 wdl.w:ptcp.t:call-tar_outputs-53 INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:26:10.282 wdl.w:ptcp.t:call-tar_outputs-53 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:26:10.319 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_plot_motifs_allele INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2192.motifs_allele.trgt_plots.zip"
2025-09-15 20:26:10.334 wdl.w:ptcp.w:call-paraphase-88.t:call-run_paraphase NOTICE done
2025-09-15 20:26:10.341 wdl.w:ptcp.w:call-paraphase-88 NOTICE finish :: job: "call-run_paraphase"
2025-09-15 20:26:10.341 wdl.w:ptcp.w:call-paraphase-88 INFO output :: job: "call-run_paraphase", values: {"havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-88/call-run_paraphase/out/m84036_250809_035451_s4.bc2185.havanno.json", "paraphase_vcfs": [], "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-88/call-run_paraphase/out/m84036_250809_035451_s4.bc2185_paraphase/m84036_250809_035451_s4.bc2185.paraphase.json", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-88/call-run_paraphase/out/m84036_250809_035451_s4.bc2185_paraphase/m84036_250809_035451_s4.bc2185.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-88/call-run_paraphase/out/m84036_250809_035451_s4.bc2185_paraphase/m84036_250809_035451_s4.bc2185.paraphase.bam"}
2025-09-15 20:26:10.342 wdl.w:ptcp.w:call-paraphase-88 NOTICE ready :: job: "call-call_f8", callee: "call_f8"
2025-09-15 20:26:10.342 wdl.w:ptcp.w:call-paraphase-88 INFO input :: job: "call-call_f8", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "out_prefix": "m84036_250809_035451_s4.bc2185", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-88/call-run_paraphase/out/m84036_250809_035451_s4.bc2185_paraphase/m84036_250809_035451_s4.bc2185.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-88/call-run_paraphase/out/m84036_250809_035451_s4.bc2185_paraphase/m84036_250809_035451_s4.bc2185.paraphase.bam", "sex": "F"}
2025-09-15 20:26:10.343 wdl.w:ptcp.w:call-paraphase-88 INFO visit :: node: "output-havanno_json", values: {"havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-88/call-run_paraphase/out/m84036_250809_035451_s4.bc2185.havanno.json"}
2025-09-15 20:26:10.343 wdl.w:ptcp.w:call-paraphase-88 INFO visit :: node: "output-paraphase_bam", values: {"paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-88/call-run_paraphase/out/m84036_250809_035451_s4.bc2185_paraphase/m84036_250809_035451_s4.bc2185.paraphase.bam"}
2025-09-15 20:26:10.343 wdl.w:ptcp.w:call-paraphase-88 INFO visit :: node: "output-paraphase_bam_bai", values: {"paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-88/call-run_paraphase/out/m84036_250809_035451_s4.bc2185_paraphase/m84036_250809_035451_s4.bc2185.paraphase.bam.bai"}
2025-09-15 20:26:10.343 wdl.w:ptcp.w:call-paraphase-88 INFO visit :: node: "output-paraphase_json", values: {"paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-88/call-run_paraphase/out/m84036_250809_035451_s4.bc2185_paraphase/m84036_250809_035451_s4.bc2185.paraphase.json"}
2025-09-15 20:26:10.343 wdl.w:ptcp.w:call-paraphase-88 INFO visit :: node: "output-paraphase_vcfs", values: {"paraphase_vcfs": []}
2025-09-15 20:26:10.344 wdl.w:ptcp.w:call-trgt-85 NOTICE done
2025-09-15 20:26:10.349 wdl.w:ptcp.t:call-tar_outputs-49 NOTICE task setup :: name: "tar_outputs", source: "./common.wdl", line: 279, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-49", thread: 140613034948160
2025-09-15 20:26:10.350 wdl.w:ptcp NOTICE finish :: job: "call-trgt-85"
2025-09-15 20:26:10.351 wdl.w:ptcp INFO output :: job: "call-trgt-85", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-85/out/m84036_250809_035451_s4.bc2182.motifs_waterfall.trgt_plots.zip", "images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-85/out/m84036_250809_035451_s4.bc2182.meth_allele.trgt_plots.zip", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-85/out/m84036_250809_035451_s4.bc2182.trgt.sorted.spanning.bam.bai", "images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-85/out/m84036_250809_035451_s4.bc2182.motifs_allele.trgt_plots.zip", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-85/out/m84036_250809_035451_s4.bc2182.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-85/out/m84036_250809_035451_s4.bc2182.trgt.vcf", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-85/out/m84036_250809_035451_s4.bc2182.repeats.bam", "images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-85/out/m84036_250809_035451_s4.bc2182.meth_waterfall.trgt_plots.zip", "reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-85/out/m84036_250809_035451_s4.bc2182.repeats.bam.bai"}
2025-09-15 20:26:10.360 wdl.w:ptcp.w:call-trgt-90.t:call-trgt_plot_meth_allele.slurm_singularity INFO srun: job 51798163 queued and waiting for resources
2025-09-15 20:26:10.360 wdl.w:ptcp.w:call-trgt-90.t:call-trgt_plot_meth_allele.slurm_singularity INFO srun: job 51798163 has been allocated resources
2025-09-15 20:26:10.360 wdl.w:ptcp.w:call-trgt-90.t:call-trgt_plot_meth_allele.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:26:10.380 wdl.w:ptcp.t:call-tar_outputs-49 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:26:10.380 wdl.w:ptcp.t:call-tar_outputs-49 INFO input :: name: "sawfish_vcf_tbi", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2146.sv.vcf.gz.tbi"
2025-09-15 20:26:10.380 wdl.w:ptcp.t:call-tar_outputs-49 INFO input :: name: "sawfish_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2146.sv.vcf.gz"
2025-09-15 20:26:10.380 wdl.w:ptcp.t:call-tar_outputs-49 INFO input :: name: "f8_json", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2146.f8inversion.json"
2025-09-15 20:26:10.380 wdl.w:ptcp.t:call-tar_outputs-49 INFO input :: name: "paraphase_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2146.paraphase.bam.bai"
2025-09-15 20:26:10.380 wdl.w:ptcp.t:call-tar_outputs-49 INFO input :: name: "paraphase_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2146.paraphase.bam"
2025-09-15 20:26:10.380 wdl.w:ptcp.t:call-tar_outputs-49 INFO input :: name: "paraphase_json", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2146.paraphase.json"
2025-09-15 20:26:10.381 wdl.w:ptcp.t:call-tar_outputs-49 INFO input :: name: "trgt_spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2146.trgt.sorted.spanning.bam.bai"
2025-09-15 20:26:10.381 wdl.w:ptcp.t:call-tar_outputs-49 INFO input :: name: "trgt_spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2146.trgt.sorted.spanning.bam"
2025-09-15 20:26:10.381 wdl.w:ptcp.t:call-tar_outputs-49 INFO input :: name: "trgt_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2146.trgt.vcf"
2025-09-15 20:26:10.381 wdl.w:ptcp.t:call-tar_outputs-49 INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2146.mapped.bam.bai"
2025-09-15 20:26:10.381 wdl.w:ptcp.t:call-tar_outputs-49 INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2146.mapped.bam"
2025-09-15 20:26:10.381 wdl.w:ptcp.t:call-tar_outputs-49 INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2146"
2025-09-15 20:26:10.381 wdl.w:ptcp.t:call-tar_outputs-49 INFO eval :: name: "threads", value: 1
2025-09-15 20:26:10.381 wdl.w:ptcp.t:call-tar_outputs-49 INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:26:10.381 wdl.w:ptcp.t:call-tar_outputs-49 INFO eval :: name: "disk_size", value: 6
2025-09-15 20:26:10.382 wdl.w:ptcp.t:call-tar_outputs-49 INFO eval :: name: "output_tarball", value: "m84036_250809_035451_s4.bc2146.tar"
2025-09-15 20:26:10.382 wdl.w:ptcp.t:call-tar_outputs-49 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:26:10.382 wdl.w:ptcp.t:call-tar_outputs-49 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:26:10.383 wdl.w:ptcp.t:call-tar_outputs-49 INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:26:10.383 wdl.w:ptcp.t:call-tar_outputs-49 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:26:10.404 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_plot_motifs_allele NOTICE done
2025-09-15 20:26:10.409 wdl.w:ptcp.w:call-trgt-95 NOTICE finish :: job: "call-trgt_plot_motifs_allele"
2025-09-15 20:26:10.409 wdl.w:ptcp.w:call-trgt-95 INFO output :: job: "call-trgt_plot_motifs_allele", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-95/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2192.motifs_allele.trgt_plots.zip"}
2025-09-15 20:26:10.409 wdl.w:ptcp.w:call-trgt-95 INFO visit :: node: "output-images_motifs_allele", values: {"images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-95/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2192.motifs_allele.trgt_plots.zip"}
2025-09-15 20:26:10.410 wdl.w:ptcp.t:call-tar_outputs-53 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 17, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-53/_singularity_tmpdir_gb8evci_"
2025-09-15 20:26:10.410 wdl.w:ptcp.t:call-tar_outputs-53 INFO Slurm invocation: srun --job-name call-tar_outputs-53 --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-53/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-53/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-53/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-53/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-53/out/m84036_250809_035451_s4.bc2150.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2150.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-53/out/m84036_250809_035451_s4.bc2150.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2150.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-53/out/m84036_250809_035451_s4.bc2150_paraphase/m84036_250809_035451_s4.bc2150.paraphase.json:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2150.paraphase.json:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-53/out/m84036_250809_035451_s4.bc2150_paraphase/m84036_250809_035451_s4.bc2150.paraphase.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2150.paraphase.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-53/out/m84036_250809_035451_s4.bc2150_paraphase/m84036_250809_035451_s4.bc2150.paraphase.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2150.paraphase.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-53/out/m84036_250809_035451_s4.bc2150.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2150.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-53/out/m84036_250809_035451_s4.bc2150.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2150.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-53/out/m84036_250809_035451_s4.bc2150.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2150.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-53/out/m84036_250809_035451_s4.bc2150_sawfish/m84036_250809_035451_s4.bc2150.sv.vcf.gz:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2150.sv.vcf.gz:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-53/out/m84036_250809_035451_s4.bc2150_sawfish/m84036_250809_035451_s4.bc2150.sv.vcf.gz.tbi:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2150.sv.vcf.gz.tbi:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-53/out/m84036_250809_035451_s4.bc2150.f8inversion.json:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2150.f8inversion.json:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-53/_singularity_tmpdir_gb8evci_/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-53/_singularity_tmpdir_gb8evci_/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:26:10.416 wdl.w:ptcp.t:call-tar_outputs-68 NOTICE task setup :: name: "tar_outputs", source: "./common.wdl", line: 279, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-68", thread: 140610342200896
2025-09-15 20:26:10.440 wdl.w:ptcp.t:call-tar_outputs-53 NOTICE slurm_singularity run :: pid: 1207242, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-53/slurm_singularity.log.txt"
2025-09-15 20:26:10.442 wdl.w:ptcp.t:call-tar_outputs-68 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:26:10.442 wdl.w:ptcp.t:call-tar_outputs-68 INFO input :: name: "sawfish_vcf_tbi", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2165.sv.vcf.gz.tbi"
2025-09-15 20:26:10.442 wdl.w:ptcp.t:call-tar_outputs-68 INFO input :: name: "sawfish_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2165.sv.vcf.gz"
2025-09-15 20:26:10.442 wdl.w:ptcp.t:call-tar_outputs-68 INFO input :: name: "f8_json", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2165.f8inversion.json"
2025-09-15 20:26:10.442 wdl.w:ptcp.t:call-tar_outputs-68 INFO input :: name: "paraphase_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2165.paraphase.bam.bai"
2025-09-15 20:26:10.442 wdl.w:ptcp.t:call-tar_outputs-68 INFO input :: name: "paraphase_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2165.paraphase.bam"
2025-09-15 20:26:10.442 wdl.w:ptcp.t:call-tar_outputs-68 INFO input :: name: "paraphase_json", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2165.paraphase.json"
2025-09-15 20:26:10.442 wdl.w:ptcp.t:call-tar_outputs-68 INFO input :: name: "trgt_spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2165.trgt.sorted.spanning.bam.bai"
2025-09-15 20:26:10.442 wdl.w:ptcp.t:call-tar_outputs-68 INFO input :: name: "trgt_spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2165.trgt.sorted.spanning.bam"
2025-09-15 20:26:10.442 wdl.w:ptcp.t:call-tar_outputs-68 INFO input :: name: "trgt_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2165.trgt.vcf"
2025-09-15 20:26:10.442 wdl.w:ptcp.t:call-tar_outputs-68 INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2165.mapped.bam.bai"
2025-09-15 20:26:10.442 wdl.w:ptcp.t:call-tar_outputs-68 INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2165.mapped.bam"
2025-09-15 20:26:10.442 wdl.w:ptcp.t:call-tar_outputs-68 INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2165"
2025-09-15 20:26:10.443 wdl.w:ptcp.t:call-tar_outputs-68 INFO eval :: name: "threads", value: 1
2025-09-15 20:26:10.443 wdl.w:ptcp.t:call-tar_outputs-68 INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:26:10.443 wdl.w:ptcp.t:call-tar_outputs-68 INFO eval :: name: "disk_size", value: 6
2025-09-15 20:26:10.443 wdl.w:ptcp.t:call-tar_outputs-68 INFO eval :: name: "output_tarball", value: "m84036_250809_035451_s4.bc2165.tar"
2025-09-15 20:26:10.444 wdl.w:ptcp.t:call-tar_outputs-68 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:26:10.444 wdl.w:ptcp.t:call-tar_outputs-68 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:26:10.444 wdl.w:ptcp.t:call-tar_outputs-68 INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:26:10.444 wdl.w:ptcp.t:call-tar_outputs-68 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:26:10.488 wdl.w:ptcp.t:call-tar_outputs-49 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 17, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-49/_singularity_tmpdir_ba_uqb9j"
2025-09-15 20:26:10.488 wdl.w:ptcp.t:call-tar_outputs-49 INFO Slurm invocation: srun --job-name call-tar_outputs-49 --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-49/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-49/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-49/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-49/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-49/out/m84036_250809_035451_s4.bc2146_sawfish/m84036_250809_035451_s4.bc2146.sv.vcf.gz.tbi:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2146.sv.vcf.gz.tbi:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-49/out/m84036_250809_035451_s4.bc2146_sawfish/m84036_250809_035451_s4.bc2146.sv.vcf.gz:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2146.sv.vcf.gz:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-49/out/m84036_250809_035451_s4.bc2146.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2146.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-49/out/m84036_250809_035451_s4.bc2146.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2146.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-49/out/m84036_250809_035451_s4.bc2146.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2146.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-49/out/m84036_250809_035451_s4.bc2146.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2146.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-49/out/m84036_250809_035451_s4.bc2146.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2146.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-49/out/m84036_250809_035451_s4.bc2146_paraphase/m84036_250809_035451_s4.bc2146.paraphase.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2146.paraphase.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-49/out/m84036_250809_035451_s4.bc2146_paraphase/m84036_250809_035451_s4.bc2146.paraphase.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2146.paraphase.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-49/out/m84036_250809_035451_s4.bc2146_paraphase/m84036_250809_035451_s4.bc2146.paraphase.json:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2146.paraphase.json:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-49/out/m84036_250809_035451_s4.bc2146.f8inversion.json:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2146.f8inversion.json:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-49/_singularity_tmpdir_ba_uqb9j/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-49/_singularity_tmpdir_ba_uqb9j/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:26:10.498 wdl.w:ptcp.t:call-tar_outputs-49 NOTICE slurm_singularity run :: pid: 1207244, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-49/slurm_singularity.log.txt"
2025-09-15 20:26:10.526 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:26:09 [ERROR] - No reads found for TRID=SCA7_ATXN7
2025-09-15 20:26:10.526 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:26:09 [ERROR] - No reads found for TRID=SBMA_AR
2025-09-15 20:26:10.542 wdl.w:ptcp.t:call-tar_outputs-68 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 17, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-68/_singularity_tmpdir_o5z5jvjz"
2025-09-15 20:26:10.542 wdl.w:ptcp.t:call-tar_outputs-68 INFO Slurm invocation: srun --job-name call-tar_outputs-68 --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-68/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-68/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-68/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-68/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-68/out/m84036_250809_035451_s4.bc2165_sawfish/m84036_250809_035451_s4.bc2165.sv.vcf.gz:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2165.sv.vcf.gz:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-68/out/m84036_250809_035451_s4.bc2165_sawfish/m84036_250809_035451_s4.bc2165.sv.vcf.gz.tbi:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2165.sv.vcf.gz.tbi:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-68/out/m84036_250809_035451_s4.bc2165_paraphase/m84036_250809_035451_s4.bc2165.paraphase.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2165.paraphase.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-68/out/m84036_250809_035451_s4.bc2165_paraphase/m84036_250809_035451_s4.bc2165.paraphase.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2165.paraphase.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-68/out/m84036_250809_035451_s4.bc2165_paraphase/m84036_250809_035451_s4.bc2165.paraphase.json:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2165.paraphase.json:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-68/out/m84036_250809_035451_s4.bc2165.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2165.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-68/out/m84036_250809_035451_s4.bc2165.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2165.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-68/out/m84036_250809_035451_s4.bc2165.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2165.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-68/out/m84036_250809_035451_s4.bc2165.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2165.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-68/out/m84036_250809_035451_s4.bc2165.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2165.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-68/out/m84036_250809_035451_s4.bc2165.f8inversion.json:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2165.f8inversion.json:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-68/_singularity_tmpdir_o5z5jvjz/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-68/_singularity_tmpdir_o5z5jvjz/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:26:10.554 wdl.w:ptcp.t:call-tar_outputs-68 NOTICE slurm_singularity run :: pid: 1207252, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-68/slurm_singularity.log.txt"
2025-09-15 20:26:10.567 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_plot_meth_waterfall INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2192.meth_waterfall.trgt_plots.zip"
2025-09-15 20:26:10.637 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_plot_meth_waterfall NOTICE done
2025-09-15 20:26:10.642 wdl.w:ptcp.w:call-trgt-95 NOTICE finish :: job: "call-trgt_plot_meth_waterfall"
2025-09-15 20:26:10.642 wdl.w:ptcp.w:call-trgt-95 INFO output :: job: "call-trgt_plot_meth_waterfall", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-95/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2192.meth_waterfall.trgt_plots.zip"}
2025-09-15 20:26:10.642 wdl.w:ptcp.w:call-trgt-95 INFO visit :: node: "output-images_meth_waterfall", values: {"images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-95/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2192.meth_waterfall.trgt_plots.zip"}
2025-09-15 20:26:10.647 wdl.w:ptcp.t:call-tar_outputs-15 NOTICE task setup :: name: "tar_outputs", source: "./common.wdl", line: 279, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-15", thread: 140607649453632
2025-09-15 20:26:10.672 wdl.w:ptcp.t:call-tar_outputs-15 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:26:10.672 wdl.w:ptcp.t:call-tar_outputs-15 INFO input :: name: "sawfish_vcf_tbi", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2112.sv.vcf.gz.tbi"
2025-09-15 20:26:10.672 wdl.w:ptcp.t:call-tar_outputs-15 INFO input :: name: "sawfish_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2112.sv.vcf.gz"
2025-09-15 20:26:10.672 wdl.w:ptcp.t:call-tar_outputs-15 INFO input :: name: "f8_json", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2112.f8inversion.json"
2025-09-15 20:26:10.673 wdl.w:ptcp.t:call-tar_outputs-15 INFO input :: name: "paraphase_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2112.paraphase.bam.bai"
2025-09-15 20:26:10.673 wdl.w:ptcp.t:call-tar_outputs-15 INFO input :: name: "paraphase_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2112.paraphase.bam"
2025-09-15 20:26:10.673 wdl.w:ptcp.t:call-tar_outputs-15 INFO input :: name: "paraphase_json", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2112.paraphase.json"
2025-09-15 20:26:10.673 wdl.w:ptcp.t:call-tar_outputs-15 INFO input :: name: "trgt_spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2112.trgt.sorted.spanning.bam.bai"
2025-09-15 20:26:10.673 wdl.w:ptcp.t:call-tar_outputs-15 INFO input :: name: "trgt_spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2112.trgt.sorted.spanning.bam"
2025-09-15 20:26:10.673 wdl.w:ptcp.t:call-tar_outputs-15 INFO input :: name: "trgt_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2112.trgt.vcf"
2025-09-15 20:26:10.673 wdl.w:ptcp.t:call-tar_outputs-15 INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2112.mapped.bam.bai"
2025-09-15 20:26:10.673 wdl.w:ptcp.t:call-tar_outputs-15 INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2112.mapped.bam"
2025-09-15 20:26:10.673 wdl.w:ptcp.t:call-tar_outputs-15 INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2112"
2025-09-15 20:26:10.673 wdl.w:ptcp.t:call-tar_outputs-15 INFO eval :: name: "threads", value: 1
2025-09-15 20:26:10.673 wdl.w:ptcp.t:call-tar_outputs-15 INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:26:10.673 wdl.w:ptcp.t:call-tar_outputs-15 INFO eval :: name: "disk_size", value: 6
2025-09-15 20:26:10.674 wdl.w:ptcp.t:call-tar_outputs-15 INFO eval :: name: "output_tarball", value: "m84036_250809_035451_s4.bc2112.tar"
2025-09-15 20:26:10.674 wdl.w:ptcp.t:call-tar_outputs-15 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:26:10.674 wdl.w:ptcp.t:call-tar_outputs-15 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:26:10.674 wdl.w:ptcp.t:call-tar_outputs-15 INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:26:10.675 wdl.w:ptcp.t:call-tar_outputs-15 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:26:10.702 wdl.w:ptcp.w:call-sawfish-72.t:call-run_sawfish.stderr VERBOSE [M::mm_idx_gen::42.386*1.65] sorted minimizers
2025-09-15 20:26:10.702 wdl.w:ptcp.w:call-sawfish-72.t:call-run_sawfish.stderr VERBOSE [M::main::42.386*1.65] loaded/built the index for 195 target sequence(s)
2025-09-15 20:26:10.702 wdl.w:ptcp.w:call-sawfish-72.t:call-run_sawfish.stderr VERBOSE [M::mm_mapopt_update::45.455*1.60] mid_occ = 136
2025-09-15 20:26:10.702 wdl.w:ptcp.w:call-sawfish-72.t:call-run_sawfish.stderr VERBOSE [M::mm_idx_stat] kmer size: 19; skip: 19; is_hpc: 0; #seq: 195
2025-09-15 20:26:10.702 wdl.w:ptcp.w:call-sawfish-72.t:call-run_sawfish.stderr VERBOSE [M::mm_idx_stat::48.089*1.57] distinct minimizers: 214664461 (92.23% are singletons); average occurrences: 1.372; average spacing: 10.529; total length: 3099922541
2025-09-15 20:26:10.702 wdl.w:ptcp.w:call-sawfish-72.t:call-run_sawfish.stderr VERBOSE [M::worker_pipeline::48.093*1.57] mapped 1 sequences
2025-09-15 20:26:10.702 wdl.w:ptcp.w:call-sawfish-72.t:call-run_sawfish.stderr VERBOSE [M::main] Version: 2.26-r1175
2025-09-15 20:26:10.702 wdl.w:ptcp.w:call-sawfish-72.t:call-run_sawfish.stderr VERBOSE [M::main] CMD: /opt/pacbio/smrttools/install/smrtlink-release_25.1.0.257715/bundles/smrttools/install/smrttools-release_25.1.0.257715/private/thirdparty/minimap2/minimap2_2.26-pacbio2/binwrap/../../../../../private/thirdparty/minimap2/minimap2_2.26-pacbio2/bin/minimap2 -a -y -x map-hifi -Y -E 1,0 /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa -
2025-09-15 20:26:10.702 wdl.w:ptcp.w:call-sawfish-72.t:call-run_sawfish.stderr VERBOSE [M::main] Real time: 48.403 sec; CPU: 75.749 sec; Peak RSS: 11.886 GB
2025-09-15 20:26:10.753 wdl.w:ptcp.t:call-tar_outputs-52 INFO output :: name: "sample_tarball", value: "m84036_250809_035451_s4.bc2149.tar"
2025-09-15 20:26:10.755 wdl.w:ptcp.w:call-paraphase-34.t:call-call_f8 INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2131.f8inversion.vcf"
2025-09-15 20:26:10.760 wdl.w:ptcp.w:call-paraphase-34.t:call-call_f8 INFO output :: name: "json", value: "m84036_250809_035451_s4.bc2131.f8inversion.json"
2025-09-15 20:26:10.785 wdl.w:ptcp.t:call-tar_outputs-15 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 17, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-15/_singularity_tmpdir_g6x79e5k"
2025-09-15 20:26:10.785 wdl.w:ptcp.t:call-tar_outputs-15 INFO Slurm invocation: srun --job-name call-tar_outputs-15 --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-15/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-15/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-15/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-15/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-15/out/m84036_250809_035451_s4.bc2112_paraphase/m84036_250809_035451_s4.bc2112.paraphase.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2112.paraphase.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-15/out/m84036_250809_035451_s4.bc2112_paraphase/m84036_250809_035451_s4.bc2112.paraphase.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2112.paraphase.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-15/out/m84036_250809_035451_s4.bc2112_paraphase/m84036_250809_035451_s4.bc2112.paraphase.json:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2112.paraphase.json:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-15/out/m84036_250809_035451_s4.bc2112.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2112.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-15/out/m84036_250809_035451_s4.bc2112.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2112.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-15/out/m84036_250809_035451_s4.bc2112.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2112.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-15/out/m84036_250809_035451_s4.bc2112.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2112.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-15/out/m84036_250809_035451_s4.bc2112.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2112.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-15/out/m84036_250809_035451_s4.bc2112.f8inversion.json:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2112.f8inversion.json:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-15/out/m84036_250809_035451_s4.bc2112_sawfish/m84036_250809_035451_s4.bc2112.sv.vcf.gz.tbi:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2112.sv.vcf.gz.tbi:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-15/out/m84036_250809_035451_s4.bc2112_sawfish/m84036_250809_035451_s4.bc2112.sv.vcf.gz:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2112.sv.vcf.gz:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-15/_singularity_tmpdir_g6x79e5k/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-15/_singularity_tmpdir_g6x79e5k/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:26:10.808 wdl.w:ptcp.t:call-tar_outputs-15 NOTICE slurm_singularity run :: pid: 1207266, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-15/slurm_singularity.log.txt"
2025-09-15 20:26:10.832 wdl.w:ptcp.t:call-tar_outputs-52 NOTICE done
2025-09-15 20:26:10.836 wdl.w:ptcp.w:call-trgt-90.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:26:10 [ERROR] - No reads found for TRID=SCA37_DAB1
2025-09-15 20:26:10.836 wdl.w:ptcp.w:call-trgt-90.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:26:10 [ERROR] - No reads found for TRID=NIID_NOTCH2NLC
2025-09-15 20:26:10.836 wdl.w:ptcp.w:call-trgt-90.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:26:10 [ERROR] - No reads found for TRID=SCA8_ATXN8OS
2025-09-15 20:26:10.836 wdl.w:ptcp.w:call-trgt-90.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:26:10 [ERROR] - No reads found for TRID=SCA27B_FGF14
2025-09-15 20:26:10.836 wdl.w:ptcp.w:call-trgt-90.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:26:10 [ERROR] - No reads found for TRID=OPDM4_RILPL1
2025-09-15 20:26:10.839 wdl.w:ptcp NOTICE finish :: job: "call-tar_outputs-52"
2025-09-15 20:26:10.839 wdl.w:ptcp INFO output :: job: "call-tar_outputs-52", values: {"sample_tarball": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-52/out/m84036_250809_035451_s4.bc2149.tar"}
2025-09-15 20:26:10.846 wdl.w:ptcp.w:call-paraphase-34.t:call-call_f8 NOTICE done
2025-09-15 20:26:10.848 wdl.w:ptcp.t:call-tar_outputs-65 NOTICE task setup :: name: "tar_outputs", source: "./common.wdl", line: 279, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-65", thread: 140611441120832
2025-09-15 20:26:10.850 wdl.w:ptcp.w:call-trgt-90.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO srun: job 51798164 queued and waiting for resources
2025-09-15 20:26:10.851 wdl.w:ptcp.w:call-trgt-90.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO srun: job 51798164 has been allocated resources
2025-09-15 20:26:10.851 wdl.w:ptcp.w:call-trgt-90.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:26:10.852 wdl.w:ptcp.w:call-paraphase-34 NOTICE finish :: job: "call-call_f8"
2025-09-15 20:26:10.852 wdl.w:ptcp.w:call-paraphase-34 INFO output :: job: "call-call_f8", values: {"json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-34/call-call_f8/out/m84036_250809_035451_s4.bc2131.f8inversion.json", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-34/call-call_f8/out/m84036_250809_035451_s4.bc2131.f8inversion.vcf"}
2025-09-15 20:26:10.852 wdl.w:ptcp.w:call-paraphase-34 INFO visit :: node: "output-f8_json", values: {"f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-34/call-call_f8/out/m84036_250809_035451_s4.bc2131.f8inversion.json"}
2025-09-15 20:26:10.852 wdl.w:ptcp.w:call-paraphase-34 INFO visit :: node: "output-f8_vcf", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-34/call-call_f8/out/m84036_250809_035451_s4.bc2131.f8inversion.vcf"}
2025-09-15 20:26:10.853 wdl.w:ptcp.w:call-paraphase-34 INFO visit :: node: "outputs", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-34/call-call_f8/out/m84036_250809_035451_s4.bc2131.f8inversion.vcf", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-34/call-run_paraphase/out/m84036_250809_035451_s4.bc2131_paraphase/m84036_250809_035451_s4.bc2131.paraphase.json", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-34/call-run_paraphase/out/m84036_250809_035451_s4.bc2131_paraphase/m84036_250809_035451_s4.bc2131.paraphase.bam", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-34/call-run_paraphase/out/m84036_250809_035451_s4.bc2131_paraphase/m84036_250809_035451_s4.bc2131.paraphase.bam.bai", "paraphase_vcfs": ["/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-34/call-run_paraphase/out/m84036_250809_035451_s4.bc2131_paraphase/m84036_250809_035451_s4.bc2131_paraphase_vcfs/m84036_250809_035451_s4.bc2131_cyp21.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-34/call-run_paraphase/out/m84036_250809_035451_s4.bc2131_paraphase/m84036_250809_035451_s4.bc2131_paraphase_vcfs/m84036_250809_035451_s4.bc2131_f8inv1.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-34/call-run_paraphase/out/m84036_250809_035451_s4.bc2131_paraphase/m84036_250809_035451_s4.bc2131_paraphase_vcfs/m84036_250809_035451_s4.bc2131_f8inv22.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-34/call-run_paraphase/out/m84036_250809_035451_s4.bc2131_paraphase/m84036_250809_035451_s4.bc2131_paraphase_vcfs/m84036_250809_035451_s4.bc2131_gba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-34/call-run_paraphase/out/m84036_250809_035451_s4.bc2131_paraphase/m84036_250809_035451_s4.bc2131_paraphase_vcfs/m84036_250809_035451_s4.bc2131_hba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-34/call-run_paraphase/out/m84036_250809_035451_s4.bc2131_paraphase/m84036_250809_035451_s4.bc2131_paraphase_vcfs/m84036_250809_035451_s4.bc2131_hbb.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-34/call-run_paraphase/out/m84036_250809_035451_s4.bc2131_paraphase/m84036_250809_035451_s4.bc2131_paraphase_vcfs/m84036_250809_035451_s4.bc2131_rpgr.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-34/call-run_paraphase/out/m84036_250809_035451_s4.bc2131_paraphase/m84036_250809_035451_s4.bc2131_paraphase_vcfs/m84036_250809_035451_s4.bc2131_smn1.vcf"], "havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-34/call-run_paraphase/out/m84036_250809_035451_s4.bc2131.havanno.json", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-34/call-call_f8/out/m84036_250809_035451_s4.bc2131.f8inversion.json"}
2025-09-15 20:26:10.864 wdl.w:ptcp.t:call-tar_outputs-48 NOTICE task setup :: name: "tar_outputs", source: "./common.wdl", line: 279, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-48", thread: 140609822115392
2025-09-15 20:26:10.873 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_meth_allele INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2191.meth_allele.trgt_plots.zip"
2025-09-15 20:26:10.876 wdl.w:ptcp.t:call-tar_outputs-65 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:26:10.876 wdl.w:ptcp.t:call-tar_outputs-65 INFO input :: name: "sawfish_vcf_tbi", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2162.sv.vcf.gz.tbi"
2025-09-15 20:26:10.876 wdl.w:ptcp.t:call-tar_outputs-65 INFO input :: name: "sawfish_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2162.sv.vcf.gz"
2025-09-15 20:26:10.877 wdl.w:ptcp.t:call-tar_outputs-65 INFO input :: name: "f8_json", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2162.f8inversion.json"
2025-09-15 20:26:10.877 wdl.w:ptcp.t:call-tar_outputs-65 INFO input :: name: "paraphase_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2162.paraphase.bam.bai"
2025-09-15 20:26:10.877 wdl.w:ptcp.t:call-tar_outputs-65 INFO input :: name: "paraphase_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2162.paraphase.bam"
2025-09-15 20:26:10.877 wdl.w:ptcp.t:call-tar_outputs-65 INFO input :: name: "paraphase_json", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2162.paraphase.json"
2025-09-15 20:26:10.878 wdl.w:ptcp.t:call-tar_outputs-65 INFO input :: name: "trgt_spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2162.trgt.sorted.spanning.bam.bai"
2025-09-15 20:26:10.878 wdl.w:ptcp.t:call-tar_outputs-65 INFO input :: name: "trgt_spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2162.trgt.sorted.spanning.bam"
2025-09-15 20:26:10.878 wdl.w:ptcp.t:call-tar_outputs-65 INFO input :: name: "trgt_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2162.trgt.vcf"
2025-09-15 20:26:10.878 wdl.w:ptcp.t:call-tar_outputs-65 INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2162.mapped.bam.bai"
2025-09-15 20:26:10.879 wdl.w:ptcp.t:call-tar_outputs-65 INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2162.mapped.bam"
2025-09-15 20:26:10.879 wdl.w:ptcp.t:call-tar_outputs-65 INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2162"
2025-09-15 20:26:10.879 wdl.w:ptcp.t:call-tar_outputs-65 INFO eval :: name: "threads", value: 1
2025-09-15 20:26:10.879 wdl.w:ptcp.t:call-tar_outputs-65 INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:26:10.879 wdl.w:ptcp.t:call-tar_outputs-65 INFO eval :: name: "disk_size", value: 6
2025-09-15 20:26:10.880 wdl.w:ptcp.t:call-tar_outputs-65 INFO eval :: name: "output_tarball", value: "m84036_250809_035451_s4.bc2162.tar"
2025-09-15 20:26:10.880 wdl.w:ptcp.t:call-tar_outputs-65 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:26:10.880 wdl.w:ptcp.t:call-tar_outputs-65 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:26:10.881 wdl.w:ptcp.w:call-trgt-93.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:26:10 [ERROR] - No reads found for TRID=PRTS_ARX
2025-09-15 20:26:10.881 wdl.w:ptcp.w:call-trgt-93.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:26:10 [ERROR] - No reads found for TRID=EIEE1_ARX
2025-09-15 20:26:10.882 wdl.w:ptcp.t:call-tar_outputs-65 INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:26:10.882 wdl.w:ptcp.t:call-tar_outputs-65 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:26:10.895 wdl.w:ptcp.t:call-tar_outputs-48 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:26:10.896 wdl.w:ptcp.t:call-tar_outputs-48 INFO input :: name: "sawfish_vcf_tbi", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2145.sv.vcf.gz.tbi"
2025-09-15 20:26:10.896 wdl.w:ptcp.t:call-tar_outputs-48 INFO input :: name: "sawfish_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2145.sv.vcf.gz"
2025-09-15 20:26:10.896 wdl.w:ptcp.t:call-tar_outputs-48 INFO input :: name: "f8_json", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2145.f8inversion.json"
2025-09-15 20:26:10.896 wdl.w:ptcp.t:call-tar_outputs-48 INFO input :: name: "paraphase_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2145.paraphase.bam.bai"
2025-09-15 20:26:10.896 wdl.w:ptcp.t:call-tar_outputs-48 INFO input :: name: "paraphase_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2145.paraphase.bam"
2025-09-15 20:26:10.896 wdl.w:ptcp.t:call-tar_outputs-48 INFO input :: name: "paraphase_json", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2145.paraphase.json"
2025-09-15 20:26:10.896 wdl.w:ptcp.t:call-tar_outputs-48 INFO input :: name: "trgt_spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2145.trgt.sorted.spanning.bam.bai"
2025-09-15 20:26:10.896 wdl.w:ptcp.t:call-tar_outputs-48 INFO input :: name: "trgt_spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2145.trgt.sorted.spanning.bam"
2025-09-15 20:26:10.896 wdl.w:ptcp.t:call-tar_outputs-48 INFO input :: name: "trgt_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2145.trgt.vcf"
2025-09-15 20:26:10.896 wdl.w:ptcp.t:call-tar_outputs-48 INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2145.mapped.bam.bai"
2025-09-15 20:26:10.896 wdl.w:ptcp.t:call-tar_outputs-48 INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2145.mapped.bam"
2025-09-15 20:26:10.896 wdl.w:ptcp.t:call-tar_outputs-48 INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2145"
2025-09-15 20:26:10.896 wdl.w:ptcp.t:call-tar_outputs-48 INFO eval :: name: "threads", value: 1
2025-09-15 20:26:10.897 wdl.w:ptcp.t:call-tar_outputs-48 INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:26:10.897 wdl.w:ptcp.t:call-tar_outputs-48 INFO eval :: name: "disk_size", value: 6
2025-09-15 20:26:10.897 wdl.w:ptcp.t:call-tar_outputs-48 INFO eval :: name: "output_tarball", value: "m84036_250809_035451_s4.bc2145.tar"
2025-09-15 20:26:10.897 wdl.w:ptcp.t:call-tar_outputs-48 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:26:10.899 wdl.w:ptcp.t:call-tar_outputs-48 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:26:10.900 wdl.w:ptcp.t:call-tar_outputs-48 INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:26:10.900 wdl.w:ptcp.t:call-tar_outputs-48 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:26:10.980 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_meth_allele NOTICE done
2025-09-15 20:26:10.986 wdl.w:ptcp.w:call-trgt-94 NOTICE finish :: job: "call-trgt_plot_meth_allele"
2025-09-15 20:26:10.987 wdl.w:ptcp.w:call-trgt-94 INFO output :: job: "call-trgt_plot_meth_allele", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-94/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2191.meth_allele.trgt_plots.zip"}
2025-09-15 20:26:10.987 wdl.w:ptcp.w:call-trgt-94 INFO visit :: node: "output-images_meth_allele", values: {"images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-94/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2191.meth_allele.trgt_plots.zip"}
2025-09-15 20:26:10.995 wdl.w:ptcp.t:call-tar_outputs-23 NOTICE task setup :: name: "tar_outputs", source: "./common.wdl", line: 279, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-23", thread: 140608748373568
2025-09-15 20:26:11.021 wdl.w:ptcp.t:call-tar_outputs-65 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 17, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-65/_singularity_tmpdir_jdzbmhpj"
2025-09-15 20:26:11.022 wdl.w:ptcp.t:call-tar_outputs-65 INFO Slurm invocation: srun --job-name call-tar_outputs-65 --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-65/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-65/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-65/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-65/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-65/out/m84036_250809_035451_s4.bc2162_sawfish/m84036_250809_035451_s4.bc2162.sv.vcf.gz.tbi:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2162.sv.vcf.gz.tbi:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-65/out/m84036_250809_035451_s4.bc2162_sawfish/m84036_250809_035451_s4.bc2162.sv.vcf.gz:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2162.sv.vcf.gz:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-65/out/m84036_250809_035451_s4.bc2162_paraphase/m84036_250809_035451_s4.bc2162.paraphase.json:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2162.paraphase.json:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-65/out/m84036_250809_035451_s4.bc2162_paraphase/m84036_250809_035451_s4.bc2162.paraphase.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2162.paraphase.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-65/out/m84036_250809_035451_s4.bc2162_paraphase/m84036_250809_035451_s4.bc2162.paraphase.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2162.paraphase.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-65/out/m84036_250809_035451_s4.bc2162.f8inversion.json:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2162.f8inversion.json:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-65/out/m84036_250809_035451_s4.bc2162.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2162.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-65/out/m84036_250809_035451_s4.bc2162.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2162.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-65/out/m84036_250809_035451_s4.bc2162.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2162.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-65/out/m84036_250809_035451_s4.bc2162.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2162.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-65/out/m84036_250809_035451_s4.bc2162.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2162.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-65/_singularity_tmpdir_jdzbmhpj/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-65/_singularity_tmpdir_jdzbmhpj/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:26:11.026 wdl.w:ptcp.t:call-tar_outputs-48 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 17, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-48/_singularity_tmpdir_2y773ml3"
2025-09-15 20:26:11.026 wdl.w:ptcp.t:call-tar_outputs-48 INFO Slurm invocation: srun --job-name call-tar_outputs-48 --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-48/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-48/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-48/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-48/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-48/out/m84036_250809_035451_s4.bc2145.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2145.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-48/out/m84036_250809_035451_s4.bc2145.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2145.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-48/out/m84036_250809_035451_s4.bc2145.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2145.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-48/out/m84036_250809_035451_s4.bc2145.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2145.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-48/out/m84036_250809_035451_s4.bc2145.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2145.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-48/out/m84036_250809_035451_s4.bc2145_paraphase/m84036_250809_035451_s4.bc2145.paraphase.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2145.paraphase.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-48/out/m84036_250809_035451_s4.bc2145_paraphase/m84036_250809_035451_s4.bc2145.paraphase.json:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2145.paraphase.json:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-48/out/m84036_250809_035451_s4.bc2145_paraphase/m84036_250809_035451_s4.bc2145.paraphase.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2145.paraphase.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-48/out/m84036_250809_035451_s4.bc2145_sawfish/m84036_250809_035451_s4.bc2145.sv.vcf.gz:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2145.sv.vcf.gz:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-48/out/m84036_250809_035451_s4.bc2145_sawfish/m84036_250809_035451_s4.bc2145.sv.vcf.gz.tbi:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2145.sv.vcf.gz.tbi:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-48/out/m84036_250809_035451_s4.bc2145.f8inversion.json:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2145.f8inversion.json:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-48/_singularity_tmpdir_2y773ml3/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-48/_singularity_tmpdir_2y773ml3/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:26:11.033 wdl.w:ptcp.w:call-paraphase-34 NOTICE done
2025-09-15 20:26:11.034 wdl.w:ptcp.t:call-tar_outputs-23 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:26:11.034 wdl.w:ptcp.t:call-tar_outputs-23 INFO input :: name: "sawfish_vcf_tbi", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2120.sv.vcf.gz.tbi"
2025-09-15 20:26:11.034 wdl.w:ptcp.t:call-tar_outputs-23 INFO input :: name: "sawfish_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2120.sv.vcf.gz"
2025-09-15 20:26:11.034 wdl.w:ptcp.t:call-tar_outputs-23 INFO input :: name: "f8_json", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2120.f8inversion.json"
2025-09-15 20:26:11.034 wdl.w:ptcp.t:call-tar_outputs-23 INFO input :: name: "paraphase_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2120.paraphase.bam.bai"
2025-09-15 20:26:11.035 wdl.w:ptcp.t:call-tar_outputs-23 INFO input :: name: "paraphase_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2120.paraphase.bam"
2025-09-15 20:26:11.035 wdl.w:ptcp.t:call-tar_outputs-23 INFO input :: name: "paraphase_json", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2120.paraphase.json"
2025-09-15 20:26:11.035 wdl.w:ptcp.t:call-tar_outputs-23 INFO input :: name: "trgt_spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2120.trgt.sorted.spanning.bam.bai"
2025-09-15 20:26:11.035 wdl.w:ptcp.t:call-tar_outputs-23 INFO input :: name: "trgt_spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2120.trgt.sorted.spanning.bam"
2025-09-15 20:26:11.035 wdl.w:ptcp.t:call-tar_outputs-23 INFO input :: name: "trgt_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2120.trgt.vcf"
2025-09-15 20:26:11.035 wdl.w:ptcp.t:call-tar_outputs-23 INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2120.mapped.bam.bai"
2025-09-15 20:26:11.036 wdl.w:ptcp.t:call-tar_outputs-23 INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2120.mapped.bam"
2025-09-15 20:26:11.035 wdl.w:ptcp.w:call-trgt-93.t:call-trgt_plot_motifs_allele INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2190.motifs_allele.trgt_plots.zip"
2025-09-15 20:26:11.036 wdl.w:ptcp.t:call-tar_outputs-23 INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2120"
2025-09-15 20:26:11.036 wdl.w:ptcp.w:call-trgt-90.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:26:10 [ERROR] - No reads found for TRID=SCA37_DAB1
2025-09-15 20:26:11.036 wdl.w:ptcp.t:call-tar_outputs-23 INFO eval :: name: "threads", value: 1
2025-09-15 20:26:11.036 wdl.w:ptcp.w:call-trgt-90.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:26:10 [ERROR] - No reads found for TRID=NIID_NOTCH2NLC
2025-09-15 20:26:11.036 wdl.w:ptcp.t:call-tar_outputs-23 INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:26:11.036 wdl.w:ptcp.w:call-trgt-90.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:26:10 [ERROR] - No reads found for TRID=SCA8_ATXN8OS
2025-09-15 20:26:11.037 wdl.w:ptcp.w:call-trgt-90.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:26:10 [ERROR] - No reads found for TRID=SCA27B_FGF14
2025-09-15 20:26:11.037 wdl.w:ptcp.t:call-tar_outputs-23 INFO eval :: name: "disk_size", value: 6
2025-09-15 20:26:11.037 wdl.w:ptcp.w:call-trgt-90.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:26:10 [ERROR] - No reads found for TRID=OPDM4_RILPL1
2025-09-15 20:26:11.037 wdl.w:ptcp.t:call-tar_outputs-23 INFO eval :: name: "output_tarball", value: "m84036_250809_035451_s4.bc2120.tar"
2025-09-15 20:26:11.037 wdl.w:ptcp.w:call-trgt-90.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:26:10 [ERROR] - No reads found for TRID=SCA3_ATXN3
2025-09-15 20:26:11.038 wdl.w:ptcp.w:call-trgt-90.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:26:10 [ERROR] - No reads found for TRID=OPDM_ABCD3
2025-09-15 20:26:11.038 wdl.w:ptcp.w:call-trgt-90.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:26:10 [ERROR] - No reads found for TRID=HDL2_JPH3
2025-09-15 20:26:11.038 wdl.w:ptcp.t:call-tar_outputs-23 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:26:11.038 wdl.w:ptcp.w:call-trgt-90.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:26:11 [ERROR] - No reads found for TRID=SCA4_ZFHX3
2025-09-15 20:26:11.038 wdl.w:ptcp.t:call-tar_outputs-23 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:26:11.039 wdl.w:ptcp.t:call-tar_outputs-23 INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:26:11.039 wdl.w:ptcp.t:call-tar_outputs-23 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:26:11.039 wdl.w:ptcp NOTICE finish :: job: "call-paraphase-34"
2025-09-15 20:26:11.040 wdl.w:ptcp INFO output :: job: "call-paraphase-34", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-34/out/m84036_250809_035451_s4.bc2131.f8inversion.vcf", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-34/out/m84036_250809_035451_s4.bc2131_paraphase/m84036_250809_035451_s4.bc2131.paraphase.json", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-34/out/m84036_250809_035451_s4.bc2131_paraphase/m84036_250809_035451_s4.bc2131.paraphase.bam", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-34/out/m84036_250809_035451_s4.bc2131_paraphase/m84036_250809_035451_s4.bc2131.paraphase.bam.bai", "paraphase_vcfs": ["/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-34/out/m84036_250809_035451_s4.bc2131_paraphase/m84036_250809_035451_s4.bc2131_paraphase_vcfs/m84036_250809_035451_s4.bc2131_cyp21.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-34/out/m84036_250809_035451_s4.bc2131_paraphase/m84036_250809_035451_s4.bc2131_paraphase_vcfs/m84036_250809_035451_s4.bc2131_f8inv1.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-34/out/m84036_250809_035451_s4.bc2131_paraphase/m84036_250809_035451_s4.bc2131_paraphase_vcfs/m84036_250809_035451_s4.bc2131_f8inv22.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-34/out/m84036_250809_035451_s4.bc2131_paraphase/m84036_250809_035451_s4.bc2131_paraphase_vcfs/m84036_250809_035451_s4.bc2131_gba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-34/out/m84036_250809_035451_s4.bc2131_paraphase/m84036_250809_035451_s4.bc2131_paraphase_vcfs/m84036_250809_035451_s4.bc2131_hba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-34/out/m84036_250809_035451_s4.bc2131_paraphase/m84036_250809_035451_s4.bc2131_paraphase_vcfs/m84036_250809_035451_s4.bc2131_hbb.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-34/out/m84036_250809_035451_s4.bc2131_paraphase/m84036_250809_035451_s4.bc2131_paraphase_vcfs/m84036_250809_035451_s4.bc2131_rpgr.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-34/out/m84036_250809_035451_s4.bc2131_paraphase/m84036_250809_035451_s4.bc2131_paraphase_vcfs/m84036_250809_035451_s4.bc2131_smn1.vcf"], "havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-34/out/m84036_250809_035451_s4.bc2131.havanno.json", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-34/out/m84036_250809_035451_s4.bc2131.f8inversion.json"}
2025-09-15 20:26:11.040 wdl.w:ptcp NOTICE ready :: job: "call-tar_outputs-34", callee: "tar_outputs"
2025-09-15 20:26:11.041 wdl.w:ptcp INFO input :: job: "call-tar_outputs-34", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "sawfish_vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-34/out/m84036_250809_035451_s4.bc2131_sawfish/m84036_250809_035451_s4.bc2131.sv.vcf.gz.tbi", "sawfish_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-34/out/m84036_250809_035451_s4.bc2131_sawfish/m84036_250809_035451_s4.bc2131.sv.vcf.gz", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-34/out/m84036_250809_035451_s4.bc2131.f8inversion.json", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-34/out/m84036_250809_035451_s4.bc2131_paraphase/m84036_250809_035451_s4.bc2131.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-34/out/m84036_250809_035451_s4.bc2131_paraphase/m84036_250809_035451_s4.bc2131.paraphase.bam", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-34/out/m84036_250809_035451_s4.bc2131_paraphase/m84036_250809_035451_s4.bc2131.paraphase.json", "trgt_spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-34/out/m84036_250809_035451_s4.bc2131.trgt.sorted.spanning.bam.bai", "trgt_spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-34/out/m84036_250809_035451_s4.bc2131.trgt.sorted.spanning.bam", "trgt_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-34/out/m84036_250809_035451_s4.bc2131.trgt.vcf", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-34/out/m84036_250809_035451_s4.bc2131.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-34/out/m84036_250809_035451_s4.bc2131.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2131"}
2025-09-15 20:26:11.050 wdl.w:ptcp.w:call-trgt-90.t:call-trgt_plot_motifs_allele.slurm_singularity INFO srun: job 51798165 queued and waiting for resources
2025-09-15 20:26:11.050 wdl.w:ptcp.t:call-tar_outputs-65 NOTICE slurm_singularity run :: pid: 1207275, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-65/slurm_singularity.log.txt"
2025-09-15 20:26:11.050 wdl.w:ptcp.w:call-trgt-90.t:call-trgt_plot_motifs_allele.slurm_singularity INFO srun: job 51798165 has been allocated resources
2025-09-15 20:26:11.050 wdl.w:ptcp.w:call-trgt-90.t:call-trgt_plot_motifs_allele.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:26:11.052 wdl.w:ptcp.t:call-tar_outputs-48 NOTICE slurm_singularity run :: pid: 1207276, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-48/slurm_singularity.log.txt"
2025-09-15 20:26:11.101 wdl.w:ptcp.w:call-sawfish-62.t:call-run_sawfish.stderr VERBOSE [M::mm_idx_gen::47.679*1.53] collected minimizers
2025-09-15 20:26:11.102 wdl.w:ptcp.w:call-sawfish-62.t:call-run_sawfish.stderr VERBOSE [M::mm_idx_gen::57.861*1.78] sorted minimizers
2025-09-15 20:26:11.102 wdl.w:ptcp.w:call-sawfish-62.t:call-run_sawfish.stderr VERBOSE [M::main::57.861*1.78] loaded/built the index for 195 target sequence(s)
2025-09-15 20:26:11.102 wdl.w:ptcp.w:call-sawfish-62.t:call-run_sawfish.stderr VERBOSE [M::mm_mapopt_update::64.509*1.70] mid_occ = 136
2025-09-15 20:26:11.102 wdl.w:ptcp.w:call-sawfish-62.t:call-run_sawfish.stderr VERBOSE [M::mm_idx_stat] kmer size: 19; skip: 19; is_hpc: 0; #seq: 195
2025-09-15 20:26:11.102 wdl.w:ptcp.w:call-sawfish-62.t:call-run_sawfish.stderr VERBOSE [M::mm_idx_stat::71.073*1.63] distinct minimizers: 214664461 (92.23% are singletons); average occurrences: 1.372; average spacing: 10.529; total length: 3099922541
2025-09-15 20:26:11.103 wdl.w:ptcp.w:call-sawfish-62.t:call-run_sawfish.stderr VERBOSE [M::bam2fq_mainloop] discarded 0 singletons
2025-09-15 20:26:11.103 wdl.w:ptcp.w:call-sawfish-62.t:call-run_sawfish.stderr VERBOSE [M::bam2fq_mainloop] processed 411 reads
2025-09-15 20:26:11.103 wdl.w:ptcp.w:call-sawfish-62.t:call-run_sawfish.stderr VERBOSE [M::worker_pipeline::71.946*1.64] mapped 411 sequences
2025-09-15 20:26:11.103 wdl.w:ptcp.w:call-sawfish-62.t:call-run_sawfish.stderr VERBOSE [M::main] Version: 2.26-r1175
2025-09-15 20:26:11.103 wdl.w:ptcp.w:call-sawfish-62.t:call-run_sawfish.stderr VERBOSE [M::main] CMD: /opt/pacbio/smrttools/install/smrtlink-release_25.1.0.257715/bundles/smrttools/install/smrttools-release_25.1.0.257715/private/thirdparty/minimap2/minimap2_2.26-pacbio2/binwrap/../../../../../private/thirdparty/minimap2/minimap2_2.26-pacbio2/bin/minimap2 -a -y -x map-hifi -Y -E 1,0 /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa -
2025-09-15 20:26:11.103 wdl.w:ptcp.w:call-sawfish-62.t:call-run_sawfish.stderr VERBOSE [M::main] Real time: 72.303 sec; CPU: 118.288 sec; Peak RSS: 11.887 GB
2025-09-15 20:26:11.103 wdl.w:ptcp.w:call-sawfish-62.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:49][sawfish][INFO] Starting sawfish 2.0.3
2025-09-15 20:26:11.103 wdl.w:ptcp.w:call-sawfish-62.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:49][sawfish][INFO] cmdline: sawfish discover --disable-cnv --threads 16 --ref /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa --bam m84036_250809_035451_s4.bc2159.minimap2.bam --output-dir m84036_250809_035451_s4.bc2159_sawfish_discover
2025-09-15 20:26:11.103 wdl.w:ptcp.w:call-sawfish-62.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:49][sawfish][INFO] Running on 16 threads
2025-09-15 20:26:11.103 wdl.w:ptcp.w:call-sawfish-62.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:49][sawfish][INFO] Writing discover settings to file: 'm84036_250809_035451_s4.bc2159_sawfish_discover/discover.settings.json'
2025-09-15 20:26:11.103 wdl.w:ptcp.w:call-sawfish-62.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:49][sawfish][INFO] Reading reference genome from file '/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa'
2025-09-15 20:26:11.103 wdl.w:ptcp.w:call-sawfish-62.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:55][sawfish][INFO] Processing alignment file '/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2159.minimap2.bam'
2025-09-15 20:26:11.103 wdl.w:ptcp.w:call-sawfish-62.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:55][sawfish][INFO] Finished processing all alignments
2025-09-15 20:26:11.103 wdl.w:ptcp.w:call-sawfish-62.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:55][sawfish][INFO] Writing depth bins to binary file: 'm84036_250809_035451_s4.bc2159_sawfish_discover/depth.mpack'
2025-09-15 20:26:11.103 wdl.w:ptcp.w:call-sawfish-62.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:55][sawfish][INFO] Writing max sv depth genome regions to bed file: 'm84036_250809_035451_s4.bc2159_sawfish_discover/max.depth.bed'
2025-09-15 20:26:11.103 wdl.w:ptcp.w:call-sawfish-62.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:55][sawfish][INFO] Completing breakpoint observation clustering
2025-09-15 20:26:11.103 wdl.w:ptcp.w:call-sawfish-62.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:55][sawfish][INFO] Finished breakpoint observation clustering
2025-09-15 20:26:11.104 wdl.w:ptcp.w:call-sawfish-62.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:55][sawfish][INFO] Consolidating adjacent indel candidates
2025-09-15 20:26:11.104 wdl.w:ptcp.w:call-sawfish-62.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:55][sawfish][INFO] Finding large insertion candidates
2025-09-15 20:26:11.104 wdl.w:ptcp.w:call-sawfish-62.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:55][sawfish][INFO] Writing breakpoint_cluster debug bed file: 'm84036_250809_035451_s4.bc2159_sawfish_discover/debug.breakpoint_clusters.bed'
2025-09-15 20:26:11.104 wdl.w:ptcp.w:call-sawfish-62.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:55][sawfish][INFO] Refining SV Candidates
2025-09-15 20:26:11.104 wdl.w:ptcp.w:call-sawfish-62.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:55][sawfish][INFO] Writing debug assembly region bed file: 'm84036_250809_035451_s4.bc2159_sawfish_discover/assembly.regions.bed'
2025-09-15 20:26:11.104 wdl.w:ptcp.w:call-sawfish-62.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:55][sawfish][INFO] Starting refinement of breakpoint evidence clusters
2025-09-15 20:26:11.104 wdl.w:ptcp.w:call-sawfish-62.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:56][sawfish][INFO] Finished refining all breakpoint evidence clusters
2025-09-15 20:26:11.104 wdl.w:ptcp.w:call-sawfish-62.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:56][sawfish][INFO] Writing all contig alignments to bam file: 'm84036_250809_035451_s4.bc2159_sawfish_discover/contig.alignment.bam'
2025-09-15 20:26:11.104 wdl.w:ptcp.w:call-sawfish-62.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:56][sawfish][INFO] Writing candidate structural variants to file: 'm84036_250809_035451_s4.bc2159_sawfish_discover/candidate.sv.bcf'
2025-09-15 20:26:11.104 wdl.w:ptcp.w:call-sawfish-62.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:56][sawfish][INFO] Writing run statistics to file: 'm84036_250809_035451_s4.bc2159_sawfish_discover/run.stats.json'
2025-09-15 20:26:11.104 wdl.w:ptcp.w:call-sawfish-62.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:56][sawfish][INFO] sawfish completed. Total Runtime: 00:00:07.652
2025-09-15 20:26:11.104 wdl.w:ptcp.w:call-sawfish-62.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:56][sawfish][INFO] Starting sawfish 2.0.3
2025-09-15 20:26:11.104 wdl.w:ptcp.w:call-sawfish-62.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:56][sawfish][INFO] cmdline: sawfish joint-call --threads 16 --sample m84036_250809_035451_s4.bc2159_sawfish_discover --output-dir m84036_250809_035451_s4.bc2159_sawfish
2025-09-15 20:26:11.104 wdl.w:ptcp.w:call-sawfish-62.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:56][sawfish][INFO] Running on 16 threads
2025-09-15 20:26:11.105 wdl.w:ptcp.w:call-sawfish-62.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:56][sawfish][INFO] Reading reference genome from file '/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa'
2025-09-15 20:26:11.156 wdl.w:ptcp.t:call-tar_outputs-23 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 17, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-23/_singularity_tmpdir_es8yxm4j"
2025-09-15 20:26:11.156 wdl.w:ptcp.t:call-tar_outputs-23 INFO Slurm invocation: srun --job-name call-tar_outputs-23 --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-23/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-23/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-23/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-23/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-23/out/m84036_250809_035451_s4.bc2120.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2120.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-23/out/m84036_250809_035451_s4.bc2120.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2120.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-23/out/m84036_250809_035451_s4.bc2120.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2120.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-23/out/m84036_250809_035451_s4.bc2120_paraphase/m84036_250809_035451_s4.bc2120.paraphase.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2120.paraphase.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-23/out/m84036_250809_035451_s4.bc2120_paraphase/m84036_250809_035451_s4.bc2120.paraphase.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2120.paraphase.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-23/out/m84036_250809_035451_s4.bc2120_paraphase/m84036_250809_035451_s4.bc2120.paraphase.json:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2120.paraphase.json:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-23/out/m84036_250809_035451_s4.bc2120.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2120.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-23/out/m84036_250809_035451_s4.bc2120.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2120.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-23/out/m84036_250809_035451_s4.bc2120_sawfish/m84036_250809_035451_s4.bc2120.sv.vcf.gz.tbi:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2120.sv.vcf.gz.tbi:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-23/out/m84036_250809_035451_s4.bc2120_sawfish/m84036_250809_035451_s4.bc2120.sv.vcf.gz:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2120.sv.vcf.gz:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-23/out/m84036_250809_035451_s4.bc2120.f8inversion.json:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2120.f8inversion.json:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-23/_singularity_tmpdir_es8yxm4j/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-23/_singularity_tmpdir_es8yxm4j/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:26:11.173 wdl.w:ptcp.t:call-tar_outputs-23 NOTICE slurm_singularity run :: pid: 1207279, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-23/slurm_singularity.log.txt"
2025-09-15 20:26:11.173 wdl.w:ptcp.w:call-trgt-90.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:26:10 [ERROR] - No reads found for TRID=SCA37_DAB1
2025-09-15 20:26:11.173 wdl.w:ptcp.w:call-trgt-90.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:26:10 [ERROR] - No reads found for TRID=NIID_NOTCH2NLC
2025-09-15 20:26:11.173 wdl.w:ptcp.w:call-trgt-90.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:26:10 [ERROR] - No reads found for TRID=SCA8_ATXN8OS
2025-09-15 20:26:11.173 wdl.w:ptcp.w:call-trgt-90.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:26:11 [ERROR] - No reads found for TRID=SCA27B_FGF14
2025-09-15 20:26:11.173 wdl.w:ptcp.w:call-trgt-90.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:26:11 [ERROR] - No reads found for TRID=OPDM4_RILPL1
2025-09-15 20:26:11.174 wdl.w:ptcp.w:call-trgt-90.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:26:11 [ERROR] - No reads found for TRID=SCA3_ATXN3
2025-09-15 20:26:11.177 wdl.w:ptcp.w:call-trgt-93.t:call-trgt_plot_motifs_allele NOTICE done
2025-09-15 20:26:11.182 wdl.w:ptcp.w:call-trgt-93 NOTICE finish :: job: "call-trgt_plot_motifs_allele"
2025-09-15 20:26:11.182 wdl.w:ptcp.w:call-trgt-93 INFO output :: job: "call-trgt_plot_motifs_allele", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-93/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2190.motifs_allele.trgt_plots.zip"}
2025-09-15 20:26:11.183 wdl.w:ptcp.w:call-trgt-93 INFO visit :: node: "output-images_motifs_allele", values: {"images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-93/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2190.motifs_allele.trgt_plots.zip"}
2025-09-15 20:26:11.188 wdl.w:ptcp.w:call-trgt-90.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO srun: job 51798166 queued and waiting for resources
2025-09-15 20:26:11.188 wdl.w:ptcp.w:call-trgt-90.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO srun: job 51798166 has been allocated resources
2025-09-15 20:26:11.188 wdl.w:ptcp.w:call-trgt-90.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:26:11.189 wdl.w:ptcp.w:call-trgt-86.t:call-trgt_plot_meth_allele NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-86/call-trgt_plot_meth_allele", thread: 140608731588160
2025-09-15 20:26:11.205 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:26:08 [ERROR] - No reads found for TRID=SCA37_DAB1
2025-09-15 20:26:11.205 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:26:08 [ERROR] - No reads found for TRID=OPDM4_RILPL1
2025-09-15 20:26:11.205 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:26:08 [ERROR] - No reads found for TRID=DRPLA_ATN1
2025-09-15 20:26:11.205 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:26:08 [ERROR] - No reads found for TRID=SCA2_ATXN2
2025-09-15 20:26:11.206 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:26:08 [ERROR] - No reads found for TRID=OPMD_PABPN1
2025-09-15 20:26:11.206 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:26:08 [ERROR] - No reads found for TRID=SCA31_BEAN1
2025-09-15 20:26:11.206 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:26:08 [ERROR] - No reads found for TRID=SCA4_ZFHX3
2025-09-15 20:26:11.206 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:26:08 [ERROR] - No reads found for TRID=SCA27B_FGF14
2025-09-15 20:26:11.206 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:26:08 [ERROR] - No reads found for TRID=FECD3_TCF4
2025-09-15 20:26:11.206 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:26:08 [ERROR] - No reads found for TRID=SCA6_CACNA1A
2025-09-15 20:26:11.206 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:26:09 [ERROR] - No reads found for TRID=OPDM2_GIPC1
2025-09-15 20:26:11.206 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:26:09 [ERROR] - No reads found for TRID=DM1_DMPK
2025-09-15 20:26:11.206 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:26:09 [ERROR] - No reads found for TRID=FRA2A_AFF3
2025-09-15 20:26:11.206 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:26:09 [ERROR] - No reads found for TRID=SD5_HOXD13
2025-09-15 20:26:11.207 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:26:09 [ERROR] - No reads found for TRID=SCA36_NOP56
2025-09-15 20:26:11.207 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:26:09 [ERROR] - No reads found for TRID=CJD_PRNP
2025-09-15 20:26:11.207 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:26:09 [ERROR] - No reads found for TRID=EPM1_CSTB
2025-09-15 20:26:11.207 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:26:10 [ERROR] - No reads found for TRID=SCA3_ATXN3
2025-09-15 20:26:11.207 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:26:10 [ERROR] - No reads found for TRID=HDL2_JPH3
2025-09-15 20:26:11.207 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:26:10 [ERROR] - No reads found for TRID=CANVAS_RFC1
2025-09-15 20:26:11.207 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:26:11 [ERROR] - No reads found for TRID=SCA12_PPP2R2B
2025-09-15 20:26:11.211 wdl.w:ptcp.w:call-trgt-86.t:call-trgt_plot_meth_allele INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:26:11.211 wdl.w:ptcp.w:call-trgt-86.t:call-trgt_plot_meth_allele INFO input :: name: "waterfall", value: false
2025-09-15 20:26:11.211 wdl.w:ptcp.w:call-trgt-86.t:call-trgt_plot_meth_allele INFO input :: name: "methylation", value: true
2025-09-15 20:26:11.211 wdl.w:ptcp.w:call-trgt-86.t:call-trgt_plot_meth_allele INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:26:11.211 wdl.w:ptcp.w:call-trgt-86.t:call-trgt_plot_meth_allele INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:26:11.212 wdl.w:ptcp.w:call-trgt-86.t:call-trgt_plot_meth_allele INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:26:11.212 wdl.w:ptcp.w:call-trgt-86.t:call-trgt_plot_meth_allele INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2183.trgt.sorted.spanning.bam.bai"
2025-09-15 20:26:11.212 wdl.w:ptcp.w:call-trgt-86.t:call-trgt_plot_meth_allele INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2183.trgt.sorted.spanning.bam"
2025-09-15 20:26:11.212 wdl.w:ptcp.w:call-trgt-86.t:call-trgt_plot_meth_allele INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2183.trgt.vcf"
2025-09-15 20:26:11.212 wdl.w:ptcp.w:call-trgt-86.t:call-trgt_plot_meth_allele INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2183"
2025-09-15 20:26:11.212 wdl.w:ptcp.w:call-trgt-86.t:call-trgt_plot_meth_allele INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:26:11.212 wdl.w:ptcp.w:call-trgt-86.t:call-trgt_plot_meth_allele INFO eval :: name: "plot_type", value: "allele"
2025-09-15 20:26:11.212 wdl.w:ptcp.w:call-trgt-86.t:call-trgt_plot_meth_allele INFO eval :: name: "show", value: "meth"
2025-09-15 20:26:11.213 wdl.w:ptcp.w:call-trgt-86.t:call-trgt_plot_meth_allele INFO eval :: name: "threads", value: 1
2025-09-15 20:26:11.213 wdl.w:ptcp.w:call-trgt-86.t:call-trgt_plot_meth_allele INFO eval :: name: "disk_size", value: 27
2025-09-15 20:26:11.213 wdl.w:ptcp.w:call-trgt-86.t:call-trgt_plot_meth_allele INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2183.meth_allele"
2025-09-15 20:26:11.213 wdl.w:ptcp.w:call-trgt-86.t:call-trgt_plot_meth_allele INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:26:11.213 wdl.w:ptcp.w:call-trgt-86.t:call-trgt_plot_meth_allele WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:26:11.214 wdl.w:ptcp.w:call-trgt-86.t:call-trgt_plot_meth_allele INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:26:11.214 wdl.w:ptcp.w:call-trgt-86.t:call-trgt_plot_meth_allele INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:26:11.257 wdl.w:ptcp.t:call-tar_outputs-53.stderr VERBOSE tar: Removing leading `/' from member names
2025-09-15 20:26:11.257 wdl.w:ptcp.t:call-tar_outputs-53.stderr VERBOSE tar: Removing leading `/' from hard link targets
2025-09-15 20:26:11.266 wdl.w:ptcp.t:call-tar_outputs-53.slurm_singularity INFO srun: job 51798167 queued and waiting for resources
2025-09-15 20:26:11.266 wdl.w:ptcp.t:call-tar_outputs-53.slurm_singularity INFO srun: job 51798167 has been allocated resources
2025-09-15 20:26:11.266 wdl.w:ptcp.t:call-tar_outputs-53.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:26:11.293 wdl.w:ptcp.w:call-trgt-86.t:call-trgt_plot_meth_allele INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-86/call-trgt_plot_meth_allele/_singularity_tmpdir_ei1kl1dn"
2025-09-15 20:26:11.293 wdl.w:ptcp.w:call-trgt-86.t:call-trgt_plot_meth_allele INFO Slurm invocation: srun --job-name call-trgt_plot_meth_allele --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-86/call-trgt_plot_meth_allele/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-86/call-trgt_plot_meth_allele/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-86/call-trgt_plot_meth_allele/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-86/call-trgt_plot_meth_allele/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-86/call-trgt_genotype/out/m84036_250809_035451_s4.bc2183.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2183.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-86/call-trgt_genotype/out/m84036_250809_035451_s4.bc2183.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2183.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-86/call-trgt_genotype/out/m84036_250809_035451_s4.bc2183.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2183.trgt.sorted.spanning.bam.bai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-86/call-trgt_plot_meth_allele/_singularity_tmpdir_ei1kl1dn/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-86/call-trgt_plot_meth_allele/_singularity_tmpdir_ei1kl1dn/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:26:11.302 wdl.w:ptcp.t:call-tar_outputs-53 INFO output :: name: "sample_tarball", value: "m84036_250809_035451_s4.bc2150.tar"
2025-09-15 20:26:11.303 wdl.w:ptcp.w:call-paraphase-07.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for hbb for sample m84036_250809_035451_s4.bc2104 at 2025-09-15 20:25:24.125513...
2025-09-15 20:26:11.303 wdl.w:ptcp.w:call-paraphase-07.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for hbb for sample m84036_250809_035451_s4.bc2104 at 2025-09-15 20:25:24.662998...
2025-09-15 20:26:11.325 wdl.w:ptcp.w:call-trgt-86.t:call-trgt_plot_meth_allele NOTICE slurm_singularity run :: pid: 1207297, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-86/call-trgt_plot_meth_allele/slurm_singularity.log.txt"
2025-09-15 20:26:11.370 wdl.w:ptcp.t:call-tar_outputs-53 NOTICE done
2025-09-15 20:26:11.406 wdl.w:ptcp NOTICE finish :: job: "call-tar_outputs-53"
2025-09-15 20:26:11.407 wdl.w:ptcp INFO output :: job: "call-tar_outputs-53", values: {"sample_tarball": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-53/out/m84036_250809_035451_s4.bc2150.tar"}
2025-09-15 20:26:11.412 wdl.w:ptcp.w:call-trgt-86.t:call-trgt_plot_meth_waterfall NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-86/call-trgt_plot_meth_waterfall", thread: 140611944420928
2025-09-15 20:26:11.430 wdl.w:ptcp.w:call-trgt-86.t:call-trgt_plot_meth_waterfall INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:26:11.430 wdl.w:ptcp.w:call-trgt-86.t:call-trgt_plot_meth_waterfall INFO input :: name: "waterfall", value: true
2025-09-15 20:26:11.430 wdl.w:ptcp.w:call-trgt-86.t:call-trgt_plot_meth_waterfall INFO input :: name: "methylation", value: true
2025-09-15 20:26:11.430 wdl.w:ptcp.w:call-trgt-86.t:call-trgt_plot_meth_waterfall INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:26:11.430 wdl.w:ptcp.w:call-trgt-86.t:call-trgt_plot_meth_waterfall INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:26:11.430 wdl.w:ptcp.w:call-trgt-86.t:call-trgt_plot_meth_waterfall INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:26:11.430 wdl.w:ptcp.w:call-trgt-86.t:call-trgt_plot_meth_waterfall INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2183.trgt.sorted.spanning.bam.bai"
2025-09-15 20:26:11.430 wdl.w:ptcp.w:call-trgt-86.t:call-trgt_plot_meth_waterfall INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2183.trgt.sorted.spanning.bam"
2025-09-15 20:26:11.430 wdl.w:ptcp.w:call-trgt-86.t:call-trgt_plot_meth_waterfall INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2183.trgt.vcf"
2025-09-15 20:26:11.430 wdl.w:ptcp.w:call-trgt-86.t:call-trgt_plot_meth_waterfall INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2183"
2025-09-15 20:26:11.430 wdl.w:ptcp.w:call-trgt-86.t:call-trgt_plot_meth_waterfall INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:26:11.430 wdl.w:ptcp.w:call-trgt-86.t:call-trgt_plot_meth_waterfall INFO eval :: name: "plot_type", value: "waterfall"
2025-09-15 20:26:11.431 wdl.w:ptcp.w:call-trgt-86.t:call-trgt_plot_meth_waterfall INFO eval :: name: "show", value: "meth"
2025-09-15 20:26:11.431 wdl.w:ptcp.w:call-trgt-86.t:call-trgt_plot_meth_waterfall INFO eval :: name: "threads", value: 1
2025-09-15 20:26:11.431 wdl.w:ptcp.w:call-trgt-86.t:call-trgt_plot_meth_waterfall INFO eval :: name: "disk_size", value: 27
2025-09-15 20:26:11.431 wdl.w:ptcp.w:call-trgt-86.t:call-trgt_plot_meth_waterfall INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2183.meth_waterfall"
2025-09-15 20:26:11.431 wdl.w:ptcp.w:call-trgt-86.t:call-trgt_plot_meth_waterfall INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:26:11.431 wdl.w:ptcp.w:call-trgt-86.t:call-trgt_plot_meth_waterfall WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:26:11.432 wdl.w:ptcp.w:call-trgt-86.t:call-trgt_plot_meth_waterfall INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:26:11.432 wdl.w:ptcp.w:call-trgt-86.t:call-trgt_plot_meth_waterfall INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:26:11.494 wdl.w:ptcp.w:call-trgt-86.t:call-trgt_plot_meth_waterfall INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-86/call-trgt_plot_meth_waterfall/_singularity_tmpdir_1xgd98vj"
2025-09-15 20:26:11.494 wdl.w:ptcp.w:call-trgt-86.t:call-trgt_plot_meth_waterfall INFO Slurm invocation: srun --job-name call-trgt_plot_meth_waterfall --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-86/call-trgt_plot_meth_waterfall/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-86/call-trgt_plot_meth_waterfall/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-86/call-trgt_plot_meth_waterfall/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-86/call-trgt_plot_meth_waterfall/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-86/call-trgt_genotype/out/m84036_250809_035451_s4.bc2183.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2183.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-86/call-trgt_genotype/out/m84036_250809_035451_s4.bc2183.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2183.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-86/call-trgt_genotype/out/m84036_250809_035451_s4.bc2183.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2183.trgt.sorted.spanning.bam.bai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-86/call-trgt_plot_meth_waterfall/_singularity_tmpdir_1xgd98vj/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-86/call-trgt_plot_meth_waterfall/_singularity_tmpdir_1xgd98vj/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:26:11.506 wdl.w:ptcp.w:call-trgt-86.t:call-trgt_plot_meth_waterfall NOTICE slurm_singularity run :: pid: 1207300, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-86/call-trgt_plot_meth_waterfall/slurm_singularity.log.txt"
2025-09-15 20:26:11.507 wdl.w:ptcp.t:call-tar_outputs-49.slurm_singularity INFO srun: job 51798168 queued and waiting for resources
2025-09-15 20:26:11.507 wdl.w:ptcp.t:call-tar_outputs-49.slurm_singularity INFO srun: job 51798168 has been allocated resources
2025-09-15 20:26:11.507 wdl.w:ptcp.t:call-tar_outputs-49.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:26:11.566 wdl.w:ptcp.t:call-tar_outputs-68.slurm_singularity INFO srun: job 51798169 queued and waiting for resources
2025-09-15 20:26:11.566 wdl.w:ptcp.t:call-tar_outputs-68.slurm_singularity INFO srun: job 51798169 has been allocated resources
2025-09-15 20:26:11.566 wdl.w:ptcp.t:call-tar_outputs-68.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:26:11.579 wdl.w:ptcp.t:call-tar_outputs-64 INFO output :: name: "sample_tarball", value: "m84036_250809_035451_s4.bc2161.tar"
2025-09-15 20:26:11.594 wdl.w:ptcp.t:call-tar_outputs-40 INFO output :: name: "sample_tarball", value: "m84036_250809_035451_s4.bc2137.tar"
2025-09-15 20:26:11.673 wdl.w:ptcp.t:call-tar_outputs-64 NOTICE done
2025-09-15 20:26:11.676 wdl.w:ptcp.t:call-tar_outputs-40 NOTICE done
2025-09-15 20:26:11.678 wdl.w:ptcp NOTICE finish :: job: "call-tar_outputs-64"
2025-09-15 20:26:11.679 wdl.w:ptcp INFO output :: job: "call-tar_outputs-64", values: {"sample_tarball": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-64/out/m84036_250809_035451_s4.bc2161.tar"}
2025-09-15 20:26:11.681 wdl.w:ptcp NOTICE finish :: job: "call-tar_outputs-40"
2025-09-15 20:26:11.682 wdl.w:ptcp INFO output :: job: "call-tar_outputs-40", values: {"sample_tarball": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-40/out/m84036_250809_035451_s4.bc2137.tar"}
2025-09-15 20:26:11.684 wdl.w:ptcp.w:call-trgt-86.t:call-trgt_plot_motifs_allele NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-86/call-trgt_plot_motifs_allele", thread: 140607683024448
2025-09-15 20:26:11.687 wdl.w:ptcp.w:call-trgt-86.t:call-trgt_plot_motifs_waterfall NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-86/call-trgt_plot_motifs_waterfall", thread: 140613043340864
2025-09-15 20:26:11.709 wdl.w:ptcp.w:call-trgt-86.t:call-trgt_plot_motifs_allele INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:26:11.709 wdl.w:ptcp.w:call-trgt-86.t:call-trgt_plot_motifs_allele INFO input :: name: "waterfall", value: false
2025-09-15 20:26:11.709 wdl.w:ptcp.w:call-trgt-86.t:call-trgt_plot_motifs_allele INFO input :: name: "methylation", value: false
2025-09-15 20:26:11.709 wdl.w:ptcp.w:call-trgt-86.t:call-trgt_plot_motifs_allele INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:26:11.709 wdl.w:ptcp.w:call-trgt-86.t:call-trgt_plot_motifs_allele INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:26:11.709 wdl.w:ptcp.w:call-trgt-86.t:call-trgt_plot_motifs_allele INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:26:11.709 wdl.w:ptcp.w:call-trgt-86.t:call-trgt_plot_motifs_allele INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2183.trgt.sorted.spanning.bam.bai"
2025-09-15 20:26:11.709 wdl.w:ptcp.w:call-trgt-86.t:call-trgt_plot_motifs_allele INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2183.trgt.sorted.spanning.bam"
2025-09-15 20:26:11.709 wdl.w:ptcp.w:call-trgt-86.t:call-trgt_plot_motifs_allele INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2183.trgt.vcf"
2025-09-15 20:26:11.709 wdl.w:ptcp.w:call-trgt-86.t:call-trgt_plot_motifs_allele INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2183"
2025-09-15 20:26:11.709 wdl.w:ptcp.w:call-trgt-86.t:call-trgt_plot_motifs_allele INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:26:11.710 wdl.w:ptcp.w:call-trgt-86.t:call-trgt_plot_motifs_allele INFO eval :: name: "plot_type", value: "allele"
2025-09-15 20:26:11.710 wdl.w:ptcp.w:call-trgt-86.t:call-trgt_plot_motifs_allele INFO eval :: name: "show", value: "motifs"
2025-09-15 20:26:11.710 wdl.w:ptcp.w:call-trgt-86.t:call-trgt_plot_motifs_allele INFO eval :: name: "threads", value: 1
2025-09-15 20:26:11.710 wdl.w:ptcp.w:call-trgt-86.t:call-trgt_plot_motifs_allele INFO eval :: name: "disk_size", value: 27
2025-09-15 20:26:11.710 wdl.w:ptcp.w:call-trgt-86.t:call-trgt_plot_motifs_allele INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2183.motifs_allele"
2025-09-15 20:26:11.711 wdl.w:ptcp.w:call-trgt-86.t:call-trgt_plot_motifs_allele INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:26:11.711 wdl.w:ptcp.w:call-trgt-86.t:call-trgt_plot_motifs_allele WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:26:11.711 wdl.w:ptcp.w:call-trgt-86.t:call-trgt_plot_motifs_allele INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:26:11.711 wdl.w:ptcp.w:call-trgt-86.t:call-trgt_plot_motifs_allele INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:26:11.711 wdl.w:ptcp.w:call-trgt-86.t:call-trgt_plot_motifs_waterfall INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:26:11.712 wdl.w:ptcp.w:call-trgt-86.t:call-trgt_plot_motifs_waterfall INFO input :: name: "waterfall", value: true
2025-09-15 20:26:11.712 wdl.w:ptcp.w:call-trgt-86.t:call-trgt_plot_motifs_waterfall INFO input :: name: "methylation", value: false
2025-09-15 20:26:11.712 wdl.w:ptcp.w:call-trgt-86.t:call-trgt_plot_motifs_waterfall INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:26:11.712 wdl.w:ptcp.w:call-trgt-86.t:call-trgt_plot_motifs_waterfall INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:26:11.712 wdl.w:ptcp.w:call-trgt-86.t:call-trgt_plot_motifs_waterfall INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:26:11.712 wdl.w:ptcp.w:call-trgt-86.t:call-trgt_plot_motifs_waterfall INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2183.trgt.sorted.spanning.bam.bai"
2025-09-15 20:26:11.712 wdl.w:ptcp.w:call-trgt-86.t:call-trgt_plot_motifs_waterfall INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2183.trgt.sorted.spanning.bam"
2025-09-15 20:26:11.712 wdl.w:ptcp.w:call-trgt-86.t:call-trgt_plot_motifs_waterfall INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2183.trgt.vcf"
2025-09-15 20:26:11.712 wdl.w:ptcp.w:call-trgt-86.t:call-trgt_plot_motifs_waterfall INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2183"
2025-09-15 20:26:11.712 wdl.w:ptcp.w:call-trgt-86.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:26:11.712 wdl.w:ptcp.w:call-trgt-86.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "plot_type", value: "waterfall"
2025-09-15 20:26:11.712 wdl.w:ptcp.w:call-trgt-86.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "show", value: "motifs"
2025-09-15 20:26:11.713 wdl.w:ptcp.w:call-trgt-86.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "threads", value: 1
2025-09-15 20:26:11.713 wdl.w:ptcp.w:call-trgt-86.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "disk_size", value: 27
2025-09-15 20:26:11.713 wdl.w:ptcp.w:call-trgt-86.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2183.motifs_waterfall"
2025-09-15 20:26:11.713 wdl.w:ptcp.w:call-trgt-86.t:call-trgt_plot_motifs_waterfall INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:26:11.713 wdl.w:ptcp.w:call-trgt-86.t:call-trgt_plot_motifs_waterfall WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:26:11.714 wdl.w:ptcp.w:call-trgt-86.t:call-trgt_plot_motifs_waterfall INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:26:11.714 wdl.w:ptcp.w:call-trgt-86.t:call-trgt_plot_motifs_waterfall INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:26:11.797 wdl.w:ptcp.w:call-trgt-86.t:call-trgt_plot_motifs_allele INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-86/call-trgt_plot_motifs_allele/_singularity_tmpdir_dmd8yzxh"
2025-09-15 20:26:11.797 wdl.w:ptcp.w:call-trgt-86.t:call-trgt_plot_motifs_allele INFO Slurm invocation: srun --job-name call-trgt_plot_motifs_allele --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-86/call-trgt_plot_motifs_allele/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-86/call-trgt_plot_motifs_allele/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-86/call-trgt_plot_motifs_allele/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-86/call-trgt_plot_motifs_allele/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-86/call-trgt_genotype/out/m84036_250809_035451_s4.bc2183.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2183.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-86/call-trgt_genotype/out/m84036_250809_035451_s4.bc2183.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2183.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-86/call-trgt_genotype/out/m84036_250809_035451_s4.bc2183.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2183.trgt.sorted.spanning.bam.bai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-86/call-trgt_plot_motifs_allele/_singularity_tmpdir_dmd8yzxh/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-86/call-trgt_plot_motifs_allele/_singularity_tmpdir_dmd8yzxh/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:26:11.807 wdl.w:ptcp.w:call-trgt-86.t:call-trgt_plot_motifs_waterfall INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-86/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_xjk07xuz"
2025-09-15 20:26:11.807 wdl.w:ptcp.w:call-trgt-86.t:call-trgt_plot_motifs_waterfall INFO Slurm invocation: srun --job-name call-trgt_plot_motifs_waterfall --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-86/call-trgt_plot_motifs_waterfall/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-86/call-trgt_plot_motifs_waterfall/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-86/call-trgt_plot_motifs_waterfall/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-86/call-trgt_plot_motifs_waterfall/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-86/call-trgt_genotype/out/m84036_250809_035451_s4.bc2183.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2183.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-86/call-trgt_genotype/out/m84036_250809_035451_s4.bc2183.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2183.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-86/call-trgt_genotype/out/m84036_250809_035451_s4.bc2183.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2183.trgt.sorted.spanning.bam.bai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-86/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_xjk07xuz/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-86/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_xjk07xuz/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:26:11.818 wdl.w:ptcp.t:call-tar_outputs-15.stderr VERBOSE tar: Removing leading `/' from member names
2025-09-15 20:26:11.818 wdl.w:ptcp.t:call-tar_outputs-15.stderr VERBOSE tar: Removing leading `/' from hard link targets
2025-09-15 20:26:11.818 wdl.w:ptcp.w:call-trgt-86.t:call-trgt_plot_motifs_waterfall NOTICE slurm_singularity run :: pid: 1207317, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-86/call-trgt_plot_motifs_waterfall/slurm_singularity.log.txt"
2025-09-15 20:26:11.818 wdl.w:ptcp.w:call-trgt-86.t:call-trgt_plot_motifs_allele NOTICE slurm_singularity run :: pid: 1207315, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-86/call-trgt_plot_motifs_allele/slurm_singularity.log.txt"
2025-09-15 20:26:11.832 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:26:08 [ERROR] - No reads found for TRID=OPDM_ABCD3
2025-09-15 20:26:11.832 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:26:09 [ERROR] - No reads found for TRID=SCA37_DAB1
2025-09-15 20:26:11.832 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:26:09 [ERROR] - No reads found for TRID=NIID_NOTCH2NLC
2025-09-15 20:26:11.833 wdl.w:ptcp.t:call-tar_outputs-15.slurm_singularity INFO srun: job 51798170 queued and waiting for resources
2025-09-15 20:26:11.833 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:26:09 [ERROR] - No reads found for TRID=OPDM4_RILPL1
2025-09-15 20:26:11.833 wdl.w:ptcp.t:call-tar_outputs-15.slurm_singularity INFO srun: job 51798170 has been allocated resources
2025-09-15 20:26:11.833 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:26:09 [ERROR] - No reads found for TRID=SCA8_ATXN8OS
2025-09-15 20:26:11.833 wdl.w:ptcp.t:call-tar_outputs-15.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:26:11.833 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:26:09 [ERROR] - No reads found for TRID=SCA27B_FGF14
2025-09-15 20:26:11.833 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:26:09 [ERROR] - No reads found for TRID=SCA2_ATXN2
2025-09-15 20:26:11.833 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:26:09 [ERROR] - No reads found for TRID=SCA3_ATXN3
2025-09-15 20:26:11.833 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:26:10 [ERROR] - No reads found for TRID=SCA31_BEAN1
2025-09-15 20:26:11.833 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:26:10 [ERROR] - No reads found for TRID=HDL2_JPH3
2025-09-15 20:26:11.833 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:26:10 [ERROR] - No reads found for TRID=SCA6_CACNA1A
2025-09-15 20:26:11.833 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:26:10 [ERROR] - No reads found for TRID=DM1_DMPK
2025-09-15 20:26:11.833 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:26:11 [ERROR] - No reads found for TRID=OPDM2_GIPC1
2025-09-15 20:26:11.833 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:26:11 [ERROR] - No reads found for TRID=SCA4_ZFHX3
2025-09-15 20:26:11.833 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:26:11 [ERROR] - No reads found for TRID=SCA36_NOP56
2025-09-15 20:26:11.841 wdl.w:ptcp.t:call-tar_outputs-49 INFO output :: name: "sample_tarball", value: "m84036_250809_035451_s4.bc2146.tar"
2025-09-15 20:26:11.885 wdl.w:ptcp.t:call-tar_outputs-15 INFO output :: name: "sample_tarball", value: "m84036_250809_035451_s4.bc2112.tar"
2025-09-15 20:26:11.895 wdl.w:ptcp.w:call-trgt-92.t:call-trgt_plot_meth_waterfall INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2189.meth_waterfall.trgt_plots.zip"
2025-09-15 20:26:11.910 wdl.w:ptcp.t:call-tar_outputs-49 NOTICE done
2025-09-15 20:26:11.914 wdl.w:ptcp NOTICE finish :: job: "call-tar_outputs-49"
2025-09-15 20:26:11.914 wdl.w:ptcp INFO output :: job: "call-tar_outputs-49", values: {"sample_tarball": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-49/out/m84036_250809_035451_s4.bc2146.tar"}
2025-09-15 20:26:11.920 wdl.w:ptcp.t:call-tar_outputs-57 NOTICE task setup :: name: "tar_outputs", source: "./common.wdl", line: 279, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-57", thread: 140613034948160
2025-09-15 20:26:11.950 wdl.w:ptcp.t:call-tar_outputs-57 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:26:11.950 wdl.w:ptcp.t:call-tar_outputs-57 INFO input :: name: "sawfish_vcf_tbi", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2154.sv.vcf.gz.tbi"
2025-09-15 20:26:11.951 wdl.w:ptcp.t:call-tar_outputs-57 INFO input :: name: "sawfish_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2154.sv.vcf.gz"
2025-09-15 20:26:11.951 wdl.w:ptcp.t:call-tar_outputs-57 INFO input :: name: "f8_json", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2154.f8inversion.json"
2025-09-15 20:26:11.951 wdl.w:ptcp.t:call-tar_outputs-57 INFO input :: name: "paraphase_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2154.paraphase.bam.bai"
2025-09-15 20:26:11.951 wdl.w:ptcp.t:call-tar_outputs-57 INFO input :: name: "paraphase_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2154.paraphase.bam"
2025-09-15 20:26:11.951 wdl.w:ptcp.t:call-tar_outputs-57 INFO input :: name: "paraphase_json", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2154.paraphase.json"
2025-09-15 20:26:11.951 wdl.w:ptcp.t:call-tar_outputs-57 INFO input :: name: "trgt_spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2154.trgt.sorted.spanning.bam.bai"
2025-09-15 20:26:11.951 wdl.w:ptcp.t:call-tar_outputs-57 INFO input :: name: "trgt_spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2154.trgt.sorted.spanning.bam"
2025-09-15 20:26:11.951 wdl.w:ptcp.t:call-tar_outputs-57 INFO input :: name: "trgt_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2154.trgt.vcf"
2025-09-15 20:26:11.951 wdl.w:ptcp.t:call-tar_outputs-57 INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2154.mapped.bam.bai"
2025-09-15 20:26:11.951 wdl.w:ptcp.t:call-tar_outputs-57 INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2154.mapped.bam"
2025-09-15 20:26:11.951 wdl.w:ptcp.t:call-tar_outputs-57 INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2154"
2025-09-15 20:26:11.951 wdl.w:ptcp.t:call-tar_outputs-57 INFO eval :: name: "threads", value: 1
2025-09-15 20:26:11.951 wdl.w:ptcp.t:call-tar_outputs-57 INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:26:11.952 wdl.w:ptcp.t:call-tar_outputs-57 INFO eval :: name: "disk_size", value: 6
2025-09-15 20:26:11.952 wdl.w:ptcp.t:call-tar_outputs-57 INFO eval :: name: "output_tarball", value: "m84036_250809_035451_s4.bc2154.tar"
2025-09-15 20:26:11.952 wdl.w:ptcp.t:call-tar_outputs-57 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:26:11.952 wdl.w:ptcp.t:call-tar_outputs-57 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:26:11.953 wdl.w:ptcp.t:call-tar_outputs-57 INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:26:11.953 wdl.w:ptcp.t:call-tar_outputs-57 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:26:11.959 wdl.w:ptcp.t:call-tar_outputs-15 NOTICE done
2025-09-15 20:26:11.966 wdl.w:ptcp NOTICE finish :: job: "call-tar_outputs-15"
2025-09-15 20:26:11.966 wdl.w:ptcp INFO output :: job: "call-tar_outputs-15", values: {"sample_tarball": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-15/out/m84036_250809_035451_s4.bc2112.tar"}
2025-09-15 20:26:11.972 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_meth_allele NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-83/call-trgt_plot_meth_allele", thread: 140607649453632
2025-09-15 20:26:11.977 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:26:09 [ERROR] - No reads found for TRID=OPDM_ABCD3
2025-09-15 20:26:11.978 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:26:09 [ERROR] - No reads found for TRID=SCA37_DAB1
2025-09-15 20:26:11.978 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:26:09 [ERROR] - No reads found for TRID=NIID_NOTCH2NLC
2025-09-15 20:26:11.978 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:26:09 [ERROR] - No reads found for TRID=OPDM4_RILPL1
2025-09-15 20:26:11.978 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:26:10 [ERROR] - No reads found for TRID=SCA8_ATXN8OS
2025-09-15 20:26:11.978 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:26:10 [ERROR] - No reads found for TRID=SCA27B_FGF14
2025-09-15 20:26:11.978 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:26:10 [ERROR] - No reads found for TRID=SCA2_ATXN2
2025-09-15 20:26:11.978 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:26:11 [ERROR] - No reads found for TRID=SCA3_ATXN3
2025-09-15 20:26:11.978 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:26:11 [ERROR] - No reads found for TRID=SCA31_BEAN1
2025-09-15 20:26:11.978 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:26:11 [ERROR] - No reads found for TRID=HDL2_JPH3
2025-09-15 20:26:11.978 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:26:11 [ERROR] - No reads found for TRID=SCA6_CACNA1A
2025-09-15 20:26:11.978 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:26:11 [ERROR] - No reads found for TRID=DM1_DMPK
2025-09-15 20:26:11.978 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:26:11 [ERROR] - No reads found for TRID=OPDM2_GIPC1
2025-09-15 20:26:12.016 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_meth_allele INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:26:12.016 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_meth_allele INFO input :: name: "waterfall", value: false
2025-09-15 20:26:12.016 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_meth_allele INFO input :: name: "methylation", value: true
2025-09-15 20:26:12.017 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_meth_allele INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:26:12.017 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_meth_allele INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:26:12.017 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_meth_allele INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:26:12.017 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_meth_allele INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2180.trgt.sorted.spanning.bam.bai"
2025-09-15 20:26:12.017 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_meth_allele INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2180.trgt.sorted.spanning.bam"
2025-09-15 20:26:12.017 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_meth_allele INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2180.trgt.vcf"
2025-09-15 20:26:12.017 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_meth_allele INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2180"
2025-09-15 20:26:12.017 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_meth_allele INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:26:12.017 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_meth_allele INFO eval :: name: "plot_type", value: "allele"
2025-09-15 20:26:12.017 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_meth_allele INFO eval :: name: "show", value: "meth"
2025-09-15 20:26:12.018 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_meth_allele INFO eval :: name: "threads", value: 1
2025-09-15 20:26:12.018 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_meth_allele INFO eval :: name: "disk_size", value: 27
2025-09-15 20:26:12.018 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_meth_allele INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2180.meth_allele"
2025-09-15 20:26:12.018 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_meth_allele INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:26:12.018 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_meth_allele WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:26:12.019 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_meth_allele INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:26:12.019 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_meth_allele INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:26:12.052 wdl.w:ptcp.w:call-trgt-92.t:call-trgt_plot_meth_waterfall NOTICE done
2025-09-15 20:26:12.057 wdl.w:ptcp.w:call-trgt-92 NOTICE finish :: job: "call-trgt_plot_meth_waterfall"
2025-09-15 20:26:12.057 wdl.w:ptcp.w:call-trgt-92 INFO output :: job: "call-trgt_plot_meth_waterfall", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-92/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2189.meth_waterfall.trgt_plots.zip"}
2025-09-15 20:26:12.058 wdl.w:ptcp.w:call-trgt-92 INFO visit :: node: "output-images_meth_waterfall", values: {"images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-92/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2189.meth_waterfall.trgt_plots.zip"}
2025-09-15 20:26:12.058 wdl.w:ptcp.w:call-trgt-92 INFO visit :: node: "outputs", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-92/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2189.motifs_waterfall.trgt_plots.zip", "images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-92/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2189.meth_allele.trgt_plots.zip", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-92/call-trgt_genotype/out/m84036_250809_035451_s4.bc2189.trgt.sorted.spanning.bam.bai", "images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-92/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2189.motifs_allele.trgt_plots.zip", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-92/call-trgt_genotype/out/m84036_250809_035451_s4.bc2189.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-92/call-trgt_genotype/out/m84036_250809_035451_s4.bc2189.trgt.vcf", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-92/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2189.repeats.bam", "images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-92/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2189.meth_waterfall.trgt_plots.zip", "reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-92/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2189.repeats.bam.bai"}
2025-09-15 20:26:12.062 wdl.w:ptcp.t:call-tar_outputs-65.slurm_singularity INFO srun: job 51798171 queued and waiting for resources
2025-09-15 20:26:12.063 wdl.w:ptcp.t:call-tar_outputs-65.slurm_singularity INFO srun: job 51798171 has been allocated resources
2025-09-15 20:26:12.063 wdl.w:ptcp.t:call-tar_outputs-65.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:26:12.071 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_meth_waterfall NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-83/call-trgt_plot_meth_waterfall", thread: 140608203109952
2025-09-15 20:26:12.071 wdl.w:ptcp.t:call-tar_outputs-48.slurm_singularity INFO srun: job 51798172 queued and waiting for resources
2025-09-15 20:26:12.071 wdl.w:ptcp.t:call-tar_outputs-48.slurm_singularity INFO srun: job 51798172 has been allocated resources
2025-09-15 20:26:12.072 wdl.w:ptcp.t:call-tar_outputs-48.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:26:12.083 wdl.w:ptcp.t:call-tar_outputs-57 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 17, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-57/_singularity_tmpdir_9qnvxql7"
2025-09-15 20:26:12.084 wdl.w:ptcp.t:call-tar_outputs-57 INFO Slurm invocation: srun --job-name call-tar_outputs-57 --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-57/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-57/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-57/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-57/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-57/out/m84036_250809_035451_s4.bc2154_sawfish/m84036_250809_035451_s4.bc2154.sv.vcf.gz.tbi:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2154.sv.vcf.gz.tbi:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-57/out/m84036_250809_035451_s4.bc2154_sawfish/m84036_250809_035451_s4.bc2154.sv.vcf.gz:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2154.sv.vcf.gz:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-57/out/m84036_250809_035451_s4.bc2154.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2154.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-57/out/m84036_250809_035451_s4.bc2154.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2154.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-57/out/m84036_250809_035451_s4.bc2154.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2154.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-57/out/m84036_250809_035451_s4.bc2154_paraphase/m84036_250809_035451_s4.bc2154.paraphase.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2154.paraphase.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-57/out/m84036_250809_035451_s4.bc2154_paraphase/m84036_250809_035451_s4.bc2154.paraphase.json:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2154.paraphase.json:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-57/out/m84036_250809_035451_s4.bc2154_paraphase/m84036_250809_035451_s4.bc2154.paraphase.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2154.paraphase.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-57/out/m84036_250809_035451_s4.bc2154.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2154.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-57/out/m84036_250809_035451_s4.bc2154.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2154.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-57/out/m84036_250809_035451_s4.bc2154.f8inversion.json:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2154.f8inversion.json:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-57/_singularity_tmpdir_9qnvxql7/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-57/_singularity_tmpdir_9qnvxql7/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:26:12.092 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_meth_waterfall INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:26:12.092 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_meth_waterfall INFO input :: name: "waterfall", value: true
2025-09-15 20:26:12.092 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_meth_waterfall INFO input :: name: "methylation", value: true
2025-09-15 20:26:12.092 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_meth_waterfall INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:26:12.092 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_meth_waterfall INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:26:12.092 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_meth_waterfall INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:26:12.092 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_meth_waterfall INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2180.trgt.sorted.spanning.bam.bai"
2025-09-15 20:26:12.092 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_meth_waterfall INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2180.trgt.sorted.spanning.bam"
2025-09-15 20:26:12.092 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_meth_waterfall INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2180.trgt.vcf"
2025-09-15 20:26:12.092 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_meth_waterfall INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2180"
2025-09-15 20:26:12.092 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_meth_waterfall INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:26:12.092 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_meth_waterfall INFO eval :: name: "plot_type", value: "waterfall"
2025-09-15 20:26:12.093 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_meth_waterfall INFO eval :: name: "show", value: "meth"
2025-09-15 20:26:12.093 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_meth_waterfall INFO eval :: name: "threads", value: 1
2025-09-15 20:26:12.093 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_meth_waterfall INFO eval :: name: "disk_size", value: 27
2025-09-15 20:26:12.093 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_meth_waterfall INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2180.meth_waterfall"
2025-09-15 20:26:12.093 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_meth_waterfall INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:26:12.093 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_meth_waterfall WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:26:12.094 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_meth_waterfall INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:26:12.094 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_meth_waterfall INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:26:12.110 wdl.w:ptcp.w:call-trgt-89.t:call-trgt_plot_meth_waterfall INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2186.meth_waterfall.trgt_plots.zip"
2025-09-15 20:26:12.118 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_meth_allele INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-83/call-trgt_plot_meth_allele/_singularity_tmpdir_e9z8s0dv"
2025-09-15 20:26:12.118 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_meth_allele INFO Slurm invocation: srun --job-name call-trgt_plot_meth_allele --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-83/call-trgt_plot_meth_allele/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-83/call-trgt_plot_meth_allele/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-83/call-trgt_plot_meth_allele/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-83/call-trgt_plot_meth_allele/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-83/call-trgt_genotype/out/m84036_250809_035451_s4.bc2180.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2180.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-83/call-trgt_genotype/out/m84036_250809_035451_s4.bc2180.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2180.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-83/call-trgt_genotype/out/m84036_250809_035451_s4.bc2180.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2180.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-83/call-trgt_plot_meth_allele/_singularity_tmpdir_e9z8s0dv/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-83/call-trgt_plot_meth_allele/_singularity_tmpdir_e9z8s0dv/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:26:12.134 wdl.w:ptcp.t:call-tar_outputs-57 NOTICE slurm_singularity run :: pid: 1207332, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-57/slurm_singularity.log.txt"
2025-09-15 20:26:12.135 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_meth_allele NOTICE slurm_singularity run :: pid: 1207333, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-83/call-trgt_plot_meth_allele/slurm_singularity.log.txt"
2025-09-15 20:26:12.174 wdl.w:ptcp.w:call-trgt-92 NOTICE done
2025-09-15 20:26:12.175 wdl.w:ptcp.t:call-tar_outputs-23.stderr VERBOSE tar: Removing leading `/' from member names
2025-09-15 20:26:12.176 wdl.w:ptcp.t:call-tar_outputs-23.stderr VERBOSE tar: Removing leading `/' from hard link targets
2025-09-15 20:26:12.181 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:26:09 [ERROR] - No reads found for TRID=OPDM_ABCD3
2025-09-15 20:26:12.181 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:26:09 [ERROR] - No reads found for TRID=SCA37_DAB1
2025-09-15 20:26:12.182 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:26:09 [ERROR] - No reads found for TRID=NIID_NOTCH2NLC
2025-09-15 20:26:12.182 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:26:09 [ERROR] - No reads found for TRID=OPDM4_RILPL1
2025-09-15 20:26:12.182 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:26:10 [ERROR] - No reads found for TRID=SCA8_ATXN8OS
2025-09-15 20:26:12.182 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:26:10 [ERROR] - No reads found for TRID=SCA27B_FGF14
2025-09-15 20:26:12.182 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:26:10 [ERROR] - No reads found for TRID=SCA2_ATXN2
2025-09-15 20:26:12.182 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:26:10 [ERROR] - No reads found for TRID=SCA3_ATXN3
2025-09-15 20:26:12.182 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:26:11 [ERROR] - No reads found for TRID=SCA31_BEAN1
2025-09-15 20:26:12.182 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:26:11 [ERROR] - No reads found for TRID=HDL2_JPH3
2025-09-15 20:26:12.182 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:26:11 [ERROR] - No reads found for TRID=SCA6_CACNA1A
2025-09-15 20:26:12.182 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:26:11 [ERROR] - No reads found for TRID=DM1_DMPK
2025-09-15 20:26:12.182 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:26:11 [ERROR] - No reads found for TRID=OPDM2_GIPC1
2025-09-15 20:26:12.183 wdl.w:ptcp NOTICE finish :: job: "call-trgt-92"
2025-09-15 20:26:12.182 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_meth_waterfall INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-83/call-trgt_plot_meth_waterfall/_singularity_tmpdir_6a54gzty"
2025-09-15 20:26:12.183 wdl.w:ptcp INFO output :: job: "call-trgt-92", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-92/out/m84036_250809_035451_s4.bc2189.motifs_waterfall.trgt_plots.zip", "images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-92/out/m84036_250809_035451_s4.bc2189.meth_allele.trgt_plots.zip", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-92/out/m84036_250809_035451_s4.bc2189.trgt.sorted.spanning.bam.bai", "images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-92/out/m84036_250809_035451_s4.bc2189.motifs_allele.trgt_plots.zip", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-92/out/m84036_250809_035451_s4.bc2189.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-92/out/m84036_250809_035451_s4.bc2189.trgt.vcf", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-92/out/m84036_250809_035451_s4.bc2189.repeats.bam", "images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-92/out/m84036_250809_035451_s4.bc2189.meth_waterfall.trgt_plots.zip", "reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-92/out/m84036_250809_035451_s4.bc2189.repeats.bam.bai"}
2025-09-15 20:26:12.183 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_meth_waterfall INFO Slurm invocation: srun --job-name call-trgt_plot_meth_waterfall --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-83/call-trgt_plot_meth_waterfall/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-83/call-trgt_plot_meth_waterfall/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-83/call-trgt_plot_meth_waterfall/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-83/call-trgt_plot_meth_waterfall/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-83/call-trgt_genotype/out/m84036_250809_035451_s4.bc2180.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2180.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-83/call-trgt_genotype/out/m84036_250809_035451_s4.bc2180.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2180.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-83/call-trgt_genotype/out/m84036_250809_035451_s4.bc2180.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2180.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-83/call-trgt_plot_meth_waterfall/_singularity_tmpdir_6a54gzty/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-83/call-trgt_plot_meth_waterfall/_singularity_tmpdir_6a54gzty/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:26:12.188 wdl.w:ptcp.t:call-tar_outputs-23.slurm_singularity INFO srun: job 51798173 queued and waiting for resources
2025-09-15 20:26:12.188 wdl.w:ptcp.t:call-tar_outputs-23.slurm_singularity INFO srun: job 51798173 has been allocated resources
2025-09-15 20:26:12.188 wdl.w:ptcp.t:call-tar_outputs-23.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:26:12.204 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_meth_waterfall NOTICE slurm_singularity run :: pid: 1207336, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-83/call-trgt_plot_meth_waterfall/slurm_singularity.log.txt"
2025-09-15 20:26:12.243 wdl.w:ptcp.w:call-trgt-89.t:call-trgt_plot_meth_waterfall NOTICE done
2025-09-15 20:26:12.247 wdl.w:ptcp.w:call-trgt-89 NOTICE finish :: job: "call-trgt_plot_meth_waterfall"
2025-09-15 20:26:12.247 wdl.w:ptcp.w:call-trgt-89 INFO output :: job: "call-trgt_plot_meth_waterfall", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-89/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2186.meth_waterfall.trgt_plots.zip"}
2025-09-15 20:26:12.248 wdl.w:ptcp.w:call-trgt-89 INFO visit :: node: "output-images_meth_waterfall", values: {"images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-89/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2186.meth_waterfall.trgt_plots.zip"}
2025-09-15 20:26:12.255 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_motifs_allele NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-83/call-trgt_plot_motifs_allele", thread: 140611969599040
2025-09-15 20:26:12.273 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_motifs_allele INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:26:12.273 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_motifs_allele INFO input :: name: "waterfall", value: false
2025-09-15 20:26:12.274 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_motifs_allele INFO input :: name: "methylation", value: false
2025-09-15 20:26:12.274 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_motifs_allele INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:26:12.274 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_motifs_allele INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:26:12.274 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_motifs_allele INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:26:12.274 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_motifs_allele INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2180.trgt.sorted.spanning.bam.bai"
2025-09-15 20:26:12.274 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_motifs_allele INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2180.trgt.sorted.spanning.bam"
2025-09-15 20:26:12.274 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_motifs_allele INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2180.trgt.vcf"
2025-09-15 20:26:12.274 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_motifs_allele INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2180"
2025-09-15 20:26:12.274 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_motifs_allele INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:26:12.274 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_motifs_allele INFO eval :: name: "plot_type", value: "allele"
2025-09-15 20:26:12.274 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_motifs_allele INFO eval :: name: "show", value: "motifs"
2025-09-15 20:26:12.274 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_motifs_allele INFO eval :: name: "threads", value: 1
2025-09-15 20:26:12.275 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_motifs_allele INFO eval :: name: "disk_size", value: 27
2025-09-15 20:26:12.275 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_motifs_allele INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2180.motifs_allele"
2025-09-15 20:26:12.275 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_motifs_allele INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:26:12.275 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_motifs_allele WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:26:12.276 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_motifs_allele INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:26:12.276 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_motifs_allele INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:26:12.334 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_motifs_allele INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-83/call-trgt_plot_motifs_allele/_singularity_tmpdir_fqdcntqx"
2025-09-15 20:26:12.334 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_motifs_allele INFO Slurm invocation: srun --job-name call-trgt_plot_motifs_allele --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-83/call-trgt_plot_motifs_allele/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-83/call-trgt_plot_motifs_allele/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-83/call-trgt_plot_motifs_allele/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-83/call-trgt_plot_motifs_allele/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-83/call-trgt_genotype/out/m84036_250809_035451_s4.bc2180.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2180.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-83/call-trgt_genotype/out/m84036_250809_035451_s4.bc2180.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2180.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-83/call-trgt_genotype/out/m84036_250809_035451_s4.bc2180.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2180.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-83/call-trgt_plot_motifs_allele/_singularity_tmpdir_fqdcntqx/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-83/call-trgt_plot_motifs_allele/_singularity_tmpdir_fqdcntqx/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:26:12.336 wdl.w:ptcp.w:call-trgt-86.t:call-trgt_plot_meth_allele.slurm_singularity INFO srun: job 51798174 queued and waiting for resources
2025-09-15 20:26:12.336 wdl.w:ptcp.w:call-trgt-86.t:call-trgt_plot_meth_allele.slurm_singularity INFO srun: job 51798174 has been allocated resources
2025-09-15 20:26:12.336 wdl.w:ptcp.w:call-trgt-86.t:call-trgt_plot_meth_allele.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:26:12.347 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_motifs_allele NOTICE slurm_singularity run :: pid: 1207338, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-83/call-trgt_plot_motifs_allele/slurm_singularity.log.txt"
2025-09-15 20:26:12.431 wdl.w:ptcp.t:call-tar_outputs-65 INFO output :: name: "sample_tarball", value: "m84036_250809_035451_s4.bc2162.tar"
2025-09-15 20:26:12.433 wdl.w:ptcp.t:call-tar_outputs-48 INFO output :: name: "sample_tarball", value: "m84036_250809_035451_s4.bc2145.tar"
2025-09-15 20:26:12.462 wdl.w:ptcp.t:call-tar_outputs-23 INFO output :: name: "sample_tarball", value: "m84036_250809_035451_s4.bc2120.tar"
2025-09-15 20:26:12.513 wdl.w:ptcp.t:call-tar_outputs-65 NOTICE done
2025-09-15 20:26:12.515 wdl.w:ptcp.t:call-tar_outputs-48 NOTICE done
2025-09-15 20:26:12.517 wdl.w:ptcp.w:call-trgt-86.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO srun: job 51798175 queued and waiting for resources
2025-09-15 20:26:12.517 wdl.w:ptcp.w:call-trgt-86.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO srun: job 51798175 has been allocated resources
2025-09-15 20:26:12.517 wdl.w:ptcp.w:call-trgt-86.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:26:12.520 wdl.w:ptcp NOTICE finish :: job: "call-tar_outputs-65"
2025-09-15 20:26:12.520 wdl.w:ptcp INFO output :: job: "call-tar_outputs-65", values: {"sample_tarball": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-65/out/m84036_250809_035451_s4.bc2162.tar"}
2025-09-15 20:26:12.523 wdl.w:ptcp NOTICE finish :: job: "call-tar_outputs-48"
2025-09-15 20:26:12.523 wdl.w:ptcp INFO output :: job: "call-tar_outputs-48", values: {"sample_tarball": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-48/out/m84036_250809_035451_s4.bc2145.tar"}
2025-09-15 20:26:12.527 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_motifs_waterfall NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-83/call-trgt_plot_motifs_waterfall", thread: 140611441120832
2025-09-15 20:26:12.535 wdl.w:ptcp.t:call-tar_outputs-41 NOTICE task setup :: name: "tar_outputs", source: "./common.wdl", line: 279, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-41", thread: 140609822115392
2025-09-15 20:26:12.543 wdl.w:ptcp.t:call-tar_outputs-23 NOTICE done
2025-09-15 20:26:12.547 wdl.w:ptcp NOTICE finish :: job: "call-tar_outputs-23"
2025-09-15 20:26:12.547 wdl.w:ptcp INFO output :: job: "call-tar_outputs-23", values: {"sample_tarball": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-23/out/m84036_250809_035451_s4.bc2120.tar"}
2025-09-15 20:26:12.551 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_motifs_waterfall INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:26:12.551 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_motifs_waterfall INFO input :: name: "waterfall", value: true
2025-09-15 20:26:12.551 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_motifs_waterfall INFO input :: name: "methylation", value: false
2025-09-15 20:26:12.551 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_motifs_waterfall INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:26:12.551 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_motifs_waterfall INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:26:12.551 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_motifs_waterfall INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:26:12.551 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_motifs_waterfall INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2180.trgt.sorted.spanning.bam.bai"
2025-09-15 20:26:12.552 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_motifs_waterfall INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2180.trgt.sorted.spanning.bam"
2025-09-15 20:26:12.552 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_motifs_waterfall INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2180.trgt.vcf"
2025-09-15 20:26:12.552 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_motifs_waterfall INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2180"
2025-09-15 20:26:12.552 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:26:12.552 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "plot_type", value: "waterfall"
2025-09-15 20:26:12.552 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "show", value: "motifs"
2025-09-15 20:26:12.552 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "threads", value: 1
2025-09-15 20:26:12.552 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "disk_size", value: 27
2025-09-15 20:26:12.552 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2180.motifs_waterfall"
2025-09-15 20:26:12.553 wdl.w:ptcp.w:call-trgt-88.t:call-trgt_plot_meth_allele NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-88/call-trgt_plot_meth_allele", thread: 140608748373568
2025-09-15 20:26:12.553 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_motifs_waterfall INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:26:12.553 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_motifs_waterfall WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:26:12.553 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_motifs_waterfall INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:26:12.554 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_motifs_waterfall INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:26:12.562 wdl.w:ptcp.t:call-tar_outputs-41 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:26:12.562 wdl.w:ptcp.t:call-tar_outputs-41 INFO input :: name: "sawfish_vcf_tbi", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2138.sv.vcf.gz.tbi"
2025-09-15 20:26:12.562 wdl.w:ptcp.t:call-tar_outputs-41 INFO input :: name: "sawfish_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2138.sv.vcf.gz"
2025-09-15 20:26:12.563 wdl.w:ptcp.t:call-tar_outputs-41 INFO input :: name: "f8_json", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2138.f8inversion.json"
2025-09-15 20:26:12.563 wdl.w:ptcp.t:call-tar_outputs-41 INFO input :: name: "paraphase_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2138.paraphase.bam.bai"
2025-09-15 20:26:12.563 wdl.w:ptcp.t:call-tar_outputs-41 INFO input :: name: "paraphase_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2138.paraphase.bam"
2025-09-15 20:26:12.563 wdl.w:ptcp.t:call-tar_outputs-41 INFO input :: name: "paraphase_json", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2138.paraphase.json"
2025-09-15 20:26:12.563 wdl.w:ptcp.t:call-tar_outputs-41 INFO input :: name: "trgt_spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2138.trgt.sorted.spanning.bam.bai"
2025-09-15 20:26:12.563 wdl.w:ptcp.t:call-tar_outputs-41 INFO input :: name: "trgt_spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2138.trgt.sorted.spanning.bam"
2025-09-15 20:26:12.563 wdl.w:ptcp.t:call-tar_outputs-41 INFO input :: name: "trgt_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2138.trgt.vcf"
2025-09-15 20:26:12.563 wdl.w:ptcp.t:call-tar_outputs-41 INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2138.mapped.bam.bai"
2025-09-15 20:26:12.563 wdl.w:ptcp.t:call-tar_outputs-41 INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2138.mapped.bam"
2025-09-15 20:26:12.563 wdl.w:ptcp.t:call-tar_outputs-41 INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2138"
2025-09-15 20:26:12.564 wdl.w:ptcp.t:call-tar_outputs-41 INFO eval :: name: "threads", value: 1
2025-09-15 20:26:12.564 wdl.w:ptcp.t:call-tar_outputs-41 INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:26:12.564 wdl.w:ptcp.t:call-tar_outputs-41 INFO eval :: name: "disk_size", value: 6
2025-09-15 20:26:12.564 wdl.w:ptcp.t:call-tar_outputs-41 INFO eval :: name: "output_tarball", value: "m84036_250809_035451_s4.bc2138.tar"
2025-09-15 20:26:12.565 wdl.w:ptcp.t:call-tar_outputs-41 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:26:12.565 wdl.w:ptcp.t:call-tar_outputs-41 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:26:12.566 wdl.w:ptcp.t:call-tar_outputs-41 INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:26:12.566 wdl.w:ptcp.t:call-tar_outputs-41 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:26:12.572 wdl.w:ptcp.w:call-trgt-88.t:call-trgt_plot_meth_allele INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:26:12.572 wdl.w:ptcp.w:call-trgt-88.t:call-trgt_plot_meth_allele INFO input :: name: "waterfall", value: false
2025-09-15 20:26:12.572 wdl.w:ptcp.w:call-trgt-88.t:call-trgt_plot_meth_allele INFO input :: name: "methylation", value: true
2025-09-15 20:26:12.572 wdl.w:ptcp.w:call-trgt-88.t:call-trgt_plot_meth_allele INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:26:12.572 wdl.w:ptcp.w:call-trgt-88.t:call-trgt_plot_meth_allele INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:26:12.572 wdl.w:ptcp.w:call-trgt-88.t:call-trgt_plot_meth_allele INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:26:12.572 wdl.w:ptcp.w:call-trgt-88.t:call-trgt_plot_meth_allele INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2185.trgt.sorted.spanning.bam.bai"
2025-09-15 20:26:12.572 wdl.w:ptcp.w:call-trgt-88.t:call-trgt_plot_meth_allele INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2185.trgt.sorted.spanning.bam"
2025-09-15 20:26:12.573 wdl.w:ptcp.w:call-trgt-88.t:call-trgt_plot_meth_allele INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2185.trgt.vcf"
2025-09-15 20:26:12.573 wdl.w:ptcp.w:call-trgt-88.t:call-trgt_plot_meth_allele INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2185"
2025-09-15 20:26:12.573 wdl.w:ptcp.w:call-trgt-88.t:call-trgt_plot_meth_allele INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:26:12.573 wdl.w:ptcp.w:call-trgt-88.t:call-trgt_plot_meth_allele INFO eval :: name: "plot_type", value: "allele"
2025-09-15 20:26:12.573 wdl.w:ptcp.w:call-trgt-88.t:call-trgt_plot_meth_allele INFO eval :: name: "show", value: "meth"
2025-09-15 20:26:12.573 wdl.w:ptcp.w:call-trgt-88.t:call-trgt_plot_meth_allele INFO eval :: name: "threads", value: 1
2025-09-15 20:26:12.573 wdl.w:ptcp.w:call-trgt-88.t:call-trgt_plot_meth_allele INFO eval :: name: "disk_size", value: 27
2025-09-15 20:26:12.573 wdl.w:ptcp.w:call-trgt-88.t:call-trgt_plot_meth_allele INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2185.meth_allele"
2025-09-15 20:26:12.574 wdl.w:ptcp.w:call-trgt-88.t:call-trgt_plot_meth_allele INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:26:12.574 wdl.w:ptcp.w:call-trgt-88.t:call-trgt_plot_meth_allele WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:26:12.574 wdl.w:ptcp.w:call-trgt-88.t:call-trgt_plot_meth_allele INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:26:12.574 wdl.w:ptcp.w:call-trgt-88.t:call-trgt_plot_meth_allele INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:26:12.577 wdl.w:ptcp.w:call-sawfish-85.t:call-run_sawfish.stderr VERBOSE [M::mm_idx_gen::33.442*1.43] collected minimizers
2025-09-15 20:26:12.649 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_motifs_waterfall INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-83/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_9njd17ad"
2025-09-15 20:26:12.649 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_motifs_waterfall INFO Slurm invocation: srun --job-name call-trgt_plot_motifs_waterfall --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-83/call-trgt_plot_motifs_waterfall/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-83/call-trgt_plot_motifs_waterfall/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-83/call-trgt_plot_motifs_waterfall/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-83/call-trgt_plot_motifs_waterfall/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-83/call-trgt_genotype/out/m84036_250809_035451_s4.bc2180.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2180.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-83/call-trgt_genotype/out/m84036_250809_035451_s4.bc2180.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2180.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-83/call-trgt_genotype/out/m84036_250809_035451_s4.bc2180.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2180.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-83/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_9njd17ad/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-83/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_9njd17ad/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:26:12.660 wdl.w:ptcp.w:call-trgt-88.t:call-trgt_plot_meth_allele INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-88/call-trgt_plot_meth_allele/_singularity_tmpdir_245g6ts7"
2025-09-15 20:26:12.660 wdl.w:ptcp.w:call-trgt-88.t:call-trgt_plot_meth_allele INFO Slurm invocation: srun --job-name call-trgt_plot_meth_allele --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-88/call-trgt_plot_meth_allele/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-88/call-trgt_plot_meth_allele/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-88/call-trgt_plot_meth_allele/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-88/call-trgt_plot_meth_allele/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-88/call-trgt_genotype/out/m84036_250809_035451_s4.bc2185.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2185.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-88/call-trgt_genotype/out/m84036_250809_035451_s4.bc2185.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2185.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-88/call-trgt_genotype/out/m84036_250809_035451_s4.bc2185.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2185.trgt.vcf:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-88/call-trgt_plot_meth_allele/_singularity_tmpdir_245g6ts7/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-88/call-trgt_plot_meth_allele/_singularity_tmpdir_245g6ts7/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:26:12.676 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_motifs_waterfall NOTICE slurm_singularity run :: pid: 1207363, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-83/call-trgt_plot_motifs_waterfall/slurm_singularity.log.txt"
2025-09-15 20:26:12.676 wdl.w:ptcp.w:call-trgt-88.t:call-trgt_plot_meth_allele NOTICE slurm_singularity run :: pid: 1207364, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-88/call-trgt_plot_meth_allele/slurm_singularity.log.txt"
2025-09-15 20:26:12.698 wdl.w:ptcp.t:call-tar_outputs-41 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 17, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-41/_singularity_tmpdir_arcu2i45"
2025-09-15 20:26:12.698 wdl.w:ptcp.t:call-tar_outputs-41 INFO Slurm invocation: srun --job-name call-tar_outputs-41 --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-41/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-41/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-41/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-41/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-41/out/m84036_250809_035451_s4.bc2138_sawfish/m84036_250809_035451_s4.bc2138.sv.vcf.gz:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2138.sv.vcf.gz:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-41/out/m84036_250809_035451_s4.bc2138_sawfish/m84036_250809_035451_s4.bc2138.sv.vcf.gz.tbi:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2138.sv.vcf.gz.tbi:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-41/out/m84036_250809_035451_s4.bc2138.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2138.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-41/out/m84036_250809_035451_s4.bc2138.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2138.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-41/out/m84036_250809_035451_s4.bc2138.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2138.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-41/out/m84036_250809_035451_s4.bc2138_paraphase/m84036_250809_035451_s4.bc2138.paraphase.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2138.paraphase.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-41/out/m84036_250809_035451_s4.bc2138_paraphase/m84036_250809_035451_s4.bc2138.paraphase.json:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2138.paraphase.json:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-41/out/m84036_250809_035451_s4.bc2138_paraphase/m84036_250809_035451_s4.bc2138.paraphase.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2138.paraphase.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-41/out/m84036_250809_035451_s4.bc2138.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2138.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-41/out/m84036_250809_035451_s4.bc2138.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2138.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-41/out/m84036_250809_035451_s4.bc2138.f8inversion.json:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2138.f8inversion.json:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-41/_singularity_tmpdir_arcu2i45/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-41/_singularity_tmpdir_arcu2i45/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:26:12.708 wdl.w:ptcp.t:call-tar_outputs-41 NOTICE slurm_singularity run :: pid: 1207367, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-41/slurm_singularity.log.txt"
2025-09-15 20:26:12.745 wdl.w:ptcp.w:call-paraphase-83.t:call-run_paraphase.stderr VERBOSE INFO:root:Processing sample m84036_250809_035451_s4.bc2180 at 2025-09-15 20:26:08.462696...
2025-09-15 20:26:12.746 wdl.w:ptcp.w:call-paraphase-83.t:call-run_paraphase.stderr VERBOSE INFO:root:Checking sample sex at 2025-09-15 20:26:08.463684...
2025-09-15 20:26:12.746 wdl.w:ptcp.w:call-paraphase-83.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for cyp21 for sample m84036_250809_035451_s4.bc2180 at 2025-09-15 20:26:08.516415...
2025-09-15 20:26:12.746 wdl.w:ptcp.w:call-paraphase-83.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for cyp21 for sample m84036_250809_035451_s4.bc2180 at 2025-09-15 20:26:08.517173...
2025-09-15 20:26:12.746 wdl.w:ptcp.w:call-paraphase-83.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for smn1 for sample m84036_250809_035451_s4.bc2180 at 2025-09-15 20:26:08.516665...
2025-09-15 20:26:12.746 wdl.w:ptcp.w:call-paraphase-83.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for smn1 for sample m84036_250809_035451_s4.bc2180 at 2025-09-15 20:26:08.517313...
2025-09-15 20:26:12.746 wdl.w:ptcp.w:call-paraphase-83.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for gba for sample m84036_250809_035451_s4.bc2180 at 2025-09-15 20:26:08.518828...
2025-09-15 20:26:12.746 wdl.w:ptcp.w:call-paraphase-83.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for hba for sample m84036_250809_035451_s4.bc2180 at 2025-09-15 20:26:08.518840...
2025-09-15 20:26:12.746 wdl.w:ptcp.w:call-paraphase-83.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for hba for sample m84036_250809_035451_s4.bc2180 at 2025-09-15 20:26:08.519516...
2025-09-15 20:26:12.746 wdl.w:ptcp.w:call-paraphase-83.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for gba for sample m84036_250809_035451_s4.bc2180 at 2025-09-15 20:26:08.519515...
2025-09-15 20:26:12.820 wdl.w:ptcp.w:call-trgt-86.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:26:12 [ERROR] - No reads found for TRID=OPDM_ABCD3
2025-09-15 20:26:12.821 wdl.w:ptcp.w:call-trgt-86.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:26:12 [ERROR] - No reads found for TRID=OPDM_ABCD3
2025-09-15 20:26:12.821 wdl.w:ptcp.w:call-trgt-86.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:26:12 [ERROR] - No reads found for TRID=SCA37_DAB1
2025-09-15 20:26:12.821 wdl.w:ptcp.w:call-trgt-86.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:26:12 [ERROR] - No reads found for TRID=NIID_NOTCH2NLC
2025-09-15 20:26:12.822 wdl.w:ptcp.w:call-trgt-86.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:26:12 [ERROR] - No reads found for TRID=OPDM4_RILPL1
2025-09-15 20:26:12.822 wdl.w:ptcp.w:call-trgt-86.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:26:12 [ERROR] - No reads found for TRID=SCA2_ATXN2
2025-09-15 20:26:12.830 wdl.w:ptcp.w:call-trgt-86.t:call-trgt_plot_motifs_allele.slurm_singularity INFO srun: job 51798176 queued and waiting for resources
2025-09-15 20:26:12.831 wdl.w:ptcp.w:call-trgt-86.t:call-trgt_plot_motifs_allele.slurm_singularity INFO srun: job 51798176 has been allocated resources
2025-09-15 20:26:12.831 wdl.w:ptcp.w:call-trgt-86.t:call-trgt_plot_motifs_allele.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:26:12.834 wdl.w:ptcp.w:call-trgt-86.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO srun: job 51798177 queued and waiting for resources
2025-09-15 20:26:12.835 wdl.w:ptcp.w:call-trgt-86.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO srun: job 51798177 has been allocated resources
2025-09-15 20:26:12.835 wdl.w:ptcp.w:call-trgt-86.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:26:12.843 wdl.w:ptcp.w:call-trgt-90.t:call-trgt_plot_motifs_allele INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2187.motifs_allele.trgt_plots.zip"
2025-09-15 20:26:12.894 wdl.w:ptcp.t:call-tar_outputs-68 INFO output :: name: "sample_tarball", value: "m84036_250809_035451_s4.bc2165.tar"
2025-09-15 20:26:12.930 wdl.w:ptcp.w:call-trgt-90.t:call-trgt_plot_motifs_allele NOTICE done
2025-09-15 20:26:12.961 wdl.w:ptcp.t:call-tar_outputs-68 NOTICE done
2025-09-15 20:26:12.967 wdl.w:ptcp NOTICE finish :: job: "call-tar_outputs-68"
2025-09-15 20:26:12.968 wdl.w:ptcp INFO output :: job: "call-tar_outputs-68", values: {"sample_tarball": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-68/out/m84036_250809_035451_s4.bc2165.tar"}
2025-09-15 20:26:12.973 wdl.w:ptcp.w:call-trgt-88.t:call-trgt_plot_meth_waterfall NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-88/call-trgt_plot_meth_waterfall", thread: 140610342200896
2025-09-15 20:26:12.997 wdl.w:ptcp.w:call-trgt-90 NOTICE finish :: job: "call-trgt_plot_motifs_allele"
2025-09-15 20:26:12.998 wdl.w:ptcp.w:call-trgt-90 INFO output :: job: "call-trgt_plot_motifs_allele", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-90/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2187.motifs_allele.trgt_plots.zip"}
2025-09-15 20:26:12.998 wdl.w:ptcp.w:call-trgt-90 INFO visit :: node: "output-images_motifs_allele", values: {"images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-90/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2187.motifs_allele.trgt_plots.zip"}
2025-09-15 20:26:13.003 wdl.w:ptcp.w:call-trgt-88.t:call-trgt_plot_motifs_allele NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-88/call-trgt_plot_motifs_allele", thread: 140607129368128
2025-09-15 20:26:13.004 wdl.w:ptcp.w:call-trgt-88.t:call-trgt_plot_meth_waterfall INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:26:13.004 wdl.w:ptcp.w:call-trgt-88.t:call-trgt_plot_meth_waterfall INFO input :: name: "waterfall", value: true
2025-09-15 20:26:13.004 wdl.w:ptcp.w:call-trgt-88.t:call-trgt_plot_meth_waterfall INFO input :: name: "methylation", value: true
2025-09-15 20:26:13.004 wdl.w:ptcp.w:call-trgt-88.t:call-trgt_plot_meth_waterfall INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:26:13.004 wdl.w:ptcp.w:call-trgt-88.t:call-trgt_plot_meth_waterfall INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:26:13.004 wdl.w:ptcp.w:call-trgt-88.t:call-trgt_plot_meth_waterfall INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:26:13.004 wdl.w:ptcp.w:call-trgt-88.t:call-trgt_plot_meth_waterfall INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2185.trgt.sorted.spanning.bam.bai"
2025-09-15 20:26:13.005 wdl.w:ptcp.w:call-trgt-88.t:call-trgt_plot_meth_waterfall INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2185.trgt.sorted.spanning.bam"
2025-09-15 20:26:13.005 wdl.w:ptcp.w:call-trgt-88.t:call-trgt_plot_meth_waterfall INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2185.trgt.vcf"
2025-09-15 20:26:13.005 wdl.w:ptcp.w:call-trgt-88.t:call-trgt_plot_meth_waterfall INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2185"
2025-09-15 20:26:13.005 wdl.w:ptcp.w:call-trgt-88.t:call-trgt_plot_meth_waterfall INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:26:13.005 wdl.w:ptcp.w:call-trgt-88.t:call-trgt_plot_meth_waterfall INFO eval :: name: "plot_type", value: "waterfall"
2025-09-15 20:26:13.005 wdl.w:ptcp.w:call-trgt-88.t:call-trgt_plot_meth_waterfall INFO eval :: name: "show", value: "meth"
2025-09-15 20:26:13.005 wdl.w:ptcp.w:call-trgt-88.t:call-trgt_plot_meth_waterfall INFO eval :: name: "threads", value: 1
2025-09-15 20:26:13.005 wdl.w:ptcp.w:call-trgt-88.t:call-trgt_plot_meth_waterfall INFO eval :: name: "disk_size", value: 27
2025-09-15 20:26:13.005 wdl.w:ptcp.w:call-trgt-88.t:call-trgt_plot_meth_waterfall INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2185.meth_waterfall"
2025-09-15 20:26:13.006 wdl.w:ptcp.w:call-trgt-88.t:call-trgt_plot_meth_waterfall INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:26:13.006 wdl.w:ptcp.w:call-trgt-88.t:call-trgt_plot_meth_waterfall WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:26:13.006 wdl.w:ptcp.w:call-trgt-88.t:call-trgt_plot_meth_waterfall INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:26:13.006 wdl.w:ptcp.w:call-trgt-88.t:call-trgt_plot_meth_waterfall INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:26:13.020 wdl.w:ptcp.w:call-trgt-88.t:call-trgt_plot_motifs_allele INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:26:13.021 wdl.w:ptcp.w:call-trgt-88.t:call-trgt_plot_motifs_allele INFO input :: name: "waterfall", value: false
2025-09-15 20:26:13.021 wdl.w:ptcp.w:call-trgt-88.t:call-trgt_plot_motifs_allele INFO input :: name: "methylation", value: false
2025-09-15 20:26:13.021 wdl.w:ptcp.w:call-trgt-88.t:call-trgt_plot_motifs_allele INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:26:13.021 wdl.w:ptcp.w:call-trgt-88.t:call-trgt_plot_motifs_allele INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:26:13.021 wdl.w:ptcp.w:call-trgt-88.t:call-trgt_plot_motifs_allele INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:26:13.021 wdl.w:ptcp.w:call-trgt-88.t:call-trgt_plot_motifs_allele INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2185.trgt.sorted.spanning.bam.bai"
2025-09-15 20:26:13.021 wdl.w:ptcp.w:call-trgt-88.t:call-trgt_plot_motifs_allele INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2185.trgt.sorted.spanning.bam"
2025-09-15 20:26:13.021 wdl.w:ptcp.w:call-trgt-88.t:call-trgt_plot_motifs_allele INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2185.trgt.vcf"
2025-09-15 20:26:13.021 wdl.w:ptcp.w:call-trgt-88.t:call-trgt_plot_motifs_allele INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2185"
2025-09-15 20:26:13.021 wdl.w:ptcp.w:call-trgt-88.t:call-trgt_plot_motifs_allele INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:26:13.021 wdl.w:ptcp.w:call-trgt-88.t:call-trgt_plot_motifs_allele INFO eval :: name: "plot_type", value: "allele"
2025-09-15 20:26:13.022 wdl.w:ptcp.w:call-trgt-88.t:call-trgt_plot_motifs_allele INFO eval :: name: "show", value: "motifs"
2025-09-15 20:26:13.022 wdl.w:ptcp.w:call-trgt-88.t:call-trgt_plot_motifs_allele INFO eval :: name: "threads", value: 1
2025-09-15 20:26:13.022 wdl.w:ptcp.w:call-trgt-88.t:call-trgt_plot_motifs_allele INFO eval :: name: "disk_size", value: 27
2025-09-15 20:26:13.022 wdl.w:ptcp.w:call-trgt-88.t:call-trgt_plot_motifs_allele INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2185.motifs_allele"
2025-09-15 20:26:13.022 wdl.w:ptcp.w:call-trgt-88.t:call-trgt_plot_motifs_allele INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:26:13.022 wdl.w:ptcp.w:call-trgt-88.t:call-trgt_plot_motifs_allele WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:26:13.023 wdl.w:ptcp.w:call-trgt-88.t:call-trgt_plot_motifs_allele INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:26:13.023 wdl.w:ptcp.w:call-trgt-88.t:call-trgt_plot_motifs_allele INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:26:13.076 wdl.w:ptcp.w:call-trgt-88.t:call-trgt_plot_meth_waterfall INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-88/call-trgt_plot_meth_waterfall/_singularity_tmpdir_0l8k5el0"
2025-09-15 20:26:13.077 wdl.w:ptcp.w:call-trgt-88.t:call-trgt_plot_meth_waterfall INFO Slurm invocation: srun --job-name call-trgt_plot_meth_waterfall --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-88/call-trgt_plot_meth_waterfall/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-88/call-trgt_plot_meth_waterfall/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-88/call-trgt_plot_meth_waterfall/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-88/call-trgt_plot_meth_waterfall/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-88/call-trgt_genotype/out/m84036_250809_035451_s4.bc2185.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2185.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-88/call-trgt_genotype/out/m84036_250809_035451_s4.bc2185.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2185.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-88/call-trgt_genotype/out/m84036_250809_035451_s4.bc2185.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2185.trgt.vcf:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-88/call-trgt_plot_meth_waterfall/_singularity_tmpdir_0l8k5el0/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-88/call-trgt_plot_meth_waterfall/_singularity_tmpdir_0l8k5el0/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:26:13.101 wdl.w:ptcp.w:call-trgt-88.t:call-trgt_plot_meth_waterfall NOTICE slurm_singularity run :: pid: 1207387, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-88/call-trgt_plot_meth_waterfall/slurm_singularity.log.txt"
2025-09-15 20:26:13.107 wdl.w:ptcp.w:call-trgt-88.t:call-trgt_plot_motifs_allele INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-88/call-trgt_plot_motifs_allele/_singularity_tmpdir_rdu9uuk1"
2025-09-15 20:26:13.108 wdl.w:ptcp.w:call-trgt-88.t:call-trgt_plot_motifs_allele INFO Slurm invocation: srun --job-name call-trgt_plot_motifs_allele --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-88/call-trgt_plot_motifs_allele/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-88/call-trgt_plot_motifs_allele/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-88/call-trgt_plot_motifs_allele/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-88/call-trgt_plot_motifs_allele/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-88/call-trgt_genotype/out/m84036_250809_035451_s4.bc2185.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2185.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-88/call-trgt_genotype/out/m84036_250809_035451_s4.bc2185.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2185.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-88/call-trgt_genotype/out/m84036_250809_035451_s4.bc2185.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2185.trgt.vcf:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-88/call-trgt_plot_motifs_allele/_singularity_tmpdir_rdu9uuk1/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-88/call-trgt_plot_motifs_allele/_singularity_tmpdir_rdu9uuk1/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:26:13.116 wdl.w:ptcp.w:call-trgt-90.t:call-trgt_plot_motifs_waterfall INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2187.motifs_waterfall.trgt_plots.zip"
2025-09-15 20:26:13.116 wdl.w:ptcp.w:call-trgt-88.t:call-trgt_plot_motifs_allele NOTICE slurm_singularity run :: pid: 1207388, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-88/call-trgt_plot_motifs_allele/slurm_singularity.log.txt"
2025-09-15 20:26:13.145 wdl.w:ptcp.t:call-tar_outputs-57.slurm_singularity INFO srun: job 51798178 queued and waiting for resources
2025-09-15 20:26:13.146 wdl.w:ptcp.t:call-tar_outputs-57.slurm_singularity INFO srun: job 51798178 has been allocated resources
2025-09-15 20:26:13.146 wdl.w:ptcp.t:call-tar_outputs-57.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:26:13.147 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_meth_allele.slurm_singularity INFO srun: job 51798179 queued and waiting for resources
2025-09-15 20:26:13.147 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_meth_allele.slurm_singularity INFO srun: job 51798179 has been allocated resources
2025-09-15 20:26:13.147 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_meth_allele.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:26:13.192 wdl.w:ptcp.w:call-trgt-89.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:26:08 [ERROR] - No reads found for TRID=PRTS_ARX
2025-09-15 20:26:13.193 wdl.w:ptcp.w:call-trgt-89.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:26:08 [ERROR] - No reads found for TRID=EIEE1_ARX
2025-09-15 20:26:13.195 wdl.w:ptcp.w:call-trgt-90.t:call-trgt_plot_motifs_waterfall NOTICE done
2025-09-15 20:26:13.200 wdl.w:ptcp.w:call-trgt-90 NOTICE finish :: job: "call-trgt_plot_motifs_waterfall"
2025-09-15 20:26:13.200 wdl.w:ptcp.w:call-trgt-90 INFO output :: job: "call-trgt_plot_motifs_waterfall", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-90/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2187.motifs_waterfall.trgt_plots.zip"}
2025-09-15 20:26:13.200 wdl.w:ptcp.w:call-trgt-90 INFO visit :: node: "output-images_motifs_waterfall", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-90/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2187.motifs_waterfall.trgt_plots.zip"}
2025-09-15 20:26:13.207 wdl.w:ptcp.w:call-trgt-88.t:call-trgt_plot_motifs_waterfall NOTICE task setup :: name: "trgt_plot", source: "./trgt.wdl", line: 385, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-88/call-trgt_plot_motifs_waterfall", thread: 140613580211776
2025-09-15 20:26:13.216 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO srun: job 51798180 queued and waiting for resources
2025-09-15 20:26:13.216 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO srun: job 51798180 has been allocated resources
2025-09-15 20:26:13.216 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:26:13.234 wdl.w:ptcp.w:call-trgt-88.t:call-trgt_plot_motifs_waterfall INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:26:13.235 wdl.w:ptcp.w:call-trgt-88.t:call-trgt_plot_motifs_waterfall INFO input :: name: "waterfall", value: true
2025-09-15 20:26:13.235 wdl.w:ptcp.w:call-trgt-88.t:call-trgt_plot_motifs_waterfall INFO input :: name: "methylation", value: false
2025-09-15 20:26:13.235 wdl.w:ptcp.w:call-trgt-88.t:call-trgt_plot_motifs_waterfall INFO input :: name: "trgt_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed"
2025-09-15 20:26:13.235 wdl.w:ptcp.w:call-trgt-88.t:call-trgt_plot_motifs_waterfall INFO input :: name: "ref_index", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai"
2025-09-15 20:26:13.235 wdl.w:ptcp.w:call-trgt-88.t:call-trgt_plot_motifs_waterfall INFO input :: name: "ref_fasta", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa"
2025-09-15 20:26:13.235 wdl.w:ptcp.w:call-trgt-88.t:call-trgt_plot_motifs_waterfall INFO input :: name: "spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2185.trgt.sorted.spanning.bam.bai"
2025-09-15 20:26:13.235 wdl.w:ptcp.w:call-trgt-88.t:call-trgt_plot_motifs_waterfall INFO input :: name: "spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2185.trgt.sorted.spanning.bam"
2025-09-15 20:26:13.235 wdl.w:ptcp.w:call-trgt-88.t:call-trgt_plot_motifs_waterfall INFO input :: name: "vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2185.trgt.vcf"
2025-09-15 20:26:13.235 wdl.w:ptcp.w:call-trgt-88.t:call-trgt_plot_motifs_waterfall INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2185"
2025-09-15 20:26:13.235 wdl.w:ptcp.w:call-trgt-88.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:26:13.235 wdl.w:ptcp.w:call-trgt-88.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "plot_type", value: "waterfall"
2025-09-15 20:26:13.235 wdl.w:ptcp.w:call-trgt-88.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "show", value: "motifs"
2025-09-15 20:26:13.236 wdl.w:ptcp.w:call-trgt-88.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "threads", value: 1
2025-09-15 20:26:13.236 wdl.w:ptcp.w:call-trgt-88.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "disk_size", value: 27
2025-09-15 20:26:13.236 wdl.w:ptcp.w:call-trgt-88.t:call-trgt_plot_motifs_waterfall INFO eval :: name: "output_prefix", value: "m84036_250809_035451_s4.bc2185.motifs_waterfall"
2025-09-15 20:26:13.236 wdl.w:ptcp.w:call-trgt-88.t:call-trgt_plot_motifs_waterfall INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:26:13.236 wdl.w:ptcp.w:call-trgt-88.t:call-trgt_plot_motifs_waterfall WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:26:13.237 wdl.w:ptcp.w:call-trgt-88.t:call-trgt_plot_motifs_waterfall INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:26:13.237 wdl.w:ptcp.w:call-trgt-88.t:call-trgt_plot_motifs_waterfall INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:26:13.301 wdl.w:ptcp.w:call-trgt-88.t:call-trgt_plot_motifs_waterfall INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 12, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-88/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_8rsz6leq"
2025-09-15 20:26:13.302 wdl.w:ptcp.w:call-trgt-88.t:call-trgt_plot_motifs_waterfall INFO Slurm invocation: srun --job-name call-trgt_plot_motifs_waterfall --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-88/call-trgt_plot_motifs_waterfall/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-88/call-trgt_plot_motifs_waterfall/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-88/call-trgt_plot_motifs_waterfall/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-88/call-trgt_plot_motifs_waterfall/command:/mnt/miniwdl_task_container/command:ro --bind /meta/refs/hg38.fa:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa:ro --bind /meta/refs/hg38.fa.fai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa.fai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-88/call-trgt_genotype/out/m84036_250809_035451_s4.bc2185.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2185.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-88/call-trgt_genotype/out/m84036_250809_035451_s4.bc2185.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2185.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-88/call-trgt_genotype/out/m84036_250809_035451_s4.bc2185.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2185.trgt.vcf:ro --bind /ptcp/meta/trgt/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/PureTarget_repeat_expansion_panel_2.0.repeat_definition.GRCh38.bed:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-88/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_8rsz6leq/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-88/call-trgt_plot_motifs_waterfall/_singularity_tmpdir_8rsz6leq/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:26:13.318 wdl.w:ptcp.w:call-trgt-88.t:call-trgt_plot_motifs_waterfall NOTICE slurm_singularity run :: pid: 1207402, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-88/call-trgt_plot_motifs_waterfall/slurm_singularity.log.txt"
2025-09-15 20:26:13.351 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:26:12 [ERROR] - No reads found for TRID=DRPLA_ATN1
2025-09-15 20:26:13.351 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:26:12 [ERROR] - No reads found for TRID=SCA2_ATXN2
2025-09-15 20:26:13.351 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:26:12 [ERROR] - No reads found for TRID=OPDM4_RILPL1
2025-09-15 20:26:13.351 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:26:13 [ERROR] - No reads found for TRID=NIID_NOTCH2NLC
2025-09-15 20:26:13.352 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:26:13 [ERROR] - No reads found for TRID=OPMD_PABPN1
2025-09-15 20:26:13.352 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:26:13 [ERROR] - No reads found for TRID=SCA27B_FGF14
2025-09-15 20:26:13.352 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:26:13 [ERROR] - No reads found for TRID=SCA37_DAB1
2025-09-15 20:26:13.352 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:26:13 [ERROR] - No reads found for TRID=SCA3_ATXN3
2025-09-15 20:26:13.352 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:26:13 [ERROR] - No reads found for TRID=FECD3_TCF4
2025-09-15 20:26:13.352 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:26:13 [ERROR] - No reads found for TRID=SCA31_BEAN1
2025-09-15 20:26:13.359 wdl.w:ptcp.w:call-trgt-89.t:call-trgt_plot_motifs_waterfall INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2186.motifs_waterfall.trgt_plots.zip"
2025-09-15 20:26:13.360 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_motifs_allele.slurm_singularity INFO srun: job 51798181 queued and waiting for resources
2025-09-15 20:26:13.360 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_motifs_allele.slurm_singularity INFO srun: job 51798181 has been allocated resources
2025-09-15 20:26:13.360 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_motifs_allele.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:26:13.392 wdl.w:ptcp.w:call-sawfish-76.t:call-run_sawfish INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2173_sawfish/m84036_250809_035451_s4.bc2173.sv.vcf.gz"
2025-09-15 20:26:13.394 wdl.w:ptcp.w:call-trgt-90.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:26:11 [ERROR] - No reads found for TRID=SCA37_DAB1
2025-09-15 20:26:13.394 wdl.w:ptcp.w:call-trgt-90.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:26:11 [ERROR] - No reads found for TRID=NIID_NOTCH2NLC
2025-09-15 20:26:13.395 wdl.w:ptcp.w:call-trgt-90.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:26:11 [ERROR] - No reads found for TRID=SCA8_ATXN8OS
2025-09-15 20:26:13.395 wdl.w:ptcp.w:call-trgt-90.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:26:11 [ERROR] - No reads found for TRID=SCA27B_FGF14
2025-09-15 20:26:13.395 wdl.w:ptcp.w:call-trgt-90.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:26:11 [ERROR] - No reads found for TRID=OPDM4_RILPL1
2025-09-15 20:26:13.395 wdl.w:ptcp.w:call-trgt-90.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:26:11 [ERROR] - No reads found for TRID=SCA3_ATXN3
2025-09-15 20:26:13.395 wdl.w:ptcp.w:call-trgt-90.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:26:12 [ERROR] - No reads found for TRID=OPDM_ABCD3
2025-09-15 20:26:13.395 wdl.w:ptcp.w:call-trgt-90.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:26:12 [ERROR] - No reads found for TRID=HDL2_JPH3
2025-09-15 20:26:13.395 wdl.w:ptcp.w:call-trgt-90.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:26:12 [ERROR] - No reads found for TRID=SCA4_ZFHX3
2025-09-15 20:26:13.395 wdl.w:ptcp.w:call-trgt-90.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:26:12 [ERROR] - No reads found for TRID=SCA31_BEAN1
2025-09-15 20:26:13.395 wdl.w:ptcp.w:call-trgt-90.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:26:13 [ERROR] - No reads found for TRID=SCA6_CACNA1A
2025-09-15 20:26:13.395 wdl.w:ptcp.w:call-trgt-90.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:26:13 [ERROR] - No reads found for TRID=OPDM2_GIPC1
2025-09-15 20:26:13.396 wdl.w:ptcp.w:call-sawfish-76.t:call-run_sawfish INFO output :: name: "vcf_tbi", value: "m84036_250809_035451_s4.bc2173_sawfish/m84036_250809_035451_s4.bc2173.sv.vcf.gz.tbi"
2025-09-15 20:26:13.397 wdl.w:ptcp.w:call-sawfish-76.t:call-run_sawfish INFO output :: name: "minimap2_bam", value: "m84036_250809_035451_s4.bc2173.minimap2.bam"
2025-09-15 20:26:13.399 wdl.w:ptcp.w:call-sawfish-76.t:call-run_sawfish INFO output :: name: "minimap2_bam_bai", value: "m84036_250809_035451_s4.bc2173.minimap2.bam.bai"
2025-09-15 20:26:13.447 wdl.w:ptcp.w:call-trgt-90.t:call-trgt_plot_meth_waterfall INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2187.meth_waterfall.trgt_plots.zip"
2025-09-15 20:26:13.494 wdl.w:ptcp.w:call-sawfish-84.t:call-run_sawfish INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2181_sawfish/m84036_250809_035451_s4.bc2181.sv.vcf.gz"
2025-09-15 20:26:13.501 wdl.w:ptcp.w:call-sawfish-84.t:call-run_sawfish INFO output :: name: "vcf_tbi", value: "m84036_250809_035451_s4.bc2181_sawfish/m84036_250809_035451_s4.bc2181.sv.vcf.gz.tbi"
2025-09-15 20:26:13.503 wdl.w:ptcp.w:call-sawfish-84.t:call-run_sawfish INFO output :: name: "minimap2_bam", value: "m84036_250809_035451_s4.bc2181.minimap2.bam"
2025-09-15 20:26:13.505 wdl.w:ptcp.w:call-sawfish-84.t:call-run_sawfish INFO output :: name: "minimap2_bam_bai", value: "m84036_250809_035451_s4.bc2181.minimap2.bam.bai"
2025-09-15 20:26:13.513 wdl.w:ptcp.w:call-trgt-89.t:call-trgt_plot_motifs_waterfall NOTICE done
2025-09-15 20:26:13.519 wdl.w:ptcp.w:call-trgt-89 NOTICE finish :: job: "call-trgt_plot_motifs_waterfall"
2025-09-15 20:26:13.520 wdl.w:ptcp.w:call-trgt-89 INFO output :: job: "call-trgt_plot_motifs_waterfall", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-89/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2186.motifs_waterfall.trgt_plots.zip"}
2025-09-15 20:26:13.520 wdl.w:ptcp.w:call-trgt-89 INFO visit :: node: "output-images_motifs_waterfall", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-89/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2186.motifs_waterfall.trgt_plots.zip"}
2025-09-15 20:26:13.527 wdl.w:ptcp.t:call-tar_outputs-31 NOTICE task setup :: name: "tar_outputs", source: "./common.wdl", line: 279, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-31", thread: 140607120975424
2025-09-15 20:26:13.551 wdl.w:ptcp.w:call-trgt-90.t:call-trgt_plot_meth_waterfall NOTICE done
2025-09-15 20:26:13.557 wdl.w:ptcp.w:call-trgt-90 NOTICE finish :: job: "call-trgt_plot_meth_waterfall"
2025-09-15 20:26:13.557 wdl.w:ptcp.w:call-trgt-90 INFO output :: job: "call-trgt_plot_meth_waterfall", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-90/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2187.meth_waterfall.trgt_plots.zip"}
2025-09-15 20:26:13.557 wdl.w:ptcp.w:call-trgt-90 INFO visit :: node: "output-images_meth_waterfall", values: {"images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-90/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2187.meth_waterfall.trgt_plots.zip"}
2025-09-15 20:26:13.563 wdl.w:ptcp.t:call-tar_outputs-31 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:26:13.563 wdl.w:ptcp.t:call-tar_outputs-31 INFO input :: name: "sawfish_vcf_tbi", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2128.sv.vcf.gz.tbi"
2025-09-15 20:26:13.563 wdl.w:ptcp.t:call-tar_outputs-31 INFO input :: name: "sawfish_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2128.sv.vcf.gz"
2025-09-15 20:26:13.563 wdl.w:ptcp.t:call-tar_outputs-31 INFO input :: name: "f8_json", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2128.f8inversion.json"
2025-09-15 20:26:13.563 wdl.w:ptcp.t:call-tar_outputs-31 INFO input :: name: "paraphase_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2128.paraphase.bam.bai"
2025-09-15 20:26:13.563 wdl.w:ptcp.t:call-tar_outputs-31 INFO input :: name: "paraphase_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2128.paraphase.bam"
2025-09-15 20:26:13.563 wdl.w:ptcp.t:call-tar_outputs-31 INFO input :: name: "paraphase_json", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2128.paraphase.json"
2025-09-15 20:26:13.563 wdl.w:ptcp.t:call-tar_outputs-31 INFO input :: name: "trgt_spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2128.trgt.sorted.spanning.bam.bai"
2025-09-15 20:26:13.563 wdl.w:ptcp.t:call-tar_outputs-31 INFO input :: name: "trgt_spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2128.trgt.sorted.spanning.bam"
2025-09-15 20:26:13.563 wdl.w:ptcp.t:call-tar_outputs-31 INFO input :: name: "trgt_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2128.trgt.vcf"
2025-09-15 20:26:13.563 wdl.w:ptcp.t:call-tar_outputs-31 INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2128.mapped.bam.bai"
2025-09-15 20:26:13.563 wdl.w:ptcp.t:call-tar_outputs-31 INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2128.mapped.bam"
2025-09-15 20:26:13.563 wdl.w:ptcp.w:call-paraphase-88.t:call-call_f8 NOTICE task setup :: name: "call_f8", source: "./paraphase.wdl", line: 232, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-88/call-call_f8", thread: 140607674631744
2025-09-15 20:26:13.563 wdl.w:ptcp.t:call-tar_outputs-31 INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2128"
2025-09-15 20:26:13.564 wdl.w:ptcp.t:call-tar_outputs-31 INFO eval :: name: "threads", value: 1
2025-09-15 20:26:13.564 wdl.w:ptcp.t:call-tar_outputs-31 INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:26:13.564 wdl.w:ptcp.t:call-tar_outputs-31 INFO eval :: name: "disk_size", value: 6
2025-09-15 20:26:13.564 wdl.w:ptcp.t:call-tar_outputs-31 INFO eval :: name: "output_tarball", value: "m84036_250809_035451_s4.bc2128.tar"
2025-09-15 20:26:13.565 wdl.w:ptcp.t:call-tar_outputs-31 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:26:13.565 wdl.w:ptcp.t:call-tar_outputs-31 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:26:13.565 wdl.w:ptcp.t:call-tar_outputs-31 INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:26:13.565 wdl.w:ptcp.t:call-tar_outputs-31 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:26:13.570 wdl.w:ptcp.w:call-sawfish-76.t:call-run_sawfish NOTICE done
2025-09-15 20:26:13.576 wdl.w:ptcp.w:call-sawfish-76 NOTICE finish :: job: "call-run_sawfish"
2025-09-15 20:26:13.577 wdl.w:ptcp.w:call-sawfish-76 INFO output :: job: "call-run_sawfish", values: {"minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-76/call-run_sawfish/out/m84036_250809_035451_s4.bc2173.minimap2.bam.bai", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-76/call-run_sawfish/out/m84036_250809_035451_s4.bc2173.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-76/call-run_sawfish/out/m84036_250809_035451_s4.bc2173_sawfish/m84036_250809_035451_s4.bc2173.sv.vcf.gz.tbi", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-76/call-run_sawfish/out/m84036_250809_035451_s4.bc2173_sawfish/m84036_250809_035451_s4.bc2173.sv.vcf.gz"}
2025-09-15 20:26:13.577 wdl.w:ptcp.w:call-sawfish-76 INFO visit :: node: "output-minimap2_bam", values: {"minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-76/call-run_sawfish/out/m84036_250809_035451_s4.bc2173.minimap2.bam"}
2025-09-15 20:26:13.578 wdl.w:ptcp.w:call-sawfish-76 INFO visit :: node: "output-minimap2_bam_bai", values: {"minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-76/call-run_sawfish/out/m84036_250809_035451_s4.bc2173.minimap2.bam.bai"}
2025-09-15 20:26:13.578 wdl.w:ptcp.w:call-sawfish-76 INFO visit :: node: "output-vcf", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-76/call-run_sawfish/out/m84036_250809_035451_s4.bc2173_sawfish/m84036_250809_035451_s4.bc2173.sv.vcf.gz"}
2025-09-15 20:26:13.578 wdl.w:ptcp.w:call-sawfish-76 INFO visit :: node: "output-vcf_tbi", values: {"vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-76/call-run_sawfish/out/m84036_250809_035451_s4.bc2173_sawfish/m84036_250809_035451_s4.bc2173.sv.vcf.gz.tbi"}
2025-09-15 20:26:13.578 wdl.w:ptcp.w:call-sawfish-76 INFO visit :: node: "outputs", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-76/call-run_sawfish/out/m84036_250809_035451_s4.bc2173_sawfish/m84036_250809_035451_s4.bc2173.sv.vcf.gz", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-76/call-run_sawfish/out/m84036_250809_035451_s4.bc2173.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-76/call-run_sawfish/out/m84036_250809_035451_s4.bc2173_sawfish/m84036_250809_035451_s4.bc2173.sv.vcf.gz.tbi", "minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-76/call-run_sawfish/out/m84036_250809_035451_s4.bc2173.minimap2.bam.bai"}
2025-09-15 20:26:13.584 wdl.w:ptcp.t:call-tar_outputs-34 NOTICE task setup :: name: "tar_outputs", source: "./common.wdl", line: 279, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-34", thread: 140609838900800
2025-09-15 20:26:13.586 wdl.w:ptcp.w:call-paraphase-88.t:call-call_f8 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:26:13.586 wdl.w:ptcp.w:call-paraphase-88.t:call-call_f8 INFO input :: name: "genome_version", value: "38"
2025-09-15 20:26:13.586 wdl.w:ptcp.w:call-paraphase-88.t:call-call_f8 INFO input :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2185"
2025-09-15 20:26:13.587 wdl.w:ptcp.w:call-paraphase-88.t:call-call_f8 INFO input :: name: "paraphase_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2185.paraphase.bam.bai"
2025-09-15 20:26:13.587 wdl.w:ptcp.w:call-paraphase-88.t:call-call_f8 INFO input :: name: "paraphase_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2185.paraphase.bam"
2025-09-15 20:26:13.587 wdl.w:ptcp.w:call-paraphase-88.t:call-call_f8 INFO input :: name: "sex", value: "F"
2025-09-15 20:26:13.587 wdl.w:ptcp.w:call-paraphase-88.t:call-call_f8 INFO eval :: name: "threads", value: 1
2025-09-15 20:26:13.587 wdl.w:ptcp.w:call-paraphase-88.t:call-call_f8 INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:26:13.587 wdl.w:ptcp.w:call-paraphase-88.t:call-call_f8 INFO eval :: name: "disk_size", value: 11
2025-09-15 20:26:13.587 wdl.w:ptcp.w:call-paraphase-88.t:call-call_f8 INFO eval :: name: "sample_sex", value: "F"
2025-09-15 20:26:13.588 wdl.w:ptcp.w:call-paraphase-88.t:call-call_f8 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:26:13.588 wdl.w:ptcp.w:call-paraphase-88.t:call-call_f8 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:26:13.588 wdl.w:ptcp.w:call-paraphase-88.t:call-call_f8 INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:26:13.588 wdl.w:ptcp.w:call-paraphase-88.t:call-call_f8 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:26:13.616 wdl.w:ptcp.t:call-tar_outputs-34 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:26:13.616 wdl.w:ptcp.t:call-tar_outputs-34 INFO input :: name: "sawfish_vcf_tbi", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2131.sv.vcf.gz.tbi"
2025-09-15 20:26:13.616 wdl.w:ptcp.t:call-tar_outputs-34 INFO input :: name: "sawfish_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2131.sv.vcf.gz"
2025-09-15 20:26:13.617 wdl.w:ptcp.t:call-tar_outputs-34 INFO input :: name: "f8_json", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2131.f8inversion.json"
2025-09-15 20:26:13.617 wdl.w:ptcp.t:call-tar_outputs-34 INFO input :: name: "paraphase_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2131.paraphase.bam.bai"
2025-09-15 20:26:13.617 wdl.w:ptcp.t:call-tar_outputs-34 INFO input :: name: "paraphase_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2131.paraphase.bam"
2025-09-15 20:26:13.617 wdl.w:ptcp.t:call-tar_outputs-34 INFO input :: name: "paraphase_json", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2131.paraphase.json"
2025-09-15 20:26:13.617 wdl.w:ptcp.t:call-tar_outputs-34 INFO input :: name: "trgt_spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2131.trgt.sorted.spanning.bam.bai"
2025-09-15 20:26:13.617 wdl.w:ptcp.t:call-tar_outputs-34 INFO input :: name: "trgt_spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2131.trgt.sorted.spanning.bam"
2025-09-15 20:26:13.617 wdl.w:ptcp.t:call-tar_outputs-34 INFO input :: name: "trgt_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2131.trgt.vcf"
2025-09-15 20:26:13.617 wdl.w:ptcp.t:call-tar_outputs-34 INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2131.mapped.bam.bai"
2025-09-15 20:26:13.617 wdl.w:ptcp.t:call-tar_outputs-34 INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2131.mapped.bam"
2025-09-15 20:26:13.617 wdl.w:ptcp.t:call-tar_outputs-34 INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2131"
2025-09-15 20:26:13.617 wdl.w:ptcp.t:call-tar_outputs-34 INFO eval :: name: "threads", value: 1
2025-09-15 20:26:13.617 wdl.w:ptcp.t:call-tar_outputs-34 INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:26:13.618 wdl.w:ptcp.t:call-tar_outputs-34 INFO eval :: name: "disk_size", value: 6
2025-09-15 20:26:13.618 wdl.w:ptcp.t:call-tar_outputs-34 INFO eval :: name: "output_tarball", value: "m84036_250809_035451_s4.bc2131.tar"
2025-09-15 20:26:13.618 wdl.w:ptcp.t:call-tar_outputs-34 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:26:13.618 wdl.w:ptcp.t:call-tar_outputs-34 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:26:13.619 wdl.w:ptcp.t:call-tar_outputs-34 INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:26:13.619 wdl.w:ptcp.t:call-tar_outputs-34 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:26:13.631 wdl.w:ptcp.w:call-paraphase-11.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for rpgr for sample m84036_250809_035451_s4.bc2108 at 2025-09-15 20:25:56.990637...
2025-09-15 20:26:13.631 wdl.w:ptcp.w:call-paraphase-11.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for rpgr for sample m84036_250809_035451_s4.bc2108 at 2025-09-15 20:25:57.942919...
2025-09-15 20:26:13.631 wdl.w:ptcp.w:call-paraphase-11.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for rpgr for sample m84036_250809_035451_s4.bc2108 at 2025-09-15 20:25:58.142730...
2025-09-15 20:26:13.631 wdl.w:ptcp.w:call-paraphase-11.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for f8inv22 for sample m84036_250809_035451_s4.bc2108 at 2025-09-15 20:26:09.704946...
2025-09-15 20:26:13.631 wdl.w:ptcp.w:call-paraphase-11.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for f8inv22 for sample m84036_250809_035451_s4.bc2108 at 2025-09-15 20:26:09.710155...
2025-09-15 20:26:13.665 wdl.w:ptcp.w:call-paraphase-88.t:call-call_f8 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 8, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-88/call-call_f8/_singularity_tmpdir_7lbvwm4k"
2025-09-15 20:26:13.665 wdl.w:ptcp.w:call-paraphase-88.t:call-call_f8 INFO Slurm invocation: srun --job-name call-call_f8 --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-88/call-call_f8/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-88/call-call_f8/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-88/call-call_f8/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-88/call-call_f8/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-88/call-run_paraphase/out/m84036_250809_035451_s4.bc2185_paraphase/m84036_250809_035451_s4.bc2185.paraphase.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2185.paraphase.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-88/call-run_paraphase/out/m84036_250809_035451_s4.bc2185_paraphase/m84036_250809_035451_s4.bc2185.paraphase.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2185.paraphase.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-88/call-call_f8/_singularity_tmpdir_7lbvwm4k/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-88/call-call_f8/_singularity_tmpdir_7lbvwm4k/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:26:13.666 wdl.w:ptcp.w:call-sawfish-76 NOTICE done
2025-09-15 20:26:13.677 wdl.w:ptcp.t:call-tar_outputs-41.stderr VERBOSE tar: Removing leading `/' from member names
2025-09-15 20:26:13.678 wdl.w:ptcp.t:call-tar_outputs-41.stderr VERBOSE tar: Removing leading `/' from hard link targets
2025-09-15 20:26:13.681 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:26:13 [ERROR] - No reads found for TRID=DRPLA_ATN1
2025-09-15 20:26:13.681 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:26:13 [ERROR] - No reads found for TRID=SCA2_ATXN2
2025-09-15 20:26:13.681 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:26:13 [ERROR] - No reads found for TRID=OPDM4_RILPL1
2025-09-15 20:26:13.681 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:26:13 [ERROR] - No reads found for TRID=NIID_NOTCH2NLC
2025-09-15 20:26:13.681 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:26:13 [ERROR] - No reads found for TRID=OPMD_PABPN1
2025-09-15 20:26:13.681 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:26:13 [ERROR] - No reads found for TRID=SCA27B_FGF14
2025-09-15 20:26:13.681 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:26:13 [ERROR] - No reads found for TRID=SCA37_DAB1
2025-09-15 20:26:13.695 wdl.w:ptcp NOTICE finish :: job: "call-sawfish-76"
2025-09-15 20:26:13.695 wdl.w:ptcp INFO output :: job: "call-sawfish-76", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-76/out/m84036_250809_035451_s4.bc2173_sawfish/m84036_250809_035451_s4.bc2173.sv.vcf.gz", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-76/out/m84036_250809_035451_s4.bc2173.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-76/out/m84036_250809_035451_s4.bc2173_sawfish/m84036_250809_035451_s4.bc2173.sv.vcf.gz.tbi", "minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-76/out/m84036_250809_035451_s4.bc2173.minimap2.bam.bai"}
2025-09-15 20:26:13.696 wdl.w:ptcp NOTICE ready :: job: "call-tar_outputs-76", callee: "tar_outputs"
2025-09-15 20:26:13.696 wdl.w:ptcp INFO input :: job: "call-tar_outputs-76", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "sawfish_vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-76/out/m84036_250809_035451_s4.bc2173_sawfish/m84036_250809_035451_s4.bc2173.sv.vcf.gz.tbi", "sawfish_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-76/out/m84036_250809_035451_s4.bc2173_sawfish/m84036_250809_035451_s4.bc2173.sv.vcf.gz", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-76/out/m84036_250809_035451_s4.bc2173.f8inversion.json", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-76/out/m84036_250809_035451_s4.bc2173_paraphase/m84036_250809_035451_s4.bc2173.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-76/out/m84036_250809_035451_s4.bc2173_paraphase/m84036_250809_035451_s4.bc2173.paraphase.bam", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-76/out/m84036_250809_035451_s4.bc2173_paraphase/m84036_250809_035451_s4.bc2173.paraphase.json", "trgt_spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-76/out/m84036_250809_035451_s4.bc2173.trgt.sorted.spanning.bam.bai", "trgt_spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-76/out/m84036_250809_035451_s4.bc2173.trgt.sorted.spanning.bam", "trgt_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-76/out/m84036_250809_035451_s4.bc2173.trgt.vcf", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-76/out/m84036_250809_035451_s4.bc2173.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-76/out/m84036_250809_035451_s4.bc2173.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2173"}
2025-09-15 20:26:13.700 wdl.w:ptcp.w:call-trgt-88.t:call-trgt_plot_meth_allele.slurm_singularity INFO srun: job 51798183 queued and waiting for resources
2025-09-15 20:26:13.700 wdl.w:ptcp.w:call-trgt-88.t:call-trgt_plot_meth_allele.slurm_singularity INFO srun: job 51798183 has been allocated resources
2025-09-15 20:26:13.700 wdl.w:ptcp.w:call-trgt-88.t:call-trgt_plot_meth_allele.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:26:13.702 wdl.w:ptcp.t:call-tar_outputs-41.slurm_singularity INFO srun: job 51798184 queued and waiting for resources
2025-09-15 20:26:13.702 wdl.w:ptcp.t:call-tar_outputs-41.slurm_singularity INFO srun: job 51798184 has been allocated resources
2025-09-15 20:26:13.702 wdl.w:ptcp.t:call-tar_outputs-41.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:26:13.705 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO srun: job 51798182 queued and waiting for resources
2025-09-15 20:26:13.705 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO srun: job 51798182 has been allocated resources
2025-09-15 20:26:13.706 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:26:13.707 wdl.w:ptcp.w:call-sawfish-84.t:call-run_sawfish NOTICE done
2025-09-15 20:26:13.709 wdl.w:ptcp.w:call-sawfish-74.t:call-run_sawfish INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2171_sawfish/m84036_250809_035451_s4.bc2171.sv.vcf.gz"
2025-09-15 20:26:13.713 wdl.w:ptcp.w:call-sawfish-84 NOTICE finish :: job: "call-run_sawfish"
2025-09-15 20:26:13.713 wdl.w:ptcp.w:call-sawfish-84 INFO output :: job: "call-run_sawfish", values: {"minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-84/call-run_sawfish/out/m84036_250809_035451_s4.bc2181.minimap2.bam.bai", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-84/call-run_sawfish/out/m84036_250809_035451_s4.bc2181.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-84/call-run_sawfish/out/m84036_250809_035451_s4.bc2181_sawfish/m84036_250809_035451_s4.bc2181.sv.vcf.gz.tbi", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-84/call-run_sawfish/out/m84036_250809_035451_s4.bc2181_sawfish/m84036_250809_035451_s4.bc2181.sv.vcf.gz"}
2025-09-15 20:26:13.713 wdl.w:ptcp.w:call-sawfish-84 INFO visit :: node: "output-minimap2_bam", values: {"minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-84/call-run_sawfish/out/m84036_250809_035451_s4.bc2181.minimap2.bam"}
2025-09-15 20:26:13.713 wdl.w:ptcp.w:call-sawfish-84 INFO visit :: node: "output-minimap2_bam_bai", values: {"minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-84/call-run_sawfish/out/m84036_250809_035451_s4.bc2181.minimap2.bam.bai"}
2025-09-15 20:26:13.714 wdl.w:ptcp.w:call-sawfish-84 INFO visit :: node: "output-vcf", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-84/call-run_sawfish/out/m84036_250809_035451_s4.bc2181_sawfish/m84036_250809_035451_s4.bc2181.sv.vcf.gz"}
2025-09-15 20:26:13.714 wdl.w:ptcp.w:call-sawfish-84 INFO visit :: node: "output-vcf_tbi", values: {"vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-84/call-run_sawfish/out/m84036_250809_035451_s4.bc2181_sawfish/m84036_250809_035451_s4.bc2181.sv.vcf.gz.tbi"}
2025-09-15 20:26:13.714 wdl.w:ptcp.w:call-sawfish-84 INFO visit :: node: "outputs", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-84/call-run_sawfish/out/m84036_250809_035451_s4.bc2181_sawfish/m84036_250809_035451_s4.bc2181.sv.vcf.gz", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-84/call-run_sawfish/out/m84036_250809_035451_s4.bc2181.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-84/call-run_sawfish/out/m84036_250809_035451_s4.bc2181_sawfish/m84036_250809_035451_s4.bc2181.sv.vcf.gz.tbi", "minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-84/call-run_sawfish/out/m84036_250809_035451_s4.bc2181.minimap2.bam.bai"}
2025-09-15 20:26:13.717 wdl.w:ptcp.w:call-paraphase-88.t:call-call_f8 NOTICE slurm_singularity run :: pid: 1207415, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-88/call-call_f8/slurm_singularity.log.txt"
2025-09-15 20:26:13.717 wdl.w:ptcp.w:call-sawfish-74.t:call-run_sawfish INFO output :: name: "vcf_tbi", value: "m84036_250809_035451_s4.bc2171_sawfish/m84036_250809_035451_s4.bc2171.sv.vcf.gz.tbi"
2025-09-15 20:26:13.719 wdl.w:ptcp.w:call-sawfish-74.t:call-run_sawfish INFO output :: name: "minimap2_bam", value: "m84036_250809_035451_s4.bc2171.minimap2.bam"
2025-09-15 20:26:13.721 wdl.w:ptcp.w:call-sawfish-74.t:call-run_sawfish INFO output :: name: "minimap2_bam_bai", value: "m84036_250809_035451_s4.bc2171.minimap2.bam.bai"
2025-09-15 20:26:13.723 wdl.w:ptcp.t:call-tar_outputs-76 NOTICE task setup :: name: "tar_outputs", source: "./common.wdl", line: 279, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-76", thread: 140613060126272
2025-09-15 20:26:13.738 wdl.w:ptcp.t:call-tar_outputs-31 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 17, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-31/_singularity_tmpdir_5wy37tyj"
2025-09-15 20:26:13.738 wdl.w:ptcp.t:call-tar_outputs-31 INFO Slurm invocation: srun --job-name call-tar_outputs-31 --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-31/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-31/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-31/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-31/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-31/out/m84036_250809_035451_s4.bc2128_sawfish/m84036_250809_035451_s4.bc2128.sv.vcf.gz:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2128.sv.vcf.gz:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-31/out/m84036_250809_035451_s4.bc2128_sawfish/m84036_250809_035451_s4.bc2128.sv.vcf.gz.tbi:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2128.sv.vcf.gz.tbi:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-31/out/m84036_250809_035451_s4.bc2128.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2128.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-31/out/m84036_250809_035451_s4.bc2128.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2128.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-31/out/m84036_250809_035451_s4.bc2128.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2128.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-31/out/m84036_250809_035451_s4.bc2128_paraphase/m84036_250809_035451_s4.bc2128.paraphase.json:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2128.paraphase.json:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-31/out/m84036_250809_035451_s4.bc2128_paraphase/m84036_250809_035451_s4.bc2128.paraphase.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2128.paraphase.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-31/out/m84036_250809_035451_s4.bc2128_paraphase/m84036_250809_035451_s4.bc2128.paraphase.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2128.paraphase.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-31/out/m84036_250809_035451_s4.bc2128.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2128.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-31/out/m84036_250809_035451_s4.bc2128.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2128.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-31/out/m84036_250809_035451_s4.bc2128.f8inversion.json:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2128.f8inversion.json:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-31/_singularity_tmpdir_5wy37tyj/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-31/_singularity_tmpdir_5wy37tyj/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:26:13.739 wdl.w:ptcp.w:call-trgt-89.t:call-trgt_plot_meth_allele INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2186.meth_allele.trgt_plots.zip"
2025-09-15 20:26:13.748 wdl.w:ptcp.w:call-sawfish-72.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:10][sawfish][INFO] Starting sawfish 2.0.3
2025-09-15 20:26:13.748 wdl.w:ptcp.w:call-sawfish-72.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:10][sawfish][INFO] cmdline: sawfish discover --disable-cnv --threads 16 --ref /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa --bam m84036_250809_035451_s4.bc2169.minimap2.bam --output-dir m84036_250809_035451_s4.bc2169_sawfish_discover
2025-09-15 20:26:13.749 wdl.w:ptcp.w:call-sawfish-72.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:10][sawfish][INFO] Running on 16 threads
2025-09-15 20:26:13.749 wdl.w:ptcp.w:call-sawfish-72.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:10][sawfish][INFO] Writing discover settings to file: 'm84036_250809_035451_s4.bc2169_sawfish_discover/discover.settings.json'
2025-09-15 20:26:13.749 wdl.w:ptcp.w:call-sawfish-72.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:10][sawfish][INFO] Reading reference genome from file '/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa'
2025-09-15 20:26:13.754 wdl.w:ptcp.t:call-tar_outputs-41 INFO output :: name: "sample_tarball", value: "m84036_250809_035451_s4.bc2138.tar"
2025-09-15 20:26:13.766 wdl.w:ptcp.t:call-tar_outputs-76 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:26:13.766 wdl.w:ptcp.t:call-tar_outputs-76 INFO input :: name: "sawfish_vcf_tbi", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2173.sv.vcf.gz.tbi"
2025-09-15 20:26:13.766 wdl.w:ptcp.t:call-tar_outputs-76 INFO input :: name: "sawfish_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2173.sv.vcf.gz"
2025-09-15 20:26:13.766 wdl.w:ptcp.t:call-tar_outputs-76 INFO input :: name: "f8_json", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2173.f8inversion.json"
2025-09-15 20:26:13.766 wdl.w:ptcp.t:call-tar_outputs-76 INFO input :: name: "paraphase_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2173.paraphase.bam.bai"
2025-09-15 20:26:13.766 wdl.w:ptcp.t:call-tar_outputs-76 INFO input :: name: "paraphase_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2173.paraphase.bam"
2025-09-15 20:26:13.767 wdl.w:ptcp.t:call-tar_outputs-76 INFO input :: name: "paraphase_json", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2173.paraphase.json"
2025-09-15 20:26:13.767 wdl.w:ptcp.t:call-tar_outputs-76 INFO input :: name: "trgt_spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2173.trgt.sorted.spanning.bam.bai"
2025-09-15 20:26:13.767 wdl.w:ptcp.t:call-tar_outputs-76 INFO input :: name: "trgt_spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2173.trgt.sorted.spanning.bam"
2025-09-15 20:26:13.767 wdl.w:ptcp.t:call-tar_outputs-76 INFO input :: name: "trgt_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2173.trgt.vcf"
2025-09-15 20:26:13.767 wdl.w:ptcp.t:call-tar_outputs-76 INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2173.mapped.bam.bai"
2025-09-15 20:26:13.767 wdl.w:ptcp.t:call-tar_outputs-76 INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2173.mapped.bam"
2025-09-15 20:26:13.767 wdl.w:ptcp.t:call-tar_outputs-76 INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2173"
2025-09-15 20:26:13.767 wdl.w:ptcp.t:call-tar_outputs-76 INFO eval :: name: "threads", value: 1
2025-09-15 20:26:13.767 wdl.w:ptcp.t:call-tar_outputs-76 INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:26:13.768 wdl.w:ptcp.t:call-tar_outputs-76 INFO eval :: name: "disk_size", value: 6
2025-09-15 20:26:13.768 wdl.w:ptcp.t:call-tar_outputs-76 INFO eval :: name: "output_tarball", value: "m84036_250809_035451_s4.bc2173.tar"
2025-09-15 20:26:13.769 wdl.w:ptcp.t:call-tar_outputs-76 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:26:13.769 wdl.w:ptcp.t:call-tar_outputs-76 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:26:13.770 wdl.w:ptcp.t:call-tar_outputs-76 INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:26:13.770 wdl.w:ptcp.t:call-tar_outputs-76 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:26:13.772 wdl.w:ptcp.t:call-tar_outputs-31 NOTICE slurm_singularity run :: pid: 1207417, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-31/slurm_singularity.log.txt"
2025-09-15 20:26:13.792 wdl.w:ptcp.t:call-tar_outputs-34 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 17, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-34/_singularity_tmpdir_0_oak9ij"
2025-09-15 20:26:13.792 wdl.w:ptcp.t:call-tar_outputs-34 INFO Slurm invocation: srun --job-name call-tar_outputs-34 --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-34/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-34/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-34/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-34/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-34/out/m84036_250809_035451_s4.bc2131_paraphase/m84036_250809_035451_s4.bc2131.paraphase.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2131.paraphase.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-34/out/m84036_250809_035451_s4.bc2131_paraphase/m84036_250809_035451_s4.bc2131.paraphase.json:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2131.paraphase.json:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-34/out/m84036_250809_035451_s4.bc2131_paraphase/m84036_250809_035451_s4.bc2131.paraphase.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2131.paraphase.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-34/out/m84036_250809_035451_s4.bc2131.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2131.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-34/out/m84036_250809_035451_s4.bc2131.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2131.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-34/out/m84036_250809_035451_s4.bc2131.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2131.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-34/out/m84036_250809_035451_s4.bc2131.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2131.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-34/out/m84036_250809_035451_s4.bc2131.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2131.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-34/out/m84036_250809_035451_s4.bc2131_sawfish/m84036_250809_035451_s4.bc2131.sv.vcf.gz.tbi:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2131.sv.vcf.gz.tbi:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-34/out/m84036_250809_035451_s4.bc2131_sawfish/m84036_250809_035451_s4.bc2131.sv.vcf.gz:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2131.sv.vcf.gz:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-34/out/m84036_250809_035451_s4.bc2131.f8inversion.json:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2131.f8inversion.json:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-34/_singularity_tmpdir_0_oak9ij/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-34/_singularity_tmpdir_0_oak9ij/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:26:13.803 wdl.w:ptcp.w:call-sawfish-84 NOTICE done
2025-09-15 20:26:13.804 wdl.w:ptcp.t:call-tar_outputs-34 NOTICE slurm_singularity run :: pid: 1207419, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-34/slurm_singularity.log.txt"
2025-09-15 20:26:13.810 wdl.w:ptcp NOTICE finish :: job: "call-sawfish-84"
2025-09-15 20:26:13.810 wdl.w:ptcp INFO output :: job: "call-sawfish-84", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-84/out/m84036_250809_035451_s4.bc2181_sawfish/m84036_250809_035451_s4.bc2181.sv.vcf.gz", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-84/out/m84036_250809_035451_s4.bc2181.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-84/out/m84036_250809_035451_s4.bc2181_sawfish/m84036_250809_035451_s4.bc2181.sv.vcf.gz.tbi", "minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-84/out/m84036_250809_035451_s4.bc2181.minimap2.bam.bai"}
2025-09-15 20:26:13.811 wdl.w:ptcp NOTICE ready :: job: "call-tar_outputs-84", callee: "tar_outputs"
2025-09-15 20:26:13.811 wdl.w:ptcp INFO input :: job: "call-tar_outputs-84", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "sawfish_vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-84/out/m84036_250809_035451_s4.bc2181_sawfish/m84036_250809_035451_s4.bc2181.sv.vcf.gz.tbi", "sawfish_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-84/out/m84036_250809_035451_s4.bc2181_sawfish/m84036_250809_035451_s4.bc2181.sv.vcf.gz", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-84/out/m84036_250809_035451_s4.bc2181.f8inversion.json", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-84/out/m84036_250809_035451_s4.bc2181_paraphase/m84036_250809_035451_s4.bc2181.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-84/out/m84036_250809_035451_s4.bc2181_paraphase/m84036_250809_035451_s4.bc2181.paraphase.bam", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-84/out/m84036_250809_035451_s4.bc2181_paraphase/m84036_250809_035451_s4.bc2181.paraphase.json", "trgt_spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-84/out/m84036_250809_035451_s4.bc2181.trgt.sorted.spanning.bam.bai", "trgt_spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-84/out/m84036_250809_035451_s4.bc2181.trgt.sorted.spanning.bam", "trgt_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-84/out/m84036_250809_035451_s4.bc2181.trgt.vcf", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-84/out/m84036_250809_035451_s4.bc2181.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-84/out/m84036_250809_035451_s4.bc2181.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2181"}
2025-09-15 20:26:13.839 wdl.w:ptcp.t:call-tar_outputs-41 NOTICE done
2025-09-15 20:26:13.845 wdl.w:ptcp NOTICE finish :: job: "call-tar_outputs-41"
2025-09-15 20:26:13.845 wdl.w:ptcp INFO output :: job: "call-tar_outputs-41", values: {"sample_tarball": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-41/out/m84036_250809_035451_s4.bc2138.tar"}
2025-09-15 20:26:13.855 wdl.w:ptcp.t:call-tar_outputs-84 NOTICE task setup :: name: "tar_outputs", source: "./common.wdl", line: 279, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-84", thread: 140609822115392
2025-09-15 20:26:13.885 wdl.w:ptcp.t:call-tar_outputs-84 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:26:13.885 wdl.w:ptcp.t:call-tar_outputs-84 INFO input :: name: "sawfish_vcf_tbi", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2181.sv.vcf.gz.tbi"
2025-09-15 20:26:13.885 wdl.w:ptcp.t:call-tar_outputs-84 INFO input :: name: "sawfish_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2181.sv.vcf.gz"
2025-09-15 20:26:13.885 wdl.w:ptcp.t:call-tar_outputs-84 INFO input :: name: "f8_json", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2181.f8inversion.json"
2025-09-15 20:26:13.885 wdl.w:ptcp.t:call-tar_outputs-84 INFO input :: name: "paraphase_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2181.paraphase.bam.bai"
2025-09-15 20:26:13.885 wdl.w:ptcp.t:call-tar_outputs-84 INFO input :: name: "paraphase_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2181.paraphase.bam"
2025-09-15 20:26:13.885 wdl.w:ptcp.t:call-tar_outputs-84 INFO input :: name: "paraphase_json", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2181.paraphase.json"
2025-09-15 20:26:13.885 wdl.w:ptcp.t:call-tar_outputs-84 INFO input :: name: "trgt_spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2181.trgt.sorted.spanning.bam.bai"
2025-09-15 20:26:13.885 wdl.w:ptcp.t:call-tar_outputs-84 INFO input :: name: "trgt_spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2181.trgt.sorted.spanning.bam"
2025-09-15 20:26:13.885 wdl.w:ptcp.t:call-tar_outputs-84 INFO input :: name: "trgt_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2181.trgt.vcf"
2025-09-15 20:26:13.886 wdl.w:ptcp.t:call-tar_outputs-84 INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2181.mapped.bam.bai"
2025-09-15 20:26:13.886 wdl.w:ptcp.t:call-tar_outputs-84 INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2181.mapped.bam"
2025-09-15 20:26:13.886 wdl.w:ptcp.t:call-tar_outputs-84 INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2181"
2025-09-15 20:26:13.886 wdl.w:ptcp.t:call-tar_outputs-84 INFO eval :: name: "threads", value: 1
2025-09-15 20:26:13.886 wdl.w:ptcp.t:call-tar_outputs-84 INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:26:13.887 wdl.w:ptcp.t:call-tar_outputs-84 INFO eval :: name: "disk_size", value: 6
2025-09-15 20:26:13.887 wdl.w:ptcp.t:call-tar_outputs-84 INFO eval :: name: "output_tarball", value: "m84036_250809_035451_s4.bc2181.tar"
2025-09-15 20:26:13.887 wdl.w:ptcp.t:call-tar_outputs-84 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:26:13.887 wdl.w:ptcp.t:call-tar_outputs-84 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:26:13.888 wdl.w:ptcp.t:call-tar_outputs-84 INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:26:13.888 wdl.w:ptcp.t:call-tar_outputs-84 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:26:13.903 wdl.w:ptcp.t:call-tar_outputs-76 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 17, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-76/_singularity_tmpdir_g9z7zv6z"
2025-09-15 20:26:13.903 wdl.w:ptcp.t:call-tar_outputs-76 INFO Slurm invocation: srun --job-name call-tar_outputs-76 --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-76/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-76/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-76/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-76/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-76/out/m84036_250809_035451_s4.bc2173.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2173.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-76/out/m84036_250809_035451_s4.bc2173.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2173.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-76/out/m84036_250809_035451_s4.bc2173.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2173.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-76/out/m84036_250809_035451_s4.bc2173.f8inversion.json:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2173.f8inversion.json:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-76/out/m84036_250809_035451_s4.bc2173_sawfish/m84036_250809_035451_s4.bc2173.sv.vcf.gz:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2173.sv.vcf.gz:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-76/out/m84036_250809_035451_s4.bc2173_sawfish/m84036_250809_035451_s4.bc2173.sv.vcf.gz.tbi:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2173.sv.vcf.gz.tbi:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-76/out/m84036_250809_035451_s4.bc2173_paraphase/m84036_250809_035451_s4.bc2173.paraphase.json:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2173.paraphase.json:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-76/out/m84036_250809_035451_s4.bc2173_paraphase/m84036_250809_035451_s4.bc2173.paraphase.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2173.paraphase.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-76/out/m84036_250809_035451_s4.bc2173_paraphase/m84036_250809_035451_s4.bc2173.paraphase.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2173.paraphase.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-76/out/m84036_250809_035451_s4.bc2173.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2173.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-76/out/m84036_250809_035451_s4.bc2173.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2173.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-76/_singularity_tmpdir_g9z7zv6z/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-76/_singularity_tmpdir_g9z7zv6z/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:26:13.912 wdl.w:ptcp.t:call-tar_outputs-76 NOTICE slurm_singularity run :: pid: 1207421, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-76/slurm_singularity.log.txt"
2025-09-15 20:26:13.914 wdl.w:ptcp.w:call-sawfish-74.t:call-run_sawfish NOTICE done
2025-09-15 20:26:13.920 wdl.w:ptcp.w:call-sawfish-74 NOTICE finish :: job: "call-run_sawfish"
2025-09-15 20:26:13.920 wdl.w:ptcp.w:call-sawfish-74 INFO output :: job: "call-run_sawfish", values: {"minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-74/call-run_sawfish/out/m84036_250809_035451_s4.bc2171.minimap2.bam.bai", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-74/call-run_sawfish/out/m84036_250809_035451_s4.bc2171.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-74/call-run_sawfish/out/m84036_250809_035451_s4.bc2171_sawfish/m84036_250809_035451_s4.bc2171.sv.vcf.gz.tbi", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-74/call-run_sawfish/out/m84036_250809_035451_s4.bc2171_sawfish/m84036_250809_035451_s4.bc2171.sv.vcf.gz"}
2025-09-15 20:26:13.921 wdl.w:ptcp.w:call-sawfish-74 INFO visit :: node: "output-minimap2_bam", values: {"minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-74/call-run_sawfish/out/m84036_250809_035451_s4.bc2171.minimap2.bam"}
2025-09-15 20:26:13.921 wdl.w:ptcp.w:call-sawfish-74 INFO visit :: node: "output-minimap2_bam_bai", values: {"minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-74/call-run_sawfish/out/m84036_250809_035451_s4.bc2171.minimap2.bam.bai"}
2025-09-15 20:26:13.921 wdl.w:ptcp.w:call-sawfish-74 INFO visit :: node: "output-vcf", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-74/call-run_sawfish/out/m84036_250809_035451_s4.bc2171_sawfish/m84036_250809_035451_s4.bc2171.sv.vcf.gz"}
2025-09-15 20:26:13.921 wdl.w:ptcp.w:call-sawfish-74 INFO visit :: node: "output-vcf_tbi", values: {"vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-74/call-run_sawfish/out/m84036_250809_035451_s4.bc2171_sawfish/m84036_250809_035451_s4.bc2171.sv.vcf.gz.tbi"}
2025-09-15 20:26:13.921 wdl.w:ptcp.w:call-sawfish-74 INFO visit :: node: "outputs", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-74/call-run_sawfish/out/m84036_250809_035451_s4.bc2171_sawfish/m84036_250809_035451_s4.bc2171.sv.vcf.gz", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-74/call-run_sawfish/out/m84036_250809_035451_s4.bc2171.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-74/call-run_sawfish/out/m84036_250809_035451_s4.bc2171_sawfish/m84036_250809_035451_s4.bc2171.sv.vcf.gz.tbi", "minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-74/call-run_sawfish/out/m84036_250809_035451_s4.bc2171.minimap2.bam.bai"}
2025-09-15 20:26:13.924 wdl.w:ptcp.w:call-trgt-89.t:call-trgt_plot_meth_allele NOTICE done
2025-09-15 20:26:13.940 wdl.w:ptcp.w:call-trgt-89 NOTICE finish :: job: "call-trgt_plot_meth_allele"
2025-09-15 20:26:13.940 wdl.w:ptcp.w:call-trgt-89 INFO output :: job: "call-trgt_plot_meth_allele", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-89/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2186.meth_allele.trgt_plots.zip"}
2025-09-15 20:26:13.942 wdl.w:ptcp.w:call-trgt-89 INFO visit :: node: "output-images_meth_allele", values: {"images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-89/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2186.meth_allele.trgt_plots.zip"}
2025-09-15 20:26:13.943 wdl.w:ptcp.w:call-trgt-89 INFO visit :: node: "outputs", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-89/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2186.motifs_waterfall.trgt_plots.zip", "images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-89/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2186.meth_allele.trgt_plots.zip", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-89/call-trgt_genotype/out/m84036_250809_035451_s4.bc2186.trgt.sorted.spanning.bam.bai", "images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-89/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2186.motifs_allele.trgt_plots.zip", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-89/call-trgt_genotype/out/m84036_250809_035451_s4.bc2186.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-89/call-trgt_genotype/out/m84036_250809_035451_s4.bc2186.trgt.vcf", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-89/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2186.repeats.bam", "images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-89/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2186.meth_waterfall.trgt_plots.zip", "reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-89/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2186.repeats.bam.bai"}
2025-09-15 20:26:13.978 wdl.w:ptcp.w:call-sawfish-74 NOTICE done
2025-09-15 20:26:13.984 wdl.w:ptcp NOTICE finish :: job: "call-sawfish-74"
2025-09-15 20:26:13.984 wdl.w:ptcp INFO output :: job: "call-sawfish-74", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-74/out/m84036_250809_035451_s4.bc2171_sawfish/m84036_250809_035451_s4.bc2171.sv.vcf.gz", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-74/out/m84036_250809_035451_s4.bc2171.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-74/out/m84036_250809_035451_s4.bc2171_sawfish/m84036_250809_035451_s4.bc2171.sv.vcf.gz.tbi", "minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-74/out/m84036_250809_035451_s4.bc2171.minimap2.bam.bai"}
2025-09-15 20:26:13.991 wdl.w:ptcp.t:call-tar_outputs-84 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 17, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-84/_singularity_tmpdir_uv6hnit4"
2025-09-15 20:26:13.991 wdl.w:ptcp.t:call-tar_outputs-84 INFO Slurm invocation: srun --job-name call-tar_outputs-84 --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-84/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-84/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-84/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-84/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-84/out/m84036_250809_035451_s4.bc2181.f8inversion.json:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2181.f8inversion.json:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-84/out/m84036_250809_035451_s4.bc2181_paraphase/m84036_250809_035451_s4.bc2181.paraphase.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2181.paraphase.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-84/out/m84036_250809_035451_s4.bc2181_paraphase/m84036_250809_035451_s4.bc2181.paraphase.json:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2181.paraphase.json:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-84/out/m84036_250809_035451_s4.bc2181_paraphase/m84036_250809_035451_s4.bc2181.paraphase.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2181.paraphase.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-84/out/m84036_250809_035451_s4.bc2181_sawfish/m84036_250809_035451_s4.bc2181.sv.vcf.gz.tbi:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2181.sv.vcf.gz.tbi:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-84/out/m84036_250809_035451_s4.bc2181_sawfish/m84036_250809_035451_s4.bc2181.sv.vcf.gz:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2181.sv.vcf.gz:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-84/out/m84036_250809_035451_s4.bc2181.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2181.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-84/out/m84036_250809_035451_s4.bc2181.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2181.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-84/out/m84036_250809_035451_s4.bc2181.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2181.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-84/out/m84036_250809_035451_s4.bc2181.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2181.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-84/out/m84036_250809_035451_s4.bc2181.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2181.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-84/_singularity_tmpdir_uv6hnit4/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-84/_singularity_tmpdir_uv6hnit4/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:26:13.998 wdl.w:ptcp.t:call-tar_outputs-84 NOTICE slurm_singularity run :: pid: 1207423, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-84/slurm_singularity.log.txt"
2025-09-15 20:26:14.046 wdl.w:ptcp.w:call-trgt-89 NOTICE done
2025-09-15 20:26:14.051 wdl.w:ptcp NOTICE finish :: job: "call-trgt-89"
2025-09-15 20:26:14.051 wdl.w:ptcp INFO output :: job: "call-trgt-89", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-89/out/m84036_250809_035451_s4.bc2186.motifs_waterfall.trgt_plots.zip", "images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-89/out/m84036_250809_035451_s4.bc2186.meth_allele.trgt_plots.zip", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-89/out/m84036_250809_035451_s4.bc2186.trgt.sorted.spanning.bam.bai", "images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-89/out/m84036_250809_035451_s4.bc2186.motifs_allele.trgt_plots.zip", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-89/out/m84036_250809_035451_s4.bc2186.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-89/out/m84036_250809_035451_s4.bc2186.trgt.vcf", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-89/out/m84036_250809_035451_s4.bc2186.repeats.bam", "images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-89/out/m84036_250809_035451_s4.bc2186.meth_waterfall.trgt_plots.zip", "reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-89/out/m84036_250809_035451_s4.bc2186.repeats.bam.bai"}
2025-09-15 20:26:14.104 wdl.w:ptcp.t:call-tar_outputs-57 INFO output :: name: "sample_tarball", value: "m84036_250809_035451_s4.bc2154.tar"
2025-09-15 20:26:14.169 wdl.w:ptcp.w:call-trgt-88.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO srun: job 51798185 queued and waiting for resources
2025-09-15 20:26:14.169 wdl.w:ptcp.w:call-trgt-88.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO srun: job 51798185 has been allocated resources
2025-09-15 20:26:14.169 wdl.w:ptcp.w:call-trgt-88.t:call-trgt_plot_meth_waterfall.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:26:14.179 wdl.w:ptcp.w:call-trgt-88.t:call-trgt_plot_motifs_allele.slurm_singularity INFO srun: job 51798186 queued and waiting for resources
2025-09-15 20:26:14.179 wdl.w:ptcp.w:call-trgt-88.t:call-trgt_plot_motifs_allele.slurm_singularity INFO srun: job 51798186 has been allocated resources
2025-09-15 20:26:14.179 wdl.w:ptcp.w:call-trgt-88.t:call-trgt_plot_motifs_allele.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:26:14.221 wdl.w:ptcp.w:call-trgt-93.t:call-trgt_plot_meth_allele INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2190.meth_allele.trgt_plots.zip"
2025-09-15 20:26:14.225 wdl.w:ptcp.w:call-sawfish-63.t:call-run_sawfish INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2160_sawfish/m84036_250809_035451_s4.bc2160.sv.vcf.gz"
2025-09-15 20:26:14.237 wdl.w:ptcp.w:call-sawfish-63.t:call-run_sawfish INFO output :: name: "vcf_tbi", value: "m84036_250809_035451_s4.bc2160_sawfish/m84036_250809_035451_s4.bc2160.sv.vcf.gz.tbi"
2025-09-15 20:26:14.238 wdl.w:ptcp.w:call-sawfish-63.t:call-run_sawfish INFO output :: name: "minimap2_bam", value: "m84036_250809_035451_s4.bc2160.minimap2.bam"
2025-09-15 20:26:14.240 wdl.w:ptcp.w:call-sawfish-63.t:call-run_sawfish INFO output :: name: "minimap2_bam_bai", value: "m84036_250809_035451_s4.bc2160.minimap2.bam.bai"
2025-09-15 20:26:14.242 wdl.w:ptcp.t:call-tar_outputs-57 NOTICE done
2025-09-15 20:26:14.246 wdl.w:ptcp NOTICE finish :: job: "call-tar_outputs-57"
2025-09-15 20:26:14.246 wdl.w:ptcp INFO output :: job: "call-tar_outputs-57", values: {"sample_tarball": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-57/out/m84036_250809_035451_s4.bc2154.tar"}
2025-09-15 20:26:14.249 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:26:11 [ERROR] - No reads found for TRID=CCHS_PHOX2B
2025-09-15 20:26:14.249 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:26:11 [ERROR] - No reads found for TRID=HD_HTT
2025-09-15 20:26:14.249 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:26:11 [ERROR] - No reads found for TRID=DM2_CNBP
2025-09-15 20:26:14.249 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:26:11 [ERROR] - No reads found for TRID=FAME1_SAMD12
2025-09-15 20:26:14.249 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:26:12 [ERROR] - No reads found for TRID=FTDALS1_C9orf72
2025-09-15 20:26:14.249 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:26:12 [ERROR] - No reads found for TRID=OPDM1_LRP12
2025-09-15 20:26:14.249 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:26:12 [ERROR] - No reads found for TRID=SCA1_ATXN1
2025-09-15 20:26:14.249 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:26:12 [ERROR] - No reads found for TRID=SCA7_ATXN7
2025-09-15 20:26:14.249 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:26:12 [ERROR] - No reads found for TRID=SBMA_AR
2025-09-15 20:26:14.260 wdl.w:ptcp.w:call-paraphase-62.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for cyp21 for sample m84036_250809_035451_s4.bc2159 at 2025-09-15 20:25:28.830215...
2025-09-15 20:26:14.261 wdl.w:ptcp.w:call-paraphase-62.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for cyp21 for sample m84036_250809_035451_s4.bc2159 at 2025-09-15 20:25:29.988736...
2025-09-15 20:26:14.261 wdl.w:ptcp.w:call-paraphase-62.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for hba for sample m84036_250809_035451_s4.bc2159 at 2025-09-15 20:25:38.201902...
2025-09-15 20:26:14.261 wdl.w:ptcp.w:call-paraphase-62.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for hba for sample m84036_250809_035451_s4.bc2159 at 2025-09-15 20:25:38.805341...
2025-09-15 20:26:14.261 wdl.w:ptcp.w:call-paraphase-62.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for gba for sample m84036_250809_035451_s4.bc2159 at 2025-09-15 20:25:40.693942...
2025-09-15 20:26:14.261 wdl.w:ptcp.w:call-paraphase-62.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for gba for sample m84036_250809_035451_s4.bc2159 at 2025-09-15 20:25:41.351469...
2025-09-15 20:26:14.261 wdl.w:ptcp.w:call-paraphase-62.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for hbb for sample m84036_250809_035451_s4.bc2159 at 2025-09-15 20:26:08.814812...
2025-09-15 20:26:14.261 wdl.w:ptcp.w:call-paraphase-62.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for hbb for sample m84036_250809_035451_s4.bc2159 at 2025-09-15 20:26:08.814962...
2025-09-15 20:26:14.261 wdl.w:ptcp.w:call-paraphase-62.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for hbb for sample m84036_250809_035451_s4.bc2159 at 2025-09-15 20:26:10.193271...
2025-09-15 20:26:14.334 wdl.w:ptcp.w:call-trgt-88.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO srun: job 51798187 queued and waiting for resources
2025-09-15 20:26:14.334 wdl.w:ptcp.w:call-trgt-88.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO srun: job 51798187 has been allocated resources
2025-09-15 20:26:14.334 wdl.w:ptcp.w:call-trgt-88.t:call-trgt_plot_motifs_waterfall.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:26:14.390 wdl.w:ptcp.w:call-trgt-93.t:call-trgt_plot_meth_allele NOTICE done
2025-09-15 20:26:14.395 wdl.w:ptcp.w:call-trgt-93 NOTICE finish :: job: "call-trgt_plot_meth_allele"
2025-09-15 20:26:14.395 wdl.w:ptcp.w:call-trgt-93 INFO output :: job: "call-trgt_plot_meth_allele", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-93/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2190.meth_allele.trgt_plots.zip"}
2025-09-15 20:26:14.396 wdl.w:ptcp.w:call-trgt-93 INFO visit :: node: "output-images_meth_allele", values: {"images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-93/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2190.meth_allele.trgt_plots.zip"}
2025-09-15 20:26:14.413 wdl.w:ptcp.w:call-sawfish-63.t:call-run_sawfish NOTICE done
2025-09-15 20:26:14.420 wdl.w:ptcp.w:call-sawfish-63 NOTICE finish :: job: "call-run_sawfish"
2025-09-15 20:26:14.421 wdl.w:ptcp.w:call-sawfish-63 INFO output :: job: "call-run_sawfish", values: {"minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-63/call-run_sawfish/out/m84036_250809_035451_s4.bc2160.minimap2.bam.bai", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-63/call-run_sawfish/out/m84036_250809_035451_s4.bc2160.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-63/call-run_sawfish/out/m84036_250809_035451_s4.bc2160_sawfish/m84036_250809_035451_s4.bc2160.sv.vcf.gz.tbi", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-63/call-run_sawfish/out/m84036_250809_035451_s4.bc2160_sawfish/m84036_250809_035451_s4.bc2160.sv.vcf.gz"}
2025-09-15 20:26:14.421 wdl.w:ptcp.w:call-sawfish-63 INFO visit :: node: "output-minimap2_bam", values: {"minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-63/call-run_sawfish/out/m84036_250809_035451_s4.bc2160.minimap2.bam"}
2025-09-15 20:26:14.421 wdl.w:ptcp.w:call-sawfish-63 INFO visit :: node: "output-minimap2_bam_bai", values: {"minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-63/call-run_sawfish/out/m84036_250809_035451_s4.bc2160.minimap2.bam.bai"}
2025-09-15 20:26:14.421 wdl.w:ptcp.w:call-sawfish-63 INFO visit :: node: "output-vcf", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-63/call-run_sawfish/out/m84036_250809_035451_s4.bc2160_sawfish/m84036_250809_035451_s4.bc2160.sv.vcf.gz"}
2025-09-15 20:26:14.421 wdl.w:ptcp.w:call-sawfish-63 INFO visit :: node: "output-vcf_tbi", values: {"vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-63/call-run_sawfish/out/m84036_250809_035451_s4.bc2160_sawfish/m84036_250809_035451_s4.bc2160.sv.vcf.gz.tbi"}
2025-09-15 20:26:14.421 wdl.w:ptcp.w:call-sawfish-63 INFO visit :: node: "outputs", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-63/call-run_sawfish/out/m84036_250809_035451_s4.bc2160_sawfish/m84036_250809_035451_s4.bc2160.sv.vcf.gz", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-63/call-run_sawfish/out/m84036_250809_035451_s4.bc2160.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-63/call-run_sawfish/out/m84036_250809_035451_s4.bc2160_sawfish/m84036_250809_035451_s4.bc2160.sv.vcf.gz.tbi", "minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-63/call-run_sawfish/out/m84036_250809_035451_s4.bc2160.minimap2.bam.bai"}
2025-09-15 20:26:14.474 wdl.w:ptcp.w:call-sawfish-63 NOTICE done
2025-09-15 20:26:14.481 wdl.w:ptcp NOTICE finish :: job: "call-sawfish-63"
2025-09-15 20:26:14.481 wdl.w:ptcp INFO output :: job: "call-sawfish-63", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-63/out/m84036_250809_035451_s4.bc2160_sawfish/m84036_250809_035451_s4.bc2160.sv.vcf.gz", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-63/out/m84036_250809_035451_s4.bc2160.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-63/out/m84036_250809_035451_s4.bc2160_sawfish/m84036_250809_035451_s4.bc2160.sv.vcf.gz.tbi", "minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-63/out/m84036_250809_035451_s4.bc2160.minimap2.bam.bai"}
2025-09-15 20:26:14.521 wdl.w:ptcp.w:call-sawfish-56.t:call-run_sawfish.stderr VERBOSE [M::mm_idx_gen::53.935*1.75] collected minimizers
2025-09-15 20:26:14.522 wdl.w:ptcp.w:call-sawfish-56.t:call-run_sawfish.stderr VERBOSE [M::mm_idx_gen::64.604*1.93] sorted minimizers
2025-09-15 20:26:14.522 wdl.w:ptcp.w:call-sawfish-56.t:call-run_sawfish.stderr VERBOSE [M::main::64.609*1.93] loaded/built the index for 195 target sequence(s)
2025-09-15 20:26:14.522 wdl.w:ptcp.w:call-sawfish-56.t:call-run_sawfish.stderr VERBOSE [M::mm_mapopt_update::71.328*1.84] mid_occ = 136
2025-09-15 20:26:14.522 wdl.w:ptcp.w:call-sawfish-56.t:call-run_sawfish.stderr VERBOSE [M::mm_idx_stat] kmer size: 19; skip: 19; is_hpc: 0; #seq: 195
2025-09-15 20:26:14.522 wdl.w:ptcp.w:call-sawfish-56.t:call-run_sawfish.stderr VERBOSE [M::mm_idx_stat::76.517*1.79] distinct minimizers: 214664461 (92.23% are singletons); average occurrences: 1.372; average spacing: 10.529; total length: 3099922541
2025-09-15 20:26:14.522 wdl.w:ptcp.w:call-sawfish-56.t:call-run_sawfish.stderr VERBOSE [M::worker_pipeline::76.519*1.79] mapped 1 sequences
2025-09-15 20:26:14.522 wdl.w:ptcp.w:call-sawfish-56.t:call-run_sawfish.stderr VERBOSE [M::main] Version: 2.26-r1175
2025-09-15 20:26:14.522 wdl.w:ptcp.w:call-sawfish-56.t:call-run_sawfish.stderr VERBOSE [M::main] CMD: /opt/pacbio/smrttools/install/smrtlink-release_25.1.0.257715/bundles/smrttools/install/smrttools-release_25.1.0.257715/private/thirdparty/minimap2/minimap2_2.26-pacbio2/binwrap/../../../../../private/thirdparty/minimap2/minimap2_2.26-pacbio2/bin/minimap2 -a -y -x map-hifi -Y -E 1,0 /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa -
2025-09-15 20:26:14.522 wdl.w:ptcp.w:call-sawfish-56.t:call-run_sawfish.stderr VERBOSE [M::main] Real time: 77.126 sec; CPU: 137.336 sec; Peak RSS: 11.886 GB
2025-09-15 20:26:14.522 wdl.w:ptcp.w:call-sawfish-56.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:58][sawfish][INFO] Starting sawfish 2.0.3
2025-09-15 20:26:14.522 wdl.w:ptcp.w:call-sawfish-56.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:58][sawfish][INFO] cmdline: sawfish discover --disable-cnv --threads 16 --ref /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa --bam m84036_250809_035451_s4.bc2153.minimap2.bam --output-dir m84036_250809_035451_s4.bc2153_sawfish_discover
2025-09-15 20:26:14.522 wdl.w:ptcp.w:call-sawfish-56.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:58][sawfish][INFO] Running on 16 threads
2025-09-15 20:26:14.522 wdl.w:ptcp.w:call-sawfish-56.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:58][sawfish][INFO] Writing discover settings to file: 'm84036_250809_035451_s4.bc2153_sawfish_discover/discover.settings.json'
2025-09-15 20:26:14.522 wdl.w:ptcp.w:call-sawfish-56.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:58][sawfish][INFO] Reading reference genome from file '/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa'
2025-09-15 20:26:14.522 wdl.w:ptcp.w:call-sawfish-56.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:07][sawfish][INFO] Processing alignment file '/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2153.minimap2.bam'
2025-09-15 20:26:14.522 wdl.w:ptcp.w:call-sawfish-56.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:07][sawfish][INFO] Finished processing all alignments
2025-09-15 20:26:14.523 wdl.w:ptcp.w:call-sawfish-56.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:07][sawfish][INFO] Writing depth bins to binary file: 'm84036_250809_035451_s4.bc2153_sawfish_discover/depth.mpack'
2025-09-15 20:26:14.523 wdl.w:ptcp.w:call-sawfish-56.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:07][sawfish][INFO] Writing max sv depth genome regions to bed file: 'm84036_250809_035451_s4.bc2153_sawfish_discover/max.depth.bed'
2025-09-15 20:26:14.523 wdl.w:ptcp.w:call-sawfish-56.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:07][sawfish][INFO] Completing breakpoint observation clustering
2025-09-15 20:26:14.523 wdl.w:ptcp.w:call-sawfish-56.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:07][sawfish][INFO] Finished breakpoint observation clustering
2025-09-15 20:26:14.523 wdl.w:ptcp.w:call-sawfish-56.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:07][sawfish][INFO] Consolidating adjacent indel candidates
2025-09-15 20:26:14.523 wdl.w:ptcp.w:call-sawfish-56.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:07][sawfish][INFO] Finding large insertion candidates
2025-09-15 20:26:14.523 wdl.w:ptcp.w:call-sawfish-56.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:07][sawfish][INFO] Writing breakpoint_cluster debug bed file: 'm84036_250809_035451_s4.bc2153_sawfish_discover/debug.breakpoint_clusters.bed'
2025-09-15 20:26:14.523 wdl.w:ptcp.w:call-sawfish-56.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:07][sawfish][INFO] Refining SV Candidates
2025-09-15 20:26:14.523 wdl.w:ptcp.w:call-sawfish-56.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:07][sawfish][INFO] Writing debug assembly region bed file: 'm84036_250809_035451_s4.bc2153_sawfish_discover/assembly.regions.bed'
2025-09-15 20:26:14.523 wdl.w:ptcp.w:call-sawfish-56.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:07][sawfish][INFO] Starting refinement of breakpoint evidence clusters
2025-09-15 20:26:14.523 wdl.w:ptcp.w:call-sawfish-56.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:07][sawfish][INFO] Finished refining all breakpoint evidence clusters
2025-09-15 20:26:14.523 wdl.w:ptcp.w:call-sawfish-56.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:07][sawfish][INFO] Writing all contig alignments to bam file: 'm84036_250809_035451_s4.bc2153_sawfish_discover/contig.alignment.bam'
2025-09-15 20:26:14.523 wdl.w:ptcp.w:call-sawfish-56.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:08][sawfish][INFO] Writing candidate structural variants to file: 'm84036_250809_035451_s4.bc2153_sawfish_discover/candidate.sv.bcf'
2025-09-15 20:26:14.523 wdl.w:ptcp.w:call-sawfish-56.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:08][sawfish][INFO] Writing run statistics to file: 'm84036_250809_035451_s4.bc2153_sawfish_discover/run.stats.json'
2025-09-15 20:26:14.523 wdl.w:ptcp.w:call-sawfish-56.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:08][sawfish][INFO] sawfish completed. Total Runtime: 00:00:10.465
2025-09-15 20:26:14.699 wdl.w:ptcp.w:call-trgt-86.t:call-trgt_plot_motifs_waterfall INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2183.motifs_waterfall.trgt_plots.zip"
2025-09-15 20:26:14.732 wdl.w:ptcp.w:call-paraphase-88.t:call-call_f8.slurm_singularity INFO srun: job 51798188 queued and waiting for resources
2025-09-15 20:26:14.732 wdl.w:ptcp.w:call-paraphase-88.t:call-call_f8.slurm_singularity INFO srun: job 51798188 has been allocated resources
2025-09-15 20:26:14.732 wdl.w:ptcp.w:call-paraphase-88.t:call-call_f8.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:26:14.766 wdl.w:ptcp.w:call-trgt-86.t:call-trgt_plot_motifs_waterfall NOTICE done
2025-09-15 20:26:14.771 wdl.w:ptcp.w:call-trgt-86 NOTICE finish :: job: "call-trgt_plot_motifs_waterfall"
2025-09-15 20:26:14.771 wdl.w:ptcp.w:call-trgt-86 INFO output :: job: "call-trgt_plot_motifs_waterfall", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-86/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2183.motifs_waterfall.trgt_plots.zip"}
2025-09-15 20:26:14.771 wdl.w:ptcp.w:call-trgt-86 INFO visit :: node: "output-images_motifs_waterfall", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-86/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2183.motifs_waterfall.trgt_plots.zip"}
2025-09-15 20:26:14.786 wdl.w:ptcp.t:call-tar_outputs-31.slurm_singularity INFO srun: job 51798189 queued and waiting for resources
2025-09-15 20:26:14.786 wdl.w:ptcp.t:call-tar_outputs-31.slurm_singularity INFO srun: job 51798189 has been allocated resources
2025-09-15 20:26:14.786 wdl.w:ptcp.t:call-tar_outputs-31.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:26:14.813 wdl.w:ptcp.t:call-tar_outputs-34.slurm_singularity INFO srun: job 51798190 queued and waiting for resources
2025-09-15 20:26:14.813 wdl.w:ptcp.t:call-tar_outputs-34.slurm_singularity INFO srun: job 51798190 has been allocated resources
2025-09-15 20:26:14.813 wdl.w:ptcp.t:call-tar_outputs-34.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:26:14.876 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:26:11 [ERROR] - No reads found for TRID=CJD_PRNP
2025-09-15 20:26:14.877 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:26:12 [ERROR] - No reads found for TRID=EPM1_CSTB
2025-09-15 20:26:14.877 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:26:12 [ERROR] - No reads found for TRID=SD5_HOXD13
2025-09-15 20:26:14.877 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:26:12 [ERROR] - No reads found for TRID=SCA7_ATXN7
2025-09-15 20:26:14.877 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:26:12 [ERROR] - No reads found for TRID=FRA2A_AFF3
2025-09-15 20:26:14.877 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:26:13 [ERROR] - No reads found for TRID=HD_HTT
2025-09-15 20:26:14.877 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:26:13 [ERROR] - No reads found for TRID=CCHS_PHOX2B
2025-09-15 20:26:14.877 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:26:13 [ERROR] - No reads found for TRID=SCA12_PPP2R2B
2025-09-15 20:26:14.877 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:26:13 [ERROR] - No reads found for TRID=DM2_CNBP
2025-09-15 20:26:14.877 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:26:13 [ERROR] - No reads found for TRID=SCA1_ATXN1
2025-09-15 20:26:14.877 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:26:14 [ERROR] - No reads found for TRID=OPDM1_LRP12
2025-09-15 20:26:14.877 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:26:14 [ERROR] - No reads found for TRID=SCA10_ATXN10
2025-09-15 20:26:14.877 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:26:14 [ERROR] - No reads found for TRID=FTDALS1_C9orf72
2025-09-15 20:26:14.923 wdl.w:ptcp.t:call-tar_outputs-76.slurm_singularity INFO srun: job 51798191 queued and waiting for resources
2025-09-15 20:26:14.923 wdl.w:ptcp.t:call-tar_outputs-76.slurm_singularity INFO srun: job 51798191 has been allocated resources
2025-09-15 20:26:14.923 wdl.w:ptcp.t:call-tar_outputs-76.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:26:14.997 wdl.w:ptcp.w:call-trgt-93.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:26:10 [ERROR] - No reads found for TRID=PRTS_ARX
2025-09-15 20:26:14.997 wdl.w:ptcp.w:call-trgt-93.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:26:10 [ERROR] - No reads found for TRID=EIEE1_ARX
2025-09-15 20:26:15.001 wdl.w:ptcp.t:call-tar_outputs-84.stderr VERBOSE tar: Removing leading `/' from member names
2025-09-15 20:26:15.001 wdl.w:ptcp.t:call-tar_outputs-84.stderr VERBOSE tar: Removing leading `/' from hard link targets
2025-09-15 20:26:15.013 wdl.w:ptcp.t:call-tar_outputs-84.slurm_singularity INFO srun: job 51798192 queued and waiting for resources
2025-09-15 20:26:15.013 wdl.w:ptcp.t:call-tar_outputs-84.slurm_singularity INFO srun: job 51798192 has been allocated resources
2025-09-15 20:26:15.013 wdl.w:ptcp.t:call-tar_outputs-84.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:26:15.014 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:26:12 [ERROR] - No reads found for TRID=SCA4_ZFHX3
2025-09-15 20:26:15.014 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:26:12 [ERROR] - No reads found for TRID=SCA36_NOP56
2025-09-15 20:26:15.014 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:26:12 [ERROR] - No reads found for TRID=CJD_PRNP
2025-09-15 20:26:15.014 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:26:12 [ERROR] - No reads found for TRID=EPM1_CSTB
2025-09-15 20:26:15.014 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:26:13 [ERROR] - No reads found for TRID=SD5_HOXD13
2025-09-15 20:26:15.014 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:26:13 [ERROR] - No reads found for TRID=SCA7_ATXN7
2025-09-15 20:26:15.014 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:26:13 [ERROR] - No reads found for TRID=FRA2A_AFF3
2025-09-15 20:26:15.014 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:26:13 [ERROR] - No reads found for TRID=HD_HTT
2025-09-15 20:26:15.014 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:26:14 [ERROR] - No reads found for TRID=CCHS_PHOX2B
2025-09-15 20:26:15.015 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:26:14 [ERROR] - No reads found for TRID=SCA12_PPP2R2B
2025-09-15 20:26:15.015 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:26:14 [ERROR] - No reads found for TRID=DM2_CNBP
2025-09-15 20:26:15.015 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:26:14 [ERROR] - No reads found for TRID=SCA1_ATXN1
2025-09-15 20:26:15.015 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:26:14 [ERROR] - No reads found for TRID=OPDM1_LRP12
2025-09-15 20:26:15.029 wdl.w:ptcp.w:call-trgt-86.t:call-trgt_plot_motifs_allele INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2183.motifs_allele.trgt_plots.zip"
2025-09-15 20:26:15.041 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_motifs_allele INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2180.motifs_allele.trgt_plots.zip"
2025-09-15 20:26:15.049 wdl.w:ptcp.w:call-trgt-93.t:call-trgt_plot_meth_waterfall INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2190.meth_waterfall.trgt_plots.zip"
2025-09-15 20:26:15.109 wdl.w:ptcp.w:call-trgt-86.t:call-trgt_plot_motifs_allele NOTICE done
2025-09-15 20:26:15.115 wdl.w:ptcp.w:call-trgt-86 NOTICE finish :: job: "call-trgt_plot_motifs_allele"
2025-09-15 20:26:15.115 wdl.w:ptcp.w:call-trgt-86 INFO output :: job: "call-trgt_plot_motifs_allele", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-86/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2183.motifs_allele.trgt_plots.zip"}
2025-09-15 20:26:15.115 wdl.w:ptcp.w:call-trgt-86 INFO visit :: node: "output-images_motifs_allele", values: {"images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-86/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2183.motifs_allele.trgt_plots.zip"}
2025-09-15 20:26:15.127 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_motifs_allele NOTICE done
2025-09-15 20:26:15.129 wdl.w:ptcp.t:call-tar_outputs-84 INFO output :: name: "sample_tarball", value: "m84036_250809_035451_s4.bc2181.tar"
2025-09-15 20:26:15.132 wdl.w:ptcp.w:call-trgt-83 NOTICE finish :: job: "call-trgt_plot_motifs_allele"
2025-09-15 20:26:15.132 wdl.w:ptcp.w:call-trgt-83 INFO output :: job: "call-trgt_plot_motifs_allele", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-83/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2180.motifs_allele.trgt_plots.zip"}
2025-09-15 20:26:15.132 wdl.w:ptcp.w:call-trgt-83 INFO visit :: node: "output-images_motifs_allele", values: {"images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-83/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2180.motifs_allele.trgt_plots.zip"}
2025-09-15 20:26:15.149 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_plot_motifs_waterfall INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2192.motifs_waterfall.trgt_plots.zip"
2025-09-15 20:26:15.205 wdl.w:ptcp.w:call-trgt-93.t:call-trgt_plot_meth_waterfall NOTICE done
2025-09-15 20:26:15.211 wdl.w:ptcp.w:call-paraphase-10.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for hbb for sample m84036_250809_035451_s4.bc2107 at 2025-09-15 20:26:06.656967...
2025-09-15 20:26:15.211 wdl.w:ptcp.w:call-trgt-93 NOTICE finish :: job: "call-trgt_plot_meth_waterfall"
2025-09-15 20:26:15.212 wdl.w:ptcp.w:call-paraphase-10.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for hbb for sample m84036_250809_035451_s4.bc2107 at 2025-09-15 20:26:07.227775...
2025-09-15 20:26:15.212 wdl.w:ptcp.w:call-trgt-93 INFO output :: job: "call-trgt_plot_meth_waterfall", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-93/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2190.meth_waterfall.trgt_plots.zip"}
2025-09-15 20:26:15.212 wdl.w:ptcp.w:call-trgt-93 INFO visit :: node: "output-images_meth_waterfall", values: {"images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-93/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2190.meth_waterfall.trgt_plots.zip"}
2025-09-15 20:26:15.218 wdl.w:ptcp.t:call-tar_outputs-84 NOTICE done
2025-09-15 20:26:15.222 wdl.w:ptcp NOTICE finish :: job: "call-tar_outputs-84"
2025-09-15 20:26:15.223 wdl.w:ptcp INFO output :: job: "call-tar_outputs-84", values: {"sample_tarball": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-84/out/m84036_250809_035451_s4.bc2181.tar"}
2025-09-15 20:26:15.233 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:26:12 [ERROR] - No reads found for TRID=SCA4_ZFHX3
2025-09-15 20:26:15.233 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:26:12 [ERROR] - No reads found for TRID=SCA36_NOP56
2025-09-15 20:26:15.233 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:26:12 [ERROR] - No reads found for TRID=CJD_PRNP
2025-09-15 20:26:15.234 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:26:12 [ERROR] - No reads found for TRID=EPM1_CSTB
2025-09-15 20:26:15.234 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:26:13 [ERROR] - No reads found for TRID=SD5_HOXD13
2025-09-15 20:26:15.234 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:26:13 [ERROR] - No reads found for TRID=SCA7_ATXN7
2025-09-15 20:26:15.234 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:26:13 [ERROR] - No reads found for TRID=FRA2A_AFF3
2025-09-15 20:26:15.234 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:26:13 [ERROR] - No reads found for TRID=HD_HTT
2025-09-15 20:26:15.234 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:26:14 [ERROR] - No reads found for TRID=CCHS_PHOX2B
2025-09-15 20:26:15.234 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:26:14 [ERROR] - No reads found for TRID=SCA12_PPP2R2B
2025-09-15 20:26:15.234 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:26:14 [ERROR] - No reads found for TRID=DM2_CNBP
2025-09-15 20:26:15.234 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:26:14 [ERROR] - No reads found for TRID=SCA1_ATXN1
2025-09-15 20:26:15.234 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:26:14 [ERROR] - No reads found for TRID=OPDM1_LRP12
2025-09-15 20:26:15.234 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:26:15 [ERROR] - No reads found for TRID=SCA10_ATXN10
2025-09-15 20:26:15.246 wdl.w:ptcp.w:call-trgt-95.t:call-trgt_plot_motifs_waterfall NOTICE done
2025-09-15 20:26:15.250 wdl.w:ptcp.w:call-trgt-95 NOTICE finish :: job: "call-trgt_plot_motifs_waterfall"
2025-09-15 20:26:15.250 wdl.w:ptcp.w:call-trgt-95 INFO output :: job: "call-trgt_plot_motifs_waterfall", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-95/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2192.motifs_waterfall.trgt_plots.zip"}
2025-09-15 20:26:15.251 wdl.w:ptcp.w:call-trgt-95 INFO visit :: node: "output-images_motifs_waterfall", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-95/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2192.motifs_waterfall.trgt_plots.zip"}
2025-09-15 20:26:15.251 wdl.w:ptcp.w:call-trgt-95 INFO visit :: node: "outputs", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-95/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2192.motifs_waterfall.trgt_plots.zip", "images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-95/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2192.meth_allele.trgt_plots.zip", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-95/call-trgt_genotype/out/m84036_250809_035451_s4.bc2192.trgt.sorted.spanning.bam.bai", "images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-95/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2192.motifs_allele.trgt_plots.zip", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-95/call-trgt_genotype/out/m84036_250809_035451_s4.bc2192.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-95/call-trgt_genotype/out/m84036_250809_035451_s4.bc2192.trgt.vcf", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-95/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2192.repeats.bam", "images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-95/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2192.meth_waterfall.trgt_plots.zip", "reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-95/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2192.repeats.bam.bai"}
2025-09-15 20:26:15.258 wdl.w:ptcp.w:call-trgt-93.t:call-trgt_plot_motifs_waterfall INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2190.motifs_waterfall.trgt_plots.zip"
2025-09-15 20:26:15.284 wdl.w:ptcp.w:call-paraphase-54.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for f8inv22 for sample m84036_250809_035451_s4.bc2151 at 2025-09-15 20:26:03.836886...
2025-09-15 20:26:15.284 wdl.w:ptcp.w:call-paraphase-54.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for f8inv22 for sample m84036_250809_035451_s4.bc2151 at 2025-09-15 20:26:06.479274...
2025-09-15 20:26:15.284 wdl.w:ptcp.w:call-paraphase-54.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for f8inv22 for sample m84036_250809_035451_s4.bc2151 at 2025-09-15 20:26:06.726547...
2025-09-15 20:26:15.295 wdl.w:ptcp.w:call-paraphase-88.t:call-call_f8 INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2185.f8inversion.vcf"
2025-09-15 20:26:15.300 wdl.w:ptcp.w:call-paraphase-88.t:call-call_f8 INFO output :: name: "json", value: "m84036_250809_035451_s4.bc2185.f8inversion.json"
2025-09-15 20:26:15.338 wdl.w:ptcp.w:call-trgt-95 NOTICE done
2025-09-15 20:26:15.343 wdl.w:ptcp NOTICE finish :: job: "call-trgt-95"
2025-09-15 20:26:15.343 wdl.w:ptcp INFO output :: job: "call-trgt-95", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-95/out/m84036_250809_035451_s4.bc2192.motifs_waterfall.trgt_plots.zip", "images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-95/out/m84036_250809_035451_s4.bc2192.meth_allele.trgt_plots.zip", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-95/out/m84036_250809_035451_s4.bc2192.trgt.sorted.spanning.bam.bai", "images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-95/out/m84036_250809_035451_s4.bc2192.motifs_allele.trgt_plots.zip", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-95/out/m84036_250809_035451_s4.bc2192.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-95/out/m84036_250809_035451_s4.bc2192.trgt.vcf", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-95/out/m84036_250809_035451_s4.bc2192.repeats.bam", "images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-95/out/m84036_250809_035451_s4.bc2192.meth_waterfall.trgt_plots.zip", "reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-95/out/m84036_250809_035451_s4.bc2192.repeats.bam.bai"}
2025-09-15 20:26:15.364 wdl.w:ptcp.w:call-paraphase-42.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for gba for sample m84036_250809_035451_s4.bc2139 at 2025-09-15 20:26:01.725228...
2025-09-15 20:26:15.365 wdl.w:ptcp.w:call-paraphase-42.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for gba for sample m84036_250809_035451_s4.bc2139 at 2025-09-15 20:26:02.387390...
2025-09-15 20:26:15.365 wdl.w:ptcp.w:call-paraphase-42.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for hbb for sample m84036_250809_035451_s4.bc2139 at 2025-09-15 20:26:11.465316...
2025-09-15 20:26:15.365 wdl.w:ptcp.w:call-paraphase-42.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for hbb for sample m84036_250809_035451_s4.bc2139 at 2025-09-15 20:26:11.466183...
2025-09-15 20:26:15.365 wdl.w:ptcp.w:call-paraphase-42.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for hbb for sample m84036_250809_035451_s4.bc2139 at 2025-09-15 20:26:14.176601...
2025-09-15 20:26:15.365 wdl.w:ptcp.w:call-paraphase-42.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for f8inv1 for sample m84036_250809_035451_s4.bc2139 at 2025-09-15 20:26:14.202621...
2025-09-15 20:26:15.365 wdl.w:ptcp.w:call-paraphase-42.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for f8inv1 for sample m84036_250809_035451_s4.bc2139 at 2025-09-15 20:26:14.202912...
2025-09-15 20:26:15.366 wdl.w:ptcp.w:call-paraphase-88.t:call-call_f8 NOTICE done
2025-09-15 20:26:15.372 wdl.w:ptcp.w:call-paraphase-88 NOTICE finish :: job: "call-call_f8"
2025-09-15 20:26:15.372 wdl.w:ptcp.w:call-paraphase-88 INFO output :: job: "call-call_f8", values: {"json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-88/call-call_f8/out/m84036_250809_035451_s4.bc2185.f8inversion.json", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-88/call-call_f8/out/m84036_250809_035451_s4.bc2185.f8inversion.vcf"}
2025-09-15 20:26:15.373 wdl.w:ptcp.w:call-paraphase-88 INFO visit :: node: "output-f8_json", values: {"f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-88/call-call_f8/out/m84036_250809_035451_s4.bc2185.f8inversion.json"}
2025-09-15 20:26:15.373 wdl.w:ptcp.w:call-paraphase-88 INFO visit :: node: "output-f8_vcf", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-88/call-call_f8/out/m84036_250809_035451_s4.bc2185.f8inversion.vcf"}
2025-09-15 20:26:15.373 wdl.w:ptcp.w:call-paraphase-88 INFO visit :: node: "outputs", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-88/call-call_f8/out/m84036_250809_035451_s4.bc2185.f8inversion.vcf", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-88/call-run_paraphase/out/m84036_250809_035451_s4.bc2185_paraphase/m84036_250809_035451_s4.bc2185.paraphase.json", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-88/call-run_paraphase/out/m84036_250809_035451_s4.bc2185_paraphase/m84036_250809_035451_s4.bc2185.paraphase.bam", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-88/call-run_paraphase/out/m84036_250809_035451_s4.bc2185_paraphase/m84036_250809_035451_s4.bc2185.paraphase.bam.bai", "paraphase_vcfs": [], "havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-88/call-run_paraphase/out/m84036_250809_035451_s4.bc2185.havanno.json", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-88/call-call_f8/out/m84036_250809_035451_s4.bc2185.f8inversion.json"}
2025-09-15 20:26:15.383 wdl.w:ptcp.w:call-trgt-86.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:26:12 [ERROR] - No reads found for TRID=OPDM_ABCD3
2025-09-15 20:26:15.384 wdl.w:ptcp.w:call-trgt-86.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:26:13 [ERROR] - No reads found for TRID=SCA37_DAB1
2025-09-15 20:26:15.384 wdl.w:ptcp.w:call-trgt-86.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:26:13 [ERROR] - No reads found for TRID=NIID_NOTCH2NLC
2025-09-15 20:26:15.384 wdl.w:ptcp.w:call-trgt-86.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:26:13 [ERROR] - No reads found for TRID=OPDM4_RILPL1
2025-09-15 20:26:15.384 wdl.w:ptcp.w:call-trgt-86.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:26:13 [ERROR] - No reads found for TRID=SCA2_ATXN2
2025-09-15 20:26:15.384 wdl.w:ptcp.w:call-trgt-86.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:26:13 [ERROR] - No reads found for TRID=SCA8_ATXN8OS
2025-09-15 20:26:15.384 wdl.w:ptcp.w:call-trgt-86.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:26:14 [ERROR] - No reads found for TRID=SCA27B_FGF14
2025-09-15 20:26:15.384 wdl.w:ptcp.w:call-trgt-86.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:26:14 [ERROR] - No reads found for TRID=OPMD_PABPN1
2025-09-15 20:26:15.384 wdl.w:ptcp.w:call-trgt-86.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:26:14 [ERROR] - No reads found for TRID=SCA3_ATXN3
2025-09-15 20:26:15.384 wdl.w:ptcp.w:call-trgt-86.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:26:14 [ERROR] - No reads found for TRID=DRPLA_ATN1
2025-09-15 20:26:15.384 wdl.w:ptcp.w:call-trgt-86.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:26:14 [ERROR] - No reads found for TRID=SCA31_BEAN1
2025-09-15 20:26:15.384 wdl.w:ptcp.w:call-trgt-86.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:26:15 [ERROR] - No reads found for TRID=HDL2_JPH3
2025-09-15 20:26:15.384 wdl.w:ptcp.w:call-trgt-86.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:26:15 [ERROR] - No reads found for TRID=FECD3_TCF4
2025-09-15 20:26:15.394 wdl.w:ptcp.w:call-trgt-93.t:call-trgt_plot_motifs_waterfall NOTICE done
2025-09-15 20:26:15.399 wdl.w:ptcp.w:call-trgt-93 NOTICE finish :: job: "call-trgt_plot_motifs_waterfall"
2025-09-15 20:26:15.399 wdl.w:ptcp.w:call-trgt-93 INFO output :: job: "call-trgt_plot_motifs_waterfall", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-93/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2190.motifs_waterfall.trgt_plots.zip"}
2025-09-15 20:26:15.400 wdl.w:ptcp.w:call-trgt-93 INFO visit :: node: "output-images_motifs_waterfall", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-93/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2190.motifs_waterfall.trgt_plots.zip"}
2025-09-15 20:26:15.400 wdl.w:ptcp.w:call-trgt-93 INFO visit :: node: "outputs", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-93/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2190.motifs_waterfall.trgt_plots.zip", "images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-93/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2190.meth_allele.trgt_plots.zip", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-93/call-trgt_genotype/out/m84036_250809_035451_s4.bc2190.trgt.sorted.spanning.bam.bai", "images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-93/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2190.motifs_allele.trgt_plots.zip", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-93/call-trgt_genotype/out/m84036_250809_035451_s4.bc2190.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-93/call-trgt_genotype/out/m84036_250809_035451_s4.bc2190.trgt.vcf", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-93/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2190.repeats.bam", "images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-93/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2190.meth_waterfall.trgt_plots.zip", "reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-93/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2190.repeats.bam.bai"}
2025-09-15 20:26:15.446 wdl.w:ptcp.w:call-paraphase-88 NOTICE done
2025-09-15 20:26:15.454 wdl.w:ptcp NOTICE finish :: job: "call-paraphase-88"
2025-09-15 20:26:15.454 wdl.w:ptcp INFO output :: job: "call-paraphase-88", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-88/out/m84036_250809_035451_s4.bc2185.f8inversion.vcf", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-88/out/m84036_250809_035451_s4.bc2185_paraphase/m84036_250809_035451_s4.bc2185.paraphase.json", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-88/out/m84036_250809_035451_s4.bc2185_paraphase/m84036_250809_035451_s4.bc2185.paraphase.bam", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-88/out/m84036_250809_035451_s4.bc2185_paraphase/m84036_250809_035451_s4.bc2185.paraphase.bam.bai", "paraphase_vcfs": [], "havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-88/out/m84036_250809_035451_s4.bc2185.havanno.json", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-88/out/m84036_250809_035451_s4.bc2185.f8inversion.json"}
2025-09-15 20:26:15.477 wdl.w:ptcp.w:call-trgt-86.t:call-trgt_plot_meth_waterfall INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2183.meth_waterfall.trgt_plots.zip"
2025-09-15 20:26:15.489 wdl.w:ptcp.w:call-trgt-93 NOTICE done
2025-09-15 20:26:15.490 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_motifs_waterfall INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2180.motifs_waterfall.trgt_plots.zip"
2025-09-15 20:26:15.495 wdl.w:ptcp NOTICE finish :: job: "call-trgt-93"
2025-09-15 20:26:15.495 wdl.w:ptcp INFO output :: job: "call-trgt-93", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-93/out/m84036_250809_035451_s4.bc2190.motifs_waterfall.trgt_plots.zip", "images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-93/out/m84036_250809_035451_s4.bc2190.meth_allele.trgt_plots.zip", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-93/out/m84036_250809_035451_s4.bc2190.trgt.sorted.spanning.bam.bai", "images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-93/out/m84036_250809_035451_s4.bc2190.motifs_allele.trgt_plots.zip", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-93/out/m84036_250809_035451_s4.bc2190.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-93/out/m84036_250809_035451_s4.bc2190.trgt.vcf", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-93/out/m84036_250809_035451_s4.bc2190.repeats.bam", "images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-93/out/m84036_250809_035451_s4.bc2190.meth_waterfall.trgt_plots.zip", "reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-93/out/m84036_250809_035451_s4.bc2190.repeats.bam.bai"}
2025-09-15 20:26:15.548 wdl.w:ptcp.w:call-trgt-86.t:call-trgt_plot_meth_waterfall NOTICE done
2025-09-15 20:26:15.553 wdl.w:ptcp.w:call-trgt-86 NOTICE finish :: job: "call-trgt_plot_meth_waterfall"
2025-09-15 20:26:15.553 wdl.w:ptcp.w:call-trgt-86 INFO output :: job: "call-trgt_plot_meth_waterfall", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-86/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2183.meth_waterfall.trgt_plots.zip"}
2025-09-15 20:26:15.554 wdl.w:ptcp.w:call-trgt-86 INFO visit :: node: "output-images_meth_waterfall", values: {"images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-86/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2183.meth_waterfall.trgt_plots.zip"}
2025-09-15 20:26:15.558 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_motifs_waterfall NOTICE done
2025-09-15 20:26:15.563 wdl.w:ptcp.w:call-trgt-83 NOTICE finish :: job: "call-trgt_plot_motifs_waterfall"
2025-09-15 20:26:15.563 wdl.w:ptcp.w:call-trgt-83 INFO output :: job: "call-trgt_plot_motifs_waterfall", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-83/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2180.motifs_waterfall.trgt_plots.zip"}
2025-09-15 20:26:15.564 wdl.w:ptcp.w:call-trgt-83 INFO visit :: node: "output-images_motifs_waterfall", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-83/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2180.motifs_waterfall.trgt_plots.zip"}
2025-09-15 20:26:15.649 wdl.w:ptcp.w:call-sawfish-85.t:call-run_sawfish.stderr VERBOSE [M::mm_idx_gen::40.382*1.69] sorted minimizers
2025-09-15 20:26:15.650 wdl.w:ptcp.w:call-sawfish-85.t:call-run_sawfish.stderr VERBOSE [M::main::40.382*1.69] loaded/built the index for 195 target sequence(s)
2025-09-15 20:26:15.650 wdl.w:ptcp.w:call-sawfish-85.t:call-run_sawfish.stderr VERBOSE [M::mm_mapopt_update::43.484*1.64] mid_occ = 136
2025-09-15 20:26:15.650 wdl.w:ptcp.w:call-sawfish-85.t:call-run_sawfish.stderr VERBOSE [M::mm_idx_stat] kmer size: 19; skip: 19; is_hpc: 0; #seq: 195
2025-09-15 20:26:15.650 wdl.w:ptcp.w:call-sawfish-85.t:call-run_sawfish.stderr VERBOSE [M::mm_idx_stat::46.135*1.61] distinct minimizers: 214664461 (92.23% are singletons); average occurrences: 1.372; average spacing: 10.529; total length: 3099922541
2025-09-15 20:26:15.650 wdl.w:ptcp.w:call-sawfish-85.t:call-run_sawfish.stderr VERBOSE [M::main] Version: 2.26-r1175
2025-09-15 20:26:15.650 wdl.w:ptcp.w:call-sawfish-85.t:call-run_sawfish.stderr VERBOSE [M::main] CMD: /opt/pacbio/smrttools/install/smrtlink-release_25.1.0.257715/bundles/smrttools/install/smrttools-release_25.1.0.257715/private/thirdparty/minimap2/minimap2_2.26-pacbio2/binwrap/../../../../../private/thirdparty/minimap2/minimap2_2.26-pacbio2/bin/minimap2 -a -y -x map-hifi -Y -E 1,0 /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa -
2025-09-15 20:26:15.650 wdl.w:ptcp.w:call-sawfish-85.t:call-run_sawfish.stderr VERBOSE [M::main] Real time: 46.450 sec; CPU: 74.414 sec; Peak RSS: 11.887 GB
2025-09-15 20:26:15.732 wdl.w:ptcp.w:call-paraphase-39.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for rpgr for sample m84036_250809_035451_s4.bc2136 at 2025-09-15 20:26:13.275882...
2025-09-15 20:26:15.732 wdl.w:ptcp.w:call-paraphase-39.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for rpgr for sample m84036_250809_035451_s4.bc2136 at 2025-09-15 20:26:13.276553...
2025-09-15 20:26:16.196 wdl.w:ptcp.w:call-paraphase-54.t:call-run_paraphase INFO output :: name: "paraphase_bam", value: "m84036_250809_035451_s4.bc2151_paraphase/m84036_250809_035451_s4.bc2151.paraphase.bam"
2025-09-15 20:26:16.199 wdl.w:ptcp.w:call-paraphase-54.t:call-run_paraphase INFO output :: name: "paraphase_bam_bai", value: "m84036_250809_035451_s4.bc2151_paraphase/m84036_250809_035451_s4.bc2151.paraphase.bam.bai"
2025-09-15 20:26:16.201 wdl.w:ptcp.w:call-paraphase-54.t:call-run_paraphase INFO output :: name: "paraphase_json", value: "m84036_250809_035451_s4.bc2151_paraphase/m84036_250809_035451_s4.bc2151.paraphase.json"
2025-09-15 20:26:16.205 wdl.w:ptcp.w:call-paraphase-54.t:call-run_paraphase INFO output :: name: "paraphase_vcfs", value: ["/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2151_paraphase/m84036_250809_035451_s4.bc2151_paraphase_vcfs/m84036_250809_035451_s4.bc2151_cyp21.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2151_paraphase/m84036_250809_035451_s4.bc2151_paraphase_vcfs/m84036_250809_035451_s4.bc2151_f8inv1.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2151_paraphase/m84036_250809_035451_s4.bc2151_paraphase_vcfs/m84036_250809_035451_s4.bc2151_f8inv22.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2151_paraphase/m84036_250809_035451_s4.bc2151_paraphase_vcfs/m84036_250809_035451_s4.bc2151_gba.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2151_paraphase/m84036_250809_035451_s4.bc2151_paraphase_vcfs/m84036_250809_035451_s4.bc2151_hba.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2151_paraphase/m84036_250809_035451_s4.bc2151_paraphase_vcfs/m84036_250809_035451_s4.bc2151_hbb.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2151_paraphase/m84036_250809_035451_s4.bc2151_paraphase_vcfs/m84036_250809_035451_s4.bc2151_rpgr.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2151_paraphase/m84036_250809_035451_s4.bc2151_paraphase_vcfs/m84036_250809_035451_s4.bc2151_smn1.vcf"]
2025-09-15 20:26:16.208 wdl.w:ptcp.w:call-paraphase-54.t:call-run_paraphase INFO output :: name: "havanno_json", value: "m84036_250809_035451_s4.bc2151.havanno.json"
2025-09-15 20:26:16.211 wdl.w:ptcp.w:call-paraphase-71.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for smn1 for sample m84036_250809_035451_s4.bc2168 at 2025-09-15 20:25:38.031277...
2025-09-15 20:26:16.212 wdl.w:ptcp.w:call-paraphase-71.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for cyp21 for sample m84036_250809_035451_s4.bc2168 at 2025-09-15 20:26:04.392620...
2025-09-15 20:26:16.212 wdl.w:ptcp.w:call-paraphase-71.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for cyp21 for sample m84036_250809_035451_s4.bc2168 at 2025-09-15 20:26:05.537084...
2025-09-15 20:26:16.212 wdl.w:ptcp.w:call-paraphase-71.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for hba for sample m84036_250809_035451_s4.bc2168 at 2025-09-15 20:26:06.636996...
2025-09-15 20:26:16.212 wdl.w:ptcp.w:call-paraphase-71.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for hba for sample m84036_250809_035451_s4.bc2168 at 2025-09-15 20:26:07.009250...
2025-09-15 20:26:16.219 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:26:13 [ERROR] - No reads found for TRID=DRPLA_ATN1
2025-09-15 20:26:16.219 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:26:13 [ERROR] - No reads found for TRID=SCA2_ATXN2
2025-09-15 20:26:16.219 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:26:13 [ERROR] - No reads found for TRID=OPDM4_RILPL1
2025-09-15 20:26:16.219 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:26:14 [ERROR] - No reads found for TRID=NIID_NOTCH2NLC
2025-09-15 20:26:16.219 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:26:14 [ERROR] - No reads found for TRID=OPMD_PABPN1
2025-09-15 20:26:16.219 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:26:14 [ERROR] - No reads found for TRID=SCA27B_FGF14
2025-09-15 20:26:16.219 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:26:14 [ERROR] - No reads found for TRID=SCA37_DAB1
2025-09-15 20:26:16.219 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:26:14 [ERROR] - No reads found for TRID=SCA3_ATXN3
2025-09-15 20:26:16.219 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:26:14 [ERROR] - No reads found for TRID=FECD3_TCF4
2025-09-15 20:26:16.219 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:26:14 [ERROR] - No reads found for TRID=SCA31_BEAN1
2025-09-15 20:26:16.219 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:26:15 [ERROR] - No reads found for TRID=SCA6_CACNA1A
2025-09-15 20:26:16.220 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:26:15 [ERROR] - No reads found for TRID=SCA4_ZFHX3
2025-09-15 20:26:16.220 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:26:15 [ERROR] - No reads found for TRID=HDL2_JPH3
2025-09-15 20:26:16.220 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:26:15 [ERROR] - No reads found for TRID=SD5_HOXD13
2025-09-15 20:26:16.220 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:26:16 [ERROR] - No reads found for TRID=FRA2A_AFF3
2025-09-15 20:26:16.257 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:26:13 [ERROR] - No reads found for TRID=DRPLA_ATN1
2025-09-15 20:26:16.257 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:26:13 [ERROR] - No reads found for TRID=SCA2_ATXN2
2025-09-15 20:26:16.257 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:26:13 [ERROR] - No reads found for TRID=OPDM4_RILPL1
2025-09-15 20:26:16.257 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:26:13 [ERROR] - No reads found for TRID=NIID_NOTCH2NLC
2025-09-15 20:26:16.257 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:26:14 [ERROR] - No reads found for TRID=OPMD_PABPN1
2025-09-15 20:26:16.258 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:26:14 [ERROR] - No reads found for TRID=SCA27B_FGF14
2025-09-15 20:26:16.258 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:26:14 [ERROR] - No reads found for TRID=SCA37_DAB1
2025-09-15 20:26:16.258 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:26:14 [ERROR] - No reads found for TRID=SCA3_ATXN3
2025-09-15 20:26:16.258 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:26:14 [ERROR] - No reads found for TRID=FECD3_TCF4
2025-09-15 20:26:16.258 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:26:14 [ERROR] - No reads found for TRID=SCA31_BEAN1
2025-09-15 20:26:16.258 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:26:15 [ERROR] - No reads found for TRID=SCA6_CACNA1A
2025-09-15 20:26:16.258 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:26:15 [ERROR] - No reads found for TRID=SCA4_ZFHX3
2025-09-15 20:26:16.258 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:26:15 [ERROR] - No reads found for TRID=HDL2_JPH3
2025-09-15 20:26:16.258 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:26:15 [ERROR] - No reads found for TRID=SD5_HOXD13
2025-09-15 20:26:16.258 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:26:16 [ERROR] - No reads found for TRID=FRA2A_AFF3
2025-09-15 20:26:16.258 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:26:16 [ERROR] - No reads found for TRID=OPDM2_GIPC1
2025-09-15 20:26:16.306 wdl.w:ptcp.t:call-tar_outputs-31 INFO output :: name: "sample_tarball", value: "m84036_250809_035451_s4.bc2128.tar"
2025-09-15 20:26:16.372 wdl.w:ptcp.t:call-tar_outputs-31 NOTICE done
2025-09-15 20:26:16.376 wdl.w:ptcp NOTICE finish :: job: "call-tar_outputs-31"
2025-09-15 20:26:16.377 wdl.w:ptcp INFO output :: job: "call-tar_outputs-31", values: {"sample_tarball": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-31/out/m84036_250809_035451_s4.bc2128.tar"}
2025-09-15 20:26:16.391 wdl.w:ptcp.t:call-tar_outputs-34 INFO output :: name: "sample_tarball", value: "m84036_250809_035451_s4.bc2131.tar"
2025-09-15 20:26:16.408 wdl.w:ptcp.t:call-tar_outputs-76 INFO output :: name: "sample_tarball", value: "m84036_250809_035451_s4.bc2173.tar"
2025-09-15 20:26:16.421 wdl.w:ptcp.w:call-paraphase-54.t:call-run_paraphase NOTICE done
2025-09-15 20:26:16.428 wdl.w:ptcp.w:call-paraphase-54 NOTICE finish :: job: "call-run_paraphase"
2025-09-15 20:26:16.429 wdl.w:ptcp.w:call-paraphase-54 INFO output :: job: "call-run_paraphase", values: {"havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-54/call-run_paraphase/out/m84036_250809_035451_s4.bc2151.havanno.json", "paraphase_vcfs": ["/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-54/call-run_paraphase/out/m84036_250809_035451_s4.bc2151_paraphase/m84036_250809_035451_s4.bc2151_paraphase_vcfs/m84036_250809_035451_s4.bc2151_cyp21.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-54/call-run_paraphase/out/m84036_250809_035451_s4.bc2151_paraphase/m84036_250809_035451_s4.bc2151_paraphase_vcfs/m84036_250809_035451_s4.bc2151_f8inv1.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-54/call-run_paraphase/out/m84036_250809_035451_s4.bc2151_paraphase/m84036_250809_035451_s4.bc2151_paraphase_vcfs/m84036_250809_035451_s4.bc2151_f8inv22.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-54/call-run_paraphase/out/m84036_250809_035451_s4.bc2151_paraphase/m84036_250809_035451_s4.bc2151_paraphase_vcfs/m84036_250809_035451_s4.bc2151_gba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-54/call-run_paraphase/out/m84036_250809_035451_s4.bc2151_paraphase/m84036_250809_035451_s4.bc2151_paraphase_vcfs/m84036_250809_035451_s4.bc2151_hba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-54/call-run_paraphase/out/m84036_250809_035451_s4.bc2151_paraphase/m84036_250809_035451_s4.bc2151_paraphase_vcfs/m84036_250809_035451_s4.bc2151_hbb.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-54/call-run_paraphase/out/m84036_250809_035451_s4.bc2151_paraphase/m84036_250809_035451_s4.bc2151_paraphase_vcfs/m84036_250809_035451_s4.bc2151_rpgr.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-54/call-run_paraphase/out/m84036_250809_035451_s4.bc2151_paraphase/m84036_250809_035451_s4.bc2151_paraphase_vcfs/m84036_250809_035451_s4.bc2151_smn1.vcf"], "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-54/call-run_paraphase/out/m84036_250809_035451_s4.bc2151_paraphase/m84036_250809_035451_s4.bc2151.paraphase.json", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-54/call-run_paraphase/out/m84036_250809_035451_s4.bc2151_paraphase/m84036_250809_035451_s4.bc2151.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-54/call-run_paraphase/out/m84036_250809_035451_s4.bc2151_paraphase/m84036_250809_035451_s4.bc2151.paraphase.bam"}
2025-09-15 20:26:16.429 wdl.w:ptcp.w:call-paraphase-54 NOTICE ready :: job: "call-call_f8", callee: "call_f8"
2025-09-15 20:26:16.429 wdl.w:ptcp.w:call-paraphase-54 INFO input :: job: "call-call_f8", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "out_prefix": "m84036_250809_035451_s4.bc2151", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-54/call-run_paraphase/out/m84036_250809_035451_s4.bc2151_paraphase/m84036_250809_035451_s4.bc2151.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-54/call-run_paraphase/out/m84036_250809_035451_s4.bc2151_paraphase/m84036_250809_035451_s4.bc2151.paraphase.bam", "sex": "F"}
2025-09-15 20:26:16.430 wdl.w:ptcp.w:call-paraphase-54 INFO visit :: node: "output-havanno_json", values: {"havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-54/call-run_paraphase/out/m84036_250809_035451_s4.bc2151.havanno.json"}
2025-09-15 20:26:16.430 wdl.w:ptcp.w:call-paraphase-54 INFO visit :: node: "output-paraphase_bam", values: {"paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-54/call-run_paraphase/out/m84036_250809_035451_s4.bc2151_paraphase/m84036_250809_035451_s4.bc2151.paraphase.bam"}
2025-09-15 20:26:16.431 wdl.w:ptcp.w:call-paraphase-54 INFO visit :: node: "output-paraphase_bam_bai", values: {"paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-54/call-run_paraphase/out/m84036_250809_035451_s4.bc2151_paraphase/m84036_250809_035451_s4.bc2151.paraphase.bam.bai"}
2025-09-15 20:26:16.431 wdl.w:ptcp.w:call-paraphase-54 INFO visit :: node: "output-paraphase_json", values: {"paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-54/call-run_paraphase/out/m84036_250809_035451_s4.bc2151_paraphase/m84036_250809_035451_s4.bc2151.paraphase.json"}
2025-09-15 20:26:16.431 wdl.w:ptcp.w:call-paraphase-54 INFO visit :: node: "output-paraphase_vcfs", values: {"paraphase_vcfs": ["/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-54/call-run_paraphase/out/m84036_250809_035451_s4.bc2151_paraphase/m84036_250809_035451_s4.bc2151_paraphase_vcfs/m84036_250809_035451_s4.bc2151_cyp21.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-54/call-run_paraphase/out/m84036_250809_035451_s4.bc2151_paraphase/m84036_250809_035451_s4.bc2151_paraphase_vcfs/m84036_250809_035451_s4.bc2151_f8inv1.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-54/call-run_paraphase/out/m84036_250809_035451_s4.bc2151_paraphase/m84036_250809_035451_s4.bc2151_paraphase_vcfs/m84036_250809_035451_s4.bc2151_f8inv22.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-54/call-run_paraphase/out/m84036_250809_035451_s4.bc2151_paraphase/m84036_250809_035451_s4.bc2151_paraphase_vcfs/m84036_250809_035451_s4.bc2151_gba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-54/call-run_paraphase/out/m84036_250809_035451_s4.bc2151_paraphase/m84036_250809_035451_s4.bc2151_paraphase_vcfs/m84036_250809_035451_s4.bc2151_hba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-54/call-run_paraphase/out/m84036_250809_035451_s4.bc2151_paraphase/m84036_250809_035451_s4.bc2151_paraphase_vcfs/m84036_250809_035451_s4.bc2151_hbb.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-54/call-run_paraphase/out/m84036_250809_035451_s4.bc2151_paraphase/m84036_250809_035451_s4.bc2151_paraphase_vcfs/m84036_250809_035451_s4.bc2151_rpgr.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-54/call-run_paraphase/out/m84036_250809_035451_s4.bc2151_paraphase/m84036_250809_035451_s4.bc2151_paraphase_vcfs/m84036_250809_035451_s4.bc2151_smn1.vcf"]}
2025-09-15 20:26:16.432 wdl.w:ptcp.w:call-trgt-90.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:26:13 [ERROR] - No reads found for TRID=SCA2_ATXN2
2025-09-15 20:26:16.432 wdl.w:ptcp.w:call-trgt-90.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:26:13 [ERROR] - No reads found for TRID=FRA2A_AFF3
2025-09-15 20:26:16.432 wdl.w:ptcp.w:call-trgt-90.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:26:13 [ERROR] - No reads found for TRID=OPMD_PABPN1
2025-09-15 20:26:16.432 wdl.w:ptcp.w:call-trgt-90.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:26:14 [ERROR] - No reads found for TRID=CJD_PRNP
2025-09-15 20:26:16.432 wdl.w:ptcp.w:call-trgt-90.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:26:14 [ERROR] - No reads found for TRID=EPM1_CSTB
2025-09-15 20:26:16.433 wdl.w:ptcp.w:call-trgt-90.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:26:14 [ERROR] - No reads found for TRID=SCA7_ATXN7
2025-09-15 20:26:16.433 wdl.w:ptcp.w:call-trgt-90.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:26:15 [ERROR] - No reads found for TRID=HD_HTT
2025-09-15 20:26:16.433 wdl.w:ptcp.w:call-trgt-90.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:26:15 [ERROR] - No reads found for TRID=CCHS_PHOX2B
2025-09-15 20:26:16.433 wdl.w:ptcp.w:call-trgt-90.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:26:16 [ERROR] - No reads found for TRID=SCA1_ATXN1
2025-09-15 20:26:16.437 wdl.w:ptcp.w:call-paraphase-54.t:call-call_f8 NOTICE task setup :: name: "call_f8", source: "./paraphase.wdl", line: 232, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-54/call-call_f8", thread: 140613068518976
2025-09-15 20:26:16.458 wdl.w:ptcp.w:call-paraphase-54.t:call-call_f8 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:26:16.458 wdl.w:ptcp.w:call-paraphase-54.t:call-call_f8 INFO input :: name: "genome_version", value: "38"
2025-09-15 20:26:16.458 wdl.w:ptcp.w:call-paraphase-54.t:call-call_f8 INFO input :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2151"
2025-09-15 20:26:16.459 wdl.w:ptcp.w:call-paraphase-54.t:call-call_f8 INFO input :: name: "paraphase_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2151.paraphase.bam.bai"
2025-09-15 20:26:16.459 wdl.w:ptcp.w:call-paraphase-54.t:call-call_f8 INFO input :: name: "paraphase_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2151.paraphase.bam"
2025-09-15 20:26:16.459 wdl.w:ptcp.w:call-paraphase-54.t:call-call_f8 INFO input :: name: "sex", value: "F"
2025-09-15 20:26:16.459 wdl.w:ptcp.w:call-paraphase-54.t:call-call_f8 INFO eval :: name: "threads", value: 1
2025-09-15 20:26:16.459 wdl.w:ptcp.w:call-paraphase-54.t:call-call_f8 INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:26:16.459 wdl.w:ptcp.w:call-paraphase-54.t:call-call_f8 INFO eval :: name: "disk_size", value: 11
2025-09-15 20:26:16.460 wdl.w:ptcp.w:call-paraphase-54.t:call-call_f8 INFO eval :: name: "sample_sex", value: "F"
2025-09-15 20:26:16.460 wdl.w:ptcp.w:call-paraphase-54.t:call-call_f8 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:26:16.460 wdl.w:ptcp.w:call-paraphase-54.t:call-call_f8 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:26:16.461 wdl.w:ptcp.w:call-paraphase-54.t:call-call_f8 INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:26:16.461 wdl.w:ptcp.w:call-paraphase-54.t:call-call_f8 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:26:16.465 wdl.w:ptcp.t:call-tar_outputs-34 NOTICE done
2025-09-15 20:26:16.473 wdl.w:ptcp NOTICE finish :: job: "call-tar_outputs-34"
2025-09-15 20:26:16.473 wdl.w:ptcp INFO output :: job: "call-tar_outputs-34", values: {"sample_tarball": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-34/out/m84036_250809_035451_s4.bc2131.tar"}
2025-09-15 20:26:16.482 wdl.w:ptcp.t:call-tar_outputs-76 NOTICE done
2025-09-15 20:26:16.502 wdl.w:ptcp.w:call-paraphase-54.t:call-call_f8 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 8, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-54/call-call_f8/_singularity_tmpdir_khh5wzo4"
2025-09-15 20:26:16.503 wdl.w:ptcp.w:call-paraphase-54.t:call-call_f8 INFO Slurm invocation: srun --job-name call-call_f8 --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-54/call-call_f8/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-54/call-call_f8/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-54/call-call_f8/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-54/call-call_f8/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-54/call-run_paraphase/out/m84036_250809_035451_s4.bc2151_paraphase/m84036_250809_035451_s4.bc2151.paraphase.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2151.paraphase.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-54/call-run_paraphase/out/m84036_250809_035451_s4.bc2151_paraphase/m84036_250809_035451_s4.bc2151.paraphase.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2151.paraphase.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-54/call-call_f8/_singularity_tmpdir_khh5wzo4/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-54/call-call_f8/_singularity_tmpdir_khh5wzo4/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:26:16.503 wdl.w:ptcp NOTICE finish :: job: "call-tar_outputs-76"
2025-09-15 20:26:16.504 wdl.w:ptcp INFO output :: job: "call-tar_outputs-76", values: {"sample_tarball": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-76/out/m84036_250809_035451_s4.bc2173.tar"}
2025-09-15 20:26:16.543 wdl.w:ptcp.w:call-paraphase-54.t:call-call_f8 NOTICE slurm_singularity run :: pid: 1207469, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-54/call-call_f8/slurm_singularity.log.txt"
2025-09-15 20:26:16.746 wdl.w:ptcp.w:call-trgt-88.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:26:15 [ERROR] - No reads found for TRID=PRTS_ARX
2025-09-15 20:26:16.746 wdl.w:ptcp.w:call-trgt-88.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:26:15 [ERROR] - No reads found for TRID=EIEE1_ARX
2025-09-15 20:26:16.804 wdl.w:ptcp.w:call-sawfish-72.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:14][sawfish][INFO] Processing alignment file '/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2169.minimap2.bam'
2025-09-15 20:26:16.804 wdl.w:ptcp.w:call-sawfish-72.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:14][sawfish][INFO] Finished processing all alignments
2025-09-15 20:26:16.804 wdl.w:ptcp.w:call-sawfish-72.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:14][sawfish][INFO] Writing depth bins to binary file: 'm84036_250809_035451_s4.bc2169_sawfish_discover/depth.mpack'
2025-09-15 20:26:16.804 wdl.w:ptcp.w:call-sawfish-72.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:14][sawfish][INFO] Writing max sv depth genome regions to bed file: 'm84036_250809_035451_s4.bc2169_sawfish_discover/max.depth.bed'
2025-09-15 20:26:16.804 wdl.w:ptcp.w:call-sawfish-72.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:14][sawfish][INFO] Completing breakpoint observation clustering
2025-09-15 20:26:16.804 wdl.w:ptcp.w:call-sawfish-72.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:14][sawfish][INFO] Finished breakpoint observation clustering
2025-09-15 20:26:16.804 wdl.w:ptcp.w:call-sawfish-72.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:14][sawfish][INFO] Consolidating adjacent indel candidates
2025-09-15 20:26:16.804 wdl.w:ptcp.w:call-sawfish-72.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:14][sawfish][INFO] Finding large insertion candidates
2025-09-15 20:26:16.804 wdl.w:ptcp.w:call-sawfish-72.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:14][sawfish][INFO] Writing breakpoint_cluster debug bed file: 'm84036_250809_035451_s4.bc2169_sawfish_discover/debug.breakpoint_clusters.bed'
2025-09-15 20:26:16.805 wdl.w:ptcp.w:call-sawfish-72.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:14][sawfish][INFO] Refining SV Candidates
2025-09-15 20:26:16.805 wdl.w:ptcp.w:call-sawfish-72.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:14][sawfish][INFO] Writing debug assembly region bed file: 'm84036_250809_035451_s4.bc2169_sawfish_discover/assembly.regions.bed'
2025-09-15 20:26:16.805 wdl.w:ptcp.w:call-sawfish-72.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:14][sawfish][INFO] Starting refinement of breakpoint evidence clusters
2025-09-15 20:26:16.805 wdl.w:ptcp.w:call-sawfish-72.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:14][sawfish][INFO] Finished refining all breakpoint evidence clusters
2025-09-15 20:26:16.805 wdl.w:ptcp.w:call-sawfish-72.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:14][sawfish][INFO] Writing all contig alignments to bam file: 'm84036_250809_035451_s4.bc2169_sawfish_discover/contig.alignment.bam'
2025-09-15 20:26:16.805 wdl.w:ptcp.w:call-sawfish-72.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:14][sawfish][INFO] Writing candidate structural variants to file: 'm84036_250809_035451_s4.bc2169_sawfish_discover/candidate.sv.bcf'
2025-09-15 20:26:16.805 wdl.w:ptcp.w:call-sawfish-72.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:14][sawfish][INFO] Writing run statistics to file: 'm84036_250809_035451_s4.bc2169_sawfish_discover/run.stats.json'
2025-09-15 20:26:16.805 wdl.w:ptcp.w:call-sawfish-72.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:14][sawfish][INFO] sawfish completed. Total Runtime: 00:00:03.753
2025-09-15 20:26:17.551 wdl.w:ptcp.w:call-paraphase-54.t:call-call_f8.slurm_singularity INFO srun: job 51798193 queued and waiting for resources
2025-09-15 20:26:17.551 wdl.w:ptcp.w:call-paraphase-54.t:call-call_f8.slurm_singularity INFO srun: job 51798193 has been allocated resources
2025-09-15 20:26:17.551 wdl.w:ptcp.w:call-paraphase-54.t:call-call_f8.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:26:17.911 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:26:15 [ERROR] - No reads found for TRID=FAME1_SAMD12
2025-09-15 20:26:17.969 wdl.w:ptcp.w:call-trgt-88.t:call-trgt_plot_meth_allele INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2185.meth_allele.trgt_plots.zip"
2025-09-15 20:26:18.051 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:26:15 [ERROR] - No reads found for TRID=SCA10_ATXN10
2025-09-15 20:26:18.051 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:26:15 [ERROR] - No reads found for TRID=FTDALS1_C9orf72
2025-09-15 20:26:18.051 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:26:16 [ERROR] - No reads found for TRID=FAME1_SAMD12
2025-09-15 20:26:18.061 wdl.w:ptcp.w:call-trgt-88.t:call-trgt_plot_meth_allele NOTICE done
2025-09-15 20:26:18.087 wdl.w:ptcp.w:call-trgt-88 NOTICE finish :: job: "call-trgt_plot_meth_allele"
2025-09-15 20:26:18.088 wdl.w:ptcp.w:call-trgt-88 INFO output :: job: "call-trgt_plot_meth_allele", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-88/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2185.meth_allele.trgt_plots.zip"}
2025-09-15 20:26:18.088 wdl.w:ptcp.w:call-trgt-88 INFO visit :: node: "output-images_meth_allele", values: {"images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-88/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2185.meth_allele.trgt_plots.zip"}
2025-09-15 20:26:18.124 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_meth_waterfall INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2191.meth_waterfall.trgt_plots.zip"
2025-09-15 20:26:18.185 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_meth_waterfall NOTICE done
2025-09-15 20:26:18.191 wdl.w:ptcp.w:call-trgt-94 NOTICE finish :: job: "call-trgt_plot_meth_waterfall"
2025-09-15 20:26:18.191 wdl.w:ptcp.w:call-trgt-94 INFO output :: job: "call-trgt_plot_meth_waterfall", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-94/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2191.meth_waterfall.trgt_plots.zip"}
2025-09-15 20:26:18.191 wdl.w:ptcp.w:call-trgt-94 INFO visit :: node: "output-images_meth_waterfall", values: {"images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-94/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2191.meth_waterfall.trgt_plots.zip"}
2025-09-15 20:26:18.276 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:26:15 [ERROR] - No reads found for TRID=FTDALS1_C9orf72
2025-09-15 20:26:18.276 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_motifs_waterfall.stderr VERBOSE 2025-09-15 20:26:16 [ERROR] - No reads found for TRID=FAME1_SAMD12
2025-09-15 20:26:18.407 wdl.w:ptcp.w:call-paraphase-42.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for f8inv1 for sample m84036_250809_035451_s4.bc2139 at 2025-09-15 20:26:16.356542...
2025-09-15 20:26:18.423 wdl.w:ptcp.w:call-trgt-86.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:26:15 [ERROR] - No reads found for TRID=SCA6_CACNA1A
2025-09-15 20:26:18.423 wdl.w:ptcp.w:call-trgt-86.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:26:15 [ERROR] - No reads found for TRID=OPDM2_GIPC1
2025-09-15 20:26:18.424 wdl.w:ptcp.w:call-trgt-86.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:26:16 [ERROR] - No reads found for TRID=DM1_DMPK
2025-09-15 20:26:18.424 wdl.w:ptcp.w:call-trgt-86.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:26:16 [ERROR] - No reads found for TRID=SCA4_ZFHX3
2025-09-15 20:26:18.424 wdl.w:ptcp.w:call-trgt-86.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:26:16 [ERROR] - No reads found for TRID=SCA36_NOP56
2025-09-15 20:26:18.424 wdl.w:ptcp.w:call-trgt-86.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:26:16 [ERROR] - No reads found for TRID=CJD_PRNP
2025-09-15 20:26:18.424 wdl.w:ptcp.w:call-trgt-86.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:26:17 [ERROR] - No reads found for TRID=EPM1_CSTB
2025-09-15 20:26:18.424 wdl.w:ptcp.w:call-trgt-86.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:26:17 [ERROR] - No reads found for TRID=SD5_HOXD13
2025-09-15 20:26:18.424 wdl.w:ptcp.w:call-trgt-86.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:26:17 [ERROR] - No reads found for TRID=FRA2A_AFF3
2025-09-15 20:26:18.424 wdl.w:ptcp.w:call-trgt-86.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:26:17 [ERROR] - No reads found for TRID=DM2_CNBP
2025-09-15 20:26:18.424 wdl.w:ptcp.w:call-trgt-86.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:26:18 [ERROR] - No reads found for TRID=HD_HTT
2025-09-15 20:26:18.424 wdl.w:ptcp.w:call-trgt-86.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:26:18 [ERROR] - No reads found for TRID=CCHS_PHOX2B
2025-09-15 20:26:18.631 wdl.w:ptcp.w:call-paraphase-74.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for f8inv1 for sample m84036_250809_035451_s4.bc2171 at 2025-09-15 20:26:16.929752...
2025-09-15 20:26:18.631 wdl.w:ptcp.w:call-paraphase-74.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for f8inv1 for sample m84036_250809_035451_s4.bc2171 at 2025-09-15 20:26:16.930743...
2025-09-15 20:26:18.687 wdl.w:ptcp.w:call-sawfish-85.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:13][sawfish][INFO] Starting sawfish 2.0.3
2025-09-15 20:26:18.687 wdl.w:ptcp.w:call-sawfish-85.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:13][sawfish][INFO] cmdline: sawfish discover --disable-cnv --threads 16 --ref /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa --bam m84036_250809_035451_s4.bc2182.minimap2.bam --output-dir m84036_250809_035451_s4.bc2182_sawfish_discover
2025-09-15 20:26:18.687 wdl.w:ptcp.w:call-sawfish-85.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:13][sawfish][INFO] Running on 16 threads
2025-09-15 20:26:18.687 wdl.w:ptcp.w:call-sawfish-85.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:13][sawfish][INFO] Writing discover settings to file: 'm84036_250809_035451_s4.bc2182_sawfish_discover/discover.settings.json'
2025-09-15 20:26:18.687 wdl.w:ptcp.w:call-sawfish-85.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:14][sawfish][INFO] Reading reference genome from file '/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa'
2025-09-15 20:26:18.687 wdl.w:ptcp.w:call-sawfish-85.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:17][sawfish][INFO] Processing alignment file '/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2182.minimap2.bam'
2025-09-15 20:26:18.687 wdl.w:ptcp.w:call-sawfish-85.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:17][sawfish][INFO] Finished processing all alignments
2025-09-15 20:26:18.687 wdl.w:ptcp.w:call-sawfish-85.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:17][sawfish][INFO] Writing depth bins to binary file: 'm84036_250809_035451_s4.bc2182_sawfish_discover/depth.mpack'
2025-09-15 20:26:18.687 wdl.w:ptcp.w:call-sawfish-85.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:17][sawfish][INFO] Writing max sv depth genome regions to bed file: 'm84036_250809_035451_s4.bc2182_sawfish_discover/max.depth.bed'
2025-09-15 20:26:18.687 wdl.w:ptcp.w:call-sawfish-85.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:17][sawfish][INFO] Completing breakpoint observation clustering
2025-09-15 20:26:18.687 wdl.w:ptcp.w:call-sawfish-85.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:17][sawfish][INFO] Finished breakpoint observation clustering
2025-09-15 20:26:18.687 wdl.w:ptcp.w:call-sawfish-85.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:17][sawfish][INFO] Consolidating adjacent indel candidates
2025-09-15 20:26:18.687 wdl.w:ptcp.w:call-sawfish-85.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:17][sawfish][INFO] Finding large insertion candidates
2025-09-15 20:26:18.687 wdl.w:ptcp.w:call-sawfish-85.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:17][sawfish][INFO] Writing breakpoint_cluster debug bed file: 'm84036_250809_035451_s4.bc2182_sawfish_discover/debug.breakpoint_clusters.bed'
2025-09-15 20:26:18.687 wdl.w:ptcp.w:call-sawfish-85.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:17][sawfish][INFO] Refining SV Candidates
2025-09-15 20:26:18.687 wdl.w:ptcp.w:call-sawfish-85.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:17][sawfish][INFO] Writing debug assembly region bed file: 'm84036_250809_035451_s4.bc2182_sawfish_discover/assembly.regions.bed'
2025-09-15 20:26:18.687 wdl.w:ptcp.w:call-sawfish-85.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:17][sawfish][INFO] Starting refinement of breakpoint evidence clusters
2025-09-15 20:26:18.688 wdl.w:ptcp.w:call-sawfish-85.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:17][sawfish][INFO] Finished refining all breakpoint evidence clusters
2025-09-15 20:26:18.688 wdl.w:ptcp.w:call-sawfish-85.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:17][sawfish][INFO] Writing all contig alignments to bam file: 'm84036_250809_035451_s4.bc2182_sawfish_discover/contig.alignment.bam'
2025-09-15 20:26:18.688 wdl.w:ptcp.w:call-sawfish-85.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:17][sawfish][INFO] Writing candidate structural variants to file: 'm84036_250809_035451_s4.bc2182_sawfish_discover/candidate.sv.bcf'
2025-09-15 20:26:18.688 wdl.w:ptcp.w:call-sawfish-85.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:17][sawfish][INFO] Writing run statistics to file: 'm84036_250809_035451_s4.bc2182_sawfish_discover/run.stats.json'
2025-09-15 20:26:18.688 wdl.w:ptcp.w:call-sawfish-85.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:17][sawfish][INFO] sawfish completed. Total Runtime: 00:00:03.728
2025-09-15 20:26:18.765 wdl.w:ptcp.w:call-paraphase-94.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for smn1 for sample m84036_250809_035451_s4.bc2191 at 2025-09-15 20:25:57.277666...
2025-09-15 20:26:18.766 wdl.w:ptcp.w:call-paraphase-94.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for hba for sample m84036_250809_035451_s4.bc2191 at 2025-09-15 20:25:57.647763...
2025-09-15 20:26:18.766 wdl.w:ptcp.w:call-paraphase-94.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for gba for sample m84036_250809_035451_s4.bc2191 at 2025-09-15 20:25:58.210028...
2025-09-15 20:26:18.766 wdl.w:ptcp.w:call-paraphase-94.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for cyp21 for sample m84036_250809_035451_s4.bc2191 at 2025-09-15 20:25:59.576468...
2025-09-15 20:26:18.766 wdl.w:ptcp.w:call-paraphase-94.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for smn1 for sample m84036_250809_035451_s4.bc2191 at 2025-09-15 20:26:16.258941...
2025-09-15 20:26:18.767 wdl.w:ptcp.w:call-paraphase-94.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning to gene2 region for smn1 for sample m84036_250809_035451_s4.bc2191 at 2025-09-15 20:26:16.620124...
2025-09-15 20:26:19.141 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_motifs_waterfall INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2191.motifs_waterfall.trgt_plots.zip"
2025-09-15 20:26:19.205 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_motifs_waterfall NOTICE done
2025-09-15 20:26:19.210 wdl.w:ptcp.w:call-trgt-94 NOTICE finish :: job: "call-trgt_plot_motifs_waterfall"
2025-09-15 20:26:19.210 wdl.w:ptcp.w:call-trgt-94 INFO output :: job: "call-trgt_plot_motifs_waterfall", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-94/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2191.motifs_waterfall.trgt_plots.zip"}
2025-09-15 20:26:19.210 wdl.w:ptcp.w:call-trgt-94 INFO visit :: node: "output-images_motifs_waterfall", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-94/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2191.motifs_waterfall.trgt_plots.zip"}
2025-09-15 20:26:19.222 wdl.w:ptcp.w:call-paraphase-54.t:call-call_f8 INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2151.f8inversion.vcf"
2025-09-15 20:26:19.225 wdl.w:ptcp.w:call-paraphase-54.t:call-call_f8 INFO output :: name: "json", value: "m84036_250809_035451_s4.bc2151.f8inversion.json"
2025-09-15 20:26:19.266 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:26:16 [ERROR] - No reads found for TRID=OPDM2_GIPC1
2025-09-15 20:26:19.266 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:26:16 [ERROR] - No reads found for TRID=EPM1_CSTB
2025-09-15 20:26:19.267 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:26:16 [ERROR] - No reads found for TRID=SCA10_ATXN10
2025-09-15 20:26:19.267 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:26:16 [ERROR] - No reads found for TRID=SCA7_ATXN7
2025-09-15 20:26:19.267 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:26:17 [ERROR] - No reads found for TRID=DM2_CNBP
2025-09-15 20:26:19.267 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:26:17 [ERROR] - No reads found for TRID=DM1_DMPK
2025-09-15 20:26:19.267 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:26:17 [ERROR] - No reads found for TRID=SCA36_NOP56
2025-09-15 20:26:19.267 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:26:17 [ERROR] - No reads found for TRID=HD_HTT
2025-09-15 20:26:19.267 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:26:17 [ERROR] - No reads found for TRID=SCA1_ATXN1
2025-09-15 20:26:19.267 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:26:18 [ERROR] - No reads found for TRID=OPDM1_LRP12
2025-09-15 20:26:19.267 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:26:18 [ERROR] - No reads found for TRID=SCA17_TBP
2025-09-15 20:26:19.267 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:26:18 [ERROR] - No reads found for TRID=CJD_PRNP
2025-09-15 20:26:19.267 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:26:18 [ERROR] - No reads found for TRID=CCHS_PHOX2B
2025-09-15 20:26:19.268 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:26:19 [ERROR] - No reads found for TRID=SCA12_PPP2R2B
2025-09-15 20:26:19.287 wdl.w:ptcp.w:call-paraphase-54.t:call-call_f8 NOTICE done
2025-09-15 20:26:19.294 wdl.w:ptcp.w:call-paraphase-54 NOTICE finish :: job: "call-call_f8"
2025-09-15 20:26:19.294 wdl.w:ptcp.w:call-paraphase-54 INFO output :: job: "call-call_f8", values: {"json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-54/call-call_f8/out/m84036_250809_035451_s4.bc2151.f8inversion.json", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-54/call-call_f8/out/m84036_250809_035451_s4.bc2151.f8inversion.vcf"}
2025-09-15 20:26:19.294 wdl.w:ptcp.w:call-paraphase-54 INFO visit :: node: "output-f8_json", values: {"f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-54/call-call_f8/out/m84036_250809_035451_s4.bc2151.f8inversion.json"}
2025-09-15 20:26:19.294 wdl.w:ptcp.w:call-paraphase-54 INFO visit :: node: "output-f8_vcf", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-54/call-call_f8/out/m84036_250809_035451_s4.bc2151.f8inversion.vcf"}
2025-09-15 20:26:19.295 wdl.w:ptcp.w:call-paraphase-54 INFO visit :: node: "outputs", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-54/call-call_f8/out/m84036_250809_035451_s4.bc2151.f8inversion.vcf", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-54/call-run_paraphase/out/m84036_250809_035451_s4.bc2151_paraphase/m84036_250809_035451_s4.bc2151.paraphase.json", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-54/call-run_paraphase/out/m84036_250809_035451_s4.bc2151_paraphase/m84036_250809_035451_s4.bc2151.paraphase.bam", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-54/call-run_paraphase/out/m84036_250809_035451_s4.bc2151_paraphase/m84036_250809_035451_s4.bc2151.paraphase.bam.bai", "paraphase_vcfs": ["/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-54/call-run_paraphase/out/m84036_250809_035451_s4.bc2151_paraphase/m84036_250809_035451_s4.bc2151_paraphase_vcfs/m84036_250809_035451_s4.bc2151_cyp21.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-54/call-run_paraphase/out/m84036_250809_035451_s4.bc2151_paraphase/m84036_250809_035451_s4.bc2151_paraphase_vcfs/m84036_250809_035451_s4.bc2151_f8inv1.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-54/call-run_paraphase/out/m84036_250809_035451_s4.bc2151_paraphase/m84036_250809_035451_s4.bc2151_paraphase_vcfs/m84036_250809_035451_s4.bc2151_f8inv22.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-54/call-run_paraphase/out/m84036_250809_035451_s4.bc2151_paraphase/m84036_250809_035451_s4.bc2151_paraphase_vcfs/m84036_250809_035451_s4.bc2151_gba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-54/call-run_paraphase/out/m84036_250809_035451_s4.bc2151_paraphase/m84036_250809_035451_s4.bc2151_paraphase_vcfs/m84036_250809_035451_s4.bc2151_hba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-54/call-run_paraphase/out/m84036_250809_035451_s4.bc2151_paraphase/m84036_250809_035451_s4.bc2151_paraphase_vcfs/m84036_250809_035451_s4.bc2151_hbb.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-54/call-run_paraphase/out/m84036_250809_035451_s4.bc2151_paraphase/m84036_250809_035451_s4.bc2151_paraphase_vcfs/m84036_250809_035451_s4.bc2151_rpgr.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-54/call-run_paraphase/out/m84036_250809_035451_s4.bc2151_paraphase/m84036_250809_035451_s4.bc2151_paraphase_vcfs/m84036_250809_035451_s4.bc2151_smn1.vcf"], "havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-54/call-run_paraphase/out/m84036_250809_035451_s4.bc2151.havanno.json", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-54/call-call_f8/out/m84036_250809_035451_s4.bc2151.f8inversion.json"}
2025-09-15 20:26:19.294 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:26:16 [ERROR] - No reads found for TRID=EPM1_CSTB
2025-09-15 20:26:19.295 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:26:16 [ERROR] - No reads found for TRID=SCA10_ATXN10
2025-09-15 20:26:19.295 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:26:16 [ERROR] - No reads found for TRID=SCA7_ATXN7
2025-09-15 20:26:19.295 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:26:16 [ERROR] - No reads found for TRID=DM2_CNBP
2025-09-15 20:26:19.295 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:26:17 [ERROR] - No reads found for TRID=DM1_DMPK
2025-09-15 20:26:19.295 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:26:17 [ERROR] - No reads found for TRID=SCA36_NOP56
2025-09-15 20:26:19.295 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:26:17 [ERROR] - No reads found for TRID=HD_HTT
2025-09-15 20:26:19.296 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:26:17 [ERROR] - No reads found for TRID=SCA1_ATXN1
2025-09-15 20:26:19.296 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:26:17 [ERROR] - No reads found for TRID=OPDM1_LRP12
2025-09-15 20:26:19.296 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:26:18 [ERROR] - No reads found for TRID=SCA17_TBP
2025-09-15 20:26:19.296 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:26:18 [ERROR] - No reads found for TRID=CJD_PRNP
2025-09-15 20:26:19.296 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:26:18 [ERROR] - No reads found for TRID=CCHS_PHOX2B
2025-09-15 20:26:19.296 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:26:19 [ERROR] - No reads found for TRID=SCA12_PPP2R2B
2025-09-15 20:26:19.377 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_motifs_allele INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2191.motifs_allele.trgt_plots.zip"
2025-09-15 20:26:19.418 wdl.w:ptcp.w:call-paraphase-54 NOTICE done
2025-09-15 20:26:19.425 wdl.w:ptcp NOTICE finish :: job: "call-paraphase-54"
2025-09-15 20:26:19.425 wdl.w:ptcp INFO output :: job: "call-paraphase-54", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-54/out/m84036_250809_035451_s4.bc2151.f8inversion.vcf", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-54/out/m84036_250809_035451_s4.bc2151_paraphase/m84036_250809_035451_s4.bc2151.paraphase.json", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-54/out/m84036_250809_035451_s4.bc2151_paraphase/m84036_250809_035451_s4.bc2151.paraphase.bam", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-54/out/m84036_250809_035451_s4.bc2151_paraphase/m84036_250809_035451_s4.bc2151.paraphase.bam.bai", "paraphase_vcfs": ["/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-54/out/m84036_250809_035451_s4.bc2151_paraphase/m84036_250809_035451_s4.bc2151_paraphase_vcfs/m84036_250809_035451_s4.bc2151_cyp21.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-54/out/m84036_250809_035451_s4.bc2151_paraphase/m84036_250809_035451_s4.bc2151_paraphase_vcfs/m84036_250809_035451_s4.bc2151_f8inv1.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-54/out/m84036_250809_035451_s4.bc2151_paraphase/m84036_250809_035451_s4.bc2151_paraphase_vcfs/m84036_250809_035451_s4.bc2151_f8inv22.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-54/out/m84036_250809_035451_s4.bc2151_paraphase/m84036_250809_035451_s4.bc2151_paraphase_vcfs/m84036_250809_035451_s4.bc2151_gba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-54/out/m84036_250809_035451_s4.bc2151_paraphase/m84036_250809_035451_s4.bc2151_paraphase_vcfs/m84036_250809_035451_s4.bc2151_hba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-54/out/m84036_250809_035451_s4.bc2151_paraphase/m84036_250809_035451_s4.bc2151_paraphase_vcfs/m84036_250809_035451_s4.bc2151_hbb.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-54/out/m84036_250809_035451_s4.bc2151_paraphase/m84036_250809_035451_s4.bc2151_paraphase_vcfs/m84036_250809_035451_s4.bc2151_rpgr.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-54/out/m84036_250809_035451_s4.bc2151_paraphase/m84036_250809_035451_s4.bc2151_paraphase_vcfs/m84036_250809_035451_s4.bc2151_smn1.vcf"], "havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-54/out/m84036_250809_035451_s4.bc2151.havanno.json", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-54/out/m84036_250809_035451_s4.bc2151.f8inversion.json"}
2025-09-15 20:26:19.426 wdl.w:ptcp NOTICE ready :: job: "call-tar_outputs-54", callee: "tar_outputs"
2025-09-15 20:26:19.426 wdl.w:ptcp INFO input :: job: "call-tar_outputs-54", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "sawfish_vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-54/out/m84036_250809_035451_s4.bc2151_sawfish/m84036_250809_035451_s4.bc2151.sv.vcf.gz.tbi", "sawfish_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-54/out/m84036_250809_035451_s4.bc2151_sawfish/m84036_250809_035451_s4.bc2151.sv.vcf.gz", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-54/out/m84036_250809_035451_s4.bc2151.f8inversion.json", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-54/out/m84036_250809_035451_s4.bc2151_paraphase/m84036_250809_035451_s4.bc2151.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-54/out/m84036_250809_035451_s4.bc2151_paraphase/m84036_250809_035451_s4.bc2151.paraphase.bam", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-54/out/m84036_250809_035451_s4.bc2151_paraphase/m84036_250809_035451_s4.bc2151.paraphase.json", "trgt_spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-54/out/m84036_250809_035451_s4.bc2151.trgt.sorted.spanning.bam.bai", "trgt_spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-54/out/m84036_250809_035451_s4.bc2151.trgt.sorted.spanning.bam", "trgt_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-54/out/m84036_250809_035451_s4.bc2151.trgt.vcf", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-54/out/m84036_250809_035451_s4.bc2151.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-54/out/m84036_250809_035451_s4.bc2151.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2151"}
2025-09-15 20:26:19.434 wdl.w:ptcp.t:call-tar_outputs-54 NOTICE task setup :: name: "tar_outputs", source: "./common.wdl", line: 279, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-54", thread: 140613034948160
2025-09-15 20:26:19.458 wdl.w:ptcp.t:call-tar_outputs-54 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:26:19.459 wdl.w:ptcp.t:call-tar_outputs-54 INFO input :: name: "sawfish_vcf_tbi", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2151.sv.vcf.gz.tbi"
2025-09-15 20:26:19.459 wdl.w:ptcp.t:call-tar_outputs-54 INFO input :: name: "sawfish_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2151.sv.vcf.gz"
2025-09-15 20:26:19.459 wdl.w:ptcp.t:call-tar_outputs-54 INFO input :: name: "f8_json", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2151.f8inversion.json"
2025-09-15 20:26:19.459 wdl.w:ptcp.t:call-tar_outputs-54 INFO input :: name: "paraphase_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2151.paraphase.bam.bai"
2025-09-15 20:26:19.459 wdl.w:ptcp.t:call-tar_outputs-54 INFO input :: name: "paraphase_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2151.paraphase.bam"
2025-09-15 20:26:19.459 wdl.w:ptcp.t:call-tar_outputs-54 INFO input :: name: "paraphase_json", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2151.paraphase.json"
2025-09-15 20:26:19.459 wdl.w:ptcp.t:call-tar_outputs-54 INFO input :: name: "trgt_spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2151.trgt.sorted.spanning.bam.bai"
2025-09-15 20:26:19.459 wdl.w:ptcp.t:call-tar_outputs-54 INFO input :: name: "trgt_spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2151.trgt.sorted.spanning.bam"
2025-09-15 20:26:19.459 wdl.w:ptcp.t:call-tar_outputs-54 INFO input :: name: "trgt_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2151.trgt.vcf"
2025-09-15 20:26:19.459 wdl.w:ptcp.t:call-tar_outputs-54 INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2151.mapped.bam.bai"
2025-09-15 20:26:19.459 wdl.w:ptcp.t:call-tar_outputs-54 INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2151.mapped.bam"
2025-09-15 20:26:19.459 wdl.w:ptcp.t:call-tar_outputs-54 INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2151"
2025-09-15 20:26:19.459 wdl.w:ptcp.t:call-tar_outputs-54 INFO eval :: name: "threads", value: 1
2025-09-15 20:26:19.460 wdl.w:ptcp.t:call-tar_outputs-54 INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:26:19.460 wdl.w:ptcp.t:call-tar_outputs-54 INFO eval :: name: "disk_size", value: 6
2025-09-15 20:26:19.460 wdl.w:ptcp.t:call-tar_outputs-54 INFO eval :: name: "output_tarball", value: "m84036_250809_035451_s4.bc2151.tar"
2025-09-15 20:26:19.460 wdl.w:ptcp.t:call-tar_outputs-54 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:26:19.460 wdl.w:ptcp.t:call-tar_outputs-54 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:26:19.461 wdl.w:ptcp.t:call-tar_outputs-54 INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:26:19.461 wdl.w:ptcp.t:call-tar_outputs-54 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:26:19.467 wdl.w:ptcp.w:call-trgt-94.t:call-trgt_plot_motifs_allele NOTICE done
2025-09-15 20:26:19.472 wdl.w:ptcp.w:call-trgt-94 NOTICE finish :: job: "call-trgt_plot_motifs_allele"
2025-09-15 20:26:19.472 wdl.w:ptcp.w:call-trgt-94 INFO output :: job: "call-trgt_plot_motifs_allele", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-94/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2191.motifs_allele.trgt_plots.zip"}
2025-09-15 20:26:19.473 wdl.w:ptcp.w:call-trgt-94 INFO visit :: node: "output-images_motifs_allele", values: {"images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-94/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2191.motifs_allele.trgt_plots.zip"}
2025-09-15 20:26:19.473 wdl.w:ptcp.w:call-trgt-94 INFO visit :: node: "outputs", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-94/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2191.motifs_waterfall.trgt_plots.zip", "images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-94/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2191.meth_allele.trgt_plots.zip", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-94/call-trgt_genotype/out/m84036_250809_035451_s4.bc2191.trgt.sorted.spanning.bam.bai", "images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-94/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2191.motifs_allele.trgt_plots.zip", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-94/call-trgt_genotype/out/m84036_250809_035451_s4.bc2191.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-94/call-trgt_genotype/out/m84036_250809_035451_s4.bc2191.trgt.vcf", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-94/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2191.repeats.bam", "images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-94/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2191.meth_waterfall.trgt_plots.zip", "reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-94/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2191.repeats.bam.bai"}
2025-09-15 20:26:19.476 wdl.w:ptcp.w:call-trgt-90.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:26:16 [ERROR] - No reads found for TRID=SCA12_PPP2R2B
2025-09-15 20:26:19.476 wdl.w:ptcp.w:call-trgt-90.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:26:17 [ERROR] - No reads found for TRID=DM2_CNBP
2025-09-15 20:26:19.476 wdl.w:ptcp.w:call-trgt-90.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:26:17 [ERROR] - No reads found for TRID=SCA36_NOP56
2025-09-15 20:26:19.476 wdl.w:ptcp.w:call-trgt-90.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:26:17 [ERROR] - No reads found for TRID=FAME1_SAMD12
2025-09-15 20:26:19.476 wdl.w:ptcp.w:call-trgt-90.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:26:18 [ERROR] - No reads found for TRID=FTDALS1_C9orf72
2025-09-15 20:26:19.476 wdl.w:ptcp.w:call-trgt-90.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:26:18 [ERROR] - No reads found for TRID=SBMA_AR
2025-09-15 20:26:19.559 wdl.w:ptcp.t:call-tar_outputs-54 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 17, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-54/_singularity_tmpdir_2xm0oyt9"
2025-09-15 20:26:19.559 wdl.w:ptcp.t:call-tar_outputs-54 INFO Slurm invocation: srun --job-name call-tar_outputs-54 --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-54/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-54/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-54/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-54/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-54/out/m84036_250809_035451_s4.bc2151.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2151.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-54/out/m84036_250809_035451_s4.bc2151.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2151.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-54/out/m84036_250809_035451_s4.bc2151_paraphase/m84036_250809_035451_s4.bc2151.paraphase.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2151.paraphase.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-54/out/m84036_250809_035451_s4.bc2151_paraphase/m84036_250809_035451_s4.bc2151.paraphase.json:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2151.paraphase.json:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-54/out/m84036_250809_035451_s4.bc2151_paraphase/m84036_250809_035451_s4.bc2151.paraphase.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2151.paraphase.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-54/out/m84036_250809_035451_s4.bc2151_sawfish/m84036_250809_035451_s4.bc2151.sv.vcf.gz.tbi:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2151.sv.vcf.gz.tbi:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-54/out/m84036_250809_035451_s4.bc2151_sawfish/m84036_250809_035451_s4.bc2151.sv.vcf.gz:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2151.sv.vcf.gz:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-54/out/m84036_250809_035451_s4.bc2151.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2151.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-54/out/m84036_250809_035451_s4.bc2151.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2151.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-54/out/m84036_250809_035451_s4.bc2151.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2151.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-54/out/m84036_250809_035451_s4.bc2151.f8inversion.json:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2151.f8inversion.json:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-54/_singularity_tmpdir_2xm0oyt9/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-54/_singularity_tmpdir_2xm0oyt9/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:26:19.568 wdl.w:ptcp.w:call-trgt-94 NOTICE done
2025-09-15 20:26:19.585 wdl.w:ptcp.t:call-tar_outputs-54 NOTICE slurm_singularity run :: pid: 1207481, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-54/slurm_singularity.log.txt"
2025-09-15 20:26:19.614 wdl.w:ptcp NOTICE finish :: job: "call-trgt-94"
2025-09-15 20:26:19.614 wdl.w:ptcp INFO output :: job: "call-trgt-94", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-94/out/m84036_250809_035451_s4.bc2191.motifs_waterfall.trgt_plots.zip", "images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-94/out/m84036_250809_035451_s4.bc2191.meth_allele.trgt_plots.zip", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-94/out/m84036_250809_035451_s4.bc2191.trgt.sorted.spanning.bam.bai", "images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-94/out/m84036_250809_035451_s4.bc2191.motifs_allele.trgt_plots.zip", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-94/out/m84036_250809_035451_s4.bc2191.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-94/out/m84036_250809_035451_s4.bc2191.trgt.vcf", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-94/out/m84036_250809_035451_s4.bc2191.repeats.bam", "images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-94/out/m84036_250809_035451_s4.bc2191.meth_waterfall.trgt_plots.zip", "reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-94/out/m84036_250809_035451_s4.bc2191.repeats.bam.bai"}
2025-09-15 20:26:19.805 wdl.w:ptcp.w:call-sawfish-72.t:call-run_sawfish INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2169_sawfish/m84036_250809_035451_s4.bc2169.sv.vcf.gz"
2025-09-15 20:26:19.809 wdl.w:ptcp.w:call-sawfish-72.t:call-run_sawfish INFO output :: name: "vcf_tbi", value: "m84036_250809_035451_s4.bc2169_sawfish/m84036_250809_035451_s4.bc2169.sv.vcf.gz.tbi"
2025-09-15 20:26:19.810 wdl.w:ptcp.w:call-sawfish-72.t:call-run_sawfish INFO output :: name: "minimap2_bam", value: "m84036_250809_035451_s4.bc2169.minimap2.bam"
2025-09-15 20:26:19.811 wdl.w:ptcp.w:call-sawfish-72.t:call-run_sawfish INFO output :: name: "minimap2_bam_bai", value: "m84036_250809_035451_s4.bc2169.minimap2.bam.bai"
2025-09-15 20:26:19.938 wdl.w:ptcp.w:call-sawfish-72.t:call-run_sawfish NOTICE done
2025-09-15 20:26:19.943 wdl.w:ptcp.w:call-sawfish-72 NOTICE finish :: job: "call-run_sawfish"
2025-09-15 20:26:19.943 wdl.w:ptcp.w:call-sawfish-72 INFO output :: job: "call-run_sawfish", values: {"minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-72/call-run_sawfish/out/m84036_250809_035451_s4.bc2169.minimap2.bam.bai", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-72/call-run_sawfish/out/m84036_250809_035451_s4.bc2169.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-72/call-run_sawfish/out/m84036_250809_035451_s4.bc2169_sawfish/m84036_250809_035451_s4.bc2169.sv.vcf.gz.tbi", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-72/call-run_sawfish/out/m84036_250809_035451_s4.bc2169_sawfish/m84036_250809_035451_s4.bc2169.sv.vcf.gz"}
2025-09-15 20:26:19.944 wdl.w:ptcp.w:call-sawfish-72 INFO visit :: node: "output-minimap2_bam", values: {"minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-72/call-run_sawfish/out/m84036_250809_035451_s4.bc2169.minimap2.bam"}
2025-09-15 20:26:19.944 wdl.w:ptcp.w:call-sawfish-72 INFO visit :: node: "output-minimap2_bam_bai", values: {"minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-72/call-run_sawfish/out/m84036_250809_035451_s4.bc2169.minimap2.bam.bai"}
2025-09-15 20:26:19.944 wdl.w:ptcp.w:call-sawfish-72 INFO visit :: node: "output-vcf", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-72/call-run_sawfish/out/m84036_250809_035451_s4.bc2169_sawfish/m84036_250809_035451_s4.bc2169.sv.vcf.gz"}
2025-09-15 20:26:19.944 wdl.w:ptcp.w:call-sawfish-72 INFO visit :: node: "output-vcf_tbi", values: {"vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-72/call-run_sawfish/out/m84036_250809_035451_s4.bc2169_sawfish/m84036_250809_035451_s4.bc2169.sv.vcf.gz.tbi"}
2025-09-15 20:26:19.944 wdl.w:ptcp.w:call-sawfish-72 INFO visit :: node: "outputs", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-72/call-run_sawfish/out/m84036_250809_035451_s4.bc2169_sawfish/m84036_250809_035451_s4.bc2169.sv.vcf.gz", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-72/call-run_sawfish/out/m84036_250809_035451_s4.bc2169.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-72/call-run_sawfish/out/m84036_250809_035451_s4.bc2169_sawfish/m84036_250809_035451_s4.bc2169.sv.vcf.gz.tbi", "minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-72/call-run_sawfish/out/m84036_250809_035451_s4.bc2169.minimap2.bam.bai"}
2025-09-15 20:26:19.986 wdl.w:ptcp.w:call-sawfish-72 NOTICE done
2025-09-15 20:26:19.991 wdl.w:ptcp NOTICE finish :: job: "call-sawfish-72"
2025-09-15 20:26:19.991 wdl.w:ptcp INFO output :: job: "call-sawfish-72", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-72/out/m84036_250809_035451_s4.bc2169_sawfish/m84036_250809_035451_s4.bc2169.sv.vcf.gz", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-72/out/m84036_250809_035451_s4.bc2169.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-72/out/m84036_250809_035451_s4.bc2169_sawfish/m84036_250809_035451_s4.bc2169.sv.vcf.gz.tbi", "minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-72/out/m84036_250809_035451_s4.bc2169.minimap2.bam.bai"}
2025-09-15 20:26:19.992 wdl.w:ptcp NOTICE ready :: job: "call-tar_outputs-72", callee: "tar_outputs"
2025-09-15 20:26:19.992 wdl.w:ptcp INFO input :: job: "call-tar_outputs-72", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "sawfish_vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-72/out/m84036_250809_035451_s4.bc2169_sawfish/m84036_250809_035451_s4.bc2169.sv.vcf.gz.tbi", "sawfish_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-72/out/m84036_250809_035451_s4.bc2169_sawfish/m84036_250809_035451_s4.bc2169.sv.vcf.gz", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-72/out/m84036_250809_035451_s4.bc2169.f8inversion.json", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-72/out/m84036_250809_035451_s4.bc2169_paraphase/m84036_250809_035451_s4.bc2169.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-72/out/m84036_250809_035451_s4.bc2169_paraphase/m84036_250809_035451_s4.bc2169.paraphase.bam", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-72/out/m84036_250809_035451_s4.bc2169_paraphase/m84036_250809_035451_s4.bc2169.paraphase.json", "trgt_spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-72/out/m84036_250809_035451_s4.bc2169.trgt.sorted.spanning.bam.bai", "trgt_spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-72/out/m84036_250809_035451_s4.bc2169.trgt.sorted.spanning.bam", "trgt_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-72/out/m84036_250809_035451_s4.bc2169.trgt.vcf", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-72/out/m84036_250809_035451_s4.bc2169.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-72/out/m84036_250809_035451_s4.bc2169.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2169"}
2025-09-15 20:26:19.999 wdl.w:ptcp.t:call-tar_outputs-72 NOTICE task setup :: name: "tar_outputs", source: "./common.wdl", line: 279, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-72", thread: 140612489684544
2025-09-15 20:26:20.016 wdl.w:ptcp.t:call-tar_outputs-72 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:26:20.016 wdl.w:ptcp.t:call-tar_outputs-72 INFO input :: name: "sawfish_vcf_tbi", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2169.sv.vcf.gz.tbi"
2025-09-15 20:26:20.016 wdl.w:ptcp.t:call-tar_outputs-72 INFO input :: name: "sawfish_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2169.sv.vcf.gz"
2025-09-15 20:26:20.016 wdl.w:ptcp.t:call-tar_outputs-72 INFO input :: name: "f8_json", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2169.f8inversion.json"
2025-09-15 20:26:20.016 wdl.w:ptcp.t:call-tar_outputs-72 INFO input :: name: "paraphase_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2169.paraphase.bam.bai"
2025-09-15 20:26:20.016 wdl.w:ptcp.t:call-tar_outputs-72 INFO input :: name: "paraphase_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2169.paraphase.bam"
2025-09-15 20:26:20.016 wdl.w:ptcp.t:call-tar_outputs-72 INFO input :: name: "paraphase_json", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2169.paraphase.json"
2025-09-15 20:26:20.016 wdl.w:ptcp.t:call-tar_outputs-72 INFO input :: name: "trgt_spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2169.trgt.sorted.spanning.bam.bai"
2025-09-15 20:26:20.016 wdl.w:ptcp.t:call-tar_outputs-72 INFO input :: name: "trgt_spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2169.trgt.sorted.spanning.bam"
2025-09-15 20:26:20.016 wdl.w:ptcp.t:call-tar_outputs-72 INFO input :: name: "trgt_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2169.trgt.vcf"
2025-09-15 20:26:20.016 wdl.w:ptcp.t:call-tar_outputs-72 INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2169.mapped.bam.bai"
2025-09-15 20:26:20.016 wdl.w:ptcp.t:call-tar_outputs-72 INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2169.mapped.bam"
2025-09-15 20:26:20.017 wdl.w:ptcp.t:call-tar_outputs-72 INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2169"
2025-09-15 20:26:20.017 wdl.w:ptcp.t:call-tar_outputs-72 INFO eval :: name: "threads", value: 1
2025-09-15 20:26:20.017 wdl.w:ptcp.t:call-tar_outputs-72 INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:26:20.017 wdl.w:ptcp.t:call-tar_outputs-72 INFO eval :: name: "disk_size", value: 6
2025-09-15 20:26:20.017 wdl.w:ptcp.t:call-tar_outputs-72 INFO eval :: name: "output_tarball", value: "m84036_250809_035451_s4.bc2169.tar"
2025-09-15 20:26:20.018 wdl.w:ptcp.t:call-tar_outputs-72 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:26:20.018 wdl.w:ptcp.t:call-tar_outputs-72 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:26:20.018 wdl.w:ptcp.t:call-tar_outputs-72 INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:26:20.018 wdl.w:ptcp.t:call-tar_outputs-72 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:26:20.102 wdl.w:ptcp.w:call-sawfish-56.t:call-run_sawfish INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2153_sawfish/m84036_250809_035451_s4.bc2153.sv.vcf.gz"
2025-09-15 20:26:20.108 wdl.w:ptcp.w:call-sawfish-56.t:call-run_sawfish INFO output :: name: "vcf_tbi", value: "m84036_250809_035451_s4.bc2153_sawfish/m84036_250809_035451_s4.bc2153.sv.vcf.gz.tbi"
2025-09-15 20:26:20.109 wdl.w:ptcp.w:call-sawfish-56.t:call-run_sawfish INFO output :: name: "minimap2_bam", value: "m84036_250809_035451_s4.bc2153.minimap2.bam"
2025-09-15 20:26:20.110 wdl.w:ptcp.w:call-sawfish-56.t:call-run_sawfish INFO output :: name: "minimap2_bam_bai", value: "m84036_250809_035451_s4.bc2153.minimap2.bam.bai"
2025-09-15 20:26:20.115 wdl.w:ptcp.t:call-tar_outputs-72 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 17, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-72/_singularity_tmpdir_6mp7mydp"
2025-09-15 20:26:20.115 wdl.w:ptcp.t:call-tar_outputs-72 INFO Slurm invocation: srun --job-name call-tar_outputs-72 --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-72/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-72/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-72/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-72/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-72/out/m84036_250809_035451_s4.bc2169_sawfish/m84036_250809_035451_s4.bc2169.sv.vcf.gz.tbi:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2169.sv.vcf.gz.tbi:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-72/out/m84036_250809_035451_s4.bc2169_sawfish/m84036_250809_035451_s4.bc2169.sv.vcf.gz:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2169.sv.vcf.gz:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-72/out/m84036_250809_035451_s4.bc2169.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2169.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-72/out/m84036_250809_035451_s4.bc2169.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2169.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-72/out/m84036_250809_035451_s4.bc2169_paraphase/m84036_250809_035451_s4.bc2169.paraphase.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2169.paraphase.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-72/out/m84036_250809_035451_s4.bc2169_paraphase/m84036_250809_035451_s4.bc2169.paraphase.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2169.paraphase.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-72/out/m84036_250809_035451_s4.bc2169_paraphase/m84036_250809_035451_s4.bc2169.paraphase.json:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2169.paraphase.json:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-72/out/m84036_250809_035451_s4.bc2169.f8inversion.json:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2169.f8inversion.json:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-72/out/m84036_250809_035451_s4.bc2169.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2169.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-72/out/m84036_250809_035451_s4.bc2169.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2169.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-72/out/m84036_250809_035451_s4.bc2169.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2169.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-72/_singularity_tmpdir_6mp7mydp/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-72/_singularity_tmpdir_6mp7mydp/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:26:20.131 wdl.w:ptcp.t:call-tar_outputs-72 NOTICE slurm_singularity run :: pid: 1207557, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-72/slurm_singularity.log.txt"
2025-09-15 20:26:20.234 wdl.w:ptcp.w:call-sawfish-56.t:call-run_sawfish NOTICE done
2025-09-15 20:26:20.240 wdl.w:ptcp.w:call-sawfish-56 NOTICE finish :: job: "call-run_sawfish"
2025-09-15 20:26:20.240 wdl.w:ptcp.w:call-sawfish-56 INFO output :: job: "call-run_sawfish", values: {"minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-56/call-run_sawfish/out/m84036_250809_035451_s4.bc2153.minimap2.bam.bai", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-56/call-run_sawfish/out/m84036_250809_035451_s4.bc2153.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-56/call-run_sawfish/out/m84036_250809_035451_s4.bc2153_sawfish/m84036_250809_035451_s4.bc2153.sv.vcf.gz.tbi", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-56/call-run_sawfish/out/m84036_250809_035451_s4.bc2153_sawfish/m84036_250809_035451_s4.bc2153.sv.vcf.gz"}
2025-09-15 20:26:20.241 wdl.w:ptcp.w:call-sawfish-56 INFO visit :: node: "output-minimap2_bam", values: {"minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-56/call-run_sawfish/out/m84036_250809_035451_s4.bc2153.minimap2.bam"}
2025-09-15 20:26:20.241 wdl.w:ptcp.w:call-sawfish-56 INFO visit :: node: "output-minimap2_bam_bai", values: {"minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-56/call-run_sawfish/out/m84036_250809_035451_s4.bc2153.minimap2.bam.bai"}
2025-09-15 20:26:20.241 wdl.w:ptcp.w:call-sawfish-56 INFO visit :: node: "output-vcf", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-56/call-run_sawfish/out/m84036_250809_035451_s4.bc2153_sawfish/m84036_250809_035451_s4.bc2153.sv.vcf.gz"}
2025-09-15 20:26:20.241 wdl.w:ptcp.w:call-sawfish-56 INFO visit :: node: "output-vcf_tbi", values: {"vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-56/call-run_sawfish/out/m84036_250809_035451_s4.bc2153_sawfish/m84036_250809_035451_s4.bc2153.sv.vcf.gz.tbi"}
2025-09-15 20:26:20.241 wdl.w:ptcp.w:call-sawfish-56 INFO visit :: node: "outputs", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-56/call-run_sawfish/out/m84036_250809_035451_s4.bc2153_sawfish/m84036_250809_035451_s4.bc2153.sv.vcf.gz", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-56/call-run_sawfish/out/m84036_250809_035451_s4.bc2153.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-56/call-run_sawfish/out/m84036_250809_035451_s4.bc2153_sawfish/m84036_250809_035451_s4.bc2153.sv.vcf.gz.tbi", "minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-56/call-run_sawfish/out/m84036_250809_035451_s4.bc2153.minimap2.bam.bai"}
2025-09-15 20:26:20.289 wdl.w:ptcp.w:call-sawfish-56 NOTICE done
2025-09-15 20:26:20.295 wdl.w:ptcp NOTICE finish :: job: "call-sawfish-56"
2025-09-15 20:26:20.295 wdl.w:ptcp INFO output :: job: "call-sawfish-56", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-56/out/m84036_250809_035451_s4.bc2153_sawfish/m84036_250809_035451_s4.bc2153.sv.vcf.gz", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-56/out/m84036_250809_035451_s4.bc2153.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-56/out/m84036_250809_035451_s4.bc2153_sawfish/m84036_250809_035451_s4.bc2153.sv.vcf.gz.tbi", "minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-56/out/m84036_250809_035451_s4.bc2153.minimap2.bam.bai"}
2025-09-15 20:26:20.296 wdl.w:ptcp NOTICE ready :: job: "call-tar_outputs-56", callee: "tar_outputs"
2025-09-15 20:26:20.296 wdl.w:ptcp INFO input :: job: "call-tar_outputs-56", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "sawfish_vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-56/out/m84036_250809_035451_s4.bc2153_sawfish/m84036_250809_035451_s4.bc2153.sv.vcf.gz.tbi", "sawfish_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-56/out/m84036_250809_035451_s4.bc2153_sawfish/m84036_250809_035451_s4.bc2153.sv.vcf.gz", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-56/out/m84036_250809_035451_s4.bc2153.f8inversion.json", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-56/out/m84036_250809_035451_s4.bc2153_paraphase/m84036_250809_035451_s4.bc2153.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-56/out/m84036_250809_035451_s4.bc2153_paraphase/m84036_250809_035451_s4.bc2153.paraphase.bam", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-56/out/m84036_250809_035451_s4.bc2153_paraphase/m84036_250809_035451_s4.bc2153.paraphase.json", "trgt_spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-56/out/m84036_250809_035451_s4.bc2153.trgt.sorted.spanning.bam.bai", "trgt_spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-56/out/m84036_250809_035451_s4.bc2153.trgt.sorted.spanning.bam", "trgt_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-56/out/m84036_250809_035451_s4.bc2153.trgt.vcf", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-56/out/m84036_250809_035451_s4.bc2153.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-56/out/m84036_250809_035451_s4.bc2153.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2153"}
2025-09-15 20:26:20.302 wdl.w:ptcp.w:call-paraphase-30.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for rpgr for sample m84036_250809_035451_s4.bc2127 at 2025-09-15 20:25:35.178771...
2025-09-15 20:26:20.302 wdl.w:ptcp.w:call-paraphase-30.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for rpgr for sample m84036_250809_035451_s4.bc2127 at 2025-09-15 20:25:36.132250...
2025-09-15 20:26:20.302 wdl.w:ptcp.w:call-paraphase-30.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for rpgr for sample m84036_250809_035451_s4.bc2127 at 2025-09-15 20:25:36.367676...
2025-09-15 20:26:20.311 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:26:19 [ERROR] - No reads found for TRID=FAME1_SAMD12
2025-09-15 20:26:20.312 wdl.w:ptcp.t:call-tar_outputs-56 NOTICE task setup :: name: "tar_outputs", source: "./common.wdl", line: 279, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-56", thread: 140607683024448
2025-09-15 20:26:20.346 wdl.w:ptcp.t:call-tar_outputs-56 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:26:20.346 wdl.w:ptcp.t:call-tar_outputs-56 INFO input :: name: "sawfish_vcf_tbi", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2153.sv.vcf.gz.tbi"
2025-09-15 20:26:20.346 wdl.w:ptcp.t:call-tar_outputs-56 INFO input :: name: "sawfish_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2153.sv.vcf.gz"
2025-09-15 20:26:20.346 wdl.w:ptcp.t:call-tar_outputs-56 INFO input :: name: "f8_json", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2153.f8inversion.json"
2025-09-15 20:26:20.346 wdl.w:ptcp.t:call-tar_outputs-56 INFO input :: name: "paraphase_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2153.paraphase.bam.bai"
2025-09-15 20:26:20.346 wdl.w:ptcp.t:call-tar_outputs-56 INFO input :: name: "paraphase_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2153.paraphase.bam"
2025-09-15 20:26:20.347 wdl.w:ptcp.t:call-tar_outputs-56 INFO input :: name: "paraphase_json", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2153.paraphase.json"
2025-09-15 20:26:20.347 wdl.w:ptcp.t:call-tar_outputs-56 INFO input :: name: "trgt_spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2153.trgt.sorted.spanning.bam.bai"
2025-09-15 20:26:20.347 wdl.w:ptcp.t:call-tar_outputs-56 INFO input :: name: "trgt_spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2153.trgt.sorted.spanning.bam"
2025-09-15 20:26:20.347 wdl.w:ptcp.t:call-tar_outputs-56 INFO input :: name: "trgt_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2153.trgt.vcf"
2025-09-15 20:26:20.347 wdl.w:ptcp.t:call-tar_outputs-56 INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2153.mapped.bam.bai"
2025-09-15 20:26:20.347 wdl.w:ptcp.t:call-tar_outputs-56 INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2153.mapped.bam"
2025-09-15 20:26:20.347 wdl.w:ptcp.t:call-tar_outputs-56 INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2153"
2025-09-15 20:26:20.347 wdl.w:ptcp.t:call-tar_outputs-56 INFO eval :: name: "threads", value: 1
2025-09-15 20:26:20.347 wdl.w:ptcp.t:call-tar_outputs-56 INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:26:20.347 wdl.w:ptcp.t:call-tar_outputs-56 INFO eval :: name: "disk_size", value: 6
2025-09-15 20:26:20.347 wdl.w:ptcp.t:call-tar_outputs-56 INFO eval :: name: "output_tarball", value: "m84036_250809_035451_s4.bc2153.tar"
2025-09-15 20:26:20.348 wdl.w:ptcp.t:call-tar_outputs-56 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:26:20.348 wdl.w:ptcp.t:call-tar_outputs-56 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:26:20.348 wdl.w:ptcp.t:call-tar_outputs-56 INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:26:20.348 wdl.w:ptcp.t:call-tar_outputs-56 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:26:20.439 wdl.w:ptcp.t:call-tar_outputs-56 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 17, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-56/_singularity_tmpdir_5g4y17n5"
2025-09-15 20:26:20.439 wdl.w:ptcp.t:call-tar_outputs-56 INFO Slurm invocation: srun --job-name call-tar_outputs-56 --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-56/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-56/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-56/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-56/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-56/out/m84036_250809_035451_s4.bc2153.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2153.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-56/out/m84036_250809_035451_s4.bc2153.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2153.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-56/out/m84036_250809_035451_s4.bc2153.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2153.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-56/out/m84036_250809_035451_s4.bc2153.f8inversion.json:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2153.f8inversion.json:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-56/out/m84036_250809_035451_s4.bc2153_paraphase/m84036_250809_035451_s4.bc2153.paraphase.json:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2153.paraphase.json:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-56/out/m84036_250809_035451_s4.bc2153_paraphase/m84036_250809_035451_s4.bc2153.paraphase.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2153.paraphase.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-56/out/m84036_250809_035451_s4.bc2153_paraphase/m84036_250809_035451_s4.bc2153.paraphase.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2153.paraphase.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-56/out/m84036_250809_035451_s4.bc2153_sawfish/m84036_250809_035451_s4.bc2153.sv.vcf.gz.tbi:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2153.sv.vcf.gz.tbi:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-56/out/m84036_250809_035451_s4.bc2153_sawfish/m84036_250809_035451_s4.bc2153.sv.vcf.gz:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2153.sv.vcf.gz:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-56/out/m84036_250809_035451_s4.bc2153.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2153.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-56/out/m84036_250809_035451_s4.bc2153.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2153.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-56/_singularity_tmpdir_5g4y17n5/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-56/_singularity_tmpdir_5g4y17n5/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:26:20.454 wdl.w:ptcp.t:call-tar_outputs-56 NOTICE slurm_singularity run :: pid: 1207566, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-56/slurm_singularity.log.txt"
2025-09-15 20:26:20.475 wdl.w:ptcp.w:call-trgt-88.t:call-trgt_plot_meth_waterfall INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2185.meth_waterfall.trgt_plots.zip"
2025-09-15 20:26:20.568 wdl.w:ptcp.w:call-trgt-88.t:call-trgt_plot_meth_waterfall NOTICE done
2025-09-15 20:26:20.573 wdl.w:ptcp.w:call-trgt-88 NOTICE finish :: job: "call-trgt_plot_meth_waterfall"
2025-09-15 20:26:20.573 wdl.w:ptcp.w:call-trgt-88 INFO output :: job: "call-trgt_plot_meth_waterfall", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-88/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2185.meth_waterfall.trgt_plots.zip"}
2025-09-15 20:26:20.573 wdl.w:ptcp.w:call-trgt-88 INFO visit :: node: "output-images_meth_waterfall", values: {"images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-88/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2185.meth_waterfall.trgt_plots.zip"}
2025-09-15 20:26:20.592 wdl.w:ptcp.t:call-tar_outputs-54.slurm_singularity INFO srun: job 51798194 queued and waiting for resources
2025-09-15 20:26:20.592 wdl.w:ptcp.t:call-tar_outputs-54.slurm_singularity INFO srun: job 51798194 has been allocated resources
2025-09-15 20:26:20.592 wdl.w:ptcp.t:call-tar_outputs-54.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:26:20.912 wdl.w:ptcp.w:call-trgt-90.t:call-trgt_plot_meth_allele INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2187.meth_allele.trgt_plots.zip"
2025-09-15 20:26:20.938 wdl.w:ptcp.w:call-sawfish-61.t:call-run_sawfish.stderr VERBOSE [M::mm_idx_gen::46.898*1.22] collected minimizers
2025-09-15 20:26:20.939 wdl.w:ptcp.w:call-sawfish-61.t:call-run_sawfish.stderr VERBOSE [M::mm_idx_gen::54.072*1.45] sorted minimizers
2025-09-15 20:26:20.939 wdl.w:ptcp.w:call-sawfish-61.t:call-run_sawfish.stderr VERBOSE [M::main::54.074*1.45] loaded/built the index for 195 target sequence(s)
2025-09-15 20:26:20.939 wdl.w:ptcp.w:call-sawfish-61.t:call-run_sawfish.stderr VERBOSE [M::mm_mapopt_update::59.347*1.41] mid_occ = 136
2025-09-15 20:26:20.939 wdl.w:ptcp.w:call-sawfish-61.t:call-run_sawfish.stderr VERBOSE [M::mm_idx_stat] kmer size: 19; skip: 19; is_hpc: 0; #seq: 195
2025-09-15 20:26:20.939 wdl.w:ptcp.w:call-sawfish-61.t:call-run_sawfish.stderr VERBOSE [M::mm_idx_stat::64.692*1.38] distinct minimizers: 214664461 (92.23% are singletons); average occurrences: 1.372; average spacing: 10.529; total length: 3099922541
2025-09-15 20:26:20.939 wdl.w:ptcp.w:call-sawfish-61.t:call-run_sawfish.stderr VERBOSE [M::main] Version: 2.26-r1175
2025-09-15 20:26:20.939 wdl.w:ptcp.w:call-sawfish-61.t:call-run_sawfish.stderr VERBOSE [M::main] CMD: /opt/pacbio/smrttools/install/smrtlink-release_25.1.0.257715/bundles/smrttools/install/smrttools-release_25.1.0.257715/private/thirdparty/minimap2/minimap2_2.26-pacbio2/binwrap/../../../../../private/thirdparty/minimap2/minimap2_2.26-pacbio2/bin/minimap2 -a -y -x map-hifi -Y -E 1,0 /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa -
2025-09-15 20:26:20.939 wdl.w:ptcp.w:call-sawfish-61.t:call-run_sawfish.stderr VERBOSE [M::main] Real time: 65.012 sec; CPU: 89.470 sec; Peak RSS: 11.886 GB
2025-09-15 20:26:20.939 wdl.w:ptcp.w:call-sawfish-61.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:51][sawfish][INFO] Starting sawfish 2.0.3
2025-09-15 20:26:20.939 wdl.w:ptcp.w:call-sawfish-61.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:51][sawfish][INFO] cmdline: sawfish discover --disable-cnv --threads 16 --ref /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa --bam m84036_250809_035451_s4.bc2158.minimap2.bam --output-dir m84036_250809_035451_s4.bc2158_sawfish_discover
2025-09-15 20:26:20.939 wdl.w:ptcp.w:call-sawfish-61.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:51][sawfish][INFO] Running on 16 threads
2025-09-15 20:26:20.939 wdl.w:ptcp.w:call-sawfish-61.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:51][sawfish][INFO] Writing discover settings to file: 'm84036_250809_035451_s4.bc2158_sawfish_discover/discover.settings.json'
2025-09-15 20:26:20.940 wdl.w:ptcp.w:call-sawfish-61.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:51][sawfish][INFO] Reading reference genome from file '/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa'
2025-09-15 20:26:20.940 wdl.w:ptcp.w:call-sawfish-61.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:55][sawfish][INFO] Processing alignment file '/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2158.minimap2.bam'
2025-09-15 20:26:20.940 wdl.w:ptcp.w:call-sawfish-61.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:55][sawfish][INFO] Finished processing all alignments
2025-09-15 20:26:20.940 wdl.w:ptcp.w:call-sawfish-61.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:55][sawfish][INFO] Writing depth bins to binary file: 'm84036_250809_035451_s4.bc2158_sawfish_discover/depth.mpack'
2025-09-15 20:26:20.940 wdl.w:ptcp.w:call-sawfish-61.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:55][sawfish][INFO] Writing max sv depth genome regions to bed file: 'm84036_250809_035451_s4.bc2158_sawfish_discover/max.depth.bed'
2025-09-15 20:26:20.940 wdl.w:ptcp.w:call-sawfish-61.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:55][sawfish][INFO] Completing breakpoint observation clustering
2025-09-15 20:26:20.940 wdl.w:ptcp.w:call-sawfish-61.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:55][sawfish][INFO] Finished breakpoint observation clustering
2025-09-15 20:26:20.940 wdl.w:ptcp.w:call-sawfish-61.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:55][sawfish][INFO] Consolidating adjacent indel candidates
2025-09-15 20:26:20.940 wdl.w:ptcp.w:call-sawfish-61.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:55][sawfish][INFO] Finding large insertion candidates
2025-09-15 20:26:20.940 wdl.w:ptcp.w:call-sawfish-61.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:55][sawfish][INFO] Writing breakpoint_cluster debug bed file: 'm84036_250809_035451_s4.bc2158_sawfish_discover/debug.breakpoint_clusters.bed'
2025-09-15 20:26:20.940 wdl.w:ptcp.w:call-sawfish-61.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:55][sawfish][INFO] Refining SV Candidates
2025-09-15 20:26:20.940 wdl.w:ptcp.w:call-sawfish-61.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:55][sawfish][INFO] Writing debug assembly region bed file: 'm84036_250809_035451_s4.bc2158_sawfish_discover/assembly.regions.bed'
2025-09-15 20:26:20.940 wdl.w:ptcp.w:call-sawfish-61.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:55][sawfish][INFO] Starting refinement of breakpoint evidence clusters
2025-09-15 20:26:20.940 wdl.w:ptcp.w:call-sawfish-61.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:55][sawfish][INFO] Finished refining all breakpoint evidence clusters
2025-09-15 20:26:20.940 wdl.w:ptcp.w:call-sawfish-61.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:55][sawfish][INFO] Writing all contig alignments to bam file: 'm84036_250809_035451_s4.bc2158_sawfish_discover/contig.alignment.bam'
2025-09-15 20:26:20.940 wdl.w:ptcp.w:call-sawfish-61.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:55][sawfish][INFO] Writing candidate structural variants to file: 'm84036_250809_035451_s4.bc2158_sawfish_discover/candidate.sv.bcf'
2025-09-15 20:26:20.940 wdl.w:ptcp.w:call-sawfish-61.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:55][sawfish][INFO] Writing run statistics to file: 'm84036_250809_035451_s4.bc2158_sawfish_discover/run.stats.json'
2025-09-15 20:26:20.940 wdl.w:ptcp.w:call-sawfish-61.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:55][sawfish][INFO] sawfish completed. Total Runtime: 00:00:04.025
2025-09-15 20:26:20.940 wdl.w:ptcp.w:call-sawfish-61.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:55][sawfish][INFO] Starting sawfish 2.0.3
2025-09-15 20:26:20.941 wdl.w:ptcp.w:call-sawfish-61.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:55][sawfish][INFO] cmdline: sawfish joint-call --threads 16 --sample m84036_250809_035451_s4.bc2158_sawfish_discover --output-dir m84036_250809_035451_s4.bc2158_sawfish
2025-09-15 20:26:20.941 wdl.w:ptcp.w:call-sawfish-61.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:55][sawfish][INFO] Running on 16 threads
2025-09-15 20:26:20.941 wdl.w:ptcp.w:call-sawfish-61.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:25:55][sawfish][INFO] Reading reference genome from file '/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa'
2025-09-15 20:26:20.946 wdl.w:ptcp.w:call-trgt-88.t:call-trgt_plot_motifs_waterfall INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2185.motifs_waterfall.trgt_plots.zip"
2025-09-15 20:26:20.993 wdl.w:ptcp.w:call-trgt-90.t:call-trgt_plot_meth_allele NOTICE done
2025-09-15 20:26:20.998 wdl.w:ptcp.w:call-trgt-90 NOTICE finish :: job: "call-trgt_plot_meth_allele"
2025-09-15 20:26:20.998 wdl.w:ptcp.w:call-trgt-90 INFO output :: job: "call-trgt_plot_meth_allele", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-90/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2187.meth_allele.trgt_plots.zip"}
2025-09-15 20:26:20.998 wdl.w:ptcp.w:call-trgt-90 INFO visit :: node: "output-images_meth_allele", values: {"images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-90/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2187.meth_allele.trgt_plots.zip"}
2025-09-15 20:26:20.998 wdl.w:ptcp.w:call-trgt-90 INFO visit :: node: "outputs", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-90/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2187.motifs_waterfall.trgt_plots.zip", "images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-90/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2187.meth_allele.trgt_plots.zip", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-90/call-trgt_genotype/out/m84036_250809_035451_s4.bc2187.trgt.sorted.spanning.bam.bai", "images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-90/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2187.motifs_allele.trgt_plots.zip", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-90/call-trgt_genotype/out/m84036_250809_035451_s4.bc2187.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-90/call-trgt_genotype/out/m84036_250809_035451_s4.bc2187.trgt.vcf", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-90/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2187.repeats.bam", "images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-90/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2187.meth_waterfall.trgt_plots.zip", "reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-90/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2187.repeats.bam.bai"}
2025-09-15 20:26:21.052 wdl.w:ptcp.w:call-trgt-88.t:call-trgt_plot_motifs_waterfall NOTICE done
2025-09-15 20:26:21.058 wdl.w:ptcp.w:call-trgt-88 NOTICE finish :: job: "call-trgt_plot_motifs_waterfall"
2025-09-15 20:26:21.058 wdl.w:ptcp.w:call-trgt-88 INFO output :: job: "call-trgt_plot_motifs_waterfall", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-88/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2185.motifs_waterfall.trgt_plots.zip"}
2025-09-15 20:26:21.058 wdl.w:ptcp.w:call-trgt-88 INFO visit :: node: "output-images_motifs_waterfall", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-88/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2185.motifs_waterfall.trgt_plots.zip"}
2025-09-15 20:26:21.081 wdl.w:ptcp.w:call-trgt-90 NOTICE done
2025-09-15 20:26:21.085 wdl.w:ptcp NOTICE finish :: job: "call-trgt-90"
2025-09-15 20:26:21.085 wdl.w:ptcp INFO output :: job: "call-trgt-90", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-90/out/m84036_250809_035451_s4.bc2187.motifs_waterfall.trgt_plots.zip", "images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-90/out/m84036_250809_035451_s4.bc2187.meth_allele.trgt_plots.zip", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-90/out/m84036_250809_035451_s4.bc2187.trgt.sorted.spanning.bam.bai", "images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-90/out/m84036_250809_035451_s4.bc2187.motifs_allele.trgt_plots.zip", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-90/out/m84036_250809_035451_s4.bc2187.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-90/out/m84036_250809_035451_s4.bc2187.trgt.vcf", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-90/out/m84036_250809_035451_s4.bc2187.repeats.bam", "images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-90/out/m84036_250809_035451_s4.bc2187.meth_waterfall.trgt_plots.zip", "reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-90/out/m84036_250809_035451_s4.bc2187.repeats.bam.bai"}
2025-09-15 20:26:21.133 wdl.w:ptcp.t:call-tar_outputs-72.stderr VERBOSE tar: Removing leading `/' from member names
2025-09-15 20:26:21.133 wdl.w:ptcp.t:call-tar_outputs-72.stderr VERBOSE tar: Removing leading `/' from hard link targets
2025-09-15 20:26:21.141 wdl.w:ptcp.t:call-tar_outputs-72.slurm_singularity INFO srun: job 51798195 queued and waiting for resources
2025-09-15 20:26:21.141 wdl.w:ptcp.t:call-tar_outputs-72.slurm_singularity INFO srun: job 51798195 has been allocated resources
2025-09-15 20:26:21.141 wdl.w:ptcp.t:call-tar_outputs-72.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:26:21.291 wdl.w:ptcp.t:call-tar_outputs-72 INFO output :: name: "sample_tarball", value: "m84036_250809_035451_s4.bc2169.tar"
2025-09-15 20:26:21.326 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_meth_waterfall.stderr VERBOSE 2025-09-15 20:26:19 [ERROR] - No reads found for TRID=SBMA_AR
2025-09-15 20:26:21.364 wdl.w:ptcp.t:call-tar_outputs-72 NOTICE done
2025-09-15 20:26:21.397 wdl.w:ptcp NOTICE finish :: job: "call-tar_outputs-72"
2025-09-15 20:26:21.397 wdl.w:ptcp INFO output :: job: "call-tar_outputs-72", values: {"sample_tarball": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-72/out/m84036_250809_035451_s4.bc2169.tar"}
2025-09-15 20:26:21.442 wdl.w:ptcp.t:call-tar_outputs-54 INFO output :: name: "sample_tarball", value: "m84036_250809_035451_s4.bc2151.tar"
2025-09-15 20:26:21.468 wdl.w:ptcp.t:call-tar_outputs-56.slurm_singularity INFO srun: job 51798196 queued and waiting for resources
2025-09-15 20:26:21.469 wdl.w:ptcp.t:call-tar_outputs-56.slurm_singularity INFO srun: job 51798196 has been allocated resources
2025-09-15 20:26:21.469 wdl.w:ptcp.t:call-tar_outputs-56.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:26:21.472 wdl.w:ptcp.w:call-trgt-86.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:26:18 [ERROR] - No reads found for TRID=SCA12_PPP2R2B
2025-09-15 20:26:21.472 wdl.w:ptcp.w:call-trgt-86.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:26:18 [ERROR] - No reads found for TRID=SCA1_ATXN1
2025-09-15 20:26:21.472 wdl.w:ptcp.w:call-trgt-86.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:26:18 [ERROR] - No reads found for TRID=CANVAS_RFC1
2025-09-15 20:26:21.472 wdl.w:ptcp.w:call-trgt-86.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:26:18 [ERROR] - No reads found for TRID=FAME1_SAMD12
2025-09-15 20:26:21.472 wdl.w:ptcp.w:call-trgt-86.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:26:19 [ERROR] - No reads found for TRID=FTDALS1_C9orf72
2025-09-15 20:26:21.472 wdl.w:ptcp.w:call-trgt-86.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:26:19 [ERROR] - No reads found for TRID=OPDM1_LRP12
2025-09-15 20:26:21.472 wdl.w:ptcp.w:call-trgt-86.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:26:19 [ERROR] - No reads found for TRID=SCA7_ATXN7
2025-09-15 20:26:21.472 wdl.w:ptcp.w:call-trgt-86.t:call-trgt_plot_meth_allele.stderr VERBOSE 2025-09-15 20:26:19 [ERROR] - No reads found for TRID=SBMA_AR
2025-09-15 20:26:21.503 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_meth_waterfall INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2180.meth_waterfall.trgt_plots.zip"
2025-09-15 20:26:21.516 wdl.w:ptcp.w:call-trgt-86.t:call-trgt_plot_meth_allele INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2183.meth_allele.trgt_plots.zip"
2025-09-15 20:26:21.519 wdl.w:ptcp.t:call-tar_outputs-54 NOTICE done
2025-09-15 20:26:21.524 wdl.w:ptcp NOTICE finish :: job: "call-tar_outputs-54"
2025-09-15 20:26:21.525 wdl.w:ptcp INFO output :: job: "call-tar_outputs-54", values: {"sample_tarball": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-54/out/m84036_250809_035451_s4.bc2151.tar"}
2025-09-15 20:26:21.574 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_meth_waterfall NOTICE done
2025-09-15 20:26:21.580 wdl.w:ptcp.w:call-trgt-83 NOTICE finish :: job: "call-trgt_plot_meth_waterfall"
2025-09-15 20:26:21.581 wdl.w:ptcp.w:call-trgt-83 INFO output :: job: "call-trgt_plot_meth_waterfall", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-83/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2180.meth_waterfall.trgt_plots.zip"}
2025-09-15 20:26:21.581 wdl.w:ptcp.w:call-trgt-83 INFO visit :: node: "output-images_meth_waterfall", values: {"images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-83/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2180.meth_waterfall.trgt_plots.zip"}
2025-09-15 20:26:21.592 wdl.w:ptcp.w:call-trgt-86.t:call-trgt_plot_meth_allele NOTICE done
2025-09-15 20:26:21.601 wdl.w:ptcp.w:call-trgt-86 NOTICE finish :: job: "call-trgt_plot_meth_allele"
2025-09-15 20:26:21.601 wdl.w:ptcp.w:call-trgt-86 INFO output :: job: "call-trgt_plot_meth_allele", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-86/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2183.meth_allele.trgt_plots.zip"}
2025-09-15 20:26:21.601 wdl.w:ptcp.w:call-trgt-86 INFO visit :: node: "output-images_meth_allele", values: {"images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-86/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2183.meth_allele.trgt_plots.zip"}
2025-09-15 20:26:21.602 wdl.w:ptcp.w:call-trgt-86 INFO visit :: node: "outputs", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-86/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2183.motifs_waterfall.trgt_plots.zip", "images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-86/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2183.meth_allele.trgt_plots.zip", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-86/call-trgt_genotype/out/m84036_250809_035451_s4.bc2183.trgt.sorted.spanning.bam.bai", "images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-86/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2183.motifs_allele.trgt_plots.zip", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-86/call-trgt_genotype/out/m84036_250809_035451_s4.bc2183.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-86/call-trgt_genotype/out/m84036_250809_035451_s4.bc2183.trgt.vcf", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-86/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2183.repeats.bam", "images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-86/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2183.meth_waterfall.trgt_plots.zip", "reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-86/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2183.repeats.bam.bai"}
2025-09-15 20:26:21.618 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_meth_allele INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2180.meth_allele.trgt_plots.zip"
2025-09-15 20:26:21.667 wdl.w:ptcp.w:call-paraphase-74.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for f8inv1 for sample m84036_250809_035451_s4.bc2171 at 2025-09-15 20:26:18.169557...
2025-09-15 20:26:21.687 wdl.w:ptcp.w:call-trgt-86 NOTICE done
2025-09-15 20:26:21.688 wdl.w:ptcp.w:call-trgt-83.t:call-trgt_plot_meth_allele NOTICE done
2025-09-15 20:26:21.692 wdl.w:ptcp NOTICE finish :: job: "call-trgt-86"
2025-09-15 20:26:21.692 wdl.w:ptcp INFO output :: job: "call-trgt-86", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-86/out/m84036_250809_035451_s4.bc2183.motifs_waterfall.trgt_plots.zip", "images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-86/out/m84036_250809_035451_s4.bc2183.meth_allele.trgt_plots.zip", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-86/out/m84036_250809_035451_s4.bc2183.trgt.sorted.spanning.bam.bai", "images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-86/out/m84036_250809_035451_s4.bc2183.motifs_allele.trgt_plots.zip", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-86/out/m84036_250809_035451_s4.bc2183.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-86/out/m84036_250809_035451_s4.bc2183.trgt.vcf", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-86/out/m84036_250809_035451_s4.bc2183.repeats.bam", "images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-86/out/m84036_250809_035451_s4.bc2183.meth_waterfall.trgt_plots.zip", "reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-86/out/m84036_250809_035451_s4.bc2183.repeats.bam.bai"}
2025-09-15 20:26:21.693 wdl.w:ptcp.w:call-trgt-83 NOTICE finish :: job: "call-trgt_plot_meth_allele"
2025-09-15 20:26:21.693 wdl.w:ptcp.w:call-trgt-83 INFO output :: job: "call-trgt_plot_meth_allele", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-83/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2180.meth_allele.trgt_plots.zip"}
2025-09-15 20:26:21.693 wdl.w:ptcp.w:call-trgt-83 INFO visit :: node: "output-images_meth_allele", values: {"images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-83/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2180.meth_allele.trgt_plots.zip"}
2025-09-15 20:26:21.693 wdl.w:ptcp.w:call-trgt-83 INFO visit :: node: "outputs", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-83/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2180.motifs_waterfall.trgt_plots.zip", "images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-83/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2180.meth_allele.trgt_plots.zip", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-83/call-trgt_genotype/out/m84036_250809_035451_s4.bc2180.trgt.sorted.spanning.bam.bai", "images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-83/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2180.motifs_allele.trgt_plots.zip", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-83/call-trgt_genotype/out/m84036_250809_035451_s4.bc2180.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-83/call-trgt_genotype/out/m84036_250809_035451_s4.bc2180.trgt.vcf", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-83/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2180.repeats.bam", "images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-83/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2180.meth_waterfall.trgt_plots.zip", "reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-83/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2180.repeats.bam.bai"}
2025-09-15 20:26:21.728 wdl.w:ptcp.w:call-sawfish-85.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:17][sawfish][INFO] Starting sawfish 2.0.3
2025-09-15 20:26:21.728 wdl.w:ptcp.w:call-sawfish-85.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:17][sawfish][INFO] cmdline: sawfish joint-call --threads 16 --sample m84036_250809_035451_s4.bc2182_sawfish_discover --output-dir m84036_250809_035451_s4.bc2182_sawfish
2025-09-15 20:26:21.728 wdl.w:ptcp.w:call-sawfish-85.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:17][sawfish][INFO] Running on 16 threads
2025-09-15 20:26:21.728 wdl.w:ptcp.w:call-sawfish-85.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:17][sawfish][INFO] Reading reference genome from file '/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa'
2025-09-15 20:26:21.782 wdl.w:ptcp.w:call-trgt-83 NOTICE done
2025-09-15 20:26:21.787 wdl.w:ptcp NOTICE finish :: job: "call-trgt-83"
2025-09-15 20:26:21.787 wdl.w:ptcp INFO output :: job: "call-trgt-83", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-83/out/m84036_250809_035451_s4.bc2180.motifs_waterfall.trgt_plots.zip", "images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-83/out/m84036_250809_035451_s4.bc2180.meth_allele.trgt_plots.zip", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-83/out/m84036_250809_035451_s4.bc2180.trgt.sorted.spanning.bam.bai", "images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-83/out/m84036_250809_035451_s4.bc2180.motifs_allele.trgt_plots.zip", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-83/out/m84036_250809_035451_s4.bc2180.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-83/out/m84036_250809_035451_s4.bc2180.trgt.vcf", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-83/out/m84036_250809_035451_s4.bc2180.repeats.bam", "images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-83/out/m84036_250809_035451_s4.bc2180.meth_waterfall.trgt_plots.zip", "reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-83/out/m84036_250809_035451_s4.bc2180.repeats.bam.bai"}
2025-09-15 20:26:21.788 wdl.w:ptcp.t:call-tar_outputs-56 INFO output :: name: "sample_tarball", value: "m84036_250809_035451_s4.bc2153.tar"
2025-09-15 20:26:21.848 wdl.w:ptcp.t:call-tar_outputs-56 NOTICE done
2025-09-15 20:26:21.852 wdl.w:ptcp NOTICE finish :: job: "call-tar_outputs-56"
2025-09-15 20:26:21.852 wdl.w:ptcp INFO output :: job: "call-tar_outputs-56", values: {"sample_tarball": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-56/out/m84036_250809_035451_s4.bc2153.tar"}
2025-09-15 20:26:23.328 wdl.w:ptcp.w:call-trgt-88.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:26:21 [ERROR] - No reads found for TRID=PRTS_ARX
2025-09-15 20:26:23.330 wdl.w:ptcp.w:call-trgt-88.t:call-trgt_plot_motifs_allele.stderr VERBOSE 2025-09-15 20:26:21 [ERROR] - No reads found for TRID=EIEE1_ARX
2025-09-15 20:26:23.371 wdl.w:ptcp.w:call-paraphase-62.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for hbb for sample m84036_250809_035451_s4.bc2159 at 2025-09-15 20:26:14.534344...
2025-09-15 20:26:23.371 wdl.w:ptcp.w:call-paraphase-62.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for hbb for sample m84036_250809_035451_s4.bc2159 at 2025-09-15 20:26:15.032570...
2025-09-15 20:26:23.371 wdl.w:ptcp.w:call-paraphase-62.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for f8inv1 for sample m84036_250809_035451_s4.bc2159 at 2025-09-15 20:26:21.139630...
2025-09-15 20:26:23.371 wdl.w:ptcp.w:call-paraphase-62.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for f8inv1 for sample m84036_250809_035451_s4.bc2159 at 2025-09-15 20:26:21.139781...
2025-09-15 20:26:23.799 wdl.w:ptcp.w:call-paraphase-03.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for hbb for sample m84036_250809_035451_s4.bc2100 at 2025-09-15 20:25:38.296907...
2025-09-15 20:26:23.799 wdl.w:ptcp.w:call-paraphase-03.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for hbb for sample m84036_250809_035451_s4.bc2100 at 2025-09-15 20:25:41.796173...
2025-09-15 20:26:23.799 wdl.w:ptcp.w:call-paraphase-03.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for hbb for sample m84036_250809_035451_s4.bc2100 at 2025-09-15 20:25:42.142002...
2025-09-15 20:26:23.841 wdl.w:ptcp.w:call-paraphase-43.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for rpgr for sample m84036_250809_035451_s4.bc2140 at 2025-09-15 20:25:59.657306...
2025-09-15 20:26:23.842 wdl.w:ptcp.w:call-paraphase-43.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for rpgr for sample m84036_250809_035451_s4.bc2140 at 2025-09-15 20:26:00.564327...
2025-09-15 20:26:23.842 wdl.w:ptcp.w:call-paraphase-43.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for rpgr for sample m84036_250809_035451_s4.bc2140 at 2025-09-15 20:26:00.818281...
2025-09-15 20:26:24.798 wdl.w:ptcp.w:call-paraphase-90.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for smn1 for sample m84036_250809_035451_s4.bc2187 at 2025-09-15 20:26:01.980405...
2025-09-15 20:26:24.800 wdl.w:ptcp.w:call-paraphase-90.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for hba for sample m84036_250809_035451_s4.bc2187 at 2025-09-15 20:26:02.060685...
2025-09-15 20:26:24.800 wdl.w:ptcp.w:call-paraphase-90.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for gba for sample m84036_250809_035451_s4.bc2187 at 2025-09-15 20:26:02.992960...
2025-09-15 20:26:24.800 wdl.w:ptcp.w:call-paraphase-90.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for cyp21 for sample m84036_250809_035451_s4.bc2187 at 2025-09-15 20:26:04.142641...
2025-09-15 20:26:24.800 wdl.w:ptcp.w:call-paraphase-90.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for smn1 for sample m84036_250809_035451_s4.bc2187 at 2025-09-15 20:26:21.508232...
2025-09-15 20:26:24.800 wdl.w:ptcp.w:call-paraphase-90.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning to gene2 region for smn1 for sample m84036_250809_035451_s4.bc2187 at 2025-09-15 20:26:21.995500...
2025-09-15 20:26:24.897 wdl.w:ptcp.w:call-trgt-88.t:call-trgt_plot_motifs_allele INFO output :: name: "images", value: "m84036_250809_035451_s4.bc2185.motifs_allele.trgt_plots.zip"
2025-09-15 20:26:24.931 wdl.w:ptcp.w:call-paraphase-91.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for smn1 for sample m84036_250809_035451_s4.bc2188 at 2025-09-15 20:25:39.711915...
2025-09-15 20:26:24.932 wdl.w:ptcp.w:call-paraphase-91.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for hba for sample m84036_250809_035451_s4.bc2188 at 2025-09-15 20:25:40.086263...
2025-09-15 20:26:24.932 wdl.w:ptcp.w:call-paraphase-91.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for gba for sample m84036_250809_035451_s4.bc2188 at 2025-09-15 20:25:41.339391...
2025-09-15 20:26:24.932 wdl.w:ptcp.w:call-paraphase-91.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for cyp21 for sample m84036_250809_035451_s4.bc2188 at 2025-09-15 20:25:43.858897...
2025-09-15 20:26:24.932 wdl.w:ptcp.w:call-paraphase-91.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for smn1 for sample m84036_250809_035451_s4.bc2188 at 2025-09-15 20:26:04.396170...
2025-09-15 20:26:24.932 wdl.w:ptcp.w:call-paraphase-91.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning to gene2 region for smn1 for sample m84036_250809_035451_s4.bc2188 at 2025-09-15 20:26:04.840988...
2025-09-15 20:26:24.932 wdl.w:ptcp.w:call-paraphase-91.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for smn1 for sample m84036_250809_035451_s4.bc2188 at 2025-09-15 20:26:07.497506...
2025-09-15 20:26:24.946 wdl.w:ptcp.w:call-paraphase-27.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for rpgr for sample m84036_250809_035451_s4.bc2124 at 2025-09-15 20:25:53.903411...
2025-09-15 20:26:24.947 wdl.w:ptcp.w:call-paraphase-27.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for rpgr for sample m84036_250809_035451_s4.bc2124 at 2025-09-15 20:25:53.904410...
2025-09-15 20:26:25.002 wdl.w:ptcp.w:call-trgt-88.t:call-trgt_plot_motifs_allele NOTICE done
2025-09-15 20:26:25.009 wdl.w:ptcp.w:call-trgt-88 NOTICE finish :: job: "call-trgt_plot_motifs_allele"
2025-09-15 20:26:25.010 wdl.w:ptcp.w:call-trgt-88 INFO output :: job: "call-trgt_plot_motifs_allele", values: {"images": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-88/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2185.motifs_allele.trgt_plots.zip"}
2025-09-15 20:26:25.010 wdl.w:ptcp.w:call-trgt-88 INFO visit :: node: "output-images_motifs_allele", values: {"images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-88/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2185.motifs_allele.trgt_plots.zip"}
2025-09-15 20:26:25.010 wdl.w:ptcp.w:call-trgt-88 INFO visit :: node: "outputs", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-88/call-trgt_plot_motifs_waterfall/out/m84036_250809_035451_s4.bc2185.motifs_waterfall.trgt_plots.zip", "images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-88/call-trgt_plot_meth_allele/out/m84036_250809_035451_s4.bc2185.meth_allele.trgt_plots.zip", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-88/call-trgt_genotype/out/m84036_250809_035451_s4.bc2185.trgt.sorted.spanning.bam.bai", "images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-88/call-trgt_plot_motifs_allele/out/m84036_250809_035451_s4.bc2185.motifs_allele.trgt_plots.zip", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-88/call-trgt_genotype/out/m84036_250809_035451_s4.bc2185.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-88/call-trgt_genotype/out/m84036_250809_035451_s4.bc2185.trgt.vcf", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-88/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2185.repeats.bam", "images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-88/call-trgt_plot_meth_waterfall/out/m84036_250809_035451_s4.bc2185.meth_waterfall.trgt_plots.zip", "reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-88/call-get_reads_overlapping_repeats/out/m84036_250809_035451_s4.bc2185.repeats.bam.bai"}
2025-09-15 20:26:25.080 wdl.w:ptcp.w:call-trgt-88 NOTICE done
2025-09-15 20:26:25.089 wdl.w:ptcp NOTICE finish :: job: "call-trgt-88"
2025-09-15 20:26:25.089 wdl.w:ptcp INFO output :: job: "call-trgt-88", values: {"images_motifs_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-88/out/m84036_250809_035451_s4.bc2185.motifs_waterfall.trgt_plots.zip", "images_meth_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-88/out/m84036_250809_035451_s4.bc2185.meth_allele.trgt_plots.zip", "spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-88/out/m84036_250809_035451_s4.bc2185.trgt.sorted.spanning.bam.bai", "images_motifs_allele": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-88/out/m84036_250809_035451_s4.bc2185.motifs_allele.trgt_plots.zip", "spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-88/out/m84036_250809_035451_s4.bc2185.trgt.sorted.spanning.bam", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-88/out/m84036_250809_035451_s4.bc2185.trgt.vcf", "reads_overlapping_repeats": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-88/out/m84036_250809_035451_s4.bc2185.repeats.bam", "images_meth_waterfall": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-88/out/m84036_250809_035451_s4.bc2185.meth_waterfall.trgt_plots.zip", "reads_overlapping_repeats_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-88/out/m84036_250809_035451_s4.bc2185.repeats.bam.bai"}
2025-09-15 20:26:25.092 wdl.w:ptcp INFO visit :: node: "gather-call-trgt", values: "(((large)))"
2025-09-15 20:26:25.093 wdl.w:ptcp INFO visit :: node: "output-images_meth_allele", values: "(((large)))"
2025-09-15 20:26:25.094 wdl.w:ptcp INFO visit :: node: "output-images_meth_waterfall", values: "(((large)))"
2025-09-15 20:26:25.094 wdl.w:ptcp INFO visit :: node: "output-images_motifs_allele", values: "(((large)))"
2025-09-15 20:26:25.095 wdl.w:ptcp INFO visit :: node: "output-images_motifs_waterfall", values: "(((large)))"
2025-09-15 20:26:25.095 wdl.w:ptcp INFO visit :: node: "output-reads_overlapping_repeats", values: "(((large)))"
2025-09-15 20:26:25.096 wdl.w:ptcp INFO visit :: node: "output-reads_overlapping_repeats_bai", values: "(((large)))"
2025-09-15 20:26:25.096 wdl.w:ptcp INFO visit :: node: "output-trgt_spanning_bam", values: "(((large)))"
2025-09-15 20:26:25.097 wdl.w:ptcp INFO visit :: node: "output-trgt_spanning_bam_bai", values: "(((large)))"
2025-09-15 20:26:25.097 wdl.w:ptcp INFO visit :: node: "output-trgt_vcf", values: "(((large)))"
2025-09-15 20:26:25.789 wdl.w:ptcp.w:call-paraphase-50.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for f8inv22 for sample m84036_250809_035451_s4.bc2147 at 2025-09-15 20:26:22.401646...
2025-09-15 20:26:25.790 wdl.w:ptcp.w:call-paraphase-50.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for f8inv22 for sample m84036_250809_035451_s4.bc2147 at 2025-09-15 20:26:22.402587...
2025-09-15 20:26:26.289 wdl.w:ptcp.w:call-sawfish-71.t:call-run_sawfish INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2168_sawfish/m84036_250809_035451_s4.bc2168.sv.vcf.gz"
2025-09-15 20:26:26.292 wdl.w:ptcp.w:call-sawfish-71.t:call-run_sawfish INFO output :: name: "vcf_tbi", value: "m84036_250809_035451_s4.bc2168_sawfish/m84036_250809_035451_s4.bc2168.sv.vcf.gz.tbi"
2025-09-15 20:26:26.294 wdl.w:ptcp.w:call-sawfish-71.t:call-run_sawfish INFO output :: name: "minimap2_bam", value: "m84036_250809_035451_s4.bc2168.minimap2.bam"
2025-09-15 20:26:26.295 wdl.w:ptcp.w:call-sawfish-71.t:call-run_sawfish INFO output :: name: "minimap2_bam_bai", value: "m84036_250809_035451_s4.bc2168.minimap2.bam.bai"
2025-09-15 20:26:26.411 wdl.w:ptcp.w:call-sawfish-71.t:call-run_sawfish NOTICE done
2025-09-15 20:26:26.421 wdl.w:ptcp.w:call-sawfish-71 NOTICE finish :: job: "call-run_sawfish"
2025-09-15 20:26:26.421 wdl.w:ptcp.w:call-sawfish-71 INFO output :: job: "call-run_sawfish", values: {"minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-71/call-run_sawfish/out/m84036_250809_035451_s4.bc2168.minimap2.bam.bai", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-71/call-run_sawfish/out/m84036_250809_035451_s4.bc2168.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-71/call-run_sawfish/out/m84036_250809_035451_s4.bc2168_sawfish/m84036_250809_035451_s4.bc2168.sv.vcf.gz.tbi", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-71/call-run_sawfish/out/m84036_250809_035451_s4.bc2168_sawfish/m84036_250809_035451_s4.bc2168.sv.vcf.gz"}
2025-09-15 20:26:26.421 wdl.w:ptcp.w:call-sawfish-71 INFO visit :: node: "output-minimap2_bam", values: {"minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-71/call-run_sawfish/out/m84036_250809_035451_s4.bc2168.minimap2.bam"}
2025-09-15 20:26:26.421 wdl.w:ptcp.w:call-sawfish-71 INFO visit :: node: "output-minimap2_bam_bai", values: {"minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-71/call-run_sawfish/out/m84036_250809_035451_s4.bc2168.minimap2.bam.bai"}
2025-09-15 20:26:26.421 wdl.w:ptcp.w:call-sawfish-71 INFO visit :: node: "output-vcf", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-71/call-run_sawfish/out/m84036_250809_035451_s4.bc2168_sawfish/m84036_250809_035451_s4.bc2168.sv.vcf.gz"}
2025-09-15 20:26:26.422 wdl.w:ptcp.w:call-sawfish-71 INFO visit :: node: "output-vcf_tbi", values: {"vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-71/call-run_sawfish/out/m84036_250809_035451_s4.bc2168_sawfish/m84036_250809_035451_s4.bc2168.sv.vcf.gz.tbi"}
2025-09-15 20:26:26.422 wdl.w:ptcp.w:call-sawfish-71 INFO visit :: node: "outputs", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-71/call-run_sawfish/out/m84036_250809_035451_s4.bc2168_sawfish/m84036_250809_035451_s4.bc2168.sv.vcf.gz", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-71/call-run_sawfish/out/m84036_250809_035451_s4.bc2168.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-71/call-run_sawfish/out/m84036_250809_035451_s4.bc2168_sawfish/m84036_250809_035451_s4.bc2168.sv.vcf.gz.tbi", "minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-71/call-run_sawfish/out/m84036_250809_035451_s4.bc2168.minimap2.bam.bai"}
2025-09-15 20:26:26.462 wdl.w:ptcp.w:call-sawfish-71 NOTICE done
2025-09-15 20:26:26.468 wdl.w:ptcp NOTICE finish :: job: "call-sawfish-71"
2025-09-15 20:26:26.468 wdl.w:ptcp INFO output :: job: "call-sawfish-71", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-71/out/m84036_250809_035451_s4.bc2168_sawfish/m84036_250809_035451_s4.bc2168.sv.vcf.gz", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-71/out/m84036_250809_035451_s4.bc2168.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-71/out/m84036_250809_035451_s4.bc2168_sawfish/m84036_250809_035451_s4.bc2168.sv.vcf.gz.tbi", "minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-71/out/m84036_250809_035451_s4.bc2168.minimap2.bam.bai"}
2025-09-15 20:26:27.239 wdl.w:ptcp.w:call-paraphase-67.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for hba for sample m84036_250809_035451_s4.bc2164 at 2025-09-15 20:25:54.550366...
2025-09-15 20:26:27.240 wdl.w:ptcp.w:call-paraphase-67.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for hba for sample m84036_250809_035451_s4.bc2164 at 2025-09-15 20:25:55.090787...
2025-09-15 20:26:27.240 wdl.w:ptcp.w:call-paraphase-67.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for cyp21 for sample m84036_250809_035451_s4.bc2164 at 2025-09-15 20:25:59.793813...
2025-09-15 20:26:27.240 wdl.w:ptcp.w:call-paraphase-67.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for cyp21 for sample m84036_250809_035451_s4.bc2164 at 2025-09-15 20:26:01.196611...
2025-09-15 20:26:27.240 wdl.w:ptcp.w:call-paraphase-67.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for gba for sample m84036_250809_035451_s4.bc2164 at 2025-09-15 20:26:19.824045...
2025-09-15 20:26:27.240 wdl.w:ptcp.w:call-paraphase-67.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for gba for sample m84036_250809_035451_s4.bc2164 at 2025-09-15 20:26:20.703659...
2025-09-15 20:26:27.740 wdl.w:ptcp.w:call-paraphase-11.t:call-run_paraphase INFO output :: name: "paraphase_bam", value: "m84036_250809_035451_s4.bc2108_paraphase/m84036_250809_035451_s4.bc2108.paraphase.bam"
2025-09-15 20:26:27.743 wdl.w:ptcp.w:call-paraphase-11.t:call-run_paraphase INFO output :: name: "paraphase_bam_bai", value: "m84036_250809_035451_s4.bc2108_paraphase/m84036_250809_035451_s4.bc2108.paraphase.bam.bai"
2025-09-15 20:26:27.744 wdl.w:ptcp.w:call-paraphase-11.t:call-run_paraphase INFO output :: name: "paraphase_json", value: "m84036_250809_035451_s4.bc2108_paraphase/m84036_250809_035451_s4.bc2108.paraphase.json"
2025-09-15 20:26:27.749 wdl.w:ptcp.w:call-paraphase-11.t:call-run_paraphase INFO output :: name: "paraphase_vcfs", value: ["/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2108_paraphase/m84036_250809_035451_s4.bc2108_paraphase_vcfs/m84036_250809_035451_s4.bc2108_cyp21.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2108_paraphase/m84036_250809_035451_s4.bc2108_paraphase_vcfs/m84036_250809_035451_s4.bc2108_f8inv1.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2108_paraphase/m84036_250809_035451_s4.bc2108_paraphase_vcfs/m84036_250809_035451_s4.bc2108_f8inv22.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2108_paraphase/m84036_250809_035451_s4.bc2108_paraphase_vcfs/m84036_250809_035451_s4.bc2108_gba.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2108_paraphase/m84036_250809_035451_s4.bc2108_paraphase_vcfs/m84036_250809_035451_s4.bc2108_hba.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2108_paraphase/m84036_250809_035451_s4.bc2108_paraphase_vcfs/m84036_250809_035451_s4.bc2108_hbb.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2108_paraphase/m84036_250809_035451_s4.bc2108_paraphase_vcfs/m84036_250809_035451_s4.bc2108_rpgr.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2108_paraphase/m84036_250809_035451_s4.bc2108_paraphase_vcfs/m84036_250809_035451_s4.bc2108_smn1.vcf"]
2025-09-15 20:26:27.751 wdl.w:ptcp.w:call-paraphase-11.t:call-run_paraphase INFO output :: name: "havanno_json", value: "m84036_250809_035451_s4.bc2108.havanno.json"
2025-09-15 20:26:27.887 wdl.w:ptcp.w:call-paraphase-94.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for smn1 for sample m84036_250809_035451_s4.bc2191 at 2025-09-15 20:26:18.422764...
2025-09-15 20:26:27.920 wdl.w:ptcp.w:call-paraphase-11.t:call-run_paraphase NOTICE done
2025-09-15 20:26:27.931 wdl.w:ptcp.w:call-paraphase-11 NOTICE finish :: job: "call-run_paraphase"
2025-09-15 20:26:27.931 wdl.w:ptcp.w:call-paraphase-11 INFO output :: job: "call-run_paraphase", values: {"havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-11/call-run_paraphase/out/m84036_250809_035451_s4.bc2108.havanno.json", "paraphase_vcfs": ["/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-11/call-run_paraphase/out/m84036_250809_035451_s4.bc2108_paraphase/m84036_250809_035451_s4.bc2108_paraphase_vcfs/m84036_250809_035451_s4.bc2108_cyp21.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-11/call-run_paraphase/out/m84036_250809_035451_s4.bc2108_paraphase/m84036_250809_035451_s4.bc2108_paraphase_vcfs/m84036_250809_035451_s4.bc2108_f8inv1.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-11/call-run_paraphase/out/m84036_250809_035451_s4.bc2108_paraphase/m84036_250809_035451_s4.bc2108_paraphase_vcfs/m84036_250809_035451_s4.bc2108_f8inv22.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-11/call-run_paraphase/out/m84036_250809_035451_s4.bc2108_paraphase/m84036_250809_035451_s4.bc2108_paraphase_vcfs/m84036_250809_035451_s4.bc2108_gba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-11/call-run_paraphase/out/m84036_250809_035451_s4.bc2108_paraphase/m84036_250809_035451_s4.bc2108_paraphase_vcfs/m84036_250809_035451_s4.bc2108_hba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-11/call-run_paraphase/out/m84036_250809_035451_s4.bc2108_paraphase/m84036_250809_035451_s4.bc2108_paraphase_vcfs/m84036_250809_035451_s4.bc2108_hbb.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-11/call-run_paraphase/out/m84036_250809_035451_s4.bc2108_paraphase/m84036_250809_035451_s4.bc2108_paraphase_vcfs/m84036_250809_035451_s4.bc2108_rpgr.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-11/call-run_paraphase/out/m84036_250809_035451_s4.bc2108_paraphase/m84036_250809_035451_s4.bc2108_paraphase_vcfs/m84036_250809_035451_s4.bc2108_smn1.vcf"], "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-11/call-run_paraphase/out/m84036_250809_035451_s4.bc2108_paraphase/m84036_250809_035451_s4.bc2108.paraphase.json", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-11/call-run_paraphase/out/m84036_250809_035451_s4.bc2108_paraphase/m84036_250809_035451_s4.bc2108.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-11/call-run_paraphase/out/m84036_250809_035451_s4.bc2108_paraphase/m84036_250809_035451_s4.bc2108.paraphase.bam"}
2025-09-15 20:26:27.931 wdl.w:ptcp.w:call-paraphase-11 NOTICE ready :: job: "call-call_f8", callee: "call_f8"
2025-09-15 20:26:27.931 wdl.w:ptcp.w:call-paraphase-11 INFO input :: job: "call-call_f8", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "out_prefix": "m84036_250809_035451_s4.bc2108", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-11/call-run_paraphase/out/m84036_250809_035451_s4.bc2108_paraphase/m84036_250809_035451_s4.bc2108.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-11/call-run_paraphase/out/m84036_250809_035451_s4.bc2108_paraphase/m84036_250809_035451_s4.bc2108.paraphase.bam", "sex": "F"}
2025-09-15 20:26:27.932 wdl.w:ptcp.w:call-paraphase-11 INFO visit :: node: "output-havanno_json", values: {"havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-11/call-run_paraphase/out/m84036_250809_035451_s4.bc2108.havanno.json"}
2025-09-15 20:26:27.932 wdl.w:ptcp.w:call-paraphase-11 INFO visit :: node: "output-paraphase_bam", values: {"paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-11/call-run_paraphase/out/m84036_250809_035451_s4.bc2108_paraphase/m84036_250809_035451_s4.bc2108.paraphase.bam"}
2025-09-15 20:26:27.933 wdl.w:ptcp.w:call-paraphase-11 INFO visit :: node: "output-paraphase_bam_bai", values: {"paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-11/call-run_paraphase/out/m84036_250809_035451_s4.bc2108_paraphase/m84036_250809_035451_s4.bc2108.paraphase.bam.bai"}
2025-09-15 20:26:27.933 wdl.w:ptcp.w:call-paraphase-11 INFO visit :: node: "output-paraphase_json", values: {"paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-11/call-run_paraphase/out/m84036_250809_035451_s4.bc2108_paraphase/m84036_250809_035451_s4.bc2108.paraphase.json"}
2025-09-15 20:26:27.933 wdl.w:ptcp.w:call-paraphase-11 INFO visit :: node: "output-paraphase_vcfs", values: {"paraphase_vcfs": ["/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-11/call-run_paraphase/out/m84036_250809_035451_s4.bc2108_paraphase/m84036_250809_035451_s4.bc2108_paraphase_vcfs/m84036_250809_035451_s4.bc2108_cyp21.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-11/call-run_paraphase/out/m84036_250809_035451_s4.bc2108_paraphase/m84036_250809_035451_s4.bc2108_paraphase_vcfs/m84036_250809_035451_s4.bc2108_f8inv1.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-11/call-run_paraphase/out/m84036_250809_035451_s4.bc2108_paraphase/m84036_250809_035451_s4.bc2108_paraphase_vcfs/m84036_250809_035451_s4.bc2108_f8inv22.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-11/call-run_paraphase/out/m84036_250809_035451_s4.bc2108_paraphase/m84036_250809_035451_s4.bc2108_paraphase_vcfs/m84036_250809_035451_s4.bc2108_gba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-11/call-run_paraphase/out/m84036_250809_035451_s4.bc2108_paraphase/m84036_250809_035451_s4.bc2108_paraphase_vcfs/m84036_250809_035451_s4.bc2108_hba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-11/call-run_paraphase/out/m84036_250809_035451_s4.bc2108_paraphase/m84036_250809_035451_s4.bc2108_paraphase_vcfs/m84036_250809_035451_s4.bc2108_hbb.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-11/call-run_paraphase/out/m84036_250809_035451_s4.bc2108_paraphase/m84036_250809_035451_s4.bc2108_paraphase_vcfs/m84036_250809_035451_s4.bc2108_rpgr.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-11/call-run_paraphase/out/m84036_250809_035451_s4.bc2108_paraphase/m84036_250809_035451_s4.bc2108_paraphase_vcfs/m84036_250809_035451_s4.bc2108_smn1.vcf"]}
2025-09-15 20:26:27.937 wdl.w:ptcp.w:call-paraphase-11.t:call-call_f8 NOTICE task setup :: name: "call_f8", source: "./paraphase.wdl", line: 232, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-11/call-call_f8", thread: 140611432728128
2025-09-15 20:26:27.953 wdl.w:ptcp.w:call-paraphase-11.t:call-call_f8 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:26:27.953 wdl.w:ptcp.w:call-paraphase-11.t:call-call_f8 INFO input :: name: "genome_version", value: "38"
2025-09-15 20:26:27.954 wdl.w:ptcp.w:call-paraphase-11.t:call-call_f8 INFO input :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2108"
2025-09-15 20:26:27.954 wdl.w:ptcp.w:call-paraphase-11.t:call-call_f8 INFO input :: name: "paraphase_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2108.paraphase.bam.bai"
2025-09-15 20:26:27.954 wdl.w:ptcp.w:call-paraphase-11.t:call-call_f8 INFO input :: name: "paraphase_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2108.paraphase.bam"
2025-09-15 20:26:27.954 wdl.w:ptcp.w:call-paraphase-11.t:call-call_f8 INFO input :: name: "sex", value: "F"
2025-09-15 20:26:27.954 wdl.w:ptcp.w:call-paraphase-11.t:call-call_f8 INFO eval :: name: "threads", value: 1
2025-09-15 20:26:27.954 wdl.w:ptcp.w:call-paraphase-11.t:call-call_f8 INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:26:27.954 wdl.w:ptcp.w:call-paraphase-11.t:call-call_f8 INFO eval :: name: "disk_size", value: 11
2025-09-15 20:26:27.954 wdl.w:ptcp.w:call-paraphase-11.t:call-call_f8 INFO eval :: name: "sample_sex", value: "F"
2025-09-15 20:26:27.955 wdl.w:ptcp.w:call-paraphase-11.t:call-call_f8 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:26:27.955 wdl.w:ptcp.w:call-paraphase-11.t:call-call_f8 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:26:27.955 wdl.w:ptcp.w:call-paraphase-11.t:call-call_f8 INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:26:27.955 wdl.w:ptcp.w:call-paraphase-11.t:call-call_f8 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:26:27.983 wdl.w:ptcp.w:call-paraphase-27.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for rpgr for sample m84036_250809_035451_s4.bc2124 at 2025-09-15 20:25:55.900919...
2025-09-15 20:26:27.983 wdl.w:ptcp.w:call-paraphase-27.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for rpgr for sample m84036_250809_035451_s4.bc2124 at 2025-09-15 20:25:56.888923...
2025-09-15 20:26:27.983 wdl.w:ptcp.w:call-paraphase-27.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for rpgr for sample m84036_250809_035451_s4.bc2124 at 2025-09-15 20:25:57.029772...
2025-09-15 20:26:28.005 wdl.w:ptcp.w:call-paraphase-11.t:call-call_f8 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 8, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-11/call-call_f8/_singularity_tmpdir_iru1_rku"
2025-09-15 20:26:28.005 wdl.w:ptcp.w:call-paraphase-11.t:call-call_f8 INFO Slurm invocation: srun --job-name call-call_f8 --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-11/call-call_f8/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-11/call-call_f8/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-11/call-call_f8/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-11/call-call_f8/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-11/call-run_paraphase/out/m84036_250809_035451_s4.bc2108_paraphase/m84036_250809_035451_s4.bc2108.paraphase.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2108.paraphase.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-11/call-run_paraphase/out/m84036_250809_035451_s4.bc2108_paraphase/m84036_250809_035451_s4.bc2108.paraphase.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2108.paraphase.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-11/call-call_f8/_singularity_tmpdir_iru1_rku/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-11/call-call_f8/_singularity_tmpdir_iru1_rku/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:26:28.051 wdl.w:ptcp.w:call-paraphase-11.t:call-call_f8 NOTICE slurm_singularity run :: pid: 1207584, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-11/call-call_f8/slurm_singularity.log.txt"
2025-09-15 20:26:28.158 wdl.w:ptcp.w:call-paraphase-86.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for hba for sample m84036_250809_035451_s4.bc2183 at 2025-09-15 20:26:04.749428...
2025-09-15 20:26:28.159 wdl.w:ptcp.w:call-paraphase-86.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for smn1 for sample m84036_250809_035451_s4.bc2183 at 2025-09-15 20:26:04.865180...
2025-09-15 20:26:28.159 wdl.w:ptcp.w:call-paraphase-86.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for gba for sample m84036_250809_035451_s4.bc2183 at 2025-09-15 20:26:05.426662...
2025-09-15 20:26:28.159 wdl.w:ptcp.w:call-paraphase-86.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for cyp21 for sample m84036_250809_035451_s4.bc2183 at 2025-09-15 20:26:06.485632...
2025-09-15 20:26:28.159 wdl.w:ptcp.w:call-paraphase-86.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for smn1 for sample m84036_250809_035451_s4.bc2183 at 2025-09-15 20:26:17.824030...
2025-09-15 20:26:28.159 wdl.w:ptcp.w:call-paraphase-86.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning to gene2 region for smn1 for sample m84036_250809_035451_s4.bc2183 at 2025-09-15 20:26:18.279570...
2025-09-15 20:26:28.442 wdl.w:ptcp.w:call-paraphase-66.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for smn1 for sample m84036_250809_035451_s4.bc2163 at 2025-09-15 20:25:44.452821...
2025-09-15 20:26:28.444 wdl.w:ptcp.w:call-paraphase-66.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for hba for sample m84036_250809_035451_s4.bc2163 at 2025-09-15 20:26:21.150114...
2025-09-15 20:26:28.444 wdl.w:ptcp.w:call-paraphase-66.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for hba for sample m84036_250809_035451_s4.bc2163 at 2025-09-15 20:26:21.824676...
2025-09-15 20:26:28.764 wdl.w:ptcp.w:call-sawfish-66.t:call-run_sawfish INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2163_sawfish/m84036_250809_035451_s4.bc2163.sv.vcf.gz"
2025-09-15 20:26:28.768 wdl.w:ptcp.w:call-sawfish-66.t:call-run_sawfish INFO output :: name: "vcf_tbi", value: "m84036_250809_035451_s4.bc2163_sawfish/m84036_250809_035451_s4.bc2163.sv.vcf.gz.tbi"
2025-09-15 20:26:28.769 wdl.w:ptcp.w:call-sawfish-66.t:call-run_sawfish INFO output :: name: "minimap2_bam", value: "m84036_250809_035451_s4.bc2163.minimap2.bam"
2025-09-15 20:26:28.771 wdl.w:ptcp.w:call-sawfish-66.t:call-run_sawfish INFO output :: name: "minimap2_bam_bai", value: "m84036_250809_035451_s4.bc2163.minimap2.bam.bai"
2025-09-15 20:26:28.826 wdl.w:ptcp.w:call-paraphase-50.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for f8inv22 for sample m84036_250809_035451_s4.bc2147 at 2025-09-15 20:26:23.157043...
2025-09-15 20:26:28.826 wdl.w:ptcp.w:call-paraphase-50.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for f8inv22 for sample m84036_250809_035451_s4.bc2147 at 2025-09-15 20:26:26.463321...
2025-09-15 20:26:28.826 wdl.w:ptcp.w:call-paraphase-50.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for f8inv22 for sample m84036_250809_035451_s4.bc2147 at 2025-09-15 20:26:26.746303...
2025-09-15 20:26:28.899 wdl.w:ptcp.w:call-sawfish-66.t:call-run_sawfish NOTICE done
2025-09-15 20:26:28.905 wdl.w:ptcp.w:call-sawfish-66 NOTICE finish :: job: "call-run_sawfish"
2025-09-15 20:26:28.905 wdl.w:ptcp.w:call-sawfish-66 INFO output :: job: "call-run_sawfish", values: {"minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-66/call-run_sawfish/out/m84036_250809_035451_s4.bc2163.minimap2.bam.bai", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-66/call-run_sawfish/out/m84036_250809_035451_s4.bc2163.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-66/call-run_sawfish/out/m84036_250809_035451_s4.bc2163_sawfish/m84036_250809_035451_s4.bc2163.sv.vcf.gz.tbi", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-66/call-run_sawfish/out/m84036_250809_035451_s4.bc2163_sawfish/m84036_250809_035451_s4.bc2163.sv.vcf.gz"}
2025-09-15 20:26:28.905 wdl.w:ptcp.w:call-sawfish-66 INFO visit :: node: "output-minimap2_bam", values: {"minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-66/call-run_sawfish/out/m84036_250809_035451_s4.bc2163.minimap2.bam"}
2025-09-15 20:26:28.905 wdl.w:ptcp.w:call-sawfish-66 INFO visit :: node: "output-minimap2_bam_bai", values: {"minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-66/call-run_sawfish/out/m84036_250809_035451_s4.bc2163.minimap2.bam.bai"}
2025-09-15 20:26:28.905 wdl.w:ptcp.w:call-sawfish-66 INFO visit :: node: "output-vcf", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-66/call-run_sawfish/out/m84036_250809_035451_s4.bc2163_sawfish/m84036_250809_035451_s4.bc2163.sv.vcf.gz"}
2025-09-15 20:26:28.906 wdl.w:ptcp.w:call-sawfish-66 INFO visit :: node: "output-vcf_tbi", values: {"vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-66/call-run_sawfish/out/m84036_250809_035451_s4.bc2163_sawfish/m84036_250809_035451_s4.bc2163.sv.vcf.gz.tbi"}
2025-09-15 20:26:28.906 wdl.w:ptcp.w:call-sawfish-66 INFO visit :: node: "outputs", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-66/call-run_sawfish/out/m84036_250809_035451_s4.bc2163_sawfish/m84036_250809_035451_s4.bc2163.sv.vcf.gz", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-66/call-run_sawfish/out/m84036_250809_035451_s4.bc2163.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-66/call-run_sawfish/out/m84036_250809_035451_s4.bc2163_sawfish/m84036_250809_035451_s4.bc2163.sv.vcf.gz.tbi", "minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-66/call-run_sawfish/out/m84036_250809_035451_s4.bc2163.minimap2.bam.bai"}
2025-09-15 20:26:28.946 wdl.w:ptcp.w:call-sawfish-66 NOTICE done
2025-09-15 20:26:28.953 wdl.w:ptcp NOTICE finish :: job: "call-sawfish-66"
2025-09-15 20:26:28.953 wdl.w:ptcp INFO output :: job: "call-sawfish-66", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-66/out/m84036_250809_035451_s4.bc2163_sawfish/m84036_250809_035451_s4.bc2163.sv.vcf.gz", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-66/out/m84036_250809_035451_s4.bc2163.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-66/out/m84036_250809_035451_s4.bc2163_sawfish/m84036_250809_035451_s4.bc2163.sv.vcf.gz.tbi", "minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-66/out/m84036_250809_035451_s4.bc2163.minimap2.bam.bai"}
2025-09-15 20:26:29.059 wdl.w:ptcp.w:call-paraphase-11.t:call-call_f8.slurm_singularity INFO srun: job 51798197 queued and waiting for resources
2025-09-15 20:26:29.059 wdl.w:ptcp.w:call-paraphase-11.t:call-call_f8.slurm_singularity INFO srun: job 51798197 has been allocated resources
2025-09-15 20:26:29.059 wdl.w:ptcp.w:call-paraphase-11.t:call-call_f8.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:26:29.417 wdl.w:ptcp.w:call-paraphase-11.t:call-call_f8 INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2108.f8inversion.vcf"
2025-09-15 20:26:29.421 wdl.w:ptcp.w:call-paraphase-11.t:call-call_f8 INFO output :: name: "json", value: "m84036_250809_035451_s4.bc2108.f8inversion.json"
2025-09-15 20:26:29.482 wdl.w:ptcp.w:call-paraphase-11.t:call-call_f8 NOTICE done
2025-09-15 20:26:29.487 wdl.w:ptcp.w:call-paraphase-11 NOTICE finish :: job: "call-call_f8"
2025-09-15 20:26:29.487 wdl.w:ptcp.w:call-paraphase-11 INFO output :: job: "call-call_f8", values: {"json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-11/call-call_f8/out/m84036_250809_035451_s4.bc2108.f8inversion.json", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-11/call-call_f8/out/m84036_250809_035451_s4.bc2108.f8inversion.vcf"}
2025-09-15 20:26:29.487 wdl.w:ptcp.w:call-paraphase-11 INFO visit :: node: "output-f8_json", values: {"f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-11/call-call_f8/out/m84036_250809_035451_s4.bc2108.f8inversion.json"}
2025-09-15 20:26:29.488 wdl.w:ptcp.w:call-paraphase-11 INFO visit :: node: "output-f8_vcf", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-11/call-call_f8/out/m84036_250809_035451_s4.bc2108.f8inversion.vcf"}
2025-09-15 20:26:29.488 wdl.w:ptcp.w:call-paraphase-11 INFO visit :: node: "outputs", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-11/call-call_f8/out/m84036_250809_035451_s4.bc2108.f8inversion.vcf", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-11/call-run_paraphase/out/m84036_250809_035451_s4.bc2108_paraphase/m84036_250809_035451_s4.bc2108.paraphase.json", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-11/call-run_paraphase/out/m84036_250809_035451_s4.bc2108_paraphase/m84036_250809_035451_s4.bc2108.paraphase.bam", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-11/call-run_paraphase/out/m84036_250809_035451_s4.bc2108_paraphase/m84036_250809_035451_s4.bc2108.paraphase.bam.bai", "paraphase_vcfs": ["/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-11/call-run_paraphase/out/m84036_250809_035451_s4.bc2108_paraphase/m84036_250809_035451_s4.bc2108_paraphase_vcfs/m84036_250809_035451_s4.bc2108_cyp21.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-11/call-run_paraphase/out/m84036_250809_035451_s4.bc2108_paraphase/m84036_250809_035451_s4.bc2108_paraphase_vcfs/m84036_250809_035451_s4.bc2108_f8inv1.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-11/call-run_paraphase/out/m84036_250809_035451_s4.bc2108_paraphase/m84036_250809_035451_s4.bc2108_paraphase_vcfs/m84036_250809_035451_s4.bc2108_f8inv22.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-11/call-run_paraphase/out/m84036_250809_035451_s4.bc2108_paraphase/m84036_250809_035451_s4.bc2108_paraphase_vcfs/m84036_250809_035451_s4.bc2108_gba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-11/call-run_paraphase/out/m84036_250809_035451_s4.bc2108_paraphase/m84036_250809_035451_s4.bc2108_paraphase_vcfs/m84036_250809_035451_s4.bc2108_hba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-11/call-run_paraphase/out/m84036_250809_035451_s4.bc2108_paraphase/m84036_250809_035451_s4.bc2108_paraphase_vcfs/m84036_250809_035451_s4.bc2108_hbb.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-11/call-run_paraphase/out/m84036_250809_035451_s4.bc2108_paraphase/m84036_250809_035451_s4.bc2108_paraphase_vcfs/m84036_250809_035451_s4.bc2108_rpgr.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-11/call-run_paraphase/out/m84036_250809_035451_s4.bc2108_paraphase/m84036_250809_035451_s4.bc2108_paraphase_vcfs/m84036_250809_035451_s4.bc2108_smn1.vcf"], "havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-11/call-run_paraphase/out/m84036_250809_035451_s4.bc2108.havanno.json", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-11/call-call_f8/out/m84036_250809_035451_s4.bc2108.f8inversion.json"}
2025-09-15 20:26:29.529 wdl.w:ptcp.w:call-paraphase-19.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for rpgr for sample m84036_250809_035451_s4.bc2116 at 2025-09-15 20:25:53.813228...
2025-09-15 20:26:29.529 wdl.w:ptcp.w:call-paraphase-19.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for rpgr for sample m84036_250809_035451_s4.bc2116 at 2025-09-15 20:25:53.814110...
2025-09-15 20:26:29.529 wdl.w:ptcp.w:call-paraphase-19.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for rpgr for sample m84036_250809_035451_s4.bc2116 at 2025-09-15 20:25:56.968303...
2025-09-15 20:26:29.530 wdl.w:ptcp.w:call-paraphase-19.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for rpgr for sample m84036_250809_035451_s4.bc2116 at 2025-09-15 20:25:58.122499...
2025-09-15 20:26:29.530 wdl.w:ptcp.w:call-paraphase-19.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for rpgr for sample m84036_250809_035451_s4.bc2116 at 2025-09-15 20:25:58.286681...
2025-09-15 20:26:29.595 wdl.w:ptcp.w:call-paraphase-11 NOTICE done
2025-09-15 20:26:29.617 wdl.w:ptcp NOTICE finish :: job: "call-paraphase-11"
2025-09-15 20:26:29.617 wdl.w:ptcp INFO output :: job: "call-paraphase-11", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-11/out/m84036_250809_035451_s4.bc2108.f8inversion.vcf", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-11/out/m84036_250809_035451_s4.bc2108_paraphase/m84036_250809_035451_s4.bc2108.paraphase.json", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-11/out/m84036_250809_035451_s4.bc2108_paraphase/m84036_250809_035451_s4.bc2108.paraphase.bam", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-11/out/m84036_250809_035451_s4.bc2108_paraphase/m84036_250809_035451_s4.bc2108.paraphase.bam.bai", "paraphase_vcfs": ["/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-11/out/m84036_250809_035451_s4.bc2108_paraphase/m84036_250809_035451_s4.bc2108_paraphase_vcfs/m84036_250809_035451_s4.bc2108_cyp21.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-11/out/m84036_250809_035451_s4.bc2108_paraphase/m84036_250809_035451_s4.bc2108_paraphase_vcfs/m84036_250809_035451_s4.bc2108_f8inv1.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-11/out/m84036_250809_035451_s4.bc2108_paraphase/m84036_250809_035451_s4.bc2108_paraphase_vcfs/m84036_250809_035451_s4.bc2108_f8inv22.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-11/out/m84036_250809_035451_s4.bc2108_paraphase/m84036_250809_035451_s4.bc2108_paraphase_vcfs/m84036_250809_035451_s4.bc2108_gba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-11/out/m84036_250809_035451_s4.bc2108_paraphase/m84036_250809_035451_s4.bc2108_paraphase_vcfs/m84036_250809_035451_s4.bc2108_hba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-11/out/m84036_250809_035451_s4.bc2108_paraphase/m84036_250809_035451_s4.bc2108_paraphase_vcfs/m84036_250809_035451_s4.bc2108_hbb.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-11/out/m84036_250809_035451_s4.bc2108_paraphase/m84036_250809_035451_s4.bc2108_paraphase_vcfs/m84036_250809_035451_s4.bc2108_rpgr.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-11/out/m84036_250809_035451_s4.bc2108_paraphase/m84036_250809_035451_s4.bc2108_paraphase_vcfs/m84036_250809_035451_s4.bc2108_smn1.vcf"], "havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-11/out/m84036_250809_035451_s4.bc2108.havanno.json", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-11/out/m84036_250809_035451_s4.bc2108.f8inversion.json"}
2025-09-15 20:26:29.618 wdl.w:ptcp NOTICE ready :: job: "call-tar_outputs-11", callee: "tar_outputs"
2025-09-15 20:26:29.618 wdl.w:ptcp INFO input :: job: "call-tar_outputs-11", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "sawfish_vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-11/out/m84036_250809_035451_s4.bc2108_sawfish/m84036_250809_035451_s4.bc2108.sv.vcf.gz.tbi", "sawfish_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-11/out/m84036_250809_035451_s4.bc2108_sawfish/m84036_250809_035451_s4.bc2108.sv.vcf.gz", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-11/out/m84036_250809_035451_s4.bc2108.f8inversion.json", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-11/out/m84036_250809_035451_s4.bc2108_paraphase/m84036_250809_035451_s4.bc2108.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-11/out/m84036_250809_035451_s4.bc2108_paraphase/m84036_250809_035451_s4.bc2108.paraphase.bam", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-11/out/m84036_250809_035451_s4.bc2108_paraphase/m84036_250809_035451_s4.bc2108.paraphase.json", "trgt_spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-11/out/m84036_250809_035451_s4.bc2108.trgt.sorted.spanning.bam.bai", "trgt_spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-11/out/m84036_250809_035451_s4.bc2108.trgt.sorted.spanning.bam", "trgt_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-11/out/m84036_250809_035451_s4.bc2108.trgt.vcf", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-11/out/m84036_250809_035451_s4.bc2108.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-11/out/m84036_250809_035451_s4.bc2108.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2108"}
2025-09-15 20:26:29.624 wdl.w:ptcp.t:call-tar_outputs-11 NOTICE task setup :: name: "tar_outputs", source: "./common.wdl", line: 279, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-11", thread: 140610879071808
2025-09-15 20:26:29.648 wdl.w:ptcp.t:call-tar_outputs-11 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:26:29.648 wdl.w:ptcp.t:call-tar_outputs-11 INFO input :: name: "sawfish_vcf_tbi", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2108.sv.vcf.gz.tbi"
2025-09-15 20:26:29.648 wdl.w:ptcp.t:call-tar_outputs-11 INFO input :: name: "sawfish_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2108.sv.vcf.gz"
2025-09-15 20:26:29.648 wdl.w:ptcp.t:call-tar_outputs-11 INFO input :: name: "f8_json", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2108.f8inversion.json"
2025-09-15 20:26:29.648 wdl.w:ptcp.t:call-tar_outputs-11 INFO input :: name: "paraphase_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2108.paraphase.bam.bai"
2025-09-15 20:26:29.648 wdl.w:ptcp.t:call-tar_outputs-11 INFO input :: name: "paraphase_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2108.paraphase.bam"
2025-09-15 20:26:29.648 wdl.w:ptcp.t:call-tar_outputs-11 INFO input :: name: "paraphase_json", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2108.paraphase.json"
2025-09-15 20:26:29.648 wdl.w:ptcp.t:call-tar_outputs-11 INFO input :: name: "trgt_spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2108.trgt.sorted.spanning.bam.bai"
2025-09-15 20:26:29.648 wdl.w:ptcp.t:call-tar_outputs-11 INFO input :: name: "trgt_spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2108.trgt.sorted.spanning.bam"
2025-09-15 20:26:29.648 wdl.w:ptcp.t:call-tar_outputs-11 INFO input :: name: "trgt_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2108.trgt.vcf"
2025-09-15 20:26:29.649 wdl.w:ptcp.t:call-tar_outputs-11 INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2108.mapped.bam.bai"
2025-09-15 20:26:29.649 wdl.w:ptcp.t:call-tar_outputs-11 INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2108.mapped.bam"
2025-09-15 20:26:29.649 wdl.w:ptcp.t:call-tar_outputs-11 INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2108"
2025-09-15 20:26:29.649 wdl.w:ptcp.t:call-tar_outputs-11 INFO eval :: name: "threads", value: 1
2025-09-15 20:26:29.649 wdl.w:ptcp.t:call-tar_outputs-11 INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:26:29.649 wdl.w:ptcp.t:call-tar_outputs-11 INFO eval :: name: "disk_size", value: 6
2025-09-15 20:26:29.649 wdl.w:ptcp.t:call-tar_outputs-11 INFO eval :: name: "output_tarball", value: "m84036_250809_035451_s4.bc2108.tar"
2025-09-15 20:26:29.650 wdl.w:ptcp.t:call-tar_outputs-11 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:26:29.650 wdl.w:ptcp.t:call-tar_outputs-11 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:26:29.650 wdl.w:ptcp.t:call-tar_outputs-11 INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:26:29.650 wdl.w:ptcp.t:call-tar_outputs-11 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:26:29.727 wdl.w:ptcp.t:call-tar_outputs-11 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 17, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-11/_singularity_tmpdir_msi3yt6q"
2025-09-15 20:26:29.728 wdl.w:ptcp.t:call-tar_outputs-11 INFO Slurm invocation: srun --job-name call-tar_outputs-11 --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-11/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-11/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-11/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-11/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-11/out/m84036_250809_035451_s4.bc2108.f8inversion.json:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2108.f8inversion.json:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-11/out/m84036_250809_035451_s4.bc2108_sawfish/m84036_250809_035451_s4.bc2108.sv.vcf.gz:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2108.sv.vcf.gz:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-11/out/m84036_250809_035451_s4.bc2108_sawfish/m84036_250809_035451_s4.bc2108.sv.vcf.gz.tbi:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2108.sv.vcf.gz.tbi:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-11/out/m84036_250809_035451_s4.bc2108.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2108.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-11/out/m84036_250809_035451_s4.bc2108.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2108.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-11/out/m84036_250809_035451_s4.bc2108.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2108.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-11/out/m84036_250809_035451_s4.bc2108.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2108.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-11/out/m84036_250809_035451_s4.bc2108.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2108.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-11/out/m84036_250809_035451_s4.bc2108_paraphase/m84036_250809_035451_s4.bc2108.paraphase.json:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2108.paraphase.json:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-11/out/m84036_250809_035451_s4.bc2108_paraphase/m84036_250809_035451_s4.bc2108.paraphase.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2108.paraphase.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-11/out/m84036_250809_035451_s4.bc2108_paraphase/m84036_250809_035451_s4.bc2108.paraphase.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2108.paraphase.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-11/_singularity_tmpdir_msi3yt6q/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-11/_singularity_tmpdir_msi3yt6q/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:26:29.736 wdl.w:ptcp.t:call-tar_outputs-11 NOTICE slurm_singularity run :: pid: 1207650, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-11/slurm_singularity.log.txt"
2025-09-15 20:26:29.825 wdl.w:ptcp.w:call-paraphase-95.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for smn1 for sample m84036_250809_035451_s4.bc2192 at 2025-09-15 20:26:08.811592...
2025-09-15 20:26:30.046 wdl.w:ptcp.w:call-sawfish-61.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:28][sawfish][INFO] Reading sawfish-discover results from 1 samples
2025-09-15 20:26:30.046 wdl.w:ptcp.w:call-sawfish-61.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:29][sawfish][INFO] Writing depth track to bigwig file: 'm84036_250809_035451_s4.bc2158_sawfish/samples/sample0001_UnknownSampleName/depth.bw'
2025-09-15 20:26:30.046 wdl.w:ptcp.w:call-sawfish-61.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:29][sawfish][INFO] Merging SV haplotypes
2025-09-15 20:26:30.046 wdl.w:ptcp.w:call-sawfish-61.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:29][sawfish][INFO] Finished merging SV haplotypes across samples
2025-09-15 20:26:30.046 wdl.w:ptcp.w:call-sawfish-61.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:29][sawfish][INFO] Writing merged contig alignments to bam file: 'm84036_250809_035451_s4.bc2158_sawfish/contig.alignment.bam'
2025-09-15 20:26:30.046 wdl.w:ptcp.w:call-sawfish-61.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:29][sawfish][INFO] Starting SV candidate cluster genotyping
2025-09-15 20:26:30.046 wdl.w:ptcp.w:call-sawfish-61.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:29][sawfish][INFO] Finished genotyping all SV candidate clusters
2025-09-15 20:26:30.046 wdl.w:ptcp.w:call-sawfish-61.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:29][sawfish][INFO] Starting joint CNV/SV refinement
2025-09-15 20:26:30.047 wdl.w:ptcp.w:call-sawfish-61.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:29][sawfish][INFO] Merged 0 CNVs into corresponding breakpoint-based SVs
2025-09-15 20:26:30.047 wdl.w:ptcp.w:call-sawfish-61.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:29][sawfish][INFO] Writing genotyped structural variants to file: 'm84036_250809_035451_s4.bc2158_sawfish/genotyped.sv.vcf.gz'
2025-09-15 20:26:30.047 wdl.w:ptcp.w:call-sawfish-61.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:29][sawfish][INFO] Writing run statistics to file: 'm84036_250809_035451_s4.bc2158_sawfish/run.stats.json'
2025-09-15 20:26:30.047 wdl.w:ptcp.w:call-sawfish-61.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:29][sawfish][INFO] sawfish completed. Total Runtime: 00:00:34.007
2025-09-15 20:26:30.209 wdl.w:ptcp.w:call-sawfish-93.t:call-run_sawfish.stderr VERBOSE [M::mm_idx_gen::33.796*1.46] collected minimizers
2025-09-15 20:26:30.210 wdl.w:ptcp.w:call-sawfish-93.t:call-run_sawfish.stderr VERBOSE [M::mm_idx_gen::40.661*1.71] sorted minimizers
2025-09-15 20:26:30.210 wdl.w:ptcp.w:call-sawfish-93.t:call-run_sawfish.stderr VERBOSE [M::main::40.662*1.71] loaded/built the index for 195 target sequence(s)
2025-09-15 20:26:30.210 wdl.w:ptcp.w:call-sawfish-93.t:call-run_sawfish.stderr VERBOSE [M::mm_mapopt_update::43.707*1.66] mid_occ = 136
2025-09-15 20:26:30.210 wdl.w:ptcp.w:call-sawfish-93.t:call-run_sawfish.stderr VERBOSE [M::mm_idx_stat] kmer size: 19; skip: 19; is_hpc: 0; #seq: 195
2025-09-15 20:26:30.453 wdl.w:ptcp.w:call-sawfish-61.t:call-run_sawfish INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2158_sawfish/m84036_250809_035451_s4.bc2158.sv.vcf.gz"
2025-09-15 20:26:30.456 wdl.w:ptcp.w:call-sawfish-61.t:call-run_sawfish INFO output :: name: "vcf_tbi", value: "m84036_250809_035451_s4.bc2158_sawfish/m84036_250809_035451_s4.bc2158.sv.vcf.gz.tbi"
2025-09-15 20:26:30.458 wdl.w:ptcp.w:call-sawfish-61.t:call-run_sawfish INFO output :: name: "minimap2_bam", value: "m84036_250809_035451_s4.bc2158.minimap2.bam"
2025-09-15 20:26:30.459 wdl.w:ptcp.w:call-sawfish-61.t:call-run_sawfish INFO output :: name: "minimap2_bam_bai", value: "m84036_250809_035451_s4.bc2158.minimap2.bam.bai"
2025-09-15 20:26:30.583 wdl.w:ptcp.w:call-sawfish-61.t:call-run_sawfish NOTICE done
2025-09-15 20:26:30.583 wdl.w:ptcp.w:call-paraphase-82.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for smn1 for sample m84036_250809_035451_s4.bc2179 at 2025-09-15 20:26:18.041816...
2025-09-15 20:26:30.584 wdl.w:ptcp.w:call-paraphase-82.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning to gene2 region for smn1 for sample m84036_250809_035451_s4.bc2179 at 2025-09-15 20:26:18.824553...
2025-09-15 20:26:30.608 wdl.w:ptcp.w:call-sawfish-61 NOTICE finish :: job: "call-run_sawfish"
2025-09-15 20:26:30.608 wdl.w:ptcp.w:call-sawfish-61 INFO output :: job: "call-run_sawfish", values: {"minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-61/call-run_sawfish/out/m84036_250809_035451_s4.bc2158.minimap2.bam.bai", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-61/call-run_sawfish/out/m84036_250809_035451_s4.bc2158.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-61/call-run_sawfish/out/m84036_250809_035451_s4.bc2158_sawfish/m84036_250809_035451_s4.bc2158.sv.vcf.gz.tbi", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-61/call-run_sawfish/out/m84036_250809_035451_s4.bc2158_sawfish/m84036_250809_035451_s4.bc2158.sv.vcf.gz"}
2025-09-15 20:26:30.608 wdl.w:ptcp.w:call-sawfish-61 INFO visit :: node: "output-minimap2_bam", values: {"minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-61/call-run_sawfish/out/m84036_250809_035451_s4.bc2158.minimap2.bam"}
2025-09-15 20:26:30.609 wdl.w:ptcp.w:call-sawfish-61 INFO visit :: node: "output-minimap2_bam_bai", values: {"minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-61/call-run_sawfish/out/m84036_250809_035451_s4.bc2158.minimap2.bam.bai"}
2025-09-15 20:26:30.609 wdl.w:ptcp.w:call-sawfish-61 INFO visit :: node: "output-vcf", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-61/call-run_sawfish/out/m84036_250809_035451_s4.bc2158_sawfish/m84036_250809_035451_s4.bc2158.sv.vcf.gz"}
2025-09-15 20:26:30.609 wdl.w:ptcp.w:call-sawfish-61 INFO visit :: node: "output-vcf_tbi", values: {"vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-61/call-run_sawfish/out/m84036_250809_035451_s4.bc2158_sawfish/m84036_250809_035451_s4.bc2158.sv.vcf.gz.tbi"}
2025-09-15 20:26:30.609 wdl.w:ptcp.w:call-sawfish-61 INFO visit :: node: "outputs", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-61/call-run_sawfish/out/m84036_250809_035451_s4.bc2158_sawfish/m84036_250809_035451_s4.bc2158.sv.vcf.gz", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-61/call-run_sawfish/out/m84036_250809_035451_s4.bc2158.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-61/call-run_sawfish/out/m84036_250809_035451_s4.bc2158_sawfish/m84036_250809_035451_s4.bc2158.sv.vcf.gz.tbi", "minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-61/call-run_sawfish/out/m84036_250809_035451_s4.bc2158.minimap2.bam.bai"}
2025-09-15 20:26:30.650 wdl.w:ptcp.w:call-sawfish-61 NOTICE done
2025-09-15 20:26:30.656 wdl.w:ptcp NOTICE finish :: job: "call-sawfish-61"
2025-09-15 20:26:30.656 wdl.w:ptcp INFO output :: job: "call-sawfish-61", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-61/out/m84036_250809_035451_s4.bc2158_sawfish/m84036_250809_035451_s4.bc2158.sv.vcf.gz", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-61/out/m84036_250809_035451_s4.bc2158.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-61/out/m84036_250809_035451_s4.bc2158_sawfish/m84036_250809_035451_s4.bc2158.sv.vcf.gz.tbi", "minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-61/out/m84036_250809_035451_s4.bc2158.minimap2.bam.bai"}
2025-09-15 20:26:30.657 wdl.w:ptcp NOTICE ready :: job: "call-tar_outputs-61", callee: "tar_outputs"
2025-09-15 20:26:30.657 wdl.w:ptcp INFO input :: job: "call-tar_outputs-61", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "sawfish_vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-61/out/m84036_250809_035451_s4.bc2158_sawfish/m84036_250809_035451_s4.bc2158.sv.vcf.gz.tbi", "sawfish_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-61/out/m84036_250809_035451_s4.bc2158_sawfish/m84036_250809_035451_s4.bc2158.sv.vcf.gz", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-61/out/m84036_250809_035451_s4.bc2158.f8inversion.json", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-61/out/m84036_250809_035451_s4.bc2158_paraphase/m84036_250809_035451_s4.bc2158.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-61/out/m84036_250809_035451_s4.bc2158_paraphase/m84036_250809_035451_s4.bc2158.paraphase.bam", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-61/out/m84036_250809_035451_s4.bc2158_paraphase/m84036_250809_035451_s4.bc2158.paraphase.json", "trgt_spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-61/out/m84036_250809_035451_s4.bc2158.trgt.sorted.spanning.bam.bai", "trgt_spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-61/out/m84036_250809_035451_s4.bc2158.trgt.sorted.spanning.bam", "trgt_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-61/out/m84036_250809_035451_s4.bc2158.trgt.vcf", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-61/out/m84036_250809_035451_s4.bc2158.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-61/out/m84036_250809_035451_s4.bc2158.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2158"}
2025-09-15 20:26:30.665 wdl.w:ptcp.t:call-tar_outputs-61 NOTICE task setup :: name: "tar_outputs", source: "./common.wdl", line: 279, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-61", thread: 140611977991744
2025-09-15 20:26:30.708 wdl.w:ptcp.t:call-tar_outputs-61 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:26:30.708 wdl.w:ptcp.t:call-tar_outputs-61 INFO input :: name: "sawfish_vcf_tbi", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2158.sv.vcf.gz.tbi"
2025-09-15 20:26:30.708 wdl.w:ptcp.t:call-tar_outputs-61 INFO input :: name: "sawfish_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2158.sv.vcf.gz"
2025-09-15 20:26:30.708 wdl.w:ptcp.t:call-tar_outputs-61 INFO input :: name: "f8_json", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2158.f8inversion.json"
2025-09-15 20:26:30.708 wdl.w:ptcp.t:call-tar_outputs-61 INFO input :: name: "paraphase_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2158.paraphase.bam.bai"
2025-09-15 20:26:30.708 wdl.w:ptcp.t:call-tar_outputs-61 INFO input :: name: "paraphase_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2158.paraphase.bam"
2025-09-15 20:26:30.708 wdl.w:ptcp.t:call-tar_outputs-61 INFO input :: name: "paraphase_json", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2158.paraphase.json"
2025-09-15 20:26:30.709 wdl.w:ptcp.t:call-tar_outputs-61 INFO input :: name: "trgt_spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2158.trgt.sorted.spanning.bam.bai"
2025-09-15 20:26:30.709 wdl.w:ptcp.t:call-tar_outputs-61 INFO input :: name: "trgt_spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2158.trgt.sorted.spanning.bam"
2025-09-15 20:26:30.709 wdl.w:ptcp.t:call-tar_outputs-61 INFO input :: name: "trgt_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2158.trgt.vcf"
2025-09-15 20:26:30.709 wdl.w:ptcp.t:call-tar_outputs-61 INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2158.mapped.bam.bai"
2025-09-15 20:26:30.709 wdl.w:ptcp.t:call-tar_outputs-61 INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2158.mapped.bam"
2025-09-15 20:26:30.709 wdl.w:ptcp.t:call-tar_outputs-61 INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2158"
2025-09-15 20:26:30.709 wdl.w:ptcp.t:call-tar_outputs-61 INFO eval :: name: "threads", value: 1
2025-09-15 20:26:30.709 wdl.w:ptcp.t:call-tar_outputs-61 INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:26:30.709 wdl.w:ptcp.t:call-tar_outputs-61 INFO eval :: name: "disk_size", value: 6
2025-09-15 20:26:30.709 wdl.w:ptcp.t:call-tar_outputs-61 INFO eval :: name: "output_tarball", value: "m84036_250809_035451_s4.bc2158.tar"
2025-09-15 20:26:30.710 wdl.w:ptcp.t:call-tar_outputs-61 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:26:30.710 wdl.w:ptcp.t:call-tar_outputs-61 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:26:30.710 wdl.w:ptcp.t:call-tar_outputs-61 INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:26:30.710 wdl.w:ptcp.t:call-tar_outputs-61 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:26:30.726 wdl.w:ptcp.w:call-sawfish-62.t:call-run_sawfish INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2159_sawfish/m84036_250809_035451_s4.bc2159.sv.vcf.gz"
2025-09-15 20:26:30.732 wdl.w:ptcp.w:call-sawfish-62.t:call-run_sawfish INFO output :: name: "vcf_tbi", value: "m84036_250809_035451_s4.bc2159_sawfish/m84036_250809_035451_s4.bc2159.sv.vcf.gz.tbi"
2025-09-15 20:26:30.733 wdl.w:ptcp.w:call-sawfish-62.t:call-run_sawfish INFO output :: name: "minimap2_bam", value: "m84036_250809_035451_s4.bc2159.minimap2.bam"
2025-09-15 20:26:30.734 wdl.w:ptcp.w:call-sawfish-62.t:call-run_sawfish INFO output :: name: "minimap2_bam_bai", value: "m84036_250809_035451_s4.bc2159.minimap2.bam.bai"
2025-09-15 20:26:30.739 wdl.w:ptcp.t:call-tar_outputs-11.stderr VERBOSE tar: Removing leading `/' from member names
2025-09-15 20:26:30.739 wdl.w:ptcp.t:call-tar_outputs-11.stderr VERBOSE tar: Removing leading `/' from hard link targets
2025-09-15 20:26:30.751 wdl.w:ptcp.t:call-tar_outputs-11.slurm_singularity INFO srun: job 51798198 queued and waiting for resources
2025-09-15 20:26:30.751 wdl.w:ptcp.t:call-tar_outputs-11.slurm_singularity INFO srun: job 51798198 has been allocated resources
2025-09-15 20:26:30.751 wdl.w:ptcp.t:call-tar_outputs-11.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:26:30.766 wdl.w:ptcp.w:call-paraphase-74.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for f8inv1 for sample m84036_250809_035451_s4.bc2171 at 2025-09-15 20:26:22.431011...
2025-09-15 20:26:30.766 wdl.w:ptcp.w:call-paraphase-74.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for f8inv1 for sample m84036_250809_035451_s4.bc2171 at 2025-09-15 20:26:22.751807...
2025-09-15 20:26:30.792 wdl.w:ptcp.w:call-sawfish-85.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:29][sawfish][INFO] Reading sawfish-discover results from 1 samples
2025-09-15 20:26:30.792 wdl.w:ptcp.w:call-sawfish-85.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:29][sawfish][INFO] Writing depth track to bigwig file: 'm84036_250809_035451_s4.bc2182_sawfish/samples/sample0001_UnknownSampleName/depth.bw'
2025-09-15 20:26:30.792 wdl.w:ptcp.w:call-sawfish-85.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:29][sawfish][INFO] Merging SV haplotypes
2025-09-15 20:26:30.792 wdl.w:ptcp.w:call-sawfish-85.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:29][sawfish][INFO] Finished merging SV haplotypes across samples
2025-09-15 20:26:30.792 wdl.w:ptcp.w:call-sawfish-85.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:29][sawfish][INFO] Writing merged contig alignments to bam file: 'm84036_250809_035451_s4.bc2182_sawfish/contig.alignment.bam'
2025-09-15 20:26:30.792 wdl.w:ptcp.w:call-sawfish-85.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:30][sawfish][INFO] Starting SV candidate cluster genotyping
2025-09-15 20:26:30.792 wdl.w:ptcp.w:call-sawfish-85.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:30][sawfish][INFO] Finished genotyping all SV candidate clusters
2025-09-15 20:26:30.792 wdl.w:ptcp.w:call-sawfish-85.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:30][sawfish][INFO] Starting joint CNV/SV refinement
2025-09-15 20:26:30.792 wdl.w:ptcp.w:call-sawfish-85.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:30][sawfish][INFO] Merged 0 CNVs into corresponding breakpoint-based SVs
2025-09-15 20:26:30.792 wdl.w:ptcp.w:call-sawfish-85.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:30][sawfish][INFO] Writing genotyped structural variants to file: 'm84036_250809_035451_s4.bc2182_sawfish/genotyped.sv.vcf.gz'
2025-09-15 20:26:30.792 wdl.w:ptcp.w:call-sawfish-85.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:30][sawfish][INFO] Writing run statistics to file: 'm84036_250809_035451_s4.bc2182_sawfish/run.stats.json'
2025-09-15 20:26:30.792 wdl.w:ptcp.w:call-sawfish-85.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:30][sawfish][INFO] sawfish completed. Total Runtime: 00:00:12.593
2025-09-15 20:26:30.803 wdl.w:ptcp.w:call-sawfish-85.t:call-run_sawfish INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2182_sawfish/m84036_250809_035451_s4.bc2182.sv.vcf.gz"
2025-09-15 20:26:30.808 wdl.w:ptcp.w:call-sawfish-85.t:call-run_sawfish INFO output :: name: "vcf_tbi", value: "m84036_250809_035451_s4.bc2182_sawfish/m84036_250809_035451_s4.bc2182.sv.vcf.gz.tbi"
2025-09-15 20:26:30.809 wdl.w:ptcp.w:call-sawfish-85.t:call-run_sawfish INFO output :: name: "minimap2_bam", value: "m84036_250809_035451_s4.bc2182.minimap2.bam"
2025-09-15 20:26:30.810 wdl.w:ptcp.w:call-sawfish-85.t:call-run_sawfish INFO output :: name: "minimap2_bam_bai", value: "m84036_250809_035451_s4.bc2182.minimap2.bam.bai"
2025-09-15 20:26:30.815 wdl.w:ptcp.t:call-tar_outputs-61 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 17, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-61/_singularity_tmpdir_7_vvrzz_"
2025-09-15 20:26:30.815 wdl.w:ptcp.t:call-tar_outputs-61 INFO Slurm invocation: srun --job-name call-tar_outputs-61 --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-61/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-61/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-61/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-61/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-61/out/m84036_250809_035451_s4.bc2158.f8inversion.json:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2158.f8inversion.json:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-61/out/m84036_250809_035451_s4.bc2158_sawfish/m84036_250809_035451_s4.bc2158.sv.vcf.gz:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2158.sv.vcf.gz:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-61/out/m84036_250809_035451_s4.bc2158_sawfish/m84036_250809_035451_s4.bc2158.sv.vcf.gz.tbi:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2158.sv.vcf.gz.tbi:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-61/out/m84036_250809_035451_s4.bc2158.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2158.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-61/out/m84036_250809_035451_s4.bc2158.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2158.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-61/out/m84036_250809_035451_s4.bc2158.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2158.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-61/out/m84036_250809_035451_s4.bc2158_paraphase/m84036_250809_035451_s4.bc2158.paraphase.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2158.paraphase.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-61/out/m84036_250809_035451_s4.bc2158_paraphase/m84036_250809_035451_s4.bc2158.paraphase.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2158.paraphase.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-61/out/m84036_250809_035451_s4.bc2158_paraphase/m84036_250809_035451_s4.bc2158.paraphase.json:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2158.paraphase.json:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-61/out/m84036_250809_035451_s4.bc2158.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2158.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-61/out/m84036_250809_035451_s4.bc2158.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2158.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-61/_singularity_tmpdir_7_vvrzz_/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-61/_singularity_tmpdir_7_vvrzz_/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:26:30.839 wdl.w:ptcp.t:call-tar_outputs-61 NOTICE slurm_singularity run :: pid: 1207673, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-61/slurm_singularity.log.txt"
2025-09-15 20:26:30.895 wdl.w:ptcp.w:call-sawfish-62.t:call-run_sawfish NOTICE done
2025-09-15 20:26:30.903 wdl.w:ptcp.w:call-sawfish-62 NOTICE finish :: job: "call-run_sawfish"
2025-09-15 20:26:30.903 wdl.w:ptcp.w:call-sawfish-62 INFO output :: job: "call-run_sawfish", values: {"minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-62/call-run_sawfish/out/m84036_250809_035451_s4.bc2159.minimap2.bam.bai", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-62/call-run_sawfish/out/m84036_250809_035451_s4.bc2159.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-62/call-run_sawfish/out/m84036_250809_035451_s4.bc2159_sawfish/m84036_250809_035451_s4.bc2159.sv.vcf.gz.tbi", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-62/call-run_sawfish/out/m84036_250809_035451_s4.bc2159_sawfish/m84036_250809_035451_s4.bc2159.sv.vcf.gz"}
2025-09-15 20:26:30.903 wdl.w:ptcp.w:call-sawfish-62 INFO visit :: node: "output-minimap2_bam", values: {"minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-62/call-run_sawfish/out/m84036_250809_035451_s4.bc2159.minimap2.bam"}
2025-09-15 20:26:30.903 wdl.w:ptcp.w:call-sawfish-62 INFO visit :: node: "output-minimap2_bam_bai", values: {"minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-62/call-run_sawfish/out/m84036_250809_035451_s4.bc2159.minimap2.bam.bai"}
2025-09-15 20:26:30.903 wdl.w:ptcp.w:call-sawfish-62 INFO visit :: node: "output-vcf", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-62/call-run_sawfish/out/m84036_250809_035451_s4.bc2159_sawfish/m84036_250809_035451_s4.bc2159.sv.vcf.gz"}
2025-09-15 20:26:30.903 wdl.w:ptcp.w:call-sawfish-62 INFO visit :: node: "output-vcf_tbi", values: {"vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-62/call-run_sawfish/out/m84036_250809_035451_s4.bc2159_sawfish/m84036_250809_035451_s4.bc2159.sv.vcf.gz.tbi"}
2025-09-15 20:26:30.904 wdl.w:ptcp.w:call-sawfish-62 INFO visit :: node: "outputs", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-62/call-run_sawfish/out/m84036_250809_035451_s4.bc2159_sawfish/m84036_250809_035451_s4.bc2159.sv.vcf.gz", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-62/call-run_sawfish/out/m84036_250809_035451_s4.bc2159.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-62/call-run_sawfish/out/m84036_250809_035451_s4.bc2159_sawfish/m84036_250809_035451_s4.bc2159.sv.vcf.gz.tbi", "minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-62/call-run_sawfish/out/m84036_250809_035451_s4.bc2159.minimap2.bam.bai"}
2025-09-15 20:26:30.958 wdl.w:ptcp.w:call-sawfish-85.t:call-run_sawfish NOTICE done
2025-09-15 20:26:30.966 wdl.w:ptcp.t:call-tar_outputs-11 INFO output :: name: "sample_tarball", value: "m84036_250809_035451_s4.bc2108.tar"
2025-09-15 20:26:30.968 wdl.w:ptcp.w:call-sawfish-62 NOTICE done
2025-09-15 20:26:30.974 wdl.w:ptcp NOTICE finish :: job: "call-sawfish-62"
2025-09-15 20:26:30.974 wdl.w:ptcp INFO output :: job: "call-sawfish-62", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-62/out/m84036_250809_035451_s4.bc2159_sawfish/m84036_250809_035451_s4.bc2159.sv.vcf.gz", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-62/out/m84036_250809_035451_s4.bc2159.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-62/out/m84036_250809_035451_s4.bc2159_sawfish/m84036_250809_035451_s4.bc2159.sv.vcf.gz.tbi", "minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-62/out/m84036_250809_035451_s4.bc2159.minimap2.bam.bai"}
2025-09-15 20:26:30.981 wdl.w:ptcp.w:call-sawfish-85 NOTICE finish :: job: "call-run_sawfish"
2025-09-15 20:26:30.981 wdl.w:ptcp.w:call-sawfish-85 INFO output :: job: "call-run_sawfish", values: {"minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-85/call-run_sawfish/out/m84036_250809_035451_s4.bc2182.minimap2.bam.bai", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-85/call-run_sawfish/out/m84036_250809_035451_s4.bc2182.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-85/call-run_sawfish/out/m84036_250809_035451_s4.bc2182_sawfish/m84036_250809_035451_s4.bc2182.sv.vcf.gz.tbi", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-85/call-run_sawfish/out/m84036_250809_035451_s4.bc2182_sawfish/m84036_250809_035451_s4.bc2182.sv.vcf.gz"}
2025-09-15 20:26:30.981 wdl.w:ptcp.w:call-sawfish-85 INFO visit :: node: "output-minimap2_bam", values: {"minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-85/call-run_sawfish/out/m84036_250809_035451_s4.bc2182.minimap2.bam"}
2025-09-15 20:26:30.981 wdl.w:ptcp.w:call-sawfish-85 INFO visit :: node: "output-minimap2_bam_bai", values: {"minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-85/call-run_sawfish/out/m84036_250809_035451_s4.bc2182.minimap2.bam.bai"}
2025-09-15 20:26:30.981 wdl.w:ptcp.w:call-sawfish-85 INFO visit :: node: "output-vcf", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-85/call-run_sawfish/out/m84036_250809_035451_s4.bc2182_sawfish/m84036_250809_035451_s4.bc2182.sv.vcf.gz"}
2025-09-15 20:26:30.982 wdl.w:ptcp.w:call-sawfish-85 INFO visit :: node: "output-vcf_tbi", values: {"vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-85/call-run_sawfish/out/m84036_250809_035451_s4.bc2182_sawfish/m84036_250809_035451_s4.bc2182.sv.vcf.gz.tbi"}
2025-09-15 20:26:30.982 wdl.w:ptcp.w:call-sawfish-85 INFO visit :: node: "outputs", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-85/call-run_sawfish/out/m84036_250809_035451_s4.bc2182_sawfish/m84036_250809_035451_s4.bc2182.sv.vcf.gz", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-85/call-run_sawfish/out/m84036_250809_035451_s4.bc2182.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-85/call-run_sawfish/out/m84036_250809_035451_s4.bc2182_sawfish/m84036_250809_035451_s4.bc2182.sv.vcf.gz.tbi", "minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-85/call-run_sawfish/out/m84036_250809_035451_s4.bc2182.minimap2.bam.bai"}
2025-09-15 20:26:31.028 wdl.w:ptcp.w:call-sawfish-85 NOTICE done
2025-09-15 20:26:31.035 wdl.w:ptcp NOTICE finish :: job: "call-sawfish-85"
2025-09-15 20:26:31.036 wdl.w:ptcp INFO output :: job: "call-sawfish-85", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-85/out/m84036_250809_035451_s4.bc2182_sawfish/m84036_250809_035451_s4.bc2182.sv.vcf.gz", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-85/out/m84036_250809_035451_s4.bc2182.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-85/out/m84036_250809_035451_s4.bc2182_sawfish/m84036_250809_035451_s4.bc2182.sv.vcf.gz.tbi", "minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-85/out/m84036_250809_035451_s4.bc2182.minimap2.bam.bai"}
2025-09-15 20:26:31.037 wdl.w:ptcp NOTICE ready :: job: "call-tar_outputs-85", callee: "tar_outputs"
2025-09-15 20:26:31.037 wdl.w:ptcp INFO input :: job: "call-tar_outputs-85", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "sawfish_vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-85/out/m84036_250809_035451_s4.bc2182_sawfish/m84036_250809_035451_s4.bc2182.sv.vcf.gz.tbi", "sawfish_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-85/out/m84036_250809_035451_s4.bc2182_sawfish/m84036_250809_035451_s4.bc2182.sv.vcf.gz", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-85/out/m84036_250809_035451_s4.bc2182.f8inversion.json", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-85/out/m84036_250809_035451_s4.bc2182_paraphase/m84036_250809_035451_s4.bc2182.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-85/out/m84036_250809_035451_s4.bc2182_paraphase/m84036_250809_035451_s4.bc2182.paraphase.bam", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-85/out/m84036_250809_035451_s4.bc2182_paraphase/m84036_250809_035451_s4.bc2182.paraphase.json", "trgt_spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-85/out/m84036_250809_035451_s4.bc2182.trgt.sorted.spanning.bam.bai", "trgt_spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-85/out/m84036_250809_035451_s4.bc2182.trgt.sorted.spanning.bam", "trgt_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-85/out/m84036_250809_035451_s4.bc2182.trgt.vcf", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-85/out/m84036_250809_035451_s4.bc2182.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-85/out/m84036_250809_035451_s4.bc2182.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2182"}
2025-09-15 20:26:31.038 wdl.w:ptcp.t:call-tar_outputs-11 NOTICE done
2025-09-15 20:26:31.042 wdl.w:ptcp NOTICE finish :: job: "call-tar_outputs-11"
2025-09-15 20:26:31.042 wdl.w:ptcp INFO output :: job: "call-tar_outputs-11", values: {"sample_tarball": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-11/out/m84036_250809_035451_s4.bc2108.tar"}
2025-09-15 20:26:31.045 wdl.w:ptcp.t:call-tar_outputs-85 NOTICE task setup :: name: "tar_outputs", source: "./common.wdl", line: 279, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-85", thread: 140611441120832
2025-09-15 20:26:31.065 wdl.w:ptcp.t:call-tar_outputs-85 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:26:31.065 wdl.w:ptcp.t:call-tar_outputs-85 INFO input :: name: "sawfish_vcf_tbi", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2182.sv.vcf.gz.tbi"
2025-09-15 20:26:31.065 wdl.w:ptcp.t:call-tar_outputs-85 INFO input :: name: "sawfish_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2182.sv.vcf.gz"
2025-09-15 20:26:31.065 wdl.w:ptcp.t:call-tar_outputs-85 INFO input :: name: "f8_json", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2182.f8inversion.json"
2025-09-15 20:26:31.065 wdl.w:ptcp.t:call-tar_outputs-85 INFO input :: name: "paraphase_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2182.paraphase.bam.bai"
2025-09-15 20:26:31.065 wdl.w:ptcp.t:call-tar_outputs-85 INFO input :: name: "paraphase_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2182.paraphase.bam"
2025-09-15 20:26:31.065 wdl.w:ptcp.t:call-tar_outputs-85 INFO input :: name: "paraphase_json", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2182.paraphase.json"
2025-09-15 20:26:31.065 wdl.w:ptcp.t:call-tar_outputs-85 INFO input :: name: "trgt_spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2182.trgt.sorted.spanning.bam.bai"
2025-09-15 20:26:31.065 wdl.w:ptcp.t:call-tar_outputs-85 INFO input :: name: "trgt_spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2182.trgt.sorted.spanning.bam"
2025-09-15 20:26:31.065 wdl.w:ptcp.t:call-tar_outputs-85 INFO input :: name: "trgt_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2182.trgt.vcf"
2025-09-15 20:26:31.065 wdl.w:ptcp.t:call-tar_outputs-85 INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2182.mapped.bam.bai"
2025-09-15 20:26:31.065 wdl.w:ptcp.t:call-tar_outputs-85 INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2182.mapped.bam"
2025-09-15 20:26:31.065 wdl.w:ptcp.t:call-tar_outputs-85 INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2182"
2025-09-15 20:26:31.066 wdl.w:ptcp.t:call-tar_outputs-85 INFO eval :: name: "threads", value: 1
2025-09-15 20:26:31.066 wdl.w:ptcp.t:call-tar_outputs-85 INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:26:31.066 wdl.w:ptcp.t:call-tar_outputs-85 INFO eval :: name: "disk_size", value: 6
2025-09-15 20:26:31.066 wdl.w:ptcp.t:call-tar_outputs-85 INFO eval :: name: "output_tarball", value: "m84036_250809_035451_s4.bc2182.tar"
2025-09-15 20:26:31.067 wdl.w:ptcp.t:call-tar_outputs-85 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:26:31.067 wdl.w:ptcp.t:call-tar_outputs-85 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:26:31.067 wdl.w:ptcp.t:call-tar_outputs-85 INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:26:31.067 wdl.w:ptcp.t:call-tar_outputs-85 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:26:31.143 wdl.w:ptcp.t:call-tar_outputs-85 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 17, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-85/_singularity_tmpdir_qq9816w7"
2025-09-15 20:26:31.143 wdl.w:ptcp.t:call-tar_outputs-85 INFO Slurm invocation: srun --job-name call-tar_outputs-85 --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-85/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-85/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-85/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-85/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-85/out/m84036_250809_035451_s4.bc2182_sawfish/m84036_250809_035451_s4.bc2182.sv.vcf.gz:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2182.sv.vcf.gz:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-85/out/m84036_250809_035451_s4.bc2182_sawfish/m84036_250809_035451_s4.bc2182.sv.vcf.gz.tbi:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2182.sv.vcf.gz.tbi:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-85/out/m84036_250809_035451_s4.bc2182_paraphase/m84036_250809_035451_s4.bc2182.paraphase.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2182.paraphase.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-85/out/m84036_250809_035451_s4.bc2182_paraphase/m84036_250809_035451_s4.bc2182.paraphase.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2182.paraphase.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-85/out/m84036_250809_035451_s4.bc2182_paraphase/m84036_250809_035451_s4.bc2182.paraphase.json:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2182.paraphase.json:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-85/out/m84036_250809_035451_s4.bc2182.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2182.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-85/out/m84036_250809_035451_s4.bc2182.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2182.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-85/out/m84036_250809_035451_s4.bc2182.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2182.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-85/out/m84036_250809_035451_s4.bc2182.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2182.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-85/out/m84036_250809_035451_s4.bc2182.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2182.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-85/out/m84036_250809_035451_s4.bc2182.f8inversion.json:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2182.f8inversion.json:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-85/_singularity_tmpdir_qq9816w7/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-85/_singularity_tmpdir_qq9816w7/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:26:31.149 wdl.w:ptcp.t:call-tar_outputs-85 NOTICE slurm_singularity run :: pid: 1207682, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-85/slurm_singularity.log.txt"
2025-09-15 20:26:31.705 wdl.w:ptcp.t:call-tar_outputs-61.stderr VERBOSE tar: Removing leading `/' from member names
2025-09-15 20:26:31.705 wdl.w:ptcp.t:call-tar_outputs-61.stderr VERBOSE tar: Removing leading `/' from hard link targets
2025-09-15 20:26:31.713 wdl.w:ptcp.t:call-tar_outputs-61.slurm_singularity INFO srun: job 51798199 queued and waiting for resources
2025-09-15 20:26:31.713 wdl.w:ptcp.t:call-tar_outputs-61.slurm_singularity INFO srun: job 51798199 has been allocated resources
2025-09-15 20:26:31.713 wdl.w:ptcp.t:call-tar_outputs-61.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:26:31.752 wdl.w:ptcp.t:call-tar_outputs-61 INFO output :: name: "sample_tarball", value: "m84036_250809_035451_s4.bc2158.tar"
2025-09-15 20:26:31.813 wdl.w:ptcp.t:call-tar_outputs-61 NOTICE done
2025-09-15 20:26:31.817 wdl.w:ptcp NOTICE finish :: job: "call-tar_outputs-61"
2025-09-15 20:26:31.817 wdl.w:ptcp INFO output :: job: "call-tar_outputs-61", values: {"sample_tarball": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-61/out/m84036_250809_035451_s4.bc2158.tar"}
2025-09-15 20:26:32.151 wdl.w:ptcp.t:call-tar_outputs-85.stderr VERBOSE tar: Removing leading `/' from member names
2025-09-15 20:26:32.151 wdl.w:ptcp.t:call-tar_outputs-85.stderr VERBOSE tar: Removing leading `/' from hard link targets
2025-09-15 20:26:32.158 wdl.w:ptcp.t:call-tar_outputs-85.slurm_singularity INFO srun: job 51798200 queued and waiting for resources
2025-09-15 20:26:32.158 wdl.w:ptcp.t:call-tar_outputs-85.slurm_singularity INFO srun: job 51798200 has been allocated resources
2025-09-15 20:26:32.158 wdl.w:ptcp.t:call-tar_outputs-85.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:26:32.311 wdl.w:ptcp.t:call-tar_outputs-85 INFO output :: name: "sample_tarball", value: "m84036_250809_035451_s4.bc2182.tar"
2025-09-15 20:26:32.363 wdl.w:ptcp.t:call-tar_outputs-85 NOTICE done
2025-09-15 20:26:32.366 wdl.w:ptcp NOTICE finish :: job: "call-tar_outputs-85"
2025-09-15 20:26:32.367 wdl.w:ptcp INFO output :: job: "call-tar_outputs-85", values: {"sample_tarball": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-85/out/m84036_250809_035451_s4.bc2182.tar"}
2025-09-15 20:26:32.672 wdl.w:ptcp.w:call-sawfish-79.t:call-run_sawfish INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2176_sawfish/m84036_250809_035451_s4.bc2176.sv.vcf.gz"
2025-09-15 20:26:32.676 wdl.w:ptcp.w:call-sawfish-79.t:call-run_sawfish INFO output :: name: "vcf_tbi", value: "m84036_250809_035451_s4.bc2176_sawfish/m84036_250809_035451_s4.bc2176.sv.vcf.gz.tbi"
2025-09-15 20:26:32.677 wdl.w:ptcp.w:call-sawfish-79.t:call-run_sawfish INFO output :: name: "minimap2_bam", value: "m84036_250809_035451_s4.bc2176.minimap2.bam"
2025-09-15 20:26:32.678 wdl.w:ptcp.w:call-sawfish-79.t:call-run_sawfish INFO output :: name: "minimap2_bam_bai", value: "m84036_250809_035451_s4.bc2176.minimap2.bam.bai"
2025-09-15 20:26:32.802 wdl.w:ptcp.w:call-sawfish-79.t:call-run_sawfish NOTICE done
2025-09-15 20:26:32.808 wdl.w:ptcp.w:call-sawfish-79 NOTICE finish :: job: "call-run_sawfish"
2025-09-15 20:26:32.808 wdl.w:ptcp.w:call-sawfish-79 INFO output :: job: "call-run_sawfish", values: {"minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-79/call-run_sawfish/out/m84036_250809_035451_s4.bc2176.minimap2.bam.bai", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-79/call-run_sawfish/out/m84036_250809_035451_s4.bc2176.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-79/call-run_sawfish/out/m84036_250809_035451_s4.bc2176_sawfish/m84036_250809_035451_s4.bc2176.sv.vcf.gz.tbi", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-79/call-run_sawfish/out/m84036_250809_035451_s4.bc2176_sawfish/m84036_250809_035451_s4.bc2176.sv.vcf.gz"}
2025-09-15 20:26:32.808 wdl.w:ptcp.w:call-sawfish-79 INFO visit :: node: "output-minimap2_bam", values: {"minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-79/call-run_sawfish/out/m84036_250809_035451_s4.bc2176.minimap2.bam"}
2025-09-15 20:26:32.808 wdl.w:ptcp.w:call-sawfish-79 INFO visit :: node: "output-minimap2_bam_bai", values: {"minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-79/call-run_sawfish/out/m84036_250809_035451_s4.bc2176.minimap2.bam.bai"}
2025-09-15 20:26:32.808 wdl.w:ptcp.w:call-sawfish-79 INFO visit :: node: "output-vcf", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-79/call-run_sawfish/out/m84036_250809_035451_s4.bc2176_sawfish/m84036_250809_035451_s4.bc2176.sv.vcf.gz"}
2025-09-15 20:26:32.808 wdl.w:ptcp.w:call-sawfish-79 INFO visit :: node: "output-vcf_tbi", values: {"vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-79/call-run_sawfish/out/m84036_250809_035451_s4.bc2176_sawfish/m84036_250809_035451_s4.bc2176.sv.vcf.gz.tbi"}
2025-09-15 20:26:32.809 wdl.w:ptcp.w:call-sawfish-79 INFO visit :: node: "outputs", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-79/call-run_sawfish/out/m84036_250809_035451_s4.bc2176_sawfish/m84036_250809_035451_s4.bc2176.sv.vcf.gz", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-79/call-run_sawfish/out/m84036_250809_035451_s4.bc2176.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-79/call-run_sawfish/out/m84036_250809_035451_s4.bc2176_sawfish/m84036_250809_035451_s4.bc2176.sv.vcf.gz.tbi", "minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-79/call-run_sawfish/out/m84036_250809_035451_s4.bc2176.minimap2.bam.bai"}
2025-09-15 20:26:32.851 wdl.w:ptcp.w:call-sawfish-79 NOTICE done
2025-09-15 20:26:32.878 wdl.w:ptcp NOTICE finish :: job: "call-sawfish-79"
2025-09-15 20:26:32.878 wdl.w:ptcp INFO output :: job: "call-sawfish-79", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-79/out/m84036_250809_035451_s4.bc2176_sawfish/m84036_250809_035451_s4.bc2176.sv.vcf.gz", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-79/out/m84036_250809_035451_s4.bc2176.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-79/out/m84036_250809_035451_s4.bc2176_sawfish/m84036_250809_035451_s4.bc2176.sv.vcf.gz.tbi", "minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-79/out/m84036_250809_035451_s4.bc2176.minimap2.bam.bai"}
2025-09-15 20:26:32.907 wdl.w:ptcp.w:call-sawfish-95.t:call-run_sawfish.stderr VERBOSE [M::mm_idx_gen::33.479*1.45] collected minimizers
2025-09-15 20:26:32.908 wdl.w:ptcp.w:call-sawfish-95.t:call-run_sawfish.stderr VERBOSE [M::mm_idx_gen::40.253*1.70] sorted minimizers
2025-09-15 20:26:32.908 wdl.w:ptcp.w:call-sawfish-95.t:call-run_sawfish.stderr VERBOSE [M::main::40.253*1.70] loaded/built the index for 195 target sequence(s)
2025-09-15 20:26:33.116 wdl.w:ptcp.w:call-paraphase-55.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for f8inv22 for sample m84036_250809_035451_s4.bc2152 at 2025-09-15 20:26:26.328720...
2025-09-15 20:26:33.117 wdl.w:ptcp.w:call-paraphase-55.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for f8inv22 for sample m84036_250809_035451_s4.bc2152 at 2025-09-15 20:26:26.330550...
2025-09-15 20:26:33.129 wdl.w:ptcp.w:call-sawfish-70.t:call-run_sawfish INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2167_sawfish/m84036_250809_035451_s4.bc2167.sv.vcf.gz"
2025-09-15 20:26:33.133 wdl.w:ptcp.w:call-sawfish-70.t:call-run_sawfish INFO output :: name: "vcf_tbi", value: "m84036_250809_035451_s4.bc2167_sawfish/m84036_250809_035451_s4.bc2167.sv.vcf.gz.tbi"
2025-09-15 20:26:33.134 wdl.w:ptcp.w:call-sawfish-70.t:call-run_sawfish INFO output :: name: "minimap2_bam", value: "m84036_250809_035451_s4.bc2167.minimap2.bam"
2025-09-15 20:26:33.135 wdl.w:ptcp.w:call-sawfish-70.t:call-run_sawfish INFO output :: name: "minimap2_bam_bai", value: "m84036_250809_035451_s4.bc2167.minimap2.bam.bai"
2025-09-15 20:26:33.241 wdl.w:ptcp.w:call-sawfish-93.t:call-run_sawfish.stderr VERBOSE [M::mm_idx_stat::46.334*1.62] distinct minimizers: 214664461 (92.23% are singletons); average occurrences: 1.372; average spacing: 10.529; total length: 3099922541
2025-09-15 20:26:33.241 wdl.w:ptcp.w:call-sawfish-70.t:call-run_sawfish NOTICE done
2025-09-15 20:26:33.241 wdl.w:ptcp.w:call-sawfish-93.t:call-run_sawfish.stderr VERBOSE [M::main] Version: 2.26-r1175
2025-09-15 20:26:33.241 wdl.w:ptcp.w:call-sawfish-93.t:call-run_sawfish.stderr VERBOSE [M::main] CMD: /opt/pacbio/smrttools/install/smrtlink-release_25.1.0.257715/bundles/smrttools/install/smrttools-release_25.1.0.257715/private/thirdparty/minimap2/minimap2_2.26-pacbio2/binwrap/../../../../../private/thirdparty/minimap2/minimap2_2.26-pacbio2/bin/minimap2 -a -y -x map-hifi -Y -E 1,0 /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa -
2025-09-15 20:26:33.241 wdl.w:ptcp.w:call-sawfish-93.t:call-run_sawfish.stderr VERBOSE [M::main] Real time: 46.603 sec; CPU: 75.393 sec; Peak RSS: 11.885 GB
2025-09-15 20:26:33.246 wdl.w:ptcp.w:call-sawfish-70 NOTICE finish :: job: "call-run_sawfish"
2025-09-15 20:26:33.246 wdl.w:ptcp.w:call-sawfish-70 INFO output :: job: "call-run_sawfish", values: {"minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-70/call-run_sawfish/out/m84036_250809_035451_s4.bc2167.minimap2.bam.bai", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-70/call-run_sawfish/out/m84036_250809_035451_s4.bc2167.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-70/call-run_sawfish/out/m84036_250809_035451_s4.bc2167_sawfish/m84036_250809_035451_s4.bc2167.sv.vcf.gz.tbi", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-70/call-run_sawfish/out/m84036_250809_035451_s4.bc2167_sawfish/m84036_250809_035451_s4.bc2167.sv.vcf.gz"}
2025-09-15 20:26:33.247 wdl.w:ptcp.w:call-sawfish-70 INFO visit :: node: "output-minimap2_bam", values: {"minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-70/call-run_sawfish/out/m84036_250809_035451_s4.bc2167.minimap2.bam"}
2025-09-15 20:26:33.247 wdl.w:ptcp.w:call-sawfish-70 INFO visit :: node: "output-minimap2_bam_bai", values: {"minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-70/call-run_sawfish/out/m84036_250809_035451_s4.bc2167.minimap2.bam.bai"}
2025-09-15 20:26:33.247 wdl.w:ptcp.w:call-sawfish-70 INFO visit :: node: "output-vcf", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-70/call-run_sawfish/out/m84036_250809_035451_s4.bc2167_sawfish/m84036_250809_035451_s4.bc2167.sv.vcf.gz"}
2025-09-15 20:26:33.247 wdl.w:ptcp.w:call-sawfish-70 INFO visit :: node: "output-vcf_tbi", values: {"vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-70/call-run_sawfish/out/m84036_250809_035451_s4.bc2167_sawfish/m84036_250809_035451_s4.bc2167.sv.vcf.gz.tbi"}
2025-09-15 20:26:33.247 wdl.w:ptcp.w:call-sawfish-70 INFO visit :: node: "outputs", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-70/call-run_sawfish/out/m84036_250809_035451_s4.bc2167_sawfish/m84036_250809_035451_s4.bc2167.sv.vcf.gz", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-70/call-run_sawfish/out/m84036_250809_035451_s4.bc2167.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-70/call-run_sawfish/out/m84036_250809_035451_s4.bc2167_sawfish/m84036_250809_035451_s4.bc2167.sv.vcf.gz.tbi", "minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-70/call-run_sawfish/out/m84036_250809_035451_s4.bc2167.minimap2.bam.bai"}
2025-09-15 20:26:33.288 wdl.w:ptcp.w:call-sawfish-70 NOTICE done
2025-09-15 20:26:33.293 wdl.w:ptcp NOTICE finish :: job: "call-sawfish-70"
2025-09-15 20:26:33.293 wdl.w:ptcp INFO output :: job: "call-sawfish-70", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-70/out/m84036_250809_035451_s4.bc2167_sawfish/m84036_250809_035451_s4.bc2167.sv.vcf.gz", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-70/out/m84036_250809_035451_s4.bc2167.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-70/out/m84036_250809_035451_s4.bc2167_sawfish/m84036_250809_035451_s4.bc2167.sv.vcf.gz.tbi", "minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-70/out/m84036_250809_035451_s4.bc2167.minimap2.bam.bai"}
2025-09-15 20:26:33.926 wdl.w:ptcp.w:call-paraphase-90.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for smn1 for sample m84036_250809_035451_s4.bc2187 at 2025-09-15 20:26:23.865769...
2025-09-15 20:26:35.939 wdl.w:ptcp.w:call-sawfish-95.t:call-run_sawfish.stderr VERBOSE [M::mm_mapopt_update::43.260*1.65] mid_occ = 136
2025-09-15 20:26:35.939 wdl.w:ptcp.w:call-sawfish-95.t:call-run_sawfish.stderr VERBOSE [M::mm_idx_stat] kmer size: 19; skip: 19; is_hpc: 0; #seq: 195
2025-09-15 20:26:35.939 wdl.w:ptcp.w:call-sawfish-95.t:call-run_sawfish.stderr VERBOSE [M::mm_idx_stat::45.905*1.61] distinct minimizers: 214664461 (92.23% are singletons); average occurrences: 1.372; average spacing: 10.529; total length: 3099922541
2025-09-15 20:26:35.939 wdl.w:ptcp.w:call-sawfish-95.t:call-run_sawfish.stderr VERBOSE [M::bam2fq_mainloop] discarded 0 singletons
2025-09-15 20:26:35.939 wdl.w:ptcp.w:call-sawfish-95.t:call-run_sawfish.stderr VERBOSE [M::bam2fq_mainloop] processed 331 reads
2025-09-15 20:26:35.939 wdl.w:ptcp.w:call-sawfish-95.t:call-run_sawfish.stderr VERBOSE [M::worker_pipeline::46.320*1.62] mapped 331 sequences
2025-09-15 20:26:35.939 wdl.w:ptcp.w:call-sawfish-95.t:call-run_sawfish.stderr VERBOSE [M::main] Version: 2.26-r1175
2025-09-15 20:26:35.939 wdl.w:ptcp.w:call-sawfish-95.t:call-run_sawfish.stderr VERBOSE [M::main] CMD: /opt/pacbio/smrttools/install/smrtlink-release_25.1.0.257715/bundles/smrttools/install/smrttools-release_25.1.0.257715/private/thirdparty/minimap2/minimap2_2.26-pacbio2/binwrap/../../../../../private/thirdparty/minimap2/minimap2_2.26-pacbio2/bin/minimap2 -a -y -x map-hifi -Y -E 1,0 /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa -
2025-09-15 20:26:35.939 wdl.w:ptcp.w:call-sawfish-95.t:call-run_sawfish.stderr VERBOSE [M::main] Real time: 46.621 sec; CPU: 75.156 sec; Peak RSS: 11.886 GB
2025-09-15 20:26:35.939 wdl.w:ptcp.w:call-sawfish-95.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:34][sawfish][INFO] Starting sawfish 2.0.3
2025-09-15 20:26:35.939 wdl.w:ptcp.w:call-sawfish-95.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:34][sawfish][INFO] cmdline: sawfish discover --disable-cnv --threads 16 --ref /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa --bam m84036_250809_035451_s4.bc2192.minimap2.bam --output-dir m84036_250809_035451_s4.bc2192_sawfish_discover
2025-09-15 20:26:35.939 wdl.w:ptcp.w:call-sawfish-95.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:34][sawfish][INFO] Running on 16 threads
2025-09-15 20:26:35.939 wdl.w:ptcp.w:call-sawfish-95.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:34][sawfish][INFO] Writing discover settings to file: 'm84036_250809_035451_s4.bc2192_sawfish_discover/discover.settings.json'
2025-09-15 20:26:35.939 wdl.w:ptcp.w:call-sawfish-95.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:34][sawfish][INFO] Reading reference genome from file '/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa'
2025-09-15 20:26:36.275 wdl.w:ptcp.w:call-sawfish-93.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:31][sawfish][INFO] Starting sawfish 2.0.3
2025-09-15 20:26:36.275 wdl.w:ptcp.w:call-sawfish-93.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:31][sawfish][INFO] cmdline: sawfish discover --disable-cnv --threads 16 --ref /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa --bam m84036_250809_035451_s4.bc2190.minimap2.bam --output-dir m84036_250809_035451_s4.bc2190_sawfish_discover
2025-09-15 20:26:36.275 wdl.w:ptcp.w:call-sawfish-93.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:31][sawfish][INFO] Running on 16 threads
2025-09-15 20:26:36.275 wdl.w:ptcp.w:call-sawfish-93.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:31][sawfish][INFO] Writing discover settings to file: 'm84036_250809_035451_s4.bc2190_sawfish_discover/discover.settings.json'
2025-09-15 20:26:36.275 wdl.w:ptcp.w:call-sawfish-93.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:31][sawfish][INFO] Reading reference genome from file '/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa'
2025-09-15 20:26:36.475 wdl.w:ptcp.w:call-paraphase-63.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for cyp21 for sample m84036_250809_035451_s4.bc2160 at 2025-09-15 20:25:42.322544...
2025-09-15 20:26:36.476 wdl.w:ptcp.w:call-paraphase-63.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for cyp21 for sample m84036_250809_035451_s4.bc2160 at 2025-09-15 20:25:43.602164...
2025-09-15 20:26:36.476 wdl.w:ptcp.w:call-paraphase-63.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for hba for sample m84036_250809_035451_s4.bc2160 at 2025-09-15 20:25:47.452185...
2025-09-15 20:26:36.476 wdl.w:ptcp.w:call-paraphase-63.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for hba for sample m84036_250809_035451_s4.bc2160 at 2025-09-15 20:25:48.148240...
2025-09-15 20:26:36.476 wdl.w:ptcp.w:call-paraphase-63.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for gba for sample m84036_250809_035451_s4.bc2160 at 2025-09-15 20:26:02.909876...
2025-09-15 20:26:36.476 wdl.w:ptcp.w:call-paraphase-63.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for gba for sample m84036_250809_035451_s4.bc2160 at 2025-09-15 20:26:03.738689...
2025-09-15 20:26:36.997 wdl.w:ptcp.w:call-paraphase-39.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for rpgr for sample m84036_250809_035451_s4.bc2136 at 2025-09-15 20:26:14.673693...
2025-09-15 20:26:36.998 wdl.w:ptcp.w:call-paraphase-39.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for rpgr for sample m84036_250809_035451_s4.bc2136 at 2025-09-15 20:26:15.400823...
2025-09-15 20:26:36.998 wdl.w:ptcp.w:call-paraphase-39.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for rpgr for sample m84036_250809_035451_s4.bc2136 at 2025-09-15 20:26:15.529540...
2025-09-15 20:26:37.119 wdl.w:ptcp.w:call-paraphase-27.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for f8inv22 for sample m84036_250809_035451_s4.bc2124 at 2025-09-15 20:26:35.877545...
2025-09-15 20:26:37.119 wdl.w:ptcp.w:call-paraphase-27.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for f8inv22 for sample m84036_250809_035451_s4.bc2124 at 2025-09-15 20:26:35.878508...
2025-09-15 20:26:37.466 wdl.w:ptcp.w:call-paraphase-71.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for gba for sample m84036_250809_035451_s4.bc2168 at 2025-09-15 20:26:28.656058...
2025-09-15 20:26:37.467 wdl.w:ptcp.w:call-paraphase-71.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for gba for sample m84036_250809_035451_s4.bc2168 at 2025-09-15 20:26:29.346263...
2025-09-15 20:26:37.467 wdl.w:ptcp.w:call-paraphase-71.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for hbb for sample m84036_250809_035451_s4.bc2168 at 2025-09-15 20:26:30.041117...
2025-09-15 20:26:37.467 wdl.w:ptcp.w:call-paraphase-71.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for hbb for sample m84036_250809_035451_s4.bc2168 at 2025-09-15 20:26:30.041278...
2025-09-15 20:26:38.613 wdl.w:ptcp.w:call-paraphase-06.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for rpgr for sample m84036_250809_035451_s4.bc2103 at 2025-09-15 20:26:28.080707...
2025-09-15 20:26:38.615 wdl.w:ptcp.w:call-paraphase-06.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for rpgr for sample m84036_250809_035451_s4.bc2103 at 2025-09-15 20:26:28.081933...
2025-09-15 20:26:38.615 wdl.w:ptcp.w:call-paraphase-06.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for rpgr for sample m84036_250809_035451_s4.bc2103 at 2025-09-15 20:26:29.711286...
2025-09-15 20:26:38.615 wdl.w:ptcp.w:call-paraphase-06.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for rpgr for sample m84036_250809_035451_s4.bc2103 at 2025-09-15 20:26:31.147979...
2025-09-15 20:26:38.615 wdl.w:ptcp.w:call-paraphase-06.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for rpgr for sample m84036_250809_035451_s4.bc2103 at 2025-09-15 20:26:31.402008...
2025-09-15 20:26:38.934 wdl.w:ptcp.w:call-paraphase-95.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for hba for sample m84036_250809_035451_s4.bc2192 at 2025-09-15 20:26:24.915309...
2025-09-15 20:26:38.934 wdl.w:ptcp.w:call-paraphase-95.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for hba for sample m84036_250809_035451_s4.bc2192 at 2025-09-15 20:26:25.401560...
2025-09-15 20:26:39.217 wdl.w:ptcp.w:call-paraphase-79.t:call-run_paraphase INFO output :: name: "paraphase_bam", value: "m84036_250809_035451_s4.bc2176_paraphase/m84036_250809_035451_s4.bc2176.paraphase.bam"
2025-09-15 20:26:39.221 wdl.w:ptcp.w:call-paraphase-79.t:call-run_paraphase INFO output :: name: "paraphase_bam_bai", value: "m84036_250809_035451_s4.bc2176_paraphase/m84036_250809_035451_s4.bc2176.paraphase.bam.bai"
2025-09-15 20:26:39.222 wdl.w:ptcp.w:call-paraphase-79.t:call-run_paraphase INFO output :: name: "paraphase_json", value: "m84036_250809_035451_s4.bc2176_paraphase/m84036_250809_035451_s4.bc2176.paraphase.json"
2025-09-15 20:26:39.227 wdl.w:ptcp.w:call-paraphase-79.t:call-run_paraphase INFO output :: name: "paraphase_vcfs", value: ["/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2176_paraphase/m84036_250809_035451_s4.bc2176_paraphase_vcfs/m84036_250809_035451_s4.bc2176_cyp21.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2176_paraphase/m84036_250809_035451_s4.bc2176_paraphase_vcfs/m84036_250809_035451_s4.bc2176_f8inv1.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2176_paraphase/m84036_250809_035451_s4.bc2176_paraphase_vcfs/m84036_250809_035451_s4.bc2176_f8inv22.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2176_paraphase/m84036_250809_035451_s4.bc2176_paraphase_vcfs/m84036_250809_035451_s4.bc2176_gba.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2176_paraphase/m84036_250809_035451_s4.bc2176_paraphase_vcfs/m84036_250809_035451_s4.bc2176_hba.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2176_paraphase/m84036_250809_035451_s4.bc2176_paraphase_vcfs/m84036_250809_035451_s4.bc2176_hbb.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2176_paraphase/m84036_250809_035451_s4.bc2176_paraphase_vcfs/m84036_250809_035451_s4.bc2176_rpgr.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2176_paraphase/m84036_250809_035451_s4.bc2176_paraphase_vcfs/m84036_250809_035451_s4.bc2176_smn1.vcf"]
2025-09-15 20:26:39.230 wdl.w:ptcp.w:call-paraphase-79.t:call-run_paraphase INFO output :: name: "havanno_json", value: "m84036_250809_035451_s4.bc2176.havanno.json"
2025-09-15 20:26:39.338 wdl.w:ptcp.w:call-sawfish-73.t:call-run_sawfish INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2170_sawfish/m84036_250809_035451_s4.bc2170.sv.vcf.gz"
2025-09-15 20:26:39.342 wdl.w:ptcp.w:call-sawfish-73.t:call-run_sawfish INFO output :: name: "vcf_tbi", value: "m84036_250809_035451_s4.bc2170_sawfish/m84036_250809_035451_s4.bc2170.sv.vcf.gz.tbi"
2025-09-15 20:26:39.344 wdl.w:ptcp.w:call-sawfish-73.t:call-run_sawfish INFO output :: name: "minimap2_bam", value: "m84036_250809_035451_s4.bc2170.minimap2.bam"
2025-09-15 20:26:39.345 wdl.w:ptcp.w:call-sawfish-73.t:call-run_sawfish INFO output :: name: "minimap2_bam_bai", value: "m84036_250809_035451_s4.bc2170.minimap2.bam.bai"
2025-09-15 20:26:39.394 wdl.w:ptcp.w:call-paraphase-79.t:call-run_paraphase NOTICE done
2025-09-15 20:26:39.401 wdl.w:ptcp.w:call-paraphase-79 NOTICE finish :: job: "call-run_paraphase"
2025-09-15 20:26:39.401 wdl.w:ptcp.w:call-paraphase-79 INFO output :: job: "call-run_paraphase", values: {"havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-79/call-run_paraphase/out/m84036_250809_035451_s4.bc2176.havanno.json", "paraphase_vcfs": ["/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-79/call-run_paraphase/out/m84036_250809_035451_s4.bc2176_paraphase/m84036_250809_035451_s4.bc2176_paraphase_vcfs/m84036_250809_035451_s4.bc2176_cyp21.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-79/call-run_paraphase/out/m84036_250809_035451_s4.bc2176_paraphase/m84036_250809_035451_s4.bc2176_paraphase_vcfs/m84036_250809_035451_s4.bc2176_f8inv1.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-79/call-run_paraphase/out/m84036_250809_035451_s4.bc2176_paraphase/m84036_250809_035451_s4.bc2176_paraphase_vcfs/m84036_250809_035451_s4.bc2176_f8inv22.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-79/call-run_paraphase/out/m84036_250809_035451_s4.bc2176_paraphase/m84036_250809_035451_s4.bc2176_paraphase_vcfs/m84036_250809_035451_s4.bc2176_gba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-79/call-run_paraphase/out/m84036_250809_035451_s4.bc2176_paraphase/m84036_250809_035451_s4.bc2176_paraphase_vcfs/m84036_250809_035451_s4.bc2176_hba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-79/call-run_paraphase/out/m84036_250809_035451_s4.bc2176_paraphase/m84036_250809_035451_s4.bc2176_paraphase_vcfs/m84036_250809_035451_s4.bc2176_hbb.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-79/call-run_paraphase/out/m84036_250809_035451_s4.bc2176_paraphase/m84036_250809_035451_s4.bc2176_paraphase_vcfs/m84036_250809_035451_s4.bc2176_rpgr.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-79/call-run_paraphase/out/m84036_250809_035451_s4.bc2176_paraphase/m84036_250809_035451_s4.bc2176_paraphase_vcfs/m84036_250809_035451_s4.bc2176_smn1.vcf"], "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-79/call-run_paraphase/out/m84036_250809_035451_s4.bc2176_paraphase/m84036_250809_035451_s4.bc2176.paraphase.json", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-79/call-run_paraphase/out/m84036_250809_035451_s4.bc2176_paraphase/m84036_250809_035451_s4.bc2176.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-79/call-run_paraphase/out/m84036_250809_035451_s4.bc2176_paraphase/m84036_250809_035451_s4.bc2176.paraphase.bam"}
2025-09-15 20:26:39.402 wdl.w:ptcp.w:call-paraphase-79 NOTICE ready :: job: "call-call_f8", callee: "call_f8"
2025-09-15 20:26:39.402 wdl.w:ptcp.w:call-paraphase-79 INFO input :: job: "call-call_f8", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "out_prefix": "m84036_250809_035451_s4.bc2176", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-79/call-run_paraphase/out/m84036_250809_035451_s4.bc2176_paraphase/m84036_250809_035451_s4.bc2176.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-79/call-run_paraphase/out/m84036_250809_035451_s4.bc2176_paraphase/m84036_250809_035451_s4.bc2176.paraphase.bam", "sex": "F"}
2025-09-15 20:26:39.402 wdl.w:ptcp.w:call-paraphase-79 INFO visit :: node: "output-havanno_json", values: {"havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-79/call-run_paraphase/out/m84036_250809_035451_s4.bc2176.havanno.json"}
2025-09-15 20:26:39.403 wdl.w:ptcp.w:call-paraphase-79 INFO visit :: node: "output-paraphase_bam", values: {"paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-79/call-run_paraphase/out/m84036_250809_035451_s4.bc2176_paraphase/m84036_250809_035451_s4.bc2176.paraphase.bam"}
2025-09-15 20:26:39.403 wdl.w:ptcp.w:call-paraphase-79 INFO visit :: node: "output-paraphase_bam_bai", values: {"paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-79/call-run_paraphase/out/m84036_250809_035451_s4.bc2176_paraphase/m84036_250809_035451_s4.bc2176.paraphase.bam.bai"}
2025-09-15 20:26:39.403 wdl.w:ptcp.w:call-paraphase-79 INFO visit :: node: "output-paraphase_json", values: {"paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-79/call-run_paraphase/out/m84036_250809_035451_s4.bc2176_paraphase/m84036_250809_035451_s4.bc2176.paraphase.json"}
2025-09-15 20:26:39.403 wdl.w:ptcp.w:call-paraphase-79 INFO visit :: node: "output-paraphase_vcfs", values: {"paraphase_vcfs": ["/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-79/call-run_paraphase/out/m84036_250809_035451_s4.bc2176_paraphase/m84036_250809_035451_s4.bc2176_paraphase_vcfs/m84036_250809_035451_s4.bc2176_cyp21.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-79/call-run_paraphase/out/m84036_250809_035451_s4.bc2176_paraphase/m84036_250809_035451_s4.bc2176_paraphase_vcfs/m84036_250809_035451_s4.bc2176_f8inv1.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-79/call-run_paraphase/out/m84036_250809_035451_s4.bc2176_paraphase/m84036_250809_035451_s4.bc2176_paraphase_vcfs/m84036_250809_035451_s4.bc2176_f8inv22.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-79/call-run_paraphase/out/m84036_250809_035451_s4.bc2176_paraphase/m84036_250809_035451_s4.bc2176_paraphase_vcfs/m84036_250809_035451_s4.bc2176_gba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-79/call-run_paraphase/out/m84036_250809_035451_s4.bc2176_paraphase/m84036_250809_035451_s4.bc2176_paraphase_vcfs/m84036_250809_035451_s4.bc2176_hba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-79/call-run_paraphase/out/m84036_250809_035451_s4.bc2176_paraphase/m84036_250809_035451_s4.bc2176_paraphase_vcfs/m84036_250809_035451_s4.bc2176_hbb.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-79/call-run_paraphase/out/m84036_250809_035451_s4.bc2176_paraphase/m84036_250809_035451_s4.bc2176_paraphase_vcfs/m84036_250809_035451_s4.bc2176_rpgr.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-79/call-run_paraphase/out/m84036_250809_035451_s4.bc2176_paraphase/m84036_250809_035451_s4.bc2176_paraphase_vcfs/m84036_250809_035451_s4.bc2176_smn1.vcf"]}
2025-09-15 20:26:39.408 wdl.w:ptcp.w:call-paraphase-79.t:call-call_f8 NOTICE task setup :: name: "call_f8", source: "./paraphase.wdl", line: 232, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-79/call-call_f8", thread: 140608194717248
2025-09-15 20:26:39.424 wdl.w:ptcp.w:call-paraphase-79.t:call-call_f8 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:26:39.424 wdl.w:ptcp.w:call-paraphase-79.t:call-call_f8 INFO input :: name: "genome_version", value: "38"
2025-09-15 20:26:39.424 wdl.w:ptcp.w:call-paraphase-79.t:call-call_f8 INFO input :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2176"
2025-09-15 20:26:39.424 wdl.w:ptcp.w:call-paraphase-79.t:call-call_f8 INFO input :: name: "paraphase_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2176.paraphase.bam.bai"
2025-09-15 20:26:39.424 wdl.w:ptcp.w:call-paraphase-79.t:call-call_f8 INFO input :: name: "paraphase_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2176.paraphase.bam"
2025-09-15 20:26:39.424 wdl.w:ptcp.w:call-paraphase-79.t:call-call_f8 INFO input :: name: "sex", value: "F"
2025-09-15 20:26:39.425 wdl.w:ptcp.w:call-paraphase-79.t:call-call_f8 INFO eval :: name: "threads", value: 1
2025-09-15 20:26:39.425 wdl.w:ptcp.w:call-paraphase-79.t:call-call_f8 INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:26:39.425 wdl.w:ptcp.w:call-paraphase-79.t:call-call_f8 INFO eval :: name: "disk_size", value: 11
2025-09-15 20:26:39.425 wdl.w:ptcp.w:call-paraphase-79.t:call-call_f8 INFO eval :: name: "sample_sex", value: "F"
2025-09-15 20:26:39.426 wdl.w:ptcp.w:call-paraphase-79.t:call-call_f8 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:26:39.426 wdl.w:ptcp.w:call-paraphase-79.t:call-call_f8 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:26:39.426 wdl.w:ptcp.w:call-paraphase-79.t:call-call_f8 INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:26:39.426 wdl.w:ptcp.w:call-paraphase-79.t:call-call_f8 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:26:39.467 wdl.w:ptcp.w:call-sawfish-73.t:call-run_sawfish NOTICE done
2025-09-15 20:26:39.469 wdl.w:ptcp.w:call-paraphase-79.t:call-call_f8 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 8, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-79/call-call_f8/_singularity_tmpdir_10zo_61r"
2025-09-15 20:26:39.469 wdl.w:ptcp.w:call-paraphase-79.t:call-call_f8 INFO Slurm invocation: srun --job-name call-call_f8 --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-79/call-call_f8/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-79/call-call_f8/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-79/call-call_f8/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-79/call-call_f8/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-79/call-run_paraphase/out/m84036_250809_035451_s4.bc2176_paraphase/m84036_250809_035451_s4.bc2176.paraphase.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2176.paraphase.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-79/call-run_paraphase/out/m84036_250809_035451_s4.bc2176_paraphase/m84036_250809_035451_s4.bc2176.paraphase.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2176.paraphase.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-79/call-call_f8/_singularity_tmpdir_10zo_61r/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-79/call-call_f8/_singularity_tmpdir_10zo_61r/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:26:39.472 wdl.w:ptcp.w:call-sawfish-73 NOTICE finish :: job: "call-run_sawfish"
2025-09-15 20:26:39.472 wdl.w:ptcp.w:call-sawfish-73 INFO output :: job: "call-run_sawfish", values: {"minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-73/call-run_sawfish/out/m84036_250809_035451_s4.bc2170.minimap2.bam.bai", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-73/call-run_sawfish/out/m84036_250809_035451_s4.bc2170.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-73/call-run_sawfish/out/m84036_250809_035451_s4.bc2170_sawfish/m84036_250809_035451_s4.bc2170.sv.vcf.gz.tbi", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-73/call-run_sawfish/out/m84036_250809_035451_s4.bc2170_sawfish/m84036_250809_035451_s4.bc2170.sv.vcf.gz"}
2025-09-15 20:26:39.472 wdl.w:ptcp.w:call-sawfish-73 INFO visit :: node: "output-minimap2_bam", values: {"minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-73/call-run_sawfish/out/m84036_250809_035451_s4.bc2170.minimap2.bam"}
2025-09-15 20:26:39.473 wdl.w:ptcp.w:call-sawfish-73 INFO visit :: node: "output-minimap2_bam_bai", values: {"minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-73/call-run_sawfish/out/m84036_250809_035451_s4.bc2170.minimap2.bam.bai"}
2025-09-15 20:26:39.473 wdl.w:ptcp.w:call-sawfish-73 INFO visit :: node: "output-vcf", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-73/call-run_sawfish/out/m84036_250809_035451_s4.bc2170_sawfish/m84036_250809_035451_s4.bc2170.sv.vcf.gz"}
2025-09-15 20:26:39.473 wdl.w:ptcp.w:call-sawfish-73 INFO visit :: node: "output-vcf_tbi", values: {"vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-73/call-run_sawfish/out/m84036_250809_035451_s4.bc2170_sawfish/m84036_250809_035451_s4.bc2170.sv.vcf.gz.tbi"}
2025-09-15 20:26:39.473 wdl.w:ptcp.w:call-sawfish-73 INFO visit :: node: "outputs", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-73/call-run_sawfish/out/m84036_250809_035451_s4.bc2170_sawfish/m84036_250809_035451_s4.bc2170.sv.vcf.gz", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-73/call-run_sawfish/out/m84036_250809_035451_s4.bc2170.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-73/call-run_sawfish/out/m84036_250809_035451_s4.bc2170_sawfish/m84036_250809_035451_s4.bc2170.sv.vcf.gz.tbi", "minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-73/call-run_sawfish/out/m84036_250809_035451_s4.bc2170.minimap2.bam.bai"}
2025-09-15 20:26:39.479 wdl.w:ptcp.w:call-paraphase-79.t:call-call_f8 NOTICE slurm_singularity run :: pid: 1207726, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-79/call-call_f8/slurm_singularity.log.txt"
2025-09-15 20:26:39.517 wdl.w:ptcp.w:call-sawfish-73 NOTICE done
2025-09-15 20:26:39.522 wdl.w:ptcp NOTICE finish :: job: "call-sawfish-73"
2025-09-15 20:26:39.522 wdl.w:ptcp INFO output :: job: "call-sawfish-73", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-73/out/m84036_250809_035451_s4.bc2170_sawfish/m84036_250809_035451_s4.bc2170.sv.vcf.gz", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-73/out/m84036_250809_035451_s4.bc2170.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-73/out/m84036_250809_035451_s4.bc2170_sawfish/m84036_250809_035451_s4.bc2170.sv.vcf.gz.tbi", "minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-73/out/m84036_250809_035451_s4.bc2170.minimap2.bam.bai"}
2025-09-15 20:26:39.523 wdl.w:ptcp NOTICE ready :: job: "call-tar_outputs-73", callee: "tar_outputs"
2025-09-15 20:26:39.523 wdl.w:ptcp INFO input :: job: "call-tar_outputs-73", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "sawfish_vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-73/out/m84036_250809_035451_s4.bc2170_sawfish/m84036_250809_035451_s4.bc2170.sv.vcf.gz.tbi", "sawfish_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-73/out/m84036_250809_035451_s4.bc2170_sawfish/m84036_250809_035451_s4.bc2170.sv.vcf.gz", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-73/out/m84036_250809_035451_s4.bc2170.f8inversion.json", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-73/out/m84036_250809_035451_s4.bc2170_paraphase/m84036_250809_035451_s4.bc2170.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-73/out/m84036_250809_035451_s4.bc2170_paraphase/m84036_250809_035451_s4.bc2170.paraphase.bam", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-73/out/m84036_250809_035451_s4.bc2170_paraphase/m84036_250809_035451_s4.bc2170.paraphase.json", "trgt_spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-73/out/m84036_250809_035451_s4.bc2170.trgt.sorted.spanning.bam.bai", "trgt_spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-73/out/m84036_250809_035451_s4.bc2170.trgt.sorted.spanning.bam", "trgt_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-73/out/m84036_250809_035451_s4.bc2170.trgt.vcf", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-73/out/m84036_250809_035451_s4.bc2170.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-73/out/m84036_250809_035451_s4.bc2170.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2170"}
2025-09-15 20:26:39.529 wdl.w:ptcp.t:call-tar_outputs-73 NOTICE task setup :: name: "tar_outputs", source: "./common.wdl", line: 279, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-73", thread: 140609838900800
2025-09-15 20:26:39.548 wdl.w:ptcp.t:call-tar_outputs-73 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:26:39.548 wdl.w:ptcp.t:call-tar_outputs-73 INFO input :: name: "sawfish_vcf_tbi", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2170.sv.vcf.gz.tbi"
2025-09-15 20:26:39.548 wdl.w:ptcp.t:call-tar_outputs-73 INFO input :: name: "sawfish_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2170.sv.vcf.gz"
2025-09-15 20:26:39.548 wdl.w:ptcp.t:call-tar_outputs-73 INFO input :: name: "f8_json", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2170.f8inversion.json"
2025-09-15 20:26:39.548 wdl.w:ptcp.t:call-tar_outputs-73 INFO input :: name: "paraphase_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2170.paraphase.bam.bai"
2025-09-15 20:26:39.548 wdl.w:ptcp.t:call-tar_outputs-73 INFO input :: name: "paraphase_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2170.paraphase.bam"
2025-09-15 20:26:39.548 wdl.w:ptcp.t:call-tar_outputs-73 INFO input :: name: "paraphase_json", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2170.paraphase.json"
2025-09-15 20:26:39.548 wdl.w:ptcp.t:call-tar_outputs-73 INFO input :: name: "trgt_spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2170.trgt.sorted.spanning.bam.bai"
2025-09-15 20:26:39.548 wdl.w:ptcp.t:call-tar_outputs-73 INFO input :: name: "trgt_spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2170.trgt.sorted.spanning.bam"
2025-09-15 20:26:39.548 wdl.w:ptcp.t:call-tar_outputs-73 INFO input :: name: "trgt_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2170.trgt.vcf"
2025-09-15 20:26:39.548 wdl.w:ptcp.t:call-tar_outputs-73 INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2170.mapped.bam.bai"
2025-09-15 20:26:39.548 wdl.w:ptcp.t:call-tar_outputs-73 INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2170.mapped.bam"
2025-09-15 20:26:39.548 wdl.w:ptcp.t:call-tar_outputs-73 INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2170"
2025-09-15 20:26:39.548 wdl.w:ptcp.t:call-tar_outputs-73 INFO eval :: name: "threads", value: 1
2025-09-15 20:26:39.549 wdl.w:ptcp.t:call-tar_outputs-73 INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:26:39.549 wdl.w:ptcp.t:call-tar_outputs-73 INFO eval :: name: "disk_size", value: 6
2025-09-15 20:26:39.549 wdl.w:ptcp.t:call-tar_outputs-73 INFO eval :: name: "output_tarball", value: "m84036_250809_035451_s4.bc2170.tar"
2025-09-15 20:26:39.549 wdl.w:ptcp.t:call-tar_outputs-73 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:26:39.549 wdl.w:ptcp.t:call-tar_outputs-73 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:26:39.550 wdl.w:ptcp.t:call-tar_outputs-73 INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:26:39.550 wdl.w:ptcp.t:call-tar_outputs-73 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:26:39.634 wdl.w:ptcp.t:call-tar_outputs-73 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 17, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-73/_singularity_tmpdir_mm6kkhkn"
2025-09-15 20:26:39.635 wdl.w:ptcp.t:call-tar_outputs-73 INFO Slurm invocation: srun --job-name call-tar_outputs-73 --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-73/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-73/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-73/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-73/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-73/out/m84036_250809_035451_s4.bc2170_sawfish/m84036_250809_035451_s4.bc2170.sv.vcf.gz:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2170.sv.vcf.gz:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-73/out/m84036_250809_035451_s4.bc2170_sawfish/m84036_250809_035451_s4.bc2170.sv.vcf.gz.tbi:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2170.sv.vcf.gz.tbi:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-73/out/m84036_250809_035451_s4.bc2170_paraphase/m84036_250809_035451_s4.bc2170.paraphase.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2170.paraphase.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-73/out/m84036_250809_035451_s4.bc2170_paraphase/m84036_250809_035451_s4.bc2170.paraphase.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2170.paraphase.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-73/out/m84036_250809_035451_s4.bc2170_paraphase/m84036_250809_035451_s4.bc2170.paraphase.json:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2170.paraphase.json:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-73/out/m84036_250809_035451_s4.bc2170.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2170.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-73/out/m84036_250809_035451_s4.bc2170.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2170.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-73/out/m84036_250809_035451_s4.bc2170.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2170.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-73/out/m84036_250809_035451_s4.bc2170.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2170.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-73/out/m84036_250809_035451_s4.bc2170.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2170.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-73/out/m84036_250809_035451_s4.bc2170.f8inversion.json:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2170.f8inversion.json:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-73/_singularity_tmpdir_mm6kkhkn/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-73/_singularity_tmpdir_mm6kkhkn/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:26:39.645 wdl.w:ptcp.t:call-tar_outputs-73 NOTICE slurm_singularity run :: pid: 1207781, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-73/slurm_singularity.log.txt"
2025-09-15 20:26:40.002 wdl.w:ptcp.w:call-paraphase-55.t:call-run_paraphase INFO output :: name: "paraphase_bam", value: "m84036_250809_035451_s4.bc2152_paraphase/m84036_250809_035451_s4.bc2152.paraphase.bam"
2025-09-15 20:26:40.005 wdl.w:ptcp.w:call-paraphase-55.t:call-run_paraphase INFO output :: name: "paraphase_bam_bai", value: "m84036_250809_035451_s4.bc2152_paraphase/m84036_250809_035451_s4.bc2152.paraphase.bam.bai"
2025-09-15 20:26:40.007 wdl.w:ptcp.w:call-paraphase-55.t:call-run_paraphase INFO output :: name: "paraphase_json", value: "m84036_250809_035451_s4.bc2152_paraphase/m84036_250809_035451_s4.bc2152.paraphase.json"
2025-09-15 20:26:40.012 wdl.w:ptcp.w:call-paraphase-55.t:call-run_paraphase INFO output :: name: "paraphase_vcfs", value: ["/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2152_paraphase/m84036_250809_035451_s4.bc2152_paraphase_vcfs/m84036_250809_035451_s4.bc2152_cyp21.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2152_paraphase/m84036_250809_035451_s4.bc2152_paraphase_vcfs/m84036_250809_035451_s4.bc2152_f8inv1.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2152_paraphase/m84036_250809_035451_s4.bc2152_paraphase_vcfs/m84036_250809_035451_s4.bc2152_f8inv22.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2152_paraphase/m84036_250809_035451_s4.bc2152_paraphase_vcfs/m84036_250809_035451_s4.bc2152_gba.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2152_paraphase/m84036_250809_035451_s4.bc2152_paraphase_vcfs/m84036_250809_035451_s4.bc2152_hba.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2152_paraphase/m84036_250809_035451_s4.bc2152_paraphase_vcfs/m84036_250809_035451_s4.bc2152_hbb.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2152_paraphase/m84036_250809_035451_s4.bc2152_paraphase_vcfs/m84036_250809_035451_s4.bc2152_rpgr.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2152_paraphase/m84036_250809_035451_s4.bc2152_paraphase_vcfs/m84036_250809_035451_s4.bc2152_smn1.vcf"]
2025-09-15 20:26:40.015 wdl.w:ptcp.w:call-paraphase-55.t:call-run_paraphase INFO output :: name: "havanno_json", value: "m84036_250809_035451_s4.bc2152.havanno.json"
2025-09-15 20:26:40.206 wdl.w:ptcp.w:call-paraphase-55.t:call-run_paraphase NOTICE done
2025-09-15 20:26:40.246 wdl.w:ptcp.w:call-paraphase-55 NOTICE finish :: job: "call-run_paraphase"
2025-09-15 20:26:40.246 wdl.w:ptcp.w:call-paraphase-55 INFO output :: job: "call-run_paraphase", values: {"havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-55/call-run_paraphase/out/m84036_250809_035451_s4.bc2152.havanno.json", "paraphase_vcfs": ["/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-55/call-run_paraphase/out/m84036_250809_035451_s4.bc2152_paraphase/m84036_250809_035451_s4.bc2152_paraphase_vcfs/m84036_250809_035451_s4.bc2152_cyp21.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-55/call-run_paraphase/out/m84036_250809_035451_s4.bc2152_paraphase/m84036_250809_035451_s4.bc2152_paraphase_vcfs/m84036_250809_035451_s4.bc2152_f8inv1.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-55/call-run_paraphase/out/m84036_250809_035451_s4.bc2152_paraphase/m84036_250809_035451_s4.bc2152_paraphase_vcfs/m84036_250809_035451_s4.bc2152_f8inv22.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-55/call-run_paraphase/out/m84036_250809_035451_s4.bc2152_paraphase/m84036_250809_035451_s4.bc2152_paraphase_vcfs/m84036_250809_035451_s4.bc2152_gba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-55/call-run_paraphase/out/m84036_250809_035451_s4.bc2152_paraphase/m84036_250809_035451_s4.bc2152_paraphase_vcfs/m84036_250809_035451_s4.bc2152_hba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-55/call-run_paraphase/out/m84036_250809_035451_s4.bc2152_paraphase/m84036_250809_035451_s4.bc2152_paraphase_vcfs/m84036_250809_035451_s4.bc2152_hbb.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-55/call-run_paraphase/out/m84036_250809_035451_s4.bc2152_paraphase/m84036_250809_035451_s4.bc2152_paraphase_vcfs/m84036_250809_035451_s4.bc2152_rpgr.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-55/call-run_paraphase/out/m84036_250809_035451_s4.bc2152_paraphase/m84036_250809_035451_s4.bc2152_paraphase_vcfs/m84036_250809_035451_s4.bc2152_smn1.vcf"], "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-55/call-run_paraphase/out/m84036_250809_035451_s4.bc2152_paraphase/m84036_250809_035451_s4.bc2152.paraphase.json", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-55/call-run_paraphase/out/m84036_250809_035451_s4.bc2152_paraphase/m84036_250809_035451_s4.bc2152.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-55/call-run_paraphase/out/m84036_250809_035451_s4.bc2152_paraphase/m84036_250809_035451_s4.bc2152.paraphase.bam"}
2025-09-15 20:26:40.247 wdl.w:ptcp.w:call-paraphase-55 NOTICE ready :: job: "call-call_f8", callee: "call_f8"
2025-09-15 20:26:40.247 wdl.w:ptcp.w:call-paraphase-55 INFO input :: job: "call-call_f8", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "out_prefix": "m84036_250809_035451_s4.bc2152", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-55/call-run_paraphase/out/m84036_250809_035451_s4.bc2152_paraphase/m84036_250809_035451_s4.bc2152.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-55/call-run_paraphase/out/m84036_250809_035451_s4.bc2152_paraphase/m84036_250809_035451_s4.bc2152.paraphase.bam", "sex": "F"}
2025-09-15 20:26:40.247 wdl.w:ptcp.w:call-paraphase-55 INFO visit :: node: "output-havanno_json", values: {"havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-55/call-run_paraphase/out/m84036_250809_035451_s4.bc2152.havanno.json"}
2025-09-15 20:26:40.248 wdl.w:ptcp.w:call-paraphase-55 INFO visit :: node: "output-paraphase_bam", values: {"paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-55/call-run_paraphase/out/m84036_250809_035451_s4.bc2152_paraphase/m84036_250809_035451_s4.bc2152.paraphase.bam"}
2025-09-15 20:26:40.248 wdl.w:ptcp.w:call-paraphase-55 INFO visit :: node: "output-paraphase_bam_bai", values: {"paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-55/call-run_paraphase/out/m84036_250809_035451_s4.bc2152_paraphase/m84036_250809_035451_s4.bc2152.paraphase.bam.bai"}
2025-09-15 20:26:40.248 wdl.w:ptcp.w:call-paraphase-55 INFO visit :: node: "output-paraphase_json", values: {"paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-55/call-run_paraphase/out/m84036_250809_035451_s4.bc2152_paraphase/m84036_250809_035451_s4.bc2152.paraphase.json"}
2025-09-15 20:26:40.248 wdl.w:ptcp.w:call-paraphase-55 INFO visit :: node: "output-paraphase_vcfs", values: {"paraphase_vcfs": ["/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-55/call-run_paraphase/out/m84036_250809_035451_s4.bc2152_paraphase/m84036_250809_035451_s4.bc2152_paraphase_vcfs/m84036_250809_035451_s4.bc2152_cyp21.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-55/call-run_paraphase/out/m84036_250809_035451_s4.bc2152_paraphase/m84036_250809_035451_s4.bc2152_paraphase_vcfs/m84036_250809_035451_s4.bc2152_f8inv1.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-55/call-run_paraphase/out/m84036_250809_035451_s4.bc2152_paraphase/m84036_250809_035451_s4.bc2152_paraphase_vcfs/m84036_250809_035451_s4.bc2152_f8inv22.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-55/call-run_paraphase/out/m84036_250809_035451_s4.bc2152_paraphase/m84036_250809_035451_s4.bc2152_paraphase_vcfs/m84036_250809_035451_s4.bc2152_gba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-55/call-run_paraphase/out/m84036_250809_035451_s4.bc2152_paraphase/m84036_250809_035451_s4.bc2152_paraphase_vcfs/m84036_250809_035451_s4.bc2152_hba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-55/call-run_paraphase/out/m84036_250809_035451_s4.bc2152_paraphase/m84036_250809_035451_s4.bc2152_paraphase_vcfs/m84036_250809_035451_s4.bc2152_hbb.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-55/call-run_paraphase/out/m84036_250809_035451_s4.bc2152_paraphase/m84036_250809_035451_s4.bc2152_paraphase_vcfs/m84036_250809_035451_s4.bc2152_rpgr.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-55/call-run_paraphase/out/m84036_250809_035451_s4.bc2152_paraphase/m84036_250809_035451_s4.bc2152_paraphase_vcfs/m84036_250809_035451_s4.bc2152_smn1.vcf"]}
2025-09-15 20:26:40.254 wdl.w:ptcp.w:call-paraphase-55.t:call-call_f8 NOTICE task setup :: name: "call_f8", source: "./paraphase.wdl", line: 232, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-55/call-call_f8", thread: 140608748373568
2025-09-15 20:26:40.272 wdl.w:ptcp.w:call-paraphase-55.t:call-call_f8 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:26:40.273 wdl.w:ptcp.w:call-paraphase-55.t:call-call_f8 INFO input :: name: "genome_version", value: "38"
2025-09-15 20:26:40.273 wdl.w:ptcp.w:call-paraphase-55.t:call-call_f8 INFO input :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2152"
2025-09-15 20:26:40.273 wdl.w:ptcp.w:call-paraphase-55.t:call-call_f8 INFO input :: name: "paraphase_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2152.paraphase.bam.bai"
2025-09-15 20:26:40.273 wdl.w:ptcp.w:call-paraphase-55.t:call-call_f8 INFO input :: name: "paraphase_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2152.paraphase.bam"
2025-09-15 20:26:40.273 wdl.w:ptcp.w:call-paraphase-55.t:call-call_f8 INFO input :: name: "sex", value: "F"
2025-09-15 20:26:40.273 wdl.w:ptcp.w:call-paraphase-55.t:call-call_f8 INFO eval :: name: "threads", value: 1
2025-09-15 20:26:40.273 wdl.w:ptcp.w:call-paraphase-55.t:call-call_f8 INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:26:40.273 wdl.w:ptcp.w:call-paraphase-55.t:call-call_f8 INFO eval :: name: "disk_size", value: 11
2025-09-15 20:26:40.274 wdl.w:ptcp.w:call-paraphase-55.t:call-call_f8 INFO eval :: name: "sample_sex", value: "F"
2025-09-15 20:26:40.275 wdl.w:ptcp.w:call-paraphase-55.t:call-call_f8 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:26:40.275 wdl.w:ptcp.w:call-paraphase-55.t:call-call_f8 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:26:40.276 wdl.w:ptcp.w:call-paraphase-55.t:call-call_f8 INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:26:40.276 wdl.w:ptcp.w:call-paraphase-55.t:call-call_f8 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:26:40.320 wdl.w:ptcp.w:call-paraphase-55.t:call-call_f8 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 8, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-55/call-call_f8/_singularity_tmpdir_gafzh7jo"
2025-09-15 20:26:40.320 wdl.w:ptcp.w:call-paraphase-55.t:call-call_f8 INFO Slurm invocation: srun --job-name call-call_f8 --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-55/call-call_f8/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-55/call-call_f8/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-55/call-call_f8/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-55/call-call_f8/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-55/call-run_paraphase/out/m84036_250809_035451_s4.bc2152_paraphase/m84036_250809_035451_s4.bc2152.paraphase.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2152.paraphase.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-55/call-run_paraphase/out/m84036_250809_035451_s4.bc2152_paraphase/m84036_250809_035451_s4.bc2152.paraphase.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2152.paraphase.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-55/call-call_f8/_singularity_tmpdir_gafzh7jo/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-55/call-call_f8/_singularity_tmpdir_gafzh7jo/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:26:40.328 wdl.w:ptcp.w:call-paraphase-55.t:call-call_f8 NOTICE slurm_singularity run :: pid: 1207797, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-55/call-call_f8/slurm_singularity.log.txt"
2025-09-15 20:26:40.487 wdl.w:ptcp.w:call-paraphase-79.t:call-call_f8.slurm_singularity INFO srun: job 51798202 queued and waiting for resources
2025-09-15 20:26:40.488 wdl.w:ptcp.w:call-paraphase-79.t:call-call_f8.slurm_singularity INFO srun: job 51798202 has been allocated resources
2025-09-15 20:26:40.488 wdl.w:ptcp.w:call-paraphase-79.t:call-call_f8.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:26:40.564 wdl.w:ptcp.w:call-paraphase-50.t:call-run_paraphase INFO output :: name: "paraphase_bam", value: "m84036_250809_035451_s4.bc2147_paraphase/m84036_250809_035451_s4.bc2147.paraphase.bam"
2025-09-15 20:26:40.567 wdl.w:ptcp.w:call-paraphase-50.t:call-run_paraphase INFO output :: name: "paraphase_bam_bai", value: "m84036_250809_035451_s4.bc2147_paraphase/m84036_250809_035451_s4.bc2147.paraphase.bam.bai"
2025-09-15 20:26:40.569 wdl.w:ptcp.w:call-paraphase-50.t:call-run_paraphase INFO output :: name: "paraphase_json", value: "m84036_250809_035451_s4.bc2147_paraphase/m84036_250809_035451_s4.bc2147.paraphase.json"
2025-09-15 20:26:40.577 wdl.w:ptcp.w:call-paraphase-50.t:call-run_paraphase INFO output :: name: "paraphase_vcfs", value: ["/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2147_paraphase/m84036_250809_035451_s4.bc2147_paraphase_vcfs/m84036_250809_035451_s4.bc2147_cyp21.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2147_paraphase/m84036_250809_035451_s4.bc2147_paraphase_vcfs/m84036_250809_035451_s4.bc2147_f8inv1.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2147_paraphase/m84036_250809_035451_s4.bc2147_paraphase_vcfs/m84036_250809_035451_s4.bc2147_f8inv22.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2147_paraphase/m84036_250809_035451_s4.bc2147_paraphase_vcfs/m84036_250809_035451_s4.bc2147_gba.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2147_paraphase/m84036_250809_035451_s4.bc2147_paraphase_vcfs/m84036_250809_035451_s4.bc2147_hba.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2147_paraphase/m84036_250809_035451_s4.bc2147_paraphase_vcfs/m84036_250809_035451_s4.bc2147_hbb.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2147_paraphase/m84036_250809_035451_s4.bc2147_paraphase_vcfs/m84036_250809_035451_s4.bc2147_rpgr.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2147_paraphase/m84036_250809_035451_s4.bc2147_paraphase_vcfs/m84036_250809_035451_s4.bc2147_smn1.vcf"]
2025-09-15 20:26:40.580 wdl.w:ptcp.w:call-paraphase-50.t:call-run_paraphase INFO output :: name: "havanno_json", value: "m84036_250809_035451_s4.bc2147.havanno.json"
2025-09-15 20:26:40.665 wdl.w:ptcp.t:call-tar_outputs-73.slurm_singularity INFO srun: job 51798203 queued and waiting for resources
2025-09-15 20:26:40.665 wdl.w:ptcp.t:call-tar_outputs-73.slurm_singularity INFO srun: job 51798203 has been allocated resources
2025-09-15 20:26:40.665 wdl.w:ptcp.t:call-tar_outputs-73.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:26:40.766 wdl.w:ptcp.w:call-paraphase-50.t:call-run_paraphase NOTICE done
2025-09-15 20:26:40.771 wdl.w:ptcp.w:call-paraphase-50 NOTICE finish :: job: "call-run_paraphase"
2025-09-15 20:26:40.772 wdl.w:ptcp.w:call-paraphase-50 INFO output :: job: "call-run_paraphase", values: {"havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-50/call-run_paraphase/out/m84036_250809_035451_s4.bc2147.havanno.json", "paraphase_vcfs": ["/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-50/call-run_paraphase/out/m84036_250809_035451_s4.bc2147_paraphase/m84036_250809_035451_s4.bc2147_paraphase_vcfs/m84036_250809_035451_s4.bc2147_cyp21.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-50/call-run_paraphase/out/m84036_250809_035451_s4.bc2147_paraphase/m84036_250809_035451_s4.bc2147_paraphase_vcfs/m84036_250809_035451_s4.bc2147_f8inv1.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-50/call-run_paraphase/out/m84036_250809_035451_s4.bc2147_paraphase/m84036_250809_035451_s4.bc2147_paraphase_vcfs/m84036_250809_035451_s4.bc2147_f8inv22.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-50/call-run_paraphase/out/m84036_250809_035451_s4.bc2147_paraphase/m84036_250809_035451_s4.bc2147_paraphase_vcfs/m84036_250809_035451_s4.bc2147_gba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-50/call-run_paraphase/out/m84036_250809_035451_s4.bc2147_paraphase/m84036_250809_035451_s4.bc2147_paraphase_vcfs/m84036_250809_035451_s4.bc2147_hba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-50/call-run_paraphase/out/m84036_250809_035451_s4.bc2147_paraphase/m84036_250809_035451_s4.bc2147_paraphase_vcfs/m84036_250809_035451_s4.bc2147_hbb.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-50/call-run_paraphase/out/m84036_250809_035451_s4.bc2147_paraphase/m84036_250809_035451_s4.bc2147_paraphase_vcfs/m84036_250809_035451_s4.bc2147_rpgr.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-50/call-run_paraphase/out/m84036_250809_035451_s4.bc2147_paraphase/m84036_250809_035451_s4.bc2147_paraphase_vcfs/m84036_250809_035451_s4.bc2147_smn1.vcf"], "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-50/call-run_paraphase/out/m84036_250809_035451_s4.bc2147_paraphase/m84036_250809_035451_s4.bc2147.paraphase.json", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-50/call-run_paraphase/out/m84036_250809_035451_s4.bc2147_paraphase/m84036_250809_035451_s4.bc2147.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-50/call-run_paraphase/out/m84036_250809_035451_s4.bc2147_paraphase/m84036_250809_035451_s4.bc2147.paraphase.bam"}
2025-09-15 20:26:40.772 wdl.w:ptcp.w:call-paraphase-50 NOTICE ready :: job: "call-call_f8", callee: "call_f8"
2025-09-15 20:26:40.772 wdl.w:ptcp.w:call-paraphase-50 INFO input :: job: "call-call_f8", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "out_prefix": "m84036_250809_035451_s4.bc2147", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-50/call-run_paraphase/out/m84036_250809_035451_s4.bc2147_paraphase/m84036_250809_035451_s4.bc2147.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-50/call-run_paraphase/out/m84036_250809_035451_s4.bc2147_paraphase/m84036_250809_035451_s4.bc2147.paraphase.bam", "sex": "F"}
2025-09-15 20:26:40.773 wdl.w:ptcp.w:call-paraphase-50 INFO visit :: node: "output-havanno_json", values: {"havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-50/call-run_paraphase/out/m84036_250809_035451_s4.bc2147.havanno.json"}
2025-09-15 20:26:40.773 wdl.w:ptcp.w:call-paraphase-50 INFO visit :: node: "output-paraphase_bam", values: {"paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-50/call-run_paraphase/out/m84036_250809_035451_s4.bc2147_paraphase/m84036_250809_035451_s4.bc2147.paraphase.bam"}
2025-09-15 20:26:40.773 wdl.w:ptcp.w:call-paraphase-50 INFO visit :: node: "output-paraphase_bam_bai", values: {"paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-50/call-run_paraphase/out/m84036_250809_035451_s4.bc2147_paraphase/m84036_250809_035451_s4.bc2147.paraphase.bam.bai"}
2025-09-15 20:26:40.773 wdl.w:ptcp.w:call-paraphase-50 INFO visit :: node: "output-paraphase_json", values: {"paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-50/call-run_paraphase/out/m84036_250809_035451_s4.bc2147_paraphase/m84036_250809_035451_s4.bc2147.paraphase.json"}
2025-09-15 20:26:40.774 wdl.w:ptcp.w:call-paraphase-50 INFO visit :: node: "output-paraphase_vcfs", values: {"paraphase_vcfs": ["/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-50/call-run_paraphase/out/m84036_250809_035451_s4.bc2147_paraphase/m84036_250809_035451_s4.bc2147_paraphase_vcfs/m84036_250809_035451_s4.bc2147_cyp21.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-50/call-run_paraphase/out/m84036_250809_035451_s4.bc2147_paraphase/m84036_250809_035451_s4.bc2147_paraphase_vcfs/m84036_250809_035451_s4.bc2147_f8inv1.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-50/call-run_paraphase/out/m84036_250809_035451_s4.bc2147_paraphase/m84036_250809_035451_s4.bc2147_paraphase_vcfs/m84036_250809_035451_s4.bc2147_f8inv22.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-50/call-run_paraphase/out/m84036_250809_035451_s4.bc2147_paraphase/m84036_250809_035451_s4.bc2147_paraphase_vcfs/m84036_250809_035451_s4.bc2147_gba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-50/call-run_paraphase/out/m84036_250809_035451_s4.bc2147_paraphase/m84036_250809_035451_s4.bc2147_paraphase_vcfs/m84036_250809_035451_s4.bc2147_hba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-50/call-run_paraphase/out/m84036_250809_035451_s4.bc2147_paraphase/m84036_250809_035451_s4.bc2147_paraphase_vcfs/m84036_250809_035451_s4.bc2147_hbb.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-50/call-run_paraphase/out/m84036_250809_035451_s4.bc2147_paraphase/m84036_250809_035451_s4.bc2147_paraphase_vcfs/m84036_250809_035451_s4.bc2147_rpgr.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-50/call-run_paraphase/out/m84036_250809_035451_s4.bc2147_paraphase/m84036_250809_035451_s4.bc2147_paraphase_vcfs/m84036_250809_035451_s4.bc2147_smn1.vcf"]}
2025-09-15 20:26:40.779 wdl.w:ptcp.w:call-paraphase-50.t:call-call_f8 NOTICE task setup :: name: "call_f8", source: "./paraphase.wdl", line: 232, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-50/call-call_f8", thread: 140608765158976
2025-09-15 20:26:40.800 wdl.w:ptcp.w:call-paraphase-50.t:call-call_f8 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:26:40.800 wdl.w:ptcp.w:call-paraphase-50.t:call-call_f8 INFO input :: name: "genome_version", value: "38"
2025-09-15 20:26:40.800 wdl.w:ptcp.w:call-paraphase-50.t:call-call_f8 INFO input :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2147"
2025-09-15 20:26:40.800 wdl.w:ptcp.w:call-paraphase-50.t:call-call_f8 INFO input :: name: "paraphase_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2147.paraphase.bam.bai"
2025-09-15 20:26:40.800 wdl.w:ptcp.w:call-paraphase-50.t:call-call_f8 INFO input :: name: "paraphase_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2147.paraphase.bam"
2025-09-15 20:26:40.800 wdl.w:ptcp.w:call-paraphase-50.t:call-call_f8 INFO input :: name: "sex", value: "F"
2025-09-15 20:26:40.800 wdl.w:ptcp.w:call-paraphase-50.t:call-call_f8 INFO eval :: name: "threads", value: 1
2025-09-15 20:26:40.800 wdl.w:ptcp.w:call-paraphase-50.t:call-call_f8 INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:26:40.801 wdl.w:ptcp.w:call-paraphase-50.t:call-call_f8 INFO eval :: name: "disk_size", value: 11
2025-09-15 20:26:40.801 wdl.w:ptcp.w:call-paraphase-50.t:call-call_f8 INFO eval :: name: "sample_sex", value: "F"
2025-09-15 20:26:40.801 wdl.w:ptcp.w:call-paraphase-50.t:call-call_f8 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:26:40.801 wdl.w:ptcp.w:call-paraphase-50.t:call-call_f8 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:26:40.802 wdl.w:ptcp.w:call-paraphase-50.t:call-call_f8 INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:26:40.802 wdl.w:ptcp.w:call-paraphase-50.t:call-call_f8 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:26:40.844 wdl.w:ptcp.w:call-paraphase-50.t:call-call_f8 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 8, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-50/call-call_f8/_singularity_tmpdir_mxigo9q1"
2025-09-15 20:26:40.844 wdl.w:ptcp.w:call-paraphase-50.t:call-call_f8 INFO Slurm invocation: srun --job-name call-call_f8 --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-50/call-call_f8/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-50/call-call_f8/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-50/call-call_f8/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-50/call-call_f8/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-50/call-run_paraphase/out/m84036_250809_035451_s4.bc2147_paraphase/m84036_250809_035451_s4.bc2147.paraphase.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2147.paraphase.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-50/call-run_paraphase/out/m84036_250809_035451_s4.bc2147_paraphase/m84036_250809_035451_s4.bc2147.paraphase.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2147.paraphase.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-50/call-call_f8/_singularity_tmpdir_mxigo9q1/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-50/call-call_f8/_singularity_tmpdir_mxigo9q1/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:26:40.855 wdl.w:ptcp.w:call-paraphase-50.t:call-call_f8 NOTICE slurm_singularity run :: pid: 1207807, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-50/call-call_f8/slurm_singularity.log.txt"
2025-09-15 20:26:41.020 wdl.w:ptcp.t:call-tar_outputs-73 INFO output :: name: "sample_tarball", value: "m84036_250809_035451_s4.bc2170.tar"
2025-09-15 20:26:41.080 wdl.w:ptcp.t:call-tar_outputs-73 NOTICE done
2025-09-15 20:26:41.084 wdl.w:ptcp NOTICE finish :: job: "call-tar_outputs-73"
2025-09-15 20:26:41.084 wdl.w:ptcp INFO output :: job: "call-tar_outputs-73", values: {"sample_tarball": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-73/out/m84036_250809_035451_s4.bc2170.tar"}
2025-09-15 20:26:41.137 wdl.w:ptcp.w:call-paraphase-79.t:call-call_f8 INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2176.f8inversion.vcf"
2025-09-15 20:26:41.141 wdl.w:ptcp.w:call-paraphase-79.t:call-call_f8 INFO output :: name: "json", value: "m84036_250809_035451_s4.bc2176.f8inversion.json"
2025-09-15 20:26:41.202 wdl.w:ptcp.w:call-paraphase-79.t:call-call_f8 NOTICE done
2025-09-15 20:26:41.207 wdl.w:ptcp.w:call-paraphase-79 NOTICE finish :: job: "call-call_f8"
2025-09-15 20:26:41.207 wdl.w:ptcp.w:call-paraphase-79 INFO output :: job: "call-call_f8", values: {"json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-79/call-call_f8/out/m84036_250809_035451_s4.bc2176.f8inversion.json", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-79/call-call_f8/out/m84036_250809_035451_s4.bc2176.f8inversion.vcf"}
2025-09-15 20:26:41.207 wdl.w:ptcp.w:call-paraphase-79 INFO visit :: node: "output-f8_json", values: {"f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-79/call-call_f8/out/m84036_250809_035451_s4.bc2176.f8inversion.json"}
2025-09-15 20:26:41.208 wdl.w:ptcp.w:call-paraphase-79 INFO visit :: node: "output-f8_vcf", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-79/call-call_f8/out/m84036_250809_035451_s4.bc2176.f8inversion.vcf"}
2025-09-15 20:26:41.208 wdl.w:ptcp.w:call-paraphase-79 INFO visit :: node: "outputs", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-79/call-call_f8/out/m84036_250809_035451_s4.bc2176.f8inversion.vcf", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-79/call-run_paraphase/out/m84036_250809_035451_s4.bc2176_paraphase/m84036_250809_035451_s4.bc2176.paraphase.json", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-79/call-run_paraphase/out/m84036_250809_035451_s4.bc2176_paraphase/m84036_250809_035451_s4.bc2176.paraphase.bam", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-79/call-run_paraphase/out/m84036_250809_035451_s4.bc2176_paraphase/m84036_250809_035451_s4.bc2176.paraphase.bam.bai", "paraphase_vcfs": ["/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-79/call-run_paraphase/out/m84036_250809_035451_s4.bc2176_paraphase/m84036_250809_035451_s4.bc2176_paraphase_vcfs/m84036_250809_035451_s4.bc2176_cyp21.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-79/call-run_paraphase/out/m84036_250809_035451_s4.bc2176_paraphase/m84036_250809_035451_s4.bc2176_paraphase_vcfs/m84036_250809_035451_s4.bc2176_f8inv1.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-79/call-run_paraphase/out/m84036_250809_035451_s4.bc2176_paraphase/m84036_250809_035451_s4.bc2176_paraphase_vcfs/m84036_250809_035451_s4.bc2176_f8inv22.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-79/call-run_paraphase/out/m84036_250809_035451_s4.bc2176_paraphase/m84036_250809_035451_s4.bc2176_paraphase_vcfs/m84036_250809_035451_s4.bc2176_gba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-79/call-run_paraphase/out/m84036_250809_035451_s4.bc2176_paraphase/m84036_250809_035451_s4.bc2176_paraphase_vcfs/m84036_250809_035451_s4.bc2176_hba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-79/call-run_paraphase/out/m84036_250809_035451_s4.bc2176_paraphase/m84036_250809_035451_s4.bc2176_paraphase_vcfs/m84036_250809_035451_s4.bc2176_hbb.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-79/call-run_paraphase/out/m84036_250809_035451_s4.bc2176_paraphase/m84036_250809_035451_s4.bc2176_paraphase_vcfs/m84036_250809_035451_s4.bc2176_rpgr.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-79/call-run_paraphase/out/m84036_250809_035451_s4.bc2176_paraphase/m84036_250809_035451_s4.bc2176_paraphase_vcfs/m84036_250809_035451_s4.bc2176_smn1.vcf"], "havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-79/call-run_paraphase/out/m84036_250809_035451_s4.bc2176.havanno.json", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-79/call-call_f8/out/m84036_250809_035451_s4.bc2176.f8inversion.json"}
2025-09-15 20:26:41.328 wdl.w:ptcp.w:call-paraphase-79 NOTICE done
2025-09-15 20:26:41.330 wdl.w:ptcp.w:call-paraphase-55.t:call-call_f8.stderr VERBOSE 2025-09-15 20:26:41,183 INFO  Started analysis for m84036_250809_035451_s4.bc2152 at 2025-09-15 20:26:41.183072...
2025-09-15 20:26:41.330 wdl.w:ptcp.w:call-paraphase-55.t:call-call_f8.stderr VERBOSE 2025-09-15 20:26:41,254 INFO  Completed analysis for m84036_250809_035451_s4.bc2152
2025-09-15 20:26:41.335 wdl.w:ptcp NOTICE finish :: job: "call-paraphase-79"
2025-09-15 20:26:41.335 wdl.w:ptcp INFO output :: job: "call-paraphase-79", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-79/out/m84036_250809_035451_s4.bc2176.f8inversion.vcf", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-79/out/m84036_250809_035451_s4.bc2176_paraphase/m84036_250809_035451_s4.bc2176.paraphase.json", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-79/out/m84036_250809_035451_s4.bc2176_paraphase/m84036_250809_035451_s4.bc2176.paraphase.bam", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-79/out/m84036_250809_035451_s4.bc2176_paraphase/m84036_250809_035451_s4.bc2176.paraphase.bam.bai", "paraphase_vcfs": ["/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-79/out/m84036_250809_035451_s4.bc2176_paraphase/m84036_250809_035451_s4.bc2176_paraphase_vcfs/m84036_250809_035451_s4.bc2176_cyp21.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-79/out/m84036_250809_035451_s4.bc2176_paraphase/m84036_250809_035451_s4.bc2176_paraphase_vcfs/m84036_250809_035451_s4.bc2176_f8inv1.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-79/out/m84036_250809_035451_s4.bc2176_paraphase/m84036_250809_035451_s4.bc2176_paraphase_vcfs/m84036_250809_035451_s4.bc2176_f8inv22.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-79/out/m84036_250809_035451_s4.bc2176_paraphase/m84036_250809_035451_s4.bc2176_paraphase_vcfs/m84036_250809_035451_s4.bc2176_gba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-79/out/m84036_250809_035451_s4.bc2176_paraphase/m84036_250809_035451_s4.bc2176_paraphase_vcfs/m84036_250809_035451_s4.bc2176_hba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-79/out/m84036_250809_035451_s4.bc2176_paraphase/m84036_250809_035451_s4.bc2176_paraphase_vcfs/m84036_250809_035451_s4.bc2176_hbb.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-79/out/m84036_250809_035451_s4.bc2176_paraphase/m84036_250809_035451_s4.bc2176_paraphase_vcfs/m84036_250809_035451_s4.bc2176_rpgr.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-79/out/m84036_250809_035451_s4.bc2176_paraphase/m84036_250809_035451_s4.bc2176_paraphase_vcfs/m84036_250809_035451_s4.bc2176_smn1.vcf"], "havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-79/out/m84036_250809_035451_s4.bc2176.havanno.json", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-79/out/m84036_250809_035451_s4.bc2176.f8inversion.json"}
2025-09-15 20:26:41.335 wdl.w:ptcp NOTICE ready :: job: "call-tar_outputs-79", callee: "tar_outputs"
2025-09-15 20:26:41.336 wdl.w:ptcp INFO input :: job: "call-tar_outputs-79", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "sawfish_vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-79/out/m84036_250809_035451_s4.bc2176_sawfish/m84036_250809_035451_s4.bc2176.sv.vcf.gz.tbi", "sawfish_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-79/out/m84036_250809_035451_s4.bc2176_sawfish/m84036_250809_035451_s4.bc2176.sv.vcf.gz", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-79/out/m84036_250809_035451_s4.bc2176.f8inversion.json", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-79/out/m84036_250809_035451_s4.bc2176_paraphase/m84036_250809_035451_s4.bc2176.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-79/out/m84036_250809_035451_s4.bc2176_paraphase/m84036_250809_035451_s4.bc2176.paraphase.bam", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-79/out/m84036_250809_035451_s4.bc2176_paraphase/m84036_250809_035451_s4.bc2176.paraphase.json", "trgt_spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-79/out/m84036_250809_035451_s4.bc2176.trgt.sorted.spanning.bam.bai", "trgt_spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-79/out/m84036_250809_035451_s4.bc2176.trgt.sorted.spanning.bam", "trgt_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-79/out/m84036_250809_035451_s4.bc2176.trgt.vcf", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-79/out/m84036_250809_035451_s4.bc2176.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-79/out/m84036_250809_035451_s4.bc2176.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2176"}
2025-09-15 20:26:41.339 wdl.w:ptcp.w:call-paraphase-55.t:call-call_f8.slurm_singularity INFO srun: job 51798204 queued and waiting for resources
2025-09-15 20:26:41.339 wdl.w:ptcp.w:call-paraphase-55.t:call-call_f8.slurm_singularity INFO srun: job 51798204 has been allocated resources
2025-09-15 20:26:41.339 wdl.w:ptcp.w:call-paraphase-55.t:call-call_f8.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:26:41.344 wdl.w:ptcp.t:call-tar_outputs-79 NOTICE task setup :: name: "tar_outputs", source: "./common.wdl", line: 279, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-79", thread: 140610887464512
2025-09-15 20:26:41.363 wdl.w:ptcp.t:call-tar_outputs-79 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:26:41.363 wdl.w:ptcp.t:call-tar_outputs-79 INFO input :: name: "sawfish_vcf_tbi", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2176.sv.vcf.gz.tbi"
2025-09-15 20:26:41.363 wdl.w:ptcp.t:call-tar_outputs-79 INFO input :: name: "sawfish_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2176.sv.vcf.gz"
2025-09-15 20:26:41.363 wdl.w:ptcp.t:call-tar_outputs-79 INFO input :: name: "f8_json", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2176.f8inversion.json"
2025-09-15 20:26:41.363 wdl.w:ptcp.t:call-tar_outputs-79 INFO input :: name: "paraphase_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2176.paraphase.bam.bai"
2025-09-15 20:26:41.363 wdl.w:ptcp.t:call-tar_outputs-79 INFO input :: name: "paraphase_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2176.paraphase.bam"
2025-09-15 20:26:41.363 wdl.w:ptcp.t:call-tar_outputs-79 INFO input :: name: "paraphase_json", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2176.paraphase.json"
2025-09-15 20:26:41.363 wdl.w:ptcp.t:call-tar_outputs-79 INFO input :: name: "trgt_spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2176.trgt.sorted.spanning.bam.bai"
2025-09-15 20:26:41.363 wdl.w:ptcp.t:call-tar_outputs-79 INFO input :: name: "trgt_spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2176.trgt.sorted.spanning.bam"
2025-09-15 20:26:41.364 wdl.w:ptcp.t:call-tar_outputs-79 INFO input :: name: "trgt_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2176.trgt.vcf"
2025-09-15 20:26:41.364 wdl.w:ptcp.t:call-tar_outputs-79 INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2176.mapped.bam.bai"
2025-09-15 20:26:41.364 wdl.w:ptcp.t:call-tar_outputs-79 INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2176.mapped.bam"
2025-09-15 20:26:41.364 wdl.w:ptcp.t:call-tar_outputs-79 INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2176"
2025-09-15 20:26:41.364 wdl.w:ptcp.t:call-tar_outputs-79 INFO eval :: name: "threads", value: 1
2025-09-15 20:26:41.364 wdl.w:ptcp.t:call-tar_outputs-79 INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:26:41.364 wdl.w:ptcp.t:call-tar_outputs-79 INFO eval :: name: "disk_size", value: 6
2025-09-15 20:26:41.364 wdl.w:ptcp.t:call-tar_outputs-79 INFO eval :: name: "output_tarball", value: "m84036_250809_035451_s4.bc2176.tar"
2025-09-15 20:26:41.365 wdl.w:ptcp.t:call-tar_outputs-79 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:26:41.365 wdl.w:ptcp.t:call-tar_outputs-79 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:26:41.365 wdl.w:ptcp.t:call-tar_outputs-79 INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:26:41.365 wdl.w:ptcp.t:call-tar_outputs-79 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:26:41.414 wdl.w:ptcp.w:call-paraphase-55.t:call-call_f8 INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2152.f8inversion.vcf"
2025-09-15 20:26:41.417 wdl.w:ptcp.w:call-paraphase-55.t:call-call_f8 INFO output :: name: "json", value: "m84036_250809_035451_s4.bc2152.f8inversion.json"
2025-09-15 20:26:41.456 wdl.w:ptcp.t:call-tar_outputs-79 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 17, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-79/_singularity_tmpdir_q6_q08_5"
2025-09-15 20:26:41.457 wdl.w:ptcp.t:call-tar_outputs-79 INFO Slurm invocation: srun --job-name call-tar_outputs-79 --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-79/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-79/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-79/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-79/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-79/out/m84036_250809_035451_s4.bc2176.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2176.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-79/out/m84036_250809_035451_s4.bc2176.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2176.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-79/out/m84036_250809_035451_s4.bc2176.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2176.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-79/out/m84036_250809_035451_s4.bc2176.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2176.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-79/out/m84036_250809_035451_s4.bc2176.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2176.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-79/out/m84036_250809_035451_s4.bc2176.f8inversion.json:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2176.f8inversion.json:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-79/out/m84036_250809_035451_s4.bc2176_paraphase/m84036_250809_035451_s4.bc2176.paraphase.json:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2176.paraphase.json:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-79/out/m84036_250809_035451_s4.bc2176_paraphase/m84036_250809_035451_s4.bc2176.paraphase.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2176.paraphase.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-79/out/m84036_250809_035451_s4.bc2176_paraphase/m84036_250809_035451_s4.bc2176.paraphase.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2176.paraphase.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-79/out/m84036_250809_035451_s4.bc2176_sawfish/m84036_250809_035451_s4.bc2176.sv.vcf.gz.tbi:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2176.sv.vcf.gz.tbi:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-79/out/m84036_250809_035451_s4.bc2176_sawfish/m84036_250809_035451_s4.bc2176.sv.vcf.gz:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2176.sv.vcf.gz:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-79/_singularity_tmpdir_q6_q08_5/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-79/_singularity_tmpdir_q6_q08_5/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:26:41.466 wdl.w:ptcp.t:call-tar_outputs-79 NOTICE slurm_singularity run :: pid: 1207817, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-79/slurm_singularity.log.txt"
2025-09-15 20:26:41.474 wdl.w:ptcp.w:call-paraphase-55.t:call-call_f8 NOTICE done
2025-09-15 20:26:41.479 wdl.w:ptcp.w:call-paraphase-55 NOTICE finish :: job: "call-call_f8"
2025-09-15 20:26:41.479 wdl.w:ptcp.w:call-paraphase-55 INFO output :: job: "call-call_f8", values: {"json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-55/call-call_f8/out/m84036_250809_035451_s4.bc2152.f8inversion.json", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-55/call-call_f8/out/m84036_250809_035451_s4.bc2152.f8inversion.vcf"}
2025-09-15 20:26:41.479 wdl.w:ptcp.w:call-paraphase-55 INFO visit :: node: "output-f8_json", values: {"f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-55/call-call_f8/out/m84036_250809_035451_s4.bc2152.f8inversion.json"}
2025-09-15 20:26:41.479 wdl.w:ptcp.w:call-paraphase-55 INFO visit :: node: "output-f8_vcf", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-55/call-call_f8/out/m84036_250809_035451_s4.bc2152.f8inversion.vcf"}
2025-09-15 20:26:41.480 wdl.w:ptcp.w:call-paraphase-55 INFO visit :: node: "outputs", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-55/call-call_f8/out/m84036_250809_035451_s4.bc2152.f8inversion.vcf", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-55/call-run_paraphase/out/m84036_250809_035451_s4.bc2152_paraphase/m84036_250809_035451_s4.bc2152.paraphase.json", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-55/call-run_paraphase/out/m84036_250809_035451_s4.bc2152_paraphase/m84036_250809_035451_s4.bc2152.paraphase.bam", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-55/call-run_paraphase/out/m84036_250809_035451_s4.bc2152_paraphase/m84036_250809_035451_s4.bc2152.paraphase.bam.bai", "paraphase_vcfs": ["/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-55/call-run_paraphase/out/m84036_250809_035451_s4.bc2152_paraphase/m84036_250809_035451_s4.bc2152_paraphase_vcfs/m84036_250809_035451_s4.bc2152_cyp21.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-55/call-run_paraphase/out/m84036_250809_035451_s4.bc2152_paraphase/m84036_250809_035451_s4.bc2152_paraphase_vcfs/m84036_250809_035451_s4.bc2152_f8inv1.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-55/call-run_paraphase/out/m84036_250809_035451_s4.bc2152_paraphase/m84036_250809_035451_s4.bc2152_paraphase_vcfs/m84036_250809_035451_s4.bc2152_f8inv22.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-55/call-run_paraphase/out/m84036_250809_035451_s4.bc2152_paraphase/m84036_250809_035451_s4.bc2152_paraphase_vcfs/m84036_250809_035451_s4.bc2152_gba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-55/call-run_paraphase/out/m84036_250809_035451_s4.bc2152_paraphase/m84036_250809_035451_s4.bc2152_paraphase_vcfs/m84036_250809_035451_s4.bc2152_hba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-55/call-run_paraphase/out/m84036_250809_035451_s4.bc2152_paraphase/m84036_250809_035451_s4.bc2152_paraphase_vcfs/m84036_250809_035451_s4.bc2152_hbb.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-55/call-run_paraphase/out/m84036_250809_035451_s4.bc2152_paraphase/m84036_250809_035451_s4.bc2152_paraphase_vcfs/m84036_250809_035451_s4.bc2152_rpgr.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-55/call-run_paraphase/out/m84036_250809_035451_s4.bc2152_paraphase/m84036_250809_035451_s4.bc2152_paraphase_vcfs/m84036_250809_035451_s4.bc2152_smn1.vcf"], "havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-55/call-run_paraphase/out/m84036_250809_035451_s4.bc2152.havanno.json", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-55/call-call_f8/out/m84036_250809_035451_s4.bc2152.f8inversion.json"}
2025-09-15 20:26:41.588 wdl.w:ptcp.w:call-paraphase-55 NOTICE done
2025-09-15 20:26:41.594 wdl.w:ptcp NOTICE finish :: job: "call-paraphase-55"
2025-09-15 20:26:41.594 wdl.w:ptcp INFO output :: job: "call-paraphase-55", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-55/out/m84036_250809_035451_s4.bc2152.f8inversion.vcf", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-55/out/m84036_250809_035451_s4.bc2152_paraphase/m84036_250809_035451_s4.bc2152.paraphase.json", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-55/out/m84036_250809_035451_s4.bc2152_paraphase/m84036_250809_035451_s4.bc2152.paraphase.bam", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-55/out/m84036_250809_035451_s4.bc2152_paraphase/m84036_250809_035451_s4.bc2152.paraphase.bam.bai", "paraphase_vcfs": ["/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-55/out/m84036_250809_035451_s4.bc2152_paraphase/m84036_250809_035451_s4.bc2152_paraphase_vcfs/m84036_250809_035451_s4.bc2152_cyp21.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-55/out/m84036_250809_035451_s4.bc2152_paraphase/m84036_250809_035451_s4.bc2152_paraphase_vcfs/m84036_250809_035451_s4.bc2152_f8inv1.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-55/out/m84036_250809_035451_s4.bc2152_paraphase/m84036_250809_035451_s4.bc2152_paraphase_vcfs/m84036_250809_035451_s4.bc2152_f8inv22.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-55/out/m84036_250809_035451_s4.bc2152_paraphase/m84036_250809_035451_s4.bc2152_paraphase_vcfs/m84036_250809_035451_s4.bc2152_gba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-55/out/m84036_250809_035451_s4.bc2152_paraphase/m84036_250809_035451_s4.bc2152_paraphase_vcfs/m84036_250809_035451_s4.bc2152_hba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-55/out/m84036_250809_035451_s4.bc2152_paraphase/m84036_250809_035451_s4.bc2152_paraphase_vcfs/m84036_250809_035451_s4.bc2152_hbb.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-55/out/m84036_250809_035451_s4.bc2152_paraphase/m84036_250809_035451_s4.bc2152_paraphase_vcfs/m84036_250809_035451_s4.bc2152_rpgr.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-55/out/m84036_250809_035451_s4.bc2152_paraphase/m84036_250809_035451_s4.bc2152_paraphase_vcfs/m84036_250809_035451_s4.bc2152_smn1.vcf"], "havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-55/out/m84036_250809_035451_s4.bc2152.havanno.json", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-55/out/m84036_250809_035451_s4.bc2152.f8inversion.json"}
2025-09-15 20:26:41.595 wdl.w:ptcp NOTICE ready :: job: "call-tar_outputs-55", callee: "tar_outputs"
2025-09-15 20:26:41.595 wdl.w:ptcp INFO input :: job: "call-tar_outputs-55", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "sawfish_vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-55/out/m84036_250809_035451_s4.bc2152_sawfish/m84036_250809_035451_s4.bc2152.sv.vcf.gz.tbi", "sawfish_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-55/out/m84036_250809_035451_s4.bc2152_sawfish/m84036_250809_035451_s4.bc2152.sv.vcf.gz", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-55/out/m84036_250809_035451_s4.bc2152.f8inversion.json", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-55/out/m84036_250809_035451_s4.bc2152_paraphase/m84036_250809_035451_s4.bc2152.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-55/out/m84036_250809_035451_s4.bc2152_paraphase/m84036_250809_035451_s4.bc2152.paraphase.bam", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-55/out/m84036_250809_035451_s4.bc2152_paraphase/m84036_250809_035451_s4.bc2152.paraphase.json", "trgt_spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-55/out/m84036_250809_035451_s4.bc2152.trgt.sorted.spanning.bam.bai", "trgt_spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-55/out/m84036_250809_035451_s4.bc2152.trgt.sorted.spanning.bam", "trgt_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-55/out/m84036_250809_035451_s4.bc2152.trgt.vcf", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-55/out/m84036_250809_035451_s4.bc2152.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-55/out/m84036_250809_035451_s4.bc2152.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2152"}
2025-09-15 20:26:41.600 wdl.w:ptcp.t:call-tar_outputs-55 NOTICE task setup :: name: "tar_outputs", source: "./common.wdl", line: 279, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-55", thread: 140609285244480
2025-09-15 20:26:41.617 wdl.w:ptcp.w:call-paraphase-30.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for f8inv22 for sample m84036_250809_035451_s4.bc2127 at 2025-09-15 20:26:32.608623...
2025-09-15 20:26:41.617 wdl.w:ptcp.w:call-paraphase-30.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for f8inv22 for sample m84036_250809_035451_s4.bc2127 at 2025-09-15 20:26:32.608819...
2025-09-15 20:26:41.622 wdl.w:ptcp.t:call-tar_outputs-55 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:26:41.622 wdl.w:ptcp.t:call-tar_outputs-55 INFO input :: name: "sawfish_vcf_tbi", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2152.sv.vcf.gz.tbi"
2025-09-15 20:26:41.622 wdl.w:ptcp.t:call-tar_outputs-55 INFO input :: name: "sawfish_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2152.sv.vcf.gz"
2025-09-15 20:26:41.622 wdl.w:ptcp.t:call-tar_outputs-55 INFO input :: name: "f8_json", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2152.f8inversion.json"
2025-09-15 20:26:41.622 wdl.w:ptcp.t:call-tar_outputs-55 INFO input :: name: "paraphase_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2152.paraphase.bam.bai"
2025-09-15 20:26:41.622 wdl.w:ptcp.t:call-tar_outputs-55 INFO input :: name: "paraphase_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2152.paraphase.bam"
2025-09-15 20:26:41.622 wdl.w:ptcp.t:call-tar_outputs-55 INFO input :: name: "paraphase_json", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2152.paraphase.json"
2025-09-15 20:26:41.622 wdl.w:ptcp.t:call-tar_outputs-55 INFO input :: name: "trgt_spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2152.trgt.sorted.spanning.bam.bai"
2025-09-15 20:26:41.622 wdl.w:ptcp.t:call-tar_outputs-55 INFO input :: name: "trgt_spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2152.trgt.sorted.spanning.bam"
2025-09-15 20:26:41.622 wdl.w:ptcp.t:call-tar_outputs-55 INFO input :: name: "trgt_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2152.trgt.vcf"
2025-09-15 20:26:41.622 wdl.w:ptcp.t:call-tar_outputs-55 INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2152.mapped.bam.bai"
2025-09-15 20:26:41.622 wdl.w:ptcp.t:call-tar_outputs-55 INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2152.mapped.bam"
2025-09-15 20:26:41.623 wdl.w:ptcp.t:call-tar_outputs-55 INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2152"
2025-09-15 20:26:41.623 wdl.w:ptcp.t:call-tar_outputs-55 INFO eval :: name: "threads", value: 1
2025-09-15 20:26:41.623 wdl.w:ptcp.t:call-tar_outputs-55 INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:26:41.623 wdl.w:ptcp.t:call-tar_outputs-55 INFO eval :: name: "disk_size", value: 6
2025-09-15 20:26:41.623 wdl.w:ptcp.t:call-tar_outputs-55 INFO eval :: name: "output_tarball", value: "m84036_250809_035451_s4.bc2152.tar"
2025-09-15 20:26:41.624 wdl.w:ptcp.t:call-tar_outputs-55 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:26:41.624 wdl.w:ptcp.t:call-tar_outputs-55 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:26:41.624 wdl.w:ptcp.t:call-tar_outputs-55 INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:26:41.624 wdl.w:ptcp.t:call-tar_outputs-55 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:26:41.726 wdl.w:ptcp.t:call-tar_outputs-55 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 17, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-55/_singularity_tmpdir_i02jgq6v"
2025-09-15 20:26:41.726 wdl.w:ptcp.t:call-tar_outputs-55 INFO Slurm invocation: srun --job-name call-tar_outputs-55 --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-55/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-55/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-55/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-55/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-55/out/m84036_250809_035451_s4.bc2152.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2152.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-55/out/m84036_250809_035451_s4.bc2152.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2152.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-55/out/m84036_250809_035451_s4.bc2152.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2152.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-55/out/m84036_250809_035451_s4.bc2152_paraphase/m84036_250809_035451_s4.bc2152.paraphase.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2152.paraphase.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-55/out/m84036_250809_035451_s4.bc2152_paraphase/m84036_250809_035451_s4.bc2152.paraphase.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2152.paraphase.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-55/out/m84036_250809_035451_s4.bc2152_paraphase/m84036_250809_035451_s4.bc2152.paraphase.json:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2152.paraphase.json:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-55/out/m84036_250809_035451_s4.bc2152_sawfish/m84036_250809_035451_s4.bc2152.sv.vcf.gz:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2152.sv.vcf.gz:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-55/out/m84036_250809_035451_s4.bc2152_sawfish/m84036_250809_035451_s4.bc2152.sv.vcf.gz.tbi:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2152.sv.vcf.gz.tbi:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-55/out/m84036_250809_035451_s4.bc2152.f8inversion.json:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2152.f8inversion.json:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-55/out/m84036_250809_035451_s4.bc2152.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2152.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-55/out/m84036_250809_035451_s4.bc2152.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2152.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-55/_singularity_tmpdir_i02jgq6v/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-55/_singularity_tmpdir_i02jgq6v/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:26:41.735 wdl.w:ptcp.t:call-tar_outputs-55 NOTICE slurm_singularity run :: pid: 1207821, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-55/slurm_singularity.log.txt"
2025-09-15 20:26:41.862 wdl.w:ptcp.w:call-paraphase-50.t:call-call_f8.slurm_singularity INFO srun: job 51798205 queued and waiting for resources
2025-09-15 20:26:41.862 wdl.w:ptcp.w:call-paraphase-50.t:call-call_f8.slurm_singularity INFO srun: job 51798205 has been allocated resources
2025-09-15 20:26:41.862 wdl.w:ptcp.w:call-paraphase-50.t:call-call_f8.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:26:42.117 wdl.w:ptcp.w:call-paraphase-50.t:call-call_f8 INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2147.f8inversion.vcf"
2025-09-15 20:26:42.120 wdl.w:ptcp.w:call-paraphase-50.t:call-call_f8 INFO output :: name: "json", value: "m84036_250809_035451_s4.bc2147.f8inversion.json"
2025-09-15 20:26:42.171 wdl.w:ptcp.w:call-paraphase-50.t:call-call_f8 NOTICE done
2025-09-15 20:26:42.176 wdl.w:ptcp.w:call-paraphase-50 NOTICE finish :: job: "call-call_f8"
2025-09-15 20:26:42.176 wdl.w:ptcp.w:call-paraphase-50 INFO output :: job: "call-call_f8", values: {"json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-50/call-call_f8/out/m84036_250809_035451_s4.bc2147.f8inversion.json", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-50/call-call_f8/out/m84036_250809_035451_s4.bc2147.f8inversion.vcf"}
2025-09-15 20:26:42.176 wdl.w:ptcp.w:call-paraphase-50 INFO visit :: node: "output-f8_json", values: {"f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-50/call-call_f8/out/m84036_250809_035451_s4.bc2147.f8inversion.json"}
2025-09-15 20:26:42.176 wdl.w:ptcp.w:call-paraphase-50 INFO visit :: node: "output-f8_vcf", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-50/call-call_f8/out/m84036_250809_035451_s4.bc2147.f8inversion.vcf"}
2025-09-15 20:26:42.177 wdl.w:ptcp.w:call-paraphase-50 INFO visit :: node: "outputs", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-50/call-call_f8/out/m84036_250809_035451_s4.bc2147.f8inversion.vcf", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-50/call-run_paraphase/out/m84036_250809_035451_s4.bc2147_paraphase/m84036_250809_035451_s4.bc2147.paraphase.json", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-50/call-run_paraphase/out/m84036_250809_035451_s4.bc2147_paraphase/m84036_250809_035451_s4.bc2147.paraphase.bam", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-50/call-run_paraphase/out/m84036_250809_035451_s4.bc2147_paraphase/m84036_250809_035451_s4.bc2147.paraphase.bam.bai", "paraphase_vcfs": ["/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-50/call-run_paraphase/out/m84036_250809_035451_s4.bc2147_paraphase/m84036_250809_035451_s4.bc2147_paraphase_vcfs/m84036_250809_035451_s4.bc2147_cyp21.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-50/call-run_paraphase/out/m84036_250809_035451_s4.bc2147_paraphase/m84036_250809_035451_s4.bc2147_paraphase_vcfs/m84036_250809_035451_s4.bc2147_f8inv1.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-50/call-run_paraphase/out/m84036_250809_035451_s4.bc2147_paraphase/m84036_250809_035451_s4.bc2147_paraphase_vcfs/m84036_250809_035451_s4.bc2147_f8inv22.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-50/call-run_paraphase/out/m84036_250809_035451_s4.bc2147_paraphase/m84036_250809_035451_s4.bc2147_paraphase_vcfs/m84036_250809_035451_s4.bc2147_gba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-50/call-run_paraphase/out/m84036_250809_035451_s4.bc2147_paraphase/m84036_250809_035451_s4.bc2147_paraphase_vcfs/m84036_250809_035451_s4.bc2147_hba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-50/call-run_paraphase/out/m84036_250809_035451_s4.bc2147_paraphase/m84036_250809_035451_s4.bc2147_paraphase_vcfs/m84036_250809_035451_s4.bc2147_hbb.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-50/call-run_paraphase/out/m84036_250809_035451_s4.bc2147_paraphase/m84036_250809_035451_s4.bc2147_paraphase_vcfs/m84036_250809_035451_s4.bc2147_rpgr.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-50/call-run_paraphase/out/m84036_250809_035451_s4.bc2147_paraphase/m84036_250809_035451_s4.bc2147_paraphase_vcfs/m84036_250809_035451_s4.bc2147_smn1.vcf"], "havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-50/call-run_paraphase/out/m84036_250809_035451_s4.bc2147.havanno.json", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-50/call-call_f8/out/m84036_250809_035451_s4.bc2147.f8inversion.json"}
2025-09-15 20:26:42.292 wdl.w:ptcp.w:call-paraphase-50 NOTICE done
2025-09-15 20:26:42.298 wdl.w:ptcp NOTICE finish :: job: "call-paraphase-50"
2025-09-15 20:26:42.298 wdl.w:ptcp INFO output :: job: "call-paraphase-50", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-50/out/m84036_250809_035451_s4.bc2147.f8inversion.vcf", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-50/out/m84036_250809_035451_s4.bc2147_paraphase/m84036_250809_035451_s4.bc2147.paraphase.json", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-50/out/m84036_250809_035451_s4.bc2147_paraphase/m84036_250809_035451_s4.bc2147.paraphase.bam", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-50/out/m84036_250809_035451_s4.bc2147_paraphase/m84036_250809_035451_s4.bc2147.paraphase.bam.bai", "paraphase_vcfs": ["/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-50/out/m84036_250809_035451_s4.bc2147_paraphase/m84036_250809_035451_s4.bc2147_paraphase_vcfs/m84036_250809_035451_s4.bc2147_cyp21.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-50/out/m84036_250809_035451_s4.bc2147_paraphase/m84036_250809_035451_s4.bc2147_paraphase_vcfs/m84036_250809_035451_s4.bc2147_f8inv1.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-50/out/m84036_250809_035451_s4.bc2147_paraphase/m84036_250809_035451_s4.bc2147_paraphase_vcfs/m84036_250809_035451_s4.bc2147_f8inv22.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-50/out/m84036_250809_035451_s4.bc2147_paraphase/m84036_250809_035451_s4.bc2147_paraphase_vcfs/m84036_250809_035451_s4.bc2147_gba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-50/out/m84036_250809_035451_s4.bc2147_paraphase/m84036_250809_035451_s4.bc2147_paraphase_vcfs/m84036_250809_035451_s4.bc2147_hba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-50/out/m84036_250809_035451_s4.bc2147_paraphase/m84036_250809_035451_s4.bc2147_paraphase_vcfs/m84036_250809_035451_s4.bc2147_hbb.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-50/out/m84036_250809_035451_s4.bc2147_paraphase/m84036_250809_035451_s4.bc2147_paraphase_vcfs/m84036_250809_035451_s4.bc2147_rpgr.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-50/out/m84036_250809_035451_s4.bc2147_paraphase/m84036_250809_035451_s4.bc2147_paraphase_vcfs/m84036_250809_035451_s4.bc2147_smn1.vcf"], "havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-50/out/m84036_250809_035451_s4.bc2147.havanno.json", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-50/out/m84036_250809_035451_s4.bc2147.f8inversion.json"}
2025-09-15 20:26:42.299 wdl.w:ptcp NOTICE ready :: job: "call-tar_outputs-50", callee: "tar_outputs"
2025-09-15 20:26:42.299 wdl.w:ptcp INFO input :: job: "call-tar_outputs-50", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "sawfish_vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-50/out/m84036_250809_035451_s4.bc2147_sawfish/m84036_250809_035451_s4.bc2147.sv.vcf.gz.tbi", "sawfish_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-50/out/m84036_250809_035451_s4.bc2147_sawfish/m84036_250809_035451_s4.bc2147.sv.vcf.gz", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-50/out/m84036_250809_035451_s4.bc2147.f8inversion.json", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-50/out/m84036_250809_035451_s4.bc2147_paraphase/m84036_250809_035451_s4.bc2147.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-50/out/m84036_250809_035451_s4.bc2147_paraphase/m84036_250809_035451_s4.bc2147.paraphase.bam", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-50/out/m84036_250809_035451_s4.bc2147_paraphase/m84036_250809_035451_s4.bc2147.paraphase.json", "trgt_spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-50/out/m84036_250809_035451_s4.bc2147.trgt.sorted.spanning.bam.bai", "trgt_spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-50/out/m84036_250809_035451_s4.bc2147.trgt.sorted.spanning.bam", "trgt_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-50/out/m84036_250809_035451_s4.bc2147.trgt.vcf", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-50/out/m84036_250809_035451_s4.bc2147.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-50/out/m84036_250809_035451_s4.bc2147.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2147"}
2025-09-15 20:26:42.306 wdl.w:ptcp.t:call-tar_outputs-50 NOTICE task setup :: name: "tar_outputs", source: "./common.wdl", line: 279, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-50", thread: 140608723195456
2025-09-15 20:26:42.327 wdl.w:ptcp.t:call-tar_outputs-50 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:26:42.327 wdl.w:ptcp.t:call-tar_outputs-50 INFO input :: name: "sawfish_vcf_tbi", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2147.sv.vcf.gz.tbi"
2025-09-15 20:26:42.327 wdl.w:ptcp.t:call-tar_outputs-50 INFO input :: name: "sawfish_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2147.sv.vcf.gz"
2025-09-15 20:26:42.327 wdl.w:ptcp.t:call-tar_outputs-50 INFO input :: name: "f8_json", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2147.f8inversion.json"
2025-09-15 20:26:42.327 wdl.w:ptcp.t:call-tar_outputs-50 INFO input :: name: "paraphase_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2147.paraphase.bam.bai"
2025-09-15 20:26:42.327 wdl.w:ptcp.t:call-tar_outputs-50 INFO input :: name: "paraphase_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2147.paraphase.bam"
2025-09-15 20:26:42.327 wdl.w:ptcp.t:call-tar_outputs-50 INFO input :: name: "paraphase_json", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2147.paraphase.json"
2025-09-15 20:26:42.327 wdl.w:ptcp.t:call-tar_outputs-50 INFO input :: name: "trgt_spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2147.trgt.sorted.spanning.bam.bai"
2025-09-15 20:26:42.327 wdl.w:ptcp.t:call-tar_outputs-50 INFO input :: name: "trgt_spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2147.trgt.sorted.spanning.bam"
2025-09-15 20:26:42.327 wdl.w:ptcp.t:call-tar_outputs-50 INFO input :: name: "trgt_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2147.trgt.vcf"
2025-09-15 20:26:42.328 wdl.w:ptcp.t:call-tar_outputs-50 INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2147.mapped.bam.bai"
2025-09-15 20:26:42.328 wdl.w:ptcp.t:call-tar_outputs-50 INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2147.mapped.bam"
2025-09-15 20:26:42.328 wdl.w:ptcp.t:call-tar_outputs-50 INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2147"
2025-09-15 20:26:42.328 wdl.w:ptcp.t:call-tar_outputs-50 INFO eval :: name: "threads", value: 1
2025-09-15 20:26:42.328 wdl.w:ptcp.t:call-tar_outputs-50 INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:26:42.328 wdl.w:ptcp.t:call-tar_outputs-50 INFO eval :: name: "disk_size", value: 6
2025-09-15 20:26:42.328 wdl.w:ptcp.t:call-tar_outputs-50 INFO eval :: name: "output_tarball", value: "m84036_250809_035451_s4.bc2147.tar"
2025-09-15 20:26:42.329 wdl.w:ptcp.t:call-tar_outputs-50 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:26:42.329 wdl.w:ptcp.t:call-tar_outputs-50 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:26:42.329 wdl.w:ptcp.t:call-tar_outputs-50 INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:26:42.329 wdl.w:ptcp.t:call-tar_outputs-50 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:26:42.413 wdl.w:ptcp.t:call-tar_outputs-50 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 17, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-50/_singularity_tmpdir__otgepza"
2025-09-15 20:26:42.414 wdl.w:ptcp.t:call-tar_outputs-50 INFO Slurm invocation: srun --job-name call-tar_outputs-50 --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-50/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-50/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-50/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-50/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-50/out/m84036_250809_035451_s4.bc2147_paraphase/m84036_250809_035451_s4.bc2147.paraphase.json:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2147.paraphase.json:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-50/out/m84036_250809_035451_s4.bc2147_paraphase/m84036_250809_035451_s4.bc2147.paraphase.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2147.paraphase.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-50/out/m84036_250809_035451_s4.bc2147_paraphase/m84036_250809_035451_s4.bc2147.paraphase.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2147.paraphase.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-50/out/m84036_250809_035451_s4.bc2147_sawfish/m84036_250809_035451_s4.bc2147.sv.vcf.gz.tbi:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2147.sv.vcf.gz.tbi:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-50/out/m84036_250809_035451_s4.bc2147_sawfish/m84036_250809_035451_s4.bc2147.sv.vcf.gz:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2147.sv.vcf.gz:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-50/out/m84036_250809_035451_s4.bc2147.f8inversion.json:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2147.f8inversion.json:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-50/out/m84036_250809_035451_s4.bc2147.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2147.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-50/out/m84036_250809_035451_s4.bc2147.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2147.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-50/out/m84036_250809_035451_s4.bc2147.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2147.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-50/out/m84036_250809_035451_s4.bc2147.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2147.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-50/out/m84036_250809_035451_s4.bc2147.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2147.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-50/_singularity_tmpdir__otgepza/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-50/_singularity_tmpdir__otgepza/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:26:42.423 wdl.w:ptcp.t:call-tar_outputs-50 NOTICE slurm_singularity run :: pid: 1207835, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-50/slurm_singularity.log.txt"
2025-09-15 20:26:42.474 wdl.w:ptcp.t:call-tar_outputs-79.slurm_singularity INFO srun: job 51798206 queued and waiting for resources
2025-09-15 20:26:42.474 wdl.w:ptcp.t:call-tar_outputs-79.slurm_singularity INFO srun: job 51798206 has been allocated resources
2025-09-15 20:26:42.474 wdl.w:ptcp.t:call-tar_outputs-79.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:26:42.742 wdl.w:ptcp.t:call-tar_outputs-55.slurm_singularity INFO srun: job 51798207 queued and waiting for resources
2025-09-15 20:26:42.742 wdl.w:ptcp.t:call-tar_outputs-55.slurm_singularity INFO srun: job 51798207 has been allocated resources
2025-09-15 20:26:42.742 wdl.w:ptcp.t:call-tar_outputs-55.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:26:42.818 wdl.w:ptcp.w:call-paraphase-70.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for cyp21 for sample m84036_250809_035451_s4.bc2167 at 2025-09-15 20:25:56.377421...
2025-09-15 20:26:42.819 wdl.w:ptcp.w:call-paraphase-70.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for cyp21 for sample m84036_250809_035451_s4.bc2167 at 2025-09-15 20:25:57.388713...
2025-09-15 20:26:42.819 wdl.w:ptcp.w:call-paraphase-70.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for hba for sample m84036_250809_035451_s4.bc2167 at 2025-09-15 20:25:58.054136...
2025-09-15 20:26:42.819 wdl.w:ptcp.w:call-paraphase-70.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for hba for sample m84036_250809_035451_s4.bc2167 at 2025-09-15 20:25:58.580833...
2025-09-15 20:26:42.819 wdl.w:ptcp.w:call-paraphase-70.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for gba for sample m84036_250809_035451_s4.bc2167 at 2025-09-15 20:26:10.269469...
2025-09-15 20:26:42.819 wdl.w:ptcp.w:call-paraphase-70.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for gba for sample m84036_250809_035451_s4.bc2167 at 2025-09-15 20:26:10.850644...
2025-09-15 20:26:42.998 wdl.w:ptcp.t:call-tar_outputs-55 INFO output :: name: "sample_tarball", value: "m84036_250809_035451_s4.bc2152.tar"
2025-09-15 20:26:43.037 wdl.w:ptcp.t:call-tar_outputs-79 INFO output :: name: "sample_tarball", value: "m84036_250809_035451_s4.bc2176.tar"
2025-09-15 20:26:43.074 wdl.w:ptcp.t:call-tar_outputs-55 NOTICE done
2025-09-15 20:26:43.079 wdl.w:ptcp NOTICE finish :: job: "call-tar_outputs-55"
2025-09-15 20:26:43.079 wdl.w:ptcp INFO output :: job: "call-tar_outputs-55", values: {"sample_tarball": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-55/out/m84036_250809_035451_s4.bc2152.tar"}
2025-09-15 20:26:43.107 wdl.w:ptcp.t:call-tar_outputs-79 NOTICE done
2025-09-15 20:26:43.111 wdl.w:ptcp NOTICE finish :: job: "call-tar_outputs-79"
2025-09-15 20:26:43.111 wdl.w:ptcp INFO output :: job: "call-tar_outputs-79", values: {"sample_tarball": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-79/out/m84036_250809_035451_s4.bc2176.tar"}
2025-09-15 20:26:43.215 wdl.w:ptcp.w:call-paraphase-59.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for f8inv1 for sample m84036_250809_035451_s4.bc2156 at 2025-09-15 20:25:50.925857...
2025-09-15 20:26:43.216 wdl.w:ptcp.w:call-paraphase-59.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for f8inv1 for sample m84036_250809_035451_s4.bc2156 at 2025-09-15 20:25:55.195191...
2025-09-15 20:26:43.216 wdl.w:ptcp.w:call-paraphase-59.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for f8inv1 for sample m84036_250809_035451_s4.bc2156 at 2025-09-15 20:25:55.506785...
2025-09-15 20:26:43.216 wdl.w:ptcp.w:call-paraphase-59.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for rpgr for sample m84036_250809_035451_s4.bc2156 at 2025-09-15 20:26:23.404968...
2025-09-15 20:26:43.216 wdl.w:ptcp.w:call-paraphase-59.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for rpgr for sample m84036_250809_035451_s4.bc2156 at 2025-09-15 20:26:23.405683...
2025-09-15 20:26:43.216 wdl.w:ptcp.w:call-paraphase-59.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for rpgr for sample m84036_250809_035451_s4.bc2156 at 2025-09-15 20:26:24.665665...
2025-09-15 20:26:43.216 wdl.w:ptcp.w:call-paraphase-59.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for rpgr for sample m84036_250809_035451_s4.bc2156 at 2025-09-15 20:26:25.688253...
2025-09-15 20:26:43.216 wdl.w:ptcp.w:call-paraphase-59.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for rpgr for sample m84036_250809_035451_s4.bc2156 at 2025-09-15 20:26:25.843949...
2025-09-15 20:26:43.432 wdl.w:ptcp.t:call-tar_outputs-50.slurm_singularity INFO srun: job 51798208 queued and waiting for resources
2025-09-15 20:26:43.432 wdl.w:ptcp.t:call-tar_outputs-50.slurm_singularity INFO srun: job 51798208 has been allocated resources
2025-09-15 20:26:43.432 wdl.w:ptcp.t:call-tar_outputs-50.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:26:43.980 wdl.w:ptcp.t:call-tar_outputs-50 INFO output :: name: "sample_tarball", value: "m84036_250809_035451_s4.bc2147.tar"
2025-09-15 20:26:44.048 wdl.w:ptcp.t:call-tar_outputs-50 NOTICE done
2025-09-15 20:26:44.051 wdl.w:ptcp NOTICE finish :: job: "call-tar_outputs-50"
2025-09-15 20:26:44.051 wdl.w:ptcp INFO output :: job: "call-tar_outputs-50", values: {"sample_tarball": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-50/out/m84036_250809_035451_s4.bc2147.tar"}
2025-09-15 20:26:44.238 wdl.w:ptcp.w:call-sawfish-78.t:call-run_sawfish.stderr VERBOSE [M::mm_idx_gen::60.282*1.56] collected minimizers
2025-09-15 20:26:44.240 wdl.w:ptcp.w:call-sawfish-78.t:call-run_sawfish.stderr VERBOSE [M::mm_idx_gen::71.510*1.78] sorted minimizers
2025-09-15 20:26:44.240 wdl.w:ptcp.w:call-sawfish-78.t:call-run_sawfish.stderr VERBOSE [M::main::71.512*1.78] loaded/built the index for 195 target sequence(s)
2025-09-15 20:26:44.240 wdl.w:ptcp.w:call-sawfish-78.t:call-run_sawfish.stderr VERBOSE [M::mm_mapopt_update::77.793*1.71] mid_occ = 136
2025-09-15 20:26:44.240 wdl.w:ptcp.w:call-sawfish-78.t:call-run_sawfish.stderr VERBOSE [M::mm_idx_stat] kmer size: 19; skip: 19; is_hpc: 0; #seq: 195
2025-09-15 20:26:44.240 wdl.w:ptcp.w:call-sawfish-78.t:call-run_sawfish.stderr VERBOSE [M::mm_idx_stat::83.068*1.67] distinct minimizers: 214664461 (92.23% are singletons); average occurrences: 1.372; average spacing: 10.529; total length: 3099922541
2025-09-15 20:26:44.240 wdl.w:ptcp.w:call-sawfish-78.t:call-run_sawfish.stderr VERBOSE [M::bam2fq_mainloop] discarded 0 singletons
2025-09-15 20:26:44.240 wdl.w:ptcp.w:call-sawfish-78.t:call-run_sawfish.stderr VERBOSE [M::bam2fq_mainloop] processed 228 reads
2025-09-15 20:26:44.240 wdl.w:ptcp.w:call-sawfish-78.t:call-run_sawfish.stderr VERBOSE [M::worker_pipeline::83.571*1.67] mapped 228 sequences
2025-09-15 20:26:44.240 wdl.w:ptcp.w:call-sawfish-78.t:call-run_sawfish.stderr VERBOSE [M::main] Version: 2.26-r1175
2025-09-15 20:26:44.241 wdl.w:ptcp.w:call-sawfish-78.t:call-run_sawfish.stderr VERBOSE [M::main] CMD: /opt/pacbio/smrttools/install/smrtlink-release_25.1.0.257715/bundles/smrttools/install/smrttools-release_25.1.0.257715/private/thirdparty/minimap2/minimap2_2.26-pacbio2/binwrap/../../../../../private/thirdparty/minimap2/minimap2_2.26-pacbio2/bin/minimap2 -a -y -x map-hifi -Y -E 1,0 /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa -
2025-09-15 20:26:44.241 wdl.w:ptcp.w:call-sawfish-78.t:call-run_sawfish.stderr VERBOSE [M::main] Real time: 83.910 sec; CPU: 140.054 sec; Peak RSS: 11.886 GB
2025-09-15 20:26:44.241 wdl.w:ptcp.w:call-sawfish-78.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:34][sawfish][INFO] Starting sawfish 2.0.3
2025-09-15 20:26:44.241 wdl.w:ptcp.w:call-sawfish-78.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:34][sawfish][INFO] cmdline: sawfish discover --disable-cnv --threads 16 --ref /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa --bam m84036_250809_035451_s4.bc2175.minimap2.bam --output-dir m84036_250809_035451_s4.bc2175_sawfish_discover
2025-09-15 20:26:44.241 wdl.w:ptcp.w:call-sawfish-78.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:34][sawfish][INFO] Running on 16 threads
2025-09-15 20:26:44.241 wdl.w:ptcp.w:call-sawfish-78.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:34][sawfish][INFO] Writing discover settings to file: 'm84036_250809_035451_s4.bc2175_sawfish_discover/discover.settings.json'
2025-09-15 20:26:44.241 wdl.w:ptcp.w:call-sawfish-78.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:34][sawfish][INFO] Reading reference genome from file '/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa'
2025-09-15 20:26:44.241 wdl.w:ptcp.w:call-sawfish-78.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:40][sawfish][INFO] Processing alignment file '/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2175.minimap2.bam'
2025-09-15 20:26:44.241 wdl.w:ptcp.w:call-sawfish-78.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:40][sawfish][INFO] Finished processing all alignments
2025-09-15 20:26:44.241 wdl.w:ptcp.w:call-sawfish-78.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:40][sawfish][INFO] Writing depth bins to binary file: 'm84036_250809_035451_s4.bc2175_sawfish_discover/depth.mpack'
2025-09-15 20:26:44.241 wdl.w:ptcp.w:call-sawfish-78.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:40][sawfish][INFO] Writing max sv depth genome regions to bed file: 'm84036_250809_035451_s4.bc2175_sawfish_discover/max.depth.bed'
2025-09-15 20:26:44.241 wdl.w:ptcp.w:call-sawfish-78.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:40][sawfish][INFO] Completing breakpoint observation clustering
2025-09-15 20:26:44.241 wdl.w:ptcp.w:call-sawfish-78.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:40][sawfish][INFO] Finished breakpoint observation clustering
2025-09-15 20:26:44.241 wdl.w:ptcp.w:call-sawfish-78.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:40][sawfish][INFO] Consolidating adjacent indel candidates
2025-09-15 20:26:44.241 wdl.w:ptcp.w:call-sawfish-78.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:40][sawfish][INFO] Finding large insertion candidates
2025-09-15 20:26:44.241 wdl.w:ptcp.w:call-sawfish-78.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:40][sawfish][INFO] Writing breakpoint_cluster debug bed file: 'm84036_250809_035451_s4.bc2175_sawfish_discover/debug.breakpoint_clusters.bed'
2025-09-15 20:26:44.241 wdl.w:ptcp.w:call-sawfish-78.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:40][sawfish][INFO] Refining SV Candidates
2025-09-15 20:26:44.241 wdl.w:ptcp.w:call-sawfish-78.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:40][sawfish][INFO] Writing debug assembly region bed file: 'm84036_250809_035451_s4.bc2175_sawfish_discover/assembly.regions.bed'
2025-09-15 20:26:44.241 wdl.w:ptcp.w:call-sawfish-78.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:40][sawfish][INFO] Starting refinement of breakpoint evidence clusters
2025-09-15 20:26:44.242 wdl.w:ptcp.w:call-sawfish-78.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:41][sawfish][INFO] Finished refining all breakpoint evidence clusters
2025-09-15 20:26:44.242 wdl.w:ptcp.w:call-sawfish-78.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:41][sawfish][INFO] Writing all contig alignments to bam file: 'm84036_250809_035451_s4.bc2175_sawfish_discover/contig.alignment.bam'
2025-09-15 20:26:44.242 wdl.w:ptcp.w:call-sawfish-78.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:41][sawfish][INFO] Writing candidate structural variants to file: 'm84036_250809_035451_s4.bc2175_sawfish_discover/candidate.sv.bcf'
2025-09-15 20:26:44.242 wdl.w:ptcp.w:call-sawfish-78.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:41][sawfish][INFO] Writing run statistics to file: 'm84036_250809_035451_s4.bc2175_sawfish_discover/run.stats.json'
2025-09-15 20:26:44.242 wdl.w:ptcp.w:call-sawfish-78.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:41][sawfish][INFO] sawfish completed. Total Runtime: 00:00:07.018
2025-09-15 20:26:44.650 wdl.w:ptcp.w:call-paraphase-30.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for f8inv22 for sample m84036_250809_035451_s4.bc2127 at 2025-09-15 20:26:33.286152...
2025-09-15 20:26:44.650 wdl.w:ptcp.w:call-paraphase-30.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for f8inv22 for sample m84036_250809_035451_s4.bc2127 at 2025-09-15 20:26:36.466176...
2025-09-15 20:26:44.650 wdl.w:ptcp.w:call-paraphase-30.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for f8inv22 for sample m84036_250809_035451_s4.bc2127 at 2025-09-15 20:26:36.763390...
2025-09-15 20:26:45.048 wdl.w:ptcp.w:call-sawfish-95.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:42][sawfish][INFO] Processing alignment file '/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2192.minimap2.bam'
2025-09-15 20:26:45.048 wdl.w:ptcp.w:call-sawfish-95.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:42][sawfish][INFO] Finished processing all alignments
2025-09-15 20:26:45.049 wdl.w:ptcp.w:call-sawfish-95.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:42][sawfish][INFO] Writing depth bins to binary file: 'm84036_250809_035451_s4.bc2192_sawfish_discover/depth.mpack'
2025-09-15 20:26:45.049 wdl.w:ptcp.w:call-sawfish-95.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:42][sawfish][INFO] Writing max sv depth genome regions to bed file: 'm84036_250809_035451_s4.bc2192_sawfish_discover/max.depth.bed'
2025-09-15 20:26:45.049 wdl.w:ptcp.w:call-sawfish-95.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:42][sawfish][INFO] Completing breakpoint observation clustering
2025-09-15 20:26:45.049 wdl.w:ptcp.w:call-sawfish-95.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:42][sawfish][INFO] Finished breakpoint observation clustering
2025-09-15 20:26:45.049 wdl.w:ptcp.w:call-sawfish-95.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:42][sawfish][INFO] Consolidating adjacent indel candidates
2025-09-15 20:26:45.049 wdl.w:ptcp.w:call-sawfish-95.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:42][sawfish][INFO] Finding large insertion candidates
2025-09-15 20:26:45.049 wdl.w:ptcp.w:call-sawfish-95.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:42][sawfish][INFO] Writing breakpoint_cluster debug bed file: 'm84036_250809_035451_s4.bc2192_sawfish_discover/debug.breakpoint_clusters.bed'
2025-09-15 20:26:45.049 wdl.w:ptcp.w:call-sawfish-95.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:42][sawfish][INFO] Refining SV Candidates
2025-09-15 20:26:45.049 wdl.w:ptcp.w:call-sawfish-95.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:42][sawfish][INFO] Writing debug assembly region bed file: 'm84036_250809_035451_s4.bc2192_sawfish_discover/assembly.regions.bed'
2025-09-15 20:26:45.049 wdl.w:ptcp.w:call-sawfish-95.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:42][sawfish][INFO] Starting refinement of breakpoint evidence clusters
2025-09-15 20:26:45.049 wdl.w:ptcp.w:call-sawfish-95.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:43][sawfish][INFO] Finished refining all breakpoint evidence clusters
2025-09-15 20:26:45.049 wdl.w:ptcp.w:call-sawfish-95.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:43][sawfish][INFO] Writing all contig alignments to bam file: 'm84036_250809_035451_s4.bc2192_sawfish_discover/contig.alignment.bam'
2025-09-15 20:26:45.049 wdl.w:ptcp.w:call-sawfish-95.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:43][sawfish][INFO] Writing candidate structural variants to file: 'm84036_250809_035451_s4.bc2192_sawfish_discover/candidate.sv.bcf'
2025-09-15 20:26:45.049 wdl.w:ptcp.w:call-sawfish-95.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:43][sawfish][INFO] Writing run statistics to file: 'm84036_250809_035451_s4.bc2192_sawfish_discover/run.stats.json'
2025-09-15 20:26:45.049 wdl.w:ptcp.w:call-sawfish-95.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:43][sawfish][INFO] sawfish completed. Total Runtime: 00:00:08.600
2025-09-15 20:26:45.373 wdl.w:ptcp.w:call-sawfish-93.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:42][sawfish][INFO] Processing alignment file '/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2190.minimap2.bam'
2025-09-15 20:26:45.374 wdl.w:ptcp.w:call-sawfish-93.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:42][sawfish][INFO] Finished processing all alignments
2025-09-15 20:26:45.374 wdl.w:ptcp.w:call-sawfish-93.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:42][sawfish][INFO] Writing depth bins to binary file: 'm84036_250809_035451_s4.bc2190_sawfish_discover/depth.mpack'
2025-09-15 20:26:45.374 wdl.w:ptcp.w:call-sawfish-93.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:42][sawfish][INFO] Writing max sv depth genome regions to bed file: 'm84036_250809_035451_s4.bc2190_sawfish_discover/max.depth.bed'
2025-09-15 20:26:45.374 wdl.w:ptcp.w:call-sawfish-93.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:42][sawfish][INFO] Completing breakpoint observation clustering
2025-09-15 20:26:45.374 wdl.w:ptcp.w:call-sawfish-93.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:42][sawfish][INFO] Finished breakpoint observation clustering
2025-09-15 20:26:45.374 wdl.w:ptcp.w:call-sawfish-93.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:42][sawfish][INFO] Consolidating adjacent indel candidates
2025-09-15 20:26:45.374 wdl.w:ptcp.w:call-sawfish-93.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:42][sawfish][INFO] Finding large insertion candidates
2025-09-15 20:26:45.374 wdl.w:ptcp.w:call-sawfish-93.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:42][sawfish][INFO] Writing breakpoint_cluster debug bed file: 'm84036_250809_035451_s4.bc2190_sawfish_discover/debug.breakpoint_clusters.bed'
2025-09-15 20:26:45.374 wdl.w:ptcp.w:call-sawfish-93.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:42][sawfish][INFO] Refining SV Candidates
2025-09-15 20:26:45.374 wdl.w:ptcp.w:call-sawfish-93.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:42][sawfish][INFO] Writing debug assembly region bed file: 'm84036_250809_035451_s4.bc2190_sawfish_discover/assembly.regions.bed'
2025-09-15 20:26:45.374 wdl.w:ptcp.w:call-sawfish-93.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:42][sawfish][INFO] Starting refinement of breakpoint evidence clusters
2025-09-15 20:26:45.374 wdl.w:ptcp.w:call-sawfish-93.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:42][sawfish][INFO] Finished refining all breakpoint evidence clusters
2025-09-15 20:26:45.374 wdl.w:ptcp.w:call-sawfish-93.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:42][sawfish][INFO] Writing all contig alignments to bam file: 'm84036_250809_035451_s4.bc2190_sawfish_discover/contig.alignment.bam'
2025-09-15 20:26:45.374 wdl.w:ptcp.w:call-sawfish-93.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:42][sawfish][INFO] Writing candidate structural variants to file: 'm84036_250809_035451_s4.bc2190_sawfish_discover/candidate.sv.bcf'
2025-09-15 20:26:45.374 wdl.w:ptcp.w:call-sawfish-93.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:42][sawfish][INFO] Writing run statistics to file: 'm84036_250809_035451_s4.bc2190_sawfish_discover/run.stats.json'
2025-09-15 20:26:45.375 wdl.w:ptcp.w:call-sawfish-93.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:42][sawfish][INFO] sawfish completed. Total Runtime: 00:00:11.264
2025-09-15 20:26:45.851 wdl.w:ptcp.w:call-paraphase-70.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for hbb for sample m84036_250809_035451_s4.bc2167 at 2025-09-15 20:26:44.137020...
2025-09-15 20:26:45.851 wdl.w:ptcp.w:call-paraphase-70.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for hbb for sample m84036_250809_035451_s4.bc2167 at 2025-09-15 20:26:44.137734...
2025-09-15 20:26:45.931 wdl.w:ptcp.w:call-paraphase-18.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for rpgr for sample m84036_250809_035451_s4.bc2115 at 2025-09-15 20:26:18.362828...
2025-09-15 20:26:45.932 wdl.w:ptcp.w:call-paraphase-18.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for rpgr for sample m84036_250809_035451_s4.bc2115 at 2025-09-15 20:26:18.363680...
2025-09-15 20:26:45.932 wdl.w:ptcp.w:call-paraphase-18.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for rpgr for sample m84036_250809_035451_s4.bc2115 at 2025-09-15 20:26:20.446911...
2025-09-15 20:26:45.932 wdl.w:ptcp.w:call-paraphase-18.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for rpgr for sample m84036_250809_035451_s4.bc2115 at 2025-09-15 20:26:21.526908...
2025-09-15 20:26:45.932 wdl.w:ptcp.w:call-paraphase-18.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for rpgr for sample m84036_250809_035451_s4.bc2115 at 2025-09-15 20:26:21.679826...
2025-09-15 20:26:45.932 wdl.w:ptcp.w:call-paraphase-18.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for f8inv22 for sample m84036_250809_035451_s4.bc2115 at 2025-09-15 20:26:41.571459...
2025-09-15 20:26:45.932 wdl.w:ptcp.w:call-paraphase-18.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for f8inv22 for sample m84036_250809_035451_s4.bc2115 at 2025-09-15 20:26:41.572238...
2025-09-15 20:26:46.253 wdl.w:ptcp.w:call-paraphase-27.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for f8inv22 for sample m84036_250809_035451_s4.bc2124 at 2025-09-15 20:26:36.569982...
2025-09-15 20:26:46.254 wdl.w:ptcp.w:call-paraphase-27.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for f8inv22 for sample m84036_250809_035451_s4.bc2124 at 2025-09-15 20:26:39.743043...
2025-09-15 20:26:46.254 wdl.w:ptcp.w:call-paraphase-27.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for f8inv22 for sample m84036_250809_035451_s4.bc2124 at 2025-09-15 20:26:40.005122...
2025-09-15 20:26:46.341 wdl.w:ptcp.w:call-paraphase-58.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for hba for sample m84036_250809_035451_s4.bc2155 at 2025-09-15 20:26:07.253135...
2025-09-15 20:26:46.343 wdl.w:ptcp.w:call-paraphase-58.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for hba for sample m84036_250809_035451_s4.bc2155 at 2025-09-15 20:26:07.944070...
2025-09-15 20:26:46.343 wdl.w:ptcp.w:call-paraphase-58.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for cyp21 for sample m84036_250809_035451_s4.bc2155 at 2025-09-15 20:26:10.489857...
2025-09-15 20:26:46.343 wdl.w:ptcp.w:call-paraphase-58.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for cyp21 for sample m84036_250809_035451_s4.bc2155 at 2025-09-15 20:26:12.103488...
2025-09-15 20:26:47.387 wdl.w:ptcp.w:call-paraphase-30.t:call-run_paraphase INFO output :: name: "paraphase_bam", value: "m84036_250809_035451_s4.bc2127_paraphase/m84036_250809_035451_s4.bc2127.paraphase.bam"
2025-09-15 20:26:47.391 wdl.w:ptcp.w:call-paraphase-30.t:call-run_paraphase INFO output :: name: "paraphase_bam_bai", value: "m84036_250809_035451_s4.bc2127_paraphase/m84036_250809_035451_s4.bc2127.paraphase.bam.bai"
2025-09-15 20:26:47.392 wdl.w:ptcp.w:call-paraphase-30.t:call-run_paraphase INFO output :: name: "paraphase_json", value: "m84036_250809_035451_s4.bc2127_paraphase/m84036_250809_035451_s4.bc2127.paraphase.json"
2025-09-15 20:26:47.396 wdl.w:ptcp.w:call-paraphase-30.t:call-run_paraphase INFO output :: name: "paraphase_vcfs", value: ["/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2127_paraphase/m84036_250809_035451_s4.bc2127_paraphase_vcfs/m84036_250809_035451_s4.bc2127_cyp21.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2127_paraphase/m84036_250809_035451_s4.bc2127_paraphase_vcfs/m84036_250809_035451_s4.bc2127_f8inv1.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2127_paraphase/m84036_250809_035451_s4.bc2127_paraphase_vcfs/m84036_250809_035451_s4.bc2127_f8inv22.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2127_paraphase/m84036_250809_035451_s4.bc2127_paraphase_vcfs/m84036_250809_035451_s4.bc2127_gba.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2127_paraphase/m84036_250809_035451_s4.bc2127_paraphase_vcfs/m84036_250809_035451_s4.bc2127_hba.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2127_paraphase/m84036_250809_035451_s4.bc2127_paraphase_vcfs/m84036_250809_035451_s4.bc2127_hbb.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2127_paraphase/m84036_250809_035451_s4.bc2127_paraphase_vcfs/m84036_250809_035451_s4.bc2127_rpgr.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2127_paraphase/m84036_250809_035451_s4.bc2127_paraphase_vcfs/m84036_250809_035451_s4.bc2127_smn1.vcf"]
2025-09-15 20:26:47.400 wdl.w:ptcp.w:call-paraphase-30.t:call-run_paraphase INFO output :: name: "havanno_json", value: "m84036_250809_035451_s4.bc2127.havanno.json"
2025-09-15 20:26:47.545 wdl.w:ptcp.w:call-paraphase-30.t:call-run_paraphase NOTICE done
2025-09-15 20:26:47.550 wdl.w:ptcp.w:call-paraphase-30 NOTICE finish :: job: "call-run_paraphase"
2025-09-15 20:26:47.550 wdl.w:ptcp.w:call-paraphase-30 INFO output :: job: "call-run_paraphase", values: {"havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-30/call-run_paraphase/out/m84036_250809_035451_s4.bc2127.havanno.json", "paraphase_vcfs": ["/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-30/call-run_paraphase/out/m84036_250809_035451_s4.bc2127_paraphase/m84036_250809_035451_s4.bc2127_paraphase_vcfs/m84036_250809_035451_s4.bc2127_cyp21.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-30/call-run_paraphase/out/m84036_250809_035451_s4.bc2127_paraphase/m84036_250809_035451_s4.bc2127_paraphase_vcfs/m84036_250809_035451_s4.bc2127_f8inv1.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-30/call-run_paraphase/out/m84036_250809_035451_s4.bc2127_paraphase/m84036_250809_035451_s4.bc2127_paraphase_vcfs/m84036_250809_035451_s4.bc2127_f8inv22.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-30/call-run_paraphase/out/m84036_250809_035451_s4.bc2127_paraphase/m84036_250809_035451_s4.bc2127_paraphase_vcfs/m84036_250809_035451_s4.bc2127_gba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-30/call-run_paraphase/out/m84036_250809_035451_s4.bc2127_paraphase/m84036_250809_035451_s4.bc2127_paraphase_vcfs/m84036_250809_035451_s4.bc2127_hba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-30/call-run_paraphase/out/m84036_250809_035451_s4.bc2127_paraphase/m84036_250809_035451_s4.bc2127_paraphase_vcfs/m84036_250809_035451_s4.bc2127_hbb.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-30/call-run_paraphase/out/m84036_250809_035451_s4.bc2127_paraphase/m84036_250809_035451_s4.bc2127_paraphase_vcfs/m84036_250809_035451_s4.bc2127_rpgr.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-30/call-run_paraphase/out/m84036_250809_035451_s4.bc2127_paraphase/m84036_250809_035451_s4.bc2127_paraphase_vcfs/m84036_250809_035451_s4.bc2127_smn1.vcf"], "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-30/call-run_paraphase/out/m84036_250809_035451_s4.bc2127_paraphase/m84036_250809_035451_s4.bc2127.paraphase.json", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-30/call-run_paraphase/out/m84036_250809_035451_s4.bc2127_paraphase/m84036_250809_035451_s4.bc2127.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-30/call-run_paraphase/out/m84036_250809_035451_s4.bc2127_paraphase/m84036_250809_035451_s4.bc2127.paraphase.bam"}
2025-09-15 20:26:47.551 wdl.w:ptcp.w:call-paraphase-30 NOTICE ready :: job: "call-call_f8", callee: "call_f8"
2025-09-15 20:26:47.551 wdl.w:ptcp.w:call-paraphase-30 INFO input :: job: "call-call_f8", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "out_prefix": "m84036_250809_035451_s4.bc2127", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-30/call-run_paraphase/out/m84036_250809_035451_s4.bc2127_paraphase/m84036_250809_035451_s4.bc2127.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-30/call-run_paraphase/out/m84036_250809_035451_s4.bc2127_paraphase/m84036_250809_035451_s4.bc2127.paraphase.bam", "sex": "F"}
2025-09-15 20:26:47.551 wdl.w:ptcp.w:call-paraphase-30 INFO visit :: node: "output-havanno_json", values: {"havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-30/call-run_paraphase/out/m84036_250809_035451_s4.bc2127.havanno.json"}
2025-09-15 20:26:47.551 wdl.w:ptcp.w:call-paraphase-30 INFO visit :: node: "output-paraphase_bam", values: {"paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-30/call-run_paraphase/out/m84036_250809_035451_s4.bc2127_paraphase/m84036_250809_035451_s4.bc2127.paraphase.bam"}
2025-09-15 20:26:47.552 wdl.w:ptcp.w:call-paraphase-30 INFO visit :: node: "output-paraphase_bam_bai", values: {"paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-30/call-run_paraphase/out/m84036_250809_035451_s4.bc2127_paraphase/m84036_250809_035451_s4.bc2127.paraphase.bam.bai"}
2025-09-15 20:26:47.552 wdl.w:ptcp.w:call-paraphase-30 INFO visit :: node: "output-paraphase_json", values: {"paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-30/call-run_paraphase/out/m84036_250809_035451_s4.bc2127_paraphase/m84036_250809_035451_s4.bc2127.paraphase.json"}
2025-09-15 20:26:47.552 wdl.w:ptcp.w:call-paraphase-30 INFO visit :: node: "output-paraphase_vcfs", values: {"paraphase_vcfs": ["/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-30/call-run_paraphase/out/m84036_250809_035451_s4.bc2127_paraphase/m84036_250809_035451_s4.bc2127_paraphase_vcfs/m84036_250809_035451_s4.bc2127_cyp21.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-30/call-run_paraphase/out/m84036_250809_035451_s4.bc2127_paraphase/m84036_250809_035451_s4.bc2127_paraphase_vcfs/m84036_250809_035451_s4.bc2127_f8inv1.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-30/call-run_paraphase/out/m84036_250809_035451_s4.bc2127_paraphase/m84036_250809_035451_s4.bc2127_paraphase_vcfs/m84036_250809_035451_s4.bc2127_f8inv22.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-30/call-run_paraphase/out/m84036_250809_035451_s4.bc2127_paraphase/m84036_250809_035451_s4.bc2127_paraphase_vcfs/m84036_250809_035451_s4.bc2127_gba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-30/call-run_paraphase/out/m84036_250809_035451_s4.bc2127_paraphase/m84036_250809_035451_s4.bc2127_paraphase_vcfs/m84036_250809_035451_s4.bc2127_hba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-30/call-run_paraphase/out/m84036_250809_035451_s4.bc2127_paraphase/m84036_250809_035451_s4.bc2127_paraphase_vcfs/m84036_250809_035451_s4.bc2127_hbb.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-30/call-run_paraphase/out/m84036_250809_035451_s4.bc2127_paraphase/m84036_250809_035451_s4.bc2127_paraphase_vcfs/m84036_250809_035451_s4.bc2127_rpgr.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-30/call-run_paraphase/out/m84036_250809_035451_s4.bc2127_paraphase/m84036_250809_035451_s4.bc2127_paraphase_vcfs/m84036_250809_035451_s4.bc2127_smn1.vcf"]}
2025-09-15 20:26:47.557 wdl.w:ptcp.w:call-paraphase-30.t:call-call_f8 NOTICE task setup :: name: "call_f8", source: "./paraphase.wdl", line: 232, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-30/call-call_f8", thread: 140610342200896
2025-09-15 20:26:47.576 wdl.w:ptcp.w:call-paraphase-30.t:call-call_f8 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:26:47.576 wdl.w:ptcp.w:call-paraphase-30.t:call-call_f8 INFO input :: name: "genome_version", value: "38"
2025-09-15 20:26:47.576 wdl.w:ptcp.w:call-paraphase-30.t:call-call_f8 INFO input :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2127"
2025-09-15 20:26:47.576 wdl.w:ptcp.w:call-paraphase-30.t:call-call_f8 INFO input :: name: "paraphase_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2127.paraphase.bam.bai"
2025-09-15 20:26:47.576 wdl.w:ptcp.w:call-paraphase-30.t:call-call_f8 INFO input :: name: "paraphase_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2127.paraphase.bam"
2025-09-15 20:26:47.576 wdl.w:ptcp.w:call-paraphase-30.t:call-call_f8 INFO input :: name: "sex", value: "F"
2025-09-15 20:26:47.578 wdl.w:ptcp.w:call-paraphase-30.t:call-call_f8 INFO eval :: name: "threads", value: 1
2025-09-15 20:26:47.578 wdl.w:ptcp.w:call-paraphase-30.t:call-call_f8 INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:26:47.578 wdl.w:ptcp.w:call-paraphase-30.t:call-call_f8 INFO eval :: name: "disk_size", value: 11
2025-09-15 20:26:47.578 wdl.w:ptcp.w:call-paraphase-30.t:call-call_f8 INFO eval :: name: "sample_sex", value: "F"
2025-09-15 20:26:47.578 wdl.w:ptcp.w:call-paraphase-30.t:call-call_f8 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:26:47.579 wdl.w:ptcp.w:call-paraphase-30.t:call-call_f8 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:26:47.579 wdl.w:ptcp.w:call-paraphase-30.t:call-call_f8 INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:26:47.579 wdl.w:ptcp.w:call-paraphase-30.t:call-call_f8 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:26:47.629 wdl.w:ptcp.w:call-paraphase-30.t:call-call_f8 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 8, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-30/call-call_f8/_singularity_tmpdir_4h7ubr4g"
2025-09-15 20:26:47.629 wdl.w:ptcp.w:call-paraphase-30.t:call-call_f8 INFO Slurm invocation: srun --job-name call-call_f8 --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-30/call-call_f8/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-30/call-call_f8/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-30/call-call_f8/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-30/call-call_f8/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-30/call-run_paraphase/out/m84036_250809_035451_s4.bc2127_paraphase/m84036_250809_035451_s4.bc2127.paraphase.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2127.paraphase.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-30/call-run_paraphase/out/m84036_250809_035451_s4.bc2127_paraphase/m84036_250809_035451_s4.bc2127.paraphase.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2127.paraphase.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-30/call-call_f8/_singularity_tmpdir_4h7ubr4g/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-30/call-call_f8/_singularity_tmpdir_4h7ubr4g/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:26:47.654 wdl.w:ptcp.w:call-paraphase-30.t:call-call_f8 NOTICE slurm_singularity run :: pid: 1207848, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-30/call-call_f8/slurm_singularity.log.txt"
2025-09-15 20:26:47.704 wdl.w:ptcp.w:call-sawfish-93.t:call-run_sawfish INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2190_sawfish/m84036_250809_035451_s4.bc2190.sv.vcf.gz"
2025-09-15 20:26:47.708 wdl.w:ptcp.w:call-sawfish-93.t:call-run_sawfish INFO output :: name: "vcf_tbi", value: "m84036_250809_035451_s4.bc2190_sawfish/m84036_250809_035451_s4.bc2190.sv.vcf.gz.tbi"
2025-09-15 20:26:47.709 wdl.w:ptcp.w:call-sawfish-93.t:call-run_sawfish INFO output :: name: "minimap2_bam", value: "m84036_250809_035451_s4.bc2190.minimap2.bam"
2025-09-15 20:26:47.710 wdl.w:ptcp.w:call-sawfish-93.t:call-run_sawfish INFO output :: name: "minimap2_bam_bai", value: "m84036_250809_035451_s4.bc2190.minimap2.bam.bai"
2025-09-15 20:26:47.864 wdl.w:ptcp.w:call-sawfish-93.t:call-run_sawfish NOTICE done
2025-09-15 20:26:47.872 wdl.w:ptcp.w:call-sawfish-93 NOTICE finish :: job: "call-run_sawfish"
2025-09-15 20:26:47.872 wdl.w:ptcp.w:call-sawfish-93 INFO output :: job: "call-run_sawfish", values: {"minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-93/call-run_sawfish/out/m84036_250809_035451_s4.bc2190.minimap2.bam.bai", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-93/call-run_sawfish/out/m84036_250809_035451_s4.bc2190.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-93/call-run_sawfish/out/m84036_250809_035451_s4.bc2190_sawfish/m84036_250809_035451_s4.bc2190.sv.vcf.gz.tbi", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-93/call-run_sawfish/out/m84036_250809_035451_s4.bc2190_sawfish/m84036_250809_035451_s4.bc2190.sv.vcf.gz"}
2025-09-15 20:26:47.873 wdl.w:ptcp.w:call-sawfish-93 INFO visit :: node: "output-minimap2_bam", values: {"minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-93/call-run_sawfish/out/m84036_250809_035451_s4.bc2190.minimap2.bam"}
2025-09-15 20:26:47.873 wdl.w:ptcp.w:call-sawfish-93 INFO visit :: node: "output-minimap2_bam_bai", values: {"minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-93/call-run_sawfish/out/m84036_250809_035451_s4.bc2190.minimap2.bam.bai"}
2025-09-15 20:26:47.873 wdl.w:ptcp.w:call-sawfish-93 INFO visit :: node: "output-vcf", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-93/call-run_sawfish/out/m84036_250809_035451_s4.bc2190_sawfish/m84036_250809_035451_s4.bc2190.sv.vcf.gz"}
2025-09-15 20:26:47.873 wdl.w:ptcp.w:call-sawfish-93 INFO visit :: node: "output-vcf_tbi", values: {"vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-93/call-run_sawfish/out/m84036_250809_035451_s4.bc2190_sawfish/m84036_250809_035451_s4.bc2190.sv.vcf.gz.tbi"}
2025-09-15 20:26:47.873 wdl.w:ptcp.w:call-sawfish-93 INFO visit :: node: "outputs", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-93/call-run_sawfish/out/m84036_250809_035451_s4.bc2190_sawfish/m84036_250809_035451_s4.bc2190.sv.vcf.gz", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-93/call-run_sawfish/out/m84036_250809_035451_s4.bc2190.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-93/call-run_sawfish/out/m84036_250809_035451_s4.bc2190_sawfish/m84036_250809_035451_s4.bc2190.sv.vcf.gz.tbi", "minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-93/call-run_sawfish/out/m84036_250809_035451_s4.bc2190.minimap2.bam.bai"}
2025-09-15 20:26:47.919 wdl.w:ptcp.w:call-sawfish-93 NOTICE done
2025-09-15 20:26:47.925 wdl.w:ptcp NOTICE finish :: job: "call-sawfish-93"
2025-09-15 20:26:47.925 wdl.w:ptcp INFO output :: job: "call-sawfish-93", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-93/out/m84036_250809_035451_s4.bc2190_sawfish/m84036_250809_035451_s4.bc2190.sv.vcf.gz", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-93/out/m84036_250809_035451_s4.bc2190.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-93/out/m84036_250809_035451_s4.bc2190_sawfish/m84036_250809_035451_s4.bc2190.sv.vcf.gz.tbi", "minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-93/out/m84036_250809_035451_s4.bc2190.minimap2.bam.bai"}
2025-09-15 20:26:47.926 wdl.w:ptcp NOTICE ready :: job: "call-tar_outputs-93", callee: "tar_outputs"
2025-09-15 20:26:47.926 wdl.w:ptcp INFO input :: job: "call-tar_outputs-93", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "sawfish_vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-93/out/m84036_250809_035451_s4.bc2190_sawfish/m84036_250809_035451_s4.bc2190.sv.vcf.gz.tbi", "sawfish_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-93/out/m84036_250809_035451_s4.bc2190_sawfish/m84036_250809_035451_s4.bc2190.sv.vcf.gz", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-93/out/m84036_250809_035451_s4.bc2190.f8inversion.json", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-93/out/m84036_250809_035451_s4.bc2190_paraphase/m84036_250809_035451_s4.bc2190.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-93/out/m84036_250809_035451_s4.bc2190_paraphase/m84036_250809_035451_s4.bc2190.paraphase.bam", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-93/out/m84036_250809_035451_s4.bc2190_paraphase/m84036_250809_035451_s4.bc2190.paraphase.json", "trgt_spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-93/out/m84036_250809_035451_s4.bc2190.trgt.sorted.spanning.bam.bai", "trgt_spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-93/out/m84036_250809_035451_s4.bc2190.trgt.sorted.spanning.bam", "trgt_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-93/out/m84036_250809_035451_s4.bc2190.trgt.vcf", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-93/out/m84036_250809_035451_s4.bc2190.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-93/out/m84036_250809_035451_s4.bc2190.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2190"}
2025-09-15 20:26:47.933 wdl.w:ptcp.t:call-tar_outputs-93 NOTICE task setup :: name: "tar_outputs", source: "./common.wdl", line: 279, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-93", thread: 140613580211776
2025-09-15 20:26:47.954 wdl.w:ptcp.t:call-tar_outputs-93 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:26:47.954 wdl.w:ptcp.t:call-tar_outputs-93 INFO input :: name: "sawfish_vcf_tbi", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2190.sv.vcf.gz.tbi"
2025-09-15 20:26:47.954 wdl.w:ptcp.t:call-tar_outputs-93 INFO input :: name: "sawfish_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2190.sv.vcf.gz"
2025-09-15 20:26:47.954 wdl.w:ptcp.t:call-tar_outputs-93 INFO input :: name: "f8_json", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2190.f8inversion.json"
2025-09-15 20:26:47.954 wdl.w:ptcp.t:call-tar_outputs-93 INFO input :: name: "paraphase_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2190.paraphase.bam.bai"
2025-09-15 20:26:47.954 wdl.w:ptcp.t:call-tar_outputs-93 INFO input :: name: "paraphase_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2190.paraphase.bam"
2025-09-15 20:26:47.954 wdl.w:ptcp.t:call-tar_outputs-93 INFO input :: name: "paraphase_json", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2190.paraphase.json"
2025-09-15 20:26:47.954 wdl.w:ptcp.t:call-tar_outputs-93 INFO input :: name: "trgt_spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2190.trgt.sorted.spanning.bam.bai"
2025-09-15 20:26:47.954 wdl.w:ptcp.t:call-tar_outputs-93 INFO input :: name: "trgt_spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2190.trgt.sorted.spanning.bam"
2025-09-15 20:26:47.954 wdl.w:ptcp.t:call-tar_outputs-93 INFO input :: name: "trgt_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2190.trgt.vcf"
2025-09-15 20:26:47.954 wdl.w:ptcp.t:call-tar_outputs-93 INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2190.mapped.bam.bai"
2025-09-15 20:26:47.954 wdl.w:ptcp.t:call-tar_outputs-93 INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2190.mapped.bam"
2025-09-15 20:26:47.954 wdl.w:ptcp.t:call-tar_outputs-93 INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2190"
2025-09-15 20:26:47.955 wdl.w:ptcp.t:call-tar_outputs-93 INFO eval :: name: "threads", value: 1
2025-09-15 20:26:47.955 wdl.w:ptcp.t:call-tar_outputs-93 INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:26:47.955 wdl.w:ptcp.t:call-tar_outputs-93 INFO eval :: name: "disk_size", value: 6
2025-09-15 20:26:47.955 wdl.w:ptcp.t:call-tar_outputs-93 INFO eval :: name: "output_tarball", value: "m84036_250809_035451_s4.bc2190.tar"
2025-09-15 20:26:47.955 wdl.w:ptcp.t:call-tar_outputs-93 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:26:47.955 wdl.w:ptcp.t:call-tar_outputs-93 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:26:47.956 wdl.w:ptcp.t:call-tar_outputs-93 INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:26:47.956 wdl.w:ptcp.t:call-tar_outputs-93 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:26:48.039 wdl.w:ptcp.t:call-tar_outputs-93 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 17, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-93/_singularity_tmpdir_uqkzwuku"
2025-09-15 20:26:48.039 wdl.w:ptcp.t:call-tar_outputs-93 INFO Slurm invocation: srun --job-name call-tar_outputs-93 --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-93/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-93/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-93/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-93/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-93/out/m84036_250809_035451_s4.bc2190.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2190.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-93/out/m84036_250809_035451_s4.bc2190.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2190.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-93/out/m84036_250809_035451_s4.bc2190.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2190.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-93/out/m84036_250809_035451_s4.bc2190_paraphase/m84036_250809_035451_s4.bc2190.paraphase.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2190.paraphase.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-93/out/m84036_250809_035451_s4.bc2190_paraphase/m84036_250809_035451_s4.bc2190.paraphase.json:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2190.paraphase.json:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-93/out/m84036_250809_035451_s4.bc2190_paraphase/m84036_250809_035451_s4.bc2190.paraphase.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2190.paraphase.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-93/out/m84036_250809_035451_s4.bc2190.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2190.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-93/out/m84036_250809_035451_s4.bc2190.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2190.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-93/out/m84036_250809_035451_s4.bc2190.f8inversion.json:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2190.f8inversion.json:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-93/out/m84036_250809_035451_s4.bc2190_sawfish/m84036_250809_035451_s4.bc2190.sv.vcf.gz.tbi:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2190.sv.vcf.gz.tbi:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-93/out/m84036_250809_035451_s4.bc2190_sawfish/m84036_250809_035451_s4.bc2190.sv.vcf.gz:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2190.sv.vcf.gz:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-93/_singularity_tmpdir_uqkzwuku/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-93/_singularity_tmpdir_uqkzwuku/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:26:48.042 wdl.w:ptcp.w:call-paraphase-95.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for cyp21 for sample m84036_250809_035451_s4.bc2192 at 2025-09-15 20:26:42.393206...
2025-09-15 20:26:48.042 wdl.w:ptcp.w:call-paraphase-95.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for gba for sample m84036_250809_035451_s4.bc2192 at 2025-09-15 20:26:42.981021...
2025-09-15 20:26:48.042 wdl.w:ptcp.w:call-paraphase-95.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for cyp21 for sample m84036_250809_035451_s4.bc2192 at 2025-09-15 20:26:43.488566...
2025-09-15 20:26:48.042 wdl.w:ptcp.w:call-paraphase-95.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for gba for sample m84036_250809_035451_s4.bc2192 at 2025-09-15 20:26:43.607766...
2025-09-15 20:26:48.043 wdl.w:ptcp.w:call-paraphase-95.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for f8inv1 for sample m84036_250809_035451_s4.bc2192 at 2025-09-15 20:26:44.226107...
2025-09-15 20:26:48.043 wdl.w:ptcp.w:call-paraphase-95.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for f8inv1 for sample m84036_250809_035451_s4.bc2192 at 2025-09-15 20:26:44.226257...
2025-09-15 20:26:48.058 wdl.w:ptcp.t:call-tar_outputs-93 NOTICE slurm_singularity run :: pid: 1207851, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-93/slurm_singularity.log.txt"
2025-09-15 20:26:48.088 wdl.w:ptcp.w:call-sawfish-95.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:43][sawfish][INFO] Starting sawfish 2.0.3
2025-09-15 20:26:48.088 wdl.w:ptcp.w:call-sawfish-95.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:43][sawfish][INFO] cmdline: sawfish joint-call --threads 16 --sample m84036_250809_035451_s4.bc2192_sawfish_discover --output-dir m84036_250809_035451_s4.bc2192_sawfish
2025-09-15 20:26:48.089 wdl.w:ptcp.w:call-sawfish-95.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:43][sawfish][INFO] Running on 16 threads
2025-09-15 20:26:48.089 wdl.w:ptcp.w:call-sawfish-95.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:43][sawfish][INFO] Reading reference genome from file '/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa'
2025-09-15 20:26:48.089 wdl.w:ptcp.w:call-sawfish-95.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:46][sawfish][INFO] Reading sawfish-discover results from 1 samples
2025-09-15 20:26:48.089 wdl.w:ptcp.w:call-sawfish-95.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:46][sawfish][INFO] Writing depth track to bigwig file: 'm84036_250809_035451_s4.bc2192_sawfish/samples/sample0001_UnknownSampleName/depth.bw'
2025-09-15 20:26:48.089 wdl.w:ptcp.w:call-sawfish-95.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:47][sawfish][INFO] Merging SV haplotypes
2025-09-15 20:26:48.089 wdl.w:ptcp.w:call-sawfish-95.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:47][sawfish][INFO] Finished merging SV haplotypes across samples
2025-09-15 20:26:48.089 wdl.w:ptcp.w:call-sawfish-95.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:47][sawfish][INFO] Writing merged contig alignments to bam file: 'm84036_250809_035451_s4.bc2192_sawfish/contig.alignment.bam'
2025-09-15 20:26:48.089 wdl.w:ptcp.w:call-sawfish-95.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:47][sawfish][INFO] Starting SV candidate cluster genotyping
2025-09-15 20:26:48.089 wdl.w:ptcp.w:call-sawfish-95.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:47][sawfish][INFO] Finished genotyping all SV candidate clusters
2025-09-15 20:26:48.089 wdl.w:ptcp.w:call-sawfish-95.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:47][sawfish][INFO] Starting joint CNV/SV refinement
2025-09-15 20:26:48.089 wdl.w:ptcp.w:call-sawfish-95.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:47][sawfish][INFO] Merged 0 CNVs into corresponding breakpoint-based SVs
2025-09-15 20:26:48.089 wdl.w:ptcp.w:call-sawfish-95.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:47][sawfish][INFO] Writing genotyped structural variants to file: 'm84036_250809_035451_s4.bc2192_sawfish/genotyped.sv.vcf.gz'
2025-09-15 20:26:48.089 wdl.w:ptcp.w:call-sawfish-95.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:47][sawfish][INFO] Writing run statistics to file: 'm84036_250809_035451_s4.bc2192_sawfish/run.stats.json'
2025-09-15 20:26:48.089 wdl.w:ptcp.w:call-sawfish-95.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:47][sawfish][INFO] sawfish completed. Total Runtime: 00:00:04.509
2025-09-15 20:26:48.147 wdl.w:ptcp.w:call-sawfish-95.t:call-run_sawfish INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2192_sawfish/m84036_250809_035451_s4.bc2192.sv.vcf.gz"
2025-09-15 20:26:48.155 wdl.w:ptcp.w:call-sawfish-95.t:call-run_sawfish INFO output :: name: "vcf_tbi", value: "m84036_250809_035451_s4.bc2192_sawfish/m84036_250809_035451_s4.bc2192.sv.vcf.gz.tbi"
2025-09-15 20:26:48.157 wdl.w:ptcp.w:call-sawfish-95.t:call-run_sawfish INFO output :: name: "minimap2_bam", value: "m84036_250809_035451_s4.bc2192.minimap2.bam"
2025-09-15 20:26:48.181 wdl.w:ptcp.w:call-sawfish-95.t:call-run_sawfish INFO output :: name: "minimap2_bam_bai", value: "m84036_250809_035451_s4.bc2192.minimap2.bam.bai"
2025-09-15 20:26:48.330 wdl.w:ptcp.w:call-sawfish-95.t:call-run_sawfish NOTICE done
2025-09-15 20:26:48.337 wdl.w:ptcp.w:call-sawfish-95 NOTICE finish :: job: "call-run_sawfish"
2025-09-15 20:26:48.337 wdl.w:ptcp.w:call-sawfish-95 INFO output :: job: "call-run_sawfish", values: {"minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-95/call-run_sawfish/out/m84036_250809_035451_s4.bc2192.minimap2.bam.bai", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-95/call-run_sawfish/out/m84036_250809_035451_s4.bc2192.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-95/call-run_sawfish/out/m84036_250809_035451_s4.bc2192_sawfish/m84036_250809_035451_s4.bc2192.sv.vcf.gz.tbi", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-95/call-run_sawfish/out/m84036_250809_035451_s4.bc2192_sawfish/m84036_250809_035451_s4.bc2192.sv.vcf.gz"}
2025-09-15 20:26:48.337 wdl.w:ptcp.w:call-sawfish-95 INFO visit :: node: "output-minimap2_bam", values: {"minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-95/call-run_sawfish/out/m84036_250809_035451_s4.bc2192.minimap2.bam"}
2025-09-15 20:26:48.337 wdl.w:ptcp.w:call-sawfish-95 INFO visit :: node: "output-minimap2_bam_bai", values: {"minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-95/call-run_sawfish/out/m84036_250809_035451_s4.bc2192.minimap2.bam.bai"}
2025-09-15 20:26:48.337 wdl.w:ptcp.w:call-sawfish-95 INFO visit :: node: "output-vcf", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-95/call-run_sawfish/out/m84036_250809_035451_s4.bc2192_sawfish/m84036_250809_035451_s4.bc2192.sv.vcf.gz"}
2025-09-15 20:26:48.337 wdl.w:ptcp.w:call-sawfish-95 INFO visit :: node: "output-vcf_tbi", values: {"vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-95/call-run_sawfish/out/m84036_250809_035451_s4.bc2192_sawfish/m84036_250809_035451_s4.bc2192.sv.vcf.gz.tbi"}
2025-09-15 20:26:48.337 wdl.w:ptcp.w:call-sawfish-95 INFO visit :: node: "outputs", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-95/call-run_sawfish/out/m84036_250809_035451_s4.bc2192_sawfish/m84036_250809_035451_s4.bc2192.sv.vcf.gz", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-95/call-run_sawfish/out/m84036_250809_035451_s4.bc2192.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-95/call-run_sawfish/out/m84036_250809_035451_s4.bc2192_sawfish/m84036_250809_035451_s4.bc2192.sv.vcf.gz.tbi", "minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-95/call-run_sawfish/out/m84036_250809_035451_s4.bc2192.minimap2.bam.bai"}
2025-09-15 20:26:48.388 wdl.w:ptcp.w:call-sawfish-95 NOTICE done
2025-09-15 20:26:48.396 wdl.w:ptcp NOTICE finish :: job: "call-sawfish-95"
2025-09-15 20:26:48.396 wdl.w:ptcp INFO output :: job: "call-sawfish-95", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-95/out/m84036_250809_035451_s4.bc2192_sawfish/m84036_250809_035451_s4.bc2192.sv.vcf.gz", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-95/out/m84036_250809_035451_s4.bc2192.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-95/out/m84036_250809_035451_s4.bc2192_sawfish/m84036_250809_035451_s4.bc2192.sv.vcf.gz.tbi", "minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-95/out/m84036_250809_035451_s4.bc2192.minimap2.bam.bai"}
2025-09-15 20:26:48.662 wdl.w:ptcp.w:call-paraphase-30.t:call-call_f8.slurm_singularity INFO srun: job 51798209 queued and waiting for resources
2025-09-15 20:26:48.662 wdl.w:ptcp.w:call-paraphase-30.t:call-call_f8.slurm_singularity INFO srun: job 51798209 has been allocated resources
2025-09-15 20:26:48.662 wdl.w:ptcp.w:call-paraphase-30.t:call-call_f8.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:26:48.887 wdl.w:ptcp.w:call-paraphase-70.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for hbb for sample m84036_250809_035451_s4.bc2167 at 2025-09-15 20:26:45.594829...
2025-09-15 20:26:49.061 wdl.w:ptcp.t:call-tar_outputs-93.stderr VERBOSE tar: Removing leading `/' from member names
2025-09-15 20:26:49.061 wdl.w:ptcp.t:call-tar_outputs-93.stderr VERBOSE tar: Removing leading `/' from hard link targets
2025-09-15 20:26:49.070 wdl.w:ptcp.t:call-tar_outputs-93.slurm_singularity INFO srun: job 51798210 queued and waiting for resources
2025-09-15 20:26:49.070 wdl.w:ptcp.t:call-tar_outputs-93.slurm_singularity INFO srun: job 51798210 has been allocated resources
2025-09-15 20:26:49.070 wdl.w:ptcp.t:call-tar_outputs-93.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:26:49.102 wdl.w:ptcp.t:call-tar_outputs-93 INFO output :: name: "sample_tarball", value: "m84036_250809_035451_s4.bc2190.tar"
2025-09-15 20:26:49.157 wdl.w:ptcp.t:call-tar_outputs-93 NOTICE done
2025-09-15 20:26:49.169 wdl.w:ptcp.w:call-paraphase-94.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for hba for sample m84036_250809_035451_s4.bc2191 at 2025-09-15 20:26:42.159100...
2025-09-15 20:26:49.170 wdl.w:ptcp.w:call-paraphase-94.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for hba for sample m84036_250809_035451_s4.bc2191 at 2025-09-15 20:26:42.632276...
2025-09-15 20:26:49.172 wdl.w:ptcp NOTICE finish :: job: "call-tar_outputs-93"
2025-09-15 20:26:49.172 wdl.w:ptcp INFO output :: job: "call-tar_outputs-93", values: {"sample_tarball": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-93/out/m84036_250809_035451_s4.bc2190.tar"}
2025-09-15 20:26:49.315 wdl.w:ptcp.w:call-sawfish-78.t:call-run_sawfish INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2175_sawfish/m84036_250809_035451_s4.bc2175.sv.vcf.gz"
2025-09-15 20:26:49.320 wdl.w:ptcp.w:call-paraphase-30.t:call-call_f8 INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2127.f8inversion.vcf"
2025-09-15 20:26:49.321 wdl.w:ptcp.w:call-sawfish-78.t:call-run_sawfish INFO output :: name: "vcf_tbi", value: "m84036_250809_035451_s4.bc2175_sawfish/m84036_250809_035451_s4.bc2175.sv.vcf.gz.tbi"
2025-09-15 20:26:49.323 wdl.w:ptcp.w:call-paraphase-30.t:call-call_f8 INFO output :: name: "json", value: "m84036_250809_035451_s4.bc2127.f8inversion.json"
2025-09-15 20:26:49.323 wdl.w:ptcp.w:call-sawfish-78.t:call-run_sawfish INFO output :: name: "minimap2_bam", value: "m84036_250809_035451_s4.bc2175.minimap2.bam"
2025-09-15 20:26:49.325 wdl.w:ptcp.w:call-sawfish-78.t:call-run_sawfish INFO output :: name: "minimap2_bam_bai", value: "m84036_250809_035451_s4.bc2175.minimap2.bam.bai"
2025-09-15 20:26:49.381 wdl.w:ptcp.w:call-paraphase-30.t:call-call_f8 NOTICE done
2025-09-15 20:26:49.389 wdl.w:ptcp.w:call-paraphase-86.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for smn1 for sample m84036_250809_035451_s4.bc2183 at 2025-09-15 20:26:19.893206...
2025-09-15 20:26:49.389 wdl.w:ptcp.w:call-paraphase-86.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for hba for sample m84036_250809_035451_s4.bc2183 at 2025-09-15 20:26:33.235600...
2025-09-15 20:26:49.389 wdl.w:ptcp.w:call-paraphase-86.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for hba for sample m84036_250809_035451_s4.bc2183 at 2025-09-15 20:26:34.152476...
2025-09-15 20:26:49.427 wdl.w:ptcp.w:call-paraphase-30 NOTICE finish :: job: "call-call_f8"
2025-09-15 20:26:49.427 wdl.w:ptcp.w:call-paraphase-30 INFO output :: job: "call-call_f8", values: {"json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-30/call-call_f8/out/m84036_250809_035451_s4.bc2127.f8inversion.json", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-30/call-call_f8/out/m84036_250809_035451_s4.bc2127.f8inversion.vcf"}
2025-09-15 20:26:49.428 wdl.w:ptcp.w:call-paraphase-30 INFO visit :: node: "output-f8_json", values: {"f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-30/call-call_f8/out/m84036_250809_035451_s4.bc2127.f8inversion.json"}
2025-09-15 20:26:49.428 wdl.w:ptcp.w:call-paraphase-30 INFO visit :: node: "output-f8_vcf", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-30/call-call_f8/out/m84036_250809_035451_s4.bc2127.f8inversion.vcf"}
2025-09-15 20:26:49.428 wdl.w:ptcp.w:call-paraphase-30 INFO visit :: node: "outputs", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-30/call-call_f8/out/m84036_250809_035451_s4.bc2127.f8inversion.vcf", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-30/call-run_paraphase/out/m84036_250809_035451_s4.bc2127_paraphase/m84036_250809_035451_s4.bc2127.paraphase.json", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-30/call-run_paraphase/out/m84036_250809_035451_s4.bc2127_paraphase/m84036_250809_035451_s4.bc2127.paraphase.bam", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-30/call-run_paraphase/out/m84036_250809_035451_s4.bc2127_paraphase/m84036_250809_035451_s4.bc2127.paraphase.bam.bai", "paraphase_vcfs": ["/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-30/call-run_paraphase/out/m84036_250809_035451_s4.bc2127_paraphase/m84036_250809_035451_s4.bc2127_paraphase_vcfs/m84036_250809_035451_s4.bc2127_cyp21.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-30/call-run_paraphase/out/m84036_250809_035451_s4.bc2127_paraphase/m84036_250809_035451_s4.bc2127_paraphase_vcfs/m84036_250809_035451_s4.bc2127_f8inv1.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-30/call-run_paraphase/out/m84036_250809_035451_s4.bc2127_paraphase/m84036_250809_035451_s4.bc2127_paraphase_vcfs/m84036_250809_035451_s4.bc2127_f8inv22.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-30/call-run_paraphase/out/m84036_250809_035451_s4.bc2127_paraphase/m84036_250809_035451_s4.bc2127_paraphase_vcfs/m84036_250809_035451_s4.bc2127_gba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-30/call-run_paraphase/out/m84036_250809_035451_s4.bc2127_paraphase/m84036_250809_035451_s4.bc2127_paraphase_vcfs/m84036_250809_035451_s4.bc2127_hba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-30/call-run_paraphase/out/m84036_250809_035451_s4.bc2127_paraphase/m84036_250809_035451_s4.bc2127_paraphase_vcfs/m84036_250809_035451_s4.bc2127_hbb.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-30/call-run_paraphase/out/m84036_250809_035451_s4.bc2127_paraphase/m84036_250809_035451_s4.bc2127_paraphase_vcfs/m84036_250809_035451_s4.bc2127_rpgr.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-30/call-run_paraphase/out/m84036_250809_035451_s4.bc2127_paraphase/m84036_250809_035451_s4.bc2127_paraphase_vcfs/m84036_250809_035451_s4.bc2127_smn1.vcf"], "havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-30/call-run_paraphase/out/m84036_250809_035451_s4.bc2127.havanno.json", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-30/call-call_f8/out/m84036_250809_035451_s4.bc2127.f8inversion.json"}
2025-09-15 20:26:49.460 wdl.w:ptcp.w:call-sawfish-78.t:call-run_sawfish NOTICE done
2025-09-15 20:26:49.465 wdl.w:ptcp.w:call-sawfish-78 NOTICE finish :: job: "call-run_sawfish"
2025-09-15 20:26:49.465 wdl.w:ptcp.w:call-sawfish-78 INFO output :: job: "call-run_sawfish", values: {"minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-78/call-run_sawfish/out/m84036_250809_035451_s4.bc2175.minimap2.bam.bai", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-78/call-run_sawfish/out/m84036_250809_035451_s4.bc2175.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-78/call-run_sawfish/out/m84036_250809_035451_s4.bc2175_sawfish/m84036_250809_035451_s4.bc2175.sv.vcf.gz.tbi", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-78/call-run_sawfish/out/m84036_250809_035451_s4.bc2175_sawfish/m84036_250809_035451_s4.bc2175.sv.vcf.gz"}
2025-09-15 20:26:49.466 wdl.w:ptcp.w:call-sawfish-78 INFO visit :: node: "output-minimap2_bam", values: {"minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-78/call-run_sawfish/out/m84036_250809_035451_s4.bc2175.minimap2.bam"}
2025-09-15 20:26:49.466 wdl.w:ptcp.w:call-sawfish-78 INFO visit :: node: "output-minimap2_bam_bai", values: {"minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-78/call-run_sawfish/out/m84036_250809_035451_s4.bc2175.minimap2.bam.bai"}
2025-09-15 20:26:49.466 wdl.w:ptcp.w:call-sawfish-78 INFO visit :: node: "output-vcf", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-78/call-run_sawfish/out/m84036_250809_035451_s4.bc2175_sawfish/m84036_250809_035451_s4.bc2175.sv.vcf.gz"}
2025-09-15 20:26:49.466 wdl.w:ptcp.w:call-sawfish-78 INFO visit :: node: "output-vcf_tbi", values: {"vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-78/call-run_sawfish/out/m84036_250809_035451_s4.bc2175_sawfish/m84036_250809_035451_s4.bc2175.sv.vcf.gz.tbi"}
2025-09-15 20:26:49.466 wdl.w:ptcp.w:call-sawfish-78 INFO visit :: node: "outputs", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-78/call-run_sawfish/out/m84036_250809_035451_s4.bc2175_sawfish/m84036_250809_035451_s4.bc2175.sv.vcf.gz", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-78/call-run_sawfish/out/m84036_250809_035451_s4.bc2175.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-78/call-run_sawfish/out/m84036_250809_035451_s4.bc2175_sawfish/m84036_250809_035451_s4.bc2175.sv.vcf.gz.tbi", "minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-78/call-run_sawfish/out/m84036_250809_035451_s4.bc2175.minimap2.bam.bai"}
2025-09-15 20:26:49.516 wdl.w:ptcp.w:call-sawfish-78 NOTICE done
2025-09-15 20:26:49.521 wdl.w:ptcp NOTICE finish :: job: "call-sawfish-78"
2025-09-15 20:26:49.521 wdl.w:ptcp INFO output :: job: "call-sawfish-78", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-78/out/m84036_250809_035451_s4.bc2175_sawfish/m84036_250809_035451_s4.bc2175.sv.vcf.gz", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-78/out/m84036_250809_035451_s4.bc2175.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-78/out/m84036_250809_035451_s4.bc2175_sawfish/m84036_250809_035451_s4.bc2175.sv.vcf.gz.tbi", "minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-78/out/m84036_250809_035451_s4.bc2175.minimap2.bam.bai"}
2025-09-15 20:26:49.552 wdl.w:ptcp.w:call-paraphase-30 NOTICE done
2025-09-15 20:26:49.557 wdl.w:ptcp NOTICE finish :: job: "call-paraphase-30"
2025-09-15 20:26:49.557 wdl.w:ptcp INFO output :: job: "call-paraphase-30", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-30/out/m84036_250809_035451_s4.bc2127.f8inversion.vcf", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-30/out/m84036_250809_035451_s4.bc2127_paraphase/m84036_250809_035451_s4.bc2127.paraphase.json", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-30/out/m84036_250809_035451_s4.bc2127_paraphase/m84036_250809_035451_s4.bc2127.paraphase.bam", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-30/out/m84036_250809_035451_s4.bc2127_paraphase/m84036_250809_035451_s4.bc2127.paraphase.bam.bai", "paraphase_vcfs": ["/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-30/out/m84036_250809_035451_s4.bc2127_paraphase/m84036_250809_035451_s4.bc2127_paraphase_vcfs/m84036_250809_035451_s4.bc2127_cyp21.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-30/out/m84036_250809_035451_s4.bc2127_paraphase/m84036_250809_035451_s4.bc2127_paraphase_vcfs/m84036_250809_035451_s4.bc2127_f8inv1.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-30/out/m84036_250809_035451_s4.bc2127_paraphase/m84036_250809_035451_s4.bc2127_paraphase_vcfs/m84036_250809_035451_s4.bc2127_f8inv22.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-30/out/m84036_250809_035451_s4.bc2127_paraphase/m84036_250809_035451_s4.bc2127_paraphase_vcfs/m84036_250809_035451_s4.bc2127_gba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-30/out/m84036_250809_035451_s4.bc2127_paraphase/m84036_250809_035451_s4.bc2127_paraphase_vcfs/m84036_250809_035451_s4.bc2127_hba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-30/out/m84036_250809_035451_s4.bc2127_paraphase/m84036_250809_035451_s4.bc2127_paraphase_vcfs/m84036_250809_035451_s4.bc2127_hbb.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-30/out/m84036_250809_035451_s4.bc2127_paraphase/m84036_250809_035451_s4.bc2127_paraphase_vcfs/m84036_250809_035451_s4.bc2127_rpgr.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-30/out/m84036_250809_035451_s4.bc2127_paraphase/m84036_250809_035451_s4.bc2127_paraphase_vcfs/m84036_250809_035451_s4.bc2127_smn1.vcf"], "havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-30/out/m84036_250809_035451_s4.bc2127.havanno.json", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-30/out/m84036_250809_035451_s4.bc2127.f8inversion.json"}
2025-09-15 20:26:49.557 wdl.w:ptcp NOTICE ready :: job: "call-tar_outputs-30", callee: "tar_outputs"
2025-09-15 20:26:49.557 wdl.w:ptcp INFO input :: job: "call-tar_outputs-30", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "sawfish_vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-30/out/m84036_250809_035451_s4.bc2127_sawfish/m84036_250809_035451_s4.bc2127.sv.vcf.gz.tbi", "sawfish_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-30/out/m84036_250809_035451_s4.bc2127_sawfish/m84036_250809_035451_s4.bc2127.sv.vcf.gz", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-30/out/m84036_250809_035451_s4.bc2127.f8inversion.json", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-30/out/m84036_250809_035451_s4.bc2127_paraphase/m84036_250809_035451_s4.bc2127.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-30/out/m84036_250809_035451_s4.bc2127_paraphase/m84036_250809_035451_s4.bc2127.paraphase.bam", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-30/out/m84036_250809_035451_s4.bc2127_paraphase/m84036_250809_035451_s4.bc2127.paraphase.json", "trgt_spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-30/out/m84036_250809_035451_s4.bc2127.trgt.sorted.spanning.bam.bai", "trgt_spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-30/out/m84036_250809_035451_s4.bc2127.trgt.sorted.spanning.bam", "trgt_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-30/out/m84036_250809_035451_s4.bc2127.trgt.vcf", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-30/out/m84036_250809_035451_s4.bc2127.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-30/out/m84036_250809_035451_s4.bc2127.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2127"}
2025-09-15 20:26:49.563 wdl.w:ptcp.t:call-tar_outputs-30 NOTICE task setup :: name: "tar_outputs", source: "./common.wdl", line: 279, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-30", thread: 140613034948160
2025-09-15 20:26:49.590 wdl.w:ptcp.t:call-tar_outputs-30 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:26:49.591 wdl.w:ptcp.t:call-tar_outputs-30 INFO input :: name: "sawfish_vcf_tbi", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2127.sv.vcf.gz.tbi"
2025-09-15 20:26:49.591 wdl.w:ptcp.t:call-tar_outputs-30 INFO input :: name: "sawfish_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2127.sv.vcf.gz"
2025-09-15 20:26:49.591 wdl.w:ptcp.t:call-tar_outputs-30 INFO input :: name: "f8_json", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2127.f8inversion.json"
2025-09-15 20:26:49.591 wdl.w:ptcp.t:call-tar_outputs-30 INFO input :: name: "paraphase_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2127.paraphase.bam.bai"
2025-09-15 20:26:49.591 wdl.w:ptcp.t:call-tar_outputs-30 INFO input :: name: "paraphase_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2127.paraphase.bam"
2025-09-15 20:26:49.591 wdl.w:ptcp.t:call-tar_outputs-30 INFO input :: name: "paraphase_json", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2127.paraphase.json"
2025-09-15 20:26:49.591 wdl.w:ptcp.t:call-tar_outputs-30 INFO input :: name: "trgt_spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2127.trgt.sorted.spanning.bam.bai"
2025-09-15 20:26:49.591 wdl.w:ptcp.t:call-tar_outputs-30 INFO input :: name: "trgt_spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2127.trgt.sorted.spanning.bam"
2025-09-15 20:26:49.591 wdl.w:ptcp.t:call-tar_outputs-30 INFO input :: name: "trgt_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2127.trgt.vcf"
2025-09-15 20:26:49.591 wdl.w:ptcp.t:call-tar_outputs-30 INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2127.mapped.bam.bai"
2025-09-15 20:26:49.591 wdl.w:ptcp.t:call-tar_outputs-30 INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2127.mapped.bam"
2025-09-15 20:26:49.591 wdl.w:ptcp.t:call-tar_outputs-30 INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2127"
2025-09-15 20:26:49.591 wdl.w:ptcp.t:call-tar_outputs-30 INFO eval :: name: "threads", value: 1
2025-09-15 20:26:49.591 wdl.w:ptcp.t:call-tar_outputs-30 INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:26:49.592 wdl.w:ptcp.t:call-tar_outputs-30 INFO eval :: name: "disk_size", value: 6
2025-09-15 20:26:49.592 wdl.w:ptcp.t:call-tar_outputs-30 INFO eval :: name: "output_tarball", value: "m84036_250809_035451_s4.bc2127.tar"
2025-09-15 20:26:49.592 wdl.w:ptcp.t:call-tar_outputs-30 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:26:49.592 wdl.w:ptcp.t:call-tar_outputs-30 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:26:49.592 wdl.w:ptcp.t:call-tar_outputs-30 INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:26:49.593 wdl.w:ptcp.t:call-tar_outputs-30 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:26:49.673 wdl.w:ptcp.t:call-tar_outputs-30 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 17, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-30/_singularity_tmpdir_ot2dtm6v"
2025-09-15 20:26:49.674 wdl.w:ptcp.t:call-tar_outputs-30 INFO Slurm invocation: srun --job-name call-tar_outputs-30 --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-30/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-30/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-30/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-30/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-30/out/m84036_250809_035451_s4.bc2127_paraphase/m84036_250809_035451_s4.bc2127.paraphase.json:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2127.paraphase.json:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-30/out/m84036_250809_035451_s4.bc2127_paraphase/m84036_250809_035451_s4.bc2127.paraphase.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2127.paraphase.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-30/out/m84036_250809_035451_s4.bc2127_paraphase/m84036_250809_035451_s4.bc2127.paraphase.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2127.paraphase.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-30/out/m84036_250809_035451_s4.bc2127.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2127.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-30/out/m84036_250809_035451_s4.bc2127.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2127.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-30/out/m84036_250809_035451_s4.bc2127.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2127.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-30/out/m84036_250809_035451_s4.bc2127_sawfish/m84036_250809_035451_s4.bc2127.sv.vcf.gz:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2127.sv.vcf.gz:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-30/out/m84036_250809_035451_s4.bc2127_sawfish/m84036_250809_035451_s4.bc2127.sv.vcf.gz.tbi:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2127.sv.vcf.gz.tbi:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-30/out/m84036_250809_035451_s4.bc2127.f8inversion.json:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2127.f8inversion.json:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-30/out/m84036_250809_035451_s4.bc2127.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2127.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-30/out/m84036_250809_035451_s4.bc2127.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2127.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-30/_singularity_tmpdir_ot2dtm6v/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-30/_singularity_tmpdir_ot2dtm6v/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:26:49.685 wdl.w:ptcp.t:call-tar_outputs-30 NOTICE slurm_singularity run :: pid: 1207869, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-30/slurm_singularity.log.txt"
2025-09-15 20:26:49.800 wdl.w:ptcp.w:call-sawfish-77.t:call-run_sawfish.stderr VERBOSE [M::mm_idx_gen::60.693*1.58] collected minimizers
2025-09-15 20:26:49.801 wdl.w:ptcp.w:call-sawfish-77.t:call-run_sawfish.stderr VERBOSE [M::mm_idx_gen::72.432*1.80] sorted minimizers
2025-09-15 20:26:49.801 wdl.w:ptcp.w:call-sawfish-77.t:call-run_sawfish.stderr VERBOSE [M::main::72.433*1.80] loaded/built the index for 195 target sequence(s)
2025-09-15 20:26:49.801 wdl.w:ptcp.w:call-sawfish-77.t:call-run_sawfish.stderr VERBOSE [M::mm_mapopt_update::79.516*1.73] mid_occ = 136
2025-09-15 20:26:49.801 wdl.w:ptcp.w:call-sawfish-77.t:call-run_sawfish.stderr VERBOSE [M::mm_idx_stat] kmer size: 19; skip: 19; is_hpc: 0; #seq: 195
2025-09-15 20:26:49.801 wdl.w:ptcp.w:call-sawfish-77.t:call-run_sawfish.stderr VERBOSE [M::mm_idx_stat::85.298*1.68] distinct minimizers: 214664461 (92.23% are singletons); average occurrences: 1.372; average spacing: 10.529; total length: 3099922541
2025-09-15 20:26:49.801 wdl.w:ptcp.w:call-sawfish-77.t:call-run_sawfish.stderr VERBOSE [M::main] Version: 2.26-r1175
2025-09-15 20:26:49.801 wdl.w:ptcp.w:call-sawfish-77.t:call-run_sawfish.stderr VERBOSE [M::main] CMD: /opt/pacbio/smrttools/install/smrtlink-release_25.1.0.257715/bundles/smrttools/install/smrttools-release_25.1.0.257715/private/thirdparty/minimap2/minimap2_2.26-pacbio2/binwrap/../../../../../private/thirdparty/minimap2/minimap2_2.26-pacbio2/bin/minimap2 -a -y -x map-hifi -Y -E 1,0 /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa -
2025-09-15 20:26:49.801 wdl.w:ptcp.w:call-sawfish-77.t:call-run_sawfish.stderr VERBOSE [M::main] Real time: 85.659 sec; CPU: 143.475 sec; Peak RSS: 11.886 GB
2025-09-15 20:26:49.802 wdl.w:ptcp.w:call-sawfish-77.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:41][sawfish][INFO] Starting sawfish 2.0.3
2025-09-15 20:26:49.802 wdl.w:ptcp.w:call-sawfish-77.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:41][sawfish][INFO] cmdline: sawfish discover --disable-cnv --threads 16 --ref /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa --bam m84036_250809_035451_s4.bc2174.minimap2.bam --output-dir m84036_250809_035451_s4.bc2174_sawfish_discover
2025-09-15 20:26:49.802 wdl.w:ptcp.w:call-sawfish-77.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:41][sawfish][INFO] Running on 16 threads
2025-09-15 20:26:49.802 wdl.w:ptcp.w:call-sawfish-77.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:41][sawfish][INFO] Writing discover settings to file: 'm84036_250809_035451_s4.bc2174_sawfish_discover/discover.settings.json'
2025-09-15 20:26:49.802 wdl.w:ptcp.w:call-sawfish-77.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:41][sawfish][INFO] Reading reference genome from file '/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa'
2025-09-15 20:26:49.802 wdl.w:ptcp.w:call-sawfish-77.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:47][sawfish][INFO] Processing alignment file '/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2174.minimap2.bam'
2025-09-15 20:26:49.802 wdl.w:ptcp.w:call-sawfish-77.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:47][sawfish][INFO] Finished processing all alignments
2025-09-15 20:26:49.802 wdl.w:ptcp.w:call-sawfish-77.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:47][sawfish][INFO] Writing depth bins to binary file: 'm84036_250809_035451_s4.bc2174_sawfish_discover/depth.mpack'
2025-09-15 20:26:49.802 wdl.w:ptcp.w:call-sawfish-77.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:47][sawfish][INFO] Writing max sv depth genome regions to bed file: 'm84036_250809_035451_s4.bc2174_sawfish_discover/max.depth.bed'
2025-09-15 20:26:49.802 wdl.w:ptcp.w:call-sawfish-77.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:47][sawfish][INFO] Completing breakpoint observation clustering
2025-09-15 20:26:49.802 wdl.w:ptcp.w:call-sawfish-77.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:47][sawfish][INFO] Finished breakpoint observation clustering
2025-09-15 20:26:49.802 wdl.w:ptcp.w:call-sawfish-77.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:47][sawfish][INFO] Consolidating adjacent indel candidates
2025-09-15 20:26:49.802 wdl.w:ptcp.w:call-sawfish-77.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:47][sawfish][INFO] Finding large insertion candidates
2025-09-15 20:26:49.802 wdl.w:ptcp.w:call-sawfish-77.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:47][sawfish][INFO] Writing breakpoint_cluster debug bed file: 'm84036_250809_035451_s4.bc2174_sawfish_discover/debug.breakpoint_clusters.bed'
2025-09-15 20:26:49.802 wdl.w:ptcp.w:call-sawfish-77.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:47][sawfish][INFO] Refining SV Candidates
2025-09-15 20:26:49.802 wdl.w:ptcp.w:call-sawfish-77.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:47][sawfish][INFO] Writing debug assembly region bed file: 'm84036_250809_035451_s4.bc2174_sawfish_discover/assembly.regions.bed'
2025-09-15 20:26:49.802 wdl.w:ptcp.w:call-sawfish-77.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:47][sawfish][INFO] Starting refinement of breakpoint evidence clusters
2025-09-15 20:26:49.802 wdl.w:ptcp.w:call-sawfish-77.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:47][sawfish][INFO] Finished refining all breakpoint evidence clusters
2025-09-15 20:26:49.803 wdl.w:ptcp.w:call-sawfish-77.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:47][sawfish][INFO] Writing all contig alignments to bam file: 'm84036_250809_035451_s4.bc2174_sawfish_discover/contig.alignment.bam'
2025-09-15 20:26:49.803 wdl.w:ptcp.w:call-sawfish-77.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:47][sawfish][INFO] Writing candidate structural variants to file: 'm84036_250809_035451_s4.bc2174_sawfish_discover/candidate.sv.bcf'
2025-09-15 20:26:49.803 wdl.w:ptcp.w:call-sawfish-77.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:47][sawfish][INFO] Writing run statistics to file: 'm84036_250809_035451_s4.bc2174_sawfish_discover/run.stats.json'
2025-09-15 20:26:49.803 wdl.w:ptcp.w:call-sawfish-77.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:47][sawfish][INFO] sawfish completed. Total Runtime: 00:00:06.212
2025-09-15 20:26:49.833 wdl.w:ptcp.w:call-paraphase-66.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for cyp21 for sample m84036_250809_035451_s4.bc2163 at 2025-09-15 20:26:28.009785...
2025-09-15 20:26:49.833 wdl.w:ptcp.w:call-paraphase-66.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for cyp21 for sample m84036_250809_035451_s4.bc2163 at 2025-09-15 20:26:30.595749...
2025-09-15 20:26:50.277 wdl.w:ptcp.w:call-paraphase-78.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for hba for sample m84036_250809_035451_s4.bc2175 at 2025-09-15 20:26:06.061059...
2025-09-15 20:26:50.278 wdl.w:ptcp.w:call-paraphase-78.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for hba for sample m84036_250809_035451_s4.bc2175 at 2025-09-15 20:26:06.576109...
2025-09-15 20:26:50.507 wdl.w:ptcp.w:call-sawfish-92.t:call-run_sawfish INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2189_sawfish/m84036_250809_035451_s4.bc2189.sv.vcf.gz"
2025-09-15 20:26:50.511 wdl.w:ptcp.w:call-sawfish-92.t:call-run_sawfish INFO output :: name: "vcf_tbi", value: "m84036_250809_035451_s4.bc2189_sawfish/m84036_250809_035451_s4.bc2189.sv.vcf.gz.tbi"
2025-09-15 20:26:50.512 wdl.w:ptcp.w:call-sawfish-92.t:call-run_sawfish INFO output :: name: "minimap2_bam", value: "m84036_250809_035451_s4.bc2189.minimap2.bam"
2025-09-15 20:26:50.513 wdl.w:ptcp.w:call-sawfish-92.t:call-run_sawfish INFO output :: name: "minimap2_bam_bai", value: "m84036_250809_035451_s4.bc2189.minimap2.bam.bai"
2025-09-15 20:26:50.622 wdl.w:ptcp.w:call-sawfish-92.t:call-run_sawfish NOTICE done
2025-09-15 20:26:50.628 wdl.w:ptcp.w:call-sawfish-92 NOTICE finish :: job: "call-run_sawfish"
2025-09-15 20:26:50.628 wdl.w:ptcp.w:call-sawfish-92 INFO output :: job: "call-run_sawfish", values: {"minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-92/call-run_sawfish/out/m84036_250809_035451_s4.bc2189.minimap2.bam.bai", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-92/call-run_sawfish/out/m84036_250809_035451_s4.bc2189.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-92/call-run_sawfish/out/m84036_250809_035451_s4.bc2189_sawfish/m84036_250809_035451_s4.bc2189.sv.vcf.gz.tbi", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-92/call-run_sawfish/out/m84036_250809_035451_s4.bc2189_sawfish/m84036_250809_035451_s4.bc2189.sv.vcf.gz"}
2025-09-15 20:26:50.628 wdl.w:ptcp.w:call-sawfish-92 INFO visit :: node: "output-minimap2_bam", values: {"minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-92/call-run_sawfish/out/m84036_250809_035451_s4.bc2189.minimap2.bam"}
2025-09-15 20:26:50.628 wdl.w:ptcp.w:call-sawfish-92 INFO visit :: node: "output-minimap2_bam_bai", values: {"minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-92/call-run_sawfish/out/m84036_250809_035451_s4.bc2189.minimap2.bam.bai"}
2025-09-15 20:26:50.628 wdl.w:ptcp.w:call-sawfish-92 INFO visit :: node: "output-vcf", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-92/call-run_sawfish/out/m84036_250809_035451_s4.bc2189_sawfish/m84036_250809_035451_s4.bc2189.sv.vcf.gz"}
2025-09-15 20:26:50.629 wdl.w:ptcp.w:call-sawfish-92 INFO visit :: node: "output-vcf_tbi", values: {"vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-92/call-run_sawfish/out/m84036_250809_035451_s4.bc2189_sawfish/m84036_250809_035451_s4.bc2189.sv.vcf.gz.tbi"}
2025-09-15 20:26:50.629 wdl.w:ptcp.w:call-sawfish-92 INFO visit :: node: "outputs", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-92/call-run_sawfish/out/m84036_250809_035451_s4.bc2189_sawfish/m84036_250809_035451_s4.bc2189.sv.vcf.gz", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-92/call-run_sawfish/out/m84036_250809_035451_s4.bc2189.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-92/call-run_sawfish/out/m84036_250809_035451_s4.bc2189_sawfish/m84036_250809_035451_s4.bc2189.sv.vcf.gz.tbi", "minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-92/call-run_sawfish/out/m84036_250809_035451_s4.bc2189.minimap2.bam.bai"}
2025-09-15 20:26:50.672 wdl.w:ptcp.w:call-sawfish-92 NOTICE done
2025-09-15 20:26:50.679 wdl.w:ptcp NOTICE finish :: job: "call-sawfish-92"
2025-09-15 20:26:50.679 wdl.w:ptcp INFO output :: job: "call-sawfish-92", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-92/out/m84036_250809_035451_s4.bc2189_sawfish/m84036_250809_035451_s4.bc2189.sv.vcf.gz", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-92/out/m84036_250809_035451_s4.bc2189.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-92/out/m84036_250809_035451_s4.bc2189_sawfish/m84036_250809_035451_s4.bc2189.sv.vcf.gz.tbi", "minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-92/out/m84036_250809_035451_s4.bc2189.minimap2.bam.bai"}
2025-09-15 20:26:50.680 wdl.w:ptcp NOTICE ready :: job: "call-tar_outputs-92", callee: "tar_outputs"
2025-09-15 20:26:50.680 wdl.w:ptcp INFO input :: job: "call-tar_outputs-92", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "sawfish_vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-92/out/m84036_250809_035451_s4.bc2189_sawfish/m84036_250809_035451_s4.bc2189.sv.vcf.gz.tbi", "sawfish_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-92/out/m84036_250809_035451_s4.bc2189_sawfish/m84036_250809_035451_s4.bc2189.sv.vcf.gz", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-92/out/m84036_250809_035451_s4.bc2189.f8inversion.json", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-92/out/m84036_250809_035451_s4.bc2189_paraphase/m84036_250809_035451_s4.bc2189.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-92/out/m84036_250809_035451_s4.bc2189_paraphase/m84036_250809_035451_s4.bc2189.paraphase.bam", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-92/out/m84036_250809_035451_s4.bc2189_paraphase/m84036_250809_035451_s4.bc2189.paraphase.json", "trgt_spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-92/out/m84036_250809_035451_s4.bc2189.trgt.sorted.spanning.bam.bai", "trgt_spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-92/out/m84036_250809_035451_s4.bc2189.trgt.sorted.spanning.bam", "trgt_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-92/out/m84036_250809_035451_s4.bc2189.trgt.vcf", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-92/out/m84036_250809_035451_s4.bc2189.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-92/out/m84036_250809_035451_s4.bc2189.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2189"}
2025-09-15 20:26:50.689 wdl.w:ptcp.t:call-tar_outputs-92 NOTICE task setup :: name: "tar_outputs", source: "./common.wdl", line: 279, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-92", thread: 140608731588160
2025-09-15 20:26:50.697 wdl.w:ptcp.t:call-tar_outputs-30.slurm_singularity INFO srun: job 51798211 queued and waiting for resources
2025-09-15 20:26:50.697 wdl.w:ptcp.t:call-tar_outputs-30.slurm_singularity INFO srun: job 51798211 has been allocated resources
2025-09-15 20:26:50.697 wdl.w:ptcp.t:call-tar_outputs-30.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:26:50.716 wdl.w:ptcp.t:call-tar_outputs-92 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:26:50.716 wdl.w:ptcp.t:call-tar_outputs-92 INFO input :: name: "sawfish_vcf_tbi", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2189.sv.vcf.gz.tbi"
2025-09-15 20:26:50.716 wdl.w:ptcp.t:call-tar_outputs-92 INFO input :: name: "sawfish_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2189.sv.vcf.gz"
2025-09-15 20:26:50.716 wdl.w:ptcp.t:call-tar_outputs-92 INFO input :: name: "f8_json", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2189.f8inversion.json"
2025-09-15 20:26:50.716 wdl.w:ptcp.t:call-tar_outputs-92 INFO input :: name: "paraphase_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2189.paraphase.bam.bai"
2025-09-15 20:26:50.716 wdl.w:ptcp.t:call-tar_outputs-92 INFO input :: name: "paraphase_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2189.paraphase.bam"
2025-09-15 20:26:50.716 wdl.w:ptcp.t:call-tar_outputs-92 INFO input :: name: "paraphase_json", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2189.paraphase.json"
2025-09-15 20:26:50.716 wdl.w:ptcp.t:call-tar_outputs-92 INFO input :: name: "trgt_spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2189.trgt.sorted.spanning.bam.bai"
2025-09-15 20:26:50.716 wdl.w:ptcp.t:call-tar_outputs-92 INFO input :: name: "trgt_spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2189.trgt.sorted.spanning.bam"
2025-09-15 20:26:50.716 wdl.w:ptcp.t:call-tar_outputs-92 INFO input :: name: "trgt_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2189.trgt.vcf"
2025-09-15 20:26:50.716 wdl.w:ptcp.t:call-tar_outputs-92 INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2189.mapped.bam.bai"
2025-09-15 20:26:50.716 wdl.w:ptcp.t:call-tar_outputs-92 INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2189.mapped.bam"
2025-09-15 20:26:50.716 wdl.w:ptcp.t:call-tar_outputs-92 INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2189"
2025-09-15 20:26:50.716 wdl.w:ptcp.t:call-tar_outputs-92 INFO eval :: name: "threads", value: 1
2025-09-15 20:26:50.716 wdl.w:ptcp.t:call-tar_outputs-92 INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:26:50.717 wdl.w:ptcp.t:call-tar_outputs-92 INFO eval :: name: "disk_size", value: 6
2025-09-15 20:26:50.717 wdl.w:ptcp.t:call-tar_outputs-92 INFO eval :: name: "output_tarball", value: "m84036_250809_035451_s4.bc2189.tar"
2025-09-15 20:26:50.717 wdl.w:ptcp.t:call-tar_outputs-92 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:26:50.717 wdl.w:ptcp.t:call-tar_outputs-92 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:26:50.718 wdl.w:ptcp.t:call-tar_outputs-92 INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:26:50.718 wdl.w:ptcp.t:call-tar_outputs-92 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:26:50.803 wdl.w:ptcp.t:call-tar_outputs-92 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 17, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-92/_singularity_tmpdir_cx0tlhyd"
2025-09-15 20:26:50.803 wdl.w:ptcp.t:call-tar_outputs-92 INFO Slurm invocation: srun --job-name call-tar_outputs-92 --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-92/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-92/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-92/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-92/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-92/out/m84036_250809_035451_s4.bc2189_paraphase/m84036_250809_035451_s4.bc2189.paraphase.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2189.paraphase.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-92/out/m84036_250809_035451_s4.bc2189_paraphase/m84036_250809_035451_s4.bc2189.paraphase.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2189.paraphase.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-92/out/m84036_250809_035451_s4.bc2189_paraphase/m84036_250809_035451_s4.bc2189.paraphase.json:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2189.paraphase.json:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-92/out/m84036_250809_035451_s4.bc2189.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2189.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-92/out/m84036_250809_035451_s4.bc2189.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2189.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-92/out/m84036_250809_035451_s4.bc2189.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2189.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-92/out/m84036_250809_035451_s4.bc2189_sawfish/m84036_250809_035451_s4.bc2189.sv.vcf.gz.tbi:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2189.sv.vcf.gz.tbi:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-92/out/m84036_250809_035451_s4.bc2189_sawfish/m84036_250809_035451_s4.bc2189.sv.vcf.gz:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2189.sv.vcf.gz:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-92/out/m84036_250809_035451_s4.bc2189.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2189.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-92/out/m84036_250809_035451_s4.bc2189.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2189.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-92/out/m84036_250809_035451_s4.bc2189.f8inversion.json:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2189.f8inversion.json:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-92/_singularity_tmpdir_cx0tlhyd/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-92/_singularity_tmpdir_cx0tlhyd/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:26:50.818 wdl.w:ptcp.t:call-tar_outputs-92 NOTICE slurm_singularity run :: pid: 1207945, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-92/slurm_singularity.log.txt"
2025-09-15 20:26:50.822 wdl.w:ptcp.w:call-paraphase-19.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for f8inv22 for sample m84036_250809_035451_s4.bc2116 at 2025-09-15 20:26:47.425307...
2025-09-15 20:26:50.823 wdl.w:ptcp.w:call-paraphase-19.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for f8inv22 for sample m84036_250809_035451_s4.bc2116 at 2025-09-15 20:26:47.426259...
2025-09-15 20:26:51.079 wdl.w:ptcp.w:call-paraphase-95.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for f8inv1 for sample m84036_250809_035451_s4.bc2192 at 2025-09-15 20:26:45.888897...
2025-09-15 20:26:51.080 wdl.w:ptcp.w:call-paraphase-95.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for hbb for sample m84036_250809_035451_s4.bc2192 at 2025-09-15 20:26:49.070328...
2025-09-15 20:26:51.080 wdl.w:ptcp.w:call-paraphase-95.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for hbb for sample m84036_250809_035451_s4.bc2192 at 2025-09-15 20:26:49.070475...
2025-09-15 20:26:51.087 wdl.w:ptcp.w:call-paraphase-87.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for hba for sample m84036_250809_035451_s4.bc2184 at 2025-09-15 20:26:30.115376...
2025-09-15 20:26:51.088 wdl.w:ptcp.w:call-paraphase-87.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for hba for sample m84036_250809_035451_s4.bc2184 at 2025-09-15 20:26:30.481353...
2025-09-15 20:26:51.089 wdl.w:ptcp.w:call-paraphase-87.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for cyp21 for sample m84036_250809_035451_s4.bc2184 at 2025-09-15 20:26:32.479124...
2025-09-15 20:26:51.089 wdl.w:ptcp.w:call-paraphase-87.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for cyp21 for sample m84036_250809_035451_s4.bc2184 at 2025-09-15 20:26:33.359268...
2025-09-15 20:26:51.089 wdl.w:ptcp.w:call-paraphase-87.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for f8inv1 for sample m84036_250809_035451_s4.bc2184 at 2025-09-15 20:26:38.530133...
2025-09-15 20:26:51.089 wdl.w:ptcp.w:call-paraphase-87.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for f8inv1 for sample m84036_250809_035451_s4.bc2184 at 2025-09-15 20:26:38.531321...
2025-09-15 20:26:51.402 wdl.w:ptcp.t:call-tar_outputs-30 INFO output :: name: "sample_tarball", value: "m84036_250809_035451_s4.bc2127.tar"
2025-09-15 20:26:51.462 wdl.w:ptcp.t:call-tar_outputs-30 NOTICE done
2025-09-15 20:26:51.465 wdl.w:ptcp NOTICE finish :: job: "call-tar_outputs-30"
2025-09-15 20:26:51.466 wdl.w:ptcp INFO output :: job: "call-tar_outputs-30", values: {"sample_tarball": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-30/out/m84036_250809_035451_s4.bc2127.tar"}
2025-09-15 20:26:51.832 wdl.w:ptcp.t:call-tar_outputs-92.slurm_singularity INFO srun: job 51798212 queued and waiting for resources
2025-09-15 20:26:51.832 wdl.w:ptcp.t:call-tar_outputs-92.slurm_singularity INFO srun: job 51798212 has been allocated resources
2025-09-15 20:26:51.832 wdl.w:ptcp.t:call-tar_outputs-92.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:26:51.884 wdl.w:ptcp.w:call-paraphase-82.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for smn1 for sample m84036_250809_035451_s4.bc2179 at 2025-09-15 20:26:21.754907...
2025-09-15 20:26:52.191 wdl.w:ptcp.t:call-tar_outputs-92 INFO output :: name: "sample_tarball", value: "m84036_250809_035451_s4.bc2189.tar"
2025-09-15 20:26:52.286 wdl.w:ptcp.t:call-tar_outputs-92 NOTICE done
2025-09-15 20:26:52.290 wdl.w:ptcp NOTICE finish :: job: "call-tar_outputs-92"
2025-09-15 20:26:52.290 wdl.w:ptcp INFO output :: job: "call-tar_outputs-92", values: {"sample_tarball": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-92/out/m84036_250809_035451_s4.bc2189.tar"}
2025-09-15 20:26:52.375 wdl.w:ptcp.w:call-paraphase-47.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for rpgr for sample m84036_250809_035451_s4.bc2144 at 2025-09-15 20:26:06.245551...
2025-09-15 20:26:52.375 wdl.w:ptcp.w:call-paraphase-47.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for rpgr for sample m84036_250809_035451_s4.bc2144 at 2025-09-15 20:26:07.086457...
2025-09-15 20:26:52.375 wdl.w:ptcp.w:call-paraphase-47.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for rpgr for sample m84036_250809_035451_s4.bc2144 at 2025-09-15 20:26:07.331928...
2025-09-15 20:26:52.427 wdl.w:ptcp.w:call-paraphase-86.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for gba for sample m84036_250809_035451_s4.bc2183 at 2025-09-15 20:26:45.559426...
2025-09-15 20:26:52.427 wdl.w:ptcp.w:call-paraphase-86.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for gba for sample m84036_250809_035451_s4.bc2183 at 2025-09-15 20:26:46.027402...
2025-09-15 20:26:52.427 wdl.w:ptcp.w:call-paraphase-86.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for cyp21 for sample m84036_250809_035451_s4.bc2183 at 2025-09-15 20:26:48.695808...
2025-09-15 20:26:52.428 wdl.w:ptcp.w:call-paraphase-86.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for cyp21 for sample m84036_250809_035451_s4.bc2183 at 2025-09-15 20:26:49.585408...
2025-09-15 20:26:52.428 wdl.w:ptcp.w:call-paraphase-86.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for f8inv1 for sample m84036_250809_035451_s4.bc2183 at 2025-09-15 20:26:50.339884...
2025-09-15 20:26:52.428 wdl.w:ptcp.w:call-paraphase-86.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for f8inv1 for sample m84036_250809_035451_s4.bc2183 at 2025-09-15 20:26:50.340081...
2025-09-15 20:26:52.598 wdl.w:ptcp.w:call-paraphase-27.t:call-run_paraphase INFO output :: name: "paraphase_bam", value: "m84036_250809_035451_s4.bc2124_paraphase/m84036_250809_035451_s4.bc2124.paraphase.bam"
2025-09-15 20:26:52.601 wdl.w:ptcp.w:call-paraphase-27.t:call-run_paraphase INFO output :: name: "paraphase_bam_bai", value: "m84036_250809_035451_s4.bc2124_paraphase/m84036_250809_035451_s4.bc2124.paraphase.bam.bai"
2025-09-15 20:26:52.602 wdl.w:ptcp.w:call-paraphase-27.t:call-run_paraphase INFO output :: name: "paraphase_json", value: "m84036_250809_035451_s4.bc2124_paraphase/m84036_250809_035451_s4.bc2124.paraphase.json"
2025-09-15 20:26:52.606 wdl.w:ptcp.w:call-paraphase-27.t:call-run_paraphase INFO output :: name: "paraphase_vcfs", value: ["/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2124_paraphase/m84036_250809_035451_s4.bc2124_paraphase_vcfs/m84036_250809_035451_s4.bc2124_cyp21.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2124_paraphase/m84036_250809_035451_s4.bc2124_paraphase_vcfs/m84036_250809_035451_s4.bc2124_f8inv1.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2124_paraphase/m84036_250809_035451_s4.bc2124_paraphase_vcfs/m84036_250809_035451_s4.bc2124_f8inv22.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2124_paraphase/m84036_250809_035451_s4.bc2124_paraphase_vcfs/m84036_250809_035451_s4.bc2124_gba.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2124_paraphase/m84036_250809_035451_s4.bc2124_paraphase_vcfs/m84036_250809_035451_s4.bc2124_hba.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2124_paraphase/m84036_250809_035451_s4.bc2124_paraphase_vcfs/m84036_250809_035451_s4.bc2124_hbb.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2124_paraphase/m84036_250809_035451_s4.bc2124_paraphase_vcfs/m84036_250809_035451_s4.bc2124_rpgr.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2124_paraphase/m84036_250809_035451_s4.bc2124_paraphase_vcfs/m84036_250809_035451_s4.bc2124_smn1.vcf"]
2025-09-15 20:26:52.609 wdl.w:ptcp.w:call-paraphase-27.t:call-run_paraphase INFO output :: name: "havanno_json", value: "m84036_250809_035451_s4.bc2124.havanno.json"
2025-09-15 20:26:52.696 wdl.w:ptcp.w:call-sawfish-82.t:call-run_sawfish INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2179_sawfish/m84036_250809_035451_s4.bc2179.sv.vcf.gz"
2025-09-15 20:26:52.701 wdl.w:ptcp.w:call-sawfish-82.t:call-run_sawfish INFO output :: name: "vcf_tbi", value: "m84036_250809_035451_s4.bc2179_sawfish/m84036_250809_035451_s4.bc2179.sv.vcf.gz.tbi"
2025-09-15 20:26:52.703 wdl.w:ptcp.w:call-sawfish-82.t:call-run_sawfish INFO output :: name: "minimap2_bam", value: "m84036_250809_035451_s4.bc2179.minimap2.bam"
2025-09-15 20:26:52.705 wdl.w:ptcp.w:call-sawfish-82.t:call-run_sawfish INFO output :: name: "minimap2_bam_bai", value: "m84036_250809_035451_s4.bc2179.minimap2.bam.bai"
2025-09-15 20:26:52.782 wdl.w:ptcp.w:call-paraphase-27.t:call-run_paraphase NOTICE done
2025-09-15 20:26:52.787 wdl.w:ptcp.w:call-paraphase-27 NOTICE finish :: job: "call-run_paraphase"
2025-09-15 20:26:52.787 wdl.w:ptcp.w:call-paraphase-27 INFO output :: job: "call-run_paraphase", values: {"havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-27/call-run_paraphase/out/m84036_250809_035451_s4.bc2124.havanno.json", "paraphase_vcfs": ["/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-27/call-run_paraphase/out/m84036_250809_035451_s4.bc2124_paraphase/m84036_250809_035451_s4.bc2124_paraphase_vcfs/m84036_250809_035451_s4.bc2124_cyp21.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-27/call-run_paraphase/out/m84036_250809_035451_s4.bc2124_paraphase/m84036_250809_035451_s4.bc2124_paraphase_vcfs/m84036_250809_035451_s4.bc2124_f8inv1.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-27/call-run_paraphase/out/m84036_250809_035451_s4.bc2124_paraphase/m84036_250809_035451_s4.bc2124_paraphase_vcfs/m84036_250809_035451_s4.bc2124_f8inv22.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-27/call-run_paraphase/out/m84036_250809_035451_s4.bc2124_paraphase/m84036_250809_035451_s4.bc2124_paraphase_vcfs/m84036_250809_035451_s4.bc2124_gba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-27/call-run_paraphase/out/m84036_250809_035451_s4.bc2124_paraphase/m84036_250809_035451_s4.bc2124_paraphase_vcfs/m84036_250809_035451_s4.bc2124_hba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-27/call-run_paraphase/out/m84036_250809_035451_s4.bc2124_paraphase/m84036_250809_035451_s4.bc2124_paraphase_vcfs/m84036_250809_035451_s4.bc2124_hbb.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-27/call-run_paraphase/out/m84036_250809_035451_s4.bc2124_paraphase/m84036_250809_035451_s4.bc2124_paraphase_vcfs/m84036_250809_035451_s4.bc2124_rpgr.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-27/call-run_paraphase/out/m84036_250809_035451_s4.bc2124_paraphase/m84036_250809_035451_s4.bc2124_paraphase_vcfs/m84036_250809_035451_s4.bc2124_smn1.vcf"], "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-27/call-run_paraphase/out/m84036_250809_035451_s4.bc2124_paraphase/m84036_250809_035451_s4.bc2124.paraphase.json", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-27/call-run_paraphase/out/m84036_250809_035451_s4.bc2124_paraphase/m84036_250809_035451_s4.bc2124.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-27/call-run_paraphase/out/m84036_250809_035451_s4.bc2124_paraphase/m84036_250809_035451_s4.bc2124.paraphase.bam"}
2025-09-15 20:26:52.788 wdl.w:ptcp.w:call-paraphase-27 NOTICE ready :: job: "call-call_f8", callee: "call_f8"
2025-09-15 20:26:52.788 wdl.w:ptcp.w:call-paraphase-27 INFO input :: job: "call-call_f8", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "out_prefix": "m84036_250809_035451_s4.bc2124", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-27/call-run_paraphase/out/m84036_250809_035451_s4.bc2124_paraphase/m84036_250809_035451_s4.bc2124.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-27/call-run_paraphase/out/m84036_250809_035451_s4.bc2124_paraphase/m84036_250809_035451_s4.bc2124.paraphase.bam", "sex": "F"}
2025-09-15 20:26:52.789 wdl.w:ptcp.w:call-paraphase-27 INFO visit :: node: "output-havanno_json", values: {"havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-27/call-run_paraphase/out/m84036_250809_035451_s4.bc2124.havanno.json"}
2025-09-15 20:26:52.789 wdl.w:ptcp.w:call-paraphase-27 INFO visit :: node: "output-paraphase_bam", values: {"paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-27/call-run_paraphase/out/m84036_250809_035451_s4.bc2124_paraphase/m84036_250809_035451_s4.bc2124.paraphase.bam"}
2025-09-15 20:26:52.789 wdl.w:ptcp.w:call-paraphase-27 INFO visit :: node: "output-paraphase_bam_bai", values: {"paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-27/call-run_paraphase/out/m84036_250809_035451_s4.bc2124_paraphase/m84036_250809_035451_s4.bc2124.paraphase.bam.bai"}
2025-09-15 20:26:52.789 wdl.w:ptcp.w:call-paraphase-27 INFO visit :: node: "output-paraphase_json", values: {"paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-27/call-run_paraphase/out/m84036_250809_035451_s4.bc2124_paraphase/m84036_250809_035451_s4.bc2124.paraphase.json"}
2025-09-15 20:26:52.789 wdl.w:ptcp.w:call-paraphase-27 INFO visit :: node: "output-paraphase_vcfs", values: {"paraphase_vcfs": ["/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-27/call-run_paraphase/out/m84036_250809_035451_s4.bc2124_paraphase/m84036_250809_035451_s4.bc2124_paraphase_vcfs/m84036_250809_035451_s4.bc2124_cyp21.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-27/call-run_paraphase/out/m84036_250809_035451_s4.bc2124_paraphase/m84036_250809_035451_s4.bc2124_paraphase_vcfs/m84036_250809_035451_s4.bc2124_f8inv1.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-27/call-run_paraphase/out/m84036_250809_035451_s4.bc2124_paraphase/m84036_250809_035451_s4.bc2124_paraphase_vcfs/m84036_250809_035451_s4.bc2124_f8inv22.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-27/call-run_paraphase/out/m84036_250809_035451_s4.bc2124_paraphase/m84036_250809_035451_s4.bc2124_paraphase_vcfs/m84036_250809_035451_s4.bc2124_gba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-27/call-run_paraphase/out/m84036_250809_035451_s4.bc2124_paraphase/m84036_250809_035451_s4.bc2124_paraphase_vcfs/m84036_250809_035451_s4.bc2124_hba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-27/call-run_paraphase/out/m84036_250809_035451_s4.bc2124_paraphase/m84036_250809_035451_s4.bc2124_paraphase_vcfs/m84036_250809_035451_s4.bc2124_hbb.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-27/call-run_paraphase/out/m84036_250809_035451_s4.bc2124_paraphase/m84036_250809_035451_s4.bc2124_paraphase_vcfs/m84036_250809_035451_s4.bc2124_rpgr.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-27/call-run_paraphase/out/m84036_250809_035451_s4.bc2124_paraphase/m84036_250809_035451_s4.bc2124_paraphase_vcfs/m84036_250809_035451_s4.bc2124_smn1.vcf"]}
2025-09-15 20:26:52.794 wdl.w:ptcp.w:call-paraphase-27.t:call-call_f8 NOTICE task setup :: name: "call_f8", source: "./paraphase.wdl", line: 232, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-27/call-call_f8", thread: 140607683024448
2025-09-15 20:26:52.812 wdl.w:ptcp.w:call-paraphase-27.t:call-call_f8 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:26:52.812 wdl.w:ptcp.w:call-paraphase-27.t:call-call_f8 INFO input :: name: "genome_version", value: "38"
2025-09-15 20:26:52.812 wdl.w:ptcp.w:call-paraphase-27.t:call-call_f8 INFO input :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2124"
2025-09-15 20:26:52.812 wdl.w:ptcp.w:call-paraphase-27.t:call-call_f8 INFO input :: name: "paraphase_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2124.paraphase.bam.bai"
2025-09-15 20:26:52.812 wdl.w:ptcp.w:call-paraphase-27.t:call-call_f8 INFO input :: name: "paraphase_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2124.paraphase.bam"
2025-09-15 20:26:52.812 wdl.w:ptcp.w:call-paraphase-27.t:call-call_f8 INFO input :: name: "sex", value: "F"
2025-09-15 20:26:52.812 wdl.w:ptcp.w:call-paraphase-27.t:call-call_f8 INFO eval :: name: "threads", value: 1
2025-09-15 20:26:52.812 wdl.w:ptcp.w:call-paraphase-27.t:call-call_f8 INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:26:52.813 wdl.w:ptcp.w:call-paraphase-27.t:call-call_f8 INFO eval :: name: "disk_size", value: 11
2025-09-15 20:26:52.813 wdl.w:ptcp.w:call-paraphase-27.t:call-call_f8 INFO eval :: name: "sample_sex", value: "F"
2025-09-15 20:26:52.813 wdl.w:ptcp.w:call-paraphase-27.t:call-call_f8 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:26:52.813 wdl.w:ptcp.w:call-paraphase-27.t:call-call_f8 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:26:52.814 wdl.w:ptcp.w:call-paraphase-27.t:call-call_f8 INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:26:52.814 wdl.w:ptcp.w:call-paraphase-27.t:call-call_f8 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:26:52.843 wdl.w:ptcp.w:call-sawfish-82.t:call-run_sawfish NOTICE done
2025-09-15 20:26:52.851 wdl.w:ptcp.w:call-sawfish-82 NOTICE finish :: job: "call-run_sawfish"
2025-09-15 20:26:52.851 wdl.w:ptcp.w:call-sawfish-82 INFO output :: job: "call-run_sawfish", values: {"minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-82/call-run_sawfish/out/m84036_250809_035451_s4.bc2179.minimap2.bam.bai", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-82/call-run_sawfish/out/m84036_250809_035451_s4.bc2179.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-82/call-run_sawfish/out/m84036_250809_035451_s4.bc2179_sawfish/m84036_250809_035451_s4.bc2179.sv.vcf.gz.tbi", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-82/call-run_sawfish/out/m84036_250809_035451_s4.bc2179_sawfish/m84036_250809_035451_s4.bc2179.sv.vcf.gz"}
2025-09-15 20:26:52.851 wdl.w:ptcp.w:call-sawfish-82 INFO visit :: node: "output-minimap2_bam", values: {"minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-82/call-run_sawfish/out/m84036_250809_035451_s4.bc2179.minimap2.bam"}
2025-09-15 20:26:52.851 wdl.w:ptcp.w:call-sawfish-82 INFO visit :: node: "output-minimap2_bam_bai", values: {"minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-82/call-run_sawfish/out/m84036_250809_035451_s4.bc2179.minimap2.bam.bai"}
2025-09-15 20:26:52.852 wdl.w:ptcp.w:call-sawfish-82 INFO visit :: node: "output-vcf", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-82/call-run_sawfish/out/m84036_250809_035451_s4.bc2179_sawfish/m84036_250809_035451_s4.bc2179.sv.vcf.gz"}
2025-09-15 20:26:52.852 wdl.w:ptcp.w:call-sawfish-82 INFO visit :: node: "output-vcf_tbi", values: {"vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-82/call-run_sawfish/out/m84036_250809_035451_s4.bc2179_sawfish/m84036_250809_035451_s4.bc2179.sv.vcf.gz.tbi"}
2025-09-15 20:26:52.852 wdl.w:ptcp.w:call-sawfish-82 INFO visit :: node: "outputs", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-82/call-run_sawfish/out/m84036_250809_035451_s4.bc2179_sawfish/m84036_250809_035451_s4.bc2179.sv.vcf.gz", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-82/call-run_sawfish/out/m84036_250809_035451_s4.bc2179.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-82/call-run_sawfish/out/m84036_250809_035451_s4.bc2179_sawfish/m84036_250809_035451_s4.bc2179.sv.vcf.gz.tbi", "minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-82/call-run_sawfish/out/m84036_250809_035451_s4.bc2179.minimap2.bam.bai"}
2025-09-15 20:26:52.868 wdl.w:ptcp.w:call-paraphase-27.t:call-call_f8 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 8, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-27/call-call_f8/_singularity_tmpdir_etk32mf5"
2025-09-15 20:26:52.868 wdl.w:ptcp.w:call-paraphase-27.t:call-call_f8 INFO Slurm invocation: srun --job-name call-call_f8 --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-27/call-call_f8/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-27/call-call_f8/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-27/call-call_f8/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-27/call-call_f8/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-27/call-run_paraphase/out/m84036_250809_035451_s4.bc2124_paraphase/m84036_250809_035451_s4.bc2124.paraphase.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2124.paraphase.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-27/call-run_paraphase/out/m84036_250809_035451_s4.bc2124_paraphase/m84036_250809_035451_s4.bc2124.paraphase.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2124.paraphase.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-27/call-call_f8/_singularity_tmpdir_etk32mf5/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-27/call-call_f8/_singularity_tmpdir_etk32mf5/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:26:52.876 wdl.w:ptcp.w:call-paraphase-66.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for gba for sample m84036_250809_035451_s4.bc2163 at 2025-09-15 20:26:48.278599...
2025-09-15 20:26:52.881 wdl.w:ptcp.w:call-paraphase-66.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for gba for sample m84036_250809_035451_s4.bc2163 at 2025-09-15 20:26:49.084426...
2025-09-15 20:26:52.912 wdl.w:ptcp.w:call-sawfish-82 NOTICE done
2025-09-15 20:26:52.913 wdl.w:ptcp.w:call-paraphase-27.t:call-call_f8 NOTICE slurm_singularity run :: pid: 1207957, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-27/call-call_f8/slurm_singularity.log.txt"
2025-09-15 20:26:52.921 wdl.w:ptcp NOTICE finish :: job: "call-sawfish-82"
2025-09-15 20:26:52.921 wdl.w:ptcp INFO output :: job: "call-sawfish-82", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-82/out/m84036_250809_035451_s4.bc2179_sawfish/m84036_250809_035451_s4.bc2179.sv.vcf.gz", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-82/out/m84036_250809_035451_s4.bc2179.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-82/out/m84036_250809_035451_s4.bc2179_sawfish/m84036_250809_035451_s4.bc2179.sv.vcf.gz.tbi", "minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-82/out/m84036_250809_035451_s4.bc2179.minimap2.bam.bai"}
2025-09-15 20:26:53.863 wdl.w:ptcp.w:call-paraphase-19.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for f8inv22 for sample m84036_250809_035451_s4.bc2116 at 2025-09-15 20:26:48.273478...
2025-09-15 20:26:53.911 wdl.w:ptcp.w:call-sawfish-75.t:call-run_sawfish.stderr VERBOSE [M::mm_idx_gen::62.444*1.57] collected minimizers
2025-09-15 20:26:53.912 wdl.w:ptcp.w:call-sawfish-75.t:call-run_sawfish.stderr VERBOSE [M::mm_idx_gen::73.748*1.78] sorted minimizers
2025-09-15 20:26:53.912 wdl.w:ptcp.w:call-sawfish-75.t:call-run_sawfish.stderr VERBOSE [M::main::73.749*1.78] loaded/built the index for 195 target sequence(s)
2025-09-15 20:26:53.912 wdl.w:ptcp.w:call-sawfish-75.t:call-run_sawfish.stderr VERBOSE [M::mm_mapopt_update::80.778*1.71] mid_occ = 136
2025-09-15 20:26:53.912 wdl.w:ptcp.w:call-sawfish-75.t:call-run_sawfish.stderr VERBOSE [M::mm_idx_stat] kmer size: 19; skip: 19; is_hpc: 0; #seq: 195
2025-09-15 20:26:53.912 wdl.w:ptcp.w:call-sawfish-75.t:call-run_sawfish.stderr VERBOSE [M::mm_idx_stat::85.894*1.67] distinct minimizers: 214664461 (92.23% are singletons); average occurrences: 1.372; average spacing: 10.529; total length: 3099922541
2025-09-15 20:26:53.912 wdl.w:ptcp.w:call-sawfish-75.t:call-run_sawfish.stderr VERBOSE [M::bam2fq_mainloop] discarded 0 singletons
2025-09-15 20:26:53.912 wdl.w:ptcp.w:call-sawfish-75.t:call-run_sawfish.stderr VERBOSE [M::bam2fq_mainloop] processed 332 reads
2025-09-15 20:26:53.912 wdl.w:ptcp.w:call-sawfish-75.t:call-run_sawfish.stderr VERBOSE [M::worker_pipeline::86.689*1.67] mapped 332 sequences
2025-09-15 20:26:53.912 wdl.w:ptcp.w:call-sawfish-75.t:call-run_sawfish.stderr VERBOSE [M::main] Version: 2.26-r1175
2025-09-15 20:26:53.912 wdl.w:ptcp.w:call-sawfish-75.t:call-run_sawfish.stderr VERBOSE [M::main] CMD: /opt/pacbio/smrttools/install/smrtlink-release_25.1.0.257715/bundles/smrttools/install/smrttools-release_25.1.0.257715/private/thirdparty/minimap2/minimap2_2.26-pacbio2/binwrap/../../../../../private/thirdparty/minimap2/minimap2_2.26-pacbio2/bin/minimap2 -a -y -x map-hifi -Y -E 1,0 /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa -
2025-09-15 20:26:53.912 wdl.w:ptcp.w:call-sawfish-75.t:call-run_sawfish.stderr VERBOSE [M::main] Real time: 87.085 sec; CPU: 145.177 sec; Peak RSS: 11.886 GB
2025-09-15 20:26:53.927 wdl.w:ptcp.w:call-paraphase-27.t:call-call_f8.slurm_singularity INFO srun: job 51798213 queued and waiting for resources
2025-09-15 20:26:54.729 wdl.w:ptcp.w:call-sawfish-81.t:call-run_sawfish.stderr VERBOSE [M::mm_idx_gen::60.340*1.57] collected minimizers
2025-09-15 20:26:54.730 wdl.w:ptcp.w:call-sawfish-81.t:call-run_sawfish.stderr VERBOSE [M::mm_idx_gen::71.809*1.79] sorted minimizers
2025-09-15 20:26:54.730 wdl.w:ptcp.w:call-sawfish-81.t:call-run_sawfish.stderr VERBOSE [M::main::71.810*1.79] loaded/built the index for 195 target sequence(s)
2025-09-15 20:26:54.730 wdl.w:ptcp.w:call-sawfish-81.t:call-run_sawfish.stderr VERBOSE [M::mm_mapopt_update::78.350*1.72] mid_occ = 136
2025-09-15 20:26:54.730 wdl.w:ptcp.w:call-sawfish-81.t:call-run_sawfish.stderr VERBOSE [M::mm_idx_stat] kmer size: 19; skip: 19; is_hpc: 0; #seq: 195
2025-09-15 20:26:54.730 wdl.w:ptcp.w:call-sawfish-81.t:call-run_sawfish.stderr VERBOSE [M::mm_idx_stat::83.272*1.68] distinct minimizers: 214664461 (92.23% are singletons); average occurrences: 1.372; average spacing: 10.529; total length: 3099922541
2025-09-15 20:26:54.730 wdl.w:ptcp.w:call-sawfish-81.t:call-run_sawfish.stderr VERBOSE [M::worker_pipeline::83.275*1.68] mapped 1 sequences
2025-09-15 20:26:54.730 wdl.w:ptcp.w:call-sawfish-81.t:call-run_sawfish.stderr VERBOSE [M::main] Version: 2.26-r1175
2025-09-15 20:26:54.730 wdl.w:ptcp.w:call-sawfish-81.t:call-run_sawfish.stderr VERBOSE [M::main] CMD: /opt/pacbio/smrttools/install/smrtlink-release_25.1.0.257715/bundles/smrttools/install/smrttools-release_25.1.0.257715/private/thirdparty/minimap2/minimap2_2.26-pacbio2/binwrap/../../../../../private/thirdparty/minimap2/minimap2_2.26-pacbio2/bin/minimap2 -a -y -x map-hifi -Y -E 1,0 /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa -
2025-09-15 20:26:54.730 wdl.w:ptcp.w:call-sawfish-81.t:call-run_sawfish.stderr VERBOSE [M::main] Real time: 83.629 sec; CPU: 140.176 sec; Peak RSS: 11.886 GB
2025-09-15 20:26:54.730 wdl.w:ptcp.w:call-sawfish-81.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:44][sawfish][INFO] Starting sawfish 2.0.3
2025-09-15 20:26:54.730 wdl.w:ptcp.w:call-sawfish-81.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:44][sawfish][INFO] cmdline: sawfish discover --disable-cnv --threads 16 --ref /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa --bam m84036_250809_035451_s4.bc2178.minimap2.bam --output-dir m84036_250809_035451_s4.bc2178_sawfish_discover
2025-09-15 20:26:54.730 wdl.w:ptcp.w:call-sawfish-81.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:44][sawfish][INFO] Running on 16 threads
2025-09-15 20:26:54.731 wdl.w:ptcp.w:call-sawfish-81.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:44][sawfish][INFO] Writing discover settings to file: 'm84036_250809_035451_s4.bc2178_sawfish_discover/discover.settings.json'
2025-09-15 20:26:54.731 wdl.w:ptcp.w:call-sawfish-81.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:44][sawfish][INFO] Reading reference genome from file '/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa'
2025-09-15 20:26:54.731 wdl.w:ptcp.w:call-sawfish-81.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:50][sawfish][INFO] Processing alignment file '/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2178.minimap2.bam'
2025-09-15 20:26:54.731 wdl.w:ptcp.w:call-sawfish-81.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:50][sawfish][INFO] Finished processing all alignments
2025-09-15 20:26:54.731 wdl.w:ptcp.w:call-sawfish-81.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:50][sawfish][INFO] Writing depth bins to binary file: 'm84036_250809_035451_s4.bc2178_sawfish_discover/depth.mpack'
2025-09-15 20:26:54.731 wdl.w:ptcp.w:call-sawfish-81.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:50][sawfish][INFO] Writing max sv depth genome regions to bed file: 'm84036_250809_035451_s4.bc2178_sawfish_discover/max.depth.bed'
2025-09-15 20:26:54.731 wdl.w:ptcp.w:call-sawfish-81.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:50][sawfish][INFO] Completing breakpoint observation clustering
2025-09-15 20:26:54.731 wdl.w:ptcp.w:call-sawfish-81.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:50][sawfish][INFO] Finished breakpoint observation clustering
2025-09-15 20:26:54.731 wdl.w:ptcp.w:call-sawfish-81.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:50][sawfish][INFO] Consolidating adjacent indel candidates
2025-09-15 20:26:54.731 wdl.w:ptcp.w:call-sawfish-81.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:50][sawfish][INFO] Finding large insertion candidates
2025-09-15 20:26:54.731 wdl.w:ptcp.w:call-sawfish-81.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:50][sawfish][INFO] Writing breakpoint_cluster debug bed file: 'm84036_250809_035451_s4.bc2178_sawfish_discover/debug.breakpoint_clusters.bed'
2025-09-15 20:26:54.731 wdl.w:ptcp.w:call-sawfish-81.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:50][sawfish][INFO] Refining SV Candidates
2025-09-15 20:26:54.731 wdl.w:ptcp.w:call-sawfish-81.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:50][sawfish][INFO] Writing debug assembly region bed file: 'm84036_250809_035451_s4.bc2178_sawfish_discover/assembly.regions.bed'
2025-09-15 20:26:54.731 wdl.w:ptcp.w:call-sawfish-81.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:50][sawfish][INFO] Starting refinement of breakpoint evidence clusters
2025-09-15 20:26:54.731 wdl.w:ptcp.w:call-sawfish-81.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:50][sawfish][INFO] Finished refining all breakpoint evidence clusters
2025-09-15 20:26:54.731 wdl.w:ptcp.w:call-sawfish-81.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:50][sawfish][INFO] Writing all contig alignments to bam file: 'm84036_250809_035451_s4.bc2178_sawfish_discover/contig.alignment.bam'
2025-09-15 20:26:54.731 wdl.w:ptcp.w:call-sawfish-81.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:50][sawfish][INFO] Writing candidate structural variants to file: 'm84036_250809_035451_s4.bc2178_sawfish_discover/candidate.sv.bcf'
2025-09-15 20:26:54.731 wdl.w:ptcp.w:call-sawfish-81.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:50][sawfish][INFO] Writing run statistics to file: 'm84036_250809_035451_s4.bc2178_sawfish_discover/run.stats.json'
2025-09-15 20:26:54.731 wdl.w:ptcp.w:call-sawfish-81.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:50][sawfish][INFO] sawfish completed. Total Runtime: 00:00:06.497
2025-09-15 20:26:54.941 wdl.w:ptcp.w:call-paraphase-27.t:call-call_f8.slurm_singularity INFO srun: job 51798213 has been allocated resources
2025-09-15 20:26:54.942 wdl.w:ptcp.w:call-paraphase-27.t:call-call_f8.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:26:55.044 wdl.w:ptcp.w:call-paraphase-18.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for f8inv22 for sample m84036_250809_035451_s4.bc2115 at 2025-09-15 20:26:42.254663...
2025-09-15 20:26:55.044 wdl.w:ptcp.w:call-paraphase-18.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for f8inv22 for sample m84036_250809_035451_s4.bc2115 at 2025-09-15 20:26:45.522331...
2025-09-15 20:26:55.044 wdl.w:ptcp.w:call-paraphase-18.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for f8inv22 for sample m84036_250809_035451_s4.bc2115 at 2025-09-15 20:26:45.742661...
2025-09-15 20:26:55.167 wdl.w:ptcp.w:call-paraphase-90.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for hba for sample m84036_250809_035451_s4.bc2187 at 2025-09-15 20:26:46.043554...
2025-09-15 20:26:55.167 wdl.w:ptcp.w:call-paraphase-90.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for hba for sample m84036_250809_035451_s4.bc2187 at 2025-09-15 20:26:46.501367...
2025-09-15 20:26:55.332 wdl.w:ptcp.w:call-sawfish-77.t:call-run_sawfish INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2174_sawfish/m84036_250809_035451_s4.bc2174.sv.vcf.gz"
2025-09-15 20:26:55.336 wdl.w:ptcp.w:call-sawfish-77.t:call-run_sawfish INFO output :: name: "vcf_tbi", value: "m84036_250809_035451_s4.bc2174_sawfish/m84036_250809_035451_s4.bc2174.sv.vcf.gz.tbi"
2025-09-15 20:26:55.337 wdl.w:ptcp.w:call-sawfish-77.t:call-run_sawfish INFO output :: name: "minimap2_bam", value: "m84036_250809_035451_s4.bc2174.minimap2.bam"
2025-09-15 20:26:55.338 wdl.w:ptcp.w:call-sawfish-77.t:call-run_sawfish INFO output :: name: "minimap2_bam_bai", value: "m84036_250809_035451_s4.bc2174.minimap2.bam.bai"
2025-09-15 20:26:55.454 wdl.w:ptcp.w:call-sawfish-77.t:call-run_sawfish NOTICE done
2025-09-15 20:26:55.460 wdl.w:ptcp.w:call-sawfish-77 NOTICE finish :: job: "call-run_sawfish"
2025-09-15 20:26:55.460 wdl.w:ptcp.w:call-sawfish-77 INFO output :: job: "call-run_sawfish", values: {"minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-77/call-run_sawfish/out/m84036_250809_035451_s4.bc2174.minimap2.bam.bai", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-77/call-run_sawfish/out/m84036_250809_035451_s4.bc2174.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-77/call-run_sawfish/out/m84036_250809_035451_s4.bc2174_sawfish/m84036_250809_035451_s4.bc2174.sv.vcf.gz.tbi", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-77/call-run_sawfish/out/m84036_250809_035451_s4.bc2174_sawfish/m84036_250809_035451_s4.bc2174.sv.vcf.gz"}
2025-09-15 20:26:55.460 wdl.w:ptcp.w:call-sawfish-77 INFO visit :: node: "output-minimap2_bam", values: {"minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-77/call-run_sawfish/out/m84036_250809_035451_s4.bc2174.minimap2.bam"}
2025-09-15 20:26:55.460 wdl.w:ptcp.w:call-sawfish-77 INFO visit :: node: "output-minimap2_bam_bai", values: {"minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-77/call-run_sawfish/out/m84036_250809_035451_s4.bc2174.minimap2.bam.bai"}
2025-09-15 20:26:55.461 wdl.w:ptcp.w:call-sawfish-77 INFO visit :: node: "output-vcf", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-77/call-run_sawfish/out/m84036_250809_035451_s4.bc2174_sawfish/m84036_250809_035451_s4.bc2174.sv.vcf.gz"}
2025-09-15 20:26:55.461 wdl.w:ptcp.w:call-sawfish-77 INFO visit :: node: "output-vcf_tbi", values: {"vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-77/call-run_sawfish/out/m84036_250809_035451_s4.bc2174_sawfish/m84036_250809_035451_s4.bc2174.sv.vcf.gz.tbi"}
2025-09-15 20:26:55.461 wdl.w:ptcp.w:call-sawfish-77 INFO visit :: node: "outputs", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-77/call-run_sawfish/out/m84036_250809_035451_s4.bc2174_sawfish/m84036_250809_035451_s4.bc2174.sv.vcf.gz", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-77/call-run_sawfish/out/m84036_250809_035451_s4.bc2174.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-77/call-run_sawfish/out/m84036_250809_035451_s4.bc2174_sawfish/m84036_250809_035451_s4.bc2174.sv.vcf.gz.tbi", "minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-77/call-run_sawfish/out/m84036_250809_035451_s4.bc2174.minimap2.bam.bai"}
2025-09-15 20:26:55.462 wdl.w:ptcp.w:call-paraphase-86.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for f8inv1 for sample m84036_250809_035451_s4.bc2183 at 2025-09-15 20:26:51.537815...
2025-09-15 20:26:55.462 wdl.w:ptcp.w:call-paraphase-86.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for hbb for sample m84036_250809_035451_s4.bc2183 at 2025-09-15 20:26:53.625124...
2025-09-15 20:26:55.463 wdl.w:ptcp.w:call-paraphase-86.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for hbb for sample m84036_250809_035451_s4.bc2183 at 2025-09-15 20:26:53.627843...
2025-09-15 20:26:55.497 wdl.w:ptcp.w:call-paraphase-27.t:call-call_f8 INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2124.f8inversion.vcf"
2025-09-15 20:26:55.501 wdl.w:ptcp.w:call-paraphase-27.t:call-call_f8 INFO output :: name: "json", value: "m84036_250809_035451_s4.bc2124.f8inversion.json"
2025-09-15 20:26:55.502 wdl.w:ptcp.w:call-sawfish-77 NOTICE done
2025-09-15 20:26:55.514 wdl.w:ptcp NOTICE finish :: job: "call-sawfish-77"
2025-09-15 20:26:55.514 wdl.w:ptcp INFO output :: job: "call-sawfish-77", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-77/out/m84036_250809_035451_s4.bc2174_sawfish/m84036_250809_035451_s4.bc2174.sv.vcf.gz", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-77/out/m84036_250809_035451_s4.bc2174.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-77/out/m84036_250809_035451_s4.bc2174_sawfish/m84036_250809_035451_s4.bc2174.sv.vcf.gz.tbi", "minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-77/out/m84036_250809_035451_s4.bc2174.minimap2.bam.bai"}
2025-09-15 20:26:55.515 wdl.w:ptcp NOTICE ready :: job: "call-tar_outputs-77", callee: "tar_outputs"
2025-09-15 20:26:55.515 wdl.w:ptcp INFO input :: job: "call-tar_outputs-77", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "sawfish_vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-77/out/m84036_250809_035451_s4.bc2174_sawfish/m84036_250809_035451_s4.bc2174.sv.vcf.gz.tbi", "sawfish_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-77/out/m84036_250809_035451_s4.bc2174_sawfish/m84036_250809_035451_s4.bc2174.sv.vcf.gz", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-77/out/m84036_250809_035451_s4.bc2174.f8inversion.json", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-77/out/m84036_250809_035451_s4.bc2174_paraphase/m84036_250809_035451_s4.bc2174.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-77/out/m84036_250809_035451_s4.bc2174_paraphase/m84036_250809_035451_s4.bc2174.paraphase.bam", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-77/out/m84036_250809_035451_s4.bc2174_paraphase/m84036_250809_035451_s4.bc2174.paraphase.json", "trgt_spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-77/out/m84036_250809_035451_s4.bc2174.trgt.sorted.spanning.bam.bai", "trgt_spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-77/out/m84036_250809_035451_s4.bc2174.trgt.sorted.spanning.bam", "trgt_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-77/out/m84036_250809_035451_s4.bc2174.trgt.vcf", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-77/out/m84036_250809_035451_s4.bc2174.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-77/out/m84036_250809_035451_s4.bc2174.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2174"}
2025-09-15 20:26:55.524 wdl.w:ptcp.t:call-tar_outputs-77 NOTICE task setup :: name: "tar_outputs", source: "./common.wdl", line: 279, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-77", thread: 140612481291840
2025-09-15 20:26:55.556 wdl.w:ptcp.t:call-tar_outputs-77 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:26:55.556 wdl.w:ptcp.t:call-tar_outputs-77 INFO input :: name: "sawfish_vcf_tbi", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2174.sv.vcf.gz.tbi"
2025-09-15 20:26:55.556 wdl.w:ptcp.t:call-tar_outputs-77 INFO input :: name: "sawfish_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2174.sv.vcf.gz"
2025-09-15 20:26:55.556 wdl.w:ptcp.t:call-tar_outputs-77 INFO input :: name: "f8_json", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2174.f8inversion.json"
2025-09-15 20:26:55.556 wdl.w:ptcp.t:call-tar_outputs-77 INFO input :: name: "paraphase_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2174.paraphase.bam.bai"
2025-09-15 20:26:55.557 wdl.w:ptcp.t:call-tar_outputs-77 INFO input :: name: "paraphase_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2174.paraphase.bam"
2025-09-15 20:26:55.557 wdl.w:ptcp.t:call-tar_outputs-77 INFO input :: name: "paraphase_json", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2174.paraphase.json"
2025-09-15 20:26:55.557 wdl.w:ptcp.t:call-tar_outputs-77 INFO input :: name: "trgt_spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2174.trgt.sorted.spanning.bam.bai"
2025-09-15 20:26:55.557 wdl.w:ptcp.t:call-tar_outputs-77 INFO input :: name: "trgt_spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2174.trgt.sorted.spanning.bam"
2025-09-15 20:26:55.557 wdl.w:ptcp.t:call-tar_outputs-77 INFO input :: name: "trgt_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2174.trgt.vcf"
2025-09-15 20:26:55.557 wdl.w:ptcp.t:call-tar_outputs-77 INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2174.mapped.bam.bai"
2025-09-15 20:26:55.557 wdl.w:ptcp.t:call-tar_outputs-77 INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2174.mapped.bam"
2025-09-15 20:26:55.557 wdl.w:ptcp.t:call-tar_outputs-77 INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2174"
2025-09-15 20:26:55.557 wdl.w:ptcp.t:call-tar_outputs-77 INFO eval :: name: "threads", value: 1
2025-09-15 20:26:55.557 wdl.w:ptcp.t:call-tar_outputs-77 INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:26:55.557 wdl.w:ptcp.t:call-tar_outputs-77 INFO eval :: name: "disk_size", value: 6
2025-09-15 20:26:55.557 wdl.w:ptcp.t:call-tar_outputs-77 INFO eval :: name: "output_tarball", value: "m84036_250809_035451_s4.bc2174.tar"
2025-09-15 20:26:55.558 wdl.w:ptcp.t:call-tar_outputs-77 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:26:55.558 wdl.w:ptcp.t:call-tar_outputs-77 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:26:55.558 wdl.w:ptcp.t:call-tar_outputs-77 INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:26:55.558 wdl.w:ptcp.t:call-tar_outputs-77 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:26:55.561 wdl.w:ptcp.w:call-paraphase-27.t:call-call_f8 NOTICE done
2025-09-15 20:26:55.566 wdl.w:ptcp.w:call-paraphase-27 NOTICE finish :: job: "call-call_f8"
2025-09-15 20:26:55.567 wdl.w:ptcp.w:call-paraphase-27 INFO output :: job: "call-call_f8", values: {"json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-27/call-call_f8/out/m84036_250809_035451_s4.bc2124.f8inversion.json", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-27/call-call_f8/out/m84036_250809_035451_s4.bc2124.f8inversion.vcf"}
2025-09-15 20:26:55.567 wdl.w:ptcp.w:call-paraphase-27 INFO visit :: node: "output-f8_json", values: {"f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-27/call-call_f8/out/m84036_250809_035451_s4.bc2124.f8inversion.json"}
2025-09-15 20:26:55.567 wdl.w:ptcp.w:call-paraphase-27 INFO visit :: node: "output-f8_vcf", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-27/call-call_f8/out/m84036_250809_035451_s4.bc2124.f8inversion.vcf"}
2025-09-15 20:26:55.567 wdl.w:ptcp.w:call-paraphase-27 INFO visit :: node: "outputs", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-27/call-call_f8/out/m84036_250809_035451_s4.bc2124.f8inversion.vcf", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-27/call-run_paraphase/out/m84036_250809_035451_s4.bc2124_paraphase/m84036_250809_035451_s4.bc2124.paraphase.json", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-27/call-run_paraphase/out/m84036_250809_035451_s4.bc2124_paraphase/m84036_250809_035451_s4.bc2124.paraphase.bam", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-27/call-run_paraphase/out/m84036_250809_035451_s4.bc2124_paraphase/m84036_250809_035451_s4.bc2124.paraphase.bam.bai", "paraphase_vcfs": ["/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-27/call-run_paraphase/out/m84036_250809_035451_s4.bc2124_paraphase/m84036_250809_035451_s4.bc2124_paraphase_vcfs/m84036_250809_035451_s4.bc2124_cyp21.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-27/call-run_paraphase/out/m84036_250809_035451_s4.bc2124_paraphase/m84036_250809_035451_s4.bc2124_paraphase_vcfs/m84036_250809_035451_s4.bc2124_f8inv1.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-27/call-run_paraphase/out/m84036_250809_035451_s4.bc2124_paraphase/m84036_250809_035451_s4.bc2124_paraphase_vcfs/m84036_250809_035451_s4.bc2124_f8inv22.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-27/call-run_paraphase/out/m84036_250809_035451_s4.bc2124_paraphase/m84036_250809_035451_s4.bc2124_paraphase_vcfs/m84036_250809_035451_s4.bc2124_gba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-27/call-run_paraphase/out/m84036_250809_035451_s4.bc2124_paraphase/m84036_250809_035451_s4.bc2124_paraphase_vcfs/m84036_250809_035451_s4.bc2124_hba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-27/call-run_paraphase/out/m84036_250809_035451_s4.bc2124_paraphase/m84036_250809_035451_s4.bc2124_paraphase_vcfs/m84036_250809_035451_s4.bc2124_hbb.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-27/call-run_paraphase/out/m84036_250809_035451_s4.bc2124_paraphase/m84036_250809_035451_s4.bc2124_paraphase_vcfs/m84036_250809_035451_s4.bc2124_rpgr.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-27/call-run_paraphase/out/m84036_250809_035451_s4.bc2124_paraphase/m84036_250809_035451_s4.bc2124_paraphase_vcfs/m84036_250809_035451_s4.bc2124_smn1.vcf"], "havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-27/call-run_paraphase/out/m84036_250809_035451_s4.bc2124.havanno.json", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-27/call-call_f8/out/m84036_250809_035451_s4.bc2124.f8inversion.json"}
2025-09-15 20:26:55.649 wdl.w:ptcp.t:call-tar_outputs-77 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 17, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-77/_singularity_tmpdir_rxaqckgb"
2025-09-15 20:26:55.649 wdl.w:ptcp.t:call-tar_outputs-77 INFO Slurm invocation: srun --job-name call-tar_outputs-77 --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-77/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-77/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-77/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-77/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-77/out/m84036_250809_035451_s4.bc2174_sawfish/m84036_250809_035451_s4.bc2174.sv.vcf.gz:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2174.sv.vcf.gz:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-77/out/m84036_250809_035451_s4.bc2174_sawfish/m84036_250809_035451_s4.bc2174.sv.vcf.gz.tbi:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2174.sv.vcf.gz.tbi:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-77/out/m84036_250809_035451_s4.bc2174.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2174.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-77/out/m84036_250809_035451_s4.bc2174.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2174.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-77/out/m84036_250809_035451_s4.bc2174.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2174.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-77/out/m84036_250809_035451_s4.bc2174_paraphase/m84036_250809_035451_s4.bc2174.paraphase.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2174.paraphase.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-77/out/m84036_250809_035451_s4.bc2174_paraphase/m84036_250809_035451_s4.bc2174.paraphase.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2174.paraphase.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-77/out/m84036_250809_035451_s4.bc2174_paraphase/m84036_250809_035451_s4.bc2174.paraphase.json:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2174.paraphase.json:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-77/out/m84036_250809_035451_s4.bc2174.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2174.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-77/out/m84036_250809_035451_s4.bc2174.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2174.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-77/out/m84036_250809_035451_s4.bc2174.f8inversion.json:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2174.f8inversion.json:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-77/_singularity_tmpdir_rxaqckgb/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-77/_singularity_tmpdir_rxaqckgb/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:26:55.665 wdl.w:ptcp.t:call-tar_outputs-77 NOTICE slurm_singularity run :: pid: 1207967, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-77/slurm_singularity.log.txt"
2025-09-15 20:26:55.684 wdl.w:ptcp.w:call-paraphase-27 NOTICE done
2025-09-15 20:26:55.712 wdl.w:ptcp NOTICE finish :: job: "call-paraphase-27"
2025-09-15 20:26:55.713 wdl.w:ptcp INFO output :: job: "call-paraphase-27", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-27/out/m84036_250809_035451_s4.bc2124.f8inversion.vcf", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-27/out/m84036_250809_035451_s4.bc2124_paraphase/m84036_250809_035451_s4.bc2124.paraphase.json", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-27/out/m84036_250809_035451_s4.bc2124_paraphase/m84036_250809_035451_s4.bc2124.paraphase.bam", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-27/out/m84036_250809_035451_s4.bc2124_paraphase/m84036_250809_035451_s4.bc2124.paraphase.bam.bai", "paraphase_vcfs": ["/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-27/out/m84036_250809_035451_s4.bc2124_paraphase/m84036_250809_035451_s4.bc2124_paraphase_vcfs/m84036_250809_035451_s4.bc2124_cyp21.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-27/out/m84036_250809_035451_s4.bc2124_paraphase/m84036_250809_035451_s4.bc2124_paraphase_vcfs/m84036_250809_035451_s4.bc2124_f8inv1.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-27/out/m84036_250809_035451_s4.bc2124_paraphase/m84036_250809_035451_s4.bc2124_paraphase_vcfs/m84036_250809_035451_s4.bc2124_f8inv22.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-27/out/m84036_250809_035451_s4.bc2124_paraphase/m84036_250809_035451_s4.bc2124_paraphase_vcfs/m84036_250809_035451_s4.bc2124_gba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-27/out/m84036_250809_035451_s4.bc2124_paraphase/m84036_250809_035451_s4.bc2124_paraphase_vcfs/m84036_250809_035451_s4.bc2124_hba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-27/out/m84036_250809_035451_s4.bc2124_paraphase/m84036_250809_035451_s4.bc2124_paraphase_vcfs/m84036_250809_035451_s4.bc2124_hbb.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-27/out/m84036_250809_035451_s4.bc2124_paraphase/m84036_250809_035451_s4.bc2124_paraphase_vcfs/m84036_250809_035451_s4.bc2124_rpgr.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-27/out/m84036_250809_035451_s4.bc2124_paraphase/m84036_250809_035451_s4.bc2124_paraphase_vcfs/m84036_250809_035451_s4.bc2124_smn1.vcf"], "havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-27/out/m84036_250809_035451_s4.bc2124.havanno.json", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-27/out/m84036_250809_035451_s4.bc2124.f8inversion.json"}
2025-09-15 20:26:55.714 wdl.w:ptcp NOTICE ready :: job: "call-tar_outputs-27", callee: "tar_outputs"
2025-09-15 20:26:55.714 wdl.w:ptcp INFO input :: job: "call-tar_outputs-27", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "sawfish_vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-27/out/m84036_250809_035451_s4.bc2124_sawfish/m84036_250809_035451_s4.bc2124.sv.vcf.gz.tbi", "sawfish_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-27/out/m84036_250809_035451_s4.bc2124_sawfish/m84036_250809_035451_s4.bc2124.sv.vcf.gz", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-27/out/m84036_250809_035451_s4.bc2124.f8inversion.json", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-27/out/m84036_250809_035451_s4.bc2124_paraphase/m84036_250809_035451_s4.bc2124.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-27/out/m84036_250809_035451_s4.bc2124_paraphase/m84036_250809_035451_s4.bc2124.paraphase.bam", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-27/out/m84036_250809_035451_s4.bc2124_paraphase/m84036_250809_035451_s4.bc2124.paraphase.json", "trgt_spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-27/out/m84036_250809_035451_s4.bc2124.trgt.sorted.spanning.bam.bai", "trgt_spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-27/out/m84036_250809_035451_s4.bc2124.trgt.sorted.spanning.bam", "trgt_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-27/out/m84036_250809_035451_s4.bc2124.trgt.vcf", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-27/out/m84036_250809_035451_s4.bc2124.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-27/out/m84036_250809_035451_s4.bc2124.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2124"}
2025-09-15 20:26:55.720 wdl.w:ptcp.t:call-tar_outputs-27 NOTICE task setup :: name: "tar_outputs", source: "./common.wdl", line: 279, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-27", thread: 140609822115392
2025-09-15 20:26:55.739 wdl.w:ptcp.t:call-tar_outputs-27 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:26:55.739 wdl.w:ptcp.t:call-tar_outputs-27 INFO input :: name: "sawfish_vcf_tbi", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2124.sv.vcf.gz.tbi"
2025-09-15 20:26:55.739 wdl.w:ptcp.t:call-tar_outputs-27 INFO input :: name: "sawfish_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2124.sv.vcf.gz"
2025-09-15 20:26:55.739 wdl.w:ptcp.t:call-tar_outputs-27 INFO input :: name: "f8_json", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2124.f8inversion.json"
2025-09-15 20:26:55.739 wdl.w:ptcp.t:call-tar_outputs-27 INFO input :: name: "paraphase_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2124.paraphase.bam.bai"
2025-09-15 20:26:55.739 wdl.w:ptcp.t:call-tar_outputs-27 INFO input :: name: "paraphase_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2124.paraphase.bam"
2025-09-15 20:26:55.739 wdl.w:ptcp.t:call-tar_outputs-27 INFO input :: name: "paraphase_json", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2124.paraphase.json"
2025-09-15 20:26:55.740 wdl.w:ptcp.t:call-tar_outputs-27 INFO input :: name: "trgt_spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2124.trgt.sorted.spanning.bam.bai"
2025-09-15 20:26:55.740 wdl.w:ptcp.t:call-tar_outputs-27 INFO input :: name: "trgt_spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2124.trgt.sorted.spanning.bam"
2025-09-15 20:26:55.740 wdl.w:ptcp.t:call-tar_outputs-27 INFO input :: name: "trgt_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2124.trgt.vcf"
2025-09-15 20:26:55.740 wdl.w:ptcp.t:call-tar_outputs-27 INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2124.mapped.bam.bai"
2025-09-15 20:26:55.740 wdl.w:ptcp.t:call-tar_outputs-27 INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2124.mapped.bam"
2025-09-15 20:26:55.740 wdl.w:ptcp.t:call-tar_outputs-27 INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2124"
2025-09-15 20:26:55.740 wdl.w:ptcp.t:call-tar_outputs-27 INFO eval :: name: "threads", value: 1
2025-09-15 20:26:55.740 wdl.w:ptcp.t:call-tar_outputs-27 INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:26:55.740 wdl.w:ptcp.t:call-tar_outputs-27 INFO eval :: name: "disk_size", value: 6
2025-09-15 20:26:55.740 wdl.w:ptcp.t:call-tar_outputs-27 INFO eval :: name: "output_tarball", value: "m84036_250809_035451_s4.bc2124.tar"
2025-09-15 20:26:55.741 wdl.w:ptcp.t:call-tar_outputs-27 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:26:55.741 wdl.w:ptcp.t:call-tar_outputs-27 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:26:55.741 wdl.w:ptcp.t:call-tar_outputs-27 INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:26:55.741 wdl.w:ptcp.t:call-tar_outputs-27 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:26:55.822 wdl.w:ptcp.t:call-tar_outputs-27 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 17, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-27/_singularity_tmpdir_78f5vc5t"
2025-09-15 20:26:55.823 wdl.w:ptcp.t:call-tar_outputs-27 INFO Slurm invocation: srun --job-name call-tar_outputs-27 --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-27/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-27/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-27/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-27/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-27/out/m84036_250809_035451_s4.bc2124_sawfish/m84036_250809_035451_s4.bc2124.sv.vcf.gz.tbi:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2124.sv.vcf.gz.tbi:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-27/out/m84036_250809_035451_s4.bc2124_sawfish/m84036_250809_035451_s4.bc2124.sv.vcf.gz:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2124.sv.vcf.gz:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-27/out/m84036_250809_035451_s4.bc2124.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2124.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-27/out/m84036_250809_035451_s4.bc2124.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2124.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-27/out/m84036_250809_035451_s4.bc2124.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2124.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-27/out/m84036_250809_035451_s4.bc2124.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2124.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-27/out/m84036_250809_035451_s4.bc2124.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2124.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-27/out/m84036_250809_035451_s4.bc2124_paraphase/m84036_250809_035451_s4.bc2124.paraphase.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2124.paraphase.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-27/out/m84036_250809_035451_s4.bc2124_paraphase/m84036_250809_035451_s4.bc2124.paraphase.json:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2124.paraphase.json:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-27/out/m84036_250809_035451_s4.bc2124_paraphase/m84036_250809_035451_s4.bc2124.paraphase.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2124.paraphase.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-27/out/m84036_250809_035451_s4.bc2124.f8inversion.json:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2124.f8inversion.json:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-27/_singularity_tmpdir_78f5vc5t/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-27/_singularity_tmpdir_78f5vc5t/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:26:55.828 wdl.w:ptcp.t:call-tar_outputs-27 NOTICE slurm_singularity run :: pid: 1207970, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-27/slurm_singularity.log.txt"
2025-09-15 20:26:55.873 wdl.w:ptcp.w:call-paraphase-75.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for hba for sample m84036_250809_035451_s4.bc2172 at 2025-09-15 20:26:46.625291...
2025-09-15 20:26:55.874 wdl.w:ptcp.w:call-paraphase-75.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for hba for sample m84036_250809_035451_s4.bc2172 at 2025-09-15 20:26:47.289653...
2025-09-15 20:26:55.883 wdl.w:ptcp.w:call-sawfish-60.t:call-run_sawfish INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2157_sawfish/m84036_250809_035451_s4.bc2157.sv.vcf.gz"
2025-09-15 20:26:55.889 wdl.w:ptcp.w:call-sawfish-60.t:call-run_sawfish INFO output :: name: "vcf_tbi", value: "m84036_250809_035451_s4.bc2157_sawfish/m84036_250809_035451_s4.bc2157.sv.vcf.gz.tbi"
2025-09-15 20:26:55.890 wdl.w:ptcp.w:call-sawfish-60.t:call-run_sawfish INFO output :: name: "minimap2_bam", value: "m84036_250809_035451_s4.bc2157.minimap2.bam"
2025-09-15 20:26:55.892 wdl.w:ptcp.w:call-sawfish-60.t:call-run_sawfish INFO output :: name: "minimap2_bam_bai", value: "m84036_250809_035451_s4.bc2157.minimap2.bam.bai"
2025-09-15 20:26:56.014 wdl.w:ptcp.w:call-sawfish-60.t:call-run_sawfish NOTICE done
2025-09-15 20:26:56.019 wdl.w:ptcp.w:call-sawfish-91.t:call-run_sawfish INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2188_sawfish/m84036_250809_035451_s4.bc2188.sv.vcf.gz"
2025-09-15 20:26:56.023 wdl.w:ptcp.w:call-sawfish-91.t:call-run_sawfish INFO output :: name: "vcf_tbi", value: "m84036_250809_035451_s4.bc2188_sawfish/m84036_250809_035451_s4.bc2188.sv.vcf.gz.tbi"
2025-09-15 20:26:56.024 wdl.w:ptcp.w:call-sawfish-91.t:call-run_sawfish INFO output :: name: "minimap2_bam", value: "m84036_250809_035451_s4.bc2188.minimap2.bam"
2025-09-15 20:26:56.026 wdl.w:ptcp.w:call-sawfish-91.t:call-run_sawfish INFO output :: name: "minimap2_bam_bai", value: "m84036_250809_035451_s4.bc2188.minimap2.bam.bai"
2025-09-15 20:26:56.034 wdl.w:ptcp.w:call-sawfish-60 NOTICE finish :: job: "call-run_sawfish"
2025-09-15 20:26:56.034 wdl.w:ptcp.w:call-sawfish-60 INFO output :: job: "call-run_sawfish", values: {"minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-60/call-run_sawfish/out/m84036_250809_035451_s4.bc2157.minimap2.bam.bai", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-60/call-run_sawfish/out/m84036_250809_035451_s4.bc2157.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-60/call-run_sawfish/out/m84036_250809_035451_s4.bc2157_sawfish/m84036_250809_035451_s4.bc2157.sv.vcf.gz.tbi", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-60/call-run_sawfish/out/m84036_250809_035451_s4.bc2157_sawfish/m84036_250809_035451_s4.bc2157.sv.vcf.gz"}
2025-09-15 20:26:56.034 wdl.w:ptcp.w:call-sawfish-60 INFO visit :: node: "output-minimap2_bam", values: {"minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-60/call-run_sawfish/out/m84036_250809_035451_s4.bc2157.minimap2.bam"}
2025-09-15 20:26:56.034 wdl.w:ptcp.w:call-sawfish-60 INFO visit :: node: "output-minimap2_bam_bai", values: {"minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-60/call-run_sawfish/out/m84036_250809_035451_s4.bc2157.minimap2.bam.bai"}
2025-09-15 20:26:56.034 wdl.w:ptcp.w:call-sawfish-60 INFO visit :: node: "output-vcf", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-60/call-run_sawfish/out/m84036_250809_035451_s4.bc2157_sawfish/m84036_250809_035451_s4.bc2157.sv.vcf.gz"}
2025-09-15 20:26:56.035 wdl.w:ptcp.w:call-sawfish-60 INFO visit :: node: "output-vcf_tbi", values: {"vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-60/call-run_sawfish/out/m84036_250809_035451_s4.bc2157_sawfish/m84036_250809_035451_s4.bc2157.sv.vcf.gz.tbi"}
2025-09-15 20:26:56.035 wdl.w:ptcp.w:call-sawfish-60 INFO visit :: node: "outputs", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-60/call-run_sawfish/out/m84036_250809_035451_s4.bc2157_sawfish/m84036_250809_035451_s4.bc2157.sv.vcf.gz", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-60/call-run_sawfish/out/m84036_250809_035451_s4.bc2157.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-60/call-run_sawfish/out/m84036_250809_035451_s4.bc2157_sawfish/m84036_250809_035451_s4.bc2157.sv.vcf.gz.tbi", "minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-60/call-run_sawfish/out/m84036_250809_035451_s4.bc2157.minimap2.bam.bai"}
2025-09-15 20:26:56.079 wdl.w:ptcp.w:call-sawfish-60 NOTICE done
2025-09-15 20:26:56.084 wdl.w:ptcp NOTICE finish :: job: "call-sawfish-60"
2025-09-15 20:26:56.085 wdl.w:ptcp INFO output :: job: "call-sawfish-60", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-60/out/m84036_250809_035451_s4.bc2157_sawfish/m84036_250809_035451_s4.bc2157.sv.vcf.gz", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-60/out/m84036_250809_035451_s4.bc2157.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-60/out/m84036_250809_035451_s4.bc2157_sawfish/m84036_250809_035451_s4.bc2157.sv.vcf.gz.tbi", "minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-60/out/m84036_250809_035451_s4.bc2157.minimap2.bam.bai"}
2025-09-15 20:26:56.085 wdl.w:ptcp NOTICE ready :: job: "call-tar_outputs-60", callee: "tar_outputs"
2025-09-15 20:26:56.085 wdl.w:ptcp INFO input :: job: "call-tar_outputs-60", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "sawfish_vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-60/out/m84036_250809_035451_s4.bc2157_sawfish/m84036_250809_035451_s4.bc2157.sv.vcf.gz.tbi", "sawfish_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-60/out/m84036_250809_035451_s4.bc2157_sawfish/m84036_250809_035451_s4.bc2157.sv.vcf.gz", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-60/out/m84036_250809_035451_s4.bc2157.f8inversion.json", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-60/out/m84036_250809_035451_s4.bc2157_paraphase/m84036_250809_035451_s4.bc2157.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-60/out/m84036_250809_035451_s4.bc2157_paraphase/m84036_250809_035451_s4.bc2157.paraphase.bam", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-60/out/m84036_250809_035451_s4.bc2157_paraphase/m84036_250809_035451_s4.bc2157.paraphase.json", "trgt_spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-60/out/m84036_250809_035451_s4.bc2157.trgt.sorted.spanning.bam.bai", "trgt_spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-60/out/m84036_250809_035451_s4.bc2157.trgt.sorted.spanning.bam", "trgt_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-60/out/m84036_250809_035451_s4.bc2157.trgt.vcf", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-60/out/m84036_250809_035451_s4.bc2157.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-60/out/m84036_250809_035451_s4.bc2157.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2157"}
2025-09-15 20:26:56.093 wdl.w:ptcp.t:call-tar_outputs-60 NOTICE task setup :: name: "tar_outputs", source: "./common.wdl", line: 279, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-60", thread: 140611432728128
2025-09-15 20:26:56.116 wdl.w:ptcp.t:call-tar_outputs-60 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:26:56.116 wdl.w:ptcp.t:call-tar_outputs-60 INFO input :: name: "sawfish_vcf_tbi", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2157.sv.vcf.gz.tbi"
2025-09-15 20:26:56.116 wdl.w:ptcp.t:call-tar_outputs-60 INFO input :: name: "sawfish_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2157.sv.vcf.gz"
2025-09-15 20:26:56.116 wdl.w:ptcp.t:call-tar_outputs-60 INFO input :: name: "f8_json", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2157.f8inversion.json"
2025-09-15 20:26:56.116 wdl.w:ptcp.t:call-tar_outputs-60 INFO input :: name: "paraphase_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2157.paraphase.bam.bai"
2025-09-15 20:26:56.116 wdl.w:ptcp.t:call-tar_outputs-60 INFO input :: name: "paraphase_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2157.paraphase.bam"
2025-09-15 20:26:56.116 wdl.w:ptcp.t:call-tar_outputs-60 INFO input :: name: "paraphase_json", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2157.paraphase.json"
2025-09-15 20:26:56.116 wdl.w:ptcp.t:call-tar_outputs-60 INFO input :: name: "trgt_spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2157.trgt.sorted.spanning.bam.bai"
2025-09-15 20:26:56.116 wdl.w:ptcp.t:call-tar_outputs-60 INFO input :: name: "trgt_spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2157.trgt.sorted.spanning.bam"
2025-09-15 20:26:56.116 wdl.w:ptcp.t:call-tar_outputs-60 INFO input :: name: "trgt_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2157.trgt.vcf"
2025-09-15 20:26:56.116 wdl.w:ptcp.t:call-tar_outputs-60 INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2157.mapped.bam.bai"
2025-09-15 20:26:56.116 wdl.w:ptcp.t:call-tar_outputs-60 INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2157.mapped.bam"
2025-09-15 20:26:56.117 wdl.w:ptcp.t:call-tar_outputs-60 INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2157"
2025-09-15 20:26:56.117 wdl.w:ptcp.t:call-tar_outputs-60 INFO eval :: name: "threads", value: 1
2025-09-15 20:26:56.117 wdl.w:ptcp.t:call-tar_outputs-60 INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:26:56.117 wdl.w:ptcp.t:call-tar_outputs-60 INFO eval :: name: "disk_size", value: 6
2025-09-15 20:26:56.117 wdl.w:ptcp.t:call-tar_outputs-60 INFO eval :: name: "output_tarball", value: "m84036_250809_035451_s4.bc2157.tar"
2025-09-15 20:26:56.117 wdl.w:ptcp.t:call-tar_outputs-60 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:26:56.118 wdl.w:ptcp.t:call-tar_outputs-60 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:26:56.118 wdl.w:ptcp.t:call-tar_outputs-60 INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:26:56.118 wdl.w:ptcp.t:call-tar_outputs-60 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:26:56.148 wdl.w:ptcp.w:call-sawfish-91.t:call-run_sawfish NOTICE done
2025-09-15 20:26:56.163 wdl.w:ptcp.w:call-sawfish-91 NOTICE finish :: job: "call-run_sawfish"
2025-09-15 20:26:56.163 wdl.w:ptcp.w:call-sawfish-91 INFO output :: job: "call-run_sawfish", values: {"minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-91/call-run_sawfish/out/m84036_250809_035451_s4.bc2188.minimap2.bam.bai", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-91/call-run_sawfish/out/m84036_250809_035451_s4.bc2188.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-91/call-run_sawfish/out/m84036_250809_035451_s4.bc2188_sawfish/m84036_250809_035451_s4.bc2188.sv.vcf.gz.tbi", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-91/call-run_sawfish/out/m84036_250809_035451_s4.bc2188_sawfish/m84036_250809_035451_s4.bc2188.sv.vcf.gz"}
2025-09-15 20:26:56.163 wdl.w:ptcp.w:call-sawfish-91 INFO visit :: node: "output-minimap2_bam", values: {"minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-91/call-run_sawfish/out/m84036_250809_035451_s4.bc2188.minimap2.bam"}
2025-09-15 20:26:56.163 wdl.w:ptcp.w:call-sawfish-91 INFO visit :: node: "output-minimap2_bam_bai", values: {"minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-91/call-run_sawfish/out/m84036_250809_035451_s4.bc2188.minimap2.bam.bai"}
2025-09-15 20:26:56.163 wdl.w:ptcp.w:call-sawfish-91 INFO visit :: node: "output-vcf", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-91/call-run_sawfish/out/m84036_250809_035451_s4.bc2188_sawfish/m84036_250809_035451_s4.bc2188.sv.vcf.gz"}
2025-09-15 20:26:56.163 wdl.w:ptcp.w:call-sawfish-91 INFO visit :: node: "output-vcf_tbi", values: {"vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-91/call-run_sawfish/out/m84036_250809_035451_s4.bc2188_sawfish/m84036_250809_035451_s4.bc2188.sv.vcf.gz.tbi"}
2025-09-15 20:26:56.164 wdl.w:ptcp.w:call-sawfish-91 INFO visit :: node: "outputs", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-91/call-run_sawfish/out/m84036_250809_035451_s4.bc2188_sawfish/m84036_250809_035451_s4.bc2188.sv.vcf.gz", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-91/call-run_sawfish/out/m84036_250809_035451_s4.bc2188.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-91/call-run_sawfish/out/m84036_250809_035451_s4.bc2188_sawfish/m84036_250809_035451_s4.bc2188.sv.vcf.gz.tbi", "minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-91/call-run_sawfish/out/m84036_250809_035451_s4.bc2188.minimap2.bam.bai"}
2025-09-15 20:26:56.208 wdl.w:ptcp.w:call-sawfish-91 NOTICE done
2025-09-15 20:26:56.214 wdl.w:ptcp NOTICE finish :: job: "call-sawfish-91"
2025-09-15 20:26:56.214 wdl.w:ptcp INFO output :: job: "call-sawfish-91", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-91/out/m84036_250809_035451_s4.bc2188_sawfish/m84036_250809_035451_s4.bc2188.sv.vcf.gz", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-91/out/m84036_250809_035451_s4.bc2188.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-91/out/m84036_250809_035451_s4.bc2188_sawfish/m84036_250809_035451_s4.bc2188.sv.vcf.gz.tbi", "minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-91/out/m84036_250809_035451_s4.bc2188.minimap2.bam.bai"}
2025-09-15 20:26:56.223 wdl.w:ptcp.t:call-tar_outputs-60 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 17, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-60/_singularity_tmpdir_x4rc29a8"
2025-09-15 20:26:56.223 wdl.w:ptcp.t:call-tar_outputs-60 INFO Slurm invocation: srun --job-name call-tar_outputs-60 --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-60/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-60/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-60/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-60/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-60/out/m84036_250809_035451_s4.bc2157.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2157.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-60/out/m84036_250809_035451_s4.bc2157.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2157.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-60/out/m84036_250809_035451_s4.bc2157.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2157.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-60/out/m84036_250809_035451_s4.bc2157_sawfish/m84036_250809_035451_s4.bc2157.sv.vcf.gz.tbi:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2157.sv.vcf.gz.tbi:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-60/out/m84036_250809_035451_s4.bc2157_sawfish/m84036_250809_035451_s4.bc2157.sv.vcf.gz:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2157.sv.vcf.gz:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-60/out/m84036_250809_035451_s4.bc2157.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2157.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-60/out/m84036_250809_035451_s4.bc2157.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2157.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-60/out/m84036_250809_035451_s4.bc2157_paraphase/m84036_250809_035451_s4.bc2157.paraphase.json:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2157.paraphase.json:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-60/out/m84036_250809_035451_s4.bc2157_paraphase/m84036_250809_035451_s4.bc2157.paraphase.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2157.paraphase.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-60/out/m84036_250809_035451_s4.bc2157_paraphase/m84036_250809_035451_s4.bc2157.paraphase.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2157.paraphase.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-60/out/m84036_250809_035451_s4.bc2157.f8inversion.json:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2157.f8inversion.json:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-60/_singularity_tmpdir_x4rc29a8/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-60/_singularity_tmpdir_x4rc29a8/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:26:56.233 wdl.w:ptcp.t:call-tar_outputs-60 NOTICE slurm_singularity run :: pid: 1207985, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-60/slurm_singularity.log.txt"
2025-09-15 20:26:56.287 wdl.w:ptcp.w:call-paraphase-38.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for rpgr for sample m84036_250809_035451_s4.bc2135 at 2025-09-15 20:26:22.231106...
2025-09-15 20:26:56.288 wdl.w:ptcp.w:call-paraphase-38.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for rpgr for sample m84036_250809_035451_s4.bc2135 at 2025-09-15 20:26:22.232269...
2025-09-15 20:26:56.288 wdl.w:ptcp.w:call-paraphase-38.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for rpgr for sample m84036_250809_035451_s4.bc2135 at 2025-09-15 20:26:23.835244...
2025-09-15 20:26:56.288 wdl.w:ptcp.w:call-paraphase-38.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for rpgr for sample m84036_250809_035451_s4.bc2135 at 2025-09-15 20:26:25.167844...
2025-09-15 20:26:56.288 wdl.w:ptcp.w:call-paraphase-38.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for rpgr for sample m84036_250809_035451_s4.bc2135 at 2025-09-15 20:26:25.331923...
2025-09-15 20:26:56.667 wdl.w:ptcp.t:call-tar_outputs-77.stderr VERBOSE tar: Removing leading `/' from member names
2025-09-15 20:26:56.667 wdl.w:ptcp.t:call-tar_outputs-77.stderr VERBOSE tar: Removing leading `/' from hard link targets
2025-09-15 20:26:56.673 wdl.w:ptcp.t:call-tar_outputs-77.slurm_singularity INFO srun: job 51798214 queued and waiting for resources
2025-09-15 20:26:56.673 wdl.w:ptcp.t:call-tar_outputs-77.slurm_singularity INFO srun: job 51798214 has been allocated resources
2025-09-15 20:26:56.673 wdl.w:ptcp.t:call-tar_outputs-77.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:26:56.783 wdl.w:ptcp.t:call-tar_outputs-77 INFO output :: name: "sample_tarball", value: "m84036_250809_035451_s4.bc2174.tar"
2025-09-15 20:26:56.830 wdl.w:ptcp.t:call-tar_outputs-27.stderr VERBOSE tar: Removing leading `/' from member names
2025-09-15 20:26:56.830 wdl.w:ptcp.t:call-tar_outputs-27.stderr VERBOSE tar: Removing leading `/' from hard link targets
2025-09-15 20:26:56.836 wdl.w:ptcp.t:call-tar_outputs-77 NOTICE done
2025-09-15 20:26:56.837 wdl.w:ptcp.t:call-tar_outputs-27.slurm_singularity INFO srun: job 51798215 queued and waiting for resources
2025-09-15 20:26:56.837 wdl.w:ptcp.t:call-tar_outputs-27.slurm_singularity INFO srun: job 51798215 has been allocated resources
2025-09-15 20:26:56.837 wdl.w:ptcp.t:call-tar_outputs-27.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:26:56.885 wdl.w:ptcp NOTICE finish :: job: "call-tar_outputs-77"
2025-09-15 20:26:56.885 wdl.w:ptcp INFO output :: job: "call-tar_outputs-77", values: {"sample_tarball": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-77/out/m84036_250809_035451_s4.bc2174.tar"}
2025-09-15 20:26:56.957 wdl.w:ptcp.w:call-sawfish-75.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:47][sawfish][INFO] Starting sawfish 2.0.3
2025-09-15 20:26:56.958 wdl.w:ptcp.w:call-sawfish-75.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:47][sawfish][INFO] cmdline: sawfish discover --disable-cnv --threads 16 --ref /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa --bam m84036_250809_035451_s4.bc2172.minimap2.bam --output-dir m84036_250809_035451_s4.bc2172_sawfish_discover
2025-09-15 20:26:56.958 wdl.w:ptcp.w:call-sawfish-75.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:47][sawfish][INFO] Running on 16 threads
2025-09-15 20:26:56.958 wdl.w:ptcp.w:call-sawfish-75.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:47][sawfish][INFO] Writing discover settings to file: 'm84036_250809_035451_s4.bc2172_sawfish_discover/discover.settings.json'
2025-09-15 20:26:56.958 wdl.w:ptcp.w:call-sawfish-75.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:47][sawfish][INFO] Reading reference genome from file '/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa'
2025-09-15 20:26:56.958 wdl.w:ptcp.w:call-sawfish-75.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:54][sawfish][INFO] Processing alignment file '/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2172.minimap2.bam'
2025-09-15 20:26:56.958 wdl.w:ptcp.w:call-sawfish-75.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:54][sawfish][INFO] Finished processing all alignments
2025-09-15 20:26:56.958 wdl.w:ptcp.w:call-sawfish-75.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:54][sawfish][INFO] Writing depth bins to binary file: 'm84036_250809_035451_s4.bc2172_sawfish_discover/depth.mpack'
2025-09-15 20:26:56.958 wdl.w:ptcp.w:call-sawfish-75.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:54][sawfish][INFO] Writing max sv depth genome regions to bed file: 'm84036_250809_035451_s4.bc2172_sawfish_discover/max.depth.bed'
2025-09-15 20:26:56.958 wdl.w:ptcp.w:call-sawfish-75.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:54][sawfish][INFO] Completing breakpoint observation clustering
2025-09-15 20:26:56.958 wdl.w:ptcp.w:call-sawfish-75.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:54][sawfish][INFO] Finished breakpoint observation clustering
2025-09-15 20:26:56.958 wdl.w:ptcp.w:call-sawfish-75.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:54][sawfish][INFO] Consolidating adjacent indel candidates
2025-09-15 20:26:56.958 wdl.w:ptcp.w:call-sawfish-75.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:54][sawfish][INFO] Finding large insertion candidates
2025-09-15 20:26:56.958 wdl.w:ptcp.w:call-sawfish-75.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:54][sawfish][INFO] Writing breakpoint_cluster debug bed file: 'm84036_250809_035451_s4.bc2172_sawfish_discover/debug.breakpoint_clusters.bed'
2025-09-15 20:26:56.958 wdl.w:ptcp.w:call-sawfish-75.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:54][sawfish][INFO] Refining SV Candidates
2025-09-15 20:26:56.958 wdl.w:ptcp.w:call-sawfish-75.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:54][sawfish][INFO] Writing debug assembly region bed file: 'm84036_250809_035451_s4.bc2172_sawfish_discover/assembly.regions.bed'
2025-09-15 20:26:56.959 wdl.w:ptcp.w:call-sawfish-75.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:55][sawfish][INFO] Starting refinement of breakpoint evidence clusters
2025-09-15 20:26:56.959 wdl.w:ptcp.w:call-sawfish-75.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:56][sawfish][INFO] Finished refining all breakpoint evidence clusters
2025-09-15 20:26:56.959 wdl.w:ptcp.w:call-sawfish-75.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:56][sawfish][INFO] Writing all contig alignments to bam file: 'm84036_250809_035451_s4.bc2172_sawfish_discover/contig.alignment.bam'
2025-09-15 20:26:56.959 wdl.w:ptcp.w:call-sawfish-75.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:56][sawfish][INFO] Writing candidate structural variants to file: 'm84036_250809_035451_s4.bc2172_sawfish_discover/candidate.sv.bcf'
2025-09-15 20:26:56.959 wdl.w:ptcp.w:call-sawfish-75.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:56][sawfish][INFO] Writing run statistics to file: 'm84036_250809_035451_s4.bc2172_sawfish_discover/run.stats.json'
2025-09-15 20:26:56.959 wdl.w:ptcp.w:call-sawfish-75.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:56][sawfish][INFO] sawfish completed. Total Runtime: 00:00:09.311
2025-09-15 20:26:56.991 wdl.w:ptcp.t:call-tar_outputs-27 INFO output :: name: "sample_tarball", value: "m84036_250809_035451_s4.bc2124.tar"
2025-09-15 20:26:57.049 wdl.w:ptcp.t:call-tar_outputs-27 NOTICE done
2025-09-15 20:26:57.052 wdl.w:ptcp NOTICE finish :: job: "call-tar_outputs-27"
2025-09-15 20:26:57.052 wdl.w:ptcp INFO output :: job: "call-tar_outputs-27", values: {"sample_tarball": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-27/out/m84036_250809_035451_s4.bc2124.tar"}
2025-09-15 20:26:57.243 wdl.w:ptcp.t:call-tar_outputs-60.slurm_singularity INFO srun: job 51798216 queued and waiting for resources
2025-09-15 20:26:57.244 wdl.w:ptcp.t:call-tar_outputs-60.slurm_singularity INFO srun: job 51798216 has been allocated resources
2025-09-15 20:26:57.244 wdl.w:ptcp.t:call-tar_outputs-60.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:26:57.542 wdl.w:ptcp.t:call-tar_outputs-60 INFO output :: name: "sample_tarball", value: "m84036_250809_035451_s4.bc2157.tar"
2025-09-15 20:26:57.594 wdl.w:ptcp.t:call-tar_outputs-60 NOTICE done
2025-09-15 20:26:57.597 wdl.w:ptcp NOTICE finish :: job: "call-tar_outputs-60"
2025-09-15 20:26:57.597 wdl.w:ptcp INFO output :: job: "call-tar_outputs-60", values: {"sample_tarball": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-60/out/m84036_250809_035451_s4.bc2157.tar"}
2025-09-15 20:26:57.670 wdl.w:ptcp.w:call-sawfish-87.t:call-run_sawfish INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2184_sawfish/m84036_250809_035451_s4.bc2184.sv.vcf.gz"
2025-09-15 20:26:57.674 wdl.w:ptcp.w:call-sawfish-87.t:call-run_sawfish INFO output :: name: "vcf_tbi", value: "m84036_250809_035451_s4.bc2184_sawfish/m84036_250809_035451_s4.bc2184.sv.vcf.gz.tbi"
2025-09-15 20:26:57.675 wdl.w:ptcp.w:call-sawfish-87.t:call-run_sawfish INFO output :: name: "minimap2_bam", value: "m84036_250809_035451_s4.bc2184.minimap2.bam"
2025-09-15 20:26:57.676 wdl.w:ptcp.w:call-sawfish-87.t:call-run_sawfish INFO output :: name: "minimap2_bam_bai", value: "m84036_250809_035451_s4.bc2184.minimap2.bam.bai"
2025-09-15 20:26:57.736 wdl.w:ptcp.w:call-paraphase-63.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for hbb for sample m84036_250809_035451_s4.bc2160 at 2025-09-15 20:26:51.877431...
2025-09-15 20:26:57.737 wdl.w:ptcp.w:call-paraphase-63.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for hbb for sample m84036_250809_035451_s4.bc2160 at 2025-09-15 20:26:51.882368...
2025-09-15 20:26:57.789 wdl.w:ptcp.w:call-sawfish-87.t:call-run_sawfish NOTICE done
2025-09-15 20:26:57.795 wdl.w:ptcp.w:call-sawfish-87 NOTICE finish :: job: "call-run_sawfish"
2025-09-15 20:26:57.795 wdl.w:ptcp.w:call-sawfish-87 INFO output :: job: "call-run_sawfish", values: {"minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-87/call-run_sawfish/out/m84036_250809_035451_s4.bc2184.minimap2.bam.bai", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-87/call-run_sawfish/out/m84036_250809_035451_s4.bc2184.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-87/call-run_sawfish/out/m84036_250809_035451_s4.bc2184_sawfish/m84036_250809_035451_s4.bc2184.sv.vcf.gz.tbi", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-87/call-run_sawfish/out/m84036_250809_035451_s4.bc2184_sawfish/m84036_250809_035451_s4.bc2184.sv.vcf.gz"}
2025-09-15 20:26:57.795 wdl.w:ptcp.w:call-sawfish-87 INFO visit :: node: "output-minimap2_bam", values: {"minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-87/call-run_sawfish/out/m84036_250809_035451_s4.bc2184.minimap2.bam"}
2025-09-15 20:26:57.795 wdl.w:ptcp.w:call-sawfish-87 INFO visit :: node: "output-minimap2_bam_bai", values: {"minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-87/call-run_sawfish/out/m84036_250809_035451_s4.bc2184.minimap2.bam.bai"}
2025-09-15 20:26:57.795 wdl.w:ptcp.w:call-sawfish-87 INFO visit :: node: "output-vcf", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-87/call-run_sawfish/out/m84036_250809_035451_s4.bc2184_sawfish/m84036_250809_035451_s4.bc2184.sv.vcf.gz"}
2025-09-15 20:26:57.796 wdl.w:ptcp.w:call-sawfish-87 INFO visit :: node: "output-vcf_tbi", values: {"vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-87/call-run_sawfish/out/m84036_250809_035451_s4.bc2184_sawfish/m84036_250809_035451_s4.bc2184.sv.vcf.gz.tbi"}
2025-09-15 20:26:57.796 wdl.w:ptcp.w:call-sawfish-87 INFO visit :: node: "outputs", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-87/call-run_sawfish/out/m84036_250809_035451_s4.bc2184_sawfish/m84036_250809_035451_s4.bc2184.sv.vcf.gz", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-87/call-run_sawfish/out/m84036_250809_035451_s4.bc2184.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-87/call-run_sawfish/out/m84036_250809_035451_s4.bc2184_sawfish/m84036_250809_035451_s4.bc2184.sv.vcf.gz.tbi", "minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-87/call-run_sawfish/out/m84036_250809_035451_s4.bc2184.minimap2.bam.bai"}
2025-09-15 20:26:57.836 wdl.w:ptcp.w:call-sawfish-87 NOTICE done
2025-09-15 20:26:57.842 wdl.w:ptcp NOTICE finish :: job: "call-sawfish-87"
2025-09-15 20:26:57.842 wdl.w:ptcp INFO output :: job: "call-sawfish-87", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-87/out/m84036_250809_035451_s4.bc2184_sawfish/m84036_250809_035451_s4.bc2184.sv.vcf.gz", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-87/out/m84036_250809_035451_s4.bc2184.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-87/out/m84036_250809_035451_s4.bc2184_sawfish/m84036_250809_035451_s4.bc2184.sv.vcf.gz.tbi", "minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-87/out/m84036_250809_035451_s4.bc2184.minimap2.bam.bai"}
2025-09-15 20:26:57.984 wdl.w:ptcp.w:call-paraphase-70.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for hbb for sample m84036_250809_035451_s4.bc2167 at 2025-09-15 20:26:50.876397...
2025-09-15 20:26:57.984 wdl.w:ptcp.w:call-paraphase-70.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for hbb for sample m84036_250809_035451_s4.bc2167 at 2025-09-15 20:26:51.186372...
2025-09-15 20:26:58.051 wdl.w:ptcp.w:call-paraphase-18.t:call-run_paraphase INFO output :: name: "paraphase_bam", value: "m84036_250809_035451_s4.bc2115_paraphase/m84036_250809_035451_s4.bc2115.paraphase.bam"
2025-09-15 20:26:58.054 wdl.w:ptcp.w:call-paraphase-18.t:call-run_paraphase INFO output :: name: "paraphase_bam_bai", value: "m84036_250809_035451_s4.bc2115_paraphase/m84036_250809_035451_s4.bc2115.paraphase.bam.bai"
2025-09-15 20:26:58.055 wdl.w:ptcp.w:call-paraphase-18.t:call-run_paraphase INFO output :: name: "paraphase_json", value: "m84036_250809_035451_s4.bc2115_paraphase/m84036_250809_035451_s4.bc2115.paraphase.json"
2025-09-15 20:26:58.065 wdl.w:ptcp.w:call-paraphase-18.t:call-run_paraphase INFO output :: name: "paraphase_vcfs", value: ["/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2115_paraphase/m84036_250809_035451_s4.bc2115_paraphase_vcfs/m84036_250809_035451_s4.bc2115_cyp21.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2115_paraphase/m84036_250809_035451_s4.bc2115_paraphase_vcfs/m84036_250809_035451_s4.bc2115_f8inv1.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2115_paraphase/m84036_250809_035451_s4.bc2115_paraphase_vcfs/m84036_250809_035451_s4.bc2115_f8inv22.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2115_paraphase/m84036_250809_035451_s4.bc2115_paraphase_vcfs/m84036_250809_035451_s4.bc2115_gba.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2115_paraphase/m84036_250809_035451_s4.bc2115_paraphase_vcfs/m84036_250809_035451_s4.bc2115_hba.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2115_paraphase/m84036_250809_035451_s4.bc2115_paraphase_vcfs/m84036_250809_035451_s4.bc2115_hbb.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2115_paraphase/m84036_250809_035451_s4.bc2115_paraphase_vcfs/m84036_250809_035451_s4.bc2115_rpgr.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2115_paraphase/m84036_250809_035451_s4.bc2115_paraphase_vcfs/m84036_250809_035451_s4.bc2115_smn1.vcf"]
2025-09-15 20:26:58.068 wdl.w:ptcp.w:call-paraphase-18.t:call-run_paraphase INFO output :: name: "havanno_json", value: "m84036_250809_035451_s4.bc2115.havanno.json"
2025-09-15 20:26:58.229 wdl.w:ptcp.w:call-paraphase-18.t:call-run_paraphase NOTICE done
2025-09-15 20:26:58.235 wdl.w:ptcp.w:call-paraphase-18 NOTICE finish :: job: "call-run_paraphase"
2025-09-15 20:26:58.235 wdl.w:ptcp.w:call-paraphase-18 INFO output :: job: "call-run_paraphase", values: {"havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-18/call-run_paraphase/out/m84036_250809_035451_s4.bc2115.havanno.json", "paraphase_vcfs": ["/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-18/call-run_paraphase/out/m84036_250809_035451_s4.bc2115_paraphase/m84036_250809_035451_s4.bc2115_paraphase_vcfs/m84036_250809_035451_s4.bc2115_cyp21.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-18/call-run_paraphase/out/m84036_250809_035451_s4.bc2115_paraphase/m84036_250809_035451_s4.bc2115_paraphase_vcfs/m84036_250809_035451_s4.bc2115_f8inv1.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-18/call-run_paraphase/out/m84036_250809_035451_s4.bc2115_paraphase/m84036_250809_035451_s4.bc2115_paraphase_vcfs/m84036_250809_035451_s4.bc2115_f8inv22.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-18/call-run_paraphase/out/m84036_250809_035451_s4.bc2115_paraphase/m84036_250809_035451_s4.bc2115_paraphase_vcfs/m84036_250809_035451_s4.bc2115_gba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-18/call-run_paraphase/out/m84036_250809_035451_s4.bc2115_paraphase/m84036_250809_035451_s4.bc2115_paraphase_vcfs/m84036_250809_035451_s4.bc2115_hba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-18/call-run_paraphase/out/m84036_250809_035451_s4.bc2115_paraphase/m84036_250809_035451_s4.bc2115_paraphase_vcfs/m84036_250809_035451_s4.bc2115_hbb.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-18/call-run_paraphase/out/m84036_250809_035451_s4.bc2115_paraphase/m84036_250809_035451_s4.bc2115_paraphase_vcfs/m84036_250809_035451_s4.bc2115_rpgr.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-18/call-run_paraphase/out/m84036_250809_035451_s4.bc2115_paraphase/m84036_250809_035451_s4.bc2115_paraphase_vcfs/m84036_250809_035451_s4.bc2115_smn1.vcf"], "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-18/call-run_paraphase/out/m84036_250809_035451_s4.bc2115_paraphase/m84036_250809_035451_s4.bc2115.paraphase.json", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-18/call-run_paraphase/out/m84036_250809_035451_s4.bc2115_paraphase/m84036_250809_035451_s4.bc2115.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-18/call-run_paraphase/out/m84036_250809_035451_s4.bc2115_paraphase/m84036_250809_035451_s4.bc2115.paraphase.bam"}
2025-09-15 20:26:58.236 wdl.w:ptcp.w:call-paraphase-18 NOTICE ready :: job: "call-call_f8", callee: "call_f8"
2025-09-15 20:26:58.236 wdl.w:ptcp.w:call-paraphase-18 INFO input :: job: "call-call_f8", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "out_prefix": "m84036_250809_035451_s4.bc2115", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-18/call-run_paraphase/out/m84036_250809_035451_s4.bc2115_paraphase/m84036_250809_035451_s4.bc2115.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-18/call-run_paraphase/out/m84036_250809_035451_s4.bc2115_paraphase/m84036_250809_035451_s4.bc2115.paraphase.bam", "sex": "F"}
2025-09-15 20:26:58.236 wdl.w:ptcp.w:call-paraphase-18 INFO visit :: node: "output-havanno_json", values: {"havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-18/call-run_paraphase/out/m84036_250809_035451_s4.bc2115.havanno.json"}
2025-09-15 20:26:58.236 wdl.w:ptcp.w:call-paraphase-18 INFO visit :: node: "output-paraphase_bam", values: {"paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-18/call-run_paraphase/out/m84036_250809_035451_s4.bc2115_paraphase/m84036_250809_035451_s4.bc2115.paraphase.bam"}
2025-09-15 20:26:58.236 wdl.w:ptcp.w:call-paraphase-18 INFO visit :: node: "output-paraphase_bam_bai", values: {"paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-18/call-run_paraphase/out/m84036_250809_035451_s4.bc2115_paraphase/m84036_250809_035451_s4.bc2115.paraphase.bam.bai"}
2025-09-15 20:26:58.237 wdl.w:ptcp.w:call-paraphase-18 INFO visit :: node: "output-paraphase_json", values: {"paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-18/call-run_paraphase/out/m84036_250809_035451_s4.bc2115_paraphase/m84036_250809_035451_s4.bc2115.paraphase.json"}
2025-09-15 20:26:58.237 wdl.w:ptcp.w:call-paraphase-18 INFO visit :: node: "output-paraphase_vcfs", values: {"paraphase_vcfs": ["/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-18/call-run_paraphase/out/m84036_250809_035451_s4.bc2115_paraphase/m84036_250809_035451_s4.bc2115_paraphase_vcfs/m84036_250809_035451_s4.bc2115_cyp21.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-18/call-run_paraphase/out/m84036_250809_035451_s4.bc2115_paraphase/m84036_250809_035451_s4.bc2115_paraphase_vcfs/m84036_250809_035451_s4.bc2115_f8inv1.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-18/call-run_paraphase/out/m84036_250809_035451_s4.bc2115_paraphase/m84036_250809_035451_s4.bc2115_paraphase_vcfs/m84036_250809_035451_s4.bc2115_f8inv22.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-18/call-run_paraphase/out/m84036_250809_035451_s4.bc2115_paraphase/m84036_250809_035451_s4.bc2115_paraphase_vcfs/m84036_250809_035451_s4.bc2115_gba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-18/call-run_paraphase/out/m84036_250809_035451_s4.bc2115_paraphase/m84036_250809_035451_s4.bc2115_paraphase_vcfs/m84036_250809_035451_s4.bc2115_hba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-18/call-run_paraphase/out/m84036_250809_035451_s4.bc2115_paraphase/m84036_250809_035451_s4.bc2115_paraphase_vcfs/m84036_250809_035451_s4.bc2115_hbb.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-18/call-run_paraphase/out/m84036_250809_035451_s4.bc2115_paraphase/m84036_250809_035451_s4.bc2115_paraphase_vcfs/m84036_250809_035451_s4.bc2115_rpgr.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-18/call-run_paraphase/out/m84036_250809_035451_s4.bc2115_paraphase/m84036_250809_035451_s4.bc2115_paraphase_vcfs/m84036_250809_035451_s4.bc2115_smn1.vcf"]}
2025-09-15 20:26:58.241 wdl.w:ptcp.w:call-paraphase-18.t:call-call_f8 NOTICE task setup :: name: "call_f8", source: "./paraphase.wdl", line: 232, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-18/call-call_f8", thread: 140610904249920
2025-09-15 20:26:58.257 wdl.w:ptcp.w:call-paraphase-18.t:call-call_f8 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:26:58.257 wdl.w:ptcp.w:call-paraphase-18.t:call-call_f8 INFO input :: name: "genome_version", value: "38"
2025-09-15 20:26:58.257 wdl.w:ptcp.w:call-paraphase-18.t:call-call_f8 INFO input :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2115"
2025-09-15 20:26:58.257 wdl.w:ptcp.w:call-paraphase-18.t:call-call_f8 INFO input :: name: "paraphase_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2115.paraphase.bam.bai"
2025-09-15 20:26:58.257 wdl.w:ptcp.w:call-paraphase-18.t:call-call_f8 INFO input :: name: "paraphase_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2115.paraphase.bam"
2025-09-15 20:26:58.257 wdl.w:ptcp.w:call-paraphase-18.t:call-call_f8 INFO input :: name: "sex", value: "F"
2025-09-15 20:26:58.258 wdl.w:ptcp.w:call-paraphase-18.t:call-call_f8 INFO eval :: name: "threads", value: 1
2025-09-15 20:26:58.258 wdl.w:ptcp.w:call-paraphase-18.t:call-call_f8 INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:26:58.258 wdl.w:ptcp.w:call-paraphase-18.t:call-call_f8 INFO eval :: name: "disk_size", value: 11
2025-09-15 20:26:58.258 wdl.w:ptcp.w:call-paraphase-18.t:call-call_f8 INFO eval :: name: "sample_sex", value: "F"
2025-09-15 20:26:58.258 wdl.w:ptcp.w:call-paraphase-18.t:call-call_f8 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:26:58.258 wdl.w:ptcp.w:call-paraphase-18.t:call-call_f8 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:26:58.259 wdl.w:ptcp.w:call-paraphase-18.t:call-call_f8 INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:26:58.259 wdl.w:ptcp.w:call-paraphase-18.t:call-call_f8 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:26:58.293 wdl.w:ptcp.w:call-paraphase-18.t:call-call_f8 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 8, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-18/call-call_f8/_singularity_tmpdir_3854z6dx"
2025-09-15 20:26:58.293 wdl.w:ptcp.w:call-paraphase-18.t:call-call_f8 INFO Slurm invocation: srun --job-name call-call_f8 --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-18/call-call_f8/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-18/call-call_f8/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-18/call-call_f8/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-18/call-call_f8/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-18/call-run_paraphase/out/m84036_250809_035451_s4.bc2115_paraphase/m84036_250809_035451_s4.bc2115.paraphase.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2115.paraphase.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-18/call-run_paraphase/out/m84036_250809_035451_s4.bc2115_paraphase/m84036_250809_035451_s4.bc2115.paraphase.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2115.paraphase.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-18/call-call_f8/_singularity_tmpdir_3854z6dx/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-18/call-call_f8/_singularity_tmpdir_3854z6dx/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:26:58.309 wdl.w:ptcp.w:call-paraphase-18.t:call-call_f8 NOTICE slurm_singularity run :: pid: 1207998, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-18/call-call_f8/slurm_singularity.log.txt"
2025-09-15 20:26:58.337 wdl.w:ptcp.w:call-paraphase-83.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for smn1 for sample m84036_250809_035451_s4.bc2180 at 2025-09-15 20:26:12.088334...
2025-09-15 20:26:58.338 wdl.w:ptcp.w:call-paraphase-83.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for hba for sample m84036_250809_035451_s4.bc2180 at 2025-09-15 20:26:13.024681...
2025-09-15 20:26:58.338 wdl.w:ptcp.w:call-paraphase-83.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for gba for sample m84036_250809_035451_s4.bc2180 at 2025-09-15 20:26:13.447745...
2025-09-15 20:26:58.338 wdl.w:ptcp.w:call-paraphase-83.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for cyp21 for sample m84036_250809_035451_s4.bc2180 at 2025-09-15 20:26:15.544413...
2025-09-15 20:26:58.338 wdl.w:ptcp.w:call-paraphase-83.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for smn1 for sample m84036_250809_035451_s4.bc2180 at 2025-09-15 20:26:36.862078...
2025-09-15 20:26:58.338 wdl.w:ptcp.w:call-paraphase-83.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning to gene2 region for smn1 for sample m84036_250809_035451_s4.bc2180 at 2025-09-15 20:26:37.303087...
2025-09-15 20:26:58.338 wdl.w:ptcp.w:call-paraphase-83.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for smn1 for sample m84036_250809_035451_s4.bc2180 at 2025-09-15 20:26:39.540680...
2025-09-15 20:26:58.489 wdl.w:ptcp.w:call-sawfish-80.t:call-run_sawfish.stderr VERBOSE [M::mm_idx_gen::62.737*1.57] collected minimizers
2025-09-15 20:26:58.490 wdl.w:ptcp.w:call-sawfish-80.t:call-run_sawfish.stderr VERBOSE [M::mm_idx_gen::75.429*1.80] sorted minimizers
2025-09-15 20:26:58.490 wdl.w:ptcp.w:call-sawfish-80.t:call-run_sawfish.stderr VERBOSE [M::main::75.431*1.80] loaded/built the index for 195 target sequence(s)
2025-09-15 20:26:58.490 wdl.w:ptcp.w:call-sawfish-80.t:call-run_sawfish.stderr VERBOSE [M::mm_mapopt_update::83.296*1.72] mid_occ = 136
2025-09-15 20:26:58.491 wdl.w:ptcp.w:call-sawfish-80.t:call-run_sawfish.stderr VERBOSE [M::mm_idx_stat] kmer size: 19; skip: 19; is_hpc: 0; #seq: 195
2025-09-15 20:26:58.491 wdl.w:ptcp.w:call-sawfish-80.t:call-run_sawfish.stderr VERBOSE [M::mm_idx_stat::89.939*1.67] distinct minimizers: 214664461 (92.23% are singletons); average occurrences: 1.372; average spacing: 10.529; total length: 3099922541
2025-09-15 20:26:58.491 wdl.w:ptcp.w:call-sawfish-80.t:call-run_sawfish.stderr VERBOSE [M::main] Version: 2.26-r1175
2025-09-15 20:26:58.491 wdl.w:ptcp.w:call-sawfish-80.t:call-run_sawfish.stderr VERBOSE [M::main] CMD: /opt/pacbio/smrttools/install/smrtlink-release_25.1.0.257715/bundles/smrttools/install/smrttools-release_25.1.0.257715/private/thirdparty/minimap2/minimap2_2.26-pacbio2/binwrap/../../../../../private/thirdparty/minimap2/minimap2_2.26-pacbio2/bin/minimap2 -a -y -x map-hifi -Y -E 1,0 /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa -
2025-09-15 20:26:58.491 wdl.w:ptcp.w:call-sawfish-80.t:call-run_sawfish.stderr VERBOSE [M::main] Real time: 90.414 sec; CPU: 150.567 sec; Peak RSS: 11.887 GB
2025-09-15 20:26:58.655 wdl.w:ptcp.w:call-sawfish-81.t:call-run_sawfish INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2178_sawfish/m84036_250809_035451_s4.bc2178.sv.vcf.gz"
2025-09-15 20:26:58.659 wdl.w:ptcp.w:call-sawfish-81.t:call-run_sawfish INFO output :: name: "vcf_tbi", value: "m84036_250809_035451_s4.bc2178_sawfish/m84036_250809_035451_s4.bc2178.sv.vcf.gz.tbi"
2025-09-15 20:26:58.661 wdl.w:ptcp.w:call-sawfish-81.t:call-run_sawfish INFO output :: name: "minimap2_bam", value: "m84036_250809_035451_s4.bc2178.minimap2.bam"
2025-09-15 20:26:58.662 wdl.w:ptcp.w:call-sawfish-81.t:call-run_sawfish INFO output :: name: "minimap2_bam_bai", value: "m84036_250809_035451_s4.bc2178.minimap2.bam.bai"
2025-09-15 20:26:58.785 wdl.w:ptcp.w:call-sawfish-81.t:call-run_sawfish NOTICE done
2025-09-15 20:26:58.875 wdl.w:ptcp.w:call-sawfish-81 NOTICE finish :: job: "call-run_sawfish"
2025-09-15 20:26:58.875 wdl.w:ptcp.w:call-sawfish-81 INFO output :: job: "call-run_sawfish", values: {"minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-81/call-run_sawfish/out/m84036_250809_035451_s4.bc2178.minimap2.bam.bai", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-81/call-run_sawfish/out/m84036_250809_035451_s4.bc2178.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-81/call-run_sawfish/out/m84036_250809_035451_s4.bc2178_sawfish/m84036_250809_035451_s4.bc2178.sv.vcf.gz.tbi", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-81/call-run_sawfish/out/m84036_250809_035451_s4.bc2178_sawfish/m84036_250809_035451_s4.bc2178.sv.vcf.gz"}
2025-09-15 20:26:58.875 wdl.w:ptcp.w:call-sawfish-81 INFO visit :: node: "output-minimap2_bam", values: {"minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-81/call-run_sawfish/out/m84036_250809_035451_s4.bc2178.minimap2.bam"}
2025-09-15 20:26:58.875 wdl.w:ptcp.w:call-sawfish-81 INFO visit :: node: "output-minimap2_bam_bai", values: {"minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-81/call-run_sawfish/out/m84036_250809_035451_s4.bc2178.minimap2.bam.bai"}
2025-09-15 20:26:58.876 wdl.w:ptcp.w:call-sawfish-81 INFO visit :: node: "output-vcf", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-81/call-run_sawfish/out/m84036_250809_035451_s4.bc2178_sawfish/m84036_250809_035451_s4.bc2178.sv.vcf.gz"}
2025-09-15 20:26:58.876 wdl.w:ptcp.w:call-sawfish-81 INFO visit :: node: "output-vcf_tbi", values: {"vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-81/call-run_sawfish/out/m84036_250809_035451_s4.bc2178_sawfish/m84036_250809_035451_s4.bc2178.sv.vcf.gz.tbi"}
2025-09-15 20:26:58.876 wdl.w:ptcp.w:call-sawfish-81 INFO visit :: node: "outputs", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-81/call-run_sawfish/out/m84036_250809_035451_s4.bc2178_sawfish/m84036_250809_035451_s4.bc2178.sv.vcf.gz", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-81/call-run_sawfish/out/m84036_250809_035451_s4.bc2178.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-81/call-run_sawfish/out/m84036_250809_035451_s4.bc2178_sawfish/m84036_250809_035451_s4.bc2178.sv.vcf.gz.tbi", "minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-81/call-run_sawfish/out/m84036_250809_035451_s4.bc2178.minimap2.bam.bai"}
2025-09-15 20:26:58.915 wdl.w:ptcp.w:call-sawfish-81 NOTICE done
2025-09-15 20:26:58.923 wdl.w:ptcp NOTICE finish :: job: "call-sawfish-81"
2025-09-15 20:26:58.923 wdl.w:ptcp INFO output :: job: "call-sawfish-81", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-81/out/m84036_250809_035451_s4.bc2178_sawfish/m84036_250809_035451_s4.bc2178.sv.vcf.gz", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-81/out/m84036_250809_035451_s4.bc2178.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-81/out/m84036_250809_035451_s4.bc2178_sawfish/m84036_250809_035451_s4.bc2178.sv.vcf.gz.tbi", "minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-81/out/m84036_250809_035451_s4.bc2178.minimap2.bam.bai"}
2025-09-15 20:26:58.924 wdl.w:ptcp NOTICE ready :: job: "call-tar_outputs-81", callee: "tar_outputs"
2025-09-15 20:26:58.924 wdl.w:ptcp INFO input :: job: "call-tar_outputs-81", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "sawfish_vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-81/out/m84036_250809_035451_s4.bc2178_sawfish/m84036_250809_035451_s4.bc2178.sv.vcf.gz.tbi", "sawfish_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-81/out/m84036_250809_035451_s4.bc2178_sawfish/m84036_250809_035451_s4.bc2178.sv.vcf.gz", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-81/out/m84036_250809_035451_s4.bc2178.f8inversion.json", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-81/out/m84036_250809_035451_s4.bc2178_paraphase/m84036_250809_035451_s4.bc2178.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-81/out/m84036_250809_035451_s4.bc2178_paraphase/m84036_250809_035451_s4.bc2178.paraphase.bam", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-81/out/m84036_250809_035451_s4.bc2178_paraphase/m84036_250809_035451_s4.bc2178.paraphase.json", "trgt_spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-81/out/m84036_250809_035451_s4.bc2178.trgt.sorted.spanning.bam.bai", "trgt_spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-81/out/m84036_250809_035451_s4.bc2178.trgt.sorted.spanning.bam", "trgt_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-81/out/m84036_250809_035451_s4.bc2178.trgt.vcf", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-81/out/m84036_250809_035451_s4.bc2178.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-81/out/m84036_250809_035451_s4.bc2178.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2178"}
2025-09-15 20:26:58.930 wdl.w:ptcp.t:call-tar_outputs-81 NOTICE task setup :: name: "tar_outputs", source: "./common.wdl", line: 279, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-81", thread: 140606626068032
2025-09-15 20:26:58.955 wdl.w:ptcp.t:call-tar_outputs-81 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:26:58.955 wdl.w:ptcp.t:call-tar_outputs-81 INFO input :: name: "sawfish_vcf_tbi", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2178.sv.vcf.gz.tbi"
2025-09-15 20:26:58.955 wdl.w:ptcp.t:call-tar_outputs-81 INFO input :: name: "sawfish_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2178.sv.vcf.gz"
2025-09-15 20:26:58.955 wdl.w:ptcp.t:call-tar_outputs-81 INFO input :: name: "f8_json", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2178.f8inversion.json"
2025-09-15 20:26:58.956 wdl.w:ptcp.t:call-tar_outputs-81 INFO input :: name: "paraphase_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2178.paraphase.bam.bai"
2025-09-15 20:26:58.956 wdl.w:ptcp.t:call-tar_outputs-81 INFO input :: name: "paraphase_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2178.paraphase.bam"
2025-09-15 20:26:58.956 wdl.w:ptcp.t:call-tar_outputs-81 INFO input :: name: "paraphase_json", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2178.paraphase.json"
2025-09-15 20:26:58.956 wdl.w:ptcp.t:call-tar_outputs-81 INFO input :: name: "trgt_spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2178.trgt.sorted.spanning.bam.bai"
2025-09-15 20:26:58.956 wdl.w:ptcp.t:call-tar_outputs-81 INFO input :: name: "trgt_spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2178.trgt.sorted.spanning.bam"
2025-09-15 20:26:58.956 wdl.w:ptcp.t:call-tar_outputs-81 INFO input :: name: "trgt_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2178.trgt.vcf"
2025-09-15 20:26:58.956 wdl.w:ptcp.t:call-tar_outputs-81 INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2178.mapped.bam.bai"
2025-09-15 20:26:58.956 wdl.w:ptcp.t:call-tar_outputs-81 INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2178.mapped.bam"
2025-09-15 20:26:58.956 wdl.w:ptcp.t:call-tar_outputs-81 INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2178"
2025-09-15 20:26:58.956 wdl.w:ptcp.t:call-tar_outputs-81 INFO eval :: name: "threads", value: 1
2025-09-15 20:26:58.956 wdl.w:ptcp.t:call-tar_outputs-81 INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:26:58.956 wdl.w:ptcp.t:call-tar_outputs-81 INFO eval :: name: "disk_size", value: 6
2025-09-15 20:26:58.957 wdl.w:ptcp.t:call-tar_outputs-81 INFO eval :: name: "output_tarball", value: "m84036_250809_035451_s4.bc2178.tar"
2025-09-15 20:26:58.957 wdl.w:ptcp.t:call-tar_outputs-81 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:26:58.957 wdl.w:ptcp.t:call-tar_outputs-81 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:26:58.957 wdl.w:ptcp.t:call-tar_outputs-81 INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:26:58.958 wdl.w:ptcp.t:call-tar_outputs-81 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:26:59.062 wdl.w:ptcp.t:call-tar_outputs-81 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 17, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-81/_singularity_tmpdir_aiodsk1l"
2025-09-15 20:26:59.062 wdl.w:ptcp.t:call-tar_outputs-81 INFO Slurm invocation: srun --job-name call-tar_outputs-81 --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-81/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-81/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-81/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-81/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-81/out/m84036_250809_035451_s4.bc2178.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2178.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-81/out/m84036_250809_035451_s4.bc2178.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2178.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-81/out/m84036_250809_035451_s4.bc2178.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2178.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-81/out/m84036_250809_035451_s4.bc2178_sawfish/m84036_250809_035451_s4.bc2178.sv.vcf.gz:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2178.sv.vcf.gz:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-81/out/m84036_250809_035451_s4.bc2178_sawfish/m84036_250809_035451_s4.bc2178.sv.vcf.gz.tbi:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2178.sv.vcf.gz.tbi:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-81/out/m84036_250809_035451_s4.bc2178.f8inversion.json:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2178.f8inversion.json:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-81/out/m84036_250809_035451_s4.bc2178.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2178.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-81/out/m84036_250809_035451_s4.bc2178.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2178.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-81/out/m84036_250809_035451_s4.bc2178_paraphase/m84036_250809_035451_s4.bc2178.paraphase.json:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2178.paraphase.json:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-81/out/m84036_250809_035451_s4.bc2178_paraphase/m84036_250809_035451_s4.bc2178.paraphase.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2178.paraphase.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-81/out/m84036_250809_035451_s4.bc2178_paraphase/m84036_250809_035451_s4.bc2178.paraphase.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2178.paraphase.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-81/_singularity_tmpdir_aiodsk1l/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-81/_singularity_tmpdir_aiodsk1l/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:26:59.074 wdl.w:ptcp.t:call-tar_outputs-81 NOTICE slurm_singularity run :: pid: 1208007, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-81/slurm_singularity.log.txt"
2025-09-15 20:26:59.317 wdl.w:ptcp.w:call-paraphase-18.t:call-call_f8.slurm_singularity INFO srun: job 51798217 queued and waiting for resources
2025-09-15 20:26:59.318 wdl.w:ptcp.w:call-paraphase-18.t:call-call_f8.slurm_singularity INFO srun: job 51798217 has been allocated resources
2025-09-15 20:26:59.318 wdl.w:ptcp.w:call-paraphase-18.t:call-call_f8.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:26:59.369 wdl.w:ptcp.w:call-paraphase-78.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for cyp21 for sample m84036_250809_035451_s4.bc2175 at 2025-09-15 20:26:39.894598...
2025-09-15 20:26:59.370 wdl.w:ptcp.w:call-paraphase-78.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for cyp21 for sample m84036_250809_035451_s4.bc2175 at 2025-09-15 20:26:41.230061...
2025-09-15 20:26:59.370 wdl.w:ptcp.w:call-paraphase-78.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for gba for sample m84036_250809_035451_s4.bc2175 at 2025-09-15 20:26:44.266672...
2025-09-15 20:26:59.370 wdl.w:ptcp.w:call-paraphase-78.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for gba for sample m84036_250809_035451_s4.bc2175 at 2025-09-15 20:26:44.987042...
2025-09-15 20:26:59.370 wdl.w:ptcp.w:call-paraphase-78.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for f8inv1 for sample m84036_250809_035451_s4.bc2175 at 2025-09-15 20:26:54.460969...
2025-09-15 20:26:59.370 wdl.w:ptcp.w:call-paraphase-78.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for f8inv1 for sample m84036_250809_035451_s4.bc2175 at 2025-09-15 20:26:54.461825...
2025-09-15 20:26:59.667 wdl.w:ptcp.w:call-paraphase-18.t:call-call_f8 INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2115.f8inversion.vcf"
2025-09-15 20:26:59.670 wdl.w:ptcp.w:call-paraphase-18.t:call-call_f8 INFO output :: name: "json", value: "m84036_250809_035451_s4.bc2115.f8inversion.json"
2025-09-15 20:26:59.718 wdl.w:ptcp.w:call-paraphase-18.t:call-call_f8 NOTICE done
2025-09-15 20:26:59.724 wdl.w:ptcp.w:call-paraphase-18 NOTICE finish :: job: "call-call_f8"
2025-09-15 20:26:59.724 wdl.w:ptcp.w:call-paraphase-18 INFO output :: job: "call-call_f8", values: {"json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-18/call-call_f8/out/m84036_250809_035451_s4.bc2115.f8inversion.json", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-18/call-call_f8/out/m84036_250809_035451_s4.bc2115.f8inversion.vcf"}
2025-09-15 20:26:59.724 wdl.w:ptcp.w:call-paraphase-18 INFO visit :: node: "output-f8_json", values: {"f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-18/call-call_f8/out/m84036_250809_035451_s4.bc2115.f8inversion.json"}
2025-09-15 20:26:59.724 wdl.w:ptcp.w:call-paraphase-18 INFO visit :: node: "output-f8_vcf", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-18/call-call_f8/out/m84036_250809_035451_s4.bc2115.f8inversion.vcf"}
2025-09-15 20:26:59.724 wdl.w:ptcp.w:call-paraphase-18 INFO visit :: node: "outputs", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-18/call-call_f8/out/m84036_250809_035451_s4.bc2115.f8inversion.vcf", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-18/call-run_paraphase/out/m84036_250809_035451_s4.bc2115_paraphase/m84036_250809_035451_s4.bc2115.paraphase.json", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-18/call-run_paraphase/out/m84036_250809_035451_s4.bc2115_paraphase/m84036_250809_035451_s4.bc2115.paraphase.bam", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-18/call-run_paraphase/out/m84036_250809_035451_s4.bc2115_paraphase/m84036_250809_035451_s4.bc2115.paraphase.bam.bai", "paraphase_vcfs": ["/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-18/call-run_paraphase/out/m84036_250809_035451_s4.bc2115_paraphase/m84036_250809_035451_s4.bc2115_paraphase_vcfs/m84036_250809_035451_s4.bc2115_cyp21.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-18/call-run_paraphase/out/m84036_250809_035451_s4.bc2115_paraphase/m84036_250809_035451_s4.bc2115_paraphase_vcfs/m84036_250809_035451_s4.bc2115_f8inv1.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-18/call-run_paraphase/out/m84036_250809_035451_s4.bc2115_paraphase/m84036_250809_035451_s4.bc2115_paraphase_vcfs/m84036_250809_035451_s4.bc2115_f8inv22.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-18/call-run_paraphase/out/m84036_250809_035451_s4.bc2115_paraphase/m84036_250809_035451_s4.bc2115_paraphase_vcfs/m84036_250809_035451_s4.bc2115_gba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-18/call-run_paraphase/out/m84036_250809_035451_s4.bc2115_paraphase/m84036_250809_035451_s4.bc2115_paraphase_vcfs/m84036_250809_035451_s4.bc2115_hba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-18/call-run_paraphase/out/m84036_250809_035451_s4.bc2115_paraphase/m84036_250809_035451_s4.bc2115_paraphase_vcfs/m84036_250809_035451_s4.bc2115_hbb.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-18/call-run_paraphase/out/m84036_250809_035451_s4.bc2115_paraphase/m84036_250809_035451_s4.bc2115_paraphase_vcfs/m84036_250809_035451_s4.bc2115_rpgr.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-18/call-run_paraphase/out/m84036_250809_035451_s4.bc2115_paraphase/m84036_250809_035451_s4.bc2115_paraphase_vcfs/m84036_250809_035451_s4.bc2115_smn1.vcf"], "havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-18/call-run_paraphase/out/m84036_250809_035451_s4.bc2115.havanno.json", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-18/call-call_f8/out/m84036_250809_035451_s4.bc2115.f8inversion.json"}
2025-09-15 20:26:59.834 wdl.w:ptcp.w:call-paraphase-18 NOTICE done
2025-09-15 20:26:59.848 wdl.w:ptcp NOTICE finish :: job: "call-paraphase-18"
2025-09-15 20:26:59.848 wdl.w:ptcp INFO output :: job: "call-paraphase-18", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-18/out/m84036_250809_035451_s4.bc2115.f8inversion.vcf", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-18/out/m84036_250809_035451_s4.bc2115_paraphase/m84036_250809_035451_s4.bc2115.paraphase.json", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-18/out/m84036_250809_035451_s4.bc2115_paraphase/m84036_250809_035451_s4.bc2115.paraphase.bam", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-18/out/m84036_250809_035451_s4.bc2115_paraphase/m84036_250809_035451_s4.bc2115.paraphase.bam.bai", "paraphase_vcfs": ["/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-18/out/m84036_250809_035451_s4.bc2115_paraphase/m84036_250809_035451_s4.bc2115_paraphase_vcfs/m84036_250809_035451_s4.bc2115_cyp21.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-18/out/m84036_250809_035451_s4.bc2115_paraphase/m84036_250809_035451_s4.bc2115_paraphase_vcfs/m84036_250809_035451_s4.bc2115_f8inv1.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-18/out/m84036_250809_035451_s4.bc2115_paraphase/m84036_250809_035451_s4.bc2115_paraphase_vcfs/m84036_250809_035451_s4.bc2115_f8inv22.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-18/out/m84036_250809_035451_s4.bc2115_paraphase/m84036_250809_035451_s4.bc2115_paraphase_vcfs/m84036_250809_035451_s4.bc2115_gba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-18/out/m84036_250809_035451_s4.bc2115_paraphase/m84036_250809_035451_s4.bc2115_paraphase_vcfs/m84036_250809_035451_s4.bc2115_hba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-18/out/m84036_250809_035451_s4.bc2115_paraphase/m84036_250809_035451_s4.bc2115_paraphase_vcfs/m84036_250809_035451_s4.bc2115_hbb.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-18/out/m84036_250809_035451_s4.bc2115_paraphase/m84036_250809_035451_s4.bc2115_paraphase_vcfs/m84036_250809_035451_s4.bc2115_rpgr.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-18/out/m84036_250809_035451_s4.bc2115_paraphase/m84036_250809_035451_s4.bc2115_paraphase_vcfs/m84036_250809_035451_s4.bc2115_smn1.vcf"], "havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-18/out/m84036_250809_035451_s4.bc2115.havanno.json", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-18/out/m84036_250809_035451_s4.bc2115.f8inversion.json"}
2025-09-15 20:26:59.849 wdl.w:ptcp NOTICE ready :: job: "call-tar_outputs-18", callee: "tar_outputs"
2025-09-15 20:26:59.849 wdl.w:ptcp INFO input :: job: "call-tar_outputs-18", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "sawfish_vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-18/out/m84036_250809_035451_s4.bc2115_sawfish/m84036_250809_035451_s4.bc2115.sv.vcf.gz.tbi", "sawfish_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-18/out/m84036_250809_035451_s4.bc2115_sawfish/m84036_250809_035451_s4.bc2115.sv.vcf.gz", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-18/out/m84036_250809_035451_s4.bc2115.f8inversion.json", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-18/out/m84036_250809_035451_s4.bc2115_paraphase/m84036_250809_035451_s4.bc2115.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-18/out/m84036_250809_035451_s4.bc2115_paraphase/m84036_250809_035451_s4.bc2115.paraphase.bam", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-18/out/m84036_250809_035451_s4.bc2115_paraphase/m84036_250809_035451_s4.bc2115.paraphase.json", "trgt_spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-18/out/m84036_250809_035451_s4.bc2115.trgt.sorted.spanning.bam.bai", "trgt_spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-18/out/m84036_250809_035451_s4.bc2115.trgt.sorted.spanning.bam", "trgt_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-18/out/m84036_250809_035451_s4.bc2115.trgt.vcf", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-18/out/m84036_250809_035451_s4.bc2115.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-18/out/m84036_250809_035451_s4.bc2115.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2115"}
2025-09-15 20:26:59.855 wdl.w:ptcp.t:call-tar_outputs-18 NOTICE task setup :: name: "tar_outputs", source: "./common.wdl", line: 279, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-18", thread: 140607120975424
2025-09-15 20:26:59.876 wdl.w:ptcp.t:call-tar_outputs-18 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:26:59.876 wdl.w:ptcp.t:call-tar_outputs-18 INFO input :: name: "sawfish_vcf_tbi", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2115.sv.vcf.gz.tbi"
2025-09-15 20:26:59.876 wdl.w:ptcp.t:call-tar_outputs-18 INFO input :: name: "sawfish_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2115.sv.vcf.gz"
2025-09-15 20:26:59.876 wdl.w:ptcp.t:call-tar_outputs-18 INFO input :: name: "f8_json", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2115.f8inversion.json"
2025-09-15 20:26:59.876 wdl.w:ptcp.t:call-tar_outputs-18 INFO input :: name: "paraphase_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2115.paraphase.bam.bai"
2025-09-15 20:26:59.876 wdl.w:ptcp.t:call-tar_outputs-18 INFO input :: name: "paraphase_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2115.paraphase.bam"
2025-09-15 20:26:59.876 wdl.w:ptcp.t:call-tar_outputs-18 INFO input :: name: "paraphase_json", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2115.paraphase.json"
2025-09-15 20:26:59.876 wdl.w:ptcp.t:call-tar_outputs-18 INFO input :: name: "trgt_spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2115.trgt.sorted.spanning.bam.bai"
2025-09-15 20:26:59.877 wdl.w:ptcp.t:call-tar_outputs-18 INFO input :: name: "trgt_spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2115.trgt.sorted.spanning.bam"
2025-09-15 20:26:59.877 wdl.w:ptcp.t:call-tar_outputs-18 INFO input :: name: "trgt_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2115.trgt.vcf"
2025-09-15 20:26:59.877 wdl.w:ptcp.t:call-tar_outputs-18 INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2115.mapped.bam.bai"
2025-09-15 20:26:59.877 wdl.w:ptcp.t:call-tar_outputs-18 INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2115.mapped.bam"
2025-09-15 20:26:59.877 wdl.w:ptcp.t:call-tar_outputs-18 INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2115"
2025-09-15 20:26:59.877 wdl.w:ptcp.t:call-tar_outputs-18 INFO eval :: name: "threads", value: 1
2025-09-15 20:26:59.877 wdl.w:ptcp.t:call-tar_outputs-18 INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:26:59.877 wdl.w:ptcp.t:call-tar_outputs-18 INFO eval :: name: "disk_size", value: 6
2025-09-15 20:26:59.877 wdl.w:ptcp.t:call-tar_outputs-18 INFO eval :: name: "output_tarball", value: "m84036_250809_035451_s4.bc2115.tar"
2025-09-15 20:26:59.878 wdl.w:ptcp.t:call-tar_outputs-18 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:26:59.878 wdl.w:ptcp.t:call-tar_outputs-18 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:26:59.878 wdl.w:ptcp.t:call-tar_outputs-18 INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:26:59.878 wdl.w:ptcp.t:call-tar_outputs-18 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:26:59.962 wdl.w:ptcp.t:call-tar_outputs-18 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 17, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-18/_singularity_tmpdir_1n18hhsx"
2025-09-15 20:26:59.962 wdl.w:ptcp.t:call-tar_outputs-18 INFO Slurm invocation: srun --job-name call-tar_outputs-18 --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-18/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-18/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-18/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-18/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-18/out/m84036_250809_035451_s4.bc2115_paraphase/m84036_250809_035451_s4.bc2115.paraphase.json:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2115.paraphase.json:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-18/out/m84036_250809_035451_s4.bc2115_paraphase/m84036_250809_035451_s4.bc2115.paraphase.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2115.paraphase.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-18/out/m84036_250809_035451_s4.bc2115_paraphase/m84036_250809_035451_s4.bc2115.paraphase.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2115.paraphase.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-18/out/m84036_250809_035451_s4.bc2115.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2115.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-18/out/m84036_250809_035451_s4.bc2115.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2115.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-18/out/m84036_250809_035451_s4.bc2115.f8inversion.json:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2115.f8inversion.json:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-18/out/m84036_250809_035451_s4.bc2115.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2115.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-18/out/m84036_250809_035451_s4.bc2115.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2115.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-18/out/m84036_250809_035451_s4.bc2115.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2115.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-18/out/m84036_250809_035451_s4.bc2115_sawfish/m84036_250809_035451_s4.bc2115.sv.vcf.gz.tbi:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2115.sv.vcf.gz.tbi:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-18/out/m84036_250809_035451_s4.bc2115_sawfish/m84036_250809_035451_s4.bc2115.sv.vcf.gz:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2115.sv.vcf.gz:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-18/_singularity_tmpdir_1n18hhsx/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-18/_singularity_tmpdir_1n18hhsx/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:26:59.973 wdl.w:ptcp.t:call-tar_outputs-18 NOTICE slurm_singularity run :: pid: 1208083, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-18/slurm_singularity.log.txt"
2025-09-15 20:27:00.081 wdl.w:ptcp.t:call-tar_outputs-81.slurm_singularity INFO srun: job 51798218 queued and waiting for resources
2025-09-15 20:27:00.081 wdl.w:ptcp.t:call-tar_outputs-81.slurm_singularity INFO srun: job 51798218 has been allocated resources
2025-09-15 20:27:00.081 wdl.w:ptcp.t:call-tar_outputs-81.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:27:00.203 wdl.w:ptcp.w:call-paraphase-87.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for f8inv1 for sample m84036_250809_035451_s4.bc2184 at 2025-09-15 20:26:40.872030...
2025-09-15 20:27:00.203 wdl.w:ptcp.w:call-paraphase-87.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for f8inv1 for sample m84036_250809_035451_s4.bc2184 at 2025-09-15 20:26:45.384765...
2025-09-15 20:27:00.203 wdl.w:ptcp.w:call-paraphase-87.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for f8inv1 for sample m84036_250809_035451_s4.bc2184 at 2025-09-15 20:26:45.701010...
2025-09-15 20:27:00.203 wdl.w:ptcp.w:call-paraphase-87.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for gba for sample m84036_250809_035451_s4.bc2184 at 2025-09-15 20:26:56.949754...
2025-09-15 20:27:00.203 wdl.w:ptcp.w:call-paraphase-87.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for gba for sample m84036_250809_035451_s4.bc2184 at 2025-09-15 20:26:57.544848...
2025-09-15 20:27:00.432 wdl.w:ptcp.t:call-tar_outputs-81 INFO output :: name: "sample_tarball", value: "m84036_250809_035451_s4.bc2178.tar"
2025-09-15 20:27:00.486 wdl.w:ptcp.t:call-tar_outputs-81 NOTICE done
2025-09-15 20:27:00.490 wdl.w:ptcp NOTICE finish :: job: "call-tar_outputs-81"
2025-09-15 20:27:00.490 wdl.w:ptcp INFO output :: job: "call-tar_outputs-81", values: {"sample_tarball": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-81/out/m84036_250809_035451_s4.bc2178.tar"}
2025-09-15 20:27:00.779 wdl.w:ptcp.w:call-paraphase-63.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for hbb for sample m84036_250809_035451_s4.bc2160 at 2025-09-15 20:26:53.728497...
2025-09-15 20:27:00.975 wdl.w:ptcp.t:call-tar_outputs-18.stderr VERBOSE tar: Removing leading `/' from member names
2025-09-15 20:27:00.975 wdl.w:ptcp.t:call-tar_outputs-18.stderr VERBOSE tar: Removing leading `/' from hard link targets
2025-09-15 20:27:00.986 wdl.w:ptcp.t:call-tar_outputs-18.slurm_singularity INFO srun: job 51798219 queued and waiting for resources
2025-09-15 20:27:00.986 wdl.w:ptcp.t:call-tar_outputs-18.slurm_singularity INFO srun: job 51798219 has been allocated resources
2025-09-15 20:27:00.986 wdl.w:ptcp.t:call-tar_outputs-18.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:27:01.029 wdl.w:ptcp.t:call-tar_outputs-18 INFO output :: name: "sample_tarball", value: "m84036_250809_035451_s4.bc2115.tar"
2025-09-15 20:27:01.094 wdl.w:ptcp.t:call-tar_outputs-18 NOTICE done
2025-09-15 20:27:01.098 wdl.w:ptcp NOTICE finish :: job: "call-tar_outputs-18"
2025-09-15 20:27:01.098 wdl.w:ptcp INFO output :: job: "call-tar_outputs-18", values: {"sample_tarball": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-18/out/m84036_250809_035451_s4.bc2115.tar"}
2025-09-15 20:27:02.048 wdl.w:ptcp.w:call-paraphase-66.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for hbb for sample m84036_250809_035451_s4.bc2163 at 2025-09-15 20:26:58.451189...
2025-09-15 20:27:02.049 wdl.w:ptcp.w:call-paraphase-66.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for hbb for sample m84036_250809_035451_s4.bc2163 at 2025-09-15 20:26:58.456978...
2025-09-15 20:27:02.405 wdl.w:ptcp.w:call-paraphase-78.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for f8inv1 for sample m84036_250809_035451_s4.bc2175 at 2025-09-15 20:26:56.857687...
2025-09-15 20:27:02.405 wdl.w:ptcp.w:call-paraphase-78.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for hbb for sample m84036_250809_035451_s4.bc2175 at 2025-09-15 20:27:02.038535...
2025-09-15 20:27:02.405 wdl.w:ptcp.w:call-paraphase-78.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for hbb for sample m84036_250809_035451_s4.bc2175 at 2025-09-15 20:27:02.039473...
2025-09-15 20:27:04.008 wdl.w:ptcp.w:call-paraphase-42.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for hbb for sample m84036_250809_035451_s4.bc2139 at 2025-09-15 20:26:19.984426...
2025-09-15 20:27:04.009 wdl.w:ptcp.w:call-paraphase-42.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for hbb for sample m84036_250809_035451_s4.bc2139 at 2025-09-15 20:26:20.313472...
2025-09-15 20:27:04.009 wdl.w:ptcp.w:call-paraphase-42.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for f8inv1 for sample m84036_250809_035451_s4.bc2139 at 2025-09-15 20:26:23.025846...
2025-09-15 20:27:04.009 wdl.w:ptcp.w:call-paraphase-42.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for f8inv1 for sample m84036_250809_035451_s4.bc2139 at 2025-09-15 20:26:23.416879...
2025-09-15 20:27:04.481 wdl.w:ptcp.w:call-paraphase-59.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for f8inv22 for sample m84036_250809_035451_s4.bc2156 at 2025-09-15 20:26:58.914773...
2025-09-15 20:27:04.481 wdl.w:ptcp.w:call-paraphase-59.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for f8inv22 for sample m84036_250809_035451_s4.bc2156 at 2025-09-15 20:26:58.914927...
2025-09-15 20:27:04.576 wdl.w:ptcp.w:call-paraphase-86.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for hbb for sample m84036_250809_035451_s4.bc2183 at 2025-09-15 20:26:54.418684...
2025-09-15 20:27:04.576 wdl.w:ptcp.w:call-paraphase-86.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for f8inv1 for sample m84036_250809_035451_s4.bc2183 at 2025-09-15 20:26:55.967815...
2025-09-15 20:27:04.576 wdl.w:ptcp.w:call-paraphase-86.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for f8inv1 for sample m84036_250809_035451_s4.bc2183 at 2025-09-15 20:26:56.348705...
2025-09-15 20:27:04.576 wdl.w:ptcp.w:call-paraphase-86.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for hbb for sample m84036_250809_035451_s4.bc2183 at 2025-09-15 20:26:57.946894...
2025-09-15 20:27:04.576 wdl.w:ptcp.w:call-paraphase-86.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for hbb for sample m84036_250809_035451_s4.bc2183 at 2025-09-15 20:26:58.287308...
2025-09-15 20:27:05.440 wdl.w:ptcp.w:call-paraphase-78.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for hbb for sample m84036_250809_035451_s4.bc2175 at 2025-09-15 20:27:03.741109...
2025-09-15 20:27:06.009 wdl.w:ptcp.w:call-paraphase-14.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for rpgr for sample m84036_250809_035451_s4.bc2111 at 2025-09-15 20:26:41.468736...
2025-09-15 20:27:06.009 wdl.w:ptcp.w:call-paraphase-14.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for rpgr for sample m84036_250809_035451_s4.bc2111 at 2025-09-15 20:26:41.469797...
2025-09-15 20:27:06.009 wdl.w:ptcp.w:call-paraphase-14.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for rpgr for sample m84036_250809_035451_s4.bc2111 at 2025-09-15 20:26:44.034127...
2025-09-15 20:27:06.010 wdl.w:ptcp.w:call-paraphase-14.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for rpgr for sample m84036_250809_035451_s4.bc2111 at 2025-09-15 20:26:45.285906...
2025-09-15 20:27:06.010 wdl.w:ptcp.w:call-paraphase-14.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for rpgr for sample m84036_250809_035451_s4.bc2111 at 2025-09-15 20:26:45.452507...
2025-09-15 20:27:06.144 wdl.w:ptcp.w:call-paraphase-19.t:call-run_paraphase INFO output :: name: "paraphase_bam", value: "m84036_250809_035451_s4.bc2116_paraphase/m84036_250809_035451_s4.bc2116.paraphase.bam"
2025-09-15 20:27:06.147 wdl.w:ptcp.w:call-paraphase-19.t:call-run_paraphase INFO output :: name: "paraphase_bam_bai", value: "m84036_250809_035451_s4.bc2116_paraphase/m84036_250809_035451_s4.bc2116.paraphase.bam.bai"
2025-09-15 20:27:06.149 wdl.w:ptcp.w:call-paraphase-19.t:call-run_paraphase INFO output :: name: "paraphase_json", value: "m84036_250809_035451_s4.bc2116_paraphase/m84036_250809_035451_s4.bc2116.paraphase.json"
2025-09-15 20:27:06.153 wdl.w:ptcp.w:call-paraphase-19.t:call-run_paraphase INFO output :: name: "paraphase_vcfs", value: ["/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2116_paraphase/m84036_250809_035451_s4.bc2116_paraphase_vcfs/m84036_250809_035451_s4.bc2116_cyp21.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2116_paraphase/m84036_250809_035451_s4.bc2116_paraphase_vcfs/m84036_250809_035451_s4.bc2116_f8inv1.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2116_paraphase/m84036_250809_035451_s4.bc2116_paraphase_vcfs/m84036_250809_035451_s4.bc2116_f8inv22.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2116_paraphase/m84036_250809_035451_s4.bc2116_paraphase_vcfs/m84036_250809_035451_s4.bc2116_gba.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2116_paraphase/m84036_250809_035451_s4.bc2116_paraphase_vcfs/m84036_250809_035451_s4.bc2116_hba.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2116_paraphase/m84036_250809_035451_s4.bc2116_paraphase_vcfs/m84036_250809_035451_s4.bc2116_hbb.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2116_paraphase/m84036_250809_035451_s4.bc2116_paraphase_vcfs/m84036_250809_035451_s4.bc2116_rpgr.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2116_paraphase/m84036_250809_035451_s4.bc2116_paraphase_vcfs/m84036_250809_035451_s4.bc2116_smn1.vcf"]
2025-09-15 20:27:06.156 wdl.w:ptcp.w:call-paraphase-19.t:call-run_paraphase INFO output :: name: "havanno_json", value: "m84036_250809_035451_s4.bc2116.havanno.json"
2025-09-15 20:27:06.315 wdl.w:ptcp.w:call-paraphase-19.t:call-run_paraphase NOTICE done
2025-09-15 20:27:06.321 wdl.w:ptcp.w:call-paraphase-19 NOTICE finish :: job: "call-run_paraphase"
2025-09-15 20:27:06.321 wdl.w:ptcp.w:call-paraphase-19 INFO output :: job: "call-run_paraphase", values: {"havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-19/call-run_paraphase/out/m84036_250809_035451_s4.bc2116.havanno.json", "paraphase_vcfs": ["/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-19/call-run_paraphase/out/m84036_250809_035451_s4.bc2116_paraphase/m84036_250809_035451_s4.bc2116_paraphase_vcfs/m84036_250809_035451_s4.bc2116_cyp21.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-19/call-run_paraphase/out/m84036_250809_035451_s4.bc2116_paraphase/m84036_250809_035451_s4.bc2116_paraphase_vcfs/m84036_250809_035451_s4.bc2116_f8inv1.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-19/call-run_paraphase/out/m84036_250809_035451_s4.bc2116_paraphase/m84036_250809_035451_s4.bc2116_paraphase_vcfs/m84036_250809_035451_s4.bc2116_f8inv22.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-19/call-run_paraphase/out/m84036_250809_035451_s4.bc2116_paraphase/m84036_250809_035451_s4.bc2116_paraphase_vcfs/m84036_250809_035451_s4.bc2116_gba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-19/call-run_paraphase/out/m84036_250809_035451_s4.bc2116_paraphase/m84036_250809_035451_s4.bc2116_paraphase_vcfs/m84036_250809_035451_s4.bc2116_hba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-19/call-run_paraphase/out/m84036_250809_035451_s4.bc2116_paraphase/m84036_250809_035451_s4.bc2116_paraphase_vcfs/m84036_250809_035451_s4.bc2116_hbb.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-19/call-run_paraphase/out/m84036_250809_035451_s4.bc2116_paraphase/m84036_250809_035451_s4.bc2116_paraphase_vcfs/m84036_250809_035451_s4.bc2116_rpgr.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-19/call-run_paraphase/out/m84036_250809_035451_s4.bc2116_paraphase/m84036_250809_035451_s4.bc2116_paraphase_vcfs/m84036_250809_035451_s4.bc2116_smn1.vcf"], "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-19/call-run_paraphase/out/m84036_250809_035451_s4.bc2116_paraphase/m84036_250809_035451_s4.bc2116.paraphase.json", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-19/call-run_paraphase/out/m84036_250809_035451_s4.bc2116_paraphase/m84036_250809_035451_s4.bc2116.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-19/call-run_paraphase/out/m84036_250809_035451_s4.bc2116_paraphase/m84036_250809_035451_s4.bc2116.paraphase.bam"}
2025-09-15 20:27:06.321 wdl.w:ptcp.w:call-paraphase-19 NOTICE ready :: job: "call-call_f8", callee: "call_f8"
2025-09-15 20:27:06.322 wdl.w:ptcp.w:call-paraphase-19 INFO input :: job: "call-call_f8", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "out_prefix": "m84036_250809_035451_s4.bc2116", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-19/call-run_paraphase/out/m84036_250809_035451_s4.bc2116_paraphase/m84036_250809_035451_s4.bc2116.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-19/call-run_paraphase/out/m84036_250809_035451_s4.bc2116_paraphase/m84036_250809_035451_s4.bc2116.paraphase.bam", "sex": "F"}
2025-09-15 20:27:06.322 wdl.w:ptcp.w:call-paraphase-19 INFO visit :: node: "output-havanno_json", values: {"havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-19/call-run_paraphase/out/m84036_250809_035451_s4.bc2116.havanno.json"}
2025-09-15 20:27:06.322 wdl.w:ptcp.w:call-paraphase-19 INFO visit :: node: "output-paraphase_bam", values: {"paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-19/call-run_paraphase/out/m84036_250809_035451_s4.bc2116_paraphase/m84036_250809_035451_s4.bc2116.paraphase.bam"}
2025-09-15 20:27:06.322 wdl.w:ptcp.w:call-paraphase-19 INFO visit :: node: "output-paraphase_bam_bai", values: {"paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-19/call-run_paraphase/out/m84036_250809_035451_s4.bc2116_paraphase/m84036_250809_035451_s4.bc2116.paraphase.bam.bai"}
2025-09-15 20:27:06.323 wdl.w:ptcp.w:call-paraphase-19 INFO visit :: node: "output-paraphase_json", values: {"paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-19/call-run_paraphase/out/m84036_250809_035451_s4.bc2116_paraphase/m84036_250809_035451_s4.bc2116.paraphase.json"}
2025-09-15 20:27:06.323 wdl.w:ptcp.w:call-paraphase-19 INFO visit :: node: "output-paraphase_vcfs", values: {"paraphase_vcfs": ["/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-19/call-run_paraphase/out/m84036_250809_035451_s4.bc2116_paraphase/m84036_250809_035451_s4.bc2116_paraphase_vcfs/m84036_250809_035451_s4.bc2116_cyp21.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-19/call-run_paraphase/out/m84036_250809_035451_s4.bc2116_paraphase/m84036_250809_035451_s4.bc2116_paraphase_vcfs/m84036_250809_035451_s4.bc2116_f8inv1.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-19/call-run_paraphase/out/m84036_250809_035451_s4.bc2116_paraphase/m84036_250809_035451_s4.bc2116_paraphase_vcfs/m84036_250809_035451_s4.bc2116_f8inv22.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-19/call-run_paraphase/out/m84036_250809_035451_s4.bc2116_paraphase/m84036_250809_035451_s4.bc2116_paraphase_vcfs/m84036_250809_035451_s4.bc2116_gba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-19/call-run_paraphase/out/m84036_250809_035451_s4.bc2116_paraphase/m84036_250809_035451_s4.bc2116_paraphase_vcfs/m84036_250809_035451_s4.bc2116_hba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-19/call-run_paraphase/out/m84036_250809_035451_s4.bc2116_paraphase/m84036_250809_035451_s4.bc2116_paraphase_vcfs/m84036_250809_035451_s4.bc2116_hbb.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-19/call-run_paraphase/out/m84036_250809_035451_s4.bc2116_paraphase/m84036_250809_035451_s4.bc2116_paraphase_vcfs/m84036_250809_035451_s4.bc2116_rpgr.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-19/call-run_paraphase/out/m84036_250809_035451_s4.bc2116_paraphase/m84036_250809_035451_s4.bc2116_paraphase_vcfs/m84036_250809_035451_s4.bc2116_smn1.vcf"]}
2025-09-15 20:27:06.329 wdl.w:ptcp.w:call-paraphase-19.t:call-call_f8 NOTICE task setup :: name: "call_f8", source: "./paraphase.wdl", line: 232, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-19/call-call_f8", thread: 140611977991744
2025-09-15 20:27:06.353 wdl.w:ptcp.w:call-paraphase-19.t:call-call_f8 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:27:06.353 wdl.w:ptcp.w:call-paraphase-19.t:call-call_f8 INFO input :: name: "genome_version", value: "38"
2025-09-15 20:27:06.353 wdl.w:ptcp.w:call-paraphase-19.t:call-call_f8 INFO input :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2116"
2025-09-15 20:27:06.353 wdl.w:ptcp.w:call-paraphase-19.t:call-call_f8 INFO input :: name: "paraphase_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2116.paraphase.bam.bai"
2025-09-15 20:27:06.353 wdl.w:ptcp.w:call-paraphase-19.t:call-call_f8 INFO input :: name: "paraphase_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2116.paraphase.bam"
2025-09-15 20:27:06.353 wdl.w:ptcp.w:call-paraphase-19.t:call-call_f8 INFO input :: name: "sex", value: "F"
2025-09-15 20:27:06.354 wdl.w:ptcp.w:call-paraphase-19.t:call-call_f8 INFO eval :: name: "threads", value: 1
2025-09-15 20:27:06.354 wdl.w:ptcp.w:call-paraphase-19.t:call-call_f8 INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:27:06.354 wdl.w:ptcp.w:call-paraphase-19.t:call-call_f8 INFO eval :: name: "disk_size", value: 11
2025-09-15 20:27:06.354 wdl.w:ptcp.w:call-paraphase-19.t:call-call_f8 INFO eval :: name: "sample_sex", value: "F"
2025-09-15 20:27:06.354 wdl.w:ptcp.w:call-paraphase-19.t:call-call_f8 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:27:06.354 wdl.w:ptcp.w:call-paraphase-19.t:call-call_f8 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:27:06.355 wdl.w:ptcp.w:call-paraphase-19.t:call-call_f8 INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:27:06.359 wdl.w:ptcp.w:call-paraphase-19.t:call-call_f8 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:27:06.395 wdl.w:ptcp.w:call-paraphase-19.t:call-call_f8 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 8, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-19/call-call_f8/_singularity_tmpdir_bvs6vwgx"
2025-09-15 20:27:06.395 wdl.w:ptcp.w:call-paraphase-19.t:call-call_f8 INFO Slurm invocation: srun --job-name call-call_f8 --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-19/call-call_f8/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-19/call-call_f8/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-19/call-call_f8/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-19/call-call_f8/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-19/call-run_paraphase/out/m84036_250809_035451_s4.bc2116_paraphase/m84036_250809_035451_s4.bc2116.paraphase.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2116.paraphase.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-19/call-run_paraphase/out/m84036_250809_035451_s4.bc2116_paraphase/m84036_250809_035451_s4.bc2116.paraphase.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2116.paraphase.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-19/call-call_f8/_singularity_tmpdir_bvs6vwgx/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-19/call-call_f8/_singularity_tmpdir_bvs6vwgx/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:27:06.412 wdl.w:ptcp.w:call-paraphase-19.t:call-call_f8 NOTICE slurm_singularity run :: pid: 1208095, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-19/call-call_f8/slurm_singularity.log.txt"
2025-09-15 20:27:07.075 wdl.w:ptcp.w:call-paraphase-35.t:call-run_paraphase INFO output :: name: "paraphase_bam", value: "m84036_250809_035451_s4.bc2132_paraphase/m84036_250809_035451_s4.bc2132.paraphase.bam"
2025-09-15 20:27:07.081 wdl.w:ptcp.w:call-sawfish-75.t:call-run_sawfish INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2172_sawfish/m84036_250809_035451_s4.bc2172.sv.vcf.gz"
2025-09-15 20:27:07.082 wdl.w:ptcp.w:call-paraphase-35.t:call-run_paraphase INFO output :: name: "paraphase_bam_bai", value: "m84036_250809_035451_s4.bc2132_paraphase/m84036_250809_035451_s4.bc2132.paraphase.bam.bai"
2025-09-15 20:27:07.084 wdl.w:ptcp.w:call-paraphase-35.t:call-run_paraphase INFO output :: name: "paraphase_json", value: "m84036_250809_035451_s4.bc2132_paraphase/m84036_250809_035451_s4.bc2132.paraphase.json"
2025-09-15 20:27:07.086 wdl.w:ptcp.w:call-sawfish-75.t:call-run_sawfish INFO output :: name: "vcf_tbi", value: "m84036_250809_035451_s4.bc2172_sawfish/m84036_250809_035451_s4.bc2172.sv.vcf.gz.tbi"
2025-09-15 20:27:07.087 wdl.w:ptcp.w:call-sawfish-75.t:call-run_sawfish INFO output :: name: "minimap2_bam", value: "m84036_250809_035451_s4.bc2172.minimap2.bam"
2025-09-15 20:27:07.089 wdl.w:ptcp.w:call-sawfish-75.t:call-run_sawfish INFO output :: name: "minimap2_bam_bai", value: "m84036_250809_035451_s4.bc2172.minimap2.bam.bai"
2025-09-15 20:27:07.089 wdl.w:ptcp.w:call-paraphase-35.t:call-run_paraphase INFO output :: name: "paraphase_vcfs", value: ["/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2132_paraphase/m84036_250809_035451_s4.bc2132_paraphase_vcfs/m84036_250809_035451_s4.bc2132_cyp21.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2132_paraphase/m84036_250809_035451_s4.bc2132_paraphase_vcfs/m84036_250809_035451_s4.bc2132_f8inv1.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2132_paraphase/m84036_250809_035451_s4.bc2132_paraphase_vcfs/m84036_250809_035451_s4.bc2132_f8inv22.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2132_paraphase/m84036_250809_035451_s4.bc2132_paraphase_vcfs/m84036_250809_035451_s4.bc2132_gba.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2132_paraphase/m84036_250809_035451_s4.bc2132_paraphase_vcfs/m84036_250809_035451_s4.bc2132_hba.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2132_paraphase/m84036_250809_035451_s4.bc2132_paraphase_vcfs/m84036_250809_035451_s4.bc2132_hbb.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2132_paraphase/m84036_250809_035451_s4.bc2132_paraphase_vcfs/m84036_250809_035451_s4.bc2132_rpgr.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2132_paraphase/m84036_250809_035451_s4.bc2132_paraphase_vcfs/m84036_250809_035451_s4.bc2132_smn1.vcf"]
2025-09-15 20:27:07.092 wdl.w:ptcp.w:call-paraphase-35.t:call-run_paraphase INFO output :: name: "havanno_json", value: "m84036_250809_035451_s4.bc2132.havanno.json"
2025-09-15 20:27:07.229 wdl.w:ptcp.w:call-sawfish-75.t:call-run_sawfish NOTICE done
2025-09-15 20:27:07.235 wdl.w:ptcp.w:call-sawfish-75 NOTICE finish :: job: "call-run_sawfish"
2025-09-15 20:27:07.235 wdl.w:ptcp.w:call-sawfish-75 INFO output :: job: "call-run_sawfish", values: {"minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-75/call-run_sawfish/out/m84036_250809_035451_s4.bc2172.minimap2.bam.bai", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-75/call-run_sawfish/out/m84036_250809_035451_s4.bc2172.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-75/call-run_sawfish/out/m84036_250809_035451_s4.bc2172_sawfish/m84036_250809_035451_s4.bc2172.sv.vcf.gz.tbi", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-75/call-run_sawfish/out/m84036_250809_035451_s4.bc2172_sawfish/m84036_250809_035451_s4.bc2172.sv.vcf.gz"}
2025-09-15 20:27:07.235 wdl.w:ptcp.w:call-sawfish-75 INFO visit :: node: "output-minimap2_bam", values: {"minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-75/call-run_sawfish/out/m84036_250809_035451_s4.bc2172.minimap2.bam"}
2025-09-15 20:27:07.235 wdl.w:ptcp.w:call-sawfish-75 INFO visit :: node: "output-minimap2_bam_bai", values: {"minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-75/call-run_sawfish/out/m84036_250809_035451_s4.bc2172.minimap2.bam.bai"}
2025-09-15 20:27:07.235 wdl.w:ptcp.w:call-sawfish-75 INFO visit :: node: "output-vcf", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-75/call-run_sawfish/out/m84036_250809_035451_s4.bc2172_sawfish/m84036_250809_035451_s4.bc2172.sv.vcf.gz"}
2025-09-15 20:27:07.236 wdl.w:ptcp.w:call-sawfish-75 INFO visit :: node: "output-vcf_tbi", values: {"vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-75/call-run_sawfish/out/m84036_250809_035451_s4.bc2172_sawfish/m84036_250809_035451_s4.bc2172.sv.vcf.gz.tbi"}
2025-09-15 20:27:07.236 wdl.w:ptcp.w:call-sawfish-75 INFO visit :: node: "outputs", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-75/call-run_sawfish/out/m84036_250809_035451_s4.bc2172_sawfish/m84036_250809_035451_s4.bc2172.sv.vcf.gz", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-75/call-run_sawfish/out/m84036_250809_035451_s4.bc2172.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-75/call-run_sawfish/out/m84036_250809_035451_s4.bc2172_sawfish/m84036_250809_035451_s4.bc2172.sv.vcf.gz.tbi", "minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-75/call-run_sawfish/out/m84036_250809_035451_s4.bc2172.minimap2.bam.bai"}
2025-09-15 20:27:07.279 wdl.w:ptcp.w:call-paraphase-35.t:call-run_paraphase NOTICE done
2025-09-15 20:27:07.281 wdl.w:ptcp.w:call-sawfish-75 NOTICE done
2025-09-15 20:27:07.284 wdl.w:ptcp.w:call-paraphase-35 NOTICE finish :: job: "call-run_paraphase"
2025-09-15 20:27:07.285 wdl.w:ptcp.w:call-paraphase-35 INFO output :: job: "call-run_paraphase", values: {"havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-35/call-run_paraphase/out/m84036_250809_035451_s4.bc2132.havanno.json", "paraphase_vcfs": ["/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-35/call-run_paraphase/out/m84036_250809_035451_s4.bc2132_paraphase/m84036_250809_035451_s4.bc2132_paraphase_vcfs/m84036_250809_035451_s4.bc2132_cyp21.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-35/call-run_paraphase/out/m84036_250809_035451_s4.bc2132_paraphase/m84036_250809_035451_s4.bc2132_paraphase_vcfs/m84036_250809_035451_s4.bc2132_f8inv1.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-35/call-run_paraphase/out/m84036_250809_035451_s4.bc2132_paraphase/m84036_250809_035451_s4.bc2132_paraphase_vcfs/m84036_250809_035451_s4.bc2132_f8inv22.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-35/call-run_paraphase/out/m84036_250809_035451_s4.bc2132_paraphase/m84036_250809_035451_s4.bc2132_paraphase_vcfs/m84036_250809_035451_s4.bc2132_gba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-35/call-run_paraphase/out/m84036_250809_035451_s4.bc2132_paraphase/m84036_250809_035451_s4.bc2132_paraphase_vcfs/m84036_250809_035451_s4.bc2132_hba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-35/call-run_paraphase/out/m84036_250809_035451_s4.bc2132_paraphase/m84036_250809_035451_s4.bc2132_paraphase_vcfs/m84036_250809_035451_s4.bc2132_hbb.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-35/call-run_paraphase/out/m84036_250809_035451_s4.bc2132_paraphase/m84036_250809_035451_s4.bc2132_paraphase_vcfs/m84036_250809_035451_s4.bc2132_rpgr.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-35/call-run_paraphase/out/m84036_250809_035451_s4.bc2132_paraphase/m84036_250809_035451_s4.bc2132_paraphase_vcfs/m84036_250809_035451_s4.bc2132_smn1.vcf"], "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-35/call-run_paraphase/out/m84036_250809_035451_s4.bc2132_paraphase/m84036_250809_035451_s4.bc2132.paraphase.json", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-35/call-run_paraphase/out/m84036_250809_035451_s4.bc2132_paraphase/m84036_250809_035451_s4.bc2132.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-35/call-run_paraphase/out/m84036_250809_035451_s4.bc2132_paraphase/m84036_250809_035451_s4.bc2132.paraphase.bam"}
2025-09-15 20:27:07.285 wdl.w:ptcp.w:call-paraphase-35 NOTICE ready :: job: "call-call_f8", callee: "call_f8"
2025-09-15 20:27:07.285 wdl.w:ptcp.w:call-paraphase-35 INFO input :: job: "call-call_f8", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "out_prefix": "m84036_250809_035451_s4.bc2132", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-35/call-run_paraphase/out/m84036_250809_035451_s4.bc2132_paraphase/m84036_250809_035451_s4.bc2132.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-35/call-run_paraphase/out/m84036_250809_035451_s4.bc2132_paraphase/m84036_250809_035451_s4.bc2132.paraphase.bam", "sex": "F"}
2025-09-15 20:27:07.286 wdl.w:ptcp.w:call-paraphase-35 INFO visit :: node: "output-havanno_json", values: {"havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-35/call-run_paraphase/out/m84036_250809_035451_s4.bc2132.havanno.json"}
2025-09-15 20:27:07.286 wdl.w:ptcp.w:call-paraphase-35 INFO visit :: node: "output-paraphase_bam", values: {"paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-35/call-run_paraphase/out/m84036_250809_035451_s4.bc2132_paraphase/m84036_250809_035451_s4.bc2132.paraphase.bam"}
2025-09-15 20:27:07.286 wdl.w:ptcp.w:call-paraphase-35 INFO visit :: node: "output-paraphase_bam_bai", values: {"paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-35/call-run_paraphase/out/m84036_250809_035451_s4.bc2132_paraphase/m84036_250809_035451_s4.bc2132.paraphase.bam.bai"}
2025-09-15 20:27:07.286 wdl.w:ptcp.w:call-paraphase-35 INFO visit :: node: "output-paraphase_json", values: {"paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-35/call-run_paraphase/out/m84036_250809_035451_s4.bc2132_paraphase/m84036_250809_035451_s4.bc2132.paraphase.json"}
2025-09-15 20:27:07.286 wdl.w:ptcp.w:call-paraphase-35 INFO visit :: node: "output-paraphase_vcfs", values: {"paraphase_vcfs": ["/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-35/call-run_paraphase/out/m84036_250809_035451_s4.bc2132_paraphase/m84036_250809_035451_s4.bc2132_paraphase_vcfs/m84036_250809_035451_s4.bc2132_cyp21.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-35/call-run_paraphase/out/m84036_250809_035451_s4.bc2132_paraphase/m84036_250809_035451_s4.bc2132_paraphase_vcfs/m84036_250809_035451_s4.bc2132_f8inv1.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-35/call-run_paraphase/out/m84036_250809_035451_s4.bc2132_paraphase/m84036_250809_035451_s4.bc2132_paraphase_vcfs/m84036_250809_035451_s4.bc2132_f8inv22.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-35/call-run_paraphase/out/m84036_250809_035451_s4.bc2132_paraphase/m84036_250809_035451_s4.bc2132_paraphase_vcfs/m84036_250809_035451_s4.bc2132_gba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-35/call-run_paraphase/out/m84036_250809_035451_s4.bc2132_paraphase/m84036_250809_035451_s4.bc2132_paraphase_vcfs/m84036_250809_035451_s4.bc2132_hba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-35/call-run_paraphase/out/m84036_250809_035451_s4.bc2132_paraphase/m84036_250809_035451_s4.bc2132_paraphase_vcfs/m84036_250809_035451_s4.bc2132_hbb.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-35/call-run_paraphase/out/m84036_250809_035451_s4.bc2132_paraphase/m84036_250809_035451_s4.bc2132_paraphase_vcfs/m84036_250809_035451_s4.bc2132_rpgr.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-35/call-run_paraphase/out/m84036_250809_035451_s4.bc2132_paraphase/m84036_250809_035451_s4.bc2132_paraphase_vcfs/m84036_250809_035451_s4.bc2132_smn1.vcf"]}
2025-09-15 20:27:07.287 wdl.w:ptcp NOTICE finish :: job: "call-sawfish-75"
2025-09-15 20:27:07.287 wdl.w:ptcp INFO output :: job: "call-sawfish-75", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-75/out/m84036_250809_035451_s4.bc2172_sawfish/m84036_250809_035451_s4.bc2172.sv.vcf.gz", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-75/out/m84036_250809_035451_s4.bc2172.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-75/out/m84036_250809_035451_s4.bc2172_sawfish/m84036_250809_035451_s4.bc2172.sv.vcf.gz.tbi", "minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-75/out/m84036_250809_035451_s4.bc2172.minimap2.bam.bai"}
2025-09-15 20:27:07.291 wdl.w:ptcp.w:call-paraphase-35.t:call-call_f8 NOTICE task setup :: name: "call_f8", source: "./paraphase.wdl", line: 232, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-35/call-call_f8", thread: 140608236680768
2025-09-15 20:27:07.309 wdl.w:ptcp.w:call-paraphase-35.t:call-call_f8 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:27:07.309 wdl.w:ptcp.w:call-paraphase-35.t:call-call_f8 INFO input :: name: "genome_version", value: "38"
2025-09-15 20:27:07.309 wdl.w:ptcp.w:call-paraphase-35.t:call-call_f8 INFO input :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2132"
2025-09-15 20:27:07.309 wdl.w:ptcp.w:call-paraphase-35.t:call-call_f8 INFO input :: name: "paraphase_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2132.paraphase.bam.bai"
2025-09-15 20:27:07.309 wdl.w:ptcp.w:call-paraphase-35.t:call-call_f8 INFO input :: name: "paraphase_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2132.paraphase.bam"
2025-09-15 20:27:07.310 wdl.w:ptcp.w:call-paraphase-35.t:call-call_f8 INFO input :: name: "sex", value: "F"
2025-09-15 20:27:07.310 wdl.w:ptcp.w:call-paraphase-35.t:call-call_f8 INFO eval :: name: "threads", value: 1
2025-09-15 20:27:07.310 wdl.w:ptcp.w:call-paraphase-35.t:call-call_f8 INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:27:07.310 wdl.w:ptcp.w:call-paraphase-35.t:call-call_f8 INFO eval :: name: "disk_size", value: 11
2025-09-15 20:27:07.310 wdl.w:ptcp.w:call-paraphase-35.t:call-call_f8 INFO eval :: name: "sample_sex", value: "F"
2025-09-15 20:27:07.311 wdl.w:ptcp.w:call-paraphase-35.t:call-call_f8 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:27:07.311 wdl.w:ptcp.w:call-paraphase-35.t:call-call_f8 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:27:07.311 wdl.w:ptcp.w:call-paraphase-35.t:call-call_f8 INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:27:07.311 wdl.w:ptcp.w:call-paraphase-35.t:call-call_f8 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:27:07.352 wdl.w:ptcp.w:call-paraphase-35.t:call-call_f8 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 8, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-35/call-call_f8/_singularity_tmpdir_v312buw_"
2025-09-15 20:27:07.352 wdl.w:ptcp.w:call-paraphase-35.t:call-call_f8 INFO Slurm invocation: srun --job-name call-call_f8 --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-35/call-call_f8/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-35/call-call_f8/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-35/call-call_f8/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-35/call-call_f8/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-35/call-run_paraphase/out/m84036_250809_035451_s4.bc2132_paraphase/m84036_250809_035451_s4.bc2132.paraphase.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2132.paraphase.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-35/call-run_paraphase/out/m84036_250809_035451_s4.bc2132_paraphase/m84036_250809_035451_s4.bc2132.paraphase.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2132.paraphase.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-35/call-call_f8/_singularity_tmpdir_v312buw_/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-35/call-call_f8/_singularity_tmpdir_v312buw_/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:27:07.360 wdl.w:ptcp.w:call-paraphase-35.t:call-call_f8 NOTICE slurm_singularity run :: pid: 1208107, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-35/call-call_f8/slurm_singularity.log.txt"
2025-09-15 20:27:07.422 wdl.w:ptcp.w:call-paraphase-19.t:call-call_f8.slurm_singularity INFO srun: job 51798220 queued and waiting for resources
2025-09-15 20:27:07.422 wdl.w:ptcp.w:call-paraphase-19.t:call-call_f8.slurm_singularity INFO srun: job 51798220 has been allocated resources
2025-09-15 20:27:07.422 wdl.w:ptcp.w:call-paraphase-19.t:call-call_f8.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:27:07.600 wdl.w:ptcp.w:call-paraphase-58.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for gba for sample m84036_250809_035451_s4.bc2155 at 2025-09-15 20:27:00.429361...
2025-09-15 20:27:07.600 wdl.w:ptcp.w:call-paraphase-58.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for gba for sample m84036_250809_035451_s4.bc2155 at 2025-09-15 20:27:01.381733...
2025-09-15 20:27:07.606 wdl.w:ptcp.w:call-sawfish-80.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:55][sawfish][INFO] Starting sawfish 2.0.3
2025-09-15 20:27:07.606 wdl.w:ptcp.w:call-sawfish-80.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:55][sawfish][INFO] cmdline: sawfish discover --disable-cnv --threads 16 --ref /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa --bam m84036_250809_035451_s4.bc2177.minimap2.bam --output-dir m84036_250809_035451_s4.bc2177_sawfish_discover
2025-09-15 20:27:07.607 wdl.w:ptcp.w:call-sawfish-80.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:55][sawfish][INFO] Running on 16 threads
2025-09-15 20:27:07.607 wdl.w:ptcp.w:call-sawfish-80.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:55][sawfish][INFO] Writing discover settings to file: 'm84036_250809_035451_s4.bc2177_sawfish_discover/discover.settings.json'
2025-09-15 20:27:07.607 wdl.w:ptcp.w:call-sawfish-80.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:55][sawfish][INFO] Reading reference genome from file '/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa'
2025-09-15 20:27:07.607 wdl.w:ptcp.w:call-sawfish-80.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:27:01][sawfish][INFO] Processing alignment file '/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2177.minimap2.bam'
2025-09-15 20:27:07.607 wdl.w:ptcp.w:call-sawfish-80.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:27:01][sawfish][INFO] Finished processing all alignments
2025-09-15 20:27:07.607 wdl.w:ptcp.w:call-sawfish-80.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:27:02][sawfish][INFO] Writing depth bins to binary file: 'm84036_250809_035451_s4.bc2177_sawfish_discover/depth.mpack'
2025-09-15 20:27:07.607 wdl.w:ptcp.w:call-sawfish-80.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:27:02][sawfish][INFO] Writing max sv depth genome regions to bed file: 'm84036_250809_035451_s4.bc2177_sawfish_discover/max.depth.bed'
2025-09-15 20:27:07.607 wdl.w:ptcp.w:call-sawfish-80.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:27:02][sawfish][INFO] Completing breakpoint observation clustering
2025-09-15 20:27:07.607 wdl.w:ptcp.w:call-sawfish-80.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:27:02][sawfish][INFO] Finished breakpoint observation clustering
2025-09-15 20:27:07.607 wdl.w:ptcp.w:call-sawfish-80.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:27:02][sawfish][INFO] Consolidating adjacent indel candidates
2025-09-15 20:27:07.607 wdl.w:ptcp.w:call-sawfish-80.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:27:02][sawfish][INFO] Finding large insertion candidates
2025-09-15 20:27:07.607 wdl.w:ptcp.w:call-sawfish-80.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:27:02][sawfish][INFO] Writing breakpoint_cluster debug bed file: 'm84036_250809_035451_s4.bc2177_sawfish_discover/debug.breakpoint_clusters.bed'
2025-09-15 20:27:07.607 wdl.w:ptcp.w:call-sawfish-80.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:27:02][sawfish][INFO] Refining SV Candidates
2025-09-15 20:27:07.607 wdl.w:ptcp.w:call-sawfish-80.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:27:02][sawfish][INFO] Writing debug assembly region bed file: 'm84036_250809_035451_s4.bc2177_sawfish_discover/assembly.regions.bed'
2025-09-15 20:27:07.607 wdl.w:ptcp.w:call-sawfish-80.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:27:02][sawfish][INFO] Starting refinement of breakpoint evidence clusters
2025-09-15 20:27:07.607 wdl.w:ptcp.w:call-sawfish-80.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:27:02][sawfish][INFO] Finished refining all breakpoint evidence clusters
2025-09-15 20:27:07.607 wdl.w:ptcp.w:call-sawfish-80.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:27:02][sawfish][INFO] Writing all contig alignments to bam file: 'm84036_250809_035451_s4.bc2177_sawfish_discover/contig.alignment.bam'
2025-09-15 20:27:07.607 wdl.w:ptcp.w:call-sawfish-80.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:27:02][sawfish][INFO] Writing candidate structural variants to file: 'm84036_250809_035451_s4.bc2177_sawfish_discover/candidate.sv.bcf'
2025-09-15 20:27:07.607 wdl.w:ptcp.w:call-sawfish-80.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:27:02][sawfish][INFO] Writing run statistics to file: 'm84036_250809_035451_s4.bc2177_sawfish_discover/run.stats.json'
2025-09-15 20:27:07.607 wdl.w:ptcp.w:call-sawfish-80.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:27:02][sawfish][INFO] sawfish completed. Total Runtime: 00:00:07.161
2025-09-15 20:27:07.629 wdl.w:ptcp.w:call-paraphase-19.t:call-call_f8 INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2116.f8inversion.vcf"
2025-09-15 20:27:07.632 wdl.w:ptcp.w:call-paraphase-19.t:call-call_f8 INFO output :: name: "json", value: "m84036_250809_035451_s4.bc2116.f8inversion.json"
2025-09-15 20:27:07.689 wdl.w:ptcp.w:call-paraphase-19.t:call-call_f8 NOTICE done
2025-09-15 20:27:07.695 wdl.w:ptcp.w:call-paraphase-19 NOTICE finish :: job: "call-call_f8"
2025-09-15 20:27:07.695 wdl.w:ptcp.w:call-paraphase-19 INFO output :: job: "call-call_f8", values: {"json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-19/call-call_f8/out/m84036_250809_035451_s4.bc2116.f8inversion.json", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-19/call-call_f8/out/m84036_250809_035451_s4.bc2116.f8inversion.vcf"}
2025-09-15 20:27:07.696 wdl.w:ptcp.w:call-paraphase-19 INFO visit :: node: "output-f8_json", values: {"f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-19/call-call_f8/out/m84036_250809_035451_s4.bc2116.f8inversion.json"}
2025-09-15 20:27:07.696 wdl.w:ptcp.w:call-paraphase-19 INFO visit :: node: "output-f8_vcf", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-19/call-call_f8/out/m84036_250809_035451_s4.bc2116.f8inversion.vcf"}
2025-09-15 20:27:07.696 wdl.w:ptcp.w:call-paraphase-19 INFO visit :: node: "outputs", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-19/call-call_f8/out/m84036_250809_035451_s4.bc2116.f8inversion.vcf", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-19/call-run_paraphase/out/m84036_250809_035451_s4.bc2116_paraphase/m84036_250809_035451_s4.bc2116.paraphase.json", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-19/call-run_paraphase/out/m84036_250809_035451_s4.bc2116_paraphase/m84036_250809_035451_s4.bc2116.paraphase.bam", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-19/call-run_paraphase/out/m84036_250809_035451_s4.bc2116_paraphase/m84036_250809_035451_s4.bc2116.paraphase.bam.bai", "paraphase_vcfs": ["/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-19/call-run_paraphase/out/m84036_250809_035451_s4.bc2116_paraphase/m84036_250809_035451_s4.bc2116_paraphase_vcfs/m84036_250809_035451_s4.bc2116_cyp21.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-19/call-run_paraphase/out/m84036_250809_035451_s4.bc2116_paraphase/m84036_250809_035451_s4.bc2116_paraphase_vcfs/m84036_250809_035451_s4.bc2116_f8inv1.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-19/call-run_paraphase/out/m84036_250809_035451_s4.bc2116_paraphase/m84036_250809_035451_s4.bc2116_paraphase_vcfs/m84036_250809_035451_s4.bc2116_f8inv22.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-19/call-run_paraphase/out/m84036_250809_035451_s4.bc2116_paraphase/m84036_250809_035451_s4.bc2116_paraphase_vcfs/m84036_250809_035451_s4.bc2116_gba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-19/call-run_paraphase/out/m84036_250809_035451_s4.bc2116_paraphase/m84036_250809_035451_s4.bc2116_paraphase_vcfs/m84036_250809_035451_s4.bc2116_hba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-19/call-run_paraphase/out/m84036_250809_035451_s4.bc2116_paraphase/m84036_250809_035451_s4.bc2116_paraphase_vcfs/m84036_250809_035451_s4.bc2116_hbb.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-19/call-run_paraphase/out/m84036_250809_035451_s4.bc2116_paraphase/m84036_250809_035451_s4.bc2116_paraphase_vcfs/m84036_250809_035451_s4.bc2116_rpgr.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-19/call-run_paraphase/out/m84036_250809_035451_s4.bc2116_paraphase/m84036_250809_035451_s4.bc2116_paraphase_vcfs/m84036_250809_035451_s4.bc2116_smn1.vcf"], "havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-19/call-run_paraphase/out/m84036_250809_035451_s4.bc2116.havanno.json", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-19/call-call_f8/out/m84036_250809_035451_s4.bc2116.f8inversion.json"}
2025-09-15 20:27:07.817 wdl.w:ptcp.w:call-paraphase-19 NOTICE done
2025-09-15 20:27:07.824 wdl.w:ptcp NOTICE finish :: job: "call-paraphase-19"
2025-09-15 20:27:07.824 wdl.w:ptcp INFO output :: job: "call-paraphase-19", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-19/out/m84036_250809_035451_s4.bc2116.f8inversion.vcf", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-19/out/m84036_250809_035451_s4.bc2116_paraphase/m84036_250809_035451_s4.bc2116.paraphase.json", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-19/out/m84036_250809_035451_s4.bc2116_paraphase/m84036_250809_035451_s4.bc2116.paraphase.bam", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-19/out/m84036_250809_035451_s4.bc2116_paraphase/m84036_250809_035451_s4.bc2116.paraphase.bam.bai", "paraphase_vcfs": ["/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-19/out/m84036_250809_035451_s4.bc2116_paraphase/m84036_250809_035451_s4.bc2116_paraphase_vcfs/m84036_250809_035451_s4.bc2116_cyp21.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-19/out/m84036_250809_035451_s4.bc2116_paraphase/m84036_250809_035451_s4.bc2116_paraphase_vcfs/m84036_250809_035451_s4.bc2116_f8inv1.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-19/out/m84036_250809_035451_s4.bc2116_paraphase/m84036_250809_035451_s4.bc2116_paraphase_vcfs/m84036_250809_035451_s4.bc2116_f8inv22.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-19/out/m84036_250809_035451_s4.bc2116_paraphase/m84036_250809_035451_s4.bc2116_paraphase_vcfs/m84036_250809_035451_s4.bc2116_gba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-19/out/m84036_250809_035451_s4.bc2116_paraphase/m84036_250809_035451_s4.bc2116_paraphase_vcfs/m84036_250809_035451_s4.bc2116_hba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-19/out/m84036_250809_035451_s4.bc2116_paraphase/m84036_250809_035451_s4.bc2116_paraphase_vcfs/m84036_250809_035451_s4.bc2116_hbb.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-19/out/m84036_250809_035451_s4.bc2116_paraphase/m84036_250809_035451_s4.bc2116_paraphase_vcfs/m84036_250809_035451_s4.bc2116_rpgr.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-19/out/m84036_250809_035451_s4.bc2116_paraphase/m84036_250809_035451_s4.bc2116_paraphase_vcfs/m84036_250809_035451_s4.bc2116_smn1.vcf"], "havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-19/out/m84036_250809_035451_s4.bc2116.havanno.json", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-19/out/m84036_250809_035451_s4.bc2116.f8inversion.json"}
2025-09-15 20:27:07.825 wdl.w:ptcp NOTICE ready :: job: "call-tar_outputs-19", callee: "tar_outputs"
2025-09-15 20:27:07.825 wdl.w:ptcp INFO input :: job: "call-tar_outputs-19", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "sawfish_vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-19/out/m84036_250809_035451_s4.bc2116_sawfish/m84036_250809_035451_s4.bc2116.sv.vcf.gz.tbi", "sawfish_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-19/out/m84036_250809_035451_s4.bc2116_sawfish/m84036_250809_035451_s4.bc2116.sv.vcf.gz", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-19/out/m84036_250809_035451_s4.bc2116.f8inversion.json", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-19/out/m84036_250809_035451_s4.bc2116_paraphase/m84036_250809_035451_s4.bc2116.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-19/out/m84036_250809_035451_s4.bc2116_paraphase/m84036_250809_035451_s4.bc2116.paraphase.bam", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-19/out/m84036_250809_035451_s4.bc2116_paraphase/m84036_250809_035451_s4.bc2116.paraphase.json", "trgt_spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-19/out/m84036_250809_035451_s4.bc2116.trgt.sorted.spanning.bam.bai", "trgt_spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-19/out/m84036_250809_035451_s4.bc2116.trgt.sorted.spanning.bam", "trgt_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-19/out/m84036_250809_035451_s4.bc2116.trgt.vcf", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-19/out/m84036_250809_035451_s4.bc2116.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-19/out/m84036_250809_035451_s4.bc2116.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2116"}
2025-09-15 20:27:07.832 wdl.w:ptcp.t:call-tar_outputs-19 NOTICE task setup :: name: "tar_outputs", source: "./common.wdl", line: 279, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-19", thread: 140609847293504
2025-09-15 20:27:07.852 wdl.w:ptcp.t:call-tar_outputs-19 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:27:07.853 wdl.w:ptcp.t:call-tar_outputs-19 INFO input :: name: "sawfish_vcf_tbi", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2116.sv.vcf.gz.tbi"
2025-09-15 20:27:07.853 wdl.w:ptcp.t:call-tar_outputs-19 INFO input :: name: "sawfish_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2116.sv.vcf.gz"
2025-09-15 20:27:07.853 wdl.w:ptcp.t:call-tar_outputs-19 INFO input :: name: "f8_json", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2116.f8inversion.json"
2025-09-15 20:27:07.853 wdl.w:ptcp.t:call-tar_outputs-19 INFO input :: name: "paraphase_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2116.paraphase.bam.bai"
2025-09-15 20:27:07.853 wdl.w:ptcp.t:call-tar_outputs-19 INFO input :: name: "paraphase_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2116.paraphase.bam"
2025-09-15 20:27:07.853 wdl.w:ptcp.t:call-tar_outputs-19 INFO input :: name: "paraphase_json", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2116.paraphase.json"
2025-09-15 20:27:07.853 wdl.w:ptcp.t:call-tar_outputs-19 INFO input :: name: "trgt_spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2116.trgt.sorted.spanning.bam.bai"
2025-09-15 20:27:07.853 wdl.w:ptcp.t:call-tar_outputs-19 INFO input :: name: "trgt_spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2116.trgt.sorted.spanning.bam"
2025-09-15 20:27:07.853 wdl.w:ptcp.t:call-tar_outputs-19 INFO input :: name: "trgt_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2116.trgt.vcf"
2025-09-15 20:27:07.853 wdl.w:ptcp.t:call-tar_outputs-19 INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2116.mapped.bam.bai"
2025-09-15 20:27:07.853 wdl.w:ptcp.t:call-tar_outputs-19 INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2116.mapped.bam"
2025-09-15 20:27:07.853 wdl.w:ptcp.t:call-tar_outputs-19 INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2116"
2025-09-15 20:27:07.853 wdl.w:ptcp.t:call-tar_outputs-19 INFO eval :: name: "threads", value: 1
2025-09-15 20:27:07.853 wdl.w:ptcp.t:call-tar_outputs-19 INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:27:07.854 wdl.w:ptcp.t:call-tar_outputs-19 INFO eval :: name: "disk_size", value: 6
2025-09-15 20:27:07.854 wdl.w:ptcp.t:call-tar_outputs-19 INFO eval :: name: "output_tarball", value: "m84036_250809_035451_s4.bc2116.tar"
2025-09-15 20:27:07.854 wdl.w:ptcp.t:call-tar_outputs-19 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:27:07.854 wdl.w:ptcp.t:call-tar_outputs-19 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:27:07.855 wdl.w:ptcp.t:call-tar_outputs-19 INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:27:07.855 wdl.w:ptcp.t:call-tar_outputs-19 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:27:07.937 wdl.w:ptcp.t:call-tar_outputs-19 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 17, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-19/_singularity_tmpdir_vkdpkplt"
2025-09-15 20:27:07.937 wdl.w:ptcp.t:call-tar_outputs-19 INFO Slurm invocation: srun --job-name call-tar_outputs-19 --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-19/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-19/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-19/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-19/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-19/out/m84036_250809_035451_s4.bc2116.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2116.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-19/out/m84036_250809_035451_s4.bc2116.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2116.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-19/out/m84036_250809_035451_s4.bc2116.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2116.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-19/out/m84036_250809_035451_s4.bc2116_paraphase/m84036_250809_035451_s4.bc2116.paraphase.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2116.paraphase.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-19/out/m84036_250809_035451_s4.bc2116_paraphase/m84036_250809_035451_s4.bc2116.paraphase.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2116.paraphase.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-19/out/m84036_250809_035451_s4.bc2116_paraphase/m84036_250809_035451_s4.bc2116.paraphase.json:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2116.paraphase.json:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-19/out/m84036_250809_035451_s4.bc2116_sawfish/m84036_250809_035451_s4.bc2116.sv.vcf.gz.tbi:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2116.sv.vcf.gz.tbi:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-19/out/m84036_250809_035451_s4.bc2116_sawfish/m84036_250809_035451_s4.bc2116.sv.vcf.gz:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2116.sv.vcf.gz:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-19/out/m84036_250809_035451_s4.bc2116.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2116.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-19/out/m84036_250809_035451_s4.bc2116.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2116.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-19/out/m84036_250809_035451_s4.bc2116.f8inversion.json:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2116.f8inversion.json:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-19/_singularity_tmpdir_vkdpkplt/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-19/_singularity_tmpdir_vkdpkplt/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:27:07.949 wdl.w:ptcp.t:call-tar_outputs-19 NOTICE slurm_singularity run :: pid: 1208115, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-19/slurm_singularity.log.txt"
2025-09-15 20:27:08.367 wdl.w:ptcp.w:call-paraphase-35.t:call-call_f8.slurm_singularity INFO srun: job 51798221 queued and waiting for resources
2025-09-15 20:27:08.367 wdl.w:ptcp.w:call-paraphase-35.t:call-call_f8.slurm_singularity INFO srun: job 51798221 has been allocated resources
2025-09-15 20:27:08.367 wdl.w:ptcp.w:call-paraphase-35.t:call-call_f8.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:27:08.672 wdl.w:ptcp.w:call-paraphase-35.t:call-call_f8 INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2132.f8inversion.vcf"
2025-09-15 20:27:08.675 wdl.w:ptcp.w:call-paraphase-35.t:call-call_f8 INFO output :: name: "json", value: "m84036_250809_035451_s4.bc2132.f8inversion.json"
2025-09-15 20:27:08.742 wdl.w:ptcp.w:call-paraphase-35.t:call-call_f8 NOTICE done
2025-09-15 20:27:08.747 wdl.w:ptcp.w:call-paraphase-35 NOTICE finish :: job: "call-call_f8"
2025-09-15 20:27:08.747 wdl.w:ptcp.w:call-paraphase-35 INFO output :: job: "call-call_f8", values: {"json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-35/call-call_f8/out/m84036_250809_035451_s4.bc2132.f8inversion.json", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-35/call-call_f8/out/m84036_250809_035451_s4.bc2132.f8inversion.vcf"}
2025-09-15 20:27:08.748 wdl.w:ptcp.w:call-paraphase-35 INFO visit :: node: "output-f8_json", values: {"f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-35/call-call_f8/out/m84036_250809_035451_s4.bc2132.f8inversion.json"}
2025-09-15 20:27:08.748 wdl.w:ptcp.w:call-paraphase-35 INFO visit :: node: "output-f8_vcf", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-35/call-call_f8/out/m84036_250809_035451_s4.bc2132.f8inversion.vcf"}
2025-09-15 20:27:08.748 wdl.w:ptcp.w:call-paraphase-35 INFO visit :: node: "outputs", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-35/call-call_f8/out/m84036_250809_035451_s4.bc2132.f8inversion.vcf", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-35/call-run_paraphase/out/m84036_250809_035451_s4.bc2132_paraphase/m84036_250809_035451_s4.bc2132.paraphase.json", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-35/call-run_paraphase/out/m84036_250809_035451_s4.bc2132_paraphase/m84036_250809_035451_s4.bc2132.paraphase.bam", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-35/call-run_paraphase/out/m84036_250809_035451_s4.bc2132_paraphase/m84036_250809_035451_s4.bc2132.paraphase.bam.bai", "paraphase_vcfs": ["/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-35/call-run_paraphase/out/m84036_250809_035451_s4.bc2132_paraphase/m84036_250809_035451_s4.bc2132_paraphase_vcfs/m84036_250809_035451_s4.bc2132_cyp21.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-35/call-run_paraphase/out/m84036_250809_035451_s4.bc2132_paraphase/m84036_250809_035451_s4.bc2132_paraphase_vcfs/m84036_250809_035451_s4.bc2132_f8inv1.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-35/call-run_paraphase/out/m84036_250809_035451_s4.bc2132_paraphase/m84036_250809_035451_s4.bc2132_paraphase_vcfs/m84036_250809_035451_s4.bc2132_f8inv22.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-35/call-run_paraphase/out/m84036_250809_035451_s4.bc2132_paraphase/m84036_250809_035451_s4.bc2132_paraphase_vcfs/m84036_250809_035451_s4.bc2132_gba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-35/call-run_paraphase/out/m84036_250809_035451_s4.bc2132_paraphase/m84036_250809_035451_s4.bc2132_paraphase_vcfs/m84036_250809_035451_s4.bc2132_hba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-35/call-run_paraphase/out/m84036_250809_035451_s4.bc2132_paraphase/m84036_250809_035451_s4.bc2132_paraphase_vcfs/m84036_250809_035451_s4.bc2132_hbb.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-35/call-run_paraphase/out/m84036_250809_035451_s4.bc2132_paraphase/m84036_250809_035451_s4.bc2132_paraphase_vcfs/m84036_250809_035451_s4.bc2132_rpgr.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-35/call-run_paraphase/out/m84036_250809_035451_s4.bc2132_paraphase/m84036_250809_035451_s4.bc2132_paraphase_vcfs/m84036_250809_035451_s4.bc2132_smn1.vcf"], "havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-35/call-run_paraphase/out/m84036_250809_035451_s4.bc2132.havanno.json", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-35/call-call_f8/out/m84036_250809_035451_s4.bc2132.f8inversion.json"}
2025-09-15 20:27:08.847 wdl.w:ptcp.w:call-paraphase-35 NOTICE done
2025-09-15 20:27:08.852 wdl.w:ptcp NOTICE finish :: job: "call-paraphase-35"
2025-09-15 20:27:08.852 wdl.w:ptcp INFO output :: job: "call-paraphase-35", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-35/out/m84036_250809_035451_s4.bc2132.f8inversion.vcf", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-35/out/m84036_250809_035451_s4.bc2132_paraphase/m84036_250809_035451_s4.bc2132.paraphase.json", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-35/out/m84036_250809_035451_s4.bc2132_paraphase/m84036_250809_035451_s4.bc2132.paraphase.bam", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-35/out/m84036_250809_035451_s4.bc2132_paraphase/m84036_250809_035451_s4.bc2132.paraphase.bam.bai", "paraphase_vcfs": ["/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-35/out/m84036_250809_035451_s4.bc2132_paraphase/m84036_250809_035451_s4.bc2132_paraphase_vcfs/m84036_250809_035451_s4.bc2132_cyp21.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-35/out/m84036_250809_035451_s4.bc2132_paraphase/m84036_250809_035451_s4.bc2132_paraphase_vcfs/m84036_250809_035451_s4.bc2132_f8inv1.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-35/out/m84036_250809_035451_s4.bc2132_paraphase/m84036_250809_035451_s4.bc2132_paraphase_vcfs/m84036_250809_035451_s4.bc2132_f8inv22.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-35/out/m84036_250809_035451_s4.bc2132_paraphase/m84036_250809_035451_s4.bc2132_paraphase_vcfs/m84036_250809_035451_s4.bc2132_gba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-35/out/m84036_250809_035451_s4.bc2132_paraphase/m84036_250809_035451_s4.bc2132_paraphase_vcfs/m84036_250809_035451_s4.bc2132_hba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-35/out/m84036_250809_035451_s4.bc2132_paraphase/m84036_250809_035451_s4.bc2132_paraphase_vcfs/m84036_250809_035451_s4.bc2132_hbb.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-35/out/m84036_250809_035451_s4.bc2132_paraphase/m84036_250809_035451_s4.bc2132_paraphase_vcfs/m84036_250809_035451_s4.bc2132_rpgr.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-35/out/m84036_250809_035451_s4.bc2132_paraphase/m84036_250809_035451_s4.bc2132_paraphase_vcfs/m84036_250809_035451_s4.bc2132_smn1.vcf"], "havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-35/out/m84036_250809_035451_s4.bc2132.havanno.json", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-35/out/m84036_250809_035451_s4.bc2132.f8inversion.json"}
2025-09-15 20:27:08.853 wdl.w:ptcp NOTICE ready :: job: "call-tar_outputs-35", callee: "tar_outputs"
2025-09-15 20:27:08.853 wdl.w:ptcp INFO input :: job: "call-tar_outputs-35", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "sawfish_vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-35/out/m84036_250809_035451_s4.bc2132_sawfish/m84036_250809_035451_s4.bc2132.sv.vcf.gz.tbi", "sawfish_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-35/out/m84036_250809_035451_s4.bc2132_sawfish/m84036_250809_035451_s4.bc2132.sv.vcf.gz", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-35/out/m84036_250809_035451_s4.bc2132.f8inversion.json", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-35/out/m84036_250809_035451_s4.bc2132_paraphase/m84036_250809_035451_s4.bc2132.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-35/out/m84036_250809_035451_s4.bc2132_paraphase/m84036_250809_035451_s4.bc2132.paraphase.bam", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-35/out/m84036_250809_035451_s4.bc2132_paraphase/m84036_250809_035451_s4.bc2132.paraphase.json", "trgt_spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-35/out/m84036_250809_035451_s4.bc2132.trgt.sorted.spanning.bam.bai", "trgt_spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-35/out/m84036_250809_035451_s4.bc2132.trgt.sorted.spanning.bam", "trgt_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-35/out/m84036_250809_035451_s4.bc2132.trgt.vcf", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-35/out/m84036_250809_035451_s4.bc2132.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-35/out/m84036_250809_035451_s4.bc2132.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2132"}
2025-09-15 20:27:08.859 wdl.w:ptcp.t:call-tar_outputs-35 NOTICE task setup :: name: "tar_outputs", source: "./common.wdl", line: 279, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-35", thread: 140609276851776
2025-09-15 20:27:08.881 wdl.w:ptcp.t:call-tar_outputs-35 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:27:08.881 wdl.w:ptcp.t:call-tar_outputs-35 INFO input :: name: "sawfish_vcf_tbi", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2132.sv.vcf.gz.tbi"
2025-09-15 20:27:08.881 wdl.w:ptcp.t:call-tar_outputs-35 INFO input :: name: "sawfish_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2132.sv.vcf.gz"
2025-09-15 20:27:08.881 wdl.w:ptcp.t:call-tar_outputs-35 INFO input :: name: "f8_json", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2132.f8inversion.json"
2025-09-15 20:27:08.881 wdl.w:ptcp.t:call-tar_outputs-35 INFO input :: name: "paraphase_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2132.paraphase.bam.bai"
2025-09-15 20:27:08.881 wdl.w:ptcp.t:call-tar_outputs-35 INFO input :: name: "paraphase_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2132.paraphase.bam"
2025-09-15 20:27:08.881 wdl.w:ptcp.t:call-tar_outputs-35 INFO input :: name: "paraphase_json", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2132.paraphase.json"
2025-09-15 20:27:08.881 wdl.w:ptcp.t:call-tar_outputs-35 INFO input :: name: "trgt_spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2132.trgt.sorted.spanning.bam.bai"
2025-09-15 20:27:08.881 wdl.w:ptcp.t:call-tar_outputs-35 INFO input :: name: "trgt_spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2132.trgt.sorted.spanning.bam"
2025-09-15 20:27:08.881 wdl.w:ptcp.t:call-tar_outputs-35 INFO input :: name: "trgt_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2132.trgt.vcf"
2025-09-15 20:27:08.881 wdl.w:ptcp.t:call-tar_outputs-35 INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2132.mapped.bam.bai"
2025-09-15 20:27:08.881 wdl.w:ptcp.t:call-tar_outputs-35 INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2132.mapped.bam"
2025-09-15 20:27:08.881 wdl.w:ptcp.t:call-tar_outputs-35 INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2132"
2025-09-15 20:27:08.882 wdl.w:ptcp.t:call-tar_outputs-35 INFO eval :: name: "threads", value: 1
2025-09-15 20:27:08.882 wdl.w:ptcp.t:call-tar_outputs-35 INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:27:08.882 wdl.w:ptcp.t:call-tar_outputs-35 INFO eval :: name: "disk_size", value: 6
2025-09-15 20:27:08.882 wdl.w:ptcp.t:call-tar_outputs-35 INFO eval :: name: "output_tarball", value: "m84036_250809_035451_s4.bc2132.tar"
2025-09-15 20:27:08.882 wdl.w:ptcp.t:call-tar_outputs-35 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:27:08.882 wdl.w:ptcp.t:call-tar_outputs-35 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:27:08.883 wdl.w:ptcp.t:call-tar_outputs-35 INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:27:08.883 wdl.w:ptcp.t:call-tar_outputs-35 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:27:08.891 wdl.w:ptcp.w:call-paraphase-62.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for f8inv1 for sample m84036_250809_035451_s4.bc2159 at 2025-09-15 20:26:22.710439...
2025-09-15 20:27:08.891 wdl.w:ptcp.w:call-paraphase-62.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for f8inv1 for sample m84036_250809_035451_s4.bc2159 at 2025-09-15 20:26:27.766658...
2025-09-15 20:27:08.891 wdl.w:ptcp.w:call-paraphase-62.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for f8inv1 for sample m84036_250809_035451_s4.bc2159 at 2025-09-15 20:26:28.625663...
2025-09-15 20:27:08.963 wdl.w:ptcp.t:call-tar_outputs-19.slurm_singularity INFO srun: job 51798222 queued and waiting for resources
2025-09-15 20:27:08.963 wdl.w:ptcp.t:call-tar_outputs-19.slurm_singularity INFO srun: job 51798222 has been allocated resources
2025-09-15 20:27:08.964 wdl.w:ptcp.t:call-tar_outputs-19.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:27:08.989 wdl.w:ptcp.t:call-tar_outputs-35 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 17, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-35/_singularity_tmpdir_dpaubjjf"
2025-09-15 20:27:08.989 wdl.w:ptcp.t:call-tar_outputs-35 INFO Slurm invocation: srun --job-name call-tar_outputs-35 --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-35/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-35/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-35/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-35/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-35/out/m84036_250809_035451_s4.bc2132.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2132.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-35/out/m84036_250809_035451_s4.bc2132.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2132.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-35/out/m84036_250809_035451_s4.bc2132.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2132.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-35/out/m84036_250809_035451_s4.bc2132_paraphase/m84036_250809_035451_s4.bc2132.paraphase.json:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2132.paraphase.json:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-35/out/m84036_250809_035451_s4.bc2132_paraphase/m84036_250809_035451_s4.bc2132.paraphase.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2132.paraphase.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-35/out/m84036_250809_035451_s4.bc2132_paraphase/m84036_250809_035451_s4.bc2132.paraphase.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2132.paraphase.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-35/out/m84036_250809_035451_s4.bc2132_sawfish/m84036_250809_035451_s4.bc2132.sv.vcf.gz:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2132.sv.vcf.gz:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-35/out/m84036_250809_035451_s4.bc2132_sawfish/m84036_250809_035451_s4.bc2132.sv.vcf.gz.tbi:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2132.sv.vcf.gz.tbi:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-35/out/m84036_250809_035451_s4.bc2132.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2132.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-35/out/m84036_250809_035451_s4.bc2132.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2132.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-35/out/m84036_250809_035451_s4.bc2132.f8inversion.json:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2132.f8inversion.json:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-35/_singularity_tmpdir_dpaubjjf/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-35/_singularity_tmpdir_dpaubjjf/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:27:08.998 wdl.w:ptcp.t:call-tar_outputs-35 NOTICE slurm_singularity run :: pid: 1208125, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-35/slurm_singularity.log.txt"
2025-09-15 20:27:09.314 wdl.w:ptcp.w:call-paraphase-87.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for hbb for sample m84036_250809_035451_s4.bc2184 at 2025-09-15 20:27:04.020944...
2025-09-15 20:27:09.315 wdl.w:ptcp.w:call-paraphase-87.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for hbb for sample m84036_250809_035451_s4.bc2184 at 2025-09-15 20:27:04.021917...
2025-09-15 20:27:09.443 wdl.w:ptcp.w:call-paraphase-43.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for f8inv22 for sample m84036_250809_035451_s4.bc2140 at 2025-09-15 20:27:02.531311...
2025-09-15 20:27:09.444 wdl.w:ptcp.w:call-paraphase-43.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for f8inv22 for sample m84036_250809_035451_s4.bc2140 at 2025-09-15 20:27:02.532357...
2025-09-15 20:27:09.521 wdl.w:ptcp.t:call-tar_outputs-19 INFO output :: name: "sample_tarball", value: "m84036_250809_035451_s4.bc2116.tar"
2025-09-15 20:27:09.574 wdl.w:ptcp.t:call-tar_outputs-19 NOTICE done
2025-09-15 20:27:09.577 wdl.w:ptcp NOTICE finish :: job: "call-tar_outputs-19"
2025-09-15 20:27:09.577 wdl.w:ptcp INFO output :: job: "call-tar_outputs-19", values: {"sample_tarball": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-19/out/m84036_250809_035451_s4.bc2116.tar"}
2025-09-15 20:27:09.845 wdl.w:ptcp.w:call-sawfish-89.t:call-run_sawfish.stderr VERBOSE [M::mm_idx_gen::60.253*1.56] collected minimizers
2025-09-15 20:27:09.845 wdl.w:ptcp.w:call-sawfish-89.t:call-run_sawfish.stderr VERBOSE [M::mm_idx_gen::72.527*1.79] sorted minimizers
2025-09-15 20:27:09.846 wdl.w:ptcp.w:call-sawfish-89.t:call-run_sawfish.stderr VERBOSE [M::main::72.528*1.79] loaded/built the index for 195 target sequence(s)
2025-09-15 20:27:09.846 wdl.w:ptcp.w:call-sawfish-89.t:call-run_sawfish.stderr VERBOSE [M::mm_mapopt_update::83.504*1.69] mid_occ = 136
2025-09-15 20:27:09.846 wdl.w:ptcp.w:call-sawfish-89.t:call-run_sawfish.stderr VERBOSE [M::mm_idx_stat] kmer size: 19; skip: 19; is_hpc: 0; #seq: 195
2025-09-15 20:27:09.846 wdl.w:ptcp.w:call-sawfish-89.t:call-run_sawfish.stderr VERBOSE [M::mm_idx_stat::90.064*1.64] distinct minimizers: 214664461 (92.23% are singletons); average occurrences: 1.372; average spacing: 10.529; total length: 3099922541
2025-09-15 20:27:09.846 wdl.w:ptcp.w:call-sawfish-89.t:call-run_sawfish.stderr VERBOSE [M::main] Version: 2.26-r1175
2025-09-15 20:27:09.846 wdl.w:ptcp.w:call-sawfish-89.t:call-run_sawfish.stderr VERBOSE [M::main] CMD: /opt/pacbio/smrttools/install/smrtlink-release_25.1.0.257715/bundles/smrttools/install/smrttools-release_25.1.0.257715/private/thirdparty/minimap2/minimap2_2.26-pacbio2/binwrap/../../../../../private/thirdparty/minimap2/minimap2_2.26-pacbio2/bin/minimap2 -a -y -x map-hifi -Y -E 1,0 /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa -
2025-09-15 20:27:09.846 wdl.w:ptcp.w:call-sawfish-89.t:call-run_sawfish.stderr VERBOSE [M::main] Real time: 90.587 sec; CPU: 148.073 sec; Peak RSS: 11.887 GB
2025-09-15 20:27:09.880 wdl.w:ptcp.w:call-paraphase-63.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for hbb for sample m84036_250809_035451_s4.bc2160 at 2025-09-15 20:27:00.454494...
2025-09-15 20:27:09.881 wdl.w:ptcp.w:call-paraphase-63.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for hbb for sample m84036_250809_035451_s4.bc2160 at 2025-09-15 20:27:00.893221...
2025-09-15 20:27:09.950 wdl.w:ptcp.w:call-sawfish-80.t:call-run_sawfish INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2177_sawfish/m84036_250809_035451_s4.bc2177.sv.vcf.gz"
2025-09-15 20:27:09.953 wdl.w:ptcp.w:call-sawfish-80.t:call-run_sawfish INFO output :: name: "vcf_tbi", value: "m84036_250809_035451_s4.bc2177_sawfish/m84036_250809_035451_s4.bc2177.sv.vcf.gz.tbi"
2025-09-15 20:27:09.954 wdl.w:ptcp.w:call-sawfish-80.t:call-run_sawfish INFO output :: name: "minimap2_bam", value: "m84036_250809_035451_s4.bc2177.minimap2.bam"
2025-09-15 20:27:09.955 wdl.w:ptcp.w:call-sawfish-80.t:call-run_sawfish INFO output :: name: "minimap2_bam_bai", value: "m84036_250809_035451_s4.bc2177.minimap2.bam.bai"
2025-09-15 20:27:10.008 wdl.w:ptcp.t:call-tar_outputs-35.slurm_singularity INFO srun: job 51798223 queued and waiting for resources
2025-09-15 20:27:10.008 wdl.w:ptcp.t:call-tar_outputs-35.slurm_singularity INFO srun: job 51798223 has been allocated resources
2025-09-15 20:27:10.008 wdl.w:ptcp.t:call-tar_outputs-35.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:27:10.065 wdl.w:ptcp.w:call-sawfish-80.t:call-run_sawfish NOTICE done
2025-09-15 20:27:10.072 wdl.w:ptcp.w:call-sawfish-80 NOTICE finish :: job: "call-run_sawfish"
2025-09-15 20:27:10.072 wdl.w:ptcp.w:call-sawfish-80 INFO output :: job: "call-run_sawfish", values: {"minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-80/call-run_sawfish/out/m84036_250809_035451_s4.bc2177.minimap2.bam.bai", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-80/call-run_sawfish/out/m84036_250809_035451_s4.bc2177.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-80/call-run_sawfish/out/m84036_250809_035451_s4.bc2177_sawfish/m84036_250809_035451_s4.bc2177.sv.vcf.gz.tbi", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-80/call-run_sawfish/out/m84036_250809_035451_s4.bc2177_sawfish/m84036_250809_035451_s4.bc2177.sv.vcf.gz"}
2025-09-15 20:27:10.072 wdl.w:ptcp.w:call-sawfish-80 INFO visit :: node: "output-minimap2_bam", values: {"minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-80/call-run_sawfish/out/m84036_250809_035451_s4.bc2177.minimap2.bam"}
2025-09-15 20:27:10.073 wdl.w:ptcp.w:call-sawfish-80 INFO visit :: node: "output-minimap2_bam_bai", values: {"minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-80/call-run_sawfish/out/m84036_250809_035451_s4.bc2177.minimap2.bam.bai"}
2025-09-15 20:27:10.073 wdl.w:ptcp.w:call-sawfish-80 INFO visit :: node: "output-vcf", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-80/call-run_sawfish/out/m84036_250809_035451_s4.bc2177_sawfish/m84036_250809_035451_s4.bc2177.sv.vcf.gz"}
2025-09-15 20:27:10.073 wdl.w:ptcp.w:call-sawfish-80 INFO visit :: node: "output-vcf_tbi", values: {"vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-80/call-run_sawfish/out/m84036_250809_035451_s4.bc2177_sawfish/m84036_250809_035451_s4.bc2177.sv.vcf.gz.tbi"}
2025-09-15 20:27:10.073 wdl.w:ptcp.w:call-sawfish-80 INFO visit :: node: "outputs", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-80/call-run_sawfish/out/m84036_250809_035451_s4.bc2177_sawfish/m84036_250809_035451_s4.bc2177.sv.vcf.gz", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-80/call-run_sawfish/out/m84036_250809_035451_s4.bc2177.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-80/call-run_sawfish/out/m84036_250809_035451_s4.bc2177_sawfish/m84036_250809_035451_s4.bc2177.sv.vcf.gz.tbi", "minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-80/call-run_sawfish/out/m84036_250809_035451_s4.bc2177.minimap2.bam.bai"}
2025-09-15 20:27:10.112 wdl.w:ptcp.w:call-sawfish-80 NOTICE done
2025-09-15 20:27:10.117 wdl.w:ptcp NOTICE finish :: job: "call-sawfish-80"
2025-09-15 20:27:10.117 wdl.w:ptcp INFO output :: job: "call-sawfish-80", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-80/out/m84036_250809_035451_s4.bc2177_sawfish/m84036_250809_035451_s4.bc2177.sv.vcf.gz", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-80/out/m84036_250809_035451_s4.bc2177.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-80/out/m84036_250809_035451_s4.bc2177_sawfish/m84036_250809_035451_s4.bc2177.sv.vcf.gz.tbi", "minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-80/out/m84036_250809_035451_s4.bc2177.minimap2.bam.bai"}
2025-09-15 20:27:10.118 wdl.w:ptcp NOTICE ready :: job: "call-tar_outputs-80", callee: "tar_outputs"
2025-09-15 20:27:10.118 wdl.w:ptcp INFO input :: job: "call-tar_outputs-80", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "sawfish_vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-80/out/m84036_250809_035451_s4.bc2177_sawfish/m84036_250809_035451_s4.bc2177.sv.vcf.gz.tbi", "sawfish_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-80/out/m84036_250809_035451_s4.bc2177_sawfish/m84036_250809_035451_s4.bc2177.sv.vcf.gz", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-80/out/m84036_250809_035451_s4.bc2177.f8inversion.json", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-80/out/m84036_250809_035451_s4.bc2177_paraphase/m84036_250809_035451_s4.bc2177.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-80/out/m84036_250809_035451_s4.bc2177_paraphase/m84036_250809_035451_s4.bc2177.paraphase.bam", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-80/out/m84036_250809_035451_s4.bc2177_paraphase/m84036_250809_035451_s4.bc2177.paraphase.json", "trgt_spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-80/out/m84036_250809_035451_s4.bc2177.trgt.sorted.spanning.bam.bai", "trgt_spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-80/out/m84036_250809_035451_s4.bc2177.trgt.sorted.spanning.bam", "trgt_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-80/out/m84036_250809_035451_s4.bc2177.trgt.vcf", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-80/out/m84036_250809_035451_s4.bc2177.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-80/out/m84036_250809_035451_s4.bc2177.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2177"}
2025-09-15 20:27:10.125 wdl.w:ptcp.t:call-tar_outputs-80 NOTICE task setup :: name: "tar_outputs", source: "./common.wdl", line: 279, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-80", thread: 140613555033664
2025-09-15 20:27:10.152 wdl.w:ptcp.t:call-tar_outputs-80 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:27:10.152 wdl.w:ptcp.t:call-tar_outputs-80 INFO input :: name: "sawfish_vcf_tbi", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2177.sv.vcf.gz.tbi"
2025-09-15 20:27:10.152 wdl.w:ptcp.t:call-tar_outputs-80 INFO input :: name: "sawfish_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2177.sv.vcf.gz"
2025-09-15 20:27:10.152 wdl.w:ptcp.t:call-tar_outputs-80 INFO input :: name: "f8_json", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2177.f8inversion.json"
2025-09-15 20:27:10.152 wdl.w:ptcp.t:call-tar_outputs-80 INFO input :: name: "paraphase_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2177.paraphase.bam.bai"
2025-09-15 20:27:10.152 wdl.w:ptcp.t:call-tar_outputs-80 INFO input :: name: "paraphase_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2177.paraphase.bam"
2025-09-15 20:27:10.152 wdl.w:ptcp.t:call-tar_outputs-80 INFO input :: name: "paraphase_json", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2177.paraphase.json"
2025-09-15 20:27:10.153 wdl.w:ptcp.t:call-tar_outputs-80 INFO input :: name: "trgt_spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2177.trgt.sorted.spanning.bam.bai"
2025-09-15 20:27:10.153 wdl.w:ptcp.t:call-tar_outputs-80 INFO input :: name: "trgt_spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2177.trgt.sorted.spanning.bam"
2025-09-15 20:27:10.153 wdl.w:ptcp.t:call-tar_outputs-80 INFO input :: name: "trgt_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2177.trgt.vcf"
2025-09-15 20:27:10.153 wdl.w:ptcp.t:call-tar_outputs-80 INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2177.mapped.bam.bai"
2025-09-15 20:27:10.153 wdl.w:ptcp.t:call-tar_outputs-80 INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2177.mapped.bam"
2025-09-15 20:27:10.153 wdl.w:ptcp.t:call-tar_outputs-80 INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2177"
2025-09-15 20:27:10.153 wdl.w:ptcp.t:call-tar_outputs-80 INFO eval :: name: "threads", value: 1
2025-09-15 20:27:10.153 wdl.w:ptcp.t:call-tar_outputs-80 INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:27:10.153 wdl.w:ptcp.t:call-tar_outputs-80 INFO eval :: name: "disk_size", value: 6
2025-09-15 20:27:10.153 wdl.w:ptcp.t:call-tar_outputs-80 INFO eval :: name: "output_tarball", value: "m84036_250809_035451_s4.bc2177.tar"
2025-09-15 20:27:10.154 wdl.w:ptcp.t:call-tar_outputs-80 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:27:10.154 wdl.w:ptcp.t:call-tar_outputs-80 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:27:10.154 wdl.w:ptcp.t:call-tar_outputs-80 INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:27:10.154 wdl.w:ptcp.t:call-tar_outputs-80 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:27:10.234 wdl.w:ptcp.t:call-tar_outputs-80 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 17, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-80/_singularity_tmpdir_a9vtd1aq"
2025-09-15 20:27:10.234 wdl.w:ptcp.t:call-tar_outputs-80 INFO Slurm invocation: srun --job-name call-tar_outputs-80 --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-80/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-80/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-80/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-80/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-80/out/m84036_250809_035451_s4.bc2177.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2177.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-80/out/m84036_250809_035451_s4.bc2177.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2177.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-80/out/m84036_250809_035451_s4.bc2177.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2177.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-80/out/m84036_250809_035451_s4.bc2177.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2177.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-80/out/m84036_250809_035451_s4.bc2177.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2177.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-80/out/m84036_250809_035451_s4.bc2177_paraphase/m84036_250809_035451_s4.bc2177.paraphase.json:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2177.paraphase.json:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-80/out/m84036_250809_035451_s4.bc2177_paraphase/m84036_250809_035451_s4.bc2177.paraphase.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2177.paraphase.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-80/out/m84036_250809_035451_s4.bc2177_paraphase/m84036_250809_035451_s4.bc2177.paraphase.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2177.paraphase.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-80/out/m84036_250809_035451_s4.bc2177_sawfish/m84036_250809_035451_s4.bc2177.sv.vcf.gz.tbi:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2177.sv.vcf.gz.tbi:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-80/out/m84036_250809_035451_s4.bc2177_sawfish/m84036_250809_035451_s4.bc2177.sv.vcf.gz:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2177.sv.vcf.gz:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-80/out/m84036_250809_035451_s4.bc2177.f8inversion.json:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2177.f8inversion.json:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-80/_singularity_tmpdir_a9vtd1aq/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-80/_singularity_tmpdir_a9vtd1aq/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:27:10.246 wdl.w:ptcp.t:call-tar_outputs-80 NOTICE slurm_singularity run :: pid: 1208204, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-80/slurm_singularity.log.txt"
2025-09-15 20:27:10.332 wdl.w:ptcp.t:call-tar_outputs-35 INFO output :: name: "sample_tarball", value: "m84036_250809_035451_s4.bc2132.tar"
2025-09-15 20:27:10.394 wdl.w:ptcp.t:call-tar_outputs-35 NOTICE done
2025-09-15 20:27:10.397 wdl.w:ptcp NOTICE finish :: job: "call-tar_outputs-35"
2025-09-15 20:27:10.397 wdl.w:ptcp INFO output :: job: "call-tar_outputs-35", values: {"sample_tarball": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-35/out/m84036_250809_035451_s4.bc2132.tar"}
2025-09-15 20:27:10.515 wdl.w:ptcp.w:call-paraphase-91.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for hba for sample m84036_250809_035451_s4.bc2188 at 2025-09-15 20:26:27.679484...
2025-09-15 20:27:10.516 wdl.w:ptcp.w:call-paraphase-91.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for hba for sample m84036_250809_035451_s4.bc2188 at 2025-09-15 20:26:28.110129...
2025-09-15 20:27:10.516 wdl.w:ptcp.w:call-paraphase-91.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for hbb for sample m84036_250809_035451_s4.bc2188 at 2025-09-15 20:27:03.457532...
2025-09-15 20:27:10.516 wdl.w:ptcp.w:call-paraphase-91.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for hbb for sample m84036_250809_035451_s4.bc2188 at 2025-09-15 20:27:03.458276...
2025-09-15 20:27:11.148 wdl.w:ptcp.w:call-paraphase-66.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for hbb for sample m84036_250809_035451_s4.bc2163 at 2025-09-15 20:27:02.010889...
2025-09-15 20:27:11.162 wdl.w:ptcp.t:call-tar_outputs-80.stderr VERBOSE tar: Removing leading `/' from member names
2025-09-15 20:27:11.162 wdl.w:ptcp.t:call-tar_outputs-80.stderr VERBOSE tar: Removing leading `/' from hard link targets
2025-09-15 20:27:11.169 wdl.w:ptcp.t:call-tar_outputs-80.slurm_singularity INFO srun: job 51798224 queued and waiting for resources
2025-09-15 20:27:11.169 wdl.w:ptcp.t:call-tar_outputs-80.slurm_singularity INFO srun: job 51798224 has been allocated resources
2025-09-15 20:27:11.169 wdl.w:ptcp.t:call-tar_outputs-80.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:27:11.196 wdl.w:ptcp.t:call-tar_outputs-80 INFO output :: name: "sample_tarball", value: "m84036_250809_035451_s4.bc2177.tar"
2025-09-15 20:27:11.248 wdl.w:ptcp.t:call-tar_outputs-80 NOTICE done
2025-09-15 20:27:11.251 wdl.w:ptcp NOTICE finish :: job: "call-tar_outputs-80"
2025-09-15 20:27:11.251 wdl.w:ptcp INFO output :: job: "call-tar_outputs-80", values: {"sample_tarball": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-80/out/m84036_250809_035451_s4.bc2177.tar"}
2025-09-15 20:27:12.356 wdl.w:ptcp.w:call-paraphase-87.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for hbb for sample m84036_250809_035451_s4.bc2184 at 2025-09-15 20:27:05.435659...
2025-09-15 20:27:12.399 wdl.w:ptcp.w:call-paraphase-95.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for hbb for sample m84036_250809_035451_s4.bc2192 at 2025-09-15 20:26:50.451442...
2025-09-15 20:27:12.399 wdl.w:ptcp.w:call-paraphase-95.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for f8inv1 for sample m84036_250809_035451_s4.bc2192 at 2025-09-15 20:26:51.913787...
2025-09-15 20:27:12.400 wdl.w:ptcp.w:call-paraphase-95.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for f8inv1 for sample m84036_250809_035451_s4.bc2192 at 2025-09-15 20:26:52.371432...
2025-09-15 20:27:12.400 wdl.w:ptcp.w:call-paraphase-95.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for hbb for sample m84036_250809_035451_s4.bc2192 at 2025-09-15 20:26:55.394460...
2025-09-15 20:27:12.400 wdl.w:ptcp.w:call-paraphase-95.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for hbb for sample m84036_250809_035451_s4.bc2192 at 2025-09-15 20:26:55.767194...
2025-09-15 20:27:12.739 wdl.w:ptcp.w:call-paraphase-67.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for hbb for sample m84036_250809_035451_s4.bc2164 at 2025-09-15 20:26:50.087683...
2025-09-15 20:27:12.740 wdl.w:ptcp.w:call-paraphase-67.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for hbb for sample m84036_250809_035451_s4.bc2164 at 2025-09-15 20:26:50.088401...
2025-09-15 20:27:12.740 wdl.w:ptcp.w:call-paraphase-67.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for hbb for sample m84036_250809_035451_s4.bc2164 at 2025-09-15 20:26:51.896893...
2025-09-15 20:27:12.740 wdl.w:ptcp.w:call-paraphase-67.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for hbb for sample m84036_250809_035451_s4.bc2164 at 2025-09-15 20:26:58.233361...
2025-09-15 20:27:12.740 wdl.w:ptcp.w:call-paraphase-67.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for hbb for sample m84036_250809_035451_s4.bc2164 at 2025-09-15 20:26:58.575492...
2025-09-15 20:27:13.178 wdl.w:ptcp.w:call-paraphase-82.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for hba for sample m84036_250809_035451_s4.bc2179 at 2025-09-15 20:26:59.796904...
2025-09-15 20:27:13.178 wdl.w:ptcp.w:call-paraphase-82.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for hba for sample m84036_250809_035451_s4.bc2179 at 2025-09-15 20:27:00.510853...
2025-09-15 20:27:13.582 wdl.w:ptcp.w:call-paraphase-59.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for f8inv22 for sample m84036_250809_035451_s4.bc2156 at 2025-09-15 20:26:59.993997...
2025-09-15 20:27:13.582 wdl.w:ptcp.w:call-paraphase-59.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for f8inv22 for sample m84036_250809_035451_s4.bc2156 at 2025-09-15 20:27:05.187349...
2025-09-15 20:27:13.582 wdl.w:ptcp.w:call-paraphase-59.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for f8inv22 for sample m84036_250809_035451_s4.bc2156 at 2025-09-15 20:27:05.569923...
2025-09-15 20:27:14.194 wdl.w:ptcp.w:call-paraphase-66.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for hbb for sample m84036_250809_035451_s4.bc2163 at 2025-09-15 20:27:12.160734...
2025-09-15 20:27:14.194 wdl.w:ptcp.w:call-paraphase-66.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for hbb for sample m84036_250809_035451_s4.bc2163 at 2025-09-15 20:27:13.301715...
2025-09-15 20:27:16.301 wdl.w:ptcp.w:call-paraphase-74.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for rpgr for sample m84036_250809_035451_s4.bc2171 at 2025-09-15 20:27:00.202902...
2025-09-15 20:27:16.302 wdl.w:ptcp.w:call-paraphase-74.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for rpgr for sample m84036_250809_035451_s4.bc2171 at 2025-09-15 20:27:00.204081...
2025-09-15 20:27:16.302 wdl.w:ptcp.w:call-paraphase-74.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for rpgr for sample m84036_250809_035451_s4.bc2171 at 2025-09-15 20:27:01.823739...
2025-09-15 20:27:16.302 wdl.w:ptcp.w:call-paraphase-74.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for rpgr for sample m84036_250809_035451_s4.bc2171 at 2025-09-15 20:27:02.953075...
2025-09-15 20:27:16.302 wdl.w:ptcp.w:call-paraphase-74.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for rpgr for sample m84036_250809_035451_s4.bc2171 at 2025-09-15 20:27:03.214505...
2025-09-15 20:27:16.418 wdl.w:ptcp.w:call-paraphase-90.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for cyp21 for sample m84036_250809_035451_s4.bc2187 at 2025-09-15 20:27:05.239083...
2025-09-15 20:27:16.418 wdl.w:ptcp.w:call-paraphase-90.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for cyp21 for sample m84036_250809_035451_s4.bc2187 at 2025-09-15 20:27:06.299168...
2025-09-15 20:27:16.418 wdl.w:ptcp.w:call-paraphase-90.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for f8inv1 for sample m84036_250809_035451_s4.bc2187 at 2025-09-15 20:27:09.976272...
2025-09-15 20:27:16.418 wdl.w:ptcp.w:call-paraphase-90.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for f8inv1 for sample m84036_250809_035451_s4.bc2187 at 2025-09-15 20:27:09.976636...
2025-09-15 20:27:16.418 wdl.w:ptcp.w:call-paraphase-90.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for f8inv1 for sample m84036_250809_035451_s4.bc2187 at 2025-09-15 20:27:12.131178...
2025-09-15 20:27:16.418 wdl.w:ptcp.w:call-paraphase-90.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for hbb for sample m84036_250809_035451_s4.bc2187 at 2025-09-15 20:27:13.409795...
2025-09-15 20:27:16.418 wdl.w:ptcp.w:call-paraphase-90.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for hbb for sample m84036_250809_035451_s4.bc2187 at 2025-09-15 20:27:13.411194...
2025-09-15 20:27:16.718 wdl.w:ptcp.w:call-paraphase-58.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for hbb for sample m84036_250809_035451_s4.bc2155 at 2025-09-15 20:27:11.637148...
2025-09-15 20:27:16.718 wdl.w:ptcp.w:call-paraphase-58.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for hbb for sample m84036_250809_035451_s4.bc2155 at 2025-09-15 20:27:11.637835...
2025-09-15 20:27:18.564 wdl.w:ptcp.w:call-paraphase-43.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for f8inv22 for sample m84036_250809_035451_s4.bc2140 at 2025-09-15 20:27:03.364039...
2025-09-15 20:27:18.565 wdl.w:ptcp.w:call-paraphase-43.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for f8inv22 for sample m84036_250809_035451_s4.bc2140 at 2025-09-15 20:27:06.962917...
2025-09-15 20:27:18.565 wdl.w:ptcp.w:call-paraphase-43.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for f8inv22 for sample m84036_250809_035451_s4.bc2140 at 2025-09-15 20:27:07.370492...
2025-09-15 20:27:18.939 wdl.w:ptcp.w:call-sawfish-89.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:27:06][sawfish][INFO] Starting sawfish 2.0.3
2025-09-15 20:27:18.939 wdl.w:ptcp.w:call-sawfish-89.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:27:06][sawfish][INFO] cmdline: sawfish discover --disable-cnv --threads 16 --ref /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa --bam m84036_250809_035451_s4.bc2186.minimap2.bam --output-dir m84036_250809_035451_s4.bc2186_sawfish_discover
2025-09-15 20:27:18.939 wdl.w:ptcp.w:call-sawfish-89.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:27:06][sawfish][INFO] Running on 16 threads
2025-09-15 20:27:18.940 wdl.w:ptcp.w:call-sawfish-89.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:27:06][sawfish][INFO] Writing discover settings to file: 'm84036_250809_035451_s4.bc2186_sawfish_discover/discover.settings.json'
2025-09-15 20:27:18.940 wdl.w:ptcp.w:call-sawfish-89.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:27:06][sawfish][INFO] Reading reference genome from file '/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa'
2025-09-15 20:27:18.940 wdl.w:ptcp.w:call-sawfish-89.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:27:12][sawfish][INFO] Processing alignment file '/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2186.minimap2.bam'
2025-09-15 20:27:18.940 wdl.w:ptcp.w:call-sawfish-89.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:27:12][sawfish][INFO] Finished processing all alignments
2025-09-15 20:27:18.940 wdl.w:ptcp.w:call-sawfish-89.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:27:13][sawfish][INFO] Writing depth bins to binary file: 'm84036_250809_035451_s4.bc2186_sawfish_discover/depth.mpack'
2025-09-15 20:27:18.940 wdl.w:ptcp.w:call-sawfish-89.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:27:13][sawfish][INFO] Writing max sv depth genome regions to bed file: 'm84036_250809_035451_s4.bc2186_sawfish_discover/max.depth.bed'
2025-09-15 20:27:18.940 wdl.w:ptcp.w:call-sawfish-89.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:27:13][sawfish][INFO] Completing breakpoint observation clustering
2025-09-15 20:27:18.940 wdl.w:ptcp.w:call-sawfish-89.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:27:13][sawfish][INFO] Finished breakpoint observation clustering
2025-09-15 20:27:18.940 wdl.w:ptcp.w:call-sawfish-89.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:27:13][sawfish][INFO] Consolidating adjacent indel candidates
2025-09-15 20:27:18.940 wdl.w:ptcp.w:call-sawfish-89.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:27:13][sawfish][INFO] Finding large insertion candidates
2025-09-15 20:27:18.940 wdl.w:ptcp.w:call-sawfish-89.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:27:13][sawfish][INFO] Writing breakpoint_cluster debug bed file: 'm84036_250809_035451_s4.bc2186_sawfish_discover/debug.breakpoint_clusters.bed'
2025-09-15 20:27:18.940 wdl.w:ptcp.w:call-sawfish-89.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:27:13][sawfish][INFO] Refining SV Candidates
2025-09-15 20:27:18.940 wdl.w:ptcp.w:call-sawfish-89.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:27:13][sawfish][INFO] Writing debug assembly region bed file: 'm84036_250809_035451_s4.bc2186_sawfish_discover/assembly.regions.bed'
2025-09-15 20:27:18.940 wdl.w:ptcp.w:call-sawfish-89.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:27:13][sawfish][INFO] Starting refinement of breakpoint evidence clusters
2025-09-15 20:27:18.940 wdl.w:ptcp.w:call-sawfish-89.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:27:13][sawfish][INFO] Finished refining all breakpoint evidence clusters
2025-09-15 20:27:18.940 wdl.w:ptcp.w:call-sawfish-89.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:27:13][sawfish][INFO] Writing all contig alignments to bam file: 'm84036_250809_035451_s4.bc2186_sawfish_discover/contig.alignment.bam'
2025-09-15 20:27:18.940 wdl.w:ptcp.w:call-sawfish-89.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:27:13][sawfish][INFO] Writing candidate structural variants to file: 'm84036_250809_035451_s4.bc2186_sawfish_discover/candidate.sv.bcf'
2025-09-15 20:27:18.940 wdl.w:ptcp.w:call-sawfish-89.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:27:13][sawfish][INFO] Writing run statistics to file: 'm84036_250809_035451_s4.bc2186_sawfish_discover/run.stats.json'
2025-09-15 20:27:18.940 wdl.w:ptcp.w:call-sawfish-89.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:27:13][sawfish][INFO] sawfish completed. Total Runtime: 00:00:06.421
2025-09-15 20:27:19.455 wdl.w:ptcp.w:call-paraphase-90.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for gba for sample m84036_250809_035451_s4.bc2187 at 2025-09-15 20:27:14.318801...
2025-09-15 20:27:19.455 wdl.w:ptcp.w:call-paraphase-90.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for hbb for sample m84036_250809_035451_s4.bc2187 at 2025-09-15 20:27:15.157815...
2025-09-15 20:27:19.455 wdl.w:ptcp.w:call-paraphase-90.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for gba for sample m84036_250809_035451_s4.bc2187 at 2025-09-15 20:27:15.251932...
2025-09-15 20:27:19.664 wdl.w:ptcp.w:call-paraphase-43.t:call-run_paraphase INFO output :: name: "paraphase_bam", value: "m84036_250809_035451_s4.bc2140_paraphase/m84036_250809_035451_s4.bc2140.paraphase.bam"
2025-09-15 20:27:19.670 wdl.w:ptcp.w:call-paraphase-43.t:call-run_paraphase INFO output :: name: "paraphase_bam_bai", value: "m84036_250809_035451_s4.bc2140_paraphase/m84036_250809_035451_s4.bc2140.paraphase.bam.bai"
2025-09-15 20:27:19.671 wdl.w:ptcp.w:call-paraphase-43.t:call-run_paraphase INFO output :: name: "paraphase_json", value: "m84036_250809_035451_s4.bc2140_paraphase/m84036_250809_035451_s4.bc2140.paraphase.json"
2025-09-15 20:27:19.675 wdl.w:ptcp.w:call-paraphase-43.t:call-run_paraphase INFO output :: name: "paraphase_vcfs", value: ["/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2140_paraphase/m84036_250809_035451_s4.bc2140_paraphase_vcfs/m84036_250809_035451_s4.bc2140_cyp21.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2140_paraphase/m84036_250809_035451_s4.bc2140_paraphase_vcfs/m84036_250809_035451_s4.bc2140_f8inv1.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2140_paraphase/m84036_250809_035451_s4.bc2140_paraphase_vcfs/m84036_250809_035451_s4.bc2140_f8inv22.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2140_paraphase/m84036_250809_035451_s4.bc2140_paraphase_vcfs/m84036_250809_035451_s4.bc2140_gba.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2140_paraphase/m84036_250809_035451_s4.bc2140_paraphase_vcfs/m84036_250809_035451_s4.bc2140_hba.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2140_paraphase/m84036_250809_035451_s4.bc2140_paraphase_vcfs/m84036_250809_035451_s4.bc2140_hbb.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2140_paraphase/m84036_250809_035451_s4.bc2140_paraphase_vcfs/m84036_250809_035451_s4.bc2140_rpgr.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2140_paraphase/m84036_250809_035451_s4.bc2140_paraphase_vcfs/m84036_250809_035451_s4.bc2140_smn1.vcf"]
2025-09-15 20:27:19.678 wdl.w:ptcp.w:call-paraphase-43.t:call-run_paraphase INFO output :: name: "havanno_json", value: "m84036_250809_035451_s4.bc2140.havanno.json"
2025-09-15 20:27:19.830 wdl.w:ptcp.w:call-paraphase-43.t:call-run_paraphase NOTICE done
2025-09-15 20:27:19.835 wdl.w:ptcp.w:call-paraphase-43 NOTICE finish :: job: "call-run_paraphase"
2025-09-15 20:27:19.835 wdl.w:ptcp.w:call-paraphase-43 INFO output :: job: "call-run_paraphase", values: {"havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-43/call-run_paraphase/out/m84036_250809_035451_s4.bc2140.havanno.json", "paraphase_vcfs": ["/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-43/call-run_paraphase/out/m84036_250809_035451_s4.bc2140_paraphase/m84036_250809_035451_s4.bc2140_paraphase_vcfs/m84036_250809_035451_s4.bc2140_cyp21.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-43/call-run_paraphase/out/m84036_250809_035451_s4.bc2140_paraphase/m84036_250809_035451_s4.bc2140_paraphase_vcfs/m84036_250809_035451_s4.bc2140_f8inv1.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-43/call-run_paraphase/out/m84036_250809_035451_s4.bc2140_paraphase/m84036_250809_035451_s4.bc2140_paraphase_vcfs/m84036_250809_035451_s4.bc2140_f8inv22.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-43/call-run_paraphase/out/m84036_250809_035451_s4.bc2140_paraphase/m84036_250809_035451_s4.bc2140_paraphase_vcfs/m84036_250809_035451_s4.bc2140_gba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-43/call-run_paraphase/out/m84036_250809_035451_s4.bc2140_paraphase/m84036_250809_035451_s4.bc2140_paraphase_vcfs/m84036_250809_035451_s4.bc2140_hba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-43/call-run_paraphase/out/m84036_250809_035451_s4.bc2140_paraphase/m84036_250809_035451_s4.bc2140_paraphase_vcfs/m84036_250809_035451_s4.bc2140_hbb.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-43/call-run_paraphase/out/m84036_250809_035451_s4.bc2140_paraphase/m84036_250809_035451_s4.bc2140_paraphase_vcfs/m84036_250809_035451_s4.bc2140_rpgr.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-43/call-run_paraphase/out/m84036_250809_035451_s4.bc2140_paraphase/m84036_250809_035451_s4.bc2140_paraphase_vcfs/m84036_250809_035451_s4.bc2140_smn1.vcf"], "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-43/call-run_paraphase/out/m84036_250809_035451_s4.bc2140_paraphase/m84036_250809_035451_s4.bc2140.paraphase.json", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-43/call-run_paraphase/out/m84036_250809_035451_s4.bc2140_paraphase/m84036_250809_035451_s4.bc2140.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-43/call-run_paraphase/out/m84036_250809_035451_s4.bc2140_paraphase/m84036_250809_035451_s4.bc2140.paraphase.bam"}
2025-09-15 20:27:19.836 wdl.w:ptcp.w:call-paraphase-43 NOTICE ready :: job: "call-call_f8", callee: "call_f8"
2025-09-15 20:27:19.836 wdl.w:ptcp.w:call-paraphase-43 INFO input :: job: "call-call_f8", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "out_prefix": "m84036_250809_035451_s4.bc2140", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-43/call-run_paraphase/out/m84036_250809_035451_s4.bc2140_paraphase/m84036_250809_035451_s4.bc2140.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-43/call-run_paraphase/out/m84036_250809_035451_s4.bc2140_paraphase/m84036_250809_035451_s4.bc2140.paraphase.bam", "sex": "F"}
2025-09-15 20:27:19.836 wdl.w:ptcp.w:call-paraphase-43 INFO visit :: node: "output-havanno_json", values: {"havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-43/call-run_paraphase/out/m84036_250809_035451_s4.bc2140.havanno.json"}
2025-09-15 20:27:19.837 wdl.w:ptcp.w:call-paraphase-43 INFO visit :: node: "output-paraphase_bam", values: {"paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-43/call-run_paraphase/out/m84036_250809_035451_s4.bc2140_paraphase/m84036_250809_035451_s4.bc2140.paraphase.bam"}
2025-09-15 20:27:19.837 wdl.w:ptcp.w:call-paraphase-43 INFO visit :: node: "output-paraphase_bam_bai", values: {"paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-43/call-run_paraphase/out/m84036_250809_035451_s4.bc2140_paraphase/m84036_250809_035451_s4.bc2140.paraphase.bam.bai"}
2025-09-15 20:27:19.837 wdl.w:ptcp.w:call-paraphase-43 INFO visit :: node: "output-paraphase_json", values: {"paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-43/call-run_paraphase/out/m84036_250809_035451_s4.bc2140_paraphase/m84036_250809_035451_s4.bc2140.paraphase.json"}
2025-09-15 20:27:19.837 wdl.w:ptcp.w:call-paraphase-43 INFO visit :: node: "output-paraphase_vcfs", values: {"paraphase_vcfs": ["/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-43/call-run_paraphase/out/m84036_250809_035451_s4.bc2140_paraphase/m84036_250809_035451_s4.bc2140_paraphase_vcfs/m84036_250809_035451_s4.bc2140_cyp21.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-43/call-run_paraphase/out/m84036_250809_035451_s4.bc2140_paraphase/m84036_250809_035451_s4.bc2140_paraphase_vcfs/m84036_250809_035451_s4.bc2140_f8inv1.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-43/call-run_paraphase/out/m84036_250809_035451_s4.bc2140_paraphase/m84036_250809_035451_s4.bc2140_paraphase_vcfs/m84036_250809_035451_s4.bc2140_f8inv22.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-43/call-run_paraphase/out/m84036_250809_035451_s4.bc2140_paraphase/m84036_250809_035451_s4.bc2140_paraphase_vcfs/m84036_250809_035451_s4.bc2140_gba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-43/call-run_paraphase/out/m84036_250809_035451_s4.bc2140_paraphase/m84036_250809_035451_s4.bc2140_paraphase_vcfs/m84036_250809_035451_s4.bc2140_hba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-43/call-run_paraphase/out/m84036_250809_035451_s4.bc2140_paraphase/m84036_250809_035451_s4.bc2140_paraphase_vcfs/m84036_250809_035451_s4.bc2140_hbb.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-43/call-run_paraphase/out/m84036_250809_035451_s4.bc2140_paraphase/m84036_250809_035451_s4.bc2140_paraphase_vcfs/m84036_250809_035451_s4.bc2140_rpgr.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-43/call-run_paraphase/out/m84036_250809_035451_s4.bc2140_paraphase/m84036_250809_035451_s4.bc2140_paraphase_vcfs/m84036_250809_035451_s4.bc2140_smn1.vcf"]}
2025-09-15 20:27:19.842 wdl.w:ptcp.w:call-paraphase-43.t:call-call_f8 NOTICE task setup :: name: "call_f8", source: "./paraphase.wdl", line: 232, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-43/call-call_f8", thread: 140608219895360
2025-09-15 20:27:19.856 wdl.w:ptcp.w:call-paraphase-43.t:call-call_f8 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:27:19.856 wdl.w:ptcp.w:call-paraphase-43.t:call-call_f8 INFO input :: name: "genome_version", value: "38"
2025-09-15 20:27:19.856 wdl.w:ptcp.w:call-paraphase-43.t:call-call_f8 INFO input :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2140"
2025-09-15 20:27:19.856 wdl.w:ptcp.w:call-paraphase-43.t:call-call_f8 INFO input :: name: "paraphase_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2140.paraphase.bam.bai"
2025-09-15 20:27:19.856 wdl.w:ptcp.w:call-paraphase-43.t:call-call_f8 INFO input :: name: "paraphase_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2140.paraphase.bam"
2025-09-15 20:27:19.857 wdl.w:ptcp.w:call-paraphase-43.t:call-call_f8 INFO input :: name: "sex", value: "F"
2025-09-15 20:27:19.857 wdl.w:ptcp.w:call-paraphase-43.t:call-call_f8 INFO eval :: name: "threads", value: 1
2025-09-15 20:27:19.857 wdl.w:ptcp.w:call-paraphase-43.t:call-call_f8 INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:27:19.857 wdl.w:ptcp.w:call-paraphase-43.t:call-call_f8 INFO eval :: name: "disk_size", value: 11
2025-09-15 20:27:19.857 wdl.w:ptcp.w:call-paraphase-43.t:call-call_f8 INFO eval :: name: "sample_sex", value: "F"
2025-09-15 20:27:19.858 wdl.w:ptcp.w:call-paraphase-43.t:call-call_f8 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:27:19.858 wdl.w:ptcp.w:call-paraphase-43.t:call-call_f8 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:27:19.858 wdl.w:ptcp.w:call-paraphase-43.t:call-call_f8 INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:27:19.858 wdl.w:ptcp.w:call-paraphase-43.t:call-call_f8 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:27:19.893 wdl.w:ptcp.w:call-paraphase-43.t:call-call_f8 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 8, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-43/call-call_f8/_singularity_tmpdir_lhfldpeh"
2025-09-15 20:27:19.893 wdl.w:ptcp.w:call-paraphase-43.t:call-call_f8 INFO Slurm invocation: srun --job-name call-call_f8 --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-43/call-call_f8/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-43/call-call_f8/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-43/call-call_f8/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-43/call-call_f8/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-43/call-run_paraphase/out/m84036_250809_035451_s4.bc2140_paraphase/m84036_250809_035451_s4.bc2140.paraphase.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2140.paraphase.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-43/call-run_paraphase/out/m84036_250809_035451_s4.bc2140_paraphase/m84036_250809_035451_s4.bc2140.paraphase.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2140.paraphase.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-43/call-call_f8/_singularity_tmpdir_lhfldpeh/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-43/call-call_f8/_singularity_tmpdir_lhfldpeh/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:27:19.897 wdl.w:ptcp.w:call-paraphase-43.t:call-call_f8 NOTICE slurm_singularity run :: pid: 1208290, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-43/call-call_f8/slurm_singularity.log.txt"
2025-09-15 20:27:20.804 wdl.w:ptcp.w:call-sawfish-89.t:call-run_sawfish INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2186_sawfish/m84036_250809_035451_s4.bc2186.sv.vcf.gz"
2025-09-15 20:27:20.807 wdl.w:ptcp.w:call-sawfish-89.t:call-run_sawfish INFO output :: name: "vcf_tbi", value: "m84036_250809_035451_s4.bc2186_sawfish/m84036_250809_035451_s4.bc2186.sv.vcf.gz.tbi"
2025-09-15 20:27:20.808 wdl.w:ptcp.w:call-sawfish-89.t:call-run_sawfish INFO output :: name: "minimap2_bam", value: "m84036_250809_035451_s4.bc2186.minimap2.bam"
2025-09-15 20:27:20.810 wdl.w:ptcp.w:call-sawfish-89.t:call-run_sawfish INFO output :: name: "minimap2_bam_bai", value: "m84036_250809_035451_s4.bc2186.minimap2.bam.bai"
2025-09-15 20:27:20.907 wdl.w:ptcp.w:call-paraphase-43.t:call-call_f8.slurm_singularity INFO srun: job 51798225 queued and waiting for resources
2025-09-15 20:27:20.907 wdl.w:ptcp.w:call-paraphase-43.t:call-call_f8.slurm_singularity INFO srun: job 51798225 has been allocated resources
2025-09-15 20:27:20.907 wdl.w:ptcp.w:call-paraphase-43.t:call-call_f8.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:27:20.917 wdl.w:ptcp.w:call-sawfish-89.t:call-run_sawfish NOTICE done
2025-09-15 20:27:20.922 wdl.w:ptcp.w:call-sawfish-89 NOTICE finish :: job: "call-run_sawfish"
2025-09-15 20:27:20.923 wdl.w:ptcp.w:call-sawfish-89 INFO output :: job: "call-run_sawfish", values: {"minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-89/call-run_sawfish/out/m84036_250809_035451_s4.bc2186.minimap2.bam.bai", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-89/call-run_sawfish/out/m84036_250809_035451_s4.bc2186.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-89/call-run_sawfish/out/m84036_250809_035451_s4.bc2186_sawfish/m84036_250809_035451_s4.bc2186.sv.vcf.gz.tbi", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-89/call-run_sawfish/out/m84036_250809_035451_s4.bc2186_sawfish/m84036_250809_035451_s4.bc2186.sv.vcf.gz"}
2025-09-15 20:27:20.923 wdl.w:ptcp.w:call-sawfish-89 INFO visit :: node: "output-minimap2_bam", values: {"minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-89/call-run_sawfish/out/m84036_250809_035451_s4.bc2186.minimap2.bam"}
2025-09-15 20:27:20.923 wdl.w:ptcp.w:call-sawfish-89 INFO visit :: node: "output-minimap2_bam_bai", values: {"minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-89/call-run_sawfish/out/m84036_250809_035451_s4.bc2186.minimap2.bam.bai"}
2025-09-15 20:27:20.923 wdl.w:ptcp.w:call-sawfish-89 INFO visit :: node: "output-vcf", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-89/call-run_sawfish/out/m84036_250809_035451_s4.bc2186_sawfish/m84036_250809_035451_s4.bc2186.sv.vcf.gz"}
2025-09-15 20:27:20.923 wdl.w:ptcp.w:call-sawfish-89 INFO visit :: node: "output-vcf_tbi", values: {"vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-89/call-run_sawfish/out/m84036_250809_035451_s4.bc2186_sawfish/m84036_250809_035451_s4.bc2186.sv.vcf.gz.tbi"}
2025-09-15 20:27:20.923 wdl.w:ptcp.w:call-sawfish-89 INFO visit :: node: "outputs", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-89/call-run_sawfish/out/m84036_250809_035451_s4.bc2186_sawfish/m84036_250809_035451_s4.bc2186.sv.vcf.gz", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-89/call-run_sawfish/out/m84036_250809_035451_s4.bc2186.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-89/call-run_sawfish/out/m84036_250809_035451_s4.bc2186_sawfish/m84036_250809_035451_s4.bc2186.sv.vcf.gz.tbi", "minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-89/call-run_sawfish/out/m84036_250809_035451_s4.bc2186.minimap2.bam.bai"}
2025-09-15 20:27:20.979 wdl.w:ptcp.w:call-sawfish-89 NOTICE done
2025-09-15 20:27:20.985 wdl.w:ptcp NOTICE finish :: job: "call-sawfish-89"
2025-09-15 20:27:20.985 wdl.w:ptcp INFO output :: job: "call-sawfish-89", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-89/out/m84036_250809_035451_s4.bc2186_sawfish/m84036_250809_035451_s4.bc2186.sv.vcf.gz", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-89/out/m84036_250809_035451_s4.bc2186.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-89/out/m84036_250809_035451_s4.bc2186_sawfish/m84036_250809_035451_s4.bc2186.sv.vcf.gz.tbi", "minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-89/out/m84036_250809_035451_s4.bc2186.minimap2.bam.bai"}
2025-09-15 20:27:20.986 wdl.w:ptcp NOTICE ready :: job: "call-tar_outputs-89", callee: "tar_outputs"
2025-09-15 20:27:20.986 wdl.w:ptcp INFO input :: job: "call-tar_outputs-89", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "sawfish_vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-89/out/m84036_250809_035451_s4.bc2186_sawfish/m84036_250809_035451_s4.bc2186.sv.vcf.gz.tbi", "sawfish_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-89/out/m84036_250809_035451_s4.bc2186_sawfish/m84036_250809_035451_s4.bc2186.sv.vcf.gz", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-89/out/m84036_250809_035451_s4.bc2186.f8inversion.json", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-89/out/m84036_250809_035451_s4.bc2186_paraphase/m84036_250809_035451_s4.bc2186.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-89/out/m84036_250809_035451_s4.bc2186_paraphase/m84036_250809_035451_s4.bc2186.paraphase.bam", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-89/out/m84036_250809_035451_s4.bc2186_paraphase/m84036_250809_035451_s4.bc2186.paraphase.json", "trgt_spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-89/out/m84036_250809_035451_s4.bc2186.trgt.sorted.spanning.bam.bai", "trgt_spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-89/out/m84036_250809_035451_s4.bc2186.trgt.sorted.spanning.bam", "trgt_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-89/out/m84036_250809_035451_s4.bc2186.trgt.vcf", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-89/out/m84036_250809_035451_s4.bc2186.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-89/out/m84036_250809_035451_s4.bc2186.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2186"}
2025-09-15 20:27:20.991 wdl.w:ptcp.t:call-tar_outputs-89 NOTICE task setup :: name: "tar_outputs", source: "./common.wdl", line: 279, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-89", thread: 140609838900800
2025-09-15 20:27:21.012 wdl.w:ptcp.t:call-tar_outputs-89 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:27:21.012 wdl.w:ptcp.t:call-tar_outputs-89 INFO input :: name: "sawfish_vcf_tbi", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2186.sv.vcf.gz.tbi"
2025-09-15 20:27:21.012 wdl.w:ptcp.t:call-tar_outputs-89 INFO input :: name: "sawfish_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2186.sv.vcf.gz"
2025-09-15 20:27:21.012 wdl.w:ptcp.t:call-tar_outputs-89 INFO input :: name: "f8_json", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2186.f8inversion.json"
2025-09-15 20:27:21.012 wdl.w:ptcp.t:call-tar_outputs-89 INFO input :: name: "paraphase_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2186.paraphase.bam.bai"
2025-09-15 20:27:21.012 wdl.w:ptcp.t:call-tar_outputs-89 INFO input :: name: "paraphase_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2186.paraphase.bam"
2025-09-15 20:27:21.012 wdl.w:ptcp.t:call-tar_outputs-89 INFO input :: name: "paraphase_json", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2186.paraphase.json"
2025-09-15 20:27:21.012 wdl.w:ptcp.t:call-tar_outputs-89 INFO input :: name: "trgt_spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2186.trgt.sorted.spanning.bam.bai"
2025-09-15 20:27:21.012 wdl.w:ptcp.t:call-tar_outputs-89 INFO input :: name: "trgt_spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2186.trgt.sorted.spanning.bam"
2025-09-15 20:27:21.012 wdl.w:ptcp.t:call-tar_outputs-89 INFO input :: name: "trgt_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2186.trgt.vcf"
2025-09-15 20:27:21.012 wdl.w:ptcp.t:call-tar_outputs-89 INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2186.mapped.bam.bai"
2025-09-15 20:27:21.012 wdl.w:ptcp.t:call-tar_outputs-89 INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2186.mapped.bam"
2025-09-15 20:27:21.012 wdl.w:ptcp.t:call-tar_outputs-89 INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2186"
2025-09-15 20:27:21.012 wdl.w:ptcp.t:call-tar_outputs-89 INFO eval :: name: "threads", value: 1
2025-09-15 20:27:21.013 wdl.w:ptcp.t:call-tar_outputs-89 INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:27:21.013 wdl.w:ptcp.t:call-tar_outputs-89 INFO eval :: name: "disk_size", value: 6
2025-09-15 20:27:21.013 wdl.w:ptcp.t:call-tar_outputs-89 INFO eval :: name: "output_tarball", value: "m84036_250809_035451_s4.bc2186.tar"
2025-09-15 20:27:21.013 wdl.w:ptcp.t:call-tar_outputs-89 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:27:21.013 wdl.w:ptcp.t:call-tar_outputs-89 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:27:21.014 wdl.w:ptcp.t:call-tar_outputs-89 INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:27:21.014 wdl.w:ptcp.t:call-tar_outputs-89 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:27:21.092 wdl.w:ptcp.t:call-tar_outputs-89 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 17, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-89/_singularity_tmpdir_x_90ag8k"
2025-09-15 20:27:21.092 wdl.w:ptcp.t:call-tar_outputs-89 INFO Slurm invocation: srun --job-name call-tar_outputs-89 --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-89/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-89/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-89/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-89/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-89/out/m84036_250809_035451_s4.bc2186_sawfish/m84036_250809_035451_s4.bc2186.sv.vcf.gz.tbi:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2186.sv.vcf.gz.tbi:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-89/out/m84036_250809_035451_s4.bc2186_sawfish/m84036_250809_035451_s4.bc2186.sv.vcf.gz:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2186.sv.vcf.gz:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-89/out/m84036_250809_035451_s4.bc2186.f8inversion.json:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2186.f8inversion.json:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-89/out/m84036_250809_035451_s4.bc2186.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2186.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-89/out/m84036_250809_035451_s4.bc2186.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2186.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-89/out/m84036_250809_035451_s4.bc2186.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2186.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-89/out/m84036_250809_035451_s4.bc2186.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2186.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-89/out/m84036_250809_035451_s4.bc2186.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2186.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-89/out/m84036_250809_035451_s4.bc2186_paraphase/m84036_250809_035451_s4.bc2186.paraphase.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2186.paraphase.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-89/out/m84036_250809_035451_s4.bc2186_paraphase/m84036_250809_035451_s4.bc2186.paraphase.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2186.paraphase.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-89/out/m84036_250809_035451_s4.bc2186_paraphase/m84036_250809_035451_s4.bc2186.paraphase.json:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2186.paraphase.json:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-89/_singularity_tmpdir_x_90ag8k/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-89/_singularity_tmpdir_x_90ag8k/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:27:21.098 wdl.w:ptcp.t:call-tar_outputs-89 NOTICE slurm_singularity run :: pid: 1208299, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-89/slurm_singularity.log.txt"
2025-09-15 20:27:21.457 wdl.w:ptcp.w:call-paraphase-87.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for hbb for sample m84036_250809_035451_s4.bc2184 at 2025-09-15 20:27:11.310773...
2025-09-15 20:27:21.457 wdl.w:ptcp.w:call-paraphase-87.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for hbb for sample m84036_250809_035451_s4.bc2184 at 2025-09-15 20:27:11.657866...
2025-09-15 20:27:21.705 wdl.w:ptcp.w:call-paraphase-43.t:call-call_f8 INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2140.f8inversion.vcf"
2025-09-15 20:27:21.708 wdl.w:ptcp.w:call-paraphase-43.t:call-call_f8 INFO output :: name: "json", value: "m84036_250809_035451_s4.bc2140.f8inversion.json"
2025-09-15 20:27:21.760 wdl.w:ptcp.w:call-paraphase-43.t:call-call_f8 NOTICE done
2025-09-15 20:27:21.766 wdl.w:ptcp.w:call-paraphase-43 NOTICE finish :: job: "call-call_f8"
2025-09-15 20:27:21.766 wdl.w:ptcp.w:call-paraphase-43 INFO output :: job: "call-call_f8", values: {"json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-43/call-call_f8/out/m84036_250809_035451_s4.bc2140.f8inversion.json", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-43/call-call_f8/out/m84036_250809_035451_s4.bc2140.f8inversion.vcf"}
2025-09-15 20:27:21.766 wdl.w:ptcp.w:call-paraphase-43 INFO visit :: node: "output-f8_json", values: {"f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-43/call-call_f8/out/m84036_250809_035451_s4.bc2140.f8inversion.json"}
2025-09-15 20:27:21.766 wdl.w:ptcp.w:call-paraphase-43 INFO visit :: node: "output-f8_vcf", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-43/call-call_f8/out/m84036_250809_035451_s4.bc2140.f8inversion.vcf"}
2025-09-15 20:27:21.766 wdl.w:ptcp.w:call-paraphase-43 INFO visit :: node: "outputs", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-43/call-call_f8/out/m84036_250809_035451_s4.bc2140.f8inversion.vcf", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-43/call-run_paraphase/out/m84036_250809_035451_s4.bc2140_paraphase/m84036_250809_035451_s4.bc2140.paraphase.json", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-43/call-run_paraphase/out/m84036_250809_035451_s4.bc2140_paraphase/m84036_250809_035451_s4.bc2140.paraphase.bam", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-43/call-run_paraphase/out/m84036_250809_035451_s4.bc2140_paraphase/m84036_250809_035451_s4.bc2140.paraphase.bam.bai", "paraphase_vcfs": ["/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-43/call-run_paraphase/out/m84036_250809_035451_s4.bc2140_paraphase/m84036_250809_035451_s4.bc2140_paraphase_vcfs/m84036_250809_035451_s4.bc2140_cyp21.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-43/call-run_paraphase/out/m84036_250809_035451_s4.bc2140_paraphase/m84036_250809_035451_s4.bc2140_paraphase_vcfs/m84036_250809_035451_s4.bc2140_f8inv1.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-43/call-run_paraphase/out/m84036_250809_035451_s4.bc2140_paraphase/m84036_250809_035451_s4.bc2140_paraphase_vcfs/m84036_250809_035451_s4.bc2140_f8inv22.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-43/call-run_paraphase/out/m84036_250809_035451_s4.bc2140_paraphase/m84036_250809_035451_s4.bc2140_paraphase_vcfs/m84036_250809_035451_s4.bc2140_gba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-43/call-run_paraphase/out/m84036_250809_035451_s4.bc2140_paraphase/m84036_250809_035451_s4.bc2140_paraphase_vcfs/m84036_250809_035451_s4.bc2140_hba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-43/call-run_paraphase/out/m84036_250809_035451_s4.bc2140_paraphase/m84036_250809_035451_s4.bc2140_paraphase_vcfs/m84036_250809_035451_s4.bc2140_hbb.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-43/call-run_paraphase/out/m84036_250809_035451_s4.bc2140_paraphase/m84036_250809_035451_s4.bc2140_paraphase_vcfs/m84036_250809_035451_s4.bc2140_rpgr.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-43/call-run_paraphase/out/m84036_250809_035451_s4.bc2140_paraphase/m84036_250809_035451_s4.bc2140_paraphase_vcfs/m84036_250809_035451_s4.bc2140_smn1.vcf"], "havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-43/call-run_paraphase/out/m84036_250809_035451_s4.bc2140.havanno.json", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-43/call-call_f8/out/m84036_250809_035451_s4.bc2140.f8inversion.json"}
2025-09-15 20:27:21.878 wdl.w:ptcp.w:call-paraphase-43 NOTICE done
2025-09-15 20:27:21.883 wdl.w:ptcp NOTICE finish :: job: "call-paraphase-43"
2025-09-15 20:27:21.883 wdl.w:ptcp INFO output :: job: "call-paraphase-43", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-43/out/m84036_250809_035451_s4.bc2140.f8inversion.vcf", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-43/out/m84036_250809_035451_s4.bc2140_paraphase/m84036_250809_035451_s4.bc2140.paraphase.json", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-43/out/m84036_250809_035451_s4.bc2140_paraphase/m84036_250809_035451_s4.bc2140.paraphase.bam", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-43/out/m84036_250809_035451_s4.bc2140_paraphase/m84036_250809_035451_s4.bc2140.paraphase.bam.bai", "paraphase_vcfs": ["/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-43/out/m84036_250809_035451_s4.bc2140_paraphase/m84036_250809_035451_s4.bc2140_paraphase_vcfs/m84036_250809_035451_s4.bc2140_cyp21.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-43/out/m84036_250809_035451_s4.bc2140_paraphase/m84036_250809_035451_s4.bc2140_paraphase_vcfs/m84036_250809_035451_s4.bc2140_f8inv1.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-43/out/m84036_250809_035451_s4.bc2140_paraphase/m84036_250809_035451_s4.bc2140_paraphase_vcfs/m84036_250809_035451_s4.bc2140_f8inv22.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-43/out/m84036_250809_035451_s4.bc2140_paraphase/m84036_250809_035451_s4.bc2140_paraphase_vcfs/m84036_250809_035451_s4.bc2140_gba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-43/out/m84036_250809_035451_s4.bc2140_paraphase/m84036_250809_035451_s4.bc2140_paraphase_vcfs/m84036_250809_035451_s4.bc2140_hba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-43/out/m84036_250809_035451_s4.bc2140_paraphase/m84036_250809_035451_s4.bc2140_paraphase_vcfs/m84036_250809_035451_s4.bc2140_hbb.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-43/out/m84036_250809_035451_s4.bc2140_paraphase/m84036_250809_035451_s4.bc2140_paraphase_vcfs/m84036_250809_035451_s4.bc2140_rpgr.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-43/out/m84036_250809_035451_s4.bc2140_paraphase/m84036_250809_035451_s4.bc2140_paraphase_vcfs/m84036_250809_035451_s4.bc2140_smn1.vcf"], "havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-43/out/m84036_250809_035451_s4.bc2140.havanno.json", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-43/out/m84036_250809_035451_s4.bc2140.f8inversion.json"}
2025-09-15 20:27:21.884 wdl.w:ptcp NOTICE ready :: job: "call-tar_outputs-43", callee: "tar_outputs"
2025-09-15 20:27:21.884 wdl.w:ptcp INFO input :: job: "call-tar_outputs-43", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "sawfish_vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-43/out/m84036_250809_035451_s4.bc2140_sawfish/m84036_250809_035451_s4.bc2140.sv.vcf.gz.tbi", "sawfish_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-43/out/m84036_250809_035451_s4.bc2140_sawfish/m84036_250809_035451_s4.bc2140.sv.vcf.gz", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-43/out/m84036_250809_035451_s4.bc2140.f8inversion.json", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-43/out/m84036_250809_035451_s4.bc2140_paraphase/m84036_250809_035451_s4.bc2140.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-43/out/m84036_250809_035451_s4.bc2140_paraphase/m84036_250809_035451_s4.bc2140.paraphase.bam", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-43/out/m84036_250809_035451_s4.bc2140_paraphase/m84036_250809_035451_s4.bc2140.paraphase.json", "trgt_spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-43/out/m84036_250809_035451_s4.bc2140.trgt.sorted.spanning.bam.bai", "trgt_spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-43/out/m84036_250809_035451_s4.bc2140.trgt.sorted.spanning.bam", "trgt_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-43/out/m84036_250809_035451_s4.bc2140.trgt.vcf", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-43/out/m84036_250809_035451_s4.bc2140.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-43/out/m84036_250809_035451_s4.bc2140.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2140"}
2025-09-15 20:27:21.890 wdl.w:ptcp.t:call-tar_outputs-43 NOTICE task setup :: name: "tar_outputs", source: "./common.wdl", line: 279, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-43", thread: 140606575711808
2025-09-15 20:27:21.910 wdl.w:ptcp.t:call-tar_outputs-43 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:27:21.911 wdl.w:ptcp.t:call-tar_outputs-43 INFO input :: name: "sawfish_vcf_tbi", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2140.sv.vcf.gz.tbi"
2025-09-15 20:27:21.911 wdl.w:ptcp.t:call-tar_outputs-43 INFO input :: name: "sawfish_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2140.sv.vcf.gz"
2025-09-15 20:27:21.911 wdl.w:ptcp.t:call-tar_outputs-43 INFO input :: name: "f8_json", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2140.f8inversion.json"
2025-09-15 20:27:21.911 wdl.w:ptcp.t:call-tar_outputs-43 INFO input :: name: "paraphase_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2140.paraphase.bam.bai"
2025-09-15 20:27:21.911 wdl.w:ptcp.t:call-tar_outputs-43 INFO input :: name: "paraphase_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2140.paraphase.bam"
2025-09-15 20:27:21.911 wdl.w:ptcp.t:call-tar_outputs-43 INFO input :: name: "paraphase_json", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2140.paraphase.json"
2025-09-15 20:27:21.911 wdl.w:ptcp.t:call-tar_outputs-43 INFO input :: name: "trgt_spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2140.trgt.sorted.spanning.bam.bai"
2025-09-15 20:27:21.911 wdl.w:ptcp.t:call-tar_outputs-43 INFO input :: name: "trgt_spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2140.trgt.sorted.spanning.bam"
2025-09-15 20:27:21.911 wdl.w:ptcp.t:call-tar_outputs-43 INFO input :: name: "trgt_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2140.trgt.vcf"
2025-09-15 20:27:21.911 wdl.w:ptcp.t:call-tar_outputs-43 INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2140.mapped.bam.bai"
2025-09-15 20:27:21.911 wdl.w:ptcp.t:call-tar_outputs-43 INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2140.mapped.bam"
2025-09-15 20:27:21.911 wdl.w:ptcp.t:call-tar_outputs-43 INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2140"
2025-09-15 20:27:21.911 wdl.w:ptcp.t:call-tar_outputs-43 INFO eval :: name: "threads", value: 1
2025-09-15 20:27:21.912 wdl.w:ptcp.t:call-tar_outputs-43 INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:27:21.912 wdl.w:ptcp.t:call-tar_outputs-43 INFO eval :: name: "disk_size", value: 6
2025-09-15 20:27:21.912 wdl.w:ptcp.t:call-tar_outputs-43 INFO eval :: name: "output_tarball", value: "m84036_250809_035451_s4.bc2140.tar"
2025-09-15 20:27:21.912 wdl.w:ptcp.t:call-tar_outputs-43 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:27:21.912 wdl.w:ptcp.t:call-tar_outputs-43 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:27:21.913 wdl.w:ptcp.t:call-tar_outputs-43 INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:27:21.913 wdl.w:ptcp.t:call-tar_outputs-43 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:27:21.988 wdl.w:ptcp.t:call-tar_outputs-43 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 17, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-43/_singularity_tmpdir_d43_ks9_"
2025-09-15 20:27:21.988 wdl.w:ptcp.t:call-tar_outputs-43 INFO Slurm invocation: srun --job-name call-tar_outputs-43 --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-43/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-43/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-43/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-43/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-43/out/m84036_250809_035451_s4.bc2140.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2140.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-43/out/m84036_250809_035451_s4.bc2140.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2140.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-43/out/m84036_250809_035451_s4.bc2140.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2140.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-43/out/m84036_250809_035451_s4.bc2140.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2140.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-43/out/m84036_250809_035451_s4.bc2140.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2140.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-43/out/m84036_250809_035451_s4.bc2140_paraphase/m84036_250809_035451_s4.bc2140.paraphase.json:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2140.paraphase.json:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-43/out/m84036_250809_035451_s4.bc2140_paraphase/m84036_250809_035451_s4.bc2140.paraphase.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2140.paraphase.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-43/out/m84036_250809_035451_s4.bc2140_paraphase/m84036_250809_035451_s4.bc2140.paraphase.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2140.paraphase.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-43/out/m84036_250809_035451_s4.bc2140.f8inversion.json:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2140.f8inversion.json:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-43/out/m84036_250809_035451_s4.bc2140_sawfish/m84036_250809_035451_s4.bc2140.sv.vcf.gz.tbi:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2140.sv.vcf.gz.tbi:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-43/out/m84036_250809_035451_s4.bc2140_sawfish/m84036_250809_035451_s4.bc2140.sv.vcf.gz:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2140.sv.vcf.gz:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-43/_singularity_tmpdir_d43_ks9_/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-43/_singularity_tmpdir_d43_ks9_/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:27:21.996 wdl.w:ptcp.t:call-tar_outputs-43 NOTICE slurm_singularity run :: pid: 1208308, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-43/slurm_singularity.log.txt"
2025-09-15 20:27:22.106 wdl.w:ptcp.t:call-tar_outputs-89.slurm_singularity INFO srun: job 51798226 queued and waiting for resources
2025-09-15 20:27:22.106 wdl.w:ptcp.t:call-tar_outputs-89.slurm_singularity INFO srun: job 51798226 has been allocated resources
2025-09-15 20:27:22.107 wdl.w:ptcp.t:call-tar_outputs-89.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:27:22.571 wdl.w:ptcp.t:call-tar_outputs-89 INFO output :: name: "sample_tarball", value: "m84036_250809_035451_s4.bc2186.tar"
2025-09-15 20:27:22.626 wdl.w:ptcp.w:call-paraphase-39.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for f8inv22 for sample m84036_250809_035451_s4.bc2136 at 2025-09-15 20:27:19.248801...
2025-09-15 20:27:22.627 wdl.w:ptcp.w:call-paraphase-39.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for f8inv22 for sample m84036_250809_035451_s4.bc2136 at 2025-09-15 20:27:19.249429...
2025-09-15 20:27:22.653 wdl.w:ptcp.t:call-tar_outputs-89 NOTICE done
2025-09-15 20:27:22.657 wdl.w:ptcp NOTICE finish :: job: "call-tar_outputs-89"
2025-09-15 20:27:22.657 wdl.w:ptcp INFO output :: job: "call-tar_outputs-89", values: {"sample_tarball": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-89/out/m84036_250809_035451_s4.bc2186.tar"}
2025-09-15 20:27:22.756 wdl.w:ptcp.w:call-sawfish-94.t:call-run_sawfish.stderr VERBOSE [M::mm_idx_gen::47.811*1.58] collected minimizers
2025-09-15 20:27:22.761 wdl.w:ptcp.w:call-sawfish-94.t:call-run_sawfish.stderr VERBOSE [M::mm_idx_gen::57.699*1.82] sorted minimizers
2025-09-15 20:27:22.761 wdl.w:ptcp.w:call-sawfish-94.t:call-run_sawfish.stderr VERBOSE [M::main::57.701*1.82] loaded/built the index for 195 target sequence(s)
2025-09-15 20:27:22.761 wdl.w:ptcp.w:call-sawfish-94.t:call-run_sawfish.stderr VERBOSE [M::mm_mapopt_update::62.282*1.76] mid_occ = 136
2025-09-15 20:27:22.761 wdl.w:ptcp.w:call-sawfish-94.t:call-run_sawfish.stderr VERBOSE [M::mm_idx_stat] kmer size: 19; skip: 19; is_hpc: 0; #seq: 195
2025-09-15 20:27:22.761 wdl.w:ptcp.w:call-sawfish-94.t:call-run_sawfish.stderr VERBOSE [M::mm_idx_stat::65.925*1.72] distinct minimizers: 214664461 (92.23% are singletons); average occurrences: 1.372; average spacing: 10.529; total length: 3099922541
2025-09-15 20:27:22.761 wdl.w:ptcp.w:call-sawfish-94.t:call-run_sawfish.stderr VERBOSE [M::bam2fq_mainloop] discarded 0 singletons
2025-09-15 20:27:22.761 wdl.w:ptcp.w:call-sawfish-94.t:call-run_sawfish.stderr VERBOSE [M::bam2fq_mainloop] processed 285 reads
2025-09-15 20:27:22.761 wdl.w:ptcp.w:call-sawfish-94.t:call-run_sawfish.stderr VERBOSE [M::worker_pipeline::66.474*1.72] mapped 285 sequences
2025-09-15 20:27:22.761 wdl.w:ptcp.w:call-sawfish-94.t:call-run_sawfish.stderr VERBOSE [M::main] Version: 2.26-r1175
2025-09-15 20:27:22.761 wdl.w:ptcp.w:call-sawfish-94.t:call-run_sawfish.stderr VERBOSE [M::main] CMD: /opt/pacbio/smrttools/install/smrtlink-release_25.1.0.257715/bundles/smrttools/install/smrttools-release_25.1.0.257715/private/thirdparty/minimap2/minimap2_2.26-pacbio2/binwrap/../../../../../private/thirdparty/minimap2/minimap2_2.26-pacbio2/bin/minimap2 -a -y -x map-hifi -Y -E 1,0 /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa -
2025-09-15 20:27:22.762 wdl.w:ptcp.w:call-sawfish-94.t:call-run_sawfish.stderr VERBOSE [M::main] Real time: 66.769 sec; CPU: 114.517 sec; Peak RSS: 11.887 GB
2025-09-15 20:27:22.762 wdl.w:ptcp.w:call-sawfish-94.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:55][sawfish][INFO] Starting sawfish 2.0.3
2025-09-15 20:27:22.762 wdl.w:ptcp.w:call-sawfish-94.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:55][sawfish][INFO] cmdline: sawfish discover --disable-cnv --threads 16 --ref /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa --bam m84036_250809_035451_s4.bc2191.minimap2.bam --output-dir m84036_250809_035451_s4.bc2191_sawfish_discover
2025-09-15 20:27:22.762 wdl.w:ptcp.w:call-sawfish-94.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:55][sawfish][INFO] Running on 16 threads
2025-09-15 20:27:22.762 wdl.w:ptcp.w:call-sawfish-94.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:55][sawfish][INFO] Writing discover settings to file: 'm84036_250809_035451_s4.bc2191_sawfish_discover/discover.settings.json'
2025-09-15 20:27:22.762 wdl.w:ptcp.w:call-sawfish-94.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:26:55][sawfish][INFO] Reading reference genome from file '/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa'
2025-09-15 20:27:22.762 wdl.w:ptcp.w:call-sawfish-94.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:27:16][sawfish][INFO] Processing alignment file '/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2191.minimap2.bam'
2025-09-15 20:27:22.762 wdl.w:ptcp.w:call-sawfish-94.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:27:16][sawfish][INFO] Finished processing all alignments
2025-09-15 20:27:22.762 wdl.w:ptcp.w:call-sawfish-94.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:27:16][sawfish][INFO] Writing depth bins to binary file: 'm84036_250809_035451_s4.bc2191_sawfish_discover/depth.mpack'
2025-09-15 20:27:22.762 wdl.w:ptcp.w:call-sawfish-94.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:27:16][sawfish][INFO] Writing max sv depth genome regions to bed file: 'm84036_250809_035451_s4.bc2191_sawfish_discover/max.depth.bed'
2025-09-15 20:27:22.762 wdl.w:ptcp.w:call-sawfish-94.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:27:16][sawfish][INFO] Completing breakpoint observation clustering
2025-09-15 20:27:22.762 wdl.w:ptcp.w:call-sawfish-94.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:27:16][sawfish][INFO] Finished breakpoint observation clustering
2025-09-15 20:27:22.762 wdl.w:ptcp.w:call-sawfish-94.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:27:16][sawfish][INFO] Consolidating adjacent indel candidates
2025-09-15 20:27:22.762 wdl.w:ptcp.w:call-sawfish-94.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:27:16][sawfish][INFO] Finding large insertion candidates
2025-09-15 20:27:22.762 wdl.w:ptcp.w:call-sawfish-94.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:27:16][sawfish][INFO] Writing breakpoint_cluster debug bed file: 'm84036_250809_035451_s4.bc2191_sawfish_discover/debug.breakpoint_clusters.bed'
2025-09-15 20:27:22.762 wdl.w:ptcp.w:call-sawfish-94.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:27:16][sawfish][INFO] Refining SV Candidates
2025-09-15 20:27:22.762 wdl.w:ptcp.w:call-sawfish-94.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:27:16][sawfish][INFO] Writing debug assembly region bed file: 'm84036_250809_035451_s4.bc2191_sawfish_discover/assembly.regions.bed'
2025-09-15 20:27:22.762 wdl.w:ptcp.w:call-sawfish-94.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:27:16][sawfish][INFO] Starting refinement of breakpoint evidence clusters
2025-09-15 20:27:22.762 wdl.w:ptcp.w:call-sawfish-94.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:27:17][sawfish][INFO] Finished refining all breakpoint evidence clusters
2025-09-15 20:27:22.762 wdl.w:ptcp.w:call-sawfish-94.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:27:17][sawfish][INFO] Writing all contig alignments to bam file: 'm84036_250809_035451_s4.bc2191_sawfish_discover/contig.alignment.bam'
2025-09-15 20:27:22.763 wdl.w:ptcp.w:call-sawfish-94.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:27:17][sawfish][INFO] Writing candidate structural variants to file: 'm84036_250809_035451_s4.bc2191_sawfish_discover/candidate.sv.bcf'
2025-09-15 20:27:22.763 wdl.w:ptcp.w:call-sawfish-94.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:27:17][sawfish][INFO] Writing run statistics to file: 'm84036_250809_035451_s4.bc2191_sawfish_discover/run.stats.json'
2025-09-15 20:27:22.763 wdl.w:ptcp.w:call-sawfish-94.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:27:17][sawfish][INFO] sawfish completed. Total Runtime: 00:00:21.728
2025-09-15 20:27:22.763 wdl.w:ptcp.w:call-sawfish-94.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:27:17][sawfish][INFO] Starting sawfish 2.0.3
2025-09-15 20:27:22.763 wdl.w:ptcp.w:call-sawfish-94.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:27:17][sawfish][INFO] cmdline: sawfish joint-call --threads 16 --sample m84036_250809_035451_s4.bc2191_sawfish_discover --output-dir m84036_250809_035451_s4.bc2191_sawfish
2025-09-15 20:27:22.763 wdl.w:ptcp.w:call-sawfish-94.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:27:17][sawfish][INFO] Running on 16 threads
2025-09-15 20:27:22.763 wdl.w:ptcp.w:call-sawfish-94.t:call-run_sawfish.stderr VERBOSE [2025-09-15][20:27:17][sawfish][INFO] Reading reference genome from file '/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/hg38.fa'
2025-09-15 20:27:23.004 wdl.w:ptcp.t:call-tar_outputs-43.slurm_singularity INFO srun: job 51798227 queued and waiting for resources
2025-09-15 20:27:23.004 wdl.w:ptcp.t:call-tar_outputs-43.slurm_singularity INFO srun: job 51798227 has been allocated resources
2025-09-15 20:27:23.004 wdl.w:ptcp.t:call-tar_outputs-43.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:27:23.043 wdl.w:ptcp.w:call-paraphase-71.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for hbb for sample m84036_250809_035451_s4.bc2168 at 2025-09-15 20:26:31.176878...
2025-09-15 20:27:23.044 wdl.w:ptcp.w:call-paraphase-71.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for hbb for sample m84036_250809_035451_s4.bc2168 at 2025-09-15 20:26:34.656238...
2025-09-15 20:27:23.044 wdl.w:ptcp.w:call-paraphase-71.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for hbb for sample m84036_250809_035451_s4.bc2168 at 2025-09-15 20:26:34.917532...
2025-09-15 20:27:23.044 wdl.w:ptcp.w:call-paraphase-71.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for f8inv1 for sample m84036_250809_035451_s4.bc2168 at 2025-09-15 20:27:02.508664...
2025-09-15 20:27:23.044 wdl.w:ptcp.w:call-paraphase-71.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for f8inv1 for sample m84036_250809_035451_s4.bc2168 at 2025-09-15 20:27:02.508918...
2025-09-15 20:27:23.356 wdl.w:ptcp.t:call-tar_outputs-43 INFO output :: name: "sample_tarball", value: "m84036_250809_035451_s4.bc2140.tar"
2025-09-15 20:27:23.408 wdl.w:ptcp.t:call-tar_outputs-43 NOTICE done
2025-09-15 20:27:23.412 wdl.w:ptcp NOTICE finish :: job: "call-tar_outputs-43"
2025-09-15 20:27:23.413 wdl.w:ptcp INFO output :: job: "call-tar_outputs-43", values: {"sample_tarball": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-43/out/m84036_250809_035451_s4.bc2140.tar"}
2025-09-15 20:27:24.869 wdl.w:ptcp.w:call-sawfish-90.t:call-run_sawfish INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2187_sawfish/m84036_250809_035451_s4.bc2187.sv.vcf.gz"
2025-09-15 20:27:24.874 wdl.w:ptcp.w:call-sawfish-90.t:call-run_sawfish INFO output :: name: "vcf_tbi", value: "m84036_250809_035451_s4.bc2187_sawfish/m84036_250809_035451_s4.bc2187.sv.vcf.gz.tbi"
2025-09-15 20:27:24.875 wdl.w:ptcp.w:call-sawfish-90.t:call-run_sawfish INFO output :: name: "minimap2_bam", value: "m84036_250809_035451_s4.bc2187.minimap2.bam"
2025-09-15 20:27:24.877 wdl.w:ptcp.w:call-sawfish-90.t:call-run_sawfish INFO output :: name: "minimap2_bam_bai", value: "m84036_250809_035451_s4.bc2187.minimap2.bam.bai"
2025-09-15 20:27:24.998 wdl.w:ptcp.w:call-sawfish-90.t:call-run_sawfish NOTICE done
2025-09-15 20:27:25.003 wdl.w:ptcp.w:call-sawfish-90 NOTICE finish :: job: "call-run_sawfish"
2025-09-15 20:27:25.003 wdl.w:ptcp.w:call-sawfish-90 INFO output :: job: "call-run_sawfish", values: {"minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-90/call-run_sawfish/out/m84036_250809_035451_s4.bc2187.minimap2.bam.bai", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-90/call-run_sawfish/out/m84036_250809_035451_s4.bc2187.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-90/call-run_sawfish/out/m84036_250809_035451_s4.bc2187_sawfish/m84036_250809_035451_s4.bc2187.sv.vcf.gz.tbi", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-90/call-run_sawfish/out/m84036_250809_035451_s4.bc2187_sawfish/m84036_250809_035451_s4.bc2187.sv.vcf.gz"}
2025-09-15 20:27:25.003 wdl.w:ptcp.w:call-sawfish-90 INFO visit :: node: "output-minimap2_bam", values: {"minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-90/call-run_sawfish/out/m84036_250809_035451_s4.bc2187.minimap2.bam"}
2025-09-15 20:27:25.003 wdl.w:ptcp.w:call-sawfish-90 INFO visit :: node: "output-minimap2_bam_bai", values: {"minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-90/call-run_sawfish/out/m84036_250809_035451_s4.bc2187.minimap2.bam.bai"}
2025-09-15 20:27:25.004 wdl.w:ptcp.w:call-sawfish-90 INFO visit :: node: "output-vcf", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-90/call-run_sawfish/out/m84036_250809_035451_s4.bc2187_sawfish/m84036_250809_035451_s4.bc2187.sv.vcf.gz"}
2025-09-15 20:27:25.004 wdl.w:ptcp.w:call-sawfish-90 INFO visit :: node: "output-vcf_tbi", values: {"vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-90/call-run_sawfish/out/m84036_250809_035451_s4.bc2187_sawfish/m84036_250809_035451_s4.bc2187.sv.vcf.gz.tbi"}
2025-09-15 20:27:25.004 wdl.w:ptcp.w:call-sawfish-90 INFO visit :: node: "outputs", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-90/call-run_sawfish/out/m84036_250809_035451_s4.bc2187_sawfish/m84036_250809_035451_s4.bc2187.sv.vcf.gz", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-90/call-run_sawfish/out/m84036_250809_035451_s4.bc2187.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-90/call-run_sawfish/out/m84036_250809_035451_s4.bc2187_sawfish/m84036_250809_035451_s4.bc2187.sv.vcf.gz.tbi", "minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-90/call-run_sawfish/out/m84036_250809_035451_s4.bc2187.minimap2.bam.bai"}
2025-09-15 20:27:25.043 wdl.w:ptcp.w:call-sawfish-90 NOTICE done
2025-09-15 20:27:25.049 wdl.w:ptcp NOTICE finish :: job: "call-sawfish-90"
2025-09-15 20:27:25.049 wdl.w:ptcp INFO output :: job: "call-sawfish-90", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-90/out/m84036_250809_035451_s4.bc2187_sawfish/m84036_250809_035451_s4.bc2187.sv.vcf.gz", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-90/out/m84036_250809_035451_s4.bc2187.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-90/out/m84036_250809_035451_s4.bc2187_sawfish/m84036_250809_035451_s4.bc2187.sv.vcf.gz.tbi", "minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-90/out/m84036_250809_035451_s4.bc2187.minimap2.bam.bai"}
2025-09-15 20:27:25.248 wdl.w:ptcp.w:call-paraphase-42.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for rpgr for sample m84036_250809_035451_s4.bc2139 at 2025-09-15 20:27:22.848456...
2025-09-15 20:27:25.248 wdl.w:ptcp.w:call-paraphase-42.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for rpgr for sample m84036_250809_035451_s4.bc2139 at 2025-09-15 20:27:22.849013...
2025-09-15 20:27:25.827 wdl.w:ptcp.w:call-paraphase-58.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for hbb for sample m84036_250809_035451_s4.bc2155 at 2025-09-15 20:27:13.982499...
2025-09-15 20:27:26.716 wdl.w:ptcp.w:call-paraphase-78.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for f8inv1 for sample m84036_250809_035451_s4.bc2175 at 2025-09-15 20:27:05.023496...
2025-09-15 20:27:26.716 wdl.w:ptcp.w:call-paraphase-78.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for f8inv1 for sample m84036_250809_035451_s4.bc2175 at 2025-09-15 20:27:05.513113...
2025-09-15 20:27:26.716 wdl.w:ptcp.w:call-paraphase-78.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for hbb for sample m84036_250809_035451_s4.bc2175 at 2025-09-15 20:27:10.847054...
2025-09-15 20:27:26.716 wdl.w:ptcp.w:call-paraphase-78.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for hbb for sample m84036_250809_035451_s4.bc2175 at 2025-09-15 20:27:11.197011...
2025-09-15 20:27:26.841 wdl.w:ptcp.w:call-paraphase-59.t:call-run_paraphase INFO output :: name: "paraphase_bam", value: "m84036_250809_035451_s4.bc2156_paraphase/m84036_250809_035451_s4.bc2156.paraphase.bam"
2025-09-15 20:27:26.846 wdl.w:ptcp.w:call-paraphase-59.t:call-run_paraphase INFO output :: name: "paraphase_bam_bai", value: "m84036_250809_035451_s4.bc2156_paraphase/m84036_250809_035451_s4.bc2156.paraphase.bam.bai"
2025-09-15 20:27:26.847 wdl.w:ptcp.w:call-paraphase-59.t:call-run_paraphase INFO output :: name: "paraphase_json", value: "m84036_250809_035451_s4.bc2156_paraphase/m84036_250809_035451_s4.bc2156.paraphase.json"
2025-09-15 20:27:26.852 wdl.w:ptcp.w:call-paraphase-59.t:call-run_paraphase INFO output :: name: "paraphase_vcfs", value: ["/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2156_paraphase/m84036_250809_035451_s4.bc2156_paraphase_vcfs/m84036_250809_035451_s4.bc2156_cyp21.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2156_paraphase/m84036_250809_035451_s4.bc2156_paraphase_vcfs/m84036_250809_035451_s4.bc2156_f8inv1.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2156_paraphase/m84036_250809_035451_s4.bc2156_paraphase_vcfs/m84036_250809_035451_s4.bc2156_f8inv22.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2156_paraphase/m84036_250809_035451_s4.bc2156_paraphase_vcfs/m84036_250809_035451_s4.bc2156_gba.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2156_paraphase/m84036_250809_035451_s4.bc2156_paraphase_vcfs/m84036_250809_035451_s4.bc2156_hba.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2156_paraphase/m84036_250809_035451_s4.bc2156_paraphase_vcfs/m84036_250809_035451_s4.bc2156_hbb.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2156_paraphase/m84036_250809_035451_s4.bc2156_paraphase_vcfs/m84036_250809_035451_s4.bc2156_rpgr.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2156_paraphase/m84036_250809_035451_s4.bc2156_paraphase_vcfs/m84036_250809_035451_s4.bc2156_smn1.vcf"]
2025-09-15 20:27:26.854 wdl.w:ptcp.w:call-paraphase-59.t:call-run_paraphase INFO output :: name: "havanno_json", value: "m84036_250809_035451_s4.bc2156.havanno.json"
2025-09-15 20:27:27.002 wdl.w:ptcp.w:call-paraphase-59.t:call-run_paraphase NOTICE done
2025-09-15 20:27:27.008 wdl.w:ptcp.w:call-paraphase-59 NOTICE finish :: job: "call-run_paraphase"
2025-09-15 20:27:27.008 wdl.w:ptcp.w:call-paraphase-59 INFO output :: job: "call-run_paraphase", values: {"havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-59/call-run_paraphase/out/m84036_250809_035451_s4.bc2156.havanno.json", "paraphase_vcfs": ["/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-59/call-run_paraphase/out/m84036_250809_035451_s4.bc2156_paraphase/m84036_250809_035451_s4.bc2156_paraphase_vcfs/m84036_250809_035451_s4.bc2156_cyp21.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-59/call-run_paraphase/out/m84036_250809_035451_s4.bc2156_paraphase/m84036_250809_035451_s4.bc2156_paraphase_vcfs/m84036_250809_035451_s4.bc2156_f8inv1.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-59/call-run_paraphase/out/m84036_250809_035451_s4.bc2156_paraphase/m84036_250809_035451_s4.bc2156_paraphase_vcfs/m84036_250809_035451_s4.bc2156_f8inv22.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-59/call-run_paraphase/out/m84036_250809_035451_s4.bc2156_paraphase/m84036_250809_035451_s4.bc2156_paraphase_vcfs/m84036_250809_035451_s4.bc2156_gba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-59/call-run_paraphase/out/m84036_250809_035451_s4.bc2156_paraphase/m84036_250809_035451_s4.bc2156_paraphase_vcfs/m84036_250809_035451_s4.bc2156_hba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-59/call-run_paraphase/out/m84036_250809_035451_s4.bc2156_paraphase/m84036_250809_035451_s4.bc2156_paraphase_vcfs/m84036_250809_035451_s4.bc2156_hbb.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-59/call-run_paraphase/out/m84036_250809_035451_s4.bc2156_paraphase/m84036_250809_035451_s4.bc2156_paraphase_vcfs/m84036_250809_035451_s4.bc2156_rpgr.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-59/call-run_paraphase/out/m84036_250809_035451_s4.bc2156_paraphase/m84036_250809_035451_s4.bc2156_paraphase_vcfs/m84036_250809_035451_s4.bc2156_smn1.vcf"], "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-59/call-run_paraphase/out/m84036_250809_035451_s4.bc2156_paraphase/m84036_250809_035451_s4.bc2156.paraphase.json", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-59/call-run_paraphase/out/m84036_250809_035451_s4.bc2156_paraphase/m84036_250809_035451_s4.bc2156.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-59/call-run_paraphase/out/m84036_250809_035451_s4.bc2156_paraphase/m84036_250809_035451_s4.bc2156.paraphase.bam"}
2025-09-15 20:27:27.008 wdl.w:ptcp.w:call-paraphase-59 NOTICE ready :: job: "call-call_f8", callee: "call_f8"
2025-09-15 20:27:27.008 wdl.w:ptcp.w:call-paraphase-59 INFO input :: job: "call-call_f8", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "out_prefix": "m84036_250809_035451_s4.bc2156", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-59/call-run_paraphase/out/m84036_250809_035451_s4.bc2156_paraphase/m84036_250809_035451_s4.bc2156.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-59/call-run_paraphase/out/m84036_250809_035451_s4.bc2156_paraphase/m84036_250809_035451_s4.bc2156.paraphase.bam", "sex": "F"}
2025-09-15 20:27:27.009 wdl.w:ptcp.w:call-paraphase-59 INFO visit :: node: "output-havanno_json", values: {"havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-59/call-run_paraphase/out/m84036_250809_035451_s4.bc2156.havanno.json"}
2025-09-15 20:27:27.009 wdl.w:ptcp.w:call-paraphase-59 INFO visit :: node: "output-paraphase_bam", values: {"paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-59/call-run_paraphase/out/m84036_250809_035451_s4.bc2156_paraphase/m84036_250809_035451_s4.bc2156.paraphase.bam"}
2025-09-15 20:27:27.009 wdl.w:ptcp.w:call-paraphase-59 INFO visit :: node: "output-paraphase_bam_bai", values: {"paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-59/call-run_paraphase/out/m84036_250809_035451_s4.bc2156_paraphase/m84036_250809_035451_s4.bc2156.paraphase.bam.bai"}
2025-09-15 20:27:27.009 wdl.w:ptcp.w:call-paraphase-59 INFO visit :: node: "output-paraphase_json", values: {"paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-59/call-run_paraphase/out/m84036_250809_035451_s4.bc2156_paraphase/m84036_250809_035451_s4.bc2156.paraphase.json"}
2025-09-15 20:27:27.009 wdl.w:ptcp.w:call-paraphase-59 INFO visit :: node: "output-paraphase_vcfs", values: {"paraphase_vcfs": ["/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-59/call-run_paraphase/out/m84036_250809_035451_s4.bc2156_paraphase/m84036_250809_035451_s4.bc2156_paraphase_vcfs/m84036_250809_035451_s4.bc2156_cyp21.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-59/call-run_paraphase/out/m84036_250809_035451_s4.bc2156_paraphase/m84036_250809_035451_s4.bc2156_paraphase_vcfs/m84036_250809_035451_s4.bc2156_f8inv1.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-59/call-run_paraphase/out/m84036_250809_035451_s4.bc2156_paraphase/m84036_250809_035451_s4.bc2156_paraphase_vcfs/m84036_250809_035451_s4.bc2156_f8inv22.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-59/call-run_paraphase/out/m84036_250809_035451_s4.bc2156_paraphase/m84036_250809_035451_s4.bc2156_paraphase_vcfs/m84036_250809_035451_s4.bc2156_gba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-59/call-run_paraphase/out/m84036_250809_035451_s4.bc2156_paraphase/m84036_250809_035451_s4.bc2156_paraphase_vcfs/m84036_250809_035451_s4.bc2156_hba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-59/call-run_paraphase/out/m84036_250809_035451_s4.bc2156_paraphase/m84036_250809_035451_s4.bc2156_paraphase_vcfs/m84036_250809_035451_s4.bc2156_hbb.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-59/call-run_paraphase/out/m84036_250809_035451_s4.bc2156_paraphase/m84036_250809_035451_s4.bc2156_paraphase_vcfs/m84036_250809_035451_s4.bc2156_rpgr.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-59/call-run_paraphase/out/m84036_250809_035451_s4.bc2156_paraphase/m84036_250809_035451_s4.bc2156_paraphase_vcfs/m84036_250809_035451_s4.bc2156_smn1.vcf"]}
2025-09-15 20:27:27.015 wdl.w:ptcp.w:call-paraphase-59.t:call-call_f8 NOTICE task setup :: name: "call_f8", source: "./paraphase.wdl", line: 232, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-59/call-call_f8", thread: 140613043340864
2025-09-15 20:27:27.030 wdl.w:ptcp.w:call-paraphase-59.t:call-call_f8 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:27:27.030 wdl.w:ptcp.w:call-paraphase-59.t:call-call_f8 INFO input :: name: "genome_version", value: "38"
2025-09-15 20:27:27.030 wdl.w:ptcp.w:call-paraphase-59.t:call-call_f8 INFO input :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2156"
2025-09-15 20:27:27.030 wdl.w:ptcp.w:call-paraphase-59.t:call-call_f8 INFO input :: name: "paraphase_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2156.paraphase.bam.bai"
2025-09-15 20:27:27.030 wdl.w:ptcp.w:call-paraphase-59.t:call-call_f8 INFO input :: name: "paraphase_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2156.paraphase.bam"
2025-09-15 20:27:27.030 wdl.w:ptcp.w:call-paraphase-59.t:call-call_f8 INFO input :: name: "sex", value: "F"
2025-09-15 20:27:27.030 wdl.w:ptcp.w:call-paraphase-59.t:call-call_f8 INFO eval :: name: "threads", value: 1
2025-09-15 20:27:27.030 wdl.w:ptcp.w:call-paraphase-59.t:call-call_f8 INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:27:27.030 wdl.w:ptcp.w:call-paraphase-59.t:call-call_f8 INFO eval :: name: "disk_size", value: 11
2025-09-15 20:27:27.030 wdl.w:ptcp.w:call-paraphase-59.t:call-call_f8 INFO eval :: name: "sample_sex", value: "F"
2025-09-15 20:27:27.031 wdl.w:ptcp.w:call-paraphase-59.t:call-call_f8 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:27:27.031 wdl.w:ptcp.w:call-paraphase-59.t:call-call_f8 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:27:27.031 wdl.w:ptcp.w:call-paraphase-59.t:call-call_f8 INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:27:27.031 wdl.w:ptcp.w:call-paraphase-59.t:call-call_f8 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:27:27.068 wdl.w:ptcp.w:call-paraphase-59.t:call-call_f8 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 8, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-59/call-call_f8/_singularity_tmpdir_7tcmf1m_"
2025-09-15 20:27:27.068 wdl.w:ptcp.w:call-paraphase-59.t:call-call_f8 INFO Slurm invocation: srun --job-name call-call_f8 --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-59/call-call_f8/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-59/call-call_f8/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-59/call-call_f8/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-59/call-call_f8/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-59/call-run_paraphase/out/m84036_250809_035451_s4.bc2156_paraphase/m84036_250809_035451_s4.bc2156.paraphase.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2156.paraphase.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-59/call-run_paraphase/out/m84036_250809_035451_s4.bc2156_paraphase/m84036_250809_035451_s4.bc2156.paraphase.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2156.paraphase.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-59/call-call_f8/_singularity_tmpdir_7tcmf1m_/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-59/call-call_f8/_singularity_tmpdir_7tcmf1m_/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:27:27.079 wdl.w:ptcp.w:call-paraphase-59.t:call-call_f8 NOTICE slurm_singularity run :: pid: 1208320, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-59/call-call_f8/slurm_singularity.log.txt"
2025-09-15 20:27:27.334 wdl.w:ptcp.w:call-sawfish-88.t:call-run_sawfish INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2185_sawfish/m84036_250809_035451_s4.bc2185.sv.vcf.gz"
2025-09-15 20:27:27.337 wdl.w:ptcp.w:call-sawfish-88.t:call-run_sawfish INFO output :: name: "vcf_tbi", value: "m84036_250809_035451_s4.bc2185_sawfish/m84036_250809_035451_s4.bc2185.sv.vcf.gz.tbi"
2025-09-15 20:27:27.338 wdl.w:ptcp.w:call-sawfish-88.t:call-run_sawfish INFO output :: name: "minimap2_bam", value: "m84036_250809_035451_s4.bc2185.minimap2.bam"
2025-09-15 20:27:27.339 wdl.w:ptcp.w:call-sawfish-88.t:call-run_sawfish INFO output :: name: "minimap2_bam_bai", value: "m84036_250809_035451_s4.bc2185.minimap2.bam.bai"
2025-09-15 20:27:27.444 wdl.w:ptcp.w:call-sawfish-88.t:call-run_sawfish NOTICE done
2025-09-15 20:27:27.449 wdl.w:ptcp.w:call-sawfish-88 NOTICE finish :: job: "call-run_sawfish"
2025-09-15 20:27:27.449 wdl.w:ptcp.w:call-sawfish-88 INFO output :: job: "call-run_sawfish", values: {"minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-88/call-run_sawfish/out/m84036_250809_035451_s4.bc2185.minimap2.bam.bai", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-88/call-run_sawfish/out/m84036_250809_035451_s4.bc2185.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-88/call-run_sawfish/out/m84036_250809_035451_s4.bc2185_sawfish/m84036_250809_035451_s4.bc2185.sv.vcf.gz.tbi", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-88/call-run_sawfish/out/m84036_250809_035451_s4.bc2185_sawfish/m84036_250809_035451_s4.bc2185.sv.vcf.gz"}
2025-09-15 20:27:27.450 wdl.w:ptcp.w:call-sawfish-88 INFO visit :: node: "output-minimap2_bam", values: {"minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-88/call-run_sawfish/out/m84036_250809_035451_s4.bc2185.minimap2.bam"}
2025-09-15 20:27:27.450 wdl.w:ptcp.w:call-sawfish-88 INFO visit :: node: "output-minimap2_bam_bai", values: {"minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-88/call-run_sawfish/out/m84036_250809_035451_s4.bc2185.minimap2.bam.bai"}
2025-09-15 20:27:27.450 wdl.w:ptcp.w:call-sawfish-88 INFO visit :: node: "output-vcf", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-88/call-run_sawfish/out/m84036_250809_035451_s4.bc2185_sawfish/m84036_250809_035451_s4.bc2185.sv.vcf.gz"}
2025-09-15 20:27:27.450 wdl.w:ptcp.w:call-sawfish-88 INFO visit :: node: "output-vcf_tbi", values: {"vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-88/call-run_sawfish/out/m84036_250809_035451_s4.bc2185_sawfish/m84036_250809_035451_s4.bc2185.sv.vcf.gz.tbi"}
2025-09-15 20:27:27.450 wdl.w:ptcp.w:call-sawfish-88 INFO visit :: node: "outputs", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-88/call-run_sawfish/out/m84036_250809_035451_s4.bc2185_sawfish/m84036_250809_035451_s4.bc2185.sv.vcf.gz", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-88/call-run_sawfish/out/m84036_250809_035451_s4.bc2185.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-88/call-run_sawfish/out/m84036_250809_035451_s4.bc2185_sawfish/m84036_250809_035451_s4.bc2185.sv.vcf.gz.tbi", "minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-88/call-run_sawfish/out/m84036_250809_035451_s4.bc2185.minimap2.bam.bai"}
2025-09-15 20:27:27.486 wdl.w:ptcp.w:call-sawfish-88 NOTICE done
2025-09-15 20:27:27.492 wdl.w:ptcp NOTICE finish :: job: "call-sawfish-88"
2025-09-15 20:27:27.492 wdl.w:ptcp INFO output :: job: "call-sawfish-88", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-88/out/m84036_250809_035451_s4.bc2185_sawfish/m84036_250809_035451_s4.bc2185.sv.vcf.gz", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-88/out/m84036_250809_035451_s4.bc2185.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-88/out/m84036_250809_035451_s4.bc2185_sawfish/m84036_250809_035451_s4.bc2185.sv.vcf.gz.tbi", "minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-88/out/m84036_250809_035451_s4.bc2185.minimap2.bam.bai"}
2025-09-15 20:27:27.493 wdl.w:ptcp NOTICE ready :: job: "call-tar_outputs-88", callee: "tar_outputs"
2025-09-15 20:27:27.493 wdl.w:ptcp INFO input :: job: "call-tar_outputs-88", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "sawfish_vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-88/out/m84036_250809_035451_s4.bc2185_sawfish/m84036_250809_035451_s4.bc2185.sv.vcf.gz.tbi", "sawfish_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-88/out/m84036_250809_035451_s4.bc2185_sawfish/m84036_250809_035451_s4.bc2185.sv.vcf.gz", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-88/out/m84036_250809_035451_s4.bc2185.f8inversion.json", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-88/out/m84036_250809_035451_s4.bc2185_paraphase/m84036_250809_035451_s4.bc2185.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-88/out/m84036_250809_035451_s4.bc2185_paraphase/m84036_250809_035451_s4.bc2185.paraphase.bam", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-88/out/m84036_250809_035451_s4.bc2185_paraphase/m84036_250809_035451_s4.bc2185.paraphase.json", "trgt_spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-88/out/m84036_250809_035451_s4.bc2185.trgt.sorted.spanning.bam.bai", "trgt_spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-88/out/m84036_250809_035451_s4.bc2185.trgt.sorted.spanning.bam", "trgt_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-88/out/m84036_250809_035451_s4.bc2185.trgt.vcf", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-88/out/m84036_250809_035451_s4.bc2185.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-88/out/m84036_250809_035451_s4.bc2185.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2185"}
2025-09-15 20:27:27.499 wdl.w:ptcp.t:call-tar_outputs-88 NOTICE task setup :: name: "tar_outputs", source: "./common.wdl", line: 279, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-88", thread: 140611969599040
2025-09-15 20:27:27.518 wdl.w:ptcp.t:call-tar_outputs-88 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:27:27.518 wdl.w:ptcp.t:call-tar_outputs-88 INFO input :: name: "sawfish_vcf_tbi", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2185.sv.vcf.gz.tbi"
2025-09-15 20:27:27.518 wdl.w:ptcp.t:call-tar_outputs-88 INFO input :: name: "sawfish_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2185.sv.vcf.gz"
2025-09-15 20:27:27.518 wdl.w:ptcp.t:call-tar_outputs-88 INFO input :: name: "f8_json", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2185.f8inversion.json"
2025-09-15 20:27:27.518 wdl.w:ptcp.t:call-tar_outputs-88 INFO input :: name: "paraphase_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2185.paraphase.bam.bai"
2025-09-15 20:27:27.518 wdl.w:ptcp.t:call-tar_outputs-88 INFO input :: name: "paraphase_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2185.paraphase.bam"
2025-09-15 20:27:27.518 wdl.w:ptcp.t:call-tar_outputs-88 INFO input :: name: "paraphase_json", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2185.paraphase.json"
2025-09-15 20:27:27.519 wdl.w:ptcp.t:call-tar_outputs-88 INFO input :: name: "trgt_spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2185.trgt.sorted.spanning.bam.bai"
2025-09-15 20:27:27.519 wdl.w:ptcp.t:call-tar_outputs-88 INFO input :: name: "trgt_spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2185.trgt.sorted.spanning.bam"
2025-09-15 20:27:27.519 wdl.w:ptcp.t:call-tar_outputs-88 INFO input :: name: "trgt_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2185.trgt.vcf"
2025-09-15 20:27:27.519 wdl.w:ptcp.t:call-tar_outputs-88 INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2185.mapped.bam.bai"
2025-09-15 20:27:27.519 wdl.w:ptcp.t:call-tar_outputs-88 INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2185.mapped.bam"
2025-09-15 20:27:27.519 wdl.w:ptcp.t:call-tar_outputs-88 INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2185"
2025-09-15 20:27:27.519 wdl.w:ptcp.t:call-tar_outputs-88 INFO eval :: name: "threads", value: 1
2025-09-15 20:27:27.519 wdl.w:ptcp.t:call-tar_outputs-88 INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:27:27.519 wdl.w:ptcp.t:call-tar_outputs-88 INFO eval :: name: "disk_size", value: 6
2025-09-15 20:27:27.519 wdl.w:ptcp.t:call-tar_outputs-88 INFO eval :: name: "output_tarball", value: "m84036_250809_035451_s4.bc2185.tar"
2025-09-15 20:27:27.520 wdl.w:ptcp.t:call-tar_outputs-88 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:27:27.520 wdl.w:ptcp.t:call-tar_outputs-88 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:27:27.520 wdl.w:ptcp.t:call-tar_outputs-88 INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:27:27.520 wdl.w:ptcp.t:call-tar_outputs-88 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:27:27.606 wdl.w:ptcp.t:call-tar_outputs-88 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 17, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-88/_singularity_tmpdir_tvnroh9w"
2025-09-15 20:27:27.606 wdl.w:ptcp.t:call-tar_outputs-88 INFO Slurm invocation: srun --job-name call-tar_outputs-88 --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-88/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-88/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-88/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-88/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-88/out/m84036_250809_035451_s4.bc2185.f8inversion.json:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2185.f8inversion.json:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-88/out/m84036_250809_035451_s4.bc2185_sawfish/m84036_250809_035451_s4.bc2185.sv.vcf.gz.tbi:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2185.sv.vcf.gz.tbi:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-88/out/m84036_250809_035451_s4.bc2185_sawfish/m84036_250809_035451_s4.bc2185.sv.vcf.gz:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2185.sv.vcf.gz:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-88/out/m84036_250809_035451_s4.bc2185_paraphase/m84036_250809_035451_s4.bc2185.paraphase.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2185.paraphase.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-88/out/m84036_250809_035451_s4.bc2185_paraphase/m84036_250809_035451_s4.bc2185.paraphase.json:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2185.paraphase.json:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-88/out/m84036_250809_035451_s4.bc2185_paraphase/m84036_250809_035451_s4.bc2185.paraphase.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2185.paraphase.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-88/out/m84036_250809_035451_s4.bc2185.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2185.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-88/out/m84036_250809_035451_s4.bc2185.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2185.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-88/out/m84036_250809_035451_s4.bc2185.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2185.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-88/out/m84036_250809_035451_s4.bc2185.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2185.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-88/out/m84036_250809_035451_s4.bc2185.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2185.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-88/_singularity_tmpdir_tvnroh9w/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-88/_singularity_tmpdir_tvnroh9w/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:27:27.612 wdl.w:ptcp.t:call-tar_outputs-88 NOTICE slurm_singularity run :: pid: 1208329, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-88/slurm_singularity.log.txt"
2025-09-15 20:27:28.087 wdl.w:ptcp.w:call-paraphase-59.t:call-call_f8.slurm_singularity INFO srun: job 51798228 queued and waiting for resources
2025-09-15 20:27:28.087 wdl.w:ptcp.w:call-paraphase-59.t:call-call_f8.slurm_singularity INFO srun: job 51798228 has been allocated resources
2025-09-15 20:27:28.087 wdl.w:ptcp.w:call-paraphase-59.t:call-call_f8.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:27:28.277 wdl.w:ptcp.w:call-paraphase-42.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for rpgr for sample m84036_250809_035451_s4.bc2139 at 2025-09-15 20:27:25.421901...
2025-09-15 20:27:28.277 wdl.w:ptcp.w:call-paraphase-42.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for rpgr for sample m84036_250809_035451_s4.bc2139 at 2025-09-15 20:27:26.753588...
2025-09-15 20:27:28.277 wdl.w:ptcp.w:call-paraphase-42.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for rpgr for sample m84036_250809_035451_s4.bc2139 at 2025-09-15 20:27:26.939185...
2025-09-15 20:27:28.568 wdl.w:ptcp.w:call-paraphase-90.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for f8inv1 for sample m84036_250809_035451_s4.bc2187 at 2025-09-15 20:27:18.294316...
2025-09-15 20:27:28.568 wdl.w:ptcp.w:call-paraphase-90.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for f8inv1 for sample m84036_250809_035451_s4.bc2187 at 2025-09-15 20:27:18.723998...
2025-09-15 20:27:28.568 wdl.w:ptcp.w:call-paraphase-90.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for hbb for sample m84036_250809_035451_s4.bc2187 at 2025-09-15 20:27:21.639675...
2025-09-15 20:27:28.568 wdl.w:ptcp.w:call-paraphase-90.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for hbb for sample m84036_250809_035451_s4.bc2187 at 2025-09-15 20:27:22.131671...
2025-09-15 20:27:28.614 wdl.w:ptcp.t:call-tar_outputs-88.stderr VERBOSE tar: Removing leading `/' from member names
2025-09-15 20:27:28.614 wdl.w:ptcp.t:call-tar_outputs-88.stderr VERBOSE tar: Removing leading `/' from hard link targets
2025-09-15 20:27:28.625 wdl.w:ptcp.t:call-tar_outputs-88.slurm_singularity INFO srun: job 51798229 queued and waiting for resources
2025-09-15 20:27:28.625 wdl.w:ptcp.t:call-tar_outputs-88.slurm_singularity INFO srun: job 51798229 has been allocated resources
2025-09-15 20:27:28.625 wdl.w:ptcp.t:call-tar_outputs-88.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:27:28.698 wdl.w:ptcp.t:call-tar_outputs-88 INFO output :: name: "sample_tarball", value: "m84036_250809_035451_s4.bc2185.tar"
2025-09-15 20:27:28.703 wdl.w:ptcp.w:call-paraphase-59.t:call-call_f8 INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2156.f8inversion.vcf"
2025-09-15 20:27:28.708 wdl.w:ptcp.w:call-paraphase-59.t:call-call_f8 INFO output :: name: "json", value: "m84036_250809_035451_s4.bc2156.f8inversion.json"
2025-09-15 20:27:28.792 wdl.w:ptcp.t:call-tar_outputs-88 NOTICE done
2025-09-15 20:27:28.796 wdl.w:ptcp NOTICE finish :: job: "call-tar_outputs-88"
2025-09-15 20:27:28.796 wdl.w:ptcp INFO output :: job: "call-tar_outputs-88", values: {"sample_tarball": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-88/out/m84036_250809_035451_s4.bc2185.tar"}
2025-09-15 20:27:28.802 wdl.w:ptcp.w:call-paraphase-59.t:call-call_f8 NOTICE done
2025-09-15 20:27:28.832 wdl.w:ptcp.w:call-paraphase-59 NOTICE finish :: job: "call-call_f8"
2025-09-15 20:27:28.832 wdl.w:ptcp.w:call-paraphase-59 INFO output :: job: "call-call_f8", values: {"json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-59/call-call_f8/out/m84036_250809_035451_s4.bc2156.f8inversion.json", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-59/call-call_f8/out/m84036_250809_035451_s4.bc2156.f8inversion.vcf"}
2025-09-15 20:27:28.833 wdl.w:ptcp.w:call-paraphase-59 INFO visit :: node: "output-f8_json", values: {"f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-59/call-call_f8/out/m84036_250809_035451_s4.bc2156.f8inversion.json"}
2025-09-15 20:27:28.833 wdl.w:ptcp.w:call-paraphase-59 INFO visit :: node: "output-f8_vcf", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-59/call-call_f8/out/m84036_250809_035451_s4.bc2156.f8inversion.vcf"}
2025-09-15 20:27:28.833 wdl.w:ptcp.w:call-paraphase-59 INFO visit :: node: "outputs", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-59/call-call_f8/out/m84036_250809_035451_s4.bc2156.f8inversion.vcf", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-59/call-run_paraphase/out/m84036_250809_035451_s4.bc2156_paraphase/m84036_250809_035451_s4.bc2156.paraphase.json", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-59/call-run_paraphase/out/m84036_250809_035451_s4.bc2156_paraphase/m84036_250809_035451_s4.bc2156.paraphase.bam", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-59/call-run_paraphase/out/m84036_250809_035451_s4.bc2156_paraphase/m84036_250809_035451_s4.bc2156.paraphase.bam.bai", "paraphase_vcfs": ["/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-59/call-run_paraphase/out/m84036_250809_035451_s4.bc2156_paraphase/m84036_250809_035451_s4.bc2156_paraphase_vcfs/m84036_250809_035451_s4.bc2156_cyp21.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-59/call-run_paraphase/out/m84036_250809_035451_s4.bc2156_paraphase/m84036_250809_035451_s4.bc2156_paraphase_vcfs/m84036_250809_035451_s4.bc2156_f8inv1.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-59/call-run_paraphase/out/m84036_250809_035451_s4.bc2156_paraphase/m84036_250809_035451_s4.bc2156_paraphase_vcfs/m84036_250809_035451_s4.bc2156_f8inv22.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-59/call-run_paraphase/out/m84036_250809_035451_s4.bc2156_paraphase/m84036_250809_035451_s4.bc2156_paraphase_vcfs/m84036_250809_035451_s4.bc2156_gba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-59/call-run_paraphase/out/m84036_250809_035451_s4.bc2156_paraphase/m84036_250809_035451_s4.bc2156_paraphase_vcfs/m84036_250809_035451_s4.bc2156_hba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-59/call-run_paraphase/out/m84036_250809_035451_s4.bc2156_paraphase/m84036_250809_035451_s4.bc2156_paraphase_vcfs/m84036_250809_035451_s4.bc2156_hbb.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-59/call-run_paraphase/out/m84036_250809_035451_s4.bc2156_paraphase/m84036_250809_035451_s4.bc2156_paraphase_vcfs/m84036_250809_035451_s4.bc2156_rpgr.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-59/call-run_paraphase/out/m84036_250809_035451_s4.bc2156_paraphase/m84036_250809_035451_s4.bc2156_paraphase_vcfs/m84036_250809_035451_s4.bc2156_smn1.vcf"], "havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-59/call-run_paraphase/out/m84036_250809_035451_s4.bc2156.havanno.json", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-59/call-call_f8/out/m84036_250809_035451_s4.bc2156.f8inversion.json"}
2025-09-15 20:27:28.860 wdl.w:ptcp.w:call-paraphase-58.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for hbb for sample m84036_250809_035451_s4.bc2155 at 2025-09-15 20:27:21.868503...
2025-09-15 20:27:28.860 wdl.w:ptcp.w:call-paraphase-58.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for hbb for sample m84036_250809_035451_s4.bc2155 at 2025-09-15 20:27:22.339062...
2025-09-15 20:27:28.963 wdl.w:ptcp.w:call-paraphase-59 NOTICE done
2025-09-15 20:27:28.981 wdl.w:ptcp NOTICE finish :: job: "call-paraphase-59"
2025-09-15 20:27:28.981 wdl.w:ptcp INFO output :: job: "call-paraphase-59", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-59/out/m84036_250809_035451_s4.bc2156.f8inversion.vcf", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-59/out/m84036_250809_035451_s4.bc2156_paraphase/m84036_250809_035451_s4.bc2156.paraphase.json", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-59/out/m84036_250809_035451_s4.bc2156_paraphase/m84036_250809_035451_s4.bc2156.paraphase.bam", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-59/out/m84036_250809_035451_s4.bc2156_paraphase/m84036_250809_035451_s4.bc2156.paraphase.bam.bai", "paraphase_vcfs": ["/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-59/out/m84036_250809_035451_s4.bc2156_paraphase/m84036_250809_035451_s4.bc2156_paraphase_vcfs/m84036_250809_035451_s4.bc2156_cyp21.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-59/out/m84036_250809_035451_s4.bc2156_paraphase/m84036_250809_035451_s4.bc2156_paraphase_vcfs/m84036_250809_035451_s4.bc2156_f8inv1.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-59/out/m84036_250809_035451_s4.bc2156_paraphase/m84036_250809_035451_s4.bc2156_paraphase_vcfs/m84036_250809_035451_s4.bc2156_f8inv22.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-59/out/m84036_250809_035451_s4.bc2156_paraphase/m84036_250809_035451_s4.bc2156_paraphase_vcfs/m84036_250809_035451_s4.bc2156_gba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-59/out/m84036_250809_035451_s4.bc2156_paraphase/m84036_250809_035451_s4.bc2156_paraphase_vcfs/m84036_250809_035451_s4.bc2156_hba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-59/out/m84036_250809_035451_s4.bc2156_paraphase/m84036_250809_035451_s4.bc2156_paraphase_vcfs/m84036_250809_035451_s4.bc2156_hbb.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-59/out/m84036_250809_035451_s4.bc2156_paraphase/m84036_250809_035451_s4.bc2156_paraphase_vcfs/m84036_250809_035451_s4.bc2156_rpgr.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-59/out/m84036_250809_035451_s4.bc2156_paraphase/m84036_250809_035451_s4.bc2156_paraphase_vcfs/m84036_250809_035451_s4.bc2156_smn1.vcf"], "havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-59/out/m84036_250809_035451_s4.bc2156.havanno.json", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-59/out/m84036_250809_035451_s4.bc2156.f8inversion.json"}
2025-09-15 20:27:28.982 wdl.w:ptcp NOTICE ready :: job: "call-tar_outputs-59", callee: "tar_outputs"
2025-09-15 20:27:28.982 wdl.w:ptcp INFO input :: job: "call-tar_outputs-59", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "sawfish_vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-59/out/m84036_250809_035451_s4.bc2156_sawfish/m84036_250809_035451_s4.bc2156.sv.vcf.gz.tbi", "sawfish_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-59/out/m84036_250809_035451_s4.bc2156_sawfish/m84036_250809_035451_s4.bc2156.sv.vcf.gz", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-59/out/m84036_250809_035451_s4.bc2156.f8inversion.json", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-59/out/m84036_250809_035451_s4.bc2156_paraphase/m84036_250809_035451_s4.bc2156.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-59/out/m84036_250809_035451_s4.bc2156_paraphase/m84036_250809_035451_s4.bc2156.paraphase.bam", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-59/out/m84036_250809_035451_s4.bc2156_paraphase/m84036_250809_035451_s4.bc2156.paraphase.json", "trgt_spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-59/out/m84036_250809_035451_s4.bc2156.trgt.sorted.spanning.bam.bai", "trgt_spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-59/out/m84036_250809_035451_s4.bc2156.trgt.sorted.spanning.bam", "trgt_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-59/out/m84036_250809_035451_s4.bc2156.trgt.vcf", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-59/out/m84036_250809_035451_s4.bc2156.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-59/out/m84036_250809_035451_s4.bc2156.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2156"}
2025-09-15 20:27:28.988 wdl.w:ptcp.t:call-tar_outputs-59 NOTICE task setup :: name: "tar_outputs", source: "./common.wdl", line: 279, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-59", thread: 140610887464512
2025-09-15 20:27:29.009 wdl.w:ptcp.t:call-tar_outputs-59 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:27:29.009 wdl.w:ptcp.t:call-tar_outputs-59 INFO input :: name: "sawfish_vcf_tbi", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2156.sv.vcf.gz.tbi"
2025-09-15 20:27:29.009 wdl.w:ptcp.t:call-tar_outputs-59 INFO input :: name: "sawfish_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2156.sv.vcf.gz"
2025-09-15 20:27:29.009 wdl.w:ptcp.t:call-tar_outputs-59 INFO input :: name: "f8_json", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2156.f8inversion.json"
2025-09-15 20:27:29.009 wdl.w:ptcp.t:call-tar_outputs-59 INFO input :: name: "paraphase_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2156.paraphase.bam.bai"
2025-09-15 20:27:29.010 wdl.w:ptcp.t:call-tar_outputs-59 INFO input :: name: "paraphase_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2156.paraphase.bam"
2025-09-15 20:27:29.010 wdl.w:ptcp.t:call-tar_outputs-59 INFO input :: name: "paraphase_json", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2156.paraphase.json"
2025-09-15 20:27:29.010 wdl.w:ptcp.t:call-tar_outputs-59 INFO input :: name: "trgt_spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2156.trgt.sorted.spanning.bam.bai"
2025-09-15 20:27:29.010 wdl.w:ptcp.t:call-tar_outputs-59 INFO input :: name: "trgt_spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2156.trgt.sorted.spanning.bam"
2025-09-15 20:27:29.010 wdl.w:ptcp.t:call-tar_outputs-59 INFO input :: name: "trgt_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2156.trgt.vcf"
2025-09-15 20:27:29.010 wdl.w:ptcp.t:call-tar_outputs-59 INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2156.mapped.bam.bai"
2025-09-15 20:27:29.010 wdl.w:ptcp.t:call-tar_outputs-59 INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2156.mapped.bam"
2025-09-15 20:27:29.010 wdl.w:ptcp.t:call-tar_outputs-59 INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2156"
2025-09-15 20:27:29.010 wdl.w:ptcp.t:call-tar_outputs-59 INFO eval :: name: "threads", value: 1
2025-09-15 20:27:29.010 wdl.w:ptcp.t:call-tar_outputs-59 INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:27:29.010 wdl.w:ptcp.t:call-tar_outputs-59 INFO eval :: name: "disk_size", value: 6
2025-09-15 20:27:29.010 wdl.w:ptcp.t:call-tar_outputs-59 INFO eval :: name: "output_tarball", value: "m84036_250809_035451_s4.bc2156.tar"
2025-09-15 20:27:29.011 wdl.w:ptcp.t:call-tar_outputs-59 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:27:29.011 wdl.w:ptcp.t:call-tar_outputs-59 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:27:29.011 wdl.w:ptcp.t:call-tar_outputs-59 INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:27:29.011 wdl.w:ptcp.t:call-tar_outputs-59 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:27:29.087 wdl.w:ptcp.t:call-tar_outputs-59 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 17, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-59/_singularity_tmpdir__v1lr7w5"
2025-09-15 20:27:29.087 wdl.w:ptcp.t:call-tar_outputs-59 INFO Slurm invocation: srun --job-name call-tar_outputs-59 --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-59/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-59/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-59/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-59/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-59/out/m84036_250809_035451_s4.bc2156.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2156.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-59/out/m84036_250809_035451_s4.bc2156.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2156.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-59/out/m84036_250809_035451_s4.bc2156_sawfish/m84036_250809_035451_s4.bc2156.sv.vcf.gz.tbi:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2156.sv.vcf.gz.tbi:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-59/out/m84036_250809_035451_s4.bc2156_sawfish/m84036_250809_035451_s4.bc2156.sv.vcf.gz:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2156.sv.vcf.gz:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-59/out/m84036_250809_035451_s4.bc2156_paraphase/m84036_250809_035451_s4.bc2156.paraphase.json:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2156.paraphase.json:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-59/out/m84036_250809_035451_s4.bc2156_paraphase/m84036_250809_035451_s4.bc2156.paraphase.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2156.paraphase.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-59/out/m84036_250809_035451_s4.bc2156_paraphase/m84036_250809_035451_s4.bc2156.paraphase.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2156.paraphase.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-59/out/m84036_250809_035451_s4.bc2156.f8inversion.json:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2156.f8inversion.json:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-59/out/m84036_250809_035451_s4.bc2156.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2156.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-59/out/m84036_250809_035451_s4.bc2156.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2156.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-59/out/m84036_250809_035451_s4.bc2156.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2156.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-59/_singularity_tmpdir__v1lr7w5/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-59/_singularity_tmpdir__v1lr7w5/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:27:29.096 wdl.w:ptcp.t:call-tar_outputs-59 NOTICE slurm_singularity run :: pid: 1208339, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-59/slurm_singularity.log.txt"
2025-09-15 20:27:30.105 wdl.w:ptcp.t:call-tar_outputs-59.slurm_singularity INFO srun: job 51798230 queued and waiting for resources
2025-09-15 20:27:30.105 wdl.w:ptcp.t:call-tar_outputs-59.slurm_singularity INFO srun: job 51798230 has been allocated resources
2025-09-15 20:27:30.134 wdl.w:ptcp.w:call-paraphase-62.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for rpgr for sample m84036_250809_035451_s4.bc2159 at 2025-09-15 20:27:18.858977...
2025-09-15 20:27:30.134 wdl.w:ptcp.w:call-paraphase-62.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for rpgr for sample m84036_250809_035451_s4.bc2159 at 2025-09-15 20:27:18.859137...
2025-09-15 20:27:30.395 wdl.w:ptcp.w:call-sawfish-94.t:call-run_sawfish INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2191_sawfish/m84036_250809_035451_s4.bc2191.sv.vcf.gz"
2025-09-15 20:27:30.399 wdl.w:ptcp.w:call-sawfish-94.t:call-run_sawfish INFO output :: name: "vcf_tbi", value: "m84036_250809_035451_s4.bc2191_sawfish/m84036_250809_035451_s4.bc2191.sv.vcf.gz.tbi"
2025-09-15 20:27:30.400 wdl.w:ptcp.w:call-sawfish-94.t:call-run_sawfish INFO output :: name: "minimap2_bam", value: "m84036_250809_035451_s4.bc2191.minimap2.bam"
2025-09-15 20:27:30.401 wdl.w:ptcp.w:call-sawfish-94.t:call-run_sawfish INFO output :: name: "minimap2_bam_bai", value: "m84036_250809_035451_s4.bc2191.minimap2.bam.bai"
2025-09-15 20:27:30.513 wdl.w:ptcp.w:call-sawfish-94.t:call-run_sawfish NOTICE done
2025-09-15 20:27:30.518 wdl.w:ptcp.w:call-sawfish-94 NOTICE finish :: job: "call-run_sawfish"
2025-09-15 20:27:30.518 wdl.w:ptcp.w:call-sawfish-94 INFO output :: job: "call-run_sawfish", values: {"minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-94/call-run_sawfish/out/m84036_250809_035451_s4.bc2191.minimap2.bam.bai", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-94/call-run_sawfish/out/m84036_250809_035451_s4.bc2191.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-94/call-run_sawfish/out/m84036_250809_035451_s4.bc2191_sawfish/m84036_250809_035451_s4.bc2191.sv.vcf.gz.tbi", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-94/call-run_sawfish/out/m84036_250809_035451_s4.bc2191_sawfish/m84036_250809_035451_s4.bc2191.sv.vcf.gz"}
2025-09-15 20:27:30.518 wdl.w:ptcp.w:call-sawfish-94 INFO visit :: node: "output-minimap2_bam", values: {"minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-94/call-run_sawfish/out/m84036_250809_035451_s4.bc2191.minimap2.bam"}
2025-09-15 20:27:30.518 wdl.w:ptcp.w:call-sawfish-94 INFO visit :: node: "output-minimap2_bam_bai", values: {"minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-94/call-run_sawfish/out/m84036_250809_035451_s4.bc2191.minimap2.bam.bai"}
2025-09-15 20:27:30.518 wdl.w:ptcp.w:call-sawfish-94 INFO visit :: node: "output-vcf", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-94/call-run_sawfish/out/m84036_250809_035451_s4.bc2191_sawfish/m84036_250809_035451_s4.bc2191.sv.vcf.gz"}
2025-09-15 20:27:30.519 wdl.w:ptcp.w:call-sawfish-94 INFO visit :: node: "output-vcf_tbi", values: {"vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-94/call-run_sawfish/out/m84036_250809_035451_s4.bc2191_sawfish/m84036_250809_035451_s4.bc2191.sv.vcf.gz.tbi"}
2025-09-15 20:27:30.519 wdl.w:ptcp.w:call-sawfish-94 INFO visit :: node: "outputs", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-94/call-run_sawfish/out/m84036_250809_035451_s4.bc2191_sawfish/m84036_250809_035451_s4.bc2191.sv.vcf.gz", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-94/call-run_sawfish/out/m84036_250809_035451_s4.bc2191.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-94/call-run_sawfish/out/m84036_250809_035451_s4.bc2191_sawfish/m84036_250809_035451_s4.bc2191.sv.vcf.gz.tbi", "minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-94/call-run_sawfish/out/m84036_250809_035451_s4.bc2191.minimap2.bam.bai"}
2025-09-15 20:27:30.560 wdl.w:ptcp.w:call-sawfish-94 NOTICE done
2025-09-15 20:27:30.566 wdl.w:ptcp NOTICE finish :: job: "call-sawfish-94"
2025-09-15 20:27:30.566 wdl.w:ptcp INFO output :: job: "call-sawfish-94", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-94/out/m84036_250809_035451_s4.bc2191_sawfish/m84036_250809_035451_s4.bc2191.sv.vcf.gz", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-94/out/m84036_250809_035451_s4.bc2191.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-94/out/m84036_250809_035451_s4.bc2191_sawfish/m84036_250809_035451_s4.bc2191.sv.vcf.gz.tbi", "minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-94/out/m84036_250809_035451_s4.bc2191.minimap2.bam.bai"}
2025-09-15 20:27:30.879 wdl.w:ptcp.t:call-tar_outputs-59.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:27:30.909 wdl.w:ptcp.t:call-tar_outputs-59 INFO output :: name: "sample_tarball", value: "m84036_250809_035451_s4.bc2156.tar"
2025-09-15 20:27:30.964 wdl.w:ptcp.t:call-tar_outputs-59 NOTICE done
2025-09-15 20:27:30.967 wdl.w:ptcp NOTICE finish :: job: "call-tar_outputs-59"
2025-09-15 20:27:30.967 wdl.w:ptcp INFO output :: job: "call-tar_outputs-59", values: {"sample_tarball": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-59/out/m84036_250809_035451_s4.bc2156.tar"}
2025-09-15 20:27:31.145 wdl.w:ptcp.w:call-paraphase-63.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for f8inv1 for sample m84036_250809_035451_s4.bc2160 at 2025-09-15 20:27:24.579935...
2025-09-15 20:27:31.145 wdl.w:ptcp.w:call-paraphase-63.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for f8inv1 for sample m84036_250809_035451_s4.bc2160 at 2025-09-15 20:27:24.581075...
2025-09-15 20:27:31.754 wdl.w:ptcp.w:call-paraphase-91.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for hbb for sample m84036_250809_035451_s4.bc2188 at 2025-09-15 20:27:05.606598...
2025-09-15 20:27:31.754 wdl.w:ptcp.w:call-paraphase-91.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for cyp21 for sample m84036_250809_035451_s4.bc2188 at 2025-09-15 20:27:07.077645...
2025-09-15 20:27:31.754 wdl.w:ptcp.w:call-paraphase-91.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for cyp21 for sample m84036_250809_035451_s4.bc2188 at 2025-09-15 20:27:08.364789...
2025-09-15 20:27:31.754 wdl.w:ptcp.w:call-paraphase-91.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for hbb for sample m84036_250809_035451_s4.bc2188 at 2025-09-15 20:27:12.130377...
2025-09-15 20:27:31.754 wdl.w:ptcp.w:call-paraphase-91.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for hbb for sample m84036_250809_035451_s4.bc2188 at 2025-09-15 20:27:12.491560...
2025-09-15 20:27:31.754 wdl.w:ptcp.w:call-paraphase-91.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for gba for sample m84036_250809_035451_s4.bc2188 at 2025-09-15 20:27:16.620074...
2025-09-15 20:27:31.754 wdl.w:ptcp.w:call-paraphase-91.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for gba for sample m84036_250809_035451_s4.bc2188 at 2025-09-15 20:27:17.471992...
2025-09-15 20:27:32.601 wdl.w:ptcp.w:call-sawfish-83.t:call-run_sawfish INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2180_sawfish/m84036_250809_035451_s4.bc2180.sv.vcf.gz"
2025-09-15 20:27:32.607 wdl.w:ptcp.w:call-sawfish-83.t:call-run_sawfish INFO output :: name: "vcf_tbi", value: "m84036_250809_035451_s4.bc2180_sawfish/m84036_250809_035451_s4.bc2180.sv.vcf.gz.tbi"
2025-09-15 20:27:32.608 wdl.w:ptcp.w:call-sawfish-83.t:call-run_sawfish INFO output :: name: "minimap2_bam", value: "m84036_250809_035451_s4.bc2180.minimap2.bam"
2025-09-15 20:27:32.609 wdl.w:ptcp.w:call-sawfish-83.t:call-run_sawfish INFO output :: name: "minimap2_bam_bai", value: "m84036_250809_035451_s4.bc2180.minimap2.bam.bai"
2025-09-15 20:27:32.619 wdl.w:ptcp.w:call-sawfish-86.t:call-run_sawfish INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2183_sawfish/m84036_250809_035451_s4.bc2183.sv.vcf.gz"
2025-09-15 20:27:32.623 wdl.w:ptcp.w:call-sawfish-86.t:call-run_sawfish INFO output :: name: "vcf_tbi", value: "m84036_250809_035451_s4.bc2183_sawfish/m84036_250809_035451_s4.bc2183.sv.vcf.gz.tbi"
2025-09-15 20:27:32.624 wdl.w:ptcp.w:call-sawfish-86.t:call-run_sawfish INFO output :: name: "minimap2_bam", value: "m84036_250809_035451_s4.bc2183.minimap2.bam"
2025-09-15 20:27:32.626 wdl.w:ptcp.w:call-sawfish-86.t:call-run_sawfish INFO output :: name: "minimap2_bam_bai", value: "m84036_250809_035451_s4.bc2183.minimap2.bam.bai"
2025-09-15 20:27:32.728 wdl.w:ptcp.w:call-sawfish-83.t:call-run_sawfish NOTICE done
2025-09-15 20:27:32.734 wdl.w:ptcp.w:call-sawfish-83 NOTICE finish :: job: "call-run_sawfish"
2025-09-15 20:27:32.735 wdl.w:ptcp.w:call-sawfish-83 INFO output :: job: "call-run_sawfish", values: {"minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-83/call-run_sawfish/out/m84036_250809_035451_s4.bc2180.minimap2.bam.bai", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-83/call-run_sawfish/out/m84036_250809_035451_s4.bc2180.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-83/call-run_sawfish/out/m84036_250809_035451_s4.bc2180_sawfish/m84036_250809_035451_s4.bc2180.sv.vcf.gz.tbi", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-83/call-run_sawfish/out/m84036_250809_035451_s4.bc2180_sawfish/m84036_250809_035451_s4.bc2180.sv.vcf.gz"}
2025-09-15 20:27:32.735 wdl.w:ptcp.w:call-sawfish-83 INFO visit :: node: "output-minimap2_bam", values: {"minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-83/call-run_sawfish/out/m84036_250809_035451_s4.bc2180.minimap2.bam"}
2025-09-15 20:27:32.735 wdl.w:ptcp.w:call-sawfish-83 INFO visit :: node: "output-minimap2_bam_bai", values: {"minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-83/call-run_sawfish/out/m84036_250809_035451_s4.bc2180.minimap2.bam.bai"}
2025-09-15 20:27:32.735 wdl.w:ptcp.w:call-sawfish-83 INFO visit :: node: "output-vcf", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-83/call-run_sawfish/out/m84036_250809_035451_s4.bc2180_sawfish/m84036_250809_035451_s4.bc2180.sv.vcf.gz"}
2025-09-15 20:27:32.735 wdl.w:ptcp.w:call-sawfish-83 INFO visit :: node: "output-vcf_tbi", values: {"vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-83/call-run_sawfish/out/m84036_250809_035451_s4.bc2180_sawfish/m84036_250809_035451_s4.bc2180.sv.vcf.gz.tbi"}
2025-09-15 20:27:32.736 wdl.w:ptcp.w:call-sawfish-83 INFO visit :: node: "outputs", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-83/call-run_sawfish/out/m84036_250809_035451_s4.bc2180_sawfish/m84036_250809_035451_s4.bc2180.sv.vcf.gz", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-83/call-run_sawfish/out/m84036_250809_035451_s4.bc2180.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-83/call-run_sawfish/out/m84036_250809_035451_s4.bc2180_sawfish/m84036_250809_035451_s4.bc2180.sv.vcf.gz.tbi", "minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-83/call-run_sawfish/out/m84036_250809_035451_s4.bc2180.minimap2.bam.bai"}
2025-09-15 20:27:32.760 wdl.w:ptcp.w:call-sawfish-86.t:call-run_sawfish NOTICE done
2025-09-15 20:27:32.766 wdl.w:ptcp.w:call-sawfish-86 NOTICE finish :: job: "call-run_sawfish"
2025-09-15 20:27:32.766 wdl.w:ptcp.w:call-sawfish-86 INFO output :: job: "call-run_sawfish", values: {"minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-86/call-run_sawfish/out/m84036_250809_035451_s4.bc2183.minimap2.bam.bai", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-86/call-run_sawfish/out/m84036_250809_035451_s4.bc2183.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-86/call-run_sawfish/out/m84036_250809_035451_s4.bc2183_sawfish/m84036_250809_035451_s4.bc2183.sv.vcf.gz.tbi", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-86/call-run_sawfish/out/m84036_250809_035451_s4.bc2183_sawfish/m84036_250809_035451_s4.bc2183.sv.vcf.gz"}
2025-09-15 20:27:32.766 wdl.w:ptcp.w:call-sawfish-86 INFO visit :: node: "output-minimap2_bam", values: {"minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-86/call-run_sawfish/out/m84036_250809_035451_s4.bc2183.minimap2.bam"}
2025-09-15 20:27:32.767 wdl.w:ptcp.w:call-sawfish-86 INFO visit :: node: "output-minimap2_bam_bai", values: {"minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-86/call-run_sawfish/out/m84036_250809_035451_s4.bc2183.minimap2.bam.bai"}
2025-09-15 20:27:32.767 wdl.w:ptcp.w:call-sawfish-86 INFO visit :: node: "output-vcf", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-86/call-run_sawfish/out/m84036_250809_035451_s4.bc2183_sawfish/m84036_250809_035451_s4.bc2183.sv.vcf.gz"}
2025-09-15 20:27:32.767 wdl.w:ptcp.w:call-sawfish-86 INFO visit :: node: "output-vcf_tbi", values: {"vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-86/call-run_sawfish/out/m84036_250809_035451_s4.bc2183_sawfish/m84036_250809_035451_s4.bc2183.sv.vcf.gz.tbi"}
2025-09-15 20:27:32.767 wdl.w:ptcp.w:call-sawfish-86 INFO visit :: node: "outputs", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-86/call-run_sawfish/out/m84036_250809_035451_s4.bc2183_sawfish/m84036_250809_035451_s4.bc2183.sv.vcf.gz", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-86/call-run_sawfish/out/m84036_250809_035451_s4.bc2183.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-86/call-run_sawfish/out/m84036_250809_035451_s4.bc2183_sawfish/m84036_250809_035451_s4.bc2183.sv.vcf.gz.tbi", "minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-86/call-run_sawfish/out/m84036_250809_035451_s4.bc2183.minimap2.bam.bai"}
2025-09-15 20:27:32.784 wdl.w:ptcp.w:call-sawfish-83 NOTICE done
2025-09-15 20:27:32.792 wdl.w:ptcp NOTICE finish :: job: "call-sawfish-83"
2025-09-15 20:27:32.792 wdl.w:ptcp INFO output :: job: "call-sawfish-83", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-83/out/m84036_250809_035451_s4.bc2180_sawfish/m84036_250809_035451_s4.bc2180.sv.vcf.gz", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-83/out/m84036_250809_035451_s4.bc2180.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-83/out/m84036_250809_035451_s4.bc2180_sawfish/m84036_250809_035451_s4.bc2180.sv.vcf.gz.tbi", "minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-83/out/m84036_250809_035451_s4.bc2180.minimap2.bam.bai"}
2025-09-15 20:27:32.813 wdl.w:ptcp.w:call-sawfish-86 NOTICE done
2025-09-15 20:27:32.819 wdl.w:ptcp NOTICE finish :: job: "call-sawfish-86"
2025-09-15 20:27:32.819 wdl.w:ptcp INFO output :: job: "call-sawfish-86", values: {"vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-86/out/m84036_250809_035451_s4.bc2183_sawfish/m84036_250809_035451_s4.bc2183.sv.vcf.gz", "minimap2_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-86/out/m84036_250809_035451_s4.bc2183.minimap2.bam", "vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-86/out/m84036_250809_035451_s4.bc2183_sawfish/m84036_250809_035451_s4.bc2183.sv.vcf.gz.tbi", "minimap2_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-86/out/m84036_250809_035451_s4.bc2183.minimap2.bam.bai"}
2025-09-15 20:27:32.820 wdl.w:ptcp INFO visit :: node: "gather-call-sawfish", values: "(((large)))"
2025-09-15 20:27:32.821 wdl.w:ptcp INFO visit :: node: "output-sawfish_minimap2_bam", values: "(((large)))"
2025-09-15 20:27:32.821 wdl.w:ptcp INFO visit :: node: "output-sawfish_minimap2_bam_bai", values: "(((large)))"
2025-09-15 20:27:32.821 wdl.w:ptcp INFO visit :: node: "output-sawfish_vcf", values: "(((large)))"
2025-09-15 20:27:32.822 wdl.w:ptcp INFO visit :: node: "output-sawfish_vcf_tbi", values: "(((large)))"
2025-09-15 20:27:34.390 wdl.w:ptcp.w:call-paraphase-82.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for f8inv1 for sample m84036_250809_035451_s4.bc2179 at 2025-09-15 20:27:23.378940...
2025-09-15 20:27:34.390 wdl.w:ptcp.w:call-paraphase-82.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for f8inv1 for sample m84036_250809_035451_s4.bc2179 at 2025-09-15 20:27:23.380253...
2025-09-15 20:27:34.764 wdl.w:ptcp.w:call-paraphase-94.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for gba for sample m84036_250809_035451_s4.bc2191 at 2025-09-15 20:27:11.722986...
2025-09-15 20:27:34.765 wdl.w:ptcp.w:call-paraphase-94.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for gba for sample m84036_250809_035451_s4.bc2191 at 2025-09-15 20:27:12.343329...
2025-09-15 20:27:34.765 wdl.w:ptcp.w:call-paraphase-94.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for cyp21 for sample m84036_250809_035451_s4.bc2191 at 2025-09-15 20:27:12.689612...
2025-09-15 20:27:34.765 wdl.w:ptcp.w:call-paraphase-94.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for cyp21 for sample m84036_250809_035451_s4.bc2191 at 2025-09-15 20:27:13.940395...
2025-09-15 20:27:34.765 wdl.w:ptcp.w:call-paraphase-94.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for f8inv1 for sample m84036_250809_035451_s4.bc2191 at 2025-09-15 20:27:23.366571...
2025-09-15 20:27:34.765 wdl.w:ptcp.w:call-paraphase-94.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for f8inv1 for sample m84036_250809_035451_s4.bc2191 at 2025-09-15 20:27:23.367321...
2025-09-15 20:27:35.829 wdl.w:ptcp.w:call-paraphase-39.t:call-run_paraphase INFO output :: name: "paraphase_bam", value: "m84036_250809_035451_s4.bc2136_paraphase/m84036_250809_035451_s4.bc2136.paraphase.bam"
2025-09-15 20:27:35.832 wdl.w:ptcp.w:call-paraphase-39.t:call-run_paraphase INFO output :: name: "paraphase_bam_bai", value: "m84036_250809_035451_s4.bc2136_paraphase/m84036_250809_035451_s4.bc2136.paraphase.bam.bai"
2025-09-15 20:27:35.833 wdl.w:ptcp.w:call-paraphase-39.t:call-run_paraphase INFO output :: name: "paraphase_json", value: "m84036_250809_035451_s4.bc2136_paraphase/m84036_250809_035451_s4.bc2136.paraphase.json"
2025-09-15 20:27:35.836 wdl.w:ptcp.w:call-paraphase-39.t:call-run_paraphase INFO output :: name: "paraphase_vcfs", value: ["/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2136_paraphase/m84036_250809_035451_s4.bc2136_paraphase_vcfs/m84036_250809_035451_s4.bc2136_cyp21.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2136_paraphase/m84036_250809_035451_s4.bc2136_paraphase_vcfs/m84036_250809_035451_s4.bc2136_f8inv1.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2136_paraphase/m84036_250809_035451_s4.bc2136_paraphase_vcfs/m84036_250809_035451_s4.bc2136_f8inv22.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2136_paraphase/m84036_250809_035451_s4.bc2136_paraphase_vcfs/m84036_250809_035451_s4.bc2136_gba.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2136_paraphase/m84036_250809_035451_s4.bc2136_paraphase_vcfs/m84036_250809_035451_s4.bc2136_hba.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2136_paraphase/m84036_250809_035451_s4.bc2136_paraphase_vcfs/m84036_250809_035451_s4.bc2136_hbb.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2136_paraphase/m84036_250809_035451_s4.bc2136_paraphase_vcfs/m84036_250809_035451_s4.bc2136_rpgr.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2136_paraphase/m84036_250809_035451_s4.bc2136_paraphase_vcfs/m84036_250809_035451_s4.bc2136_smn1.vcf"]
2025-09-15 20:27:35.839 wdl.w:ptcp.w:call-paraphase-39.t:call-run_paraphase INFO output :: name: "havanno_json", value: "m84036_250809_035451_s4.bc2136.havanno.json"
2025-09-15 20:27:36.008 wdl.w:ptcp.w:call-paraphase-39.t:call-run_paraphase NOTICE done
2025-09-15 20:27:36.014 wdl.w:ptcp.w:call-paraphase-39 NOTICE finish :: job: "call-run_paraphase"
2025-09-15 20:27:36.014 wdl.w:ptcp.w:call-paraphase-39 INFO output :: job: "call-run_paraphase", values: {"havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-39/call-run_paraphase/out/m84036_250809_035451_s4.bc2136.havanno.json", "paraphase_vcfs": ["/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-39/call-run_paraphase/out/m84036_250809_035451_s4.bc2136_paraphase/m84036_250809_035451_s4.bc2136_paraphase_vcfs/m84036_250809_035451_s4.bc2136_cyp21.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-39/call-run_paraphase/out/m84036_250809_035451_s4.bc2136_paraphase/m84036_250809_035451_s4.bc2136_paraphase_vcfs/m84036_250809_035451_s4.bc2136_f8inv1.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-39/call-run_paraphase/out/m84036_250809_035451_s4.bc2136_paraphase/m84036_250809_035451_s4.bc2136_paraphase_vcfs/m84036_250809_035451_s4.bc2136_f8inv22.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-39/call-run_paraphase/out/m84036_250809_035451_s4.bc2136_paraphase/m84036_250809_035451_s4.bc2136_paraphase_vcfs/m84036_250809_035451_s4.bc2136_gba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-39/call-run_paraphase/out/m84036_250809_035451_s4.bc2136_paraphase/m84036_250809_035451_s4.bc2136_paraphase_vcfs/m84036_250809_035451_s4.bc2136_hba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-39/call-run_paraphase/out/m84036_250809_035451_s4.bc2136_paraphase/m84036_250809_035451_s4.bc2136_paraphase_vcfs/m84036_250809_035451_s4.bc2136_hbb.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-39/call-run_paraphase/out/m84036_250809_035451_s4.bc2136_paraphase/m84036_250809_035451_s4.bc2136_paraphase_vcfs/m84036_250809_035451_s4.bc2136_rpgr.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-39/call-run_paraphase/out/m84036_250809_035451_s4.bc2136_paraphase/m84036_250809_035451_s4.bc2136_paraphase_vcfs/m84036_250809_035451_s4.bc2136_smn1.vcf"], "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-39/call-run_paraphase/out/m84036_250809_035451_s4.bc2136_paraphase/m84036_250809_035451_s4.bc2136.paraphase.json", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-39/call-run_paraphase/out/m84036_250809_035451_s4.bc2136_paraphase/m84036_250809_035451_s4.bc2136.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-39/call-run_paraphase/out/m84036_250809_035451_s4.bc2136_paraphase/m84036_250809_035451_s4.bc2136.paraphase.bam"}
2025-09-15 20:27:36.015 wdl.w:ptcp.w:call-paraphase-39 NOTICE ready :: job: "call-call_f8", callee: "call_f8"
2025-09-15 20:27:36.015 wdl.w:ptcp.w:call-paraphase-39 INFO input :: job: "call-call_f8", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "out_prefix": "m84036_250809_035451_s4.bc2136", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-39/call-run_paraphase/out/m84036_250809_035451_s4.bc2136_paraphase/m84036_250809_035451_s4.bc2136.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-39/call-run_paraphase/out/m84036_250809_035451_s4.bc2136_paraphase/m84036_250809_035451_s4.bc2136.paraphase.bam", "sex": "F"}
2025-09-15 20:27:36.016 wdl.w:ptcp.w:call-paraphase-39 INFO visit :: node: "output-havanno_json", values: {"havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-39/call-run_paraphase/out/m84036_250809_035451_s4.bc2136.havanno.json"}
2025-09-15 20:27:36.016 wdl.w:ptcp.w:call-paraphase-39 INFO visit :: node: "output-paraphase_bam", values: {"paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-39/call-run_paraphase/out/m84036_250809_035451_s4.bc2136_paraphase/m84036_250809_035451_s4.bc2136.paraphase.bam"}
2025-09-15 20:27:36.016 wdl.w:ptcp.w:call-paraphase-39 INFO visit :: node: "output-paraphase_bam_bai", values: {"paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-39/call-run_paraphase/out/m84036_250809_035451_s4.bc2136_paraphase/m84036_250809_035451_s4.bc2136.paraphase.bam.bai"}
2025-09-15 20:27:36.016 wdl.w:ptcp.w:call-paraphase-39 INFO visit :: node: "output-paraphase_json", values: {"paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-39/call-run_paraphase/out/m84036_250809_035451_s4.bc2136_paraphase/m84036_250809_035451_s4.bc2136.paraphase.json"}
2025-09-15 20:27:36.016 wdl.w:ptcp.w:call-paraphase-39 INFO visit :: node: "output-paraphase_vcfs", values: {"paraphase_vcfs": ["/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-39/call-run_paraphase/out/m84036_250809_035451_s4.bc2136_paraphase/m84036_250809_035451_s4.bc2136_paraphase_vcfs/m84036_250809_035451_s4.bc2136_cyp21.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-39/call-run_paraphase/out/m84036_250809_035451_s4.bc2136_paraphase/m84036_250809_035451_s4.bc2136_paraphase_vcfs/m84036_250809_035451_s4.bc2136_f8inv1.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-39/call-run_paraphase/out/m84036_250809_035451_s4.bc2136_paraphase/m84036_250809_035451_s4.bc2136_paraphase_vcfs/m84036_250809_035451_s4.bc2136_f8inv22.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-39/call-run_paraphase/out/m84036_250809_035451_s4.bc2136_paraphase/m84036_250809_035451_s4.bc2136_paraphase_vcfs/m84036_250809_035451_s4.bc2136_gba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-39/call-run_paraphase/out/m84036_250809_035451_s4.bc2136_paraphase/m84036_250809_035451_s4.bc2136_paraphase_vcfs/m84036_250809_035451_s4.bc2136_hba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-39/call-run_paraphase/out/m84036_250809_035451_s4.bc2136_paraphase/m84036_250809_035451_s4.bc2136_paraphase_vcfs/m84036_250809_035451_s4.bc2136_hbb.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-39/call-run_paraphase/out/m84036_250809_035451_s4.bc2136_paraphase/m84036_250809_035451_s4.bc2136_paraphase_vcfs/m84036_250809_035451_s4.bc2136_rpgr.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-39/call-run_paraphase/out/m84036_250809_035451_s4.bc2136_paraphase/m84036_250809_035451_s4.bc2136_paraphase_vcfs/m84036_250809_035451_s4.bc2136_smn1.vcf"]}
2025-09-15 20:27:36.022 wdl.w:ptcp.w:call-paraphase-39.t:call-call_f8 NOTICE task setup :: name: "call_f8", source: "./paraphase.wdl", line: 232, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-39/call-call_f8", thread: 140610350593600
2025-09-15 20:27:36.037 wdl.w:ptcp.w:call-paraphase-39.t:call-call_f8 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:27:36.037 wdl.w:ptcp.w:call-paraphase-39.t:call-call_f8 INFO input :: name: "genome_version", value: "38"
2025-09-15 20:27:36.037 wdl.w:ptcp.w:call-paraphase-39.t:call-call_f8 INFO input :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2136"
2025-09-15 20:27:36.037 wdl.w:ptcp.w:call-paraphase-39.t:call-call_f8 INFO input :: name: "paraphase_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2136.paraphase.bam.bai"
2025-09-15 20:27:36.037 wdl.w:ptcp.w:call-paraphase-39.t:call-call_f8 INFO input :: name: "paraphase_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2136.paraphase.bam"
2025-09-15 20:27:36.037 wdl.w:ptcp.w:call-paraphase-39.t:call-call_f8 INFO input :: name: "sex", value: "F"
2025-09-15 20:27:36.038 wdl.w:ptcp.w:call-paraphase-39.t:call-call_f8 INFO eval :: name: "threads", value: 1
2025-09-15 20:27:36.038 wdl.w:ptcp.w:call-paraphase-39.t:call-call_f8 INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:27:36.038 wdl.w:ptcp.w:call-paraphase-39.t:call-call_f8 INFO eval :: name: "disk_size", value: 11
2025-09-15 20:27:36.038 wdl.w:ptcp.w:call-paraphase-39.t:call-call_f8 INFO eval :: name: "sample_sex", value: "F"
2025-09-15 20:27:36.038 wdl.w:ptcp.w:call-paraphase-39.t:call-call_f8 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:27:36.039 wdl.w:ptcp.w:call-paraphase-39.t:call-call_f8 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:27:36.039 wdl.w:ptcp.w:call-paraphase-39.t:call-call_f8 INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:27:36.039 wdl.w:ptcp.w:call-paraphase-39.t:call-call_f8 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:27:36.079 wdl.w:ptcp.w:call-paraphase-39.t:call-call_f8 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 8, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-39/call-call_f8/_singularity_tmpdir_up25104d"
2025-09-15 20:27:36.079 wdl.w:ptcp.w:call-paraphase-39.t:call-call_f8 INFO Slurm invocation: srun --job-name call-call_f8 --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-39/call-call_f8/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-39/call-call_f8/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-39/call-call_f8/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-39/call-call_f8/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-39/call-run_paraphase/out/m84036_250809_035451_s4.bc2136_paraphase/m84036_250809_035451_s4.bc2136.paraphase.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2136.paraphase.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-39/call-run_paraphase/out/m84036_250809_035451_s4.bc2136_paraphase/m84036_250809_035451_s4.bc2136.paraphase.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2136.paraphase.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-39/call-call_f8/_singularity_tmpdir_up25104d/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-39/call-call_f8/_singularity_tmpdir_up25104d/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:27:36.085 wdl.w:ptcp.w:call-paraphase-39.t:call-call_f8 NOTICE slurm_singularity run :: pid: 1208420, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-39/call-call_f8/slurm_singularity.log.txt"
2025-09-15 20:27:37.095 wdl.w:ptcp.w:call-paraphase-39.t:call-call_f8.slurm_singularity INFO srun: job 51798231 queued and waiting for resources
2025-09-15 20:27:37.095 wdl.w:ptcp.w:call-paraphase-39.t:call-call_f8.slurm_singularity INFO srun: job 51798231 has been allocated resources
2025-09-15 20:27:37.095 wdl.w:ptcp.w:call-paraphase-39.t:call-call_f8.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:27:37.514 wdl.w:ptcp.w:call-paraphase-74.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for f8inv22 for sample m84036_250809_035451_s4.bc2171 at 2025-09-15 20:27:34.297032...
2025-09-15 20:27:37.514 wdl.w:ptcp.w:call-paraphase-74.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for f8inv22 for sample m84036_250809_035451_s4.bc2171 at 2025-09-15 20:27:34.297188...
2025-09-15 20:27:37.706 wdl.w:ptcp.w:call-paraphase-39.t:call-call_f8 INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2136.f8inversion.vcf"
2025-09-15 20:27:37.709 wdl.w:ptcp.w:call-paraphase-39.t:call-call_f8 INFO output :: name: "json", value: "m84036_250809_035451_s4.bc2136.f8inversion.json"
2025-09-15 20:27:37.769 wdl.w:ptcp.w:call-paraphase-39.t:call-call_f8 NOTICE done
2025-09-15 20:27:37.774 wdl.w:ptcp.w:call-paraphase-39 NOTICE finish :: job: "call-call_f8"
2025-09-15 20:27:37.774 wdl.w:ptcp.w:call-paraphase-39 INFO output :: job: "call-call_f8", values: {"json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-39/call-call_f8/out/m84036_250809_035451_s4.bc2136.f8inversion.json", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-39/call-call_f8/out/m84036_250809_035451_s4.bc2136.f8inversion.vcf"}
2025-09-15 20:27:37.774 wdl.w:ptcp.w:call-paraphase-39 INFO visit :: node: "output-f8_json", values: {"f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-39/call-call_f8/out/m84036_250809_035451_s4.bc2136.f8inversion.json"}
2025-09-15 20:27:37.774 wdl.w:ptcp.w:call-paraphase-39 INFO visit :: node: "output-f8_vcf", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-39/call-call_f8/out/m84036_250809_035451_s4.bc2136.f8inversion.vcf"}
2025-09-15 20:27:37.775 wdl.w:ptcp.w:call-paraphase-39 INFO visit :: node: "outputs", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-39/call-call_f8/out/m84036_250809_035451_s4.bc2136.f8inversion.vcf", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-39/call-run_paraphase/out/m84036_250809_035451_s4.bc2136_paraphase/m84036_250809_035451_s4.bc2136.paraphase.json", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-39/call-run_paraphase/out/m84036_250809_035451_s4.bc2136_paraphase/m84036_250809_035451_s4.bc2136.paraphase.bam", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-39/call-run_paraphase/out/m84036_250809_035451_s4.bc2136_paraphase/m84036_250809_035451_s4.bc2136.paraphase.bam.bai", "paraphase_vcfs": ["/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-39/call-run_paraphase/out/m84036_250809_035451_s4.bc2136_paraphase/m84036_250809_035451_s4.bc2136_paraphase_vcfs/m84036_250809_035451_s4.bc2136_cyp21.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-39/call-run_paraphase/out/m84036_250809_035451_s4.bc2136_paraphase/m84036_250809_035451_s4.bc2136_paraphase_vcfs/m84036_250809_035451_s4.bc2136_f8inv1.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-39/call-run_paraphase/out/m84036_250809_035451_s4.bc2136_paraphase/m84036_250809_035451_s4.bc2136_paraphase_vcfs/m84036_250809_035451_s4.bc2136_f8inv22.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-39/call-run_paraphase/out/m84036_250809_035451_s4.bc2136_paraphase/m84036_250809_035451_s4.bc2136_paraphase_vcfs/m84036_250809_035451_s4.bc2136_gba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-39/call-run_paraphase/out/m84036_250809_035451_s4.bc2136_paraphase/m84036_250809_035451_s4.bc2136_paraphase_vcfs/m84036_250809_035451_s4.bc2136_hba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-39/call-run_paraphase/out/m84036_250809_035451_s4.bc2136_paraphase/m84036_250809_035451_s4.bc2136_paraphase_vcfs/m84036_250809_035451_s4.bc2136_hbb.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-39/call-run_paraphase/out/m84036_250809_035451_s4.bc2136_paraphase/m84036_250809_035451_s4.bc2136_paraphase_vcfs/m84036_250809_035451_s4.bc2136_rpgr.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-39/call-run_paraphase/out/m84036_250809_035451_s4.bc2136_paraphase/m84036_250809_035451_s4.bc2136_paraphase_vcfs/m84036_250809_035451_s4.bc2136_smn1.vcf"], "havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-39/call-run_paraphase/out/m84036_250809_035451_s4.bc2136.havanno.json", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-39/call-call_f8/out/m84036_250809_035451_s4.bc2136.f8inversion.json"}
2025-09-15 20:27:37.881 wdl.w:ptcp.w:call-paraphase-39 NOTICE done
2025-09-15 20:27:37.887 wdl.w:ptcp NOTICE finish :: job: "call-paraphase-39"
2025-09-15 20:27:37.887 wdl.w:ptcp INFO output :: job: "call-paraphase-39", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-39/out/m84036_250809_035451_s4.bc2136.f8inversion.vcf", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-39/out/m84036_250809_035451_s4.bc2136_paraphase/m84036_250809_035451_s4.bc2136.paraphase.json", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-39/out/m84036_250809_035451_s4.bc2136_paraphase/m84036_250809_035451_s4.bc2136.paraphase.bam", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-39/out/m84036_250809_035451_s4.bc2136_paraphase/m84036_250809_035451_s4.bc2136.paraphase.bam.bai", "paraphase_vcfs": ["/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-39/out/m84036_250809_035451_s4.bc2136_paraphase/m84036_250809_035451_s4.bc2136_paraphase_vcfs/m84036_250809_035451_s4.bc2136_cyp21.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-39/out/m84036_250809_035451_s4.bc2136_paraphase/m84036_250809_035451_s4.bc2136_paraphase_vcfs/m84036_250809_035451_s4.bc2136_f8inv1.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-39/out/m84036_250809_035451_s4.bc2136_paraphase/m84036_250809_035451_s4.bc2136_paraphase_vcfs/m84036_250809_035451_s4.bc2136_f8inv22.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-39/out/m84036_250809_035451_s4.bc2136_paraphase/m84036_250809_035451_s4.bc2136_paraphase_vcfs/m84036_250809_035451_s4.bc2136_gba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-39/out/m84036_250809_035451_s4.bc2136_paraphase/m84036_250809_035451_s4.bc2136_paraphase_vcfs/m84036_250809_035451_s4.bc2136_hba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-39/out/m84036_250809_035451_s4.bc2136_paraphase/m84036_250809_035451_s4.bc2136_paraphase_vcfs/m84036_250809_035451_s4.bc2136_hbb.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-39/out/m84036_250809_035451_s4.bc2136_paraphase/m84036_250809_035451_s4.bc2136_paraphase_vcfs/m84036_250809_035451_s4.bc2136_rpgr.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-39/out/m84036_250809_035451_s4.bc2136_paraphase/m84036_250809_035451_s4.bc2136_paraphase_vcfs/m84036_250809_035451_s4.bc2136_smn1.vcf"], "havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-39/out/m84036_250809_035451_s4.bc2136.havanno.json", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-39/out/m84036_250809_035451_s4.bc2136.f8inversion.json"}
2025-09-15 20:27:37.888 wdl.w:ptcp NOTICE ready :: job: "call-tar_outputs-39", callee: "tar_outputs"
2025-09-15 20:27:37.888 wdl.w:ptcp.w:call-paraphase-47.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for f8inv22 for sample m84036_250809_035451_s4.bc2144 at 2025-09-15 20:27:22.059088...
2025-09-15 20:27:37.888 wdl.w:ptcp INFO input :: job: "call-tar_outputs-39", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "sawfish_vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-39/out/m84036_250809_035451_s4.bc2136_sawfish/m84036_250809_035451_s4.bc2136.sv.vcf.gz.tbi", "sawfish_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-39/out/m84036_250809_035451_s4.bc2136_sawfish/m84036_250809_035451_s4.bc2136.sv.vcf.gz", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-39/out/m84036_250809_035451_s4.bc2136.f8inversion.json", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-39/out/m84036_250809_035451_s4.bc2136_paraphase/m84036_250809_035451_s4.bc2136.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-39/out/m84036_250809_035451_s4.bc2136_paraphase/m84036_250809_035451_s4.bc2136.paraphase.bam", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-39/out/m84036_250809_035451_s4.bc2136_paraphase/m84036_250809_035451_s4.bc2136.paraphase.json", "trgt_spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-39/out/m84036_250809_035451_s4.bc2136.trgt.sorted.spanning.bam.bai", "trgt_spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-39/out/m84036_250809_035451_s4.bc2136.trgt.sorted.spanning.bam", "trgt_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-39/out/m84036_250809_035451_s4.bc2136.trgt.vcf", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-39/out/m84036_250809_035451_s4.bc2136.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-39/out/m84036_250809_035451_s4.bc2136.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2136"}
2025-09-15 20:27:37.889 wdl.w:ptcp.w:call-paraphase-47.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for f8inv22 for sample m84036_250809_035451_s4.bc2144 at 2025-09-15 20:27:22.059293...
2025-09-15 20:27:37.889 wdl.w:ptcp.w:call-paraphase-47.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for f8inv22 for sample m84036_250809_035451_s4.bc2144 at 2025-09-15 20:27:22.779128...
2025-09-15 20:27:37.889 wdl.w:ptcp.w:call-paraphase-47.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for f8inv22 for sample m84036_250809_035451_s4.bc2144 at 2025-09-15 20:27:25.822450...
2025-09-15 20:27:37.889 wdl.w:ptcp.w:call-paraphase-47.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for f8inv22 for sample m84036_250809_035451_s4.bc2144 at 2025-09-15 20:27:26.102863...
2025-09-15 20:27:37.896 wdl.w:ptcp.t:call-tar_outputs-39 NOTICE task setup :: name: "tar_outputs", source: "./common.wdl", line: 279, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-39", thread: 140610912642624
2025-09-15 20:27:37.919 wdl.w:ptcp.t:call-tar_outputs-39 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:27:37.919 wdl.w:ptcp.t:call-tar_outputs-39 INFO input :: name: "sawfish_vcf_tbi", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2136.sv.vcf.gz.tbi"
2025-09-15 20:27:37.919 wdl.w:ptcp.t:call-tar_outputs-39 INFO input :: name: "sawfish_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2136.sv.vcf.gz"
2025-09-15 20:27:37.919 wdl.w:ptcp.t:call-tar_outputs-39 INFO input :: name: "f8_json", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2136.f8inversion.json"
2025-09-15 20:27:37.919 wdl.w:ptcp.t:call-tar_outputs-39 INFO input :: name: "paraphase_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2136.paraphase.bam.bai"
2025-09-15 20:27:37.919 wdl.w:ptcp.t:call-tar_outputs-39 INFO input :: name: "paraphase_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2136.paraphase.bam"
2025-09-15 20:27:37.919 wdl.w:ptcp.t:call-tar_outputs-39 INFO input :: name: "paraphase_json", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2136.paraphase.json"
2025-09-15 20:27:37.919 wdl.w:ptcp.t:call-tar_outputs-39 INFO input :: name: "trgt_spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2136.trgt.sorted.spanning.bam.bai"
2025-09-15 20:27:37.919 wdl.w:ptcp.t:call-tar_outputs-39 INFO input :: name: "trgt_spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2136.trgt.sorted.spanning.bam"
2025-09-15 20:27:37.919 wdl.w:ptcp.t:call-tar_outputs-39 INFO input :: name: "trgt_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2136.trgt.vcf"
2025-09-15 20:27:37.919 wdl.w:ptcp.t:call-tar_outputs-39 INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2136.mapped.bam.bai"
2025-09-15 20:27:37.919 wdl.w:ptcp.t:call-tar_outputs-39 INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2136.mapped.bam"
2025-09-15 20:27:37.919 wdl.w:ptcp.t:call-tar_outputs-39 INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2136"
2025-09-15 20:27:37.919 wdl.w:ptcp.t:call-tar_outputs-39 INFO eval :: name: "threads", value: 1
2025-09-15 20:27:37.920 wdl.w:ptcp.t:call-tar_outputs-39 INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:27:37.920 wdl.w:ptcp.t:call-tar_outputs-39 INFO eval :: name: "disk_size", value: 6
2025-09-15 20:27:37.920 wdl.w:ptcp.t:call-tar_outputs-39 INFO eval :: name: "output_tarball", value: "m84036_250809_035451_s4.bc2136.tar"
2025-09-15 20:27:37.920 wdl.w:ptcp.t:call-tar_outputs-39 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:27:37.920 wdl.w:ptcp.t:call-tar_outputs-39 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:27:37.921 wdl.w:ptcp.t:call-tar_outputs-39 INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:27:37.921 wdl.w:ptcp.t:call-tar_outputs-39 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:27:38.006 wdl.w:ptcp.t:call-tar_outputs-39 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 17, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-39/_singularity_tmpdir_3q4kfka8"
2025-09-15 20:27:38.006 wdl.w:ptcp.t:call-tar_outputs-39 INFO Slurm invocation: srun --job-name call-tar_outputs-39 --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-39/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-39/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-39/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-39/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-39/out/m84036_250809_035451_s4.bc2136_sawfish/m84036_250809_035451_s4.bc2136.sv.vcf.gz:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2136.sv.vcf.gz:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-39/out/m84036_250809_035451_s4.bc2136_sawfish/m84036_250809_035451_s4.bc2136.sv.vcf.gz.tbi:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2136.sv.vcf.gz.tbi:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-39/out/m84036_250809_035451_s4.bc2136.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2136.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-39/out/m84036_250809_035451_s4.bc2136.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2136.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-39/out/m84036_250809_035451_s4.bc2136_paraphase/m84036_250809_035451_s4.bc2136.paraphase.json:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2136.paraphase.json:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-39/out/m84036_250809_035451_s4.bc2136_paraphase/m84036_250809_035451_s4.bc2136.paraphase.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2136.paraphase.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-39/out/m84036_250809_035451_s4.bc2136_paraphase/m84036_250809_035451_s4.bc2136.paraphase.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2136.paraphase.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-39/out/m84036_250809_035451_s4.bc2136.f8inversion.json:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2136.f8inversion.json:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-39/out/m84036_250809_035451_s4.bc2136.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2136.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-39/out/m84036_250809_035451_s4.bc2136.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2136.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-39/out/m84036_250809_035451_s4.bc2136.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2136.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-39/_singularity_tmpdir_3q4kfka8/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-39/_singularity_tmpdir_3q4kfka8/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:27:38.015 wdl.w:ptcp.t:call-tar_outputs-39 NOTICE slurm_singularity run :: pid: 1208429, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-39/slurm_singularity.log.txt"
2025-09-15 20:27:38.673 wdl.w:ptcp.w:call-paraphase-47.t:call-run_paraphase INFO output :: name: "paraphase_bam", value: "m84036_250809_035451_s4.bc2144_paraphase/m84036_250809_035451_s4.bc2144.paraphase.bam"
2025-09-15 20:27:38.679 wdl.w:ptcp.w:call-paraphase-47.t:call-run_paraphase INFO output :: name: "paraphase_bam_bai", value: "m84036_250809_035451_s4.bc2144_paraphase/m84036_250809_035451_s4.bc2144.paraphase.bam.bai"
2025-09-15 20:27:38.680 wdl.w:ptcp.w:call-paraphase-47.t:call-run_paraphase INFO output :: name: "paraphase_json", value: "m84036_250809_035451_s4.bc2144_paraphase/m84036_250809_035451_s4.bc2144.paraphase.json"
2025-09-15 20:27:38.686 wdl.w:ptcp.w:call-paraphase-47.t:call-run_paraphase INFO output :: name: "paraphase_vcfs", value: ["/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2144_paraphase/m84036_250809_035451_s4.bc2144_paraphase_vcfs/m84036_250809_035451_s4.bc2144_cyp21.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2144_paraphase/m84036_250809_035451_s4.bc2144_paraphase_vcfs/m84036_250809_035451_s4.bc2144_f8inv1.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2144_paraphase/m84036_250809_035451_s4.bc2144_paraphase_vcfs/m84036_250809_035451_s4.bc2144_f8inv22.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2144_paraphase/m84036_250809_035451_s4.bc2144_paraphase_vcfs/m84036_250809_035451_s4.bc2144_gba.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2144_paraphase/m84036_250809_035451_s4.bc2144_paraphase_vcfs/m84036_250809_035451_s4.bc2144_hba.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2144_paraphase/m84036_250809_035451_s4.bc2144_paraphase_vcfs/m84036_250809_035451_s4.bc2144_hbb.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2144_paraphase/m84036_250809_035451_s4.bc2144_paraphase_vcfs/m84036_250809_035451_s4.bc2144_rpgr.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2144_paraphase/m84036_250809_035451_s4.bc2144_paraphase_vcfs/m84036_250809_035451_s4.bc2144_smn1.vcf"]
2025-09-15 20:27:38.689 wdl.w:ptcp.w:call-paraphase-47.t:call-run_paraphase INFO output :: name: "havanno_json", value: "m84036_250809_035451_s4.bc2144.havanno.json"
2025-09-15 20:27:38.890 wdl.w:ptcp.w:call-paraphase-47.t:call-run_paraphase NOTICE done
2025-09-15 20:27:38.896 wdl.w:ptcp.w:call-paraphase-47 NOTICE finish :: job: "call-run_paraphase"
2025-09-15 20:27:38.896 wdl.w:ptcp.w:call-paraphase-47 INFO output :: job: "call-run_paraphase", values: {"havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-47/call-run_paraphase/out/m84036_250809_035451_s4.bc2144.havanno.json", "paraphase_vcfs": ["/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-47/call-run_paraphase/out/m84036_250809_035451_s4.bc2144_paraphase/m84036_250809_035451_s4.bc2144_paraphase_vcfs/m84036_250809_035451_s4.bc2144_cyp21.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-47/call-run_paraphase/out/m84036_250809_035451_s4.bc2144_paraphase/m84036_250809_035451_s4.bc2144_paraphase_vcfs/m84036_250809_035451_s4.bc2144_f8inv1.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-47/call-run_paraphase/out/m84036_250809_035451_s4.bc2144_paraphase/m84036_250809_035451_s4.bc2144_paraphase_vcfs/m84036_250809_035451_s4.bc2144_f8inv22.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-47/call-run_paraphase/out/m84036_250809_035451_s4.bc2144_paraphase/m84036_250809_035451_s4.bc2144_paraphase_vcfs/m84036_250809_035451_s4.bc2144_gba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-47/call-run_paraphase/out/m84036_250809_035451_s4.bc2144_paraphase/m84036_250809_035451_s4.bc2144_paraphase_vcfs/m84036_250809_035451_s4.bc2144_hba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-47/call-run_paraphase/out/m84036_250809_035451_s4.bc2144_paraphase/m84036_250809_035451_s4.bc2144_paraphase_vcfs/m84036_250809_035451_s4.bc2144_hbb.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-47/call-run_paraphase/out/m84036_250809_035451_s4.bc2144_paraphase/m84036_250809_035451_s4.bc2144_paraphase_vcfs/m84036_250809_035451_s4.bc2144_rpgr.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-47/call-run_paraphase/out/m84036_250809_035451_s4.bc2144_paraphase/m84036_250809_035451_s4.bc2144_paraphase_vcfs/m84036_250809_035451_s4.bc2144_smn1.vcf"], "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-47/call-run_paraphase/out/m84036_250809_035451_s4.bc2144_paraphase/m84036_250809_035451_s4.bc2144.paraphase.json", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-47/call-run_paraphase/out/m84036_250809_035451_s4.bc2144_paraphase/m84036_250809_035451_s4.bc2144.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-47/call-run_paraphase/out/m84036_250809_035451_s4.bc2144_paraphase/m84036_250809_035451_s4.bc2144.paraphase.bam"}
2025-09-15 20:27:38.897 wdl.w:ptcp.w:call-paraphase-47 NOTICE ready :: job: "call-call_f8", callee: "call_f8"
2025-09-15 20:27:38.897 wdl.w:ptcp.w:call-paraphase-47 INFO input :: job: "call-call_f8", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "out_prefix": "m84036_250809_035451_s4.bc2144", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-47/call-run_paraphase/out/m84036_250809_035451_s4.bc2144_paraphase/m84036_250809_035451_s4.bc2144.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-47/call-run_paraphase/out/m84036_250809_035451_s4.bc2144_paraphase/m84036_250809_035451_s4.bc2144.paraphase.bam", "sex": "F"}
2025-09-15 20:27:38.897 wdl.w:ptcp.w:call-paraphase-47 INFO visit :: node: "output-havanno_json", values: {"havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-47/call-run_paraphase/out/m84036_250809_035451_s4.bc2144.havanno.json"}
2025-09-15 20:27:38.898 wdl.w:ptcp.w:call-paraphase-47 INFO visit :: node: "output-paraphase_bam", values: {"paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-47/call-run_paraphase/out/m84036_250809_035451_s4.bc2144_paraphase/m84036_250809_035451_s4.bc2144.paraphase.bam"}
2025-09-15 20:27:38.898 wdl.w:ptcp.w:call-paraphase-47 INFO visit :: node: "output-paraphase_bam_bai", values: {"paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-47/call-run_paraphase/out/m84036_250809_035451_s4.bc2144_paraphase/m84036_250809_035451_s4.bc2144.paraphase.bam.bai"}
2025-09-15 20:27:38.898 wdl.w:ptcp.w:call-paraphase-47 INFO visit :: node: "output-paraphase_json", values: {"paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-47/call-run_paraphase/out/m84036_250809_035451_s4.bc2144_paraphase/m84036_250809_035451_s4.bc2144.paraphase.json"}
2025-09-15 20:27:38.898 wdl.w:ptcp.w:call-paraphase-47 INFO visit :: node: "output-paraphase_vcfs", values: {"paraphase_vcfs": ["/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-47/call-run_paraphase/out/m84036_250809_035451_s4.bc2144_paraphase/m84036_250809_035451_s4.bc2144_paraphase_vcfs/m84036_250809_035451_s4.bc2144_cyp21.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-47/call-run_paraphase/out/m84036_250809_035451_s4.bc2144_paraphase/m84036_250809_035451_s4.bc2144_paraphase_vcfs/m84036_250809_035451_s4.bc2144_f8inv1.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-47/call-run_paraphase/out/m84036_250809_035451_s4.bc2144_paraphase/m84036_250809_035451_s4.bc2144_paraphase_vcfs/m84036_250809_035451_s4.bc2144_f8inv22.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-47/call-run_paraphase/out/m84036_250809_035451_s4.bc2144_paraphase/m84036_250809_035451_s4.bc2144_paraphase_vcfs/m84036_250809_035451_s4.bc2144_gba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-47/call-run_paraphase/out/m84036_250809_035451_s4.bc2144_paraphase/m84036_250809_035451_s4.bc2144_paraphase_vcfs/m84036_250809_035451_s4.bc2144_hba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-47/call-run_paraphase/out/m84036_250809_035451_s4.bc2144_paraphase/m84036_250809_035451_s4.bc2144_paraphase_vcfs/m84036_250809_035451_s4.bc2144_hbb.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-47/call-run_paraphase/out/m84036_250809_035451_s4.bc2144_paraphase/m84036_250809_035451_s4.bc2144_paraphase_vcfs/m84036_250809_035451_s4.bc2144_rpgr.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-47/call-run_paraphase/out/m84036_250809_035451_s4.bc2144_paraphase/m84036_250809_035451_s4.bc2144_paraphase_vcfs/m84036_250809_035451_s4.bc2144_smn1.vcf"]}
2025-09-15 20:27:38.902 wdl.w:ptcp.w:call-paraphase-47.t:call-call_f8 NOTICE task setup :: name: "call_f8", source: "./paraphase.wdl", line: 232, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-47/call-call_f8", thread: 140607137760832
2025-09-15 20:27:38.917 wdl.w:ptcp.w:call-paraphase-47.t:call-call_f8 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:27:38.917 wdl.w:ptcp.w:call-paraphase-47.t:call-call_f8 INFO input :: name: "genome_version", value: "38"
2025-09-15 20:27:38.917 wdl.w:ptcp.w:call-paraphase-47.t:call-call_f8 INFO input :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2144"
2025-09-15 20:27:38.917 wdl.w:ptcp.w:call-paraphase-47.t:call-call_f8 INFO input :: name: "paraphase_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2144.paraphase.bam.bai"
2025-09-15 20:27:38.917 wdl.w:ptcp.w:call-paraphase-47.t:call-call_f8 INFO input :: name: "paraphase_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2144.paraphase.bam"
2025-09-15 20:27:38.917 wdl.w:ptcp.w:call-paraphase-47.t:call-call_f8 INFO input :: name: "sex", value: "F"
2025-09-15 20:27:38.917 wdl.w:ptcp.w:call-paraphase-47.t:call-call_f8 INFO eval :: name: "threads", value: 1
2025-09-15 20:27:38.917 wdl.w:ptcp.w:call-paraphase-47.t:call-call_f8 INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:27:38.918 wdl.w:ptcp.w:call-paraphase-47.t:call-call_f8 INFO eval :: name: "disk_size", value: 11
2025-09-15 20:27:38.918 wdl.w:ptcp.w:call-paraphase-47.t:call-call_f8 INFO eval :: name: "sample_sex", value: "F"
2025-09-15 20:27:38.918 wdl.w:ptcp.w:call-paraphase-47.t:call-call_f8 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:27:38.918 wdl.w:ptcp.w:call-paraphase-47.t:call-call_f8 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:27:38.919 wdl.w:ptcp.w:call-paraphase-47.t:call-call_f8 INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:27:38.919 wdl.w:ptcp.w:call-paraphase-47.t:call-call_f8 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:27:38.957 wdl.w:ptcp.w:call-paraphase-47.t:call-call_f8 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 8, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-47/call-call_f8/_singularity_tmpdir_7xi35201"
2025-09-15 20:27:38.957 wdl.w:ptcp.w:call-paraphase-47.t:call-call_f8 INFO Slurm invocation: srun --job-name call-call_f8 --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-47/call-call_f8/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-47/call-call_f8/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-47/call-call_f8/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-47/call-call_f8/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-47/call-run_paraphase/out/m84036_250809_035451_s4.bc2144_paraphase/m84036_250809_035451_s4.bc2144.paraphase.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2144.paraphase.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-47/call-run_paraphase/out/m84036_250809_035451_s4.bc2144_paraphase/m84036_250809_035451_s4.bc2144.paraphase.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2144.paraphase.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-47/call-call_f8/_singularity_tmpdir_7xi35201/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-47/call-call_f8/_singularity_tmpdir_7xi35201/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:27:38.963 wdl.w:ptcp.w:call-paraphase-47.t:call-call_f8 NOTICE slurm_singularity run :: pid: 1208438, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-47/call-call_f8/slurm_singularity.log.txt"
2025-09-15 20:27:39.022 wdl.w:ptcp.t:call-tar_outputs-39.slurm_singularity INFO srun: job 51798232 queued and waiting for resources
2025-09-15 20:27:39.022 wdl.w:ptcp.t:call-tar_outputs-39.slurm_singularity INFO srun: job 51798232 has been allocated resources
2025-09-15 20:27:39.022 wdl.w:ptcp.t:call-tar_outputs-39.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:27:39.335 wdl.w:ptcp.t:call-tar_outputs-39 INFO output :: name: "sample_tarball", value: "m84036_250809_035451_s4.bc2136.tar"
2025-09-15 20:27:39.396 wdl.w:ptcp.t:call-tar_outputs-39 NOTICE done
2025-09-15 20:27:39.401 wdl.w:ptcp NOTICE finish :: job: "call-tar_outputs-39"
2025-09-15 20:27:39.401 wdl.w:ptcp INFO output :: job: "call-tar_outputs-39", values: {"sample_tarball": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-39/out/m84036_250809_035451_s4.bc2136.tar"}
2025-09-15 20:27:39.973 wdl.w:ptcp.w:call-paraphase-47.t:call-call_f8.slurm_singularity INFO srun: job 51798233 queued and waiting for resources
2025-09-15 20:27:39.973 wdl.w:ptcp.w:call-paraphase-47.t:call-call_f8.slurm_singularity INFO srun: job 51798233 has been allocated resources
2025-09-15 20:27:39.973 wdl.w:ptcp.w:call-paraphase-47.t:call-call_f8.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:27:40.258 wdl.w:ptcp.w:call-paraphase-63.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for f8inv1 for sample m84036_250809_035451_s4.bc2160 at 2025-09-15 20:27:27.268774...
2025-09-15 20:27:40.258 wdl.w:ptcp.w:call-paraphase-63.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for f8inv1 for sample m84036_250809_035451_s4.bc2160 at 2025-09-15 20:27:33.961864...
2025-09-15 20:27:40.258 wdl.w:ptcp.w:call-paraphase-63.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for f8inv1 for sample m84036_250809_035451_s4.bc2160 at 2025-09-15 20:27:34.417538...
2025-09-15 20:27:40.328 wdl.w:ptcp.w:call-paraphase-47.t:call-call_f8 INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2144.f8inversion.vcf"
2025-09-15 20:27:40.331 wdl.w:ptcp.w:call-paraphase-47.t:call-call_f8 INFO output :: name: "json", value: "m84036_250809_035451_s4.bc2144.f8inversion.json"
2025-09-15 20:27:40.382 wdl.w:ptcp.w:call-paraphase-47.t:call-call_f8 NOTICE done
2025-09-15 20:27:40.387 wdl.w:ptcp.w:call-paraphase-47 NOTICE finish :: job: "call-call_f8"
2025-09-15 20:27:40.387 wdl.w:ptcp.w:call-paraphase-47 INFO output :: job: "call-call_f8", values: {"json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-47/call-call_f8/out/m84036_250809_035451_s4.bc2144.f8inversion.json", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-47/call-call_f8/out/m84036_250809_035451_s4.bc2144.f8inversion.vcf"}
2025-09-15 20:27:40.388 wdl.w:ptcp.w:call-paraphase-47 INFO visit :: node: "output-f8_json", values: {"f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-47/call-call_f8/out/m84036_250809_035451_s4.bc2144.f8inversion.json"}
2025-09-15 20:27:40.388 wdl.w:ptcp.w:call-paraphase-47 INFO visit :: node: "output-f8_vcf", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-47/call-call_f8/out/m84036_250809_035451_s4.bc2144.f8inversion.vcf"}
2025-09-15 20:27:40.388 wdl.w:ptcp.w:call-paraphase-47 INFO visit :: node: "outputs", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-47/call-call_f8/out/m84036_250809_035451_s4.bc2144.f8inversion.vcf", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-47/call-run_paraphase/out/m84036_250809_035451_s4.bc2144_paraphase/m84036_250809_035451_s4.bc2144.paraphase.json", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-47/call-run_paraphase/out/m84036_250809_035451_s4.bc2144_paraphase/m84036_250809_035451_s4.bc2144.paraphase.bam", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-47/call-run_paraphase/out/m84036_250809_035451_s4.bc2144_paraphase/m84036_250809_035451_s4.bc2144.paraphase.bam.bai", "paraphase_vcfs": ["/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-47/call-run_paraphase/out/m84036_250809_035451_s4.bc2144_paraphase/m84036_250809_035451_s4.bc2144_paraphase_vcfs/m84036_250809_035451_s4.bc2144_cyp21.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-47/call-run_paraphase/out/m84036_250809_035451_s4.bc2144_paraphase/m84036_250809_035451_s4.bc2144_paraphase_vcfs/m84036_250809_035451_s4.bc2144_f8inv1.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-47/call-run_paraphase/out/m84036_250809_035451_s4.bc2144_paraphase/m84036_250809_035451_s4.bc2144_paraphase_vcfs/m84036_250809_035451_s4.bc2144_f8inv22.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-47/call-run_paraphase/out/m84036_250809_035451_s4.bc2144_paraphase/m84036_250809_035451_s4.bc2144_paraphase_vcfs/m84036_250809_035451_s4.bc2144_gba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-47/call-run_paraphase/out/m84036_250809_035451_s4.bc2144_paraphase/m84036_250809_035451_s4.bc2144_paraphase_vcfs/m84036_250809_035451_s4.bc2144_hba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-47/call-run_paraphase/out/m84036_250809_035451_s4.bc2144_paraphase/m84036_250809_035451_s4.bc2144_paraphase_vcfs/m84036_250809_035451_s4.bc2144_hbb.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-47/call-run_paraphase/out/m84036_250809_035451_s4.bc2144_paraphase/m84036_250809_035451_s4.bc2144_paraphase_vcfs/m84036_250809_035451_s4.bc2144_rpgr.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-47/call-run_paraphase/out/m84036_250809_035451_s4.bc2144_paraphase/m84036_250809_035451_s4.bc2144_paraphase_vcfs/m84036_250809_035451_s4.bc2144_smn1.vcf"], "havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-47/call-run_paraphase/out/m84036_250809_035451_s4.bc2144.havanno.json", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-47/call-call_f8/out/m84036_250809_035451_s4.bc2144.f8inversion.json"}
2025-09-15 20:27:40.516 wdl.w:ptcp.w:call-paraphase-47 NOTICE done
2025-09-15 20:27:40.521 wdl.w:ptcp NOTICE finish :: job: "call-paraphase-47"
2025-09-15 20:27:40.521 wdl.w:ptcp INFO output :: job: "call-paraphase-47", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-47/out/m84036_250809_035451_s4.bc2144.f8inversion.vcf", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-47/out/m84036_250809_035451_s4.bc2144_paraphase/m84036_250809_035451_s4.bc2144.paraphase.json", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-47/out/m84036_250809_035451_s4.bc2144_paraphase/m84036_250809_035451_s4.bc2144.paraphase.bam", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-47/out/m84036_250809_035451_s4.bc2144_paraphase/m84036_250809_035451_s4.bc2144.paraphase.bam.bai", "paraphase_vcfs": ["/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-47/out/m84036_250809_035451_s4.bc2144_paraphase/m84036_250809_035451_s4.bc2144_paraphase_vcfs/m84036_250809_035451_s4.bc2144_cyp21.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-47/out/m84036_250809_035451_s4.bc2144_paraphase/m84036_250809_035451_s4.bc2144_paraphase_vcfs/m84036_250809_035451_s4.bc2144_f8inv1.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-47/out/m84036_250809_035451_s4.bc2144_paraphase/m84036_250809_035451_s4.bc2144_paraphase_vcfs/m84036_250809_035451_s4.bc2144_f8inv22.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-47/out/m84036_250809_035451_s4.bc2144_paraphase/m84036_250809_035451_s4.bc2144_paraphase_vcfs/m84036_250809_035451_s4.bc2144_gba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-47/out/m84036_250809_035451_s4.bc2144_paraphase/m84036_250809_035451_s4.bc2144_paraphase_vcfs/m84036_250809_035451_s4.bc2144_hba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-47/out/m84036_250809_035451_s4.bc2144_paraphase/m84036_250809_035451_s4.bc2144_paraphase_vcfs/m84036_250809_035451_s4.bc2144_hbb.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-47/out/m84036_250809_035451_s4.bc2144_paraphase/m84036_250809_035451_s4.bc2144_paraphase_vcfs/m84036_250809_035451_s4.bc2144_rpgr.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-47/out/m84036_250809_035451_s4.bc2144_paraphase/m84036_250809_035451_s4.bc2144_paraphase_vcfs/m84036_250809_035451_s4.bc2144_smn1.vcf"], "havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-47/out/m84036_250809_035451_s4.bc2144.havanno.json", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-47/out/m84036_250809_035451_s4.bc2144.f8inversion.json"}
2025-09-15 20:27:40.522 wdl.w:ptcp NOTICE ready :: job: "call-tar_outputs-47", callee: "tar_outputs"
2025-09-15 20:27:40.522 wdl.w:ptcp INFO input :: job: "call-tar_outputs-47", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "sawfish_vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-47/out/m84036_250809_035451_s4.bc2144_sawfish/m84036_250809_035451_s4.bc2144.sv.vcf.gz.tbi", "sawfish_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-47/out/m84036_250809_035451_s4.bc2144_sawfish/m84036_250809_035451_s4.bc2144.sv.vcf.gz", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-47/out/m84036_250809_035451_s4.bc2144.f8inversion.json", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-47/out/m84036_250809_035451_s4.bc2144_paraphase/m84036_250809_035451_s4.bc2144.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-47/out/m84036_250809_035451_s4.bc2144_paraphase/m84036_250809_035451_s4.bc2144.paraphase.bam", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-47/out/m84036_250809_035451_s4.bc2144_paraphase/m84036_250809_035451_s4.bc2144.paraphase.json", "trgt_spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-47/out/m84036_250809_035451_s4.bc2144.trgt.sorted.spanning.bam.bai", "trgt_spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-47/out/m84036_250809_035451_s4.bc2144.trgt.sorted.spanning.bam", "trgt_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-47/out/m84036_250809_035451_s4.bc2144.trgt.vcf", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-47/out/m84036_250809_035451_s4.bc2144.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-47/out/m84036_250809_035451_s4.bc2144.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2144"}
2025-09-15 20:27:40.528 wdl.w:ptcp.t:call-tar_outputs-47 NOTICE task setup :: name: "tar_outputs", source: "./common.wdl", line: 279, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-47", thread: 140610342200896
2025-09-15 20:27:40.550 wdl.w:ptcp.t:call-tar_outputs-47 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:27:40.550 wdl.w:ptcp.t:call-tar_outputs-47 INFO input :: name: "sawfish_vcf_tbi", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2144.sv.vcf.gz.tbi"
2025-09-15 20:27:40.550 wdl.w:ptcp.t:call-tar_outputs-47 INFO input :: name: "sawfish_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2144.sv.vcf.gz"
2025-09-15 20:27:40.550 wdl.w:ptcp.t:call-tar_outputs-47 INFO input :: name: "f8_json", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2144.f8inversion.json"
2025-09-15 20:27:40.550 wdl.w:ptcp.t:call-tar_outputs-47 INFO input :: name: "paraphase_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2144.paraphase.bam.bai"
2025-09-15 20:27:40.551 wdl.w:ptcp.t:call-tar_outputs-47 INFO input :: name: "paraphase_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2144.paraphase.bam"
2025-09-15 20:27:40.551 wdl.w:ptcp.t:call-tar_outputs-47 INFO input :: name: "paraphase_json", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2144.paraphase.json"
2025-09-15 20:27:40.551 wdl.w:ptcp.t:call-tar_outputs-47 INFO input :: name: "trgt_spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2144.trgt.sorted.spanning.bam.bai"
2025-09-15 20:27:40.551 wdl.w:ptcp.t:call-tar_outputs-47 INFO input :: name: "trgt_spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2144.trgt.sorted.spanning.bam"
2025-09-15 20:27:40.551 wdl.w:ptcp.t:call-tar_outputs-47 INFO input :: name: "trgt_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2144.trgt.vcf"
2025-09-15 20:27:40.551 wdl.w:ptcp.t:call-tar_outputs-47 INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2144.mapped.bam.bai"
2025-09-15 20:27:40.551 wdl.w:ptcp.t:call-tar_outputs-47 INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2144.mapped.bam"
2025-09-15 20:27:40.551 wdl.w:ptcp.t:call-tar_outputs-47 INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2144"
2025-09-15 20:27:40.551 wdl.w:ptcp.t:call-tar_outputs-47 INFO eval :: name: "threads", value: 1
2025-09-15 20:27:40.551 wdl.w:ptcp.t:call-tar_outputs-47 INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:27:40.551 wdl.w:ptcp.t:call-tar_outputs-47 INFO eval :: name: "disk_size", value: 6
2025-09-15 20:27:40.551 wdl.w:ptcp.t:call-tar_outputs-47 INFO eval :: name: "output_tarball", value: "m84036_250809_035451_s4.bc2144.tar"
2025-09-15 20:27:40.552 wdl.w:ptcp.t:call-tar_outputs-47 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:27:40.552 wdl.w:ptcp.t:call-tar_outputs-47 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:27:40.552 wdl.w:ptcp.t:call-tar_outputs-47 INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:27:40.552 wdl.w:ptcp.t:call-tar_outputs-47 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:27:40.626 wdl.w:ptcp.t:call-tar_outputs-47 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 17, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-47/_singularity_tmpdir__yjnbclp"
2025-09-15 20:27:40.626 wdl.w:ptcp.t:call-tar_outputs-47 INFO Slurm invocation: srun --job-name call-tar_outputs-47 --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-47/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-47/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-47/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-47/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-47/out/m84036_250809_035451_s4.bc2144.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2144.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-47/out/m84036_250809_035451_s4.bc2144.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2144.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-47/out/m84036_250809_035451_s4.bc2144.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2144.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-47/out/m84036_250809_035451_s4.bc2144.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2144.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-47/out/m84036_250809_035451_s4.bc2144.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2144.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-47/out/m84036_250809_035451_s4.bc2144_paraphase/m84036_250809_035451_s4.bc2144.paraphase.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2144.paraphase.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-47/out/m84036_250809_035451_s4.bc2144_paraphase/m84036_250809_035451_s4.bc2144.paraphase.json:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2144.paraphase.json:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-47/out/m84036_250809_035451_s4.bc2144_paraphase/m84036_250809_035451_s4.bc2144.paraphase.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2144.paraphase.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-47/out/m84036_250809_035451_s4.bc2144.f8inversion.json:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2144.f8inversion.json:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-47/out/m84036_250809_035451_s4.bc2144_sawfish/m84036_250809_035451_s4.bc2144.sv.vcf.gz:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2144.sv.vcf.gz:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-47/out/m84036_250809_035451_s4.bc2144_sawfish/m84036_250809_035451_s4.bc2144.sv.vcf.gz.tbi:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2144.sv.vcf.gz.tbi:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-47/_singularity_tmpdir__yjnbclp/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-47/_singularity_tmpdir__yjnbclp/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:27:40.631 wdl.w:ptcp.t:call-tar_outputs-47 NOTICE slurm_singularity run :: pid: 1208531, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-47/slurm_singularity.log.txt"
2025-09-15 20:27:40.863 wdl.w:ptcp.w:call-paraphase-91.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for f8inv1 for sample m84036_250809_035451_s4.bc2188 at 2025-09-15 20:27:36.944749...
2025-09-15 20:27:40.863 wdl.w:ptcp.w:call-paraphase-91.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for f8inv1 for sample m84036_250809_035451_s4.bc2188 at 2025-09-15 20:27:36.945686...
2025-09-15 20:27:41.389 wdl.w:ptcp.w:call-paraphase-75.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for cyp21 for sample m84036_250809_035451_s4.bc2172 at 2025-09-15 20:27:09.219812...
2025-09-15 20:27:41.389 wdl.w:ptcp.w:call-paraphase-75.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for cyp21 for sample m84036_250809_035451_s4.bc2172 at 2025-09-15 20:27:11.390250...
2025-09-15 20:27:41.389 wdl.w:ptcp.w:call-paraphase-75.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for gba for sample m84036_250809_035451_s4.bc2172 at 2025-09-15 20:27:23.931669...
2025-09-15 20:27:41.389 wdl.w:ptcp.w:call-paraphase-75.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for gba for sample m84036_250809_035451_s4.bc2172 at 2025-09-15 20:27:24.796624...
2025-09-15 20:27:41.390 wdl.w:ptcp.w:call-paraphase-75.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for f8inv1 for sample m84036_250809_035451_s4.bc2172 at 2025-09-15 20:27:25.525619...
2025-09-15 20:27:41.390 wdl.w:ptcp.w:call-paraphase-75.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for f8inv1 for sample m84036_250809_035451_s4.bc2172 at 2025-09-15 20:27:25.526429...
2025-09-15 20:27:41.390 wdl.w:ptcp.w:call-paraphase-75.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for f8inv1 for sample m84036_250809_035451_s4.bc2172 at 2025-09-15 20:27:28.676801...
2025-09-15 20:27:41.390 wdl.w:ptcp.w:call-paraphase-75.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for f8inv1 for sample m84036_250809_035451_s4.bc2172 at 2025-09-15 20:27:38.919483...
2025-09-15 20:27:41.643 wdl.w:ptcp.t:call-tar_outputs-47.slurm_singularity INFO srun: job 51798234 queued and waiting for resources
2025-09-15 20:27:42.445 wdl.w:ptcp.w:call-paraphase-46.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for f8inv22 for sample m84036_250809_035451_s4.bc2143 at 2025-09-15 20:27:25.439452...
2025-09-15 20:27:42.446 wdl.w:ptcp.w:call-paraphase-46.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for f8inv22 for sample m84036_250809_035451_s4.bc2143 at 2025-09-15 20:27:25.442597...
2025-09-15 20:27:43.479 wdl.w:ptcp.t:call-tar_outputs-47.slurm_singularity INFO srun: job 51798234 has been allocated resources
2025-09-15 20:27:43.479 wdl.w:ptcp.t:call-tar_outputs-47.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:27:43.507 wdl.w:ptcp.t:call-tar_outputs-47 INFO output :: name: "sample_tarball", value: "m84036_250809_035451_s4.bc2144.tar"
2025-09-15 20:27:43.564 wdl.w:ptcp.t:call-tar_outputs-47 NOTICE done
2025-09-15 20:27:43.569 wdl.w:ptcp NOTICE finish :: job: "call-tar_outputs-47"
2025-09-15 20:27:43.569 wdl.w:ptcp INFO output :: job: "call-tar_outputs-47", values: {"sample_tarball": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-47/out/m84036_250809_035451_s4.bc2144.tar"}
2025-09-15 20:27:43.893 wdl.w:ptcp.w:call-paraphase-91.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for f8inv1 for sample m84036_250809_035451_s4.bc2188 at 2025-09-15 20:27:40.772865...
2025-09-15 20:27:44.313 wdl.w:ptcp.w:call-paraphase-71.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for f8inv1 for sample m84036_250809_035451_s4.bc2168 at 2025-09-15 20:27:04.315072...
2025-09-15 20:27:44.314 wdl.w:ptcp.w:call-paraphase-71.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for f8inv1 for sample m84036_250809_035451_s4.bc2168 at 2025-09-15 20:27:10.169608...
2025-09-15 20:27:44.314 wdl.w:ptcp.w:call-paraphase-71.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for f8inv1 for sample m84036_250809_035451_s4.bc2168 at 2025-09-15 20:27:10.529300...
2025-09-15 20:27:44.427 wdl.w:ptcp.w:call-paraphase-75.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for f8inv1 for sample m84036_250809_035451_s4.bc2172 at 2025-09-15 20:27:39.567051...
2025-09-15 20:27:45.484 wdl.w:ptcp.w:call-paraphase-46.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for f8inv22 for sample m84036_250809_035451_s4.bc2143 at 2025-09-15 20:27:26.559812...
2025-09-15 20:27:45.484 wdl.w:ptcp.w:call-paraphase-46.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for f8inv22 for sample m84036_250809_035451_s4.bc2143 at 2025-09-15 20:27:30.607970...
2025-09-15 20:27:45.484 wdl.w:ptcp.w:call-paraphase-46.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for f8inv22 for sample m84036_250809_035451_s4.bc2143 at 2025-09-15 20:27:30.977223...
2025-09-15 20:27:45.484 wdl.w:ptcp.w:call-paraphase-46.t:call-run_paraphase.stderr VERBOSE INFO:root:Merging all bams for sample m84036_250809_035451_s4.bc2143 at 2025-09-15 20:27:43.991624...
2025-09-15 20:27:45.757 wdl.w:ptcp.w:call-paraphase-26.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for rpgr for sample m84036_250809_035451_s4.bc2123 at 2025-09-15 20:26:54.934786...
2025-09-15 20:27:45.758 wdl.w:ptcp.w:call-paraphase-26.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for rpgr for sample m84036_250809_035451_s4.bc2123 at 2025-09-15 20:26:54.935876...
2025-09-15 20:27:45.758 wdl.w:ptcp.w:call-paraphase-26.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for rpgr for sample m84036_250809_035451_s4.bc2123 at 2025-09-15 20:26:56.748906...
2025-09-15 20:27:45.758 wdl.w:ptcp.w:call-paraphase-26.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for rpgr for sample m84036_250809_035451_s4.bc2123 at 2025-09-15 20:26:57.900041...
2025-09-15 20:27:45.758 wdl.w:ptcp.w:call-paraphase-26.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for rpgr for sample m84036_250809_035451_s4.bc2123 at 2025-09-15 20:26:58.062428...
2025-09-15 20:27:47.835 wdl.w:ptcp.w:call-paraphase-46.t:call-run_paraphase INFO output :: name: "paraphase_bam", value: "m84036_250809_035451_s4.bc2143_paraphase/m84036_250809_035451_s4.bc2143.paraphase.bam"
2025-09-15 20:27:47.838 wdl.w:ptcp.w:call-paraphase-46.t:call-run_paraphase INFO output :: name: "paraphase_bam_bai", value: "m84036_250809_035451_s4.bc2143_paraphase/m84036_250809_035451_s4.bc2143.paraphase.bam.bai"
2025-09-15 20:27:47.839 wdl.w:ptcp.w:call-paraphase-46.t:call-run_paraphase INFO output :: name: "paraphase_json", value: "m84036_250809_035451_s4.bc2143_paraphase/m84036_250809_035451_s4.bc2143.paraphase.json"
2025-09-15 20:27:47.843 wdl.w:ptcp.w:call-paraphase-46.t:call-run_paraphase INFO output :: name: "paraphase_vcfs", value: ["/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2143_paraphase/m84036_250809_035451_s4.bc2143_paraphase_vcfs/m84036_250809_035451_s4.bc2143_cyp21.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2143_paraphase/m84036_250809_035451_s4.bc2143_paraphase_vcfs/m84036_250809_035451_s4.bc2143_f8inv1.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2143_paraphase/m84036_250809_035451_s4.bc2143_paraphase_vcfs/m84036_250809_035451_s4.bc2143_f8inv22.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2143_paraphase/m84036_250809_035451_s4.bc2143_paraphase_vcfs/m84036_250809_035451_s4.bc2143_gba.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2143_paraphase/m84036_250809_035451_s4.bc2143_paraphase_vcfs/m84036_250809_035451_s4.bc2143_hba.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2143_paraphase/m84036_250809_035451_s4.bc2143_paraphase_vcfs/m84036_250809_035451_s4.bc2143_hbb.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2143_paraphase/m84036_250809_035451_s4.bc2143_paraphase_vcfs/m84036_250809_035451_s4.bc2143_rpgr.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2143_paraphase/m84036_250809_035451_s4.bc2143_paraphase_vcfs/m84036_250809_035451_s4.bc2143_smn1.vcf"]
2025-09-15 20:27:47.846 wdl.w:ptcp.w:call-paraphase-46.t:call-run_paraphase INFO output :: name: "havanno_json", value: "m84036_250809_035451_s4.bc2143.havanno.json"
2025-09-15 20:27:47.995 wdl.w:ptcp.w:call-paraphase-46.t:call-run_paraphase NOTICE done
2025-09-15 20:27:48.002 wdl.w:ptcp.w:call-paraphase-46 NOTICE finish :: job: "call-run_paraphase"
2025-09-15 20:27:48.002 wdl.w:ptcp.w:call-paraphase-46 INFO output :: job: "call-run_paraphase", values: {"havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-46/call-run_paraphase/out/m84036_250809_035451_s4.bc2143.havanno.json", "paraphase_vcfs": ["/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-46/call-run_paraphase/out/m84036_250809_035451_s4.bc2143_paraphase/m84036_250809_035451_s4.bc2143_paraphase_vcfs/m84036_250809_035451_s4.bc2143_cyp21.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-46/call-run_paraphase/out/m84036_250809_035451_s4.bc2143_paraphase/m84036_250809_035451_s4.bc2143_paraphase_vcfs/m84036_250809_035451_s4.bc2143_f8inv1.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-46/call-run_paraphase/out/m84036_250809_035451_s4.bc2143_paraphase/m84036_250809_035451_s4.bc2143_paraphase_vcfs/m84036_250809_035451_s4.bc2143_f8inv22.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-46/call-run_paraphase/out/m84036_250809_035451_s4.bc2143_paraphase/m84036_250809_035451_s4.bc2143_paraphase_vcfs/m84036_250809_035451_s4.bc2143_gba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-46/call-run_paraphase/out/m84036_250809_035451_s4.bc2143_paraphase/m84036_250809_035451_s4.bc2143_paraphase_vcfs/m84036_250809_035451_s4.bc2143_hba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-46/call-run_paraphase/out/m84036_250809_035451_s4.bc2143_paraphase/m84036_250809_035451_s4.bc2143_paraphase_vcfs/m84036_250809_035451_s4.bc2143_hbb.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-46/call-run_paraphase/out/m84036_250809_035451_s4.bc2143_paraphase/m84036_250809_035451_s4.bc2143_paraphase_vcfs/m84036_250809_035451_s4.bc2143_rpgr.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-46/call-run_paraphase/out/m84036_250809_035451_s4.bc2143_paraphase/m84036_250809_035451_s4.bc2143_paraphase_vcfs/m84036_250809_035451_s4.bc2143_smn1.vcf"], "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-46/call-run_paraphase/out/m84036_250809_035451_s4.bc2143_paraphase/m84036_250809_035451_s4.bc2143.paraphase.json", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-46/call-run_paraphase/out/m84036_250809_035451_s4.bc2143_paraphase/m84036_250809_035451_s4.bc2143.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-46/call-run_paraphase/out/m84036_250809_035451_s4.bc2143_paraphase/m84036_250809_035451_s4.bc2143.paraphase.bam"}
2025-09-15 20:27:48.003 wdl.w:ptcp.w:call-paraphase-46 NOTICE ready :: job: "call-call_f8", callee: "call_f8"
2025-09-15 20:27:48.003 wdl.w:ptcp.w:call-paraphase-46 INFO input :: job: "call-call_f8", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "out_prefix": "m84036_250809_035451_s4.bc2143", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-46/call-run_paraphase/out/m84036_250809_035451_s4.bc2143_paraphase/m84036_250809_035451_s4.bc2143.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-46/call-run_paraphase/out/m84036_250809_035451_s4.bc2143_paraphase/m84036_250809_035451_s4.bc2143.paraphase.bam", "sex": "F"}
2025-09-15 20:27:48.003 wdl.w:ptcp.w:call-paraphase-46 INFO visit :: node: "output-havanno_json", values: {"havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-46/call-run_paraphase/out/m84036_250809_035451_s4.bc2143.havanno.json"}
2025-09-15 20:27:48.003 wdl.w:ptcp.w:call-paraphase-46 INFO visit :: node: "output-paraphase_bam", values: {"paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-46/call-run_paraphase/out/m84036_250809_035451_s4.bc2143_paraphase/m84036_250809_035451_s4.bc2143.paraphase.bam"}
2025-09-15 20:27:48.003 wdl.w:ptcp.w:call-paraphase-46 INFO visit :: node: "output-paraphase_bam_bai", values: {"paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-46/call-run_paraphase/out/m84036_250809_035451_s4.bc2143_paraphase/m84036_250809_035451_s4.bc2143.paraphase.bam.bai"}
2025-09-15 20:27:48.004 wdl.w:ptcp.w:call-paraphase-46 INFO visit :: node: "output-paraphase_json", values: {"paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-46/call-run_paraphase/out/m84036_250809_035451_s4.bc2143_paraphase/m84036_250809_035451_s4.bc2143.paraphase.json"}
2025-09-15 20:27:48.004 wdl.w:ptcp.w:call-paraphase-46 INFO visit :: node: "output-paraphase_vcfs", values: {"paraphase_vcfs": ["/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-46/call-run_paraphase/out/m84036_250809_035451_s4.bc2143_paraphase/m84036_250809_035451_s4.bc2143_paraphase_vcfs/m84036_250809_035451_s4.bc2143_cyp21.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-46/call-run_paraphase/out/m84036_250809_035451_s4.bc2143_paraphase/m84036_250809_035451_s4.bc2143_paraphase_vcfs/m84036_250809_035451_s4.bc2143_f8inv1.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-46/call-run_paraphase/out/m84036_250809_035451_s4.bc2143_paraphase/m84036_250809_035451_s4.bc2143_paraphase_vcfs/m84036_250809_035451_s4.bc2143_f8inv22.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-46/call-run_paraphase/out/m84036_250809_035451_s4.bc2143_paraphase/m84036_250809_035451_s4.bc2143_paraphase_vcfs/m84036_250809_035451_s4.bc2143_gba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-46/call-run_paraphase/out/m84036_250809_035451_s4.bc2143_paraphase/m84036_250809_035451_s4.bc2143_paraphase_vcfs/m84036_250809_035451_s4.bc2143_hba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-46/call-run_paraphase/out/m84036_250809_035451_s4.bc2143_paraphase/m84036_250809_035451_s4.bc2143_paraphase_vcfs/m84036_250809_035451_s4.bc2143_hbb.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-46/call-run_paraphase/out/m84036_250809_035451_s4.bc2143_paraphase/m84036_250809_035451_s4.bc2143_paraphase_vcfs/m84036_250809_035451_s4.bc2143_rpgr.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-46/call-run_paraphase/out/m84036_250809_035451_s4.bc2143_paraphase/m84036_250809_035451_s4.bc2143_paraphase_vcfs/m84036_250809_035451_s4.bc2143_smn1.vcf"]}
2025-09-15 20:27:48.008 wdl.w:ptcp.w:call-paraphase-46.t:call-call_f8 NOTICE task setup :: name: "call_f8", source: "./paraphase.wdl", line: 232, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-46/call-call_f8", thread: 140608203109952
2025-09-15 20:27:48.023 wdl.w:ptcp.w:call-paraphase-46.t:call-call_f8 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:27:48.023 wdl.w:ptcp.w:call-paraphase-46.t:call-call_f8 INFO input :: name: "genome_version", value: "38"
2025-09-15 20:27:48.024 wdl.w:ptcp.w:call-paraphase-46.t:call-call_f8 INFO input :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2143"
2025-09-15 20:27:48.024 wdl.w:ptcp.w:call-paraphase-46.t:call-call_f8 INFO input :: name: "paraphase_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2143.paraphase.bam.bai"
2025-09-15 20:27:48.024 wdl.w:ptcp.w:call-paraphase-46.t:call-call_f8 INFO input :: name: "paraphase_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2143.paraphase.bam"
2025-09-15 20:27:48.024 wdl.w:ptcp.w:call-paraphase-46.t:call-call_f8 INFO input :: name: "sex", value: "F"
2025-09-15 20:27:48.024 wdl.w:ptcp.w:call-paraphase-46.t:call-call_f8 INFO eval :: name: "threads", value: 1
2025-09-15 20:27:48.024 wdl.w:ptcp.w:call-paraphase-46.t:call-call_f8 INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:27:48.024 wdl.w:ptcp.w:call-paraphase-46.t:call-call_f8 INFO eval :: name: "disk_size", value: 11
2025-09-15 20:27:48.024 wdl.w:ptcp.w:call-paraphase-46.t:call-call_f8 INFO eval :: name: "sample_sex", value: "F"
2025-09-15 20:27:48.025 wdl.w:ptcp.w:call-paraphase-46.t:call-call_f8 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:27:48.025 wdl.w:ptcp.w:call-paraphase-46.t:call-call_f8 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:27:48.025 wdl.w:ptcp.w:call-paraphase-46.t:call-call_f8 INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:27:48.025 wdl.w:ptcp.w:call-paraphase-46.t:call-call_f8 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:27:48.060 wdl.w:ptcp.w:call-paraphase-46.t:call-call_f8 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 8, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-46/call-call_f8/_singularity_tmpdir_wee6d8ft"
2025-09-15 20:27:48.060 wdl.w:ptcp.w:call-paraphase-46.t:call-call_f8 INFO Slurm invocation: srun --job-name call-call_f8 --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-46/call-call_f8/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-46/call-call_f8/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-46/call-call_f8/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-46/call-call_f8/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-46/call-run_paraphase/out/m84036_250809_035451_s4.bc2143_paraphase/m84036_250809_035451_s4.bc2143.paraphase.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2143.paraphase.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-46/call-run_paraphase/out/m84036_250809_035451_s4.bc2143_paraphase/m84036_250809_035451_s4.bc2143.paraphase.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2143.paraphase.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-46/call-call_f8/_singularity_tmpdir_wee6d8ft/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-46/call-call_f8/_singularity_tmpdir_wee6d8ft/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:27:48.067 wdl.w:ptcp.w:call-paraphase-46.t:call-call_f8 NOTICE slurm_singularity run :: pid: 1208541, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-46/call-call_f8/slurm_singularity.log.txt"
2025-09-15 20:27:49.075 wdl.w:ptcp.w:call-paraphase-46.t:call-call_f8.slurm_singularity INFO srun: job 51798235 queued and waiting for resources
2025-09-15 20:27:49.075 wdl.w:ptcp.w:call-paraphase-46.t:call-call_f8.slurm_singularity INFO srun: job 51798235 has been allocated resources
2025-09-15 20:27:49.075 wdl.w:ptcp.w:call-paraphase-46.t:call-call_f8.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:27:49.383 wdl.w:ptcp.w:call-paraphase-14.t:call-run_paraphase INFO output :: name: "paraphase_bam", value: "m84036_250809_035451_s4.bc2111_paraphase/m84036_250809_035451_s4.bc2111.paraphase.bam"
2025-09-15 20:27:49.387 wdl.w:ptcp.w:call-paraphase-14.t:call-run_paraphase INFO output :: name: "paraphase_bam_bai", value: "m84036_250809_035451_s4.bc2111_paraphase/m84036_250809_035451_s4.bc2111.paraphase.bam.bai"
2025-09-15 20:27:49.388 wdl.w:ptcp.w:call-paraphase-14.t:call-run_paraphase INFO output :: name: "paraphase_json", value: "m84036_250809_035451_s4.bc2111_paraphase/m84036_250809_035451_s4.bc2111.paraphase.json"
2025-09-15 20:27:49.393 wdl.w:ptcp.w:call-paraphase-14.t:call-run_paraphase INFO output :: name: "paraphase_vcfs", value: ["/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2111_paraphase/m84036_250809_035451_s4.bc2111_paraphase_vcfs/m84036_250809_035451_s4.bc2111_cyp21.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2111_paraphase/m84036_250809_035451_s4.bc2111_paraphase_vcfs/m84036_250809_035451_s4.bc2111_f8inv1.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2111_paraphase/m84036_250809_035451_s4.bc2111_paraphase_vcfs/m84036_250809_035451_s4.bc2111_f8inv22.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2111_paraphase/m84036_250809_035451_s4.bc2111_paraphase_vcfs/m84036_250809_035451_s4.bc2111_gba.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2111_paraphase/m84036_250809_035451_s4.bc2111_paraphase_vcfs/m84036_250809_035451_s4.bc2111_hba.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2111_paraphase/m84036_250809_035451_s4.bc2111_paraphase_vcfs/m84036_250809_035451_s4.bc2111_hbb.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2111_paraphase/m84036_250809_035451_s4.bc2111_paraphase_vcfs/m84036_250809_035451_s4.bc2111_rpgr.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2111_paraphase/m84036_250809_035451_s4.bc2111_paraphase_vcfs/m84036_250809_035451_s4.bc2111_smn1.vcf"]
2025-09-15 20:27:49.396 wdl.w:ptcp.w:call-paraphase-14.t:call-run_paraphase INFO output :: name: "havanno_json", value: "m84036_250809_035451_s4.bc2111.havanno.json"
2025-09-15 20:27:49.546 wdl.w:ptcp.w:call-paraphase-14.t:call-run_paraphase NOTICE done
2025-09-15 20:27:49.552 wdl.w:ptcp.w:call-paraphase-14 NOTICE finish :: job: "call-run_paraphase"
2025-09-15 20:27:49.552 wdl.w:ptcp.w:call-paraphase-14 INFO output :: job: "call-run_paraphase", values: {"havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-14/call-run_paraphase/out/m84036_250809_035451_s4.bc2111.havanno.json", "paraphase_vcfs": ["/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-14/call-run_paraphase/out/m84036_250809_035451_s4.bc2111_paraphase/m84036_250809_035451_s4.bc2111_paraphase_vcfs/m84036_250809_035451_s4.bc2111_cyp21.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-14/call-run_paraphase/out/m84036_250809_035451_s4.bc2111_paraphase/m84036_250809_035451_s4.bc2111_paraphase_vcfs/m84036_250809_035451_s4.bc2111_f8inv1.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-14/call-run_paraphase/out/m84036_250809_035451_s4.bc2111_paraphase/m84036_250809_035451_s4.bc2111_paraphase_vcfs/m84036_250809_035451_s4.bc2111_f8inv22.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-14/call-run_paraphase/out/m84036_250809_035451_s4.bc2111_paraphase/m84036_250809_035451_s4.bc2111_paraphase_vcfs/m84036_250809_035451_s4.bc2111_gba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-14/call-run_paraphase/out/m84036_250809_035451_s4.bc2111_paraphase/m84036_250809_035451_s4.bc2111_paraphase_vcfs/m84036_250809_035451_s4.bc2111_hba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-14/call-run_paraphase/out/m84036_250809_035451_s4.bc2111_paraphase/m84036_250809_035451_s4.bc2111_paraphase_vcfs/m84036_250809_035451_s4.bc2111_hbb.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-14/call-run_paraphase/out/m84036_250809_035451_s4.bc2111_paraphase/m84036_250809_035451_s4.bc2111_paraphase_vcfs/m84036_250809_035451_s4.bc2111_rpgr.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-14/call-run_paraphase/out/m84036_250809_035451_s4.bc2111_paraphase/m84036_250809_035451_s4.bc2111_paraphase_vcfs/m84036_250809_035451_s4.bc2111_smn1.vcf"], "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-14/call-run_paraphase/out/m84036_250809_035451_s4.bc2111_paraphase/m84036_250809_035451_s4.bc2111.paraphase.json", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-14/call-run_paraphase/out/m84036_250809_035451_s4.bc2111_paraphase/m84036_250809_035451_s4.bc2111.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-14/call-run_paraphase/out/m84036_250809_035451_s4.bc2111_paraphase/m84036_250809_035451_s4.bc2111.paraphase.bam"}
2025-09-15 20:27:49.553 wdl.w:ptcp.w:call-paraphase-14 NOTICE ready :: job: "call-call_f8", callee: "call_f8"
2025-09-15 20:27:49.553 wdl.w:ptcp.w:call-paraphase-14 INFO input :: job: "call-call_f8", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "out_prefix": "m84036_250809_035451_s4.bc2111", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-14/call-run_paraphase/out/m84036_250809_035451_s4.bc2111_paraphase/m84036_250809_035451_s4.bc2111.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-14/call-run_paraphase/out/m84036_250809_035451_s4.bc2111_paraphase/m84036_250809_035451_s4.bc2111.paraphase.bam", "sex": "F"}
2025-09-15 20:27:49.553 wdl.w:ptcp.w:call-paraphase-14 INFO visit :: node: "output-havanno_json", values: {"havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-14/call-run_paraphase/out/m84036_250809_035451_s4.bc2111.havanno.json"}
2025-09-15 20:27:49.553 wdl.w:ptcp.w:call-paraphase-14 INFO visit :: node: "output-paraphase_bam", values: {"paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-14/call-run_paraphase/out/m84036_250809_035451_s4.bc2111_paraphase/m84036_250809_035451_s4.bc2111.paraphase.bam"}
2025-09-15 20:27:49.553 wdl.w:ptcp.w:call-paraphase-14 INFO visit :: node: "output-paraphase_bam_bai", values: {"paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-14/call-run_paraphase/out/m84036_250809_035451_s4.bc2111_paraphase/m84036_250809_035451_s4.bc2111.paraphase.bam.bai"}
2025-09-15 20:27:49.554 wdl.w:ptcp.w:call-paraphase-14 INFO visit :: node: "output-paraphase_json", values: {"paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-14/call-run_paraphase/out/m84036_250809_035451_s4.bc2111_paraphase/m84036_250809_035451_s4.bc2111.paraphase.json"}
2025-09-15 20:27:49.554 wdl.w:ptcp.w:call-paraphase-14 INFO visit :: node: "output-paraphase_vcfs", values: {"paraphase_vcfs": ["/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-14/call-run_paraphase/out/m84036_250809_035451_s4.bc2111_paraphase/m84036_250809_035451_s4.bc2111_paraphase_vcfs/m84036_250809_035451_s4.bc2111_cyp21.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-14/call-run_paraphase/out/m84036_250809_035451_s4.bc2111_paraphase/m84036_250809_035451_s4.bc2111_paraphase_vcfs/m84036_250809_035451_s4.bc2111_f8inv1.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-14/call-run_paraphase/out/m84036_250809_035451_s4.bc2111_paraphase/m84036_250809_035451_s4.bc2111_paraphase_vcfs/m84036_250809_035451_s4.bc2111_f8inv22.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-14/call-run_paraphase/out/m84036_250809_035451_s4.bc2111_paraphase/m84036_250809_035451_s4.bc2111_paraphase_vcfs/m84036_250809_035451_s4.bc2111_gba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-14/call-run_paraphase/out/m84036_250809_035451_s4.bc2111_paraphase/m84036_250809_035451_s4.bc2111_paraphase_vcfs/m84036_250809_035451_s4.bc2111_hba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-14/call-run_paraphase/out/m84036_250809_035451_s4.bc2111_paraphase/m84036_250809_035451_s4.bc2111_paraphase_vcfs/m84036_250809_035451_s4.bc2111_hbb.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-14/call-run_paraphase/out/m84036_250809_035451_s4.bc2111_paraphase/m84036_250809_035451_s4.bc2111_paraphase_vcfs/m84036_250809_035451_s4.bc2111_rpgr.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-14/call-run_paraphase/out/m84036_250809_035451_s4.bc2111_paraphase/m84036_250809_035451_s4.bc2111_paraphase_vcfs/m84036_250809_035451_s4.bc2111_smn1.vcf"]}
2025-09-15 20:27:49.559 wdl.w:ptcp.w:call-paraphase-14.t:call-call_f8 NOTICE task setup :: name: "call_f8", source: "./paraphase.wdl", line: 232, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-14/call-call_f8", thread: 140607649453632
2025-09-15 20:27:49.574 wdl.w:ptcp.w:call-paraphase-14.t:call-call_f8 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:27:49.574 wdl.w:ptcp.w:call-paraphase-14.t:call-call_f8 INFO input :: name: "genome_version", value: "38"
2025-09-15 20:27:49.575 wdl.w:ptcp.w:call-paraphase-14.t:call-call_f8 INFO input :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2111"
2025-09-15 20:27:49.575 wdl.w:ptcp.w:call-paraphase-14.t:call-call_f8 INFO input :: name: "paraphase_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2111.paraphase.bam.bai"
2025-09-15 20:27:49.575 wdl.w:ptcp.w:call-paraphase-14.t:call-call_f8 INFO input :: name: "paraphase_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2111.paraphase.bam"
2025-09-15 20:27:49.575 wdl.w:ptcp.w:call-paraphase-14.t:call-call_f8 INFO input :: name: "sex", value: "F"
2025-09-15 20:27:49.575 wdl.w:ptcp.w:call-paraphase-14.t:call-call_f8 INFO eval :: name: "threads", value: 1
2025-09-15 20:27:49.575 wdl.w:ptcp.w:call-paraphase-14.t:call-call_f8 INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:27:49.575 wdl.w:ptcp.w:call-paraphase-14.t:call-call_f8 INFO eval :: name: "disk_size", value: 11
2025-09-15 20:27:49.575 wdl.w:ptcp.w:call-paraphase-14.t:call-call_f8 INFO eval :: name: "sample_sex", value: "F"
2025-09-15 20:27:49.576 wdl.w:ptcp.w:call-paraphase-14.t:call-call_f8 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:27:49.576 wdl.w:ptcp.w:call-paraphase-14.t:call-call_f8 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:27:49.576 wdl.w:ptcp.w:call-paraphase-14.t:call-call_f8 INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:27:49.576 wdl.w:ptcp.w:call-paraphase-14.t:call-call_f8 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:27:49.617 wdl.w:ptcp.w:call-paraphase-14.t:call-call_f8 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 8, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-14/call-call_f8/_singularity_tmpdir_9jd2ja48"
2025-09-15 20:27:49.617 wdl.w:ptcp.w:call-paraphase-14.t:call-call_f8 INFO Slurm invocation: srun --job-name call-call_f8 --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-14/call-call_f8/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-14/call-call_f8/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-14/call-call_f8/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-14/call-call_f8/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-14/call-run_paraphase/out/m84036_250809_035451_s4.bc2111_paraphase/m84036_250809_035451_s4.bc2111.paraphase.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2111.paraphase.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-14/call-run_paraphase/out/m84036_250809_035451_s4.bc2111_paraphase/m84036_250809_035451_s4.bc2111.paraphase.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2111.paraphase.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-14/call-call_f8/_singularity_tmpdir_9jd2ja48/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-14/call-call_f8/_singularity_tmpdir_9jd2ja48/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:27:49.623 wdl.w:ptcp.w:call-paraphase-14.t:call-call_f8 NOTICE slurm_singularity run :: pid: 1208550, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-14/call-call_f8/slurm_singularity.log.txt"
2025-09-15 20:27:49.773 wdl.w:ptcp.w:call-paraphase-46.t:call-call_f8 INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2143.f8inversion.vcf"
2025-09-15 20:27:49.776 wdl.w:ptcp.w:call-paraphase-46.t:call-call_f8 INFO output :: name: "json", value: "m84036_250809_035451_s4.bc2143.f8inversion.json"
2025-09-15 20:27:49.835 wdl.w:ptcp.w:call-paraphase-46.t:call-call_f8 NOTICE done
2025-09-15 20:27:49.842 wdl.w:ptcp.w:call-paraphase-46 NOTICE finish :: job: "call-call_f8"
2025-09-15 20:27:49.842 wdl.w:ptcp.w:call-paraphase-46 INFO output :: job: "call-call_f8", values: {"json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-46/call-call_f8/out/m84036_250809_035451_s4.bc2143.f8inversion.json", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-46/call-call_f8/out/m84036_250809_035451_s4.bc2143.f8inversion.vcf"}
2025-09-15 20:27:49.842 wdl.w:ptcp.w:call-paraphase-46 INFO visit :: node: "output-f8_json", values: {"f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-46/call-call_f8/out/m84036_250809_035451_s4.bc2143.f8inversion.json"}
2025-09-15 20:27:49.843 wdl.w:ptcp.w:call-paraphase-46 INFO visit :: node: "output-f8_vcf", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-46/call-call_f8/out/m84036_250809_035451_s4.bc2143.f8inversion.vcf"}
2025-09-15 20:27:49.843 wdl.w:ptcp.w:call-paraphase-46 INFO visit :: node: "outputs", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-46/call-call_f8/out/m84036_250809_035451_s4.bc2143.f8inversion.vcf", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-46/call-run_paraphase/out/m84036_250809_035451_s4.bc2143_paraphase/m84036_250809_035451_s4.bc2143.paraphase.json", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-46/call-run_paraphase/out/m84036_250809_035451_s4.bc2143_paraphase/m84036_250809_035451_s4.bc2143.paraphase.bam", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-46/call-run_paraphase/out/m84036_250809_035451_s4.bc2143_paraphase/m84036_250809_035451_s4.bc2143.paraphase.bam.bai", "paraphase_vcfs": ["/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-46/call-run_paraphase/out/m84036_250809_035451_s4.bc2143_paraphase/m84036_250809_035451_s4.bc2143_paraphase_vcfs/m84036_250809_035451_s4.bc2143_cyp21.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-46/call-run_paraphase/out/m84036_250809_035451_s4.bc2143_paraphase/m84036_250809_035451_s4.bc2143_paraphase_vcfs/m84036_250809_035451_s4.bc2143_f8inv1.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-46/call-run_paraphase/out/m84036_250809_035451_s4.bc2143_paraphase/m84036_250809_035451_s4.bc2143_paraphase_vcfs/m84036_250809_035451_s4.bc2143_f8inv22.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-46/call-run_paraphase/out/m84036_250809_035451_s4.bc2143_paraphase/m84036_250809_035451_s4.bc2143_paraphase_vcfs/m84036_250809_035451_s4.bc2143_gba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-46/call-run_paraphase/out/m84036_250809_035451_s4.bc2143_paraphase/m84036_250809_035451_s4.bc2143_paraphase_vcfs/m84036_250809_035451_s4.bc2143_hba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-46/call-run_paraphase/out/m84036_250809_035451_s4.bc2143_paraphase/m84036_250809_035451_s4.bc2143_paraphase_vcfs/m84036_250809_035451_s4.bc2143_hbb.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-46/call-run_paraphase/out/m84036_250809_035451_s4.bc2143_paraphase/m84036_250809_035451_s4.bc2143_paraphase_vcfs/m84036_250809_035451_s4.bc2143_rpgr.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-46/call-run_paraphase/out/m84036_250809_035451_s4.bc2143_paraphase/m84036_250809_035451_s4.bc2143_paraphase_vcfs/m84036_250809_035451_s4.bc2143_smn1.vcf"], "havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-46/call-run_paraphase/out/m84036_250809_035451_s4.bc2143.havanno.json", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-46/call-call_f8/out/m84036_250809_035451_s4.bc2143.f8inversion.json"}
2025-09-15 20:27:49.947 wdl.w:ptcp.w:call-paraphase-46 NOTICE done
2025-09-15 20:27:49.952 wdl.w:ptcp NOTICE finish :: job: "call-paraphase-46"
2025-09-15 20:27:49.953 wdl.w:ptcp INFO output :: job: "call-paraphase-46", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-46/out/m84036_250809_035451_s4.bc2143.f8inversion.vcf", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-46/out/m84036_250809_035451_s4.bc2143_paraphase/m84036_250809_035451_s4.bc2143.paraphase.json", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-46/out/m84036_250809_035451_s4.bc2143_paraphase/m84036_250809_035451_s4.bc2143.paraphase.bam", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-46/out/m84036_250809_035451_s4.bc2143_paraphase/m84036_250809_035451_s4.bc2143.paraphase.bam.bai", "paraphase_vcfs": ["/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-46/out/m84036_250809_035451_s4.bc2143_paraphase/m84036_250809_035451_s4.bc2143_paraphase_vcfs/m84036_250809_035451_s4.bc2143_cyp21.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-46/out/m84036_250809_035451_s4.bc2143_paraphase/m84036_250809_035451_s4.bc2143_paraphase_vcfs/m84036_250809_035451_s4.bc2143_f8inv1.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-46/out/m84036_250809_035451_s4.bc2143_paraphase/m84036_250809_035451_s4.bc2143_paraphase_vcfs/m84036_250809_035451_s4.bc2143_f8inv22.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-46/out/m84036_250809_035451_s4.bc2143_paraphase/m84036_250809_035451_s4.bc2143_paraphase_vcfs/m84036_250809_035451_s4.bc2143_gba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-46/out/m84036_250809_035451_s4.bc2143_paraphase/m84036_250809_035451_s4.bc2143_paraphase_vcfs/m84036_250809_035451_s4.bc2143_hba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-46/out/m84036_250809_035451_s4.bc2143_paraphase/m84036_250809_035451_s4.bc2143_paraphase_vcfs/m84036_250809_035451_s4.bc2143_hbb.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-46/out/m84036_250809_035451_s4.bc2143_paraphase/m84036_250809_035451_s4.bc2143_paraphase_vcfs/m84036_250809_035451_s4.bc2143_rpgr.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-46/out/m84036_250809_035451_s4.bc2143_paraphase/m84036_250809_035451_s4.bc2143_paraphase_vcfs/m84036_250809_035451_s4.bc2143_smn1.vcf"], "havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-46/out/m84036_250809_035451_s4.bc2143.havanno.json", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-46/out/m84036_250809_035451_s4.bc2143.f8inversion.json"}
2025-09-15 20:27:49.953 wdl.w:ptcp NOTICE ready :: job: "call-tar_outputs-46", callee: "tar_outputs"
2025-09-15 20:27:49.954 wdl.w:ptcp INFO input :: job: "call-tar_outputs-46", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "sawfish_vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-46/out/m84036_250809_035451_s4.bc2143_sawfish/m84036_250809_035451_s4.bc2143.sv.vcf.gz.tbi", "sawfish_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-46/out/m84036_250809_035451_s4.bc2143_sawfish/m84036_250809_035451_s4.bc2143.sv.vcf.gz", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-46/out/m84036_250809_035451_s4.bc2143.f8inversion.json", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-46/out/m84036_250809_035451_s4.bc2143_paraphase/m84036_250809_035451_s4.bc2143.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-46/out/m84036_250809_035451_s4.bc2143_paraphase/m84036_250809_035451_s4.bc2143.paraphase.bam", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-46/out/m84036_250809_035451_s4.bc2143_paraphase/m84036_250809_035451_s4.bc2143.paraphase.json", "trgt_spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-46/out/m84036_250809_035451_s4.bc2143.trgt.sorted.spanning.bam.bai", "trgt_spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-46/out/m84036_250809_035451_s4.bc2143.trgt.sorted.spanning.bam", "trgt_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-46/out/m84036_250809_035451_s4.bc2143.trgt.vcf", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-46/out/m84036_250809_035451_s4.bc2143.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-46/out/m84036_250809_035451_s4.bc2143.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2143"}
2025-09-15 20:27:49.959 wdl.w:ptcp.t:call-tar_outputs-46 NOTICE task setup :: name: "tar_outputs", source: "./common.wdl", line: 279, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-46", thread: 140608731588160
2025-09-15 20:27:49.986 wdl.w:ptcp.t:call-tar_outputs-46 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:27:49.986 wdl.w:ptcp.t:call-tar_outputs-46 INFO input :: name: "sawfish_vcf_tbi", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2143.sv.vcf.gz.tbi"
2025-09-15 20:27:49.986 wdl.w:ptcp.t:call-tar_outputs-46 INFO input :: name: "sawfish_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2143.sv.vcf.gz"
2025-09-15 20:27:49.986 wdl.w:ptcp.t:call-tar_outputs-46 INFO input :: name: "f8_json", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2143.f8inversion.json"
2025-09-15 20:27:49.986 wdl.w:ptcp.t:call-tar_outputs-46 INFO input :: name: "paraphase_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2143.paraphase.bam.bai"
2025-09-15 20:27:49.986 wdl.w:ptcp.t:call-tar_outputs-46 INFO input :: name: "paraphase_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2143.paraphase.bam"
2025-09-15 20:27:49.986 wdl.w:ptcp.t:call-tar_outputs-46 INFO input :: name: "paraphase_json", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2143.paraphase.json"
2025-09-15 20:27:49.986 wdl.w:ptcp.t:call-tar_outputs-46 INFO input :: name: "trgt_spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2143.trgt.sorted.spanning.bam.bai"
2025-09-15 20:27:49.986 wdl.w:ptcp.t:call-tar_outputs-46 INFO input :: name: "trgt_spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2143.trgt.sorted.spanning.bam"
2025-09-15 20:27:49.986 wdl.w:ptcp.t:call-tar_outputs-46 INFO input :: name: "trgt_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2143.trgt.vcf"
2025-09-15 20:27:49.986 wdl.w:ptcp.t:call-tar_outputs-46 INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2143.mapped.bam.bai"
2025-09-15 20:27:49.986 wdl.w:ptcp.t:call-tar_outputs-46 INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2143.mapped.bam"
2025-09-15 20:27:49.986 wdl.w:ptcp.t:call-tar_outputs-46 INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2143"
2025-09-15 20:27:49.987 wdl.w:ptcp.t:call-tar_outputs-46 INFO eval :: name: "threads", value: 1
2025-09-15 20:27:49.987 wdl.w:ptcp.t:call-tar_outputs-46 INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:27:49.987 wdl.w:ptcp.t:call-tar_outputs-46 INFO eval :: name: "disk_size", value: 6
2025-09-15 20:27:49.987 wdl.w:ptcp.t:call-tar_outputs-46 INFO eval :: name: "output_tarball", value: "m84036_250809_035451_s4.bc2143.tar"
2025-09-15 20:27:49.988 wdl.w:ptcp.t:call-tar_outputs-46 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:27:49.988 wdl.w:ptcp.t:call-tar_outputs-46 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:27:49.988 wdl.w:ptcp.t:call-tar_outputs-46 INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:27:49.988 wdl.w:ptcp.t:call-tar_outputs-46 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:27:50.064 wdl.w:ptcp.t:call-tar_outputs-46 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 17, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-46/_singularity_tmpdir_moc9jnjk"
2025-09-15 20:27:50.065 wdl.w:ptcp.t:call-tar_outputs-46 INFO Slurm invocation: srun --job-name call-tar_outputs-46 --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-46/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-46/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-46/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-46/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-46/out/m84036_250809_035451_s4.bc2143.f8inversion.json:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2143.f8inversion.json:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-46/out/m84036_250809_035451_s4.bc2143.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2143.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-46/out/m84036_250809_035451_s4.bc2143.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2143.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-46/out/m84036_250809_035451_s4.bc2143.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2143.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-46/out/m84036_250809_035451_s4.bc2143_sawfish/m84036_250809_035451_s4.bc2143.sv.vcf.gz:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2143.sv.vcf.gz:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-46/out/m84036_250809_035451_s4.bc2143_sawfish/m84036_250809_035451_s4.bc2143.sv.vcf.gz.tbi:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2143.sv.vcf.gz.tbi:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-46/out/m84036_250809_035451_s4.bc2143.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2143.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-46/out/m84036_250809_035451_s4.bc2143.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2143.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-46/out/m84036_250809_035451_s4.bc2143_paraphase/m84036_250809_035451_s4.bc2143.paraphase.json:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2143.paraphase.json:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-46/out/m84036_250809_035451_s4.bc2143_paraphase/m84036_250809_035451_s4.bc2143.paraphase.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2143.paraphase.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-46/out/m84036_250809_035451_s4.bc2143_paraphase/m84036_250809_035451_s4.bc2143.paraphase.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2143.paraphase.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-46/_singularity_tmpdir_moc9jnjk/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-46/_singularity_tmpdir_moc9jnjk/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:27:50.072 wdl.w:ptcp.t:call-tar_outputs-46 NOTICE slurm_singularity run :: pid: 1208625, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-46/slurm_singularity.log.txt"
2025-09-15 20:27:50.630 wdl.w:ptcp.w:call-paraphase-14.t:call-call_f8.slurm_singularity INFO srun: job 51798236 queued and waiting for resources
2025-09-15 20:27:50.630 wdl.w:ptcp.w:call-paraphase-14.t:call-call_f8.slurm_singularity INFO srun: job 51798236 has been allocated resources
2025-09-15 20:27:50.630 wdl.w:ptcp.w:call-paraphase-14.t:call-call_f8.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:27:50.789 wdl.w:ptcp.w:call-paraphase-14.t:call-call_f8 INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2111.f8inversion.vcf"
2025-09-15 20:27:50.792 wdl.w:ptcp.w:call-paraphase-14.t:call-call_f8 INFO output :: name: "json", value: "m84036_250809_035451_s4.bc2111.f8inversion.json"
2025-09-15 20:27:50.849 wdl.w:ptcp.w:call-paraphase-14.t:call-call_f8 NOTICE done
2025-09-15 20:27:50.854 wdl.w:ptcp.w:call-paraphase-14 NOTICE finish :: job: "call-call_f8"
2025-09-15 20:27:50.854 wdl.w:ptcp.w:call-paraphase-14 INFO output :: job: "call-call_f8", values: {"json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-14/call-call_f8/out/m84036_250809_035451_s4.bc2111.f8inversion.json", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-14/call-call_f8/out/m84036_250809_035451_s4.bc2111.f8inversion.vcf"}
2025-09-15 20:27:50.855 wdl.w:ptcp.w:call-paraphase-14 INFO visit :: node: "output-f8_json", values: {"f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-14/call-call_f8/out/m84036_250809_035451_s4.bc2111.f8inversion.json"}
2025-09-15 20:27:50.855 wdl.w:ptcp.w:call-paraphase-14 INFO visit :: node: "output-f8_vcf", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-14/call-call_f8/out/m84036_250809_035451_s4.bc2111.f8inversion.vcf"}
2025-09-15 20:27:50.855 wdl.w:ptcp.w:call-paraphase-14 INFO visit :: node: "outputs", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-14/call-call_f8/out/m84036_250809_035451_s4.bc2111.f8inversion.vcf", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-14/call-run_paraphase/out/m84036_250809_035451_s4.bc2111_paraphase/m84036_250809_035451_s4.bc2111.paraphase.json", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-14/call-run_paraphase/out/m84036_250809_035451_s4.bc2111_paraphase/m84036_250809_035451_s4.bc2111.paraphase.bam", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-14/call-run_paraphase/out/m84036_250809_035451_s4.bc2111_paraphase/m84036_250809_035451_s4.bc2111.paraphase.bam.bai", "paraphase_vcfs": ["/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-14/call-run_paraphase/out/m84036_250809_035451_s4.bc2111_paraphase/m84036_250809_035451_s4.bc2111_paraphase_vcfs/m84036_250809_035451_s4.bc2111_cyp21.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-14/call-run_paraphase/out/m84036_250809_035451_s4.bc2111_paraphase/m84036_250809_035451_s4.bc2111_paraphase_vcfs/m84036_250809_035451_s4.bc2111_f8inv1.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-14/call-run_paraphase/out/m84036_250809_035451_s4.bc2111_paraphase/m84036_250809_035451_s4.bc2111_paraphase_vcfs/m84036_250809_035451_s4.bc2111_f8inv22.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-14/call-run_paraphase/out/m84036_250809_035451_s4.bc2111_paraphase/m84036_250809_035451_s4.bc2111_paraphase_vcfs/m84036_250809_035451_s4.bc2111_gba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-14/call-run_paraphase/out/m84036_250809_035451_s4.bc2111_paraphase/m84036_250809_035451_s4.bc2111_paraphase_vcfs/m84036_250809_035451_s4.bc2111_hba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-14/call-run_paraphase/out/m84036_250809_035451_s4.bc2111_paraphase/m84036_250809_035451_s4.bc2111_paraphase_vcfs/m84036_250809_035451_s4.bc2111_hbb.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-14/call-run_paraphase/out/m84036_250809_035451_s4.bc2111_paraphase/m84036_250809_035451_s4.bc2111_paraphase_vcfs/m84036_250809_035451_s4.bc2111_rpgr.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-14/call-run_paraphase/out/m84036_250809_035451_s4.bc2111_paraphase/m84036_250809_035451_s4.bc2111_paraphase_vcfs/m84036_250809_035451_s4.bc2111_smn1.vcf"], "havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-14/call-run_paraphase/out/m84036_250809_035451_s4.bc2111.havanno.json", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-14/call-call_f8/out/m84036_250809_035451_s4.bc2111.f8inversion.json"}
2025-09-15 20:27:50.983 wdl.w:ptcp.w:call-paraphase-14 NOTICE done
2025-09-15 20:27:50.989 wdl.w:ptcp NOTICE finish :: job: "call-paraphase-14"
2025-09-15 20:27:50.989 wdl.w:ptcp INFO output :: job: "call-paraphase-14", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-14/out/m84036_250809_035451_s4.bc2111.f8inversion.vcf", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-14/out/m84036_250809_035451_s4.bc2111_paraphase/m84036_250809_035451_s4.bc2111.paraphase.json", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-14/out/m84036_250809_035451_s4.bc2111_paraphase/m84036_250809_035451_s4.bc2111.paraphase.bam", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-14/out/m84036_250809_035451_s4.bc2111_paraphase/m84036_250809_035451_s4.bc2111.paraphase.bam.bai", "paraphase_vcfs": ["/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-14/out/m84036_250809_035451_s4.bc2111_paraphase/m84036_250809_035451_s4.bc2111_paraphase_vcfs/m84036_250809_035451_s4.bc2111_cyp21.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-14/out/m84036_250809_035451_s4.bc2111_paraphase/m84036_250809_035451_s4.bc2111_paraphase_vcfs/m84036_250809_035451_s4.bc2111_f8inv1.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-14/out/m84036_250809_035451_s4.bc2111_paraphase/m84036_250809_035451_s4.bc2111_paraphase_vcfs/m84036_250809_035451_s4.bc2111_f8inv22.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-14/out/m84036_250809_035451_s4.bc2111_paraphase/m84036_250809_035451_s4.bc2111_paraphase_vcfs/m84036_250809_035451_s4.bc2111_gba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-14/out/m84036_250809_035451_s4.bc2111_paraphase/m84036_250809_035451_s4.bc2111_paraphase_vcfs/m84036_250809_035451_s4.bc2111_hba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-14/out/m84036_250809_035451_s4.bc2111_paraphase/m84036_250809_035451_s4.bc2111_paraphase_vcfs/m84036_250809_035451_s4.bc2111_hbb.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-14/out/m84036_250809_035451_s4.bc2111_paraphase/m84036_250809_035451_s4.bc2111_paraphase_vcfs/m84036_250809_035451_s4.bc2111_rpgr.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-14/out/m84036_250809_035451_s4.bc2111_paraphase/m84036_250809_035451_s4.bc2111_paraphase_vcfs/m84036_250809_035451_s4.bc2111_smn1.vcf"], "havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-14/out/m84036_250809_035451_s4.bc2111.havanno.json", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-14/out/m84036_250809_035451_s4.bc2111.f8inversion.json"}
2025-09-15 20:27:50.990 wdl.w:ptcp NOTICE ready :: job: "call-tar_outputs-14", callee: "tar_outputs"
2025-09-15 20:27:50.990 wdl.w:ptcp INFO input :: job: "call-tar_outputs-14", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "sawfish_vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-14/out/m84036_250809_035451_s4.bc2111_sawfish/m84036_250809_035451_s4.bc2111.sv.vcf.gz.tbi", "sawfish_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-14/out/m84036_250809_035451_s4.bc2111_sawfish/m84036_250809_035451_s4.bc2111.sv.vcf.gz", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-14/out/m84036_250809_035451_s4.bc2111.f8inversion.json", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-14/out/m84036_250809_035451_s4.bc2111_paraphase/m84036_250809_035451_s4.bc2111.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-14/out/m84036_250809_035451_s4.bc2111_paraphase/m84036_250809_035451_s4.bc2111.paraphase.bam", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-14/out/m84036_250809_035451_s4.bc2111_paraphase/m84036_250809_035451_s4.bc2111.paraphase.json", "trgt_spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-14/out/m84036_250809_035451_s4.bc2111.trgt.sorted.spanning.bam.bai", "trgt_spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-14/out/m84036_250809_035451_s4.bc2111.trgt.sorted.spanning.bam", "trgt_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-14/out/m84036_250809_035451_s4.bc2111.trgt.vcf", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-14/out/m84036_250809_035451_s4.bc2111.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-14/out/m84036_250809_035451_s4.bc2111.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2111"}
2025-09-15 20:27:50.995 wdl.w:ptcp.t:call-tar_outputs-14 NOTICE task setup :: name: "tar_outputs", source: "./common.wdl", line: 279, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-14", thread: 140607129368128
2025-09-15 20:27:51.020 wdl.w:ptcp.t:call-tar_outputs-14 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:27:51.020 wdl.w:ptcp.t:call-tar_outputs-14 INFO input :: name: "sawfish_vcf_tbi", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2111.sv.vcf.gz.tbi"
2025-09-15 20:27:51.020 wdl.w:ptcp.t:call-tar_outputs-14 INFO input :: name: "sawfish_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2111.sv.vcf.gz"
2025-09-15 20:27:51.020 wdl.w:ptcp.t:call-tar_outputs-14 INFO input :: name: "f8_json", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2111.f8inversion.json"
2025-09-15 20:27:51.020 wdl.w:ptcp.t:call-tar_outputs-14 INFO input :: name: "paraphase_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2111.paraphase.bam.bai"
2025-09-15 20:27:51.020 wdl.w:ptcp.t:call-tar_outputs-14 INFO input :: name: "paraphase_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2111.paraphase.bam"
2025-09-15 20:27:51.020 wdl.w:ptcp.t:call-tar_outputs-14 INFO input :: name: "paraphase_json", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2111.paraphase.json"
2025-09-15 20:27:51.020 wdl.w:ptcp.t:call-tar_outputs-14 INFO input :: name: "trgt_spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2111.trgt.sorted.spanning.bam.bai"
2025-09-15 20:27:51.020 wdl.w:ptcp.t:call-tar_outputs-14 INFO input :: name: "trgt_spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2111.trgt.sorted.spanning.bam"
2025-09-15 20:27:51.021 wdl.w:ptcp.t:call-tar_outputs-14 INFO input :: name: "trgt_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2111.trgt.vcf"
2025-09-15 20:27:51.021 wdl.w:ptcp.t:call-tar_outputs-14 INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2111.mapped.bam.bai"
2025-09-15 20:27:51.021 wdl.w:ptcp.t:call-tar_outputs-14 INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2111.mapped.bam"
2025-09-15 20:27:51.021 wdl.w:ptcp.t:call-tar_outputs-14 INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2111"
2025-09-15 20:27:51.021 wdl.w:ptcp.t:call-tar_outputs-14 INFO eval :: name: "threads", value: 1
2025-09-15 20:27:51.021 wdl.w:ptcp.t:call-tar_outputs-14 INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:27:51.021 wdl.w:ptcp.t:call-tar_outputs-14 INFO eval :: name: "disk_size", value: 6
2025-09-15 20:27:51.021 wdl.w:ptcp.t:call-tar_outputs-14 INFO eval :: name: "output_tarball", value: "m84036_250809_035451_s4.bc2111.tar"
2025-09-15 20:27:51.022 wdl.w:ptcp.t:call-tar_outputs-14 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:27:51.022 wdl.w:ptcp.t:call-tar_outputs-14 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:27:51.022 wdl.w:ptcp.t:call-tar_outputs-14 INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:27:51.022 wdl.w:ptcp.t:call-tar_outputs-14 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:27:51.082 wdl.w:ptcp.t:call-tar_outputs-46.slurm_singularity INFO srun: job 51798237 queued and waiting for resources
2025-09-15 20:27:51.082 wdl.w:ptcp.t:call-tar_outputs-46.slurm_singularity INFO srun: job 51798237 has been allocated resources
2025-09-15 20:27:51.082 wdl.w:ptcp.t:call-tar_outputs-46.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:27:51.103 wdl.w:ptcp.t:call-tar_outputs-14 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 17, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-14/_singularity_tmpdir_sppdjudt"
2025-09-15 20:27:51.103 wdl.w:ptcp.t:call-tar_outputs-14 INFO Slurm invocation: srun --job-name call-tar_outputs-14 --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-14/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-14/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-14/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-14/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-14/out/m84036_250809_035451_s4.bc2111_paraphase/m84036_250809_035451_s4.bc2111.paraphase.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2111.paraphase.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-14/out/m84036_250809_035451_s4.bc2111_paraphase/m84036_250809_035451_s4.bc2111.paraphase.json:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2111.paraphase.json:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-14/out/m84036_250809_035451_s4.bc2111_paraphase/m84036_250809_035451_s4.bc2111.paraphase.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2111.paraphase.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-14/out/m84036_250809_035451_s4.bc2111.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2111.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-14/out/m84036_250809_035451_s4.bc2111.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2111.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-14/out/m84036_250809_035451_s4.bc2111.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2111.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-14/out/m84036_250809_035451_s4.bc2111.f8inversion.json:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2111.f8inversion.json:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-14/out/m84036_250809_035451_s4.bc2111.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2111.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-14/out/m84036_250809_035451_s4.bc2111.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2111.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-14/out/m84036_250809_035451_s4.bc2111_sawfish/m84036_250809_035451_s4.bc2111.sv.vcf.gz:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2111.sv.vcf.gz:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-14/out/m84036_250809_035451_s4.bc2111_sawfish/m84036_250809_035451_s4.bc2111.sv.vcf.gz.tbi:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2111.sv.vcf.gz.tbi:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-14/_singularity_tmpdir_sppdjudt/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-14/_singularity_tmpdir_sppdjudt/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:27:51.107 wdl.w:ptcp.t:call-tar_outputs-14 NOTICE slurm_singularity run :: pid: 1208635, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-14/slurm_singularity.log.txt"
2025-09-15 20:27:51.367 wdl.w:ptcp.w:call-paraphase-62.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for rpgr for sample m84036_250809_035451_s4.bc2159 at 2025-09-15 20:27:21.625842...
2025-09-15 20:27:51.367 wdl.w:ptcp.w:call-paraphase-62.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for rpgr for sample m84036_250809_035451_s4.bc2159 at 2025-09-15 20:27:23.170581...
2025-09-15 20:27:51.367 wdl.w:ptcp.w:call-paraphase-62.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for rpgr for sample m84036_250809_035451_s4.bc2159 at 2025-09-15 20:27:23.548523...
2025-09-15 20:27:51.560 wdl.w:ptcp.t:call-tar_outputs-46 INFO output :: name: "sample_tarball", value: "m84036_250809_035451_s4.bc2143.tar"
2025-09-15 20:27:51.616 wdl.w:ptcp.t:call-tar_outputs-46 NOTICE done
2025-09-15 20:27:51.639 wdl.w:ptcp NOTICE finish :: job: "call-tar_outputs-46"
2025-09-15 20:27:51.639 wdl.w:ptcp INFO output :: job: "call-tar_outputs-46", values: {"sample_tarball": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-46/out/m84036_250809_035451_s4.bc2143.tar"}
2025-09-15 20:27:52.127 wdl.w:ptcp.t:call-tar_outputs-14.slurm_singularity INFO srun: job 51798238 queued and waiting for resources
2025-09-15 20:27:52.127 wdl.w:ptcp.t:call-tar_outputs-14.slurm_singularity INFO srun: job 51798238 has been allocated resources
2025-09-15 20:27:52.127 wdl.w:ptcp.t:call-tar_outputs-14.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:27:52.331 wdl.w:ptcp.t:call-tar_outputs-14 INFO output :: name: "sample_tarball", value: "m84036_250809_035451_s4.bc2111.tar"
2025-09-15 20:27:52.384 wdl.w:ptcp.t:call-tar_outputs-14 NOTICE done
2025-09-15 20:27:52.388 wdl.w:ptcp NOTICE finish :: job: "call-tar_outputs-14"
2025-09-15 20:27:52.388 wdl.w:ptcp INFO output :: job: "call-tar_outputs-14", values: {"sample_tarball": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-14/out/m84036_250809_035451_s4.bc2111.tar"}
2025-09-15 20:27:53.004 wdl.w:ptcp.w:call-paraphase-91.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for f8inv1 for sample m84036_250809_035451_s4.bc2188 at 2025-09-15 20:27:47.762090...
2025-09-15 20:27:53.004 wdl.w:ptcp.w:call-paraphase-91.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for f8inv1 for sample m84036_250809_035451_s4.bc2188 at 2025-09-15 20:27:48.170853...
2025-09-15 20:27:54.867 wdl.w:ptcp.w:call-paraphase-26.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for f8inv22 for sample m84036_250809_035451_s4.bc2123 at 2025-09-15 20:27:52.779804...
2025-09-15 20:27:54.867 wdl.w:ptcp.w:call-paraphase-26.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for f8inv22 for sample m84036_250809_035451_s4.bc2123 at 2025-09-15 20:27:52.780735...
2025-09-15 20:27:55.604 wdl.w:ptcp.w:call-paraphase-82.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for f8inv1 for sample m84036_250809_035451_s4.bc2179 at 2025-09-15 20:27:26.335693...
2025-09-15 20:27:55.605 wdl.w:ptcp.w:call-paraphase-82.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for cyp21 for sample m84036_250809_035451_s4.bc2179 at 2025-09-15 20:27:31.112100...
2025-09-15 20:27:55.605 wdl.w:ptcp.w:call-paraphase-82.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for cyp21 for sample m84036_250809_035451_s4.bc2179 at 2025-09-15 20:27:32.655534...
2025-09-15 20:27:55.605 wdl.w:ptcp.w:call-paraphase-82.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for f8inv1 for sample m84036_250809_035451_s4.bc2179 at 2025-09-15 20:27:35.536181...
2025-09-15 20:27:55.605 wdl.w:ptcp.w:call-paraphase-82.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for f8inv1 for sample m84036_250809_035451_s4.bc2179 at 2025-09-15 20:27:36.212189...
2025-09-15 20:27:55.605 wdl.w:ptcp.w:call-paraphase-82.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for gba for sample m84036_250809_035451_s4.bc2179 at 2025-09-15 20:27:37.349659...
2025-09-15 20:27:55.605 wdl.w:ptcp.w:call-paraphase-82.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for gba for sample m84036_250809_035451_s4.bc2179 at 2025-09-15 20:27:38.242988...
2025-09-15 20:27:56.036 wdl.w:ptcp.w:call-paraphase-94.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for f8inv1 for sample m84036_250809_035451_s4.bc2191 at 2025-09-15 20:27:25.761150...
2025-09-15 20:27:56.036 wdl.w:ptcp.w:call-paraphase-94.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for f8inv1 for sample m84036_250809_035451_s4.bc2191 at 2025-09-15 20:27:32.462850...
2025-09-15 20:27:56.036 wdl.w:ptcp.w:call-paraphase-94.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for f8inv1 for sample m84036_250809_035451_s4.bc2191 at 2025-09-15 20:27:32.861280...
2025-09-15 20:27:56.036 wdl.w:ptcp.w:call-paraphase-94.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for hbb for sample m84036_250809_035451_s4.bc2191 at 2025-09-15 20:27:45.333274...
2025-09-15 20:27:56.036 wdl.w:ptcp.w:call-paraphase-94.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for hbb for sample m84036_250809_035451_s4.bc2191 at 2025-09-15 20:27:45.334097...
2025-09-15 20:27:56.036 wdl.w:ptcp.w:call-paraphase-94.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for hbb for sample m84036_250809_035451_s4.bc2191 at 2025-09-15 20:27:47.662573...
2025-09-15 20:27:57.916 wdl.w:ptcp.w:call-paraphase-03.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for rpgr for sample m84036_250809_035451_s4.bc2100 at 2025-09-15 20:27:51.957708...
2025-09-15 20:27:57.917 wdl.w:ptcp.w:call-paraphase-03.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for rpgr for sample m84036_250809_035451_s4.bc2100 at 2025-09-15 20:27:51.958341...
2025-09-15 20:27:58.773 wdl.w:ptcp.w:call-paraphase-74.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for f8inv22 for sample m84036_250809_035451_s4.bc2171 at 2025-09-15 20:27:35.574938...
2025-09-15 20:27:58.773 wdl.w:ptcp.w:call-paraphase-74.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for f8inv22 for sample m84036_250809_035451_s4.bc2171 at 2025-09-15 20:27:41.274857...
2025-09-15 20:27:58.773 wdl.w:ptcp.w:call-paraphase-74.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for f8inv22 for sample m84036_250809_035451_s4.bc2171 at 2025-09-15 20:27:41.775283...
2025-09-15 20:27:59.720 wdl.w:ptcp.w:call-paraphase-66.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for f8inv1 for sample m84036_250809_035451_s4.bc2163 at 2025-09-15 20:27:55.738369...
2025-09-15 20:27:59.721 wdl.w:ptcp.w:call-paraphase-66.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for f8inv1 for sample m84036_250809_035451_s4.bc2163 at 2025-09-15 20:27:55.739544...
2025-09-15 20:28:03.597 wdl.w:ptcp.w:call-paraphase-74.t:call-run_paraphase INFO output :: name: "paraphase_bam", value: "m84036_250809_035451_s4.bc2171_paraphase/m84036_250809_035451_s4.bc2171.paraphase.bam"
2025-09-15 20:28:03.603 wdl.w:ptcp.w:call-paraphase-74.t:call-run_paraphase INFO output :: name: "paraphase_bam_bai", value: "m84036_250809_035451_s4.bc2171_paraphase/m84036_250809_035451_s4.bc2171.paraphase.bam.bai"
2025-09-15 20:28:03.604 wdl.w:ptcp.w:call-paraphase-74.t:call-run_paraphase INFO output :: name: "paraphase_json", value: "m84036_250809_035451_s4.bc2171_paraphase/m84036_250809_035451_s4.bc2171.paraphase.json"
2025-09-15 20:28:03.609 wdl.w:ptcp.w:call-paraphase-74.t:call-run_paraphase INFO output :: name: "paraphase_vcfs", value: ["/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2171_paraphase/m84036_250809_035451_s4.bc2171_paraphase_vcfs/m84036_250809_035451_s4.bc2171_cyp21.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2171_paraphase/m84036_250809_035451_s4.bc2171_paraphase_vcfs/m84036_250809_035451_s4.bc2171_f8inv1.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2171_paraphase/m84036_250809_035451_s4.bc2171_paraphase_vcfs/m84036_250809_035451_s4.bc2171_f8inv22.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2171_paraphase/m84036_250809_035451_s4.bc2171_paraphase_vcfs/m84036_250809_035451_s4.bc2171_gba.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2171_paraphase/m84036_250809_035451_s4.bc2171_paraphase_vcfs/m84036_250809_035451_s4.bc2171_hba.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2171_paraphase/m84036_250809_035451_s4.bc2171_paraphase_vcfs/m84036_250809_035451_s4.bc2171_hbb.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2171_paraphase/m84036_250809_035451_s4.bc2171_paraphase_vcfs/m84036_250809_035451_s4.bc2171_rpgr.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2171_paraphase/m84036_250809_035451_s4.bc2171_paraphase_vcfs/m84036_250809_035451_s4.bc2171_smn1.vcf"]
2025-09-15 20:28:03.612 wdl.w:ptcp.w:call-paraphase-74.t:call-run_paraphase INFO output :: name: "havanno_json", value: "m84036_250809_035451_s4.bc2171.havanno.json"
2025-09-15 20:28:03.783 wdl.w:ptcp.w:call-paraphase-74.t:call-run_paraphase NOTICE done
2025-09-15 20:28:03.789 wdl.w:ptcp.w:call-paraphase-74 NOTICE finish :: job: "call-run_paraphase"
2025-09-15 20:28:03.789 wdl.w:ptcp.w:call-paraphase-74 INFO output :: job: "call-run_paraphase", values: {"havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-74/call-run_paraphase/out/m84036_250809_035451_s4.bc2171.havanno.json", "paraphase_vcfs": ["/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-74/call-run_paraphase/out/m84036_250809_035451_s4.bc2171_paraphase/m84036_250809_035451_s4.bc2171_paraphase_vcfs/m84036_250809_035451_s4.bc2171_cyp21.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-74/call-run_paraphase/out/m84036_250809_035451_s4.bc2171_paraphase/m84036_250809_035451_s4.bc2171_paraphase_vcfs/m84036_250809_035451_s4.bc2171_f8inv1.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-74/call-run_paraphase/out/m84036_250809_035451_s4.bc2171_paraphase/m84036_250809_035451_s4.bc2171_paraphase_vcfs/m84036_250809_035451_s4.bc2171_f8inv22.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-74/call-run_paraphase/out/m84036_250809_035451_s4.bc2171_paraphase/m84036_250809_035451_s4.bc2171_paraphase_vcfs/m84036_250809_035451_s4.bc2171_gba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-74/call-run_paraphase/out/m84036_250809_035451_s4.bc2171_paraphase/m84036_250809_035451_s4.bc2171_paraphase_vcfs/m84036_250809_035451_s4.bc2171_hba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-74/call-run_paraphase/out/m84036_250809_035451_s4.bc2171_paraphase/m84036_250809_035451_s4.bc2171_paraphase_vcfs/m84036_250809_035451_s4.bc2171_hbb.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-74/call-run_paraphase/out/m84036_250809_035451_s4.bc2171_paraphase/m84036_250809_035451_s4.bc2171_paraphase_vcfs/m84036_250809_035451_s4.bc2171_rpgr.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-74/call-run_paraphase/out/m84036_250809_035451_s4.bc2171_paraphase/m84036_250809_035451_s4.bc2171_paraphase_vcfs/m84036_250809_035451_s4.bc2171_smn1.vcf"], "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-74/call-run_paraphase/out/m84036_250809_035451_s4.bc2171_paraphase/m84036_250809_035451_s4.bc2171.paraphase.json", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-74/call-run_paraphase/out/m84036_250809_035451_s4.bc2171_paraphase/m84036_250809_035451_s4.bc2171.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-74/call-run_paraphase/out/m84036_250809_035451_s4.bc2171_paraphase/m84036_250809_035451_s4.bc2171.paraphase.bam"}
2025-09-15 20:28:03.790 wdl.w:ptcp.w:call-paraphase-74 NOTICE ready :: job: "call-call_f8", callee: "call_f8"
2025-09-15 20:28:03.790 wdl.w:ptcp.w:call-paraphase-74 INFO input :: job: "call-call_f8", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "out_prefix": "m84036_250809_035451_s4.bc2171", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-74/call-run_paraphase/out/m84036_250809_035451_s4.bc2171_paraphase/m84036_250809_035451_s4.bc2171.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-74/call-run_paraphase/out/m84036_250809_035451_s4.bc2171_paraphase/m84036_250809_035451_s4.bc2171.paraphase.bam", "sex": "F"}
2025-09-15 20:28:03.791 wdl.w:ptcp.w:call-paraphase-74 INFO visit :: node: "output-havanno_json", values: {"havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-74/call-run_paraphase/out/m84036_250809_035451_s4.bc2171.havanno.json"}
2025-09-15 20:28:03.791 wdl.w:ptcp.w:call-paraphase-74 INFO visit :: node: "output-paraphase_bam", values: {"paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-74/call-run_paraphase/out/m84036_250809_035451_s4.bc2171_paraphase/m84036_250809_035451_s4.bc2171.paraphase.bam"}
2025-09-15 20:28:03.791 wdl.w:ptcp.w:call-paraphase-74 INFO visit :: node: "output-paraphase_bam_bai", values: {"paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-74/call-run_paraphase/out/m84036_250809_035451_s4.bc2171_paraphase/m84036_250809_035451_s4.bc2171.paraphase.bam.bai"}
2025-09-15 20:28:03.791 wdl.w:ptcp.w:call-paraphase-74 INFO visit :: node: "output-paraphase_json", values: {"paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-74/call-run_paraphase/out/m84036_250809_035451_s4.bc2171_paraphase/m84036_250809_035451_s4.bc2171.paraphase.json"}
2025-09-15 20:28:03.791 wdl.w:ptcp.w:call-paraphase-74 INFO visit :: node: "output-paraphase_vcfs", values: {"paraphase_vcfs": ["/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-74/call-run_paraphase/out/m84036_250809_035451_s4.bc2171_paraphase/m84036_250809_035451_s4.bc2171_paraphase_vcfs/m84036_250809_035451_s4.bc2171_cyp21.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-74/call-run_paraphase/out/m84036_250809_035451_s4.bc2171_paraphase/m84036_250809_035451_s4.bc2171_paraphase_vcfs/m84036_250809_035451_s4.bc2171_f8inv1.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-74/call-run_paraphase/out/m84036_250809_035451_s4.bc2171_paraphase/m84036_250809_035451_s4.bc2171_paraphase_vcfs/m84036_250809_035451_s4.bc2171_f8inv22.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-74/call-run_paraphase/out/m84036_250809_035451_s4.bc2171_paraphase/m84036_250809_035451_s4.bc2171_paraphase_vcfs/m84036_250809_035451_s4.bc2171_gba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-74/call-run_paraphase/out/m84036_250809_035451_s4.bc2171_paraphase/m84036_250809_035451_s4.bc2171_paraphase_vcfs/m84036_250809_035451_s4.bc2171_hba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-74/call-run_paraphase/out/m84036_250809_035451_s4.bc2171_paraphase/m84036_250809_035451_s4.bc2171_paraphase_vcfs/m84036_250809_035451_s4.bc2171_hbb.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-74/call-run_paraphase/out/m84036_250809_035451_s4.bc2171_paraphase/m84036_250809_035451_s4.bc2171_paraphase_vcfs/m84036_250809_035451_s4.bc2171_rpgr.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-74/call-run_paraphase/out/m84036_250809_035451_s4.bc2171_paraphase/m84036_250809_035451_s4.bc2171_paraphase_vcfs/m84036_250809_035451_s4.bc2171_smn1.vcf"]}
2025-09-15 20:28:03.795 wdl.w:ptcp.w:call-paraphase-74.t:call-call_f8 NOTICE task setup :: name: "call_f8", source: "./paraphase.wdl", line: 232, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-74/call-call_f8", thread: 140611424335424
2025-09-15 20:28:03.813 wdl.w:ptcp.w:call-paraphase-74.t:call-call_f8 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:28:03.813 wdl.w:ptcp.w:call-paraphase-74.t:call-call_f8 INFO input :: name: "genome_version", value: "38"
2025-09-15 20:28:03.814 wdl.w:ptcp.w:call-paraphase-74.t:call-call_f8 INFO input :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2171"
2025-09-15 20:28:03.814 wdl.w:ptcp.w:call-paraphase-74.t:call-call_f8 INFO input :: name: "paraphase_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2171.paraphase.bam.bai"
2025-09-15 20:28:03.814 wdl.w:ptcp.w:call-paraphase-74.t:call-call_f8 INFO input :: name: "paraphase_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2171.paraphase.bam"
2025-09-15 20:28:03.814 wdl.w:ptcp.w:call-paraphase-74.t:call-call_f8 INFO input :: name: "sex", value: "F"
2025-09-15 20:28:03.814 wdl.w:ptcp.w:call-paraphase-74.t:call-call_f8 INFO eval :: name: "threads", value: 1
2025-09-15 20:28:03.814 wdl.w:ptcp.w:call-paraphase-74.t:call-call_f8 INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:28:03.814 wdl.w:ptcp.w:call-paraphase-74.t:call-call_f8 INFO eval :: name: "disk_size", value: 11
2025-09-15 20:28:03.814 wdl.w:ptcp.w:call-paraphase-74.t:call-call_f8 INFO eval :: name: "sample_sex", value: "F"
2025-09-15 20:28:03.815 wdl.w:ptcp.w:call-paraphase-74.t:call-call_f8 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:28:03.815 wdl.w:ptcp.w:call-paraphase-74.t:call-call_f8 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:28:03.815 wdl.w:ptcp.w:call-paraphase-74.t:call-call_f8 INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:28:03.815 wdl.w:ptcp.w:call-paraphase-74.t:call-call_f8 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:28:03.850 wdl.w:ptcp.w:call-paraphase-74.t:call-call_f8 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 8, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-74/call-call_f8/_singularity_tmpdir_87eq144_"
2025-09-15 20:28:03.850 wdl.w:ptcp.w:call-paraphase-74.t:call-call_f8 INFO Slurm invocation: srun --job-name call-call_f8 --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-74/call-call_f8/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-74/call-call_f8/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-74/call-call_f8/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-74/call-call_f8/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-74/call-run_paraphase/out/m84036_250809_035451_s4.bc2171_paraphase/m84036_250809_035451_s4.bc2171.paraphase.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2171.paraphase.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-74/call-run_paraphase/out/m84036_250809_035451_s4.bc2171_paraphase/m84036_250809_035451_s4.bc2171.paraphase.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2171.paraphase.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-74/call-call_f8/_singularity_tmpdir_87eq144_/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-74/call-call_f8/_singularity_tmpdir_87eq144_/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:28:03.855 wdl.w:ptcp.w:call-paraphase-74.t:call-call_f8 NOTICE slurm_singularity run :: pid: 1208840, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-74/call-call_f8/slurm_singularity.log.txt"
2025-09-15 20:28:04.863 wdl.w:ptcp.w:call-paraphase-74.t:call-call_f8.slurm_singularity INFO srun: job 51798241 queued and waiting for resources
2025-09-15 20:28:04.863 wdl.w:ptcp.w:call-paraphase-74.t:call-call_f8.slurm_singularity INFO srun: job 51798241 has been allocated resources
2025-09-15 20:28:04.863 wdl.w:ptcp.w:call-paraphase-74.t:call-call_f8.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:28:05.151 wdl.w:ptcp.w:call-paraphase-94.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for hbb for sample m84036_250809_035451_s4.bc2191 at 2025-09-15 20:27:54.523247...
2025-09-15 20:28:05.151 wdl.w:ptcp.w:call-paraphase-94.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for hbb for sample m84036_250809_035451_s4.bc2191 at 2025-09-15 20:27:54.906649...
2025-09-15 20:28:05.210 wdl.w:ptcp.w:call-paraphase-74.t:call-call_f8 INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2171.f8inversion.vcf"
2025-09-15 20:28:05.213 wdl.w:ptcp.w:call-paraphase-74.t:call-call_f8 INFO output :: name: "json", value: "m84036_250809_035451_s4.bc2171.f8inversion.json"
2025-09-15 20:28:05.263 wdl.w:ptcp.w:call-paraphase-74.t:call-call_f8 NOTICE done
2025-09-15 20:28:05.268 wdl.w:ptcp.w:call-paraphase-74 NOTICE finish :: job: "call-call_f8"
2025-09-15 20:28:05.269 wdl.w:ptcp.w:call-paraphase-74 INFO output :: job: "call-call_f8", values: {"json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-74/call-call_f8/out/m84036_250809_035451_s4.bc2171.f8inversion.json", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-74/call-call_f8/out/m84036_250809_035451_s4.bc2171.f8inversion.vcf"}
2025-09-15 20:28:05.269 wdl.w:ptcp.w:call-paraphase-74 INFO visit :: node: "output-f8_json", values: {"f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-74/call-call_f8/out/m84036_250809_035451_s4.bc2171.f8inversion.json"}
2025-09-15 20:28:05.269 wdl.w:ptcp.w:call-paraphase-74 INFO visit :: node: "output-f8_vcf", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-74/call-call_f8/out/m84036_250809_035451_s4.bc2171.f8inversion.vcf"}
2025-09-15 20:28:05.269 wdl.w:ptcp.w:call-paraphase-74 INFO visit :: node: "outputs", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-74/call-call_f8/out/m84036_250809_035451_s4.bc2171.f8inversion.vcf", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-74/call-run_paraphase/out/m84036_250809_035451_s4.bc2171_paraphase/m84036_250809_035451_s4.bc2171.paraphase.json", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-74/call-run_paraphase/out/m84036_250809_035451_s4.bc2171_paraphase/m84036_250809_035451_s4.bc2171.paraphase.bam", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-74/call-run_paraphase/out/m84036_250809_035451_s4.bc2171_paraphase/m84036_250809_035451_s4.bc2171.paraphase.bam.bai", "paraphase_vcfs": ["/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-74/call-run_paraphase/out/m84036_250809_035451_s4.bc2171_paraphase/m84036_250809_035451_s4.bc2171_paraphase_vcfs/m84036_250809_035451_s4.bc2171_cyp21.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-74/call-run_paraphase/out/m84036_250809_035451_s4.bc2171_paraphase/m84036_250809_035451_s4.bc2171_paraphase_vcfs/m84036_250809_035451_s4.bc2171_f8inv1.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-74/call-run_paraphase/out/m84036_250809_035451_s4.bc2171_paraphase/m84036_250809_035451_s4.bc2171_paraphase_vcfs/m84036_250809_035451_s4.bc2171_f8inv22.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-74/call-run_paraphase/out/m84036_250809_035451_s4.bc2171_paraphase/m84036_250809_035451_s4.bc2171_paraphase_vcfs/m84036_250809_035451_s4.bc2171_gba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-74/call-run_paraphase/out/m84036_250809_035451_s4.bc2171_paraphase/m84036_250809_035451_s4.bc2171_paraphase_vcfs/m84036_250809_035451_s4.bc2171_hba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-74/call-run_paraphase/out/m84036_250809_035451_s4.bc2171_paraphase/m84036_250809_035451_s4.bc2171_paraphase_vcfs/m84036_250809_035451_s4.bc2171_hbb.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-74/call-run_paraphase/out/m84036_250809_035451_s4.bc2171_paraphase/m84036_250809_035451_s4.bc2171_paraphase_vcfs/m84036_250809_035451_s4.bc2171_rpgr.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-74/call-run_paraphase/out/m84036_250809_035451_s4.bc2171_paraphase/m84036_250809_035451_s4.bc2171_paraphase_vcfs/m84036_250809_035451_s4.bc2171_smn1.vcf"], "havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-74/call-run_paraphase/out/m84036_250809_035451_s4.bc2171.havanno.json", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-74/call-call_f8/out/m84036_250809_035451_s4.bc2171.f8inversion.json"}
2025-09-15 20:28:05.373 wdl.w:ptcp.w:call-paraphase-74 NOTICE done
2025-09-15 20:28:05.378 wdl.w:ptcp NOTICE finish :: job: "call-paraphase-74"
2025-09-15 20:28:05.378 wdl.w:ptcp INFO output :: job: "call-paraphase-74", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-74/out/m84036_250809_035451_s4.bc2171.f8inversion.vcf", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-74/out/m84036_250809_035451_s4.bc2171_paraphase/m84036_250809_035451_s4.bc2171.paraphase.json", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-74/out/m84036_250809_035451_s4.bc2171_paraphase/m84036_250809_035451_s4.bc2171.paraphase.bam", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-74/out/m84036_250809_035451_s4.bc2171_paraphase/m84036_250809_035451_s4.bc2171.paraphase.bam.bai", "paraphase_vcfs": ["/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-74/out/m84036_250809_035451_s4.bc2171_paraphase/m84036_250809_035451_s4.bc2171_paraphase_vcfs/m84036_250809_035451_s4.bc2171_cyp21.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-74/out/m84036_250809_035451_s4.bc2171_paraphase/m84036_250809_035451_s4.bc2171_paraphase_vcfs/m84036_250809_035451_s4.bc2171_f8inv1.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-74/out/m84036_250809_035451_s4.bc2171_paraphase/m84036_250809_035451_s4.bc2171_paraphase_vcfs/m84036_250809_035451_s4.bc2171_f8inv22.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-74/out/m84036_250809_035451_s4.bc2171_paraphase/m84036_250809_035451_s4.bc2171_paraphase_vcfs/m84036_250809_035451_s4.bc2171_gba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-74/out/m84036_250809_035451_s4.bc2171_paraphase/m84036_250809_035451_s4.bc2171_paraphase_vcfs/m84036_250809_035451_s4.bc2171_hba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-74/out/m84036_250809_035451_s4.bc2171_paraphase/m84036_250809_035451_s4.bc2171_paraphase_vcfs/m84036_250809_035451_s4.bc2171_hbb.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-74/out/m84036_250809_035451_s4.bc2171_paraphase/m84036_250809_035451_s4.bc2171_paraphase_vcfs/m84036_250809_035451_s4.bc2171_rpgr.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-74/out/m84036_250809_035451_s4.bc2171_paraphase/m84036_250809_035451_s4.bc2171_paraphase_vcfs/m84036_250809_035451_s4.bc2171_smn1.vcf"], "havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-74/out/m84036_250809_035451_s4.bc2171.havanno.json", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-74/out/m84036_250809_035451_s4.bc2171.f8inversion.json"}
2025-09-15 20:28:05.379 wdl.w:ptcp NOTICE ready :: job: "call-tar_outputs-74", callee: "tar_outputs"
2025-09-15 20:28:05.379 wdl.w:ptcp INFO input :: job: "call-tar_outputs-74", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "sawfish_vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-74/out/m84036_250809_035451_s4.bc2171_sawfish/m84036_250809_035451_s4.bc2171.sv.vcf.gz.tbi", "sawfish_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-74/out/m84036_250809_035451_s4.bc2171_sawfish/m84036_250809_035451_s4.bc2171.sv.vcf.gz", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-74/out/m84036_250809_035451_s4.bc2171.f8inversion.json", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-74/out/m84036_250809_035451_s4.bc2171_paraphase/m84036_250809_035451_s4.bc2171.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-74/out/m84036_250809_035451_s4.bc2171_paraphase/m84036_250809_035451_s4.bc2171.paraphase.bam", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-74/out/m84036_250809_035451_s4.bc2171_paraphase/m84036_250809_035451_s4.bc2171.paraphase.json", "trgt_spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-74/out/m84036_250809_035451_s4.bc2171.trgt.sorted.spanning.bam.bai", "trgt_spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-74/out/m84036_250809_035451_s4.bc2171.trgt.sorted.spanning.bam", "trgt_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-74/out/m84036_250809_035451_s4.bc2171.trgt.vcf", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-74/out/m84036_250809_035451_s4.bc2171.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-74/out/m84036_250809_035451_s4.bc2171.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2171"}
2025-09-15 20:28:05.385 wdl.w:ptcp.t:call-tar_outputs-74 NOTICE task setup :: name: "tar_outputs", source: "./common.wdl", line: 279, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-74", thread: 140607683024448
2025-09-15 20:28:05.405 wdl.w:ptcp.t:call-tar_outputs-74 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:28:05.406 wdl.w:ptcp.t:call-tar_outputs-74 INFO input :: name: "sawfish_vcf_tbi", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2171.sv.vcf.gz.tbi"
2025-09-15 20:28:05.406 wdl.w:ptcp.t:call-tar_outputs-74 INFO input :: name: "sawfish_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2171.sv.vcf.gz"
2025-09-15 20:28:05.406 wdl.w:ptcp.t:call-tar_outputs-74 INFO input :: name: "f8_json", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2171.f8inversion.json"
2025-09-15 20:28:05.406 wdl.w:ptcp.t:call-tar_outputs-74 INFO input :: name: "paraphase_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2171.paraphase.bam.bai"
2025-09-15 20:28:05.406 wdl.w:ptcp.t:call-tar_outputs-74 INFO input :: name: "paraphase_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2171.paraphase.bam"
2025-09-15 20:28:05.406 wdl.w:ptcp.t:call-tar_outputs-74 INFO input :: name: "paraphase_json", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2171.paraphase.json"
2025-09-15 20:28:05.406 wdl.w:ptcp.t:call-tar_outputs-74 INFO input :: name: "trgt_spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2171.trgt.sorted.spanning.bam.bai"
2025-09-15 20:28:05.406 wdl.w:ptcp.t:call-tar_outputs-74 INFO input :: name: "trgt_spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2171.trgt.sorted.spanning.bam"
2025-09-15 20:28:05.406 wdl.w:ptcp.t:call-tar_outputs-74 INFO input :: name: "trgt_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2171.trgt.vcf"
2025-09-15 20:28:05.406 wdl.w:ptcp.t:call-tar_outputs-74 INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2171.mapped.bam.bai"
2025-09-15 20:28:05.406 wdl.w:ptcp.t:call-tar_outputs-74 INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2171.mapped.bam"
2025-09-15 20:28:05.406 wdl.w:ptcp.t:call-tar_outputs-74 INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2171"
2025-09-15 20:28:05.406 wdl.w:ptcp.t:call-tar_outputs-74 INFO eval :: name: "threads", value: 1
2025-09-15 20:28:05.406 wdl.w:ptcp.t:call-tar_outputs-74 INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:28:05.407 wdl.w:ptcp.t:call-tar_outputs-74 INFO eval :: name: "disk_size", value: 6
2025-09-15 20:28:05.407 wdl.w:ptcp.t:call-tar_outputs-74 INFO eval :: name: "output_tarball", value: "m84036_250809_035451_s4.bc2171.tar"
2025-09-15 20:28:05.407 wdl.w:ptcp.t:call-tar_outputs-74 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:28:05.407 wdl.w:ptcp.t:call-tar_outputs-74 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:28:05.407 wdl.w:ptcp.t:call-tar_outputs-74 INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:28:05.408 wdl.w:ptcp.t:call-tar_outputs-74 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:28:05.480 wdl.w:ptcp.t:call-tar_outputs-74 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 17, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-74/_singularity_tmpdir_jx9vsqtj"
2025-09-15 20:28:05.481 wdl.w:ptcp.t:call-tar_outputs-74 INFO Slurm invocation: srun --job-name call-tar_outputs-74 --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-74/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-74/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-74/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-74/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-74/out/m84036_250809_035451_s4.bc2171_sawfish/m84036_250809_035451_s4.bc2171.sv.vcf.gz.tbi:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2171.sv.vcf.gz.tbi:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-74/out/m84036_250809_035451_s4.bc2171_sawfish/m84036_250809_035451_s4.bc2171.sv.vcf.gz:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2171.sv.vcf.gz:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-74/out/m84036_250809_035451_s4.bc2171.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2171.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-74/out/m84036_250809_035451_s4.bc2171.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2171.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-74/out/m84036_250809_035451_s4.bc2171.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2171.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-74/out/m84036_250809_035451_s4.bc2171.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2171.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-74/out/m84036_250809_035451_s4.bc2171.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2171.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-74/out/m84036_250809_035451_s4.bc2171_paraphase/m84036_250809_035451_s4.bc2171.paraphase.json:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2171.paraphase.json:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-74/out/m84036_250809_035451_s4.bc2171_paraphase/m84036_250809_035451_s4.bc2171.paraphase.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2171.paraphase.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-74/out/m84036_250809_035451_s4.bc2171_paraphase/m84036_250809_035451_s4.bc2171.paraphase.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2171.paraphase.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-74/out/m84036_250809_035451_s4.bc2171.f8inversion.json:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2171.f8inversion.json:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-74/_singularity_tmpdir_jx9vsqtj/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-74/_singularity_tmpdir_jx9vsqtj/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:28:05.487 wdl.w:ptcp.t:call-tar_outputs-74 NOTICE slurm_singularity run :: pid: 1208848, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-74/slurm_singularity.log.txt"
2025-09-15 20:28:05.568 wdl.w:ptcp.w:call-paraphase-71.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for rpgr for sample m84036_250809_035451_s4.bc2168 at 2025-09-15 20:27:55.800633...
2025-09-15 20:28:05.569 wdl.w:ptcp.w:call-paraphase-71.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for rpgr for sample m84036_250809_035451_s4.bc2168 at 2025-09-15 20:27:55.801197...
2025-09-15 20:28:06.489 wdl.w:ptcp.t:call-tar_outputs-74.stderr VERBOSE tar: Removing leading `/' from member names
2025-09-15 20:28:06.489 wdl.w:ptcp.t:call-tar_outputs-74.stderr VERBOSE tar: Removing leading `/' from hard link targets
2025-09-15 20:28:06.498 wdl.w:ptcp.t:call-tar_outputs-74.slurm_singularity INFO srun: job 51798242 queued and waiting for resources
2025-09-15 20:28:06.498 wdl.w:ptcp.t:call-tar_outputs-74.slurm_singularity INFO srun: job 51798242 has been allocated resources
2025-09-15 20:28:06.498 wdl.w:ptcp.t:call-tar_outputs-74.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:28:06.647 wdl.w:ptcp.t:call-tar_outputs-74 INFO output :: name: "sample_tarball", value: "m84036_250809_035451_s4.bc2171.tar"
2025-09-15 20:28:06.718 wdl.w:ptcp.t:call-tar_outputs-74 NOTICE done
2025-09-15 20:28:06.723 wdl.w:ptcp NOTICE finish :: job: "call-tar_outputs-74"
2025-09-15 20:28:06.724 wdl.w:ptcp INFO output :: job: "call-tar_outputs-74", values: {"sample_tarball": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-74/out/m84036_250809_035451_s4.bc2171.tar"}
2025-09-15 20:28:08.823 wdl.w:ptcp.w:call-paraphase-66.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for f8inv1 for sample m84036_250809_035451_s4.bc2163 at 2025-09-15 20:27:59.283607...
2025-09-15 20:28:10.404 wdl.w:ptcp.w:call-paraphase-26.t:call-run_paraphase INFO output :: name: "paraphase_bam", value: "m84036_250809_035451_s4.bc2123_paraphase/m84036_250809_035451_s4.bc2123.paraphase.bam"
2025-09-15 20:28:10.409 wdl.w:ptcp.w:call-paraphase-26.t:call-run_paraphase INFO output :: name: "paraphase_bam_bai", value: "m84036_250809_035451_s4.bc2123_paraphase/m84036_250809_035451_s4.bc2123.paraphase.bam.bai"
2025-09-15 20:28:10.410 wdl.w:ptcp.w:call-paraphase-26.t:call-run_paraphase INFO output :: name: "paraphase_json", value: "m84036_250809_035451_s4.bc2123_paraphase/m84036_250809_035451_s4.bc2123.paraphase.json"
2025-09-15 20:28:10.413 wdl.w:ptcp.w:call-paraphase-26.t:call-run_paraphase INFO output :: name: "paraphase_vcfs", value: ["/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2123_paraphase/m84036_250809_035451_s4.bc2123_paraphase_vcfs/m84036_250809_035451_s4.bc2123_cyp21.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2123_paraphase/m84036_250809_035451_s4.bc2123_paraphase_vcfs/m84036_250809_035451_s4.bc2123_f8inv1.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2123_paraphase/m84036_250809_035451_s4.bc2123_paraphase_vcfs/m84036_250809_035451_s4.bc2123_f8inv22.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2123_paraphase/m84036_250809_035451_s4.bc2123_paraphase_vcfs/m84036_250809_035451_s4.bc2123_gba.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2123_paraphase/m84036_250809_035451_s4.bc2123_paraphase_vcfs/m84036_250809_035451_s4.bc2123_hba.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2123_paraphase/m84036_250809_035451_s4.bc2123_paraphase_vcfs/m84036_250809_035451_s4.bc2123_hbb.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2123_paraphase/m84036_250809_035451_s4.bc2123_paraphase_vcfs/m84036_250809_035451_s4.bc2123_rpgr.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2123_paraphase/m84036_250809_035451_s4.bc2123_paraphase_vcfs/m84036_250809_035451_s4.bc2123_smn1.vcf"]
2025-09-15 20:28:10.416 wdl.w:ptcp.w:call-paraphase-26.t:call-run_paraphase INFO output :: name: "havanno_json", value: "m84036_250809_035451_s4.bc2123.havanno.json"
2025-09-15 20:28:10.562 wdl.w:ptcp.w:call-paraphase-26.t:call-run_paraphase NOTICE done
2025-09-15 20:28:10.666 wdl.w:ptcp.w:call-paraphase-26 NOTICE finish :: job: "call-run_paraphase"
2025-09-15 20:28:10.666 wdl.w:ptcp.w:call-paraphase-26 INFO output :: job: "call-run_paraphase", values: {"havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-26/call-run_paraphase/out/m84036_250809_035451_s4.bc2123.havanno.json", "paraphase_vcfs": ["/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-26/call-run_paraphase/out/m84036_250809_035451_s4.bc2123_paraphase/m84036_250809_035451_s4.bc2123_paraphase_vcfs/m84036_250809_035451_s4.bc2123_cyp21.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-26/call-run_paraphase/out/m84036_250809_035451_s4.bc2123_paraphase/m84036_250809_035451_s4.bc2123_paraphase_vcfs/m84036_250809_035451_s4.bc2123_f8inv1.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-26/call-run_paraphase/out/m84036_250809_035451_s4.bc2123_paraphase/m84036_250809_035451_s4.bc2123_paraphase_vcfs/m84036_250809_035451_s4.bc2123_f8inv22.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-26/call-run_paraphase/out/m84036_250809_035451_s4.bc2123_paraphase/m84036_250809_035451_s4.bc2123_paraphase_vcfs/m84036_250809_035451_s4.bc2123_gba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-26/call-run_paraphase/out/m84036_250809_035451_s4.bc2123_paraphase/m84036_250809_035451_s4.bc2123_paraphase_vcfs/m84036_250809_035451_s4.bc2123_hba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-26/call-run_paraphase/out/m84036_250809_035451_s4.bc2123_paraphase/m84036_250809_035451_s4.bc2123_paraphase_vcfs/m84036_250809_035451_s4.bc2123_hbb.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-26/call-run_paraphase/out/m84036_250809_035451_s4.bc2123_paraphase/m84036_250809_035451_s4.bc2123_paraphase_vcfs/m84036_250809_035451_s4.bc2123_rpgr.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-26/call-run_paraphase/out/m84036_250809_035451_s4.bc2123_paraphase/m84036_250809_035451_s4.bc2123_paraphase_vcfs/m84036_250809_035451_s4.bc2123_smn1.vcf"], "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-26/call-run_paraphase/out/m84036_250809_035451_s4.bc2123_paraphase/m84036_250809_035451_s4.bc2123.paraphase.json", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-26/call-run_paraphase/out/m84036_250809_035451_s4.bc2123_paraphase/m84036_250809_035451_s4.bc2123.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-26/call-run_paraphase/out/m84036_250809_035451_s4.bc2123_paraphase/m84036_250809_035451_s4.bc2123.paraphase.bam"}
2025-09-15 20:28:10.667 wdl.w:ptcp.w:call-paraphase-26 NOTICE ready :: job: "call-call_f8", callee: "call_f8"
2025-09-15 20:28:10.667 wdl.w:ptcp.w:call-paraphase-26 INFO input :: job: "call-call_f8", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "out_prefix": "m84036_250809_035451_s4.bc2123", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-26/call-run_paraphase/out/m84036_250809_035451_s4.bc2123_paraphase/m84036_250809_035451_s4.bc2123.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-26/call-run_paraphase/out/m84036_250809_035451_s4.bc2123_paraphase/m84036_250809_035451_s4.bc2123.paraphase.bam", "sex": "F"}
2025-09-15 20:28:10.667 wdl.w:ptcp.w:call-paraphase-26 INFO visit :: node: "output-havanno_json", values: {"havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-26/call-run_paraphase/out/m84036_250809_035451_s4.bc2123.havanno.json"}
2025-09-15 20:28:10.667 wdl.w:ptcp.w:call-paraphase-26 INFO visit :: node: "output-paraphase_bam", values: {"paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-26/call-run_paraphase/out/m84036_250809_035451_s4.bc2123_paraphase/m84036_250809_035451_s4.bc2123.paraphase.bam"}
2025-09-15 20:28:10.668 wdl.w:ptcp.w:call-paraphase-26 INFO visit :: node: "output-paraphase_bam_bai", values: {"paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-26/call-run_paraphase/out/m84036_250809_035451_s4.bc2123_paraphase/m84036_250809_035451_s4.bc2123.paraphase.bam.bai"}
2025-09-15 20:28:10.668 wdl.w:ptcp.w:call-paraphase-26 INFO visit :: node: "output-paraphase_json", values: {"paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-26/call-run_paraphase/out/m84036_250809_035451_s4.bc2123_paraphase/m84036_250809_035451_s4.bc2123.paraphase.json"}
2025-09-15 20:28:10.668 wdl.w:ptcp.w:call-paraphase-26 INFO visit :: node: "output-paraphase_vcfs", values: {"paraphase_vcfs": ["/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-26/call-run_paraphase/out/m84036_250809_035451_s4.bc2123_paraphase/m84036_250809_035451_s4.bc2123_paraphase_vcfs/m84036_250809_035451_s4.bc2123_cyp21.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-26/call-run_paraphase/out/m84036_250809_035451_s4.bc2123_paraphase/m84036_250809_035451_s4.bc2123_paraphase_vcfs/m84036_250809_035451_s4.bc2123_f8inv1.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-26/call-run_paraphase/out/m84036_250809_035451_s4.bc2123_paraphase/m84036_250809_035451_s4.bc2123_paraphase_vcfs/m84036_250809_035451_s4.bc2123_f8inv22.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-26/call-run_paraphase/out/m84036_250809_035451_s4.bc2123_paraphase/m84036_250809_035451_s4.bc2123_paraphase_vcfs/m84036_250809_035451_s4.bc2123_gba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-26/call-run_paraphase/out/m84036_250809_035451_s4.bc2123_paraphase/m84036_250809_035451_s4.bc2123_paraphase_vcfs/m84036_250809_035451_s4.bc2123_hba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-26/call-run_paraphase/out/m84036_250809_035451_s4.bc2123_paraphase/m84036_250809_035451_s4.bc2123_paraphase_vcfs/m84036_250809_035451_s4.bc2123_hbb.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-26/call-run_paraphase/out/m84036_250809_035451_s4.bc2123_paraphase/m84036_250809_035451_s4.bc2123_paraphase_vcfs/m84036_250809_035451_s4.bc2123_rpgr.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-26/call-run_paraphase/out/m84036_250809_035451_s4.bc2123_paraphase/m84036_250809_035451_s4.bc2123_paraphase_vcfs/m84036_250809_035451_s4.bc2123_smn1.vcf"]}
2025-09-15 20:28:10.672 wdl.w:ptcp.w:call-paraphase-26.t:call-call_f8 NOTICE task setup :: name: "call_f8", source: "./paraphase.wdl", line: 232, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-26/call-call_f8", thread: 140609302029888
2025-09-15 20:28:10.696 wdl.w:ptcp.w:call-paraphase-26.t:call-call_f8 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:28:10.696 wdl.w:ptcp.w:call-paraphase-26.t:call-call_f8 INFO input :: name: "genome_version", value: "38"
2025-09-15 20:28:10.696 wdl.w:ptcp.w:call-paraphase-26.t:call-call_f8 INFO input :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2123"
2025-09-15 20:28:10.696 wdl.w:ptcp.w:call-paraphase-26.t:call-call_f8 INFO input :: name: "paraphase_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2123.paraphase.bam.bai"
2025-09-15 20:28:10.696 wdl.w:ptcp.w:call-paraphase-26.t:call-call_f8 INFO input :: name: "paraphase_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2123.paraphase.bam"
2025-09-15 20:28:10.696 wdl.w:ptcp.w:call-paraphase-26.t:call-call_f8 INFO input :: name: "sex", value: "F"
2025-09-15 20:28:10.697 wdl.w:ptcp.w:call-paraphase-26.t:call-call_f8 INFO eval :: name: "threads", value: 1
2025-09-15 20:28:10.697 wdl.w:ptcp.w:call-paraphase-26.t:call-call_f8 INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:28:10.697 wdl.w:ptcp.w:call-paraphase-26.t:call-call_f8 INFO eval :: name: "disk_size", value: 11
2025-09-15 20:28:10.697 wdl.w:ptcp.w:call-paraphase-26.t:call-call_f8 INFO eval :: name: "sample_sex", value: "F"
2025-09-15 20:28:10.697 wdl.w:ptcp.w:call-paraphase-26.t:call-call_f8 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:28:10.697 wdl.w:ptcp.w:call-paraphase-26.t:call-call_f8 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:28:10.698 wdl.w:ptcp.w:call-paraphase-26.t:call-call_f8 INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:28:10.699 wdl.w:ptcp.w:call-paraphase-26.t:call-call_f8 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:28:10.736 wdl.w:ptcp.w:call-paraphase-26.t:call-call_f8 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 8, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-26/call-call_f8/_singularity_tmpdir_6_cn92ln"
2025-09-15 20:28:10.737 wdl.w:ptcp.w:call-paraphase-26.t:call-call_f8 INFO Slurm invocation: srun --job-name call-call_f8 --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-26/call-call_f8/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-26/call-call_f8/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-26/call-call_f8/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-26/call-call_f8/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-26/call-run_paraphase/out/m84036_250809_035451_s4.bc2123_paraphase/m84036_250809_035451_s4.bc2123.paraphase.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2123.paraphase.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-26/call-run_paraphase/out/m84036_250809_035451_s4.bc2123_paraphase/m84036_250809_035451_s4.bc2123.paraphase.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2123.paraphase.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-26/call-call_f8/_singularity_tmpdir_6_cn92ln/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-26/call-call_f8/_singularity_tmpdir_6_cn92ln/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:28:10.744 wdl.w:ptcp.w:call-paraphase-26.t:call-call_f8 NOTICE slurm_singularity run :: pid: 1209011, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-26/call-call_f8/slurm_singularity.log.txt"
2025-09-15 20:28:11.760 wdl.w:ptcp.w:call-paraphase-26.t:call-call_f8.slurm_singularity INFO srun: job 51798243 queued and waiting for resources
2025-09-15 20:28:11.760 wdl.w:ptcp.w:call-paraphase-26.t:call-call_f8.slurm_singularity INFO srun: job 51798243 has been allocated resources
2025-09-15 20:28:11.760 wdl.w:ptcp.w:call-paraphase-26.t:call-call_f8.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:28:11.862 wdl.w:ptcp.w:call-paraphase-66.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for f8inv1 for sample m84036_250809_035451_s4.bc2163 at 2025-09-15 20:28:06.502843...
2025-09-15 20:28:11.862 wdl.w:ptcp.w:call-paraphase-66.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for f8inv1 for sample m84036_250809_035451_s4.bc2163 at 2025-09-15 20:28:07.009024...
2025-09-15 20:28:11.970 wdl.w:ptcp.w:call-paraphase-26.t:call-call_f8 INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2123.f8inversion.vcf"
2025-09-15 20:28:11.972 wdl.w:ptcp.w:call-paraphase-26.t:call-call_f8 INFO output :: name: "json", value: "m84036_250809_035451_s4.bc2123.f8inversion.json"
2025-09-15 20:28:12.020 wdl.w:ptcp.w:call-paraphase-26.t:call-call_f8 NOTICE done
2025-09-15 20:28:12.024 wdl.w:ptcp.w:call-paraphase-26 NOTICE finish :: job: "call-call_f8"
2025-09-15 20:28:12.025 wdl.w:ptcp.w:call-paraphase-26 INFO output :: job: "call-call_f8", values: {"json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-26/call-call_f8/out/m84036_250809_035451_s4.bc2123.f8inversion.json", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-26/call-call_f8/out/m84036_250809_035451_s4.bc2123.f8inversion.vcf"}
2025-09-15 20:28:12.025 wdl.w:ptcp.w:call-paraphase-26 INFO visit :: node: "output-f8_json", values: {"f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-26/call-call_f8/out/m84036_250809_035451_s4.bc2123.f8inversion.json"}
2025-09-15 20:28:12.025 wdl.w:ptcp.w:call-paraphase-26 INFO visit :: node: "output-f8_vcf", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-26/call-call_f8/out/m84036_250809_035451_s4.bc2123.f8inversion.vcf"}
2025-09-15 20:28:12.025 wdl.w:ptcp.w:call-paraphase-26 INFO visit :: node: "outputs", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-26/call-call_f8/out/m84036_250809_035451_s4.bc2123.f8inversion.vcf", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-26/call-run_paraphase/out/m84036_250809_035451_s4.bc2123_paraphase/m84036_250809_035451_s4.bc2123.paraphase.json", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-26/call-run_paraphase/out/m84036_250809_035451_s4.bc2123_paraphase/m84036_250809_035451_s4.bc2123.paraphase.bam", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-26/call-run_paraphase/out/m84036_250809_035451_s4.bc2123_paraphase/m84036_250809_035451_s4.bc2123.paraphase.bam.bai", "paraphase_vcfs": ["/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-26/call-run_paraphase/out/m84036_250809_035451_s4.bc2123_paraphase/m84036_250809_035451_s4.bc2123_paraphase_vcfs/m84036_250809_035451_s4.bc2123_cyp21.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-26/call-run_paraphase/out/m84036_250809_035451_s4.bc2123_paraphase/m84036_250809_035451_s4.bc2123_paraphase_vcfs/m84036_250809_035451_s4.bc2123_f8inv1.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-26/call-run_paraphase/out/m84036_250809_035451_s4.bc2123_paraphase/m84036_250809_035451_s4.bc2123_paraphase_vcfs/m84036_250809_035451_s4.bc2123_f8inv22.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-26/call-run_paraphase/out/m84036_250809_035451_s4.bc2123_paraphase/m84036_250809_035451_s4.bc2123_paraphase_vcfs/m84036_250809_035451_s4.bc2123_gba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-26/call-run_paraphase/out/m84036_250809_035451_s4.bc2123_paraphase/m84036_250809_035451_s4.bc2123_paraphase_vcfs/m84036_250809_035451_s4.bc2123_hba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-26/call-run_paraphase/out/m84036_250809_035451_s4.bc2123_paraphase/m84036_250809_035451_s4.bc2123_paraphase_vcfs/m84036_250809_035451_s4.bc2123_hbb.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-26/call-run_paraphase/out/m84036_250809_035451_s4.bc2123_paraphase/m84036_250809_035451_s4.bc2123_paraphase_vcfs/m84036_250809_035451_s4.bc2123_rpgr.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-26/call-run_paraphase/out/m84036_250809_035451_s4.bc2123_paraphase/m84036_250809_035451_s4.bc2123_paraphase_vcfs/m84036_250809_035451_s4.bc2123_smn1.vcf"], "havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-26/call-run_paraphase/out/m84036_250809_035451_s4.bc2123.havanno.json", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-26/call-call_f8/out/m84036_250809_035451_s4.bc2123.f8inversion.json"}
2025-09-15 20:28:12.133 wdl.w:ptcp.w:call-paraphase-26 NOTICE done
2025-09-15 20:28:12.140 wdl.w:ptcp NOTICE finish :: job: "call-paraphase-26"
2025-09-15 20:28:12.140 wdl.w:ptcp INFO output :: job: "call-paraphase-26", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-26/out/m84036_250809_035451_s4.bc2123.f8inversion.vcf", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-26/out/m84036_250809_035451_s4.bc2123_paraphase/m84036_250809_035451_s4.bc2123.paraphase.json", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-26/out/m84036_250809_035451_s4.bc2123_paraphase/m84036_250809_035451_s4.bc2123.paraphase.bam", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-26/out/m84036_250809_035451_s4.bc2123_paraphase/m84036_250809_035451_s4.bc2123.paraphase.bam.bai", "paraphase_vcfs": ["/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-26/out/m84036_250809_035451_s4.bc2123_paraphase/m84036_250809_035451_s4.bc2123_paraphase_vcfs/m84036_250809_035451_s4.bc2123_cyp21.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-26/out/m84036_250809_035451_s4.bc2123_paraphase/m84036_250809_035451_s4.bc2123_paraphase_vcfs/m84036_250809_035451_s4.bc2123_f8inv1.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-26/out/m84036_250809_035451_s4.bc2123_paraphase/m84036_250809_035451_s4.bc2123_paraphase_vcfs/m84036_250809_035451_s4.bc2123_f8inv22.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-26/out/m84036_250809_035451_s4.bc2123_paraphase/m84036_250809_035451_s4.bc2123_paraphase_vcfs/m84036_250809_035451_s4.bc2123_gba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-26/out/m84036_250809_035451_s4.bc2123_paraphase/m84036_250809_035451_s4.bc2123_paraphase_vcfs/m84036_250809_035451_s4.bc2123_hba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-26/out/m84036_250809_035451_s4.bc2123_paraphase/m84036_250809_035451_s4.bc2123_paraphase_vcfs/m84036_250809_035451_s4.bc2123_hbb.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-26/out/m84036_250809_035451_s4.bc2123_paraphase/m84036_250809_035451_s4.bc2123_paraphase_vcfs/m84036_250809_035451_s4.bc2123_rpgr.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-26/out/m84036_250809_035451_s4.bc2123_paraphase/m84036_250809_035451_s4.bc2123_paraphase_vcfs/m84036_250809_035451_s4.bc2123_smn1.vcf"], "havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-26/out/m84036_250809_035451_s4.bc2123.havanno.json", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-26/out/m84036_250809_035451_s4.bc2123.f8inversion.json"}
2025-09-15 20:28:12.140 wdl.w:ptcp NOTICE ready :: job: "call-tar_outputs-26", callee: "tar_outputs"
2025-09-15 20:28:12.141 wdl.w:ptcp INFO input :: job: "call-tar_outputs-26", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "sawfish_vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-26/out/m84036_250809_035451_s4.bc2123_sawfish/m84036_250809_035451_s4.bc2123.sv.vcf.gz.tbi", "sawfish_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-26/out/m84036_250809_035451_s4.bc2123_sawfish/m84036_250809_035451_s4.bc2123.sv.vcf.gz", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-26/out/m84036_250809_035451_s4.bc2123.f8inversion.json", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-26/out/m84036_250809_035451_s4.bc2123_paraphase/m84036_250809_035451_s4.bc2123.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-26/out/m84036_250809_035451_s4.bc2123_paraphase/m84036_250809_035451_s4.bc2123.paraphase.bam", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-26/out/m84036_250809_035451_s4.bc2123_paraphase/m84036_250809_035451_s4.bc2123.paraphase.json", "trgt_spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-26/out/m84036_250809_035451_s4.bc2123.trgt.sorted.spanning.bam.bai", "trgt_spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-26/out/m84036_250809_035451_s4.bc2123.trgt.sorted.spanning.bam", "trgt_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-26/out/m84036_250809_035451_s4.bc2123.trgt.vcf", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-26/out/m84036_250809_035451_s4.bc2123.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-26/out/m84036_250809_035451_s4.bc2123.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2123"}
2025-09-15 20:28:12.146 wdl.w:ptcp.t:call-tar_outputs-26 NOTICE task setup :: name: "tar_outputs", source: "./common.wdl", line: 279, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-26", thread: 140610895857216
2025-09-15 20:28:12.165 wdl.w:ptcp.t:call-tar_outputs-26 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:28:12.165 wdl.w:ptcp.t:call-tar_outputs-26 INFO input :: name: "sawfish_vcf_tbi", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2123.sv.vcf.gz.tbi"
2025-09-15 20:28:12.165 wdl.w:ptcp.t:call-tar_outputs-26 INFO input :: name: "sawfish_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2123.sv.vcf.gz"
2025-09-15 20:28:12.165 wdl.w:ptcp.t:call-tar_outputs-26 INFO input :: name: "f8_json", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2123.f8inversion.json"
2025-09-15 20:28:12.165 wdl.w:ptcp.t:call-tar_outputs-26 INFO input :: name: "paraphase_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2123.paraphase.bam.bai"
2025-09-15 20:28:12.165 wdl.w:ptcp.t:call-tar_outputs-26 INFO input :: name: "paraphase_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2123.paraphase.bam"
2025-09-15 20:28:12.165 wdl.w:ptcp.t:call-tar_outputs-26 INFO input :: name: "paraphase_json", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2123.paraphase.json"
2025-09-15 20:28:12.165 wdl.w:ptcp.t:call-tar_outputs-26 INFO input :: name: "trgt_spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2123.trgt.sorted.spanning.bam.bai"
2025-09-15 20:28:12.165 wdl.w:ptcp.t:call-tar_outputs-26 INFO input :: name: "trgt_spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2123.trgt.sorted.spanning.bam"
2025-09-15 20:28:12.165 wdl.w:ptcp.t:call-tar_outputs-26 INFO input :: name: "trgt_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2123.trgt.vcf"
2025-09-15 20:28:12.166 wdl.w:ptcp.t:call-tar_outputs-26 INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2123.mapped.bam.bai"
2025-09-15 20:28:12.166 wdl.w:ptcp.t:call-tar_outputs-26 INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2123.mapped.bam"
2025-09-15 20:28:12.166 wdl.w:ptcp.t:call-tar_outputs-26 INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2123"
2025-09-15 20:28:12.166 wdl.w:ptcp.t:call-tar_outputs-26 INFO eval :: name: "threads", value: 1
2025-09-15 20:28:12.166 wdl.w:ptcp.t:call-tar_outputs-26 INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:28:12.166 wdl.w:ptcp.t:call-tar_outputs-26 INFO eval :: name: "disk_size", value: 6
2025-09-15 20:28:12.166 wdl.w:ptcp.t:call-tar_outputs-26 INFO eval :: name: "output_tarball", value: "m84036_250809_035451_s4.bc2123.tar"
2025-09-15 20:28:12.167 wdl.w:ptcp.t:call-tar_outputs-26 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:28:12.167 wdl.w:ptcp.t:call-tar_outputs-26 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:28:12.167 wdl.w:ptcp.t:call-tar_outputs-26 INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:28:12.167 wdl.w:ptcp.t:call-tar_outputs-26 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:28:12.269 wdl.w:ptcp.t:call-tar_outputs-26 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 17, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-26/_singularity_tmpdir_uk_kv3k3"
2025-09-15 20:28:12.270 wdl.w:ptcp.t:call-tar_outputs-26 INFO Slurm invocation: srun --job-name call-tar_outputs-26 --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-26/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-26/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-26/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-26/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-26/out/m84036_250809_035451_s4.bc2123_sawfish/m84036_250809_035451_s4.bc2123.sv.vcf.gz.tbi:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2123.sv.vcf.gz.tbi:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-26/out/m84036_250809_035451_s4.bc2123_sawfish/m84036_250809_035451_s4.bc2123.sv.vcf.gz:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2123.sv.vcf.gz:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-26/out/m84036_250809_035451_s4.bc2123_paraphase/m84036_250809_035451_s4.bc2123.paraphase.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2123.paraphase.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-26/out/m84036_250809_035451_s4.bc2123_paraphase/m84036_250809_035451_s4.bc2123.paraphase.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2123.paraphase.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-26/out/m84036_250809_035451_s4.bc2123_paraphase/m84036_250809_035451_s4.bc2123.paraphase.json:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2123.paraphase.json:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-26/out/m84036_250809_035451_s4.bc2123.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2123.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-26/out/m84036_250809_035451_s4.bc2123.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2123.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-26/out/m84036_250809_035451_s4.bc2123.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2123.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-26/out/m84036_250809_035451_s4.bc2123.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2123.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-26/out/m84036_250809_035451_s4.bc2123.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2123.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-26/out/m84036_250809_035451_s4.bc2123.f8inversion.json:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2123.f8inversion.json:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-26/_singularity_tmpdir_uk_kv3k3/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-26/_singularity_tmpdir_uk_kv3k3/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:28:12.275 wdl.w:ptcp.t:call-tar_outputs-26 NOTICE slurm_singularity run :: pid: 1209025, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-26/slurm_singularity.log.txt"
2025-09-15 20:28:12.798 wdl.w:ptcp.w:call-paraphase-06.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for f8inv22 for sample m84036_250809_035451_s4.bc2103 at 2025-09-15 20:28:03.360637...
2025-09-15 20:28:12.799 wdl.w:ptcp.w:call-paraphase-06.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for f8inv22 for sample m84036_250809_035451_s4.bc2103 at 2025-09-15 20:28:03.361208...
2025-09-15 20:28:13.284 wdl.w:ptcp.t:call-tar_outputs-26.slurm_singularity INFO srun: job 51798244 queued and waiting for resources
2025-09-15 20:28:13.801 wdl.w:ptcp.w:call-paraphase-42.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for f8inv22 for sample m84036_250809_035451_s4.bc2139 at 2025-09-15 20:28:02.039471...
2025-09-15 20:28:13.802 wdl.w:ptcp.w:call-paraphase-42.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for f8inv22 for sample m84036_250809_035451_s4.bc2139 at 2025-09-15 20:28:02.040044...
2025-09-15 20:28:14.294 wdl.w:ptcp.t:call-tar_outputs-26.slurm_singularity INFO srun: job 51798244 has been allocated resources
2025-09-15 20:28:14.294 wdl.w:ptcp.t:call-tar_outputs-26.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:28:14.745 wdl.w:ptcp.t:call-tar_outputs-26 INFO output :: name: "sample_tarball", value: "m84036_250809_035451_s4.bc2123.tar"
2025-09-15 20:28:14.797 wdl.w:ptcp.t:call-tar_outputs-26 NOTICE done
2025-09-15 20:28:14.802 wdl.w:ptcp NOTICE finish :: job: "call-tar_outputs-26"
2025-09-15 20:28:14.802 wdl.w:ptcp INFO output :: job: "call-tar_outputs-26", values: {"sample_tarball": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-26/out/m84036_250809_035451_s4.bc2123.tar"}
2025-09-15 20:28:25.718 wdl.w:ptcp.w:call-paraphase-63.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for rpgr for sample m84036_250809_035451_s4.bc2160 at 2025-09-15 20:28:18.302830...
2025-09-15 20:28:25.718 wdl.w:ptcp.w:call-paraphase-63.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for rpgr for sample m84036_250809_035451_s4.bc2160 at 2025-09-15 20:28:18.304821...
2025-09-15 20:28:25.718 wdl.w:ptcp.w:call-paraphase-63.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for rpgr for sample m84036_250809_035451_s4.bc2160 at 2025-09-15 20:28:20.941108...
2025-09-15 20:28:25.718 wdl.w:ptcp.w:call-paraphase-63.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for rpgr for sample m84036_250809_035451_s4.bc2160 at 2025-09-15 20:28:22.245315...
2025-09-15 20:28:25.718 wdl.w:ptcp.w:call-paraphase-63.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for rpgr for sample m84036_250809_035451_s4.bc2160 at 2025-09-15 20:28:22.452852...
2025-09-15 20:28:26.638 wdl.w:ptcp.w:call-paraphase-42.t:call-run_paraphase INFO output :: name: "paraphase_bam", value: "m84036_250809_035451_s4.bc2139_paraphase/m84036_250809_035451_s4.bc2139.paraphase.bam"
2025-09-15 20:28:26.641 wdl.w:ptcp.w:call-paraphase-42.t:call-run_paraphase INFO output :: name: "paraphase_bam_bai", value: "m84036_250809_035451_s4.bc2139_paraphase/m84036_250809_035451_s4.bc2139.paraphase.bam.bai"
2025-09-15 20:28:26.642 wdl.w:ptcp.w:call-paraphase-42.t:call-run_paraphase INFO output :: name: "paraphase_json", value: "m84036_250809_035451_s4.bc2139_paraphase/m84036_250809_035451_s4.bc2139.paraphase.json"
2025-09-15 20:28:26.646 wdl.w:ptcp.w:call-paraphase-42.t:call-run_paraphase INFO output :: name: "paraphase_vcfs", value: ["/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2139_paraphase/m84036_250809_035451_s4.bc2139_paraphase_vcfs/m84036_250809_035451_s4.bc2139_cyp21.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2139_paraphase/m84036_250809_035451_s4.bc2139_paraphase_vcfs/m84036_250809_035451_s4.bc2139_f8inv1.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2139_paraphase/m84036_250809_035451_s4.bc2139_paraphase_vcfs/m84036_250809_035451_s4.bc2139_f8inv22.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2139_paraphase/m84036_250809_035451_s4.bc2139_paraphase_vcfs/m84036_250809_035451_s4.bc2139_gba.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2139_paraphase/m84036_250809_035451_s4.bc2139_paraphase_vcfs/m84036_250809_035451_s4.bc2139_hba.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2139_paraphase/m84036_250809_035451_s4.bc2139_paraphase_vcfs/m84036_250809_035451_s4.bc2139_hbb.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2139_paraphase/m84036_250809_035451_s4.bc2139_paraphase_vcfs/m84036_250809_035451_s4.bc2139_rpgr.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2139_paraphase/m84036_250809_035451_s4.bc2139_paraphase_vcfs/m84036_250809_035451_s4.bc2139_smn1.vcf"]
2025-09-15 20:28:26.649 wdl.w:ptcp.w:call-paraphase-42.t:call-run_paraphase INFO output :: name: "havanno_json", value: "m84036_250809_035451_s4.bc2139.havanno.json"
2025-09-15 20:28:26.789 wdl.w:ptcp.w:call-paraphase-71.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for rpgr for sample m84036_250809_035451_s4.bc2168 at 2025-09-15 20:27:59.119196...
2025-09-15 20:28:26.789 wdl.w:ptcp.w:call-paraphase-71.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for rpgr for sample m84036_250809_035451_s4.bc2168 at 2025-09-15 20:28:00.094328...
2025-09-15 20:28:26.789 wdl.w:ptcp.w:call-paraphase-71.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for rpgr for sample m84036_250809_035451_s4.bc2168 at 2025-09-15 20:28:00.228159...
2025-09-15 20:28:26.793 wdl.w:ptcp.w:call-paraphase-42.t:call-run_paraphase NOTICE done
2025-09-15 20:28:26.798 wdl.w:ptcp.w:call-paraphase-42 NOTICE finish :: job: "call-run_paraphase"
2025-09-15 20:28:26.799 wdl.w:ptcp.w:call-paraphase-42 INFO output :: job: "call-run_paraphase", values: {"havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-42/call-run_paraphase/out/m84036_250809_035451_s4.bc2139.havanno.json", "paraphase_vcfs": ["/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-42/call-run_paraphase/out/m84036_250809_035451_s4.bc2139_paraphase/m84036_250809_035451_s4.bc2139_paraphase_vcfs/m84036_250809_035451_s4.bc2139_cyp21.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-42/call-run_paraphase/out/m84036_250809_035451_s4.bc2139_paraphase/m84036_250809_035451_s4.bc2139_paraphase_vcfs/m84036_250809_035451_s4.bc2139_f8inv1.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-42/call-run_paraphase/out/m84036_250809_035451_s4.bc2139_paraphase/m84036_250809_035451_s4.bc2139_paraphase_vcfs/m84036_250809_035451_s4.bc2139_f8inv22.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-42/call-run_paraphase/out/m84036_250809_035451_s4.bc2139_paraphase/m84036_250809_035451_s4.bc2139_paraphase_vcfs/m84036_250809_035451_s4.bc2139_gba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-42/call-run_paraphase/out/m84036_250809_035451_s4.bc2139_paraphase/m84036_250809_035451_s4.bc2139_paraphase_vcfs/m84036_250809_035451_s4.bc2139_hba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-42/call-run_paraphase/out/m84036_250809_035451_s4.bc2139_paraphase/m84036_250809_035451_s4.bc2139_paraphase_vcfs/m84036_250809_035451_s4.bc2139_hbb.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-42/call-run_paraphase/out/m84036_250809_035451_s4.bc2139_paraphase/m84036_250809_035451_s4.bc2139_paraphase_vcfs/m84036_250809_035451_s4.bc2139_rpgr.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-42/call-run_paraphase/out/m84036_250809_035451_s4.bc2139_paraphase/m84036_250809_035451_s4.bc2139_paraphase_vcfs/m84036_250809_035451_s4.bc2139_smn1.vcf"], "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-42/call-run_paraphase/out/m84036_250809_035451_s4.bc2139_paraphase/m84036_250809_035451_s4.bc2139.paraphase.json", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-42/call-run_paraphase/out/m84036_250809_035451_s4.bc2139_paraphase/m84036_250809_035451_s4.bc2139.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-42/call-run_paraphase/out/m84036_250809_035451_s4.bc2139_paraphase/m84036_250809_035451_s4.bc2139.paraphase.bam"}
2025-09-15 20:28:26.799 wdl.w:ptcp.w:call-paraphase-42 NOTICE ready :: job: "call-call_f8", callee: "call_f8"
2025-09-15 20:28:26.800 wdl.w:ptcp.w:call-paraphase-42 INFO input :: job: "call-call_f8", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "out_prefix": "m84036_250809_035451_s4.bc2139", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-42/call-run_paraphase/out/m84036_250809_035451_s4.bc2139_paraphase/m84036_250809_035451_s4.bc2139.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-42/call-run_paraphase/out/m84036_250809_035451_s4.bc2139_paraphase/m84036_250809_035451_s4.bc2139.paraphase.bam", "sex": "F"}
2025-09-15 20:28:26.800 wdl.w:ptcp.w:call-paraphase-42 INFO visit :: node: "output-havanno_json", values: {"havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-42/call-run_paraphase/out/m84036_250809_035451_s4.bc2139.havanno.json"}
2025-09-15 20:28:26.800 wdl.w:ptcp.w:call-paraphase-42 INFO visit :: node: "output-paraphase_bam", values: {"paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-42/call-run_paraphase/out/m84036_250809_035451_s4.bc2139_paraphase/m84036_250809_035451_s4.bc2139.paraphase.bam"}
2025-09-15 20:28:26.800 wdl.w:ptcp.w:call-paraphase-42 INFO visit :: node: "output-paraphase_bam_bai", values: {"paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-42/call-run_paraphase/out/m84036_250809_035451_s4.bc2139_paraphase/m84036_250809_035451_s4.bc2139.paraphase.bam.bai"}
2025-09-15 20:28:26.800 wdl.w:ptcp.w:call-paraphase-42 INFO visit :: node: "output-paraphase_json", values: {"paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-42/call-run_paraphase/out/m84036_250809_035451_s4.bc2139_paraphase/m84036_250809_035451_s4.bc2139.paraphase.json"}
2025-09-15 20:28:26.800 wdl.w:ptcp.w:call-paraphase-42 INFO visit :: node: "output-paraphase_vcfs", values: {"paraphase_vcfs": ["/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-42/call-run_paraphase/out/m84036_250809_035451_s4.bc2139_paraphase/m84036_250809_035451_s4.bc2139_paraphase_vcfs/m84036_250809_035451_s4.bc2139_cyp21.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-42/call-run_paraphase/out/m84036_250809_035451_s4.bc2139_paraphase/m84036_250809_035451_s4.bc2139_paraphase_vcfs/m84036_250809_035451_s4.bc2139_f8inv1.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-42/call-run_paraphase/out/m84036_250809_035451_s4.bc2139_paraphase/m84036_250809_035451_s4.bc2139_paraphase_vcfs/m84036_250809_035451_s4.bc2139_f8inv22.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-42/call-run_paraphase/out/m84036_250809_035451_s4.bc2139_paraphase/m84036_250809_035451_s4.bc2139_paraphase_vcfs/m84036_250809_035451_s4.bc2139_gba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-42/call-run_paraphase/out/m84036_250809_035451_s4.bc2139_paraphase/m84036_250809_035451_s4.bc2139_paraphase_vcfs/m84036_250809_035451_s4.bc2139_hba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-42/call-run_paraphase/out/m84036_250809_035451_s4.bc2139_paraphase/m84036_250809_035451_s4.bc2139_paraphase_vcfs/m84036_250809_035451_s4.bc2139_hbb.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-42/call-run_paraphase/out/m84036_250809_035451_s4.bc2139_paraphase/m84036_250809_035451_s4.bc2139_paraphase_vcfs/m84036_250809_035451_s4.bc2139_rpgr.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-42/call-run_paraphase/out/m84036_250809_035451_s4.bc2139_paraphase/m84036_250809_035451_s4.bc2139_paraphase_vcfs/m84036_250809_035451_s4.bc2139_smn1.vcf"]}
2025-09-15 20:28:26.805 wdl.w:ptcp.w:call-paraphase-42.t:call-call_f8 NOTICE task setup :: name: "call_f8", source: "./paraphase.wdl", line: 232, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-42/call-call_f8", thread: 140609822115392
2025-09-15 20:28:26.819 wdl.w:ptcp.w:call-paraphase-42.t:call-call_f8 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:28:26.819 wdl.w:ptcp.w:call-paraphase-42.t:call-call_f8 INFO input :: name: "genome_version", value: "38"
2025-09-15 20:28:26.819 wdl.w:ptcp.w:call-paraphase-42.t:call-call_f8 INFO input :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2139"
2025-09-15 20:28:26.819 wdl.w:ptcp.w:call-paraphase-42.t:call-call_f8 INFO input :: name: "paraphase_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2139.paraphase.bam.bai"
2025-09-15 20:28:26.819 wdl.w:ptcp.w:call-paraphase-42.t:call-call_f8 INFO input :: name: "paraphase_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2139.paraphase.bam"
2025-09-15 20:28:26.819 wdl.w:ptcp.w:call-paraphase-42.t:call-call_f8 INFO input :: name: "sex", value: "F"
2025-09-15 20:28:26.820 wdl.w:ptcp.w:call-paraphase-42.t:call-call_f8 INFO eval :: name: "threads", value: 1
2025-09-15 20:28:26.820 wdl.w:ptcp.w:call-paraphase-42.t:call-call_f8 INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:28:26.820 wdl.w:ptcp.w:call-paraphase-42.t:call-call_f8 INFO eval :: name: "disk_size", value: 11
2025-09-15 20:28:26.820 wdl.w:ptcp.w:call-paraphase-42.t:call-call_f8 INFO eval :: name: "sample_sex", value: "F"
2025-09-15 20:28:26.820 wdl.w:ptcp.w:call-paraphase-42.t:call-call_f8 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:28:26.820 wdl.w:ptcp.w:call-paraphase-42.t:call-call_f8 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:28:26.821 wdl.w:ptcp.w:call-paraphase-42.t:call-call_f8 INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:28:26.821 wdl.w:ptcp.w:call-paraphase-42.t:call-call_f8 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:28:26.859 wdl.w:ptcp.w:call-paraphase-42.t:call-call_f8 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 8, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-42/call-call_f8/_singularity_tmpdir_o3nu573p"
2025-09-15 20:28:26.859 wdl.w:ptcp.w:call-paraphase-42.t:call-call_f8 INFO Slurm invocation: srun --job-name call-call_f8 --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-42/call-call_f8/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-42/call-call_f8/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-42/call-call_f8/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-42/call-call_f8/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-42/call-run_paraphase/out/m84036_250809_035451_s4.bc2139_paraphase/m84036_250809_035451_s4.bc2139.paraphase.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2139.paraphase.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-42/call-run_paraphase/out/m84036_250809_035451_s4.bc2139_paraphase/m84036_250809_035451_s4.bc2139.paraphase.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2139.paraphase.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-42/call-call_f8/_singularity_tmpdir_o3nu573p/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-42/call-call_f8/_singularity_tmpdir_o3nu573p/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:28:26.869 wdl.w:ptcp.w:call-paraphase-42.t:call-call_f8 NOTICE slurm_singularity run :: pid: 1209108, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-42/call-call_f8/slurm_singularity.log.txt"
2025-09-15 20:28:26.946 wdl.w:ptcp.w:call-paraphase-02.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for rpgr for sample m84036_250809_035451_s4.bc2099 at 2025-09-15 20:28:24.691640...
2025-09-15 20:28:26.946 wdl.w:ptcp.w:call-paraphase-02.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for rpgr for sample m84036_250809_035451_s4.bc2099 at 2025-09-15 20:28:24.693122...
2025-09-15 20:28:27.878 wdl.w:ptcp.w:call-paraphase-42.t:call-call_f8.slurm_singularity INFO srun: job 51798247 queued and waiting for resources
2025-09-15 20:28:27.878 wdl.w:ptcp.w:call-paraphase-42.t:call-call_f8.slurm_singularity INFO srun: job 51798247 has been allocated resources
2025-09-15 20:28:27.878 wdl.w:ptcp.w:call-paraphase-42.t:call-call_f8.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:28:28.125 wdl.w:ptcp.w:call-paraphase-42.t:call-call_f8 INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2139.f8inversion.vcf"
2025-09-15 20:28:28.127 wdl.w:ptcp.w:call-paraphase-42.t:call-call_f8 INFO output :: name: "json", value: "m84036_250809_035451_s4.bc2139.f8inversion.json"
2025-09-15 20:28:28.179 wdl.w:ptcp.w:call-paraphase-42.t:call-call_f8 NOTICE done
2025-09-15 20:28:28.184 wdl.w:ptcp.w:call-paraphase-42 NOTICE finish :: job: "call-call_f8"
2025-09-15 20:28:28.184 wdl.w:ptcp.w:call-paraphase-42 INFO output :: job: "call-call_f8", values: {"json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-42/call-call_f8/out/m84036_250809_035451_s4.bc2139.f8inversion.json", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-42/call-call_f8/out/m84036_250809_035451_s4.bc2139.f8inversion.vcf"}
2025-09-15 20:28:28.185 wdl.w:ptcp.w:call-paraphase-42 INFO visit :: node: "output-f8_json", values: {"f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-42/call-call_f8/out/m84036_250809_035451_s4.bc2139.f8inversion.json"}
2025-09-15 20:28:28.185 wdl.w:ptcp.w:call-paraphase-42 INFO visit :: node: "output-f8_vcf", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-42/call-call_f8/out/m84036_250809_035451_s4.bc2139.f8inversion.vcf"}
2025-09-15 20:28:28.185 wdl.w:ptcp.w:call-paraphase-42 INFO visit :: node: "outputs", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-42/call-call_f8/out/m84036_250809_035451_s4.bc2139.f8inversion.vcf", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-42/call-run_paraphase/out/m84036_250809_035451_s4.bc2139_paraphase/m84036_250809_035451_s4.bc2139.paraphase.json", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-42/call-run_paraphase/out/m84036_250809_035451_s4.bc2139_paraphase/m84036_250809_035451_s4.bc2139.paraphase.bam", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-42/call-run_paraphase/out/m84036_250809_035451_s4.bc2139_paraphase/m84036_250809_035451_s4.bc2139.paraphase.bam.bai", "paraphase_vcfs": ["/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-42/call-run_paraphase/out/m84036_250809_035451_s4.bc2139_paraphase/m84036_250809_035451_s4.bc2139_paraphase_vcfs/m84036_250809_035451_s4.bc2139_cyp21.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-42/call-run_paraphase/out/m84036_250809_035451_s4.bc2139_paraphase/m84036_250809_035451_s4.bc2139_paraphase_vcfs/m84036_250809_035451_s4.bc2139_f8inv1.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-42/call-run_paraphase/out/m84036_250809_035451_s4.bc2139_paraphase/m84036_250809_035451_s4.bc2139_paraphase_vcfs/m84036_250809_035451_s4.bc2139_f8inv22.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-42/call-run_paraphase/out/m84036_250809_035451_s4.bc2139_paraphase/m84036_250809_035451_s4.bc2139_paraphase_vcfs/m84036_250809_035451_s4.bc2139_gba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-42/call-run_paraphase/out/m84036_250809_035451_s4.bc2139_paraphase/m84036_250809_035451_s4.bc2139_paraphase_vcfs/m84036_250809_035451_s4.bc2139_hba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-42/call-run_paraphase/out/m84036_250809_035451_s4.bc2139_paraphase/m84036_250809_035451_s4.bc2139_paraphase_vcfs/m84036_250809_035451_s4.bc2139_hbb.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-42/call-run_paraphase/out/m84036_250809_035451_s4.bc2139_paraphase/m84036_250809_035451_s4.bc2139_paraphase_vcfs/m84036_250809_035451_s4.bc2139_rpgr.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-42/call-run_paraphase/out/m84036_250809_035451_s4.bc2139_paraphase/m84036_250809_035451_s4.bc2139_paraphase_vcfs/m84036_250809_035451_s4.bc2139_smn1.vcf"], "havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-42/call-run_paraphase/out/m84036_250809_035451_s4.bc2139.havanno.json", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-42/call-call_f8/out/m84036_250809_035451_s4.bc2139.f8inversion.json"}
2025-09-15 20:28:28.288 wdl.w:ptcp.w:call-paraphase-42 NOTICE done
2025-09-15 20:28:28.294 wdl.w:ptcp NOTICE finish :: job: "call-paraphase-42"
2025-09-15 20:28:28.294 wdl.w:ptcp INFO output :: job: "call-paraphase-42", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-42/out/m84036_250809_035451_s4.bc2139.f8inversion.vcf", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-42/out/m84036_250809_035451_s4.bc2139_paraphase/m84036_250809_035451_s4.bc2139.paraphase.json", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-42/out/m84036_250809_035451_s4.bc2139_paraphase/m84036_250809_035451_s4.bc2139.paraphase.bam", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-42/out/m84036_250809_035451_s4.bc2139_paraphase/m84036_250809_035451_s4.bc2139.paraphase.bam.bai", "paraphase_vcfs": ["/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-42/out/m84036_250809_035451_s4.bc2139_paraphase/m84036_250809_035451_s4.bc2139_paraphase_vcfs/m84036_250809_035451_s4.bc2139_cyp21.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-42/out/m84036_250809_035451_s4.bc2139_paraphase/m84036_250809_035451_s4.bc2139_paraphase_vcfs/m84036_250809_035451_s4.bc2139_f8inv1.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-42/out/m84036_250809_035451_s4.bc2139_paraphase/m84036_250809_035451_s4.bc2139_paraphase_vcfs/m84036_250809_035451_s4.bc2139_f8inv22.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-42/out/m84036_250809_035451_s4.bc2139_paraphase/m84036_250809_035451_s4.bc2139_paraphase_vcfs/m84036_250809_035451_s4.bc2139_gba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-42/out/m84036_250809_035451_s4.bc2139_paraphase/m84036_250809_035451_s4.bc2139_paraphase_vcfs/m84036_250809_035451_s4.bc2139_hba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-42/out/m84036_250809_035451_s4.bc2139_paraphase/m84036_250809_035451_s4.bc2139_paraphase_vcfs/m84036_250809_035451_s4.bc2139_hbb.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-42/out/m84036_250809_035451_s4.bc2139_paraphase/m84036_250809_035451_s4.bc2139_paraphase_vcfs/m84036_250809_035451_s4.bc2139_rpgr.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-42/out/m84036_250809_035451_s4.bc2139_paraphase/m84036_250809_035451_s4.bc2139_paraphase_vcfs/m84036_250809_035451_s4.bc2139_smn1.vcf"], "havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-42/out/m84036_250809_035451_s4.bc2139.havanno.json", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-42/out/m84036_250809_035451_s4.bc2139.f8inversion.json"}
2025-09-15 20:28:28.295 wdl.w:ptcp NOTICE ready :: job: "call-tar_outputs-42", callee: "tar_outputs"
2025-09-15 20:28:28.295 wdl.w:ptcp INFO input :: job: "call-tar_outputs-42", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "sawfish_vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-42/out/m84036_250809_035451_s4.bc2139_sawfish/m84036_250809_035451_s4.bc2139.sv.vcf.gz.tbi", "sawfish_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-42/out/m84036_250809_035451_s4.bc2139_sawfish/m84036_250809_035451_s4.bc2139.sv.vcf.gz", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-42/out/m84036_250809_035451_s4.bc2139.f8inversion.json", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-42/out/m84036_250809_035451_s4.bc2139_paraphase/m84036_250809_035451_s4.bc2139.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-42/out/m84036_250809_035451_s4.bc2139_paraphase/m84036_250809_035451_s4.bc2139.paraphase.bam", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-42/out/m84036_250809_035451_s4.bc2139_paraphase/m84036_250809_035451_s4.bc2139.paraphase.json", "trgt_spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-42/out/m84036_250809_035451_s4.bc2139.trgt.sorted.spanning.bam.bai", "trgt_spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-42/out/m84036_250809_035451_s4.bc2139.trgt.sorted.spanning.bam", "trgt_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-42/out/m84036_250809_035451_s4.bc2139.trgt.vcf", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-42/out/m84036_250809_035451_s4.bc2139.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-42/out/m84036_250809_035451_s4.bc2139.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2139"}
2025-09-15 20:28:28.301 wdl.w:ptcp.t:call-tar_outputs-42 NOTICE task setup :: name: "tar_outputs", source: "./common.wdl", line: 279, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-42", thread: 140612506469952
2025-09-15 20:28:28.322 wdl.w:ptcp.t:call-tar_outputs-42 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:28:28.322 wdl.w:ptcp.t:call-tar_outputs-42 INFO input :: name: "sawfish_vcf_tbi", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2139.sv.vcf.gz.tbi"
2025-09-15 20:28:28.322 wdl.w:ptcp.t:call-tar_outputs-42 INFO input :: name: "sawfish_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2139.sv.vcf.gz"
2025-09-15 20:28:28.322 wdl.w:ptcp.t:call-tar_outputs-42 INFO input :: name: "f8_json", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2139.f8inversion.json"
2025-09-15 20:28:28.322 wdl.w:ptcp.t:call-tar_outputs-42 INFO input :: name: "paraphase_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2139.paraphase.bam.bai"
2025-09-15 20:28:28.322 wdl.w:ptcp.t:call-tar_outputs-42 INFO input :: name: "paraphase_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2139.paraphase.bam"
2025-09-15 20:28:28.322 wdl.w:ptcp.t:call-tar_outputs-42 INFO input :: name: "paraphase_json", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2139.paraphase.json"
2025-09-15 20:28:28.322 wdl.w:ptcp.t:call-tar_outputs-42 INFO input :: name: "trgt_spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2139.trgt.sorted.spanning.bam.bai"
2025-09-15 20:28:28.322 wdl.w:ptcp.t:call-tar_outputs-42 INFO input :: name: "trgt_spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2139.trgt.sorted.spanning.bam"
2025-09-15 20:28:28.322 wdl.w:ptcp.t:call-tar_outputs-42 INFO input :: name: "trgt_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2139.trgt.vcf"
2025-09-15 20:28:28.322 wdl.w:ptcp.t:call-tar_outputs-42 INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2139.mapped.bam.bai"
2025-09-15 20:28:28.322 wdl.w:ptcp.t:call-tar_outputs-42 INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2139.mapped.bam"
2025-09-15 20:28:28.322 wdl.w:ptcp.t:call-tar_outputs-42 INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2139"
2025-09-15 20:28:28.323 wdl.w:ptcp.t:call-tar_outputs-42 INFO eval :: name: "threads", value: 1
2025-09-15 20:28:28.323 wdl.w:ptcp.t:call-tar_outputs-42 INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:28:28.323 wdl.w:ptcp.t:call-tar_outputs-42 INFO eval :: name: "disk_size", value: 6
2025-09-15 20:28:28.323 wdl.w:ptcp.t:call-tar_outputs-42 INFO eval :: name: "output_tarball", value: "m84036_250809_035451_s4.bc2139.tar"
2025-09-15 20:28:28.323 wdl.w:ptcp.t:call-tar_outputs-42 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:28:28.323 wdl.w:ptcp.t:call-tar_outputs-42 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:28:28.324 wdl.w:ptcp.t:call-tar_outputs-42 INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:28:28.324 wdl.w:ptcp.t:call-tar_outputs-42 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:28:28.396 wdl.w:ptcp.t:call-tar_outputs-42 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 17, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-42/_singularity_tmpdir_1i35qv_f"
2025-09-15 20:28:28.396 wdl.w:ptcp.t:call-tar_outputs-42 INFO Slurm invocation: srun --job-name call-tar_outputs-42 --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-42/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-42/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-42/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-42/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-42/out/m84036_250809_035451_s4.bc2139.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2139.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-42/out/m84036_250809_035451_s4.bc2139.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2139.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-42/out/m84036_250809_035451_s4.bc2139.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2139.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-42/out/m84036_250809_035451_s4.bc2139.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2139.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-42/out/m84036_250809_035451_s4.bc2139.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2139.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-42/out/m84036_250809_035451_s4.bc2139.f8inversion.json:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2139.f8inversion.json:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-42/out/m84036_250809_035451_s4.bc2139_paraphase/m84036_250809_035451_s4.bc2139.paraphase.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2139.paraphase.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-42/out/m84036_250809_035451_s4.bc2139_paraphase/m84036_250809_035451_s4.bc2139.paraphase.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2139.paraphase.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-42/out/m84036_250809_035451_s4.bc2139_paraphase/m84036_250809_035451_s4.bc2139.paraphase.json:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2139.paraphase.json:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-42/out/m84036_250809_035451_s4.bc2139_sawfish/m84036_250809_035451_s4.bc2139.sv.vcf.gz.tbi:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2139.sv.vcf.gz.tbi:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-42/out/m84036_250809_035451_s4.bc2139_sawfish/m84036_250809_035451_s4.bc2139.sv.vcf.gz:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2139.sv.vcf.gz:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-42/_singularity_tmpdir_1i35qv_f/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-42/_singularity_tmpdir_1i35qv_f/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:28:28.404 wdl.w:ptcp.t:call-tar_outputs-42 NOTICE slurm_singularity run :: pid: 1209117, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-42/slurm_singularity.log.txt"
2025-09-15 20:28:29.416 wdl.w:ptcp.t:call-tar_outputs-42.slurm_singularity INFO srun: job 51798248 queued and waiting for resources
2025-09-15 20:28:29.955 wdl.w:ptcp.w:call-paraphase-75.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for hbb for sample m84036_250809_035451_s4.bc2172 at 2025-09-15 20:28:16.906498...
2025-09-15 20:28:29.955 wdl.w:ptcp.w:call-paraphase-75.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for hbb for sample m84036_250809_035451_s4.bc2172 at 2025-09-15 20:28:16.909513...
2025-09-15 20:28:29.955 wdl.w:ptcp.w:call-paraphase-75.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for hbb for sample m84036_250809_035451_s4.bc2172 at 2025-09-15 20:28:19.214779...
2025-09-15 20:28:29.977 wdl.w:ptcp.w:call-paraphase-02.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for rpgr for sample m84036_250809_035451_s4.bc2099 at 2025-09-15 20:28:27.777837...
2025-09-15 20:28:29.978 wdl.w:ptcp.w:call-paraphase-02.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for rpgr for sample m84036_250809_035451_s4.bc2099 at 2025-09-15 20:28:29.328663...
2025-09-15 20:28:29.994 wdl.w:ptcp.w:call-paraphase-38.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for f8inv22 for sample m84036_250809_035451_s4.bc2135 at 2025-09-15 20:27:58.298253...
2025-09-15 20:28:29.994 wdl.w:ptcp.w:call-paraphase-38.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for f8inv22 for sample m84036_250809_035451_s4.bc2135 at 2025-09-15 20:27:58.299082...
2025-09-15 20:28:29.994 wdl.w:ptcp.w:call-paraphase-38.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for f8inv22 for sample m84036_250809_035451_s4.bc2135 at 2025-09-15 20:27:59.441185...
2025-09-15 20:28:29.994 wdl.w:ptcp.w:call-paraphase-38.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for f8inv22 for sample m84036_250809_035451_s4.bc2135 at 2025-09-15 20:28:04.500491...
2025-09-15 20:28:29.995 wdl.w:ptcp.w:call-paraphase-38.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for f8inv22 for sample m84036_250809_035451_s4.bc2135 at 2025-09-15 20:28:04.860841...
2025-09-15 20:28:29.995 wdl.w:ptcp.w:call-paraphase-38.t:call-run_paraphase.stderr VERBOSE INFO:root:Merging all bams for sample m84036_250809_035451_s4.bc2135 at 2025-09-15 20:28:26.542581...
2025-09-15 20:28:29.995 wdl.w:ptcp.w:call-paraphase-38.t:call-run_paraphase.stderr VERBOSE INFO:root:Writing to json for sample m84036_250809_035451_s4.bc2135 at 2025-09-15 20:28:29.072754...
2025-09-15 20:28:29.995 wdl.w:ptcp.w:call-paraphase-38.t:call-run_paraphase.stderr VERBOSE INFO:root:Completed Paraphase analysis at 2025-09-15 20:28:29.242375...
2025-09-15 20:28:29.995 wdl.w:ptcp.w:call-paraphase-38.t:call-run_paraphase.stderr VERBOSE [2025-09-15 20:28:29,763] INFO - reading variant list from /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf
2025-09-15 20:28:29.995 wdl.w:ptcp.w:call-paraphase-38.t:call-run_paraphase.stderr VERBOSE [2025-09-15 20:28:29,774] INFO - reading paraphase variant list from m84036_250809_035451_s4.bc2135_paraphase/m84036_250809_035451_s4.bc2135_paraphase_vcfs/m84036_250809_035451_s4.bc2135_cyp21.vcf
2025-09-15 20:28:29.995 wdl.w:ptcp.w:call-paraphase-38.t:call-run_paraphase.stderr VERBOSE [2025-09-15 20:28:29,778] INFO - finding matches of paraphase variants in the VCF
2025-09-15 20:28:29.995 wdl.w:ptcp.w:call-paraphase-38.t:call-run_paraphase.stderr VERBOSE [2025-09-15 20:28:29,779] INFO - writing output and wrapping up...
2025-09-15 20:28:29.995 wdl.w:ptcp.w:call-paraphase-38.t:call-run_paraphase.stderr VERBOSE [2025-09-15 20:28:29,779] INFO - reading paraphase variant list from m84036_250809_035451_s4.bc2135_paraphase/m84036_250809_035451_s4.bc2135_paraphase_vcfs/m84036_250809_035451_s4.bc2135_f8inv1.vcf
2025-09-15 20:28:29.995 wdl.w:ptcp.w:call-paraphase-38.t:call-run_paraphase.stderr VERBOSE [2025-09-15 20:28:29,783] INFO - finding matches of paraphase variants in the VCF
2025-09-15 20:28:29.995 wdl.w:ptcp.w:call-paraphase-38.t:call-run_paraphase.stderr VERBOSE [2025-09-15 20:28:29,783] INFO - writing output and wrapping up...
2025-09-15 20:28:29.995 wdl.w:ptcp.w:call-paraphase-38.t:call-run_paraphase.stderr VERBOSE [2025-09-15 20:28:29,783] INFO - reading paraphase variant list from m84036_250809_035451_s4.bc2135_paraphase/m84036_250809_035451_s4.bc2135_paraphase_vcfs/m84036_250809_035451_s4.bc2135_f8inv22.vcf
2025-09-15 20:28:29.995 wdl.w:ptcp.w:call-paraphase-38.t:call-run_paraphase.stderr VERBOSE [2025-09-15 20:28:29,787] INFO - finding matches of paraphase variants in the VCF
2025-09-15 20:28:29.995 wdl.w:ptcp.w:call-paraphase-38.t:call-run_paraphase.stderr VERBOSE [2025-09-15 20:28:29,787] INFO - writing output and wrapping up...
2025-09-15 20:28:29.995 wdl.w:ptcp.w:call-paraphase-38.t:call-run_paraphase.stderr VERBOSE [2025-09-15 20:28:29,787] INFO - reading paraphase variant list from m84036_250809_035451_s4.bc2135_paraphase/m84036_250809_035451_s4.bc2135_paraphase_vcfs/m84036_250809_035451_s4.bc2135_gba.vcf
2025-09-15 20:28:29.995 wdl.w:ptcp.w:call-paraphase-38.t:call-run_paraphase.stderr VERBOSE [2025-09-15 20:28:29,794] INFO - finding matches of paraphase variants in the VCF
2025-09-15 20:28:29.995 wdl.w:ptcp.w:call-paraphase-38.t:call-run_paraphase.stderr VERBOSE [2025-09-15 20:28:29,795] INFO - writing output and wrapping up...
2025-09-15 20:28:29.995 wdl.w:ptcp.w:call-paraphase-38.t:call-run_paraphase.stderr VERBOSE [2025-09-15 20:28:29,795] INFO - reading paraphase variant list from m84036_250809_035451_s4.bc2135_paraphase/m84036_250809_035451_s4.bc2135_paraphase_vcfs/m84036_250809_035451_s4.bc2135_hba.vcf
2025-09-15 20:28:29.995 wdl.w:ptcp.w:call-paraphase-38.t:call-run_paraphase.stderr VERBOSE [2025-09-15 20:28:29,801] INFO - finding matches of paraphase variants in the VCF
2025-09-15 20:28:29.996 wdl.w:ptcp.w:call-paraphase-38.t:call-run_paraphase.stderr VERBOSE [2025-09-15 20:28:29,802] INFO - writing output and wrapping up...
2025-09-15 20:28:29.996 wdl.w:ptcp.w:call-paraphase-38.t:call-run_paraphase.stderr VERBOSE [2025-09-15 20:28:29,802] INFO - reading paraphase variant list from m84036_250809_035451_s4.bc2135_paraphase/m84036_250809_035451_s4.bc2135_paraphase_vcfs/m84036_250809_035451_s4.bc2135_hbb.vcf
2025-09-15 20:28:29.996 wdl.w:ptcp.w:call-paraphase-38.t:call-run_paraphase.stderr VERBOSE [2025-09-15 20:28:29,805] INFO - finding matches of paraphase variants in the VCF
2025-09-15 20:28:29.996 wdl.w:ptcp.w:call-paraphase-38.t:call-run_paraphase.stderr VERBOSE [2025-09-15 20:28:29,806] INFO - writing output and wrapping up...
2025-09-15 20:28:29.996 wdl.w:ptcp.w:call-paraphase-38.t:call-run_paraphase.stderr VERBOSE [2025-09-15 20:28:29,806] INFO - reading paraphase variant list from m84036_250809_035451_s4.bc2135_paraphase/m84036_250809_035451_s4.bc2135_paraphase_vcfs/m84036_250809_035451_s4.bc2135_rpgr.vcf
2025-09-15 20:28:29.996 wdl.w:ptcp.w:call-paraphase-38.t:call-run_paraphase.stderr VERBOSE [2025-09-15 20:28:29,809] INFO - finding matches of paraphase variants in the VCF
2025-09-15 20:28:29.996 wdl.w:ptcp.w:call-paraphase-38.t:call-run_paraphase.stderr VERBOSE [2025-09-15 20:28:29,809] INFO - writing output and wrapping up...
2025-09-15 20:28:29.996 wdl.w:ptcp.w:call-paraphase-38.t:call-run_paraphase.stderr VERBOSE [2025-09-15 20:28:29,809] INFO - reading paraphase variant list from m84036_250809_035451_s4.bc2135_paraphase/m84036_250809_035451_s4.bc2135_paraphase_vcfs/m84036_250809_035451_s4.bc2135_smn1.vcf
2025-09-15 20:28:29.996 wdl.w:ptcp.w:call-paraphase-38.t:call-run_paraphase.stderr VERBOSE [2025-09-15 20:28:29,813] INFO - finding matches of paraphase variants in the VCF
2025-09-15 20:28:29.996 wdl.w:ptcp.w:call-paraphase-38.t:call-run_paraphase.stderr VERBOSE [2025-09-15 20:28:29,813] INFO - writing output and wrapping up...
2025-09-15 20:28:30.033 wdl.w:ptcp.w:call-paraphase-38.t:call-run_paraphase INFO output :: name: "paraphase_bam", value: "m84036_250809_035451_s4.bc2135_paraphase/m84036_250809_035451_s4.bc2135.paraphase.bam"
2025-09-15 20:28:30.036 wdl.w:ptcp.w:call-paraphase-38.t:call-run_paraphase INFO output :: name: "paraphase_bam_bai", value: "m84036_250809_035451_s4.bc2135_paraphase/m84036_250809_035451_s4.bc2135.paraphase.bam.bai"
2025-09-15 20:28:30.037 wdl.w:ptcp.w:call-paraphase-38.t:call-run_paraphase INFO output :: name: "paraphase_json", value: "m84036_250809_035451_s4.bc2135_paraphase/m84036_250809_035451_s4.bc2135.paraphase.json"
2025-09-15 20:28:30.041 wdl.w:ptcp.w:call-paraphase-38.t:call-run_paraphase INFO output :: name: "paraphase_vcfs", value: ["/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2135_paraphase/m84036_250809_035451_s4.bc2135_paraphase_vcfs/m84036_250809_035451_s4.bc2135_cyp21.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2135_paraphase/m84036_250809_035451_s4.bc2135_paraphase_vcfs/m84036_250809_035451_s4.bc2135_f8inv1.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2135_paraphase/m84036_250809_035451_s4.bc2135_paraphase_vcfs/m84036_250809_035451_s4.bc2135_f8inv22.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2135_paraphase/m84036_250809_035451_s4.bc2135_paraphase_vcfs/m84036_250809_035451_s4.bc2135_gba.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2135_paraphase/m84036_250809_035451_s4.bc2135_paraphase_vcfs/m84036_250809_035451_s4.bc2135_hba.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2135_paraphase/m84036_250809_035451_s4.bc2135_paraphase_vcfs/m84036_250809_035451_s4.bc2135_hbb.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2135_paraphase/m84036_250809_035451_s4.bc2135_paraphase_vcfs/m84036_250809_035451_s4.bc2135_rpgr.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2135_paraphase/m84036_250809_035451_s4.bc2135_paraphase_vcfs/m84036_250809_035451_s4.bc2135_smn1.vcf"]
2025-09-15 20:28:30.044 wdl.w:ptcp.w:call-paraphase-38.t:call-run_paraphase INFO output :: name: "havanno_json", value: "m84036_250809_035451_s4.bc2135.havanno.json"
2025-09-15 20:28:30.050 wdl.w:ptcp.w:call-paraphase-51.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for rpgr for sample m84036_250809_035451_s4.bc2148 at 2025-09-15 20:27:33.332180...
2025-09-15 20:28:30.051 wdl.w:ptcp.w:call-paraphase-51.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for rpgr for sample m84036_250809_035451_s4.bc2148 at 2025-09-15 20:27:33.333886...
2025-09-15 20:28:30.051 wdl.w:ptcp.w:call-paraphase-51.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for rpgr for sample m84036_250809_035451_s4.bc2148 at 2025-09-15 20:27:35.890977...
2025-09-15 20:28:30.051 wdl.w:ptcp.w:call-paraphase-51.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for rpgr for sample m84036_250809_035451_s4.bc2148 at 2025-09-15 20:27:37.095261...
2025-09-15 20:28:30.051 wdl.w:ptcp.w:call-paraphase-51.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for rpgr for sample m84036_250809_035451_s4.bc2148 at 2025-09-15 20:27:37.553593...
2025-09-15 20:28:30.195 wdl.w:ptcp.w:call-paraphase-38.t:call-run_paraphase NOTICE done
2025-09-15 20:28:30.201 wdl.w:ptcp.w:call-paraphase-38 NOTICE finish :: job: "call-run_paraphase"
2025-09-15 20:28:30.201 wdl.w:ptcp.w:call-paraphase-38 INFO output :: job: "call-run_paraphase", values: {"havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-38/call-run_paraphase/out/m84036_250809_035451_s4.bc2135.havanno.json", "paraphase_vcfs": ["/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-38/call-run_paraphase/out/m84036_250809_035451_s4.bc2135_paraphase/m84036_250809_035451_s4.bc2135_paraphase_vcfs/m84036_250809_035451_s4.bc2135_cyp21.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-38/call-run_paraphase/out/m84036_250809_035451_s4.bc2135_paraphase/m84036_250809_035451_s4.bc2135_paraphase_vcfs/m84036_250809_035451_s4.bc2135_f8inv1.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-38/call-run_paraphase/out/m84036_250809_035451_s4.bc2135_paraphase/m84036_250809_035451_s4.bc2135_paraphase_vcfs/m84036_250809_035451_s4.bc2135_f8inv22.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-38/call-run_paraphase/out/m84036_250809_035451_s4.bc2135_paraphase/m84036_250809_035451_s4.bc2135_paraphase_vcfs/m84036_250809_035451_s4.bc2135_gba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-38/call-run_paraphase/out/m84036_250809_035451_s4.bc2135_paraphase/m84036_250809_035451_s4.bc2135_paraphase_vcfs/m84036_250809_035451_s4.bc2135_hba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-38/call-run_paraphase/out/m84036_250809_035451_s4.bc2135_paraphase/m84036_250809_035451_s4.bc2135_paraphase_vcfs/m84036_250809_035451_s4.bc2135_hbb.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-38/call-run_paraphase/out/m84036_250809_035451_s4.bc2135_paraphase/m84036_250809_035451_s4.bc2135_paraphase_vcfs/m84036_250809_035451_s4.bc2135_rpgr.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-38/call-run_paraphase/out/m84036_250809_035451_s4.bc2135_paraphase/m84036_250809_035451_s4.bc2135_paraphase_vcfs/m84036_250809_035451_s4.bc2135_smn1.vcf"], "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-38/call-run_paraphase/out/m84036_250809_035451_s4.bc2135_paraphase/m84036_250809_035451_s4.bc2135.paraphase.json", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-38/call-run_paraphase/out/m84036_250809_035451_s4.bc2135_paraphase/m84036_250809_035451_s4.bc2135.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-38/call-run_paraphase/out/m84036_250809_035451_s4.bc2135_paraphase/m84036_250809_035451_s4.bc2135.paraphase.bam"}
2025-09-15 20:28:30.202 wdl.w:ptcp.w:call-paraphase-38 NOTICE ready :: job: "call-call_f8", callee: "call_f8"
2025-09-15 20:28:30.202 wdl.w:ptcp.w:call-paraphase-38 INFO input :: job: "call-call_f8", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "out_prefix": "m84036_250809_035451_s4.bc2135", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-38/call-run_paraphase/out/m84036_250809_035451_s4.bc2135_paraphase/m84036_250809_035451_s4.bc2135.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-38/call-run_paraphase/out/m84036_250809_035451_s4.bc2135_paraphase/m84036_250809_035451_s4.bc2135.paraphase.bam", "sex": "F"}
2025-09-15 20:28:30.202 wdl.w:ptcp.w:call-paraphase-38 INFO visit :: node: "output-havanno_json", values: {"havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-38/call-run_paraphase/out/m84036_250809_035451_s4.bc2135.havanno.json"}
2025-09-15 20:28:30.203 wdl.w:ptcp.w:call-paraphase-38 INFO visit :: node: "output-paraphase_bam", values: {"paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-38/call-run_paraphase/out/m84036_250809_035451_s4.bc2135_paraphase/m84036_250809_035451_s4.bc2135.paraphase.bam"}
2025-09-15 20:28:30.203 wdl.w:ptcp.w:call-paraphase-38 INFO visit :: node: "output-paraphase_bam_bai", values: {"paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-38/call-run_paraphase/out/m84036_250809_035451_s4.bc2135_paraphase/m84036_250809_035451_s4.bc2135.paraphase.bam.bai"}
2025-09-15 20:28:30.203 wdl.w:ptcp.w:call-paraphase-38 INFO visit :: node: "output-paraphase_json", values: {"paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-38/call-run_paraphase/out/m84036_250809_035451_s4.bc2135_paraphase/m84036_250809_035451_s4.bc2135.paraphase.json"}
2025-09-15 20:28:30.203 wdl.w:ptcp.w:call-paraphase-38 INFO visit :: node: "output-paraphase_vcfs", values: {"paraphase_vcfs": ["/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-38/call-run_paraphase/out/m84036_250809_035451_s4.bc2135_paraphase/m84036_250809_035451_s4.bc2135_paraphase_vcfs/m84036_250809_035451_s4.bc2135_cyp21.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-38/call-run_paraphase/out/m84036_250809_035451_s4.bc2135_paraphase/m84036_250809_035451_s4.bc2135_paraphase_vcfs/m84036_250809_035451_s4.bc2135_f8inv1.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-38/call-run_paraphase/out/m84036_250809_035451_s4.bc2135_paraphase/m84036_250809_035451_s4.bc2135_paraphase_vcfs/m84036_250809_035451_s4.bc2135_f8inv22.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-38/call-run_paraphase/out/m84036_250809_035451_s4.bc2135_paraphase/m84036_250809_035451_s4.bc2135_paraphase_vcfs/m84036_250809_035451_s4.bc2135_gba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-38/call-run_paraphase/out/m84036_250809_035451_s4.bc2135_paraphase/m84036_250809_035451_s4.bc2135_paraphase_vcfs/m84036_250809_035451_s4.bc2135_hba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-38/call-run_paraphase/out/m84036_250809_035451_s4.bc2135_paraphase/m84036_250809_035451_s4.bc2135_paraphase_vcfs/m84036_250809_035451_s4.bc2135_hbb.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-38/call-run_paraphase/out/m84036_250809_035451_s4.bc2135_paraphase/m84036_250809_035451_s4.bc2135_paraphase_vcfs/m84036_250809_035451_s4.bc2135_rpgr.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-38/call-run_paraphase/out/m84036_250809_035451_s4.bc2135_paraphase/m84036_250809_035451_s4.bc2135_paraphase_vcfs/m84036_250809_035451_s4.bc2135_smn1.vcf"]}
2025-09-15 20:28:30.210 wdl.w:ptcp.w:call-paraphase-38.t:call-call_f8 NOTICE task setup :: name: "call_f8", source: "./paraphase.wdl", line: 232, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-38/call-call_f8", thread: 140611944420928
2025-09-15 20:28:30.225 wdl.w:ptcp.w:call-paraphase-38.t:call-call_f8 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:28:30.225 wdl.w:ptcp.w:call-paraphase-38.t:call-call_f8 INFO input :: name: "genome_version", value: "38"
2025-09-15 20:28:30.225 wdl.w:ptcp.w:call-paraphase-38.t:call-call_f8 INFO input :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2135"
2025-09-15 20:28:30.225 wdl.w:ptcp.w:call-paraphase-38.t:call-call_f8 INFO input :: name: "paraphase_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2135.paraphase.bam.bai"
2025-09-15 20:28:30.225 wdl.w:ptcp.w:call-paraphase-38.t:call-call_f8 INFO input :: name: "paraphase_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2135.paraphase.bam"
2025-09-15 20:28:30.225 wdl.w:ptcp.w:call-paraphase-38.t:call-call_f8 INFO input :: name: "sex", value: "F"
2025-09-15 20:28:30.225 wdl.w:ptcp.w:call-paraphase-38.t:call-call_f8 INFO eval :: name: "threads", value: 1
2025-09-15 20:28:30.225 wdl.w:ptcp.w:call-paraphase-38.t:call-call_f8 INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:28:30.226 wdl.w:ptcp.w:call-paraphase-38.t:call-call_f8 INFO eval :: name: "disk_size", value: 11
2025-09-15 20:28:30.226 wdl.w:ptcp.w:call-paraphase-38.t:call-call_f8 INFO eval :: name: "sample_sex", value: "F"
2025-09-15 20:28:30.227 wdl.w:ptcp.w:call-paraphase-38.t:call-call_f8 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:28:30.227 wdl.w:ptcp.w:call-paraphase-38.t:call-call_f8 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:28:30.228 wdl.w:ptcp.w:call-paraphase-38.t:call-call_f8 INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:28:30.228 wdl.w:ptcp.w:call-paraphase-38.t:call-call_f8 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:28:30.264 wdl.w:ptcp.w:call-paraphase-38.t:call-call_f8 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 8, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-38/call-call_f8/_singularity_tmpdir_4aki2v0m"
2025-09-15 20:28:30.264 wdl.w:ptcp.w:call-paraphase-38.t:call-call_f8 INFO Slurm invocation: srun --job-name call-call_f8 --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-38/call-call_f8/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-38/call-call_f8/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-38/call-call_f8/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-38/call-call_f8/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-38/call-run_paraphase/out/m84036_250809_035451_s4.bc2135_paraphase/m84036_250809_035451_s4.bc2135.paraphase.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2135.paraphase.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-38/call-run_paraphase/out/m84036_250809_035451_s4.bc2135_paraphase/m84036_250809_035451_s4.bc2135.paraphase.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2135.paraphase.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-38/call-call_f8/_singularity_tmpdir_4aki2v0m/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-38/call-call_f8/_singularity_tmpdir_4aki2v0m/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:28:30.277 wdl.w:ptcp.w:call-paraphase-38.t:call-call_f8 NOTICE slurm_singularity run :: pid: 1209194, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-38/call-call_f8/slurm_singularity.log.txt"
2025-09-15 20:28:30.426 wdl.w:ptcp.t:call-tar_outputs-42.slurm_singularity INFO srun: job 51798248 has been allocated resources
2025-09-15 20:28:30.426 wdl.w:ptcp.t:call-tar_outputs-42.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:28:30.875 wdl.w:ptcp.t:call-tar_outputs-42 INFO output :: name: "sample_tarball", value: "m84036_250809_035451_s4.bc2139.tar"
2025-09-15 20:28:30.926 wdl.w:ptcp.t:call-tar_outputs-42 NOTICE done
2025-09-15 20:28:30.933 wdl.w:ptcp NOTICE finish :: job: "call-tar_outputs-42"
2025-09-15 20:28:30.933 wdl.w:ptcp INFO output :: job: "call-tar_outputs-42", values: {"sample_tarball": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-42/out/m84036_250809_035451_s4.bc2139.tar"}
2025-09-15 20:28:31.286 wdl.w:ptcp.w:call-paraphase-38.t:call-call_f8.slurm_singularity INFO srun: job 51798249 queued and waiting for resources
2025-09-15 20:28:31.286 wdl.w:ptcp.w:call-paraphase-38.t:call-call_f8.slurm_singularity INFO srun: job 51798249 has been allocated resources
2025-09-15 20:28:31.286 wdl.w:ptcp.w:call-paraphase-38.t:call-call_f8.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:28:31.833 wdl.w:ptcp.w:call-paraphase-38.t:call-call_f8 INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2135.f8inversion.vcf"
2025-09-15 20:28:31.836 wdl.w:ptcp.w:call-paraphase-38.t:call-call_f8 INFO output :: name: "json", value: "m84036_250809_035451_s4.bc2135.f8inversion.json"
2025-09-15 20:28:31.888 wdl.w:ptcp.w:call-paraphase-38.t:call-call_f8 NOTICE done
2025-09-15 20:28:31.905 wdl.w:ptcp.w:call-paraphase-38 NOTICE finish :: job: "call-call_f8"
2025-09-15 20:28:31.906 wdl.w:ptcp.w:call-paraphase-38 INFO output :: job: "call-call_f8", values: {"json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-38/call-call_f8/out/m84036_250809_035451_s4.bc2135.f8inversion.json", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-38/call-call_f8/out/m84036_250809_035451_s4.bc2135.f8inversion.vcf"}
2025-09-15 20:28:31.906 wdl.w:ptcp.w:call-paraphase-38 INFO visit :: node: "output-f8_json", values: {"f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-38/call-call_f8/out/m84036_250809_035451_s4.bc2135.f8inversion.json"}
2025-09-15 20:28:31.906 wdl.w:ptcp.w:call-paraphase-38 INFO visit :: node: "output-f8_vcf", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-38/call-call_f8/out/m84036_250809_035451_s4.bc2135.f8inversion.vcf"}
2025-09-15 20:28:31.907 wdl.w:ptcp.w:call-paraphase-38 INFO visit :: node: "outputs", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-38/call-call_f8/out/m84036_250809_035451_s4.bc2135.f8inversion.vcf", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-38/call-run_paraphase/out/m84036_250809_035451_s4.bc2135_paraphase/m84036_250809_035451_s4.bc2135.paraphase.json", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-38/call-run_paraphase/out/m84036_250809_035451_s4.bc2135_paraphase/m84036_250809_035451_s4.bc2135.paraphase.bam", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-38/call-run_paraphase/out/m84036_250809_035451_s4.bc2135_paraphase/m84036_250809_035451_s4.bc2135.paraphase.bam.bai", "paraphase_vcfs": ["/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-38/call-run_paraphase/out/m84036_250809_035451_s4.bc2135_paraphase/m84036_250809_035451_s4.bc2135_paraphase_vcfs/m84036_250809_035451_s4.bc2135_cyp21.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-38/call-run_paraphase/out/m84036_250809_035451_s4.bc2135_paraphase/m84036_250809_035451_s4.bc2135_paraphase_vcfs/m84036_250809_035451_s4.bc2135_f8inv1.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-38/call-run_paraphase/out/m84036_250809_035451_s4.bc2135_paraphase/m84036_250809_035451_s4.bc2135_paraphase_vcfs/m84036_250809_035451_s4.bc2135_f8inv22.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-38/call-run_paraphase/out/m84036_250809_035451_s4.bc2135_paraphase/m84036_250809_035451_s4.bc2135_paraphase_vcfs/m84036_250809_035451_s4.bc2135_gba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-38/call-run_paraphase/out/m84036_250809_035451_s4.bc2135_paraphase/m84036_250809_035451_s4.bc2135_paraphase_vcfs/m84036_250809_035451_s4.bc2135_hba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-38/call-run_paraphase/out/m84036_250809_035451_s4.bc2135_paraphase/m84036_250809_035451_s4.bc2135_paraphase_vcfs/m84036_250809_035451_s4.bc2135_hbb.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-38/call-run_paraphase/out/m84036_250809_035451_s4.bc2135_paraphase/m84036_250809_035451_s4.bc2135_paraphase_vcfs/m84036_250809_035451_s4.bc2135_rpgr.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-38/call-run_paraphase/out/m84036_250809_035451_s4.bc2135_paraphase/m84036_250809_035451_s4.bc2135_paraphase_vcfs/m84036_250809_035451_s4.bc2135_smn1.vcf"], "havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-38/call-run_paraphase/out/m84036_250809_035451_s4.bc2135.havanno.json", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-38/call-call_f8/out/m84036_250809_035451_s4.bc2135.f8inversion.json"}
2025-09-15 20:28:32.008 wdl.w:ptcp.w:call-paraphase-38 NOTICE done
2025-09-15 20:28:32.013 wdl.w:ptcp NOTICE finish :: job: "call-paraphase-38"
2025-09-15 20:28:32.013 wdl.w:ptcp INFO output :: job: "call-paraphase-38", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-38/out/m84036_250809_035451_s4.bc2135.f8inversion.vcf", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-38/out/m84036_250809_035451_s4.bc2135_paraphase/m84036_250809_035451_s4.bc2135.paraphase.json", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-38/out/m84036_250809_035451_s4.bc2135_paraphase/m84036_250809_035451_s4.bc2135.paraphase.bam", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-38/out/m84036_250809_035451_s4.bc2135_paraphase/m84036_250809_035451_s4.bc2135.paraphase.bam.bai", "paraphase_vcfs": ["/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-38/out/m84036_250809_035451_s4.bc2135_paraphase/m84036_250809_035451_s4.bc2135_paraphase_vcfs/m84036_250809_035451_s4.bc2135_cyp21.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-38/out/m84036_250809_035451_s4.bc2135_paraphase/m84036_250809_035451_s4.bc2135_paraphase_vcfs/m84036_250809_035451_s4.bc2135_f8inv1.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-38/out/m84036_250809_035451_s4.bc2135_paraphase/m84036_250809_035451_s4.bc2135_paraphase_vcfs/m84036_250809_035451_s4.bc2135_f8inv22.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-38/out/m84036_250809_035451_s4.bc2135_paraphase/m84036_250809_035451_s4.bc2135_paraphase_vcfs/m84036_250809_035451_s4.bc2135_gba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-38/out/m84036_250809_035451_s4.bc2135_paraphase/m84036_250809_035451_s4.bc2135_paraphase_vcfs/m84036_250809_035451_s4.bc2135_hba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-38/out/m84036_250809_035451_s4.bc2135_paraphase/m84036_250809_035451_s4.bc2135_paraphase_vcfs/m84036_250809_035451_s4.bc2135_hbb.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-38/out/m84036_250809_035451_s4.bc2135_paraphase/m84036_250809_035451_s4.bc2135_paraphase_vcfs/m84036_250809_035451_s4.bc2135_rpgr.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-38/out/m84036_250809_035451_s4.bc2135_paraphase/m84036_250809_035451_s4.bc2135_paraphase_vcfs/m84036_250809_035451_s4.bc2135_smn1.vcf"], "havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-38/out/m84036_250809_035451_s4.bc2135.havanno.json", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-38/out/m84036_250809_035451_s4.bc2135.f8inversion.json"}
2025-09-15 20:28:32.014 wdl.w:ptcp NOTICE ready :: job: "call-tar_outputs-38", callee: "tar_outputs"
2025-09-15 20:28:32.014 wdl.w:ptcp INFO input :: job: "call-tar_outputs-38", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "sawfish_vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-38/out/m84036_250809_035451_s4.bc2135_sawfish/m84036_250809_035451_s4.bc2135.sv.vcf.gz.tbi", "sawfish_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-38/out/m84036_250809_035451_s4.bc2135_sawfish/m84036_250809_035451_s4.bc2135.sv.vcf.gz", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-38/out/m84036_250809_035451_s4.bc2135.f8inversion.json", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-38/out/m84036_250809_035451_s4.bc2135_paraphase/m84036_250809_035451_s4.bc2135.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-38/out/m84036_250809_035451_s4.bc2135_paraphase/m84036_250809_035451_s4.bc2135.paraphase.bam", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-38/out/m84036_250809_035451_s4.bc2135_paraphase/m84036_250809_035451_s4.bc2135.paraphase.json", "trgt_spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-38/out/m84036_250809_035451_s4.bc2135.trgt.sorted.spanning.bam.bai", "trgt_spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-38/out/m84036_250809_035451_s4.bc2135.trgt.sorted.spanning.bam", "trgt_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-38/out/m84036_250809_035451_s4.bc2135.trgt.vcf", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-38/out/m84036_250809_035451_s4.bc2135.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-38/out/m84036_250809_035451_s4.bc2135.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2135"}
2025-09-15 20:28:32.019 wdl.w:ptcp.t:call-tar_outputs-38 NOTICE task setup :: name: "tar_outputs", source: "./common.wdl", line: 279, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-38", thread: 140609813722688
2025-09-15 20:28:32.040 wdl.w:ptcp.t:call-tar_outputs-38 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:28:32.040 wdl.w:ptcp.t:call-tar_outputs-38 INFO input :: name: "sawfish_vcf_tbi", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2135.sv.vcf.gz.tbi"
2025-09-15 20:28:32.040 wdl.w:ptcp.t:call-tar_outputs-38 INFO input :: name: "sawfish_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2135.sv.vcf.gz"
2025-09-15 20:28:32.040 wdl.w:ptcp.t:call-tar_outputs-38 INFO input :: name: "f8_json", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2135.f8inversion.json"
2025-09-15 20:28:32.040 wdl.w:ptcp.t:call-tar_outputs-38 INFO input :: name: "paraphase_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2135.paraphase.bam.bai"
2025-09-15 20:28:32.040 wdl.w:ptcp.t:call-tar_outputs-38 INFO input :: name: "paraphase_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2135.paraphase.bam"
2025-09-15 20:28:32.041 wdl.w:ptcp.t:call-tar_outputs-38 INFO input :: name: "paraphase_json", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2135.paraphase.json"
2025-09-15 20:28:32.041 wdl.w:ptcp.t:call-tar_outputs-38 INFO input :: name: "trgt_spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2135.trgt.sorted.spanning.bam.bai"
2025-09-15 20:28:32.041 wdl.w:ptcp.t:call-tar_outputs-38 INFO input :: name: "trgt_spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2135.trgt.sorted.spanning.bam"
2025-09-15 20:28:32.041 wdl.w:ptcp.t:call-tar_outputs-38 INFO input :: name: "trgt_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2135.trgt.vcf"
2025-09-15 20:28:32.041 wdl.w:ptcp.t:call-tar_outputs-38 INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2135.mapped.bam.bai"
2025-09-15 20:28:32.041 wdl.w:ptcp.t:call-tar_outputs-38 INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2135.mapped.bam"
2025-09-15 20:28:32.041 wdl.w:ptcp.t:call-tar_outputs-38 INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2135"
2025-09-15 20:28:32.041 wdl.w:ptcp.t:call-tar_outputs-38 INFO eval :: name: "threads", value: 1
2025-09-15 20:28:32.041 wdl.w:ptcp.t:call-tar_outputs-38 INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:28:32.041 wdl.w:ptcp.t:call-tar_outputs-38 INFO eval :: name: "disk_size", value: 6
2025-09-15 20:28:32.041 wdl.w:ptcp.t:call-tar_outputs-38 INFO eval :: name: "output_tarball", value: "m84036_250809_035451_s4.bc2135.tar"
2025-09-15 20:28:32.042 wdl.w:ptcp.t:call-tar_outputs-38 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:28:32.042 wdl.w:ptcp.t:call-tar_outputs-38 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:28:32.042 wdl.w:ptcp.t:call-tar_outputs-38 INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:28:32.042 wdl.w:ptcp.t:call-tar_outputs-38 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:28:32.079 wdl.w:ptcp.w:call-paraphase-70.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for f8inv1 for sample m84036_250809_035451_s4.bc2167 at 2025-09-15 20:28:10.046941...
2025-09-15 20:28:32.080 wdl.w:ptcp.w:call-paraphase-70.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for f8inv1 for sample m84036_250809_035451_s4.bc2167 at 2025-09-15 20:28:10.047784...
2025-09-15 20:28:32.080 wdl.w:ptcp.w:call-paraphase-70.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for f8inv1 for sample m84036_250809_035451_s4.bc2167 at 2025-09-15 20:28:12.097455...
2025-09-15 20:28:32.080 wdl.w:ptcp.w:call-paraphase-70.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for f8inv1 for sample m84036_250809_035451_s4.bc2167 at 2025-09-15 20:28:18.385591...
2025-09-15 20:28:32.080 wdl.w:ptcp.w:call-paraphase-70.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for f8inv1 for sample m84036_250809_035451_s4.bc2167 at 2025-09-15 20:28:18.773778...
2025-09-15 20:28:32.120 wdl.w:ptcp.t:call-tar_outputs-38 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 17, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-38/_singularity_tmpdir_4bwqcf72"
2025-09-15 20:28:32.120 wdl.w:ptcp.t:call-tar_outputs-38 INFO Slurm invocation: srun --job-name call-tar_outputs-38 --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-38/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-38/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-38/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-38/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-38/out/m84036_250809_035451_s4.bc2135.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2135.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-38/out/m84036_250809_035451_s4.bc2135.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2135.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-38/out/m84036_250809_035451_s4.bc2135.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2135.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-38/out/m84036_250809_035451_s4.bc2135.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2135.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-38/out/m84036_250809_035451_s4.bc2135.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2135.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-38/out/m84036_250809_035451_s4.bc2135_paraphase/m84036_250809_035451_s4.bc2135.paraphase.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2135.paraphase.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-38/out/m84036_250809_035451_s4.bc2135_paraphase/m84036_250809_035451_s4.bc2135.paraphase.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2135.paraphase.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-38/out/m84036_250809_035451_s4.bc2135_paraphase/m84036_250809_035451_s4.bc2135.paraphase.json:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2135.paraphase.json:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-38/out/m84036_250809_035451_s4.bc2135.f8inversion.json:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2135.f8inversion.json:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-38/out/m84036_250809_035451_s4.bc2135_sawfish/m84036_250809_035451_s4.bc2135.sv.vcf.gz.tbi:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2135.sv.vcf.gz.tbi:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-38/out/m84036_250809_035451_s4.bc2135_sawfish/m84036_250809_035451_s4.bc2135.sv.vcf.gz:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2135.sv.vcf.gz:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-38/_singularity_tmpdir_4bwqcf72/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-38/_singularity_tmpdir_4bwqcf72/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:28:32.126 wdl.w:ptcp.t:call-tar_outputs-38 NOTICE slurm_singularity run :: pid: 1209204, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-38/slurm_singularity.log.txt"
2025-09-15 20:28:32.461 wdl.w:ptcp.w:call-paraphase-83.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for hba for sample m84036_250809_035451_s4.bc2180 at 2025-09-15 20:27:16.790477...
2025-09-15 20:28:32.462 wdl.w:ptcp.w:call-paraphase-83.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for hba for sample m84036_250809_035451_s4.bc2180 at 2025-09-15 20:27:17.307473...
2025-09-15 20:28:32.462 wdl.w:ptcp.w:call-paraphase-83.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for cyp21 for sample m84036_250809_035451_s4.bc2180 at 2025-09-15 20:27:42.993243...
2025-09-15 20:28:32.462 wdl.w:ptcp.w:call-paraphase-83.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for cyp21 for sample m84036_250809_035451_s4.bc2180 at 2025-09-15 20:27:44.353436...
2025-09-15 20:28:32.462 wdl.w:ptcp.w:call-paraphase-83.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for f8inv1 for sample m84036_250809_035451_s4.bc2180 at 2025-09-15 20:27:44.647827...
2025-09-15 20:28:32.462 wdl.w:ptcp.w:call-paraphase-83.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for f8inv1 for sample m84036_250809_035451_s4.bc2180 at 2025-09-15 20:27:44.648124...
2025-09-15 20:28:32.462 wdl.w:ptcp.w:call-paraphase-83.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for f8inv1 for sample m84036_250809_035451_s4.bc2180 at 2025-09-15 20:27:48.343345...
2025-09-15 20:28:32.462 wdl.w:ptcp.w:call-paraphase-83.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for gba for sample m84036_250809_035451_s4.bc2180 at 2025-09-15 20:27:48.596685...
2025-09-15 20:28:32.462 wdl.w:ptcp.w:call-paraphase-83.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for gba for sample m84036_250809_035451_s4.bc2180 at 2025-09-15 20:27:49.268759...
2025-09-15 20:28:32.462 wdl.w:ptcp.w:call-paraphase-83.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for f8inv1 for sample m84036_250809_035451_s4.bc2180 at 2025-09-15 20:27:57.652963...
2025-09-15 20:28:32.462 wdl.w:ptcp.w:call-paraphase-83.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for f8inv1 for sample m84036_250809_035451_s4.bc2180 at 2025-09-15 20:27:58.158932...
2025-09-15 20:28:32.462 wdl.w:ptcp.w:call-paraphase-83.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for hbb for sample m84036_250809_035451_s4.bc2180 at 2025-09-15 20:28:15.786027...
2025-09-15 20:28:32.462 wdl.w:ptcp.w:call-paraphase-83.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for hbb for sample m84036_250809_035451_s4.bc2180 at 2025-09-15 20:28:15.786972...
2025-09-15 20:28:32.462 wdl.w:ptcp.w:call-paraphase-83.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for hbb for sample m84036_250809_035451_s4.bc2180 at 2025-09-15 20:28:18.031511...
2025-09-15 20:28:33.134 wdl.w:ptcp.t:call-tar_outputs-38.slurm_singularity INFO srun: job 51798250 queued and waiting for resources
2025-09-15 20:28:33.134 wdl.w:ptcp.t:call-tar_outputs-38.slurm_singularity INFO srun: job 51798250 has been allocated resources
2025-09-15 20:28:33.134 wdl.w:ptcp.t:call-tar_outputs-38.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:28:33.735 wdl.w:ptcp.t:call-tar_outputs-38 INFO output :: name: "sample_tarball", value: "m84036_250809_035451_s4.bc2135.tar"
2025-09-15 20:28:33.790 wdl.w:ptcp.t:call-tar_outputs-38 NOTICE done
2025-09-15 20:28:33.793 wdl.w:ptcp NOTICE finish :: job: "call-tar_outputs-38"
2025-09-15 20:28:33.793 wdl.w:ptcp INFO output :: job: "call-tar_outputs-38", values: {"sample_tarball": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-38/out/m84036_250809_035451_s4.bc2135.tar"}
2025-09-15 20:28:34.052 wdl.w:ptcp.w:call-paraphase-06.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for f8inv22 for sample m84036_250809_035451_s4.bc2103 at 2025-09-15 20:28:04.728417...
2025-09-15 20:28:34.053 wdl.w:ptcp.w:call-paraphase-06.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for f8inv22 for sample m84036_250809_035451_s4.bc2103 at 2025-09-15 20:28:11.219425...
2025-09-15 20:28:34.053 wdl.w:ptcp.w:call-paraphase-06.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for f8inv22 for sample m84036_250809_035451_s4.bc2103 at 2025-09-15 20:28:11.687475...
2025-09-15 20:28:34.053 wdl.w:ptcp.w:call-paraphase-06.t:call-run_paraphase.stderr VERBOSE INFO:root:Merging all bams for sample m84036_250809_035451_s4.bc2103 at 2025-09-15 20:28:32.696744...
2025-09-15 20:28:35.115 wdl.w:ptcp.w:call-paraphase-70.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for rpgr for sample m84036_250809_035451_s4.bc2167 at 2025-09-15 20:28:32.555031...
2025-09-15 20:28:35.115 wdl.w:ptcp.w:call-paraphase-70.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for rpgr for sample m84036_250809_035451_s4.bc2167 at 2025-09-15 20:28:32.555836...
2025-09-15 20:28:36.489 wdl.w:ptcp.w:call-paraphase-06.t:call-run_paraphase INFO output :: name: "paraphase_bam", value: "m84036_250809_035451_s4.bc2103_paraphase/m84036_250809_035451_s4.bc2103.paraphase.bam"
2025-09-15 20:28:36.492 wdl.w:ptcp.w:call-paraphase-06.t:call-run_paraphase INFO output :: name: "paraphase_bam_bai", value: "m84036_250809_035451_s4.bc2103_paraphase/m84036_250809_035451_s4.bc2103.paraphase.bam.bai"
2025-09-15 20:28:36.493 wdl.w:ptcp.w:call-paraphase-06.t:call-run_paraphase INFO output :: name: "paraphase_json", value: "m84036_250809_035451_s4.bc2103_paraphase/m84036_250809_035451_s4.bc2103.paraphase.json"
2025-09-15 20:28:36.498 wdl.w:ptcp.w:call-paraphase-06.t:call-run_paraphase INFO output :: name: "paraphase_vcfs", value: ["/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2103_paraphase/m84036_250809_035451_s4.bc2103_paraphase_vcfs/m84036_250809_035451_s4.bc2103_cyp21.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2103_paraphase/m84036_250809_035451_s4.bc2103_paraphase_vcfs/m84036_250809_035451_s4.bc2103_f8inv1.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2103_paraphase/m84036_250809_035451_s4.bc2103_paraphase_vcfs/m84036_250809_035451_s4.bc2103_f8inv22.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2103_paraphase/m84036_250809_035451_s4.bc2103_paraphase_vcfs/m84036_250809_035451_s4.bc2103_gba.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2103_paraphase/m84036_250809_035451_s4.bc2103_paraphase_vcfs/m84036_250809_035451_s4.bc2103_hba.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2103_paraphase/m84036_250809_035451_s4.bc2103_paraphase_vcfs/m84036_250809_035451_s4.bc2103_hbb.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2103_paraphase/m84036_250809_035451_s4.bc2103_paraphase_vcfs/m84036_250809_035451_s4.bc2103_rpgr.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2103_paraphase/m84036_250809_035451_s4.bc2103_paraphase_vcfs/m84036_250809_035451_s4.bc2103_smn1.vcf"]
2025-09-15 20:28:36.501 wdl.w:ptcp.w:call-paraphase-06.t:call-run_paraphase INFO output :: name: "havanno_json", value: "m84036_250809_035451_s4.bc2103.havanno.json"
2025-09-15 20:28:36.645 wdl.w:ptcp.w:call-paraphase-06.t:call-run_paraphase NOTICE done
2025-09-15 20:28:36.651 wdl.w:ptcp.w:call-paraphase-06 NOTICE finish :: job: "call-run_paraphase"
2025-09-15 20:28:36.652 wdl.w:ptcp.w:call-paraphase-06 INFO output :: job: "call-run_paraphase", values: {"havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-06/call-run_paraphase/out/m84036_250809_035451_s4.bc2103.havanno.json", "paraphase_vcfs": ["/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-06/call-run_paraphase/out/m84036_250809_035451_s4.bc2103_paraphase/m84036_250809_035451_s4.bc2103_paraphase_vcfs/m84036_250809_035451_s4.bc2103_cyp21.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-06/call-run_paraphase/out/m84036_250809_035451_s4.bc2103_paraphase/m84036_250809_035451_s4.bc2103_paraphase_vcfs/m84036_250809_035451_s4.bc2103_f8inv1.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-06/call-run_paraphase/out/m84036_250809_035451_s4.bc2103_paraphase/m84036_250809_035451_s4.bc2103_paraphase_vcfs/m84036_250809_035451_s4.bc2103_f8inv22.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-06/call-run_paraphase/out/m84036_250809_035451_s4.bc2103_paraphase/m84036_250809_035451_s4.bc2103_paraphase_vcfs/m84036_250809_035451_s4.bc2103_gba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-06/call-run_paraphase/out/m84036_250809_035451_s4.bc2103_paraphase/m84036_250809_035451_s4.bc2103_paraphase_vcfs/m84036_250809_035451_s4.bc2103_hba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-06/call-run_paraphase/out/m84036_250809_035451_s4.bc2103_paraphase/m84036_250809_035451_s4.bc2103_paraphase_vcfs/m84036_250809_035451_s4.bc2103_hbb.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-06/call-run_paraphase/out/m84036_250809_035451_s4.bc2103_paraphase/m84036_250809_035451_s4.bc2103_paraphase_vcfs/m84036_250809_035451_s4.bc2103_rpgr.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-06/call-run_paraphase/out/m84036_250809_035451_s4.bc2103_paraphase/m84036_250809_035451_s4.bc2103_paraphase_vcfs/m84036_250809_035451_s4.bc2103_smn1.vcf"], "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-06/call-run_paraphase/out/m84036_250809_035451_s4.bc2103_paraphase/m84036_250809_035451_s4.bc2103.paraphase.json", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-06/call-run_paraphase/out/m84036_250809_035451_s4.bc2103_paraphase/m84036_250809_035451_s4.bc2103.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-06/call-run_paraphase/out/m84036_250809_035451_s4.bc2103_paraphase/m84036_250809_035451_s4.bc2103.paraphase.bam"}
2025-09-15 20:28:36.652 wdl.w:ptcp.w:call-paraphase-06 NOTICE ready :: job: "call-call_f8", callee: "call_f8"
2025-09-15 20:28:36.653 wdl.w:ptcp.w:call-paraphase-06 INFO input :: job: "call-call_f8", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "out_prefix": "m84036_250809_035451_s4.bc2103", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-06/call-run_paraphase/out/m84036_250809_035451_s4.bc2103_paraphase/m84036_250809_035451_s4.bc2103.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-06/call-run_paraphase/out/m84036_250809_035451_s4.bc2103_paraphase/m84036_250809_035451_s4.bc2103.paraphase.bam", "sex": "F"}
2025-09-15 20:28:36.653 wdl.w:ptcp.w:call-paraphase-06 INFO visit :: node: "output-havanno_json", values: {"havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-06/call-run_paraphase/out/m84036_250809_035451_s4.bc2103.havanno.json"}
2025-09-15 20:28:36.653 wdl.w:ptcp.w:call-paraphase-06 INFO visit :: node: "output-paraphase_bam", values: {"paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-06/call-run_paraphase/out/m84036_250809_035451_s4.bc2103_paraphase/m84036_250809_035451_s4.bc2103.paraphase.bam"}
2025-09-15 20:28:36.653 wdl.w:ptcp.w:call-paraphase-06 INFO visit :: node: "output-paraphase_bam_bai", values: {"paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-06/call-run_paraphase/out/m84036_250809_035451_s4.bc2103_paraphase/m84036_250809_035451_s4.bc2103.paraphase.bam.bai"}
2025-09-15 20:28:36.653 wdl.w:ptcp.w:call-paraphase-06 INFO visit :: node: "output-paraphase_json", values: {"paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-06/call-run_paraphase/out/m84036_250809_035451_s4.bc2103_paraphase/m84036_250809_035451_s4.bc2103.paraphase.json"}
2025-09-15 20:28:36.654 wdl.w:ptcp.w:call-paraphase-06 INFO visit :: node: "output-paraphase_vcfs", values: {"paraphase_vcfs": ["/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-06/call-run_paraphase/out/m84036_250809_035451_s4.bc2103_paraphase/m84036_250809_035451_s4.bc2103_paraphase_vcfs/m84036_250809_035451_s4.bc2103_cyp21.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-06/call-run_paraphase/out/m84036_250809_035451_s4.bc2103_paraphase/m84036_250809_035451_s4.bc2103_paraphase_vcfs/m84036_250809_035451_s4.bc2103_f8inv1.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-06/call-run_paraphase/out/m84036_250809_035451_s4.bc2103_paraphase/m84036_250809_035451_s4.bc2103_paraphase_vcfs/m84036_250809_035451_s4.bc2103_f8inv22.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-06/call-run_paraphase/out/m84036_250809_035451_s4.bc2103_paraphase/m84036_250809_035451_s4.bc2103_paraphase_vcfs/m84036_250809_035451_s4.bc2103_gba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-06/call-run_paraphase/out/m84036_250809_035451_s4.bc2103_paraphase/m84036_250809_035451_s4.bc2103_paraphase_vcfs/m84036_250809_035451_s4.bc2103_hba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-06/call-run_paraphase/out/m84036_250809_035451_s4.bc2103_paraphase/m84036_250809_035451_s4.bc2103_paraphase_vcfs/m84036_250809_035451_s4.bc2103_hbb.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-06/call-run_paraphase/out/m84036_250809_035451_s4.bc2103_paraphase/m84036_250809_035451_s4.bc2103_paraphase_vcfs/m84036_250809_035451_s4.bc2103_rpgr.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-06/call-run_paraphase/out/m84036_250809_035451_s4.bc2103_paraphase/m84036_250809_035451_s4.bc2103_paraphase_vcfs/m84036_250809_035451_s4.bc2103_smn1.vcf"]}
2025-09-15 20:28:36.659 wdl.w:ptcp.w:call-paraphase-06.t:call-call_f8 NOTICE task setup :: name: "call_f8", source: "./paraphase.wdl", line: 232, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-06/call-call_f8", thread: 140610879071808
2025-09-15 20:28:36.676 wdl.w:ptcp.w:call-paraphase-06.t:call-call_f8 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:28:36.676 wdl.w:ptcp.w:call-paraphase-06.t:call-call_f8 INFO input :: name: "genome_version", value: "38"
2025-09-15 20:28:36.676 wdl.w:ptcp.w:call-paraphase-06.t:call-call_f8 INFO input :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2103"
2025-09-15 20:28:36.676 wdl.w:ptcp.w:call-paraphase-06.t:call-call_f8 INFO input :: name: "paraphase_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2103.paraphase.bam.bai"
2025-09-15 20:28:36.676 wdl.w:ptcp.w:call-paraphase-06.t:call-call_f8 INFO input :: name: "paraphase_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2103.paraphase.bam"
2025-09-15 20:28:36.676 wdl.w:ptcp.w:call-paraphase-06.t:call-call_f8 INFO input :: name: "sex", value: "F"
2025-09-15 20:28:36.676 wdl.w:ptcp.w:call-paraphase-06.t:call-call_f8 INFO eval :: name: "threads", value: 1
2025-09-15 20:28:36.676 wdl.w:ptcp.w:call-paraphase-06.t:call-call_f8 INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:28:36.677 wdl.w:ptcp.w:call-paraphase-06.t:call-call_f8 INFO eval :: name: "disk_size", value: 11
2025-09-15 20:28:36.677 wdl.w:ptcp.w:call-paraphase-06.t:call-call_f8 INFO eval :: name: "sample_sex", value: "F"
2025-09-15 20:28:36.677 wdl.w:ptcp.w:call-paraphase-06.t:call-call_f8 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:28:36.677 wdl.w:ptcp.w:call-paraphase-06.t:call-call_f8 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:28:36.678 wdl.w:ptcp.w:call-paraphase-06.t:call-call_f8 INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:28:36.678 wdl.w:ptcp.w:call-paraphase-06.t:call-call_f8 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:28:36.714 wdl.w:ptcp.w:call-paraphase-06.t:call-call_f8 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 8, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-06/call-call_f8/_singularity_tmpdir_z4s7idk2"
2025-09-15 20:28:36.714 wdl.w:ptcp.w:call-paraphase-06.t:call-call_f8 INFO Slurm invocation: srun --job-name call-call_f8 --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-06/call-call_f8/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-06/call-call_f8/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-06/call-call_f8/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-06/call-call_f8/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-06/call-run_paraphase/out/m84036_250809_035451_s4.bc2103_paraphase/m84036_250809_035451_s4.bc2103.paraphase.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2103.paraphase.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-06/call-run_paraphase/out/m84036_250809_035451_s4.bc2103_paraphase/m84036_250809_035451_s4.bc2103.paraphase.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2103.paraphase.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-06/call-call_f8/_singularity_tmpdir_z4s7idk2/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-06/call-call_f8/_singularity_tmpdir_z4s7idk2/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:28:36.719 wdl.w:ptcp.w:call-paraphase-06.t:call-call_f8 NOTICE slurm_singularity run :: pid: 1209214, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-06/call-call_f8/slurm_singularity.log.txt"
2025-09-15 20:28:36.824 wdl.w:ptcp.w:call-paraphase-62.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for f8inv22 for sample m84036_250809_035451_s4.bc2159 at 2025-09-15 20:28:19.480886...
2025-09-15 20:28:36.824 wdl.w:ptcp.w:call-paraphase-62.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for f8inv22 for sample m84036_250809_035451_s4.bc2159 at 2025-09-15 20:28:19.481034...
2025-09-15 20:28:37.726 wdl.w:ptcp.w:call-paraphase-06.t:call-call_f8.slurm_singularity INFO srun: job 51798251 queued and waiting for resources
2025-09-15 20:28:37.726 wdl.w:ptcp.w:call-paraphase-06.t:call-call_f8.slurm_singularity INFO srun: job 51798251 has been allocated resources
2025-09-15 20:28:37.726 wdl.w:ptcp.w:call-paraphase-06.t:call-call_f8.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:28:38.125 wdl.w:ptcp.w:call-paraphase-06.t:call-call_f8 INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2103.f8inversion.vcf"
2025-09-15 20:28:38.127 wdl.w:ptcp.w:call-paraphase-06.t:call-call_f8 INFO output :: name: "json", value: "m84036_250809_035451_s4.bc2103.f8inversion.json"
2025-09-15 20:28:38.179 wdl.w:ptcp.w:call-paraphase-06.t:call-call_f8 NOTICE done
2025-09-15 20:28:38.184 wdl.w:ptcp.w:call-paraphase-06 NOTICE finish :: job: "call-call_f8"
2025-09-15 20:28:38.184 wdl.w:ptcp.w:call-paraphase-06 INFO output :: job: "call-call_f8", values: {"json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-06/call-call_f8/out/m84036_250809_035451_s4.bc2103.f8inversion.json", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-06/call-call_f8/out/m84036_250809_035451_s4.bc2103.f8inversion.vcf"}
2025-09-15 20:28:38.184 wdl.w:ptcp.w:call-paraphase-06 INFO visit :: node: "output-f8_json", values: {"f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-06/call-call_f8/out/m84036_250809_035451_s4.bc2103.f8inversion.json"}
2025-09-15 20:28:38.185 wdl.w:ptcp.w:call-paraphase-06 INFO visit :: node: "output-f8_vcf", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-06/call-call_f8/out/m84036_250809_035451_s4.bc2103.f8inversion.vcf"}
2025-09-15 20:28:38.185 wdl.w:ptcp.w:call-paraphase-06 INFO visit :: node: "outputs", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-06/call-call_f8/out/m84036_250809_035451_s4.bc2103.f8inversion.vcf", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-06/call-run_paraphase/out/m84036_250809_035451_s4.bc2103_paraphase/m84036_250809_035451_s4.bc2103.paraphase.json", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-06/call-run_paraphase/out/m84036_250809_035451_s4.bc2103_paraphase/m84036_250809_035451_s4.bc2103.paraphase.bam", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-06/call-run_paraphase/out/m84036_250809_035451_s4.bc2103_paraphase/m84036_250809_035451_s4.bc2103.paraphase.bam.bai", "paraphase_vcfs": ["/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-06/call-run_paraphase/out/m84036_250809_035451_s4.bc2103_paraphase/m84036_250809_035451_s4.bc2103_paraphase_vcfs/m84036_250809_035451_s4.bc2103_cyp21.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-06/call-run_paraphase/out/m84036_250809_035451_s4.bc2103_paraphase/m84036_250809_035451_s4.bc2103_paraphase_vcfs/m84036_250809_035451_s4.bc2103_f8inv1.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-06/call-run_paraphase/out/m84036_250809_035451_s4.bc2103_paraphase/m84036_250809_035451_s4.bc2103_paraphase_vcfs/m84036_250809_035451_s4.bc2103_f8inv22.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-06/call-run_paraphase/out/m84036_250809_035451_s4.bc2103_paraphase/m84036_250809_035451_s4.bc2103_paraphase_vcfs/m84036_250809_035451_s4.bc2103_gba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-06/call-run_paraphase/out/m84036_250809_035451_s4.bc2103_paraphase/m84036_250809_035451_s4.bc2103_paraphase_vcfs/m84036_250809_035451_s4.bc2103_hba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-06/call-run_paraphase/out/m84036_250809_035451_s4.bc2103_paraphase/m84036_250809_035451_s4.bc2103_paraphase_vcfs/m84036_250809_035451_s4.bc2103_hbb.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-06/call-run_paraphase/out/m84036_250809_035451_s4.bc2103_paraphase/m84036_250809_035451_s4.bc2103_paraphase_vcfs/m84036_250809_035451_s4.bc2103_rpgr.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-06/call-run_paraphase/out/m84036_250809_035451_s4.bc2103_paraphase/m84036_250809_035451_s4.bc2103_paraphase_vcfs/m84036_250809_035451_s4.bc2103_smn1.vcf"], "havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-06/call-run_paraphase/out/m84036_250809_035451_s4.bc2103.havanno.json", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-06/call-call_f8/out/m84036_250809_035451_s4.bc2103.f8inversion.json"}
2025-09-15 20:28:38.186 wdl.w:ptcp.w:call-paraphase-70.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for rpgr for sample m84036_250809_035451_s4.bc2167 at 2025-09-15 20:28:35.847937...
2025-09-15 20:28:38.280 wdl.w:ptcp.w:call-paraphase-06 NOTICE done
2025-09-15 20:28:38.286 wdl.w:ptcp NOTICE finish :: job: "call-paraphase-06"
2025-09-15 20:28:38.286 wdl.w:ptcp INFO output :: job: "call-paraphase-06", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-06/out/m84036_250809_035451_s4.bc2103.f8inversion.vcf", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-06/out/m84036_250809_035451_s4.bc2103_paraphase/m84036_250809_035451_s4.bc2103.paraphase.json", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-06/out/m84036_250809_035451_s4.bc2103_paraphase/m84036_250809_035451_s4.bc2103.paraphase.bam", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-06/out/m84036_250809_035451_s4.bc2103_paraphase/m84036_250809_035451_s4.bc2103.paraphase.bam.bai", "paraphase_vcfs": ["/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-06/out/m84036_250809_035451_s4.bc2103_paraphase/m84036_250809_035451_s4.bc2103_paraphase_vcfs/m84036_250809_035451_s4.bc2103_cyp21.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-06/out/m84036_250809_035451_s4.bc2103_paraphase/m84036_250809_035451_s4.bc2103_paraphase_vcfs/m84036_250809_035451_s4.bc2103_f8inv1.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-06/out/m84036_250809_035451_s4.bc2103_paraphase/m84036_250809_035451_s4.bc2103_paraphase_vcfs/m84036_250809_035451_s4.bc2103_f8inv22.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-06/out/m84036_250809_035451_s4.bc2103_paraphase/m84036_250809_035451_s4.bc2103_paraphase_vcfs/m84036_250809_035451_s4.bc2103_gba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-06/out/m84036_250809_035451_s4.bc2103_paraphase/m84036_250809_035451_s4.bc2103_paraphase_vcfs/m84036_250809_035451_s4.bc2103_hba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-06/out/m84036_250809_035451_s4.bc2103_paraphase/m84036_250809_035451_s4.bc2103_paraphase_vcfs/m84036_250809_035451_s4.bc2103_hbb.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-06/out/m84036_250809_035451_s4.bc2103_paraphase/m84036_250809_035451_s4.bc2103_paraphase_vcfs/m84036_250809_035451_s4.bc2103_rpgr.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-06/out/m84036_250809_035451_s4.bc2103_paraphase/m84036_250809_035451_s4.bc2103_paraphase_vcfs/m84036_250809_035451_s4.bc2103_smn1.vcf"], "havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-06/out/m84036_250809_035451_s4.bc2103.havanno.json", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-06/out/m84036_250809_035451_s4.bc2103.f8inversion.json"}
2025-09-15 20:28:38.287 wdl.w:ptcp NOTICE ready :: job: "call-tar_outputs-06", callee: "tar_outputs"
2025-09-15 20:28:38.287 wdl.w:ptcp INFO input :: job: "call-tar_outputs-06", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "sawfish_vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-06/out/m84036_250809_035451_s4.bc2103_sawfish/m84036_250809_035451_s4.bc2103.sv.vcf.gz.tbi", "sawfish_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-06/out/m84036_250809_035451_s4.bc2103_sawfish/m84036_250809_035451_s4.bc2103.sv.vcf.gz", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-06/out/m84036_250809_035451_s4.bc2103.f8inversion.json", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-06/out/m84036_250809_035451_s4.bc2103_paraphase/m84036_250809_035451_s4.bc2103.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-06/out/m84036_250809_035451_s4.bc2103_paraphase/m84036_250809_035451_s4.bc2103.paraphase.bam", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-06/out/m84036_250809_035451_s4.bc2103_paraphase/m84036_250809_035451_s4.bc2103.paraphase.json", "trgt_spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-06/out/m84036_250809_035451_s4.bc2103.trgt.sorted.spanning.bam.bai", "trgt_spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-06/out/m84036_250809_035451_s4.bc2103.trgt.sorted.spanning.bam", "trgt_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-06/out/m84036_250809_035451_s4.bc2103.trgt.vcf", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-06/out/m84036_250809_035451_s4.bc2103.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-06/out/m84036_250809_035451_s4.bc2103.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2103"}
2025-09-15 20:28:38.292 wdl.w:ptcp.t:call-tar_outputs-06 NOTICE task setup :: name: "tar_outputs", source: "./common.wdl", line: 279, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-06", thread: 140607120975424
2025-09-15 20:28:38.311 wdl.w:ptcp.t:call-tar_outputs-06 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:28:38.311 wdl.w:ptcp.t:call-tar_outputs-06 INFO input :: name: "sawfish_vcf_tbi", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2103.sv.vcf.gz.tbi"
2025-09-15 20:28:38.311 wdl.w:ptcp.t:call-tar_outputs-06 INFO input :: name: "sawfish_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2103.sv.vcf.gz"
2025-09-15 20:28:38.311 wdl.w:ptcp.t:call-tar_outputs-06 INFO input :: name: "f8_json", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2103.f8inversion.json"
2025-09-15 20:28:38.311 wdl.w:ptcp.t:call-tar_outputs-06 INFO input :: name: "paraphase_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2103.paraphase.bam.bai"
2025-09-15 20:28:38.311 wdl.w:ptcp.t:call-tar_outputs-06 INFO input :: name: "paraphase_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2103.paraphase.bam"
2025-09-15 20:28:38.312 wdl.w:ptcp.t:call-tar_outputs-06 INFO input :: name: "paraphase_json", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2103.paraphase.json"
2025-09-15 20:28:38.312 wdl.w:ptcp.t:call-tar_outputs-06 INFO input :: name: "trgt_spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2103.trgt.sorted.spanning.bam.bai"
2025-09-15 20:28:38.312 wdl.w:ptcp.t:call-tar_outputs-06 INFO input :: name: "trgt_spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2103.trgt.sorted.spanning.bam"
2025-09-15 20:28:38.312 wdl.w:ptcp.t:call-tar_outputs-06 INFO input :: name: "trgt_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2103.trgt.vcf"
2025-09-15 20:28:38.312 wdl.w:ptcp.t:call-tar_outputs-06 INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2103.mapped.bam.bai"
2025-09-15 20:28:38.312 wdl.w:ptcp.t:call-tar_outputs-06 INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2103.mapped.bam"
2025-09-15 20:28:38.312 wdl.w:ptcp.t:call-tar_outputs-06 INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2103"
2025-09-15 20:28:38.312 wdl.w:ptcp.t:call-tar_outputs-06 INFO eval :: name: "threads", value: 1
2025-09-15 20:28:38.312 wdl.w:ptcp.t:call-tar_outputs-06 INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:28:38.312 wdl.w:ptcp.t:call-tar_outputs-06 INFO eval :: name: "disk_size", value: 6
2025-09-15 20:28:38.312 wdl.w:ptcp.t:call-tar_outputs-06 INFO eval :: name: "output_tarball", value: "m84036_250809_035451_s4.bc2103.tar"
2025-09-15 20:28:38.313 wdl.w:ptcp.t:call-tar_outputs-06 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:28:38.313 wdl.w:ptcp.t:call-tar_outputs-06 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:28:38.313 wdl.w:ptcp.t:call-tar_outputs-06 INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:28:38.313 wdl.w:ptcp.t:call-tar_outputs-06 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:28:38.391 wdl.w:ptcp.t:call-tar_outputs-06 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 17, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-06/_singularity_tmpdir_317nr43o"
2025-09-15 20:28:38.391 wdl.w:ptcp.t:call-tar_outputs-06 INFO Slurm invocation: srun --job-name call-tar_outputs-06 --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-06/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-06/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-06/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-06/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-06/out/m84036_250809_035451_s4.bc2103.f8inversion.json:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2103.f8inversion.json:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-06/out/m84036_250809_035451_s4.bc2103.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2103.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-06/out/m84036_250809_035451_s4.bc2103.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2103.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-06/out/m84036_250809_035451_s4.bc2103_paraphase/m84036_250809_035451_s4.bc2103.paraphase.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2103.paraphase.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-06/out/m84036_250809_035451_s4.bc2103_paraphase/m84036_250809_035451_s4.bc2103.paraphase.json:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2103.paraphase.json:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-06/out/m84036_250809_035451_s4.bc2103_paraphase/m84036_250809_035451_s4.bc2103.paraphase.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2103.paraphase.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-06/out/m84036_250809_035451_s4.bc2103.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2103.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-06/out/m84036_250809_035451_s4.bc2103.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2103.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-06/out/m84036_250809_035451_s4.bc2103.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2103.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-06/out/m84036_250809_035451_s4.bc2103_sawfish/m84036_250809_035451_s4.bc2103.sv.vcf.gz:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2103.sv.vcf.gz:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-06/out/m84036_250809_035451_s4.bc2103_sawfish/m84036_250809_035451_s4.bc2103.sv.vcf.gz.tbi:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2103.sv.vcf.gz.tbi:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-06/_singularity_tmpdir_317nr43o/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-06/_singularity_tmpdir_317nr43o/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:28:38.400 wdl.w:ptcp.t:call-tar_outputs-06 NOTICE slurm_singularity run :: pid: 1209223, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-06/slurm_singularity.log.txt"
2025-09-15 20:28:38.639 wdl.w:ptcp.w:call-paraphase-86.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for rpgr for sample m84036_250809_035451_s4.bc2183 at 2025-09-15 20:28:10.767313...
2025-09-15 20:28:38.640 wdl.w:ptcp.w:call-paraphase-86.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for rpgr for sample m84036_250809_035451_s4.bc2183 at 2025-09-15 20:28:10.768058...
2025-09-15 20:28:38.640 wdl.w:ptcp.w:call-paraphase-86.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for rpgr for sample m84036_250809_035451_s4.bc2183 at 2025-09-15 20:28:12.230434...
2025-09-15 20:28:38.640 wdl.w:ptcp.w:call-paraphase-86.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for rpgr for sample m84036_250809_035451_s4.bc2183 at 2025-09-15 20:28:13.292037...
2025-09-15 20:28:38.640 wdl.w:ptcp.w:call-paraphase-86.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for rpgr for sample m84036_250809_035451_s4.bc2183 at 2025-09-15 20:28:13.501900...
2025-09-15 20:28:39.047 wdl.w:ptcp.w:call-paraphase-75.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for hbb for sample m84036_250809_035451_s4.bc2172 at 2025-09-15 20:28:29.536382...
2025-09-15 20:28:39.047 wdl.w:ptcp.w:call-paraphase-75.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for hbb for sample m84036_250809_035451_s4.bc2172 at 2025-09-15 20:28:30.147982...
2025-09-15 20:28:39.066 wdl.w:ptcp.w:call-paraphase-02.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for rpgr for sample m84036_250809_035451_s4.bc2099 at 2025-09-15 20:28:29.635638...
2025-09-15 20:28:39.410 wdl.w:ptcp.t:call-tar_outputs-06.slurm_singularity INFO srun: job 51798252 queued and waiting for resources
2025-09-15 20:28:40.419 wdl.w:ptcp.t:call-tar_outputs-06.slurm_singularity INFO srun: job 51798252 has been allocated resources
2025-09-15 20:28:40.419 wdl.w:ptcp.t:call-tar_outputs-06.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:28:40.916 wdl.w:ptcp.t:call-tar_outputs-06 INFO output :: name: "sample_tarball", value: "m84036_250809_035451_s4.bc2103.tar"
2025-09-15 20:28:40.966 wdl.w:ptcp.t:call-tar_outputs-06 NOTICE done
2025-09-15 20:28:40.971 wdl.w:ptcp NOTICE finish :: job: "call-tar_outputs-06"
2025-09-15 20:28:40.971 wdl.w:ptcp INFO output :: job: "call-tar_outputs-06", values: {"sample_tarball": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-06/out/m84036_250809_035451_s4.bc2103.tar"}
2025-09-15 20:28:41.127 wdl.w:ptcp.w:call-paraphase-82.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for hbb for sample m84036_250809_035451_s4.bc2179 at 2025-09-15 20:28:18.350732...
2025-09-15 20:28:41.127 wdl.w:ptcp.w:call-paraphase-82.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for hbb for sample m84036_250809_035451_s4.bc2179 at 2025-09-15 20:28:18.352630...
2025-09-15 20:28:41.127 wdl.w:ptcp.w:call-paraphase-82.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for hbb for sample m84036_250809_035451_s4.bc2179 at 2025-09-15 20:28:20.534794...
2025-09-15 20:28:41.127 wdl.w:ptcp.w:call-paraphase-82.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for hbb for sample m84036_250809_035451_s4.bc2179 at 2025-09-15 20:28:29.438411...
2025-09-15 20:28:41.127 wdl.w:ptcp.w:call-paraphase-82.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for hbb for sample m84036_250809_035451_s4.bc2179 at 2025-09-15 20:28:29.997229...
2025-09-15 20:28:43.442 wdl.w:ptcp.w:call-paraphase-03.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for rpgr for sample m84036_250809_035451_s4.bc2100 at 2025-09-15 20:27:53.878822...
2025-09-15 20:28:43.442 wdl.w:ptcp.w:call-paraphase-03.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for rpgr for sample m84036_250809_035451_s4.bc2100 at 2025-09-15 20:27:55.386661...
2025-09-15 20:28:43.442 wdl.w:ptcp.w:call-paraphase-03.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for rpgr for sample m84036_250809_035451_s4.bc2100 at 2025-09-15 20:27:55.632555...
2025-09-15 20:28:46.183 wdl.w:ptcp.w:call-paraphase-07.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for rpgr for sample m84036_250809_035451_s4.bc2104 at 2025-09-15 20:28:11.448145...
2025-09-15 20:28:46.184 wdl.w:ptcp.w:call-paraphase-07.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for rpgr for sample m84036_250809_035451_s4.bc2104 at 2025-09-15 20:28:11.448828...
2025-09-15 20:28:46.184 wdl.w:ptcp.w:call-paraphase-07.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for rpgr for sample m84036_250809_035451_s4.bc2104 at 2025-09-15 20:28:15.085733...
2025-09-15 20:28:46.184 wdl.w:ptcp.w:call-paraphase-07.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for rpgr for sample m84036_250809_035451_s4.bc2104 at 2025-09-15 20:28:16.996447...
2025-09-15 20:28:46.184 wdl.w:ptcp.w:call-paraphase-07.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for rpgr for sample m84036_250809_035451_s4.bc2104 at 2025-09-15 20:28:17.223294...
2025-09-15 20:28:47.269 wdl.w:ptcp.w:call-paraphase-70.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for rpgr for sample m84036_250809_035451_s4.bc2167 at 2025-09-15 20:28:37.559130...
2025-09-15 20:28:47.269 wdl.w:ptcp.w:call-paraphase-70.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for rpgr for sample m84036_250809_035451_s4.bc2167 at 2025-09-15 20:28:37.732239...
2025-09-15 20:28:48.008 wdl.w:ptcp.w:call-paraphase-71.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for f8inv22 for sample m84036_250809_035451_s4.bc2168 at 2025-09-15 20:28:38.140606...
2025-09-15 20:28:48.008 wdl.w:ptcp.w:call-paraphase-71.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for f8inv22 for sample m84036_250809_035451_s4.bc2168 at 2025-09-15 20:28:38.141414...
2025-09-15 20:28:50.122 wdl.w:ptcp.w:call-paraphase-10.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for rpgr for sample m84036_250809_035451_s4.bc2107 at 2025-09-15 20:27:55.920600...
2025-09-15 20:28:50.123 wdl.w:ptcp.w:call-paraphase-10.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for rpgr for sample m84036_250809_035451_s4.bc2107 at 2025-09-15 20:27:55.922256...
2025-09-15 20:28:50.123 wdl.w:ptcp.w:call-paraphase-10.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for rpgr for sample m84036_250809_035451_s4.bc2107 at 2025-09-15 20:27:58.580676...
2025-09-15 20:28:50.123 wdl.w:ptcp.w:call-paraphase-10.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for rpgr for sample m84036_250809_035451_s4.bc2107 at 2025-09-15 20:28:00.011216...
2025-09-15 20:28:50.123 wdl.w:ptcp.w:call-paraphase-10.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for rpgr for sample m84036_250809_035451_s4.bc2107 at 2025-09-15 20:28:00.273571...
2025-09-15 20:28:58.036 wdl.w:ptcp.w:call-paraphase-62.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for f8inv22 for sample m84036_250809_035451_s4.bc2159 at 2025-09-15 20:28:20.962964...
2025-09-15 20:28:58.036 wdl.w:ptcp.w:call-paraphase-62.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for f8inv22 for sample m84036_250809_035451_s4.bc2159 at 2025-09-15 20:28:27.651215...
2025-09-15 20:28:58.036 wdl.w:ptcp.w:call-paraphase-62.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for f8inv22 for sample m84036_250809_035451_s4.bc2159 at 2025-09-15 20:28:28.319810...
2025-09-15 20:28:58.036 wdl.w:ptcp.w:call-paraphase-62.t:call-run_paraphase.stderr VERBOSE INFO:root:Merging all bams for sample m84036_250809_035451_s4.bc2159 at 2025-09-15 20:28:53.126387...
2025-09-15 20:28:58.036 wdl.w:ptcp.w:call-paraphase-62.t:call-run_paraphase.stderr VERBOSE INFO:root:Writing to json for sample m84036_250809_035451_s4.bc2159 at 2025-09-15 20:28:57.134654...
2025-09-15 20:28:58.036 wdl.w:ptcp.w:call-paraphase-62.t:call-run_paraphase.stderr VERBOSE INFO:root:Completed Paraphase analysis at 2025-09-15 20:28:57.568775...
2025-09-15 20:28:58.491 wdl.w:ptcp.w:call-paraphase-62.t:call-run_paraphase INFO output :: name: "paraphase_bam", value: "m84036_250809_035451_s4.bc2159_paraphase/m84036_250809_035451_s4.bc2159.paraphase.bam"
2025-09-15 20:28:58.494 wdl.w:ptcp.w:call-paraphase-62.t:call-run_paraphase INFO output :: name: "paraphase_bam_bai", value: "m84036_250809_035451_s4.bc2159_paraphase/m84036_250809_035451_s4.bc2159.paraphase.bam.bai"
2025-09-15 20:28:58.495 wdl.w:ptcp.w:call-paraphase-62.t:call-run_paraphase INFO output :: name: "paraphase_json", value: "m84036_250809_035451_s4.bc2159_paraphase/m84036_250809_035451_s4.bc2159.paraphase.json"
2025-09-15 20:28:58.499 wdl.w:ptcp.w:call-paraphase-62.t:call-run_paraphase INFO output :: name: "paraphase_vcfs", value: ["/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2159_paraphase/m84036_250809_035451_s4.bc2159_paraphase_vcfs/m84036_250809_035451_s4.bc2159_cyp21.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2159_paraphase/m84036_250809_035451_s4.bc2159_paraphase_vcfs/m84036_250809_035451_s4.bc2159_f8inv1.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2159_paraphase/m84036_250809_035451_s4.bc2159_paraphase_vcfs/m84036_250809_035451_s4.bc2159_f8inv22.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2159_paraphase/m84036_250809_035451_s4.bc2159_paraphase_vcfs/m84036_250809_035451_s4.bc2159_gba.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2159_paraphase/m84036_250809_035451_s4.bc2159_paraphase_vcfs/m84036_250809_035451_s4.bc2159_hba.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2159_paraphase/m84036_250809_035451_s4.bc2159_paraphase_vcfs/m84036_250809_035451_s4.bc2159_hbb.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2159_paraphase/m84036_250809_035451_s4.bc2159_paraphase_vcfs/m84036_250809_035451_s4.bc2159_rpgr.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2159_paraphase/m84036_250809_035451_s4.bc2159_paraphase_vcfs/m84036_250809_035451_s4.bc2159_smn1.vcf"]
2025-09-15 20:28:58.502 wdl.w:ptcp.w:call-paraphase-62.t:call-run_paraphase INFO output :: name: "havanno_json", value: "m84036_250809_035451_s4.bc2159.havanno.json"
2025-09-15 20:28:58.644 wdl.w:ptcp.w:call-paraphase-62.t:call-run_paraphase NOTICE done
2025-09-15 20:28:58.649 wdl.w:ptcp.w:call-paraphase-62 NOTICE finish :: job: "call-run_paraphase"
2025-09-15 20:28:58.650 wdl.w:ptcp.w:call-paraphase-62 INFO output :: job: "call-run_paraphase", values: {"havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-62/call-run_paraphase/out/m84036_250809_035451_s4.bc2159.havanno.json", "paraphase_vcfs": ["/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-62/call-run_paraphase/out/m84036_250809_035451_s4.bc2159_paraphase/m84036_250809_035451_s4.bc2159_paraphase_vcfs/m84036_250809_035451_s4.bc2159_cyp21.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-62/call-run_paraphase/out/m84036_250809_035451_s4.bc2159_paraphase/m84036_250809_035451_s4.bc2159_paraphase_vcfs/m84036_250809_035451_s4.bc2159_f8inv1.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-62/call-run_paraphase/out/m84036_250809_035451_s4.bc2159_paraphase/m84036_250809_035451_s4.bc2159_paraphase_vcfs/m84036_250809_035451_s4.bc2159_f8inv22.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-62/call-run_paraphase/out/m84036_250809_035451_s4.bc2159_paraphase/m84036_250809_035451_s4.bc2159_paraphase_vcfs/m84036_250809_035451_s4.bc2159_gba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-62/call-run_paraphase/out/m84036_250809_035451_s4.bc2159_paraphase/m84036_250809_035451_s4.bc2159_paraphase_vcfs/m84036_250809_035451_s4.bc2159_hba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-62/call-run_paraphase/out/m84036_250809_035451_s4.bc2159_paraphase/m84036_250809_035451_s4.bc2159_paraphase_vcfs/m84036_250809_035451_s4.bc2159_hbb.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-62/call-run_paraphase/out/m84036_250809_035451_s4.bc2159_paraphase/m84036_250809_035451_s4.bc2159_paraphase_vcfs/m84036_250809_035451_s4.bc2159_rpgr.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-62/call-run_paraphase/out/m84036_250809_035451_s4.bc2159_paraphase/m84036_250809_035451_s4.bc2159_paraphase_vcfs/m84036_250809_035451_s4.bc2159_smn1.vcf"], "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-62/call-run_paraphase/out/m84036_250809_035451_s4.bc2159_paraphase/m84036_250809_035451_s4.bc2159.paraphase.json", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-62/call-run_paraphase/out/m84036_250809_035451_s4.bc2159_paraphase/m84036_250809_035451_s4.bc2159.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-62/call-run_paraphase/out/m84036_250809_035451_s4.bc2159_paraphase/m84036_250809_035451_s4.bc2159.paraphase.bam"}
2025-09-15 20:28:58.650 wdl.w:ptcp.w:call-paraphase-62 NOTICE ready :: job: "call-call_f8", callee: "call_f8"
2025-09-15 20:28:58.650 wdl.w:ptcp.w:call-paraphase-62 INFO input :: job: "call-call_f8", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "out_prefix": "m84036_250809_035451_s4.bc2159", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-62/call-run_paraphase/out/m84036_250809_035451_s4.bc2159_paraphase/m84036_250809_035451_s4.bc2159.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-62/call-run_paraphase/out/m84036_250809_035451_s4.bc2159_paraphase/m84036_250809_035451_s4.bc2159.paraphase.bam", "sex": "F"}
2025-09-15 20:28:58.651 wdl.w:ptcp.w:call-paraphase-62 INFO visit :: node: "output-havanno_json", values: {"havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-62/call-run_paraphase/out/m84036_250809_035451_s4.bc2159.havanno.json"}
2025-09-15 20:28:58.651 wdl.w:ptcp.w:call-paraphase-62 INFO visit :: node: "output-paraphase_bam", values: {"paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-62/call-run_paraphase/out/m84036_250809_035451_s4.bc2159_paraphase/m84036_250809_035451_s4.bc2159.paraphase.bam"}
2025-09-15 20:28:58.651 wdl.w:ptcp.w:call-paraphase-62 INFO visit :: node: "output-paraphase_bam_bai", values: {"paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-62/call-run_paraphase/out/m84036_250809_035451_s4.bc2159_paraphase/m84036_250809_035451_s4.bc2159.paraphase.bam.bai"}
2025-09-15 20:28:58.651 wdl.w:ptcp.w:call-paraphase-62 INFO visit :: node: "output-paraphase_json", values: {"paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-62/call-run_paraphase/out/m84036_250809_035451_s4.bc2159_paraphase/m84036_250809_035451_s4.bc2159.paraphase.json"}
2025-09-15 20:28:58.651 wdl.w:ptcp.w:call-paraphase-62 INFO visit :: node: "output-paraphase_vcfs", values: {"paraphase_vcfs": ["/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-62/call-run_paraphase/out/m84036_250809_035451_s4.bc2159_paraphase/m84036_250809_035451_s4.bc2159_paraphase_vcfs/m84036_250809_035451_s4.bc2159_cyp21.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-62/call-run_paraphase/out/m84036_250809_035451_s4.bc2159_paraphase/m84036_250809_035451_s4.bc2159_paraphase_vcfs/m84036_250809_035451_s4.bc2159_f8inv1.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-62/call-run_paraphase/out/m84036_250809_035451_s4.bc2159_paraphase/m84036_250809_035451_s4.bc2159_paraphase_vcfs/m84036_250809_035451_s4.bc2159_f8inv22.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-62/call-run_paraphase/out/m84036_250809_035451_s4.bc2159_paraphase/m84036_250809_035451_s4.bc2159_paraphase_vcfs/m84036_250809_035451_s4.bc2159_gba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-62/call-run_paraphase/out/m84036_250809_035451_s4.bc2159_paraphase/m84036_250809_035451_s4.bc2159_paraphase_vcfs/m84036_250809_035451_s4.bc2159_hba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-62/call-run_paraphase/out/m84036_250809_035451_s4.bc2159_paraphase/m84036_250809_035451_s4.bc2159_paraphase_vcfs/m84036_250809_035451_s4.bc2159_hbb.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-62/call-run_paraphase/out/m84036_250809_035451_s4.bc2159_paraphase/m84036_250809_035451_s4.bc2159_paraphase_vcfs/m84036_250809_035451_s4.bc2159_rpgr.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-62/call-run_paraphase/out/m84036_250809_035451_s4.bc2159_paraphase/m84036_250809_035451_s4.bc2159_paraphase_vcfs/m84036_250809_035451_s4.bc2159_smn1.vcf"]}
2025-09-15 20:28:58.655 wdl.w:ptcp.w:call-paraphase-62.t:call-call_f8 NOTICE task setup :: name: "call_f8", source: "./paraphase.wdl", line: 232, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-62/call-call_f8", thread: 140611441120832
2025-09-15 20:28:58.670 wdl.w:ptcp.w:call-paraphase-62.t:call-call_f8 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:28:58.670 wdl.w:ptcp.w:call-paraphase-62.t:call-call_f8 INFO input :: name: "genome_version", value: "38"
2025-09-15 20:28:58.670 wdl.w:ptcp.w:call-paraphase-62.t:call-call_f8 INFO input :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2159"
2025-09-15 20:28:58.670 wdl.w:ptcp.w:call-paraphase-62.t:call-call_f8 INFO input :: name: "paraphase_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2159.paraphase.bam.bai"
2025-09-15 20:28:58.670 wdl.w:ptcp.w:call-paraphase-62.t:call-call_f8 INFO input :: name: "paraphase_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2159.paraphase.bam"
2025-09-15 20:28:58.670 wdl.w:ptcp.w:call-paraphase-62.t:call-call_f8 INFO input :: name: "sex", value: "F"
2025-09-15 20:28:58.671 wdl.w:ptcp.w:call-paraphase-62.t:call-call_f8 INFO eval :: name: "threads", value: 1
2025-09-15 20:28:58.671 wdl.w:ptcp.w:call-paraphase-62.t:call-call_f8 INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:28:58.671 wdl.w:ptcp.w:call-paraphase-62.t:call-call_f8 INFO eval :: name: "disk_size", value: 11
2025-09-15 20:28:58.671 wdl.w:ptcp.w:call-paraphase-62.t:call-call_f8 INFO eval :: name: "sample_sex", value: "F"
2025-09-15 20:28:58.671 wdl.w:ptcp.w:call-paraphase-62.t:call-call_f8 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:28:58.671 wdl.w:ptcp.w:call-paraphase-62.t:call-call_f8 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:28:58.672 wdl.w:ptcp.w:call-paraphase-62.t:call-call_f8 INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:28:58.672 wdl.w:ptcp.w:call-paraphase-62.t:call-call_f8 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:28:58.706 wdl.w:ptcp.w:call-paraphase-62.t:call-call_f8 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 8, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-62/call-call_f8/_singularity_tmpdir__yhq0s1d"
2025-09-15 20:28:58.706 wdl.w:ptcp.w:call-paraphase-62.t:call-call_f8 INFO Slurm invocation: srun --job-name call-call_f8 --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-62/call-call_f8/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-62/call-call_f8/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-62/call-call_f8/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-62/call-call_f8/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-62/call-run_paraphase/out/m84036_250809_035451_s4.bc2159_paraphase/m84036_250809_035451_s4.bc2159.paraphase.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2159.paraphase.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-62/call-run_paraphase/out/m84036_250809_035451_s4.bc2159_paraphase/m84036_250809_035451_s4.bc2159.paraphase.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2159.paraphase.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-62/call-call_f8/_singularity_tmpdir__yhq0s1d/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-62/call-call_f8/_singularity_tmpdir__yhq0s1d/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:28:58.710 wdl.w:ptcp.w:call-paraphase-62.t:call-call_f8 NOTICE slurm_singularity run :: pid: 1209384, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-62/call-call_f8/slurm_singularity.log.txt"
2025-09-15 20:28:59.719 wdl.w:ptcp.w:call-paraphase-62.t:call-call_f8.slurm_singularity INFO srun: job 51798262 queued and waiting for resources
2025-09-15 20:28:59.719 wdl.w:ptcp.w:call-paraphase-62.t:call-call_f8.slurm_singularity INFO srun: job 51798262 has been allocated resources
2025-09-15 20:28:59.719 wdl.w:ptcp.w:call-paraphase-62.t:call-call_f8.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:29:00.217 wdl.w:ptcp.w:call-paraphase-62.t:call-call_f8 INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2159.f8inversion.vcf"
2025-09-15 20:29:00.219 wdl.w:ptcp.w:call-paraphase-62.t:call-call_f8 INFO output :: name: "json", value: "m84036_250809_035451_s4.bc2159.f8inversion.json"
2025-09-15 20:29:00.270 wdl.w:ptcp.w:call-paraphase-62.t:call-call_f8 NOTICE done
2025-09-15 20:29:00.275 wdl.w:ptcp.w:call-paraphase-62 NOTICE finish :: job: "call-call_f8"
2025-09-15 20:29:00.275 wdl.w:ptcp.w:call-paraphase-62 INFO output :: job: "call-call_f8", values: {"json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-62/call-call_f8/out/m84036_250809_035451_s4.bc2159.f8inversion.json", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-62/call-call_f8/out/m84036_250809_035451_s4.bc2159.f8inversion.vcf"}
2025-09-15 20:29:00.276 wdl.w:ptcp.w:call-paraphase-62 INFO visit :: node: "output-f8_json", values: {"f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-62/call-call_f8/out/m84036_250809_035451_s4.bc2159.f8inversion.json"}
2025-09-15 20:29:00.276 wdl.w:ptcp.w:call-paraphase-62 INFO visit :: node: "output-f8_vcf", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-62/call-call_f8/out/m84036_250809_035451_s4.bc2159.f8inversion.vcf"}
2025-09-15 20:29:00.276 wdl.w:ptcp.w:call-paraphase-62 INFO visit :: node: "outputs", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-62/call-call_f8/out/m84036_250809_035451_s4.bc2159.f8inversion.vcf", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-62/call-run_paraphase/out/m84036_250809_035451_s4.bc2159_paraphase/m84036_250809_035451_s4.bc2159.paraphase.json", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-62/call-run_paraphase/out/m84036_250809_035451_s4.bc2159_paraphase/m84036_250809_035451_s4.bc2159.paraphase.bam", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-62/call-run_paraphase/out/m84036_250809_035451_s4.bc2159_paraphase/m84036_250809_035451_s4.bc2159.paraphase.bam.bai", "paraphase_vcfs": ["/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-62/call-run_paraphase/out/m84036_250809_035451_s4.bc2159_paraphase/m84036_250809_035451_s4.bc2159_paraphase_vcfs/m84036_250809_035451_s4.bc2159_cyp21.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-62/call-run_paraphase/out/m84036_250809_035451_s4.bc2159_paraphase/m84036_250809_035451_s4.bc2159_paraphase_vcfs/m84036_250809_035451_s4.bc2159_f8inv1.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-62/call-run_paraphase/out/m84036_250809_035451_s4.bc2159_paraphase/m84036_250809_035451_s4.bc2159_paraphase_vcfs/m84036_250809_035451_s4.bc2159_f8inv22.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-62/call-run_paraphase/out/m84036_250809_035451_s4.bc2159_paraphase/m84036_250809_035451_s4.bc2159_paraphase_vcfs/m84036_250809_035451_s4.bc2159_gba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-62/call-run_paraphase/out/m84036_250809_035451_s4.bc2159_paraphase/m84036_250809_035451_s4.bc2159_paraphase_vcfs/m84036_250809_035451_s4.bc2159_hba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-62/call-run_paraphase/out/m84036_250809_035451_s4.bc2159_paraphase/m84036_250809_035451_s4.bc2159_paraphase_vcfs/m84036_250809_035451_s4.bc2159_hbb.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-62/call-run_paraphase/out/m84036_250809_035451_s4.bc2159_paraphase/m84036_250809_035451_s4.bc2159_paraphase_vcfs/m84036_250809_035451_s4.bc2159_rpgr.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-62/call-run_paraphase/out/m84036_250809_035451_s4.bc2159_paraphase/m84036_250809_035451_s4.bc2159_paraphase_vcfs/m84036_250809_035451_s4.bc2159_smn1.vcf"], "havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-62/call-run_paraphase/out/m84036_250809_035451_s4.bc2159.havanno.json", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-62/call-call_f8/out/m84036_250809_035451_s4.bc2159.f8inversion.json"}
2025-09-15 20:29:00.381 wdl.w:ptcp.w:call-paraphase-62 NOTICE done
2025-09-15 20:29:00.387 wdl.w:ptcp NOTICE finish :: job: "call-paraphase-62"
2025-09-15 20:29:00.387 wdl.w:ptcp INFO output :: job: "call-paraphase-62", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-62/out/m84036_250809_035451_s4.bc2159.f8inversion.vcf", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-62/out/m84036_250809_035451_s4.bc2159_paraphase/m84036_250809_035451_s4.bc2159.paraphase.json", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-62/out/m84036_250809_035451_s4.bc2159_paraphase/m84036_250809_035451_s4.bc2159.paraphase.bam", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-62/out/m84036_250809_035451_s4.bc2159_paraphase/m84036_250809_035451_s4.bc2159.paraphase.bam.bai", "paraphase_vcfs": ["/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-62/out/m84036_250809_035451_s4.bc2159_paraphase/m84036_250809_035451_s4.bc2159_paraphase_vcfs/m84036_250809_035451_s4.bc2159_cyp21.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-62/out/m84036_250809_035451_s4.bc2159_paraphase/m84036_250809_035451_s4.bc2159_paraphase_vcfs/m84036_250809_035451_s4.bc2159_f8inv1.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-62/out/m84036_250809_035451_s4.bc2159_paraphase/m84036_250809_035451_s4.bc2159_paraphase_vcfs/m84036_250809_035451_s4.bc2159_f8inv22.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-62/out/m84036_250809_035451_s4.bc2159_paraphase/m84036_250809_035451_s4.bc2159_paraphase_vcfs/m84036_250809_035451_s4.bc2159_gba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-62/out/m84036_250809_035451_s4.bc2159_paraphase/m84036_250809_035451_s4.bc2159_paraphase_vcfs/m84036_250809_035451_s4.bc2159_hba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-62/out/m84036_250809_035451_s4.bc2159_paraphase/m84036_250809_035451_s4.bc2159_paraphase_vcfs/m84036_250809_035451_s4.bc2159_hbb.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-62/out/m84036_250809_035451_s4.bc2159_paraphase/m84036_250809_035451_s4.bc2159_paraphase_vcfs/m84036_250809_035451_s4.bc2159_rpgr.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-62/out/m84036_250809_035451_s4.bc2159_paraphase/m84036_250809_035451_s4.bc2159_paraphase_vcfs/m84036_250809_035451_s4.bc2159_smn1.vcf"], "havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-62/out/m84036_250809_035451_s4.bc2159.havanno.json", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-62/out/m84036_250809_035451_s4.bc2159.f8inversion.json"}
2025-09-15 20:29:00.387 wdl.w:ptcp NOTICE ready :: job: "call-tar_outputs-62", callee: "tar_outputs"
2025-09-15 20:29:00.387 wdl.w:ptcp INFO input :: job: "call-tar_outputs-62", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "sawfish_vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-62/out/m84036_250809_035451_s4.bc2159_sawfish/m84036_250809_035451_s4.bc2159.sv.vcf.gz.tbi", "sawfish_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-62/out/m84036_250809_035451_s4.bc2159_sawfish/m84036_250809_035451_s4.bc2159.sv.vcf.gz", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-62/out/m84036_250809_035451_s4.bc2159.f8inversion.json", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-62/out/m84036_250809_035451_s4.bc2159_paraphase/m84036_250809_035451_s4.bc2159.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-62/out/m84036_250809_035451_s4.bc2159_paraphase/m84036_250809_035451_s4.bc2159.paraphase.bam", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-62/out/m84036_250809_035451_s4.bc2159_paraphase/m84036_250809_035451_s4.bc2159.paraphase.json", "trgt_spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-62/out/m84036_250809_035451_s4.bc2159.trgt.sorted.spanning.bam.bai", "trgt_spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-62/out/m84036_250809_035451_s4.bc2159.trgt.sorted.spanning.bam", "trgt_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-62/out/m84036_250809_035451_s4.bc2159.trgt.vcf", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-62/out/m84036_250809_035451_s4.bc2159.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-62/out/m84036_250809_035451_s4.bc2159.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2159"}
2025-09-15 20:29:00.395 wdl.w:ptcp.t:call-tar_outputs-62 NOTICE task setup :: name: "tar_outputs", source: "./common.wdl", line: 279, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-62", thread: 140613596997184
2025-09-15 20:29:00.431 wdl.w:ptcp.t:call-tar_outputs-62 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:29:00.431 wdl.w:ptcp.t:call-tar_outputs-62 INFO input :: name: "sawfish_vcf_tbi", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2159.sv.vcf.gz.tbi"
2025-09-15 20:29:00.431 wdl.w:ptcp.t:call-tar_outputs-62 INFO input :: name: "sawfish_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2159.sv.vcf.gz"
2025-09-15 20:29:00.431 wdl.w:ptcp.t:call-tar_outputs-62 INFO input :: name: "f8_json", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2159.f8inversion.json"
2025-09-15 20:29:00.431 wdl.w:ptcp.t:call-tar_outputs-62 INFO input :: name: "paraphase_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2159.paraphase.bam.bai"
2025-09-15 20:29:00.431 wdl.w:ptcp.t:call-tar_outputs-62 INFO input :: name: "paraphase_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2159.paraphase.bam"
2025-09-15 20:29:00.431 wdl.w:ptcp.t:call-tar_outputs-62 INFO input :: name: "paraphase_json", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2159.paraphase.json"
2025-09-15 20:29:00.431 wdl.w:ptcp.t:call-tar_outputs-62 INFO input :: name: "trgt_spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2159.trgt.sorted.spanning.bam.bai"
2025-09-15 20:29:00.431 wdl.w:ptcp.t:call-tar_outputs-62 INFO input :: name: "trgt_spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2159.trgt.sorted.spanning.bam"
2025-09-15 20:29:00.431 wdl.w:ptcp.t:call-tar_outputs-62 INFO input :: name: "trgt_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2159.trgt.vcf"
2025-09-15 20:29:00.431 wdl.w:ptcp.t:call-tar_outputs-62 INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2159.mapped.bam.bai"
2025-09-15 20:29:00.431 wdl.w:ptcp.t:call-tar_outputs-62 INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2159.mapped.bam"
2025-09-15 20:29:00.431 wdl.w:ptcp.t:call-tar_outputs-62 INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2159"
2025-09-15 20:29:00.431 wdl.w:ptcp.t:call-tar_outputs-62 INFO eval :: name: "threads", value: 1
2025-09-15 20:29:00.431 wdl.w:ptcp.t:call-tar_outputs-62 INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:29:00.432 wdl.w:ptcp.t:call-tar_outputs-62 INFO eval :: name: "disk_size", value: 6
2025-09-15 20:29:00.432 wdl.w:ptcp.t:call-tar_outputs-62 INFO eval :: name: "output_tarball", value: "m84036_250809_035451_s4.bc2159.tar"
2025-09-15 20:29:00.432 wdl.w:ptcp.t:call-tar_outputs-62 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:29:00.432 wdl.w:ptcp.t:call-tar_outputs-62 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:29:00.433 wdl.w:ptcp.t:call-tar_outputs-62 INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:29:00.433 wdl.w:ptcp.t:call-tar_outputs-62 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:29:00.502 wdl.w:ptcp.t:call-tar_outputs-62 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 17, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-62/_singularity_tmpdir__dk02w3p"
2025-09-15 20:29:00.503 wdl.w:ptcp.t:call-tar_outputs-62 INFO Slurm invocation: srun --job-name call-tar_outputs-62 --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-62/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-62/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-62/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-62/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-62/out/m84036_250809_035451_s4.bc2159.f8inversion.json:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2159.f8inversion.json:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-62/out/m84036_250809_035451_s4.bc2159_paraphase/m84036_250809_035451_s4.bc2159.paraphase.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2159.paraphase.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-62/out/m84036_250809_035451_s4.bc2159_paraphase/m84036_250809_035451_s4.bc2159.paraphase.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2159.paraphase.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-62/out/m84036_250809_035451_s4.bc2159_paraphase/m84036_250809_035451_s4.bc2159.paraphase.json:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2159.paraphase.json:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-62/out/m84036_250809_035451_s4.bc2159.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2159.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-62/out/m84036_250809_035451_s4.bc2159.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2159.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-62/out/m84036_250809_035451_s4.bc2159.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2159.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-62/out/m84036_250809_035451_s4.bc2159.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2159.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-62/out/m84036_250809_035451_s4.bc2159.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2159.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-62/out/m84036_250809_035451_s4.bc2159_sawfish/m84036_250809_035451_s4.bc2159.sv.vcf.gz.tbi:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2159.sv.vcf.gz.tbi:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-62/out/m84036_250809_035451_s4.bc2159_sawfish/m84036_250809_035451_s4.bc2159.sv.vcf.gz:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2159.sv.vcf.gz:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-62/_singularity_tmpdir__dk02w3p/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-62/_singularity_tmpdir__dk02w3p/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:29:00.507 wdl.w:ptcp.t:call-tar_outputs-62 NOTICE slurm_singularity run :: pid: 1209461, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-62/slurm_singularity.log.txt"
2025-09-15 20:29:01.516 wdl.w:ptcp.t:call-tar_outputs-62.slurm_singularity INFO srun: job 51798263 queued and waiting for resources
2025-09-15 20:29:02.526 wdl.w:ptcp.t:call-tar_outputs-62.slurm_singularity INFO srun: job 51798263 has been allocated resources
2025-09-15 20:29:02.526 wdl.w:ptcp.t:call-tar_outputs-62.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:29:02.936 wdl.w:ptcp.w:call-paraphase-58.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for f8inv1 for sample m84036_250809_035451_s4.bc2155 at 2025-09-15 20:28:53.894071...
2025-09-15 20:29:02.937 wdl.w:ptcp.w:call-paraphase-58.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for f8inv1 for sample m84036_250809_035451_s4.bc2155 at 2025-09-15 20:28:53.896854...
2025-09-15 20:29:02.937 wdl.w:ptcp.w:call-paraphase-58.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for f8inv1 for sample m84036_250809_035451_s4.bc2155 at 2025-09-15 20:28:56.267738...
2025-09-15 20:29:02.973 wdl.w:ptcp.t:call-tar_outputs-62 INFO output :: name: "sample_tarball", value: "m84036_250809_035451_s4.bc2159.tar"
2025-09-15 20:29:03.022 wdl.w:ptcp.t:call-tar_outputs-62 NOTICE done
2025-09-15 20:29:03.026 wdl.w:ptcp NOTICE finish :: job: "call-tar_outputs-62"
2025-09-15 20:29:03.026 wdl.w:ptcp INFO output :: job: "call-tar_outputs-62", values: {"sample_tarball": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-62/out/m84036_250809_035451_s4.bc2159.tar"}
2025-09-15 20:29:09.231 wdl.w:ptcp.w:call-paraphase-71.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for f8inv22 for sample m84036_250809_035451_s4.bc2168 at 2025-09-15 20:28:39.554711...
2025-09-15 20:29:09.231 wdl.w:ptcp.w:call-paraphase-71.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for f8inv22 for sample m84036_250809_035451_s4.bc2168 at 2025-09-15 20:28:45.340251...
2025-09-15 20:29:09.231 wdl.w:ptcp.w:call-paraphase-71.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for f8inv22 for sample m84036_250809_035451_s4.bc2168 at 2025-09-15 20:28:45.735334...
2025-09-15 20:29:09.986 wdl.w:ptcp.w:call-paraphase-71.t:call-run_paraphase INFO output :: name: "paraphase_bam", value: "m84036_250809_035451_s4.bc2168_paraphase/m84036_250809_035451_s4.bc2168.paraphase.bam"
2025-09-15 20:29:09.989 wdl.w:ptcp.w:call-paraphase-71.t:call-run_paraphase INFO output :: name: "paraphase_bam_bai", value: "m84036_250809_035451_s4.bc2168_paraphase/m84036_250809_035451_s4.bc2168.paraphase.bam.bai"
2025-09-15 20:29:09.990 wdl.w:ptcp.w:call-paraphase-71.t:call-run_paraphase INFO output :: name: "paraphase_json", value: "m84036_250809_035451_s4.bc2168_paraphase/m84036_250809_035451_s4.bc2168.paraphase.json"
2025-09-15 20:29:09.994 wdl.w:ptcp.w:call-paraphase-71.t:call-run_paraphase INFO output :: name: "paraphase_vcfs", value: ["/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2168_paraphase/m84036_250809_035451_s4.bc2168_paraphase_vcfs/m84036_250809_035451_s4.bc2168_cyp21.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2168_paraphase/m84036_250809_035451_s4.bc2168_paraphase_vcfs/m84036_250809_035451_s4.bc2168_f8inv1.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2168_paraphase/m84036_250809_035451_s4.bc2168_paraphase_vcfs/m84036_250809_035451_s4.bc2168_f8inv22.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2168_paraphase/m84036_250809_035451_s4.bc2168_paraphase_vcfs/m84036_250809_035451_s4.bc2168_gba.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2168_paraphase/m84036_250809_035451_s4.bc2168_paraphase_vcfs/m84036_250809_035451_s4.bc2168_hba.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2168_paraphase/m84036_250809_035451_s4.bc2168_paraphase_vcfs/m84036_250809_035451_s4.bc2168_hbb.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2168_paraphase/m84036_250809_035451_s4.bc2168_paraphase_vcfs/m84036_250809_035451_s4.bc2168_rpgr.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2168_paraphase/m84036_250809_035451_s4.bc2168_paraphase_vcfs/m84036_250809_035451_s4.bc2168_smn1.vcf"]
2025-09-15 20:29:09.997 wdl.w:ptcp.w:call-paraphase-71.t:call-run_paraphase INFO output :: name: "havanno_json", value: "m84036_250809_035451_s4.bc2168.havanno.json"
2025-09-15 20:29:10.174 wdl.w:ptcp.w:call-paraphase-71.t:call-run_paraphase NOTICE done
2025-09-15 20:29:10.180 wdl.w:ptcp.w:call-paraphase-71 NOTICE finish :: job: "call-run_paraphase"
2025-09-15 20:29:10.180 wdl.w:ptcp.w:call-paraphase-71 INFO output :: job: "call-run_paraphase", values: {"havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-71/call-run_paraphase/out/m84036_250809_035451_s4.bc2168.havanno.json", "paraphase_vcfs": ["/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-71/call-run_paraphase/out/m84036_250809_035451_s4.bc2168_paraphase/m84036_250809_035451_s4.bc2168_paraphase_vcfs/m84036_250809_035451_s4.bc2168_cyp21.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-71/call-run_paraphase/out/m84036_250809_035451_s4.bc2168_paraphase/m84036_250809_035451_s4.bc2168_paraphase_vcfs/m84036_250809_035451_s4.bc2168_f8inv1.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-71/call-run_paraphase/out/m84036_250809_035451_s4.bc2168_paraphase/m84036_250809_035451_s4.bc2168_paraphase_vcfs/m84036_250809_035451_s4.bc2168_f8inv22.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-71/call-run_paraphase/out/m84036_250809_035451_s4.bc2168_paraphase/m84036_250809_035451_s4.bc2168_paraphase_vcfs/m84036_250809_035451_s4.bc2168_gba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-71/call-run_paraphase/out/m84036_250809_035451_s4.bc2168_paraphase/m84036_250809_035451_s4.bc2168_paraphase_vcfs/m84036_250809_035451_s4.bc2168_hba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-71/call-run_paraphase/out/m84036_250809_035451_s4.bc2168_paraphase/m84036_250809_035451_s4.bc2168_paraphase_vcfs/m84036_250809_035451_s4.bc2168_hbb.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-71/call-run_paraphase/out/m84036_250809_035451_s4.bc2168_paraphase/m84036_250809_035451_s4.bc2168_paraphase_vcfs/m84036_250809_035451_s4.bc2168_rpgr.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-71/call-run_paraphase/out/m84036_250809_035451_s4.bc2168_paraphase/m84036_250809_035451_s4.bc2168_paraphase_vcfs/m84036_250809_035451_s4.bc2168_smn1.vcf"], "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-71/call-run_paraphase/out/m84036_250809_035451_s4.bc2168_paraphase/m84036_250809_035451_s4.bc2168.paraphase.json", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-71/call-run_paraphase/out/m84036_250809_035451_s4.bc2168_paraphase/m84036_250809_035451_s4.bc2168.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-71/call-run_paraphase/out/m84036_250809_035451_s4.bc2168_paraphase/m84036_250809_035451_s4.bc2168.paraphase.bam"}
2025-09-15 20:29:10.181 wdl.w:ptcp.w:call-paraphase-71 NOTICE ready :: job: "call-call_f8", callee: "call_f8"
2025-09-15 20:29:10.181 wdl.w:ptcp.w:call-paraphase-71 INFO input :: job: "call-call_f8", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "out_prefix": "m84036_250809_035451_s4.bc2168", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-71/call-run_paraphase/out/m84036_250809_035451_s4.bc2168_paraphase/m84036_250809_035451_s4.bc2168.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-71/call-run_paraphase/out/m84036_250809_035451_s4.bc2168_paraphase/m84036_250809_035451_s4.bc2168.paraphase.bam", "sex": "F"}
2025-09-15 20:29:10.182 wdl.w:ptcp.w:call-paraphase-71 INFO visit :: node: "output-havanno_json", values: {"havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-71/call-run_paraphase/out/m84036_250809_035451_s4.bc2168.havanno.json"}
2025-09-15 20:29:10.182 wdl.w:ptcp.w:call-paraphase-71 INFO visit :: node: "output-paraphase_bam", values: {"paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-71/call-run_paraphase/out/m84036_250809_035451_s4.bc2168_paraphase/m84036_250809_035451_s4.bc2168.paraphase.bam"}
2025-09-15 20:29:10.182 wdl.w:ptcp.w:call-paraphase-71 INFO visit :: node: "output-paraphase_bam_bai", values: {"paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-71/call-run_paraphase/out/m84036_250809_035451_s4.bc2168_paraphase/m84036_250809_035451_s4.bc2168.paraphase.bam.bai"}
2025-09-15 20:29:10.182 wdl.w:ptcp.w:call-paraphase-71 INFO visit :: node: "output-paraphase_json", values: {"paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-71/call-run_paraphase/out/m84036_250809_035451_s4.bc2168_paraphase/m84036_250809_035451_s4.bc2168.paraphase.json"}
2025-09-15 20:29:10.182 wdl.w:ptcp.w:call-paraphase-71 INFO visit :: node: "output-paraphase_vcfs", values: {"paraphase_vcfs": ["/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-71/call-run_paraphase/out/m84036_250809_035451_s4.bc2168_paraphase/m84036_250809_035451_s4.bc2168_paraphase_vcfs/m84036_250809_035451_s4.bc2168_cyp21.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-71/call-run_paraphase/out/m84036_250809_035451_s4.bc2168_paraphase/m84036_250809_035451_s4.bc2168_paraphase_vcfs/m84036_250809_035451_s4.bc2168_f8inv1.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-71/call-run_paraphase/out/m84036_250809_035451_s4.bc2168_paraphase/m84036_250809_035451_s4.bc2168_paraphase_vcfs/m84036_250809_035451_s4.bc2168_f8inv22.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-71/call-run_paraphase/out/m84036_250809_035451_s4.bc2168_paraphase/m84036_250809_035451_s4.bc2168_paraphase_vcfs/m84036_250809_035451_s4.bc2168_gba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-71/call-run_paraphase/out/m84036_250809_035451_s4.bc2168_paraphase/m84036_250809_035451_s4.bc2168_paraphase_vcfs/m84036_250809_035451_s4.bc2168_hba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-71/call-run_paraphase/out/m84036_250809_035451_s4.bc2168_paraphase/m84036_250809_035451_s4.bc2168_paraphase_vcfs/m84036_250809_035451_s4.bc2168_hbb.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-71/call-run_paraphase/out/m84036_250809_035451_s4.bc2168_paraphase/m84036_250809_035451_s4.bc2168_paraphase_vcfs/m84036_250809_035451_s4.bc2168_rpgr.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-71/call-run_paraphase/out/m84036_250809_035451_s4.bc2168_paraphase/m84036_250809_035451_s4.bc2168_paraphase_vcfs/m84036_250809_035451_s4.bc2168_smn1.vcf"]}
2025-09-15 20:29:10.186 wdl.w:ptcp.w:call-paraphase-71.t:call-call_f8 NOTICE task setup :: name: "call_f8", source: "./paraphase.wdl", line: 232, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-71/call-call_f8", thread: 140611977991744
2025-09-15 20:29:10.200 wdl.w:ptcp.w:call-paraphase-71.t:call-call_f8 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:29:10.200 wdl.w:ptcp.w:call-paraphase-71.t:call-call_f8 INFO input :: name: "genome_version", value: "38"
2025-09-15 20:29:10.200 wdl.w:ptcp.w:call-paraphase-71.t:call-call_f8 INFO input :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2168"
2025-09-15 20:29:10.200 wdl.w:ptcp.w:call-paraphase-71.t:call-call_f8 INFO input :: name: "paraphase_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2168.paraphase.bam.bai"
2025-09-15 20:29:10.200 wdl.w:ptcp.w:call-paraphase-71.t:call-call_f8 INFO input :: name: "paraphase_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2168.paraphase.bam"
2025-09-15 20:29:10.200 wdl.w:ptcp.w:call-paraphase-71.t:call-call_f8 INFO input :: name: "sex", value: "F"
2025-09-15 20:29:10.201 wdl.w:ptcp.w:call-paraphase-71.t:call-call_f8 INFO eval :: name: "threads", value: 1
2025-09-15 20:29:10.201 wdl.w:ptcp.w:call-paraphase-71.t:call-call_f8 INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:29:10.201 wdl.w:ptcp.w:call-paraphase-71.t:call-call_f8 INFO eval :: name: "disk_size", value: 11
2025-09-15 20:29:10.201 wdl.w:ptcp.w:call-paraphase-71.t:call-call_f8 INFO eval :: name: "sample_sex", value: "F"
2025-09-15 20:29:10.201 wdl.w:ptcp.w:call-paraphase-71.t:call-call_f8 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:29:10.202 wdl.w:ptcp.w:call-paraphase-71.t:call-call_f8 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:29:10.202 wdl.w:ptcp.w:call-paraphase-71.t:call-call_f8 INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:29:10.202 wdl.w:ptcp.w:call-paraphase-71.t:call-call_f8 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:29:10.237 wdl.w:ptcp.w:call-paraphase-71.t:call-call_f8 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 8, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-71/call-call_f8/_singularity_tmpdir_40zq4o7u"
2025-09-15 20:29:10.237 wdl.w:ptcp.w:call-paraphase-71.t:call-call_f8 INFO Slurm invocation: srun --job-name call-call_f8 --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-71/call-call_f8/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-71/call-call_f8/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-71/call-call_f8/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-71/call-call_f8/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-71/call-run_paraphase/out/m84036_250809_035451_s4.bc2168_paraphase/m84036_250809_035451_s4.bc2168.paraphase.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2168.paraphase.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-71/call-run_paraphase/out/m84036_250809_035451_s4.bc2168_paraphase/m84036_250809_035451_s4.bc2168.paraphase.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2168.paraphase.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-71/call-call_f8/_singularity_tmpdir_40zq4o7u/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-71/call-call_f8/_singularity_tmpdir_40zq4o7u/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:29:10.243 wdl.w:ptcp.w:call-paraphase-71.t:call-call_f8 NOTICE slurm_singularity run :: pid: 1209544, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-71/call-call_f8/slurm_singularity.log.txt"
2025-09-15 20:29:11.176 wdl.w:ptcp.w:call-paraphase-63.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for f8inv22 for sample m84036_250809_035451_s4.bc2160 at 2025-09-15 20:29:08.708224...
2025-09-15 20:29:11.176 wdl.w:ptcp.w:call-paraphase-63.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for f8inv22 for sample m84036_250809_035451_s4.bc2160 at 2025-09-15 20:29:08.709052...
2025-09-15 20:29:11.250 wdl.w:ptcp.w:call-paraphase-71.t:call-call_f8.slurm_singularity INFO srun: job 51798264 queued and waiting for resources
2025-09-15 20:29:11.251 wdl.w:ptcp.w:call-paraphase-71.t:call-call_f8.slurm_singularity INFO srun: job 51798264 has been allocated resources
2025-09-15 20:29:12.031 wdl.w:ptcp.w:call-paraphase-58.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for f8inv1 for sample m84036_250809_035451_s4.bc2155 at 2025-09-15 20:29:04.421672...
2025-09-15 20:29:12.032 wdl.w:ptcp.w:call-paraphase-58.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for f8inv1 for sample m84036_250809_035451_s4.bc2155 at 2025-09-15 20:29:04.917081...
2025-09-15 20:29:12.260 wdl.w:ptcp.w:call-paraphase-71.t:call-call_f8.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:29:12.459 wdl.w:ptcp.w:call-paraphase-71.t:call-call_f8 INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2168.f8inversion.vcf"
2025-09-15 20:29:12.462 wdl.w:ptcp.w:call-paraphase-71.t:call-call_f8 INFO output :: name: "json", value: "m84036_250809_035451_s4.bc2168.f8inversion.json"
2025-09-15 20:29:12.509 wdl.w:ptcp.w:call-paraphase-71.t:call-call_f8 NOTICE done
2025-09-15 20:29:12.514 wdl.w:ptcp.w:call-paraphase-71 NOTICE finish :: job: "call-call_f8"
2025-09-15 20:29:12.514 wdl.w:ptcp.w:call-paraphase-71 INFO output :: job: "call-call_f8", values: {"json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-71/call-call_f8/out/m84036_250809_035451_s4.bc2168.f8inversion.json", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-71/call-call_f8/out/m84036_250809_035451_s4.bc2168.f8inversion.vcf"}
2025-09-15 20:29:12.514 wdl.w:ptcp.w:call-paraphase-71 INFO visit :: node: "output-f8_json", values: {"f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-71/call-call_f8/out/m84036_250809_035451_s4.bc2168.f8inversion.json"}
2025-09-15 20:29:12.514 wdl.w:ptcp.w:call-paraphase-71 INFO visit :: node: "output-f8_vcf", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-71/call-call_f8/out/m84036_250809_035451_s4.bc2168.f8inversion.vcf"}
2025-09-15 20:29:12.515 wdl.w:ptcp.w:call-paraphase-71 INFO visit :: node: "outputs", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-71/call-call_f8/out/m84036_250809_035451_s4.bc2168.f8inversion.vcf", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-71/call-run_paraphase/out/m84036_250809_035451_s4.bc2168_paraphase/m84036_250809_035451_s4.bc2168.paraphase.json", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-71/call-run_paraphase/out/m84036_250809_035451_s4.bc2168_paraphase/m84036_250809_035451_s4.bc2168.paraphase.bam", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-71/call-run_paraphase/out/m84036_250809_035451_s4.bc2168_paraphase/m84036_250809_035451_s4.bc2168.paraphase.bam.bai", "paraphase_vcfs": ["/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-71/call-run_paraphase/out/m84036_250809_035451_s4.bc2168_paraphase/m84036_250809_035451_s4.bc2168_paraphase_vcfs/m84036_250809_035451_s4.bc2168_cyp21.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-71/call-run_paraphase/out/m84036_250809_035451_s4.bc2168_paraphase/m84036_250809_035451_s4.bc2168_paraphase_vcfs/m84036_250809_035451_s4.bc2168_f8inv1.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-71/call-run_paraphase/out/m84036_250809_035451_s4.bc2168_paraphase/m84036_250809_035451_s4.bc2168_paraphase_vcfs/m84036_250809_035451_s4.bc2168_f8inv22.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-71/call-run_paraphase/out/m84036_250809_035451_s4.bc2168_paraphase/m84036_250809_035451_s4.bc2168_paraphase_vcfs/m84036_250809_035451_s4.bc2168_gba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-71/call-run_paraphase/out/m84036_250809_035451_s4.bc2168_paraphase/m84036_250809_035451_s4.bc2168_paraphase_vcfs/m84036_250809_035451_s4.bc2168_hba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-71/call-run_paraphase/out/m84036_250809_035451_s4.bc2168_paraphase/m84036_250809_035451_s4.bc2168_paraphase_vcfs/m84036_250809_035451_s4.bc2168_hbb.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-71/call-run_paraphase/out/m84036_250809_035451_s4.bc2168_paraphase/m84036_250809_035451_s4.bc2168_paraphase_vcfs/m84036_250809_035451_s4.bc2168_rpgr.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-71/call-run_paraphase/out/m84036_250809_035451_s4.bc2168_paraphase/m84036_250809_035451_s4.bc2168_paraphase_vcfs/m84036_250809_035451_s4.bc2168_smn1.vcf"], "havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-71/call-run_paraphase/out/m84036_250809_035451_s4.bc2168.havanno.json", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-71/call-call_f8/out/m84036_250809_035451_s4.bc2168.f8inversion.json"}
2025-09-15 20:29:12.616 wdl.w:ptcp.w:call-paraphase-71 NOTICE done
2025-09-15 20:29:12.679 wdl.w:ptcp NOTICE finish :: job: "call-paraphase-71"
2025-09-15 20:29:12.679 wdl.w:ptcp INFO output :: job: "call-paraphase-71", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-71/out/m84036_250809_035451_s4.bc2168.f8inversion.vcf", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-71/out/m84036_250809_035451_s4.bc2168_paraphase/m84036_250809_035451_s4.bc2168.paraphase.json", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-71/out/m84036_250809_035451_s4.bc2168_paraphase/m84036_250809_035451_s4.bc2168.paraphase.bam", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-71/out/m84036_250809_035451_s4.bc2168_paraphase/m84036_250809_035451_s4.bc2168.paraphase.bam.bai", "paraphase_vcfs": ["/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-71/out/m84036_250809_035451_s4.bc2168_paraphase/m84036_250809_035451_s4.bc2168_paraphase_vcfs/m84036_250809_035451_s4.bc2168_cyp21.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-71/out/m84036_250809_035451_s4.bc2168_paraphase/m84036_250809_035451_s4.bc2168_paraphase_vcfs/m84036_250809_035451_s4.bc2168_f8inv1.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-71/out/m84036_250809_035451_s4.bc2168_paraphase/m84036_250809_035451_s4.bc2168_paraphase_vcfs/m84036_250809_035451_s4.bc2168_f8inv22.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-71/out/m84036_250809_035451_s4.bc2168_paraphase/m84036_250809_035451_s4.bc2168_paraphase_vcfs/m84036_250809_035451_s4.bc2168_gba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-71/out/m84036_250809_035451_s4.bc2168_paraphase/m84036_250809_035451_s4.bc2168_paraphase_vcfs/m84036_250809_035451_s4.bc2168_hba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-71/out/m84036_250809_035451_s4.bc2168_paraphase/m84036_250809_035451_s4.bc2168_paraphase_vcfs/m84036_250809_035451_s4.bc2168_hbb.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-71/out/m84036_250809_035451_s4.bc2168_paraphase/m84036_250809_035451_s4.bc2168_paraphase_vcfs/m84036_250809_035451_s4.bc2168_rpgr.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-71/out/m84036_250809_035451_s4.bc2168_paraphase/m84036_250809_035451_s4.bc2168_paraphase_vcfs/m84036_250809_035451_s4.bc2168_smn1.vcf"], "havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-71/out/m84036_250809_035451_s4.bc2168.havanno.json", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-71/out/m84036_250809_035451_s4.bc2168.f8inversion.json"}
2025-09-15 20:29:12.680 wdl.w:ptcp NOTICE ready :: job: "call-tar_outputs-71", callee: "tar_outputs"
2025-09-15 20:29:12.680 wdl.w:ptcp INFO input :: job: "call-tar_outputs-71", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "sawfish_vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-71/out/m84036_250809_035451_s4.bc2168_sawfish/m84036_250809_035451_s4.bc2168.sv.vcf.gz.tbi", "sawfish_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-71/out/m84036_250809_035451_s4.bc2168_sawfish/m84036_250809_035451_s4.bc2168.sv.vcf.gz", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-71/out/m84036_250809_035451_s4.bc2168.f8inversion.json", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-71/out/m84036_250809_035451_s4.bc2168_paraphase/m84036_250809_035451_s4.bc2168.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-71/out/m84036_250809_035451_s4.bc2168_paraphase/m84036_250809_035451_s4.bc2168.paraphase.bam", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-71/out/m84036_250809_035451_s4.bc2168_paraphase/m84036_250809_035451_s4.bc2168.paraphase.json", "trgt_spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-71/out/m84036_250809_035451_s4.bc2168.trgt.sorted.spanning.bam.bai", "trgt_spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-71/out/m84036_250809_035451_s4.bc2168.trgt.sorted.spanning.bam", "trgt_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-71/out/m84036_250809_035451_s4.bc2168.trgt.vcf", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-71/out/m84036_250809_035451_s4.bc2168.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-71/out/m84036_250809_035451_s4.bc2168.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2168"}
2025-09-15 20:29:12.686 wdl.w:ptcp.t:call-tar_outputs-71 NOTICE task setup :: name: "tar_outputs", source: "./common.wdl", line: 279, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-71", thread: 140608236680768
2025-09-15 20:29:12.715 wdl.w:ptcp.t:call-tar_outputs-71 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:29:12.715 wdl.w:ptcp.t:call-tar_outputs-71 INFO input :: name: "sawfish_vcf_tbi", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2168.sv.vcf.gz.tbi"
2025-09-15 20:29:12.715 wdl.w:ptcp.t:call-tar_outputs-71 INFO input :: name: "sawfish_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2168.sv.vcf.gz"
2025-09-15 20:29:12.715 wdl.w:ptcp.t:call-tar_outputs-71 INFO input :: name: "f8_json", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2168.f8inversion.json"
2025-09-15 20:29:12.715 wdl.w:ptcp.t:call-tar_outputs-71 INFO input :: name: "paraphase_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2168.paraphase.bam.bai"
2025-09-15 20:29:12.715 wdl.w:ptcp.t:call-tar_outputs-71 INFO input :: name: "paraphase_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2168.paraphase.bam"
2025-09-15 20:29:12.715 wdl.w:ptcp.t:call-tar_outputs-71 INFO input :: name: "paraphase_json", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2168.paraphase.json"
2025-09-15 20:29:12.715 wdl.w:ptcp.t:call-tar_outputs-71 INFO input :: name: "trgt_spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2168.trgt.sorted.spanning.bam.bai"
2025-09-15 20:29:12.715 wdl.w:ptcp.t:call-tar_outputs-71 INFO input :: name: "trgt_spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2168.trgt.sorted.spanning.bam"
2025-09-15 20:29:12.715 wdl.w:ptcp.t:call-tar_outputs-71 INFO input :: name: "trgt_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2168.trgt.vcf"
2025-09-15 20:29:12.715 wdl.w:ptcp.t:call-tar_outputs-71 INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2168.mapped.bam.bai"
2025-09-15 20:29:12.715 wdl.w:ptcp.t:call-tar_outputs-71 INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2168.mapped.bam"
2025-09-15 20:29:12.716 wdl.w:ptcp.t:call-tar_outputs-71 INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2168"
2025-09-15 20:29:12.716 wdl.w:ptcp.t:call-tar_outputs-71 INFO eval :: name: "threads", value: 1
2025-09-15 20:29:12.716 wdl.w:ptcp.t:call-tar_outputs-71 INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:29:12.716 wdl.w:ptcp.t:call-tar_outputs-71 INFO eval :: name: "disk_size", value: 6
2025-09-15 20:29:12.716 wdl.w:ptcp.t:call-tar_outputs-71 INFO eval :: name: "output_tarball", value: "m84036_250809_035451_s4.bc2168.tar"
2025-09-15 20:29:12.717 wdl.w:ptcp.t:call-tar_outputs-71 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:29:12.717 wdl.w:ptcp.t:call-tar_outputs-71 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:29:12.717 wdl.w:ptcp.t:call-tar_outputs-71 INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:29:12.718 wdl.w:ptcp.t:call-tar_outputs-71 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:29:12.790 wdl.w:ptcp.t:call-tar_outputs-71 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 17, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-71/_singularity_tmpdir_y_cos_nb"
2025-09-15 20:29:12.791 wdl.w:ptcp.t:call-tar_outputs-71 INFO Slurm invocation: srun --job-name call-tar_outputs-71 --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-71/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-71/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-71/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-71/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-71/out/m84036_250809_035451_s4.bc2168_paraphase/m84036_250809_035451_s4.bc2168.paraphase.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2168.paraphase.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-71/out/m84036_250809_035451_s4.bc2168_paraphase/m84036_250809_035451_s4.bc2168.paraphase.json:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2168.paraphase.json:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-71/out/m84036_250809_035451_s4.bc2168_paraphase/m84036_250809_035451_s4.bc2168.paraphase.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2168.paraphase.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-71/out/m84036_250809_035451_s4.bc2168.f8inversion.json:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2168.f8inversion.json:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-71/out/m84036_250809_035451_s4.bc2168.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2168.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-71/out/m84036_250809_035451_s4.bc2168.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2168.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-71/out/m84036_250809_035451_s4.bc2168.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2168.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-71/out/m84036_250809_035451_s4.bc2168.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2168.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-71/out/m84036_250809_035451_s4.bc2168.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2168.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-71/out/m84036_250809_035451_s4.bc2168_sawfish/m84036_250809_035451_s4.bc2168.sv.vcf.gz:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2168.sv.vcf.gz:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-71/out/m84036_250809_035451_s4.bc2168_sawfish/m84036_250809_035451_s4.bc2168.sv.vcf.gz.tbi:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2168.sv.vcf.gz.tbi:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-71/_singularity_tmpdir_y_cos_nb/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-71/_singularity_tmpdir_y_cos_nb/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:29:12.799 wdl.w:ptcp.t:call-tar_outputs-71 NOTICE slurm_singularity run :: pid: 1209558, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-71/slurm_singularity.log.txt"
2025-09-15 20:29:13.810 wdl.w:ptcp.t:call-tar_outputs-71.slurm_singularity INFO srun: job 51798269 queued and waiting for resources
2025-09-15 20:29:13.811 wdl.w:ptcp.t:call-tar_outputs-71.slurm_singularity INFO srun: job 51798269 has been allocated resources
2025-09-15 20:29:14.205 wdl.w:ptcp.w:call-paraphase-63.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for f8inv22 for sample m84036_250809_035451_s4.bc2160 at 2025-09-15 20:29:09.939288...
2025-09-15 20:29:14.583 wdl.w:ptcp.t:call-tar_outputs-71.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:29:14.607 wdl.w:ptcp.t:call-tar_outputs-71 INFO output :: name: "sample_tarball", value: "m84036_250809_035451_s4.bc2168.tar"
2025-09-15 20:29:14.655 wdl.w:ptcp.t:call-tar_outputs-71 NOTICE done
2025-09-15 20:29:14.658 wdl.w:ptcp NOTICE finish :: job: "call-tar_outputs-71"
2025-09-15 20:29:14.658 wdl.w:ptcp INFO output :: job: "call-tar_outputs-71", values: {"sample_tarball": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-71/out/m84036_250809_035451_s4.bc2168.tar"}
2025-09-15 20:29:17.958 wdl.w:ptcp.w:call-paraphase-83.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for hbb for sample m84036_250809_035451_s4.bc2180 at 2025-09-15 20:28:26.181616...
2025-09-15 20:29:17.958 wdl.w:ptcp.w:call-paraphase-83.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for hbb for sample m84036_250809_035451_s4.bc2180 at 2025-09-15 20:28:26.559593...
2025-09-15 20:29:32.754 wdl.w:ptcp.w:call-paraphase-70.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for f8inv22 for sample m84036_250809_035451_s4.bc2167 at 2025-09-15 20:29:27.576114...
2025-09-15 20:29:32.754 wdl.w:ptcp.w:call-paraphase-70.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for f8inv22 for sample m84036_250809_035451_s4.bc2167 at 2025-09-15 20:29:27.576799...
2025-09-15 20:29:32.754 wdl.w:ptcp.w:call-paraphase-70.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for f8inv22 for sample m84036_250809_035451_s4.bc2167 at 2025-09-15 20:29:28.773236...
2025-09-15 20:29:35.410 wdl.w:ptcp.w:call-paraphase-63.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for f8inv22 for sample m84036_250809_035451_s4.bc2160 at 2025-09-15 20:29:15.095177...
2025-09-15 20:29:35.410 wdl.w:ptcp.w:call-paraphase-63.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for f8inv22 for sample m84036_250809_035451_s4.bc2160 at 2025-09-15 20:29:15.511954...
2025-09-15 20:29:35.564 wdl.w:ptcp.w:call-paraphase-10.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for f8inv22 for sample m84036_250809_035451_s4.bc2107 at 2025-09-15 20:29:28.620560...
2025-09-15 20:29:35.564 wdl.w:ptcp.w:call-paraphase-10.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for f8inv22 for sample m84036_250809_035451_s4.bc2107 at 2025-09-15 20:29:28.622602...
2025-09-15 20:29:37.502 wdl.w:ptcp.w:call-paraphase-63.t:call-run_paraphase INFO output :: name: "paraphase_bam", value: "m84036_250809_035451_s4.bc2160_paraphase/m84036_250809_035451_s4.bc2160.paraphase.bam"
2025-09-15 20:29:37.505 wdl.w:ptcp.w:call-paraphase-63.t:call-run_paraphase INFO output :: name: "paraphase_bam_bai", value: "m84036_250809_035451_s4.bc2160_paraphase/m84036_250809_035451_s4.bc2160.paraphase.bam.bai"
2025-09-15 20:29:37.506 wdl.w:ptcp.w:call-paraphase-63.t:call-run_paraphase INFO output :: name: "paraphase_json", value: "m84036_250809_035451_s4.bc2160_paraphase/m84036_250809_035451_s4.bc2160.paraphase.json"
2025-09-15 20:29:37.510 wdl.w:ptcp.w:call-paraphase-63.t:call-run_paraphase INFO output :: name: "paraphase_vcfs", value: ["/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2160_paraphase/m84036_250809_035451_s4.bc2160_paraphase_vcfs/m84036_250809_035451_s4.bc2160_cyp21.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2160_paraphase/m84036_250809_035451_s4.bc2160_paraphase_vcfs/m84036_250809_035451_s4.bc2160_f8inv1.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2160_paraphase/m84036_250809_035451_s4.bc2160_paraphase_vcfs/m84036_250809_035451_s4.bc2160_f8inv22.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2160_paraphase/m84036_250809_035451_s4.bc2160_paraphase_vcfs/m84036_250809_035451_s4.bc2160_gba.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2160_paraphase/m84036_250809_035451_s4.bc2160_paraphase_vcfs/m84036_250809_035451_s4.bc2160_hba.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2160_paraphase/m84036_250809_035451_s4.bc2160_paraphase_vcfs/m84036_250809_035451_s4.bc2160_hbb.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2160_paraphase/m84036_250809_035451_s4.bc2160_paraphase_vcfs/m84036_250809_035451_s4.bc2160_rpgr.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2160_paraphase/m84036_250809_035451_s4.bc2160_paraphase_vcfs/m84036_250809_035451_s4.bc2160_smn1.vcf"]
2025-09-15 20:29:37.513 wdl.w:ptcp.w:call-paraphase-63.t:call-run_paraphase INFO output :: name: "havanno_json", value: "m84036_250809_035451_s4.bc2160.havanno.json"
2025-09-15 20:29:37.655 wdl.w:ptcp.w:call-paraphase-63.t:call-run_paraphase NOTICE done
2025-09-15 20:29:37.661 wdl.w:ptcp.w:call-paraphase-63 NOTICE finish :: job: "call-run_paraphase"
2025-09-15 20:29:37.661 wdl.w:ptcp.w:call-paraphase-63 INFO output :: job: "call-run_paraphase", values: {"havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-63/call-run_paraphase/out/m84036_250809_035451_s4.bc2160.havanno.json", "paraphase_vcfs": ["/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-63/call-run_paraphase/out/m84036_250809_035451_s4.bc2160_paraphase/m84036_250809_035451_s4.bc2160_paraphase_vcfs/m84036_250809_035451_s4.bc2160_cyp21.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-63/call-run_paraphase/out/m84036_250809_035451_s4.bc2160_paraphase/m84036_250809_035451_s4.bc2160_paraphase_vcfs/m84036_250809_035451_s4.bc2160_f8inv1.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-63/call-run_paraphase/out/m84036_250809_035451_s4.bc2160_paraphase/m84036_250809_035451_s4.bc2160_paraphase_vcfs/m84036_250809_035451_s4.bc2160_f8inv22.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-63/call-run_paraphase/out/m84036_250809_035451_s4.bc2160_paraphase/m84036_250809_035451_s4.bc2160_paraphase_vcfs/m84036_250809_035451_s4.bc2160_gba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-63/call-run_paraphase/out/m84036_250809_035451_s4.bc2160_paraphase/m84036_250809_035451_s4.bc2160_paraphase_vcfs/m84036_250809_035451_s4.bc2160_hba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-63/call-run_paraphase/out/m84036_250809_035451_s4.bc2160_paraphase/m84036_250809_035451_s4.bc2160_paraphase_vcfs/m84036_250809_035451_s4.bc2160_hbb.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-63/call-run_paraphase/out/m84036_250809_035451_s4.bc2160_paraphase/m84036_250809_035451_s4.bc2160_paraphase_vcfs/m84036_250809_035451_s4.bc2160_rpgr.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-63/call-run_paraphase/out/m84036_250809_035451_s4.bc2160_paraphase/m84036_250809_035451_s4.bc2160_paraphase_vcfs/m84036_250809_035451_s4.bc2160_smn1.vcf"], "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-63/call-run_paraphase/out/m84036_250809_035451_s4.bc2160_paraphase/m84036_250809_035451_s4.bc2160.paraphase.json", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-63/call-run_paraphase/out/m84036_250809_035451_s4.bc2160_paraphase/m84036_250809_035451_s4.bc2160.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-63/call-run_paraphase/out/m84036_250809_035451_s4.bc2160_paraphase/m84036_250809_035451_s4.bc2160.paraphase.bam"}
2025-09-15 20:29:37.662 wdl.w:ptcp.w:call-paraphase-63 NOTICE ready :: job: "call-call_f8", callee: "call_f8"
2025-09-15 20:29:37.662 wdl.w:ptcp.w:call-paraphase-63 INFO input :: job: "call-call_f8", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "out_prefix": "m84036_250809_035451_s4.bc2160", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-63/call-run_paraphase/out/m84036_250809_035451_s4.bc2160_paraphase/m84036_250809_035451_s4.bc2160.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-63/call-run_paraphase/out/m84036_250809_035451_s4.bc2160_paraphase/m84036_250809_035451_s4.bc2160.paraphase.bam", "sex": "F"}
2025-09-15 20:29:37.662 wdl.w:ptcp.w:call-paraphase-63 INFO visit :: node: "output-havanno_json", values: {"havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-63/call-run_paraphase/out/m84036_250809_035451_s4.bc2160.havanno.json"}
2025-09-15 20:29:37.662 wdl.w:ptcp.w:call-paraphase-63 INFO visit :: node: "output-paraphase_bam", values: {"paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-63/call-run_paraphase/out/m84036_250809_035451_s4.bc2160_paraphase/m84036_250809_035451_s4.bc2160.paraphase.bam"}
2025-09-15 20:29:37.663 wdl.w:ptcp.w:call-paraphase-63 INFO visit :: node: "output-paraphase_bam_bai", values: {"paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-63/call-run_paraphase/out/m84036_250809_035451_s4.bc2160_paraphase/m84036_250809_035451_s4.bc2160.paraphase.bam.bai"}
2025-09-15 20:29:37.663 wdl.w:ptcp.w:call-paraphase-63 INFO visit :: node: "output-paraphase_json", values: {"paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-63/call-run_paraphase/out/m84036_250809_035451_s4.bc2160_paraphase/m84036_250809_035451_s4.bc2160.paraphase.json"}
2025-09-15 20:29:37.663 wdl.w:ptcp.w:call-paraphase-63 INFO visit :: node: "output-paraphase_vcfs", values: {"paraphase_vcfs": ["/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-63/call-run_paraphase/out/m84036_250809_035451_s4.bc2160_paraphase/m84036_250809_035451_s4.bc2160_paraphase_vcfs/m84036_250809_035451_s4.bc2160_cyp21.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-63/call-run_paraphase/out/m84036_250809_035451_s4.bc2160_paraphase/m84036_250809_035451_s4.bc2160_paraphase_vcfs/m84036_250809_035451_s4.bc2160_f8inv1.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-63/call-run_paraphase/out/m84036_250809_035451_s4.bc2160_paraphase/m84036_250809_035451_s4.bc2160_paraphase_vcfs/m84036_250809_035451_s4.bc2160_f8inv22.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-63/call-run_paraphase/out/m84036_250809_035451_s4.bc2160_paraphase/m84036_250809_035451_s4.bc2160_paraphase_vcfs/m84036_250809_035451_s4.bc2160_gba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-63/call-run_paraphase/out/m84036_250809_035451_s4.bc2160_paraphase/m84036_250809_035451_s4.bc2160_paraphase_vcfs/m84036_250809_035451_s4.bc2160_hba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-63/call-run_paraphase/out/m84036_250809_035451_s4.bc2160_paraphase/m84036_250809_035451_s4.bc2160_paraphase_vcfs/m84036_250809_035451_s4.bc2160_hbb.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-63/call-run_paraphase/out/m84036_250809_035451_s4.bc2160_paraphase/m84036_250809_035451_s4.bc2160_paraphase_vcfs/m84036_250809_035451_s4.bc2160_rpgr.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-63/call-run_paraphase/out/m84036_250809_035451_s4.bc2160_paraphase/m84036_250809_035451_s4.bc2160_paraphase_vcfs/m84036_250809_035451_s4.bc2160_smn1.vcf"]}
2025-09-15 20:29:37.667 wdl.w:ptcp.w:call-paraphase-63.t:call-call_f8 NOTICE task setup :: name: "call_f8", source: "./paraphase.wdl", line: 232, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-63/call-call_f8", thread: 140609847293504
2025-09-15 20:29:37.681 wdl.w:ptcp.w:call-paraphase-63.t:call-call_f8 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:29:37.681 wdl.w:ptcp.w:call-paraphase-63.t:call-call_f8 INFO input :: name: "genome_version", value: "38"
2025-09-15 20:29:37.681 wdl.w:ptcp.w:call-paraphase-63.t:call-call_f8 INFO input :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2160"
2025-09-15 20:29:37.681 wdl.w:ptcp.w:call-paraphase-63.t:call-call_f8 INFO input :: name: "paraphase_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2160.paraphase.bam.bai"
2025-09-15 20:29:37.681 wdl.w:ptcp.w:call-paraphase-63.t:call-call_f8 INFO input :: name: "paraphase_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2160.paraphase.bam"
2025-09-15 20:29:37.681 wdl.w:ptcp.w:call-paraphase-63.t:call-call_f8 INFO input :: name: "sex", value: "F"
2025-09-15 20:29:37.682 wdl.w:ptcp.w:call-paraphase-63.t:call-call_f8 INFO eval :: name: "threads", value: 1
2025-09-15 20:29:37.682 wdl.w:ptcp.w:call-paraphase-63.t:call-call_f8 INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:29:37.682 wdl.w:ptcp.w:call-paraphase-63.t:call-call_f8 INFO eval :: name: "disk_size", value: 11
2025-09-15 20:29:37.682 wdl.w:ptcp.w:call-paraphase-63.t:call-call_f8 INFO eval :: name: "sample_sex", value: "F"
2025-09-15 20:29:37.683 wdl.w:ptcp.w:call-paraphase-63.t:call-call_f8 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:29:37.683 wdl.w:ptcp.w:call-paraphase-63.t:call-call_f8 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:29:37.683 wdl.w:ptcp.w:call-paraphase-63.t:call-call_f8 INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:29:37.683 wdl.w:ptcp.w:call-paraphase-63.t:call-call_f8 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:29:37.719 wdl.w:ptcp.w:call-paraphase-63.t:call-call_f8 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 8, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-63/call-call_f8/_singularity_tmpdir_wt5y5sxr"
2025-09-15 20:29:37.719 wdl.w:ptcp.w:call-paraphase-63.t:call-call_f8 INFO Slurm invocation: srun --job-name call-call_f8 --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-63/call-call_f8/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-63/call-call_f8/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-63/call-call_f8/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-63/call-call_f8/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-63/call-run_paraphase/out/m84036_250809_035451_s4.bc2160_paraphase/m84036_250809_035451_s4.bc2160.paraphase.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2160.paraphase.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-63/call-run_paraphase/out/m84036_250809_035451_s4.bc2160_paraphase/m84036_250809_035451_s4.bc2160.paraphase.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2160.paraphase.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-63/call-call_f8/_singularity_tmpdir_wt5y5sxr/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-63/call-call_f8/_singularity_tmpdir_wt5y5sxr/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:29:37.726 wdl.w:ptcp.w:call-paraphase-63.t:call-call_f8 NOTICE slurm_singularity run :: pid: 1209708, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-63/call-call_f8/slurm_singularity.log.txt"
2025-09-15 20:29:38.733 wdl.w:ptcp.w:call-paraphase-63.t:call-call_f8.slurm_singularity INFO srun: job 51798274 queued and waiting for resources
2025-09-15 20:29:38.733 wdl.w:ptcp.w:call-paraphase-63.t:call-call_f8.slurm_singularity INFO srun: job 51798274 has been allocated resources
2025-09-15 20:29:38.733 wdl.w:ptcp.w:call-paraphase-63.t:call-call_f8.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:29:39.633 wdl.w:ptcp.w:call-paraphase-63.t:call-call_f8 INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2160.f8inversion.vcf"
2025-09-15 20:29:39.636 wdl.w:ptcp.w:call-paraphase-63.t:call-call_f8 INFO output :: name: "json", value: "m84036_250809_035451_s4.bc2160.f8inversion.json"
2025-09-15 20:29:39.686 wdl.w:ptcp.w:call-paraphase-63.t:call-call_f8 NOTICE done
2025-09-15 20:29:39.692 wdl.w:ptcp.w:call-paraphase-63 NOTICE finish :: job: "call-call_f8"
2025-09-15 20:29:39.692 wdl.w:ptcp.w:call-paraphase-63 INFO output :: job: "call-call_f8", values: {"json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-63/call-call_f8/out/m84036_250809_035451_s4.bc2160.f8inversion.json", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-63/call-call_f8/out/m84036_250809_035451_s4.bc2160.f8inversion.vcf"}
2025-09-15 20:29:39.693 wdl.w:ptcp.w:call-paraphase-63 INFO visit :: node: "output-f8_json", values: {"f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-63/call-call_f8/out/m84036_250809_035451_s4.bc2160.f8inversion.json"}
2025-09-15 20:29:39.693 wdl.w:ptcp.w:call-paraphase-63 INFO visit :: node: "output-f8_vcf", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-63/call-call_f8/out/m84036_250809_035451_s4.bc2160.f8inversion.vcf"}
2025-09-15 20:29:39.693 wdl.w:ptcp.w:call-paraphase-63 INFO visit :: node: "outputs", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-63/call-call_f8/out/m84036_250809_035451_s4.bc2160.f8inversion.vcf", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-63/call-run_paraphase/out/m84036_250809_035451_s4.bc2160_paraphase/m84036_250809_035451_s4.bc2160.paraphase.json", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-63/call-run_paraphase/out/m84036_250809_035451_s4.bc2160_paraphase/m84036_250809_035451_s4.bc2160.paraphase.bam", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-63/call-run_paraphase/out/m84036_250809_035451_s4.bc2160_paraphase/m84036_250809_035451_s4.bc2160.paraphase.bam.bai", "paraphase_vcfs": ["/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-63/call-run_paraphase/out/m84036_250809_035451_s4.bc2160_paraphase/m84036_250809_035451_s4.bc2160_paraphase_vcfs/m84036_250809_035451_s4.bc2160_cyp21.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-63/call-run_paraphase/out/m84036_250809_035451_s4.bc2160_paraphase/m84036_250809_035451_s4.bc2160_paraphase_vcfs/m84036_250809_035451_s4.bc2160_f8inv1.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-63/call-run_paraphase/out/m84036_250809_035451_s4.bc2160_paraphase/m84036_250809_035451_s4.bc2160_paraphase_vcfs/m84036_250809_035451_s4.bc2160_f8inv22.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-63/call-run_paraphase/out/m84036_250809_035451_s4.bc2160_paraphase/m84036_250809_035451_s4.bc2160_paraphase_vcfs/m84036_250809_035451_s4.bc2160_gba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-63/call-run_paraphase/out/m84036_250809_035451_s4.bc2160_paraphase/m84036_250809_035451_s4.bc2160_paraphase_vcfs/m84036_250809_035451_s4.bc2160_hba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-63/call-run_paraphase/out/m84036_250809_035451_s4.bc2160_paraphase/m84036_250809_035451_s4.bc2160_paraphase_vcfs/m84036_250809_035451_s4.bc2160_hbb.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-63/call-run_paraphase/out/m84036_250809_035451_s4.bc2160_paraphase/m84036_250809_035451_s4.bc2160_paraphase_vcfs/m84036_250809_035451_s4.bc2160_rpgr.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-63/call-run_paraphase/out/m84036_250809_035451_s4.bc2160_paraphase/m84036_250809_035451_s4.bc2160_paraphase_vcfs/m84036_250809_035451_s4.bc2160_smn1.vcf"], "havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-63/call-run_paraphase/out/m84036_250809_035451_s4.bc2160.havanno.json", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-63/call-call_f8/out/m84036_250809_035451_s4.bc2160.f8inversion.json"}
2025-09-15 20:29:39.799 wdl.w:ptcp.w:call-paraphase-63 NOTICE done
2025-09-15 20:29:39.804 wdl.w:ptcp NOTICE finish :: job: "call-paraphase-63"
2025-09-15 20:29:39.805 wdl.w:ptcp INFO output :: job: "call-paraphase-63", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-63/out/m84036_250809_035451_s4.bc2160.f8inversion.vcf", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-63/out/m84036_250809_035451_s4.bc2160_paraphase/m84036_250809_035451_s4.bc2160.paraphase.json", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-63/out/m84036_250809_035451_s4.bc2160_paraphase/m84036_250809_035451_s4.bc2160.paraphase.bam", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-63/out/m84036_250809_035451_s4.bc2160_paraphase/m84036_250809_035451_s4.bc2160.paraphase.bam.bai", "paraphase_vcfs": ["/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-63/out/m84036_250809_035451_s4.bc2160_paraphase/m84036_250809_035451_s4.bc2160_paraphase_vcfs/m84036_250809_035451_s4.bc2160_cyp21.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-63/out/m84036_250809_035451_s4.bc2160_paraphase/m84036_250809_035451_s4.bc2160_paraphase_vcfs/m84036_250809_035451_s4.bc2160_f8inv1.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-63/out/m84036_250809_035451_s4.bc2160_paraphase/m84036_250809_035451_s4.bc2160_paraphase_vcfs/m84036_250809_035451_s4.bc2160_f8inv22.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-63/out/m84036_250809_035451_s4.bc2160_paraphase/m84036_250809_035451_s4.bc2160_paraphase_vcfs/m84036_250809_035451_s4.bc2160_gba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-63/out/m84036_250809_035451_s4.bc2160_paraphase/m84036_250809_035451_s4.bc2160_paraphase_vcfs/m84036_250809_035451_s4.bc2160_hba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-63/out/m84036_250809_035451_s4.bc2160_paraphase/m84036_250809_035451_s4.bc2160_paraphase_vcfs/m84036_250809_035451_s4.bc2160_hbb.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-63/out/m84036_250809_035451_s4.bc2160_paraphase/m84036_250809_035451_s4.bc2160_paraphase_vcfs/m84036_250809_035451_s4.bc2160_rpgr.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-63/out/m84036_250809_035451_s4.bc2160_paraphase/m84036_250809_035451_s4.bc2160_paraphase_vcfs/m84036_250809_035451_s4.bc2160_smn1.vcf"], "havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-63/out/m84036_250809_035451_s4.bc2160.havanno.json", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-63/out/m84036_250809_035451_s4.bc2160.f8inversion.json"}
2025-09-15 20:29:39.805 wdl.w:ptcp NOTICE ready :: job: "call-tar_outputs-63", callee: "tar_outputs"
2025-09-15 20:29:39.805 wdl.w:ptcp INFO input :: job: "call-tar_outputs-63", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "sawfish_vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-63/out/m84036_250809_035451_s4.bc2160_sawfish/m84036_250809_035451_s4.bc2160.sv.vcf.gz.tbi", "sawfish_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-63/out/m84036_250809_035451_s4.bc2160_sawfish/m84036_250809_035451_s4.bc2160.sv.vcf.gz", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-63/out/m84036_250809_035451_s4.bc2160.f8inversion.json", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-63/out/m84036_250809_035451_s4.bc2160_paraphase/m84036_250809_035451_s4.bc2160.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-63/out/m84036_250809_035451_s4.bc2160_paraphase/m84036_250809_035451_s4.bc2160.paraphase.bam", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-63/out/m84036_250809_035451_s4.bc2160_paraphase/m84036_250809_035451_s4.bc2160.paraphase.json", "trgt_spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-63/out/m84036_250809_035451_s4.bc2160.trgt.sorted.spanning.bam.bai", "trgt_spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-63/out/m84036_250809_035451_s4.bc2160.trgt.sorted.spanning.bam", "trgt_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-63/out/m84036_250809_035451_s4.bc2160.trgt.vcf", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-63/out/m84036_250809_035451_s4.bc2160.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-63/out/m84036_250809_035451_s4.bc2160.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2160"}
2025-09-15 20:29:39.810 wdl.w:ptcp.t:call-tar_outputs-63 NOTICE task setup :: name: "tar_outputs", source: "./common.wdl", line: 279, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-63", thread: 140613563426368
2025-09-15 20:29:39.830 wdl.w:ptcp.t:call-tar_outputs-63 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:29:39.830 wdl.w:ptcp.t:call-tar_outputs-63 INFO input :: name: "sawfish_vcf_tbi", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2160.sv.vcf.gz.tbi"
2025-09-15 20:29:39.830 wdl.w:ptcp.t:call-tar_outputs-63 INFO input :: name: "sawfish_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2160.sv.vcf.gz"
2025-09-15 20:29:39.830 wdl.w:ptcp.t:call-tar_outputs-63 INFO input :: name: "f8_json", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2160.f8inversion.json"
2025-09-15 20:29:39.830 wdl.w:ptcp.t:call-tar_outputs-63 INFO input :: name: "paraphase_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2160.paraphase.bam.bai"
2025-09-15 20:29:39.830 wdl.w:ptcp.t:call-tar_outputs-63 INFO input :: name: "paraphase_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2160.paraphase.bam"
2025-09-15 20:29:39.830 wdl.w:ptcp.t:call-tar_outputs-63 INFO input :: name: "paraphase_json", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2160.paraphase.json"
2025-09-15 20:29:39.830 wdl.w:ptcp.t:call-tar_outputs-63 INFO input :: name: "trgt_spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2160.trgt.sorted.spanning.bam.bai"
2025-09-15 20:29:39.830 wdl.w:ptcp.t:call-tar_outputs-63 INFO input :: name: "trgt_spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2160.trgt.sorted.spanning.bam"
2025-09-15 20:29:39.831 wdl.w:ptcp.t:call-tar_outputs-63 INFO input :: name: "trgt_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2160.trgt.vcf"
2025-09-15 20:29:39.831 wdl.w:ptcp.t:call-tar_outputs-63 INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2160.mapped.bam.bai"
2025-09-15 20:29:39.831 wdl.w:ptcp.t:call-tar_outputs-63 INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2160.mapped.bam"
2025-09-15 20:29:39.831 wdl.w:ptcp.t:call-tar_outputs-63 INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2160"
2025-09-15 20:29:39.831 wdl.w:ptcp.t:call-tar_outputs-63 INFO eval :: name: "threads", value: 1
2025-09-15 20:29:39.831 wdl.w:ptcp.t:call-tar_outputs-63 INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:29:39.831 wdl.w:ptcp.t:call-tar_outputs-63 INFO eval :: name: "disk_size", value: 6
2025-09-15 20:29:39.831 wdl.w:ptcp.t:call-tar_outputs-63 INFO eval :: name: "output_tarball", value: "m84036_250809_035451_s4.bc2160.tar"
2025-09-15 20:29:39.832 wdl.w:ptcp.t:call-tar_outputs-63 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:29:39.832 wdl.w:ptcp.t:call-tar_outputs-63 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:29:39.832 wdl.w:ptcp.t:call-tar_outputs-63 INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:29:39.832 wdl.w:ptcp.t:call-tar_outputs-63 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:29:39.906 wdl.w:ptcp.t:call-tar_outputs-63 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 17, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-63/_singularity_tmpdir_mbhpczs8"
2025-09-15 20:29:39.906 wdl.w:ptcp.t:call-tar_outputs-63 INFO Slurm invocation: srun --job-name call-tar_outputs-63 --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-63/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-63/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-63/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-63/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-63/out/m84036_250809_035451_s4.bc2160.f8inversion.json:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2160.f8inversion.json:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-63/out/m84036_250809_035451_s4.bc2160.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2160.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-63/out/m84036_250809_035451_s4.bc2160.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2160.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-63/out/m84036_250809_035451_s4.bc2160.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2160.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-63/out/m84036_250809_035451_s4.bc2160_paraphase/m84036_250809_035451_s4.bc2160.paraphase.json:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2160.paraphase.json:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-63/out/m84036_250809_035451_s4.bc2160_paraphase/m84036_250809_035451_s4.bc2160.paraphase.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2160.paraphase.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-63/out/m84036_250809_035451_s4.bc2160_paraphase/m84036_250809_035451_s4.bc2160.paraphase.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2160.paraphase.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-63/out/m84036_250809_035451_s4.bc2160_sawfish/m84036_250809_035451_s4.bc2160.sv.vcf.gz.tbi:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2160.sv.vcf.gz.tbi:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-63/out/m84036_250809_035451_s4.bc2160_sawfish/m84036_250809_035451_s4.bc2160.sv.vcf.gz:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2160.sv.vcf.gz:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-63/out/m84036_250809_035451_s4.bc2160.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2160.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-63/out/m84036_250809_035451_s4.bc2160.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2160.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-63/_singularity_tmpdir_mbhpczs8/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-63/_singularity_tmpdir_mbhpczs8/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:29:39.909 wdl.w:ptcp.t:call-tar_outputs-63 NOTICE slurm_singularity run :: pid: 1209789, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-63/slurm_singularity.log.txt"
2025-09-15 20:29:40.917 wdl.w:ptcp.t:call-tar_outputs-63.slurm_singularity INFO srun: job 51798275 queued and waiting for resources
2025-09-15 20:29:41.861 wdl.w:ptcp.w:call-paraphase-70.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for f8inv22 for sample m84036_250809_035451_s4.bc2167 at 2025-09-15 20:29:33.901297...
2025-09-15 20:29:41.861 wdl.w:ptcp.w:call-paraphase-70.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for f8inv22 for sample m84036_250809_035451_s4.bc2167 at 2025-09-15 20:29:34.245764...
2025-09-15 20:29:41.926 wdl.w:ptcp.t:call-tar_outputs-63.slurm_singularity INFO srun: job 51798275 has been allocated resources
2025-09-15 20:29:41.926 wdl.w:ptcp.t:call-tar_outputs-63.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:29:42.322 wdl.w:ptcp.t:call-tar_outputs-63 INFO output :: name: "sample_tarball", value: "m84036_250809_035451_s4.bc2160.tar"
2025-09-15 20:29:42.375 wdl.w:ptcp.t:call-tar_outputs-63 NOTICE done
2025-09-15 20:29:42.379 wdl.w:ptcp NOTICE finish :: job: "call-tar_outputs-63"
2025-09-15 20:29:42.379 wdl.w:ptcp INFO output :: job: "call-tar_outputs-63", values: {"sample_tarball": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-63/out/m84036_250809_035451_s4.bc2160.tar"}
2025-09-15 20:29:44.659 wdl.w:ptcp.w:call-paraphase-10.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for f8inv22 for sample m84036_250809_035451_s4.bc2107 at 2025-09-15 20:29:30.003537...
2025-09-15 20:29:44.660 wdl.w:ptcp.w:call-paraphase-10.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for f8inv22 for sample m84036_250809_035451_s4.bc2107 at 2025-09-15 20:29:35.695106...
2025-09-15 20:29:44.660 wdl.w:ptcp.w:call-paraphase-10.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for f8inv22 for sample m84036_250809_035451_s4.bc2107 at 2025-09-15 20:29:36.147290...
2025-09-15 20:29:45.908 wdl.w:ptcp.w:call-paraphase-66.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for rpgr for sample m84036_250809_035451_s4.bc2163 at 2025-09-15 20:29:38.168989...
2025-09-15 20:29:45.909 wdl.w:ptcp.w:call-paraphase-66.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for rpgr for sample m84036_250809_035451_s4.bc2163 at 2025-09-15 20:29:38.169829...
2025-09-15 20:29:47.185 wdl.w:ptcp.w:call-paraphase-95.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for rpgr for sample m84036_250809_035451_s4.bc2192 at 2025-09-15 20:29:26.106181...
2025-09-15 20:29:47.186 wdl.w:ptcp.w:call-paraphase-95.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for rpgr for sample m84036_250809_035451_s4.bc2192 at 2025-09-15 20:29:26.110557...
2025-09-15 20:29:47.186 wdl.w:ptcp.w:call-paraphase-95.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for rpgr for sample m84036_250809_035451_s4.bc2192 at 2025-09-15 20:29:28.074663...
2025-09-15 20:29:47.186 wdl.w:ptcp.w:call-paraphase-95.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for rpgr for sample m84036_250809_035451_s4.bc2192 at 2025-09-15 20:29:29.425217...
2025-09-15 20:29:47.186 wdl.w:ptcp.w:call-paraphase-95.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for rpgr for sample m84036_250809_035451_s4.bc2192 at 2025-09-15 20:29:29.638416...
2025-09-15 20:29:47.407 wdl.w:ptcp.w:call-paraphase-67.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for f8inv1 for sample m84036_250809_035451_s4.bc2164 at 2025-09-15 20:28:55.701512...
2025-09-15 20:29:47.408 wdl.w:ptcp.w:call-paraphase-67.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for f8inv1 for sample m84036_250809_035451_s4.bc2164 at 2025-09-15 20:28:55.702096...
2025-09-15 20:29:47.408 wdl.w:ptcp.w:call-paraphase-67.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for f8inv1 for sample m84036_250809_035451_s4.bc2164 at 2025-09-15 20:28:58.076129...
2025-09-15 20:29:47.408 wdl.w:ptcp.w:call-paraphase-67.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for f8inv1 for sample m84036_250809_035451_s4.bc2164 at 2025-09-15 20:29:05.850753...
2025-09-15 20:29:47.408 wdl.w:ptcp.w:call-paraphase-67.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for f8inv1 for sample m84036_250809_035451_s4.bc2164 at 2025-09-15 20:29:06.295352...
2025-09-15 20:29:47.408 wdl.w:ptcp.w:call-paraphase-67.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for rpgr for sample m84036_250809_035451_s4.bc2164 at 2025-09-15 20:29:27.283741...
2025-09-15 20:29:47.408 wdl.w:ptcp.w:call-paraphase-67.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for rpgr for sample m84036_250809_035451_s4.bc2164 at 2025-09-15 20:29:27.284548...
2025-09-15 20:29:47.408 wdl.w:ptcp.w:call-paraphase-67.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for rpgr for sample m84036_250809_035451_s4.bc2164 at 2025-09-15 20:29:30.395057...
2025-09-15 20:29:47.408 wdl.w:ptcp.w:call-paraphase-67.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for rpgr for sample m84036_250809_035451_s4.bc2164 at 2025-09-15 20:29:31.775897...
2025-09-15 20:29:47.408 wdl.w:ptcp.w:call-paraphase-67.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for rpgr for sample m84036_250809_035451_s4.bc2164 at 2025-09-15 20:29:31.950090...
2025-09-15 20:29:55.018 wdl.w:ptcp.w:call-paraphase-66.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for rpgr for sample m84036_250809_035451_s4.bc2163 at 2025-09-15 20:29:40.572207...
2025-09-15 20:29:55.018 wdl.w:ptcp.w:call-paraphase-66.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for rpgr for sample m84036_250809_035451_s4.bc2163 at 2025-09-15 20:29:41.709277...
2025-09-15 20:29:55.018 wdl.w:ptcp.w:call-paraphase-66.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for rpgr for sample m84036_250809_035451_s4.bc2163 at 2025-09-15 20:29:42.073069...
2025-09-15 20:29:56.099 wdl.w:ptcp.w:call-paraphase-87.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for rpgr for sample m84036_250809_035451_s4.bc2184 at 2025-09-15 20:29:00.224264...
2025-09-15 20:29:56.100 wdl.w:ptcp.w:call-paraphase-87.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for rpgr for sample m84036_250809_035451_s4.bc2184 at 2025-09-15 20:29:00.225009...
2025-09-15 20:29:56.100 wdl.w:ptcp.w:call-paraphase-87.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for rpgr for sample m84036_250809_035451_s4.bc2184 at 2025-09-15 20:29:02.564729...
2025-09-15 20:29:56.100 wdl.w:ptcp.w:call-paraphase-87.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for rpgr for sample m84036_250809_035451_s4.bc2184 at 2025-09-15 20:29:03.817691...
2025-09-15 20:29:56.100 wdl.w:ptcp.w:call-paraphase-87.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for rpgr for sample m84036_250809_035451_s4.bc2184 at 2025-09-15 20:29:04.045660...
2025-09-15 20:29:56.580 wdl.w:ptcp.w:call-paraphase-70.t:call-run_paraphase INFO output :: name: "paraphase_bam", value: "m84036_250809_035451_s4.bc2167_paraphase/m84036_250809_035451_s4.bc2167.paraphase.bam"
2025-09-15 20:29:56.583 wdl.w:ptcp.w:call-paraphase-70.t:call-run_paraphase INFO output :: name: "paraphase_bam_bai", value: "m84036_250809_035451_s4.bc2167_paraphase/m84036_250809_035451_s4.bc2167.paraphase.bam.bai"
2025-09-15 20:29:56.583 wdl.w:ptcp.w:call-paraphase-70.t:call-run_paraphase INFO output :: name: "paraphase_json", value: "m84036_250809_035451_s4.bc2167_paraphase/m84036_250809_035451_s4.bc2167.paraphase.json"
2025-09-15 20:29:56.586 wdl.w:ptcp.w:call-paraphase-70.t:call-run_paraphase INFO output :: name: "paraphase_vcfs", value: ["/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2167_paraphase/m84036_250809_035451_s4.bc2167_paraphase_vcfs/m84036_250809_035451_s4.bc2167_cyp21.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2167_paraphase/m84036_250809_035451_s4.bc2167_paraphase_vcfs/m84036_250809_035451_s4.bc2167_f8inv1.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2167_paraphase/m84036_250809_035451_s4.bc2167_paraphase_vcfs/m84036_250809_035451_s4.bc2167_f8inv22.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2167_paraphase/m84036_250809_035451_s4.bc2167_paraphase_vcfs/m84036_250809_035451_s4.bc2167_gba.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2167_paraphase/m84036_250809_035451_s4.bc2167_paraphase_vcfs/m84036_250809_035451_s4.bc2167_hba.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2167_paraphase/m84036_250809_035451_s4.bc2167_paraphase_vcfs/m84036_250809_035451_s4.bc2167_hbb.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2167_paraphase/m84036_250809_035451_s4.bc2167_paraphase_vcfs/m84036_250809_035451_s4.bc2167_rpgr.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2167_paraphase/m84036_250809_035451_s4.bc2167_paraphase_vcfs/m84036_250809_035451_s4.bc2167_smn1.vcf"]
2025-09-15 20:29:56.589 wdl.w:ptcp.w:call-paraphase-70.t:call-run_paraphase INFO output :: name: "havanno_json", value: "m84036_250809_035451_s4.bc2167.havanno.json"
2025-09-15 20:29:56.731 wdl.w:ptcp.w:call-paraphase-70.t:call-run_paraphase NOTICE done
2025-09-15 20:29:56.738 wdl.w:ptcp.w:call-paraphase-70 NOTICE finish :: job: "call-run_paraphase"
2025-09-15 20:29:56.738 wdl.w:ptcp.w:call-paraphase-70 INFO output :: job: "call-run_paraphase", values: {"havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-70/call-run_paraphase/out/m84036_250809_035451_s4.bc2167.havanno.json", "paraphase_vcfs": ["/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-70/call-run_paraphase/out/m84036_250809_035451_s4.bc2167_paraphase/m84036_250809_035451_s4.bc2167_paraphase_vcfs/m84036_250809_035451_s4.bc2167_cyp21.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-70/call-run_paraphase/out/m84036_250809_035451_s4.bc2167_paraphase/m84036_250809_035451_s4.bc2167_paraphase_vcfs/m84036_250809_035451_s4.bc2167_f8inv1.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-70/call-run_paraphase/out/m84036_250809_035451_s4.bc2167_paraphase/m84036_250809_035451_s4.bc2167_paraphase_vcfs/m84036_250809_035451_s4.bc2167_f8inv22.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-70/call-run_paraphase/out/m84036_250809_035451_s4.bc2167_paraphase/m84036_250809_035451_s4.bc2167_paraphase_vcfs/m84036_250809_035451_s4.bc2167_gba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-70/call-run_paraphase/out/m84036_250809_035451_s4.bc2167_paraphase/m84036_250809_035451_s4.bc2167_paraphase_vcfs/m84036_250809_035451_s4.bc2167_hba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-70/call-run_paraphase/out/m84036_250809_035451_s4.bc2167_paraphase/m84036_250809_035451_s4.bc2167_paraphase_vcfs/m84036_250809_035451_s4.bc2167_hbb.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-70/call-run_paraphase/out/m84036_250809_035451_s4.bc2167_paraphase/m84036_250809_035451_s4.bc2167_paraphase_vcfs/m84036_250809_035451_s4.bc2167_rpgr.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-70/call-run_paraphase/out/m84036_250809_035451_s4.bc2167_paraphase/m84036_250809_035451_s4.bc2167_paraphase_vcfs/m84036_250809_035451_s4.bc2167_smn1.vcf"], "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-70/call-run_paraphase/out/m84036_250809_035451_s4.bc2167_paraphase/m84036_250809_035451_s4.bc2167.paraphase.json", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-70/call-run_paraphase/out/m84036_250809_035451_s4.bc2167_paraphase/m84036_250809_035451_s4.bc2167.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-70/call-run_paraphase/out/m84036_250809_035451_s4.bc2167_paraphase/m84036_250809_035451_s4.bc2167.paraphase.bam"}
2025-09-15 20:29:56.738 wdl.w:ptcp.w:call-paraphase-70 NOTICE ready :: job: "call-call_f8", callee: "call_f8"
2025-09-15 20:29:56.738 wdl.w:ptcp.w:call-paraphase-70 INFO input :: job: "call-call_f8", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "out_prefix": "m84036_250809_035451_s4.bc2167", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-70/call-run_paraphase/out/m84036_250809_035451_s4.bc2167_paraphase/m84036_250809_035451_s4.bc2167.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-70/call-run_paraphase/out/m84036_250809_035451_s4.bc2167_paraphase/m84036_250809_035451_s4.bc2167.paraphase.bam", "sex": "F"}
2025-09-15 20:29:56.739 wdl.w:ptcp.w:call-paraphase-70 INFO visit :: node: "output-havanno_json", values: {"havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-70/call-run_paraphase/out/m84036_250809_035451_s4.bc2167.havanno.json"}
2025-09-15 20:29:56.739 wdl.w:ptcp.w:call-paraphase-70 INFO visit :: node: "output-paraphase_bam", values: {"paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-70/call-run_paraphase/out/m84036_250809_035451_s4.bc2167_paraphase/m84036_250809_035451_s4.bc2167.paraphase.bam"}
2025-09-15 20:29:56.739 wdl.w:ptcp.w:call-paraphase-70 INFO visit :: node: "output-paraphase_bam_bai", values: {"paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-70/call-run_paraphase/out/m84036_250809_035451_s4.bc2167_paraphase/m84036_250809_035451_s4.bc2167.paraphase.bam.bai"}
2025-09-15 20:29:56.739 wdl.w:ptcp.w:call-paraphase-70 INFO visit :: node: "output-paraphase_json", values: {"paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-70/call-run_paraphase/out/m84036_250809_035451_s4.bc2167_paraphase/m84036_250809_035451_s4.bc2167.paraphase.json"}
2025-09-15 20:29:56.739 wdl.w:ptcp.w:call-paraphase-70 INFO visit :: node: "output-paraphase_vcfs", values: {"paraphase_vcfs": ["/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-70/call-run_paraphase/out/m84036_250809_035451_s4.bc2167_paraphase/m84036_250809_035451_s4.bc2167_paraphase_vcfs/m84036_250809_035451_s4.bc2167_cyp21.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-70/call-run_paraphase/out/m84036_250809_035451_s4.bc2167_paraphase/m84036_250809_035451_s4.bc2167_paraphase_vcfs/m84036_250809_035451_s4.bc2167_f8inv1.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-70/call-run_paraphase/out/m84036_250809_035451_s4.bc2167_paraphase/m84036_250809_035451_s4.bc2167_paraphase_vcfs/m84036_250809_035451_s4.bc2167_f8inv22.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-70/call-run_paraphase/out/m84036_250809_035451_s4.bc2167_paraphase/m84036_250809_035451_s4.bc2167_paraphase_vcfs/m84036_250809_035451_s4.bc2167_gba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-70/call-run_paraphase/out/m84036_250809_035451_s4.bc2167_paraphase/m84036_250809_035451_s4.bc2167_paraphase_vcfs/m84036_250809_035451_s4.bc2167_hba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-70/call-run_paraphase/out/m84036_250809_035451_s4.bc2167_paraphase/m84036_250809_035451_s4.bc2167_paraphase_vcfs/m84036_250809_035451_s4.bc2167_hbb.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-70/call-run_paraphase/out/m84036_250809_035451_s4.bc2167_paraphase/m84036_250809_035451_s4.bc2167_paraphase_vcfs/m84036_250809_035451_s4.bc2167_rpgr.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-70/call-run_paraphase/out/m84036_250809_035451_s4.bc2167_paraphase/m84036_250809_035451_s4.bc2167_paraphase_vcfs/m84036_250809_035451_s4.bc2167_smn1.vcf"]}
2025-09-15 20:29:56.744 wdl.w:ptcp.w:call-paraphase-70.t:call-call_f8 NOTICE task setup :: name: "call_f8", source: "./paraphase.wdl", line: 232, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-70/call-call_f8", thread: 140613555033664
2025-09-15 20:29:56.759 wdl.w:ptcp.w:call-paraphase-70.t:call-call_f8 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:29:56.759 wdl.w:ptcp.w:call-paraphase-70.t:call-call_f8 INFO input :: name: "genome_version", value: "38"
2025-09-15 20:29:56.759 wdl.w:ptcp.w:call-paraphase-70.t:call-call_f8 INFO input :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2167"
2025-09-15 20:29:56.759 wdl.w:ptcp.w:call-paraphase-70.t:call-call_f8 INFO input :: name: "paraphase_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2167.paraphase.bam.bai"
2025-09-15 20:29:56.759 wdl.w:ptcp.w:call-paraphase-70.t:call-call_f8 INFO input :: name: "paraphase_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2167.paraphase.bam"
2025-09-15 20:29:56.760 wdl.w:ptcp.w:call-paraphase-70.t:call-call_f8 INFO input :: name: "sex", value: "F"
2025-09-15 20:29:56.760 wdl.w:ptcp.w:call-paraphase-70.t:call-call_f8 INFO eval :: name: "threads", value: 1
2025-09-15 20:29:56.760 wdl.w:ptcp.w:call-paraphase-70.t:call-call_f8 INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:29:56.760 wdl.w:ptcp.w:call-paraphase-70.t:call-call_f8 INFO eval :: name: "disk_size", value: 11
2025-09-15 20:29:56.760 wdl.w:ptcp.w:call-paraphase-70.t:call-call_f8 INFO eval :: name: "sample_sex", value: "F"
2025-09-15 20:29:56.761 wdl.w:ptcp.w:call-paraphase-70.t:call-call_f8 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:29:56.761 wdl.w:ptcp.w:call-paraphase-70.t:call-call_f8 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:29:56.761 wdl.w:ptcp.w:call-paraphase-70.t:call-call_f8 INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:29:56.761 wdl.w:ptcp.w:call-paraphase-70.t:call-call_f8 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:29:56.801 wdl.w:ptcp.w:call-paraphase-70.t:call-call_f8 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 8, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-70/call-call_f8/_singularity_tmpdir_can7e44a"
2025-09-15 20:29:56.801 wdl.w:ptcp.w:call-paraphase-70.t:call-call_f8 INFO Slurm invocation: srun --job-name call-call_f8 --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-70/call-call_f8/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-70/call-call_f8/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-70/call-call_f8/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-70/call-call_f8/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-70/call-run_paraphase/out/m84036_250809_035451_s4.bc2167_paraphase/m84036_250809_035451_s4.bc2167.paraphase.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2167.paraphase.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-70/call-run_paraphase/out/m84036_250809_035451_s4.bc2167_paraphase/m84036_250809_035451_s4.bc2167.paraphase.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2167.paraphase.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-70/call-call_f8/_singularity_tmpdir_can7e44a/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-70/call-call_f8/_singularity_tmpdir_can7e44a/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:29:56.812 wdl.w:ptcp.w:call-paraphase-70.t:call-call_f8 NOTICE slurm_singularity run :: pid: 1209881, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-70/call-call_f8/slurm_singularity.log.txt"
2025-09-15 20:29:57.823 wdl.w:ptcp.w:call-paraphase-70.t:call-call_f8.slurm_singularity INFO srun: job 51798289 queued and waiting for resources
2025-09-15 20:29:58.835 wdl.w:ptcp.w:call-paraphase-70.t:call-call_f8.slurm_singularity INFO srun: job 51798289 has been allocated resources
2025-09-15 20:29:58.835 wdl.w:ptcp.w:call-paraphase-70.t:call-call_f8.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:29:58.980 wdl.w:ptcp.w:call-paraphase-10.t:call-run_paraphase INFO output :: name: "paraphase_bam", value: "m84036_250809_035451_s4.bc2107_paraphase/m84036_250809_035451_s4.bc2107.paraphase.bam"
2025-09-15 20:29:58.983 wdl.w:ptcp.w:call-paraphase-10.t:call-run_paraphase INFO output :: name: "paraphase_bam_bai", value: "m84036_250809_035451_s4.bc2107_paraphase/m84036_250809_035451_s4.bc2107.paraphase.bam.bai"
2025-09-15 20:29:58.984 wdl.w:ptcp.w:call-paraphase-10.t:call-run_paraphase INFO output :: name: "paraphase_json", value: "m84036_250809_035451_s4.bc2107_paraphase/m84036_250809_035451_s4.bc2107.paraphase.json"
2025-09-15 20:29:58.988 wdl.w:ptcp.w:call-paraphase-10.t:call-run_paraphase INFO output :: name: "paraphase_vcfs", value: ["/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2107_paraphase/m84036_250809_035451_s4.bc2107_paraphase_vcfs/m84036_250809_035451_s4.bc2107_cyp21.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2107_paraphase/m84036_250809_035451_s4.bc2107_paraphase_vcfs/m84036_250809_035451_s4.bc2107_f8inv1.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2107_paraphase/m84036_250809_035451_s4.bc2107_paraphase_vcfs/m84036_250809_035451_s4.bc2107_f8inv22.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2107_paraphase/m84036_250809_035451_s4.bc2107_paraphase_vcfs/m84036_250809_035451_s4.bc2107_gba.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2107_paraphase/m84036_250809_035451_s4.bc2107_paraphase_vcfs/m84036_250809_035451_s4.bc2107_hba.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2107_paraphase/m84036_250809_035451_s4.bc2107_paraphase_vcfs/m84036_250809_035451_s4.bc2107_hbb.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2107_paraphase/m84036_250809_035451_s4.bc2107_paraphase_vcfs/m84036_250809_035451_s4.bc2107_rpgr.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2107_paraphase/m84036_250809_035451_s4.bc2107_paraphase_vcfs/m84036_250809_035451_s4.bc2107_smn1.vcf"]
2025-09-15 20:29:58.991 wdl.w:ptcp.w:call-paraphase-10.t:call-run_paraphase INFO output :: name: "havanno_json", value: "m84036_250809_035451_s4.bc2107.havanno.json"
2025-09-15 20:29:59.162 wdl.w:ptcp.w:call-paraphase-10.t:call-run_paraphase NOTICE done
2025-09-15 20:29:59.169 wdl.w:ptcp.w:call-paraphase-10 NOTICE finish :: job: "call-run_paraphase"
2025-09-15 20:29:59.170 wdl.w:ptcp.w:call-paraphase-10 INFO output :: job: "call-run_paraphase", values: {"havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-10/call-run_paraphase/out/m84036_250809_035451_s4.bc2107.havanno.json", "paraphase_vcfs": ["/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-10/call-run_paraphase/out/m84036_250809_035451_s4.bc2107_paraphase/m84036_250809_035451_s4.bc2107_paraphase_vcfs/m84036_250809_035451_s4.bc2107_cyp21.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-10/call-run_paraphase/out/m84036_250809_035451_s4.bc2107_paraphase/m84036_250809_035451_s4.bc2107_paraphase_vcfs/m84036_250809_035451_s4.bc2107_f8inv1.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-10/call-run_paraphase/out/m84036_250809_035451_s4.bc2107_paraphase/m84036_250809_035451_s4.bc2107_paraphase_vcfs/m84036_250809_035451_s4.bc2107_f8inv22.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-10/call-run_paraphase/out/m84036_250809_035451_s4.bc2107_paraphase/m84036_250809_035451_s4.bc2107_paraphase_vcfs/m84036_250809_035451_s4.bc2107_gba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-10/call-run_paraphase/out/m84036_250809_035451_s4.bc2107_paraphase/m84036_250809_035451_s4.bc2107_paraphase_vcfs/m84036_250809_035451_s4.bc2107_hba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-10/call-run_paraphase/out/m84036_250809_035451_s4.bc2107_paraphase/m84036_250809_035451_s4.bc2107_paraphase_vcfs/m84036_250809_035451_s4.bc2107_hbb.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-10/call-run_paraphase/out/m84036_250809_035451_s4.bc2107_paraphase/m84036_250809_035451_s4.bc2107_paraphase_vcfs/m84036_250809_035451_s4.bc2107_rpgr.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-10/call-run_paraphase/out/m84036_250809_035451_s4.bc2107_paraphase/m84036_250809_035451_s4.bc2107_paraphase_vcfs/m84036_250809_035451_s4.bc2107_smn1.vcf"], "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-10/call-run_paraphase/out/m84036_250809_035451_s4.bc2107_paraphase/m84036_250809_035451_s4.bc2107.paraphase.json", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-10/call-run_paraphase/out/m84036_250809_035451_s4.bc2107_paraphase/m84036_250809_035451_s4.bc2107.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-10/call-run_paraphase/out/m84036_250809_035451_s4.bc2107_paraphase/m84036_250809_035451_s4.bc2107.paraphase.bam"}
2025-09-15 20:29:59.171 wdl.w:ptcp.w:call-paraphase-10 NOTICE ready :: job: "call-call_f8", callee: "call_f8"
2025-09-15 20:29:59.172 wdl.w:ptcp.w:call-paraphase-10 INFO input :: job: "call-call_f8", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "out_prefix": "m84036_250809_035451_s4.bc2107", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-10/call-run_paraphase/out/m84036_250809_035451_s4.bc2107_paraphase/m84036_250809_035451_s4.bc2107.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-10/call-run_paraphase/out/m84036_250809_035451_s4.bc2107_paraphase/m84036_250809_035451_s4.bc2107.paraphase.bam", "sex": "F"}
2025-09-15 20:29:59.172 wdl.w:ptcp.w:call-paraphase-10 INFO visit :: node: "output-havanno_json", values: {"havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-10/call-run_paraphase/out/m84036_250809_035451_s4.bc2107.havanno.json"}
2025-09-15 20:29:59.172 wdl.w:ptcp.w:call-paraphase-10 INFO visit :: node: "output-paraphase_bam", values: {"paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-10/call-run_paraphase/out/m84036_250809_035451_s4.bc2107_paraphase/m84036_250809_035451_s4.bc2107.paraphase.bam"}
2025-09-15 20:29:59.172 wdl.w:ptcp.w:call-paraphase-10 INFO visit :: node: "output-paraphase_bam_bai", values: {"paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-10/call-run_paraphase/out/m84036_250809_035451_s4.bc2107_paraphase/m84036_250809_035451_s4.bc2107.paraphase.bam.bai"}
2025-09-15 20:29:59.172 wdl.w:ptcp.w:call-paraphase-10 INFO visit :: node: "output-paraphase_json", values: {"paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-10/call-run_paraphase/out/m84036_250809_035451_s4.bc2107_paraphase/m84036_250809_035451_s4.bc2107.paraphase.json"}
2025-09-15 20:29:59.173 wdl.w:ptcp.w:call-paraphase-10 INFO visit :: node: "output-paraphase_vcfs", values: {"paraphase_vcfs": ["/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-10/call-run_paraphase/out/m84036_250809_035451_s4.bc2107_paraphase/m84036_250809_035451_s4.bc2107_paraphase_vcfs/m84036_250809_035451_s4.bc2107_cyp21.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-10/call-run_paraphase/out/m84036_250809_035451_s4.bc2107_paraphase/m84036_250809_035451_s4.bc2107_paraphase_vcfs/m84036_250809_035451_s4.bc2107_f8inv1.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-10/call-run_paraphase/out/m84036_250809_035451_s4.bc2107_paraphase/m84036_250809_035451_s4.bc2107_paraphase_vcfs/m84036_250809_035451_s4.bc2107_f8inv22.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-10/call-run_paraphase/out/m84036_250809_035451_s4.bc2107_paraphase/m84036_250809_035451_s4.bc2107_paraphase_vcfs/m84036_250809_035451_s4.bc2107_gba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-10/call-run_paraphase/out/m84036_250809_035451_s4.bc2107_paraphase/m84036_250809_035451_s4.bc2107_paraphase_vcfs/m84036_250809_035451_s4.bc2107_hba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-10/call-run_paraphase/out/m84036_250809_035451_s4.bc2107_paraphase/m84036_250809_035451_s4.bc2107_paraphase_vcfs/m84036_250809_035451_s4.bc2107_hbb.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-10/call-run_paraphase/out/m84036_250809_035451_s4.bc2107_paraphase/m84036_250809_035451_s4.bc2107_paraphase_vcfs/m84036_250809_035451_s4.bc2107_rpgr.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-10/call-run_paraphase/out/m84036_250809_035451_s4.bc2107_paraphase/m84036_250809_035451_s4.bc2107_paraphase_vcfs/m84036_250809_035451_s4.bc2107_smn1.vcf"]}
2025-09-15 20:29:59.183 wdl.w:ptcp.w:call-paraphase-10.t:call-call_f8 NOTICE task setup :: name: "call_f8", source: "./paraphase.wdl", line: 232, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-10/call-call_f8", thread: 140613068518976
2025-09-15 20:29:59.197 wdl.w:ptcp.w:call-paraphase-10.t:call-call_f8 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:29:59.197 wdl.w:ptcp.w:call-paraphase-10.t:call-call_f8 INFO input :: name: "genome_version", value: "38"
2025-09-15 20:29:59.197 wdl.w:ptcp.w:call-paraphase-10.t:call-call_f8 INFO input :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2107"
2025-09-15 20:29:59.197 wdl.w:ptcp.w:call-paraphase-10.t:call-call_f8 INFO input :: name: "paraphase_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2107.paraphase.bam.bai"
2025-09-15 20:29:59.197 wdl.w:ptcp.w:call-paraphase-10.t:call-call_f8 INFO input :: name: "paraphase_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2107.paraphase.bam"
2025-09-15 20:29:59.197 wdl.w:ptcp.w:call-paraphase-10.t:call-call_f8 INFO input :: name: "sex", value: "F"
2025-09-15 20:29:59.197 wdl.w:ptcp.w:call-paraphase-10.t:call-call_f8 INFO eval :: name: "threads", value: 1
2025-09-15 20:29:59.198 wdl.w:ptcp.w:call-paraphase-10.t:call-call_f8 INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:29:59.198 wdl.w:ptcp.w:call-paraphase-10.t:call-call_f8 INFO eval :: name: "disk_size", value: 11
2025-09-15 20:29:59.198 wdl.w:ptcp.w:call-paraphase-10.t:call-call_f8 INFO eval :: name: "sample_sex", value: "F"
2025-09-15 20:29:59.198 wdl.w:ptcp.w:call-paraphase-10.t:call-call_f8 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:29:59.198 wdl.w:ptcp.w:call-paraphase-10.t:call-call_f8 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:29:59.199 wdl.w:ptcp.w:call-paraphase-10.t:call-call_f8 INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:29:59.199 wdl.w:ptcp.w:call-paraphase-10.t:call-call_f8 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:29:59.236 wdl.w:ptcp.w:call-paraphase-10.t:call-call_f8 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 8, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-10/call-call_f8/_singularity_tmpdir_7_sto7z7"
2025-09-15 20:29:59.236 wdl.w:ptcp.w:call-paraphase-10.t:call-call_f8 INFO Slurm invocation: srun --job-name call-call_f8 --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-10/call-call_f8/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-10/call-call_f8/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-10/call-call_f8/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-10/call-call_f8/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-10/call-run_paraphase/out/m84036_250809_035451_s4.bc2107_paraphase/m84036_250809_035451_s4.bc2107.paraphase.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2107.paraphase.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-10/call-run_paraphase/out/m84036_250809_035451_s4.bc2107_paraphase/m84036_250809_035451_s4.bc2107.paraphase.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2107.paraphase.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-10/call-call_f8/_singularity_tmpdir_7_sto7z7/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-10/call-call_f8/_singularity_tmpdir_7_sto7z7/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:29:59.240 wdl.w:ptcp.w:call-paraphase-10.t:call-call_f8 NOTICE slurm_singularity run :: pid: 1209890, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-10/call-call_f8/slurm_singularity.log.txt"
2025-09-15 20:29:59.585 wdl.w:ptcp.w:call-paraphase-70.t:call-call_f8 INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2167.f8inversion.vcf"
2025-09-15 20:29:59.588 wdl.w:ptcp.w:call-paraphase-70.t:call-call_f8 INFO output :: name: "json", value: "m84036_250809_035451_s4.bc2167.f8inversion.json"
2025-09-15 20:29:59.638 wdl.w:ptcp.w:call-paraphase-70.t:call-call_f8 NOTICE done
2025-09-15 20:29:59.643 wdl.w:ptcp.w:call-paraphase-70 NOTICE finish :: job: "call-call_f8"
2025-09-15 20:29:59.643 wdl.w:ptcp.w:call-paraphase-70 INFO output :: job: "call-call_f8", values: {"json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-70/call-call_f8/out/m84036_250809_035451_s4.bc2167.f8inversion.json", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-70/call-call_f8/out/m84036_250809_035451_s4.bc2167.f8inversion.vcf"}
2025-09-15 20:29:59.643 wdl.w:ptcp.w:call-paraphase-70 INFO visit :: node: "output-f8_json", values: {"f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-70/call-call_f8/out/m84036_250809_035451_s4.bc2167.f8inversion.json"}
2025-09-15 20:29:59.643 wdl.w:ptcp.w:call-paraphase-70 INFO visit :: node: "output-f8_vcf", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-70/call-call_f8/out/m84036_250809_035451_s4.bc2167.f8inversion.vcf"}
2025-09-15 20:29:59.644 wdl.w:ptcp.w:call-paraphase-70 INFO visit :: node: "outputs", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-70/call-call_f8/out/m84036_250809_035451_s4.bc2167.f8inversion.vcf", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-70/call-run_paraphase/out/m84036_250809_035451_s4.bc2167_paraphase/m84036_250809_035451_s4.bc2167.paraphase.json", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-70/call-run_paraphase/out/m84036_250809_035451_s4.bc2167_paraphase/m84036_250809_035451_s4.bc2167.paraphase.bam", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-70/call-run_paraphase/out/m84036_250809_035451_s4.bc2167_paraphase/m84036_250809_035451_s4.bc2167.paraphase.bam.bai", "paraphase_vcfs": ["/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-70/call-run_paraphase/out/m84036_250809_035451_s4.bc2167_paraphase/m84036_250809_035451_s4.bc2167_paraphase_vcfs/m84036_250809_035451_s4.bc2167_cyp21.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-70/call-run_paraphase/out/m84036_250809_035451_s4.bc2167_paraphase/m84036_250809_035451_s4.bc2167_paraphase_vcfs/m84036_250809_035451_s4.bc2167_f8inv1.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-70/call-run_paraphase/out/m84036_250809_035451_s4.bc2167_paraphase/m84036_250809_035451_s4.bc2167_paraphase_vcfs/m84036_250809_035451_s4.bc2167_f8inv22.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-70/call-run_paraphase/out/m84036_250809_035451_s4.bc2167_paraphase/m84036_250809_035451_s4.bc2167_paraphase_vcfs/m84036_250809_035451_s4.bc2167_gba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-70/call-run_paraphase/out/m84036_250809_035451_s4.bc2167_paraphase/m84036_250809_035451_s4.bc2167_paraphase_vcfs/m84036_250809_035451_s4.bc2167_hba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-70/call-run_paraphase/out/m84036_250809_035451_s4.bc2167_paraphase/m84036_250809_035451_s4.bc2167_paraphase_vcfs/m84036_250809_035451_s4.bc2167_hbb.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-70/call-run_paraphase/out/m84036_250809_035451_s4.bc2167_paraphase/m84036_250809_035451_s4.bc2167_paraphase_vcfs/m84036_250809_035451_s4.bc2167_rpgr.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-70/call-run_paraphase/out/m84036_250809_035451_s4.bc2167_paraphase/m84036_250809_035451_s4.bc2167_paraphase_vcfs/m84036_250809_035451_s4.bc2167_smn1.vcf"], "havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-70/call-run_paraphase/out/m84036_250809_035451_s4.bc2167.havanno.json", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-70/call-call_f8/out/m84036_250809_035451_s4.bc2167.f8inversion.json"}
2025-09-15 20:29:59.740 wdl.w:ptcp.w:call-paraphase-70 NOTICE done
2025-09-15 20:29:59.745 wdl.w:ptcp NOTICE finish :: job: "call-paraphase-70"
2025-09-15 20:29:59.745 wdl.w:ptcp INFO output :: job: "call-paraphase-70", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-70/out/m84036_250809_035451_s4.bc2167.f8inversion.vcf", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-70/out/m84036_250809_035451_s4.bc2167_paraphase/m84036_250809_035451_s4.bc2167.paraphase.json", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-70/out/m84036_250809_035451_s4.bc2167_paraphase/m84036_250809_035451_s4.bc2167.paraphase.bam", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-70/out/m84036_250809_035451_s4.bc2167_paraphase/m84036_250809_035451_s4.bc2167.paraphase.bam.bai", "paraphase_vcfs": ["/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-70/out/m84036_250809_035451_s4.bc2167_paraphase/m84036_250809_035451_s4.bc2167_paraphase_vcfs/m84036_250809_035451_s4.bc2167_cyp21.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-70/out/m84036_250809_035451_s4.bc2167_paraphase/m84036_250809_035451_s4.bc2167_paraphase_vcfs/m84036_250809_035451_s4.bc2167_f8inv1.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-70/out/m84036_250809_035451_s4.bc2167_paraphase/m84036_250809_035451_s4.bc2167_paraphase_vcfs/m84036_250809_035451_s4.bc2167_f8inv22.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-70/out/m84036_250809_035451_s4.bc2167_paraphase/m84036_250809_035451_s4.bc2167_paraphase_vcfs/m84036_250809_035451_s4.bc2167_gba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-70/out/m84036_250809_035451_s4.bc2167_paraphase/m84036_250809_035451_s4.bc2167_paraphase_vcfs/m84036_250809_035451_s4.bc2167_hba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-70/out/m84036_250809_035451_s4.bc2167_paraphase/m84036_250809_035451_s4.bc2167_paraphase_vcfs/m84036_250809_035451_s4.bc2167_hbb.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-70/out/m84036_250809_035451_s4.bc2167_paraphase/m84036_250809_035451_s4.bc2167_paraphase_vcfs/m84036_250809_035451_s4.bc2167_rpgr.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-70/out/m84036_250809_035451_s4.bc2167_paraphase/m84036_250809_035451_s4.bc2167_paraphase_vcfs/m84036_250809_035451_s4.bc2167_smn1.vcf"], "havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-70/out/m84036_250809_035451_s4.bc2167.havanno.json", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-70/out/m84036_250809_035451_s4.bc2167.f8inversion.json"}
2025-09-15 20:29:59.746 wdl.w:ptcp NOTICE ready :: job: "call-tar_outputs-70", callee: "tar_outputs"
2025-09-15 20:29:59.747 wdl.w:ptcp INFO input :: job: "call-tar_outputs-70", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "sawfish_vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-70/out/m84036_250809_035451_s4.bc2167_sawfish/m84036_250809_035451_s4.bc2167.sv.vcf.gz.tbi", "sawfish_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-70/out/m84036_250809_035451_s4.bc2167_sawfish/m84036_250809_035451_s4.bc2167.sv.vcf.gz", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-70/out/m84036_250809_035451_s4.bc2167.f8inversion.json", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-70/out/m84036_250809_035451_s4.bc2167_paraphase/m84036_250809_035451_s4.bc2167.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-70/out/m84036_250809_035451_s4.bc2167_paraphase/m84036_250809_035451_s4.bc2167.paraphase.bam", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-70/out/m84036_250809_035451_s4.bc2167_paraphase/m84036_250809_035451_s4.bc2167.paraphase.json", "trgt_spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-70/out/m84036_250809_035451_s4.bc2167.trgt.sorted.spanning.bam.bai", "trgt_spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-70/out/m84036_250809_035451_s4.bc2167.trgt.sorted.spanning.bam", "trgt_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-70/out/m84036_250809_035451_s4.bc2167.trgt.vcf", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-70/out/m84036_250809_035451_s4.bc2167.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-70/out/m84036_250809_035451_s4.bc2167.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2167"}
2025-09-15 20:29:59.752 wdl.w:ptcp.t:call-tar_outputs-70 NOTICE task setup :: name: "tar_outputs", source: "./common.wdl", line: 279, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-70", thread: 140608194717248
2025-09-15 20:29:59.771 wdl.w:ptcp.t:call-tar_outputs-70 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:29:59.771 wdl.w:ptcp.t:call-tar_outputs-70 INFO input :: name: "sawfish_vcf_tbi", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2167.sv.vcf.gz.tbi"
2025-09-15 20:29:59.771 wdl.w:ptcp.t:call-tar_outputs-70 INFO input :: name: "sawfish_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2167.sv.vcf.gz"
2025-09-15 20:29:59.771 wdl.w:ptcp.t:call-tar_outputs-70 INFO input :: name: "f8_json", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2167.f8inversion.json"
2025-09-15 20:29:59.771 wdl.w:ptcp.t:call-tar_outputs-70 INFO input :: name: "paraphase_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2167.paraphase.bam.bai"
2025-09-15 20:29:59.771 wdl.w:ptcp.t:call-tar_outputs-70 INFO input :: name: "paraphase_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2167.paraphase.bam"
2025-09-15 20:29:59.771 wdl.w:ptcp.t:call-tar_outputs-70 INFO input :: name: "paraphase_json", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2167.paraphase.json"
2025-09-15 20:29:59.771 wdl.w:ptcp.t:call-tar_outputs-70 INFO input :: name: "trgt_spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2167.trgt.sorted.spanning.bam.bai"
2025-09-15 20:29:59.771 wdl.w:ptcp.t:call-tar_outputs-70 INFO input :: name: "trgt_spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2167.trgt.sorted.spanning.bam"
2025-09-15 20:29:59.771 wdl.w:ptcp.t:call-tar_outputs-70 INFO input :: name: "trgt_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2167.trgt.vcf"
2025-09-15 20:29:59.771 wdl.w:ptcp.t:call-tar_outputs-70 INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2167.mapped.bam.bai"
2025-09-15 20:29:59.771 wdl.w:ptcp.t:call-tar_outputs-70 INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2167.mapped.bam"
2025-09-15 20:29:59.771 wdl.w:ptcp.t:call-tar_outputs-70 INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2167"
2025-09-15 20:29:59.771 wdl.w:ptcp.t:call-tar_outputs-70 INFO eval :: name: "threads", value: 1
2025-09-15 20:29:59.771 wdl.w:ptcp.t:call-tar_outputs-70 INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:29:59.772 wdl.w:ptcp.t:call-tar_outputs-70 INFO eval :: name: "disk_size", value: 6
2025-09-15 20:29:59.772 wdl.w:ptcp.t:call-tar_outputs-70 INFO eval :: name: "output_tarball", value: "m84036_250809_035451_s4.bc2167.tar"
2025-09-15 20:29:59.772 wdl.w:ptcp.t:call-tar_outputs-70 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:29:59.772 wdl.w:ptcp.t:call-tar_outputs-70 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:29:59.773 wdl.w:ptcp.t:call-tar_outputs-70 INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:29:59.773 wdl.w:ptcp.t:call-tar_outputs-70 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:29:59.848 wdl.w:ptcp.t:call-tar_outputs-70 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 17, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-70/_singularity_tmpdir__s564ao4"
2025-09-15 20:29:59.848 wdl.w:ptcp.t:call-tar_outputs-70 INFO Slurm invocation: srun --job-name call-tar_outputs-70 --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-70/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-70/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-70/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-70/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-70/out/m84036_250809_035451_s4.bc2167_sawfish/m84036_250809_035451_s4.bc2167.sv.vcf.gz:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2167.sv.vcf.gz:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-70/out/m84036_250809_035451_s4.bc2167_sawfish/m84036_250809_035451_s4.bc2167.sv.vcf.gz.tbi:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2167.sv.vcf.gz.tbi:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-70/out/m84036_250809_035451_s4.bc2167.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2167.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-70/out/m84036_250809_035451_s4.bc2167.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2167.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-70/out/m84036_250809_035451_s4.bc2167.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2167.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-70/out/m84036_250809_035451_s4.bc2167_paraphase/m84036_250809_035451_s4.bc2167.paraphase.json:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2167.paraphase.json:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-70/out/m84036_250809_035451_s4.bc2167_paraphase/m84036_250809_035451_s4.bc2167.paraphase.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2167.paraphase.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-70/out/m84036_250809_035451_s4.bc2167_paraphase/m84036_250809_035451_s4.bc2167.paraphase.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2167.paraphase.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-70/out/m84036_250809_035451_s4.bc2167.f8inversion.json:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2167.f8inversion.json:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-70/out/m84036_250809_035451_s4.bc2167.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2167.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-70/out/m84036_250809_035451_s4.bc2167.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2167.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-70/_singularity_tmpdir__s564ao4/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-70/_singularity_tmpdir__s564ao4/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:29:59.855 wdl.w:ptcp.t:call-tar_outputs-70 NOTICE slurm_singularity run :: pid: 1209901, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-70/slurm_singularity.log.txt"
2025-09-15 20:30:00.248 wdl.w:ptcp.w:call-paraphase-10.t:call-call_f8.slurm_singularity INFO srun: job 51798290 queued and waiting for resources
2025-09-15 20:30:00.248 wdl.w:ptcp.w:call-paraphase-10.t:call-call_f8.slurm_singularity INFO srun: job 51798290 has been allocated resources
2025-09-15 20:30:00.248 wdl.w:ptcp.w:call-paraphase-10.t:call-call_f8.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:30:00.857 wdl.w:ptcp.t:call-tar_outputs-70.stderr VERBOSE tar: Removing leading `/' from member names
2025-09-15 20:30:00.857 wdl.w:ptcp.t:call-tar_outputs-70.stderr VERBOSE tar: Removing leading `/' from hard link targets
2025-09-15 20:30:00.866 wdl.w:ptcp.t:call-tar_outputs-70.slurm_singularity INFO srun: job 51798291 queued and waiting for resources
2025-09-15 20:30:00.866 wdl.w:ptcp.t:call-tar_outputs-70.slurm_singularity INFO srun: job 51798291 has been allocated resources
2025-09-15 20:30:00.866 wdl.w:ptcp.t:call-tar_outputs-70.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:30:00.945 wdl.w:ptcp.w:call-paraphase-10.t:call-call_f8 INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2107.f8inversion.vcf"
2025-09-15 20:30:00.947 wdl.w:ptcp.w:call-paraphase-10.t:call-call_f8 INFO output :: name: "json", value: "m84036_250809_035451_s4.bc2107.f8inversion.json"
2025-09-15 20:30:00.999 wdl.w:ptcp.w:call-paraphase-10.t:call-call_f8 NOTICE done
2025-09-15 20:30:01.005 wdl.w:ptcp.w:call-paraphase-10 NOTICE finish :: job: "call-call_f8"
2025-09-15 20:30:01.005 wdl.w:ptcp.w:call-paraphase-10 INFO output :: job: "call-call_f8", values: {"json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-10/call-call_f8/out/m84036_250809_035451_s4.bc2107.f8inversion.json", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-10/call-call_f8/out/m84036_250809_035451_s4.bc2107.f8inversion.vcf"}
2025-09-15 20:30:01.005 wdl.w:ptcp.w:call-paraphase-10 INFO visit :: node: "output-f8_json", values: {"f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-10/call-call_f8/out/m84036_250809_035451_s4.bc2107.f8inversion.json"}
2025-09-15 20:30:01.006 wdl.w:ptcp.w:call-paraphase-10 INFO visit :: node: "output-f8_vcf", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-10/call-call_f8/out/m84036_250809_035451_s4.bc2107.f8inversion.vcf"}
2025-09-15 20:30:01.006 wdl.w:ptcp.w:call-paraphase-10 INFO visit :: node: "outputs", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-10/call-call_f8/out/m84036_250809_035451_s4.bc2107.f8inversion.vcf", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-10/call-run_paraphase/out/m84036_250809_035451_s4.bc2107_paraphase/m84036_250809_035451_s4.bc2107.paraphase.json", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-10/call-run_paraphase/out/m84036_250809_035451_s4.bc2107_paraphase/m84036_250809_035451_s4.bc2107.paraphase.bam", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-10/call-run_paraphase/out/m84036_250809_035451_s4.bc2107_paraphase/m84036_250809_035451_s4.bc2107.paraphase.bam.bai", "paraphase_vcfs": ["/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-10/call-run_paraphase/out/m84036_250809_035451_s4.bc2107_paraphase/m84036_250809_035451_s4.bc2107_paraphase_vcfs/m84036_250809_035451_s4.bc2107_cyp21.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-10/call-run_paraphase/out/m84036_250809_035451_s4.bc2107_paraphase/m84036_250809_035451_s4.bc2107_paraphase_vcfs/m84036_250809_035451_s4.bc2107_f8inv1.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-10/call-run_paraphase/out/m84036_250809_035451_s4.bc2107_paraphase/m84036_250809_035451_s4.bc2107_paraphase_vcfs/m84036_250809_035451_s4.bc2107_f8inv22.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-10/call-run_paraphase/out/m84036_250809_035451_s4.bc2107_paraphase/m84036_250809_035451_s4.bc2107_paraphase_vcfs/m84036_250809_035451_s4.bc2107_gba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-10/call-run_paraphase/out/m84036_250809_035451_s4.bc2107_paraphase/m84036_250809_035451_s4.bc2107_paraphase_vcfs/m84036_250809_035451_s4.bc2107_hba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-10/call-run_paraphase/out/m84036_250809_035451_s4.bc2107_paraphase/m84036_250809_035451_s4.bc2107_paraphase_vcfs/m84036_250809_035451_s4.bc2107_hbb.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-10/call-run_paraphase/out/m84036_250809_035451_s4.bc2107_paraphase/m84036_250809_035451_s4.bc2107_paraphase_vcfs/m84036_250809_035451_s4.bc2107_rpgr.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-10/call-run_paraphase/out/m84036_250809_035451_s4.bc2107_paraphase/m84036_250809_035451_s4.bc2107_paraphase_vcfs/m84036_250809_035451_s4.bc2107_smn1.vcf"], "havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-10/call-run_paraphase/out/m84036_250809_035451_s4.bc2107.havanno.json", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-10/call-call_f8/out/m84036_250809_035451_s4.bc2107.f8inversion.json"}
2025-09-15 20:30:01.065 wdl.w:ptcp.t:call-tar_outputs-70 INFO output :: name: "sample_tarball", value: "m84036_250809_035451_s4.bc2167.tar"
2025-09-15 20:30:01.112 wdl.w:ptcp.w:call-paraphase-10 NOTICE done
2025-09-15 20:30:01.117 wdl.w:ptcp NOTICE finish :: job: "call-paraphase-10"
2025-09-15 20:30:01.118 wdl.w:ptcp INFO output :: job: "call-paraphase-10", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-10/out/m84036_250809_035451_s4.bc2107.f8inversion.vcf", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-10/out/m84036_250809_035451_s4.bc2107_paraphase/m84036_250809_035451_s4.bc2107.paraphase.json", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-10/out/m84036_250809_035451_s4.bc2107_paraphase/m84036_250809_035451_s4.bc2107.paraphase.bam", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-10/out/m84036_250809_035451_s4.bc2107_paraphase/m84036_250809_035451_s4.bc2107.paraphase.bam.bai", "paraphase_vcfs": ["/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-10/out/m84036_250809_035451_s4.bc2107_paraphase/m84036_250809_035451_s4.bc2107_paraphase_vcfs/m84036_250809_035451_s4.bc2107_cyp21.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-10/out/m84036_250809_035451_s4.bc2107_paraphase/m84036_250809_035451_s4.bc2107_paraphase_vcfs/m84036_250809_035451_s4.bc2107_f8inv1.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-10/out/m84036_250809_035451_s4.bc2107_paraphase/m84036_250809_035451_s4.bc2107_paraphase_vcfs/m84036_250809_035451_s4.bc2107_f8inv22.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-10/out/m84036_250809_035451_s4.bc2107_paraphase/m84036_250809_035451_s4.bc2107_paraphase_vcfs/m84036_250809_035451_s4.bc2107_gba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-10/out/m84036_250809_035451_s4.bc2107_paraphase/m84036_250809_035451_s4.bc2107_paraphase_vcfs/m84036_250809_035451_s4.bc2107_hba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-10/out/m84036_250809_035451_s4.bc2107_paraphase/m84036_250809_035451_s4.bc2107_paraphase_vcfs/m84036_250809_035451_s4.bc2107_hbb.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-10/out/m84036_250809_035451_s4.bc2107_paraphase/m84036_250809_035451_s4.bc2107_paraphase_vcfs/m84036_250809_035451_s4.bc2107_rpgr.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-10/out/m84036_250809_035451_s4.bc2107_paraphase/m84036_250809_035451_s4.bc2107_paraphase_vcfs/m84036_250809_035451_s4.bc2107_smn1.vcf"], "havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-10/out/m84036_250809_035451_s4.bc2107.havanno.json", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-10/out/m84036_250809_035451_s4.bc2107.f8inversion.json"}
2025-09-15 20:30:01.118 wdl.w:ptcp NOTICE ready :: job: "call-tar_outputs-10", callee: "tar_outputs"
2025-09-15 20:30:01.118 wdl.w:ptcp.t:call-tar_outputs-70 NOTICE done
2025-09-15 20:30:01.118 wdl.w:ptcp INFO input :: job: "call-tar_outputs-10", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "sawfish_vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-10/out/m84036_250809_035451_s4.bc2107_sawfish/m84036_250809_035451_s4.bc2107.sv.vcf.gz.tbi", "sawfish_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-10/out/m84036_250809_035451_s4.bc2107_sawfish/m84036_250809_035451_s4.bc2107.sv.vcf.gz", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-10/out/m84036_250809_035451_s4.bc2107.f8inversion.json", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-10/out/m84036_250809_035451_s4.bc2107_paraphase/m84036_250809_035451_s4.bc2107.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-10/out/m84036_250809_035451_s4.bc2107_paraphase/m84036_250809_035451_s4.bc2107.paraphase.bam", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-10/out/m84036_250809_035451_s4.bc2107_paraphase/m84036_250809_035451_s4.bc2107.paraphase.json", "trgt_spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-10/out/m84036_250809_035451_s4.bc2107.trgt.sorted.spanning.bam.bai", "trgt_spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-10/out/m84036_250809_035451_s4.bc2107.trgt.sorted.spanning.bam", "trgt_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-10/out/m84036_250809_035451_s4.bc2107.trgt.vcf", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-10/out/m84036_250809_035451_s4.bc2107.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-10/out/m84036_250809_035451_s4.bc2107.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2107"}
2025-09-15 20:30:01.122 wdl.w:ptcp NOTICE finish :: job: "call-tar_outputs-70"
2025-09-15 20:30:01.122 wdl.w:ptcp INFO output :: job: "call-tar_outputs-70", values: {"sample_tarball": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-70/out/m84036_250809_035451_s4.bc2167.tar"}
2025-09-15 20:30:01.124 wdl.w:ptcp.t:call-tar_outputs-10 NOTICE task setup :: name: "tar_outputs", source: "./common.wdl", line: 279, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-10", thread: 140608748373568
2025-09-15 20:30:01.145 wdl.w:ptcp.t:call-tar_outputs-10 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:30:01.145 wdl.w:ptcp.t:call-tar_outputs-10 INFO input :: name: "sawfish_vcf_tbi", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2107.sv.vcf.gz.tbi"
2025-09-15 20:30:01.145 wdl.w:ptcp.t:call-tar_outputs-10 INFO input :: name: "sawfish_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2107.sv.vcf.gz"
2025-09-15 20:30:01.145 wdl.w:ptcp.t:call-tar_outputs-10 INFO input :: name: "f8_json", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2107.f8inversion.json"
2025-09-15 20:30:01.145 wdl.w:ptcp.t:call-tar_outputs-10 INFO input :: name: "paraphase_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2107.paraphase.bam.bai"
2025-09-15 20:30:01.145 wdl.w:ptcp.t:call-tar_outputs-10 INFO input :: name: "paraphase_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2107.paraphase.bam"
2025-09-15 20:30:01.145 wdl.w:ptcp.t:call-tar_outputs-10 INFO input :: name: "paraphase_json", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2107.paraphase.json"
2025-09-15 20:30:01.145 wdl.w:ptcp.t:call-tar_outputs-10 INFO input :: name: "trgt_spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2107.trgt.sorted.spanning.bam.bai"
2025-09-15 20:30:01.145 wdl.w:ptcp.t:call-tar_outputs-10 INFO input :: name: "trgt_spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2107.trgt.sorted.spanning.bam"
2025-09-15 20:30:01.145 wdl.w:ptcp.t:call-tar_outputs-10 INFO input :: name: "trgt_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2107.trgt.vcf"
2025-09-15 20:30:01.145 wdl.w:ptcp.t:call-tar_outputs-10 INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2107.mapped.bam.bai"
2025-09-15 20:30:01.146 wdl.w:ptcp.t:call-tar_outputs-10 INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2107.mapped.bam"
2025-09-15 20:30:01.146 wdl.w:ptcp.t:call-tar_outputs-10 INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2107"
2025-09-15 20:30:01.146 wdl.w:ptcp.t:call-tar_outputs-10 INFO eval :: name: "threads", value: 1
2025-09-15 20:30:01.146 wdl.w:ptcp.t:call-tar_outputs-10 INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:30:01.146 wdl.w:ptcp.t:call-tar_outputs-10 INFO eval :: name: "disk_size", value: 6
2025-09-15 20:30:01.146 wdl.w:ptcp.t:call-tar_outputs-10 INFO eval :: name: "output_tarball", value: "m84036_250809_035451_s4.bc2107.tar"
2025-09-15 20:30:01.146 wdl.w:ptcp.t:call-tar_outputs-10 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:30:01.147 wdl.w:ptcp.t:call-tar_outputs-10 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:30:01.147 wdl.w:ptcp.t:call-tar_outputs-10 INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:30:01.147 wdl.w:ptcp.t:call-tar_outputs-10 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:30:01.216 wdl.w:ptcp.t:call-tar_outputs-10 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 17, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-10/_singularity_tmpdir_mxoc4inq"
2025-09-15 20:30:01.217 wdl.w:ptcp.t:call-tar_outputs-10 INFO Slurm invocation: srun --job-name call-tar_outputs-10 --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-10/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-10/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-10/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-10/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-10/out/m84036_250809_035451_s4.bc2107.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2107.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-10/out/m84036_250809_035451_s4.bc2107.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2107.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-10/out/m84036_250809_035451_s4.bc2107.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2107.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-10/out/m84036_250809_035451_s4.bc2107_sawfish/m84036_250809_035451_s4.bc2107.sv.vcf.gz:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2107.sv.vcf.gz:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-10/out/m84036_250809_035451_s4.bc2107_sawfish/m84036_250809_035451_s4.bc2107.sv.vcf.gz.tbi:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2107.sv.vcf.gz.tbi:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-10/out/m84036_250809_035451_s4.bc2107_paraphase/m84036_250809_035451_s4.bc2107.paraphase.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2107.paraphase.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-10/out/m84036_250809_035451_s4.bc2107_paraphase/m84036_250809_035451_s4.bc2107.paraphase.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2107.paraphase.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-10/out/m84036_250809_035451_s4.bc2107_paraphase/m84036_250809_035451_s4.bc2107.paraphase.json:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2107.paraphase.json:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-10/out/m84036_250809_035451_s4.bc2107.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2107.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-10/out/m84036_250809_035451_s4.bc2107.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2107.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-10/out/m84036_250809_035451_s4.bc2107.f8inversion.json:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2107.f8inversion.json:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-10/_singularity_tmpdir_mxoc4inq/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-10/_singularity_tmpdir_mxoc4inq/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:30:01.220 wdl.w:ptcp.t:call-tar_outputs-10 NOTICE slurm_singularity run :: pid: 1209987, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-10/slurm_singularity.log.txt"
2025-09-15 20:30:02.227 wdl.w:ptcp.t:call-tar_outputs-10.slurm_singularity INFO srun: job 51798292 queued and waiting for resources
2025-09-15 20:30:03.237 wdl.w:ptcp.t:call-tar_outputs-10.slurm_singularity INFO srun: job 51798292 has been allocated resources
2025-09-15 20:30:03.237 wdl.w:ptcp.t:call-tar_outputs-10.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:30:03.375 wdl.w:ptcp.w:call-paraphase-90.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for rpgr for sample m84036_250809_035451_s4.bc2187 at 2025-09-15 20:29:09.209304...
2025-09-15 20:30:03.376 wdl.w:ptcp.w:call-paraphase-90.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for rpgr for sample m84036_250809_035451_s4.bc2187 at 2025-09-15 20:29:09.210479...
2025-09-15 20:30:03.376 wdl.w:ptcp.w:call-paraphase-90.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for rpgr for sample m84036_250809_035451_s4.bc2187 at 2025-09-15 20:29:11.423967...
2025-09-15 20:30:03.377 wdl.w:ptcp.w:call-paraphase-90.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for rpgr for sample m84036_250809_035451_s4.bc2187 at 2025-09-15 20:29:12.622230...
2025-09-15 20:30:03.377 wdl.w:ptcp.w:call-paraphase-90.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for rpgr for sample m84036_250809_035451_s4.bc2187 at 2025-09-15 20:29:12.876379...
2025-09-15 20:30:03.435 wdl.w:ptcp.t:call-tar_outputs-10 INFO output :: name: "sample_tarball", value: "m84036_250809_035451_s4.bc2107.tar"
2025-09-15 20:30:03.485 wdl.w:ptcp.t:call-tar_outputs-10 NOTICE done
2025-09-15 20:30:03.489 wdl.w:ptcp NOTICE finish :: job: "call-tar_outputs-10"
2025-09-15 20:30:03.489 wdl.w:ptcp INFO output :: job: "call-tar_outputs-10", values: {"sample_tarball": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-10/out/m84036_250809_035451_s4.bc2107.tar"}
2025-09-15 20:30:04.120 wdl.w:ptcp.w:call-paraphase-51.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for f8inv22 for sample m84036_250809_035451_s4.bc2148 at 2025-09-15 20:29:40.402495...
2025-09-15 20:30:04.121 wdl.w:ptcp.w:call-paraphase-51.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for f8inv22 for sample m84036_250809_035451_s4.bc2148 at 2025-09-15 20:29:40.404216...
2025-09-15 20:30:04.121 wdl.w:ptcp.w:call-paraphase-51.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for f8inv22 for sample m84036_250809_035451_s4.bc2148 at 2025-09-15 20:29:41.658292...
2025-09-15 20:30:04.121 wdl.w:ptcp.w:call-paraphase-51.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for f8inv22 for sample m84036_250809_035451_s4.bc2148 at 2025-09-15 20:29:46.810290...
2025-09-15 20:30:04.121 wdl.w:ptcp.w:call-paraphase-51.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for f8inv22 for sample m84036_250809_035451_s4.bc2148 at 2025-09-15 20:29:47.245708...
2025-09-15 20:30:08.425 wdl.w:ptcp.w:call-paraphase-51.t:call-run_paraphase INFO output :: name: "paraphase_bam", value: "m84036_250809_035451_s4.bc2148_paraphase/m84036_250809_035451_s4.bc2148.paraphase.bam"
2025-09-15 20:30:08.428 wdl.w:ptcp.w:call-paraphase-51.t:call-run_paraphase INFO output :: name: "paraphase_bam_bai", value: "m84036_250809_035451_s4.bc2148_paraphase/m84036_250809_035451_s4.bc2148.paraphase.bam.bai"
2025-09-15 20:30:08.429 wdl.w:ptcp.w:call-paraphase-51.t:call-run_paraphase INFO output :: name: "paraphase_json", value: "m84036_250809_035451_s4.bc2148_paraphase/m84036_250809_035451_s4.bc2148.paraphase.json"
2025-09-15 20:30:08.433 wdl.w:ptcp.w:call-paraphase-51.t:call-run_paraphase INFO output :: name: "paraphase_vcfs", value: ["/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2148_paraphase/m84036_250809_035451_s4.bc2148_paraphase_vcfs/m84036_250809_035451_s4.bc2148_cyp21.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2148_paraphase/m84036_250809_035451_s4.bc2148_paraphase_vcfs/m84036_250809_035451_s4.bc2148_f8inv1.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2148_paraphase/m84036_250809_035451_s4.bc2148_paraphase_vcfs/m84036_250809_035451_s4.bc2148_f8inv22.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2148_paraphase/m84036_250809_035451_s4.bc2148_paraphase_vcfs/m84036_250809_035451_s4.bc2148_gba.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2148_paraphase/m84036_250809_035451_s4.bc2148_paraphase_vcfs/m84036_250809_035451_s4.bc2148_hba.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2148_paraphase/m84036_250809_035451_s4.bc2148_paraphase_vcfs/m84036_250809_035451_s4.bc2148_hbb.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2148_paraphase/m84036_250809_035451_s4.bc2148_paraphase_vcfs/m84036_250809_035451_s4.bc2148_rpgr.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2148_paraphase/m84036_250809_035451_s4.bc2148_paraphase_vcfs/m84036_250809_035451_s4.bc2148_smn1.vcf"]
2025-09-15 20:30:08.436 wdl.w:ptcp.w:call-paraphase-51.t:call-run_paraphase INFO output :: name: "havanno_json", value: "m84036_250809_035451_s4.bc2148.havanno.json"
2025-09-15 20:30:08.582 wdl.w:ptcp.w:call-paraphase-51.t:call-run_paraphase NOTICE done
2025-09-15 20:30:08.589 wdl.w:ptcp.w:call-paraphase-51 NOTICE finish :: job: "call-run_paraphase"
2025-09-15 20:30:08.589 wdl.w:ptcp.w:call-paraphase-51 INFO output :: job: "call-run_paraphase", values: {"havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-51/call-run_paraphase/out/m84036_250809_035451_s4.bc2148.havanno.json", "paraphase_vcfs": ["/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-51/call-run_paraphase/out/m84036_250809_035451_s4.bc2148_paraphase/m84036_250809_035451_s4.bc2148_paraphase_vcfs/m84036_250809_035451_s4.bc2148_cyp21.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-51/call-run_paraphase/out/m84036_250809_035451_s4.bc2148_paraphase/m84036_250809_035451_s4.bc2148_paraphase_vcfs/m84036_250809_035451_s4.bc2148_f8inv1.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-51/call-run_paraphase/out/m84036_250809_035451_s4.bc2148_paraphase/m84036_250809_035451_s4.bc2148_paraphase_vcfs/m84036_250809_035451_s4.bc2148_f8inv22.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-51/call-run_paraphase/out/m84036_250809_035451_s4.bc2148_paraphase/m84036_250809_035451_s4.bc2148_paraphase_vcfs/m84036_250809_035451_s4.bc2148_gba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-51/call-run_paraphase/out/m84036_250809_035451_s4.bc2148_paraphase/m84036_250809_035451_s4.bc2148_paraphase_vcfs/m84036_250809_035451_s4.bc2148_hba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-51/call-run_paraphase/out/m84036_250809_035451_s4.bc2148_paraphase/m84036_250809_035451_s4.bc2148_paraphase_vcfs/m84036_250809_035451_s4.bc2148_hbb.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-51/call-run_paraphase/out/m84036_250809_035451_s4.bc2148_paraphase/m84036_250809_035451_s4.bc2148_paraphase_vcfs/m84036_250809_035451_s4.bc2148_rpgr.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-51/call-run_paraphase/out/m84036_250809_035451_s4.bc2148_paraphase/m84036_250809_035451_s4.bc2148_paraphase_vcfs/m84036_250809_035451_s4.bc2148_smn1.vcf"], "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-51/call-run_paraphase/out/m84036_250809_035451_s4.bc2148_paraphase/m84036_250809_035451_s4.bc2148.paraphase.json", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-51/call-run_paraphase/out/m84036_250809_035451_s4.bc2148_paraphase/m84036_250809_035451_s4.bc2148.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-51/call-run_paraphase/out/m84036_250809_035451_s4.bc2148_paraphase/m84036_250809_035451_s4.bc2148.paraphase.bam"}
2025-09-15 20:30:08.590 wdl.w:ptcp.w:call-paraphase-51 NOTICE ready :: job: "call-call_f8", callee: "call_f8"
2025-09-15 20:30:08.590 wdl.w:ptcp.w:call-paraphase-51 INFO input :: job: "call-call_f8", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "out_prefix": "m84036_250809_035451_s4.bc2148", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-51/call-run_paraphase/out/m84036_250809_035451_s4.bc2148_paraphase/m84036_250809_035451_s4.bc2148.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-51/call-run_paraphase/out/m84036_250809_035451_s4.bc2148_paraphase/m84036_250809_035451_s4.bc2148.paraphase.bam", "sex": "F"}
2025-09-15 20:30:08.590 wdl.w:ptcp.w:call-paraphase-51 INFO visit :: node: "output-havanno_json", values: {"havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-51/call-run_paraphase/out/m84036_250809_035451_s4.bc2148.havanno.json"}
2025-09-15 20:30:08.591 wdl.w:ptcp.w:call-paraphase-51 INFO visit :: node: "output-paraphase_bam", values: {"paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-51/call-run_paraphase/out/m84036_250809_035451_s4.bc2148_paraphase/m84036_250809_035451_s4.bc2148.paraphase.bam"}
2025-09-15 20:30:08.591 wdl.w:ptcp.w:call-paraphase-51 INFO visit :: node: "output-paraphase_bam_bai", values: {"paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-51/call-run_paraphase/out/m84036_250809_035451_s4.bc2148_paraphase/m84036_250809_035451_s4.bc2148.paraphase.bam.bai"}
2025-09-15 20:30:08.591 wdl.w:ptcp.w:call-paraphase-51 INFO visit :: node: "output-paraphase_json", values: {"paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-51/call-run_paraphase/out/m84036_250809_035451_s4.bc2148_paraphase/m84036_250809_035451_s4.bc2148.paraphase.json"}
2025-09-15 20:30:08.591 wdl.w:ptcp.w:call-paraphase-51 INFO visit :: node: "output-paraphase_vcfs", values: {"paraphase_vcfs": ["/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-51/call-run_paraphase/out/m84036_250809_035451_s4.bc2148_paraphase/m84036_250809_035451_s4.bc2148_paraphase_vcfs/m84036_250809_035451_s4.bc2148_cyp21.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-51/call-run_paraphase/out/m84036_250809_035451_s4.bc2148_paraphase/m84036_250809_035451_s4.bc2148_paraphase_vcfs/m84036_250809_035451_s4.bc2148_f8inv1.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-51/call-run_paraphase/out/m84036_250809_035451_s4.bc2148_paraphase/m84036_250809_035451_s4.bc2148_paraphase_vcfs/m84036_250809_035451_s4.bc2148_f8inv22.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-51/call-run_paraphase/out/m84036_250809_035451_s4.bc2148_paraphase/m84036_250809_035451_s4.bc2148_paraphase_vcfs/m84036_250809_035451_s4.bc2148_gba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-51/call-run_paraphase/out/m84036_250809_035451_s4.bc2148_paraphase/m84036_250809_035451_s4.bc2148_paraphase_vcfs/m84036_250809_035451_s4.bc2148_hba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-51/call-run_paraphase/out/m84036_250809_035451_s4.bc2148_paraphase/m84036_250809_035451_s4.bc2148_paraphase_vcfs/m84036_250809_035451_s4.bc2148_hbb.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-51/call-run_paraphase/out/m84036_250809_035451_s4.bc2148_paraphase/m84036_250809_035451_s4.bc2148_paraphase_vcfs/m84036_250809_035451_s4.bc2148_rpgr.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-51/call-run_paraphase/out/m84036_250809_035451_s4.bc2148_paraphase/m84036_250809_035451_s4.bc2148_paraphase_vcfs/m84036_250809_035451_s4.bc2148_smn1.vcf"]}
2025-09-15 20:30:08.598 wdl.w:ptcp.w:call-paraphase-51.t:call-call_f8 NOTICE task setup :: name: "call_f8", source: "./paraphase.wdl", line: 232, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-51/call-call_f8", thread: 140606575711808
2025-09-15 20:30:08.615 wdl.w:ptcp.w:call-paraphase-51.t:call-call_f8 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:30:08.616 wdl.w:ptcp.w:call-paraphase-51.t:call-call_f8 INFO input :: name: "genome_version", value: "38"
2025-09-15 20:30:08.616 wdl.w:ptcp.w:call-paraphase-51.t:call-call_f8 INFO input :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2148"
2025-09-15 20:30:08.616 wdl.w:ptcp.w:call-paraphase-51.t:call-call_f8 INFO input :: name: "paraphase_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2148.paraphase.bam.bai"
2025-09-15 20:30:08.616 wdl.w:ptcp.w:call-paraphase-51.t:call-call_f8 INFO input :: name: "paraphase_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2148.paraphase.bam"
2025-09-15 20:30:08.616 wdl.w:ptcp.w:call-paraphase-51.t:call-call_f8 INFO input :: name: "sex", value: "F"
2025-09-15 20:30:08.616 wdl.w:ptcp.w:call-paraphase-51.t:call-call_f8 INFO eval :: name: "threads", value: 1
2025-09-15 20:30:08.616 wdl.w:ptcp.w:call-paraphase-51.t:call-call_f8 INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:30:08.616 wdl.w:ptcp.w:call-paraphase-51.t:call-call_f8 INFO eval :: name: "disk_size", value: 11
2025-09-15 20:30:08.616 wdl.w:ptcp.w:call-paraphase-51.t:call-call_f8 INFO eval :: name: "sample_sex", value: "F"
2025-09-15 20:30:08.617 wdl.w:ptcp.w:call-paraphase-51.t:call-call_f8 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:30:08.617 wdl.w:ptcp.w:call-paraphase-51.t:call-call_f8 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:30:08.617 wdl.w:ptcp.w:call-paraphase-51.t:call-call_f8 INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:30:08.617 wdl.w:ptcp.w:call-paraphase-51.t:call-call_f8 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:30:08.657 wdl.w:ptcp.w:call-paraphase-51.t:call-call_f8 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 8, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-51/call-call_f8/_singularity_tmpdir_h7lkkqns"
2025-09-15 20:30:08.657 wdl.w:ptcp.w:call-paraphase-51.t:call-call_f8 INFO Slurm invocation: srun --job-name call-call_f8 --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-51/call-call_f8/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-51/call-call_f8/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-51/call-call_f8/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-51/call-call_f8/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-51/call-run_paraphase/out/m84036_250809_035451_s4.bc2148_paraphase/m84036_250809_035451_s4.bc2148.paraphase.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2148.paraphase.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-51/call-run_paraphase/out/m84036_250809_035451_s4.bc2148_paraphase/m84036_250809_035451_s4.bc2148.paraphase.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2148.paraphase.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-51/call-call_f8/_singularity_tmpdir_h7lkkqns/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-51/call-call_f8/_singularity_tmpdir_h7lkkqns/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:30:08.663 wdl.w:ptcp.w:call-paraphase-51.t:call-call_f8 NOTICE slurm_singularity run :: pid: 1209998, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-51/call-call_f8/slurm_singularity.log.txt"
2025-09-15 20:30:09.670 wdl.w:ptcp.w:call-paraphase-51.t:call-call_f8.slurm_singularity INFO srun: job 51798295 queued and waiting for resources
2025-09-15 20:30:09.671 wdl.w:ptcp.w:call-paraphase-51.t:call-call_f8.slurm_singularity INFO srun: job 51798295 has been allocated resources
2025-09-15 20:30:09.671 wdl.w:ptcp.w:call-paraphase-51.t:call-call_f8.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:30:10.686 wdl.w:ptcp.w:call-paraphase-51.t:call-call_f8 INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2148.f8inversion.vcf"
2025-09-15 20:30:10.689 wdl.w:ptcp.w:call-paraphase-51.t:call-call_f8 INFO output :: name: "json", value: "m84036_250809_035451_s4.bc2148.f8inversion.json"
2025-09-15 20:30:10.759 wdl.w:ptcp.w:call-paraphase-51.t:call-call_f8 NOTICE done
2025-09-15 20:30:10.790 wdl.w:ptcp.w:call-paraphase-51 NOTICE finish :: job: "call-call_f8"
2025-09-15 20:30:10.790 wdl.w:ptcp.w:call-paraphase-51 INFO output :: job: "call-call_f8", values: {"json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-51/call-call_f8/out/m84036_250809_035451_s4.bc2148.f8inversion.json", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-51/call-call_f8/out/m84036_250809_035451_s4.bc2148.f8inversion.vcf"}
2025-09-15 20:30:10.790 wdl.w:ptcp.w:call-paraphase-51 INFO visit :: node: "output-f8_json", values: {"f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-51/call-call_f8/out/m84036_250809_035451_s4.bc2148.f8inversion.json"}
2025-09-15 20:30:10.791 wdl.w:ptcp.w:call-paraphase-51 INFO visit :: node: "output-f8_vcf", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-51/call-call_f8/out/m84036_250809_035451_s4.bc2148.f8inversion.vcf"}
2025-09-15 20:30:10.791 wdl.w:ptcp.w:call-paraphase-51 INFO visit :: node: "outputs", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-51/call-call_f8/out/m84036_250809_035451_s4.bc2148.f8inversion.vcf", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-51/call-run_paraphase/out/m84036_250809_035451_s4.bc2148_paraphase/m84036_250809_035451_s4.bc2148.paraphase.json", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-51/call-run_paraphase/out/m84036_250809_035451_s4.bc2148_paraphase/m84036_250809_035451_s4.bc2148.paraphase.bam", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-51/call-run_paraphase/out/m84036_250809_035451_s4.bc2148_paraphase/m84036_250809_035451_s4.bc2148.paraphase.bam.bai", "paraphase_vcfs": ["/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-51/call-run_paraphase/out/m84036_250809_035451_s4.bc2148_paraphase/m84036_250809_035451_s4.bc2148_paraphase_vcfs/m84036_250809_035451_s4.bc2148_cyp21.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-51/call-run_paraphase/out/m84036_250809_035451_s4.bc2148_paraphase/m84036_250809_035451_s4.bc2148_paraphase_vcfs/m84036_250809_035451_s4.bc2148_f8inv1.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-51/call-run_paraphase/out/m84036_250809_035451_s4.bc2148_paraphase/m84036_250809_035451_s4.bc2148_paraphase_vcfs/m84036_250809_035451_s4.bc2148_f8inv22.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-51/call-run_paraphase/out/m84036_250809_035451_s4.bc2148_paraphase/m84036_250809_035451_s4.bc2148_paraphase_vcfs/m84036_250809_035451_s4.bc2148_gba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-51/call-run_paraphase/out/m84036_250809_035451_s4.bc2148_paraphase/m84036_250809_035451_s4.bc2148_paraphase_vcfs/m84036_250809_035451_s4.bc2148_hba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-51/call-run_paraphase/out/m84036_250809_035451_s4.bc2148_paraphase/m84036_250809_035451_s4.bc2148_paraphase_vcfs/m84036_250809_035451_s4.bc2148_hbb.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-51/call-run_paraphase/out/m84036_250809_035451_s4.bc2148_paraphase/m84036_250809_035451_s4.bc2148_paraphase_vcfs/m84036_250809_035451_s4.bc2148_rpgr.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-51/call-run_paraphase/out/m84036_250809_035451_s4.bc2148_paraphase/m84036_250809_035451_s4.bc2148_paraphase_vcfs/m84036_250809_035451_s4.bc2148_smn1.vcf"], "havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-51/call-run_paraphase/out/m84036_250809_035451_s4.bc2148.havanno.json", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-51/call-call_f8/out/m84036_250809_035451_s4.bc2148.f8inversion.json"}
2025-09-15 20:30:10.900 wdl.w:ptcp.w:call-paraphase-51 NOTICE done
2025-09-15 20:30:10.905 wdl.w:ptcp NOTICE finish :: job: "call-paraphase-51"
2025-09-15 20:30:10.905 wdl.w:ptcp INFO output :: job: "call-paraphase-51", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-51/out/m84036_250809_035451_s4.bc2148.f8inversion.vcf", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-51/out/m84036_250809_035451_s4.bc2148_paraphase/m84036_250809_035451_s4.bc2148.paraphase.json", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-51/out/m84036_250809_035451_s4.bc2148_paraphase/m84036_250809_035451_s4.bc2148.paraphase.bam", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-51/out/m84036_250809_035451_s4.bc2148_paraphase/m84036_250809_035451_s4.bc2148.paraphase.bam.bai", "paraphase_vcfs": ["/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-51/out/m84036_250809_035451_s4.bc2148_paraphase/m84036_250809_035451_s4.bc2148_paraphase_vcfs/m84036_250809_035451_s4.bc2148_cyp21.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-51/out/m84036_250809_035451_s4.bc2148_paraphase/m84036_250809_035451_s4.bc2148_paraphase_vcfs/m84036_250809_035451_s4.bc2148_f8inv1.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-51/out/m84036_250809_035451_s4.bc2148_paraphase/m84036_250809_035451_s4.bc2148_paraphase_vcfs/m84036_250809_035451_s4.bc2148_f8inv22.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-51/out/m84036_250809_035451_s4.bc2148_paraphase/m84036_250809_035451_s4.bc2148_paraphase_vcfs/m84036_250809_035451_s4.bc2148_gba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-51/out/m84036_250809_035451_s4.bc2148_paraphase/m84036_250809_035451_s4.bc2148_paraphase_vcfs/m84036_250809_035451_s4.bc2148_hba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-51/out/m84036_250809_035451_s4.bc2148_paraphase/m84036_250809_035451_s4.bc2148_paraphase_vcfs/m84036_250809_035451_s4.bc2148_hbb.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-51/out/m84036_250809_035451_s4.bc2148_paraphase/m84036_250809_035451_s4.bc2148_paraphase_vcfs/m84036_250809_035451_s4.bc2148_rpgr.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-51/out/m84036_250809_035451_s4.bc2148_paraphase/m84036_250809_035451_s4.bc2148_paraphase_vcfs/m84036_250809_035451_s4.bc2148_smn1.vcf"], "havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-51/out/m84036_250809_035451_s4.bc2148.havanno.json", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-51/out/m84036_250809_035451_s4.bc2148.f8inversion.json"}
2025-09-15 20:30:10.906 wdl.w:ptcp NOTICE ready :: job: "call-tar_outputs-51", callee: "tar_outputs"
2025-09-15 20:30:10.906 wdl.w:ptcp INFO input :: job: "call-tar_outputs-51", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "sawfish_vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-51/out/m84036_250809_035451_s4.bc2148_sawfish/m84036_250809_035451_s4.bc2148.sv.vcf.gz.tbi", "sawfish_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-51/out/m84036_250809_035451_s4.bc2148_sawfish/m84036_250809_035451_s4.bc2148.sv.vcf.gz", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-51/out/m84036_250809_035451_s4.bc2148.f8inversion.json", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-51/out/m84036_250809_035451_s4.bc2148_paraphase/m84036_250809_035451_s4.bc2148.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-51/out/m84036_250809_035451_s4.bc2148_paraphase/m84036_250809_035451_s4.bc2148.paraphase.bam", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-51/out/m84036_250809_035451_s4.bc2148_paraphase/m84036_250809_035451_s4.bc2148.paraphase.json", "trgt_spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-51/out/m84036_250809_035451_s4.bc2148.trgt.sorted.spanning.bam.bai", "trgt_spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-51/out/m84036_250809_035451_s4.bc2148.trgt.sorted.spanning.bam", "trgt_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-51/out/m84036_250809_035451_s4.bc2148.trgt.vcf", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-51/out/m84036_250809_035451_s4.bc2148.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-51/out/m84036_250809_035451_s4.bc2148.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2148"}
2025-09-15 20:30:10.912 wdl.w:ptcp.t:call-tar_outputs-51 NOTICE task setup :: name: "tar_outputs", source: "./common.wdl", line: 279, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-51", thread: 140607162938944
2025-09-15 20:30:10.931 wdl.w:ptcp.t:call-tar_outputs-51 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:30:10.931 wdl.w:ptcp.t:call-tar_outputs-51 INFO input :: name: "sawfish_vcf_tbi", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2148.sv.vcf.gz.tbi"
2025-09-15 20:30:10.931 wdl.w:ptcp.t:call-tar_outputs-51 INFO input :: name: "sawfish_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2148.sv.vcf.gz"
2025-09-15 20:30:10.931 wdl.w:ptcp.t:call-tar_outputs-51 INFO input :: name: "f8_json", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2148.f8inversion.json"
2025-09-15 20:30:10.931 wdl.w:ptcp.t:call-tar_outputs-51 INFO input :: name: "paraphase_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2148.paraphase.bam.bai"
2025-09-15 20:30:10.932 wdl.w:ptcp.t:call-tar_outputs-51 INFO input :: name: "paraphase_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2148.paraphase.bam"
2025-09-15 20:30:10.932 wdl.w:ptcp.t:call-tar_outputs-51 INFO input :: name: "paraphase_json", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2148.paraphase.json"
2025-09-15 20:30:10.932 wdl.w:ptcp.t:call-tar_outputs-51 INFO input :: name: "trgt_spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2148.trgt.sorted.spanning.bam.bai"
2025-09-15 20:30:10.932 wdl.w:ptcp.t:call-tar_outputs-51 INFO input :: name: "trgt_spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2148.trgt.sorted.spanning.bam"
2025-09-15 20:30:10.932 wdl.w:ptcp.t:call-tar_outputs-51 INFO input :: name: "trgt_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2148.trgt.vcf"
2025-09-15 20:30:10.932 wdl.w:ptcp.t:call-tar_outputs-51 INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2148.mapped.bam.bai"
2025-09-15 20:30:10.932 wdl.w:ptcp.t:call-tar_outputs-51 INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2148.mapped.bam"
2025-09-15 20:30:10.932 wdl.w:ptcp.t:call-tar_outputs-51 INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2148"
2025-09-15 20:30:10.932 wdl.w:ptcp.t:call-tar_outputs-51 INFO eval :: name: "threads", value: 1
2025-09-15 20:30:10.932 wdl.w:ptcp.t:call-tar_outputs-51 INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:30:10.932 wdl.w:ptcp.t:call-tar_outputs-51 INFO eval :: name: "disk_size", value: 6
2025-09-15 20:30:10.932 wdl.w:ptcp.t:call-tar_outputs-51 INFO eval :: name: "output_tarball", value: "m84036_250809_035451_s4.bc2148.tar"
2025-09-15 20:30:10.933 wdl.w:ptcp.t:call-tar_outputs-51 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:30:10.933 wdl.w:ptcp.t:call-tar_outputs-51 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:30:10.933 wdl.w:ptcp.t:call-tar_outputs-51 INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:30:10.933 wdl.w:ptcp.t:call-tar_outputs-51 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:30:11.015 wdl.w:ptcp.t:call-tar_outputs-51 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 17, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-51/_singularity_tmpdir_l1evg075"
2025-09-15 20:30:11.015 wdl.w:ptcp.t:call-tar_outputs-51 INFO Slurm invocation: srun --job-name call-tar_outputs-51 --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-51/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-51/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-51/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-51/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-51/out/m84036_250809_035451_s4.bc2148.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2148.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-51/out/m84036_250809_035451_s4.bc2148.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2148.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-51/out/m84036_250809_035451_s4.bc2148.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2148.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-51/out/m84036_250809_035451_s4.bc2148_paraphase/m84036_250809_035451_s4.bc2148.paraphase.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2148.paraphase.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-51/out/m84036_250809_035451_s4.bc2148_paraphase/m84036_250809_035451_s4.bc2148.paraphase.json:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2148.paraphase.json:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-51/out/m84036_250809_035451_s4.bc2148_paraphase/m84036_250809_035451_s4.bc2148.paraphase.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2148.paraphase.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-51/out/m84036_250809_035451_s4.bc2148.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2148.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-51/out/m84036_250809_035451_s4.bc2148.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2148.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-51/out/m84036_250809_035451_s4.bc2148_sawfish/m84036_250809_035451_s4.bc2148.sv.vcf.gz.tbi:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2148.sv.vcf.gz.tbi:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-51/out/m84036_250809_035451_s4.bc2148_sawfish/m84036_250809_035451_s4.bc2148.sv.vcf.gz:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2148.sv.vcf.gz:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-51/out/m84036_250809_035451_s4.bc2148.f8inversion.json:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2148.f8inversion.json:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-51/_singularity_tmpdir_l1evg075/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-51/_singularity_tmpdir_l1evg075/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:30:11.019 wdl.w:ptcp.t:call-tar_outputs-51 NOTICE slurm_singularity run :: pid: 1210098, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-51/slurm_singularity.log.txt"
2025-09-15 20:30:12.028 wdl.w:ptcp.t:call-tar_outputs-51.slurm_singularity INFO srun: job 51798296 queued and waiting for resources
2025-09-15 20:30:12.985 wdl.w:ptcp.w:call-paraphase-02.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for f8inv22 for sample m84036_250809_035451_s4.bc2099 at 2025-09-15 20:30:04.353979...
2025-09-15 20:30:12.986 wdl.w:ptcp.w:call-paraphase-02.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for f8inv22 for sample m84036_250809_035451_s4.bc2099 at 2025-09-15 20:30:04.355035...
2025-09-15 20:30:13.038 wdl.w:ptcp.t:call-tar_outputs-51.slurm_singularity INFO srun: job 51798296 has been allocated resources
2025-09-15 20:30:13.038 wdl.w:ptcp.t:call-tar_outputs-51.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:30:13.436 wdl.w:ptcp.t:call-tar_outputs-51 INFO output :: name: "sample_tarball", value: "m84036_250809_035451_s4.bc2148.tar"
2025-09-15 20:30:13.483 wdl.w:ptcp.t:call-tar_outputs-51 NOTICE done
2025-09-15 20:30:13.487 wdl.w:ptcp NOTICE finish :: job: "call-tar_outputs-51"
2025-09-15 20:30:13.487 wdl.w:ptcp INFO output :: job: "call-tar_outputs-51", values: {"sample_tarball": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-51/out/m84036_250809_035451_s4.bc2148.tar"}
2025-09-15 20:30:19.931 wdl.w:ptcp.w:call-paraphase-07.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for f8inv22 for sample m84036_250809_035451_s4.bc2104 at 2025-09-15 20:29:45.200854...
2025-09-15 20:30:19.932 wdl.w:ptcp.w:call-paraphase-07.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for f8inv22 for sample m84036_250809_035451_s4.bc2104 at 2025-09-15 20:29:45.201716...
2025-09-15 20:30:19.932 wdl.w:ptcp.w:call-paraphase-07.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for f8inv22 for sample m84036_250809_035451_s4.bc2104 at 2025-09-15 20:29:46.605895...
2025-09-15 20:30:19.932 wdl.w:ptcp.w:call-paraphase-07.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for f8inv22 for sample m84036_250809_035451_s4.bc2104 at 2025-09-15 20:29:53.409345...
2025-09-15 20:30:19.932 wdl.w:ptcp.w:call-paraphase-07.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for f8inv22 for sample m84036_250809_035451_s4.bc2104 at 2025-09-15 20:29:53.848893...
2025-09-15 20:30:19.932 wdl.w:ptcp.w:call-paraphase-07.t:call-run_paraphase.stderr VERBOSE INFO:root:Merging all bams for sample m84036_250809_035451_s4.bc2104 at 2025-09-15 20:30:15.580310...
2025-09-15 20:30:19.932 wdl.w:ptcp.w:call-paraphase-07.t:call-run_paraphase.stderr VERBOSE INFO:root:Writing to json for sample m84036_250809_035451_s4.bc2104 at 2025-09-15 20:30:19.164393...
2025-09-15 20:30:19.932 wdl.w:ptcp.w:call-paraphase-07.t:call-run_paraphase.stderr VERBOSE INFO:root:Completed Paraphase analysis at 2025-09-15 20:30:19.341619...
2025-09-15 20:30:19.932 wdl.w:ptcp.w:call-paraphase-07.t:call-run_paraphase.stderr VERBOSE [2025-09-15 20:30:19,704] INFO - reading variant list from /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/variant_list.GRCh38.vcf
2025-09-15 20:30:19.933 wdl.w:ptcp.w:call-paraphase-07.t:call-run_paraphase.stderr VERBOSE [2025-09-15 20:30:19,716] INFO - reading paraphase variant list from m84036_250809_035451_s4.bc2104_paraphase/m84036_250809_035451_s4.bc2104_paraphase_vcfs/m84036_250809_035451_s4.bc2104_cyp21.vcf
2025-09-15 20:30:19.933 wdl.w:ptcp.w:call-paraphase-07.t:call-run_paraphase.stderr VERBOSE [2025-09-15 20:30:19,721] INFO - finding matches of paraphase variants in the VCF
2025-09-15 20:30:19.933 wdl.w:ptcp.w:call-paraphase-07.t:call-run_paraphase.stderr VERBOSE [2025-09-15 20:30:19,722] INFO - writing output and wrapping up...
2025-09-15 20:30:19.933 wdl.w:ptcp.w:call-paraphase-07.t:call-run_paraphase.stderr VERBOSE [2025-09-15 20:30:19,722] INFO - reading paraphase variant list from m84036_250809_035451_s4.bc2104_paraphase/m84036_250809_035451_s4.bc2104_paraphase_vcfs/m84036_250809_035451_s4.bc2104_f8inv1.vcf
2025-09-15 20:30:19.933 wdl.w:ptcp.w:call-paraphase-07.t:call-run_paraphase.stderr VERBOSE [2025-09-15 20:30:19,726] INFO - finding matches of paraphase variants in the VCF
2025-09-15 20:30:19.933 wdl.w:ptcp.w:call-paraphase-07.t:call-run_paraphase.stderr VERBOSE [2025-09-15 20:30:19,726] INFO - writing output and wrapping up...
2025-09-15 20:30:19.933 wdl.w:ptcp.w:call-paraphase-07.t:call-run_paraphase.stderr VERBOSE [2025-09-15 20:30:19,726] INFO - reading paraphase variant list from m84036_250809_035451_s4.bc2104_paraphase/m84036_250809_035451_s4.bc2104_paraphase_vcfs/m84036_250809_035451_s4.bc2104_f8inv22.vcf
2025-09-15 20:30:19.933 wdl.w:ptcp.w:call-paraphase-07.t:call-run_paraphase.stderr VERBOSE [2025-09-15 20:30:19,730] INFO - finding matches of paraphase variants in the VCF
2025-09-15 20:30:19.933 wdl.w:ptcp.w:call-paraphase-07.t:call-run_paraphase.stderr VERBOSE [2025-09-15 20:30:19,731] INFO - writing output and wrapping up...
2025-09-15 20:30:19.933 wdl.w:ptcp.w:call-paraphase-07.t:call-run_paraphase.stderr VERBOSE [2025-09-15 20:30:19,731] INFO - reading paraphase variant list from m84036_250809_035451_s4.bc2104_paraphase/m84036_250809_035451_s4.bc2104_paraphase_vcfs/m84036_250809_035451_s4.bc2104_gba.vcf
2025-09-15 20:30:19.933 wdl.w:ptcp.w:call-paraphase-07.t:call-run_paraphase.stderr VERBOSE [2025-09-15 20:30:19,738] INFO - finding matches of paraphase variants in the VCF
2025-09-15 20:30:19.933 wdl.w:ptcp.w:call-paraphase-07.t:call-run_paraphase.stderr VERBOSE [2025-09-15 20:30:19,739] INFO - writing output and wrapping up...
2025-09-15 20:30:19.933 wdl.w:ptcp.w:call-paraphase-07.t:call-run_paraphase.stderr VERBOSE [2025-09-15 20:30:19,739] INFO - reading paraphase variant list from m84036_250809_035451_s4.bc2104_paraphase/m84036_250809_035451_s4.bc2104_paraphase_vcfs/m84036_250809_035451_s4.bc2104_hba.vcf
2025-09-15 20:30:19.933 wdl.w:ptcp.w:call-paraphase-07.t:call-run_paraphase.stderr VERBOSE [2025-09-15 20:30:19,744] INFO - finding matches of paraphase variants in the VCF
2025-09-15 20:30:19.933 wdl.w:ptcp.w:call-paraphase-07.t:call-run_paraphase.stderr VERBOSE [2025-09-15 20:30:19,745] INFO - writing output and wrapping up...
2025-09-15 20:30:19.933 wdl.w:ptcp.w:call-paraphase-07.t:call-run_paraphase.stderr VERBOSE [2025-09-15 20:30:19,745] INFO - reading paraphase variant list from m84036_250809_035451_s4.bc2104_paraphase/m84036_250809_035451_s4.bc2104_paraphase_vcfs/m84036_250809_035451_s4.bc2104_hbb.vcf
2025-09-15 20:30:19.933 wdl.w:ptcp.w:call-paraphase-07.t:call-run_paraphase.stderr VERBOSE [2025-09-15 20:30:19,751] INFO - finding matches of paraphase variants in the VCF
2025-09-15 20:30:19.933 wdl.w:ptcp.w:call-paraphase-07.t:call-run_paraphase.stderr VERBOSE [2025-09-15 20:30:19,751] INFO - writing output and wrapping up...
2025-09-15 20:30:19.933 wdl.w:ptcp.w:call-paraphase-07.t:call-run_paraphase.stderr VERBOSE [2025-09-15 20:30:19,751] INFO - reading paraphase variant list from m84036_250809_035451_s4.bc2104_paraphase/m84036_250809_035451_s4.bc2104_paraphase_vcfs/m84036_250809_035451_s4.bc2104_rpgr.vcf
2025-09-15 20:30:19.933 wdl.w:ptcp.w:call-paraphase-07.t:call-run_paraphase.stderr VERBOSE [2025-09-15 20:30:19,755] INFO - finding matches of paraphase variants in the VCF
2025-09-15 20:30:19.933 wdl.w:ptcp.w:call-paraphase-07.t:call-run_paraphase.stderr VERBOSE [2025-09-15 20:30:19,755] INFO - writing output and wrapping up...
2025-09-15 20:30:19.933 wdl.w:ptcp.w:call-paraphase-07.t:call-run_paraphase.stderr VERBOSE [2025-09-15 20:30:19,755] INFO - reading paraphase variant list from m84036_250809_035451_s4.bc2104_paraphase/m84036_250809_035451_s4.bc2104_paraphase_vcfs/m84036_250809_035451_s4.bc2104_smn1.vcf
2025-09-15 20:30:19.934 wdl.w:ptcp.w:call-paraphase-07.t:call-run_paraphase.stderr VERBOSE [2025-09-15 20:30:19,758] INFO - finding matches of paraphase variants in the VCF
2025-09-15 20:30:19.934 wdl.w:ptcp.w:call-paraphase-07.t:call-run_paraphase.stderr VERBOSE [2025-09-15 20:30:19,759] INFO - writing output and wrapping up...
2025-09-15 20:30:19.969 wdl.w:ptcp.w:call-paraphase-07.t:call-run_paraphase INFO output :: name: "paraphase_bam", value: "m84036_250809_035451_s4.bc2104_paraphase/m84036_250809_035451_s4.bc2104.paraphase.bam"
2025-09-15 20:30:19.972 wdl.w:ptcp.w:call-paraphase-07.t:call-run_paraphase INFO output :: name: "paraphase_bam_bai", value: "m84036_250809_035451_s4.bc2104_paraphase/m84036_250809_035451_s4.bc2104.paraphase.bam.bai"
2025-09-15 20:30:19.973 wdl.w:ptcp.w:call-paraphase-07.t:call-run_paraphase INFO output :: name: "paraphase_json", value: "m84036_250809_035451_s4.bc2104_paraphase/m84036_250809_035451_s4.bc2104.paraphase.json"
2025-09-15 20:30:19.977 wdl.w:ptcp.w:call-paraphase-07.t:call-run_paraphase INFO output :: name: "paraphase_vcfs", value: ["/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2104_paraphase/m84036_250809_035451_s4.bc2104_paraphase_vcfs/m84036_250809_035451_s4.bc2104_cyp21.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2104_paraphase/m84036_250809_035451_s4.bc2104_paraphase_vcfs/m84036_250809_035451_s4.bc2104_f8inv1.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2104_paraphase/m84036_250809_035451_s4.bc2104_paraphase_vcfs/m84036_250809_035451_s4.bc2104_f8inv22.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2104_paraphase/m84036_250809_035451_s4.bc2104_paraphase_vcfs/m84036_250809_035451_s4.bc2104_gba.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2104_paraphase/m84036_250809_035451_s4.bc2104_paraphase_vcfs/m84036_250809_035451_s4.bc2104_hba.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2104_paraphase/m84036_250809_035451_s4.bc2104_paraphase_vcfs/m84036_250809_035451_s4.bc2104_hbb.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2104_paraphase/m84036_250809_035451_s4.bc2104_paraphase_vcfs/m84036_250809_035451_s4.bc2104_rpgr.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2104_paraphase/m84036_250809_035451_s4.bc2104_paraphase_vcfs/m84036_250809_035451_s4.bc2104_smn1.vcf"]
2025-09-15 20:30:19.979 wdl.w:ptcp.w:call-paraphase-07.t:call-run_paraphase INFO output :: name: "havanno_json", value: "m84036_250809_035451_s4.bc2104.havanno.json"
2025-09-15 20:30:20.123 wdl.w:ptcp.w:call-paraphase-07.t:call-run_paraphase NOTICE done
2025-09-15 20:30:20.128 wdl.w:ptcp.w:call-paraphase-07 NOTICE finish :: job: "call-run_paraphase"
2025-09-15 20:30:20.129 wdl.w:ptcp.w:call-paraphase-07 INFO output :: job: "call-run_paraphase", values: {"havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-07/call-run_paraphase/out/m84036_250809_035451_s4.bc2104.havanno.json", "paraphase_vcfs": ["/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-07/call-run_paraphase/out/m84036_250809_035451_s4.bc2104_paraphase/m84036_250809_035451_s4.bc2104_paraphase_vcfs/m84036_250809_035451_s4.bc2104_cyp21.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-07/call-run_paraphase/out/m84036_250809_035451_s4.bc2104_paraphase/m84036_250809_035451_s4.bc2104_paraphase_vcfs/m84036_250809_035451_s4.bc2104_f8inv1.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-07/call-run_paraphase/out/m84036_250809_035451_s4.bc2104_paraphase/m84036_250809_035451_s4.bc2104_paraphase_vcfs/m84036_250809_035451_s4.bc2104_f8inv22.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-07/call-run_paraphase/out/m84036_250809_035451_s4.bc2104_paraphase/m84036_250809_035451_s4.bc2104_paraphase_vcfs/m84036_250809_035451_s4.bc2104_gba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-07/call-run_paraphase/out/m84036_250809_035451_s4.bc2104_paraphase/m84036_250809_035451_s4.bc2104_paraphase_vcfs/m84036_250809_035451_s4.bc2104_hba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-07/call-run_paraphase/out/m84036_250809_035451_s4.bc2104_paraphase/m84036_250809_035451_s4.bc2104_paraphase_vcfs/m84036_250809_035451_s4.bc2104_hbb.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-07/call-run_paraphase/out/m84036_250809_035451_s4.bc2104_paraphase/m84036_250809_035451_s4.bc2104_paraphase_vcfs/m84036_250809_035451_s4.bc2104_rpgr.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-07/call-run_paraphase/out/m84036_250809_035451_s4.bc2104_paraphase/m84036_250809_035451_s4.bc2104_paraphase_vcfs/m84036_250809_035451_s4.bc2104_smn1.vcf"], "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-07/call-run_paraphase/out/m84036_250809_035451_s4.bc2104_paraphase/m84036_250809_035451_s4.bc2104.paraphase.json", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-07/call-run_paraphase/out/m84036_250809_035451_s4.bc2104_paraphase/m84036_250809_035451_s4.bc2104.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-07/call-run_paraphase/out/m84036_250809_035451_s4.bc2104_paraphase/m84036_250809_035451_s4.bc2104.paraphase.bam"}
2025-09-15 20:30:20.130 wdl.w:ptcp.w:call-paraphase-07 NOTICE ready :: job: "call-call_f8", callee: "call_f8"
2025-09-15 20:30:20.130 wdl.w:ptcp.w:call-paraphase-07 INFO input :: job: "call-call_f8", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "out_prefix": "m84036_250809_035451_s4.bc2104", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-07/call-run_paraphase/out/m84036_250809_035451_s4.bc2104_paraphase/m84036_250809_035451_s4.bc2104.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-07/call-run_paraphase/out/m84036_250809_035451_s4.bc2104_paraphase/m84036_250809_035451_s4.bc2104.paraphase.bam", "sex": "F"}
2025-09-15 20:30:20.131 wdl.w:ptcp.w:call-paraphase-07 INFO visit :: node: "output-havanno_json", values: {"havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-07/call-run_paraphase/out/m84036_250809_035451_s4.bc2104.havanno.json"}
2025-09-15 20:30:20.131 wdl.w:ptcp.w:call-paraphase-07 INFO visit :: node: "output-paraphase_bam", values: {"paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-07/call-run_paraphase/out/m84036_250809_035451_s4.bc2104_paraphase/m84036_250809_035451_s4.bc2104.paraphase.bam"}
2025-09-15 20:30:20.131 wdl.w:ptcp.w:call-paraphase-07 INFO visit :: node: "output-paraphase_bam_bai", values: {"paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-07/call-run_paraphase/out/m84036_250809_035451_s4.bc2104_paraphase/m84036_250809_035451_s4.bc2104.paraphase.bam.bai"}
2025-09-15 20:30:20.131 wdl.w:ptcp.w:call-paraphase-07 INFO visit :: node: "output-paraphase_json", values: {"paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-07/call-run_paraphase/out/m84036_250809_035451_s4.bc2104_paraphase/m84036_250809_035451_s4.bc2104.paraphase.json"}
2025-09-15 20:30:20.131 wdl.w:ptcp.w:call-paraphase-07 INFO visit :: node: "output-paraphase_vcfs", values: {"paraphase_vcfs": ["/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-07/call-run_paraphase/out/m84036_250809_035451_s4.bc2104_paraphase/m84036_250809_035451_s4.bc2104_paraphase_vcfs/m84036_250809_035451_s4.bc2104_cyp21.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-07/call-run_paraphase/out/m84036_250809_035451_s4.bc2104_paraphase/m84036_250809_035451_s4.bc2104_paraphase_vcfs/m84036_250809_035451_s4.bc2104_f8inv1.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-07/call-run_paraphase/out/m84036_250809_035451_s4.bc2104_paraphase/m84036_250809_035451_s4.bc2104_paraphase_vcfs/m84036_250809_035451_s4.bc2104_f8inv22.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-07/call-run_paraphase/out/m84036_250809_035451_s4.bc2104_paraphase/m84036_250809_035451_s4.bc2104_paraphase_vcfs/m84036_250809_035451_s4.bc2104_gba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-07/call-run_paraphase/out/m84036_250809_035451_s4.bc2104_paraphase/m84036_250809_035451_s4.bc2104_paraphase_vcfs/m84036_250809_035451_s4.bc2104_hba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-07/call-run_paraphase/out/m84036_250809_035451_s4.bc2104_paraphase/m84036_250809_035451_s4.bc2104_paraphase_vcfs/m84036_250809_035451_s4.bc2104_hbb.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-07/call-run_paraphase/out/m84036_250809_035451_s4.bc2104_paraphase/m84036_250809_035451_s4.bc2104_paraphase_vcfs/m84036_250809_035451_s4.bc2104_rpgr.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-07/call-run_paraphase/out/m84036_250809_035451_s4.bc2104_paraphase/m84036_250809_035451_s4.bc2104_paraphase_vcfs/m84036_250809_035451_s4.bc2104_smn1.vcf"]}
2025-09-15 20:30:20.136 wdl.w:ptcp.w:call-paraphase-07.t:call-call_f8 NOTICE task setup :: name: "call_f8", source: "./paraphase.wdl", line: 232, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-07/call-call_f8", thread: 140609310422592
2025-09-15 20:30:20.166 wdl.w:ptcp.w:call-paraphase-07.t:call-call_f8 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:30:20.166 wdl.w:ptcp.w:call-paraphase-07.t:call-call_f8 INFO input :: name: "genome_version", value: "38"
2025-09-15 20:30:20.166 wdl.w:ptcp.w:call-paraphase-07.t:call-call_f8 INFO input :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2104"
2025-09-15 20:30:20.166 wdl.w:ptcp.w:call-paraphase-07.t:call-call_f8 INFO input :: name: "paraphase_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2104.paraphase.bam.bai"
2025-09-15 20:30:20.166 wdl.w:ptcp.w:call-paraphase-07.t:call-call_f8 INFO input :: name: "paraphase_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2104.paraphase.bam"
2025-09-15 20:30:20.166 wdl.w:ptcp.w:call-paraphase-07.t:call-call_f8 INFO input :: name: "sex", value: "F"
2025-09-15 20:30:20.166 wdl.w:ptcp.w:call-paraphase-07.t:call-call_f8 INFO eval :: name: "threads", value: 1
2025-09-15 20:30:20.166 wdl.w:ptcp.w:call-paraphase-07.t:call-call_f8 INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:30:20.167 wdl.w:ptcp.w:call-paraphase-07.t:call-call_f8 INFO eval :: name: "disk_size", value: 11
2025-09-15 20:30:20.167 wdl.w:ptcp.w:call-paraphase-07.t:call-call_f8 INFO eval :: name: "sample_sex", value: "F"
2025-09-15 20:30:20.167 wdl.w:ptcp.w:call-paraphase-07.t:call-call_f8 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:30:20.167 wdl.w:ptcp.w:call-paraphase-07.t:call-call_f8 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:30:20.167 wdl.w:ptcp.w:call-paraphase-07.t:call-call_f8 INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:30:20.170 wdl.w:ptcp.w:call-paraphase-07.t:call-call_f8 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:30:20.213 wdl.w:ptcp.w:call-paraphase-07.t:call-call_f8 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 8, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-07/call-call_f8/_singularity_tmpdir_2t7z9pb0"
2025-09-15 20:30:20.213 wdl.w:ptcp.w:call-paraphase-07.t:call-call_f8 INFO Slurm invocation: srun --job-name call-call_f8 --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-07/call-call_f8/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-07/call-call_f8/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-07/call-call_f8/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-07/call-call_f8/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-07/call-run_paraphase/out/m84036_250809_035451_s4.bc2104_paraphase/m84036_250809_035451_s4.bc2104.paraphase.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2104.paraphase.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-07/call-run_paraphase/out/m84036_250809_035451_s4.bc2104_paraphase/m84036_250809_035451_s4.bc2104.paraphase.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2104.paraphase.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-07/call-call_f8/_singularity_tmpdir_2t7z9pb0/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-07/call-call_f8/_singularity_tmpdir_2t7z9pb0/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:30:20.217 wdl.w:ptcp.w:call-paraphase-07.t:call-call_f8 NOTICE slurm_singularity run :: pid: 1210202, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-07/call-call_f8/slurm_singularity.log.txt"
2025-09-15 20:30:21.228 wdl.w:ptcp.w:call-paraphase-07.t:call-call_f8.slurm_singularity INFO srun: job 51798314 queued and waiting for resources
2025-09-15 20:30:21.228 wdl.w:ptcp.w:call-paraphase-07.t:call-call_f8.slurm_singularity INFO srun: job 51798314 has been allocated resources
2025-09-15 20:30:21.228 wdl.w:ptcp.w:call-paraphase-07.t:call-call_f8.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:30:21.791 wdl.w:ptcp.w:call-paraphase-07.t:call-call_f8 INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2104.f8inversion.vcf"
2025-09-15 20:30:21.794 wdl.w:ptcp.w:call-paraphase-07.t:call-call_f8 INFO output :: name: "json", value: "m84036_250809_035451_s4.bc2104.f8inversion.json"
2025-09-15 20:30:21.853 wdl.w:ptcp.w:call-paraphase-07.t:call-call_f8 NOTICE done
2025-09-15 20:30:21.861 wdl.w:ptcp.w:call-paraphase-07 NOTICE finish :: job: "call-call_f8"
2025-09-15 20:30:21.861 wdl.w:ptcp.w:call-paraphase-07 INFO output :: job: "call-call_f8", values: {"json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-07/call-call_f8/out/m84036_250809_035451_s4.bc2104.f8inversion.json", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-07/call-call_f8/out/m84036_250809_035451_s4.bc2104.f8inversion.vcf"}
2025-09-15 20:30:21.861 wdl.w:ptcp.w:call-paraphase-07 INFO visit :: node: "output-f8_json", values: {"f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-07/call-call_f8/out/m84036_250809_035451_s4.bc2104.f8inversion.json"}
2025-09-15 20:30:21.861 wdl.w:ptcp.w:call-paraphase-07 INFO visit :: node: "output-f8_vcf", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-07/call-call_f8/out/m84036_250809_035451_s4.bc2104.f8inversion.vcf"}
2025-09-15 20:30:21.861 wdl.w:ptcp.w:call-paraphase-07 INFO visit :: node: "outputs", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-07/call-call_f8/out/m84036_250809_035451_s4.bc2104.f8inversion.vcf", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-07/call-run_paraphase/out/m84036_250809_035451_s4.bc2104_paraphase/m84036_250809_035451_s4.bc2104.paraphase.json", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-07/call-run_paraphase/out/m84036_250809_035451_s4.bc2104_paraphase/m84036_250809_035451_s4.bc2104.paraphase.bam", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-07/call-run_paraphase/out/m84036_250809_035451_s4.bc2104_paraphase/m84036_250809_035451_s4.bc2104.paraphase.bam.bai", "paraphase_vcfs": ["/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-07/call-run_paraphase/out/m84036_250809_035451_s4.bc2104_paraphase/m84036_250809_035451_s4.bc2104_paraphase_vcfs/m84036_250809_035451_s4.bc2104_cyp21.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-07/call-run_paraphase/out/m84036_250809_035451_s4.bc2104_paraphase/m84036_250809_035451_s4.bc2104_paraphase_vcfs/m84036_250809_035451_s4.bc2104_f8inv1.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-07/call-run_paraphase/out/m84036_250809_035451_s4.bc2104_paraphase/m84036_250809_035451_s4.bc2104_paraphase_vcfs/m84036_250809_035451_s4.bc2104_f8inv22.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-07/call-run_paraphase/out/m84036_250809_035451_s4.bc2104_paraphase/m84036_250809_035451_s4.bc2104_paraphase_vcfs/m84036_250809_035451_s4.bc2104_gba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-07/call-run_paraphase/out/m84036_250809_035451_s4.bc2104_paraphase/m84036_250809_035451_s4.bc2104_paraphase_vcfs/m84036_250809_035451_s4.bc2104_hba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-07/call-run_paraphase/out/m84036_250809_035451_s4.bc2104_paraphase/m84036_250809_035451_s4.bc2104_paraphase_vcfs/m84036_250809_035451_s4.bc2104_hbb.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-07/call-run_paraphase/out/m84036_250809_035451_s4.bc2104_paraphase/m84036_250809_035451_s4.bc2104_paraphase_vcfs/m84036_250809_035451_s4.bc2104_rpgr.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-07/call-run_paraphase/out/m84036_250809_035451_s4.bc2104_paraphase/m84036_250809_035451_s4.bc2104_paraphase_vcfs/m84036_250809_035451_s4.bc2104_smn1.vcf"], "havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-07/call-run_paraphase/out/m84036_250809_035451_s4.bc2104.havanno.json", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-07/call-call_f8/out/m84036_250809_035451_s4.bc2104.f8inversion.json"}
2025-09-15 20:30:21.971 wdl.w:ptcp.w:call-paraphase-07 NOTICE done
2025-09-15 20:30:21.977 wdl.w:ptcp NOTICE finish :: job: "call-paraphase-07"
2025-09-15 20:30:21.977 wdl.w:ptcp INFO output :: job: "call-paraphase-07", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-07/out/m84036_250809_035451_s4.bc2104.f8inversion.vcf", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-07/out/m84036_250809_035451_s4.bc2104_paraphase/m84036_250809_035451_s4.bc2104.paraphase.json", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-07/out/m84036_250809_035451_s4.bc2104_paraphase/m84036_250809_035451_s4.bc2104.paraphase.bam", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-07/out/m84036_250809_035451_s4.bc2104_paraphase/m84036_250809_035451_s4.bc2104.paraphase.bam.bai", "paraphase_vcfs": ["/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-07/out/m84036_250809_035451_s4.bc2104_paraphase/m84036_250809_035451_s4.bc2104_paraphase_vcfs/m84036_250809_035451_s4.bc2104_cyp21.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-07/out/m84036_250809_035451_s4.bc2104_paraphase/m84036_250809_035451_s4.bc2104_paraphase_vcfs/m84036_250809_035451_s4.bc2104_f8inv1.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-07/out/m84036_250809_035451_s4.bc2104_paraphase/m84036_250809_035451_s4.bc2104_paraphase_vcfs/m84036_250809_035451_s4.bc2104_f8inv22.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-07/out/m84036_250809_035451_s4.bc2104_paraphase/m84036_250809_035451_s4.bc2104_paraphase_vcfs/m84036_250809_035451_s4.bc2104_gba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-07/out/m84036_250809_035451_s4.bc2104_paraphase/m84036_250809_035451_s4.bc2104_paraphase_vcfs/m84036_250809_035451_s4.bc2104_hba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-07/out/m84036_250809_035451_s4.bc2104_paraphase/m84036_250809_035451_s4.bc2104_paraphase_vcfs/m84036_250809_035451_s4.bc2104_hbb.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-07/out/m84036_250809_035451_s4.bc2104_paraphase/m84036_250809_035451_s4.bc2104_paraphase_vcfs/m84036_250809_035451_s4.bc2104_rpgr.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-07/out/m84036_250809_035451_s4.bc2104_paraphase/m84036_250809_035451_s4.bc2104_paraphase_vcfs/m84036_250809_035451_s4.bc2104_smn1.vcf"], "havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-07/out/m84036_250809_035451_s4.bc2104.havanno.json", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-07/out/m84036_250809_035451_s4.bc2104.f8inversion.json"}
2025-09-15 20:30:21.978 wdl.w:ptcp NOTICE ready :: job: "call-tar_outputs-07", callee: "tar_outputs"
2025-09-15 20:30:21.978 wdl.w:ptcp INFO input :: job: "call-tar_outputs-07", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "sawfish_vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-07/out/m84036_250809_035451_s4.bc2104_sawfish/m84036_250809_035451_s4.bc2104.sv.vcf.gz.tbi", "sawfish_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-07/out/m84036_250809_035451_s4.bc2104_sawfish/m84036_250809_035451_s4.bc2104.sv.vcf.gz", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-07/out/m84036_250809_035451_s4.bc2104.f8inversion.json", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-07/out/m84036_250809_035451_s4.bc2104_paraphase/m84036_250809_035451_s4.bc2104.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-07/out/m84036_250809_035451_s4.bc2104_paraphase/m84036_250809_035451_s4.bc2104.paraphase.bam", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-07/out/m84036_250809_035451_s4.bc2104_paraphase/m84036_250809_035451_s4.bc2104.paraphase.json", "trgt_spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-07/out/m84036_250809_035451_s4.bc2104.trgt.sorted.spanning.bam.bai", "trgt_spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-07/out/m84036_250809_035451_s4.bc2104.trgt.sorted.spanning.bam", "trgt_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-07/out/m84036_250809_035451_s4.bc2104.trgt.vcf", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-07/out/m84036_250809_035451_s4.bc2104.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-07/out/m84036_250809_035451_s4.bc2104.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2104"}
2025-09-15 20:30:21.987 wdl.w:ptcp.t:call-tar_outputs-07 NOTICE task setup :: name: "tar_outputs", source: "./common.wdl", line: 279, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-07", thread: 140611969599040
2025-09-15 20:30:22.009 wdl.w:ptcp.t:call-tar_outputs-07 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:30:22.009 wdl.w:ptcp.t:call-tar_outputs-07 INFO input :: name: "sawfish_vcf_tbi", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2104.sv.vcf.gz.tbi"
2025-09-15 20:30:22.009 wdl.w:ptcp.t:call-tar_outputs-07 INFO input :: name: "sawfish_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2104.sv.vcf.gz"
2025-09-15 20:30:22.009 wdl.w:ptcp.t:call-tar_outputs-07 INFO input :: name: "f8_json", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2104.f8inversion.json"
2025-09-15 20:30:22.009 wdl.w:ptcp.t:call-tar_outputs-07 INFO input :: name: "paraphase_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2104.paraphase.bam.bai"
2025-09-15 20:30:22.009 wdl.w:ptcp.t:call-tar_outputs-07 INFO input :: name: "paraphase_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2104.paraphase.bam"
2025-09-15 20:30:22.010 wdl.w:ptcp.t:call-tar_outputs-07 INFO input :: name: "paraphase_json", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2104.paraphase.json"
2025-09-15 20:30:22.010 wdl.w:ptcp.t:call-tar_outputs-07 INFO input :: name: "trgt_spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2104.trgt.sorted.spanning.bam.bai"
2025-09-15 20:30:22.010 wdl.w:ptcp.t:call-tar_outputs-07 INFO input :: name: "trgt_spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2104.trgt.sorted.spanning.bam"
2025-09-15 20:30:22.010 wdl.w:ptcp.t:call-tar_outputs-07 INFO input :: name: "trgt_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2104.trgt.vcf"
2025-09-15 20:30:22.010 wdl.w:ptcp.t:call-tar_outputs-07 INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2104.mapped.bam.bai"
2025-09-15 20:30:22.010 wdl.w:ptcp.t:call-tar_outputs-07 INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2104.mapped.bam"
2025-09-15 20:30:22.010 wdl.w:ptcp.t:call-tar_outputs-07 INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2104"
2025-09-15 20:30:22.010 wdl.w:ptcp.t:call-tar_outputs-07 INFO eval :: name: "threads", value: 1
2025-09-15 20:30:22.010 wdl.w:ptcp.t:call-tar_outputs-07 INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:30:22.011 wdl.w:ptcp.t:call-tar_outputs-07 INFO eval :: name: "disk_size", value: 6
2025-09-15 20:30:22.011 wdl.w:ptcp.t:call-tar_outputs-07 INFO eval :: name: "output_tarball", value: "m84036_250809_035451_s4.bc2104.tar"
2025-09-15 20:30:22.011 wdl.w:ptcp.t:call-tar_outputs-07 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:30:22.011 wdl.w:ptcp.t:call-tar_outputs-07 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:30:22.011 wdl.w:ptcp.t:call-tar_outputs-07 INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:30:22.012 wdl.w:ptcp.t:call-tar_outputs-07 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:30:22.085 wdl.w:ptcp.w:call-paraphase-02.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for f8inv22 for sample m84036_250809_035451_s4.bc2099 at 2025-09-15 20:30:05.687442...
2025-09-15 20:30:22.085 wdl.w:ptcp.w:call-paraphase-02.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for f8inv22 for sample m84036_250809_035451_s4.bc2099 at 2025-09-15 20:30:11.519750...
2025-09-15 20:30:22.085 wdl.w:ptcp.w:call-paraphase-02.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for f8inv22 for sample m84036_250809_035451_s4.bc2099 at 2025-09-15 20:30:12.069474...
2025-09-15 20:30:22.102 wdl.w:ptcp.t:call-tar_outputs-07 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 17, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-07/_singularity_tmpdir_4yjbs2m7"
2025-09-15 20:30:22.102 wdl.w:ptcp.t:call-tar_outputs-07 INFO Slurm invocation: srun --job-name call-tar_outputs-07 --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-07/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-07/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-07/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-07/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-07/out/m84036_250809_035451_s4.bc2104_paraphase/m84036_250809_035451_s4.bc2104.paraphase.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2104.paraphase.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-07/out/m84036_250809_035451_s4.bc2104_paraphase/m84036_250809_035451_s4.bc2104.paraphase.json:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2104.paraphase.json:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-07/out/m84036_250809_035451_s4.bc2104_paraphase/m84036_250809_035451_s4.bc2104.paraphase.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2104.paraphase.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-07/out/m84036_250809_035451_s4.bc2104.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2104.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-07/out/m84036_250809_035451_s4.bc2104.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2104.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-07/out/m84036_250809_035451_s4.bc2104.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2104.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-07/out/m84036_250809_035451_s4.bc2104.f8inversion.json:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2104.f8inversion.json:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-07/out/m84036_250809_035451_s4.bc2104_sawfish/m84036_250809_035451_s4.bc2104.sv.vcf.gz:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2104.sv.vcf.gz:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-07/out/m84036_250809_035451_s4.bc2104_sawfish/m84036_250809_035451_s4.bc2104.sv.vcf.gz.tbi:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2104.sv.vcf.gz.tbi:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-07/out/m84036_250809_035451_s4.bc2104.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2104.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-07/out/m84036_250809_035451_s4.bc2104.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2104.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-07/_singularity_tmpdir_4yjbs2m7/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-07/_singularity_tmpdir_4yjbs2m7/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:30:22.111 wdl.w:ptcp.t:call-tar_outputs-07 NOTICE slurm_singularity run :: pid: 1210211, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-07/slurm_singularity.log.txt"
2025-09-15 20:30:23.121 wdl.w:ptcp.t:call-tar_outputs-07.slurm_singularity INFO srun: job 51798317 queued and waiting for resources
2025-09-15 20:30:24.130 wdl.w:ptcp.t:call-tar_outputs-07.slurm_singularity INFO srun: job 51798317 has been allocated resources
2025-09-15 20:30:24.130 wdl.w:ptcp.t:call-tar_outputs-07.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:30:24.427 wdl.w:ptcp.t:call-tar_outputs-07 INFO output :: name: "sample_tarball", value: "m84036_250809_035451_s4.bc2104.tar"
2025-09-15 20:30:24.478 wdl.w:ptcp.t:call-tar_outputs-07 NOTICE done
2025-09-15 20:30:24.520 wdl.w:ptcp NOTICE finish :: job: "call-tar_outputs-07"
2025-09-15 20:30:24.520 wdl.w:ptcp INFO output :: job: "call-tar_outputs-07", values: {"sample_tarball": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-07/out/m84036_250809_035451_s4.bc2104.tar"}
2025-09-15 20:30:35.315 wdl.w:ptcp.w:call-paraphase-02.t:call-run_paraphase INFO output :: name: "paraphase_bam", value: "m84036_250809_035451_s4.bc2099_paraphase/m84036_250809_035451_s4.bc2099.paraphase.bam"
2025-09-15 20:30:35.318 wdl.w:ptcp.w:call-paraphase-02.t:call-run_paraphase INFO output :: name: "paraphase_bam_bai", value: "m84036_250809_035451_s4.bc2099_paraphase/m84036_250809_035451_s4.bc2099.paraphase.bam.bai"
2025-09-15 20:30:35.319 wdl.w:ptcp.w:call-paraphase-02.t:call-run_paraphase INFO output :: name: "paraphase_json", value: "m84036_250809_035451_s4.bc2099_paraphase/m84036_250809_035451_s4.bc2099.paraphase.json"
2025-09-15 20:30:35.324 wdl.w:ptcp.w:call-paraphase-02.t:call-run_paraphase INFO output :: name: "paraphase_vcfs", value: ["/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2099_paraphase/m84036_250809_035451_s4.bc2099_paraphase_vcfs/m84036_250809_035451_s4.bc2099_cyp21.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2099_paraphase/m84036_250809_035451_s4.bc2099_paraphase_vcfs/m84036_250809_035451_s4.bc2099_f8inv1.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2099_paraphase/m84036_250809_035451_s4.bc2099_paraphase_vcfs/m84036_250809_035451_s4.bc2099_f8inv22.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2099_paraphase/m84036_250809_035451_s4.bc2099_paraphase_vcfs/m84036_250809_035451_s4.bc2099_gba.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2099_paraphase/m84036_250809_035451_s4.bc2099_paraphase_vcfs/m84036_250809_035451_s4.bc2099_hba.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2099_paraphase/m84036_250809_035451_s4.bc2099_paraphase_vcfs/m84036_250809_035451_s4.bc2099_hbb.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2099_paraphase/m84036_250809_035451_s4.bc2099_paraphase_vcfs/m84036_250809_035451_s4.bc2099_rpgr.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2099_paraphase/m84036_250809_035451_s4.bc2099_paraphase_vcfs/m84036_250809_035451_s4.bc2099_smn1.vcf"]
2025-09-15 20:30:35.327 wdl.w:ptcp.w:call-paraphase-02.t:call-run_paraphase INFO output :: name: "havanno_json", value: "m84036_250809_035451_s4.bc2099.havanno.json"
2025-09-15 20:30:35.477 wdl.w:ptcp.w:call-paraphase-02.t:call-run_paraphase NOTICE done
2025-09-15 20:30:35.497 wdl.w:ptcp.w:call-paraphase-02 NOTICE finish :: job: "call-run_paraphase"
2025-09-15 20:30:35.497 wdl.w:ptcp.w:call-paraphase-02 INFO output :: job: "call-run_paraphase", values: {"havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-02/call-run_paraphase/out/m84036_250809_035451_s4.bc2099.havanno.json", "paraphase_vcfs": ["/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-02/call-run_paraphase/out/m84036_250809_035451_s4.bc2099_paraphase/m84036_250809_035451_s4.bc2099_paraphase_vcfs/m84036_250809_035451_s4.bc2099_cyp21.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-02/call-run_paraphase/out/m84036_250809_035451_s4.bc2099_paraphase/m84036_250809_035451_s4.bc2099_paraphase_vcfs/m84036_250809_035451_s4.bc2099_f8inv1.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-02/call-run_paraphase/out/m84036_250809_035451_s4.bc2099_paraphase/m84036_250809_035451_s4.bc2099_paraphase_vcfs/m84036_250809_035451_s4.bc2099_f8inv22.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-02/call-run_paraphase/out/m84036_250809_035451_s4.bc2099_paraphase/m84036_250809_035451_s4.bc2099_paraphase_vcfs/m84036_250809_035451_s4.bc2099_gba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-02/call-run_paraphase/out/m84036_250809_035451_s4.bc2099_paraphase/m84036_250809_035451_s4.bc2099_paraphase_vcfs/m84036_250809_035451_s4.bc2099_hba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-02/call-run_paraphase/out/m84036_250809_035451_s4.bc2099_paraphase/m84036_250809_035451_s4.bc2099_paraphase_vcfs/m84036_250809_035451_s4.bc2099_hbb.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-02/call-run_paraphase/out/m84036_250809_035451_s4.bc2099_paraphase/m84036_250809_035451_s4.bc2099_paraphase_vcfs/m84036_250809_035451_s4.bc2099_rpgr.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-02/call-run_paraphase/out/m84036_250809_035451_s4.bc2099_paraphase/m84036_250809_035451_s4.bc2099_paraphase_vcfs/m84036_250809_035451_s4.bc2099_smn1.vcf"], "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-02/call-run_paraphase/out/m84036_250809_035451_s4.bc2099_paraphase/m84036_250809_035451_s4.bc2099.paraphase.json", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-02/call-run_paraphase/out/m84036_250809_035451_s4.bc2099_paraphase/m84036_250809_035451_s4.bc2099.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-02/call-run_paraphase/out/m84036_250809_035451_s4.bc2099_paraphase/m84036_250809_035451_s4.bc2099.paraphase.bam"}
2025-09-15 20:30:35.497 wdl.w:ptcp.w:call-paraphase-02 NOTICE ready :: job: "call-call_f8", callee: "call_f8"
2025-09-15 20:30:35.497 wdl.w:ptcp.w:call-paraphase-02 INFO input :: job: "call-call_f8", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "out_prefix": "m84036_250809_035451_s4.bc2099", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-02/call-run_paraphase/out/m84036_250809_035451_s4.bc2099_paraphase/m84036_250809_035451_s4.bc2099.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-02/call-run_paraphase/out/m84036_250809_035451_s4.bc2099_paraphase/m84036_250809_035451_s4.bc2099.paraphase.bam", "sex": "F"}
2025-09-15 20:30:35.498 wdl.w:ptcp.w:call-paraphase-02 INFO visit :: node: "output-havanno_json", values: {"havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-02/call-run_paraphase/out/m84036_250809_035451_s4.bc2099.havanno.json"}
2025-09-15 20:30:35.498 wdl.w:ptcp.w:call-paraphase-02 INFO visit :: node: "output-paraphase_bam", values: {"paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-02/call-run_paraphase/out/m84036_250809_035451_s4.bc2099_paraphase/m84036_250809_035451_s4.bc2099.paraphase.bam"}
2025-09-15 20:30:35.499 wdl.w:ptcp.w:call-paraphase-02 INFO visit :: node: "output-paraphase_bam_bai", values: {"paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-02/call-run_paraphase/out/m84036_250809_035451_s4.bc2099_paraphase/m84036_250809_035451_s4.bc2099.paraphase.bam.bai"}
2025-09-15 20:30:35.499 wdl.w:ptcp.w:call-paraphase-02 INFO visit :: node: "output-paraphase_json", values: {"paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-02/call-run_paraphase/out/m84036_250809_035451_s4.bc2099_paraphase/m84036_250809_035451_s4.bc2099.paraphase.json"}
2025-09-15 20:30:35.499 wdl.w:ptcp.w:call-paraphase-02 INFO visit :: node: "output-paraphase_vcfs", values: {"paraphase_vcfs": ["/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-02/call-run_paraphase/out/m84036_250809_035451_s4.bc2099_paraphase/m84036_250809_035451_s4.bc2099_paraphase_vcfs/m84036_250809_035451_s4.bc2099_cyp21.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-02/call-run_paraphase/out/m84036_250809_035451_s4.bc2099_paraphase/m84036_250809_035451_s4.bc2099_paraphase_vcfs/m84036_250809_035451_s4.bc2099_f8inv1.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-02/call-run_paraphase/out/m84036_250809_035451_s4.bc2099_paraphase/m84036_250809_035451_s4.bc2099_paraphase_vcfs/m84036_250809_035451_s4.bc2099_f8inv22.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-02/call-run_paraphase/out/m84036_250809_035451_s4.bc2099_paraphase/m84036_250809_035451_s4.bc2099_paraphase_vcfs/m84036_250809_035451_s4.bc2099_gba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-02/call-run_paraphase/out/m84036_250809_035451_s4.bc2099_paraphase/m84036_250809_035451_s4.bc2099_paraphase_vcfs/m84036_250809_035451_s4.bc2099_hba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-02/call-run_paraphase/out/m84036_250809_035451_s4.bc2099_paraphase/m84036_250809_035451_s4.bc2099_paraphase_vcfs/m84036_250809_035451_s4.bc2099_hbb.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-02/call-run_paraphase/out/m84036_250809_035451_s4.bc2099_paraphase/m84036_250809_035451_s4.bc2099_paraphase_vcfs/m84036_250809_035451_s4.bc2099_rpgr.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-02/call-run_paraphase/out/m84036_250809_035451_s4.bc2099_paraphase/m84036_250809_035451_s4.bc2099_paraphase_vcfs/m84036_250809_035451_s4.bc2099_smn1.vcf"]}
2025-09-15 20:30:35.503 wdl.w:ptcp.w:call-paraphase-02.t:call-call_f8 NOTICE task setup :: name: "call_f8", source: "./paraphase.wdl", line: 232, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-02/call-call_f8", thread: 140608723195456
2025-09-15 20:30:35.521 wdl.w:ptcp.w:call-paraphase-02.t:call-call_f8 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:30:35.521 wdl.w:ptcp.w:call-paraphase-02.t:call-call_f8 INFO input :: name: "genome_version", value: "38"
2025-09-15 20:30:35.521 wdl.w:ptcp.w:call-paraphase-02.t:call-call_f8 INFO input :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2099"
2025-09-15 20:30:35.521 wdl.w:ptcp.w:call-paraphase-02.t:call-call_f8 INFO input :: name: "paraphase_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2099.paraphase.bam.bai"
2025-09-15 20:30:35.522 wdl.w:ptcp.w:call-paraphase-02.t:call-call_f8 INFO input :: name: "paraphase_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2099.paraphase.bam"
2025-09-15 20:30:35.522 wdl.w:ptcp.w:call-paraphase-02.t:call-call_f8 INFO input :: name: "sex", value: "F"
2025-09-15 20:30:35.522 wdl.w:ptcp.w:call-paraphase-02.t:call-call_f8 INFO eval :: name: "threads", value: 1
2025-09-15 20:30:35.522 wdl.w:ptcp.w:call-paraphase-02.t:call-call_f8 INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:30:35.522 wdl.w:ptcp.w:call-paraphase-02.t:call-call_f8 INFO eval :: name: "disk_size", value: 11
2025-09-15 20:30:35.522 wdl.w:ptcp.w:call-paraphase-02.t:call-call_f8 INFO eval :: name: "sample_sex", value: "F"
2025-09-15 20:30:35.523 wdl.w:ptcp.w:call-paraphase-02.t:call-call_f8 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:30:35.523 wdl.w:ptcp.w:call-paraphase-02.t:call-call_f8 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:30:35.523 wdl.w:ptcp.w:call-paraphase-02.t:call-call_f8 INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:30:35.523 wdl.w:ptcp.w:call-paraphase-02.t:call-call_f8 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:30:35.560 wdl.w:ptcp.w:call-paraphase-02.t:call-call_f8 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 8, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-02/call-call_f8/_singularity_tmpdir_qk4w2nno"
2025-09-15 20:30:35.560 wdl.w:ptcp.w:call-paraphase-02.t:call-call_f8 INFO Slurm invocation: srun --job-name call-call_f8 --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-02/call-call_f8/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-02/call-call_f8/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-02/call-call_f8/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-02/call-call_f8/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-02/call-run_paraphase/out/m84036_250809_035451_s4.bc2099_paraphase/m84036_250809_035451_s4.bc2099.paraphase.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2099.paraphase.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-02/call-run_paraphase/out/m84036_250809_035451_s4.bc2099_paraphase/m84036_250809_035451_s4.bc2099.paraphase.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2099.paraphase.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-02/call-call_f8/_singularity_tmpdir_qk4w2nno/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-02/call-call_f8/_singularity_tmpdir_qk4w2nno/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:30:35.564 wdl.w:ptcp.w:call-paraphase-02.t:call-call_f8 NOTICE slurm_singularity run :: pid: 1210314, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-02/call-call_f8/slurm_singularity.log.txt"
2025-09-15 20:30:36.573 wdl.w:ptcp.w:call-paraphase-02.t:call-call_f8.slurm_singularity INFO srun: job 51798329 queued and waiting for resources
2025-09-15 20:30:36.573 wdl.w:ptcp.w:call-paraphase-02.t:call-call_f8.slurm_singularity INFO srun: job 51798329 has been allocated resources
2025-09-15 20:30:36.573 wdl.w:ptcp.w:call-paraphase-02.t:call-call_f8.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:30:36.970 wdl.w:ptcp.w:call-paraphase-02.t:call-call_f8 INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2099.f8inversion.vcf"
2025-09-15 20:30:36.974 wdl.w:ptcp.w:call-paraphase-02.t:call-call_f8 INFO output :: name: "json", value: "m84036_250809_035451_s4.bc2099.f8inversion.json"
2025-09-15 20:30:37.032 wdl.w:ptcp.w:call-paraphase-02.t:call-call_f8 NOTICE done
2025-09-15 20:30:37.045 wdl.w:ptcp.w:call-paraphase-02 NOTICE finish :: job: "call-call_f8"
2025-09-15 20:30:37.045 wdl.w:ptcp.w:call-paraphase-02 INFO output :: job: "call-call_f8", values: {"json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-02/call-call_f8/out/m84036_250809_035451_s4.bc2099.f8inversion.json", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-02/call-call_f8/out/m84036_250809_035451_s4.bc2099.f8inversion.vcf"}
2025-09-15 20:30:37.045 wdl.w:ptcp.w:call-paraphase-02 INFO visit :: node: "output-f8_json", values: {"f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-02/call-call_f8/out/m84036_250809_035451_s4.bc2099.f8inversion.json"}
2025-09-15 20:30:37.045 wdl.w:ptcp.w:call-paraphase-02 INFO visit :: node: "output-f8_vcf", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-02/call-call_f8/out/m84036_250809_035451_s4.bc2099.f8inversion.vcf"}
2025-09-15 20:30:37.046 wdl.w:ptcp.w:call-paraphase-02 INFO visit :: node: "outputs", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-02/call-call_f8/out/m84036_250809_035451_s4.bc2099.f8inversion.vcf", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-02/call-run_paraphase/out/m84036_250809_035451_s4.bc2099_paraphase/m84036_250809_035451_s4.bc2099.paraphase.json", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-02/call-run_paraphase/out/m84036_250809_035451_s4.bc2099_paraphase/m84036_250809_035451_s4.bc2099.paraphase.bam", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-02/call-run_paraphase/out/m84036_250809_035451_s4.bc2099_paraphase/m84036_250809_035451_s4.bc2099.paraphase.bam.bai", "paraphase_vcfs": ["/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-02/call-run_paraphase/out/m84036_250809_035451_s4.bc2099_paraphase/m84036_250809_035451_s4.bc2099_paraphase_vcfs/m84036_250809_035451_s4.bc2099_cyp21.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-02/call-run_paraphase/out/m84036_250809_035451_s4.bc2099_paraphase/m84036_250809_035451_s4.bc2099_paraphase_vcfs/m84036_250809_035451_s4.bc2099_f8inv1.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-02/call-run_paraphase/out/m84036_250809_035451_s4.bc2099_paraphase/m84036_250809_035451_s4.bc2099_paraphase_vcfs/m84036_250809_035451_s4.bc2099_f8inv22.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-02/call-run_paraphase/out/m84036_250809_035451_s4.bc2099_paraphase/m84036_250809_035451_s4.bc2099_paraphase_vcfs/m84036_250809_035451_s4.bc2099_gba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-02/call-run_paraphase/out/m84036_250809_035451_s4.bc2099_paraphase/m84036_250809_035451_s4.bc2099_paraphase_vcfs/m84036_250809_035451_s4.bc2099_hba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-02/call-run_paraphase/out/m84036_250809_035451_s4.bc2099_paraphase/m84036_250809_035451_s4.bc2099_paraphase_vcfs/m84036_250809_035451_s4.bc2099_hbb.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-02/call-run_paraphase/out/m84036_250809_035451_s4.bc2099_paraphase/m84036_250809_035451_s4.bc2099_paraphase_vcfs/m84036_250809_035451_s4.bc2099_rpgr.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-02/call-run_paraphase/out/m84036_250809_035451_s4.bc2099_paraphase/m84036_250809_035451_s4.bc2099_paraphase_vcfs/m84036_250809_035451_s4.bc2099_smn1.vcf"], "havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-02/call-run_paraphase/out/m84036_250809_035451_s4.bc2099.havanno.json", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-02/call-call_f8/out/m84036_250809_035451_s4.bc2099.f8inversion.json"}
2025-09-15 20:30:37.148 wdl.w:ptcp.w:call-paraphase-02 NOTICE done
2025-09-15 20:30:37.153 wdl.w:ptcp NOTICE finish :: job: "call-paraphase-02"
2025-09-15 20:30:37.153 wdl.w:ptcp INFO output :: job: "call-paraphase-02", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-02/out/m84036_250809_035451_s4.bc2099.f8inversion.vcf", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-02/out/m84036_250809_035451_s4.bc2099_paraphase/m84036_250809_035451_s4.bc2099.paraphase.json", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-02/out/m84036_250809_035451_s4.bc2099_paraphase/m84036_250809_035451_s4.bc2099.paraphase.bam", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-02/out/m84036_250809_035451_s4.bc2099_paraphase/m84036_250809_035451_s4.bc2099.paraphase.bam.bai", "paraphase_vcfs": ["/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-02/out/m84036_250809_035451_s4.bc2099_paraphase/m84036_250809_035451_s4.bc2099_paraphase_vcfs/m84036_250809_035451_s4.bc2099_cyp21.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-02/out/m84036_250809_035451_s4.bc2099_paraphase/m84036_250809_035451_s4.bc2099_paraphase_vcfs/m84036_250809_035451_s4.bc2099_f8inv1.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-02/out/m84036_250809_035451_s4.bc2099_paraphase/m84036_250809_035451_s4.bc2099_paraphase_vcfs/m84036_250809_035451_s4.bc2099_f8inv22.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-02/out/m84036_250809_035451_s4.bc2099_paraphase/m84036_250809_035451_s4.bc2099_paraphase_vcfs/m84036_250809_035451_s4.bc2099_gba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-02/out/m84036_250809_035451_s4.bc2099_paraphase/m84036_250809_035451_s4.bc2099_paraphase_vcfs/m84036_250809_035451_s4.bc2099_hba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-02/out/m84036_250809_035451_s4.bc2099_paraphase/m84036_250809_035451_s4.bc2099_paraphase_vcfs/m84036_250809_035451_s4.bc2099_hbb.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-02/out/m84036_250809_035451_s4.bc2099_paraphase/m84036_250809_035451_s4.bc2099_paraphase_vcfs/m84036_250809_035451_s4.bc2099_rpgr.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-02/out/m84036_250809_035451_s4.bc2099_paraphase/m84036_250809_035451_s4.bc2099_paraphase_vcfs/m84036_250809_035451_s4.bc2099_smn1.vcf"], "havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-02/out/m84036_250809_035451_s4.bc2099.havanno.json", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-02/out/m84036_250809_035451_s4.bc2099.f8inversion.json"}
2025-09-15 20:30:37.154 wdl.w:ptcp NOTICE ready :: job: "call-tar_outputs-02", callee: "tar_outputs"
2025-09-15 20:30:37.154 wdl.w:ptcp INFO input :: job: "call-tar_outputs-02", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "sawfish_vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-02/out/m84036_250809_035451_s4.bc2099_sawfish/m84036_250809_035451_s4.bc2099.sv.vcf.gz.tbi", "sawfish_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-02/out/m84036_250809_035451_s4.bc2099_sawfish/m84036_250809_035451_s4.bc2099.sv.vcf.gz", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-02/out/m84036_250809_035451_s4.bc2099.f8inversion.json", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-02/out/m84036_250809_035451_s4.bc2099_paraphase/m84036_250809_035451_s4.bc2099.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-02/out/m84036_250809_035451_s4.bc2099_paraphase/m84036_250809_035451_s4.bc2099.paraphase.bam", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-02/out/m84036_250809_035451_s4.bc2099_paraphase/m84036_250809_035451_s4.bc2099.paraphase.json", "trgt_spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-02/out/m84036_250809_035451_s4.bc2099.trgt.sorted.spanning.bam.bai", "trgt_spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-02/out/m84036_250809_035451_s4.bc2099.trgt.sorted.spanning.bam", "trgt_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-02/out/m84036_250809_035451_s4.bc2099.trgt.vcf", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-02/out/m84036_250809_035451_s4.bc2099.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-02/out/m84036_250809_035451_s4.bc2099.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2099"}
2025-09-15 20:30:37.160 wdl.w:ptcp.t:call-tar_outputs-02 NOTICE task setup :: name: "tar_outputs", source: "./common.wdl", line: 279, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-02", thread: 140610887464512
2025-09-15 20:30:37.181 wdl.w:ptcp.t:call-tar_outputs-02 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:30:37.181 wdl.w:ptcp.t:call-tar_outputs-02 INFO input :: name: "sawfish_vcf_tbi", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2099.sv.vcf.gz.tbi"
2025-09-15 20:30:37.181 wdl.w:ptcp.t:call-tar_outputs-02 INFO input :: name: "sawfish_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2099.sv.vcf.gz"
2025-09-15 20:30:37.181 wdl.w:ptcp.t:call-tar_outputs-02 INFO input :: name: "f8_json", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2099.f8inversion.json"
2025-09-15 20:30:37.181 wdl.w:ptcp.t:call-tar_outputs-02 INFO input :: name: "paraphase_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2099.paraphase.bam.bai"
2025-09-15 20:30:37.181 wdl.w:ptcp.t:call-tar_outputs-02 INFO input :: name: "paraphase_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2099.paraphase.bam"
2025-09-15 20:30:37.181 wdl.w:ptcp.t:call-tar_outputs-02 INFO input :: name: "paraphase_json", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2099.paraphase.json"
2025-09-15 20:30:37.181 wdl.w:ptcp.t:call-tar_outputs-02 INFO input :: name: "trgt_spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2099.trgt.sorted.spanning.bam.bai"
2025-09-15 20:30:37.181 wdl.w:ptcp.t:call-tar_outputs-02 INFO input :: name: "trgt_spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2099.trgt.sorted.spanning.bam"
2025-09-15 20:30:37.181 wdl.w:ptcp.t:call-tar_outputs-02 INFO input :: name: "trgt_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2099.trgt.vcf"
2025-09-15 20:30:37.181 wdl.w:ptcp.t:call-tar_outputs-02 INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2099.mapped.bam.bai"
2025-09-15 20:30:37.181 wdl.w:ptcp.t:call-tar_outputs-02 INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2099.mapped.bam"
2025-09-15 20:30:37.181 wdl.w:ptcp.t:call-tar_outputs-02 INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2099"
2025-09-15 20:30:37.181 wdl.w:ptcp.t:call-tar_outputs-02 INFO eval :: name: "threads", value: 1
2025-09-15 20:30:37.181 wdl.w:ptcp.t:call-tar_outputs-02 INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:30:37.182 wdl.w:ptcp.t:call-tar_outputs-02 INFO eval :: name: "disk_size", value: 6
2025-09-15 20:30:37.182 wdl.w:ptcp.t:call-tar_outputs-02 INFO eval :: name: "output_tarball", value: "m84036_250809_035451_s4.bc2099.tar"
2025-09-15 20:30:37.182 wdl.w:ptcp.t:call-tar_outputs-02 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:30:37.182 wdl.w:ptcp.t:call-tar_outputs-02 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:30:37.183 wdl.w:ptcp.t:call-tar_outputs-02 INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:30:37.183 wdl.w:ptcp.t:call-tar_outputs-02 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:30:37.256 wdl.w:ptcp.t:call-tar_outputs-02 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 17, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-02/_singularity_tmpdir_oeubdcu_"
2025-09-15 20:30:37.256 wdl.w:ptcp.t:call-tar_outputs-02 INFO Slurm invocation: srun --job-name call-tar_outputs-02 --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-02/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-02/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-02/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-02/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-02/out/m84036_250809_035451_s4.bc2099_sawfish/m84036_250809_035451_s4.bc2099.sv.vcf.gz.tbi:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2099.sv.vcf.gz.tbi:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-02/out/m84036_250809_035451_s4.bc2099_sawfish/m84036_250809_035451_s4.bc2099.sv.vcf.gz:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2099.sv.vcf.gz:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-02/out/m84036_250809_035451_s4.bc2099.f8inversion.json:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2099.f8inversion.json:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-02/out/m84036_250809_035451_s4.bc2099.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2099.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-02/out/m84036_250809_035451_s4.bc2099.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2099.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-02/out/m84036_250809_035451_s4.bc2099_paraphase/m84036_250809_035451_s4.bc2099.paraphase.json:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2099.paraphase.json:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-02/out/m84036_250809_035451_s4.bc2099_paraphase/m84036_250809_035451_s4.bc2099.paraphase.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2099.paraphase.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-02/out/m84036_250809_035451_s4.bc2099_paraphase/m84036_250809_035451_s4.bc2099.paraphase.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2099.paraphase.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-02/out/m84036_250809_035451_s4.bc2099.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2099.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-02/out/m84036_250809_035451_s4.bc2099.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2099.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-02/out/m84036_250809_035451_s4.bc2099.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2099.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-02/_singularity_tmpdir_oeubdcu_/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-02/_singularity_tmpdir_oeubdcu_/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:30:37.260 wdl.w:ptcp.t:call-tar_outputs-02 NOTICE slurm_singularity run :: pid: 1210324, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-02/slurm_singularity.log.txt"
2025-09-15 20:30:38.268 wdl.w:ptcp.t:call-tar_outputs-02.slurm_singularity INFO srun: job 51798330 queued and waiting for resources
2025-09-15 20:30:39.277 wdl.w:ptcp.t:call-tar_outputs-02.slurm_singularity INFO srun: job 51798330 has been allocated resources
2025-09-15 20:30:39.277 wdl.w:ptcp.t:call-tar_outputs-02.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:30:39.636 wdl.w:ptcp.t:call-tar_outputs-02 INFO output :: name: "sample_tarball", value: "m84036_250809_035451_s4.bc2099.tar"
2025-09-15 20:30:39.686 wdl.w:ptcp.t:call-tar_outputs-02 NOTICE done
2025-09-15 20:30:39.689 wdl.w:ptcp NOTICE finish :: job: "call-tar_outputs-02"
2025-09-15 20:30:39.690 wdl.w:ptcp INFO output :: job: "call-tar_outputs-02", values: {"sample_tarball": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-02/out/m84036_250809_035451_s4.bc2099.tar"}
2025-09-15 20:30:40.023 wdl.w:ptcp.w:call-paraphase-94.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for rpgr for sample m84036_250809_035451_s4.bc2191 at 2025-09-15 20:30:23.952644...
2025-09-15 20:30:40.023 wdl.w:ptcp.w:call-paraphase-94.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for rpgr for sample m84036_250809_035451_s4.bc2191 at 2025-09-15 20:30:23.953314...
2025-09-15 20:30:40.023 wdl.w:ptcp.w:call-paraphase-94.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for rpgr for sample m84036_250809_035451_s4.bc2191 at 2025-09-15 20:30:25.505955...
2025-09-15 20:30:40.024 wdl.w:ptcp.w:call-paraphase-94.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for rpgr for sample m84036_250809_035451_s4.bc2191 at 2025-09-15 20:30:26.653018...
2025-09-15 20:30:40.024 wdl.w:ptcp.w:call-paraphase-94.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for rpgr for sample m84036_250809_035451_s4.bc2191 at 2025-09-15 20:30:26.827000...
2025-09-15 20:30:41.567 wdl.w:ptcp.w:call-paraphase-87.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for f8inv22 for sample m84036_250809_035451_s4.bc2184 at 2025-09-15 20:30:36.099511...
2025-09-15 20:30:41.567 wdl.w:ptcp.w:call-paraphase-87.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for f8inv22 for sample m84036_250809_035451_s4.bc2184 at 2025-09-15 20:30:36.100287...
2025-09-15 20:30:41.567 wdl.w:ptcp.w:call-paraphase-87.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for f8inv22 for sample m84036_250809_035451_s4.bc2184 at 2025-09-15 20:30:37.084637...
2025-09-15 20:30:46.081 wdl.w:ptcp.w:call-paraphase-58.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for rpgr for sample m84036_250809_035451_s4.bc2155 at 2025-09-15 20:30:06.742499...
2025-09-15 20:30:46.082 wdl.w:ptcp.w:call-paraphase-58.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for rpgr for sample m84036_250809_035451_s4.bc2155 at 2025-09-15 20:30:06.743138...
2025-09-15 20:30:46.082 wdl.w:ptcp.w:call-paraphase-58.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for rpgr for sample m84036_250809_035451_s4.bc2155 at 2025-09-15 20:30:09.893856...
2025-09-15 20:30:46.082 wdl.w:ptcp.w:call-paraphase-58.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for rpgr for sample m84036_250809_035451_s4.bc2155 at 2025-09-15 20:30:11.470552...
2025-09-15 20:30:46.082 wdl.w:ptcp.w:call-paraphase-58.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for rpgr for sample m84036_250809_035451_s4.bc2155 at 2025-09-15 20:30:11.679348...
2025-09-15 20:30:50.658 wdl.w:ptcp.w:call-paraphase-87.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for f8inv22 for sample m84036_250809_035451_s4.bc2184 at 2025-09-15 20:30:42.208179...
2025-09-15 20:30:50.658 wdl.w:ptcp.w:call-paraphase-87.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for f8inv22 for sample m84036_250809_035451_s4.bc2184 at 2025-09-15 20:30:42.538007...
2025-09-15 20:30:52.006 wdl.w:ptcp.w:call-paraphase-83.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for rpgr for sample m84036_250809_035451_s4.bc2180 at 2025-09-15 20:30:43.850042...
2025-09-15 20:30:52.006 wdl.w:ptcp.w:call-paraphase-83.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for rpgr for sample m84036_250809_035451_s4.bc2180 at 2025-09-15 20:30:43.850777...
2025-09-15 20:30:58.566 wdl.w:ptcp.w:call-paraphase-86.t:call-run_paraphase INFO output :: name: "paraphase_bam", value: "m84036_250809_035451_s4.bc2183_paraphase/m84036_250809_035451_s4.bc2183.paraphase.bam"
2025-09-15 20:30:58.571 wdl.w:ptcp.w:call-paraphase-86.t:call-run_paraphase INFO output :: name: "paraphase_bam_bai", value: "m84036_250809_035451_s4.bc2183_paraphase/m84036_250809_035451_s4.bc2183.paraphase.bam.bai"
2025-09-15 20:30:58.572 wdl.w:ptcp.w:call-paraphase-86.t:call-run_paraphase INFO output :: name: "paraphase_json", value: "m84036_250809_035451_s4.bc2183_paraphase/m84036_250809_035451_s4.bc2183.paraphase.json"
2025-09-15 20:30:58.576 wdl.w:ptcp.w:call-paraphase-86.t:call-run_paraphase INFO output :: name: "paraphase_vcfs", value: ["/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2183_paraphase/m84036_250809_035451_s4.bc2183_paraphase_vcfs/m84036_250809_035451_s4.bc2183_cyp21.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2183_paraphase/m84036_250809_035451_s4.bc2183_paraphase_vcfs/m84036_250809_035451_s4.bc2183_f8inv1.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2183_paraphase/m84036_250809_035451_s4.bc2183_paraphase_vcfs/m84036_250809_035451_s4.bc2183_f8inv22.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2183_paraphase/m84036_250809_035451_s4.bc2183_paraphase_vcfs/m84036_250809_035451_s4.bc2183_gba.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2183_paraphase/m84036_250809_035451_s4.bc2183_paraphase_vcfs/m84036_250809_035451_s4.bc2183_hba.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2183_paraphase/m84036_250809_035451_s4.bc2183_paraphase_vcfs/m84036_250809_035451_s4.bc2183_hbb.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2183_paraphase/m84036_250809_035451_s4.bc2183_paraphase_vcfs/m84036_250809_035451_s4.bc2183_rpgr.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2183_paraphase/m84036_250809_035451_s4.bc2183_paraphase_vcfs/m84036_250809_035451_s4.bc2183_smn1.vcf"]
2025-09-15 20:30:58.578 wdl.w:ptcp.w:call-paraphase-86.t:call-run_paraphase INFO output :: name: "havanno_json", value: "m84036_250809_035451_s4.bc2183.havanno.json"
2025-09-15 20:30:58.752 wdl.w:ptcp.w:call-paraphase-86.t:call-run_paraphase NOTICE done
2025-09-15 20:30:58.764 wdl.w:ptcp.w:call-paraphase-86 NOTICE finish :: job: "call-run_paraphase"
2025-09-15 20:30:58.764 wdl.w:ptcp.w:call-paraphase-86 INFO output :: job: "call-run_paraphase", values: {"havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-86/call-run_paraphase/out/m84036_250809_035451_s4.bc2183.havanno.json", "paraphase_vcfs": ["/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-86/call-run_paraphase/out/m84036_250809_035451_s4.bc2183_paraphase/m84036_250809_035451_s4.bc2183_paraphase_vcfs/m84036_250809_035451_s4.bc2183_cyp21.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-86/call-run_paraphase/out/m84036_250809_035451_s4.bc2183_paraphase/m84036_250809_035451_s4.bc2183_paraphase_vcfs/m84036_250809_035451_s4.bc2183_f8inv1.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-86/call-run_paraphase/out/m84036_250809_035451_s4.bc2183_paraphase/m84036_250809_035451_s4.bc2183_paraphase_vcfs/m84036_250809_035451_s4.bc2183_f8inv22.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-86/call-run_paraphase/out/m84036_250809_035451_s4.bc2183_paraphase/m84036_250809_035451_s4.bc2183_paraphase_vcfs/m84036_250809_035451_s4.bc2183_gba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-86/call-run_paraphase/out/m84036_250809_035451_s4.bc2183_paraphase/m84036_250809_035451_s4.bc2183_paraphase_vcfs/m84036_250809_035451_s4.bc2183_hba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-86/call-run_paraphase/out/m84036_250809_035451_s4.bc2183_paraphase/m84036_250809_035451_s4.bc2183_paraphase_vcfs/m84036_250809_035451_s4.bc2183_hbb.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-86/call-run_paraphase/out/m84036_250809_035451_s4.bc2183_paraphase/m84036_250809_035451_s4.bc2183_paraphase_vcfs/m84036_250809_035451_s4.bc2183_rpgr.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-86/call-run_paraphase/out/m84036_250809_035451_s4.bc2183_paraphase/m84036_250809_035451_s4.bc2183_paraphase_vcfs/m84036_250809_035451_s4.bc2183_smn1.vcf"], "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-86/call-run_paraphase/out/m84036_250809_035451_s4.bc2183_paraphase/m84036_250809_035451_s4.bc2183.paraphase.json", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-86/call-run_paraphase/out/m84036_250809_035451_s4.bc2183_paraphase/m84036_250809_035451_s4.bc2183.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-86/call-run_paraphase/out/m84036_250809_035451_s4.bc2183_paraphase/m84036_250809_035451_s4.bc2183.paraphase.bam"}
2025-09-15 20:30:58.764 wdl.w:ptcp.w:call-paraphase-86 NOTICE ready :: job: "call-call_f8", callee: "call_f8"
2025-09-15 20:30:58.765 wdl.w:ptcp.w:call-paraphase-86 INFO input :: job: "call-call_f8", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "out_prefix": "m84036_250809_035451_s4.bc2183", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-86/call-run_paraphase/out/m84036_250809_035451_s4.bc2183_paraphase/m84036_250809_035451_s4.bc2183.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-86/call-run_paraphase/out/m84036_250809_035451_s4.bc2183_paraphase/m84036_250809_035451_s4.bc2183.paraphase.bam", "sex": "F"}
2025-09-15 20:30:58.765 wdl.w:ptcp.w:call-paraphase-86 INFO visit :: node: "output-havanno_json", values: {"havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-86/call-run_paraphase/out/m84036_250809_035451_s4.bc2183.havanno.json"}
2025-09-15 20:30:58.765 wdl.w:ptcp.w:call-paraphase-86 INFO visit :: node: "output-paraphase_bam", values: {"paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-86/call-run_paraphase/out/m84036_250809_035451_s4.bc2183_paraphase/m84036_250809_035451_s4.bc2183.paraphase.bam"}
2025-09-15 20:30:58.765 wdl.w:ptcp.w:call-paraphase-86 INFO visit :: node: "output-paraphase_bam_bai", values: {"paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-86/call-run_paraphase/out/m84036_250809_035451_s4.bc2183_paraphase/m84036_250809_035451_s4.bc2183.paraphase.bam.bai"}
2025-09-15 20:30:58.765 wdl.w:ptcp.w:call-paraphase-86 INFO visit :: node: "output-paraphase_json", values: {"paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-86/call-run_paraphase/out/m84036_250809_035451_s4.bc2183_paraphase/m84036_250809_035451_s4.bc2183.paraphase.json"}
2025-09-15 20:30:58.766 wdl.w:ptcp.w:call-paraphase-86 INFO visit :: node: "output-paraphase_vcfs", values: {"paraphase_vcfs": ["/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-86/call-run_paraphase/out/m84036_250809_035451_s4.bc2183_paraphase/m84036_250809_035451_s4.bc2183_paraphase_vcfs/m84036_250809_035451_s4.bc2183_cyp21.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-86/call-run_paraphase/out/m84036_250809_035451_s4.bc2183_paraphase/m84036_250809_035451_s4.bc2183_paraphase_vcfs/m84036_250809_035451_s4.bc2183_f8inv1.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-86/call-run_paraphase/out/m84036_250809_035451_s4.bc2183_paraphase/m84036_250809_035451_s4.bc2183_paraphase_vcfs/m84036_250809_035451_s4.bc2183_f8inv22.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-86/call-run_paraphase/out/m84036_250809_035451_s4.bc2183_paraphase/m84036_250809_035451_s4.bc2183_paraphase_vcfs/m84036_250809_035451_s4.bc2183_gba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-86/call-run_paraphase/out/m84036_250809_035451_s4.bc2183_paraphase/m84036_250809_035451_s4.bc2183_paraphase_vcfs/m84036_250809_035451_s4.bc2183_hba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-86/call-run_paraphase/out/m84036_250809_035451_s4.bc2183_paraphase/m84036_250809_035451_s4.bc2183_paraphase_vcfs/m84036_250809_035451_s4.bc2183_hbb.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-86/call-run_paraphase/out/m84036_250809_035451_s4.bc2183_paraphase/m84036_250809_035451_s4.bc2183_paraphase_vcfs/m84036_250809_035451_s4.bc2183_rpgr.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-86/call-run_paraphase/out/m84036_250809_035451_s4.bc2183_paraphase/m84036_250809_035451_s4.bc2183_paraphase_vcfs/m84036_250809_035451_s4.bc2183_smn1.vcf"]}
2025-09-15 20:30:58.776 wdl.w:ptcp.w:call-paraphase-86.t:call-call_f8 NOTICE task setup :: name: "call_f8", source: "./paraphase.wdl", line: 232, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-86/call-call_f8", thread: 140608186324544
2025-09-15 20:30:58.792 wdl.w:ptcp.w:call-paraphase-86.t:call-call_f8 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:30:58.792 wdl.w:ptcp.w:call-paraphase-86.t:call-call_f8 INFO input :: name: "genome_version", value: "38"
2025-09-15 20:30:58.792 wdl.w:ptcp.w:call-paraphase-86.t:call-call_f8 INFO input :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2183"
2025-09-15 20:30:58.792 wdl.w:ptcp.w:call-paraphase-86.t:call-call_f8 INFO input :: name: "paraphase_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2183.paraphase.bam.bai"
2025-09-15 20:30:58.792 wdl.w:ptcp.w:call-paraphase-86.t:call-call_f8 INFO input :: name: "paraphase_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2183.paraphase.bam"
2025-09-15 20:30:58.792 wdl.w:ptcp.w:call-paraphase-86.t:call-call_f8 INFO input :: name: "sex", value: "F"
2025-09-15 20:30:58.793 wdl.w:ptcp.w:call-paraphase-86.t:call-call_f8 INFO eval :: name: "threads", value: 1
2025-09-15 20:30:58.793 wdl.w:ptcp.w:call-paraphase-86.t:call-call_f8 INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:30:58.793 wdl.w:ptcp.w:call-paraphase-86.t:call-call_f8 INFO eval :: name: "disk_size", value: 11
2025-09-15 20:30:58.793 wdl.w:ptcp.w:call-paraphase-86.t:call-call_f8 INFO eval :: name: "sample_sex", value: "F"
2025-09-15 20:30:58.793 wdl.w:ptcp.w:call-paraphase-86.t:call-call_f8 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:30:58.793 wdl.w:ptcp.w:call-paraphase-86.t:call-call_f8 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:30:58.794 wdl.w:ptcp.w:call-paraphase-86.t:call-call_f8 INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:30:58.794 wdl.w:ptcp.w:call-paraphase-86.t:call-call_f8 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:30:58.844 wdl.w:ptcp.w:call-paraphase-86.t:call-call_f8 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 8, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-86/call-call_f8/_singularity_tmpdir_sb08s4ig"
2025-09-15 20:30:58.844 wdl.w:ptcp.w:call-paraphase-86.t:call-call_f8 INFO Slurm invocation: srun --job-name call-call_f8 --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-86/call-call_f8/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-86/call-call_f8/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-86/call-call_f8/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-86/call-call_f8/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-86/call-run_paraphase/out/m84036_250809_035451_s4.bc2183_paraphase/m84036_250809_035451_s4.bc2183.paraphase.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2183.paraphase.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-86/call-run_paraphase/out/m84036_250809_035451_s4.bc2183_paraphase/m84036_250809_035451_s4.bc2183.paraphase.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2183.paraphase.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-86/call-call_f8/_singularity_tmpdir_sb08s4ig/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-86/call-call_f8/_singularity_tmpdir_sb08s4ig/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:30:58.849 wdl.w:ptcp.w:call-paraphase-86.t:call-call_f8 NOTICE slurm_singularity run :: pid: 1210531, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-86/call-call_f8/slurm_singularity.log.txt"
2025-09-15 20:30:59.857 wdl.w:ptcp.w:call-paraphase-86.t:call-call_f8.slurm_singularity INFO srun: job 51798346 queued and waiting for resources
2025-09-15 20:30:59.857 wdl.w:ptcp.w:call-paraphase-86.t:call-call_f8.slurm_singularity INFO srun: job 51798346 has been allocated resources
2025-09-15 20:31:00.866 wdl.w:ptcp.w:call-paraphase-86.t:call-call_f8.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:31:01.070 wdl.w:ptcp.w:call-paraphase-86.t:call-call_f8 INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2183.f8inversion.vcf"
2025-09-15 20:31:01.073 wdl.w:ptcp.w:call-paraphase-86.t:call-call_f8 INFO output :: name: "json", value: "m84036_250809_035451_s4.bc2183.f8inversion.json"
2025-09-15 20:31:01.125 wdl.w:ptcp.w:call-paraphase-86.t:call-call_f8 NOTICE done
2025-09-15 20:31:01.129 wdl.w:ptcp.w:call-paraphase-86 NOTICE finish :: job: "call-call_f8"
2025-09-15 20:31:01.130 wdl.w:ptcp.w:call-paraphase-86 INFO output :: job: "call-call_f8", values: {"json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-86/call-call_f8/out/m84036_250809_035451_s4.bc2183.f8inversion.json", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-86/call-call_f8/out/m84036_250809_035451_s4.bc2183.f8inversion.vcf"}
2025-09-15 20:31:01.130 wdl.w:ptcp.w:call-paraphase-86 INFO visit :: node: "output-f8_json", values: {"f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-86/call-call_f8/out/m84036_250809_035451_s4.bc2183.f8inversion.json"}
2025-09-15 20:31:01.130 wdl.w:ptcp.w:call-paraphase-86 INFO visit :: node: "output-f8_vcf", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-86/call-call_f8/out/m84036_250809_035451_s4.bc2183.f8inversion.vcf"}
2025-09-15 20:31:01.130 wdl.w:ptcp.w:call-paraphase-86 INFO visit :: node: "outputs", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-86/call-call_f8/out/m84036_250809_035451_s4.bc2183.f8inversion.vcf", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-86/call-run_paraphase/out/m84036_250809_035451_s4.bc2183_paraphase/m84036_250809_035451_s4.bc2183.paraphase.json", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-86/call-run_paraphase/out/m84036_250809_035451_s4.bc2183_paraphase/m84036_250809_035451_s4.bc2183.paraphase.bam", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-86/call-run_paraphase/out/m84036_250809_035451_s4.bc2183_paraphase/m84036_250809_035451_s4.bc2183.paraphase.bam.bai", "paraphase_vcfs": ["/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-86/call-run_paraphase/out/m84036_250809_035451_s4.bc2183_paraphase/m84036_250809_035451_s4.bc2183_paraphase_vcfs/m84036_250809_035451_s4.bc2183_cyp21.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-86/call-run_paraphase/out/m84036_250809_035451_s4.bc2183_paraphase/m84036_250809_035451_s4.bc2183_paraphase_vcfs/m84036_250809_035451_s4.bc2183_f8inv1.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-86/call-run_paraphase/out/m84036_250809_035451_s4.bc2183_paraphase/m84036_250809_035451_s4.bc2183_paraphase_vcfs/m84036_250809_035451_s4.bc2183_f8inv22.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-86/call-run_paraphase/out/m84036_250809_035451_s4.bc2183_paraphase/m84036_250809_035451_s4.bc2183_paraphase_vcfs/m84036_250809_035451_s4.bc2183_gba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-86/call-run_paraphase/out/m84036_250809_035451_s4.bc2183_paraphase/m84036_250809_035451_s4.bc2183_paraphase_vcfs/m84036_250809_035451_s4.bc2183_hba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-86/call-run_paraphase/out/m84036_250809_035451_s4.bc2183_paraphase/m84036_250809_035451_s4.bc2183_paraphase_vcfs/m84036_250809_035451_s4.bc2183_hbb.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-86/call-run_paraphase/out/m84036_250809_035451_s4.bc2183_paraphase/m84036_250809_035451_s4.bc2183_paraphase_vcfs/m84036_250809_035451_s4.bc2183_rpgr.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-86/call-run_paraphase/out/m84036_250809_035451_s4.bc2183_paraphase/m84036_250809_035451_s4.bc2183_paraphase_vcfs/m84036_250809_035451_s4.bc2183_smn1.vcf"], "havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-86/call-run_paraphase/out/m84036_250809_035451_s4.bc2183.havanno.json", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-86/call-call_f8/out/m84036_250809_035451_s4.bc2183.f8inversion.json"}
2025-09-15 20:31:01.230 wdl.w:ptcp.w:call-paraphase-86 NOTICE done
2025-09-15 20:31:01.236 wdl.w:ptcp NOTICE finish :: job: "call-paraphase-86"
2025-09-15 20:31:01.236 wdl.w:ptcp INFO output :: job: "call-paraphase-86", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-86/out/m84036_250809_035451_s4.bc2183.f8inversion.vcf", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-86/out/m84036_250809_035451_s4.bc2183_paraphase/m84036_250809_035451_s4.bc2183.paraphase.json", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-86/out/m84036_250809_035451_s4.bc2183_paraphase/m84036_250809_035451_s4.bc2183.paraphase.bam", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-86/out/m84036_250809_035451_s4.bc2183_paraphase/m84036_250809_035451_s4.bc2183.paraphase.bam.bai", "paraphase_vcfs": ["/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-86/out/m84036_250809_035451_s4.bc2183_paraphase/m84036_250809_035451_s4.bc2183_paraphase_vcfs/m84036_250809_035451_s4.bc2183_cyp21.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-86/out/m84036_250809_035451_s4.bc2183_paraphase/m84036_250809_035451_s4.bc2183_paraphase_vcfs/m84036_250809_035451_s4.bc2183_f8inv1.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-86/out/m84036_250809_035451_s4.bc2183_paraphase/m84036_250809_035451_s4.bc2183_paraphase_vcfs/m84036_250809_035451_s4.bc2183_f8inv22.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-86/out/m84036_250809_035451_s4.bc2183_paraphase/m84036_250809_035451_s4.bc2183_paraphase_vcfs/m84036_250809_035451_s4.bc2183_gba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-86/out/m84036_250809_035451_s4.bc2183_paraphase/m84036_250809_035451_s4.bc2183_paraphase_vcfs/m84036_250809_035451_s4.bc2183_hba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-86/out/m84036_250809_035451_s4.bc2183_paraphase/m84036_250809_035451_s4.bc2183_paraphase_vcfs/m84036_250809_035451_s4.bc2183_hbb.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-86/out/m84036_250809_035451_s4.bc2183_paraphase/m84036_250809_035451_s4.bc2183_paraphase_vcfs/m84036_250809_035451_s4.bc2183_rpgr.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-86/out/m84036_250809_035451_s4.bc2183_paraphase/m84036_250809_035451_s4.bc2183_paraphase_vcfs/m84036_250809_035451_s4.bc2183_smn1.vcf"], "havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-86/out/m84036_250809_035451_s4.bc2183.havanno.json", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-86/out/m84036_250809_035451_s4.bc2183.f8inversion.json"}
2025-09-15 20:31:01.237 wdl.w:ptcp NOTICE ready :: job: "call-tar_outputs-86", callee: "tar_outputs"
2025-09-15 20:31:01.237 wdl.w:ptcp INFO input :: job: "call-tar_outputs-86", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "sawfish_vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-86/out/m84036_250809_035451_s4.bc2183_sawfish/m84036_250809_035451_s4.bc2183.sv.vcf.gz.tbi", "sawfish_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-86/out/m84036_250809_035451_s4.bc2183_sawfish/m84036_250809_035451_s4.bc2183.sv.vcf.gz", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-86/out/m84036_250809_035451_s4.bc2183.f8inversion.json", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-86/out/m84036_250809_035451_s4.bc2183_paraphase/m84036_250809_035451_s4.bc2183.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-86/out/m84036_250809_035451_s4.bc2183_paraphase/m84036_250809_035451_s4.bc2183.paraphase.bam", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-86/out/m84036_250809_035451_s4.bc2183_paraphase/m84036_250809_035451_s4.bc2183.paraphase.json", "trgt_spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-86/out/m84036_250809_035451_s4.bc2183.trgt.sorted.spanning.bam.bai", "trgt_spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-86/out/m84036_250809_035451_s4.bc2183.trgt.sorted.spanning.bam", "trgt_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-86/out/m84036_250809_035451_s4.bc2183.trgt.vcf", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-86/out/m84036_250809_035451_s4.bc2183.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-86/out/m84036_250809_035451_s4.bc2183.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2183"}
2025-09-15 20:31:01.246 wdl.w:ptcp.t:call-tar_outputs-86 NOTICE task setup :: name: "tar_outputs", source: "./common.wdl", line: 279, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-86", thread: 140613823374912
2025-09-15 20:31:01.270 wdl.w:ptcp.t:call-tar_outputs-86 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:31:01.270 wdl.w:ptcp.t:call-tar_outputs-86 INFO input :: name: "sawfish_vcf_tbi", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2183.sv.vcf.gz.tbi"
2025-09-15 20:31:01.270 wdl.w:ptcp.t:call-tar_outputs-86 INFO input :: name: "sawfish_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2183.sv.vcf.gz"
2025-09-15 20:31:01.270 wdl.w:ptcp.t:call-tar_outputs-86 INFO input :: name: "f8_json", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2183.f8inversion.json"
2025-09-15 20:31:01.270 wdl.w:ptcp.t:call-tar_outputs-86 INFO input :: name: "paraphase_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2183.paraphase.bam.bai"
2025-09-15 20:31:01.270 wdl.w:ptcp.t:call-tar_outputs-86 INFO input :: name: "paraphase_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2183.paraphase.bam"
2025-09-15 20:31:01.270 wdl.w:ptcp.t:call-tar_outputs-86 INFO input :: name: "paraphase_json", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2183.paraphase.json"
2025-09-15 20:31:01.270 wdl.w:ptcp.t:call-tar_outputs-86 INFO input :: name: "trgt_spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2183.trgt.sorted.spanning.bam.bai"
2025-09-15 20:31:01.270 wdl.w:ptcp.t:call-tar_outputs-86 INFO input :: name: "trgt_spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2183.trgt.sorted.spanning.bam"
2025-09-15 20:31:01.270 wdl.w:ptcp.t:call-tar_outputs-86 INFO input :: name: "trgt_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2183.trgt.vcf"
2025-09-15 20:31:01.270 wdl.w:ptcp.t:call-tar_outputs-86 INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2183.mapped.bam.bai"
2025-09-15 20:31:01.270 wdl.w:ptcp.t:call-tar_outputs-86 INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2183.mapped.bam"
2025-09-15 20:31:01.271 wdl.w:ptcp.t:call-tar_outputs-86 INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2183"
2025-09-15 20:31:01.271 wdl.w:ptcp.t:call-tar_outputs-86 INFO eval :: name: "threads", value: 1
2025-09-15 20:31:01.271 wdl.w:ptcp.t:call-tar_outputs-86 INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:31:01.271 wdl.w:ptcp.t:call-tar_outputs-86 INFO eval :: name: "disk_size", value: 6
2025-09-15 20:31:01.271 wdl.w:ptcp.t:call-tar_outputs-86 INFO eval :: name: "output_tarball", value: "m84036_250809_035451_s4.bc2183.tar"
2025-09-15 20:31:01.271 wdl.w:ptcp.t:call-tar_outputs-86 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:31:01.272 wdl.w:ptcp.t:call-tar_outputs-86 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:31:01.272 wdl.w:ptcp.t:call-tar_outputs-86 INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:31:01.272 wdl.w:ptcp.t:call-tar_outputs-86 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:31:01.353 wdl.w:ptcp.t:call-tar_outputs-86 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 17, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-86/_singularity_tmpdir_xjaxkuxv"
2025-09-15 20:31:01.353 wdl.w:ptcp.t:call-tar_outputs-86 INFO Slurm invocation: srun --job-name call-tar_outputs-86 --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-86/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-86/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-86/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-86/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-86/out/m84036_250809_035451_s4.bc2183_sawfish/m84036_250809_035451_s4.bc2183.sv.vcf.gz:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2183.sv.vcf.gz:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-86/out/m84036_250809_035451_s4.bc2183_sawfish/m84036_250809_035451_s4.bc2183.sv.vcf.gz.tbi:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2183.sv.vcf.gz.tbi:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-86/out/m84036_250809_035451_s4.bc2183.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2183.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-86/out/m84036_250809_035451_s4.bc2183.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2183.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-86/out/m84036_250809_035451_s4.bc2183.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2183.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-86/out/m84036_250809_035451_s4.bc2183.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2183.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-86/out/m84036_250809_035451_s4.bc2183.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2183.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-86/out/m84036_250809_035451_s4.bc2183_paraphase/m84036_250809_035451_s4.bc2183.paraphase.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2183.paraphase.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-86/out/m84036_250809_035451_s4.bc2183_paraphase/m84036_250809_035451_s4.bc2183.paraphase.json:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2183.paraphase.json:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-86/out/m84036_250809_035451_s4.bc2183_paraphase/m84036_250809_035451_s4.bc2183.paraphase.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2183.paraphase.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-86/out/m84036_250809_035451_s4.bc2183.f8inversion.json:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2183.f8inversion.json:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-86/_singularity_tmpdir_xjaxkuxv/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-86/_singularity_tmpdir_xjaxkuxv/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:31:01.356 wdl.w:ptcp.t:call-tar_outputs-86 NOTICE slurm_singularity run :: pid: 1210629, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-86/slurm_singularity.log.txt"
2025-09-15 20:31:02.300 wdl.w:ptcp.w:call-paraphase-78.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for rpgr for sample m84036_250809_035451_s4.bc2175 at 2025-09-15 20:30:23.624020...
2025-09-15 20:31:02.301 wdl.w:ptcp.w:call-paraphase-78.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for rpgr for sample m84036_250809_035451_s4.bc2175 at 2025-09-15 20:30:23.624916...
2025-09-15 20:31:02.301 wdl.w:ptcp.w:call-paraphase-78.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for rpgr for sample m84036_250809_035451_s4.bc2175 at 2025-09-15 20:30:27.283580...
2025-09-15 20:31:02.301 wdl.w:ptcp.w:call-paraphase-78.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for rpgr for sample m84036_250809_035451_s4.bc2175 at 2025-09-15 20:30:28.615505...
2025-09-15 20:31:02.301 wdl.w:ptcp.w:call-paraphase-78.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for rpgr for sample m84036_250809_035451_s4.bc2175 at 2025-09-15 20:30:28.818820...
2025-09-15 20:31:02.363 wdl.w:ptcp.t:call-tar_outputs-86.slurm_singularity INFO srun: job 51798347 queued and waiting for resources
2025-09-15 20:31:03.372 wdl.w:ptcp.t:call-tar_outputs-86.slurm_singularity INFO srun: job 51798347 has been allocated resources
2025-09-15 20:31:03.372 wdl.w:ptcp.t:call-tar_outputs-86.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:31:03.785 wdl.w:ptcp.t:call-tar_outputs-86 INFO output :: name: "sample_tarball", value: "m84036_250809_035451_s4.bc2183.tar"
2025-09-15 20:31:03.836 wdl.w:ptcp.t:call-tar_outputs-86 NOTICE done
2025-09-15 20:31:03.840 wdl.w:ptcp NOTICE finish :: job: "call-tar_outputs-86"
2025-09-15 20:31:03.840 wdl.w:ptcp INFO output :: job: "call-tar_outputs-86", values: {"sample_tarball": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-86/out/m84036_250809_035451_s4.bc2183.tar"}
2025-09-15 20:31:07.305 wdl.w:ptcp.w:call-paraphase-58.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for f8inv22 for sample m84036_250809_035451_s4.bc2155 at 2025-09-15 20:31:06.236044...
2025-09-15 20:31:07.305 wdl.w:ptcp.w:call-paraphase-58.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for f8inv22 for sample m84036_250809_035451_s4.bc2155 at 2025-09-15 20:31:06.236914...
2025-09-15 20:31:11.880 wdl.w:ptcp.w:call-paraphase-87.t:call-run_paraphase.stderr VERBOSE INFO:root:Merging all bams for sample m84036_250809_035451_s4.bc2184 at 2025-09-15 20:31:08.949117...
2025-09-15 20:31:11.880 wdl.w:ptcp.w:call-paraphase-87.t:call-run_paraphase.stderr VERBOSE INFO:root:Writing to json for sample m84036_250809_035451_s4.bc2184 at 2025-09-15 20:31:11.410724...
2025-09-15 20:31:11.880 wdl.w:ptcp.w:call-paraphase-87.t:call-run_paraphase.stderr VERBOSE INFO:root:Completed Paraphase analysis at 2025-09-15 20:31:11.706586...
2025-09-15 20:31:12.283 wdl.w:ptcp.w:call-paraphase-87.t:call-run_paraphase INFO output :: name: "paraphase_bam", value: "m84036_250809_035451_s4.bc2184_paraphase/m84036_250809_035451_s4.bc2184.paraphase.bam"
2025-09-15 20:31:12.286 wdl.w:ptcp.w:call-paraphase-87.t:call-run_paraphase INFO output :: name: "paraphase_bam_bai", value: "m84036_250809_035451_s4.bc2184_paraphase/m84036_250809_035451_s4.bc2184.paraphase.bam.bai"
2025-09-15 20:31:12.287 wdl.w:ptcp.w:call-paraphase-87.t:call-run_paraphase INFO output :: name: "paraphase_json", value: "m84036_250809_035451_s4.bc2184_paraphase/m84036_250809_035451_s4.bc2184.paraphase.json"
2025-09-15 20:31:12.291 wdl.w:ptcp.w:call-paraphase-87.t:call-run_paraphase INFO output :: name: "paraphase_vcfs", value: ["/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2184_paraphase/m84036_250809_035451_s4.bc2184_paraphase_vcfs/m84036_250809_035451_s4.bc2184_cyp21.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2184_paraphase/m84036_250809_035451_s4.bc2184_paraphase_vcfs/m84036_250809_035451_s4.bc2184_f8inv1.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2184_paraphase/m84036_250809_035451_s4.bc2184_paraphase_vcfs/m84036_250809_035451_s4.bc2184_f8inv22.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2184_paraphase/m84036_250809_035451_s4.bc2184_paraphase_vcfs/m84036_250809_035451_s4.bc2184_gba.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2184_paraphase/m84036_250809_035451_s4.bc2184_paraphase_vcfs/m84036_250809_035451_s4.bc2184_hba.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2184_paraphase/m84036_250809_035451_s4.bc2184_paraphase_vcfs/m84036_250809_035451_s4.bc2184_hbb.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2184_paraphase/m84036_250809_035451_s4.bc2184_paraphase_vcfs/m84036_250809_035451_s4.bc2184_rpgr.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2184_paraphase/m84036_250809_035451_s4.bc2184_paraphase_vcfs/m84036_250809_035451_s4.bc2184_smn1.vcf"]
2025-09-15 20:31:12.294 wdl.w:ptcp.w:call-paraphase-87.t:call-run_paraphase INFO output :: name: "havanno_json", value: "m84036_250809_035451_s4.bc2184.havanno.json"
2025-09-15 20:31:12.434 wdl.w:ptcp.w:call-paraphase-87.t:call-run_paraphase NOTICE done
2025-09-15 20:31:12.442 wdl.w:ptcp.w:call-paraphase-87 NOTICE finish :: job: "call-run_paraphase"
2025-09-15 20:31:12.442 wdl.w:ptcp.w:call-paraphase-87 INFO output :: job: "call-run_paraphase", values: {"havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-87/call-run_paraphase/out/m84036_250809_035451_s4.bc2184.havanno.json", "paraphase_vcfs": ["/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-87/call-run_paraphase/out/m84036_250809_035451_s4.bc2184_paraphase/m84036_250809_035451_s4.bc2184_paraphase_vcfs/m84036_250809_035451_s4.bc2184_cyp21.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-87/call-run_paraphase/out/m84036_250809_035451_s4.bc2184_paraphase/m84036_250809_035451_s4.bc2184_paraphase_vcfs/m84036_250809_035451_s4.bc2184_f8inv1.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-87/call-run_paraphase/out/m84036_250809_035451_s4.bc2184_paraphase/m84036_250809_035451_s4.bc2184_paraphase_vcfs/m84036_250809_035451_s4.bc2184_f8inv22.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-87/call-run_paraphase/out/m84036_250809_035451_s4.bc2184_paraphase/m84036_250809_035451_s4.bc2184_paraphase_vcfs/m84036_250809_035451_s4.bc2184_gba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-87/call-run_paraphase/out/m84036_250809_035451_s4.bc2184_paraphase/m84036_250809_035451_s4.bc2184_paraphase_vcfs/m84036_250809_035451_s4.bc2184_hba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-87/call-run_paraphase/out/m84036_250809_035451_s4.bc2184_paraphase/m84036_250809_035451_s4.bc2184_paraphase_vcfs/m84036_250809_035451_s4.bc2184_hbb.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-87/call-run_paraphase/out/m84036_250809_035451_s4.bc2184_paraphase/m84036_250809_035451_s4.bc2184_paraphase_vcfs/m84036_250809_035451_s4.bc2184_rpgr.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-87/call-run_paraphase/out/m84036_250809_035451_s4.bc2184_paraphase/m84036_250809_035451_s4.bc2184_paraphase_vcfs/m84036_250809_035451_s4.bc2184_smn1.vcf"], "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-87/call-run_paraphase/out/m84036_250809_035451_s4.bc2184_paraphase/m84036_250809_035451_s4.bc2184.paraphase.json", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-87/call-run_paraphase/out/m84036_250809_035451_s4.bc2184_paraphase/m84036_250809_035451_s4.bc2184.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-87/call-run_paraphase/out/m84036_250809_035451_s4.bc2184_paraphase/m84036_250809_035451_s4.bc2184.paraphase.bam"}
2025-09-15 20:31:12.442 wdl.w:ptcp.w:call-paraphase-87 NOTICE ready :: job: "call-call_f8", callee: "call_f8"
2025-09-15 20:31:12.442 wdl.w:ptcp.w:call-paraphase-87 INFO input :: job: "call-call_f8", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "out_prefix": "m84036_250809_035451_s4.bc2184", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-87/call-run_paraphase/out/m84036_250809_035451_s4.bc2184_paraphase/m84036_250809_035451_s4.bc2184.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-87/call-run_paraphase/out/m84036_250809_035451_s4.bc2184_paraphase/m84036_250809_035451_s4.bc2184.paraphase.bam", "sex": "F"}
2025-09-15 20:31:12.443 wdl.w:ptcp.w:call-paraphase-87 INFO visit :: node: "output-havanno_json", values: {"havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-87/call-run_paraphase/out/m84036_250809_035451_s4.bc2184.havanno.json"}
2025-09-15 20:31:12.443 wdl.w:ptcp.w:call-paraphase-87 INFO visit :: node: "output-paraphase_bam", values: {"paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-87/call-run_paraphase/out/m84036_250809_035451_s4.bc2184_paraphase/m84036_250809_035451_s4.bc2184.paraphase.bam"}
2025-09-15 20:31:12.443 wdl.w:ptcp.w:call-paraphase-87 INFO visit :: node: "output-paraphase_bam_bai", values: {"paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-87/call-run_paraphase/out/m84036_250809_035451_s4.bc2184_paraphase/m84036_250809_035451_s4.bc2184.paraphase.bam.bai"}
2025-09-15 20:31:12.443 wdl.w:ptcp.w:call-paraphase-87 INFO visit :: node: "output-paraphase_json", values: {"paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-87/call-run_paraphase/out/m84036_250809_035451_s4.bc2184_paraphase/m84036_250809_035451_s4.bc2184.paraphase.json"}
2025-09-15 20:31:12.443 wdl.w:ptcp.w:call-paraphase-87 INFO visit :: node: "output-paraphase_vcfs", values: {"paraphase_vcfs": ["/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-87/call-run_paraphase/out/m84036_250809_035451_s4.bc2184_paraphase/m84036_250809_035451_s4.bc2184_paraphase_vcfs/m84036_250809_035451_s4.bc2184_cyp21.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-87/call-run_paraphase/out/m84036_250809_035451_s4.bc2184_paraphase/m84036_250809_035451_s4.bc2184_paraphase_vcfs/m84036_250809_035451_s4.bc2184_f8inv1.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-87/call-run_paraphase/out/m84036_250809_035451_s4.bc2184_paraphase/m84036_250809_035451_s4.bc2184_paraphase_vcfs/m84036_250809_035451_s4.bc2184_f8inv22.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-87/call-run_paraphase/out/m84036_250809_035451_s4.bc2184_paraphase/m84036_250809_035451_s4.bc2184_paraphase_vcfs/m84036_250809_035451_s4.bc2184_gba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-87/call-run_paraphase/out/m84036_250809_035451_s4.bc2184_paraphase/m84036_250809_035451_s4.bc2184_paraphase_vcfs/m84036_250809_035451_s4.bc2184_hba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-87/call-run_paraphase/out/m84036_250809_035451_s4.bc2184_paraphase/m84036_250809_035451_s4.bc2184_paraphase_vcfs/m84036_250809_035451_s4.bc2184_hbb.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-87/call-run_paraphase/out/m84036_250809_035451_s4.bc2184_paraphase/m84036_250809_035451_s4.bc2184_paraphase_vcfs/m84036_250809_035451_s4.bc2184_rpgr.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-87/call-run_paraphase/out/m84036_250809_035451_s4.bc2184_paraphase/m84036_250809_035451_s4.bc2184_paraphase_vcfs/m84036_250809_035451_s4.bc2184_smn1.vcf"]}
2025-09-15 20:31:12.448 wdl.w:ptcp.w:call-paraphase-87.t:call-call_f8 NOTICE task setup :: name: "call_f8", source: "./paraphase.wdl", line: 232, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-87/call-call_f8", thread: 140612489684544
2025-09-15 20:31:12.462 wdl.w:ptcp.w:call-paraphase-87.t:call-call_f8 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:31:12.462 wdl.w:ptcp.w:call-paraphase-87.t:call-call_f8 INFO input :: name: "genome_version", value: "38"
2025-09-15 20:31:12.462 wdl.w:ptcp.w:call-paraphase-87.t:call-call_f8 INFO input :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2184"
2025-09-15 20:31:12.462 wdl.w:ptcp.w:call-paraphase-87.t:call-call_f8 INFO input :: name: "paraphase_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2184.paraphase.bam.bai"
2025-09-15 20:31:12.462 wdl.w:ptcp.w:call-paraphase-87.t:call-call_f8 INFO input :: name: "paraphase_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2184.paraphase.bam"
2025-09-15 20:31:12.462 wdl.w:ptcp.w:call-paraphase-87.t:call-call_f8 INFO input :: name: "sex", value: "F"
2025-09-15 20:31:12.462 wdl.w:ptcp.w:call-paraphase-87.t:call-call_f8 INFO eval :: name: "threads", value: 1
2025-09-15 20:31:12.462 wdl.w:ptcp.w:call-paraphase-87.t:call-call_f8 INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:31:12.463 wdl.w:ptcp.w:call-paraphase-87.t:call-call_f8 INFO eval :: name: "disk_size", value: 11
2025-09-15 20:31:12.463 wdl.w:ptcp.w:call-paraphase-87.t:call-call_f8 INFO eval :: name: "sample_sex", value: "F"
2025-09-15 20:31:12.463 wdl.w:ptcp.w:call-paraphase-87.t:call-call_f8 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:31:12.463 wdl.w:ptcp.w:call-paraphase-87.t:call-call_f8 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:31:12.463 wdl.w:ptcp.w:call-paraphase-87.t:call-call_f8 INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:31:12.464 wdl.w:ptcp.w:call-paraphase-87.t:call-call_f8 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:31:12.501 wdl.w:ptcp.w:call-paraphase-87.t:call-call_f8 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 8, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-87/call-call_f8/_singularity_tmpdir_ou_su4wc"
2025-09-15 20:31:12.502 wdl.w:ptcp.w:call-paraphase-87.t:call-call_f8 INFO Slurm invocation: srun --job-name call-call_f8 --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-87/call-call_f8/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-87/call-call_f8/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-87/call-call_f8/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-87/call-call_f8/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-87/call-run_paraphase/out/m84036_250809_035451_s4.bc2184_paraphase/m84036_250809_035451_s4.bc2184.paraphase.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2184.paraphase.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-87/call-run_paraphase/out/m84036_250809_035451_s4.bc2184_paraphase/m84036_250809_035451_s4.bc2184.paraphase.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2184.paraphase.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-87/call-call_f8/_singularity_tmpdir_ou_su4wc/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-87/call-call_f8/_singularity_tmpdir_ou_su4wc/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:31:12.506 wdl.w:ptcp.w:call-paraphase-87.t:call-call_f8 NOTICE slurm_singularity run :: pid: 1210737, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-87/call-call_f8/slurm_singularity.log.txt"
2025-09-15 20:31:13.514 wdl.w:ptcp.w:call-paraphase-87.t:call-call_f8.slurm_singularity INFO srun: job 51798362 queued and waiting for resources
2025-09-15 20:31:13.514 wdl.w:ptcp.w:call-paraphase-87.t:call-call_f8.slurm_singularity INFO srun: job 51798362 has been allocated resources
2025-09-15 20:31:13.514 wdl.w:ptcp.w:call-paraphase-87.t:call-call_f8.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:31:13.812 wdl.w:ptcp.w:call-paraphase-87.t:call-call_f8 INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2184.f8inversion.vcf"
2025-09-15 20:31:13.814 wdl.w:ptcp.w:call-paraphase-87.t:call-call_f8 INFO output :: name: "json", value: "m84036_250809_035451_s4.bc2184.f8inversion.json"
2025-09-15 20:31:13.866 wdl.w:ptcp.w:call-paraphase-87.t:call-call_f8 NOTICE done
2025-09-15 20:31:13.871 wdl.w:ptcp.w:call-paraphase-87 NOTICE finish :: job: "call-call_f8"
2025-09-15 20:31:13.871 wdl.w:ptcp.w:call-paraphase-87 INFO output :: job: "call-call_f8", values: {"json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-87/call-call_f8/out/m84036_250809_035451_s4.bc2184.f8inversion.json", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-87/call-call_f8/out/m84036_250809_035451_s4.bc2184.f8inversion.vcf"}
2025-09-15 20:31:13.871 wdl.w:ptcp.w:call-paraphase-87 INFO visit :: node: "output-f8_json", values: {"f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-87/call-call_f8/out/m84036_250809_035451_s4.bc2184.f8inversion.json"}
2025-09-15 20:31:13.871 wdl.w:ptcp.w:call-paraphase-87 INFO visit :: node: "output-f8_vcf", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-87/call-call_f8/out/m84036_250809_035451_s4.bc2184.f8inversion.vcf"}
2025-09-15 20:31:13.871 wdl.w:ptcp.w:call-paraphase-87 INFO visit :: node: "outputs", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-87/call-call_f8/out/m84036_250809_035451_s4.bc2184.f8inversion.vcf", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-87/call-run_paraphase/out/m84036_250809_035451_s4.bc2184_paraphase/m84036_250809_035451_s4.bc2184.paraphase.json", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-87/call-run_paraphase/out/m84036_250809_035451_s4.bc2184_paraphase/m84036_250809_035451_s4.bc2184.paraphase.bam", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-87/call-run_paraphase/out/m84036_250809_035451_s4.bc2184_paraphase/m84036_250809_035451_s4.bc2184.paraphase.bam.bai", "paraphase_vcfs": ["/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-87/call-run_paraphase/out/m84036_250809_035451_s4.bc2184_paraphase/m84036_250809_035451_s4.bc2184_paraphase_vcfs/m84036_250809_035451_s4.bc2184_cyp21.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-87/call-run_paraphase/out/m84036_250809_035451_s4.bc2184_paraphase/m84036_250809_035451_s4.bc2184_paraphase_vcfs/m84036_250809_035451_s4.bc2184_f8inv1.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-87/call-run_paraphase/out/m84036_250809_035451_s4.bc2184_paraphase/m84036_250809_035451_s4.bc2184_paraphase_vcfs/m84036_250809_035451_s4.bc2184_f8inv22.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-87/call-run_paraphase/out/m84036_250809_035451_s4.bc2184_paraphase/m84036_250809_035451_s4.bc2184_paraphase_vcfs/m84036_250809_035451_s4.bc2184_gba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-87/call-run_paraphase/out/m84036_250809_035451_s4.bc2184_paraphase/m84036_250809_035451_s4.bc2184_paraphase_vcfs/m84036_250809_035451_s4.bc2184_hba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-87/call-run_paraphase/out/m84036_250809_035451_s4.bc2184_paraphase/m84036_250809_035451_s4.bc2184_paraphase_vcfs/m84036_250809_035451_s4.bc2184_hbb.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-87/call-run_paraphase/out/m84036_250809_035451_s4.bc2184_paraphase/m84036_250809_035451_s4.bc2184_paraphase_vcfs/m84036_250809_035451_s4.bc2184_rpgr.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-87/call-run_paraphase/out/m84036_250809_035451_s4.bc2184_paraphase/m84036_250809_035451_s4.bc2184_paraphase_vcfs/m84036_250809_035451_s4.bc2184_smn1.vcf"], "havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-87/call-run_paraphase/out/m84036_250809_035451_s4.bc2184.havanno.json", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-87/call-call_f8/out/m84036_250809_035451_s4.bc2184.f8inversion.json"}
2025-09-15 20:31:13.977 wdl.w:ptcp.w:call-paraphase-87 NOTICE done
2025-09-15 20:31:13.983 wdl.w:ptcp NOTICE finish :: job: "call-paraphase-87"
2025-09-15 20:31:13.983 wdl.w:ptcp INFO output :: job: "call-paraphase-87", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-87/out/m84036_250809_035451_s4.bc2184.f8inversion.vcf", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-87/out/m84036_250809_035451_s4.bc2184_paraphase/m84036_250809_035451_s4.bc2184.paraphase.json", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-87/out/m84036_250809_035451_s4.bc2184_paraphase/m84036_250809_035451_s4.bc2184.paraphase.bam", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-87/out/m84036_250809_035451_s4.bc2184_paraphase/m84036_250809_035451_s4.bc2184.paraphase.bam.bai", "paraphase_vcfs": ["/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-87/out/m84036_250809_035451_s4.bc2184_paraphase/m84036_250809_035451_s4.bc2184_paraphase_vcfs/m84036_250809_035451_s4.bc2184_cyp21.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-87/out/m84036_250809_035451_s4.bc2184_paraphase/m84036_250809_035451_s4.bc2184_paraphase_vcfs/m84036_250809_035451_s4.bc2184_f8inv1.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-87/out/m84036_250809_035451_s4.bc2184_paraphase/m84036_250809_035451_s4.bc2184_paraphase_vcfs/m84036_250809_035451_s4.bc2184_f8inv22.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-87/out/m84036_250809_035451_s4.bc2184_paraphase/m84036_250809_035451_s4.bc2184_paraphase_vcfs/m84036_250809_035451_s4.bc2184_gba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-87/out/m84036_250809_035451_s4.bc2184_paraphase/m84036_250809_035451_s4.bc2184_paraphase_vcfs/m84036_250809_035451_s4.bc2184_hba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-87/out/m84036_250809_035451_s4.bc2184_paraphase/m84036_250809_035451_s4.bc2184_paraphase_vcfs/m84036_250809_035451_s4.bc2184_hbb.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-87/out/m84036_250809_035451_s4.bc2184_paraphase/m84036_250809_035451_s4.bc2184_paraphase_vcfs/m84036_250809_035451_s4.bc2184_rpgr.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-87/out/m84036_250809_035451_s4.bc2184_paraphase/m84036_250809_035451_s4.bc2184_paraphase_vcfs/m84036_250809_035451_s4.bc2184_smn1.vcf"], "havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-87/out/m84036_250809_035451_s4.bc2184.havanno.json", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-87/out/m84036_250809_035451_s4.bc2184.f8inversion.json"}
2025-09-15 20:31:13.984 wdl.w:ptcp NOTICE ready :: job: "call-tar_outputs-87", callee: "tar_outputs"
2025-09-15 20:31:13.984 wdl.w:ptcp INFO input :: job: "call-tar_outputs-87", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "sawfish_vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-87/out/m84036_250809_035451_s4.bc2184_sawfish/m84036_250809_035451_s4.bc2184.sv.vcf.gz.tbi", "sawfish_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-87/out/m84036_250809_035451_s4.bc2184_sawfish/m84036_250809_035451_s4.bc2184.sv.vcf.gz", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-87/out/m84036_250809_035451_s4.bc2184.f8inversion.json", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-87/out/m84036_250809_035451_s4.bc2184_paraphase/m84036_250809_035451_s4.bc2184.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-87/out/m84036_250809_035451_s4.bc2184_paraphase/m84036_250809_035451_s4.bc2184.paraphase.bam", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-87/out/m84036_250809_035451_s4.bc2184_paraphase/m84036_250809_035451_s4.bc2184.paraphase.json", "trgt_spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-87/out/m84036_250809_035451_s4.bc2184.trgt.sorted.spanning.bam.bai", "trgt_spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-87/out/m84036_250809_035451_s4.bc2184.trgt.sorted.spanning.bam", "trgt_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-87/out/m84036_250809_035451_s4.bc2184.trgt.vcf", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-87/out/m84036_250809_035451_s4.bc2184.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-87/out/m84036_250809_035451_s4.bc2184.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2184"}
2025-09-15 20:31:13.989 wdl.w:ptcp.t:call-tar_outputs-87 NOTICE task setup :: name: "tar_outputs", source: "./common.wdl", line: 279, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-87", thread: 140613580211776
2025-09-15 20:31:14.009 wdl.w:ptcp.t:call-tar_outputs-87 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:31:14.009 wdl.w:ptcp.t:call-tar_outputs-87 INFO input :: name: "sawfish_vcf_tbi", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2184.sv.vcf.gz.tbi"
2025-09-15 20:31:14.009 wdl.w:ptcp.t:call-tar_outputs-87 INFO input :: name: "sawfish_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2184.sv.vcf.gz"
2025-09-15 20:31:14.009 wdl.w:ptcp.t:call-tar_outputs-87 INFO input :: name: "f8_json", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2184.f8inversion.json"
2025-09-15 20:31:14.009 wdl.w:ptcp.t:call-tar_outputs-87 INFO input :: name: "paraphase_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2184.paraphase.bam.bai"
2025-09-15 20:31:14.009 wdl.w:ptcp.t:call-tar_outputs-87 INFO input :: name: "paraphase_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2184.paraphase.bam"
2025-09-15 20:31:14.009 wdl.w:ptcp.t:call-tar_outputs-87 INFO input :: name: "paraphase_json", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2184.paraphase.json"
2025-09-15 20:31:14.009 wdl.w:ptcp.t:call-tar_outputs-87 INFO input :: name: "trgt_spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2184.trgt.sorted.spanning.bam.bai"
2025-09-15 20:31:14.009 wdl.w:ptcp.t:call-tar_outputs-87 INFO input :: name: "trgt_spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2184.trgt.sorted.spanning.bam"
2025-09-15 20:31:14.009 wdl.w:ptcp.t:call-tar_outputs-87 INFO input :: name: "trgt_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2184.trgt.vcf"
2025-09-15 20:31:14.009 wdl.w:ptcp.t:call-tar_outputs-87 INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2184.mapped.bam.bai"
2025-09-15 20:31:14.009 wdl.w:ptcp.t:call-tar_outputs-87 INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2184.mapped.bam"
2025-09-15 20:31:14.009 wdl.w:ptcp.t:call-tar_outputs-87 INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2184"
2025-09-15 20:31:14.010 wdl.w:ptcp.t:call-tar_outputs-87 INFO eval :: name: "threads", value: 1
2025-09-15 20:31:14.010 wdl.w:ptcp.t:call-tar_outputs-87 INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:31:14.010 wdl.w:ptcp.t:call-tar_outputs-87 INFO eval :: name: "disk_size", value: 6
2025-09-15 20:31:14.010 wdl.w:ptcp.t:call-tar_outputs-87 INFO eval :: name: "output_tarball", value: "m84036_250809_035451_s4.bc2184.tar"
2025-09-15 20:31:14.010 wdl.w:ptcp.t:call-tar_outputs-87 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:31:14.011 wdl.w:ptcp.t:call-tar_outputs-87 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:31:14.011 wdl.w:ptcp.t:call-tar_outputs-87 INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:31:14.011 wdl.w:ptcp.t:call-tar_outputs-87 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:31:14.083 wdl.w:ptcp.t:call-tar_outputs-87 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 17, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-87/_singularity_tmpdir_wg815hub"
2025-09-15 20:31:14.083 wdl.w:ptcp.t:call-tar_outputs-87 INFO Slurm invocation: srun --job-name call-tar_outputs-87 --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-87/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-87/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-87/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-87/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-87/out/m84036_250809_035451_s4.bc2184_sawfish/m84036_250809_035451_s4.bc2184.sv.vcf.gz:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2184.sv.vcf.gz:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-87/out/m84036_250809_035451_s4.bc2184_sawfish/m84036_250809_035451_s4.bc2184.sv.vcf.gz.tbi:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2184.sv.vcf.gz.tbi:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-87/out/m84036_250809_035451_s4.bc2184.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2184.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-87/out/m84036_250809_035451_s4.bc2184.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2184.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-87/out/m84036_250809_035451_s4.bc2184.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2184.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-87/out/m84036_250809_035451_s4.bc2184_paraphase/m84036_250809_035451_s4.bc2184.paraphase.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2184.paraphase.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-87/out/m84036_250809_035451_s4.bc2184_paraphase/m84036_250809_035451_s4.bc2184.paraphase.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2184.paraphase.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-87/out/m84036_250809_035451_s4.bc2184_paraphase/m84036_250809_035451_s4.bc2184.paraphase.json:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2184.paraphase.json:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-87/out/m84036_250809_035451_s4.bc2184.f8inversion.json:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2184.f8inversion.json:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-87/out/m84036_250809_035451_s4.bc2184.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2184.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-87/out/m84036_250809_035451_s4.bc2184.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2184.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-87/_singularity_tmpdir_wg815hub/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-87/_singularity_tmpdir_wg815hub/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:31:14.086 wdl.w:ptcp.t:call-tar_outputs-87 NOTICE slurm_singularity run :: pid: 1210747, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-87/slurm_singularity.log.txt"
2025-09-15 20:31:15.088 wdl.w:ptcp.t:call-tar_outputs-87.stderr VERBOSE tar: Removing leading `/' from member names
2025-09-15 20:31:15.089 wdl.w:ptcp.t:call-tar_outputs-87.stderr VERBOSE tar: Removing leading `/' from hard link targets
2025-09-15 20:31:15.095 wdl.w:ptcp.t:call-tar_outputs-87.slurm_singularity INFO srun: job 51798363 queued and waiting for resources
2025-09-15 20:31:15.095 wdl.w:ptcp.t:call-tar_outputs-87.slurm_singularity INFO srun: job 51798363 has been allocated resources
2025-09-15 20:31:15.095 wdl.w:ptcp.t:call-tar_outputs-87.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:31:15.296 wdl.w:ptcp.t:call-tar_outputs-87 INFO output :: name: "sample_tarball", value: "m84036_250809_035451_s4.bc2184.tar"
2025-09-15 20:31:15.344 wdl.w:ptcp.t:call-tar_outputs-87 NOTICE done
2025-09-15 20:31:15.348 wdl.w:ptcp NOTICE finish :: job: "call-tar_outputs-87"
2025-09-15 20:31:15.348 wdl.w:ptcp INFO output :: job: "call-tar_outputs-87", values: {"sample_tarball": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-87/out/m84036_250809_035451_s4.bc2184.tar"}
2025-09-15 20:31:16.412 wdl.w:ptcp.w:call-paraphase-58.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for f8inv22 for sample m84036_250809_035451_s4.bc2155 at 2025-09-15 20:31:08.063884...
2025-09-15 20:31:18.249 wdl.w:ptcp.w:call-paraphase-03.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for f8inv22 for sample m84036_250809_035451_s4.bc2100 at 2025-09-15 20:30:50.057974...
2025-09-15 20:31:18.250 wdl.w:ptcp.w:call-paraphase-03.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for f8inv22 for sample m84036_250809_035451_s4.bc2100 at 2025-09-15 20:30:50.060351...
2025-09-15 20:31:21.479 wdl.w:ptcp.w:call-paraphase-67.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for f8inv22 for sample m84036_250809_035451_s4.bc2164 at 2025-09-15 20:30:48.023420...
2025-09-15 20:31:21.480 wdl.w:ptcp.w:call-paraphase-67.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for f8inv22 for sample m84036_250809_035451_s4.bc2164 at 2025-09-15 20:30:48.024155...
2025-09-15 20:31:21.480 wdl.w:ptcp.w:call-paraphase-67.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for f8inv22 for sample m84036_250809_035451_s4.bc2164 at 2025-09-15 20:30:49.414177...
2025-09-15 20:31:21.480 wdl.w:ptcp.w:call-paraphase-67.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for f8inv22 for sample m84036_250809_035451_s4.bc2164 at 2025-09-15 20:30:56.037900...
2025-09-15 20:31:21.480 wdl.w:ptcp.w:call-paraphase-67.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for f8inv22 for sample m84036_250809_035451_s4.bc2164 at 2025-09-15 20:30:56.500121...
2025-09-15 20:31:25.531 wdl.w:ptcp.w:call-paraphase-58.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for f8inv22 for sample m84036_250809_035451_s4.bc2155 at 2025-09-15 20:31:15.932089...
2025-09-15 20:31:25.531 wdl.w:ptcp.w:call-paraphase-58.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for f8inv22 for sample m84036_250809_035451_s4.bc2155 at 2025-09-15 20:31:16.510363...
2025-09-15 20:31:27.357 wdl.w:ptcp.w:call-paraphase-03.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for f8inv22 for sample m84036_250809_035451_s4.bc2100 at 2025-09-15 20:30:51.483770...
2025-09-15 20:31:27.357 wdl.w:ptcp.w:call-paraphase-03.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for f8inv22 for sample m84036_250809_035451_s4.bc2100 at 2025-09-15 20:30:58.807990...
2025-09-15 20:31:27.357 wdl.w:ptcp.w:call-paraphase-03.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for f8inv22 for sample m84036_250809_035451_s4.bc2100 at 2025-09-15 20:30:59.417523...
2025-09-15 20:31:27.405 wdl.w:ptcp.w:call-paraphase-67.t:call-run_paraphase INFO output :: name: "paraphase_bam", value: "m84036_250809_035451_s4.bc2164_paraphase/m84036_250809_035451_s4.bc2164.paraphase.bam"
2025-09-15 20:31:27.407 wdl.w:ptcp.w:call-paraphase-67.t:call-run_paraphase INFO output :: name: "paraphase_bam_bai", value: "m84036_250809_035451_s4.bc2164_paraphase/m84036_250809_035451_s4.bc2164.paraphase.bam.bai"
2025-09-15 20:31:27.408 wdl.w:ptcp.w:call-paraphase-67.t:call-run_paraphase INFO output :: name: "paraphase_json", value: "m84036_250809_035451_s4.bc2164_paraphase/m84036_250809_035451_s4.bc2164.paraphase.json"
2025-09-15 20:31:27.411 wdl.w:ptcp.w:call-paraphase-67.t:call-run_paraphase INFO output :: name: "paraphase_vcfs", value: ["/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2164_paraphase/m84036_250809_035451_s4.bc2164_paraphase_vcfs/m84036_250809_035451_s4.bc2164_cyp21.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2164_paraphase/m84036_250809_035451_s4.bc2164_paraphase_vcfs/m84036_250809_035451_s4.bc2164_f8inv1.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2164_paraphase/m84036_250809_035451_s4.bc2164_paraphase_vcfs/m84036_250809_035451_s4.bc2164_f8inv22.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2164_paraphase/m84036_250809_035451_s4.bc2164_paraphase_vcfs/m84036_250809_035451_s4.bc2164_gba.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2164_paraphase/m84036_250809_035451_s4.bc2164_paraphase_vcfs/m84036_250809_035451_s4.bc2164_hba.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2164_paraphase/m84036_250809_035451_s4.bc2164_paraphase_vcfs/m84036_250809_035451_s4.bc2164_hbb.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2164_paraphase/m84036_250809_035451_s4.bc2164_paraphase_vcfs/m84036_250809_035451_s4.bc2164_rpgr.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2164_paraphase/m84036_250809_035451_s4.bc2164_paraphase_vcfs/m84036_250809_035451_s4.bc2164_smn1.vcf"]
2025-09-15 20:31:27.414 wdl.w:ptcp.w:call-paraphase-67.t:call-run_paraphase INFO output :: name: "havanno_json", value: "m84036_250809_035451_s4.bc2164.havanno.json"
2025-09-15 20:31:27.604 wdl.w:ptcp.w:call-paraphase-67.t:call-run_paraphase NOTICE done
2025-09-15 20:31:27.639 wdl.w:ptcp.w:call-paraphase-67 NOTICE finish :: job: "call-run_paraphase"
2025-09-15 20:31:27.640 wdl.w:ptcp.w:call-paraphase-67 INFO output :: job: "call-run_paraphase", values: {"havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-67/call-run_paraphase/out/m84036_250809_035451_s4.bc2164.havanno.json", "paraphase_vcfs": ["/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-67/call-run_paraphase/out/m84036_250809_035451_s4.bc2164_paraphase/m84036_250809_035451_s4.bc2164_paraphase_vcfs/m84036_250809_035451_s4.bc2164_cyp21.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-67/call-run_paraphase/out/m84036_250809_035451_s4.bc2164_paraphase/m84036_250809_035451_s4.bc2164_paraphase_vcfs/m84036_250809_035451_s4.bc2164_f8inv1.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-67/call-run_paraphase/out/m84036_250809_035451_s4.bc2164_paraphase/m84036_250809_035451_s4.bc2164_paraphase_vcfs/m84036_250809_035451_s4.bc2164_f8inv22.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-67/call-run_paraphase/out/m84036_250809_035451_s4.bc2164_paraphase/m84036_250809_035451_s4.bc2164_paraphase_vcfs/m84036_250809_035451_s4.bc2164_gba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-67/call-run_paraphase/out/m84036_250809_035451_s4.bc2164_paraphase/m84036_250809_035451_s4.bc2164_paraphase_vcfs/m84036_250809_035451_s4.bc2164_hba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-67/call-run_paraphase/out/m84036_250809_035451_s4.bc2164_paraphase/m84036_250809_035451_s4.bc2164_paraphase_vcfs/m84036_250809_035451_s4.bc2164_hbb.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-67/call-run_paraphase/out/m84036_250809_035451_s4.bc2164_paraphase/m84036_250809_035451_s4.bc2164_paraphase_vcfs/m84036_250809_035451_s4.bc2164_rpgr.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-67/call-run_paraphase/out/m84036_250809_035451_s4.bc2164_paraphase/m84036_250809_035451_s4.bc2164_paraphase_vcfs/m84036_250809_035451_s4.bc2164_smn1.vcf"], "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-67/call-run_paraphase/out/m84036_250809_035451_s4.bc2164_paraphase/m84036_250809_035451_s4.bc2164.paraphase.json", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-67/call-run_paraphase/out/m84036_250809_035451_s4.bc2164_paraphase/m84036_250809_035451_s4.bc2164.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-67/call-run_paraphase/out/m84036_250809_035451_s4.bc2164_paraphase/m84036_250809_035451_s4.bc2164.paraphase.bam"}
2025-09-15 20:31:27.640 wdl.w:ptcp.w:call-paraphase-67 NOTICE ready :: job: "call-call_f8", callee: "call_f8"
2025-09-15 20:31:27.640 wdl.w:ptcp.w:call-paraphase-67 INFO input :: job: "call-call_f8", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "out_prefix": "m84036_250809_035451_s4.bc2164", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-67/call-run_paraphase/out/m84036_250809_035451_s4.bc2164_paraphase/m84036_250809_035451_s4.bc2164.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-67/call-run_paraphase/out/m84036_250809_035451_s4.bc2164_paraphase/m84036_250809_035451_s4.bc2164.paraphase.bam", "sex": "F"}
2025-09-15 20:31:27.641 wdl.w:ptcp.w:call-paraphase-67 INFO visit :: node: "output-havanno_json", values: {"havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-67/call-run_paraphase/out/m84036_250809_035451_s4.bc2164.havanno.json"}
2025-09-15 20:31:27.641 wdl.w:ptcp.w:call-paraphase-67 INFO visit :: node: "output-paraphase_bam", values: {"paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-67/call-run_paraphase/out/m84036_250809_035451_s4.bc2164_paraphase/m84036_250809_035451_s4.bc2164.paraphase.bam"}
2025-09-15 20:31:27.641 wdl.w:ptcp.w:call-paraphase-67 INFO visit :: node: "output-paraphase_bam_bai", values: {"paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-67/call-run_paraphase/out/m84036_250809_035451_s4.bc2164_paraphase/m84036_250809_035451_s4.bc2164.paraphase.bam.bai"}
2025-09-15 20:31:27.641 wdl.w:ptcp.w:call-paraphase-67 INFO visit :: node: "output-paraphase_json", values: {"paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-67/call-run_paraphase/out/m84036_250809_035451_s4.bc2164_paraphase/m84036_250809_035451_s4.bc2164.paraphase.json"}
2025-09-15 20:31:27.641 wdl.w:ptcp.w:call-paraphase-67 INFO visit :: node: "output-paraphase_vcfs", values: {"paraphase_vcfs": ["/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-67/call-run_paraphase/out/m84036_250809_035451_s4.bc2164_paraphase/m84036_250809_035451_s4.bc2164_paraphase_vcfs/m84036_250809_035451_s4.bc2164_cyp21.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-67/call-run_paraphase/out/m84036_250809_035451_s4.bc2164_paraphase/m84036_250809_035451_s4.bc2164_paraphase_vcfs/m84036_250809_035451_s4.bc2164_f8inv1.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-67/call-run_paraphase/out/m84036_250809_035451_s4.bc2164_paraphase/m84036_250809_035451_s4.bc2164_paraphase_vcfs/m84036_250809_035451_s4.bc2164_f8inv22.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-67/call-run_paraphase/out/m84036_250809_035451_s4.bc2164_paraphase/m84036_250809_035451_s4.bc2164_paraphase_vcfs/m84036_250809_035451_s4.bc2164_gba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-67/call-run_paraphase/out/m84036_250809_035451_s4.bc2164_paraphase/m84036_250809_035451_s4.bc2164_paraphase_vcfs/m84036_250809_035451_s4.bc2164_hba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-67/call-run_paraphase/out/m84036_250809_035451_s4.bc2164_paraphase/m84036_250809_035451_s4.bc2164_paraphase_vcfs/m84036_250809_035451_s4.bc2164_hbb.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-67/call-run_paraphase/out/m84036_250809_035451_s4.bc2164_paraphase/m84036_250809_035451_s4.bc2164_paraphase_vcfs/m84036_250809_035451_s4.bc2164_rpgr.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-67/call-run_paraphase/out/m84036_250809_035451_s4.bc2164_paraphase/m84036_250809_035451_s4.bc2164_paraphase_vcfs/m84036_250809_035451_s4.bc2164_smn1.vcf"]}
2025-09-15 20:31:27.646 wdl.w:ptcp.w:call-paraphase-67.t:call-call_f8 NOTICE task setup :: name: "call_f8", source: "./paraphase.wdl", line: 232, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-67/call-call_f8", thread: 140607137760832
2025-09-15 20:31:27.670 wdl.w:ptcp.w:call-paraphase-67.t:call-call_f8 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:31:27.670 wdl.w:ptcp.w:call-paraphase-67.t:call-call_f8 INFO input :: name: "genome_version", value: "38"
2025-09-15 20:31:27.670 wdl.w:ptcp.w:call-paraphase-67.t:call-call_f8 INFO input :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2164"
2025-09-15 20:31:27.670 wdl.w:ptcp.w:call-paraphase-67.t:call-call_f8 INFO input :: name: "paraphase_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2164.paraphase.bam.bai"
2025-09-15 20:31:27.670 wdl.w:ptcp.w:call-paraphase-67.t:call-call_f8 INFO input :: name: "paraphase_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2164.paraphase.bam"
2025-09-15 20:31:27.670 wdl.w:ptcp.w:call-paraphase-67.t:call-call_f8 INFO input :: name: "sex", value: "F"
2025-09-15 20:31:27.671 wdl.w:ptcp.w:call-paraphase-67.t:call-call_f8 INFO eval :: name: "threads", value: 1
2025-09-15 20:31:27.671 wdl.w:ptcp.w:call-paraphase-67.t:call-call_f8 INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:31:27.671 wdl.w:ptcp.w:call-paraphase-67.t:call-call_f8 INFO eval :: name: "disk_size", value: 11
2025-09-15 20:31:27.671 wdl.w:ptcp.w:call-paraphase-67.t:call-call_f8 INFO eval :: name: "sample_sex", value: "F"
2025-09-15 20:31:27.671 wdl.w:ptcp.w:call-paraphase-67.t:call-call_f8 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:31:27.672 wdl.w:ptcp.w:call-paraphase-67.t:call-call_f8 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:31:27.672 wdl.w:ptcp.w:call-paraphase-67.t:call-call_f8 INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:31:27.673 wdl.w:ptcp.w:call-paraphase-67.t:call-call_f8 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:31:27.708 wdl.w:ptcp.w:call-paraphase-67.t:call-call_f8 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 8, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-67/call-call_f8/_singularity_tmpdir_b56pxoiy"
2025-09-15 20:31:27.708 wdl.w:ptcp.w:call-paraphase-67.t:call-call_f8 INFO Slurm invocation: srun --job-name call-call_f8 --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-67/call-call_f8/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-67/call-call_f8/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-67/call-call_f8/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-67/call-call_f8/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-67/call-run_paraphase/out/m84036_250809_035451_s4.bc2164_paraphase/m84036_250809_035451_s4.bc2164.paraphase.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2164.paraphase.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-67/call-run_paraphase/out/m84036_250809_035451_s4.bc2164_paraphase/m84036_250809_035451_s4.bc2164.paraphase.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2164.paraphase.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-67/call-call_f8/_singularity_tmpdir_b56pxoiy/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-67/call-call_f8/_singularity_tmpdir_b56pxoiy/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:31:27.718 wdl.w:ptcp.w:call-paraphase-67.t:call-call_f8 NOTICE slurm_singularity run :: pid: 1210849, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-67/call-call_f8/slurm_singularity.log.txt"
2025-09-15 20:31:28.726 wdl.w:ptcp.w:call-paraphase-67.t:call-call_f8.slurm_singularity INFO srun: job 51798365 queued and waiting for resources
2025-09-15 20:31:28.726 wdl.w:ptcp.w:call-paraphase-67.t:call-call_f8.slurm_singularity INFO srun: job 51798365 has been allocated resources
2025-09-15 20:31:28.726 wdl.w:ptcp.w:call-paraphase-67.t:call-call_f8.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:31:28.994 wdl.w:ptcp.w:call-paraphase-66.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for f8inv22 for sample m84036_250809_035451_s4.bc2163 at 2025-09-15 20:30:55.681744...
2025-09-15 20:31:28.995 wdl.w:ptcp.w:call-paraphase-66.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for f8inv22 for sample m84036_250809_035451_s4.bc2163 at 2025-09-15 20:30:55.682523...
2025-09-15 20:31:28.995 wdl.w:ptcp.w:call-paraphase-66.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for f8inv22 for sample m84036_250809_035451_s4.bc2163 at 2025-09-15 20:30:57.277726...
2025-09-15 20:31:28.995 wdl.w:ptcp.w:call-paraphase-66.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for f8inv22 for sample m84036_250809_035451_s4.bc2163 at 2025-09-15 20:31:03.724707...
2025-09-15 20:31:28.995 wdl.w:ptcp.w:call-paraphase-66.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for f8inv22 for sample m84036_250809_035451_s4.bc2163 at 2025-09-15 20:31:04.237282...
2025-09-15 20:31:29.223 wdl.w:ptcp.w:call-paraphase-67.t:call-call_f8 INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2164.f8inversion.vcf"
2025-09-15 20:31:29.226 wdl.w:ptcp.w:call-paraphase-67.t:call-call_f8 INFO output :: name: "json", value: "m84036_250809_035451_s4.bc2164.f8inversion.json"
2025-09-15 20:31:29.273 wdl.w:ptcp.w:call-paraphase-67.t:call-call_f8 NOTICE done
2025-09-15 20:31:29.279 wdl.w:ptcp.w:call-paraphase-67 NOTICE finish :: job: "call-call_f8"
2025-09-15 20:31:29.280 wdl.w:ptcp.w:call-paraphase-67 INFO output :: job: "call-call_f8", values: {"json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-67/call-call_f8/out/m84036_250809_035451_s4.bc2164.f8inversion.json", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-67/call-call_f8/out/m84036_250809_035451_s4.bc2164.f8inversion.vcf"}
2025-09-15 20:31:29.280 wdl.w:ptcp.w:call-paraphase-67 INFO visit :: node: "output-f8_json", values: {"f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-67/call-call_f8/out/m84036_250809_035451_s4.bc2164.f8inversion.json"}
2025-09-15 20:31:29.280 wdl.w:ptcp.w:call-paraphase-67 INFO visit :: node: "output-f8_vcf", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-67/call-call_f8/out/m84036_250809_035451_s4.bc2164.f8inversion.vcf"}
2025-09-15 20:31:29.280 wdl.w:ptcp.w:call-paraphase-67 INFO visit :: node: "outputs", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-67/call-call_f8/out/m84036_250809_035451_s4.bc2164.f8inversion.vcf", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-67/call-run_paraphase/out/m84036_250809_035451_s4.bc2164_paraphase/m84036_250809_035451_s4.bc2164.paraphase.json", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-67/call-run_paraphase/out/m84036_250809_035451_s4.bc2164_paraphase/m84036_250809_035451_s4.bc2164.paraphase.bam", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-67/call-run_paraphase/out/m84036_250809_035451_s4.bc2164_paraphase/m84036_250809_035451_s4.bc2164.paraphase.bam.bai", "paraphase_vcfs": ["/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-67/call-run_paraphase/out/m84036_250809_035451_s4.bc2164_paraphase/m84036_250809_035451_s4.bc2164_paraphase_vcfs/m84036_250809_035451_s4.bc2164_cyp21.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-67/call-run_paraphase/out/m84036_250809_035451_s4.bc2164_paraphase/m84036_250809_035451_s4.bc2164_paraphase_vcfs/m84036_250809_035451_s4.bc2164_f8inv1.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-67/call-run_paraphase/out/m84036_250809_035451_s4.bc2164_paraphase/m84036_250809_035451_s4.bc2164_paraphase_vcfs/m84036_250809_035451_s4.bc2164_f8inv22.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-67/call-run_paraphase/out/m84036_250809_035451_s4.bc2164_paraphase/m84036_250809_035451_s4.bc2164_paraphase_vcfs/m84036_250809_035451_s4.bc2164_gba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-67/call-run_paraphase/out/m84036_250809_035451_s4.bc2164_paraphase/m84036_250809_035451_s4.bc2164_paraphase_vcfs/m84036_250809_035451_s4.bc2164_hba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-67/call-run_paraphase/out/m84036_250809_035451_s4.bc2164_paraphase/m84036_250809_035451_s4.bc2164_paraphase_vcfs/m84036_250809_035451_s4.bc2164_hbb.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-67/call-run_paraphase/out/m84036_250809_035451_s4.bc2164_paraphase/m84036_250809_035451_s4.bc2164_paraphase_vcfs/m84036_250809_035451_s4.bc2164_rpgr.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-67/call-run_paraphase/out/m84036_250809_035451_s4.bc2164_paraphase/m84036_250809_035451_s4.bc2164_paraphase_vcfs/m84036_250809_035451_s4.bc2164_smn1.vcf"], "havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-67/call-run_paraphase/out/m84036_250809_035451_s4.bc2164.havanno.json", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-67/call-call_f8/out/m84036_250809_035451_s4.bc2164.f8inversion.json"}
2025-09-15 20:31:29.376 wdl.w:ptcp.w:call-paraphase-67 NOTICE done
2025-09-15 20:31:29.397 wdl.w:ptcp NOTICE finish :: job: "call-paraphase-67"
2025-09-15 20:31:29.397 wdl.w:ptcp INFO output :: job: "call-paraphase-67", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-67/out/m84036_250809_035451_s4.bc2164.f8inversion.vcf", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-67/out/m84036_250809_035451_s4.bc2164_paraphase/m84036_250809_035451_s4.bc2164.paraphase.json", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-67/out/m84036_250809_035451_s4.bc2164_paraphase/m84036_250809_035451_s4.bc2164.paraphase.bam", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-67/out/m84036_250809_035451_s4.bc2164_paraphase/m84036_250809_035451_s4.bc2164.paraphase.bam.bai", "paraphase_vcfs": ["/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-67/out/m84036_250809_035451_s4.bc2164_paraphase/m84036_250809_035451_s4.bc2164_paraphase_vcfs/m84036_250809_035451_s4.bc2164_cyp21.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-67/out/m84036_250809_035451_s4.bc2164_paraphase/m84036_250809_035451_s4.bc2164_paraphase_vcfs/m84036_250809_035451_s4.bc2164_f8inv1.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-67/out/m84036_250809_035451_s4.bc2164_paraphase/m84036_250809_035451_s4.bc2164_paraphase_vcfs/m84036_250809_035451_s4.bc2164_f8inv22.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-67/out/m84036_250809_035451_s4.bc2164_paraphase/m84036_250809_035451_s4.bc2164_paraphase_vcfs/m84036_250809_035451_s4.bc2164_gba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-67/out/m84036_250809_035451_s4.bc2164_paraphase/m84036_250809_035451_s4.bc2164_paraphase_vcfs/m84036_250809_035451_s4.bc2164_hba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-67/out/m84036_250809_035451_s4.bc2164_paraphase/m84036_250809_035451_s4.bc2164_paraphase_vcfs/m84036_250809_035451_s4.bc2164_hbb.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-67/out/m84036_250809_035451_s4.bc2164_paraphase/m84036_250809_035451_s4.bc2164_paraphase_vcfs/m84036_250809_035451_s4.bc2164_rpgr.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-67/out/m84036_250809_035451_s4.bc2164_paraphase/m84036_250809_035451_s4.bc2164_paraphase_vcfs/m84036_250809_035451_s4.bc2164_smn1.vcf"], "havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-67/out/m84036_250809_035451_s4.bc2164.havanno.json", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-67/out/m84036_250809_035451_s4.bc2164.f8inversion.json"}
2025-09-15 20:31:29.398 wdl.w:ptcp NOTICE ready :: job: "call-tar_outputs-67", callee: "tar_outputs"
2025-09-15 20:31:29.398 wdl.w:ptcp INFO input :: job: "call-tar_outputs-67", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "sawfish_vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-67/out/m84036_250809_035451_s4.bc2164_sawfish/m84036_250809_035451_s4.bc2164.sv.vcf.gz.tbi", "sawfish_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-67/out/m84036_250809_035451_s4.bc2164_sawfish/m84036_250809_035451_s4.bc2164.sv.vcf.gz", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-67/out/m84036_250809_035451_s4.bc2164.f8inversion.json", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-67/out/m84036_250809_035451_s4.bc2164_paraphase/m84036_250809_035451_s4.bc2164.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-67/out/m84036_250809_035451_s4.bc2164_paraphase/m84036_250809_035451_s4.bc2164.paraphase.bam", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-67/out/m84036_250809_035451_s4.bc2164_paraphase/m84036_250809_035451_s4.bc2164.paraphase.json", "trgt_spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-67/out/m84036_250809_035451_s4.bc2164.trgt.sorted.spanning.bam.bai", "trgt_spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-67/out/m84036_250809_035451_s4.bc2164.trgt.sorted.spanning.bam", "trgt_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-67/out/m84036_250809_035451_s4.bc2164.trgt.vcf", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-67/out/m84036_250809_035451_s4.bc2164.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-67/out/m84036_250809_035451_s4.bc2164.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2164"}
2025-09-15 20:31:29.403 wdl.w:ptcp.t:call-tar_outputs-67 NOTICE task setup :: name: "tar_outputs", source: "./common.wdl", line: 279, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-67", thread: 140610342200896
2025-09-15 20:31:29.422 wdl.w:ptcp.t:call-tar_outputs-67 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:31:29.422 wdl.w:ptcp.t:call-tar_outputs-67 INFO input :: name: "sawfish_vcf_tbi", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2164.sv.vcf.gz.tbi"
2025-09-15 20:31:29.422 wdl.w:ptcp.t:call-tar_outputs-67 INFO input :: name: "sawfish_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2164.sv.vcf.gz"
2025-09-15 20:31:29.422 wdl.w:ptcp.t:call-tar_outputs-67 INFO input :: name: "f8_json", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2164.f8inversion.json"
2025-09-15 20:31:29.422 wdl.w:ptcp.t:call-tar_outputs-67 INFO input :: name: "paraphase_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2164.paraphase.bam.bai"
2025-09-15 20:31:29.422 wdl.w:ptcp.t:call-tar_outputs-67 INFO input :: name: "paraphase_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2164.paraphase.bam"
2025-09-15 20:31:29.422 wdl.w:ptcp.t:call-tar_outputs-67 INFO input :: name: "paraphase_json", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2164.paraphase.json"
2025-09-15 20:31:29.423 wdl.w:ptcp.t:call-tar_outputs-67 INFO input :: name: "trgt_spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2164.trgt.sorted.spanning.bam.bai"
2025-09-15 20:31:29.423 wdl.w:ptcp.t:call-tar_outputs-67 INFO input :: name: "trgt_spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2164.trgt.sorted.spanning.bam"
2025-09-15 20:31:29.423 wdl.w:ptcp.t:call-tar_outputs-67 INFO input :: name: "trgt_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2164.trgt.vcf"
2025-09-15 20:31:29.423 wdl.w:ptcp.t:call-tar_outputs-67 INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2164.mapped.bam.bai"
2025-09-15 20:31:29.423 wdl.w:ptcp.t:call-tar_outputs-67 INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2164.mapped.bam"
2025-09-15 20:31:29.423 wdl.w:ptcp.t:call-tar_outputs-67 INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2164"
2025-09-15 20:31:29.423 wdl.w:ptcp.t:call-tar_outputs-67 INFO eval :: name: "threads", value: 1
2025-09-15 20:31:29.423 wdl.w:ptcp.t:call-tar_outputs-67 INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:31:29.423 wdl.w:ptcp.t:call-tar_outputs-67 INFO eval :: name: "disk_size", value: 6
2025-09-15 20:31:29.423 wdl.w:ptcp.t:call-tar_outputs-67 INFO eval :: name: "output_tarball", value: "m84036_250809_035451_s4.bc2164.tar"
2025-09-15 20:31:29.424 wdl.w:ptcp.t:call-tar_outputs-67 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:31:29.424 wdl.w:ptcp.t:call-tar_outputs-67 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:31:29.424 wdl.w:ptcp.t:call-tar_outputs-67 INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:31:29.424 wdl.w:ptcp.t:call-tar_outputs-67 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:31:29.537 wdl.w:ptcp.t:call-tar_outputs-67 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 17, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-67/_singularity_tmpdir_s9jgea62"
2025-09-15 20:31:29.537 wdl.w:ptcp.t:call-tar_outputs-67 INFO Slurm invocation: srun --job-name call-tar_outputs-67 --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-67/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-67/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-67/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-67/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-67/out/m84036_250809_035451_s4.bc2164_paraphase/m84036_250809_035451_s4.bc2164.paraphase.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2164.paraphase.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-67/out/m84036_250809_035451_s4.bc2164_paraphase/m84036_250809_035451_s4.bc2164.paraphase.json:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2164.paraphase.json:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-67/out/m84036_250809_035451_s4.bc2164_paraphase/m84036_250809_035451_s4.bc2164.paraphase.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2164.paraphase.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-67/out/m84036_250809_035451_s4.bc2164.f8inversion.json:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2164.f8inversion.json:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-67/out/m84036_250809_035451_s4.bc2164.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2164.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-67/out/m84036_250809_035451_s4.bc2164.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2164.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-67/out/m84036_250809_035451_s4.bc2164.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2164.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-67/out/m84036_250809_035451_s4.bc2164_sawfish/m84036_250809_035451_s4.bc2164.sv.vcf.gz:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2164.sv.vcf.gz:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-67/out/m84036_250809_035451_s4.bc2164_sawfish/m84036_250809_035451_s4.bc2164.sv.vcf.gz.tbi:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2164.sv.vcf.gz.tbi:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-67/out/m84036_250809_035451_s4.bc2164.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2164.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-67/out/m84036_250809_035451_s4.bc2164.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2164.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-67/_singularity_tmpdir_s9jgea62/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-67/_singularity_tmpdir_s9jgea62/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:31:29.544 wdl.w:ptcp.t:call-tar_outputs-67 NOTICE slurm_singularity run :: pid: 1210859, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-67/slurm_singularity.log.txt"
2025-09-15 20:31:30.396 wdl.w:ptcp.w:call-paraphase-03.t:call-run_paraphase.stderr VERBOSE INFO:root:Merging all bams for sample m84036_250809_035451_s4.bc2100 at 2025-09-15 20:31:26.357422...
2025-09-15 20:31:30.397 wdl.w:ptcp.w:call-paraphase-03.t:call-run_paraphase.stderr VERBOSE INFO:root:Writing to json for sample m84036_250809_035451_s4.bc2100 at 2025-09-15 20:31:29.842449...
2025-09-15 20:31:30.397 wdl.w:ptcp.w:call-paraphase-03.t:call-run_paraphase.stderr VERBOSE INFO:root:Completed Paraphase analysis at 2025-09-15 20:31:30.190147...
2025-09-15 20:31:30.552 wdl.w:ptcp.t:call-tar_outputs-67.slurm_singularity INFO srun: job 51798366 queued and waiting for resources
2025-09-15 20:31:30.552 wdl.w:ptcp.t:call-tar_outputs-67.slurm_singularity INFO srun: job 51798366 has been allocated resources
2025-09-15 20:31:30.552 wdl.w:ptcp.t:call-tar_outputs-67.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:31:30.914 wdl.w:ptcp.w:call-paraphase-03.t:call-run_paraphase INFO output :: name: "paraphase_bam", value: "m84036_250809_035451_s4.bc2100_paraphase/m84036_250809_035451_s4.bc2100.paraphase.bam"
2025-09-15 20:31:30.919 wdl.w:ptcp.w:call-paraphase-03.t:call-run_paraphase INFO output :: name: "paraphase_bam_bai", value: "m84036_250809_035451_s4.bc2100_paraphase/m84036_250809_035451_s4.bc2100.paraphase.bam.bai"
2025-09-15 20:31:30.921 wdl.w:ptcp.w:call-paraphase-03.t:call-run_paraphase INFO output :: name: "paraphase_json", value: "m84036_250809_035451_s4.bc2100_paraphase/m84036_250809_035451_s4.bc2100.paraphase.json"
2025-09-15 20:31:30.926 wdl.w:ptcp.w:call-paraphase-03.t:call-run_paraphase INFO output :: name: "paraphase_vcfs", value: ["/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2100_paraphase/m84036_250809_035451_s4.bc2100_paraphase_vcfs/m84036_250809_035451_s4.bc2100_cyp21.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2100_paraphase/m84036_250809_035451_s4.bc2100_paraphase_vcfs/m84036_250809_035451_s4.bc2100_f8inv1.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2100_paraphase/m84036_250809_035451_s4.bc2100_paraphase_vcfs/m84036_250809_035451_s4.bc2100_f8inv22.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2100_paraphase/m84036_250809_035451_s4.bc2100_paraphase_vcfs/m84036_250809_035451_s4.bc2100_gba.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2100_paraphase/m84036_250809_035451_s4.bc2100_paraphase_vcfs/m84036_250809_035451_s4.bc2100_hba.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2100_paraphase/m84036_250809_035451_s4.bc2100_paraphase_vcfs/m84036_250809_035451_s4.bc2100_hbb.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2100_paraphase/m84036_250809_035451_s4.bc2100_paraphase_vcfs/m84036_250809_035451_s4.bc2100_rpgr.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2100_paraphase/m84036_250809_035451_s4.bc2100_paraphase_vcfs/m84036_250809_035451_s4.bc2100_smn1.vcf"]
2025-09-15 20:31:30.929 wdl.w:ptcp.w:call-paraphase-03.t:call-run_paraphase INFO output :: name: "havanno_json", value: "m84036_250809_035451_s4.bc2100.havanno.json"
2025-09-15 20:31:31.006 wdl.w:ptcp.t:call-tar_outputs-67 INFO output :: name: "sample_tarball", value: "m84036_250809_035451_s4.bc2164.tar"
2025-09-15 20:31:31.073 wdl.w:ptcp.t:call-tar_outputs-67 NOTICE done
2025-09-15 20:31:31.077 wdl.w:ptcp NOTICE finish :: job: "call-tar_outputs-67"
2025-09-15 20:31:31.077 wdl.w:ptcp INFO output :: job: "call-tar_outputs-67", values: {"sample_tarball": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-67/out/m84036_250809_035451_s4.bc2164.tar"}
2025-09-15 20:31:31.102 wdl.w:ptcp.w:call-paraphase-03.t:call-run_paraphase NOTICE done
2025-09-15 20:31:31.108 wdl.w:ptcp.w:call-paraphase-03 NOTICE finish :: job: "call-run_paraphase"
2025-09-15 20:31:31.108 wdl.w:ptcp.w:call-paraphase-03 INFO output :: job: "call-run_paraphase", values: {"havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-03/call-run_paraphase/out/m84036_250809_035451_s4.bc2100.havanno.json", "paraphase_vcfs": ["/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-03/call-run_paraphase/out/m84036_250809_035451_s4.bc2100_paraphase/m84036_250809_035451_s4.bc2100_paraphase_vcfs/m84036_250809_035451_s4.bc2100_cyp21.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-03/call-run_paraphase/out/m84036_250809_035451_s4.bc2100_paraphase/m84036_250809_035451_s4.bc2100_paraphase_vcfs/m84036_250809_035451_s4.bc2100_f8inv1.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-03/call-run_paraphase/out/m84036_250809_035451_s4.bc2100_paraphase/m84036_250809_035451_s4.bc2100_paraphase_vcfs/m84036_250809_035451_s4.bc2100_f8inv22.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-03/call-run_paraphase/out/m84036_250809_035451_s4.bc2100_paraphase/m84036_250809_035451_s4.bc2100_paraphase_vcfs/m84036_250809_035451_s4.bc2100_gba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-03/call-run_paraphase/out/m84036_250809_035451_s4.bc2100_paraphase/m84036_250809_035451_s4.bc2100_paraphase_vcfs/m84036_250809_035451_s4.bc2100_hba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-03/call-run_paraphase/out/m84036_250809_035451_s4.bc2100_paraphase/m84036_250809_035451_s4.bc2100_paraphase_vcfs/m84036_250809_035451_s4.bc2100_hbb.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-03/call-run_paraphase/out/m84036_250809_035451_s4.bc2100_paraphase/m84036_250809_035451_s4.bc2100_paraphase_vcfs/m84036_250809_035451_s4.bc2100_rpgr.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-03/call-run_paraphase/out/m84036_250809_035451_s4.bc2100_paraphase/m84036_250809_035451_s4.bc2100_paraphase_vcfs/m84036_250809_035451_s4.bc2100_smn1.vcf"], "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-03/call-run_paraphase/out/m84036_250809_035451_s4.bc2100_paraphase/m84036_250809_035451_s4.bc2100.paraphase.json", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-03/call-run_paraphase/out/m84036_250809_035451_s4.bc2100_paraphase/m84036_250809_035451_s4.bc2100.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-03/call-run_paraphase/out/m84036_250809_035451_s4.bc2100_paraphase/m84036_250809_035451_s4.bc2100.paraphase.bam"}
2025-09-15 20:31:31.109 wdl.w:ptcp.w:call-paraphase-03 NOTICE ready :: job: "call-call_f8", callee: "call_f8"
2025-09-15 20:31:31.109 wdl.w:ptcp.w:call-paraphase-03 INFO input :: job: "call-call_f8", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "out_prefix": "m84036_250809_035451_s4.bc2100", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-03/call-run_paraphase/out/m84036_250809_035451_s4.bc2100_paraphase/m84036_250809_035451_s4.bc2100.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-03/call-run_paraphase/out/m84036_250809_035451_s4.bc2100_paraphase/m84036_250809_035451_s4.bc2100.paraphase.bam", "sex": "F"}
2025-09-15 20:31:31.109 wdl.w:ptcp.w:call-paraphase-03 INFO visit :: node: "output-havanno_json", values: {"havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-03/call-run_paraphase/out/m84036_250809_035451_s4.bc2100.havanno.json"}
2025-09-15 20:31:31.110 wdl.w:ptcp.w:call-paraphase-03 INFO visit :: node: "output-paraphase_bam", values: {"paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-03/call-run_paraphase/out/m84036_250809_035451_s4.bc2100_paraphase/m84036_250809_035451_s4.bc2100.paraphase.bam"}
2025-09-15 20:31:31.110 wdl.w:ptcp.w:call-paraphase-03 INFO visit :: node: "output-paraphase_bam_bai", values: {"paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-03/call-run_paraphase/out/m84036_250809_035451_s4.bc2100_paraphase/m84036_250809_035451_s4.bc2100.paraphase.bam.bai"}
2025-09-15 20:31:31.110 wdl.w:ptcp.w:call-paraphase-03 INFO visit :: node: "output-paraphase_json", values: {"paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-03/call-run_paraphase/out/m84036_250809_035451_s4.bc2100_paraphase/m84036_250809_035451_s4.bc2100.paraphase.json"}
2025-09-15 20:31:31.110 wdl.w:ptcp.w:call-paraphase-03 INFO visit :: node: "output-paraphase_vcfs", values: {"paraphase_vcfs": ["/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-03/call-run_paraphase/out/m84036_250809_035451_s4.bc2100_paraphase/m84036_250809_035451_s4.bc2100_paraphase_vcfs/m84036_250809_035451_s4.bc2100_cyp21.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-03/call-run_paraphase/out/m84036_250809_035451_s4.bc2100_paraphase/m84036_250809_035451_s4.bc2100_paraphase_vcfs/m84036_250809_035451_s4.bc2100_f8inv1.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-03/call-run_paraphase/out/m84036_250809_035451_s4.bc2100_paraphase/m84036_250809_035451_s4.bc2100_paraphase_vcfs/m84036_250809_035451_s4.bc2100_f8inv22.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-03/call-run_paraphase/out/m84036_250809_035451_s4.bc2100_paraphase/m84036_250809_035451_s4.bc2100_paraphase_vcfs/m84036_250809_035451_s4.bc2100_gba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-03/call-run_paraphase/out/m84036_250809_035451_s4.bc2100_paraphase/m84036_250809_035451_s4.bc2100_paraphase_vcfs/m84036_250809_035451_s4.bc2100_hba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-03/call-run_paraphase/out/m84036_250809_035451_s4.bc2100_paraphase/m84036_250809_035451_s4.bc2100_paraphase_vcfs/m84036_250809_035451_s4.bc2100_hbb.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-03/call-run_paraphase/out/m84036_250809_035451_s4.bc2100_paraphase/m84036_250809_035451_s4.bc2100_paraphase_vcfs/m84036_250809_035451_s4.bc2100_rpgr.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-03/call-run_paraphase/out/m84036_250809_035451_s4.bc2100_paraphase/m84036_250809_035451_s4.bc2100_paraphase_vcfs/m84036_250809_035451_s4.bc2100_smn1.vcf"]}
2025-09-15 20:31:31.115 wdl.w:ptcp.w:call-paraphase-03.t:call-call_f8 NOTICE task setup :: name: "call_f8", source: "./paraphase.wdl", line: 232, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-03/call-call_f8", thread: 140611415942720
2025-09-15 20:31:31.141 wdl.w:ptcp.w:call-paraphase-03.t:call-call_f8 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:31:31.141 wdl.w:ptcp.w:call-paraphase-03.t:call-call_f8 INFO input :: name: "genome_version", value: "38"
2025-09-15 20:31:31.141 wdl.w:ptcp.w:call-paraphase-03.t:call-call_f8 INFO input :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2100"
2025-09-15 20:31:31.141 wdl.w:ptcp.w:call-paraphase-03.t:call-call_f8 INFO input :: name: "paraphase_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2100.paraphase.bam.bai"
2025-09-15 20:31:31.141 wdl.w:ptcp.w:call-paraphase-03.t:call-call_f8 INFO input :: name: "paraphase_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2100.paraphase.bam"
2025-09-15 20:31:31.141 wdl.w:ptcp.w:call-paraphase-03.t:call-call_f8 INFO input :: name: "sex", value: "F"
2025-09-15 20:31:31.143 wdl.w:ptcp.w:call-paraphase-03.t:call-call_f8 INFO eval :: name: "threads", value: 1
2025-09-15 20:31:31.143 wdl.w:ptcp.w:call-paraphase-03.t:call-call_f8 INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:31:31.143 wdl.w:ptcp.w:call-paraphase-03.t:call-call_f8 INFO eval :: name: "disk_size", value: 11
2025-09-15 20:31:31.143 wdl.w:ptcp.w:call-paraphase-03.t:call-call_f8 INFO eval :: name: "sample_sex", value: "F"
2025-09-15 20:31:31.143 wdl.w:ptcp.w:call-paraphase-03.t:call-call_f8 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:31:31.144 wdl.w:ptcp.w:call-paraphase-03.t:call-call_f8 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:31:31.144 wdl.w:ptcp.w:call-paraphase-03.t:call-call_f8 INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:31:31.144 wdl.w:ptcp.w:call-paraphase-03.t:call-call_f8 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:31:31.181 wdl.w:ptcp.w:call-paraphase-03.t:call-call_f8 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 8, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-03/call-call_f8/_singularity_tmpdir_6e9iu_my"
2025-09-15 20:31:31.181 wdl.w:ptcp.w:call-paraphase-03.t:call-call_f8 INFO Slurm invocation: srun --job-name call-call_f8 --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-03/call-call_f8/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-03/call-call_f8/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-03/call-call_f8/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-03/call-call_f8/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-03/call-run_paraphase/out/m84036_250809_035451_s4.bc2100_paraphase/m84036_250809_035451_s4.bc2100.paraphase.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2100.paraphase.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-03/call-run_paraphase/out/m84036_250809_035451_s4.bc2100_paraphase/m84036_250809_035451_s4.bc2100.paraphase.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2100.paraphase.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-03/call-call_f8/_singularity_tmpdir_6e9iu_my/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-03/call-call_f8/_singularity_tmpdir_6e9iu_my/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:31:31.185 wdl.w:ptcp.w:call-paraphase-03.t:call-call_f8 NOTICE slurm_singularity run :: pid: 1210959, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-03/call-call_f8/slurm_singularity.log.txt"
2025-09-15 20:31:32.193 wdl.w:ptcp.w:call-paraphase-03.t:call-call_f8.slurm_singularity INFO srun: job 51798367 queued and waiting for resources
2025-09-15 20:31:33.990 wdl.w:ptcp.w:call-paraphase-66.t:call-run_paraphase INFO output :: name: "paraphase_bam", value: "m84036_250809_035451_s4.bc2163_paraphase/m84036_250809_035451_s4.bc2163.paraphase.bam"
2025-09-15 20:31:33.994 wdl.w:ptcp.w:call-paraphase-66.t:call-run_paraphase INFO output :: name: "paraphase_bam_bai", value: "m84036_250809_035451_s4.bc2163_paraphase/m84036_250809_035451_s4.bc2163.paraphase.bam.bai"
2025-09-15 20:31:33.995 wdl.w:ptcp.w:call-paraphase-66.t:call-run_paraphase INFO output :: name: "paraphase_json", value: "m84036_250809_035451_s4.bc2163_paraphase/m84036_250809_035451_s4.bc2163.paraphase.json"
2025-09-15 20:31:33.999 wdl.w:ptcp.w:call-paraphase-66.t:call-run_paraphase INFO output :: name: "paraphase_vcfs", value: ["/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2163_paraphase/m84036_250809_035451_s4.bc2163_paraphase_vcfs/m84036_250809_035451_s4.bc2163_cyp21.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2163_paraphase/m84036_250809_035451_s4.bc2163_paraphase_vcfs/m84036_250809_035451_s4.bc2163_f8inv1.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2163_paraphase/m84036_250809_035451_s4.bc2163_paraphase_vcfs/m84036_250809_035451_s4.bc2163_f8inv22.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2163_paraphase/m84036_250809_035451_s4.bc2163_paraphase_vcfs/m84036_250809_035451_s4.bc2163_gba.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2163_paraphase/m84036_250809_035451_s4.bc2163_paraphase_vcfs/m84036_250809_035451_s4.bc2163_hba.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2163_paraphase/m84036_250809_035451_s4.bc2163_paraphase_vcfs/m84036_250809_035451_s4.bc2163_hbb.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2163_paraphase/m84036_250809_035451_s4.bc2163_paraphase_vcfs/m84036_250809_035451_s4.bc2163_rpgr.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2163_paraphase/m84036_250809_035451_s4.bc2163_paraphase_vcfs/m84036_250809_035451_s4.bc2163_smn1.vcf"]
2025-09-15 20:31:34.002 wdl.w:ptcp.w:call-paraphase-66.t:call-run_paraphase INFO output :: name: "havanno_json", value: "m84036_250809_035451_s4.bc2163.havanno.json"
2025-09-15 20:31:34.181 wdl.w:ptcp.w:call-paraphase-66.t:call-run_paraphase NOTICE done
2025-09-15 20:31:34.187 wdl.w:ptcp.w:call-paraphase-66 NOTICE finish :: job: "call-run_paraphase"
2025-09-15 20:31:34.187 wdl.w:ptcp.w:call-paraphase-66 INFO output :: job: "call-run_paraphase", values: {"havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-66/call-run_paraphase/out/m84036_250809_035451_s4.bc2163.havanno.json", "paraphase_vcfs": ["/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-66/call-run_paraphase/out/m84036_250809_035451_s4.bc2163_paraphase/m84036_250809_035451_s4.bc2163_paraphase_vcfs/m84036_250809_035451_s4.bc2163_cyp21.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-66/call-run_paraphase/out/m84036_250809_035451_s4.bc2163_paraphase/m84036_250809_035451_s4.bc2163_paraphase_vcfs/m84036_250809_035451_s4.bc2163_f8inv1.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-66/call-run_paraphase/out/m84036_250809_035451_s4.bc2163_paraphase/m84036_250809_035451_s4.bc2163_paraphase_vcfs/m84036_250809_035451_s4.bc2163_f8inv22.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-66/call-run_paraphase/out/m84036_250809_035451_s4.bc2163_paraphase/m84036_250809_035451_s4.bc2163_paraphase_vcfs/m84036_250809_035451_s4.bc2163_gba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-66/call-run_paraphase/out/m84036_250809_035451_s4.bc2163_paraphase/m84036_250809_035451_s4.bc2163_paraphase_vcfs/m84036_250809_035451_s4.bc2163_hba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-66/call-run_paraphase/out/m84036_250809_035451_s4.bc2163_paraphase/m84036_250809_035451_s4.bc2163_paraphase_vcfs/m84036_250809_035451_s4.bc2163_hbb.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-66/call-run_paraphase/out/m84036_250809_035451_s4.bc2163_paraphase/m84036_250809_035451_s4.bc2163_paraphase_vcfs/m84036_250809_035451_s4.bc2163_rpgr.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-66/call-run_paraphase/out/m84036_250809_035451_s4.bc2163_paraphase/m84036_250809_035451_s4.bc2163_paraphase_vcfs/m84036_250809_035451_s4.bc2163_smn1.vcf"], "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-66/call-run_paraphase/out/m84036_250809_035451_s4.bc2163_paraphase/m84036_250809_035451_s4.bc2163.paraphase.json", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-66/call-run_paraphase/out/m84036_250809_035451_s4.bc2163_paraphase/m84036_250809_035451_s4.bc2163.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-66/call-run_paraphase/out/m84036_250809_035451_s4.bc2163_paraphase/m84036_250809_035451_s4.bc2163.paraphase.bam"}
2025-09-15 20:31:34.188 wdl.w:ptcp.w:call-paraphase-66 NOTICE ready :: job: "call-call_f8", callee: "call_f8"
2025-09-15 20:31:34.188 wdl.w:ptcp.w:call-paraphase-66 INFO input :: job: "call-call_f8", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "out_prefix": "m84036_250809_035451_s4.bc2163", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-66/call-run_paraphase/out/m84036_250809_035451_s4.bc2163_paraphase/m84036_250809_035451_s4.bc2163.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-66/call-run_paraphase/out/m84036_250809_035451_s4.bc2163_paraphase/m84036_250809_035451_s4.bc2163.paraphase.bam", "sex": "F"}
2025-09-15 20:31:34.189 wdl.w:ptcp.w:call-paraphase-66 INFO visit :: node: "output-havanno_json", values: {"havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-66/call-run_paraphase/out/m84036_250809_035451_s4.bc2163.havanno.json"}
2025-09-15 20:31:34.189 wdl.w:ptcp.w:call-paraphase-66 INFO visit :: node: "output-paraphase_bam", values: {"paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-66/call-run_paraphase/out/m84036_250809_035451_s4.bc2163_paraphase/m84036_250809_035451_s4.bc2163.paraphase.bam"}
2025-09-15 20:31:34.189 wdl.w:ptcp.w:call-paraphase-66 INFO visit :: node: "output-paraphase_bam_bai", values: {"paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-66/call-run_paraphase/out/m84036_250809_035451_s4.bc2163_paraphase/m84036_250809_035451_s4.bc2163.paraphase.bam.bai"}
2025-09-15 20:31:34.189 wdl.w:ptcp.w:call-paraphase-66 INFO visit :: node: "output-paraphase_json", values: {"paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-66/call-run_paraphase/out/m84036_250809_035451_s4.bc2163_paraphase/m84036_250809_035451_s4.bc2163.paraphase.json"}
2025-09-15 20:31:34.189 wdl.w:ptcp.w:call-paraphase-66 INFO visit :: node: "output-paraphase_vcfs", values: {"paraphase_vcfs": ["/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-66/call-run_paraphase/out/m84036_250809_035451_s4.bc2163_paraphase/m84036_250809_035451_s4.bc2163_paraphase_vcfs/m84036_250809_035451_s4.bc2163_cyp21.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-66/call-run_paraphase/out/m84036_250809_035451_s4.bc2163_paraphase/m84036_250809_035451_s4.bc2163_paraphase_vcfs/m84036_250809_035451_s4.bc2163_f8inv1.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-66/call-run_paraphase/out/m84036_250809_035451_s4.bc2163_paraphase/m84036_250809_035451_s4.bc2163_paraphase_vcfs/m84036_250809_035451_s4.bc2163_f8inv22.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-66/call-run_paraphase/out/m84036_250809_035451_s4.bc2163_paraphase/m84036_250809_035451_s4.bc2163_paraphase_vcfs/m84036_250809_035451_s4.bc2163_gba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-66/call-run_paraphase/out/m84036_250809_035451_s4.bc2163_paraphase/m84036_250809_035451_s4.bc2163_paraphase_vcfs/m84036_250809_035451_s4.bc2163_hba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-66/call-run_paraphase/out/m84036_250809_035451_s4.bc2163_paraphase/m84036_250809_035451_s4.bc2163_paraphase_vcfs/m84036_250809_035451_s4.bc2163_hbb.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-66/call-run_paraphase/out/m84036_250809_035451_s4.bc2163_paraphase/m84036_250809_035451_s4.bc2163_paraphase_vcfs/m84036_250809_035451_s4.bc2163_rpgr.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-66/call-run_paraphase/out/m84036_250809_035451_s4.bc2163_paraphase/m84036_250809_035451_s4.bc2163_paraphase_vcfs/m84036_250809_035451_s4.bc2163_smn1.vcf"]}
2025-09-15 20:31:34.193 wdl.w:ptcp.w:call-paraphase-66.t:call-call_f8 NOTICE task setup :: name: "call_f8", source: "./paraphase.wdl", line: 232, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-66/call-call_f8", thread: 140613034948160
2025-09-15 20:31:34.209 wdl.w:ptcp.w:call-paraphase-66.t:call-call_f8 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:31:34.209 wdl.w:ptcp.w:call-paraphase-66.t:call-call_f8 INFO input :: name: "genome_version", value: "38"
2025-09-15 20:31:34.209 wdl.w:ptcp.w:call-paraphase-66.t:call-call_f8 INFO input :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2163"
2025-09-15 20:31:34.209 wdl.w:ptcp.w:call-paraphase-66.t:call-call_f8 INFO input :: name: "paraphase_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2163.paraphase.bam.bai"
2025-09-15 20:31:34.209 wdl.w:ptcp.w:call-paraphase-66.t:call-call_f8 INFO input :: name: "paraphase_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2163.paraphase.bam"
2025-09-15 20:31:34.209 wdl.w:ptcp.w:call-paraphase-66.t:call-call_f8 INFO input :: name: "sex", value: "F"
2025-09-15 20:31:34.209 wdl.w:ptcp.w:call-paraphase-66.t:call-call_f8 INFO eval :: name: "threads", value: 1
2025-09-15 20:31:34.209 wdl.w:ptcp.w:call-paraphase-66.t:call-call_f8 INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:31:34.209 wdl.w:ptcp.w:call-paraphase-66.t:call-call_f8 INFO eval :: name: "disk_size", value: 11
2025-09-15 20:31:34.210 wdl.w:ptcp.w:call-paraphase-66.t:call-call_f8 INFO eval :: name: "sample_sex", value: "F"
2025-09-15 20:31:34.210 wdl.w:ptcp.w:call-paraphase-66.t:call-call_f8 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:31:34.210 wdl.w:ptcp.w:call-paraphase-66.t:call-call_f8 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:31:34.210 wdl.w:ptcp.w:call-paraphase-66.t:call-call_f8 INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:31:34.210 wdl.w:ptcp.w:call-paraphase-66.t:call-call_f8 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:31:34.219 wdl.w:ptcp.w:call-paraphase-03.t:call-call_f8.slurm_singularity INFO srun: job 51798367 has been allocated resources
2025-09-15 20:31:34.220 wdl.w:ptcp.w:call-paraphase-03.t:call-call_f8.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:31:34.249 wdl.w:ptcp.w:call-paraphase-66.t:call-call_f8 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 8, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-66/call-call_f8/_singularity_tmpdir_ah24de_o"
2025-09-15 20:31:34.249 wdl.w:ptcp.w:call-paraphase-66.t:call-call_f8 INFO Slurm invocation: srun --job-name call-call_f8 --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-66/call-call_f8/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-66/call-call_f8/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-66/call-call_f8/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-66/call-call_f8/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-66/call-run_paraphase/out/m84036_250809_035451_s4.bc2163_paraphase/m84036_250809_035451_s4.bc2163.paraphase.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2163.paraphase.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-66/call-run_paraphase/out/m84036_250809_035451_s4.bc2163_paraphase/m84036_250809_035451_s4.bc2163.paraphase.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2163.paraphase.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-66/call-call_f8/_singularity_tmpdir_ah24de_o/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-66/call-call_f8/_singularity_tmpdir_ah24de_o/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:31:34.256 wdl.w:ptcp.w:call-paraphase-66.t:call-call_f8 NOTICE slurm_singularity run :: pid: 1210968, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-66/call-call_f8/slurm_singularity.log.txt"
2025-09-15 20:31:35.192 wdl.w:ptcp.w:call-paraphase-03.t:call-call_f8.stderr VERBOSE 2025-09-15 20:31:34,881 INFO  Started analysis for m84036_250809_035451_s4.bc2100 at 2025-09-15 20:31:34.881552...
2025-09-15 20:31:35.193 wdl.w:ptcp.w:call-paraphase-03.t:call-call_f8.stderr VERBOSE 2025-09-15 20:31:35,001 INFO  Completed analysis for m84036_250809_035451_s4.bc2100
2025-09-15 20:31:35.225 wdl.w:ptcp.w:call-paraphase-03.t:call-call_f8 INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2100.f8inversion.vcf"
2025-09-15 20:31:35.228 wdl.w:ptcp.w:call-paraphase-03.t:call-call_f8 INFO output :: name: "json", value: "m84036_250809_035451_s4.bc2100.f8inversion.json"
2025-09-15 20:31:35.265 wdl.w:ptcp.w:call-paraphase-66.t:call-call_f8.slurm_singularity INFO srun: job 51798374 queued and waiting for resources
2025-09-15 20:31:35.265 wdl.w:ptcp.w:call-paraphase-66.t:call-call_f8.slurm_singularity INFO srun: job 51798374 has been allocated resources
2025-09-15 20:31:35.278 wdl.w:ptcp.w:call-paraphase-03.t:call-call_f8 NOTICE done
2025-09-15 20:31:35.299 wdl.w:ptcp.w:call-paraphase-03 NOTICE finish :: job: "call-call_f8"
2025-09-15 20:31:35.299 wdl.w:ptcp.w:call-paraphase-03 INFO output :: job: "call-call_f8", values: {"json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-03/call-call_f8/out/m84036_250809_035451_s4.bc2100.f8inversion.json", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-03/call-call_f8/out/m84036_250809_035451_s4.bc2100.f8inversion.vcf"}
2025-09-15 20:31:35.300 wdl.w:ptcp.w:call-paraphase-03 INFO visit :: node: "output-f8_json", values: {"f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-03/call-call_f8/out/m84036_250809_035451_s4.bc2100.f8inversion.json"}
2025-09-15 20:31:35.300 wdl.w:ptcp.w:call-paraphase-03 INFO visit :: node: "output-f8_vcf", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-03/call-call_f8/out/m84036_250809_035451_s4.bc2100.f8inversion.vcf"}
2025-09-15 20:31:35.300 wdl.w:ptcp.w:call-paraphase-03 INFO visit :: node: "outputs", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-03/call-call_f8/out/m84036_250809_035451_s4.bc2100.f8inversion.vcf", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-03/call-run_paraphase/out/m84036_250809_035451_s4.bc2100_paraphase/m84036_250809_035451_s4.bc2100.paraphase.json", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-03/call-run_paraphase/out/m84036_250809_035451_s4.bc2100_paraphase/m84036_250809_035451_s4.bc2100.paraphase.bam", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-03/call-run_paraphase/out/m84036_250809_035451_s4.bc2100_paraphase/m84036_250809_035451_s4.bc2100.paraphase.bam.bai", "paraphase_vcfs": ["/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-03/call-run_paraphase/out/m84036_250809_035451_s4.bc2100_paraphase/m84036_250809_035451_s4.bc2100_paraphase_vcfs/m84036_250809_035451_s4.bc2100_cyp21.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-03/call-run_paraphase/out/m84036_250809_035451_s4.bc2100_paraphase/m84036_250809_035451_s4.bc2100_paraphase_vcfs/m84036_250809_035451_s4.bc2100_f8inv1.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-03/call-run_paraphase/out/m84036_250809_035451_s4.bc2100_paraphase/m84036_250809_035451_s4.bc2100_paraphase_vcfs/m84036_250809_035451_s4.bc2100_f8inv22.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-03/call-run_paraphase/out/m84036_250809_035451_s4.bc2100_paraphase/m84036_250809_035451_s4.bc2100_paraphase_vcfs/m84036_250809_035451_s4.bc2100_gba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-03/call-run_paraphase/out/m84036_250809_035451_s4.bc2100_paraphase/m84036_250809_035451_s4.bc2100_paraphase_vcfs/m84036_250809_035451_s4.bc2100_hba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-03/call-run_paraphase/out/m84036_250809_035451_s4.bc2100_paraphase/m84036_250809_035451_s4.bc2100_paraphase_vcfs/m84036_250809_035451_s4.bc2100_hbb.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-03/call-run_paraphase/out/m84036_250809_035451_s4.bc2100_paraphase/m84036_250809_035451_s4.bc2100_paraphase_vcfs/m84036_250809_035451_s4.bc2100_rpgr.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-03/call-run_paraphase/out/m84036_250809_035451_s4.bc2100_paraphase/m84036_250809_035451_s4.bc2100_paraphase_vcfs/m84036_250809_035451_s4.bc2100_smn1.vcf"], "havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-03/call-run_paraphase/out/m84036_250809_035451_s4.bc2100.havanno.json", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-03/call-call_f8/out/m84036_250809_035451_s4.bc2100.f8inversion.json"}
2025-09-15 20:31:35.399 wdl.w:ptcp.w:call-paraphase-03 NOTICE done
2025-09-15 20:31:35.405 wdl.w:ptcp NOTICE finish :: job: "call-paraphase-03"
2025-09-15 20:31:35.405 wdl.w:ptcp INFO output :: job: "call-paraphase-03", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-03/out/m84036_250809_035451_s4.bc2100.f8inversion.vcf", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-03/out/m84036_250809_035451_s4.bc2100_paraphase/m84036_250809_035451_s4.bc2100.paraphase.json", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-03/out/m84036_250809_035451_s4.bc2100_paraphase/m84036_250809_035451_s4.bc2100.paraphase.bam", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-03/out/m84036_250809_035451_s4.bc2100_paraphase/m84036_250809_035451_s4.bc2100.paraphase.bam.bai", "paraphase_vcfs": ["/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-03/out/m84036_250809_035451_s4.bc2100_paraphase/m84036_250809_035451_s4.bc2100_paraphase_vcfs/m84036_250809_035451_s4.bc2100_cyp21.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-03/out/m84036_250809_035451_s4.bc2100_paraphase/m84036_250809_035451_s4.bc2100_paraphase_vcfs/m84036_250809_035451_s4.bc2100_f8inv1.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-03/out/m84036_250809_035451_s4.bc2100_paraphase/m84036_250809_035451_s4.bc2100_paraphase_vcfs/m84036_250809_035451_s4.bc2100_f8inv22.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-03/out/m84036_250809_035451_s4.bc2100_paraphase/m84036_250809_035451_s4.bc2100_paraphase_vcfs/m84036_250809_035451_s4.bc2100_gba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-03/out/m84036_250809_035451_s4.bc2100_paraphase/m84036_250809_035451_s4.bc2100_paraphase_vcfs/m84036_250809_035451_s4.bc2100_hba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-03/out/m84036_250809_035451_s4.bc2100_paraphase/m84036_250809_035451_s4.bc2100_paraphase_vcfs/m84036_250809_035451_s4.bc2100_hbb.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-03/out/m84036_250809_035451_s4.bc2100_paraphase/m84036_250809_035451_s4.bc2100_paraphase_vcfs/m84036_250809_035451_s4.bc2100_rpgr.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-03/out/m84036_250809_035451_s4.bc2100_paraphase/m84036_250809_035451_s4.bc2100_paraphase_vcfs/m84036_250809_035451_s4.bc2100_smn1.vcf"], "havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-03/out/m84036_250809_035451_s4.bc2100.havanno.json", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-03/out/m84036_250809_035451_s4.bc2100.f8inversion.json"}
2025-09-15 20:31:35.406 wdl.w:ptcp NOTICE ready :: job: "call-tar_outputs-03", callee: "tar_outputs"
2025-09-15 20:31:35.406 wdl.w:ptcp INFO input :: job: "call-tar_outputs-03", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "sawfish_vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-03/out/m84036_250809_035451_s4.bc2100_sawfish/m84036_250809_035451_s4.bc2100.sv.vcf.gz.tbi", "sawfish_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-03/out/m84036_250809_035451_s4.bc2100_sawfish/m84036_250809_035451_s4.bc2100.sv.vcf.gz", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-03/out/m84036_250809_035451_s4.bc2100.f8inversion.json", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-03/out/m84036_250809_035451_s4.bc2100_paraphase/m84036_250809_035451_s4.bc2100.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-03/out/m84036_250809_035451_s4.bc2100_paraphase/m84036_250809_035451_s4.bc2100.paraphase.bam", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-03/out/m84036_250809_035451_s4.bc2100_paraphase/m84036_250809_035451_s4.bc2100.paraphase.json", "trgt_spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-03/out/m84036_250809_035451_s4.bc2100.trgt.sorted.spanning.bam.bai", "trgt_spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-03/out/m84036_250809_035451_s4.bc2100.trgt.sorted.spanning.bam", "trgt_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-03/out/m84036_250809_035451_s4.bc2100.trgt.vcf", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-03/out/m84036_250809_035451_s4.bc2100.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-03/out/m84036_250809_035451_s4.bc2100.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2100"}
2025-09-15 20:31:35.411 wdl.w:ptcp.t:call-tar_outputs-03 NOTICE task setup :: name: "tar_outputs", source: "./common.wdl", line: 279, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-03", thread: 140608756766272
2025-09-15 20:31:35.431 wdl.w:ptcp.t:call-tar_outputs-03 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:31:35.431 wdl.w:ptcp.t:call-tar_outputs-03 INFO input :: name: "sawfish_vcf_tbi", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2100.sv.vcf.gz.tbi"
2025-09-15 20:31:35.431 wdl.w:ptcp.t:call-tar_outputs-03 INFO input :: name: "sawfish_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2100.sv.vcf.gz"
2025-09-15 20:31:35.431 wdl.w:ptcp.t:call-tar_outputs-03 INFO input :: name: "f8_json", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2100.f8inversion.json"
2025-09-15 20:31:35.431 wdl.w:ptcp.t:call-tar_outputs-03 INFO input :: name: "paraphase_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2100.paraphase.bam.bai"
2025-09-15 20:31:35.431 wdl.w:ptcp.t:call-tar_outputs-03 INFO input :: name: "paraphase_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2100.paraphase.bam"
2025-09-15 20:31:35.431 wdl.w:ptcp.t:call-tar_outputs-03 INFO input :: name: "paraphase_json", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2100.paraphase.json"
2025-09-15 20:31:35.431 wdl.w:ptcp.t:call-tar_outputs-03 INFO input :: name: "trgt_spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2100.trgt.sorted.spanning.bam.bai"
2025-09-15 20:31:35.431 wdl.w:ptcp.t:call-tar_outputs-03 INFO input :: name: "trgt_spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2100.trgt.sorted.spanning.bam"
2025-09-15 20:31:35.431 wdl.w:ptcp.t:call-tar_outputs-03 INFO input :: name: "trgt_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2100.trgt.vcf"
2025-09-15 20:31:35.431 wdl.w:ptcp.t:call-tar_outputs-03 INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2100.mapped.bam.bai"
2025-09-15 20:31:35.431 wdl.w:ptcp.t:call-tar_outputs-03 INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2100.mapped.bam"
2025-09-15 20:31:35.431 wdl.w:ptcp.t:call-tar_outputs-03 INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2100"
2025-09-15 20:31:35.432 wdl.w:ptcp.t:call-tar_outputs-03 INFO eval :: name: "threads", value: 1
2025-09-15 20:31:35.432 wdl.w:ptcp.t:call-tar_outputs-03 INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:31:35.432 wdl.w:ptcp.t:call-tar_outputs-03 INFO eval :: name: "disk_size", value: 6
2025-09-15 20:31:35.432 wdl.w:ptcp.t:call-tar_outputs-03 INFO eval :: name: "output_tarball", value: "m84036_250809_035451_s4.bc2100.tar"
2025-09-15 20:31:35.432 wdl.w:ptcp.t:call-tar_outputs-03 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:31:35.432 wdl.w:ptcp.t:call-tar_outputs-03 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:31:35.433 wdl.w:ptcp.t:call-tar_outputs-03 INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:31:35.433 wdl.w:ptcp.t:call-tar_outputs-03 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:31:35.510 wdl.w:ptcp.t:call-tar_outputs-03 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 17, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-03/_singularity_tmpdir_byvaesmd"
2025-09-15 20:31:35.510 wdl.w:ptcp.t:call-tar_outputs-03 INFO Slurm invocation: srun --job-name call-tar_outputs-03 --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-03/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-03/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-03/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-03/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-03/out/m84036_250809_035451_s4.bc2100.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2100.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-03/out/m84036_250809_035451_s4.bc2100.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2100.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-03/out/m84036_250809_035451_s4.bc2100_sawfish/m84036_250809_035451_s4.bc2100.sv.vcf.gz:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2100.sv.vcf.gz:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-03/out/m84036_250809_035451_s4.bc2100_sawfish/m84036_250809_035451_s4.bc2100.sv.vcf.gz.tbi:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2100.sv.vcf.gz.tbi:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-03/out/m84036_250809_035451_s4.bc2100.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2100.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-03/out/m84036_250809_035451_s4.bc2100.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2100.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-03/out/m84036_250809_035451_s4.bc2100.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2100.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-03/out/m84036_250809_035451_s4.bc2100_paraphase/m84036_250809_035451_s4.bc2100.paraphase.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2100.paraphase.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-03/out/m84036_250809_035451_s4.bc2100_paraphase/m84036_250809_035451_s4.bc2100.paraphase.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2100.paraphase.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-03/out/m84036_250809_035451_s4.bc2100_paraphase/m84036_250809_035451_s4.bc2100.paraphase.json:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2100.paraphase.json:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-03/out/m84036_250809_035451_s4.bc2100.f8inversion.json:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2100.f8inversion.json:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-03/_singularity_tmpdir_byvaesmd/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-03/_singularity_tmpdir_byvaesmd/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:31:35.515 wdl.w:ptcp.t:call-tar_outputs-03 NOTICE slurm_singularity run :: pid: 1210977, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-03/slurm_singularity.log.txt"
2025-09-15 20:31:36.276 wdl.w:ptcp.w:call-paraphase-66.t:call-call_f8.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:31:36.517 wdl.w:ptcp.t:call-tar_outputs-03.stderr VERBOSE tar: Removing leading `/' from member names
2025-09-15 20:31:36.517 wdl.w:ptcp.t:call-tar_outputs-03.stderr VERBOSE tar: Removing leading `/' from hard link targets
2025-09-15 20:31:36.525 wdl.w:ptcp.t:call-tar_outputs-03.slurm_singularity INFO srun: job 51798375 queued and waiting for resources
2025-09-15 20:31:36.525 wdl.w:ptcp.t:call-tar_outputs-03.slurm_singularity INFO srun: job 51798375 has been allocated resources
2025-09-15 20:31:36.525 wdl.w:ptcp.t:call-tar_outputs-03.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:31:36.571 wdl.w:ptcp.w:call-paraphase-66.t:call-call_f8 INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2163.f8inversion.vcf"
2025-09-15 20:31:36.574 wdl.w:ptcp.w:call-paraphase-66.t:call-call_f8 INFO output :: name: "json", value: "m84036_250809_035451_s4.bc2163.f8inversion.json"
2025-09-15 20:31:36.623 wdl.w:ptcp.w:call-paraphase-66.t:call-call_f8 NOTICE done
2025-09-15 20:31:36.628 wdl.w:ptcp.w:call-paraphase-66 NOTICE finish :: job: "call-call_f8"
2025-09-15 20:31:36.628 wdl.w:ptcp.w:call-paraphase-66 INFO output :: job: "call-call_f8", values: {"json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-66/call-call_f8/out/m84036_250809_035451_s4.bc2163.f8inversion.json", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-66/call-call_f8/out/m84036_250809_035451_s4.bc2163.f8inversion.vcf"}
2025-09-15 20:31:36.628 wdl.w:ptcp.w:call-paraphase-66 INFO visit :: node: "output-f8_json", values: {"f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-66/call-call_f8/out/m84036_250809_035451_s4.bc2163.f8inversion.json"}
2025-09-15 20:31:36.628 wdl.w:ptcp.w:call-paraphase-66 INFO visit :: node: "output-f8_vcf", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-66/call-call_f8/out/m84036_250809_035451_s4.bc2163.f8inversion.vcf"}
2025-09-15 20:31:36.628 wdl.w:ptcp.w:call-paraphase-66 INFO visit :: node: "outputs", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-66/call-call_f8/out/m84036_250809_035451_s4.bc2163.f8inversion.vcf", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-66/call-run_paraphase/out/m84036_250809_035451_s4.bc2163_paraphase/m84036_250809_035451_s4.bc2163.paraphase.json", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-66/call-run_paraphase/out/m84036_250809_035451_s4.bc2163_paraphase/m84036_250809_035451_s4.bc2163.paraphase.bam", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-66/call-run_paraphase/out/m84036_250809_035451_s4.bc2163_paraphase/m84036_250809_035451_s4.bc2163.paraphase.bam.bai", "paraphase_vcfs": ["/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-66/call-run_paraphase/out/m84036_250809_035451_s4.bc2163_paraphase/m84036_250809_035451_s4.bc2163_paraphase_vcfs/m84036_250809_035451_s4.bc2163_cyp21.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-66/call-run_paraphase/out/m84036_250809_035451_s4.bc2163_paraphase/m84036_250809_035451_s4.bc2163_paraphase_vcfs/m84036_250809_035451_s4.bc2163_f8inv1.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-66/call-run_paraphase/out/m84036_250809_035451_s4.bc2163_paraphase/m84036_250809_035451_s4.bc2163_paraphase_vcfs/m84036_250809_035451_s4.bc2163_f8inv22.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-66/call-run_paraphase/out/m84036_250809_035451_s4.bc2163_paraphase/m84036_250809_035451_s4.bc2163_paraphase_vcfs/m84036_250809_035451_s4.bc2163_gba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-66/call-run_paraphase/out/m84036_250809_035451_s4.bc2163_paraphase/m84036_250809_035451_s4.bc2163_paraphase_vcfs/m84036_250809_035451_s4.bc2163_hba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-66/call-run_paraphase/out/m84036_250809_035451_s4.bc2163_paraphase/m84036_250809_035451_s4.bc2163_paraphase_vcfs/m84036_250809_035451_s4.bc2163_hbb.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-66/call-run_paraphase/out/m84036_250809_035451_s4.bc2163_paraphase/m84036_250809_035451_s4.bc2163_paraphase_vcfs/m84036_250809_035451_s4.bc2163_rpgr.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-66/call-run_paraphase/out/m84036_250809_035451_s4.bc2163_paraphase/m84036_250809_035451_s4.bc2163_paraphase_vcfs/m84036_250809_035451_s4.bc2163_smn1.vcf"], "havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-66/call-run_paraphase/out/m84036_250809_035451_s4.bc2163.havanno.json", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-66/call-call_f8/out/m84036_250809_035451_s4.bc2163.f8inversion.json"}
2025-09-15 20:31:36.681 wdl.w:ptcp.t:call-tar_outputs-03 INFO output :: name: "sample_tarball", value: "m84036_250809_035451_s4.bc2100.tar"
2025-09-15 20:31:36.736 wdl.w:ptcp.t:call-tar_outputs-03 NOTICE done
2025-09-15 20:31:36.740 wdl.w:ptcp NOTICE finish :: job: "call-tar_outputs-03"
2025-09-15 20:31:36.740 wdl.w:ptcp INFO output :: job: "call-tar_outputs-03", values: {"sample_tarball": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-03/out/m84036_250809_035451_s4.bc2100.tar"}
2025-09-15 20:31:36.749 wdl.w:ptcp.w:call-paraphase-66 NOTICE done
2025-09-15 20:31:36.778 wdl.w:ptcp NOTICE finish :: job: "call-paraphase-66"
2025-09-15 20:31:36.778 wdl.w:ptcp INFO output :: job: "call-paraphase-66", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-66/out/m84036_250809_035451_s4.bc2163.f8inversion.vcf", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-66/out/m84036_250809_035451_s4.bc2163_paraphase/m84036_250809_035451_s4.bc2163.paraphase.json", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-66/out/m84036_250809_035451_s4.bc2163_paraphase/m84036_250809_035451_s4.bc2163.paraphase.bam", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-66/out/m84036_250809_035451_s4.bc2163_paraphase/m84036_250809_035451_s4.bc2163.paraphase.bam.bai", "paraphase_vcfs": ["/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-66/out/m84036_250809_035451_s4.bc2163_paraphase/m84036_250809_035451_s4.bc2163_paraphase_vcfs/m84036_250809_035451_s4.bc2163_cyp21.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-66/out/m84036_250809_035451_s4.bc2163_paraphase/m84036_250809_035451_s4.bc2163_paraphase_vcfs/m84036_250809_035451_s4.bc2163_f8inv1.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-66/out/m84036_250809_035451_s4.bc2163_paraphase/m84036_250809_035451_s4.bc2163_paraphase_vcfs/m84036_250809_035451_s4.bc2163_f8inv22.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-66/out/m84036_250809_035451_s4.bc2163_paraphase/m84036_250809_035451_s4.bc2163_paraphase_vcfs/m84036_250809_035451_s4.bc2163_gba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-66/out/m84036_250809_035451_s4.bc2163_paraphase/m84036_250809_035451_s4.bc2163_paraphase_vcfs/m84036_250809_035451_s4.bc2163_hba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-66/out/m84036_250809_035451_s4.bc2163_paraphase/m84036_250809_035451_s4.bc2163_paraphase_vcfs/m84036_250809_035451_s4.bc2163_hbb.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-66/out/m84036_250809_035451_s4.bc2163_paraphase/m84036_250809_035451_s4.bc2163_paraphase_vcfs/m84036_250809_035451_s4.bc2163_rpgr.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-66/out/m84036_250809_035451_s4.bc2163_paraphase/m84036_250809_035451_s4.bc2163_paraphase_vcfs/m84036_250809_035451_s4.bc2163_smn1.vcf"], "havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-66/out/m84036_250809_035451_s4.bc2163.havanno.json", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-66/out/m84036_250809_035451_s4.bc2163.f8inversion.json"}
2025-09-15 20:31:36.779 wdl.w:ptcp NOTICE ready :: job: "call-tar_outputs-66", callee: "tar_outputs"
2025-09-15 20:31:36.779 wdl.w:ptcp INFO input :: job: "call-tar_outputs-66", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "sawfish_vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-66/out/m84036_250809_035451_s4.bc2163_sawfish/m84036_250809_035451_s4.bc2163.sv.vcf.gz.tbi", "sawfish_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-66/out/m84036_250809_035451_s4.bc2163_sawfish/m84036_250809_035451_s4.bc2163.sv.vcf.gz", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-66/out/m84036_250809_035451_s4.bc2163.f8inversion.json", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-66/out/m84036_250809_035451_s4.bc2163_paraphase/m84036_250809_035451_s4.bc2163.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-66/out/m84036_250809_035451_s4.bc2163_paraphase/m84036_250809_035451_s4.bc2163.paraphase.bam", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-66/out/m84036_250809_035451_s4.bc2163_paraphase/m84036_250809_035451_s4.bc2163.paraphase.json", "trgt_spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-66/out/m84036_250809_035451_s4.bc2163.trgt.sorted.spanning.bam.bai", "trgt_spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-66/out/m84036_250809_035451_s4.bc2163.trgt.sorted.spanning.bam", "trgt_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-66/out/m84036_250809_035451_s4.bc2163.trgt.vcf", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-66/out/m84036_250809_035451_s4.bc2163.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-66/out/m84036_250809_035451_s4.bc2163.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2163"}
2025-09-15 20:31:36.784 wdl.w:ptcp.t:call-tar_outputs-66 NOTICE task setup :: name: "tar_outputs", source: "./common.wdl", line: 279, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-66", thread: 140607146153536
2025-09-15 20:31:36.804 wdl.w:ptcp.t:call-tar_outputs-66 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:31:36.804 wdl.w:ptcp.t:call-tar_outputs-66 INFO input :: name: "sawfish_vcf_tbi", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2163.sv.vcf.gz.tbi"
2025-09-15 20:31:36.804 wdl.w:ptcp.t:call-tar_outputs-66 INFO input :: name: "sawfish_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2163.sv.vcf.gz"
2025-09-15 20:31:36.804 wdl.w:ptcp.t:call-tar_outputs-66 INFO input :: name: "f8_json", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2163.f8inversion.json"
2025-09-15 20:31:36.804 wdl.w:ptcp.t:call-tar_outputs-66 INFO input :: name: "paraphase_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2163.paraphase.bam.bai"
2025-09-15 20:31:36.804 wdl.w:ptcp.t:call-tar_outputs-66 INFO input :: name: "paraphase_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2163.paraphase.bam"
2025-09-15 20:31:36.804 wdl.w:ptcp.t:call-tar_outputs-66 INFO input :: name: "paraphase_json", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2163.paraphase.json"
2025-09-15 20:31:36.804 wdl.w:ptcp.t:call-tar_outputs-66 INFO input :: name: "trgt_spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2163.trgt.sorted.spanning.bam.bai"
2025-09-15 20:31:36.804 wdl.w:ptcp.t:call-tar_outputs-66 INFO input :: name: "trgt_spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2163.trgt.sorted.spanning.bam"
2025-09-15 20:31:36.804 wdl.w:ptcp.t:call-tar_outputs-66 INFO input :: name: "trgt_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2163.trgt.vcf"
2025-09-15 20:31:36.804 wdl.w:ptcp.t:call-tar_outputs-66 INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2163.mapped.bam.bai"
2025-09-15 20:31:36.804 wdl.w:ptcp.t:call-tar_outputs-66 INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2163.mapped.bam"
2025-09-15 20:31:36.804 wdl.w:ptcp.t:call-tar_outputs-66 INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2163"
2025-09-15 20:31:36.805 wdl.w:ptcp.t:call-tar_outputs-66 INFO eval :: name: "threads", value: 1
2025-09-15 20:31:36.805 wdl.w:ptcp.t:call-tar_outputs-66 INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:31:36.805 wdl.w:ptcp.t:call-tar_outputs-66 INFO eval :: name: "disk_size", value: 6
2025-09-15 20:31:36.805 wdl.w:ptcp.t:call-tar_outputs-66 INFO eval :: name: "output_tarball", value: "m84036_250809_035451_s4.bc2163.tar"
2025-09-15 20:31:36.805 wdl.w:ptcp.t:call-tar_outputs-66 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:31:36.805 wdl.w:ptcp.t:call-tar_outputs-66 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:31:36.806 wdl.w:ptcp.t:call-tar_outputs-66 INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:31:36.806 wdl.w:ptcp.t:call-tar_outputs-66 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:31:36.886 wdl.w:ptcp.t:call-tar_outputs-66 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 17, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-66/_singularity_tmpdir_80na04vj"
2025-09-15 20:31:36.886 wdl.w:ptcp.t:call-tar_outputs-66 INFO Slurm invocation: srun --job-name call-tar_outputs-66 --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-66/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-66/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-66/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-66/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-66/out/m84036_250809_035451_s4.bc2163_sawfish/m84036_250809_035451_s4.bc2163.sv.vcf.gz:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2163.sv.vcf.gz:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-66/out/m84036_250809_035451_s4.bc2163_sawfish/m84036_250809_035451_s4.bc2163.sv.vcf.gz.tbi:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2163.sv.vcf.gz.tbi:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-66/out/m84036_250809_035451_s4.bc2163.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2163.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-66/out/m84036_250809_035451_s4.bc2163.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2163.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-66/out/m84036_250809_035451_s4.bc2163.f8inversion.json:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2163.f8inversion.json:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-66/out/m84036_250809_035451_s4.bc2163_paraphase/m84036_250809_035451_s4.bc2163.paraphase.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2163.paraphase.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-66/out/m84036_250809_035451_s4.bc2163_paraphase/m84036_250809_035451_s4.bc2163.paraphase.json:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2163.paraphase.json:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-66/out/m84036_250809_035451_s4.bc2163_paraphase/m84036_250809_035451_s4.bc2163.paraphase.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2163.paraphase.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-66/out/m84036_250809_035451_s4.bc2163.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2163.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-66/out/m84036_250809_035451_s4.bc2163.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2163.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-66/out/m84036_250809_035451_s4.bc2163.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2163.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-66/_singularity_tmpdir_80na04vj/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-66/_singularity_tmpdir_80na04vj/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:31:36.889 wdl.w:ptcp.t:call-tar_outputs-66 NOTICE slurm_singularity run :: pid: 1210987, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-66/slurm_singularity.log.txt"
2025-09-15 20:31:37.482 wdl.w:ptcp.w:call-paraphase-83.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for rpgr for sample m84036_250809_035451_s4.bc2180 at 2025-09-15 20:30:46.872011...
2025-09-15 20:31:37.482 wdl.w:ptcp.w:call-paraphase-83.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for rpgr for sample m84036_250809_035451_s4.bc2180 at 2025-09-15 20:30:48.349568...
2025-09-15 20:31:37.482 wdl.w:ptcp.w:call-paraphase-83.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for rpgr for sample m84036_250809_035451_s4.bc2180 at 2025-09-15 20:30:48.522959...
2025-09-15 20:31:37.484 wdl.w:ptcp.w:call-paraphase-90.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for f8inv22 for sample m84036_250809_035451_s4.bc2187 at 2025-09-15 20:31:27.550659...
2025-09-15 20:31:37.485 wdl.w:ptcp.w:call-paraphase-90.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for f8inv22 for sample m84036_250809_035451_s4.bc2187 at 2025-09-15 20:31:27.552940...
2025-09-15 20:31:37.486 wdl.w:ptcp.w:call-paraphase-90.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for f8inv22 for sample m84036_250809_035451_s4.bc2187 at 2025-09-15 20:31:28.568305...
2025-09-15 20:31:37.891 wdl.w:ptcp.t:call-tar_outputs-66.stderr VERBOSE tar: Removing leading `/' from member names
2025-09-15 20:31:37.891 wdl.w:ptcp.t:call-tar_outputs-66.stderr VERBOSE tar: Removing leading `/' from hard link targets
2025-09-15 20:31:37.898 wdl.w:ptcp.t:call-tar_outputs-66.slurm_singularity INFO srun: job 51798376 queued and waiting for resources
2025-09-15 20:31:37.898 wdl.w:ptcp.t:call-tar_outputs-66.slurm_singularity INFO srun: job 51798376 has been allocated resources
2025-09-15 20:31:37.898 wdl.w:ptcp.t:call-tar_outputs-66.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:31:37.923 wdl.w:ptcp.t:call-tar_outputs-66 INFO output :: name: "sample_tarball", value: "m84036_250809_035451_s4.bc2163.tar"
2025-09-15 20:31:37.974 wdl.w:ptcp.t:call-tar_outputs-66 NOTICE done
2025-09-15 20:31:37.977 wdl.w:ptcp NOTICE finish :: job: "call-tar_outputs-66"
2025-09-15 20:31:37.977 wdl.w:ptcp INFO output :: job: "call-tar_outputs-66", values: {"sample_tarball": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-66/out/m84036_250809_035451_s4.bc2163.tar"}
2025-09-15 20:31:40.526 wdl.w:ptcp.w:call-paraphase-90.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for f8inv22 for sample m84036_250809_035451_s4.bc2187 at 2025-09-15 20:31:33.969746...
2025-09-15 20:31:40.527 wdl.w:ptcp.w:call-paraphase-90.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for f8inv22 for sample m84036_250809_035451_s4.bc2187 at 2025-09-15 20:31:34.337426...
2025-09-15 20:31:51.107 wdl.w:ptcp.w:call-paraphase-58.t:call-run_paraphase INFO output :: name: "paraphase_bam", value: "m84036_250809_035451_s4.bc2155_paraphase/m84036_250809_035451_s4.bc2155.paraphase.bam"
2025-09-15 20:31:51.110 wdl.w:ptcp.w:call-paraphase-58.t:call-run_paraphase INFO output :: name: "paraphase_bam_bai", value: "m84036_250809_035451_s4.bc2155_paraphase/m84036_250809_035451_s4.bc2155.paraphase.bam.bai"
2025-09-15 20:31:51.111 wdl.w:ptcp.w:call-paraphase-58.t:call-run_paraphase INFO output :: name: "paraphase_json", value: "m84036_250809_035451_s4.bc2155_paraphase/m84036_250809_035451_s4.bc2155.paraphase.json"
2025-09-15 20:31:51.115 wdl.w:ptcp.w:call-paraphase-58.t:call-run_paraphase INFO output :: name: "paraphase_vcfs", value: ["/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2155_paraphase/m84036_250809_035451_s4.bc2155_paraphase_vcfs/m84036_250809_035451_s4.bc2155_cyp21.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2155_paraphase/m84036_250809_035451_s4.bc2155_paraphase_vcfs/m84036_250809_035451_s4.bc2155_f8inv1.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2155_paraphase/m84036_250809_035451_s4.bc2155_paraphase_vcfs/m84036_250809_035451_s4.bc2155_f8inv22.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2155_paraphase/m84036_250809_035451_s4.bc2155_paraphase_vcfs/m84036_250809_035451_s4.bc2155_gba.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2155_paraphase/m84036_250809_035451_s4.bc2155_paraphase_vcfs/m84036_250809_035451_s4.bc2155_hba.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2155_paraphase/m84036_250809_035451_s4.bc2155_paraphase_vcfs/m84036_250809_035451_s4.bc2155_hbb.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2155_paraphase/m84036_250809_035451_s4.bc2155_paraphase_vcfs/m84036_250809_035451_s4.bc2155_rpgr.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2155_paraphase/m84036_250809_035451_s4.bc2155_paraphase_vcfs/m84036_250809_035451_s4.bc2155_smn1.vcf"]
2025-09-15 20:31:51.118 wdl.w:ptcp.w:call-paraphase-58.t:call-run_paraphase INFO output :: name: "havanno_json", value: "m84036_250809_035451_s4.bc2155.havanno.json"
2025-09-15 20:31:51.252 wdl.w:ptcp.w:call-paraphase-58.t:call-run_paraphase NOTICE done
2025-09-15 20:31:51.257 wdl.w:ptcp.w:call-paraphase-58 NOTICE finish :: job: "call-run_paraphase"
2025-09-15 20:31:51.257 wdl.w:ptcp.w:call-paraphase-58 INFO output :: job: "call-run_paraphase", values: {"havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-58/call-run_paraphase/out/m84036_250809_035451_s4.bc2155.havanno.json", "paraphase_vcfs": ["/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-58/call-run_paraphase/out/m84036_250809_035451_s4.bc2155_paraphase/m84036_250809_035451_s4.bc2155_paraphase_vcfs/m84036_250809_035451_s4.bc2155_cyp21.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-58/call-run_paraphase/out/m84036_250809_035451_s4.bc2155_paraphase/m84036_250809_035451_s4.bc2155_paraphase_vcfs/m84036_250809_035451_s4.bc2155_f8inv1.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-58/call-run_paraphase/out/m84036_250809_035451_s4.bc2155_paraphase/m84036_250809_035451_s4.bc2155_paraphase_vcfs/m84036_250809_035451_s4.bc2155_f8inv22.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-58/call-run_paraphase/out/m84036_250809_035451_s4.bc2155_paraphase/m84036_250809_035451_s4.bc2155_paraphase_vcfs/m84036_250809_035451_s4.bc2155_gba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-58/call-run_paraphase/out/m84036_250809_035451_s4.bc2155_paraphase/m84036_250809_035451_s4.bc2155_paraphase_vcfs/m84036_250809_035451_s4.bc2155_hba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-58/call-run_paraphase/out/m84036_250809_035451_s4.bc2155_paraphase/m84036_250809_035451_s4.bc2155_paraphase_vcfs/m84036_250809_035451_s4.bc2155_hbb.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-58/call-run_paraphase/out/m84036_250809_035451_s4.bc2155_paraphase/m84036_250809_035451_s4.bc2155_paraphase_vcfs/m84036_250809_035451_s4.bc2155_rpgr.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-58/call-run_paraphase/out/m84036_250809_035451_s4.bc2155_paraphase/m84036_250809_035451_s4.bc2155_paraphase_vcfs/m84036_250809_035451_s4.bc2155_smn1.vcf"], "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-58/call-run_paraphase/out/m84036_250809_035451_s4.bc2155_paraphase/m84036_250809_035451_s4.bc2155.paraphase.json", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-58/call-run_paraphase/out/m84036_250809_035451_s4.bc2155_paraphase/m84036_250809_035451_s4.bc2155.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-58/call-run_paraphase/out/m84036_250809_035451_s4.bc2155_paraphase/m84036_250809_035451_s4.bc2155.paraphase.bam"}
2025-09-15 20:31:51.258 wdl.w:ptcp.w:call-paraphase-58 NOTICE ready :: job: "call-call_f8", callee: "call_f8"
2025-09-15 20:31:51.258 wdl.w:ptcp.w:call-paraphase-58 INFO input :: job: "call-call_f8", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "out_prefix": "m84036_250809_035451_s4.bc2155", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-58/call-run_paraphase/out/m84036_250809_035451_s4.bc2155_paraphase/m84036_250809_035451_s4.bc2155.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-58/call-run_paraphase/out/m84036_250809_035451_s4.bc2155_paraphase/m84036_250809_035451_s4.bc2155.paraphase.bam", "sex": "F"}
2025-09-15 20:31:51.258 wdl.w:ptcp.w:call-paraphase-58 INFO visit :: node: "output-havanno_json", values: {"havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-58/call-run_paraphase/out/m84036_250809_035451_s4.bc2155.havanno.json"}
2025-09-15 20:31:51.259 wdl.w:ptcp.w:call-paraphase-58 INFO visit :: node: "output-paraphase_bam", values: {"paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-58/call-run_paraphase/out/m84036_250809_035451_s4.bc2155_paraphase/m84036_250809_035451_s4.bc2155.paraphase.bam"}
2025-09-15 20:31:51.259 wdl.w:ptcp.w:call-paraphase-58 INFO visit :: node: "output-paraphase_bam_bai", values: {"paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-58/call-run_paraphase/out/m84036_250809_035451_s4.bc2155_paraphase/m84036_250809_035451_s4.bc2155.paraphase.bam.bai"}
2025-09-15 20:31:51.259 wdl.w:ptcp.w:call-paraphase-58 INFO visit :: node: "output-paraphase_json", values: {"paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-58/call-run_paraphase/out/m84036_250809_035451_s4.bc2155_paraphase/m84036_250809_035451_s4.bc2155.paraphase.json"}
2025-09-15 20:31:51.259 wdl.w:ptcp.w:call-paraphase-58 INFO visit :: node: "output-paraphase_vcfs", values: {"paraphase_vcfs": ["/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-58/call-run_paraphase/out/m84036_250809_035451_s4.bc2155_paraphase/m84036_250809_035451_s4.bc2155_paraphase_vcfs/m84036_250809_035451_s4.bc2155_cyp21.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-58/call-run_paraphase/out/m84036_250809_035451_s4.bc2155_paraphase/m84036_250809_035451_s4.bc2155_paraphase_vcfs/m84036_250809_035451_s4.bc2155_f8inv1.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-58/call-run_paraphase/out/m84036_250809_035451_s4.bc2155_paraphase/m84036_250809_035451_s4.bc2155_paraphase_vcfs/m84036_250809_035451_s4.bc2155_f8inv22.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-58/call-run_paraphase/out/m84036_250809_035451_s4.bc2155_paraphase/m84036_250809_035451_s4.bc2155_paraphase_vcfs/m84036_250809_035451_s4.bc2155_gba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-58/call-run_paraphase/out/m84036_250809_035451_s4.bc2155_paraphase/m84036_250809_035451_s4.bc2155_paraphase_vcfs/m84036_250809_035451_s4.bc2155_hba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-58/call-run_paraphase/out/m84036_250809_035451_s4.bc2155_paraphase/m84036_250809_035451_s4.bc2155_paraphase_vcfs/m84036_250809_035451_s4.bc2155_hbb.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-58/call-run_paraphase/out/m84036_250809_035451_s4.bc2155_paraphase/m84036_250809_035451_s4.bc2155_paraphase_vcfs/m84036_250809_035451_s4.bc2155_rpgr.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-58/call-run_paraphase/out/m84036_250809_035451_s4.bc2155_paraphase/m84036_250809_035451_s4.bc2155_paraphase_vcfs/m84036_250809_035451_s4.bc2155_smn1.vcf"]}
2025-09-15 20:31:51.264 wdl.w:ptcp.w:call-paraphase-58.t:call-call_f8 NOTICE task setup :: name: "call_f8", source: "./paraphase.wdl", line: 232, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-58/call-call_f8", thread: 140607129368128
2025-09-15 20:31:51.277 wdl.w:ptcp.w:call-paraphase-58.t:call-call_f8 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:31:51.278 wdl.w:ptcp.w:call-paraphase-58.t:call-call_f8 INFO input :: name: "genome_version", value: "38"
2025-09-15 20:31:51.278 wdl.w:ptcp.w:call-paraphase-58.t:call-call_f8 INFO input :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2155"
2025-09-15 20:31:51.278 wdl.w:ptcp.w:call-paraphase-58.t:call-call_f8 INFO input :: name: "paraphase_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2155.paraphase.bam.bai"
2025-09-15 20:31:51.278 wdl.w:ptcp.w:call-paraphase-58.t:call-call_f8 INFO input :: name: "paraphase_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2155.paraphase.bam"
2025-09-15 20:31:51.278 wdl.w:ptcp.w:call-paraphase-58.t:call-call_f8 INFO input :: name: "sex", value: "F"
2025-09-15 20:31:51.278 wdl.w:ptcp.w:call-paraphase-58.t:call-call_f8 INFO eval :: name: "threads", value: 1
2025-09-15 20:31:51.278 wdl.w:ptcp.w:call-paraphase-58.t:call-call_f8 INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:31:51.279 wdl.w:ptcp.w:call-paraphase-58.t:call-call_f8 INFO eval :: name: "disk_size", value: 11
2025-09-15 20:31:51.279 wdl.w:ptcp.w:call-paraphase-58.t:call-call_f8 INFO eval :: name: "sample_sex", value: "F"
2025-09-15 20:31:51.279 wdl.w:ptcp.w:call-paraphase-58.t:call-call_f8 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:31:51.279 wdl.w:ptcp.w:call-paraphase-58.t:call-call_f8 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:31:51.279 wdl.w:ptcp.w:call-paraphase-58.t:call-call_f8 INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:31:51.280 wdl.w:ptcp.w:call-paraphase-58.t:call-call_f8 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:31:51.314 wdl.w:ptcp.w:call-paraphase-58.t:call-call_f8 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 8, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-58/call-call_f8/_singularity_tmpdir_qg21j3zl"
2025-09-15 20:31:51.314 wdl.w:ptcp.w:call-paraphase-58.t:call-call_f8 INFO Slurm invocation: srun --job-name call-call_f8 --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-58/call-call_f8/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-58/call-call_f8/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-58/call-call_f8/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-58/call-call_f8/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-58/call-run_paraphase/out/m84036_250809_035451_s4.bc2155_paraphase/m84036_250809_035451_s4.bc2155.paraphase.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2155.paraphase.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-58/call-run_paraphase/out/m84036_250809_035451_s4.bc2155_paraphase/m84036_250809_035451_s4.bc2155.paraphase.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2155.paraphase.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-58/call-call_f8/_singularity_tmpdir_qg21j3zl/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-58/call-call_f8/_singularity_tmpdir_qg21j3zl/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:31:51.318 wdl.w:ptcp.w:call-paraphase-58.t:call-call_f8 NOTICE slurm_singularity run :: pid: 1211589, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-58/call-call_f8/slurm_singularity.log.txt"
2025-09-15 20:31:52.326 wdl.w:ptcp.w:call-paraphase-58.t:call-call_f8.slurm_singularity INFO srun: job 51798382 queued and waiting for resources
2025-09-15 20:31:52.326 wdl.w:ptcp.w:call-paraphase-58.t:call-call_f8.slurm_singularity INFO srun: job 51798382 has been allocated resources
2025-09-15 20:31:52.326 wdl.w:ptcp.w:call-paraphase-58.t:call-call_f8.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:31:53.326 wdl.w:ptcp.w:call-paraphase-58.t:call-call_f8 INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2155.f8inversion.vcf"
2025-09-15 20:31:53.328 wdl.w:ptcp.w:call-paraphase-58.t:call-call_f8 INFO output :: name: "json", value: "m84036_250809_035451_s4.bc2155.f8inversion.json"
2025-09-15 20:31:53.377 wdl.w:ptcp.w:call-paraphase-58.t:call-call_f8 NOTICE done
2025-09-15 20:31:53.382 wdl.w:ptcp.w:call-paraphase-58 NOTICE finish :: job: "call-call_f8"
2025-09-15 20:31:53.382 wdl.w:ptcp.w:call-paraphase-58 INFO output :: job: "call-call_f8", values: {"json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-58/call-call_f8/out/m84036_250809_035451_s4.bc2155.f8inversion.json", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-58/call-call_f8/out/m84036_250809_035451_s4.bc2155.f8inversion.vcf"}
2025-09-15 20:31:53.382 wdl.w:ptcp.w:call-paraphase-58 INFO visit :: node: "output-f8_json", values: {"f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-58/call-call_f8/out/m84036_250809_035451_s4.bc2155.f8inversion.json"}
2025-09-15 20:31:53.382 wdl.w:ptcp.w:call-paraphase-58 INFO visit :: node: "output-f8_vcf", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-58/call-call_f8/out/m84036_250809_035451_s4.bc2155.f8inversion.vcf"}
2025-09-15 20:31:53.382 wdl.w:ptcp.w:call-paraphase-58 INFO visit :: node: "outputs", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-58/call-call_f8/out/m84036_250809_035451_s4.bc2155.f8inversion.vcf", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-58/call-run_paraphase/out/m84036_250809_035451_s4.bc2155_paraphase/m84036_250809_035451_s4.bc2155.paraphase.json", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-58/call-run_paraphase/out/m84036_250809_035451_s4.bc2155_paraphase/m84036_250809_035451_s4.bc2155.paraphase.bam", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-58/call-run_paraphase/out/m84036_250809_035451_s4.bc2155_paraphase/m84036_250809_035451_s4.bc2155.paraphase.bam.bai", "paraphase_vcfs": ["/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-58/call-run_paraphase/out/m84036_250809_035451_s4.bc2155_paraphase/m84036_250809_035451_s4.bc2155_paraphase_vcfs/m84036_250809_035451_s4.bc2155_cyp21.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-58/call-run_paraphase/out/m84036_250809_035451_s4.bc2155_paraphase/m84036_250809_035451_s4.bc2155_paraphase_vcfs/m84036_250809_035451_s4.bc2155_f8inv1.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-58/call-run_paraphase/out/m84036_250809_035451_s4.bc2155_paraphase/m84036_250809_035451_s4.bc2155_paraphase_vcfs/m84036_250809_035451_s4.bc2155_f8inv22.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-58/call-run_paraphase/out/m84036_250809_035451_s4.bc2155_paraphase/m84036_250809_035451_s4.bc2155_paraphase_vcfs/m84036_250809_035451_s4.bc2155_gba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-58/call-run_paraphase/out/m84036_250809_035451_s4.bc2155_paraphase/m84036_250809_035451_s4.bc2155_paraphase_vcfs/m84036_250809_035451_s4.bc2155_hba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-58/call-run_paraphase/out/m84036_250809_035451_s4.bc2155_paraphase/m84036_250809_035451_s4.bc2155_paraphase_vcfs/m84036_250809_035451_s4.bc2155_hbb.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-58/call-run_paraphase/out/m84036_250809_035451_s4.bc2155_paraphase/m84036_250809_035451_s4.bc2155_paraphase_vcfs/m84036_250809_035451_s4.bc2155_rpgr.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-58/call-run_paraphase/out/m84036_250809_035451_s4.bc2155_paraphase/m84036_250809_035451_s4.bc2155_paraphase_vcfs/m84036_250809_035451_s4.bc2155_smn1.vcf"], "havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-58/call-run_paraphase/out/m84036_250809_035451_s4.bc2155.havanno.json", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-58/call-call_f8/out/m84036_250809_035451_s4.bc2155.f8inversion.json"}
2025-09-15 20:31:53.482 wdl.w:ptcp.w:call-paraphase-58 NOTICE done
2025-09-15 20:31:53.487 wdl.w:ptcp NOTICE finish :: job: "call-paraphase-58"
2025-09-15 20:31:53.487 wdl.w:ptcp INFO output :: job: "call-paraphase-58", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-58/out/m84036_250809_035451_s4.bc2155.f8inversion.vcf", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-58/out/m84036_250809_035451_s4.bc2155_paraphase/m84036_250809_035451_s4.bc2155.paraphase.json", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-58/out/m84036_250809_035451_s4.bc2155_paraphase/m84036_250809_035451_s4.bc2155.paraphase.bam", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-58/out/m84036_250809_035451_s4.bc2155_paraphase/m84036_250809_035451_s4.bc2155.paraphase.bam.bai", "paraphase_vcfs": ["/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-58/out/m84036_250809_035451_s4.bc2155_paraphase/m84036_250809_035451_s4.bc2155_paraphase_vcfs/m84036_250809_035451_s4.bc2155_cyp21.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-58/out/m84036_250809_035451_s4.bc2155_paraphase/m84036_250809_035451_s4.bc2155_paraphase_vcfs/m84036_250809_035451_s4.bc2155_f8inv1.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-58/out/m84036_250809_035451_s4.bc2155_paraphase/m84036_250809_035451_s4.bc2155_paraphase_vcfs/m84036_250809_035451_s4.bc2155_f8inv22.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-58/out/m84036_250809_035451_s4.bc2155_paraphase/m84036_250809_035451_s4.bc2155_paraphase_vcfs/m84036_250809_035451_s4.bc2155_gba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-58/out/m84036_250809_035451_s4.bc2155_paraphase/m84036_250809_035451_s4.bc2155_paraphase_vcfs/m84036_250809_035451_s4.bc2155_hba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-58/out/m84036_250809_035451_s4.bc2155_paraphase/m84036_250809_035451_s4.bc2155_paraphase_vcfs/m84036_250809_035451_s4.bc2155_hbb.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-58/out/m84036_250809_035451_s4.bc2155_paraphase/m84036_250809_035451_s4.bc2155_paraphase_vcfs/m84036_250809_035451_s4.bc2155_rpgr.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-58/out/m84036_250809_035451_s4.bc2155_paraphase/m84036_250809_035451_s4.bc2155_paraphase_vcfs/m84036_250809_035451_s4.bc2155_smn1.vcf"], "havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-58/out/m84036_250809_035451_s4.bc2155.havanno.json", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-58/out/m84036_250809_035451_s4.bc2155.f8inversion.json"}
2025-09-15 20:31:53.488 wdl.w:ptcp NOTICE ready :: job: "call-tar_outputs-58", callee: "tar_outputs"
2025-09-15 20:31:53.488 wdl.w:ptcp INFO input :: job: "call-tar_outputs-58", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "sawfish_vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-58/out/m84036_250809_035451_s4.bc2155_sawfish/m84036_250809_035451_s4.bc2155.sv.vcf.gz.tbi", "sawfish_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-58/out/m84036_250809_035451_s4.bc2155_sawfish/m84036_250809_035451_s4.bc2155.sv.vcf.gz", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-58/out/m84036_250809_035451_s4.bc2155.f8inversion.json", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-58/out/m84036_250809_035451_s4.bc2155_paraphase/m84036_250809_035451_s4.bc2155.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-58/out/m84036_250809_035451_s4.bc2155_paraphase/m84036_250809_035451_s4.bc2155.paraphase.bam", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-58/out/m84036_250809_035451_s4.bc2155_paraphase/m84036_250809_035451_s4.bc2155.paraphase.json", "trgt_spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-58/out/m84036_250809_035451_s4.bc2155.trgt.sorted.spanning.bam.bai", "trgt_spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-58/out/m84036_250809_035451_s4.bc2155.trgt.sorted.spanning.bam", "trgt_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-58/out/m84036_250809_035451_s4.bc2155.trgt.vcf", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-58/out/m84036_250809_035451_s4.bc2155.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-58/out/m84036_250809_035451_s4.bc2155.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2155"}
2025-09-15 20:31:53.494 wdl.w:ptcp.t:call-tar_outputs-58 NOTICE task setup :: name: "tar_outputs", source: "./common.wdl", line: 279, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-58", thread: 140611952813632
2025-09-15 20:31:53.513 wdl.w:ptcp.t:call-tar_outputs-58 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:31:53.513 wdl.w:ptcp.t:call-tar_outputs-58 INFO input :: name: "sawfish_vcf_tbi", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2155.sv.vcf.gz.tbi"
2025-09-15 20:31:53.513 wdl.w:ptcp.t:call-tar_outputs-58 INFO input :: name: "sawfish_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2155.sv.vcf.gz"
2025-09-15 20:31:53.513 wdl.w:ptcp.t:call-tar_outputs-58 INFO input :: name: "f8_json", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2155.f8inversion.json"
2025-09-15 20:31:53.513 wdl.w:ptcp.t:call-tar_outputs-58 INFO input :: name: "paraphase_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2155.paraphase.bam.bai"
2025-09-15 20:31:53.513 wdl.w:ptcp.t:call-tar_outputs-58 INFO input :: name: "paraphase_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2155.paraphase.bam"
2025-09-15 20:31:53.514 wdl.w:ptcp.t:call-tar_outputs-58 INFO input :: name: "paraphase_json", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2155.paraphase.json"
2025-09-15 20:31:53.514 wdl.w:ptcp.t:call-tar_outputs-58 INFO input :: name: "trgt_spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2155.trgt.sorted.spanning.bam.bai"
2025-09-15 20:31:53.514 wdl.w:ptcp.t:call-tar_outputs-58 INFO input :: name: "trgt_spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2155.trgt.sorted.spanning.bam"
2025-09-15 20:31:53.514 wdl.w:ptcp.t:call-tar_outputs-58 INFO input :: name: "trgt_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2155.trgt.vcf"
2025-09-15 20:31:53.514 wdl.w:ptcp.t:call-tar_outputs-58 INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2155.mapped.bam.bai"
2025-09-15 20:31:53.514 wdl.w:ptcp.t:call-tar_outputs-58 INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2155.mapped.bam"
2025-09-15 20:31:53.514 wdl.w:ptcp.t:call-tar_outputs-58 INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2155"
2025-09-15 20:31:53.514 wdl.w:ptcp.t:call-tar_outputs-58 INFO eval :: name: "threads", value: 1
2025-09-15 20:31:53.514 wdl.w:ptcp.t:call-tar_outputs-58 INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:31:53.514 wdl.w:ptcp.t:call-tar_outputs-58 INFO eval :: name: "disk_size", value: 6
2025-09-15 20:31:53.514 wdl.w:ptcp.t:call-tar_outputs-58 INFO eval :: name: "output_tarball", value: "m84036_250809_035451_s4.bc2155.tar"
2025-09-15 20:31:53.515 wdl.w:ptcp.t:call-tar_outputs-58 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:31:53.515 wdl.w:ptcp.t:call-tar_outputs-58 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:31:53.515 wdl.w:ptcp.t:call-tar_outputs-58 INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:31:53.515 wdl.w:ptcp.t:call-tar_outputs-58 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:31:53.581 wdl.w:ptcp.t:call-tar_outputs-58 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 17, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-58/_singularity_tmpdir_5dszuivg"
2025-09-15 20:31:53.581 wdl.w:ptcp.t:call-tar_outputs-58 INFO Slurm invocation: srun --job-name call-tar_outputs-58 --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-58/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-58/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-58/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-58/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-58/out/m84036_250809_035451_s4.bc2155_sawfish/m84036_250809_035451_s4.bc2155.sv.vcf.gz.tbi:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2155.sv.vcf.gz.tbi:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-58/out/m84036_250809_035451_s4.bc2155_sawfish/m84036_250809_035451_s4.bc2155.sv.vcf.gz:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2155.sv.vcf.gz:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-58/out/m84036_250809_035451_s4.bc2155_paraphase/m84036_250809_035451_s4.bc2155.paraphase.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2155.paraphase.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-58/out/m84036_250809_035451_s4.bc2155_paraphase/m84036_250809_035451_s4.bc2155.paraphase.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2155.paraphase.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-58/out/m84036_250809_035451_s4.bc2155_paraphase/m84036_250809_035451_s4.bc2155.paraphase.json:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2155.paraphase.json:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-58/out/m84036_250809_035451_s4.bc2155.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2155.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-58/out/m84036_250809_035451_s4.bc2155.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2155.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-58/out/m84036_250809_035451_s4.bc2155.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2155.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-58/out/m84036_250809_035451_s4.bc2155.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2155.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-58/out/m84036_250809_035451_s4.bc2155.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2155.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-58/out/m84036_250809_035451_s4.bc2155.f8inversion.json:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2155.f8inversion.json:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-58/_singularity_tmpdir_5dszuivg/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-58/_singularity_tmpdir_5dszuivg/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:31:53.584 wdl.w:ptcp.t:call-tar_outputs-58 NOTICE slurm_singularity run :: pid: 1211599, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-58/slurm_singularity.log.txt"
2025-09-15 20:31:54.592 wdl.w:ptcp.t:call-tar_outputs-58.slurm_singularity INFO srun: job 51798386 queued and waiting for resources
2025-09-15 20:31:54.593 wdl.w:ptcp.t:call-tar_outputs-58.slurm_singularity INFO srun: job 51798386 has been allocated resources
2025-09-15 20:31:55.416 wdl.w:ptcp.t:call-tar_outputs-58.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:31:55.440 wdl.w:ptcp.t:call-tar_outputs-58 INFO output :: name: "sample_tarball", value: "m84036_250809_035451_s4.bc2155.tar"
2025-09-15 20:31:55.490 wdl.w:ptcp.t:call-tar_outputs-58 NOTICE done
2025-09-15 20:31:55.493 wdl.w:ptcp NOTICE finish :: job: "call-tar_outputs-58"
2025-09-15 20:31:55.493 wdl.w:ptcp INFO output :: job: "call-tar_outputs-58", values: {"sample_tarball": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-58/out/m84036_250809_035451_s4.bc2155.tar"}
2025-09-15 20:32:06.843 wdl.w:ptcp.w:call-paraphase-90.t:call-run_paraphase INFO output :: name: "paraphase_bam", value: "m84036_250809_035451_s4.bc2187_paraphase/m84036_250809_035451_s4.bc2187.paraphase.bam"
2025-09-15 20:32:06.847 wdl.w:ptcp.w:call-paraphase-90.t:call-run_paraphase INFO output :: name: "paraphase_bam_bai", value: "m84036_250809_035451_s4.bc2187_paraphase/m84036_250809_035451_s4.bc2187.paraphase.bam.bai"
2025-09-15 20:32:06.848 wdl.w:ptcp.w:call-paraphase-90.t:call-run_paraphase INFO output :: name: "paraphase_json", value: "m84036_250809_035451_s4.bc2187_paraphase/m84036_250809_035451_s4.bc2187.paraphase.json"
2025-09-15 20:32:06.854 wdl.w:ptcp.w:call-paraphase-90.t:call-run_paraphase INFO output :: name: "paraphase_vcfs", value: ["/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2187_paraphase/m84036_250809_035451_s4.bc2187_paraphase_vcfs/m84036_250809_035451_s4.bc2187_cyp21.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2187_paraphase/m84036_250809_035451_s4.bc2187_paraphase_vcfs/m84036_250809_035451_s4.bc2187_f8inv1.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2187_paraphase/m84036_250809_035451_s4.bc2187_paraphase_vcfs/m84036_250809_035451_s4.bc2187_f8inv22.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2187_paraphase/m84036_250809_035451_s4.bc2187_paraphase_vcfs/m84036_250809_035451_s4.bc2187_gba.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2187_paraphase/m84036_250809_035451_s4.bc2187_paraphase_vcfs/m84036_250809_035451_s4.bc2187_hba.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2187_paraphase/m84036_250809_035451_s4.bc2187_paraphase_vcfs/m84036_250809_035451_s4.bc2187_hbb.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2187_paraphase/m84036_250809_035451_s4.bc2187_paraphase_vcfs/m84036_250809_035451_s4.bc2187_rpgr.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2187_paraphase/m84036_250809_035451_s4.bc2187_paraphase_vcfs/m84036_250809_035451_s4.bc2187_smn1.vcf"]
2025-09-15 20:32:06.857 wdl.w:ptcp.w:call-paraphase-90.t:call-run_paraphase INFO output :: name: "havanno_json", value: "m84036_250809_035451_s4.bc2187.havanno.json"
2025-09-15 20:32:07.004 wdl.w:ptcp.w:call-paraphase-90.t:call-run_paraphase NOTICE done
2025-09-15 20:32:07.010 wdl.w:ptcp.w:call-paraphase-90 NOTICE finish :: job: "call-run_paraphase"
2025-09-15 20:32:07.010 wdl.w:ptcp.w:call-paraphase-90 INFO output :: job: "call-run_paraphase", values: {"havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-90/call-run_paraphase/out/m84036_250809_035451_s4.bc2187.havanno.json", "paraphase_vcfs": ["/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-90/call-run_paraphase/out/m84036_250809_035451_s4.bc2187_paraphase/m84036_250809_035451_s4.bc2187_paraphase_vcfs/m84036_250809_035451_s4.bc2187_cyp21.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-90/call-run_paraphase/out/m84036_250809_035451_s4.bc2187_paraphase/m84036_250809_035451_s4.bc2187_paraphase_vcfs/m84036_250809_035451_s4.bc2187_f8inv1.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-90/call-run_paraphase/out/m84036_250809_035451_s4.bc2187_paraphase/m84036_250809_035451_s4.bc2187_paraphase_vcfs/m84036_250809_035451_s4.bc2187_f8inv22.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-90/call-run_paraphase/out/m84036_250809_035451_s4.bc2187_paraphase/m84036_250809_035451_s4.bc2187_paraphase_vcfs/m84036_250809_035451_s4.bc2187_gba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-90/call-run_paraphase/out/m84036_250809_035451_s4.bc2187_paraphase/m84036_250809_035451_s4.bc2187_paraphase_vcfs/m84036_250809_035451_s4.bc2187_hba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-90/call-run_paraphase/out/m84036_250809_035451_s4.bc2187_paraphase/m84036_250809_035451_s4.bc2187_paraphase_vcfs/m84036_250809_035451_s4.bc2187_hbb.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-90/call-run_paraphase/out/m84036_250809_035451_s4.bc2187_paraphase/m84036_250809_035451_s4.bc2187_paraphase_vcfs/m84036_250809_035451_s4.bc2187_rpgr.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-90/call-run_paraphase/out/m84036_250809_035451_s4.bc2187_paraphase/m84036_250809_035451_s4.bc2187_paraphase_vcfs/m84036_250809_035451_s4.bc2187_smn1.vcf"], "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-90/call-run_paraphase/out/m84036_250809_035451_s4.bc2187_paraphase/m84036_250809_035451_s4.bc2187.paraphase.json", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-90/call-run_paraphase/out/m84036_250809_035451_s4.bc2187_paraphase/m84036_250809_035451_s4.bc2187.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-90/call-run_paraphase/out/m84036_250809_035451_s4.bc2187_paraphase/m84036_250809_035451_s4.bc2187.paraphase.bam"}
2025-09-15 20:32:07.011 wdl.w:ptcp.w:call-paraphase-90 NOTICE ready :: job: "call-call_f8", callee: "call_f8"
2025-09-15 20:32:07.011 wdl.w:ptcp.w:call-paraphase-90 INFO input :: job: "call-call_f8", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "out_prefix": "m84036_250809_035451_s4.bc2187", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-90/call-run_paraphase/out/m84036_250809_035451_s4.bc2187_paraphase/m84036_250809_035451_s4.bc2187.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-90/call-run_paraphase/out/m84036_250809_035451_s4.bc2187_paraphase/m84036_250809_035451_s4.bc2187.paraphase.bam", "sex": "F"}
2025-09-15 20:32:07.011 wdl.w:ptcp.w:call-paraphase-90 INFO visit :: node: "output-havanno_json", values: {"havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-90/call-run_paraphase/out/m84036_250809_035451_s4.bc2187.havanno.json"}
2025-09-15 20:32:07.011 wdl.w:ptcp.w:call-paraphase-90 INFO visit :: node: "output-paraphase_bam", values: {"paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-90/call-run_paraphase/out/m84036_250809_035451_s4.bc2187_paraphase/m84036_250809_035451_s4.bc2187.paraphase.bam"}
2025-09-15 20:32:07.012 wdl.w:ptcp.w:call-paraphase-90 INFO visit :: node: "output-paraphase_bam_bai", values: {"paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-90/call-run_paraphase/out/m84036_250809_035451_s4.bc2187_paraphase/m84036_250809_035451_s4.bc2187.paraphase.bam.bai"}
2025-09-15 20:32:07.012 wdl.w:ptcp.w:call-paraphase-90 INFO visit :: node: "output-paraphase_json", values: {"paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-90/call-run_paraphase/out/m84036_250809_035451_s4.bc2187_paraphase/m84036_250809_035451_s4.bc2187.paraphase.json"}
2025-09-15 20:32:07.012 wdl.w:ptcp.w:call-paraphase-90 INFO visit :: node: "output-paraphase_vcfs", values: {"paraphase_vcfs": ["/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-90/call-run_paraphase/out/m84036_250809_035451_s4.bc2187_paraphase/m84036_250809_035451_s4.bc2187_paraphase_vcfs/m84036_250809_035451_s4.bc2187_cyp21.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-90/call-run_paraphase/out/m84036_250809_035451_s4.bc2187_paraphase/m84036_250809_035451_s4.bc2187_paraphase_vcfs/m84036_250809_035451_s4.bc2187_f8inv1.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-90/call-run_paraphase/out/m84036_250809_035451_s4.bc2187_paraphase/m84036_250809_035451_s4.bc2187_paraphase_vcfs/m84036_250809_035451_s4.bc2187_f8inv22.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-90/call-run_paraphase/out/m84036_250809_035451_s4.bc2187_paraphase/m84036_250809_035451_s4.bc2187_paraphase_vcfs/m84036_250809_035451_s4.bc2187_gba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-90/call-run_paraphase/out/m84036_250809_035451_s4.bc2187_paraphase/m84036_250809_035451_s4.bc2187_paraphase_vcfs/m84036_250809_035451_s4.bc2187_hba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-90/call-run_paraphase/out/m84036_250809_035451_s4.bc2187_paraphase/m84036_250809_035451_s4.bc2187_paraphase_vcfs/m84036_250809_035451_s4.bc2187_hbb.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-90/call-run_paraphase/out/m84036_250809_035451_s4.bc2187_paraphase/m84036_250809_035451_s4.bc2187_paraphase_vcfs/m84036_250809_035451_s4.bc2187_rpgr.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-90/call-run_paraphase/out/m84036_250809_035451_s4.bc2187_paraphase/m84036_250809_035451_s4.bc2187_paraphase_vcfs/m84036_250809_035451_s4.bc2187_smn1.vcf"]}
2025-09-15 20:32:07.015 wdl.w:ptcp.w:call-paraphase-90.t:call-call_f8 NOTICE task setup :: name: "call_f8", source: "./paraphase.wdl", line: 232, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-90/call-call_f8", thread: 140607112582720
2025-09-15 20:32:07.029 wdl.w:ptcp.w:call-paraphase-90.t:call-call_f8 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:32:07.029 wdl.w:ptcp.w:call-paraphase-90.t:call-call_f8 INFO input :: name: "genome_version", value: "38"
2025-09-15 20:32:07.029 wdl.w:ptcp.w:call-paraphase-90.t:call-call_f8 INFO input :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2187"
2025-09-15 20:32:07.029 wdl.w:ptcp.w:call-paraphase-90.t:call-call_f8 INFO input :: name: "paraphase_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2187.paraphase.bam.bai"
2025-09-15 20:32:07.029 wdl.w:ptcp.w:call-paraphase-90.t:call-call_f8 INFO input :: name: "paraphase_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2187.paraphase.bam"
2025-09-15 20:32:07.030 wdl.w:ptcp.w:call-paraphase-90.t:call-call_f8 INFO input :: name: "sex", value: "F"
2025-09-15 20:32:07.030 wdl.w:ptcp.w:call-paraphase-90.t:call-call_f8 INFO eval :: name: "threads", value: 1
2025-09-15 20:32:07.030 wdl.w:ptcp.w:call-paraphase-90.t:call-call_f8 INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:32:07.030 wdl.w:ptcp.w:call-paraphase-90.t:call-call_f8 INFO eval :: name: "disk_size", value: 11
2025-09-15 20:32:07.030 wdl.w:ptcp.w:call-paraphase-90.t:call-call_f8 INFO eval :: name: "sample_sex", value: "F"
2025-09-15 20:32:07.031 wdl.w:ptcp.w:call-paraphase-90.t:call-call_f8 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:32:07.031 wdl.w:ptcp.w:call-paraphase-90.t:call-call_f8 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:32:07.031 wdl.w:ptcp.w:call-paraphase-90.t:call-call_f8 INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:32:07.031 wdl.w:ptcp.w:call-paraphase-90.t:call-call_f8 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:32:07.067 wdl.w:ptcp.w:call-paraphase-90.t:call-call_f8 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 8, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-90/call-call_f8/_singularity_tmpdir_1ebq8do5"
2025-09-15 20:32:07.067 wdl.w:ptcp.w:call-paraphase-90.t:call-call_f8 INFO Slurm invocation: srun --job-name call-call_f8 --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-90/call-call_f8/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-90/call-call_f8/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-90/call-call_f8/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-90/call-call_f8/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-90/call-run_paraphase/out/m84036_250809_035451_s4.bc2187_paraphase/m84036_250809_035451_s4.bc2187.paraphase.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2187.paraphase.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-90/call-run_paraphase/out/m84036_250809_035451_s4.bc2187_paraphase/m84036_250809_035451_s4.bc2187.paraphase.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2187.paraphase.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-90/call-call_f8/_singularity_tmpdir_1ebq8do5/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-90/call-call_f8/_singularity_tmpdir_1ebq8do5/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:32:07.071 wdl.w:ptcp.w:call-paraphase-90.t:call-call_f8 NOTICE slurm_singularity run :: pid: 1211699, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-90/call-call_f8/slurm_singularity.log.txt"
2025-09-15 20:32:08.079 wdl.w:ptcp.w:call-paraphase-90.t:call-call_f8.slurm_singularity INFO srun: job 51798390 queued and waiting for resources
2025-09-15 20:32:08.080 wdl.w:ptcp.w:call-paraphase-90.t:call-call_f8.slurm_singularity INFO srun: job 51798390 has been allocated resources
2025-09-15 20:32:08.080 wdl.w:ptcp.w:call-paraphase-90.t:call-call_f8.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:32:08.378 wdl.w:ptcp.w:call-paraphase-90.t:call-call_f8 INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2187.f8inversion.vcf"
2025-09-15 20:32:08.381 wdl.w:ptcp.w:call-paraphase-90.t:call-call_f8 INFO output :: name: "json", value: "m84036_250809_035451_s4.bc2187.f8inversion.json"
2025-09-15 20:32:08.428 wdl.w:ptcp.w:call-paraphase-90.t:call-call_f8 NOTICE done
2025-09-15 20:32:08.433 wdl.w:ptcp.w:call-paraphase-90 NOTICE finish :: job: "call-call_f8"
2025-09-15 20:32:08.434 wdl.w:ptcp.w:call-paraphase-90 INFO output :: job: "call-call_f8", values: {"json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-90/call-call_f8/out/m84036_250809_035451_s4.bc2187.f8inversion.json", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-90/call-call_f8/out/m84036_250809_035451_s4.bc2187.f8inversion.vcf"}
2025-09-15 20:32:08.434 wdl.w:ptcp.w:call-paraphase-90 INFO visit :: node: "output-f8_json", values: {"f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-90/call-call_f8/out/m84036_250809_035451_s4.bc2187.f8inversion.json"}
2025-09-15 20:32:08.434 wdl.w:ptcp.w:call-paraphase-90 INFO visit :: node: "output-f8_vcf", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-90/call-call_f8/out/m84036_250809_035451_s4.bc2187.f8inversion.vcf"}
2025-09-15 20:32:08.434 wdl.w:ptcp.w:call-paraphase-90 INFO visit :: node: "outputs", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-90/call-call_f8/out/m84036_250809_035451_s4.bc2187.f8inversion.vcf", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-90/call-run_paraphase/out/m84036_250809_035451_s4.bc2187_paraphase/m84036_250809_035451_s4.bc2187.paraphase.json", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-90/call-run_paraphase/out/m84036_250809_035451_s4.bc2187_paraphase/m84036_250809_035451_s4.bc2187.paraphase.bam", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-90/call-run_paraphase/out/m84036_250809_035451_s4.bc2187_paraphase/m84036_250809_035451_s4.bc2187.paraphase.bam.bai", "paraphase_vcfs": ["/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-90/call-run_paraphase/out/m84036_250809_035451_s4.bc2187_paraphase/m84036_250809_035451_s4.bc2187_paraphase_vcfs/m84036_250809_035451_s4.bc2187_cyp21.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-90/call-run_paraphase/out/m84036_250809_035451_s4.bc2187_paraphase/m84036_250809_035451_s4.bc2187_paraphase_vcfs/m84036_250809_035451_s4.bc2187_f8inv1.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-90/call-run_paraphase/out/m84036_250809_035451_s4.bc2187_paraphase/m84036_250809_035451_s4.bc2187_paraphase_vcfs/m84036_250809_035451_s4.bc2187_f8inv22.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-90/call-run_paraphase/out/m84036_250809_035451_s4.bc2187_paraphase/m84036_250809_035451_s4.bc2187_paraphase_vcfs/m84036_250809_035451_s4.bc2187_gba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-90/call-run_paraphase/out/m84036_250809_035451_s4.bc2187_paraphase/m84036_250809_035451_s4.bc2187_paraphase_vcfs/m84036_250809_035451_s4.bc2187_hba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-90/call-run_paraphase/out/m84036_250809_035451_s4.bc2187_paraphase/m84036_250809_035451_s4.bc2187_paraphase_vcfs/m84036_250809_035451_s4.bc2187_hbb.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-90/call-run_paraphase/out/m84036_250809_035451_s4.bc2187_paraphase/m84036_250809_035451_s4.bc2187_paraphase_vcfs/m84036_250809_035451_s4.bc2187_rpgr.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-90/call-run_paraphase/out/m84036_250809_035451_s4.bc2187_paraphase/m84036_250809_035451_s4.bc2187_paraphase_vcfs/m84036_250809_035451_s4.bc2187_smn1.vcf"], "havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-90/call-run_paraphase/out/m84036_250809_035451_s4.bc2187.havanno.json", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-90/call-call_f8/out/m84036_250809_035451_s4.bc2187.f8inversion.json"}
2025-09-15 20:32:08.532 wdl.w:ptcp.w:call-paraphase-90 NOTICE done
2025-09-15 20:32:08.538 wdl.w:ptcp NOTICE finish :: job: "call-paraphase-90"
2025-09-15 20:32:08.538 wdl.w:ptcp INFO output :: job: "call-paraphase-90", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-90/out/m84036_250809_035451_s4.bc2187.f8inversion.vcf", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-90/out/m84036_250809_035451_s4.bc2187_paraphase/m84036_250809_035451_s4.bc2187.paraphase.json", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-90/out/m84036_250809_035451_s4.bc2187_paraphase/m84036_250809_035451_s4.bc2187.paraphase.bam", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-90/out/m84036_250809_035451_s4.bc2187_paraphase/m84036_250809_035451_s4.bc2187.paraphase.bam.bai", "paraphase_vcfs": ["/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-90/out/m84036_250809_035451_s4.bc2187_paraphase/m84036_250809_035451_s4.bc2187_paraphase_vcfs/m84036_250809_035451_s4.bc2187_cyp21.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-90/out/m84036_250809_035451_s4.bc2187_paraphase/m84036_250809_035451_s4.bc2187_paraphase_vcfs/m84036_250809_035451_s4.bc2187_f8inv1.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-90/out/m84036_250809_035451_s4.bc2187_paraphase/m84036_250809_035451_s4.bc2187_paraphase_vcfs/m84036_250809_035451_s4.bc2187_f8inv22.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-90/out/m84036_250809_035451_s4.bc2187_paraphase/m84036_250809_035451_s4.bc2187_paraphase_vcfs/m84036_250809_035451_s4.bc2187_gba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-90/out/m84036_250809_035451_s4.bc2187_paraphase/m84036_250809_035451_s4.bc2187_paraphase_vcfs/m84036_250809_035451_s4.bc2187_hba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-90/out/m84036_250809_035451_s4.bc2187_paraphase/m84036_250809_035451_s4.bc2187_paraphase_vcfs/m84036_250809_035451_s4.bc2187_hbb.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-90/out/m84036_250809_035451_s4.bc2187_paraphase/m84036_250809_035451_s4.bc2187_paraphase_vcfs/m84036_250809_035451_s4.bc2187_rpgr.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-90/out/m84036_250809_035451_s4.bc2187_paraphase/m84036_250809_035451_s4.bc2187_paraphase_vcfs/m84036_250809_035451_s4.bc2187_smn1.vcf"], "havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-90/out/m84036_250809_035451_s4.bc2187.havanno.json", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-90/out/m84036_250809_035451_s4.bc2187.f8inversion.json"}
2025-09-15 20:32:08.539 wdl.w:ptcp NOTICE ready :: job: "call-tar_outputs-90", callee: "tar_outputs"
2025-09-15 20:32:08.539 wdl.w:ptcp INFO input :: job: "call-tar_outputs-90", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "sawfish_vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-90/out/m84036_250809_035451_s4.bc2187_sawfish/m84036_250809_035451_s4.bc2187.sv.vcf.gz.tbi", "sawfish_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-90/out/m84036_250809_035451_s4.bc2187_sawfish/m84036_250809_035451_s4.bc2187.sv.vcf.gz", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-90/out/m84036_250809_035451_s4.bc2187.f8inversion.json", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-90/out/m84036_250809_035451_s4.bc2187_paraphase/m84036_250809_035451_s4.bc2187.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-90/out/m84036_250809_035451_s4.bc2187_paraphase/m84036_250809_035451_s4.bc2187.paraphase.bam", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-90/out/m84036_250809_035451_s4.bc2187_paraphase/m84036_250809_035451_s4.bc2187.paraphase.json", "trgt_spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-90/out/m84036_250809_035451_s4.bc2187.trgt.sorted.spanning.bam.bai", "trgt_spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-90/out/m84036_250809_035451_s4.bc2187.trgt.sorted.spanning.bam", "trgt_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-90/out/m84036_250809_035451_s4.bc2187.trgt.vcf", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-90/out/m84036_250809_035451_s4.bc2187.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-90/out/m84036_250809_035451_s4.bc2187.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2187"}
2025-09-15 20:32:08.545 wdl.w:ptcp.t:call-tar_outputs-90 NOTICE task setup :: name: "tar_outputs", source: "./common.wdl", line: 279, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-90", thread: 140606089197120
2025-09-15 20:32:08.566 wdl.w:ptcp.t:call-tar_outputs-90 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:32:08.566 wdl.w:ptcp.t:call-tar_outputs-90 INFO input :: name: "sawfish_vcf_tbi", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2187.sv.vcf.gz.tbi"
2025-09-15 20:32:08.566 wdl.w:ptcp.t:call-tar_outputs-90 INFO input :: name: "sawfish_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2187.sv.vcf.gz"
2025-09-15 20:32:08.566 wdl.w:ptcp.t:call-tar_outputs-90 INFO input :: name: "f8_json", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2187.f8inversion.json"
2025-09-15 20:32:08.566 wdl.w:ptcp.t:call-tar_outputs-90 INFO input :: name: "paraphase_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2187.paraphase.bam.bai"
2025-09-15 20:32:08.566 wdl.w:ptcp.t:call-tar_outputs-90 INFO input :: name: "paraphase_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2187.paraphase.bam"
2025-09-15 20:32:08.566 wdl.w:ptcp.t:call-tar_outputs-90 INFO input :: name: "paraphase_json", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2187.paraphase.json"
2025-09-15 20:32:08.566 wdl.w:ptcp.t:call-tar_outputs-90 INFO input :: name: "trgt_spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2187.trgt.sorted.spanning.bam.bai"
2025-09-15 20:32:08.566 wdl.w:ptcp.t:call-tar_outputs-90 INFO input :: name: "trgt_spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2187.trgt.sorted.spanning.bam"
2025-09-15 20:32:08.566 wdl.w:ptcp.t:call-tar_outputs-90 INFO input :: name: "trgt_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2187.trgt.vcf"
2025-09-15 20:32:08.566 wdl.w:ptcp.t:call-tar_outputs-90 INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2187.mapped.bam.bai"
2025-09-15 20:32:08.567 wdl.w:ptcp.t:call-tar_outputs-90 INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2187.mapped.bam"
2025-09-15 20:32:08.567 wdl.w:ptcp.t:call-tar_outputs-90 INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2187"
2025-09-15 20:32:08.567 wdl.w:ptcp.t:call-tar_outputs-90 INFO eval :: name: "threads", value: 1
2025-09-15 20:32:08.567 wdl.w:ptcp.t:call-tar_outputs-90 INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:32:08.567 wdl.w:ptcp.t:call-tar_outputs-90 INFO eval :: name: "disk_size", value: 6
2025-09-15 20:32:08.567 wdl.w:ptcp.t:call-tar_outputs-90 INFO eval :: name: "output_tarball", value: "m84036_250809_035451_s4.bc2187.tar"
2025-09-15 20:32:08.568 wdl.w:ptcp.t:call-tar_outputs-90 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:32:08.568 wdl.w:ptcp.t:call-tar_outputs-90 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:32:08.568 wdl.w:ptcp.t:call-tar_outputs-90 INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:32:08.568 wdl.w:ptcp.t:call-tar_outputs-90 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:32:08.637 wdl.w:ptcp.t:call-tar_outputs-90 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 17, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-90/_singularity_tmpdir_xy5lqs14"
2025-09-15 20:32:08.637 wdl.w:ptcp.t:call-tar_outputs-90 INFO Slurm invocation: srun --job-name call-tar_outputs-90 --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-90/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-90/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-90/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-90/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-90/out/m84036_250809_035451_s4.bc2187.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2187.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-90/out/m84036_250809_035451_s4.bc2187.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2187.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-90/out/m84036_250809_035451_s4.bc2187.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2187.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-90/out/m84036_250809_035451_s4.bc2187_paraphase/m84036_250809_035451_s4.bc2187.paraphase.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2187.paraphase.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-90/out/m84036_250809_035451_s4.bc2187_paraphase/m84036_250809_035451_s4.bc2187.paraphase.json:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2187.paraphase.json:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-90/out/m84036_250809_035451_s4.bc2187_paraphase/m84036_250809_035451_s4.bc2187.paraphase.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2187.paraphase.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-90/out/m84036_250809_035451_s4.bc2187_sawfish/m84036_250809_035451_s4.bc2187.sv.vcf.gz.tbi:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2187.sv.vcf.gz.tbi:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-90/out/m84036_250809_035451_s4.bc2187_sawfish/m84036_250809_035451_s4.bc2187.sv.vcf.gz:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2187.sv.vcf.gz:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-90/out/m84036_250809_035451_s4.bc2187.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2187.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-90/out/m84036_250809_035451_s4.bc2187.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2187.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-90/out/m84036_250809_035451_s4.bc2187.f8inversion.json:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2187.f8inversion.json:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-90/_singularity_tmpdir_xy5lqs14/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-90/_singularity_tmpdir_xy5lqs14/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:32:08.640 wdl.w:ptcp.t:call-tar_outputs-90 NOTICE slurm_singularity run :: pid: 1211708, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-90/slurm_singularity.log.txt"
2025-09-15 20:32:09.657 wdl.w:ptcp.t:call-tar_outputs-90.slurm_singularity INFO srun: job 51798391 queued and waiting for resources
2025-09-15 20:32:10.680 wdl.w:ptcp.t:call-tar_outputs-90.slurm_singularity INFO srun: job 51798391 has been allocated resources
2025-09-15 20:32:10.680 wdl.w:ptcp.t:call-tar_outputs-90.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:32:11.135 wdl.w:ptcp.t:call-tar_outputs-90 INFO output :: name: "sample_tarball", value: "m84036_250809_035451_s4.bc2187.tar"
2025-09-15 20:32:11.188 wdl.w:ptcp.t:call-tar_outputs-90 NOTICE done
2025-09-15 20:32:11.192 wdl.w:ptcp NOTICE finish :: job: "call-tar_outputs-90"
2025-09-15 20:32:11.192 wdl.w:ptcp INFO output :: job: "call-tar_outputs-90", values: {"sample_tarball": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-90/out/m84036_250809_035451_s4.bc2187.tar"}
2025-09-15 20:32:14.261 wdl.w:ptcp.w:call-paraphase-75.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for rpgr for sample m84036_250809_035451_s4.bc2172 at 2025-09-15 20:31:43.405806...
2025-09-15 20:32:14.262 wdl.w:ptcp.w:call-paraphase-75.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for rpgr for sample m84036_250809_035451_s4.bc2172 at 2025-09-15 20:31:43.407053...
2025-09-15 20:32:14.262 wdl.w:ptcp.w:call-paraphase-75.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for rpgr for sample m84036_250809_035451_s4.bc2172 at 2025-09-15 20:31:47.874675...
2025-09-15 20:32:14.262 wdl.w:ptcp.w:call-paraphase-75.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for rpgr for sample m84036_250809_035451_s4.bc2172 at 2025-09-15 20:31:49.518970...
2025-09-15 20:32:14.262 wdl.w:ptcp.w:call-paraphase-75.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for rpgr for sample m84036_250809_035451_s4.bc2172 at 2025-09-15 20:31:49.817503...
2025-09-15 20:32:16.342 wdl.w:ptcp.w:call-paraphase-82.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for rpgr for sample m84036_250809_035451_s4.bc2179 at 2025-09-15 20:31:50.893177...
2025-09-15 20:32:16.343 wdl.w:ptcp.w:call-paraphase-82.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for rpgr for sample m84036_250809_035451_s4.bc2179 at 2025-09-15 20:31:50.894838...
2025-09-15 20:32:16.343 wdl.w:ptcp.w:call-paraphase-82.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for rpgr for sample m84036_250809_035451_s4.bc2179 at 2025-09-15 20:31:53.951905...
2025-09-15 20:32:16.343 wdl.w:ptcp.w:call-paraphase-82.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for rpgr for sample m84036_250809_035451_s4.bc2179 at 2025-09-15 20:31:55.481296...
2025-09-15 20:32:16.343 wdl.w:ptcp.w:call-paraphase-82.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for rpgr for sample m84036_250809_035451_s4.bc2179 at 2025-09-15 20:31:55.769746...
2025-09-15 20:33:11.562 wdl.w:ptcp.w:call-paraphase-83.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for f8inv22 for sample m84036_250809_035451_s4.bc2180 at 2025-09-15 20:32:58.357869...
2025-09-15 20:33:11.563 wdl.w:ptcp.w:call-paraphase-83.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for f8inv22 for sample m84036_250809_035451_s4.bc2180 at 2025-09-15 20:32:58.358696...
2025-09-15 20:33:12.841 wdl.w:ptcp.w:call-paraphase-94.t:call-run_paraphase INFO output :: name: "paraphase_bam", value: "m84036_250809_035451_s4.bc2191_paraphase/m84036_250809_035451_s4.bc2191.paraphase.bam"
2025-09-15 20:33:12.844 wdl.w:ptcp.w:call-paraphase-94.t:call-run_paraphase INFO output :: name: "paraphase_bam_bai", value: "m84036_250809_035451_s4.bc2191_paraphase/m84036_250809_035451_s4.bc2191.paraphase.bam.bai"
2025-09-15 20:33:12.846 wdl.w:ptcp.w:call-paraphase-94.t:call-run_paraphase INFO output :: name: "paraphase_json", value: "m84036_250809_035451_s4.bc2191_paraphase/m84036_250809_035451_s4.bc2191.paraphase.json"
2025-09-15 20:33:12.849 wdl.w:ptcp.w:call-paraphase-94.t:call-run_paraphase INFO output :: name: "paraphase_vcfs", value: ["/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2191_paraphase/m84036_250809_035451_s4.bc2191_paraphase_vcfs/m84036_250809_035451_s4.bc2191_cyp21.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2191_paraphase/m84036_250809_035451_s4.bc2191_paraphase_vcfs/m84036_250809_035451_s4.bc2191_f8inv1.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2191_paraphase/m84036_250809_035451_s4.bc2191_paraphase_vcfs/m84036_250809_035451_s4.bc2191_f8inv22.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2191_paraphase/m84036_250809_035451_s4.bc2191_paraphase_vcfs/m84036_250809_035451_s4.bc2191_gba.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2191_paraphase/m84036_250809_035451_s4.bc2191_paraphase_vcfs/m84036_250809_035451_s4.bc2191_hba.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2191_paraphase/m84036_250809_035451_s4.bc2191_paraphase_vcfs/m84036_250809_035451_s4.bc2191_hbb.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2191_paraphase/m84036_250809_035451_s4.bc2191_paraphase_vcfs/m84036_250809_035451_s4.bc2191_rpgr.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2191_paraphase/m84036_250809_035451_s4.bc2191_paraphase_vcfs/m84036_250809_035451_s4.bc2191_smn1.vcf"]
2025-09-15 20:33:12.852 wdl.w:ptcp.w:call-paraphase-94.t:call-run_paraphase INFO output :: name: "havanno_json", value: "m84036_250809_035451_s4.bc2191.havanno.json"
2025-09-15 20:33:13.004 wdl.w:ptcp.w:call-paraphase-94.t:call-run_paraphase NOTICE done
2025-09-15 20:33:13.010 wdl.w:ptcp.w:call-paraphase-94 NOTICE finish :: job: "call-run_paraphase"
2025-09-15 20:33:13.010 wdl.w:ptcp.w:call-paraphase-94 INFO output :: job: "call-run_paraphase", values: {"havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-94/call-run_paraphase/out/m84036_250809_035451_s4.bc2191.havanno.json", "paraphase_vcfs": ["/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-94/call-run_paraphase/out/m84036_250809_035451_s4.bc2191_paraphase/m84036_250809_035451_s4.bc2191_paraphase_vcfs/m84036_250809_035451_s4.bc2191_cyp21.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-94/call-run_paraphase/out/m84036_250809_035451_s4.bc2191_paraphase/m84036_250809_035451_s4.bc2191_paraphase_vcfs/m84036_250809_035451_s4.bc2191_f8inv1.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-94/call-run_paraphase/out/m84036_250809_035451_s4.bc2191_paraphase/m84036_250809_035451_s4.bc2191_paraphase_vcfs/m84036_250809_035451_s4.bc2191_f8inv22.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-94/call-run_paraphase/out/m84036_250809_035451_s4.bc2191_paraphase/m84036_250809_035451_s4.bc2191_paraphase_vcfs/m84036_250809_035451_s4.bc2191_gba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-94/call-run_paraphase/out/m84036_250809_035451_s4.bc2191_paraphase/m84036_250809_035451_s4.bc2191_paraphase_vcfs/m84036_250809_035451_s4.bc2191_hba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-94/call-run_paraphase/out/m84036_250809_035451_s4.bc2191_paraphase/m84036_250809_035451_s4.bc2191_paraphase_vcfs/m84036_250809_035451_s4.bc2191_hbb.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-94/call-run_paraphase/out/m84036_250809_035451_s4.bc2191_paraphase/m84036_250809_035451_s4.bc2191_paraphase_vcfs/m84036_250809_035451_s4.bc2191_rpgr.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-94/call-run_paraphase/out/m84036_250809_035451_s4.bc2191_paraphase/m84036_250809_035451_s4.bc2191_paraphase_vcfs/m84036_250809_035451_s4.bc2191_smn1.vcf"], "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-94/call-run_paraphase/out/m84036_250809_035451_s4.bc2191_paraphase/m84036_250809_035451_s4.bc2191.paraphase.json", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-94/call-run_paraphase/out/m84036_250809_035451_s4.bc2191_paraphase/m84036_250809_035451_s4.bc2191.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-94/call-run_paraphase/out/m84036_250809_035451_s4.bc2191_paraphase/m84036_250809_035451_s4.bc2191.paraphase.bam"}
2025-09-15 20:33:13.011 wdl.w:ptcp.w:call-paraphase-94 NOTICE ready :: job: "call-call_f8", callee: "call_f8"
2025-09-15 20:33:13.011 wdl.w:ptcp.w:call-paraphase-94 INFO input :: job: "call-call_f8", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "out_prefix": "m84036_250809_035451_s4.bc2191", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-94/call-run_paraphase/out/m84036_250809_035451_s4.bc2191_paraphase/m84036_250809_035451_s4.bc2191.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-94/call-run_paraphase/out/m84036_250809_035451_s4.bc2191_paraphase/m84036_250809_035451_s4.bc2191.paraphase.bam", "sex": "F"}
2025-09-15 20:33:13.011 wdl.w:ptcp.w:call-paraphase-94 INFO visit :: node: "output-havanno_json", values: {"havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-94/call-run_paraphase/out/m84036_250809_035451_s4.bc2191.havanno.json"}
2025-09-15 20:33:13.011 wdl.w:ptcp.w:call-paraphase-94 INFO visit :: node: "output-paraphase_bam", values: {"paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-94/call-run_paraphase/out/m84036_250809_035451_s4.bc2191_paraphase/m84036_250809_035451_s4.bc2191.paraphase.bam"}
2025-09-15 20:33:13.012 wdl.w:ptcp.w:call-paraphase-94 INFO visit :: node: "output-paraphase_bam_bai", values: {"paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-94/call-run_paraphase/out/m84036_250809_035451_s4.bc2191_paraphase/m84036_250809_035451_s4.bc2191.paraphase.bam.bai"}
2025-09-15 20:33:13.012 wdl.w:ptcp.w:call-paraphase-94 INFO visit :: node: "output-paraphase_json", values: {"paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-94/call-run_paraphase/out/m84036_250809_035451_s4.bc2191_paraphase/m84036_250809_035451_s4.bc2191.paraphase.json"}
2025-09-15 20:33:13.012 wdl.w:ptcp.w:call-paraphase-94 INFO visit :: node: "output-paraphase_vcfs", values: {"paraphase_vcfs": ["/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-94/call-run_paraphase/out/m84036_250809_035451_s4.bc2191_paraphase/m84036_250809_035451_s4.bc2191_paraphase_vcfs/m84036_250809_035451_s4.bc2191_cyp21.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-94/call-run_paraphase/out/m84036_250809_035451_s4.bc2191_paraphase/m84036_250809_035451_s4.bc2191_paraphase_vcfs/m84036_250809_035451_s4.bc2191_f8inv1.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-94/call-run_paraphase/out/m84036_250809_035451_s4.bc2191_paraphase/m84036_250809_035451_s4.bc2191_paraphase_vcfs/m84036_250809_035451_s4.bc2191_f8inv22.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-94/call-run_paraphase/out/m84036_250809_035451_s4.bc2191_paraphase/m84036_250809_035451_s4.bc2191_paraphase_vcfs/m84036_250809_035451_s4.bc2191_gba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-94/call-run_paraphase/out/m84036_250809_035451_s4.bc2191_paraphase/m84036_250809_035451_s4.bc2191_paraphase_vcfs/m84036_250809_035451_s4.bc2191_hba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-94/call-run_paraphase/out/m84036_250809_035451_s4.bc2191_paraphase/m84036_250809_035451_s4.bc2191_paraphase_vcfs/m84036_250809_035451_s4.bc2191_hbb.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-94/call-run_paraphase/out/m84036_250809_035451_s4.bc2191_paraphase/m84036_250809_035451_s4.bc2191_paraphase_vcfs/m84036_250809_035451_s4.bc2191_rpgr.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-94/call-run_paraphase/out/m84036_250809_035451_s4.bc2191_paraphase/m84036_250809_035451_s4.bc2191_paraphase_vcfs/m84036_250809_035451_s4.bc2191_smn1.vcf"]}
2025-09-15 20:33:13.016 wdl.w:ptcp.w:call-paraphase-94.t:call-call_f8 NOTICE task setup :: name: "call_f8", source: "./paraphase.wdl", line: 232, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-94/call-call_f8", thread: 140609302029888
2025-09-15 20:33:13.040 wdl.w:ptcp.w:call-paraphase-94.t:call-call_f8 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:33:13.040 wdl.w:ptcp.w:call-paraphase-94.t:call-call_f8 INFO input :: name: "genome_version", value: "38"
2025-09-15 20:33:13.040 wdl.w:ptcp.w:call-paraphase-94.t:call-call_f8 INFO input :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2191"
2025-09-15 20:33:13.040 wdl.w:ptcp.w:call-paraphase-94.t:call-call_f8 INFO input :: name: "paraphase_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2191.paraphase.bam.bai"
2025-09-15 20:33:13.040 wdl.w:ptcp.w:call-paraphase-94.t:call-call_f8 INFO input :: name: "paraphase_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2191.paraphase.bam"
2025-09-15 20:33:13.040 wdl.w:ptcp.w:call-paraphase-94.t:call-call_f8 INFO input :: name: "sex", value: "F"
2025-09-15 20:33:13.040 wdl.w:ptcp.w:call-paraphase-94.t:call-call_f8 INFO eval :: name: "threads", value: 1
2025-09-15 20:33:13.041 wdl.w:ptcp.w:call-paraphase-94.t:call-call_f8 INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:33:13.041 wdl.w:ptcp.w:call-paraphase-94.t:call-call_f8 INFO eval :: name: "disk_size", value: 11
2025-09-15 20:33:13.041 wdl.w:ptcp.w:call-paraphase-94.t:call-call_f8 INFO eval :: name: "sample_sex", value: "F"
2025-09-15 20:33:13.041 wdl.w:ptcp.w:call-paraphase-94.t:call-call_f8 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:33:13.041 wdl.w:ptcp.w:call-paraphase-94.t:call-call_f8 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:33:13.041 wdl.w:ptcp.w:call-paraphase-94.t:call-call_f8 INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:33:13.043 wdl.w:ptcp.w:call-paraphase-94.t:call-call_f8 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:33:13.079 wdl.w:ptcp.w:call-paraphase-94.t:call-call_f8 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 8, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-94/call-call_f8/_singularity_tmpdir_owz2yt3j"
2025-09-15 20:33:13.079 wdl.w:ptcp.w:call-paraphase-94.t:call-call_f8 INFO Slurm invocation: srun --job-name call-call_f8 --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-94/call-call_f8/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-94/call-call_f8/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-94/call-call_f8/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-94/call-call_f8/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-94/call-run_paraphase/out/m84036_250809_035451_s4.bc2191_paraphase/m84036_250809_035451_s4.bc2191.paraphase.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2191.paraphase.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-94/call-run_paraphase/out/m84036_250809_035451_s4.bc2191_paraphase/m84036_250809_035451_s4.bc2191.paraphase.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2191.paraphase.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-94/call-call_f8/_singularity_tmpdir_owz2yt3j/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-94/call-call_f8/_singularity_tmpdir_owz2yt3j/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:33:13.087 wdl.w:ptcp.w:call-paraphase-94.t:call-call_f8 NOTICE slurm_singularity run :: pid: 1212309, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-94/call-call_f8/slurm_singularity.log.txt"
2025-09-15 20:33:14.096 wdl.w:ptcp.w:call-paraphase-94.t:call-call_f8.slurm_singularity INFO srun: job 51798401 queued and waiting for resources
2025-09-15 20:33:14.096 wdl.w:ptcp.w:call-paraphase-94.t:call-call_f8.slurm_singularity INFO srun: job 51798401 has been allocated resources
2025-09-15 20:33:14.096 wdl.w:ptcp.w:call-paraphase-94.t:call-call_f8.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:33:14.600 wdl.w:ptcp.w:call-paraphase-94.t:call-call_f8 INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2191.f8inversion.vcf"
2025-09-15 20:33:14.603 wdl.w:ptcp.w:call-paraphase-94.t:call-call_f8 INFO output :: name: "json", value: "m84036_250809_035451_s4.bc2191.f8inversion.json"
2025-09-15 20:33:14.655 wdl.w:ptcp.w:call-paraphase-94.t:call-call_f8 NOTICE done
2025-09-15 20:33:14.660 wdl.w:ptcp.w:call-paraphase-94 NOTICE finish :: job: "call-call_f8"
2025-09-15 20:33:14.660 wdl.w:ptcp.w:call-paraphase-94 INFO output :: job: "call-call_f8", values: {"json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-94/call-call_f8/out/m84036_250809_035451_s4.bc2191.f8inversion.json", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-94/call-call_f8/out/m84036_250809_035451_s4.bc2191.f8inversion.vcf"}
2025-09-15 20:33:14.660 wdl.w:ptcp.w:call-paraphase-94 INFO visit :: node: "output-f8_json", values: {"f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-94/call-call_f8/out/m84036_250809_035451_s4.bc2191.f8inversion.json"}
2025-09-15 20:33:14.661 wdl.w:ptcp.w:call-paraphase-94 INFO visit :: node: "output-f8_vcf", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-94/call-call_f8/out/m84036_250809_035451_s4.bc2191.f8inversion.vcf"}
2025-09-15 20:33:14.661 wdl.w:ptcp.w:call-paraphase-94 INFO visit :: node: "outputs", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-94/call-call_f8/out/m84036_250809_035451_s4.bc2191.f8inversion.vcf", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-94/call-run_paraphase/out/m84036_250809_035451_s4.bc2191_paraphase/m84036_250809_035451_s4.bc2191.paraphase.json", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-94/call-run_paraphase/out/m84036_250809_035451_s4.bc2191_paraphase/m84036_250809_035451_s4.bc2191.paraphase.bam", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-94/call-run_paraphase/out/m84036_250809_035451_s4.bc2191_paraphase/m84036_250809_035451_s4.bc2191.paraphase.bam.bai", "paraphase_vcfs": ["/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-94/call-run_paraphase/out/m84036_250809_035451_s4.bc2191_paraphase/m84036_250809_035451_s4.bc2191_paraphase_vcfs/m84036_250809_035451_s4.bc2191_cyp21.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-94/call-run_paraphase/out/m84036_250809_035451_s4.bc2191_paraphase/m84036_250809_035451_s4.bc2191_paraphase_vcfs/m84036_250809_035451_s4.bc2191_f8inv1.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-94/call-run_paraphase/out/m84036_250809_035451_s4.bc2191_paraphase/m84036_250809_035451_s4.bc2191_paraphase_vcfs/m84036_250809_035451_s4.bc2191_f8inv22.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-94/call-run_paraphase/out/m84036_250809_035451_s4.bc2191_paraphase/m84036_250809_035451_s4.bc2191_paraphase_vcfs/m84036_250809_035451_s4.bc2191_gba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-94/call-run_paraphase/out/m84036_250809_035451_s4.bc2191_paraphase/m84036_250809_035451_s4.bc2191_paraphase_vcfs/m84036_250809_035451_s4.bc2191_hba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-94/call-run_paraphase/out/m84036_250809_035451_s4.bc2191_paraphase/m84036_250809_035451_s4.bc2191_paraphase_vcfs/m84036_250809_035451_s4.bc2191_hbb.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-94/call-run_paraphase/out/m84036_250809_035451_s4.bc2191_paraphase/m84036_250809_035451_s4.bc2191_paraphase_vcfs/m84036_250809_035451_s4.bc2191_rpgr.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-94/call-run_paraphase/out/m84036_250809_035451_s4.bc2191_paraphase/m84036_250809_035451_s4.bc2191_paraphase_vcfs/m84036_250809_035451_s4.bc2191_smn1.vcf"], "havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-94/call-run_paraphase/out/m84036_250809_035451_s4.bc2191.havanno.json", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-94/call-call_f8/out/m84036_250809_035451_s4.bc2191.f8inversion.json"}
2025-09-15 20:33:14.756 wdl.w:ptcp.w:call-paraphase-94 NOTICE done
2025-09-15 20:33:14.761 wdl.w:ptcp NOTICE finish :: job: "call-paraphase-94"
2025-09-15 20:33:14.761 wdl.w:ptcp INFO output :: job: "call-paraphase-94", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-94/out/m84036_250809_035451_s4.bc2191.f8inversion.vcf", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-94/out/m84036_250809_035451_s4.bc2191_paraphase/m84036_250809_035451_s4.bc2191.paraphase.json", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-94/out/m84036_250809_035451_s4.bc2191_paraphase/m84036_250809_035451_s4.bc2191.paraphase.bam", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-94/out/m84036_250809_035451_s4.bc2191_paraphase/m84036_250809_035451_s4.bc2191.paraphase.bam.bai", "paraphase_vcfs": ["/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-94/out/m84036_250809_035451_s4.bc2191_paraphase/m84036_250809_035451_s4.bc2191_paraphase_vcfs/m84036_250809_035451_s4.bc2191_cyp21.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-94/out/m84036_250809_035451_s4.bc2191_paraphase/m84036_250809_035451_s4.bc2191_paraphase_vcfs/m84036_250809_035451_s4.bc2191_f8inv1.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-94/out/m84036_250809_035451_s4.bc2191_paraphase/m84036_250809_035451_s4.bc2191_paraphase_vcfs/m84036_250809_035451_s4.bc2191_f8inv22.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-94/out/m84036_250809_035451_s4.bc2191_paraphase/m84036_250809_035451_s4.bc2191_paraphase_vcfs/m84036_250809_035451_s4.bc2191_gba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-94/out/m84036_250809_035451_s4.bc2191_paraphase/m84036_250809_035451_s4.bc2191_paraphase_vcfs/m84036_250809_035451_s4.bc2191_hba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-94/out/m84036_250809_035451_s4.bc2191_paraphase/m84036_250809_035451_s4.bc2191_paraphase_vcfs/m84036_250809_035451_s4.bc2191_hbb.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-94/out/m84036_250809_035451_s4.bc2191_paraphase/m84036_250809_035451_s4.bc2191_paraphase_vcfs/m84036_250809_035451_s4.bc2191_rpgr.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-94/out/m84036_250809_035451_s4.bc2191_paraphase/m84036_250809_035451_s4.bc2191_paraphase_vcfs/m84036_250809_035451_s4.bc2191_smn1.vcf"], "havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-94/out/m84036_250809_035451_s4.bc2191.havanno.json", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-94/out/m84036_250809_035451_s4.bc2191.f8inversion.json"}
2025-09-15 20:33:14.762 wdl.w:ptcp NOTICE ready :: job: "call-tar_outputs-94", callee: "tar_outputs"
2025-09-15 20:33:14.762 wdl.w:ptcp INFO input :: job: "call-tar_outputs-94", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "sawfish_vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-94/out/m84036_250809_035451_s4.bc2191_sawfish/m84036_250809_035451_s4.bc2191.sv.vcf.gz.tbi", "sawfish_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-94/out/m84036_250809_035451_s4.bc2191_sawfish/m84036_250809_035451_s4.bc2191.sv.vcf.gz", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-94/out/m84036_250809_035451_s4.bc2191.f8inversion.json", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-94/out/m84036_250809_035451_s4.bc2191_paraphase/m84036_250809_035451_s4.bc2191.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-94/out/m84036_250809_035451_s4.bc2191_paraphase/m84036_250809_035451_s4.bc2191.paraphase.bam", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-94/out/m84036_250809_035451_s4.bc2191_paraphase/m84036_250809_035451_s4.bc2191.paraphase.json", "trgt_spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-94/out/m84036_250809_035451_s4.bc2191.trgt.sorted.spanning.bam.bai", "trgt_spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-94/out/m84036_250809_035451_s4.bc2191.trgt.sorted.spanning.bam", "trgt_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-94/out/m84036_250809_035451_s4.bc2191.trgt.vcf", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-94/out/m84036_250809_035451_s4.bc2191.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-94/out/m84036_250809_035451_s4.bc2191.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2191"}
2025-09-15 20:33:14.767 wdl.w:ptcp.t:call-tar_outputs-94 NOTICE task setup :: name: "tar_outputs", source: "./common.wdl", line: 279, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-94", thread: 140610895857216
2025-09-15 20:33:14.786 wdl.w:ptcp.t:call-tar_outputs-94 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:33:14.786 wdl.w:ptcp.t:call-tar_outputs-94 INFO input :: name: "sawfish_vcf_tbi", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2191.sv.vcf.gz.tbi"
2025-09-15 20:33:14.786 wdl.w:ptcp.t:call-tar_outputs-94 INFO input :: name: "sawfish_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2191.sv.vcf.gz"
2025-09-15 20:33:14.786 wdl.w:ptcp.t:call-tar_outputs-94 INFO input :: name: "f8_json", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2191.f8inversion.json"
2025-09-15 20:33:14.786 wdl.w:ptcp.t:call-tar_outputs-94 INFO input :: name: "paraphase_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2191.paraphase.bam.bai"
2025-09-15 20:33:14.786 wdl.w:ptcp.t:call-tar_outputs-94 INFO input :: name: "paraphase_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2191.paraphase.bam"
2025-09-15 20:33:14.786 wdl.w:ptcp.t:call-tar_outputs-94 INFO input :: name: "paraphase_json", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2191.paraphase.json"
2025-09-15 20:33:14.786 wdl.w:ptcp.t:call-tar_outputs-94 INFO input :: name: "trgt_spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2191.trgt.sorted.spanning.bam.bai"
2025-09-15 20:33:14.786 wdl.w:ptcp.t:call-tar_outputs-94 INFO input :: name: "trgt_spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2191.trgt.sorted.spanning.bam"
2025-09-15 20:33:14.786 wdl.w:ptcp.t:call-tar_outputs-94 INFO input :: name: "trgt_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2191.trgt.vcf"
2025-09-15 20:33:14.786 wdl.w:ptcp.t:call-tar_outputs-94 INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2191.mapped.bam.bai"
2025-09-15 20:33:14.786 wdl.w:ptcp.t:call-tar_outputs-94 INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2191.mapped.bam"
2025-09-15 20:33:14.786 wdl.w:ptcp.t:call-tar_outputs-94 INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2191"
2025-09-15 20:33:14.787 wdl.w:ptcp.t:call-tar_outputs-94 INFO eval :: name: "threads", value: 1
2025-09-15 20:33:14.787 wdl.w:ptcp.t:call-tar_outputs-94 INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:33:14.787 wdl.w:ptcp.t:call-tar_outputs-94 INFO eval :: name: "disk_size", value: 6
2025-09-15 20:33:14.787 wdl.w:ptcp.t:call-tar_outputs-94 INFO eval :: name: "output_tarball", value: "m84036_250809_035451_s4.bc2191.tar"
2025-09-15 20:33:14.787 wdl.w:ptcp.t:call-tar_outputs-94 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:33:14.787 wdl.w:ptcp.t:call-tar_outputs-94 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:33:14.788 wdl.w:ptcp.t:call-tar_outputs-94 INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:33:14.788 wdl.w:ptcp.t:call-tar_outputs-94 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:33:14.853 wdl.w:ptcp.t:call-tar_outputs-94 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 17, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-94/_singularity_tmpdir_1f4j45kf"
2025-09-15 20:33:14.854 wdl.w:ptcp.t:call-tar_outputs-94 INFO Slurm invocation: srun --job-name call-tar_outputs-94 --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-94/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-94/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-94/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-94/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-94/out/m84036_250809_035451_s4.bc2191_paraphase/m84036_250809_035451_s4.bc2191.paraphase.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2191.paraphase.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-94/out/m84036_250809_035451_s4.bc2191_paraphase/m84036_250809_035451_s4.bc2191.paraphase.json:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2191.paraphase.json:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-94/out/m84036_250809_035451_s4.bc2191_paraphase/m84036_250809_035451_s4.bc2191.paraphase.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2191.paraphase.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-94/out/m84036_250809_035451_s4.bc2191.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2191.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-94/out/m84036_250809_035451_s4.bc2191.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2191.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-94/out/m84036_250809_035451_s4.bc2191.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2191.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-94/out/m84036_250809_035451_s4.bc2191.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2191.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-94/out/m84036_250809_035451_s4.bc2191.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2191.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-94/out/m84036_250809_035451_s4.bc2191_sawfish/m84036_250809_035451_s4.bc2191.sv.vcf.gz:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2191.sv.vcf.gz:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-94/out/m84036_250809_035451_s4.bc2191_sawfish/m84036_250809_035451_s4.bc2191.sv.vcf.gz.tbi:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2191.sv.vcf.gz.tbi:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-94/out/m84036_250809_035451_s4.bc2191.f8inversion.json:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2191.f8inversion.json:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-94/_singularity_tmpdir_1f4j45kf/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-94/_singularity_tmpdir_1f4j45kf/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:33:14.856 wdl.w:ptcp.t:call-tar_outputs-94 NOTICE slurm_singularity run :: pid: 1212321, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-94/slurm_singularity.log.txt"
2025-09-15 20:33:15.865 wdl.w:ptcp.t:call-tar_outputs-94.slurm_singularity INFO srun: job 51798402 queued and waiting for resources
2025-09-15 20:33:16.875 wdl.w:ptcp.t:call-tar_outputs-94.slurm_singularity INFO srun: job 51798402 has been allocated resources
2025-09-15 20:33:16.875 wdl.w:ptcp.t:call-tar_outputs-94.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:33:17.271 wdl.w:ptcp.t:call-tar_outputs-94 INFO output :: name: "sample_tarball", value: "m84036_250809_035451_s4.bc2191.tar"
2025-09-15 20:33:17.320 wdl.w:ptcp.t:call-tar_outputs-94 NOTICE done
2025-09-15 20:33:17.323 wdl.w:ptcp NOTICE finish :: job: "call-tar_outputs-94"
2025-09-15 20:33:17.323 wdl.w:ptcp INFO output :: job: "call-tar_outputs-94", values: {"sample_tarball": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-94/out/m84036_250809_035451_s4.bc2191.tar"}
2025-09-15 20:33:22.683 wdl.w:ptcp.w:call-paraphase-95.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for f8inv22 for sample m84036_250809_035451_s4.bc2192 at 2025-09-15 20:32:33.925540...
2025-09-15 20:33:22.684 wdl.w:ptcp.w:call-paraphase-95.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for f8inv22 for sample m84036_250809_035451_s4.bc2192 at 2025-09-15 20:32:33.926695...
2025-09-15 20:33:22.684 wdl.w:ptcp.w:call-paraphase-95.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for f8inv22 for sample m84036_250809_035451_s4.bc2192 at 2025-09-15 20:32:35.234437...
2025-09-15 20:33:22.684 wdl.w:ptcp.w:call-paraphase-95.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for f8inv22 for sample m84036_250809_035451_s4.bc2192 at 2025-09-15 20:32:41.800646...
2025-09-15 20:33:22.684 wdl.w:ptcp.w:call-paraphase-95.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for f8inv22 for sample m84036_250809_035451_s4.bc2192 at 2025-09-15 20:32:42.220704...
2025-09-15 20:33:24.499 wdl.w:ptcp.w:call-paraphase-95.t:call-run_paraphase INFO output :: name: "paraphase_bam", value: "m84036_250809_035451_s4.bc2192_paraphase/m84036_250809_035451_s4.bc2192.paraphase.bam"
2025-09-15 20:33:24.502 wdl.w:ptcp.w:call-paraphase-95.t:call-run_paraphase INFO output :: name: "paraphase_bam_bai", value: "m84036_250809_035451_s4.bc2192_paraphase/m84036_250809_035451_s4.bc2192.paraphase.bam.bai"
2025-09-15 20:33:24.503 wdl.w:ptcp.w:call-paraphase-95.t:call-run_paraphase INFO output :: name: "paraphase_json", value: "m84036_250809_035451_s4.bc2192_paraphase/m84036_250809_035451_s4.bc2192.paraphase.json"
2025-09-15 20:33:24.507 wdl.w:ptcp.w:call-paraphase-95.t:call-run_paraphase INFO output :: name: "paraphase_vcfs", value: ["/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2192_paraphase/m84036_250809_035451_s4.bc2192_paraphase_vcfs/m84036_250809_035451_s4.bc2192_cyp21.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2192_paraphase/m84036_250809_035451_s4.bc2192_paraphase_vcfs/m84036_250809_035451_s4.bc2192_f8inv1.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2192_paraphase/m84036_250809_035451_s4.bc2192_paraphase_vcfs/m84036_250809_035451_s4.bc2192_f8inv22.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2192_paraphase/m84036_250809_035451_s4.bc2192_paraphase_vcfs/m84036_250809_035451_s4.bc2192_gba.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2192_paraphase/m84036_250809_035451_s4.bc2192_paraphase_vcfs/m84036_250809_035451_s4.bc2192_hba.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2192_paraphase/m84036_250809_035451_s4.bc2192_paraphase_vcfs/m84036_250809_035451_s4.bc2192_hbb.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2192_paraphase/m84036_250809_035451_s4.bc2192_paraphase_vcfs/m84036_250809_035451_s4.bc2192_rpgr.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2192_paraphase/m84036_250809_035451_s4.bc2192_paraphase_vcfs/m84036_250809_035451_s4.bc2192_smn1.vcf"]
2025-09-15 20:33:24.510 wdl.w:ptcp.w:call-paraphase-95.t:call-run_paraphase INFO output :: name: "havanno_json", value: "m84036_250809_035451_s4.bc2192.havanno.json"
2025-09-15 20:33:24.669 wdl.w:ptcp.w:call-paraphase-95.t:call-run_paraphase NOTICE done
2025-09-15 20:33:24.674 wdl.w:ptcp.w:call-paraphase-95 NOTICE finish :: job: "call-run_paraphase"
2025-09-15 20:33:24.674 wdl.w:ptcp.w:call-paraphase-95 INFO output :: job: "call-run_paraphase", values: {"havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-95/call-run_paraphase/out/m84036_250809_035451_s4.bc2192.havanno.json", "paraphase_vcfs": ["/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-95/call-run_paraphase/out/m84036_250809_035451_s4.bc2192_paraphase/m84036_250809_035451_s4.bc2192_paraphase_vcfs/m84036_250809_035451_s4.bc2192_cyp21.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-95/call-run_paraphase/out/m84036_250809_035451_s4.bc2192_paraphase/m84036_250809_035451_s4.bc2192_paraphase_vcfs/m84036_250809_035451_s4.bc2192_f8inv1.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-95/call-run_paraphase/out/m84036_250809_035451_s4.bc2192_paraphase/m84036_250809_035451_s4.bc2192_paraphase_vcfs/m84036_250809_035451_s4.bc2192_f8inv22.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-95/call-run_paraphase/out/m84036_250809_035451_s4.bc2192_paraphase/m84036_250809_035451_s4.bc2192_paraphase_vcfs/m84036_250809_035451_s4.bc2192_gba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-95/call-run_paraphase/out/m84036_250809_035451_s4.bc2192_paraphase/m84036_250809_035451_s4.bc2192_paraphase_vcfs/m84036_250809_035451_s4.bc2192_hba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-95/call-run_paraphase/out/m84036_250809_035451_s4.bc2192_paraphase/m84036_250809_035451_s4.bc2192_paraphase_vcfs/m84036_250809_035451_s4.bc2192_hbb.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-95/call-run_paraphase/out/m84036_250809_035451_s4.bc2192_paraphase/m84036_250809_035451_s4.bc2192_paraphase_vcfs/m84036_250809_035451_s4.bc2192_rpgr.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-95/call-run_paraphase/out/m84036_250809_035451_s4.bc2192_paraphase/m84036_250809_035451_s4.bc2192_paraphase_vcfs/m84036_250809_035451_s4.bc2192_smn1.vcf"], "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-95/call-run_paraphase/out/m84036_250809_035451_s4.bc2192_paraphase/m84036_250809_035451_s4.bc2192.paraphase.json", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-95/call-run_paraphase/out/m84036_250809_035451_s4.bc2192_paraphase/m84036_250809_035451_s4.bc2192.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-95/call-run_paraphase/out/m84036_250809_035451_s4.bc2192_paraphase/m84036_250809_035451_s4.bc2192.paraphase.bam"}
2025-09-15 20:33:24.675 wdl.w:ptcp.w:call-paraphase-95 NOTICE ready :: job: "call-call_f8", callee: "call_f8"
2025-09-15 20:33:24.675 wdl.w:ptcp.w:call-paraphase-95 INFO input :: job: "call-call_f8", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "out_prefix": "m84036_250809_035451_s4.bc2192", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-95/call-run_paraphase/out/m84036_250809_035451_s4.bc2192_paraphase/m84036_250809_035451_s4.bc2192.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-95/call-run_paraphase/out/m84036_250809_035451_s4.bc2192_paraphase/m84036_250809_035451_s4.bc2192.paraphase.bam", "sex": "F"}
2025-09-15 20:33:24.675 wdl.w:ptcp.w:call-paraphase-95 INFO visit :: node: "output-havanno_json", values: {"havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-95/call-run_paraphase/out/m84036_250809_035451_s4.bc2192.havanno.json"}
2025-09-15 20:33:24.675 wdl.w:ptcp.w:call-paraphase-95 INFO visit :: node: "output-paraphase_bam", values: {"paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-95/call-run_paraphase/out/m84036_250809_035451_s4.bc2192_paraphase/m84036_250809_035451_s4.bc2192.paraphase.bam"}
2025-09-15 20:33:24.676 wdl.w:ptcp.w:call-paraphase-95 INFO visit :: node: "output-paraphase_bam_bai", values: {"paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-95/call-run_paraphase/out/m84036_250809_035451_s4.bc2192_paraphase/m84036_250809_035451_s4.bc2192.paraphase.bam.bai"}
2025-09-15 20:33:24.676 wdl.w:ptcp.w:call-paraphase-95 INFO visit :: node: "output-paraphase_json", values: {"paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-95/call-run_paraphase/out/m84036_250809_035451_s4.bc2192_paraphase/m84036_250809_035451_s4.bc2192.paraphase.json"}
2025-09-15 20:33:24.676 wdl.w:ptcp.w:call-paraphase-95 INFO visit :: node: "output-paraphase_vcfs", values: {"paraphase_vcfs": ["/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-95/call-run_paraphase/out/m84036_250809_035451_s4.bc2192_paraphase/m84036_250809_035451_s4.bc2192_paraphase_vcfs/m84036_250809_035451_s4.bc2192_cyp21.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-95/call-run_paraphase/out/m84036_250809_035451_s4.bc2192_paraphase/m84036_250809_035451_s4.bc2192_paraphase_vcfs/m84036_250809_035451_s4.bc2192_f8inv1.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-95/call-run_paraphase/out/m84036_250809_035451_s4.bc2192_paraphase/m84036_250809_035451_s4.bc2192_paraphase_vcfs/m84036_250809_035451_s4.bc2192_f8inv22.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-95/call-run_paraphase/out/m84036_250809_035451_s4.bc2192_paraphase/m84036_250809_035451_s4.bc2192_paraphase_vcfs/m84036_250809_035451_s4.bc2192_gba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-95/call-run_paraphase/out/m84036_250809_035451_s4.bc2192_paraphase/m84036_250809_035451_s4.bc2192_paraphase_vcfs/m84036_250809_035451_s4.bc2192_hba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-95/call-run_paraphase/out/m84036_250809_035451_s4.bc2192_paraphase/m84036_250809_035451_s4.bc2192_paraphase_vcfs/m84036_250809_035451_s4.bc2192_hbb.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-95/call-run_paraphase/out/m84036_250809_035451_s4.bc2192_paraphase/m84036_250809_035451_s4.bc2192_paraphase_vcfs/m84036_250809_035451_s4.bc2192_rpgr.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-95/call-run_paraphase/out/m84036_250809_035451_s4.bc2192_paraphase/m84036_250809_035451_s4.bc2192_paraphase_vcfs/m84036_250809_035451_s4.bc2192_smn1.vcf"]}
2025-09-15 20:33:24.680 wdl.w:ptcp.w:call-paraphase-95.t:call-call_f8 NOTICE task setup :: name: "call_f8", source: "./paraphase.wdl", line: 232, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-95/call-call_f8", thread: 140611432728128
2025-09-15 20:33:24.694 wdl.w:ptcp.w:call-paraphase-95.t:call-call_f8 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:33:24.694 wdl.w:ptcp.w:call-paraphase-95.t:call-call_f8 INFO input :: name: "genome_version", value: "38"
2025-09-15 20:33:24.694 wdl.w:ptcp.w:call-paraphase-95.t:call-call_f8 INFO input :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2192"
2025-09-15 20:33:24.694 wdl.w:ptcp.w:call-paraphase-95.t:call-call_f8 INFO input :: name: "paraphase_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2192.paraphase.bam.bai"
2025-09-15 20:33:24.694 wdl.w:ptcp.w:call-paraphase-95.t:call-call_f8 INFO input :: name: "paraphase_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2192.paraphase.bam"
2025-09-15 20:33:24.694 wdl.w:ptcp.w:call-paraphase-95.t:call-call_f8 INFO input :: name: "sex", value: "F"
2025-09-15 20:33:24.694 wdl.w:ptcp.w:call-paraphase-95.t:call-call_f8 INFO eval :: name: "threads", value: 1
2025-09-15 20:33:24.694 wdl.w:ptcp.w:call-paraphase-95.t:call-call_f8 INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:33:24.694 wdl.w:ptcp.w:call-paraphase-95.t:call-call_f8 INFO eval :: name: "disk_size", value: 11
2025-09-15 20:33:24.695 wdl.w:ptcp.w:call-paraphase-95.t:call-call_f8 INFO eval :: name: "sample_sex", value: "F"
2025-09-15 20:33:24.695 wdl.w:ptcp.w:call-paraphase-95.t:call-call_f8 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:33:24.695 wdl.w:ptcp.w:call-paraphase-95.t:call-call_f8 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:33:24.695 wdl.w:ptcp.w:call-paraphase-95.t:call-call_f8 INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:33:24.695 wdl.w:ptcp.w:call-paraphase-95.t:call-call_f8 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:33:24.732 wdl.w:ptcp.w:call-paraphase-95.t:call-call_f8 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 8, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-95/call-call_f8/_singularity_tmpdir_to1ppj1q"
2025-09-15 20:33:24.732 wdl.w:ptcp.w:call-paraphase-95.t:call-call_f8 INFO Slurm invocation: srun --job-name call-call_f8 --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-95/call-call_f8/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-95/call-call_f8/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-95/call-call_f8/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-95/call-call_f8/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-95/call-run_paraphase/out/m84036_250809_035451_s4.bc2192_paraphase/m84036_250809_035451_s4.bc2192.paraphase.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2192.paraphase.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-95/call-run_paraphase/out/m84036_250809_035451_s4.bc2192_paraphase/m84036_250809_035451_s4.bc2192.paraphase.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2192.paraphase.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-95/call-call_f8/_singularity_tmpdir_to1ppj1q/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-95/call-call_f8/_singularity_tmpdir_to1ppj1q/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:33:24.736 wdl.w:ptcp.w:call-paraphase-95.t:call-call_f8 NOTICE slurm_singularity run :: pid: 1212401, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-95/call-call_f8/slurm_singularity.log.txt"
2025-09-15 20:33:25.744 wdl.w:ptcp.w:call-paraphase-95.t:call-call_f8.slurm_singularity INFO srun: job 51798403 queued and waiting for resources
2025-09-15 20:33:25.744 wdl.w:ptcp.w:call-paraphase-95.t:call-call_f8.slurm_singularity INFO srun: job 51798403 has been allocated resources
2025-09-15 20:33:25.744 wdl.w:ptcp.w:call-paraphase-95.t:call-call_f8.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:33:26.650 wdl.w:ptcp.w:call-paraphase-95.t:call-call_f8 INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2192.f8inversion.vcf"
2025-09-15 20:33:26.653 wdl.w:ptcp.w:call-paraphase-95.t:call-call_f8 INFO output :: name: "json", value: "m84036_250809_035451_s4.bc2192.f8inversion.json"
2025-09-15 20:33:26.700 wdl.w:ptcp.w:call-paraphase-95.t:call-call_f8 NOTICE done
2025-09-15 20:33:26.705 wdl.w:ptcp.w:call-paraphase-95 NOTICE finish :: job: "call-call_f8"
2025-09-15 20:33:26.705 wdl.w:ptcp.w:call-paraphase-95 INFO output :: job: "call-call_f8", values: {"json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-95/call-call_f8/out/m84036_250809_035451_s4.bc2192.f8inversion.json", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-95/call-call_f8/out/m84036_250809_035451_s4.bc2192.f8inversion.vcf"}
2025-09-15 20:33:26.705 wdl.w:ptcp.w:call-paraphase-95 INFO visit :: node: "output-f8_json", values: {"f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-95/call-call_f8/out/m84036_250809_035451_s4.bc2192.f8inversion.json"}
2025-09-15 20:33:26.706 wdl.w:ptcp.w:call-paraphase-95 INFO visit :: node: "output-f8_vcf", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-95/call-call_f8/out/m84036_250809_035451_s4.bc2192.f8inversion.vcf"}
2025-09-15 20:33:26.707 wdl.w:ptcp.w:call-paraphase-95 INFO visit :: node: "outputs", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-95/call-call_f8/out/m84036_250809_035451_s4.bc2192.f8inversion.vcf", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-95/call-run_paraphase/out/m84036_250809_035451_s4.bc2192_paraphase/m84036_250809_035451_s4.bc2192.paraphase.json", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-95/call-run_paraphase/out/m84036_250809_035451_s4.bc2192_paraphase/m84036_250809_035451_s4.bc2192.paraphase.bam", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-95/call-run_paraphase/out/m84036_250809_035451_s4.bc2192_paraphase/m84036_250809_035451_s4.bc2192.paraphase.bam.bai", "paraphase_vcfs": ["/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-95/call-run_paraphase/out/m84036_250809_035451_s4.bc2192_paraphase/m84036_250809_035451_s4.bc2192_paraphase_vcfs/m84036_250809_035451_s4.bc2192_cyp21.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-95/call-run_paraphase/out/m84036_250809_035451_s4.bc2192_paraphase/m84036_250809_035451_s4.bc2192_paraphase_vcfs/m84036_250809_035451_s4.bc2192_f8inv1.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-95/call-run_paraphase/out/m84036_250809_035451_s4.bc2192_paraphase/m84036_250809_035451_s4.bc2192_paraphase_vcfs/m84036_250809_035451_s4.bc2192_f8inv22.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-95/call-run_paraphase/out/m84036_250809_035451_s4.bc2192_paraphase/m84036_250809_035451_s4.bc2192_paraphase_vcfs/m84036_250809_035451_s4.bc2192_gba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-95/call-run_paraphase/out/m84036_250809_035451_s4.bc2192_paraphase/m84036_250809_035451_s4.bc2192_paraphase_vcfs/m84036_250809_035451_s4.bc2192_hba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-95/call-run_paraphase/out/m84036_250809_035451_s4.bc2192_paraphase/m84036_250809_035451_s4.bc2192_paraphase_vcfs/m84036_250809_035451_s4.bc2192_hbb.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-95/call-run_paraphase/out/m84036_250809_035451_s4.bc2192_paraphase/m84036_250809_035451_s4.bc2192_paraphase_vcfs/m84036_250809_035451_s4.bc2192_rpgr.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-95/call-run_paraphase/out/m84036_250809_035451_s4.bc2192_paraphase/m84036_250809_035451_s4.bc2192_paraphase_vcfs/m84036_250809_035451_s4.bc2192_smn1.vcf"], "havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-95/call-run_paraphase/out/m84036_250809_035451_s4.bc2192.havanno.json", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-95/call-call_f8/out/m84036_250809_035451_s4.bc2192.f8inversion.json"}
2025-09-15 20:33:26.805 wdl.w:ptcp.w:call-paraphase-95 NOTICE done
2025-09-15 20:33:26.810 wdl.w:ptcp NOTICE finish :: job: "call-paraphase-95"
2025-09-15 20:33:26.810 wdl.w:ptcp INFO output :: job: "call-paraphase-95", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-95/out/m84036_250809_035451_s4.bc2192.f8inversion.vcf", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-95/out/m84036_250809_035451_s4.bc2192_paraphase/m84036_250809_035451_s4.bc2192.paraphase.json", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-95/out/m84036_250809_035451_s4.bc2192_paraphase/m84036_250809_035451_s4.bc2192.paraphase.bam", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-95/out/m84036_250809_035451_s4.bc2192_paraphase/m84036_250809_035451_s4.bc2192.paraphase.bam.bai", "paraphase_vcfs": ["/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-95/out/m84036_250809_035451_s4.bc2192_paraphase/m84036_250809_035451_s4.bc2192_paraphase_vcfs/m84036_250809_035451_s4.bc2192_cyp21.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-95/out/m84036_250809_035451_s4.bc2192_paraphase/m84036_250809_035451_s4.bc2192_paraphase_vcfs/m84036_250809_035451_s4.bc2192_f8inv1.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-95/out/m84036_250809_035451_s4.bc2192_paraphase/m84036_250809_035451_s4.bc2192_paraphase_vcfs/m84036_250809_035451_s4.bc2192_f8inv22.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-95/out/m84036_250809_035451_s4.bc2192_paraphase/m84036_250809_035451_s4.bc2192_paraphase_vcfs/m84036_250809_035451_s4.bc2192_gba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-95/out/m84036_250809_035451_s4.bc2192_paraphase/m84036_250809_035451_s4.bc2192_paraphase_vcfs/m84036_250809_035451_s4.bc2192_hba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-95/out/m84036_250809_035451_s4.bc2192_paraphase/m84036_250809_035451_s4.bc2192_paraphase_vcfs/m84036_250809_035451_s4.bc2192_hbb.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-95/out/m84036_250809_035451_s4.bc2192_paraphase/m84036_250809_035451_s4.bc2192_paraphase_vcfs/m84036_250809_035451_s4.bc2192_rpgr.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-95/out/m84036_250809_035451_s4.bc2192_paraphase/m84036_250809_035451_s4.bc2192_paraphase_vcfs/m84036_250809_035451_s4.bc2192_smn1.vcf"], "havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-95/out/m84036_250809_035451_s4.bc2192.havanno.json", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-95/out/m84036_250809_035451_s4.bc2192.f8inversion.json"}
2025-09-15 20:33:26.810 wdl.w:ptcp NOTICE ready :: job: "call-tar_outputs-95", callee: "tar_outputs"
2025-09-15 20:33:26.810 wdl.w:ptcp INFO input :: job: "call-tar_outputs-95", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "sawfish_vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-95/out/m84036_250809_035451_s4.bc2192_sawfish/m84036_250809_035451_s4.bc2192.sv.vcf.gz.tbi", "sawfish_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-95/out/m84036_250809_035451_s4.bc2192_sawfish/m84036_250809_035451_s4.bc2192.sv.vcf.gz", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-95/out/m84036_250809_035451_s4.bc2192.f8inversion.json", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-95/out/m84036_250809_035451_s4.bc2192_paraphase/m84036_250809_035451_s4.bc2192.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-95/out/m84036_250809_035451_s4.bc2192_paraphase/m84036_250809_035451_s4.bc2192.paraphase.bam", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-95/out/m84036_250809_035451_s4.bc2192_paraphase/m84036_250809_035451_s4.bc2192.paraphase.json", "trgt_spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-95/out/m84036_250809_035451_s4.bc2192.trgt.sorted.spanning.bam.bai", "trgt_spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-95/out/m84036_250809_035451_s4.bc2192.trgt.sorted.spanning.bam", "trgt_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-95/out/m84036_250809_035451_s4.bc2192.trgt.vcf", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-95/out/m84036_250809_035451_s4.bc2192.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-95/out/m84036_250809_035451_s4.bc2192.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2192"}
2025-09-15 20:33:26.816 wdl.w:ptcp.t:call-tar_outputs-95 NOTICE task setup :: name: "tar_outputs", source: "./common.wdl", line: 279, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-95", thread: 140613605389888
2025-09-15 20:33:26.835 wdl.w:ptcp.t:call-tar_outputs-95 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:33:26.835 wdl.w:ptcp.t:call-tar_outputs-95 INFO input :: name: "sawfish_vcf_tbi", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2192.sv.vcf.gz.tbi"
2025-09-15 20:33:26.835 wdl.w:ptcp.t:call-tar_outputs-95 INFO input :: name: "sawfish_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2192.sv.vcf.gz"
2025-09-15 20:33:26.835 wdl.w:ptcp.t:call-tar_outputs-95 INFO input :: name: "f8_json", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2192.f8inversion.json"
2025-09-15 20:33:26.835 wdl.w:ptcp.t:call-tar_outputs-95 INFO input :: name: "paraphase_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2192.paraphase.bam.bai"
2025-09-15 20:33:26.835 wdl.w:ptcp.t:call-tar_outputs-95 INFO input :: name: "paraphase_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2192.paraphase.bam"
2025-09-15 20:33:26.835 wdl.w:ptcp.t:call-tar_outputs-95 INFO input :: name: "paraphase_json", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2192.paraphase.json"
2025-09-15 20:33:26.835 wdl.w:ptcp.t:call-tar_outputs-95 INFO input :: name: "trgt_spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2192.trgt.sorted.spanning.bam.bai"
2025-09-15 20:33:26.835 wdl.w:ptcp.t:call-tar_outputs-95 INFO input :: name: "trgt_spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2192.trgt.sorted.spanning.bam"
2025-09-15 20:33:26.836 wdl.w:ptcp.t:call-tar_outputs-95 INFO input :: name: "trgt_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2192.trgt.vcf"
2025-09-15 20:33:26.836 wdl.w:ptcp.t:call-tar_outputs-95 INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2192.mapped.bam.bai"
2025-09-15 20:33:26.836 wdl.w:ptcp.t:call-tar_outputs-95 INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2192.mapped.bam"
2025-09-15 20:33:26.836 wdl.w:ptcp.t:call-tar_outputs-95 INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2192"
2025-09-15 20:33:26.836 wdl.w:ptcp.t:call-tar_outputs-95 INFO eval :: name: "threads", value: 1
2025-09-15 20:33:26.836 wdl.w:ptcp.t:call-tar_outputs-95 INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:33:26.836 wdl.w:ptcp.t:call-tar_outputs-95 INFO eval :: name: "disk_size", value: 6
2025-09-15 20:33:26.836 wdl.w:ptcp.t:call-tar_outputs-95 INFO eval :: name: "output_tarball", value: "m84036_250809_035451_s4.bc2192.tar"
2025-09-15 20:33:26.837 wdl.w:ptcp.t:call-tar_outputs-95 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:33:26.837 wdl.w:ptcp.t:call-tar_outputs-95 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:33:26.837 wdl.w:ptcp.t:call-tar_outputs-95 INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:33:26.837 wdl.w:ptcp.t:call-tar_outputs-95 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:33:26.927 wdl.w:ptcp.t:call-tar_outputs-95 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 17, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-95/_singularity_tmpdir_cxrnpjs0"
2025-09-15 20:33:26.927 wdl.w:ptcp.t:call-tar_outputs-95 INFO Slurm invocation: srun --job-name call-tar_outputs-95 --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-95/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-95/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-95/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-95/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-95/out/m84036_250809_035451_s4.bc2192_sawfish/m84036_250809_035451_s4.bc2192.sv.vcf.gz:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2192.sv.vcf.gz:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-95/out/m84036_250809_035451_s4.bc2192_sawfish/m84036_250809_035451_s4.bc2192.sv.vcf.gz.tbi:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2192.sv.vcf.gz.tbi:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-95/out/m84036_250809_035451_s4.bc2192_paraphase/m84036_250809_035451_s4.bc2192.paraphase.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2192.paraphase.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-95/out/m84036_250809_035451_s4.bc2192_paraphase/m84036_250809_035451_s4.bc2192.paraphase.json:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2192.paraphase.json:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-95/out/m84036_250809_035451_s4.bc2192_paraphase/m84036_250809_035451_s4.bc2192.paraphase.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2192.paraphase.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-95/out/m84036_250809_035451_s4.bc2192.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2192.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-95/out/m84036_250809_035451_s4.bc2192.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2192.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-95/out/m84036_250809_035451_s4.bc2192.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2192.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-95/out/m84036_250809_035451_s4.bc2192.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2192.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-95/out/m84036_250809_035451_s4.bc2192.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2192.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-95/out/m84036_250809_035451_s4.bc2192.f8inversion.json:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2192.f8inversion.json:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-95/_singularity_tmpdir_cxrnpjs0/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-95/_singularity_tmpdir_cxrnpjs0/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:33:26.931 wdl.w:ptcp.t:call-tar_outputs-95 NOTICE slurm_singularity run :: pid: 1212412, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-95/slurm_singularity.log.txt"
2025-09-15 20:33:27.941 wdl.w:ptcp.t:call-tar_outputs-95.slurm_singularity INFO srun: job 51798404 queued and waiting for resources
2025-09-15 20:33:28.949 wdl.w:ptcp.t:call-tar_outputs-95.slurm_singularity INFO srun: job 51798404 has been allocated resources
2025-09-15 20:33:28.950 wdl.w:ptcp.t:call-tar_outputs-95.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:33:29.348 wdl.w:ptcp.t:call-tar_outputs-95 INFO output :: name: "sample_tarball", value: "m84036_250809_035451_s4.bc2192.tar"
2025-09-15 20:33:29.402 wdl.w:ptcp.t:call-tar_outputs-95 NOTICE done
2025-09-15 20:33:29.406 wdl.w:ptcp NOTICE finish :: job: "call-tar_outputs-95"
2025-09-15 20:33:29.406 wdl.w:ptcp INFO output :: job: "call-tar_outputs-95", values: {"sample_tarball": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-95/out/m84036_250809_035451_s4.bc2192.tar"}
2025-09-15 20:33:29.876 wdl.w:ptcp.w:call-paraphase-91.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for rpgr for sample m84036_250809_035451_s4.bc2188 at 2025-09-15 20:32:38.133615...
2025-09-15 20:33:29.877 wdl.w:ptcp.w:call-paraphase-91.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for rpgr for sample m84036_250809_035451_s4.bc2188 at 2025-09-15 20:32:38.134502...
2025-09-15 20:33:29.877 wdl.w:ptcp.w:call-paraphase-91.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for rpgr for sample m84036_250809_035451_s4.bc2188 at 2025-09-15 20:32:42.691467...
2025-09-15 20:33:29.877 wdl.w:ptcp.w:call-paraphase-91.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for rpgr for sample m84036_250809_035451_s4.bc2188 at 2025-09-15 20:32:44.414450...
2025-09-15 20:33:29.877 wdl.w:ptcp.w:call-paraphase-91.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for rpgr for sample m84036_250809_035451_s4.bc2188 at 2025-09-15 20:32:44.612720...
2025-09-15 20:33:36.954 wdl.w:ptcp.w:call-paraphase-78.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for f8inv22 for sample m84036_250809_035451_s4.bc2175 at 2025-09-15 20:33:35.669844...
2025-09-15 20:33:36.956 wdl.w:ptcp.w:call-paraphase-78.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for f8inv22 for sample m84036_250809_035451_s4.bc2175 at 2025-09-15 20:33:35.670605...
2025-09-15 20:33:46.063 wdl.w:ptcp.w:call-paraphase-78.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for f8inv22 for sample m84036_250809_035451_s4.bc2175 at 2025-09-15 20:33:36.785295...
2025-09-15 20:33:49.100 wdl.w:ptcp.w:call-paraphase-78.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for f8inv22 for sample m84036_250809_035451_s4.bc2175 at 2025-09-15 20:33:42.626651...
2025-09-15 20:33:49.100 wdl.w:ptcp.w:call-paraphase-78.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for f8inv22 for sample m84036_250809_035451_s4.bc2175 at 2025-09-15 20:33:42.975127...
2025-09-15 20:33:53.081 wdl.w:ptcp.w:call-paraphase-83.t:call-run_paraphase INFO output :: name: "paraphase_bam", value: "m84036_250809_035451_s4.bc2180_paraphase/m84036_250809_035451_s4.bc2180.paraphase.bam"
2025-09-15 20:33:53.084 wdl.w:ptcp.w:call-paraphase-83.t:call-run_paraphase INFO output :: name: "paraphase_bam_bai", value: "m84036_250809_035451_s4.bc2180_paraphase/m84036_250809_035451_s4.bc2180.paraphase.bam.bai"
2025-09-15 20:33:53.085 wdl.w:ptcp.w:call-paraphase-83.t:call-run_paraphase INFO output :: name: "paraphase_json", value: "m84036_250809_035451_s4.bc2180_paraphase/m84036_250809_035451_s4.bc2180.paraphase.json"
2025-09-15 20:33:53.090 wdl.w:ptcp.w:call-paraphase-83.t:call-run_paraphase INFO output :: name: "paraphase_vcfs", value: ["/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2180_paraphase/m84036_250809_035451_s4.bc2180_paraphase_vcfs/m84036_250809_035451_s4.bc2180_cyp21.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2180_paraphase/m84036_250809_035451_s4.bc2180_paraphase_vcfs/m84036_250809_035451_s4.bc2180_f8inv1.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2180_paraphase/m84036_250809_035451_s4.bc2180_paraphase_vcfs/m84036_250809_035451_s4.bc2180_f8inv22.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2180_paraphase/m84036_250809_035451_s4.bc2180_paraphase_vcfs/m84036_250809_035451_s4.bc2180_gba.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2180_paraphase/m84036_250809_035451_s4.bc2180_paraphase_vcfs/m84036_250809_035451_s4.bc2180_hba.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2180_paraphase/m84036_250809_035451_s4.bc2180_paraphase_vcfs/m84036_250809_035451_s4.bc2180_hbb.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2180_paraphase/m84036_250809_035451_s4.bc2180_paraphase_vcfs/m84036_250809_035451_s4.bc2180_rpgr.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2180_paraphase/m84036_250809_035451_s4.bc2180_paraphase_vcfs/m84036_250809_035451_s4.bc2180_smn1.vcf"]
2025-09-15 20:33:53.093 wdl.w:ptcp.w:call-paraphase-83.t:call-run_paraphase INFO output :: name: "havanno_json", value: "m84036_250809_035451_s4.bc2180.havanno.json"
2025-09-15 20:33:53.235 wdl.w:ptcp.w:call-paraphase-83.t:call-run_paraphase NOTICE done
2025-09-15 20:33:53.240 wdl.w:ptcp.w:call-paraphase-83 NOTICE finish :: job: "call-run_paraphase"
2025-09-15 20:33:53.241 wdl.w:ptcp.w:call-paraphase-83 INFO output :: job: "call-run_paraphase", values: {"havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-83/call-run_paraphase/out/m84036_250809_035451_s4.bc2180.havanno.json", "paraphase_vcfs": ["/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-83/call-run_paraphase/out/m84036_250809_035451_s4.bc2180_paraphase/m84036_250809_035451_s4.bc2180_paraphase_vcfs/m84036_250809_035451_s4.bc2180_cyp21.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-83/call-run_paraphase/out/m84036_250809_035451_s4.bc2180_paraphase/m84036_250809_035451_s4.bc2180_paraphase_vcfs/m84036_250809_035451_s4.bc2180_f8inv1.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-83/call-run_paraphase/out/m84036_250809_035451_s4.bc2180_paraphase/m84036_250809_035451_s4.bc2180_paraphase_vcfs/m84036_250809_035451_s4.bc2180_f8inv22.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-83/call-run_paraphase/out/m84036_250809_035451_s4.bc2180_paraphase/m84036_250809_035451_s4.bc2180_paraphase_vcfs/m84036_250809_035451_s4.bc2180_gba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-83/call-run_paraphase/out/m84036_250809_035451_s4.bc2180_paraphase/m84036_250809_035451_s4.bc2180_paraphase_vcfs/m84036_250809_035451_s4.bc2180_hba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-83/call-run_paraphase/out/m84036_250809_035451_s4.bc2180_paraphase/m84036_250809_035451_s4.bc2180_paraphase_vcfs/m84036_250809_035451_s4.bc2180_hbb.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-83/call-run_paraphase/out/m84036_250809_035451_s4.bc2180_paraphase/m84036_250809_035451_s4.bc2180_paraphase_vcfs/m84036_250809_035451_s4.bc2180_rpgr.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-83/call-run_paraphase/out/m84036_250809_035451_s4.bc2180_paraphase/m84036_250809_035451_s4.bc2180_paraphase_vcfs/m84036_250809_035451_s4.bc2180_smn1.vcf"], "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-83/call-run_paraphase/out/m84036_250809_035451_s4.bc2180_paraphase/m84036_250809_035451_s4.bc2180.paraphase.json", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-83/call-run_paraphase/out/m84036_250809_035451_s4.bc2180_paraphase/m84036_250809_035451_s4.bc2180.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-83/call-run_paraphase/out/m84036_250809_035451_s4.bc2180_paraphase/m84036_250809_035451_s4.bc2180.paraphase.bam"}
2025-09-15 20:33:53.241 wdl.w:ptcp.w:call-paraphase-83 NOTICE ready :: job: "call-call_f8", callee: "call_f8"
2025-09-15 20:33:53.242 wdl.w:ptcp.w:call-paraphase-83 INFO input :: job: "call-call_f8", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "out_prefix": "m84036_250809_035451_s4.bc2180", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-83/call-run_paraphase/out/m84036_250809_035451_s4.bc2180_paraphase/m84036_250809_035451_s4.bc2180.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-83/call-run_paraphase/out/m84036_250809_035451_s4.bc2180_paraphase/m84036_250809_035451_s4.bc2180.paraphase.bam", "sex": "F"}
2025-09-15 20:33:53.242 wdl.w:ptcp.w:call-paraphase-83 INFO visit :: node: "output-havanno_json", values: {"havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-83/call-run_paraphase/out/m84036_250809_035451_s4.bc2180.havanno.json"}
2025-09-15 20:33:53.242 wdl.w:ptcp.w:call-paraphase-83 INFO visit :: node: "output-paraphase_bam", values: {"paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-83/call-run_paraphase/out/m84036_250809_035451_s4.bc2180_paraphase/m84036_250809_035451_s4.bc2180.paraphase.bam"}
2025-09-15 20:33:53.242 wdl.w:ptcp.w:call-paraphase-83 INFO visit :: node: "output-paraphase_bam_bai", values: {"paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-83/call-run_paraphase/out/m84036_250809_035451_s4.bc2180_paraphase/m84036_250809_035451_s4.bc2180.paraphase.bam.bai"}
2025-09-15 20:33:53.243 wdl.w:ptcp.w:call-paraphase-83 INFO visit :: node: "output-paraphase_json", values: {"paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-83/call-run_paraphase/out/m84036_250809_035451_s4.bc2180_paraphase/m84036_250809_035451_s4.bc2180.paraphase.json"}
2025-09-15 20:33:53.243 wdl.w:ptcp.w:call-paraphase-83 INFO visit :: node: "output-paraphase_vcfs", values: {"paraphase_vcfs": ["/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-83/call-run_paraphase/out/m84036_250809_035451_s4.bc2180_paraphase/m84036_250809_035451_s4.bc2180_paraphase_vcfs/m84036_250809_035451_s4.bc2180_cyp21.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-83/call-run_paraphase/out/m84036_250809_035451_s4.bc2180_paraphase/m84036_250809_035451_s4.bc2180_paraphase_vcfs/m84036_250809_035451_s4.bc2180_f8inv1.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-83/call-run_paraphase/out/m84036_250809_035451_s4.bc2180_paraphase/m84036_250809_035451_s4.bc2180_paraphase_vcfs/m84036_250809_035451_s4.bc2180_f8inv22.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-83/call-run_paraphase/out/m84036_250809_035451_s4.bc2180_paraphase/m84036_250809_035451_s4.bc2180_paraphase_vcfs/m84036_250809_035451_s4.bc2180_gba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-83/call-run_paraphase/out/m84036_250809_035451_s4.bc2180_paraphase/m84036_250809_035451_s4.bc2180_paraphase_vcfs/m84036_250809_035451_s4.bc2180_hba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-83/call-run_paraphase/out/m84036_250809_035451_s4.bc2180_paraphase/m84036_250809_035451_s4.bc2180_paraphase_vcfs/m84036_250809_035451_s4.bc2180_hbb.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-83/call-run_paraphase/out/m84036_250809_035451_s4.bc2180_paraphase/m84036_250809_035451_s4.bc2180_paraphase_vcfs/m84036_250809_035451_s4.bc2180_rpgr.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-83/call-run_paraphase/out/m84036_250809_035451_s4.bc2180_paraphase/m84036_250809_035451_s4.bc2180_paraphase_vcfs/m84036_250809_035451_s4.bc2180_smn1.vcf"]}
2025-09-15 20:33:53.247 wdl.w:ptcp.w:call-paraphase-83.t:call-call_f8 NOTICE task setup :: name: "call_f8", source: "./paraphase.wdl", line: 232, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-83/call-call_f8", thread: 140611961206336
2025-09-15 20:33:53.262 wdl.w:ptcp.w:call-paraphase-83.t:call-call_f8 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:33:53.262 wdl.w:ptcp.w:call-paraphase-83.t:call-call_f8 INFO input :: name: "genome_version", value: "38"
2025-09-15 20:33:53.262 wdl.w:ptcp.w:call-paraphase-83.t:call-call_f8 INFO input :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2180"
2025-09-15 20:33:53.262 wdl.w:ptcp.w:call-paraphase-83.t:call-call_f8 INFO input :: name: "paraphase_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2180.paraphase.bam.bai"
2025-09-15 20:33:53.262 wdl.w:ptcp.w:call-paraphase-83.t:call-call_f8 INFO input :: name: "paraphase_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2180.paraphase.bam"
2025-09-15 20:33:53.262 wdl.w:ptcp.w:call-paraphase-83.t:call-call_f8 INFO input :: name: "sex", value: "F"
2025-09-15 20:33:53.262 wdl.w:ptcp.w:call-paraphase-83.t:call-call_f8 INFO eval :: name: "threads", value: 1
2025-09-15 20:33:53.262 wdl.w:ptcp.w:call-paraphase-83.t:call-call_f8 INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:33:53.262 wdl.w:ptcp.w:call-paraphase-83.t:call-call_f8 INFO eval :: name: "disk_size", value: 11
2025-09-15 20:33:53.262 wdl.w:ptcp.w:call-paraphase-83.t:call-call_f8 INFO eval :: name: "sample_sex", value: "F"
2025-09-15 20:33:53.263 wdl.w:ptcp.w:call-paraphase-83.t:call-call_f8 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:33:53.263 wdl.w:ptcp.w:call-paraphase-83.t:call-call_f8 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:33:53.263 wdl.w:ptcp.w:call-paraphase-83.t:call-call_f8 INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:33:53.263 wdl.w:ptcp.w:call-paraphase-83.t:call-call_f8 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:33:53.299 wdl.w:ptcp.w:call-paraphase-83.t:call-call_f8 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 8, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-83/call-call_f8/_singularity_tmpdir_3o24trk3"
2025-09-15 20:33:53.299 wdl.w:ptcp.w:call-paraphase-83.t:call-call_f8 INFO Slurm invocation: srun --job-name call-call_f8 --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-83/call-call_f8/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-83/call-call_f8/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-83/call-call_f8/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-83/call-call_f8/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-83/call-run_paraphase/out/m84036_250809_035451_s4.bc2180_paraphase/m84036_250809_035451_s4.bc2180.paraphase.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2180.paraphase.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-83/call-run_paraphase/out/m84036_250809_035451_s4.bc2180_paraphase/m84036_250809_035451_s4.bc2180.paraphase.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2180.paraphase.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-83/call-call_f8/_singularity_tmpdir_3o24trk3/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-83/call-call_f8/_singularity_tmpdir_3o24trk3/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:33:53.305 wdl.w:ptcp.w:call-paraphase-83.t:call-call_f8 NOTICE slurm_singularity run :: pid: 1212640, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-83/call-call_f8/slurm_singularity.log.txt"
2025-09-15 20:33:54.313 wdl.w:ptcp.w:call-paraphase-83.t:call-call_f8.slurm_singularity INFO srun: job 51798406 queued and waiting for resources
2025-09-15 20:33:54.314 wdl.w:ptcp.w:call-paraphase-83.t:call-call_f8.slurm_singularity INFO srun: job 51798406 has been allocated resources
2025-09-15 20:33:54.314 wdl.w:ptcp.w:call-paraphase-83.t:call-call_f8.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:33:54.761 wdl.w:ptcp.w:call-paraphase-83.t:call-call_f8 INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2180.f8inversion.vcf"
2025-09-15 20:33:54.764 wdl.w:ptcp.w:call-paraphase-83.t:call-call_f8 INFO output :: name: "json", value: "m84036_250809_035451_s4.bc2180.f8inversion.json"
2025-09-15 20:33:54.813 wdl.w:ptcp.w:call-paraphase-83.t:call-call_f8 NOTICE done
2025-09-15 20:33:54.817 wdl.w:ptcp.w:call-paraphase-83 NOTICE finish :: job: "call-call_f8"
2025-09-15 20:33:54.817 wdl.w:ptcp.w:call-paraphase-83 INFO output :: job: "call-call_f8", values: {"json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-83/call-call_f8/out/m84036_250809_035451_s4.bc2180.f8inversion.json", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-83/call-call_f8/out/m84036_250809_035451_s4.bc2180.f8inversion.vcf"}
2025-09-15 20:33:54.818 wdl.w:ptcp.w:call-paraphase-83 INFO visit :: node: "output-f8_json", values: {"f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-83/call-call_f8/out/m84036_250809_035451_s4.bc2180.f8inversion.json"}
2025-09-15 20:33:54.818 wdl.w:ptcp.w:call-paraphase-83 INFO visit :: node: "output-f8_vcf", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-83/call-call_f8/out/m84036_250809_035451_s4.bc2180.f8inversion.vcf"}
2025-09-15 20:33:54.818 wdl.w:ptcp.w:call-paraphase-83 INFO visit :: node: "outputs", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-83/call-call_f8/out/m84036_250809_035451_s4.bc2180.f8inversion.vcf", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-83/call-run_paraphase/out/m84036_250809_035451_s4.bc2180_paraphase/m84036_250809_035451_s4.bc2180.paraphase.json", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-83/call-run_paraphase/out/m84036_250809_035451_s4.bc2180_paraphase/m84036_250809_035451_s4.bc2180.paraphase.bam", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-83/call-run_paraphase/out/m84036_250809_035451_s4.bc2180_paraphase/m84036_250809_035451_s4.bc2180.paraphase.bam.bai", "paraphase_vcfs": ["/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-83/call-run_paraphase/out/m84036_250809_035451_s4.bc2180_paraphase/m84036_250809_035451_s4.bc2180_paraphase_vcfs/m84036_250809_035451_s4.bc2180_cyp21.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-83/call-run_paraphase/out/m84036_250809_035451_s4.bc2180_paraphase/m84036_250809_035451_s4.bc2180_paraphase_vcfs/m84036_250809_035451_s4.bc2180_f8inv1.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-83/call-run_paraphase/out/m84036_250809_035451_s4.bc2180_paraphase/m84036_250809_035451_s4.bc2180_paraphase_vcfs/m84036_250809_035451_s4.bc2180_f8inv22.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-83/call-run_paraphase/out/m84036_250809_035451_s4.bc2180_paraphase/m84036_250809_035451_s4.bc2180_paraphase_vcfs/m84036_250809_035451_s4.bc2180_gba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-83/call-run_paraphase/out/m84036_250809_035451_s4.bc2180_paraphase/m84036_250809_035451_s4.bc2180_paraphase_vcfs/m84036_250809_035451_s4.bc2180_hba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-83/call-run_paraphase/out/m84036_250809_035451_s4.bc2180_paraphase/m84036_250809_035451_s4.bc2180_paraphase_vcfs/m84036_250809_035451_s4.bc2180_hbb.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-83/call-run_paraphase/out/m84036_250809_035451_s4.bc2180_paraphase/m84036_250809_035451_s4.bc2180_paraphase_vcfs/m84036_250809_035451_s4.bc2180_rpgr.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-83/call-run_paraphase/out/m84036_250809_035451_s4.bc2180_paraphase/m84036_250809_035451_s4.bc2180_paraphase_vcfs/m84036_250809_035451_s4.bc2180_smn1.vcf"], "havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-83/call-run_paraphase/out/m84036_250809_035451_s4.bc2180.havanno.json", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-83/call-call_f8/out/m84036_250809_035451_s4.bc2180.f8inversion.json"}
2025-09-15 20:33:54.919 wdl.w:ptcp.w:call-paraphase-83 NOTICE done
2025-09-15 20:33:54.924 wdl.w:ptcp NOTICE finish :: job: "call-paraphase-83"
2025-09-15 20:33:54.924 wdl.w:ptcp INFO output :: job: "call-paraphase-83", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-83/out/m84036_250809_035451_s4.bc2180.f8inversion.vcf", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-83/out/m84036_250809_035451_s4.bc2180_paraphase/m84036_250809_035451_s4.bc2180.paraphase.json", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-83/out/m84036_250809_035451_s4.bc2180_paraphase/m84036_250809_035451_s4.bc2180.paraphase.bam", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-83/out/m84036_250809_035451_s4.bc2180_paraphase/m84036_250809_035451_s4.bc2180.paraphase.bam.bai", "paraphase_vcfs": ["/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-83/out/m84036_250809_035451_s4.bc2180_paraphase/m84036_250809_035451_s4.bc2180_paraphase_vcfs/m84036_250809_035451_s4.bc2180_cyp21.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-83/out/m84036_250809_035451_s4.bc2180_paraphase/m84036_250809_035451_s4.bc2180_paraphase_vcfs/m84036_250809_035451_s4.bc2180_f8inv1.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-83/out/m84036_250809_035451_s4.bc2180_paraphase/m84036_250809_035451_s4.bc2180_paraphase_vcfs/m84036_250809_035451_s4.bc2180_f8inv22.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-83/out/m84036_250809_035451_s4.bc2180_paraphase/m84036_250809_035451_s4.bc2180_paraphase_vcfs/m84036_250809_035451_s4.bc2180_gba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-83/out/m84036_250809_035451_s4.bc2180_paraphase/m84036_250809_035451_s4.bc2180_paraphase_vcfs/m84036_250809_035451_s4.bc2180_hba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-83/out/m84036_250809_035451_s4.bc2180_paraphase/m84036_250809_035451_s4.bc2180_paraphase_vcfs/m84036_250809_035451_s4.bc2180_hbb.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-83/out/m84036_250809_035451_s4.bc2180_paraphase/m84036_250809_035451_s4.bc2180_paraphase_vcfs/m84036_250809_035451_s4.bc2180_rpgr.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-83/out/m84036_250809_035451_s4.bc2180_paraphase/m84036_250809_035451_s4.bc2180_paraphase_vcfs/m84036_250809_035451_s4.bc2180_smn1.vcf"], "havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-83/out/m84036_250809_035451_s4.bc2180.havanno.json", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-83/out/m84036_250809_035451_s4.bc2180.f8inversion.json"}
2025-09-15 20:33:54.925 wdl.w:ptcp NOTICE ready :: job: "call-tar_outputs-83", callee: "tar_outputs"
2025-09-15 20:33:54.926 wdl.w:ptcp INFO input :: job: "call-tar_outputs-83", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "sawfish_vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-83/out/m84036_250809_035451_s4.bc2180_sawfish/m84036_250809_035451_s4.bc2180.sv.vcf.gz.tbi", "sawfish_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-83/out/m84036_250809_035451_s4.bc2180_sawfish/m84036_250809_035451_s4.bc2180.sv.vcf.gz", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-83/out/m84036_250809_035451_s4.bc2180.f8inversion.json", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-83/out/m84036_250809_035451_s4.bc2180_paraphase/m84036_250809_035451_s4.bc2180.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-83/out/m84036_250809_035451_s4.bc2180_paraphase/m84036_250809_035451_s4.bc2180.paraphase.bam", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-83/out/m84036_250809_035451_s4.bc2180_paraphase/m84036_250809_035451_s4.bc2180.paraphase.json", "trgt_spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-83/out/m84036_250809_035451_s4.bc2180.trgt.sorted.spanning.bam.bai", "trgt_spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-83/out/m84036_250809_035451_s4.bc2180.trgt.sorted.spanning.bam", "trgt_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-83/out/m84036_250809_035451_s4.bc2180.trgt.vcf", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-83/out/m84036_250809_035451_s4.bc2180.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-83/out/m84036_250809_035451_s4.bc2180.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2180"}
2025-09-15 20:33:54.933 wdl.w:ptcp.t:call-tar_outputs-83 NOTICE task setup :: name: "tar_outputs", source: "./common.wdl", line: 279, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-83", thread: 140611944420928
2025-09-15 20:33:54.953 wdl.w:ptcp.t:call-tar_outputs-83 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:33:54.954 wdl.w:ptcp.t:call-tar_outputs-83 INFO input :: name: "sawfish_vcf_tbi", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2180.sv.vcf.gz.tbi"
2025-09-15 20:33:54.954 wdl.w:ptcp.t:call-tar_outputs-83 INFO input :: name: "sawfish_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2180.sv.vcf.gz"
2025-09-15 20:33:54.954 wdl.w:ptcp.t:call-tar_outputs-83 INFO input :: name: "f8_json", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2180.f8inversion.json"
2025-09-15 20:33:54.954 wdl.w:ptcp.t:call-tar_outputs-83 INFO input :: name: "paraphase_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2180.paraphase.bam.bai"
2025-09-15 20:33:54.954 wdl.w:ptcp.t:call-tar_outputs-83 INFO input :: name: "paraphase_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2180.paraphase.bam"
2025-09-15 20:33:54.954 wdl.w:ptcp.t:call-tar_outputs-83 INFO input :: name: "paraphase_json", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2180.paraphase.json"
2025-09-15 20:33:54.954 wdl.w:ptcp.t:call-tar_outputs-83 INFO input :: name: "trgt_spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2180.trgt.sorted.spanning.bam.bai"
2025-09-15 20:33:54.954 wdl.w:ptcp.t:call-tar_outputs-83 INFO input :: name: "trgt_spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2180.trgt.sorted.spanning.bam"
2025-09-15 20:33:54.954 wdl.w:ptcp.t:call-tar_outputs-83 INFO input :: name: "trgt_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2180.trgt.vcf"
2025-09-15 20:33:54.954 wdl.w:ptcp.t:call-tar_outputs-83 INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2180.mapped.bam.bai"
2025-09-15 20:33:54.954 wdl.w:ptcp.t:call-tar_outputs-83 INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2180.mapped.bam"
2025-09-15 20:33:54.954 wdl.w:ptcp.t:call-tar_outputs-83 INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2180"
2025-09-15 20:33:54.954 wdl.w:ptcp.t:call-tar_outputs-83 INFO eval :: name: "threads", value: 1
2025-09-15 20:33:54.954 wdl.w:ptcp.t:call-tar_outputs-83 INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:33:54.955 wdl.w:ptcp.t:call-tar_outputs-83 INFO eval :: name: "disk_size", value: 6
2025-09-15 20:33:54.955 wdl.w:ptcp.t:call-tar_outputs-83 INFO eval :: name: "output_tarball", value: "m84036_250809_035451_s4.bc2180.tar"
2025-09-15 20:33:54.955 wdl.w:ptcp.t:call-tar_outputs-83 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:33:54.955 wdl.w:ptcp.t:call-tar_outputs-83 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:33:54.955 wdl.w:ptcp.t:call-tar_outputs-83 INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:33:54.956 wdl.w:ptcp.t:call-tar_outputs-83 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:33:55.032 wdl.w:ptcp.t:call-tar_outputs-83 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 17, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-83/_singularity_tmpdir_7pwwa37_"
2025-09-15 20:33:55.033 wdl.w:ptcp.t:call-tar_outputs-83 INFO Slurm invocation: srun --job-name call-tar_outputs-83 --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-83/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-83/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-83/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-83/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-83/out/m84036_250809_035451_s4.bc2180.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2180.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-83/out/m84036_250809_035451_s4.bc2180.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2180.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-83/out/m84036_250809_035451_s4.bc2180.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2180.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-83/out/m84036_250809_035451_s4.bc2180_paraphase/m84036_250809_035451_s4.bc2180.paraphase.json:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2180.paraphase.json:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-83/out/m84036_250809_035451_s4.bc2180_paraphase/m84036_250809_035451_s4.bc2180.paraphase.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2180.paraphase.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-83/out/m84036_250809_035451_s4.bc2180_paraphase/m84036_250809_035451_s4.bc2180.paraphase.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2180.paraphase.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-83/out/m84036_250809_035451_s4.bc2180_sawfish/m84036_250809_035451_s4.bc2180.sv.vcf.gz:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2180.sv.vcf.gz:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-83/out/m84036_250809_035451_s4.bc2180_sawfish/m84036_250809_035451_s4.bc2180.sv.vcf.gz.tbi:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2180.sv.vcf.gz.tbi:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-83/out/m84036_250809_035451_s4.bc2180.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2180.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-83/out/m84036_250809_035451_s4.bc2180.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2180.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-83/out/m84036_250809_035451_s4.bc2180.f8inversion.json:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2180.f8inversion.json:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-83/_singularity_tmpdir_7pwwa37_/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-83/_singularity_tmpdir_7pwwa37_/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:33:55.036 wdl.w:ptcp.t:call-tar_outputs-83 NOTICE slurm_singularity run :: pid: 1212650, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-83/slurm_singularity.log.txt"
2025-09-15 20:33:56.046 wdl.w:ptcp.t:call-tar_outputs-83.slurm_singularity INFO srun: job 51798407 queued and waiting for resources
2025-09-15 20:33:57.055 wdl.w:ptcp.t:call-tar_outputs-83.slurm_singularity INFO srun: job 51798407 has been allocated resources
2025-09-15 20:33:57.055 wdl.w:ptcp.t:call-tar_outputs-83.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:33:57.460 wdl.w:ptcp.t:call-tar_outputs-83 INFO output :: name: "sample_tarball", value: "m84036_250809_035451_s4.bc2180.tar"
2025-09-15 20:33:57.518 wdl.w:ptcp.t:call-tar_outputs-83 NOTICE done
2025-09-15 20:33:57.522 wdl.w:ptcp NOTICE finish :: job: "call-tar_outputs-83"
2025-09-15 20:33:57.522 wdl.w:ptcp INFO output :: job: "call-tar_outputs-83", values: {"sample_tarball": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-83/out/m84036_250809_035451_s4.bc2180.tar"}
2025-09-15 20:34:18.475 wdl.w:ptcp.w:call-paraphase-78.t:call-run_paraphase INFO output :: name: "paraphase_bam", value: "m84036_250809_035451_s4.bc2175_paraphase/m84036_250809_035451_s4.bc2175.paraphase.bam"
2025-09-15 20:34:18.478 wdl.w:ptcp.w:call-paraphase-78.t:call-run_paraphase INFO output :: name: "paraphase_bam_bai", value: "m84036_250809_035451_s4.bc2175_paraphase/m84036_250809_035451_s4.bc2175.paraphase.bam.bai"
2025-09-15 20:34:18.479 wdl.w:ptcp.w:call-paraphase-78.t:call-run_paraphase INFO output :: name: "paraphase_json", value: "m84036_250809_035451_s4.bc2175_paraphase/m84036_250809_035451_s4.bc2175.paraphase.json"
2025-09-15 20:34:18.482 wdl.w:ptcp.w:call-paraphase-78.t:call-run_paraphase INFO output :: name: "paraphase_vcfs", value: ["/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2175_paraphase/m84036_250809_035451_s4.bc2175_paraphase_vcfs/m84036_250809_035451_s4.bc2175_cyp21.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2175_paraphase/m84036_250809_035451_s4.bc2175_paraphase_vcfs/m84036_250809_035451_s4.bc2175_f8inv1.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2175_paraphase/m84036_250809_035451_s4.bc2175_paraphase_vcfs/m84036_250809_035451_s4.bc2175_f8inv22.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2175_paraphase/m84036_250809_035451_s4.bc2175_paraphase_vcfs/m84036_250809_035451_s4.bc2175_gba.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2175_paraphase/m84036_250809_035451_s4.bc2175_paraphase_vcfs/m84036_250809_035451_s4.bc2175_hba.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2175_paraphase/m84036_250809_035451_s4.bc2175_paraphase_vcfs/m84036_250809_035451_s4.bc2175_hbb.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2175_paraphase/m84036_250809_035451_s4.bc2175_paraphase_vcfs/m84036_250809_035451_s4.bc2175_rpgr.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2175_paraphase/m84036_250809_035451_s4.bc2175_paraphase_vcfs/m84036_250809_035451_s4.bc2175_smn1.vcf"]
2025-09-15 20:34:18.485 wdl.w:ptcp.w:call-paraphase-78.t:call-run_paraphase INFO output :: name: "havanno_json", value: "m84036_250809_035451_s4.bc2175.havanno.json"
2025-09-15 20:34:18.627 wdl.w:ptcp.w:call-paraphase-78.t:call-run_paraphase NOTICE done
2025-09-15 20:34:18.636 wdl.w:ptcp.w:call-paraphase-78 NOTICE finish :: job: "call-run_paraphase"
2025-09-15 20:34:18.636 wdl.w:ptcp.w:call-paraphase-78 INFO output :: job: "call-run_paraphase", values: {"havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-78/call-run_paraphase/out/m84036_250809_035451_s4.bc2175.havanno.json", "paraphase_vcfs": ["/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-78/call-run_paraphase/out/m84036_250809_035451_s4.bc2175_paraphase/m84036_250809_035451_s4.bc2175_paraphase_vcfs/m84036_250809_035451_s4.bc2175_cyp21.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-78/call-run_paraphase/out/m84036_250809_035451_s4.bc2175_paraphase/m84036_250809_035451_s4.bc2175_paraphase_vcfs/m84036_250809_035451_s4.bc2175_f8inv1.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-78/call-run_paraphase/out/m84036_250809_035451_s4.bc2175_paraphase/m84036_250809_035451_s4.bc2175_paraphase_vcfs/m84036_250809_035451_s4.bc2175_f8inv22.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-78/call-run_paraphase/out/m84036_250809_035451_s4.bc2175_paraphase/m84036_250809_035451_s4.bc2175_paraphase_vcfs/m84036_250809_035451_s4.bc2175_gba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-78/call-run_paraphase/out/m84036_250809_035451_s4.bc2175_paraphase/m84036_250809_035451_s4.bc2175_paraphase_vcfs/m84036_250809_035451_s4.bc2175_hba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-78/call-run_paraphase/out/m84036_250809_035451_s4.bc2175_paraphase/m84036_250809_035451_s4.bc2175_paraphase_vcfs/m84036_250809_035451_s4.bc2175_hbb.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-78/call-run_paraphase/out/m84036_250809_035451_s4.bc2175_paraphase/m84036_250809_035451_s4.bc2175_paraphase_vcfs/m84036_250809_035451_s4.bc2175_rpgr.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-78/call-run_paraphase/out/m84036_250809_035451_s4.bc2175_paraphase/m84036_250809_035451_s4.bc2175_paraphase_vcfs/m84036_250809_035451_s4.bc2175_smn1.vcf"], "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-78/call-run_paraphase/out/m84036_250809_035451_s4.bc2175_paraphase/m84036_250809_035451_s4.bc2175.paraphase.json", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-78/call-run_paraphase/out/m84036_250809_035451_s4.bc2175_paraphase/m84036_250809_035451_s4.bc2175.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-78/call-run_paraphase/out/m84036_250809_035451_s4.bc2175_paraphase/m84036_250809_035451_s4.bc2175.paraphase.bam"}
2025-09-15 20:34:18.636 wdl.w:ptcp.w:call-paraphase-78 NOTICE ready :: job: "call-call_f8", callee: "call_f8"
2025-09-15 20:34:18.637 wdl.w:ptcp.w:call-paraphase-78 INFO input :: job: "call-call_f8", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "out_prefix": "m84036_250809_035451_s4.bc2175", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-78/call-run_paraphase/out/m84036_250809_035451_s4.bc2175_paraphase/m84036_250809_035451_s4.bc2175.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-78/call-run_paraphase/out/m84036_250809_035451_s4.bc2175_paraphase/m84036_250809_035451_s4.bc2175.paraphase.bam", "sex": "F"}
2025-09-15 20:34:18.637 wdl.w:ptcp.w:call-paraphase-78 INFO visit :: node: "output-havanno_json", values: {"havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-78/call-run_paraphase/out/m84036_250809_035451_s4.bc2175.havanno.json"}
2025-09-15 20:34:18.637 wdl.w:ptcp.w:call-paraphase-78 INFO visit :: node: "output-paraphase_bam", values: {"paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-78/call-run_paraphase/out/m84036_250809_035451_s4.bc2175_paraphase/m84036_250809_035451_s4.bc2175.paraphase.bam"}
2025-09-15 20:34:18.637 wdl.w:ptcp.w:call-paraphase-78 INFO visit :: node: "output-paraphase_bam_bai", values: {"paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-78/call-run_paraphase/out/m84036_250809_035451_s4.bc2175_paraphase/m84036_250809_035451_s4.bc2175.paraphase.bam.bai"}
2025-09-15 20:34:18.637 wdl.w:ptcp.w:call-paraphase-78 INFO visit :: node: "output-paraphase_json", values: {"paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-78/call-run_paraphase/out/m84036_250809_035451_s4.bc2175_paraphase/m84036_250809_035451_s4.bc2175.paraphase.json"}
2025-09-15 20:34:18.638 wdl.w:ptcp.w:call-paraphase-78 INFO visit :: node: "output-paraphase_vcfs", values: {"paraphase_vcfs": ["/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-78/call-run_paraphase/out/m84036_250809_035451_s4.bc2175_paraphase/m84036_250809_035451_s4.bc2175_paraphase_vcfs/m84036_250809_035451_s4.bc2175_cyp21.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-78/call-run_paraphase/out/m84036_250809_035451_s4.bc2175_paraphase/m84036_250809_035451_s4.bc2175_paraphase_vcfs/m84036_250809_035451_s4.bc2175_f8inv1.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-78/call-run_paraphase/out/m84036_250809_035451_s4.bc2175_paraphase/m84036_250809_035451_s4.bc2175_paraphase_vcfs/m84036_250809_035451_s4.bc2175_f8inv22.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-78/call-run_paraphase/out/m84036_250809_035451_s4.bc2175_paraphase/m84036_250809_035451_s4.bc2175_paraphase_vcfs/m84036_250809_035451_s4.bc2175_gba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-78/call-run_paraphase/out/m84036_250809_035451_s4.bc2175_paraphase/m84036_250809_035451_s4.bc2175_paraphase_vcfs/m84036_250809_035451_s4.bc2175_hba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-78/call-run_paraphase/out/m84036_250809_035451_s4.bc2175_paraphase/m84036_250809_035451_s4.bc2175_paraphase_vcfs/m84036_250809_035451_s4.bc2175_hbb.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-78/call-run_paraphase/out/m84036_250809_035451_s4.bc2175_paraphase/m84036_250809_035451_s4.bc2175_paraphase_vcfs/m84036_250809_035451_s4.bc2175_rpgr.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-78/call-run_paraphase/out/m84036_250809_035451_s4.bc2175_paraphase/m84036_250809_035451_s4.bc2175_paraphase_vcfs/m84036_250809_035451_s4.bc2175_smn1.vcf"]}
2025-09-15 20:34:18.642 wdl.w:ptcp.w:call-paraphase-78.t:call-call_f8 NOTICE task setup :: name: "call_f8", source: "./paraphase.wdl", line: 232, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-78/call-call_f8", thread: 140609813722688
2025-09-15 20:34:18.666 wdl.w:ptcp.w:call-paraphase-78.t:call-call_f8 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:34:18.666 wdl.w:ptcp.w:call-paraphase-78.t:call-call_f8 INFO input :: name: "genome_version", value: "38"
2025-09-15 20:34:18.666 wdl.w:ptcp.w:call-paraphase-78.t:call-call_f8 INFO input :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2175"
2025-09-15 20:34:18.666 wdl.w:ptcp.w:call-paraphase-78.t:call-call_f8 INFO input :: name: "paraphase_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2175.paraphase.bam.bai"
2025-09-15 20:34:18.666 wdl.w:ptcp.w:call-paraphase-78.t:call-call_f8 INFO input :: name: "paraphase_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2175.paraphase.bam"
2025-09-15 20:34:18.666 wdl.w:ptcp.w:call-paraphase-78.t:call-call_f8 INFO input :: name: "sex", value: "F"
2025-09-15 20:34:18.667 wdl.w:ptcp.w:call-paraphase-78.t:call-call_f8 INFO eval :: name: "threads", value: 1
2025-09-15 20:34:18.667 wdl.w:ptcp.w:call-paraphase-78.t:call-call_f8 INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:34:18.667 wdl.w:ptcp.w:call-paraphase-78.t:call-call_f8 INFO eval :: name: "disk_size", value: 11
2025-09-15 20:34:18.667 wdl.w:ptcp.w:call-paraphase-78.t:call-call_f8 INFO eval :: name: "sample_sex", value: "F"
2025-09-15 20:34:18.668 wdl.w:ptcp.w:call-paraphase-78.t:call-call_f8 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:34:18.668 wdl.w:ptcp.w:call-paraphase-78.t:call-call_f8 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:34:18.668 wdl.w:ptcp.w:call-paraphase-78.t:call-call_f8 INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:34:18.669 wdl.w:ptcp.w:call-paraphase-78.t:call-call_f8 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:34:18.704 wdl.w:ptcp.w:call-paraphase-78.t:call-call_f8 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 8, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-78/call-call_f8/_singularity_tmpdir_lnpqyjt0"
2025-09-15 20:34:18.704 wdl.w:ptcp.w:call-paraphase-78.t:call-call_f8 INFO Slurm invocation: srun --job-name call-call_f8 --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-78/call-call_f8/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-78/call-call_f8/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-78/call-call_f8/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-78/call-call_f8/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-78/call-run_paraphase/out/m84036_250809_035451_s4.bc2175_paraphase/m84036_250809_035451_s4.bc2175.paraphase.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2175.paraphase.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-78/call-run_paraphase/out/m84036_250809_035451_s4.bc2175_paraphase/m84036_250809_035451_s4.bc2175.paraphase.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2175.paraphase.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-78/call-call_f8/_singularity_tmpdir_lnpqyjt0/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-78/call-call_f8/_singularity_tmpdir_lnpqyjt0/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:34:18.710 wdl.w:ptcp.w:call-paraphase-78.t:call-call_f8 NOTICE slurm_singularity run :: pid: 1212805, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-78/call-call_f8/slurm_singularity.log.txt"
2025-09-15 20:34:19.718 wdl.w:ptcp.w:call-paraphase-78.t:call-call_f8.slurm_singularity INFO srun: job 51798409 queued and waiting for resources
2025-09-15 20:34:19.718 wdl.w:ptcp.w:call-paraphase-78.t:call-call_f8.slurm_singularity INFO srun: job 51798409 has been allocated resources
2025-09-15 20:34:19.718 wdl.w:ptcp.w:call-paraphase-78.t:call-call_f8.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:34:20.800 wdl.w:ptcp.w:call-paraphase-78.t:call-call_f8 INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2175.f8inversion.vcf"
2025-09-15 20:34:20.803 wdl.w:ptcp.w:call-paraphase-78.t:call-call_f8 INFO output :: name: "json", value: "m84036_250809_035451_s4.bc2175.f8inversion.json"
2025-09-15 20:34:20.858 wdl.w:ptcp.w:call-paraphase-78.t:call-call_f8 NOTICE done
2025-09-15 20:34:20.864 wdl.w:ptcp.w:call-paraphase-78 NOTICE finish :: job: "call-call_f8"
2025-09-15 20:34:20.864 wdl.w:ptcp.w:call-paraphase-78 INFO output :: job: "call-call_f8", values: {"json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-78/call-call_f8/out/m84036_250809_035451_s4.bc2175.f8inversion.json", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-78/call-call_f8/out/m84036_250809_035451_s4.bc2175.f8inversion.vcf"}
2025-09-15 20:34:20.864 wdl.w:ptcp.w:call-paraphase-78 INFO visit :: node: "output-f8_json", values: {"f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-78/call-call_f8/out/m84036_250809_035451_s4.bc2175.f8inversion.json"}
2025-09-15 20:34:20.864 wdl.w:ptcp.w:call-paraphase-78 INFO visit :: node: "output-f8_vcf", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-78/call-call_f8/out/m84036_250809_035451_s4.bc2175.f8inversion.vcf"}
2025-09-15 20:34:20.865 wdl.w:ptcp.w:call-paraphase-78 INFO visit :: node: "outputs", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-78/call-call_f8/out/m84036_250809_035451_s4.bc2175.f8inversion.vcf", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-78/call-run_paraphase/out/m84036_250809_035451_s4.bc2175_paraphase/m84036_250809_035451_s4.bc2175.paraphase.json", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-78/call-run_paraphase/out/m84036_250809_035451_s4.bc2175_paraphase/m84036_250809_035451_s4.bc2175.paraphase.bam", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-78/call-run_paraphase/out/m84036_250809_035451_s4.bc2175_paraphase/m84036_250809_035451_s4.bc2175.paraphase.bam.bai", "paraphase_vcfs": ["/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-78/call-run_paraphase/out/m84036_250809_035451_s4.bc2175_paraphase/m84036_250809_035451_s4.bc2175_paraphase_vcfs/m84036_250809_035451_s4.bc2175_cyp21.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-78/call-run_paraphase/out/m84036_250809_035451_s4.bc2175_paraphase/m84036_250809_035451_s4.bc2175_paraphase_vcfs/m84036_250809_035451_s4.bc2175_f8inv1.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-78/call-run_paraphase/out/m84036_250809_035451_s4.bc2175_paraphase/m84036_250809_035451_s4.bc2175_paraphase_vcfs/m84036_250809_035451_s4.bc2175_f8inv22.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-78/call-run_paraphase/out/m84036_250809_035451_s4.bc2175_paraphase/m84036_250809_035451_s4.bc2175_paraphase_vcfs/m84036_250809_035451_s4.bc2175_gba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-78/call-run_paraphase/out/m84036_250809_035451_s4.bc2175_paraphase/m84036_250809_035451_s4.bc2175_paraphase_vcfs/m84036_250809_035451_s4.bc2175_hba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-78/call-run_paraphase/out/m84036_250809_035451_s4.bc2175_paraphase/m84036_250809_035451_s4.bc2175_paraphase_vcfs/m84036_250809_035451_s4.bc2175_hbb.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-78/call-run_paraphase/out/m84036_250809_035451_s4.bc2175_paraphase/m84036_250809_035451_s4.bc2175_paraphase_vcfs/m84036_250809_035451_s4.bc2175_rpgr.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-78/call-run_paraphase/out/m84036_250809_035451_s4.bc2175_paraphase/m84036_250809_035451_s4.bc2175_paraphase_vcfs/m84036_250809_035451_s4.bc2175_smn1.vcf"], "havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-78/call-run_paraphase/out/m84036_250809_035451_s4.bc2175.havanno.json", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-78/call-call_f8/out/m84036_250809_035451_s4.bc2175.f8inversion.json"}
2025-09-15 20:34:20.966 wdl.w:ptcp.w:call-paraphase-78 NOTICE done
2025-09-15 20:34:20.971 wdl.w:ptcp NOTICE finish :: job: "call-paraphase-78"
2025-09-15 20:34:20.972 wdl.w:ptcp INFO output :: job: "call-paraphase-78", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-78/out/m84036_250809_035451_s4.bc2175.f8inversion.vcf", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-78/out/m84036_250809_035451_s4.bc2175_paraphase/m84036_250809_035451_s4.bc2175.paraphase.json", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-78/out/m84036_250809_035451_s4.bc2175_paraphase/m84036_250809_035451_s4.bc2175.paraphase.bam", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-78/out/m84036_250809_035451_s4.bc2175_paraphase/m84036_250809_035451_s4.bc2175.paraphase.bam.bai", "paraphase_vcfs": ["/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-78/out/m84036_250809_035451_s4.bc2175_paraphase/m84036_250809_035451_s4.bc2175_paraphase_vcfs/m84036_250809_035451_s4.bc2175_cyp21.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-78/out/m84036_250809_035451_s4.bc2175_paraphase/m84036_250809_035451_s4.bc2175_paraphase_vcfs/m84036_250809_035451_s4.bc2175_f8inv1.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-78/out/m84036_250809_035451_s4.bc2175_paraphase/m84036_250809_035451_s4.bc2175_paraphase_vcfs/m84036_250809_035451_s4.bc2175_f8inv22.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-78/out/m84036_250809_035451_s4.bc2175_paraphase/m84036_250809_035451_s4.bc2175_paraphase_vcfs/m84036_250809_035451_s4.bc2175_gba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-78/out/m84036_250809_035451_s4.bc2175_paraphase/m84036_250809_035451_s4.bc2175_paraphase_vcfs/m84036_250809_035451_s4.bc2175_hba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-78/out/m84036_250809_035451_s4.bc2175_paraphase/m84036_250809_035451_s4.bc2175_paraphase_vcfs/m84036_250809_035451_s4.bc2175_hbb.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-78/out/m84036_250809_035451_s4.bc2175_paraphase/m84036_250809_035451_s4.bc2175_paraphase_vcfs/m84036_250809_035451_s4.bc2175_rpgr.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-78/out/m84036_250809_035451_s4.bc2175_paraphase/m84036_250809_035451_s4.bc2175_paraphase_vcfs/m84036_250809_035451_s4.bc2175_smn1.vcf"], "havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-78/out/m84036_250809_035451_s4.bc2175.havanno.json", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-78/out/m84036_250809_035451_s4.bc2175.f8inversion.json"}
2025-09-15 20:34:20.972 wdl.w:ptcp NOTICE ready :: job: "call-tar_outputs-78", callee: "tar_outputs"
2025-09-15 20:34:20.972 wdl.w:ptcp INFO input :: job: "call-tar_outputs-78", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "sawfish_vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-78/out/m84036_250809_035451_s4.bc2175_sawfish/m84036_250809_035451_s4.bc2175.sv.vcf.gz.tbi", "sawfish_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-78/out/m84036_250809_035451_s4.bc2175_sawfish/m84036_250809_035451_s4.bc2175.sv.vcf.gz", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-78/out/m84036_250809_035451_s4.bc2175.f8inversion.json", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-78/out/m84036_250809_035451_s4.bc2175_paraphase/m84036_250809_035451_s4.bc2175.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-78/out/m84036_250809_035451_s4.bc2175_paraphase/m84036_250809_035451_s4.bc2175.paraphase.bam", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-78/out/m84036_250809_035451_s4.bc2175_paraphase/m84036_250809_035451_s4.bc2175.paraphase.json", "trgt_spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-78/out/m84036_250809_035451_s4.bc2175.trgt.sorted.spanning.bam.bai", "trgt_spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-78/out/m84036_250809_035451_s4.bc2175.trgt.sorted.spanning.bam", "trgt_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-78/out/m84036_250809_035451_s4.bc2175.trgt.vcf", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-78/out/m84036_250809_035451_s4.bc2175.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-78/out/m84036_250809_035451_s4.bc2175.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2175"}
2025-09-15 20:34:20.979 wdl.w:ptcp.t:call-tar_outputs-78 NOTICE task setup :: name: "tar_outputs", source: "./common.wdl", line: 279, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-78", thread: 140606626068032
2025-09-15 20:34:20.999 wdl.w:ptcp.t:call-tar_outputs-78 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:34:21.000 wdl.w:ptcp.t:call-tar_outputs-78 INFO input :: name: "sawfish_vcf_tbi", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2175.sv.vcf.gz.tbi"
2025-09-15 20:34:21.000 wdl.w:ptcp.t:call-tar_outputs-78 INFO input :: name: "sawfish_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2175.sv.vcf.gz"
2025-09-15 20:34:21.000 wdl.w:ptcp.t:call-tar_outputs-78 INFO input :: name: "f8_json", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2175.f8inversion.json"
2025-09-15 20:34:21.000 wdl.w:ptcp.t:call-tar_outputs-78 INFO input :: name: "paraphase_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2175.paraphase.bam.bai"
2025-09-15 20:34:21.000 wdl.w:ptcp.t:call-tar_outputs-78 INFO input :: name: "paraphase_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2175.paraphase.bam"
2025-09-15 20:34:21.000 wdl.w:ptcp.t:call-tar_outputs-78 INFO input :: name: "paraphase_json", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2175.paraphase.json"
2025-09-15 20:34:21.000 wdl.w:ptcp.t:call-tar_outputs-78 INFO input :: name: "trgt_spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2175.trgt.sorted.spanning.bam.bai"
2025-09-15 20:34:21.000 wdl.w:ptcp.t:call-tar_outputs-78 INFO input :: name: "trgt_spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2175.trgt.sorted.spanning.bam"
2025-09-15 20:34:21.000 wdl.w:ptcp.t:call-tar_outputs-78 INFO input :: name: "trgt_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2175.trgt.vcf"
2025-09-15 20:34:21.000 wdl.w:ptcp.t:call-tar_outputs-78 INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2175.mapped.bam.bai"
2025-09-15 20:34:21.000 wdl.w:ptcp.t:call-tar_outputs-78 INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2175.mapped.bam"
2025-09-15 20:34:21.000 wdl.w:ptcp.t:call-tar_outputs-78 INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2175"
2025-09-15 20:34:21.000 wdl.w:ptcp.t:call-tar_outputs-78 INFO eval :: name: "threads", value: 1
2025-09-15 20:34:21.000 wdl.w:ptcp.t:call-tar_outputs-78 INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:34:21.000 wdl.w:ptcp.t:call-tar_outputs-78 INFO eval :: name: "disk_size", value: 6
2025-09-15 20:34:21.001 wdl.w:ptcp.t:call-tar_outputs-78 INFO eval :: name: "output_tarball", value: "m84036_250809_035451_s4.bc2175.tar"
2025-09-15 20:34:21.001 wdl.w:ptcp.t:call-tar_outputs-78 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:34:21.001 wdl.w:ptcp.t:call-tar_outputs-78 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:34:21.001 wdl.w:ptcp.t:call-tar_outputs-78 INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:34:21.001 wdl.w:ptcp.t:call-tar_outputs-78 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:34:21.077 wdl.w:ptcp.t:call-tar_outputs-78 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 17, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-78/_singularity_tmpdir_emmxhmgq"
2025-09-15 20:34:21.078 wdl.w:ptcp.t:call-tar_outputs-78 INFO Slurm invocation: srun --job-name call-tar_outputs-78 --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-78/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-78/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-78/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-78/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-78/out/m84036_250809_035451_s4.bc2175.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2175.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-78/out/m84036_250809_035451_s4.bc2175.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2175.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-78/out/m84036_250809_035451_s4.bc2175.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2175.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-78/out/m84036_250809_035451_s4.bc2175.f8inversion.json:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2175.f8inversion.json:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-78/out/m84036_250809_035451_s4.bc2175_paraphase/m84036_250809_035451_s4.bc2175.paraphase.json:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2175.paraphase.json:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-78/out/m84036_250809_035451_s4.bc2175_paraphase/m84036_250809_035451_s4.bc2175.paraphase.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2175.paraphase.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-78/out/m84036_250809_035451_s4.bc2175_paraphase/m84036_250809_035451_s4.bc2175.paraphase.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2175.paraphase.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-78/out/m84036_250809_035451_s4.bc2175_sawfish/m84036_250809_035451_s4.bc2175.sv.vcf.gz.tbi:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2175.sv.vcf.gz.tbi:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-78/out/m84036_250809_035451_s4.bc2175_sawfish/m84036_250809_035451_s4.bc2175.sv.vcf.gz:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2175.sv.vcf.gz:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-78/out/m84036_250809_035451_s4.bc2175.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2175.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-78/out/m84036_250809_035451_s4.bc2175.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2175.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-78/_singularity_tmpdir_emmxhmgq/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-78/_singularity_tmpdir_emmxhmgq/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:34:21.080 wdl.w:ptcp.t:call-tar_outputs-78 NOTICE slurm_singularity run :: pid: 1212882, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-78/slurm_singularity.log.txt"
2025-09-15 20:34:22.090 wdl.w:ptcp.t:call-tar_outputs-78.slurm_singularity INFO srun: job 51798410 queued and waiting for resources
2025-09-15 20:34:23.102 wdl.w:ptcp.t:call-tar_outputs-78.slurm_singularity INFO srun: job 51798410 has been allocated resources
2025-09-15 20:34:23.102 wdl.w:ptcp.t:call-tar_outputs-78.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:34:23.453 wdl.w:ptcp.t:call-tar_outputs-78 INFO output :: name: "sample_tarball", value: "m84036_250809_035451_s4.bc2175.tar"
2025-09-15 20:34:23.502 wdl.w:ptcp.t:call-tar_outputs-78 NOTICE done
2025-09-15 20:34:23.506 wdl.w:ptcp NOTICE finish :: job: "call-tar_outputs-78"
2025-09-15 20:34:23.506 wdl.w:ptcp INFO output :: job: "call-tar_outputs-78", values: {"sample_tarball": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-78/out/m84036_250809_035451_s4.bc2175.tar"}
2025-09-15 20:35:51.530 wdl.w:ptcp.w:call-paraphase-82.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for f8inv22 for sample m84036_250809_035451_s4.bc2179 at 2025-09-15 20:35:34.484135...
2025-09-15 20:35:51.531 wdl.w:ptcp.w:call-paraphase-82.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for f8inv22 for sample m84036_250809_035451_s4.bc2179 at 2025-09-15 20:35:34.485382...
2025-09-15 20:35:51.531 wdl.w:ptcp.w:call-paraphase-82.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for f8inv22 for sample m84036_250809_035451_s4.bc2179 at 2025-09-15 20:35:35.918227...
2025-09-15 20:35:51.531 wdl.w:ptcp.w:call-paraphase-82.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for f8inv22 for sample m84036_250809_035451_s4.bc2179 at 2025-09-15 20:35:43.949788...
2025-09-15 20:35:51.531 wdl.w:ptcp.w:call-paraphase-82.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for f8inv22 for sample m84036_250809_035451_s4.bc2179 at 2025-09-15 20:35:44.441776...
2025-09-15 20:36:30.820 wdl.w:ptcp.w:call-paraphase-82.t:call-run_paraphase INFO output :: name: "paraphase_bam", value: "m84036_250809_035451_s4.bc2179_paraphase/m84036_250809_035451_s4.bc2179.paraphase.bam"
2025-09-15 20:36:30.823 wdl.w:ptcp.w:call-paraphase-82.t:call-run_paraphase INFO output :: name: "paraphase_bam_bai", value: "m84036_250809_035451_s4.bc2179_paraphase/m84036_250809_035451_s4.bc2179.paraphase.bam.bai"
2025-09-15 20:36:30.825 wdl.w:ptcp.w:call-paraphase-82.t:call-run_paraphase INFO output :: name: "paraphase_json", value: "m84036_250809_035451_s4.bc2179_paraphase/m84036_250809_035451_s4.bc2179.paraphase.json"
2025-09-15 20:36:30.828 wdl.w:ptcp.w:call-paraphase-82.t:call-run_paraphase INFO output :: name: "paraphase_vcfs", value: ["/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2179_paraphase/m84036_250809_035451_s4.bc2179_paraphase_vcfs/m84036_250809_035451_s4.bc2179_cyp21.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2179_paraphase/m84036_250809_035451_s4.bc2179_paraphase_vcfs/m84036_250809_035451_s4.bc2179_f8inv1.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2179_paraphase/m84036_250809_035451_s4.bc2179_paraphase_vcfs/m84036_250809_035451_s4.bc2179_f8inv22.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2179_paraphase/m84036_250809_035451_s4.bc2179_paraphase_vcfs/m84036_250809_035451_s4.bc2179_gba.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2179_paraphase/m84036_250809_035451_s4.bc2179_paraphase_vcfs/m84036_250809_035451_s4.bc2179_hba.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2179_paraphase/m84036_250809_035451_s4.bc2179_paraphase_vcfs/m84036_250809_035451_s4.bc2179_hbb.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2179_paraphase/m84036_250809_035451_s4.bc2179_paraphase_vcfs/m84036_250809_035451_s4.bc2179_rpgr.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2179_paraphase/m84036_250809_035451_s4.bc2179_paraphase_vcfs/m84036_250809_035451_s4.bc2179_smn1.vcf"]
2025-09-15 20:36:30.831 wdl.w:ptcp.w:call-paraphase-82.t:call-run_paraphase INFO output :: name: "havanno_json", value: "m84036_250809_035451_s4.bc2179.havanno.json"
2025-09-15 20:36:30.994 wdl.w:ptcp.w:call-paraphase-82.t:call-run_paraphase NOTICE done
2025-09-15 20:36:31.002 wdl.w:ptcp.w:call-paraphase-82 NOTICE finish :: job: "call-run_paraphase"
2025-09-15 20:36:31.002 wdl.w:ptcp.w:call-paraphase-82 INFO output :: job: "call-run_paraphase", values: {"havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-82/call-run_paraphase/out/m84036_250809_035451_s4.bc2179.havanno.json", "paraphase_vcfs": ["/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-82/call-run_paraphase/out/m84036_250809_035451_s4.bc2179_paraphase/m84036_250809_035451_s4.bc2179_paraphase_vcfs/m84036_250809_035451_s4.bc2179_cyp21.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-82/call-run_paraphase/out/m84036_250809_035451_s4.bc2179_paraphase/m84036_250809_035451_s4.bc2179_paraphase_vcfs/m84036_250809_035451_s4.bc2179_f8inv1.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-82/call-run_paraphase/out/m84036_250809_035451_s4.bc2179_paraphase/m84036_250809_035451_s4.bc2179_paraphase_vcfs/m84036_250809_035451_s4.bc2179_f8inv22.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-82/call-run_paraphase/out/m84036_250809_035451_s4.bc2179_paraphase/m84036_250809_035451_s4.bc2179_paraphase_vcfs/m84036_250809_035451_s4.bc2179_gba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-82/call-run_paraphase/out/m84036_250809_035451_s4.bc2179_paraphase/m84036_250809_035451_s4.bc2179_paraphase_vcfs/m84036_250809_035451_s4.bc2179_hba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-82/call-run_paraphase/out/m84036_250809_035451_s4.bc2179_paraphase/m84036_250809_035451_s4.bc2179_paraphase_vcfs/m84036_250809_035451_s4.bc2179_hbb.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-82/call-run_paraphase/out/m84036_250809_035451_s4.bc2179_paraphase/m84036_250809_035451_s4.bc2179_paraphase_vcfs/m84036_250809_035451_s4.bc2179_rpgr.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-82/call-run_paraphase/out/m84036_250809_035451_s4.bc2179_paraphase/m84036_250809_035451_s4.bc2179_paraphase_vcfs/m84036_250809_035451_s4.bc2179_smn1.vcf"], "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-82/call-run_paraphase/out/m84036_250809_035451_s4.bc2179_paraphase/m84036_250809_035451_s4.bc2179.paraphase.json", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-82/call-run_paraphase/out/m84036_250809_035451_s4.bc2179_paraphase/m84036_250809_035451_s4.bc2179.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-82/call-run_paraphase/out/m84036_250809_035451_s4.bc2179_paraphase/m84036_250809_035451_s4.bc2179.paraphase.bam"}
2025-09-15 20:36:31.003 wdl.w:ptcp.w:call-paraphase-82 NOTICE ready :: job: "call-call_f8", callee: "call_f8"
2025-09-15 20:36:31.003 wdl.w:ptcp.w:call-paraphase-82 INFO input :: job: "call-call_f8", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "out_prefix": "m84036_250809_035451_s4.bc2179", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-82/call-run_paraphase/out/m84036_250809_035451_s4.bc2179_paraphase/m84036_250809_035451_s4.bc2179.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-82/call-run_paraphase/out/m84036_250809_035451_s4.bc2179_paraphase/m84036_250809_035451_s4.bc2179.paraphase.bam", "sex": "F"}
2025-09-15 20:36:31.003 wdl.w:ptcp.w:call-paraphase-82 INFO visit :: node: "output-havanno_json", values: {"havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-82/call-run_paraphase/out/m84036_250809_035451_s4.bc2179.havanno.json"}
2025-09-15 20:36:31.004 wdl.w:ptcp.w:call-paraphase-82 INFO visit :: node: "output-paraphase_bam", values: {"paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-82/call-run_paraphase/out/m84036_250809_035451_s4.bc2179_paraphase/m84036_250809_035451_s4.bc2179.paraphase.bam"}
2025-09-15 20:36:31.004 wdl.w:ptcp.w:call-paraphase-82 INFO visit :: node: "output-paraphase_bam_bai", values: {"paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-82/call-run_paraphase/out/m84036_250809_035451_s4.bc2179_paraphase/m84036_250809_035451_s4.bc2179.paraphase.bam.bai"}
2025-09-15 20:36:31.004 wdl.w:ptcp.w:call-paraphase-82 INFO visit :: node: "output-paraphase_json", values: {"paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-82/call-run_paraphase/out/m84036_250809_035451_s4.bc2179_paraphase/m84036_250809_035451_s4.bc2179.paraphase.json"}
2025-09-15 20:36:31.004 wdl.w:ptcp.w:call-paraphase-82 INFO visit :: node: "output-paraphase_vcfs", values: {"paraphase_vcfs": ["/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-82/call-run_paraphase/out/m84036_250809_035451_s4.bc2179_paraphase/m84036_250809_035451_s4.bc2179_paraphase_vcfs/m84036_250809_035451_s4.bc2179_cyp21.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-82/call-run_paraphase/out/m84036_250809_035451_s4.bc2179_paraphase/m84036_250809_035451_s4.bc2179_paraphase_vcfs/m84036_250809_035451_s4.bc2179_f8inv1.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-82/call-run_paraphase/out/m84036_250809_035451_s4.bc2179_paraphase/m84036_250809_035451_s4.bc2179_paraphase_vcfs/m84036_250809_035451_s4.bc2179_f8inv22.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-82/call-run_paraphase/out/m84036_250809_035451_s4.bc2179_paraphase/m84036_250809_035451_s4.bc2179_paraphase_vcfs/m84036_250809_035451_s4.bc2179_gba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-82/call-run_paraphase/out/m84036_250809_035451_s4.bc2179_paraphase/m84036_250809_035451_s4.bc2179_paraphase_vcfs/m84036_250809_035451_s4.bc2179_hba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-82/call-run_paraphase/out/m84036_250809_035451_s4.bc2179_paraphase/m84036_250809_035451_s4.bc2179_paraphase_vcfs/m84036_250809_035451_s4.bc2179_hbb.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-82/call-run_paraphase/out/m84036_250809_035451_s4.bc2179_paraphase/m84036_250809_035451_s4.bc2179_paraphase_vcfs/m84036_250809_035451_s4.bc2179_rpgr.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-82/call-run_paraphase/out/m84036_250809_035451_s4.bc2179_paraphase/m84036_250809_035451_s4.bc2179_paraphase_vcfs/m84036_250809_035451_s4.bc2179_smn1.vcf"]}
2025-09-15 20:36:31.008 wdl.w:ptcp.w:call-paraphase-82.t:call-call_f8 NOTICE task setup :: name: "call_f8", source: "./paraphase.wdl", line: 232, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-82/call-call_f8", thread: 140611994777152
2025-09-15 20:36:31.032 wdl.w:ptcp.w:call-paraphase-82.t:call-call_f8 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:36:31.032 wdl.w:ptcp.w:call-paraphase-82.t:call-call_f8 INFO input :: name: "genome_version", value: "38"
2025-09-15 20:36:31.032 wdl.w:ptcp.w:call-paraphase-82.t:call-call_f8 INFO input :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2179"
2025-09-15 20:36:31.032 wdl.w:ptcp.w:call-paraphase-82.t:call-call_f8 INFO input :: name: "paraphase_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2179.paraphase.bam.bai"
2025-09-15 20:36:31.032 wdl.w:ptcp.w:call-paraphase-82.t:call-call_f8 INFO input :: name: "paraphase_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2179.paraphase.bam"
2025-09-15 20:36:31.032 wdl.w:ptcp.w:call-paraphase-82.t:call-call_f8 INFO input :: name: "sex", value: "F"
2025-09-15 20:36:31.032 wdl.w:ptcp.w:call-paraphase-82.t:call-call_f8 INFO eval :: name: "threads", value: 1
2025-09-15 20:36:31.032 wdl.w:ptcp.w:call-paraphase-82.t:call-call_f8 INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:36:31.033 wdl.w:ptcp.w:call-paraphase-82.t:call-call_f8 INFO eval :: name: "disk_size", value: 11
2025-09-15 20:36:31.033 wdl.w:ptcp.w:call-paraphase-82.t:call-call_f8 INFO eval :: name: "sample_sex", value: "F"
2025-09-15 20:36:31.033 wdl.w:ptcp.w:call-paraphase-82.t:call-call_f8 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:36:31.033 wdl.w:ptcp.w:call-paraphase-82.t:call-call_f8 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:36:31.033 wdl.w:ptcp.w:call-paraphase-82.t:call-call_f8 INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:36:31.034 wdl.w:ptcp.w:call-paraphase-82.t:call-call_f8 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:36:31.069 wdl.w:ptcp.w:call-paraphase-82.t:call-call_f8 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 8, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-82/call-call_f8/_singularity_tmpdir__y0s0aj3"
2025-09-15 20:36:31.069 wdl.w:ptcp.w:call-paraphase-82.t:call-call_f8 INFO Slurm invocation: srun --job-name call-call_f8 --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-82/call-call_f8/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-82/call-call_f8/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-82/call-call_f8/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-82/call-call_f8/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-82/call-run_paraphase/out/m84036_250809_035451_s4.bc2179_paraphase/m84036_250809_035451_s4.bc2179.paraphase.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2179.paraphase.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-82/call-run_paraphase/out/m84036_250809_035451_s4.bc2179_paraphase/m84036_250809_035451_s4.bc2179.paraphase.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2179.paraphase.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-82/call-call_f8/_singularity_tmpdir__y0s0aj3/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-82/call-call_f8/_singularity_tmpdir__y0s0aj3/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:36:31.074 wdl.w:ptcp.w:call-paraphase-82.t:call-call_f8 NOTICE slurm_singularity run :: pid: 1213831, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-82/call-call_f8/slurm_singularity.log.txt"
2025-09-15 20:36:32.083 wdl.w:ptcp.w:call-paraphase-82.t:call-call_f8.slurm_singularity INFO srun: job 51798413 queued and waiting for resources
2025-09-15 20:36:32.083 wdl.w:ptcp.w:call-paraphase-82.t:call-call_f8.slurm_singularity INFO srun: job 51798413 has been allocated resources
2025-09-15 20:36:32.083 wdl.w:ptcp.w:call-paraphase-82.t:call-call_f8.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:36:33.082 wdl.w:ptcp.w:call-paraphase-82.t:call-call_f8 INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2179.f8inversion.vcf"
2025-09-15 20:36:33.084 wdl.w:ptcp.w:call-paraphase-82.t:call-call_f8 INFO output :: name: "json", value: "m84036_250809_035451_s4.bc2179.f8inversion.json"
2025-09-15 20:36:33.131 wdl.w:ptcp.w:call-paraphase-82.t:call-call_f8 NOTICE done
2025-09-15 20:36:33.136 wdl.w:ptcp.w:call-paraphase-82 NOTICE finish :: job: "call-call_f8"
2025-09-15 20:36:33.136 wdl.w:ptcp.w:call-paraphase-82 INFO output :: job: "call-call_f8", values: {"json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-82/call-call_f8/out/m84036_250809_035451_s4.bc2179.f8inversion.json", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-82/call-call_f8/out/m84036_250809_035451_s4.bc2179.f8inversion.vcf"}
2025-09-15 20:36:33.136 wdl.w:ptcp.w:call-paraphase-82 INFO visit :: node: "output-f8_json", values: {"f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-82/call-call_f8/out/m84036_250809_035451_s4.bc2179.f8inversion.json"}
2025-09-15 20:36:33.136 wdl.w:ptcp.w:call-paraphase-82 INFO visit :: node: "output-f8_vcf", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-82/call-call_f8/out/m84036_250809_035451_s4.bc2179.f8inversion.vcf"}
2025-09-15 20:36:33.137 wdl.w:ptcp.w:call-paraphase-82 INFO visit :: node: "outputs", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-82/call-call_f8/out/m84036_250809_035451_s4.bc2179.f8inversion.vcf", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-82/call-run_paraphase/out/m84036_250809_035451_s4.bc2179_paraphase/m84036_250809_035451_s4.bc2179.paraphase.json", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-82/call-run_paraphase/out/m84036_250809_035451_s4.bc2179_paraphase/m84036_250809_035451_s4.bc2179.paraphase.bam", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-82/call-run_paraphase/out/m84036_250809_035451_s4.bc2179_paraphase/m84036_250809_035451_s4.bc2179.paraphase.bam.bai", "paraphase_vcfs": ["/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-82/call-run_paraphase/out/m84036_250809_035451_s4.bc2179_paraphase/m84036_250809_035451_s4.bc2179_paraphase_vcfs/m84036_250809_035451_s4.bc2179_cyp21.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-82/call-run_paraphase/out/m84036_250809_035451_s4.bc2179_paraphase/m84036_250809_035451_s4.bc2179_paraphase_vcfs/m84036_250809_035451_s4.bc2179_f8inv1.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-82/call-run_paraphase/out/m84036_250809_035451_s4.bc2179_paraphase/m84036_250809_035451_s4.bc2179_paraphase_vcfs/m84036_250809_035451_s4.bc2179_f8inv22.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-82/call-run_paraphase/out/m84036_250809_035451_s4.bc2179_paraphase/m84036_250809_035451_s4.bc2179_paraphase_vcfs/m84036_250809_035451_s4.bc2179_gba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-82/call-run_paraphase/out/m84036_250809_035451_s4.bc2179_paraphase/m84036_250809_035451_s4.bc2179_paraphase_vcfs/m84036_250809_035451_s4.bc2179_hba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-82/call-run_paraphase/out/m84036_250809_035451_s4.bc2179_paraphase/m84036_250809_035451_s4.bc2179_paraphase_vcfs/m84036_250809_035451_s4.bc2179_hbb.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-82/call-run_paraphase/out/m84036_250809_035451_s4.bc2179_paraphase/m84036_250809_035451_s4.bc2179_paraphase_vcfs/m84036_250809_035451_s4.bc2179_rpgr.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-82/call-run_paraphase/out/m84036_250809_035451_s4.bc2179_paraphase/m84036_250809_035451_s4.bc2179_paraphase_vcfs/m84036_250809_035451_s4.bc2179_smn1.vcf"], "havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-82/call-run_paraphase/out/m84036_250809_035451_s4.bc2179.havanno.json", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-82/call-call_f8/out/m84036_250809_035451_s4.bc2179.f8inversion.json"}
2025-09-15 20:36:33.233 wdl.w:ptcp.w:call-paraphase-82 NOTICE done
2025-09-15 20:36:33.241 wdl.w:ptcp NOTICE finish :: job: "call-paraphase-82"
2025-09-15 20:36:33.241 wdl.w:ptcp INFO output :: job: "call-paraphase-82", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-82/out/m84036_250809_035451_s4.bc2179.f8inversion.vcf", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-82/out/m84036_250809_035451_s4.bc2179_paraphase/m84036_250809_035451_s4.bc2179.paraphase.json", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-82/out/m84036_250809_035451_s4.bc2179_paraphase/m84036_250809_035451_s4.bc2179.paraphase.bam", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-82/out/m84036_250809_035451_s4.bc2179_paraphase/m84036_250809_035451_s4.bc2179.paraphase.bam.bai", "paraphase_vcfs": ["/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-82/out/m84036_250809_035451_s4.bc2179_paraphase/m84036_250809_035451_s4.bc2179_paraphase_vcfs/m84036_250809_035451_s4.bc2179_cyp21.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-82/out/m84036_250809_035451_s4.bc2179_paraphase/m84036_250809_035451_s4.bc2179_paraphase_vcfs/m84036_250809_035451_s4.bc2179_f8inv1.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-82/out/m84036_250809_035451_s4.bc2179_paraphase/m84036_250809_035451_s4.bc2179_paraphase_vcfs/m84036_250809_035451_s4.bc2179_f8inv22.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-82/out/m84036_250809_035451_s4.bc2179_paraphase/m84036_250809_035451_s4.bc2179_paraphase_vcfs/m84036_250809_035451_s4.bc2179_gba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-82/out/m84036_250809_035451_s4.bc2179_paraphase/m84036_250809_035451_s4.bc2179_paraphase_vcfs/m84036_250809_035451_s4.bc2179_hba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-82/out/m84036_250809_035451_s4.bc2179_paraphase/m84036_250809_035451_s4.bc2179_paraphase_vcfs/m84036_250809_035451_s4.bc2179_hbb.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-82/out/m84036_250809_035451_s4.bc2179_paraphase/m84036_250809_035451_s4.bc2179_paraphase_vcfs/m84036_250809_035451_s4.bc2179_rpgr.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-82/out/m84036_250809_035451_s4.bc2179_paraphase/m84036_250809_035451_s4.bc2179_paraphase_vcfs/m84036_250809_035451_s4.bc2179_smn1.vcf"], "havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-82/out/m84036_250809_035451_s4.bc2179.havanno.json", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-82/out/m84036_250809_035451_s4.bc2179.f8inversion.json"}
2025-09-15 20:36:33.242 wdl.w:ptcp NOTICE ready :: job: "call-tar_outputs-82", callee: "tar_outputs"
2025-09-15 20:36:33.242 wdl.w:ptcp INFO input :: job: "call-tar_outputs-82", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "sawfish_vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-82/out/m84036_250809_035451_s4.bc2179_sawfish/m84036_250809_035451_s4.bc2179.sv.vcf.gz.tbi", "sawfish_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-82/out/m84036_250809_035451_s4.bc2179_sawfish/m84036_250809_035451_s4.bc2179.sv.vcf.gz", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-82/out/m84036_250809_035451_s4.bc2179.f8inversion.json", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-82/out/m84036_250809_035451_s4.bc2179_paraphase/m84036_250809_035451_s4.bc2179.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-82/out/m84036_250809_035451_s4.bc2179_paraphase/m84036_250809_035451_s4.bc2179.paraphase.bam", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-82/out/m84036_250809_035451_s4.bc2179_paraphase/m84036_250809_035451_s4.bc2179.paraphase.json", "trgt_spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-82/out/m84036_250809_035451_s4.bc2179.trgt.sorted.spanning.bam.bai", "trgt_spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-82/out/m84036_250809_035451_s4.bc2179.trgt.sorted.spanning.bam", "trgt_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-82/out/m84036_250809_035451_s4.bc2179.trgt.vcf", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-82/out/m84036_250809_035451_s4.bc2179.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-82/out/m84036_250809_035451_s4.bc2179.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2179"}
2025-09-15 20:36:33.248 wdl.w:ptcp.t:call-tar_outputs-82 NOTICE task setup :: name: "tar_outputs", source: "./common.wdl", line: 279, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-82", thread: 140606617675328
2025-09-15 20:36:33.267 wdl.w:ptcp.t:call-tar_outputs-82 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:36:33.267 wdl.w:ptcp.t:call-tar_outputs-82 INFO input :: name: "sawfish_vcf_tbi", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2179.sv.vcf.gz.tbi"
2025-09-15 20:36:33.267 wdl.w:ptcp.t:call-tar_outputs-82 INFO input :: name: "sawfish_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2179.sv.vcf.gz"
2025-09-15 20:36:33.267 wdl.w:ptcp.t:call-tar_outputs-82 INFO input :: name: "f8_json", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2179.f8inversion.json"
2025-09-15 20:36:33.267 wdl.w:ptcp.t:call-tar_outputs-82 INFO input :: name: "paraphase_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2179.paraphase.bam.bai"
2025-09-15 20:36:33.267 wdl.w:ptcp.t:call-tar_outputs-82 INFO input :: name: "paraphase_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2179.paraphase.bam"
2025-09-15 20:36:33.267 wdl.w:ptcp.t:call-tar_outputs-82 INFO input :: name: "paraphase_json", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2179.paraphase.json"
2025-09-15 20:36:33.267 wdl.w:ptcp.t:call-tar_outputs-82 INFO input :: name: "trgt_spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2179.trgt.sorted.spanning.bam.bai"
2025-09-15 20:36:33.267 wdl.w:ptcp.t:call-tar_outputs-82 INFO input :: name: "trgt_spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2179.trgt.sorted.spanning.bam"
2025-09-15 20:36:33.267 wdl.w:ptcp.t:call-tar_outputs-82 INFO input :: name: "trgt_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2179.trgt.vcf"
2025-09-15 20:36:33.267 wdl.w:ptcp.t:call-tar_outputs-82 INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2179.mapped.bam.bai"
2025-09-15 20:36:33.267 wdl.w:ptcp.t:call-tar_outputs-82 INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2179.mapped.bam"
2025-09-15 20:36:33.267 wdl.w:ptcp.t:call-tar_outputs-82 INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2179"
2025-09-15 20:36:33.267 wdl.w:ptcp.t:call-tar_outputs-82 INFO eval :: name: "threads", value: 1
2025-09-15 20:36:33.268 wdl.w:ptcp.t:call-tar_outputs-82 INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:36:33.268 wdl.w:ptcp.t:call-tar_outputs-82 INFO eval :: name: "disk_size", value: 6
2025-09-15 20:36:33.268 wdl.w:ptcp.t:call-tar_outputs-82 INFO eval :: name: "output_tarball", value: "m84036_250809_035451_s4.bc2179.tar"
2025-09-15 20:36:33.268 wdl.w:ptcp.t:call-tar_outputs-82 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:36:33.268 wdl.w:ptcp.t:call-tar_outputs-82 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:36:33.269 wdl.w:ptcp.t:call-tar_outputs-82 INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:36:33.269 wdl.w:ptcp.t:call-tar_outputs-82 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:36:33.340 wdl.w:ptcp.t:call-tar_outputs-82 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 17, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-82/_singularity_tmpdir_p1tikt0q"
2025-09-15 20:36:33.340 wdl.w:ptcp.t:call-tar_outputs-82 INFO Slurm invocation: srun --job-name call-tar_outputs-82 --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-82/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-82/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-82/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-82/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-82/out/m84036_250809_035451_s4.bc2179_paraphase/m84036_250809_035451_s4.bc2179.paraphase.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2179.paraphase.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-82/out/m84036_250809_035451_s4.bc2179_paraphase/m84036_250809_035451_s4.bc2179.paraphase.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2179.paraphase.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-82/out/m84036_250809_035451_s4.bc2179_paraphase/m84036_250809_035451_s4.bc2179.paraphase.json:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2179.paraphase.json:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-82/out/m84036_250809_035451_s4.bc2179.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2179.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-82/out/m84036_250809_035451_s4.bc2179.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2179.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-82/out/m84036_250809_035451_s4.bc2179.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2179.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-82/out/m84036_250809_035451_s4.bc2179.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2179.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-82/out/m84036_250809_035451_s4.bc2179.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2179.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-82/out/m84036_250809_035451_s4.bc2179_sawfish/m84036_250809_035451_s4.bc2179.sv.vcf.gz.tbi:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2179.sv.vcf.gz.tbi:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-82/out/m84036_250809_035451_s4.bc2179_sawfish/m84036_250809_035451_s4.bc2179.sv.vcf.gz:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2179.sv.vcf.gz:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-82/out/m84036_250809_035451_s4.bc2179.f8inversion.json:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2179.f8inversion.json:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-82/_singularity_tmpdir_p1tikt0q/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-82/_singularity_tmpdir_p1tikt0q/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:36:33.343 wdl.w:ptcp.t:call-tar_outputs-82 NOTICE slurm_singularity run :: pid: 1213841, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-82/slurm_singularity.log.txt"
2025-09-15 20:36:34.352 wdl.w:ptcp.t:call-tar_outputs-82.slurm_singularity INFO srun: job 51798414 queued and waiting for resources
2025-09-15 20:36:35.361 wdl.w:ptcp.t:call-tar_outputs-82.slurm_singularity INFO srun: job 51798414 has been allocated resources
2025-09-15 20:36:35.361 wdl.w:ptcp.t:call-tar_outputs-82.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:36:35.760 wdl.w:ptcp.t:call-tar_outputs-82 INFO output :: name: "sample_tarball", value: "m84036_250809_035451_s4.bc2179.tar"
2025-09-15 20:36:35.813 wdl.w:ptcp.t:call-tar_outputs-82 NOTICE done
2025-09-15 20:36:35.816 wdl.w:ptcp NOTICE finish :: job: "call-tar_outputs-82"
2025-09-15 20:36:35.816 wdl.w:ptcp INFO output :: job: "call-tar_outputs-82", values: {"sample_tarball": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-82/out/m84036_250809_035451_s4.bc2179.tar"}
2025-09-15 20:37:50.774 wdl.w:ptcp.w:call-paraphase-75.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for f8inv22 for sample m84036_250809_035451_s4.bc2172 at 2025-09-15 20:36:52.654193...
2025-09-15 20:37:50.775 wdl.w:ptcp.w:call-paraphase-75.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for f8inv22 for sample m84036_250809_035451_s4.bc2172 at 2025-09-15 20:36:52.656348...
2025-09-15 20:37:50.775 wdl.w:ptcp.w:call-paraphase-75.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for f8inv22 for sample m84036_250809_035451_s4.bc2172 at 2025-09-15 20:36:54.269021...
2025-09-15 20:37:50.775 wdl.w:ptcp.w:call-paraphase-75.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for f8inv22 for sample m84036_250809_035451_s4.bc2172 at 2025-09-15 20:37:02.314839...
2025-09-15 20:37:50.775 wdl.w:ptcp.w:call-paraphase-75.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for f8inv22 for sample m84036_250809_035451_s4.bc2172 at 2025-09-15 20:37:02.921708...
2025-09-15 20:37:52.443 wdl.w:ptcp.w:call-paraphase-75.t:call-run_paraphase INFO output :: name: "paraphase_bam", value: "m84036_250809_035451_s4.bc2172_paraphase/m84036_250809_035451_s4.bc2172.paraphase.bam"
2025-09-15 20:37:52.447 wdl.w:ptcp.w:call-paraphase-75.t:call-run_paraphase INFO output :: name: "paraphase_bam_bai", value: "m84036_250809_035451_s4.bc2172_paraphase/m84036_250809_035451_s4.bc2172.paraphase.bam.bai"
2025-09-15 20:37:52.448 wdl.w:ptcp.w:call-paraphase-75.t:call-run_paraphase INFO output :: name: "paraphase_json", value: "m84036_250809_035451_s4.bc2172_paraphase/m84036_250809_035451_s4.bc2172.paraphase.json"
2025-09-15 20:37:52.452 wdl.w:ptcp.w:call-paraphase-75.t:call-run_paraphase INFO output :: name: "paraphase_vcfs", value: ["/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2172_paraphase/m84036_250809_035451_s4.bc2172_paraphase_vcfs/m84036_250809_035451_s4.bc2172_cyp21.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2172_paraphase/m84036_250809_035451_s4.bc2172_paraphase_vcfs/m84036_250809_035451_s4.bc2172_f8inv1.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2172_paraphase/m84036_250809_035451_s4.bc2172_paraphase_vcfs/m84036_250809_035451_s4.bc2172_f8inv22.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2172_paraphase/m84036_250809_035451_s4.bc2172_paraphase_vcfs/m84036_250809_035451_s4.bc2172_gba.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2172_paraphase/m84036_250809_035451_s4.bc2172_paraphase_vcfs/m84036_250809_035451_s4.bc2172_hba.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2172_paraphase/m84036_250809_035451_s4.bc2172_paraphase_vcfs/m84036_250809_035451_s4.bc2172_hbb.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2172_paraphase/m84036_250809_035451_s4.bc2172_paraphase_vcfs/m84036_250809_035451_s4.bc2172_rpgr.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2172_paraphase/m84036_250809_035451_s4.bc2172_paraphase_vcfs/m84036_250809_035451_s4.bc2172_smn1.vcf"]
2025-09-15 20:37:52.455 wdl.w:ptcp.w:call-paraphase-75.t:call-run_paraphase INFO output :: name: "havanno_json", value: "m84036_250809_035451_s4.bc2172.havanno.json"
2025-09-15 20:37:52.621 wdl.w:ptcp.w:call-paraphase-75.t:call-run_paraphase NOTICE done
2025-09-15 20:37:52.628 wdl.w:ptcp.w:call-paraphase-75 NOTICE finish :: job: "call-run_paraphase"
2025-09-15 20:37:52.628 wdl.w:ptcp.w:call-paraphase-75 INFO output :: job: "call-run_paraphase", values: {"havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-75/call-run_paraphase/out/m84036_250809_035451_s4.bc2172.havanno.json", "paraphase_vcfs": ["/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-75/call-run_paraphase/out/m84036_250809_035451_s4.bc2172_paraphase/m84036_250809_035451_s4.bc2172_paraphase_vcfs/m84036_250809_035451_s4.bc2172_cyp21.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-75/call-run_paraphase/out/m84036_250809_035451_s4.bc2172_paraphase/m84036_250809_035451_s4.bc2172_paraphase_vcfs/m84036_250809_035451_s4.bc2172_f8inv1.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-75/call-run_paraphase/out/m84036_250809_035451_s4.bc2172_paraphase/m84036_250809_035451_s4.bc2172_paraphase_vcfs/m84036_250809_035451_s4.bc2172_f8inv22.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-75/call-run_paraphase/out/m84036_250809_035451_s4.bc2172_paraphase/m84036_250809_035451_s4.bc2172_paraphase_vcfs/m84036_250809_035451_s4.bc2172_gba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-75/call-run_paraphase/out/m84036_250809_035451_s4.bc2172_paraphase/m84036_250809_035451_s4.bc2172_paraphase_vcfs/m84036_250809_035451_s4.bc2172_hba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-75/call-run_paraphase/out/m84036_250809_035451_s4.bc2172_paraphase/m84036_250809_035451_s4.bc2172_paraphase_vcfs/m84036_250809_035451_s4.bc2172_hbb.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-75/call-run_paraphase/out/m84036_250809_035451_s4.bc2172_paraphase/m84036_250809_035451_s4.bc2172_paraphase_vcfs/m84036_250809_035451_s4.bc2172_rpgr.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-75/call-run_paraphase/out/m84036_250809_035451_s4.bc2172_paraphase/m84036_250809_035451_s4.bc2172_paraphase_vcfs/m84036_250809_035451_s4.bc2172_smn1.vcf"], "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-75/call-run_paraphase/out/m84036_250809_035451_s4.bc2172_paraphase/m84036_250809_035451_s4.bc2172.paraphase.json", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-75/call-run_paraphase/out/m84036_250809_035451_s4.bc2172_paraphase/m84036_250809_035451_s4.bc2172.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-75/call-run_paraphase/out/m84036_250809_035451_s4.bc2172_paraphase/m84036_250809_035451_s4.bc2172.paraphase.bam"}
2025-09-15 20:37:52.629 wdl.w:ptcp.w:call-paraphase-75 NOTICE ready :: job: "call-call_f8", callee: "call_f8"
2025-09-15 20:37:52.629 wdl.w:ptcp.w:call-paraphase-75 INFO input :: job: "call-call_f8", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "out_prefix": "m84036_250809_035451_s4.bc2172", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-75/call-run_paraphase/out/m84036_250809_035451_s4.bc2172_paraphase/m84036_250809_035451_s4.bc2172.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-75/call-run_paraphase/out/m84036_250809_035451_s4.bc2172_paraphase/m84036_250809_035451_s4.bc2172.paraphase.bam", "sex": "F"}
2025-09-15 20:37:52.630 wdl.w:ptcp.w:call-paraphase-75 INFO visit :: node: "output-havanno_json", values: {"havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-75/call-run_paraphase/out/m84036_250809_035451_s4.bc2172.havanno.json"}
2025-09-15 20:37:52.630 wdl.w:ptcp.w:call-paraphase-75 INFO visit :: node: "output-paraphase_bam", values: {"paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-75/call-run_paraphase/out/m84036_250809_035451_s4.bc2172_paraphase/m84036_250809_035451_s4.bc2172.paraphase.bam"}
2025-09-15 20:37:52.630 wdl.w:ptcp.w:call-paraphase-75 INFO visit :: node: "output-paraphase_bam_bai", values: {"paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-75/call-run_paraphase/out/m84036_250809_035451_s4.bc2172_paraphase/m84036_250809_035451_s4.bc2172.paraphase.bam.bai"}
2025-09-15 20:37:52.630 wdl.w:ptcp.w:call-paraphase-75 INFO visit :: node: "output-paraphase_json", values: {"paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-75/call-run_paraphase/out/m84036_250809_035451_s4.bc2172_paraphase/m84036_250809_035451_s4.bc2172.paraphase.json"}
2025-09-15 20:37:52.630 wdl.w:ptcp.w:call-paraphase-75 INFO visit :: node: "output-paraphase_vcfs", values: {"paraphase_vcfs": ["/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-75/call-run_paraphase/out/m84036_250809_035451_s4.bc2172_paraphase/m84036_250809_035451_s4.bc2172_paraphase_vcfs/m84036_250809_035451_s4.bc2172_cyp21.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-75/call-run_paraphase/out/m84036_250809_035451_s4.bc2172_paraphase/m84036_250809_035451_s4.bc2172_paraphase_vcfs/m84036_250809_035451_s4.bc2172_f8inv1.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-75/call-run_paraphase/out/m84036_250809_035451_s4.bc2172_paraphase/m84036_250809_035451_s4.bc2172_paraphase_vcfs/m84036_250809_035451_s4.bc2172_f8inv22.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-75/call-run_paraphase/out/m84036_250809_035451_s4.bc2172_paraphase/m84036_250809_035451_s4.bc2172_paraphase_vcfs/m84036_250809_035451_s4.bc2172_gba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-75/call-run_paraphase/out/m84036_250809_035451_s4.bc2172_paraphase/m84036_250809_035451_s4.bc2172_paraphase_vcfs/m84036_250809_035451_s4.bc2172_hba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-75/call-run_paraphase/out/m84036_250809_035451_s4.bc2172_paraphase/m84036_250809_035451_s4.bc2172_paraphase_vcfs/m84036_250809_035451_s4.bc2172_hbb.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-75/call-run_paraphase/out/m84036_250809_035451_s4.bc2172_paraphase/m84036_250809_035451_s4.bc2172_paraphase_vcfs/m84036_250809_035451_s4.bc2172_rpgr.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-75/call-run_paraphase/out/m84036_250809_035451_s4.bc2172_paraphase/m84036_250809_035451_s4.bc2172_paraphase_vcfs/m84036_250809_035451_s4.bc2172_smn1.vcf"]}
2025-09-15 20:37:52.636 wdl.w:ptcp.w:call-paraphase-75.t:call-call_f8 NOTICE task setup :: name: "call_f8", source: "./paraphase.wdl", line: 232, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-75/call-call_f8", thread: 140611441120832
2025-09-15 20:37:52.667 wdl.w:ptcp.w:call-paraphase-75.t:call-call_f8 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:37:52.667 wdl.w:ptcp.w:call-paraphase-75.t:call-call_f8 INFO input :: name: "genome_version", value: "38"
2025-09-15 20:37:52.667 wdl.w:ptcp.w:call-paraphase-75.t:call-call_f8 INFO input :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2172"
2025-09-15 20:37:52.667 wdl.w:ptcp.w:call-paraphase-75.t:call-call_f8 INFO input :: name: "paraphase_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2172.paraphase.bam.bai"
2025-09-15 20:37:52.667 wdl.w:ptcp.w:call-paraphase-75.t:call-call_f8 INFO input :: name: "paraphase_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2172.paraphase.bam"
2025-09-15 20:37:52.667 wdl.w:ptcp.w:call-paraphase-75.t:call-call_f8 INFO input :: name: "sex", value: "F"
2025-09-15 20:37:52.668 wdl.w:ptcp.w:call-paraphase-75.t:call-call_f8 INFO eval :: name: "threads", value: 1
2025-09-15 20:37:52.668 wdl.w:ptcp.w:call-paraphase-75.t:call-call_f8 INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:37:52.668 wdl.w:ptcp.w:call-paraphase-75.t:call-call_f8 INFO eval :: name: "disk_size", value: 11
2025-09-15 20:37:52.668 wdl.w:ptcp.w:call-paraphase-75.t:call-call_f8 INFO eval :: name: "sample_sex", value: "F"
2025-09-15 20:37:52.668 wdl.w:ptcp.w:call-paraphase-75.t:call-call_f8 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:37:52.668 wdl.w:ptcp.w:call-paraphase-75.t:call-call_f8 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:37:52.669 wdl.w:ptcp.w:call-paraphase-75.t:call-call_f8 INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:37:52.673 wdl.w:ptcp.w:call-paraphase-75.t:call-call_f8 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:37:52.710 wdl.w:ptcp.w:call-paraphase-75.t:call-call_f8 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 8, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-75/call-call_f8/_singularity_tmpdir_giq46irh"
2025-09-15 20:37:52.710 wdl.w:ptcp.w:call-paraphase-75.t:call-call_f8 INFO Slurm invocation: srun --job-name call-call_f8 --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-75/call-call_f8/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-75/call-call_f8/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-75/call-call_f8/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-75/call-call_f8/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-75/call-run_paraphase/out/m84036_250809_035451_s4.bc2172_paraphase/m84036_250809_035451_s4.bc2172.paraphase.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2172.paraphase.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-75/call-run_paraphase/out/m84036_250809_035451_s4.bc2172_paraphase/m84036_250809_035451_s4.bc2172.paraphase.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2172.paraphase.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-75/call-call_f8/_singularity_tmpdir_giq46irh/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-75/call-call_f8/_singularity_tmpdir_giq46irh/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:37:52.716 wdl.w:ptcp.w:call-paraphase-75.t:call-call_f8 NOTICE slurm_singularity run :: pid: 1214434, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-75/call-call_f8/slurm_singularity.log.txt"
2025-09-15 20:37:53.724 wdl.w:ptcp.w:call-paraphase-75.t:call-call_f8.slurm_singularity INFO srun: job 51798418 queued and waiting for resources
2025-09-15 20:37:53.724 wdl.w:ptcp.w:call-paraphase-75.t:call-call_f8.slurm_singularity INFO srun: job 51798418 has been allocated resources
2025-09-15 20:37:53.724 wdl.w:ptcp.w:call-paraphase-75.t:call-call_f8.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:37:54.224 wdl.w:ptcp.w:call-paraphase-75.t:call-call_f8 INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2172.f8inversion.vcf"
2025-09-15 20:37:54.227 wdl.w:ptcp.w:call-paraphase-75.t:call-call_f8 INFO output :: name: "json", value: "m84036_250809_035451_s4.bc2172.f8inversion.json"
2025-09-15 20:37:54.273 wdl.w:ptcp.w:call-paraphase-75.t:call-call_f8 NOTICE done
2025-09-15 20:37:54.278 wdl.w:ptcp.w:call-paraphase-75 NOTICE finish :: job: "call-call_f8"
2025-09-15 20:37:54.278 wdl.w:ptcp.w:call-paraphase-75 INFO output :: job: "call-call_f8", values: {"json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-75/call-call_f8/out/m84036_250809_035451_s4.bc2172.f8inversion.json", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-75/call-call_f8/out/m84036_250809_035451_s4.bc2172.f8inversion.vcf"}
2025-09-15 20:37:54.278 wdl.w:ptcp.w:call-paraphase-75 INFO visit :: node: "output-f8_json", values: {"f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-75/call-call_f8/out/m84036_250809_035451_s4.bc2172.f8inversion.json"}
2025-09-15 20:37:54.278 wdl.w:ptcp.w:call-paraphase-75 INFO visit :: node: "output-f8_vcf", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-75/call-call_f8/out/m84036_250809_035451_s4.bc2172.f8inversion.vcf"}
2025-09-15 20:37:54.279 wdl.w:ptcp.w:call-paraphase-75 INFO visit :: node: "outputs", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-75/call-call_f8/out/m84036_250809_035451_s4.bc2172.f8inversion.vcf", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-75/call-run_paraphase/out/m84036_250809_035451_s4.bc2172_paraphase/m84036_250809_035451_s4.bc2172.paraphase.json", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-75/call-run_paraphase/out/m84036_250809_035451_s4.bc2172_paraphase/m84036_250809_035451_s4.bc2172.paraphase.bam", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-75/call-run_paraphase/out/m84036_250809_035451_s4.bc2172_paraphase/m84036_250809_035451_s4.bc2172.paraphase.bam.bai", "paraphase_vcfs": ["/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-75/call-run_paraphase/out/m84036_250809_035451_s4.bc2172_paraphase/m84036_250809_035451_s4.bc2172_paraphase_vcfs/m84036_250809_035451_s4.bc2172_cyp21.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-75/call-run_paraphase/out/m84036_250809_035451_s4.bc2172_paraphase/m84036_250809_035451_s4.bc2172_paraphase_vcfs/m84036_250809_035451_s4.bc2172_f8inv1.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-75/call-run_paraphase/out/m84036_250809_035451_s4.bc2172_paraphase/m84036_250809_035451_s4.bc2172_paraphase_vcfs/m84036_250809_035451_s4.bc2172_f8inv22.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-75/call-run_paraphase/out/m84036_250809_035451_s4.bc2172_paraphase/m84036_250809_035451_s4.bc2172_paraphase_vcfs/m84036_250809_035451_s4.bc2172_gba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-75/call-run_paraphase/out/m84036_250809_035451_s4.bc2172_paraphase/m84036_250809_035451_s4.bc2172_paraphase_vcfs/m84036_250809_035451_s4.bc2172_hba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-75/call-run_paraphase/out/m84036_250809_035451_s4.bc2172_paraphase/m84036_250809_035451_s4.bc2172_paraphase_vcfs/m84036_250809_035451_s4.bc2172_hbb.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-75/call-run_paraphase/out/m84036_250809_035451_s4.bc2172_paraphase/m84036_250809_035451_s4.bc2172_paraphase_vcfs/m84036_250809_035451_s4.bc2172_rpgr.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-75/call-run_paraphase/out/m84036_250809_035451_s4.bc2172_paraphase/m84036_250809_035451_s4.bc2172_paraphase_vcfs/m84036_250809_035451_s4.bc2172_smn1.vcf"], "havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-75/call-run_paraphase/out/m84036_250809_035451_s4.bc2172.havanno.json", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-75/call-call_f8/out/m84036_250809_035451_s4.bc2172.f8inversion.json"}
2025-09-15 20:37:54.378 wdl.w:ptcp.w:call-paraphase-75 NOTICE done
2025-09-15 20:37:54.384 wdl.w:ptcp NOTICE finish :: job: "call-paraphase-75"
2025-09-15 20:37:54.384 wdl.w:ptcp INFO output :: job: "call-paraphase-75", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-75/out/m84036_250809_035451_s4.bc2172.f8inversion.vcf", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-75/out/m84036_250809_035451_s4.bc2172_paraphase/m84036_250809_035451_s4.bc2172.paraphase.json", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-75/out/m84036_250809_035451_s4.bc2172_paraphase/m84036_250809_035451_s4.bc2172.paraphase.bam", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-75/out/m84036_250809_035451_s4.bc2172_paraphase/m84036_250809_035451_s4.bc2172.paraphase.bam.bai", "paraphase_vcfs": ["/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-75/out/m84036_250809_035451_s4.bc2172_paraphase/m84036_250809_035451_s4.bc2172_paraphase_vcfs/m84036_250809_035451_s4.bc2172_cyp21.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-75/out/m84036_250809_035451_s4.bc2172_paraphase/m84036_250809_035451_s4.bc2172_paraphase_vcfs/m84036_250809_035451_s4.bc2172_f8inv1.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-75/out/m84036_250809_035451_s4.bc2172_paraphase/m84036_250809_035451_s4.bc2172_paraphase_vcfs/m84036_250809_035451_s4.bc2172_f8inv22.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-75/out/m84036_250809_035451_s4.bc2172_paraphase/m84036_250809_035451_s4.bc2172_paraphase_vcfs/m84036_250809_035451_s4.bc2172_gba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-75/out/m84036_250809_035451_s4.bc2172_paraphase/m84036_250809_035451_s4.bc2172_paraphase_vcfs/m84036_250809_035451_s4.bc2172_hba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-75/out/m84036_250809_035451_s4.bc2172_paraphase/m84036_250809_035451_s4.bc2172_paraphase_vcfs/m84036_250809_035451_s4.bc2172_hbb.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-75/out/m84036_250809_035451_s4.bc2172_paraphase/m84036_250809_035451_s4.bc2172_paraphase_vcfs/m84036_250809_035451_s4.bc2172_rpgr.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-75/out/m84036_250809_035451_s4.bc2172_paraphase/m84036_250809_035451_s4.bc2172_paraphase_vcfs/m84036_250809_035451_s4.bc2172_smn1.vcf"], "havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-75/out/m84036_250809_035451_s4.bc2172.havanno.json", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-75/out/m84036_250809_035451_s4.bc2172.f8inversion.json"}
2025-09-15 20:37:54.385 wdl.w:ptcp NOTICE ready :: job: "call-tar_outputs-75", callee: "tar_outputs"
2025-09-15 20:37:54.386 wdl.w:ptcp INFO input :: job: "call-tar_outputs-75", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "sawfish_vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-75/out/m84036_250809_035451_s4.bc2172_sawfish/m84036_250809_035451_s4.bc2172.sv.vcf.gz.tbi", "sawfish_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-75/out/m84036_250809_035451_s4.bc2172_sawfish/m84036_250809_035451_s4.bc2172.sv.vcf.gz", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-75/out/m84036_250809_035451_s4.bc2172.f8inversion.json", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-75/out/m84036_250809_035451_s4.bc2172_paraphase/m84036_250809_035451_s4.bc2172.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-75/out/m84036_250809_035451_s4.bc2172_paraphase/m84036_250809_035451_s4.bc2172.paraphase.bam", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-75/out/m84036_250809_035451_s4.bc2172_paraphase/m84036_250809_035451_s4.bc2172.paraphase.json", "trgt_spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-75/out/m84036_250809_035451_s4.bc2172.trgt.sorted.spanning.bam.bai", "trgt_spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-75/out/m84036_250809_035451_s4.bc2172.trgt.sorted.spanning.bam", "trgt_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-75/out/m84036_250809_035451_s4.bc2172.trgt.vcf", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-75/out/m84036_250809_035451_s4.bc2172.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-75/out/m84036_250809_035451_s4.bc2172.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2172"}
2025-09-15 20:37:54.396 wdl.w:ptcp.t:call-tar_outputs-75 NOTICE task setup :: name: "tar_outputs", source: "./common.wdl", line: 279, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-75", thread: 140613596997184
2025-09-15 20:37:54.415 wdl.w:ptcp.t:call-tar_outputs-75 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:37:54.415 wdl.w:ptcp.t:call-tar_outputs-75 INFO input :: name: "sawfish_vcf_tbi", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2172.sv.vcf.gz.tbi"
2025-09-15 20:37:54.415 wdl.w:ptcp.t:call-tar_outputs-75 INFO input :: name: "sawfish_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2172.sv.vcf.gz"
2025-09-15 20:37:54.415 wdl.w:ptcp.t:call-tar_outputs-75 INFO input :: name: "f8_json", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2172.f8inversion.json"
2025-09-15 20:37:54.415 wdl.w:ptcp.t:call-tar_outputs-75 INFO input :: name: "paraphase_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2172.paraphase.bam.bai"
2025-09-15 20:37:54.415 wdl.w:ptcp.t:call-tar_outputs-75 INFO input :: name: "paraphase_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2172.paraphase.bam"
2025-09-15 20:37:54.415 wdl.w:ptcp.t:call-tar_outputs-75 INFO input :: name: "paraphase_json", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2172.paraphase.json"
2025-09-15 20:37:54.415 wdl.w:ptcp.t:call-tar_outputs-75 INFO input :: name: "trgt_spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2172.trgt.sorted.spanning.bam.bai"
2025-09-15 20:37:54.415 wdl.w:ptcp.t:call-tar_outputs-75 INFO input :: name: "trgt_spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2172.trgt.sorted.spanning.bam"
2025-09-15 20:37:54.415 wdl.w:ptcp.t:call-tar_outputs-75 INFO input :: name: "trgt_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2172.trgt.vcf"
2025-09-15 20:37:54.415 wdl.w:ptcp.t:call-tar_outputs-75 INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2172.mapped.bam.bai"
2025-09-15 20:37:54.415 wdl.w:ptcp.t:call-tar_outputs-75 INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2172.mapped.bam"
2025-09-15 20:37:54.415 wdl.w:ptcp.t:call-tar_outputs-75 INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2172"
2025-09-15 20:37:54.415 wdl.w:ptcp.t:call-tar_outputs-75 INFO eval :: name: "threads", value: 1
2025-09-15 20:37:54.416 wdl.w:ptcp.t:call-tar_outputs-75 INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:37:54.416 wdl.w:ptcp.t:call-tar_outputs-75 INFO eval :: name: "disk_size", value: 6
2025-09-15 20:37:54.416 wdl.w:ptcp.t:call-tar_outputs-75 INFO eval :: name: "output_tarball", value: "m84036_250809_035451_s4.bc2172.tar"
2025-09-15 20:37:54.416 wdl.w:ptcp.t:call-tar_outputs-75 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:37:54.416 wdl.w:ptcp.t:call-tar_outputs-75 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:37:54.417 wdl.w:ptcp.t:call-tar_outputs-75 INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:37:54.417 wdl.w:ptcp.t:call-tar_outputs-75 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:37:54.492 wdl.w:ptcp.t:call-tar_outputs-75 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 17, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-75/_singularity_tmpdir_8hyvyspu"
2025-09-15 20:37:54.492 wdl.w:ptcp.t:call-tar_outputs-75 INFO Slurm invocation: srun --job-name call-tar_outputs-75 --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-75/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-75/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-75/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-75/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-75/out/m84036_250809_035451_s4.bc2172.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2172.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-75/out/m84036_250809_035451_s4.bc2172.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2172.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-75/out/m84036_250809_035451_s4.bc2172.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2172.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-75/out/m84036_250809_035451_s4.bc2172_sawfish/m84036_250809_035451_s4.bc2172.sv.vcf.gz:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2172.sv.vcf.gz:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-75/out/m84036_250809_035451_s4.bc2172_sawfish/m84036_250809_035451_s4.bc2172.sv.vcf.gz.tbi:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2172.sv.vcf.gz.tbi:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-75/out/m84036_250809_035451_s4.bc2172.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2172.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-75/out/m84036_250809_035451_s4.bc2172.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2172.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-75/out/m84036_250809_035451_s4.bc2172_paraphase/m84036_250809_035451_s4.bc2172.paraphase.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2172.paraphase.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-75/out/m84036_250809_035451_s4.bc2172_paraphase/m84036_250809_035451_s4.bc2172.paraphase.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2172.paraphase.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-75/out/m84036_250809_035451_s4.bc2172_paraphase/m84036_250809_035451_s4.bc2172.paraphase.json:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2172.paraphase.json:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-75/out/m84036_250809_035451_s4.bc2172.f8inversion.json:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2172.f8inversion.json:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-75/_singularity_tmpdir_8hyvyspu/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-75/_singularity_tmpdir_8hyvyspu/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:37:54.495 wdl.w:ptcp.t:call-tar_outputs-75 NOTICE slurm_singularity run :: pid: 1214446, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-75/slurm_singularity.log.txt"
2025-09-15 20:37:55.502 wdl.w:ptcp.t:call-tar_outputs-75.slurm_singularity INFO srun: job 51798419 queued and waiting for resources
2025-09-15 20:37:56.511 wdl.w:ptcp.t:call-tar_outputs-75.slurm_singularity INFO srun: job 51798419 has been allocated resources
2025-09-15 20:37:56.511 wdl.w:ptcp.t:call-tar_outputs-75.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:37:57.008 wdl.w:ptcp.t:call-tar_outputs-75 INFO output :: name: "sample_tarball", value: "m84036_250809_035451_s4.bc2172.tar"
2025-09-15 20:37:57.054 wdl.w:ptcp.t:call-tar_outputs-75 NOTICE done
2025-09-15 20:37:57.076 wdl.w:ptcp NOTICE finish :: job: "call-tar_outputs-75"
2025-09-15 20:37:57.076 wdl.w:ptcp INFO output :: job: "call-tar_outputs-75", values: {"sample_tarball": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-75/out/m84036_250809_035451_s4.bc2172.tar"}
2025-09-15 20:38:05.925 wdl.w:ptcp.w:call-paraphase-91.t:call-run_paraphase.stderr VERBOSE INFO:root:Running analysis for f8inv22 for sample m84036_250809_035451_s4.bc2188 at 2025-09-15 20:37:32.819677...
2025-09-15 20:38:05.926 wdl.w:ptcp.w:call-paraphase-91.t:call-run_paraphase.stderr VERBOSE INFO:root:Realigning reads for f8inv22 for sample m84036_250809_035451_s4.bc2188 at 2025-09-15 20:37:32.820561...
2025-09-15 20:38:05.926 wdl.w:ptcp.w:call-paraphase-91.t:call-run_paraphase.stderr VERBOSE INFO:root:Phasing haplotypes for f8inv22 for sample m84036_250809_035451_s4.bc2188 at 2025-09-15 20:37:34.383271...
2025-09-15 20:38:05.926 wdl.w:ptcp.w:call-paraphase-91.t:call-run_paraphase.stderr VERBOSE INFO:root:Tagging reads for f8inv22 for sample m84036_250809_035451_s4.bc2188 at 2025-09-15 20:37:42.109736...
2025-09-15 20:38:05.926 wdl.w:ptcp.w:call-paraphase-91.t:call-run_paraphase.stderr VERBOSE INFO:root:Generating VCFs for f8inv22 for sample m84036_250809_035451_s4.bc2188 at 2025-09-15 20:37:42.600570...
2025-09-15 20:38:31.440 wdl.w:ptcp.w:call-paraphase-91.t:call-run_paraphase INFO output :: name: "paraphase_bam", value: "m84036_250809_035451_s4.bc2188_paraphase/m84036_250809_035451_s4.bc2188.paraphase.bam"
2025-09-15 20:38:31.443 wdl.w:ptcp.w:call-paraphase-91.t:call-run_paraphase INFO output :: name: "paraphase_bam_bai", value: "m84036_250809_035451_s4.bc2188_paraphase/m84036_250809_035451_s4.bc2188.paraphase.bam.bai"
2025-09-15 20:38:31.445 wdl.w:ptcp.w:call-paraphase-91.t:call-run_paraphase INFO output :: name: "paraphase_json", value: "m84036_250809_035451_s4.bc2188_paraphase/m84036_250809_035451_s4.bc2188.paraphase.json"
2025-09-15 20:38:31.448 wdl.w:ptcp.w:call-paraphase-91.t:call-run_paraphase INFO output :: name: "paraphase_vcfs", value: ["/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2188_paraphase/m84036_250809_035451_s4.bc2188_paraphase_vcfs/m84036_250809_035451_s4.bc2188_cyp21.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2188_paraphase/m84036_250809_035451_s4.bc2188_paraphase_vcfs/m84036_250809_035451_s4.bc2188_f8inv1.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2188_paraphase/m84036_250809_035451_s4.bc2188_paraphase_vcfs/m84036_250809_035451_s4.bc2188_f8inv22.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2188_paraphase/m84036_250809_035451_s4.bc2188_paraphase_vcfs/m84036_250809_035451_s4.bc2188_gba.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2188_paraphase/m84036_250809_035451_s4.bc2188_paraphase_vcfs/m84036_250809_035451_s4.bc2188_hba.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2188_paraphase/m84036_250809_035451_s4.bc2188_paraphase_vcfs/m84036_250809_035451_s4.bc2188_hbb.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2188_paraphase/m84036_250809_035451_s4.bc2188_paraphase_vcfs/m84036_250809_035451_s4.bc2188_rpgr.vcf", "/mnt/miniwdl_task_container/work/m84036_250809_035451_s4.bc2188_paraphase/m84036_250809_035451_s4.bc2188_paraphase_vcfs/m84036_250809_035451_s4.bc2188_smn1.vcf"]
2025-09-15 20:38:31.451 wdl.w:ptcp.w:call-paraphase-91.t:call-run_paraphase INFO output :: name: "havanno_json", value: "m84036_250809_035451_s4.bc2188.havanno.json"
2025-09-15 20:38:31.592 wdl.w:ptcp.w:call-paraphase-91.t:call-run_paraphase NOTICE done
2025-09-15 20:38:31.638 wdl.w:ptcp.w:call-paraphase-91 NOTICE finish :: job: "call-run_paraphase"
2025-09-15 20:38:31.639 wdl.w:ptcp.w:call-paraphase-91 INFO output :: job: "call-run_paraphase", values: {"havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-91/call-run_paraphase/out/m84036_250809_035451_s4.bc2188.havanno.json", "paraphase_vcfs": ["/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-91/call-run_paraphase/out/m84036_250809_035451_s4.bc2188_paraphase/m84036_250809_035451_s4.bc2188_paraphase_vcfs/m84036_250809_035451_s4.bc2188_cyp21.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-91/call-run_paraphase/out/m84036_250809_035451_s4.bc2188_paraphase/m84036_250809_035451_s4.bc2188_paraphase_vcfs/m84036_250809_035451_s4.bc2188_f8inv1.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-91/call-run_paraphase/out/m84036_250809_035451_s4.bc2188_paraphase/m84036_250809_035451_s4.bc2188_paraphase_vcfs/m84036_250809_035451_s4.bc2188_f8inv22.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-91/call-run_paraphase/out/m84036_250809_035451_s4.bc2188_paraphase/m84036_250809_035451_s4.bc2188_paraphase_vcfs/m84036_250809_035451_s4.bc2188_gba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-91/call-run_paraphase/out/m84036_250809_035451_s4.bc2188_paraphase/m84036_250809_035451_s4.bc2188_paraphase_vcfs/m84036_250809_035451_s4.bc2188_hba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-91/call-run_paraphase/out/m84036_250809_035451_s4.bc2188_paraphase/m84036_250809_035451_s4.bc2188_paraphase_vcfs/m84036_250809_035451_s4.bc2188_hbb.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-91/call-run_paraphase/out/m84036_250809_035451_s4.bc2188_paraphase/m84036_250809_035451_s4.bc2188_paraphase_vcfs/m84036_250809_035451_s4.bc2188_rpgr.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-91/call-run_paraphase/out/m84036_250809_035451_s4.bc2188_paraphase/m84036_250809_035451_s4.bc2188_paraphase_vcfs/m84036_250809_035451_s4.bc2188_smn1.vcf"], "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-91/call-run_paraphase/out/m84036_250809_035451_s4.bc2188_paraphase/m84036_250809_035451_s4.bc2188.paraphase.json", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-91/call-run_paraphase/out/m84036_250809_035451_s4.bc2188_paraphase/m84036_250809_035451_s4.bc2188.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-91/call-run_paraphase/out/m84036_250809_035451_s4.bc2188_paraphase/m84036_250809_035451_s4.bc2188.paraphase.bam"}
2025-09-15 20:38:31.639 wdl.w:ptcp.w:call-paraphase-91 NOTICE ready :: job: "call-call_f8", callee: "call_f8"
2025-09-15 20:38:31.639 wdl.w:ptcp.w:call-paraphase-91 INFO input :: job: "call-call_f8", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "genome_version": "38", "out_prefix": "m84036_250809_035451_s4.bc2188", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-91/call-run_paraphase/out/m84036_250809_035451_s4.bc2188_paraphase/m84036_250809_035451_s4.bc2188.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-91/call-run_paraphase/out/m84036_250809_035451_s4.bc2188_paraphase/m84036_250809_035451_s4.bc2188.paraphase.bam", "sex": "F"}
2025-09-15 20:38:31.640 wdl.w:ptcp.w:call-paraphase-91 INFO visit :: node: "output-havanno_json", values: {"havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-91/call-run_paraphase/out/m84036_250809_035451_s4.bc2188.havanno.json"}
2025-09-15 20:38:31.640 wdl.w:ptcp.w:call-paraphase-91 INFO visit :: node: "output-paraphase_bam", values: {"paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-91/call-run_paraphase/out/m84036_250809_035451_s4.bc2188_paraphase/m84036_250809_035451_s4.bc2188.paraphase.bam"}
2025-09-15 20:38:31.640 wdl.w:ptcp.w:call-paraphase-91 INFO visit :: node: "output-paraphase_bam_bai", values: {"paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-91/call-run_paraphase/out/m84036_250809_035451_s4.bc2188_paraphase/m84036_250809_035451_s4.bc2188.paraphase.bam.bai"}
2025-09-15 20:38:31.640 wdl.w:ptcp.w:call-paraphase-91 INFO visit :: node: "output-paraphase_json", values: {"paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-91/call-run_paraphase/out/m84036_250809_035451_s4.bc2188_paraphase/m84036_250809_035451_s4.bc2188.paraphase.json"}
2025-09-15 20:38:31.640 wdl.w:ptcp.w:call-paraphase-91 INFO visit :: node: "output-paraphase_vcfs", values: {"paraphase_vcfs": ["/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-91/call-run_paraphase/out/m84036_250809_035451_s4.bc2188_paraphase/m84036_250809_035451_s4.bc2188_paraphase_vcfs/m84036_250809_035451_s4.bc2188_cyp21.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-91/call-run_paraphase/out/m84036_250809_035451_s4.bc2188_paraphase/m84036_250809_035451_s4.bc2188_paraphase_vcfs/m84036_250809_035451_s4.bc2188_f8inv1.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-91/call-run_paraphase/out/m84036_250809_035451_s4.bc2188_paraphase/m84036_250809_035451_s4.bc2188_paraphase_vcfs/m84036_250809_035451_s4.bc2188_f8inv22.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-91/call-run_paraphase/out/m84036_250809_035451_s4.bc2188_paraphase/m84036_250809_035451_s4.bc2188_paraphase_vcfs/m84036_250809_035451_s4.bc2188_gba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-91/call-run_paraphase/out/m84036_250809_035451_s4.bc2188_paraphase/m84036_250809_035451_s4.bc2188_paraphase_vcfs/m84036_250809_035451_s4.bc2188_hba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-91/call-run_paraphase/out/m84036_250809_035451_s4.bc2188_paraphase/m84036_250809_035451_s4.bc2188_paraphase_vcfs/m84036_250809_035451_s4.bc2188_hbb.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-91/call-run_paraphase/out/m84036_250809_035451_s4.bc2188_paraphase/m84036_250809_035451_s4.bc2188_paraphase_vcfs/m84036_250809_035451_s4.bc2188_rpgr.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-91/call-run_paraphase/out/m84036_250809_035451_s4.bc2188_paraphase/m84036_250809_035451_s4.bc2188_paraphase_vcfs/m84036_250809_035451_s4.bc2188_smn1.vcf"]}
2025-09-15 20:38:31.646 wdl.w:ptcp.w:call-paraphase-91.t:call-call_f8 NOTICE task setup :: name: "call_f8", source: "./paraphase.wdl", line: 232, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-91/call-call_f8", thread: 140611449513536
2025-09-15 20:38:31.660 wdl.w:ptcp.w:call-paraphase-91.t:call-call_f8 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:38:31.660 wdl.w:ptcp.w:call-paraphase-91.t:call-call_f8 INFO input :: name: "genome_version", value: "38"
2025-09-15 20:38:31.660 wdl.w:ptcp.w:call-paraphase-91.t:call-call_f8 INFO input :: name: "out_prefix", value: "m84036_250809_035451_s4.bc2188"
2025-09-15 20:38:31.660 wdl.w:ptcp.w:call-paraphase-91.t:call-call_f8 INFO input :: name: "paraphase_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2188.paraphase.bam.bai"
2025-09-15 20:38:31.660 wdl.w:ptcp.w:call-paraphase-91.t:call-call_f8 INFO input :: name: "paraphase_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2188.paraphase.bam"
2025-09-15 20:38:31.660 wdl.w:ptcp.w:call-paraphase-91.t:call-call_f8 INFO input :: name: "sex", value: "F"
2025-09-15 20:38:31.661 wdl.w:ptcp.w:call-paraphase-91.t:call-call_f8 INFO eval :: name: "threads", value: 1
2025-09-15 20:38:31.661 wdl.w:ptcp.w:call-paraphase-91.t:call-call_f8 INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:38:31.661 wdl.w:ptcp.w:call-paraphase-91.t:call-call_f8 INFO eval :: name: "disk_size", value: 11
2025-09-15 20:38:31.661 wdl.w:ptcp.w:call-paraphase-91.t:call-call_f8 INFO eval :: name: "sample_sex", value: "F"
2025-09-15 20:38:31.661 wdl.w:ptcp.w:call-paraphase-91.t:call-call_f8 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:38:31.661 wdl.w:ptcp.w:call-paraphase-91.t:call-call_f8 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:38:31.662 wdl.w:ptcp.w:call-paraphase-91.t:call-call_f8 INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:38:31.662 wdl.w:ptcp.w:call-paraphase-91.t:call-call_f8 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:38:31.706 wdl.w:ptcp.w:call-paraphase-91.t:call-call_f8 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 8, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-91/call-call_f8/_singularity_tmpdir_zrzkab7f"
2025-09-15 20:38:31.707 wdl.w:ptcp.w:call-paraphase-91.t:call-call_f8 INFO Slurm invocation: srun --job-name call-call_f8 --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-91/call-call_f8/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-91/call-call_f8/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-91/call-call_f8/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-91/call-call_f8/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-91/call-run_paraphase/out/m84036_250809_035451_s4.bc2188_paraphase/m84036_250809_035451_s4.bc2188.paraphase.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2188.paraphase.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-91/call-run_paraphase/out/m84036_250809_035451_s4.bc2188_paraphase/m84036_250809_035451_s4.bc2188.paraphase.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2188.paraphase.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-91/call-call_f8/_singularity_tmpdir_zrzkab7f/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-91/call-call_f8/_singularity_tmpdir_zrzkab7f/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:38:31.711 wdl.w:ptcp.w:call-paraphase-91.t:call-call_f8 NOTICE slurm_singularity run :: pid: 1214744, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-91/call-call_f8/slurm_singularity.log.txt"
2025-09-15 20:38:32.719 wdl.w:ptcp.w:call-paraphase-91.t:call-call_f8.slurm_singularity INFO srun: job 51798421 queued and waiting for resources
2025-09-15 20:38:32.719 wdl.w:ptcp.w:call-paraphase-91.t:call-call_f8.slurm_singularity INFO srun: job 51798421 has been allocated resources
2025-09-15 20:38:32.719 wdl.w:ptcp.w:call-paraphase-91.t:call-call_f8.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:38:33.522 wdl.w:ptcp.w:call-paraphase-91.t:call-call_f8 INFO output :: name: "vcf", value: "m84036_250809_035451_s4.bc2188.f8inversion.vcf"
2025-09-15 20:38:33.524 wdl.w:ptcp.w:call-paraphase-91.t:call-call_f8 INFO output :: name: "json", value: "m84036_250809_035451_s4.bc2188.f8inversion.json"
2025-09-15 20:38:33.572 wdl.w:ptcp.w:call-paraphase-91.t:call-call_f8 NOTICE done
2025-09-15 20:38:33.577 wdl.w:ptcp.w:call-paraphase-91 NOTICE finish :: job: "call-call_f8"
2025-09-15 20:38:33.577 wdl.w:ptcp.w:call-paraphase-91 INFO output :: job: "call-call_f8", values: {"json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-91/call-call_f8/out/m84036_250809_035451_s4.bc2188.f8inversion.json", "vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-91/call-call_f8/out/m84036_250809_035451_s4.bc2188.f8inversion.vcf"}
2025-09-15 20:38:33.577 wdl.w:ptcp.w:call-paraphase-91 INFO visit :: node: "output-f8_json", values: {"f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-91/call-call_f8/out/m84036_250809_035451_s4.bc2188.f8inversion.json"}
2025-09-15 20:38:33.577 wdl.w:ptcp.w:call-paraphase-91 INFO visit :: node: "output-f8_vcf", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-91/call-call_f8/out/m84036_250809_035451_s4.bc2188.f8inversion.vcf"}
2025-09-15 20:38:33.578 wdl.w:ptcp.w:call-paraphase-91 INFO visit :: node: "outputs", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-91/call-call_f8/out/m84036_250809_035451_s4.bc2188.f8inversion.vcf", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-91/call-run_paraphase/out/m84036_250809_035451_s4.bc2188_paraphase/m84036_250809_035451_s4.bc2188.paraphase.json", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-91/call-run_paraphase/out/m84036_250809_035451_s4.bc2188_paraphase/m84036_250809_035451_s4.bc2188.paraphase.bam", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-91/call-run_paraphase/out/m84036_250809_035451_s4.bc2188_paraphase/m84036_250809_035451_s4.bc2188.paraphase.bam.bai", "paraphase_vcfs": ["/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-91/call-run_paraphase/out/m84036_250809_035451_s4.bc2188_paraphase/m84036_250809_035451_s4.bc2188_paraphase_vcfs/m84036_250809_035451_s4.bc2188_cyp21.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-91/call-run_paraphase/out/m84036_250809_035451_s4.bc2188_paraphase/m84036_250809_035451_s4.bc2188_paraphase_vcfs/m84036_250809_035451_s4.bc2188_f8inv1.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-91/call-run_paraphase/out/m84036_250809_035451_s4.bc2188_paraphase/m84036_250809_035451_s4.bc2188_paraphase_vcfs/m84036_250809_035451_s4.bc2188_f8inv22.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-91/call-run_paraphase/out/m84036_250809_035451_s4.bc2188_paraphase/m84036_250809_035451_s4.bc2188_paraphase_vcfs/m84036_250809_035451_s4.bc2188_gba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-91/call-run_paraphase/out/m84036_250809_035451_s4.bc2188_paraphase/m84036_250809_035451_s4.bc2188_paraphase_vcfs/m84036_250809_035451_s4.bc2188_hba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-91/call-run_paraphase/out/m84036_250809_035451_s4.bc2188_paraphase/m84036_250809_035451_s4.bc2188_paraphase_vcfs/m84036_250809_035451_s4.bc2188_hbb.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-91/call-run_paraphase/out/m84036_250809_035451_s4.bc2188_paraphase/m84036_250809_035451_s4.bc2188_paraphase_vcfs/m84036_250809_035451_s4.bc2188_rpgr.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-91/call-run_paraphase/out/m84036_250809_035451_s4.bc2188_paraphase/m84036_250809_035451_s4.bc2188_paraphase_vcfs/m84036_250809_035451_s4.bc2188_smn1.vcf"], "havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-91/call-run_paraphase/out/m84036_250809_035451_s4.bc2188.havanno.json", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-91/call-call_f8/out/m84036_250809_035451_s4.bc2188.f8inversion.json"}
2025-09-15 20:38:33.688 wdl.w:ptcp.w:call-paraphase-91 NOTICE done
2025-09-15 20:38:33.719 wdl.w:ptcp NOTICE finish :: job: "call-paraphase-91"
2025-09-15 20:38:33.720 wdl.w:ptcp INFO output :: job: "call-paraphase-91", values: {"f8_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-91/out/m84036_250809_035451_s4.bc2188.f8inversion.vcf", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-91/out/m84036_250809_035451_s4.bc2188_paraphase/m84036_250809_035451_s4.bc2188.paraphase.json", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-91/out/m84036_250809_035451_s4.bc2188_paraphase/m84036_250809_035451_s4.bc2188.paraphase.bam", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-91/out/m84036_250809_035451_s4.bc2188_paraphase/m84036_250809_035451_s4.bc2188.paraphase.bam.bai", "paraphase_vcfs": ["/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-91/out/m84036_250809_035451_s4.bc2188_paraphase/m84036_250809_035451_s4.bc2188_paraphase_vcfs/m84036_250809_035451_s4.bc2188_cyp21.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-91/out/m84036_250809_035451_s4.bc2188_paraphase/m84036_250809_035451_s4.bc2188_paraphase_vcfs/m84036_250809_035451_s4.bc2188_f8inv1.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-91/out/m84036_250809_035451_s4.bc2188_paraphase/m84036_250809_035451_s4.bc2188_paraphase_vcfs/m84036_250809_035451_s4.bc2188_f8inv22.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-91/out/m84036_250809_035451_s4.bc2188_paraphase/m84036_250809_035451_s4.bc2188_paraphase_vcfs/m84036_250809_035451_s4.bc2188_gba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-91/out/m84036_250809_035451_s4.bc2188_paraphase/m84036_250809_035451_s4.bc2188_paraphase_vcfs/m84036_250809_035451_s4.bc2188_hba.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-91/out/m84036_250809_035451_s4.bc2188_paraphase/m84036_250809_035451_s4.bc2188_paraphase_vcfs/m84036_250809_035451_s4.bc2188_hbb.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-91/out/m84036_250809_035451_s4.bc2188_paraphase/m84036_250809_035451_s4.bc2188_paraphase_vcfs/m84036_250809_035451_s4.bc2188_rpgr.vcf", "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-91/out/m84036_250809_035451_s4.bc2188_paraphase/m84036_250809_035451_s4.bc2188_paraphase_vcfs/m84036_250809_035451_s4.bc2188_smn1.vcf"], "havanno_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-91/out/m84036_250809_035451_s4.bc2188.havanno.json", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-91/out/m84036_250809_035451_s4.bc2188.f8inversion.json"}
2025-09-15 20:38:33.720 wdl.w:ptcp NOTICE ready :: job: "call-tar_outputs-91", callee: "tar_outputs"
2025-09-15 20:38:33.720 wdl.w:ptcp INFO input :: job: "call-tar_outputs-91", values: {"docker_smrttools": "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "sawfish_vcf_tbi": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-91/out/m84036_250809_035451_s4.bc2188_sawfish/m84036_250809_035451_s4.bc2188.sv.vcf.gz.tbi", "sawfish_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-91/out/m84036_250809_035451_s4.bc2188_sawfish/m84036_250809_035451_s4.bc2188.sv.vcf.gz", "f8_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-91/out/m84036_250809_035451_s4.bc2188.f8inversion.json", "paraphase_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-91/out/m84036_250809_035451_s4.bc2188_paraphase/m84036_250809_035451_s4.bc2188.paraphase.bam.bai", "paraphase_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-91/out/m84036_250809_035451_s4.bc2188_paraphase/m84036_250809_035451_s4.bc2188.paraphase.bam", "paraphase_json": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-91/out/m84036_250809_035451_s4.bc2188_paraphase/m84036_250809_035451_s4.bc2188.paraphase.json", "trgt_spanning_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-91/out/m84036_250809_035451_s4.bc2188.trgt.sorted.spanning.bam.bai", "trgt_spanning_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-91/out/m84036_250809_035451_s4.bc2188.trgt.sorted.spanning.bam", "trgt_vcf": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-91/out/m84036_250809_035451_s4.bc2188.trgt.vcf", "mapped_bam_bai": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-91/out/m84036_250809_035451_s4.bc2188.mapped.bam.bai", "mapped_bam": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-91/out/m84036_250809_035451_s4.bc2188.mapped.bam", "sample_name": "m84036_250809_035451_s4.bc2188"}
2025-09-15 20:38:33.723 wdl.w:ptcp INFO visit :: node: "gather-call-paraphase", values: "(((large)))"
2025-09-15 20:38:33.724 wdl.w:ptcp INFO visit :: node: "output-f8_json", values: "(((large)))"
2025-09-15 20:38:33.725 wdl.w:ptcp INFO visit :: node: "output-f8_vcf", values: "(((large)))"
2025-09-15 20:38:33.726 wdl.w:ptcp INFO visit :: node: "output-havanno_json", values: "(((large)))"
2025-09-15 20:38:33.726 wdl.w:ptcp INFO visit :: node: "output-paraphase_bam", values: "(((large)))"
2025-09-15 20:38:33.727 wdl.w:ptcp INFO visit :: node: "output-paraphase_bam_bai", values: "(((large)))"
2025-09-15 20:38:33.728 wdl.w:ptcp INFO visit :: node: "output-paraphase_json", values: "(((large)))"
2025-09-15 20:38:33.729 wdl.w:ptcp INFO visit :: node: "output-paraphase_vcfs", values: "(((large)))"
2025-09-15 20:38:33.730 wdl.w:ptcp.t:call-tar_outputs-91 NOTICE task setup :: name: "tar_outputs", source: "./common.wdl", line: 279, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-91", thread: 140613060126272
2025-09-15 20:38:33.751 wdl.w:ptcp.t:call-tar_outputs-91 INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:38:33.751 wdl.w:ptcp.t:call-tar_outputs-91 INFO input :: name: "sawfish_vcf_tbi", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2188.sv.vcf.gz.tbi"
2025-09-15 20:38:33.752 wdl.w:ptcp.t:call-tar_outputs-91 INFO input :: name: "sawfish_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2188.sv.vcf.gz"
2025-09-15 20:38:33.752 wdl.w:ptcp.t:call-tar_outputs-91 INFO input :: name: "f8_json", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2188.f8inversion.json"
2025-09-15 20:38:33.752 wdl.w:ptcp.t:call-tar_outputs-91 INFO input :: name: "paraphase_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2188.paraphase.bam.bai"
2025-09-15 20:38:33.752 wdl.w:ptcp.t:call-tar_outputs-91 INFO input :: name: "paraphase_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2188.paraphase.bam"
2025-09-15 20:38:33.752 wdl.w:ptcp.t:call-tar_outputs-91 INFO input :: name: "paraphase_json", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2188.paraphase.json"
2025-09-15 20:38:33.752 wdl.w:ptcp.t:call-tar_outputs-91 INFO input :: name: "trgt_spanning_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2188.trgt.sorted.spanning.bam.bai"
2025-09-15 20:38:33.752 wdl.w:ptcp.t:call-tar_outputs-91 INFO input :: name: "trgt_spanning_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2188.trgt.sorted.spanning.bam"
2025-09-15 20:38:33.752 wdl.w:ptcp.t:call-tar_outputs-91 INFO input :: name: "trgt_vcf", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2188.trgt.vcf"
2025-09-15 20:38:33.752 wdl.w:ptcp.t:call-tar_outputs-91 INFO input :: name: "mapped_bam_bai", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2188.mapped.bam.bai"
2025-09-15 20:38:33.752 wdl.w:ptcp.t:call-tar_outputs-91 INFO input :: name: "mapped_bam", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2188.mapped.bam"
2025-09-15 20:38:33.752 wdl.w:ptcp.t:call-tar_outputs-91 INFO input :: name: "sample_name", value: "m84036_250809_035451_s4.bc2188"
2025-09-15 20:38:33.752 wdl.w:ptcp.t:call-tar_outputs-91 INFO eval :: name: "threads", value: 1
2025-09-15 20:38:33.752 wdl.w:ptcp.t:call-tar_outputs-91 INFO eval :: name: "mem_gb", value: 4
2025-09-15 20:38:33.752 wdl.w:ptcp.t:call-tar_outputs-91 INFO eval :: name: "disk_size", value: 6
2025-09-15 20:38:33.753 wdl.w:ptcp.t:call-tar_outputs-91 INFO eval :: name: "output_tarball", value: "m84036_250809_035451_s4.bc2188.tar"
2025-09-15 20:38:33.753 wdl.w:ptcp.t:call-tar_outputs-91 INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 1, memory_reservation: 4000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:38:33.753 wdl.w:ptcp.t:call-tar_outputs-91 WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:38:33.753 wdl.w:ptcp.t:call-tar_outputs-91 INFO provisioned :: seconds_waited: 0, cpu: 1, mem_bytes: 4000000000
2025-09-15 20:38:33.753 wdl.w:ptcp.t:call-tar_outputs-91 INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:38:33.827 wdl.w:ptcp.t:call-tar_outputs-91 INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 17, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-91/_singularity_tmpdir_9s25vd8o"
2025-09-15 20:38:33.827 wdl.w:ptcp.t:call-tar_outputs-91 INFO Slurm invocation: srun --job-name call-tar_outputs-91 --partition compute,compute9 --cpus-per-task 1 --mem 3815M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-91/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-91/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-91/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-91/command:/mnt/miniwdl_task_container/command:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-91/out/m84036_250809_035451_s4.bc2188.f8inversion.json:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2188.f8inversion.json:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-91/out/m84036_250809_035451_s4.bc2188.mapped.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2188.mapped.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-pbmm2_align_hifi-91/out/m84036_250809_035451_s4.bc2188.mapped.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2188.mapped.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-91/out/m84036_250809_035451_s4.bc2188_sawfish/m84036_250809_035451_s4.bc2188.sv.vcf.gz:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2188.sv.vcf.gz:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-sawfish-91/out/m84036_250809_035451_s4.bc2188_sawfish/m84036_250809_035451_s4.bc2188.sv.vcf.gz.tbi:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2188.sv.vcf.gz.tbi:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-91/out/m84036_250809_035451_s4.bc2188.trgt.vcf:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2188.trgt.vcf:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-91/out/m84036_250809_035451_s4.bc2188.trgt.sorted.spanning.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2188.trgt.sorted.spanning.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-trgt-91/out/m84036_250809_035451_s4.bc2188.trgt.sorted.spanning.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2188.trgt.sorted.spanning.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-91/out/m84036_250809_035451_s4.bc2188_paraphase/m84036_250809_035451_s4.bc2188.paraphase.json:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2188.paraphase.json:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-91/out/m84036_250809_035451_s4.bc2188_paraphase/m84036_250809_035451_s4.bc2188.paraphase.bam.bai:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2188.paraphase.bam.bai:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-paraphase-91/out/m84036_250809_035451_s4.bc2188_paraphase/m84036_250809_035451_s4.bc2188.paraphase.bam:/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/m84036_250809_035451_s4.bc2188.paraphase.bam:ro --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-91/_singularity_tmpdir_9s25vd8o/tmp:/tmp --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-91/_singularity_tmpdir_9s25vd8o/var_tmp:/var/tmp /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif
2025-09-15 20:38:33.830 wdl.w:ptcp.t:call-tar_outputs-91 NOTICE slurm_singularity run :: pid: 1214753, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-91/slurm_singularity.log.txt"
2025-09-15 20:38:34.838 wdl.w:ptcp.t:call-tar_outputs-91.slurm_singularity INFO srun: job 51798422 queued and waiting for resources
2025-09-15 20:38:35.847 wdl.w:ptcp.t:call-tar_outputs-91.slurm_singularity INFO srun: job 51798422 has been allocated resources
2025-09-15 20:38:35.847 wdl.w:ptcp.t:call-tar_outputs-91.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:38:36.095 wdl.w:ptcp.t:call-tar_outputs-91 INFO output :: name: "sample_tarball", value: "m84036_250809_035451_s4.bc2188.tar"
2025-09-15 20:38:36.144 wdl.w:ptcp.t:call-tar_outputs-91 NOTICE done
2025-09-15 20:38:36.148 wdl.w:ptcp NOTICE finish :: job: "call-tar_outputs-91"
2025-09-15 20:38:36.149 wdl.w:ptcp INFO output :: job: "call-tar_outputs-91", values: {"sample_tarball": "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-tar_outputs-91/out/m84036_250809_035451_s4.bc2188.tar"}
2025-09-15 20:38:36.149 wdl.w:ptcp INFO visit :: node: "gather-call-tar_outputs", values: "(((large)))"
2025-09-15 20:38:36.150 wdl.w:ptcp NOTICE ready :: job: "call-ptcp_qc", callee: "ptcp_qc"
2025-09-15 20:38:36.150 wdl.w:ptcp INFO input :: job: "call-ptcp_qc", values: "(((large)))"
2025-09-15 20:38:36.155 wdl.w:ptcp.t:call-ptcp_qc NOTICE task setup :: name: "ptcp_qc", source: "./common.wdl", line: 394, column: 1, dir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-ptcp_qc", thread: 140607657846336
2025-09-15 20:38:36.273 wdl.w:ptcp.t:call-ptcp_qc INFO input :: name: "docker_smrttools", value: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
2025-09-15 20:38:36.273 wdl.w:ptcp.t:call-ptcp_qc INFO input :: name: "pt_linear_regression", value: null
2025-09-15 20:38:36.273 wdl.w:ptcp.t:call-ptcp_qc INFO input :: name: "qc_bed", value: "/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/ptcp-qc.GRCh38.bed"
2025-09-15 20:38:36.273 wdl.w:ptcp.t:call-ptcp_qc INFO input :: name: "tarballs", value: "(((large)))"
2025-09-15 20:38:36.274 wdl.w:ptcp.t:call-ptcp_qc INFO eval :: name: "mem_gb", value: 8
2025-09-15 20:38:36.274 wdl.w:ptcp.t:call-ptcp_qc INFO eval :: name: "threads", value: 16
2025-09-15 20:38:36.274 wdl.w:ptcp.t:call-ptcp_qc INFO eval :: name: "disk_size", value: 192
2025-09-15 20:38:36.274 wdl.w:ptcp.t:call-ptcp_qc INFO eval :: name: "output_dir", value: "ptcp_qc"
2025-09-15 20:38:36.274 wdl.w:ptcp.t:call-ptcp_qc INFO eval :: name: "output_prefix", value: "qc"
2025-09-15 20:38:36.274 wdl.w:ptcp.t:call-ptcp_qc INFO eval :: name: "manifest_filename", value: "input_manifest.json"
2025-09-15 20:38:36.274 wdl.w:ptcp.t:call-ptcp_qc INFO effective runtime :: docker: "quay.io/pacbio/smrttools@sha256:01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", cpu: 16, memory_reservation: 8000000000, maxRetries: 2, slurm_partition: "compute,compute9"
2025-09-15 20:38:36.275 wdl.w:ptcp.t:call-ptcp_qc WARNING ignored runtime settings :: keys: ["disk", "disks"]
2025-09-15 20:38:36.276 wdl.w:ptcp.t:call-ptcp_qc INFO provisioned :: seconds_waited: 0, cpu: 16, mem_bytes: 8000000000
2025-09-15 20:38:36.276 wdl.w:ptcp.t:call-ptcp_qc INFO Singularity SIF found in image cache directory :: sif: "/home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif"
2025-09-15 20:38:36.716 wdl.w:ptcp.t:call-ptcp_qc INFO singularity invocation :: args: "/usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv /home/dnasko/projects/griffin/run_ptcp/ptcp-v3.1.0/miniwdl_singularity_cache/docker___quay.io_pacbio_smrttools@sha256_01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b.sif", binds: 103, tmpdir: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-ptcp_qc/_singularity_tmpdir_i_n0nmhi"
2025-09-15 20:38:36.717 wdl.w:ptcp.t:call-ptcp_qc INFO Slurm invocation: srun --job-name call-ptcp_qc --partition compute,compute9 --cpus-per-task 16 --mem 7629M /usr/bin/singularity exec --pwd /mnt/miniwdl_task_container/work --containall --nv --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-ptcp_qc/stdout.txt:/mnt/miniwdl_task_container/stdout.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-ptcp_qc/stderr.txt:/mnt/miniwdl_task_container/stderr.txt --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-ptcp_qc/work:/mnt/miniwdl_task_container/work --bind /datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-ptcp_qc/command:/mnt/miniwdl_task_container/command:ro --bind 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2025-09-15 20:38:36.720 wdl.w:ptcp.t:call-ptcp_qc NOTICE slurm_singularity run :: pid: 1214763, log: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-ptcp_qc/slurm_singularity.log.txt"
2025-09-15 20:38:37.729 wdl.w:ptcp.t:call-ptcp_qc.slurm_singularity INFO srun: job 51798423 queued and waiting for resources
2025-09-15 20:38:38.739 wdl.w:ptcp.t:call-ptcp_qc.slurm_singularity INFO srun: job 51798423 has been allocated resources
2025-09-15 20:38:38.739 wdl.w:ptcp.t:call-ptcp_qc.slurm_singularity INFO WARNING: Could not find any nv files on this host!
2025-09-15 20:40:11.680 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:39:27 [INFO] - Running ptcp-qc-0.8.0 [analyze]
2025-09-15 20:40:11.681 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:39:27 [WARN] - Subgroup overlap in the input targets bed file: 'AFF2:AFF2_v1' (chrX:148499250-148502505) overlaps with 'AFF2:FRAXE_AFF2' (chrX:148500605-148500753), read assignment within the subgroups of a group may be ambiguous.
2025-09-15 20:40:11.681 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:39:27 [WARN] - Subgroup overlap in the input targets bed file: 'hba:hba_MEDII_BRIT' (chr16:146738-185285) overlaps with 'hba:hba_alpha20.5_BRIT' (chr16:156652-185285), read assignment within the subgroups of a group may be ambiguous.
2025-09-15 20:40:11.681 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:39:27 [WARN] - Subgroup overlap in the input targets bed file: 'hba:hba_MEDII_BRIT' (chr16:146738-185285) overlaps with 'hba:hba_4.2_3.7' (chr16:168820-178426), read assignment within the subgroups of a group may be ambiguous.
2025-09-15 20:40:11.681 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:39:27 [WARN] - Subgroup overlap in the input targets bed file: 'hba:hba_alpha20.5_BRIT' (chr16:156652-185285) overlaps with 'hba:hba_4.2_3.7' (chr16:168820-178426), read assignment within the subgroups of a group may be ambiguous.
2025-09-15 20:40:11.681 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:39:27 [INFO] - Analyzing 96 samples with 48 carrier groups.
2025-09-15 20:40:11.681 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:39:27 [INFO] - Running analysis for sample m84036_250809_035451_s4.bc2145
2025-09-15 20:40:11.681 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:39:27 [INFO] - Running analysis for sample m84036_250809_035451_s4.bc2110
2025-09-15 20:40:11.681 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:39:27 [INFO] - Running analysis for sample m84036_250809_035451_s4.bc2146
2025-09-15 20:40:11.681 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:39:27 [INFO] - Running analysis for sample m84036_250809_035451_s4.bc2119
2025-09-15 20:40:11.681 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:39:27 [INFO] - Running analysis for sample m84036_250809_035451_s4.bc2109
2025-09-15 20:40:11.681 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:39:27 [INFO] - Running analysis for sample m84036_250809_035451_s4.bc2121
2025-09-15 20:40:11.681 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:39:27 [INFO] - Running analysis for sample m84036_250809_035451_s4.bc2151
2025-09-15 20:40:11.681 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:39:27 [INFO] - Running analysis for sample m84036_250809_035451_s4.bc2169
2025-09-15 20:40:11.681 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:39:27 [INFO] - Running analysis for sample m84036_250809_035451_s4.bc2120
2025-09-15 20:40:11.681 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:39:27 [INFO] - Running analysis for sample m84036_250809_035451_s4.bc2147
2025-09-15 20:40:11.681 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:39:27 [INFO] - Running analysis for sample m84036_250809_035451_s4.bc2097
2025-09-15 20:40:11.681 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:39:27 [INFO] - Running analysis for sample m84036_250809_035451_s4.bc2112
2025-09-15 20:40:11.681 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:39:27 [INFO] - Running analysis for sample m84036_250809_035451_s4.bc2118
2025-09-15 20:40:11.681 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:39:27 [INFO] - Running analysis for sample m84036_250809_035451_s4.bc2148
2025-09-15 20:40:11.681 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:39:27 [INFO] - Running analysis for sample m84036_250809_035451_s4.bc2115
2025-09-15 20:40:11.682 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:39:27 [INFO] - Running analysis for sample m84036_250809_035451_s4.bc2157
2025-09-15 20:40:11.682 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:39:49 [DEBUG] - Writing to ptcp_qc/qc.m84036_250809_035451_s4.bc2148.json
2025-09-15 20:40:11.682 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:39:49 [DEBUG] - Writing to ptcp_qc/qc.m84036_250809_035451_s4.bc2147.json
2025-09-15 20:40:11.682 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:39:49 [DEBUG] - Writing to ptcp_qc/qc.m84036_250809_035451_s4.bc2151.json
2025-09-15 20:40:11.682 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:39:49 [DEBUG] - Writing to ptcp_qc/qc.m84036_250809_035451_s4.bc2120.json
2025-09-15 20:40:11.682 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:39:49 [INFO] - Running analysis for sample m84036_250809_035451_s4.bc2149
2025-09-15 20:40:11.682 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:39:49 [DEBUG] - Writing to ptcp_qc/qc.m84036_250809_035451_s4.bc2157.json
2025-09-15 20:40:11.682 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:39:49 [DEBUG] - Writing to ptcp_qc/qc.m84036_250809_035451_s4.bc2119.json
2025-09-15 20:40:11.682 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:39:49 [DEBUG] - Writing to ptcp_qc/qc.m84036_250809_035451_s4.bc2118.json
2025-09-15 20:40:11.682 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:39:49 [DEBUG] - Writing to ptcp_qc/qc.m84036_250809_035451_s4.bc2109.json
2025-09-15 20:40:11.682 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:39:49 [INFO] - Running analysis for sample m84036_250809_035451_s4.bc2133
2025-09-15 20:40:11.682 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:39:49 [DEBUG] - Writing to ptcp_qc/qc.m84036_250809_035451_s4.bc2145.json
2025-09-15 20:40:11.682 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:39:49 [DEBUG] - Writing to ptcp_qc/qc.m84036_250809_035451_s4.bc2169.json
2025-09-15 20:40:11.682 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:39:49 [INFO] - Running analysis for sample m84036_250809_035451_s4.bc2152
2025-09-15 20:40:11.682 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:39:49 [DEBUG] - Writing to ptcp_qc/qc.m84036_250809_035451_s4.bc2121.json
2025-09-15 20:40:11.682 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:39:49 [INFO] - Running analysis for sample m84036_250809_035451_s4.bc2116
2025-09-15 20:40:11.682 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:39:49 [DEBUG] - Writing to ptcp_qc/qc.m84036_250809_035451_s4.bc2146.json
2025-09-15 20:40:11.682 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:39:49 [DEBUG] - Writing to ptcp_qc/qc.m84036_250809_035451_s4.bc2115.json
2025-09-15 20:40:11.682 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:39:49 [DEBUG] - Writing to ptcp_qc/qc.m84036_250809_035451_s4.bc2110.json
2025-09-15 20:40:11.682 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:39:49 [INFO] - Running analysis for sample m84036_250809_035451_s4.bc2150
2025-09-15 20:40:11.682 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:39:49 [INFO] - Running analysis for sample m84036_250809_035451_s4.bc2158
2025-09-15 20:40:11.682 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:39:49 [DEBUG] - Writing to ptcp_qc/qc.m84036_250809_035451_s4.bc2112.json
2025-09-15 20:40:11.682 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:39:50 [INFO] - Running analysis for sample m84036_250809_035451_s4.bc2154
2025-09-15 20:40:11.683 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:39:53 [INFO] - Running analysis for sample m84036_250809_035451_s4.bc2139
2025-09-15 20:40:11.683 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:39:53 [INFO] - Running analysis for sample m84036_250809_035451_s4.bc2153
2025-09-15 20:40:11.683 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:39:53 [INFO] - Running analysis for sample m84036_250809_035451_s4.bc2170
2025-09-15 20:40:11.683 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:39:53 [INFO] - Running analysis for sample m84036_250809_035451_s4.bc2122
2025-09-15 20:40:11.683 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:39:53 [INFO] - Running analysis for sample m84036_250809_035451_s4.bc2136
2025-09-15 20:40:11.683 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:39:53 [INFO] - Running analysis for sample m84036_250809_035451_s4.bc2155
2025-09-15 20:40:11.683 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:39:55 [INFO] - Running analysis for sample m84036_250809_035451_s4.bc2113
2025-09-15 20:40:11.683 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:39:56 [INFO] - Running analysis for sample m84036_250809_035451_s4.bc2111
2025-09-15 20:40:11.683 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:39:59 [DEBUG] - Writing to ptcp_qc/qc.m84036_250809_035451_s4.bc2097.json
2025-09-15 20:40:11.683 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:40:01 [INFO] - Running analysis for sample m84036_250809_035451_s4.bc2098
2025-09-15 20:40:11.683 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:40:05 [DEBUG] - Writing to ptcp_qc/qc.m84036_250809_035451_s4.bc2152.json
2025-09-15 20:40:11.683 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:40:05 [DEBUG] - Writing to ptcp_qc/qc.m84036_250809_035451_s4.bc2158.json
2025-09-15 20:40:11.683 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:40:05 [DEBUG] - Writing to ptcp_qc/qc.m84036_250809_035451_s4.bc2149.json
2025-09-15 20:40:11.683 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:40:05 [DEBUG] - Writing to ptcp_qc/qc.m84036_250809_035451_s4.bc2150.json
2025-09-15 20:40:11.683 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:40:05 [DEBUG] - Writing to ptcp_qc/qc.m84036_250809_035451_s4.bc2133.json
2025-09-15 20:40:11.683 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:40:05 [INFO] - Running analysis for sample m84036_250809_035451_s4.bc2163
2025-09-15 20:40:11.683 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:40:06 [INFO] - Running analysis for sample m84036_250809_035451_s4.bc2159
2025-09-15 20:40:11.683 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:40:07 [INFO] - Running analysis for sample m84036_250809_035451_s4.bc2137
2025-09-15 20:40:11.683 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:40:08 [INFO] - Running analysis for sample m84036_250809_035451_s4.bc2138
2025-09-15 20:40:11.683 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:40:08 [INFO] - Running analysis for sample m84036_250809_035451_s4.bc2134
2025-09-15 20:40:11.683 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:40:08 [DEBUG] - Writing to ptcp_qc/qc.m84036_250809_035451_s4.bc2154.json
2025-09-15 20:40:11.683 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:40:08 [DEBUG] - Writing to ptcp_qc/qc.m84036_250809_035451_s4.bc2153.json
2025-09-15 20:40:11.683 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:40:08 [DEBUG] - Writing to ptcp_qc/qc.m84036_250809_035451_s4.bc2170.json
2025-09-15 20:40:11.684 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:40:08 [DEBUG] - Writing to ptcp_qc/qc.m84036_250809_035451_s4.bc2116.json
2025-09-15 20:40:20.772 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:40:10 [INFO] - Running analysis for sample m84036_250809_035451_s4.bc2156
2025-09-15 20:40:20.772 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:40:11 [DEBUG] - Writing to ptcp_qc/qc.m84036_250809_035451_s4.bc2155.json
2025-09-15 20:40:20.772 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:40:14 [INFO] - Running analysis for sample m84036_250809_035451_s4.bc2166
2025-09-15 20:40:20.772 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:40:15 [INFO] - Running analysis for sample m84036_250809_035451_s4.bc2171
2025-09-15 20:40:20.772 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:40:15 [INFO] - Running analysis for sample m84036_250809_035451_s4.bc2117
2025-09-15 20:40:20.772 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:40:15 [DEBUG] - Writing to ptcp_qc/qc.m84036_250809_035451_s4.bc2122.json
2025-09-15 20:40:20.772 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:40:15 [INFO] - Running analysis for sample m84036_250809_035451_s4.bc2135
2025-09-15 20:40:20.772 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:40:15 [INFO] - Running analysis for sample m84036_250809_035451_s4.bc2123
2025-09-15 20:40:20.772 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:40:16 [DEBUG] - Writing to ptcp_qc/qc.m84036_250809_035451_s4.bc2139.json
2025-09-15 20:40:29.874 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:40:20 [DEBUG] - Writing to ptcp_qc/qc.m84036_250809_035451_s4.bc2136.json
2025-09-15 20:40:29.875 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:40:20 [DEBUG] - Writing to ptcp_qc/qc.m84036_250809_035451_s4.bc2113.json
2025-09-15 20:40:29.875 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:40:20 [INFO] - Running analysis for sample m84036_250809_035451_s4.bc2140
2025-09-15 20:40:29.875 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:40:21 [DEBUG] - Writing to ptcp_qc/qc.m84036_250809_035451_s4.bc2111.json
2025-09-15 20:40:29.875 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:40:21 [INFO] - Running analysis for sample m84036_250809_035451_s4.bc2181
2025-09-15 20:40:29.875 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:40:21 [DEBUG] - Writing to ptcp_qc/qc.m84036_250809_035451_s4.bc2163.json
2025-09-15 20:40:29.875 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:40:21 [INFO] - Running analysis for sample m84036_250809_035451_s4.bc2114
2025-09-15 20:40:29.875 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:40:24 [INFO] - Running analysis for sample m84036_250809_035451_s4.bc2187
2025-09-15 20:40:29.875 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:40:25 [INFO] - Running analysis for sample m84036_250809_035451_s4.bc2164
2025-09-15 20:40:29.875 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:40:25 [DEBUG] - Writing to ptcp_qc/qc.m84036_250809_035451_s4.bc2159.json
2025-09-15 20:40:29.875 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:40:25 [DEBUG] - Writing to ptcp_qc/qc.m84036_250809_035451_s4.bc2098.json
2025-09-15 20:40:32.909 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:40:27 [INFO] - Running analysis for sample m84036_250809_035451_s4.bc2160
2025-09-15 20:40:32.909 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:40:28 [INFO] - Running analysis for sample m84036_250809_035451_s4.bc2099
2025-09-15 20:40:32.909 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:40:28 [DEBUG] - Writing to ptcp_qc/qc.m84036_250809_035451_s4.bc2134.json
2025-09-15 20:40:32.909 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:40:28 [DEBUG] - Writing to ptcp_qc/qc.m84036_250809_035451_s4.bc2138.json
2025-09-15 20:40:32.909 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:40:28 [DEBUG] - Writing to ptcp_qc/qc.m84036_250809_035451_s4.bc2137.json
2025-09-15 20:40:32.910 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:40:28 [INFO] - Running analysis for sample m84036_250809_035451_s4.bc2184
2025-09-15 20:40:32.910 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:40:29 [DEBUG] - Writing to ptcp_qc/qc.m84036_250809_035451_s4.bc2166.json
2025-09-15 20:40:32.910 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:40:29 [INFO] - Running analysis for sample m84036_250809_035451_s4.bc2142
2025-09-15 20:40:32.910 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:40:29 [DEBUG] - Writing to ptcp_qc/qc.m84036_250809_035451_s4.bc2117.json
2025-09-15 20:40:32.910 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:40:29 [DEBUG] - Writing to ptcp_qc/qc.m84036_250809_035451_s4.bc2171.json
2025-09-15 20:40:32.910 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:40:29 [INFO] - Running analysis for sample m84036_250809_035451_s4.bc2127
2025-09-15 20:40:32.910 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:40:30 [INFO] - Running analysis for sample m84036_250809_035451_s4.bc2167
2025-09-15 20:40:42.001 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:40:31 [DEBUG] - Writing to ptcp_qc/qc.m84036_250809_035451_s4.bc2135.json
2025-09-15 20:40:42.002 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:40:31 [INFO] - Running analysis for sample m84036_250809_035451_s4.bc2124
2025-09-15 20:40:42.002 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:40:31 [DEBUG] - Writing to ptcp_qc/qc.m84036_250809_035451_s4.bc2181.json
2025-09-15 20:40:42.002 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:40:31 [INFO] - Running analysis for sample m84036_250809_035451_s4.bc2172
2025-09-15 20:40:42.002 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:40:33 [INFO] - Running analysis for sample m84036_250809_035451_s4.bc2190
2025-09-15 20:40:42.002 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:40:36 [INFO] - Running analysis for sample m84036_250809_035451_s4.bc2182
2025-09-15 20:40:42.002 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:40:38 [DEBUG] - Writing to ptcp_qc/qc.m84036_250809_035451_s4.bc2123.json
2025-09-15 20:40:42.002 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:40:38 [DEBUG] - Writing to ptcp_qc/qc.m84036_250809_035451_s4.bc2156.json
2025-09-15 20:40:42.002 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:40:38 [DEBUG] - Writing to ptcp_qc/qc.m84036_250809_035451_s4.bc2164.json
2025-09-15 20:40:42.002 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:40:38 [INFO] - Running analysis for sample m84036_250809_035451_s4.bc2161
2025-09-15 20:40:42.002 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:40:38 [INFO] - Running analysis for sample m84036_250809_035451_s4.bc2141
2025-09-15 20:40:42.002 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:40:38 [DEBUG] - Writing to ptcp_qc/qc.m84036_250809_035451_s4.bc2187.json
2025-09-15 20:40:42.002 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:40:38 [INFO] - Running analysis for sample m84036_250809_035451_s4.bc2165
2025-09-15 20:40:42.002 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:40:38 [DEBUG] - Writing to ptcp_qc/qc.m84036_250809_035451_s4.bc2140.json
2025-09-15 20:40:42.002 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:40:38 [DEBUG] - Writing to ptcp_qc/qc.m84036_250809_035451_s4.bc2114.json
2025-09-15 20:40:42.002 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:40:38 [INFO] - Running analysis for sample m84036_250809_035451_s4.bc2188
2025-09-15 20:40:42.002 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:40:39 [INFO] - Running analysis for sample m84036_250809_035451_s4.bc2143
2025-09-15 20:40:51.097 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:40:43 [INFO] - Running analysis for sample m84036_250809_035451_s4.bc2191
2025-09-15 20:40:51.097 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:40:43 [DEBUG] - Writing to ptcp_qc/qc.m84036_250809_035451_s4.bc2184.json
2025-09-15 20:40:51.097 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:40:44 [INFO] - Running analysis for sample m84036_250809_035451_s4.bc2185
2025-09-15 20:40:51.097 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:40:45 [DEBUG] - Writing to ptcp_qc/qc.m84036_250809_035451_s4.bc2160.json
2025-09-15 20:40:51.097 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:40:45 [DEBUG] - Writing to ptcp_qc/qc.m84036_250809_035451_s4.bc2167.json
2025-09-15 20:40:51.097 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:40:45 [DEBUG] - Writing to ptcp_qc/qc.m84036_250809_035451_s4.bc2172.json
2025-09-15 20:40:51.097 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:40:45 [INFO] - Running analysis for sample m84036_250809_035451_s4.bc2189
2025-09-15 20:40:51.097 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:40:45 [DEBUG] - Writing to ptcp_qc/qc.m84036_250809_035451_s4.bc2099.json
2025-09-15 20:40:51.097 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:40:45 [INFO] - Running analysis for sample m84036_250809_035451_s4.bc2168
2025-09-15 20:40:51.097 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:40:45 [INFO] - Running analysis for sample m84036_250809_035451_s4.bc2173
2025-09-15 20:40:51.097 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:40:45 [DEBUG] - Writing to ptcp_qc/qc.m84036_250809_035451_s4.bc2142.json
2025-09-15 20:40:51.097 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:40:45 [DEBUG] - Writing to ptcp_qc/qc.m84036_250809_035451_s4.bc2127.json
2025-09-15 20:40:51.098 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:40:45 [DEBUG] - Writing to ptcp_qc/qc.m84036_250809_035451_s4.bc2190.json
2025-09-15 20:40:51.098 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:40:45 [INFO] - Running analysis for sample m84036_250809_035451_s4.bc2100
2025-09-15 20:40:51.098 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:40:45 [DEBUG] - Writing to ptcp_qc/qc.m84036_250809_035451_s4.bc2182.json
2025-09-15 20:40:51.098 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:40:45 [DEBUG] - Writing to ptcp_qc/qc.m84036_250809_035451_s4.bc2165.json
2025-09-15 20:40:51.098 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:40:46 [DEBUG] - Writing to ptcp_qc/qc.m84036_250809_035451_s4.bc2124.json
2025-09-15 20:40:51.098 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:40:46 [INFO] - Running analysis for sample m84036_250809_035451_s4.bc2128
2025-09-15 20:40:51.098 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:40:46 [INFO] - Running analysis for sample m84036_250809_035451_s4.bc2125
2025-09-15 20:40:51.098 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:40:46 [DEBUG] - Writing to ptcp_qc/qc.m84036_250809_035451_s4.bc2141.json
2025-09-15 20:40:51.098 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:40:46 [INFO] - Running analysis for sample m84036_250809_035451_s4.bc2175
2025-09-15 20:40:51.098 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:40:46 [INFO] - Running analysis for sample m84036_250809_035451_s4.bc2183
2025-09-15 20:40:54.127 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:40:48 [DEBUG] - Writing to ptcp_qc/qc.m84036_250809_035451_s4.bc2191.json
2025-09-15 20:40:54.127 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:40:48 [INFO] - Running analysis for sample m84036_250809_035451_s4.bc2126
2025-09-15 20:40:54.128 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:40:51 [INFO] - Running analysis for sample m84036_250809_035451_s4.bc2144
2025-09-15 20:41:03.222 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:40:54 [INFO] - Running analysis for sample m84036_250809_035451_s4.bc2186
2025-09-15 20:41:03.222 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:40:54 [INFO] - Running analysis for sample m84036_250809_035451_s4.bc2192
2025-09-15 20:41:03.222 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:40:54 [DEBUG] - Writing to ptcp_qc/qc.m84036_250809_035451_s4.bc2188.json
2025-09-15 20:41:03.223 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:40:58 [INFO] - Running analysis for sample m84036_250809_035451_s4.bc2174
2025-09-15 20:41:03.223 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:40:58 [DEBUG] - Writing to ptcp_qc/qc.m84036_250809_035451_s4.bc2143.json
2025-09-15 20:41:03.223 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:40:58 [DEBUG] - Writing to ptcp_qc/qc.m84036_250809_035451_s4.bc2161.json
2025-09-15 20:41:03.223 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:40:58 [INFO] - Running analysis for sample m84036_250809_035451_s4.bc2178
2025-09-15 20:41:03.223 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:40:58 [INFO] - Running analysis for sample m84036_250809_035451_s4.bc2162
2025-09-15 20:41:03.223 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:40:58 [DEBUG] - Writing to ptcp_qc/qc.m84036_250809_035451_s4.bc2185.json
2025-09-15 20:41:03.223 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:40:58 [DEBUG] - Writing to ptcp_qc/qc.m84036_250809_035451_s4.bc2173.json
2025-09-15 20:41:03.223 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:40:58 [DEBUG] - Writing to ptcp_qc/qc.m84036_250809_035451_s4.bc2189.json
2025-09-15 20:41:03.223 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:40:58 [INFO] - Running analysis for sample m84036_250809_035451_s4.bc2179
2025-09-15 20:41:03.223 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:40:58 [INFO] - Running analysis for sample m84036_250809_035451_s4.bc2176
2025-09-15 20:41:06.253 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:40:59 [INFO] - Running analysis for sample m84036_250809_035451_s4.bc2103
2025-09-15 20:41:06.253 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:41:01 [DEBUG] - Writing to ptcp_qc/qc.m84036_250809_035451_s4.bc2168.json
2025-09-15 20:41:06.253 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:41:02 [DEBUG] - Writing to ptcp_qc/qc.m84036_250809_035451_s4.bc2183.json
2025-09-15 20:41:06.253 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:41:02 [DEBUG] - Writing to ptcp_qc/qc.m84036_250809_035451_s4.bc2175.json
2025-09-15 20:41:06.253 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:41:02 [INFO] - Running analysis for sample m84036_250809_035451_s4.bc2106
2025-09-15 20:41:06.253 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:41:02 [INFO] - Running analysis for sample m84036_250809_035451_s4.bc2107
2025-09-15 20:41:06.253 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:41:02 [INFO] - Running analysis for sample m84036_250809_035451_s4.bc2177
2025-09-15 20:41:06.253 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:41:02 [DEBUG] - Writing to ptcp_qc/qc.m84036_250809_035451_s4.bc2186.json
2025-09-15 20:41:06.253 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:41:03 [DEBUG] - Writing to ptcp_qc/qc.m84036_250809_035451_s4.bc2100.json
2025-09-15 20:41:06.253 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:41:03 [DEBUG] - Writing to ptcp_qc/qc.m84036_250809_035451_s4.bc2125.json
2025-09-15 20:41:09.285 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:41:04 [DEBUG] - Writing to ptcp_qc/qc.m84036_250809_035451_s4.bc2128.json
2025-09-15 20:41:18.392 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:41:11 [DEBUG] - Writing to ptcp_qc/qc.m84036_250809_035451_s4.bc2144.json
2025-09-15 20:41:18.392 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:41:11 [DEBUG] - Writing to ptcp_qc/qc.m84036_250809_035451_s4.bc2126.json
2025-09-15 20:41:18.392 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:41:11 [INFO] - Running analysis for sample m84036_250809_035451_s4.bc2104
2025-09-15 20:41:18.392 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:41:11 [INFO] - Running analysis for sample m84036_250809_035451_s4.bc2101
2025-09-15 20:41:18.392 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:41:11 [INFO] - Running analysis for sample m84036_250809_035451_s4.bc2129
2025-09-15 20:41:18.392 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:41:11 [INFO] - Running analysis for sample m84036_250809_035451_s4.bc2102
2025-09-15 20:41:18.392 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:41:12 [INFO] - Running analysis for sample m84036_250809_035451_s4.bc2180
2025-09-15 20:41:18.392 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:41:15 [INFO] - Running analysis for sample m84036_250809_035451_s4.bc2130
2025-09-15 20:41:27.481 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:41:16 [DEBUG] - Writing to ptcp_qc/qc.m84036_250809_035451_s4.bc2192.json
2025-09-15 20:41:27.482 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:41:16 [DEBUG] - Writing to ptcp_qc/qc.m84036_250809_035451_s4.bc2176.json
2025-09-15 20:41:30.530 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:41:20 [DEBUG] - Writing to ptcp_qc/qc.m84036_250809_035451_s4.bc2179.json
2025-09-15 20:41:30.530 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:41:24 [INFO] - Running analysis for sample m84036_250809_035451_s4.bc2131
2025-09-15 20:41:30.530 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:41:24 [DEBUG] - Writing to ptcp_qc/qc.m84036_250809_035451_s4.bc2174.json
2025-09-15 20:41:30.530 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:41:24 [DEBUG] - Writing to ptcp_qc/qc.m84036_250809_035451_s4.bc2178.json
2025-09-15 20:41:30.530 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:41:26 [INFO] - Running analysis for sample m84036_250809_035451_s4.bc2105
2025-09-15 20:41:30.530 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:41:27 [INFO] - Running analysis for sample m84036_250809_035451_s4.bc2108
2025-09-15 20:41:30.530 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:41:27 [INFO] - Running analysis for sample m84036_250809_035451_s4.bc2132
2025-09-15 20:41:33.563 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:41:28 [DEBUG] - Writing to ptcp_qc/qc.m84036_250809_035451_s4.bc2162.json
2025-09-15 20:41:42.657 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:41:35 [DEBUG] - Writing to ptcp_qc/qc.m84036_250809_035451_s4.bc2177.json
2025-09-15 20:41:42.657 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:41:39 [DEBUG] - Writing to ptcp_qc/qc.m84036_250809_035451_s4.bc2106.json
2025-09-15 20:41:42.657 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:41:39 [DEBUG] - Writing to ptcp_qc/qc.m84036_250809_035451_s4.bc2103.json
2025-09-15 20:41:42.657 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:41:39 [DEBUG] - Writing to ptcp_qc/qc.m84036_250809_035451_s4.bc2180.json
2025-09-15 20:41:42.657 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:41:39 [DEBUG] - Writing to ptcp_qc/qc.m84036_250809_035451_s4.bc2101.json
2025-09-15 20:41:42.657 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:41:39 [DEBUG] - Writing to ptcp_qc/qc.m84036_250809_035451_s4.bc2107.json
2025-09-15 20:41:42.657 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:41:39 [DEBUG] - Writing to ptcp_qc/qc.m84036_250809_035451_s4.bc2104.json
2025-09-15 20:41:42.657 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:41:39 [DEBUG] - Writing to ptcp_qc/qc.m84036_250809_035451_s4.bc2129.json
2025-09-15 20:41:42.657 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:41:39 [DEBUG] - Writing to ptcp_qc/qc.m84036_250809_035451_s4.bc2102.json
2025-09-15 20:41:42.657 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:41:40 [DEBUG] - Writing to ptcp_qc/qc.m84036_250809_035451_s4.bc2130.json
2025-09-15 20:41:42.657 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:41:40 [DEBUG] - Writing to ptcp_qc/qc.m84036_250809_035451_s4.bc2108.json
2025-09-15 20:41:42.657 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:41:40 [DEBUG] - Writing to ptcp_qc/qc.m84036_250809_035451_s4.bc2131.json
2025-09-15 20:41:42.657 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:41:40 [DEBUG] - Writing to ptcp_qc/qc.m84036_250809_035451_s4.bc2105.json
2025-09-15 20:41:42.657 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:41:40 [DEBUG] - Writing to ptcp_qc/qc.m84036_250809_035451_s4.bc2132.json
2025-09-15 20:41:42.657 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:41:40 [DEBUG] - Writing to ptcp_qc/qc.aggregate.json
2025-09-15 20:41:42.657 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:41:40 [INFO] - Total execution time: 133.22s
2025-09-15 20:41:42.658 wdl.w:ptcp.t:call-ptcp_qc.stderr VERBOSE 2025-09-15 20:41:40 [INFO] - ptcp-qc end
2025-09-15 20:41:51.142 wdl.w:ptcp.t:call-ptcp_qc INFO command stdout unused; consider output `File cmd_out = stdout()` or redirect command to stderr log >&2 :: stdout_file: "/datasets-for-launch/Carrier_Nanobind_96plex_RevioSRPQ/ptcp_v3.1.0_output/20250915_201807_ptcp/call-ptcp_qc/stdout.txt"
2025-09-15 20:41:51.154 wdl.w:ptcp.t:call-ptcp_qc INFO output :: name: "qc_reports", value: "(((large)))"
2025-09-15 20:41:52.105 wdl.w:ptcp.t:call-ptcp_qc NOTICE done
2025-09-15 20:41:52.124 wdl.w:ptcp NOTICE finish :: job: "call-ptcp_qc"
2025-09-15 20:41:52.124 wdl.w:ptcp INFO output :: job: "call-ptcp_qc", values: "(((large)))"
2025-09-15 20:41:52.124 wdl.w:ptcp INFO visit :: node: "output-ptcp_qc_reports", values: "(((large)))"
2025-09-15 20:41:52.134 wdl.w:ptcp INFO visit :: node: "outputs", values: "(((large)))"
2025-09-15 20:42:10.616 wdl.w:ptcp NOTICE done